Repository: JLSteenwyk/ClipKIT (language: python)

Issue:
2023-08-24: Use numpy to accelerate the trimming process
Hi - I'm suggesting to use some numpy implementation instead of for loop for trimming.

Below is an example codes that I tried. I slightly modified the original function ClipKIT used for the trimming process but the concept should be the same. Note that I'm using Biopython MultipleSeqAlignment objects as input. I noticed you have already convert them to numpy array so I guess you can simply skip the conversion step. Also the trimD definition might be different from the original one since I just use it to store the index should be trimmed.
```python
def original_clipkit(msa: MultipleSeqAlignment, gaps: int = 0.9):    
    keepD = msa[:, :0]
    trimD = []
    for idx in range(msa.get_alignment_length()):
        _, gappyness = report_column_features(msa, idx, get_gap_chars(SeqType.aa))
        if gappyness <= gaps:
            keepD += msa[:, idx : idx + 1]
        else:
            trimD.append(idx)

    return keepD, trimD
```
I tested it with jupyter %%timeit function and here is the results:
`67.1 ms ± 1.67 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)`

And here is the rewrite with numpy methods.
```python
def numpy_clipkit(msa: MultipleSeqAlignment, gaps: int = 0.9):
    infoList = [{"id": rec.id, "name": rec.name, "description": rec.description} for rec in msa]
    msa_array = np.array([list(rec) for rec in msa])
    gappyness = (msa_array == "-").mean(axis=0)
    trimD = np.where(gappyness > gaps)[0]
    keepD = np.delete(msa_array, trimD, axis=1)

    return MultipleSeqAlignment([SeqRecord(Seq("".join(rec)), **info) for rec, info in zip(keepD.tolist(), infoList)]), trimD.tolist()
```
And there is a significant speed up:
`616 µs ± 2.73 µs per loop (mean ± std. dev. of 7 runs, 1,000 loops each)`

Since I'm only using the gappy mode to do the trimming, I'm not sure if this implementation is applicable to other trimming mode.


Discussion / hints:
Hi Cheng-Hung,

Thanks for this suggestion! At first glance, it looks like a great enhancement!

I will take a close look early next week.

Thanks again!

best,

Jacob

Fix patch:
diff --git a/change_log.txt b/change_log.txt
index 174dea3..2c3d22c 100644
--- a/change_log.txt
+++ b/change_log.txt
@@ -1,5 +1,8 @@
 Major changes to ClipKIT are summarized here.
 
+2.0.0 through 2.1.0
+Introduce and refactor MSA class. Rely on Numpy functionality to accelerate processes.
+
 1.3.0
 long description of sequences, rather than identifiers, are kept in the ClipKIT output
 
diff --git a/clipkit/api.py b/clipkit/api.py
index 1baef8c..4db0061 100644
--- a/clipkit/api.py
+++ b/clipkit/api.py
@@ -3,7 +3,7 @@
 
 from .clipkit import run
 from .files import FileFormat
-from .helpers import SeqType, write_keep_msa
+from .helpers import SeqType, write_msa
 from .logger import logger
 from .modes import TrimmingMode
 
@@ -59,5 +59,5 @@ def clipkit(
     if not output_file_path:
         return trim_run, stats
     else:
-        write_keep_msa(trim_run.keep_msa, output_file_path, trim_run.output_file_format)
+        write_msa(trim_run.msa, output_file_path, trim_run.output_file_format)
         return output_file_path, stats
diff --git a/clipkit/clipkit.py b/clipkit/clipkit.py
index 9fee2aa..bdb66c9 100644
--- a/clipkit/clipkit.py
+++ b/clipkit/clipkit.py
@@ -8,13 +8,13 @@
 from Bio.Align import MultipleSeqAlignment
 from .args_processing import process_args
 from .exceptions import InvalidInputFileFormat
-from .files import get_alignment_and_format, FileFormat
+from .files import get_alignment_and_format, FileFormat, write_debug_log_file
 from .helpers import (
+    create_msa,
     get_seq_type,
     get_gap_chars,
-    keep_trim_and_log,
-    write_keep_msa,
-    write_trim_msa,
+    write_msa,
+    write_complement,
     SeqType,
 )
 from .logger import logger, log_file_logger
@@ -23,16 +23,16 @@
 from .parser import create_parser
 from .settings import DEFAULT_AA_GAP_CHARS, DEFAULT_NT_GAP_CHARS
 from .smart_gap_helper import smart_gap_threshold_determination
-from .stats import TrimmingStats
 from .version import __version__ as current_version
 from .warnings import (
     warn_if_all_sites_were_trimmed,
     warn_if_entry_contains_only_gaps,
 )
 from .write import (
-    write_determining_smart_gap_threshold,
     write_user_args,
     write_output_stats,
+    write_processing_aln,
+    write_output_files_message,
 )
 
 from dataclasses import dataclass
@@ -41,23 +41,21 @@
 @dataclass
 class TrimRun:
     alignment: MultipleSeqAlignment
-    keep_msa: MSA
-    trim_msa: MSA
+    msa: MSA
     gap_characters: list
     sequence_type: SeqType
     input_file_format: FileFormat
     output_file_format: FileFormat
-    site_classification_counts: dict
     gaps: float
     version: str = current_version
 
     @property
     def complement(self):
-        return self.trim_msa.to_bio_msa() if self.trim_msa else None
+        return self.msa.complement_to_bio_msa()
 
     @property
     def trimmed(self):
-        return self.keep_msa.to_bio_msa()
+        return self.msa.to_bio_msa()
 
 
 def run(
@@ -98,28 +96,22 @@ def run(
         TrimmingMode.kpi_smart_gap,
         TrimmingMode.kpic_smart_gap,
     }:
-        write_determining_smart_gap_threshold()
-        gaps = smart_gap_threshold_determination(alignment, gap_characters, quiet)
+        gaps = smart_gap_threshold_determination(alignment, gap_characters)
 
-    # instantiates MSAs to track what we keep/trim from the alignment
-    keep_msa, trim_msa, site_classification_counts = keep_trim_and_log(
-        alignment, gaps, mode, use_log, output_file, complement, gap_characters, quiet
-    )
+    msa = create_msa(alignment, gap_characters)
+    msa.trim(mode, gap_threshold=gaps)
 
     trim_run = TrimRun(
         alignment,
-        keep_msa,
-        trim_msa,
+        msa,
         gap_characters,
         sequence_type,
         input_file_format,
         output_file_format,
-        site_classification_counts,
         gaps,
     )
-    stats = TrimmingStats(trim_run.alignment, trim_run.keep_msa, trim_run.trim_msa)
 
-    return trim_run, stats
+    return trim_run, msa.stats
 
 
 def execute(
@@ -149,6 +141,7 @@ def execute(
     # for reporting runtime duration to user
     start_time = time.time()
 
+    write_processing_aln()
     trim_run, stats = run(
         input_file,
         input_file_format,
@@ -162,6 +155,7 @@ def execute(
         use_log,
         quiet,
     )
+    write_output_files_message(output_file, complement, use_log)
 
     # display to user what args are being used in stdout
     write_user_args(
@@ -178,14 +172,15 @@ def execute(
     )
 
     if use_log:
-        warn_if_all_sites_were_trimmed(trim_run.keep_msa)
-        warn_if_entry_contains_only_gaps(trim_run.keep_msa, trim_run.sequence_type)
+        warn_if_all_sites_were_trimmed(trim_run.msa)
+        warn_if_entry_contains_only_gaps(trim_run.msa)
+        write_debug_log_file(trim_run.msa)
 
-    write_keep_msa(trim_run.keep_msa, output_file, trim_run.output_file_format)
+    write_msa(trim_run.msa, output_file, trim_run.output_file_format)
 
     # if the -c/--complementary argument was used, create an alignment of the trimmed sequences
     if complement:
-        write_trim_msa(trim_run.trim_msa, output_file, trim_run.output_file_format)
+        write_complement(trim_run.msa, output_file, trim_run.output_file_format)
 
     write_output_stats(stats, start_time)
 
diff --git a/clipkit/files.py b/clipkit/files.py
index c37038b..b88d093 100644
--- a/clipkit/files.py
+++ b/clipkit/files.py
@@ -1,5 +1,5 @@
 from enum import Enum
-import logging
+from .logger import log_file_logger
 
 from Bio import AlignIO
 from Bio.Align import MultipleSeqAlignment
@@ -7,9 +7,6 @@
 from .exceptions import InvalidInputFileFormat
 
 
-log = logging.getLogger(__name__)
-
-
 class FileFormat(Enum):
     fasta = "fasta"
     clustal = "clustal"
@@ -47,3 +44,8 @@ def get_alignment_and_format(
                 continue
 
         raise InvalidInputFileFormat("File could not be read")
+
+
+def write_debug_log_file(msa):
+    for info in msa.generate_debug_log_info():
+        log_file_logger.debug(f"{str(info[0] + 1)} {info[1]} {info[2].value} {info[3]}")
diff --git a/clipkit/helpers.py b/clipkit/helpers.py
index c6405ff..29ed4de 100644
--- a/clipkit/helpers.py
+++ b/clipkit/helpers.py
@@ -5,10 +5,10 @@
 from tqdm import tqdm
 
 from .msa import MSA
-from .modes import SiteClassificationType, TrimmingMode, trim
+from .modes import TrimmingMode
 from .settings import DEFAULT_AA_GAP_CHARS, DEFAULT_NT_GAP_CHARS
 from .files import FileFormat
-from .write import write_processing_aln, write_output_files_message
+from .stats import TrimmingStats
 
 from enum import Enum
 
@@ -38,12 +38,6 @@ def get_seq_type(alignment: MultipleSeqAlignment) -> SeqType:
     return sequence_type
 
 
-def get_alignment_column(alignment: MultipleSeqAlignment, index: int) -> str:
-    alignment_column = ""
-    alignment_column += alignment[:, index]
-    return alignment_column.upper()
-
-
 def get_gap_chars(seq_type: SeqType) -> list[str]:
     if seq_type == SeqType.nt:
         return DEFAULT_NT_GAP_CHARS
@@ -51,89 +45,18 @@ def get_gap_chars(seq_type: SeqType) -> list[str]:
         return DEFAULT_AA_GAP_CHARS
 
 
-def report_column_features(
-    alignment: MultipleSeqAlignment, index: int, gap_chars: list
-) -> tuple[str, float]:
-    """
-    Count the occurence of each character at a given position
-    in an alignment. This information is used to determine
-    if the alignment is parsimony informative or not. When
-    counting characters, gaps are excluded.
-    """
-    alignment_column = get_alignment_column(alignment, index)
-
-    column_length = len(alignment_column)
-
-    number_of_gaps = sum([alignment_column.count(char) for char in gap_chars])
-    gappyness = number_of_gaps / column_length
-
-    return alignment_column, gappyness
-
-
-def count_characters_at_position(alignment_column: str, gap_chars: list) -> dict:
-    character_counts = {}
-
-    alignment_column = remove_gaps(alignment_column, gap_chars)
-    for char in set(alignment_column):
-        character_counts[char] = alignment_column.count(char)
-    return character_counts
-
-
-def determine_site_classification_type(
-    character_counts: dict,
-) -> SiteClassificationType:
-    """
-    Determines if a site is parsimony informative or constant.
-    A site is parsimony-informative if it contains at least two types of nucleotides
-    (or amino acids), and at least two of them occur with a minimum frequency of two.
-    https://www.megasoftware.net/web_help_7/rh_parsimony_informative_site.htm
-
-    A site is constant if it contains only one character and that character occurs
-    at least twice. https://www.megasoftware.net/web_help_7/rh_constant_site.htm
-
-    A singleton is a site that contains at least two types of characters with, at most,
-    one occuring multiple times. https://www.megasoftware.net/web_help_7/rh_singleton_sites.htm
-    """
-    parsimony_informative_threshold = 2
-    counts_gte_threshold = 0
-
-    for count in character_counts.values():
-        if count >= 2:
-            counts_gte_threshold += 1
-        if counts_gte_threshold >= parsimony_informative_threshold:
-            return SiteClassificationType.parsimony_informative
-
-    if counts_gte_threshold == 1 and len(character_counts) == 1:
-        return SiteClassificationType.constant
-    elif counts_gte_threshold == 1 and len(character_counts) > 1:
-        return SiteClassificationType.singleton
-
-    return SiteClassificationType.other
-
-
-def create_keep_and_trim_msas(
-    alignment: MultipleSeqAlignment, complement: bool
-) -> tuple[MSA, MSA]:
+def create_msa(alignment: MultipleSeqAlignment, gap_chars: list[str] = None) -> MSA:
     """
-    Creates MSA classes to track sites kept and trimmed
+    Create MSA class
     """
+    return MSA.from_bio_msa(alignment, gap_chars)
 
-    keep_msa = MSA.from_bio_msa(alignment)
-    if complement:
-        trim_msa = MSA.from_bio_msa(alignment)
-    else:
-        trim_msa = None
-
-    return keep_msa, trim_msa
 
-
-def write_keep_msa(
-    keep_msa: MSA, out_file_name: str, out_file_format: FileFormat
-) -> None:
+def write_msa(msa: MSA, out_file_name: str, out_file_format: FileFormat) -> None:
     """
-    keep_msa is populated with sites that are kept after trimming is finished
+    msa is populated with sites that are kept after trimming is finished
     """
-    output_msa = keep_msa.to_bio_msa()
+    output_msa = msa.to_bio_msa()
     if out_file_format.value == "phylip_relaxed":
         SeqIO.write(output_msa, out_file_name, "phylip-relaxed")
     elif out_file_format.value == "phylip_sequential":
@@ -142,65 +65,14 @@ def write_keep_msa(
         SeqIO.write(output_msa, out_file_name, out_file_format.value)
 
 
-def write_trim_msa(trim_msa: MSA, out_file: str, out_file_format: FileFormat) -> None:
+def write_complement(msa: MSA, out_file: str, out_file_format: FileFormat) -> None:
     """
-    trim_msa is populated with sites that are trimmed after trimming is finished
+    msa is populated with sites that are trimmed after trimming is finished
     """
-    output_msa = trim_msa.to_bio_msa()
+    output_msa = msa.complement_to_bio_msa()
     completmentOut = str(out_file) + ".complement"
     if out_file_format.value == "phylip_relaxed":
         SeqIO.write(output_msa, out_file, "phylip-relaxed")
     elif out_file_format.value == "phylip_sequential":
         SeqIO.write(output_msa, out_file, "phylip-sequential")
     SeqIO.write(output_msa, completmentOut, out_file_format.value)
-
-
-def keep_trim_and_log(
-    alignment: MultipleSeqAlignment,
-    gaps: float,
-    mode: TrimmingMode,
-    use_log: bool,
-    out_file_name: str,
-    complement: bool,
-    gap_chars: list,
-    quiet: bool,
-) -> tuple[MSA, MSA]:
-    """
-    Determines positions to keep or trim and saves these positions on the MSA classes.
-    """
-    # initialize MSA classes
-    keep_msa, trim_msa = create_keep_and_trim_msas(alignment, complement)
-
-    alignment_length = alignment.get_alignment_length()
-
-    site_classification_counts = dict()
-    site_classification_counts[SiteClassificationType.parsimony_informative] = 0
-    site_classification_counts[SiteClassificationType.constant] = 0
-    site_classification_counts[SiteClassificationType.singleton] = 0
-    site_classification_counts[SiteClassificationType.other] = 0
-
-    write_processing_aln()
-    for i in tqdm(range(alignment_length), disable=quiet, postfix="trimmer"):
-        sequence_at_index, gappyness = report_column_features(alignment, i, gap_chars)
-
-        character_counts = count_characters_at_position(sequence_at_index, gap_chars)
-
-        # determine if a site is parsimony informative, singleton, or constant
-        site_classification_type = determine_site_classification_type(character_counts)
-
-        keep_msa, trim_msa = trim(
-            gappyness,
-            site_classification_type,
-            site_classification_counts,
-            keep_msa,
-            trim_msa,
-            i,
-            gaps,
-            alignment,
-            mode,
-            use_log,
-        )
-
-    # inform user that output files are being written
-    write_output_files_message(out_file_name, complement, use_log)
-    return keep_msa, trim_msa, site_classification_counts
diff --git a/clipkit/modes.py b/clipkit/modes.py
index 3606498..e4001a2 100644
--- a/clipkit/modes.py
+++ b/clipkit/modes.py
@@ -7,13 +7,6 @@
     from .msa import MSA
 
 
-class SiteClassificationType(Enum):
-    parsimony_informative = "parsimony-informative"
-    constant = "constant"
-    singleton = "singleton"
-    other = "other"
-
-
 class TrimmingMode(Enum):
     gappy = "gappy"
     smart_gap = "smart-gap"
@@ -23,80 +16,3 @@ class TrimmingMode(Enum):
     kpic = "kpic"
     kpic_gappy = "kpic-gappy"
     kpic_smart_gap = "kpic-smart-gap"
-
-
-def should_keep_site(
-    mode: TrimmingMode,
-    site_classification_type: "SiteClassificationType",
-    gappyness: float,
-    gaps: float,
-) -> bool:
-    if mode == TrimmingMode.kpi_gappy:
-        return (
-            gappyness <= gaps
-            and site_classification_type == SiteClassificationType.parsimony_informative
-        )
-    elif mode == TrimmingMode.gappy:
-        return gappyness <= gaps
-    elif mode == TrimmingMode.kpi:
-        return site_classification_type == SiteClassificationType.parsimony_informative
-    elif mode == TrimmingMode.kpic:
-        return (
-            site_classification_type == SiteClassificationType.parsimony_informative
-            or site_classification_type == SiteClassificationType.constant
-        )
-    elif mode == TrimmingMode.kpic_gappy:
-        return gappyness <= gaps and (
-            site_classification_type == SiteClassificationType.parsimony_informative
-            or site_classification_type == SiteClassificationType.constant
-        )
-    elif mode == TrimmingMode.smart_gap:
-        return round(gappyness, 4) < gaps
-    elif mode == TrimmingMode.kpic_smart_gap:
-        return round(gappyness, 4) < gaps and (
-            site_classification_type == SiteClassificationType.parsimony_informative
-            or site_classification_type == SiteClassificationType.constant
-        )
-    elif mode == TrimmingMode.kpi_smart_gap:
-        return (
-            round(gappyness, 4) < gaps
-            and site_classification_type == SiteClassificationType.parsimony_informative
-        )
-
-
-def trim(
-    gappyness: float,
-    site_classification_type: "SiteClassificationType",
-    site_classification_counts: dict,
-    keep_msa: "MSA",
-    trim_msa: "MSA",
-    alignment_position: int,
-    gaps: float,
-    alignment: "MultipleSeqAlignment",
-    mode: TrimmingMode,
-    use_log: bool,
-) -> tuple["MSA", "MSA"]:
-    if should_keep_site(mode, site_classification_type, gappyness, gaps):
-        site_classification_counts[site_classification_type] += 1
-        for entry in alignment:
-            new_value = entry.seq._data[alignment_position : alignment_position + 1]
-            keep_msa.set_entry_sequence_at_position(
-                entry.description, alignment_position, new_value
-            )
-        if use_log:
-            log_file_logger.debug(
-                f"{str(alignment_position + 1)} keep {site_classification_type.value} {gappyness}"
-            )
-    else:
-        if trim_msa is not None:
-            for entry in alignment:
-                new_value = entry.seq._data[alignment_position : alignment_position + 1]
-                trim_msa.set_entry_sequence_at_position(
-                    entry.description, alignment_position, new_value
-                )
-        if use_log:
-            log_file_logger.debug(
-                f"{str(alignment_position + 1)} trim {site_classification_type.value} {gappyness}"
-            )
-
-    return keep_msa, trim_msa
diff --git a/clipkit/msa.py b/clipkit/msa.py
index e63d638..a72beec 100644
--- a/clipkit/msa.py
+++ b/clipkit/msa.py
@@ -4,75 +4,210 @@
 import numpy as np
 from typing import Union
 
+from .modes import TrimmingMode
+from .site_classification import (
+    SiteClassificationType,
+    determine_site_classification_type,
+)
 from .settings import DEFAULT_AA_GAP_CHARS
+from .stats import TrimmingStats
 
 
 class MSA:
-    def __init__(self, entries: list[str], starting_length: int) -> None:
-        self.starting_length = starting_length
-        self.entries = entries
-        self._data = self._init_data()
-        self._joined = None
+    def __init__(
+        self, header_info, seq_records, gap_chars=DEFAULT_AA_GAP_CHARS
+    ) -> None:
+        self.header_info = header_info
+        self.seq_records = seq_records
+        self._original_length = len(self.seq_records[0])
+        self._site_positions_to_keep = np.arange(self._original_length)
+        self._site_positions_to_trim = np.array([])
+        self._site_classification_types = None
+        self._column_character_frequencies = None
+        self._gap_chars = gap_chars
+
+    @staticmethod
+    def from_bio_msa(alignment: MultipleSeqAlignment, gap_chars=None) -> "MSA":
+        header_info = [
+            {"id": rec.id, "name": rec.name, "description": rec.description}
+            for rec in alignment
+        ]
+        seq_records = np.array([list(rec) for rec in alignment])
+        return MSA(header_info, seq_records, gap_chars)
+
+    def to_bio_msa(self) -> MultipleSeqAlignment:
+        return self._to_bio_msa(self.sites_kept)
 
-    def _init_data(self) -> dict[str, np.array]:
-        data = {}
-        for entry in self.entries:
-            data[entry] = np.zeros([self.starting_length], dtype=bytes)
-        return data
+    def complement_to_bio_msa(self) -> MultipleSeqAlignment:
+        return self._to_bio_msa(self.sites_trimmed)
 
-    def _reset_joined(self) -> None:
-        self._joined = None
+    def _to_bio_msa(self, sites) -> MultipleSeqAlignment:
+        # NOTE: we use the description as the id to preserve the full sequence description - see issue #20
+        return MultipleSeqAlignment(
+            [
+                SeqRecord(
+                    Seq("".join(rec)), id=str(info["description"]), description=""
+                )
+                for rec, info in zip(sites.tolist(), self.header_info)
+            ]
+        )
+
+    @property
+    def trimmed(self):
+        if len(self._site_positions_to_trim) == 0:
+            return self.seq_records
+        return np.delete(self.seq_records, self._site_positions_to_trim, axis=1)
+
+    @property
+    def sites_kept(self):
+        return np.take(self.seq_records, self._site_positions_to_keep, axis=1)
+
+    @property
+    def sites_trimmed(self):
+        return np.take(self.seq_records, self._site_positions_to_trim, axis=1)
 
     @property
     def length(self) -> int:
-        return np.count_nonzero(next(iter(self._data.values())))
+        return len(self._site_positions_to_keep)
+
+    @property
+    def original_length(self):
+        return self._original_length
+
+    @property
+    def gap_chars(self):
+        return self._gap_chars
+
+    @property
+    def site_gappyness(self) -> np.floating:
+        site_gappyness = (np.isin(self.seq_records, self._gap_chars)).mean(axis=0)
+        return np.around(site_gappyness, decimals=4)
 
     @property
     def is_empty(self) -> bool:
-        all_zeros = np.all(self._data[self.entries[0]] == b"")
+        all_zeros = np.all(self.sites_kept[0] == "")
         return all_zeros
 
     @property
-    def string_sequences(self) -> dict[str, str]:
-        if self._joined:
-            return self._joined
-        else:
-            joined = {}
-            for entry, sequence in self._data.items():
-                joined[entry] = "".join(np.char.decode(sequence))
-            self._joined = joined
-        return self._joined
+    def stats(self) -> TrimmingStats:
+        return TrimmingStats(self)
 
-    @staticmethod
-    def from_bio_msa(alignment: MultipleSeqAlignment) -> "MSA":
-        entries = [entry.description for entry in alignment]
-        length = alignment.get_alignment_length()
-        return MSA(entries, length)
+    def is_any_entry_sequence_only_gaps(self) -> tuple[bool, Union[str, None]]:
+        for idx, row in enumerate(self.trimmed):
+            if np.all(row == row[0]) and (  # all values the same
+                row[0] in self.gap_chars
+            ):
+                return True, self.header_info[idx].get("id")
+        return False, None
 
-    def to_bio_msa(self) -> MultipleSeqAlignment:
-        seqList = []
-        for entry, joined in self.string_sequences.items():
-            seqList.append(SeqRecord(Seq(str(joined)), id=str(entry), description=""))
-        return MultipleSeqAlignment(seqList)
+    def trim(
+        self,
+        mode: TrimmingMode,
+        gap_threshold=None,
+    ) -> np.array:
+        self._site_positions_to_trim = self.determine_site_positions_to_trim(
+            mode, gap_threshold
+        )
+        self._site_positions_to_keep = np.delete(
+            np.arange(self._original_length), self._site_positions_to_trim
+        )
 
-    def set_entry_sequence_at_position(
-        self, entry: str, position: int, value: str
-    ) -> None:
-        self._data[entry][position] = value
-
-        # since we've mutated the sequence data we need to release our cached _joined
-        self._reset_joined()
-
-    def is_any_entry_sequence_only_gaps(
-        self, gap_chars=DEFAULT_AA_GAP_CHARS
-    ) -> tuple[bool, Union[str, None]]:
-        for entry, sequence in self._data.items():
-            first_sequence_value = sequence[0]
-            sequence_values_all_same = np.all(sequence == first_sequence_value)
-            if (
-                sequence_values_all_same
-                and first_sequence_value.decode("utf-8") in gap_chars
-            ):
-                return True, entry
+    @property
+    def column_character_frequencies(self):
+        if self._column_character_frequencies is not None:
+            return self._column_character_frequencies
 
-        return False, None
+        column_character_frequencies = []
+        for column in self.seq_records.T:
+            col_sorted_unique_values_for, col_counts_per_char = np.unique(
+                [char.upper() for char in column], return_counts=True
+            )
+            freqs = dict(zip(col_sorted_unique_values_for, col_counts_per_char))
+            for gap_char in self.gap_chars:
+                try:
+                    del freqs[gap_char]
+                except KeyError:
+                    continue
+            column_character_frequencies.append(freqs)
+        self._column_character_frequencies = column_character_frequencies
+        return self._column_character_frequencies
+
+    @property
+    def site_classification_types(self):
+        if self._site_classification_types is not None:
+            return self._site_classification_types
+
+        site_classification_types = np.array(
+            [
+                determine_site_classification_type(col_char_freq)
+                for col_char_freq in self.column_character_frequencies
+            ]
+        )
+        self._site_classification_types = site_classification_types
+        return self._site_classification_types
+
+    def determine_site_positions_to_trim(self, mode, gap_threshold):
+        if mode in (TrimmingMode.gappy, TrimmingMode.smart_gap):
+            sites_to_trim = np.where(self.site_gappyness >= gap_threshold)[0]
+        elif mode == TrimmingMode.kpi:
+            col_char_freqs = self.column_character_frequencies
+            site_classification_types = self.site_classification_types
+            sites_to_trim = np.where(
+                site_classification_types
+                != SiteClassificationType.parsimony_informative
+            )[0]
+        elif mode in (TrimmingMode.kpi_gappy, TrimmingMode.kpi_smart_gap):
+            sites_to_trim_gaps_based = np.where(self.site_gappyness > gap_threshold)[0]
+            col_char_freqs = self.column_character_frequencies
+            site_classification_types = self.site_classification_types
+            sites_to_trim_classification_based = np.where(
+                site_classification_types
+                != SiteClassificationType.parsimony_informative
+            )[0]
+            sites_to_trim = np.unique(
+                np.concatenate(
+                    (sites_to_trim_gaps_based, sites_to_trim_classification_based)
+                )
+            )
+        elif mode == TrimmingMode.kpic:
+            col_char_freqs = self.column_character_frequencies
+            site_classification_types = self.site_classification_types
+            sites_to_trim = np.where(
+                (site_classification_types == SiteClassificationType.other)
+                | (site_classification_types == SiteClassificationType.singleton)
+            )[0]
+        elif mode in (TrimmingMode.kpic_gappy, TrimmingMode.kpic_smart_gap):
+            sites_to_trim_gaps_based = np.where(self.site_gappyness >= gap_threshold)[0]
+
+            col_char_freqs = self.column_character_frequencies
+            site_classification_types = self.site_classification_types
+            sites_to_trim_classification_based = np.where(
+                (site_classification_types == SiteClassificationType.other)
+                | (site_classification_types == SiteClassificationType.singleton)
+            )[0]
+
+            sites_to_trim = np.unique(
+                np.concatenate(
+                    (sites_to_trim_gaps_based, sites_to_trim_classification_based)
+                )
+            )
+
+        return sites_to_trim
+
+    def generate_debug_log_info(self):
+        """
+        Returns tuples of site position, keep or trim, site classification type, and gappyness
+        """
+        keep_or_trim_lookup = {}
+        for keep_idx in self._site_positions_to_keep:
+            keep_or_trim_lookup[keep_idx] = "keep"
+        for trim_idx in self._site_positions_to_trim:
+            keep_or_trim_lookup[trim_idx] = "trim"
+
+        for idx, gappyness in enumerate(self.site_gappyness):
+            yield (
+                idx,
+                keep_or_trim_lookup[idx],
+                self.site_classification_types[idx],
+                gappyness,
+            )
diff --git a/clipkit/site_classification.py b/clipkit/site_classification.py
new file mode 100644
index 0000000..eeb3073
--- /dev/null
+++ b/clipkit/site_classification.py
@@ -0,0 +1,40 @@
+from enum import Enum
+
+
+class SiteClassificationType(Enum):
+    parsimony_informative = "parsimony-informative"
+    constant = "constant"
+    singleton = "singleton"
+    other = "other"
+
+
+def determine_site_classification_type(
+    character_counts: dict,
+) -> SiteClassificationType:
+    """
+    Determines if a site is parsimony informative or constant.
+    A site is parsimony-informative if it contains at least two types of nucleotides
+    (or amino acids), and at least two of them occur with a minimum frequency of two.
+    https://www.megasoftware.net/web_help_7/rh_parsimony_informative_site.htm
+
+    A site is constant if it contains only one character and that character occurs
+    at least twice. https://www.megasoftware.net/web_help_7/rh_constant_site.htm
+
+    A singleton is a site that contains at least two types of characters with, at most,
+    one occuring multiple times. https://www.megasoftware.net/web_help_7/rh_singleton_sites.htm
+    """
+    parsimony_informative_threshold = 2
+    counts_gte_threshold = 0
+
+    for count in character_counts.values():
+        if count >= 2:
+            counts_gte_threshold += 1
+        if counts_gte_threshold >= parsimony_informative_threshold:
+            return SiteClassificationType.parsimony_informative
+
+    if counts_gte_threshold == 1 and len(character_counts) == 1:
+        return SiteClassificationType.constant
+    elif counts_gte_threshold == 1 and len(character_counts) > 1:
+        return SiteClassificationType.singleton
+
+    return SiteClassificationType.other
diff --git a/clipkit/smart_gap_helper.py b/clipkit/smart_gap_helper.py
index 25c6f11..8a8a4f4 100644
--- a/clipkit/smart_gap_helper.py
+++ b/clipkit/smart_gap_helper.py
@@ -4,17 +4,16 @@
 import numpy as np
 from tqdm import tqdm
 
-from .helpers import report_column_features
 from .logger import logger
 
 
 def smart_gap_threshold_determination(
-    alignment: MultipleSeqAlignment, gap_chars: list, quiet: bool
+    alignment: MultipleSeqAlignment, gap_chars: list
 ) -> float:
     alignment_length = alignment.get_alignment_length()
 
     # get distribution of gaps rounded to the fourth decimal place
-    gaps_dist = get_gaps_distribution(alignment, alignment_length, gap_chars, quiet)
+    gaps_dist = get_gaps_distribution(alignment, gap_chars)
 
     # count freq of gaps and convert to sorted np array
     gaps_arr = count_and_sort_gaps(gaps_dist)
@@ -57,15 +56,12 @@ def gap_to_gap_slope(gaps_arr: np.array, alignment_length: int) -> list[float]:
 
 
 def get_gaps_distribution(
-    alignment: MultipleSeqAlignment, alignment_length: int, gap_chars: list, quiet: bool
+    alignment: MultipleSeqAlignment, gap_chars: list
 ) -> list[float]:
-    gaps_dist = []
-    for i in tqdm(range(0, alignment_length), disable=quiet, postfix="smart-gap"):
-        _, gappyness = report_column_features(alignment, i, gap_chars)
-        gappyness = round(gappyness, 4)
-        gaps_dist.append(gappyness)
+    msa_array = np.array([list(rec) for rec in alignment])
+    gaps_dist = (np.isin(msa_array, gap_chars)).mean(axis=0)
 
-    return gaps_dist
+    return np.round(gaps_dist, decimals=4).tolist()
 
 
 def count_and_sort_gaps(gaps_dist: list) -> list:
diff --git a/clipkit/stats.py b/clipkit/stats.py
index 7cb05d6..5d7ae8b 100644
--- a/clipkit/stats.py
+++ b/clipkit/stats.py
@@ -1,23 +1,23 @@
 from dataclasses import dataclass
+from typing import TYPE_CHECKING
 
 from Bio.Align import MultipleSeqAlignment
 
-from .msa import MSA
+if TYPE_CHECKING:
+    from .msa import MSA
 
 
 @dataclass
 class TrimmingStats:
-    alignment: MultipleSeqAlignment
-    keep_msa: MSA
-    trim_msa: MSA
+    msa: "MSA"
 
     @property
     def alignment_length(self) -> int:
-        return self.alignment.get_alignment_length()
+        return self.msa.original_length
 
     @property
     def output_length(self) -> int:
-        return self.keep_msa.length
+        return self.msa.length
 
     @property
     def trimmed_length(self) -> int:
diff --git a/clipkit/version.py b/clipkit/version.py
index 159d48b..9aa3f90 100644
--- a/clipkit/version.py
+++ b/clipkit/version.py
@@ -1,1 +1,1 @@
-__version__ = "2.0.1"
+__version__ = "2.1.0"
diff --git a/clipkit/warnings.py b/clipkit/warnings.py
index 92eba1a..0f669e0 100644
--- a/clipkit/warnings.py
+++ b/clipkit/warnings.py
@@ -12,18 +12,14 @@
 logger = logging.getLogger(__name__)
 
 
-def warn_if_all_sites_were_trimmed(keep_msa: "MSA") -> None:
-    if keep_msa.is_empty:
+def warn_if_all_sites_were_trimmed(msa: "MSA") -> None:
+    if msa.is_empty:
         logger.warning(
             "WARNING: All sites trimmed from alignment. Please use different parameters."
         )
 
 
-def warn_if_entry_contains_only_gaps(keep_msa: "MSA", sequence_type: SeqType) -> None:
-    if sequence_type == SeqType.aa:
-        gap_chars = DEFAULT_AA_GAP_CHARS
-    else:
-        gap_chars = DEFAULT_NT_GAP_CHARS
-    should_warn, entry = keep_msa.is_any_entry_sequence_only_gaps(gap_chars)
+def warn_if_entry_contains_only_gaps(msa: "MSA") -> None:
+    should_warn, entry = msa.is_any_entry_sequence_only_gaps()
     if should_warn:
         logger.warning(f"WARNING: header id '{entry}' contains only gaps")
diff --git a/clipkit/write.py b/clipkit/write.py
index 2f9475f..0173311 100644
--- a/clipkit/write.py
+++ b/clipkit/write.py
@@ -105,18 +105,3 @@ def write_output_stats(stats: "TrimmingStats", start_time: float) -> None:
     """
         )
     )
-
-
-def write_determining_smart_gap_threshold() -> None:
-    """
-    Function to inform using that the smart-gap threshold is being determined
-    """
-    logger.info(
-        textwrap.dedent(
-            """\
-        -----------------------------------
-        | Determining smart-gap threshold |
-        -----------------------------------
-        """
-        )
-    )
diff --git a/eg b/eg
deleted file mode 100644
index 2a39c28..0000000
--- a/eg
+++ /dev/null
@@ -1,10 +0,0 @@
->1
-AGAT
->2
-AGAT
->3
-AGTA
->4
-AATA
->5
-AaT-
diff --git a/eg.log b/eg.log
deleted file mode 100644
index 8a37254..0000000
--- a/eg.log
+++ /dev/null
@@ -1,1026 +0,0 @@
-1 trim constant 0.0
-2 trim constant 0.0
-3 keep parsimony-informative 0.0
-4 trim constant 0.0
-5 trim constant 0.0
-6 trim singleton 0.0
-7 trim constant 0.0
-8 trim constant 0.0
-9 trim constant 0.0
-10 trim constant 0.0
-11 keep parsimony-informative 0.0
-12 trim singleton 0.0
-13 keep parsimony-informative 0.0
-14 trim constant 0.0
-15 keep parsimony-informative 0.0
-16 keep parsimony-informative 0.0
-17 keep parsimony-informative 0.0
-18 trim constant 0.0
-19 keep parsimony-informative 0.0
-20 keep parsimony-informative 0.0
-21 keep parsimony-informative 0.0
-22 trim constant 0.0
-23 keep parsimony-informative 0.0
-24 trim constant 0.0
-25 keep parsimony-informative 0.0
-26 trim singleton 0.0
-27 trim constant 0.0
-28 keep parsimony-informative 0.0
-29 trim singleton 0.0
-30 trim constant 0.0
-31 trim constant 0.0
-32 trim constant 0.0
-33 trim singleton 0.0
-34 keep parsimony-informative 0.0
-35 keep parsimony-informative 0.0
-36 keep parsimony-informative 0.0
-37 keep parsimony-informative 0.0
-38 trim constant 0.0
-39 keep parsimony-informative 0.0
-40 keep parsimony-informative 0.0
-41 trim singleton 0.0
-42 keep parsimony-informative 0.0
-43 keep parsimony-informative 0.0
-44 keep parsimony-informative 0.0
-45 trim singleton 0.0
-46 trim constant 0.0
-47 keep parsimony-informative 0.0
-48 keep parsimony-informative 0.0
-49 trim constant 0.0
-50 keep parsimony-informative 0.0
-51 keep parsimony-informative 0.0
-52 keep parsimony-informative 0.0
-53 keep parsimony-informative 0.0
-54 trim constant 0.0
-55 trim constant 0.0
-56 keep parsimony-informative 0.0
-57 trim singleton 0.0
-58 trim constant 0.0
-59 keep parsimony-informative 0.0
-60 keep parsimony-informative 0.0
-61 trim constant 0.0
-62 trim singleton 0.0
-63 trim constant 0.0
-64 trim singleton 0.0
-65 trim constant 0.0
-66 trim constant 0.0
-67 keep parsimony-informative 0.0
-68 keep parsimony-informative 0.0
-69 trim singleton 0.0
-70 keep parsimony-informative 0.05982905982905983
-71 trim other 0.9829059829059829
-72 keep parsimony-informative 0.05982905982905983
-73 trim other 0.9914529914529915
-74 trim parsimony-informative 0.9401709401709402
-75 keep parsimony-informative 0.08547008547008547
-76 trim constant 0.9829059829059829
-77 keep parsimony-informative 0.03418803418803419
-78 trim singleton 0.02564102564102564
-79 trim singleton 0.02564102564102564
-80 trim singleton 0.07692307692307693
-81 trim constant 0.11965811965811966
-82 trim singleton 0.8803418803418803
-83 trim parsimony-informative 0.8803418803418803
-84 keep parsimony-informative 0.0
-85 keep parsimony-informative 0.0
-86 keep parsimony-informative 0.0
-87 keep parsimony-informative 0.0
-88 keep parsimony-informative 0.0
-89 keep parsimony-informative 0.017094017094017096
-90 keep parsimony-informative 0.0
-91 keep parsimony-informative 0.0
-92 keep parsimony-informative 0.0
-93 trim constant 0.7521367521367521
-94 keep parsimony-informative 0.0
-95 trim constant 0.0
-96 keep parsimony-informative 0.0
-97 keep parsimony-informative 0.02564102564102564
-98 trim parsimony-informative 0.9487179487179487
-99 trim constant 0.9487179487179487
-100 trim singleton 0.9487179487179487
-101 keep parsimony-informative 0.0
-102 trim constant 0.0
-103 trim constant 0.0
-104 keep parsimony-informative 0.0
-105 keep parsimony-informative 0.8376068376068376
-106 keep parsimony-informative 0.008547008547008548
-107 trim constant 0.0
-108 trim constant 0.0
-109 keep parsimony-informative 0.0
-110 keep parsimony-informative 0.0
-111 keep parsimony-informative 0.0
-112 keep parsimony-informative 0.0
-113 keep parsimony-informative 0.0
-114 keep parsimony-informative 0.0
-115 keep parsimony-informative 0.0
-116 trim constant 0.9487179487179487
-117 trim other 0.9914529914529915
-118 trim other 0.9914529914529915
-119 trim other 0.9914529914529915
-120 trim other 0.9914529914529915
-121 trim constant 0.9487179487179487
-122 trim singleton 0.9487179487179487
-123 trim other 0.9914529914529915
-124 trim other 0.9914529914529915
-125 trim other 0.9914529914529915
-126 trim other 0.9914529914529915
-127 trim other 0.9914529914529915
-128 trim other 0.9914529914529915
-129 trim other 0.9914529914529915
-130 trim other 0.9914529914529915
-131 trim other 0.9914529914529915
-132 trim other 0.9914529914529915
-133 trim other 0.9914529914529915
-134 trim other 0.9914529914529915
-135 trim other 0.9914529914529915
-136 trim other 0.9914529914529915
-137 trim other 0.9914529914529915
-138 trim other 0.9914529914529915
-139 trim other 0.9914529914529915
-140 trim other 0.9914529914529915
-141 trim other 0.9914529914529915
-142 trim other 0.9914529914529915
-143 trim other 0.9914529914529915
-144 trim other 0.9914529914529915
-145 trim other 0.9914529914529915
-146 trim other 0.9914529914529915
-147 trim other 0.9914529914529915
-148 trim other 0.9914529914529915
-149 trim other 0.9914529914529915
-150 trim other 0.9914529914529915
-151 trim other 0.9914529914529915
-152 trim other 0.9914529914529915
-153 trim other 0.9914529914529915
-154 trim other 0.9914529914529915
-155 trim other 0.9914529914529915
-156 trim other 0.9914529914529915
-157 trim other 0.9914529914529915
-158 trim other 0.9914529914529915
-159 trim other 0.9914529914529915
-160 trim other 0.9914529914529915
-161 trim other 0.9914529914529915
-162 trim other 0.9914529914529915
-163 trim other 0.9914529914529915
-164 trim other 0.9914529914529915
-165 trim other 0.9914529914529915
-166 trim other 0.9914529914529915
-167 trim other 0.9914529914529915
-168 trim other 0.9914529914529915
-169 trim other 0.9914529914529915
-170 trim other 0.9914529914529915
-171 trim other 0.9914529914529915
-172 trim other 0.9914529914529915
-173 trim other 0.9914529914529915
-174 trim other 0.9914529914529915
-175 trim other 0.9914529914529915
-176 trim other 0.9914529914529915
-177 trim other 0.9914529914529915
-178 trim other 0.9914529914529915
-179 trim other 0.9914529914529915
-180 trim other 0.9914529914529915
-181 trim other 0.9914529914529915
-182 trim other 0.9914529914529915
-183 trim other 0.9914529914529915
-184 trim other 0.9914529914529915
-185 trim other 0.9914529914529915
-186 trim other 0.9914529914529915
-187 trim other 0.9914529914529915
-188 trim other 0.9914529914529915
-189 trim other 0.9914529914529915
-190 trim other 0.9914529914529915
-191 trim other 0.9914529914529915
-192 trim other 0.9914529914529915
-193 trim other 0.9914529914529915
-194 trim other 0.9914529914529915
-195 trim other 0.9914529914529915
-196 trim other 0.9914529914529915
-197 trim other 0.9914529914529915
-198 trim other 0.9914529914529915
-199 trim other 0.9914529914529915
-200 trim other 0.9914529914529915
-201 trim other 0.9914529914529915
-202 trim other 0.9914529914529915
-203 trim singleton 0.9487179487179487
-204 keep parsimony-informative 0.0
-205 keep parsimony-informative 0.0
-206 trim constant 0.8461538461538461
-207 trim constant 0.8461538461538461
-208 trim constant 0.8034188034188035
-209 trim constant 0.8034188034188035
-210 trim constant 0.8034188034188035
-211 trim constant 0.8034188034188035
-212 keep parsimony-informative 0.7948717948717948
-213 keep parsimony-informative 0.7606837606837606
-214 keep parsimony-informative 0.7606837606837606
-215 trim constant 0.7692307692307693
-216 trim constant 0.7692307692307693
-217 trim constant 0.7692307692307693
-218 trim constant 0.7692307692307693
-219 trim constant 0.9829059829059829
-220 trim constant 0.7692307692307693
-221 trim constant 0.7692307692307693
-222 trim constant 0.7692307692307693
-223 trim constant 0.7692307692307693
-224 trim constant 0.7692307692307693
-225 trim constant 0.7692307692307693
-226 trim constant 0.7692307692307693
-227 trim constant 0.7692307692307693
-228 trim constant 0.7692307692307693
-229 trim constant 0.7692307692307693
-230 trim constant 0.7692307692307693
-231 trim constant 0.7692307692307693
-232 trim constant 0.7692307692307693
-233 trim constant 0.7692307692307693
-234 trim singleton 0.7606837606837606
-235 trim constant 0.7606837606837606
-236 trim constant 0.7692307692307693
-237 trim constant 0.7692307692307693
-238 trim constant 0.7692307692307693
-239 trim constant 0.7692307692307693
-240 trim constant 0.7606837606837606
-241 trim singleton 0.7606837606837606
-242 trim singleton 0.7606837606837606
-243 trim constant 0.7606837606837606
-244 trim constant 0.7606837606837606
-245 trim constant 0.7692307692307693
-246 trim constant 0.7692307692307693
-247 trim constant 0.7692307692307693
-248 trim constant 0.7692307692307693
-249 trim constant 0.7692307692307693
-250 trim constant 0.7692307692307693
-251 trim constant 0.7692307692307693
-252 trim constant 0.7606837606837606
-253 trim singleton 0.7606837606837606
-254 trim constant 0.7692307692307693
-255 trim constant 0.7692307692307693
-256 trim constant 0.7692307692307693
-257 trim constant 0.7692307692307693
-258 trim constant 0.7692307692307693
-259 trim constant 0.7692307692307693
-260 trim constant 0.7692307692307693
-261 trim constant 0.7692307692307693
-262 trim constant 0.7692307692307693
-263 trim constant 0.7692307692307693
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-766 trim singleton 0.7606837606837606
-767 trim singleton 0.7606837606837606
-768 trim singleton 0.7606837606837606
-769 trim singleton 0.7606837606837606
-770 trim singleton 0.7606837606837606
-771 keep parsimony-informative 0.7606837606837606
-772 trim singleton 0.7606837606837606
-773 keep parsimony-informative 0.7606837606837606
-774 trim singleton 0.7606837606837606
-775 keep parsimony-informative 0.7606837606837606
-776 trim constant 0.7606837606837606
-777 trim singleton 0.7606837606837606
-778 trim singleton 0.7606837606837606
-779 trim singleton 0.7606837606837606
-780 keep parsimony-informative 0.7606837606837606
-781 keep parsimony-informative 0.7606837606837606
-782 trim constant 0.7606837606837606
-783 trim singleton 0.7606837606837606
-784 trim singleton 0.7606837606837606
-785 trim singleton 0.7521367521367521
-786 trim constant 0.7606837606837606
-787 trim singleton 0.7606837606837606
-788 trim singleton 0.7606837606837606
-789 trim singleton 0.7606837606837606
-790 trim singleton 0.7606837606837606
-791 trim singleton 0.7606837606837606
-792 trim constant 0.7606837606837606
-793 trim singleton 0.7606837606837606
-794 trim singleton 0.7606837606837606
-795 trim constant 0.7606837606837606
-796 trim singleton 0.7606837606837606
-797 trim singleton 0.7606837606837606
-798 trim singleton 0.7606837606837606
-799 trim singleton 0.7606837606837606
-800 trim singleton 0.7606837606837606
-801 trim singleton 0.7606837606837606
-802 trim singleton 0.7606837606837606
-803 trim singleton 0.7606837606837606
-804 trim constant 0.7606837606837606
-805 trim singleton 0.7606837606837606
-806 trim singleton 0.7606837606837606
-807 trim singleton 0.7606837606837606
-808 trim singleton 0.7606837606837606
-809 trim singleton 0.7606837606837606
-810 keep parsimony-informative 0.7606837606837606
-811 trim singleton 0.7606837606837606
-812 trim singleton 0.7606837606837606
-813 trim constant 0.7606837606837606
-814 trim singleton 0.7606837606837606
-815 trim singleton 0.7606837606837606
-816 trim constant 0.7606837606837606
-817 trim singleton 0.7606837606837606
-818 keep parsimony-informative 0.7606837606837606
-819 trim constant 0.7692307692307693
-820 trim constant 0.7692307692307693
-821 trim constant 0.7692307692307693
-822 trim constant 0.7692307692307693
-823 trim constant 0.7692307692307693
-824 trim constant 0.7692307692307693
-825 keep parsimony-informative 0.7606837606837606
-826 trim singleton 0.7606837606837606
-827 trim singleton 0.7606837606837606
-828 trim constant 0.7606837606837606
-829 keep parsimony-informative 0.7606837606837606
-830 trim constant 0.7606837606837606
-831 trim singleton 0.7692307692307693
-832 trim constant 0.7692307692307693
-833 trim constant 0.7692307692307693
-834 trim constant 0.7692307692307693
-835 trim singleton 0.7692307692307693
-836 trim constant 0.7606837606837606
-837 trim singleton 0.7606837606837606
-838 trim constant 0.7606837606837606
-839 trim singleton 0.7606837606837606
-840 trim singleton 0.7606837606837606
-841 trim other 0.9914529914529915
-842 trim singleton 0.7606837606837606
-843 trim constant 0.7606837606837606
-844 trim constant 0.7606837606837606
-845 trim singleton 0.7606837606837606
-846 trim singleton 0.7606837606837606
-847 trim singleton 0.7606837606837606
-848 trim constant 0.7606837606837606
-849 trim other 0.9914529914529915
-850 trim other 0.9914529914529915
-851 trim other 0.9914529914529915
-852 trim other 0.9914529914529915
-853 trim other 0.9914529914529915
-854 trim other 0.9914529914529915
-855 trim other 0.9914529914529915
-856 trim singleton 0.7606837606837606
-857 trim singleton 0.7606837606837606
-858 trim constant 0.7606837606837606
-859 keep parsimony-informative 0.7606837606837606
-860 trim other 0.9914529914529915
-861 trim other 0.9914529914529915
-862 trim other 0.9914529914529915
-863 trim other 0.9914529914529915
-864 trim other 0.9914529914529915
-865 trim other 0.9914529914529915
-866 trim other 0.9914529914529915
-867 trim other 0.9914529914529915
-868 trim other 0.9914529914529915
-869 trim other 0.9914529914529915
-870 trim other 0.9914529914529915
-871 trim other 0.9914529914529915
-872 trim other 0.9914529914529915
-873 trim other 0.9914529914529915
-874 trim singleton 0.7606837606837606
-875 trim singleton 0.7606837606837606
-876 trim singleton 0.7606837606837606
-877 trim constant 0.7606837606837606
-878 trim singleton 0.7606837606837606
-879 trim singleton 0.7606837606837606
-880 trim constant 0.7606837606837606
-881 trim constant 0.7606837606837606
-882 trim other 0.9914529914529915
-883 trim other 0.9914529914529915
-884 trim other 0.9914529914529915
-885 trim singleton 0.7606837606837606
-886 trim singleton 0.7606837606837606
-887 trim constant 0.7606837606837606
-888 trim constant 0.7606837606837606
-889 trim singleton 0.7606837606837606
-890 trim singleton 0.7606837606837606
-891 trim singleton 0.7606837606837606
-892 trim singleton 0.7606837606837606
-893 trim singleton 0.7606837606837606
-894 trim singleton 0.7606837606837606
-895 trim constant 0.7692307692307693
-896 trim constant 0.7692307692307693
-897 trim constant 0.7606837606837606
-898 trim constant 0.7692307692307693
-899 trim singleton 0.7606837606837606
-900 trim singleton 0.7606837606837606
-901 trim constant 0.7606837606837606
-902 trim constant 0.7692307692307693
-903 trim constant 0.7692307692307693
-904 trim constant 0.7692307692307693
-905 trim constant 0.7692307692307693
-906 trim constant 0.7692307692307693
-907 trim constant 0.7692307692307693
-908 keep parsimony-informative 0.7692307692307693
-909 trim singleton 0.7606837606837606
-910 trim singleton 0.7606837606837606
-911 trim constant 0.7606837606837606
-912 trim singleton 0.7606837606837606
-913 trim singleton 0.7606837606837606
-914 trim singleton 0.7606837606837606
-915 keep parsimony-informative 0.7606837606837606
-916 trim constant 0.7606837606837606
-917 trim constant 0.7692307692307693
-918 trim constant 0.7692307692307693
-919 trim constant 0.7692307692307693
-920 trim constant 0.7692307692307693
-921 trim constant 0.7692307692307693
-922 trim constant 0.7692307692307693
-923 trim constant 0.7692307692307693
-924 trim constant 0.7692307692307693
-925 trim constant 0.8034188034188035
-926 trim singleton 0.8034188034188035
-927 keep parsimony-informative 0.8034188034188035
-928 trim constant 0.8034188034188035
-929 trim constant 0.8034188034188035
-930 trim singleton 0.8034188034188035
-931 trim singleton 0.8034188034188035
-932 trim singleton 0.8034188034188035
-933 trim constant 0.8034188034188035
-934 keep parsimony-informative 0.8034188034188035
-935 trim singleton 0.8034188034188035
-936 trim constant 0.811965811965812
-937 trim constant 0.811965811965812
-938 trim constant 0.811965811965812
-939 trim constant 0.811965811965812
-940 trim constant 0.811965811965812
-941 trim constant 0.811965811965812
-942 trim constant 0.811965811965812
-943 trim singleton 0.8034188034188035
-944 trim singleton 0.8034188034188035
-945 trim singleton 0.8034188034188035
-946 trim constant 0.8034188034188035
-947 trim singleton 0.8461538461538461
-948 keep parsimony-informative 0.8461538461538461
-949 keep parsimony-informative 0.8461538461538461
-950 keep parsimony-informative 0.8461538461538461
-951 trim singleton 0.8461538461538461
-952 keep parsimony-informative 0.8461538461538461
-953 keep parsimony-informative 0.8461538461538461
-954 trim singleton 0.8461538461538461
-955 keep parsimony-informative 0.8461538461538461
-956 keep parsimony-informative 0.8461538461538461
-957 trim singleton 0.8461538461538461
-958 keep parsimony-informative 0.8461538461538461
-959 trim singleton 0.8461538461538461
-960 trim constant 0.8461538461538461
-961 trim singleton 0.8461538461538461
-962 trim singleton 0.8461538461538461
-963 keep parsimony-informative 0.8717948717948718
-964 trim singleton 0.8717948717948718
-965 trim constant 0.8717948717948718
-966 keep parsimony-informative 0.8717948717948718
-967 keep parsimony-informative 0.8717948717948718
-968 trim constant 0.8717948717948718
-969 trim constant 0.8717948717948718
-970 trim constant 0.8717948717948718
-971 trim constant 0.8717948717948718
-972 trim constant 0.8717948717948718
-973 trim constant 0.8717948717948718
-974 trim constant 0.8717948717948718
-975 trim constant 0.8717948717948718
-976 trim singleton 0.8717948717948718
-977 trim constant 0.8717948717948718
-978 trim constant 0.8632478632478633
-979 trim constant 0.8632478632478633
-980 trim constant 0.8632478632478633
-981 trim singleton 0.8632478632478633
-982 trim singleton 0.8632478632478633
-983 trim constant 0.8632478632478633
-984 trim singleton 0.8632478632478633
-985 trim singleton 0.8632478632478633
-986 trim singleton 0.8632478632478633
-987 trim singleton 0.8632478632478633
-988 trim singleton 0.8632478632478633
-989 trim constant 0.8632478632478633
-990 trim constant 0.8717948717948718
-991 trim constant 0.8717948717948718
-992 trim constant 0.8717948717948718
-993 keep parsimony-informative 0.8717948717948718
-994 trim constant 0.8717948717948718
-995 trim constant 0.8717948717948718
-996 trim singleton 0.8717948717948718
-997 trim constant 0.8888888888888888
-998 trim singleton 0.8888888888888888
-999 trim constant 0.8888888888888888
-1000 trim parsimony-informative 0.8888888888888888
-1001 trim parsimony-informative 0.8888888888888888
-1002 trim parsimony-informative 0.8888888888888888
-1003 trim parsimony-informative 0.8888888888888888
-1004 trim singleton 0.8888888888888888
-1005 trim singleton 0.8888888888888888
-1006 trim singleton 0.8888888888888888
-1007 trim singleton 0.8888888888888888
-1008 trim other 0.9829059829059829
-1009 trim other 0.9914529914529915
-1010 trim other 0.9914529914529915
-1011 trim other 0.9914529914529915
-1012 trim other 0.9914529914529915
-1013 trim other 0.9914529914529915
-1014 trim other 0.9914529914529915
-1015 trim other 0.9914529914529915
-1016 trim other 0.9914529914529915
-1017 trim other 0.9914529914529915
-1018 trim other 0.9914529914529915
-1019 trim other 0.9914529914529915
-1020 trim other 0.9914529914529915
-1021 trim other 0.9914529914529915
-1022 trim other 0.9914529914529915
-1023 trim other 0.9914529914529915
-1024 trim other 0.9914529914529915
-1025 trim other 0.9914529914529915
-1026 trim singleton 0.8974358974358975


Test patch:
diff --git a/test-api.py b/test-api.py
index 181faca..9967aea 100644
--- a/test-api.py
+++ b/test-api.py
@@ -1,7 +1,7 @@
 from clipkit import clipkit
 from clipkit.files import FileFormat
 
-trim_run = clipkit(
+trim_run, stats = clipkit(
     # raw_alignment=">1\nA-GTAT\n>2\nA-G-AT\n>3\nA-G-TA\n>4\nAGA-TA\n>5\nACa-T-\n",
     input_file_path="tests/integration/samples/simple.fa",
     # output_file_path="./programmatic-temp.phylip",
@@ -12,4 +12,4 @@
     sequence_type="nt",
 )
 
-print(trim_run.site_classification_counts)
+print(trim_run.version)
diff --git a/tests/integration/expected/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit.log b/tests/integration/expected/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit.log
index 1e4b970..2d94155 100644
--- a/tests/integration/expected/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit.log
+++ b/tests/integration/expected/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit.log
@@ -1,27 +1,27 @@
 1 keep constant 0.0
 2 keep constant 0.0
 3 keep constant 0.0
-4 keep other 0.8333333333333334
-5 keep other 0.8333333333333334
-6 keep other 0.8333333333333334
-7 keep constant 0.08333333333333333
-8 keep constant 0.08333333333333333
-9 keep parsimony-informative 0.08333333333333333
-10 keep parsimony-informative 0.08333333333333333
-11 keep parsimony-informative 0.08333333333333333
-12 keep parsimony-informative 0.08333333333333333
-13 keep parsimony-informative 0.08333333333333333
-14 keep constant 0.08333333333333333
-15 keep parsimony-informative 0.08333333333333333
+4 keep other 0.8333
+5 keep other 0.8333
+6 keep other 0.8333
+7 keep constant 0.0833
+8 keep constant 0.0833
+9 keep parsimony-informative 0.0833
+10 keep parsimony-informative 0.0833
+11 keep parsimony-informative 0.0833
+12 keep parsimony-informative 0.0833
+13 keep parsimony-informative 0.0833
+14 keep constant 0.0833
+15 keep parsimony-informative 0.0833
 16 keep parsimony-informative 0.0
 17 keep parsimony-informative 0.0
 18 keep parsimony-informative 0.0
 19 keep singleton 0.0
 20 keep constant 0.0
 21 keep parsimony-informative 0.0
-22 trim other 0.9166666666666666
-23 trim other 0.9166666666666666
-24 trim other 0.9166666666666666
+22 trim other 0.9167
+23 trim other 0.9167
+24 trim other 0.9167
 25 keep constant 0.0
 26 keep constant 0.0
 27 keep parsimony-informative 0.0
@@ -76,9 +76,9 @@
 76 keep singleton 0.0
 77 keep parsimony-informative 0.0
 78 keep parsimony-informative 0.0
-79 trim other 0.9166666666666666
-80 trim other 0.9166666666666666
-81 trim other 0.9166666666666666
+79 trim other 0.9167
+80 trim other 0.9167
+81 trim other 0.9167
 82 keep parsimony-informative 0.0
 83 keep parsimony-informative 0.0
 84 keep parsimony-informative 0.0
@@ -97,9 +97,9 @@
 97 keep singleton 0.0
 98 keep parsimony-informative 0.0
 99 keep parsimony-informative 0.0
-100 keep other 0.8333333333333334
-101 keep other 0.8333333333333334
-102 keep other 0.8333333333333334
+100 keep other 0.8333
+101 keep other 0.8333
+102 keep other 0.8333
 103 keep parsimony-informative 0.0
 104 keep singleton 0.0
 105 keep parsimony-informative 0.0
@@ -148,18 +148,18 @@
 148 keep singleton 0.0
 149 keep constant 0.0
 150 keep parsimony-informative 0.0
-151 trim other 0.9166666666666666
-152 trim other 0.9166666666666666
-153 trim other 0.9166666666666666
-154 trim other 0.9166666666666666
-155 trim other 0.9166666666666666
-156 trim other 0.9166666666666666
-157 trim other 0.9166666666666666
-158 trim other 0.9166666666666666
-159 trim other 0.9166666666666666
-160 trim other 0.9166666666666666
-161 trim other 0.9166666666666666
-162 trim other 0.9166666666666666
+151 trim other 0.9167
+152 trim other 0.9167
+153 trim other 0.9167
+154 trim other 0.9167
+155 trim other 0.9167
+156 trim other 0.9167
+157 trim other 0.9167
+158 trim other 0.9167
+159 trim other 0.9167
+160 trim other 0.9167
+161 trim other 0.9167
+162 trim other 0.9167
 163 keep parsimony-informative 0.0
 164 keep parsimony-informative 0.0
 165 keep parsimony-informative 0.0
@@ -250,78 +250,78 @@
 250 keep parsimony-informative 0.0
 251 keep parsimony-informative 0.0
 252 keep parsimony-informative 0.0
-253 trim other 0.9166666666666666
-254 trim other 0.9166666666666666
-255 trim other 0.9166666666666666
-256 trim other 0.9166666666666666
-257 trim other 0.9166666666666666
-258 trim other 0.9166666666666666
-259 trim other 0.9166666666666666
-260 trim other 0.9166666666666666
-261 trim other 0.9166666666666666
-262 trim other 0.9166666666666666
-263 trim other 0.9166666666666666
-264 trim other 0.9166666666666666
-265 trim other 0.9166666666666666
-266 trim other 0.9166666666666666
-267 trim other 0.9166666666666666
-268 trim other 0.9166666666666666
-269 trim other 0.9166666666666666
-270 trim other 0.9166666666666666
-271 trim other 0.9166666666666666
-272 trim other 0.9166666666666666
-273 trim other 0.9166666666666666
-274 trim other 0.9166666666666666
-275 trim other 0.9166666666666666
-276 trim other 0.9166666666666666
-277 trim other 0.9166666666666666
-278 trim other 0.9166666666666666
-279 trim other 0.9166666666666666
-280 trim other 0.9166666666666666
-281 trim other 0.9166666666666666
-282 trim other 0.9166666666666666
-283 trim other 0.9166666666666666
-284 trim other 0.9166666666666666
-285 trim other 0.9166666666666666
-286 keep other 0.8333333333333334
-287 keep constant 0.8333333333333334
-288 keep other 0.8333333333333334
-289 keep constant 0.8333333333333334
-290 keep other 0.8333333333333334
-291 keep other 0.8333333333333334
-292 keep constant 0.8333333333333334
-293 keep other 0.8333333333333334
-294 keep other 0.8333333333333334
-295 keep other 0.8333333333333334
-296 keep other 0.8333333333333334
-297 keep other 0.8333333333333334
-298 keep other 0.8333333333333334
-299 keep constant 0.8333333333333334
-300 keep constant 0.8333333333333334
-301 keep constant 0.8333333333333334
-302 keep constant 0.8333333333333334
-303 keep other 0.8333333333333334
-304 keep constant 0.8333333333333334
-305 keep constant 0.8333333333333334
-306 keep constant 0.8333333333333334
-307 trim other 0.9166666666666666
-308 trim other 0.9166666666666666
-309 trim other 0.9166666666666666
-310 trim other 0.9166666666666666
-311 trim other 0.9166666666666666
-312 trim other 0.9166666666666666
-313 trim other 0.9166666666666666
-314 trim other 0.9166666666666666
-315 trim other 0.9166666666666666
-316 keep singleton 0.4166666666666667
-317 keep parsimony-informative 0.4166666666666667
-318 keep parsimony-informative 0.4166666666666667
-319 keep parsimony-informative 0.4166666666666667
-320 keep parsimony-informative 0.4166666666666667
-321 keep parsimony-informative 0.4166666666666667
-322 keep singleton 0.3333333333333333
-323 keep parsimony-informative 0.3333333333333333
-324 keep parsimony-informative 0.3333333333333333
+253 trim other 0.9167
+254 trim other 0.9167
+255 trim other 0.9167
+256 trim other 0.9167
+257 trim other 0.9167
+258 trim other 0.9167
+259 trim other 0.9167
+260 trim other 0.9167
+261 trim other 0.9167
+262 trim other 0.9167
+263 trim other 0.9167
+264 trim other 0.9167
+265 trim other 0.9167
+266 trim other 0.9167
+267 trim other 0.9167
+268 trim other 0.9167
+269 trim other 0.9167
+270 trim other 0.9167
+271 trim other 0.9167
+272 trim other 0.9167
+273 trim other 0.9167
+274 trim other 0.9167
+275 trim other 0.9167
+276 trim other 0.9167
+277 trim other 0.9167
+278 trim other 0.9167
+279 trim other 0.9167
+280 trim other 0.9167
+281 trim other 0.9167
+282 trim other 0.9167
+283 trim other 0.9167
+284 trim other 0.9167
+285 trim other 0.9167
+286 keep other 0.8333
+287 keep constant 0.8333
+288 keep other 0.8333
+289 keep constant 0.8333
+290 keep other 0.8333
+291 keep other 0.8333
+292 keep constant 0.8333
+293 keep other 0.8333
+294 keep other 0.8333
+295 keep other 0.8333
+296 keep other 0.8333
+297 keep other 0.8333
+298 keep other 0.8333
+299 keep constant 0.8333
+300 keep constant 0.8333
+301 keep constant 0.8333
+302 keep constant 0.8333
+303 keep other 0.8333
+304 keep constant 0.8333
+305 keep constant 0.8333
+306 keep constant 0.8333
+307 trim other 0.9167
+308 trim other 0.9167
+309 trim other 0.9167
+310 trim other 0.9167
+311 trim other 0.9167
+312 trim other 0.9167
+313 trim other 0.9167
+314 trim other 0.9167
+315 trim other 0.9167
+316 keep singleton 0.4167
+317 keep parsimony-informative 0.4167
+318 keep parsimony-informative 0.4167
+319 keep parsimony-informative 0.4167
+320 keep parsimony-informative 0.4167
+321 keep parsimony-informative 0.4167
+322 keep singleton 0.3333
+323 keep parsimony-informative 0.3333
+324 keep parsimony-informative 0.3333
 325 keep parsimony-informative 0.5
 326 keep parsimony-informative 0.5
 327 keep parsimony-informative 0.5
@@ -331,15 +331,15 @@
 331 keep parsimony-informative 0.0
 332 keep singleton 0.0
 333 keep parsimony-informative 0.0
-334 keep parsimony-informative 0.08333333333333333
-335 keep parsimony-informative 0.08333333333333333
-336 keep parsimony-informative 0.08333333333333333
-337 keep parsimony-informative 0.08333333333333333
-338 keep parsimony-informative 0.08333333333333333
-339 keep parsimony-informative 0.08333333333333333
-340 keep parsimony-informative 0.08333333333333333
-341 keep parsimony-informative 0.08333333333333333
-342 keep parsimony-informative 0.08333333333333333
+334 keep parsimony-informative 0.0833
+335 keep parsimony-informative 0.0833
+336 keep parsimony-informative 0.0833
+337 keep parsimony-informative 0.0833
+338 keep parsimony-informative 0.0833
+339 keep parsimony-informative 0.0833
+340 keep parsimony-informative 0.0833
+341 keep parsimony-informative 0.0833
+342 keep parsimony-informative 0.0833
 343 keep singleton 0.0
 344 keep singleton 0.0
 345 keep singleton 0.0
@@ -349,9 +349,9 @@
 349 keep singleton 0.0
 350 keep parsimony-informative 0.0
 351 keep parsimony-informative 0.0
-352 keep other 0.8333333333333334
-353 keep other 0.8333333333333334
-354 keep other 0.8333333333333334
+352 keep other 0.8333
+353 keep other 0.8333
+354 keep other 0.8333
 355 keep parsimony-informative 0.0
 356 keep parsimony-informative 0.0
 357 keep parsimony-informative 0.0
@@ -391,9 +391,9 @@
 391 keep parsimony-informative 0.0
 392 keep parsimony-informative 0.0
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 1933 keep singleton 0.5
 1934 keep singleton 0.5
 1935 keep singleton 0.5
 1936 keep singleton 0.5
 1937 keep parsimony-informative 0.5
 1938 keep parsimony-informative 0.5
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 1948 keep constant 0.0
 1949 keep constant 0.0
 1950 keep parsimony-informative 0.0
@@ -1981,63 +1981,63 @@
 1981 keep singleton 0.75
 1982 keep other 0.75
 1983 keep singleton 0.75
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 2002 keep parsimony-informative 0.25
 2003 keep parsimony-informative 0.25
 2004 keep singleton 0.25
 2005 keep singleton 0.25
 2006 keep singleton 0.25
 2007 keep parsimony-informative 0.25
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 2041 keep singleton 0.75
 2042 keep singleton 0.75
 2043 keep singleton 0.75
@@ -2053,144 +2053,144 @@
 2053 keep constant 0.75
 2054 keep singleton 0.75
 2055 keep singleton 0.75
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 2074 keep singleton 0.75
 2075 keep singleton 0.75
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 2194 keep singleton 0.75
 2195 keep singleton 0.75
 2196 keep singleton 0.75
@@ -2209,33 +2209,33 @@
 2209 keep constant 0.0
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 2239 keep singleton 0.0
 2240 keep parsimony-informative 0.0
 2241 keep parsimony-informative 0.0
@@ -2266,39 +2266,39 @@
 2266 keep parsimony-informative 0.0
 2267 keep singleton 0.0
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 2282 keep singleton 0.5
 2283 keep singleton 0.5
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 2302 keep parsimony-informative 0.5
 2303 keep singleton 0.5
 2304 keep singleton 0.5
@@ -2332,75 +2332,75 @@
 2332 keep constant 0.0
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 3876 keep parsimony-informative 0.25
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 3886 keep parsimony-informative 0.0
 3887 keep constant 0.0
 3888 keep parsimony-informative 0.0
@@ -3901,69 +3901,69 @@
 3901 keep parsimony-informative 0.0
 3902 keep parsimony-informative 0.0
 3903 keep parsimony-informative 0.0
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 3967 keep singleton 0.75
 3968 keep singleton 0.75
 3969 keep singleton 0.75
@@ -4009,15 +4009,15 @@
 4009 keep singleton 0.0
 4010 keep singleton 0.0
 4011 keep parsimony-informative 0.0
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 4021 keep singleton 0.0
 4022 keep singleton 0.0
 4023 keep parsimony-informative 0.0
@@ -4057,15 +4057,15 @@
 4057 keep parsimony-informative 0.5
 4058 keep singleton 0.5
 4059 keep parsimony-informative 0.5
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 4069 keep parsimony-informative 0.0
 4070 keep parsimony-informative 0.0
 4071 keep parsimony-informative 0.0
@@ -4129,9 +4129,9 @@
 4129 keep parsimony-informative 0.0
 4130 keep constant 0.0
 4131 keep parsimony-informative 0.0
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 4135 keep parsimony-informative 0.0
 4136 keep singleton 0.0
 4137 keep parsimony-informative 0.0
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 4147 keep parsimony-informative 0.0
 4148 keep singleton 0.0
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 4156 keep constant 0.0
 4157 keep constant 0.0
 4158 keep singleton 0.0
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 4162 keep parsimony-informative 0.0
 4163 keep constant 0.0
 4164 keep parsimony-informative 0.0
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 4183 keep singleton 0.0
 4184 keep parsimony-informative 0.0
 4185 keep parsimony-informative 0.0
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 4189 keep parsimony-informative 0.0
 4190 keep parsimony-informative 0.0
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 4204 keep parsimony-informative 0.25
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 4228 keep constant 0.75
 4229 keep singleton 0.75
 4230 keep singleton 0.75
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 4252 keep singleton 0.75
 4253 keep singleton 0.75
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 4312 keep parsimony-informative 0.0
 4313 keep parsimony-informative 0.0
 4314 keep parsimony-informative 0.0
@@ -4327,108 +4327,108 @@
 4327 keep singleton 0.0
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-6172 keep parsimony-informative 0.08333333333333333
-6173 keep parsimony-informative 0.08333333333333333
-6174 keep parsimony-informative 0.08333333333333333
-6175 keep parsimony-informative 0.08333333333333333
-6176 keep parsimony-informative 0.08333333333333333
-6177 keep parsimony-informative 0.08333333333333333
-6178 keep parsimony-informative 0.08333333333333333
-6179 keep parsimony-informative 0.08333333333333333
-6180 keep parsimony-informative 0.08333333333333333
-6181 keep singleton 0.08333333333333333
-6182 keep parsimony-informative 0.08333333333333333
-6183 keep parsimony-informative 0.08333333333333333
-6184 keep parsimony-informative 0.08333333333333333
-6185 keep parsimony-informative 0.08333333333333333
-6186 keep parsimony-informative 0.08333333333333333
+6169 keep singleton 0.0833
+6170 keep parsimony-informative 0.0833
+6171 keep parsimony-informative 0.0833
+6172 keep parsimony-informative 0.0833
+6173 keep parsimony-informative 0.0833
+6174 keep parsimony-informative 0.0833
+6175 keep parsimony-informative 0.0833
+6176 keep parsimony-informative 0.0833
+6177 keep parsimony-informative 0.0833
+6178 keep parsimony-informative 0.0833
+6179 keep parsimony-informative 0.0833
+6180 keep parsimony-informative 0.0833
+6181 keep singleton 0.0833
+6182 keep parsimony-informative 0.0833
+6183 keep parsimony-informative 0.0833
+6184 keep parsimony-informative 0.0833
+6185 keep parsimony-informative 0.0833
+6186 keep parsimony-informative 0.0833
 6187 keep parsimony-informative 0.0
 6188 keep parsimony-informative 0.0
 6189 keep parsimony-informative 0.0
@@ -6199,18 +6199,18 @@
 6199 keep parsimony-informative 0.0
 6200 keep parsimony-informative 0.0
 6201 keep parsimony-informative 0.0
-6202 keep parsimony-informative 0.08333333333333333
-6203 keep parsimony-informative 0.08333333333333333
-6204 keep parsimony-informative 0.08333333333333333
+6202 keep parsimony-informative 0.0833
+6203 keep parsimony-informative 0.0833
+6204 keep parsimony-informative 0.0833
 6205 keep parsimony-informative 0.5
 6206 keep singleton 0.5
 6207 keep parsimony-informative 0.5
-6208 keep parsimony-informative 0.16666666666666666
-6209 keep parsimony-informative 0.16666666666666666
-6210 keep parsimony-informative 0.16666666666666666
-6211 keep parsimony-informative 0.08333333333333333
-6212 keep parsimony-informative 0.08333333333333333
-6213 keep parsimony-informative 0.08333333333333333
+6208 keep parsimony-informative 0.1667
+6209 keep parsimony-informative 0.1667
+6210 keep parsimony-informative 0.1667
+6211 keep parsimony-informative 0.0833
+6212 keep parsimony-informative 0.0833
+6213 keep parsimony-informative 0.0833
 6214 keep parsimony-informative 0.0
 6215 keep singleton 0.0
 6216 keep parsimony-informative 0.0
@@ -6226,27 +6226,27 @@
 6226 keep singleton 0.0
 6227 keep parsimony-informative 0.0
 6228 keep parsimony-informative 0.0
-6229 keep constant 0.8333333333333334
-6230 keep constant 0.8333333333333334
-6231 keep other 0.8333333333333334
-6232 keep constant 0.8333333333333334
-6233 keep other 0.8333333333333334
-6234 keep other 0.8333333333333334
-6235 keep other 0.8333333333333334
-6236 keep constant 0.8333333333333334
-6237 keep other 0.8333333333333334
-6238 keep constant 0.8333333333333334
-6239 keep other 0.8333333333333334
-6240 keep other 0.8333333333333334
-6241 keep other 0.8333333333333334
-6242 keep other 0.8333333333333334
-6243 keep other 0.8333333333333334
-6244 keep other 0.8333333333333334
-6245 keep other 0.8333333333333334
-6246 keep other 0.8333333333333334
-6247 keep constant 0.8333333333333334
-6248 keep constant 0.8333333333333334
-6249 keep other 0.8333333333333334
+6229 keep constant 0.8333
+6230 keep constant 0.8333
+6231 keep other 0.8333
+6232 keep constant 0.8333
+6233 keep other 0.8333
+6234 keep other 0.8333
+6235 keep other 0.8333
+6236 keep constant 0.8333
+6237 keep other 0.8333
+6238 keep constant 0.8333
+6239 keep other 0.8333
+6240 keep other 0.8333
+6241 keep other 0.8333
+6242 keep other 0.8333
+6243 keep other 0.8333
+6244 keep other 0.8333
+6245 keep other 0.8333
+6246 keep other 0.8333
+6247 keep constant 0.8333
+6248 keep constant 0.8333
+6249 keep other 0.8333
 6250 keep parsimony-informative 0.0
 6251 keep parsimony-informative 0.0
 6252 keep parsimony-informative 0.0
@@ -6325,12 +6325,12 @@
 6325 keep singleton 0.0
 6326 keep parsimony-informative 0.0
 6327 keep parsimony-informative 0.0
-6328 keep parsimony-informative 0.08333333333333333
-6329 keep singleton 0.08333333333333333
-6330 keep parsimony-informative 0.08333333333333333
-6331 keep parsimony-informative 0.16666666666666666
-6332 keep singleton 0.16666666666666666
-6333 keep parsimony-informative 0.16666666666666666
+6328 keep parsimony-informative 0.0833
+6329 keep singleton 0.0833
+6330 keep parsimony-informative 0.0833
+6331 keep parsimony-informative 0.1667
+6332 keep singleton 0.1667
+6333 keep parsimony-informative 0.1667
 6334 keep parsimony-informative 0.25
 6335 keep parsimony-informative 0.25
 6336 keep parsimony-informative 0.25
@@ -6340,12 +6340,12 @@
 6340 keep parsimony-informative 0.25
 6341 keep parsimony-informative 0.25
 6342 keep singleton 0.25
-6343 trim other 0.9166666666666666
-6344 trim other 0.9166666666666666
-6345 trim other 0.9166666666666666
-6346 trim other 0.9166666666666666
-6347 trim other 0.9166666666666666
-6348 trim other 0.9166666666666666
+6343 trim other 0.9167
+6344 trim other 0.9167
+6345 trim other 0.9167
+6346 trim other 0.9167
+6347 trim other 0.9167
+6348 trim other 0.9167
 6349 keep parsimony-informative 0.25
 6350 keep parsimony-informative 0.25
 6351 keep parsimony-informative 0.25
diff --git a/tests/integration/expected/EOG091N44M8_aa.clipkit_kpi_smart_gaps b/tests/integration/expected/EOG091N44M8_aa.clipkit_kpi_smart_gaps
index e6b6001..f2c118e 100644
--- a/tests/integration/expected/EOG091N44M8_aa.clipkit_kpi_smart_gaps
+++ b/tests/integration/expected/EOG091N44M8_aa.clipkit_kpi_smart_gaps
@@ -1,468 +1,468 @@
 >200_S38|EOG091N44M8
-YAATEATSAIASAEGDLEVISQGDLQESSASG-GAAAAAGGAEAPAEKVK-ESDEDMGFG
-ISEYVGISPSNYAKIIDQYSHDDKKERVIIGAHVAAREMPDAISIRKIAKIVKVVGGMSD
-PYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
+YAATEATSAIASAEGDLEVISQGDLQESSASG-GAA-AAAGGAEAPAEKVK-ESDEDMGF
+GISEYVGISMPPSNYPLVDIPVDFENDAKIIDQYSHDDKKERVIIGAHVAAREMPDAISI
+RKIAKIVKVVGGMSDPYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
 >203_S40|EOG091N44M8
-YAATEATSAIASAEGDLEVISQGDLQESSASG-GAAAAAGGAEAPAEKVK-ESDEDMGFG
-ISEYVGISPSNYAKIIDQYSHDDKKERVIIGAHVAAREMPDAISIRKIAKIVKVVGGMSD
-PYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
+YAATEATSAIASAEGDLEVISQGDLQESSASG-GAA-AAAGGAEAPAEKVK-ESDEDMGF
+GISEYVGISMPPSNYPLVDIPVDFENDAKIIDQYSHDDKKERVIIGAHVAAREMPDAISI
+RKIAKIVKVVGGMSDPYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
 >206_S41|EOG091N44M8
-YAANESSSAIASAEGDLEVVSQGDLNEASTSGAAA-AAPAGGAAPAEKKE-KSDEDMGFG
-THEYVGIS------VLEQHAREDKRDKVVVAAGAAVKQMSEAVTLRKVEKVIMVIGGKSD
-HYTITAIFDTIQEASQEAIVLLEFLIALRNEEEDKVSAHL
+YAANESSSAIASAEGDLEVVSQGDLNEASTSGAAA--AAPAGGAAPAEKKE-KSDEDMGF
+GTHEYVGIS--------------------VLEQHAREDKRDKVVVAAGAAVKQMSEAVTL
+RKVEKVIMVIGGKSDHYTITAIFDTIQEASQEAIVLLEFLIALRNEEEDKVSAHL
 >207_S42|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFA
-G---ISLS----------------------------------------------------
-----------------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+AG---ISLS---------------------------------------------------
+-------------------------------------------------------
 >209_S43|EOG091N44M8
-YAATEASAAIASAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAATEASAAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >212_S45|EOG091N44M8
-HAANAESAAIGSADSELDVVAQGDIQESTTSGAGAAAAGGDAAAPAEKKE-KSDEDMGFG
-C-----------------------------------------------------------
--------TG-------------------------------
+HAANAESAAIGSADSELDVVAQGDIQESTTSGAGAA-AAGGDAAAPAEKKE-KSDEDMGF
+GC----------------------------------------------------------
+----------------------TG-------------------------------
 >215_S46|EOG091N44M8
-YAATEATSAIASAEGDLEVISQGDLQESSASG-GAAAAAGGAEAPAEKVK-ESDEDMGFG
-ISEYVGISPSNYAKIIDQYSHDDKKERVIIGAHVAAREMPDAISIRKIAKIVKVVGGMSD
-PYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
+YAATEATSAIASAEGDLEVISQGDLQESSASG-GAA-AAAGGAEAPAEKVK-ESDEDMGF
+GISEYVGISMPPSNYPLVDIPVDFENDAKIIDQYSHDDKKERVIIGAHVAAREMPDAISI
+RKIAKIVKVVGGMSDPYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
 >220_S48|EOG091N44M8
-YAANESSSAIASAEGDLEVVSQGDLNEASTSGAAA-AAPAGGAAPAEKKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSSAIASAEGDLEVVSQGDLNEASTSGAAA--AAPAGGAAPAEKKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >231_51|EOG091N44M8
-YAATEASAAIASAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAATEASAAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >232-S52|EOG091N44M8
-YAATEASAAIASAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAATEASAAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >236_53|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFA
-G---ISLS----------------------------------------------------
-----------------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+AG---ISLS---------------------------------------------------
+-------------------------------------------------------
 >244-S54|EOG091N44M8
-HAANESSAAIASADSELEVVAQGNLQESSTSAGGAAAAGGAAAAPAEKKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSAAIASADSELEVVAQGNLQESSTSAGGAA-AAGGAAAAPAEKKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >245_S55|EOG091N44M8
-YAATEATSAIASAEGDLEVISQGDLQESSASG-GAAAAAGGAEAPAEKVK-ESDEDMGFG
-ISEYVGISPSNYAKIIDQYSHDDKKERVIIGAHVAAREMPDAISIRKIAKVVKVVGGMSD
-PYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
+YAATEATSAIASAEGDLEVISQGDLQESSASG-GAA-AAAGGAEAPAEKVK-ESDEDMGF
+GISEYVGISMPPSNYPLVDIPVDFENDAKIIDQYSHDDKKERVIIGAHVAAREMPDAISI
+RKIAKVVKVVGGMSDPYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
 >247_s46|EOG091N44M8
-HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAAAAGGAAAAPAEKKE-KSDEDMGFG
-F-----------------------------------------------------------
--------KM-------------------------------
+HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAA-AAGGAAAAPAEKKE-KSDEDMGF
+GF----------------------------------------------------------
+----------------------KM-------------------------------
 >250_S57|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >252_S58|EOG091N44M8
-HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAAAAGGAAAAPAEKKE-KSDEDMGFG
-S-----------------------------------------------------------
--------KM-------------------------------
+HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAA-AAGGAAAAPAEKKE-KSDEDMGF
+GS----------------------------------------------------------
+----------------------KM-------------------------------
 >256_S59|EOG091N44M8
-HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAAAAGGAAAAPAEKKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAA-AAGGAAAAPAEKKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >257_S60|EOG091N44M8
-YAANEASAAIASAEGDVEVISKDDLQVSSASGGAAAAAAGGAAAPAEKKK-EDCDSSXIS
-AIEYVGIS------LIDQHSREDKKERVIIGANVAVRELSDVTSIRKVAKVIRYIAANSN
-PYNLAAVFDSIHEASREAIVVMEYHITMRSEEEASISTSI
+YAANEASAAIASAEGDVEVISKDDLQVSSASGGAAA-AAAGGAAAPAEKKK-EDCDSSXI
+SAIEYVGIS--------------------LIDQHSREDKKERVIIGANVAVRELSDVTSI
+RKVAKVIRYIAANSNPYNLAAVFDSIHEASREAIVVMEYHITMRSEEEASISTSI
 >258_S61|EOG091N44M8
-YAATEASAAIASAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFA
-G---ISLS----------------------------------------------------
-----------------------------------------
+YAATEASAAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+AG---ISLS---------------------------------------------------
+-------------------------------------------------------
 >259_S62|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >261_S63|EOG091N44M8
-YAATEASAAIASAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFA
-G---ISLV----------------------------------------------------
-----------------------------------------
+YAATEASAAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+AG---ISLV---------------------------------------------------
+-------------------------------------------------------
 >262_S64|EOG091N44M8
-YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >267_S66|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >269_S67|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >271_S68|EOG091N44M8
-YAATEASAAISSAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFA
-G---ISLS----------------------------------------------------
-----------------------------------------
+YAATEASAAISSAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+AG---ISLS---------------------------------------------------
+-------------------------------------------------------
 >274_S69|EOG091N44M8
-HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAAAAGGAAAAPAEKKE-KSDEDMGFG
-F-----------------------------------------------------------
--------FV-------------------------------
+HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAA-AAGGAAAAPAEKKE-KSDEDMGF
+GF----------------------------------------------------------
+----------------------FV-------------------------------
 >275_S70|EOG091N44M8
-YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >276_S71|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >277_S72|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFA
-G---ISLS----------------------------------------------------
-----------------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+AG---ISLS---------------------------------------------------
+-------------------------------------------------------
 >278_S73|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFA
-G---ISLS----------------------------------------------------
-----------------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+AG---ISLS---------------------------------------------------
+-------------------------------------------------------
 >280_S74|EOG091N44M8
-YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >284_S76|EOG091N44M8
-HAANESSAAIASADSELEVVAQGNLQESSTSAGGAAAAGGAAAAPAEKKE-KSDEDMGFG
-F-----------------------------------------------------------
--------VG-------------------------------
+HAANESSAAIASADSELEVVAQGNLQESSTSAGGAA-AAGGAAAAPAEKKE-KSDEDMGF
+GF----------------------------------------------------------
+----------------------VG-------------------------------
 >285_S77|EOG091N44M8
-HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAAAAGGAAAAPAEKKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAA-AAGGAAAAPAEKKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >288_S78|EOG091N44M8
-YAANESSSAIASAEGDLEVVSQGDLNEASTSGAAA-AAPAGGAAPAEKKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSSAIASAEGDLEVVSQGDLNEASTSGAAA--AAPAGGAAPAEKKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >289_S79|EOG091N44M8
-HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAAAAGGAAAAPAEKKE-KSDEDMGFG
-F-----------------------------------------------------------
--------FV-------------------------------
+HAANESSAAIASADSELEVVAQGNLQDSSTSAGGAA-AAGGAAAAPAEKKE-KSDEDMGF
+GF----------------------------------------------------------
+----------------------FV-------------------------------
 >Aspergillus_fumigatus_Af293_GCF_000002655.1|EOG091N44M8
-HAANTSSSEVASADEELNLIAEGDLQEASTSGAAAAAAAGGAAAPAEKKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANTSSSEVASADEELNLIAEGDLQEASTSGAAAAGAAAGGAAAPAEKKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Aspergillus_niger_GCF_000002855.3|EOG091N44M8
-YAANNTSAEISSAEEELQLLAEGDLQESTQSGAGAAGGAAAAEAPAEKKA-ASDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANNTSAEISSAEEELQLLAEGDLQESTQSGAGAA-GGAAAAEAPAEKKA-ASDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Aspergillus_oryzae_RIB40_GCF_000184455.2|EOG091N44M8
-HAANSTSVEISSADEELQVISEGDLQQTSESGAGAAAAAGG-DAPAE-KE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANSTSVEISSADEELQVISEGDLQQTSESGAGAAGAAAGG-DAPAE-KE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_antarcticum_GCA_002072345.1|EOG091N44M8
-YAANETSAAISSAEGDLDVIAEGNLQESSTSGAGAAAAAGGAAAPAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANETSAAISSAEGDLDVIAEGNLQESSTSGAGAA-AAAGGAAAPAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_biforme_FM169_GCA_000577785.1|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_brasilianum_GCA_000769745.1|EOG091N44M8
-YAANEASAAIASVEGDVEVISQGDLQESSASGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-IMEYVGISSTEGLHIIDKLSRDDKKERVIIGAHVAVREMPDAISIRKIAAVIRFIGGMSD
-LFTITAIFDSIQESSREAIELLEYYI--------------
+YAANEASAAIASVEGDVEVISQGDLQESSASGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GIMEYVGISSTSTEGQIAEMSCRSQSQLHIIDKLSRDDKKERVIIGAHVAVREMPDAISI
+RKIAAVIRFIGGMSDLFTITAIFDSIQESSREAIELLEYYI--------------
 >Penicillium_brasilianum_GCA_001048715.1|EOG091N44M8
-HAANESSVSIESADSELEVVAQGNLQDASASGAGAAAAAGGAAEAPAAKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSVSIESADSELEVVAQGNLQDASASGAGAA-AAAGGAAEAPAAKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_brasilianum_GCA_002016555.1|EOG091N44M8
-HAANESSVSIESADSELEVVAQGNLQDASASGAGAAAAAGGAAEAPAAKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSVSIESADSELEVVAQGNLQDASASGAGAA-AAAGGAAEAPAAKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_brasilianum_GCA_004916855.1|EOG091N44M8
-HAANESSVSIESADSELEVVAQGNLQDASASGAGAAAAAGGAAEAPAAKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSVSIESADSELEVVAQGNLQDASASGAGAA-AAAGGAAEAPAAKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_camemberti_FM_013_GCA_000513335.1|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_capsulatum_GCA_000943765.1|EOG091N44M8
-YAANESSAAISSAEGDLDVIAEGNLQESSTSGGAAAAAAGGAAAPAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAISSAEGDLDVIAEGNLQESSTSGGAAA-AAAGGAAAPAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_capsulatum_GCA_000943775.1|EOG091N44M8
-YAANESSAAISSAEGDLDVIAEGNLQESSTSGGAAAAAAGGAAAPAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAISSAEGDLDVIAEGNLQESSTSGGAAA-AAAGGAAAPAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_chrysogenum_GCA_000710275.1|EOG091N44M8
-YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_chrysogenum_GCA_000801355.1|EOG091N44M8
-YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_chrysogenum_GCA_002080375.1|EOG091N44M8
-YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_chrysogenum_KF-25_GCA_000816005.1|EOG091N44M8
-YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_chrysogenum_NCPC10086_GCA_000523475.1|EOG091N44M8
-YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_chrysogenum_NCPC10086_GCA_001773325.1|EOG091N44M8
-YAANETSAAISSAEGDLDVIAEGNLQESSTSGGGAAAAAGGAAAPAEKKKEESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANETSAAISSAEGDLDVIAEGNLQESSTSGGGAA-AAAGGAAAPAEKKKEESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_citrinum_GCA_001399475.1|EOG091N44M8
-HAANAESAAIGSADSELDVVAQGDIQESTTSGAGAAAAGGDAAAPAEKKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANAESAAIGSADSELDVVAQGDIQESTTSGAGAA-AAGGDAAAPAEKKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_citrinum_GCA_001950535.1|EOG091N44M8
-HAANAESAAIGSADSELDVVAQGDIQESTTSGAGAAAAGGDAAAPAEKKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANAESAAIGSADSELDVVAQGDIQESTTSGAGAA-AAGGDAAAPAEKKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_commune_162_3FA|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_coprophilum_GCA_002072405.1|EOG091N44M8
-YAANEASSAIASAEGDLEVISQGDLQEASTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAIASAEGDLEVISQGDLQEASTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_decumbens_GCA_000226395.1|EOG091N44M8
-YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_decumbens_GCA_002072245.1|EOG091N44M8
-YSANESSAAIGSADSELDLIAQGNLQEASTSAAGAAAAGGAADAPAE-KE-KSDDDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YSANESSAAIGSADSELDLIAQGNLQEASTSAAGAA-AAGGAADAPAE-KE-KSDDDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_digitatum_Pd01-ZJU_GCA_000485865.1|EOG091N44M8
-YAANEASSDIASAEGDLEVISQGDLQESSASGSAAAAAAGGAAAPAEKVK-ESDEDMGFD
-V-WMIGIS------VLDQYSRDNNKESIIIGVHVVVREMSGAISICRIAKVIRFTARERD
-PYTITSIFDSLQQASQGAMELLEYYV--------------
+YAANEASSDIASAEGDLEVISQGDLQESSASGSAAA-AAAGGAAAPAEKVK-ESDEDMGF
+DV-WMIGIS--------------------VLDQYSRDNNKESIIIGVHVVVREMSGAISI
+CRIAKVIRFTARERDPYTITSIFDSLQQASQGAMELLEYYV--------------
 >Penicillium_digitatum_PDC_102_GCA_001307865.1|EOG091N44M8
-YAANEASSDIASAEGDLEVISQGDLQESSASGSAAAAAAGGAAAPAEKVK-ESDEDMGFD
-V-WMIGISLSKGS-FLDQYSRDNNKESIIIGVHVVVREMSGAISICRIAKVIRFTARERD
-PYTITSIFDSLQQASQGAMELLEYYVAMKSVDEANI----
+YAANEASSDIASAEGDLEVISQGDLQESSASGSAAA-AAAGGAAAPAEKVK-ESDEDMGF
+DV-WMIGIS--LSKG------------S-FLDQYSRDNNKESIIIGVHVVVREMSGAISI
+CRIAKVIRFTARERDPYTITSIFDSLQQASQGAMELLEYYVAMKSVDEANI----
 >Penicillium_digitatum_PHI26_GCA_000315665.1|EOG091N44M8
-YAANEASSDIASAEGDLEVISQGDLQESSASGSAAAAAAGGAAAPAEKVK-ESDEDMGFD
-V-WMIGIS------VLDQYSRDNNKESIIIGVHVVVREMSGAISICRIAKVIRFTARERD
-PYTITSIFDSLQQASQGAMELLEYYVAMKSVDEANI----
+YAANEASSDIASAEGDLEVISQGDLQESSASGSAAA-AAAGGAAAPAEKVK-ESDEDMGF
+DV-WMIGIS--------------------VLDQYSRDNNKESIIIGVHVVVREMSGAISI
+CRIAKVIRFTARERDPYTITSIFDSLQQASQGAMELLEYYVAMKSVDEANI----
 >Penicillium_expansum_GCA_000688875.1|EOG091N44M8
-YAANEASAAIASVEGDVEVISQGDLQESSASGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-IMEYVGISSTEGLHIIDKLSRDDKKERVIIGAHVAVREMPDAISIRKIAAVIRFIGGMSD
-LFTITAIFDSIQESSREAIELLEYYIAM------------
+YAANEASAAIASVEGDVEVISQGDLQESSASGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GIMEYVGISSTSTEGQIAEMSCRSQSQLHIIDKLSRDDKKERVIIGAHVAVREMPDAISI
+RKIAAVIRFIGGMSDLFTITAIFDSIQESSREAIELLEYYIAM------------
 >Penicillium_expansum_GCA_000769735.1|EOG091N44M8
-YAANEASAAIASVEGDVEVISQGDLQESSASGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-IMEYVGISSTEGLHIIDKLSRDDKKERVIIGAHVAVREMPDAISIRKIAAVIRFIGGMSD
-LFTITAIFDSIQESSREAIELLEYYI--------------
+YAANEASAAIASVEGDVEVISQGDLQESSASGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GIMEYVGISSTSTEGQIAEMSCRSQSQLHIIDKLSRDDKKERVIIGAHVAVREMPDAISI
+RKIAAVIRFIGGMSDLFTITAIFDSIQESSREAIELLEYYI--------------
 >Penicillium_expansum_GCA_000769755.1|EOG091N44M8
-YAANEASAAIASVEGDVEVISQGDLQESSASGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-IMEYVGISSTEGLHIIDKLSRDDKKERVIIGAHVAVREMPDAISIRKIAAVIRFIGGMSD
-LFTITAIFDSIQESSREAIELLEYYIAM------------
+YAANEASAAIASVEGDVEVISQGDLQESSASGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GIMEYVGISSTSTEGQIAEMSCRSQSQLHIIDKLSRDDKKERVIIGAHVAVREMPDAISI
+RKIAAVIRFIGGMSDLFTITAIFDSIQESSREAIELLEYYIAM------------
 >Penicillium_expansum_GCA_001750045.2|EOG091N44M8
-YAANEASAAIASVEGDVEVISQGDLQESSASGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-IMEYVGISSTEGLHIIDKLSRDDKKERVIIGAHVAVREMPDAISIRKIAAVIRFIGGMSD
-LFTITAIFDSIQESSREAIELLEYYIAM------------
+YAANEASAAIASVEGDVEVISQGDLQESSASGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GIMEYVGISSTSTEGQIAEMSCRSQSQLHIIDKLSRDDKKERVIIGAHVAVREMPDAISI
+RKIAAVIRFIGGMSDLFTITAIFDSIQESSREAIELLEYYIAM------------
 >Penicillium_expansum_GCA_004302965.1|EOG091N44M8
-YAANEASAAIASVEGDVEVISQGDLQESSASGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-IMEYVGISSTEGLHIIDKLSRDDKKERVIIGAHVAVREMPDAISIRKIAAVIRFIGGMSD
-LFTITAIFDSIQESSREAIELLEYYIAM------------
+YAANEASAAIASVEGDVEVISQGDLQESSASGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GIMEYVGISSTSTEGQIAEMSCRSQSQLHIIDKLSRDDKKERVIIGAHVAVREMPDAISI
+RKIAAVIRFIGGMSDLFTITAIFDSIQESSREAIELLEYYIAM------------
 >Penicillium_expansum_NRRL_62431_GCA_000584915.1|EOG091N44M8
-YAANEASAAIASVEGDVEVISQGDLQESSASGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-IMEYVGISSTEGLHIIDKLSRDDKKERVIIGAHVAVREMPDAISIRKIAAVIRFIGGMSD
-LFTITAIFDSIQESSREAIELLEYYIAM------------
+YAANEASAAIASVEGDVEVISQGDLQESSASGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GIMEYVGISSTSTEGQIAEMSCRSQSQLHIIDKLSRDDKKERVIIGAHVAVREMPDAISI
+RKIAAVIRFIGGMSDLFTITAIFDSIQESSREAIELLEYYIAM------------
 >Penicillium_expansum_T01_GCA_001008385.1|EOG091N44M8
-YAANEASAAIASVEGDVEVISQGDLQESSASGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-IMEYVGISSTEGLHIIDKLSRDDKKERVIIGAHVAVREMPDAISIRKIAAVIRFIGGMSD
-LFTITAIFDSIQESSREAIELLEYYI--------------
+YAANEASAAIASVEGDVEVISQGDLQESSASGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GIMEYVGISSTSTEGQIAEMSCRSQSQLHIIDKLSRDDKKERVIIGAHVAVREMPDAISI
+RKIAAVIRFIGGMSDLFTITAIFDSIQESSREAIELLEYYI--------------
 >Penicillium_expansum_YT02_GCA_002072455.1|EOG091N44M8
-HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAGGAAEAPAAKE-KSDDDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAAGGAAEAPAAKE-KSDDDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_flavigenum_GCA_002072365.1|EOG091N44M8
-YAANEASAAIDSAEADLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASAAIDSAEADLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_freii_GCA_001513925.1|EOG091N44M8
-YAATEASAAISSAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAATEASAAISSAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_fuscoglaucum_FM041_GCA_000576735.1|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFA
-G---ISLS----------------------------------------------------
-----------------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+AG---ISLS---------------------------------------------------
+-------------------------------------------------------
 >Penicillium_griseofulvum_GCA_001561935.1|EOG091N44M8
-YAANEASSDIASAEGDLEVISQGDLQEASTTGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSDIASAEGDLEVISQGDLQEASTTGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_griseofulvum_GCA_001735785.1|EOG091N44M8
-YAANEASSDIASAEGDLEVISQGDLQEASTTGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSDIASAEGDLEVISQGDLQEASTTGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_italicum_GCA_000769765.1|EOG091N44M8
-YAANEASSAIASAEGDLEVISQGDLQESSASGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_italicum_GCA_001008395.1|EOG091N44M8
-YAANEASSAIASAEGDLEVISQGDLQESSASGAGAAAAAGGAAAPAEKEK-ESDEDMGFG
-IVEYVGIS------VIDQHSRDDNEERVIIGAHVAVREMSDLISTRKIATVTRFIGGMSD
-PYNITAIFDSIQEASREAIELLEYHIAMTNADEARISASV
+YAANEASSAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGAAAPAEKEK-ESDEDMGF
+GIVEYVGIS--------------------VIDQHSRDDNEERVIIGAHVAVREMSDLIST
+RKIATVTRFIGGMSDPYNITAIFDSIQEASREAIELLEYHIAMTNADEARISASV
 >Penicillium_italicum_GCA_002116305.1|EOG091N44M8
-YAANEASSAIASAEGDLEVISQGDLQESSASGAGAAAAAGGAAAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_janthinellum_GCA_002369805.1|EOG091N44M8
-HAANESSASIESADSDLEVVAQGNLQDASASGAGGAAAAGGAAEAPAAKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSASIESADSDLEVVAQGNLQDASASGAGGAGAAAGGAAEAPAAKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_nalgiovense_FM193_GCA_000577395.2|EOG091N44M8
-YAANEASTAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASTAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_nalgiovense_GCA_002072425.1|EOG091N44M8
-YAANEASTAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASTAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_nordicum_GCA_000315645.2|EOG091N44M8
-YAANEASSDIASAEGDLEVISQGDLQESSASGSAAAAAAGGAAAPAEKVK-ESDEDMGFD
-V-WMIGIS------VLDQYSRDNNKESIIIGVHVVVREMSGAISICRIAKVIRFTARERD
-PYTITSIFDSLQQASQGAMELLEYYVA-GLCSQEEV----
+YAANEASSDIASAEGDLEVISQGDLQESSASGSAAA-AAAGGAAAPAEKVK-ESDEDMGF
+DV-WMIGIS--------------------VLDQYSRDNNKESIIIGVHVVVREMSGAISI
+CRIAKVIRFTARERDPYTITSIFDSLQQASQGAMELLEYYVA-GLCSQEEV----
 >Penicillium_nordicum_GCA_000733025.2|EOG091N44M8
-YAATEATSAIASAEGDLEVISQGDLQESSASG-GAAAAAGGAEAPAEKVK-ESDEDMGFG
-ISEYVGISPSNYAKIIDQYSHDDKKERVIIGAHVAAREMSDAISIRKIAKIVKVVGGMSD
-PYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
+YAATEATSAIASAEGDLEVISQGDLQESSASG-GAA-AAAGGAEAPAEKVK-ESDEDMGF
+GISEYVGISMPPSNYPLVDIPVDFENDAKIIDQYSHDDKKERVIIGAHVAAREMSDAISI
+RKIAKIVKVVGGMSDPYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
 >Penicillium_nordicum_GCA_001278595.1|EOG091N44M8
-YAATEATSAIASAEGDLEVISQGDLQESSASG-GAAAAAGGAEAPAEKVK-ESDEDMGFG
-ISEYVGIS----AKIIDQYSHDDKKERVIIGAHVAAREMSDAISIRKIAKIVKAVGGMSD
-PYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
+YAATEATSAIASAEGDLEVISQGDLQESSASG-GAA-AAAGGAEAPAEKVK-ESDEDMGF
+GISEYVGIS------------------AKIIDQYSHDDKKERVIIGAHVAAREMSDAISI
+RKIAKIVKAVGGMSDPYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
 >Penicillium_oxalicum_114-2_GCA_000346795.1|EOG091N44M8
-HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAGGAAEAPAAKE-KSDDDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAAGGAAEAPAAKE-KSDDDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_oxalicum_GCA_001723175.2|EOG091N44M8
-HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAGGAAEAPAAKE-KSDDDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAAGGAAEAPAAKE-KSDDDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_oxalicum_GCA_004153425.1|EOG091N44M8
-HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAGGAAEAPAAKE-KSDDDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAAGGAAEAPAAKE-KSDDDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_oxalicum_GCA_004521935.1|EOG091N44M8
-HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAGGAAEAPAAKE-KSDDDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAAGGAAEAPAAKE-KSDDDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_oxalicum_GCA_005546515.1|EOG091N44M8
-HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAGGAAEAPAAKE-KSDDDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAAGGAAEAPAAKE-KSDDDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_oxalicum_JU-A10-T_GCA_000383025.1|EOG091N44M8
-HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAGGAAEAPAAKE-KSDDDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSASIESADSELEVVSQGNLQDSSSSGA--AAAAAGGAAEAPAAKE-KSDDDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_paneum_FM227_GCA_000577715.1|EOG091N44M8
-YAGNDDPSAIASAEGDVEVISKGDLQESSASGGGGAAAAAGAAAPAEKKKEESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAGNDDPSAIASAEGDVEVISKGDLQESSASGGGGA-AAAAGAAAPAEKKKEESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_paxilli_ATCC_26601_GCA_000347475.1|EOG091N44M8
-HAANESSAAIASADSDLDVVAQGDIQEASSSGAGAAAGGAAADAPAEKEK--SDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSAAIASADSDLDVVAQGDIQEASSSGAGAA-AGGAAADAPAEKEK--SDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_polonicum_GCA_002072265.1|EOG091N44M8
-YAATEASAAIASAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFA
-G---ISLS----------------------------------------------------
-----------------------------------------
+YAATEASAAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+AG---ISLS---------------------------------------------------
+-------------------------------------------------------
 >Penicillium_polonicum_GCA_003344595.1|EOG091N44M8
-YAATEASAAIASAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAATEASAAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_roqueforti_FM164_GCA_000513255.1|EOG091N44M8
-YAANEASAAIASAEGDVEVISKDDLQVSSASGGAAAAAAGGAAAPAEKKK-EDCDSSXIS
-AIEYVGIS------VIDQHSREDKKERVIIGANVAVRELSDVTSIRKVAKVIRYIAANSN
-PYNLAAVFDSIHEASREAIVVMEYHITMRSEEEASISTSI
+YAANEASAAIASAEGDVEVISKDDLQVSSASGGAAA-AAAGGAAAPAEKKK-EDCDSSXI
+SAIEYVGIS--------------------VIDQHSREDKKERVIIGANVAVRELSDVTSI
+RKVAKVIRYIAANSNPYNLAAVFDSIHEASREAIVVMEYHITMRSEEEASISTSI
 >Penicillium_roqueforti_GCA_000737485.2|EOG091N44M8
-YAANEASAAIASAEGDVEVISKDDLQVSSASGGAAAAAAGGAAAPAEKKK-EDCDSSXIS
-AIEYVGIS------LIDQHSREDKKERVIIGANVAVRELSDVTSIRKVAKVIRYIAANSN
-PYNLAAVFDSIHEASREAIVVMEYHITMRSEEEASISTSI
+YAANEASAAIASAEGDVEVISKDDLQVSSASGGAAA-AAAGGAAAPAEKKK-EDCDSSXI
+SAIEYVGIS--------------------LIDQHSREDKKERVIIGANVAVRELSDVTSI
+RKVAKVIRYIAANSNPYNLAAVFDSIHEASREAIVVMEYHITMRSEEEASISTSI
 >Penicillium_roqueforti_GCA_001599855.1|EOG091N44M8
-YAANEASAAIASAEGDVEVISKDDLQVSSASGGAAAAAAGGAAAPAEKKK-EDCDSSXIS
-AIEYVGIS------LIDQHSREDKKERVIIGANVAVRELSDVTSIRKVAKVIRYIAANSN
-PYNLAAVFDSIHEASREAIVVMEYHITMRSEEEASISTSI
+YAANEASAAIASAEGDVEVISKDDLQVSSASGGAAA-AAAGGAAAPAEKKK-EDCDSSXI
+SAIEYVGIS--------------------LIDQHSREDKKERVIIGANVAVRELSDVTSI
+RKVAKVIRYIAANSNPYNLAAVFDSIHEASREAIVVMEYHITMRSEEEASISTSI
 >Penicillium_roqueforti_GCA_001939915.1|EOG091N44M8
-YAANEASAAIASAEGDVEVISKDDLQVSSASGGAAAAAAGGAAAPAEKKK-EDCDSSXIS
-AIEYVGIS------VIDQHSREDKKERVIIGANVAVRELSDVTSIRKVAKVIRYIAANSN
-PYNLAAVFDSIHEASREAIVVMEYHITMRSEEEASISTSI
+YAANEASAAIASAEGDVEVISKDDLQVSSASGGAAA-AAAGGAAAPAEKKK-EDCDSSXI
+SAIEYVGIS--------------------VIDQHSREDKKERVIIGANVAVRELSDVTSI
+RKVAKVIRYIAANSNPYNLAAVFDSIHEASREAIVVMEYHITMRSEEEASISTSI
 >Penicillium_sclerotiorum_GCA_001750025.1|EOG091N44M8
-YAANAQSAAVESADSELDLIAQGDINEASTSGAGAAGGATTTEAAPAAKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANAQSAAVESADSELDLIAQGDINEASTSGAGAA-GGATTTEAAPAAKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_solitum_GCA_000952775.2|EOG091N44M8
-YAATEASAAIASAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFA
-G---ISLS----------------------------------------------------
-----------------------------------------
+YAATEASAAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+AG---ISLS---------------------------------------------------
+-------------------------------------------------------
 >Penicillium_solitum_GCA_001750005.1|EOG091N44M8
-YAANEAASAISSAEGDLEVIAQGDLQESSASGAGAAAAAGGDAAPAEKAK-ESDEDMGFG
-V-----------------------------------------------------------
--------FG-------------------------------
+YAANEAASAISSAEGDLEVIAQGDLQESSASGAGAA-AAAGGDAAPAEKAK-ESDEDMGF
+GV----------------------------------------------------------
+----------------------FG-------------------------------
 >Penicillium_solitum_GCA_002072235.1|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_sp.12|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_sp._CF05_GCA_002916455.1|EOG091N44M8
-YAANEASTAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASTAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_sp._MA_6036_GCA_003138045.1|EOG091N44M8
-YAANEASSAIASAEGDLEVVSQGSLDEASTSGAG--AAAGG-AAPAEKEE-KSDEDMGFG
-THEYVGIS------LLEQHAREDKRDKVVVAAGATVKQMSDGVTLRKVEKVIMVTGGNSN
-HYTITAIFDTIQEASQTAIVLLQFLIALSSEDEEKISAHV
+YAANEASSAIASAEGDLEVVSQGSLDEASTSGAG---AAAGG-AAPAEKEE-KSDEDMGF
+GTHEYVGIS--------------------LLEQHAREDKRDKVVVAAGATVKQMSDGVTL
+RKVEKVIMVTGGNSNHYTITAIFDTIQEASQTAIVLLQFLIALSSEDEEKISAHV
 >Penicillium_sp._MA_6040_GCA_003138025.1|EOG091N44M8
-YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAAAAAGGAEAAAEKKKVESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANESSAAIDSAEGDLEVIAQGDLQEASTSGGAAA-AAAGGAEAAAEKKKVESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_sp.MB|EOG091N44M8
-YAATEASAAIASAEGDLEVISQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFA
-G---ISLV----------------------------------------------------
-----------------------------------------
+YAATEASAAIASAEGDLEVISQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+AG---ISLV---------------------------------------------------
+-------------------------------------------------------
 >Penicillium_sp._MT2_MMC-2018_GCA_003852855.1|EOG091N44M8
-HAANESSASIESADSDLEVVAQGNLQDASASGAGGAAAAGGAAEAPAAKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSASIESADSDLEVVAQGNLQDASASGAGGAGAAAGGAAEAPAAKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_sp._occitanis_GCA_002382835.1|EOG091N44M8
-HGANASSASINEADEELELLAEGDIQEASSSGAG-GATAAGGAAAAEKKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HGANASSASINEADEELELLAEGDIQEASSSGAG-GGATAAGGAAAAEKKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_sp._occitanis_GCA_002382855.1|EOG091N44M8
-HGANASSASINEADEELELLAEGDIQEASSSGAG-GATAAGGAAAAEKKE-KSDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HGANASSASINEADEELELLAEGDIQEASSSGAG-GGATAAGGAAAAEKKE-KSDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_sp._SPG-F15_GCA_003800485.1|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAAAAAGGAAAPAEKVK-ESDEDMGFA
-G---ISLS----------------------------------------------------
-----------------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSTSGAGAA-AAAGGAAAPAEKVK-ESDEDMGF
+AG---ISLS---------------------------------------------------
+-------------------------------------------------------
 >Penicillium_sp._SPG-F1_GCA_003800495.1|EOG091N44M8
-YAANEASSAISSAEGDLEVIAQGDLQESSASGAGAAAAAGGADAPAEKVK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASSAISSAEGDLEVIAQGDLQESSASGAGAA-AAAGGADAPAEKVK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_sp._W3_MMC-2018_GCA_004959885.1|EOG091N44M8
-YNGKANAAAISSSEEEVSLISADDISEAQETGTVAAGAAASSDAPAE-KE-KSDDDMGFG
-VNDY-------------------------T--------EEPPRKLKH--QQYKTKKPPGI
-I--II--ED--TELDTSNLVLLQL-L-L------------
+YNGKANAAAISSSEEEVSLISADDISEAQETGTVAA-GAAASSDAPAE-KE-KSDDDMGF
+GVNDY---------------------------------------T--------EEPPRKL
+KH--QQYKTKKPPGII--II--ED--TELDTSNLVLLQL-L-L------------
 >Penicillium_steckii_GCA_002072375.1|EOG091N44M8
-HAANAESAAIGSADSELDVVAQGDIQESTTSGAGAAAAGGDAAAPAEKKE-KSDEDMGFV
-M-----------------------------------------------------------
--------WC-------------------------------
+HAANAESAAIGSADSELDVVAQGDIQESTTSGAGAA-AAGGDAAAPAEKKE-KSDEDMGF
+VM----------------------------------------------------------
+----------------------WC-------------------------------
 >Penicillium_subrubescens_GCA_001908125.1|EOG091N44M8
-HAANESSASIESADSELEVVAQGNLQDASTSGAGGAAAAGGAAEAPAAKE-KSDDDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+HAANESSASIESADSELEVVAQGNLQDASTSGAGGAGAAAGGAAEAPAAKE-KSDDDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
 >Penicillium_verrucosum_GCA_000970515.2|EOG091N44M8
-YAATEATSAIASAEGDLEVISQGDLQESSASG-GAAAAAGGAEAPAEKVK-ESDEDMGFG
-ISEYVGISPSNYAKIIDQYSHDDKKERVIIGAHVAAREMPDAISIRKIAKIVKVVGGMSD
-PYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
+YAATEATSAIASAEGDLEVISQGDLQESSASG-GAA-AAAGGAEAPAEKVK-ESDEDMGF
+GISEYVGISMPPSNYPLVDIPVDFENDAKIIDQYSHDDKKERVIIGAHVAAREMPDAISI
+RKIAKIVKVVGGMSDPYTITAIFDSIQEAARETIELMEYYIAMTSADQAMIGASI
 >Penicillium_vulpinum_GCA_002072255.1|EOG091N44M8
-YAANEASAAIASAEGDLDVISQGDLQQASTSGAGAAAGGAAAAAPAEKEK-ESDEDMGFG
-L-----------------------------------------------------------
--------FD-------------------------------
+YAANEASAAIASAEGDLDVISQGDLQQASTSGAGAA-AGGAAAAAPAEKEK-ESDEDMGF
+GL----------------------------------------------------------
+----------------------FD-------------------------------
diff --git a/tests/integration/expected/EOG091N44M8_nt.clipkit_kpi_smart_gaps b/tests/integration/expected/EOG091N44M8_nt.clipkit_kpi_smart_gaps
index 564d519..5cf7a3a 100644
--- a/tests/integration/expected/EOG091N44M8_nt.clipkit_kpi_smart_gaps
+++ b/tests/integration/expected/EOG091N44M8_nt.clipkit_kpi_smart_gaps
@@ -1,1404 +1,1521 @@
 >200_S38|EOG091N44M8
 ttcctcccccccctccctgaggcccactccgcccagcccctcccccccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgct---gtccctctctccgctgccgtg
-tccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatactct
-cttctctcccgcgtacctccccctcttactaaagctacagatacgcccattatatgaact
-ggttgtaaatggcgctctcaaccagcactaacacaactgtcgtcgccgccccatcattaa
-cacccgcgggatgaacctgccttccagccatcgatgcgtcacctgaactcgaatggtttg
-ggggtgcctgccagtaaggtgttggcgggatgtgagccttgttcgccacgtattacccta
-tacggttgctttacgttcgattagctcttgacttcggcgctactactccttgataggggc
-ccgaccatctaggaacgacatctccttcgtccacgtgcagttcatgccgcctagcccgat
-ccttgttagttttgatcttttacttccgtaggtagcctattcttttgactcgtagtcgcc
-agtcgtcactgcaaggtgcagcgtttcccccgatg
+gcactcccggccggagcgctccttgccctctccgct---gtccctctct---ccgctgcc
+gtgtccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatac
+tctcttctctcccgcgtacctccccccaatgcatcttactacccgtcccaagtggactgc
+aagtaagctacagatacgcccattatatgaactggttgtaaatggcgctctcaaccagca
+ctaacacaactgtcgtcgccgccccatcattaacacccgcgggatgaacctgccttccag
+ccatcgatgcgtcacctgaactcgaatggtttgggggtgcctgccagtaaggtgttggcg
+ggatgtgagccttgttcgccacgtattaccctatacggttgctttacgttcgattagctc
+ttgacttcggcgctactactccttgataggggcccgaccatctaggaacgacatctcctt
+cgtccacgtgcagttcatgccgcctagcccgatccttgttagttttgatcttttacttcc
+gtaggtagcctattcttttgactcgtagtcgccagtcgtcactgcaaggtgcagcgtttc
+ccccgatg
 >203_S40|EOG091N44M8
 ttcctcccccccctccctgaggcccactccgcccagcccctcccccccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgct---gtccctctctccgctgccgtg
-tccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatactct
-cttctctcccgcgtacctccccctcttactaaagctacagatacgcccattatatgaact
-ggttgtaaatggcgctctcaaccagcactaacacaactgtcgtcgccgccccatcattaa
-cacccgcgggatgaacctgccttccagccatcgatgcgtcacctgaactcgaatggtttg
-ggggtgcctgccagtaaggtgttggcgggatgtgagccttgttcgccacgtattacccta
-tacggttgctttacgttcgattagctcttgacttcggcgctactactccttgataggggc
-ccgaccatctaggaacgacatctccttcgtccacgtgcagttcatgccgcctagcccgat
-ccttgttagttttgatcttttacttccgtaggtagcctattcttttgactcgtagtcgcc
-agtcgtcactgcaaggtgcagcgtttcccccgatg
+gcactcccggccggagcgctccttgccctctccgct---gtccctctct---ccgctgcc
+gtgtccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatac
+tctcttctctcccgcgtacctccccccaatgcatcttactacccgtcccaagtggactgc
+aagtaagctacagatacgcccattatatgaactggttgtaaatggcgctctcaaccagca
+ctaacacaactgtcgtcgccgccccatcattaacacccgcgggatgaacctgccttccag
+ccatcgatgcgtcacctgaactcgaatggtttgggggtgcctgccagtaaggtgttggcg
+ggatgtgagccttgttcgccacgtattaccctatacggttgctttacgttcgattagctc
+ttgacttcggcgctactactccttgataggggcccgaccatctaggaacgacatctcctt
+cgtccacgtgcagttcatgccgcctagcccgatccttgttagttttgatcttttacttcc
+gtaggtagcctattcttttgactcgtagtcgccagtcgtcactgcaaggtgcagcgtttc
+ccccgatg
 >206_S41|EOG091N44M8
 tccctcccccccctctacgagtccctctccgcccagcccctcccccccctgggtccccgg
-gcgctcccggcacgagcgtgtttcaccccttccgttgctccct-----cccgctcccccg
-cgtctctccgtagaagaagaag--agtccgatggacatgctcggaactcacgaatactct
-ctcttcccccgcgtacctcccc------------------gcccacccgccacggtcgcg
-agctagcgctctaagtcgtcgtccgttaacgggcgctgcgtgtcccagtcaggcaggcta
-cctgtaaaacgccgaagcatacctgtctgaacggtgtcccccaggagggagaactgctct
-actgtgctcgcggactgggtattgatggtaaatgagtactctccatcgtgaatcacttta
-catagccaccccagttttgactagcagcaaactcgagcggcgtagtggccttcaaagggc
-gagaatcccgataaatagatcgttccccgcccccgagctgcctgcccccttccccctgag
-cttctctcgtcttttctccctgcccccttgggctacccattgagacggtcaactatctag
-aatagagaaaatggagcgccatgctctttcctcgc
+gcgctcccggcacgagcgtgtttcaccccttccgttgctccct-----c---ccgctccc
+ccgcgtctctccgtagaagaagaag--agtccgatggacatgctcggaactcacgaatac
+tctctcttcccccgcgtacctcccc-----------------------------------
+-------------gcccacccgccacggtcgcgagctagcgctctaagtcgtcgtccgtt
+aacgggcgctgcgtgtcccagtcaggcaggctacctgtaaaacgccgaagcatacctgtc
+tgaacggtgtcccccaggagggagaactgctctactgtgctcgcggactgggtattgatg
+gtaaatgagtactctccatcgtgaatcactttacatagccaccccagttttgactagcag
+caaactcgagcggcgtagtggccttcaaagggcgagaatcccgataaatagatcgttccc
+cgcccccgagctgcctgcccccttccccctgagcttctctcgtcttttctccctgccccc
+ttgggctacccattgagacggtcaactatctagaatagagaaaatggagcgccatgctct
+ttcctcgc
 >207_S42|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga------------
-----------aaactattcc----------------------------------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga---------
+-------------aaactattcc-------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >209_S43|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccagcccctcccctccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcggtctc------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >212_S45|EOG091N44M8
 ccccaccctgcctgccacgccgagctcgccgcctaggccctccccttcctctctgcccgc
-gcgcgtccggacggagtgctctataccccttccgttgctgtctcccc--ctgctggtgta
-cccctccccgtagaagaagggg--agtccgatggacatgctcggttgt------------
-----a-------------------------------------------------------
+gcgcgtccggacggagtgctctataccccttccgttgctgtctcccc-----ctgctggt
+gtacccctccccgtagaagaagggg--agtccgatggacatgctcggttgt---------
+-------a----------------------------------------------------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------accggc------
 ------------------------------------------------------------
----------------accggc---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >215_S46|EOG091N44M8
 ttcctcccccccctccctgaggcccactccgcccagcccctcccccccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgct---gtccctctctccgctgccgtg
-tccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatactct
-cttctctcccgcgtacctccccctcttactaaagctacagatacgcccattatatgaact
-ggttgtaaatggcgctctcaaccagcactaacacaactgtcgtcgccgccccatcattaa
-cacccgcgggatgaacctgccttccagccatcgatgcgtcacctgaactcgaatggtttg
-ggggtgcctgccagtaaggtgttggcgggatgtgagccttgttcgccacgtattacccta
-tacggttgctttacgttcgattagctcttgacttcggcgctactactccttgataggggc
-ccgaccatctaggaacgacatctccttcgtccacgtgcagttcatgccgcctagcccgat
-ccttgttagttttgatcttttacttccgtaggtagcctattcttttgactcgtagtcgcc
-agtcgtcactgcaaggtgcagcgtttcccccgatg
+gcactcccggccggagcgctccttgccctctccgct---gtccctctct---ccgctgcc
+gtgtccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatac
+tctcttctctcccgcgtacctccccccaatgcatcttactacccgtcccaagtggactgc
+aagtaagctacagatacgcccattatatgaactggttgtaaatggcgctctcaaccagca
+ctaacacaactgtcgtcgccgccccatcattaacacccgcgggatgaacctgccttccag
+ccatcgatgcgtcacctgaactcgaatggtttgggggtgcctgccagtaaggtgttggcg
+ggatgtgagccttgttcgccacgtattaccctatacggttgctttacgttcgattagctc
+ttgacttcggcgctactactccttgataggggcccgaccatctaggaacgacatctcctt
+cgtccacgtgcagttcatgccgcctagcccgatccttgttagttttgatcttttacttcc
+gtaggtagcctattcttttgactcgtagtcgccagtcgtcactgcaaggtgcagcgtttc
+ccccgatg
 >220_S48|EOG091N44M8
 tccctcccccccctctacgagtccctctccgcccagcccctcccccccctgggtccccgg
-gcgctcccggcacgagcgtgtttcaccccttccgttgctccct-----cccgctcccccg
-cgtctctccgtagaagaagaag--agtccgatggacatgctcggtctc------------
+gcgctcccggcacgagcgtgtttcaccccttccgttgctccct-----c---ccgctccc
+ccgcgtctctccgtagaagaagaag--agtccgatggacatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >231_51|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccagcccctcccctccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcggtctc------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >232-S52|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccagcccctcccctccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcggtctc------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >236_53|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga------------
-----------aaactattcc----------------------------------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga---------
+-------------aaactattcc-------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >244-S54|EOG091N44M8
 ccccatccactcctccacgagtccctcgccgcccagctcctcccctctctcagcgcccgg
-gtgcgtgcgaccggagcgctcttcaccccctcgcctggtgtctctctc-ctgccggagtc
-tccccccccgtagaagaagggg--agtccgatggacatgctcggtctc------------
+gtgcgtgcgaccggagcgctcttcaccccctcgcctggtgtctctctc----ctgccgga
+gtctccccccccgtagaagaagggg--agtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >245_S55|EOG091N44M8
 ttcctcccccccctccctgaggcccactccgcccagcccctcccccccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgct---gtccctctctccgctgccgtg
-tccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatactct
-cttctctcccgcgtacctccccctcttactaaagctacagatacgcccattatatgaact
-ggttgtaaatggcgctctcaaccagcactaacacaactgtcgtcgctgccccatcattaa
-cccccgcgggatgaacctgccttccagccatcgatgcgtcacctgaactcgaatggtttg
-ggggtgcctgcgggtaaggtgttggcgggatgtgagccttgttcgccacgtattacccta
-tacggttgctttacgttcgattagctcttgactccggcgctactactccttgatgggggc
-ccgaccatctaggaacgacatctccttcgtccacgtgcagttcatgccgcctagcccgat
-ccttgttagttttgatcttttacttccgtaggtagcctattcttttgactcgtagtcgcc
-agtcgtcactgcaaggtgcagcgtttcccccgatg
+gcactcccggccggagcgctccttgccctctccgct---gtccctctct---ccgctgcc
+gtgtccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatac
+tctcttctctcccgcgtacctccccccaatgcatcttactacccgtcccaagtggactgc
+aagtaagctacagatacgcccattatatgaactggttgtaaatggcgctctcaaccagca
+ctaacacaactgtcgtcgctgccccatcattaacccccgcgggatgaacctgccttccag
+ccatcgatgcgtcacctgaactcgaatggtttgggggtgcctgcgggtaaggtgttggcg
+ggatgtgagccttgttcgccacgtattaccctatacggttgctttacgttcgattagctc
+ttgactccggcgctactactccttgatgggggcccgaccatctaggaacgacatctcctt
+cgtccacgtgcagttcatgccgcctagcccgatccttgttagttttgatcttttacttcc
+gtaggtagcctattcttttgactcgtagtcgccagtcgtcactgcaaggtgcagcgtttc
+ccccgatg
 >247_s46|EOG091N44M8
 ccccatccgctcccctacgagtccctcgccgcccagctcctcccctctctcagcgcccgg
-gcgcgttcgaccggaccgctcttcaccccctcgcctggtgtctctccc-ctgccggtgtc
-cccccctccgtagaagaagggg--agtccgacggacatgctcggcttc------------
+gcgcgttcgaccggaccgctcttcaccccctcgcctggtgtctctccc----ctgccggt
+gtccccccctccgtagaagaagggg--agtccgacggacatgctcggcttc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------aaaatg------
 ------------------------------------------------------------
----------------aaaatg---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >250_S57|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >252_S58|EOG091N44M8
 ccccatccgctcccctacgagtccctcgccgcccagctcctcccctctctcagcgcccgg
-gcgcgttcgaccggaccgctcttcaccccctcgcctggtgtctctccc-ctgccggtgtc
-cccccctccgtagaagaagggg--agtccgacggatatgctcggctcc------------
+gcgcgttcgaccggaccgctcttcaccccctcgcctggtgtctctccc----ctgccggt
+gtccccccctccgtagaagaagggg--agtccgacggatatgctcggctcc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------aaaatg------
 ------------------------------------------------------------
----------------aaaatg---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >256_S59|EOG091N44M8
 ccccatccgctcccctacgagtccctcgccgcccagctcctcccctctctcagcgcccgg
-gcgcgtgcgaccggaccgctcttcaccccctcgcctggtgtctctccc-ctgccggtgtc
-cccccctccgtagaagaagggg--agtccgacggacatgctcggtctc------------
+gcgcgtgcgaccggaccgctcttcaccccctcgcctggtgtctctccc----ctgccggt
+gtccccccctccgtagaagaagggg--agtccgacggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >257_S60|EOG091N44M8
 ttctccctgcccccccacgaggccctcgccgcctagctcctcccctccctgggtccgcgg
-gcactccaagccggtgcgctccttgccctctccgtcggtctctctctctccgctgccgtg
-tccctctctgtagaagaaggga--gggattgcctcttca-aatctgcaatcgaatactct
-tctctcttctgcgtacctccttt-----------------ctatacccgccacatgagcg
-ggttgcaaatggcgcggccgaccaggatcaatatggtagccatcgccacctaaccattag
-cctgcgcgggatgattccgtctccgggtcattgacgtgtcatccgagcccgaatatcttt
-gtggtgtccgcggatgggtaatccaggcaaacctaatctcattcgacgtggatcgatccc
-tgcggttattctgcatttgacaaactgctgattaagaagccattactcttaggttgaggt
-ccagccactcatggatggtttccccttcgtattcacactccttatgcgctcgagctcgat
-tcttgtcagtcctgaccttttaccctcgcggacagtttatttttttaactcgtagtcctg
-ggcaaagacgctaaagcatagcatgtccctcgatg
+gcactccaagccggtgcgctccttgccctctccgtcggtctctctctct---ccgctgcc
+gtgtccctctctgtagaagaaggga--gggattgcctcttca-aatctgcaatcgaatac
+tcttctctcttctgcgtacctccttt----------------------------------
+-------------ctatacccgccacatgagcgggttgcaaatggcgcggccgaccagga
+tcaatatggtagccatcgccacctaaccattagcctgcgcgggatgattccgtctccggg
+tcattgacgtgtcatccgagcccgaatatctttgtggtgtccgcggatgggtaatccagg
+caaacctaatctcattcgacgtggatcgatccctgcggttattctgcatttgacaaactg
+ctgattaagaagccattactcttaggttgaggtccagccactcatggatggtttcccctt
+cgtattcacactccttatgcgctcgagctcgattcttgtcagtcctgaccttttaccctc
+gcggacagtttatttttttaactcgtagtcctgggcaaagacgctaaagcatagcatgtc
+cctcgatg
 >258_S61|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccagcccctcccctccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga------------
-----------aaactattct----------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga---------
+-------------aaactattct-------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >259_S62|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctccccaccctgggtctccgg
-gcacgcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >261_S63|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccagcccctcccctccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga------------
-----------aaactacgtg----------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga---------
+-------------aaactacgtg-------------------------------------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >262_S64|EOG091N44M8
 tcccctccgcccctccacgagtccctcgccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >267_S66|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctccccaccctgggtctccgg
-gcacgcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >269_S67|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >271_S68|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccatcccctcccccccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga------------
-----------aaactattct----------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga---------
+-------------aaactattct-------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >274_S69|EOG091N44M8
 ccccatccgctcccctacgagtccctcgccgcccagctcctcccctctctcagcgcccgg
-gcgcgtgcgaccggaccgctcttcaccccctcgcctggtgtctctccc-ctgccggtgtc
-cccccctccgtagaagaagggg--agtccgacggacatgctcggcttt------------
+gcgcgtgcgaccggaccgctcttcaccccctcgcctggtgtctctccc----ctgccggt
+gtccccccctccgtagaagaagggg--agtccgacggacatgctcggcttt---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------tttgtc------
 ------------------------------------------------------------
----------------tttgtc---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >275_S70|EOG091N44M8
 tcccctccgcccctccacgagtccctcgccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >276_S71|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >277_S72|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga------------
-----------aaactattcc----------------------------------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga---------
+-------------aaactattcc-------------------------------------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >278_S73|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga------------
-----------aaactattcc----------------------------------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga---------
+-------------aaactattcc-------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >280_S74|EOG091N44M8
 tcccctccgcccctccacgagtccctcgccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >284_S76|EOG091N44M8
 ccccatccactcctccacgagtccctcgccgcccagctcctcccctctctcagcgcccgg
-gtgcgtgcgaccggagcgctcttcaccccctcgcctggtgtctctctc-ctgccggagtc
-tccccccccgtagaagaagggg--agtccgatggacatgctcggcttc------------
+gtgcgtgcgaccggagcgctcttcaccccctcgcctggtgtctctctc----ctgccgga
+gtctccccccccgtagaagaagggg--agtccgatggacatgctcggcttc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------gtagga------
 ------------------------------------------------------------
----------------gtagga---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >285_S77|EOG091N44M8
 ccccatccgctcccctacgagtccctcgccgcccagctcctcccctctctcagcgcccgg
-gcgcgttcgaccggaccgctcttcaccccctcgcctggtgtctctccc-ctgccggtgtc
-cccccctccgtagaagaagggg--agtccgacggacatgctcggtctc------------
+gcgcgttcgaccggaccgctcttcaccccctcgcctggtgtctctccc----ctgccggt
+gtccccccctccgtagaagaagggg--agtccgacggacatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >288_S78|EOG091N44M8
 tccctcccccccctctacgagtccctctccgcccagcccctcccccccctgggtccccgg
-gcgctcccggcacgagcgtgtttcaccccttccgttgctccct-----cccgctcccccg
-cgtctctccgtagaagaagaag--agtccgatggacatgctcggtctc------------
+gcgctcccggcacgagcgtgtttcaccccttccgttgctccct-----c---ccgctccc
+ccgcgtctctccgtagaagaagaag--agtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >289_S79|EOG091N44M8
 ccccatccgctcccctacgagtccctcgccgcccagctcctcccctctctcagcgcccgg
-gcgcgtgcgaccggaccgctcttcaccccctcgcctggtgtctctccc-ctgccggtgtc
-cccccctccgtagaagaagggg--agtccgacggacatgctcggcttt------------
+gcgcgtgcgaccggaccgctcttcaccccctcgcctggtgtctctccc----ctgccggt
+gtccccccctccgtagaagaagggg--agtccgacggacatgctcggcttt---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------tttgtc------
 ------------------------------------------------------------
----------------tttgtc---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Aspergillus_fumigatus_Af293_GCF_000002655.1|EOG091N44M8
 ccccctccccccctctacacctccgtctctgagtggcccctctctcttcctgaggccgac
-ccatgtcgggccggagcccgcttcaccctttccgttgctccccctttctccgctgccgtg
-tctctctctgtagaagaagggg--agtccgacggacatgctcggtctt------------
+ccatgtcgggccggagcccgcttcaccctttccgttgctccccctttctcgtccgctgcc
+gtgtctctctctgtagaagaagggg--agtccgacggacatgctcggtctt---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Aspergillus_niger_GCF_000002855.3|EOG091N44M8
 tccccccctggcctctacaacaccctcgctgagcatcccctccccctcctggaggccccg
-ccctgttgggccggagccctctaccagctttccgttgccgtccctcctcgtggcgccctc
-tctagctccgtagaagaagggg--ggtccgatggacatgctcggtctc------------
+ccctgttgggccggagccctctaccagctttccgttgccgtccctcctc---gtggcgcc
+ctctctagctccgtagaagaagggg--ggtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Aspergillus_oryzae_RIB40_GCF_000184455.2|EOG091N44M8
 ccctctccccccccctactccaccctcgttgagcaagctctctcctttcctgaggccccg
-gcactccgggccgcagcgcattacgagctttccgttgctgtccctctttccgctgccgtg
-t--acccccgtag---aaggag--agtccgatggacatgctcggtctc------------
+gcactccgggccgcagcgcattacgagctttccgttgctgtccctctttcgtccgctgcc
+gtgt--acccccgtag---aaggag--agtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_antarcticum_GCA_002072345.1|EOG091N44M8
 tccctccctcccctccacgagaccctcgctgcccatcccctcccctccctgggtctctgc
-gcacgtcggaccggagccctccttaccccttccgttgctgtctcctcccccgctgccgtg
-tccctctccgtagaagaagggattggtccgatggacatgatcggactc------------
+gcacgtcggaccggagccctccttaccccttccgttgctgtctcctccc---ccgctgcc
+gtgtccctctccgtagaagaagggattggtccgatggacatgatcggactc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_biforme_FM169_GCA_000577785.1|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_brasilianum_GCA_000769745.1|EOG091N44M8
 ttccccccgcccctccacgaggccctcgccgcccagcccctcccccccttgggtctgcgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatactcc
-cctttcccccgcgtacctcccccatagggggcgttactctatacaccaacctcatgagtt
-ggtcgtaaacggcgcagccaaccagcatcaatacggcggtcgtcgccgcctcatcattaa
-cttgcacgggatgaacccgcatttgggtaatccatgcgtcacctgaactcggctggtttg
-ttagtatctacggatgagttattggtggaatgtgagctttgtccgctgtggttcacccta
-tacggttactttacctttgactaatcgttcacctagacaccactactcccagcgagagtc
-ccggccacctatggacagtatctcctttgtttacatgcagcccatgccgtctcgaccgat
-tcctgtcggctttaaccctttacttccgtggatagtctattttcc---------------
------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatac
+tcccctttcccccgcgtacctccccctttctatatagggggaaaccggtcgtgccgacca
+tccacgttactctatacaccaacctcatgagttggtcgtaaacggcgcagccaaccagca
+tcaatacggcggtcgtcgccgcctcatcattaacttgcacgggatgaacccgcatttggg
+taatccatgcgtcacctgaactcggctggtttgttagtatctacggatgagttattggtg
+gaatgtgagctttgtccgctgtggttcaccctatacggttactttacctttgactaatcg
+ttcacctagacaccactactcccagcgagagtcccggccacctatggacagtatctcctt
+tgtttacatgcagcccatgccgtctcgaccgattcctgtcggctttaaccctttacttcc
+gtggatagtctattttcc------------------------------------------
+--------
 >Penicillium_brasilianum_GCA_001048715.1|EOG091N44M8
 ccccatccccccccctacgagtctctcgtctcccagagtctcccccccctctccgcccgg
-gtgcgtccgaccggaccgcgtttcgccccctccgttgccgtctctccctctgccgctgtg
-tccccaggtccccgccaagggg--agtccgacggacatgatcggtctc------------
+gtgcgtccgaccggaccgcgtttcgccccctccgttgccgtctctccct---ctgccgct
+gtgtccccaggtccccgccaagggg--agtccgacggacatgatcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_brasilianum_GCA_002016555.1|EOG091N44M8
 ccccatccccccccctacgagtctctcgtctcccagagcctcccccccctctccgcccgg
-gtgcgtccgaccggaccgcgtttcgccccttccgttgccgtctctccctctgccgctgtg
-tccccaggtccccgccaagggg--agtccgacggacatgatcggtctc------------
+gtgcgtccgaccggaccgcgtttcgccccttccgttgccgtctctccct---ctgccgct
+gtgtccccaggtccccgccaagggg--agtccgacggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_brasilianum_GCA_004916855.1|EOG091N44M8
 ccccatccccccccctacgagtctctcgtctcccagagcctcccccccctctccgcccgg
-gtgcgtccgaccggaccgcgtttcgccccttccgttgccgtctctccctctgccgctgtg
-tccccaggtccccgccaagggg--agtccgacggacatgatcggtctc------------
+gtgcgtccgaccggaccgcgtttcgccccttccgttgccgtctctccct---ctgccgct
+gtgtccccaggtccccgccaagggg--agtccgacggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_camemberti_FM_013_GCA_000513335.1|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_capsulatum_GCA_000943765.1|EOG091N44M8
 tccctccctcccctccacgagtccctcgctgcccatcccctccccctcctgggtctctgc
-gcacgtcggaccggagcgctcctcaccccttccgttggtctctctctccccgccgccgtg
-tccccctccgtagaagaagggattggtccgatggacatgatcggactc------------
+gcacgtcggaccggagcgctcctcaccccttccgttggtctctctctcc---ccgccgcc
+gtgtccccctccgtagaagaagggattggtccgatggacatgatcggactc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_capsulatum_GCA_000943775.1|EOG091N44M8
 tccctccctcccctccacgagtccctcgctgcccatcccctccccctcctgggtctctgc
-gcacgtcggaccggagcgctcctcaccccttccgttggtctctctctccccgccgccgtg
-tccccctccgtagaagaagggattggtccgatggacatgatcggactc------------
+gcacgtcggaccggagcgctcctcaccccttccgttggtctctctctcc---ccgccgcc
+gtgtccccctccgtagaagaagggattggtccgatggacatgatcggactc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_chrysogenum_GCA_000710275.1|EOG091N44M8
 tcccctccgcccctccacgagtccctcgccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_chrysogenum_GCA_000801355.1|EOG091N44M8
 tcccctccgcccctccacgagtccctcgccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_chrysogenum_GCA_002080375.1|EOG091N44M8
 tcccctccgcccctccacgagtccctcgccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_chrysogenum_KF-25_GCA_000816005.1|EOG091N44M8
 tcccctccgcccctccacgagtccctcgccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_chrysogenum_NCPC10086_GCA_000523475.1|EOG091N44M8
 tcccctccgcccctccacgagtccctcgccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_chrysogenum_NCPC10086_GCA_001773325.1|EOG091N44M8
 tccctccctcccctccacgagaccctcgctgcccatcccctcccccccctgggtctctgc
-gcacgtcggaccggagcgctcctcaccccttccgttggtgtctctccccccgccgccgtg
-tccccctccgtagaagaagggaagggtccgacggacatgatcggactc------------
+gcacgtcggaccggagcgctcctcaccccttccgttggtgtctctcccc---ccgccgcc
+gtgtccccctccgtagaagaagggaagggtccgacggacatgatcggactc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_citrinum_GCA_001399475.1|EOG091N44M8
 ccccaccctgcctgccacgccgagctcgccgcctaggccctccccttcctctctgcccgc
-gcgcgtccggacggagtgctctataccccttccgttgctgtctcccc--ctgctggtgta
-cccctccccgtagaagaagggg--agtccgatggacatgctcggtctc------------
+gcgcgtccggacggagtgctctataccccttccgttgctgtctcccc-----ctgctggt
+gtacccctccccgtagaagaagggg--agtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_citrinum_GCA_001950535.1|EOG091N44M8
 ccccaccctgcctgccacgccgagctcgccgcctaggccctccccttcctctctgcccgc
-gcgcgtccggacggagtgctctataccccttccgttgctgtctcccc--ctgctggtgta
-cccctccccgtagaagaagggg--agtccgatggacatgctcggtctc------------
+gcgcgtccggacggagtgctctataccccttccgttgctgtctcccc-----ctgctggt
+gtacccctccccgtagaagaagggg--agtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_commune_162_3FA|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_coprophilum_GCA_002072405.1|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcctagctcctcccccccctgggtctccgg
-gcactcccggccggagcgcgtcttaccctttccgctgctgtctctctctccgctgccgtg
-tccccctccgtagaaggtcgga--ggtccgatggatatgctcggtctc------------
+gcactcccggccggagcgcgtcttaccctttccgctgctgtctctctct---ccgctgcc
+gtgtccccctccgtagaaggtcgga--ggtccgatggatatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_decumbens_GCA_000226395.1|EOG091N44M8
 tcccctccgcccctccacgagtccctcgccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_decumbens_GCA_002072245.1|EOG091N44M8
 tcccctccccgccgctacgagtctctcgccgcccaggccctcccctctccctccgcccgc
-ccacgtccgaccggagcgcgcttcaccccttcccttgctgtccctctccctgccggtgtc
-cctacctccgtag---aagggg--agtccgatcgacatgattggtctc------------
+ccacgtccgaccggagcgcgcttcaccccttcccttgctgtccctctcc---ctgccggt
+gtccctacctccgtag---aagggg--agtccgatcgacatgattggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_digitatum_Pd01-ZJU_GCA_000485865.1|EOG091N44M8
 tcccccccgcccctctacgaggccctttccgaccagcccctccccctcctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgcttctccctctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggacatgctcgatgtt---tggatgtct
-cctttttctcacgtacctcccc------------------gtccattcactatatgagct
-gatctcaaacagagcagtcaaccgacatcaatacggcggccggtgtcgctccatcattca
-tttgcacgggacgaatctgccatcgggtcgtcgatacgttacttagattcaaatggttcc
-gtgccattcgcagatgagttactcgtagagagcgcgtcttattagccgtagaccacccta
-taagtttgctttaattttgataggttgctgcctcagatgccaccactcggcgcgaggcgc
-ccggccacctctaggcagcgactttttcgcgtatatgtagatcgtgtcgtctcgctcggt
-ccttgccgattttgacccctcgtatctgtgaatagcctgtcttct---------------
------------------------------------
+gcactcccggccggagcgctccttgccctctccgcttctccctctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggacatgctcgatgtt---tggatg
+tctcctttttctcacgtacctcccc-----------------------------------
+-------------gtccattcactatatgagctgatctcaaacagagcagtcaaccgaca
+tcaatacggcggccggtgtcgctccatcattcatttgcacgggacgaatctgccatcggg
+tcgtcgatacgttacttagattcaaatggttccgtgccattcgcagatgagttactcgta
+gagagcgcgtcttattagccgtagaccaccctataagtttgctttaattttgataggttg
+ctgcctcagatgccaccactcggcgcgaggcgcccggccacctctaggcagcgacttttt
+cgcgtatatgtagatcgtgtcgtctcgctcggtccttgccgattttgacccctcgtatct
+gtgaatagcctgtcttct------------------------------------------
+--------
 >Penicillium_digitatum_PDC_102_GCA_001307865.1|EOG091N44M8
 tcccccccgcccctctacgaggccctttccgaccagcccctccccctcctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgcttctccctctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggacatgctcgatgtt---tggatgtct
-cctttttctcacgtacctccccccctcaaggagtcc----ttccattcactatatgagct
-gatctcaaacagagcagtcaaccgacatcaatacggcggccggtgtcgctccatcattca
-tttgcacgggacgaatctgccatcgggtcgtcgatacgttacttagattcaaatggttcc
-gtgccatccgcagatgagttactcgtagagagcgcgtcttattagccgtagaccacccta
-taagtttgctttaattttgataggttgctgcctcagatgccaccactcggcgcgaggcgc
-ccggccacctctaggcagcgactttttcgcgtatatgtagatcgtgtcgtctcgctcggt
-ccttgccgattttgacccctcgtatctgtgaatagcctgtcttcttgattcgtagccgta
-agttgcggcactaa---------------------
+gcactcccggccggagcgctccttgccctctccgcttctccctctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggacatgctcgatgtt---tggatg
+tctcctttttctcacgtacctccccc-------cctcaagg-------------------
+----agtcc----ttccattcactatatgagctgatctcaaacagagcagtcaaccgaca
+tcaatacggcggccggtgtcgctccatcattcatttgcacgggacgaatctgccatcggg
+tcgtcgatacgttacttagattcaaatggttccgtgccatccgcagatgagttactcgta
+gagagcgcgtcttattagccgtagaccaccctataagtttgctttaattttgataggttg
+ctgcctcagatgccaccactcggcgcgaggcgcccggccacctctaggcagcgacttttt
+cgcgtatatgtagatcgtgtcgtctcgctcggtccttgccgattttgacccctcgtatct
+gtgaatagcctgtcttcttgattcgtagccgtaagttgcggcactaa-------------
+--------
 >Penicillium_digitatum_PHI26_GCA_000315665.1|EOG091N44M8
 tcccccccgcccctctacgaggccctttccgaccagcccctccccctcctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgcttctccctctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggacatgctcgatgtt---tggatgtct
-cctttttctcacgtacctcccc------------------gtccattcactatatgagct
-gatctcaaacagagcagtcaaccgacatcaatacggcggccggtgtcgctccatcattca
-tttgcacgggacgaatctgccatcgggtcgtcgatacgttacttagattcaaatggttcc
-gtgccatccgcagatgagttactcgtagagagcgcgtcttattagccgtagaccacccta
-taagtttgctttaattttgataggttgctgcctcagatgccaccactcggcgcgaggcgc
-ccggccacctctaggcagcgactttttcgcgtatatgtagatcgtgtcgtctcgctcggt
-ccttgccgattttgacccctcgtatctgtgaatagcctgtcttcttgattcgtagccgta
-agttgcggcactaa---------------------
+gcactcccggccggagcgctccttgccctctccgcttctccctctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggacatgctcgatgtt---tggatg
+tctcctttttctcacgtacctcccc-----------------------------------
+-------------gtccattcactatatgagctgatctcaaacagagcagtcaaccgaca
+tcaatacggcggccggtgtcgctccatcattcatttgcacgggacgaatctgccatcggg
+tcgtcgatacgttacttagattcaaatggttccgtgccatccgcagatgagttactcgta
+gagagcgcgtcttattagccgtagaccaccctataagtttgctttaattttgataggttg
+ctgcctcagatgccaccactcggcgcgaggcgcccggccacctctaggcagcgacttttt
+cgcgtatatgtagatcgtgtcgtctcgctcggtccttgccgattttgacccctcgtatct
+gtgaatagcctgtcttcttgattcgtagccgtaagttgcggcactaa-------------
+--------
 >Penicillium_expansum_GCA_000688875.1|EOG091N44M8
 ttccccccgcccctccacgaggccctcgccgcccagcccctcccccccttgggtctgcgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatactcc
-cctttcccccgcgtacctcccccatagggggcgttactctatacaccaacctcatgagtt
-ggtcgtaaacggcgcagccaaccagcatcaatacggcggtcgtcgccgcctcatcattaa
-cttgcacgggatgaacccgcatttgggtaatccatgcgtcacctgaactcggctggtttg
-ttagtatctacggatgagttattggtggaatgtgagctttgtccgctgtggttcacccta
-tacggttactttacctttgactaatcgttcacctagacaccactactcccagcgagagtc
-ccggccacctatggacagtatctcctttgtttacatgcagcccatgccgtctcgaccgat
-tcctgtcggctttaaccctttacttccgtggatagtctactttcctgacccgtagctgt-
------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatac
+tcccctttcccccgcgtacctccccctttctatatagggggaaaccggtcgtgccgacca
+tccacgttactctatacaccaacctcatgagttggtcgtaaacggcgcagccaaccagca
+tcaatacggcggtcgtcgccgcctcatcattaacttgcacgggatgaacccgcatttggg
+taatccatgcgtcacctgaactcggctggtttgttagtatctacggatgagttattggtg
+gaatgtgagctttgtccgctgtggttcaccctatacggttactttacctttgactaatcg
+ttcacctagacaccactactcccagcgagagtcccggccacctatggacagtatctcctt
+tgtttacatgcagcccatgccgtctcgaccgattcctgtcggctttaaccctttacttcc
+gtggatagtctactttcctgacccgtagctgt----------------------------
+--------
 >Penicillium_expansum_GCA_000769735.1|EOG091N44M8
 ttccccccgcccctccacgaggccctcgccgcccagcccctcccccccttgggtctgcgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatactcc
-cctttcccccgcgtacctcccccatagggggcgttactctatacaccaacctcatgagtt
-ggtcgtaaacggcgcagccaaccagcatcaatacggcggtcgtcgccgcctcatcattaa
-cttgcacgggatgaacccgcatttgggtaatccatgcgtcacctgaactcggctggtttg
-ttagtatctacggatgagttattggtggaatgtgagctttgtccgctgtggttcacccta
-tacggttactttacctttgactaatcgttcacctagacaccactactcccagcgagagtc
-ccggccacctatggacagtatctcctttgtttacatgcagcccatgccgtctcgaccgat
-tcctgtcggctttaaccctttacttccgtggatagtctattttcc---------------
------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatac
+tcccctttcccccgcgtacctccccctttctatatagggggaaaccggtcgtgccgacca
+tccacgttactctatacaccaacctcatgagttggtcgtaaacggcgcagccaaccagca
+tcaatacggcggtcgtcgccgcctcatcattaacttgcacgggatgaacccgcatttggg
+taatccatgcgtcacctgaactcggctggtttgttagtatctacggatgagttattggtg
+gaatgtgagctttgtccgctgtggttcaccctatacggttactttacctttgactaatcg
+ttcacctagacaccactactcccagcgagagtcccggccacctatggacagtatctcctt
+tgtttacatgcagcccatgccgtctcgaccgattcctgtcggctttaaccctttacttcc
+gtggatagtctattttcc------------------------------------------
+--------
 >Penicillium_expansum_GCA_000769755.1|EOG091N44M8
 ttccccccgcccctccacgaggccctcgccgcccagcccctcccccccttgggtctgcgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatactcc
-cctttcccccgcgtacctcccccatagggggcgttactctatacaccaacctcatgagtt
-ggtcgtaaacggcgcagccaaccagcatcaatacggcggtcgtcgccgcctcatcattaa
-cttgcacgggatgaacccgcatttgggtaatccatgcgtcacctgaactcggctggtttg
-ttagtatctacggatgagttattggtggaatgtgagctttgtccgctgtggttcacccta
-tacggttactttacctttgactaatcgttcacctagacaccactactcccagcgagagtc
-ccggccacctatggacagtatctcctttgtttacatgcagcccatgccgtctcgaccgat
-tcctgtcggctttaaccctttacttccgtggatagtctattttcctgacccgtagctgt-
------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatac
+tcccctttcccccgcgtacctccccctttctatatagggggaaaccggtcgtgccgacca
+tccacgttactctatacaccaacctcatgagttggtcgtaaacggcgcagccaaccagca
+tcaatacggcggtcgtcgccgcctcatcattaacttgcacgggatgaacccgcatttggg
+taatccatgcgtcacctgaactcggctggtttgttagtatctacggatgagttattggtg
+gaatgtgagctttgtccgctgtggttcaccctatacggttactttacctttgactaatcg
+ttcacctagacaccactactcccagcgagagtcccggccacctatggacagtatctcctt
+tgtttacatgcagcccatgccgtctcgaccgattcctgtcggctttaaccctttacttcc
+gtggatagtctattttcctgacccgtagctgt----------------------------
+--------
 >Penicillium_expansum_GCA_001750045.2|EOG091N44M8
 ttccccccgcccctccacgaggccctcgccgcccagcccctcccccccttgggtctgcgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatactcc
-cctttcccccgcgtacctcccccatagggggcgttactctatacaccaacctcatgagtt
-ggtcgtaaacggcgcagccaaccagcatcaatacggcggtcgtcgccgcctcatcattaa
-cttgcacgggatgaacccgcatttgggtaatccatgcgtcacctgaactcggctggtttg
-ttagtatctacggatgagttattggtggaatgtgagctttgtccgctgtggttcacccta
-tacggttactttacctttgactaatcgttcacctagacaccactactcccagcgagagtc
-ccggccacctatggacagtatctcctttgtttacatgcagcccatgccgtctcgaccgat
-tcctgtcggctttaaccctttacttccgtggatagtctattttcctgacccgtagctgt-
------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatac
+tcccctttcccccgcgtacctccccctttctatatagggggaaaccggtcgtgccgacca
+tccacgttactctatacaccaacctcatgagttggtcgtaaacggcgcagccaaccagca
+tcaatacggcggtcgtcgccgcctcatcattaacttgcacgggatgaacccgcatttggg
+taatccatgcgtcacctgaactcggctggtttgttagtatctacggatgagttattggtg
+gaatgtgagctttgtccgctgtggttcaccctatacggttactttacctttgactaatcg
+ttcacctagacaccactactcccagcgagagtcccggccacctatggacagtatctcctt
+tgtttacatgcagcccatgccgtctcgaccgattcctgtcggctttaaccctttacttcc
+gtggatagtctattttcctgacccgtagctgt----------------------------
+--------
 >Penicillium_expansum_GCA_004302965.1|EOG091N44M8
 ttccccccgcccctccacgaggccctcgccgcccagcccctcccccccttgggtctgcgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatactcc
-cctttcccccgcgtacctcccccatagggggcgttactctatacaccaacctcatgagtt
-ggtcgtaaacggcgcagccaaccagcatcaatacggcggtcgtcgccgcctcatcattaa
-cttgcacgggatgaacccgcatttgggtaatccatgcgtcacctgaactcggctggtttg
-ttagtatctacggatgagttattggtggaatgtgagctttgtccgctgtggttcacccta
-tacggttactttacctttgactaatcgttcacctagacaccactactcccagcgagagtc
-ccggccacctatggacagtatctcctttgtttacatgcagcccatgccgtctcgaccgat
-tcctgtcggctttaaccctttacttccgtggatagtctactttcctgacccgtagctgt-
------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatac
+tcccctttcccccgcgtacctccccctttctatatagggggaaaccggtcgtgccgacca
+tccacgttactctatacaccaacctcatgagttggtcgtaaacggcgcagccaaccagca
+tcaatacggcggtcgtcgccgcctcatcattaacttgcacgggatgaacccgcatttggg
+taatccatgcgtcacctgaactcggctggtttgttagtatctacggatgagttattggtg
+gaatgtgagctttgtccgctgtggttcaccctatacggttactttacctttgactaatcg
+ttcacctagacaccactactcccagcgagagtcccggccacctatggacagtatctcctt
+tgtttacatgcagcccatgccgtctcgaccgattcctgtcggctttaaccctttacttcc
+gtggatagtctactttcctgacccgtagctgt----------------------------
+--------
 >Penicillium_expansum_NRRL_62431_GCA_000584915.1|EOG091N44M8
 ttccccccgcccctccacgaggccctcgccgcccagcccctcccccccttgggtctgcgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatactcc
-cctttcccccgcgtacctcccccatagggggcgttactctatacaccaacctcatgagtt
-ggtcgtaaacggcgcagccaaccagcatcaatacggcggtcgtcgccgcctcatcattaa
-cttgcacgggatgaacccgcatttgggtaatccatgcgtcacctgaactcggctggtttg
-ttagtatctacggatgagttattggtggaatgtgagctttgtccgctgtggttcacccta
-tacggttactttacctttgactaatcgttcacctagacaccactactcccagcgagagtc
-ccggccacctatggacagtatctcctttgtttacatgcagcccatgccgtctcgaccgat
-tcctgtcggctttaaccctttacttccgtggatagtctattttcctgacccgtagctgt-
------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatac
+tcccctttcccccgcgtacctccccctttctatatagggggaaaccggtcgtgccgacca
+tccacgttactctatacaccaacctcatgagttggtcgtaaacggcgcagccaaccagca
+tcaatacggcggtcgtcgccgcctcatcattaacttgcacgggatgaacccgcatttggg
+taatccatgcgtcacctgaactcggctggtttgttagtatctacggatgagttattggtg
+gaatgtgagctttgtccgctgtggttcaccctatacggttactttacctttgactaatcg
+ttcacctagacaccactactcccagcgagagtcccggccacctatggacagtatctcctt
+tgtttacatgcagcccatgccgtctcgaccgattcctgtcggctttaaccctttacttcc
+gtggatagtctattttcctgacccgtagctgt----------------------------
+--------
 >Penicillium_expansum_T01_GCA_001008385.1|EOG091N44M8
 ttccccccgcccctccacgaggccctcgccgcccagcccctcccccccttgggtctgcgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatactcc
-cctttcccccgcgtacctcccccatagggggcgttactctatacaccaacctcatgagtt
-ggtcgtaaacggcgcagccaaccagcatcaatacggcggtcgtcgccgcctcatcattaa
-cttgcacgggatgaacccgcatttgggtaatccatgcgtcacctgaactcggctggtttg
-ttagtatctacggatgagttattggtggaatgtgagctttgtccgctgtggttcacccta
-tacggttactttacctttgactaatcgttcacctagacaccactactcccagcgagagtc
-ccggccacctatggacagtatctcctttgtttacatgcagcccatgccgtctcgaccgat
-tcctgtcggctttaaccctttacttccgtggatagtctattttcc---------------
------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtctccctccgtagaaggttgga--ggtccgatggacatgctcggaataatggaatac
+tcccctttcccccgcgtacctccccctttctatatagggggaaaccggtcgtgccgacca
+tccacgttactctatacaccaacctcatgagttggtcgtaaacggcgcagccaaccagca
+tcaatacggcggtcgtcgccgcctcatcattaacttgcacgggatgaacccgcatttggg
+taatccatgcgtcacctgaactcggctggtttgttagtatctacggatgagttattggtg
+gaatgtgagctttgtccgctgtggttcaccctatacggttactttacctttgactaatcg
+ttcacctagacaccactactcccagcgagagtcccggccacctatggacagtatctcctt
+tgtttacatgcagcccatgccgtctcgaccgattcctgtcggctttaaccctttacttcc
+gtggatagtctattttcc------------------------------------------
+--------
 >Penicillium_expansum_YT02_GCA_002072455.1|EOG091N44M8
 ccccacccccccctctacgagtcccttgcctctcagagcctccccctcctctccgcccgg
-gtgcttccgaccggactgcttttctccctttccgccgct----ctcctcccgctgccgtg
-tctctaggcccccgccaagggg--agtccgaccgacatgatcggactc------------
+gtgcttccgaccggactgcttttctccctttccgccgct----ctcctctccccgctgcc
+gtgtctctaggcccccgccaagggg--agtccgaccgacatgatcggactc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_flavigenum_GCA_002072365.1|EOG091N44M8
 ttccctccgcccctccacgaggccctcgccgcccagatcctcccctccctggctctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_freii_GCA_001513925.1|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccatcccctcccccccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcggtctc------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_fuscoglaucum_FM041_GCA_000576735.1|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga------------
-----------aaactattcc----------------------------------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga---------
+-------------aaactattcc-------------------------------------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_griseofulvum_GCA_001561935.1|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgactagctcctcccctctctgggtctccgg
-gcactcccggccggagcgcgtcttacctttaccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggtcgga--ggtccgatggatatgctcggtctc------------
+gcactcccggccggagcgcgtcttacctttaccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggtcgga--ggtccgatggatatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_griseofulvum_GCA_001735785.1|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgactagctcctcccctctctgggtctccgg
-gcactcccggccggagcgcgtcttacctttaccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggtcgga--ggtccgatggatatgctcggtctc------------
+gcactcccggccggagcgcgtcttacctttaccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggtcgga--ggtccgatggatatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_italicum_GCA_000769765.1|EOG091N44M8
 ttccccccgcccctccacgaggccctctccgcccagcccctccccttcctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggacatgctcggtctc------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_italicum_GCA_001008395.1|EOG091N44M8
 ttccccccgcccctccacgaggccctctccgcccagcccctccccttcctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggaggga--ggtccgatggacatgctcggaatagtcgaatactcc
-ccttcctcccgcgcacctccccc-----------------gcacatacgccacatgagct
-ggtctcgaacggcgtagccaaccgggatcaatacggtggtcattgccgccccatctttaa
-cttgcgcgggatgaatctaccctcgagtcattgatgcgccagctgaactcgactggtttg
-gtggagtttgcggatgagttattgatgggatgtgagtcttgttcgccgtgaatcaatcta
-tatggacactttactttcgactagccgctcacttagacgccactactcccagcgagaggc
-ccggacacccctggacggcatcttattcgtttacaagcagcccgcgttatttcgctcgat
-acctaccggttcttaccttttactcccttggacagctcattttcctgtcttgtagccgtc
-aaccgcgacgataaagcgaagtgtttcccttggtg
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggaggga--ggtccgatggacatgctcggaatagtcgaatac
+tccccttcctcccgcgcacctccccc----------------------------------
+-------------gcacatacgccacatgagctggtctcgaacggcgtagccaaccggga
+tcaatacggtggtcattgccgccccatctttaacttgcgcgggatgaatctaccctcgag
+tcattgatgcgccagctgaactcgactggtttggtggagtttgcggatgagttattgatg
+ggatgtgagtcttgttcgccgtgaatcaatctatatggacactttactttcgactagccg
+ctcacttagacgccactactcccagcgagaggcccggacacccctggacggcatcttatt
+cgtttacaagcagcccgcgttatttcgctcgatacctaccggttcttaccttttactccc
+ttggacagctcattttcctgtcttgtagccgtcaaccgcgacgataaagcgaagtgtttc
+ccttggtg
 >Penicillium_italicum_GCA_002116305.1|EOG091N44M8
 ttccccccgcccctccacgaggccctctccgcccagcccctccccttcctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggacatgctcggtctc------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggacatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_janthinellum_GCA_002369805.1|EOG091N44M8
 ccccattcccccccctacgagtcccttgcctcccagagcctcctcctcctctccccccgg
-gcgtgtccgaccggaccgcgtttcgccctctccgctgctgtgtctccctctgccgctgcg
-tccccaggtcccagccaagggg--agtccgacggacatgctcggtctc------------
+gcgtgtccgaccggaccgcgtttcgccctctccgctgctgtgtctcccttgtctgccgct
+gcgtccccaggtcccagccaagggg--agtccgacggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_nalgiovense_FM193_GCA_000577395.2|EOG091N44M8
 ttccccccgcccctccacgaggccctcaccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_nalgiovense_GCA_002072425.1|EOG091N44M8
 ttccccccgcccctccacgaggccctcaccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_nordicum_GCA_000315645.2|EOG091N44M8
 tcccccccgcccctctacgaggccctttccgaccagcccctccccctcctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgcttctccctctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggacatgctcgatgtt---tggatgtct
-cctttttctcacgtacctcccc------------------gtccattcactatatgagct
-gatctcaaacagagcagtcaaccgacatcaatacggcggccggtgtcgctccatcattca
-tttgcacgggacgaatctgccatcgggtcgtcgatacgttacttagattcaaatggttcc
-gtgccatccgcagatgagttactcgtagagagcgcgtcttattagccgtagaccacccta
-taagtttgctttaattttgataggttgctgcctcagatgccaccactcggcgcgaggcgc
-ccggccacctctaggcagcgactttttcgcgtatatgtagatcgtgtcgtctcgctcggt
-ccttgccgattttgacccctcgtatctgtgaatagcctgtcttcttgatg--------cg
-ctggtgcgaagagc---------------------
+gcactcccggccggagcgctccttgccctctccgcttctccctctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggacatgctcgatgtt---tggatg
+tctcctttttctcacgtacctcccc-----------------------------------
+-------------gtccattcactatatgagctgatctcaaacagagcagtcaaccgaca
+tcaatacggcggccggtgtcgctccatcattcatttgcacgggacgaatctgccatcggg
+tcgtcgatacgttacttagattcaaatggttccgtgccatccgcagatgagttactcgta
+gagagcgcgtcttattagccgtagaccaccctataagtttgctttaattttgataggttg
+ctgcctcagatgccaccactcggcgcgaggcgcccggccacctctaggcagcgacttttt
+cgcgtatatgtagatcgtgtcgtctcgctcggtccttgccgattttgacccctcgtatct
+gtgaatagcctgtcttcttgatg--------cgctggtgcgaagagc-------------
+--------
 >Penicillium_nordicum_GCA_000733025.2|EOG091N44M8
 ttcctcccccccctccctgaggcccactccgcccagcccctcccccccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgct---gtccctctctccgctgccgtg
-tccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatactct
-cttctctcccgtgtacctcccc-ccttactaaagctacagatacgtccattacatgaact
-ggttgtaaatggcgctctcaaccagcaccaacacaacagtcgtcgccgccccatcattaa
-cacccgcgggatgaatctgccttccagccatcgatgcgtcacctgaactcgaatggtttg
-ggggtgcctgccagtaaggtgttggcgggatgtgagccttgttcgccccgtatcacccta
-tacggttgctttacgttcgatcagctcttgacttcggcgctactactccttgtcaggggc
-ccggccatctaggaacgacatctccttcgtccacgtgcagctcatgccgcctagcccgat
-ccttgttagttttgatcttttacttccgcaggtagcccatttttttgactcgtagtcgcc
-agtcgtcactgtaagatgcagcgtttcccccgatg
+gcactcccggccggagcgctccttgccctctccgct---gtccctctct---ccgctgcc
+gtgtccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatac
+tctcttctctcccgtgtacctcccc-caatgccccttactacccgttccaagtggactgc
+aagtaagctacagatacgtccattacatgaactggttgtaaatggcgctctcaaccagca
+ccaacacaacagtcgtcgccgccccatcattaacacccgcgggatgaatctgccttccag
+ccatcgatgcgtcacctgaactcgaatggtttgggggtgcctgccagtaaggtgttggcg
+ggatgtgagccttgttcgccccgtatcaccctatacggttgctttacgttcgatcagctc
+ttgacttcggcgctactactccttgtcaggggcccggccatctaggaacgacatctcctt
+cgtccacgtgcagctcatgccgcctagcccgatccttgttagttttgatcttttacttcc
+gcaggtagcccatttttttgactcgtagtcgccagtcgtcactgtaagatgcagcgtttc
+ccccgatg
 >Penicillium_nordicum_GCA_001278595.1|EOG091N44M8
 ttcctcccccccctccctgaggcccactccgcccagcccctcccccccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgct---gtccctctctccgctgccgtg
-tccagctccgtagaaggtcgga--ggtccgatggatatgcttggaataagtgaatactct
-cttctctcccgtgtacctcccct--------aagctacagatacgtccattacatgaact
-ggttgtaaatggcgctctcaaccagcaccaacacaacagtcgtcgccgtcccatcattaa
-cacccgcgggatgaatctgccttccagccatcgatgcgtcacctgaactcgaatggtttg
-ggggtgcctgccagtaaggcgttggcgggatgtgagccttgttcgccacgtatcacccta
-tacggttgctttacgttcgatcagctcttgacttcggcgctactactccttgtcaggggc
-ccggccatctaggaacgacatctccttcgtccacgtgcagctcatgccgcctagcccgat
-ccttgttagttttgatcttttacttccgcaggtagcccatttttttgactcgtagtcgcc
-agtcgtcactgtaagatgcagcgtttcccccgatg
+gcactcccggccggagcgctccttgccctctccgct---gtccctctct---ccgctgcc
+gtgtccagctccgtagaaggtcgga--ggtccgatggatatgcttggaataagtgaatac
+tctcttctctcccgtgtacctcccct----------------------------------
+----aagctacagatacgtccattacatgaactggttgtaaatggcgctctcaaccagca
+ccaacacaacagtcgtcgccgtcccatcattaacacccgcgggatgaatctgccttccag
+ccatcgatgcgtcacctgaactcgaatggtttgggggtgcctgccagtaaggcgttggcg
+ggatgtgagccttgttcgccacgtatcaccctatacggttgctttacgttcgatcagctc
+ttgacttcggcgctactactccttgtcaggggcccggccatctaggaacgacatctcctt
+cgtccacgtgcagctcatgccgcctagcccgatccttgttagttttgatcttttacttcc
+gcaggtagcccatttttttgactcgtagtcgccagtcgtcactgtaagatgcagcgtttc
+ccccgatg
 >Penicillium_oxalicum_114-2_GCA_000346795.1|EOG091N44M8
 ccccacccccccctctacgagtcccttgcctctcagagcctccccctcctctccgcccgg
-gtgcttccgaccggactgcttttctccctttccgccgct----ctcctcccgctgccgtg
-tctctaggcccccgccaagggg--agtccgaccgacatgatcggactc------------
+gtgcttccgaccggactgcttttctccctttccgccgct----ctcctctccccgctgcc
+gtgtctctaggcccccgccaagggg--agtccgaccgacatgatcggactc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_oxalicum_GCA_001723175.2|EOG091N44M8
 ccccacccccccctctacgagtcccttgcctctcagagcctccccctcctctccgcccgg
-gtgcttccgaccggactgcttttctccctttccgccgct----ctcctcccgctgccgtg
-tctctaggcccccgccaagggg--agtccgaccgacatgatcggactc------------
+gtgcttccgaccggactgcttttctccctttccgccgct----ctcctctccccgctgcc
+gtgtctctaggcccccgccaagggg--agtccgaccgacatgatcggactc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_oxalicum_GCA_004153425.1|EOG091N44M8
 ccccacccccccctctacgagtcccttgcctctcagagcctccccctcctctccgcccgg
-gtgcttccgaccggactgcttttctccctttccgccgct----ctcctcccgctgccgtg
-tctctaggcccccgccaagggg--agtccgaccgacatgatcggactc------------
+gtgcttccgaccggactgcttttctccctttccgccgct----ctcctctccccgctgcc
+gtgtctctaggcccccgccaagggg--agtccgaccgacatgatcggactc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_oxalicum_GCA_004521935.1|EOG091N44M8
 ccccacccccccctctacgagtcccttgcctctcagagcctccccctcctctccgcccgg
-gtgcttccgaccggactgcttttctccctttccgccgct----ctcctcccgctgccgtg
-tctctaggcccccgccaagggg--agtccgaccgacatgatcggactc------------
+gtgcttccgaccggactgcttttctccctttccgccgct----ctcctctccccgctgcc
+gtgtctctaggcccccgccaagggg--agtccgaccgacatgatcggactc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_oxalicum_GCA_005546515.1|EOG091N44M8
 ccccacccgcccctctacgagtcccttgcctctcagagcctccccctcctctccgcccgg
-gtgcttccgaccggactgcttttctccctttccgccgct----ctcctcccgctgccgtg
-tctctaggcccccgccaagggg--agtccgaccgacatgatcggactc------------
+gtgcttccgaccggactgcttttctccctttccgccgct----ctcctctccccgctgcc
+gtgtctctaggcccccgccaagggg--agtccgaccgacatgatcggactc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_oxalicum_JU-A10-T_GCA_000383025.1|EOG091N44M8
 ccccacccccccctctacgagtcccttgcctctcagagcctccccctcctctccgcccgg
-gtgcttccgaccggactgcttttctccctttccgccgct----ctcctcccgctgccgtg
-tctctaggcccccgccaagggg--agtccgaccgacatgatcggactc------------
+gtgcttccgaccggactgcttttctccctttccgccgct----ctcctctccccgctgcc
+gtgtctctaggcccccgccaagggg--agtccgaccgacatgatcggactc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_paneum_FM227_GCA_000577715.1|EOG091N44M8
 ttcctccctcccccgcacgacgacccctccgcctagcttctcccccccctgggtctgcgg
-gcactccaggccggagcgctccttgccctctccgctggtgtgtcttct-ccgctgccctg
-tccctctctgtagaagaagggaagggtccgatggatatgatcggactc------------
+gcactccaggccggagcgctccttgccctctccgctggtgtgtcttct----ccgctgcc
+ctgtccctctctgtagaagaagggaagggtccgatggatatgatcggactc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_paxilli_ATCC_26601_GCA_000347475.1|EOG091N44M8
 ccccaccctgccctccacgagtcccttgccgcccagcctgtccccctcctctccctccgc
-gtgcgtccggacggagcgcgtttctccgtttccgttgctgtccctcc-cccggtggtctc
-cctacctccgtagaaggaggga---gtccgacggacatgatcggtctt------------
+gtgcgtccggacggagcgcgtttctccgtttccgttgctgtccctcc-c---ccggtggt
+ctccctacctccgtagaaggaggga---gtccgacggacatgatcggtctt---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_polonicum_GCA_002072265.1|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccagcccctcccctccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga------------
-----------aaactattct----------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga---------
+-------------aaactattct-------------------------------------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_polonicum_GCA_003344595.1|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccagcccctcccctccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcggtctc------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_roqueforti_FM164_GCA_000513255.1|EOG091N44M8
 ttctccctgcccccccacgaggccctcgccgcctagctcctcccctccctgggtccgcgg
-gcactccaagccggtgcgctccttgccctctccgtcggtctctctctctccgctgccgtg
-tccctctctgtagaagaaggga--gggattgcctcttca-aatctgcaatcgaataccat
-tctctcttctgcgtacctccttt-----------------gtatacccgccacatgagcg
-ggttgcaaatggcgcggccgaccaggatcaatacggtagccatcgccacctaaccattag
-cctgcgcgggatgattccgtctccgggtcattgacgtgtcatccgagcccgaatatcttt
-gtggtgtccgcggatgggtaatccaggcaaacctaatctcattcgacgtggatcgatccc
-tgcggttattctgcatttgacaaactgctgattaagaagccattactcttaggttgaggt
-ccagccactcatggatggtttccccttcgtattcacactccttatgcgctcgagctcgat
-tcttgtcagtcctgaccttttaccctcgcggacagtttatttttttaactcgtagtcctg
-ggcaaagacgctaaagcatagcatgtccctcgatg
+gcactccaagccggtgcgctccttgccctctccgtcggtctctctctct---ccgctgcc
+gtgtccctctctgtagaagaaggga--gggattgcctcttca-aatctgcaatcgaatac
+cattctctcttctgcgtacctccttt----------------------------------
+-------------gtatacccgccacatgagcgggttgcaaatggcgcggccgaccagga
+tcaatacggtagccatcgccacctaaccattagcctgcgcgggatgattccgtctccggg
+tcattgacgtgtcatccgagcccgaatatctttgtggtgtccgcggatgggtaatccagg
+caaacctaatctcattcgacgtggatcgatccctgcggttattctgcatttgacaaactg
+ctgattaagaagccattactcttaggttgaggtccagccactcatggatggtttcccctt
+cgtattcacactccttatgcgctcgagctcgattcttgtcagtcctgaccttttaccctc
+gcggacagtttatttttttaactcgtagtcctgggcaaagacgctaaagcatagcatgtc
+cctcgatg
 >Penicillium_roqueforti_GCA_000737485.2|EOG091N44M8
 ttctccctgcccccccacgaggccctcgccgcctagctcctcccctccctgggtccgcgg
-gcactccaagccggtgcgctccttgccctctccgtcggtctctctctctccgctgccgtg
-tccctctctgtagaagaaggga--gggattgcctcttca-aatctgcaatcgaatactct
-tctctcttctgcgtacctccttt-----------------ctatacccgccacatgagcg
-ggttgcaaatggcgcggccgaccaggatcaatacggtagccatcgccacctaaccattag
-cctgcgcgggatgattccgtctccgggtcattgacgtgtcatccgagcccgaatatcttt
-gtggtgtccgcggatgggtaatccaggcaaacctaatctcattcgacgtggatcgatccc
-tgcggttattctgcatttgacaaactgctgattaagaagccattactcttaggttgaggt
-ccagccactcatggatggtttccccttcgtattcacactccttatgcgctcgagctcgat
-tcttgtcagtcctgaccttttaccctcgcggacagtttatttttttaactcgtagtcctg
-ggcaaagacgctaaagcatagcatgtccctcgatg
+gcactccaagccggtgcgctccttgccctctccgtcggtctctctctct---ccgctgcc
+gtgtccctctctgtagaagaaggga--gggattgcctcttca-aatctgcaatcgaatac
+tcttctctcttctgcgtacctccttt----------------------------------
+-------------ctatacccgccacatgagcgggttgcaaatggcgcggccgaccagga
+tcaatacggtagccatcgccacctaaccattagcctgcgcgggatgattccgtctccggg
+tcattgacgtgtcatccgagcccgaatatctttgtggtgtccgcggatgggtaatccagg
+caaacctaatctcattcgacgtggatcgatccctgcggttattctgcatttgacaaactg
+ctgattaagaagccattactcttaggttgaggtccagccactcatggatggtttcccctt
+cgtattcacactccttatgcgctcgagctcgattcttgtcagtcctgaccttttaccctc
+gcggacagtttatttttttaactcgtagtcctgggcaaagacgctaaagcatagcatgtc
+cctcgatg
 >Penicillium_roqueforti_GCA_001599855.1|EOG091N44M8
 ttctccctgcccccccacgaggccctcgccgcctagctcctcccctccctgggtccgcgg
-gcactccaagccggtgcgctccttgccctctccgtcggtctctctctctccgctgccgtg
-tccctctctgtagaagaaggga--gggattgcctcttca-aatctgcaatcgaatactct
-tctctcttctgcgtacctccttt-----------------ctatacccgccacatgagcg
-ggttgcaaatggcgcggccgaccaggatcaatatggtagccatcgccacctaaccattag
-cctgcgcgggatgattccgtctccgggtcattgacgtgtcatccgagcccgaatatcttt
-gtggtgtccgcggatgggtaatccaggcaaacctaatctcattcgacgtggatcgatccc
-tgcggttattctgcatttgacaaactgctgattaagaagccattactcttaggttgaggt
-ccagccactcatggatggtttccccttcgtattcacactccttatgcgctcgagctcgat
-tcttgtcagtcctgaccttttaccctcgcggacagtttatttttttaactcgtagtcctg
-ggcaaagacgctaaagcatagcatgtccctcgatg
+gcactccaagccggtgcgctccttgccctctccgtcggtctctctctct---ccgctgcc
+gtgtccctctctgtagaagaaggga--gggattgcctcttca-aatctgcaatcgaatac
+tcttctctcttctgcgtacctccttt----------------------------------
+-------------ctatacccgccacatgagcgggttgcaaatggcgcggccgaccagga
+tcaatatggtagccatcgccacctaaccattagcctgcgcgggatgattccgtctccggg
+tcattgacgtgtcatccgagcccgaatatctttgtggtgtccgcggatgggtaatccagg
+caaacctaatctcattcgacgtggatcgatccctgcggttattctgcatttgacaaactg
+ctgattaagaagccattactcttaggttgaggtccagccactcatggatggtttcccctt
+cgtattcacactccttatgcgctcgagctcgattcttgtcagtcctgaccttttaccctc
+gcggacagtttatttttttaactcgtagtcctgggcaaagacgctaaagcatagcatgtc
+cctcgatg
 >Penicillium_roqueforti_GCA_001939915.1|EOG091N44M8
 ttctccctgcccccccacgaggccctcgccgcctagctcctcccctccctgggtccgcgg
-gcactccaagccggtgcgctccttgccctctccgtcggtctctctctctccgctgccgtg
-tccctctctgtagaagaaggga--gggattgcctcttca-aatctgcaatcgaataccat
-tctctcttctgcgtacctcctt------------------gtatacccgccacatgagcg
-ggttgcaaatggcgcggccgaccaggatcaatatggtagccatcgccacctaaccattag
-cctgcgcgggatgattccgtctccgggtcattgacgtgtcatccgagcccgaatatcttt
-gtggtgtccgcggatgggtaatccaggcaaacctaatctcattcgacgtggatcgatccc
-tgcggttattctgcatttgacaaactgctgattaagaagccattactcttaggttgaggt
-ccagccactcatggatggtttccccttcgtattcacactccttatgcgctcgagctcgat
-tcttgtcagtcctgaccttttaccctcgcggacagtttatttttttaactcgtagtcctg
-ggcaaagacgctaaagcatagcatgtccctcgatg
+gcactccaagccggtgcgctccttgccctctccgtcggtctctctctct---ccgctgcc
+gtgtccctctctgtagaagaaggga--gggattgcctcttca-aatctgcaatcgaatac
+cattctctcttctgcgtacctcctt-----------------------------------
+-------------gtatacccgccacatgagcgggttgcaaatggcgcggccgaccagga
+tcaatatggtagccatcgccacctaaccattagcctgcgcgggatgattccgtctccggg
+tcattgacgtgtcatccgagcccgaatatctttgtggtgtccgcggatgggtaatccagg
+caaacctaatctcattcgacgtggatcgatccctgcggttattctgcatttgacaaactg
+ctgattaagaagccattactcttaggttgaggtccagccactcatggatggtttcccctt
+cgtattcacactccttatgcgctcgagctcgattcttgtcagtcctgaccttttaccctc
+gcggacagtttatttttttaactcgtagtcctgggcaaagacgctaaagcatagcatgtc
+cctcgatg
 >Penicillium_sclerotiorum_GCA_001750025.1|EOG091N44M8
 tccctcccgcgcttccacgctcagctcgctgcctggagtctcccctccctctccgcccgc
-ccatgtccggaacgagcgcgtttcaccccttccgttgctgtctctcctcgtggtgctccc
-cccagctgcccccgccaagggg--agtccgacggacatgatcggtctc------------
+ccatgtccggaacgagcgcgtttcaccccttccgttgctgtctctcctc---gtggtgct
+ccccccagctgcccccgccaagggg--agtccgacggacatgatcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_solitum_GCA_000952775.2|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccagcccctcccctccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga------------
-----------aaactattct----------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga---------
+-------------aaactattct-------------------------------------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_solitum_GCA_001750005.1|EOG091N44M8
 ttccttccccccctccacgaggcctgctccgcccatcccctcccctccctgggtctccgg
-gcacgcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tacccctccgtagaaggccgga--ggtccgatggatatgctcggtgta------------
+gcacgcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtacccctccgtagaaggccgga--ggtccgatggatatgctcggtgta---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcggag-----
+--------------------------------------------------------ag--
 ------------------------------------------------------------
----------------ttcggag--------------------------------------
------------------------ag-----------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_solitum_GCA_002072235.1|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctccccaccctgggtctccgg
-gcacgcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_sp.12|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctccccaccctgggtctccgg
-gcacgcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_sp._CF05_GCA_002916455.1|EOG091N44M8
 ttccccccgcccctccacgaggccctcaccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_sp._MA_6036_GCA_003138045.1|EOG091N44M8
 tccctcccccccctccacgaggctctctccgcccagcccctcccccccctgggtctccgg
-gcgctcccgacgcgagcccgtttcaccccttccgttgctgt----cctcctgccgctgcg
-t--ctctccgtagaaggaaggg--agtccgatggacatgctcggaactcacgaatactct
-ctcttcccctgtgtacctccccc-----------------ccccacccgccacggtcgtg
-agctagcgctctaagtcgtcgttcgttgacgggcgacgcgtgtcccagcccggcatgctg
-cctgtaaaacgcggaagtgtccctgtccgatgggtgccctccaggaggtagaactcccct
-agcgcgttcgaggattgagtaccgatggtaattgaatactcaccatcgtgcactacatta
-cacagccaccccagcttcgactagcagcaaactcgagcggcgtagtggccacccaagggc
-gaaaatcccgataactagatcgttccccacctccgagctgcttgcgccgcctccccccgg
-cttcttttgtctgttctccccgcctccttgggctactgactgagacggccaactagctgg
-cgtaatgaaaatagagcgacatgcgctttcttggc
+gcgctcccgacgcgagcccgtttcaccccttccgttgctgt----cctc---ctgccgct
+gcgt--ctctccgtagaaggaaggg--agtccgatggacatgctcggaactcacgaatac
+tctctcttcccctgtgtacctccccc----------------------------------
+-------------ccccacccgccacggtcgtgagctagcgctctaagtcgtcgttcgtt
+gacgggcgacgcgtgtcccagcccggcatgctgcctgtaaaacgcggaagtgtccctgtc
+cgatgggtgccctccaggaggtagaactcccctagcgcgttcgaggattgagtaccgatg
+gtaattgaatactcaccatcgtgcactacattacacagccaccccagcttcgactagcag
+caaactcgagcggcgtagtggccacccaagggcgaaaatcccgataactagatcgttccc
+cacctccgagctgcttgcgccgcctccccccggcttcttttgtctgttctccccgcctcc
+ttgggctactgactgagacggccaactagctggcgtaatgaaaatagagcgacatgcgct
+ttcttggc
 >Penicillium_sp._MA_6040_GCA_003138025.1|EOG091N44M8
 tcccctccgcccctccacgagtccctcgccgcccagatcctcccccccctgggtctccgg
-gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctctccgctgccgtg
-tccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc------------
+gcacgtccggccggagcgcgtcttaccctttccgttggtctccccctct---ccgctgcc
+gtgtccagctgcgtagaagaagggatcggtccgatggacatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_sp.MB|EOG091N44M8
 ttcctcccccccctccctgaggccctcgccgcccagcccctcccctccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga------------
-----------aaactacgtg----------------------------------------
+gcactcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggtcgga--ggtccgatggacatgctcgctgga---------
+-------------aaactacgtg-------------------------------------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_sp._MT2_MMC-2018_GCA_003852855.1|EOG091N44M8
 ccccatcccctcccctacgagtcccttgcctcccagagcctccccctcctctccccccgg
-gcgcgtccgaccggaccgcgtttcgccctctccgctgctgtgtctccttctgccgctgcg
-tccccaggtccccgccaagggg--agtctgacggacatgctcggtctc------------
+gcgcgtccgaccggaccgcgtttcgccctctccgctgctgtgtctcctttgtctgccgct
+gcgtccccaggtccccgccaagggg--agtctgacggacatgctcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_sp._occitanis_GCA_002382835.1|EOG091N44M8
 cctagccccccgctccacgcctccttcgcctctcaaacctgagtctctcctgaggtccgg
-ccctgccgggacggagtgtgtttttcccccagcgttgctgt--gtttttccaccgccccg
-tgtctctgtgcagaagaagggg--aatccgacggacatgatcggtctt------------
+ccctgccgggacggagtgtgtttttcccccagcgttgctgt--gttttttgtccaccgcc
+ccgtgtctctgtgcagaagaagggg--aatccgacggacatgatcggtctt---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_sp._occitanis_GCA_002382855.1|EOG091N44M8
 cctagccccccgctccacgcctccttcgcctctcaaacctgagtctctcctgaggtccgg
-ccctgccgggacggagtgtgtttttcccccagcgttgctgt--gtttttccaccgccccg
-tgtctctgtgcagaagaagggg--aatccgacggacatgatcggtctt------------
+ccctgccgggacggagtgtgtttttcccccagcgttgctgt--gttttttgtccaccgcc
+ccgtgtctctgtgcagaagaagggg--aatccgacggacatgatcggtctt---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_sp._SPG-F15_GCA_003800485.1|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctcccccccctgggtctccgg
-gcacgcccggccggagcgctccttaccctctccgctgctgtccctctctccgctgccgtg
-tccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga------------
-----------aaactattcc----------------------------------------
+gcacgcccggccggagcgctccttaccctctccgctgctgtccctctct---ccgctgcc
+gtgtccccctccgtagaaggttgga--ggtccgatggatatgctcgctgga---------
+-------------aaactattcc-------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_sp._SPG-F1_GCA_003800495.1|EOG091N44M8
 ttcctcccccccctccacgaggccctctccgcccatcccctccccaccctgggtctccgg
-gcacgcccggccggagcgctccttgccctctccgctgctgtccctctctccgctgccgtg
-tccacctccgtagaaggttgga--ggtccgatggatatgctcggtctc------------
+gcacgcccggccggagcgctccttgccctctccgctgctgtccctctct---ccgctgcc
+gtgtccacctccgtagaaggttgga--ggtccgatggatatgctcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_sp._W3_MMC-2018_GCA_004959885.1|EOG091N44M8
 ttcctttctccactgtaggccaactgcgccgcttatcccgagcctttactagagatgttt
-tgactttgagattgagcctgttcagaggttactgttactttcccttc--gtgccgctctc
-tctatccctgtag---aagagg--aatctgattgatatgttcggcgtcaatgactat---
-a--------------------c--------------------------------------
------------------acattta--------ataagg----------------------
-------------cgggaaaggtggaattacactagataaac-aaaa-----caacgcctg
-actgcacagaaactcagaacaagaatccacccaggaattaaatcaaggaa----c---aa
-tata-----------gaagac----------------------ttcagctttaaacagct
--gacccgtgtagcacctatactac-atgactgttggagtgagacccttg---tgtttc--
--ctccatacctcgttggaggtttg-t-a------gtttta----------agtta-----
---------------------------tccc-----
+tgactttgagattgagcctgttcagaggttactgttactttcccttc-----gtgccgct
+ctctctatccctgtag---aagagg--aatctgattgatatgttcggcgtcaatgactat
+---a--------------------c-----------------------------------
+--------------------------------------------------acattta---
+-----ataagg----------------------------------cgggaaaggtggaat
+tacactagataaac-aaaa-----caacgcctgactgcacagaaactcagaacaagaatc
+cacccaggaattaaatcaaggaa----c---aatata-----------gaagac------
+----------------ttcagctttaaacagct-gacccgtgtagcacctatactac-at
+gactgttggagtgagacccttg---tgtttc---ctccatacctcgttggaggtttg-t-
+a------gtttta----------agtta-------------------------------t
+ccc-----
 >Penicillium_steckii_GCA_002072375.1|EOG091N44M8
 ccccaccctgcctgccacgccgagctcgccgcccaggctgtcccctccctctctgcccgc
-gcgcgtccggacggagtgctctacaccccttccgttgctgtcccccc--ccgctggtgta
-cccctccccgtagaagaagggg--agtccgatggacatgctcgtgatg------------
-----a-------------------------------------------------------
+gcgcgtccggacggagtgctctacaccccttccgttgctgtcccccc-----ccgctggt
+gtacccctccccgtagaagaagggg--agtccgatggacatgctcgtgatg---------
+-------a----------------------------------------------------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------tggtgc------
 ------------------------------------------------------------
----------------tggtgc---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
 >Penicillium_subrubescens_GCA_001908125.1|EOG091N44M8
 ccccatccccccccctacgagtcccttgcttcccagagcctcccccccctctccgcccgg
-gcgcgtccgaccggaccgcgtttcaccctcagcgctgctgtgtcttcccctgccgctgcg
-tccccaggtccccgccaagggg--agtccgactgacatgatcggtctc------------
+gcgcgtccgaccggaccgcgtttcaccctcagcgctgctgtgtcttccctgtctgccgct
+gcgtccccaggtccccgccaagggg--agtccgactgacatgatcggtctc---------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------ttcgac---------------------------------------
+------------------------------------------------ttcgac------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+------------------------------------------------------------
+--------
 >Penicillium_verrucosum_GCA_000970515.2|EOG091N44M8
 ttcctcccccccctccctgaggcccactccgcccagcccctcccccccctgggtctccgg
-gcactcccggccggagcgctccttgccctctccgct---gtccctctctccgctgccgtg
-tccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatactct
-cttctctcccgcgtacctccccctcttactaaagctacagatacgcccattatatgaact
-ggttgtaaatggcgctctcaaccagcactaacacaactgtcgtcgccgccccatcattaa
-cacccgcgggatgaacctgccttccagccatcgatgcgtcacctgaactcgaatggtttg
-ggggtgcctgccagtaaggtgttggcgggatgtgagccttgttcgccacgtattacccta
-tacggttgctttacgttcgattagctcttgacttcggcgctactactccttgataggggc
-ccgaccatctaggaacgacatctccttcgtccacgtgcagttcatgccgcctagcccgat
-ccttgttagttttgatcttttacttccgtaggtagcctattcttttgactcgtagtcgcc
-agtcgtcactgcaaggtgcagcgtttcccccgatg
+gcactcccggccggagcgctccttgccctctccgct---gtccctctct---ccgctgcc
+gtgtccagctccgtagaaggtcgga--ggtccgatggatatgctcggaataagtgaatac
+tctcttctctcccgcgtacctccccccaatgcatcttactacccgtcccaagtggactgc
+aagtaagctacagatacgcccattatatgaactggttgtaaatggcgctctcaaccagca
+ctaacacaactgtcgtcgccgccccatcattaacacccgcgggatgaacctgccttccag
+ccatcgatgcgtcacctgaactcgaatggtttgggggtgcctgccagtaaggtgttggcg
+ggatgtgagccttgttcgccacgtattaccctatacggttgctttacgttcgattagctc
+ttgacttcggcgctactactccttgataggggcccgaccatctaggaacgacatctcctt
+cgtccacgtgcagttcatgccgcctagcccgatccttgttagttttgatcttttacttcc
+gtaggtagcctattcttttgactcgtagtcgccagtcgtcactgcaaggtgcagcgtttc
+ccccgatg
 >Penicillium_vulpinum_GCA_002072255.1|EOG091N44M8
 ttcctcccccccctctacgaggctctcgccgcctagcttctcccctccctgggtctccgc
-gcactcccggccgcagcgtgtcttaccctttccgctgctgtctctctctccggcggtccc
-cccccctccgtagaaggaggga--ggtccgacggatatgatcggtctc------------
+gcactcccggccgcagcgtgtcttaccctttccgctgctgtctctctct---ccggcggt
+ccccccccctccgtagaaggaggga--ggtccgacggatatgatcggtctc---------
+------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+------------------------------------------------ttcgat------
 ------------------------------------------------------------
----------------ttcgat---------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
------------------------------------
+--------
diff --git a/tests/integration/expected/EOG091N44M8_nt.fa.clipkit.log b/tests/integration/expected/EOG091N44M8_nt.fa.clipkit.log
index 12f1a47..bf61c87 100644
--- a/tests/integration/expected/EOG091N44M8_nt.fa.clipkit.log
+++ b/tests/integration/expected/EOG091N44M8_nt.fa.clipkit.log
@@ -205,48 +205,48 @@
 205 keep singleton 0.0
 206 keep constant 0.0
 207 keep parsimony-informative 0.0
-208 keep parsimony-informative 0.05982905982905983
-209 keep parsimony-informative 0.05982905982905983
-210 keep parsimony-informative 0.05982905982905983
-211 trim constant 0.9829059829059829
-212 trim other 0.9829059829059829
-213 trim other 0.9829059829059829
-214 keep constant 0.05982905982905983
-215 keep parsimony-informative 0.05982905982905983
-216 keep parsimony-informative 0.05982905982905983
-217 trim other 0.9914529914529915
-218 trim other 0.9914529914529915
-219 trim other 0.9914529914529915
-220 trim constant 0.9401709401709402
-221 trim parsimony-informative 0.9401709401709402
-222 trim parsimony-informative 0.9401709401709402
-223 keep constant 0.08547008547008547
-224 keep parsimony-informative 0.08547008547008547
-225 keep parsimony-informative 0.08547008547008547
-226 trim constant 0.9829059829059829
-227 trim constant 0.9829059829059829
-228 trim constant 0.9829059829059829
-229 keep constant 0.03418803418803419
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-231 keep parsimony-informative 0.03418803418803419
-232 keep singleton 0.02564102564102564
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-235 keep singleton 0.02564102564102564
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-237 keep parsimony-informative 0.02564102564102564
-238 keep singleton 0.07692307692307693
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-241 keep constant 0.11965811965811966
-242 keep constant 0.11965811965811966
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-244 keep constant 0.8803418803418803
-245 keep singleton 0.8803418803418803
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-249 keep parsimony-informative 0.8803418803418803
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 250 keep constant 0.0
 251 keep parsimony-informative 0.0
 252 keep parsimony-informative 0.0
@@ -262,9 +262,9 @@
 262 keep singleton 0.0
 263 keep parsimony-informative 0.0
 264 keep parsimony-informative 0.0
-265 keep singleton 0.017094017094017096
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-267 keep parsimony-informative 0.017094017094017096
+265 keep singleton 0.0171
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 268 keep constant 0.0
 269 keep parsimony-informative 0.0
 270 keep parsimony-informative 0.0
@@ -274,9 +274,9 @@
 274 keep parsimony-informative 0.0
 275 keep constant 0.0
 276 keep parsimony-informative 0.0
-277 keep constant 0.7521367521367521
-278 keep constant 0.7521367521367521
-279 keep singleton 0.7521367521367521
+277 keep constant 0.7521
+278 keep constant 0.7521
+279 keep singleton 0.7521
 280 keep parsimony-informative 0.0
 281 keep constant 0.0
 282 keep parsimony-informative 0.0
@@ -286,18 +286,18 @@
 286 keep constant 0.0
 287 keep parsimony-informative 0.0
 288 keep parsimony-informative 0.0
-289 keep parsimony-informative 0.02564102564102564
-290 keep parsimony-informative 0.02564102564102564
-291 keep parsimony-informative 0.02564102564102564
-292 trim parsimony-informative 0.9487179487179487
-293 trim parsimony-informative 0.9487179487179487
-294 trim parsimony-informative 0.9487179487179487
-295 trim constant 0.9487179487179487
-296 trim constant 0.9487179487179487
-297 trim parsimony-informative 0.9487179487179487
-298 trim singleton 0.9487179487179487
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-300 trim constant 0.9487179487179487
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 301 keep parsimony-informative 0.0
 302 keep parsimony-informative 0.0
 303 keep parsimony-informative 0.0
@@ -310,12 +310,12 @@
 310 keep parsimony-informative 0.0
 311 keep singleton 0.0
 312 keep singleton 0.0
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 319 keep constant 0.0
 320 keep constant 0.0
 321 keep parsimony-informative 0.0
@@ -337,2742 +337,2742 @@
 337 keep parsimony-informative 0.0
 338 keep parsimony-informative 0.0
 339 keep parsimony-informative 0.0
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 343 keep parsimony-informative 0.0
 344 keep constant 0.0
 345 keep parsimony-informative 0.0
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+2964 keep singleton 0.8632
+2965 keep constant 0.8632
+2966 keep constant 0.8632
+2967 keep singleton 0.8632
+2968 keep parsimony-informative 0.8718
+2969 keep constant 0.8718
+2970 keep singleton 0.8718
+2971 keep constant 0.8718
+2972 keep constant 0.8718
+2973 keep constant 0.8718
+2974 keep constant 0.8718
+2975 keep constant 0.8718
+2976 keep parsimony-informative 0.8718
+2977 keep parsimony-informative 0.8718
+2978 keep constant 0.8718
+2979 keep parsimony-informative 0.8718
+2980 keep constant 0.8718
+2981 keep constant 0.8718
+2982 keep parsimony-informative 0.8718
+2983 keep constant 0.8718
+2984 keep constant 0.8718
+2985 keep constant 0.8718
+2986 keep singleton 0.8718
+2987 keep constant 0.8718
+2988 keep constant 0.8718
+2989 keep constant 0.8889
+2990 keep constant 0.8889
+2991 keep constant 0.8889
+2992 keep singleton 0.8889
+2993 keep constant 0.8889
+2994 keep constant 0.8889
+2995 keep constant 0.8889
+2996 keep constant 0.8889
+2997 keep constant 0.8889
+2998 keep constant 0.8889
+2999 keep parsimony-informative 0.8889
+3000 keep singleton 0.8889
+3001 keep singleton 0.8889
+3002 keep parsimony-informative 0.8889
+3003 keep singleton 0.8889
+3004 keep parsimony-informative 0.8889
+3005 keep parsimony-informative 0.8889
+3006 keep parsimony-informative 0.8889
+3007 keep parsimony-informative 0.8889
+3008 keep constant 0.8889
+3009 keep constant 0.8889
+3010 keep singleton 0.8889
+3011 keep singleton 0.8889
+3012 keep singleton 0.8889
+3013 keep constant 0.8889
+3014 keep singleton 0.8889
+3015 keep parsimony-informative 0.8889
+3016 keep constant 0.8889
+3017 keep singleton 0.8889
+3018 keep parsimony-informative 0.8889
+3019 keep singleton 0.8889
+3020 keep constant 0.8889
+3021 keep parsimony-informative 0.8889
+3022 trim constant 0.9829
+3023 trim other 0.9829
+3024 trim other 0.9829
+3025 trim other 0.9915
+3026 trim other 0.9915
+3027 trim other 0.9915
+3028 trim other 0.9915
+3029 trim other 0.9915
+3030 trim other 0.9915
+3031 trim other 0.9915
+3032 trim other 0.9915
+3033 trim other 0.9915
+3034 trim other 0.9915
+3035 trim other 0.9915
+3036 trim other 0.9915
+3037 trim other 0.9915
+3038 trim other 0.9915
+3039 trim other 0.9915
+3040 trim other 0.9915
+3041 trim other 0.9915
+3042 trim other 0.9915
+3043 trim other 0.9915
+3044 trim other 0.9915
+3045 trim other 0.9915
+3046 trim other 0.9915
+3047 trim other 0.9915
+3048 trim other 0.9915
+3049 trim other 0.9915
+3050 trim other 0.9915
+3051 trim other 0.9915
+3052 trim other 0.9915
+3053 trim other 0.9915
+3054 trim other 0.9915
+3055 trim other 0.9915
+3056 trim other 0.9915
+3057 trim other 0.9915
+3058 trim other 0.9915
+3059 trim other 0.9915
+3060 trim other 0.9915
+3061 trim other 0.9915
+3062 trim other 0.9915
+3063 trim other 0.9915
+3064 trim other 0.9915
+3065 trim other 0.9915
+3066 trim other 0.9915
+3067 trim other 0.9915
+3068 trim other 0.9915
+3069 trim other 0.9915
+3070 trim other 0.9915
+3071 trim other 0.9915
+3072 trim other 0.9915
+3073 trim other 0.9915
+3074 trim other 0.9915
+3075 trim other 0.9915
+3076 keep singleton 0.8974
+3077 keep constant 0.8974
+3078 keep singleton 0.8974
diff --git a/tests/integration/expected/simple.fa_gappy_gaps_set_to_0.2 b/tests/integration/expected/simple.fa_gappy_gaps_set_to_0.2
index 2a39c28..d3744bf 100644
--- a/tests/integration/expected/simple.fa_gappy_gaps_set_to_0.2
+++ b/tests/integration/expected/simple.fa_gappy_gaps_set_to_0.2
@@ -1,10 +1,10 @@
 >1
-AGAT
+AGA
 >2
-AGAT
+AGA
 >3
-AGTA
+AGT
 >4
-AATA
+AAT
 >5
-AaT-
+AaT
diff --git a/tests/integration/samples/simple.fa.clipkit b/tests/integration/samples/simple.fa.clipkit
index da4f9f8..0cef391 100644
--- a/tests/integration/samples/simple.fa.clipkit
+++ b/tests/integration/samples/simple.fa.clipkit
@@ -1,10 +1,10 @@
 >1
-A-GAT
+A-GTAT
 >2
-A-GAT
+A-G-AT
 >3
-A-GTA
+A-G-TA
 >4
-AGATA
+AGA-TA
 >5
-ACaT-
+ACa-T-
diff --git a/tests/integration/test_api.py b/tests/integration/test_api.py
index d237dc8..005e280 100644
--- a/tests/integration/test_api.py
+++ b/tests/integration/test_api.py
@@ -6,12 +6,13 @@
 from clipkit.modes import TrimmingMode
 from clipkit.msa import MSA
 
+
 @pytest.mark.integration
 class TestApiInvocation(object):
     def test_input_file(self):
         trim_run, stats = clipkit(
             input_file_path="tests/integration/samples/simple.fa",
-            mode="gappy",
+            mode=TrimmingMode.gappy,
             gaps=0.3,
             sequence_type="nt",
         )
@@ -20,10 +21,9 @@ def test_input_file(self):
             "alignment_length": 6,
             "output_length": 4,
             "trimmed_length": 2,
-            "trimmed_percentage": 33.333
+            "trimmed_percentage": 33.333,
         }
         assert isinstance(trim_run.version, str)
-        assert trim_run.complement is None
         assert isinstance(trim_run.trimmed, MultipleSeqAlignment)
 
     def test_raw_alignment(self):
@@ -37,7 +37,6 @@ def test_raw_alignment(self):
             "alignment_length": 6,
             "output_length": 5,
             "trimmed_length": 1,
-            "trimmed_percentage": 16.667
+            "trimmed_percentage": 16.667,
         }
         assert isinstance(trim_run.version, str)
-        assert trim_run.complement is None
diff --git a/tests/unit/test_helpers.py b/tests/unit/test_helpers.py
deleted file mode 100644
index 1a36ccb..0000000
--- a/tests/unit/test_helpers.py
+++ /dev/null
@@ -1,221 +0,0 @@
-import pytest
-import pytest_mock
-from pathlib import Path
-
-
-import numpy as np
-from Bio import AlignIO
-from Bio import SeqIO
-from Bio.Seq import Seq
-from Bio.SeqRecord import SeqRecord
-from Bio.Align import MultipleSeqAlignment
-
-from clipkit.helpers import (
-    count_characters_at_position,
-    get_gap_chars,
-    report_column_features,
-    determine_site_classification_type,
-    create_keep_and_trim_msas,
-    write_trim_msa,
-    write_keep_msa,
-    SeqType,
-)
-from clipkit.files import FileFormat
-from clipkit.modes import SiteClassificationType, TrimmingMode, trim, should_keep_site
-from clipkit.settings import DEFAULT_AA_GAP_CHARS, DEFAULT_NT_GAP_CHARS
-
-
-here = Path(__file__)
-
-
-@pytest.fixture
-def sample_msa():
-    return MultipleSeqAlignment(
-        [
-            SeqRecord(
-                seq=Seq("['A']"),
-                id="1",
-                name="<unknown name>",
-                description="",
-                dbxrefs=[],
-            ),
-            SeqRecord(
-                seq=Seq("['A']"),
-                id="2",
-                name="<unknown name>",
-                description="",
-                dbxrefs=[],
-            ),
-            SeqRecord(
-                seq=Seq("['A']"),
-                id="3",
-                name="<unknown name>",
-                description="",
-                dbxrefs=[],
-            ),
-            SeqRecord(
-                seq=Seq("['A']"),
-                id="4",
-                name="<unknown name>",
-                description="",
-                dbxrefs=[],
-            ),
-            SeqRecord(
-                seq=Seq("['A']"),
-                id="5",
-                name="<unknown name>",
-                description="",
-                dbxrefs=[],
-            ),
-        ]
-    )
-
-
-class TestCountCharactersAtPosition(object):
-    def test_gives_count_for_each_char(self):
-        ## setup
-        s = "ACTTTGGG"
-
-        ## execution
-        res = count_characters_at_position(s, DEFAULT_NT_GAP_CHARS)
-
-        ## check results
-        # test that each character has an associated key
-        for char in s:
-            assert char in res.keys()
-
-        # test that the len of the res is equal to the
-        # number of unique string characters
-        assert len(res) == len(set(s))
-
-
-class TestGetSequenceAtPositionAndReportFeatures(object):
-    def test_gets_sequence_and_gappyness(self):
-        ## setup
-        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
-        i = 5
-
-        ## execution
-        seq, gappyness = report_column_features(alignment, i, DEFAULT_AA_GAP_CHARS)
-
-        ## check results
-        # test output types
-        assert isinstance(seq, str)
-        assert isinstance(gappyness, float)
-
-
-class TestParsimonyInformativeOrConstant(object):
-    def test_determine_site_classification_type(self):
-        ## set up
-        num_occurences_pi = {"A": 5, "T": 10, "G": 2, "C": 4}
-        num_occurences_const = {"T": 10}
-        num_occurences_singleton = {"A": 1, "T": 2}
-        num_occurences_other = {"A": 1}
-
-        ## execution
-        res_num_occurences_pi = determine_site_classification_type(num_occurences_pi)
-        res_num_occurences_const = determine_site_classification_type(
-            num_occurences_const
-        )
-        res_num_occurences_singleton = determine_site_classification_type(
-            num_occurences_singleton
-        )
-        res_num_occurences_other = determine_site_classification_type(
-            num_occurences_other
-        )
-
-        ## check results
-        assert res_num_occurences_pi is SiteClassificationType.parsimony_informative
-        assert res_num_occurences_const is SiteClassificationType.constant
-        assert res_num_occurences_singleton is SiteClassificationType.singleton
-        assert res_num_occurences_other is SiteClassificationType.other
-
-
-class TestPopulateEmptyKeepDAndTrimD(object):
-    def test_create_keep_and_trim_msas(self):
-        ## set up
-        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
-
-        ## execution
-        keep_msa, trim_msa = create_keep_and_trim_msas(alignment, True)
-
-        ## check results
-        expected_keep_data = {
-            "1": np.array([b"", b"", b"", b"", b"", b""]),
-            "2": np.array([b"", b"", b"", b"", b"", b""]),
-            "3": np.array([b"", b"", b"", b"", b"", b""]),
-            "4": np.array([b"", b"", b"", b"", b"", b""]),
-            "5": np.array([b"", b"", b"", b"", b"", b""]),
-        }
-        expected_trim_data = {
-            "1": np.array([b"", b"", b"", b"", b"", b""]),
-            "2": np.array([b"", b"", b"", b"", b"", b""]),
-            "3": np.array([b"", b"", b"", b"", b"", b""]),
-            "4": np.array([b"", b"", b"", b"", b"", b""]),
-            "5": np.array([b"", b"", b"", b"", b"", b""]),
-        }
-
-        assert expected_keep_data.keys() == keep_msa._data.keys()
-        assert all(
-            np.array_equal(expected_keep_data[key], keep_msa._data[key])
-            for key in expected_keep_data
-        )
-        assert expected_trim_data.keys() == trim_msa._data.keys()
-        assert all(
-            np.array_equal(expected_trim_data[key], trim_msa._data[key])
-            for key in expected_trim_data
-        )
-
-
-class TestWriteKeepD(object):
-    def test_write_keep_msa_writes_file(self, mocker, sample_msa):
-        ## set up
-        alignment = AlignIO.read(f"{here.parent}/examples/single_site.fa", "fasta")
-        keep_msa, _ = create_keep_and_trim_msas(alignment, True)
-
-        out_file = "output_file_name.fa"
-        out_file_format = FileFormat.fasta
-        mock_msa = mocker.patch("clipkit.msa.MultipleSeqAlignment")
-        mock_msa.return_value = sample_msa
-        mock_write = mocker.patch("clipkit.helpers.SeqIO.write")
-
-        ## execution
-        write_keep_msa(keep_msa, out_file, out_file_format)
-
-        ## check results
-        mock_write.assert_called_once_with(sample_msa, out_file, out_file_format.value)
-
-
-class TestWriteTrimD(object):
-    def test_write_trim_msa_calls_seqio_write(self, mocker, sample_msa):
-        ## set up
-        alignment = AlignIO.read(f"{here.parent}/examples/single_site.fa", "fasta")
-        _, trim_msa = create_keep_and_trim_msas(alignment, True)
-
-        out_file = "output_file_name.fa"
-        out_file_format = FileFormat.fasta
-        mock_msa = mocker.patch("clipkit.msa.MultipleSeqAlignment")
-        mock_msa.return_value = sample_msa
-        mock_write = mocker.patch("clipkit.helpers.SeqIO.write")
-
-        ## execution
-        write_trim_msa(trim_msa, out_file, out_file_format)
-
-        ## check results
-        expected_completmentOut = f"{out_file}.complement"
-        mock_write.assert_called_once_with(
-            sample_msa, expected_completmentOut, out_file_format.value
-        )
-
-
-class TestGetGapChars(object):
-    def test_get_gap_chars(self):
-        ## set up
-        seq_type = SeqType.aa
-
-        ## execution
-        res_seq_type = get_gap_chars(seq_type)
-
-        ## check results
-        expected_res = DEFAULT_AA_GAP_CHARS
-        assert expected_res == res_seq_type
diff --git a/tests/unit/test_modes.py b/tests/unit/test_modes.py
deleted file mode 100644
index a647f12..0000000
--- a/tests/unit/test_modes.py
+++ /dev/null
@@ -1,421 +0,0 @@
-import pytest
-from pathlib import Path
-
-import numpy as np
-from Bio import AlignIO
-from clipkit.modes import SiteClassificationType, TrimmingMode, trim, should_keep_site
-from clipkit.msa import MSA
-from clipkit.helpers import create_keep_and_trim_msas
-
-
-here = Path(__file__)
-
-
-class TestModes(object):
-    def test_should_keep_site_kpi_gappy_keep(self):
-        ## setup
-        mode = TrimmingMode.kpi_gappy
-        gappyness = 0.00
-        gaps = 0.9
-
-        assert (
-            should_keep_site(
-                mode, SiteClassificationType.parsimony_informative, gappyness, gaps
-            )
-            is True
-        )
-
-    def test_should_keep_site_kpi_gappy_trim(self):
-        ## setup
-        mode = TrimmingMode.kpi_gappy
-        gappyness = 0.00
-        gaps = 0.9
-
-        assert (
-            should_keep_site(mode, SiteClassificationType.constant, gappyness, gaps)
-            is False
-        )
-
-    def test_should_keep_site_gappy_keep(self):
-        ## setup
-        mode = TrimmingMode.gappy
-        site_classification_type = SiteClassificationType.parsimony_informative
-        gappyness = 0.00
-        gaps_threshold = 0.9
-
-        assert (
-            should_keep_site(mode, site_classification_type, gappyness, gaps_threshold)
-            is True
-        )
-
-    def test_should_keep_site_gappy_trim(self):
-        ## setup
-        mode = TrimmingMode.gappy
-        site_classification_type = SiteClassificationType.parsimony_informative
-        gappyness = 0.95
-        gaps_threshold = 0.9
-
-        assert (
-            should_keep_site(mode, site_classification_type, gappyness, gaps_threshold)
-            is False
-        )
-
-    def test_should_keep_site_kpi_keep(self):
-        ## setup
-        mode = TrimmingMode.kpi
-        site_classification_type = SiteClassificationType.parsimony_informative
-        gappyness = 0.00
-        gaps_threshold = 0.9
-
-        assert should_keep_site(
-            mode, site_classification_type, gappyness, gaps_threshold
-        )
-
-    def test_should_keep_site_kpi_trim(self):
-        ## setup
-        mode = TrimmingMode.kpi
-        site_classification_type = SiteClassificationType.other
-        gappyness = 0.95
-        gaps_threshold = 0.9
-
-        assert (
-            should_keep_site(mode, site_classification_type, gappyness, gaps_threshold)
-            is False
-        )
-
-    def test_should_keep_site_kpic_keep(self):
-        ## setup
-        mode = TrimmingMode.kpic
-        site_classification_type = SiteClassificationType.constant
-        gappyness = 0.95
-        gaps_threshold = 0.9
-
-        assert should_keep_site(
-            mode, site_classification_type, gappyness, gaps_threshold
-        )
-
-    def test_should_keep_site_kpic_trim(self):
-        ## setup
-        mode = TrimmingMode.kpic
-        site_classification_type = SiteClassificationType.other
-        gappyness = 0.95
-        gaps_threshold = 0.9
-
-        assert (
-            should_keep_site(mode, site_classification_type, gappyness, gaps_threshold)
-            is False
-        )
-
-    def test_should_keep_site_kpic_gappy_keep(self):
-        ## setup
-        mode = TrimmingMode.kpic_gappy
-        site_classification_type = SiteClassificationType.constant
-        gappyness = 0.2
-        gaps_threshold = 0.9
-
-        assert should_keep_site(
-            mode, site_classification_type, gappyness, gaps_threshold
-        )
-
-    def test_should_keep_site_kpic_gappy_trim(self):
-        ## setup
-        mode = TrimmingMode.kpic_gappy
-        site_classification_type = SiteClassificationType.constant
-        gappyness = 0.95
-        gaps_threshold = 0.9
-
-        assert (
-            should_keep_site(mode, site_classification_type, gappyness, gaps_threshold)
-            is False
-        )
-
-    def test_gappy_mode(self):
-        ## setup
-        gappyness = 0
-        site_classification_type = SiteClassificationType.constant
-        site_classification_counts = {
-            SiteClassificationType.parsimony_informative: 0,
-            SiteClassificationType.constant: 0,
-            SiteClassificationType.singleton: 0,
-            SiteClassificationType.other: 0,
-        }
-        i = 2
-        gaps_threshold = 0.9
-        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
-        use_log = False
-
-        keep_msa, trim_msa = create_keep_and_trim_msas(alignment, True)
-
-        ## execution
-        keep_msa, trim_msa = trim(
-            gappyness,
-            site_classification_type,
-            site_classification_counts,
-            keep_msa,
-            trim_msa,
-            i,
-            gaps_threshold,
-            alignment,
-            TrimmingMode.gappy,
-            use_log,
-        )
-
-        ## check results
-        expected_keep_data = {
-            "1": np.array([b"", b"", b"G", b"", b"", b""]),
-            "2": np.array([b"", b"", b"G", b"", b"", b""]),
-            "3": np.array([b"", b"", b"G", b"", b"", b""]),
-            "4": np.array([b"", b"", b"A", b"", b"", b""]),
-            "5": np.array([b"", b"", b"a", b"", b"", b""]),
-        }
-        expected_trim_data = {
-            "1": np.array([b"", b"", b"", b"", b"", b""]),
-            "2": np.array([b"", b"", b"", b"", b"", b""]),
-            "3": np.array([b"", b"", b"", b"", b"", b""]),
-            "4": np.array([b"", b"", b"", b"", b"", b""]),
-            "5": np.array([b"", b"", b"", b"", b"", b""]),
-        }
-
-        assert expected_keep_data.keys() == keep_msa._data.keys()
-        assert all(
-            np.array_equal(expected_keep_data[key], keep_msa._data[key])
-            for key in expected_keep_data
-        )
-        assert expected_trim_data.keys() == trim_msa._data.keys()
-        assert all(
-            np.array_equal(expected_trim_data[key], trim_msa._data[key])
-            for key in expected_trim_data
-        )
-
-    def test_kpi_gappy_mode(self):
-        ## setup
-        gappyness = 0
-        site_classification_type = SiteClassificationType.constant
-        site_classification_counts = {
-            SiteClassificationType.parsimony_informative: 0,
-            SiteClassificationType.constant: 0,
-            SiteClassificationType.singleton: 0,
-            SiteClassificationType.other: 0,
-        }
-        i = 1
-        gaps_threshold = 0.9
-        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
-        use_log = False
-
-        keep_msa, trim_msa = create_keep_and_trim_msas(alignment, True)
-
-        ## execution
-        keep_msa, trim_msa = trim(
-            gappyness,
-            site_classification_type,
-            site_classification_counts,
-            keep_msa,
-            trim_msa,
-            i,
-            gaps_threshold,
-            alignment,
-            TrimmingMode.kpi_gappy,
-            use_log,
-        )
-
-        ## check results
-        expected_keep_data = {
-            "1": np.array([b"", b"", b"", b"", b"", b""]),
-            "2": np.array([b"", b"", b"", b"", b"", b""]),
-            "3": np.array([b"", b"", b"", b"", b"", b""]),
-            "4": np.array([b"", b"", b"", b"", b"", b""]),
-            "5": np.array([b"", b"", b"", b"", b"", b""]),
-        }
-        expected_trim_data = {
-            "1": np.array([b"", b"-", b"", b"", b"", b""]),
-            "2": np.array([b"", b"-", b"", b"", b"", b""]),
-            "3": np.array([b"", b"-", b"", b"", b"", b""]),
-            "4": np.array([b"", b"G", b"", b"", b"", b""]),
-            "5": np.array([b"", b"C", b"", b"", b"", b""]),
-        }
-
-        assert expected_keep_data.keys() == keep_msa._data.keys()
-        assert all(
-            np.array_equal(expected_keep_data[key], keep_msa._data[key])
-            for key in expected_keep_data
-        )
-        assert expected_trim_data.keys() == trim_msa._data.keys()
-        assert all(
-            np.array_equal(expected_trim_data[key], trim_msa._data[key])
-            for key in expected_trim_data
-        )
-
-    def test_kpi_mode(self):
-        ## setup
-        gappyness = 0
-        site_classification_type = SiteClassificationType.parsimony_informative
-        site_classification_counts = {
-            SiteClassificationType.parsimony_informative: 0,
-            SiteClassificationType.constant: 0,
-            SiteClassificationType.singleton: 0,
-            SiteClassificationType.other: 0,
-        }
-        i = 5
-        gaps_threshold = 0.9
-        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
-        use_log = False
-
-        keep_msa, trim_msa = create_keep_and_trim_msas(alignment, True)
-
-        ## execution
-        keep_msa, trim_msa = trim(
-            gappyness,
-            site_classification_type,
-            site_classification_counts,
-            keep_msa,
-            trim_msa,
-            i,
-            gaps_threshold,
-            alignment,
-            TrimmingMode.kpi,
-            use_log,
-        )
-
-        ## check results
-        expected_keep_data = {
-            "1": np.array([b"", b"", b"", b"", b"", b"T"]),
-            "2": np.array([b"", b"", b"", b"", b"", b"T"]),
-            "3": np.array([b"", b"", b"", b"", b"", b"A"]),
-            "4": np.array([b"", b"", b"", b"", b"", b"A"]),
-            "5": np.array([b"", b"", b"", b"", b"", b"-"]),
-        }
-        expected_trim_data = {
-            "1": np.array([b"", b"", b"", b"", b"", b""]),
-            "2": np.array([b"", b"", b"", b"", b"", b""]),
-            "3": np.array([b"", b"", b"", b"", b"", b""]),
-            "4": np.array([b"", b"", b"", b"", b"", b""]),
-            "5": np.array([b"", b"", b"", b"", b"", b""]),
-        }
-
-        assert expected_keep_data.keys() == keep_msa._data.keys()
-        assert all(
-            np.array_equal(expected_keep_data[key], keep_msa._data[key])
-            for key in expected_keep_data
-        )
-        assert expected_trim_data.keys() == trim_msa._data.keys()
-        assert all(
-            np.array_equal(expected_trim_data[key], trim_msa._data[key])
-            for key in expected_trim_data
-        )
-
-    def test_kpic_mode(self):
-        ## setup
-        gappyness = 0
-        site_classification_type = SiteClassificationType.constant
-        site_classification_counts = {
-            SiteClassificationType.parsimony_informative: 0,
-            SiteClassificationType.constant: 0,
-            SiteClassificationType.singleton: 0,
-            SiteClassificationType.other: 0,
-        }
-        i = 0
-        gaps_threshold = 0.9
-        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
-        use_log = False
-
-        keep_msa, trim_msa = create_keep_and_trim_msas(alignment, True)
-
-        ## execution
-        keep_msa, trim_msa = trim(
-            gappyness,
-            site_classification_type,
-            site_classification_counts,
-            keep_msa,
-            trim_msa,
-            i,
-            gaps_threshold,
-            alignment,
-            TrimmingMode.kpic_gappy,
-            use_log,
-        )
-
-        ## check results
-        expected_keep_data = {
-            "1": np.array([b"A", b"", b"", b"", b"", b""]),
-            "2": np.array([b"A", b"", b"", b"", b"", b""]),
-            "3": np.array([b"A", b"", b"", b"", b"", b""]),
-            "4": np.array([b"A", b"", b"", b"", b"", b""]),
-            "5": np.array([b"A", b"", b"", b"", b"", b""]),
-        }
-        expected_trim_data = {
-            "1": np.array([b"", b"", b"", b"", b"", b""]),
-            "2": np.array([b"", b"", b"", b"", b"", b""]),
-            "3": np.array([b"", b"", b"", b"", b"", b""]),
-            "4": np.array([b"", b"", b"", b"", b"", b""]),
-            "5": np.array([b"", b"", b"", b"", b"", b""]),
-        }
-
-        assert expected_keep_data.keys() == keep_msa._data.keys()
-        assert all(
-            np.array_equal(expected_keep_data[key], keep_msa._data[key])
-            for key in expected_keep_data
-        )
-        assert expected_trim_data.keys() == trim_msa._data.keys()
-        assert all(
-            np.array_equal(expected_trim_data[key], trim_msa._data[key])
-            for key in expected_trim_data
-        )
-
-    def test_kpic_gappy_mode(self):
-        ## setup
-        gappyness = 0.2
-        site_classification_type = SiteClassificationType.singleton
-        site_classification_counts = {
-            SiteClassificationType.parsimony_informative: 0,
-            SiteClassificationType.constant: 0,
-            SiteClassificationType.singleton: 0,
-            SiteClassificationType.other: 0,
-        }
-
-        i = 3
-        gaps_threshold = 0.9
-        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
-        use_log = False
-
-        keep_msa, trim_msa = create_keep_and_trim_msas(alignment, True)
-
-        ## execution
-        keep_msa, trim_msa = trim(
-            gappyness,
-            site_classification_type,
-            site_classification_counts,
-            keep_msa,
-            trim_msa,
-            i,
-            gaps_threshold,
-            alignment,
-            TrimmingMode.kpic_gappy,
-            use_log,
-        )
-
-        ## check results
-        expected_keep_data = {
-            "1": np.array([b"", b"", b"", b"", b"", b""]),
-            "2": np.array([b"", b"", b"", b"", b"", b""]),
-            "3": np.array([b"", b"", b"", b"", b"", b""]),
-            "4": np.array([b"", b"", b"", b"", b"", b""]),
-            "5": np.array([b"", b"", b"", b"", b"", b""]),
-        }
-        expected_trim_data = {
-            "1": np.array([b"", b"", b"", b"T", b"", b""]),
-            "2": np.array([b"", b"", b"", b"-", b"", b""]),
-            "3": np.array([b"", b"", b"", b"-", b"", b""]),
-            "4": np.array([b"", b"", b"", b"-", b"", b""]),
-            "5": np.array([b"", b"", b"", b"-", b"", b""]),
-        }
-
-        assert expected_keep_data.keys() == keep_msa._data.keys()
-        assert all(
-            np.array_equal(expected_keep_data[key], keep_msa._data[key])
-            for key in expected_keep_data
-        )
-        assert expected_trim_data.keys() == trim_msa._data.keys()
-        assert all(
-            np.array_equal(expected_trim_data[key], trim_msa._data[key])
-            for key in expected_trim_data
-        )
diff --git a/tests/unit/test_smart_gap_helper.py b/tests/unit/test_smart_gap_helper.py
index 8565d82..c755168 100644
--- a/tests/unit/test_smart_gap_helper.py
+++ b/tests/unit/test_smart_gap_helper.py
@@ -32,7 +32,7 @@ def test_smart_gap_threshold_simple_case(self):
         expected_gaps = 0.8
 
         ## execution
-        gaps = smart_gap_threshold_determination(alignment, DEFAULT_AA_GAP_CHARS, True)
+        gaps = smart_gap_threshold_determination(alignment, DEFAULT_AA_GAP_CHARS)
 
         ## check results
         assert expected_gaps == gaps
@@ -42,7 +42,7 @@ def test_smart_gap_threshold_standard_case(self):
         alignment = AlignIO.read(f"{here.parent}/examples/EOG091N44M8_aa.fa", "fasta")
 
         ## execution
-        gaps = smart_gap_threshold_determination(alignment, DEFAULT_AA_GAP_CHARS, True)
+        gaps = smart_gap_threshold_determination(alignment, DEFAULT_AA_GAP_CHARS)
         expected_gaps = 0.8803
 
         ## check results
@@ -136,12 +136,9 @@ def test_gap_to_gap_slope_simple_case(self):
     def test_get_gaps_distribution(self):
         ## set up
         alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
-        alignment_length = 6
 
         ## execution
-        gaps_arr = get_gaps_distribution(
-            alignment, alignment_length, DEFAULT_NT_GAP_CHARS, True
-        )
+        gaps_arr = get_gaps_distribution(alignment, DEFAULT_NT_GAP_CHARS)
         expected_gaps_arr = [0.0, 0.6, 0.0, 0.8, 0.0, 0.2]
 
         ## check results
diff --git a/tests/unit/test_warnings.py b/tests/unit/test_warnings.py
index 9b0cae7..0e4bca8 100644
--- a/tests/unit/test_warnings.py
+++ b/tests/unit/test_warnings.py
@@ -10,27 +10,90 @@
 
 
 class TestWarnings(object):
-    def test_all_sites_trimmed(self, mocker):
+    @pytest.mark.parametrize(
+        "header_info, seq_records, should_warn",
+        [
+            (
+                [
+                    {"id": "1", "name": "1", "description": "1"},
+                    {"id": "2", "name": "2", "description": "2"},
+                ],
+                np.array([["", "", "", "", "", ""], ["", "", "", "", "", ""]]),
+                True,
+            ),
+            (
+                [
+                    {"id": "1", "name": "1", "description": "1"},
+                    {"id": "2", "name": "2", "description": "2"},
+                ],
+                np.array(
+                    [["A", "-", "G", "T", "A", "T"], ["A", "-", "G", "-", "A", "T"]]
+                ),
+                False,
+            ),
+        ],
+    )
+    def test_warn_all_sites_trimmed(
+        self, mocker, header_info, seq_records, should_warn
+    ):
         mocked_warning = mocker.patch("clipkit.warnings.logger.warning")
 
-        entries = ["some_id"]
-        length = 10
-        keep_msa = MSA(entries, length)
-        warn_if_all_sites_were_trimmed(keep_msa)
+        msa = MSA(header_info, seq_records)
+        warn_if_all_sites_were_trimmed(msa)
 
-        mocked_warning.assert_called_once_with(
-            "WARNING: All sites trimmed from alignment. Please use different parameters."
-        )
+        if should_warn:
+            mocked_warning.assert_called_once_with(
+                "WARNING: All sites trimmed from alignment. Please use different parameters."
+            )
+        else:
+            mocked_warning.assert_not_called()
 
-    def test_gaps_only(self, mocker):
+    @pytest.mark.parametrize(
+        "header_info, seq_records, gap_only_header_id",
+        [
+            (
+                [
+                    {"id": "1", "name": "1", "description": "1"},
+                    {"id": "2", "name": "2", "description": "2"},
+                ],
+                np.array(
+                    [["-", "-", "-", "-", "-", "-"], ["A", "G", "G", "T", "A", "C"]]
+                ),
+                "1",
+            ),
+            (
+                [
+                    {"id": "1", "name": "1", "description": "1"},
+                    {"id": "2", "name": "2", "description": "2"},
+                ],
+                np.array(
+                    [["A", "G", "G", "T", "A", "C"], ["-", "-", "-", "-", "-", "-"]]
+                ),
+                "2",
+            ),
+            (
+                [
+                    {"id": "1", "name": "1", "description": "1"},
+                    {"id": "2", "name": "2", "description": "2"},
+                ],
+                np.array(
+                    [["A", "-", "G", "T", "A", "T"], ["A", "-", "G", "-", "A", "T"]]
+                ),
+                None,
+            ),
+        ],
+    )
+    def test_warn_if_entry_contains_only_gaps(
+        self, mocker, header_info, seq_records, gap_only_header_id
+    ):
         mocked_warning = mocker.patch("clipkit.warnings.logger.warning")
 
-        entries = ["some_id"]
-        length = 1
-        keep_msa = MSA(entries, length)
-        keep_msa.set_entry_sequence_at_position("some_id", 0, "-")
-        warn_if_entry_contains_only_gaps(keep_msa, SeqType.aa)
+        msa = MSA(header_info, seq_records)
+        warn_if_entry_contains_only_gaps(msa)
 
-        mocked_warning.assert_called_once_with(
-            """WARNING: header id 'some_id' contains only gaps"""
-        )
+        if gap_only_header_id:
+            mocked_warning.assert_called_once_with(
+                f"""WARNING: header id '{gap_only_header_id}' contains only gaps"""
+            )
+        else:
+            mocked_warning.assert_not_called()