Spreadsheet: 252b02d8-635a-44aa-a22b-05fb408a2c40
Sheet: Sheet1

Supplemental Table 2: List of all sequence features analyzed | Unnamed: 1 | Unnamed: 2
Feature | Source | Description
All Repeats | RepeatMasker | All repetitive elements annotated by RepeatMasker
AcHobo | RepeatMasker | AcHobo repeat family, DNA transposon class
Alu | RepeatMasker | Alu repeat family, non-LTR retrotransposon, SINE class
centr | RepeatMasker | Centromeric repeat family, satellite repeat class
CR1 | RepeatMasker | CR1 (chicken repeat 1) repeat familiy, non-LTR retrotransposon, LINE class
DNA | RepeatMasker | DNA transposons
ERV | RepeatMasker | ERV (endogenous retrovirus) repeat family, LTR class
ERV1 | RepeatMasker | ERV1 (endogenous retrovirus) repeat family, LTR class
ERVK | RepeatMasker | ERVK (endogenous retrovirus) repeat family, LTR class
ERVL | RepeatMasker | ERVL (endogenous retrovirus) repeat family, LTR class
L1 | RepeatMasker | L1 repeat family, non-LTR retrotransposon class
L2 | RepeatMasker | L2 repeat family, non-LTR retrotransposon, LINE class
Low_complexity | RepeatMasker | Low complexity repeat family
MaLR | RepeatMasker | MaLR repeat family, LTR class
Mariner | RepeatMasker | Mariner repeat family, DNA transposon class
MER1_type | RepeatMasker | [NAME] repeat family, DNA transposon class
MER1_type? | RepeatMasker | [NAME] repeat family, DNA transposon class
MER2_type | RepeatMasker | MER2 repeat family, DNA transposon class
Merlin | RepeatMasker | Merlin repeat family, DNA transposon class
MIR | RepeatMasker | MIR (mammalian interspersed repeat) family, SINE class
Other | RepeatMasker | Other repeats
PiggyBac | RepeatMasker | PiggyBac repeat family, DNA transposon class
RNA | RepeatMasker | RNA repeat family, [NAME] repeat class
rRNA | RepeatMasker | Ribosomal RNA repeat family, [NAME] repeat class
Satellite | RepeatMasker | Satellite repeat family, Satellite repeat class
scRNA | RepeatMasker | scRNA repeat family, scRNA repeat class
Simple_repeat | RepeatMasker | Simple repeat family, simple repeat class
snRNA | RepeatMasker | small nuclear repeat family, snRNA repeat class
srpRNA | RepeatMasker | srpRNA repeat family, srpRNA repeat class
Tc2 | RepeatMasker | Tc2 repeat family, DNA transposon class
[NAME] | RepeatMasker | Telomeric repeat family, satellite repeat class
Tip100 | RepeatMasker | Tip100 repeat family, DNA transposon repeat class
tRNA | RepeatMasker | tRNA repeat family, tRNA repeat class
Unknown | RepeatMasker | Unknown repeat family, unknown repeat class
acro | RepeatMasker | Acrocentric repeat family, satellite repeat class
ARTEFACT | RepeatMasker | ARTEFACT repeat family, ARTEFACT repeat class
DNA | RepeatMasker | DNA transposons repeat class
LINE | RepeatMasker | LINE (long interspersed nuclear elements) repeat class
Low_complexity | RepeatMasker | Low complexity repeat class
LTR | RepeatMasker | LTR (long terminal repeats) repeat class
Other | RepeatMasker | Other repeat class
RNA | RepeatMasker | RNA repeat class
rRNA | RepeatMasker | rRNA repeat class
Satellite | RepeatMasker | Satellite repeat class
scRNA | RepeatMasker | scRNA repeat class
Simple_repeat | RepeatMasker | Somple repeat class
SINE | RepeatMasker | SINE (chort intersersed nuclear element) repeat class
snRNA | RepeatMasker | snRNA repeat class
srpRNA | RepeatMasker | srpRNA repeat class
tRNA | RepeatMasker | tRNA repeat class
Unknown | RepeatMasker | Unknown repeat class
ARTEFACT | RepeatMasker | ARTEFACT repeat class
Tandem_Repeats | TRF | Tandem repeats
Inv_Repeats | IRF | Inverted repeats
CpG_Islands | UCSC Genome Database | CpG islands
CpG_Content | Genome sequence | CG dinucleotide content
GC_Content | Genome sequence | G and C base content
Conserved | phastCons | Top ~5% most evolutionarily conserved elements
Chromatin | [NAME], et [NAME]. (2005) | Average log2 open ratio
Transcribed | UCSC Genome Database | Transcribed sequence as annotated in Known Genes annotation
Translated | UCSC Genome Database | Translated sequence as annotated in Known Genes annotation
Genes | UCSC Genome Database | Number of genes as annotated in Known Genes annotation
Promoters | [NAME], et [NAME]. (2005) | Number of active promoters
Micro_RNAs | miRBase, [NAME] | Micro RNAs from miRBase
SNPs | dbSNP | SNPs (single nucleotide polymorphisms)
Chromosome_Band | [NAME] and [NAME] (2003) | Stain of chromosome band