Repository: biopython/biopython

Issue:
Duplicate files in Tests/Motif and Tests/motifs
The files in Test/motifs seem to be a copy of those in Test/Motif plus some more. Has the Motif directory been deprecated since renaming Bio.Motif to Bio.motifs?


Discussion:
That is likely what happened, probably ``Tests/Motif`` can be removed (after moving any still in use files under ``Tests/motifs``)? Do you agree @mdehoon?
@peterjc , @victorlin  Yes I think `Tests/Motif` can be removed.
@victorlin would you like to try doing this as a pull request?

Resolving patch:
diff --git a/Bio/motifs/__init__.py b/Bio/motifs/__init__.py
--- a/Bio/motifs/__init__.py
+++ b/Bio/motifs/__init__.py
@@ -44,7 +44,7 @@ def parse(handle, format, strict=True):
     For example:
 
     >>> from Bio import motifs
-    >>> with open("Motif/alignace.out") as handle:
+    >>> with open("motifs/alignace.out") as handle:
     ...     for m in motifs.parse(handle, "AlignAce"):
     ...         print(m.consensus)
     ...


Test patch:
diff --git a/Tests/Motif/Arnt.sites b/Tests/Motif/Arnt.sites
deleted file mode 100644
--- a/Tests/Motif/Arnt.sites
+++ /dev/null
@@ -1,40 +0,0 @@
->MA0004	ARNT	1
-CACGTGatgtcctc
->MA0004	ARNT	2
-CACGTGggaggtac
->MA0004	ARNT	3
-CACGTGccgcgcgc
->MA0004	ARNT	4
-CACGTGaagttgtc
->MA0004	ARNT	5
-taaatgcCACGTG
->MA0004	ARNT	6
-aggtataCACGTG
->MA0004	ARNT	7
-agtCACGTGttcc
->MA0004	ARNT	8
-gggatCACGTGgt
->MA0004	ARNT	9
-gggtCACGTGttc
->MA0004	ARNT	10
-catgtCACGTGcc
->MA0004	ARNT	11
-agttcgCACGTGc
->MA0004	ARNT	12
-taagCACGTGgtc
->MA0004	ARNT	13
-tgaatacCACGTG
->MA0004	ARNT	14
-tgaCACGTGtccg
->MA0004	ARNT	15
-attgtgCACGTGg
->MA0004	ARNT	16
-AACGTGacttcgtacc
->MA0004	ARNT	17
-AACGTGcgtgatgtcc
->MA0004	ARNT	18
-AACGTGacagccctcc
->MA0004	ARNT	19
-AACGTGcacatcgtcc
->MA0004	ARNT	20
-aggaatCGCGTGc
diff --git a/Tests/Motif/REB1.pfm b/Tests/Motif/REB1.pfm
deleted file mode 100644
--- a/Tests/Motif/REB1.pfm
+++ /dev/null
@@ -1,5 +0,0 @@
-30   0   0 100   0   0   0   0  15
-10   0   0   0 100 100 100   0  15
-50   0   0   0   0   0   0  60  55
-10 100 100   0   0   0   0  40  15
-
diff --git a/Tests/Motif/SRF.pfm b/Tests/Motif/SRF.pfm
deleted file mode 100644
--- a/Tests/Motif/SRF.pfm
+++ /dev/null
@@ -1,4 +0,0 @@
- 2  9  0  1 32  3 46  1 43 15  2  2
- 1 33 45 45  1  1  0  0  0  1  0  1
-39  2  1  0  0  0  0  0  0  0 44 43
- 4  2  0  0 13 42  0 45  3 30  0  0
diff --git a/Tests/Motif/alignace.out b/Tests/Motif/alignace.out
deleted file mode 100644
--- a/Tests/Motif/alignace.out
+++ /dev/null
@@ -1,354 +0,0 @@
-AlignACE 4.0 05/13/04
-./AlignACE -i test.fa 
-Parameter values:
- expect =      	10
- gcback =      	0.38
- minpass =     	200
- seed =        	1227623309
- numcols =     	10
- undersample = 	1
- oversample = 	1
-
-Input sequences:
-#0	SEQ1; M: CTCAATCGTAGA at 52
-#1	SEQ2; M: CTCAATCGTAGA at 172
-#2	SEQ3; M: CTCAATCGTAGA at 112
-#3	SEQ4; M: CTCAATCGTAGA at 173
-#4	SEQ5; M: CTCAATCGTAGA at 185
-#5	SEQ6; M: CTCAATCGTAGA at 105
-#6	SEQ7; M: CTCAATCGTAGA at 177
-#7	SEQ8; M: CTCAATCGTAGA at 172
-#8	SEQ9; M: CTCAATCGTAGA at 93
-#9	SEQ10; M: CTCAATCGTAGA at 3
-
-Motif 1
-TCTACGATTGAG	0	51	0
-TCTACGATTGAG	1	171	0
-TCTACGATTGAG	2	111	0
-TCTACGATTGAG	3	172	0
-TCTACGATTGAG	4	184	0
-TCTACGATTGAG	5	104	0
-TCTACGATTGAG	6	176	0
-TCTACGATTGAG	7	171	0
-TCTACGATTGAG	8	92	0
-TCAAAGATAGAG	8	155	1
-TCTACGATTGAG	9	2	0
-** ***** ***
-MAP Score: 57.9079
-
-Motif 2
-GCGAAGGAAGCAGCGCGTGTG	0	7	1
-GGCACCGCCTCTACGATTGAG	0	51	0
-CAGAGCTTAGCATTGAACGCG	0	93	0
-CTAATGAAAGCAATGAGAGTG	0	154	1
-CTTGTGCCCTCTAAGCGTCCG	1	73	1
-GAGCACGACGCTTTGTACCTG	1	153	0
-CGGCACTTAGCAGCGTATCGT	2	36	0
-CTGGTTTCATCTACGATTGAG	2	111	0
-GGGCCAATAGCGGCGCCGGAG	2	133	0
-GTGGAGTTATCTTAGTGCGCG	2	158	0
-GAGAGGTTATCTACGATTGAG	3	172	0
-CTGCTCCCCGCATACAGCGCG	4	62	0
-CAGAACCGAGGTCCGGTACGG	4	157	1
-GTGCCCCAAGCTTACCCAGGG	5	40	1
-CGCCTCTGATCTACGATTGAG	5	104	0
-GTGCTCATAGGGACGTCGCGG	6	2	1
-CTGCCCCCCGCATAGTAGGGG	6	45	1
-GTAAAGAAATCGATGTGCCAG	6	72	0
-CACCTGCAATTGCTGGCAGCG	6	128	0
-GGCGGGCCATCCCTGTATGAA	8	65	0
-CTCCAGGTCGCATGGAGAGAG	9	89	1
-CCTCGGATCGCTTGGGAAGAG	9	134	0
-* ** *  ***   *   * *
-MAP Score: 19.6235
-
-Motif 3
-GTGCGCGAAGGAAGCAGCGCG	0	3	1
-CAGAGCTTAGCATTGAACGCG	0	93	0
-GTGCCCGATGACCACCCGTCG	0	117	0
-GCCCTCTAAGCGTCCGCGGAT	1	78	1
-GAGCACGACGCTTTGTACCTG	1	153	0
-CGGCACTTAGCAGCGTATCGT	2	36	0
-GGGCCAATAGCGGCGCCGGAG	2	133	0
-GCGCACTAAGATAACTCCACG	2	159	1
-CGGCCCGTTGTCCAGCAGACG	3	2	0
-CTGCTCCCCGCATACAGCGCG	4	62	0
-GTGCCCCAAGCTTACCCAGGG	5	40	1
-GTGCTCATAGGGACGTCGCGG	6	2	1
-CTGCCCCCCGCATAGTAGGGG	6	45	1
-CGCCGCCATGCGACGCAGAGG	8	39	0
-AACCTCTAAGCATACTCTACG	9	8	0
-GACCTGGAGGCTTAGACTTGG	9	77	0
-GCGCTCTTCCCAAGCGATCCG	9	131	1
-GGGCCGTCAGCTCTCAAGTCT	9	153	1
-* ** *   **   * *  **
-MAP Score: 19.1804
-
-Motif 4
-GCCCCAAGCTTACCCAGGGAC	5	42	1
-GCCGTCTGCTGGACAACGGGC	3	0	1
-GCCGACGGGTGGTCATCGGGC	0	115	1
-GCCAATAGCGGCGCCGGAGTC	2	131	0
-GCCCCCCGCATAGTAGGGGGA	6	47	1
-GCCCGTACCGGACCTCGGTTC	4	159	0
-GCCTCATGTACCGGAAGGGAC	3	24	1
-GACACGCGCCTGGGAGGGTTC	2	11	1
-GCCTTTGGCCTTGGATGAGAA	7	76	0
-GGCCCTCGGATCGCTTGGGAA	9	137	0
-GCATGTTGGGAATCCGCGGAC	1	89	0
-GACACGCGCTGTATGCGGGGA	4	58	1
-GCCAGGTACAAAGCGTCGTGC	1	151	1
-GCGATCAGCTTGTGGGCGTGC	4	82	1
-GACAAATCGGATACTGGGGCA	3	75	0
-GCACTTAGCAGCGTATCGTTA	2	34	0
-***    **    *  *** *
-MAP Score: 18.0097
-
-Motif 5
-CGGCACAGAGCTT	0	106	0
-ATCCGCGGACGCT	1	86	0
-CGCCTGGGAGGGT	2	17	1
-CGGAAGGGACGTT	3	35	1
-ACACACAGACGGT	3	122	0
-TGCCAGAGAGGTT	3	185	0
-AGACTGAGACGTT	4	114	1
-AATCGTAGAGGAT	4	187	1
-CGTCTCGTAGGGT	5	61	0
-CGTCGCGGAGGAT	6	15	1
-CTTCTTAGACGCT	6	119	1
-CGACGCAGAGGAT	8	37	0
-ATGCTTAGAGGTT	9	16	1
-AGACTTGGGCGAT	9	72	0
-CGACCTGGAGGCT	9	86	0
-** * ****** *
-MAP Score: 16.8287
-
-Motif 6
-GTGCGCGAAGGAAGCAGCGCGTG	0	3	1
-TTGAGCCGAGTAAAGGGCTGGTG	0	33	0
-CAATGCTAAGCTCTGTGCCGACG	0	99	1
-CAACTCTCTATGTAGTGCCCGAG	1	28	0
-CGACGCTTTGTACCTGGCTTGCG	1	146	0
-CGAGTCAATGACACGCGCCTGGG	2	2	1
-CGATACGCTGCTAAGTGCCGTCC	2	37	1
-CCGGGCCAATAGCGGCGCCGGAG	2	133	0
-CCACGCTTCGACACGTGGTATAG	2	175	1
-CCGAGCCTCATGTACCGGAAGGG	3	20	1
-CTGCTCCCCGCATACAGCGCGTG	4	60	0
-CCGAGGTCCGGTACGGGCAAGCC	4	162	1
-GTGCTCATAGGGACGTCGCGGAG	6	2	1
-CCCTACTATGCGGGGGGCAGGTC	6	42	0
-GCCAGCAATTGCAGGTGGTCGTG	6	132	1
-CTCTGCGTCGCATGGCGGCGTGG	8	40	1
-GGAGGCTTAGACTTGGGCGATAC	9	70	0
-GCATGGAGAGAGATCCGGAGGAG	9	98	1
-* * **   *    * **  * *
-MAP Score: 15.0441
-
-Motif 7
-GCGCGTGTGTGTAAC	0	19	1
-GCACAGAGCTTAGCA	0	102	0
-GGTGGTCATCGGGCA	0	122	1
-GCGCGTGTCATTGAC	2	5	0
-GGACGGCACTTAGCA	2	45	0
-GCGCGTCCCGGGCCA	2	148	0
-GCTCGGCCCGTTGTC	3	11	0
-GCGCGTGTCCTTTAA	4	52	0
-GCTGATCGCTGCTCC	4	76	0
-GCCCGTACCGGACCT	4	165	0
-GGACGTCGCGGAGGA	6	12	1
-GCGGGGGGCAGGTCA	6	41	0
-GGACGTACTGGCACA	6	65	1
-GCAGGTGGTCGTGCA	6	142	1
-GCGCATACCTTAACA	7	21	0
-GCACGGGACTTCAAC	7	38	0
-GCACGTAGCTGGTAA	7	116	0
-GCTCGTCTATGGTCA	8	139	0
-GCGCATGCTGGATCC	9	120	0
-GGCCGTCAGCTCTCA	9	154	1
-** **** * *  **
-MAP Score: 13.3145
-
-Motif 8
-GAACCGAGGTCCGGTACGGGC	4	159	1
-GCCCCCCGCATAGTAGGGGGA	6	47	1
-GTCCCTGGGTAAGCTTGGGGC	5	42	0
-ACTCCACGCTTCGACACGTGG	2	172	1
-ATCCTCTGCGTCGCATGGCGG	8	37	1
-GTTCAATGCTAAGCTCTGTGC	0	96	1
-GCTCATAGGGACGTCGCGGAG	6	4	1
-GTCCCGGGCCAATAGCGGCGC	2	138	0
-GCACTTAGCAGCGTATCGTTA	2	34	0
-GGCCCTCGGATCGCTTGGGAA	9	137	0
-CTGCTGGACAACGGGCCGAGC	3	5	1
-GGGCACTACATAGAGAGTTGC	1	31	1
-AGCCTCCAGGTCGCATGGAGA	9	86	1
-AATCGTAGATCAGAGGCGAGA	5	107	1
-GAACTCCACTAAGACTTGAGA	9	164	0
-GAGCAGCGATCAGCTTGTGGG	4	77	1
-GCCAGGTACAAAGCGTCGTGC	1	151	1
-AGTCAATGACACGCGCCTGGG	2	4	1
-GGTCATGGAATCTTATGTAGC	4	5	1
-GTAGATAACAGAGGTCGGGGG	1	178	1
-*  *   **  **   ** **
-MAP Score: 11.6098
-
-Motif 9
-CCGAGTAAAGGGCTG	0	36	0
-GTGGTCATCGGGCAC	0	123	1
-GATAACAGAGGTCGG	1	181	1
-CGGCGCCGGAGTCTG	2	129	0
-GCGCGTCCCGGGCCA	2	148	0
-CTGGACAACGGGCCG	3	8	1
-CGGATACTGGGGCAG	3	74	0
-GGGAGCAGCGATCAG	4	75	1
-CAGAACCGAGGTCCG	4	157	1
-GGGTCCCTGGGTAAG	5	50	0
-GTGCTCATAGGGACG	6	2	1
-GAGATCCGGAGGAGG	9	107	1
-GCGATCCGAGGGCCG	9	144	1
-GAGTTCACATGGCTG	9	179	1
-* *  ** ***** *
-MAP Score: 11.2943
-
-Motif 10
-TAGAGGCGGTG	0	59	1
-GCTAAGCTCTG	0	103	1
-TGGAAGCAGTG	1	121	1
-GCGAGGCTGTG	1	138	0
-ACGACGCTTTG	1	159	0
-GGGACGCGCAC	2	154	1
-TCGAAGCGTGG	2	175	0
-TGTATGCGGGG	4	67	1
-GGTAAGCTTGG	5	45	0
-TGTACGCTGGG	5	148	1
-ACTATGCGGGG	6	50	0
-GGTATGCGCTG	7	27	1
-GGTACCCGGAG	7	157	1
-GCGACGCAGAG	8	40	0
-TGGCGGCGTGG	8	52	1
-TCTAGGCGGGC	8	79	0
-AGTATGCTTAG	9	13	1
-TGGAGGCTTAG	9	83	0
-**** ******
-MAP Score: 9.7924
-
-Motif 11
-GCACAGAGCTTAGCATTGAAC	0	96	0
-GTCCGCGGATTCCCAACATGC	1	89	1
-ATACACAGCCTCGCAAGCCAG	1	135	1
-GGCCCGGGACGCGCACTAAGA	2	149	1
-GCCCGTTGTCCAGCAGACGGC	3	0	0
-GAGCAGCGATCAGCTTGTGGG	4	77	1
-GAACCGAGGTCCGGTACGGGC	4	159	1
-GTCCCTGGGTAAGCTTGGGGC	5	42	0
-GACCTGCCCCCCGCATAGTAG	6	42	1
-AACCAGCGCATACCTTAACAG	7	20	0
-ATCCTCTGCGTCGCATGGCGG	8	37	1
-GACCATAGACGAGCATCAAAG	8	140	1
-GGCCCTCGGATCGCTTGGGAA	9	137	0
-* **   *   ****    **
-MAP Score: 9.01393
-
-Motif 12
-GCCGTCCGTC	2	53	1
-GGCGTGCGCG	0	0	1
-GGCGCGTGTC	2	11	0
-AGCGCGTGTG	0	18	1
-GCGGTGCGTG	8	108	0
-AGCGCGTGTC	4	58	0
-AGCGTCCGCG	1	86	1
-ACCGTCTGTG	3	122	1
-GCCATGCGAC	8	46	0
-ACCACCCGTC	0	118	0
-GGCGCCGGAG	2	133	0
-ACCACGTGTC	2	184	0
-GGCTTGCGAG	1	144	0
-GCGATCCGAG	9	144	1
-AGTGCGCGTC	2	156	0
-AGTGCCCGAG	1	28	0
-**********
-MAP Score: 7.51121
-
-Motif 13
-GCCGACGGGTGGTCATCGGG	0	115	1
-GCACGACGCTTTGTACCTGG	1	152	0
-CCTGGGAGGGTTCAATAACG	2	19	1
-GCGCGTCCCGGGCCAATAGC	2	143	0
-GCCGTCTGCTGGACAACGGG	3	0	1
-GTCCCTTCCGGTACATGAGG	3	25	0
-GCTGCTCCCCGCATACAGCG	4	64	0
-GCCCCAAGCTTACCCAGGGA	5	42	1
-ACCGGCTGACGCTAATACGG	5	84	0
-GCGGGGGGCAGGTCATTACA	6	36	0
-GCTGGCAGCGTCTAAGAAGG	6	118	0
-GCAGGTGGTCGTGCAATACG	6	142	1
-GCTGGTTGAAGTCCCGTGCG	7	34	1
-GCACGTAGCTGGTAAATAGG	7	111	0
-GCGGCGTGGATTTCATACAG	8	54	1
-CCTGGAGGCTTAGACTTGGG	9	76	0
-** **  ** *   *   **
-MAP Score: 5.63667
-
-Motif 14
-GCCGACGGGTGGTCATCGGG	0	115	1
-ATCCGCGGACGCTTAGAGGG	1	79	0
-ACGCTTTGTACCTGGCTTGC	1	147	0
-ACGGACGGCACTTAGCAGCG	2	42	0
-GCCGTCTGCTGGACAACGGG	3	0	1
-ACACACAGACGGTTGAAAGG	3	115	0
-GCCGATAGTGCTTAAGTTCG	3	147	1
-CTTGCCCGTACCGGACCTCG	4	163	0
-ACCGGCTGACGCTAATACGG	5	84	0
-GCCCCCCGCATAGTAGGGGG	6	47	1
-GCTGGCAGCGTCTAAGAAGG	6	118	0
-GCAGGTGGTCGTGCAATACG	6	142	1
-ACGCACGGGACTTCAACCAG	7	35	0
-GCACGTAGCTGGTAAATAGG	7	111	0
-ATCCTCTGCGTCGCATGGCG	8	37	1
-** * * *  * * *   **
-MAP Score: 3.89842
-
-Motif 15
-GAGGCTGTGTAT	1	135	0
-GAGGTCGGGGGT	1	188	1
-GACGGACGGCAC	2	51	0
-TTGGCCCGGGAC	2	147	1
-GAGGCTCGGCCC	3	17	0
-CACGCGCTGTAT	4	60	1
-TAGGCCAGGTAT	4	127	0
-GAGGTCCGGTAC	4	164	1
-TACGCTGGGGAT	5	150	1
-GTCGCGGAGGAT	6	16	1
-TACGCACGGGAC	7	44	0
-TACTCCGGGTAC	7	158	0
-GACGCAGAGGAT	8	37	0
-TAGGCGGGCCAT	8	76	0
-***** *** **
-MAP Score: 3.33444
-
-Motif 16
-CGGCTCAATCGTAGAGGC	0	48	1
-CGACGGGTGGTCATCGGG	0	117	1
-CGCTTAGAGGGCACAAGC	1	72	0
-TGACACGCGCCTGGGAGG	2	10	1
-CGATACGCTGCTAAGTGC	2	37	1
-CGTCCCGGGCCAATAGCG	2	142	0
-CCACGCTTCGACACGTGG	2	175	1
-CGTCTGCTGGACAACGGG	3	2	1
-ACACAGACGGTTGAAAGG	3	115	0
-TGCTCCCCGCATACAGCG	4	64	0
-TGAGGCTTGCCCGTACCG	4	170	0
-TGCCCCAAGCTTACCCAG	5	41	1
-CGGCTGACGCTAATACGG	5	84	0
-CGCGACGTCCCTATGAGC	6	4	0
-TGCCCCCCGCATAGTAGG	6	46	1
-CGTTGCCTTCTTAGACGC	6	113	1
-TGACTCAATCGTAGACCC	6	173	1
-AGTCCCGTGCGTATGTGG	7	43	1
-AGGCTCGCACGTAGCTGG	7	119	0
-CCACGCCGCCATGCGACG	8	45	0
-AGCCTCCAGGTCGCATGG	9	86	1
-** * *  ** **   **
-MAP Score: 1.0395
-
diff --git a/Tests/Motif/mast.dna.oops.txt b/Tests/Motif/mast.dna.oops.txt
deleted file mode 100644
--- a/Tests/Motif/mast.dna.oops.txt
+++ /dev/null
@@ -1,301 +0,0 @@
-********************************************************************************
-MAST - Motif Alignment and Search Tool
-********************************************************************************
-	MAST version 3.0 (Release date: 2004/08/18 09:07:01)
-
-	For further information on how to interpret these results or to get
-	a copy of the MAST software please access http://meme.sdsc.edu.
-********************************************************************************
-
-
-********************************************************************************
-REFERENCE
-********************************************************************************
-	If you use this program in your research, please cite:
-
-	Timothy L. Bailey and Michael Gribskov,
-	"Combining evidence using p-values: application to sequence homology
-	searches", Bioinformatics, 14(48-54), 1998.
-********************************************************************************
-
-
-********************************************************************************
-DATABASE AND MOTIFS
-********************************************************************************
-	DATABASE INO_up800.s (nucleotide)
-	Last updated on Mon Aug 16 21:19:59 2004
-	Database contains 7 sequences, 5600 residues
-
-	Scores for positive and reverse complement strands are combined.
-
-	MOTIFS meme.INO_up800.oops.txt (nucleotide)
-	MOTIF WIDTH BEST POSSIBLE MATCH
-	----- ----- -------------------
-	  1    12   TTCACATGCCGC
-	  2    10   TCTGGCACAG
-
-	PAIRWISE MOTIF CORRELATIONS:
-	MOTIF     1
-	----- -----
-	   2   0.32
-	No overly similar pairs (correlation > 0.60) found.
-
-	Random model letter frequencies (from non-redundant database):
-	A 0.281 C 0.222 G 0.229 T 0.267 
-********************************************************************************
-
-
-********************************************************************************
-SECTION I: HIGH-SCORING SEQUENCES
-********************************************************************************
-	- Each of the following 7 sequences has E-value less than 10.
-	- The E-value of a sequence is the expected number of sequences
-	  in a random database of the same size that would match the motifs as
-	  well as the sequence does and is equal to the combined p-value of the
-	  sequence times the number of sequences in the database.
-	- The combined p-value of a sequence measures the strength of the
-	  match of the sequence to all the motifs and is calculated by
-	    o finding the score of the single best match of each motif
-	      to the sequence (best matches may overlap),
-	    o calculating the sequence p-value of each score,
-	    o forming the product of the p-values,
-	    o taking the p-value of the product.
-	- The sequence p-value of a score is defined as the
-	  probability of a random sequence of the same length containing
-	  some match with as good or better a score.
-	- The score for the match of a position in a sequence to a motif
-	  is computed by by summing the appropriate entry from each column of
-	  the position-dependent scoring matrix that represents the motif.
-	- Sequences shorter than one or more of the motifs are skipped.
-	- The table is sorted by increasing E-value.
-********************************************************************************
-
-SEQUENCE NAME                      DESCRIPTION                   E-VALUE  LENGTH
--------------                      -----------                   -------- ------
-ACC1                               sequence of the region up...    6.1e-05    800
-CHO1                               sequence of the region up...    0.00016    800
-INO1                               sequence of the region up...    0.00019    800
-FAS1                               sequence of the region up...    0.00022    800
-OPI3                               sequence of the region up...    0.00092    800
-CHO2                               sequence of the region up...     0.0029    800
-FAS2                               sequence of the region up...     0.0093    800
-
-********************************************************************************
-
-
-
-********************************************************************************
-SECTION II: MOTIF DIAGRAMS
-********************************************************************************
-	- The ordering and spacing of all non-overlapping motif occurrences
-	  are shown for each high-scoring sequence listed in Section I.
-	- A motif occurrence is defined as a position in the sequence whose
-	  match to the motif has POSITION p-value less than 0.0001.
-	- The POSITION p-value of a match is the probability of
-	  a single random subsequence of the length of the motif
-	  scoring at least as well as the observed match.
-	- For each sequence, all motif occurrences are shown unless there
-	  are overlaps.  In that case, a motif occurrence is shown only if its
-	  p-value is less than the product of the p-values of the other
-	  (lower-numbered) motif occurrences that it overlaps.
-	- The table also shows the E-value of each sequence.
-	- Spacers and motif occurences are indicated by
-	   o -d-    `d' residues separate the end of the preceding motif 
-		    occurrence and the start of the following motif occurrence
-	   o [sn]  occurrence of motif `n' with p-value less than 0.0001.
-		    A minus sign indicates that the occurrence is on the
-		    reverse complement strand.
-********************************************************************************
-
-SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
--------------                      --------  -------------
-ACC1                                6.1e-05  82_[+1]_137_[+2]_559
-CHO1                                0.00016  152_[+2]_396_[-2]_42_[+1]_17_
-                                             [+1]_149
-INO1                                0.00019  282_[-2]_327_[-1]_55_[+1]_102
-FAS1                                0.00022  43_[+2]_41_[+1]_694
-OPI3                                0.00092  185_[-2]_144_[+1]_449
-CHO2                                 0.0029  353_[+1]_47_[-2]_378
-FAS2                                 0.0093  184_[-2]_372_[+1]_222
-
-********************************************************************************
-
-
-
-********************************************************************************
-SECTION III: ANNOTATED SEQUENCES
-********************************************************************************
-	- The positions and p-values of the non-overlapping motif occurrences
-	  are shown above the actual sequence for each of the high-scoring
-	  sequences from Section I.
-	- A motif occurrence is defined as a position in the sequence whose
-	  match to the motif has POSITION p-value less than 0.0001 as 
-	  defined in Section II.
-	- For each sequence, the first line specifies the name of the sequence.
-	- The second (and possibly more) lines give a description of the 
-	  sequence.
-	- Following the description line(s) is a line giving the length, 
-	  combined p-value, and E-value of the sequence as defined in Section I.
-	- The next line reproduces the motif diagram from Section II.
-	- The entire sequence is printed on the following lines.
-	- Motif occurrences are indicated directly above their positions in the
-	  sequence on lines showing
-	   o the motif number of the occurrence (a minus sign indicates that
-	  the occurrence is on the reverse complement strand),
-	   o the position p-value of the occurrence,
-	   o the best possible match to the motif (or its reverse complement), and
-	   o columns whose match to the motif has a positive score (indicated 
-	     by a plus sign).
-********************************************************************************
-
-
-ACC1
-  sequence of the region upstream from YNR016C
-  LENGTH = 800  COMBINED P-VALUE = 8.78e-06  E-VALUE =  6.1e-05
-  DIAGRAM: 82_[+1]_137_[+2]_559
-
-
-            [+1]
-            3.1e-07
-            TTCACATGCCGC
-            ++++++++++ +
-76   TAAAATCTTCACATGGCCCGGCCGCGCGCGCGTTGTGCCAACAAGTCGCAGTCGAAATTCAACCGCTCATTGCCA
-
-           [+2]
-           7.4e-07
-           TCTGGCACAG
-           ++++++++++
-226  TCGTATTCTGGCACAGTATAGCCTAGCACAATCACTGTCACAATTGTTATCGGTTCTACAATTGTTCTGCTCTCT
-
-
-CHO1
-  sequence of the region upstream from YER026C
-  LENGTH = 800  COMBINED P-VALUE = 2.30e-05  E-VALUE =  0.00016
-  DIAGRAM: 152_[+2]_396_[-2]_42_[+1]_17_[+1]_149
-
-
-       [+2]
-       3.9e-05
-       TCTGGCACAG
-       ++++++ +
-151  CGTCTGGCGCCCTTCCCATTCCGAACCATGTTATATTGAACCATCTGGCGACAAGCAGTATTAAGCATAATACAT
-
-                                      [-2]
-                                      7.4e-07
-                                      CTGTGCCAGA
-                                      ++++++++++
-526  CAATCCCCACTCCTTCTCAATGTGTGCAGACTTCTGTGCCAGACACTGAATATATATCAGTAATTGGTCAAAATC
-
-               [+1]                         [+1]
-               8.7e-07                      2.2e-05
-               TTCACATGCCGC                 TTCACATGCCGC
-               ++++++ +++ +                 +++++++++  +
-601  ACTTTGAACGTTCACACGGCACCCTCACGCCTTTGAGCTTTCACATGGACCCATCTAAAGATGAAGATCCGTATT
-
-
-INO1
-  sequence of the region upstream from YJL153C
-  LENGTH = 800  COMBINED P-VALUE = 2.71e-05  E-VALUE =  0.00019
-  DIAGRAM: 282_[-2]_327_[-1]_55_[+1]_102
-
-
-                                                              [-2]
-                                                              1.8e-05
-                                                              CTGTGCCAGA
-                                                              +++ +++ ++
-226  ACGTTGTATATGAAACGAGTAGTGAACGTTCGTACGATCTTTCACGCAGACATGCGACTGCGCCCGCCGTAGACC
-
-                        [-1]
-                        4.2e-08
-                        GCGGCATGTGAA
-                        ++++++++++++
-601  TGCGCTTCGGCGGCTAAATGCGGCATGTGAAAAGTATTGTCTATTTTATCTTCATCCTTCTTTCCCAGAATATTG
-
-                [+1]
-                1.3e-05
-                TTCACATGCCGC
-                +++++++++ ++
-676  AACTTATTTAATTCACATGGAGCAGAGAAAGCGCACCTCTGCGTTGGCGGCAATGTTAATTTGAGACGTATATAA
-
-
-FAS1
-  sequence of the region upstream from YKL182W
-  LENGTH = 800  COMBINED P-VALUE = 3.19e-05  E-VALUE =  0.00022
-  DIAGRAM: 43_[+2]_41_[+1]_694
-
-                                                [+2]
-                                                2.2e-05
-                                                TCTGGCACAG
-                                                ++ +++++ +
-1    CCGGGTTATAGCAGCGTCTGCTCCGCATCACGATACACGAGGTGCAGGCACGGTTCACTACTCCCCTGGCCTCCA
-
-                        [+1]
-                        4.2e-08
-                        TTCACATGCCGC
-                        ++++++++++++
-76   ACAAACGACGGCCAAAAACTTCACATGCCGCCCAGCCAAGCATAATTACGCAACAGCGATCTTTCCGTCGCACAA
-
-
-OPI3
-  sequence of the region upstream from YJR073C
-  LENGTH = 800  COMBINED P-VALUE = 1.32e-04  E-VALUE =  0.00092
-  DIAGRAM: 185_[-2]_144_[+1]_449
-
-
-                                        [-2]
-                                        7.4e-07
-                                        CTGTGCCAGA
-                                        ++++++++++
-151  GTTAATCTGATCAACGCTACGCCGATGACAACGGTCTGTGCCAGATCTGGTTTTCCCCACTTATTTGCTACTTCC
-
-                                            [+1]
-                                            5.8e-06
-                                            TTCACATGCCGC
-                                            ++++ ++ ++ +
-301  AACTCCGTCAGGTCTTCCACGTGGAACTGCCAAGCCTCCTTCAGATCGCTCTTGTCGACCGTCTCCAAGAGATCC
-
-
-CHO2
-  sequence of the region upstream from YGR157W
-  LENGTH = 800  COMBINED P-VALUE = 4.18e-04  E-VALUE =   0.0029
-  DIAGRAM: 353_[+1]_47_[-2]_378
-
-
-                                                          [+1]
-                                                          5.2e-07
-                                                          TTCACATGCCGC
-                                                          +++ ++++++++
-301  ATATATATTTTTGCCTTGGTTTAAATTGGTCAAGACAGTCAATTGCCACACTTTTCTCATGCCGCATTCATTATT
-
-                                          [-2]
-                                          2.9e-05
-                                          CTGTGCCAGA
-                                          +  +++++++
-376  CGCGAAGTTTTCCACACAAAACTGTGAAAATGAACGGCGATGCCAGAAACGGCAAAACCTCAAATGTTAGATAAC
-
-
-FAS2
-  sequence of the region upstream from YPL231W
-  LENGTH = 800  COMBINED P-VALUE = 1.33e-03  E-VALUE =   0.0093
-  DIAGRAM: 184_[-2]_372_[+1]_222
-
-
-                                       [-2]
-                                       2.9e-05
-                                       CTGTGCCAGA
-                                         ++++++++
-151  AACAGGGTGTCGGTCATACCGATAAAGCCGTCAAGAGTGCCAGAAAAGCAAGAAAGAACAAGATTAGATGTTGGT
-
-                                              [+1]
-                                              1.9e-06
-                                              TTCACATGCCGC
-                                              +++++++++  +
-526  GCTTAGCAAAATCCAACCATTTTTTTTTTATCTCCCGCGTTTTCACATGCTACCTCATTCGCCTCGTAACGTTAC
-
-********************************************************************************
-
-
-CPU: pmgm2
-Time 0.030000 secs.
-
-mast meme.INO_up800.oops.txt -text -stdout
diff --git a/Tests/Motif/mast.protein.oops.txt b/Tests/Motif/mast.protein.oops.txt
deleted file mode 100644
--- a/Tests/Motif/mast.protein.oops.txt
+++ /dev/null
@@ -1,885 +0,0 @@
-********************************************************************************
-MAST - Motif Alignment and Search Tool
-********************************************************************************
-	MAST version 3.0 (Release date: 2004/08/18 09:07:01)
-
-	For further information on how to interpret these results or to get
-	a copy of the MAST software please access http://meme.sdsc.edu.
-********************************************************************************
-
-
-********************************************************************************
-REFERENCE
-********************************************************************************
-	If you use this program in your research, please cite:
-
-	Timothy L. Bailey and Michael Gribskov,
-	"Combining evidence using p-values: application to sequence homology
-	searches", Bioinformatics, 14(48-54), 1998.
-********************************************************************************
-
-
-********************************************************************************
-DATABASE AND MOTIFS
-********************************************************************************
-	DATABASE adh.s (peptide)
-	Last updated on Mon Aug 16 21:19:59 2004
-	Database contains 33 sequences, 9996 residues
-
-	MOTIFS meme.adh.oops.txt (peptide)
-	MOTIF WIDTH BEST POSSIBLE MATCH
-	----- ----- -------------------
-	  1    29   YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-	  2    29   KVVLITGCSSGIGKATAKHLHKEGAKVVL
-
-	PAIRWISE MOTIF CORRELATIONS:
-	MOTIF     1
-	----- -----
-	   2   0.30
-	No overly similar pairs (correlation > 0.60) found.
-
-	Random model letter frequencies (from non-redundant database):
-	A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 
-	L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 
-	W 0.013 Y 0.033 
-********************************************************************************
-
-
-********************************************************************************
-SECTION I: HIGH-SCORING SEQUENCES
-********************************************************************************
-	- Each of the following 33 sequences has E-value less than 10.
-	- The E-value of a sequence is the expected number of sequences
-	  in a random database of the same size that would match the motifs as
-	  well as the sequence does and is equal to the combined p-value of the
-	  sequence times the number of sequences in the database.
-	- The combined p-value of a sequence measures the strength of the
-	  match of the sequence to all the motifs and is calculated by
-	    o finding the score of the single best match of each motif
-	      to the sequence (best matches may overlap),
-	    o calculating the sequence p-value of each score,
-	    o forming the product of the p-values,
-	    o taking the p-value of the product.
-	- The sequence p-value of a score is defined as the
-	  probability of a random sequence of the same length containing
-	  some match with as good or better a score.
-	- The score for the match of a position in a sequence to a motif
-	  is computed by by summing the appropriate entry from each column of
-	  the position-dependent scoring matrix that represents the motif.
-	- Sequences shorter than one or more of the motifs are skipped.
-	- The table is sorted by increasing E-value.
-********************************************************************************
-
-SEQUENCE NAME                      DESCRIPTION                   E-VALUE  LENGTH
--------------                      -----------                   -------- ------
-BUDC_KLETE                         ACETOIN(DIACETYL) REDUCTA...    2.6e-33    241
-YRTP_BACSU                         HYPOTHETICAL 25.3 KD PROT...    4.3e-33    238
-AP27_MOUSE                         ADIPOCYTE P27 PROTEIN (AP...    4.5e-33    244
-HDE_CANTR                          HYDRATASE-DEHYDROGENASE-E...    1.6e-32    906
-HDHA_ECOLI                         7-ALPHA-HYDROXYSTEROID DE...    4.9e-31    255
-DHII_HUMAN                         CORTICOSTEROID 11-BETA-DE...    8.2e-31    292
-FIXR_BRAJA                         FIXR PROTEIN                   2.6e-30    278
-DHGB_BACME                         GLUCOSE 1-DEHYDROGENASE B...    3.2e-30    262
-NODG_RHIME                         NODULATION PROTEIN G (HOS...    3.4e-29    245
-RIDH_KLEAE                         RIBITOL 2-DEHYDROGENASE (...    6.2e-29    249
-YINL_LISMO                         HYPOTHETICAL 26.8 KD PROT...    6.6e-29    248
-DHMA_FLAS1                         N-ACYLMANNOSAMINE 1-DEHYD...    1.2e-28    270
-HMTR_LEIMA                         no comment                     5.1e-28    287
-2BHD_STREX                         20-BETA-HYDROXYSTEROID DE...    5.9e-28    255
-ENTA_ECOLI                         2,3-DIHYDRO-2,3-DIHYDROXY...    4.8e-27    248
-DHB2_HUMAN                         no comment                     1.7e-26    387
-BDH_HUMAN                          D-BETA-HYDROXYBUTYRATE DE...    2.8e-26    343
-BA72_EUBSP                         7-ALPHA-HYDROXYSTEROID DE...    4.2e-26    249
-FVT1_HUMAN                         no comment                     8.9e-26    332
-GUTD_ECOLI                         SORBITOL-6-PHOSPHATE 2-DE...    5.1e-25    259
-DHB3_HUMAN                         no comment                     8.3e-25    310
-3BHD_COMTE                         3-BETA-HYDROXYSTEROID DEH...    1.4e-24    253
-LIGD_PSEPA                         C ALPHA-DEHYDROGENASE (EC...    8.1e-24    305
-DHES_HUMAN                         ESTRADIOL 17 BETA-DEHYDRO...    2.4e-22    327
-RFBB_NEIGO                         no comment                     3.2e-19    346
-BPHB_PSEPS                         BIPHENYL-CIS-DIOL DEHYDRO...      1e-18    275
-YURA_MYXXA                         no comment                     1.9e-18    258
-PCR_PEA                            no comment                     7.2e-18    399
-DHCA_HUMAN                         no comment                     1.1e-17    276
-ADH_DROME                          ALCOHOL DEHYDROGENASE (EC...    2.7e-14    255
-MAS1_AGRRA                         no comment                       3e-14    476
-FABI_ECOLI                         no comment                     9.7e-14    262
-CSGA_MYXXA                         no comment                     2.5e-12    166
-
-********************************************************************************
-
-
-
-********************************************************************************
-SECTION II: MOTIF DIAGRAMS
-********************************************************************************
-	- The ordering and spacing of all non-overlapping motif occurrences
-	  are shown for each high-scoring sequence listed in Section I.
-	- A motif occurrence is defined as a position in the sequence whose
-	  match to the motif has POSITION p-value less than 0.0001.
-	- The POSITION p-value of a match is the probability of
-	  a single random subsequence of the length of the motif
-	  scoring at least as well as the observed match.
-	- For each sequence, all motif occurrences are shown unless there
-	  are overlaps.  In that case, a motif occurrence is shown only if its
-	  p-value is less than the product of the p-values of the other
-	  (lower-numbered) motif occurrences that it overlaps.
-	- The table also shows the E-value of each sequence.
-	- Spacers and motif occurences are indicated by
-	   o -d-    `d' residues separate the end of the preceding motif 
-		    occurrence and the start of the following motif occurrence
-	   o [n]  occurrence of motif `n' with p-value less than 0.0001.
-********************************************************************************
-
-SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
--------------                      --------  -------------
-BUDC_KLETE                          2.6e-33  2_[2]_120_[1]_61
-YRTP_BACSU                          4.3e-33  6_[2]_119_[1]_55
-AP27_MOUSE                          4.5e-33  7_[2]_112_[1]_67
-HDE_CANTR                           1.6e-32  8_[2]_125_[1]_131_[2]_115_[1]_411
-HDHA_ECOLI                          4.9e-31  11_[2]_74_[1]_15_[1]_68
-DHII_HUMAN                          8.2e-31  34_[2]_119_[1]_81
-FIXR_BRAJA                          2.6e-30  36_[2]_123_[1]_61
-DHGB_BACME                          3.2e-30  7_[2]_123_[1]_74
-NODG_RHIME                          3.4e-29  6_[2]_116_[1]_65
-RIDH_KLEAE                          6.2e-29  14_[2]_116_[1]_61
-YINL_LISMO                          6.6e-29  5_[2]_75_[2]_15_[1]_66
-DHMA_FLAS1                          1.2e-28  14_[2]_121_[1]_77
-HMTR_LEIMA                          5.1e-28  6_[2]_157_[1]_66
-2BHD_STREX                          5.9e-28  6_[2]_116_[1]_75
-ENTA_ECOLI                          4.8e-27  5_[2]_109_[1]_76
-DHB2_HUMAN                          1.7e-26  82_[2]_120_[1]_127
-BDH_HUMAN                           2.8e-26  55_[2]_123_[1]_107
-BA72_EUBSP                          4.2e-26  6_[2]_121_[1]_64
-FVT1_HUMAN                          8.9e-26  32_[2]_124_[1]_118
-GUTD_ECOLI                          5.1e-25  2_[2]_122_[1]_77
-DHB3_HUMAN                          8.3e-25  48_[2]_120_[1]_84
-3BHD_COMTE                          1.4e-24  6_[2]_115_[1]_74
-LIGD_PSEPA                          8.1e-24  6_[2]_121_[1]_120
-DHES_HUMAN                          2.4e-22  2_[2]_50_[2]_44_[1]_144
-RFBB_NEIGO                          3.2e-19  6_[2]_129_[1]_153
-BPHB_PSEPS                            1e-18  5_[2]_118_[1]_94
-YURA_MYXXA                          1.9e-18  65_[2]_22_[2]_14_[1]_70
-PCR_PEA                             7.2e-18  25_[1]_32_[2]_284
-DHCA_HUMAN                          1.1e-17  4_[2]_159_[1]_55
-ADH_DROME                           2.7e-14  6_[2]_116_[1]_75
-MAS1_AGRRA                            3e-14  245_[2]_74_[1]_14_[1]_56
-FABI_ECOLI                          9.7e-14  6_[2]_123_[1]_75
-CSGA_MYXXA                          2.5e-12  51_[2]_7_[1]_50
-
-********************************************************************************
-
-
-
-********************************************************************************
-SECTION III: ANNOTATED SEQUENCES
-********************************************************************************
-	- The positions and p-values of the non-overlapping motif occurrences
-	  are shown above the actual sequence for each of the high-scoring
-	  sequences from Section I.
-	- A motif occurrence is defined as a position in the sequence whose
-	  match to the motif has POSITION p-value less than 0.0001 as 
-	  defined in Section II.
-	- For each sequence, the first line specifies the name of the sequence.
-	- The second (and possibly more) lines give a description of the 
-	  sequence.
-	- Following the description line(s) is a line giving the length, 
-	  combined p-value, and E-value of the sequence as defined in Section I.
-	- The next line reproduces the motif diagram from Section II.
-	- The entire sequence is printed on the following lines.
-	- Motif occurrences are indicated directly above their positions in the
-	  sequence on lines showing
-	   o the motif number of the occurrence,
-	   o the position p-value of the occurrence,
-	   o the best possible match to the motif, and
-	   o columns whose match to the motif has a positive score (indicated 
-	     by a plus sign).
-********************************************************************************
-
-
-BUDC_KLETE
-  ACETOIN(DIACETYL) REDUCTASE (EC 1.1.1.5) (ACETOIN DEHYDROGENASE)
-  LENGTH = 241  COMBINED P-VALUE = 7.82e-35  E-VALUE =  2.6e-33
-  DIAGRAM: 2_[2]_120_[1]_61
-
-       [2]
-       7.9e-21
-       KVVLITGCSSGIGKATAKHLHKEGAKVVL
-       +++++++++++++++++++++++++ + +
-1    MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATATAVAAEINQAGGRAVAIKVDVSRRDQVFAAVEQARK
-
-      [1]
-      2.6e-21
-      YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-      +++++++++++++++++++++ ++++++
-151  VYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTPMWAEIDRQCRKRRANRWATARLNLPNASPLAACRSLK
-
-
-YRTP_BACSU
-  HYPOTHETICAL 25.3 KD PROTEIN IN RTP 5'REGION (ORF238)
-  LENGTH = 238  COMBINED P-VALUE = 1.31e-34  E-VALUE =  4.3e-33
-  DIAGRAM: 6_[2]_119_[1]_55
-
-           [2]
-           2.8e-19
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-           ++++++++++++++++++++++++ ++ +
-1    MQSLQHKTALITGGGRGIGRATALALAKEGVNIGLIGRTSANVEKVAEEVKALGVKAAFAAADVKDADQVNQAVA
-
-         [1]
-         1.3e-22
-         YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-         ++++++++ ++++++++++++++++++++
-151  VTSAYSASKFAVLGLTESLMQEVRKHNIRVSALTPSTVASDMSIELNLTDGNPEKVMQPEDLAEYMVAQLKLDPR
-
-
-AP27_MOUSE
-  ADIPOCYTE P27 PROTEIN (AP27)
-  LENGTH = 244  COMBINED P-VALUE = 1.37e-34  E-VALUE =  4.5e-33
-  DIAGRAM: 7_[2]_112_[1]_67
-
-            [2]
-            7.4e-20
-            KVVLITGCSSGIGKATAKHLHKEGAKVVL
-             +++++++++++++ ++++++++++++++
-1    MKLNFSGLRALVTGAGKGIGRDTVKALHASGAKVVAVTRTNSDLVSLAKECPGIEPVCVDLGDWDATEKALGGIG
-
-                                                                              [1
-                                                                              4.
-                                                                              YS
-                                                                              ++
-76   PVDLLVNNAALVIMQPFLEVTKEAFDRSFSVNLRSVFQVSQMVARDMINRGVPGSIVNVSSMVAHVTFPNLITYS
-
-     ]
-     8e-22
-     ASKFAVRMLTRSMAHEYAPHGIRVNCI
-     ++++++++++++++++++++ ++++++
-151  STKGAMTMLTKAMAMELGPHKIRVNSVNPTVVLTDMGKKVSADPEFARKLKERHPLRKFAEVEDVVNSILFLLSD
-
-
-HDE_CANTR
-  HYDRATASE-DEHYDROGENASE-EPIMERASE (HDE)
-  LENGTH = 906  COMBINED P-VALUE = 4.94e-34  E-VALUE =  1.6e-32
-  DIAGRAM: 8_[2]_125_[1]_131_[2]_115_[1]_411
-
-             [2]
-             2.5e-19
-             KVVLITGCSSGIGKATAKHLHKEGAKVVL
-             ++++++++++++++ + +++++ ++++++
-1    MSPVDFKDKVVIITGAGGGLGKYYSLEFAKLGAKVVVNDLGGALNGQGGNSKAADVVVDEIVKNGGVAVADYNNV
-
-                 [1]
-                 2.8e-13
-                 YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                 + +++ ++ ++ ++++++ ++++++ +++
-151  PAGLYGNFGQANYASAKSALLGFAETLAKEGAKYNIKANAIAPLARSRMTESILPPPMLEKLGPEKVAPLVLYLS
-
-                           [2]
-                           1.5e-24
-                           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-                           +++++++++ +++++++++++++++++++
-301  TNEARKLPANDASGAPTVSLKDKVVLITGAGAGLGKEYAKWFAKYGAKVVVNDFKDATKTVDEIKAAGGEAWPDQ
-
-                     [1]
-                     5.2e-18
-                     YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                     ++++++++ +++++++ + ++ +++++++
-451  NITSTSGIYGNFGQANYSSSKAGILGLSKTMAIEGAKNNIKVNIVAPHAETAMTLTIFREQDKNLYHADQVAPLL
-
-
-HDHA_ECOLI
-  7-ALPHA-HYDROXYSTEROID DEHYDROGENASE (EC 1.1.1.159) (HSDH)
-  LENGTH = 255  COMBINED P-VALUE = 1.49e-32  E-VALUE =  4.9e-31
-  DIAGRAM: 11_[2]_74_[1]_15_[1]_68
-
-                [2]
-                4.3e-21
-                KVVLITGCSSGIGKATAKHLHKEGAKVVL
-                +++++++++ +++++++++++++++++++
-1    MFNSDNLRLDGKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANHVVDEIQQLGGQAFACRCDITSEQEL
-
-                                            [1]
-                                            2.9e-05
-                                            YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                                            +    ++  ++++  + ++++ +  +
-76   SALADFAISKLGKVDILVNNAGGGGPKPFDMPMADFRRAYELNVFSFFHLSQLVAPEMEKNGGGVILTITSMAAE
-
-             [1]
-             8.6e-19
-             YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-             + +++++ +++++ +++++++++++++++
-151  NKNINMTSYASSKAAASHLVRNMAFDLGEKNIRVNGIAPGAILTDALKSVITPEIEQKMLQHTPIRRLGQPQDIA
-
-
-DHII_HUMAN
-  CORTICOSTEROID 11-BETA-DEHYDROGENASE (EC 1.1.1.146) (11-DH) (11-BETA- 
-  HYDROXYSTEROID DEHYDROGENASE) (11-BETA-HSD)
-  LENGTH = 292  COMBINED P-VALUE = 2.49e-32  E-VALUE =  8.2e-31
-  DIAGRAM: 34_[2]_119_[1]_81
-
-                                       [2]
-                                       3.9e-24
-                                       KVVLITGCSSGIGKATAKHLHKEGAKVVL
-                                       +++++++++++++++++++++++++++++
-1    MAFMKKYLLPILGLFMAYYYYSANEEFRPEMLQGKKVIVTGASKGIGREMAYHLAKMGAHVVVTARSKETLQKVV
-
-                                     [1]
-                                     1.2e-15
-                                     YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                                     +++++++++++ ++ +++++ +++++++
-151  TVAALPMLKQSNGSIVVVSSLAGKVAYPMVAAYSASKFALDGFFSSIRKEYSVSRVNVSITLCVLGLIDTETAMK
-
-
-FIXR_BRAJA
-  FIXR PROTEIN
-  LENGTH = 278  COMBINED P-VALUE = 7.83e-32  E-VALUE =  2.6e-30
-  DIAGRAM: 36_[2]_123_[1]_61
-
-                                         [2]
-                                         3.2e-18
-                                         KVVLITGCSSGIGKATAKHLHKEGAKVVL
-                                         ++++ +++++++++++++ + ++++++
-1    MGLDLPNDNLIRGPLPEAHLDRLVDAVNARVDRGEPKVMLLTGASRGIGHATAKLFSEAGWRIISCARQPFDGER
-
-                                           [1]
-                                           5.1e-21
-                                           YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                                           +  +++++ ++++++++++++++++++++
-151  APILLAQGLFDELRAASGSIVNVTSIAGSRVHPFAGSAYATSKAALASLTRELAHDYAPHGIRVNAIAPGEIRTD
-
-
-DHGB_BACME
-  GLUCOSE 1-DEHYDROGENASE B (EC 1.1.1.47)
-  LENGTH = 262  COMBINED P-VALUE = 9.77e-32  E-VALUE =  3.2e-30
-  DIAGRAM: 7_[2]_123_[1]_74
-
-            [2]
-            4.4e-19
-            KVVLITGCSSGIGKATAKHLHKEGAKVVL
-            +++++++ + +++++++++++++ +++++
-1    MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEEIKKVGGEAIAVKGDVTVESDVIN
-
-              [1]
-              5.3e-20
-              YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-              + +++++++ +++++++++++++++++++
-151  KIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEE
-
-
-NODG_RHIME
-  NODULATION PROTEIN G (HOST-SPECIFICITY OF NODULATION PROTEIN C)
-  LENGTH = 245  COMBINED P-VALUE = 1.03e-30  E-VALUE =  3.4e-29
-  DIAGRAM: 6_[2]_116_[1]_65
-
-           [2]
-           4.0e-16
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-            +++++++++ ++ ++++ ++++++ + +
-1    MFELTGRKALVTGASGAIGGAIARVLHAQGAIVGLHGTQIEKLETLATELGDRVKLFPANLANRDEVKALGQRAE
-
-      [1]
-      7.3e-22
-      YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-      +++++++++++++++++++++ +++++++
-151  NYCASKAGMIGFSKSLAQEIATRNITVNCVAPGFIESAMTDKLNHKQKEKIMVAIPIHRMGTGTEVASAVAYLAS
-
-
-RIDH_KLEAE
-  RIBITOL 2-DEHYDROGENASE (EC 1.1.1.56) (RDH)
-  LENGTH = 249  COMBINED P-VALUE = 1.88e-30  E-VALUE =  6.2e-29
-  DIAGRAM: 14_[2]_116_[1]_61
-
-                   [2]
-                   7.0e-21
-                   KVVLITGCSSGIGKATAKHLHKEGAKVVL
-                   +++ +++++++++++++++++ +++++++
-1    MKHSVSSMNTSLSGKVAAITGAASGIGLECARTLLGAGAKVVLIDREGEKLNKLVAELGENAFALQVDLMQADQV
-
-              [1]
-              7.4e-17
-              YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-              ++++++++++++++ +++++++++++ ++
-151  VVPVIWEPVYTASKFAVQAFVHTTRRQVAQYGVRVGAVLPGPVVTALLDDWPKAKMDEALANGSLMQPIEVAESV
-
-
-YINL_LISMO
-  HYPOTHETICAL 26.8 KD PROTEIN IN INLA 5'REGION (ORFA)
-  LENGTH = 248  COMBINED P-VALUE = 1.99e-30  E-VALUE =  6.6e-29
-  DIAGRAM: 5_[2]_75_[2]_15_[1]_66
-
-          [2]
-          2.9e-23
-          KVVLITGCSSGIGKATAKHLHKEGAKVVL
-          ++++++++++++++++++ +++++++ ++
-1    MTIKNKVIIITGASSGIGKATALLLAEKGAKLVLAARRVEKLEKIVQIIKANSGEAIFAKTDVTKREDNKKLVEL
-
-                                       [2]
-                                       3.8e-05
-                                       KVVLITGCSSGIGKATAKHLHKEGAKVVL
-                                         + + +   ++   +    +++  ++ +
-76   AIERYGKVDAIFLNAGIMPNSPLSALKEDEWEQMIDINIKGVLNGIAAVLPSFIAQKSGHIIATSSVAGLKAYPG
-
-        [1]
-        1.9e-14
-        YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-        +++++++++ +++ ++++ ++++ ++++
-151  GAVYGATKWAVRDLMEVLRMESAQEGTNIRTATIYPAAINTELLETITDKETEQGMTSLYKQYGITPDRIASIVA
-
-
-DHMA_FLAS1
-  N-ACYLMANNOSAMINE 1-DEHYDROGENASE (EC 1.1.1.233) (NAM-DH) 
-  LENGTH = 270  COMBINED P-VALUE = 3.65e-30  E-VALUE =  1.2e-28
-  DIAGRAM: 14_[2]_121_[1]_77
-
-                   [2]
-                   2.0e-19
-                   KVVLITGCSSGIGKATAKHLHKEGAKVVL
-                   + +++++++++++++++++ +++++++++
-1    TTAGVSRRPGRLAGKAAIVTGAAGGIGRATVEAYLREGASVVAMDLAPRLAATRYEEPGAIPIACDLADRAAIDA
-
-                   [1]
-                   4.2e-18
-                   YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                   + ++++++ +++++++++++++++ ++++
-151  GSVNSFMAEPEAAAYVAAKGGVAMLTRAMAVDLARHGILVNMIAPGPVDVTGNNTGYSEPRLAEQVLDEVALGRP
-
-
-HMTR_LEIMA
-  no comment
-  LENGTH = 287  COMBINED P-VALUE = 1.55e-29  E-VALUE =  5.1e-28
-  DIAGRAM: 6_[2]_157_[1]_66
-
-           [2]
-           1.6e-17
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-           ++++++++++ +++++++ ++++++ +++
-1    MTAPTVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPVS
-
-                                               [1]
-                                               2.1e-19
-                                               YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                                               +++++++++++++++++++++ +++++++
-151  PYFLIKAFAHRSRHPSQASRTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGL
-
-
-2BHD_STREX
-  20-BETA-HYDROXYSTEROID DEHYDROGENASE (EC 1.1.1.53)
-  LENGTH = 255  COMBINED P-VALUE = 1.78e-29  E-VALUE =  5.9e-28
-  DIAGRAM: 6_[2]_116_[1]_75
-
-           [2]
-           7.1e-18
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-           +++++++++++++ + +++ +++++++++
-1    MNDLSGKTVIITGGARGLGAEAARQAVAAGARVVLADVLDEEGAATARELGDAARYQHLDVTIEEDWQRVVAYAR
-
-      [1]
-      6.8e-19
-      YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-      +++++++++++++ +++++++ +++++++
-151  SYGASKWGVRGLSKLAAVELGTDRIRVNSVHPGMTYTPMTAETGIRQGEGNYPNTPMGRVGNEPGEIAGAVVKLL
-
-
-ENTA_ECOLI
-  2,3-DIHYDRO-2,3-DIHYDROXYBENZOATE DEHYDROGENASE (EC 1.3.1.28)
-  LENGTH = 248  COMBINED P-VALUE = 1.45e-28  E-VALUE =  4.8e-27
-  DIAGRAM: 5_[2]_109_[1]_76
-
-          [2]
-          3.7e-20
-          KVVLITGCSSGIGKATAKHLHKEGAKVVL
-          +++++++++++++++++++++++++++
-1    MDFSGKNVWVTGAGKGIGYATALAFVEAGAKVTGFDQAFTQEQYPFATEVMDVADAAQVAQVCQRLLAETERLDA
-
-                                                                         [1]
-                                                                         1.2e-15
-                                                                         YSASKFA
-                                                                         +++++++
-76   LVNAAGILRMGATDQLSKEDWQQTFAVNVGGAFNLFQQTMNQFRRQRGGAIVTVASDAAHTPRIGMSAYGASKAA
-
-     
-     
-     VRMLTRSMAHEYAPHGIRVNCI
-     ++++  +  ++++ ++++++++
-151  LKSLALSVGLELAGSGVRCNVVSPGSTDTDMQRTLWVSDDAEEQRIRGFGEQFKLGIPLGKIARPQEIANTILFL
-
-
-DHB2_HUMAN
-  no comment
-  LENGTH = 387  COMBINED P-VALUE = 5.05e-28  E-VALUE =  1.7e-26
-  DIAGRAM: 82_[2]_120_[1]_127
-
-
-            [2]
-            3.4e-17
-            KVVLITGCSSGIGKATAKHLHKEGAKVVL
-            + ++++++++++++++++++ + ++ +++
-76   ELLPVDQKAVLVTGGDCGLGHALCKYLDELGFTVFAGVLNENGPGAEELRRTCSPRLSVLQMDITKPVQIKDAYS
-
-           [1]
-           1.7e-18
-           YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-           +++++++++++++ ++++++++++++ ++
-226  MERLASYGSSKAAVTMFSSVMRLELSKWGIKVASIQPGGFLTNIAGTSDKWEKLEKDILDHLPAEVQEDYGQDYI
-
-
-BDH_HUMAN
-  D-BETA-HYDROXYBUTYRATE DEHYDROGENASE PRECURSOR (EC 1.1.1.30) (BDH) 
-  (3-HYDROXYBUTYRATE DEHYDROGENASE) (FRAGMENT)
-  LENGTH = 343  COMBINED P-VALUE = 8.57e-28  E-VALUE =  2.8e-26
-  DIAGRAM: 55_[2]_123_[1]_107
-
-                                                            [2]
-                                                            2.3e-18
-                                                            KVVLITGCSSGIGKATAKHL
-                                                            + +++++++++ ++++++++
-1    GLRPPPPGRFSRLPGKTLSACDRENGARRPLLLGSTSFIPIGRRTYASAAEPVGSKAVLVTGCDSGFGFSLAKHL
-
-     
-     
-     HKEGAKVVL
-     +++++ +++
-76   HSKGFLVFAGCLMKDKGHDGVKELDSLNSDRLRTVQLNVFRSEEVEKVVGDCPFEPEGPEKGMWGLVNNAGISTF
-
-                                                              [1]
-                                                              5.5e-17
-                                                              YSASKFAVRMLTRSMAHE
-                                                              ++ +++++++++++++++
-151  GEVEFTSLETYKQVAEVNLWGTVRMTKSFLPLIRRAKGRVVNISSMLGRMANPARSPYCITKFGVEAFSDCLRYE
-
-     
-     
-     YAPHGIRVNCI
-     +++ +++++++
-226  MYPLGVKVSVVEPGNFIAATSLYNPESIQAIAKKMWEELPEVVRKDYGKKYFDEKIAKMETYCSSGSTDTSPVID
-
-
-BA72_EUBSP
-  7-ALPHA-HYDROXYSTEROID DEHYDROGENASE (EC 1.1.1.159) (BILE ACID 
-  7-DEHYDROXYLASE) (BILE ACID-INDUCIBLE PROTEIN)
-  LENGTH = 249  COMBINED P-VALUE = 1.28e-27  E-VALUE =  4.2e-26
-  DIAGRAM: 6_[2]_121_[1]_64
-
-           [2]
-           2.6e-18
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-           ++++++++ ++++++ ++ ++ +++++ +
-1    MNLVQDKVTIITGGTRGIGFAAAKIFIDNGAKVSIFGETQEEVDTALAQLKELYPEEEVLGFAPDLTSRDAVMAA
-
-           [1]
-           1.5e-16
-           YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-           + +++++++++++ + +++ +++++++++
-151  SLSGVGYPASKASVIGLTHGLGREIIRKNIRVVGVAPGVVNTDMTNGNPPEIMEGYLKALPMKRMLEPEEIANVY
-
-
-FVT1_HUMAN
-  no comment
-  LENGTH = 332  COMBINED P-VALUE = 2.70e-27  E-VALUE =  8.9e-26
-  DIAGRAM: 32_[2]_124_[1]_118
-
-                                     [2]
-                                     2.3e-17
-                                     KVVLITGCSSGIGKATAKHLHKEGAKVVL
-                                      ++++++++++++++++++++++++ + +
-1    MLLLAAAFLVAFVLLLYMVSPLISPKPLALPGAHVVVTGGSSGIGKCIAIECYKQGAFITLVARNEDKLLQAKKE
-
-                                        [1]
-                                        1.9e-17
-                                        YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                                        +++++++++++ ++++++++++++++++
-151  YPSRAVITTMKERRVGRIVFVSSQAGQLGLFGFTAYSASKFAIRGLAEALQMEVKPYNVYITVAYPPDTDTPGFA
-
-
-GUTD_ECOLI
-  SORBITOL-6-PHOSPHATE 2-DEHYDROGENASE (EC 1.1.1.140) (GLUCITOL-6- PHOSPHATE 
-  DEHYDROGENASE) (KETOSEPHOSPHATE REDUCTASE)
-  LENGTH = 259  COMBINED P-VALUE = 1.54e-26  E-VALUE =  5.1e-25
-  DIAGRAM: 2_[2]_122_[1]_77
-
-       [2]
-       1.5e-14
-       KVVLITGCSSGIGKATAKHLHKEGAKVVL
-       +++++ ++++ ++  +++ ++++++++ +
-1    MNQVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSDKAANVAQEINAEYGESMAYGFGADATSEQSCLALSRGV
-
-        [1]
-        3.0e-19
-        YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-        +++++++ +++++++++++++++++++++
-151  NSGYSAAKFGGVGLTQSLALDLAEYGITVHSLMLGNLLKSPMFQSLLPQYATKLGIKPDQVEQYYIDKVPLKRGC
-
-
-DHB3_HUMAN
-  no comment
-  LENGTH = 310  COMBINED P-VALUE = 2.53e-26  E-VALUE =  8.3e-25
-  DIAGRAM: 48_[2]_120_[1]_84
-
-                                                     [2]
-                                                     7.4e-19
-                                                     KVVLITGCSSGIGKATAKHLHKEGAKV
-                                                     +++++++++ ++++++  ++++++ ++
-1    MGDVLEQFFILTGLLVCLACLAKCVRFSRCVLLNYYKVLPKSFLRSMGQWAVITGAGDGIGKAYSFELAKRGLNV
-
-     
-     
-     VL
-     ++
-76   VLISRTLEKLEAIATEIERTTGRSVKIIQADFTKDDIYEHIKEKLAGLEIGILVNNVGMLPNLLPSHFLNAPDEI
-
-                                                    [1]
-                                                    6.7e-15
-                                                    YSASKFAVRMLTRSMAHEYAPHGIRVNC
-                                                    ++++++++++++++++ +++ + + +++
-151  QSLIHCNITSVVKMTQLILKHMESRQKGLILNISSGIALFPWPLYSMYSASKAFVCAFSKALQEEYKAKEVIIQV
-
-     
-     
-     I
-     +
-226  LTPYAVSTAMTKYLNTNVITKTADEFVKESLNYVTIGGETCGCLAHEILAGFLSLIPAWAFYSGAFQRLLLTHYV
-
-
-3BHD_COMTE
-  3-BETA-HYDROXYSTEROID DEHYDROGENASE (EC 1.1.1.51)
-  LENGTH = 253  COMBINED P-VALUE = 4.25e-26  E-VALUE =  1.4e-24
-  DIAGRAM: 6_[2]_115_[1]_74
-
-           [2]
-           2.6e-18
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-           +++++++++++ ++++++ ++ +++++
-1    TNRLQGKVALVTGGASGVGLEVVKLLLGEGAKVAFSDINEAAGQQLAAELGERSMFVRHDVSSEADWTLVMAAVQ
-
-     [1]
-     5.1e-15
-     YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-     +++++++++++++++++ +++++  +++
-151  YSASKAAVSALTRAAALSCRKQGYAIRVNSIHPDGIYTPMMQASLPKGVSKEMVLHDPKLNRAGRAYMPERIAQL
-
-
-LIGD_PSEPA
-  C ALPHA-DEHYDROGENASE (EC -.-.-.-)
-  LENGTH = 305  COMBINED P-VALUE = 2.45e-25  E-VALUE =  8.1e-24
-  DIAGRAM: 6_[2]_121_[1]_120
-
-           [2]
-           6.5e-17
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-           +++ +++++++ ++  ++ + ++++++++
-1    MKDFQDQVAFITGGASGAGFGQAKVFGQAGAKIVVADVRAEAVEKAVAELEGLGITAHGIVLDIMDREAYARAAD
-
-           [1]
-           7.9e-16
-           YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-           +++++++ +++++ +++ ++++++ ++++
-151  SALAGPYSAAKAASINLMEGYRQGLEKYGIGVSVCTPANIKSNIAEASRLRPAKYGTSGYVENEESIASLHSIHQ
-
-
-DHES_HUMAN
-  ESTRADIOL 17 BETA-DEHYDROGENASE (EC 1.1.1.62) (20 ALPHA-HYDROXYSTEROID 
-  DEHYDROGENASE) (E2DH) (17-BETA-HSD) (PLACENTAL 17-BETA-HYDROXYSTEROID 
-  DEHYDROGENASE)
-  LENGTH = 327  COMBINED P-VALUE = 7.31e-24  E-VALUE =  2.4e-22
-  DIAGRAM: 2_[2]_50_[2]_44_[1]_144
-
-       [2]
-       1.4e-14
-       KVVLITGCSSGIGKATAKHLHKEGAKVVL
-       +++++++++++++++++ +++++ ++ +
-1    ARTVVLITGCSSGIGLHLAVRLASDPSQSFKVYATLRDLKTQGRLWEAARALACPPGSLETLQLDVRDSKSVAAA
-
-           [2]
-           9.3e-05
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-            ++ +  ++ ++++   ++ + + +   +
-76   RERVTEGRVDVLVCNAGLGLLGPLEALGEDAVASVLDVNVVGTVRMLQAFLPDMKRRGSGRVLVTGSVGGLMGLP
-
-         [1]
-         1.0e-16
-         YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-         +++++++++++++++++ + + +++ + +
-151  FNDVYCASKFALEGLCESLAVLLLPFGVHLSLIECGPVHTAFMEKVLGSPEEVLDRTDIHTFHRFYQYLAHSKQV
-
-
-RFBB_NEIGO
-  no comment
-  LENGTH = 346  COMBINED P-VALUE = 9.68e-21  E-VALUE =  3.2e-19
-  DIAGRAM: 6_[2]_129_[1]_153
-
-           [2]
-           1.8e-13
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-           ++++++++++ ++ +++++ +++    ++
-1    MQTEGKKNILVTGGAGFIGSAVVRHIIQNTRDSVVNLDKLTYAGNLESLTDIADNPRYAFEQVDICDRAELDRVF
-
-                   [1]
-                   1.0e-14
-                   YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                   +++++++ +++++++++ ++   ++ ++
-151  DLFTETTPYAPSSPYSASKAAADHLVRAWQRTYRLPSIVSNCSNNYGPRQFPEKLIPLMILNALSGKPLPVYGDG
-
-
-BPHB_PSEPS
-  BIPHENYL-CIS-DIOL DEHYDROGENASE (EC 1.3.1.-)
-  LENGTH = 275  COMBINED P-VALUE = 3.02e-20  E-VALUE =    1e-18
-  DIAGRAM: 5_[2]_118_[1]_94
-
-          [2]
-          8.6e-15
-          KVVLITGCSSGIGKATAKHLHKEGAKVVL
-            +++++++++++++++ +++++    ++
-1    MKLKGEAVLITGGASGLGRALVDRFVAEAKVAVLDKSAERLAELETDLGDNVLGIVGDVRSLEDQKQAASRCVAR
-
-       [1]
-       1.2e-12
-       YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-       ++++++++++++++++++++++  +  +
-151  PLYTAAKQAIVGLVRELAFELAPYVRVNGVGPGGMNSDMRGPSSLGMGSKAISTVPLADMLKSVLPIGRMPEVEE
-
-
-YURA_MYXXA
-  no comment
-  LENGTH = 258  COMBINED P-VALUE = 5.64e-20  E-VALUE =  1.9e-18
-  DIAGRAM: 65_[2]_22_[2]_14_[1]_70
-
-                                                                      [2]
-                                                                      5.6e-05
-                                                                      KVVLITGCSS
-                                                                        + ++ ++
-1    RQHTGGLHGGDELPDGVGDGCLQRPGTRAGAVARQAGVRVFAAGRRLPQLQAADEAPGGRRHRGARGVDVTKADA
-
-                                              [2]
-                                              5.7e-08
-     GIGKATAKHLHKEGAKVVL                      KVVLITGCSSGIGKATAKHLHKEGAKVVL
-      + +  +++  + +   ++                        + +++++  +   + ++  ++  + +
-76   TLERIRALDAEAGGLDLVVANAGVGGTTNAKRLPWERVRGIIDTNVTGAAATLSAVLPQMVERKRGHLVGVSSLA
-
-              [1]
-              3.8e-19
-              YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-              +++++++++ ++++++++++ ++++++++
-151  GFRGLPATRYSASKAFLSTFMESLRVDLRGTGVRVTCIYPGFVKSELTATNNFPMPFLMETHDAVELMGKGIVRG
-
-
-PCR_PEA
-  no comment
-  LENGTH = 399  COMBINED P-VALUE = 2.17e-19  E-VALUE =  7.2e-18
-  DIAGRAM: 25_[1]_32_[2]_284
-
-                              [1]
-                              1.7e-08
-                              YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                                ++ ++++++++++  +   +  +++ +
-1    MALQTASMLPASFSIPKEGKIGASLKDSTLFGVSSLSDSLKGDFTSSALRCKELRQKVGAVRAETAAPATPAVNK
-
-                [2]
-                1.9e-18
-                KVVLITGCSSGIGKATAKHLHKEGAKVVL
-                 +++++++++++++++++++++++ + ++
-76   SSSEGKKTLRKGNVVITGASSGLGLATAKALAESGKWHVIMACRDYLKAARAAKSAGLAKENYTIMHLDLASLDS
-
-
-DHCA_HUMAN
-  no comment
-  LENGTH = 276  COMBINED P-VALUE = 3.43e-19  E-VALUE =  1.1e-17
-  DIAGRAM: 4_[2]_159_[1]_55
-
-         [2]
-         4.0e-16
-         KVVLITGCSSGIGKATAKHLHKEGAKVVL
-         ++++++++++++++++++++++  +  ++
-1    SSGIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTARDVTRGQAAVQQLQAEGLSPRFHQLDIDDLQSIRALRDF
-
-                                               [1]
-                                               2.9e-10
-                                               YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-                                               ++ ++ +++ +++ +++ +++++   +++
-151  PELQQKFRSETITEEELVGLMNKFVEDTKKGVHQKEGWPSSAYGVTKIGVTVLSRIHARKLSEQRKGDKILLNAC
-
-
-ADH_DROME
-  ALCOHOL DEHYDROGENASE (EC 1.1.1.1)
-  LENGTH = 255  COMBINED P-VALUE = 8.17e-16  E-VALUE =  2.7e-14
-  DIAGRAM: 6_[2]_116_[1]_75
-
-           [2]
-           1.1e-10
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-           ++++   + +++++ + ++++++  +  +
-1    SFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENPAAIAELKAINPKVTVTFYPYDVTVPIAETTKL
-
-      [1]
-      3.6e-12
-      YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-      ++ ++++++++++++++    ++++ +++
-151  VYSGTKAAVVNFTSSLAKLAPITGVTAYTVNPGITRTTLVHKFNSWLDVEPQVAEKLLAHPTQPSLACAENFVKA
-
-
-MAS1_AGRRA
-  no comment
-  LENGTH = 476  COMBINED P-VALUE = 9.22e-16  E-VALUE =    3e-14
-  DIAGRAM: 245_[2]_74_[1]_14_[1]_56
-
-
-                         [2]
-                         2.9e-15
-                         KVVLITGCSSGIGKATAKHLHKEGAKVVL
-                         +++++ + +++ ++++++++++++++  +
-226  GRVLHFRRGFSHWTVEIHQSPVILVSGSNRGVGKAIAEDLIAHGYRLSLGARKVKDLEVAFGPQDEWLHYARFDA
-
-                                                     [1]
-                                                     4.0e-08
-                                                     YSASKFAVRMLTRSMAHEYAPHGIRVN
-                                                     +  + + +++   ++ + +++   +++
-301  EDHGTMAAWVTAAVEKFGRIDGLVNNAGYGEPVNLDKHVDYQRFHLQWYINCVAPLRMTELCLPHLYETGSGRIV
-
-                     [1]
-                     8.7e-05
-     CI              YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-     ++              + +++ ++ +++++ ++     +     +
-376  NINSMSGQRVLNPLVGYNMTKHALGGLTKTTQHVGWDRRCAAIDICLGFVATDMSAWTDLIASKDMIQPEDIAKL
-
-
-FABI_ECOLI
-  no comment
-  LENGTH = 262  COMBINED P-VALUE = 2.94e-15  E-VALUE =  9.7e-14
-  DIAGRAM: 6_[2]_123_[1]_75
-
-           [2]
-           4.5e-10
-           KVVLITGCSSGIGKATAKHLHKEGAKVVL
-           +++++++ ++ +  ++ ++ +++     +
-1    MGFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRVEEFAAQLGSDIVLQCDVAEDASIDTMF
-
-             [1]
-             3.1e-12
-             YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-             ++ +++++++ +++++  +++++++++++
-151  RAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAASGIKDFRKMLAHCEAVTPIRRTVTIEDV
-
-
-CSGA_MYXXA
-  no comment
-  LENGTH = 166  COMBINED P-VALUE = 7.50e-14  E-VALUE =  2.5e-12
-  DIAGRAM: 51_[2]_7_[1]_50
-
-                                                        [2]
-                                                        9.0e-08
-                                                        KVVLITGCSSGIGKATAKHLHKEG
-                                                        + ++  +  ++  + +++   +++
-1    MRAFATNVCTGPVDVLINNAGVSGLWCALGDVDYADMARTFTINALGPLRVTSAMLPGLRQGALRRVAHVTSRMG
-
-                 [1]
-                 1.3e-12
-     AKVVL       YSASKFAVRMLTRSMAHEYAPHGIRVNCI
-     +           + ++++++ + ++++  ++++++ + + +
-76   SLAANTDGGAYAYRMSKAALNMAVRSMSTDLRPEGFVTVLLHPGWVQTDMGGPDATLPAPDSVRGMLRVIDGLNP
-
-********************************************************************************
-
-
-CPU: pmgm2
-Time 0.250000 secs.
-
-mast meme.adh.oops.txt -text -stdout
diff --git a/Tests/Motif/mast.protein.tcm.txt b/Tests/Motif/mast.protein.tcm.txt
deleted file mode 100644
--- a/Tests/Motif/mast.protein.tcm.txt
+++ /dev/null
@@ -1,332 +0,0 @@
-********************************************************************************
-MAST - Motif Alignment and Search Tool
-********************************************************************************
-	MAST version 3.0 (Release date: 2004/08/18 09:07:01)
-
-	For further information on how to interpret these results or to get
-	a copy of the MAST software please access http://meme.sdsc.edu.
-********************************************************************************
-
-
-********************************************************************************
-REFERENCE
-********************************************************************************
-	If you use this program in your research, please cite:
-
-	Timothy L. Bailey and Michael Gribskov,
-	"Combining evidence using p-values: application to sequence homology
-	searches", Bioinformatics, 14(48-54), 1998.
-********************************************************************************
-
-
-********************************************************************************
-DATABASE AND MOTIFS
-********************************************************************************
-	DATABASE farntrans5.s (peptide)
-	Last updated on Mon Aug 16 21:19:59 2004
-	Database contains 5 sequences, 1900 residues
-
-	MOTIFS meme.farntrans5.tcm.txt (peptide)
-	MOTIF WIDTH BEST POSSIBLE MATCH
-	----- ----- -------------------
-	  1    30   GGFQGRPNKEVHTCYTYWALAALAILNKLH
-	  2    14   INKEKLIQWIKSCQ
-
-	PAIRWISE MOTIF CORRELATIONS:
-	MOTIF     1
-	----- -----
-	   2   0.22
-	No overly similar pairs (correlation > 0.60) found.
-
-	Random model letter frequencies (from non-redundant database):
-	A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 
-	L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 
-	W 0.013 Y 0.033 
-********************************************************************************
-
-
-********************************************************************************
-SECTION I: HIGH-SCORING SEQUENCES
-********************************************************************************
-	- Each of the following 5 sequences has E-value less than 10.
-	- The E-value of a sequence is the expected number of sequences
-	  in a random database of the same size that would match the motifs as
-	  well as the sequence does and is equal to the combined p-value of the
-	  sequence times the number of sequences in the database.
-	- The combined p-value of a sequence measures the strength of the
-	  match of the sequence to all the motifs and is calculated by
-	    o finding the score of the single best match of each motif
-	      to the sequence (best matches may overlap),
-	    o calculating the sequence p-value of each score,
-	    o forming the product of the p-values,
-	    o taking the p-value of the product.
-	- The sequence p-value of a score is defined as the
-	  probability of a random sequence of the same length containing
-	  some match with as good or better a score.
-	- The score for the match of a position in a sequence to a motif
-	  is computed by by summing the appropriate entry from each column of
-	  the position-dependent scoring matrix that represents the motif.
-	- Sequences shorter than one or more of the motifs are skipped.
-	- The table is sorted by increasing E-value.
-********************************************************************************
-
-SEQUENCE NAME                      DESCRIPTION                   E-VALUE  LENGTH
--------------                      -----------                   -------- ------
-BET2_YEAST                         YPT1/SEC4 PROTEINS GERANY...    2.9e-27    325
-RATRABGERB                         Rat rab geranylgeranyl tr...    1.4e-25    331
-CAL1_YEAST                         RAS PROTEINS GERANYLGERAN...    9.7e-22    376
-PFTB_RAT                           PROTEIN FARNESYLTRANSFERA...    7.6e-21    437
-RAM1_YEAST                         PROTEIN FARNESYLTRANSFERA...    6.2e-20    431
-
-********************************************************************************
-
-
-
-********************************************************************************
-SECTION II: MOTIF DIAGRAMS
-********************************************************************************
-	- The ordering and spacing of all non-overlapping motif occurrences
-	  are shown for each high-scoring sequence listed in Section I.
-	- A motif occurrence is defined as a position in the sequence whose
-	  match to the motif has POSITION p-value less than 0.0001.
-	- The POSITION p-value of a match is the probability of
-	  a single random subsequence of the length of the motif
-	  scoring at least as well as the observed match.
-	- For each sequence, all motif occurrences are shown unless there
-	  are overlaps.  In that case, a motif occurrence is shown only if its
-	  p-value is less than the product of the p-values of the other
-	  (lower-numbered) motif occurrences that it overlaps.
-	- The table also shows the E-value of each sequence.
-	- Spacers and motif occurences are indicated by
-	   o -d-    `d' residues separate the end of the preceding motif 
-		    occurrence and the start of the following motif occurrence
-	   o [n]  occurrence of motif `n' with p-value less than 0.0001.
-********************************************************************************
-
-SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
--------------                      --------  -------------
-BET2_YEAST                          2.9e-27  6_[2]_3_[1]_1_[2]_4_[1]_4_[2]_
-                                             3_[1]_1_[2]_3_[1]_21_[1]_1_[2]_
-                                             4_[1]_24
-RATRABGERB                          1.4e-25  65_[2]_3_[1]_1_[2]_3_[1]_1_[2]_
-                                             3_[1]_18_[1]_1_[2]_4_[1]_26
-CAL1_YEAST                          9.7e-22  125_[2]_50_[2]_1_[1]_4_[2]_22_
-                                             [1]_22_[1]_5_[2]_1
-PFTB_RAT                            7.6e-21  120_[2]_3_[1]_4_[2]_3_[1]_1_[2]_
-                                             3_[1]_1_[2]_4_[1]_14_[2]_4_[1]_60
-RAM1_YEAST                          6.2e-20  144_[1]_5_[2]_4_[1]_1_[2]_4_[1]_
-                                             1_[2]_4_[1]_4_[2]_5_[1]_35_[2]_4
-
-********************************************************************************
-
-
-
-********************************************************************************
-SECTION III: ANNOTATED SEQUENCES
-********************************************************************************
-	- The positions and p-values of the non-overlapping motif occurrences
-	  are shown above the actual sequence for each of the high-scoring
-	  sequences from Section I.
-	- A motif occurrence is defined as a position in the sequence whose
-	  match to the motif has POSITION p-value less than 0.0001 as 
-	  defined in Section II.
-	- For each sequence, the first line specifies the name of the sequence.
-	- The second (and possibly more) lines give a description of the 
-	  sequence.
-	- Following the description line(s) is a line giving the length, 
-	  combined p-value, and E-value of the sequence as defined in Section I.
-	- The next line reproduces the motif diagram from Section II.
-	- The entire sequence is printed on the following lines.
-	- Motif occurrences are indicated directly above their positions in the
-	  sequence on lines showing
-	   o the motif number of the occurrence,
-	   o the position p-value of the occurrence,
-	   o the best possible match to the motif, and
-	   o columns whose match to the motif has a positive score (indicated 
-	     by a plus sign).
-********************************************************************************
-
-
-BET2_YEAST
-  YPT1/SEC4 PROTEINS GERANYLGERANYLTRANSFERASE BETA SUBUNIT (EC 2.
-  LENGTH = 325  COMBINED P-VALUE = 5.77e-28  E-VALUE =  2.9e-27
-  DIAGRAM: 6_[2]_3_[1]_1_[2]_4_[1]_4_[2]_3_[1]_1_[2]_3_[1]_21_[1]_1_[2]_4_[1]_24
-
-           [2]              [1]                            [2]               [1]
-           5.2e-05          2.7e-10                        6.6e-10           5.9
-           INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGF
-             +++ +++++++     ++  + +++ +++ +++++ +++++++ + ++++++++++++++    + +
-1    MSGSLTLLKEKHIRYIESLDTNKHNFEYWLTEHLRLNGIYWGLTALCVLDSPETFVKEEVISFVLSCWDDKYGAF
-
-                                    [2]              [1]
-     e-14                           4.8e-07          2.3e-17
-     QGRPNKEVHTCYTYWALAALAILNKLH    INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILN
-     +  +++++++  +  ++++++ +++++    +++ +++++++ ++   + ++++  +++++++ +++++++++++
-76   APFPRHDAHLLTTLSAVQILATYDALDVLGKDRKVRLISFIRGNQLEDGSFQGDRFGEVDTRFVYTALSALSILG
-
-         [2]              [1]                                                [1]
-         5.1e-07          1.4e-18                                            4.6
-     KLH INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH                     GGF
-     +++ ++++ ++++++++    ++++  ++++++++++++++++++++++++                     +++
-151  ELTSEVVDPAVDFVLKCYNFDGGFGLCPNAESHAAQAFTCLGALAIANKLDMLSDDQLEEIGWWLCERQLPEGGL
-
-                                 [2]               [1]
-     e-22                        2.0e-13           3.8e-17
-     QGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGFQGRPNKEVHTCYTYWALAALAILNKL
-     ++++ ++++++++++++++++++++++ ++ +++++++++++    ++++++++++++++++ ++++++++++ +
-226  NGRPSKLPDVCYSWWVLSSLAIIGRLDWINYEKLTEFILKCQDEKKGGISDRPENEVDVFHTVFGVAGLSLMGYD
-
-     
-     
-     H
-     +
-301  NLVPIDPIYCMPKSVTSKFKKYPYK
-
-
-RATRABGERB
-  Rat rab geranylgeranyl transferase beta-subunit
-  LENGTH = 331  COMBINED P-VALUE = 2.83e-26  E-VALUE =  1.4e-25
-  DIAGRAM: 65_[2]_3_[1]_1_[2]_3_[1]_1_[2]_3_[1]_18_[1]_1_[2]_4_[1]_26
-
-                                                                      [2]
-                                                                      1.0e-11
-                                                                      INKEKLIQWI
-                                                                      +++++++ ++
-1    MGTQQKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFI
-
-            [1]                            [2]              [1]
-            1.6e-14                        1.4e-09          5.4e-19
-     KSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWAL
-     ++++   ++ +  +++++++ ++  ++++++++++++ +++++++ ++++++   + ++++++++++++++++++
-76   KSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAV
-
-                [2]              [1]
-                3.8e-12          4.8e-19
-     AALAILNKLH INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH
-     ++++++++++ ++++++++++++++   ++++++++ ++++++++++++ ++++++++
-151  ATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLP
-
-      [1]                            [2]               [1]
-      3.9e-21                        1.2e-12           9.6e-18
-      GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGFQGRPNKEVHTCYTYWALAALAI
-      +++++++++++++++++++++++ ++++++ ++++++++++++++    ++++++++++++ +++ ++++++++
-226  SGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSL
-
-     
-     
-     LNKLH
-     +++++
-301  LGEEQIKPVSPVFCMPEEVLQRVNVQPELVS
-
-
-CAL1_YEAST
-  RAS PROTEINS GERANYLGERANYLTRANSFERASE (EC 2.5.1.-) (PROTEIN GER
-  LENGTH = 376  COMBINED P-VALUE = 1.94e-22  E-VALUE =  9.7e-22
-  DIAGRAM: 125_[2]_50_[2]_1_[1]_4_[2]_22_[1]_22_[1]_5_[2]_1
-
-
-                                                       [2]
-                                                       1.8e-08
-                                                       INKEKLIQWIKSCQ
-                                                        +++++++++++++
-76   LDDTENTVISGFVGSLVMNIPHATTINLPNTLFALLSMIMLRDYEYFETILDKRSLARFVSKCQRPDRGSFVSCL
-
-                                            [2]            [1]
-                                            4.8e-10        8.7e-14
-                                            INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALA
-                                            +++++++ ++++++  + + + +++++ +++ ++++
-151  DYKTNCGSSVDSDDLRFCYIAVAILYICGCRSKEDFDEYIDTEKLLGYIMSQQCYNGAFGAHNEPHSGYTSCALS
-
-                  [2]                                 [1]
-                  5.9e-08                             5.9e-20
-     ALAILNKLH    INKEKLIQWIKSCQ                      GGFQGRPNKEVHTCYTYWALAALAIL
-     +++++++++      ++++++++++++                      +++++++++ +++++++++++++ ++
-226  TLALLSSLEKLSDKFKEDTITWLLHRQVSSHGCMKFESELNASYDQSDDGGFQGRENKFADTCYAFWCLNSLHLL
-
-                               [1]                                [2]
-                               4.0e-13                            2.1e-07
-     NKLH                      GGFQGRPNKEVHTCYTYWALAALAILNKLH     INKEKLIQWIKSCQ
-     ++++                      ++++ + ++++++++++ + +++++++        + ++ +++++++++
-301  TKDWKMLCQTELVTNYLLDRTQKTLTGGFSKNDEEDADLYHSCLGSAALALIEGKFNGELCIPQEIFNDFSKRCC
-
-
-PFTB_RAT
-  PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARNES
-  LENGTH = 437  COMBINED P-VALUE = 1.53e-21  E-VALUE =  7.6e-21
-  DIAGRAM: 120_[2]_3_[1]_4_[2]_3_[1]_1_[2]_3_[1]_1_[2]_4_[1]_14_[2]_4_[1]_60
-
-
-                                                  [2]              [1]
-                                                  1.3e-07          2.8e-19
-                                                  INKEKLIQWIKSCQ   GGFQGRPNKEVHT
-                                                  ++ ++++++++ ++   +++++++++ +++
-76   EKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPDGGFGGGPGQYPHL
-
-                          [2]              [1]                            [2]
-                          2.3e-09          2.1e-14                        1.8e-0
-     CYTYWALAALAILNKLH    INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKL
-     + +++++++++++++++    ++++++++++ +++   + + ++ +++++++ +++++++++++++++ +  +++
-151  APTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGT
-
-                [1]                            [2]               [1]
-     8          7.4e-20                        1.8e-08           2.2e-16
-     IQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGFQGRPNKEVHTCY
-     ++++ +++   +++++ +++++++++++++++++ ++++++  + +++++++++++    ++++++ ++++++++
-226  AEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCY
-
-                                  [2]               [1]
-                                  5.0e-08           3.1e-15
-     TYWALAALAILNKLH              INKEKLIQWIKSCQ    GGFQGRPNKEVHTCYTYWALAALAILNK
-     ++++++ + ++++                ++++++++++++++    +++ +++++  +++++++++++++++++
-301  SFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQH
-
-     
-     
-     LH
-     +
-376  FGSGAMLHDVVMGVPENVLQPTHPVYNIGPDKVIQATTHFLQKPVPGFEECEDAVTSDPATD
-
-
-RAM1_YEAST
-  PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARN
-  LENGTH = 431  COMBINED P-VALUE = 1.24e-20  E-VALUE =  6.2e-20
-  DIAGRAM: 144_[1]_5_[2]_4_[1]_1_[2]_4_[1]_1_[2]_4_[1]_4_[2]_5_[1]_35_[2]_4
-
-
-                                                                          [1]
-                                                                          8.8e-1
-                                                                          GGFQGR
-                                                                          + ++++
-76   PALTKEFHKMYLDVAFEISLPPQMTALDASQPWMLYWIANSLKVMDRDWLSDDTKRKIVVKLFTISPSGGPFGGG
-
-                                  [2]               [1]
-     7                            6.4e-07           1.0e-13
-     PNKEVHTCYTYWALAALAILNKLH     INKEKLIQWIKSCQ    GGFQGRPNKEVHTCYTYWALAALAILNK
-     ++++++++ ++++++++++ ++++     ++++++++++ +++    +  ++ ++++++++ +++++++++++++
-151  PGQLSHLASTYAAINALSLCDNIDGCWDRIDRKGIYQWLISLKEPNGGFKTCLEVGEVDTRGIYCALSIATLLNI
-
-        [2]               [1]                            [2]               [1]
-        2.5e-08           3.1e-17                        4.7e-11           2.4e-
-     LH INKEKLIQWIKSCQ    GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGFQG
-     ++ + ++++++++++++    +  ++  +++++++++++++++++++++++ ++++++++++++++     ++ +
-226  LTEELTEGVLNYLKNCQNYEGGFGSCPHVDEAHGGYTFCATASLAILRSMDQINVEKLLEWSSARQLQEERGFCG
-
-                                  [2]                [1]
-     16                           4.9e-09            2.7e-13
-     RPNKEVHTCYTYWALAALAILNKLH    INKEKLIQWIKSCQ     GGFQGRPNKEVHTCYTYWALAALAILN
-     + ++++++++++++ +++++++++     +++++++++++ ++      +++++++++++++++ +++ ++++++
-301  RSNKLVDGCYSFWVGGSAAILEAFGYGQCFNKHALRDYILYCCQEKEQPGLRDKPGAHSDFYHTNYCLLGLAVAE
-
-                                           [2]
-                                           9.8e-05
-     KLH                                   INKEKLIQWIKSCQ
-     +                                     +++++++ + +++
-376  SSYSCTPNDSPHNIKCTPDRLIGSSKLTDVNPVYGLPIENVRKIIHYFKSNLSSPS
-
-********************************************************************************
-
-
-CPU: pmgm2
-Time 0.130000 secs.
-
-mast meme.farntrans5.tcm.txt -text -stdout
diff --git a/Tests/Motif/meme.dna.oops.txt b/Tests/Motif/meme.dna.oops.txt
deleted file mode 100644
--- a/Tests/Motif/meme.dna.oops.txt
+++ /dev/null
@@ -1,324 +0,0 @@
-********************************************************************************
-MEME - Motif discovery tool
-********************************************************************************
-MEME version 3.0 (Release date: 2004/08/18 09:07:01)
-
-For further information on how to interpret these results or to get
-a copy of the MEME software please access http://meme.sdsc.edu.
-
-This file may be used as input to the MAST algorithm for searching
-sequence databases for matches to groups of motifs.  MAST is available
-for interactive use and downloading at http://meme.sdsc.edu.
-********************************************************************************
-
-
-********************************************************************************
-REFERENCE
-********************************************************************************
-If you use this program in your research, please cite:
-
-Timothy L. Bailey and Charles Elkan,
-"Fitting a mixture model by expectation maximization to discover
-motifs in biopolymers", Proceedings of the Second International
-Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
-AAAI Press, Menlo Park, California, 1994.
-********************************************************************************
-
-
-********************************************************************************
-TRAINING SET
-********************************************************************************
-DATAFILE= INO_up800.s
-ALPHABET= ACGT
-Sequence name            Weight Length  Sequence name            Weight Length  
--------------            ------ ------  -------------            ------ ------  
-CHO1                     1.0000    800  CHO2                     1.0000    800  
-FAS1                     1.0000    800  FAS2                     1.0000    800  
-ACC1                     1.0000    800  INO1                     1.0000    800  
-OPI3                     1.0000    800  
-********************************************************************************
-
-********************************************************************************
-COMMAND LINE SUMMARY
-********************************************************************************
-This information can also be useful in the event you wish to report a
-problem with the MEME software.
-
-command: meme -mod oops -dna -revcomp -nmotifs 2 -bfile yeast.nc.6.freq INO_up800.s 
-
-model:  mod=          oops    nmotifs=         2    evt=           inf
-object function=  E-value of product of p-values
-width:  minw=            8    maxw=           50    minic=        0.00
-width:  wg=             11    ws=              1    endgaps=       yes
-nsites: minsites=        7    maxsites=        7    wnsites=       0.8
-theta:  prob=            1    spmap=         uni    spfuzz=        0.5
-em:     prior=   dirichlet    b=            0.01    maxiter=        50
-        distance=    1e-05
-data:   n=            5600    N=               7
-strands: + -
-sample: seed=            0    seqfrac=         1
-Letter frequencies in dataset:
-A 0.304 C 0.196 G 0.196 T 0.304 
-Background letter frequencies (from yeast.nc.6.freq):
-A 0.324 C 0.176 G 0.176 T 0.324 
-********************************************************************************
-
-
-********************************************************************************
-MOTIF  1	width =   12   sites =   7   llr = 95   E-value = 2.0e-001
-********************************************************************************
---------------------------------------------------------------------------------
-	Motif 1 Description
---------------------------------------------------------------------------------
-Simplified        A  :::9:a::::3:
-pos.-specific     C  ::a:9:11691a
-probability       G  ::::1::94:4:
-matrix            T  aa:1::9::11:
-
-         bits    2.5   *        *
-                 2.3   *        *
-                 2.0   * *  *   *
-                 1.8   * *  * * *
-Information      1.5 *** ** *** *
-content          1.3 *** ****** *
-(19.5 bits)      1.0 ********** *
-                 0.8 ********** *
-                 0.5 ********** *
-                 0.3 ************
-                 0.0 ------------
-
-Multilevel           TTCACATGCCGC
-consensus                    G A 
-sequence                         
-                                 
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 sites sorted by position p-value
---------------------------------------------------------------------------------
-Sequence name            Strand  Start   P-value                Site  
--------------            ------  ----- ---------            ------------
-INO1                         -    620  1.85e-08 GACAATACTT TTCACATGCCGC ATTTAGCCGC
-FAS1                         +     95  1.85e-08 GGCCAAAAAC TTCACATGCCGC CCAGCCAAGC
-ACC1                         +     83  1.52e-07 CGTTAAAATC TTCACATGGCCC GGCCGCGCGC
-CHO2                         +    354  2.52e-07 TGCCACACTT TTCTCATGCCGC ATTCATTATT
-CHO1                         +    611  4.23e-07 ACTTTGAACG TTCACACGGCAC CCTCACGCCT
-FAS2                         +    567  9.43e-07 CTCCCGCGTT TTCACATGCTAC CTCATTCGCC
-OPI3                         +    340  3.32e-06 CCAAGCCTCC TTCAGATCGCTC TTGTCGACCG
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 block diagrams
---------------------------------------------------------------------------------
-SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-INO1                              1.8e-08  619_[-1]_169
-FAS1                              1.8e-08  94_[+1]_694
-ACC1                              1.5e-07  82_[+1]_706
-CHO2                              2.5e-07  353_[+1]_435
-CHO1                              4.2e-07  610_[+1]_178
-FAS2                              9.4e-07  566_[+1]_222
-OPI3                              3.3e-06  339_[+1]_449
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 in BLOCKS format
---------------------------------------------------------------------------------
-BL   MOTIF 1 width=12 seqs=7
-INO1                     (  620) TTCACATGCCGC  1 
-FAS1                     (   95) TTCACATGCCGC  1 
-ACC1                     (   83) TTCACATGGCCC  1 
-CHO2                     (  354) TTCTCATGCCGC  1 
-CHO1                     (  611) TTCACACGGCAC  1 
-FAS2                     (  567) TTCACATGCTAC  1 
-OPI3                     (  340) TTCAGATCGCTC  1 
-//
-
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 position-specific scoring matrix
---------------------------------------------------------------------------------
-log-odds matrix: alength= 4 w= 12 n= 5523 bayes= 9.62205 E= 2.0e-001 
-  -945   -945   -945    162 
-  -945   -945   -945    162 
-  -945    251   -945   -945 
-   140   -945   -945   -118 
-  -945    229    -30   -945 
-   162   -945   -945   -945 
-  -945    -30   -945    140 
-  -945    -30    229   -945 
-  -945    170    129   -945 
-  -945    229   -945   -118 
-   -18    -30    129   -118 
-  -945    251   -945   -945 
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 position-specific probability matrix
---------------------------------------------------------------------------------
-letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 2.0e-001 
- 0.000000  0.000000  0.000000  1.000000 
- 0.000000  0.000000  0.000000  1.000000 
- 0.000000  1.000000  0.000000  0.000000 
- 0.857143  0.000000  0.000000  0.142857 
- 0.000000  0.857143  0.142857  0.000000 
- 1.000000  0.000000  0.000000  0.000000 
- 0.000000  0.142857  0.000000  0.857143 
- 0.000000  0.142857  0.857143  0.000000 
- 0.000000  0.571429  0.428571  0.000000 
- 0.000000  0.857143  0.000000  0.142857 
- 0.285714  0.142857  0.428571  0.142857 
- 0.000000  1.000000  0.000000  0.000000 
---------------------------------------------------------------------------------
-
-
-
-
-
-Time 20.91 secs.
-
-********************************************************************************
-
-
-********************************************************************************
-MOTIF  2	width =   10   sites =   7   llr = 81   E-value = 1.1e+002
-********************************************************************************
---------------------------------------------------------------------------------
-	Motif 2 Description
---------------------------------------------------------------------------------
-Simplified        A  ::1:::9:6:
-pos.-specific     C  :a:::a:911
-probability       G  3:1aa:1:19
-matrix            T  7:7::::11:
-
-         bits    2.5  * ***    
-                 2.3  * ***    
-                 2.0  * ***   *
-                 1.8  * *** * *
-Information      1.5  * *** * *
-content          1.3  * ***** *
-(16.7 bits)      1.0 ** ***** *
-                 0.8 ** ***** *
-                 0.5 ******** *
-                 0.3 **********
-                 0.0 ----------
-
-Multilevel           TCTGGCACAG
-consensus            G         
-sequence                       
-                               
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 sites sorted by position p-value
---------------------------------------------------------------------------------
-Sequence name            Strand  Start   P-value               Site 
--------------            ------  ----- ---------            ----------
-OPI3                         -    186  3.24e-07 GAAAACCAGA TCTGGCACAG ACCGTTGTCA
-ACC1                         +    232  3.24e-07 CCAGTCGTAT TCTGGCACAG TATAGCCTAG
-CHO1                         -    559  3.24e-07 ATATTCAGTG TCTGGCACAG AAGTCTGCAC
-INO1                         -    283  5.29e-06 ACGGTCTACG GCGGGCGCAG TCGCATGTCT
-FAS1                         +     44  6.25e-06 TACACGAGGT GCAGGCACGG TTCACTACTC
-FAS2                         -    185  8.48e-06 TTCTTGCTTT TCTGGCACTC TTGACGGCTT
-CHO2                         -    413  8.48e-06 TTTTGCCGTT TCTGGCATCG CCGTTCATTT
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 block diagrams
---------------------------------------------------------------------------------
-SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-OPI3                              3.2e-07  185_[-2]_605
-ACC1                              3.2e-07  231_[+2]_559
-CHO1                              3.2e-07  558_[-2]_232
-INO1                              5.3e-06  282_[-2]_508
-FAS1                              6.3e-06  43_[+2]_747
-FAS2                              8.5e-06  184_[-2]_606
-CHO2                              8.5e-06  412_[-2]_378
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 in BLOCKS format
---------------------------------------------------------------------------------
-BL   MOTIF 2 width=10 seqs=7
-OPI3                     (  186) TCTGGCACAG  1 
-ACC1                     (  232) TCTGGCACAG  1 
-CHO1                     (  559) TCTGGCACAG  1 
-INO1                     (  283) GCGGGCGCAG  1 
-FAS1                     (   44) GCAGGCACGG  1 
-FAS2                     (  185) TCTGGCACTC  1 
-CHO2                     (  413) TCTGGCATCG  1 
-//
-
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 position-specific scoring matrix
---------------------------------------------------------------------------------
-log-odds matrix: alength= 4 w= 10 n= 5537 bayes= 9.62571 E= 1.1e+002 
-  -945   -945     70    114 
-  -945    251   -945   -945 
-  -118   -945    -30    114 
-  -945   -945    251   -945 
-  -945   -945    251   -945 
-  -945    251   -945   -945 
-   140   -945    -30   -945 
-  -945    229   -945   -118 
-    82    -30    -30   -118 
-  -945    -30    229   -945 
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 position-specific probability matrix
---------------------------------------------------------------------------------
-letter-probability matrix: alength= 4 w= 10 nsites= 7 E= 1.1e+002 
- 0.000000  0.000000  0.285714  0.714286 
- 0.000000  1.000000  0.000000  0.000000 
- 0.142857  0.000000  0.142857  0.714286 
- 0.000000  0.000000  1.000000  0.000000 
- 0.000000  0.000000  1.000000  0.000000 
- 0.000000  1.000000  0.000000  0.000000 
- 0.857143  0.000000  0.142857  0.000000 
- 0.000000  0.857143  0.000000  0.142857 
- 0.571429  0.142857  0.142857  0.142857 
- 0.000000  0.142857  0.857143  0.000000 
---------------------------------------------------------------------------------
-
-
-
-
-
-Time 41.19 secs.
-
-********************************************************************************
-
-
-********************************************************************************
-SUMMARY OF MOTIFS
-********************************************************************************
-
---------------------------------------------------------------------------------
-	Combined block diagrams: non-overlapping sites with p-value < 0.0001
---------------------------------------------------------------------------------
-SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-CHO1                             5.44e-06  152_[+2(1.10e-05)]_396_[-2(3.24e-07)]_42_[+1(4.23e-07)]_17_[+1(1.23e-05)]_149
-CHO2                             6.96e-05  353_[+1(2.52e-07)]_47_[-2(8.48e-06)]_378
-FAS1                             4.61e-06  43_[+2(6.25e-06)]_41_[+1(1.85e-08)]_694
-FAS2                             2.34e-04  184_[-2(8.48e-06)]_372_[+1(9.43e-07)]_222
-ACC1                             2.09e-06  82_[+1(1.52e-07)]_137_[+2(3.24e-07)]_559
-INO1                             3.95e-06  282_[-2(5.29e-06)]_327_[-1(1.85e-08)]_55_[+1(7.55e-06)]_102
-OPI3                             3.70e-05  185_[-2(3.24e-07)]_144_[+1(3.32e-06)]_449
---------------------------------------------------------------------------------
-
-********************************************************************************
-
-
-********************************************************************************
-Stopped because nmotifs = 2 reached.
-********************************************************************************
-
-CPU: pmgm2
-
-********************************************************************************
diff --git a/Tests/Motif/meme.out b/Tests/Motif/meme.out
deleted file mode 100644
--- a/Tests/Motif/meme.out
+++ /dev/null
@@ -1,225 +0,0 @@
-********************************************************************************
-MEME - Motif discovery tool
-********************************************************************************
-MEME version 3.5.7 (Release date: 2007-12-17 16:56:19 -0800 (Mon, 17 Dec 2007))
-
-For further information on how to interpret these results or to get
-a copy of the MEME software please access http://meme.nbcr.net.
-
-This file may be used as input to the MAST algorithm for searching
-sequence databases for matches to groups of motifs.  MAST is available
-for interactive use and downloading at http://meme.nbcr.net.
-********************************************************************************
-
-
-********************************************************************************
-REFERENCE
-********************************************************************************
-If you use this program in your research, please cite:
-
-Timothy L. Bailey and Charles Elkan,
-"Fitting a mixture model by expectation maximization to discover
-motifs in biopolymers", Proceedings of the Second International
-Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
-AAAI Press, Menlo Park, California, 1994.
-********************************************************************************
-
-
-********************************************************************************
-TRAINING SET
-********************************************************************************
-DATAFILE= test.fa
-ALPHABET= ACGT
-Sequence name            Weight Length  Sequence name            Weight Length  
--------------            ------ ------  -------------            ------ ------  
-SEQ1;                    1.0000    200  SEQ2;                    1.0000    200  
-SEQ3;                    1.0000    200  SEQ4;                    1.0000    200  
-SEQ5;                    1.0000    200  SEQ6;                    1.0000    200  
-SEQ7;                    1.0000    200  SEQ8;                    1.0000    200  
-SEQ9;                    1.0000    200  SEQ10;                   1.0000    200  
-********************************************************************************
-
-********************************************************************************
-COMMAND LINE SUMMARY
-********************************************************************************
-This information can also be useful in the event you wish to report a
-problem with the MEME software.
-
-command: meme test.fa -dna -w 10 -dir /home/bartek/MetaMotif/meme 
-
-model:  mod=         zoops    nmotifs=         1    evt=           inf
-object function=  E-value of product of p-values
-width:  minw=           10    maxw=           10    minic=        0.00
-width:  wg=             11    ws=              1    endgaps=       yes
-nsites: minsites=        2    maxsites=       10    wnsites=       0.8
-theta:  prob=            1    spmap=         uni    spfuzz=        0.5
-em:     prior=   dirichlet    b=            0.01    maxiter=        50
-        distance=    1e-05
-data:   n=            2000    N=              10
-strands: +
-sample: seed=            0    seqfrac=         1
-Letter frequencies in dataset:
-A 0.255 C 0.235 G 0.261 T 0.249 
-Background letter frequencies (from dataset with add-one prior applied):
-A 0.255 C 0.236 G 0.260 T 0.249 
-********************************************************************************
-
-
-********************************************************************************
-MOTIF  1	width =   10   sites =  10   llr = 140   E-value = 1.1e-022
-********************************************************************************
---------------------------------------------------------------------------------
-	Motif 1 Description
---------------------------------------------------------------------------------
-Simplified        A  :::aa::::a
-pos.-specific     C  a:a:::a:::
-probability       G  :::::::a::
-matrix            T  :a:::a::a:
-
-         bits    2.1 ***  ** * 
-                 1.9 **********
-                 1.7 **********
-                 1.5 **********
-Information      1.3 **********
-content          1.0 **********
-(20.1 bits)      0.8 **********
-                 0.6 **********
-                 0.4 **********
-                 0.2 **********
-                 0.0 ----------
-
-Multilevel           CTCAATCGTA
-consensus                      
-sequence                       
-                               
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 sites sorted by position p-value
---------------------------------------------------------------------------------
-Sequence name             Start   P-value               Site 
--------------             ----- ---------            ----------
-SEQ10;                        3  8.71e-07         TT CTCAATCGTA GAGTATGCTT
-SEQ9;                        93  8.71e-07 CGCCTAGAAA CTCAATCGTA GAGTATCACG
-SEQ8;                       172  8.71e-07 CCCGGAGTAT CTCAATCGTA GATGAATACC
-SEQ7;                       177  8.71e-07 AAGTCTTTGA CTCAATCGTA GACCCAACAC
-SEQ6;                       105  8.71e-07 GTCAGCCGGT CTCAATCGTA GATCAGAGGC
-SEQ5;                       185  8.71e-07 ACGGGCAAGC CTCAATCGTA GAGGAT    
-SEQ4;                       173  8.71e-07 GTTCGAGAGC CTCAATCGTA GATAACCTCT
-SEQ3;                       112  8.71e-07 GTTATATTGG CTCAATCGTA GATGAAACCA
-SEQ2;                       172  8.71e-07 AAGCGTCGTG CTCAATCGTA GATAACAGAG
-SEQ1;                        52  8.71e-07 CTTTACTCGG CTCAATCGTA GAGGCGGTGC
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 block diagrams
---------------------------------------------------------------------------------
-SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-SEQ10;                            8.7e-07  2_[1]_188
-SEQ9;                             8.7e-07  92_[1]_98
-SEQ8;                             8.7e-07  171_[1]_19
-SEQ7;                             8.7e-07  176_[1]_14
-SEQ6;                             8.7e-07  104_[1]_86
-SEQ5;                             8.7e-07  184_[1]_6
-SEQ4;                             8.7e-07  172_[1]_18
-SEQ3;                             8.7e-07  111_[1]_79
-SEQ2;                             8.7e-07  171_[1]_19
-SEQ1;                             8.7e-07  51_[1]_139
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 in BLOCKS format
---------------------------------------------------------------------------------
-BL   MOTIF 1 width=10 seqs=10
-SEQ10;                   (    3) CTCAATCGTA  1 
-SEQ9;                    (   93) CTCAATCGTA  1 
-SEQ8;                    (  172) CTCAATCGTA  1 
-SEQ7;                    (  177) CTCAATCGTA  1 
-SEQ6;                    (  105) CTCAATCGTA  1 
-SEQ5;                    (  185) CTCAATCGTA  1 
-SEQ4;                    (  173) CTCAATCGTA  1 
-SEQ3;                    (  112) CTCAATCGTA  1 
-SEQ2;                    (  172) CTCAATCGTA  1 
-SEQ1;                    (   52) CTCAATCGTA  1 
-//
-
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 position-specific scoring matrix
---------------------------------------------------------------------------------
-log-odds matrix: alength= 4 w= 10 n= 1910 bayes= 8.51691 E= 1.1e-022 
-  -997    208   -997   -997 
-  -997   -997   -997    200 
-  -997    208   -997   -997 
-   197   -997   -997   -997 
-   197   -997   -997   -997 
-  -997   -997   -997    200 
-  -997    208   -997   -997 
-  -997   -997    194   -997 
-  -997   -997   -997    200 
-   197   -997   -997   -997 
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 position-specific probability matrix
---------------------------------------------------------------------------------
-letter-probability matrix: alength= 4 w= 10 nsites= 10 E= 1.1e-022 
- 0.000000  1.000000  0.000000  0.000000 
- 0.000000  0.000000  0.000000  1.000000 
- 0.000000  1.000000  0.000000  0.000000 
- 1.000000  0.000000  0.000000  0.000000 
- 1.000000  0.000000  0.000000  0.000000 
- 0.000000  0.000000  0.000000  1.000000 
- 0.000000  1.000000  0.000000  0.000000 
- 0.000000  0.000000  1.000000  0.000000 
- 0.000000  0.000000  0.000000  1.000000 
- 1.000000  0.000000  0.000000  0.000000 
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 regular expression
---------------------------------------------------------------------------------
-CTCAATCGTA
---------------------------------------------------------------------------------
-
-
-
-
-Time  0.26 secs.
-
-********************************************************************************
-
-
-********************************************************************************
-SUMMARY OF MOTIFS
-********************************************************************************
-
---------------------------------------------------------------------------------
-	Combined block diagrams: non-overlapping sites with p-value < 0.0001
---------------------------------------------------------------------------------
-SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-SEQ1;                            1.66e-04  51_[1(8.71e-07)]_139
-SEQ2;                            1.66e-04  171_[1(8.71e-07)]_19
-SEQ3;                            1.66e-04  111_[1(8.71e-07)]_79
-SEQ4;                            1.66e-04  172_[1(8.71e-07)]_18
-SEQ5;                            1.66e-04  184_[1(8.71e-07)]_6
-SEQ6;                            1.66e-04  104_[1(8.71e-07)]_86
-SEQ7;                            1.66e-04  176_[1(8.71e-07)]_14
-SEQ8;                            1.66e-04  171_[1(8.71e-07)]_19
-SEQ9;                            1.66e-04  92_[1(8.71e-07)]_98
-SEQ10;                           1.66e-04  2_[1(8.71e-07)]_188
---------------------------------------------------------------------------------
-
-********************************************************************************
-
-
-********************************************************************************
-Stopped because nmotifs = 1 reached.
-********************************************************************************
-
-CPU: pc-arendt9
-
-********************************************************************************
diff --git a/Tests/Motif/meme.protein.oops.txt b/Tests/Motif/meme.protein.oops.txt
deleted file mode 100644
--- a/Tests/Motif/meme.protein.oops.txt
+++ /dev/null
@@ -1,630 +0,0 @@
-********************************************************************************
-MEME - Motif discovery tool
-********************************************************************************
-MEME version 3.0 (Release date: 2004/08/18 09:07:01)
-
-For further information on how to interpret these results or to get
-a copy of the MEME software please access http://meme.sdsc.edu.
-
-This file may be used as input to the MAST algorithm for searching
-sequence databases for matches to groups of motifs.  MAST is available
-for interactive use and downloading at http://meme.sdsc.edu.
-********************************************************************************
-
-
-********************************************************************************
-REFERENCE
-********************************************************************************
-If you use this program in your research, please cite:
-
-Timothy L. Bailey and Charles Elkan,
-"Fitting a mixture model by expectation maximization to discover
-motifs in biopolymers", Proceedings of the Second International
-Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
-AAAI Press, Menlo Park, California, 1994.
-********************************************************************************
-
-
-********************************************************************************
-TRAINING SET
-********************************************************************************
-DATAFILE= adh.s
-ALPHABET= ACDEFGHIKLMNPQRSTVWY
-Sequence name            Weight Length  Sequence name            Weight Length  
--------------            ------ ------  -------------            ------ ------  
-2BHD_STREX               1.0000    255  3BHD_COMTE               1.0000    253  
-ADH_DROME                1.0000    255  AP27_MOUSE               1.0000    244  
-BA72_EUBSP               1.0000    249  BDH_HUMAN                1.0000    343  
-BPHB_PSEPS               1.0000    275  BUDC_KLETE               1.0000    241  
-DHES_HUMAN               1.0000    327  DHGB_BACME               1.0000    262  
-DHII_HUMAN               1.0000    292  DHMA_FLAS1               1.0000    270  
-ENTA_ECOLI               1.0000    248  FIXR_BRAJA               1.0000    278  
-GUTD_ECOLI               1.0000    259  HDE_CANTR                1.0000    906  
-HDHA_ECOLI               1.0000    255  LIGD_PSEPA               1.0000    305  
-NODG_RHIME               1.0000    245  RIDH_KLEAE               1.0000    249  
-YINL_LISMO               1.0000    248  YRTP_BACSU               1.0000    238  
-CSGA_MYXXA               1.0000    166  DHB2_HUMAN               1.0000    387  
-DHB3_HUMAN               1.0000    310  DHCA_HUMAN               1.0000    276  
-FABI_ECOLI               1.0000    262  FVT1_HUMAN               1.0000    332  
-HMTR_LEIMA               1.0000    287  MAS1_AGRRA               1.0000    476  
-PCR_PEA                  1.0000    399  RFBB_NEIGO               1.0000    346  
-YURA_MYXXA               1.0000    258  
-********************************************************************************
-
-********************************************************************************
-COMMAND LINE SUMMARY
-********************************************************************************
-This information can also be useful in the event you wish to report a
-problem with the MEME software.
-
-command: meme adh.s -mod oops -protein -nmotifs 2 
-
-model:  mod=          oops    nmotifs=         2    evt=           inf
-object function=  E-value of product of p-values
-width:  minw=            8    maxw=           50    minic=        0.00
-width:  wg=             11    ws=              1    endgaps=       yes
-nsites: minsites=       33    maxsites=       33    wnsites=       0.8
-theta:  prob=            1    spmap=         pam    spfuzz=        120
-em:     prior=        dmix    b=               0    maxiter=        50
-        distance=    1e-05
-data:   n=            9996    N=              33
-
-sample: seed=            0    seqfrac=         1
-Dirichlet mixture priors file: prior30.plib
-Letter frequencies in dataset:
-A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052 
-L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083 
-W 0.010 Y 0.027 
-Background letter frequencies (from dataset with add-one prior applied):
-A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052 
-L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083 
-W 0.010 Y 0.027 
-********************************************************************************
-
-
-********************************************************************************
-MOTIF  1	width =   29   sites =  33   llr = 1118   E-value = 3.6e-165
-********************************************************************************
---------------------------------------------------------------------------------
-	Motif 1 Description
---------------------------------------------------------------------------------
-Simplified        A  :162:56112:1:215:::4:::::::11
-pos.-specific     C  :1:::::::::::1:::::::::::1:1:
-probability       D  ::::::::1:::1::::2:::::::::::
-matrix            E  ::::::::1:::21:::5:111:::::::
-                  F  :::::31:::2:::::1::::::::::::
-                  G  :2:::13::4:::1:1:::11:5:1:11:
-                  H  :::::::::1::1:::1::::1:::::::
-                  I  :::::::11:::::::::1::::5:2:13
-                  K  ::::9:::1:::2:::1::121::1:1::
-                  L  :::::::31:6:1:5:215::1:::::12
-                  M  ::1::::1:2:1::2:1:1::::::::::
-                  N  :::::::::1::::::::::::2:1:41:
-                  P  ::::::::::::::::::::3::::::::
-                  Q  ::::::::::::1::11:::11:::::::
-                  R  ::::::::2:::3::22::21:1:4:1::
-                  S  :426::1:11:213:::::1:11:::21:
-                  T  :1:2::::1::3:1::::::11::1:11:
-                  V  :::::::41::2:1::1:1::::316123
-                  W  :::::1:::::::::::::::::::::::
-                  Y  9:::::::::::::::::2::2:::::::
-
-         bits    6.7                              
-                 6.0                              
-                 5.4                              
-                 4.7 *                            
-Information      4.0 *   *                        
-content          3.4 *   *                        
-(48.9 bits)      2.7 *  **     *                  
-                 2.0 *  ****   *   *  *     * *   
-                 1.3 ******** ******* ** * ***** *
-                 0.7 *****************************
-                 0.0 -----------------------------
-
-Multilevel           YSASKAAVxGLTRSLAxELAPxGIRVNVV
-consensus                 FGL  FSE MR D     V    I
-sequence                                          
-                                                  
-                                                  
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 sites sorted by position p-value
---------------------------------------------------------------------------------
-Sequence name             Start   P-value                        Site           
--------------             ----- ---------            -----------------------------
-YRTP_BACSU                  155  1.64e-22 GQRGAAVTSA YSASKFAVLGLTESLMQEVRKHNIRVSAL TPSTVASDMS
-AP27_MOUSE                  149  6.32e-22 AHVTFPNLIT YSSTKGAMTMLTKAMAMELGPHKIRVNSV NPTVVLTDMG
-NODG_RHIME                  152  1.13e-21 GAIGNPGQTN YCASKAGMIGFSKSLAQEIATRNITVNCV APGFIESAMT
-BUDC_KLETE                  152  4.04e-21 GHVGNPELAV YSSSKFAVRGLTQTAARDLAPLGITVNGF CPGIVKTPMW
-FIXR_BRAJA                  189  6.12e-21 SRVHPFAGSA YATSKAALASLTRELAHDYAPHGIRVNAI APGEIRTDML
-DHGB_BACME                  160  7.52e-20 WKIPWPLFVH YAASKGGMKLMTETLALEYAPKGIRVNNI GPGAINTPIN
-HMTR_LEIMA                  193  3.35e-19 TNQPLLGYTI YTMAKGALEGLTRSAALELAPLQIRVNGV GPGLSVLVDD
-YURA_MYXXA                  160  4.82e-19 AGFRGLPATR YSASKAFLSTFMESLRVDLRGTGVRVTCI YPGFVKSELT
-GUTD_ECOLI                  154  4.82e-19 GKVGSKHNSG YSAAKFGGVGLTQSLALDLAEYGITVHSL MLGNLLKSPM
-2BHD_STREX                  152  1.11e-18 GLMGLALTSS YGASKWGVRGLSKLAAVELGTDRIRVNSV HPGMTYTPMT
-HDHA_ECOLI                  159  1.25e-18 AENKNINMTS YASSKAAASHLVRNMAFDLGEKNIRVNGI APGAILTDAL
-DHB2_HUMAN                  232  2.23e-18 GGAPMERLAS YGSSKAAVTMFSSVMRLELSKWGIKVASI QPGGFLTNIA
-DHMA_FLAS1                  165  5.53e-18 SFMAEPEAAA YVAAKGGVAMLTRAMAVDLARHGILVNMI APGPVDVTGN
-HDE_CANTR                   467  9.65e-18 GIYGNFGQAN YSSSKAGILGLSKTMAIEGAKNNIKVNIV APHAETAMTL
-FVT1_HUMAN                  186  2.86e-17 GQLGLFGFTA YSASKFAIRGLAEALQMEVKPYNVYITVA YPPDTDTPGF
-BDH_HUMAN                   208  8.20e-17 GRMANPARSP YCITKFGVEAFSDCLRYEMYPLGVKVSVV EPGNFIAATS
-RIDH_KLEAE                  160  9.09e-17 GVVPVIWEPV YTASKFAVQAFVHTTRRQVAQYGVRVGAV LPGPVVTALL
-DHES_HUMAN                  155  1.37e-16 GLMGLPFNDV YCASKFALEGLCESLAVLLLPFGVHLSLI ECGPVHTAFM
-BA72_EUBSP                  157  2.52e-16 GIFGSLSGVG YPASKASVIGLTHGLGREIIRKNIRVVGV APGVVNTDMT
-LIGD_PSEPA                  157  1.21e-15 GFMGSALAGP YSAAKAASINLMEGYRQGLEKYGIGVSVC TPANIKSNIA
-DHII_HUMAN                  183  1.61e-15 GKVAYPMVAA YSASKFALDGFFSSIRKEYSVSRVNVSIT LCVLGLIDTE
-ENTA_ECOLI                  144  1.77e-15 AHTPRIGMSA YGASKAALKSLALSVGLELAGSGVRCNVV SPGSTDTDMQ
-3BHD_COMTE                  151  7.81e-15 SWLPIEQYAG YSASKAAVSALTRAAALSCRKQGYAIRVN SIHPDGIYTP
-DHB3_HUMAN                  198  8.55e-15 ALFPWPLYSM YSASKAFVCAFSKALQEEYKAKEVIIQVL TPYAVSTAMT
-RFBB_NEIGO                  165  1.47e-14 ETTPYAPSSP YSASKAAADHLVRAWQRTYRLPSIVSNCS NNYGPRQFPE
-YINL_LISMO                  154  3.24e-14 GLKAYPGGAV YGATKWAVRDLMEVLRMESAQEGTNIRTA TIYPAAINTE
-BPHB_PSEPS                  153  1.80e-12 GFYPNGGGPL YTAAKQAIVGLVRELAFELAPYVRVNGVG PGGMNSDMRG
-CSGA_MYXXA                   88  2.10e-12 AANTDGGAYA YRMSKAALNMAVRSMSTDLRPEGFVTVLL HPGWVQTDMG
-FABI_ECOLI                  159  4.15e-12 AERAIPNYNV MGLAKASLEANVRYMANAMGPEGVRVNAI SAGPIRTLAA
-ADH_DROME                   152  5.20e-12 GFNAIYQVPV YSGTKAAVVNFTSSLAKLAPITGVTAYTV NPGITRTTLV
-DHCA_HUMAN                  193  4.80e-10 HQKEGWPSSA YGVTKIGVTVLSRIHARKLSEQRKGDKIL LNACCPGWVR
-PCR_PEA                      26  2.77e-08 PKEGKIGASL KDSTLFGVSSLSDSLKGDFTSSALRCKEL RQKVGAVRAE
-MAS1_AGRRA                  349  5.72e-08 VDYQRFHLQW YINCVAPLRMTELCLPHLYETGSGRIVNI NSMSGQRVLN
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 block diagrams
---------------------------------------------------------------------------------
-SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-YRTP_BACSU                        1.6e-22  154_[1]_55
-AP27_MOUSE                        6.3e-22  148_[1]_67
-NODG_RHIME                        1.1e-21  151_[1]_65
-BUDC_KLETE                          4e-21  151_[1]_61
-FIXR_BRAJA                        6.1e-21  188_[1]_61
-DHGB_BACME                        7.5e-20  159_[1]_74
-HMTR_LEIMA                        3.4e-19  192_[1]_66
-YURA_MYXXA                        4.8e-19  159_[1]_70
-GUTD_ECOLI                        4.8e-19  153_[1]_77
-2BHD_STREX                        1.1e-18  151_[1]_75
-HDHA_ECOLI                        1.2e-18  158_[1]_68
-DHB2_HUMAN                        2.2e-18  231_[1]_127
-DHMA_FLAS1                        5.5e-18  164_[1]_77
-HDE_CANTR                         9.7e-18  466_[1]_411
-FVT1_HUMAN                        2.9e-17  185_[1]_118
-BDH_HUMAN                         8.2e-17  207_[1]_107
-RIDH_KLEAE                        9.1e-17  159_[1]_61
-DHES_HUMAN                        1.4e-16  154_[1]_144
-BA72_EUBSP                        2.5e-16  156_[1]_64
-LIGD_PSEPA                        1.2e-15  156_[1]_120
-DHII_HUMAN                        1.6e-15  182_[1]_81
-ENTA_ECOLI                        1.8e-15  143_[1]_76
-3BHD_COMTE                        7.8e-15  150_[1]_74
-DHB3_HUMAN                        8.6e-15  197_[1]_84
-RFBB_NEIGO                        1.5e-14  164_[1]_153
-YINL_LISMO                        3.2e-14  153_[1]_66
-BPHB_PSEPS                        1.8e-12  152_[1]_94
-CSGA_MYXXA                        2.1e-12  87_[1]_50
-FABI_ECOLI                        4.2e-12  158_[1]_75
-ADH_DROME                         5.2e-12  151_[1]_75
-DHCA_HUMAN                        4.8e-10  192_[1]_55
-PCR_PEA                           2.8e-08  25_[1]_345
-MAS1_AGRRA                        5.7e-08  348_[1]_99
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 in BLOCKS format
---------------------------------------------------------------------------------
-BL   MOTIF 1 width=29 seqs=33
-YRTP_BACSU               (  155) YSASKFAVLGLTESLMQEVRKHNIRVSAL  1 
-AP27_MOUSE               (  149) YSSTKGAMTMLTKAMAMELGPHKIRVNSV  1 
-NODG_RHIME               (  152) YCASKAGMIGFSKSLAQEIATRNITVNCV  1 
-BUDC_KLETE               (  152) YSSSKFAVRGLTQTAARDLAPLGITVNGF  1 
-FIXR_BRAJA               (  189) YATSKAALASLTRELAHDYAPHGIRVNAI  1 
-DHGB_BACME               (  160) YAASKGGMKLMTETLALEYAPKGIRVNNI  1 
-HMTR_LEIMA               (  193) YTMAKGALEGLTRSAALELAPLQIRVNGV  1 
-YURA_MYXXA               (  160) YSASKAFLSTFMESLRVDLRGTGVRVTCI  1 
-GUTD_ECOLI               (  154) YSAAKFGGVGLTQSLALDLAEYGITVHSL  1 
-2BHD_STREX               (  152) YGASKWGVRGLSKLAAVELGTDRIRVNSV  1 
-HDHA_ECOLI               (  159) YASSKAAASHLVRNMAFDLGEKNIRVNGI  1 
-DHB2_HUMAN               (  232) YGSSKAAVTMFSSVMRLELSKWGIKVASI  1 
-DHMA_FLAS1               (  165) YVAAKGGVAMLTRAMAVDLARHGILVNMI  1 
-HDE_CANTR                (  467) YSSSKAGILGLSKTMAIEGAKNNIKVNIV  1 
-FVT1_HUMAN               (  186) YSASKFAIRGLAEALQMEVKPYNVYITVA  1 
-BDH_HUMAN                (  208) YCITKFGVEAFSDCLRYEMYPLGVKVSVV  1 
-RIDH_KLEAE               (  160) YTASKFAVQAFVHTTRRQVAQYGVRVGAV  1 
-DHES_HUMAN               (  155) YCASKFALEGLCESLAVLLLPFGVHLSLI  1 
-BA72_EUBSP               (  157) YPASKASVIGLTHGLGREIIRKNIRVVGV  1 
-LIGD_PSEPA               (  157) YSAAKAASINLMEGYRQGLEKYGIGVSVC  1 
-DHII_HUMAN               (  183) YSASKFALDGFFSSIRKEYSVSRVNVSIT  1 
-ENTA_ECOLI               (  144) YGASKAALKSLALSVGLELAGSGVRCNVV  1 
-3BHD_COMTE               (  151) YSASKAAVSALTRAAALSCRKQGYAIRVN  1 
-DHB3_HUMAN               (  198) YSASKAFVCAFSKALQEEYKAKEVIIQVL  1 
-RFBB_NEIGO               (  165) YSASKAAADHLVRAWQRTYRLPSIVSNCS  1 
-YINL_LISMO               (  154) YGATKWAVRDLMEVLRMESAQEGTNIRTA  1 
-BPHB_PSEPS               (  153) YTAAKQAIVGLVRELAFELAPYVRVNGVG  1 
-CSGA_MYXXA               (   88) YRMSKAALNMAVRSMSTDLRPEGFVTVLL  1 
-FABI_ECOLI               (  159) MGLAKASLEANVRYMANAMGPEGVRVNAI  1 
-ADH_DROME                (  152) YSGTKAAVVNFTSSLAKLAPITGVTAYTV  1 
-DHCA_HUMAN               (  193) YGVTKIGVTVLSRIHARKLSEQRKGDKIL  1 
-PCR_PEA                  (   26) KDSTLFGVSSLSDSLKGDFTSSALRCKEL  1 
-MAS1_AGRRA               (  349) YINCVAPLRMTELCLPHLYETGSGRIVNI  1 
-//
-
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 position-specific scoring matrix
---------------------------------------------------------------------------------
-log-odds matrix: alength= 20 w= 29 n= 9072 bayes= 8.09755 E= 3.6e-165 
-  -716   -497   -698   -691   -172   -730   -304   -562    -80   -507     12   -550   -661   -513   -563   -605   -625   -609   -217    508 
-   -51    240    -90   -249   -334     53   -232   -106   -219   -337   -278   -209    -72   -192    -79    276     81   -153   -332   -306 
-   257    -64   -390   -343   -320   -160   -326   -144   -343   -193     26   -120   -436   -313   -349     86   -117   -123   -309   -358 
-    57    116   -511   -541   -504   -420   -453   -532   -481   -549   -470   -353   -434   -438   -470    325    161   -493   -485   -492 
-  -433   -317   -482   -429   -524   -520   -342   -409    413   -326   -416   -349   -435   -343    -57   -433   -392   -321   -375   -453 
-   205   -259   -559   -505    282     34   -356    -70   -475   -333   -299   -445   -475     -1   -468   -326   -334   -312    255   -226 
-   235   -273   -630   -622     68    154   -557   -603   -636   -616   -544   -517    -44   -518   -595      5   -371   -482   -571   -615 
-   -80   -195   -498   -421   -234   -161   -307     78   -389    146    165   -378   -410   -325   -384    -96   -250    223   -275   -265 
-   -75    107     27    110   -355   -358   -150     45     46    -69   -279    -14   -296     44    145     85     61     -5   -331   -279 
-    33   -283    -54   -168   -321    176    159   -291   -150   -137    223     56   -315   -120   -208     49    -61   -125   -319   -277 
-  -215   -277   -532   -447    217   -558   -360   -167   -423    288     23    -95   -427   -325   -396   -413   -122   -250   -311   -327 
-   -89    117   -466   -101    -26   -476   -318   -198   -376   -255    156   -325   -415   -315   -380    173    259     99   -304   -300 
-  -295   -344     26    181   -386   -383    160   -385    151    -69   -304   -196   -322    112    242     49   -236   -378   -354   -305 
-    56    211   -348      6   -258    -72   -244    -52   -256   -112   -197    -40   -364   -217   -294    224    101    -30   -286     10 
-    -3   -202   -498   -419   -224   -471     54    -37   -388    234    272   -382   -407   -317   -379   -325    -74    -85    143      8 
-   204   -306   -264   -189   -396    -69   -189   -390    -14   -378      3   -217    -51    156    193    -72   -251   -369   -361   -322 
-  -277   -280   -236    -39     57   -152    158    -80     39     79    153    -21   -313    156    145   -204    -60     39   -315      8 
-  -164   -464    216    305   -496   -158   -268   -472    -47    -16   -396   -277   -379     31   -306    -90    -81   -452   -469   -411 
-  -157    123   -496   -418    -13   -163   -303     31   -385    220    113   -376   -406   -318   -379    -98   -251     25   -270    253 
-   149   -311   -209     33   -354     22   -151    -97     45   -149   -278   -172    -46    -92    145     50    -59   -348   -330      5 
-  -142   -318   -208     76   -356    -68   -151    -97    147   -150   -280   -172    276    112     34    -61     60   -140   -332   -280 
-  -268   -317    -47     77    -38   -150    250   -359    121    -18   -279    -15    -46    112    -37     50     13   -352    139    222 
-  -156   -338   -229    -48   -391    239   -183   -396    -30   -386   -318    190   -329     27     74     -6   -247   -151   -356   -313 
-  -372   -253   -410   -399   -123   -293   -366    345   -197    -52   -102   -354   -429   -337   -203   -342   -171    118   -313   -110 
-  -144   -290   -233   -162   -327    -68     73    -84     85   -139   -256     56   -312   -113    285   -203     97      1   -321      8 
-  -146     94   -193   -329   -285   -443   -265     73   -337   -177   -228   -168   -320   -310   -312   -198   -113    308   -344   -389 
-  -142   -319   -207   -138   -356    -68     75   -360     46   -347   -280    302   -296     44     34    113     13     -5   -332      6 
-     6    273   -480    -92   -230     26   -297     77   -371    -32     33     44   -403   -310   -372     80     13    130   -270   -259 
-   -80    123   -491   -416    -13   -162   -302    217   -383     93   -169    -51   -405   -320   -379    -96    -66    178   -270   -260 
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 position-specific probability matrix
---------------------------------------------------------------------------------
-letter-probability matrix: alength= 20 w= 29 nsites= 33 E= 3.6e-165 
- 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.939394 
- 0.090909  0.090909  0.030303  0.000000  0.000000  0.181818  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.030303  0.393939  0.090909  0.030303  0.000000  0.000000 
- 0.575758  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.030303  0.000000  0.030303  0.060606  0.030303  0.000000  0.000000  0.000000  0.181818  0.030303  0.030303  0.000000  0.000000 
- 0.181818  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.606061  0.181818  0.000000  0.000000  0.000000 
- 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.939394  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000 
- 0.484848  0.000000  0.000000  0.000000  0.272727  0.121212  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.060606  0.000000 
- 0.575758  0.000000  0.000000  0.000000  0.060606  0.272727  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.060606  0.000000  0.000000  0.000000  0.000000 
- 0.060606  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.090909  0.000000  0.272727  0.090909  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.424242  0.000000  0.000000 
- 0.060606  0.030303  0.060606  0.121212  0.000000  0.000000  0.000000  0.090909  0.060606  0.060606  0.000000  0.030303  0.000000  0.030303  0.151515  0.121212  0.090909  0.090909  0.000000  0.000000 
- 0.151515  0.000000  0.030303  0.000000  0.000000  0.363636  0.060606  0.000000  0.000000  0.030303  0.151515  0.060606  0.000000  0.000000  0.000000  0.090909  0.030303  0.030303  0.000000  0.000000 
- 0.030303  0.000000  0.000000  0.000000  0.242424  0.000000  0.000000  0.000000  0.000000  0.636364  0.030303  0.030303  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.000000 
- 0.060606  0.030303  0.000000  0.030303  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.090909  0.000000  0.000000  0.000000  0.000000  0.242424  0.333333  0.181818  0.000000  0.000000 
- 0.000000  0.000000  0.060606  0.212121  0.000000  0.000000  0.060606  0.000000  0.151515  0.060606  0.000000  0.000000  0.000000  0.060606  0.303030  0.090909  0.000000  0.000000  0.000000  0.000000 
- 0.181818  0.060606  0.000000  0.060606  0.000000  0.060606  0.000000  0.030303  0.000000  0.030303  0.000000  0.030303  0.000000  0.000000  0.000000  0.333333  0.121212  0.060606  0.000000  0.030303 
- 0.121212  0.000000  0.000000  0.000000  0.000000  0.000000  0.030303  0.030303  0.000000  0.484848  0.212121  0.000000  0.000000  0.000000  0.000000  0.000000  0.030303  0.030303  0.030303  0.030303 
- 0.515152  0.000000  0.000000  0.000000  0.000000  0.060606  0.000000  0.000000  0.030303  0.000000  0.030303  0.000000  0.030303  0.090909  0.212121  0.030303  0.000000  0.000000  0.000000  0.000000 
- 0.000000  0.000000  0.000000  0.030303  0.060606  0.030303  0.060606  0.030303  0.060606  0.181818  0.090909  0.030303  0.000000  0.090909  0.151515  0.000000  0.030303  0.121212  0.000000  0.030303 
- 0.030303  0.000000  0.242424  0.484848  0.000000  0.030303  0.000000  0.000000  0.030303  0.090909  0.000000  0.000000  0.000000  0.030303  0.000000  0.030303  0.030303  0.000000  0.000000  0.000000 
- 0.030303  0.030303  0.000000  0.000000  0.030303  0.030303  0.000000  0.060606  0.000000  0.454545  0.060606  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.090909  0.000000  0.181818 
- 0.363636  0.000000  0.000000  0.060606  0.000000  0.121212  0.000000  0.030303  0.060606  0.030303  0.000000  0.000000  0.030303  0.000000  0.151515  0.090909  0.030303  0.000000  0.000000  0.030303 
- 0.030303  0.000000  0.000000  0.090909  0.000000  0.060606  0.000000  0.030303  0.151515  0.030303  0.000000  0.000000  0.333333  0.060606  0.060606  0.030303  0.090909  0.030303  0.000000  0.000000 
- 0.000000  0.000000  0.030303  0.090909  0.030303  0.030303  0.121212  0.000000  0.121212  0.090909  0.000000  0.030303  0.030303  0.060606  0.030303  0.090909  0.060606  0.000000  0.030303  0.151515 
- 0.030303  0.000000  0.000000  0.030303  0.000000  0.515152  0.000000  0.000000  0.030303  0.000000  0.000000  0.181818  0.000000  0.030303  0.090909  0.060606  0.000000  0.030303  0.000000  0.000000 
- 0.000000  0.000000  0.000000  0.000000  0.030303  0.030303  0.000000  0.484848  0.030303  0.030303  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.030303  0.303030  0.000000  0.030303 
- 0.030303  0.000000  0.000000  0.000000  0.000000  0.060606  0.030303  0.030303  0.090909  0.030303  0.000000  0.060606  0.000000  0.000000  0.424242  0.000000  0.121212  0.090909  0.000000  0.030303 
- 0.030303  0.060606  0.030303  0.000000  0.000000  0.000000  0.000000  0.151515  0.000000  0.030303  0.000000  0.030303  0.000000  0.000000  0.000000  0.030303  0.030303  0.606061  0.000000  0.000000 
- 0.030303  0.000000  0.000000  0.000000  0.000000  0.060606  0.030303  0.000000  0.060606  0.000000  0.000000  0.393939  0.000000  0.030303  0.060606  0.151515  0.060606  0.090909  0.000000  0.030303 
- 0.121212  0.090909  0.000000  0.030303  0.000000  0.121212  0.000000  0.090909  0.000000  0.060606  0.030303  0.060606  0.000000  0.000000  0.000000  0.121212  0.060606  0.212121  0.000000  0.000000 
- 0.060606  0.030303  0.000000  0.000000  0.030303  0.030303  0.000000  0.272727  0.000000  0.181818  0.000000  0.030303  0.000000  0.000000  0.000000  0.030303  0.030303  0.303030  0.000000  0.000000 
---------------------------------------------------------------------------------
-
-
-
-
-
-Time 36.66 secs.
-
-********************************************************************************
-
-
-********************************************************************************
-MOTIF  2	width =   29   sites =  33   llr = 1106   E-value = 2.3e-159
-********************************************************************************
---------------------------------------------------------------------------------
-	Motif 2 Description
---------------------------------------------------------------------------------
-Simplified        A  :14::::531:1:1516:2:322:51111
-pos.-specific     C  :::::::1::::::::1::::::::::::
-probability       D  ::::::::1:::::1:::1:::1::::::
-matrix            E  ::::::::::::::2::11::22::::::
-                  F  :::::::::::::1:::::2::::1::1:
-                  G  ::::::a4218:9:::::1::1:8:1:11
-                  H  :::::::::::::1:::11:1:1::1:::
-                  I  ::124::::::5:::2:1::1:::::1:1
-                  K  61:::::::2:::2:::3:::21:13:::
-                  L  :::51::::::3:2:2:1151:1:111:3
-                  M  :::::::::::::::1::::::1::::::
-                  N  :1::::::1:::::::::::::1::1:::
-                  P  1::::::::::::::::::::::::::::
-                  Q  1::::::::1:::::::::::11::::::
-                  R  :1:::::::2:::2:::21::111:1:::
-                  S  :::::::123::1:1:1:::111:1111:
-                  T  111::9::::1::::2::1::1:::::1:
-                  V  :4425::::::1:::12:1:1:::::553
-                  W  :::::::::::::::::::::::::::::
-                  Y  :::::::::::::::1::::::::1::::
-
-         bits    6.7                              
-                 6.0                              
-                 5.4                              
-                 4.7                              
-Information      4.0                              
-content          3.4      **                      
-(48.4 bits)      2.7     ***   * *                
-                 2.0 * ******  ***   *  *   *     
-                 1.3 ****************** * * ** ***
-                 0.7 *****************************
-                 0.0 -----------------------------
-
-Multilevel           KVALVTGAASGIGKATAKxLAAEGAKVVL
-consensus              VII  GG  L R I   F K      V
-sequence                     S                    
-                                                  
-                                                  
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 sites sorted by position p-value
---------------------------------------------------------------------------------
-Sequence name             Start   P-value                        Site           
--------------             ----- ---------            -----------------------------
-HDE_CANTR                   323  2.44e-23 SGAPTVSLKD KVVLITGAGAGLGKEYAKWFAKYGAKVVV NDFKDATKTV
-DHII_HUMAN                   35  5.50e-23 EEFRPEMLQG KKVIVTGASKGIGREMAYHLAKMGAHVVV TARSKETLQK
-YINL_LISMO                    6  5.38e-22      MTIKN KVIIITGASSGIGKATALLLAEKGAKLVL AARRVEKLEK
-HDHA_ECOLI                   12  5.65e-20 FNSDNLRLDG KCAIITGAGAGIGKEIAITFATAGASVVV SDINADAANH
-RIDH_KLEAE                   15  1.17e-19 VSSMNTSLSG KVAAITGAASGIGLECARTLLGAGAKVVL IDREGEKLNK
-BUDC_KLETE                    3  1.17e-19         MQ KVALVTGAGQGIGKAIALRLVKDGFAVAI ADYNDATATA
-ENTA_ECOLI                    6  4.74e-19      MDFSG KNVWVTGAGKGIGYATALAFVEAGAKVTG FDQAFTQEQY
-AP27_MOUSE                    8  9.31e-19    MKLNFSG LRALVTGAGKGIGRDTVKALHASGAKVVA VTRTNSDLVS
-DHMA_FLAS1                   15  2.50e-18 VSRRPGRLAG KAAIVTGAAGGIGRATVEAYLREGASVVA MDLAPRLAAT
-YRTP_BACSU                    7  3.45e-18     MQSLQH KTALITGGGRGIGRATALALAKEGVNIGL IGRTSANVEK
-DHGB_BACME                    8  5.86e-18    MYKDLEG KVVVITGSSTGLGKSMAIRFATEKAKVVV NYRSKEDEAN
-DHB3_HUMAN                   49  9.86e-18 LPKSFLRSMG QWAVITGAGDGIGKAYSFELAKRGLNVVL ISRTLEKLEA
-PCR_PEA                      87  2.47e-17 SSEGKKTLRK GNVVITGASSGLGLATAKALAESGKWHVI MACRDYLKAA
-BDH_HUMAN                    56  3.01e-17 YASAAEPVGS KAVLVTGCDSGFGFSLAKHLHSKGFLVFA GCLMKDKGHD
-BA72_EUBSP                    7  3.33e-17     MNLVQD KVTIITGGTRGIGFAAAKIFIDNGAKVSI FGETQEEVDT
-FIXR_BRAJA                   37  4.06e-17 VNARVDRGEP KVMLLTGASRGIGHATAKLFSEAGWRIIS CARQPFDGER
-3BHD_COMTE                    7  4.06e-17     TNRLQG KVALVTGGASGVGLEVVKLLLGEGAKVAF SDINEAAGQQ
-2BHD_STREX                    7  8.05e-17     MNDLSG KTVIITGGARGLGAEAARQAVAAGARVVL ADVLDEEGAA
-HMTR_LEIMA                    7  1.90e-16     MTAPTV PVALVTGAAKRLGRSIAEGLHAEGYAVCL HYHRSAAEAN
-FVT1_HUMAN                   33  2.77e-16 ISPKPLALPG AHVVVTGGSSGIGKCIAIECYKQGAFITL VARNEDKLLQ
-DHB2_HUMAN                   83  3.65e-16 SGQELLPVDQ KAVLVTGGDCGLGHALCKYLDELGFTVFA GVLNENGPGA
-LIGD_PSEPA                    7  8.31e-16     MKDFQD QVAFITGGASGAGFGQAKVFGQAGAKIVV ADVRAEAVEK
-NODG_RHIME                    7  4.05e-15     MFELTG RKALVTGASGAIGGAIARVLHAQGAIVGL HGTQIEKLET
-DHCA_HUMAN                    5  5.24e-15       SSGI HVALVTGGNKGIGLAIVRDLCRLFSGDVV LTARDVTRGQ
-MAS1_AGRRA                  246  3.00e-14 SHWTVEIHQS PVILVSGSNRGVGKAIAEDLIAHGYRLSL GARKVKDLEV
-BPHB_PSEPS                    6  8.47e-14      MKLKG EAVLITGGASGLGRALVDRFVAEAKVAVL DKSAERLAEL
-GUTD_ECOLI                    3  1.46e-13         MN QVAVVIGGGQTLGAFLCHGLAAEGYRVAV VDIQSDKAAN
-DHES_HUMAN                    3  1.46e-13         AR TVVLITGCSSGIGLHLAVRLASDPSQSFK VYATLRDLKT
-RFBB_NEIGO                    7  1.59e-12     MQTEGK KNILVTGGAGFIGSAVVRHIIQNTRDSVV NLDKLTYAGN
-ADH_DROME                     7  6.97e-10     SFTLTN KNVIFVAGLGGIGLDTSKELLKRDLKNLV ILDRIENPAA
-FABI_ECOLI                    7  3.15e-09     MGFLSG KRILVTGVASKLSIAYGIAQAMHREGAEL AFTYQNDKLK
-YURA_MYXXA                  117  2.77e-07 RLPWERVRGI IDTNVTGAAATLSAVLPQMVERKRGHLVG VSSLAGFRGL
-CSGA_MYXXA                   52  4.24e-07 TINALGPLRV TSAMLPGLRQGALRRVAHVTSRMGSLAAN TDGGAYAYRM
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 block diagrams
---------------------------------------------------------------------------------
-SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-HDE_CANTR                         2.4e-23  322_[2]_555
-DHII_HUMAN                        5.5e-23  34_[2]_229
-YINL_LISMO                        5.4e-22  5_[2]_214
-HDHA_ECOLI                        5.7e-20  11_[2]_215
-RIDH_KLEAE                        1.2e-19  14_[2]_206
-BUDC_KLETE                        1.2e-19  2_[2]_210
-ENTA_ECOLI                        4.7e-19  5_[2]_214
-AP27_MOUSE                        9.3e-19  7_[2]_208
-DHMA_FLAS1                        2.5e-18  14_[2]_227
-YRTP_BACSU                        3.4e-18  6_[2]_203
-DHGB_BACME                        5.9e-18  7_[2]_226
-DHB3_HUMAN                        9.9e-18  48_[2]_233
-PCR_PEA                           2.5e-17  86_[2]_284
-BDH_HUMAN                           3e-17  55_[2]_259
-BA72_EUBSP                        3.3e-17  6_[2]_214
-FIXR_BRAJA                        4.1e-17  36_[2]_213
-3BHD_COMTE                        4.1e-17  6_[2]_218
-2BHD_STREX                          8e-17  6_[2]_220
-HMTR_LEIMA                        1.9e-16  6_[2]_252
-FVT1_HUMAN                        2.8e-16  32_[2]_271
-DHB2_HUMAN                        3.7e-16  82_[2]_276
-LIGD_PSEPA                        8.3e-16  6_[2]_270
-NODG_RHIME                        4.1e-15  6_[2]_210
-DHCA_HUMAN                        5.2e-15  4_[2]_243
-MAS1_AGRRA                          3e-14  245_[2]_202
-BPHB_PSEPS                        8.5e-14  5_[2]_241
-GUTD_ECOLI                        1.5e-13  2_[2]_228
-DHES_HUMAN                        1.5e-13  2_[2]_296
-RFBB_NEIGO                        1.6e-12  6_[2]_311
-ADH_DROME                           7e-10  6_[2]_220
-FABI_ECOLI                        3.1e-09  6_[2]_227
-YURA_MYXXA                        2.8e-07  116_[2]_113
-CSGA_MYXXA                        4.2e-07  51_[2]_86
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 in BLOCKS format
---------------------------------------------------------------------------------
-BL   MOTIF 2 width=29 seqs=33
-HDE_CANTR                (  323) KVVLITGAGAGLGKEYAKWFAKYGAKVVV  1 
-DHII_HUMAN               (   35) KKVIVTGASKGIGREMAYHLAKMGAHVVV  1 
-YINL_LISMO               (    6) KVIIITGASSGIGKATALLLAEKGAKLVL  1 
-HDHA_ECOLI               (   12) KCAIITGAGAGIGKEIAITFATAGASVVV  1 
-RIDH_KLEAE               (   15) KVAAITGAASGIGLECARTLLGAGAKVVL  1 
-BUDC_KLETE               (    3) KVALVTGAGQGIGKAIALRLVKDGFAVAI  1 
-ENTA_ECOLI               (    6) KNVWVTGAGKGIGYATALAFVEAGAKVTG  1 
-AP27_MOUSE               (    8) LRALVTGAGKGIGRDTVKALHASGAKVVA  1 
-DHMA_FLAS1               (   15) KAAIVTGAAGGIGRATVEAYLREGASVVA  1 
-YRTP_BACSU               (    7) KTALITGGGRGIGRATALALAKEGVNIGL  1 
-DHGB_BACME               (    8) KVVVITGSSTGLGKSMAIRFATEKAKVVV  1 
-DHB3_HUMAN               (   49) QWAVITGAGDGIGKAYSFELAKRGLNVVL  1 
-PCR_PEA                  (   87) GNVVITGASSGLGLATAKALAESGKWHVI  1 
-BDH_HUMAN                (   56) KAVLVTGCDSGFGFSLAKHLHSKGFLVFA  1 
-BA72_EUBSP               (    7) KVTIITGGTRGIGFAAAKIFIDNGAKVSI  1 
-FIXR_BRAJA               (   37) KVMLLTGASRGIGHATAKLFSEAGWRIIS  1 
-3BHD_COMTE               (    7) KVALVTGGASGVGLEVVKLLLGEGAKVAF  1 
-2BHD_STREX               (    7) KTVIITGGARGLGAEAARQAVAAGARVVL  1 
-HMTR_LEIMA               (    7) PVALVTGAAKRLGRSIAEGLHAEGYAVCL  1 
-FVT1_HUMAN               (   33) AHVVVTGGSSGIGKCIAIECYKQGAFITL  1 
-DHB2_HUMAN               (   83) KAVLVTGGDCGLGHALCKYLDELGFTVFA  1 
-LIGD_PSEPA               (    7) QVAFITGGASGAGFGQAKVFGQAGAKIVV  1 
-NODG_RHIME               (    7) RKALVTGASGAIGGAIARVLHAQGAIVGL  1 
-DHCA_HUMAN               (    5) HVALVTGGNKGIGLAIVRDLCRLFSGDVV  1 
-MAS1_AGRRA               (  246) PVILVSGSNRGVGKAIAEDLIAHGYRLSL  1 
-BPHB_PSEPS               (    6) EAVLITGGASGLGRALVDRFVAEAKVAVL  1 
-GUTD_ECOLI               (    3) QVAVVIGGGQTLGAFLCHGLAAEGYRVAV  1 
-DHES_HUMAN               (    3) TVVLITGCSSGIGLHLAVRLASDPSQSFK  1 
-RFBB_NEIGO               (    7) KNILVTGGAGFIGSAVVRHIIQNTRDSVV  1 
-ADH_DROME                (    7) KNVIFVAGLGGIGLDTSKELLKRDLKNLV  1 
-FABI_ECOLI               (    7) KRILVTGVASKLSIAYGIAQAMHREGAEL  1 
-YURA_MYXXA               (  117) IDTNVTGAAATLSAVLPQMVERKRGHLVG  1 
-CSGA_MYXXA               (   52) TSAMLPGLRQGALRRVAHVTSRMGSLAAN  1 
-//
-
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 position-specific scoring matrix
---------------------------------------------------------------------------------
-log-odds matrix: alength= 20 w= 29 n= 9072 bayes= 8.09755 E= 2.3e-159 
-  -143   -322   -212    -29   -360   -150     75    -97    323   -150   -283   -174     41    159    -35   -190     13   -356   -334   -283 
-     0    103    -55   -150   -343   -365     68   -277     37   -328   -270    137   -300   -104     27    -68      8    216    134   -284 
-   184   -328   -685   -628   -415   -668   -559    121   -607   -334     17   -587   -610   -559   -621   -535      7    212   -519   -487 
-  -171   -214   -506   -425    -20   -485   -317    170   -395    240     30    -63   -412   -320   -383   -339   -272     73    137   -278 
-  -548   -378   -767   -727    -25   -789   -710    277   -719    -45   -344   -695   -699   -669   -749   -678   -480    260   -602   -574 
-  -390   -251   -433   -462   -434   -534   -365   -109   -376   -462   -320   -258    -80   -318   -390    -26    386   -153   -406   -454 
-  -198   -345   -337   -398   -504    336   -361   -523   -381   -566   -470   -293   -442   -394   -385   -308   -423   -506   -397   -449 
-   205    225   -616   -594   -556    193   -536   -552   -603   -163   -504   -510   -489   -501   -571      4   -361   -139   -540   -583 
-   131   -370     35   -219   -442    128   -213   -456   -212   -158   -382     70   -370   -181    -55    181    -71   -445   -421   -359 
-   -30    108    -48   -141   -360     23   -153   -364    148   -351   -284   -173   -299    159    146    204    -60   -357   -335   -283 
-  -204   -337   -316   -378   -112    323   -341   -505   -141   -549   -452   -272   -427   -375   -136   -296    -74   -492   -378   -430 
-   -95   -361   -677   -632    -23   -695   -554    323   -604    166   -255   -593   -615   -536   -614   -563   -440    -15   -461   -462 
-  -326   -337   -324   -385   -492    331   -348   -511   -368   -235   -458   -280   -431   -381   -372    -66   -413   -495   -385   -437 
-   -30   -269   -258   -187    114   -153    158    -74    206     82   -239   -214   -326   -135    191    -71   -224   -281   -312      9 
-   237     89    -43     92    -86   -158      5   -315   -262   -325   -263   -289   -394   -232   -114     27   -229   -127   -314   -338 
-   -79    126   -496   -418   -229   -460   -302    183   -384     95    114   -373   -406     -2   -380   -314    194     28   -269    160 
-   260    176   -422   -376   -354   -156   -358   -340   -378   -355   -293   -375   -107   -342   -381     -6   -258     55   -342   -392 
-  -270   -314    -48     76    -39   -361    159     86    236     21   -276   -175   -299     43    146   -189   -211   -138   -330      6 
-    56   -301     25     75   -338    -68    212    -90   -130    -15      8   -180   -302     41    116   -193     13     -2    141      7 
-  -177    105   -501   -421    238   -487   -316    -44   -391    257   -134   -393   -406    -19   -377   -340    -87    -96   -279     -4 
-   151    122    -87    -90   -241   -159    248     70   -331     38   -181   -340   -395   -280   -347    -10   -242     54   -276     11 
-    75   -319    -47    137   -356    -68   -150   -361    189   -347      5   -170   -296    112    117      5     13   -353   -332   -279 
-    55   -318     27    179   -355   -357    159   -360     88    -69     94     59   -295    112     34      6   -209   -352   -331      6 
-  -204   -337   -127   -377   -112    318   -341   -505   -141   -549   -452   -272   -122   -374    -52   -296   -161   -492   -378   -430 
-   225   -109   -325   -105     68   -158   -257   -288    -22    -98   -250   -283   -385   -221   -102     31   -229   -121     98    106 
-   -75   -318    -47   -137    -40    -68    159    -97    236    -69   -279     59   -295     44    117      6    -59   -140    140   -279 
-   -91   -125   -192   -330   -284   -443    -59     58   -338   -101   -228   -167   -320   -310   -312   -132   -175    304   -343   -387 
-   -59     39   -374   -175     10   -177   -269     -2   -342   -164   -220   -355   -327   -311   -318   -112    -56    295   -333   -366 
-     6   -192   -493   -415    -11    -69   -301     78    -81    174   -170    -49   -406   -318   -378    -94   -246    162   -269   -259 
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 position-specific probability matrix
---------------------------------------------------------------------------------
-letter-probability matrix: alength= 20 w= 29 nsites= 33 E= 2.3e-159 
- 0.030303  0.000000  0.000000  0.030303  0.000000  0.030303  0.030303  0.030303  0.575758  0.030303  0.000000  0.000000  0.060606  0.090909  0.030303  0.000000  0.060606  0.000000  0.000000  0.000000 
- 0.121212  0.030303  0.030303  0.000000  0.000000  0.000000  0.030303  0.000000  0.060606  0.000000  0.000000  0.121212  0.000000  0.000000  0.060606  0.030303  0.060606  0.424242  0.030303  0.000000 
- 0.424242  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.121212  0.000000  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.060606  0.363636  0.000000  0.000000 
- 0.030303  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.212121  0.000000  0.484848  0.030303  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.151515  0.030303  0.000000 
- 0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.393939  0.000000  0.060606  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.515152  0.000000  0.000000 
- 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.030303  0.878788  0.030303  0.000000  0.000000 
- 0.030303  0.000000  0.000000  0.000000  0.000000  0.969697  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
- 0.454545  0.060606  0.000000  0.000000  0.000000  0.363636  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.060606  0.000000  0.030303  0.000000  0.000000 
- 0.303030  0.000000  0.060606  0.000000  0.000000  0.242424  0.000000  0.000000  0.000000  0.030303  0.000000  0.060606  0.000000  0.000000  0.030303  0.242424  0.030303  0.000000  0.000000  0.000000 
- 0.090909  0.030303  0.030303  0.000000  0.000000  0.121212  0.000000  0.000000  0.151515  0.000000  0.000000  0.000000  0.000000  0.090909  0.151515  0.303030  0.030303  0.000000  0.000000  0.000000 
- 0.030303  0.000000  0.000000  0.000000  0.030303  0.818182  0.000000  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.060606  0.000000  0.000000  0.000000 
- 0.060606  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.545455  0.000000  0.303030  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.060606  0.000000  0.000000 
- 0.000000  0.000000  0.000000  0.000000  0.000000  0.909091  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.060606  0.000000  0.000000  0.000000  0.000000 
- 0.090909  0.000000  0.000000  0.000000  0.090909  0.030303  0.060606  0.030303  0.242424  0.181818  0.000000  0.000000  0.000000  0.000000  0.212121  0.030303  0.000000  0.000000  0.000000  0.030303 
- 0.484848  0.030303  0.060606  0.181818  0.030303  0.030303  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.030303  0.090909  0.000000  0.030303  0.000000  0.000000 
- 0.060606  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.212121  0.000000  0.181818  0.060606  0.000000  0.000000  0.030303  0.000000  0.000000  0.242424  0.090909  0.000000  0.090909 
- 0.636364  0.060606  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.060606  0.000000  0.181818  0.000000  0.000000 
- 0.000000  0.000000  0.030303  0.090909  0.030303  0.000000  0.060606  0.121212  0.303030  0.121212  0.000000  0.000000  0.000000  0.030303  0.151515  0.000000  0.000000  0.030303  0.000000  0.030303 
- 0.181818  0.000000  0.060606  0.090909  0.000000  0.060606  0.090909  0.030303  0.000000  0.090909  0.030303  0.000000  0.000000  0.030303  0.121212  0.000000  0.060606  0.090909  0.030303  0.030303 
- 0.030303  0.030303  0.000000  0.000000  0.242424  0.000000  0.000000  0.030303  0.000000  0.545455  0.000000  0.000000  0.000000  0.030303  0.000000  0.000000  0.030303  0.030303  0.000000  0.030303 
- 0.333333  0.030303  0.030303  0.030303  0.000000  0.030303  0.121212  0.090909  0.000000  0.121212  0.000000  0.000000  0.000000  0.000000  0.000000  0.060606  0.000000  0.121212  0.000000  0.030303 
- 0.212121  0.000000  0.030303  0.151515  0.000000  0.060606  0.000000  0.000000  0.212121  0.000000  0.030303  0.000000  0.000000  0.060606  0.121212  0.060606  0.060606  0.000000  0.000000  0.000000 
- 0.181818  0.000000  0.060606  0.212121  0.000000  0.000000  0.060606  0.000000  0.090909  0.060606  0.060606  0.060606  0.000000  0.060606  0.060606  0.060606  0.000000  0.000000  0.000000  0.030303 
- 0.030303  0.000000  0.030303  0.000000  0.030303  0.757576  0.000000  0.000000  0.030303  0.000000  0.000000  0.000000  0.030303  0.000000  0.060606  0.000000  0.030303  0.000000  0.000000  0.000000 
- 0.454545  0.000000  0.000000  0.030303  0.090909  0.030303  0.000000  0.000000  0.060606  0.060606  0.000000  0.000000  0.000000  0.000000  0.030303  0.090909  0.000000  0.030303  0.030303  0.090909 
- 0.060606  0.000000  0.030303  0.000000  0.030303  0.060606  0.060606  0.030303  0.303030  0.060606  0.000000  0.060606  0.000000  0.030303  0.121212  0.060606  0.030303  0.030303  0.030303  0.000000 
- 0.090909  0.000000  0.030303  0.000000  0.000000  0.000000  0.030303  0.121212  0.000000  0.090909  0.000000  0.030303  0.000000  0.000000  0.000000  0.060606  0.000000  0.545455  0.000000  0.000000 
- 0.121212  0.030303  0.000000  0.030303  0.090909  0.060606  0.000000  0.030303  0.000000  0.030303  0.000000  0.000000  0.000000  0.000000  0.000000  0.060606  0.060606  0.484848  0.000000  0.000000 
- 0.121212  0.000000  0.000000  0.000000  0.030303  0.060606  0.000000  0.090909  0.030303  0.333333  0.000000  0.030303  0.000000  0.000000  0.000000  0.030303  0.000000  0.272727  0.000000  0.000000 
---------------------------------------------------------------------------------
-
-
-
-
-
-Time 67.32 secs.
-
-********************************************************************************
-
-
-********************************************************************************
-SUMMARY OF MOTIFS
-********************************************************************************
-
---------------------------------------------------------------------------------
-	Combined block diagrams: non-overlapping sites with p-value < 0.0001
---------------------------------------------------------------------------------
-SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-2BHD_STREX                       3.15e-28  6_[2(8.05e-17)]_116_[1(1.11e-18)]_75
-3BHD_COMTE                       9.69e-25  6_[2(4.06e-17)]_115_[1(7.81e-15)]_74
-ADH_DROME                        6.95e-15  6_[2(6.97e-10)]_116_[1(5.20e-12)]_75
-AP27_MOUSE                       2.21e-33  7_[2(9.31e-19)]_112_[1(6.32e-22)]_67
-BA72_EUBSP                       2.62e-26  6_[2(3.33e-17)]_121_[1(2.52e-16)]_64
-BDH_HUMAN                        1.58e-26  55_[2(3.01e-17)]_123_[1(8.20e-17)]_107
-BPHB_PSEPS                       4.38e-19  5_[2(8.47e-14)]_118_[1(1.80e-12)]_94
-BUDC_KLETE                       1.73e-33  2_[2(1.17e-19)]_120_[1(4.04e-21)]_61
-DHES_HUMAN                       9.98e-23  2_[2(1.46e-13)]_123_[1(1.37e-16)]_144
-DHGB_BACME                       1.78e-30  7_[2(5.86e-18)]_123_[1(7.52e-20)]_74
-DHII_HUMAN                       4.64e-31  34_[2(5.50e-23)]_119_[1(1.61e-15)]_81
-DHMA_FLAS1                       5.69e-29  14_[2(2.50e-18)]_121_[1(5.53e-18)]_77
-ENTA_ECOLI                       2.69e-27  5_[2(4.74e-19)]_109_[1(1.77e-15)]_76
-FIXR_BRAJA                       1.15e-30  36_[2(4.06e-17)]_123_[1(6.12e-21)]_61
-GUTD_ECOLI                       2.33e-25  2_[2(1.46e-13)]_122_[1(4.82e-19)]_77
-HDE_CANTR                        1.43e-32  8_[2(3.45e-18)]_125_[1(4.01e-13)]_131_[2(2.44e-23)]_115_[1(9.65e-18)]_411
-HDHA_ECOLI                       2.75e-31  11_[2(5.65e-20)]_74_[1(4.42e-05)]_15_[1(1.25e-18)]_68
-LIGD_PSEPA                       4.54e-24  6_[2(8.31e-16)]_121_[1(1.21e-15)]_120
-NODG_RHIME                       1.55e-29  6_[2(4.05e-15)]_116_[1(1.13e-21)]_65
-RIDH_KLEAE                       3.67e-29  14_[2(1.17e-19)]_116_[1(9.09e-17)]_61
-YINL_LISMO                       5.92e-29  5_[2(5.38e-22)]_119_[1(3.24e-14)]_66
-YRTP_BACSU                       2.01e-33  6_[2(3.45e-18)]_119_[1(1.64e-22)]_55
-CSGA_MYXXA                       5.53e-13  51_[2(4.24e-07)]_7_[1(2.10e-12)]_50
-DHB2_HUMAN                       6.87e-27  82_[2(3.65e-16)]_120_[1(2.23e-18)]_127
-DHB3_HUMAN                       4.11e-25  48_[2(9.86e-18)]_120_[1(8.55e-15)]_84
-DHCA_HUMAN                       6.86e-18  4_[2(5.24e-15)]_159_[1(4.80e-10)]_55
-FABI_ECOLI                       2.57e-14  6_[2(3.15e-09)]_123_[1(4.15e-12)]_75
-FVT1_HUMAN                       4.64e-26  32_[2(2.77e-16)]_124_[1(2.86e-17)]_118
-HMTR_LEIMA                       2.93e-28  6_[2(1.90e-16)]_157_[1(3.35e-19)]_66
-MAS1_AGRRA                       1.26e-14  245_[2(3.00e-14)]_74_[1(5.72e-08)]_99
-PCR_PEA                          4.22e-18  25_[1(2.77e-08)]_32_[2(2.47e-17)]_284
-RFBB_NEIGO                       1.14e-19  6_[2(1.59e-12)]_129_[1(1.47e-14)]_153
-YURA_MYXXA                       3.34e-19  116_[2(2.77e-07)]_14_[1(4.82e-19)]_70
---------------------------------------------------------------------------------
-
-********************************************************************************
-
-
-********************************************************************************
-Stopped because nmotifs = 2 reached.
-********************************************************************************
-
-CPU: pmgm2
-
-********************************************************************************
diff --git a/Tests/Motif/meme.protein.tcm.txt b/Tests/Motif/meme.protein.tcm.txt
deleted file mode 100644
--- a/Tests/Motif/meme.protein.tcm.txt
+++ /dev/null
@@ -1,466 +0,0 @@
-********************************************************************************
-MEME - Motif discovery tool
-********************************************************************************
-MEME version 3.0 (Release date: 2004/08/18 09:07:01)
-
-For further information on how to interpret these results or to get
-a copy of the MEME software please access http://meme.sdsc.edu.
-
-This file may be used as input to the MAST algorithm for searching
-sequence databases for matches to groups of motifs.  MAST is available
-for interactive use and downloading at http://meme.sdsc.edu.
-********************************************************************************
-
-
-********************************************************************************
-REFERENCE
-********************************************************************************
-If you use this program in your research, please cite:
-
-Timothy L. Bailey and Charles Elkan,
-"Fitting a mixture model by expectation maximization to discover
-motifs in biopolymers", Proceedings of the Second International
-Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
-AAAI Press, Menlo Park, California, 1994.
-********************************************************************************
-
-
-********************************************************************************
-TRAINING SET
-********************************************************************************
-DATAFILE= farntrans5.s
-ALPHABET= ACDEFGHIKLMNPQRSTVWY
-Sequence name            Weight Length  Sequence name            Weight Length  
--------------            ------ ------  -------------            ------ ------  
-RAM1_YEAST               1.0000    431  PFTB_RAT                 1.0000    437  
-BET2_YEAST               1.0000    325  RATRABGERB               1.0000    331  
-CAL1_YEAST               1.0000    376  
-********************************************************************************
-
-********************************************************************************
-COMMAND LINE SUMMARY
-********************************************************************************
-This information can also be useful in the event you wish to report a
-problem with the MEME software.
-
-command: meme farntrans5.s -mod tcm -protein -nmotifs 2 
-
-model:  mod=           tcm    nmotifs=         2    evt=           inf
-object function=  E-value of product of p-values
-width:  minw=            8    maxw=           50    minic=        0.00
-width:  wg=             11    ws=              1    endgaps=       yes
-nsites: minsites=        2    maxsites=       25    wnsites=       0.8
-theta:  prob=            1    spmap=         pam    spfuzz=        120
-em:     prior=       megap    b=            9500    maxiter=        50
-        distance=    1e-05
-data:   n=            1900    N=               5
-
-sample: seed=            0    seqfrac=         1
-Dirichlet mixture priors file: prior30.plib
-Letter frequencies in dataset:
-A 0.061 C 0.037 D 0.062 E 0.061 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051 
-L 0.114 M 0.021 N 0.034 P 0.041 Q 0.038 R 0.041 S 0.078 T 0.046 V 0.057 
-W 0.018 Y 0.041 
-Background letter frequencies (from dataset with add-one prior applied):
-A 0.061 C 0.037 D 0.061 E 0.060 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051 
-L 0.113 M 0.021 N 0.034 P 0.041 Q 0.039 R 0.041 S 0.078 T 0.046 V 0.057 
-W 0.018 Y 0.041 
-********************************************************************************
-
-
-********************************************************************************
-MOTIF  1	width =   30   sites =  24   llr = 854   E-value = 2.2e-094
-********************************************************************************
---------------------------------------------------------------------------------
-	Motif 1 Description
---------------------------------------------------------------------------------
-Simplified        A  :::2::::1:2:11:1:1413314:1:1::
-pos.-specific     C  ::::1::::::::2::132::::1::::::
-probability       D  ::::21::11:6::::::::::::::2:13
-matrix            E  ::::::1114::::::::::::::::1111
-                  F  :16:::::::::111:31::::::::::1:
-                  G  861241:42:::221:::2:22::::3::1
-                  H  ::::::::11:4::2::::::::::::::1
-                  I  ::1:::1::::::::1:::1:1::42:11:
-                  K  :::::1::3::::::::::::::::::2::
-                  L  ::21:::::2::31::1::5::9:55::4:
-                  M  ::::::::::::::::::::::::::::::
-                  N  :1:1:::21:::::::::::1:::::1:::
-                  P  ::::::5:::2:::::::::::::::::::
-                  Q  :::1::::1:::::1:::::1:::::::::
-                  R  :::::3:::::::2:::::::::::::1::
-                  S  :1:2::::::2:::13:1::32:3::12::
-                  T  ::::::::::::2::5:1:1:1:1:1:::1
-                  V  :::::::1::3:2:::::12::::1:::::
-                  W  ::::::::::::::::13::::::::::::
-                  Y  :::::::::::::14:31:::::::1::::
-
-         bits    5.8                               
-                 5.2                               
-                 4.6                               
-                 4.0                               
-Information      3.5            *                  
-content          2.9 *          *          *       
-(51.4 bits)      2.3 ***        *   * **   * *     
-                 1.7 ***   ** ***  ***** * ****    
-                 1.2 ******************************
-                 0.6 ******************************
-                 0.0 ------------------------------
-
-Multilevel           GGFGGRPGKEVDLCYTFCALAALALLGSLD
-consensus                     LAH  HSYWCVSS SI     
-sequence                       P       G           
-                                                   
-                                                   
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 sites sorted by position p-value
---------------------------------------------------------------------------------
-Sequence name             Start   P-value                         Site           
--------------             ----- ---------            ------------------------------
-BET2_YEAST                  223  7.28e-22 WWLCERQLPE GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD WINYEKLTEF
-RATRABGERB                  227  6.18e-21 WWLCERQLPS GGLNGRPEKLPDVCYSWWVLASLKIIGRLH WIDREKLRSF
-CAL1_YEAST                  275  9.17e-20 LNASYDQSDD GGFQGRENKFADTCYAFWCLNSLHLLTKDW KMLCQTELVT
-PFTB_RAT                    237  1.15e-19 EWIARCQNWE GGIGGVPGMEAHGGYTFCGLAALVILKKER SLNLKSLLQW
-PFTB_RAT                    138  4.30e-19 QFLELCQSPD GGFGGGPGQYPHLAPTYAAVNALCIIGTEE AYNVINREKL
-RATRABGERB                  179  7.36e-19 EFVLSCMNFD GGFGCRPGSESHAGQIYCCTGFLAITSQLH QVNSDLLGWW
-RATRABGERB                  131  8.19e-19 AYVQSLQKED GSFAGDIWGEIDTRFSFCAVATLALLGKLD AINVEKAIEF
-BET2_YEAST                  172  2.10e-18 DFVLKCYNFD GGFGLCPNAESHAAQAFTCLGALAIANKLD MLSDDQLEEI
-RATRABGERB                  276  1.43e-17 FILACQDEET GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ IKPVSPVFCM
-BET2_YEAST                  124  3.41e-17 SFIRGNQLED GSFQGDRFGEVDTRFVYTALSALSILGELT SEVVDPAVDF
-RAM1_YEAST                  247  5.00e-17 YLKNCQNYEG GFGSCPHVDEAHGGYTFCATASLAILRSMD QINVEKLLEW
-BET2_YEAST                  272  6.64e-17 FILKCQDEKK GGISDRPENEVDVFHTVFGVAGLSLMGYDN LVPIDPIYCM
-RAM1_YEAST                  145  1.27e-16 VKLFTISPSG GPFGGGPGQLSHLASTYAAINALSLCDNID GCWDRIDRKG
-PFTB_RAT                    286  3.17e-16 WVTSRQMRFE GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL HAQGDPALSM
-RAM1_YEAST                  296  3.47e-16 WSSARQLQEE RGFCGRSNKLVDGCYSFWVGGSAAILEAFG YGQCFNKHAL
-PFTB_RAT                    348  4.30e-15 YILMCCQCPA GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG SGAMLHDVVM
-RATRABGERB                   83  2.40e-14 VFIKSCQHEC GGVSASIGHDPHLLYTLSAVQILTLYDSIH VINVDKVVAY
-PFTB_RAT                    189  2.81e-14 QYLYSLKQPD GSFLMHVGGEVDVRSAYCAASVASLTNIIT PDLFEGTAEW
-BET2_YEAST                   73  7.78e-14 FVLSCWDDKY GAFAPFPRHDAHLLTTLSAVQILATYDALD VLGKDRKVRL
-CAL1_YEAST                  205  1.14e-13 LLGYIMSQQC YNGAFGAHNEPHSGYTSCALSTLALLSSLE KLSDKFKEDT
-RAM1_YEAST                  198  1.33e-13 WLISLKEPNG GFKTCLEVGEVDTRGIYCALSIATLLNILT EELTEGVLNY
-RAM1_YEAST                  349  3.52e-13 ILYCCQEKEQ PGLRDKPGAHSDFYHTNYCLLGLAVAESSY SCTPNDSPHN
-CAL1_YEAST                  327  5.47e-13 LLDRTQKTLT GGFSKNDEEDADLYHSCLGSAALALIEGKF NGELCIPQEI
-BET2_YEAST                   24  3.11e-10 RYIESLDTNK HNFEYWLTEHLRLNGIYWGLTALCVLDSPE TFVKEEVISF
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 block diagrams
---------------------------------------------------------------------------------
-SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-BET2_YEAST                        3.1e-10  23_[1]_19_[1]_21_[1]_18_[1]_21_
-                                           [1]_19_[1]_24
-RATRABGERB                        2.4e-14  82_[1]_18_[1]_18_[1]_18_[1]_19_[1]_26
-CAL1_YEAST                        1.1e-13  204_[1]_40_[1]_22_[1]_20
-PFTB_RAT                          4.3e-15  137_[1]_21_[1]_18_[1]_19_[1]_32_
-                                           [1]_60
-RAM1_YEAST                        1.3e-13  144_[1]_23_[1]_19_[1]_19_[1]_23_
-                                           [1]_53
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 in BLOCKS format
---------------------------------------------------------------------------------
-BL   MOTIF 1 width=30 seqs=24
-BET2_YEAST               (  223) GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD  1 
-RATRABGERB               (  227) GGLNGRPEKLPDVCYSWWVLASLKIIGRLH  1 
-CAL1_YEAST               (  275) GGFQGRENKFADTCYAFWCLNSLHLLTKDW  1 
-PFTB_RAT                 (  237) GGIGGVPGMEAHGGYTFCGLAALVILKKER  1 
-PFTB_RAT                 (  138) GGFGGGPGQYPHLAPTYAAVNALCIIGTEE  1 
-RATRABGERB               (  179) GGFGCRPGSESHAGQIYCCTGFLAITSQLH  1 
-RATRABGERB               (  131) GSFAGDIWGEIDTRFSFCAVATLALLGKLD  1 
-BET2_YEAST               (  172) GGFGLCPNAESHAAQAFTCLGALAIANKLD  1 
-RATRABGERB               (  276) GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ  1 
-BET2_YEAST               (  124) GSFQGDRFGEVDTRFVYTALSALSILGELT  1 
-RAM1_YEAST               (  247) GFGSCPHVDEAHGGYTFCATASLAILRSMD  1 
-BET2_YEAST               (  272) GGISDRPENEVDVFHTVFGVAGLSLMGYDN  1 
-RAM1_YEAST               (  145) GPFGGGPGQLSHLASTYAAINALSLCDNID  1 
-PFTB_RAT                 (  286) GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL  1 
-RAM1_YEAST               (  296) RGFCGRSNKLVDGCYSFWVGGSAAILEAFG  1 
-PFTB_RAT                 (  348) GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG  1 
-RATRABGERB               (   83) GGVSASIGHDPHLLYTLSAVQILTLYDSIH  1 
-PFTB_RAT                 (  189) GSFLMHVGGEVDVRSAYCAASVASLTNIIT  1 
-BET2_YEAST               (   73) GAFAPFPRHDAHLLTTLSAVQILATYDALD  1 
-CAL1_YEAST               (  205) YNGAFGAHNEPHSGYTSCALSTLALLSSLE  1 
-RAM1_YEAST               (  198) GFKTCLEVGEVDTRGIYCALSIATLLNILT  1 
-RAM1_YEAST               (  349) PGLRDKPGAHSDFYHTNYCLLGLAVAESSY  1 
-CAL1_YEAST               (  327) GGFSKNDEEDADLYHSCLGSAALALIEGKF  1 
-BET2_YEAST               (   24) HNFEYWLTEHLRLNGIYWGLTALCVLDSPE  1 
-//
-
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 position-specific scoring matrix
---------------------------------------------------------------------------------
-log-odds matrix: alength= 20 w= 30 n= 1755 bayes= 6.12445 E= 2.2e-094 
-  -218   -476   -324   -369   -492    351    -61   -474   -334   -558   -392   -225   -103   -392    -86   -303   -361   -418   -449   -109 
-   -81   -470   -327   -377     -1    330   -398   -485   -347   -566   -404     54    -81   -396   -330     -9   -350   -421   -467   -482 
-  -244   -349   -513   -434    367    -26   -384     59    -61     38   -123   -357   -404   -371   -364   -348   -238    -14   -322   -240 
-   127    -17   -201     -5   -348    114   -187   -312    -81    -63   -205    120   -263    155     27     92      7   -262   -388   -304 
-   -26    143    115   -207    -17    219   -252   -171     -9   -112     95   -186    -16   -179   -195   -235   -164   -152   -351    -13 
-  -146    -17     33   -115    -32     45     38   -310     85   -143   -204     47    -13    -95    271    -53   -143    -50     83   -303 
-   -47    -38    -90      6   -396   -374      0     15   -233   -169   -288   -259    375   -235    -26    -97   -231    -75   -473   -424 
-  -148   -438   -204     99    -31    196     38   -302    -85   -335   -202    205   -266    -99     26    -54      6     33     83   -304 
-    47   -444     33     57   -349     84    122   -315    209   -342     79    121   -263    109   -118    -53   -144   -265   -389   -305 
-  -160   -416     82    250    -25   -316    123   -254   -111     61     85   -136   -283   -122   -146    -60   -156   -221   -375    -14 
-   161   -320   -465   -373   -228   -392   -333     13   -325    -90   -101   -301    208   -309     -7     90   -181    221   -331   -288 
-  -438   -650    318   -350   -594   -396    355   -672   -341   -686   -596   -158   -495   -373      4   -357   -386   -623   -637   -514 
-    47   -316   -480   -387     82     91   -337   -111   -338    103    -98   -307    -15   -318   -312    -83    170    152   -328   -285 
-    94    221   -398   -311     80     90   -301   -129   -266    -30   -111     21   -354   -263    179   -282   -178   -115   -329    139 
-  -167   -305   -309   -259    149    -77    196   -221   -241   -249   -153   -216    -75     19   -217    -54    -68   -205   -133    341 
-    71   -383   -460   -463   -428   -445   -427     86   -370   -442   -260   -234   -417   -351   -356    143    348    -55   -479   -484 
-  -170     21   -317   -268    232   -354    -39   -217   -250    -54   -152    -36   -288   -261   -224   -116   -223    -78    132    328 
-    46    272   -489   -397     84   -402   -334   -118   -347    -90   -105   -314   -378   -325   -320     -1     82   -106    351     88 
-   277    240   -625   -594   -564    141   -583   -514   -585   -580   -446   -452   -451      4   -521   -277   -297    107   -614   -619 
-    45   -317   -489   -395   -222    -96   -340     81   -346    184    -95   -313   -373   -323   -316    -85     81    179   -327   -285 
-   211   -440   -247   -196   -412     97   -258   -374   -166   -146   -278    178   -325    106   -202    153      0   -314   -457   -377 
-   213   -308   -476   -384     -5     88   -337    123   -337    -91    -99   -307   -372   -318   -311    118     79     12   -328   -287 
-    87   -518   -675   -601   -320   -554   -562   -243   -564    290   -164   -543   -528   -491   -503   -489   -418   -296   -502   -500 
-   317     38   -358   -284   -334   -229    -37   -276    -81   -332   -204   -260    -82   -270   -263     99     23    -47   -389   -383 
-  -408   -489   -735   -670   -387   -688   -678    294   -638    194   -240   -597   -632   -619   -631   -623    -16     84   -602   -556 
-    91      0   -492   -398   -220   -404   -343    158   -348    187    109   -317   -375   -324   -318   -313     78   -100   -329     80 
-  -159   -454    121    100   -362    163     39   -329     20   -356   -221    172   -274     38     24     13      5   -279   -402   -316 
-    47   -443   -200     57   -348    -88     38     37    160   -341   -205     47   -262     41    145    120      7   -264   -388    -19 
-   -28   -364     22     86     69   -344   -250    108     -9    153     95   -185    -17   -174   -192    -72   -165   -153   -352   -294 
-  -146   -443    171    100    -32     -6    175   -314    -80   -144   -205     47   -262     41     27   -178    126   -263     82    -19 
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 1 position-specific probability matrix
---------------------------------------------------------------------------------
-letter-probability matrix: alength= 20 w= 30 nsites= 24 E= 2.2e-094 
- 0.000000  0.000000  0.000000  0.000000  0.000000  0.833333  0.041667  0.000000  0.000000  0.000000  0.000000  0.000000  0.041667  0.000000  0.041667  0.000000  0.000000  0.000000  0.000000  0.041667 
- 0.041667  0.000000  0.000000  0.000000  0.083333  0.625000  0.000000  0.000000  0.000000  0.000000  0.000000  0.083333  0.041667  0.000000  0.000000  0.125000  0.000000  0.000000  0.000000  0.000000 
- 0.000000  0.000000  0.000000  0.000000  0.583333  0.083333  0.000000  0.083333  0.041667  0.166667  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.041667  0.000000  0.000000 
- 0.166667  0.041667  0.000000  0.041667  0.000000  0.208333  0.000000  0.000000  0.000000  0.083333  0.000000  0.083333  0.000000  0.125000  0.041667  0.166667  0.041667  0.000000  0.000000  0.000000 
- 0.041667  0.125000  0.166667  0.000000  0.041667  0.416667  0.000000  0.000000  0.041667  0.041667  0.041667  0.000000  0.041667  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.041667 
- 0.000000  0.041667  0.083333  0.000000  0.041667  0.125000  0.041667  0.000000  0.083333  0.041667  0.000000  0.041667  0.041667  0.000000  0.333333  0.041667  0.000000  0.041667  0.041667  0.000000 
- 0.041667  0.041667  0.041667  0.083333  0.000000  0.000000  0.041667  0.083333  0.000000  0.041667  0.000000  0.000000  0.500000  0.000000  0.041667  0.041667  0.000000  0.041667  0.000000  0.000000 
- 0.000000  0.000000  0.000000  0.125000  0.041667  0.375000  0.041667  0.000000  0.000000  0.000000  0.000000  0.166667  0.000000  0.000000  0.041667  0.041667  0.041667  0.083333  0.041667  0.000000 
- 0.083333  0.000000  0.083333  0.083333  0.000000  0.166667  0.083333  0.000000  0.250000  0.000000  0.041667  0.083333  0.000000  0.083333  0.000000  0.041667  0.000000  0.000000  0.000000  0.000000 
- 0.000000  0.000000  0.125000  0.416667  0.041667  0.000000  0.083333  0.000000  0.000000  0.208333  0.041667  0.000000  0.000000  0.000000  0.000000  0.041667  0.000000  0.000000  0.000000  0.041667 
- 0.208333  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.041667  0.000000  0.041667  0.000000  0.000000  0.208333  0.000000  0.041667  0.166667  0.000000  0.291667  0.000000  0.000000 
- 0.000000  0.000000  0.583333  0.000000  0.000000  0.000000  0.375000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.041667  0.000000  0.000000  0.000000  0.000000  0.000000 
- 0.083333  0.000000  0.000000  0.000000  0.083333  0.166667  0.000000  0.000000  0.000000  0.250000  0.000000  0.000000  0.041667  0.000000  0.000000  0.041667  0.166667  0.166667  0.000000  0.000000 
- 0.125000  0.208333  0.000000  0.000000  0.083333  0.166667  0.000000  0.000000  0.000000  0.083333  0.000000  0.041667  0.000000  0.000000  0.166667  0.000000  0.000000  0.000000  0.000000  0.125000 
- 0.000000  0.000000  0.000000  0.000000  0.083333  0.083333  0.208333  0.000000  0.000000  0.000000  0.000000  0.000000  0.041667  0.083333  0.000000  0.083333  0.041667  0.000000  0.000000  0.375000 
- 0.125000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.125000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.250000  0.458333  0.041667  0.000000  0.000000 
- 0.000000  0.083333  0.000000  0.000000  0.291667  0.000000  0.000000  0.000000  0.000000  0.125000  0.000000  0.041667  0.000000  0.000000  0.000000  0.041667  0.000000  0.041667  0.083333  0.291667 
- 0.083333  0.291667  0.000000  0.000000  0.083333  0.000000  0.000000  0.000000  0.000000  0.041667  0.000000  0.000000  0.000000  0.000000  0.000000  0.083333  0.083333  0.000000  0.250000  0.083333 
- 0.416667  0.208333  0.000000  0.000000  0.000000  0.208333  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.041667  0.000000  0.000000  0.000000  0.125000  0.000000  0.000000 
- 0.083333  0.000000  0.000000  0.000000  0.000000  0.041667  0.000000  0.083333  0.000000  0.458333  0.000000  0.000000  0.000000  0.000000  0.000000  0.041667  0.083333  0.208333  0.000000  0.000000 
- 0.291667  0.000000  0.000000  0.000000  0.000000  0.166667  0.000000  0.000000  0.000000  0.041667  0.000000  0.125000  0.000000  0.083333  0.000000  0.250000  0.041667  0.000000  0.000000  0.000000 
- 0.291667  0.000000  0.000000  0.000000  0.041667  0.166667  0.000000  0.125000  0.000000  0.041667  0.000000  0.000000  0.000000  0.000000  0.000000  0.208333  0.083333  0.041667  0.000000  0.000000 
- 0.125000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.875000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
- 0.416667  0.083333  0.000000  0.000000  0.000000  0.000000  0.041667  0.000000  0.041667  0.000000  0.000000  0.000000  0.041667  0.000000  0.000000  0.250000  0.083333  0.041667  0.000000  0.000000 
- 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.416667  0.000000  0.458333  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.041667  0.083333  0.000000  0.000000 
- 0.125000  0.041667  0.000000  0.000000  0.000000  0.000000  0.000000  0.166667  0.000000  0.458333  0.041667  0.000000  0.000000  0.000000  0.000000  0.000000  0.083333  0.000000  0.000000  0.083333 
- 0.000000  0.000000  0.166667  0.125000  0.000000  0.291667  0.041667  0.000000  0.041667  0.000000  0.000000  0.125000  0.000000  0.041667  0.041667  0.083333  0.041667  0.000000  0.000000  0.000000 
- 0.083333  0.000000  0.000000  0.083333  0.000000  0.041667  0.041667  0.083333  0.166667  0.000000  0.000000  0.041667  0.000000  0.041667  0.125000  0.208333  0.041667  0.000000  0.000000  0.041667 
- 0.041667  0.000000  0.083333  0.125000  0.083333  0.000000  0.000000  0.125000  0.041667  0.375000  0.041667  0.000000  0.041667  0.000000  0.000000  0.041667  0.000000  0.000000  0.000000  0.000000 
- 0.000000  0.000000  0.250000  0.125000  0.041667  0.083333  0.125000  0.000000  0.000000  0.041667  0.000000  0.041667  0.000000  0.041667  0.041667  0.000000  0.125000  0.000000  0.041667  0.041667 
---------------------------------------------------------------------------------
-
-
-
-
-
-Time 32.68 secs.
-
-********************************************************************************
-
-
-********************************************************************************
-MOTIF  2	width =   14   sites =  21   llr = 376   E-value = 3.1e-019
-********************************************************************************
---------------------------------------------------------------------------------
-	Motif 2 Description
---------------------------------------------------------------------------------
-Simplified        A  ::::111::::1::
-pos.-specific     C  ::::::::::::61
-probability       D  12:11::1::::::
-matrix            E  1::61::2::::::
-                  F  1:::::::5:::::
-                  G  ::::1:::::::::
-                  H  ::::::::::::::
-                  I  5::::12::4::::
-                  K  ::313:::::11:1
-                  L  11:::53::24:1:
-                  M  ::::::::::::::
-                  N  :4::::::::::::
-                  P  ::::::::::::::
-                  Q  ::1::::2:::::6
-                  R  ::1:::1::::11:
-                  S  ::::1::1:114::
-                  T  ::1::1::::::::
-                  V  :12::21::3::::
-                  W  ::::::::2:::::
-                  Y  ::::::::3:::::
-
-         bits    5.8               
-                 5.2               
-                 4.6               
-                 4.0               
-Information      3.5         *     
-content          2.9         *   **
-(25.8 bits)      2.3    *    **  **
-                 1.7 **** *  **  **
-                 1.2 **************
-                 0.6 **************
-                 0.0 --------------
-
-Multilevel           INKEKLLEFILSCQ
-consensus                    YV    
-sequence                     WL    
-                                   
-                                   
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 sites sorted by position p-value
---------------------------------------------------------------------------------
-Sequence name             Start   P-value                 Site   
--------------             ----- ---------            --------------
-BET2_YEAST                  254  2.24e-13 SLAIIGRLDW INYEKLTEFILKCQ DEKKGGISDR
-RATRABGERB                  258  1.30e-12 SLKIIGRLHW IDREKLRSFILACQ DEETGGFADR
-RATRABGERB                  162  4.20e-12 TLALLGKLDA INVEKAIEFVLSCM NFDGGFGCRP
-RATRABGERB                   66  9.60e-12 VMDLMGQLHR MNKEEILVFIKSCQ HECGGVSASI
-RAM1_YEAST                  278  5.08e-11 SLAILRSMDQ INVEKLLEWSSARQ LQEERGFCGR
-CAL1_YEAST                  190  5.01e-10 CRSKEDFDEY IDTEKLLGYIMSQQ CYNGAFGAHN
-BET2_YEAST                   55  6.90e-10 ALCVLDSPET FVKEEVISFVLSCW DDKYGAFAPF
-RATRABGERB                  114  1.57e-09 ILTLYDSIHV INVDKVVAYVQSLQ KEDGSFAGDI
-PFTB_RAT                    172  2.34e-09 IIGTEEAYNV INREKLLQYLYSLK QPDGSFLMHV
-RAM1_YEAST                  330  4.59e-09 ILEAFGYGQC FNKHALRDYILYCC QEKEQPGLRD
-CAL1_YEAST                  126  1.65e-08 LRDYEYFETI LDKRSLARFVSKCQ RPDRGSFVSC
-PFTB_RAT                    268  1.65e-08 ALVILKKERS LNLKSLLQWVTSRQ MRFEGGFQGR
-PFTB_RAT                    220  1.65e-08 VASLTNIITP DLFEGTAEWIARCQ NWEGGIGGVP
-RAM1_YEAST                  229  2.54e-08 IATLLNILTE ELTEGVLNYLKNCQ NYEGGFGSCP
-PFTB_RAT                    330  4.58e-08 DPALSMSHWM FHQQALQEYILMCC QCPAGGLLDK
-CAL1_YEAST                  239  5.86e-08 LLSSLEKLSD KFKEDTITWLLHRQ VSSHGCMKFE
-PFTB_RAT                    121  1.52e-07 LELLDEPIPQ IVATDVCQFLELCQ SPDGGFGGGP
-CAL1_YEAST                  362  1.91e-07 IEGKFNGELC IPQEIFNDFSKRCC F         
-BET2_YEAST                  107  4.34e-07 TYDALDVLGK DRKVRLISFIRGNQ LEDGSFQGDR
-BET2_YEAST                  155  5.01e-07 ALSILGELTS EVVDPAVDFVLKCY NFDGGFGLCP
-RAM1_YEAST                  180  5.78e-07 CDNIDGCWDR IDRKGIYQWLISLK EPNGGFKTCL
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 block diagrams
---------------------------------------------------------------------------------
-SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-BET2_YEAST                        4.3e-07  54_[2]_38_[2]_34_[2]_85_[2]_58
-RATRABGERB                        1.6e-09  65_[2]_34_[2]_34_[2]_82_[2]_60
-RAM1_YEAST                        5.8e-07  179_[2]_35_[2]_35_[2]_38_[2]_88
-CAL1_YEAST                        5.9e-08  125_[2]_50_[2]_35_[2]_109_[2]_1
-PFTB_RAT                          2.3e-09  120_[2]_37_[2]_34_[2]_34_[2]_48_
-                                           [2]_94
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 in BLOCKS format
---------------------------------------------------------------------------------
-BL   MOTIF 2 width=14 seqs=21
-BET2_YEAST               (  254) INYEKLTEFILKCQ  1 
-RATRABGERB               (  258) IDREKLRSFILACQ  1 
-RATRABGERB               (  162) INVEKAIEFVLSCM  1 
-RATRABGERB               (   66) MNKEEILVFIKSCQ  1 
-RAM1_YEAST               (  278) INVEKLLEWSSARQ  1 
-CAL1_YEAST               (  190) IDTEKLLGYIMSQQ  1 
-BET2_YEAST               (   55) FVKEEVISFVLSCW  1 
-RATRABGERB               (  114) INVDKVVAYVQSLQ  1 
-PFTB_RAT                 (  172) INREKLLQYLYSLK  1 
-RAM1_YEAST               (  330) FNKHALRDYILYCC  1 
-CAL1_YEAST               (  126) LDKRSLARFVSKCQ  1 
-PFTB_RAT                 (  268) LNLKSLLQWVTSRQ  1 
-PFTB_RAT                 (  220) DLFEGTAEWIARCQ  1 
-RAM1_YEAST               (  229) ELTEGVLNYLKNCQ  1 
-PFTB_RAT                 (  330) FHQQALQEYILMCC  1 
-CAL1_YEAST               (  239) KFKEDTITWLLHRQ  1 
-PFTB_RAT                 (  121) IVATDVCQFLELCQ  1 
-CAL1_YEAST               (  362) IPQEIFNDFSKRCC  1 
-BET2_YEAST               (  107) DRKVRLISFIRGNQ  1 
-BET2_YEAST               (  155) EVVDPAVDFVLKCY  1 
-RAM1_YEAST               (  180) IDRKGIYQWLISLK  1 
-//
-
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 position-specific scoring matrix
---------------------------------------------------------------------------------
-log-odds matrix: alength= 20 w= 14 n= 1835 bayes= 7.42721 E= 3.1e-019 
-  -180   -316     28     36    140   -376   -308    299    -24    -14    117   -265   -348   -268   -271   -280   -167    -65   -321   -275 
-  -149   -393    133   -139    -11   -301     50   -227   -104    -40   -165    317      0   -117     32   -189   -143    106   -363   -290 
-    -9   -383   -234   -146     -8   -309   -205   -210    224   -111   -154   -135   -277    119    160   -196     94    147   -356      0 
-  -174   -491     57    300   -396   -328     51   -351     95   -378   -243   -145   -289     50     33   -217     12    -38   -433   -348 
-    61   -430     48     71   -335     60   -173    -37    243   -328   -192    -95      2    -80     41     27   -130   -250   -375   -291 
-    55   -332   -507   -413     10   -422   -361     96   -365    194    -94   -334   -390   -340   -334   -331     92    167   -344   -304 
-    61     19   -456   -363   -205   -378   -316    176   -315    118    -79     32   -352     14     98   -285     19     91   -309     10 
-    -6   -431     96    174   -336    -74   -174   -302    -67   -329   -193     61   -249    205     41     72     21    -37   -376   -291 
-  -585   -591   -675   -658    339   -654   -303   -494   -585   -478   -424   -461   -604   -498   -508   -576   -538   -496    362    282 
-  -333   -431   -610   -551   -351   -574   -548    290   -506     94   -192   -471   -535   -506   -502      6   -316    227   -516   -458 
-    -7   -410   -200      4   -314   -290   -182    -28    139    137     97   -106   -256     51     38     25     20   -221   -366     -4 
-    61   -428   -188   -102   -334    -74     52   -298    141   -130     93     61   -249    -81    112    195   -129   -248   -374     -5 
-  -318    386   -431   -324   -470   -438   -297   -372    -61     20   -304     47   -439     41    186   -360   -300   -347   -474   -424 
-  -264     97   -402   -180   -325   -446   -118   -335     29   -335     49   -229   -343    411   -155   -328   -274   -317     47    -50 
---------------------------------------------------------------------------------
-
---------------------------------------------------------------------------------
-	Motif 2 position-specific probability matrix
---------------------------------------------------------------------------------
-letter-probability matrix: alength= 20 w= 14 nsites= 21 E= 3.1e-019 
- 0.000000  0.000000  0.095238  0.095238  0.142857  0.000000  0.000000  0.476190  0.047619  0.095238  0.047619  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
- 0.000000  0.000000  0.190476  0.000000  0.047619  0.000000  0.047619  0.000000  0.000000  0.095238  0.000000  0.380952  0.047619  0.000000  0.047619  0.000000  0.000000  0.142857  0.000000  0.000000 
- 0.047619  0.000000  0.000000  0.000000  0.047619  0.000000  0.000000  0.000000  0.285714  0.047619  0.000000  0.000000  0.000000  0.095238  0.142857  0.000000  0.095238  0.190476  0.000000  0.047619 
- 0.000000  0.000000  0.095238  0.571429  0.000000  0.000000  0.047619  0.000000  0.095238  0.000000  0.000000  0.000000  0.000000  0.047619  0.047619  0.000000  0.047619  0.047619  0.000000  0.000000 
- 0.095238  0.000000  0.095238  0.095238  0.000000  0.142857  0.000000  0.047619  0.333333  0.000000  0.000000  0.000000  0.047619  0.000000  0.047619  0.095238  0.000000  0.000000  0.000000  0.000000 
- 0.095238  0.000000  0.000000  0.000000  0.047619  0.000000  0.000000  0.095238  0.000000  0.476190  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.095238  0.190476  0.000000  0.000000 
- 0.095238  0.047619  0.000000  0.000000  0.000000  0.000000  0.000000  0.190476  0.000000  0.285714  0.000000  0.047619  0.000000  0.047619  0.095238  0.000000  0.047619  0.095238  0.000000  0.047619 
- 0.047619  0.000000  0.142857  0.238095  0.000000  0.047619  0.000000  0.000000  0.000000  0.000000  0.000000  0.047619  0.000000  0.190476  0.047619  0.142857  0.047619  0.047619  0.000000  0.000000 
- 0.000000  0.000000  0.000000  0.000000  0.476190  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.238095  0.285714 
- 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.380952  0.000000  0.238095  0.000000  0.000000  0.000000  0.000000  0.000000  0.095238  0.000000  0.285714  0.000000  0.000000 
- 0.047619  0.000000  0.000000  0.047619  0.000000  0.000000  0.000000  0.047619  0.142857  0.380952  0.047619  0.000000  0.000000  0.047619  0.047619  0.095238  0.047619  0.000000  0.000000  0.047619 
- 0.095238  0.000000  0.000000  0.000000  0.000000  0.047619  0.047619  0.000000  0.142857  0.047619  0.047619  0.047619  0.000000  0.000000  0.095238  0.380952  0.000000  0.000000  0.000000  0.047619 
- 0.000000  0.619048  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.142857  0.000000  0.047619  0.000000  0.047619  0.142857  0.000000  0.000000  0.000000  0.000000  0.000000 
- 0.000000  0.142857  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.095238  0.000000  0.047619  0.000000  0.000000  0.619048  0.000000  0.000000  0.000000  0.000000  0.047619  0.047619 
---------------------------------------------------------------------------------
-
-
-
-
-
-Time 51.86 secs.
-
-********************************************************************************
-
-
-********************************************************************************
-SUMMARY OF MOTIFS
-********************************************************************************
-
---------------------------------------------------------------------------------
-	Combined block diagrams: non-overlapping sites with p-value < 0.0001
---------------------------------------------------------------------------------
-SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
--------------            ----------------  -------------
-RAM1_YEAST                       2.14e-20  144_[1(1.27e-16)]_5_[2(5.78e-07)]_4_[1(1.33e-13)]_1_[2(2.54e-08)]_4_[1(5.00e-17)]_1_[2(5.08e-11)]_4_[1(3.47e-16)]_4_[2(4.59e-09)]_5_[1(3.52e-13)]_35_[2(9.16e-05)]_4
-PFTB_RAT                         2.44e-21  120_[2(1.52e-07)]_3_[1(4.30e-19)]_4_[2(2.34e-09)]_3_[1(2.81e-14)]_1_[2(1.65e-08)]_3_[1(1.15e-19)]_1_[2(1.65e-08)]_4_[1(3.17e-16)]_14_[2(4.58e-08)]_4_[1(4.30e-15)]_60
-BET2_YEAST                       1.02e-27  6_[2(5.17e-05)]_3_[1(3.11e-10)]_1_[2(6.90e-10)]_4_[1(7.78e-14)]_4_[2(4.34e-07)]_3_[1(3.41e-17)]_1_[2(5.01e-07)]_3_[1(2.10e-18)]_21_[1(7.28e-22)]_1_[2(2.24e-13)]_4_[1(6.64e-17)]_24
-RATRABGERB                       4.90e-26  65_[2(9.60e-12)]_3_[1(2.40e-14)]_1_[2(1.57e-09)]_3_[1(8.19e-19)]_1_[2(4.20e-12)]_3_[1(7.36e-19)]_18_[1(6.18e-21)]_1_[2(1.30e-12)]_4_[1(1.43e-17)]_26
-CAL1_YEAST                       3.16e-22  125_[2(1.65e-08)]_50_[2(5.01e-10)]_1_[1(1.14e-13)]_4_[2(5.86e-08)]_22_[1(9.17e-20)]_22_[1(5.47e-13)]_5_[2(1.91e-07)]_1
---------------------------------------------------------------------------------
-
-********************************************************************************
-
-
-********************************************************************************
-Stopped because nmotifs = 2 reached.
-********************************************************************************
-
-CPU: pmgm2
-
-********************************************************************************
diff --git a/Tests/Motif/transfac.dat b/Tests/Motif/transfac.dat
deleted file mode 100644
--- a/Tests/Motif/transfac.dat
+++ /dev/null
@@ -1,31 +0,0 @@
-VV  EXAMPLE January 15, 2013
-XX
-//
-ID  motif1
-P0      A      C      G      T
-01      1      2      2      0      S
-02      2      1      2      0      R
-03      3      0      1      1      A
-04      0      5      0      0      C
-05      5      0      0      0      A
-06      0      0      4      1      G
-07      0      1      4      0      G
-08      0      0      0      5      T
-09      0      0      5      0      G
-10      0      1      2      2      K
-11      0      2      0      3      Y
-12      1      0      3      1      G
-//
-ID  motif2
-P0      A      C      G      T
-01      2      1      2      0      R
-02      1      2      2      0      S
-03      0      5      0      0      C
-04      3      0      1      1      A
-05      0      0      4      1      G
-06      5      0      0      0      A
-07      0      1      4      0      G
-08      0      0      5      0      G
-09      0      0      0      5      T
-10      0      2      0      3      Y
-//