********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date: )
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= HEM1-HEM14.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YDR232W 1.0000 498 MIT_Spar_c117_4603 1.0000 498
MIT_Smik_c228_4055 1.0000 498 WashU_Skud_Contig2069.5 1.0000 498
WashU_Sbay_Contig461.5 1.0000 498 SGD_Scer_YER014W 1.0000 322
MIT_Spar_c425_6072 1.0000 322 MIT_Smik_c283_5928 1.0000 322
MIT_Sbay_c84_6418 1.0000 322
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM1-HEM14.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
model: mod= oops nmotifs= 5 evt= inf
object function= E-value of product of p-values
width: minw= 6 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 9 maxsites= 9 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 3778 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.293 C 0.207 G 0.207 T 0.293
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324
********************************************************************************
********************************************************************************
MOTIF 1 width = 20 sites = 9 llr = 202 E-value = 1.6e-028
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A a3a9:::::aa:::aa:6:1
pos.-specific C :7:::1:46::::a:::2:1
probability G :::119664::aa:::91:8
matrix T ::::9:4:::::::::11a:
bits 2.5 ***
2.3 ***
2.0 * *** *
1.8 * *** *
Information 1.5 * * * ********** **
content 1.3 ****** ********** **
(32.4 bits) 1.0 ***************** **
0.8 ***************** **
0.5 ***************** **
0.3 ********************
0.0 --------------------
Multilevel ACAATGGGCAAGGCAAGATG
consensus A TCG C
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig461.5 + 280 3.60e-13 CCGGGACAGA ACAATGGGCAAGGCAAGATG AAAAATCTCC
MIT_Smik_c228_4055 + 285 3.60e-13 TTGAATTAGA ACAATGGGCAAGGCAAGATG AAAATTTCCG
MIT_Spar_c117_4603 + 282 3.60e-13 ATGGGTCAGA ACAATGGGCAAGGCAAGATG AAAAATTTCT
SGD_Scer_YDR232W + 287 3.60e-13 ATGGATCAGA ACAATGGGCAAGGCAAGATG AAAAATTTCC
MIT_Spar_c425_6072 + 133 2.98e-11 CCGAAGCAAC AAAATGTCGAAGGCAAGATG AAAGGCGTTT
MIT_Smik_c283_5928 + 128 4.86e-11 CTCCGAAGCA ACAAGGTCGAAGGCAAGCTG AAAGGCATTT
WashU_Skud_Contig2069.5 + 285 9.69e-11 CTGGATCGGA ACAATGGGCAAGGCAATGTG AAAAATTTCC
MIT_Sbay_c84_6418 + 126 8.09e-10 CCGAAACAAC AAAATCTCGAAGGCAAGCTA AGGTAAAAAT
SGD_Scer_YER014W + 134 8.09e-10 CCGAAGCAAC AAAGTGTCGAAGGCAAGTTC AAAGGCGTTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig461.5 3.6e-13 279_[+1]_199
MIT_Smik_c228_4055 3.6e-13 284_[+1]_194
MIT_Spar_c117_4603 3.6e-13 281_[+1]_197
SGD_Scer_YDR232W 3.6e-13 286_[+1]_192
MIT_Spar_c425_6072 3e-11 132_[+1]_170
MIT_Smik_c283_5928 4.9e-11 127_[+1]_175
WashU_Skud_Contig2069.5 9.7e-11 284_[+1]_194
MIT_Sbay_c84_6418 8.1e-10 125_[+1]_177
SGD_Scer_YER014W 8.1e-10 133_[+1]_169
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig461.5 ( 280) ACAATGGGCAAGGCAAGATG 1
MIT_Smik_c228_4055 ( 285) ACAATGGGCAAGGCAAGATG 1
MIT_Spar_c117_4603 ( 282) ACAATGGGCAAGGCAAGATG 1
SGD_Scer_YDR232W ( 287) ACAATGGGCAAGGCAAGATG 1
MIT_Spar_c425_6072 ( 133) AAAATGTCGAAGGCAAGATG 1
MIT_Smik_c283_5928 ( 128) ACAAGGTCGAAGGCAAGCTG 1
WashU_Skud_Contig2069.5 ( 285) ACAATGGGCAAGGCAATGTG 1
MIT_Sbay_c84_6418 ( 126) AAAATCTCGAAGGCAAGCTA 1
SGD_Scer_YER014W ( 134) AAAGTGTCGAAGGCAAGTTC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 3607 bayes= 8.64305 E= 1.6e-028
162 -982 -982 -982
4 192 -982 -982
162 -982 -982 -982
145 -982 -66 -982
-982 -982 -66 145
-982 -66 234 -982
-982 -982 166 45
-982 134 166 -982
-982 166 134 -982
162 -982 -982 -982
162 -982 -982 -982
-982 -982 251 -982
-982 -982 251 -982
-982 251 -982 -982
162 -982 -982 -982
162 -982 -982 -982
-982 -982 234 -154
78 34 -66 -154
-982 -982 -982 162
-154 -66 215 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.6e-028
1.000000 0.000000 0.000000 0.000000
0.333333 0.666667 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.000000 0.111111 0.888889
0.000000 0.111111 0.888889 0.000000
0.000000 0.000000 0.555556 0.444444
0.000000 0.444444 0.555556 0.000000
0.000000 0.555556 0.444444 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
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 0.888889 0.111111
0.555556 0.222222 0.111111 0.111111
0.000000 0.000000 0.000000 1.000000
0.111111 0.111111 0.777778 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
A[CA]AATG[GT][GC][CG]AAGGCAAG[AC]TG
--------------------------------------------------------------------------------
Time 1.73 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 18 sites = 9 llr = 163 E-value = 9.8e-015
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 37a:aa:44:4:a27:a:
pos.-specific C 11::::a1:::::::::4
probability G 62:a:::46::a:829:1
matrix T :::::::::a6:::11:4
bits 2.5 * * *
2.3 * * *
2.0 * * * *
1.8 * * * *
Information 1.5 ***** * *** **
content 1.3 ***** * *** **
(26.1 bits) 1.0 ***** ** *** **
0.8 ************** ***
0.5 ******************
0.3 ******************
0.0 ------------------
Multilevel GAAGAACAGTTGAGAGAC
consensus AG GA A AG T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ------------------
WashU_Skud_Contig2069.5 + 163 6.31e-12 CGTGTGGAGG GAAGAACGGTTGAGAGAC AGCAGAGCAC
SGD_Scer_YDR232W + 166 6.31e-12 GCGTGTAAAG GAAGAACGGTTGAGAGAC AGCAGAGCAG
WashU_Sbay_Contig461.5 + 162 2.27e-10 CGTGTGGAGG GAAGAACCGTTGAGAGAC AACAGAGCAG
MIT_Spar_c117_4603 + 161 2.27e-10 GCGTGTAAAG GAAGAACGGTTGAGAGAG AGCAGAGCAG
MIT_Smik_c283_5928 - 71 6.85e-09 AGAGTAATGG AAAGAACAATAGAGGGAT TTGCAAAAGA
MIT_Spar_c425_6072 - 69 6.85e-09 AGAATAATAG AGAGAACAATAGAGAGAT CCGCGAAGGA
MIT_Sbay_c84_6418 - 64 1.24e-08 GAACAATAAG GAAGAACAATAGAAGGAT GCGAAAGGAC
MIT_Smik_c228_4055 + 162 3.13e-08 ACGTGTGAAG CCAGAACGGTTGAATGAC AGTAGAGGAG
SGD_Scer_YER014W - 69 3.60e-08 AGTATAATAG AGAGAACAATAGAGATAT TCGCGAAGAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2069.5 6.3e-12 162_[+2]_318
SGD_Scer_YDR232W 6.3e-12 165_[+2]_315
WashU_Sbay_Contig461.5 2.3e-10 161_[+2]_319
MIT_Spar_c117_4603 2.3e-10 160_[+2]_320
MIT_Smik_c283_5928 6.8e-09 70_[-2]_234
MIT_Spar_c425_6072 6.8e-09 68_[-2]_236
MIT_Sbay_c84_6418 1.2e-08 63_[-2]_241
MIT_Smik_c228_4055 3.1e-08 161_[+2]_319
SGD_Scer_YER014W 3.6e-08 68_[-2]_236
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=18 seqs=9
WashU_Skud_Contig2069.5 ( 163) GAAGAACGGTTGAGAGAC 1
SGD_Scer_YDR232W ( 166) GAAGAACGGTTGAGAGAC 1
WashU_Sbay_Contig461.5 ( 162) GAAGAACCGTTGAGAGAC 1
MIT_Spar_c117_4603 ( 161) GAAGAACGGTTGAGAGAG 1
MIT_Smik_c283_5928 ( 71) AAAGAACAATAGAGGGAT 1
MIT_Spar_c425_6072 ( 69) AGAGAACAATAGAGAGAT 1
MIT_Sbay_c84_6418 ( 64) GAAGAACAATAGAAGGAT 1
MIT_Smik_c228_4055 ( 162) CCAGAACGGTTGAATGAC 1
SGD_Scer_YER014W ( 69) AGAGAACAATAGAGATAT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 18 n= 3625 bayes= 8.65025 E= 9.8e-015
4 -66 166 -982
104 -66 34 -982
162 -982 -982 -982
-982 -982 251 -982
162 -982 -982 -982
162 -982 -982 -982
-982 251 -982 -982
45 -66 134 -982
45 -982 166 -982
-982 -982 -982 162
45 -982 -982 78
-982 -982 251 -982
162 -982 -982 -982
-55 -982 215 -982
104 -982 34 -154
-982 -982 234 -154
162 -982 -982 -982
-982 134 -66 45
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 18 nsites= 9 E= 9.8e-015
0.333333 0.111111 0.555556 0.000000
0.666667 0.111111 0.222222 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.444444 0.111111 0.444444 0.000000
0.444444 0.000000 0.555556 0.000000
0.000000 0.000000 0.000000 1.000000
0.444444 0.000000 0.000000 0.555556
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.222222 0.000000 0.777778 0.000000
0.666667 0.000000 0.222222 0.111111
0.000000 0.000000 0.888889 0.111111
1.000000 0.000000 0.000000 0.000000
0.000000 0.444444 0.111111 0.444444
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[GA][AG]AGAAC[AG][GA]T[TA]GA[GA][AG]GA[CT]
--------------------------------------------------------------------------------
Time 3.42 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 185 E-value = 4.5e-020
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :3a6:4a4::a::aa111:4
pos.-specific C 97:4::::a::63::::63:
probability G :::::6:6:a:46::49366
matrix T 1:::a:::::::1::4::1:
bits 2.5 **
2.3 **
2.0 * ** *
1.8 * ** *
Information 1.5 * * * * **** ** *
content 1.3 *** * * **** ** *
(29.6 bits) 1.0 *************** ****
0.8 *************** ****
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CCAATGAGCGACGAAGGCGG
consensus A C A A GC T GCA
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2069.5 + 370 1.19e-13 CGGCCGCAGA CCAATGAGCGACGAAGGCGG CCTTTCGTAG
MIT_Spar_c117_4603 + 368 1.19e-13 CGGCCGCAGA CCAATGAGCGACGAAGGCGG CCTTTCCGAG
SGD_Scer_YDR232W + 373 1.19e-13 CGGCCGCAGA CCAATGAGCGACGAAGGCGG CCTTTCCGAG
MIT_Smik_c228_4055 + 370 2.41e-11 CAAGCGCAGA CCAATGAGCGACGAAAGCGG CCTTTTGAAG
WashU_Sbay_Contig461.5 + 367 6.46e-11 CGGGCGCAGA CCAATGAGCGACGAAGACGG CTTTTGGGCG
MIT_Sbay_c84_6418 + 161 1.68e-09 AAAATATTCA CCACTAAACGAGCAATGACA GTTATATTCA
MIT_Smik_c283_5928 + 160 3.61e-09 AGGCATTTTA CAACTAAACGAGCAATGGTA GCTTTTGATT
MIT_Spar_c425_6072 + 165 3.61e-09 AGGCGTTTTG CAACTAAACGAGTAATGGCA GCTTTTAATT
SGD_Scer_YER014W + 166 5.94e-09 AGGCGTTTTG TAACTAAACGAGCAATGGCA GCTTTCAATT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2069.5 1.2e-13 369_[+3]_109
MIT_Spar_c117_4603 1.2e-13 367_[+3]_111
SGD_Scer_YDR232W 1.2e-13 372_[+3]_106
MIT_Smik_c228_4055 2.4e-11 369_[+3]_109
WashU_Sbay_Contig461.5 6.5e-11 366_[+3]_112
MIT_Sbay_c84_6418 1.7e-09 160_[+3]_142
MIT_Smik_c283_5928 3.6e-09 159_[+3]_143
MIT_Spar_c425_6072 3.6e-09 164_[+3]_138
SGD_Scer_YER014W 5.9e-09 165_[+3]_137
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
WashU_Skud_Contig2069.5 ( 370) CCAATGAGCGACGAAGGCGG 1
MIT_Spar_c117_4603 ( 368) CCAATGAGCGACGAAGGCGG 1
SGD_Scer_YDR232W ( 373) CCAATGAGCGACGAAGGCGG 1
MIT_Smik_c228_4055 ( 370) CCAATGAGCGACGAAAGCGG 1
WashU_Sbay_Contig461.5 ( 367) CCAATGAGCGACGAAGACGG 1
MIT_Sbay_c84_6418 ( 161) CCACTAAACGAGCAATGACA 1
MIT_Smik_c283_5928 ( 160) CAACTAAACGAGCAATGGTA 1
MIT_Spar_c425_6072 ( 165) CAACTAAACGAGTAATGGCA 1
SGD_Scer_YER014W ( 166) TAACTAAACGAGCAATGGCA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 3607 bayes= 8.64305 E= 4.5e-020
-982 234 -982 -154
4 192 -982 -982
162 -982 -982 -982
78 134 -982 -982
-982 -982 -982 162
45 -982 166 -982
162 -982 -982 -982
45 -982 166 -982
-982 251 -982 -982
-982 -982 251 -982
162 -982 -982 -982
-982 166 134 -982
-982 92 166 -154
162 -982 -982 -982
162 -982 -982 -982
-154 -982 134 45
-154 -982 234 -982
-154 166 92 -982
-982 92 166 -154
45 -982 166 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.5e-020
0.000000 0.888889 0.000000 0.111111
0.333333 0.666667 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.555556 0.444444 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.444444 0.000000 0.555556 0.000000
1.000000 0.000000 0.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.555556 0.444444 0.000000
0.000000 0.333333 0.555556 0.111111
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.111111 0.000000 0.444444 0.444444
0.111111 0.000000 0.888889 0.000000
0.111111 0.555556 0.333333 0.000000
0.000000 0.333333 0.555556 0.111111
0.444444 0.000000 0.555556 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
C[CA]A[AC]T[GA]A[GA]CGA[CG][GC]AA[GT]G[CG][GC][GA]
--------------------------------------------------------------------------------
Time 4.97 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 9 llr = 174 E-value = 3.1e-016
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 896a21:1:::411:::4a1
pos.-specific C ::::363778:64:8a:6::
probability G ::::4:6:32a:442:a::9
matrix T 214::312:::::4::::::
bits 2.5 * **
2.3 * **
2.0 * ** *
1.8 ** *** *
Information 1.5 * *** *** **
content 1.3 * *** *** **
(27.9 bits) 1.0 * * ******* ******
0.8 ************* ******
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel AAAAGCGCCCGCCGCCGCAG
consensus T T CTCTGG AGTG A
sequence A
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c117_4603 + 347 3.34e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
SGD_Scer_YDR232W + 352 3.34e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
WashU_Skud_Contig2069.5 + 349 3.24e-12 ACAATGACCA AAAAGCGTCCGCGGCCGCAG ACCAATGAGC
WashU_Sbay_Contig461.5 + 346 1.26e-10 CAATGACCAA AAAAACGCCGGCGGGCGCAG ACCAATGAGC
MIT_Spar_c425_6072 + 109 6.37e-10 TTCTTTTTTA AATACTCCGCGACTCCGAAG CAACAAAATG
SGD_Scer_YER014W + 110 6.37e-10 TCTTTTTTTG AATACTCCGCGACTCCGAAG CAACAAAGTG
MIT_Smik_c228_4055 + 349 6.96e-10 ACAATGACCA AAAAGCGCCCGCAAGCGCAG ACCAATGAGC
MIT_Sbay_c84_6418 + 102 3.58e-08 TCGTTTTTTT TATACTCTGCGACTCCGAAA CAACAAAATC
MIT_Smik_c283_5928 + 106 2.54e-07 TCTTTTCTTT TTTAAATACGGACTCCGAAG CAACAAGGTC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c117_4603 3.3e-14 346_[+4]_132
SGD_Scer_YDR232W 3.3e-14 351_[+4]_127
WashU_Skud_Contig2069.5 3.2e-12 348_[+4]_130
WashU_Sbay_Contig461.5 1.3e-10 345_[+4]_133
MIT_Spar_c425_6072 6.4e-10 108_[+4]_194
SGD_Scer_YER014W 6.4e-10 109_[+4]_193
MIT_Smik_c228_4055 7e-10 348_[+4]_130
MIT_Sbay_c84_6418 3.6e-08 101_[+4]_201
MIT_Smik_c283_5928 2.5e-07 105_[+4]_197
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=9
MIT_Spar_c117_4603 ( 347) AAAAGCGCCCGCGGCCGCAG 1
SGD_Scer_YDR232W ( 352) AAAAGCGCCCGCGGCCGCAG 1
WashU_Skud_Contig2069.5 ( 349) AAAAGCGTCCGCGGCCGCAG 1
WashU_Sbay_Contig461.5 ( 346) AAAAACGCCGGCGGGCGCAG 1
MIT_Spar_c425_6072 ( 109) AATACTCCGCGACTCCGAAG 1
SGD_Scer_YER014W ( 110) AATACTCCGCGACTCCGAAG 1
MIT_Smik_c228_4055 ( 349) AAAAGCGCCCGCAAGCGCAG 1
MIT_Sbay_c84_6418 ( 102) TATACTCTGCGACTCCGAAA 1
MIT_Smik_c283_5928 ( 106) TTTAAATACGGACTCCGAAG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 3607 bayes= 8.64305 E= 3.1e-016
126 -982 -982 -55
145 -982 -982 -154
78 -982 -982 45
162 -982 -982 -982
-55 92 134 -982
-154 166 -982 4
-982 92 166 -154
-154 192 -982 -55
-982 192 92 -982
-982 215 34 -982
-982 -982 251 -982
45 166 -982 -982
-154 134 134 -982
-154 -982 134 45
-982 215 34 -982
-982 251 -982 -982
-982 -982 251 -982
45 166 -982 -982
162 -982 -982 -982
-154 -982 234 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.1e-016
0.777778 0.000000 0.000000 0.222222
0.888889 0.000000 0.000000 0.111111
0.555556 0.000000 0.000000 0.444444
1.000000 0.000000 0.000000 0.000000
0.222222 0.333333 0.444444 0.000000
0.111111 0.555556 0.000000 0.333333
0.000000 0.333333 0.555556 0.111111
0.111111 0.666667 0.000000 0.222222
0.000000 0.666667 0.333333 0.000000
0.000000 0.777778 0.222222 0.000000
0.000000 0.000000 1.000000 0.000000
0.444444 0.555556 0.000000 0.000000
0.111111 0.444444 0.444444 0.000000
0.111111 0.000000 0.444444 0.444444
0.000000 0.777778 0.222222 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.444444 0.555556 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[AT]A[AT]A[GCA][CT][GC][CT][CG][CG]G[CA][CG][GT][CG]CG[CA]AG
--------------------------------------------------------------------------------
Time 6.50 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 17 sites = 9 llr = 139 E-value = 2.2e-007
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Motif 5 Description
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Simplified A 79:::a3:a39::8:3a
pos.-specific C ::79::::::::1:76:
probability G :1:19:61:61a1211:
matrix T 3:3:1:19:1::8:2::
bits 2.5 *
2.3 *
2.0 ** *
1.8 ** *
Information 1.5 *** * * *
content 1.3 ***** ** ** *
(22.3 bits) 1.0 ***** ** ** ** *
0.8 *****************
0.5 *****************
0.3 *****************
0.0 -----------------
Multilevel AACCGAGTAGAGTACCA
consensus T T A A GTA
sequence
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Motif 5 sites sorted by position p-value
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Sequence name Strand Start P-value Site
------------- ------ ----- --------- -----------------
WashU_Skud_Contig2069.5 + 201 3.60e-11 AGCGCAACAC AACCGAGTAGAGTACCA GCAGACGGAG
MIT_Smik_c228_4055 + 200 3.60e-11 GGTGCAACAC AACCGAGTAGAGTACCA GCTGACGGAA
WashU_Sbay_Contig461.5 + 196 1.71e-09 GCAGGGTGCA AACCGATTAGAGTACCA GCAGACGAGA
MIT_Spar_c117_4603 + 201 3.89e-09 TGCAACACAC AACCGAATAGAGTATCA GCTGACGGGA
SGD_Scer_YDR232W + 206 3.89e-09 TGCAACACAC AACCGAATAGAGTATCA GCTGACGGAA
SGD_Scer_YER014W - 28 4.70e-08 AATTCAAACA TATCGAGTAAAGTGCAA TTGAGAACGC
MIT_Spar_c425_6072 - 28 3.05e-07 AATTCAATCC TATCGAGGAAGGTACAA TTGGGAACGC
MIT_Sbay_c84_6418 - 9 1.50e-06 CGTAAGAAAC AGCGGAATAAAGGAGAA CTTCGACA
MIT_Smik_c283_5928 - 30 1.85e-06 AGTTTAACCA TATCTAGTATAGCGCGA TTAAAGAAAT
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Motif 5 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2069.5 3.6e-11 200_[+5]_281
MIT_Smik_c228_4055 3.6e-11 199_[+5]_282
WashU_Sbay_Contig461.5 1.7e-09 195_[+5]_286
MIT_Spar_c117_4603 3.9e-09 200_[+5]_281
SGD_Scer_YDR232W 3.9e-09 205_[+5]_276
SGD_Scer_YER014W 4.7e-08 27_[-5]_278
MIT_Spar_c425_6072 3e-07 27_[-5]_278
MIT_Sbay_c84_6418 1.5e-06 8_[-5]_297
MIT_Smik_c283_5928 1.8e-06 29_[-5]_276
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Motif 5 in BLOCKS format
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BL MOTIF 5 width=17 seqs=9
WashU_Skud_Contig2069.5 ( 201) AACCGAGTAGAGTACCA 1
MIT_Smik_c228_4055 ( 200) AACCGAGTAGAGTACCA 1
WashU_Sbay_Contig461.5 ( 196) AACCGATTAGAGTACCA 1
MIT_Spar_c117_4603 ( 201) AACCGAATAGAGTATCA 1
SGD_Scer_YDR232W ( 206) AACCGAATAGAGTATCA 1
SGD_Scer_YER014W ( 28) TATCGAGTAAAGTGCAA 1
MIT_Spar_c425_6072 ( 28) TATCGAGGAAGGTACAA 1
MIT_Sbay_c84_6418 ( 9) AGCGGAATAAAGGAGAA 1
MIT_Smik_c283_5928 ( 30) TATCTAGTATAGCGCGA 1
//
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Motif 5 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 17 n= 3634 bayes= 8.65384 E= 2.2e-007
104 -982 -982 4
145 -982 -66 -982
-982 192 -982 4
-982 234 -66 -982
-982 -982 234 -154
162 -982 -982 -982
4 -982 166 -154
-982 -982 -66 145
162 -982 -982 -982
4 -982 166 -154
145 -982 -66 -982
-982 -982 251 -982
-982 -66 -66 126
126 -982 34 -982
-982 192 -66 -55
4 166 -66 -982
162 -982 -982 -982
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Motif 5 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 17 nsites= 9 E= 2.2e-007
0.666667 0.000000 0.000000 0.333333
0.888889 0.000000 0.111111 0.000000
0.000000 0.666667 0.000000 0.333333
0.000000 0.888889 0.111111 0.000000
0.000000 0.000000 0.888889 0.111111
1.000000 0.000000 0.000000 0.000000
0.333333 0.000000 0.555556 0.111111
0.000000 0.000000 0.111111 0.888889
1.000000 0.000000 0.000000 0.000000
0.333333 0.000000 0.555556 0.111111
0.888889 0.000000 0.111111 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.111111 0.111111 0.777778
0.777778 0.000000 0.222222 0.000000
0.000000 0.666667 0.111111 0.222222
0.333333 0.555556 0.111111 0.000000
1.000000 0.000000 0.000000 0.000000
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Motif 5 regular expression
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[AT]A[CT]CGA[GA]TA[GA]AGT[AG][CT][CA]A
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Time 7.92 secs.
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SUMMARY OF MOTIFS
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR232W 1.25e-37 165_[+2(6.31e-12)]_[+5(9.28e-05)]_5_[+5(3.89e-09)]_64_[+1(3.60e-13)]_45_[+4(3.34e-14)]_1_[+3(1.19e-13)]_106
MIT_Spar_c117_4603 3.90e-36 160_[+2(2.27e-10)]_[+5(9.28e-05)]_5_[+5(3.89e-09)]_64_[+1(3.60e-13)]_45_[+4(3.34e-14)]_1_[+3(1.19e-13)]_111
MIT_Smik_c228_4055 1.05e-29 161_[+2(3.13e-08)]_[+5(1.70e-05)]_3_[+5(3.60e-11)]_68_[+1(3.60e-13)]_44_[+4(6.96e-10)]_1_[+3(2.41e-11)]_109
WashU_Skud_Contig2069.5 2.42e-35 162_[+2(6.31e-12)]_20_[+5(3.60e-11)]_67_[+1(9.69e-11)]_44_[+4(3.24e-12)]_1_[+3(1.19e-13)]_109
WashU_Sbay_Contig461.5 1.93e-30 125_[+4(6.68e-05)]_16_[+2(2.27e-10)]_16_[+5(1.71e-09)]_67_[+1(3.60e-13)]_46_[+4(1.26e-10)]_1_[+3(6.46e-11)]_19_[+1(2.50e-06)]_73
SGD_Scer_YER014W 3.02e-22 27_[-5(4.70e-08)]_24_[-2(3.60e-08)]_23_[+4(6.37e-10)]_4_[+1(8.09e-10)]_12_[+3(5.94e-09)]_137
MIT_Spar_c425_6072 1.04e-23 27_[-5(3.05e-07)]_24_[-2(6.85e-09)]_22_[+4(6.37e-10)]_4_[+1(2.98e-11)]_12_[+3(3.61e-09)]_138
MIT_Smik_c283_5928 2.42e-20 29_[-5(1.85e-06)]_24_[-2(6.85e-09)]_17_[+4(2.54e-07)]_2_[+1(4.86e-11)]_12_[+3(3.61e-09)]_143
MIT_Sbay_c84_6418 3.76e-20 8_[-5(1.50e-06)]_38_[-2(1.24e-08)]_20_[+4(3.58e-08)]_4_[+1(8.09e-10)]_15_[+3(1.68e-09)]_13_[-2(2.04e-05)]_111
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Stopped because nmotifs = 5 reached.
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CPU: dhn02990.mrc-dunn.cam.ac.uk
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