********************************************************************************
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= HEM4-HEM13.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YOR278W 1.0000 635 MIT_Spar_c261_21317 1.0000 635
MIT_Smik_c492_20940 1.0000 635 WashU_Skud_Contig1682.4 1.0000 635
WashU_Sbay_Contig635.57 1.0000 635 SGD_Scer_YDR044W 1.0000 1000
MIT_Spar_c130_3912 1.0000 1000 MIT_Sbay_c896_21290 1.0000 1000
WashU_Smik_Contig2283.3 1.0000 1000
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM4-HEM13.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= 7175 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.306 C 0.194 G 0.194 T 0.306
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 = 201 E-value = 6.7e-025
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :::::63:::::86::61::
pos.-specific C :61::4:::9:::2:a::::
probability G a46:a::a:1::2:9:::9a
matrix T ::3a::7:a:aa:21:491:
bits 2.5 * * * * *
2.3 * * * * *
2.0 * * * * ** **
1.8 * * * * ** **
Information 1.5 ** ** ***** ** **
content 1.3 ** ** ***** ** **
(32.2 bits) 1.0 ** *** ****** ** ***
0.8 ************* ******
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GCGTGATGTCTTAAGCATGG
consensus GT CA GC T
sequence T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 + 377 1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
WashU_Skud_Contig1682.4 + 370 1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
MIT_Smik_c492_20940 + 375 1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
MIT_Spar_c261_21317 + 369 1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
SGD_Scer_YOR278W + 366 1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
MIT_Spar_c130_3912 + 217 1.16e-10 TCAGCTCTTT GGTTGCAGTCTTGTGCTTGG TTCAAGCTGG
WashU_Smik_Contig2283.3 + 213 3.08e-10 ACAGTTCGTT GGCTGCAGTGTTACGCTTGG TTGAAGCTGG
SGD_Scer_YDR044W + 225 4.42e-10 TCAGCGCTTT GGTTGCAGTCTTATGCTTTG TTCAAGCTGG
MIT_Sbay_c896_21290 + 223 8.28e-10 ACAGCTCTTT GGTTGCTGTCTTGCTCTAGG TCCAAGCTGG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 1.2e-12 376_[+1]_239
WashU_Skud_Contig1682.4 1.2e-12 369_[+1]_246
MIT_Smik_c492_20940 1.2e-12 374_[+1]_241
MIT_Spar_c261_21317 1.2e-12 368_[+1]_247
SGD_Scer_YOR278W 1.2e-12 365_[+1]_250
MIT_Spar_c130_3912 1.2e-10 216_[+1]_764
WashU_Smik_Contig2283.3 3.1e-10 212_[+1]_768
SGD_Scer_YDR044W 4.4e-10 224_[+1]_756
MIT_Sbay_c896_21290 8.3e-10 222_[+1]_758
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig635.57 ( 377) GCGTGATGTCTTAAGCATGG 1
WashU_Skud_Contig1682.4 ( 370) GCGTGATGTCTTAAGCATGG 1
MIT_Smik_c492_20940 ( 375) GCGTGATGTCTTAAGCATGG 1
MIT_Spar_c261_21317 ( 369) GCGTGATGTCTTAAGCATGG 1
SGD_Scer_YOR278W ( 366) GCGTGATGTCTTAAGCATGG 1
MIT_Spar_c130_3912 ( 217) GGTTGCAGTCTTGTGCTTGG 1
WashU_Smik_Contig2283.3 ( 213) GGCTGCAGTGTTACGCTTGG 1
SGD_Scer_YDR044W ( 225) GGTTGCAGTCTTATGCTTTG 1
MIT_Sbay_c896_21290 ( 223) GGTTGCTGTCTTGCTCTAGG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 6.7e-025
-982 -982 251 -982
-982 166 134 -982
-982 -66 166 4
-982 -982 -982 162
-982 -982 251 -982
78 134 -982 -982
4 -982 -982 104
-982 -982 251 -982
-982 -982 -982 162
-982 234 -66 -982
-982 -982 -982 162
-982 -982 -982 162
126 -982 34 -982
78 34 -982 -55
-982 -982 234 -154
-982 251 -982 -982
78 -982 -982 45
-154 -982 -982 145
-982 -982 234 -154
-982 -982 251 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.7e-025
0.000000 0.000000 1.000000 0.000000
0.000000 0.555556 0.444444 0.000000
0.000000 0.111111 0.555556 0.333333
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.555556 0.444444 0.000000 0.000000
0.333333 0.000000 0.000000 0.666667
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.888889 0.111111 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.777778 0.000000 0.222222 0.000000
0.555556 0.222222 0.000000 0.222222
0.000000 0.000000 0.888889 0.111111
0.000000 1.000000 0.000000 0.000000
0.555556 0.000000 0.000000 0.444444
0.111111 0.000000 0.000000 0.888889
0.000000 0.000000 0.888889 0.111111
0.000000 0.000000 1.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
G[CG][GT]TG[AC][TA]GTCTT[AG][ACT]GC[AT]TGG
--------------------------------------------------------------------------------
Time 5.38 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 197 E-value = 4.1e-023
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 1::367a:::::::7a:4a:
pos.-specific C :646::::::6::::::::1
probability G 9461::::6a4:aa3:a::9
matrix T ::::43:a4::a:::::6::
bits 2.5 * ** *
2.3 * ** *
2.0 * * ** * *
1.8 * * ** * *
Information 1.5 *** ** ***** ** **
content 1.3 *** ** ***** ** **
(31.6 bits) 1.0 *** *********** **
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GCGCAAATGGCTGGAAGTAG
consensus GCATT T G G A
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 - 338 1.95e-13 TCTATGTCAA GCGCAAATGGCTGGAAGTAG ACCAATTTCT
WashU_Skud_Contig1682.4 - 331 1.95e-13 TCTATGTAAA GCGCAAATGGCTGGAAGTAG ACCAATCTCT
MIT_Smik_c492_20940 - 336 1.95e-13 TCTATATAAA GCGCAAATGGCTGGAAGTAG ACAAATTTCT
MIT_Spar_c261_21317 - 330 1.95e-13 TCTATATAAA GCGCAAATGGCTGGAAGTAG ACCAATTTTT
SGD_Scer_YOR278W - 327 1.95e-13 TCTATATAAA GCGCAAATGGCTGGAAGTAG ACCAATTTTT
MIT_Sbay_c896_21290 + 253 1.81e-10 TCCAAGCTGG GGCATAATTGGTGGGAGAAG CCAGAAAATG
WashU_Smik_Contig2283.3 + 243 2.62e-10 TTGAAGCTGG GGCATTATTGGTGGAAGAAG CCAGAAAAGA
MIT_Spar_c130_3912 + 247 2.73e-10 TTCAAGCTGG GGCATTATTGGTGGGAGAAG CCAGAAAAGG
SGD_Scer_YDR044W + 255 1.92e-09 TTCAAGCTGG AGCGTTATTGGTGGGAGAAC CAGAAAAGGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 1.9e-13 337_[-2]_278
WashU_Skud_Contig1682.4 1.9e-13 330_[-2]_285
MIT_Smik_c492_20940 1.9e-13 335_[-2]_280
MIT_Spar_c261_21317 1.9e-13 329_[-2]_286
SGD_Scer_YOR278W 1.9e-13 326_[-2]_289
MIT_Sbay_c896_21290 1.8e-10 252_[+2]_728
WashU_Smik_Contig2283.3 2.6e-10 242_[+2]_738
MIT_Spar_c130_3912 2.7e-10 246_[+2]_734
SGD_Scer_YDR044W 1.9e-09 254_[+2]_726
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
WashU_Sbay_Contig635.57 ( 338) GCGCAAATGGCTGGAAGTAG 1
WashU_Skud_Contig1682.4 ( 331) GCGCAAATGGCTGGAAGTAG 1
MIT_Smik_c492_20940 ( 336) GCGCAAATGGCTGGAAGTAG 1
MIT_Spar_c261_21317 ( 330) GCGCAAATGGCTGGAAGTAG 1
SGD_Scer_YOR278W ( 327) GCGCAAATGGCTGGAAGTAG 1
MIT_Sbay_c896_21290 ( 253) GGCATAATTGGTGGGAGAAG 1
WashU_Smik_Contig2283.3 ( 243) GGCATTATTGGTGGAAGAAG 1
MIT_Spar_c130_3912 ( 247) GGCATTATTGGTGGGAGAAG 1
SGD_Scer_YDR044W ( 255) AGCGTTATTGGTGGGAGAAC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 4.1e-023
-154 -982 234 -982
-982 166 134 -982
-982 134 166 -982
4 166 -66 -982
78 -982 -982 45
104 -982 -982 4
162 -982 -982 -982
-982 -982 -982 162
-982 -982 166 45
-982 -982 251 -982
-982 166 134 -982
-982 -982 -982 162
-982 -982 251 -982
-982 -982 251 -982
104 -982 92 -982
162 -982 -982 -982
-982 -982 251 -982
45 -982 -982 78
162 -982 -982 -982
-982 -66 234 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.1e-023
0.111111 0.000000 0.888889 0.000000
0.000000 0.555556 0.444444 0.000000
0.000000 0.444444 0.555556 0.000000
0.333333 0.555556 0.111111 0.000000
0.555556 0.000000 0.000000 0.444444
0.666667 0.000000 0.000000 0.333333
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.555556 0.444444
0.000000 0.000000 1.000000 0.000000
0.000000 0.555556 0.444444 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.666667 0.000000 0.333333 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.444444 0.000000 0.000000 0.555556
1.000000 0.000000 0.000000 0.000000
0.000000 0.111111 0.888889 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
G[CG][GC][CA][AT][AT]AT[GT]G[CG]TGG[AG]AG[TA]AG
--------------------------------------------------------------------------------
Time 10.47 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 184 E-value = 6.0e-018
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :21199:a::71:::6:::9
pos.-specific C 98:3::::193:::::::4:
probability G 1:961:a::1:94:13::6:
matrix T :::::1::9:::6a91aa:1
bits 2.5 *
2.3 *
2.0 * * * * *
1.8 * * * * *
Information 1.5 *** ** * * * ***
content 1.3 *** * **** * ** ***
(29.5 bits) 1.0 *************** ****
0.8 *************** ****
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CCGGAAGATCAGTTTATTGA
consensus A C C G G C
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 + 401 5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGCTC
WashU_Skud_Contig1682.4 + 394 5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
MIT_Smik_c492_20940 + 399 5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
MIT_Spar_c261_21317 + 393 5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
SGD_Scer_YOR278W + 390 5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTT
MIT_Spar_c130_3912 + 763 1.18e-11 AGAAAAATGA CCGCAAGATCCGGTTGTTCA TAACTTTCTA
SGD_Scer_YDR044W + 767 1.43e-10 AGAAAAATGA CCGCAAGATCCGGTTGTTCT CAACCTTCTA
MIT_Sbay_c896_21290 + 781 2.40e-08 GAAGGGGGTG CAAAGTGATCCGGTTGTTCA TATTTCTTCA
WashU_Smik_Contig2283.3 - 359 1.26e-07 TGGGTGGGAA GAGCAAGACGAAGTGTTTCA CGGCGGGGCC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 5.8e-12 400_[+3]_215
WashU_Skud_Contig1682.4 5.8e-12 393_[+3]_222
MIT_Smik_c492_20940 5.8e-12 398_[+3]_217
MIT_Spar_c261_21317 5.8e-12 392_[+3]_223
SGD_Scer_YOR278W 5.8e-12 389_[+3]_226
MIT_Spar_c130_3912 1.2e-11 762_[+3]_218
SGD_Scer_YDR044W 1.4e-10 766_[+3]_214
MIT_Sbay_c896_21290 2.4e-08 780_[+3]_200
WashU_Smik_Contig2283.3 1.3e-07 358_[-3]_622
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
WashU_Sbay_Contig635.57 ( 401) CCGGAAGATCAGTTTATTGA 1
WashU_Skud_Contig1682.4 ( 394) CCGGAAGATCAGTTTATTGA 1
MIT_Smik_c492_20940 ( 399) CCGGAAGATCAGTTTATTGA 1
MIT_Spar_c261_21317 ( 393) CCGGAAGATCAGTTTATTGA 1
SGD_Scer_YOR278W ( 390) CCGGAAGATCAGTTTATTGA 1
MIT_Spar_c130_3912 ( 763) CCGCAAGATCCGGTTGTTCA 1
SGD_Scer_YDR044W ( 767) CCGCAAGATCCGGTTGTTCT 1
MIT_Sbay_c896_21290 ( 781) CAAAGTGATCCGGTTGTTCA 1
WashU_Smik_Contig2283.3 ( 359) GAGCAAGACGAAGTGTTTCA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 6.0e-018
-982 234 -66 -982
-55 215 -982 -982
-154 -982 234 -982
-154 92 166 -982
145 -982 -66 -982
145 -982 -982 -154
-982 -982 251 -982
162 -982 -982 -982
-982 -66 -982 145
-982 234 -66 -982
104 92 -982 -982
-154 -982 234 -982
-982 -982 134 78
-982 -982 -982 162
-982 -982 -66 145
78 -982 92 -154
-982 -982 -982 162
-982 -982 -982 162
-982 134 166 -982
145 -982 -982 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.0e-018
0.000000 0.888889 0.111111 0.000000
0.222222 0.777778 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
0.111111 0.333333 0.555556 0.000000
0.888889 0.000000 0.111111 0.000000
0.888889 0.000000 0.000000 0.111111
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.111111 0.000000 0.888889
0.000000 0.888889 0.111111 0.000000
0.666667 0.333333 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
0.000000 0.000000 0.444444 0.555556
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.111111 0.888889
0.555556 0.000000 0.333333 0.111111
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.444444 0.555556 0.000000
0.888889 0.000000 0.000000 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
C[CA]G[GC]AAGATC[AC]G[TG]TT[AG]TT[GC]A
--------------------------------------------------------------------------------
Time 15.56 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 9 llr = 185 E-value = 1.4e-017
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 1:a91a81:6aa6::2a::6
pos.-specific C :9::3::::3::::a::::4
probability G ::::::24a1::4a:::8a:
matrix T 91:16::4:::::::8:2::
bits 2.5 * ** *
2.3 * ** *
2.0 * * ** *
1.8 * * ** *
Information 1.5 ** * * ** ** ***
content 1.3 ** * * ** ** ***
(29.7 bits) 1.0 **** ** * ***** ****
0.8 **** ** ************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel TCAATAAGGAAAAGCTAGGA
consensus C GT C G A T C
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1682.4 + 296 5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ATAAAAGAGA
MIT_Smik_c492_20940 + 301 5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ACAAAAGAAA
MIT_Spar_c261_21317 + 296 5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ACAGAAAAAT
SGD_Scer_YOR278W + 292 5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ACAAAAAAAA
MIT_Sbay_c896_21290 + 699 6.10e-11 GAGGAAAATA TCAACAAGGCAAGGCTATGC CTTTCGAAGA
MIT_Spar_c130_3912 + 693 6.60e-11 GAGAGAAATA TCAACAGGGCAAGGCAAGGC TATGCTCTTT
WashU_Smik_Contig2283.3 + 701 1.34e-09 GAGAAAAATA TTAACAAGGGAAGGCAAGGC TATGTTCTAT
WashU_Sbay_Contig635.57 + 304 1.34e-09 GGATTAGATT TCATTAAAGAAAAGCTAGGA ACAAAGAAAT
SGD_Scer_YDR044W + 701 2.68e-09 AGAAATATCA ACAAAAGGGCAAGGCTATGC CTTCTGGAAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1682.4 5e-11 295_[+4]_320
MIT_Smik_c492_20940 5e-11 300_[+4]_315
MIT_Spar_c261_21317 5e-11 295_[+4]_320
SGD_Scer_YOR278W 5e-11 291_[+4]_324
MIT_Sbay_c896_21290 6.1e-11 698_[+4]_282
MIT_Spar_c130_3912 6.6e-11 692_[+4]_288
WashU_Smik_Contig2283.3 1.3e-09 700_[+4]_280
WashU_Sbay_Contig635.57 1.3e-09 303_[+4]_312
SGD_Scer_YDR044W 2.7e-09 700_[+4]_280
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=9
WashU_Skud_Contig1682.4 ( 296) TCAATAATGAAAAGCTAGGA 1
MIT_Smik_c492_20940 ( 301) TCAATAATGAAAAGCTAGGA 1
MIT_Spar_c261_21317 ( 296) TCAATAATGAAAAGCTAGGA 1
SGD_Scer_YOR278W ( 292) TCAATAATGAAAAGCTAGGA 1
MIT_Sbay_c896_21290 ( 699) TCAACAAGGCAAGGCTATGC 1
MIT_Spar_c130_3912 ( 693) TCAACAGGGCAAGGCAAGGC 1
WashU_Smik_Contig2283.3 ( 701) TTAACAAGGGAAGGCAAGGC 1
WashU_Sbay_Contig635.57 ( 304) TCATTAAAGAAAAGCTAGGA 1
SGD_Scer_YDR044W ( 701) ACAAAAGGGCAAGGCTATGC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 1.4e-017
-154 -982 -982 145
-982 234 -982 -154
162 -982 -982 -982
145 -982 -982 -154
-154 92 -982 78
162 -982 -982 -982
126 -982 34 -982
-154 -982 134 45
-982 -982 251 -982
78 92 -66 -982
162 -982 -982 -982
162 -982 -982 -982
78 -982 134 -982
-982 -982 251 -982
-982 251 -982 -982
-55 -982 -982 126
162 -982 -982 -982
-982 -982 215 -55
-982 -982 251 -982
78 134 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.4e-017
0.111111 0.000000 0.000000 0.888889
0.000000 0.888889 0.000000 0.111111
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.000000 0.111111
0.111111 0.333333 0.000000 0.555556
1.000000 0.000000 0.000000 0.000000
0.777778 0.000000 0.222222 0.000000
0.111111 0.000000 0.444444 0.444444
0.000000 0.000000 1.000000 0.000000
0.555556 0.333333 0.111111 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.555556 0.000000 0.444444 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.222222 0.000000 0.000000 0.777778
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.777778 0.222222
0.000000 0.000000 1.000000 0.000000
0.555556 0.444444 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
TCAA[TC]A[AG][GT]G[AC]AA[AG]GC[TA]A[GT]G[AC]
--------------------------------------------------------------------------------
Time 20.51 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 178 E-value = 2.4e-015
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 61372:::::1:::aaa74:
pos.-specific C 4:::1a:6:9:::1::::::
probability G :9137:a:6::7:9::::::
matrix T ::6::::44193a::::36a
bits 2.5 **
2.3 **
2.0 * ** * *
1.8 * ** * *
Information 1.5 * ** * ***** *
content 1.3 * ** * ****** *
(28.5 bits) 1.0 ** ************** *
0.8 ** *****************
0.5 ** *****************
0.3 ********************
0.0 --------------------
Multilevel AGTAGCGCGCTGTGAAAATT
consensus C AGA TT T TA
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c261_21317 + 517 7.89e-12 CGCCGCATCA AGAAGCGCGCTGTGAAAATT TTTCGTTTTT
SGD_Scer_YOR278W + 499 2.23e-11 CGCCGCACCA AGGAGCGCGCTGTGAAAATT TTTCGCTTTA
WashU_Skud_Contig1682.4 + 512 4.09e-10 TCGCAGCGTC AGTGGCGCGTTGTGAAAAAT TTTCACTTTT
MIT_Spar_c130_3912 + 283 4.88e-10 AAGGCGAAAG CGTAGCGTTCTTTGAAATTT GGATTCTGTT
SGD_Scer_YDR044W + 290 4.88e-10 AAGGCGAAAG CGTAGCGTTCTTTGAAATTT GGCTTCTGTT
MIT_Sbay_c896_21290 + 289 5.32e-10 AATGCGAAAG CGTACCGTTCTGTGAAAAAT GGCTTCGGTT
MIT_Smik_c492_20940 + 516 1.70e-09 CATTGTGATA AGAGACGCGCAGTGAAAAAT TTTCGCTTTT
WashU_Sbay_Contig635.57 + 525 2.83e-09 TCATCGCGGA AAAGACGCGCTGTGAAAAAT TTTCTCTTTT
WashU_Smik_Contig2283.3 + 284 3.02e-09 GAAAGAGTAG CGTAGCGTTCTTTCAAATTT TGGTTTCGGG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c261_21317 7.9e-12 516_[+5]_99
SGD_Scer_YOR278W 2.2e-11 498_[+5]_117
WashU_Skud_Contig1682.4 4.1e-10 511_[+5]_104
MIT_Spar_c130_3912 4.9e-10 282_[+5]_698
SGD_Scer_YDR044W 4.9e-10 289_[+5]_691
MIT_Sbay_c896_21290 5.3e-10 288_[+5]_692
MIT_Smik_c492_20940 1.7e-09 515_[+5]_100
WashU_Sbay_Contig635.57 2.8e-09 524_[+5]_91
WashU_Smik_Contig2283.3 3e-09 283_[+5]_697
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
MIT_Spar_c261_21317 ( 517) AGAAGCGCGCTGTGAAAATT 1
SGD_Scer_YOR278W ( 499) AGGAGCGCGCTGTGAAAATT 1
WashU_Skud_Contig1682.4 ( 512) AGTGGCGCGTTGTGAAAAAT 1
MIT_Spar_c130_3912 ( 283) CGTAGCGTTCTTTGAAATTT 1
SGD_Scer_YDR044W ( 290) CGTAGCGTTCTTTGAAATTT 1
MIT_Sbay_c896_21290 ( 289) CGTACCGTTCTGTGAAAAAT 1
MIT_Smik_c492_20940 ( 516) AGAGACGCGCAGTGAAAAAT 1
WashU_Sbay_Contig635.57 ( 525) AAAGACGCGCTGTGAAAAAT 1
WashU_Smik_Contig2283.3 ( 284) CGTAGCGTTCTTTCAAATTT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 2.4e-015
78 134 -982 -982
-154 -982 234 -982
4 -982 -66 78
104 -982 92 -982
-55 -66 192 -982
-982 251 -982 -982
-982 -982 251 -982
-982 166 -982 45
-982 -982 166 45
-982 234 -982 -154
-154 -982 -982 145
-982 -982 192 4
-982 -982 -982 162
-982 -66 234 -982
162 -982 -982 -982
162 -982 -982 -982
162 -982 -982 -982
104 -982 -982 4
45 -982 -982 78
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.4e-015
0.555556 0.444444 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
0.333333 0.000000 0.111111 0.555556
0.666667 0.000000 0.333333 0.000000
0.222222 0.111111 0.666667 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.555556 0.000000 0.444444
0.000000 0.000000 0.555556 0.444444
0.000000 0.888889 0.000000 0.111111
0.111111 0.000000 0.000000 0.888889
0.000000 0.000000 0.666667 0.333333
0.000000 0.000000 0.000000 1.000000
0.000000 0.111111 0.888889 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.666667 0.000000 0.000000 0.333333
0.444444 0.000000 0.000000 0.555556
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
[AC]G[TA][AG][GA]CG[CT][GT]CT[GT]TGAAA[AT][TA]T
--------------------------------------------------------------------------------
Time 25.34 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YOR278W 1.58e-35 291_[+4(5.02e-11)]_15_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_89_[+5(2.23e-11)]_117
MIT_Spar_c261_21317 5.85e-36 260_[+4(4.80e-06)]_15_[+4(5.02e-11)]_14_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_104_[+5(7.89e-12)]_99
MIT_Smik_c492_20940 1.00e-33 265_[+4(4.99e-05)]_15_[+4(5.02e-11)]_15_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_97_[+5(1.70e-09)]_16_[+1(5.40e-05)]_64
WashU_Skud_Contig1682.4 2.57e-34 295_[+4(5.02e-11)]_15_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_98_[+5(4.09e-10)]_104
WashU_Sbay_Contig635.57 3.77e-32 303_[+4(1.34e-09)]_14_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_104_[+5(2.83e-09)]_91
SGD_Scer_YDR044W 4.25e-24 106_[+4(5.44e-05)]_98_[+1(4.42e-10)]_10_[+2(1.92e-09)]_15_[+5(4.88e-10)]_391_[+4(2.68e-09)]_46_[+3(1.43e-10)]_142_[+5(4.10e-05)]_52
MIT_Spar_c130_3912 5.41e-28 103_[+4(5.44e-05)]_93_[+1(1.16e-10)]_10_[+2(2.73e-10)]_16_[+5(4.88e-10)]_390_[+4(6.60e-11)]_50_[+3(1.18e-11)]_218
MIT_Sbay_c896_21290 3.19e-24 222_[+1(8.28e-10)]_10_[+2(1.81e-10)]_16_[+5(5.32e-10)]_390_[+4(6.10e-11)]_62_[+3(2.40e-08)]_200
WashU_Smik_Contig2283.3 7.85e-22 212_[+1(3.08e-10)]_10_[+2(2.62e-10)]_21_[+5(3.02e-09)]_55_[-3(1.26e-07)]_322_[+4(1.34e-09)]_280
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************