********************************************************************************
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-HEM13.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_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 HEM1-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= 6490 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.288 C 0.212 G 0.212 T 0.288
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 = 215 E-value = 3.2e-031
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 9:aa:aa:::2:aa4:1aa1
pos.-specific C ::::a::::::9::::9:::
probability G 1a::::::aa7:::67:::8
matrix T :::::::a::11:::3:::1
bits 2.5 * * **
2.3 * * **
2.0 * * ** * *
1.8 * * ** * *
Information 1.5 ********* *** ***
content 1.3 ********** *** *****
(34.4 bits) 1.0 ********************
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel AGAACAATGGGCAAGGCAAG
consensus A AT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig461.5 + 277 3.60e-13 GCACCGGGAC AGAACAATGGGCAAGGCAAG ATGAAAAATC
MIT_Smik_c228_4055 + 282 3.60e-13 ACATTGAATT AGAACAATGGGCAAGGCAAG ATGAAAATTT
MIT_Spar_c117_4603 + 279 3.60e-13 CGCATGGGTC AGAACAATGGGCAAGGCAAG ATGAAAAATT
SGD_Scer_YDR232W + 284 3.60e-13 CGCATGGATC AGAACAATGGGCAAGGCAAG ATGAAAAATT
SGD_Scer_YDR044W + 175 1.02e-12 TTTCGAAACG AGAACAATGGGCAAAGCAAG CTTTATCTTC
MIT_Spar_c130_3912 + 171 2.37e-11 TTTCGAAACG AGAACAATGGACAAATCAAG CTTTATCTAT
WashU_Skud_Contig2069.5 + 282 2.76e-11 ACACTGGATC GGAACAATGGGCAAGGCAAT GTGAAAAATT
WashU_Smik_Contig2283.3 + 167 1.95e-10 TTTCAAAAAG AGAACAATGGTCAAATAAAG GTTTATCTAC
MIT_Sbay_c896_21290 + 177 4.52e-10 TCTCGAAGGG AGAACAATGGATAAATCAAA GCTTATCTAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig461.5 3.6e-13 276_[+1]_202
MIT_Smik_c228_4055 3.6e-13 281_[+1]_197
MIT_Spar_c117_4603 3.6e-13 278_[+1]_200
SGD_Scer_YDR232W 3.6e-13 283_[+1]_195
SGD_Scer_YDR044W 1e-12 174_[+1]_806
MIT_Spar_c130_3912 2.4e-11 170_[+1]_810
WashU_Skud_Contig2069.5 2.8e-11 281_[+1]_197
WashU_Smik_Contig2283.3 2e-10 166_[+1]_814
MIT_Sbay_c896_21290 4.5e-10 176_[+1]_804
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig461.5 ( 277) AGAACAATGGGCAAGGCAAG 1
MIT_Smik_c228_4055 ( 282) AGAACAATGGGCAAGGCAAG 1
MIT_Spar_c117_4603 ( 279) AGAACAATGGGCAAGGCAAG 1
SGD_Scer_YDR232W ( 284) AGAACAATGGGCAAGGCAAG 1
SGD_Scer_YDR044W ( 175) AGAACAATGGGCAAAGCAAG 1
MIT_Spar_c130_3912 ( 171) AGAACAATGGACAAATCAAG 1
WashU_Skud_Contig2069.5 ( 282) GGAACAATGGGCAAGGCAAT 1
WashU_Smik_Contig2283.3 ( 167) AGAACAATGGTCAAATAAAG 1
MIT_Sbay_c896_21290 ( 177) AGAACAATGGATAAATCAAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 3.2e-031
145 -982 -66 -982
-982 -982 251 -982
162 -982 -982 -982
162 -982 -982 -982
-982 251 -982 -982
162 -982 -982 -982
162 -982 -982 -982
-982 -982 -982 162
-982 -982 251 -982
-982 -982 251 -982
-55 -982 192 -154
-982 234 -982 -154
162 -982 -982 -982
162 -982 -982 -982
45 -982 166 -982
-982 -982 192 4
-154 234 -982 -982
162 -982 -982 -982
162 -982 -982 -982
-154 -982 215 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.2e-031
0.888889 0.000000 0.111111 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
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 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.222222 0.000000 0.666667 0.111111
0.000000 0.888889 0.000000 0.111111
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.000000 0.000000 0.666667 0.333333
0.111111 0.888889 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.111111 0.000000 0.777778 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
AGAACAATGG[GA]CAA[GA][GT]CAAG
--------------------------------------------------------------------------------
Time 4.41 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 209 E-value = 1.2e-028
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A a99a2:::::::113:::7:
pos.-specific C :::::6:8a8:a:1474a:3
probability G :11:84a1:1a:98236:27
matrix T :::::::1:1::::::::1:
bits 2.5 * * ** *
2.3 * * ** *
2.0 * * *** *
1.8 * * *** *
Information 1.5 * *********** *** *
content 1.3 ************** *** *
(33.5 bits) 1.0 ************** *** *
0.8 ****************** *
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel AAAAGCGCCCGCGGCCGCAG
consensus AG AGC GC
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c117_4603 + 347 1.67e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
SGD_Scer_YDR232W + 352 1.67e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
WashU_Smik_Contig2283.3 + 337 6.44e-13 TTTAAAAAAG AAAAGGGCCCGCGGCCCCGC CGTGAAACAC
WashU_Skud_Contig2069.5 + 349 2.55e-12 ACAATGACCA AAAAGCGTCCGCGGCCGCAG ACCAATGAGC
SGD_Scer_YDR044W + 340 2.62e-11 GTTTAAAAGT AGAAGGGCCCGCGGAGCCGC TGTGAAAGAT
WashU_Sbay_Contig461.5 + 346 2.62e-11 CAATGACCAA AAAAACGCCGGCGGGCGCAG ACCAATGAGC
MIT_Sbay_c896_21290 + 339 6.92e-11 GTTTAAAAAG AAAAGGGCCCGCGCAGCCTG TGTGAAATGT
MIT_Smik_c228_4055 + 349 9.01e-11 ACAATGACCA AAAAGCGCCCGCAAGCGCAG ACCAATGAGC
MIT_Spar_c130_3912 + 332 1.10e-09 CGTTTAAAAG AAGAAGGGCTGCGGAGCCAC TGTGAAAGAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c117_4603 1.7e-14 346_[+2]_132
SGD_Scer_YDR232W 1.7e-14 351_[+2]_127
WashU_Smik_Contig2283.3 6.4e-13 336_[+2]_644
WashU_Skud_Contig2069.5 2.5e-12 348_[+2]_130
SGD_Scer_YDR044W 2.6e-11 339_[+2]_641
WashU_Sbay_Contig461.5 2.6e-11 345_[+2]_133
MIT_Sbay_c896_21290 6.9e-11 338_[+2]_642
MIT_Smik_c228_4055 9e-11 348_[+2]_130
MIT_Spar_c130_3912 1.1e-09 331_[+2]_649
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
MIT_Spar_c117_4603 ( 347) AAAAGCGCCCGCGGCCGCAG 1
SGD_Scer_YDR232W ( 352) AAAAGCGCCCGCGGCCGCAG 1
WashU_Smik_Contig2283.3 ( 337) AAAAGGGCCCGCGGCCCCGC 1
WashU_Skud_Contig2069.5 ( 349) AAAAGCGTCCGCGGCCGCAG 1
SGD_Scer_YDR044W ( 340) AGAAGGGCCCGCGGAGCCGC 1
WashU_Sbay_Contig461.5 ( 346) AAAAACGCCGGCGGGCGCAG 1
MIT_Sbay_c896_21290 ( 339) AAAAGGGCCCGCGCAGCCTG 1
MIT_Smik_c228_4055 ( 349) AAAAGCGCCCGCAAGCGCAG 1
MIT_Spar_c130_3912 ( 332) AAGAAGGGCTGCGGAGCCAC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 1.2e-028
162 -982 -982 -982
145 -982 -66 -982
145 -982 -66 -982
162 -982 -982 -982
-55 -982 215 -982
-982 166 134 -982
-982 -982 251 -982
-982 215 -66 -154
-982 251 -982 -982
-982 215 -66 -154
-982 -982 251 -982
-982 251 -982 -982
-154 -982 234 -982
-154 -66 215 -982
4 134 34 -982
-982 192 92 -982
-982 134 166 -982
-982 251 -982 -982
104 -982 34 -154
-982 92 192 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.2e-028
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.888889 0.000000 0.111111 0.000000
1.000000 0.000000 0.000000 0.000000
0.222222 0.000000 0.777778 0.000000
0.000000 0.555556 0.444444 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.777778 0.111111 0.111111
0.000000 1.000000 0.000000 0.000000
0.000000 0.777778 0.111111 0.111111
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
0.111111 0.111111 0.777778 0.000000
0.333333 0.444444 0.222222 0.000000
0.000000 0.666667 0.333333 0.000000
0.000000 0.444444 0.555556 0.000000
0.000000 1.000000 0.000000 0.000000
0.666667 0.000000 0.222222 0.111111
0.000000 0.333333 0.666667 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
AAAA[GA][CG]GCCCGCGG[CAG][CG][GC]C[AG][GC]
--------------------------------------------------------------------------------
Time 8.84 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 205 E-value = 8.3e-027
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :::::::::::::4::::::
pos.-specific C 1194:::aa::a:64:46::
probability G ::12a:::::a:4:::24::
matrix T 99:3:aa::a::6:6a3:aa
bits 2.5 * ** **
2.3 * ** **
2.0 * * ** **
1.8 * * ** **
Information 1.5 * ******** * ***
content 1.3 *** ******** * ***
(32.8 bits) 1.0 *** ************ ***
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel TTCCGTTCCTGCTCTTCCTT
consensus T GAC TG
sequence G G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2069.5 + 311 1.06e-11 TGTGAAAAAT TTCCGTTCCTGCTCTTGCTT CATATATGAC
MIT_Sbay_c896_21290 + 312 1.49e-11 GAAAAATGGC TTCGGTTCCTGCGACTCGTT TAAAAAGAAA
MIT_Smik_c228_4055 + 310 1.49e-11 AGATGAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
SGD_Scer_YDR232W + 313 1.49e-11 GATGAAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
MIT_Spar_c130_3912 + 306 1.92e-11 GAAATTTGGA TTCTGTTCCTGCGACTCGTT TAAAAGAAGA
SGD_Scer_YDR044W + 313 1.92e-11 GAAATTTGGC TTCTGTTCCTGCGACTCGTT TAAAAGTAGA
MIT_Spar_c117_4603 + 308 5.14e-11 GATGAAAAAT TTCTGTTCCTGCTCTTTCTT CATATATGAA
WashU_Sbay_Contig461.5 + 306 6.73e-11 GATGAAAAAT CTCCGTTCCTGCTCTTGCTT GATATATTAA
WashU_Smik_Contig2283.3 + 309 2.36e-10 AATTTTGGTT TCGGGTTCCTGCGACTCGTT TAAAAAAGAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2069.5 1.1e-11 310_[+3]_168
MIT_Sbay_c896_21290 1.5e-11 311_[+3]_669
MIT_Smik_c228_4055 1.5e-11 309_[+3]_169
SGD_Scer_YDR232W 1.5e-11 312_[+3]_166
MIT_Spar_c130_3912 1.9e-11 305_[+3]_675
SGD_Scer_YDR044W 1.9e-11 312_[+3]_668
MIT_Spar_c117_4603 5.1e-11 307_[+3]_171
WashU_Sbay_Contig461.5 6.7e-11 305_[+3]_173
WashU_Smik_Contig2283.3 2.4e-10 308_[+3]_672
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
WashU_Skud_Contig2069.5 ( 311) TTCCGTTCCTGCTCTTGCTT 1
MIT_Sbay_c896_21290 ( 312) TTCGGTTCCTGCGACTCGTT 1
MIT_Smik_c228_4055 ( 310) TTCCGTTCCTGCTCTTTCTT 1
SGD_Scer_YDR232W ( 313) TTCCGTTCCTGCTCTTTCTT 1
MIT_Spar_c130_3912 ( 306) TTCTGTTCCTGCGACTCGTT 1
SGD_Scer_YDR044W ( 313) TTCTGTTCCTGCGACTCGTT 1
MIT_Spar_c117_4603 ( 308) TTCTGTTCCTGCTCTTTCTT 1
WashU_Sbay_Contig461.5 ( 306) CTCCGTTCCTGCTCTTGCTT 1
WashU_Smik_Contig2283.3 ( 309) TCGGGTTCCTGCGACTCGTT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 8.3e-027
-982 -66 -982 145
-982 -66 -982 145
-982 234 -66 -982
-982 134 34 4
-982 -982 251 -982
-982 -982 -982 162
-982 -982 -982 162
-982 251 -982 -982
-982 251 -982 -982
-982 -982 -982 162
-982 -982 251 -982
-982 251 -982 -982
-982 -982 134 78
45 166 -982 -982
-982 134 -982 78
-982 -982 -982 162
-982 134 34 4
-982 166 134 -982
-982 -982 -982 162
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 8.3e-027
0.000000 0.111111 0.000000 0.888889
0.000000 0.111111 0.000000 0.888889
0.000000 0.888889 0.111111 0.000000
0.000000 0.444444 0.222222 0.333333
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
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 0.000000 0.444444 0.555556
0.444444 0.555556 0.000000 0.000000
0.000000 0.444444 0.000000 0.555556
0.000000 0.000000 0.000000 1.000000
0.000000 0.444444 0.222222 0.333333
0.000000 0.555556 0.444444 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
TTC[CTG]GTTCCTGC[TG][CA][TC]T[CTG][CG]TT
--------------------------------------------------------------------------------
Time 13.06 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 9 llr = 202 E-value = 5.2e-025
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A a1:6a:4a44:7::aa611:
pos.-specific C :6a4:::::6::a:::::9:
probability G :3:::46:6:93:a::49:a
matrix T :::::6::::1:::::::::
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 ACCAATGAGCGACGAAAGCG
consensus G C GA AA G G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2069.5 + 369 8.45e-13 GCGGCCGCAG ACCAATGAGCGACGAAGGCG GCCTTTCGTA
MIT_Spar_c117_4603 + 367 8.45e-13 GCGGCCGCAG ACCAATGAGCGACGAAGGCG GCCTTTCCGA
SGD_Scer_YDR232W + 372 8.45e-13 GCGGCCGCAG ACCAATGAGCGACGAAGGCG GCCTTTCCGA
MIT_Smik_c228_4055 + 369 2.51e-12 GCAAGCGCAG ACCAATGAGCGACGAAAGCG GCCTTTTGAA
MIT_Spar_c130_3912 + 265 5.38e-11 TGGTGGGAGA AGCCAGAAAAGGCGAAAGCG TAGCGTTCTT
WashU_Sbay_Contig461.5 + 366 5.38e-11 GCGGGCGCAG ACCAATGAGCGACGAAGACG GCTTTTGGGC
SGD_Scer_YDR044W + 272 1.99e-10 TTGGTGGGAG AACCAGAAAAGGCGAAAGCG TAGCGTTCTT
WashU_Smik_Contig2283.3 + 261 3.58e-10 TGGTGGAAGA AGCCAGAAAAGACGAAAGAG TAGCGTAGCG
MIT_Sbay_c896_21290 + 271 3.78e-10 TGGTGGGAGA AGCCAGAAAATGCGAAAGCG TACCGTTCTG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2069.5 8.5e-13 368_[+4]_110
MIT_Spar_c117_4603 8.5e-13 366_[+4]_112
SGD_Scer_YDR232W 8.5e-13 371_[+4]_107
MIT_Smik_c228_4055 2.5e-12 368_[+4]_110
MIT_Spar_c130_3912 5.4e-11 264_[+4]_716
WashU_Sbay_Contig461.5 5.4e-11 365_[+4]_113
SGD_Scer_YDR044W 2e-10 271_[+4]_709
WashU_Smik_Contig2283.3 3.6e-10 260_[+4]_720
MIT_Sbay_c896_21290 3.8e-10 270_[+4]_710
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=9
WashU_Skud_Contig2069.5 ( 369) ACCAATGAGCGACGAAGGCG 1
MIT_Spar_c117_4603 ( 367) ACCAATGAGCGACGAAGGCG 1
SGD_Scer_YDR232W ( 372) ACCAATGAGCGACGAAGGCG 1
MIT_Smik_c228_4055 ( 369) ACCAATGAGCGACGAAAGCG 1
MIT_Spar_c130_3912 ( 265) AGCCAGAAAAGGCGAAAGCG 1
WashU_Sbay_Contig461.5 ( 366) ACCAATGAGCGACGAAGACG 1
SGD_Scer_YDR044W ( 272) AACCAGAAAAGGCGAAAGCG 1
WashU_Smik_Contig2283.3 ( 261) AGCCAGAAAAGACGAAAGAG 1
MIT_Sbay_c896_21290 ( 271) AGCCAGAAAATGCGAAAGCG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 5.2e-025
162 -982 -982 -982
-154 166 92 -982
-982 251 -982 -982
78 134 -982 -982
162 -982 -982 -982
-982 -982 134 78
45 -982 166 -982
162 -982 -982 -982
45 -982 166 -982
45 166 -982 -982
-982 -982 234 -154
104 -982 92 -982
-982 251 -982 -982
-982 -982 251 -982
162 -982 -982 -982
162 -982 -982 -982
78 -982 134 -982
-154 -982 234 -982
-154 234 -982 -982
-982 -982 251 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.2e-025
1.000000 0.000000 0.000000 0.000000
0.111111 0.555556 0.333333 0.000000
0.000000 1.000000 0.000000 0.000000
0.555556 0.444444 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.444444 0.555556
0.444444 0.000000 0.555556 0.000000
1.000000 0.000000 0.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.444444 0.555556 0.000000 0.000000
0.000000 0.000000 0.888889 0.111111
0.666667 0.000000 0.333333 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
1.000000 0.000000 0.000000 0.000000
0.555556 0.000000 0.444444 0.000000
0.111111 0.000000 0.888889 0.000000
0.111111 0.888889 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
A[CG]C[AC]A[TG][GA]A[GA][CA]G[AG]CGAA[AG]GCG
--------------------------------------------------------------------------------
Time 17.20 secs.
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MOTIF 5 width = 20 sites = 9 llr = 183 E-value = 5.4e-018
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Motif 5 Description
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Simplified A ::96:a26:2a::a:12:a1
pos.-specific C 94::2::::::86::9:::8
probability G :6:32:82a:::4:a:4a::
matrix T 1:116::2:8:2::::3::1
bits 2.5 * * *
2.3 * * *
2.0 * * ** *
1.8 * * ** *
Information 1.5 ** ** * ****** **
content 1.3 ** ** * ****** ***
(29.3 bits) 1.0 *** ** * ****** ***
0.8 *** ** ******** ***
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CGAATAGAGTACCAGCGGAC
consensus C GC AG A TG T
sequence G T A
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Motif 5 sites sorted by position p-value
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Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c228_4055 + 203 3.97e-12 GCAACACAAC CGAGTAGAGTACCAGCTGAC GGAATGGAGG
WashU_Skud_Contig2069.5 + 204 8.98e-12 GCAACACAAC CGAGTAGAGTACCAGCAGAC GGAGTGGGTA
MIT_Spar_c130_3912 + 589 1.65e-11 ATTGTTTCTC CCAACAGTGTACGAGCGGAC GAAACTCTAG
MIT_Spar_c117_4603 + 204 7.31e-11 AACACACAAC CGAATAGAGTATCAGCTGAC GGGATGGAGG
SGD_Scer_YDR232W + 209 7.31e-11 AACACACAAC CGAATAGAGTATCAGCTGAC GGAATGGAGA
WashU_Sbay_Contig461.5 + 199 9.18e-11 GGGTGCAAAC CGATTAGAGTACCAGCAGAC GAGATGGGCG
SGD_Scer_YDR044W + 595 1.19e-09 ATTGTTTTTC CCAACAGTGAACGAGAGGAC AAACTCCAGA
WashU_Smik_Contig2283.3 + 595 6.61e-09 GTATTGTCTT TCAAGAAGGTACGAGCGGAT GAACTTCTTG
MIT_Sbay_c896_21290 + 597 8.76e-09 ATTGTTTTTT CCTGGAAGGAACGAGCGGAA CTCTTGGGGA
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Motif 5 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c228_4055 4e-12 202_[+5]_276
WashU_Skud_Contig2069.5 9e-12 203_[+5]_275
MIT_Spar_c130_3912 1.7e-11 588_[+5]_392
MIT_Spar_c117_4603 7.3e-11 203_[+5]_275
SGD_Scer_YDR232W 7.3e-11 208_[+5]_270
WashU_Sbay_Contig461.5 9.2e-11 198_[+5]_280
SGD_Scer_YDR044W 1.2e-09 594_[+5]_386
WashU_Smik_Contig2283.3 6.6e-09 594_[+5]_386
MIT_Sbay_c896_21290 8.8e-09 596_[+5]_384
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Motif 5 in BLOCKS format
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BL MOTIF 5 width=20 seqs=9
MIT_Smik_c228_4055 ( 203) CGAGTAGAGTACCAGCTGAC 1
WashU_Skud_Contig2069.5 ( 204) CGAGTAGAGTACCAGCAGAC 1
MIT_Spar_c130_3912 ( 589) CCAACAGTGTACGAGCGGAC 1
MIT_Spar_c117_4603 ( 204) CGAATAGAGTATCAGCTGAC 1
SGD_Scer_YDR232W ( 209) CGAATAGAGTATCAGCTGAC 1
WashU_Sbay_Contig461.5 ( 199) CGATTAGAGTACCAGCAGAC 1
SGD_Scer_YDR044W ( 595) CCAACAGTGAACGAGAGGAC 1
WashU_Smik_Contig2283.3 ( 595) TCAAGAAGGTACGAGCGGAT 1
MIT_Sbay_c896_21290 ( 597) CCTGGAAGGAACGAGCGGAA 1
//
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Motif 5 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 5.4e-018
-982 234 -982 -154
-982 134 166 -982
145 -982 -982 -154
78 -982 92 -154
-982 34 34 78
162 -982 -982 -982
-55 -982 215 -982
78 -982 34 -55
-982 -982 251 -982
-55 -982 -982 126
162 -982 -982 -982
-982 215 -982 -55
-982 166 134 -982
162 -982 -982 -982
-982 -982 251 -982
-154 234 -982 -982
-55 -982 134 4
-982 -982 251 -982
162 -982 -982 -982
-154 215 -982 -154
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Motif 5 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.4e-018
0.000000 0.888889 0.000000 0.111111
0.000000 0.444444 0.555556 0.000000
0.888889 0.000000 0.000000 0.111111
0.555556 0.000000 0.333333 0.111111
0.000000 0.222222 0.222222 0.555556
1.000000 0.000000 0.000000 0.000000
0.222222 0.000000 0.777778 0.000000
0.555556 0.000000 0.222222 0.222222
0.000000 0.000000 1.000000 0.000000
0.222222 0.000000 0.000000 0.777778
1.000000 0.000000 0.000000 0.000000
0.000000 0.777778 0.000000 0.222222
0.000000 0.555556 0.444444 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.111111 0.888889 0.000000 0.000000
0.222222 0.000000 0.444444 0.333333
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.111111 0.777778 0.000000 0.111111
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Motif 5 regular expression
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C[GC]A[AG][TCG]A[GA][AGT]G[TA]A[CT][CG]AGC[GTA]GAC
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Time 21.26 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 2.11e-38 208_[+5(7.31e-11)]_55_[+1(3.60e-13)]_9_[+3(1.49e-11)]_19_[+2(1.67e-14)]_[+4(8.45e-13)]_107
MIT_Spar_c117_4603 6.91e-38 203_[+5(7.31e-11)]_55_[+1(3.60e-13)]_9_[+3(5.14e-11)]_19_[+2(1.67e-14)]_[+4(8.45e-13)]_44_[+2(5.31e-05)]_48
MIT_Smik_c228_4055 1.40e-35 202_[+5(3.97e-12)]_59_[+1(3.60e-13)]_8_[+3(1.49e-11)]_19_[+2(9.01e-11)]_[+4(2.51e-12)]_110
WashU_Skud_Contig2069.5 1.63e-35 203_[+5(8.98e-12)]_58_[+1(2.76e-11)]_9_[+3(1.06e-11)]_18_[+2(2.55e-12)]_[+4(8.45e-13)]_110
WashU_Sbay_Contig461.5 6.88e-33 46_[-1(4.97e-05)]_100_[+4(2.76e-05)]_12_[+5(9.18e-11)]_58_[+1(3.60e-13)]_9_[+3(6.73e-11)]_20_[+2(2.62e-11)]_[+4(5.38e-11)]_17_[+1(5.86e-05)]_76
SGD_Scer_YDR044W 6.91e-30 174_[+1(1.02e-12)]_11_[-2(3.63e-05)]_46_[+4(1.99e-10)]_21_[+3(1.92e-11)]_7_[+2(2.62e-11)]_235_[+5(1.19e-09)]_386
MIT_Spar_c130_3912 2.36e-29 170_[+1(2.37e-11)]_28_[+3(2.57e-05)]_26_[+4(5.38e-11)]_21_[+3(1.92e-11)]_6_[+2(1.10e-09)]_237_[+5(1.65e-11)]_77_[+1(7.05e-05)]_23_[+3(9.81e-05)]_252
MIT_Sbay_c896_21290 5.38e-26 117_[+1(4.54e-05)]_39_[+1(4.52e-10)]_74_[+4(3.78e-10)]_21_[+3(1.49e-11)]_7_[+2(6.92e-11)]_238_[+5(8.76e-09)]_172_[+3(3.90e-05)]_192
WashU_Smik_Contig2283.3 2.87e-27 166_[+1(1.95e-10)]_74_[+4(3.58e-10)]_28_[+3(2.36e-10)]_8_[+2(6.44e-13)]_27_[+4(3.86e-05)]_191_[+5(6.61e-09)]_111_[+5(3.65e-05)]_255
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Stopped because nmotifs = 5 reached.
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CPU: dhn02990.mrc-dunn.cam.ac.uk
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