********************************************************************************
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-HEM4.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_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
********************************************************************************
********************************************************************************
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-HEM4.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= 10 maxsites= 10 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 5665 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.298 C 0.202 G 0.202 T 0.298
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 = 10 llr = 232 E-value = 3.1e-035
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :5::16:5::55a::a9:1a
pos.-specific C a45a::35:a:::aa:::::
probability G :15:447:a:55::::1:9:
matrix T ::::5::::::::::::a::
bits 2.5 * * ** **
2.3 * * ** **
2.0 * * ** ** *
1.8 * * ** ** *
Information 1.5 * ** * ** **** ***
content 1.3 * ** * ** ********
(33.4 bits) 1.0 * ** ***************
0.8 **** ***************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CACCTAGAGCAAACCAATGA
consensus CG GGCC GG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2069.5 + 357 6.68e-12 CAAAAAGCGT CCGCGGCCGCAGACCAATGA GCGACGAAGG
MIT_Spar_c117_4603 + 355 6.68e-12 CAAAAAGCGC CCGCGGCCGCAGACCAATGA GCGACGAAGG
SGD_Scer_YDR232W + 360 6.68e-12 CAAAAAGCGC CCGCGGCCGCAGACCAATGA GCGACGAAGG
WashU_Sbay_Contig461.5 + 354 1.53e-11 AAAAAAACGC CGGCGGGCGCAGACCAATGA GCGACGAAGA
WashU_Skud_Contig1682.4 + 231 1.78e-11 GAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
MIT_Spar_c261_21317 + 229 1.78e-11 TGAATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
SGD_Scer_YOR278W + 225 1.78e-11 AAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
MIT_Smik_c228_4055 + 357 3.51e-11 CAAAAAGCGC CCGCAAGCGCAGACCAATGA GCGACGAAAG
WashU_Sbay_Contig635.57 + 237 6.67e-11 AAAACATGTA CACCTAGAGCGAACCAGTGA TAATTTGCTT
MIT_Smik_c492_20940 + 234 1.29e-10 AAGATATGTA CACCTAGAGCGAACCAATAA TAATTTGTTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2069.5 6.7e-12 356_[+1]_122
MIT_Spar_c117_4603 6.7e-12 354_[+1]_124
SGD_Scer_YDR232W 6.7e-12 359_[+1]_119
WashU_Sbay_Contig461.5 1.5e-11 353_[+1]_125
WashU_Skud_Contig1682.4 1.8e-11 230_[+1]_385
MIT_Spar_c261_21317 1.8e-11 228_[+1]_387
SGD_Scer_YOR278W 1.8e-11 224_[+1]_391
MIT_Smik_c228_4055 3.5e-11 356_[+1]_122
WashU_Sbay_Contig635.57 6.7e-11 236_[+1]_379
MIT_Smik_c492_20940 1.3e-10 233_[+1]_382
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=10
WashU_Skud_Contig2069.5 ( 357) CCGCGGCCGCAGACCAATGA 1
MIT_Spar_c117_4603 ( 355) CCGCGGCCGCAGACCAATGA 1
SGD_Scer_YDR232W ( 360) CCGCGGCCGCAGACCAATGA 1
WashU_Sbay_Contig461.5 ( 354) CGGCGGGCGCAGACCAATGA 1
WashU_Skud_Contig1682.4 ( 231) CACCTAGAGCGAACCAATGA 1
MIT_Spar_c261_21317 ( 229) CACCTAGAGCGAACCAATGA 1
SGD_Scer_YOR278W ( 225) CACCTAGAGCGAACCAATGA 1
MIT_Smik_c228_4055 ( 357) CCGCAAGCGCAGACCAATGA 1
WashU_Sbay_Contig635.57 ( 237) CACCTAGAGCGAACCAGTGA 1
MIT_Smik_c492_20940 ( 234) CACCTAGAGCGAACCAATAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 3.1e-035
-997 251 -997 -997
62 119 -81 -997
-997 151 151 -997
-997 251 -997 -997
-169 -997 119 62
89 -997 119 -997
-997 77 199 -997
62 151 -997 -997
-997 -997 251 -997
-997 251 -997 -997
62 -997 151 -997
62 -997 151 -997
162 -997 -997 -997
-997 251 -997 -997
-997 251 -997 -997
162 -997 -997 -997
147 -997 -81 -997
-997 -997 -997 162
-169 -997 236 -997
162 -997 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.1e-035
0.000000 1.000000 0.000000 0.000000
0.500000 0.400000 0.100000 0.000000
0.000000 0.500000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
0.100000 0.000000 0.400000 0.500000
0.600000 0.000000 0.400000 0.000000
0.000000 0.300000 0.700000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.500000 0.000000 0.500000 0.000000
0.500000 0.000000 0.500000 0.000000
1.000000 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 0.000000
0.900000 0.000000 0.100000 0.000000
0.000000 0.000000 0.000000 1.000000
0.100000 0.000000 0.900000 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
C[AC][CG]C[TG][AG][GC][AC]GC[AG][AG]ACCAATGA
--------------------------------------------------------------------------------
Time 3.49 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 10 llr = 215 E-value = 5.3e-029
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 53::9a:a5:5::::a14:a
pos.-specific C 55:11::::a1:::::::::
probability G :2a9::a:::4a::5:4:a:
matrix T ::::::::5:::aa5:56::
bits 2.5 * * * * *
2.3 * * * * *
2.0 ** * * * *
1.8 ** * * * *
Information 1.5 ** *** * *** * **
content 1.3 ****** * *** * **
(31.1 bits) 1.0 * ****** * ***** **
0.8 ******** ******* ***
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel ACGGAAGAACAGTTGATTGA
consensus CA T G T GA
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 + 401 2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGCTC
WashU_Skud_Contig1682.4 + 394 2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
MIT_Smik_c492_20940 + 399 2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
MIT_Spar_c261_21317 + 393 2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
SGD_Scer_YOR278W + 390 2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTT
WashU_Skud_Contig2069.5 + 160 7.63e-11 AACCGTGTGG AGGGAAGAACGGTTGAGAGA CAGCAGAGCA
MIT_Spar_c117_4603 + 158 9.24e-11 AAGGCGTGTA AAGGAAGAACGGTTGAGAGA GAGCAGAGCA
SGD_Scer_YDR232W + 163 9.24e-11 AAGGCGTGTA AAGGAAGAACGGTTGAGAGA CAGCAGAGCA
WashU_Sbay_Contig461.5 + 159 2.91e-10 GAGCGTGTGG AGGGAAGAACCGTTGAGAGA CAACAGAGCA
MIT_Smik_c228_4055 + 159 1.25e-09 AGGACGTGTG AAGCCAGAACGGTTGAATGA CAGTAGAGGA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 2.3e-11 400_[+2]_215
WashU_Skud_Contig1682.4 2.3e-11 393_[+2]_222
MIT_Smik_c492_20940 2.3e-11 398_[+2]_217
MIT_Spar_c261_21317 2.3e-11 392_[+2]_223
SGD_Scer_YOR278W 2.3e-11 389_[+2]_226
WashU_Skud_Contig2069.5 7.6e-11 159_[+2]_319
MIT_Spar_c117_4603 9.2e-11 157_[+2]_321
SGD_Scer_YDR232W 9.2e-11 162_[+2]_316
WashU_Sbay_Contig461.5 2.9e-10 158_[+2]_320
MIT_Smik_c228_4055 1.3e-09 158_[+2]_320
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=10
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
WashU_Skud_Contig2069.5 ( 160) AGGGAAGAACGGTTGAGAGA 1
MIT_Spar_c117_4603 ( 158) AAGGAAGAACGGTTGAGAGA 1
SGD_Scer_YDR232W ( 163) AAGGAAGAACGGTTGAGAGA 1
WashU_Sbay_Contig461.5 ( 159) AGGGAAGAACCGTTGAGAGA 1
MIT_Smik_c228_4055 ( 159) AAGCCAGAACGGTTGAATGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 5.3e-029
62 151 -997 -997
-11 151 19 -997
-997 -997 251 -997
-997 -81 236 -997
147 -81 -997 -997
162 -997 -997 -997
-997 -997 251 -997
162 -997 -997 -997
62 -997 -997 62
-997 251 -997 -997
62 -81 119 -997
-997 -997 251 -997
-997 -997 -997 162
-997 -997 -997 162
-997 -997 151 62
162 -997 -997 -997
-169 -997 119 62
30 -997 -997 89
-997 -997 251 -997
162 -997 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.3e-029
0.500000 0.500000 0.000000 0.000000
0.300000 0.500000 0.200000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.100000 0.900000 0.000000
0.900000 0.100000 0.000000 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
0.500000 0.000000 0.000000 0.500000
0.000000 1.000000 0.000000 0.000000
0.500000 0.100000 0.400000 0.000000
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 0.000000 0.500000 0.500000
1.000000 0.000000 0.000000 0.000000
0.100000 0.000000 0.400000 0.500000
0.400000 0.000000 0.000000 0.600000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[AC][CAG]GGAAGA[AT]C[AG]GTT[GT]A[TG][TA]GA
--------------------------------------------------------------------------------
Time 6.83 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 10 llr = 212 E-value = 7.8e-027
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A ::::1:::::5:::::::4:
pos.-specific C 2:64:::aa::555:::a::
probability G ::::9:::::55::::2:::
matrix T 8a46:aa::a::55aa8:6a
bits 2.5 ** *
2.3 ** *
2.0 * ** *
1.8 * ** *
Information 1.5 * ****** * ** * *
content 1.3 ** ****** * ** * *
(30.6 bits) 1.0 ****************** *
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel TTCTGTTCCTACCCTTTCTT
consensus C TC GGTT G A
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c228_4055 + 310 8.08e-12 AGATGAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
SGD_Scer_YDR232W + 313 8.08e-12 GATGAAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
MIT_Spar_c117_4603 + 308 1.62e-11 GATGAAAAAT TTCTGTTCCTGCTCTTTCTT CATATATGAA
WashU_Skud_Contig2069.5 + 311 6.03e-11 TGTGAAAAAT TTCCGTTCCTGCTCTTGCTT CATATATGAC
MIT_Spar_c261_21317 - 302 1.25e-10 AGACCAATTT TTCTGTTCCTAGCTTTTCAT TATTGAAATC
WashU_Sbay_Contig461.5 + 306 1.76e-10 GATGAAAAAT CTCCGTTCCTGCTCTTGCTT GATATATTAA
MIT_Smik_c492_20940 - 307 3.70e-10 GACAAATTTC TTTTGTTCCTAGCTTTTCAT TATTGAAATC
SGD_Scer_YOR278W - 298 3.70e-10 GACCAATTTT TTTTGTTCCTAGCTTTTCAT TATTGAAATC
WashU_Sbay_Contig635.57 - 310 4.68e-10 AGACCAATTT CTTTGTTCCTAGCTTTTCTT TAATGAAATC
WashU_Skud_Contig1682.4 - 302 1.32e-09 GACCAATCTC TTTTATTCCTAGCTTTTCAT TATTGAAATC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c228_4055 8.1e-12 309_[+3]_169
SGD_Scer_YDR232W 8.1e-12 312_[+3]_166
MIT_Spar_c117_4603 1.6e-11 307_[+3]_171
WashU_Skud_Contig2069.5 6e-11 310_[+3]_168
MIT_Spar_c261_21317 1.2e-10 301_[-3]_314
WashU_Sbay_Contig461.5 1.8e-10 305_[+3]_173
MIT_Smik_c492_20940 3.7e-10 306_[-3]_309
SGD_Scer_YOR278W 3.7e-10 297_[-3]_318
WashU_Sbay_Contig635.57 4.7e-10 309_[-3]_306
WashU_Skud_Contig1682.4 1.3e-09 301_[-3]_314
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=10
MIT_Smik_c228_4055 ( 310) TTCCGTTCCTGCTCTTTCTT 1
SGD_Scer_YDR232W ( 313) TTCCGTTCCTGCTCTTTCTT 1
MIT_Spar_c117_4603 ( 308) TTCTGTTCCTGCTCTTTCTT 1
WashU_Skud_Contig2069.5 ( 311) TTCCGTTCCTGCTCTTGCTT 1
MIT_Spar_c261_21317 ( 302) TTCTGTTCCTAGCTTTTCAT 1
WashU_Sbay_Contig461.5 ( 306) CTCCGTTCCTGCTCTTGCTT 1
MIT_Smik_c492_20940 ( 307) TTTTGTTCCTAGCTTTTCAT 1
SGD_Scer_YOR278W ( 298) TTTTGTTCCTAGCTTTTCAT 1
WashU_Sbay_Contig635.57 ( 310) CTTTGTTCCTAGCTTTTCTT 1
WashU_Skud_Contig1682.4 ( 302) TTTTATTCCTAGCTTTTCAT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 7.8e-027
-997 19 -997 130
-997 -997 -997 162
-997 177 -997 30
-997 119 -997 89
-169 -997 236 -997
-997 -997 -997 162
-997 -997 -997 162
-997 251 -997 -997
-997 251 -997 -997
-997 -997 -997 162
62 -997 151 -997
-997 151 151 -997
-997 151 -997 62
-997 151 -997 62
-997 -997 -997 162
-997 -997 -997 162
-997 -997 19 130
-997 251 -997 -997
30 -997 -997 89
-997 -997 -997 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 7.8e-027
0.000000 0.200000 0.000000 0.800000
0.000000 0.000000 0.000000 1.000000
0.000000 0.600000 0.000000 0.400000
0.000000 0.400000 0.000000 0.600000
0.100000 0.000000 0.900000 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
0.500000 0.000000 0.500000 0.000000
0.000000 0.500000 0.500000 0.000000
0.000000 0.500000 0.000000 0.500000
0.000000 0.500000 0.000000 0.500000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.200000 0.800000
0.000000 1.000000 0.000000 0.000000
0.400000 0.000000 0.000000 0.600000
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
[TC]T[CT][TC]GTTCCT[AG][CG][CT][CT]TT[TG]C[TA]T
--------------------------------------------------------------------------------
Time 10.06 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 10 llr = 206 E-value = 2.2e-024
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A :11::::5:::::a5::955
pos.-specific C :::::5:2a::aa::aa:::
probability G :365::::::::::5:::::
matrix T a635a5a3:aa::::::155
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 TTGGTCTACTTCCAACCAAA
consensus GTT T T G TT
sequence C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 + 333 2.66e-12 AACAAAGAAA TTGGTCTACTTCCAGCCATT TGCGCTTGAC
WashU_Skud_Contig1682.4 + 326 2.66e-12 ATAAAAGAGA TTGGTCTACTTCCAGCCATT TGCGCTTTAC
MIT_Spar_c261_21317 + 325 2.66e-12 AACAGAAAAA TTGGTCTACTTCCAGCCATT TGCGCTTTAT
SGD_Scer_YOR278W + 322 2.66e-12 ACAAAAAAAA TTGGTCTACTTCCAGCCATT TGCGCTTTAT
MIT_Smik_c492_20940 + 331 1.15e-10 ACAAAAGAAA TTTGTCTACTTCCAGCCATT TGCGCTTTAT
MIT_Spar_c117_4603 + 56 2.75e-10 CTAGCTCTAT TTGTTTTCCTTCCAACCAAA CTTATATGGG
WashU_Sbay_Contig461.5 + 54 1.18e-09 TAGCTTTATT TGTTTTTTCTTCCAACCAAA CTTATATGGA
SGD_Scer_YDR232W + 58 1.27e-09 CTAGCTCTAT TAGTTTTCCTTCCAACCAAA CTTATATGGG
WashU_Skud_Contig2069.5 + 59 2.01e-09 TAGCTCTATT TGATTTTTCTTCCAACCAAA CTTATATGGA
MIT_Smik_c228_4055 + 58 2.84e-09 CAGCTTTGTT TGTTTTTTCTTCCAACCTAA CTTATATGGG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 2.7e-12 332_[+4]_283
WashU_Skud_Contig1682.4 2.7e-12 325_[+4]_290
MIT_Spar_c261_21317 2.7e-12 324_[+4]_291
SGD_Scer_YOR278W 2.7e-12 321_[+4]_294
MIT_Smik_c492_20940 1.1e-10 330_[+4]_285
MIT_Spar_c117_4603 2.7e-10 55_[+4]_423
WashU_Sbay_Contig461.5 1.2e-09 53_[+4]_425
SGD_Scer_YDR232W 1.3e-09 57_[+4]_421
WashU_Skud_Contig2069.5 2e-09 58_[+4]_420
MIT_Smik_c228_4055 2.8e-09 57_[+4]_421
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=10
WashU_Sbay_Contig635.57 ( 333) TTGGTCTACTTCCAGCCATT 1
WashU_Skud_Contig1682.4 ( 326) TTGGTCTACTTCCAGCCATT 1
MIT_Spar_c261_21317 ( 325) TTGGTCTACTTCCAGCCATT 1
SGD_Scer_YOR278W ( 322) TTGGTCTACTTCCAGCCATT 1
MIT_Smik_c492_20940 ( 331) TTTGTCTACTTCCAGCCATT 1
MIT_Spar_c117_4603 ( 56) TTGTTTTCCTTCCAACCAAA 1
WashU_Sbay_Contig461.5 ( 54) TGTTTTTTCTTCCAACCAAA 1
SGD_Scer_YDR232W ( 58) TAGTTTTCCTTCCAACCAAA 1
WashU_Skud_Contig2069.5 ( 59) TGATTTTTCTTCCAACCAAA 1
MIT_Smik_c228_4055 ( 58) TGTTTTTTCTTCCAACCTAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 2.2e-024
-997 -997 -997 162
-169 -997 77 89
-169 -997 177 -11
-997 -997 151 62
-997 -997 -997 162
-997 151 -997 62
-997 -997 -997 162
62 19 -997 -11
-997 251 -997 -997
-997 -997 -997 162
-997 -997 -997 162
-997 251 -997 -997
-997 251 -997 -997
162 -997 -997 -997
62 -997 151 -997
-997 251 -997 -997
-997 251 -997 -997
147 -997 -997 -169
62 -997 -997 62
62 -997 -997 62
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.2e-024
0.000000 0.000000 0.000000 1.000000
0.100000 0.000000 0.300000 0.600000
0.100000 0.000000 0.600000 0.300000
0.000000 0.000000 0.500000 0.500000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.000000 0.500000
0.000000 0.000000 0.000000 1.000000
0.500000 0.200000 0.000000 0.300000
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 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.500000 0.000000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.900000 0.000000 0.000000 0.100000
0.500000 0.000000 0.000000 0.500000
0.500000 0.000000 0.000000 0.500000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
T[TG][GT][GT]T[CT]T[ATC]CTTCCA[AG]CCA[AT][AT]
--------------------------------------------------------------------------------
Time 13.18 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 10 llr = 216 E-value = 2.6e-029
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A :5::6::::::56::a::::
pos.-specific C 9::5::14a::144a:::::
probability G :5:5:19::::4:6:::6a:
matrix T 1:a:49:6:aa:::::a4:a
bits 2.5 * * *
2.3 * * *
2.0 * * * * *
1.8 * * * * *
Information 1.5 * ** * *** **** **
content 1.3 * ** ** *** *******
(31.2 bits) 1.0 **** ****** ********
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CATCATGTCTTAAGCATGGT
consensus G GT C GCC T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 + 378 7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
WashU_Skud_Contig1682.4 + 371 7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
MIT_Smik_c492_20940 + 376 7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
MIT_Spar_c261_21317 + 370 7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
SGD_Scer_YOR278W + 367 7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
WashU_Sbay_Contig461.5 - 280 1.38e-10 GGAGATTTTT CATCTTGCCTTGCCCATTGT TCTGTCCCGG
MIT_Smik_c228_4055 - 285 1.38e-10 CGGAAATTTT CATCTTGCCTTGCCCATTGT TCTAATTCAA
MIT_Spar_c117_4603 - 282 1.38e-10 AGAAATTTTT CATCTTGCCTTGCCCATTGT TCTGACCCAT
SGD_Scer_YDR232W - 287 1.38e-10 GGAAATTTTT CATCTTGCCTTGCCCATTGT TCTGATCCAT
WashU_Skud_Contig2069.5 + 457 2.43e-09 GGCACCACTA TATCAGCTCTTCAGCATGGT AGGCCATTAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 7.2e-12 377_[+5]_238
WashU_Skud_Contig1682.4 7.2e-12 370_[+5]_245
MIT_Smik_c492_20940 7.2e-12 375_[+5]_240
MIT_Spar_c261_21317 7.2e-12 369_[+5]_246
SGD_Scer_YOR278W 7.2e-12 366_[+5]_249
WashU_Sbay_Contig461.5 1.4e-10 279_[-5]_199
MIT_Smik_c228_4055 1.4e-10 284_[-5]_194
MIT_Spar_c117_4603 1.4e-10 281_[-5]_197
SGD_Scer_YDR232W 1.4e-10 286_[-5]_192
WashU_Skud_Contig2069.5 2.4e-09 456_[+5]_22
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=10
WashU_Sbay_Contig635.57 ( 378) CGTGATGTCTTAAGCATGGT 1
WashU_Skud_Contig1682.4 ( 371) CGTGATGTCTTAAGCATGGT 1
MIT_Smik_c492_20940 ( 376) CGTGATGTCTTAAGCATGGT 1
MIT_Spar_c261_21317 ( 370) CGTGATGTCTTAAGCATGGT 1
SGD_Scer_YOR278W ( 367) CGTGATGTCTTAAGCATGGT 1
WashU_Sbay_Contig461.5 ( 280) CATCTTGCCTTGCCCATTGT 1
MIT_Smik_c228_4055 ( 285) CATCTTGCCTTGCCCATTGT 1
MIT_Spar_c117_4603 ( 282) CATCTTGCCTTGCCCATTGT 1
SGD_Scer_YDR232W ( 287) CATCTTGCCTTGCCCATTGT 1
WashU_Skud_Contig2069.5 ( 457) TATCAGCTCTTCAGCATGGT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 2.6e-029
-997 236 -997 -169
62 -997 151 -997
-997 -997 -997 162
-997 151 151 -997
89 -997 -997 30
-997 -997 -81 147
-997 -81 236 -997
-997 119 -997 89
-997 251 -997 -997
-997 -997 -997 162
-997 -997 -997 162
62 -81 119 -997
89 119 -997 -997
-997 119 177 -997
-997 251 -997 -997
162 -997 -997 -997
-997 -997 -997 162
-997 -997 177 30
-997 -997 251 -997
-997 -997 -997 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.6e-029
0.000000 0.900000 0.000000 0.100000
0.500000 0.000000 0.500000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.500000 0.000000
0.600000 0.000000 0.000000 0.400000
0.000000 0.000000 0.100000 0.900000
0.000000 0.100000 0.900000 0.000000
0.000000 0.400000 0.000000 0.600000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.500000 0.100000 0.400000 0.000000
0.600000 0.400000 0.000000 0.000000
0.000000 0.400000 0.600000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.600000 0.400000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
C[AG]T[CG][AT]TG[TC]CTT[AG][AC][GC]CAT[GT]GT
--------------------------------------------------------------------------------
Time 16.24 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR232W 1.48e-30 57_[+4(1.27e-09)]_29_[-3(6.67e-05)]_36_[+2(9.24e-11)]_104_[-5(1.38e-10)]_6_[+3(8.08e-12)]_27_[+1(6.68e-12)]_119
MIT_Spar_c117_4603 6.70e-31 55_[+4(2.75e-10)]_30_[-3(3.93e-05)]_32_[+2(9.24e-11)]_104_[-5(1.38e-10)]_6_[+3(1.62e-11)]_27_[+1(6.68e-12)]_124
MIT_Smik_c228_4055 1.84e-28 57_[+4(2.84e-09)]_30_[-3(3.93e-05)]_31_[+2(1.25e-09)]_106_[-5(1.38e-10)]_5_[+3(8.08e-12)]_27_[+1(3.51e-11)]_122
WashU_Skud_Contig2069.5 1.98e-28 58_[+4(2.01e-09)]_30_[-3(3.79e-05)]_31_[+2(7.63e-11)]_105_[-5(1.61e-07)]_6_[+3(6.03e-11)]_26_[+1(6.68e-12)]_80_[+5(2.43e-09)]_22
WashU_Sbay_Contig461.5 1.68e-28 53_[+4(1.18e-09)]_10_[-3(5.72e-06)]_3_[-3(3.63e-05)]_32_[+2(2.91e-10)]_6_[+1(9.53e-05)]_75_[-5(1.38e-10)]_6_[+3(1.76e-10)]_28_[+1(1.53e-11)]_125
SGD_Scer_YOR278W 2.15e-32 224_[+1(1.78e-11)]_53_[-3(3.70e-10)]_4_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_226
MIT_Spar_c261_21317 7.63e-33 228_[+1(1.78e-11)]_53_[-3(1.25e-10)]_3_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_223
MIT_Smik_c492_20940 5.17e-30 62_[-4(6.56e-06)]_151_[+1(1.29e-10)]_53_[-3(3.70e-10)]_4_[+4(1.15e-10)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_217
WashU_Skud_Contig1682.4 7.25e-32 89_[-4(8.96e-05)]_121_[+1(1.78e-11)]_51_[-3(1.32e-09)]_4_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_141_[+1(3.09e-05)]_61
WashU_Sbay_Contig635.57 9.51e-32 188_[-3(5.84e-05)]_28_[+1(6.67e-11)]_53_[-3(4.68e-10)]_3_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_215
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************