********************************************************************************
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-HEM14.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_YER014W 1.0000 322
MIT_Spar_c425_6072 1.0000 322 MIT_Smik_c283_5928 1.0000 322
MIT_Sbay_c84_6418 1.0000 322
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM4-HEM14.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
model: mod= oops nmotifs= 5 evt= inf
object function= E-value of product of p-values
width: minw= 6 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 9 maxsites= 9 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 4463 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.321 C 0.179 G 0.179 T 0.321
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 = 192 E-value = 6.5e-023
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :7:::a:6:::aa1:a9:6a
pos.-specific C 9279::4:4a:::6a::4::
probability G ::314:6:6:a::3::1:4:
matrix T 11::6::4:::::::::6::
bits 2.5 ** *
2.3 ** *
2.0 * * ** *
1.8 * * ** *
Information 1.5 * ** ** ***** ** *
content 1.3 * ** ** ***** *** *
(30.8 bits) 1.0 * ***** ************
0.8 * ******************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CACCTAGAGCGAACCAATAA
consensus CG G CTC G CG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1682.4 + 231 7.13e-12 GAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
MIT_Spar_c261_21317 + 229 7.13e-12 TGAATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
SGD_Scer_YOR278W + 225 7.13e-12 AAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
MIT_Smik_c492_20940 + 234 2.25e-11 AAGATATGTA CACCTAGAGCGAACCAATAA TAATTTGTTT
WashU_Sbay_Contig635.57 + 237 9.57e-11 AAAACATGTA CACCTAGAGCGAACCAGTGA TAATTTGCTT
MIT_Spar_c425_6072 + 115 1.35e-10 TTTAAATACT CCGCGACTCCGAAGCAACAA AATGTCGAAG
SGD_Scer_YER014W + 116 1.35e-10 TTTGAATACT CCGCGACTCCGAAGCAACAA AGTGTCGAAG
MIT_Sbay_c84_6418 + 108 1.06e-09 TTTTTATACT CTGCGACTCCGAAACAACAA AATCTCGAAG
MIT_Smik_c283_5928 + 112 1.44e-09 CTTTTTTAAA TACGGACTCCGAAGCAACAA GGTCGAAGGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1682.4 7.1e-12 230_[+1]_385
MIT_Spar_c261_21317 7.1e-12 228_[+1]_387
SGD_Scer_YOR278W 7.1e-12 224_[+1]_391
MIT_Smik_c492_20940 2.3e-11 233_[+1]_382
WashU_Sbay_Contig635.57 9.6e-11 236_[+1]_379
MIT_Spar_c425_6072 1.4e-10 114_[+1]_188
SGD_Scer_YER014W 1.4e-10 115_[+1]_187
MIT_Sbay_c84_6418 1.1e-09 107_[+1]_195
MIT_Smik_c283_5928 1.4e-09 111_[+1]_191
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Skud_Contig1682.4 ( 231) CACCTAGAGCGAACCAATGA 1
MIT_Spar_c261_21317 ( 229) CACCTAGAGCGAACCAATGA 1
SGD_Scer_YOR278W ( 225) CACCTAGAGCGAACCAATGA 1
MIT_Smik_c492_20940 ( 234) CACCTAGAGCGAACCAATAA 1
WashU_Sbay_Contig635.57 ( 237) CACCTAGAGCGAACCAGTGA 1
MIT_Spar_c425_6072 ( 115) CCGCGACTCCGAAGCAACAA 1
SGD_Scer_YER014W ( 116) CCGCGACTCCGAAGCAACAA 1
MIT_Sbay_c84_6418 ( 108) CTGCGACTCCGAAACAACAA 1
MIT_Smik_c283_5928 ( 112) TACGGACTCCGAAGCAACAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4292 bayes= 8.89448 E= 6.5e-023
-982 234 -982 -154
104 34 -982 -154
-982 192 92 -982
-982 234 -66 -982
-982 -982 134 78
162 -982 -982 -982
-982 134 166 -982
78 -982 -982 45
-982 134 166 -982
-982 251 -982 -982
-982 -982 251 -982
162 -982 -982 -982
162 -982 -982 -982
-154 166 92 -982
-982 251 -982 -982
162 -982 -982 -982
145 -982 -66 -982
-982 134 -982 78
78 -982 134 -982
162 -982 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.5e-023
0.000000 0.888889 0.000000 0.111111
0.666667 0.222222 0.000000 0.111111
0.000000 0.666667 0.333333 0.000000
0.000000 0.888889 0.111111 0.000000
0.000000 0.000000 0.444444 0.555556
1.000000 0.000000 0.000000 0.000000
0.000000 0.444444 0.555556 0.000000
0.555556 0.000000 0.000000 0.444444
0.000000 0.444444 0.555556 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.111111 0.555556 0.333333 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.444444 0.000000 0.555556
0.555556 0.000000 0.444444 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
C[AC][CG]C[TG]A[GC][AT][GC]CGAA[CG]CAA[TC][AG]A
--------------------------------------------------------------------------------
Time 2.29 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 15 sites = 9 llr = 142 E-value = 7.6e-011
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A ::a:128::::2:::
pos.-specific C a6::981:::27291
probability G :4:a:::1227:81:
matrix T ::::::198811::9
bits 2.5 * *
2.3 * *
2.0 * ** *
1.8 * ** **
Information 1.5 ****** **
content 1.3 ****** * * ***
(22.8 bits) 1.0 ****** ********
0.8 ***************
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel CCAGCCATTTGCGCT
consensus G A GGCAC
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Sbay_Contig635.57 + 344 1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TGACATAGAC
WashU_Skud_Contig1682.4 + 337 1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TTACATAGAC
MIT_Smik_c492_20940 + 342 1.85e-10 TTGTCTACTT CCAGCCATTTGCGCT TTATATAGAC
MIT_Spar_c261_21317 + 336 1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TTATATAGAC
SGD_Scer_YOR278W + 333 1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TTATATAGAC
SGD_Scer_YER014W + 174 2.34e-07 TGTAACTAAA CGAGCAATGGCAGCT TTCAATTAAA
MIT_Smik_c283_5928 + 168 4.95e-07 TACAACTAAA CGAGCAATGGTAGCT TTTGATTGAA
MIT_Spar_c425_6072 + 5 4.95e-07 TATT CGAGCCCTTTCCCGC GTTCCCAATT
MIT_Sbay_c84_6418 + 44 1.47e-06 CGGAATCCAG CGAGACTGTTGTCCT TTCGCATCCT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 1.8e-10 343_[+2]_277
WashU_Skud_Contig1682.4 1.8e-10 336_[+2]_284
MIT_Smik_c492_20940 1.8e-10 341_[+2]_279
MIT_Spar_c261_21317 1.8e-10 335_[+2]_285
SGD_Scer_YOR278W 1.8e-10 332_[+2]_288
SGD_Scer_YER014W 2.3e-07 173_[+2]_134
MIT_Smik_c283_5928 4.9e-07 167_[+2]_140
MIT_Spar_c425_6072 4.9e-07 4_[+2]_303
MIT_Sbay_c84_6418 1.5e-06 43_[+2]_264
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=15 seqs=9
WashU_Sbay_Contig635.57 ( 344) CCAGCCATTTGCGCT 1
WashU_Skud_Contig1682.4 ( 337) CCAGCCATTTGCGCT 1
MIT_Smik_c492_20940 ( 342) CCAGCCATTTGCGCT 1
MIT_Spar_c261_21317 ( 336) CCAGCCATTTGCGCT 1
SGD_Scer_YOR278W ( 333) CCAGCCATTTGCGCT 1
SGD_Scer_YER014W ( 174) CGAGCAATGGCAGCT 1
MIT_Smik_c283_5928 ( 168) CGAGCAATGGTAGCT 1
MIT_Spar_c425_6072 ( 5) CGAGCCCTTTCCCGC 1
MIT_Sbay_c84_6418 ( 44) CGAGACTGTTGTCCT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4337 bayes= 8.90956 E= 7.6e-011
-982 251 -982 -982
-982 166 134 -982
162 -982 -982 -982
-982 -982 251 -982
-154 234 -982 -982
-55 215 -982 -982
126 -66 -982 -154
-982 -982 -66 145
-982 -982 34 126
-982 -982 34 126
-982 34 192 -154
-55 192 -982 -154
-982 34 215 -982
-982 234 -66 -982
-982 -66 -982 145
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 7.6e-011
0.000000 1.000000 0.000000 0.000000
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 0.777778 0.000000 0.000000
0.777778 0.111111 0.000000 0.111111
0.000000 0.000000 0.111111 0.888889
0.000000 0.000000 0.222222 0.777778
0.000000 0.000000 0.222222 0.777778
0.000000 0.222222 0.666667 0.111111
0.222222 0.666667 0.000000 0.111111
0.000000 0.222222 0.777778 0.000000
0.000000 0.888889 0.111111 0.000000
0.000000 0.111111 0.000000 0.888889
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
C[CG]AGC[CA]AT[TG][TG][GC][CA][GC]CT
--------------------------------------------------------------------------------
Time 4.39 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 181 E-value = 1.1e-018
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A ::::4a6::a4:1:7a33:1
pos.-specific C 1:a:::::a:::2:1::66:
probability G 9::4::4a:::a6:2:1139
matrix T :a:66:::::6:1a::6:1:
bits 2.5 * ** *
2.3 * ** *
2.0 * * ** * *
1.8 * * ** * *
Information 1.5 *** * *** * * * *
content 1.3 *** * *** * * * *
(29.0 bits) 1.0 **** ***** * * * **
0.8 **************** ***
0.5 **************** ***
0.3 ********************
0.0 --------------------
Multilevel GTCTTAAGCATGGTAATCCG
consensus GA G A C G AAG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 + 384 5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
WashU_Skud_Contig1682.4 + 377 5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
MIT_Smik_c492_20940 + 382 5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
MIT_Spar_c261_21317 + 376 5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
SGD_Scer_YOR278W + 373 5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
MIT_Smik_c283_5928 + 133 7.06e-10 AAGCAACAAG GTCGAAGGCAAGCTGAAAGG CATTTTACAA
MIT_Spar_c425_6072 + 138 1.93e-09 GCAACAAAAT GTCGAAGGCAAGATGAAAGG CGTTTTGCAA
SGD_Scer_YER014W + 139 2.96e-09 GCAACAAAGT GTCGAAGGCAAGTTCAAAGG CGTTTTGTAA
MIT_Sbay_c84_6418 + 131 2.41e-08 ACAACAAAAT CTCGAAGGCAAGCTAAGGTA AAAATATTCA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 5.1e-12 383_[+3]_232
WashU_Skud_Contig1682.4 5.1e-12 376_[+3]_239
MIT_Smik_c492_20940 5.1e-12 381_[+3]_234
MIT_Spar_c261_21317 5.1e-12 375_[+3]_240
SGD_Scer_YOR278W 5.1e-12 372_[+3]_243
MIT_Smik_c283_5928 7.1e-10 132_[+3]_170
MIT_Spar_c425_6072 1.9e-09 137_[+3]_165
SGD_Scer_YER014W 3e-09 138_[+3]_164
MIT_Sbay_c84_6418 2.4e-08 130_[+3]_172
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
WashU_Sbay_Contig635.57 ( 384) GTCTTAAGCATGGTAATCCG 1
WashU_Skud_Contig1682.4 ( 377) GTCTTAAGCATGGTAATCCG 1
MIT_Smik_c492_20940 ( 382) GTCTTAAGCATGGTAATCCG 1
MIT_Spar_c261_21317 ( 376) GTCTTAAGCATGGTAATCCG 1
SGD_Scer_YOR278W ( 373) GTCTTAAGCATGGTAATCCG 1
MIT_Smik_c283_5928 ( 133) GTCGAAGGCAAGCTGAAAGG 1
MIT_Spar_c425_6072 ( 138) GTCGAAGGCAAGATGAAAGG 1
SGD_Scer_YER014W ( 139) GTCGAAGGCAAGTTCAAAGG 1
MIT_Sbay_c84_6418 ( 131) CTCGAAGGCAAGCTAAGGTA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4292 bayes= 8.89448 E= 1.1e-018
-982 -66 234 -982
-982 -982 -982 162
-982 251 -982 -982
-982 -982 134 78
45 -982 -982 78
162 -982 -982 -982
78 -982 134 -982
-982 -982 251 -982
-982 251 -982 -982
162 -982 -982 -982
45 -982 -982 78
-982 -982 251 -982
-154 34 166 -154
-982 -982 -982 162
104 -66 34 -982
162 -982 -982 -982
4 -982 -66 78
4 166 -66 -982
-982 166 92 -154
-154 -982 234 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.1e-018
0.000000 0.111111 0.888889 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.444444 0.555556
0.444444 0.000000 0.000000 0.555556
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
1.000000 0.000000 0.000000 0.000000
0.444444 0.000000 0.000000 0.555556
0.000000 0.000000 1.000000 0.000000
0.111111 0.222222 0.555556 0.111111
0.000000 0.000000 0.000000 1.000000
0.666667 0.111111 0.222222 0.000000
1.000000 0.000000 0.000000 0.000000
0.333333 0.000000 0.111111 0.555556
0.333333 0.555556 0.111111 0.000000
0.000000 0.555556 0.333333 0.111111
0.111111 0.000000 0.888889 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
GTC[TG][TA]A[AG]GCA[TA]G[GC]T[AG]A[TA][CA][CG]G
--------------------------------------------------------------------------------
Time 6.42 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 15 sites = 9 llr = 134 E-value = 6.1e-007
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A :9:a:2:::a:8499
pos.-specific C 7::::::a:::::1:
probability G :1::48:::::2::1
matrix T 3:a:6:a:a:a:6::
bits 2.5 *
2.3 *
2.0 *
1.8 *
Information 1.5 ** ******
content 1.3 **** ****** **
(21.5 bits) 1.0 ************ **
0.8 ***************
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel CATATGTCTATATAA
consensus T GA GA
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
MIT_Smik_c492_20940 - 357 1.53e-08 ATCACGCCTC CATATGTCTATATAA AGCGCAAATG
MIT_Spar_c261_21317 - 351 1.53e-08 ATCACGCCTC CATATGTCTATATAA AGCGCAAATG
SGD_Scer_YOR278W - 348 1.53e-08 ATCACGCCTC CATATGTCTATATAA AGCGCAAATG
WashU_Skud_Contig1682.4 - 352 3.10e-08 ATCACGCCTC CATATGTCTATGTAA AGCGCAAATG
MIT_Spar_c425_6072 + 280 5.61e-08 GAAGAATGAA TATAGGTCTATAAAA ATTCAATAAT
SGD_Scer_YER014W + 273 5.61e-08 AAAAATTAAA TATAGGTCTATAAAA CTCGATAATT
WashU_Sbay_Contig635.57 - 359 1.88e-07 ATCACGCCTC CATATGTCTATGTCA AGCGCAAATG
MIT_Smik_c283_5928 + 275 3.48e-07 AAATGTTAAA TATAGATCTATAAAA ATTGAATAGT
MIT_Sbay_c84_6418 + 264 7.23e-07 TTATATTAAA CGTAGATCTATAAAG TTTAAATAGT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c492_20940 1.5e-08 356_[-4]_264
MIT_Spar_c261_21317 1.5e-08 350_[-4]_270
SGD_Scer_YOR278W 1.5e-08 347_[-4]_273
WashU_Skud_Contig1682.4 3.1e-08 351_[-4]_269
MIT_Spar_c425_6072 5.6e-08 279_[+4]_28
SGD_Scer_YER014W 5.6e-08 272_[+4]_35
WashU_Sbay_Contig635.57 1.9e-07 358_[-4]_262
MIT_Smik_c283_5928 3.5e-07 274_[+4]_33
MIT_Sbay_c84_6418 7.2e-07 263_[+4]_44
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=15 seqs=9
MIT_Smik_c492_20940 ( 357) CATATGTCTATATAA 1
MIT_Spar_c261_21317 ( 351) CATATGTCTATATAA 1
SGD_Scer_YOR278W ( 348) CATATGTCTATATAA 1
WashU_Skud_Contig1682.4 ( 352) CATATGTCTATGTAA 1
MIT_Spar_c425_6072 ( 280) TATAGGTCTATAAAA 1
SGD_Scer_YER014W ( 273) TATAGGTCTATAAAA 1
WashU_Sbay_Contig635.57 ( 359) CATATGTCTATGTCA 1
MIT_Smik_c283_5928 ( 275) TATAGATCTATAAAA 1
MIT_Sbay_c84_6418 ( 264) CGTAGATCTATAAAG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4337 bayes= 8.90956 E= 6.1e-007
-982 192 -982 4
145 -982 -66 -982
-982 -982 -982 162
162 -982 -982 -982
-982 -982 134 78
-55 -982 215 -982
-982 -982 -982 162
-982 251 -982 -982
-982 -982 -982 162
162 -982 -982 -982
-982 -982 -982 162
126 -982 34 -982
45 -982 -982 78
145 -66 -982 -982
145 -982 -66 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 6.1e-007
0.000000 0.666667 0.000000 0.333333
0.888889 0.000000 0.111111 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.444444 0.555556
0.222222 0.000000 0.777778 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.777778 0.000000 0.222222 0.000000
0.444444 0.000000 0.000000 0.555556
0.888889 0.111111 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[CT]ATA[TG][GA]TCTAT[AG][TA]AA
--------------------------------------------------------------------------------
Time 8.49 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 162 E-value = 6.6e-011
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 27a973:384:aa:a9693a
pos.-specific C 1:::::6::::::9::::::
probability G 7::::74126a::::1:17:
matrix T :3:13::6:::::1::4:::
bits 2.5 *
2.3 *
2.0 * *
1.8 * *
Information 1.5 * * ***** *
content 1.3 * ** ****** ***
(25.9 bits) 1.0 * ** ** ******** ***
0.8 ******* ************
0.5 ******* ************
0.3 ********************
0.0 --------------------
Multilevel GAAAAGCTAGGAACAAAAGA
consensus AT TAGAGA T A
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c492_20940 + 309 2.27e-12 TTTCAATAAT GAAAAGCTAGGAACAAAAGA AATTTGTCTA
SGD_Scer_YOR278W + 300 7.58e-11 TTTCAATAAT GAAAAGCTAGGAACAAAAAA AATTGGTCTA
WashU_Sbay_Contig635.57 + 312 8.91e-10 TTTCATTAAA GAAAAGCTAGGAACAAAGAA ATTGGTCTAC
WashU_Skud_Contig1682.4 + 304 8.91e-10 TTTCAATAAT GAAAAGCTAGGAATAAAAGA GATTGGTCTA
MIT_Spar_c261_21317 + 304 8.91e-10 TTTCAATAAT GAAAAGCTAGGAACAGAAAA ATTGGTCTAC
MIT_Smik_c283_5928 - 76 1.57e-09 AAAGAAAAGA GTAATGGAAAGAACAATAGA GGGATTTGCA
MIT_Spar_c425_6072 - 74 3.54e-08 AAGAAAAAGA ATAATAGAGAGAACAATAGA GAGATCCGCG
SGD_Scer_YER014W - 74 3.54e-08 AAGAAATAGT ATAATAGAGAGAACAATAGA GATATTCGCG
MIT_Sbay_c84_6418 - 69 4.79e-08 AAAACGAGAA CAATAAGGAAGAACAATAGA AGGATGCGAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c492_20940 2.3e-12 308_[+5]_307
SGD_Scer_YOR278W 7.6e-11 299_[+5]_316
WashU_Sbay_Contig635.57 8.9e-10 311_[+5]_304
WashU_Skud_Contig1682.4 8.9e-10 303_[+5]_312
MIT_Spar_c261_21317 8.9e-10 303_[+5]_312
MIT_Smik_c283_5928 1.6e-09 75_[-5]_227
MIT_Spar_c425_6072 3.5e-08 73_[-5]_229
SGD_Scer_YER014W 3.5e-08 73_[-5]_229
MIT_Sbay_c84_6418 4.8e-08 68_[-5]_234
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
MIT_Smik_c492_20940 ( 309) GAAAAGCTAGGAACAAAAGA 1
SGD_Scer_YOR278W ( 300) GAAAAGCTAGGAACAAAAAA 1
WashU_Sbay_Contig635.57 ( 312) GAAAAGCTAGGAACAAAGAA 1
WashU_Skud_Contig1682.4 ( 304) GAAAAGCTAGGAATAAAAGA 1
MIT_Spar_c261_21317 ( 304) GAAAAGCTAGGAACAGAAAA 1
MIT_Smik_c283_5928 ( 76) GTAATGGAAAGAACAATAGA 1
MIT_Spar_c425_6072 ( 74) ATAATAGAGAGAACAATAGA 1
SGD_Scer_YER014W ( 74) ATAATAGAGAGAACAATAGA 1
MIT_Sbay_c84_6418 ( 69) CAATAAGGAAGAACAATAGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4292 bayes= 8.89448 E= 6.6e-011
-55 -66 192 -982
104 -982 -982 4
162 -982 -982 -982
145 -982 -982 -154
104 -982 -982 4
4 -982 192 -982
-982 166 134 -982
4 -982 -66 78
126 -982 34 -982
45 -982 166 -982
-982 -982 251 -982
162 -982 -982 -982
162 -982 -982 -982
-982 234 -982 -154
162 -982 -982 -982
145 -982 -66 -982
78 -982 -982 45
145 -982 -66 -982
4 -982 192 -982
162 -982 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.6e-011
0.222222 0.111111 0.666667 0.000000
0.666667 0.000000 0.000000 0.333333
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.000000 0.111111
0.666667 0.000000 0.000000 0.333333
0.333333 0.000000 0.666667 0.000000
0.000000 0.555556 0.444444 0.000000
0.333333 0.000000 0.111111 0.555556
0.777778 0.000000 0.222222 0.000000
0.444444 0.000000 0.555556 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 0.888889 0.000000 0.111111
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.555556 0.000000 0.000000 0.444444
0.888889 0.000000 0.111111 0.000000
0.333333 0.000000 0.666667 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
[GA][AT]AA[AT][GA][CG][TA][AG][GA]GAACAA[AT]A[GA]A
--------------------------------------------------------------------------------
Time 10.53 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 3.99e-29 224_[+1(7.13e-12)]_55_[+5(7.58e-11)]_13_[+2(1.85e-10)]_[-4(1.53e-08)]_10_[+3(5.08e-12)]_243
MIT_Spar_c261_21317 4.14e-28 228_[+1(7.13e-12)]_55_[+5(8.91e-10)]_12_[+2(1.85e-10)]_[-4(1.53e-08)]_10_[+3(5.08e-12)]_240
MIT_Smik_c492_20940 4.23e-30 233_[+1(2.25e-11)]_55_[+5(2.27e-12)]_13_[+2(1.85e-10)]_[-4(1.53e-08)]_10_[+3(5.08e-12)]_234
WashU_Skud_Contig1682.4 8.07e-28 230_[+1(7.13e-12)]_53_[+5(8.91e-10)]_13_[+2(1.85e-10)]_[-4(3.10e-08)]_10_[+3(5.08e-12)]_239
WashU_Sbay_Contig635.57 5.21e-26 27_[+2(5.31e-05)]_194_[+1(9.57e-11)]_55_[+5(8.91e-10)]_12_[+2(1.85e-10)]_[-4(1.88e-07)]_10_[+3(5.08e-12)]_232
SGD_Scer_YER014W 8.73e-21 73_[-5(3.54e-08)]_22_[+1(1.35e-10)]_3_[+3(2.96e-09)]_15_[+2(2.34e-07)]_84_[+4(5.61e-08)]_35
MIT_Spar_c425_6072 1.18e-20 4_[+2(4.95e-07)]_54_[-5(3.54e-08)]_21_[+1(1.35e-10)]_3_[+3(1.93e-09)]_15_[+2(1.10e-05)]_92_[+4(5.61e-08)]_28
MIT_Smik_c283_5928 1.26e-20 75_[-5(1.57e-09)]_16_[+1(1.44e-09)]_1_[+3(7.06e-10)]_15_[+2(4.95e-07)]_92_[+4(3.48e-07)]_33
MIT_Sbay_c84_6418 3.25e-17 43_[+2(1.47e-06)]_10_[-5(4.79e-08)]_19_[+1(1.06e-09)]_3_[+3(2.41e-08)]_113_[+4(7.23e-07)]_6_[-3(8.88e-05)]_18
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************