********************************************************************************
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-HEM15.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_YOR176W 1.0000 727
MIT_Spar_c278_20970 1.0000 727 MIT_Smik_c935_20455 1.0000 727
WashU_Skud_Contig2050.4 1.0000 727 WashU_Sbay_Contig480.2 1.0000 727
********************************************************************************
********************************************************************************
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-HEM15.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= 6810 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.314 C 0.186 G 0.186 T 0.314
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 = 217 E-value = 8.2e-028
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :9::::::24a::5::5:::
pos.-specific C :::a:15a11::::a55::a
probability G a:::::::75:2:5:5:55:
matrix T :1a:a95::::8a::::55:
bits 2.5 * * * * *
2.3 * * * * *
2.0 * * * * *
1.8 * * * * *
Information 1.5 * *** * * * ** *
content 1.3 ****** ** * * ** *
(31.3 bits) 1.0 ********* **********
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GATCTTCCGGATTACCAGGC
consensus T AA G G GCTT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 - 391 1.53e-11 TCAATAAACT GATCTTCCGGATTACCATGC TTAAGACATC
WashU_Skud_Contig1682.4 - 384 1.53e-11 TCAATAAACT GATCTTCCGGATTACCATGC TTAAGACATC
MIT_Smik_c492_20940 - 389 1.53e-11 TCAATAAACT GATCTTCCGGATTACCATGC TTAAGACATC
MIT_Spar_c261_21317 - 383 1.53e-11 TCAATAAACT GATCTTCCGGATTACCATGC TTAAGACATC
SGD_Scer_YOR278W - 380 1.53e-11 TCAATAAACT GATCTTCCGGATTACCATGC TTAAGACATC
MIT_Spar_c278_20970 + 547 2.49e-11 AAACAGTGAA GATCTTTCGAATTGCGCGTC GAAACCACAA
WashU_Sbay_Contig480.2 + 558 6.65e-11 AAATGGCAGA GATCTTTCGAAGTGCGCGTC GAAACCACAA
WashU_Skud_Contig2050.4 + 553 3.56e-10 AGCTTCACTG GATCTTTCAAAGTGCGCGTC GAAACCACAA
SGD_Scer_YOR176W + 545 3.56e-10 AAACATTGAA GATCTTTCACATTGCGCGTC GAAACCACAA
MIT_Smik_c935_20455 + 531 1.23e-09 AAACAATAGA GTTCTCTCCAATTGCGCGTC AAAACCACAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 1.5e-11 390_[-1]_225
WashU_Skud_Contig1682.4 1.5e-11 383_[-1]_232
MIT_Smik_c492_20940 1.5e-11 388_[-1]_227
MIT_Spar_c261_21317 1.5e-11 382_[-1]_233
SGD_Scer_YOR278W 1.5e-11 379_[-1]_236
MIT_Spar_c278_20970 2.5e-11 546_[+1]_161
WashU_Sbay_Contig480.2 6.6e-11 557_[+1]_150
WashU_Skud_Contig2050.4 3.6e-10 552_[+1]_155
SGD_Scer_YOR176W 3.6e-10 544_[+1]_163
MIT_Smik_c935_20455 1.2e-09 530_[+1]_177
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=10
WashU_Sbay_Contig635.57 ( 391) GATCTTCCGGATTACCATGC 1
WashU_Skud_Contig1682.4 ( 384) GATCTTCCGGATTACCATGC 1
MIT_Smik_c492_20940 ( 389) GATCTTCCGGATTACCATGC 1
MIT_Spar_c261_21317 ( 383) GATCTTCCGGATTACCATGC 1
SGD_Scer_YOR278W ( 380) GATCTTCCGGATTACCATGC 1
MIT_Spar_c278_20970 ( 547) GATCTTTCGAATTGCGCGTC 1
WashU_Sbay_Contig480.2 ( 558) GATCTTTCGAAGTGCGCGTC 1
WashU_Skud_Contig2050.4 ( 553) GATCTTTCAAAGTGCGCGTC 1
SGD_Scer_YOR176W ( 545) GATCTTTCACATTGCGCGTC 1
MIT_Smik_c935_20455 ( 531) GTTCTCTCCAATTGCGCGTC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6620 bayes= 9.36851 E= 8.2e-028
-997 -997 251 -997
147 -997 -997 -169
-997 -997 -997 162
-997 251 -997 -997
-997 -997 -997 162
-997 -81 -997 147
-997 151 -997 62
-997 251 -997 -997
-70 -81 199 -997
30 -81 151 -997
162 -997 -997 -997
-997 -997 19 130
-997 -997 -997 162
62 -997 151 -997
-997 251 -997 -997
-997 151 151 -997
62 151 -997 -997
-997 -997 151 62
-997 -997 151 62
-997 251 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 8.2e-028
0.000000 0.000000 1.000000 0.000000
0.900000 0.000000 0.000000 0.100000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.100000 0.000000 0.900000
0.000000 0.500000 0.000000 0.500000
0.000000 1.000000 0.000000 0.000000
0.200000 0.100000 0.700000 0.000000
0.400000 0.100000 0.500000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.200000 0.800000
0.000000 0.000000 0.000000 1.000000
0.500000 0.000000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.500000 0.500000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.000000 0.500000 0.500000
0.000000 0.000000 0.500000 0.500000
0.000000 1.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
GATCTT[CT]C[GA][GA]A[TG]T[AG]C[CG][AC][GT][GT]C
--------------------------------------------------------------------------------
Time 4.85 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 10 llr = 212 E-value = 9.1e-027
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A :9:1:5:9:::a5:5a9518
pos.-specific C 5179::::5a::595:::::
probability G 5:::::a15:a:::::1:9:
matrix T ::3:a5:::::::1:::5:2
bits 2.5 * **
2.3 * **
2.0 * * ** * *
1.8 * * ** * *
Information 1.5 * ** * **** * * *
content 1.3 ***** ****** * ** *
(30.7 bits) 1.0 ***** *********** **
0.8 ***** *********** **
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CACCTAGACCGAACAAAAGA
consensus G T T G C C T T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1682.4 + 231 1.46e-11 GAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
MIT_Spar_c261_21317 + 229 1.46e-11 TGAATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
SGD_Scer_YOR278W + 225 1.46e-11 AAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
SGD_Scer_YOR176W + 133 5.07e-11 AGCCAAGAGT GACCTTGACCGACCAAAAGT ATTCCTTCGC
WashU_Sbay_Contig635.57 + 237 9.06e-11 AAAACATGTA CACCTAGAGCGAACCAGTGA TAATTTGCTT
MIT_Smik_c492_20940 + 234 2.63e-10 AAGATATGTA CACCTAGAGCGAACCAATAA TAATTTGTTT
WashU_Sbay_Contig480.2 + 180 3.17e-10 GAGCCATAAT GCTCTTGACCGACCAAAAGA AGTATTCCTA
MIT_Smik_c935_20455 + 131 3.17e-10 GACCAACAGT GATCTTGGCCGACCAAAAGA CTCCTTCGCG
MIT_Spar_c278_20970 + 135 6.22e-10 AACCAAGAGT GACCTTGACCGACTAAAAGT ATTCCTTCGC
WashU_Skud_Contig2050.4 + 136 7.40e-10 GACCAACAAT GATATTGACCGACCAAAAGA AGTATTCCTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1682.4 1.5e-11 230_[+2]_385
MIT_Spar_c261_21317 1.5e-11 228_[+2]_387
SGD_Scer_YOR278W 1.5e-11 224_[+2]_391
SGD_Scer_YOR176W 5.1e-11 132_[+2]_575
WashU_Sbay_Contig635.57 9.1e-11 236_[+2]_379
MIT_Smik_c492_20940 2.6e-10 233_[+2]_382
WashU_Sbay_Contig480.2 3.2e-10 179_[+2]_528
MIT_Smik_c935_20455 3.2e-10 130_[+2]_577
MIT_Spar_c278_20970 6.2e-10 134_[+2]_573
WashU_Skud_Contig2050.4 7.4e-10 135_[+2]_572
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=10
WashU_Skud_Contig1682.4 ( 231) CACCTAGAGCGAACCAATGA 1
MIT_Spar_c261_21317 ( 229) CACCTAGAGCGAACCAATGA 1
SGD_Scer_YOR278W ( 225) CACCTAGAGCGAACCAATGA 1
SGD_Scer_YOR176W ( 133) GACCTTGACCGACCAAAAGT 1
WashU_Sbay_Contig635.57 ( 237) CACCTAGAGCGAACCAGTGA 1
MIT_Smik_c492_20940 ( 234) CACCTAGAGCGAACCAATAA 1
WashU_Sbay_Contig480.2 ( 180) GCTCTTGACCGACCAAAAGA 1
MIT_Smik_c935_20455 ( 131) GATCTTGGCCGACCAAAAGA 1
MIT_Spar_c278_20970 ( 135) GACCTTGACCGACTAAAAGT 1
WashU_Skud_Contig2050.4 ( 136) GATATTGACCGACCAAAAGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6620 bayes= 9.36851 E= 9.1e-027
-997 151 151 -997
147 -81 -997 -997
-997 199 -997 -11
-169 236 -997 -997
-997 -997 -997 162
62 -997 -997 62
-997 -997 251 -997
147 -997 -81 -997
-997 151 151 -997
-997 251 -997 -997
-997 -997 251 -997
162 -997 -997 -997
62 151 -997 -997
-997 236 -997 -169
62 151 -997 -997
162 -997 -997 -997
147 -997 -81 -997
62 -997 -997 62
-169 -997 236 -997
130 -997 -997 -70
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.1e-027
0.000000 0.500000 0.500000 0.000000
0.900000 0.100000 0.000000 0.000000
0.000000 0.700000 0.000000 0.300000
0.100000 0.900000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.500000 0.000000 0.000000 0.500000
0.000000 0.000000 1.000000 0.000000
0.900000 0.000000 0.100000 0.000000
0.000000 0.500000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.900000 0.000000 0.100000
0.500000 0.500000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.900000 0.000000 0.100000 0.000000
0.500000 0.000000 0.000000 0.500000
0.100000 0.000000 0.900000 0.000000
0.800000 0.000000 0.000000 0.200000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[CG]A[CT]CT[AT]GA[CG]CGA[AC]C[AC]AA[AT]G[AT]
--------------------------------------------------------------------------------
Time 9.66 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 10 llr = 214 E-value = 3.7e-026
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :5:::5::::5:5::::::6
pos.-specific C 25::5:::5:::5:::5:::
probability G :::a5:a5:a:a::a::::4
matrix T 8:a::5:55:5::a:a5aa:
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 TATGCAGGCGAGATGTCTTA
consensus CC GT TT T C T G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 + 370 1.12e-10 GACATAGACA TATGGAGGCGTGATGTCTTA AGCATGGTAA
WashU_Skud_Contig1682.4 + 363 1.12e-10 TACATAGACA TATGGAGGCGTGATGTCTTA AGCATGGTAA
MIT_Smik_c492_20940 + 368 1.12e-10 TATATAGACA TATGGAGGCGTGATGTCTTA AGCATGGTAA
MIT_Spar_c261_21317 + 362 1.12e-10 TATATAGACA TATGGAGGCGTGATGTCTTA AGCATGGTAA
SGD_Scer_YOR278W + 359 1.12e-10 TATATAGACA TATGGAGGCGTGATGTCTTA AGCATGGTAA
WashU_Sbay_Contig480.2 + 512 1.73e-10 TGTTTTTTGT TCTGCTGTTGAGCTGTTTTG CTCCACCTGT
WashU_Skud_Contig2050.4 + 503 1.73e-10 TGTTTTTTGT TCTGCTGTTGAGCTGTTTTG TTCCATCTGT
MIT_Smik_c935_20455 + 486 2.87e-10 CTTTTTTTGC TCTGCTGTTGAGCTGTTTTA CTTCATTGTT
MIT_Spar_c278_20970 + 502 4.84e-10 CTTTTTTTGC CCTGCTGTTGAGCTGTTTTG CTTCACTGTT
SGD_Scer_YOR176W + 500 4.84e-10 CTTTTTTTGT CCTGCTGTTGAGCTGTTTTG CTTTACTGTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 1.1e-10 369_[+3]_246
WashU_Skud_Contig1682.4 1.1e-10 362_[+3]_253
MIT_Smik_c492_20940 1.1e-10 367_[+3]_248
MIT_Spar_c261_21317 1.1e-10 361_[+3]_254
SGD_Scer_YOR278W 1.1e-10 358_[+3]_257
WashU_Sbay_Contig480.2 1.7e-10 511_[+3]_196
WashU_Skud_Contig2050.4 1.7e-10 502_[+3]_205
MIT_Smik_c935_20455 2.9e-10 485_[+3]_222
MIT_Spar_c278_20970 4.8e-10 501_[+3]_206
SGD_Scer_YOR176W 4.8e-10 499_[+3]_208
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=10
WashU_Sbay_Contig635.57 ( 370) TATGGAGGCGTGATGTCTTA 1
WashU_Skud_Contig1682.4 ( 363) TATGGAGGCGTGATGTCTTA 1
MIT_Smik_c492_20940 ( 368) TATGGAGGCGTGATGTCTTA 1
MIT_Spar_c261_21317 ( 362) TATGGAGGCGTGATGTCTTA 1
SGD_Scer_YOR278W ( 359) TATGGAGGCGTGATGTCTTA 1
WashU_Sbay_Contig480.2 ( 512) TCTGCTGTTGAGCTGTTTTG 1
WashU_Skud_Contig2050.4 ( 503) TCTGCTGTTGAGCTGTTTTG 1
MIT_Smik_c935_20455 ( 486) TCTGCTGTTGAGCTGTTTTA 1
MIT_Spar_c278_20970 ( 502) CCTGCTGTTGAGCTGTTTTG 1
SGD_Scer_YOR176W ( 500) CCTGCTGTTGAGCTGTTTTG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6620 bayes= 9.36851 E= 3.7e-026
-997 19 -997 130
62 151 -997 -997
-997 -997 -997 162
-997 -997 251 -997
-997 151 151 -997
62 -997 -997 62
-997 -997 251 -997
-997 -997 151 62
-997 151 -997 62
-997 -997 251 -997
62 -997 -997 62
-997 -997 251 -997
62 151 -997 -997
-997 -997 -997 162
-997 -997 251 -997
-997 -997 -997 162
-997 151 -997 62
-997 -997 -997 162
-997 -997 -997 162
89 -997 119 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.7e-026
0.000000 0.200000 0.000000 0.800000
0.500000 0.500000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.500000 0.500000 0.000000
0.500000 0.000000 0.000000 0.500000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.500000 0.500000
0.000000 0.500000 0.000000 0.500000
0.000000 0.000000 1.000000 0.000000
0.500000 0.000000 0.000000 0.500000
0.000000 0.000000 1.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.000000 0.500000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.600000 0.000000 0.400000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
[TC][AC]TG[CG][AT]G[GT][CT]G[AT]G[AC]TGT[CT]TT[AG]
--------------------------------------------------------------------------------
Time 14.33 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 10 llr = 183 E-value = 2.8e-014
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 41::::a4177a9a78:486
pos.-specific C :5aaa::61::::::124:1
probability G :4::::::533:::318123
matrix T 6::::a::3:::1::::1::
bits 2.5 ***
2.3 ***
2.0 ***
1.8 *** *
Information 1.5 ***** * * *
content 1.3 ****** *** *
(26.3 bits) 1.0 ******* ******** *
0.8 ******** ******** **
0.5 ***************** **
0.3 ********************
0.0 --------------------
Multilevel TCCCCTACGAAAAAAAGAAA
consensus AG ATGG G CCGG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YOR176W + 185 1.89e-12 CAATCCCATA TCCCCTACGAAAAAAAGCAG CATGAGAAAA
WashU_Sbay_Contig480.2 + 236 9.76e-11 AAGTGCCAAA TCCCCTACTGAAAAAAGCAA CATGAGAAGC
MIT_Spar_c278_20970 + 187 1.11e-10 CAATCCCATA TCCCCTACTGAAAAAAGCAG CGTGCGAAAA
WashU_Sbay_Contig635.57 - 545 7.33e-10 GCTGGATAGG AGCCCTAAGAAAAAGAGAAA ATTTTTCACA
MIT_Smik_c935_20455 + 183 3.77e-09 AAGTCTCATA TCCCCTACCAGAAAAAGTAG CAGGCGAAAA
MIT_Smik_c492_20940 - 536 4.08e-09 GTTAGATAGG AGCCCTAAGAAAAAGCGAAA ATTTTTCACT
MIT_Spar_c261_21317 - 538 7.56e-09 GTTGGATGGG AGCCCTAAGAGAAAAACGAA AAATTTTCAC
SGD_Scer_YOR278W - 521 9.27e-09 CGACAGTAGG AGCCCTAAGAGATAAAGCGA AAAATTTTCA
WashU_Skud_Contig1682.4 - 616 1.19e-08 . TACCCTACAAAAAAGAGAAA GCATTGGAAA
WashU_Skud_Contig2050.4 + 192 2.76e-08 CTGTGTCAAA TCCCCTACTGAAAAAGCAGC ATTGGGAAAG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YOR176W 1.9e-12 184_[+4]_523
WashU_Sbay_Contig480.2 9.8e-11 235_[+4]_472
MIT_Spar_c278_20970 1.1e-10 186_[+4]_521
WashU_Sbay_Contig635.57 7.3e-10 544_[-4]_71
MIT_Smik_c935_20455 3.8e-09 182_[+4]_525
MIT_Smik_c492_20940 4.1e-09 535_[-4]_80
MIT_Spar_c261_21317 7.6e-09 537_[-4]_78
SGD_Scer_YOR278W 9.3e-09 520_[-4]_95
WashU_Skud_Contig1682.4 1.2e-08 615_[-4]
WashU_Skud_Contig2050.4 2.8e-08 191_[+4]_516
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=10
SGD_Scer_YOR176W ( 185) TCCCCTACGAAAAAAAGCAG 1
WashU_Sbay_Contig480.2 ( 236) TCCCCTACTGAAAAAAGCAA 1
MIT_Spar_c278_20970 ( 187) TCCCCTACTGAAAAAAGCAG 1
WashU_Sbay_Contig635.57 ( 545) AGCCCTAAGAAAAAGAGAAA 1
MIT_Smik_c935_20455 ( 183) TCCCCTACCAGAAAAAGTAG 1
MIT_Smik_c492_20940 ( 536) AGCCCTAAGAAAAAGCGAAA 1
MIT_Spar_c261_21317 ( 538) AGCCCTAAGAGAAAAACGAA 1
SGD_Scer_YOR278W ( 521) AGCCCTAAGAGATAAAGCGA 1
WashU_Skud_Contig1682.4 ( 616) TACCCTACAAAAAAGAGAAA 1
WashU_Skud_Contig2050.4 ( 192) TCCCCTACTGAAAAAGCAGC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6620 bayes= 9.36851 E= 2.8e-014
30 -997 -997 89
-169 151 119 -997
-997 251 -997 -997
-997 251 -997 -997
-997 251 -997 -997
-997 -997 -997 162
162 -997 -997 -997
30 177 -997 -997
-169 -81 151 -11
111 -997 77 -997
111 -997 77 -997
162 -997 -997 -997
147 -997 -997 -169
162 -997 -997 -997
111 -997 77 -997
130 -81 -81 -997
-997 19 219 -997
30 119 -81 -169
130 -997 19 -997
89 -81 77 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.8e-014
0.400000 0.000000 0.000000 0.600000
0.100000 0.500000 0.400000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.400000 0.600000 0.000000 0.000000
0.100000 0.100000 0.500000 0.300000
0.700000 0.000000 0.300000 0.000000
0.700000 0.000000 0.300000 0.000000
1.000000 0.000000 0.000000 0.000000
0.900000 0.000000 0.000000 0.100000
1.000000 0.000000 0.000000 0.000000
0.700000 0.000000 0.300000 0.000000
0.800000 0.100000 0.100000 0.000000
0.000000 0.200000 0.800000 0.000000
0.400000 0.400000 0.100000 0.100000
0.800000 0.000000 0.200000 0.000000
0.600000 0.100000 0.300000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[TA][CG]CCCTA[CA][GT][AG][AG]AAA[AG]A[GC][AC][AG][AG]
--------------------------------------------------------------------------------
Time 18.90 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 10 llr = 178 E-value = 7.9e-013
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A a4::3::5:::5a9:7aa15
pos.-specific C ::1::16::a:1:1::::::
probability G :::561:::::::::2::95
matrix T :6951845a:a4::a1::::
bits 2.5 *
2.3 *
2.0 * *
1.8 * *
Information 1.5 * *** * * ***
content 1.3 * * * *** *** ***
(25.6 bits) 1.0 * ** ** *** *** ****
0.8 ******* *** ********
0.5 *********** ********
0.3 ********************
0.0 --------------------
Multilevel ATTGGTCATCTAAATAAAGA
consensus A TA TT T G G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c278_20970 + 589 2.51e-11 CGTCGAAAAT AATGGTCATCTAAATAAAGG GTTCTTATTT
SGD_Scer_YOR176W + 587 2.51e-11 CGTCGAAAAC AATGGTCATCTAAATAAAGG GTTCTTATTA
WashU_Skud_Contig2050.4 + 595 2.67e-10 CGTCGAAAAT ATTGATCATCTAAATAAAGG GTTCTTATTT
MIT_Spar_c261_21317 + 251 1.62e-09 ACCAATGATA ATTTGTTTTCTTAATAAAGA AAAACTATTA
WashU_Skud_Contig1682.4 + 253 3.66e-09 ACCAATGATA ATTTGTTTTCTTAATGAAGA AAGTATTAAA
MIT_Smik_c492_20940 + 256 9.18e-09 ACCAATAATA ATTTGTTTTCTTACTAAAGA AAAACTATTA
WashU_Sbay_Contig480.2 + 600 1.13e-08 CATCAAAAAT ATCGACCATCTAAATAAAGG GTTCTTGTTT
SGD_Scer_YOR278W + 247 1.22e-08 ACCAATGATA ATTTGTTTTCTTAATTAAGA AAAACCATTA
MIT_Smik_c935_20455 + 573 1.29e-08 CGTCGAAAAT AATGATCATCTAAATAAAAG AGTTCACGTT
WashU_Sbay_Contig635.57 + 258 5.96e-08 AACCAGTGAT AATTTGCTTCTCAATGAAGA AAAAGCGATT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c278_20970 2.5e-11 588_[+5]_119
SGD_Scer_YOR176W 2.5e-11 586_[+5]_121
WashU_Skud_Contig2050.4 2.7e-10 594_[+5]_113
MIT_Spar_c261_21317 1.6e-09 250_[+5]_365
WashU_Skud_Contig1682.4 3.7e-09 252_[+5]_363
MIT_Smik_c492_20940 9.2e-09 255_[+5]_360
WashU_Sbay_Contig480.2 1.1e-08 599_[+5]_108
SGD_Scer_YOR278W 1.2e-08 246_[+5]_369
MIT_Smik_c935_20455 1.3e-08 572_[+5]_135
WashU_Sbay_Contig635.57 6e-08 257_[+5]_358
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=10
MIT_Spar_c278_20970 ( 589) AATGGTCATCTAAATAAAGG 1
SGD_Scer_YOR176W ( 587) AATGGTCATCTAAATAAAGG 1
WashU_Skud_Contig2050.4 ( 595) ATTGATCATCTAAATAAAGG 1
MIT_Spar_c261_21317 ( 251) ATTTGTTTTCTTAATAAAGA 1
WashU_Skud_Contig1682.4 ( 253) ATTTGTTTTCTTAATGAAGA 1
MIT_Smik_c492_20940 ( 256) ATTTGTTTTCTTACTAAAGA 1
WashU_Sbay_Contig480.2 ( 600) ATCGACCATCTAAATAAAGG 1
SGD_Scer_YOR278W ( 247) ATTTGTTTTCTTAATTAAGA 1
MIT_Smik_c935_20455 ( 573) AATGATCATCTAAATAAAAG 1
WashU_Sbay_Contig635.57 ( 258) AATTTGCTTCTCAATGAAGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6620 bayes= 9.36851 E= 7.9e-013
162 -997 -997 -997
30 -997 -997 89
-997 -81 -997 147
-997 -997 151 62
-11 -997 177 -169
-997 -81 -81 130
-997 177 -997 30
62 -997 -997 62
-997 -997 -997 162
-997 251 -997 -997
-997 -997 -997 162
62 -81 -997 30
162 -997 -997 -997
147 -81 -997 -997
-997 -997 -997 162
111 -997 19 -169
162 -997 -997 -997
162 -997 -997 -997
-169 -997 236 -997
62 -997 151 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 7.9e-013
1.000000 0.000000 0.000000 0.000000
0.400000 0.000000 0.000000 0.600000
0.000000 0.100000 0.000000 0.900000
0.000000 0.000000 0.500000 0.500000
0.300000 0.000000 0.600000 0.100000
0.000000 0.100000 0.100000 0.800000
0.000000 0.600000 0.000000 0.400000
0.500000 0.000000 0.000000 0.500000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.500000 0.100000 0.000000 0.400000
1.000000 0.000000 0.000000 0.000000
0.900000 0.100000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.700000 0.000000 0.200000 0.100000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.100000 0.000000 0.900000 0.000000
0.500000 0.000000 0.500000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
A[TA]T[GT][GA]T[CT][AT]TCT[AT]AAT[AG]AAG[AG]
--------------------------------------------------------------------------------
Time 23.28 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YOR278W 1.05e-26 224_[+2(1.46e-11)]_2_[+5(1.22e-08)]_92_[+3(1.12e-10)]_1_[-1(1.53e-11)]_121_[-4(9.27e-09)]_95
MIT_Spar_c261_21317 1.29e-27 99_[-3(7.46e-05)]_109_[+2(1.46e-11)]_2_[+5(1.62e-09)]_91_[+3(1.12e-10)]_1_[-1(1.53e-11)]_29_[-1(4.35e-06)]_66_[-1(8.95e-05)]_[-4(7.56e-09)]_78
MIT_Smik_c492_20940 5.72e-26 233_[+2(2.63e-10)]_2_[+5(9.18e-09)]_92_[+3(1.12e-10)]_1_[-1(1.53e-11)]_127_[-4(4.08e-09)]_8_[+2(8.70e-06)]_52
WashU_Skud_Contig1682.4 4.27e-27 230_[+2(1.46e-11)]_2_[+5(3.66e-09)]_90_[+3(1.12e-10)]_1_[-1(1.53e-11)]_128_[-4(2.59e-06)]_64_[-4(1.19e-08)]
WashU_Sbay_Contig635.57 2.42e-26 236_[+2(9.06e-11)]_1_[+5(5.96e-08)]_92_[+3(1.12e-10)]_1_[-1(1.53e-11)]_134_[-4(7.33e-10)]_71
SGD_Scer_YOR176W 4.69e-30 132_[+2(5.07e-11)]_32_[+4(1.89e-12)]_295_[+3(4.84e-10)]_25_[+1(3.56e-10)]_22_[+5(2.51e-11)]_121
MIT_Spar_c278_20970 1.96e-28 134_[+2(6.22e-10)]_32_[+4(1.11e-10)]_91_[+1(3.86e-05)]_184_[+3(4.84e-10)]_25_[+1(2.49e-11)]_22_[+5(2.51e-11)]_119
MIT_Smik_c935_20455 2.56e-23 130_[+2(3.17e-10)]_32_[+4(3.77e-09)]_31_[+2(4.34e-05)]_24_[+4(2.18e-05)]_188_[+3(2.87e-10)]_25_[+1(1.23e-09)]_22_[+5(1.29e-08)]_135
WashU_Skud_Contig2050.4 1.85e-24 135_[+2(7.40e-10)]_36_[+4(2.76e-08)]_291_[+3(1.73e-10)]_30_[+1(3.56e-10)]_22_[+5(2.67e-10)]_113
WashU_Sbay_Contig480.2 2.83e-26 179_[+2(3.17e-10)]_36_[+4(9.76e-11)]_256_[+3(1.73e-10)]_26_[+1(6.65e-11)]_22_[+5(1.13e-08)]_108
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************