********************************************************************************
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-HEM15.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_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 HEM1-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= 6125 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.296 C 0.204 G 0.204 T 0.296
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 = 225 E-value = 1.2e-031
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 4a5::5:::5:1aa61:5:5
pos.-specific C 6::::5:a::a::::5a:55
probability G ::2:a:a:a::9::44:55:
matrix T ::3a:::::5::::::::::
bits 2.5 * *** * *
2.3 * *** * *
2.0 * *** ** *
1.8 * *** ** *
Information 1.5 * ** *** **** * *
content 1.3 ** ** *** **** * *
(32.4 bits) 1.0 ** ****** **********
0.8 ** ****** **********
0.5 ** *****************
0.3 ********************
0.0 --------------------
Multilevel CAATGAGCGACGAAACCACA
consensus A T C T GG GGC
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2069.5 + 371 4.19e-12 GGCCGCAGAC CAATGAGCGACGAAGGCGGC CTTTCGTAGC
MIT_Spar_c117_4603 + 369 4.19e-12 GGCCGCAGAC CAATGAGCGACGAAGGCGGC CTTTCCGAGT
SGD_Scer_YDR232W + 374 4.19e-12 GGCCGCAGAC CAATGAGCGACGAAGGCGGC CTTTCCGAGC
MIT_Smik_c228_4055 + 371 6.28e-12 AAGCGCAGAC CAATGAGCGACGAAAGCGGC CTTTTGAAGG
SGD_Scer_YOR176W + 554 3.36e-11 AGATCTTTCA CATTGCGCGTCGAAACCACA AACCGTCGAA
WashU_Sbay_Contig480.2 + 567 8.33e-11 AGATCTTTCG AAGTGCGCGTCGAAACCACA AACCATCAAA
WashU_Skud_Contig2050.4 + 562 8.33e-11 GGATCTTTCA AAGTGCGCGTCGAAACCACA AACCGTCGAA
WashU_Sbay_Contig461.5 + 368 8.75e-11 GGGCGCAGAC CAATGAGCGACGAAGACGGC TTTTGGGCGG
MIT_Spar_c278_20970 + 556 9.22e-11 AGATCTTTCG AATTGCGCGTCGAAACCACA AACCGTCGAA
MIT_Smik_c935_20455 + 540 3.96e-10 AGTTCTCTCC AATTGCGCGTCAAAACCACA AACCGTCGAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2069.5 4.2e-12 370_[+1]_108
MIT_Spar_c117_4603 4.2e-12 368_[+1]_110
SGD_Scer_YDR232W 4.2e-12 373_[+1]_105
MIT_Smik_c228_4055 6.3e-12 370_[+1]_108
SGD_Scer_YOR176W 3.4e-11 553_[+1]_154
WashU_Sbay_Contig480.2 8.3e-11 566_[+1]_141
WashU_Skud_Contig2050.4 8.3e-11 561_[+1]_146
WashU_Sbay_Contig461.5 8.7e-11 367_[+1]_111
MIT_Spar_c278_20970 9.2e-11 555_[+1]_152
MIT_Smik_c935_20455 4e-10 539_[+1]_168
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=10
WashU_Skud_Contig2069.5 ( 371) CAATGAGCGACGAAGGCGGC 1
MIT_Spar_c117_4603 ( 369) CAATGAGCGACGAAGGCGGC 1
SGD_Scer_YDR232W ( 374) CAATGAGCGACGAAGGCGGC 1
MIT_Smik_c228_4055 ( 371) CAATGAGCGACGAAAGCGGC 1
SGD_Scer_YOR176W ( 554) CATTGCGCGTCGAAACCACA 1
WashU_Sbay_Contig480.2 ( 567) AAGTGCGCGTCGAAACCACA 1
WashU_Skud_Contig2050.4 ( 562) AAGTGCGCGTCGAAACCACA 1
WashU_Sbay_Contig461.5 ( 368) CAATGAGCGACGAAGACGGC 1
MIT_Spar_c278_20970 ( 556) AATTGCGCGTCGAAACCACA 1
MIT_Smik_c935_20455 ( 540) AATTGCGCGTCAAAACCACA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 1.2e-031
30 177 -997 -997
162 -997 -997 -997
62 -997 19 -11
-997 -997 -997 162
-997 -997 251 -997
62 151 -997 -997
-997 -997 251 -997
-997 251 -997 -997
-997 -997 251 -997
62 -997 -997 62
-997 251 -997 -997
-169 -997 236 -997
162 -997 -997 -997
162 -997 -997 -997
89 -997 119 -997
-169 151 119 -997
-997 251 -997 -997
62 -997 151 -997
-997 151 151 -997
62 151 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.2e-031
0.400000 0.600000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.500000 0.000000 0.200000 0.300000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 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
0.000000 0.000000 1.000000 0.000000
0.500000 0.000000 0.000000 0.500000
0.000000 1.000000 0.000000 0.000000
0.100000 0.000000 0.900000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.600000 0.000000 0.400000 0.000000
0.100000 0.500000 0.400000 0.000000
0.000000 1.000000 0.000000 0.000000
0.500000 0.000000 0.500000 0.000000
0.000000 0.500000 0.500000 0.000000
0.500000 0.500000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
[CA]A[ATG]TG[AC]GCG[AT]CGAA[AG][CG]C[AG][CG][AC]
--------------------------------------------------------------------------------
Time 3.95 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 10 llr = 209 E-value = 9.7e-026
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A ::2::::1:::::::::::9
pos.-specific C 94:4:a6:3a:a41:a::9:
probability G 1:5:4:4:6:1:1:3:::1:
matrix T :6366::91:9:597:aa:1
bits 2.5 * * * *
2.3 * * * *
2.0 * * * * * *
1.8 * * * * * *
Information 1.5 * ** * * ****
content 1.3 * *** *** * *****
(30.1 bits) 1.0 ** ********* *******
0.8 ** *****************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CTGTTCCTGCTCTTTCTTCA
consensus CTCG G C C G
sequence A
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c228_4055 + 312 4.12e-12 ATGAAAATTT CCGTTCCTGCTCTTTCTTCA TATATGAACA
SGD_Scer_YDR232W + 315 4.12e-12 TGAAAAATTT CCGTTCCTGCTCTTTCTTCA TATATGAACA
MIT_Spar_c117_4603 + 310 6.47e-12 TGAAAAATTT CTGTTCCTGCTCTTTCTTCA TATATGAACA
WashU_Skud_Contig2069.5 + 313 8.03e-12 TGAAAAATTT CCGTTCCTGCTCTTGCTTCA TATATGACAA
MIT_Smik_c935_20455 + 154 7.23e-11 CAAAAGACTC CTTCGCGTCCTCCTTCTTCA AGTCTCATAT
MIT_Spar_c278_20970 + 159 7.23e-11 AAAAGTATTC CTTCGCGTCCTCCTTCTTCA ATCCCATATC
SGD_Scer_YOR176W + 157 7.23e-11 AAAAGTATTC CTTCGCGTCCTCCTTCTTCA ATCCCATATC
WashU_Sbay_Contig461.5 + 308 1.78e-10 TGAAAAATCT CCGTTCCTGCTCTTGCTTGA TATATTAACA
WashU_Sbay_Contig480.2 + 207 1.47e-09 AGAAGTATTC CTACGCGAGCTCCCTCTTCA AGTGCCAAAT
WashU_Skud_Contig2050.4 + 157 2.43e-08 ACCAAAAGAA GTATTCCTTCGCGTGCTTCT CCTTTCTGTG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c228_4055 4.1e-12 311_[+2]_167
SGD_Scer_YDR232W 4.1e-12 314_[+2]_164
MIT_Spar_c117_4603 6.5e-12 309_[+2]_169
WashU_Skud_Contig2069.5 8e-12 312_[+2]_166
MIT_Smik_c935_20455 7.2e-11 153_[+2]_554
MIT_Spar_c278_20970 7.2e-11 158_[+2]_549
SGD_Scer_YOR176W 7.2e-11 156_[+2]_551
WashU_Sbay_Contig461.5 1.8e-10 307_[+2]_171
WashU_Sbay_Contig480.2 1.5e-09 206_[+2]_501
WashU_Skud_Contig2050.4 2.4e-08 156_[+2]_551
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=10
MIT_Smik_c228_4055 ( 312) CCGTTCCTGCTCTTTCTTCA 1
SGD_Scer_YDR232W ( 315) CCGTTCCTGCTCTTTCTTCA 1
MIT_Spar_c117_4603 ( 310) CTGTTCCTGCTCTTTCTTCA 1
WashU_Skud_Contig2069.5 ( 313) CCGTTCCTGCTCTTGCTTCA 1
MIT_Smik_c935_20455 ( 154) CTTCGCGTCCTCCTTCTTCA 1
MIT_Spar_c278_20970 ( 159) CTTCGCGTCCTCCTTCTTCA 1
SGD_Scer_YOR176W ( 157) CTTCGCGTCCTCCTTCTTCA 1
WashU_Sbay_Contig461.5 ( 308) CCGTTCCTGCTCTTGCTTGA 1
WashU_Sbay_Contig480.2 ( 207) CTACGCGAGCTCCCTCTTCA 1
WashU_Skud_Contig2050.4 ( 157) GTATTCCTTCGCGTGCTTCT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 9.7e-026
-997 236 -81 -997
-997 119 -997 89
-70 -997 151 -11
-997 119 -997 89
-997 -997 119 89
-997 251 -997 -997
-997 177 119 -997
-169 -997 -997 147
-997 77 177 -169
-997 251 -997 -997
-997 -997 -81 147
-997 251 -997 -997
-997 119 -81 62
-997 -81 -997 147
-997 -997 77 111
-997 251 -997 -997
-997 -997 -997 162
-997 -997 -997 162
-997 236 -81 -997
147 -997 -997 -169
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.7e-026
0.000000 0.900000 0.100000 0.000000
0.000000 0.400000 0.000000 0.600000
0.200000 0.000000 0.500000 0.300000
0.000000 0.400000 0.000000 0.600000
0.000000 0.000000 0.400000 0.600000
0.000000 1.000000 0.000000 0.000000
0.000000 0.600000 0.400000 0.000000
0.100000 0.000000 0.000000 0.900000
0.000000 0.300000 0.600000 0.100000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.100000 0.900000
0.000000 1.000000 0.000000 0.000000
0.000000 0.400000 0.100000 0.500000
0.000000 0.100000 0.000000 0.900000
0.000000 0.000000 0.300000 0.700000
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 0.900000 0.100000 0.000000
0.900000 0.000000 0.000000 0.100000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
C[TC][GTA][TC][TG]C[CG]T[GC]CTC[TC]T[TG]CTTCA
--------------------------------------------------------------------------------
Time 7.93 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 10 llr = 194 E-value = 5.5e-020
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :1:3::111:1:11:91:::
pos.-specific C 122:6661:9::1::1:8::
probability G :::7::3:91:a:3a:9::7
matrix T 978:44:8::9:86:::2a3
bits 2.5 * *
2.3 * *
2.0 ** * * *
1.8 ** * * *
Information 1.5 ** * * ***
content 1.3 * *** **** ******
(28.0 bits) 1.0 * ***** **** ******
0.8 ************* ******
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel TTTGCCCTGCTGTTGAGCTG
consensus CCATTG G T T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c278_20970 + 497 1.95e-13 TTTAGCTTTT TTTGCCCTGCTGTTGAGCTG TTTTGCTTCA
MIT_Smik_c935_20455 + 481 1.64e-12 TTCAGCTTTT TTTGCTCTGCTGTTGAGCTG TTTTACTTCA
SGD_Scer_YOR176W + 495 1.64e-12 TTTAGCTTTT TTTGTCCTGCTGTTGAGCTG TTTTGCTTTA
WashU_Sbay_Contig480.2 + 507 8.61e-12 TTAGCTGTTT TTTGTTCTGCTGTTGAGCTG TTTTGCTCCA
WashU_Skud_Contig2050.4 + 498 8.61e-12 TCAGCTGTTT TTTGTTCTGCTGTTGAGCTG TTTTGTTCCA
MIT_Spar_c117_4603 - 457 3.51e-09 ACTGCAATGC TTCACCGTGCTGTGGAACTT GATATAGTGG
WashU_Sbay_Contig461.5 - 260 8.74e-09 TGCCCATTGT TCTGTCCCGGTGCTGCGCTG TTGGAACCAC
SGD_Scer_YDR232W - 465 2.27e-08 ACTACAATGC TTTACCGAGCAGTGGAGTTT GATATAGTGG
WashU_Skud_Contig2069.5 - 460 2.39e-08 GCTGTAATGG CCTACCATGCTGAAGAGCTG ATATAGTGGT
MIT_Smik_c228_4055 - 459 3.73e-08 ACAGCAATGT TACGCTGTACTGTGGAGTTT GATATAATGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c278_20970 1.9e-13 496_[+3]_211
MIT_Smik_c935_20455 1.6e-12 480_[+3]_227
SGD_Scer_YOR176W 1.6e-12 494_[+3]_213
WashU_Sbay_Contig480.2 8.6e-12 506_[+3]_201
WashU_Skud_Contig2050.4 8.6e-12 497_[+3]_210
MIT_Spar_c117_4603 3.5e-09 456_[-3]_22
WashU_Sbay_Contig461.5 8.7e-09 259_[-3]_219
SGD_Scer_YDR232W 2.3e-08 464_[-3]_14
WashU_Skud_Contig2069.5 2.4e-08 459_[-3]_19
MIT_Smik_c228_4055 3.7e-08 458_[-3]_20
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=10
MIT_Spar_c278_20970 ( 497) TTTGCCCTGCTGTTGAGCTG 1
MIT_Smik_c935_20455 ( 481) TTTGCTCTGCTGTTGAGCTG 1
SGD_Scer_YOR176W ( 495) TTTGTCCTGCTGTTGAGCTG 1
WashU_Sbay_Contig480.2 ( 507) TTTGTTCTGCTGTTGAGCTG 1
WashU_Skud_Contig2050.4 ( 498) TTTGTTCTGCTGTTGAGCTG 1
MIT_Spar_c117_4603 ( 457) TTCACCGTGCTGTGGAACTT 1
WashU_Sbay_Contig461.5 ( 260) TCTGTCCCGGTGCTGCGCTG 1
SGD_Scer_YDR232W ( 465) TTTACCGAGCAGTGGAGTTT 1
WashU_Skud_Contig2069.5 ( 460) CCTACCATGCTGAAGAGCTG 1
MIT_Smik_c228_4055 ( 459) TACGCTGTACTGTGGAGTTT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 5.5e-020
-997 -81 -997 147
-169 19 -997 111
-997 19 -997 130
-11 -997 199 -997
-997 177 -997 30
-997 177 -997 30
-169 177 77 -997
-169 -81 -997 130
-169 -997 236 -997
-997 236 -81 -997
-169 -997 -997 147
-997 -997 251 -997
-169 -81 -997 130
-169 -997 77 89
-997 -997 251 -997
147 -81 -997 -997
-169 -997 236 -997
-997 219 -997 -70
-997 -997 -997 162
-997 -997 199 -11
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.5e-020
0.000000 0.100000 0.000000 0.900000
0.100000 0.200000 0.000000 0.700000
0.000000 0.200000 0.000000 0.800000
0.300000 0.000000 0.700000 0.000000
0.000000 0.600000 0.000000 0.400000
0.000000 0.600000 0.000000 0.400000
0.100000 0.600000 0.300000 0.000000
0.100000 0.100000 0.000000 0.800000
0.100000 0.000000 0.900000 0.000000
0.000000 0.900000 0.100000 0.000000
0.100000 0.000000 0.000000 0.900000
0.000000 0.000000 1.000000 0.000000
0.100000 0.100000 0.000000 0.800000
0.100000 0.000000 0.300000 0.600000
0.000000 0.000000 1.000000 0.000000
0.900000 0.100000 0.000000 0.000000
0.100000 0.000000 0.900000 0.000000
0.000000 0.800000 0.000000 0.200000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.700000 0.300000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
T[TC][TC][GA][CT][CT][CG]TGCTGT[TG]GAG[CT]T[GT]
--------------------------------------------------------------------------------
Time 11.72 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 10 llr = 192 E-value = 5.7e-019
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A :1:19421:1::::1:5:9:
pos.-specific C :::9:1621:5a3::a58::
probability G :1::::2219::::9:::1:
matrix T a8a:15:58:5:7a:::2:a
bits 2.5 * *
2.3 * *
2.0 * * * **
1.8 * * * **
Information 1.5 * ** * * *** * *
content 1.3 * *** * * *** ***
(27.7 bits) 1.0 * *** * ************
0.8 ***** * ************
0.5 ***** * ************
0.3 ********************
0.0 --------------------
Multilevel TTTCATCTTGCCTTGCACAT
consensus AAC T C CT
sequence GG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig461.5 - 283 6.64e-13 AACGGAGATT TTTCATCTTGCCTTGCCCAT TGTTCTGTCC
MIT_Smik_c228_4055 - 288 6.64e-13 GAACGGAAAT TTTCATCTTGCCTTGCCCAT TGTTCTAATT
MIT_Spar_c117_4603 - 285 6.64e-13 AACAGAAATT TTTCATCTTGCCTTGCCCAT TGTTCTGACC
SGD_Scer_YDR232W - 290 6.64e-13 AACGGAAATT TTTCATCTTGCCTTGCCCAT TGTTCTGATC
WashU_Skud_Contig2069.5 - 288 1.75e-10 AACGGAAATT TTTCACATTGCCTTGCCCAT TGTTCCGATC
MIT_Spar_c278_20970 + 302 3.17e-10 AGTAGAGATA TTTCAAGCTGTCCTGCACAT GCTACATATT
MIT_Smik_c935_20455 + 298 3.30e-09 AATAAAGAAG TTTCAACGTGTCCTGCATGT TCTACAAATT
WashU_Skud_Contig2050.4 + 308 1.63e-08 ATAATTAAAA TGTCTTCAGGTCTTGCACAT ACTCCTACAT
SGD_Scer_YOR176W + 301 5.38e-08 AGCGGAGATG TTTCAAGGCATCCTACACAT GCTACATATT
WashU_Sbay_Contig480.2 + 345 5.53e-08 GAAAGATGTT TATAAAACTGTCTTGCATAT GCTCTATTTA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig461.5 6.6e-13 282_[-4]_196
MIT_Smik_c228_4055 6.6e-13 287_[-4]_191
MIT_Spar_c117_4603 6.6e-13 284_[-4]_194
SGD_Scer_YDR232W 6.6e-13 289_[-4]_189
WashU_Skud_Contig2069.5 1.7e-10 287_[-4]_191
MIT_Spar_c278_20970 3.2e-10 301_[+4]_406
MIT_Smik_c935_20455 3.3e-09 297_[+4]_410
WashU_Skud_Contig2050.4 1.6e-08 307_[+4]_400
SGD_Scer_YOR176W 5.4e-08 300_[+4]_407
WashU_Sbay_Contig480.2 5.5e-08 344_[+4]_363
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=10
WashU_Sbay_Contig461.5 ( 283) TTTCATCTTGCCTTGCCCAT 1
MIT_Smik_c228_4055 ( 288) TTTCATCTTGCCTTGCCCAT 1
MIT_Spar_c117_4603 ( 285) TTTCATCTTGCCTTGCCCAT 1
SGD_Scer_YDR232W ( 290) TTTCATCTTGCCTTGCCCAT 1
WashU_Skud_Contig2069.5 ( 288) TTTCACATTGCCTTGCCCAT 1
MIT_Spar_c278_20970 ( 302) TTTCAAGCTGTCCTGCACAT 1
MIT_Smik_c935_20455 ( 298) TTTCAACGTGTCCTGCATGT 1
WashU_Skud_Contig2050.4 ( 308) TGTCTTCAGGTCTTGCACAT 1
SGD_Scer_YOR176W ( 301) TTTCAAGGCATCCTACACAT 1
WashU_Sbay_Contig480.2 ( 345) TATAAAACTGTCTTGCATAT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 5.7e-019
-997 -997 -997 162
-169 -997 -81 130
-997 -997 -997 162
-169 236 -997 -997
147 -997 -997 -169
30 -81 -997 62
-70 177 19 -997
-169 19 19 62
-997 -81 -81 130
-169 -997 236 -997
-997 151 -997 62
-997 251 -997 -997
-997 77 -997 111
-997 -997 -997 162
-169 -997 236 -997
-997 251 -997 -997
62 151 -997 -997
-997 219 -997 -70
147 -997 -81 -997
-997 -997 -997 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.7e-019
0.000000 0.000000 0.000000 1.000000
0.100000 0.000000 0.100000 0.800000
0.000000 0.000000 0.000000 1.000000
0.100000 0.900000 0.000000 0.000000
0.900000 0.000000 0.000000 0.100000
0.400000 0.100000 0.000000 0.500000
0.200000 0.600000 0.200000 0.000000
0.100000 0.200000 0.200000 0.500000
0.000000 0.100000 0.100000 0.800000
0.100000 0.000000 0.900000 0.000000
0.000000 0.500000 0.000000 0.500000
0.000000 1.000000 0.000000 0.000000
0.000000 0.300000 0.000000 0.700000
0.000000 0.000000 0.000000 1.000000
0.100000 0.000000 0.900000 0.000000
0.000000 1.000000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.800000 0.000000 0.200000
0.900000 0.000000 0.100000 0.000000
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
TTTCA[TA][CAG][TCG]TG[CT]C[TC]TGC[AC][CT]AT
--------------------------------------------------------------------------------
Time 15.38 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 10 llr = 188 E-value = 9.3e-018
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 216895a11:3::::13:11
pos.-specific C 6931:2::5:678:7::69:
probability G 1:1:13:91a::17:972:9
matrix T 1::1::::3:13133::2::
bits 2.5 *
2.3 *
2.0 * * * * **
1.8 * * * * **
Information 1.5 * ** * * * **
content 1.3 * * ** * ****** **
(27.1 bits) 1.0 * * ** * *********
0.8 ***** ** ***********
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CCAAAAAGCGCCCGCGGCCG
consensus A C G T AT TT AG
sequence C T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c117_4603 + 344 3.06e-14 TGAACAATGA CCAAAAAGCGCCCGCGGCCG CAGACCAATG
SGD_Scer_YDR232W + 349 3.06e-14 TGAACAATGA CCAAAAAGCGCCCGCGGCCG CAGACCAATG
WashU_Skud_Contig2069.5 + 346 1.65e-12 ATGACAATGA CCAAAAAGCGTCCGCGGCCG CAGACCAATG
MIT_Smik_c228_4055 + 346 1.43e-10 TGAACAATGA CCAAAAAGCGCCCGCAAGCG CAGACCAATG
MIT_Spar_c278_20970 + 126 3.60e-09 TTGGTGCCAA ACCAAGAGTGACCTTGACCG ACTAAAAGTA
SGD_Scer_YOR176W + 124 3.90e-09 TTGGTGTCAA GCCAAGAGTGACCTTGACCG ACCAAAAGTA
WashU_Sbay_Contig461.5 + 343 4.91e-09 TAACAATGAC CAAAAAAACGCCGGCGGGCG CAGACCAATG
MIT_Smik_c935_20455 + 122 5.29e-09 TAATGATCAG ACCAACAGTGATCTTGGCCG ACCAAAAGAC
WashU_Skud_Contig2050.4 + 242 1.18e-07 TTCTCCTTCG TCGCAGAGAGCTCGCGGTAG CATTTCATTG
WashU_Sbay_Contig480.2 + 282 2.27e-07 ATGCCTCTCG CCATGCAGGGCTTGCGGTCA TGTTTTCTAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c117_4603 3.1e-14 343_[+5]_135
SGD_Scer_YDR232W 3.1e-14 348_[+5]_130
WashU_Skud_Contig2069.5 1.6e-12 345_[+5]_133
MIT_Smik_c228_4055 1.4e-10 345_[+5]_133
MIT_Spar_c278_20970 3.6e-09 125_[+5]_582
SGD_Scer_YOR176W 3.9e-09 123_[+5]_584
WashU_Sbay_Contig461.5 4.9e-09 342_[+5]_136
MIT_Smik_c935_20455 5.3e-09 121_[+5]_586
WashU_Skud_Contig2050.4 1.2e-07 241_[+5]_466
WashU_Sbay_Contig480.2 2.3e-07 281_[+5]_426
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=10
MIT_Spar_c117_4603 ( 344) CCAAAAAGCGCCCGCGGCCG 1
SGD_Scer_YDR232W ( 349) CCAAAAAGCGCCCGCGGCCG 1
WashU_Skud_Contig2069.5 ( 346) CCAAAAAGCGTCCGCGGCCG 1
MIT_Smik_c228_4055 ( 346) CCAAAAAGCGCCCGCAAGCG 1
MIT_Spar_c278_20970 ( 126) ACCAAGAGTGACCTTGACCG 1
SGD_Scer_YOR176W ( 124) GCCAAGAGTGACCTTGACCG 1
WashU_Sbay_Contig461.5 ( 343) CAAAAAAACGCCGGCGGGCG 1
MIT_Smik_c935_20455 ( 122) ACCAACAGTGATCTTGGCCG 1
WashU_Skud_Contig2050.4 ( 242) TCGCAGAGAGCTCGCGGTAG 1
WashU_Sbay_Contig480.2 ( 282) CCATGCAGGGCTTGCGGTCA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 9.3e-018
-70 177 -81 -169
-169 236 -997 -997
89 77 -81 -997
130 -81 -997 -169
147 -997 -81 -997
62 19 77 -997
162 -997 -997 -997
-169 -997 236 -997
-169 151 -81 -11
-997 -997 251 -997
-11 177 -997 -169
-997 199 -997 -11
-997 219 -81 -169
-997 -997 199 -11
-997 199 -997 -11
-169 -997 236 -997
-11 -997 199 -997
-997 177 19 -70
-169 236 -997 -997
-169 -997 236 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.3e-018
0.200000 0.600000 0.100000 0.100000
0.100000 0.900000 0.000000 0.000000
0.600000 0.300000 0.100000 0.000000
0.800000 0.100000 0.000000 0.100000
0.900000 0.000000 0.100000 0.000000
0.500000 0.200000 0.300000 0.000000
1.000000 0.000000 0.000000 0.000000
0.100000 0.000000 0.900000 0.000000
0.100000 0.500000 0.100000 0.300000
0.000000 0.000000 1.000000 0.000000
0.300000 0.600000 0.000000 0.100000
0.000000 0.700000 0.000000 0.300000
0.000000 0.800000 0.100000 0.100000
0.000000 0.000000 0.700000 0.300000
0.000000 0.700000 0.000000 0.300000
0.100000 0.000000 0.900000 0.000000
0.300000 0.000000 0.700000 0.000000
0.000000 0.600000 0.200000 0.200000
0.100000 0.900000 0.000000 0.000000
0.100000 0.000000 0.900000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
[CA]C[AC]AA[AGC]AG[CT]G[CA][CT]C[GT][CT]G[GA][CGT]CG
--------------------------------------------------------------------------------
Time 18.95 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 2.26e-35 131_[-2(4.87e-05)]_138_[-4(6.64e-13)]_5_[+2(4.12e-12)]_14_[+5(3.06e-14)]_5_[+1(4.19e-12)]_71_[-3(2.27e-08)]_14
MIT_Spar_c117_4603 5.83e-36 284_[-4(6.64e-13)]_5_[+2(6.47e-12)]_14_[+5(3.06e-14)]_5_[+1(4.19e-12)]_68_[-3(3.51e-09)]_22
MIT_Smik_c228_4055 1.73e-31 287_[-4(6.64e-13)]_4_[+2(4.12e-12)]_14_[+5(1.43e-10)]_5_[+1(6.28e-12)]_68_[-3(3.73e-08)]_20
WashU_Skud_Contig2069.5 4.17e-31 264_[-3(3.20e-06)]_3_[-4(1.75e-10)]_5_[+2(8.03e-12)]_13_[+5(1.65e-12)]_5_[+1(4.19e-12)]_69_[-3(2.39e-08)]_19
WashU_Sbay_Contig461.5 5.52e-28 168_[+1(4.58e-05)]_71_[-3(8.74e-09)]_3_[-4(6.64e-13)]_5_[+2(1.78e-10)]_15_[+5(4.91e-09)]_5_[+1(8.75e-11)]_111
SGD_Scer_YOR176W 6.45e-27 123_[+5(3.90e-09)]_13_[+2(7.23e-11)]_124_[+4(5.38e-08)]_81_[+3(6.18e-05)]_73_[+3(1.64e-12)]_39_[+1(3.36e-11)]_80_[-2(1.18e-05)]_54
MIT_Spar_c278_20970 1.57e-29 125_[+5(3.60e-09)]_13_[+2(7.23e-11)]_123_[+4(3.17e-10)]_83_[+3(6.18e-05)]_72_[+3(1.95e-13)]_39_[+1(9.22e-11)]_128_[+3(8.37e-05)]_4
MIT_Smik_c935_20455 6.31e-27 121_[+5(5.29e-09)]_12_[+2(7.23e-11)]_18_[-2(1.21e-05)]_86_[+4(3.30e-09)]_163_[+3(1.64e-12)]_39_[+1(3.96e-10)]_168
WashU_Skud_Contig2050.4 1.40e-22 67_[-1(8.16e-05)]_4_[-2(9.76e-05)]_15_[+5(6.67e-06)]_10_[+2(2.43e-08)]_65_[+5(1.18e-07)]_46_[+4(1.63e-08)]_170_[+3(8.61e-12)]_44_[+1(8.33e-11)]_146
WashU_Sbay_Contig480.2 5.90e-23 29_[-5(7.21e-05)]_121_[+5(9.26e-05)]_16_[+2(1.47e-09)]_55_[+5(2.27e-07)]_43_[+4(5.53e-08)]_142_[+3(8.61e-12)]_11_[-3(9.47e-05)]_9_[+1(8.33e-11)]_42_[-2(6.80e-06)]_14_[-4(5.59e-06)]_45
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************