********************************************************************************
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-HEM12.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_YDR047W 1.0000 1000
MIT_Spar_c130_3923 1.0000 1000 MIT_Sbay_c896_21277 1.0000 1000
WashU_Skud_Contig1362.1 1.0000 761
********************************************************************************
********************************************************************************
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-HEM12.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= 6251 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.280 C 0.220 G 0.220 T 0.280
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 = 195 E-value = 1.4e-022
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 116::::8:8:1a9::943:
pos.-specific C 9::3a172:189::2:::6:
probability G :947:63:a1:::1:a:61a
matrix T :::::3::::2:::8:1:::
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 CGAGCGCAGACCAATGAGCG
consensus GC TGC T C AA
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig461.5 + 357 3.08e-14 AAAACGCCGG CGGGCGCAGACCAATGAGCG ACGAAGACGG
WashU_Skud_Contig2069.5 + 360 1.83e-13 AAAGCGTCCG CGGCCGCAGACCAATGAGCG ACGAAGGCGG
MIT_Spar_c117_4603 + 358 1.83e-13 AAAGCGCCCG CGGCCGCAGACCAATGAGCG ACGAAGGCGG
SGD_Scer_YDR232W + 363 1.83e-13 AAAGCGCCCG CGGCCGCAGACCAATGAGCG ACGAAGGCGG
MIT_Smik_c228_4055 + 360 1.47e-11 AAAGCGCCCG CAAGCGCAGACCAATGAGCG ACGAAAGCGG
MIT_Sbay_c896_21277 + 892 2.69e-10 GCCTAATTCT CGAGCTGAGGCCAATGAAGG CAGCTTCCAG
MIT_Spar_c130_3923 + 931 7.23e-10 AGCTGATCCT CGAGCTGCGATCAACGAAAG CCCCATCCAA
SGD_Scer_YDR047W + 922 1.02e-09 ACCTGAACTT CGAGCCGCGATCAACGAAAG CTCTCATCCA
WashU_Skud_Contig1362.1 + 294 1.77e-08 AAAGAATGAC AGAGCTCAGCCAAGTGTAAG CTAAGTGTTG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig461.5 3.1e-14 356_[+1]_122
WashU_Skud_Contig2069.5 1.8e-13 359_[+1]_119
MIT_Spar_c117_4603 1.8e-13 357_[+1]_121
SGD_Scer_YDR232W 1.8e-13 362_[+1]_116
MIT_Smik_c228_4055 1.5e-11 359_[+1]_119
MIT_Sbay_c896_21277 2.7e-10 891_[+1]_89
MIT_Spar_c130_3923 7.2e-10 930_[+1]_50
SGD_Scer_YDR047W 1e-09 921_[+1]_59
WashU_Skud_Contig1362.1 1.8e-08 293_[+1]_448
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig461.5 ( 357) CGGGCGCAGACCAATGAGCG 1
WashU_Skud_Contig2069.5 ( 360) CGGCCGCAGACCAATGAGCG 1
MIT_Spar_c117_4603 ( 358) CGGCCGCAGACCAATGAGCG 1
SGD_Scer_YDR232W ( 363) CGGCCGCAGACCAATGAGCG 1
MIT_Smik_c228_4055 ( 360) CAAGCGCAGACCAATGAGCG 1
MIT_Sbay_c896_21277 ( 892) CGAGCTGAGGCCAATGAAGG 1
MIT_Spar_c130_3923 ( 931) CGAGCTGCGATCAACGAAAG 1
SGD_Scer_YDR047W ( 922) CGAGCCGCGATCAACGAAAG 1
WashU_Skud_Contig1362.1 ( 294) AGAGCTCAGCCAAGTGTAAG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 1.4e-022
-154 234 -982 -982
-154 -982 234 -982
78 -982 134 -982
-982 92 192 -982
-982 251 -982 -982
-982 -66 166 4
-982 192 92 -982
126 34 -982 -982
-982 -982 251 -982
126 -66 -66 -982
-982 215 -982 -55
-154 234 -982 -982
162 -982 -982 -982
145 -982 -66 -982
-982 34 -982 126
-982 -982 251 -982
145 -982 -982 -154
45 -982 166 -982
4 166 -66 -982
-982 -982 251 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.4e-022
0.111111 0.888889 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
0.555556 0.000000 0.444444 0.000000
0.000000 0.333333 0.666667 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.111111 0.555556 0.333333
0.000000 0.666667 0.333333 0.000000
0.777778 0.222222 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.777778 0.111111 0.111111 0.000000
0.000000 0.777778 0.000000 0.222222
0.111111 0.888889 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.222222 0.000000 0.777778
0.000000 0.000000 1.000000 0.000000
0.888889 0.000000 0.000000 0.111111
0.444444 0.000000 0.555556 0.000000
0.333333 0.555556 0.111111 0.000000
0.000000 0.000000 1.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
CG[AG][GC]C[GT][CG][AC]GA[CT]CAA[TC]GA[GA][CA]G
--------------------------------------------------------------------------------
Time 4.41 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 179 E-value = 3.0e-017
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 1:4a1a9:4::::614:8:a
pos.-specific C :14::::a111:4:1:::9:
probability G 991:9:1:46::644:a21:
matrix T :::::::::39a::36::::
bits 2.5 * *
2.3 * *
2.0 ** * * * *
1.8 ** * * * *
Information 1.5 ** *** * ** * **
content 1.3 ** ***** *** * **
(28.7 bits) 1.0 ** ***** **** ****
0.8 ************** *****
0.5 ************** *****
0.3 ********************
0.0 --------------------
Multilevel GGAAGAACAGTTGAGTGACA
consensus C GT CGTA G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2069.5 + 162 7.75e-12 CCGTGTGGAG GGAAGAACGGTTGAGAGACA GCAGAGCACA
SGD_Scer_YDR232W + 165 7.75e-12 GGCGTGTAAA GGAAGAACGGTTGAGAGACA GCAGAGCAGG
WashU_Sbay_Contig461.5 + 161 8.83e-11 GCGTGTGGAG GGAAGAACCGTTGAGAGACA ACAGAGCAGG
MIT_Spar_c117_4603 + 160 2.12e-10 GGCGTGTAAA GGAAGAACGGTTGAGAGAGA GCAGAGCAGG
MIT_Spar_c130_3923 + 170 2.30e-10 TGACAAAAAG GGCAGAACATTTCGTTGGCA AAATTTAAAC
SGD_Scer_YDR047W + 173 4.04e-10 AGATGAAAAT GGCAGAACATTTCGCTGGCA AAATTAAAAC
MIT_Smik_c228_4055 + 161 6.70e-10 GACGTGTGAA GCCAGAACGGTTGAATGACA GTAGAGGAGG
WashU_Skud_Contig1362.1 + 137 8.43e-10 ACATACGAAA GGCAGAACACCTCGTTGACA AAACTGAAAC
MIT_Sbay_c896_21277 + 143 3.02e-08 TGACACGAAT AGGAAAGCATTTCGTTGACA AAAATAAAAT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2069.5 7.7e-12 161_[+2]_317
SGD_Scer_YDR232W 7.7e-12 164_[+2]_314
WashU_Sbay_Contig461.5 8.8e-11 160_[+2]_318
MIT_Spar_c117_4603 2.1e-10 159_[+2]_319
MIT_Spar_c130_3923 2.3e-10 169_[+2]_811
SGD_Scer_YDR047W 4e-10 172_[+2]_808
MIT_Smik_c228_4055 6.7e-10 160_[+2]_318
WashU_Skud_Contig1362.1 8.4e-10 136_[+2]_605
MIT_Sbay_c896_21277 3e-08 142_[+2]_838
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
WashU_Skud_Contig2069.5 ( 162) GGAAGAACGGTTGAGAGACA 1
SGD_Scer_YDR232W ( 165) GGAAGAACGGTTGAGAGACA 1
WashU_Sbay_Contig461.5 ( 161) GGAAGAACCGTTGAGAGACA 1
MIT_Spar_c117_4603 ( 160) GGAAGAACGGTTGAGAGAGA 1
MIT_Spar_c130_3923 ( 170) GGCAGAACATTTCGTTGGCA 1
SGD_Scer_YDR047W ( 173) GGCAGAACATTTCGCTGGCA 1
MIT_Smik_c228_4055 ( 161) GCCAGAACGGTTGAATGACA 1
WashU_Skud_Contig1362.1 ( 137) GGCAGAACACCTCGTTGACA 1
MIT_Sbay_c896_21277 ( 143) AGGAAAGCATTTCGTTGACA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 3.0e-017
-154 -982 234 -982
-982 -66 234 -982
45 134 -66 -982
162 -982 -982 -982
-154 -982 234 -982
162 -982 -982 -982
145 -982 -66 -982
-982 251 -982 -982
45 -66 134 -982
-982 -66 166 4
-982 -66 -982 145
-982 -982 -982 162
-982 134 166 -982
78 -982 134 -982
-154 -66 134 4
45 -982 -982 78
-982 -982 251 -982
126 -982 34 -982
-982 234 -66 -982
162 -982 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-017
0.111111 0.000000 0.888889 0.000000
0.000000 0.111111 0.888889 0.000000
0.444444 0.444444 0.111111 0.000000
1.000000 0.000000 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 1.000000 0.000000 0.000000
0.444444 0.111111 0.444444 0.000000
0.000000 0.111111 0.555556 0.333333
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.000000 1.000000
0.000000 0.444444 0.555556 0.000000
0.555556 0.000000 0.444444 0.000000
0.111111 0.111111 0.444444 0.333333
0.444444 0.000000 0.000000 0.555556
0.000000 0.000000 1.000000 0.000000
0.777778 0.000000 0.222222 0.000000
0.000000 0.888889 0.111111 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
GG[AC]AGAAC[AG][GT]TT[GC][AG][GT][TA]G[AG]CA
--------------------------------------------------------------------------------
Time 8.63 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 181 E-value = 3.1e-017
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A 8aaa64:::::1:::1112:
pos.-specific C 1:::4:1:a9::2aa3:62a
probability G 1::::::4::a:::::81::
matrix T :::::696:1:98::6126:
bits 2.5 * * ** *
2.3 * * ** *
2.0 *** ** *
1.8 *** ** *
Information 1.5 *** *** ** *
content 1.3 *** * *** ** * *
(29.1 bits) 1.0 **** ********* * *
0.8 *************** * *
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel AAAAATTTCCGTTCCTGCTC
consensus CA G C C TA
sequence C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2069.5 + 305 9.40e-12 AGGCAATGTG AAAAATTTCCGTTCCTGCTC TTGCTTCATA
SGD_Scer_YDR232W + 307 9.40e-12 AGGCAAGATG AAAAATTTCCGTTCCTGCTC TTTCTTCATA
MIT_Smik_c228_4055 + 304 6.77e-11 AAGGCAAGAT GAAAATTTCCGTTCCTGCTC TTTCTTCATA
WashU_Sbay_Contig461.5 + 300 7.67e-11 AGGCAAGATG AAAAATCTCCGTTCCTGCTC TTGCTTGATA
SGD_Scer_YDR047W + 647 1.22e-10 CTGTGCATTT AAAACATGCCGTTCCCGTAC CAAGTTATAT
MIT_Spar_c130_3923 + 645 2.75e-10 GGCGCAATTC AAAACATGCCGTCCCCGTAC TAAGTTATGT
MIT_Spar_c117_4603 + 302 3.58e-10 AGGCAAGATG AAAAATTTCTGTTCCTGCTC TTTCTTCATA
WashU_Skud_Contig1362.1 + 647 5.76e-09 TGGAACAAAT CAAACATGCCGTCCCCTACC AGCTCTCGAA
MIT_Sbay_c896_21277 + 651 9.67e-09 TTGACAAGAC AAAACATGCCGATCCAAGCC AGGCGAAACG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2069.5 9.4e-12 304_[+3]_174
SGD_Scer_YDR232W 9.4e-12 306_[+3]_172
MIT_Smik_c228_4055 6.8e-11 303_[+3]_175
WashU_Sbay_Contig461.5 7.7e-11 299_[+3]_179
SGD_Scer_YDR047W 1.2e-10 646_[+3]_334
MIT_Spar_c130_3923 2.7e-10 644_[+3]_336
MIT_Spar_c117_4603 3.6e-10 301_[+3]_177
WashU_Skud_Contig1362.1 5.8e-09 646_[+3]_95
MIT_Sbay_c896_21277 9.7e-09 650_[+3]_330
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
WashU_Skud_Contig2069.5 ( 305) AAAAATTTCCGTTCCTGCTC 1
SGD_Scer_YDR232W ( 307) AAAAATTTCCGTTCCTGCTC 1
MIT_Smik_c228_4055 ( 304) GAAAATTTCCGTTCCTGCTC 1
WashU_Sbay_Contig461.5 ( 300) AAAAATCTCCGTTCCTGCTC 1
SGD_Scer_YDR047W ( 647) AAAACATGCCGTTCCCGTAC 1
MIT_Spar_c130_3923 ( 645) AAAACATGCCGTCCCCGTAC 1
MIT_Spar_c117_4603 ( 302) AAAAATTTCTGTTCCTGCTC 1
WashU_Skud_Contig1362.1 ( 647) CAAACATGCCGTCCCCTACC 1
MIT_Sbay_c896_21277 ( 651) AAAACATGCCGATCCAAGCC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 3.1e-017
126 -66 -66 -982
162 -982 -982 -982
162 -982 -982 -982
162 -982 -982 -982
78 134 -982 -982
45 -982 -982 78
-982 -66 -982 145
-982 -982 134 78
-982 251 -982 -982
-982 234 -982 -154
-982 -982 251 -982
-154 -982 -982 145
-982 34 -982 126
-982 251 -982 -982
-982 251 -982 -982
-154 92 -982 78
-154 -982 215 -154
-154 166 -66 -55
-55 34 -982 78
-982 251 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.1e-017
0.777778 0.111111 0.111111 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
0.555556 0.444444 0.000000 0.000000
0.444444 0.000000 0.000000 0.555556
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.444444 0.555556
0.000000 1.000000 0.000000 0.000000
0.000000 0.888889 0.000000 0.111111
0.000000 0.000000 1.000000 0.000000
0.111111 0.000000 0.000000 0.888889
0.000000 0.222222 0.000000 0.777778
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.111111 0.333333 0.000000 0.555556
0.111111 0.000000 0.777778 0.111111
0.111111 0.555556 0.111111 0.222222
0.222222 0.222222 0.000000 0.555556
0.000000 1.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
AAAA[AC][TA]T[TG]CCGT[TC]CC[TC]G[CT][TAC]C
--------------------------------------------------------------------------------
Time 12.69 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 9 llr = 171 E-value = 9.5e-014
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 23aa22::::::::::1611
pos.-specific C 7:::1:a::991::86:236
probability G 17::48:6a1:3::147:62
matrix T ::::2::4::16aa1:22:1
bits 2.5 * *
2.3 * *
2.0 * ***
1.8 * ***
Information 1.5 ** ** *** ****
content 1.3 *** ** *** ****
(27.5 bits) 1.0 **** ****** ***** *
0.8 **** ************ **
0.5 **** ***************
0.3 ********************
0.0 --------------------
Multilevel CGAAGGCGGCCTTTCCGAGC
consensus AA AA T G GTCCG
sequence T T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YDR232W + 384 4.75e-14 CAATGAGCGA CGAAGGCGGCCTTTCCGAGC GGTAGGGTAA
WashU_Skud_Contig2069.5 + 381 3.48e-12 CAATGAGCGA CGAAGGCGGCCTTTCGTAGC AGCAGGGTAA
MIT_Spar_c117_4603 + 379 6.28e-12 CAATGAGCGA CGAAGGCGGCCTTTCCGAGT GGTAGGGTAA
MIT_Spar_c130_3923 + 708 1.69e-09 ATTATACTCT AAAATGCTGCCGTTCCGTCC CATTGAGTTT
SGD_Scer_YDR047W + 708 1.69e-09 AATTTGTTAA AAAATGCTGCCGTTCCGTCC CATTGAGTTT
MIT_Smik_c228_4055 + 381 3.64e-09 CAATGAGCGA CGAAAGCGGCCTTTTGAAGG GTAGGGTAAT
WashU_Sbay_Contig461.5 + 378 5.96e-09 CAATGAGCGA CGAAGACGGCTTTTGGGCGG GGCAGGGTAA
MIT_Sbay_c896_21277 + 699 7.77e-09 ACTACGCAGC CAAACACTGGCGTTCCGCCC GTCCCATCCA
WashU_Skud_Contig1362.1 - 483 5.15e-08 AACGCTTATA GGAAAGCTGCCCTTCGTAAA ACAGCTTGCT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR232W 4.8e-14 383_[+4]_95
WashU_Skud_Contig2069.5 3.5e-12 380_[+4]_98
MIT_Spar_c117_4603 6.3e-12 378_[+4]_100
MIT_Spar_c130_3923 1.7e-09 707_[+4]_273
SGD_Scer_YDR047W 1.7e-09 707_[+4]_273
MIT_Smik_c228_4055 3.6e-09 380_[+4]_98
WashU_Sbay_Contig461.5 6e-09 377_[+4]_101
MIT_Sbay_c896_21277 7.8e-09 698_[+4]_282
WashU_Skud_Contig1362.1 5.1e-08 482_[-4]_259
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=9
SGD_Scer_YDR232W ( 384) CGAAGGCGGCCTTTCCGAGC 1
WashU_Skud_Contig2069.5 ( 381) CGAAGGCGGCCTTTCGTAGC 1
MIT_Spar_c117_4603 ( 379) CGAAGGCGGCCTTTCCGAGT 1
MIT_Spar_c130_3923 ( 708) AAAATGCTGCCGTTCCGTCC 1
SGD_Scer_YDR047W ( 708) AAAATGCTGCCGTTCCGTCC 1
MIT_Smik_c228_4055 ( 381) CGAAAGCGGCCTTTTGAAGG 1
WashU_Sbay_Contig461.5 ( 378) CGAAGACGGCTTTTGGGCGG 1
MIT_Sbay_c896_21277 ( 699) CAAACACTGGCGTTCCGCCC 1
WashU_Skud_Contig1362.1 ( 483) GGAAAGCTGCCCTTCGTAAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 9.5e-014
-55 192 -66 -982
4 -982 192 -982
162 -982 -982 -982
162 -982 -982 -982
-55 -66 134 -55
-55 -982 215 -982
-982 251 -982 -982
-982 -982 166 45
-982 -982 251 -982
-982 234 -66 -982
-982 234 -982 -154
-982 -66 92 78
-982 -982 -982 162
-982 -982 -982 162
-982 215 -66 -154
-982 166 134 -982
-154 -982 192 -55
78 34 -982 -55
-154 92 166 -982
-154 166 34 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 9.5e-014
0.222222 0.666667 0.111111 0.000000
0.333333 0.000000 0.666667 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.222222 0.111111 0.444444 0.222222
0.222222 0.000000 0.777778 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.555556 0.444444
0.000000 0.000000 1.000000 0.000000
0.000000 0.888889 0.111111 0.000000
0.000000 0.888889 0.000000 0.111111
0.000000 0.111111 0.333333 0.555556
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.777778 0.111111 0.111111
0.000000 0.555556 0.444444 0.000000
0.111111 0.000000 0.666667 0.222222
0.555556 0.222222 0.000000 0.222222
0.111111 0.333333 0.555556 0.000000
0.111111 0.555556 0.222222 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[CA][GA]AA[GAT][GA]C[GT]GCC[TG]TTC[CG][GT][ACT][GC][CG]
--------------------------------------------------------------------------------
Time 16.70 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 178 E-value = 2.7e-015
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A :68:86:::::76::27a29
pos.-specific C :::9:1:3::a134:8::::
probability G a:2:2:37aa:::69:3:71
matrix T :4:1:37::::21:1:::1:
bits 2.5 * ***
2.3 * ***
2.0 * * *** *
1.8 * * *** *
Information 1.5 * * **** *** *
content 1.3 * * **** *** * *
(28.5 bits) 1.0 * *** ***** *******
0.8 ***** ***** *******
0.5 ***** **************
0.3 ********************
0.0 --------------------
Multilevel GAACAATGGGCAAGGCAAGA
consensus TG GTGC TCC AG A
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig461.5 + 278 7.65e-13 CACCGGGACA GAACAATGGGCAAGGCAAGA TGAAAAATCT
MIT_Smik_c228_4055 + 283 7.65e-13 CATTGAATTA GAACAATGGGCAAGGCAAGA TGAAAATTTC
MIT_Spar_c117_4603 + 280 7.65e-13 GCATGGGTCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
SGD_Scer_YDR232W + 285 7.65e-13 GCATGGATCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
WashU_Skud_Contig2069.5 + 283 7.37e-10 CACTGGATCG GAACAATGGGCAAGGCAATG TGAAAAATTT
SGD_Scer_YDR047W + 871 2.30e-09 TAATGTAGCC GTGCATGCGGCTCCGCGAAA AGAGCTCTGC
WashU_Skud_Contig1362.1 + 334 3.13e-09 ACAAGGGAAG GTACATTGGGCCCCGAAAAA ATTTGCTAAT
MIT_Spar_c130_3923 + 880 4.62e-09 TTATATAGCC GTACGTGCGGCTCCTCGAGA AAGGCCCTGC
MIT_Sbay_c896_21277 + 841 2.58e-08 TTTTATAGCC GTGTGCGCGGCATCGAGAGA CAGGTTCAGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig461.5 7.6e-13 277_[+5]_201
MIT_Smik_c228_4055 7.6e-13 282_[+5]_196
MIT_Spar_c117_4603 7.6e-13 279_[+5]_199
SGD_Scer_YDR232W 7.6e-13 284_[+5]_194
WashU_Skud_Contig2069.5 7.4e-10 282_[+5]_196
SGD_Scer_YDR047W 2.3e-09 870_[+5]_110
WashU_Skud_Contig1362.1 3.1e-09 333_[+5]_408
MIT_Spar_c130_3923 4.6e-09 879_[+5]_101
MIT_Sbay_c896_21277 2.6e-08 840_[+5]_140
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
WashU_Sbay_Contig461.5 ( 278) GAACAATGGGCAAGGCAAGA 1
MIT_Smik_c228_4055 ( 283) GAACAATGGGCAAGGCAAGA 1
MIT_Spar_c117_4603 ( 280) GAACAATGGGCAAGGCAAGA 1
SGD_Scer_YDR232W ( 285) GAACAATGGGCAAGGCAAGA 1
WashU_Skud_Contig2069.5 ( 283) GAACAATGGGCAAGGCAATG 1
SGD_Scer_YDR047W ( 871) GTGCATGCGGCTCCGCGAAA 1
WashU_Skud_Contig1362.1 ( 334) GTACATTGGGCCCCGAAAAA 1
MIT_Spar_c130_3923 ( 880) GTACGTGCGGCTCCTCGAGA 1
MIT_Sbay_c896_21277 ( 841) GTGTGCGCGGCATCGAGAGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 2.7e-015
-982 -982 251 -982
78 -982 -982 45
126 -982 34 -982
-982 234 -982 -154
126 -982 34 -982
78 -66 -982 4
-982 -982 92 104
-982 92 192 -982
-982 -982 251 -982
-982 -982 251 -982
-982 251 -982 -982
104 -66 -982 -55
78 92 -982 -154
-982 134 166 -982
-982 -982 234 -154
-55 215 -982 -982
104 -982 92 -982
162 -982 -982 -982
-55 -982 192 -154
145 -982 -66 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.7e-015
0.000000 0.000000 1.000000 0.000000
0.555556 0.000000 0.000000 0.444444
0.777778 0.000000 0.222222 0.000000
0.000000 0.888889 0.000000 0.111111
0.777778 0.000000 0.222222 0.000000
0.555556 0.111111 0.000000 0.333333
0.000000 0.000000 0.333333 0.666667
0.000000 0.333333 0.666667 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.666667 0.111111 0.000000 0.222222
0.555556 0.333333 0.000000 0.111111
0.000000 0.444444 0.555556 0.000000
0.000000 0.000000 0.888889 0.111111
0.222222 0.777778 0.000000 0.000000
0.666667 0.000000 0.333333 0.000000
1.000000 0.000000 0.000000 0.000000
0.222222 0.000000 0.666667 0.111111
0.888889 0.000000 0.111111 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
G[AT][AG]C[AG][AT][TG][GC]GGC[AT][AC][GC]G[CA][AG]A[GA]A
--------------------------------------------------------------------------------
Time 20.54 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 2.02e-39 164_[+2(7.75e-12)]_100_[+5(7.65e-13)]_2_[+3(9.40e-12)]_36_[+1(1.83e-13)]_1_[+4(4.75e-14)]_95
MIT_Spar_c117_4603 1.73e-34 159_[+2(2.12e-10)]_100_[+5(7.65e-13)]_2_[+3(3.58e-10)]_36_[+1(1.83e-13)]_1_[+4(6.28e-12)]_100
MIT_Smik_c228_4055 3.04e-30 160_[+2(6.70e-10)]_102_[+5(7.65e-13)]_1_[+3(6.77e-11)]_36_[+1(1.47e-11)]_1_[+4(3.64e-09)]_98
WashU_Skud_Contig2069.5 9.14e-35 161_[+2(7.75e-12)]_101_[+5(7.37e-10)]_2_[+3(9.40e-12)]_35_[+1(1.83e-13)]_1_[+4(3.48e-12)]_98
WashU_Sbay_Contig461.5 2.20e-33 160_[+2(8.83e-11)]_7_[+1(7.03e-05)]_70_[+5(7.65e-13)]_2_[+3(7.67e-11)]_37_[+1(3.08e-14)]_1_[+4(5.96e-09)]_6_[+5(2.10e-06)]_75
SGD_Scer_YDR047W 5.13e-24 172_[+2(4.04e-10)]_47_[+3(8.04e-06)]_387_[+3(1.22e-10)]_41_[+4(1.69e-09)]_17_[-5(6.96e-05)]_106_[+5(2.30e-09)]_31_[+1(1.02e-09)]_3_[-4(1.74e-05)]_36
MIT_Spar_c130_3923 9.08e-24 169_[+2(2.30e-10)]_47_[+3(8.58e-05)]_388_[+3(2.75e-10)]_43_[+4(1.69e-09)]_17_[-5(6.49e-06)]_37_[-5(2.93e-05)]_58_[+5(4.62e-09)]_31_[+1(7.23e-10)]_8_[+4(7.15e-06)]_22
MIT_Sbay_c896_21277 2.02e-19 142_[+2(3.02e-08)]_45_[+3(6.78e-05)]_259_[-4(2.48e-06)]_144_[+3(9.67e-09)]_28_[+4(7.77e-09)]_122_[+5(2.58e-08)]_31_[+1(2.69e-10)]_89
WashU_Skud_Contig1362.1 4.91e-20 41_[-1(2.10e-05)]_75_[+2(8.43e-10)]_137_[+1(1.77e-08)]_20_[+5(3.13e-09)]_129_[-4(5.15e-08)]_144_[+3(5.76e-09)]_31_[+4(1.33e-05)]_44
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************