********************************************************************************
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= HEM2-HEM14.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YGL040C 1.0000 1000 MIT_Spar_c19_8512 1.0000 1000
MIT_Smik_c273_7756 1.0000 1000 MIT_Sbay_c77_8808 1.0000 1000
WashU_Skud_Contig2052.17 1.0000 1000 SGD_Scer_YER014W 1.0000 322
MIT_Spar_c425_6072 1.0000 322 MIT_Smik_c283_5928 1.0000 322
MIT_Sbay_c84_6418 1.0000 322
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM2-HEM14.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
model: mod= oops nmotifs= 5 evt= inf
object function= E-value of product of p-values
width: minw= 6 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 9 maxsites= 9 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 6288 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.328 C 0.172 G 0.172 T 0.328
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324
********************************************************************************
********************************************************************************
MOTIF 1 width = 20 sites = 9 llr = 192 E-value = 5.7e-022
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 96:42:191:1:::::::a:
pos.-specific C :191:34::::a:a:::::6
probability G 13::8641::9:::a::::4
matrix T ::14:1::9a::a::aaa::
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 AACAGGCATTGCTCGTTTAC
consensus G TACG G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2052.17 + 200 4.10e-12 CACCGCACCG AACAGGGATTGCTCGTTTAC CCGTTGCGTT
MIT_Spar_c19_8512 + 201 4.10e-12 CACCGCACCG AACAGGGATTGCTCGTTTAC CCGTAGTTTG
SGD_Scer_YGL040C + 200 4.10e-12 CACCGCACCG AACAGGGATTGCTCGTTTAC CCGTATTTTG
SGD_Scer_YER014W - 169 1.37e-11 TTTAATTGAA AGCTGCCATTGCTCGTTTAG TTACAAAACG
MIT_Sbay_c84_6418 - 164 1.01e-10 GTTTGAATAT AACTGTCATTGCTCGTTTAG TGGTGAATAT
MIT_Smik_c283_5928 - 163 1.09e-10 TTCAATCAAA AGCTACCATTGCTCGTTTAG TTGTAAAATG
MIT_Spar_c425_6072 - 168 2.28e-10 TTTAATTAAA AGCTGCCATTACTCGTTTAG TTGCAAAACG
MIT_Smik_c273_7756 + 199 6.00e-10 CACCGCACCG AATAAGGATTGCTCGTTTAC CCGTTGTTCG
MIT_Sbay_c77_8808 + 200 5.23e-09 TCACCGCACC GCCCGGAGATGCTCGTTTAC CGTTGTGCAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 4.1e-12 199_[+1]_781
MIT_Spar_c19_8512 4.1e-12 200_[+1]_780
SGD_Scer_YGL040C 4.1e-12 199_[+1]_781
SGD_Scer_YER014W 1.4e-11 168_[-1]_134
MIT_Sbay_c84_6418 1e-10 163_[-1]_139
MIT_Smik_c283_5928 1.1e-10 162_[-1]_140
MIT_Spar_c425_6072 2.3e-10 167_[-1]_135
MIT_Smik_c273_7756 6e-10 198_[+1]_782
MIT_Sbay_c77_8808 5.2e-09 199_[+1]_781
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2052.17 ( 200) AACAGGGATTGCTCGTTTAC 1
MIT_Spar_c19_8512 ( 201) AACAGGGATTGCTCGTTTAC 1
SGD_Scer_YGL040C ( 200) AACAGGGATTGCTCGTTTAC 1
SGD_Scer_YER014W ( 169) AGCTGCCATTGCTCGTTTAG 1
MIT_Sbay_c84_6418 ( 164) AACTGTCATTGCTCGTTTAG 1
MIT_Smik_c283_5928 ( 163) AGCTACCATTGCTCGTTTAG 1
MIT_Spar_c425_6072 ( 168) AGCTGCCATTACTCGTTTAG 1
MIT_Smik_c273_7756 ( 199) AATAAGGATTGCTCGTTTAC 1
MIT_Sbay_c77_8808 ( 200) GCCCGGAGATGCTCGTTTAC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 5.7e-022
145 -982 -66 -982
78 -66 92 -982
-982 234 -982 -154
45 -66 -982 45
-55 -982 215 -982
-982 92 166 -154
-154 134 134 -982
145 -982 -66 -982
-154 -982 -982 145
-982 -982 -982 162
-154 -982 234 -982
-982 251 -982 -982
-982 -982 -982 162
-982 251 -982 -982
-982 -982 251 -982
-982 -982 -982 162
-982 -982 -982 162
-982 -982 -982 162
162 -982 -982 -982
-982 166 134 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.7e-022
0.888889 0.000000 0.111111 0.000000
0.555556 0.111111 0.333333 0.000000
0.000000 0.888889 0.000000 0.111111
0.444444 0.111111 0.000000 0.444444
0.222222 0.000000 0.777778 0.000000
0.000000 0.333333 0.555556 0.111111
0.111111 0.444444 0.444444 0.000000
0.888889 0.000000 0.111111 0.000000
0.111111 0.000000 0.000000 0.888889
0.000000 0.000000 0.000000 1.000000
0.111111 0.000000 0.888889 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.555556 0.444444 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
A[AG]C[AT][GA][GC][CG]ATTGCTCGTTTA[CG]
--------------------------------------------------------------------------------
Time 4.20 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 15 sites = 9 llr = 154 E-value = 6.2e-015
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A :::::49:::a9:2:
pos.-specific C :169::1::a::17:
probability G 79::46:aa::19::
matrix T 3:416::::::::1a
bits 2.5 ***
2.3 ***
2.0 * * *** *
1.8 * * *** *
Information 1.5 * * **** * *
content 1.3 ** * ******* *
(24.7 bits) 1.0 ***************
0.8 ***************
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel GGCCTGAGGCAAGCT
consensus T T GA A
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Skud_Contig2052.17 - 172 1.54e-10 TGCGGTGATT GGCCTGAGGCAAGCT GCCTGCCCAA
MIT_Spar_c19_8512 - 173 1.54e-10 TGCGGTGATT GGCCTGAGGCAAGCT GCCCGCTTGA
MIT_Smik_c283_5928 + 132 1.35e-09 GAAGCAACAA GGTCGAAGGCAAGCT GAAAGGCATT
SGD_Scer_YGL040C - 172 7.15e-09 TGCGGTGATT GGCTTGAGGCAAGCT TCCCGCTTGA
MIT_Sbay_c77_8808 - 173 7.55e-09 TGCGGTGATT GGCCTGCGGCAGGCT GCCTGATTTA
MIT_Smik_c273_7756 - 171 2.10e-08 TGCGGTGATT GGCCTGAGGCAACAT ACACTCTTGA
MIT_Spar_c425_6072 + 137 2.87e-08 AGCAACAAAA TGTCGAAGGCAAGAT GAAAGGCGTT
MIT_Sbay_c84_6418 + 130 4.02e-08 AACAACAAAA TCTCGAAGGCAAGCT AAGGTAAAAA
SGD_Scer_YER014W + 138 4.64e-08 AGCAACAAAG TGTCGAAGGCAAGTT CAAAGGCGTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 1.5e-10 171_[-2]_814
MIT_Spar_c19_8512 1.5e-10 172_[-2]_813
MIT_Smik_c283_5928 1.4e-09 131_[+2]_176
SGD_Scer_YGL040C 7.1e-09 171_[-2]_814
MIT_Sbay_c77_8808 7.5e-09 172_[-2]_813
MIT_Smik_c273_7756 2.1e-08 170_[-2]_815
MIT_Spar_c425_6072 2.9e-08 136_[+2]_171
MIT_Sbay_c84_6418 4e-08 129_[+2]_178
SGD_Scer_YER014W 4.6e-08 137_[+2]_170
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=15 seqs=9
WashU_Skud_Contig2052.17 ( 172) GGCCTGAGGCAAGCT 1
MIT_Spar_c19_8512 ( 173) GGCCTGAGGCAAGCT 1
MIT_Smik_c283_5928 ( 132) GGTCGAAGGCAAGCT 1
SGD_Scer_YGL040C ( 172) GGCTTGAGGCAAGCT 1
MIT_Sbay_c77_8808 ( 173) GGCCTGCGGCAGGCT 1
MIT_Smik_c273_7756 ( 171) GGCCTGAGGCAACAT 1
MIT_Spar_c425_6072 ( 137) TGTCGAAGGCAAGAT 1
MIT_Sbay_c84_6418 ( 130) TCTCGAAGGCAAGCT 1
SGD_Scer_YER014W ( 138) TGTCGAAGGCAAGTT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 6162 bayes= 9.41715 E= 6.2e-015
-982 -982 192 4
-982 -66 234 -982
-982 166 -982 45
-982 234 -982 -154
-982 -982 134 78
45 -982 166 -982
145 -66 -982 -982
-982 -982 251 -982
-982 -982 251 -982
-982 251 -982 -982
162 -982 -982 -982
145 -982 -66 -982
-982 -66 234 -982
-55 192 -982 -154
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 6.2e-015
0.000000 0.000000 0.666667 0.333333
0.000000 0.111111 0.888889 0.000000
0.000000 0.555556 0.000000 0.444444
0.000000 0.888889 0.000000 0.111111
0.000000 0.000000 0.444444 0.555556
0.444444 0.000000 0.555556 0.000000
0.888889 0.111111 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.111111 0.888889 0.000000
0.222222 0.666667 0.000000 0.111111
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[GT]G[CT]C[TG][GA]AGGCAAG[CA]T
--------------------------------------------------------------------------------
Time 8.46 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 171 E-value = 1.2e-013
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A 8718a:aa:a:942:9:1:6
pos.-specific C :::::a::::::::::419:
probability G 2182::::::a16291:6:4
matrix T :21:::::a::::61:621:
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 AAGAACAATAGAGTGATGCA
consensus GT G AA CT G
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Sbay_c84_6418 - 61 3.82e-11 AACAATAAGG AAGAACAATAGAAGGATGCG AAAGGACAAC
MIT_Smik_c273_7756 + 99 1.39e-10 CCAATAAATC AGGAACAATAGAATGACGCA CCGAGTTTGC
MIT_Spar_c425_6072 - 66 6.11e-10 GAATAATAGA GAGAACAATAGAGAGATCCG CGAAGGATAC
WashU_Skud_Contig2052.17 + 97 7.49e-10 GCCAGAAATC ATGAACAATAGGATGACGCA TAGACGTCAC
MIT_Spar_c19_8512 + 99 1.07e-09 GCCAAAAAAC AAGGACAATAGAATGACACA TAAAGTTTGC
MIT_Sbay_c77_8808 + 102 1.50e-09 ATGAACTAAC ATTAACAATAGAGTGATGCA TAGACGTCAC
MIT_Smik_c283_5928 - 68 2.37e-09 GAGTAATGGA AAGAACAATAGAGGGATTTG CAAAAGATAG
SGD_Scer_YGL040C + 98 2.54e-09 CAAGAAAATC AAAGACAATAGAGTGGCGCA TAGATGTTGC
SGD_Scer_YER014W - 66 6.53e-09 GTATAATAGA GAGAACAATAGAGATATTCG CGAAGAACAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Sbay_c84_6418 3.8e-11 60_[-3]_242
MIT_Smik_c273_7756 1.4e-10 98_[+3]_882
MIT_Spar_c425_6072 6.1e-10 65_[-3]_237
WashU_Skud_Contig2052.17 7.5e-10 96_[+3]_884
MIT_Spar_c19_8512 1.1e-09 98_[+3]_882
MIT_Sbay_c77_8808 1.5e-09 101_[+3]_879
MIT_Smik_c283_5928 2.4e-09 67_[-3]_235
SGD_Scer_YGL040C 2.5e-09 97_[+3]_883
SGD_Scer_YER014W 6.5e-09 65_[-3]_237
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
MIT_Sbay_c84_6418 ( 61) AAGAACAATAGAAGGATGCG 1
MIT_Smik_c273_7756 ( 99) AGGAACAATAGAATGACGCA 1
MIT_Spar_c425_6072 ( 66) GAGAACAATAGAGAGATCCG 1
WashU_Skud_Contig2052.17 ( 97) ATGAACAATAGGATGACGCA 1
MIT_Spar_c19_8512 ( 99) AAGGACAATAGAATGACACA 1
MIT_Sbay_c77_8808 ( 102) ATTAACAATAGAGTGATGCA 1
MIT_Smik_c283_5928 ( 68) AAGAACAATAGAGGGATTTG 1
SGD_Scer_YGL040C ( 98) AAAGACAATAGAGTGGCGCA 1
SGD_Scer_YER014W ( 66) GAGAACAATAGAGATATTCG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 1.2e-013
126 -982 34 -982
104 -982 -66 -55
-154 -982 215 -154
126 -982 34 -982
162 -982 -982 -982
-982 251 -982 -982
162 -982 -982 -982
162 -982 -982 -982
-982 -982 -982 162
162 -982 -982 -982
-982 -982 251 -982
145 -982 -66 -982
45 -982 166 -982
-55 -982 34 78
-982 -982 234 -154
145 -982 -66 -982
-982 134 -982 78
-154 -66 166 -55
-982 234 -982 -154
78 -982 134 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.2e-013
0.777778 0.000000 0.222222 0.000000
0.666667 0.000000 0.111111 0.222222
0.111111 0.000000 0.777778 0.111111
0.777778 0.000000 0.222222 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.444444 0.000000 0.555556 0.000000
0.222222 0.000000 0.222222 0.555556
0.000000 0.000000 0.888889 0.111111
0.888889 0.000000 0.111111 0.000000
0.000000 0.444444 0.000000 0.555556
0.111111 0.111111 0.555556 0.222222
0.000000 0.888889 0.000000 0.111111
0.555556 0.000000 0.444444 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
[AG][AT]G[AG]ACAATAGA[GA][TAG]GA[TC][GT]C[AG]
--------------------------------------------------------------------------------
Time 12.41 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 9 llr = 148 E-value = 1.9e-005
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A :2:::7:11:38a7:a427a
pos.-specific C 8217119:7412::9:473:
probability G :2739:11:16::31::1::
matrix T 232::2:824::::::1:::
bits 2.5
2.3
2.0 * * *
1.8 * * *
Information 1.5 * ** * * ** *
content 1.3 * ** * * ** *
(23.7 bits) 1.0 * *** * * ***** ***
0.8 * *** ********** ***
0.5 * ******************
0.3 * ******************
0.0 --------------------
Multilevel CTGCGACTCCGAAACAACAA
consensus TATG T TTAC G CAC
sequence C
G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c425_6072 + 115 3.47e-12 TTTAAATACT CCGCGACTCCGAAGCAACAA AATGTCGAAG
SGD_Scer_YER014W + 116 3.47e-12 TTTGAATACT CCGCGACTCCGAAGCAACAA AGTGTCGAAG
MIT_Sbay_c84_6418 + 108 4.98e-12 TTTTTATACT CTGCGACTCCGAAACAACAA AATCTCGAAG
SGD_Scer_YGL040C + 316 8.20e-09 TGATGTATTT CGGCGTCTCTACAAGACCCA ATAAAGTAAT
MIT_Smik_c283_5928 + 112 1.07e-08 CTTTTTTAAA TACGGACTCCGAAGCAACAA GGTCGAAGGC
WashU_Skud_Contig2052.17 - 460 4.18e-08 GAAGAGTCTT CATCGACGCTAAAACACAAA TTCAAGAAGA
MIT_Spar_c19_8512 + 311 5.58e-08 GGGAGTATAC CTGCCTCTTTACAACACCCA ACAAAACACT
MIT_Sbay_c77_8808 + 766 8.32e-07 TGTTGCAATA TGTGGACAAGGAAACACGAA ATATATTGGG
MIT_Smik_c273_7756 - 311 8.97e-07 AATATTGTAA CTGGGCGTTTCAAACATACA AGTGTATATT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c425_6072 3.5e-12 114_[+4]_188
SGD_Scer_YER014W 3.5e-12 115_[+4]_187
MIT_Sbay_c84_6418 5e-12 107_[+4]_195
SGD_Scer_YGL040C 8.2e-09 315_[+4]_665
MIT_Smik_c283_5928 1.1e-08 111_[+4]_191
WashU_Skud_Contig2052.17 4.2e-08 459_[-4]_521
MIT_Spar_c19_8512 5.6e-08 310_[+4]_670
MIT_Sbay_c77_8808 8.3e-07 765_[+4]_215
MIT_Smik_c273_7756 9e-07 310_[-4]_670
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=9
MIT_Spar_c425_6072 ( 115) CCGCGACTCCGAAGCAACAA 1
SGD_Scer_YER014W ( 116) CCGCGACTCCGAAGCAACAA 1
MIT_Sbay_c84_6418 ( 108) CTGCGACTCCGAAACAACAA 1
SGD_Scer_YGL040C ( 316) CGGCGTCTCTACAAGACCCA 1
MIT_Smik_c283_5928 ( 112) TACGGACTCCGAAGCAACAA 1
WashU_Skud_Contig2052.17 ( 460) CATCGACGCTAAAACACAAA 1
MIT_Spar_c19_8512 ( 311) CTGCCTCTTTACAACACCCA 1
MIT_Sbay_c77_8808 ( 766) TGTGGACAAGGAAACACGAA 1
MIT_Smik_c273_7756 ( 311) CTGGGCGTTTCAAACATACA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 1.9e-005
-982 215 -982 -55
-55 34 34 4
-982 -66 192 -55
-982 192 92 -982
-982 -66 234 -982
104 -66 -982 -55
-982 234 -66 -982
-154 -982 -66 126
-154 192 -982 -55
-982 134 -66 45
4 -66 166 -982
126 34 -982 -982
162 -982 -982 -982
104 -982 92 -982
-982 234 -66 -982
162 -982 -982 -982
45 134 -982 -154
-55 192 -66 -982
104 92 -982 -982
162 -982 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.9e-005
0.000000 0.777778 0.000000 0.222222
0.222222 0.222222 0.222222 0.333333
0.000000 0.111111 0.666667 0.222222
0.000000 0.666667 0.333333 0.000000
0.000000 0.111111 0.888889 0.000000
0.666667 0.111111 0.000000 0.222222
0.000000 0.888889 0.111111 0.000000
0.111111 0.000000 0.111111 0.777778
0.111111 0.666667 0.000000 0.222222
0.000000 0.444444 0.111111 0.444444
0.333333 0.111111 0.555556 0.000000
0.777778 0.222222 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.666667 0.000000 0.333333 0.000000
0.000000 0.888889 0.111111 0.000000
1.000000 0.000000 0.000000 0.000000
0.444444 0.444444 0.000000 0.111111
0.222222 0.666667 0.111111 0.000000
0.666667 0.333333 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[CT][TACGA][GT][CG]G[AT]CT[CT][CT][GA][AC]A[AG]CA[AC][CA][AC]A
--------------------------------------------------------------------------------
Time 16.27 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 142 E-value = 8.9e-002
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A :22::::41::::128:999
pos.-specific C :1:971::6:a1::::::::
probability G ::7:1112::::2:1:1:::
matrix T a71128933a:989729111
bits 2.5 *
2.3 *
2.0 * *
1.8 * *
Information 1.5 * * **
content 1.3 * * * *** *
(22.7 bits) 1.0 * *** * ***** ****
0.8 * ***** ****** *****
0.5 ******* ************
0.3 ********************
0.0 --------------------
Multilevel TTGCCTTACTCTTTTATAAA
consensus AA T TT G AT
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c19_8512 + 143 7.75e-12 ATTTATTAGG TTGCCTTACTCTTTTATAAA TCAAGCGGGC
MIT_Sbay_c77_8808 + 147 1.19e-11 TTTTATTGTG TTGCCTTGCTCTTTTATAAA TCAGGCAGCC
WashU_Skud_Contig2052.17 + 142 1.97e-11 TTCATATAAG TTGCCTTTCTCTTTTATAAA TTGGGCAGGC
SGD_Scer_YGL040C + 142 3.83e-10 ATTTATTAGG TTGCCTTACTCTTATATAAA TCAAGCGGGA
MIT_Smik_c273_7756 + 567 2.20e-08 AACAATAAAG TTACCTTGATCTTTAATAAA ATATTCCCCC
MIT_Smik_c283_5928 + 92 1.78e-07 GTTCTTTCCA TTACTCTTTTCTTTTTTAAA TACGGACTCC
MIT_Spar_c425_6072 + 91 4.97e-07 TTCTCTCTAT TATTCTTTTTCTTTTTTAAA TACTCCGCGA
SGD_Scer_YER014W + 206 1.59e-06 AAAGAAAGGT TAGCGTTACTCTGTGATTTT TTTCATGTAA
MIT_Sbay_c84_6418 - 27 2.13e-06 GACAACAGTC TCGCTGGATTCCGTAAGAAA CAGCGGAATA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c19_8512 7.7e-12 142_[+5]_838
MIT_Sbay_c77_8808 1.2e-11 146_[+5]_834
WashU_Skud_Contig2052.17 2e-11 141_[+5]_839
SGD_Scer_YGL040C 3.8e-10 141_[+5]_839
MIT_Smik_c273_7756 2.2e-08 566_[+5]_414
MIT_Smik_c283_5928 1.8e-07 91_[+5]_211
MIT_Spar_c425_6072 5e-07 90_[+5]_212
SGD_Scer_YER014W 1.6e-06 205_[+5]_97
MIT_Sbay_c84_6418 2.1e-06 26_[-5]_276
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
MIT_Spar_c19_8512 ( 143) TTGCCTTACTCTTTTATAAA 1
MIT_Sbay_c77_8808 ( 147) TTGCCTTGCTCTTTTATAAA 1
WashU_Skud_Contig2052.17 ( 142) TTGCCTTTCTCTTTTATAAA 1
SGD_Scer_YGL040C ( 142) TTGCCTTACTCTTATATAAA 1
MIT_Smik_c273_7756 ( 567) TTACCTTGATCTTTAATAAA 1
MIT_Smik_c283_5928 ( 92) TTACTCTTTTCTTTTTTAAA 1
MIT_Spar_c425_6072 ( 91) TATTCTTTTTCTTTTTTAAA 1
SGD_Scer_YER014W ( 206) TAGCGTTACTCTGTGATTTT 1
MIT_Sbay_c84_6418 ( 27) TCGCTGGATTCCGTAAGAAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 8.9e-002
-982 -982 -982 162
-55 -66 -982 104
-55 -982 192 -154
-982 234 -982 -154
-982 192 -66 -55
-982 -66 -66 126
-982 -982 -66 145
45 -982 34 4
-154 166 -982 4
-982 -982 -982 162
-982 251 -982 -982
-982 -66 -982 145
-982 -982 34 126
-154 -982 -982 145
-55 -982 -66 104
126 -982 -982 -55
-982 -982 -66 145
145 -982 -982 -154
145 -982 -982 -154
145 -982 -982 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 8.9e-002
0.000000 0.000000 0.000000 1.000000
0.222222 0.111111 0.000000 0.666667
0.222222 0.000000 0.666667 0.111111
0.000000 0.888889 0.000000 0.111111
0.000000 0.666667 0.111111 0.222222
0.000000 0.111111 0.111111 0.777778
0.000000 0.000000 0.111111 0.888889
0.444444 0.000000 0.222222 0.333333
0.111111 0.555556 0.000000 0.333333
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.222222 0.777778
0.111111 0.000000 0.000000 0.888889
0.222222 0.000000 0.111111 0.666667
0.777778 0.000000 0.000000 0.222222
0.000000 0.000000 0.111111 0.888889
0.888889 0.000000 0.000000 0.111111
0.888889 0.000000 0.000000 0.111111
0.888889 0.000000 0.000000 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
T[TA][GA]C[CT]TT[ATG][CT]TCT[TG]T[TA][AT]TAAA
--------------------------------------------------------------------------------
Time 20.21 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YGL040C 6.13e-24 97_[+3(2.54e-09)]_24_[+5(3.83e-10)]_10_[-2(7.15e-09)]_13_[+1(4.10e-12)]_96_[+4(8.20e-09)]_665
MIT_Spar_c19_8512 1.11e-26 98_[+3(1.07e-09)]_24_[+5(7.75e-12)]_10_[-2(1.54e-10)]_13_[+1(4.10e-12)]_13_[+5(5.08e-05)]_57_[+4(5.58e-08)]_670
MIT_Smik_c273_7756 4.21e-19 98_[+3(1.39e-10)]_52_[-2(2.10e-08)]_13_[+1(6.00e-10)]_92_[-4(8.97e-07)]_236_[+5(2.20e-08)]_414
MIT_Sbay_c77_8808 9.48e-21 101_[+3(1.50e-09)]_25_[+5(1.19e-11)]_6_[-2(7.55e-09)]_12_[+1(5.23e-09)]_250_[-3(4.01e-05)]_276_[+4(8.32e-07)]_141_[+2(5.20e-05)]_59
WashU_Skud_Contig2052.17 1.47e-26 96_[+3(7.49e-10)]_25_[+5(1.97e-11)]_10_[-2(1.54e-10)]_13_[+1(4.10e-12)]_98_[-4(1.54e-05)]_122_[-4(4.18e-08)]_191_[-1(9.59e-05)]_80_[-4(2.53e-05)]_16_[-1(9.59e-05)]_174
SGD_Scer_YER014W 1.85e-24 65_[-3(6.53e-09)]_30_[+4(3.47e-12)]_2_[+2(4.64e-08)]_16_[-1(1.37e-11)]_17_[+5(1.59e-06)]_97
MIT_Spar_c425_6072 5.95e-25 65_[-3(6.11e-10)]_5_[+5(4.97e-07)]_4_[+4(3.47e-12)]_2_[+2(2.87e-08)]_16_[-1(2.28e-10)]_14_[+1(4.94e-05)]_101
MIT_Smik_c283_5928 4.38e-23 67_[-3(2.37e-09)]_4_[+5(1.78e-07)]_[+4(1.07e-08)]_[+2(1.35e-09)]_16_[-1(1.09e-10)]_140
MIT_Sbay_c84_6418 1.54e-25 26_[-5(2.13e-06)]_14_[-3(3.82e-11)]_27_[+4(4.98e-12)]_2_[+2(4.02e-08)]_19_[-1(1.01e-10)]_139
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************