********************************************************************************
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= HEM3-HEM14.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YDL205C 1.0000 860 MIT_Spar_c429_3020 1.0000 860
MIT_Smik_c193_2483 1.0000 860 MIT_Sbay_c841_3215 1.0000 860
WashU_Skud_Contig1850.5 1.0000 860 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 HEM3-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= 5588 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.311 C 0.189 G 0.189 T 0.311
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 = 197 E-value = 1.6e-024
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 4:1:::::a::1:::6::::
pos.-specific C 6:98964:::::::a:87a1
probability G :::::::::::9::::::::
matrix T :a:2146a:aa:aa:423:9
bits 2.5 * *
2.3 * *
2.0 * * * * *
1.8 * * * * *
Information 1.5 **** ******** * *
content 1.3 **** ******** ****
(31.6 bits) 1.0 *************** ****
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CTCCCCTTATTGTTCACCCT
consensus A T TC TTT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1850.5 + 706 7.49e-13 CATAGGCAAT CTCCCCTTATTGTTCACCCT TATTTCCACC
MIT_Sbay_c841_3215 + 725 7.49e-13 CATAGGCAAT CTCCCCTTATTGTTCACCCT TATTTCCACC
MIT_Spar_c429_3020 + 699 7.49e-13 CATAGGCAAC CTCCCCTTATTGTTCACCCT TATTTCCACC
SGD_Scer_YDL205C + 698 7.49e-13 CATAGGCAAT CTCCCCTTATTGTTCACCCT TATTTCCACC
MIT_Smik_c193_2483 + 699 4.36e-11 CATAGGCAAT CTCCCCTTATTATTCACCCT TATTTCCACC
MIT_Spar_c425_6072 + 69 2.43e-10 TCCTTCGCGG ATCTCTCTATTGTTCTCTCT ATTATTCTTT
MIT_Sbay_c84_6418 + 64 6.44e-10 GTCCTTTCGC ATCCTTCTATTGTTCTTCCT TATTGTTCTC
MIT_Smik_c283_5928 + 71 6.44e-10 TCTTTTGCAA ATCCCTCTATTGTTCTTTCC ATTACTCTTT
SGD_Scer_YER014W + 69 1.29e-09 TTCTTCGCGA ATATCTCTATTGTTCTCTCT ATTATACTAT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 7.5e-13 705_[+1]_135
MIT_Sbay_c841_3215 7.5e-13 724_[+1]_116
MIT_Spar_c429_3020 7.5e-13 698_[+1]_142
SGD_Scer_YDL205C 7.5e-13 697_[+1]_143
MIT_Smik_c193_2483 4.4e-11 698_[+1]_142
MIT_Spar_c425_6072 2.4e-10 68_[+1]_234
MIT_Sbay_c84_6418 6.4e-10 63_[+1]_239
MIT_Smik_c283_5928 6.4e-10 70_[+1]_232
SGD_Scer_YER014W 1.3e-09 68_[+1]_234
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Skud_Contig1850.5 ( 706) CTCCCCTTATTGTTCACCCT 1
MIT_Sbay_c841_3215 ( 725) CTCCCCTTATTGTTCACCCT 1
MIT_Spar_c429_3020 ( 699) CTCCCCTTATTGTTCACCCT 1
SGD_Scer_YDL205C ( 698) CTCCCCTTATTGTTCACCCT 1
MIT_Smik_c193_2483 ( 699) CTCCCCTTATTATTCACCCT 1
MIT_Spar_c425_6072 ( 69) ATCTCTCTATTGTTCTCTCT 1
MIT_Sbay_c84_6418 ( 64) ATCCTTCTATTGTTCTTCCT 1
MIT_Smik_c283_5928 ( 71) ATCCCTCTATTGTTCTTTCC 1
SGD_Scer_YER014W ( 69) ATATCTCTATTGTTCTCTCT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 1.6e-024
45 166 -982 -982
-982 -982 -982 162
-154 234 -982 -982
-982 215 -982 -55
-982 234 -982 -154
-982 166 -982 45
-982 134 -982 78
-982 -982 -982 162
162 -982 -982 -982
-982 -982 -982 162
-982 -982 -982 162
-154 -982 234 -982
-982 -982 -982 162
-982 -982 -982 162
-982 251 -982 -982
78 -982 -982 45
-982 215 -982 -55
-982 192 -982 4
-982 251 -982 -982
-982 -66 -982 145
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.6e-024
0.444444 0.555556 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.111111 0.888889 0.000000 0.000000
0.000000 0.777778 0.000000 0.222222
0.000000 0.888889 0.000000 0.111111
0.000000 0.555556 0.000000 0.444444
0.000000 0.444444 0.000000 0.555556
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.111111 0.000000 0.888889 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.555556 0.000000 0.000000 0.444444
0.000000 0.777778 0.000000 0.222222
0.000000 0.666667 0.000000 0.333333
0.000000 1.000000 0.000000 0.000000
0.000000 0.111111 0.000000 0.888889
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
[CA]TC[CT]C[CT][TC]TATTGTTC[AT][CT][CT]CT
--------------------------------------------------------------------------------
Time 3.32 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 193 E-value = 8.8e-023
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A ::a:::::aa7:4a:aa82:
pos.-specific C 96:a6a46:::9::6::::6
probability G 14:::::4::316::::28:
matrix T ::::4:6:::::::4::::4
bits 2.5 * *
2.3 * *
2.0 * * * *
1.8 * * * *
Information 1.5 **** * *** * * ** *
content 1.3 **** * *** * * ** *
(30.9 bits) 1.0 ********************
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CCACCCTCAAACGACAAAGC
consensus G T CG G A T GAT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Sbay_c841_3215 + 750 5.90e-12 ACCCTTATTT CCACCCTCAAACGACAAGGC TTGTTATGTT
MIT_Smik_c193_2483 + 724 8.81e-12 ACCCTTATTT CCACCCTCAAACGATAAAGC TTGCTGCGCT
MIT_Spar_c429_3020 + 724 8.81e-12 ACCCTTATTT CCACCCTCAAACGATAAAGC TTGTCTACAT
SGD_Scer_YDL205C + 723 8.81e-12 ACCCTTATTT CCACCCTCAAACGATAAAGC TTGCTACTTT
SGD_Scer_YER014W + 119 1.14e-10 GAATACTCCG CGACTCCGAAGCAACAAAGT GTCGAAGGCA
WashU_Skud_Contig1850.5 + 731 1.80e-10 ACCCTTATTT CCACCCTCAAAGGATAAAGC TTGTTGCATT
MIT_Sbay_c84_6418 + 111 4.97e-10 TTATACTCTG CGACTCCGAAACAACAAAAT CTCGAAGGCA
MIT_Spar_c425_6072 + 118 5.35e-10 AAATACTCCG CGACTCCGAAGCAACAAAAT GTCGAAGGCA
MIT_Smik_c283_5928 + 115 8.73e-10 TTTTAAATAC GGACTCCGAAGCAACAAGGT CGAAGGCAAG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Sbay_c841_3215 5.9e-12 749_[+2]_91
MIT_Smik_c193_2483 8.8e-12 723_[+2]_117
MIT_Spar_c429_3020 8.8e-12 723_[+2]_117
SGD_Scer_YDL205C 8.8e-12 722_[+2]_118
SGD_Scer_YER014W 1.1e-10 118_[+2]_184
WashU_Skud_Contig1850.5 1.8e-10 730_[+2]_110
MIT_Sbay_c84_6418 5e-10 110_[+2]_192
MIT_Spar_c425_6072 5.3e-10 117_[+2]_185
MIT_Smik_c283_5928 8.7e-10 114_[+2]_188
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
MIT_Sbay_c841_3215 ( 750) CCACCCTCAAACGACAAGGC 1
MIT_Smik_c193_2483 ( 724) CCACCCTCAAACGATAAAGC 1
MIT_Spar_c429_3020 ( 724) CCACCCTCAAACGATAAAGC 1
SGD_Scer_YDL205C ( 723) CCACCCTCAAACGATAAAGC 1
SGD_Scer_YER014W ( 119) CGACTCCGAAGCAACAAAGT 1
WashU_Skud_Contig1850.5 ( 731) CCACCCTCAAAGGATAAAGC 1
MIT_Sbay_c84_6418 ( 111) CGACTCCGAAACAACAAAAT 1
MIT_Spar_c425_6072 ( 118) CGACTCCGAAGCAACAAAAT 1
MIT_Smik_c283_5928 ( 115) GGACTCCGAAGCAACAAGGT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 8.8e-023
-982 234 -66 -982
-982 166 134 -982
162 -982 -982 -982
-982 251 -982 -982
-982 166 -982 45
-982 251 -982 -982
-982 134 -982 78
-982 166 134 -982
162 -982 -982 -982
162 -982 -982 -982
104 -982 92 -982
-982 234 -66 -982
45 -982 166 -982
162 -982 -982 -982
-982 166 -982 45
162 -982 -982 -982
162 -982 -982 -982
126 -982 34 -982
-55 -982 215 -982
-982 166 -982 45
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 8.8e-023
0.000000 0.888889 0.111111 0.000000
0.000000 0.555556 0.444444 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.555556 0.000000 0.444444
0.000000 1.000000 0.000000 0.000000
0.000000 0.444444 0.000000 0.555556
0.000000 0.555556 0.444444 0.000000
1.000000 0.000000 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
0.444444 0.000000 0.555556 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.555556 0.000000 0.444444
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.777778 0.000000 0.222222 0.000000
0.222222 0.000000 0.777778 0.000000
0.000000 0.555556 0.000000 0.444444
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
C[CG]AC[CT]C[TC][CG]AA[AG]C[GA]A[CT]AA[AG][GA][CT]
--------------------------------------------------------------------------------
Time 6.50 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 178 E-value = 2.3e-016
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A 9a::9496:41:94:34:71
pos.-specific C 1:a::6:4:::31:6::91:
probability G ::::1:1:a69::6:76:29
matrix T :::a:::::::7::4::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 AACTACAAGGGTAGCGGCAG
consensus A C A C ATAA G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YDL205C + 545 1.06e-11 AGTTAACTTA AACTACAAGGGTAGCAGCAG AATGTGTCGG
MIT_Spar_c429_3020 + 548 4.76e-11 AGTTAACTTG AACTACAAGGGTAGCAACAG AATGTCGGTG
MIT_Smik_c193_2483 + 547 1.28e-10 ACTTGACTTG AACTGCAAGGGTAGCGACGG CGTATGTCGG
MIT_Spar_c425_6072 + 166 1.56e-10 GGCGTTTTGC AACTAAACGAGTAATGGCAG CTTTTAATTA
SGD_Scer_YER014W + 167 1.77e-10 GGCGTTTTGT AACTAAACGAGCAATGGCAG CTTTCAATTA
MIT_Sbay_c84_6418 + 162 1.74e-09 AAATATTCAC CACTAAACGAGCAATGACAG TTATATTCAA
WashU_Skud_Contig1850.5 + 550 1.74e-09 CGCAAAACGG AACTACAAGGATAGCAACGG AATGTGTCGG
MIT_Smik_c283_5928 + 161 2.36e-09 GGCATTTTAC AACTAAACGAGCAATGGTAG CTTTTGATTG
MIT_Sbay_c841_3215 + 557 4.89e-09 CGTAAGATAG AACTACGAGGGTCGCGGCCA ATGTGTCGGT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDL205C 1.1e-11 544_[+3]_296
MIT_Spar_c429_3020 4.8e-11 547_[+3]_293
MIT_Smik_c193_2483 1.3e-10 546_[+3]_294
MIT_Spar_c425_6072 1.6e-10 165_[+3]_137
SGD_Scer_YER014W 1.8e-10 166_[+3]_136
MIT_Sbay_c84_6418 1.7e-09 161_[+3]_141
WashU_Skud_Contig1850.5 1.7e-09 549_[+3]_291
MIT_Smik_c283_5928 2.4e-09 160_[+3]_142
MIT_Sbay_c841_3215 4.9e-09 556_[+3]_284
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
SGD_Scer_YDL205C ( 545) AACTACAAGGGTAGCAGCAG 1
MIT_Spar_c429_3020 ( 548) AACTACAAGGGTAGCAACAG 1
MIT_Smik_c193_2483 ( 547) AACTGCAAGGGTAGCGACGG 1
MIT_Spar_c425_6072 ( 166) AACTAAACGAGTAATGGCAG 1
SGD_Scer_YER014W ( 167) AACTAAACGAGCAATGGCAG 1
MIT_Sbay_c84_6418 ( 162) CACTAAACGAGCAATGACAG 1
WashU_Skud_Contig1850.5 ( 550) AACTACAAGGATAGCAACGG 1
MIT_Smik_c283_5928 ( 161) AACTAAACGAGCAATGGTAG 1
MIT_Sbay_c841_3215 ( 557) AACTACGAGGGTCGCGGCCA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 2.3e-016
145 -66 -982 -982
162 -982 -982 -982
-982 251 -982 -982
-982 -982 -982 162
145 -982 -66 -982
45 166 -982 -982
145 -982 -66 -982
78 134 -982 -982
-982 -982 251 -982
45 -982 166 -982
-154 -982 234 -982
-982 92 -982 104
145 -66 -982 -982
45 -982 166 -982
-982 166 -982 45
4 -982 192 -982
45 -982 166 -982
-982 234 -982 -154
104 -66 34 -982
-154 -982 234 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.3e-016
0.888889 0.111111 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.888889 0.000000 0.111111 0.000000
0.444444 0.555556 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.555556 0.444444 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.111111 0.000000 0.888889 0.000000
0.000000 0.333333 0.000000 0.666667
0.888889 0.111111 0.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.000000 0.555556 0.000000 0.444444
0.333333 0.000000 0.666667 0.000000
0.444444 0.000000 0.555556 0.000000
0.000000 0.888889 0.000000 0.111111
0.666667 0.111111 0.222222 0.000000
0.111111 0.000000 0.888889 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
AACTA[CA]A[AC]G[GA]G[TC]A[GA][CT][GA][GA]C[AG]G
--------------------------------------------------------------------------------
Time 9.58 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 11 sites = 9 llr = 119 E-value = 1.7e-006
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 2aa::6a4:1:
pos.-specific C :::::4:6:8:
probability G 8::aa:::a::
matrix T :::::::::1a
bits 2.5 ** *
2.3 ** *
2.0 ** *
1.8 ** *
Information 1.5 ***** * * *
content 1.3 ***** * ***
(19.1 bits) 1.0 ***********
0.8 ***********
0.5 ***********
0.3 ***********
0.0 -----------
Multilevel GAAGGAACGCT
consensus A C A
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- -----------
WashU_Skud_Contig1850.5 - 217 1.62e-07 TGAAAAAATT GAAGGAACGCT TTATATAAAC
MIT_Smik_c193_2483 - 220 1.62e-07 GAGAAAAACT GAAGGAACGCT TAATATAAAC
MIT_Spar_c429_3020 - 218 1.62e-07 TGAAAAAAAT GAAGGAACGCT TTATATAAAC
MIT_Sbay_c84_6418 + 134 2.68e-07 ACAAAATCTC GAAGGCAAGCT AAGGTAAAAA
MIT_Smik_c283_5928 + 136 2.68e-07 CAACAAGGTC GAAGGCAAGCT GAAAGGCATT
MIT_Sbay_c841_3215 - 218 7.62e-07 CCGAAAAATT AAAGGAACGCT TATTTAAACG
SGD_Scer_YDL205C - 217 7.62e-07 ATGAAAAAGT AAAGGAACGCT TTATATAAAC
MIT_Spar_c425_6072 + 141 2.30e-06 ACAAAATGTC GAAGGCAAGAT GAAAGGCGTT
SGD_Scer_YER014W + 142 2.30e-06 ACAAAGTGTC GAAGGCAAGTT CAAAGGCGTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 1.6e-07 216_[-4]_633
MIT_Smik_c193_2483 1.6e-07 219_[-4]_630
MIT_Spar_c429_3020 1.6e-07 217_[-4]_632
MIT_Sbay_c84_6418 2.7e-07 133_[+4]_178
MIT_Smik_c283_5928 2.7e-07 135_[+4]_176
MIT_Sbay_c841_3215 7.6e-07 217_[-4]_632
SGD_Scer_YDL205C 7.6e-07 216_[-4]_633
MIT_Spar_c425_6072 2.3e-06 140_[+4]_171
SGD_Scer_YER014W 2.3e-06 141_[+4]_170
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=11 seqs=9
WashU_Skud_Contig1850.5 ( 217) GAAGGAACGCT 1
MIT_Smik_c193_2483 ( 220) GAAGGAACGCT 1
MIT_Spar_c429_3020 ( 218) GAAGGAACGCT 1
MIT_Sbay_c84_6418 ( 134) GAAGGCAAGCT 1
MIT_Smik_c283_5928 ( 136) GAAGGCAAGCT 1
MIT_Sbay_c841_3215 ( 218) AAAGGAACGCT 1
SGD_Scer_YDL205C ( 217) AAAGGAACGCT 1
MIT_Spar_c425_6072 ( 141) GAAGGCAAGAT 1
SGD_Scer_YER014W ( 142) GAAGGCAAGTT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 11 n= 5498 bayes= 9.2524 E= 1.7e-006
-55 -982 215 -982
162 -982 -982 -982
162 -982 -982 -982
-982 -982 251 -982
-982 -982 251 -982
78 134 -982 -982
162 -982 -982 -982
45 166 -982 -982
-982 -982 251 -982
-154 215 -982 -154
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 11 nsites= 9 E= 1.7e-006
0.222222 0.000000 0.777778 0.000000
1.000000 0.000000 0.000000 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
0.555556 0.444444 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.444444 0.555556 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.111111 0.777778 0.000000 0.111111
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[GA]AAGG[AC]A[CA]GCT
--------------------------------------------------------------------------------
Time 12.58 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 167 E-value = 6.6e-012
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 9:a:2:::4:a4492::7a9
pos.-specific C :6::66a::::66:1:71::
probability G 1::a2:::6::::1:2:2::
matrix T :4:::4:a:a::::783::1
bits 2.5 * *
2.3 * *
2.0 * *
1.8 * *
Information 1.5 ** ** ** *
content 1.3 * ** ** ** * * *
(26.7 bits) 1.0 **** ********* ** **
0.8 ************** *****
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel ACAGCCCTGTACCATTCAAA
consensus T AT A AA AGTG
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1850.5 + 115 6.64e-13 AAAAAGCAAT ACAGCCCTGTACCATTCAAA CACGAACGCC
MIT_Sbay_c841_3215 + 116 6.64e-13 AAAACGCAAT ACAGCCCTGTACCATTCAAA TACGAACGCC
MIT_Smik_c193_2483 + 117 6.64e-13 AAAAAGTAAT ACAGCCCTGTACCATTCAAA CACGAGCGCC
MIT_Spar_c429_3020 + 115 1.38e-12 AAAATGTAAA ACAGCCCTGTACCATGCAAA CACGAGCCTC
SGD_Scer_YDL205C + 115 1.38e-12 AAAATCTAAT ACAGCCCTGTACCATGCAAA CACGAGCGTC
MIT_Smik_c283_5928 + 276 3.37e-08 AATGTTAAAT ATAGATCTATAAAAATTGAA TAGTAATAAT
MIT_Spar_c425_6072 + 281 3.48e-08 AAGAATGAAT ATAGGTCTATAAAAATTCAA TAATTATAGA
SGD_Scer_YER014W + 274 3.63e-08 AAAATTAAAT ATAGGTCTATAAAACTCGAT AATTATAATG
MIT_Sbay_c84_6418 + 265 4.65e-08 TATATTAAAC GTAGATCTATAAAGTTTAAA TAGTTTATAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 6.6e-13 114_[+5]_726
MIT_Sbay_c841_3215 6.6e-13 115_[+5]_725
MIT_Smik_c193_2483 6.6e-13 116_[+5]_724
MIT_Spar_c429_3020 1.4e-12 114_[+5]_726
SGD_Scer_YDL205C 1.4e-12 114_[+5]_726
MIT_Smik_c283_5928 3.4e-08 275_[+5]_27
MIT_Spar_c425_6072 3.5e-08 280_[+5]_22
SGD_Scer_YER014W 3.6e-08 273_[+5]_29
MIT_Sbay_c84_6418 4.7e-08 264_[+5]_38
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
WashU_Skud_Contig1850.5 ( 115) ACAGCCCTGTACCATTCAAA 1
MIT_Sbay_c841_3215 ( 116) ACAGCCCTGTACCATTCAAA 1
MIT_Smik_c193_2483 ( 117) ACAGCCCTGTACCATTCAAA 1
MIT_Spar_c429_3020 ( 115) ACAGCCCTGTACCATGCAAA 1
SGD_Scer_YDL205C ( 115) ACAGCCCTGTACCATGCAAA 1
MIT_Smik_c283_5928 ( 276) ATAGATCTATAAAAATTGAA 1
MIT_Spar_c425_6072 ( 281) ATAGGTCTATAAAAATTCAA 1
SGD_Scer_YER014W ( 274) ATAGGTCTATAAAACTCGAT 1
MIT_Sbay_c84_6418 ( 265) GTAGATCTATAAAGTTTAAA 1
//
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Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 6.6e-012
145 -982 -66 -982
-982 166 -982 45
162 -982 -982 -982
-982 -982 251 -982
-55 166 34 -982
-982 166 -982 45
-982 251 -982 -982
-982 -982 -982 162
45 -982 166 -982
-982 -982 -982 162
162 -982 -982 -982
45 166 -982 -982
45 166 -982 -982
145 -982 -66 -982
-55 -66 -982 104
-982 -982 34 126
-982 192 -982 4
104 -66 34 -982
162 -982 -982 -982
145 -982 -982 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.6e-012
0.888889 0.000000 0.111111 0.000000
0.000000 0.555556 0.000000 0.444444
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.222222 0.555556 0.222222 0.000000
0.000000 0.555556 0.000000 0.444444
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.444444 0.000000 0.555556 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.444444 0.555556 0.000000 0.000000
0.444444 0.555556 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.222222 0.111111 0.000000 0.666667
0.000000 0.000000 0.222222 0.777778
0.000000 0.666667 0.000000 0.333333
0.666667 0.111111 0.222222 0.000000
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.000000 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
A[CT]AG[CAG][CT]CT[GA]TA[CA][CA]A[TA][TG][CT][AG]AA
--------------------------------------------------------------------------------
Time 15.70 secs.
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********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDL205C 2.08e-30 114_[+5(1.38e-12)]_82_[-4(7.62e-07)]_154_[+4(3.75e-05)]_152_[+3(1.06e-11)]_133_[+1(7.49e-13)]_5_[+2(8.81e-12)]_118
MIT_Spar_c429_3020 1.99e-30 53_[+1(9.52e-05)]_41_[+5(1.38e-12)]_83_[-4(1.62e-07)]_156_[+4(3.75e-05)]_152_[+3(4.76e-11)]_131_[+1(7.49e-13)]_5_[+2(8.81e-12)]_117
MIT_Smik_c193_2483 1.21e-28 116_[+5(6.64e-13)]_83_[-4(1.62e-07)]_316_[+3(1.28e-10)]_132_[+1(4.36e-11)]_5_[+2(8.81e-12)]_117
MIT_Sbay_c841_3215 2.40e-28 54_[+1(9.52e-05)]_41_[+5(6.64e-13)]_60_[+5(4.92e-05)]_2_[-4(7.62e-07)]_328_[+3(4.89e-09)]_107_[-1(5.66e-05)]_21_[+1(7.49e-13)]_5_[+2(5.90e-12)]_91
WashU_Skud_Contig1850.5 5.34e-28 114_[+5(6.64e-13)]_82_[-4(1.62e-07)]_289_[+2(7.24e-05)]_13_[+3(1.74e-09)]_136_[+1(7.49e-13)]_5_[+2(1.80e-10)]_110
SGD_Scer_YER014W 1.36e-22 68_[+1(1.29e-09)]_30_[+2(1.14e-10)]_3_[+4(2.30e-06)]_14_[+3(1.77e-10)]_87_[+5(3.63e-08)]_29
MIT_Spar_c425_6072 1.03e-22 68_[+1(2.43e-10)]_29_[+2(5.35e-10)]_3_[+4(2.30e-06)]_14_[+3(1.56e-10)]_57_[+4(9.30e-05)]_27_[+5(3.48e-08)]_22
MIT_Smik_c283_5928 6.69e-22 70_[+1(6.44e-10)]_24_[+2(8.73e-10)]_1_[+4(2.68e-07)]_14_[+3(2.36e-09)]_95_[+5(3.37e-08)]_27
MIT_Sbay_c84_6418 4.02e-22 63_[+1(6.44e-10)]_27_[+2(4.97e-10)]_3_[+4(2.68e-07)]_17_[+3(1.74e-09)]_83_[+5(4.65e-08)]_38
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************