********************************************************************************
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= HEM14-HEM15.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
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
SGD_Scer_YOR176W 1.0000 727 MIT_Spar_c278_20970 1.0000 727
MIT_Smik_c935_20455 1.0000 727 WashU_Skud_Contig2050.4 1.0000 727
WashU_Sbay_Contig480.2 1.0000 727
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM14-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
model: mod= oops nmotifs= 5 evt= inf
object function= E-value of product of p-values
width: minw= 6 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 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= 4923 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.317 C 0.183 G 0.183 T 0.317
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 = 199 E-value = 3.0e-025
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A ::::1aa7:4a:aa92:1:1
pos.-specific C a:4a::::a6:a:::662:9
probability G :6::9::3::::::12:71:
matrix T :46:::::::::::::4:9:
bits 2.5 * * * *
2.3 * * * *
2.0 * ** * * *
1.8 * ** * * *
Information 1.5 * **** * **** *
content 1.3 * **** * ***** ***
(31.9 bits) 1.0 *************** ****
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CGTCGAAACCACAAACCGTC
consensus TC G A ATC
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2050.4 + 569 3.57e-13 TCAAAGTGCG CGTCGAAACCACAAACCGTC GAAAATATTG
MIT_Spar_c278_20970 + 563 3.57e-13 TCGAATTGCG CGTCGAAACCACAAACCGTC GAAAATAATG
SGD_Scer_YOR176W + 561 3.57e-13 TCACATTGCG CGTCGAAACCACAAACCGTC GAAAACAATG
WashU_Sbay_Contig480.2 + 574 2.79e-11 TCGAAGTGCG CGTCGAAACCACAAACCATC AAAAATATCG
MIT_Smik_c935_20455 + 547 3.89e-11 TCCAATTGCG CGTCAAAACCACAAACCGTC GAAAATAATG
SGD_Scer_YER014W + 122 5.95e-11 TACTCCGCGA CTCCGAAGCAACAAAGTGTC GAAGGCAAGT
MIT_Spar_c425_6072 + 121 1.08e-10 TACTCCGCGA CTCCGAAGCAACAAAATGTC GAAGGCAAGA
MIT_Sbay_c84_6418 + 114 2.44e-10 TACTCTGCGA CTCCGAAACAACAAAATCTC GAAGGCAAGC
MIT_Smik_c283_5928 + 118 2.73e-09 TAAATACGGA CTCCGAAGCAACAAGGTCGA AGGCAAGCTG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2050.4 3.6e-13 568_[+1]_139
MIT_Spar_c278_20970 3.6e-13 562_[+1]_145
SGD_Scer_YOR176W 3.6e-13 560_[+1]_147
WashU_Sbay_Contig480.2 2.8e-11 573_[+1]_134
MIT_Smik_c935_20455 3.9e-11 546_[+1]_161
SGD_Scer_YER014W 6e-11 121_[+1]_181
MIT_Spar_c425_6072 1.1e-10 120_[+1]_182
MIT_Sbay_c84_6418 2.4e-10 113_[+1]_189
MIT_Smik_c283_5928 2.7e-09 117_[+1]_185
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2050.4 ( 569) CGTCGAAACCACAAACCGTC 1
MIT_Spar_c278_20970 ( 563) CGTCGAAACCACAAACCGTC 1
SGD_Scer_YOR176W ( 561) CGTCGAAACCACAAACCGTC 1
WashU_Sbay_Contig480.2 ( 574) CGTCGAAACCACAAACCATC 1
MIT_Smik_c935_20455 ( 547) CGTCAAAACCACAAACCGTC 1
SGD_Scer_YER014W ( 122) CTCCGAAGCAACAAAGTGTC 1
MIT_Spar_c425_6072 ( 121) CTCCGAAGCAACAAAATGTC 1
MIT_Sbay_c84_6418 ( 114) CTCCGAAACAACAAAATCTC 1
MIT_Smik_c283_5928 ( 118) CTCCGAAGCAACAAGGTCGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 3.0e-025
-982 251 -982 -982
-982 -982 166 45
-982 134 -982 78
-982 251 -982 -982
-154 -982 234 -982
162 -982 -982 -982
162 -982 -982 -982
104 -982 92 -982
-982 251 -982 -982
45 166 -982 -982
162 -982 -982 -982
-982 251 -982 -982
162 -982 -982 -982
162 -982 -982 -982
145 -982 -66 -982
-55 166 34 -982
-982 166 -982 45
-154 34 192 -982
-982 -982 -66 145
-154 234 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-025
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.555556 0.444444
0.000000 0.444444 0.000000 0.555556
0.000000 1.000000 0.000000 0.000000
0.111111 0.000000 0.888889 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 1.000000 0.000000 0.000000
0.444444 0.555556 0.000000 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
0.888889 0.000000 0.111111 0.000000
0.222222 0.555556 0.222222 0.000000
0.000000 0.555556 0.000000 0.444444
0.111111 0.222222 0.666667 0.000000
0.000000 0.000000 0.111111 0.888889
0.111111 0.888889 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
C[GT][TC]CGAA[AG]C[CA]ACAAA[CAG][CT][GC]TC
--------------------------------------------------------------------------------
Time 2.80 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 169 E-value = 2.7e-014
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A ::::1::1133:1:::::3:
pos.-specific C :99::9:9::36279167::
probability G ::::::9:813:::::::::
matrix T a11a911:16:47319437a
bits 2.5
2.3
2.0 ** *** *
1.8 ** *** *
Information 1.5 **** *** * *
content 1.3 **** **** *** * *
(27.1 bits) 1.0 ********* * ***** *
0.8 ********* ** *******
0.5 ********* **********
0.3 ********************
0.0 --------------------
Multilevel TCCTTCGCGTACTCCTCCTT
consensus ACTCT TTA
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c935_20455 + 152 1.72e-12 ACCAAAAGAC TCCTTCGCGTCCTCCTTCTT CAAGTCTCAT
MIT_Spar_c278_20970 + 157 1.72e-12 CTAAAAGTAT TCCTTCGCGTCCTCCTTCTT CAATCCCATA
SGD_Scer_YOR176W + 155 1.72e-12 CCAAAAGTAT TCCTTCGCGTCCTCCTTCTT CAATCCCATA
WashU_Skud_Contig2050.4 + 161 4.74e-12 AAAGAAGTAT TCCTTCGCGTGCTTCTCCTT TCTGTGTCAA
WashU_Sbay_Contig480.2 + 205 6.16e-10 AAAGAAGTAT TCCTACGCGAGCTCCCTCTT CAAGTGCCAA
MIT_Spar_c425_6072 + 59 2.17e-09 TGAATTGGTA TCCTTCGCGGATCTCTCTAT TGTTCTCTCT
SGD_Scer_YER014W + 59 3.35e-08 TGAATTGGTG TTCTTCGCGAATATCTCTAT TGTTCTCTCT
MIT_Sbay_c84_6418 + 65 9.53e-08 TCCTTTCGCA TCCTTCTATTGTTCTTCCTT ATTGTTCTCG
MIT_Smik_c283_5928 + 61 1.51e-07 TAAACTGCTA TCTTTTGCAAATCCCTCTAT TGTTCTTTCC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c935_20455 1.7e-12 151_[+2]_556
MIT_Spar_c278_20970 1.7e-12 156_[+2]_551
SGD_Scer_YOR176W 1.7e-12 154_[+2]_553
WashU_Skud_Contig2050.4 4.7e-12 160_[+2]_547
WashU_Sbay_Contig480.2 6.2e-10 204_[+2]_503
MIT_Spar_c425_6072 2.2e-09 58_[+2]_244
SGD_Scer_YER014W 3.3e-08 58_[+2]_244
MIT_Sbay_c84_6418 9.5e-08 64_[+2]_238
MIT_Smik_c283_5928 1.5e-07 60_[+2]_242
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
MIT_Smik_c935_20455 ( 152) TCCTTCGCGTCCTCCTTCTT 1
MIT_Spar_c278_20970 ( 157) TCCTTCGCGTCCTCCTTCTT 1
SGD_Scer_YOR176W ( 155) TCCTTCGCGTCCTCCTTCTT 1
WashU_Skud_Contig2050.4 ( 161) TCCTTCGCGTGCTTCTCCTT 1
WashU_Sbay_Contig480.2 ( 205) TCCTACGCGAGCTCCCTCTT 1
MIT_Spar_c425_6072 ( 59) TCCTTCGCGGATCTCTCTAT 1
SGD_Scer_YER014W ( 59) TTCTTCGCGAATATCTCTAT 1
MIT_Sbay_c84_6418 ( 65) TCCTTCTATTGTTCTTCCTT 1
MIT_Smik_c283_5928 ( 61) TCTTTTGCAAATCCCTCTAT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 2.7e-014
-982 -982 -982 162
-982 234 -982 -154
-982 234 -982 -154
-982 -982 -982 162
-154 -982 -982 145
-982 234 -982 -154
-982 -982 234 -154
-154 234 -982 -982
-154 -982 215 -154
4 -982 -66 78
4 92 92 -982
-982 166 -982 45
-154 34 -982 104
-982 192 -982 4
-982 234 -982 -154
-982 -66 -982 145
-982 166 -982 45
-982 192 -982 4
4 -982 -982 104
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.7e-014
0.000000 0.000000 0.000000 1.000000
0.000000 0.888889 0.000000 0.111111
0.000000 0.888889 0.000000 0.111111
0.000000 0.000000 0.000000 1.000000
0.111111 0.000000 0.000000 0.888889
0.000000 0.888889 0.000000 0.111111
0.000000 0.000000 0.888889 0.111111
0.111111 0.888889 0.000000 0.000000
0.111111 0.000000 0.777778 0.111111
0.333333 0.000000 0.111111 0.555556
0.333333 0.333333 0.333333 0.000000
0.000000 0.555556 0.000000 0.444444
0.111111 0.222222 0.000000 0.666667
0.000000 0.666667 0.000000 0.333333
0.000000 0.888889 0.000000 0.111111
0.000000 0.111111 0.000000 0.888889
0.000000 0.555556 0.000000 0.444444
0.000000 0.666667 0.000000 0.333333
0.333333 0.000000 0.000000 0.666667
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
TCCTTCGCG[TA][ACG][CT][TC][CT]CT[CT][CT][TA]T
--------------------------------------------------------------------------------
Time 5.45 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 159 E-value = 1.6e-009
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :1:12::::23:1:8:1:2:
pos.-specific C :::4291:6:1:21219:::
probability G 1:8::::6::6::9:8::8:
matrix T 9924619448:a7::1:a:a
bits 2.5
2.3
2.0 * * *
1.8 * * *
Information 1.5 * * * * *****
content 1.3 * * ** * * *****
(25.4 bits) 1.0 *** **** * *******
0.8 *** ******* *******
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel TTGCTCTGCTGTTGAGCTGT
consensus TTA TTAA C C A
sequence C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c935_20455 + 482 3.60e-13 TCAGCTTTTT TTGCTCTGCTGTTGAGCTGT TTTACTTCAT
MIT_Spar_c278_20970 + 498 5.54e-13 TTAGCTTTTT TTGCCCTGCTGTTGAGCTGT TTTGCTTCAC
WashU_Sbay_Contig480.2 + 508 1.71e-12 TAGCTGTTTT TTGTTCTGCTGTTGAGCTGT TTTGCTCCAC
WashU_Skud_Contig2050.4 + 499 1.71e-12 CAGCTGTTTT TTGTTCTGCTGTTGAGCTGT TTTGTTCCAT
SGD_Scer_YOR176W + 496 3.87e-12 TTAGCTTTTT TTGTCCTGCTGTTGAGCTGT TTTGCTTTAC
MIT_Sbay_c84_6418 + 8 1.48e-07 TGTCGAA GTTCTCCTTTATTCCGCTGT TTCTTACGGA
SGD_Scer_YER014W + 28 2.26e-07 GCGTTCTCAA TTGCACTTTACTCGATATGT TTGAATTGGT
MIT_Smik_c283_5928 + 19 2.82e-07 CTCTCTCCAC TATTTCTTTAATCGCGCTAT ACTAGATATG
MIT_Spar_c425_6072 - 281 8.96e-07 TCTATAATTA TTGAATTTTTATAGACCTAT ATTCATTCTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c935_20455 3.6e-13 481_[+3]_226
MIT_Spar_c278_20970 5.5e-13 497_[+3]_210
WashU_Sbay_Contig480.2 1.7e-12 507_[+3]_200
WashU_Skud_Contig2050.4 1.7e-12 498_[+3]_209
SGD_Scer_YOR176W 3.9e-12 495_[+3]_212
MIT_Sbay_c84_6418 1.5e-07 7_[+3]_295
SGD_Scer_YER014W 2.3e-07 27_[+3]_275
MIT_Smik_c283_5928 2.8e-07 18_[+3]_284
MIT_Spar_c425_6072 9e-07 280_[-3]_22
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
MIT_Smik_c935_20455 ( 482) TTGCTCTGCTGTTGAGCTGT 1
MIT_Spar_c278_20970 ( 498) TTGCCCTGCTGTTGAGCTGT 1
WashU_Sbay_Contig480.2 ( 508) TTGTTCTGCTGTTGAGCTGT 1
WashU_Skud_Contig2050.4 ( 499) TTGTTCTGCTGTTGAGCTGT 1
SGD_Scer_YOR176W ( 496) TTGTCCTGCTGTTGAGCTGT 1
MIT_Sbay_c84_6418 ( 8) GTTCTCCTTTATTCCGCTGT 1
SGD_Scer_YER014W ( 28) TTGCACTTTACTCGATATGT 1
MIT_Smik_c283_5928 ( 19) TATTTCTTTAATCGCGCTAT 1
MIT_Spar_c425_6072 ( 281) TTGAATTTTTATAGACCTAT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 1.6e-009
-982 -982 -66 145
-154 -982 -982 145
-982 -982 215 -55
-154 134 -982 45
-55 34 -982 78
-982 234 -982 -154
-982 -66 -982 145
-982 -982 166 45
-982 166 -982 45
-55 -982 -982 126
4 -66 166 -982
-982 -982 -982 162
-154 34 -982 104
-982 -66 234 -982
126 34 -982 -982
-982 -66 215 -154
-154 234 -982 -982
-982 -982 -982 162
-55 -982 215 -982
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.6e-009
0.000000 0.000000 0.111111 0.888889
0.111111 0.000000 0.000000 0.888889
0.000000 0.000000 0.777778 0.222222
0.111111 0.444444 0.000000 0.444444
0.222222 0.222222 0.000000 0.555556
0.000000 0.888889 0.000000 0.111111
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.555556 0.444444
0.000000 0.555556 0.000000 0.444444
0.222222 0.000000 0.000000 0.777778
0.333333 0.111111 0.555556 0.000000
0.000000 0.000000 0.000000 1.000000
0.111111 0.222222 0.000000 0.666667
0.000000 0.111111 0.888889 0.000000
0.777778 0.222222 0.000000 0.000000
0.000000 0.111111 0.777778 0.111111
0.111111 0.888889 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.222222 0.000000 0.777778 0.000000
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
TT[GT][CT][TAC]CT[GT][CT][TA][GA]T[TC]G[AC]GCT[GA]T
--------------------------------------------------------------------------------
Time 7.97 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 9 llr = 162 E-value = 7.2e-011
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A :412:::41:39:1aaa717
pos.-specific C :166::1:78::a4:::3::
probability G a4:2::612:71::::::91
matrix T ::3:aa34:2:::4:::::2
bits 2.5 * *
2.3 * *
2.0 * * *
1.8 * * *
Information 1.5 * ** * * *** *
content 1.3 * ** ***** *** *
(26.0 bits) 1.0 * ** ***** *****
0.8 ******* ***** *****
0.5 ******* ************
0.3 ********************
0.0 --------------------
Multilevel GACCTTGACCGACCAAAAGA
consensus GTA TTGTA T C T
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YOR176W + 133 2.43e-11 AGCCAAGAGT GACCTTGACCGACCAAAAGT ATTCCTTCGC
MIT_Spar_c278_20970 + 135 8.09e-11 AACCAAGAGT GACCTTGACCGACTAAAAGT ATTCCTTCGC
WashU_Sbay_Contig480.2 + 180 9.46e-11 GAGCCATAAT GCTCTTGACCGACCAAAAGA AGTATTCCTA
MIT_Smik_c935_20455 + 131 9.46e-11 GACCAACAGT GATCTTGGCCGACCAAAAGA CTCCTTCGCG
WashU_Skud_Contig2050.4 + 136 3.12e-10 GACCAACAAT GATATTGACCGACCAAAAGA AGTATTCCTT
MIT_Spar_c425_6072 + 156 3.11e-09 CAAGATGAAA GGCGTTTTGCAACTAAACGA GTAATGGCAG
MIT_Smik_c283_5928 + 151 1.64e-08 CAAGCTGAAA GGCATTTTACAACTAAACGA GCAATGGTAG
SGD_Scer_YER014W + 157 1.64e-08 CAAGTTCAAA GGCGTTTTGTAACTAAACGA GCAATGGCAG
MIT_Sbay_c84_6418 - 203 3.27e-07 TCTCCAGTGA GGACTTCTCTGGCAAAAAAG TAGAATGACG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YOR176W 2.4e-11 132_[+4]_575
MIT_Spar_c278_20970 8.1e-11 134_[+4]_573
WashU_Sbay_Contig480.2 9.5e-11 179_[+4]_528
MIT_Smik_c935_20455 9.5e-11 130_[+4]_577
WashU_Skud_Contig2050.4 3.1e-10 135_[+4]_572
MIT_Spar_c425_6072 3.1e-09 155_[+4]_147
MIT_Smik_c283_5928 1.6e-08 150_[+4]_152
SGD_Scer_YER014W 1.6e-08 156_[+4]_146
MIT_Sbay_c84_6418 3.3e-07 202_[-4]_100
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=9
SGD_Scer_YOR176W ( 133) GACCTTGACCGACCAAAAGT 1
MIT_Spar_c278_20970 ( 135) GACCTTGACCGACTAAAAGT 1
WashU_Sbay_Contig480.2 ( 180) GCTCTTGACCGACCAAAAGA 1
MIT_Smik_c935_20455 ( 131) GATCTTGGCCGACCAAAAGA 1
WashU_Skud_Contig2050.4 ( 136) GATATTGACCGACCAAAAGA 1
MIT_Spar_c425_6072 ( 156) GGCGTTTTGCAACTAAACGA 1
MIT_Smik_c283_5928 ( 151) GGCATTTTACAACTAAACGA 1
SGD_Scer_YER014W ( 157) GGCGTTTTGTAACTAAACGA 1
MIT_Sbay_c84_6418 ( 203) GGACTTCTCTGGCAAAAAAG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 7.2e-011
-982 -982 251 -982
45 -66 134 -982
-154 166 -982 4
-55 166 34 -982
-982 -982 -982 162
-982 -982 -982 162
-982 -66 166 4
45 -982 -66 45
-154 192 34 -982
-982 215 -982 -55
4 -982 192 -982
145 -982 -66 -982
-982 251 -982 -982
-154 134 -982 45
162 -982 -982 -982
162 -982 -982 -982
162 -982 -982 -982
104 92 -982 -982
-154 -982 234 -982
104 -982 -66 -55
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 7.2e-011
0.000000 0.000000 1.000000 0.000000
0.444444 0.111111 0.444444 0.000000
0.111111 0.555556 0.000000 0.333333
0.222222 0.555556 0.222222 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.111111 0.555556 0.333333
0.444444 0.000000 0.111111 0.444444
0.111111 0.666667 0.222222 0.000000
0.000000 0.777778 0.000000 0.222222
0.333333 0.000000 0.666667 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 1.000000 0.000000 0.000000
0.111111 0.444444 0.000000 0.444444
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.666667 0.333333 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
0.666667 0.000000 0.111111 0.222222
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
G[AG][CT][CAG]TT[GT][AT][CG][CT][GA]AC[CT]AAA[AC]G[AT]
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Time 10.39 secs.
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MOTIF 5 width = 20 sites = 9 llr = 144 E-value = 1.4e-003
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Motif 5 Description
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Simplified A a6a:::1:191169877a82
pos.-specific C ::::7a6a1:71:::11::2
probability G ::::::::2:1341221:26
matrix T :4:a3:3:6114::::1:::
bits 2.5 * *
2.3 * *
2.0 * *
1.8 * *
Information 1.5 * ** * * *
content 1.3 * **** * * *
(23.0 bits) 1.0 * **** * * *** **
0.8 ******** ** **** ***
0.5 ******** ** **** ***
0.3 ********************
0.0 --------------------
Multilevel AAATCCCCTACTAAAAAAAG
consensus T T T G GG GG GA
sequence C
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Motif 5 sites sorted by position p-value
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Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig480.2 + 233 5.39e-12 TTCAAGTGCC AAATCCCCTACTGAAAAAAG CAACATGAGA
MIT_Spar_c278_20970 + 184 1.13e-11 CTTCAATCCC ATATCCCCTACTGAAAAAAG CAGCGTGCGA
SGD_Scer_YOR176W + 182 1.61e-11 CTTCAATCCC ATATCCCCTACGAAAAAAAG CAGCATGAGA
WashU_Skud_Contig2050.4 + 189 2.93e-10 TTTCTGTGTC AAATCCCCTACTGAAAAAGC AGCATTGGGA
MIT_Smik_c935_20455 + 180 2.45e-09 TTCAAGTCTC ATATCCCCTACCAGAAAAAG TAGCAGGCGA
MIT_Spar_c425_6072 + 232 1.36e-07 TTTTCACATA AAATCCTCGAAGAAGGAAAA ATTGATAATC
MIT_Smik_c283_5928 + 228 5.40e-07 TTGTCCCACG AAATTCTCGTTGAAAGCAAG GTTCGTAAGG
MIT_Sbay_c84_6418 + 154 6.05e-07 TAAGGTAAAA ATATTCACCACTAAACGAGC AATGACAGTT
SGD_Scer_YER014W + 236 1.24e-06 TTTCATGTAA AAATTCTCAAGAGAGATAAA GTTGTTAAAA
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Motif 5 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig480.2 5.4e-12 232_[+5]_475
MIT_Spar_c278_20970 1.1e-11 183_[+5]_524
SGD_Scer_YOR176W 1.6e-11 181_[+5]_526
WashU_Skud_Contig2050.4 2.9e-10 188_[+5]_519
MIT_Smik_c935_20455 2.5e-09 179_[+5]_528
MIT_Spar_c425_6072 1.4e-07 231_[+5]_71
MIT_Smik_c283_5928 5.4e-07 227_[+5]_75
MIT_Sbay_c84_6418 6.1e-07 153_[+5]_149
SGD_Scer_YER014W 1.2e-06 235_[+5]_67
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Motif 5 in BLOCKS format
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BL MOTIF 5 width=20 seqs=9
WashU_Sbay_Contig480.2 ( 233) AAATCCCCTACTGAAAAAAG 1
MIT_Spar_c278_20970 ( 184) ATATCCCCTACTGAAAAAAG 1
SGD_Scer_YOR176W ( 182) ATATCCCCTACGAAAAAAAG 1
WashU_Skud_Contig2050.4 ( 189) AAATCCCCTACTGAAAAAGC 1
MIT_Smik_c935_20455 ( 180) ATATCCCCTACCAGAAAAAG 1
MIT_Spar_c425_6072 ( 232) AAATCCTCGAAGAAGGAAAA 1
MIT_Smik_c283_5928 ( 228) AAATTCTCGTTGAAAGCAAG 1
MIT_Sbay_c84_6418 ( 154) ATATTCACCACTAAACGAGC 1
SGD_Scer_YER014W ( 236) AAATTCTCAAGAGAGATAAA 1
//
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Motif 5 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 1.4e-003
162 -982 -982 -982
78 -982 -982 45
162 -982 -982 -982
-982 -982 -982 162
-982 192 -982 4
-982 251 -982 -982
-154 166 -982 4
-982 251 -982 -982
-154 -66 34 78
145 -982 -982 -154
-154 192 -66 -154
-154 -66 92 45
78 -982 134 -982
145 -982 -66 -982
126 -982 34 -982
104 -66 34 -982
104 -66 -66 -154
162 -982 -982 -982
126 -982 34 -982
-55 34 166 -982
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Motif 5 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.4e-003
1.000000 0.000000 0.000000 0.000000
0.555556 0.000000 0.000000 0.444444
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.666667 0.000000 0.333333
0.000000 1.000000 0.000000 0.000000
0.111111 0.555556 0.000000 0.333333
0.000000 1.000000 0.000000 0.000000
0.111111 0.111111 0.222222 0.555556
0.888889 0.000000 0.000000 0.111111
0.111111 0.666667 0.111111 0.111111
0.111111 0.111111 0.333333 0.444444
0.555556 0.000000 0.444444 0.000000
0.888889 0.000000 0.111111 0.000000
0.777778 0.000000 0.222222 0.000000
0.666667 0.111111 0.222222 0.000000
0.666667 0.111111 0.111111 0.111111
1.000000 0.000000 0.000000 0.000000
0.777778 0.000000 0.222222 0.000000
0.222222 0.222222 0.555556 0.000000
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Motif 5 regular expression
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A[AT]AT[CT]C[CT]C[TG]AC[TG][AG]A[AG][AG]AA[AG][GAC]
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Time 12.73 secs.
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SUMMARY OF MOTIFS
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YER014W 3.19e-19 27_[+3(2.26e-07)]_11_[+2(3.35e-08)]_43_[+1(5.95e-11)]_15_[+4(1.64e-08)]_59_[+5(1.24e-06)]_67
MIT_Spar_c425_6072 4.24e-21 58_[+2(2.17e-09)]_42_[+1(1.08e-10)]_15_[+4(3.11e-09)]_56_[+5(1.36e-07)]_29_[-3(8.96e-07)]_22
MIT_Smik_c283_5928 2.54e-17 18_[+3(2.82e-07)]_22_[+2(1.51e-07)]_37_[+1(2.73e-09)]_13_[+4(1.64e-08)]_57_[+5(5.40e-07)]_28_[-3(2.96e-05)]_27
MIT_Sbay_c84_6418 1.73e-17 7_[+3(1.48e-07)]_37_[+2(9.53e-08)]_29_[+1(2.44e-10)]_20_[+5(6.05e-07)]_29_[-4(3.27e-07)]_100
SGD_Scer_YOR176W 1.87e-35 132_[+4(2.43e-11)]_2_[+2(1.72e-12)]_7_[+5(1.61e-11)]_294_[+3(3.87e-12)]_45_[+1(3.57e-13)]_147
MIT_Spar_c278_20970 6.54e-36 134_[+4(8.09e-11)]_2_[+2(1.72e-12)]_7_[+5(1.13e-11)]_155_[-2(5.46e-05)]_119_[+3(5.54e-13)]_45_[+1(3.57e-13)]_145
MIT_Smik_c935_20455 7.71e-32 130_[+4(9.46e-11)]_1_[+2(1.72e-12)]_8_[+5(2.45e-09)]_282_[+3(3.60e-13)]_45_[+1(3.89e-11)]_161
WashU_Skud_Contig2050.4 4.20e-33 135_[+4(3.12e-10)]_5_[+2(4.74e-12)]_8_[+5(2.93e-10)]_290_[+3(1.71e-12)]_50_[+1(3.57e-13)]_69_[-3(1.35e-06)]_50
WashU_Sbay_Contig480.2 1.98e-31 40_[-4(5.82e-05)]_119_[+4(9.46e-11)]_5_[+2(6.16e-10)]_8_[+5(5.39e-12)]_255_[+3(1.71e-12)]_46_[+1(2.79e-11)]_134
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Stopped because nmotifs = 5 reached.
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CPU: dhn02990.mrc-dunn.cam.ac.uk
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