********************************************************************************
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= HEM13-HEM14.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YDR044W 1.0000 1000 MIT_Spar_c130_3912 1.0000 1000
MIT_Sbay_c896_21290 1.0000 1000 WashU_Smik_Contig2283.3 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 HEM13-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= 8 maxsites= 8 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 5288 N= 8
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.305 C 0.195 G 0.195 T 0.305
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 = 8 llr = 168 E-value = 5.3e-017
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 1:::::::::9:::1:114:
pos.-specific C :::494:a:1115a181:::
probability G 9556::5:a9:9::6339:9
matrix T :55:165:::::5:1:5:61
bits 2.5 ** *
2.3 ** *
2.0 *** * *
1.8 * * *** * * * * *
Information 1.5 * ** *** * * * * *
content 1.3 * ** ***** * * * *
(30.2 bits) 1.0 ************** * * *
0.8 **************** ***
0.5 **************** ***
0.3 ********************
0.0 --------------------
Multilevel GGGGCTGCGGAGCCGCTGTG
consensus TTC CT T GG A
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YDR044W + 344 3.65e-14 AAAAGTAGAA GGGCCCGCGGAGCCGCTGTG AAAGATTTCT
MIT_Spar_c425_6072 - 113 1.77e-11 TCGACATTTT GTTGCTTCGGAGTCGCGGAG TATTTAAAAA
SGD_Scer_YER014W - 114 1.77e-11 TCGACACTTT GTTGCTTCGGAGTCGCGGAG TATTCAAAAA
WashU_Smik_Contig2283.3 + 341 8.23e-11 AAAAAGAAAA GGGCCCGCGGCCCCGCCGTG AAACACTTCG
MIT_Spar_c130_3912 + 336 1.07e-10 TAAAAGAAGA AGGGCTGCGGAGCCACTGTG AAAGACTTGT
MIT_Sbay_c896_21290 + 343 2.63e-10 AAAAAGAAAA GGGCCCGCGCAGCCTGTGTG AAATGTTCGT
MIT_Sbay_c84_6418 - 106 8.94e-10 TCGAGATTTT GTTGTTTCGGAGTCGCAGAG TATAAAAAAA
MIT_Smik_c283_5928 - 110 7.48e-09 CTTCGACCTT GTTGCTTCGGAGTCCGTATT TAAAAAAGAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR044W 3.7e-14 343_[+1]_637
MIT_Spar_c425_6072 1.8e-11 112_[-1]_190
SGD_Scer_YER014W 1.8e-11 113_[-1]_189
WashU_Smik_Contig2283.3 8.2e-11 340_[+1]_640
MIT_Spar_c130_3912 1.1e-10 335_[+1]_645
MIT_Sbay_c896_21290 2.6e-10 342_[+1]_638
MIT_Sbay_c84_6418 8.9e-10 105_[-1]_197
MIT_Smik_c283_5928 7.5e-09 109_[-1]_193
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=8
SGD_Scer_YDR044W ( 344) GGGCCCGCGGAGCCGCTGTG 1
MIT_Spar_c425_6072 ( 113) GTTGCTTCGGAGTCGCGGAG 1
SGD_Scer_YER014W ( 114) GTTGCTTCGGAGTCGCGGAG 1
WashU_Smik_Contig2283.3 ( 341) GGGCCCGCGGCCCCGCCGTG 1
MIT_Spar_c130_3912 ( 336) AGGGCTGCGGAGCCACTGTG 1
MIT_Sbay_c896_21290 ( 343) GGGCCCGCGCAGCCTGTGTG 1
MIT_Sbay_c84_6418 ( 106) GTTGTTTCGGAGTCGCAGAG 1
MIT_Smik_c283_5928 ( 110) GTTGCTTCGGAGTCCGTATT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5136 bayes= 9.32418 E= 5.3e-017
-137 -965 232 -965
-965 -965 151 62
-965 -965 151 62
-965 109 183 -965
-965 232 -965 -137
-965 109 -965 95
-965 -965 151 62
-965 251 -965 -965
-965 -965 251 -965
-965 -49 232 -965
143 -49 -965 -965
-965 -49 232 -965
-965 151 -965 62
-965 251 -965 -965
-137 -49 183 -137
-965 209 51 -965
-137 -49 51 62
-137 -965 232 -965
21 -965 -965 95
-965 -965 232 -137
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 5.3e-017
0.125000 0.000000 0.875000 0.000000
0.000000 0.000000 0.500000 0.500000
0.000000 0.000000 0.500000 0.500000
0.000000 0.375000 0.625000 0.000000
0.000000 0.875000 0.000000 0.125000
0.000000 0.375000 0.000000 0.625000
0.000000 0.000000 0.500000 0.500000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.125000 0.875000 0.000000
0.875000 0.125000 0.000000 0.000000
0.000000 0.125000 0.875000 0.000000
0.000000 0.500000 0.000000 0.500000
0.000000 1.000000 0.000000 0.000000
0.125000 0.125000 0.625000 0.125000
0.000000 0.750000 0.250000 0.000000
0.125000 0.125000 0.250000 0.500000
0.125000 0.000000 0.875000 0.000000
0.375000 0.000000 0.000000 0.625000
0.000000 0.000000 0.875000 0.125000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
G[GT][GT][GC]C[TC][GT]CGGAG[CT]CG[CG][TG]G[TA]G
--------------------------------------------------------------------------------
Time 3.15 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 8 llr = 157 E-value = 1.6e-011
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 9453a:aa:aa:5:8185a:
pos.-specific C ::3:::::a::::::4::::
probability G 1638:a::::::5a1434:1
matrix T :::::::::::a::11:1:9
bits 2.5 * * *
2.3 * * *
2.0 * * *
1.8 * * *
Information 1.5 ********* * *
content 1.3 ** ********* * **
(28.3 bits) 1.0 ** *********** * **
0.8 ** ************ * **
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel AGAGAGAACAATAGACAAAT
consensus ACA G GGG
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c425_6072 - 69 2.68e-11 AAAGAATAAT AGAGAGAACAATAGAGAGAT CCGCGAAGGA
MIT_Spar_c130_3912 + 167 9.91e-11 GCCTTTTCGA AACGAGAACAATGGACAAAT CAAGCTTTAT
MIT_Sbay_c896_21290 + 173 2.20e-10 GCTTTCTCGA AGGGAGAACAATGGATAAAT CAAAGCTTAT
SGD_Scer_YER014W - 69 3.83e-10 ATAGTATAAT AGAGAGAACAATAGAGATAT TCGCGAAGAA
WashU_Smik_Contig2283.3 + 163 9.67e-10 GCCTTTTCAA AAAGAGAACAATGGTCAAAT AAAGGTTTAT
SGD_Scer_YDR044W + 171 1.97e-09 AGCCTTTCGA AACGAGAACAATGGGCAAAG CAAGCTTTAT
MIT_Smik_c283_5928 - 71 2.41e-09 AAAGAGTAAT GGAAAGAACAATAGAGGGAT TTGCAAAAGA
MIT_Sbay_c84_6418 - 64 3.09e-09 GAGAACAATA AGGAAGAACAATAGAAGGAT GCGAAAGGAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c425_6072 2.7e-11 68_[-2]_234
MIT_Spar_c130_3912 9.9e-11 166_[+2]_814
MIT_Sbay_c896_21290 2.2e-10 172_[+2]_808
SGD_Scer_YER014W 3.8e-10 68_[-2]_234
WashU_Smik_Contig2283.3 9.7e-10 162_[+2]_818
SGD_Scer_YDR044W 2e-09 170_[+2]_810
MIT_Smik_c283_5928 2.4e-09 70_[-2]_232
MIT_Sbay_c84_6418 3.1e-09 63_[-2]_239
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=8
MIT_Spar_c425_6072 ( 69) AGAGAGAACAATAGAGAGAT 1
MIT_Spar_c130_3912 ( 167) AACGAGAACAATGGACAAAT 1
MIT_Sbay_c896_21290 ( 173) AGGGAGAACAATGGATAAAT 1
SGD_Scer_YER014W ( 69) AGAGAGAACAATAGAGATAT 1
WashU_Smik_Contig2283.3 ( 163) AAAGAGAACAATGGTCAAAT 1
SGD_Scer_YDR044W ( 171) AACGAGAACAATGGGCAAAG 1
MIT_Smik_c283_5928 ( 71) GGAAAGAACAATAGAGGGAT 1
MIT_Sbay_c84_6418 ( 64) AGGAAGAACAATAGAAGGAT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5136 bayes= 9.32418 E= 1.6e-011
143 -965 -49 -965
21 -965 183 -965
62 51 51 -965
-38 -965 209 -965
162 -965 -965 -965
-965 -965 251 -965
162 -965 -965 -965
162 -965 -965 -965
-965 251 -965 -965
162 -965 -965 -965
162 -965 -965 -965
-965 -965 -965 162
62 -965 151 -965
-965 -965 251 -965
121 -965 -49 -137
-137 109 109 -137
121 -965 51 -965
62 -965 109 -137
162 -965 -965 -965
-965 -965 -49 143
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.6e-011
0.875000 0.000000 0.125000 0.000000
0.375000 0.000000 0.625000 0.000000
0.500000 0.250000 0.250000 0.000000
0.250000 0.000000 0.750000 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
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
0.500000 0.000000 0.500000 0.000000
0.000000 0.000000 1.000000 0.000000
0.750000 0.000000 0.125000 0.125000
0.125000 0.375000 0.375000 0.125000
0.750000 0.000000 0.250000 0.000000
0.500000 0.000000 0.375000 0.125000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.125000 0.875000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
A[GA][ACG][GA]AGAACAAT[AG]GA[CG][AG][AG]AT
--------------------------------------------------------------------------------
Time 6.10 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 8 llr = 156 E-value = 2.4e-010
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A ::1:1:::::51:16:9aa9
pos.-specific C :::a:5:4:4:1:::3::::
probability G ::9:45a:::58:54:1:::
matrix T aa::5::6a6::a4:8:::1
bits 2.5 * *
2.3 * *
2.0 * *
1.8 ** *
Information 1.5 **** ** * * **
content 1.3 **** ** * ** ***
(28.1 bits) 1.0 **** ******** ******
0.8 **** ***************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel TTGCTCGTTTAGTGATAAAA
consensus GG C CG TGC
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Smik_Contig2283.3 + 630 6.53e-12 TCTTGAGGAT TTGCGGGTTCGGTGATAAAA AATGTATTGT
MIT_Spar_c130_3912 + 624 2.08e-10 TCTAGAGGAT TTGCAGGCTCGGTGATAAAA TGTATTGTTG
MIT_Smik_c283_5928 - 155 3.18e-10 AAAGCTACCA TTGCTCGTTTAGTTGTAAAA TGCCTTTCAG
SGD_Scer_YER014W - 161 5.75e-10 AAAGCTGCCA TTGCTCGTTTAGTTACAAAA CGCCTTTGAA
SGD_Scer_YDR044W + 629 5.75e-10 TCCAGAGGAT TTGCGGGCTTGATGATAAAA TGTATTGTTG
MIT_Sbay_c896_21290 + 628 2.12e-09 TCTTGGGGAT TTGCGGGCTCGCTAATAAAA AGTGTCTTGT
MIT_Sbay_c84_6418 - 156 3.04e-09 ATAACTGTCA TTGCTCGTTTAGTGGTGAAT ATTTTTACCT
MIT_Spar_c425_6072 - 160 4.65e-09 AAAGCTGCCA TTACTCGTTTAGTTGCAAAA CGCCTTTCAT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Smik_Contig2283.3 6.5e-12 629_[+3]_351
MIT_Spar_c130_3912 2.1e-10 623_[+3]_357
MIT_Smik_c283_5928 3.2e-10 154_[-3]_148
SGD_Scer_YER014W 5.8e-10 160_[-3]_142
SGD_Scer_YDR044W 5.8e-10 628_[+3]_352
MIT_Sbay_c896_21290 2.1e-09 627_[+3]_353
MIT_Sbay_c84_6418 3e-09 155_[-3]_147
MIT_Spar_c425_6072 4.7e-09 159_[-3]_143
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=8
WashU_Smik_Contig2283.3 ( 630) TTGCGGGTTCGGTGATAAAA 1
MIT_Spar_c130_3912 ( 624) TTGCAGGCTCGGTGATAAAA 1
MIT_Smik_c283_5928 ( 155) TTGCTCGTTTAGTTGTAAAA 1
SGD_Scer_YER014W ( 161) TTGCTCGTTTAGTTACAAAA 1
SGD_Scer_YDR044W ( 629) TTGCGGGCTTGATGATAAAA 1
MIT_Sbay_c896_21290 ( 628) TTGCGGGCTCGCTAATAAAA 1
MIT_Sbay_c84_6418 ( 156) TTGCTCGTTTAGTGGTGAAT 1
MIT_Spar_c425_6072 ( 160) TTACTCGTTTAGTTGCAAAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5136 bayes= 9.32418 E= 2.4e-010
-965 -965 -965 162
-965 -965 -965 162
-137 -965 232 -965
-965 251 -965 -965
-137 -965 109 62
-965 151 151 -965
-965 -965 251 -965
-965 109 -965 95
-965 -965 -965 162
-965 109 -965 95
62 -965 151 -965
-137 -49 209 -965
-965 -965 -965 162
-137 -965 151 21
95 -965 109 -965
-965 51 -965 121
143 -965 -49 -965
162 -965 -965 -965
162 -965 -965 -965
143 -965 -965 -137
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 2.4e-010
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.125000 0.000000 0.875000 0.000000
0.000000 1.000000 0.000000 0.000000
0.125000 0.000000 0.375000 0.500000
0.000000 0.500000 0.500000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.375000 0.000000 0.625000
0.000000 0.000000 0.000000 1.000000
0.000000 0.375000 0.000000 0.625000
0.500000 0.000000 0.500000 0.000000
0.125000 0.125000 0.750000 0.000000
0.000000 0.000000 0.000000 1.000000
0.125000 0.000000 0.500000 0.375000
0.625000 0.000000 0.375000 0.000000
0.000000 0.250000 0.000000 0.750000
0.875000 0.000000 0.125000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.875000 0.000000 0.000000 0.125000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
TTGC[TG][CG]G[TC]T[TC][AG]GT[GT][AG][TC]AAAA
--------------------------------------------------------------------------------
Time 8.96 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 15 sites = 8 llr = 123 E-value = 9.2e-006
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 1a9:::aa:1:1a44
pos.-specific C 3::::a:::351:::
probability G 6:1aa:::a5:3:16
matrix T :::::::::155:5:
bits 2.5 *** *
2.3 *** *
2.0 *** *
1.8 *** *
Information 1.5 * ****** *
content 1.3 ******** * *
(22.2 bits) 1.0 ********* * * *
0.8 ********* * * *
0.5 *********** * *
0.3 ***************
0.0 ---------------
Multilevel GAAGGCAAGGCTATG
consensus C CTG AA
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Smik_Contig2283.3 + 710 5.26e-10 ATTAACAAGG GAAGGCAAGGCTATG TTCTATTGAG
MIT_Sbay_c896_21290 + 703 3.55e-09 AAAATATCAA CAAGGCAAGGCTATG CCTTTCGAAG
MIT_Spar_c130_3912 + 702 3.55e-09 ATCAACAGGG CAAGGCAAGGCTATG CTCTTTTGGA
MIT_Smik_c283_5928 + 136 5.90e-08 CAACAAGGTC GAAGGCAAGCTGAAA GGCATTTTAC
MIT_Sbay_c84_6418 + 134 1.20e-07 ACAAAATCTC GAAGGCAAGCTAAGG TAAAAATATT
SGD_Scer_YDR044W + 705 1.33e-07 ATATCAACAA AAGGGCAAGGCTATG CCTTCTGGAA
MIT_Spar_c425_6072 + 141 1.99e-07 ACAAAATGTC GAAGGCAAGATGAAA GGCGTTTTGC
SGD_Scer_YER014W + 142 3.03e-07 ACAAAGTGTC GAAGGCAAGTTCAAA GGCGTTTTGT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Smik_Contig2283.3 5.3e-10 709_[+4]_276
MIT_Sbay_c896_21290 3.5e-09 702_[+4]_283
MIT_Spar_c130_3912 3.5e-09 701_[+4]_284
MIT_Smik_c283_5928 5.9e-08 135_[+4]_172
MIT_Sbay_c84_6418 1.2e-07 133_[+4]_174
SGD_Scer_YDR044W 1.3e-07 704_[+4]_281
MIT_Spar_c425_6072 2e-07 140_[+4]_167
SGD_Scer_YER014W 3e-07 141_[+4]_166
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=15 seqs=8
WashU_Smik_Contig2283.3 ( 710) GAAGGCAAGGCTATG 1
MIT_Sbay_c896_21290 ( 703) CAAGGCAAGGCTATG 1
MIT_Spar_c130_3912 ( 702) CAAGGCAAGGCTATG 1
MIT_Smik_c283_5928 ( 136) GAAGGCAAGCTGAAA 1
MIT_Sbay_c84_6418 ( 134) GAAGGCAAGCTAAGG 1
SGD_Scer_YDR044W ( 705) AAGGGCAAGGCTATG 1
MIT_Spar_c425_6072 ( 141) GAAGGCAAGATGAAA 1
SGD_Scer_YER014W ( 142) GAAGGCAAGTTCAAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 5176 bayes= 9.33539 E= 9.2e-006
-137 51 183 -965
162 -965 -965 -965
143 -965 -49 -965
-965 -965 251 -965
-965 -965 251 -965
-965 251 -965 -965
162 -965 -965 -965
162 -965 -965 -965
-965 -965 251 -965
-137 51 151 -137
-965 151 -965 62
-137 -49 51 62
162 -965 -965 -965
21 -965 -49 62
21 -965 183 -965
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 9.2e-006
0.125000 0.250000 0.625000 0.000000
1.000000 0.000000 0.000000 0.000000
0.875000 0.000000 0.125000 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
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.125000 0.250000 0.500000 0.125000
0.000000 0.500000 0.000000 0.500000
0.125000 0.125000 0.250000 0.500000
1.000000 0.000000 0.000000 0.000000
0.375000 0.000000 0.125000 0.500000
0.375000 0.000000 0.625000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[GC]AAGGCAAG[GC][CT][TG]A[TA][GA]
--------------------------------------------------------------------------------
Time 11.74 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 19 sites = 8 llr = 137 E-value = 5.5e-005
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 5a559:a:3::1a5aaa98
pos.-specific C ::51:::::15:::::::1
probability G 5:::1::a8:54:::::1:
matrix T :::4:a:::9:5:5::::1
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 AAAAATAGGTCTAAAAAAA
consensus G CT A GG T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- -------------------
WashU_Smik_Contig2283.3 + 112 5.17e-11 TAACAGGTGA GACAATAGGTGGAAAAAAA GGAAAATATG
SGD_Scer_YDR044W + 119 5.17e-11 AACAAAGAAA GACAATAGGTGGAAAAAAA AAGGAAAATC
MIT_Spar_c425_6072 + 277 1.49e-09 ACCGAAGAAT GAATATAGGTCTATAAAAA TTCAATAATT
MIT_Spar_c130_3912 + 116 1.75e-09 AACAAAGAAA GACAATAGGCGGAAAAAAA GGAAAATCCG
MIT_Sbay_c896_21290 + 120 6.56e-09 ATTGGCAGCG AACAATAGGTGAAAAAAAA AAAGAAAATG
SGD_Scer_YER014W + 270 1.56e-08 TTAAAAAATT AAATATAGGTCTATAAAAC TCGATAATTA
MIT_Smik_c283_5928 + 272 2.46e-08 ATCAAATGTT AAATATAGATCTATAAAAA TTGAATAGTA
MIT_Sbay_c84_6418 + 261 1.48e-07 TATTTATATT AAACGTAGATCTATAAAGT TTAAATAGTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Smik_Contig2283.3 5.2e-11 111_[+5]_870
SGD_Scer_YDR044W 5.2e-11 118_[+5]_863
MIT_Spar_c425_6072 1.5e-09 276_[+5]_27
MIT_Spar_c130_3912 1.8e-09 115_[+5]_866
MIT_Sbay_c896_21290 6.6e-09 119_[+5]_862
SGD_Scer_YER014W 1.6e-08 269_[+5]_34
MIT_Smik_c283_5928 2.5e-08 271_[+5]_32
MIT_Sbay_c84_6418 1.5e-07 260_[+5]_43
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=19 seqs=8
WashU_Smik_Contig2283.3 ( 112) GACAATAGGTGGAAAAAAA 1
SGD_Scer_YDR044W ( 119) GACAATAGGTGGAAAAAAA 1
MIT_Spar_c425_6072 ( 277) GAATATAGGTCTATAAAAA 1
MIT_Spar_c130_3912 ( 116) GACAATAGGCGGAAAAAAA 1
MIT_Sbay_c896_21290 ( 120) AACAATAGGTGAAAAAAAA 1
SGD_Scer_YER014W ( 270) AAATATAGGTCTATAAAAC 1
MIT_Smik_c283_5928 ( 272) AAATATAGATCTATAAAAA 1
MIT_Sbay_c84_6418 ( 261) AAACGTAGATCTATAAAGT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 19 n= 5144 bayes= 9.32643 E= 5.5e-005
62 -965 151 -965
162 -965 -965 -965
62 151 -965 -965
62 -49 -965 21
143 -965 -49 -965
-965 -965 -965 162
162 -965 -965 -965
-965 -965 251 -965
-38 -965 209 -965
-965 -49 -965 143
-965 151 151 -965
-137 -965 109 62
162 -965 -965 -965
62 -965 -965 62
162 -965 -965 -965
162 -965 -965 -965
162 -965 -965 -965
143 -965 -49 -965
121 -49 -965 -137
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 19 nsites= 8 E= 5.5e-005
0.500000 0.000000 0.500000 0.000000
1.000000 0.000000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.500000 0.125000 0.000000 0.375000
0.875000 0.000000 0.125000 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
0.250000 0.000000 0.750000 0.000000
0.000000 0.125000 0.000000 0.875000
0.000000 0.500000 0.500000 0.000000
0.125000 0.000000 0.375000 0.500000
1.000000 0.000000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.875000 0.000000 0.125000 0.000000
0.750000 0.125000 0.000000 0.125000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
[AG]A[AC][AT]ATAG[GA]T[CG][TG]A[AT]AAAAA
--------------------------------------------------------------------------------
Time 14.61 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR044W 1.10e-26 118_[+5(5.17e-11)]_33_[+2(1.97e-09)]_153_[+1(3.65e-14)]_265_[+3(5.75e-10)]_56_[+4(1.33e-07)]_153_[+2(7.52e-05)]_108
MIT_Spar_c130_3912 4.24e-25 115_[+5(1.75e-09)]_32_[+2(9.91e-11)]_149_[+1(1.07e-10)]_268_[+3(2.08e-10)]_58_[+4(3.55e-09)]_254_[-4(6.48e-05)]_15
MIT_Sbay_c896_21290 6.48e-23 119_[+5(6.56e-09)]_34_[+2(2.20e-10)]_114_[+1(4.06e-05)]_16_[+1(2.63e-10)]_265_[+3(2.12e-09)]_55_[+4(3.55e-09)]_283
WashU_Smik_Contig2283.3 6.34e-28 111_[+5(5.17e-11)]_32_[+2(9.67e-10)]_158_[+1(8.23e-11)]_5_[-4(1.66e-05)]_249_[+3(6.53e-12)]_60_[+4(5.26e-10)]_276
SGD_Scer_YER014W 1.51e-24 68_[-2(3.83e-10)]_25_[-1(1.77e-11)]_8_[+4(3.03e-07)]_4_[-3(5.75e-10)]_89_[+5(1.56e-08)]_34
MIT_Spar_c425_6072 6.46e-26 68_[-2(2.68e-11)]_24_[-1(1.77e-11)]_8_[+4(1.99e-07)]_4_[-3(4.65e-09)]_97_[+5(1.49e-09)]_6_[+5(6.43e-06)]_2
MIT_Smik_c283_5928 4.72e-22 70_[-2(2.41e-09)]_19_[-1(7.48e-09)]_6_[+4(5.90e-08)]_4_[-3(3.18e-10)]_97_[+5(2.46e-08)]_32
MIT_Sbay_c84_6418 7.03e-21 63_[-2(3.09e-09)]_22_[-1(8.94e-10)]_8_[+4(1.20e-07)]_7_[-3(3.04e-09)]_85_[+5(1.48e-07)]_43
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************