********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date: )
For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.
This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs. MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************
********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:
Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************
********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM1-HEM2.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YDR232W 1.0000 498 MIT_Spar_c117_4603 1.0000 498
MIT_Smik_c228_4055 1.0000 498 WashU_Skud_Contig2069.5 1.0000 498
WashU_Sbay_Contig461.5 1.0000 498 SGD_Scer_YGL040C 1.0000 1000
MIT_Spar_c19_8512 1.0000 1000 MIT_Smik_c273_7756 1.0000 1000
MIT_Sbay_c77_8808 1.0000 1000 WashU_Skud_Contig2052.17 1.0000 1000
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM1-HEM2.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= 10 maxsites= 10 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 7490 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.310 C 0.190 G 0.190 T 0.310
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 = 10 llr = 251 E-value = 7.9e-043
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 1::::a15::aa::a:::55
pos.-specific C :8a:a:::aa:::5:5a:55
probability G 92:6::95:::::5:5:a::
matrix T :::4::::::::a:::::::
bits 2.5 * * ** **
2.3 * * ** **
2.0 * * * * ** **
1.8 *** * * ** **
Information 1.5 *** *** **********
content 1.3 ******* **********
(36.3 bits) 1.0 ********************
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GCCGCAGACCAATCACCGAA
consensus G T G G G CC
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Sbay_c77_8808 + 178 4.37e-13 CAGGCAGCCT GCCGCAGGCCAATCACCGCA CCGCCCGGAG
WashU_Skud_Contig2069.5 + 362 1.24e-12 AGCGTCCGCG GCCGCAGACCAATGAGCGAC GAAGGCGGCC
MIT_Spar_c117_4603 + 360 1.24e-12 AGCGCCCGCG GCCGCAGACCAATGAGCGAC GAAGGCGGCC
SGD_Scer_YDR232W + 365 1.24e-12 AGCGCCCGCG GCCGCAGACCAATGAGCGAC GAAGGCGGCC
WashU_Skud_Contig2052.17 + 177 1.99e-12 CAGGCAGCTT GCCTCAGGCCAATCACCGCA CCGAACAGGG
MIT_Smik_c273_7756 + 176 1.99e-12 AGTGTATGTT GCCTCAGGCCAATCACCGCA CCGAATAAGG
MIT_Spar_c19_8512 + 178 1.99e-12 CGGGCAGCTT GCCTCAGGCCAATCACCGCA CCGAACAGGG
WashU_Sbay_Contig461.5 + 359 4.86e-12 AACGCCGGCG GGCGCAGACCAATGAGCGAC GAAGACGGCT
SGD_Scer_YGL040C + 177 1.62e-11 CGGGAAGCTT GCCTCAAGCCAATCACCGCA CCGAACAGGG
MIT_Smik_c228_4055 + 362 2.67e-11 AGCGCCCGCA AGCGCAGACCAATGAGCGAC GAAAGCGGCC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Sbay_c77_8808 4.4e-13 177_[+1]_803
WashU_Skud_Contig2069.5 1.2e-12 361_[+1]_117
MIT_Spar_c117_4603 1.2e-12 359_[+1]_119
SGD_Scer_YDR232W 1.2e-12 364_[+1]_114
WashU_Skud_Contig2052.17 2e-12 176_[+1]_804
MIT_Smik_c273_7756 2e-12 175_[+1]_805
MIT_Spar_c19_8512 2e-12 177_[+1]_803
WashU_Sbay_Contig461.5 4.9e-12 358_[+1]_120
SGD_Scer_YGL040C 1.6e-11 176_[+1]_804
MIT_Smik_c228_4055 2.7e-11 361_[+1]_117
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=10
MIT_Sbay_c77_8808 ( 178) GCCGCAGGCCAATCACCGCA 1
WashU_Skud_Contig2069.5 ( 362) GCCGCAGACCAATGAGCGAC 1
MIT_Spar_c117_4603 ( 360) GCCGCAGACCAATGAGCGAC 1
SGD_Scer_YDR232W ( 365) GCCGCAGACCAATGAGCGAC 1
WashU_Skud_Contig2052.17 ( 177) GCCTCAGGCCAATCACCGCA 1
MIT_Smik_c273_7756 ( 176) GCCTCAGGCCAATCACCGCA 1
MIT_Spar_c19_8512 ( 178) GCCTCAGGCCAATCACCGCA 1
WashU_Sbay_Contig461.5 ( 359) GGCGCAGACCAATGAGCGAC 1
SGD_Scer_YGL040C ( 177) GCCTCAAGCCAATCACCGCA 1
MIT_Smik_c228_4055 ( 362) AGCGCAGACCAATGAGCGAC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7300 bayes= 9.50978 E= 7.9e-043
-169 -997 236 -997
-997 219 19 -997
-997 251 -997 -997
-997 -997 177 30
-997 251 -997 -997
162 -997 -997 -997
-169 -997 236 -997
62 -997 151 -997
-997 251 -997 -997
-997 251 -997 -997
162 -997 -997 -997
162 -997 -997 -997
-997 -997 -997 162
-997 151 151 -997
162 -997 -997 -997
-997 151 151 -997
-997 251 -997 -997
-997 -997 251 -997
62 151 -997 -997
62 151 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 7.9e-043
0.100000 0.000000 0.900000 0.000000
0.000000 0.800000 0.200000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.600000 0.400000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.100000 0.000000 0.900000 0.000000
0.500000 0.000000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.500000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.500000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
G[CG]C[GT]CAG[AG]CCAAT[CG]A[CG]CG[AC][AC]
--------------------------------------------------------------------------------
Time 5.77 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 10 llr = 206 E-value = 2.0e-023
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 9659a4:5:1a9:::aa:6:
pos.-specific C 1:5::::::7::::a::422
probability G ::::::a5a::1aa:::51:
matrix T :4:1:6:::2:::::::118
bits 2.5 * * ***
2.3 * * ***
2.0 * * ***
1.8 * * ***
Information 1.5 * * * * *****
content 1.3 * ** * * *******
(29.7 bits) 1.0 * *** ************ *
0.8 ****************** *
0.5 ****************** *
0.3 ********************
0.0 --------------------
Multilevel AAAAATGAGCAAGGCAAGAT
consensus TC A G T CCC
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig461.5 + 279 6.64e-13 ACCGGGACAG AACAATGGGCAAGGCAAGAT GAAAAATCTC
MIT_Smik_c228_4055 + 284 6.64e-13 ATTGAATTAG AACAATGGGCAAGGCAAGAT GAAAATTTCC
MIT_Spar_c117_4603 + 281 6.64e-13 CATGGGTCAG AACAATGGGCAAGGCAAGAT GAAAAATTTC
SGD_Scer_YDR232W + 286 6.64e-13 CATGGATCAG AACAATGGGCAAGGCAAGAT GAAAAATTTC
MIT_Sbay_c77_8808 - 144 2.57e-10 TGCCTGATTT ATAAAAGAGCAAGGCAACAC AATAAAAGGC
WashU_Skud_Contig2069.5 + 284 3.77e-10 ACTGGATCGG AACAATGGGCAAGGCAATGT GAAAAATTTC
MIT_Spar_c19_8512 - 140 1.08e-09 CGCTTGATTT ATAAAAGAGTAAGGCAACCT AATAAATGCT
MIT_Smik_c273_7756 - 833 1.52e-09 TCGTTTTCTA CAAAATGAGCAGGGCAAGAC GAAATTTCCG
WashU_Skud_Contig2052.17 - 139 3.25e-09 TGCCCAATTT ATAAAAGAGAAAGGCAACTT ATATGAAGAG
SGD_Scer_YGL040C - 139 3.61e-09 CGCTTGATTT ATATAAGAGTAAGGCAACCT AATAAATGCT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig461.5 6.6e-13 278_[+2]_200
MIT_Smik_c228_4055 6.6e-13 283_[+2]_195
MIT_Spar_c117_4603 6.6e-13 280_[+2]_198
SGD_Scer_YDR232W 6.6e-13 285_[+2]_193
MIT_Sbay_c77_8808 2.6e-10 143_[-2]_837
WashU_Skud_Contig2069.5 3.8e-10 283_[+2]_195
MIT_Spar_c19_8512 1.1e-09 139_[-2]_841
MIT_Smik_c273_7756 1.5e-09 832_[-2]_148
WashU_Skud_Contig2052.17 3.3e-09 138_[-2]_842
SGD_Scer_YGL040C 3.6e-09 138_[-2]_842
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=10
WashU_Sbay_Contig461.5 ( 279) AACAATGGGCAAGGCAAGAT 1
MIT_Smik_c228_4055 ( 284) AACAATGGGCAAGGCAAGAT 1
MIT_Spar_c117_4603 ( 281) AACAATGGGCAAGGCAAGAT 1
SGD_Scer_YDR232W ( 286) AACAATGGGCAAGGCAAGAT 1
MIT_Sbay_c77_8808 ( 144) ATAAAAGAGCAAGGCAACAC 1
WashU_Skud_Contig2069.5 ( 284) AACAATGGGCAAGGCAATGT 1
MIT_Spar_c19_8512 ( 140) ATAAAAGAGTAAGGCAACCT 1
MIT_Smik_c273_7756 ( 833) CAAAATGAGCAGGGCAAGAC 1
WashU_Skud_Contig2052.17 ( 139) ATAAAAGAGAAAGGCAACTT 1
SGD_Scer_YGL040C ( 139) ATATAAGAGTAAGGCAACCT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7300 bayes= 9.50978 E= 2.0e-023
147 -81 -997 -997
89 -997 -997 30
62 151 -997 -997
147 -997 -997 -169
162 -997 -997 -997
30 -997 -997 89
-997 -997 251 -997
62 -997 151 -997
-997 -997 251 -997
-169 199 -997 -70
162 -997 -997 -997
147 -997 -81 -997
-997 -997 251 -997
-997 -997 251 -997
-997 251 -997 -997
162 -997 -997 -997
162 -997 -997 -997
-997 119 151 -169
89 19 -81 -169
-997 19 -997 130
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.0e-023
0.900000 0.100000 0.000000 0.000000
0.600000 0.000000 0.000000 0.400000
0.500000 0.500000 0.000000 0.000000
0.900000 0.000000 0.000000 0.100000
1.000000 0.000000 0.000000 0.000000
0.400000 0.000000 0.000000 0.600000
0.000000 0.000000 1.000000 0.000000
0.500000 0.000000 0.500000 0.000000
0.000000 0.000000 1.000000 0.000000
0.100000 0.700000 0.000000 0.200000
1.000000 0.000000 0.000000 0.000000
0.900000 0.000000 0.100000 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 0.400000 0.500000 0.100000
0.600000 0.200000 0.100000 0.100000
0.000000 0.200000 0.000000 0.800000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
A[AT][AC]AA[TA]G[AG]G[CT]AAGGCAA[GC][AC][TC]
--------------------------------------------------------------------------------
Time 11.41 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 10 llr = 182 E-value = 4.3e-014
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A ::::1:::a5::::2:::1:
pos.-specific C :6:a:4:5:5a8:::51156
probability G 54::5::::::29:131213
matrix T 5:a:46a5::::1a728731
bits 2.5 * *
2.3 * *
2.0 * * *
1.8 * ***
Information 1.5 *** * * ****
content 1.3 *** * * ****
(26.3 bits) 1.0 **** ********* * *
0.8 ************** *** *
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GCTCGTTCAACCGTTCTTCC
consensus TG TC T C G AG GTG
sequence T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c273_7756 + 209 2.78e-11 AATAAGGATT GCTCGTTTACCCGTTGTTCG ATTTTTTTTT
MIT_Spar_c117_4603 - 160 3.34e-11 CCTGCTCTGC TCTCTCTCAACCGTTCTTCC TTTACACGCC
WashU_Skud_Contig2069.5 - 162 7.41e-11 TGTGCTCTGC TGTCTCTCAACCGTTCTTCC CTCCACACGG
SGD_Scer_YDR232W - 165 7.41e-11 CCTGCTCTGC TGTCTCTCAACCGTTCTTCC TTTACACGCC
WashU_Sbay_Contig461.5 - 161 6.43e-10 CCTGCTCTGT TGTCTCTCAACGGTTCTTCC CTCCACACGC
MIT_Spar_c19_8512 + 211 1.23e-09 AACAGGGATT GCTCGTTTACCCGTAGTTTG AATTTTTTTT
SGD_Scer_YGL040C + 210 3.72e-09 AACAGGGATT GCTCGTTTACCCGTATTTTG ATTTTTTTTT
MIT_Smik_c228_4055 - 161 8.54e-09 CCTCCTCTAC TGTCATTCAACCGTTCTGGC TTCACACGTC
WashU_Skud_Contig2052.17 + 210 1.35e-08 AACAGGGATT GCTCGTTTACCCGTTGCGTT CAAAGTTTTT
MIT_Sbay_c77_8808 + 210 2.19e-07 GCCCGGAGAT GCTCGTTTACCGTTGTGCAC CAAATTTTTC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c273_7756 2.8e-11 208_[+3]_772
MIT_Spar_c117_4603 3.3e-11 159_[-3]_319
WashU_Skud_Contig2069.5 7.4e-11 161_[-3]_317
SGD_Scer_YDR232W 7.4e-11 164_[-3]_314
WashU_Sbay_Contig461.5 6.4e-10 160_[-3]_318
MIT_Spar_c19_8512 1.2e-09 210_[+3]_770
SGD_Scer_YGL040C 3.7e-09 209_[+3]_771
MIT_Smik_c228_4055 8.5e-09 160_[-3]_318
WashU_Skud_Contig2052.17 1.3e-08 209_[+3]_771
MIT_Sbay_c77_8808 2.2e-07 209_[+3]_771
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=10
MIT_Smik_c273_7756 ( 209) GCTCGTTTACCCGTTGTTCG 1
MIT_Spar_c117_4603 ( 160) TCTCTCTCAACCGTTCTTCC 1
WashU_Skud_Contig2069.5 ( 162) TGTCTCTCAACCGTTCTTCC 1
SGD_Scer_YDR232W ( 165) TGTCTCTCAACCGTTCTTCC 1
WashU_Sbay_Contig461.5 ( 161) TGTCTCTCAACGGTTCTTCC 1
MIT_Spar_c19_8512 ( 211) GCTCGTTTACCCGTAGTTTG 1
SGD_Scer_YGL040C ( 210) GCTCGTTTACCCGTATTTTG 1
MIT_Smik_c228_4055 ( 161) TGTCATTCAACCGTTCTGGC 1
WashU_Skud_Contig2052.17 ( 210) GCTCGTTTACCCGTTGCGTT 1
MIT_Sbay_c77_8808 ( 210) GCTCGTTTACCGTTGTGCAC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7300 bayes= 9.50978 E= 4.3e-014
-997 -997 151 62
-997 177 119 -997
-997 -997 -997 162
-997 251 -997 -997
-169 -997 151 30
-997 119 -997 89
-997 -997 -997 162
-997 151 -997 62
162 -997 -997 -997
62 151 -997 -997
-997 251 -997 -997
-997 219 19 -997
-997 -997 236 -169
-997 -997 -997 162
-70 -997 -81 111
-997 151 77 -70
-997 -81 -81 130
-997 -81 19 111
-169 151 -81 -11
-997 177 77 -169
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 4.3e-014
0.000000 0.000000 0.500000 0.500000
0.000000 0.600000 0.400000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.100000 0.000000 0.500000 0.400000
0.000000 0.400000 0.000000 0.600000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.000000 0.500000
1.000000 0.000000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.800000 0.200000 0.000000
0.000000 0.000000 0.900000 0.100000
0.000000 0.000000 0.000000 1.000000
0.200000 0.000000 0.100000 0.700000
0.000000 0.500000 0.300000 0.200000
0.000000 0.100000 0.100000 0.800000
0.000000 0.100000 0.200000 0.700000
0.100000 0.500000 0.100000 0.300000
0.000000 0.600000 0.300000 0.100000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
[GT][CG]TC[GT][TC]T[CT]A[AC]C[CG]GT[TA][CGT]T[TG][CT][CG]
--------------------------------------------------------------------------------
Time 17.19 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 10 llr = 181 E-value = 1.3e-014
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A :::::::1::1211:1:9:9
pos.-specific C :::a8:17:6:1:7:1913:
probability G 8:1:2:91::::3:221:1:
matrix T 2a9::a:1a4976286::61
bits 2.5 *
2.3 *
2.0 * * *
1.8 ** * *
Information 1.5 ** **** * *
content 1.3 ******* *** ** *
(26.1 bits) 1.0 *********** ** ** *
0.8 *********** ** ****
0.5 *************** ****
0.3 ********************
0.0 --------------------
Multilevel GTTCCTGCTCTTTCTTCATA
consensus T G T AGTGG C
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c228_4055 + 314 1.23e-12 GAAAATTTCC GTTCCTGCTCTTTCTTCATA TATGAACAAT
MIT_Spar_c117_4603 + 312 1.23e-12 AAAAATTTCT GTTCCTGCTCTTTCTTCATA TATGAACAAT
SGD_Scer_YDR232W + 317 1.23e-12 AAAAATTTCC GTTCCTGCTCTTTCTTCATA TATGAACAAT
WashU_Skud_Contig2069.5 + 315 2.56e-12 AAAAATTTCC GTTCCTGCTCTTGCTTCATA TATGACAATG
WashU_Sbay_Contig461.5 + 310 7.98e-11 AAAAATCTCC GTTCCTGCTCTTGCTTGATA TATTAACAAT
MIT_Spar_c19_8512 - 909 2.03e-10 ATCTACAATA GTTCCTGCTTTTTTTTCACA TCTATTTTCA
WashU_Skud_Contig2052.17 + 317 7.48e-08 AATGATTTAT GTTCGTGTTTTCACGGCACA AAGGTAGGCA
MIT_Smik_c273_7756 - 85 8.28e-08 TCATTCTATT GTTCCTGATTTATTGGCCTA TTTAGCTATA
MIT_Sbay_c77_8808 + 596 3.07e-07 ATATCTTATT TTGCGTGGTTTATCTACAGA CACTGCTTGA
SGD_Scer_YGL040C - 741 3.58e-07 GACGGTTAGC TTTCCTCCTCATGATCCACT CTTTCGGGAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c228_4055 1.2e-12 313_[+4]_165
MIT_Spar_c117_4603 1.2e-12 311_[+4]_167
SGD_Scer_YDR232W 1.2e-12 316_[+4]_162
WashU_Skud_Contig2069.5 2.6e-12 314_[+4]_164
WashU_Sbay_Contig461.5 8e-11 309_[+4]_169
MIT_Spar_c19_8512 2e-10 908_[-4]_72
WashU_Skud_Contig2052.17 7.5e-08 316_[+4]_664
MIT_Smik_c273_7756 8.3e-08 84_[-4]_896
MIT_Sbay_c77_8808 3.1e-07 595_[+4]_385
SGD_Scer_YGL040C 3.6e-07 740_[-4]_240
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=10
MIT_Smik_c228_4055 ( 314) GTTCCTGCTCTTTCTTCATA 1
MIT_Spar_c117_4603 ( 312) GTTCCTGCTCTTTCTTCATA 1
SGD_Scer_YDR232W ( 317) GTTCCTGCTCTTTCTTCATA 1
WashU_Skud_Contig2069.5 ( 315) GTTCCTGCTCTTGCTTCATA 1
WashU_Sbay_Contig461.5 ( 310) GTTCCTGCTCTTGCTTGATA 1
MIT_Spar_c19_8512 ( 909) GTTCCTGCTTTTTTTTCACA 1
WashU_Skud_Contig2052.17 ( 317) GTTCGTGTTTTCACGGCACA 1
MIT_Smik_c273_7756 ( 85) GTTCCTGATTTATTGGCCTA 1
MIT_Sbay_c77_8808 ( 596) TTGCGTGGTTTATCTACAGA 1
SGD_Scer_YGL040C ( 741) TTTCCTCCTCATGATCCACT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7300 bayes= 9.50978 E= 1.3e-014
-997 -997 219 -70
-997 -997 -997 162
-997 -997 -81 147
-997 251 -997 -997
-997 219 19 -997
-997 -997 -997 162
-997 -81 236 -997
-169 199 -81 -169
-997 -997 -997 162
-997 177 -997 30
-169 -997 -997 147
-70 -81 -997 111
-169 -997 77 89
-169 199 -997 -70
-997 -997 19 130
-169 -81 19 89
-997 236 -81 -997
147 -81 -997 -997
-997 77 -81 89
147 -997 -997 -169
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.3e-014
0.000000 0.000000 0.800000 0.200000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.100000 0.900000
0.000000 1.000000 0.000000 0.000000
0.000000 0.800000 0.200000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.100000 0.900000 0.000000
0.100000 0.700000 0.100000 0.100000
0.000000 0.000000 0.000000 1.000000
0.000000 0.600000 0.000000 0.400000
0.100000 0.000000 0.000000 0.900000
0.200000 0.100000 0.000000 0.700000
0.100000 0.000000 0.300000 0.600000
0.100000 0.700000 0.000000 0.200000
0.000000 0.000000 0.200000 0.800000
0.100000 0.100000 0.200000 0.600000
0.000000 0.900000 0.100000 0.000000
0.900000 0.100000 0.000000 0.000000
0.000000 0.300000 0.100000 0.600000
0.900000 0.000000 0.000000 0.100000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[GT]TTC[CG]TGCT[CT]T[TA][TG][CT][TG][TG]CA[TC]A
--------------------------------------------------------------------------------
Time 22.88 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 10 llr = 171 E-value = 6.2e-010
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A :a91:9:29997843:1221
pos.-specific C 9::1:1961:::2:524861
probability G ::1:a:::::12:6:73:18
matrix T 1::8::12:1:1::212:1:
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 CAATGACCAAAAAGCGCCCG
consensus A GCAACGAA
sequence T T T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c228_4055 + 340 1.95e-13 CATATATGAA CAATGACCAAAAAGCGCCCG CAAGCGCAGA
MIT_Spar_c117_4603 + 338 1.95e-13 CATATATGAA CAATGACCAAAAAGCGCCCG CGGCCGCAGA
SGD_Scer_YDR232W + 343 1.95e-13 CATATATGAA CAATGACCAAAAAGCGCCCG CGGCCGCAGA
WashU_Skud_Contig2069.5 + 340 2.44e-12 TCATATATGA CAATGACCAAAAAGCGTCCG CGGCCGCAGA
WashU_Sbay_Contig461.5 + 336 1.31e-10 GATATATTAA CAATGACCAAAAAAACGCCG GCGGGCGCAG
MIT_Smik_c273_7756 + 527 5.44e-08 TTTTTCTTTA CAATGCTTAAAACAAGGCCG CACAGAACTA
SGD_Scer_YGL040C + 97 4.33e-07 GCAAGAAAAT CAAAGACAATAGAGTGGCGC ATAGATGTTG
MIT_Spar_c19_8512 - 459 5.04e-07 TGTGAAGATT CAGTGACACAAGAGCCAAAG AAGGCAAAAC
MIT_Sbay_c77_8808 - 889 9.84e-07 GACATCGCCA TAACGACTAAATAAAGTCTG TGAGTCTCTG
WashU_Skud_Contig2052.17 - 280 1.03e-06 ATTTCAAGAT CAATGACCAAGACATTCAAA AACGGCGTCA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c228_4055 1.9e-13 339_[+5]_139
MIT_Spar_c117_4603 1.9e-13 337_[+5]_141
SGD_Scer_YDR232W 1.9e-13 342_[+5]_136
WashU_Skud_Contig2069.5 2.4e-12 339_[+5]_139
WashU_Sbay_Contig461.5 1.3e-10 335_[+5]_143
MIT_Smik_c273_7756 5.4e-08 526_[+5]_454
SGD_Scer_YGL040C 4.3e-07 96_[+5]_884
MIT_Spar_c19_8512 5e-07 458_[-5]_522
MIT_Sbay_c77_8808 9.8e-07 888_[-5]_92
WashU_Skud_Contig2052.17 1e-06 279_[-5]_701
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=10
MIT_Smik_c228_4055 ( 340) CAATGACCAAAAAGCGCCCG 1
MIT_Spar_c117_4603 ( 338) CAATGACCAAAAAGCGCCCG 1
SGD_Scer_YDR232W ( 343) CAATGACCAAAAAGCGCCCG 1
WashU_Skud_Contig2069.5 ( 340) CAATGACCAAAAAGCGTCCG 1
WashU_Sbay_Contig461.5 ( 336) CAATGACCAAAAAAACGCCG 1
MIT_Smik_c273_7756 ( 527) CAATGCTTAAAACAAGGCCG 1
SGD_Scer_YGL040C ( 97) CAAAGACAATAGAGTGGCGC 1
MIT_Spar_c19_8512 ( 459) CAGTGACACAAGAGCCAAAG 1
MIT_Sbay_c77_8808 ( 889) TAACGACTAAATAAAGTCTG 1
WashU_Skud_Contig2052.17 ( 280) CAATGACCAAGACATTCAAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7300 bayes= 9.50978 E= 6.2e-010
-997 236 -997 -169
162 -997 -997 -997
147 -997 -81 -997
-169 -81 -997 130
-997 -997 251 -997
147 -81 -997 -997
-997 236 -997 -169
-70 177 -997 -70
147 -81 -997 -997
147 -997 -997 -169
147 -997 -81 -997
111 -997 19 -169
130 19 -997 -997
30 -997 177 -997
-11 151 -997 -70
-997 19 199 -169
-169 119 77 -70
-70 219 -997 -997
-70 177 -81 -169
-169 -81 219 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.2e-010
0.000000 0.900000 0.000000 0.100000
1.000000 0.000000 0.000000 0.000000
0.900000 0.000000 0.100000 0.000000
0.100000 0.100000 0.000000 0.800000
0.000000 0.000000 1.000000 0.000000
0.900000 0.100000 0.000000 0.000000
0.000000 0.900000 0.000000 0.100000
0.200000 0.600000 0.000000 0.200000
0.900000 0.100000 0.000000 0.000000
0.900000 0.000000 0.000000 0.100000
0.900000 0.000000 0.100000 0.000000
0.700000 0.000000 0.200000 0.100000
0.800000 0.200000 0.000000 0.000000
0.400000 0.000000 0.600000 0.000000
0.300000 0.500000 0.000000 0.200000
0.000000 0.200000 0.700000 0.100000
0.100000 0.400000 0.300000 0.200000
0.200000 0.800000 0.000000 0.000000
0.200000 0.600000 0.100000 0.100000
0.100000 0.100000 0.800000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
CAATGAC[CAT]AAA[AG][AC][GA][CAT][GC][CGT][CA][CA]G
--------------------------------------------------------------------------------
Time 28.31 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR232W 5.36e-38 124_[+2(1.97e-05)]_20_[-3(7.41e-11)]_101_[+2(6.64e-13)]_11_[+4(1.23e-12)]_6_[+5(1.95e-13)]_2_[+1(1.24e-12)]_114
MIT_Spar_c117_4603 2.49e-38 [-4(3.67e-05)]_139_[-3(3.34e-11)]_101_[+2(6.64e-13)]_11_[+4(1.23e-12)]_6_[+5(1.95e-13)]_2_[+1(1.24e-12)]_119
MIT_Smik_c228_4055 9.65e-35 120_[+2(2.17e-05)]_20_[-3(8.54e-09)]_47_[-1(1.92e-05)]_36_[+2(6.64e-13)]_10_[+4(1.23e-12)]_6_[+5(1.95e-13)]_2_[+1(2.67e-11)]_117
WashU_Skud_Contig2069.5 5.35e-34 82_[-4(9.25e-05)]_15_[-4(3.28e-05)]_24_[-3(7.41e-11)]_102_[+2(3.77e-10)]_11_[+4(2.56e-12)]_5_[+5(2.44e-12)]_2_[+1(1.24e-12)]_17_[+1(1.48e-05)]_80
WashU_Sbay_Contig461.5 4.36e-32 160_[-3(6.43e-10)]_9_[+1(4.95e-05)]_69_[+2(6.64e-13)]_11_[+4(7.98e-11)]_6_[+5(1.31e-10)]_3_[+1(4.86e-12)]_26_[+2(1.02e-05)]_74
SGD_Scer_YGL040C 4.10e-19 96_[+5(4.33e-07)]_22_[-2(3.61e-09)]_18_[+1(1.62e-11)]_13_[+3(3.72e-09)]_511_[-4(3.58e-07)]_240
MIT_Spar_c19_8512 7.03e-24 97_[+5(2.06e-05)]_22_[-2(1.08e-09)]_18_[+1(1.99e-12)]_13_[+3(1.23e-09)]_228_[-5(5.04e-07)]_430_[-4(2.03e-10)]_72
MIT_Smik_c273_7756 9.66e-24 84_[-4(8.28e-08)]_71_[+1(1.99e-12)]_13_[+3(2.78e-11)]_298_[+5(5.44e-08)]_17_[-2(1.20e-05)]_249_[-2(1.52e-09)]_148
MIT_Sbay_c77_8808 1.01e-19 143_[-2(2.57e-10)]_14_[+1(4.37e-13)]_12_[+3(2.19e-07)]_366_[+4(3.07e-07)]_147_[+2(1.67e-05)]_106_[-5(9.84e-07)]_92
WashU_Skud_Contig2052.17 9.16e-20 138_[-2(3.25e-09)]_18_[+1(1.99e-12)]_13_[+3(1.35e-08)]_50_[-5(1.03e-06)]_17_[+4(7.48e-08)]_245_[-1(8.62e-05)]_184_[-3(9.67e-05)]_195
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************