********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date: )
For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.
This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs. MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************
********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:
Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************
********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM2-HEM15.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YGL040C 1.0000 1000 MIT_Spar_c19_8512 1.0000 1000
MIT_Smik_c273_7756 1.0000 1000 MIT_Sbay_c77_8808 1.0000 1000
WashU_Skud_Contig2052.17 1.0000 1000 SGD_Scer_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 HEM2-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= 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= 8635 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.321 C 0.179 G 0.179 T 0.321
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 = 215 E-value = 5.2e-026
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 2:1861:5aa5:a::::a5:
pos.-specific C 5:5:::95:::a:5a:a:5a
probability G 314249:::::::5:5::::
matrix T :9::::1:::5::::5::::
bits 2.5 * * * *
2.3 * * * *
2.0 ** * * * *
1.8 ** * * * *
Information 1.5 ** ** **** ** *
content 1.3 * ** ** **** ** *
(31.0 bits) 1.0 ********* *********
0.8 ********** *********
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CTCAAGCAAAACACCGCAAC
consensus G GGG C T G T C
sequence A
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2052.17 + 179 2.28e-13 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
MIT_Smik_c273_7756 + 178 2.28e-13 TGTATGTTGC CTCAGGCCAATCACCGCACC GAATAAGGAT
MIT_Spar_c19_8512 + 180 2.28e-13 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
SGD_Scer_YGL040C + 179 6.49e-13 GGAAGCTTGC CTCAAGCCAATCACCGCACC GAACAGGGAT
MIT_Sbay_c77_8808 + 180 3.46e-11 GGCAGCCTGC CGCAGGCCAATCACCGCACC GCCCGGAGAT
MIT_Spar_c278_20970 - 508 1.13e-10 TTGTTGAACA GTGAAGCAAAACAGCTCAAC AGCAGGGCAA
WashU_Sbay_Contig480.2 - 518 2.09e-10 TGTTGAACAG GTGGAGCAAAACAGCTCAAC AGCAGAACAA
SGD_Scer_YOR176W - 506 5.11e-10 TTGTTGAACA GTAAAGCAAAACAGCTCAAC AGCAGGACAA
MIT_Smik_c935_20455 - 492 1.39e-09 TTGTTGAACA ATGAAGTAAAACAGCTCAAC AGCAGAGCAA
WashU_Skud_Contig2050.4 - 509 1.85e-09 TGTTGAACAG ATGGAACAAAACAGCTCAAC AGCAGAACAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 2.3e-13 178_[+1]_802
MIT_Smik_c273_7756 2.3e-13 177_[+1]_803
MIT_Spar_c19_8512 2.3e-13 179_[+1]_801
SGD_Scer_YGL040C 6.5e-13 178_[+1]_802
MIT_Sbay_c77_8808 3.5e-11 179_[+1]_801
MIT_Spar_c278_20970 1.1e-10 507_[-1]_200
WashU_Sbay_Contig480.2 2.1e-10 517_[-1]_190
SGD_Scer_YOR176W 5.1e-10 505_[-1]_202
MIT_Smik_c935_20455 1.4e-09 491_[-1]_216
WashU_Skud_Contig2050.4 1.8e-09 508_[-1]_199
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=10
WashU_Skud_Contig2052.17 ( 179) CTCAGGCCAATCACCGCACC 1
MIT_Smik_c273_7756 ( 178) CTCAGGCCAATCACCGCACC 1
MIT_Spar_c19_8512 ( 180) CTCAGGCCAATCACCGCACC 1
SGD_Scer_YGL040C ( 179) CTCAAGCCAATCACCGCACC 1
MIT_Sbay_c77_8808 ( 180) CGCAGGCCAATCACCGCACC 1
MIT_Spar_c278_20970 ( 508) GTGAAGCAAAACAGCTCAAC 1
WashU_Sbay_Contig480.2 ( 518) GTGGAGCAAAACAGCTCAAC 1
SGD_Scer_YOR176W ( 506) GTAAAGCAAAACAGCTCAAC 1
MIT_Smik_c935_20455 ( 492) ATGAAGTAAAACAGCTCAAC 1
WashU_Skud_Contig2050.4 ( 509) ATGGAACAAAACAGCTCAAC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 5.2e-026
-70 151 77 -997
-997 -997 -81 147
-169 151 119 -997
130 -997 19 -997
89 -997 119 -997
-169 -997 236 -997
-997 236 -997 -169
62 151 -997 -997
162 -997 -997 -997
162 -997 -997 -997
62 -997 -997 62
-997 251 -997 -997
162 -997 -997 -997
-997 151 151 -997
-997 251 -997 -997
-997 -997 151 62
-997 251 -997 -997
162 -997 -997 -997
62 151 -997 -997
-997 251 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.2e-026
0.200000 0.500000 0.300000 0.000000
0.000000 0.000000 0.100000 0.900000
0.100000 0.500000 0.400000 0.000000
0.800000 0.000000 0.200000 0.000000
0.600000 0.000000 0.400000 0.000000
0.100000 0.000000 0.900000 0.000000
0.000000 0.900000 0.000000 0.100000
0.500000 0.500000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
0.000000 1.000000 0.000000 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 0.500000 0.500000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
[CGA]T[CG][AG][AG]GC[AC]AA[AT]CA[CG]C[GT]CA[AC]C
--------------------------------------------------------------------------------
Time 7.72 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 10 llr = 180 E-value = 8.7e-013
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A :3:::69932:::::::49a
pos.-specific C 8:1:a11:::3627:39:1:
probability G 1::::3::41546:a:16::
matrix T 179a:::1372:23:7::::
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 CTTTCAAAGTGCGCGTCGAA
consensus A G AACGCT C A
sequence T T T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2050.4 + 556 3.60e-13 TTCACTGGAT CTTTCAAAGTGCGCGTCGAA ACCACAAACC
WashU_Sbay_Contig480.2 + 561 5.54e-13 TGGCAGAGAT CTTTCGAAGTGCGCGTCGAA ACCACAAACC
MIT_Spar_c278_20970 + 550 5.52e-12 CAGTGAAGAT CTTTCGAATTGCGCGTCGAA ACCACAAACC
SGD_Scer_YOR176W + 548 1.17e-10 CATTGAAGAT CTTTCACATTGCGCGTCGAA ACCACAAACC
MIT_Smik_c935_20455 + 534 2.24e-09 CAATAGAGTT CTCTCCAATTGCGCGTCAAA ACCACAAACC
WashU_Skud_Contig2052.17 - 268 2.94e-09 ATGACCAAGA CATTCAAAAACGGCGTCAAA AAAAAAAAAG
MIT_Smik_c273_7756 - 258 7.80e-09 TGATCAAAGT CATTCAAAGGCGCTGCCGAA AAAAATTGGT
MIT_Spar_c19_8512 - 263 1.90e-08 CGATAAAAGT CATTCAAAATTGTTGCCGAA AAAAAAAAAT
MIT_Sbay_c77_8808 - 258 8.58e-08 TGATCAAAAT TTTTCGAAAACGCTGCCAAA TAGAAAAAGG
SGD_Scer_YGL040C + 647 2.66e-07 TTTTGTATAT GTTTCAATGTTCTCGTGACA ATGCAGGCTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2050.4 3.6e-13 555_[+2]_152
WashU_Sbay_Contig480.2 5.5e-13 560_[+2]_147
MIT_Spar_c278_20970 5.5e-12 549_[+2]_158
SGD_Scer_YOR176W 1.2e-10 547_[+2]_160
MIT_Smik_c935_20455 2.2e-09 533_[+2]_174
WashU_Skud_Contig2052.17 2.9e-09 267_[-2]_713
MIT_Smik_c273_7756 7.8e-09 257_[-2]_723
MIT_Spar_c19_8512 1.9e-08 262_[-2]_718
MIT_Sbay_c77_8808 8.6e-08 257_[-2]_723
SGD_Scer_YGL040C 2.7e-07 646_[+2]_334
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=10
WashU_Skud_Contig2050.4 ( 556) CTTTCAAAGTGCGCGTCGAA 1
WashU_Sbay_Contig480.2 ( 561) CTTTCGAAGTGCGCGTCGAA 1
MIT_Spar_c278_20970 ( 550) CTTTCGAATTGCGCGTCGAA 1
SGD_Scer_YOR176W ( 548) CTTTCACATTGCGCGTCGAA 1
MIT_Smik_c935_20455 ( 534) CTCTCCAATTGCGCGTCAAA 1
WashU_Skud_Contig2052.17 ( 268) CATTCAAAAACGGCGTCAAA 1
MIT_Smik_c273_7756 ( 258) CATTCAAAGGCGCTGCCGAA 1
MIT_Spar_c19_8512 ( 263) CATTCAAAATTGTTGCCGAA 1
MIT_Sbay_c77_8808 ( 258) TTTTCGAAAACGCTGCCAAA 1
SGD_Scer_YGL040C ( 647) GTTTCAATGTTCTCGTGACA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 8.7e-013
-997 219 -81 -169
-11 -997 -997 111
-997 -81 -997 147
-997 -997 -997 162
-997 251 -997 -997
89 -81 77 -997
147 -81 -997 -997
147 -997 -997 -169
-11 -997 119 -11
-70 -997 -81 111
-997 77 151 -70
-997 177 119 -997
-997 19 177 -70
-997 199 -997 -11
-997 -997 251 -997
-997 77 -997 111
-997 236 -81 -997
30 -997 177 -997
147 -81 -997 -997
162 -997 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 8.7e-013
0.000000 0.800000 0.100000 0.100000
0.300000 0.000000 0.000000 0.700000
0.000000 0.100000 0.000000 0.900000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.600000 0.100000 0.300000 0.000000
0.900000 0.100000 0.000000 0.000000
0.900000 0.000000 0.000000 0.100000
0.300000 0.000000 0.400000 0.300000
0.200000 0.000000 0.100000 0.700000
0.000000 0.300000 0.500000 0.200000
0.000000 0.600000 0.400000 0.000000
0.000000 0.200000 0.600000 0.200000
0.000000 0.700000 0.000000 0.300000
0.000000 0.000000 1.000000 0.000000
0.000000 0.300000 0.000000 0.700000
0.000000 0.900000 0.100000 0.000000
0.400000 0.000000 0.600000 0.000000
0.900000 0.100000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
C[TA]TTC[AG]AA[GAT][TA][GCT][CG][GCT][CT]G[TC]C[GA]AA
--------------------------------------------------------------------------------
Time 15.21 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 10 llr = 185 E-value = 8.7e-014
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :556:15:255:::1:2:::
pos.-specific C 55::a:5:435:8a415::9
probability G :::::9:9:2::::::3:::
matrix T 5:54:::14::a2:59:aa1
bits 2.5 * *
2.3 * *
2.0 ** * * *
1.8 ** * * *
Information 1.5 ** * *** ***
content 1.3 ** * *** * ***
(26.7 bits) 1.0 ** **** **** * ***
0.8 ** ***** **** *****
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CAAACGAGCAATCCTTCTTC
consensus TCTT C TCC T C G
sequence AG A
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c935_20455 + 153 1.95e-11 CCAAAAGACT CCTTCGCGTCCTCCTTCTTC AAGTCTCATA
MIT_Spar_c278_20970 + 158 1.95e-11 TAAAAGTATT CCTTCGCGTCCTCCTTCTTC AATCCCATAT
SGD_Scer_YOR176W + 156 1.95e-11 CAAAAGTATT CCTTCGCGTCCTCCTTCTTC AATCCCATAT
WashU_Sbay_Contig480.2 + 206 4.98e-11 AAGAAGTATT CCTACGCGAGCTCCCTCTTC AAGTGCCAAA
WashU_Skud_Contig2052.17 - 199 4.36e-10 ACGCAACGGG TAAACGAGCAATCCCTGTTC GGTGCGGTGA
MIT_Spar_c19_8512 - 200 4.36e-10 AAACTACGGG TAAACGAGCAATCCCTGTTC GGTGCGGTGA
SGD_Scer_YGL040C - 199 4.36e-10 AAAATACGGG TAAACGAGCAATCCCTGTTC GGTGCGGTGA
MIT_Smik_c273_7756 - 198 1.99e-09 GAACAACGGG TAAACGAGCAATCCTTATTC GGTGCGGTGA
WashU_Skud_Contig2050.4 + 162 3.33e-08 AAGAAGTATT CCTTCGCGTGCTTCTCCTTT CTGTGTCAAA
MIT_Sbay_c77_8808 + 824 6.99e-07 TACATAGAAC TAAACAATAAATTCATATTC AATAATACTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c935_20455 1.9e-11 152_[+3]_555
MIT_Spar_c278_20970 1.9e-11 157_[+3]_550
SGD_Scer_YOR176W 1.9e-11 155_[+3]_552
WashU_Sbay_Contig480.2 5e-11 205_[+3]_502
WashU_Skud_Contig2052.17 4.4e-10 198_[-3]_782
MIT_Spar_c19_8512 4.4e-10 199_[-3]_781
SGD_Scer_YGL040C 4.4e-10 198_[-3]_782
MIT_Smik_c273_7756 2e-09 197_[-3]_783
WashU_Skud_Contig2050.4 3.3e-08 161_[+3]_546
MIT_Sbay_c77_8808 7e-07 823_[+3]_157
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=10
MIT_Smik_c935_20455 ( 153) CCTTCGCGTCCTCCTTCTTC 1
MIT_Spar_c278_20970 ( 158) CCTTCGCGTCCTCCTTCTTC 1
SGD_Scer_YOR176W ( 156) CCTTCGCGTCCTCCTTCTTC 1
WashU_Sbay_Contig480.2 ( 206) CCTACGCGAGCTCCCTCTTC 1
WashU_Skud_Contig2052.17 ( 199) TAAACGAGCAATCCCTGTTC 1
MIT_Spar_c19_8512 ( 200) TAAACGAGCAATCCCTGTTC 1
SGD_Scer_YGL040C ( 199) TAAACGAGCAATCCCTGTTC 1
MIT_Smik_c273_7756 ( 198) TAAACGAGCAATCCTTATTC 1
WashU_Skud_Contig2050.4 ( 162) CCTTCGCGTGCTTCTCCTTT 1
MIT_Sbay_c77_8808 ( 824) TAAACAATAAATTCATATTC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 8.7e-014
-997 151 -997 62
62 151 -997 -997
62 -997 -997 62
89 -997 -997 30
-997 251 -997 -997
-169 -997 236 -997
62 151 -997 -997
-997 -997 236 -169
-70 119 -997 30
62 77 19 -997
62 151 -997 -997
-997 -997 -997 162
-997 219 -997 -70
-997 251 -997 -997
-169 119 -997 62
-997 -81 -997 147
-70 151 77 -997
-997 -997 -997 162
-997 -997 -997 162
-997 236 -997 -169
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 8.7e-014
0.000000 0.500000 0.000000 0.500000
0.500000 0.500000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
0.600000 0.000000 0.000000 0.400000
0.000000 1.000000 0.000000 0.000000
0.100000 0.000000 0.900000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.000000 0.900000 0.100000
0.200000 0.400000 0.000000 0.400000
0.500000 0.300000 0.200000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.800000 0.000000 0.200000
0.000000 1.000000 0.000000 0.000000
0.100000 0.400000 0.000000 0.500000
0.000000 0.100000 0.000000 0.900000
0.200000 0.500000 0.300000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.900000 0.000000 0.100000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
[CT][AC][AT][AT]CG[AC]G[CTA][ACG][AC]T[CT]C[TC]T[CGA]TTC
--------------------------------------------------------------------------------
Time 22.63 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 10 llr = 177 E-value = 3.5e-011
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 7:2a19aa2:61:4969a:9
pos.-specific C 1a7:5:::5a:16::4::1:
probability G 2:::31::::4246::::::
matrix T ::1:1:::3::6::1:1:91
bits 2.5 * *
2.3 * *
2.0 * *
1.8 * *
Information 1.5 * * ** * * *
content 1.3 * * *** * *** ****
(25.6 bits) 1.0 *** *** ** ********
0.8 ******** ** ********
0.5 *********** ********
0.3 ********************
0.0 --------------------
Multilevel ACCACAAACCATCGAAAATA
consensus G A G T GGGA C
sequence A
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2050.4 + 576 3.12e-12 GCGCGTCGAA ACCACAAACCGTCGAAAATA TTGATCATCT
MIT_Smik_c935_20455 + 554 3.12e-12 GCGCGTCAAA ACCACAAACCGTCGAAAATA ATGATCATCT
MIT_Spar_c278_20970 + 570 3.12e-12 GCGCGTCGAA ACCACAAACCGTCGAAAATA ATGGTCATCT
WashU_Sbay_Contig480.2 + 581 5.53e-11 GCGCGTCGAA ACCACAAACCATCAAAAATA TCGACCATCT
SGD_Scer_YOR176W + 568 1.19e-10 GCGCGTCGAA ACCACAAACCGTCGAAAACA ATGGTCATCT
WashU_Skud_Contig2052.17 + 87 2.26e-09 AGCTAATTTA GCCAGAAATCATGAACAATA GGATGACGCA
MIT_Spar_c19_8512 + 89 2.98e-08 GGCTGATTGG GCCAAAAAACAAGGACAATA GAATGACACA
MIT_Smik_c273_7756 + 89 9.01e-08 GCTAAATAGG CCAATAAATCAGGAACAATA GAATGACGCA
SGD_Scer_YGL040C - 535 1.20e-07 TTTTTAATTA ACTAGAAATCAGCGTCAATT ATAGTTTCTG
MIT_Sbay_c77_8808 + 771 2.18e-07 CAATATGTGG ACAAGGAAACACGAAATATA TTGGGATAAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2050.4 3.1e-12 575_[+4]_132
MIT_Smik_c935_20455 3.1e-12 553_[+4]_154
MIT_Spar_c278_20970 3.1e-12 569_[+4]_138
WashU_Sbay_Contig480.2 5.5e-11 580_[+4]_127
SGD_Scer_YOR176W 1.2e-10 567_[+4]_140
WashU_Skud_Contig2052.17 2.3e-09 86_[+4]_894
MIT_Spar_c19_8512 3e-08 88_[+4]_892
MIT_Smik_c273_7756 9e-08 88_[+4]_892
SGD_Scer_YGL040C 1.2e-07 534_[-4]_446
MIT_Sbay_c77_8808 2.2e-07 770_[+4]_210
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=10
WashU_Skud_Contig2050.4 ( 576) ACCACAAACCGTCGAAAATA 1
MIT_Smik_c935_20455 ( 554) ACCACAAACCGTCGAAAATA 1
MIT_Spar_c278_20970 ( 570) ACCACAAACCGTCGAAAATA 1
WashU_Sbay_Contig480.2 ( 581) ACCACAAACCATCAAAAATA 1
SGD_Scer_YOR176W ( 568) ACCACAAACCGTCGAAAACA 1
WashU_Skud_Contig2052.17 ( 87) GCCAGAAATCATGAACAATA 1
MIT_Spar_c19_8512 ( 89) GCCAAAAAACAAGGACAATA 1
MIT_Smik_c273_7756 ( 89) CCAATAAATCAGGAACAATA 1
SGD_Scer_YGL040C ( 535) ACTAGAAATCAGCGTCAATT 1
MIT_Sbay_c77_8808 ( 771) ACAAGGAAACACGAAATATA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 3.5e-011
111 -81 19 -997
-997 251 -997 -997
-70 199 -997 -169
162 -997 -997 -997
-169 151 77 -169
147 -997 -81 -997
162 -997 -997 -997
162 -997 -997 -997
-70 151 -997 -11
-997 251 -997 -997
89 -997 119 -997
-169 -81 19 89
-997 177 119 -997
30 -997 177 -997
147 -997 -997 -169
89 119 -997 -997
147 -997 -997 -169
162 -997 -997 -997
-997 -81 -997 147
147 -997 -997 -169
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.5e-011
0.700000 0.100000 0.200000 0.000000
0.000000 1.000000 0.000000 0.000000
0.200000 0.700000 0.000000 0.100000
1.000000 0.000000 0.000000 0.000000
0.100000 0.500000 0.300000 0.100000
0.900000 0.000000 0.100000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.200000 0.500000 0.000000 0.300000
0.000000 1.000000 0.000000 0.000000
0.600000 0.000000 0.400000 0.000000
0.100000 0.100000 0.200000 0.600000
0.000000 0.600000 0.400000 0.000000
0.400000 0.000000 0.600000 0.000000
0.900000 0.000000 0.000000 0.100000
0.600000 0.400000 0.000000 0.000000
0.900000 0.000000 0.000000 0.100000
1.000000 0.000000 0.000000 0.000000
0.000000 0.100000 0.000000 0.900000
0.900000 0.000000 0.000000 0.100000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[AG]C[CA]A[CG]AAA[CTA]C[AG][TG][CG][GA]A[AC]AATA
--------------------------------------------------------------------------------
Time 29.89 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 15 sites = 10 llr = 143 E-value = 2.9e-005
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A :6::11:1::3116:
pos.-specific C ::4a::::a8:12:1
probability G 9::::8:9:118:3:
matrix T 146:91a::16:719
bits 2.5 * *
2.3 * *
2.0 * * **
1.8 * * **
Information 1.5 * * ***** *
content 1.3 * ******* * *
(20.7 bits) 1.0 * ******** * *
0.8 ********** ** *
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel GATCTGTGCCTGTAT
consensus TC A CG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Sbay_Contig480.2 - 655 3.42e-10 CTTCTTATCT GACCTGTGCCTGTAT GAAGAGCTTC
MIT_Smik_c935_20455 - 630 3.42e-10 CTTCTTGTTA GACCTGTGCCTGTAT GGAGTATTTC
MIT_Spar_c278_20970 - 645 3.42e-10 ATTCTTTCTG GACCTGTGCCTGTAT CGTGTCTTTG
SGD_Scer_YOR176W - 641 3.42e-10 CTTCTTGCTT GACCTGTGCCTGTAT TTTGTCCTTG
WashU_Skud_Contig2050.4 - 650 1.56e-08 TCTTCTTGTT GATCTGTGCCTGAAT GGAATATTTC
SGD_Scer_YGL040C + 944 5.03e-08 TGTCATCTGT GTTCTGTGCCAGTAC ACCGGACTCG
MIT_Spar_c19_8512 + 985 1.58e-07 TATGATCTGT GTTCTATGCCAGTGT A
MIT_Smik_c273_7756 - 540 3.80e-06 TTATTGTTTA GTTCTGTGCGGCCTT GTTTTAAGCA
WashU_Skud_Contig2052.17 - 662 5.05e-06 GTTATTGTTT GTTCAGTGCTAATGT ATTTATGGGT
MIT_Sbay_c77_8808 - 324 5.92e-06 GATTTGTTCA TATCTTTACCTGCGT GCCCTAAAAT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig480.2 3.4e-10 654_[-5]_58
MIT_Smik_c935_20455 3.4e-10 629_[-5]_83
MIT_Spar_c278_20970 3.4e-10 644_[-5]_68
SGD_Scer_YOR176W 3.4e-10 640_[-5]_72
WashU_Skud_Contig2050.4 1.6e-08 649_[-5]_63
SGD_Scer_YGL040C 5e-08 943_[+5]_42
MIT_Spar_c19_8512 1.6e-07 984_[+5]_1
MIT_Smik_c273_7756 3.8e-06 539_[-5]_446
WashU_Skud_Contig2052.17 5e-06 661_[-5]_324
MIT_Sbay_c77_8808 5.9e-06 323_[-5]_662
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=15 seqs=10
WashU_Sbay_Contig480.2 ( 655) GACCTGTGCCTGTAT 1
MIT_Smik_c935_20455 ( 630) GACCTGTGCCTGTAT 1
MIT_Spar_c278_20970 ( 645) GACCTGTGCCTGTAT 1
SGD_Scer_YOR176W ( 641) GACCTGTGCCTGTAT 1
WashU_Skud_Contig2050.4 ( 650) GATCTGTGCCTGAAT 1
SGD_Scer_YGL040C ( 944) GTTCTGTGCCAGTAC 1
MIT_Spar_c19_8512 ( 985) GTTCTATGCCAGTGT 1
MIT_Smik_c273_7756 ( 540) GTTCTGTGCGGCCTT 1
WashU_Skud_Contig2052.17 ( 662) GTTCAGTGCTAATGT 1
MIT_Sbay_c77_8808 ( 324) TATCTTTACCTGCGT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8495 bayes= 9.72877 E= 2.9e-005
-997 -997 236 -169
89 -997 -997 30
-997 119 -997 89
-997 251 -997 -997
-169 -997 -997 147
-169 -997 219 -169
-997 -997 -997 162
-169 -997 236 -997
-997 251 -997 -997
-997 219 -81 -169
-11 -997 -81 89
-169 -81 219 -997
-169 19 -997 111
89 -997 77 -169
-997 -81 -997 147
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 2.9e-005
0.000000 0.000000 0.900000 0.100000
0.600000 0.000000 0.000000 0.400000
0.000000 0.400000 0.000000 0.600000
0.000000 1.000000 0.000000 0.000000
0.100000 0.000000 0.000000 0.900000
0.100000 0.000000 0.800000 0.100000
0.000000 0.000000 0.000000 1.000000
0.100000 0.000000 0.900000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.800000 0.100000 0.100000
0.300000 0.000000 0.100000 0.600000
0.100000 0.100000 0.800000 0.000000
0.100000 0.200000 0.000000 0.700000
0.600000 0.000000 0.300000 0.100000
0.000000 0.100000 0.000000 0.900000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
G[AT][TC]CTGTGCC[TA]G[TC][AG]T
--------------------------------------------------------------------------------
Time 37.04 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YGL040C 7.45e-21 178_[+1(6.49e-13)]_[-3(4.36e-10)]_316_[-4(1.20e-07)]_92_[+2(2.66e-07)]_127_[+1(6.62e-05)]_130_[+5(5.03e-08)]_42
MIT_Spar_c19_8512 1.88e-22 88_[+4(2.98e-08)]_71_[+1(2.28e-13)]_[-3(4.36e-10)]_43_[-2(1.90e-08)]_150_[+3(3.32e-05)]_465_[-3(5.73e-05)]_47_[+5(1.58e-07)]_1
MIT_Smik_c273_7756 1.86e-20 88_[+4(9.01e-08)]_69_[+1(2.28e-13)]_[-3(1.99e-09)]_40_[-2(7.80e-09)]_262_[-5(3.80e-06)]_446
MIT_Sbay_c77_8808 1.33e-14 179_[+1(3.46e-11)]_58_[-2(8.58e-08)]_46_[-5(5.92e-06)]_432_[+4(2.18e-07)]_33_[+3(6.99e-07)]_90_[-1(4.25e-05)]_47
WashU_Skud_Contig2052.17 7.44e-23 86_[+4(2.26e-09)]_72_[+1(2.28e-13)]_[-3(4.36e-10)]_49_[-2(2.94e-09)]_374_[-5(5.05e-06)]_131_[+3(3.98e-05)]_143_[+1(9.33e-05)]_10
SGD_Scer_YOR176W 4.25e-28 100_[-4(3.19e-05)]_35_[+3(1.95e-11)]_136_[+3(4.98e-05)]_174_[-1(5.11e-10)]_22_[+2(1.17e-10)]_[+4(1.19e-10)]_53_[-5(3.42e-10)]_72
MIT_Spar_c278_20970 1.73e-31 48_[+3(3.79e-05)]_89_[+3(1.95e-11)]_330_[-1(1.13e-10)]_22_[+2(5.52e-12)]_[+4(3.12e-12)]_55_[-5(3.42e-10)]_68
MIT_Smik_c935_20455 5.70e-28 152_[+3(1.95e-11)]_127_[+3(4.68e-06)]_172_[-1(1.39e-09)]_22_[+2(2.24e-09)]_[+4(3.12e-12)]_56_[-5(3.42e-10)]_83
WashU_Skud_Contig2050.4 8.21e-27 161_[+3(3.33e-08)]_256_[+4(2.13e-05)]_51_[-1(1.85e-09)]_2_[+1(8.00e-05)]_5_[+2(3.60e-13)]_[+4(3.12e-12)]_54_[-5(1.56e-08)]_63
WashU_Sbay_Contig480.2 1.32e-30 205_[+3(4.98e-11)]_292_[-1(2.09e-10)]_23_[+2(5.54e-13)]_[+4(5.53e-11)]_10_[-3(4.52e-05)]_24_[-5(3.42e-10)]_58
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************