********************************************************************************
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= HEM12-HEM15.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YDR047W 1.0000 1000 MIT_Spar_c130_3923 1.0000 1000
MIT_Sbay_c896_21277 1.0000 1000 WashU_Skud_Contig1362.1 1.0000 761
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 HEM12-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
model: mod= oops nmotifs= 5 evt= inf
object function= E-value of product of p-values
width: minw= 6 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 9 maxsites= 9 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 7396 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.298 C 0.202 G 0.202 T 0.298
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324
********************************************************************************
********************************************************************************
MOTIF 1 width = 20 sites = 9 llr = 199 E-value = 4.8e-024
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A ::::1236aaa::6:6aa::
pos.-specific C 1828327::::aa4a:::9a
probability G 81816::4:::::::4::::
matrix T 11:1:6::::::::::::1:
bits 2.5 ** * *
2.3 ** * *
2.0 ** * **
1.8 * ** * **
Information 1.5 **** ***** * ****
content 1.3 **** * ***** * ****
(31.9 bits) 1.0 ***** **************
0.8 ***** **************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GCGCGTCAAAACCACAAACC
consensus C CAAG C G
sequence C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig480.2 + 571 6.74e-13 CTTTCGAAGT GCGCGTCGAAACCACAAACC ATCAAAAATA
WashU_Skud_Contig2050.4 + 566 6.74e-13 CTTTCAAAGT GCGCGTCGAAACCACAAACC GTCGAAAATA
MIT_Spar_c278_20970 + 560 6.74e-13 CTTTCGAATT GCGCGTCGAAACCACAAACC GTCGAAAATA
SGD_Scer_YOR176W + 558 6.74e-13 CTTTCACATT GCGCGTCGAAACCACAAACC GTCGAAAACA
MIT_Smik_c935_20455 + 544 1.42e-12 CTCTCCAATT GCGCGTCAAAACCACAAACC GTCGAAAATA
MIT_Sbay_c896_21277 + 203 2.13e-10 CTTTTCCATG GCGTCAAAAAACCCCGAACC CTGTATAAAC
SGD_Scer_YDR047W + 235 2.25e-10 TTCCTCTCCT GCCGCCAAAAACCCCGAACC CTGTCCTGTA
MIT_Spar_c130_3923 + 232 1.41e-09 TTTTCTCTCC TGCCACCAAAACCCCGAACC CTGTCCCGTA
WashU_Skud_Contig1362.1 + 198 2.94e-09 TTTTTTCCTG CTGCCAAAAAACCCCGAATC ATGTAGAAGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig480.2 6.7e-13 570_[+1]_137
WashU_Skud_Contig2050.4 6.7e-13 565_[+1]_142
MIT_Spar_c278_20970 6.7e-13 559_[+1]_148
SGD_Scer_YOR176W 6.7e-13 557_[+1]_150
MIT_Smik_c935_20455 1.4e-12 543_[+1]_164
MIT_Sbay_c896_21277 2.1e-10 202_[+1]_778
SGD_Scer_YDR047W 2.2e-10 234_[+1]_746
MIT_Spar_c130_3923 1.4e-09 231_[+1]_749
WashU_Skud_Contig1362.1 2.9e-09 197_[+1]_544
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig480.2 ( 571) GCGCGTCGAAACCACAAACC 1
WashU_Skud_Contig2050.4 ( 566) GCGCGTCGAAACCACAAACC 1
MIT_Spar_c278_20970 ( 560) GCGCGTCGAAACCACAAACC 1
SGD_Scer_YOR176W ( 558) GCGCGTCGAAACCACAAACC 1
MIT_Smik_c935_20455 ( 544) GCGCGTCAAAACCACAAACC 1
MIT_Sbay_c896_21277 ( 203) GCGTCAAAAAACCCCGAACC 1
SGD_Scer_YDR047W ( 235) GCCGCCAAAAACCCCGAACC 1
MIT_Spar_c130_3923 ( 232) TGCCACCAAAACCCCGAACC 1
WashU_Skud_Contig1362.1 ( 198) CTGCCAAAAAACCCCGAATC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 4.8e-024
-982 -66 215 -154
-982 215 -66 -154
-982 34 215 -982
-982 215 -66 -154
-154 92 166 -982
-55 34 -982 78
4 192 -982 -982
78 -982 134 -982
162 -982 -982 -982
162 -982 -982 -982
162 -982 -982 -982
-982 251 -982 -982
-982 251 -982 -982
78 134 -982 -982
-982 251 -982 -982
78 -982 134 -982
162 -982 -982 -982
162 -982 -982 -982
-982 234 -982 -154
-982 251 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.8e-024
0.000000 0.111111 0.777778 0.111111
0.000000 0.777778 0.111111 0.111111
0.000000 0.222222 0.777778 0.000000
0.000000 0.777778 0.111111 0.111111
0.111111 0.333333 0.555556 0.000000
0.222222 0.222222 0.000000 0.555556
0.333333 0.666667 0.000000 0.000000
0.555556 0.000000 0.444444 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.555556 0.444444 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.555556 0.000000 0.444444 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.888889 0.000000 0.111111
0.000000 1.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
GC[GC]C[GC][TAC][CA][AG]AAACC[AC]C[AG]AACC
--------------------------------------------------------------------------------
Time 5.88 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 171 E-value = 5.0e-014
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 91:a12:::6::::1::12:
pos.-specific C 1:::1:881:8:a2239:48
probability G :91:2:22::2a:827:1::
matrix T ::9:68::94::::4:1832
bits 2.5 **
2.3 **
2.0 * ** *
1.8 * ** **** *
Information 1.5 * * ** **** ** *
content 1.3 **** *** **** ** *
(27.4 bits) 1.0 **** *** **** ** *
0.8 **** ********* *** *
0.5 **** ********* *****
0.3 ********************
0.0 --------------------
Multilevel AGTATTCCTACGCGTGCTCC
consensus GAGG TG CCC TT
sequence G A
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c278_20970 + 152 2.21e-12 ACCGACTAAA AGTATTCCTTCGCGTCCTCC TTCTTCAATC
SGD_Scer_YOR176W + 150 2.21e-12 ACCGACCAAA AGTATTCCTTCGCGTCCTCC TTCTTCAATC
WashU_Skud_Contig2050.4 + 156 3.61e-12 GACCAAAAGA AGTATTCCTTCGCGTGCTTC TCCTTTCTGT
WashU_Sbay_Contig480.2 + 200 7.52e-12 GACCAAAAGA AGTATTCCTACGCGAGCTCC CTCTTCAAGT
MIT_Smik_c935_20455 + 147 3.24e-09 GGCCGACCAA AAGACTCCTTCGCGTCCTCC TTCTTCAAGT
WashU_Skud_Contig1362.1 - 674 4.27e-09 CGTTCGATCG AGTAATGCTAGGCCCGCTTC GAGAGCTGGT
SGD_Scer_YDR047W - 388 1.16e-08 AACATGTTGT AGTATACGTACGCGGGCAAT TGTGGTGACA
MIT_Spar_c130_3923 - 386 2.39e-08 ATCATATTTT AGTAGACGCACGCGGGCGAT TATAACGAAA
MIT_Sbay_c896_21277 - 675 2.87e-08 TGTTTGGCTG CGTAGTGCTAGGCCCGTTTC GCCTGGCTTG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c278_20970 2.2e-12 151_[+2]_556
SGD_Scer_YOR176W 2.2e-12 149_[+2]_558
WashU_Skud_Contig2050.4 3.6e-12 155_[+2]_552
WashU_Sbay_Contig480.2 7.5e-12 199_[+2]_508
MIT_Smik_c935_20455 3.2e-09 146_[+2]_561
WashU_Skud_Contig1362.1 4.3e-09 673_[-2]_68
SGD_Scer_YDR047W 1.2e-08 387_[-2]_593
MIT_Spar_c130_3923 2.4e-08 385_[-2]_595
MIT_Sbay_c896_21277 2.9e-08 674_[-2]_306
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
MIT_Spar_c278_20970 ( 152) AGTATTCCTTCGCGTCCTCC 1
SGD_Scer_YOR176W ( 150) AGTATTCCTTCGCGTCCTCC 1
WashU_Skud_Contig2050.4 ( 156) AGTATTCCTTCGCGTGCTTC 1
WashU_Sbay_Contig480.2 ( 200) AGTATTCCTACGCGAGCTCC 1
MIT_Smik_c935_20455 ( 147) AAGACTCCTTCGCGTCCTCC 1
WashU_Skud_Contig1362.1 ( 674) AGTAATGCTAGGCCCGCTTC 1
SGD_Scer_YDR047W ( 388) AGTATACGTACGCGGGCAAT 1
MIT_Spar_c130_3923 ( 386) AGTAGACGCACGCGGGCGAT 1
MIT_Sbay_c896_21277 ( 675) CGTAGTGCTAGGCCCGTTTC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 5.0e-014
145 -66 -982 -982
-154 -982 234 -982
-982 -982 -66 145
162 -982 -982 -982
-154 -66 34 78
-55 -982 -982 126
-982 215 34 -982
-982 215 34 -982
-982 -66 -982 145
78 -982 -982 45
-982 215 34 -982
-982 -982 251 -982
-982 251 -982 -982
-982 34 215 -982
-154 34 34 45
-982 92 192 -982
-982 234 -982 -154
-154 -982 -66 126
-55 134 -982 4
-982 215 -982 -55
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.0e-014
0.888889 0.111111 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
0.000000 0.000000 0.111111 0.888889
1.000000 0.000000 0.000000 0.000000
0.111111 0.111111 0.222222 0.555556
0.222222 0.000000 0.000000 0.777778
0.000000 0.777778 0.222222 0.000000
0.000000 0.777778 0.222222 0.000000
0.000000 0.111111 0.000000 0.888889
0.555556 0.000000 0.000000 0.444444
0.000000 0.777778 0.222222 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.222222 0.777778 0.000000
0.111111 0.222222 0.222222 0.444444
0.000000 0.333333 0.666667 0.000000
0.000000 0.888889 0.000000 0.111111
0.111111 0.000000 0.111111 0.777778
0.222222 0.444444 0.000000 0.333333
0.000000 0.777778 0.000000 0.222222
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
AGTA[TG][TA][CG][CG]T[AT][CG]GC[GC][TCG][GC]CT[CTA][CT]
--------------------------------------------------------------------------------
Time 11.70 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 168 E-value = 2.4e-011
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A ::::::::11::7:21::::
pos.-specific C :428:1a2:::2116:1:::
probability G a:::19:17:1718::8:::
matrix T :6829::7299111291aaa
bits 2.5 * *
2.3 * *
2.0 * **
1.8 * **
Information 1.5 * * ** * ****
content 1.3 * **** ** * ****
(27.0 bits) 1.0 ******* **** * *****
0.8 ************ *******
0.5 ************ *******
0.3 ********************
0.0 --------------------
Multilevel GTTCTGCTGTTGAGCTGTTT
consensus CCT CT C A
sequence T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c935_20455 + 484 3.60e-13 AGCTTTTTTT GCTCTGCTGTTGAGCTGTTT TACTTCATTG
WashU_Sbay_Contig480.2 + 510 1.02e-12 GCTGTTTTTT GTTCTGCTGTTGAGCTGTTT TGCTCCACCT
WashU_Skud_Contig2050.4 + 501 1.02e-12 GCTGTTTTTT GTTCTGCTGTTGAGCTGTTT TGTTCCATCT
MIT_Spar_c278_20970 + 500 1.41e-12 AGCTTTTTTT GCCCTGCTGTTGAGCTGTTT TGCTTCACTG
SGD_Scer_YOR176W + 498 2.49e-12 AGCTTTTTTT GTCCTGCTGTTGAGCTGTTT TGCTTTACTG
WashU_Skud_Contig1362.1 - 125 2.43e-08 TCAACGAGGT GTTCTGCCTTTCGTATGTTT ATTGCTCGAA
MIT_Spar_c130_3923 - 609 7.51e-08 CGCCAGTGGT GCTTTGCTTTGCCGTAGTTT GTAAAAAAAA
MIT_Sbay_c896_21277 + 770 1.89e-07 CTAGCAGCGT GCTTGCCGGATGAGTTTTTT CCATTTTCCT
SGD_Scer_YDR047W - 161 2.04e-07 CCAGCGAAAT GTTCTGCCATTTTCATCTTT ACCGCTCGAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c935_20455 3.6e-13 483_[+3]_224
WashU_Sbay_Contig480.2 1e-12 509_[+3]_198
WashU_Skud_Contig2050.4 1e-12 500_[+3]_207
MIT_Spar_c278_20970 1.4e-12 499_[+3]_208
SGD_Scer_YOR176W 2.5e-12 497_[+3]_210
WashU_Skud_Contig1362.1 2.4e-08 124_[-3]_617
MIT_Spar_c130_3923 7.5e-08 608_[-3]_372
MIT_Sbay_c896_21277 1.9e-07 769_[+3]_211
SGD_Scer_YDR047W 2e-07 160_[-3]_820
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
MIT_Smik_c935_20455 ( 484) GCTCTGCTGTTGAGCTGTTT 1
WashU_Sbay_Contig480.2 ( 510) GTTCTGCTGTTGAGCTGTTT 1
WashU_Skud_Contig2050.4 ( 501) GTTCTGCTGTTGAGCTGTTT 1
MIT_Spar_c278_20970 ( 500) GCCCTGCTGTTGAGCTGTTT 1
SGD_Scer_YOR176W ( 498) GTCCTGCTGTTGAGCTGTTT 1
WashU_Skud_Contig1362.1 ( 125) GTTCTGCCTTTCGTATGTTT 1
MIT_Spar_c130_3923 ( 609) GCTTTGCTTTGCCGTAGTTT 1
MIT_Sbay_c896_21277 ( 770) GCTTGCCGGATGAGTTTTTT 1
SGD_Scer_YDR047W ( 161) GTTCTGCCATTTTCATCTTT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 2.4e-011
-982 -982 251 -982
-982 134 -982 78
-982 34 -982 126
-982 215 -982 -55
-982 -982 -66 145
-982 -66 234 -982
-982 251 -982 -982
-982 34 -66 104
-154 -982 192 -55
-154 -982 -982 145
-982 -982 -66 145
-982 34 192 -154
104 -66 -66 -154
-982 -66 215 -154
-55 166 -982 -55
-154 -982 -982 145
-982 -66 215 -154
-982 -982 -982 162
-982 -982 -982 162
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.4e-011
0.000000 0.000000 1.000000 0.000000
0.000000 0.444444 0.000000 0.555556
0.000000 0.222222 0.000000 0.777778
0.000000 0.777778 0.000000 0.222222
0.000000 0.000000 0.111111 0.888889
0.000000 0.111111 0.888889 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.222222 0.111111 0.666667
0.111111 0.000000 0.666667 0.222222
0.111111 0.000000 0.000000 0.888889
0.000000 0.000000 0.111111 0.888889
0.000000 0.222222 0.666667 0.111111
0.666667 0.111111 0.111111 0.111111
0.000000 0.111111 0.777778 0.111111
0.222222 0.555556 0.000000 0.222222
0.111111 0.000000 0.000000 0.888889
0.000000 0.111111 0.777778 0.111111
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
G[TC][TC][CT]TGC[TC][GT]TT[GC]AG[CAT]TGTTT
--------------------------------------------------------------------------------
Time 17.31 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 9 llr = 165 E-value = 1.1e-009
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 8282::a:8:3::3734a93
pos.-specific C 17:1:a:a:31:a3:14:::
probability G ::17a:::2761::34::17
matrix T 111::::::::9:3:11:::
bits 2.5 ** * *
2.3 ** * *
2.0 ** * *
1.8 ** * *
Information 1.5 **** * * *
content 1.3 **** * ** ***
(26.4 bits) 1.0 * ******* ** * ***
0.8 ************* * ***
0.5 ************* * ****
0.3 ********************
0.0 --------------------
Multilevel ACAGGCACAGGTCAAGAAAG
consensus A A GCA CGAC A
sequence T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YOR176W + 643 5.51e-13 AGGACAAAAT ACAGGCACAGGTCAAGCAAG AAGACAAACC
MIT_Spar_c278_20970 + 647 1.12e-12 AAGACACGAT ACAGGCACAGGTCCAGAAAG AATACAAAAC
MIT_Smik_c935_20455 + 632 6.03e-12 AATACTCCAT ACAGGCACAGGTCTAACAAG AAGACAACGC
WashU_Sbay_Contig480.2 + 657 2.48e-10 AGCTCTTCAT ACAGGCACAGGTCAGATAAG AAGACAATTC
MIT_Spar_c130_3923 - 808 3.78e-09 GCCGGAAAAA AAAAGCACGCATCCGGCAAG GAAAGGACGC
SGD_Scer_YDR047W - 798 3.78e-09 GCCGGAAAAA AAAAGCACGCATCCGGCAAG CACACTAGTA
WashU_Skud_Contig2050.4 + 652 2.81e-08 AATATTCCAT TCAGGCACAGATCAACAAGA AGACAAAAAG
WashU_Skud_Contig1362.1 + 48 4.74e-08 AGCAAGCTCA ATTGGCACAGCTCTAAAAAA AGCCTTGTGA
MIT_Sbay_c896_21277 - 831 1.01e-07 TCTCTCGATG CCGCGCACACGGCTATAAAA CTGACCTTTC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YOR176W 5.5e-13 642_[+4]_65
MIT_Spar_c278_20970 1.1e-12 646_[+4]_61
MIT_Smik_c935_20455 6e-12 631_[+4]_76
WashU_Sbay_Contig480.2 2.5e-10 656_[+4]_51
MIT_Spar_c130_3923 3.8e-09 807_[-4]_173
SGD_Scer_YDR047W 3.8e-09 797_[-4]_183
WashU_Skud_Contig2050.4 2.8e-08 651_[+4]_56
WashU_Skud_Contig1362.1 4.7e-08 47_[+4]_694
MIT_Sbay_c896_21277 1e-07 830_[-4]_150
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=9
SGD_Scer_YOR176W ( 643) ACAGGCACAGGTCAAGCAAG 1
MIT_Spar_c278_20970 ( 647) ACAGGCACAGGTCCAGAAAG 1
MIT_Smik_c935_20455 ( 632) ACAGGCACAGGTCTAACAAG 1
WashU_Sbay_Contig480.2 ( 657) ACAGGCACAGGTCAGATAAG 1
MIT_Spar_c130_3923 ( 808) AAAAGCACGCATCCGGCAAG 1
SGD_Scer_YDR047W ( 798) AAAAGCACGCATCCGGCAAG 1
WashU_Skud_Contig2050.4 ( 652) TCAGGCACAGATCAACAAGA 1
WashU_Skud_Contig1362.1 ( 48) ATTGGCACAGCTCTAAAAAA 1
MIT_Sbay_c896_21277 ( 831) CCGCGCACACGGCTATAAAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 1.1e-009
126 -66 -982 -154
-55 192 -982 -154
126 -982 -66 -154
-55 -66 192 -982
-982 -982 251 -982
-982 251 -982 -982
162 -982 -982 -982
-982 251 -982 -982
126 -982 34 -982
-982 92 192 -982
4 -66 166 -982
-982 -982 -66 145
-982 251 -982 -982
4 92 -982 4
104 -982 92 -982
4 -66 134 -154
45 134 -982 -154
162 -982 -982 -982
145 -982 -66 -982
4 -982 192 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.1e-009
0.777778 0.111111 0.000000 0.111111
0.222222 0.666667 0.000000 0.111111
0.777778 0.000000 0.111111 0.111111
0.222222 0.111111 0.666667 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
0.000000 1.000000 0.000000 0.000000
0.777778 0.000000 0.222222 0.000000
0.000000 0.333333 0.666667 0.000000
0.333333 0.111111 0.555556 0.000000
0.000000 0.000000 0.111111 0.888889
0.000000 1.000000 0.000000 0.000000
0.333333 0.333333 0.000000 0.333333
0.666667 0.000000 0.333333 0.000000
0.333333 0.111111 0.444444 0.111111
0.444444 0.444444 0.000000 0.111111
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.333333 0.000000 0.666667 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
A[CA]A[GA]GCAC[AG][GC][GA]TC[ACT][AG][GA][AC]AA[GA]
--------------------------------------------------------------------------------
Time 22.56 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 160 E-value = 3.0e-008
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 91:1::3:::3:::::::1:
pos.-specific C :::611:::::89::613::
probability G 17::::::::121:::::4:
matrix T :2a3997aaa6::aa4974a
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 AGTCTTTTTTTCCTTCTTGT
consensus T T A AG T CT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c130_3923 + 733 2.54e-10 CGTCCCATTG AGTTTTATTTTCCTTCTCGT AGCACCTTCT
WashU_Sbay_Contig480.2 + 102 1.11e-09 AGAGAAGAAA ATTTTTTTTTTCCTTCTTGT ATGGTCAGTT
WashU_Skud_Contig2050.4 + 58 1.57e-09 ATAAGCAAGA AATCTTTTTTTCCTTCTTTT ACGGTCTATT
WashU_Skud_Contig1362.1 + 713 1.57e-09 GTTGCCGTTT AGTCTTATTTTCCTTTCCGT GCTGCGCTGC
MIT_Spar_c278_20970 + 480 1.72e-09 AAATGCGAAG AGTCTTTTTTAGCTTTTTTT GCCCTGCTGT
SGD_Scer_YDR047W + 733 3.76e-09 CGTCCCATTG AGTTTTATTTTCCTTCTCAT GGCACCTTCT
MIT_Smik_c935_20455 + 57 4.88e-09 ATATGTGATG AGTCCTTTTTACGTTCTTGT ATAACCTAAG
MIT_Sbay_c896_21277 + 10 2.83e-08 AGTGTTAAC AGTATCTTTTGCCTTTTTTT ATTCTAATAG
SGD_Scer_YOR176W + 478 3.32e-08 AGTGCGAAGA GTTCTTTTTTAGCTTTTTTT GTCCTGCTGT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c130_3923 2.5e-10 732_[+5]_248
WashU_Sbay_Contig480.2 1.1e-09 101_[+5]_606
WashU_Skud_Contig2050.4 1.6e-09 57_[+5]_650
WashU_Skud_Contig1362.1 1.6e-09 712_[+5]_29
MIT_Spar_c278_20970 1.7e-09 479_[+5]_228
SGD_Scer_YDR047W 3.8e-09 732_[+5]_248
MIT_Smik_c935_20455 4.9e-09 56_[+5]_651
MIT_Sbay_c896_21277 2.8e-08 9_[+5]_971
SGD_Scer_YOR176W 3.3e-08 477_[+5]_230
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
MIT_Spar_c130_3923 ( 733) AGTTTTATTTTCCTTCTCGT 1
WashU_Sbay_Contig480.2 ( 102) ATTTTTTTTTTCCTTCTTGT 1
WashU_Skud_Contig2050.4 ( 58) AATCTTTTTTTCCTTCTTTT 1
WashU_Skud_Contig1362.1 ( 713) AGTCTTATTTTCCTTTCCGT 1
MIT_Spar_c278_20970 ( 480) AGTCTTTTTTAGCTTTTTTT 1
SGD_Scer_YDR047W ( 733) AGTTTTATTTTCCTTCTCAT 1
MIT_Smik_c935_20455 ( 57) AGTCCTTTTTACGTTCTTGT 1
MIT_Sbay_c896_21277 ( 10) AGTATCTTTTGCCTTTTTTT 1
SGD_Scer_YOR176W ( 478) GTTCTTTTTTAGCTTTTTTT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 3.0e-008
145 -982 -66 -982
-154 -982 192 -55
-982 -982 -982 162
-154 166 -982 4
-982 -66 -982 145
-982 -66 -982 145
4 -982 -982 104
-982 -982 -982 162
-982 -982 -982 162
-982 -982 -982 162
4 -982 -66 78
-982 215 34 -982
-982 234 -66 -982
-982 -982 -982 162
-982 -982 -982 162
-982 166 -982 45
-982 -66 -982 145
-982 92 -982 104
-154 -982 134 45
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-008
0.888889 0.000000 0.111111 0.000000
0.111111 0.000000 0.666667 0.222222
0.000000 0.000000 0.000000 1.000000
0.111111 0.555556 0.000000 0.333333
0.000000 0.111111 0.000000 0.888889
0.000000 0.111111 0.000000 0.888889
0.333333 0.000000 0.000000 0.666667
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.333333 0.000000 0.111111 0.555556
0.000000 0.777778 0.222222 0.000000
0.000000 0.888889 0.111111 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.555556 0.000000 0.444444
0.000000 0.111111 0.000000 0.888889
0.000000 0.333333 0.000000 0.666667
0.111111 0.000000 0.444444 0.444444
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
A[GT]T[CT]TT[TA]TTT[TA][CG]CTT[CT]T[TC][GT]T
--------------------------------------------------------------------------------
Time 27.84 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR047W 1.02e-19 160_[-3(2.04e-07)]_31_[+5(1.41e-05)]_3_[+1(2.25e-10)]_133_[-2(1.16e-08)]_88_[+4(6.35e-05)]_217_[+5(3.76e-09)]_45_[-4(3.78e-09)]_183
MIT_Spar_c130_3923 3.55e-20 231_[+1(1.41e-09)]_134_[-2(2.39e-08)]_178_[+3(8.67e-05)]_5_[-3(7.51e-08)]_104_[+5(2.54e-10)]_55_[-4(3.78e-09)]_173
MIT_Sbay_c896_21277 2.88e-17 9_[+5(2.83e-08)]_148_[+5(7.36e-05)]_5_[+1(2.13e-10)]_452_[-2(2.87e-08)]_75_[+3(1.89e-07)]_41_[-4(1.01e-07)]_150
WashU_Skud_Contig1362.1 7.74e-20 47_[+4(4.74e-08)]_57_[-3(2.43e-08)]_53_[+1(2.94e-09)]_70_[+4(1.81e-05)]_366_[-2(4.27e-09)]_19_[+5(1.57e-09)]_29
SGD_Scer_YOR176W 1.14e-33 149_[+2(2.21e-12)]_26_[-3(1.12e-05)]_90_[+2(6.19e-05)]_152_[+5(3.32e-08)]_[+3(2.49e-12)]_40_[+1(6.74e-13)]_65_[+4(5.51e-13)]_65
MIT_Spar_c278_20970 7.69e-35 57_[+5(1.77e-06)]_29_[-4(3.91e-05)]_25_[+2(2.21e-12)]_27_[-2(6.64e-05)]_261_[+5(1.72e-09)]_[+3(1.41e-12)]_40_[+1(6.74e-13)]_67_[+4(1.12e-12)]_3_[-3(6.33e-05)]_38
MIT_Smik_c935_20455 6.08e-31 56_[+5(4.88e-09)]_70_[+2(3.24e-09)]_317_[+3(3.60e-13)]_40_[+1(1.42e-12)]_68_[+4(6.03e-12)]_76
WashU_Skud_Contig2050.4 1.32e-30 57_[+5(1.57e-09)]_78_[+2(3.61e-12)]_304_[+5(7.50e-05)]_1_[+3(1.02e-12)]_45_[+1(6.74e-13)]_66_[+4(2.81e-08)]_56
WashU_Sbay_Contig480.2 2.10e-32 101_[+5(1.11e-09)]_78_[+2(7.52e-12)]_37_[-5(3.91e-05)]_77_[+3(3.61e-05)]_44_[+2(3.84e-06)]_51_[+5(6.08e-06)]_1_[+3(1.02e-12)]_41_[+1(6.74e-13)]_66_[+4(2.48e-10)]_51
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************