********************************************************************************
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= HEM3-HEM13.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YDL205C 1.0000 860 MIT_Spar_c429_3020 1.0000 860
MIT_Smik_c193_2483 1.0000 860 MIT_Sbay_c841_3215 1.0000 860
WashU_Skud_Contig1850.5 1.0000 860 SGD_Scer_YDR044W 1.0000 1000
MIT_Spar_c130_3912 1.0000 1000 MIT_Sbay_c896_21290 1.0000 1000
WashU_Smik_Contig2283.3 1.0000 1000
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM3-HEM13.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= 8300 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.301 C 0.199 G 0.199 T 0.301
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 = 197 E-value = 2.8e-022
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :::::9692aa4:4::aa:a
pos.-specific C :::::::::::::::3::9:
probability G aa:aa1412::666:6::::
matrix T ::a:::::6:::4:a1::1:
bits 2.5 ** **
2.3 ** **
2.0 ** ** *
1.8 ** ** *
Information 1.5 ***** ** * ****
content 1.3 ****** * ** * ****
(31.6 bits) 1.0 ******** ***********
0.8 ******** ***********
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GGTGGAAATAAGGGTGAACA
consensus G A ATA C
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1850.5 - 716 1.22e-12 ATCCTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
MIT_Sbay_c841_3215 - 735 1.22e-12 GTCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
MIT_Spar_c429_3020 - 709 1.22e-12 ATCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
SGD_Scer_YDL205C - 708 1.22e-12 ATCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
MIT_Smik_c193_2483 - 709 1.22e-10 ATCGTTTGAG GGTGGAAATAAGGGTGAATA ATAAGGGGAG
MIT_Spar_c130_3912 + 679 1.35e-10 CAACGATTGT GGTGGAGAGAAATATCAACA GGGCAAGGCA
SGD_Scer_YDR044W + 684 3.84e-10 CAACAATTAC GGTGGGGAGAAATATCAACA AAAGGGCAAG
MIT_Sbay_c896_21290 + 685 5.43e-10 CGACTAAAAC GGTGGAGGAAAATATCAACA AGGCAAGGCT
WashU_Smik_Contig2283.3 + 687 5.84e-10 CAACAATTAC GGTGGAGAAAAATATTAACA AGGGAAGGCA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 1.2e-12 715_[-1]_125
MIT_Sbay_c841_3215 1.2e-12 734_[-1]_106
MIT_Spar_c429_3020 1.2e-12 708_[-1]_132
SGD_Scer_YDL205C 1.2e-12 707_[-1]_133
MIT_Smik_c193_2483 1.2e-10 708_[-1]_132
MIT_Spar_c130_3912 1.4e-10 678_[+1]_302
SGD_Scer_YDR044W 3.8e-10 683_[+1]_297
MIT_Sbay_c896_21290 5.4e-10 684_[+1]_296
WashU_Smik_Contig2283.3 5.8e-10 686_[+1]_294
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Skud_Contig1850.5 ( 716) GGTGGAAATAAGGGTGAACA 1
MIT_Sbay_c841_3215 ( 735) GGTGGAAATAAGGGTGAACA 1
MIT_Spar_c429_3020 ( 709) GGTGGAAATAAGGGTGAACA 1
SGD_Scer_YDL205C ( 708) GGTGGAAATAAGGGTGAACA 1
MIT_Smik_c193_2483 ( 709) GGTGGAAATAAGGGTGAATA 1
MIT_Spar_c130_3912 ( 679) GGTGGAGAGAAATATCAACA 1
SGD_Scer_YDR044W ( 684) GGTGGGGAGAAATATCAACA 1
MIT_Sbay_c896_21290 ( 685) GGTGGAGGAAAATATCAACA 1
WashU_Smik_Contig2283.3 ( 687) GGTGGAGAAAAATATTAACA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 2.8e-022
-982 -982 251 -982
-982 -982 251 -982
-982 -982 -982 162
-982 -982 251 -982
-982 -982 251 -982
145 -982 -66 -982
78 -982 134 -982
145 -982 -66 -982
-55 -982 34 78
162 -982 -982 -982
162 -982 -982 -982
45 -982 166 -982
-982 -982 166 45
45 -982 166 -982
-982 -982 -982 162
-982 92 166 -154
162 -982 -982 -982
162 -982 -982 -982
-982 234 -982 -154
162 -982 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.8e-022
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 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.555556 0.000000 0.444444 0.000000
0.888889 0.000000 0.111111 0.000000
0.222222 0.000000 0.222222 0.555556
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.000000 0.000000 0.555556 0.444444
0.444444 0.000000 0.555556 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.333333 0.555556 0.111111
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.888889 0.000000 0.111111
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
GGTGGA[AG]A[TAG]AA[GA][GT][GA]T[GC]AACA
--------------------------------------------------------------------------------
Time 7.14 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 199 E-value = 2.7e-023
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 3::1:a:6:::a7::::1:1
pos.-specific C ::a:6:4:::a:316:a878
probability G 7a:94:::6a:::::1:::1
matrix T ::::::644::::949:13:
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 GGCGCATAGGCAATCTCCCC
consensus A G CTT C T T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1850.5 + 692 2.30e-13 GTGACGTTTA GGCGCATAGGCAATCTCCCC TTATTGTTCA
SGD_Scer_YDL205C + 684 2.30e-13 GTGACGTTTA GGCGCATAGGCAATCTCCCC TTATTGTTCA
MIT_Sbay_c841_3215 + 711 3.52e-12 GTGACGTTTT AGCGCATAGGCAATCTCCCC TTATTGTTCA
MIT_Smik_c193_2483 + 685 3.52e-12 ATGACGTTTA AGCGCATAGGCAATCTCCCC TTATTATTCA
MIT_Spar_c429_3020 + 685 4.30e-12 GTGACGTTTA GGCGCATAGGCAACCTCCCC TTATTGTTCA
WashU_Smik_Contig2283.3 + 739 3.24e-11 ATTGAGAAGC GGCGGACTTGCACTTTCCTC GAAGAAAAAA
SGD_Scer_YDR044W + 733 3.60e-10 TCTGGAAAGT GGCAGACTTGCACTTTCCTC GAAAAGAAAA
MIT_Spar_c130_3912 + 730 1.03e-09 TTTTGGAAGT GGCGGACTTGCACTTTCTTG AAAAGAAAAA
MIT_Sbay_c896_21290 + 731 2.40e-09 TTCGAAGAAA AGCGGACTTGCAATTGCACA ACCGTATCGA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 2.3e-13 691_[+2]_149
SGD_Scer_YDL205C 2.3e-13 683_[+2]_157
MIT_Sbay_c841_3215 3.5e-12 710_[+2]_130
MIT_Smik_c193_2483 3.5e-12 684_[+2]_156
MIT_Spar_c429_3020 4.3e-12 684_[+2]_156
WashU_Smik_Contig2283.3 3.2e-11 738_[+2]_242
SGD_Scer_YDR044W 3.6e-10 732_[+2]_248
MIT_Spar_c130_3912 1e-09 729_[+2]_251
MIT_Sbay_c896_21290 2.4e-09 730_[+2]_250
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
WashU_Skud_Contig1850.5 ( 692) GGCGCATAGGCAATCTCCCC 1
SGD_Scer_YDL205C ( 684) GGCGCATAGGCAATCTCCCC 1
MIT_Sbay_c841_3215 ( 711) AGCGCATAGGCAATCTCCCC 1
MIT_Smik_c193_2483 ( 685) AGCGCATAGGCAATCTCCCC 1
MIT_Spar_c429_3020 ( 685) GGCGCATAGGCAACCTCCCC 1
WashU_Smik_Contig2283.3 ( 739) GGCGGACTTGCACTTTCCTC 1
SGD_Scer_YDR044W ( 733) GGCAGACTTGCACTTTCCTC 1
MIT_Spar_c130_3912 ( 730) GGCGGACTTGCACTTTCTTG 1
MIT_Sbay_c896_21290 ( 731) AGCGGACTTGCAATTGCACA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 2.7e-023
4 -982 192 -982
-982 -982 251 -982
-982 251 -982 -982
-154 -982 234 -982
-982 166 134 -982
162 -982 -982 -982
-982 134 -982 78
78 -982 -982 45
-982 -982 166 45
-982 -982 251 -982
-982 251 -982 -982
162 -982 -982 -982
104 92 -982 -982
-982 -66 -982 145
-982 166 -982 45
-982 -982 -66 145
-982 251 -982 -982
-154 215 -982 -154
-982 192 -982 4
-154 215 -66 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.7e-023
0.333333 0.000000 0.666667 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
0.000000 0.555556 0.444444 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.444444 0.000000 0.555556
0.555556 0.000000 0.000000 0.444444
0.000000 0.000000 0.555556 0.444444
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.666667 0.333333 0.000000 0.000000
0.000000 0.111111 0.000000 0.888889
0.000000 0.555556 0.000000 0.444444
0.000000 0.000000 0.111111 0.888889
0.000000 1.000000 0.000000 0.000000
0.111111 0.777778 0.000000 0.111111
0.000000 0.666667 0.000000 0.333333
0.111111 0.777778 0.111111 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[GA]GCG[CG]A[TC][AT][GT]GCA[AC]T[CT]TCC[CT]C
--------------------------------------------------------------------------------
Time 14.04 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 15 sites = 9 llr = 162 E-value = 1.1e-016
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A 1:::::6::6:::a:
pos.-specific C :79:1::a9:6a::a
probability G ::189:::::4:a::
matrix T 93:2:a4:14:::::
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 TCCGGTACCACCGAC
consensus T T T TG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
MIT_Smik_c193_2483 - 572 1.00e-10 TCTTGCCATA TCCGGTACCACCGAC ATACGCCGTC
MIT_Spar_c429_3020 - 571 1.00e-10 CTTTGTCACA TCCGGTACCACCGAC ATTCTGTTGC
MIT_Sbay_c896_21290 + 312 2.46e-09 GAAAAATGGC TTCGGTTCCTGCGAC TCGTTTAAAA
SGD_Scer_YDL205C - 570 2.75e-09 GCATTATCAC ACCGGTACCACCGAC ACATTCTGCT
WashU_Skud_Contig1850.5 - 575 3.32e-09 TCTTGCCACA TCCGCTACCACCGAC ACATTCCGTT
MIT_Sbay_c841_3215 - 581 6.14e-09 CTTTGCCCCA TCCGGTACTACCGAC ACATTGGCCG
WashU_Smik_Contig2283.3 + 309 6.34e-09 AATTTTGGTT TCGGGTTCCTGCGAC TCGTTTAAAA
MIT_Spar_c130_3912 + 306 1.39e-08 GAAATTTGGA TTCTGTTCCTGCGAC TCGTTTAAAA
SGD_Scer_YDR044W + 313 1.39e-08 GAAATTTGGC TTCTGTTCCTGCGAC TCGTTTAAAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c193_2483 1e-10 571_[-3]_274
MIT_Spar_c429_3020 1e-10 570_[-3]_275
MIT_Sbay_c896_21290 2.5e-09 311_[+3]_674
SGD_Scer_YDL205C 2.7e-09 569_[-3]_276
WashU_Skud_Contig1850.5 3.3e-09 574_[-3]_271
MIT_Sbay_c841_3215 6.1e-09 580_[-3]_265
WashU_Smik_Contig2283.3 6.3e-09 308_[+3]_677
MIT_Spar_c130_3912 1.4e-08 305_[+3]_680
SGD_Scer_YDR044W 1.4e-08 312_[+3]_673
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=15 seqs=9
MIT_Smik_c193_2483 ( 572) TCCGGTACCACCGAC 1
MIT_Spar_c429_3020 ( 571) TCCGGTACCACCGAC 1
MIT_Sbay_c896_21290 ( 312) TTCGGTTCCTGCGAC 1
SGD_Scer_YDL205C ( 570) ACCGGTACCACCGAC 1
WashU_Skud_Contig1850.5 ( 575) TCCGCTACCACCGAC 1
MIT_Sbay_c841_3215 ( 581) TCCGGTACTACCGAC 1
WashU_Smik_Contig2283.3 ( 309) TCGGGTTCCTGCGAC 1
MIT_Spar_c130_3912 ( 306) TTCTGTTCCTGCGAC 1
SGD_Scer_YDR044W ( 313) TTCTGTTCCTGCGAC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8174 bayes= 9.82531 E= 1.1e-016
-154 -982 -982 145
-982 192 -982 4
-982 234 -66 -982
-982 -982 215 -55
-982 -66 234 -982
-982 -982 -982 162
78 -982 -982 45
-982 251 -982 -982
-982 234 -982 -154
78 -982 -982 45
-982 166 134 -982
-982 251 -982 -982
-982 -982 251 -982
162 -982 -982 -982
-982 251 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 1.1e-016
0.111111 0.000000 0.000000 0.888889
0.000000 0.666667 0.000000 0.333333
0.000000 0.888889 0.111111 0.000000
0.000000 0.000000 0.777778 0.222222
0.000000 0.111111 0.888889 0.000000
0.000000 0.000000 0.000000 1.000000
0.555556 0.000000 0.000000 0.444444
0.000000 1.000000 0.000000 0.000000
0.000000 0.888889 0.000000 0.111111
0.555556 0.000000 0.000000 0.444444
0.000000 0.555556 0.444444 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
T[CT]C[GT]GT[AT]CC[AT][CG]CGAC
--------------------------------------------------------------------------------
Time 20.83 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 9 llr = 178 E-value = 5.9e-016
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A ::2::19a91:a:99:9a2:
pos.-specific C 1:214::::2:::::a:::1
probability G ::2:481:17a:a11:1:39
matrix T 9a3911::::::::::::4:
bits 2.5 * * *
2.3 * * *
2.0 * * * *
1.8 * * * *
Information 1.5 * * *** * * *
content 1.3 ** * ************* *
(28.5 bits) 1.0 ** *************** *
0.8 ** *************** *
0.5 ** *****************
0.3 ** *****************
0.0 --------------------
Multilevel TTTTCGAAAGGAGAACAATG
consensus A G C G
sequence C A
G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c130_3912 + 160 6.95e-11 TTATATAGCC TTTTCGAAACGAGAACAATG GACAAATCAA
MIT_Sbay_c896_21290 + 166 9.05e-11 TTATATAGCT TTCTCGAAGGGAGAACAATG GATAAATCAA
MIT_Smik_c193_2483 + 648 1.24e-10 CGCAAGGCGT TTATGGAAAGGAGGACAAGG TCAGAGGATG
SGD_Scer_YDL205C + 647 1.24e-10 CAAGGCGTTT TTGTTGAAAGGAGAACAAGG TTAGACGGTG
SGD_Scer_YDR044W + 164 4.24e-10 CTTATATAGC CTTTCGAAACGAGAACAATG GGCAAAGCAA
MIT_Spar_c429_3020 + 648 6.04e-10 CAAGGCGTTT TTATGGAAAGGAGAGCGAGG TTAGAGGGTG
MIT_Sbay_c841_3215 + 670 1.69e-09 CAAAGGCGCT TTGTGGGAAGGAGAACAAAC AACATTAGAG
WashU_Skud_Contig1850.5 + 655 2.34e-09 ACAAGGCTTT TTCCGTAAAGGAGAACAAAG TTGGAAGGTG
WashU_Smik_Contig2283.3 + 156 3.18e-09 TTATATAGCC TTTTCAAAAAGAGAACAATG GTCAAATAAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c130_3912 6.9e-11 159_[+4]_821
MIT_Sbay_c896_21290 9.1e-11 165_[+4]_815
MIT_Smik_c193_2483 1.2e-10 647_[+4]_193
SGD_Scer_YDL205C 1.2e-10 646_[+4]_194
SGD_Scer_YDR044W 4.2e-10 163_[+4]_817
MIT_Spar_c429_3020 6e-10 647_[+4]_193
MIT_Sbay_c841_3215 1.7e-09 669_[+4]_171
WashU_Skud_Contig1850.5 2.3e-09 654_[+4]_186
WashU_Smik_Contig2283.3 3.2e-09 155_[+4]_825
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=9
MIT_Spar_c130_3912 ( 160) TTTTCGAAACGAGAACAATG 1
MIT_Sbay_c896_21290 ( 166) TTCTCGAAGGGAGAACAATG 1
MIT_Smik_c193_2483 ( 648) TTATGGAAAGGAGGACAAGG 1
SGD_Scer_YDL205C ( 647) TTGTTGAAAGGAGAACAAGG 1
SGD_Scer_YDR044W ( 164) CTTTCGAAACGAGAACAATG 1
MIT_Spar_c429_3020 ( 648) TTATGGAAAGGAGAGCGAGG 1
MIT_Sbay_c841_3215 ( 670) TTGTGGGAAGGAGAACAAAC 1
WashU_Skud_Contig1850.5 ( 655) TTCCGTAAAGGAGAACAAAG 1
WashU_Smik_Contig2283.3 ( 156) TTTTCAAAAAGAGAACAATG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 5.9e-016
-982 -66 -982 145
-982 -982 -982 162
-55 34 34 4
-982 -66 -982 145
-982 134 134 -154
-154 -982 215 -154
145 -982 -66 -982
162 -982 -982 -982
145 -982 -66 -982
-154 34 192 -982
-982 -982 251 -982
162 -982 -982 -982
-982 -982 251 -982
145 -982 -66 -982
145 -982 -66 -982
-982 251 -982 -982
145 -982 -66 -982
162 -982 -982 -982
-55 -982 92 45
-982 -66 234 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.9e-016
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.000000 1.000000
0.222222 0.222222 0.222222 0.333333
0.000000 0.111111 0.000000 0.888889
0.000000 0.444444 0.444444 0.111111
0.111111 0.000000 0.777778 0.111111
0.888889 0.000000 0.111111 0.000000
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.111111 0.222222 0.666667 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 1.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
1.000000 0.000000 0.000000 0.000000
0.222222 0.000000 0.333333 0.444444
0.000000 0.111111 0.888889 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
TT[TACGA]T[CG]GAAA[GC]GAGAACAA[TGA]G
--------------------------------------------------------------------------------
Time 27.50 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 178 E-value = 5.2e-014
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A :::::::::::3:::a::::
pos.-specific C 84::1122:34:4a::::::
probability G :::::::::::1::::::a:
matrix T 26aa9988a7666:a:aa:a
bits 2.5 * *
2.3 * *
2.0 * *
1.8 * *
Information 1.5 * ** * *******
content 1.3 * **** * *******
(28.6 bits) 1.0 *********** ********
0.8 *********** ********
0.5 *********** ********
0.3 ********************
0.0 --------------------
Multilevel CTTTTTTTTTTTTCTATTGT
consensus TC CC CCAC
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Smik_Contig2283.3 - 113 4.87e-11 CACATATTTT CCTTTTTTTCCACCTATTGT CTCACCTGTT
MIT_Spar_c130_3912 - 117 1.86e-10 CACGGATTTT CCTTTTTTTCCGCCTATTGT CTTTCTTTGT
WashU_Skud_Contig1850.5 + 46 2.33e-10 AGTTTTCCTG CTTTTTTTTTTTTCTATTGT TCTAGAAACT
MIT_Smik_c193_2483 + 49 6.29e-10 ACTATCTGGC CTTTTTCTTTTTTCTATTGT TCTAGATACT
MIT_Spar_c429_3020 + 47 7.60e-10 GATTTTCTTG CCTTTTCCTTTTTCTATTGT TCTAGATACT
SGD_Scer_YDL205C + 47 1.27e-09 ATTTTCTTCG CTTTTCTTTTTTTCTATTGT TCTAGATATT
MIT_Sbay_c896_21290 - 121 1.43e-09 CGCATTTTCT TTTTTTTTTTCACCTATTGT TCGCTGCCAA
SGD_Scer_YDR044W - 120 1.50e-09 CGGATTTTCC TTTTTTTTTCCACCTATTGT CTTTCTTTGT
MIT_Sbay_c841_3215 + 48 1.62e-09 TATTTTTTTT CCTTCTTCTTTTTCTATTGT TCTAGATGCT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Smik_Contig2283.3 4.9e-11 112_[-5]_868
MIT_Spar_c130_3912 1.9e-10 116_[-5]_864
WashU_Skud_Contig1850.5 2.3e-10 45_[+5]_795
MIT_Smik_c193_2483 6.3e-10 48_[+5]_792
MIT_Spar_c429_3020 7.6e-10 46_[+5]_794
SGD_Scer_YDL205C 1.3e-09 46_[+5]_794
MIT_Sbay_c896_21290 1.4e-09 120_[-5]_860
SGD_Scer_YDR044W 1.5e-09 119_[-5]_861
MIT_Sbay_c841_3215 1.6e-09 47_[+5]_793
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
WashU_Smik_Contig2283.3 ( 113) CCTTTTTTTCCACCTATTGT 1
MIT_Spar_c130_3912 ( 117) CCTTTTTTTCCGCCTATTGT 1
WashU_Skud_Contig1850.5 ( 46) CTTTTTTTTTTTTCTATTGT 1
MIT_Smik_c193_2483 ( 49) CTTTTTCTTTTTTCTATTGT 1
MIT_Spar_c429_3020 ( 47) CCTTTTCCTTTTTCTATTGT 1
SGD_Scer_YDL205C ( 47) CTTTTCTTTTTTTCTATTGT 1
MIT_Sbay_c896_21290 ( 121) TTTTTTTTTTCACCTATTGT 1
SGD_Scer_YDR044W ( 120) TTTTTTTTTCCACCTATTGT 1
MIT_Sbay_c841_3215 ( 48) CCTTCTTCTTTTTCTATTGT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 5.2e-014
-982 215 -982 -55
-982 134 -982 78
-982 -982 -982 162
-982 -982 -982 162
-982 -66 -982 145
-982 -66 -982 145
-982 34 -982 126
-982 34 -982 126
-982 -982 -982 162
-982 92 -982 104
-982 134 -982 78
4 -982 -66 78
-982 134 -982 78
-982 251 -982 -982
-982 -982 -982 162
162 -982 -982 -982
-982 -982 -982 162
-982 -982 -982 162
-982 -982 251 -982
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.2e-014
0.000000 0.777778 0.000000 0.222222
0.000000 0.444444 0.000000 0.555556
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.111111 0.000000 0.888889
0.000000 0.111111 0.000000 0.888889
0.000000 0.222222 0.000000 0.777778
0.000000 0.222222 0.000000 0.777778
0.000000 0.000000 0.000000 1.000000
0.000000 0.333333 0.000000 0.666667
0.000000 0.444444 0.000000 0.555556
0.333333 0.000000 0.111111 0.555556
0.000000 0.444444 0.000000 0.555556
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
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 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
[CT][TC]TTTT[TC][TC]T[TC][TC][TA][TC]CTATTGT
--------------------------------------------------------------------------------
Time 34.04 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDL205C 3.32e-30 46_[+5(1.27e-09)]_156_[+5(7.84e-05)]_327_[-3(2.75e-09)]_62_[+4(1.24e-10)]_17_[+2(2.30e-13)]_4_[-1(1.22e-12)]_133
MIT_Spar_c429_3020 6.35e-30 46_[+5(7.60e-10)]_170_[+5(7.84e-05)]_251_[+1(3.79e-05)]_43_[-3(1.00e-10)]_62_[+4(6.04e-10)]_17_[+2(4.30e-12)]_4_[-1(1.22e-12)]_132
MIT_Smik_c193_2483 7.78e-29 48_[+5(6.29e-10)]_174_[+5(2.65e-05)]_309_[-3(1.00e-10)]_61_[+4(1.24e-10)]_17_[+2(3.52e-12)]_4_[-1(1.22e-10)]_132
MIT_Sbay_c841_3215 1.43e-27 47_[+5(1.62e-09)]_297_[-5(2.91e-05)]_196_[-3(6.14e-09)]_74_[+4(1.69e-09)]_21_[+2(3.52e-12)]_4_[-1(1.22e-12)]_106
WashU_Skud_Contig1850.5 1.30e-29 45_[+5(2.33e-10)]_131_[-4(6.41e-05)]_19_[+5(7.84e-05)]_319_[-3(3.32e-09)]_1_[-3(6.63e-05)]_49_[+4(2.34e-09)]_17_[+2(2.30e-13)]_4_[-1(1.22e-12)]_125
SGD_Scer_YDR044W 2.91e-23 119_[-5(1.50e-09)]_24_[+4(4.24e-10)]_18_[+3(7.91e-05)]_42_[+4(4.47e-05)]_34_[+3(1.39e-08)]_271_[+4(2.94e-05)]_65_[+1(3.84e-10)]_29_[+2(3.60e-10)]_248
MIT_Spar_c130_3912 7.46e-25 116_[-5(1.86e-10)]_23_[+4(6.95e-11)]_126_[+3(1.39e-08)]_358_[+1(1.35e-10)]_31_[+2(1.03e-09)]_251
MIT_Sbay_c896_21290 1.06e-23 85_[-5(1.91e-05)]_15_[-5(1.43e-09)]_25_[+4(9.05e-11)]_126_[+3(2.46e-09)]_140_[-5(3.09e-05)]_198_[+1(5.43e-10)]_26_[+2(2.40e-09)]_48_[+5(4.88e-05)]_182
WashU_Smik_Contig2283.3 5.66e-25 86_[+1(4.04e-05)]_6_[-5(4.87e-11)]_23_[+4(3.18e-09)]_133_[+3(6.34e-09)]_144_[-5(8.86e-05)]_199_[+1(5.84e-10)]_32_[+2(3.24e-11)]_27_[-1(3.56e-05)]_195
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************