********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date: )
For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.
This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs. MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************
********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:
Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************
********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM1-HEM3.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YDR232W 1.0000 498 MIT_Spar_c117_4603 1.0000 498
MIT_Smik_c228_4055 1.0000 498 WashU_Skud_Contig2069.5 1.0000 498
WashU_Sbay_Contig461.5 1.0000 498 SGD_Scer_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
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM1-HEM3.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= 6790 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.293 C 0.207 G 0.207 T 0.293
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 = 225 E-value = 3.0e-032
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :68:aa:1:4:aa::55a:9
pos.-specific C 1::a::::11a::::5::::
probability G 94:::::785:::aa:5:91
matrix T ::2:::a21:::::::::1:
bits 2.5 * * **
2.3 * * **
2.0 * * * ** *
1.8 * * * ** *
Information 1.5 * **** * ***** **
content 1.3 * **** * ***** ***
(32.4 bits) 1.0 ********* **********
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GAACAATGGGCAAGGAAAGA
consensus GT T A CG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig461.5 + 278 1.41e-12 CACCGGGACA GAACAATGGGCAAGGCAAGA TGAAAAATCT
MIT_Smik_c228_4055 + 283 1.41e-12 CATTGAATTA GAACAATGGGCAAGGCAAGA TGAAAATTTC
MIT_Spar_c117_4603 + 280 1.41e-12 GCATGGGTCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
SGD_Scer_YDR232W + 285 1.41e-12 GCATGGATCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
MIT_Sbay_c841_3215 + 363 6.65e-11 AGAGCCCAAG GGACAATAGACAAGGAGAGA ACCACCAACT
WashU_Skud_Contig1850.5 + 365 1.00e-10 AAAGCTCCAG GAACAATGCCCAAGGAGAGA AAGAGTGCTA
MIT_Spar_c429_3020 + 367 1.18e-10 CGCTCCCCAG GGTCAATTGACAAGGAGAGA AGGAATGTTA
SGD_Scer_YDL205C + 364 1.18e-10 CGCTCCCCAG GGTCAATTGACAAGGAGAGA AGGAATGTTA
WashU_Skud_Contig2069.5 + 283 1.74e-10 CACTGGATCG GAACAATGGGCAAGGCAATG TGAAAAATTT
MIT_Smik_c193_2483 + 366 3.73e-10 AAATCCCCAG CGACAATGTACAAGGAGAGA AGAAATGATA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig461.5 1.4e-12 277_[+1]_201
MIT_Smik_c228_4055 1.4e-12 282_[+1]_196
MIT_Spar_c117_4603 1.4e-12 279_[+1]_199
SGD_Scer_YDR232W 1.4e-12 284_[+1]_194
MIT_Sbay_c841_3215 6.6e-11 362_[+1]_478
WashU_Skud_Contig1850.5 1e-10 364_[+1]_476
MIT_Spar_c429_3020 1.2e-10 366_[+1]_474
SGD_Scer_YDL205C 1.2e-10 363_[+1]_477
WashU_Skud_Contig2069.5 1.7e-10 282_[+1]_196
MIT_Smik_c193_2483 3.7e-10 365_[+1]_475
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=10
WashU_Sbay_Contig461.5 ( 278) GAACAATGGGCAAGGCAAGA 1
MIT_Smik_c228_4055 ( 283) GAACAATGGGCAAGGCAAGA 1
MIT_Spar_c117_4603 ( 280) GAACAATGGGCAAGGCAAGA 1
SGD_Scer_YDR232W ( 285) GAACAATGGGCAAGGCAAGA 1
MIT_Sbay_c841_3215 ( 363) GGACAATAGACAAGGAGAGA 1
WashU_Skud_Contig1850.5 ( 365) GAACAATGCCCAAGGAGAGA 1
MIT_Spar_c429_3020 ( 367) GGTCAATTGACAAGGAGAGA 1
SGD_Scer_YDL205C ( 364) GGTCAATTGACAAGGAGAGA 1
WashU_Skud_Contig2069.5 ( 283) GAACAATGGGCAAGGCAATG 1
MIT_Smik_c193_2483 ( 366) CGACAATGTACAAGGAGAGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6600 bayes= 9.36413 E= 3.0e-032
-997 -81 236 -997
89 -997 119 -997
130 -997 -997 -70
-997 251 -997 -997
162 -997 -997 -997
162 -997 -997 -997
-997 -997 -997 162
-169 -997 199 -70
-997 -81 219 -169
30 -81 151 -997
-997 251 -997 -997
162 -997 -997 -997
162 -997 -997 -997
-997 -997 251 -997
-997 -997 251 -997
62 151 -997 -997
62 -997 151 -997
162 -997 -997 -997
-997 -997 236 -169
147 -997 -81 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.0e-032
0.000000 0.100000 0.900000 0.000000
0.600000 0.000000 0.400000 0.000000
0.800000 0.000000 0.000000 0.200000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.100000 0.000000 0.700000 0.200000
0.000000 0.100000 0.800000 0.100000
0.400000 0.100000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.500000 0.000000 0.500000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.900000 0.100000
0.900000 0.000000 0.100000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
G[AG][AT]CAAT[GT]G[GA]CAAGG[AC][AG]AGA
--------------------------------------------------------------------------------
Time 4.86 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 10 llr = 213 E-value = 1.1e-027
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A :::a::::::5343::::13
pos.-specific C a:5::::::9::52296593
probability G ::::::aa:::7157::5:4
matrix T :a5:aa::a15:::114:::
bits 2.5 * **
2.3 * **
2.0 * ** * * *
1.8 * ** * * *
Information 1.5 ** ******* * **
content 1.3 ** ******* * *****
(30.7 bits) 1.0 ********** * *****
0.8 ********** *********
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CTCATTGGTCAGCGGCCCCG
consensus T TAAAC TG A
sequence C C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2069.5 - 358 1.23e-13 GCCTTCGTCG CTCATTGGTCTGCGGCCGCG GACGCTTTTT
MIT_Spar_c117_4603 - 356 1.23e-13 GCCTTCGTCG CTCATTGGTCTGCGGCCGCG GGCGCTTTTT
SGD_Scer_YDR232W - 361 1.23e-13 GCCTTCGTCG CTCATTGGTCTGCGGCCGCG GGCGCTTTTT
WashU_Sbay_Contig461.5 - 355 4.09e-12 GTCTTCGTCG CTCATTGGTCTGCGCCCGCC GGCGTTTTTT
MIT_Spar_c429_3020 + 344 8.68e-11 TCATCGGTTT CTTATTGGTCAGACGCTCCC CAGGGTCAAT
SGD_Scer_YDL205C + 341 8.68e-11 TCATCGGTTT CTTATTGGTCAGACGCTCCC CAGGGTCAAT
MIT_Smik_c228_4055 - 358 3.24e-10 GCTTTCGTCG CTCATTGGTCTGCGCTTGCG GGCGCTTTTT
WashU_Skud_Contig1850.5 + 344 5.80e-10 TCATCGTTTT CTTATTGGTCAAAAGCTCCA GGAACAATGC
MIT_Sbay_c841_3215 + 342 2.64e-09 TCATCGTTAT CTTATTGGTCAAGAGCCCAA GGGACAATAG
MIT_Smik_c193_2483 + 345 5.92e-09 TCATCGTTAT CTTATTGGTTAAAATCCCCA GCGACAATGT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2069.5 1.2e-13 357_[-2]_121
MIT_Spar_c117_4603 1.2e-13 355_[-2]_123
SGD_Scer_YDR232W 1.2e-13 360_[-2]_118
WashU_Sbay_Contig461.5 4.1e-12 354_[-2]_124
MIT_Spar_c429_3020 8.7e-11 343_[+2]_497
SGD_Scer_YDL205C 8.7e-11 340_[+2]_500
MIT_Smik_c228_4055 3.2e-10 357_[-2]_121
WashU_Skud_Contig1850.5 5.8e-10 343_[+2]_497
MIT_Sbay_c841_3215 2.6e-09 341_[+2]_499
MIT_Smik_c193_2483 5.9e-09 344_[+2]_496
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=10
WashU_Skud_Contig2069.5 ( 358) CTCATTGGTCTGCGGCCGCG 1
MIT_Spar_c117_4603 ( 356) CTCATTGGTCTGCGGCCGCG 1
SGD_Scer_YDR232W ( 361) CTCATTGGTCTGCGGCCGCG 1
WashU_Sbay_Contig461.5 ( 355) CTCATTGGTCTGCGCCCGCC 1
MIT_Spar_c429_3020 ( 344) CTTATTGGTCAGACGCTCCC 1
SGD_Scer_YDL205C ( 341) CTTATTGGTCAGACGCTCCC 1
MIT_Smik_c228_4055 ( 358) CTCATTGGTCTGCGCTTGCG 1
WashU_Skud_Contig1850.5 ( 344) CTTATTGGTCAAAAGCTCCA 1
MIT_Sbay_c841_3215 ( 342) CTTATTGGTCAAGAGCCCAA 1
MIT_Smik_c193_2483 ( 345) CTTATTGGTTAAAATCCCCA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6600 bayes= 9.36413 E= 1.1e-027
-997 251 -997 -997
-997 -997 -997 162
-997 151 -997 62
162 -997 -997 -997
-997 -997 -997 162
-997 -997 -997 162
-997 -997 251 -997
-997 -997 251 -997
-997 -997 -997 162
-997 236 -997 -169
62 -997 -997 62
-11 -997 199 -997
30 151 -81 -997
-11 19 151 -997
-997 19 199 -169
-997 236 -997 -169
-997 177 -997 30
-997 151 151 -997
-169 236 -997 -997
-11 77 119 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.1e-027
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.000000 0.500000
1.000000 0.000000 0.000000 0.000000
0.000000 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 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.900000 0.000000 0.100000
0.500000 0.000000 0.000000 0.500000
0.300000 0.000000 0.700000 0.000000
0.400000 0.500000 0.100000 0.000000
0.300000 0.200000 0.500000 0.000000
0.000000 0.200000 0.700000 0.100000
0.000000 0.900000 0.000000 0.100000
0.000000 0.600000 0.000000 0.400000
0.000000 0.500000 0.500000 0.000000
0.100000 0.900000 0.000000 0.000000
0.300000 0.300000 0.400000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
CT[CT]ATTGGTC[AT][GA][CA][GAC][GC]C[CT][CG]C[GAC]
--------------------------------------------------------------------------------
Time 9.68 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 15 sites = 10 llr = 175 E-value = 1.1e-018
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :51:a:::::576::
pos.-specific C ::5a:aa5:a:::4:
probability G ::4::::5::5346a
matrix T a5::::::a::::::
bits 2.5 * ** * *
2.3 * ** * *
2.0 * ** * *
1.8 * ** * *
Information 1.5 * ******* **
content 1.3 * ******* **
(25.2 bits) 1.0 * *************
0.8 * *************
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel TACCACCCTCAAAGG
consensus TG G GGGC
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Sbay_Contig461.5 + 431 1.76e-09 AGGTCCGCTA TAGCACCGTCGAGGG GGACCGCTAT
MIT_Smik_c228_4055 + 431 3.51e-09 AAGTTTATTA TAGCACCGTCGGGGG GAAGCATTAT
MIT_Spar_c117_4603 + 430 3.51e-09 AAGCTTATTA TAGCACCGTCGGGGG GACCACTATA
SGD_Scer_YDR232W + 435 3.51e-09 AAGCTTATTA TAGCACCGTCGGGGG TACCACCACT
WashU_Skud_Contig1850.5 + 729 7.37e-09 TCACCCTTAT TTCCACCCTCAAAGG ATAAAGCTTG
MIT_Sbay_c841_3215 + 748 1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ACAAGGCTTG
MIT_Smik_c193_2483 + 722 1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ATAAAGCTTG
MIT_Spar_c429_3020 + 722 1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ATAAAGCTTG
SGD_Scer_YDL205C + 721 1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ATAAAGCTTG
WashU_Skud_Contig2069.5 + 432 2.21e-08 AAGTCCGTCA TAACACCGTCGAAGG GGCACCACTA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig461.5 1.8e-09 430_[+3]_53
MIT_Smik_c228_4055 3.5e-09 430_[+3]_53
MIT_Spar_c117_4603 3.5e-09 429_[+3]_54
SGD_Scer_YDR232W 3.5e-09 434_[+3]_49
WashU_Skud_Contig1850.5 7.4e-09 728_[+3]_117
MIT_Sbay_c841_3215 1.5e-08 747_[+3]_98
MIT_Smik_c193_2483 1.5e-08 721_[+3]_124
MIT_Spar_c429_3020 1.5e-08 721_[+3]_124
SGD_Scer_YDL205C 1.5e-08 720_[+3]_125
WashU_Skud_Contig2069.5 2.2e-08 431_[+3]_52
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=15 seqs=10
WashU_Sbay_Contig461.5 ( 431) TAGCACCGTCGAGGG 1
MIT_Smik_c228_4055 ( 431) TAGCACCGTCGGGGG 1
MIT_Spar_c117_4603 ( 430) TAGCACCGTCGGGGG 1
SGD_Scer_YDR232W ( 435) TAGCACCGTCGGGGG 1
WashU_Skud_Contig1850.5 ( 729) TTCCACCCTCAAAGG 1
MIT_Sbay_c841_3215 ( 748) TTCCACCCTCAAACG 1
MIT_Smik_c193_2483 ( 722) TTCCACCCTCAAACG 1
MIT_Spar_c429_3020 ( 722) TTCCACCCTCAAACG 1
SGD_Scer_YDL205C ( 721) TTCCACCCTCAAACG 1
WashU_Skud_Contig2069.5 ( 432) TAACACCGTCGAAGG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 6650 bayes= 9.37504 E= 1.1e-018
-997 -997 -997 162
62 -997 -997 62
-169 151 119 -997
-997 251 -997 -997
162 -997 -997 -997
-997 251 -997 -997
-997 251 -997 -997
-997 151 151 -997
-997 -997 -997 162
-997 251 -997 -997
62 -997 151 -997
111 -997 77 -997
89 -997 119 -997
-997 119 177 -997
-997 -997 251 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.1e-018
0.000000 0.000000 0.000000 1.000000
0.500000 0.000000 0.000000 0.500000
0.100000 0.500000 0.400000 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
0.000000 1.000000 0.000000 0.000000
0.000000 0.500000 0.500000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.500000 0.000000 0.500000 0.000000
0.700000 0.000000 0.300000 0.000000
0.600000 0.000000 0.400000 0.000000
0.000000 0.400000 0.600000 0.000000
0.000000 0.000000 1.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
T[AT][CG]CACC[CG]TC[AG][AG][AG][GC]G
--------------------------------------------------------------------------------
Time 14.37 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 10 llr = 206 E-value = 1.9e-024
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 4:a612::5:::::4214::
pos.-specific C 5::1::5::a4:::32:6:7
probability G 1a:398:a5:5:::168:a2
matrix T ::::::5:::1aaa2:1::1
bits 2.5 * * * *
2.3 * * * *
2.0 * * * * *
1.8 * * * * *
Information 1.5 ** ** * * *** * *
content 1.3 ** ** * * *** ****
(29.7 bits) 1.0 ** ********** *****
0.8 ************** *****
0.5 ************** *****
0.3 ********************
0.0 --------------------
Multilevel CGAAGGCGACGTTTAGGCGC
consensus A G AT G C CA A G
sequence TC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YDR232W + 384 9.38e-12 CAATGAGCGA CGAAGGCGGCCTTTCCGAGC GGTAGGGTAA
MIT_Spar_c429_3020 + 670 1.07e-11 GAGCGAGGTT AGAGGGTGACGTTTAGGCGC ATAGGCAACC
WashU_Skud_Contig1850.5 + 677 3.00e-11 GAACAAAGTT GGAAGGTGACGTTTAGGCGC ATAGGCAATC
SGD_Scer_YDL205C + 669 5.20e-11 GAACAAGGTT AGACGGTGACGTTTAGGCGC ATAGGCAATC
WashU_Skud_Contig2069.5 + 381 7.97e-11 CAATGAGCGA CGAAGGCGGCCTTTCGTAGC AGCAGGGTAA
MIT_Sbay_c841_3215 + 696 2.22e-10 AAACAACATT AGAGGGTGACGTTTTAGCGC ATAGGCAATC
MIT_Spar_c117_4603 + 379 2.42e-10 CAATGAGCGA CGAAGGCGGCCTTTCCGAGT GGTAGGGTAA
MIT_Smik_c193_2483 + 670 7.21e-10 GGACAAGGTC AGAGGATGACGTTTAAGCGC ATAGGCAATC
WashU_Sbay_Contig461.5 + 378 1.03e-09 CAATGAGCGA CGAAGACGGCTTTTGGGCGG GGCAGGGTAA
MIT_Smik_c228_4055 + 381 5.22e-09 CAATGAGCGA CGAAAGCGGCCTTTTGAAGG GTAGGGTAAT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR232W 9.4e-12 383_[+4]_95
MIT_Spar_c429_3020 1.1e-11 669_[+4]_171
WashU_Skud_Contig1850.5 3e-11 676_[+4]_164
SGD_Scer_YDL205C 5.2e-11 668_[+4]_172
WashU_Skud_Contig2069.5 8e-11 380_[+4]_98
MIT_Sbay_c841_3215 2.2e-10 695_[+4]_145
MIT_Spar_c117_4603 2.4e-10 378_[+4]_100
MIT_Smik_c193_2483 7.2e-10 669_[+4]_171
WashU_Sbay_Contig461.5 1e-09 377_[+4]_101
MIT_Smik_c228_4055 5.2e-09 380_[+4]_98
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=10
SGD_Scer_YDR232W ( 384) CGAAGGCGGCCTTTCCGAGC 1
MIT_Spar_c429_3020 ( 670) AGAGGGTGACGTTTAGGCGC 1
WashU_Skud_Contig1850.5 ( 677) GGAAGGTGACGTTTAGGCGC 1
SGD_Scer_YDL205C ( 669) AGACGGTGACGTTTAGGCGC 1
WashU_Skud_Contig2069.5 ( 381) CGAAGGCGGCCTTTCGTAGC 1
MIT_Sbay_c841_3215 ( 696) AGAGGGTGACGTTTTAGCGC 1
MIT_Spar_c117_4603 ( 379) CGAAGGCGGCCTTTCCGAGT 1
MIT_Smik_c193_2483 ( 670) AGAGGATGACGTTTAAGCGC 1
WashU_Sbay_Contig461.5 ( 378) CGAAGACGGCTTTTGGGCGG 1
MIT_Smik_c228_4055 ( 381) CGAAAGCGGCCTTTTGAAGG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6600 bayes= 9.36413 E= 1.9e-024
30 151 -81 -997
-997 -997 251 -997
162 -997 -997 -997
89 -81 77 -997
-169 -997 236 -997
-70 -997 219 -997
-997 151 -997 62
-997 -997 251 -997
62 -997 151 -997
-997 251 -997 -997
-997 119 151 -169
-997 -997 -997 162
-997 -997 -997 162
-997 -997 -997 162
30 77 -81 -70
-70 19 177 -997
-169 -997 219 -169
30 177 -997 -997
-997 -997 251 -997
-997 199 19 -169
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.9e-024
0.400000 0.500000 0.100000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.600000 0.100000 0.300000 0.000000
0.100000 0.000000 0.900000 0.000000
0.200000 0.000000 0.800000 0.000000
0.000000 0.500000 0.000000 0.500000
0.000000 0.000000 1.000000 0.000000
0.500000 0.000000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.400000 0.500000 0.100000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.400000 0.300000 0.100000 0.200000
0.200000 0.200000 0.600000 0.000000
0.100000 0.000000 0.800000 0.100000
0.400000 0.600000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.700000 0.200000 0.100000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[CA]GA[AG]G[GA][CT]G[AG]C[GC]TTT[ACT][GAC]G[CA]G[CG]
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Time 18.89 secs.
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MOTIF 5 width = 15 sites = 10 llr = 163 E-value = 1.8e-014
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Motif 5 Description
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Simplified A ::::::::4::::::
pos.-specific C a7:116a::84a11:
probability G ::9:14::61::::6
matrix T :3198::a:16:994
bits 2.5 * * *
2.3 * * *
2.0 * * * *
1.8 * * * *
Information 1.5 * * *** * *
content 1.3 **** ***** ****
(23.5 bits) 1.0 ***************
0.8 ***************
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel CCGTTCCTGCTCTTG
consensus T G A C T
sequence
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Motif 5 sites sorted by position p-value
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Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Sbay_Contig461.5 + 308 2.85e-10 TGAAAAATCT CCGTTCCTGCTCTTG CTTGATATAT
WashU_Skud_Contig2069.5 + 313 2.85e-10 TGAAAAATTT CCGTTCCTGCTCTTG CTTCATATAT
MIT_Smik_c228_4055 + 312 1.62e-09 ATGAAAATTT CCGTTCCTGCTCTTT CTTCATATAT
SGD_Scer_YDR232W + 315 1.62e-09 TGAAAAATTT CCGTTCCTGCTCTTT CTTCATATAT
MIT_Spar_c117_4603 + 310 1.17e-08 TGAAAAATTT CTGTTCCTGCTCTTT CTTCATATAT
MIT_Smik_c193_2483 - 552 1.46e-08 CCGACATACG CCGTCGCTACCCTTG CAGTTCAAGT
MIT_Spar_c429_3020 - 553 1.46e-08 CACCGACATT CTGTTGCTACCCTTG TAGTTCAAGT
WashU_Skud_Contig1850.5 - 555 4.54e-08 CCGACACATT CCGTTGCTATCCTTG TAGTTCCGTT
SGD_Scer_YDL205C - 550 6.46e-08 CCGACACATT CTGCTGCTACCCTTG TAGTTTAAGT
MIT_Sbay_c841_3215 - 516 1.21e-06 TCTTGCAAGC CCTTGCCTGGTCCCT GGCAGCGCGG
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Motif 5 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig461.5 2.8e-10 307_[+5]_176
WashU_Skud_Contig2069.5 2.8e-10 312_[+5]_171
MIT_Smik_c228_4055 1.6e-09 311_[+5]_172
SGD_Scer_YDR232W 1.6e-09 314_[+5]_169
MIT_Spar_c117_4603 1.2e-08 309_[+5]_174
MIT_Smik_c193_2483 1.5e-08 551_[-5]_294
MIT_Spar_c429_3020 1.5e-08 552_[-5]_293
WashU_Skud_Contig1850.5 4.5e-08 554_[-5]_291
SGD_Scer_YDL205C 6.5e-08 549_[-5]_296
MIT_Sbay_c841_3215 1.2e-06 515_[-5]_330
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Motif 5 in BLOCKS format
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BL MOTIF 5 width=15 seqs=10
WashU_Sbay_Contig461.5 ( 308) CCGTTCCTGCTCTTG 1
WashU_Skud_Contig2069.5 ( 313) CCGTTCCTGCTCTTG 1
MIT_Smik_c228_4055 ( 312) CCGTTCCTGCTCTTT 1
SGD_Scer_YDR232W ( 315) CCGTTCCTGCTCTTT 1
MIT_Spar_c117_4603 ( 310) CTGTTCCTGCTCTTT 1
MIT_Smik_c193_2483 ( 552) CCGTCGCTACCCTTG 1
MIT_Spar_c429_3020 ( 553) CTGTTGCTACCCTTG 1
WashU_Skud_Contig1850.5 ( 555) CCGTTGCTATCCTTG 1
SGD_Scer_YDL205C ( 550) CTGCTGCTACCCTTG 1
MIT_Sbay_c841_3215 ( 516) CCTTGCCTGGTCCCT 1
//
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Motif 5 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 15 n= 6650 bayes= 9.37504 E= 1.8e-014
-997 251 -997 -997
-997 199 -997 -11
-997 -997 236 -169
-997 -81 -997 147
-997 -81 -81 130
-997 177 119 -997
-997 251 -997 -997
-997 -997 -997 162
30 -997 177 -997
-997 219 -81 -169
-997 119 -997 89
-997 251 -997 -997
-997 -81 -997 147
-997 -81 -997 147
-997 -997 177 30
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Motif 5 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.8e-014
0.000000 1.000000 0.000000 0.000000
0.000000 0.700000 0.000000 0.300000
0.000000 0.000000 0.900000 0.100000
0.000000 0.100000 0.000000 0.900000
0.000000 0.100000 0.100000 0.800000
0.000000 0.600000 0.400000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.400000 0.000000 0.600000 0.000000
0.000000 0.800000 0.100000 0.100000
0.000000 0.400000 0.000000 0.600000
0.000000 1.000000 0.000000 0.000000
0.000000 0.100000 0.000000 0.900000
0.000000 0.100000 0.000000 0.900000
0.000000 0.000000 0.600000 0.400000
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Motif 5 regular expression
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C[CT]GTT[CG]CT[GA]C[TC]CTT[GT]
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Time 23.30 secs.
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SUMMARY OF MOTIFS
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR232W 1.98e-32 284_[+1(1.41e-12)]_10_[+5(1.62e-09)]_31_[-2(1.23e-13)]_3_[+4(9.38e-12)]_31_[+3(3.51e-09)]_49
MIT_Spar_c117_4603 2.87e-30 279_[+1(1.41e-12)]_10_[+5(1.17e-08)]_31_[-2(1.23e-13)]_3_[+4(2.42e-10)]_31_[+3(3.51e-09)]_54
MIT_Smik_c228_4055 1.44e-26 282_[+1(1.41e-12)]_9_[+5(1.62e-09)]_31_[-2(3.24e-10)]_3_[+4(5.22e-09)]_30_[+3(3.51e-09)]_53
WashU_Skud_Contig2069.5 1.65e-29 111_[-5(2.14e-05)]_156_[+1(1.74e-10)]_10_[+5(2.85e-10)]_30_[-2(1.23e-13)]_3_[+4(7.97e-11)]_31_[+3(2.21e-08)]_52
WashU_Sbay_Contig461.5 4.83e-30 185_[-2(9.76e-05)]_72_[+1(1.41e-12)]_10_[+5(2.85e-10)]_32_[-2(4.09e-12)]_3_[+4(1.03e-09)]_11_[-5(1.98e-05)]_7_[+3(1.76e-09)]_53
SGD_Scer_YDL205C 6.25e-24 48_[-1(4.94e-05)]_272_[+2(8.68e-11)]_3_[+1(1.18e-10)]_166_[-5(6.46e-08)]_104_[+4(5.20e-11)]_32_[+3(1.49e-08)]_125
MIT_Spar_c429_3020 3.47e-25 41_[-1(2.08e-05)]_282_[+2(8.68e-11)]_3_[+1(1.18e-10)]_166_[-5(1.46e-08)]_46_[-2(5.52e-05)]_36_[+4(1.07e-11)]_32_[+3(1.49e-08)]_124
MIT_Smik_c193_2483 2.83e-21 344_[+2(5.92e-09)]_1_[+1(3.73e-10)]_166_[-5(1.46e-08)]_[-3(3.86e-06)]_88_[+4(7.21e-10)]_32_[+3(1.49e-08)]_124
MIT_Sbay_c841_3215 5.49e-21 49_[-1(4.94e-05)]_272_[+2(2.64e-09)]_1_[+1(6.65e-11)]_133_[-5(1.21e-06)]_165_[+4(2.22e-10)]_32_[+3(1.49e-08)]_98
WashU_Skud_Contig1850.5 7.09e-24 47_[-1(5.92e-05)]_276_[+2(5.80e-10)]_1_[+1(1.00e-10)]_170_[-5(4.54e-08)]_107_[+4(3.00e-11)]_32_[+3(7.37e-09)]_117
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Stopped because nmotifs = 5 reached.
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CPU: dhn02990.mrc-dunn.cam.ac.uk
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