********************************************************************************
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= HEM13-HEM15.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
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
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 HEM13-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= 7635 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.304 C 0.196 G 0.196 T 0.304
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 = 204 E-value = 7.1e-025
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :9::4:::::1::::::7:1
pos.-specific C ::4::::::4:::3:8:16:
probability G a14a6:::a:9a4:::a2:9
matrix T ::1::aaa:6::67a2::4:
bits 2.5 * * * * *
2.3 * * * * *
2.0 * * * ** * *
1.8 * * * ** * *
Information 1.5 * * **** ** *** *
content 1.3 ** * **** ** *** *
(32.6 bits) 1.0 ***************** **
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GACGGTTTGTGGTTTCGACG
consensus G A C GC T GT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2050.4 - 569 1.73e-12 CAATATTTTC GACGGTTTGTGGTTTCGACG CGCACTTTGA
MIT_Spar_c278_20970 - 563 1.73e-12 CATTATTTTC GACGGTTTGTGGTTTCGACG CGCAATTCGA
SGD_Scer_YOR176W - 561 1.73e-12 CATTGTTTTC GACGGTTTGTGGTTTCGACG CGCAATGTGA
WashU_Smik_Contig2283.3 + 624 1.50e-11 TGAACTTCTT GAGGATTTGCGGGTTCGGTG ATAAAAAATG
MIT_Smik_c935_20455 - 547 2.58e-11 CATTATTTTC GACGGTTTGTGGTTTTGACG CGCAATTGGA
WashU_Sbay_Contig480.2 - 574 3.01e-11 CGATATTTTT GATGGTTTGTGGTTTCGACG CGCACTTCGA
SGD_Scer_YDR044W + 623 6.31e-11 ACAAACTCCA GAGGATTTGCGGGCTTGATG ATAAAATGTA
MIT_Spar_c130_3912 + 618 1.73e-10 CGAAACTCTA GAGGATTTGCAGGCTCGGTG ATAAAATGTA
MIT_Sbay_c896_21290 + 622 5.29e-10 CGGAACTCTT GGGGATTTGCGGGCTCGCTA ATAAAAAGTG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2050.4 1.7e-12 568_[-1]_139
MIT_Spar_c278_20970 1.7e-12 562_[-1]_145
SGD_Scer_YOR176W 1.7e-12 560_[-1]_147
WashU_Smik_Contig2283.3 1.5e-11 623_[+1]_357
MIT_Smik_c935_20455 2.6e-11 546_[-1]_161
WashU_Sbay_Contig480.2 3e-11 573_[-1]_134
SGD_Scer_YDR044W 6.3e-11 622_[+1]_358
MIT_Spar_c130_3912 1.7e-10 617_[+1]_363
MIT_Sbay_c896_21290 5.3e-10 621_[+1]_359
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2050.4 ( 569) GACGGTTTGTGGTTTCGACG 1
MIT_Spar_c278_20970 ( 563) GACGGTTTGTGGTTTCGACG 1
SGD_Scer_YOR176W ( 561) GACGGTTTGTGGTTTCGACG 1
WashU_Smik_Contig2283.3 ( 624) GAGGATTTGCGGGTTCGGTG 1
MIT_Smik_c935_20455 ( 547) GACGGTTTGTGGTTTTGACG 1
WashU_Sbay_Contig480.2 ( 574) GATGGTTTGTGGTTTCGACG 1
SGD_Scer_YDR044W ( 623) GAGGATTTGCGGGCTTGATG 1
MIT_Spar_c130_3912 ( 618) GAGGATTTGCAGGCTCGGTG 1
MIT_Sbay_c896_21290 ( 622) GGGGATTTGCGGGCTCGCTA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7464 bayes= 9.69407 E= 7.1e-025
-982 -982 251 -982
145 -982 -66 -982
-982 134 134 -154
-982 -982 251 -982
45 -982 166 -982
-982 -982 -982 162
-982 -982 -982 162
-982 -982 -982 162
-982 -982 251 -982
-982 134 -982 78
-154 -982 234 -982
-982 -982 251 -982
-982 -982 134 78
-982 92 -982 104
-982 -982 -982 162
-982 215 -982 -55
-982 -982 251 -982
104 -66 34 -982
-982 166 -982 45
-154 -982 234 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 7.1e-025
0.000000 0.000000 1.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.444444 0.444444 0.111111
0.000000 0.000000 1.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.444444 0.000000 0.555556
0.111111 0.000000 0.888889 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.444444 0.555556
0.000000 0.333333 0.000000 0.666667
0.000000 0.000000 0.000000 1.000000
0.000000 0.777778 0.000000 0.222222
0.000000 0.000000 1.000000 0.000000
0.666667 0.111111 0.222222 0.000000
0.000000 0.555556 0.000000 0.444444
0.111111 0.000000 0.888889 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
GA[CG]G[GA]TTTG[TC]GG[TG][TC]T[CT]G[AG][CT]G
--------------------------------------------------------------------------------
Time 5.96 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 177 E-value = 5.1e-015
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A :::::39::::::3:1::::
pos.-specific C 8::1:1::9111::::9168
probability G ::a:161a1:6::::4::::
matrix T 2a:99::::939a7a41942
bits 2.5 * *
2.3 * *
2.0 * ** *
1.8 * ** *
Information 1.5 *** ** * * * *
content 1.3 ***** **** ** * ** *
(28.4 bits) 1.0 ***** **** ** * ****
0.8 *************** ****
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CTGTTGAGCTGTTTTGCTCC
consensus T A T A T TT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig480.2 + 516 3.60e-13 TTTTGTTCTG CTGTTGAGCTGTTTTGCTCC ACCTGTTCAA
MIT_Spar_c278_20970 + 506 2.05e-12 TTTTGCCCTG CTGTTGAGCTGTTTTGCTTC ACTGTTCAAC
WashU_Skud_Contig2050.4 + 507 5.04e-11 TTTTGTTCTG CTGTTGAGCTGTTTTGTTCC ATCTGTTCAA
SGD_Scer_YOR176W + 504 5.04e-11 TTTTGTCCTG CTGTTGAGCTGTTTTGCTTT ACTGTTCAAC
MIT_Smik_c935_20455 + 490 5.99e-11 TTTTGCTCTG CTGTTGAGCTGTTTTACTTC ATTGTTCAAC
WashU_Smik_Contig2283.3 - 88 7.45e-10 ATTGTCTCAC CTGTTAAGCTTTTATTCCCC GTGTTTTCTT
MIT_Spar_c130_3912 - 91 1.12e-09 TTGTCTTTCT TTGTTAAGCTTTTATTCTCC AGCTTTTTTT
SGD_Scer_YDR044W - 94 1.12e-09 TTGTCTTTCT TTGTTAAGCTTTTATTCTCC GGGTTTTCTT
MIT_Sbay_c896_21290 - 335 3.38e-07 TTCACACAGG CTGCGCGGGCCCTTTTCTTT TTAAACGAGT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig480.2 3.6e-13 515_[+2]_192
MIT_Spar_c278_20970 2e-12 505_[+2]_202
WashU_Skud_Contig2050.4 5e-11 506_[+2]_201
SGD_Scer_YOR176W 5e-11 503_[+2]_204
MIT_Smik_c935_20455 6e-11 489_[+2]_218
WashU_Smik_Contig2283.3 7.5e-10 87_[-2]_893
MIT_Spar_c130_3912 1.1e-09 90_[-2]_890
SGD_Scer_YDR044W 1.1e-09 93_[-2]_887
MIT_Sbay_c896_21290 3.4e-07 334_[-2]_646
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
WashU_Sbay_Contig480.2 ( 516) CTGTTGAGCTGTTTTGCTCC 1
MIT_Spar_c278_20970 ( 506) CTGTTGAGCTGTTTTGCTTC 1
WashU_Skud_Contig2050.4 ( 507) CTGTTGAGCTGTTTTGTTCC 1
SGD_Scer_YOR176W ( 504) CTGTTGAGCTGTTTTGCTTT 1
MIT_Smik_c935_20455 ( 490) CTGTTGAGCTGTTTTACTTC 1
WashU_Smik_Contig2283.3 ( 88) CTGTTAAGCTTTTATTCCCC 1
MIT_Spar_c130_3912 ( 91) TTGTTAAGCTTTTATTCTCC 1
SGD_Scer_YDR044W ( 94) TTGTTAAGCTTTTATTCTCC 1
MIT_Sbay_c896_21290 ( 335) CTGCGCGGGCCCTTTTCTTT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7464 bayes= 9.69407 E= 5.1e-015
-982 215 -982 -55
-982 -982 -982 162
-982 -982 251 -982
-982 -66 -982 145
-982 -982 -66 145
4 -66 166 -982
145 -982 -66 -982
-982 -982 251 -982
-982 234 -66 -982
-982 -66 -982 145
-982 -66 166 4
-982 -66 -982 145
-982 -982 -982 162
4 -982 -982 104
-982 -982 -982 162
-154 -982 134 45
-982 234 -982 -154
-982 -66 -982 145
-982 166 -982 45
-982 215 -982 -55
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.1e-015
0.000000 0.777778 0.000000 0.222222
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 0.111111 0.888889
0.333333 0.111111 0.555556 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.888889 0.111111 0.000000
0.000000 0.111111 0.000000 0.888889
0.000000 0.111111 0.555556 0.333333
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.000000 1.000000
0.333333 0.000000 0.000000 0.666667
0.000000 0.000000 0.000000 1.000000
0.111111 0.000000 0.444444 0.444444
0.000000 0.888889 0.000000 0.111111
0.000000 0.111111 0.000000 0.888889
0.000000 0.555556 0.000000 0.444444
0.000000 0.777778 0.000000 0.222222
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[CT]TGTT[GA]AGCT[GT]TT[TA]T[GT]CT[CT][CT]
--------------------------------------------------------------------------------
Time 11.78 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 19 sites = 9 llr = 177 E-value = 3.0e-016
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :::3:1:1::2::::1::3
pos.-specific C 1:a7::a:a:149:46167
probability G :4:::::9:a:2:::::::
matrix T 96::a9::::731a6394:
bits 2.5 * * **
2.3 * * **
2.0 * **** *
1.8 * **** *
Information 1.5 * * **** **
content 1.3 * *** **** ** * *
(28.4 bits) 1.0 ********** *** ***
0.8 ********** ********
0.5 *******************
0.3 *******************
0.0 -------------------
Multilevel TTCCTTCGCGTCCTTCTCC
consensus G A AT CT TA
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- -------------------
MIT_Spar_c278_20970 + 156 5.34e-12 ACTAAAAGTA TTCCTTCGCGTCCTCCTTC TTCAATCCCA
SGD_Scer_YOR176W + 154 5.34e-12 ACCAAAAGTA TTCCTTCGCGTCCTCCTTC TTCAATCCCA
WashU_Skud_Contig2050.4 + 160 9.86e-12 AAAAGAAGTA TTCCTTCGCGTGCTTCTCC TTTCTGTGTC
MIT_Smik_c935_20455 + 151 6.97e-11 GACCAAAAGA CTCCTTCGCGTCCTCCTTC TTCAAGTCTC
WashU_Smik_Contig2283.3 - 660 1.04e-09 CCGTAATTGT TGCATTCGCGTTCTTTTCA ACAATACATT
MIT_Spar_c130_3912 - 652 1.04e-09 CCACAATCGT TGCATTCGCGTTCTTTTCA ACAATACATT
SGD_Scer_YDR044W - 657 2.59e-09 CCGTAATTGT TGCATTCGCGATCTTTTCA ACAATACATT
WashU_Sbay_Contig480.2 + 204 3.78e-09 AAAAGAAGTA TTCCTACGCGAGCTCCCTC TTCAAGTGCC
MIT_Sbay_c896_21290 - 440 1.61e-08 GTTCAGGGAG TGCCTTCACGCCTTTATCC CCTGGTATTC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c278_20970 5.3e-12 155_[+3]_553
SGD_Scer_YOR176W 5.3e-12 153_[+3]_555
WashU_Skud_Contig2050.4 9.9e-12 159_[+3]_549
MIT_Smik_c935_20455 7e-11 150_[+3]_558
WashU_Smik_Contig2283.3 1e-09 659_[-3]_322
MIT_Spar_c130_3912 1e-09 651_[-3]_330
SGD_Scer_YDR044W 2.6e-09 656_[-3]_325
WashU_Sbay_Contig480.2 3.8e-09 203_[+3]_505
MIT_Sbay_c896_21290 1.6e-08 439_[-3]_542
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=19 seqs=9
MIT_Spar_c278_20970 ( 156) TTCCTTCGCGTCCTCCTTC 1
SGD_Scer_YOR176W ( 154) TTCCTTCGCGTCCTCCTTC 1
WashU_Skud_Contig2050.4 ( 160) TTCCTTCGCGTGCTTCTCC 1
MIT_Smik_c935_20455 ( 151) CTCCTTCGCGTCCTCCTTC 1
WashU_Smik_Contig2283.3 ( 660) TGCATTCGCGTTCTTTTCA 1
MIT_Spar_c130_3912 ( 652) TGCATTCGCGTTCTTTTCA 1
SGD_Scer_YDR044W ( 657) TGCATTCGCGATCTTTTCA 1
WashU_Sbay_Contig480.2 ( 204) TTCCTACGCGAGCTCCCTC 1
MIT_Sbay_c896_21290 ( 440) TGCCTTCACGCCTTTATCC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 19 n= 7473 bayes= 9.69581 E= 3.0e-016
-982 -66 -982 145
-982 -982 134 78
-982 251 -982 -982
4 192 -982 -982
-982 -982 -982 162
-154 -982 -982 145
-982 251 -982 -982
-154 -982 234 -982
-982 251 -982 -982
-982 -982 251 -982
-55 -66 -982 104
-982 134 34 4
-982 234 -982 -154
-982 -982 -982 162
-982 134 -982 78
-154 166 -982 4
-982 -66 -982 145
-982 166 -982 45
4 192 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 19 nsites= 9 E= 3.0e-016
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.444444 0.555556
0.000000 1.000000 0.000000 0.000000
0.333333 0.666667 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.111111 0.000000 0.000000 0.888889
0.000000 1.000000 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.222222 0.111111 0.000000 0.666667
0.000000 0.444444 0.222222 0.333333
0.000000 0.888889 0.000000 0.111111
0.000000 0.000000 0.000000 1.000000
0.000000 0.444444 0.000000 0.555556
0.111111 0.555556 0.000000 0.333333
0.000000 0.111111 0.000000 0.888889
0.000000 0.555556 0.000000 0.444444
0.333333 0.666667 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
T[TG]C[CA]TTCGCG[TA][CTG]CT[TC][CT]T[CT][CA]
--------------------------------------------------------------------------------
Time 17.43 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 9 llr = 171 E-value = 3.0e-012
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 1a6aa:a8::32:a44:7aa
pos.-specific C :::::6::1::19::6:3::
probability G 9:4::::::a71::::1:::
matrix T :::::4:29::61:6:9:::
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 GAAAACAATGGTCATCTAAA
consensus G T T AA AA C
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YOR176W + 581 1.12e-11 ACAAACCGTC GAAAACAATGGTCATCTAAA TAAAGGGTTC
WashU_Smik_Contig2283.3 + 166 4.85e-11 TTTTCAAAAA GAGAACAATGGTCAAATAAA GGTTTATCTA
MIT_Spar_c278_20970 + 583 8.09e-11 ACAAACCGTC GAAAATAATGGTCATCTAAA TAAAGGGTTC
MIT_Spar_c130_3912 + 170 3.22e-10 TTTTCGAAAC GAGAACAATGGACAAATCAA GCTTTATCTA
MIT_Smik_c935_20455 + 567 6.16e-10 ACAAACCGTC GAAAATAATGATCATCTAAA TAAAAGAGTT
SGD_Scer_YDR044W + 174 1.95e-09 CTTTCGAAAC GAGAACAATGGGCAAAGCAA GCTTTATCTT
WashU_Skud_Contig2050.4 + 589 2.29e-09 ACAAACCGTC GAAAATATTGATCATCTAAA TAAAGGGTTC
MIT_Sbay_c896_21290 + 176 4.95e-09 TTCTCGAAGG GAGAACAATGGATAAATCAA AGCTTATCTA
WashU_Sbay_Contig480.2 + 594 3.59e-08 ACAAACCATC AAAAATATCGACCATCTAAA TAAAGGGTTC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YOR176W 1.1e-11 580_[+4]_127
WashU_Smik_Contig2283.3 4.8e-11 165_[+4]_815
MIT_Spar_c278_20970 8.1e-11 582_[+4]_125
MIT_Spar_c130_3912 3.2e-10 169_[+4]_811
MIT_Smik_c935_20455 6.2e-10 566_[+4]_141
SGD_Scer_YDR044W 2e-09 173_[+4]_807
WashU_Skud_Contig2050.4 2.3e-09 588_[+4]_119
MIT_Sbay_c896_21290 5e-09 175_[+4]_805
WashU_Sbay_Contig480.2 3.6e-08 593_[+4]_114
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=9
SGD_Scer_YOR176W ( 581) GAAAACAATGGTCATCTAAA 1
WashU_Smik_Contig2283.3 ( 166) GAGAACAATGGTCAAATAAA 1
MIT_Spar_c278_20970 ( 583) GAAAATAATGGTCATCTAAA 1
MIT_Spar_c130_3912 ( 170) GAGAACAATGGACAAATCAA 1
MIT_Smik_c935_20455 ( 567) GAAAATAATGATCATCTAAA 1
SGD_Scer_YDR044W ( 174) GAGAACAATGGGCAAAGCAA 1
WashU_Skud_Contig2050.4 ( 589) GAAAATATTGATCATCTAAA 1
MIT_Sbay_c896_21290 ( 176) GAGAACAATGGATAAATCAA 1
WashU_Sbay_Contig480.2 ( 594) AAAAATATCGACCATCTAAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7464 bayes= 9.69407 E= 3.0e-012
-154 -982 234 -982
162 -982 -982 -982
78 -982 134 -982
162 -982 -982 -982
162 -982 -982 -982
-982 166 -982 45
162 -982 -982 -982
126 -982 -982 -55
-982 -66 -982 145
-982 -982 251 -982
4 -982 192 -982
-55 -66 -66 78
-982 234 -982 -154
162 -982 -982 -982
45 -982 -982 78
45 166 -982 -982
-982 -982 -66 145
104 92 -982 -982
162 -982 -982 -982
162 -982 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-012
0.111111 0.000000 0.888889 0.000000
1.000000 0.000000 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 0.555556 0.000000 0.444444
1.000000 0.000000 0.000000 0.000000
0.777778 0.000000 0.000000 0.222222
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 1.000000 0.000000
0.333333 0.000000 0.666667 0.000000
0.222222 0.111111 0.111111 0.555556
0.000000 0.888889 0.000000 0.111111
1.000000 0.000000 0.000000 0.000000
0.444444 0.000000 0.000000 0.555556
0.444444 0.555556 0.000000 0.000000
0.000000 0.000000 0.111111 0.888889
0.666667 0.333333 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
GA[AG]AA[CT]A[AT]TG[GA][TA]CA[TA][CA]T[AC]AA
--------------------------------------------------------------------------------
Time 23.00 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 15 sites = 9 llr = 147 E-value = 3.6e-010
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 1:::4:::a::aa69
pos.-specific C 8::4:9a4:a9::::
probability G 1::61::6:::::::
matrix T :aa:41::::1::41
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 CTTGACCGACCAAAA
consensus CT C T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Sbay_Contig480.2 + 183 1.26e-09 CCATAATGCT CTTGACCGACCAAAA GAAGTATTCC
SGD_Scer_YOR176W + 136 1.26e-09 CAAGAGTGAC CTTGACCGACCAAAA GTATTCCTTC
MIT_Spar_c130_3912 - 252 1.01e-08 CCTTTTCTGG CTTCTCCCACCAATA ATGCCCCAGC
MIT_Smik_c935_20455 + 134 1.04e-08 CAACAGTGAT CTTGGCCGACCAAAA GACTCCTTCG
WashU_Skud_Contig2050.4 + 139 3.41e-08 CAACAATGAT ATTGACCGACCAAAA GAAGTATTCC
SGD_Scer_YDR044W - 260 3.41e-08 GCCTTTTCTG GTTCTCCCACCAATA ACGCTCCAGC
MIT_Sbay_c896_21290 - 258 3.54e-08 CATTTTCTGG CTTCTCCCACCAATT ATGCCCCAGC
MIT_Spar_c278_20970 + 138 4.50e-08 CAAGAGTGAC CTTGACCGACTAAAA GTATTCCTTC
WashU_Smik_Contig2283.3 - 248 9.48e-08 TCTTTTCTGG CTTCTTCCACCAATA ATGCCCCAGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig480.2 1.3e-09 182_[+5]_530
SGD_Scer_YOR176W 1.3e-09 135_[+5]_577
MIT_Spar_c130_3912 1e-08 251_[-5]_734
MIT_Smik_c935_20455 1e-08 133_[+5]_579
WashU_Skud_Contig2050.4 3.4e-08 138_[+5]_574
SGD_Scer_YDR044W 3.4e-08 259_[-5]_726
MIT_Sbay_c896_21290 3.5e-08 257_[-5]_728
MIT_Spar_c278_20970 4.5e-08 137_[+5]_575
WashU_Smik_Contig2283.3 9.5e-08 247_[-5]_738
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=15 seqs=9
WashU_Sbay_Contig480.2 ( 183) CTTGACCGACCAAAA 1
SGD_Scer_YOR176W ( 136) CTTGACCGACCAAAA 1
MIT_Spar_c130_3912 ( 252) CTTCTCCCACCAATA 1
MIT_Smik_c935_20455 ( 134) CTTGGCCGACCAAAA 1
WashU_Skud_Contig2050.4 ( 139) ATTGACCGACCAAAA 1
SGD_Scer_YDR044W ( 260) GTTCTCCCACCAATA 1
MIT_Sbay_c896_21290 ( 258) CTTCTCCCACCAATT 1
MIT_Spar_c278_20970 ( 138) CTTGACCGACTAAAA 1
WashU_Smik_Contig2283.3 ( 248) CTTCTTCCACCAATA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 7509 bayes= 9.70275 E= 3.6e-010
-154 215 -66 -982
-982 -982 -982 162
-982 -982 -982 162
-982 134 166 -982
45 -982 -66 45
-982 234 -982 -154
-982 251 -982 -982
-982 134 166 -982
162 -982 -982 -982
-982 251 -982 -982
-982 234 -982 -154
162 -982 -982 -982
162 -982 -982 -982
78 -982 -982 45
145 -982 -982 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 3.6e-010
0.111111 0.777778 0.111111 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.444444 0.555556 0.000000
0.444444 0.000000 0.111111 0.444444
0.000000 0.888889 0.000000 0.111111
0.000000 1.000000 0.000000 0.000000
0.000000 0.444444 0.555556 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.888889 0.000000 0.111111
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.555556 0.000000 0.000000 0.444444
0.888889 0.000000 0.000000 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
CTT[GC][AT]CC[GC]ACCAA[AT]A
--------------------------------------------------------------------------------
Time 28.58 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR044W 2.52e-22 93_[-2(1.12e-09)]_60_[+4(1.95e-09)]_66_[-5(3.41e-08)]_165_[-3(5.96e-05)]_164_[+1(6.31e-11)]_14_[-3(2.59e-09)]_325
MIT_Spar_c130_3912 1.62e-23 90_[-2(1.12e-09)]_59_[+4(3.22e-10)]_62_[-5(1.01e-08)]_61_[-2(1.77e-05)]_85_[-3(5.96e-05)]_166_[+1(1.73e-10)]_14_[-3(1.04e-09)]_330
MIT_Sbay_c896_21290 5.08e-18 94_[-2(2.30e-05)]_61_[+4(4.95e-09)]_62_[-5(3.54e-08)]_62_[-2(3.38e-07)]_31_[-3(3.05e-05)]_35_[-3(1.61e-08)]_163_[+1(5.29e-10)]_82_[-2(1.56e-05)]_257
WashU_Smik_Contig2283.3 1.53e-24 7_[+1(1.86e-05)]_60_[-2(7.45e-10)]_58_[+4(4.85e-11)]_62_[-5(9.48e-08)]_336_[-3(6.30e-05)]_6_[+1(1.50e-11)]_16_[-3(1.04e-09)]_204_[-3(4.16e-06)]_99
SGD_Scer_YOR176W 9.09e-32 135_[+5(1.26e-09)]_3_[+3(5.34e-12)]_20_[-2(9.24e-05)]_269_[+2(2.71e-05)]_2_[+2(5.04e-11)]_37_[-1(1.73e-12)]_[+4(1.12e-11)]_55_[-1(7.71e-05)]_52
MIT_Spar_c278_20970 8.55e-31 137_[+5(4.50e-08)]_3_[+3(5.34e-12)]_309_[+2(4.04e-05)]_2_[+2(2.05e-12)]_37_[-1(1.73e-12)]_[+4(8.09e-11)]_125
MIT_Smik_c935_20455 5.42e-27 133_[+5(1.04e-08)]_2_[+3(6.97e-11)]_298_[+2(5.34e-05)]_2_[+2(5.99e-11)]_37_[-1(2.58e-11)]_[+4(6.16e-10)]_141
WashU_Skud_Contig2050.4 5.92e-28 138_[+5(3.41e-08)]_6_[+3(9.86e-12)]_305_[+2(1.26e-05)]_3_[+2(5.04e-11)]_6_[-2(3.42e-05)]_16_[-1(1.73e-12)]_[+4(2.29e-09)]_119
WashU_Sbay_Contig480.2 1.38e-26 182_[+5(1.26e-09)]_6_[+3(3.78e-09)]_270_[+2(7.91e-05)]_3_[+2(3.60e-13)]_38_[-1(3.01e-11)]_[+4(3.59e-08)]_114
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************