********************************************************************************
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-HEM15.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_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 HEM3-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
model: mod= oops nmotifs= 5 evt= inf
object function= E-value of product of p-values
width: minw= 6 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 10 maxsites= 10 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 7935 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.308 C 0.192 G 0.192 T 0.308
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324
********************************************************************************
********************************************************************************
MOTIF 1 width = 19 sites = 10 llr = 215 E-value = 3.6e-028
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 1:aa6a:a::::55:a::a
pos.-specific C 16::::a::a5a::5:5a:
probability G 8:::::::a::::5::5::
matrix T :4::4:::::5:5:5::::
bits 2.5 * ** * *
2.3 * ** * *
2.0 * ** * *
1.8 * ** * *
Information 1.5 * ** ***** * ****
content 1.3 **** ***** * ****
(31.0 bits) 1.0 **** ******* ******
0.8 ************ ******
0.5 *******************
0.3 *******************
0.0 -------------------
Multilevel GCAAAACAGCCCAACACCA
consensus T T T TGT G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- -------------------
WashU_Skud_Contig1850.5 + 110 3.58e-11 TTTTCAAAAA GCAATACAGCCCTGTACCA TTCAAACACG
MIT_Sbay_c841_3215 + 111 3.58e-11 TATTCAAAAC GCAATACAGCCCTGTACCA TTCAAATACG
WashU_Sbay_Contig480.2 - 514 6.04e-11 AACAGGTGGA GCAAAACAGCTCAACAGCA GAACAAAAAA
MIT_Spar_c278_20970 - 504 6.04e-11 GAACAGTGAA GCAAAACAGCTCAACAGCA GGGCAAAAAA
SGD_Scer_YOR176W - 502 6.04e-11 GAACAGTAAA GCAAAACAGCTCAACAGCA GGACAAAAAA
MIT_Spar_c429_3020 + 110 1.14e-10 TATTCAAAAT GTAAAACAGCCCTGTACCA TGCAAACACG
MIT_Smik_c193_2483 + 112 1.56e-10 TATTCAAAAA GTAATACAGCCCTGTACCA TTCAAACACG
MIT_Smik_c935_20455 - 488 2.17e-10 GAACAATGAA GTAAAACAGCTCAACAGCA GAGCAAAAAA
WashU_Skud_Contig2050.4 - 505 5.56e-10 AACAGATGGA ACAAAACAGCTCAACAGCA GAACAAAAAA
SGD_Scer_YDL205C + 110 5.89e-10 TATTCAAAAT CTAATACAGCCCTGTACCA TGCAAACACG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 3.6e-11 109_[+1]_732
MIT_Sbay_c841_3215 3.6e-11 110_[+1]_731
WashU_Sbay_Contig480.2 6e-11 513_[-1]_195
MIT_Spar_c278_20970 6e-11 503_[-1]_205
SGD_Scer_YOR176W 6e-11 501_[-1]_207
MIT_Spar_c429_3020 1.1e-10 109_[+1]_732
MIT_Smik_c193_2483 1.6e-10 111_[+1]_730
MIT_Smik_c935_20455 2.2e-10 487_[-1]_221
WashU_Skud_Contig2050.4 5.6e-10 504_[-1]_204
SGD_Scer_YDL205C 5.9e-10 109_[+1]_732
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=19 seqs=10
WashU_Skud_Contig1850.5 ( 110) GCAATACAGCCCTGTACCA 1
MIT_Sbay_c841_3215 ( 111) GCAATACAGCCCTGTACCA 1
WashU_Sbay_Contig480.2 ( 514) GCAAAACAGCTCAACAGCA 1
MIT_Spar_c278_20970 ( 504) GCAAAACAGCTCAACAGCA 1
SGD_Scer_YOR176W ( 502) GCAAAACAGCTCAACAGCA 1
MIT_Spar_c429_3020 ( 110) GTAAAACAGCCCTGTACCA 1
MIT_Smik_c193_2483 ( 112) GTAATACAGCCCTGTACCA 1
MIT_Smik_c935_20455 ( 488) GTAAAACAGCTCAACAGCA 1
WashU_Skud_Contig2050.4 ( 505) ACAAAACAGCTCAACAGCA 1
SGD_Scer_YDL205C ( 110) CTAATACAGCCCTGTACCA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 19 n= 7755 bayes= 9.59712 E= 3.6e-028
-169 -81 219 -997
-997 177 -997 30
162 -997 -997 -997
162 -997 -997 -997
89 -997 -997 30
162 -997 -997 -997
-997 251 -997 -997
162 -997 -997 -997
-997 -997 251 -997
-997 251 -997 -997
-997 151 -997 62
-997 251 -997 -997
62 -997 -997 62
62 -997 151 -997
-997 151 -997 62
162 -997 -997 -997
-997 151 151 -997
-997 251 -997 -997
162 -997 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 19 nsites= 10 E= 3.6e-028
0.100000 0.100000 0.800000 0.000000
0.000000 0.600000 0.000000 0.400000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.600000 0.000000 0.000000 0.400000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.500000 0.000000 0.500000
0.000000 1.000000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
0.500000 0.000000 0.500000 0.000000
0.000000 0.500000 0.000000 0.500000
1.000000 0.000000 0.000000 0.000000
0.000000 0.500000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
G[CT]AA[AT]ACAGC[CT]C[AT][AG][CT]A[CG]CA
--------------------------------------------------------------------------------
Time 6.58 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 10 llr = 204 E-value = 3.8e-022
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A :::::3::3a5a5:a:a78:
pos.-specific C ::6:62:a::::55:a:::6
probability G :a:a:55:7::::::::31:
matrix T a:4:4:5:::5::5::::14
bits 2.5 * * * *
2.3 * * * *
2.0 * * * *
1.8 * * * *
Information 1.5 ** * * * * ***
content 1.3 ***** *** * *** *
(29.5 bits) 1.0 ***** **** ******* *
0.8 ********** *********
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel TGCGCGGCGAAAACACAAAC
consensus T TAT A T CT G T
sequence C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig480.2 + 570 1.49e-12 TCTTTCGAAG TGCGCGTCGAAACCACAAAC CATCAAAAAT
WashU_Skud_Contig2050.4 + 565 1.49e-12 TCTTTCAAAG TGCGCGTCGAAACCACAAAC CGTCGAAAAT
MIT_Spar_c278_20970 + 559 1.49e-12 TCTTTCGAAT TGCGCGTCGAAACCACAAAC CGTCGAAAAT
SGD_Scer_YOR176W + 557 1.49e-12 TCTTTCACAT TGCGCGTCGAAACCACAAAC CGTCGAAAAC
MIT_Smik_c935_20455 + 543 3.24e-11 TCTCTCCAAT TGCGCGTCAAAACCACAAAC CGTCGAAAAT
MIT_Smik_c193_2483 + 176 9.12e-10 AATCCAGCTA TGCGTAGCGATAATACAGAT GATTGTTTGA
MIT_Sbay_c841_3215 + 175 1.46e-09 AATCAAGTTA TGTGCCGCGATAATACAATC TTTTGGCCTA
WashU_Skud_Contig1850.5 + 173 3.07e-09 AATCAATCTA TGTGTCGCGATAATACAAGT GATTGATTGG
MIT_Spar_c429_3020 + 174 3.52e-09 ATCCAAGCTA TGTGTAGCAATAATACAGAT GATTGATTGG
SGD_Scer_YDL205C + 174 3.52e-09 ATTCAGGCTA TGTGTAGCAATAATACAGAT AGTTAGTAGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig480.2 1.5e-12 569_[+2]_138
WashU_Skud_Contig2050.4 1.5e-12 564_[+2]_143
MIT_Spar_c278_20970 1.5e-12 558_[+2]_149
SGD_Scer_YOR176W 1.5e-12 556_[+2]_151
MIT_Smik_c935_20455 3.2e-11 542_[+2]_165
MIT_Smik_c193_2483 9.1e-10 175_[+2]_665
MIT_Sbay_c841_3215 1.5e-09 174_[+2]_666
WashU_Skud_Contig1850.5 3.1e-09 172_[+2]_668
MIT_Spar_c429_3020 3.5e-09 173_[+2]_667
SGD_Scer_YDL205C 3.5e-09 173_[+2]_667
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=10
WashU_Sbay_Contig480.2 ( 570) TGCGCGTCGAAACCACAAAC 1
WashU_Skud_Contig2050.4 ( 565) TGCGCGTCGAAACCACAAAC 1
MIT_Spar_c278_20970 ( 559) TGCGCGTCGAAACCACAAAC 1
SGD_Scer_YOR176W ( 557) TGCGCGTCGAAACCACAAAC 1
MIT_Smik_c935_20455 ( 543) TGCGCGTCAAAACCACAAAC 1
MIT_Smik_c193_2483 ( 176) TGCGTAGCGATAATACAGAT 1
MIT_Sbay_c841_3215 ( 175) TGTGCCGCGATAATACAATC 1
WashU_Skud_Contig1850.5 ( 173) TGTGTCGCGATAATACAAGT 1
MIT_Spar_c429_3020 ( 174) TGTGTAGCAATAATACAGAT 1
SGD_Scer_YDL205C ( 174) TGTGTAGCAATAATACAGAT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 3.8e-022
-997 -997 -997 162
-997 -997 251 -997
-997 177 -997 30
-997 -997 251 -997
-997 177 -997 30
-11 19 151 -997
-997 -997 151 62
-997 251 -997 -997
-11 -997 199 -997
162 -997 -997 -997
62 -997 -997 62
162 -997 -997 -997
62 151 -997 -997
-997 151 -997 62
162 -997 -997 -997
-997 251 -997 -997
162 -997 -997 -997
111 -997 77 -997
130 -997 -81 -169
-997 177 -997 30
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.8e-022
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.600000 0.000000 0.400000
0.000000 0.000000 1.000000 0.000000
0.000000 0.600000 0.000000 0.400000
0.300000 0.200000 0.500000 0.000000
0.000000 0.000000 0.500000 0.500000
0.000000 1.000000 0.000000 0.000000
0.300000 0.000000 0.700000 0.000000
1.000000 0.000000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
1.000000 0.000000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.500000 0.000000 0.500000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.700000 0.000000 0.300000 0.000000
0.800000 0.000000 0.100000 0.100000
0.000000 0.600000 0.000000 0.400000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
TG[CT]G[CT][GAC][GT]C[GA]A[AT]A[AC][CT]ACA[AG]A[CT]
--------------------------------------------------------------------------------
Time 12.80 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 10 llr = 199 E-value = 1.7e-020
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A ::5:::a6a:9a91:1::::
pos.-specific C 1a::5::::::::14::195
probability G ::5:::::::::18681:::
matrix T 9::a5a:4:a1::::19915
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 TCATCTAAATAAAGGGTTCC
consensus G T T C T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2050.4 + 600 3.79e-11 AAAATATTGA TCATCTAAATAAAGGGTTCT TATTTGCACA
MIT_Spar_c278_20970 + 594 3.79e-11 AAAATAATGG TCATCTAAATAAAGGGTTCT TATTTGAACA
SGD_Scer_YOR176W + 592 3.79e-11 AAAACAATGG TCATCTAAATAAAGGGTTCT TATTAAACAG
WashU_Skud_Contig1850.5 + 205 4.47e-11 TTGATTGGTG TCGTTTATATAAAGCGTTCC TTCAATTTTT
MIT_Spar_c429_3020 + 206 4.47e-11 TTGATTGGCG TCGTTTATATAAAGCGTTCC TTCATTTTTT
SGD_Scer_YDL205C + 205 4.47e-11 GTTAGTAGCC TCGTTTATATAAAGCGTTCC TTTACTTTTT
WashU_Sbay_Contig480.2 + 605 2.26e-10 AAAATATCGA CCATCTAAATAAAGGGTTCT TGTTTGAATA
MIT_Smik_c193_2483 + 208 5.94e-10 TTGTTTGATG TCGTTTATATTAAGCGTTCC TTCAGTTTTT
MIT_Sbay_c841_3215 + 207 2.13e-08 TTGGCCTATA TCGTTTAAATAAGCGTTCCT TTAATTTTTC
MIT_Smik_c935_20455 + 578 3.47e-08 AAAATAATGA TCATCTAAATAAAAGAGTTC ACGTTTTCAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2050.4 3.8e-11 599_[+3]_108
MIT_Spar_c278_20970 3.8e-11 593_[+3]_114
SGD_Scer_YOR176W 3.8e-11 591_[+3]_116
WashU_Skud_Contig1850.5 4.5e-11 204_[+3]_636
MIT_Spar_c429_3020 4.5e-11 205_[+3]_635
SGD_Scer_YDL205C 4.5e-11 204_[+3]_636
WashU_Sbay_Contig480.2 2.3e-10 604_[+3]_103
MIT_Smik_c193_2483 5.9e-10 207_[+3]_633
MIT_Sbay_c841_3215 2.1e-08 206_[+3]_634
MIT_Smik_c935_20455 3.5e-08 577_[+3]_130
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=10
WashU_Skud_Contig2050.4 ( 600) TCATCTAAATAAAGGGTTCT 1
MIT_Spar_c278_20970 ( 594) TCATCTAAATAAAGGGTTCT 1
SGD_Scer_YOR176W ( 592) TCATCTAAATAAAGGGTTCT 1
WashU_Skud_Contig1850.5 ( 205) TCGTTTATATAAAGCGTTCC 1
MIT_Spar_c429_3020 ( 206) TCGTTTATATAAAGCGTTCC 1
SGD_Scer_YDL205C ( 205) TCGTTTATATAAAGCGTTCC 1
WashU_Sbay_Contig480.2 ( 605) CCATCTAAATAAAGGGTTCT 1
MIT_Smik_c193_2483 ( 208) TCGTTTATATTAAGCGTTCC 1
MIT_Sbay_c841_3215 ( 207) TCGTTTAAATAAGCGTTCCT 1
MIT_Smik_c935_20455 ( 578) TCATCTAAATAAAAGAGTTC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 1.7e-020
-997 -81 -997 147
-997 251 -997 -997
62 -997 151 -997
-997 -997 -997 162
-997 151 -997 62
-997 -997 -997 162
162 -997 -997 -997
89 -997 -997 30
162 -997 -997 -997
-997 -997 -997 162
147 -997 -997 -169
162 -997 -997 -997
147 -997 -81 -997
-169 -81 219 -997
-997 119 177 -997
-169 -997 219 -169
-997 -997 -81 147
-997 -81 -997 147
-997 236 -997 -169
-997 151 -997 62
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.7e-020
0.000000 0.100000 0.000000 0.900000
0.000000 1.000000 0.000000 0.000000
0.500000 0.000000 0.500000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.000000 0.500000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.600000 0.000000 0.000000 0.400000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.900000 0.000000 0.000000 0.100000
1.000000 0.000000 0.000000 0.000000
0.900000 0.000000 0.100000 0.000000
0.100000 0.100000 0.800000 0.000000
0.000000 0.400000 0.600000 0.000000
0.100000 0.000000 0.800000 0.100000
0.000000 0.000000 0.100000 0.900000
0.000000 0.100000 0.000000 0.900000
0.000000 0.900000 0.000000 0.100000
0.000000 0.500000 0.000000 0.500000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
TC[AG]T[CT]TA[AT]ATAAAG[GC]GTTC[CT]
--------------------------------------------------------------------------------
Time 19.05 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 10 llr = 191 E-value = 6.7e-018
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A :975::45:a7::911:::9
pos.-specific C a1::76147::::169::::
probability G ::311:412:3:a:::::a1
matrix T :::4241:1::a::3:aa::
bits 2.5 * * *
2.3 * * *
2.0 * * * *
1.8 * * * *
Information 1.5 * * ** ****
content 1.3 ** ** ** *** *****
(27.6 bits) 1.0 *** ** ****** *****
0.8 *** ** *************
0.5 *** ** *************
0.3 ********************
0.0 --------------------
Multilevel CAAACCAACAATGACCTTGA
consensus GTTTGCG G T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Sbay_c841_3215 + 145 1.51e-11 ATACGAACGC CAATCTGCCAATGACCTTGA AATCAAGTTA
MIT_Spar_c429_3020 + 144 1.51e-11 ACACGAGCCT CAATCTGCCAATGACCTTGA ATCCAAGCTA
SGD_Scer_YDL205C + 144 1.51e-11 ACACGAGCGT CAATCTGCCAATGACCTTGA ATTCAGGCTA
MIT_Spar_c278_20970 + 123 1.17e-10 TGCTTGGTGC CAAACCAAGAGTGACCTTGA CCGACTAAAA
SGD_Scer_YOR176W + 121 4.51e-10 TGTTTGGTGT CAAGCCAAGAGTGACCTTGA CCGACCAAAA
MIT_Smik_c935_20455 + 119 1.09e-09 CTTTAATGAT CAGACCAACAGTGATCTTGG CCGACCAAAA
WashU_Skud_Contig2050.4 + 124 2.63e-09 GTTTAATAAT CAGACCAACAATGATATTGA CCGACCAAAA
MIT_Smik_c193_2483 + 146 3.28e-09 ACACGAGCGC CAATTTGCCAATGAACTTGA AATCCAGCTA
WashU_Skud_Contig1850.5 + 143 8.39e-09 AACACGAACG CCAATCTGCAATGACCTTGA AATCAATCTA
WashU_Sbay_Contig480.2 + 168 3.20e-08 GTTTAGTAAG CAGAGCCATAATGCTCTTGA CCGACCAAAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Sbay_c841_3215 1.5e-11 144_[+4]_696
MIT_Spar_c429_3020 1.5e-11 143_[+4]_697
SGD_Scer_YDL205C 1.5e-11 143_[+4]_697
MIT_Spar_c278_20970 1.2e-10 122_[+4]_585
SGD_Scer_YOR176W 4.5e-10 120_[+4]_587
MIT_Smik_c935_20455 1.1e-09 118_[+4]_589
WashU_Skud_Contig2050.4 2.6e-09 123_[+4]_584
MIT_Smik_c193_2483 3.3e-09 145_[+4]_695
WashU_Skud_Contig1850.5 8.4e-09 142_[+4]_698
WashU_Sbay_Contig480.2 3.2e-08 167_[+4]_540
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=10
MIT_Sbay_c841_3215 ( 145) CAATCTGCCAATGACCTTGA 1
MIT_Spar_c429_3020 ( 144) CAATCTGCCAATGACCTTGA 1
SGD_Scer_YDL205C ( 144) CAATCTGCCAATGACCTTGA 1
MIT_Spar_c278_20970 ( 123) CAAACCAAGAGTGACCTTGA 1
SGD_Scer_YOR176W ( 121) CAAGCCAAGAGTGACCTTGA 1
MIT_Smik_c935_20455 ( 119) CAGACCAACAGTGATCTTGG 1
WashU_Skud_Contig2050.4 ( 124) CAGACCAACAATGATATTGA 1
MIT_Smik_c193_2483 ( 146) CAATTTGCCAATGAACTTGA 1
WashU_Skud_Contig1850.5 ( 143) CCAATCTGCAATGACCTTGA 1
WashU_Sbay_Contig480.2 ( 168) CAGAGCCATAATGCTCTTGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 6.7e-018
-997 251 -997 -997
147 -81 -997 -997
111 -997 77 -997
62 -997 -81 30
-997 199 -81 -70
-997 177 -997 30
30 -81 119 -169
62 119 -81 -997
-997 199 19 -169
162 -997 -997 -997
111 -997 77 -997
-997 -997 -997 162
-997 -997 251 -997
147 -81 -997 -997
-169 177 -997 -11
-169 236 -997 -997
-997 -997 -997 162
-997 -997 -997 162
-997 -997 251 -997
147 -997 -81 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.7e-018
0.000000 1.000000 0.000000 0.000000
0.900000 0.100000 0.000000 0.000000
0.700000 0.000000 0.300000 0.000000
0.500000 0.000000 0.100000 0.400000
0.000000 0.700000 0.100000 0.200000
0.000000 0.600000 0.000000 0.400000
0.400000 0.100000 0.400000 0.100000
0.500000 0.400000 0.100000 0.000000
0.000000 0.700000 0.200000 0.100000
1.000000 0.000000 0.000000 0.000000
0.700000 0.000000 0.300000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.900000 0.100000 0.000000 0.000000
0.100000 0.600000 0.000000 0.300000
0.100000 0.900000 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
0.900000 0.000000 0.100000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
CA[AG][AT][CT][CT][AG][AC][CG]A[AG]TGA[CT]CTTGA
--------------------------------------------------------------------------------
Time 25.42 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 10 llr = 190 E-value = 6.6e-017
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 219a56:::::19aa::15:
pos.-specific C ::1:541:1a11::::1::6
probability G :9::::::8::81::::1::
matrix T 8:::::9a1:9::::a9854
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 TGAAAATTGCTGAAATTTAC
consensus A CC TT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1850.5 + 282 3.68e-11 TTTTCACTTT TGAAAATTGCTGAAATTTTC GTAGCAAAAA
MIT_Sbay_c841_3215 + 280 3.68e-11 TTTTTTCACT TGAAAATTGCTGAAATTTTC GTAGCTGAAA
MIT_Smik_c193_2483 + 285 3.68e-11 TTTTCACTTT TGAAAATTGCTGAAATTTTC GTAACAAAAA
SGD_Scer_YOR176W + 415 1.86e-10 GTAAAGCTGT TGAACCTTCCTGAAATTTAC TTCTAAAATT
MIT_Spar_c429_3020 + 282 3.08e-10 TTTTCACTTT TGAAAACTGCTGAAATTTTC GTAGCAAAAA
SGD_Scer_YDL205C + 281 3.80e-09 TTTTCACTTT AAAAAATTGCTGAAATTTTC GTAGCCAAAA
WashU_Skud_Contig2050.4 + 417 5.20e-09 TGCAAAATGT TGAACCTTTCCGAAATTTAT TGCCAGAAAC
MIT_Spar_c278_20970 + 418 5.20e-09 GTAAAGCTGT TGAACCTTGCTAAAATCTAT TACTATAATT
WashU_Sbay_Contig480.2 + 453 9.34e-09 CAGAGTTGGT TGAACCTTGCTCGAATTGAT AGCTCAAAGT
MIT_Smik_c935_20455 + 419 1.01e-08 AATATGCCAA AGCACATTGCTGAAATTAAT CAGTAAAGCT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 3.7e-11 281_[+5]_559
MIT_Sbay_c841_3215 3.7e-11 279_[+5]_561
MIT_Smik_c193_2483 3.7e-11 284_[+5]_556
SGD_Scer_YOR176W 1.9e-10 414_[+5]_293
MIT_Spar_c429_3020 3.1e-10 281_[+5]_559
SGD_Scer_YDL205C 3.8e-09 280_[+5]_560
WashU_Skud_Contig2050.4 5.2e-09 416_[+5]_291
MIT_Spar_c278_20970 5.2e-09 417_[+5]_290
WashU_Sbay_Contig480.2 9.3e-09 452_[+5]_255
MIT_Smik_c935_20455 1e-08 418_[+5]_289
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=10
WashU_Skud_Contig1850.5 ( 282) TGAAAATTGCTGAAATTTTC 1
MIT_Sbay_c841_3215 ( 280) TGAAAATTGCTGAAATTTTC 1
MIT_Smik_c193_2483 ( 285) TGAAAATTGCTGAAATTTTC 1
SGD_Scer_YOR176W ( 415) TGAACCTTCCTGAAATTTAC 1
MIT_Spar_c429_3020 ( 282) TGAAAACTGCTGAAATTTTC 1
SGD_Scer_YDL205C ( 281) AAAAAATTGCTGAAATTTTC 1
WashU_Skud_Contig2050.4 ( 417) TGAACCTTTCCGAAATTTAT 1
MIT_Spar_c278_20970 ( 418) TGAACCTTGCTAAAATCTAT 1
WashU_Sbay_Contig480.2 ( 453) TGAACCTTGCTCGAATTGAT 1
MIT_Smik_c935_20455 ( 419) AGCACATTGCTGAAATTAAT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 6.6e-017
-70 -997 -997 130
-169 -997 236 -997
147 -81 -997 -997
162 -997 -997 -997
62 151 -997 -997
89 119 -997 -997
-997 -81 -997 147
-997 -997 -997 162
-997 -81 219 -169
-997 251 -997 -997
-997 -81 -997 147
-169 -81 219 -997
147 -997 -81 -997
162 -997 -997 -997
162 -997 -997 -997
-997 -997 -997 162
-997 -81 -997 147
-169 -997 -81 130
62 -997 -997 62
-997 177 -997 30
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.6e-017
0.200000 0.000000 0.000000 0.800000
0.100000 0.000000 0.900000 0.000000
0.900000 0.100000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.600000 0.400000 0.000000 0.000000
0.000000 0.100000 0.000000 0.900000
0.000000 0.000000 0.000000 1.000000
0.000000 0.100000 0.800000 0.100000
0.000000 1.000000 0.000000 0.000000
0.000000 0.100000 0.000000 0.900000
0.100000 0.100000 0.800000 0.000000
0.900000 0.000000 0.100000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.100000 0.000000 0.900000
0.100000 0.000000 0.100000 0.800000
0.500000 0.000000 0.000000 0.500000
0.000000 0.600000 0.000000 0.400000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
[TA]GAA[AC][AC]TTGCTGAAATTT[AT][CT]
--------------------------------------------------------------------------------
Time 31.23 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 8.36e-26 109_[+1(5.89e-10)]_15_[+4(1.51e-11)]_10_[+2(3.52e-09)]_11_[+3(4.47e-11)]_56_[+5(3.80e-09)]_560
MIT_Spar_c429_3020 1.64e-27 109_[+1(1.14e-10)]_15_[+4(1.51e-11)]_10_[+2(3.52e-09)]_12_[+3(4.47e-11)]_56_[+5(3.08e-10)]_494_[+2(3.35e-05)]_22_[+5(2.99e-05)]_3
MIT_Smik_c193_2483 1.55e-25 111_[+1(1.56e-10)]_15_[+4(3.28e-09)]_10_[+2(9.12e-10)]_12_[+3(5.94e-10)]_57_[+5(3.68e-11)]_556
MIT_Sbay_c841_3215 1.09e-26 110_[+1(3.58e-11)]_15_[+4(1.51e-11)]_10_[+2(1.46e-09)]_12_[+3(2.13e-08)]_53_[+5(3.68e-11)]_561
WashU_Skud_Contig1850.5 2.56e-26 109_[+1(3.58e-11)]_14_[+4(8.39e-09)]_10_[+2(3.07e-09)]_12_[+3(4.47e-11)]_57_[+5(3.68e-11)]_559
SGD_Scer_YOR176W 3.30e-30 120_[+4(4.51e-10)]_274_[+5(1.86e-10)]_67_[-1(6.04e-11)]_36_[+2(1.49e-12)]_15_[+3(3.79e-11)]_116
MIT_Spar_c278_20970 2.16e-29 122_[+4(1.17e-10)]_239_[+5(6.19e-05)]_16_[+5(5.20e-09)]_66_[-1(6.04e-11)]_36_[+2(1.49e-12)]_15_[+3(3.79e-11)]_114
MIT_Smik_c935_20455 1.31e-23 118_[+4(1.09e-09)]_280_[+5(1.01e-08)]_49_[-1(2.17e-10)]_36_[+2(3.24e-11)]_15_[+3(3.47e-08)]_130
WashU_Skud_Contig2050.4 3.42e-27 123_[+4(2.63e-09)]_235_[+1(5.68e-05)]_19_[+5(5.20e-09)]_68_[-1(5.56e-10)]_12_[+1(5.97e-05)]_10_[+2(1.49e-12)]_15_[+3(3.79e-11)]_108
WashU_Sbay_Contig480.2 4.20e-26 167_[+4(3.20e-08)]_265_[+5(9.34e-09)]_41_[-1(6.04e-11)]_37_[+2(1.49e-12)]_15_[+3(2.26e-10)]_103
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************