********************************************************************************
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= HEM2-HEM13.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YGL040C 1.0000 1000 MIT_Spar_c19_8512 1.0000 1000
MIT_Smik_c273_7756 1.0000 1000 MIT_Sbay_c77_8808 1.0000 1000
WashU_Skud_Contig2052.17 1.0000 1000 SGD_Scer_YDR044W 1.0000 1000
MIT_Spar_c130_3912 1.0000 1000 MIT_Sbay_c896_21290 1.0000 1000
WashU_Smik_Contig2283.3 1.0000 1000
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM2-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
model: mod= oops nmotifs= 5 evt= inf
object function= E-value of product of p-values
width: minw= 6 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 9 maxsites= 9 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 9000 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.314 C 0.186 G 0.186 T 0.314
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324
********************************************************************************
********************************************************************************
MOTIF 1 width = 20 sites = 9 llr = 197 E-value = 9.2e-022
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A ::::::4:12a1:::::::8
pos.-specific C a144:a::1::::::66::1
probability G :66:a:6a28:::a8::1a1
matrix T :3:6::::6::9a:2449::
bits 2.5 * ** * * *
2.3 * ** * * *
2.0 * ** * * *
1.8 * ** * * *
Information 1.5 * * ** * ** *** *
content 1.3 * * ** * ** *** **
(31.6 bits) 1.0 * ****** **********
0.8 ******** ***********
0.5 ******** ***********
0.3 ********************
0.0 --------------------
Multilevel CGGTGCGGTGATTGGCCTGA
consensus TCC A GA TTT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2052.17 - 180 1.35e-13 AATCCCTGTT CGGTGCGGTGATTGGCCTGA GGCAAGCTGC
MIT_Smik_c273_7756 - 179 1.35e-13 AATCCTTATT CGGTGCGGTGATTGGCCTGA GGCAACATAC
MIT_Spar_c19_8512 - 181 1.35e-13 AATCCCTGTT CGGTGCGGTGATTGGCCTGA GGCAAGCTGC
SGD_Scer_YGL040C - 180 1.17e-12 AATCCCTGTT CGGTGCGGTGATTGGCTTGA GGCAAGCTTC
MIT_Sbay_c77_8808 - 181 2.88e-12 CATCTCCGGG CGGTGCGGTGATTGGCCTGC GGCAGGCTGC
WashU_Smik_Contig2283.3 + 542 2.66e-10 ACGTTGAAAA CTCCGCAGGGATTGGTTTGG AAAATTATAG
SGD_Scer_YDR044W + 540 1.12e-09 ACAGTAAAAA CTCCGCAGGAAATGGTTTGA AGAATCTTAA
MIT_Spar_c130_3912 + 534 1.20e-09 ACATTGAAAA CCCCGCAGCAATTGTTCTGA AGAATCTTAA
MIT_Sbay_c896_21290 + 542 1.43e-09 ACTTTTAAAA CTCCGCAGAGATTGTTTGGA GGGACCTTGA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 1.4e-13 179_[-1]_801
MIT_Smik_c273_7756 1.4e-13 178_[-1]_802
MIT_Spar_c19_8512 1.4e-13 180_[-1]_800
SGD_Scer_YGL040C 1.2e-12 179_[-1]_801
MIT_Sbay_c77_8808 2.9e-12 180_[-1]_800
WashU_Smik_Contig2283.3 2.7e-10 541_[+1]_439
SGD_Scer_YDR044W 1.1e-09 539_[+1]_441
MIT_Spar_c130_3912 1.2e-09 533_[+1]_447
MIT_Sbay_c896_21290 1.4e-09 541_[+1]_439
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2052.17 ( 180) CGGTGCGGTGATTGGCCTGA 1
MIT_Smik_c273_7756 ( 179) CGGTGCGGTGATTGGCCTGA 1
MIT_Spar_c19_8512 ( 181) CGGTGCGGTGATTGGCCTGA 1
SGD_Scer_YGL040C ( 180) CGGTGCGGTGATTGGCTTGA 1
MIT_Sbay_c77_8808 ( 181) CGGTGCGGTGATTGGCCTGC 1
WashU_Smik_Contig2283.3 ( 542) CTCCGCAGGGATTGGTTTGG 1
SGD_Scer_YDR044W ( 540) CTCCGCAGGAAATGGTTTGA 1
MIT_Spar_c130_3912 ( 534) CCCCGCAGCAATTGTTCTGA 1
MIT_Sbay_c896_21290 ( 542) CTCCGCAGAGATTGTTTGGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 9.2e-022
-982 251 -982 -982
-982 -66 166 4
-982 134 166 -982
-982 134 -982 78
-982 -982 251 -982
-982 251 -982 -982
45 -982 166 -982
-982 -982 251 -982
-154 -66 34 78
-55 -982 215 -982
162 -982 -982 -982
-154 -982 -982 145
-982 -982 -982 162
-982 -982 251 -982
-982 -982 215 -55
-982 166 -982 45
-982 166 -982 45
-982 -982 -66 145
-982 -982 251 -982
126 -66 -66 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 9.2e-022
0.000000 1.000000 0.000000 0.000000
0.000000 0.111111 0.555556 0.333333
0.000000 0.444444 0.555556 0.000000
0.000000 0.444444 0.000000 0.555556
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.000000 0.000000 1.000000 0.000000
0.111111 0.111111 0.222222 0.555556
0.222222 0.000000 0.777778 0.000000
1.000000 0.000000 0.000000 0.000000
0.111111 0.000000 0.000000 0.888889
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.777778 0.222222
0.000000 0.555556 0.000000 0.444444
0.000000 0.555556 0.000000 0.444444
0.000000 0.000000 0.111111 0.888889
0.000000 0.000000 1.000000 0.000000
0.777778 0.111111 0.111111 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
C[GT][GC][TC]GC[GA]G[TG][GA]ATTG[GT][CT][CT]TGA
--------------------------------------------------------------------------------
Time 8.40 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 167 E-value = 2.0e-010
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 4a:aa:a:43:19464a493
pos.-specific C ::a::::::1:::4:6:11:
probability G 6::::::a62491:4::::7
matrix T :::::a:::36::1:::4::
bits 2.5 * *
2.3 * *
2.0 * * *
1.8 * * *
Information 1.5 ******* * *
content 1.3 ******* ** * **
(26.8 bits) 1.0 ********* *** *** **
0.8 ********* *** *** **
0.5 ********* ******* **
0.3 ********* **********
0.0 --------------------
Multilevel GACAATAGGATGAAACAAAG
consensus A ATG CGA T A
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2052.17 + 100 8.72e-11 AGAAATCATG AACAATAGGATGACGCATAG ACGTCACTAC
WashU_Smik_Contig2283.3 + 112 3.17e-10 TAACAGGTGA GACAATAGGTGGAAAAAAAG GAAAATATGT
MIT_Spar_c130_3912 + 116 6.61e-10 AACAAAGAAA GACAATAGGCGGAAAAAAAG GAAAATCCGT
SGD_Scer_YGL040C + 101 8.03e-10 GAAAATCAAA GACAATAGAGTGGCGCATAG ATGTTGCTAG
MIT_Spar_c19_8512 + 102 1.36e-09 AAAAAACAAG GACAATAGAATGACACATAA AGTTTGCTAG
SGD_Scer_YDR044W + 119 1.86e-09 AACAAAGAAA GACAATAGGTGGAAAAAAAA AGGAAAATCC
MIT_Sbay_c77_8808 + 105 3.82e-09 AACTAACATT AACAATAGAGTGATGCATAG ACGTCACTAG
MIT_Smik_c273_7756 + 102 5.03e-09 ATAAATCAGG AACAATAGAATGACGCACCG AGTTTGCTAG
MIT_Sbay_c896_21290 + 120 2.10e-08 ATTGGCAGCG AACAATAGGTGAAAAAAAAA AAGAAAATGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 8.7e-11 99_[+2]_881
WashU_Smik_Contig2283.3 3.2e-10 111_[+2]_869
MIT_Spar_c130_3912 6.6e-10 115_[+2]_865
SGD_Scer_YGL040C 8e-10 100_[+2]_880
MIT_Spar_c19_8512 1.4e-09 101_[+2]_879
SGD_Scer_YDR044W 1.9e-09 118_[+2]_862
MIT_Sbay_c77_8808 3.8e-09 104_[+2]_876
MIT_Smik_c273_7756 5e-09 101_[+2]_879
MIT_Sbay_c896_21290 2.1e-08 119_[+2]_861
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
WashU_Skud_Contig2052.17 ( 100) AACAATAGGATGACGCATAG 1
WashU_Smik_Contig2283.3 ( 112) GACAATAGGTGGAAAAAAAG 1
MIT_Spar_c130_3912 ( 116) GACAATAGGCGGAAAAAAAG 1
SGD_Scer_YGL040C ( 101) GACAATAGAGTGGCGCATAG 1
MIT_Spar_c19_8512 ( 102) GACAATAGAATGACACATAA 1
SGD_Scer_YDR044W ( 119) GACAATAGGTGGAAAAAAAA 1
MIT_Sbay_c77_8808 ( 105) AACAATAGAGTGATGCATAG 1
MIT_Smik_c273_7756 ( 102) AACAATAGAATGACGCACCG 1
MIT_Sbay_c896_21290 ( 120) AACAATAGGTGAAAAAAAAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 2.0e-010
45 -982 166 -982
162 -982 -982 -982
-982 251 -982 -982
162 -982 -982 -982
162 -982 -982 -982
-982 -982 -982 162
162 -982 -982 -982
-982 -982 251 -982
45 -982 166 -982
4 -66 34 4
-982 -982 134 78
-154 -982 234 -982
145 -982 -66 -982
45 134 -982 -154
78 -982 134 -982
45 166 -982 -982
162 -982 -982 -982
45 -66 -982 45
145 -66 -982 -982
4 -982 192 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.0e-010
0.444444 0.000000 0.555556 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.333333 0.111111 0.222222 0.333333
0.000000 0.000000 0.444444 0.555556
0.111111 0.000000 0.888889 0.000000
0.888889 0.000000 0.111111 0.000000
0.444444 0.444444 0.000000 0.111111
0.555556 0.000000 0.444444 0.000000
0.444444 0.555556 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.444444 0.111111 0.000000 0.444444
0.888889 0.111111 0.000000 0.000000
0.333333 0.000000 0.666667 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[GA]ACAATAG[GA][ATG][TG]GA[AC][AG][CA]A[AT]A[GA]
--------------------------------------------------------------------------------
Time 16.42 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 18 sites = 9 llr = 161 E-value = 2.9e-010
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A a97926:1a9:::8a:2:
pos.-specific C ::3::::6::::a::427
probability G ::::84a1:1aa:::34:
matrix T :1:1:::2:::::2:213
bits 2.5 * ***
2.3 * ***
2.0 * ***
1.8 * ***
Information 1.5 * * * * *** *
content 1.3 * * * ***** * *
(25.8 bits) 1.0 ******* ***** * *
0.8 ******* ******** *
0.5 ******************
0.3 ******************
0.0 ------------------
Multilevel AAAAGAGCAAGGCAACGC
consensus C AG T T GAT
sequence TC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ------------------
MIT_Spar_c130_3912 + 695 1.68e-11 GAGAAATATC AACAGGGCAAGGCAAGGC TATGCTCTTT
MIT_Sbay_c77_8808 - 144 1.90e-10 CCTGATTTAT AAAAGAGCAAGGCAACAC AATAAAAGGC
SGD_Scer_YDR044W + 703 6.56e-10 AAATATCAAC AAAAGGGCAAGGCTATGC CTTCTGGAAA
WashU_Smik_Contig2283.3 + 703 3.25e-09 GAAAAATATT AACAAGGGAAGGCAAGGC TATGTTCTAT
MIT_Spar_c19_8512 - 140 3.60e-09 CTTGATTTAT AAAAGAGTAAGGCAACCT AATAAATGCT
MIT_Sbay_c896_21290 + 701 6.28e-09 GGAAAATATC AACAAGGCAAGGCTATGC CTTTCGAAGA
MIT_Smik_c273_7756 - 833 1.56e-08 GTTTTCTACA AAATGAGCAGGGCAAGAC GAAATTTCCG
WashU_Skud_Contig2052.17 - 139 1.98e-08 CCCAATTTAT AAAAGAGAAAGGCAACTT ATATGAAGAG
SGD_Scer_YGL040C - 139 2.12e-08 CTTGATTTAT ATAAGAGTAAGGCAACCT AATAAATGCT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c130_3912 1.7e-11 694_[+3]_288
MIT_Sbay_c77_8808 1.9e-10 143_[-3]_839
SGD_Scer_YDR044W 6.6e-10 702_[+3]_280
WashU_Smik_Contig2283.3 3.3e-09 702_[+3]_280
MIT_Spar_c19_8512 3.6e-09 139_[-3]_843
MIT_Sbay_c896_21290 6.3e-09 700_[+3]_282
MIT_Smik_c273_7756 1.6e-08 832_[-3]_150
WashU_Skud_Contig2052.17 2e-08 138_[-3]_844
SGD_Scer_YGL040C 2.1e-08 138_[-3]_844
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=18 seqs=9
MIT_Spar_c130_3912 ( 695) AACAGGGCAAGGCAAGGC 1
MIT_Sbay_c77_8808 ( 144) AAAAGAGCAAGGCAACAC 1
SGD_Scer_YDR044W ( 703) AAAAGGGCAAGGCTATGC 1
WashU_Smik_Contig2283.3 ( 703) AACAAGGGAAGGCAAGGC 1
MIT_Spar_c19_8512 ( 140) AAAAGAGTAAGGCAACCT 1
MIT_Sbay_c896_21290 ( 701) AACAAGGCAAGGCTATGC 1
MIT_Smik_c273_7756 ( 833) AAATGAGCAGGGCAAGAC 1
WashU_Skud_Contig2052.17 ( 139) AAAAGAGAAAGGCAACTT 1
SGD_Scer_YGL040C ( 139) ATAAGAGTAAGGCAACCT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 18 n= 8847 bayes= 9.93958 E= 2.9e-010
162 -982 -982 -982
145 -982 -982 -154
104 92 -982 -982
145 -982 -982 -154
-55 -982 215 -982
78 -982 134 -982
-982 -982 251 -982
-154 166 -66 -55
162 -982 -982 -982
145 -982 -66 -982
-982 -982 251 -982
-982 -982 251 -982
-982 251 -982 -982
126 -982 -982 -55
162 -982 -982 -982
-982 134 92 -55
-55 34 134 -154
-982 192 -982 4
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 18 nsites= 9 E= 2.9e-010
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.000000 0.111111
0.666667 0.333333 0.000000 0.000000
0.888889 0.000000 0.000000 0.111111
0.222222 0.000000 0.777778 0.000000
0.555556 0.000000 0.444444 0.000000
0.000000 0.000000 1.000000 0.000000
0.111111 0.555556 0.111111 0.222222
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 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
0.777778 0.000000 0.000000 0.222222
1.000000 0.000000 0.000000 0.000000
0.000000 0.444444 0.333333 0.222222
0.222222 0.222222 0.444444 0.111111
0.000000 0.666667 0.000000 0.333333
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
AA[AC]A[GA][AG]G[CT]AAGGC[AT]A[CGT][GAC][CT]
--------------------------------------------------------------------------------
Time 24.29 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 15 sites = 9 llr = 139 E-value = 2.6e-006
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A :::::::2:8:::::
pos.-specific C 3:9:a:::318771:
probability G :9:::a::::1:34:
matrix T 711a::a87113:4a
bits 2.5 **
2.3 **
2.0 ** **
1.8 ** **
Information 1.5 ****** * * *
content 1.3 ****** *** *
(22.3 bits) 1.0 ******* * *** *
0.8 ***************
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel TGCTCGTTTACCCGT
consensus C AC TGT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Skud_Contig2052.17 + 209 3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT TGCGTTCAAA
MIT_Smik_c273_7756 + 208 3.42e-10 GAATAAGGAT TGCTCGTTTACCCGT TGTTCGATTT
MIT_Spar_c19_8512 + 210 3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT AGTTTGAATT
SGD_Scer_YGL040C + 209 3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT ATTTTGATTT
MIT_Sbay_c77_8808 + 209 5.96e-09 CGCCCGGAGA TGCTCGTTTACCGTT GTGCACCAAA
MIT_Spar_c130_3912 - 591 1.14e-07 GAGTTTCGTC CGCTCGTACACTGTT GGGAGAAACA
SGD_Scer_YDR044W - 597 3.16e-07 GGAGTTTGTC CTCTCGTTCACTGTT GGGAAAAACA
WashU_Smik_Contig2283.3 - 597 7.66e-07 GAAGTTCATC CGCTCGTACCTTCTT GAAAGACAAT
MIT_Sbay_c896_21290 + 366 1.10e-06 CTGTGTGAAA TGTTCGTTTTGCCCT TCCCAGAGAG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 3.4e-10 208_[+4]_777
MIT_Smik_c273_7756 3.4e-10 207_[+4]_778
MIT_Spar_c19_8512 3.4e-10 209_[+4]_776
SGD_Scer_YGL040C 3.4e-10 208_[+4]_777
MIT_Sbay_c77_8808 6e-09 208_[+4]_777
MIT_Spar_c130_3912 1.1e-07 590_[-4]_395
SGD_Scer_YDR044W 3.2e-07 596_[-4]_389
WashU_Smik_Contig2283.3 7.7e-07 596_[-4]_389
MIT_Sbay_c896_21290 1.1e-06 365_[+4]_620
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=15 seqs=9
WashU_Skud_Contig2052.17 ( 209) TGCTCGTTTACCCGT 1
MIT_Smik_c273_7756 ( 208) TGCTCGTTTACCCGT 1
MIT_Spar_c19_8512 ( 210) TGCTCGTTTACCCGT 1
SGD_Scer_YGL040C ( 209) TGCTCGTTTACCCGT 1
MIT_Sbay_c77_8808 ( 209) TGCTCGTTTACCGTT 1
MIT_Spar_c130_3912 ( 591) CGCTCGTACACTGTT 1
SGD_Scer_YDR044W ( 597) CTCTCGTTCACTGTT 1
WashU_Smik_Contig2283.3 ( 597) CGCTCGTACCTTCTT 1
MIT_Sbay_c896_21290 ( 366) TGTTCGTTTTGCCCT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8874 bayes= 9.94398 E= 2.6e-006
-982 92 -982 104
-982 -982 234 -154
-982 234 -982 -154
-982 -982 -982 162
-982 251 -982 -982
-982 -982 251 -982
-982 -982 -982 162
-55 -982 -982 126
-982 92 -982 104
126 -66 -982 -154
-982 215 -66 -154
-982 192 -982 4
-982 192 92 -982
-982 -66 134 45
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.6e-006
0.000000 0.333333 0.000000 0.666667
0.000000 0.000000 0.888889 0.111111
0.000000 0.888889 0.000000 0.111111
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.222222 0.000000 0.000000 0.777778
0.000000 0.333333 0.000000 0.666667
0.777778 0.111111 0.000000 0.111111
0.000000 0.777778 0.111111 0.111111
0.000000 0.666667 0.000000 0.333333
0.000000 0.666667 0.333333 0.000000
0.000000 0.111111 0.444444 0.444444
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[TC]GCTCGT[TA][TC]AC[CT][CG][GT]T
--------------------------------------------------------------------------------
Time 32.02 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 157 E-value = 4.5e-006
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A a:21::1178:99:1794a8
pos.-specific C ::::3::::1:1:163:1:2
probability G ::177199319::91:13::
matrix T :a72:9::::1:1:2::1::
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 ATTGGTGGAAGAAGCAAAAA
consensus ATC G TC G C
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Smik_Contig2283.3 + 249 2.56e-12 CTGGGGCATT ATTGGTGGAAGAAGCCAGAA AAGACGAAAG
MIT_Sbay_c896_21290 + 259 2.92e-12 CTGGGGCATA ATTGGTGGGAGAAGCCAGAA AATGCGAAAG
MIT_Spar_c130_3912 + 253 2.92e-12 CTGGGGCATT ATTGGTGGGAGAAGCCAGAA AAGGCGAAAG
SGD_Scer_YDR044W + 261 1.67e-09 CTGGAGCGTT ATTGGTGGGAGAACCAGAAA AGGCGAAAGC
MIT_Sbay_c77_8808 + 27 1.46e-08 TCTGGTAAGG ATATCTGGAAGAAGTAACAA TACGTATAAA
MIT_Smik_c273_7756 - 234 3.53e-08 GCCGAAAAAA ATTGGTAGAAGATGAAAAAA AAAATCGAAC
MIT_Spar_c19_8512 + 45 7.16e-08 GCAGGCAATA ATATGGGGAAGCAGTAAAAC TTTTTGTTTT
WashU_Skud_Contig2052.17 + 962 8.03e-08 AGTTTCCGTC ATGGCTGAACGAAGGAAAAC TACATCACCT
SGD_Scer_YGL040C + 26 1.04e-07 CTAGGTATGA ATTACTGGAGTAAGCAATAA TATGAGTAAG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Smik_Contig2283.3 2.6e-12 248_[+5]_732
MIT_Sbay_c896_21290 2.9e-12 258_[+5]_722
MIT_Spar_c130_3912 2.9e-12 252_[+5]_728
SGD_Scer_YDR044W 1.7e-09 260_[+5]_720
MIT_Sbay_c77_8808 1.5e-08 26_[+5]_954
MIT_Smik_c273_7756 3.5e-08 233_[-5]_747
MIT_Spar_c19_8512 7.2e-08 44_[+5]_936
WashU_Skud_Contig2052.17 8e-08 961_[+5]_19
SGD_Scer_YGL040C 1e-07 25_[+5]_955
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
WashU_Smik_Contig2283.3 ( 249) ATTGGTGGAAGAAGCCAGAA 1
MIT_Sbay_c896_21290 ( 259) ATTGGTGGGAGAAGCCAGAA 1
MIT_Spar_c130_3912 ( 253) ATTGGTGGGAGAAGCCAGAA 1
SGD_Scer_YDR044W ( 261) ATTGGTGGGAGAACCAGAAA 1
MIT_Sbay_c77_8808 ( 27) ATATCTGGAAGAAGTAACAA 1
MIT_Smik_c273_7756 ( 234) ATTGGTAGAAGATGAAAAAA 1
MIT_Spar_c19_8512 ( 45) ATATGGGGAAGCAGTAAAAC 1
WashU_Skud_Contig2052.17 ( 962) ATGGCTGAACGAAGGAAAAC 1
SGD_Scer_YGL040C ( 26) ATTACTGGAGTAAGCAATAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 4.5e-006
162 -982 -982 -982
-982 -982 -982 162
-55 -982 -66 104
-154 -982 192 -55
-982 92 192 -982
-982 -982 -66 145
-154 -982 234 -982
-154 -982 234 -982
104 -982 92 -982
126 -66 -66 -982
-982 -982 234 -154
145 -66 -982 -982
145 -982 -982 -154
-982 -66 234 -982
-154 166 -66 -55
104 92 -982 -982
145 -982 -66 -982
45 -66 92 -154
162 -982 -982 -982
126 34 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.5e-006
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.222222 0.000000 0.111111 0.666667
0.111111 0.000000 0.666667 0.222222
0.000000 0.333333 0.666667 0.000000
0.000000 0.000000 0.111111 0.888889
0.111111 0.000000 0.888889 0.000000
0.111111 0.000000 0.888889 0.000000
0.666667 0.000000 0.333333 0.000000
0.777778 0.111111 0.111111 0.000000
0.000000 0.000000 0.888889 0.111111
0.888889 0.111111 0.000000 0.000000
0.888889 0.000000 0.000000 0.111111
0.000000 0.111111 0.888889 0.000000
0.111111 0.555556 0.111111 0.222222
0.666667 0.333333 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.444444 0.111111 0.333333 0.111111
1.000000 0.000000 0.000000 0.000000
0.777778 0.222222 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
AT[TA][GT][GC]TGG[AG]AGAAG[CT][AC]A[AG]A[AC]
--------------------------------------------------------------------------------
Time 39.67 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YGL040C 1.75e-23 25_[+5(1.04e-07)]_55_[+2(8.03e-10)]_18_[-3(2.12e-08)]_23_[-1(1.17e-12)]_9_[+4(3.42e-10)]_178_[-3(7.59e-05)]_498_[-2(2.36e-05)]_63
MIT_Spar_c19_8512 4.98e-25 44_[+5(7.16e-08)]_37_[+2(1.36e-09)]_18_[-3(3.60e-09)]_23_[-1(1.35e-13)]_9_[+4(3.42e-10)]_8_[-2(8.78e-05)]_191_[-3(9.88e-05)]_101_[+2(6.40e-05)]_317_[+2(1.09e-05)]_81
MIT_Smik_c273_7756 3.49e-24 25_[+5(8.56e-07)]_56_[+2(5.03e-09)]_57_[-1(1.35e-13)]_9_[+4(3.42e-10)]_11_[-5(3.53e-08)]_529_[+5(2.17e-05)]_30_[-3(1.56e-08)]_150
MIT_Sbay_c77_8808 4.86e-24 26_[+5(1.46e-08)]_58_[+2(3.82e-09)]_19_[-3(1.90e-10)]_19_[-1(2.88e-12)]_8_[+4(5.96e-09)]_465_[-2(9.60e-06)]_54_[+5(6.34e-05)]_218
WashU_Skud_Contig2052.17 2.08e-25 99_[+2(8.72e-11)]_19_[-3(1.98e-08)]_23_[-1(1.35e-13)]_9_[+4(3.42e-10)]_322_[-5(2.17e-05)]_101_[-4(3.66e-05)]_280_[+5(8.03e-08)]_19
SGD_Scer_YDR044W 1.15e-20 118_[+2(1.86e-09)]_40_[+3(9.53e-06)]_64_[+5(1.67e-09)]_153_[+1(5.50e-05)]_86_[+1(1.12e-09)]_37_[-4(3.16e-07)]_91_[+3(6.56e-10)]_280
MIT_Spar_c130_3912 1.46e-25 115_[+2(6.61e-10)]_117_[+5(2.92e-12)]_261_[+1(1.20e-09)]_37_[-4(1.14e-07)]_89_[+3(1.68e-11)]_288
MIT_Sbay_c896_21290 9.74e-21 84_[+5(7.87e-05)]_15_[+2(2.10e-08)]_119_[+5(2.92e-12)]_87_[+4(1.10e-06)]_161_[+1(1.43e-09)]_37_[-4(1.81e-05)]_87_[+3(6.28e-09)]_282
WashU_Smik_Contig2283.3 1.35e-23 111_[+2(3.17e-10)]_81_[+1(3.33e-05)]_16_[+5(2.56e-12)]_273_[+1(2.66e-10)]_35_[-4(7.66e-07)]_91_[+3(3.25e-09)]_280
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************