********************************************************************************
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-HEM12.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_YDR047W 1.0000 1000
MIT_Spar_c130_3923 1.0000 1000 MIT_Sbay_c896_21277 1.0000 1000
WashU_Skud_Contig1362.1 1.0000 761
********************************************************************************
********************************************************************************
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-HEM12.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= 8061 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.295 C 0.205 G 0.205 T 0.295
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 = 189 E-value = 1.1e-018
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :784a4a4:::::4a::7::
pos.-specific C 4321:6::aaa4:::9a3::
probability G 1::::::6::::a::::::7
matrix T 4::4:::::::6:6:1::a3
bits 2.5 *** * *
2.3 *** * *
2.0 *** * **
1.8 *** * **
Information 1.5 * * *** * *** *
content 1.3 * * *** * *** **
(30.3 bits) 1.0 ** ********* ******
0.8 *** ****************
0.5 *** ****************
0.3 ********************
0.0 --------------------
Multilevel CAAAACAGCCCTGTACCATG
consensus TCCT A A C A C T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c429_3020 + 111 1.67e-11 ATTCAAAATG TAAAACAGCCCTGTACCATG CAAACACGAG
SGD_Scer_YDL205C + 111 1.67e-11 ATTCAAAATC TAATACAGCCCTGTACCATG CAAACACGAG
WashU_Skud_Contig1850.5 + 111 5.77e-11 TTTCAAAAAG CAATACAGCCCTGTACCATT CAAACACGAA
MIT_Sbay_c841_3215 + 112 5.77e-11 ATTCAAAACG CAATACAGCCCTGTACCATT CAAATACGAA
MIT_Smik_c193_2483 + 113 1.63e-10 ATTCAAAAAG TAATACAGCCCTGTACCATT CAAACACGAG
MIT_Sbay_c896_21277 + 206 2.60e-10 TTCCATGGCG TCAAAAAACCCCGAACCCTG TATAAACGAG
MIT_Spar_c130_3923 + 235 4.70e-10 TCTCTCCTGC CACCAAAACCCCGAACCCTG TCCCGTATAT
SGD_Scer_YDR047W + 238 7.68e-10 CTCTCCTGCC GCCAAAAACCCCGAACCCTG TCCTGTATAT
WashU_Skud_Contig1362.1 + 201 9.83e-10 TTTCCTGCTG CCAAAAAACCCCGAATCATG TAGAAGCGAG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c429_3020 1.7e-11 110_[+1]_730
SGD_Scer_YDL205C 1.7e-11 110_[+1]_730
WashU_Skud_Contig1850.5 5.8e-11 110_[+1]_730
MIT_Sbay_c841_3215 5.8e-11 111_[+1]_729
MIT_Smik_c193_2483 1.6e-10 112_[+1]_728
MIT_Sbay_c896_21277 2.6e-10 205_[+1]_775
MIT_Spar_c130_3923 4.7e-10 234_[+1]_746
SGD_Scer_YDR047W 7.7e-10 237_[+1]_743
WashU_Skud_Contig1362.1 9.8e-10 200_[+1]_541
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
MIT_Spar_c429_3020 ( 111) TAAAACAGCCCTGTACCATG 1
SGD_Scer_YDL205C ( 111) TAATACAGCCCTGTACCATG 1
WashU_Skud_Contig1850.5 ( 111) CAATACAGCCCTGTACCATT 1
MIT_Sbay_c841_3215 ( 112) CAATACAGCCCTGTACCATT 1
MIT_Smik_c193_2483 ( 113) TAATACAGCCCTGTACCATT 1
MIT_Sbay_c896_21277 ( 206) TCAAAAAACCCCGAACCCTG 1
MIT_Spar_c130_3923 ( 235) CACCAAAACCCCGAACCCTG 1
SGD_Scer_YDR047W ( 238) GCCAAAAACCCCGAACCCTG 1
WashU_Skud_Contig1362.1 ( 201) CCAAAAAACCCCGAATCATG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 1.1e-018
-982 134 -66 45
104 92 -982 -982
126 34 -982 -982
45 -66 -982 45
162 -982 -982 -982
45 166 -982 -982
162 -982 -982 -982
45 -982 166 -982
-982 251 -982 -982
-982 251 -982 -982
-982 251 -982 -982
-982 134 -982 78
-982 -982 251 -982
45 -982 -982 78
162 -982 -982 -982
-982 234 -982 -154
-982 251 -982 -982
104 92 -982 -982
-982 -982 -982 162
-982 -982 192 4
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.1e-018
0.000000 0.444444 0.111111 0.444444
0.666667 0.333333 0.000000 0.000000
0.777778 0.222222 0.000000 0.000000
0.444444 0.111111 0.000000 0.444444
1.000000 0.000000 0.000000 0.000000
0.444444 0.555556 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.444444 0.000000 0.555556 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
0.000000 0.444444 0.000000 0.555556
0.000000 0.000000 1.000000 0.000000
0.444444 0.000000 0.000000 0.555556
1.000000 0.000000 0.000000 0.000000
0.000000 0.888889 0.000000 0.111111
0.000000 1.000000 0.000000 0.000000
0.666667 0.333333 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.666667 0.333333
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
[CT][AC][AC][AT]A[CA]A[GA]CCC[TC]G[TA]ACC[AC]T[GT]
--------------------------------------------------------------------------------
Time 6.92 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 187 E-value = 6.5e-018
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A ::::1:11::4::a:3:a::
pos.-specific C 68441:6:a::7a:::4:46
probability G ::::8a:9::61::676:63
matrix T 4266::3::a:2::4::::1
bits 2.5 * * *
2.3 * * *
2.0 * ** *
1.8 * ** *
Information 1.5 * ** *** ** ***
content 1.3 * ** *** ** ****
(30.0 bits) 1.0 ****** *************
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CCTTGGCGCTGCCAGGGAGC
consensus TTCC T AT TAC CG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YDL205C + 489 3.06e-13 ACATCTTTAC CCCCGGTGCTGCCAGGGAGC AAAATAATTA
MIT_Spar_c429_3020 + 493 9.57e-12 GACATCTTAC CCCCGGTGCTGTCAGGGAGC AAAAAAATGA
MIT_Sbay_c841_3215 + 503 2.31e-11 CCCTCCCCCT TCTCCGCGCTGCCAGGGACC AGGCAAGGGC
MIT_Sbay_c896_21277 - 239 1.64e-10 TATCTGCCTT TTCTGGCGCTACCATGCAGC TTCCTCGTTT
MIT_Spar_c130_3923 - 287 2.77e-10 TTATTCGCTA TCTTGGCGCTACCATACACG ATTTTTTTTC
WashU_Skud_Contig1850.5 + 494 5.55e-10 ACATCTTCAC CTTCGGAGCTGGCAGGGAGC AAGGGACTCT
WashU_Skud_Contig1362.1 - 246 6.00e-10 TGCCCGTTTT CCTTGGCGCTACCATACACT TCCTCTGTTT
SGD_Scer_YDR047W - 289 1.18e-09 TTATCCGCCA TCTTGGCGCTATCATACACG ATCTTTTTCA
MIT_Smik_c193_2483 + 493 1.25e-09 TTCATCTTAC CCCTAGTACTGCCAGGGAGG AACTAAACCT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDL205C 3.1e-13 488_[+2]_352
MIT_Spar_c429_3020 9.6e-12 492_[+2]_348
MIT_Sbay_c841_3215 2.3e-11 502_[+2]_338
MIT_Sbay_c896_21277 1.6e-10 238_[-2]_742
MIT_Spar_c130_3923 2.8e-10 286_[-2]_694
WashU_Skud_Contig1850.5 5.6e-10 493_[+2]_347
WashU_Skud_Contig1362.1 6e-10 245_[-2]_496
SGD_Scer_YDR047W 1.2e-09 288_[-2]_692
MIT_Smik_c193_2483 1.3e-09 492_[+2]_348
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
SGD_Scer_YDL205C ( 489) CCCCGGTGCTGCCAGGGAGC 1
MIT_Spar_c429_3020 ( 493) CCCCGGTGCTGTCAGGGAGC 1
MIT_Sbay_c841_3215 ( 503) TCTCCGCGCTGCCAGGGACC 1
MIT_Sbay_c896_21277 ( 239) TTCTGGCGCTACCATGCAGC 1
MIT_Spar_c130_3923 ( 287) TCTTGGCGCTACCATACACG 1
WashU_Skud_Contig1850.5 ( 494) CTTCGGAGCTGGCAGGGAGC 1
WashU_Skud_Contig1362.1 ( 246) CCTTGGCGCTACCATACACT 1
SGD_Scer_YDR047W ( 289) TCTTGGCGCTATCATACACG 1
MIT_Smik_c193_2483 ( 493) CCCTAGTACTGCCAGGGAGG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 6.5e-018
-982 166 -982 45
-982 215 -982 -55
-982 134 -982 78
-982 134 -982 78
-154 -66 215 -982
-982 -982 251 -982
-154 166 -982 4
-154 -982 234 -982
-982 251 -982 -982
-982 -982 -982 162
45 -982 166 -982
-982 192 -66 -55
-982 251 -982 -982
162 -982 -982 -982
-982 -982 166 45
4 -982 192 -982
-982 134 166 -982
162 -982 -982 -982
-982 134 166 -982
-982 166 92 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.5e-018
0.000000 0.555556 0.000000 0.444444
0.000000 0.777778 0.000000 0.222222
0.000000 0.444444 0.000000 0.555556
0.000000 0.444444 0.000000 0.555556
0.111111 0.111111 0.777778 0.000000
0.000000 0.000000 1.000000 0.000000
0.111111 0.555556 0.000000 0.333333
0.111111 0.000000 0.888889 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.444444 0.000000 0.555556 0.000000
0.000000 0.666667 0.111111 0.222222
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.555556 0.444444
0.333333 0.000000 0.666667 0.000000
0.000000 0.444444 0.555556 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.444444 0.555556 0.000000
0.000000 0.555556 0.333333 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[CT][CT][TC][TC]GG[CT]GCT[GA][CT]CA[GT][GA][GC]A[GC][CG]
--------------------------------------------------------------------------------
Time 13.49 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 183 E-value = 1.9e-017
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :1::6:1::162::1:a:71
pos.-specific C :2::3a:1:22::a29::::
probability G a6:a1:9::::87:6::::8
matrix T :1a::::9a72:3:11:a31
bits 2.5 * * * *
2.3 * * * *
2.0 * * ** * *
1.8 * * ** * *
Information 1.5 * ** ** * * * ***
content 1.3 * ** **** *** *** *
(29.4 bits) 1.0 * ** **** *** *** *
0.8 ********* *********
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GGTGACGTTTAGGCGCATAG
consensus C C CCAT C T
sequence T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1850.5 + 681 3.00e-13 AAAGTTGGAA GGTGACGTTTAGGCGCATAG GCAATCTCCC
MIT_Spar_c429_3020 + 674 3.00e-13 GAGGTTAGAG GGTGACGTTTAGGCGCATAG GCAACCTCCC
SGD_Scer_YDL205C + 673 3.00e-13 AAGGTTAGAC GGTGACGTTTAGGCGCATAG GCAATCTCCC
MIT_Sbay_c841_3215 + 700 3.16e-11 AACATTAGAG GGTGACGTTTTAGCGCATAG GCAATCTCCC
MIT_Smik_c193_2483 + 674 1.45e-10 AAGGTCAGAG GATGACGTTTAAGCGCATAG GCAATCTCCC
MIT_Spar_c130_3923 + 713 2.43e-10 ACTCTAAAAT GCTGCCGTTCCGTCCCATTG AGTTTTATTT
SGD_Scer_YDR047W + 713 2.43e-10 GTTAAAAAAT GCTGCCGTTCCGTCCCATTG AGTTTTATTT
WashU_Skud_Contig1362.1 + 703 2.69e-08 TCGATCGAAC GTTGCCGTTTAGTCTTATTT TCCTTTCCGT
MIT_Sbay_c896_21277 - 969 4.38e-08 GGGGGCTAGT GGTGGCACTATGGCACATAA AAGCCGTGCA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 3e-13 680_[+3]_160
MIT_Spar_c429_3020 3e-13 673_[+3]_167
SGD_Scer_YDL205C 3e-13 672_[+3]_168
MIT_Sbay_c841_3215 3.2e-11 699_[+3]_141
MIT_Smik_c193_2483 1.5e-10 673_[+3]_167
MIT_Spar_c130_3923 2.4e-10 712_[+3]_268
SGD_Scer_YDR047W 2.4e-10 712_[+3]_268
WashU_Skud_Contig1362.1 2.7e-08 702_[+3]_39
MIT_Sbay_c896_21277 4.4e-08 968_[-3]_12
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
WashU_Skud_Contig1850.5 ( 681) GGTGACGTTTAGGCGCATAG 1
MIT_Spar_c429_3020 ( 674) GGTGACGTTTAGGCGCATAG 1
SGD_Scer_YDL205C ( 673) GGTGACGTTTAGGCGCATAG 1
MIT_Sbay_c841_3215 ( 700) GGTGACGTTTTAGCGCATAG 1
MIT_Smik_c193_2483 ( 674) GATGACGTTTAAGCGCATAG 1
MIT_Spar_c130_3923 ( 713) GCTGCCGTTCCGTCCCATTG 1
SGD_Scer_YDR047W ( 713) GCTGCCGTTCCGTCCCATTG 1
WashU_Skud_Contig1362.1 ( 703) GTTGCCGTTTAGTCTTATTT 1
MIT_Sbay_c896_21277 ( 969) GGTGGCACTATGGCACATAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 1.9e-017
-982 -982 251 -982
-154 34 166 -154
-982 -982 -982 162
-982 -982 251 -982
78 92 -66 -982
-982 251 -982 -982
-154 -982 234 -982
-982 -66 -982 145
-982 -982 -982 162
-154 34 -982 104
78 34 -982 -55
-55 -982 215 -982
-982 -982 192 4
-982 251 -982 -982
-154 34 166 -154
-982 234 -982 -154
162 -982 -982 -982
-982 -982 -982 162
104 -982 -982 4
-154 -982 215 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.9e-017
0.000000 0.000000 1.000000 0.000000
0.111111 0.222222 0.555556 0.111111
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.555556 0.333333 0.111111 0.000000
0.000000 1.000000 0.000000 0.000000
0.111111 0.000000 0.888889 0.000000
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.000000 1.000000
0.111111 0.222222 0.000000 0.666667
0.555556 0.222222 0.000000 0.222222
0.222222 0.000000 0.777778 0.000000
0.000000 0.000000 0.666667 0.333333
0.000000 1.000000 0.000000 0.000000
0.111111 0.222222 0.555556 0.111111
0.000000 0.888889 0.000000 0.111111
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.666667 0.000000 0.000000 0.333333
0.111111 0.000000 0.777778 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
G[GC]TG[AC]CGTT[TC][ACT][GA][GT]C[GC]CAT[AT]G
--------------------------------------------------------------------------------
Time 20.03 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 15 sites = 9 llr = 142 E-value = 2.9e-008
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A ::::9:::::8::::
pos.-specific C a8:::11:89:899:
probability G :::::1:::::11:2
matrix T :2aa189a2121:18
bits 2.5 *
2.3 *
2.0 * * **
1.8 * * **
Information 1.5 **** *** ***
content 1.3 **** **** ***
(22.8 bits) 1.0 ***** **** ****
0.8 ***************
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel CCTTATTTCCACCCT
consensus T T T G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Skud_Contig1850.5 + 723 6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAAGGATAA
MIT_Sbay_c841_3215 + 742 6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGACAA
MIT_Smik_c193_2483 + 716 6.31e-10 TATTATTCAC CCTTATTTCCACCCT CAAACGATAA
MIT_Spar_c429_3020 + 716 6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGATAA
SGD_Scer_YDL205C + 715 6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGATAA
MIT_Spar_c130_3923 - 332 8.79e-08 AACAACATAT CCTTAGCTTCACCCT GCCAATACTG
MIT_Sbay_c896_21277 + 178 6.08e-07 AAAATTGTTT CTTTATTTTTTCCCT CTTTTCCATG
SGD_Scer_YDR047W - 467 1.01e-06 GAAAAAACTT CTTTACTTCCATGCG CGCGTTTTTG
WashU_Skud_Contig1362.1 + 186 1.07e-06 AATTTTTTGG CCTTTTTTCCTGCTG CCAAAAAACC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 6.3e-10 722_[+4]_123
MIT_Sbay_c841_3215 6.3e-10 741_[+4]_104
MIT_Smik_c193_2483 6.3e-10 715_[+4]_130
MIT_Spar_c429_3020 6.3e-10 715_[+4]_130
SGD_Scer_YDL205C 6.3e-10 714_[+4]_131
MIT_Spar_c130_3923 8.8e-08 331_[-4]_654
MIT_Sbay_c896_21277 6.1e-07 177_[+4]_808
SGD_Scer_YDR047W 1e-06 466_[-4]_519
WashU_Skud_Contig1362.1 1.1e-06 185_[+4]_561
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=15 seqs=9
WashU_Skud_Contig1850.5 ( 723) CCTTATTTCCACCCT 1
MIT_Sbay_c841_3215 ( 742) CCTTATTTCCACCCT 1
MIT_Smik_c193_2483 ( 716) CCTTATTTCCACCCT 1
MIT_Spar_c429_3020 ( 716) CCTTATTTCCACCCT 1
SGD_Scer_YDL205C ( 715) CCTTATTTCCACCCT 1
MIT_Spar_c130_3923 ( 332) CCTTAGCTTCACCCT 1
MIT_Sbay_c896_21277 ( 178) CTTTATTTTTTCCCT 1
SGD_Scer_YDR047W ( 467) CTTTACTTCCATGCG 1
WashU_Skud_Contig1362.1 ( 186) CCTTTTTTCCTGCTG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 7935 bayes= 9.78245 E= 2.9e-008
-982 251 -982 -982
-982 215 -982 -55
-982 -982 -982 162
-982 -982 -982 162
145 -982 -982 -154
-982 -66 -66 126
-982 -66 -982 145
-982 -982 -982 162
-982 215 -982 -55
-982 234 -982 -154
126 -982 -982 -55
-982 215 -66 -154
-982 234 -66 -982
-982 234 -982 -154
-982 -982 34 126
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.9e-008
0.000000 1.000000 0.000000 0.000000
0.000000 0.777778 0.000000 0.222222
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.888889 0.000000 0.000000 0.111111
0.000000 0.111111 0.111111 0.777778
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.000000 1.000000
0.000000 0.777778 0.000000 0.222222
0.000000 0.888889 0.000000 0.111111
0.777778 0.000000 0.000000 0.222222
0.000000 0.777778 0.111111 0.111111
0.000000 0.888889 0.111111 0.000000
0.000000 0.888889 0.000000 0.111111
0.000000 0.000000 0.222222 0.777778
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
C[CT]TTATTT[CT]C[AT]CCC[TG]
--------------------------------------------------------------------------------
Time 26.29 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 161 E-value = 2.9e-008
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 2:6197:7:::::::22:a6
pos.-specific C :8211:6:11:9:1:::6:3
probability G 8228:2:3:6:196:88::1
matrix T :::::14:93a:13a::4::
bits 2.5
2.3
2.0 **
1.8 * **
Information 1.5 ** * *** *** *
content 1.3 ** ** * *** *** *
(25.9 bits) 1.0 ** ** *** *** *****
0.8 ** ** **************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GCAGAACATGTCGGTGGCAA
consensus AGC GTG T T AAT C
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YDL205C + 561 1.62e-11 AAGGGTAGCA GCAGAATGTGTCGGTGGTAC CGGTGTGATA
MIT_Spar_c130_3923 + 171 4.79e-11 GACAAAAAGG GCAGAACATTTCGTTGGCAA AATTTAAACT
SGD_Scer_YDR047W + 174 1.01e-10 GATGAAAATG GCAGAACATTTCGCTGGCAA AATTAAAACT
WashU_Skud_Contig1850.5 + 566 1.81e-09 AAGGATAGCA ACGGAATGTGTCGGTGGTAG CGGATGTGGC
MIT_Smik_c193_2483 + 563 3.96e-09 AAGGGTAGCG ACGGCGTATGTCGGTGGTAC CGGATATGGC
WashU_Skud_Contig1362.1 + 138 5.96e-09 CATACGAAAG GCAGAACACCTCGTTGACAA AACTGAAACT
MIT_Sbay_c841_3215 + 572 1.26e-08 CGAGGGTCGC GGCCAATGTGTCGGTAGTAC CGGATGGGGC
MIT_Sbay_c896_21277 + 144 3.29e-08 GACACGAATA GGAAAGCATTTCGTTGACAA AAATAAAATT
MIT_Spar_c429_3020 + 786 4.67e-08 GGATTGAAAA GCCGATCATGTGTGTAGCAA TAGTAGTAGT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDL205C 1.6e-11 560_[+5]_280
MIT_Spar_c130_3923 4.8e-11 170_[+5]_810
SGD_Scer_YDR047W 1e-10 173_[+5]_807
WashU_Skud_Contig1850.5 1.8e-09 565_[+5]_275
MIT_Smik_c193_2483 4e-09 562_[+5]_278
WashU_Skud_Contig1362.1 6e-09 137_[+5]_604
MIT_Sbay_c841_3215 1.3e-08 571_[+5]_269
MIT_Sbay_c896_21277 3.3e-08 143_[+5]_837
MIT_Spar_c429_3020 4.7e-08 785_[+5]_55
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
SGD_Scer_YDL205C ( 561) GCAGAATGTGTCGGTGGTAC 1
MIT_Spar_c130_3923 ( 171) GCAGAACATTTCGTTGGCAA 1
SGD_Scer_YDR047W ( 174) GCAGAACATTTCGCTGGCAA 1
WashU_Skud_Contig1850.5 ( 566) ACGGAATGTGTCGGTGGTAG 1
MIT_Smik_c193_2483 ( 563) ACGGCGTATGTCGGTGGTAC 1
WashU_Skud_Contig1362.1 ( 138) GCAGAACACCTCGTTGACAA 1
MIT_Sbay_c841_3215 ( 572) GGCCAATGTGTCGGTAGTAC 1
MIT_Sbay_c896_21277 ( 144) GGAAAGCATTTCGTTGACAA 1
MIT_Spar_c429_3020 ( 786) GCCGATCATGTGTGTAGCAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 2.9e-008
-55 -982 215 -982
-982 215 34 -982
78 34 34 -982
-154 -66 215 -982
145 -66 -982 -982
104 -982 34 -154
-982 166 -982 45
104 -982 92 -982
-982 -66 -982 145
-982 -66 166 4
-982 -982 -982 162
-982 234 -66 -982
-982 -982 234 -154
-982 -66 166 4
-982 -982 -982 162
-55 -982 215 -982
-55 -982 215 -982
-982 166 -982 45
162 -982 -982 -982
78 92 -66 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.9e-008
0.222222 0.000000 0.777778 0.000000
0.000000 0.777778 0.222222 0.000000
0.555556 0.222222 0.222222 0.000000
0.111111 0.111111 0.777778 0.000000
0.888889 0.111111 0.000000 0.000000
0.666667 0.000000 0.222222 0.111111
0.000000 0.555556 0.000000 0.444444
0.666667 0.000000 0.333333 0.000000
0.000000 0.111111 0.000000 0.888889
0.000000 0.111111 0.555556 0.333333
0.000000 0.000000 0.000000 1.000000
0.000000 0.888889 0.111111 0.000000
0.000000 0.000000 0.888889 0.111111
0.000000 0.111111 0.555556 0.333333
0.000000 0.000000 0.000000 1.000000
0.222222 0.000000 0.777778 0.000000
0.222222 0.000000 0.777778 0.000000
0.000000 0.555556 0.000000 0.444444
1.000000 0.000000 0.000000 0.000000
0.555556 0.333333 0.111111 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
[GA][CG][ACG]GA[AG][CT][AG]T[GT]TCG[GT]T[GA][GA][CT]A[AC]
--------------------------------------------------------------------------------
Time 32.47 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 6.46e-34 110_[+1(1.67e-11)]_358_[+2(3.06e-13)]_52_[+5(1.62e-11)]_92_[+3(3.00e-13)]_22_[+4(6.31e-10)]_54_[+5(2.69e-05)]_57
MIT_Spar_c429_3020 3.43e-29 110_[+1(1.67e-11)]_173_[-4(1.29e-05)]_174_[+2(9.57e-12)]_49_[+5(9.46e-05)]_92_[+3(3.00e-13)]_22_[+4(6.31e-10)]_55_[+5(4.67e-08)]_55
MIT_Smik_c193_2483 1.01e-24 112_[+1(1.63e-10)]_21_[-3(6.96e-05)]_319_[+2(1.25e-09)]_50_[+5(3.96e-09)]_91_[+3(1.45e-10)]_22_[+4(6.31e-10)]_130
MIT_Sbay_c841_3215 6.11e-27 39_[+4(6.88e-05)]_57_[+1(5.77e-11)]_371_[+2(2.31e-11)]_49_[+5(1.26e-08)]_108_[+3(3.16e-11)]_22_[+4(6.31e-10)]_104
WashU_Skud_Contig1850.5 2.40e-28 110_[+1(5.77e-11)]_272_[-3(9.23e-05)]_71_[+2(5.55e-10)]_52_[+5(1.81e-09)]_53_[-1(8.53e-05)]_22_[+3(3.00e-13)]_22_[+4(6.31e-10)]_123
SGD_Scer_YDR047W 4.48e-22 173_[+5(1.01e-10)]_44_[+1(7.68e-10)]_31_[-2(1.18e-09)]_158_[-4(1.01e-06)]_134_[+2(4.56e-05)]_77_[+3(2.43e-10)]_268
MIT_Spar_c130_3923 3.62e-24 22_[+4(6.45e-05)]_133_[+5(4.79e-11)]_44_[+1(4.70e-10)]_32_[-2(2.77e-10)]_25_[-4(8.79e-08)]_124_[-1(9.89e-05)]_222_[+3(2.43e-10)]_36_[+4(1.03e-05)]_143_[+2(2.11e-05)]_54
MIT_Sbay_c896_21277 4.53e-19 143_[+5(3.29e-08)]_14_[+4(6.08e-07)]_13_[+1(2.60e-10)]_13_[-2(1.64e-10)]_493_[+2(7.81e-05)]_197_[-3(4.38e-08)]_12
WashU_Skud_Contig1362.1 3.15e-19 137_[+5(5.96e-09)]_28_[+4(1.07e-06)]_[+1(9.83e-10)]_25_[-2(6.00e-10)]_252_[-2(2.11e-05)]_165_[+3(2.69e-08)]_39
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************