********************************************************************************
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-HEM3.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_YDL205C 1.0000 860
MIT_Spar_c429_3020 1.0000 860 MIT_Smik_c193_2483 1.0000 860
MIT_Sbay_c841_3215 1.0000 860 WashU_Skud_Contig1850.5 1.0000 860
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM2-HEM3.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
model: mod= oops nmotifs= 5 evt= inf
object function= E-value of product of p-values
width: minw= 6 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 10 maxsites= 10 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 9300 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.317 C 0.183 G 0.183 T 0.317
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324
********************************************************************************
********************************************************************************
MOTIF 1 width = 11 sites = 10 llr = 140 E-value = 1.1e-010
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :::aa1:a1::
pos.-specific C :a9:::5:9a:
probability G a:1:::5:::6
matrix T :::::9::::4
bits 2.5 ** *
2.3 ** *
2.0 *** **
1.8 *** **
Information 1.5 ***** ****
content 1.3 ***********
(20.2 bits) 1.0 ***********
0.8 ***********
0.5 ***********
0.3 ***********
0.0 -----------
Multilevel GCCAATCACCG
consensus G T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- -----------
WashU_Skud_Contig2052.17 + 184 1.14e-07 CTTGCCTCAG GCCAATCACCG CACCGAACAG
MIT_Sbay_c77_8808 + 185 1.14e-07 CCTGCCGCAG GCCAATCACCG CACCGCCCGG
MIT_Smik_c273_7756 + 183 1.14e-07 GTTGCCTCAG GCCAATCACCG CACCGAATAA
MIT_Spar_c19_8512 + 185 1.14e-07 CTTGCCTCAG GCCAATCACCG CACCGAACAG
SGD_Scer_YGL040C + 184 1.14e-07 CTTGCCTCAA GCCAATCACCG CACCGAACAG
MIT_Sbay_c841_3215 + 151 3.24e-07 ACGCCAATCT GCCAATGACCT TGAAATCAAG
MIT_Spar_c429_3020 + 150 3.24e-07 GCCTCAATCT GCCAATGACCT TGAATCCAAG
SGD_Scer_YDL205C + 150 3.24e-07 GCGTCAATCT GCCAATGACCT TGAATTCAGG
MIT_Smik_c193_2483 + 152 1.57e-06 GCGCCAATTT GCCAATGAACT TGAAATCCAG
WashU_Skud_Contig1850.5 - 817 1.69e-06 AACTGAATAA GCGAAAGACCG TCCCACTACC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 1.1e-07 183_[+1]_806
MIT_Sbay_c77_8808 1.1e-07 184_[+1]_805
MIT_Smik_c273_7756 1.1e-07 182_[+1]_807
MIT_Spar_c19_8512 1.1e-07 184_[+1]_805
SGD_Scer_YGL040C 1.1e-07 183_[+1]_806
MIT_Sbay_c841_3215 3.2e-07 150_[+1]_699
MIT_Spar_c429_3020 3.2e-07 149_[+1]_700
SGD_Scer_YDL205C 3.2e-07 149_[+1]_700
MIT_Smik_c193_2483 1.6e-06 151_[+1]_698
WashU_Skud_Contig1850.5 1.7e-06 816_[-1]_33
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=11 seqs=10
WashU_Skud_Contig2052.17 ( 184) GCCAATCACCG 1
MIT_Sbay_c77_8808 ( 185) GCCAATCACCG 1
MIT_Smik_c273_7756 ( 183) GCCAATCACCG 1
MIT_Spar_c19_8512 ( 185) GCCAATCACCG 1
SGD_Scer_YGL040C ( 184) GCCAATCACCG 1
MIT_Sbay_c841_3215 ( 151) GCCAATGACCT 1
MIT_Spar_c429_3020 ( 150) GCCAATGACCT 1
SGD_Scer_YDL205C ( 150) GCCAATGACCT 1
MIT_Smik_c193_2483 ( 152) GCCAATGAACT 1
WashU_Skud_Contig1850.5 ( 817) GCGAAAGACCG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 11 n= 9200 bayes= 9.84392 E= 1.1e-010
-997 -997 251 -997
-997 251 -997 -997
-997 236 -81 -997
162 -997 -997 -997
162 -997 -997 -997
-169 -997 -997 147
-997 151 151 -997
162 -997 -997 -997
-169 236 -997 -997
-997 251 -997 -997
-997 -997 177 30
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 11 nsites= 10 E= 1.1e-010
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.900000 0.100000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.100000 0.000000 0.000000 0.900000
0.000000 0.500000 0.500000 0.000000
1.000000 0.000000 0.000000 0.000000
0.100000 0.900000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.600000 0.400000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
GCCAAT[CG]ACC[GT]
--------------------------------------------------------------------------------
Time 9.05 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 10 llr = 196 E-value = 5.0e-018
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A ::5::1:::a:::::7:::1
pos.-specific C ::5:5:::5:aa9::::116
probability G :5:::9::::::14:1311:
matrix T a5:a5:aa5::::6a27883
bits 2.5 **
2.3 **
2.0 * ***
1.8 * ***
Information 1.5 * * *** **** *
content 1.3 * * *** **** *
(28.2 bits) 1.0 *************** ***
0.8 *************** ****
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel TGATCGTTCACCCTTATTTC
consensus TC T T G TG T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YGL040C + 209 7.10e-11 GAACAGGGAT TGCTCGTTTACCCGTATTTT GATTTTTTTT
WashU_Skud_Contig1850.5 + 712 8.92e-11 CAATCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
MIT_Sbay_c841_3215 + 731 8.92e-11 CAATCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
MIT_Spar_c429_3020 + 705 8.92e-11 CAACCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
SGD_Scer_YDL205C + 704 8.92e-11 CAATCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
MIT_Smik_c273_7756 + 208 1.21e-10 GAATAAGGAT TGCTCGTTTACCCGTTGTTC GATTTTTTTT
MIT_Spar_c19_8512 + 210 1.21e-10 GAACAGGGAT TGCTCGTTTACCCGTAGTTT GAATTTTTTT
MIT_Smik_c193_2483 + 705 2.20e-09 CAATCTCCCC TTATTATTCACCCTTATTTC CACCCTCAAA
WashU_Skud_Contig2052.17 + 209 6.11e-09 GAACAGGGAT TGCTCGTTTACCCGTTGCGT TCAAAGTTTT
MIT_Sbay_c77_8808 + 209 2.28e-08 CGCCCGGAGA TGCTCGTTTACCGTTGTGCA CCAAATTTTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YGL040C 7.1e-11 208_[+2]_772
WashU_Skud_Contig1850.5 8.9e-11 711_[+2]_129
MIT_Sbay_c841_3215 8.9e-11 730_[+2]_110
MIT_Spar_c429_3020 8.9e-11 704_[+2]_136
SGD_Scer_YDL205C 8.9e-11 703_[+2]_137
MIT_Smik_c273_7756 1.2e-10 207_[+2]_773
MIT_Spar_c19_8512 1.2e-10 209_[+2]_771
MIT_Smik_c193_2483 2.2e-09 704_[+2]_136
WashU_Skud_Contig2052.17 6.1e-09 208_[+2]_772
MIT_Sbay_c77_8808 2.3e-08 208_[+2]_772
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=10
SGD_Scer_YGL040C ( 209) TGCTCGTTTACCCGTATTTT 1
WashU_Skud_Contig1850.5 ( 712) TTATTGTTCACCCTTATTTC 1
MIT_Sbay_c841_3215 ( 731) TTATTGTTCACCCTTATTTC 1
MIT_Spar_c429_3020 ( 705) TTATTGTTCACCCTTATTTC 1
SGD_Scer_YDL205C ( 704) TTATTGTTCACCCTTATTTC 1
MIT_Smik_c273_7756 ( 208) TGCTCGTTTACCCGTTGTTC 1
MIT_Spar_c19_8512 ( 210) TGCTCGTTTACCCGTAGTTT 1
MIT_Smik_c193_2483 ( 705) TTATTATTCACCCTTATTTC 1
WashU_Skud_Contig2052.17 ( 209) TGCTCGTTTACCCGTTGCGT 1
MIT_Sbay_c77_8808 ( 209) TGCTCGTTTACCGTTGTGCA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 9110 bayes= 9.82972 E= 5.0e-018
-997 -997 -997 162
-997 -997 151 62
62 151 -997 -997
-997 -997 -997 162
-997 151 -997 62
-169 -997 236 -997
-997 -997 -997 162
-997 -997 -997 162
-997 151 -997 62
162 -997 -997 -997
-997 251 -997 -997
-997 251 -997 -997
-997 236 -81 -997
-997 -997 119 89
-997 -997 -997 162
111 -997 -81 -70
-997 -997 77 111
-997 -81 -81 130
-997 -81 -81 130
-169 177 -997 -11
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.0e-018
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.500000 0.500000
0.500000 0.500000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.000000 0.500000
0.100000 0.000000 0.900000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.000000 0.500000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.900000 0.100000 0.000000
0.000000 0.000000 0.400000 0.600000
0.000000 0.000000 0.000000 1.000000
0.700000 0.000000 0.100000 0.200000
0.000000 0.000000 0.300000 0.700000
0.000000 0.100000 0.100000 0.800000
0.000000 0.100000 0.100000 0.800000
0.100000 0.600000 0.000000 0.300000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
T[GT][AC]T[CT]GTT[CT]ACCC[TG]T[AT][TG]TT[CT]
--------------------------------------------------------------------------------
Time 18.20 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 15 sites = 10 llr = 167 E-value = 8.5e-015
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A 5:a:::a9:1:1:1:
pos.-specific C :1:::a::39:5a98
probability G :4:aa::13::3::1
matrix T 55::::::4:a1::1
bits 2.5 *** *
2.3 *** *
2.0 *** * **
1.8 *** * **
Information 1.5 ***** ** ***
content 1.3 ****** ** ***
(24.1 bits) 1.0 ****** ** ***
0.8 ******* ******
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel ATAGGCAATCTCCCC
consensus TG C G
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
MIT_Spar_c429_3020 + 690 1.51e-09 GTTTAGGCGC ATAGGCAACCTCCCC TTATTGTTCA
MIT_Spar_c19_8512 - 169 1.91e-09 GTGATTGGCC TGAGGCAAGCTGCCC GCTTGATTTA
WashU_Skud_Contig1850.5 + 697 2.59e-09 GTTTAGGCGC ATAGGCAATCTCCCC TTATTGTTCA
MIT_Sbay_c841_3215 + 716 2.59e-09 GTTTTAGCGC ATAGGCAATCTCCCC TTATTGTTCA
MIT_Smik_c193_2483 + 690 2.59e-09 GTTTAAGCGC ATAGGCAATCTCCCC TTATTATTCA
SGD_Scer_YDL205C + 689 2.59e-09 GTTTAGGCGC ATAGGCAATCTCCCC TTATTGTTCA
SGD_Scer_YGL040C - 168 8.84e-09 GTGATTGGCT TGAGGCAAGCTTCCC GCTTGATTTA
WashU_Skud_Contig2052.17 - 168 2.94e-08 GTGATTGGCC TGAGGCAAGCTGCCT GCCCAATTTA
MIT_Sbay_c77_8808 + 167 1.36e-07 CTTTTATAAA TCAGGCAGCCTGCCG CAGGCCAATC
MIT_Smik_c273_7756 - 167 3.45e-07 GTGATTGGCC TGAGGCAACATACAC TCTTGATTTA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c429_3020 1.5e-09 689_[+3]_156
MIT_Spar_c19_8512 1.9e-09 168_[-3]_817
WashU_Skud_Contig1850.5 2.6e-09 696_[+3]_149
MIT_Sbay_c841_3215 2.6e-09 715_[+3]_130
MIT_Smik_c193_2483 2.6e-09 689_[+3]_156
SGD_Scer_YDL205C 2.6e-09 688_[+3]_157
SGD_Scer_YGL040C 8.8e-09 167_[-3]_818
WashU_Skud_Contig2052.17 2.9e-08 167_[-3]_818
MIT_Sbay_c77_8808 1.4e-07 166_[+3]_819
MIT_Smik_c273_7756 3.4e-07 166_[-3]_819
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=15 seqs=10
MIT_Spar_c429_3020 ( 690) ATAGGCAACCTCCCC 1
MIT_Spar_c19_8512 ( 169) TGAGGCAAGCTGCCC 1
WashU_Skud_Contig1850.5 ( 697) ATAGGCAATCTCCCC 1
MIT_Sbay_c841_3215 ( 716) ATAGGCAATCTCCCC 1
MIT_Smik_c193_2483 ( 690) ATAGGCAATCTCCCC 1
SGD_Scer_YDL205C ( 689) ATAGGCAATCTCCCC 1
SGD_Scer_YGL040C ( 168) TGAGGCAAGCTTCCC 1
WashU_Skud_Contig2052.17 ( 168) TGAGGCAAGCTGCCT 1
MIT_Sbay_c77_8808 ( 167) TCAGGCAGCCTGCCG 1
MIT_Smik_c273_7756 ( 167) TGAGGCAACATACAC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 9160 bayes= 9.83763 E= 8.5e-015
62 -997 -997 62
-997 -81 119 62
162 -997 -997 -997
-997 -997 251 -997
-997 -997 251 -997
-997 251 -997 -997
162 -997 -997 -997
147 -997 -81 -997
-997 77 77 30
-169 236 -997 -997
-997 -997 -997 162
-169 151 77 -169
-997 251 -997 -997
-169 236 -997 -997
-997 219 -81 -169
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 8.5e-015
0.500000 0.000000 0.000000 0.500000
0.000000 0.100000 0.400000 0.500000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.900000 0.000000 0.100000 0.000000
0.000000 0.300000 0.300000 0.400000
0.100000 0.900000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.100000 0.500000 0.300000 0.100000
0.000000 1.000000 0.000000 0.000000
0.100000 0.900000 0.000000 0.000000
0.000000 0.800000 0.100000 0.100000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
[AT][TG]AGGCAA[TCG]CT[CG]CCC
--------------------------------------------------------------------------------
Time 27.22 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 18 sites = 10 llr = 176 E-value = 2.3e-013
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 92:5718a:aa:a:9855
pos.-specific C ::a:::::a:::::::::
probability G ::::182::::::a12:5
matrix T 18:521:::::a::::5:
bits 2.5 * * *
2.3 * * *
2.0 * * *
1.8 * * *
Information 1.5 * * *******
content 1.3 * * * ********
(25.4 bits) 1.0 *** *********** *
0.8 *** *********** *
0.5 ******************
0.3 ******************
0.0 ------------------
Multilevel ATCAAGAACAATAGAAAA
consensus A TT G GTG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ------------------
MIT_Sbay_c841_3215 - 57 8.38e-10 CCATATTAGC ATCTAGAACAATAGAAAA AGAAGAAGGA
MIT_Smik_c193_2483 - 58 8.38e-10 CCGTATTAGT ATCTAGAACAATAGAAAA AAGAAAAAGG
MIT_Spar_c429_3020 - 56 8.38e-10 CCGTATTAGT ATCTAGAACAATAGAAAA AGGAAAAGGC
SGD_Scer_YDL205C - 56 8.38e-10 CCGTATTAAT ATCTAGAACAATAGAAAA AAAGAAAAGC
MIT_Smik_c273_7756 + 96 2.49e-09 AGGCCAATAA ATCAGGAACAATAGAATG ACGCACCGAG
MIT_Spar_c19_8512 + 96 5.09e-09 TGGGCCAAAA AACAAGGACAATAGAATG ACACATAAAG
WashU_Skud_Contig1850.5 - 55 9.52e-09 CCATATTAGT TTCTAGAACAATAGAAAA AAAAAAAAGC
WashU_Skud_Contig2052.17 + 94 9.81e-09 TTAGCCAGAA ATCATGAACAATAGGATG ACGCATAGAC
SGD_Scer_YGL040C + 95 2.62e-08 GGGCAAGAAA ATCAAAGACAATAGAGTG GCGCATAGAT
MIT_Sbay_c77_8808 + 99 6.75e-08 GCTATGAACT AACATTAACAATAGAGTG ATGCATAGAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Sbay_c841_3215 8.4e-10 56_[-4]_786
MIT_Smik_c193_2483 8.4e-10 57_[-4]_785
MIT_Spar_c429_3020 8.4e-10 55_[-4]_787
SGD_Scer_YDL205C 8.4e-10 55_[-4]_787
MIT_Smik_c273_7756 2.5e-09 95_[+4]_887
MIT_Spar_c19_8512 5.1e-09 95_[+4]_887
WashU_Skud_Contig1850.5 9.5e-09 54_[-4]_788
WashU_Skud_Contig2052.17 9.8e-09 93_[+4]_889
SGD_Scer_YGL040C 2.6e-08 94_[+4]_888
MIT_Sbay_c77_8808 6.8e-08 98_[+4]_884
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=18 seqs=10
MIT_Sbay_c841_3215 ( 57) ATCTAGAACAATAGAAAA 1
MIT_Smik_c193_2483 ( 58) ATCTAGAACAATAGAAAA 1
MIT_Spar_c429_3020 ( 56) ATCTAGAACAATAGAAAA 1
SGD_Scer_YDL205C ( 56) ATCTAGAACAATAGAAAA 1
MIT_Smik_c273_7756 ( 96) ATCAGGAACAATAGAATG 1
MIT_Spar_c19_8512 ( 96) AACAAGGACAATAGAATG 1
WashU_Skud_Contig1850.5 ( 55) TTCTAGAACAATAGAAAA 1
WashU_Skud_Contig2052.17 ( 94) ATCATGAACAATAGGATG 1
SGD_Scer_YGL040C ( 95) ATCAAAGACAATAGAGTG 1
MIT_Sbay_c77_8808 ( 99) AACATTAACAATAGAGTG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 18 n= 9130 bayes= 9.83289 E= 2.3e-013
147 -997 -997 -169
-70 -997 -997 130
-997 251 -997 -997
62 -997 -997 62
111 -997 -81 -70
-169 -997 219 -169
130 -997 19 -997
162 -997 -997 -997
-997 251 -997 -997
162 -997 -997 -997
162 -997 -997 -997
-997 -997 -997 162
162 -997 -997 -997
-997 -997 251 -997
147 -997 -81 -997
130 -997 19 -997
62 -997 -997 62
62 -997 151 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 18 nsites= 10 E= 2.3e-013
0.900000 0.000000 0.000000 0.100000
0.200000 0.000000 0.000000 0.800000
0.000000 1.000000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
0.700000 0.000000 0.100000 0.200000
0.100000 0.000000 0.800000 0.100000
0.800000 0.000000 0.200000 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
0.900000 0.000000 0.100000 0.000000
0.800000 0.000000 0.200000 0.000000
0.500000 0.000000 0.000000 0.500000
0.500000 0.000000 0.500000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
A[TA]C[AT][AT]G[AG]ACAATAGA[AG][AT][AG]
--------------------------------------------------------------------------------
Time 35.82 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 10 llr = 179 E-value = 9.4e-012
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A ::::::8::::::1:1211:
pos.-specific C :1:11a2:12:61:49:4::
probability G ::::1::::::::41:::::
matrix T a9a98::a98a4955:859a
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 TTTTTCATTTTCTTTCTTTT
consensus C C T GC AC
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1850.5 + 231 1.09e-10 TTCCTTCAAT TTTTTCATTTTCTTTCTTTT TTTATGTTTA
MIT_Spar_c429_3020 + 232 1.09e-10 TTCCTTCATT TTTTTCATTTTCTTTCTTTT TTTATGTTTG
SGD_Scer_YDL205C + 230 1.09e-10 GTTCCTTTAC TTTTTCATTTTCTTTCTTTT TTTATGTTTG
MIT_Sbay_c77_8808 + 234 1.86e-10 GTGCACCAAA TTTTTCATTTTTTGCCTTTT TCTATTTGGC
MIT_Smik_c193_2483 + 235 1.28e-09 TCCTTCAGTT TTTCTCATTTTCTTTCTTTT TCTATGTTTT
MIT_Sbay_c841_3215 + 261 2.16e-09 TTATGTCTAA TTTTTCATTTTTTTTCACTT GAAAATTGCT
MIT_Spar_c19_8512 + 450 1.73e-08 GTACGTCTTG TTTTGCCTTCTTTGGCTCTT GTGTCACTGA
SGD_Scer_YGL040C + 446 2.06e-08 GTGTACGCCT TCTTCCCTTCTTTGCCTCTT GTGCCACTGT
WashU_Skud_Contig2052.17 + 235 3.92e-08 GCGTTCAAAG TTTTTCATTTTCCGCATCAT CTACTTTTTT
MIT_Smik_c273_7756 + 235 4.56e-08 TTCGATTTTT TTTTTCATCTTCTACCAATT TTTTTCGGCA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 1.1e-10 230_[+5]_610
MIT_Spar_c429_3020 1.1e-10 231_[+5]_609
SGD_Scer_YDL205C 1.1e-10 229_[+5]_611
MIT_Sbay_c77_8808 1.9e-10 233_[+5]_747
MIT_Smik_c193_2483 1.3e-09 234_[+5]_606
MIT_Sbay_c841_3215 2.2e-09 260_[+5]_580
MIT_Spar_c19_8512 1.7e-08 449_[+5]_531
SGD_Scer_YGL040C 2.1e-08 445_[+5]_535
WashU_Skud_Contig2052.17 3.9e-08 234_[+5]_746
MIT_Smik_c273_7756 4.6e-08 234_[+5]_746
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=10
WashU_Skud_Contig1850.5 ( 231) TTTTTCATTTTCTTTCTTTT 1
MIT_Spar_c429_3020 ( 232) TTTTTCATTTTCTTTCTTTT 1
SGD_Scer_YDL205C ( 230) TTTTTCATTTTCTTTCTTTT 1
MIT_Sbay_c77_8808 ( 234) TTTTTCATTTTTTGCCTTTT 1
MIT_Smik_c193_2483 ( 235) TTTCTCATTTTCTTTCTTTT 1
MIT_Sbay_c841_3215 ( 261) TTTTTCATTTTTTTTCACTT 1
MIT_Spar_c19_8512 ( 450) TTTTGCCTTCTTTGGCTCTT 1
SGD_Scer_YGL040C ( 446) TCTTCCCTTCTTTGCCTCTT 1
WashU_Skud_Contig2052.17 ( 235) TTTTTCATTTTCCGCATCAT 1
MIT_Smik_c273_7756 ( 235) TTTTTCATCTTCTACCAATT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 9110 bayes= 9.82972 E= 9.4e-012
-997 -997 -997 162
-997 -81 -997 147
-997 -997 -997 162
-997 -81 -997 147
-997 -81 -81 130
-997 251 -997 -997
130 19 -997 -997
-997 -997 -997 162
-997 -81 -997 147
-997 19 -997 130
-997 -997 -997 162
-997 177 -997 30
-997 -81 -997 147
-169 -997 119 62
-997 119 -81 62
-169 236 -997 -997
-70 -997 -997 130
-169 119 -997 62
-169 -997 -997 147
-997 -997 -997 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.4e-012
0.000000 0.000000 0.000000 1.000000
0.000000 0.100000 0.000000 0.900000
0.000000 0.000000 0.000000 1.000000
0.000000 0.100000 0.000000 0.900000
0.000000 0.100000 0.100000 0.800000
0.000000 1.000000 0.000000 0.000000
0.800000 0.200000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.100000 0.000000 0.900000
0.000000 0.200000 0.000000 0.800000
0.000000 0.000000 0.000000 1.000000
0.000000 0.600000 0.000000 0.400000
0.000000 0.100000 0.000000 0.900000
0.100000 0.000000 0.400000 0.500000
0.000000 0.400000 0.100000 0.500000
0.100000 0.900000 0.000000 0.000000
0.200000 0.000000 0.000000 0.800000
0.100000 0.400000 0.000000 0.500000
0.100000 0.000000 0.000000 0.900000
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
TTTTTC[AC]TT[TC]T[CT]T[TG][TC]C[TA][TC]TT
--------------------------------------------------------------------------------
Time 44.27 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YGL040C 4.71e-19 94_[+4(2.62e-08)]_55_[-3(8.84e-09)]_1_[+1(1.14e-07)]_14_[+2(7.10e-11)]_6_[+5(2.48e-05)]_191_[+5(2.06e-08)]_95_[-5(3.50e-05)]_420
MIT_Spar_c19_8512 3.44e-20 95_[+4(5.09e-09)]_55_[-3(1.91e-09)]_1_[+1(1.14e-07)]_14_[+2(1.21e-10)]_7_[+5(2.48e-05)]_193_[+5(1.73e-08)]_353_[+5(1.61e-05)]_65_[-5(3.99e-05)]_73
MIT_Smik_c273_7756 5.44e-18 43_[-5(4.67e-06)]_32_[+4(2.49e-09)]_53_[-3(3.45e-07)]_1_[+1(1.14e-07)]_14_[+2(1.21e-10)]_7_[+5(4.56e-08)]_187_[+2(8.72e-05)]_539
MIT_Sbay_c77_8808 3.80e-17 98_[+4(6.75e-08)]_50_[+3(1.36e-07)]_3_[+1(1.14e-07)]_13_[+2(2.28e-08)]_5_[+5(1.86e-10)]_508_[-5(4.64e-05)]_219
WashU_Skud_Contig2052.17 6.49e-17 93_[+4(9.81e-09)]_56_[-3(2.94e-08)]_1_[+1(1.14e-07)]_14_[+2(6.11e-09)]_6_[+5(3.92e-08)]_265_[+5(1.82e-05)]_245_[+1(9.56e-05)]_205
SGD_Scer_YDL205C 7.24e-23 55_[-4(8.38e-10)]_76_[+1(3.24e-07)]_69_[+5(1.09e-10)]_4_[+5(6.12e-05)]_50_[+2(1.32e-05)]_345_[+3(2.59e-09)]_[+2(8.92e-11)]_137
MIT_Spar_c429_3020 4.36e-23 55_[-4(8.38e-10)]_76_[+1(3.24e-07)]_71_[+5(1.09e-10)]_75_[+2(1.32e-05)]_160_[-5(7.29e-05)]_163_[+3(1.51e-09)]_[+2(8.92e-11)]_105_[+2(8.90e-05)]_11
MIT_Smik_c193_2483 6.38e-20 57_[-4(8.38e-10)]_76_[+1(1.57e-06)]_72_[+5(1.28e-09)]_11_[+5(4.42e-05)]_42_[+2(1.03e-05)]_342_[+3(2.59e-09)]_[+2(2.20e-09)]_136
MIT_Sbay_c841_3215 1.19e-21 56_[-4(8.38e-10)]_76_[+1(3.24e-07)]_69_[+5(3.18e-06)]_10_[+5(2.16e-09)]_44_[+2(1.03e-05)]_371_[+3(2.59e-09)]_[+2(8.92e-11)]_110
WashU_Skud_Contig1850.5 3.30e-21 54_[-4(9.52e-09)]_158_[+5(1.09e-10)]_4_[+5(6.08e-06)]_52_[+2(1.38e-05)]_180_[-5(8.12e-05)]_43_[+3(2.88e-05)]_92_[+3(2.59e-09)]_[+2(8.92e-11)]_85_[-1(1.69e-06)]_33
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************