********************************************************************************
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-HEM12.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_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 HEM2-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= 8761 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.309 C 0.191 G 0.191 T 0.309
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 = 201 E-value = 6.7e-025
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A ::2711:1aa1:a32::a::
pos.-specific C a272::a7:::9:66:a:99
probability G :11199:2::21:12a::1:
matrix T :7::::::::7::::::::1
bits 2.5 * * **
2.3 * * **
2.0 * *** * ** **
1.8 * *** * ** **
Information 1.5 * *** ** ** *****
content 1.3 * ****** ** *****
(32.3 bits) 1.0 * * ****** ** *****
0.8 ********** *********
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CTCAGGCCAATCACCGCACC
consensus CAC G G AA
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2052.17 + 179 5.70e-14 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
MIT_Smik_c273_7756 + 178 5.70e-14 TGTATGTTGC CTCAGGCCAATCACCGCACC GAATAAGGAT
MIT_Spar_c19_8512 + 180 5.70e-14 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
MIT_Sbay_c77_8808 + 180 4.81e-13 GGCAGCCTGC CGCAGGCCAATCACCGCACC GCCCGGAGAT
SGD_Scer_YGL040C + 179 4.85e-12 GGAAGCTTGC CTCAAGCCAATCACCGCACC GAACAGGGAT
SGD_Scer_YDR047W + 616 4.68e-10 CTTTAACAAT CCACGGCGAAACAAGGCACC GCTGTGCATT
MIT_Spar_c130_3923 + 612 4.99e-10 TTTTTACAAA CTACGGCAAAGCAAAGCACC ACTGGCGCAA
MIT_Sbay_c896_21277 + 896 5.96e-10 AATTCTCGAG CTGAGGCCAATGAAGGCAGC TTCCAGGGCT
WashU_Skud_Contig1362.1 + 614 4.38e-09 ATTTTACAAA CCCGGACGAAGCAGAGCACT TGCTGGAACA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 5.7e-14 178_[+1]_802
MIT_Smik_c273_7756 5.7e-14 177_[+1]_803
MIT_Spar_c19_8512 5.7e-14 179_[+1]_801
MIT_Sbay_c77_8808 4.8e-13 179_[+1]_801
SGD_Scer_YGL040C 4.9e-12 178_[+1]_802
SGD_Scer_YDR047W 4.7e-10 615_[+1]_365
MIT_Spar_c130_3923 5e-10 611_[+1]_369
MIT_Sbay_c896_21277 6e-10 895_[+1]_85
WashU_Skud_Contig1362.1 4.4e-09 613_[+1]_128
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2052.17 ( 179) CTCAGGCCAATCACCGCACC 1
MIT_Smik_c273_7756 ( 178) CTCAGGCCAATCACCGCACC 1
MIT_Spar_c19_8512 ( 180) CTCAGGCCAATCACCGCACC 1
MIT_Sbay_c77_8808 ( 180) CGCAGGCCAATCACCGCACC 1
SGD_Scer_YGL040C ( 179) CTCAAGCCAATCACCGCACC 1
SGD_Scer_YDR047W ( 616) CCACGGCGAAACAAGGCACC 1
MIT_Spar_c130_3923 ( 612) CTACGGCAAAGCAAAGCACC 1
MIT_Sbay_c896_21277 ( 896) CTGAGGCCAATGAAGGCAGC 1
WashU_Skud_Contig1362.1 ( 614) CCCGGACGAAGCAGAGCACT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 6.7e-025
-982 251 -982 -982
-982 34 -66 104
-55 192 -66 -982
104 34 -66 -982
-154 -982 234 -982
-154 -982 234 -982
-982 251 -982 -982
-154 192 34 -982
162 -982 -982 -982
162 -982 -982 -982
-154 -982 34 104
-982 234 -66 -982
162 -982 -982 -982
4 166 -66 -982
-55 166 34 -982
-982 -982 251 -982
-982 251 -982 -982
162 -982 -982 -982
-982 234 -66 -982
-982 234 -982 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.7e-025
0.000000 1.000000 0.000000 0.000000
0.000000 0.222222 0.111111 0.666667
0.222222 0.666667 0.111111 0.000000
0.666667 0.222222 0.111111 0.000000
0.111111 0.000000 0.888889 0.000000
0.111111 0.000000 0.888889 0.000000
0.000000 1.000000 0.000000 0.000000
0.111111 0.666667 0.222222 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.111111 0.000000 0.222222 0.666667
0.000000 0.888889 0.111111 0.000000
1.000000 0.000000 0.000000 0.000000
0.333333 0.555556 0.111111 0.000000
0.222222 0.555556 0.222222 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
0.000000 0.888889 0.111111 0.000000
0.000000 0.888889 0.000000 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
C[TC][CA][AC]GGC[CG]AA[TG]CA[CA][CAG]GCACC
--------------------------------------------------------------------------------
Time 8.20 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 174 E-value = 1.0e-012
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 8:82:391:1:::::::9::
pos.-specific C 27122::::1a17:::1:7a
probability G ::16761::8::3a13::3:
matrix T :3::11:9a::9::9791::
bits 2.5 * * *
2.3 * * *
2.0 * * *
1.8 * * *
Information 1.5 *** ** **
content 1.3 * * * ******* * **
(27.9 bits) 1.0 ** * **************
0.8 ********************
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel ACAGGGATTGCTCGTTTACC
consensus CT ACA G G G
sequence C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2052.17 + 201 3.60e-13 ACCGCACCGA ACAGGGATTGCTCGTTTACC CGTTGCGTTC
MIT_Spar_c19_8512 + 202 3.60e-13 ACCGCACCGA ACAGGGATTGCTCGTTTACC CGTAGTTTGA
SGD_Scer_YGL040C + 201 3.60e-13 ACCGCACCGA ACAGGGATTGCTCGTTTACC CGTATTTTGA
MIT_Smik_c273_7756 + 200 6.88e-11 ACCGCACCGA ATAAGGATTGCTCGTTTACC CGTTGTTCGA
SGD_Scer_YDR047W + 557 2.56e-09 TGATCCGAAG ACACCAATTGCTGGTGCAGC ATAGGAATAT
MIT_Sbay_c77_8808 + 201 4.15e-09 CACCGCACCG CCCGGAGATGCTCGTTTACC GTTGTGCACC
MIT_Sbay_c896_21277 - 39 1.46e-08 TCTTTGCTAA ATAGTGATTCCTGGGGTAGC TATTAGAATA
MIT_Spar_c130_3923 + 554 1.46e-08 ATGGTCAATG ACGCCAATTACTGGTGTAGC ATGAGAATAC
WashU_Skud_Contig1362.1 - 264 2.12e-08 GTCATTCTTT CTAAGTATTGCCCGTTTTCC TTGGCGCTAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 3.6e-13 200_[+2]_780
MIT_Spar_c19_8512 3.6e-13 201_[+2]_779
SGD_Scer_YGL040C 3.6e-13 200_[+2]_780
MIT_Smik_c273_7756 6.9e-11 199_[+2]_781
SGD_Scer_YDR047W 2.6e-09 556_[+2]_424
MIT_Sbay_c77_8808 4.1e-09 200_[+2]_780
MIT_Sbay_c896_21277 1.5e-08 38_[-2]_942
MIT_Spar_c130_3923 1.5e-08 553_[+2]_427
WashU_Skud_Contig1362.1 2.1e-08 263_[-2]_478
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
WashU_Skud_Contig2052.17 ( 201) ACAGGGATTGCTCGTTTACC 1
MIT_Spar_c19_8512 ( 202) ACAGGGATTGCTCGTTTACC 1
SGD_Scer_YGL040C ( 201) ACAGGGATTGCTCGTTTACC 1
MIT_Smik_c273_7756 ( 200) ATAAGGATTGCTCGTTTACC 1
SGD_Scer_YDR047W ( 557) ACACCAATTGCTGGTGCAGC 1
MIT_Sbay_c77_8808 ( 201) CCCGGAGATGCTCGTTTACC 1
MIT_Sbay_c896_21277 ( 39) ATAGTGATTCCTGGGGTAGC 1
MIT_Spar_c130_3923 ( 554) ACGCCAATTACTGGTGTAGC 1
WashU_Skud_Contig1362.1 ( 264) CTAAGTATTGCCCGTTTTCC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 1.0e-012
126 34 -982 -982
-982 192 -982 4
126 -66 -66 -982
-55 34 166 -982
-982 34 192 -154
4 -982 166 -154
145 -982 -66 -982
-154 -982 -982 145
-982 -982 -982 162
-154 -66 215 -982
-982 251 -982 -982
-982 -66 -982 145
-982 192 92 -982
-982 -982 251 -982
-982 -982 -66 145
-982 -982 92 104
-982 -66 -982 145
145 -982 -982 -154
-982 192 92 -982
-982 251 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.0e-012
0.777778 0.222222 0.000000 0.000000
0.000000 0.666667 0.000000 0.333333
0.777778 0.111111 0.111111 0.000000
0.222222 0.222222 0.555556 0.000000
0.000000 0.222222 0.666667 0.111111
0.333333 0.000000 0.555556 0.111111
0.888889 0.000000 0.111111 0.000000
0.111111 0.000000 0.000000 0.888889
0.000000 0.000000 0.000000 1.000000
0.111111 0.111111 0.777778 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.111111 0.000000 0.888889
0.000000 0.666667 0.333333 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.111111 0.888889
0.000000 0.000000 0.333333 0.666667
0.000000 0.111111 0.000000 0.888889
0.888889 0.000000 0.000000 0.111111
0.000000 0.666667 0.333333 0.000000
0.000000 1.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[AC][CT]A[GAC][GC][GA]ATTGCT[CG]GT[TG]TA[CG]C
--------------------------------------------------------------------------------
Time 16.04 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 9 llr = 159 E-value = 7.4e-007
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :::23:16:::9:a784:9:
pos.-specific C a73623641::::::16:::
probability G ::7:2:3::4:11::1:a19
matrix T :3:227::96a:9:3::::1
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 CCGCATCATTTATAAACGAG
consensus TCACCGC G T A
sequence TG
T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Sbay_c896_21277 + 216 1.03e-10 TCAAAAAACC CCGAACCCTGTATAAACGAG GAAGCTGCAT
MIT_Spar_c19_8512 - 151 6.18e-10 GGCAAGCTGC CCGCTTGATTTATAAAAGAG TAAGGCAACC
SGD_Scer_YDR047W + 253 7.00e-10 AAACCCCGAA CCCTGTCCTGTATATACGAG AAACATTGAA
MIT_Sbay_c77_8808 - 155 1.63e-09 CTGCGGCAGG CTGCCTGATTTATAAAAGAG CAAGGCAACA
SGD_Scer_YGL040C - 150 1.63e-09 GGCAAGCTTC CCGCTTGATTTATATAAGAG TAAGGCAACC
MIT_Spar_c130_3923 + 250 4.40e-09 AAACCCCGAA CCCTGTCCCGTATATACGAG GAACATTGAA
WashU_Skud_Contig1362.1 + 211 8.03e-09 CCAAAAAACC CCGAATCATGTAGAAGCGAG AAGTAAAACA
WashU_Skud_Contig2052.17 - 150 1.10e-08 GGCAAGCTGC CTGCCCAATTTATAAAAGAG AAAGGCAACT
MIT_Smik_c273_7756 + 871 1.32e-07 GAGTCATCAT CTCCACCCTTTGTAACCGGT GTCCTGCTCA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Sbay_c896_21277 1e-10 215_[+3]_765
MIT_Spar_c19_8512 6.2e-10 150_[-3]_830
SGD_Scer_YDR047W 7e-10 252_[+3]_728
MIT_Sbay_c77_8808 1.6e-09 154_[-3]_826
SGD_Scer_YGL040C 1.6e-09 149_[-3]_831
MIT_Spar_c130_3923 4.4e-09 249_[+3]_731
WashU_Skud_Contig1362.1 8e-09 210_[+3]_531
WashU_Skud_Contig2052.17 1.1e-08 149_[-3]_831
MIT_Smik_c273_7756 1.3e-07 870_[+3]_110
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=9
MIT_Sbay_c896_21277 ( 216) CCGAACCCTGTATAAACGAG 1
MIT_Spar_c19_8512 ( 151) CCGCTTGATTTATAAAAGAG 1
SGD_Scer_YDR047W ( 253) CCCTGTCCTGTATATACGAG 1
MIT_Sbay_c77_8808 ( 155) CTGCCTGATTTATAAAAGAG 1
SGD_Scer_YGL040C ( 150) CCGCTTGATTTATATAAGAG 1
MIT_Spar_c130_3923 ( 250) CCCTGTCCCGTATATACGAG 1
WashU_Skud_Contig1362.1 ( 211) CCGAATCATGTAGAAGCGAG 1
WashU_Skud_Contig2052.17 ( 150) CTGCCCAATTTATAAAAGAG 1
MIT_Smik_c273_7756 ( 871) CTCCACCCTTTGTAACCGGT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 7.4e-007
-982 251 -982 -982
-982 192 -982 4
-982 92 192 -982
-55 166 -982 -55
4 34 34 -55
-982 92 -982 104
-154 166 92 -982
78 134 -982 -982
-982 -66 -982 145
-982 -982 134 78
-982 -982 -982 162
145 -982 -66 -982
-982 -982 -66 145
162 -982 -982 -982
104 -982 -982 4
126 -66 -66 -982
45 166 -982 -982
-982 -982 251 -982
145 -982 -66 -982
-982 -982 234 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 7.4e-007
0.000000 1.000000 0.000000 0.000000
0.000000 0.666667 0.000000 0.333333
0.000000 0.333333 0.666667 0.000000
0.222222 0.555556 0.000000 0.222222
0.333333 0.222222 0.222222 0.222222
0.000000 0.333333 0.000000 0.666667
0.111111 0.555556 0.333333 0.000000
0.555556 0.444444 0.000000 0.000000
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.444444 0.555556
0.000000 0.000000 0.000000 1.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.000000 0.111111 0.888889
1.000000 0.000000 0.000000 0.000000
0.666667 0.000000 0.000000 0.333333
0.777778 0.111111 0.111111 0.000000
0.444444 0.555556 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.000000 0.888889 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
C[CT][GC][CAT][ACGTC][TC][CG][AC]T[TG]TATA[AT]A[CA]GAG
--------------------------------------------------------------------------------
Time 23.77 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 15 sites = 9 llr = 130 E-value = 2.3e-003
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A :::4::4:8::::18
pos.-specific C ::131::2::8:99:
probability G :921:94::92a::1
matrix T a171911821::1:1
bits 2.5 *
2.3 *
2.0 * * * ***
1.8 * * *****
Information 1.5 ** * *****
content 1.3 ** ** *****
(20.9 bits) 1.0 ** ** * *****
0.8 *** ** ********
0.5 *** ***********
0.3 ***************
0.0 ---------------
Multilevel TGTATGATAGCGCCA
consensus GC GCT G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Skud_Contig1362.1 + 248 5.26e-10 ACAGAGGAAG TGTATGGTAGCGCCA AGGAAAACGG
MIT_Spar_c130_3923 + 289 5.26e-10 AAAAAAATCG TGTATGGTAGCGCCA AGATAGCGAA
SGD_Scer_YDR047W + 291 2.07e-09 AAAAAGATCG TGTATGATAGCGCCA AGATGGCGGA
MIT_Sbay_c896_21277 + 241 3.97e-09 ACGAGGAAGC TGCATGGTAGCGCCA GAAAAGGCAG
MIT_Spar_c19_8512 + 78 7.03e-08 TTGTTTTATG TGGCTGATTGGGCCA AAAAACAAGG
MIT_Sbay_c77_8808 - 909 8.89e-08 TTAAACATGA TGTCTGACATCGCCA TAACGACTAA
SGD_Scer_YGL040C + 76 7.23e-07 TTTTTTTATT TGGCTGATTGGGCAA GAAAATCAAA
MIT_Smik_c273_7756 + 256 2.61e-06 CTACCAATTT TTTTCGGCAGCGCCT TTGAATGACT
WashU_Skud_Contig2052.17 + 462 5.54e-06 TTCTTGAATT TGTGTTTTAGCGTCG ATGAAGACTC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1362.1 5.3e-10 247_[+4]_499
MIT_Spar_c130_3923 5.3e-10 288_[+4]_697
SGD_Scer_YDR047W 2.1e-09 290_[+4]_695
MIT_Sbay_c896_21277 4e-09 240_[+4]_745
MIT_Spar_c19_8512 7e-08 77_[+4]_908
MIT_Sbay_c77_8808 8.9e-08 908_[-4]_77
SGD_Scer_YGL040C 7.2e-07 75_[+4]_910
MIT_Smik_c273_7756 2.6e-06 255_[+4]_730
WashU_Skud_Contig2052.17 5.5e-06 461_[+4]_524
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=15 seqs=9
WashU_Skud_Contig1362.1 ( 248) TGTATGGTAGCGCCA 1
MIT_Spar_c130_3923 ( 289) TGTATGGTAGCGCCA 1
SGD_Scer_YDR047W ( 291) TGTATGATAGCGCCA 1
MIT_Sbay_c896_21277 ( 241) TGCATGGTAGCGCCA 1
MIT_Spar_c19_8512 ( 78) TGGCTGATTGGGCCA 1
MIT_Sbay_c77_8808 ( 909) TGTCTGACATCGCCA 1
SGD_Scer_YGL040C ( 76) TGGCTGATTGGGCAA 1
MIT_Smik_c273_7756 ( 256) TTTTCGGCAGCGCCT 1
WashU_Skud_Contig2052.17 ( 462) TGTGTTTTAGCGTCG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8635 bayes= 9.90455 E= 2.3e-003
-982 -982 -982 162
-982 -982 234 -154
-982 -66 34 104
45 92 -66 -154
-982 -66 -982 145
-982 -982 234 -154
45 -982 134 -154
-982 34 -982 126
126 -982 -982 -55
-982 -982 234 -154
-982 215 34 -982
-982 -982 251 -982
-982 234 -982 -154
-154 234 -982 -982
126 -982 -66 -154
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.3e-003
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.888889 0.111111
0.000000 0.111111 0.222222 0.666667
0.444444 0.333333 0.111111 0.111111
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.888889 0.111111
0.444444 0.000000 0.444444 0.111111
0.000000 0.222222 0.000000 0.777778
0.777778 0.000000 0.000000 0.222222
0.000000 0.000000 0.888889 0.111111
0.000000 0.777778 0.222222 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.888889 0.000000 0.111111
0.111111 0.888889 0.000000 0.000000
0.777778 0.000000 0.111111 0.111111
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
TG[TG][AC]TG[AG][TC][AT]G[CG]GCCA
--------------------------------------------------------------------------------
Time 31.71 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 145 E-value = 2.1e-001
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 7336939a283881:9:2:8
pos.-specific C 32:::6:::2::::2:8:a2
probability G :264111:::722281:8::
matrix T :21:::::8::::7::2:::
bits 2.5 *
2.3 *
2.0 *
1.8 * *
Information 1.5 * * ***
content 1.3 * ** * *****
(23.3 bits) 1.0 * ** ** **** ******
0.8 * *********** ******
0.5 * ******************
0.3 * ******************
0.0 --------------------
Multilevel AAGAACAATAGAATGACGCA
consensus CCAG A ACAGGGC TA C
sequence G
T
--------------------------------------------------------------------------------
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Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Smik_c273_7756 + 99 6.39e-12 CCAATAAATC AGGAACAATAGAATGACGCA CCGAGTTTGC
WashU_Skud_Contig2052.17 + 97 1.53e-10 GCCAGAAATC ATGAACAATAGGATGACGCA TAGACGTCAC
MIT_Spar_c19_8512 + 99 3.15e-10 GCCAAAAAAC AAGGACAATAGAATGACACA TAAAGTTTGC
SGD_Scer_YGL040C + 98 2.76e-09 CAAGAAAATC AAAGACAATAGAGTGGCGCA TAGATGTTGC
MIT_Spar_c130_3923 - 817 3.44e-08 GATTTGTCGG CCGGAAAAAAAAAGCACGCA TCCGGCAAGG
SGD_Scer_YDR047W - 807 3.44e-08 TATGTGTCGG CCGGAAAAAAAAAGCACGCA TCCGGCAAGC
MIT_Sbay_c77_8808 + 102 4.32e-08 ATGAACTAAC ATTAACAATAGAGTGATGCA TAGACGTCAC
MIT_Sbay_c896_21277 + 549 2.76e-07 ATATGCCCAG CAAAGGGATCGGATGACGCC CAACTAACAT
WashU_Skud_Contig1362.1 - 10 8.14e-07 CTACCAATCT AGAAAAAATCAAAAGATACC ATCAACACT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Smik_c273_7756 6.4e-12 98_[+5]_882
WashU_Skud_Contig2052.17 1.5e-10 96_[+5]_884
MIT_Spar_c19_8512 3.1e-10 98_[+5]_882
SGD_Scer_YGL040C 2.8e-09 97_[+5]_883
MIT_Spar_c130_3923 3.4e-08 816_[-5]_164
SGD_Scer_YDR047W 3.4e-08 806_[-5]_174
MIT_Sbay_c77_8808 4.3e-08 101_[+5]_879
MIT_Sbay_c896_21277 2.8e-07 548_[+5]_432
WashU_Skud_Contig1362.1 8.1e-07 9_[-5]_732
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
MIT_Smik_c273_7756 ( 99) AGGAACAATAGAATGACGCA 1
WashU_Skud_Contig2052.17 ( 97) ATGAACAATAGGATGACGCA 1
MIT_Spar_c19_8512 ( 99) AAGGACAATAGAATGACACA 1
SGD_Scer_YGL040C ( 98) AAAGACAATAGAGTGGCGCA 1
MIT_Spar_c130_3923 ( 817) CCGGAAAAAAAAAGCACGCA 1
SGD_Scer_YDR047W ( 807) CCGGAAAAAAAAAGCACGCA 1
MIT_Sbay_c77_8808 ( 102) ATTAACAATAGAGTGATGCA 1
MIT_Sbay_c896_21277 ( 549) CAAAGGGATCGGATGACGCC 1
WashU_Skud_Contig1362.1 ( 10) AGAAAAAATCAAAAGATACC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 2.1e-001
104 92 -982 -982
4 34 34 -55
4 -982 166 -154
78 -982 134 -982
145 -982 -66 -982
4 166 -66 -982
145 -982 -66 -982
162 -982 -982 -982
-55 -982 -982 126
126 34 -982 -982
4 -982 192 -982
126 -982 34 -982
126 -982 34 -982
-154 -982 34 104
-982 34 215 -982
145 -982 -66 -982
-982 215 -982 -55
-55 -982 215 -982
-982 251 -982 -982
126 34 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.1e-001
0.666667 0.333333 0.000000 0.000000
0.333333 0.222222 0.222222 0.222222
0.333333 0.000000 0.555556 0.111111
0.555556 0.000000 0.444444 0.000000
0.888889 0.000000 0.111111 0.000000
0.333333 0.555556 0.111111 0.000000
0.888889 0.000000 0.111111 0.000000
1.000000 0.000000 0.000000 0.000000
0.222222 0.000000 0.000000 0.777778
0.777778 0.222222 0.000000 0.000000
0.333333 0.000000 0.666667 0.000000
0.777778 0.000000 0.222222 0.000000
0.777778 0.000000 0.222222 0.000000
0.111111 0.000000 0.222222 0.666667
0.000000 0.222222 0.777778 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.777778 0.000000 0.222222
0.222222 0.000000 0.777778 0.000000
0.000000 1.000000 0.000000 0.000000
0.777778 0.222222 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
[AC][ACGTC][GA][AG]A[CA]AA[TA][AC][GA][AG][AG][TG][GC]A[CT][GA]C[AC]
--------------------------------------------------------------------------------
Time 39.58 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YGL040C 1.84e-25 75_[+4(7.23e-07)]_7_[+5(2.76e-09)]_32_[-3(1.63e-09)]_9_[+1(4.85e-12)]_2_[+2(3.60e-13)]_780
MIT_Spar_c19_8512 1.53e-29 19_[+2(8.47e-05)]_38_[+4(7.03e-08)]_6_[+5(3.15e-10)]_32_[-3(6.18e-10)]_9_[+1(5.70e-14)]_2_[+2(3.60e-13)]_229_[-1(3.52e-05)]_530
MIT_Smik_c273_7756 2.73e-25 98_[+5(6.39e-12)]_59_[+1(5.70e-14)]_2_[+2(6.88e-11)]_3_[-5(1.42e-05)]_13_[+4(2.61e-06)]_600_[+3(1.32e-07)]_110
MIT_Sbay_c77_8808 2.58e-22 101_[+5(4.32e-08)]_33_[-3(1.63e-09)]_5_[+1(4.81e-13)]_1_[+2(4.15e-09)]_688_[-4(8.89e-08)]_77
WashU_Skud_Contig2052.17 7.43e-27 96_[+5(1.53e-10)]_33_[-3(1.10e-08)]_9_[+1(5.70e-14)]_2_[+2(3.60e-13)]_241_[+4(5.54e-06)]_44_[-5(8.79e-05)]_430_[+1(9.64e-05)]_10
SGD_Scer_YDR047W 1.12e-21 19_[-5(5.14e-05)]_166_[-5(2.78e-05)]_27_[+3(7.00e-10)]_18_[+4(2.07e-09)]_76_[+2(5.89e-06)]_155_[+2(2.56e-09)]_39_[+1(4.68e-10)]_171_[-5(3.44e-08)]_99_[+1(4.63e-05)]_55
MIT_Spar_c130_3923 9.38e-21 92_[+4(5.51e-05)]_142_[+3(4.40e-09)]_19_[+4(5.26e-10)]_250_[+2(1.46e-08)]_38_[+1(4.99e-10)]_185_[-5(3.44e-08)]_82_[+2(5.53e-06)]_62
MIT_Sbay_c896_21277 1.53e-20 38_[-2(1.46e-08)]_114_[-5(6.18e-05)]_23_[+3(1.03e-10)]_5_[+4(3.97e-09)]_293_[+5(2.76e-07)]_121_[-4(7.12e-06)]_48_[+1(6.93e-05)]_123_[+1(5.96e-10)]_85
WashU_Skud_Contig1362.1 9.11e-19 9_[-5(8.14e-07)]_55_[-1(1.36e-05)]_106_[+3(8.03e-09)]_17_[+4(5.26e-10)]_1_[-2(2.12e-08)]_330_[+1(4.38e-09)]_99_[-1(7.81e-06)]_9
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************