********************************************************************************
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= HEM12-HEM14.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
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
SGD_Scer_YER014W 1.0000 322 MIT_Spar_c425_6072 1.0000 322
MIT_Smik_c283_5928 1.0000 322 MIT_Sbay_c84_6418 1.0000 322
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM12-HEM14.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= 8 maxsites= 8 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 5049 N= 8
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.296 C 0.204 G 0.204 T 0.296
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324
********************************************************************************
********************************************************************************
MOTIF 1 width = 15 sites = 8 llr = 132 E-value = 1.4e-008
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A a:::::aa1:65:58
pos.-specific C :a5aa:::4a4:5:3
probability G :::::a::4:::5::
matrix T ::5:::::1::5:5:
bits 2.5 * *** *
2.3 * *** *
2.0 * *** *
1.8 * *** *
Information 1.5 ** ***** * *
content 1.3 ** ***** * *
(23.8 bits) 1.0 ******** ** * *
0.8 ******** ** * *
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel ACCCCGAACCAACAA
consensus T G CTGTC
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
MIT_Sbay_c896_21277 + 213 2.96e-09 GCGTCAAAAA ACCCCGAACCCTGTA TAAACGAGGA
MIT_Spar_c130_3923 + 242 1.00e-08 TGCCACCAAA ACCCCGAACCCTGTC CCGTATATAC
SGD_Scer_YDR047W + 245 1.00e-08 GCCGCCAAAA ACCCCGAACCCTGTC CTGTATATAC
MIT_Smik_c283_5928 + 117 2.85e-08 TTAAATACGG ACTCCGAAGCAACAA GGTCGAAGGC
MIT_Spar_c425_6072 + 120 2.85e-08 ATACTCCGCG ACTCCGAAGCAACAA AATGTCGAAG
SGD_Scer_YER014W + 121 2.85e-08 ATACTCCGCG ACTCCGAAGCAACAA AGTGTCGAAG
WashU_Skud_Contig1362.1 + 208 5.25e-08 CTGCCAAAAA ACCCCGAATCATGTA GAAGCGAGAA
MIT_Sbay_c84_6418 + 113 8.97e-08 ATACTCTGCG ACTCCGAAACAACAA AATCTCGAAG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Sbay_c896_21277 3e-09 212_[+1]_773
MIT_Spar_c130_3923 1e-08 241_[+1]_744
SGD_Scer_YDR047W 1e-08 244_[+1]_741
MIT_Smik_c283_5928 2.9e-08 116_[+1]_191
MIT_Spar_c425_6072 2.9e-08 119_[+1]_188
SGD_Scer_YER014W 2.9e-08 120_[+1]_187
WashU_Skud_Contig1362.1 5.3e-08 207_[+1]_539
MIT_Sbay_c84_6418 9e-08 112_[+1]_195
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=15 seqs=8
MIT_Sbay_c896_21277 ( 213) ACCCCGAACCCTGTA 1
MIT_Spar_c130_3923 ( 242) ACCCCGAACCCTGTC 1
SGD_Scer_YDR047W ( 245) ACCCCGAACCCTGTC 1
MIT_Smik_c283_5928 ( 117) ACTCCGAAGCAACAA 1
MIT_Spar_c425_6072 ( 120) ACTCCGAAGCAACAA 1
SGD_Scer_YER014W ( 121) ACTCCGAAGCAACAA 1
WashU_Skud_Contig1362.1 ( 208) ACCCCGAATCATGTA 1
MIT_Sbay_c84_6418 ( 113) ACTCCGAAACAACAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4937 bayes= 9.26708 E= 1.4e-008
162 -965 -965 -965
-965 251 -965 -965
-965 151 -965 62
-965 251 -965 -965
-965 251 -965 -965
-965 -965 251 -965
162 -965 -965 -965
162 -965 -965 -965
-137 109 109 -137
-965 251 -965 -965
95 109 -965 -965
62 -965 -965 62
-965 151 151 -965
62 -965 -965 62
121 51 -965 -965
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 1.4e-008
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.500000 0.000000 0.500000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.125000 0.375000 0.375000 0.125000
0.000000 1.000000 0.000000 0.000000
0.625000 0.375000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
0.000000 0.500000 0.500000 0.000000
0.500000 0.000000 0.000000 0.500000
0.750000 0.250000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
AC[CT]CCGAA[CG]C[AC][AT][CG][AT][AC]
--------------------------------------------------------------------------------
Time 2.78 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 8 llr = 144 E-value = 2.6e-007
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 61:888::9:166::138::
pos.-specific C 48131:a1::813:1:5::8
probability G :11::3:91a::::88:3a:
matrix T ::8:1:::::131a113::3
bits 2.5 * * *
2.3 * * *
2.0 ** * *
1.8 ** * *
Information 1.5 ** * * **
content 1.3 * ***** *** **
(26.0 bits) 1.0 ** * ****** *** ***
0.8 *********** *** ***
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel ACTAAACGAGCAATGGCAGC
consensus C C G TC AG T
sequence T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
SGD_Scer_YER014W + 168 5.54e-13 GCGTTTTGTA ACTAAACGAGCAATGGCAGC TTTCAATTAA
MIT_Smik_c283_5928 + 162 8.88e-12 GCATTTTACA ACTAAACGAGCAATGGTAGC TTTTGATTGA
MIT_Spar_c425_6072 + 167 5.42e-11 GCGTTTTGCA ACTAAACGAGTAATGGCAGC TTTTAATTAA
MIT_Sbay_c84_6418 + 163 5.99e-10 AATATTCACC ACTAAACGAGCAATGACAGT TATATTCAAA
MIT_Sbay_c896_21277 - 914 4.51e-09 TTTTCCCGAG CAGAAACGAGCCCTGGAAGC TGCCTTCATT
MIT_Spar_c130_3923 - 836 3.57e-08 TGTCTTTCCA ACTCAGCGAGATTTGTCGGC CGGAAAAAAA
WashU_Skud_Contig1362.1 + 659 6.59e-08 AACATGCCGT CCCCTACCAGCTCTCGAAGC GGGCCTAGCA
SGD_Scer_YDR047W - 382 1.24e-07 TTGTAGTATA CGTACGCGGGCAATTGTGGT GACAGTATCT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YER014W 5.5e-13 167_[+2]_135
MIT_Smik_c283_5928 8.9e-12 161_[+2]_141
MIT_Spar_c425_6072 5.4e-11 166_[+2]_136
MIT_Sbay_c84_6418 6e-10 162_[+2]_140
MIT_Sbay_c896_21277 4.5e-09 913_[-2]_67
MIT_Spar_c130_3923 3.6e-08 835_[-2]_145
WashU_Skud_Contig1362.1 6.6e-08 658_[+2]_83
SGD_Scer_YDR047W 1.2e-07 381_[-2]_599
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=8
SGD_Scer_YER014W ( 168) ACTAAACGAGCAATGGCAGC 1
MIT_Smik_c283_5928 ( 162) ACTAAACGAGCAATGGTAGC 1
MIT_Spar_c425_6072 ( 167) ACTAAACGAGTAATGGCAGC 1
MIT_Sbay_c84_6418 ( 163) ACTAAACGAGCAATGACAGT 1
MIT_Sbay_c896_21277 ( 914) CAGAAACGAGCCCTGGAAGC 1
MIT_Spar_c130_3923 ( 836) ACTCAGCGAGATTTGTCGGC 1
WashU_Skud_Contig1362.1 ( 659) CCCCTACCAGCTCTCGAAGC 1
SGD_Scer_YDR047W ( 382) CGTACGCGGGCAATTGTGGT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4897 bayes= 9.25532 E= 2.6e-007
95 109 -965 -965
-137 209 -49 -965
-965 -49 -49 121
121 51 -965 -965
121 -49 -965 -137
121 -965 51 -965
-965 251 -965 -965
-965 -49 232 -965
143 -965 -49 -965
-965 -965 251 -965
-137 209 -965 -137
95 -49 -965 -38
95 51 -965 -137
-965 -965 -965 162
-965 -49 209 -137
-137 -965 209 -137
-38 151 -965 -38
121 -965 51 -965
-965 -965 251 -965
-965 209 -965 -38
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 2.6e-007
0.625000 0.375000 0.000000 0.000000
0.125000 0.750000 0.125000 0.000000
0.000000 0.125000 0.125000 0.750000
0.750000 0.250000 0.000000 0.000000
0.750000 0.125000 0.000000 0.125000
0.750000 0.000000 0.250000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.125000 0.875000 0.000000
0.875000 0.000000 0.125000 0.000000
0.000000 0.000000 1.000000 0.000000
0.125000 0.750000 0.000000 0.125000
0.625000 0.125000 0.000000 0.250000
0.625000 0.250000 0.000000 0.125000
0.000000 0.000000 0.000000 1.000000
0.000000 0.125000 0.750000 0.125000
0.125000 0.000000 0.750000 0.125000
0.250000 0.500000 0.000000 0.250000
0.750000 0.000000 0.250000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.750000 0.000000 0.250000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[AC]CT[AC]A[AG]CGAGC[AT][AC]TGG[CAT][AG]G[CT]
--------------------------------------------------------------------------------
Time 5.72 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 18 sites = 8 llr = 139 E-value = 1.4e-007
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A ::::aa:::a63614a86
pos.-specific C 14a3::::a:::311:::
probability G 9::5::6a::48:15:34
matrix T :6:3::4:::::16::::
bits 2.5 * **
2.3 * **
2.0 * * **
1.8 * * **
Information 1.5 * * ** *** * *
content 1.3 * * ****** * *
(25.1 bits) 1.0 *** ******** ***
0.8 ************ ****
0.5 ************* ****
0.3 ******************
0.0 ------------------
Multilevel GTCGAAGGCAAGATGAAA
consensus C C T GAC A GG
sequence T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ------------------
MIT_Spar_c425_6072 + 138 4.37e-11 GCAACAAAAT GTCGAAGGCAAGATGAAA GGCGTTTTGC
MIT_Smik_c283_5928 + 133 7.23e-11 AAGCAACAAG GTCGAAGGCAAGCTGAAA GGCATTTTAC
SGD_Scer_YDR047W - 769 2.84e-09 ACACTAGTAA GTCTAATGCAGGATGAAG AAACGAAGAA
SGD_Scer_YER014W + 139 7.28e-09 GCAACAAAGT GTCGAAGGCAAGTTCAAA GGCGTTTTGT
MIT_Sbay_c896_21277 - 742 9.47e-09 ACGCTGCTAG GCCCAAGGCAGAACGAAA TAAGAAATGA
MIT_Sbay_c84_6418 + 131 1.10e-08 ACAACAAAAT CTCGAAGGCAAGCTAAGG TAAAAATATT
WashU_Skud_Contig1362.1 - 743 2.13e-08 A GCCCAATGCAAGAAAAAA GCAGCGCAGC
MIT_Spar_c130_3923 - 774 6.83e-08 ACGCTAGTAA GCCTAATGCAGAAGAAGG AAAGGACACG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c425_6072 4.4e-11 137_[+3]_167
MIT_Smik_c283_5928 7.2e-11 132_[+3]_172
SGD_Scer_YDR047W 2.8e-09 768_[-3]_214
SGD_Scer_YER014W 7.3e-09 138_[+3]_166
MIT_Sbay_c896_21277 9.5e-09 741_[-3]_241
MIT_Sbay_c84_6418 1.1e-08 130_[+3]_174
WashU_Skud_Contig1362.1 2.1e-08 742_[-3]_1
MIT_Spar_c130_3923 6.8e-08 773_[-3]_209
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=18 seqs=8
MIT_Spar_c425_6072 ( 138) GTCGAAGGCAAGATGAAA 1
MIT_Smik_c283_5928 ( 133) GTCGAAGGCAAGCTGAAA 1
SGD_Scer_YDR047W ( 769) GTCTAATGCAGGATGAAG 1
SGD_Scer_YER014W ( 139) GTCGAAGGCAAGTTCAAA 1
MIT_Sbay_c896_21277 ( 742) GCCCAAGGCAGAACGAAA 1
MIT_Sbay_c84_6418 ( 131) CTCGAAGGCAAGCTAAGG 1
WashU_Skud_Contig1362.1 ( 743) GCCCAATGCAAGAAAAAA 1
MIT_Spar_c130_3923 ( 774) GCCTAATGCAGAAGAAGG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 18 n= 4913 bayes= 9.26004 E= 1.4e-007
-965 -49 232 -965
-965 109 -965 95
-965 251 -965 -965
-965 51 151 -38
162 -965 -965 -965
162 -965 -965 -965
-965 -965 183 21
-965 -965 251 -965
-965 251 -965 -965
162 -965 -965 -965
95 -965 109 -965
-38 -965 209 -965
95 51 -965 -137
-137 -49 -49 95
21 -49 151 -965
162 -965 -965 -965
121 -965 51 -965
95 -965 109 -965
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 18 nsites= 8 E= 1.4e-007
0.000000 0.125000 0.875000 0.000000
0.000000 0.375000 0.000000 0.625000
0.000000 1.000000 0.000000 0.000000
0.000000 0.250000 0.500000 0.250000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.625000 0.375000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.625000 0.000000 0.375000 0.000000
0.250000 0.000000 0.750000 0.000000
0.625000 0.250000 0.000000 0.125000
0.125000 0.125000 0.125000 0.625000
0.375000 0.125000 0.500000 0.000000
1.000000 0.000000 0.000000 0.000000
0.750000 0.000000 0.250000 0.000000
0.625000 0.000000 0.375000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
G[TC]C[GCT]AA[GT]GCA[AG][GA][AC]T[GA]A[AG][AG]
--------------------------------------------------------------------------------
Time 8.67 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 8 llr = 132 E-value = 6.8e-002
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 6::5:93:::1955985431
pos.-specific C ::::::1a:96:::::1:36
probability G :3953:6:a:31441:4653
matrix T 481:81:::1::11:3::::
bits 2.5 **
2.3 **
2.0 **
1.8 * ***
Information 1.5 * ***
content 1.3 * *** * * *
(23.8 bits) 1.0 *********** * * *
0.8 ************ ******
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel ATGATAGCGCCAAAAAAGGC
consensus TG GG A G GG TGAAG
sequence C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Sbay_c896_21277 + 244 1.24e-12 AGGAAGCTGC ATGGTAGCGCCAGAAAAGGC AGATAACCTT
MIT_Spar_c130_3923 + 292 4.51e-10 AAAATCGTGT ATGGTAGCGCCAAGATAGCG AATAAACTAT
SGD_Scer_YDR047W + 294 7.62e-10 AAGATCGTGT ATGATAGCGCCAAGATGGCG GATAAACTAA
WashU_Skud_Contig1362.1 + 251 2.49e-09 GAGGAAGTGT ATGGTAGCGCCAAGGAAAAC GGGCAATACT
SGD_Scer_YER014W - 8 4.22e-09 TAAAGTGCAA TTGAGAACGCCAAAAAGAGC TTGTATA
MIT_Spar_c425_6072 - 8 4.66e-09 GAAGGTACAA TTGGGAACGCGGGAAAGGGC TCGAATA
MIT_Smik_c283_5928 - 22 7.67e-07 AACCATATCT AGTATAGCGCGATTAAAGAA ATAGTGGAGA
MIT_Sbay_c84_6418 - 23 1.04e-06 ACAGTCTCGC TGGATTCCGTAAGAAACAGC GGAATAAAGG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Sbay_c896_21277 1.2e-12 243_[+4]_737
MIT_Spar_c130_3923 4.5e-10 291_[+4]_689
SGD_Scer_YDR047W 7.6e-10 293_[+4]_687
WashU_Skud_Contig1362.1 2.5e-09 250_[+4]_491
SGD_Scer_YER014W 4.2e-09 7_[-4]_295
MIT_Spar_c425_6072 4.7e-09 7_[-4]_295
MIT_Smik_c283_5928 7.7e-07 21_[-4]_281
MIT_Sbay_c84_6418 1e-06 22_[-4]_280
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=8
MIT_Sbay_c896_21277 ( 244) ATGGTAGCGCCAGAAAAGGC 1
MIT_Spar_c130_3923 ( 292) ATGGTAGCGCCAAGATAGCG 1
SGD_Scer_YDR047W ( 294) ATGATAGCGCCAAGATGGCG 1
WashU_Skud_Contig1362.1 ( 251) ATGGTAGCGCCAAGGAAAAC 1
SGD_Scer_YER014W ( 8) TTGAGAACGCCAAAAAGAGC 1
MIT_Spar_c425_6072 ( 8) TTGGGAACGCGGGAAAGGGC 1
MIT_Smik_c283_5928 ( 22) AGTATAGCGCGATTAAAGAA 1
MIT_Sbay_c84_6418 ( 23) TGGATTCCGTAAGAAACAGC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4897 bayes= 9.25532 E= 6.8e-002
95 -965 -965 21
-965 -965 51 121
-965 -965 232 -137
62 -965 151 -965
-965 -965 51 121
143 -965 -965 -137
-38 -49 183 -965
-965 251 -965 -965
-965 -965 251 -965
-965 232 -965 -137
-137 183 51 -965
143 -965 -49 -965
62 -965 109 -137
62 -965 109 -137
143 -965 -49 -965
121 -965 -965 -38
62 -49 109 -965
21 -965 183 -965
-38 51 151 -965
-137 183 51 -965
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 6.8e-002
0.625000 0.000000 0.000000 0.375000
0.000000 0.000000 0.250000 0.750000
0.000000 0.000000 0.875000 0.125000
0.500000 0.000000 0.500000 0.000000
0.000000 0.000000 0.250000 0.750000
0.875000 0.000000 0.000000 0.125000
0.250000 0.125000 0.625000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.875000 0.000000 0.125000
0.125000 0.625000 0.250000 0.000000
0.875000 0.000000 0.125000 0.000000
0.500000 0.000000 0.375000 0.125000
0.500000 0.000000 0.375000 0.125000
0.875000 0.000000 0.125000 0.000000
0.750000 0.000000 0.000000 0.250000
0.500000 0.125000 0.375000 0.000000
0.375000 0.000000 0.625000 0.000000
0.250000 0.250000 0.500000 0.000000
0.125000 0.625000 0.250000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[AT][TG]G[AG][TG]A[GA]CGC[CG]A[AG][AG]A[AT][AG][GA][GAC][CG]
--------------------------------------------------------------------------------
Time 11.28 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 14 sites = 8 llr = 115 E-value = 4.7e-003
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A ::5::1::::::::
pos.-specific C a::35:::a433a5
probability G ::51:9::::4:::
matrix T :a:65:aa:648:5
bits 2.5 * * *
2.3 * * *
2.0 * * *
1.8 * * * *
Information 1.5 ** **** *
content 1.3 ** **** *
(20.8 bits) 1.0 *** ****** ***
0.8 ********** ***
0.5 **************
0.3 **************
0.0 --------------
Multilevel CTATCGTTCTGTCC
consensus GCT CTC T
sequence C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------
MIT_Spar_c130_3923 + 714 1.93e-09 CTCTAAAATG CTGCCGTTCCGTCC CATTGAGTTT
SGD_Scer_YDR047W + 714 1.93e-09 TTAAAAAATG CTGCCGTTCCGTCC CATTGAGTTT
MIT_Sbay_c896_21277 + 705 8.69e-08 CAGCCAAACA CTGGCGTTCCGCCC GTCCCATCCA
MIT_Smik_c283_5928 + 77 2.04e-07 GCAAATCCCT CTATTGTTCTTTCC ATTACTCTTT
MIT_Spar_c425_6072 + 75 3.04e-07 GCGGATCTCT CTATTGTTCTCTCT ATTATTCTTT
SGD_Scer_YER014W + 75 3.04e-07 GCGAATATCT CTATTGTTCTCTCT ATTATACTAT
MIT_Sbay_c84_6418 + 70 4.30e-07 TCGCATCCTT CTATTGTTCTTCCT TATTGTTCTC
WashU_Skud_Contig1362.1 - 282 5.90e-07 TGGCTGAGCT CTGTCATTCTTTCT AAGTATTGCC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c130_3923 1.9e-09 713_[+5]_273
SGD_Scer_YDR047W 1.9e-09 713_[+5]_273
MIT_Sbay_c896_21277 8.7e-08 704_[+5]_282
MIT_Smik_c283_5928 2e-07 76_[+5]_232
MIT_Spar_c425_6072 3e-07 74_[+5]_234
SGD_Scer_YER014W 3e-07 74_[+5]_234
MIT_Sbay_c84_6418 4.3e-07 69_[+5]_239
WashU_Skud_Contig1362.1 5.9e-07 281_[-5]_466
--------------------------------------------------------------------------------
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Motif 5 in BLOCKS format
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BL MOTIF 5 width=14 seqs=8
MIT_Spar_c130_3923 ( 714) CTGCCGTTCCGTCC 1
SGD_Scer_YDR047W ( 714) CTGCCGTTCCGTCC 1
MIT_Sbay_c896_21277 ( 705) CTGGCGTTCCGCCC 1
MIT_Smik_c283_5928 ( 77) CTATTGTTCTTTCC 1
MIT_Spar_c425_6072 ( 75) CTATTGTTCTCTCT 1
SGD_Scer_YER014W ( 75) CTATTGTTCTCTCT 1
MIT_Sbay_c84_6418 ( 70) CTATTGTTCTTCCT 1
WashU_Skud_Contig1362.1 ( 282) CTGTCATTCTTTCT 1
//
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Motif 5 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 14 n= 4945 bayes= 9.26942 E= 4.7e-003
-965 251 -965 -965
-965 -965 -965 162
62 -965 151 -965
-965 51 -49 95
-965 151 -965 62
-137 -965 232 -965
-965 -965 -965 162
-965 -965 -965 162
-965 251 -965 -965
-965 109 -965 95
-965 51 109 21
-965 51 -965 121
-965 251 -965 -965
-965 151 -965 62
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 14 nsites= 8 E= 4.7e-003
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.500000 0.000000 0.500000 0.000000
0.000000 0.250000 0.125000 0.625000
0.000000 0.500000 0.000000 0.500000
0.125000 0.000000 0.875000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.375000 0.000000 0.625000
0.000000 0.250000 0.375000 0.375000
0.000000 0.250000 0.000000 0.750000
0.000000 1.000000 0.000000 0.000000
0.000000 0.500000 0.000000 0.500000
--------------------------------------------------------------------------------
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Motif 5 regular expression
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CT[AG][TC][CT]GTTC[TC][GTC][TC]C[CT]
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Time 13.87 secs.
********************************************************************************
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SUMMARY OF MOTIFS
********************************************************************************
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR047W 7.31e-20 108_[+5(5.48e-05)]_122_[+1(1.00e-08)]_34_[+4(7.62e-10)]_68_[-2(1.24e-07)]_312_[+5(1.93e-09)]_41_[-3(2.84e-09)]_214
MIT_Spar_c130_3923 2.71e-19 241_[+1(1.00e-08)]_35_[+4(4.51e-10)]_5_[-2(1.77e-05)]_377_[+5(1.93e-09)]_46_[-3(6.83e-08)]_3_[+5(7.96e-06)]_27_[-2(3.57e-08)]_145
MIT_Sbay_c896_21277 2.82e-22 212_[+1(2.96e-09)]_16_[+4(1.24e-12)]_398_[+3(9.45e-05)]_25_[+5(8.69e-08)]_23_[-3(9.47e-09)]_154_[-2(4.51e-09)]_67
WashU_Skud_Contig1362.1 2.00e-16 207_[+1(5.25e-08)]_28_[+4(2.49e-09)]_11_[-5(5.90e-07)]_363_[+2(6.59e-08)]_64_[-3(2.13e-08)]_1
SGD_Scer_YER014W 1.10e-23 7_[-4(4.22e-09)]_47_[+5(3.04e-07)]_32_[+1(2.85e-08)]_3_[+3(7.28e-09)]_11_[+2(5.54e-13)]_135
MIT_Spar_c425_6072 7.28e-24 7_[-4(4.66e-09)]_47_[+5(3.04e-07)]_31_[+1(2.85e-08)]_3_[+3(4.37e-11)]_11_[+2(5.42e-11)]_136
MIT_Smik_c283_5928 1.78e-22 21_[-4(7.67e-07)]_35_[+5(2.04e-07)]_26_[+1(2.85e-08)]_1_[+3(7.23e-11)]_11_[+2(8.88e-12)]_141
MIT_Sbay_c84_6418 7.50e-18 22_[-4(1.04e-06)]_6_[+5(5.48e-05)]_7_[+5(4.30e-07)]_29_[+1(8.97e-08)]_3_[+3(1.10e-08)]_14_[+2(5.99e-10)]_140
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************