********************************************************************************
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-HEM13.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_YDR044W 1.0000 1000 MIT_Spar_c130_3912 1.0000 1000
MIT_Sbay_c896_21290 1.0000 1000 WashU_Smik_Contig2283.3 1.0000 1000
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM12-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
model: mod= oops nmotifs= 5 evt= inf
object function= E-value of product of p-values
width: minw= 6 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 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= 7761 N= 8
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.291 C 0.209 G 0.209 T 0.291
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 = 8 llr = 167 E-value = 1.0e-013
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :1165:9:1a::11:::1a:
pos.-specific C :::::a::4:3::11:5:::
probability G :9945:1:::1:98:559:a
matrix T a::::::a5:6a::95::::
bits 2.5 * *
2.3 * *
2.0 * *
1.8 ** * * * *
Information 1.5 *** * * * ** ****
content 1.3 *** *** * **** ****
(30.1 bits) 1.0 ******** * *********
0.8 ******** ***********
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel TGGAACATTATTGGTGCGAG
consensus GG C C TG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c130_3912 + 244 1.31e-12 TGGTTCAAGC TGGGGCATTATTGGTGGGAG AAGCCAGAAA
MIT_Sbay_c896_21290 + 250 2.00e-11 AGGTCCAAGC TGGGGCATAATTGGTGGGAG AAGCCAGAAA
SGD_Scer_YDR044W + 252 2.47e-11 TTGTTCAAGC TGGAGCGTTATTGGTGGGAG AACCAGAAAA
WashU_Smik_Contig2283.3 + 240 7.53e-11 TGGTTGAAGC TGGGGCATTATTGGTGGAAG AAGCCAGAAA
WashU_Skud_Contig1362.1 + 101 2.45e-10 TTCTTTCGTT TGGAACATTACTGCTTCGAG CAATAAACAT
MIT_Spar_c130_3923 + 134 5.96e-10 CCACTTCGTT TGAAACATCAGTGGTTCGAG CAGTAATGAC
MIT_Sbay_c896_21277 + 107 7.56e-10 CTAAGTTCTT TAGAACATCATTGGCTCGAG CATTAGTGAC
SGD_Scer_YDR047W + 137 1.93e-09 TACCTTCGTC TGGAACATCACTAATTCGAG CGGTAAAGAT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c130_3912 1.3e-12 243_[+1]_737
MIT_Sbay_c896_21290 2e-11 249_[+1]_731
SGD_Scer_YDR044W 2.5e-11 251_[+1]_729
WashU_Smik_Contig2283.3 7.5e-11 239_[+1]_741
WashU_Skud_Contig1362.1 2.5e-10 100_[+1]_641
MIT_Spar_c130_3923 6e-10 133_[+1]_847
MIT_Sbay_c896_21277 7.6e-10 106_[+1]_874
SGD_Scer_YDR047W 1.9e-09 136_[+1]_844
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=8
MIT_Spar_c130_3912 ( 244) TGGGGCATTATTGGTGGGAG 1
MIT_Sbay_c896_21290 ( 250) TGGGGCATAATTGGTGGGAG 1
SGD_Scer_YDR044W ( 252) TGGAGCGTTATTGGTGGGAG 1
WashU_Smik_Contig2283.3 ( 240) TGGGGCATTATTGGTGGAAG 1
WashU_Skud_Contig1362.1 ( 101) TGGAACATTACTGCTTCGAG 1
MIT_Spar_c130_3923 ( 134) TGAAACATCAGTGGTTCGAG 1
MIT_Sbay_c896_21277 ( 107) TAGAACATCATTGGCTCGAG 1
SGD_Scer_YDR047W ( 137) TGGAACATCACTAATTCGAG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 1.0e-013
-965 -965 -965 162
-137 -965 232 -965
-137 -965 232 -965
95 -965 109 -965
62 -965 151 -965
-965 251 -965 -965
143 -965 -49 -965
-965 -965 -965 162
-137 109 -965 62
162 -965 -965 -965
-965 51 -49 95
-965 -965 -965 162
-137 -965 232 -965
-137 -49 209 -965
-965 -49 -965 143
-965 -965 151 62
-965 151 151 -965
-137 -965 232 -965
162 -965 -965 -965
-965 -965 251 -965
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.0e-013
0.000000 0.000000 0.000000 1.000000
0.125000 0.000000 0.875000 0.000000
0.125000 0.000000 0.875000 0.000000
0.625000 0.000000 0.375000 0.000000
0.500000 0.000000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
0.875000 0.000000 0.125000 0.000000
0.000000 0.000000 0.000000 1.000000
0.125000 0.375000 0.000000 0.500000
1.000000 0.000000 0.000000 0.000000
0.000000 0.250000 0.125000 0.625000
0.000000 0.000000 0.000000 1.000000
0.125000 0.000000 0.875000 0.000000
0.125000 0.125000 0.750000 0.000000
0.000000 0.125000 0.000000 0.875000
0.000000 0.000000 0.500000 0.500000
0.000000 0.500000 0.500000 0.000000
0.125000 0.000000 0.875000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
TGG[AG][AG]CAT[TC]A[TC]TGGT[GT][CG]GAG
--------------------------------------------------------------------------------
Time 6.16 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 8 llr = 161 E-value = 5.1e-011
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A ::1:1::1:6:1:::1:98a
pos.-specific C 1::951:9::a:85:3::::
probability G 9:4:4:a:a4::154:513:
matrix T :a51:9:::::91:665:::
bits 2.5 * * *
2.3 * * *
2.0 * * * *
1.8 * * *** *
Information 1.5 ** * *** * * *
content 1.3 ** * **** * ** * *
(29.0 bits) 1.0 ** ************ ****
0.8 ** ************ ****
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel GTTCCTGCGACTCCTTGAAA
consensus G G G GGCT G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Smik_Contig2283.3 + 313 1.96e-11 TTGGTTTCGG GTTCCTGCGACTCGTTTAAA AAAGAAAAGG
MIT_Sbay_c896_21290 + 316 1.96e-11 AATGGCTTCG GTTCCTGCGACTCGTTTAAA AAGAAAAGGG
MIT_Spar_c130_3912 + 310 1.96e-11 TTTGGATTCT GTTCCTGCGACTCGTTTAAA AGAAGAAGGG
SGD_Scer_YDR044W + 317 1.96e-11 TTTGGCTTCT GTTCCTGCGACTCGTTTAAA AGTAGAAGGG
SGD_Scer_YDR047W + 871 6.56e-11 TAATGTAGCC GTGCATGCGGCTCCGCGAAA AGAGCTCTGC
MIT_Spar_c130_3923 + 880 1.43e-10 TTATATAGCC GTACGTGCGGCTCCTCGAGA AAGGCCCTGC
WashU_Skud_Contig1362.1 - 420 9.20e-09 GAAGGTGGCA CTGCGTGAGACTGCGTGGAA AGTATAAATA
MIT_Sbay_c896_21277 + 841 2.90e-08 TTTTATAGCC GTGTGCGCGGCATCGAGAGA CAGGTTCAGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Smik_Contig2283.3 2e-11 312_[+2]_668
MIT_Sbay_c896_21290 2e-11 315_[+2]_665
MIT_Spar_c130_3912 2e-11 309_[+2]_671
SGD_Scer_YDR044W 2e-11 316_[+2]_664
SGD_Scer_YDR047W 6.6e-11 870_[+2]_110
MIT_Spar_c130_3923 1.4e-10 879_[+2]_101
WashU_Skud_Contig1362.1 9.2e-09 419_[-2]_322
MIT_Sbay_c896_21277 2.9e-08 840_[+2]_140
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=8
WashU_Smik_Contig2283.3 ( 313) GTTCCTGCGACTCGTTTAAA 1
MIT_Sbay_c896_21290 ( 316) GTTCCTGCGACTCGTTTAAA 1
MIT_Spar_c130_3912 ( 310) GTTCCTGCGACTCGTTTAAA 1
SGD_Scer_YDR044W ( 317) GTTCCTGCGACTCGTTTAAA 1
SGD_Scer_YDR047W ( 871) GTGCATGCGGCTCCGCGAAA 1
MIT_Spar_c130_3923 ( 880) GTACGTGCGGCTCCTCGAGA 1
WashU_Skud_Contig1362.1 ( 420) CTGCGTGAGACTGCGTGGAA 1
MIT_Sbay_c896_21277 ( 841) GTGTGCGCGGCATCGAGAGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 5.1e-011
-965 -49 232 -965
-965 -965 -965 162
-137 -965 109 62
-965 232 -965 -137
-137 151 109 -965
-965 -49 -965 143
-965 -965 251 -965
-137 232 -965 -965
-965 -965 251 -965
95 -965 109 -965
-965 251 -965 -965
-137 -965 -965 143
-965 209 -49 -137
-965 151 151 -965
-965 -965 109 95
-137 51 -965 95
-965 -965 151 62
143 -965 -49 -965
121 -965 51 -965
162 -965 -965 -965
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 5.1e-011
0.000000 0.125000 0.875000 0.000000
0.000000 0.000000 0.000000 1.000000
0.125000 0.000000 0.375000 0.500000
0.000000 0.875000 0.000000 0.125000
0.125000 0.500000 0.375000 0.000000
0.000000 0.125000 0.000000 0.875000
0.000000 0.000000 1.000000 0.000000
0.125000 0.875000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.625000 0.000000 0.375000 0.000000
0.000000 1.000000 0.000000 0.000000
0.125000 0.000000 0.000000 0.875000
0.000000 0.750000 0.125000 0.125000
0.000000 0.500000 0.500000 0.000000
0.000000 0.000000 0.375000 0.625000
0.125000 0.250000 0.000000 0.625000
0.000000 0.000000 0.500000 0.500000
0.875000 0.000000 0.125000 0.000000
0.750000 0.000000 0.250000 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
GT[TG]C[CG]TGCG[AG]CTC[CG][TG][TC][GT]A[AG]A
--------------------------------------------------------------------------------
Time 12.22 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 15 sites = 8 llr = 136 E-value = 3.8e-008
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :9::6:::::1::::
pos.-specific C 5::::::5:5:::4:
probability G 519a4:::a59a5::
matrix T ::1::aa5::::56a
bits 2.5 * * *
2.3 * * *
2.0 * * *
1.8 ** * **
Information 1.5 * ** ** **** *
content 1.3 **** ** **** *
(24.5 bits) 1.0 ***************
0.8 ***************
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel CAGGATTCGCGGGTT
consensus G G T G TC
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
SGD_Scer_YDR044W + 623 5.51e-09 ACAAACTCCA GAGGATTTGCGGGCT TGATGATAAA
MIT_Sbay_c896_21277 - 211 5.51e-09 CTCGTTTATA CAGGGTTCGGGGTTT TTTGACGCCA
MIT_Spar_c130_3923 - 240 5.51e-09 ATATACGGGA CAGGGTTCGGGGTTT TGGTGGCAGG
SGD_Scer_YDR047W - 243 5.51e-09 ATATACAGGA CAGGGTTCGGGGTTT TTGGCGGCAG
WashU_Smik_Contig2283.3 + 624 8.25e-09 TGAACTTCTT GAGGATTTGCGGGTT CGGTGATAAA
MIT_Sbay_c896_21290 + 622 1.72e-08 CGGAACTCTT GGGGATTTGCGGGCT CGCTAATAAA
MIT_Spar_c130_3912 + 618 4.23e-08 CGAAACTCTA GAGGATTTGCAGGCT CGGTGATAAA
WashU_Skud_Contig1362.1 - 206 5.24e-08 CTCGCTTCTA CATGATTCGGGGTTT TTTGGCAGCA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDR044W 5.5e-09 622_[+3]_363
MIT_Sbay_c896_21277 5.5e-09 210_[-3]_775
MIT_Spar_c130_3923 5.5e-09 239_[-3]_746
SGD_Scer_YDR047W 5.5e-09 242_[-3]_743
WashU_Smik_Contig2283.3 8.2e-09 623_[+3]_362
MIT_Sbay_c896_21290 1.7e-08 621_[+3]_364
MIT_Spar_c130_3912 4.2e-08 617_[+3]_368
WashU_Skud_Contig1362.1 5.2e-08 205_[-3]_541
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=15 seqs=8
SGD_Scer_YDR044W ( 623) GAGGATTTGCGGGCT 1
MIT_Sbay_c896_21277 ( 211) CAGGGTTCGGGGTTT 1
MIT_Spar_c130_3923 ( 240) CAGGGTTCGGGGTTT 1
SGD_Scer_YDR047W ( 243) CAGGGTTCGGGGTTT 1
WashU_Smik_Contig2283.3 ( 624) GAGGATTTGCGGGTT 1
MIT_Sbay_c896_21290 ( 622) GGGGATTTGCGGGCT 1
MIT_Spar_c130_3912 ( 618) GAGGATTTGCAGGCT 1
WashU_Skud_Contig1362.1 ( 206) CATGATTCGGGGTTT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 7649 bayes= 9.89955 E= 3.8e-008
-965 151 151 -965
143 -965 -49 -965
-965 -965 232 -137
-965 -965 251 -965
95 -965 109 -965
-965 -965 -965 162
-965 -965 -965 162
-965 151 -965 62
-965 -965 251 -965
-965 151 151 -965
-137 -965 232 -965
-965 -965 251 -965
-965 -965 151 62
-965 109 -965 95
-965 -965 -965 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 3.8e-008
0.000000 0.500000 0.500000 0.000000
0.875000 0.000000 0.125000 0.000000
0.000000 0.000000 0.875000 0.125000
0.000000 0.000000 1.000000 0.000000
0.625000 0.000000 0.375000 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
0.000000 0.000000 1.000000 0.000000
0.000000 0.500000 0.500000 0.000000
0.125000 0.000000 0.875000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.500000 0.500000
0.000000 0.375000 0.000000 0.625000
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
[CG]AGG[AG]TT[CT]G[CG]GG[GT][TC]T
--------------------------------------------------------------------------------
Time 18.15 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 20 sites = 8 llr = 155 E-value = 1.1e-008
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A aa13::a6a415:5::::1:
pos.-specific C ::::54::::9:111a:1:4
probability G ::5856:4:6:5::4:a::6
matrix T ::4:::::::::945::99:
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 AAGGCGAAAGCATATCGTTG
consensus TAGC G A G TG C
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c130_3912 + 273 3.90e-12 GAAGCCAGAA AAGGCGAAAGCGTAGCGTTC TTTGAAATTT
SGD_Scer_YDR044W + 280 3.90e-12 AGAACCAGAA AAGGCGAAAGCGTAGCGTTC TTTGAAATTT
MIT_Sbay_c896_21290 + 279 2.45e-10 GAAGCCAGAA AATGCGAAAGCGTACCGTTC TGTGAAAAAT
MIT_Spar_c130_3923 + 167 3.43e-10 TAATGACAAA AAGGGCAGAACATTTCGTTG GCAAAATTTA
MIT_Sbay_c896_21277 + 140 1.28e-09 TAGTGACACG AATAGGAAAGCATTTCGTTG ACAAAAATAA
SGD_Scer_YDR047W + 170 3.28e-09 TAAAGATGAA AATGGCAGAACATTTCGCTG GCAAAATTAA
WashU_Smik_Contig2283.3 + 269 7.13e-09 GAAGCCAGAA AAGACGAAAGAGTAGCGTAG CGTTCTTTCA
WashU_Skud_Contig1362.1 + 134 8.94e-09 TAAACATACG AAAGGCAGAACACCTCGTTG ACAAAACTGA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c130_3912 3.9e-12 272_[+4]_708
SGD_Scer_YDR044W 3.9e-12 279_[+4]_701
MIT_Sbay_c896_21290 2.4e-10 278_[+4]_702
MIT_Spar_c130_3923 3.4e-10 166_[+4]_814
MIT_Sbay_c896_21277 1.3e-09 139_[+4]_841
SGD_Scer_YDR047W 3.3e-09 169_[+4]_811
WashU_Smik_Contig2283.3 7.1e-09 268_[+4]_712
WashU_Skud_Contig1362.1 8.9e-09 133_[+4]_608
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=20 seqs=8
MIT_Spar_c130_3912 ( 273) AAGGCGAAAGCGTAGCGTTC 1
SGD_Scer_YDR044W ( 280) AAGGCGAAAGCGTAGCGTTC 1
MIT_Sbay_c896_21290 ( 279) AATGCGAAAGCGTACCGTTC 1
MIT_Spar_c130_3923 ( 167) AAGGGCAGAACATTTCGTTG 1
MIT_Sbay_c896_21277 ( 140) AATAGGAAAGCATTTCGTTG 1
SGD_Scer_YDR047W ( 170) AATGGCAGAACATTTCGCTG 1
WashU_Smik_Contig2283.3 ( 269) AAGACGAAAGAGTAGCGTAG 1
WashU_Skud_Contig1362.1 ( 134) AAAGGCAGAACACCTCGTTG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 1.1e-008
162 -965 -965 -965
162 -965 -965 -965
-137 -965 151 21
-38 -965 209 -965
-965 151 151 -965
-965 109 183 -965
162 -965 -965 -965
95 -965 109 -965
162 -965 -965 -965
21 -965 183 -965
-137 232 -965 -965
62 -965 151 -965
-965 -49 -965 143
62 -49 -965 21
-965 -49 109 62
-965 251 -965 -965
-965 -965 251 -965
-965 -49 -965 143
-137 -965 -965 143
-965 109 183 -965
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.1e-008
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.125000 0.000000 0.500000 0.375000
0.250000 0.000000 0.750000 0.000000
0.000000 0.500000 0.500000 0.000000
0.000000 0.375000 0.625000 0.000000
1.000000 0.000000 0.000000 0.000000
0.625000 0.000000 0.375000 0.000000
1.000000 0.000000 0.000000 0.000000
0.375000 0.000000 0.625000 0.000000
0.125000 0.875000 0.000000 0.000000
0.500000 0.000000 0.500000 0.000000
0.000000 0.125000 0.000000 0.875000
0.500000 0.125000 0.000000 0.375000
0.000000 0.125000 0.375000 0.500000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.125000 0.000000 0.875000
0.125000 0.000000 0.000000 0.875000
0.000000 0.375000 0.625000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
AA[GT][GA][CG][GC]A[AG]A[GA]C[AG]T[AT][TG]CGTT[GC]
--------------------------------------------------------------------------------
Time 24.05 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 8 llr = 150 E-value = 3.2e-007
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A 1::::1a643:6:85:aa::
pos.-specific C 135:a:::44:4:11a::31
probability G :1:::9:431a:91:::::9
matrix T 865a:::::3::1:4:::8:
bits 2.5 * * *
2.3 * * *
2.0 * * * *
1.8 ** * * * *
Information 1.5 **** * * *** *
content 1.3 **** * * *** *
(27.0 bits) 1.0 ****** *** *****
0.8 ******** **** *****
0.5 ********* **** *****
0.3 ********************
0.0 --------------------
Multilevel TTCTCGAAACGAGAACAATG
consensus CT GCA C T C
sequence GT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c130_3912 + 160 8.41e-11 TTATATAGCC TTTTCGAAACGAGAACAATG GACAAATCAA
MIT_Sbay_c896_21290 + 166 1.14e-10 TTATATAGCT TTCTCGAAGGGAGAACAATG GATAAATCAA
MIT_Spar_c130_3923 + 927 2.25e-10 CACTAGCTGA TCCTCGAGCTGCGATCAACG AAAGCCCCAT
SGD_Scer_YDR044W + 164 6.26e-10 CTTATATAGC CTTTCGAAACGAGAACAATG GGCAAAGCAA
MIT_Sbay_c896_21277 + 888 1.02e-09 ATTTGCCTAA TTCTCGAGCTGAGGCCAATG AAGGCAGCTT
SGD_Scer_YDR047W + 918 1.45e-09 CTCTACCTGA ACTTCGAGCCGCGATCAACG AAAGCTCTCA
WashU_Smik_Contig2283.3 + 156 6.02e-09 TTATATAGCC TTTTCAAAAAGAGAACAATG GTCAAATAAA
WashU_Skud_Contig1362.1 + 363 3.46e-08 AATTTGCTAA TGCTCGAAGAGCTCTCAATC AATCACCCAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c130_3912 8.4e-11 159_[+5]_821
MIT_Sbay_c896_21290 1.1e-10 165_[+5]_815
MIT_Spar_c130_3923 2.2e-10 926_[+5]_54
SGD_Scer_YDR044W 6.3e-10 163_[+5]_817
MIT_Sbay_c896_21277 1e-09 887_[+5]_93
SGD_Scer_YDR047W 1.4e-09 917_[+5]_63
WashU_Smik_Contig2283.3 6e-09 155_[+5]_825
WashU_Skud_Contig1362.1 3.5e-08 362_[+5]_379
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=8
MIT_Spar_c130_3912 ( 160) TTTTCGAAACGAGAACAATG 1
MIT_Sbay_c896_21290 ( 166) TTCTCGAAGGGAGAACAATG 1
MIT_Spar_c130_3923 ( 927) TCCTCGAGCTGCGATCAACG 1
SGD_Scer_YDR044W ( 164) CTTTCGAAACGAGAACAATG 1
MIT_Sbay_c896_21277 ( 888) TTCTCGAGCTGAGGCCAATG 1
SGD_Scer_YDR047W ( 918) ACTTCGAGCCGCGATCAACG 1
WashU_Smik_Contig2283.3 ( 156) TTTTCAAAAAGAGAACAATG 1
WashU_Skud_Contig1362.1 ( 363) TGCTCGAAGAGCTCTCAATC 1
//
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--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 3.2e-007
-137 -49 -965 121
-965 51 -49 95
-965 151 -965 62
-965 -965 -965 162
-965 251 -965 -965
-137 -965 232 -965
162 -965 -965 -965
95 -965 109 -965
21 109 51 -965
-38 109 -49 -38
-965 -965 251 -965
95 109 -965 -965
-965 -965 232 -137
121 -49 -49 -965
62 -49 -965 21
-965 251 -965 -965
162 -965 -965 -965
162 -965 -965 -965
-965 51 -965 121
-965 -49 232 -965
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 3.2e-007
0.125000 0.125000 0.000000 0.750000
0.000000 0.250000 0.125000 0.625000
0.000000 0.500000 0.000000 0.500000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.125000 0.000000 0.875000 0.000000
1.000000 0.000000 0.000000 0.000000
0.625000 0.000000 0.375000 0.000000
0.375000 0.375000 0.250000 0.000000
0.250000 0.375000 0.125000 0.250000
0.000000 0.000000 1.000000 0.000000
0.625000 0.375000 0.000000 0.000000
0.000000 0.000000 0.875000 0.125000
0.750000 0.125000 0.125000 0.000000
0.500000 0.125000 0.000000 0.375000
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 0.250000 0.000000 0.750000
0.000000 0.125000 0.875000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
T[TC][CT]TCGA[AG][ACG][CAT]G[AC]GA[AT]CAA[TC]G
--------------------------------------------------------------------------------
Time 29.84 secs.
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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_YDR047W 7.45e-23 50_[+5(5.03e-05)]_66_[+1(1.93e-09)]_13_[+4(3.28e-09)]_53_[-3(5.51e-09)]_613_[+2(6.56e-11)]_27_[+5(1.45e-09)]_63
MIT_Spar_c130_3923 1.06e-24 133_[+1(5.96e-10)]_13_[+4(3.43e-10)]_53_[-3(5.51e-09)]_110_[-4(7.03e-05)]_238_[+1(6.23e-05)]_237_[+2(1.43e-10)]_27_[+5(2.25e-10)]_54
MIT_Sbay_c896_21277 2.78e-21 5_[-4(5.78e-05)]_81_[+1(7.56e-10)]_13_[+4(1.28e-09)]_51_[-3(5.51e-09)]_615_[+2(2.90e-08)]_27_[+5(1.02e-09)]_93
WashU_Skud_Contig1362.1 1.22e-19 100_[+1(2.45e-10)]_13_[+4(8.94e-09)]_52_[-3(5.24e-08)]_142_[+5(3.46e-08)]_37_[-2(9.20e-09)]_322
SGD_Scer_YDR044W 3.05e-28 163_[+5(6.26e-10)]_68_[+1(2.47e-11)]_8_[+4(3.90e-12)]_17_[+2(1.96e-11)]_286_[+3(5.51e-09)]_363
MIT_Spar_c130_3912 1.93e-29 159_[+5(8.41e-11)]_64_[+1(1.31e-12)]_9_[+4(3.90e-12)]_17_[+2(1.96e-11)]_288_[+3(4.23e-08)]_69_[-4(1.60e-05)]_279
MIT_Sbay_c896_21290 7.41e-27 165_[+5(1.14e-10)]_64_[+1(2.00e-11)]_9_[+4(2.45e-10)]_17_[+2(1.96e-11)]_8_[-3(7.60e-05)]_3_[-4(2.55e-05)]_240_[+3(1.72e-08)]_66_[-4(1.70e-05)]_278
WashU_Smik_Contig2283.3 1.31e-23 7_[+3(8.33e-05)]_39_[-5(9.82e-05)]_74_[+5(6.02e-09)]_64_[+1(7.53e-11)]_9_[+4(7.13e-09)]_24_[+2(1.96e-11)]_61_[-2(3.93e-05)]_88_[+2(7.74e-05)]_102_[+3(8.25e-09)]_362
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************