********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date: )
For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.
This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs. MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************
********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:
Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************
********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM3-HEM4.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YDL205C 1.0000 860 MIT_Spar_c429_3020 1.0000 860
MIT_Smik_c193_2483 1.0000 860 MIT_Sbay_c841_3215 1.0000 860
WashU_Skud_Contig1850.5 1.0000 860 SGD_Scer_YOR278W 1.0000 635
MIT_Spar_c261_21317 1.0000 635 MIT_Smik_c492_20940 1.0000 635
WashU_Skud_Contig1682.4 1.0000 635 WashU_Sbay_Contig635.57 1.0000 635
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM3-HEM4.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
model: mod= oops nmotifs= 5 evt= inf
object function= E-value of product of p-values
width: minw= 6 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 10 maxsites= 10 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 7475 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.310 C 0.190 G 0.190 T 0.310
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 = 10 llr = 217 E-value = 9.7e-028
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 5:a:::5:::5::5:::a5a
pos.-specific C 5a::aa5::::a55::5:2:
probability G :::a::::5:5:5::21:::
matrix T :::::::a5a::::a84:3:
bits 2.5 * *** *
2.3 * *** *
2.0 * *** *
1.8 * *** *
Information 1.5 ***** * * ** * * *
content 1.3 ***** * * ** * * *
(31.3 bits) 1.0 **************** * *
0.8 ****************** *
0.5 ****************** *
0.3 ********************
0.0 --------------------
Multilevel ACAGCCATGTACCATTCAAA
consensus C C T G GC GT T
sequence C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig1850.5 + 115 4.59e-11 AAAAAGCAAT ACAGCCCTGTACCATTCAAA CACGAACGCC
MIT_Sbay_c841_3215 + 116 4.59e-11 AAAACGCAAT ACAGCCCTGTACCATTCAAA TACGAACGCC
MIT_Smik_c193_2483 + 117 4.59e-11 AAAAAGTAAT ACAGCCCTGTACCATTCAAA CACGAGCGCC
WashU_Skud_Contig1682.4 + 337 1.14e-10 TGGTCTACTT CCAGCCATTTGCGCTTTACA TAGACATATG
MIT_Smik_c492_20940 + 342 1.41e-10 TTGTCTACTT CCAGCCATTTGCGCTTTATA TAGACATATG
MIT_Spar_c261_21317 + 336 1.41e-10 TGGTCTACTT CCAGCCATTTGCGCTTTATA TAGACATATG
SGD_Scer_YOR278W + 333 1.41e-10 TGGTCTACTT CCAGCCATTTGCGCTTTATA TAGACATATG
MIT_Spar_c429_3020 + 115 1.41e-10 AAAATGTAAA ACAGCCCTGTACCATGCAAA CACGAGCCTC
SGD_Scer_YDL205C + 115 1.41e-10 AAAATCTAAT ACAGCCCTGTACCATGCAAA CACGAGCGTC
WashU_Sbay_Contig635.57 + 344 2.72e-10 TGGTCTACTT CCAGCCATTTGCGCTTGACA TAGACATATG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig1850.5 4.6e-11 114_[+1]_726
MIT_Sbay_c841_3215 4.6e-11 115_[+1]_725
MIT_Smik_c193_2483 4.6e-11 116_[+1]_724
WashU_Skud_Contig1682.4 1.1e-10 336_[+1]_279
MIT_Smik_c492_20940 1.4e-10 341_[+1]_274
MIT_Spar_c261_21317 1.4e-10 335_[+1]_280
SGD_Scer_YOR278W 1.4e-10 332_[+1]_283
MIT_Spar_c429_3020 1.4e-10 114_[+1]_726
SGD_Scer_YDL205C 1.4e-10 114_[+1]_726
WashU_Sbay_Contig635.57 2.7e-10 343_[+1]_272
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=10
WashU_Skud_Contig1850.5 ( 115) ACAGCCCTGTACCATTCAAA 1
MIT_Sbay_c841_3215 ( 116) ACAGCCCTGTACCATTCAAA 1
MIT_Smik_c193_2483 ( 117) ACAGCCCTGTACCATTCAAA 1
WashU_Skud_Contig1682.4 ( 337) CCAGCCATTTGCGCTTTACA 1
MIT_Smik_c492_20940 ( 342) CCAGCCATTTGCGCTTTATA 1
MIT_Spar_c261_21317 ( 336) CCAGCCATTTGCGCTTTATA 1
SGD_Scer_YOR278W ( 333) CCAGCCATTTGCGCTTTATA 1
MIT_Spar_c429_3020 ( 115) ACAGCCCTGTACCATGCAAA 1
SGD_Scer_YDL205C ( 115) ACAGCCCTGTACCATGCAAA 1
WashU_Sbay_Contig635.57 ( 344) CCAGCCATTTGCGCTTGACA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 9.7e-028
62 151 -997 -997
-997 251 -997 -997
162 -997 -997 -997
-997 -997 251 -997
-997 251 -997 -997
-997 251 -997 -997
62 151 -997 -997
-997 -997 -997 162
-997 -997 151 62
-997 -997 -997 162
62 -997 151 -997
-997 251 -997 -997
-997 151 151 -997
62 151 -997 -997
-997 -997 -997 162
-997 -997 19 130
-997 151 -81 30
162 -997 -997 -997
62 19 -997 -11
162 -997 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.7e-028
0.500000 0.500000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.500000 0.500000
0.000000 0.000000 0.000000 1.000000
0.500000 0.000000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.500000 0.500000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.200000 0.800000
0.000000 0.500000 0.100000 0.400000
1.000000 0.000000 0.000000 0.000000
0.500000 0.200000 0.000000 0.300000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
[AC]CAGCC[AC]T[GT]T[AG]C[CG][AC]T[TG][CT]A[ATC]A
--------------------------------------------------------------------------------
Time 5.67 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 10 llr = 211 E-value = 3.2e-025
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 8::::::a5::a::::57::
pos.-specific C ::::a:::5:a::5:::::a
probability G 1:55:::::5:::5a2::::
matrix T 1a55:aa::5::a::853a:
bits 2.5 * * * *
2.3 * * * *
2.0 * * * *
1.8 * * * *
Information 1.5 * **** ***** **
content 1.3 * **** ***** **
(30.4 bits) 1.0 *************** **
0.8 **************** ***
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel ATGGCTTAAGCATCGTAATC
consensus TT CT G GTT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 + 382 8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
WashU_Skud_Contig1682.4 + 375 8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
MIT_Smik_c492_20940 + 380 8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
MIT_Spar_c261_21317 + 374 8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
SGD_Scer_YOR278W + 371 8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
MIT_Smik_c193_2483 + 326 8.08e-11 AGAGGCCTTC ATTGCTTACTCATCGTTATC TTATTGGTTA
MIT_Spar_c429_3020 + 325 5.11e-10 AAAGACCTTC ATTGCTTACTCATCGGTTTC TTATTGGTCA
SGD_Scer_YDL205C + 322 5.11e-10 AAAGACCTTC ATTGCTTACTCATCGGTTTC TTATTGGTCA
MIT_Sbay_c841_3215 + 323 6.64e-10 AGAGGCCTTC TTTGCTTACTCATCGTTATC TTATTGGTCA
WashU_Skud_Contig1850.5 + 325 7.76e-10 AGAGGCGTAC GTTGCTTACTCATCGTTTTC TTATTGGTCA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 8.1e-11 381_[+2]_234
WashU_Skud_Contig1682.4 8.1e-11 374_[+2]_241
MIT_Smik_c492_20940 8.1e-11 379_[+2]_236
MIT_Spar_c261_21317 8.1e-11 373_[+2]_242
SGD_Scer_YOR278W 8.1e-11 370_[+2]_245
MIT_Smik_c193_2483 8.1e-11 325_[+2]_515
MIT_Spar_c429_3020 5.1e-10 324_[+2]_516
SGD_Scer_YDL205C 5.1e-10 321_[+2]_519
MIT_Sbay_c841_3215 6.6e-10 322_[+2]_518
WashU_Skud_Contig1850.5 7.8e-10 324_[+2]_516
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=10
WashU_Sbay_Contig635.57 ( 382) ATGTCTTAAGCATGGTAATC 1
WashU_Skud_Contig1682.4 ( 375) ATGTCTTAAGCATGGTAATC 1
MIT_Smik_c492_20940 ( 380) ATGTCTTAAGCATGGTAATC 1
MIT_Spar_c261_21317 ( 374) ATGTCTTAAGCATGGTAATC 1
SGD_Scer_YOR278W ( 371) ATGTCTTAAGCATGGTAATC 1
MIT_Smik_c193_2483 ( 326) ATTGCTTACTCATCGTTATC 1
MIT_Spar_c429_3020 ( 325) ATTGCTTACTCATCGGTTTC 1
SGD_Scer_YDL205C ( 322) ATTGCTTACTCATCGGTTTC 1
MIT_Sbay_c841_3215 ( 323) TTTGCTTACTCATCGTTATC 1
WashU_Skud_Contig1850.5 ( 325) GTTGCTTACTCATCGTTTTC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 3.2e-025
130 -997 -81 -169
-997 -997 -997 162
-997 -997 151 62
-997 -997 151 62
-997 251 -997 -997
-997 -997 -997 162
-997 -997 -997 162
162 -997 -997 -997
62 151 -997 -997
-997 -997 151 62
-997 251 -997 -997
162 -997 -997 -997
-997 -997 -997 162
-997 151 151 -997
-997 -997 251 -997
-997 -997 19 130
62 -997 -997 62
111 -997 -997 -11
-997 -997 -997 162
-997 251 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.2e-025
0.800000 0.000000 0.100000 0.100000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.500000 0.500000
0.000000 0.000000 0.500000 0.500000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.000000 0.000000 0.500000 0.500000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.500000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.200000 0.800000
0.500000 0.000000 0.000000 0.500000
0.700000 0.000000 0.000000 0.300000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
AT[GT][GT]CTTA[AC][GT]CAT[CG]G[TG][AT][AT]TC
--------------------------------------------------------------------------------
Time 11.21 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 20 sites = 10 llr = 207 E-value = 5.5e-024
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A :519a:a5:a255:9:::aa
pos.-specific C 5:::::::a::::::::5::
probability G 559::a::::8::::::5::
matrix T :::1:::5:::55a1aa:::
bits 2.5 * *
2.3 * *
2.0 * * *
1.8 * * *
Information 1.5 * * *** *** * *****
content 1.3 * ***** *** *******
(29.8 bits) 1.0 ******* *** *******
0.8 ******* *** *******
0.5 ********************
0.3 ********************
0.0 --------------------
Multilevel CAGAAGAACAGAATATTCAA
consensus GG T ATT G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Sbay_Contig635.57 + 402 7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGCTCT
WashU_Skud_Contig1682.4 + 395 7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTCT
MIT_Smik_c492_20940 + 400 7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTCT
MIT_Spar_c261_21317 + 394 7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTCT
SGD_Scer_YOR278W + 391 7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTTT
MIT_Spar_c429_3020 + 87 2.07e-10 AATACGGGAT GAGAAGAACAGAATATTCAA AATGTAAAAC
SGD_Scer_YDL205C + 87 2.07e-10 AATACGGGAT GAGAAGAACAGAATATTCAA AATCTAATAC
MIT_Smik_c193_2483 + 89 1.38e-09 AATACGGGAT GAAAAGAACAGAATATTCAA AAAGTAATAC
WashU_Skud_Contig1850.5 + 87 2.47e-09 ATATGGGGAT GAGAAGAACAAAATTTTCAA AAAGCAATAC
MIT_Sbay_c841_3215 + 88 2.47e-09 AATATGGGAT GAGTAGAACAAAATATTCAA AACGCAATAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 7.3e-11 401_[+3]_214
WashU_Skud_Contig1682.4 7.3e-11 394_[+3]_221
MIT_Smik_c492_20940 7.3e-11 399_[+3]_216
MIT_Spar_c261_21317 7.3e-11 393_[+3]_222
SGD_Scer_YOR278W 7.3e-11 390_[+3]_225
MIT_Spar_c429_3020 2.1e-10 86_[+3]_754
SGD_Scer_YDL205C 2.1e-10 86_[+3]_754
MIT_Smik_c193_2483 1.4e-09 88_[+3]_752
WashU_Skud_Contig1850.5 2.5e-09 86_[+3]_754
MIT_Sbay_c841_3215 2.5e-09 87_[+3]_753
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=20 seqs=10
WashU_Sbay_Contig635.57 ( 402) CGGAAGATCAGTTTATTGAA 1
WashU_Skud_Contig1682.4 ( 395) CGGAAGATCAGTTTATTGAA 1
MIT_Smik_c492_20940 ( 400) CGGAAGATCAGTTTATTGAA 1
MIT_Spar_c261_21317 ( 394) CGGAAGATCAGTTTATTGAA 1
SGD_Scer_YOR278W ( 391) CGGAAGATCAGTTTATTGAA 1
MIT_Spar_c429_3020 ( 87) GAGAAGAACAGAATATTCAA 1
SGD_Scer_YDL205C ( 87) GAGAAGAACAGAATATTCAA 1
MIT_Smik_c193_2483 ( 89) GAAAAGAACAGAATATTCAA 1
WashU_Skud_Contig1850.5 ( 87) GAGAAGAACAAAATTTTCAA 1
MIT_Sbay_c841_3215 ( 88) GAGTAGAACAAAATATTCAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 5.5e-024
-997 151 151 -997
62 -997 151 -997
-169 -997 236 -997
147 -997 -997 -169
162 -997 -997 -997
-997 -997 251 -997
162 -997 -997 -997
62 -997 -997 62
-997 251 -997 -997
162 -997 -997 -997
-70 -997 219 -997
62 -997 -997 62
62 -997 -997 62
-997 -997 -997 162
147 -997 -997 -169
-997 -997 -997 162
-997 -997 -997 162
-997 151 151 -997
162 -997 -997 -997
162 -997 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.5e-024
0.000000 0.500000 0.500000 0.000000
0.500000 0.000000 0.500000 0.000000
0.100000 0.000000 0.900000 0.000000
0.900000 0.000000 0.000000 0.100000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.200000 0.000000 0.800000 0.000000
0.500000 0.000000 0.000000 0.500000
0.500000 0.000000 0.000000 0.500000
0.000000 0.000000 0.000000 1.000000
0.900000 0.000000 0.000000 0.100000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.500000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
[CG][AG]GAAGA[AT]CA[GA][AT][AT]TATT[CG]AA
--------------------------------------------------------------------------------
Time 16.58 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 15 sites = 10 llr = 165 E-value = 1.7e-014
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A 9:555:a:5:aa11a
pos.-specific C 1a5:::::5:::66:
probability G ::::5a:a:a::33:
matrix T :::5:::::::::::
bits 2.5 * * * *
2.3 * * * *
2.0 * * * *
1.8 * * * *
Information 1.5 * *** *** *
content 1.3 ** *** *** *
(23.9 bits) 1.0 *** ***********
0.8 *** ***********
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel ACAAAGAGAGAACCA
consensus CTG C GG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Sbay_Contig635.57 + 238 2.42e-09 AAACATGTAC ACCTAGAGCGAACCA GTGATAATTT
WashU_Skud_Contig1682.4 + 232 2.42e-09 AGATATGTAC ACCTAGAGCGAACCA ATGATAATTT
MIT_Smik_c492_20940 + 235 2.42e-09 AGATATGTAC ACCTAGAGCGAACCA ATAATAATTT
MIT_Spar_c261_21317 + 230 2.42e-09 GAATATGTAC ACCTAGAGCGAACCA ATGATAATTT
SGD_Scer_YOR278W + 226 2.42e-09 AGATATGTAC ACCTAGAGCGAACCA ATGATAATTT
MIT_Sbay_c841_3215 + 372 6.95e-09 GGGACAATAG ACAAGGAGAGAACCA CCAACTTTGG
MIT_Spar_c429_3020 + 376 3.49e-08 GGGTCAATTG ACAAGGAGAGAAGGA ATGTTACATC
SGD_Scer_YDL205C + 373 3.49e-08 GGGTCAATTG ACAAGGAGAGAAGGA ATGTTATATG
MIT_Smik_c193_2483 + 375 1.07e-07 GCGACAATGT ACAAGGAGAGAAGAA ATGATATGTC
WashU_Skud_Contig1850.5 + 374 1.53e-07 GGAACAATGC CCAAGGAGAGAAAGA GTGCTACGTC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Sbay_Contig635.57 2.4e-09 237_[+4]_383
WashU_Skud_Contig1682.4 2.4e-09 231_[+4]_389
MIT_Smik_c492_20940 2.4e-09 234_[+4]_386
MIT_Spar_c261_21317 2.4e-09 229_[+4]_391
SGD_Scer_YOR278W 2.4e-09 225_[+4]_395
MIT_Sbay_c841_3215 6.9e-09 371_[+4]_474
MIT_Spar_c429_3020 3.5e-08 375_[+4]_470
SGD_Scer_YDL205C 3.5e-08 372_[+4]_473
MIT_Smik_c193_2483 1.1e-07 374_[+4]_471
WashU_Skud_Contig1850.5 1.5e-07 373_[+4]_472
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=15 seqs=10
WashU_Sbay_Contig635.57 ( 238) ACCTAGAGCGAACCA 1
WashU_Skud_Contig1682.4 ( 232) ACCTAGAGCGAACCA 1
MIT_Smik_c492_20940 ( 235) ACCTAGAGCGAACCA 1
MIT_Spar_c261_21317 ( 230) ACCTAGAGCGAACCA 1
SGD_Scer_YOR278W ( 226) ACCTAGAGCGAACCA 1
MIT_Sbay_c841_3215 ( 372) ACAAGGAGAGAACCA 1
MIT_Spar_c429_3020 ( 376) ACAAGGAGAGAAGGA 1
SGD_Scer_YDL205C ( 373) ACAAGGAGAGAAGGA 1
MIT_Smik_c193_2483 ( 375) ACAAGGAGAGAAGAA 1
WashU_Skud_Contig1850.5 ( 374) CCAAGGAGAGAAAGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 7335 bayes= 9.51668 E= 1.7e-014
147 -81 -997 -997
-997 251 -997 -997
62 151 -997 -997
62 -997 -997 62
62 -997 151 -997
-997 -997 251 -997
162 -997 -997 -997
-997 -997 251 -997
62 151 -997 -997
-997 -997 251 -997
162 -997 -997 -997
162 -997 -997 -997
-169 177 77 -997
-169 177 77 -997
162 -997 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.7e-014
0.900000 0.100000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
0.500000 0.000000 0.500000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.500000 0.500000 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
0.100000 0.600000 0.300000 0.000000
0.100000 0.600000 0.300000 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
AC[AC][AT][AG]GAG[AC]GAA[CG][CG]A
--------------------------------------------------------------------------------
Time 21.88 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 10 llr = 194 E-value = 4.5e-019
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A aaaa:55a:5aa454a88a9
pos.-specific C :::::5::::::51::::::
probability G ::::a:::a5::::6:22:1
matrix T ::::::5:::::14::::::
bits 2.5 * *
2.3 * *
2.0 * *
1.8 * *
Information 1.5 ***** ** ** * *
content 1.3 ***** ** ** ** **
(28.0 bits) 1.0 ****** ***** ******
0.8 ****** ****** ******
0.5 ************* ******
0.3 ********************
0.0 --------------------
Multilevel AAAAGAAAGAAACAGAAAAA
consensus CT G ATA GG
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
MIT_Spar_c261_21317 + 305 8.38e-12 TTCAATAATG AAAAGCTAGGAACAGAAAAA TTGGTCTACT
SGD_Scer_YOR278W + 301 1.32e-10 TTCAATAATG AAAAGCTAGGAACAAAAAAA ATTGGTCTAC
WashU_Sbay_Contig635.57 + 313 5.24e-10 TTCATTAAAG AAAAGCTAGGAACAAAGAAA TTGGTCTACT
MIT_Smik_c492_20940 + 310 5.24e-10 TTCAATAATG AAAAGCTAGGAACAAAAGAA ATTTGTCTAC
MIT_Sbay_c841_3215 - 231 9.80e-10 TTAGACATAA AAAAGAAAGAAACCGAAAAA TTAAAGGAAC
WashU_Skud_Contig1850.5 - 231 1.03e-09 TAAACATAAA AAAAGAAAGAAAATGAAAAA ATTGAAGGAA
MIT_Spar_c429_3020 - 232 1.03e-09 CAAACATAAA AAAAGAAAGAAAATGAAAAA AATGAAGGAA
SGD_Scer_YDL205C - 230 1.03e-09 CAAACATAAA AAAAGAAAGAAAATGAAAAA GTAAAGGAAC
MIT_Smik_c193_2483 - 235 2.33e-09 AAAACATAGA AAAAGAAAGAAAATGAGAAA AACTGAAGGA
WashU_Skud_Contig1682.4 + 305 7.25e-09 TTCAATAATG AAAAGCTAGGAATAAAAGAG ATTGGTCTAC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c261_21317 8.4e-12 304_[+5]_311
SGD_Scer_YOR278W 1.3e-10 300_[+5]_315
WashU_Sbay_Contig635.57 5.2e-10 312_[+5]_303
MIT_Smik_c492_20940 5.2e-10 309_[+5]_306
MIT_Sbay_c841_3215 9.8e-10 230_[-5]_610
WashU_Skud_Contig1850.5 1e-09 230_[-5]_610
MIT_Spar_c429_3020 1e-09 231_[-5]_609
SGD_Scer_YDL205C 1e-09 229_[-5]_611
MIT_Smik_c193_2483 2.3e-09 234_[-5]_606
WashU_Skud_Contig1682.4 7.3e-09 304_[+5]_311
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=10
MIT_Spar_c261_21317 ( 305) AAAAGCTAGGAACAGAAAAA 1
SGD_Scer_YOR278W ( 301) AAAAGCTAGGAACAAAAAAA 1
WashU_Sbay_Contig635.57 ( 313) AAAAGCTAGGAACAAAGAAA 1
MIT_Smik_c492_20940 ( 310) AAAAGCTAGGAACAAAAGAA 1
MIT_Sbay_c841_3215 ( 231) AAAAGAAAGAAACCGAAAAA 1
WashU_Skud_Contig1850.5 ( 231) AAAAGAAAGAAAATGAAAAA 1
MIT_Spar_c429_3020 ( 232) AAAAGAAAGAAAATGAAAAA 1
SGD_Scer_YDL205C ( 230) AAAAGAAAGAAAATGAAAAA 1
MIT_Smik_c193_2483 ( 235) AAAAGAAAGAAAATGAGAAA 1
WashU_Skud_Contig1682.4 ( 305) AAAAGCTAGGAATAAAAGAG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 4.5e-019
162 -997 -997 -997
162 -997 -997 -997
162 -997 -997 -997
162 -997 -997 -997
-997 -997 251 -997
62 151 -997 -997
62 -997 -997 62
162 -997 -997 -997
-997 -997 251 -997
62 -997 151 -997
162 -997 -997 -997
162 -997 -997 -997
30 151 -997 -169
62 -81 -997 30
30 -997 177 -997
162 -997 -997 -997
130 -997 19 -997
130 -997 19 -997
162 -997 -997 -997
147 -997 -81 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 4.5e-019
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.500000 0.500000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 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
0.400000 0.500000 0.000000 0.100000
0.500000 0.100000 0.000000 0.400000
0.400000 0.000000 0.600000 0.000000
1.000000 0.000000 0.000000 0.000000
0.800000 0.000000 0.200000 0.000000
0.800000 0.000000 0.200000 0.000000
1.000000 0.000000 0.000000 0.000000
0.900000 0.000000 0.100000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
AAAAG[AC][AT]AG[AG]AA[CA][AT][GA]A[AG][AG]AA
--------------------------------------------------------------------------------
Time 27.05 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YDL205C 6.52e-24 48_[-5(3.42e-05)]_18_[+3(2.07e-10)]_8_[+1(1.41e-10)]_95_[-5(1.03e-09)]_72_[+2(5.11e-10)]_31_[+4(3.49e-08)]_473
MIT_Spar_c429_3020 6.52e-24 86_[+3(2.07e-10)]_8_[+1(1.41e-10)]_97_[-5(1.03e-09)]_11_[-5(7.48e-05)]_42_[+2(5.11e-10)]_31_[+4(3.49e-08)]_430_[-5(9.37e-05)]_20
MIT_Smik_c193_2483 1.47e-23 88_[+3(1.38e-09)]_8_[+1(4.59e-11)]_98_[-5(2.33e-09)]_11_[-5(5.68e-05)]_40_[+2(8.08e-11)]_29_[+4(1.07e-07)]_410_[+3(7.71e-05)]_41
MIT_Sbay_c841_3215 6.24e-24 49_[-5(2.22e-05)]_18_[+3(2.47e-09)]_8_[+1(4.59e-11)]_95_[-5(9.80e-10)]_10_[-5(1.66e-05)]_42_[+2(6.64e-10)]_29_[+4(6.95e-09)]_474
WashU_Skud_Contig1850.5 1.39e-22 30_[-5(2.12e-05)]_36_[+3(2.47e-09)]_8_[+1(4.59e-11)]_96_[-5(1.03e-09)]_4_[-5(8.25e-06)]_50_[+2(7.76e-10)]_29_[+4(1.53e-07)]_246_[-1(7.52e-05)]_206
SGD_Scer_YOR278W 1.13e-27 225_[+4(2.42e-09)]_60_[+5(1.32e-10)]_12_[+1(1.41e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_106_[-4(9.20e-05)]_24_[+3(1.41e-05)]_60
MIT_Spar_c261_21317 8.21e-29 197_[+5(7.95e-06)]_12_[+4(2.42e-09)]_60_[+5(8.38e-12)]_11_[+1(1.41e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_222
MIT_Smik_c492_20940 4.15e-27 234_[+4(2.42e-09)]_60_[+5(5.24e-10)]_12_[+1(1.41e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_196_[-5(9.37e-05)]
WashU_Skud_Contig1682.4 4.10e-26 231_[+4(2.42e-09)]_58_[+5(7.25e-09)]_12_[+1(1.14e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_221
WashU_Sbay_Contig635.57 7.73e-27 237_[+4(2.42e-09)]_60_[+5(5.24e-10)]_11_[+1(2.72e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_25_[+5(8.91e-05)]_126_[+2(8.80e-05)]_23
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************