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MEME - Motif discovery tool
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MEME version 3.0 (Release date: 2002/04/02 00:11:59)
For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.sdsc.edu.
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.sdsc.edu.
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REFERENCE
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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.
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TRAINING SET
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DATAFILE= test.fasta
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
68723 1.0000 2000 16939 1.0000 2001
20754 1.0000 2001 6707 1.0000 2000
20755 1.0000 2000 6700 1.0000 2002
20760 1.0000 2000 20761 1.0000 2000
20762 1.0000 2000
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COMMAND LINE SUMMARY
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This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme test.fasta -dna -nostatus -nmotifs 2 -minsites 8 -maxw 20 -revcomp
model: mod= zoops nmotifs= 2 evt= inf
object function= E-value of product of p-values
width: minw= 8 maxw= 20 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 8 maxsites= 9 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 18004 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.295 C 0.205 G 0.205 T 0.295
Background letter frequencies (from dataset with add-one prior applied):
A 0.295 C 0.205 G 0.205 T 0.295
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MOTIF 1 width = 20 sites = 8 llr = 147 E-value = 1.3e-002
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Motif 1 Description
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Simplified A ::a1::931:6:348:1::1
pos.-specific C aa:::8:11841:331:139
probability G :::9::::63::84::3:8:
matrix T ::::a3161::9:::969::
bits 2.3 **
2.1 **
1.8 *** *
1.6 ***** *
Information 1.4 ****** * ** * ***
content 1.1 ******* * ** ** ***
(26.5 bits) 0.9 ******* **** ** ***
0.7 ******* ***** ******
0.5 ********************
0.2 ********************
0.0 --------------------
Multilevel CCAGTCATGCATGAATTTGC
consensus T A GC AGC G C
sequence C
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Motif 1 sites sorted by position p-value
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Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
20761 + 1879 6.50e-13 TCTGATTAAG CCAGTCATGCATGGATTTGC ATTTTGGTTG
20760 + 1875 6.50e-13 CCCAGTCACG CCAGTCATGCATGGATTTGC ATTTTGATTG
6700 + 1100 2.27e-10 CCTGCTCATG CCAGTCATGGATAAATTTGC ATCTGGCTTA
20755 + 1478 5.08e-10 CCCTGTCAGG CCAGTTATGGATGAATGTGC ACTTAANNNN
6707 + 1431 6.11e-09 TCACACAGAT CCAGTCAATCCTGCCTGTCC ATCTCAATGA
20762 + 1878 1.89e-08 CCTGGTTAGG CCAGTTAAACACAGATTTGC ATTTTGGTTA
16939 - 914 2.01e-08 ACTTTTCCTT CCAATCATGCCTGCCCTTGA ACCCTATTGG
20754 + 1175 6.73e-08 GCTCACCTTG CCAGTCTCCCCTGAATACCC TACATGCCCT
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Motif 1 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
20761 6.5e-13 1878_[+1]_102
20760 6.5e-13 1874_[+1]_106
6700 2.3e-10 1099_[+1]_883
20755 5.1e-10 1477_[+1]_503
6707 6.1e-09 1430_[+1]_550
20762 1.9e-08 1877_[+1]_103
16939 2e-08 913_[-1]_1068
20754 6.7e-08 1174_[+1]_807
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Motif 1 in BLOCKS format
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BL MOTIF 1 width=20 seqs=8
20761 ( 1879) CCAGTCATGCATGGATTTGC 1
20760 ( 1875) CCAGTCATGCATGGATTTGC 1
6700 ( 1100) CCAGTCATGGATAAATTTGC 1
20755 ( 1478) CCAGTTATGGATGAATGTGC 1
6707 ( 1431) CCAGTCAATCCTGCCTGTCC 1
20762 ( 1878) CCAGTTAAACACAGATTTGC 1
16939 ( 914) CCAATCATGCCTGCCCTTGA 1
20754 ( 1175) CCAGTCTCCCCTGAATACCC 1
//
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Motif 1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 20 n= 17833 bayes= 11.1216 E= 1.3e-002
-965 229 -965 -965
-965 229 -965 -965
176 -965 -965 -965
-124 -965 210 -965
-965 -965 -965 176
-965 187 -965 -24
157 -965 -965 -124
-24 -71 -965 108
-124 -71 161 -124
-965 187 29 -965
108 87 -965 -965
-965 -71 -965 157
-24 -965 187 -965
34 29 87 -965
134 29 -965 -965
-965 -71 -965 157
-124 -965 29 108
-965 -71 -965 157
-965 29 187 -965
-124 210 -965 -965
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Motif 1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 20 n= 17833 E= 1.3e-002
0.000369 0.999007 0.000255 0.000369
0.000369 0.999007 0.000255 0.000369
0.999120 0.000255 0.000255 0.000369
0.125213 0.000255 0.874163 0.000369
0.000369 0.000255 0.000255 0.999120
0.000369 0.749319 0.000255 0.250057
0.874276 0.000255 0.000255 0.125213
0.250057 0.125099 0.000255 0.624589
0.125213 0.125099 0.624475 0.125213
0.000369 0.749319 0.249943 0.000369
0.624589 0.374787 0.000255 0.000369
0.000369 0.125099 0.000255 0.874276
0.250057 0.000255 0.749319 0.000369
0.374901 0.249943 0.374787 0.000369
0.749432 0.249943 0.000255 0.000369
0.000369 0.125099 0.000255 0.874276
0.125213 0.000255 0.249943 0.624589
0.000369 0.125099 0.000255 0.874276
0.000369 0.249943 0.749319 0.000369
0.125213 0.874163 0.000255 0.000369
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Time 75.70 secs.
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MOTIF 2 width = 15 sites = 8 llr = 117 E-value = 1.2e+003
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Motif 2 Description
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Simplified A :1a39:::::18:::
pos.-specific C ::::1:::8a:::::
probability G 96:3::1:::::4::
matrix T 13:5:a9a3:936aa
bits 2.3 *
2.1 *
1.8 * * * * **
1.6 * * * * * **
Information 1.4 * * ****** **
content 1.1 * * ******* **
(21.0 bits) 0.9 * * ***********
0.7 *** ***********
0.5 ***************
0.2 ***************
0.0 ---------------
Multilevel GGATATTTCCTATTT
consensus T A T TG
sequence G
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Motif 2 sites sorted by position p-value
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Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
20762 + 1845 2.62e-09 TCCAGGAACA GGATATTTCCTATTT TTGAGAGTCC
6700 + 1068 2.62e-09 TTTCAGAACA GGATATTTCCTATTT TGAGTATCCT
20755 + 1445 2.84e-08 GCCAAGGGTG GGATATTTTCTATTT TGTAGAGTCC
20754 - 664 5.62e-08 TTTCTTAGAA GGAAATTTCCTTGTT CTCTTTCTAT
20761 + 670 1.06e-07 GAAGAAAAAG GAAGATTTCCTAGTT AACAATTCAA
68723 - 1925 5.26e-07 TTGCTTTCTT TGAGATGTCCTAGTT CACTCCTAAA
20760 - 651 5.56e-07 TTTAAACTTG GTAAATTTTCTTTTT CTTCACATTT
16939 - 1616 6.78e-07 TAGTTCAGTT GTATCTTTCCAATTT TGATGTTTGG
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Motif 2 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
20762 2.6e-09 1844_[+2]_141
6700 2.6e-09 1067_[+2]_920
20755 2.8e-08 1444_[+2]_541
20754 5.6e-08 663_[-2]_1323
20761 1.1e-07 669_[+2]_1316
68723 5.3e-07 1924_[-2]_61
20760 5.6e-07 650_[-2]_1335
16939 6.8e-07 1615_[-2]_371
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Motif 2 in BLOCKS format
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BL MOTIF 2 width=15 seqs=8
20762 ( 1845) GGATATTTCCTATTT 1
6700 ( 1068) GGATATTTCCTATTT 1
20755 ( 1445) GGATATTTTCTATTT 1
20754 ( 664) GGAAATTTCCTTGTT 1
20761 ( 670) GAAGATTTCCTAGTT 1
68723 ( 1925) TGAGATGTCCTAGTT 1
20760 ( 651) GTAAATTTTCTTTTT 1
16939 ( 1616) GTATCTTTCCAATTT 1
//
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Motif 2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 15 n= 17878 bayes= 11.1253 E= 1.2e+003
-965 -965 210 -124
-124 -965 161 -24
176 -965 -965 -965
-24 -965 29 76
157 -71 -965 -965
-965 -965 -965 176
-965 -965 -71 157
-965 -965 -965 176
-965 187 -965 -24
-965 229 -965 -965
-124 -965 -965 157
134 -965 -965 -24
-965 -965 87 108
-965 -965 -965 176
-965 -965 -965 176
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Motif 2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 15 n= 17878 E= 1.2e+003
0.000369 0.000255 0.874163 0.125213
0.125213 0.000255 0.624475 0.250057
0.999120 0.000255 0.000255 0.000369
0.250057 0.000255 0.249943 0.499745
0.874276 0.125099 0.000255 0.000369
0.000369 0.000255 0.000255 0.999120
0.000369 0.000255 0.125099 0.874276
0.000369 0.000255 0.000255 0.999120
0.000369 0.749319 0.000255 0.250057
0.000369 0.999007 0.000255 0.000369
0.125213 0.000255 0.000255 0.874276
0.749432 0.000255 0.000255 0.250057
0.000369 0.000255 0.374787 0.624589
0.000369 0.000255 0.000255 0.999120
0.000369 0.000255 0.000255 0.999120
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Time 152.20 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
------------- ---------------- -------------
68723 2.83e-04 473_[-1(8.43e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_35_[-1(3.15e-06)]_[+1(1.38e-05)]_9_[-1(7.89e-05)]_63_[-1(2.97e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_26_[+2(4.37e-06)]_46_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_6_[-1(7.97e-06)]_24_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_1_[-2(5.92e-05)]_279_[-1(8.43e-06)]_[+1(1.38e-05)]_[+2(5.60e-05)]_157_[-2(5.26e-07)]_61
16939 3.50e-06 913_[-1(2.01e-08)]_682_[-2(6.78e-07)]_205_[+1(5.80e-05)]_146
20754 1.05e-06 39_[-2(1.78e-05)]_4_[+1(4.78e-06)]_564_[-2(7.42e-05)]_6_[-2(5.62e-08)]_146_[+2(3.98e-05)]_335_[+1(6.73e-08)]_93_[+1(5.54e-05)]_694
6707 2.26e-05 173_[+1(4.46e-05)]_655_[-2(5.60e-05)]_3_[+1(3.06e-06)]_12_[+1(4.78e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.93e-05)]_181_[-1(3.26e-05)]_251_[+1(6.11e-09)]_329_[+1(6.34e-05)]_201
20755 5.26e-09 160_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3_[+1(6.41e-06)]_219_[-1(4.80e-05)]_962_[+2(2.84e-08)]_18_[+1(5.08e-10)]_6_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_14_[+1(7.97e-06)]_83
6700 2.48e-10 48_[+1(7.97e-06)]_267_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_129_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3_[+1(4.41e-06)]_280_[+2(2.62e-09)]_17_[+1(2.27e-10)]_101_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+2(7.29e-05)]_[+1(6.41e-06)]_604_[-1(8.43e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3
20760 1.53e-10 259_[-1(6.20e-05)]_339_[-2(3.17e-05)]_17_[-2(5.56e-07)]_436_[-2(4.06e-05)]_7_[+1(2.95e-07)]_6_[-1(1.12e-05)]_705_[+1(6.50e-13)]_106
20761 3.10e-11 397_[-2(1.10e-06)]_257_[+2(1.06e-07)]_382_[-2(5.60e-05)]_[+2(7.29e-05)]_[-1(3.24e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_722_[+1(6.50e-13)]_102
20762 1.72e-08 134_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_92_[+2(9.22e-05)]_517_[+1(7.97e-06)]_7_[-1(4.78e-06)]_439_[+2(2.62e-09)]_18_[+1(1.89e-08)]_103
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Stopped because nmotifs = 2 reached.
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CPU: crick
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