| blob | cd5c24d180fc5ff5fe6f648aedf8ae215a0ae5e8 |
1 ********************************************************************************
2 MEME - Motif discovery tool
3 ********************************************************************************
4 MEME version 3.0 (Release date: 2002/04/02 00:11:59)
6 For further information on how to interpret these results or to get
7 a copy of the MEME software please access http://meme.sdsc.edu.
9 This file may be used as input to the MAST algorithm for searching
10 sequence databases for matches to groups of motifs. MAST is available
11 for interactive use and downloading at http://meme.sdsc.edu.
12 ********************************************************************************
15 ********************************************************************************
16 REFERENCE
17 ********************************************************************************
18 If you use this program in your research, please cite:
20 Timothy L. Bailey and Charles Elkan,
21 "Fitting a mixture model by expectation maximization to discover
22 motifs in biopolymers", Proceedings of the Second International
23 Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
24 AAAI Press, Menlo Park, California, 1994.
25 ********************************************************************************
28 ********************************************************************************
29 TRAINING SET
30 ********************************************************************************
31 DATAFILE= test.fasta
32 ALPHABET= ACGT
33 Sequence name Weight Length Sequence name Weight Length
34 ------------- ------ ------ ------------- ------ ------
35 68723 1.0000 2000 16939 1.0000 2001
36 20754 1.0000 2001 6707 1.0000 2000
37 20755 1.0000 2000 6700 1.0000 2002
38 20760 1.0000 2000 20761 1.0000 2000
39 20762 1.0000 2000
40 ********************************************************************************
42 ********************************************************************************
43 COMMAND LINE SUMMARY
44 ********************************************************************************
45 This information can also be useful in the event you wish to report a
46 problem with the MEME software.
48 command: meme test.fasta -dna -nostatus -nmotifs 2 -minsites 8 -maxw 20 -revcomp
50 model: mod= zoops nmotifs= 2 evt= inf
51 object function= E-value of product of p-values
52 width: minw= 8 maxw= 20 minic= 0.00
53 width: wg= 11 ws= 1 endgaps= yes
54 nsites: minsites= 8 maxsites= 9 wnsites= 0.8
55 theta: prob= 1 spmap= uni spfuzz= 0.5
56 em: prior= dirichlet b= 0.01 maxiter= 50
57 distance= 1e-05
58 data: n= 18004 N= 9
59 strands: + -
60 sample: seed= 0 seqfrac= 1
61 Letter frequencies in dataset:
62 A 0.295 C 0.205 G 0.205 T 0.295
63 Background letter frequencies (from dataset with add-one prior applied):
64 A 0.295 C 0.205 G 0.205 T 0.295
65 ********************************************************************************
68 ********************************************************************************
69 MOTIF 1 width = 20 sites = 8 llr = 147 E-value = 1.3e-002
70 ********************************************************************************
71 --------------------------------------------------------------------------------
72 Motif 1 Description
73 --------------------------------------------------------------------------------
74 Simplified A ::a1::931:6:348:1::1
75 pos.-specific C aa:::8:11841:331:139
76 probability G :::9::::63::84::3:8:
77 matrix T ::::a3161::9:::969::
79 bits 2.3 **
80 2.1 **
81 1.8 *** *
82 1.6 ***** *
83 Information 1.4 ****** * ** * ***
84 content 1.1 ******* * ** ** ***
85 (26.5 bits) 0.9 ******* **** ** ***
86 0.7 ******* ***** ******
87 0.5 ********************
88 0.2 ********************
89 0.0 --------------------
91 Multilevel CCAGTCATGCATGAATTTGC
92 consensus T A GC AGC G C
93 sequence C
95 --------------------------------------------------------------------------------
97 --------------------------------------------------------------------------------
98 Motif 1 sites sorted by position p-value
99 --------------------------------------------------------------------------------
100 Sequence name Strand Start P-value Site
101 ------------- ------ ----- --------- --------------------
102 20761 + 1879 6.50e-13 TCTGATTAAG CCAGTCATGCATGGATTTGC ATTTTGGTTG
103 20760 + 1875 6.50e-13 CCCAGTCACG CCAGTCATGCATGGATTTGC ATTTTGATTG
104 6700 + 1100 2.27e-10 CCTGCTCATG CCAGTCATGGATAAATTTGC ATCTGGCTTA
105 20755 + 1478 5.08e-10 CCCTGTCAGG CCAGTTATGGATGAATGTGC ACTTAANNNN
106 6707 + 1431 6.11e-09 TCACACAGAT CCAGTCAATCCTGCCTGTCC ATCTCAATGA
107 20762 + 1878 1.89e-08 CCTGGTTAGG CCAGTTAAACACAGATTTGC ATTTTGGTTA
108 16939 - 914 2.01e-08 ACTTTTCCTT CCAATCATGCCTGCCCTTGA ACCCTATTGG
109 20754 + 1175 6.73e-08 GCTCACCTTG CCAGTCTCCCCTGAATACCC TACATGCCCT
110 --------------------------------------------------------------------------------
112 --------------------------------------------------------------------------------
113 Motif 1 block diagrams
114 --------------------------------------------------------------------------------
115 SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
116 ------------- ---------------- -------------
117 20761 6.5e-13 1878_[+1]_102
118 20760 6.5e-13 1874_[+1]_106
119 6700 2.3e-10 1099_[+1]_883
120 20755 5.1e-10 1477_[+1]_503
121 6707 6.1e-09 1430_[+1]_550
122 20762 1.9e-08 1877_[+1]_103
123 16939 2e-08 913_[-1]_1068
124 20754 6.7e-08 1174_[+1]_807
125 --------------------------------------------------------------------------------
127 --------------------------------------------------------------------------------
128 Motif 1 in BLOCKS format
129 --------------------------------------------------------------------------------
130 BL MOTIF 1 width=20 seqs=8
131 20761 ( 1879) CCAGTCATGCATGGATTTGC 1
132 20760 ( 1875) CCAGTCATGCATGGATTTGC 1
133 6700 ( 1100) CCAGTCATGGATAAATTTGC 1
134 20755 ( 1478) CCAGTTATGGATGAATGTGC 1
135 6707 ( 1431) CCAGTCAATCCTGCCTGTCC 1
136 20762 ( 1878) CCAGTTAAACACAGATTTGC 1
137 16939 ( 914) CCAATCATGCCTGCCCTTGA 1
138 20754 ( 1175) CCAGTCTCCCCTGAATACCC 1
139 //
141 --------------------------------------------------------------------------------
143 --------------------------------------------------------------------------------
144 Motif 1 position-specific scoring matrix
145 --------------------------------------------------------------------------------
146 log-odds matrix: alength= 4 w= 20 n= 17833 bayes= 11.1216 E= 1.3e-002
147 -965 229 -965 -965
148 -965 229 -965 -965
149 176 -965 -965 -965
150 -124 -965 210 -965
151 -965 -965 -965 176
152 -965 187 -965 -24
153 157 -965 -965 -124
154 -24 -71 -965 108
155 -124 -71 161 -124
156 -965 187 29 -965
157 108 87 -965 -965
158 -965 -71 -965 157
159 -24 -965 187 -965
160 34 29 87 -965
161 134 29 -965 -965
162 -965 -71 -965 157
163 -124 -965 29 108
164 -965 -71 -965 157
165 -965 29 187 -965
166 -124 210 -965 -965
167 --------------------------------------------------------------------------------
169 --------------------------------------------------------------------------------
170 Motif 1 position-specific probability matrix
171 --------------------------------------------------------------------------------
172 letter-probability matrix: alength= 4 w= 20 n= 17833 E= 1.3e-002
173 0.000369 0.999007 0.000255 0.000369
174 0.000369 0.999007 0.000255 0.000369
175 0.999120 0.000255 0.000255 0.000369
176 0.125213 0.000255 0.874163 0.000369
177 0.000369 0.000255 0.000255 0.999120
178 0.000369 0.749319 0.000255 0.250057
179 0.874276 0.000255 0.000255 0.125213
180 0.250057 0.125099 0.000255 0.624589
181 0.125213 0.125099 0.624475 0.125213
182 0.000369 0.749319 0.249943 0.000369
183 0.624589 0.374787 0.000255 0.000369
184 0.000369 0.125099 0.000255 0.874276
185 0.250057 0.000255 0.749319 0.000369
186 0.374901 0.249943 0.374787 0.000369
187 0.749432 0.249943 0.000255 0.000369
188 0.000369 0.125099 0.000255 0.874276
189 0.125213 0.000255 0.249943 0.624589
190 0.000369 0.125099 0.000255 0.874276
191 0.000369 0.249943 0.749319 0.000369
192 0.125213 0.874163 0.000255 0.000369
193 --------------------------------------------------------------------------------
199 Time 75.70 secs.
201 ********************************************************************************
204 ********************************************************************************
205 MOTIF 2 width = 15 sites = 8 llr = 117 E-value = 1.2e+003
206 ********************************************************************************
207 --------------------------------------------------------------------------------
208 Motif 2 Description
209 --------------------------------------------------------------------------------
210 Simplified A :1a39:::::18:::
211 pos.-specific C ::::1:::8a:::::
212 probability G 96:3::1:::::4::
213 matrix T 13:5:a9a3:936aa
215 bits 2.3 *
216 2.1 *
217 1.8 * * * * **
218 1.6 * * * * * **
219 Information 1.4 * * ****** **
220 content 1.1 * * ******* **
221 (21.0 bits) 0.9 * * ***********
222 0.7 *** ***********
223 0.5 ***************
224 0.2 ***************
225 0.0 ---------------
227 Multilevel GGATATTTCCTATTT
228 consensus T A T TG
229 sequence G
231 --------------------------------------------------------------------------------
233 --------------------------------------------------------------------------------
234 Motif 2 sites sorted by position p-value
235 --------------------------------------------------------------------------------
236 Sequence name Strand Start P-value Site
237 ------------- ------ ----- --------- ---------------
238 20762 + 1845 2.62e-09 TCCAGGAACA GGATATTTCCTATTT TTGAGAGTCC
239 6700 + 1068 2.62e-09 TTTCAGAACA GGATATTTCCTATTT TGAGTATCCT
240 20755 + 1445 2.84e-08 GCCAAGGGTG GGATATTTTCTATTT TGTAGAGTCC
241 20754 - 664 5.62e-08 TTTCTTAGAA GGAAATTTCCTTGTT CTCTTTCTAT
242 20761 + 670 1.06e-07 GAAGAAAAAG GAAGATTTCCTAGTT AACAATTCAA
243 68723 - 1925 5.26e-07 TTGCTTTCTT TGAGATGTCCTAGTT CACTCCTAAA
244 20760 - 651 5.56e-07 TTTAAACTTG GTAAATTTTCTTTTT CTTCACATTT
245 16939 - 1616 6.78e-07 TAGTTCAGTT GTATCTTTCCAATTT TGATGTTTGG
246 --------------------------------------------------------------------------------
248 --------------------------------------------------------------------------------
249 Motif 2 block diagrams
250 --------------------------------------------------------------------------------
251 SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
252 ------------- ---------------- -------------
253 20762 2.6e-09 1844_[+2]_141
254 6700 2.6e-09 1067_[+2]_920
255 20755 2.8e-08 1444_[+2]_541
256 20754 5.6e-08 663_[-2]_1323
257 20761 1.1e-07 669_[+2]_1316
258 68723 5.3e-07 1924_[-2]_61
259 20760 5.6e-07 650_[-2]_1335
260 16939 6.8e-07 1615_[-2]_371
261 --------------------------------------------------------------------------------
263 --------------------------------------------------------------------------------
264 Motif 2 in BLOCKS format
265 --------------------------------------------------------------------------------
266 BL MOTIF 2 width=15 seqs=8
267 20762 ( 1845) GGATATTTCCTATTT 1
268 6700 ( 1068) GGATATTTCCTATTT 1
269 20755 ( 1445) GGATATTTTCTATTT 1
270 20754 ( 664) GGAAATTTCCTTGTT 1
271 20761 ( 670) GAAGATTTCCTAGTT 1
272 68723 ( 1925) TGAGATGTCCTAGTT 1
273 20760 ( 651) GTAAATTTTCTTTTT 1
274 16939 ( 1616) GTATCTTTCCAATTT 1
275 //
277 --------------------------------------------------------------------------------
279 --------------------------------------------------------------------------------
280 Motif 2 position-specific scoring matrix
281 --------------------------------------------------------------------------------
282 log-odds matrix: alength= 4 w= 15 n= 17878 bayes= 11.1253 E= 1.2e+003
283 -965 -965 210 -124
284 -124 -965 161 -24
285 176 -965 -965 -965
286 -24 -965 29 76
287 157 -71 -965 -965
288 -965 -965 -965 176
289 -965 -965 -71 157
290 -965 -965 -965 176
291 -965 187 -965 -24
292 -965 229 -965 -965
293 -124 -965 -965 157
294 134 -965 -965 -24
295 -965 -965 87 108
296 -965 -965 -965 176
297 -965 -965 -965 176
298 --------------------------------------------------------------------------------
300 --------------------------------------------------------------------------------
301 Motif 2 position-specific probability matrix
302 --------------------------------------------------------------------------------
303 letter-probability matrix: alength= 4 w= 15 n= 17878 E= 1.2e+003
304 0.000369 0.000255 0.874163 0.125213
305 0.125213 0.000255 0.624475 0.250057
306 0.999120 0.000255 0.000255 0.000369
307 0.250057 0.000255 0.249943 0.499745
308 0.874276 0.125099 0.000255 0.000369
309 0.000369 0.000255 0.000255 0.999120
310 0.000369 0.000255 0.125099 0.874276
311 0.000369 0.000255 0.000255 0.999120
312 0.000369 0.749319 0.000255 0.250057
313 0.000369 0.999007 0.000255 0.000369
314 0.125213 0.000255 0.000255 0.874276
315 0.749432 0.000255 0.000255 0.250057
316 0.000369 0.000255 0.374787 0.624589
317 0.000369 0.000255 0.000255 0.999120
318 0.000369 0.000255 0.000255 0.999120
319 --------------------------------------------------------------------------------
325 Time 152.20 secs.
327 ********************************************************************************
330 ********************************************************************************
331 SUMMARY OF MOTIFS
332 ********************************************************************************
334 --------------------------------------------------------------------------------
335 Combined block diagrams: non-overlapping sites with p-value < 0.0001
336 --------------------------------------------------------------------------------
337 SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
338 ------------- ---------------- -------------
339 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
340 16939 3.50e-06 913_[-1(2.01e-08)]_682_[-2(6.78e-07)]_205_[+1(5.80e-05)]_146
341 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
342 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
343 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
344 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
345 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
346 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
347 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
348 --------------------------------------------------------------------------------
350 ********************************************************************************
353 ********************************************************************************
354 Stopped because nmotifs = 2 reached.
355 ********************************************************************************
357 CPU: crick
359 ********************************************************************************