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A test to ensure Bio::PrimarySeqI->trunc() doesn't use clone() for a Bio::Seq::RichSe...
[bioperl-live.git] / t / data / meme.dat
blob1aedbfc75a9cda1f69d3f0f455b0dfb4f7c9ceb5
1 ********************************************************************************
2 MEME - Motif discovery tool
3 ********************************************************************************
4 MEME version 3.0 (Release date: 2001/03/05 14:24:28)
5
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.
8
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 ********************************************************************************
13
14
15 ********************************************************************************
16 REFERENCE
17 ********************************************************************************
18 If you use this program in your research, please cite:
19
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 ********************************************************************************
26
27
28 ********************************************************************************
29 TRAINING SET
30 ********************************************************************************
31 DATAFILE= D10Mit194.set.genbank.fasta.nref
32 ALPHABET= ACGT
33 Sequence name Weight Length Sequence name Weight Length
34 ------------- ------ ------ ------------- ------ ------
35 20218 1.0000 2000 10657 1.0000 2000
36 83796 1.0000 2000 6603 1.0000 2000
37 ********************************************************************************
38
39 ********************************************************************************
40 COMMAND LINE SUMMARY
41 ********************************************************************************
42 This information can also be useful in the event you wish to report a
43 problem with the MEME software.
44
45 command: meme D10Mit194.set.genbank.fasta.nref -dna -print_fasta -nmotifs 3 -maxw 25
46
47 model: mod= zoops nmotifs= 3 evt= inf
48 object function= E-value of product of p-values
49 width: minw= 8 maxw= 25 minic= 0.00
50 width: wg= 11 ws= 1 endgaps= yes
51 nsites: minsites= 2 maxsites= 4 wnsites= 0.8
52 theta: prob= 1 spmap= uni spfuzz= 0.5
53 em: prior= dirichlet b= 0.01 maxiter= 50
54 distance= 1e-05
55 data: n= 8000 N= 4
56 strands: +
57 sample: seed= 0 seqfrac= 1
58 Letter frequencies in dataset:
59 A 0.255 C 0.236 G 0.252 T 0.257
60 Background letter frequencies (from dataset with add-one prior applied):
61 A 0.255 C 0.236 G 0.252 T 0.257
62 ********************************************************************************
63
64
65 ********************************************************************************
66 MOTIF 1 width = 25 sites = 4 llr = 106 E-value = 1.2e-002
67 ********************************************************************************
68 --------------------------------------------------------------------------------
69 Motif 1 Description
70 --------------------------------------------------------------------------------
71 Simplified A :8:88aaa:53a8:::3:a::3::3
72 pos.-specific C a3::3:::::3:::5a8a:8a5aa8
73 probability G ::8:::::3:5::::::::3:::::
74 matrix T ::33::::85::3a5::::::3:::
75
76 bits 2.1 * * * * **
77 1.9 * *** * * * ** * **
78 1.7 * *** * * * ** * **
79 1.5 * *** * * * ** * **
80 Information 1.2 ********* *** ****** ***
81 content 1.0 ********** ********** ***
82 (38.1 bits) 0.8 ********** ********** ***
83 0.6 ********** **************
84 0.4 *************************
85 0.2 *************************
86 0.0 -------------------------
87
88 Multilevel CAGAAAAATAGAATCCCCACCCCCC
89 consensus CTTC GTA T T A G A A
90 sequence C T
91
92 --------------------------------------------------------------------------------
93
94 --------------------------------------------------------------------------------
95 Motif 1 sites sorted by position p-value
96 --------------------------------------------------------------------------------
97 Sequence name Start P-value Site
98 ------------- ----- --------- -------------------------
99 6603 1311 2.59e-15 GGCGCATTGA CAGAAAAATTGAATTCCCACCCCCC AATGAGGAGG
100 83796 1284 2.59e-15 GGAGGATTGA CAGAAAAATTGAATTCCCACCCCCC AACGAGGAGG
101 20218 938 6.34e-12 TTTTTGGTAA CCTTAAAATAAAATCCCCACCACCA CTTTTAAAAA
102 10657 1685 8.70e-12 GGCCCGCGCG CAGACAAAGACATTCCACAGCTCCC GCCCCCTCCA
103 --------------------------------------------------------------------------------
104
105 --------------------------------------------------------------------------------
106 Motif 1 block diagrams
107 --------------------------------------------------------------------------------
108 SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
109 ------------- ---------------- -------------
110 6603 2.6e-15 1310_[1]_665
111 83796 2.6e-15 1283_[1]_692
112 20218 6.3e-12 937_[1]_1038
113 10657 8.7e-12 1684_[1]_291
114 --------------------------------------------------------------------------------
115
116 --------------------------------------------------------------------------------
117 Motif 1 in FASTA format
118 --------------------------------------------------------------------------------
119 >6603 pos 1311
120 CAGAAAAATTGAATTCCCACCCCCC
121 >83796 pos 1284
122 CAGAAAAATTGAATTCCCACCCCCC
123 >20218 pos 938
124 CCTTAAAATAAAATCCCCACCACCA
125 >10657 pos 1685
126 CAGACAAAGACATTCCACAGCTCCC
127 --------------------------------------------------------------------------------
128
129 --------------------------------------------------------------------------------
130 Motif 1 position-specific scoring matrix
131 --------------------------------------------------------------------------------
132 log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 11.6849 E= 1.2e-002
133 -865 208 -865 -865
134 156 8 -865 -865
135 -865 -865 157 -4
136 156 -865 -865 -4
137 156 8 -865 -865
138 197 -865 -865 -865
139 197 -865 -865 -865
140 197 -865 -865 -865
141 -865 -865 -1 154
142 97 -865 -865 96
143 -3 8 99 -865
144 197 -865 -865 -865
145 156 -865 -865 -4
146 -865 -865 -865 196
147 -865 108 -865 96
148 -865 208 -865 -865
149 -3 166 -865 -865
150 -865 208 -865 -865
151 197 -865 -865 -865
152 -865 166 -1 -865
153 -865 208 -865 -865
154 -3 108 -865 -4
155 -865 208 -865 -865
156 -865 208 -865 -865
157 -3 166 -865 -865
158 --------------------------------------------------------------------------------
159
160 --------------------------------------------------------------------------------
161 Motif 1 position-specific probability matrix
162 --------------------------------------------------------------------------------
163 letter-probability matrix: alength= 4 w= 25 n= 7904 E= 1.2e-002
164 0.000635 0.998096 0.000629 0.000640
165 0.748765 0.249966 0.000629 0.000640
166 0.000635 0.000589 0.748759 0.250017
167 0.748765 0.000589 0.000629 0.250017
168 0.748765 0.249966 0.000629 0.000640
169 0.998141 0.000589 0.000629 0.000640
170 0.998141 0.000589 0.000629 0.000640
171 0.998141 0.000589 0.000629 0.000640
172 0.000635 0.000589 0.250006 0.748770
173 0.499388 0.000589 0.000629 0.499393
174 0.250012 0.249966 0.499382 0.000640
175 0.998141 0.000589 0.000629 0.000640
176 0.748765 0.000589 0.000629 0.250017
177 0.000635 0.000589 0.000629 0.998147
178 0.000635 0.499343 0.000629 0.499393
179 0.000635 0.998096 0.000629 0.000640
180 0.250012 0.748719 0.000629 0.000640
181 0.000635 0.998096 0.000629 0.000640
182 0.998141 0.000589 0.000629 0.000640
183 0.000635 0.748719 0.250006 0.000640
184 0.000635 0.998096 0.000629 0.000640
185 0.250012 0.499343 0.000629 0.250017
186 0.000635 0.998096 0.000629 0.000640
187 0.000635 0.998096 0.000629 0.000640
188 0.250012 0.748719 0.000629 0.000640
189 --------------------------------------------------------------------------------
190
191
192
193
194
195 Time 38.44 secs.
196
197 ********************************************************************************
198
199
200 ********************************************************************************
201 MOTIF 2 width = 25 sites = 4 llr = 101 E-value = 4.5e-001
202 ********************************************************************************
203 --------------------------------------------------------------------------------
204 Motif 2 Description
205 --------------------------------------------------------------------------------
206 Simplified A ::::a::383:5:3:::a33:83:a
207 pos.-specific C a3a8:3a33:a::5::8::::383:
208 probability G ::::::::::::::::3:38a::8:
209 matrix T :8:3:8:5:8:5a3aa::5::::::
210
211 bits 2.1 * * * * *
212 1.9 * * * * * * ** * * *
213 1.7 * * * * * * ** * * *
214 1.5 * * * * * * ** * * *
215 Information 1.2 ******* *** * **** ******
216 content 1.0 ******* ***** **** ******
217 (36.6 bits) 0.8 ******* ***** **** ******
218 0.6 ******* ********** ******
219 0.4 *************************
220 0.2 *************************
221 0.0 -------------------------
222
223 Multilevel CTCCATCTATCATCTTCATGGACGA
224 consensus C T C ACA T A G AA CAC
225 sequence C T G
226
227 --------------------------------------------------------------------------------
228
229 --------------------------------------------------------------------------------
230 Motif 2 sites sorted by position p-value
231 --------------------------------------------------------------------------------
232 Sequence name Start P-value Site
233 ------------- ----- --------- -------------------------
234 6603 1000 1.62e-15 CGGGAACATG CTCCATCTATCATCTTCATGGACGA AATCGACTCC
235 83796 978 4.69e-15 CGAGAACATG CTCCATCCATCATCTTCATGGACGA GATTGACTCT
236 20218 1545 1.69e-11 TAGCTTCTCT CCCCATCAATCTTATTCAGAGCCCA CCCCTCCCCC
237 10657 1075 3.40e-11 AGGATCTGGT CTCTACCTCACTTTTTGAAGGAAGA AACACTTAAT
238 --------------------------------------------------------------------------------
239
240 --------------------------------------------------------------------------------
241 Motif 2 block diagrams
242 --------------------------------------------------------------------------------
243 SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
244 ------------- ---------------- -------------
245 6603 1.6e-15 999_[2]_976
246 83796 4.7e-15 977_[2]_998
247 20218 1.7e-11 1544_[2]_431
248 10657 3.4e-11 1074_[2]_901
249 --------------------------------------------------------------------------------
250
251 --------------------------------------------------------------------------------
252 Motif 2 in FASTA format
253 --------------------------------------------------------------------------------
254 >6603 pos 1000
255 CTCCATCTATCATCTTCATGGACGA
256 >83796 pos 978
257 CTCCATCCATCATCTTCATGGACGA
258 >20218 pos 1545
259 CCCCATCAATCTTATTCAGAGCCCA
260 >10657 pos 1075
261 CTCTACCTCACTTTTTGAAGGAAGA
262 --------------------------------------------------------------------------------
263
264 --------------------------------------------------------------------------------
265 Motif 2 position-specific scoring matrix
266 --------------------------------------------------------------------------------
267 log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 10.9476 E= 4.5e-001
268 -865 208 -865 -865
269 -865 8 -865 154
270 -865 208 -865 -865
271 -865 166 -865 -4
272 197 -865 -865 -865
273 -865 8 -865 154
274 -865 208 -865 -865
275 -3 8 -865 96
276 156 8 -865 -865
277 -3 -865 -865 154
278 -865 208 -865 -865
279 97 -865 -865 96
280 -865 -865 -865 196
281 -3 108 -865 -4
282 -865 -865 -865 196
283 -865 -865 -865 196
284 -865 166 -1 -865
285 197 -865 -865 -865
286 -3 -865 -1 96
287 -3 -865 157 -865
288 -865 -865 198 -865
289 156 8 -865 -865
290 -3 166 -865 -865
291 -865 8 157 -865
292 197 -865 -865 -865
293 --------------------------------------------------------------------------------
294
295 --------------------------------------------------------------------------------
296 Motif 2 position-specific probability matrix
297 --------------------------------------------------------------------------------
298 letter-probability matrix: alength= 4 w= 25 n= 7904 E= 4.5e-001
299 0.000635 0.998096 0.000629 0.000640
300 0.000635 0.249966 0.000629 0.748770
301 0.000635 0.998096 0.000629 0.000640
302 0.000635 0.748719 0.000629 0.250017
303 0.998141 0.000589 0.000629 0.000640
304 0.000635 0.249966 0.000629 0.748770
305 0.000635 0.998096 0.000629 0.000640
306 0.250012 0.249966 0.000629 0.499393
307 0.748765 0.249966 0.000629 0.000640
308 0.250012 0.000589 0.000629 0.748770
309 0.000635 0.998096 0.000629 0.000640
310 0.499388 0.000589 0.000629 0.499393
311 0.000635 0.000589 0.000629 0.998147
312 0.250012 0.499343 0.000629 0.250017
313 0.000635 0.000589 0.000629 0.998147
314 0.000635 0.000589 0.000629 0.998147
315 0.000635 0.748719 0.250006 0.000640
316 0.998141 0.000589 0.000629 0.000640
317 0.250012 0.000589 0.250006 0.499393
318 0.250012 0.000589 0.748759 0.000640
319 0.000635 0.000589 0.998135 0.000640
320 0.748765 0.249966 0.000629 0.000640
321 0.250012 0.748719 0.000629 0.000640
322 0.000635 0.249966 0.748759 0.000640
323 0.998141 0.000589 0.000629 0.000640
324 --------------------------------------------------------------------------------
325
326
327
328
329
330 Time 78.29 secs.
331
332 ********************************************************************************
333
334
335 ********************************************************************************
336 MOTIF 3 width = 21 sites = 4 llr = 88 E-value = 4.8e-001
337 ********************************************************************************
338 --------------------------------------------------------------------------------
339 Motif 3 Description
340 --------------------------------------------------------------------------------
341 Simplified A :::58:::::3::::33::::
342 pos.-specific C 8:833::8:8:a:8a8:a5a8
343 probability G 3::::::3:::::3:::::::
344 matrix T :a33:aa:a38:a:::8:5:3
345
346 bits 2.1 * * * *
347 1.9 * ** * ** * * *
348 1.7 * ** * ** * * *
349 1.5 * ** * ** * * *
350 Information 1.2 *** ************** **
351 content 1.0 *** *****************
352 (31.8 bits) 0.8 *** *****************
353 0.6 *** *****************
354 0.4 *********************
355 0.2 *********************
356 0.0 ---------------------
357
358 Multilevel CTCAATTCTCTCTCCCTCCCC
359 consensus G TCC G TA G AA T T
360 sequence T
361
362 --------------------------------------------------------------------------------
363
364 --------------------------------------------------------------------------------
365 Motif 3 sites sorted by position p-value
366 --------------------------------------------------------------------------------
367 Sequence name Start P-value Site
368 ------------- ----- --------- ---------------------
369 10657 1511 1.45e-13 CCCAGGCGGT CTCAATTCTCTCTCCCTCCCC TTTCCGTGAC
370 83796 1801 7.40e-12 TGTATATGCA CTCTCTTCTCTCTCCCTCTCC AGGTCATGCA
371 6603 1811 1.22e-10 GTAACTTAAT GTTCATTCTCTCTCCCACCCC TAGGTCATGC
372 20218 606 7.57e-10 CCCAGGCCAG CTCAATTGTTACTGCATCTCT AGGATTGGAA
373 --------------------------------------------------------------------------------
374
375 --------------------------------------------------------------------------------
376 Motif 3 block diagrams
377 --------------------------------------------------------------------------------
378 SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
379 ------------- ---------------- -------------
380 10657 1.5e-13 1510_[3]_469
381 83796 7.4e-12 1800_[3]_179
382 6603 1.2e-10 1810_[3]_169
383 20218 7.6e-10 605_[3]_1374
384 --------------------------------------------------------------------------------
385
386 --------------------------------------------------------------------------------
387 Motif 3 in FASTA format
388 --------------------------------------------------------------------------------
389 >10657 pos 1511
390 CTCAATTCTCTCTCCCTCCCC
391 >83796 pos 1801
392 CTCTCTTCTCTCTCCCTCTCC
393 >6603 pos 1811
394 GTTCATTCTCTCTCCCACCCC
395 >20218 pos 606
396 CTCAATTGTTACTGCATCTCT
397 --------------------------------------------------------------------------------
398
399 --------------------------------------------------------------------------------
400 Motif 3 position-specific scoring matrix
401 --------------------------------------------------------------------------------
402 log-odds matrix: alength= 4 w= 21 n= 7920 bayes= 10.9506 E= 4.8e-001
403 -865 166 -1 -865
404 -865 -865 -865 196
405 -865 166 -865 -4
406 97 8 -865 -4
407 156 8 -865 -865
408 -865 -865 -865 196
409 -865 -865 -865 196
410 -865 166 -1 -865
411 -865 -865 -865 196
412 -865 166 -865 -4
413 -3 -865 -865 154
414 -865 208 -865 -865
415 -865 -865 -865 196
416 -865 166 -1 -865
417 -865 208 -865 -865
418 -3 166 -865 -865
419 -3 -865 -865 154
420 -865 208 -865 -865
421 -865 108 -865 96
422 -865 208 -865 -865
423 -865 166 -865 -4
424 --------------------------------------------------------------------------------
425
426 --------------------------------------------------------------------------------
427 Motif 3 position-specific probability matrix
428 --------------------------------------------------------------------------------
429 letter-probability matrix: alength= 4 w= 21 n= 7920 E= 4.8e-001
430 0.000635 0.748719 0.250006 0.000640
431 0.000635 0.000589 0.000629 0.998147
432 0.000635 0.748719 0.000629 0.250017
433 0.499388 0.249966 0.000629 0.250017
434 0.748765 0.249966 0.000629 0.000640
435 0.000635 0.000589 0.000629 0.998147
436 0.000635 0.000589 0.000629 0.998147
437 0.000635 0.748719 0.250006 0.000640
438 0.000635 0.000589 0.000629 0.998147
439 0.000635 0.748719 0.000629 0.250017
440 0.250012 0.000589 0.000629 0.748770
441 0.000635 0.998096 0.000629 0.000640
442 0.000635 0.000589 0.000629 0.998147
443 0.000635 0.748719 0.250006 0.000640
444 0.000635 0.998096 0.000629 0.000640
445 0.250012 0.748719 0.000629 0.000640
446 0.250012 0.000589 0.000629 0.748770
447 0.000635 0.998096 0.000629 0.000640
448 0.000635 0.499343 0.000629 0.499393
449 0.000635 0.998096 0.000629 0.000640
450 0.000635 0.748719 0.000629 0.250017
451 --------------------------------------------------------------------------------
452
453
454
455
456
457 Time 117.82 secs.
458
459 ********************************************************************************
460
461
462 ********************************************************************************
463 SUMMARY OF MOTIFS
464 ********************************************************************************
465
466 --------------------------------------------------------------------------------
467 Combined block diagrams: non-overlapping sites with p-value < 0.0001
468 --------------------------------------------------------------------------------
469 SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
470 ------------- ---------------- -------------
471 20218 7.77e-19 605_[3(7.57e-10)]_311_[1(6.34e-12)]_582_[2(1.69e-11)]_431
472 10657 5.46e-22 1_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_7_[1(6.00e-08)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_5_[1(1.18e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_4_[1(1.29e-07)]_332_[2(3.40e-11)]_383_[3(7.75e-07)]_7_[3(1.45e-13)]_56_[3(3.47e-05)]_76_[1(8.70e-12)]_291
473 83796 1.73e-27 977_[2(4.69e-15)]_281_[1(2.59e-15)]_492_[3(7.40e-12)]_179
474 6603 9.32e-27 597_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_327_[2(1.62e-15)]_286_[1(2.59e-15)]_475_[3(1.22e-10)]_169
475 --------------------------------------------------------------------------------
476
477 ********************************************************************************
478
479
480 ********************************************************************************
481 Stopped because nmotifs = 3 reached.
482 ********************************************************************************
483
484 CPU: hydra-1.lsd.ornl.gov
485
486 ********************************************************************************
BioPerl core