1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
|
test_MEME
Testing MEME Scanner
noevent : ***************************************************************
noevent : MEME - Motif discovery tool
noevent : ***************************************************************
_version : MEME version 3.0 (Release date: 2004/08/18 09:07:01)
noevent :
noevent : For further information on how to interpret these results or to
noevent : a copy of the MEME software please access http://meme.sdsc.edu.
noevent :
noevent : This file may be used as input to the MAST algorithm for search
noevent : sequence databases for matches to groups of motifs. MAST is av
noevent : for interactive use and downloading at http://meme.sdsc.edu.
noevent : ***************************************************************
noevent :
noevent :
noevent : ***************************************************************
noevent : REFERENCE
noevent : ***************************************************************
noevent : If you use this program in your research, please cite:
noevent :
noevent : Timothy L. Bailey and Charles Elkan,
noevent : "Fitting a mixture model by expectation maximization to discove
noevent : motifs in biopolymers", Proceedings of the Second International
noevent : Conference on Intelligent Systems for Molecular Biology, pp. 28
noevent : AAAI Press, Menlo Park, California, 1994.
noevent : ***************************************************************
noevent :
noevent :
noevent : ***************************************************************
noevent : TRAINING SET
noevent : ***************************************************************
_datafile : DATAFILE= INO_up800.s
_alphabet : ALPHABET= ACGT
noevent : Sequence name Weight Length Sequence name
noevent : ------------- ------ ------ -------------
_sequence_name : CHO1 1.0000 800 CHO2
_sequence_name : FAS1 1.0000 800 FAS2
_sequence_name : ACC1 1.0000 800 INO1
_sequence_name : OPI3 1.0000 800
noevent : ***************************************************************
noevent :
noevent : ***************************************************************
noevent : COMMAND LINE SUMMARY
noevent : ***************************************************************
noevent : This information can also be useful in the event you wish to re
noevent : problem with the MEME software.
noevent :
_commandline : command: meme -mod oops -dna -revcomp -nmotifs 2 -bfile yeast.n
noevent :
noevent : model: mod= oops nmotifs= 2 evt=
noevent : object function= E-value of product of p-values
noevent : width: minw= 8 maxw= 50 minic=
noevent : width: wg= 11 ws= 1 endgaps=
noevent : nsites: minsites= 7 maxsites= 7 wnsites=
noevent : theta: prob= 1 spmap= uni spfuzz=
noevent : em: prior= dirichlet b= 0.01 maxiter=
noevent : distance= 1e-05
noevent : data: n= 5600 N= 7
noevent : strands: + -
noevent : sample: seed= 0 seqfrac= 1
noevent : Letter frequencies in dataset:
noevent : A 0.304 C 0.196 G 0.196 T 0.304
noevent : Background letter frequencies (from yeast.nc.6.freq):
noevent : A 0.324 C 0.176 G 0.176 T 0.324
noevent : ***************************************************************
noevent :
noevent :
noevent : ***************************************************************
_add_motif_with: MOTIF 1 width = 12 sites = 7 llr = 95 E-value = 2.0e
noevent : ***************************************************************
noevent : ---------------------------------------------------------------
noevent : Motif 1 Description
noevent : ---------------------------------------------------------------
noevent : Simplified A :::9:a::::3:
noevent : pos.-specific C ::a:9:11691a
noevent : probability G ::::1::94:4:
noevent : matrix T aa:1::9::11:
noevent :
noevent : bits 2.5 * *
noevent : 2.3 * *
noevent : 2.0 * * * *
noevent : 1.8 * * * * *
noevent : Information 1.5 *** ** *** *
noevent : content 1.3 *** ****** *
noevent : (19.5 bits) 1.0 ********** *
noevent : 0.8 ********** *
noevent : 0.5 ********** *
noevent : 0.3 ************
noevent : 0.0 ------------
noevent :
noevent : Multilevel TTCACATGCCGC
noevent : consensus G A
noevent : sequence
noevent :
noevent : ---------------------------------------------------------------
noevent :
noevent : ---------------------------------------------------------------
motif_name : Motif 1 sites sorted by position p-value
noevent : ---------------------------------------------------------------
noevent : Sequence name Strand Start P-value
noevent : ------------- ------ ----- --------- ---
add_instance : INO1 - 620 1.85e-08 GACAATACTT TTCA
add_instance : FAS1 + 95 1.85e-08 GGCCAAAAAC TTCA
add_instance : ACC1 + 83 1.52e-07 CGTTAAAATC TTCA
add_instance : CHO2 + 354 2.52e-07 TGCCACACTT TTCT
add_instance : CHO1 + 611 4.23e-07 ACTTTGAACG TTCA
add_instance : FAS2 + 567 9.43e-07 CTCCCGCGTT TTCA
add_instance : OPI3 + 340 3.32e-06 CCAAGCCTCC TTCA
noevent : ---------------------------------------------------------------
noevent :
noevent : ---------------------------------------------------------------
noevent : Motif 1 block diagrams
noevent : ---------------------------------------------------------------
noevent : SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
noevent : ------------- ---------------- -------------
noevent : INO1 1.8e-08 619_[-1]_169
noevent : FAS1 1.8e-08 94_[+1]_694
noevent : ACC1 1.5e-07 82_[+1]_706
noevent : CHO2 2.5e-07 353_[+1]_435
noevent : CHO1 4.2e-07 610_[+1]_178
noevent : FAS2 9.4e-07 566_[+1]_222
noevent : OPI3 3.3e-06 339_[+1]_449
noevent : ---------------------------------------------------------------
noevent :
noevent : ---------------------------------------------------------------
noevent : Motif 1 in BLOCKS format
noevent : ---------------------------------------------------------------
noevent : BL MOTIF 1 width=12 seqs=7
noevent : INO1 ( 620) TTCACATGCCGC 1
noevent : FAS1 ( 95) TTCACATGCCGC 1
noevent : ACC1 ( 83) TTCACATGGCCC 1
noevent : CHO2 ( 354) TTCTCATGCCGC 1
noevent : CHO1 ( 611) TTCACACGGCAC 1
noevent : FAS2 ( 567) TTCACATGCTAC 1
noevent : OPI3 ( 340) TTCAGATCGCTC 1
noevent : //
noevent :
noevent : ---------------------------------------------------------------
noevent :
noevent : ---------------------------------------------------------------
noevent : Motif 1 position-specific scoring matrix
noevent : ---------------------------------------------------------------
noevent : log-odds matrix: alength= 4 w= 12 n= 5523 bayes= 9.62205 E= 2.0
add_to_logodds : -945 -945 -945 162
add_to_logodds : -945 -945 -945 162
add_to_logodds : -945 251 -945 -945
add_to_logodds : 140 -945 -945 -118
add_to_logodds : -945 229 -30 -945
add_to_logodds : 162 -945 -945 -945
add_to_logodds : -945 -30 -945 140
add_to_logodds : -945 -30 229 -945
add_to_logodds : -945 170 129 -945
add_to_logodds : -945 229 -945 -118
add_to_logodds : -18 -30 129 -118
add_to_logodds : -945 251 -945 -945
noevent : ---------------------------------------------------------------
noevent :
noevent : ---------------------------------------------------------------
noevent : Motif 1 position-specific probability matrix
noevent : ---------------------------------------------------------------
noevent : letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 2.0e-0
add_to_pssm : 0.000000 0.000000 0.000000 1.000000
add_to_pssm : 0.000000 0.000000 0.000000 1.000000
add_to_pssm : 0.000000 1.000000 0.000000 0.000000
add_to_pssm : 0.857143 0.000000 0.000000 0.142857
add_to_pssm : 0.000000 0.857143 0.142857 0.000000
add_to_pssm : 1.000000 0.000000 0.000000 0.000000
add_to_pssm : 0.000000 0.142857 0.000000 0.857143
add_to_pssm : 0.000000 0.142857 0.857143 0.000000
add_to_pssm : 0.000000 0.571429 0.428571 0.000000
add_to_pssm : 0.000000 0.857143 0.000000 0.142857
add_to_pssm : 0.285714 0.142857 0.428571 0.142857
add_to_pssm : 0.000000 1.000000 0.000000 0.000000
noevent : ---------------------------------------------------------------
noevent :
noevent :
noevent :
noevent :
noevent :
noevent : Time 20.91 secs.
noevent :
noevent : ***************************************************************
noevent :
noevent :
noevent : ***************************************************************
_add_motif_with: MOTIF 2 width = 10 sites = 7 llr = 81 E-value = 1.1e
noevent : ***************************************************************
noevent : ---------------------------------------------------------------
noevent : Motif 2 Description
noevent : ---------------------------------------------------------------
noevent : Simplified A ::1:::9:6:
noevent : pos.-specific C :a:::a:911
noevent : probability G 3:1aa:1:19
noevent : matrix T 7:7::::11:
noevent :
noevent : bits 2.5 * ***
noevent : 2.3 * ***
noevent : 2.0 * *** *
noevent : 1.8 * *** * *
noevent : Information 1.5 * *** * *
noevent : content 1.3 * ***** *
noevent : (16.7 bits) 1.0 ** ***** *
noevent : 0.8 ** ***** *
noevent : 0.5 ******** *
noevent : 0.3 **********
noevent : 0.0 ----------
noevent :
noevent : Multilevel TCTGGCACAG
noevent : consensus G
noevent : sequence
noevent :
noevent : ---------------------------------------------------------------
noevent :
noevent : ---------------------------------------------------------------
motif_name : Motif 2 sites sorted by position p-value
noevent : ---------------------------------------------------------------
noevent : Sequence name Strand Start P-value
noevent : ------------- ------ ----- --------- ---
add_instance : OPI3 - 186 3.24e-07 GAAAACCAGA TCTG
add_instance : ACC1 + 232 3.24e-07 CCAGTCGTAT TCTG
add_instance : CHO1 - 559 3.24e-07 ATATTCAGTG TCTG
add_instance : INO1 - 283 5.29e-06 ACGGTCTACG GCGG
add_instance : FAS1 + 44 6.25e-06 TACACGAGGT GCAG
add_instance : FAS2 - 185 8.48e-06 TTCTTGCTTT TCTG
add_instance : CHO2 - 413 8.48e-06 TTTTGCCGTT TCTG
noevent : ---------------------------------------------------------------
noevent :
noevent : ---------------------------------------------------------------
noevent : Motif 2 block diagrams
noevent : ---------------------------------------------------------------
noevent : SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
noevent : ------------- ---------------- -------------
noevent : OPI3 3.2e-07 185_[-2]_605
noevent : ACC1 3.2e-07 231_[+2]_559
noevent : CHO1 3.2e-07 558_[-2]_232
noevent : INO1 5.3e-06 282_[-2]_508
noevent : FAS1 6.3e-06 43_[+2]_747
noevent : FAS2 8.5e-06 184_[-2]_606
noevent : CHO2 8.5e-06 412_[-2]_378
noevent : ---------------------------------------------------------------
noevent :
noevent : ---------------------------------------------------------------
noevent : Motif 2 in BLOCKS format
noevent : ---------------------------------------------------------------
noevent : BL MOTIF 2 width=10 seqs=7
noevent : OPI3 ( 186) TCTGGCACAG 1
noevent : ACC1 ( 232) TCTGGCACAG 1
noevent : CHO1 ( 559) TCTGGCACAG 1
noevent : INO1 ( 283) GCGGGCGCAG 1
noevent : FAS1 ( 44) GCAGGCACGG 1
noevent : FAS2 ( 185) TCTGGCACTC 1
noevent : CHO2 ( 413) TCTGGCATCG 1
noevent : //
noevent :
noevent : ---------------------------------------------------------------
noevent :
noevent : ---------------------------------------------------------------
noevent : Motif 2 position-specific scoring matrix
noevent : ---------------------------------------------------------------
noevent : log-odds matrix: alength= 4 w= 10 n= 5537 bayes= 9.62571 E= 1.1
add_to_logodds : -945 -945 70 114
add_to_logodds : -945 251 -945 -945
add_to_logodds : -118 -945 -30 114
add_to_logodds : -945 -945 251 -945
add_to_logodds : -945 -945 251 -945
add_to_logodds : -945 251 -945 -945
add_to_logodds : 140 -945 -30 -945
add_to_logodds : -945 229 -945 -118
add_to_logodds : 82 -30 -30 -118
add_to_logodds : -945 -30 229 -945
noevent : ---------------------------------------------------------------
noevent :
noevent : ---------------------------------------------------------------
noevent : Motif 2 position-specific probability matrix
noevent : ---------------------------------------------------------------
noevent : letter-probability matrix: alength= 4 w= 10 nsites= 7 E= 1.1e+0
add_to_pssm : 0.000000 0.000000 0.285714 0.714286
add_to_pssm : 0.000000 1.000000 0.000000 0.000000
add_to_pssm : 0.142857 0.000000 0.142857 0.714286
add_to_pssm : 0.000000 0.000000 1.000000 0.000000
add_to_pssm : 0.000000 0.000000 1.000000 0.000000
add_to_pssm : 0.000000 1.000000 0.000000 0.000000
add_to_pssm : 0.857143 0.000000 0.142857 0.000000
add_to_pssm : 0.000000 0.857143 0.000000 0.142857
add_to_pssm : 0.571429 0.142857 0.142857 0.142857
add_to_pssm : 0.000000 0.142857 0.857143 0.000000
noevent : ---------------------------------------------------------------
noevent :
noevent :
noevent :
noevent :
noevent :
noevent : Time 41.19 secs.
noevent :
noevent : ***************************************************************
noevent :
noevent :
noevent : ***************************************************************
Running tests on MEME parser
************************************************** TESTING meme.dna.oops.txt
************************************************** TESTING meme.protein.oops.txt
************************************************** TESTING meme.protein.tcm.txt
Testing MEME Scanner
noevent : ***************************************************************
noevent : MAST - Motif Alignment and Search Tool
noevent : ***************************************************************
_version : MAST version 3.0 (Release date: 2004/08/18 09:07:01)
noevent :
noevent : For further information on how to interpret these results or t
noevent : a copy of the MAST software please access http://meme.sdsc.edu
noevent : ***************************************************************
noevent :
noevent :
noevent : ***************************************************************
noevent : REFERENCE
noevent : ***************************************************************
noevent : If you use this program in your research, please cite:
noevent :
noevent : Timothy L. Bailey and Michael Gribskov,
noevent : "Combining evidence using p-values: application to sequence ho
noevent : searches", Bioinformatics, 14(48-54), 1998.
noevent : ***************************************************************
noevent :
noevent :
noevent : ***************************************************************
noevent : DATABASE AND MOTIFS
noevent : ***************************************************************
_database : DATABASE INO_up800.s (nucleotide)
noevent : Last updated on Mon Aug 16 21:19:59 2004
noevent : Database contains 7 sequences, 5600 residues
noevent :
noevent : Scores for positive and reverse complement strands are combine
noevent :
noevent : MOTIFS meme.INO_up800.oops.txt (nucleotide)
noevent : MOTIF WIDTH BEST POSSIBLE MATCH
noevent : ----- ----- -------------------
_add_motif : 1 12 TTCACATGCCGC
_add_motif : 2 10 TCTGGCACAG
noevent :
noevent : PAIRWISE MOTIF CORRELATIONS:
noevent : MOTIF 1
noevent : ----- -----
noevent : 2 0.32
noevent : No overly similar pairs (correlation > 0.60) found.
noevent :
noevent : Random model letter frequencies (from non-redundant database):
noevent : A 0.281 C 0.222 G 0.229 T 0.267
noevent : ***************************************************************
noevent :
noevent :
noevent : ***************************************************************
noevent : SECTION I: HIGH-SCORING SEQUENCES
noevent : ***************************************************************
noevent : - Each of the following 7 sequences has E-value less than 10.
noevent : - The E-value of a sequence is the expected number of sequence
noevent : in a random database of the same size that would match the m
noevent : well as the sequence does and is equal to the combined p-val
noevent : sequence times the number of sequences in the database.
noevent : - The combined p-value of a sequence measures the strength of
noevent : match of the sequence to all the motifs and is calculated by
noevent : o finding the score of the single best match of each motif
noevent : to the sequence (best matches may overlap),
noevent : o calculating the sequence p-value of each score,
noevent : o forming the product of the p-values,
noevent : o taking the p-value of the product.
noevent : - The sequence p-value of a score is defined as the
noevent : probability of a random sequence of the same length containi
noevent : some match with as good or better a score.
noevent : - The score for the match of a position in a sequence to a mot
noevent : is computed by by summing the appropriate entry from each co
noevent : the position-dependent scoring matrix that represents the mo
noevent : - Sequences shorter than one or more of the motifs are skipped
noevent : - The table is sorted by increasing E-value.
noevent : ***************************************************************
noevent :
noevent : SEQUENCE NAME DESCRIPTION
noevent : ------------- -----------
noevent : ACC1 sequence of the region up...
noevent : CHO1 sequence of the region up...
noevent : INO1 sequence of the region up...
noevent : FAS1 sequence of the region up...
noevent : OPI3 sequence of the region up...
noevent : CHO2 sequence of the region up...
noevent : FAS2 sequence of the region up...
noevent :
noevent : ***************************************************************
noevent :
noevent :
noevent :
noevent : ***************************************************************
noevent : SECTION II: MOTIF DIAGRAMS
noevent : ***************************************************************
noevent : - The ordering and spacing of all non-overlapping motif occurr
noevent : are shown for each high-scoring sequence listed in Section I
noevent : - A motif occurrence is defined as a position in the sequence
noevent : match to the motif has POSITION p-value less than 0.0001.
noevent : - The POSITION p-value of a match is the probability of
noevent : a single random subsequence of the length of the motif
noevent : scoring at least as well as the observed match.
noevent : - For each sequence, all motif occurrences are shown unless th
noevent : are overlaps. In that case, a motif occurrence is shown onl
noevent : p-value is less than the product of the p-values of the othe
noevent : (lower-numbered) motif occurrences that it overlaps.
noevent : - The table also shows the E-value of each sequence.
noevent : - Spacers and motif occurences are indicated by
noevent : o -d- `d' residues separate the end of the preceding mot
noevent : occurrence and the start of the following motif occurrenc
noevent : o [sn] occurrence of motif `n' with p-value less than 0.00
noevent : A minus sign indicates that the occurrence is on the
noevent : reverse complement strand.
noevent : ***************************************************************
noevent :
noevent : SEQUENCE NAME E-VALUE MOTIF DIAGRAM
noevent : ------------- -------- -------------
noevent : ACC1 6.1e-05 82_[+1]_137_[+2]_5
noevent : CHO1 0.00016 152_[+2]_396_[-2]_
noevent : [+1]_149
noevent : INO1 0.00019 282_[-2]_327_[-1]_
noevent : FAS1 0.00022 43_[+2]_41_[+1]_69
noevent : OPI3 0.00092 185_[-2]_144_[+1]_
noevent : CHO2 0.0029 353_[+1]_47_[-2]_3
noevent : FAS2 0.0093 184_[-2]_372_[+1]_
noevent :
noevent : ***************************************************************
noevent :
noevent :
noevent :
noevent : ***************************************************************
noevent : SECTION III: ANNOTATED SEQUENCES
noevent : ***************************************************************
noevent : - The positions and p-values of the non-overlapping motif occu
noevent : are shown above the actual sequence for each of the high-sco
noevent : sequences from Section I.
noevent : - A motif occurrence is defined as a position in the sequence
noevent : match to the motif has POSITION p-value less than 0.0001 as
noevent : defined in Section II.
noevent : - For each sequence, the first line specifies the name of the
noevent : - The second (and possibly more) lines give a description of t
noevent : sequence.
noevent : - Following the description line(s) is a line giving the lengt
noevent : combined p-value, and E-value of the sequence as defined in
noevent : - The next line reproduces the motif diagram from Section II.
noevent : - The entire sequence is printed on the following lines.
noevent : - Motif occurrences are indicated directly above their positio
noevent : sequence on lines showing
noevent : o the motif number of the occurrence (a minus sign indicate
noevent : the occurrence is on the reverse complement strand),
noevent : o the position p-value of the occurrence,
noevent : o the best possible match to the motif (or its reverse comp
noevent : o columns whose match to the motif has a positive score (in
noevent : by a plus sign).
noevent : ***************************************************************
noevent :
noevent :
*************** _parse_buffer
*************** _blank_buffer
_set_current_se: ACC1
noevent : sequence of the region upstream from YNR016C
noevent : LENGTH = 800 COMBINED P-VALUE = 8.78e-06 E-VALUE = 6.1e-05
_add_line_to_bu: DIAGRAM: 82_[+1]_137_[+2]_559
*************** _add_diagram_from_buffer
*************** _blank_buffer
noevent :
noevent :
*************** _collapse_buffer
_add_line_to_bu: [+1]
_add_line_to_bu: 3.1e-07
_add_line_to_bu: TTCACATGCCGC
_add_line_to_bu: ++++++++++ +
_add_line_to_bu: 76 TAAAATCTTCACATGGCCCGGCCGCGCGCGCGTTGTGCCAACAAGTCGCAGTCGAAAT
noevent :
*************** _collapse_buffer
_add_line_to_bu: [+2]
_add_line_to_bu: 7.4e-07
_add_line_to_bu: TCTGGCACAG
_add_line_to_bu: ++++++++++
_add_line_to_bu: 226 TCGTATTCTGGCACAGTATAGCCTAGCACAATCACTGTCACAATTGTTATCGGTTCTA
noevent :
*************** _collapse_buffer
noevent :
*************** _parse_buffer
*************** _blank_buffer
_set_current_se: CHO1
noevent : sequence of the region upstream from YER026C
noevent : LENGTH = 800 COMBINED P-VALUE = 2.30e-05 E-VALUE = 0.00016
_add_line_to_bu: DIAGRAM: 152_[+2]_396_[-2]_42_[+1]_17_[+1]_149
*************** _add_diagram_from_buffer
*************** _blank_buffer
noevent :
noevent :
*************** _collapse_buffer
_add_line_to_bu: [+2]
_add_line_to_bu: 3.9e-05
_add_line_to_bu: TCTGGCACAG
_add_line_to_bu: ++++++ +
_add_line_to_bu: 151 CGTCTGGCGCCCTTCCCATTCCGAACCATGTTATATTGAACCATCTGGCGACAAGCAG
noevent :
*************** _collapse_buffer
_add_line_to_bu: [-2]
_add_line_to_bu: 7.4e-07
_add_line_to_bu: CTGTGCCAGA
_add_line_to_bu: ++++++++++
_add_line_to_bu: 526 CAATCCCCACTCCTTCTCAATGTGTGCAGACTTCTGTGCCAGACACTGAATATATATC
noevent :
*************** _collapse_buffer
_add_line_to_bu: [+1] [+1]
_add_line_to_bu: 8.7e-07 2.2e-05
_add_line_to_bu: TTCACATGCCGC TTCACATGCCGC
_add_line_to_bu: ++++++ +++ + +++++++++ +
_add_line_to_bu: 601 ACTTTGAACGTTCACACGGCACCCTCACGCCTTTGAGCTTTCACATGGACCCATCTAA
noevent :
*************** _collapse_buffer
noevent :
*************** _parse_buffer
*************** _blank_buffer
_set_current_se: INO1
noevent : sequence of the region upstream from YJL153C
noevent : LENGTH = 800 COMBINED P-VALUE = 2.71e-05 E-VALUE = 0.00019
_add_line_to_bu: DIAGRAM: 282_[-2]_327_[-1]_55_[+1]_102
*************** _add_diagram_from_buffer
*************** _blank_buffer
noevent :
noevent :
*************** _collapse_buffer
_add_line_to_bu: [
_add_line_to_bu: 1
_add_line_to_bu: C
_add_line_to_bu: +
_add_line_to_bu: 226 ACGTTGTATATGAAACGAGTAGTGAACGTTCGTACGATCTTTCACGCAGACATGCGAC
noevent :
*************** _collapse_buffer
_add_line_to_bu: [-1]
_add_line_to_bu: 4.2e-08
_add_line_to_bu: GCGGCATGTGAA
_add_line_to_bu: ++++++++++++
_add_line_to_bu: 601 TGCGCTTCGGCGGCTAAATGCGGCATGTGAAAAGTATTGTCTATTTTATCTTCATCCT
noevent :
*************** _collapse_buffer
_add_line_to_bu: [+1]
_add_line_to_bu: 1.3e-05
_add_line_to_bu: TTCACATGCCGC
_add_line_to_bu: +++++++++ ++
_add_line_to_bu: 676 AACTTATTTAATTCACATGGAGCAGAGAAAGCGCACCTCTGCGTTGGCGGCAATGTTA
noevent :
*************** _collapse_buffer
noevent :
*************** _parse_buffer
*************** _blank_buffer
_set_current_se: FAS1
noevent : sequence of the region upstream from YKL182W
noevent : LENGTH = 800 COMBINED P-VALUE = 3.19e-05 E-VALUE = 0.00022
_add_line_to_bu: DIAGRAM: 43_[+2]_41_[+1]_694
*************** _add_diagram_from_buffer
*************** _blank_buffer
noevent :
_add_line_to_bu: [+2]
_add_line_to_bu: 2.2e-05
_add_line_to_bu: TCTGGCACAG
_add_line_to_bu: ++ +++++ +
_add_line_to_bu: 1 CCGGGTTATAGCAGCGTCTGCTCCGCATCACGATACACGAGGTGCAGGCACGGTTCAC
noevent :
*************** _collapse_buffer
_add_line_to_bu: [+1]
_add_line_to_bu: 4.2e-08
_add_line_to_bu: TTCACATGCCGC
_add_line_to_bu: ++++++++++++
_add_line_to_bu: 76 ACAAACGACGGCCAAAAACTTCACATGCCGCCCAGCCAAGCATAATTACGCAACAGCG
noevent :
*************** _collapse_buffer
noevent :
*************** _parse_buffer
*************** _blank_buffer
_set_current_se: OPI3
noevent : sequence of the region upstream from YJR073C
noevent : LENGTH = 800 COMBINED P-VALUE = 1.32e-04 E-VALUE = 0.00092
_add_line_to_bu: DIAGRAM: 185_[-2]_144_[+1]_449
*************** _add_diagram_from_buffer
*************** _blank_buffer
noevent :
noevent :
*************** _collapse_buffer
_add_line_to_bu: [-2]
_add_line_to_bu: 7.4e-07
_add_line_to_bu: CTGTGCCAGA
_add_line_to_bu: ++++++++++
_add_line_to_bu: 151 GTTAATCTGATCAACGCTACGCCGATGACAACGGTCTGTGCCAGATCTGGTTTTCCCC
noevent :
*************** _collapse_buffer
_add_line_to_bu: [+1]
_add_line_to_bu: 5.8e-06
_add_line_to_bu: TTCACATGCCGC
_add_line_to_bu: ++++ ++ ++ +
_add_line_to_bu: 301 AACTCCGTCAGGTCTTCCACGTGGAACTGCCAAGCCTCCTTCAGATCGCTCTTGTCGA
noevent :
*************** _collapse_buffer
noevent :
*************** _parse_buffer
*************** _blank_buffer
_set_current_se: CHO2
noevent : sequence of the region upstream from YGR157W
noevent : LENGTH = 800 COMBINED P-VALUE = 4.18e-04 E-VALUE = 0.0029
_add_line_to_bu: DIAGRAM: 353_[+1]_47_[-2]_378
*************** _add_diagram_from_buffer
*************** _blank_buffer
noevent :
noevent :
*************** _collapse_buffer
_add_line_to_bu: [+1]
_add_line_to_bu: 5.2e-
_add_line_to_bu: TTCAC
_add_line_to_bu: +++ +
_add_line_to_bu: 301 ATATATATTTTTGCCTTGGTTTAAATTGGTCAAGACAGTCAATTGCCACACTTTTCTC
noevent :
*************** _collapse_buffer
_add_line_to_bu: [-2]
_add_line_to_bu: 2.9e-05
_add_line_to_bu: CTGTGCCAGA
_add_line_to_bu: + +++++++
_add_line_to_bu: 376 CGCGAAGTTTTCCACACAAAACTGTGAAAATGAACGGCGATGCCAGAAACGGCAAAAC
noevent :
*************** _collapse_buffer
noevent :
*************** _parse_buffer
*************** _blank_buffer
_set_current_se: FAS2
noevent : sequence of the region upstream from YPL231W
noevent : LENGTH = 800 COMBINED P-VALUE = 1.33e-03 E-VALUE = 0.0093
_add_line_to_bu: DIAGRAM: 184_[-2]_372_[+1]_222
*************** _add_diagram_from_buffer
*************** _blank_buffer
noevent :
noevent :
*************** _collapse_buffer
_add_line_to_bu: [-2]
_add_line_to_bu: 2.9e-05
_add_line_to_bu: CTGTGCCAGA
_add_line_to_bu: ++++++++
_add_line_to_bu: 151 AACAGGGTGTCGGTCATACCGATAAAGCCGTCAAGAGTGCCAGAAAAGCAAGAAAGAA
noevent :
*************** _collapse_buffer
_add_line_to_bu: [+1]
_add_line_to_bu: 1.9e-06
_add_line_to_bu: TTCACATGCCGC
_add_line_to_bu: +++++++++ +
_add_line_to_bu: 526 GCTTAGCAAAATCCAACCATTTTTTTTTTATCTCCCGCGTTTTCACATGCTACCTCAT
noevent :
*************** _collapse_buffer
noevent : ***************************************************************
*************** _parse_buffer
*************** _blank_buffer
Running tests on MAST parser
************************************************** TESTING mast.dna.oops.txt
************************************************** TESTING mast.protein.oops.txt
************************************************** TESTING mast.protein.tcm.txt
|
