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
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
|
********************************************************************************
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= HEM2-HEM13.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SGD_Scer_YGL040C 1.0000 1000 MIT_Spar_c19_8512 1.0000 1000
MIT_Smik_c273_7756 1.0000 1000 MIT_Sbay_c77_8808 1.0000 1000
WashU_Skud_Contig2052.17 1.0000 1000 SGD_Scer_YDR044W 1.0000 1000
MIT_Spar_c130_3912 1.0000 1000 MIT_Sbay_c896_21290 1.0000 1000
WashU_Smik_Contig2283.3 1.0000 1000
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme HEM2-HEM13.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= 9 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= 9000 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.314 C 0.186 G 0.186 T 0.314
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 = 9 llr = 197 E-value = 9.2e-022
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A ::::::4:12a1:::::::8
pos.-specific C a144:a::1::::::66::1
probability G :66:a:6a28:::a8::1a1
matrix T :3:6::::6::9a:2449::
bits 2.5 * ** * * *
2.3 * ** * * *
2.0 * ** * * *
1.8 * ** * * *
Information 1.5 * * ** * ** *** *
content 1.3 * * ** * ** *** **
(31.6 bits) 1.0 * ****** **********
0.8 ******** ***********
0.5 ******** ***********
0.3 ********************
0.0 --------------------
Multilevel CGGTGCGGTGATTGGCCTGA
consensus TCC A GA TTT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2052.17 - 180 1.35e-13 AATCCCTGTT CGGTGCGGTGATTGGCCTGA GGCAAGCTGC
MIT_Smik_c273_7756 - 179 1.35e-13 AATCCTTATT CGGTGCGGTGATTGGCCTGA GGCAACATAC
MIT_Spar_c19_8512 - 181 1.35e-13 AATCCCTGTT CGGTGCGGTGATTGGCCTGA GGCAAGCTGC
SGD_Scer_YGL040C - 180 1.17e-12 AATCCCTGTT CGGTGCGGTGATTGGCTTGA GGCAAGCTTC
MIT_Sbay_c77_8808 - 181 2.88e-12 CATCTCCGGG CGGTGCGGTGATTGGCCTGC GGCAGGCTGC
WashU_Smik_Contig2283.3 + 542 2.66e-10 ACGTTGAAAA CTCCGCAGGGATTGGTTTGG AAAATTATAG
SGD_Scer_YDR044W + 540 1.12e-09 ACAGTAAAAA CTCCGCAGGAAATGGTTTGA AGAATCTTAA
MIT_Spar_c130_3912 + 534 1.20e-09 ACATTGAAAA CCCCGCAGCAATTGTTCTGA AGAATCTTAA
MIT_Sbay_c896_21290 + 542 1.43e-09 ACTTTTAAAA CTCCGCAGAGATTGTTTGGA GGGACCTTGA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 1.4e-13 179_[-1]_801
MIT_Smik_c273_7756 1.4e-13 178_[-1]_802
MIT_Spar_c19_8512 1.4e-13 180_[-1]_800
SGD_Scer_YGL040C 1.2e-12 179_[-1]_801
MIT_Sbay_c77_8808 2.9e-12 180_[-1]_800
WashU_Smik_Contig2283.3 2.7e-10 541_[+1]_439
SGD_Scer_YDR044W 1.1e-09 539_[+1]_441
MIT_Spar_c130_3912 1.2e-09 533_[+1]_447
MIT_Sbay_c896_21290 1.4e-09 541_[+1]_439
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2052.17 ( 180) CGGTGCGGTGATTGGCCTGA 1
MIT_Smik_c273_7756 ( 179) CGGTGCGGTGATTGGCCTGA 1
MIT_Spar_c19_8512 ( 181) CGGTGCGGTGATTGGCCTGA 1
SGD_Scer_YGL040C ( 180) CGGTGCGGTGATTGGCTTGA 1
MIT_Sbay_c77_8808 ( 181) CGGTGCGGTGATTGGCCTGC 1
WashU_Smik_Contig2283.3 ( 542) CTCCGCAGGGATTGGTTTGG 1
SGD_Scer_YDR044W ( 540) CTCCGCAGGAAATGGTTTGA 1
MIT_Spar_c130_3912 ( 534) CCCCGCAGCAATTGTTCTGA 1
MIT_Sbay_c896_21290 ( 542) CTCCGCAGAGATTGTTTGGA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 9.2e-022
-982 251 -982 -982
-982 -66 166 4
-982 134 166 -982
-982 134 -982 78
-982 -982 251 -982
-982 251 -982 -982
45 -982 166 -982
-982 -982 251 -982
-154 -66 34 78
-55 -982 215 -982
162 -982 -982 -982
-154 -982 -982 145
-982 -982 -982 162
-982 -982 251 -982
-982 -982 215 -55
-982 166 -982 45
-982 166 -982 45
-982 -982 -66 145
-982 -982 251 -982
126 -66 -66 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 9.2e-022
0.000000 1.000000 0.000000 0.000000
0.000000 0.111111 0.555556 0.333333
0.000000 0.444444 0.555556 0.000000
0.000000 0.444444 0.000000 0.555556
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.000000 0.000000 1.000000 0.000000
0.111111 0.111111 0.222222 0.555556
0.222222 0.000000 0.777778 0.000000
1.000000 0.000000 0.000000 0.000000
0.111111 0.000000 0.000000 0.888889
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.777778 0.222222
0.000000 0.555556 0.000000 0.444444
0.000000 0.555556 0.000000 0.444444
0.000000 0.000000 0.111111 0.888889
0.000000 0.000000 1.000000 0.000000
0.777778 0.111111 0.111111 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
C[GT][GC][TC]GC[GA]G[TG][GA]ATTG[GT][CT][CT]TGA
--------------------------------------------------------------------------------
Time 8.40 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 20 sites = 9 llr = 167 E-value = 2.0e-010
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A 4a:aa:a:43:19464a493
pos.-specific C ::a::::::1:::4:6:11:
probability G 6::::::a62491:4::::7
matrix T :::::a:::36::1:::4::
bits 2.5 * *
2.3 * *
2.0 * * *
1.8 * * *
Information 1.5 ******* * *
content 1.3 ******* ** * **
(26.8 bits) 1.0 ********* *** *** **
0.8 ********* *** *** **
0.5 ********* ******* **
0.3 ********* **********
0.0 --------------------
Multilevel GACAATAGGATGAAACAAAG
consensus A ATG CGA T A
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Skud_Contig2052.17 + 100 8.72e-11 AGAAATCATG AACAATAGGATGACGCATAG ACGTCACTAC
WashU_Smik_Contig2283.3 + 112 3.17e-10 TAACAGGTGA GACAATAGGTGGAAAAAAAG GAAAATATGT
MIT_Spar_c130_3912 + 116 6.61e-10 AACAAAGAAA GACAATAGGCGGAAAAAAAG GAAAATCCGT
SGD_Scer_YGL040C + 101 8.03e-10 GAAAATCAAA GACAATAGAGTGGCGCATAG ATGTTGCTAG
MIT_Spar_c19_8512 + 102 1.36e-09 AAAAAACAAG GACAATAGAATGACACATAA AGTTTGCTAG
SGD_Scer_YDR044W + 119 1.86e-09 AACAAAGAAA GACAATAGGTGGAAAAAAAA AGGAAAATCC
MIT_Sbay_c77_8808 + 105 3.82e-09 AACTAACATT AACAATAGAGTGATGCATAG ACGTCACTAG
MIT_Smik_c273_7756 + 102 5.03e-09 ATAAATCAGG AACAATAGAATGACGCACCG AGTTTGCTAG
MIT_Sbay_c896_21290 + 120 2.10e-08 ATTGGCAGCG AACAATAGGTGAAAAAAAAA AAGAAAATGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 8.7e-11 99_[+2]_881
WashU_Smik_Contig2283.3 3.2e-10 111_[+2]_869
MIT_Spar_c130_3912 6.6e-10 115_[+2]_865
SGD_Scer_YGL040C 8e-10 100_[+2]_880
MIT_Spar_c19_8512 1.4e-09 101_[+2]_879
SGD_Scer_YDR044W 1.9e-09 118_[+2]_862
MIT_Sbay_c77_8808 3.8e-09 104_[+2]_876
MIT_Smik_c273_7756 5e-09 101_[+2]_879
MIT_Sbay_c896_21290 2.1e-08 119_[+2]_861
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=20 seqs=9
WashU_Skud_Contig2052.17 ( 100) AACAATAGGATGACGCATAG 1
WashU_Smik_Contig2283.3 ( 112) GACAATAGGTGGAAAAAAAG 1
MIT_Spar_c130_3912 ( 116) GACAATAGGCGGAAAAAAAG 1
SGD_Scer_YGL040C ( 101) GACAATAGAGTGGCGCATAG 1
MIT_Spar_c19_8512 ( 102) GACAATAGAATGACACATAA 1
SGD_Scer_YDR044W ( 119) GACAATAGGTGGAAAAAAAA 1
MIT_Sbay_c77_8808 ( 105) AACAATAGAGTGATGCATAG 1
MIT_Smik_c273_7756 ( 102) AACAATAGAATGACGCACCG 1
MIT_Sbay_c896_21290 ( 120) AACAATAGGTGAAAAAAAAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 2.0e-010
45 -982 166 -982
162 -982 -982 -982
-982 251 -982 -982
162 -982 -982 -982
162 -982 -982 -982
-982 -982 -982 162
162 -982 -982 -982
-982 -982 251 -982
45 -982 166 -982
4 -66 34 4
-982 -982 134 78
-154 -982 234 -982
145 -982 -66 -982
45 134 -982 -154
78 -982 134 -982
45 166 -982 -982
162 -982 -982 -982
45 -66 -982 45
145 -66 -982 -982
4 -982 192 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.0e-010
0.444444 0.000000 0.555556 0.000000
1.000000 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 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.444444 0.000000 0.555556 0.000000
0.333333 0.111111 0.222222 0.333333
0.000000 0.000000 0.444444 0.555556
0.111111 0.000000 0.888889 0.000000
0.888889 0.000000 0.111111 0.000000
0.444444 0.444444 0.000000 0.111111
0.555556 0.000000 0.444444 0.000000
0.444444 0.555556 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.444444 0.111111 0.000000 0.444444
0.888889 0.111111 0.000000 0.000000
0.333333 0.000000 0.666667 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 regular expression
--------------------------------------------------------------------------------
[GA]ACAATAG[GA][ATG][TG]GA[AC][AG][CA]A[AT]A[GA]
--------------------------------------------------------------------------------
Time 16.42 secs.
********************************************************************************
********************************************************************************
MOTIF 3 width = 18 sites = 9 llr = 161 E-value = 2.9e-010
********************************************************************************
--------------------------------------------------------------------------------
Motif 3 Description
--------------------------------------------------------------------------------
Simplified A a97926:1a9:::8a:2:
pos.-specific C ::3::::6::::a::427
probability G ::::84a1:1aa:::34:
matrix T :1:1:::2:::::2:213
bits 2.5 * ***
2.3 * ***
2.0 * ***
1.8 * ***
Information 1.5 * * * * *** *
content 1.3 * * * ***** * *
(25.8 bits) 1.0 ******* ***** * *
0.8 ******* ******** *
0.5 ******************
0.3 ******************
0.0 ------------------
Multilevel AAAAGAGCAAGGCAACGC
consensus C AG T T GAT
sequence TC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ------------------
MIT_Spar_c130_3912 + 695 1.68e-11 GAGAAATATC AACAGGGCAAGGCAAGGC TATGCTCTTT
MIT_Sbay_c77_8808 - 144 1.90e-10 CCTGATTTAT AAAAGAGCAAGGCAACAC AATAAAAGGC
SGD_Scer_YDR044W + 703 6.56e-10 AAATATCAAC AAAAGGGCAAGGCTATGC CTTCTGGAAA
WashU_Smik_Contig2283.3 + 703 3.25e-09 GAAAAATATT AACAAGGGAAGGCAAGGC TATGTTCTAT
MIT_Spar_c19_8512 - 140 3.60e-09 CTTGATTTAT AAAAGAGTAAGGCAACCT AATAAATGCT
MIT_Sbay_c896_21290 + 701 6.28e-09 GGAAAATATC AACAAGGCAAGGCTATGC CTTTCGAAGA
MIT_Smik_c273_7756 - 833 1.56e-08 GTTTTCTACA AAATGAGCAGGGCAAGAC GAAATTTCCG
WashU_Skud_Contig2052.17 - 139 1.98e-08 CCCAATTTAT AAAAGAGAAAGGCAACTT ATATGAAGAG
SGD_Scer_YGL040C - 139 2.12e-08 CTTGATTTAT ATAAGAGTAAGGCAACCT AATAAATGCT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
MIT_Spar_c130_3912 1.7e-11 694_[+3]_288
MIT_Sbay_c77_8808 1.9e-10 143_[-3]_839
SGD_Scer_YDR044W 6.6e-10 702_[+3]_280
WashU_Smik_Contig2283.3 3.3e-09 702_[+3]_280
MIT_Spar_c19_8512 3.6e-09 139_[-3]_843
MIT_Sbay_c896_21290 6.3e-09 700_[+3]_282
MIT_Smik_c273_7756 1.6e-08 832_[-3]_150
WashU_Skud_Contig2052.17 2e-08 138_[-3]_844
SGD_Scer_YGL040C 2.1e-08 138_[-3]_844
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 3 width=18 seqs=9
MIT_Spar_c130_3912 ( 695) AACAGGGCAAGGCAAGGC 1
MIT_Sbay_c77_8808 ( 144) AAAAGAGCAAGGCAACAC 1
SGD_Scer_YDR044W ( 703) AAAAGGGCAAGGCTATGC 1
WashU_Smik_Contig2283.3 ( 703) AACAAGGGAAGGCAAGGC 1
MIT_Spar_c19_8512 ( 140) AAAAGAGTAAGGCAACCT 1
MIT_Sbay_c896_21290 ( 701) AACAAGGCAAGGCTATGC 1
MIT_Smik_c273_7756 ( 833) AAATGAGCAGGGCAAGAC 1
WashU_Skud_Contig2052.17 ( 139) AAAAGAGAAAGGCAACTT 1
SGD_Scer_YGL040C ( 139) ATAAGAGTAAGGCAACCT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 18 n= 8847 bayes= 9.93958 E= 2.9e-010
162 -982 -982 -982
145 -982 -982 -154
104 92 -982 -982
145 -982 -982 -154
-55 -982 215 -982
78 -982 134 -982
-982 -982 251 -982
-154 166 -66 -55
162 -982 -982 -982
145 -982 -66 -982
-982 -982 251 -982
-982 -982 251 -982
-982 251 -982 -982
126 -982 -982 -55
162 -982 -982 -982
-982 134 92 -55
-55 34 134 -154
-982 192 -982 4
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 18 nsites= 9 E= 2.9e-010
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.000000 0.111111
0.666667 0.333333 0.000000 0.000000
0.888889 0.000000 0.000000 0.111111
0.222222 0.000000 0.777778 0.000000
0.555556 0.000000 0.444444 0.000000
0.000000 0.000000 1.000000 0.000000
0.111111 0.555556 0.111111 0.222222
1.000000 0.000000 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.777778 0.000000 0.000000 0.222222
1.000000 0.000000 0.000000 0.000000
0.000000 0.444444 0.333333 0.222222
0.222222 0.222222 0.444444 0.111111
0.000000 0.666667 0.000000 0.333333
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 3 regular expression
--------------------------------------------------------------------------------
AA[AC]A[GA][AG]G[CT]AAGGC[AT]A[CGT][GAC][CT]
--------------------------------------------------------------------------------
Time 24.29 secs.
********************************************************************************
********************************************************************************
MOTIF 4 width = 15 sites = 9 llr = 139 E-value = 2.6e-006
********************************************************************************
--------------------------------------------------------------------------------
Motif 4 Description
--------------------------------------------------------------------------------
Simplified A :::::::2:8:::::
pos.-specific C 3:9:a:::318771:
probability G :9:::a::::1:34:
matrix T 711a::a87113:4a
bits 2.5 **
2.3 **
2.0 ** **
1.8 ** **
Information 1.5 ****** * * *
content 1.3 ****** *** *
(22.3 bits) 1.0 ******* * *** *
0.8 ***************
0.5 ***************
0.3 ***************
0.0 ---------------
Multilevel TGCTCGTTTACCCGT
consensus C AC TGT
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
WashU_Skud_Contig2052.17 + 209 3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT TGCGTTCAAA
MIT_Smik_c273_7756 + 208 3.42e-10 GAATAAGGAT TGCTCGTTTACCCGT TGTTCGATTT
MIT_Spar_c19_8512 + 210 3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT AGTTTGAATT
SGD_Scer_YGL040C + 209 3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT ATTTTGATTT
MIT_Sbay_c77_8808 + 209 5.96e-09 CGCCCGGAGA TGCTCGTTTACCGTT GTGCACCAAA
MIT_Spar_c130_3912 - 591 1.14e-07 GAGTTTCGTC CGCTCGTACACTGTT GGGAGAAACA
SGD_Scer_YDR044W - 597 3.16e-07 GGAGTTTGTC CTCTCGTTCACTGTT GGGAAAAACA
WashU_Smik_Contig2283.3 - 597 7.66e-07 GAAGTTCATC CGCTCGTACCTTCTT GAAAGACAAT
MIT_Sbay_c896_21290 + 366 1.10e-06 CTGTGTGAAA TGTTCGTTTTGCCCT TCCCAGAGAG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Skud_Contig2052.17 3.4e-10 208_[+4]_777
MIT_Smik_c273_7756 3.4e-10 207_[+4]_778
MIT_Spar_c19_8512 3.4e-10 209_[+4]_776
SGD_Scer_YGL040C 3.4e-10 208_[+4]_777
MIT_Sbay_c77_8808 6e-09 208_[+4]_777
MIT_Spar_c130_3912 1.1e-07 590_[-4]_395
SGD_Scer_YDR044W 3.2e-07 596_[-4]_389
WashU_Smik_Contig2283.3 7.7e-07 596_[-4]_389
MIT_Sbay_c896_21290 1.1e-06 365_[+4]_620
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 4 width=15 seqs=9
WashU_Skud_Contig2052.17 ( 209) TGCTCGTTTACCCGT 1
MIT_Smik_c273_7756 ( 208) TGCTCGTTTACCCGT 1
MIT_Spar_c19_8512 ( 210) TGCTCGTTTACCCGT 1
SGD_Scer_YGL040C ( 209) TGCTCGTTTACCCGT 1
MIT_Sbay_c77_8808 ( 209) TGCTCGTTTACCGTT 1
MIT_Spar_c130_3912 ( 591) CGCTCGTACACTGTT 1
SGD_Scer_YDR044W ( 597) CTCTCGTTCACTGTT 1
WashU_Smik_Contig2283.3 ( 597) CGCTCGTACCTTCTT 1
MIT_Sbay_c896_21290 ( 366) TGTTCGTTTTGCCCT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8874 bayes= 9.94398 E= 2.6e-006
-982 92 -982 104
-982 -982 234 -154
-982 234 -982 -154
-982 -982 -982 162
-982 251 -982 -982
-982 -982 251 -982
-982 -982 -982 162
-55 -982 -982 126
-982 92 -982 104
126 -66 -982 -154
-982 215 -66 -154
-982 192 -982 4
-982 192 92 -982
-982 -66 134 45
-982 -982 -982 162
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.6e-006
0.000000 0.333333 0.000000 0.666667
0.000000 0.000000 0.888889 0.111111
0.000000 0.888889 0.000000 0.111111
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.222222 0.000000 0.000000 0.777778
0.000000 0.333333 0.000000 0.666667
0.777778 0.111111 0.000000 0.111111
0.000000 0.777778 0.111111 0.111111
0.000000 0.666667 0.000000 0.333333
0.000000 0.666667 0.333333 0.000000
0.000000 0.111111 0.444444 0.444444
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 4 regular expression
--------------------------------------------------------------------------------
[TC]GCTCGT[TA][TC]AC[CT][CG][GT]T
--------------------------------------------------------------------------------
Time 32.02 secs.
********************************************************************************
********************************************************************************
MOTIF 5 width = 20 sites = 9 llr = 157 E-value = 4.5e-006
********************************************************************************
--------------------------------------------------------------------------------
Motif 5 Description
--------------------------------------------------------------------------------
Simplified A a:21::1178:99:1794a8
pos.-specific C ::::3::::1:1:163:1:2
probability G ::177199319::91:13::
matrix T :a72:9::::1:1:2::1::
bits 2.5
2.3
2.0 ** * *
1.8 ** * *
Information 1.5 ** * ** * * *
content 1.3 ** **** ** * * *
(25.2 bits) 1.0 ** ****** **** ** **
0.8 ** *********** ** **
0.5 ***************** **
0.3 ********************
0.0 --------------------
Multilevel ATTGGTGGAAGAAGCAAAAA
consensus ATC G TC G C
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------------------
WashU_Smik_Contig2283.3 + 249 2.56e-12 CTGGGGCATT ATTGGTGGAAGAAGCCAGAA AAGACGAAAG
MIT_Sbay_c896_21290 + 259 2.92e-12 CTGGGGCATA ATTGGTGGGAGAAGCCAGAA AATGCGAAAG
MIT_Spar_c130_3912 + 253 2.92e-12 CTGGGGCATT ATTGGTGGGAGAAGCCAGAA AAGGCGAAAG
SGD_Scer_YDR044W + 261 1.67e-09 CTGGAGCGTT ATTGGTGGGAGAACCAGAAA AGGCGAAAGC
MIT_Sbay_c77_8808 + 27 1.46e-08 TCTGGTAAGG ATATCTGGAAGAAGTAACAA TACGTATAAA
MIT_Smik_c273_7756 - 234 3.53e-08 GCCGAAAAAA ATTGGTAGAAGATGAAAAAA AAAATCGAAC
MIT_Spar_c19_8512 + 45 7.16e-08 GCAGGCAATA ATATGGGGAAGCAGTAAAAC TTTTTGTTTT
WashU_Skud_Contig2052.17 + 962 8.03e-08 AGTTTCCGTC ATGGCTGAACGAAGGAAAAC TACATCACCT
SGD_Scer_YGL040C + 26 1.04e-07 CTAGGTATGA ATTACTGGAGTAAGCAATAA TATGAGTAAG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
WashU_Smik_Contig2283.3 2.6e-12 248_[+5]_732
MIT_Sbay_c896_21290 2.9e-12 258_[+5]_722
MIT_Spar_c130_3912 2.9e-12 252_[+5]_728
SGD_Scer_YDR044W 1.7e-09 260_[+5]_720
MIT_Sbay_c77_8808 1.5e-08 26_[+5]_954
MIT_Smik_c273_7756 3.5e-08 233_[-5]_747
MIT_Spar_c19_8512 7.2e-08 44_[+5]_936
WashU_Skud_Contig2052.17 8e-08 961_[+5]_19
SGD_Scer_YGL040C 1e-07 25_[+5]_955
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 5 width=20 seqs=9
WashU_Smik_Contig2283.3 ( 249) ATTGGTGGAAGAAGCCAGAA 1
MIT_Sbay_c896_21290 ( 259) ATTGGTGGGAGAAGCCAGAA 1
MIT_Spar_c130_3912 ( 253) ATTGGTGGGAGAAGCCAGAA 1
SGD_Scer_YDR044W ( 261) ATTGGTGGGAGAACCAGAAA 1
MIT_Sbay_c77_8808 ( 27) ATATCTGGAAGAAGTAACAA 1
MIT_Smik_c273_7756 ( 234) ATTGGTAGAAGATGAAAAAA 1
MIT_Spar_c19_8512 ( 45) ATATGGGGAAGCAGTAAAAC 1
WashU_Skud_Contig2052.17 ( 962) ATGGCTGAACGAAGGAAAAC 1
SGD_Scer_YGL040C ( 26) ATTACTGGAGTAAGCAATAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 4.5e-006
162 -982 -982 -982
-982 -982 -982 162
-55 -982 -66 104
-154 -982 192 -55
-982 92 192 -982
-982 -982 -66 145
-154 -982 234 -982
-154 -982 234 -982
104 -982 92 -982
126 -66 -66 -982
-982 -982 234 -154
145 -66 -982 -982
145 -982 -982 -154
-982 -66 234 -982
-154 166 -66 -55
104 92 -982 -982
145 -982 -66 -982
45 -66 92 -154
162 -982 -982 -982
126 34 -982 -982
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.5e-006
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.222222 0.000000 0.111111 0.666667
0.111111 0.000000 0.666667 0.222222
0.000000 0.333333 0.666667 0.000000
0.000000 0.000000 0.111111 0.888889
0.111111 0.000000 0.888889 0.000000
0.111111 0.000000 0.888889 0.000000
0.666667 0.000000 0.333333 0.000000
0.777778 0.111111 0.111111 0.000000
0.000000 0.000000 0.888889 0.111111
0.888889 0.111111 0.000000 0.000000
0.888889 0.000000 0.000000 0.111111
0.000000 0.111111 0.888889 0.000000
0.111111 0.555556 0.111111 0.222222
0.666667 0.333333 0.000000 0.000000
0.888889 0.000000 0.111111 0.000000
0.444444 0.111111 0.333333 0.111111
1.000000 0.000000 0.000000 0.000000
0.777778 0.222222 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 5 regular expression
--------------------------------------------------------------------------------
AT[TA][GT][GC]TGG[AG]AGAAG[CT][AC]A[AG]A[AC]
--------------------------------------------------------------------------------
Time 39.67 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SGD_Scer_YGL040C 1.75e-23 25_[+5(1.04e-07)]_55_[+2(8.03e-10)]_18_[-3(2.12e-08)]_23_[-1(1.17e-12)]_9_[+4(3.42e-10)]_178_[-3(7.59e-05)]_498_[-2(2.36e-05)]_63
MIT_Spar_c19_8512 4.98e-25 44_[+5(7.16e-08)]_37_[+2(1.36e-09)]_18_[-3(3.60e-09)]_23_[-1(1.35e-13)]_9_[+4(3.42e-10)]_8_[-2(8.78e-05)]_191_[-3(9.88e-05)]_101_[+2(6.40e-05)]_317_[+2(1.09e-05)]_81
MIT_Smik_c273_7756 3.49e-24 25_[+5(8.56e-07)]_56_[+2(5.03e-09)]_57_[-1(1.35e-13)]_9_[+4(3.42e-10)]_11_[-5(3.53e-08)]_529_[+5(2.17e-05)]_30_[-3(1.56e-08)]_150
MIT_Sbay_c77_8808 4.86e-24 26_[+5(1.46e-08)]_58_[+2(3.82e-09)]_19_[-3(1.90e-10)]_19_[-1(2.88e-12)]_8_[+4(5.96e-09)]_465_[-2(9.60e-06)]_54_[+5(6.34e-05)]_218
WashU_Skud_Contig2052.17 2.08e-25 99_[+2(8.72e-11)]_19_[-3(1.98e-08)]_23_[-1(1.35e-13)]_9_[+4(3.42e-10)]_322_[-5(2.17e-05)]_101_[-4(3.66e-05)]_280_[+5(8.03e-08)]_19
SGD_Scer_YDR044W 1.15e-20 118_[+2(1.86e-09)]_40_[+3(9.53e-06)]_64_[+5(1.67e-09)]_153_[+1(5.50e-05)]_86_[+1(1.12e-09)]_37_[-4(3.16e-07)]_91_[+3(6.56e-10)]_280
MIT_Spar_c130_3912 1.46e-25 115_[+2(6.61e-10)]_117_[+5(2.92e-12)]_261_[+1(1.20e-09)]_37_[-4(1.14e-07)]_89_[+3(1.68e-11)]_288
MIT_Sbay_c896_21290 9.74e-21 84_[+5(7.87e-05)]_15_[+2(2.10e-08)]_119_[+5(2.92e-12)]_87_[+4(1.10e-06)]_161_[+1(1.43e-09)]_37_[-4(1.81e-05)]_87_[+3(6.28e-09)]_282
WashU_Smik_Contig2283.3 1.35e-23 111_[+2(3.17e-10)]_81_[+1(3.33e-05)]_16_[+5(2.56e-12)]_273_[+1(2.66e-10)]_35_[-4(7.66e-07)]_91_[+3(3.25e-09)]_280
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************
CPU: dhn02990.mrc-dunn.cam.ac.uk
********************************************************************************
|
