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
804
805
806
807
808
809
810
811
|
#---------------------------------------------------------------------------------
# qrna 1.2b (Tue Dec 18 15:04:38 CST 2001) using squid 1.5m (Sept 1997)
#---------------------------------------------------------------------------------
# PAM model = BLOSUM62 scaled by 1.000
#---------------------------------------------------------------------------------
# RNA model = /mix_tied_linux.cfg
#---------------------------------------------------------------------------------
# seq file = ecoli-trna.blast.q
# #seqs: 94 (max_len = 78)
#---------------------------------------------------------------------------------
# full length version: -- length range = [0,1000]
#---------------------------------------------------------------------------------
# 1 [+ strand]
>DA0780-1- (76)
>ECOLI-225501- (76)
length alignment: 76 (id=77.63)
posX: 0-75 [0-72](73) -- (0.18 0.30 0.36 0.16)
posY: 0-75 [0-71](72) -- (0.17 0.29 0.33 0.21)
21.414226 -10.515196 16.075247
19.988807 -3.972533 12.698167
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 75
COD ends = 74 0
RNA ends = 0 12
OTH = 20.871 COD = -4.957 RNA = 15.208
logoddspostOTH = 0.000 logoddspostCOD = -25.828 logoddspostRNA = -5.663
# 2 [+ strand]
>DA0780-1- (76)
>ECOLI-4034592- (76)
length alignment: 76 (id=77.63)
posX: 0-75 [0-72](73) -- (0.18 0.30 0.36 0.16)
posY: 0-75 [0-71](72) -- (0.17 0.29 0.33 0.21)
21.414226 -10.515196 16.075247
19.988807 -3.972533 12.698167
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 75
COD ends = 74 0
RNA ends = 0 12
OTH = 20.871 COD = -4.957 RNA = 15.208
logoddspostOTH = 0.000 logoddspostCOD = -25.828 logoddspostRNA = -5.663
# 3 [+ strand]
>DA0780-1- (70)
>ECOLI-3979754- (70)
length alignment: 70 (id=72.86)
posX: 0-69 [0-68](69) -- (0.17 0.29 0.38 0.16)
posY: 0-69 [0-69](70) -- (0.16 0.30 0.36 0.19)
21.384909 12.463364 22.249356
21.249381 17.921616 22.037246
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 0 69
COD ends = 68 1
RNA ends = 3 69
OTH = 21.319 COD = 16.954 RNA = 22.147
logoddspostOTH = 0.000 logoddspostCOD = -4.365 logoddspostRNA = 0.828
# 4 [+ strand]
>DA0780-8- (56)
>ECOLI-779995- (56)
length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18)
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18)
14.761275 -0.369781 17.076846
14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 55 0
COD ends = 54 0
RNA ends = 35 19
OTH = 14.801 COD = 9.226 RNA = 20.928
logoddspostOTH = 0.000 logoddspostCOD = -5.574 logoddspostRNA = 6.127
# 5 [+ strand]
>DA0780-8- (56)
>ECOLI-780298- (56)
length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18)
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18)
14.761275 -0.369781 17.076846
14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 55 0
COD ends = 54 0
RNA ends = 35 19
OTH = 14.801 COD = 9.226 RNA = 20.928
logoddspostOTH = 0.000 logoddspostCOD = -5.574 logoddspostRNA = 6.127
# 6 [+ strand]
>DA0780-8- (56)
>ECOLI-2518730- (56)
length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18)
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18)
14.761275 -0.369781 17.076846
14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 55 0
COD ends = 54 0
RNA ends = 35 19
OTH = 14.801 COD = 9.226 RNA = 20.928
logoddspostOTH = 0.000 logoddspostCOD = -5.574 logoddspostRNA = 6.127
# 7 [+ strand]
>DA0780-8- (56)
>ECOLI-2518850- (56)
length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18)
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18)
14.761275 -0.369781 17.076846
14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 55 0
COD ends = 54 0
RNA ends = 35 19
OTH = 14.801 COD = 9.226 RNA = 20.928
logoddspostOTH = 0.000 logoddspostCOD = -5.574 logoddspostRNA = 6.127
# 8 [+ strand]
>DA0780-8- (56)
>ECOLI-2518972- (56)
length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18)
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18)
14.761275 -0.369781 17.076846
14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 55 0
COD ends = 54 0
RNA ends = 35 19
OTH = 14.801 COD = 9.226 RNA = 20.928
logoddspostOTH = 0.000 logoddspostCOD = -5.574 logoddspostRNA = 6.127
# 9 [+ strand]
>DA0780-2- (73)
>ECOLI-2284230- (73)
length alignment: 73 (id=64.38)
posX: 0-72 [0-71](72) -- (0.18 0.31 0.35 0.17)
posY: 0-72 [0-72](73) -- (0.15 0.27 0.38 0.19)
13.918545 -8.608490 24.007519
15.073192 7.016852 12.344431
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 72 0
COD ends = 72 0
RNA ends = 0 70
OTH = 14.608 COD = 6.017 RNA = 23.008
logoddspostOTH = 0.000 logoddspostCOD = -8.592 logoddspostRNA = 8.400
# 10 [+ strand]
>DA0780-7- (59)
>ECOLI-2945191- (59)
length alignment: 59 (id=67.80)
posX: 0-58 [0-55](56) -- (0.20 0.27 0.36 0.18)
posY: 0-58 [0-56](57) -- (0.19 0.28 0.32 0.21)
7.994668 -17.443195 7.730549
8.785962 -9.672509 13.155362
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 58 0
COD ends = 58 1
RNA ends = 39 21
OTH = 8.444 COD = -10.666 RNA = 12.189
logoddspostOTH = 0.000 logoddspostCOD = -19.110 logoddspostRNA = 3.745
# 11 [+ strand]
>DA0780-7- (59)
>ECOLI-2945301- (59)
length alignment: 59 (id=67.80)
posX: 0-58 [0-55](56) -- (0.20 0.27 0.36 0.18)
posY: 0-58 [0-56](57) -- (0.19 0.28 0.32 0.21)
7.994668 -17.443195 7.730549
8.785962 -9.672509 13.155362
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 58 0
COD ends = 58 1
RNA ends = 39 21
OTH = 8.444 COD = -10.666 RNA = 12.189
logoddspostOTH = 0.000 logoddspostCOD = -19.110 logoddspostRNA = 3.745
# 12 [+ strand]
>DA0780-7- (59)
>ECOLI-2945411- (59)
length alignment: 59 (id=67.80)
posX: 0-58 [0-55](56) -- (0.20 0.27 0.36 0.18)
posY: 0-58 [0-56](57) -- (0.19 0.28 0.32 0.21)
7.994668 -17.443195 7.730549
8.785962 -9.672509 13.155362
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 58 0
COD ends = 58 1
RNA ends = 39 21
OTH = 8.444 COD = -10.666 RNA = 12.189
logoddspostOTH = 0.000 logoddspostCOD = -19.110 logoddspostRNA = 3.745
# 13 [+ strand]
>DA0780-1- (76)
>ECOLI-3424373- (76)
length alignment: 76 (id=77.63)
posX: 0-75 [0-72](73) -- (0.16 0.36 0.30 0.18)
posY: 0-75 [0-71](72) -- (0.21 0.33 0.29 0.17)
20.682006 -9.755632 13.248665
21.241284 -22.237923 16.258281
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 75 0
COD ends = 1 68
RNA ends = 75 63
OTH = 20.989 COD = -10.755 RNA = 15.427
logoddspostOTH = 0.000 logoddspostCOD = -31.744 logoddspostRNA = -5.561
# 14 [+ strand]
>DA0780-6- (71)
>ECOLI-2815582- (71)
length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19)
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22)
16.431838 -14.269383 12.463979
16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 70
COD ends = 70 1
RNA ends = 24 8
OTH = 16.380 COD = -8.320 RNA = 13.225
logoddspostOTH = 0.000 logoddspostCOD = -24.700 logoddspostRNA = -3.155
# 15 [+ strand]
>DA0780-6- (71)
>ECOLI-2815857- (71)
length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19)
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22)
16.431838 -14.269383 12.463979
16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 70
COD ends = 70 1
RNA ends = 24 8
OTH = 16.380 COD = -8.320 RNA = 13.225
logoddspostOTH = 0.000 logoddspostCOD = -24.700 logoddspostRNA = -3.155
# 16 [+ strand]
>DA0780-6- (71)
>ECOLI-2815996- (71)
length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19)
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22)
16.431838 -14.269383 12.463979
16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 70
COD ends = 70 1
RNA ends = 24 8
OTH = 16.380 COD = -8.320 RNA = 13.225
logoddspostOTH = 0.000 logoddspostCOD = -24.700 logoddspostRNA = -3.155
# 17 [+ strand]
>DA0780-6- (71)
>ECOLI-2816271- (71)
length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19)
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22)
16.431838 -14.269383 12.463979
16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 70
COD ends = 70 1
RNA ends = 24 8
OTH = 16.380 COD = -8.320 RNA = 13.225
logoddspostOTH = 0.000 logoddspostCOD = -24.700 logoddspostRNA = -3.155
# 18 [+ strand]
>DA0780-1- (76)
>ECOLI-2515836- (76)
length alignment: 76 (id=71.05)
posX: 0-75 [0-72](73) -- (0.16 0.36 0.30 0.18)
posY: 0-75 [0-71](72) -- (0.21 0.33 0.26 0.19)
14.736984 -14.375325 8.884532
14.851236 -24.156886 9.868232
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 75 0
COD ends = 1 75
RNA ends = 75 63
OTH = 14.795 COD = -15.374 RNA = 9.459
logoddspostOTH = 0.000 logoddspostCOD = -30.169 logoddspostRNA = -5.337
# 19 [+ strand]
>DA0780-1- (76)
>ECOLI-2515951- (76)
length alignment: 76 (id=71.05)
posX: 0-75 [0-72](73) -- (0.16 0.36 0.30 0.18)
posY: 0-75 [0-71](72) -- (0.21 0.33 0.26 0.19)
14.736984 -14.375325 8.884532
14.851236 -24.156886 9.868232
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 75 0
COD ends = 1 75
RNA ends = 75 63
OTH = 14.795 COD = -15.374 RNA = 9.459
logoddspostOTH = 0.000 logoddspostCOD = -30.169 logoddspostRNA = -5.337
# 20 [+ strand]
>DA0780-6- (52)
>ECOLI-2155594- (52)
length alignment: 52 (id=71.15)
posX: 0-51 [0-48](49) -- (0.16 0.41 0.27 0.16)
posY: 0-51 [0-48](49) -- (0.18 0.41 0.29 0.12)
5.862400 -19.930995 -1.194701
7.783836 -15.355771 0.726735
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 51 0
COD ends = 50 0
RNA ends = 52 52
OTH = 7.122 COD = -16.296 RNA = 0.065
logoddspostOTH = 0.000 logoddspostCOD = -23.418 logoddspostRNA = -7.057
# 21 [+ strand]
>DA0780-7- (59)
>ECOLI-3315645- (59)
length alignment: 59 (id=66.10)
posX: 0-58 [0-55](56) -- (0.18 0.36 0.27 0.20)
posY: 0-58 [0-56](57) -- (0.21 0.30 0.28 0.21)
7.886726 -12.920042 12.597060
6.999592 -16.997763 6.986972
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 0 58
COD ends = 0 58
RNA ends = 20 36
OTH = 7.510 COD = -13.837 RNA = 11.626
logoddspostOTH = 0.000 logoddspostCOD = -21.347 logoddspostRNA = 4.116
# 22 [+ strand]
>DA0940-1- (77)
>ECOLI-225500- (77)
length alignment: 77 (id=75.32)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14)
posY: 0-76 [0-74](75) -- (0.16 0.31 0.33 0.20)
24.181055 -0.353323 26.401988
23.109013 11.590026 23.929123
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 0 76
COD ends = 76 0
RNA ends = 0 73
OTH = 23.742 COD = 10.590 RNA = 25.641
logoddspostOTH = 0.000 logoddspostCOD = -13.152 logoddspostRNA = 1.899
# 23 [+ strand]
>DA0940-1- (77)
>ECOLI-4034591- (77)
length alignment: 77 (id=75.32)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14)
posY: 0-76 [0-74](75) -- (0.16 0.31 0.33 0.20)
24.181055 -0.353323 26.401988
23.109013 11.590026 23.929123
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 0 76
COD ends = 76 0
RNA ends = 0 73
OTH = 23.742 COD = 10.590 RNA = 25.641
logoddspostOTH = 0.000 logoddspostCOD = -13.152 logoddspostRNA = 1.899
# 24 [+ strand]
>DA0940-1- (77)
>ECOLI-779777- (77)
length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14)
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28)
19.326669 -6.735706 19.727199
19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 76 0
COD ends = 74 1
RNA ends = 0 73
OTH = 19.344 COD = -2.948 RNA = 18.779
logoddspostOTH = 0.000 logoddspostCOD = -22.291 logoddspostRNA = -0.564
# 25 [+ strand]
>DA0940-1- (77)
>ECOLI-780066- (77)
length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14)
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28)
19.326669 -6.735706 19.727199
19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 76 0
COD ends = 74 1
RNA ends = 0 73
OTH = 19.344 COD = -2.948 RNA = 18.779
logoddspostOTH = 0.000 logoddspostCOD = -22.291 logoddspostRNA = -0.564
# 26 [+ strand]
>DA0940-1- (77)
>ECOLI-780370- (77)
length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14)
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28)
19.326669 -6.735706 19.727199
19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 76 0
COD ends = 74 1
RNA ends = 0 73
OTH = 19.344 COD = -2.948 RNA = 18.779
logoddspostOTH = 0.000 logoddspostCOD = -22.291 logoddspostRNA = -0.564
# 27 [+ strand]
>DA0940-1- (77)
>ECOLI-780592- (77)
length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14)
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28)
19.326669 -6.735706 19.727199
19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 76 0
COD ends = 74 1
RNA ends = 0 73
OTH = 19.344 COD = -2.948 RNA = 18.779
logoddspostOTH = 0.000 logoddspostCOD = -22.291 logoddspostRNA = -0.564
# 28 [+ strand]
>DA0940-1- (77)
>ECOLI-780800- (77)
length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14)
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28)
19.326669 -6.735706 19.727199
19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 76 0
COD ends = 74 1
RNA ends = 0 73
OTH = 19.344 COD = -2.948 RNA = 18.779
logoddspostOTH = 0.000 logoddspostCOD = -22.291 logoddspostRNA = -0.564
# 29 [+ strand]
>DA0940-1- (77)
>ECOLI-2519045- (77)
length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14)
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28)
19.326669 -6.735706 19.727199
19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 76 0
COD ends = 74 1
RNA ends = 0 73
OTH = 19.344 COD = -2.948 RNA = 18.779
logoddspostOTH = 0.000 logoddspostCOD = -22.291 logoddspostRNA = -0.564
# 30 [+ strand]
>DA0940-1- (78)
>ECOLI-563946- (78)
length alignment: 78 (id=69.23)
posX: 0-77 [0-75](76) -- (0.14 0.34 0.37 0.14)
posY: 0-77 [0-75](76) -- (0.18 0.30 0.32 0.20)
17.963663 -9.269558 17.104482
18.280556 -6.326426 22.143566
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 77 0
COD ends = 72 1
RNA ends = 44 28
OTH = 18.131 COD = -7.150 RNA = 21.187
logoddspostOTH = 0.000 logoddspostCOD = -25.281 logoddspostRNA = 3.056
# 31 [+ strand]
>DA0940-1- (78)
>ECOLI-3979754- (78)
length alignment: 78 (id=69.23)
posX: 0-77 [0-75](76) -- (0.14 0.34 0.37 0.14)
posY: 0-77 [0-75](76) -- (0.14 0.33 0.36 0.17)
18.718315 -12.877073 20.514241
18.551819 -5.649083 11.109117
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 0 77
COD ends = 76 1
RNA ends = 0 74
OTH = 18.637 COD = -6.639 RNA = 19.516
logoddspostOTH = 0.000 logoddspostCOD = -25.277 logoddspostRNA = 0.879
# 32 [+ strand]
>DA0940-2- (75)
>ECOLI-3980115- (75)
length alignment: 75 (id=64.00)
posX: 0-74 [0-74](75) -- (0.15 0.35 0.36 0.15)
posY: 0-74 [0-74](75) -- (0.16 0.27 0.36 0.21)
16.673417 5.650160 34.947176
16.791520 4.389619 18.597200
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 74 0
COD ends = 2 73
RNA ends = 0 70
OTH = 16.734 COD = 5.153 RNA = 33.947
logoddspostOTH = 0.000 logoddspostCOD = -11.580 logoddspostRNA = 17.214
# 33 [+ strand]
>DA0940-8- (58)
>ECOLI-3979896- (58)
length alignment: 58 (id=68.97)
posX: 0-57 [0-56](57) -- (0.18 0.32 0.33 0.18)
posY: 0-57 [0-55](56) -- (0.16 0.21 0.30 0.32)
11.514323 -1.612738 9.963681
11.181613 -0.641287 8.426787
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 57
COD ends = 57 0
RNA ends = 20 37
OTH = 11.358 COD = -1.047 RNA = 9.391
logoddspostOTH = 0.000 logoddspostCOD = -12.404 logoddspostRNA = -1.967
# 34 [+ strand]
>DA0940-1- (77)
>ECOLI-3424371- (77)
length alignment: 77 (id=75.32)
posX: 0-76 [0-75](76) -- (0.14 0.37 0.34 0.14)
posY: 0-76 [0-74](75) -- (0.20 0.33 0.31 0.16)
23.109013 5.520843 24.913393
24.181055 9.917873 33.181724
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 76 0
COD ends = 76 2
RNA ends = 76 3
OTH = 23.742 COD = 8.985 RNA = 32.186
logoddspostOTH = 0.000 logoddspostCOD = -14.758 logoddspostRNA = 8.444
# 35 [+ strand]
>DA0940-1- (77)
>ECOLI-2515834- (77)
length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.37 0.34 0.14)
posY: 0-76 [0-74](75) -- (0.20 0.33 0.28 0.19)
18.645991 3.152473 25.533618
18.627918 3.690656 29.967242
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 0 76
COD ends = 76 2
RNA ends = 76 3
OTH = 18.637 COD = 3.447 RNA = 29.033
logoddspostOTH = 0.000 logoddspostCOD = -15.190 logoddspostRNA = 10.396
# 36 [+ strand]
>DA0940-1- (77)
>ECOLI-2515949- (77)
length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.37 0.34 0.14)
posY: 0-76 [0-74](75) -- (0.20 0.33 0.28 0.19)
18.645991 3.152473 25.533618
18.627918 3.690656 29.967242
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 0 76
COD ends = 76 2
RNA ends = 76 3
OTH = 18.637 COD = 3.447 RNA = 29.033
logoddspostOTH = 0.000 logoddspostCOD = -15.190 logoddspostRNA = 10.396
# 37 [+ strand]
>DA0940-5- (76)
>ECOLI-2815580- (76)
length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15)
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21)
13.333636 -36.156781 13.057277
13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 75
COD ends = 0 73
RNA ends = 32 52
OTH = 13.249 COD = -36.263 RNA = 12.150
logoddspostOTH = 0.000 logoddspostCOD = -49.512 logoddspostRNA = -1.099
# 38 [+ strand]
>DA0940-5- (76)
>ECOLI-2815855- (76)
length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15)
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21)
13.333636 -36.156781 13.057277
13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 75
COD ends = 0 73
RNA ends = 32 52
OTH = 13.249 COD = -36.263 RNA = 12.150
logoddspostOTH = 0.000 logoddspostCOD = -49.512 logoddspostRNA = -1.099
# 39 [+ strand]
>DA0940-5- (76)
>ECOLI-2815994- (76)
length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15)
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21)
13.333636 -36.156781 13.057277
13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 75
COD ends = 0 73
RNA ends = 32 52
OTH = 13.249 COD = -36.263 RNA = 12.150
logoddspostOTH = 0.000 logoddspostCOD = -49.512 logoddspostRNA = -1.099
# 40 [+ strand]
>DA0940-5- (76)
>ECOLI-2816269- (76)
length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15)
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21)
13.333636 -36.156781 13.057277
13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 75
COD ends = 0 73
RNA ends = 32 52
OTH = 13.249 COD = -36.263 RNA = 12.150
logoddspostOTH = 0.000 logoddspostCOD = -49.512 logoddspostRNA = -1.099
# 41 [+ strand]
>DA0940-9- (69)
>ECOLI-1804478- (69)
length alignment: 69 (id=66.67)
posX: 0-68 [0-67](68) -- (0.15 0.34 0.35 0.16)
posY: 0-68 [0-66](67) -- (0.13 0.39 0.31 0.16)
10.953909 -9.639667 10.662024
12.823044 -5.075973 10.777964
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 68 0
COD ends = 66 1
RNA ends = 51 31
OTH = 12.172 COD = -6.016 RNA = 10.721
logoddspostOTH = 0.000 logoddspostCOD = -18.188 logoddspostRNA = -1.451
# 42 [+ strand]
>DA0940-8- (58)
>ECOLI-3706024- (58)
length alignment: 58 (id=68.97)
posX: 0-57 [0-55](56) -- (0.18 0.34 0.30 0.18)
posY: 0-57 [0-55](56) -- (0.20 0.39 0.25 0.16)
9.771742 -15.688073 2.357499
9.187335 -13.325765 1.773092
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 57
COD ends = 55 1
RNA ends = -1 -1
OTH = 9.509 COD = -14.069 RNA = 2.095
logoddspostOTH = 0.000 logoddspostCOD = -23.578 logoddspostRNA = -7.414
# 43 [+ strand]
>DA0940-7- (73)
>ECOLI-695888- (73)
length alignment: 73 (id=64.38)
posX: 0-72 [0-69](70) -- (0.16 0.34 0.34 0.16)
posY: 0-72 [0-69](70) -- (0.24 0.26 0.26 0.24)
10.281468 -22.207847 3.873799
9.636380 -19.716135 1.831177
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 72
COD ends = 72 1
RNA ends = 10 26
OTH = 9.995 COD = -20.480 RNA = 3.187
logoddspostOTH = 0.000 logoddspostCOD = -30.475 logoddspostRNA = -6.807
# 44 [+ strand]
>DA0940-7- (73)
>ECOLI-696281- (73)
length alignment: 73 (id=64.38)
posX: 0-72 [0-69](70) -- (0.16 0.34 0.34 0.16)
posY: 0-72 [0-69](70) -- (0.24 0.26 0.26 0.24)
10.281468 -22.207847 3.873799
9.636380 -19.716135 1.831177
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 72
COD ends = 72 1
RNA ends = 10 26
OTH = 9.995 COD = -20.480 RNA = 3.187
logoddspostOTH = 0.000 logoddspostCOD = -30.475 logoddspostRNA = -6.807
# 45 [+ strand]
>DA0940-6- (62)
>ECOLI-695990- (62)
length alignment: 62 (id=62.90)
posX: 0-61 [0-60](61) -- (0.16 0.38 0.30 0.16)
posY: 0-61 [0-60](61) -- (0.25 0.30 0.26 0.20)
10.452429 5.015902 10.936383
9.772183 2.186248 11.450894
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 0 61
COD ends = 0 61
RNA ends = 38 22
OTH = 10.152 COD = 4.206 RNA = 11.216
logoddspostOTH = 0.000 logoddspostCOD = -5.946 logoddspostRNA = 1.064
# 46 [+ strand]
>DA0940-6- (62)
>ECOLI-696099- (62)
length alignment: 62 (id=62.90)
posX: 0-61 [0-60](61) -- (0.16 0.38 0.30 0.16)
posY: 0-61 [0-60](61) -- (0.25 0.30 0.26 0.20)
10.452429 5.015902 10.936383
9.772183 2.186248 11.450894
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA
OTH ends = 0 61
COD ends = 0 61
RNA ends = 38 22
OTH = 10.152 COD = 4.206 RNA = 11.216
logoddspostOTH = 0.000 logoddspostCOD = -5.946 logoddspostRNA = 1.064
# 47 [+ strand]
>DA0940-10- (69)
>ECOLI-2816349- (69)
length alignment: 69 (id=63.77)
posX: 0-68 [0-66](67) -- (0.15 0.34 0.36 0.15)
posY: 0-68 [0-65](66) -- (0.18 0.27 0.36 0.18)
9.155278 -17.238488 5.252253
9.115589 -17.289968 6.575597
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 0 68
COD ends = 0 56
RNA ends = 26 10
OTH = 9.136 COD = -17.264 RNA = 6.061
logoddspostOTH = 0.000 logoddspostCOD = -26.400 logoddspostRNA = -3.075
|