Contig Alignment

Base A B C D E F
1 . . . G . .
2 . . . C . .
3 . . . A . .
4 . . . C . .
5 . . . G . .
6 . . . C . .
7 . . . G . .
8 . . . T . .
9 . . . T . .
10 . . . C . .
11 . . . A . .
12 . . . A . .
13 . . . T . .
14 . . . C . .
15 . . . T . .
16 . . . C . .
17 . . . T . .
18 . . . A . .
19 . . . C . .
20 . . . T . .
21 . . . C . .
22 . . . C . .
23 . . . T . .
24 . . . C . .
25 . . . T . .
26 . . . C . .
27 . . . C . .
28 . . . T . .
29 . C C C . .
30 . T T T . .
31 . C C C . .
32 . T T T . .
33 . C C C . .
34 . C C C . .
35 . T T T . .
36 . C C C . .
37 . T T T . .
38 . C C C . .
39 . C C C . .
40 . T T T . .
41 . C C C . .
42 . T T T . .
43 . C C C . .
44 . A A A . .
45 . G G G . .
46 . T T T . .
47 . C C C . .
48 . A A A . .
49 . C C C . .
50 . T T T . .
51 . C C C . .
52 . C C C C .
53 . G G G G .
54 . C C C C .
55 . A A A A .
56 . G G G G .
57 . G G G G .
58 . A A A A .
59 . G G G G .
60 . C C C C .
61 . G G G G .
62 . T T T T .
63 . C C C C .
64 . T T T T .
65 . C C C C .
66 . T T T T .
67 . C C C C .
68 . T T T T .
69 . T T T T .
70 . C C C C .
71 . T T T T .
72 . C C C T .
73 . T T T T .
74 . C C C C .
75 . C C C C .
76 . T T T T .
77 . C C C C .
78 . T T T T .
79 . T T T T .
80 . C C C T .
81 . T T T T .
82 . G G G G .
83 . T T T T .
84 . T T C T .
85 . G G G G .
86 . G G G G .
87 . T T T T .
88 . G G G G .
89 . A A A A .
90 . A A A A .
91 . G G G G .
92 . G G G G .
93 . A A A A .
94 A A A A A .
95 T T T T T .
96 C C C C C .
97 A A A A A .
98 T T T T T .
99 G G G G G .
100 C C C C C .
101 A A A A A .
102 G G G G G .
103 A A A A A .
104 G G G G G .
105 G G G G G .
106 G G G G G .
107 C C C C C .
108 A A A A A .
109 A A A A A .
110 T T T T T .
111 G G G G G .
112 C C C C C .
113 A A A A A .
114 A A A A A .
115 T T T T T .
116 C C C C C .
117 A A A A A .
118 C C C C C .
119 T T T T T .
120 G G G G G .
121 C C C C C .
122 G G G G G .
123 G G G G G .
124 C C C C C .
125 T T T T T .
126 G G G G G .
127 C C C C C .
128 A A A A A .
129 T T T T T .
130 G G G G G .
131 G G G G G .
132 A A A A A .
133 A A A A A .
134 A A A A A .
135 T T T T T .
136 G G G G G .
137 T T T T T .
138 T T T T T .
139 C C C C C .
140 T T T T T .
141 T T T T T .
142 A A A A A .
143 A A A A A .
144 A A A A A .
145 C C C C C .
146 G G G G G .
147 A A A A A .
148 G G G G G .
149 C C C C C .
150 T T T T T .
151 G G G G G .
152 T T T T T .
153 T T T T T .
154 C C C C C .
155 T T T T T .
156 C C C C C .
157 C C C C C .
158 A A A A A .
159 A A A A A .
160 C C C C C .
161 A A A A A .
162 T T T T T .
163 G G G G G .
164 T T T T T .
165 T T T T T .
166 C C C C C .
167 G G G G G .
168 A A A A A .
169 G G G G G .
170 T T T T T .
171 C C C C C .
172 A A A A A .
173 T T T T T .
174 G G G G G .
175 A A A A A .
176 A A A A A .
177 C C C C C .
178 C C C C C .
179 C C C C C .
180 C C C C C .
181 T T T T T .
182 C C C C C .
183 T T T T T .
184 G G G G G .
185 T T T T T .
186 G G G G G .
187 C C C C C .
188 T T T T T .
189 A A A A A .
190 C C C C C .
191 C C C C C .
192 A A A A A .
193 A A A A A .
194 C C C C C .
195 T T T T T .
196 G G G G G .
197 T T T T T .
198 G G G G G .
199 T T T T T .
200 T T T T T .
201 T T T T T .
202 A A A A A .
203 C C C C C .
204 C C C C C .
205 C C C C C .
206 G G G G G .
207 C C C C C .
208 T T T T T .
209 A A A A A .
210 T T T T T .
211 G G G G G .
212 A A A A A .
213 G G G G G .
214 T T T T T .
215 C C C C C .
216 A A A A A .
217 G G G G G .
218 T T T T T .
219 T T T T T .
220 T T T T T .
221 T T T T T .
222 G G G G G .
223 C C C C C .
224 C C C C C .
225 A A A A A .
226 T T T T T .
227 C C C C C .
228 A A A A A .
229 C C C C C .
230 G G G G G .
231 T T T T T .
232 T T T T T .
233 T T T T T .
234 A A A A A .
235 G G G G G .
236 A A A A A .
237 A A A A A .
238 G G G G G .
239 A A A A A .
240 G G G G G .
241 C C C C C .
242 A A A A A .
243 T T T T T .
244 G G G G G .
245 G G G G G .
246 A A A A A .
247 T T T T T .
248 T T T T T .
249 T T T T T .
250 G G G G G .
251 A A A A A .
252 A A A A A .
253 A A A A A .
254 G G G G G .
255 C C C C C .
256 A A A A A .
257 C C C C C .
258 A A A A A .
259 A A A A A .
260 C C C C C .
261 T T T T T .
262 A A A A A .
263 T T T T T .
264 C C C C C .
265 C C C C C .
266 T T T T T .
267 G G G G G .
268 G G G G G .
269 A A A A A .
270 T T T T T .
271 A A A A A .
272 T T T T T .
273 T T T T T .
274 C C C C C .
275 T T T T T .
276 C C C C C .
277 A A A A A .
278 C C C C C .
279 A A A A A .
280 G G G G G .
281 C C C C C .
282 T T T T T .
283 A A A A A .
284 A A A A A .
285 A A A A A .
286 G G G G G .
287 G G G G G .
288 G G G G G .
289 A A A A A .
290 A A A A A .
291 G G G G G .
292 A A A A A .
293 G G G G G .
294 T T T T T .
295 G G G G G .
296 C C C C C .
297 C C C C C .
298 G G G G G .
299 A A A A A .
300 T T T T T .
301 G G G G G .
302 G G G G G .
303 C C C C C .
304 T T T T T .
305 C C C C C .
306 C C C C C .
307 T T T T T .
308 G G G G G .
309 G G G G G .
310 C C C C C .
311 T T T T T .
312 G G G G G .
313 T T T T T .
314 G G G G G .
315 G G G G G .
316 T T T T T .
317 G G G G G .
318 C C C C C .
319 A A A A A .
320 C C C C C .
321 A A A A A .
322 A A A A A .
323 C C C C C .
324 T T T T T .
325 G G G G G .
326 A A A A A .
327 T T T T T .
328 G G G G G .
329 A A A A A .
330 C C C C C .
331 A A A A A .
332 C C C C C .
333 T T T T T .
334 G G G G G .
335 T T T T T .
336 T T T T T .
337 T T T T T .
338 A A A A A .
339 T T T T T .
340 G G G G G .
341 A A A A A .
342 T T T T T .
343 G G G G G .
344 C C C C C .
345 T T T T T .
346 G G G G G .
347 T T T T T .
348 C C C C C .
349 A A A A A .
350 A A A A A .
351 A A A A A .
352 T T T T T .
353 C C C C C .
354 T T T T T .
355 A A A A A .
356 T T T T T .
357 G G G G G .
358 A A A A A .
359 C C C C C .
360 A A A A A .
361 C C C C C .
362 A A A A A .
363 A A A A A .
364 C C C C C .
365 A A A A A .
366 C C C C C .
367 A A A A A .
368 A A A A A .
369 T T T T T .
370 G G G G G .
371 T T T T T .
372 T T T T T .
373 G G G G G .
374 G G G G G .
375 A A A A A .
376 G G G G G .
377 C C C C C .
378 T T T T T .
379 C C C C C .
380 T T T T T .
381 G G G G G .
382 G G G G G .
383 T T T T T .
384 G G G G G .
385 G G G G G .
386 T T T T T .
387 G G G G G .
388 G G G G G .
389 T T T T T .
390 G G G G G .
391 A A A A A .
392 A A A A A .
393 A A A A A .
394 C C C C C .
395 C C C C C .
396 A A A A A .
397 G G G G G .
398 G G G G G .
399 G G G G G .
400 G G G G G .
401 A A A A A .
402 A A A A A .
403 G G G G G .
404 A A A A A .
405 G G G G G .
406 A A A A A .
407 A A A A A .
408 G G G G G .
409 G G G G G .
410 C C C C C .
411 A A A A A .
412 A A A A A .
413 T T T T T .
414 T T T T T .
415 G G G G G .
416 C C C C C .
417 T T T T T .
418 G G G G G .
419 G G G G G .
420 T T T T T .
421 A A A A A .
422 T T T T T .
423 T T T T T .
424 G G G G G .
425 T T T T T .
426 T T T T T .
427 A A A A A .
428 C C C C C .
429 T T T T T .
430 G G G G G .
431 A A A A A .
432 G G G G G .
433 A A A A A .
434 G G G G G .
435 A A A A A .
436 G G G G G .
437 A A A A A .
438 T T T T T .
439 T T T T T .
440 A A A A A .
441 T T T T T .
442 C C C C C .
443 T T T T T .
444 C C C C C .
445 C C C C C .
446 G G G G G .
447 T T T T T .
448 A A A A A .
449 A A A A A .
450 A A A A A .
451 A A A A A .
452 T T T T T .
453 C C C C C .
454 A A A A A .
455 T T T T T .
456 T T T T T .
457 G G G G G .
458 T T T T T .
459 G G G G G .
460 C C C C C .
461 A A A A A .
462 A A A A A .
463 G G G G G .
464 G G G G G .
465 A A A A A .
466 A A A A A .
467 G G G G G .
468 A A A A A .
469 T T T T T .
470 C C C C C .
471 T T T T T .
472 T T T T T .
473 C C C C C .
474 C C C C C .
475 A A A A A .
476 A A A A A .
477 G G G G G G
478 G G G G G G
479 A A A A A A
480 A A A A A A
481 A A A A A A
482 C C C C C C
483 T T T T T T
484 A A A A A A
485 A A A A A A
486 A A A A A A
487 G G G G G G
488 T T T T T T
489 T T T T T T
490 G G G G G G
491 G G G G G G
492 T T T T T T
493 G G G G G G
494 A A A A A A
495 C C C C C C
496 A A A A A A
497 T T T T T T
498 C C C C C C
499 A A A A A A
500 T T T T T T
501 G G G G G G
502 A A A A A A
503 C C C C C C
504 T T T T T T
505 G G G G G G
506 A A A A A A
507 A A A A A A
508 G G G G G G
509 A A A A A A
510 G G G G G G
511 A A A A A A
512 A A A A A A
513 T T T T T T
514 A A A A A A
515 A A A A A A
516 A A A A A A
517 C C C C C C
518 T T T T T T
519 C T T C T T 2 transition
520 A A A A A A
521 T T T T T T
522 C C C C C C
523 A A A A A A
524 C C C C C C
525 T C C T C C 2 transition
526 G G G G G G
527 T T T T T T
528 G G G G G G
529 A A A A A A
530 C C C C C C
531 T T T T T T
532 C C C C C C
533 C C C C C C
534 A A A A A A
535 G G G G G G
536 A A A A A A
537 T T T T T T
538 A A A A A A
539 C C C C C A
540 T T T T T T
541 A A A A A A
542 A A A A A A
543 A A A A A A
544 G G G G G G
545 T T T T T T
546 A A A A A A
547 C C C C C C
548 T T T T T T
549 G G G G G G
550 C C C C C C
551 G G G G G G
552 G G G G G G
553 G G G G G G
554 C C C C C C
555 A A A A A A
556 A A A A A A
557 T T T T T T
558 G G G G G G
559 C C C C C C
560 A A A A A A
561 G G G G G G
562 C C C C C C
563 T T T T T T
564 G G G G G G
565 A A A A A A
566 T T T T T T
567 G G G G G G
568 A A A A A A
569 C C C C C C
570 A A A A A A
571 G G G G G G
572 A A A A A A
573 C C C C C C
574 A A A A A A
575 A A A A A A
576 C C C C C C
577 C C C C C C
578 G G G G G G
579 C C C C C C
580 A A A A A A
581 T T T T T T
582 T T T T T T
583 A A A A A A
584 G G G G G G
585 G G G G G G
586 C C C C C C
587 A A A A A A
588 C C C C C C
589 A A A A A A
590 T T T T T T
591 C C C C C C
592 C C C C C C
593 C C C C C C
594 C T T C T T 2 transition
595 G G G G G G
596 T T T T T T
597 G G G G G G
598 G G G G G G
599 T T T T T T
600 T T T T T T
601 G G G G G G
602 G G G G G G
603 T T T T T T
604 G G G G G G
605 A A A A A A
606 G G G G G G
607 A A A A A A
608 A A A A A A
609 A A A A A A
610 G G G G G G
611 G G G G G G
612 A A A A A A
613 A A A A A A
614 T T T T T T
615 G G G G G G
616 A A A A A A
617 T T T T T T
618 T T T T T T
619 G G G G G G
620 G G G G G G
621 A A A A A A
622 A A A A A A
623 T T T T T T
624 G G G G G G
625 G G G G G G
626 T T T T T T
627 C C C C C C
628 T T T T T T
629 C C C C C C
630 C C C C C C
631 A A A A A A
632 T T T T T T
633 T T T T T T
634 G G G G G G
635 G G G G G G
636 T T T T T T
637 G G G G G G
638 A A A A A A
639 C C C C C C
640 G G G G G G
641 T T T T T T
642 T T T T T T
643 G G G G G G
644 T T T T T T
645 T T T T T T
646 C C C C C C
647 G G G G G G
648 A A A A A A
649 G G G G G G
650 C C C C C C
651 T T T T T T
652 G G G G G G
653 T T T T T T
654 G G G G G G
655 G G G G G G
656 T T T T T T
657 G G G G G G
658 A A A A A A
659 G G G G G G
660 C C C C C C
661 G G G G G G
662 A A A A A A
663 G G G G G G
664 C C C C C C
665 A A A A A A
666 T T T T T T
667 C C C C C C
668 G G G G G G
669 T T T T T T
670 G G G G G G
671 A A A A A A
672 G G G G G G
673 G G G G G G
674 A A A A A A
675 G G G G G G
676 C C C C C C
677 T T T T T T
678 G G G G G G
679 A A A A A A
680 A A A A A A
681 T T T T T T
682 C C C C C C
683 G G G G G G
684 C C C C C C
685 C C C C C C
686 T T T T T T
687 C C C C C C
688 A A A A A A
689 A A A A A A
690 T T T T T T
691 G G G G G G
692 C C C C C C
693 T T T T T T
694 T T T T T T
695 A A A A A A
696 T T T T T T
697 A A A A A A
698 T T T T T T
699 A A A A A A
700 C C C C C C
701 A A A A A A
702 A A A A A A
703 G G G G G G
704 G G G G G G
705 A A A A A A
706 . . G G G G
707 . . G G G G
708 . . A A A A
709 . . T T T T
710 . . A A A A
711 . . C C C C
712 . . T T T T
713 . . A A A A
714 . . A A A A
715 . . G G G G
716 . . A A A A
717 . . C C C C
718 . . A A A A
719 . . A A A A
720 . . G G G G
721 . . T T T T
722 . . A A A A
723 . . G G G G
724 . . T T T T
725 . . T T T T
726 . . C C C C
727 . . C C C C
728 . . C C C C
729 . . T T T T
730 . . A A A A
731 . . G G G G
732 . . T T T T
733 . . C C C C
734 . . G G G G
735 . . A A A A
736 . . A A A A
737 . . T T T T
738 . . A A A A
739 . . A A A A
740 . . C C C C
741 . . G A G G
742 . . A A A A
743 . . T T T T
744 . . A A A A
745 . . G G G G
746 . . A A A A
747 . . C C C C
748 . . C C C C
749 . . A A A A
750 . . T T T T
751 . . A A A A
752 . . A A A A
753 . . T C T T
754 . . G G G G
755 . . A A A A
756 . . T T T T
757 . . G G G G
758 . . G G G G
759 . . C C C C
760 . . A A A A
761 . . A A A A
762 . . A A A A
763 . . A A A A
764 . . A A A A
765 . . A A A A
766 . . C C C C
767 . . C C C C
768 . . - C - -
769 . . T T T T
770 . . C C C C
771 . . T T T T
772 . . C C C C
773 . . G G G G
774 . . T T T T
775 . . T T T T
776 . . T T T T
777 . . C C C C
778 . . T T T T
779 . . T T T T
780 . . T T T G
781 . . G G G G
782 . . A A A A
783 . . G G G G
784 . . C C C C
785 . . A A A A
786 . . G G G G
787 . . A A A A
788 . . C C C C
789 . . T T T T
790 . . G G G G
791 . . C C C C
792 . . G G G G
793 . . A A A A
794 . . G G G G
795 . . C C C C
796 . . A A A A
797 . . C C C C
798 . . A A A A
799 . . T T T T
800 . . G G G G
801 . . T T T T
802 . . A A A A
803 . . C C C C
804 . . A A A A
805 . . A A A A
806 . . T T T T
807 . . T T T T
808 . . G G G G
809 . . T T T T
810 . . G G G G
811 . . C C C C
812 . . C C C C
813 . . G G G G
814 . . G G G G
815 . . T T T T
816 . . T T T T
817 . . T T T T
818 . . T T T T
819 . . C C C A
820 . . T T T T
821 . . C C C G
822 . . T T A -
823 . . A G A G 2 transition
824 . . . G G G
825 . . . T G T
826 . . . C C C
827 . . . A A A
828 . . . A A A
829 . . . G G G
830 . . . C C C
831 . . . A A A
832 . . . A A A
833 . . . A A A
834 . . . A C C
835 . . . C C C
836 . . . T T T
837 . . . A A A
838 . . . G G G
839 . . . A A A
840 . . . T T T
841 . . . C C C
842 . . . C C C
843 . . . C C C
844 . . . T T T
845 . . . G T T
846 . . . T T T
847 . . . T T T
848 . . . T T T
849 . . . C C C
850 . . . T T T
851 . . . G G G
852 . . . G G G
853 . . . C C C
854 . . . T T T
855 . . . A A A
856 . . . C C .
857 . . . T T .
858 . . . T T .
859 . . . G G .
860 . . . . A .
861 . . . . T .
862 . . . . A .
863 . . . . A .
864 . . . . A .
865 . . . . G .