Multiple sequence alignment - TraesCS5B01G423500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G423500 chr5B 100.000 2372 0 0 1 2372 599754575 599756946 0.000000e+00 4344.0
1 TraesCS5B01G423500 chr5B 97.550 653 16 0 1 653 127808880 127809532 0.000000e+00 1118.0
2 TraesCS5B01G423500 chr5B 93.913 230 12 1 2143 2372 599704731 599704958 1.750000e-91 346.0
3 TraesCS5B01G423500 chr5B 94.853 136 7 0 2237 2372 599846076 599846211 1.850000e-51 213.0
4 TraesCS5B01G423500 chr5B 92.517 147 10 1 2096 2242 599844933 599845078 2.390000e-50 209.0
5 TraesCS5B01G423500 chr5B 86.239 109 4 4 2259 2367 599693966 599694063 8.960000e-20 108.0
6 TraesCS5B01G423500 chr5B 98.039 51 1 0 2096 2146 599703885 599703935 3.250000e-14 89.8
7 TraesCS5B01G423500 chr3A 98.369 1410 23 0 664 2073 66004273 66002864 0.000000e+00 2477.0
8 TraesCS5B01G423500 chr3A 97.542 651 16 0 1 651 66004686 66004036 0.000000e+00 1114.0
9 TraesCS5B01G423500 chr3A 97.243 653 18 0 1 653 695640834 695641486 0.000000e+00 1107.0
10 TraesCS5B01G423500 chr5D 98.298 1410 24 0 664 2073 503246132 503247541 0.000000e+00 2471.0
11 TraesCS5B01G423500 chr5D 98.298 1410 24 0 664 2073 503263916 503262507 0.000000e+00 2471.0
12 TraesCS5B01G423500 chr2D 98.298 1410 24 0 664 2073 272811386 272809977 0.000000e+00 2471.0
13 TraesCS5B01G423500 chr2D 97.943 1410 29 0 664 2073 591985469 591986878 0.000000e+00 2444.0
14 TraesCS5B01G423500 chr2D 97.550 653 16 0 1 653 591985056 591985708 0.000000e+00 1118.0
15 TraesCS5B01G423500 chr6D 98.227 1410 25 0 664 2073 389244962 389243553 0.000000e+00 2466.0
16 TraesCS5B01G423500 chr6D 97.397 653 17 0 1 653 389245375 389244723 0.000000e+00 1112.0
17 TraesCS5B01G423500 chr2A 98.156 1410 26 0 664 2073 726905595 726904186 0.000000e+00 2460.0
18 TraesCS5B01G423500 chr3D 98.084 1409 27 0 664 2072 589262666 589261258 0.000000e+00 2453.0
19 TraesCS5B01G423500 chr3D 97.397 653 17 0 1 653 589263079 589262427 0.000000e+00 1112.0
20 TraesCS5B01G423500 chrUn 97.872 1410 30 0 664 2073 365939956 365941365 0.000000e+00 2438.0
21 TraesCS5B01G423500 chr7B 97.550 653 16 0 1 653 662726851 662727503 0.000000e+00 1118.0
22 TraesCS5B01G423500 chr1D 97.397 653 17 0 1 653 459904270 459903618 0.000000e+00 1112.0
23 TraesCS5B01G423500 chr1D 97.090 653 19 0 1 653 254526054 254526706 0.000000e+00 1101.0
24 TraesCS5B01G423500 chr1B 97.243 653 18 0 1 653 638729085 638729737 0.000000e+00 1107.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G423500 chr5B 599754575 599756946 2371 False 4344.0 4344 100.0000 1 2372 1 chr5B.!!$F3 2371
1 TraesCS5B01G423500 chr5B 127808880 127809532 652 False 1118.0 1118 97.5500 1 653 1 chr5B.!!$F1 652
2 TraesCS5B01G423500 chr5B 599703885 599704958 1073 False 217.9 346 95.9760 2096 2372 2 chr5B.!!$F4 276
3 TraesCS5B01G423500 chr5B 599844933 599846211 1278 False 211.0 213 93.6850 2096 2372 2 chr5B.!!$F5 276
4 TraesCS5B01G423500 chr3A 66002864 66004686 1822 True 1795.5 2477 97.9555 1 2073 2 chr3A.!!$R1 2072
5 TraesCS5B01G423500 chr3A 695640834 695641486 652 False 1107.0 1107 97.2430 1 653 1 chr3A.!!$F1 652
6 TraesCS5B01G423500 chr5D 503246132 503247541 1409 False 2471.0 2471 98.2980 664 2073 1 chr5D.!!$F1 1409
7 TraesCS5B01G423500 chr5D 503262507 503263916 1409 True 2471.0 2471 98.2980 664 2073 1 chr5D.!!$R1 1409
8 TraesCS5B01G423500 chr2D 272809977 272811386 1409 True 2471.0 2471 98.2980 664 2073 1 chr2D.!!$R1 1409
9 TraesCS5B01G423500 chr2D 591985056 591986878 1822 False 1781.0 2444 97.7465 1 2073 2 chr2D.!!$F1 2072
10 TraesCS5B01G423500 chr6D 389243553 389245375 1822 True 1789.0 2466 97.8120 1 2073 2 chr6D.!!$R1 2072
11 TraesCS5B01G423500 chr2A 726904186 726905595 1409 True 2460.0 2460 98.1560 664 2073 1 chr2A.!!$R1 1409
12 TraesCS5B01G423500 chr3D 589261258 589263079 1821 True 1782.5 2453 97.7405 1 2072 2 chr3D.!!$R1 2071
13 TraesCS5B01G423500 chrUn 365939956 365941365 1409 False 2438.0 2438 97.8720 664 2073 1 chrUn.!!$F1 1409
14 TraesCS5B01G423500 chr7B 662726851 662727503 652 False 1118.0 1118 97.5500 1 653 1 chr7B.!!$F1 652
15 TraesCS5B01G423500 chr1D 459903618 459904270 652 True 1112.0 1112 97.3970 1 653 1 chr1D.!!$R1 652
16 TraesCS5B01G423500 chr1D 254526054 254526706 652 False 1101.0 1101 97.0900 1 653 1 chr1D.!!$F1 652
17 TraesCS5B01G423500 chr1B 638729085 638729737 652 False 1107.0 1107 97.2430 1 653 1 chr1B.!!$F1 652

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
595 596 0.038166 TGGGATTCCAACTCAGCACC 59.962 55.0 4.8 0.0 40.73 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 3002 0.896479 TGCCAGAGTGTACGCCTACA 60.896 55.0 1.98 0.26 0.0 2.74 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 3.316029 TGAAACATGCCACTGAAAGACTG 59.684 43.478 0.00 0.00 37.43 3.51
101 102 6.706295 ACAAAAAGATGGGTTGTCAAAAAGA 58.294 32.000 0.00 0.00 29.57 2.52
107 108 5.649831 AGATGGGTTGTCAAAAAGATAGAGC 59.350 40.000 0.00 0.00 0.00 4.09
119 120 4.477536 AAGATAGAGCAGGTAGGATGGA 57.522 45.455 0.00 0.00 0.00 3.41
252 253 5.234972 TGCGAATAACTTGATGCACTATCTG 59.765 40.000 0.00 0.00 36.71 2.90
388 389 2.981859 GTCACGGACCAACCATAGAT 57.018 50.000 0.00 0.00 38.90 1.98
533 534 2.529389 AGCTCCCCGTTCCTGGTT 60.529 61.111 0.00 0.00 0.00 3.67
534 535 2.046217 GCTCCCCGTTCCTGGTTC 60.046 66.667 0.00 0.00 0.00 3.62
535 536 2.593956 GCTCCCCGTTCCTGGTTCT 61.594 63.158 0.00 0.00 0.00 3.01
536 537 1.597461 CTCCCCGTTCCTGGTTCTC 59.403 63.158 0.00 0.00 0.00 2.87
537 538 1.900545 CTCCCCGTTCCTGGTTCTCC 61.901 65.000 0.00 0.00 0.00 3.71
538 539 1.918800 CCCCGTTCCTGGTTCTCCT 60.919 63.158 0.00 0.00 34.23 3.69
539 540 1.296715 CCCGTTCCTGGTTCTCCTG 59.703 63.158 0.00 0.00 34.23 3.86
540 541 1.481056 CCCGTTCCTGGTTCTCCTGT 61.481 60.000 0.00 0.00 34.23 4.00
541 542 1.263356 CCGTTCCTGGTTCTCCTGTA 58.737 55.000 0.00 0.00 34.23 2.74
542 543 1.621814 CCGTTCCTGGTTCTCCTGTAA 59.378 52.381 0.00 0.00 34.23 2.41
543 544 2.612221 CCGTTCCTGGTTCTCCTGTAAC 60.612 54.545 0.00 0.00 31.64 2.50
544 545 2.299297 CGTTCCTGGTTCTCCTGTAACT 59.701 50.000 0.00 0.00 32.36 2.24
545 546 3.508793 CGTTCCTGGTTCTCCTGTAACTA 59.491 47.826 0.00 0.00 32.36 2.24
546 547 4.380655 CGTTCCTGGTTCTCCTGTAACTAG 60.381 50.000 0.00 0.00 35.77 2.57
547 548 4.669866 TCCTGGTTCTCCTGTAACTAGA 57.330 45.455 0.00 0.00 37.56 2.43
548 549 5.208294 TCCTGGTTCTCCTGTAACTAGAT 57.792 43.478 0.00 0.00 37.56 1.98
549 550 5.590818 TCCTGGTTCTCCTGTAACTAGATT 58.409 41.667 0.00 0.00 37.56 2.40
550 551 5.657302 TCCTGGTTCTCCTGTAACTAGATTC 59.343 44.000 0.00 0.00 37.56 2.52
551 552 5.163395 CCTGGTTCTCCTGTAACTAGATTCC 60.163 48.000 0.00 0.00 37.56 3.01
552 553 5.590818 TGGTTCTCCTGTAACTAGATTCCT 58.409 41.667 0.00 0.00 34.23 3.36
553 554 5.657302 TGGTTCTCCTGTAACTAGATTCCTC 59.343 44.000 0.00 0.00 34.23 3.71
554 555 5.657302 GGTTCTCCTGTAACTAGATTCCTCA 59.343 44.000 0.00 0.00 0.00 3.86
555 556 6.183360 GGTTCTCCTGTAACTAGATTCCTCAG 60.183 46.154 0.00 0.00 0.00 3.35
556 557 6.328782 TCTCCTGTAACTAGATTCCTCAGA 57.671 41.667 0.00 0.00 0.00 3.27
557 558 6.732487 TCTCCTGTAACTAGATTCCTCAGAA 58.268 40.000 0.00 0.00 36.15 3.02
558 559 6.603997 TCTCCTGTAACTAGATTCCTCAGAAC 59.396 42.308 0.00 0.00 33.97 3.01
559 560 5.657302 TCCTGTAACTAGATTCCTCAGAACC 59.343 44.000 0.00 0.00 33.97 3.62
560 561 5.422331 CCTGTAACTAGATTCCTCAGAACCA 59.578 44.000 0.00 0.00 33.97 3.67
561 562 6.282199 TGTAACTAGATTCCTCAGAACCAC 57.718 41.667 0.00 0.00 33.97 4.16
562 563 5.778241 TGTAACTAGATTCCTCAGAACCACA 59.222 40.000 0.00 0.00 33.97 4.17
563 564 5.825593 AACTAGATTCCTCAGAACCACAA 57.174 39.130 0.00 0.00 33.97 3.33
564 565 5.413309 ACTAGATTCCTCAGAACCACAAG 57.587 43.478 0.00 0.00 33.97 3.16
565 566 5.087323 ACTAGATTCCTCAGAACCACAAGA 58.913 41.667 0.00 0.00 33.97 3.02
566 567 4.982241 AGATTCCTCAGAACCACAAGAA 57.018 40.909 0.00 0.00 33.97 2.52
567 568 5.511386 AGATTCCTCAGAACCACAAGAAT 57.489 39.130 0.00 0.00 33.97 2.40
568 569 5.495640 AGATTCCTCAGAACCACAAGAATC 58.504 41.667 0.00 0.00 38.79 2.52
569 570 3.703001 TCCTCAGAACCACAAGAATCC 57.297 47.619 0.00 0.00 0.00 3.01
570 571 3.251484 TCCTCAGAACCACAAGAATCCT 58.749 45.455 0.00 0.00 0.00 3.24
571 572 3.652869 TCCTCAGAACCACAAGAATCCTT 59.347 43.478 0.00 0.00 0.00 3.36
572 573 4.844085 TCCTCAGAACCACAAGAATCCTTA 59.156 41.667 0.00 0.00 0.00 2.69
573 574 5.046304 TCCTCAGAACCACAAGAATCCTTAG 60.046 44.000 0.00 0.00 0.00 2.18
574 575 5.046304 CCTCAGAACCACAAGAATCCTTAGA 60.046 44.000 0.00 0.00 0.00 2.10
575 576 6.433847 TCAGAACCACAAGAATCCTTAGAA 57.566 37.500 0.00 0.00 0.00 2.10
576 577 7.020827 TCAGAACCACAAGAATCCTTAGAAT 57.979 36.000 0.00 0.00 0.00 2.40
577 578 6.881065 TCAGAACCACAAGAATCCTTAGAATG 59.119 38.462 0.00 0.00 0.00 2.67
578 579 6.094603 CAGAACCACAAGAATCCTTAGAATGG 59.905 42.308 0.00 0.00 31.72 3.16
579 580 4.860022 ACCACAAGAATCCTTAGAATGGG 58.140 43.478 0.00 0.00 30.62 4.00
580 581 4.540099 ACCACAAGAATCCTTAGAATGGGA 59.460 41.667 0.00 0.00 35.96 4.37
581 582 5.194537 ACCACAAGAATCCTTAGAATGGGAT 59.805 40.000 0.00 0.00 43.40 3.85
588 589 6.347061 AATCCTTAGAATGGGATTCCAACT 57.653 37.500 0.00 2.30 45.84 3.16
589 590 6.368805 AATCCTTAGAATGGGATTCCAACTC 58.631 40.000 0.00 0.00 45.84 3.01
590 591 6.068853 AATCCTTAGAATGGGATTCCAACTCA 60.069 38.462 0.00 0.00 45.84 3.41
591 592 7.857018 AATCCTTAGAATGGGATTCCAACTCAG 60.857 40.741 0.00 0.94 45.84 3.35
594 595 3.650647 TGGGATTCCAACTCAGCAC 57.349 52.632 4.80 0.00 40.73 4.40
595 596 0.038166 TGGGATTCCAACTCAGCACC 59.962 55.000 4.80 0.00 40.73 5.01
596 597 0.329596 GGGATTCCAACTCAGCACCT 59.670 55.000 4.80 0.00 0.00 4.00
597 598 1.272147 GGGATTCCAACTCAGCACCTT 60.272 52.381 4.80 0.00 0.00 3.50
598 599 2.519013 GGATTCCAACTCAGCACCTTT 58.481 47.619 0.00 0.00 0.00 3.11
599 600 2.893489 GGATTCCAACTCAGCACCTTTT 59.107 45.455 0.00 0.00 0.00 2.27
600 601 3.305608 GGATTCCAACTCAGCACCTTTTG 60.306 47.826 0.00 0.00 0.00 2.44
601 602 2.435372 TCCAACTCAGCACCTTTTGT 57.565 45.000 0.00 0.00 0.00 2.83
602 603 2.733956 TCCAACTCAGCACCTTTTGTT 58.266 42.857 0.00 0.00 0.00 2.83
603 604 3.096092 TCCAACTCAGCACCTTTTGTTT 58.904 40.909 0.00 0.00 0.00 2.83
604 605 3.513515 TCCAACTCAGCACCTTTTGTTTT 59.486 39.130 0.00 0.00 0.00 2.43
605 606 3.618150 CCAACTCAGCACCTTTTGTTTTG 59.382 43.478 0.00 0.00 0.00 2.44
606 607 4.493547 CAACTCAGCACCTTTTGTTTTGA 58.506 39.130 0.00 0.00 0.00 2.69
607 608 4.376340 ACTCAGCACCTTTTGTTTTGAG 57.624 40.909 0.00 0.00 36.84 3.02
608 609 4.016444 ACTCAGCACCTTTTGTTTTGAGA 58.984 39.130 5.68 0.00 35.55 3.27
609 610 4.646492 ACTCAGCACCTTTTGTTTTGAGAT 59.354 37.500 5.68 0.00 35.55 2.75
610 611 5.127682 ACTCAGCACCTTTTGTTTTGAGATT 59.872 36.000 5.68 0.00 35.55 2.40
611 612 5.976458 TCAGCACCTTTTGTTTTGAGATTT 58.024 33.333 0.00 0.00 0.00 2.17
612 613 6.405538 TCAGCACCTTTTGTTTTGAGATTTT 58.594 32.000 0.00 0.00 0.00 1.82
613 614 6.313411 TCAGCACCTTTTGTTTTGAGATTTTG 59.687 34.615 0.00 0.00 0.00 2.44
614 615 6.313411 CAGCACCTTTTGTTTTGAGATTTTGA 59.687 34.615 0.00 0.00 0.00 2.69
615 616 6.536224 AGCACCTTTTGTTTTGAGATTTTGAG 59.464 34.615 0.00 0.00 0.00 3.02
616 617 6.534793 GCACCTTTTGTTTTGAGATTTTGAGA 59.465 34.615 0.00 0.00 0.00 3.27
617 618 7.064490 GCACCTTTTGTTTTGAGATTTTGAGAA 59.936 33.333 0.00 0.00 0.00 2.87
618 619 8.598075 CACCTTTTGTTTTGAGATTTTGAGAAG 58.402 33.333 0.00 0.00 0.00 2.85
619 620 8.531146 ACCTTTTGTTTTGAGATTTTGAGAAGA 58.469 29.630 0.00 0.00 0.00 2.87
620 621 9.028185 CCTTTTGTTTTGAGATTTTGAGAAGAG 57.972 33.333 0.00 0.00 0.00 2.85
621 622 9.578439 CTTTTGTTTTGAGATTTTGAGAAGAGT 57.422 29.630 0.00 0.00 0.00 3.24
622 623 9.927668 TTTTGTTTTGAGATTTTGAGAAGAGTT 57.072 25.926 0.00 0.00 0.00 3.01
623 624 9.573133 TTTGTTTTGAGATTTTGAGAAGAGTTC 57.427 29.630 0.00 0.00 0.00 3.01
624 625 7.707104 TGTTTTGAGATTTTGAGAAGAGTTCC 58.293 34.615 0.00 0.00 0.00 3.62
625 626 7.557719 TGTTTTGAGATTTTGAGAAGAGTTCCT 59.442 33.333 0.00 0.00 0.00 3.36
626 627 7.736447 TTTGAGATTTTGAGAAGAGTTCCTC 57.264 36.000 0.00 0.00 0.00 3.71
627 628 6.678568 TGAGATTTTGAGAAGAGTTCCTCT 57.321 37.500 0.00 0.00 43.37 3.69
637 638 2.614259 AGAGTTCCTCTTTGGAGAGCA 58.386 47.619 0.00 0.00 46.64 4.26
638 639 2.301583 AGAGTTCCTCTTTGGAGAGCAC 59.698 50.000 0.00 0.00 46.64 4.40
639 640 2.037772 GAGTTCCTCTTTGGAGAGCACA 59.962 50.000 0.00 0.00 46.64 4.57
640 641 2.038295 AGTTCCTCTTTGGAGAGCACAG 59.962 50.000 0.00 0.00 46.64 3.66
641 642 1.722034 TCCTCTTTGGAGAGCACAGT 58.278 50.000 0.00 0.00 46.64 3.55
642 643 2.889512 TCCTCTTTGGAGAGCACAGTA 58.110 47.619 0.00 0.00 46.64 2.74
643 644 2.563179 TCCTCTTTGGAGAGCACAGTAC 59.437 50.000 0.00 0.00 46.64 2.73
644 645 2.600731 CTCTTTGGAGAGCACAGTACG 58.399 52.381 0.00 0.00 42.72 3.67
645 646 2.229062 CTCTTTGGAGAGCACAGTACGA 59.771 50.000 0.00 0.00 42.72 3.43
646 647 2.826128 TCTTTGGAGAGCACAGTACGAT 59.174 45.455 0.00 0.00 0.00 3.73
647 648 2.654749 TTGGAGAGCACAGTACGATG 57.345 50.000 0.00 0.00 0.00 3.84
648 649 1.834188 TGGAGAGCACAGTACGATGA 58.166 50.000 3.82 0.00 0.00 2.92
649 650 2.167662 TGGAGAGCACAGTACGATGAA 58.832 47.619 3.82 0.00 0.00 2.57
650 651 2.560981 TGGAGAGCACAGTACGATGAAA 59.439 45.455 3.82 0.00 0.00 2.69
651 652 3.182967 GGAGAGCACAGTACGATGAAAG 58.817 50.000 3.82 0.00 0.00 2.62
652 653 3.367498 GGAGAGCACAGTACGATGAAAGT 60.367 47.826 3.82 0.00 0.00 2.66
1034 1035 1.382557 TCCGCTTATCTCCAGCCCA 60.383 57.895 0.00 0.00 33.29 5.36
1294 1295 2.894731 AGCATAGATCCGGAGATTCCA 58.105 47.619 11.34 0.00 35.91 3.53
1355 1356 1.228245 GGCAAGAGACAACCTGGCA 60.228 57.895 0.00 0.00 0.00 4.92
1378 1379 6.293955 GCAAACTGAAACATCTTAGTAGCCAA 60.294 38.462 0.00 0.00 0.00 4.52
1396 1397 5.252547 AGCCAAAGGAAAAGAAAGCAAAAA 58.747 33.333 0.00 0.00 0.00 1.94
1458 1459 2.395651 CGTGAAAACGGGGTTGTGA 58.604 52.632 0.00 0.00 0.00 3.58
1674 1675 3.922375 ACCATGAGGGAAAGGTGAAAAA 58.078 40.909 0.00 0.00 41.15 1.94
1938 1939 1.926108 ACTAAGCAGAGGTCCGAACT 58.074 50.000 0.00 0.00 0.00 3.01
1993 1994 1.367346 TAGGGGTGAAATGCCACTCA 58.633 50.000 0.00 0.00 39.36 3.41
2059 2060 3.451178 GCAGTTAACTGGACATCTAGGGA 59.549 47.826 31.42 0.00 43.94 4.20
2073 2074 5.882557 ACATCTAGGGATAAAGCACTGTTTG 59.117 40.000 0.00 0.00 0.00 2.93
2074 2075 5.755409 TCTAGGGATAAAGCACTGTTTGA 57.245 39.130 0.00 0.00 0.00 2.69
2075 2076 6.121776 TCTAGGGATAAAGCACTGTTTGAA 57.878 37.500 0.00 0.00 0.00 2.69
2076 2077 6.721318 TCTAGGGATAAAGCACTGTTTGAAT 58.279 36.000 0.00 0.00 0.00 2.57
2077 2078 5.904362 AGGGATAAAGCACTGTTTGAATC 57.096 39.130 0.00 0.00 0.00 2.52
2078 2079 5.324409 AGGGATAAAGCACTGTTTGAATCA 58.676 37.500 0.00 0.00 0.00 2.57
2079 2080 5.183904 AGGGATAAAGCACTGTTTGAATCAC 59.816 40.000 0.00 1.66 0.00 3.06
2080 2081 5.402398 GGATAAAGCACTGTTTGAATCACC 58.598 41.667 0.00 0.00 0.00 4.02
2081 2082 5.183904 GGATAAAGCACTGTTTGAATCACCT 59.816 40.000 0.00 0.00 0.00 4.00
2082 2083 6.294731 GGATAAAGCACTGTTTGAATCACCTT 60.295 38.462 0.00 0.00 0.00 3.50
2083 2084 3.996150 AGCACTGTTTGAATCACCTTG 57.004 42.857 0.00 0.00 0.00 3.61
2084 2085 2.624838 AGCACTGTTTGAATCACCTTGG 59.375 45.455 0.00 0.00 0.00 3.61
2085 2086 2.863704 GCACTGTTTGAATCACCTTGGC 60.864 50.000 0.00 0.00 0.00 4.52
2086 2087 2.624838 CACTGTTTGAATCACCTTGGCT 59.375 45.455 0.00 0.00 0.00 4.75
2087 2088 3.068590 CACTGTTTGAATCACCTTGGCTT 59.931 43.478 0.00 0.00 0.00 4.35
2088 2089 3.319122 ACTGTTTGAATCACCTTGGCTTC 59.681 43.478 0.00 0.00 0.00 3.86
2089 2090 2.293122 TGTTTGAATCACCTTGGCTTCG 59.707 45.455 0.00 0.00 0.00 3.79
2090 2091 0.881118 TTGAATCACCTTGGCTTCGC 59.119 50.000 0.00 0.00 0.00 4.70
2177 2977 3.359033 AGATCAATTAAGCTGCTTGCCA 58.641 40.909 24.35 8.98 44.23 4.92
2202 3002 4.082571 CCTACTTGCAAGTTAGCTTTGCAT 60.083 41.667 35.20 12.41 40.37 3.96
2217 3017 1.182667 TGCATGTAGGCGTACACTCT 58.817 50.000 20.67 3.44 42.06 3.24
2263 4066 2.029964 GAAAGTGGTGGCGGACGA 59.970 61.111 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 5.531287 ACAACCCATCTTTTTGTCTCAGTAC 59.469 40.000 0.00 0.00 0.00 2.73
101 102 3.116939 ACTGTCCATCCTACCTGCTCTAT 60.117 47.826 0.00 0.00 0.00 1.98
107 108 1.909302 ACCAACTGTCCATCCTACCTG 59.091 52.381 0.00 0.00 0.00 4.00
119 120 5.023452 TCCATACTAGATGTGACCAACTGT 58.977 41.667 0.00 0.00 0.00 3.55
130 131 6.556212 GTCCATGTACGATCCATACTAGATG 58.444 44.000 0.00 0.00 0.00 2.90
252 253 0.889186 TCGCTCAAAGGGTTGAAGGC 60.889 55.000 0.00 0.00 43.18 4.35
379 380 7.056635 CCACTTATTGAACAGGATCTATGGTT 58.943 38.462 0.00 0.00 0.00 3.67
533 534 6.328782 TCTGAGGAATCTAGTTACAGGAGA 57.671 41.667 0.00 0.00 0.00 3.71
534 535 6.183360 GGTTCTGAGGAATCTAGTTACAGGAG 60.183 46.154 0.00 0.00 33.71 3.69
535 536 5.657302 GGTTCTGAGGAATCTAGTTACAGGA 59.343 44.000 0.00 0.00 33.71 3.86
536 537 5.422331 TGGTTCTGAGGAATCTAGTTACAGG 59.578 44.000 0.00 0.00 33.95 4.00
537 538 6.071334 TGTGGTTCTGAGGAATCTAGTTACAG 60.071 42.308 0.00 0.00 33.95 2.74
538 539 5.778241 TGTGGTTCTGAGGAATCTAGTTACA 59.222 40.000 0.00 0.00 33.95 2.41
539 540 6.282199 TGTGGTTCTGAGGAATCTAGTTAC 57.718 41.667 0.00 0.00 33.95 2.50
540 541 6.724441 TCTTGTGGTTCTGAGGAATCTAGTTA 59.276 38.462 0.00 0.00 33.95 2.24
541 542 5.544176 TCTTGTGGTTCTGAGGAATCTAGTT 59.456 40.000 0.00 0.00 33.95 2.24
542 543 5.087323 TCTTGTGGTTCTGAGGAATCTAGT 58.913 41.667 0.00 0.00 33.95 2.57
543 544 5.667539 TCTTGTGGTTCTGAGGAATCTAG 57.332 43.478 0.00 0.00 33.95 2.43
544 545 6.352222 GGATTCTTGTGGTTCTGAGGAATCTA 60.352 42.308 0.00 0.00 38.21 1.98
545 546 4.982241 TTCTTGTGGTTCTGAGGAATCT 57.018 40.909 0.00 0.00 33.95 2.40
546 547 4.637977 GGATTCTTGTGGTTCTGAGGAATC 59.362 45.833 0.00 0.00 37.74 2.52
547 548 4.290722 AGGATTCTTGTGGTTCTGAGGAAT 59.709 41.667 0.00 0.00 33.71 3.01
548 549 3.652869 AGGATTCTTGTGGTTCTGAGGAA 59.347 43.478 0.00 0.00 0.00 3.36
549 550 3.251484 AGGATTCTTGTGGTTCTGAGGA 58.749 45.455 0.00 0.00 0.00 3.71
550 551 3.710209 AGGATTCTTGTGGTTCTGAGG 57.290 47.619 0.00 0.00 0.00 3.86
551 552 6.042638 TCTAAGGATTCTTGTGGTTCTGAG 57.957 41.667 0.00 0.00 34.59 3.35
552 553 6.433847 TTCTAAGGATTCTTGTGGTTCTGA 57.566 37.500 0.00 0.00 34.59 3.27
553 554 6.094603 CCATTCTAAGGATTCTTGTGGTTCTG 59.905 42.308 0.00 0.00 34.59 3.02
554 555 6.183347 CCATTCTAAGGATTCTTGTGGTTCT 58.817 40.000 0.00 0.00 34.59 3.01
555 556 5.358160 CCCATTCTAAGGATTCTTGTGGTTC 59.642 44.000 0.00 0.00 34.59 3.62
556 557 5.015178 TCCCATTCTAAGGATTCTTGTGGTT 59.985 40.000 0.00 0.00 34.59 3.67
557 558 4.540099 TCCCATTCTAAGGATTCTTGTGGT 59.460 41.667 0.00 0.00 34.59 4.16
558 559 5.116084 TCCCATTCTAAGGATTCTTGTGG 57.884 43.478 0.00 0.00 34.59 4.17
566 567 5.433051 TGAGTTGGAATCCCATTCTAAGGAT 59.567 40.000 0.00 0.00 45.01 3.24
567 568 4.788075 TGAGTTGGAATCCCATTCTAAGGA 59.212 41.667 0.00 0.00 43.12 3.36
568 569 5.116084 TGAGTTGGAATCCCATTCTAAGG 57.884 43.478 0.00 0.00 43.12 2.69
569 570 4.578105 GCTGAGTTGGAATCCCATTCTAAG 59.422 45.833 0.00 0.00 43.12 2.18
570 571 4.018506 TGCTGAGTTGGAATCCCATTCTAA 60.019 41.667 0.00 0.00 43.12 2.10
571 572 3.523157 TGCTGAGTTGGAATCCCATTCTA 59.477 43.478 0.00 0.00 43.12 2.10
572 573 2.309755 TGCTGAGTTGGAATCCCATTCT 59.690 45.455 0.00 0.00 43.12 2.40
573 574 2.424956 GTGCTGAGTTGGAATCCCATTC 59.575 50.000 0.00 0.00 43.12 2.67
574 575 2.450476 GTGCTGAGTTGGAATCCCATT 58.550 47.619 0.00 0.00 43.12 3.16
575 576 1.341383 GGTGCTGAGTTGGAATCCCAT 60.341 52.381 0.00 0.00 43.12 4.00
576 577 0.038166 GGTGCTGAGTTGGAATCCCA 59.962 55.000 0.00 0.00 41.64 4.37
577 578 0.329596 AGGTGCTGAGTTGGAATCCC 59.670 55.000 0.00 0.00 0.00 3.85
578 579 2.206576 AAGGTGCTGAGTTGGAATCC 57.793 50.000 0.00 0.00 0.00 3.01
579 580 3.319122 ACAAAAGGTGCTGAGTTGGAATC 59.681 43.478 0.00 0.00 0.00 2.52
580 581 3.299503 ACAAAAGGTGCTGAGTTGGAAT 58.700 40.909 0.00 0.00 0.00 3.01
581 582 2.733956 ACAAAAGGTGCTGAGTTGGAA 58.266 42.857 0.00 0.00 0.00 3.53
582 583 2.435372 ACAAAAGGTGCTGAGTTGGA 57.565 45.000 0.00 0.00 0.00 3.53
583 584 3.525268 AAACAAAAGGTGCTGAGTTGG 57.475 42.857 0.00 0.00 0.00 3.77
584 585 4.493547 TCAAAACAAAAGGTGCTGAGTTG 58.506 39.130 0.00 0.00 0.00 3.16
585 586 4.462483 TCTCAAAACAAAAGGTGCTGAGTT 59.538 37.500 0.00 0.00 38.89 3.01
586 587 4.016444 TCTCAAAACAAAAGGTGCTGAGT 58.984 39.130 0.00 0.00 38.89 3.41
587 588 4.637483 TCTCAAAACAAAAGGTGCTGAG 57.363 40.909 0.00 0.00 39.04 3.35
588 589 5.596836 AATCTCAAAACAAAAGGTGCTGA 57.403 34.783 0.00 0.00 0.00 4.26
589 590 6.313411 TCAAAATCTCAAAACAAAAGGTGCTG 59.687 34.615 0.00 0.00 0.00 4.41
590 591 6.405538 TCAAAATCTCAAAACAAAAGGTGCT 58.594 32.000 0.00 0.00 0.00 4.40
591 592 6.534793 TCTCAAAATCTCAAAACAAAAGGTGC 59.465 34.615 0.00 0.00 0.00 5.01
592 593 8.477984 TTCTCAAAATCTCAAAACAAAAGGTG 57.522 30.769 0.00 0.00 0.00 4.00
593 594 8.531146 TCTTCTCAAAATCTCAAAACAAAAGGT 58.469 29.630 0.00 0.00 0.00 3.50
594 595 8.931385 TCTTCTCAAAATCTCAAAACAAAAGG 57.069 30.769 0.00 0.00 0.00 3.11
595 596 9.578439 ACTCTTCTCAAAATCTCAAAACAAAAG 57.422 29.630 0.00 0.00 0.00 2.27
596 597 9.927668 AACTCTTCTCAAAATCTCAAAACAAAA 57.072 25.926 0.00 0.00 0.00 2.44
597 598 9.573133 GAACTCTTCTCAAAATCTCAAAACAAA 57.427 29.630 0.00 0.00 0.00 2.83
598 599 8.190784 GGAACTCTTCTCAAAATCTCAAAACAA 58.809 33.333 0.00 0.00 0.00 2.83
599 600 7.557719 AGGAACTCTTCTCAAAATCTCAAAACA 59.442 33.333 0.00 0.00 0.00 2.83
600 601 7.935520 AGGAACTCTTCTCAAAATCTCAAAAC 58.064 34.615 0.00 0.00 0.00 2.43
625 626 2.235891 TCGTACTGTGCTCTCCAAAGA 58.764 47.619 0.00 0.00 32.77 2.52
626 627 2.724977 TCGTACTGTGCTCTCCAAAG 57.275 50.000 0.00 0.00 34.75 2.77
627 628 2.560981 TCATCGTACTGTGCTCTCCAAA 59.439 45.455 0.00 0.00 0.00 3.28
628 629 2.167662 TCATCGTACTGTGCTCTCCAA 58.832 47.619 0.00 0.00 0.00 3.53
629 630 1.834188 TCATCGTACTGTGCTCTCCA 58.166 50.000 0.00 0.00 0.00 3.86
630 631 2.941453 TTCATCGTACTGTGCTCTCC 57.059 50.000 0.00 0.00 0.00 3.71
631 632 3.839293 ACTTTCATCGTACTGTGCTCTC 58.161 45.455 0.00 0.00 0.00 3.20
632 633 3.944055 ACTTTCATCGTACTGTGCTCT 57.056 42.857 0.00 0.00 0.00 4.09
1034 1035 7.484975 GCTATCATAGTATCCGCTAAGTTCAT 58.515 38.462 0.00 0.00 0.00 2.57
1355 1356 7.040409 CCTTTGGCTACTAAGATGTTTCAGTTT 60.040 37.037 0.00 0.00 32.20 2.66
1378 1379 6.257849 GGAATCGTTTTTGCTTTCTTTTCCTT 59.742 34.615 0.00 0.00 0.00 3.36
1413 1414 2.512515 GCTCCCATTTCGCTCGCT 60.513 61.111 0.00 0.00 0.00 4.93
1458 1459 2.738846 CACAACGCTTGTATTGCTCTCT 59.261 45.455 3.60 0.00 43.23 3.10
1639 1640 6.923670 TCCCTCATGGTACTACTTCTCTATT 58.076 40.000 0.00 0.00 34.77 1.73
1644 1645 4.717280 CCTTTCCCTCATGGTACTACTTCT 59.283 45.833 0.00 0.00 34.77 2.85
1692 1693 3.562557 AGCACGGTTTCACGTTCTATTTT 59.437 39.130 0.00 0.00 46.25 1.82
1938 1939 3.681417 CGCTGATTCTTCAACATCAGTCA 59.319 43.478 10.14 0.00 45.69 3.41
2043 2044 4.721776 TGCTTTATCCCTAGATGTCCAGTT 59.278 41.667 0.00 0.00 33.67 3.16
2059 2060 6.449698 CAAGGTGATTCAAACAGTGCTTTAT 58.550 36.000 0.00 0.00 0.00 1.40
2085 2086 1.941734 GATCTCGACTGCGGCGAAG 60.942 63.158 14.72 14.72 37.32 3.79
2086 2087 2.102357 GATCTCGACTGCGGCGAA 59.898 61.111 12.98 0.00 37.32 4.70
2087 2088 3.889044 GGATCTCGACTGCGGCGA 61.889 66.667 12.98 10.80 38.28 5.54
2088 2089 4.193334 TGGATCTCGACTGCGGCG 62.193 66.667 0.51 0.51 38.28 6.46
2089 2090 2.583593 GTGGATCTCGACTGCGGC 60.584 66.667 0.00 0.00 38.28 6.53
2090 2091 1.064946 GAGTGGATCTCGACTGCGG 59.935 63.158 0.00 0.00 35.02 5.69
2091 2092 4.700037 GAGTGGATCTCGACTGCG 57.300 61.111 0.00 0.00 35.02 5.18
2177 2977 3.425162 AAGCTAACTTGCAAGTAGGCT 57.575 42.857 34.01 34.01 43.61 4.58
2182 2982 3.068590 ACATGCAAAGCTAACTTGCAAGT 59.931 39.130 26.36 26.36 40.66 3.16
2202 3002 0.896479 TGCCAGAGTGTACGCCTACA 60.896 55.000 1.98 0.26 0.00 2.74
2217 3017 6.830324 ACTTAGAATGCTAGATGAAATTGCCA 59.170 34.615 0.00 0.00 0.00 4.92


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.