Multiple sequence alignment - TraesCS6A01G023500

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 TraesCS6A01G023500 chr6A 100.000 2840 0 0 1 2840 11768463 11765624 0.000000e+00 5245
1 TraesCS6A01G023500 chr6A 79.697 2044 351 43 709 2731 11497287 11499287 0.000000e+00 1417
2 TraesCS6A01G023500 chr6A 79.725 947 177 11 1880 2817 11476358 11477298 0.000000e+00 671
3 TraesCS6A01G023500 chr6A 76.939 954 184 24 1880 2816 10931540 10930606 7.020000e-141 510
4 TraesCS6A01G023500 chr6D 98.632 2193 28 1 650 2840 10317187 10314995 0.000000e+00 3882
5 TraesCS6A01G023500 chr6D 99.041 417 4 0 1 417 10317603 10317187 0.000000e+00 749
6 TraesCS6A01G023500 chr6D 78.000 950 180 19 1880 2816 9851334 9850401 1.140000e-158 569
7 TraesCS6A01G023500 chr6D 76.955 972 178 27 1861 2815 10309321 10308379 1.950000e-141 512
8 TraesCS6A01G023500 chr6D 82.189 539 86 5 1880 2410 9914259 9914795 3.340000e-124 455
9 TraesCS6A01G023500 chr6B 94.305 2195 97 9 652 2840 18849337 18847165 0.000000e+00 3336
10 TraesCS6A01G023500 chr6B 78.422 2192 423 38 652 2820 18239663 18241827 0.000000e+00 1382
11 TraesCS6A01G023500 chr6B 77.154 1834 372 33 1007 2820 18401612 18399806 0.000000e+00 1022
12 TraesCS6A01G023500 chr6B 95.238 420 16 3 1 418 18849752 18849335 0.000000e+00 662
13 TraesCS6A01G023500 chr6B 78.750 960 182 17 1880 2825 18813942 18814893 8.640000e-175 623
14 TraesCS6A01G023500 chr6B 93.416 243 16 0 411 653 523343879 523343637 7.480000e-96 361
15 TraesCS6A01G023500 chrUn 80.189 954 169 15 1874 2817 240893045 240893988 0.000000e+00 697
16 TraesCS6A01G023500 chrUn 80.189 954 169 15 1874 2817 268930855 268929912 0.000000e+00 697
17 TraesCS6A01G023500 chr2A 93.878 245 14 1 412 655 362445894 362446138 4.470000e-98 368
18 TraesCS6A01G023500 chr1D 93.469 245 16 0 409 653 27881893 27881649 5.780000e-97 364
19 TraesCS6A01G023500 chr1D 92.623 244 18 0 410 653 249563238 249562995 4.500000e-93 351
20 TraesCS6A01G023500 chr7D 93.388 242 16 0 412 653 31061841 31062082 2.690000e-95 359
21 TraesCS6A01G023500 chr7A 92.713 247 17 1 407 653 631367664 631367419 3.480000e-94 355
22 TraesCS6A01G023500 chr2B 92.623 244 18 0 410 653 101976957 101976714 4.500000e-93 351
23 TraesCS6A01G023500 chr2B 92.946 241 16 1 413 653 399350682 399350443 1.620000e-92 350
24 TraesCS6A01G023500 chr4D 92.562 242 18 0 410 651 26895774 26896015 5.820000e-92 348


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 TraesCS6A01G023500 chr6A 11765624 11768463 2839 True 5245.0 5245 100.0000 1 2840 1 chr6A.!!$R2 2839
1 TraesCS6A01G023500 chr6A 11497287 11499287 2000 False 1417.0 1417 79.6970 709 2731 1 chr6A.!!$F2 2022
2 TraesCS6A01G023500 chr6A 11476358 11477298 940 False 671.0 671 79.7250 1880 2817 1 chr6A.!!$F1 937
3 TraesCS6A01G023500 chr6A 10930606 10931540 934 True 510.0 510 76.9390 1880 2816 1 chr6A.!!$R1 936
4 TraesCS6A01G023500 chr6D 10314995 10317603 2608 True 2315.5 3882 98.8365 1 2840 2 chr6D.!!$R3 2839
5 TraesCS6A01G023500 chr6D 9850401 9851334 933 True 569.0 569 78.0000 1880 2816 1 chr6D.!!$R1 936
6 TraesCS6A01G023500 chr6D 10308379 10309321 942 True 512.0 512 76.9550 1861 2815 1 chr6D.!!$R2 954
7 TraesCS6A01G023500 chr6D 9914259 9914795 536 False 455.0 455 82.1890 1880 2410 1 chr6D.!!$F1 530
8 TraesCS6A01G023500 chr6B 18847165 18849752 2587 True 1999.0 3336 94.7715 1 2840 2 chr6B.!!$R3 2839
9 TraesCS6A01G023500 chr6B 18239663 18241827 2164 False 1382.0 1382 78.4220 652 2820 1 chr6B.!!$F1 2168
10 TraesCS6A01G023500 chr6B 18399806 18401612 1806 True 1022.0 1022 77.1540 1007 2820 1 chr6B.!!$R1 1813
11 TraesCS6A01G023500 chr6B 18813942 18814893 951 False 623.0 623 78.7500 1880 2825 1 chr6B.!!$F2 945
12 TraesCS6A01G023500 chrUn 240893045 240893988 943 False 697.0 697 80.1890 1874 2817 1 chrUn.!!$F1 943
13 TraesCS6A01G023500 chrUn 268929912 268930855 943 True 697.0 697 80.1890 1874 2817 1 chrUn.!!$R1 943

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
639 641 0.040425 GCGGGCGCACTATATTTTGG 60.04 55.0 8.62 0.0 41.49 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2383 2414 3.20129 CAATATTGCACGGAGCTTCTCT 58.799 45.455 1.74 0.0 45.94 3.1 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
252 254 7.611467 ACTTGTGCATGTTATCTTTCTTATCCA 59.389 33.333 0.00 0.00 0.00 3.41
436 438 8.993404 ATACTACCTCCGTTCTAAAATAGAGT 57.007 34.615 0.00 0.00 35.96 3.24
437 439 7.098074 ACTACCTCCGTTCTAAAATAGAGTG 57.902 40.000 0.00 0.00 35.96 3.51
438 440 4.756502 ACCTCCGTTCTAAAATAGAGTGC 58.243 43.478 0.00 0.00 35.96 4.40
439 441 4.466726 ACCTCCGTTCTAAAATAGAGTGCT 59.533 41.667 0.00 0.00 35.96 4.40
440 442 5.046520 ACCTCCGTTCTAAAATAGAGTGCTT 60.047 40.000 0.00 0.00 35.96 3.91
441 443 5.520649 CCTCCGTTCTAAAATAGAGTGCTTC 59.479 44.000 0.00 0.00 35.96 3.86
442 444 5.416947 TCCGTTCTAAAATAGAGTGCTTCC 58.583 41.667 0.00 0.00 35.96 3.46
443 445 5.187186 TCCGTTCTAAAATAGAGTGCTTCCT 59.813 40.000 0.00 0.00 35.96 3.36
444 446 5.520649 CCGTTCTAAAATAGAGTGCTTCCTC 59.479 44.000 0.00 0.00 35.96 3.71
445 447 6.334202 CGTTCTAAAATAGAGTGCTTCCTCT 58.666 40.000 6.42 6.42 44.00 3.69
446 448 7.416438 CCGTTCTAAAATAGAGTGCTTCCTCTA 60.416 40.741 9.68 9.68 45.53 2.43
452 454 2.035632 AGAGTGCTTCCTCTATTCCCG 58.964 52.381 0.14 0.00 40.02 5.14
453 455 1.757699 GAGTGCTTCCTCTATTCCCGT 59.242 52.381 0.00 0.00 0.00 5.28
454 456 1.482593 AGTGCTTCCTCTATTCCCGTG 59.517 52.381 0.00 0.00 0.00 4.94
455 457 0.178068 TGCTTCCTCTATTCCCGTGC 59.822 55.000 0.00 0.00 0.00 5.34
456 458 0.466124 GCTTCCTCTATTCCCGTGCT 59.534 55.000 0.00 0.00 0.00 4.40
457 459 1.134371 GCTTCCTCTATTCCCGTGCTT 60.134 52.381 0.00 0.00 0.00 3.91
458 460 2.681097 GCTTCCTCTATTCCCGTGCTTT 60.681 50.000 0.00 0.00 0.00 3.51
459 461 3.431766 GCTTCCTCTATTCCCGTGCTTTA 60.432 47.826 0.00 0.00 0.00 1.85
460 462 4.766375 CTTCCTCTATTCCCGTGCTTTAA 58.234 43.478 0.00 0.00 0.00 1.52
461 463 4.133013 TCCTCTATTCCCGTGCTTTAAC 57.867 45.455 0.00 0.00 0.00 2.01
462 464 3.773119 TCCTCTATTCCCGTGCTTTAACT 59.227 43.478 0.00 0.00 0.00 2.24
463 465 4.224370 TCCTCTATTCCCGTGCTTTAACTT 59.776 41.667 0.00 0.00 0.00 2.66
464 466 4.941873 CCTCTATTCCCGTGCTTTAACTTT 59.058 41.667 0.00 0.00 0.00 2.66
465 467 5.163754 CCTCTATTCCCGTGCTTTAACTTTG 60.164 44.000 0.00 0.00 0.00 2.77
466 468 5.553123 TCTATTCCCGTGCTTTAACTTTGA 58.447 37.500 0.00 0.00 0.00 2.69
467 469 3.974871 TTCCCGTGCTTTAACTTTGAC 57.025 42.857 0.00 0.00 0.00 3.18
468 470 2.223745 TCCCGTGCTTTAACTTTGACC 58.776 47.619 0.00 0.00 0.00 4.02
469 471 1.950909 CCCGTGCTTTAACTTTGACCA 59.049 47.619 0.00 0.00 0.00 4.02
470 472 2.556622 CCCGTGCTTTAACTTTGACCAT 59.443 45.455 0.00 0.00 0.00 3.55
471 473 3.754323 CCCGTGCTTTAACTTTGACCATA 59.246 43.478 0.00 0.00 0.00 2.74
472 474 4.216687 CCCGTGCTTTAACTTTGACCATAA 59.783 41.667 0.00 0.00 0.00 1.90
473 475 5.278561 CCCGTGCTTTAACTTTGACCATAAA 60.279 40.000 0.00 0.00 0.00 1.40
474 476 6.386654 CCGTGCTTTAACTTTGACCATAAAT 58.613 36.000 0.00 0.00 0.00 1.40
475 477 6.866248 CCGTGCTTTAACTTTGACCATAAATT 59.134 34.615 0.00 0.00 0.00 1.82
476 478 7.383843 CCGTGCTTTAACTTTGACCATAAATTT 59.616 33.333 0.00 0.00 0.00 1.82
477 479 9.400638 CGTGCTTTAACTTTGACCATAAATTTA 57.599 29.630 0.00 0.00 0.00 1.40
490 492 9.489084 TGACCATAAATTTATCTAATGAGACCG 57.511 33.333 7.76 0.00 33.41 4.79
491 493 9.706691 GACCATAAATTTATCTAATGAGACCGA 57.293 33.333 7.76 0.00 33.41 4.69
492 494 9.490379 ACCATAAATTTATCTAATGAGACCGAC 57.510 33.333 7.76 0.00 33.41 4.79
493 495 9.712305 CCATAAATTTATCTAATGAGACCGACT 57.288 33.333 7.76 0.00 33.41 4.18
495 497 7.484035 AAATTTATCTAATGAGACCGACTGC 57.516 36.000 0.00 0.00 33.41 4.40
496 498 2.783828 ATCTAATGAGACCGACTGCG 57.216 50.000 0.00 0.00 33.41 5.18
519 521 2.354821 CGGGAGCAAAAGTTATACCAGC 59.645 50.000 0.00 0.00 0.00 4.85
520 522 2.354821 GGGAGCAAAAGTTATACCAGCG 59.645 50.000 0.00 0.00 0.00 5.18
521 523 3.267483 GGAGCAAAAGTTATACCAGCGA 58.733 45.455 0.00 0.00 0.00 4.93
522 524 3.687698 GGAGCAAAAGTTATACCAGCGAA 59.312 43.478 0.00 0.00 0.00 4.70
523 525 4.335594 GGAGCAAAAGTTATACCAGCGAAT 59.664 41.667 0.00 0.00 0.00 3.34
524 526 5.163652 GGAGCAAAAGTTATACCAGCGAATT 60.164 40.000 0.00 0.00 0.00 2.17
525 527 5.880341 AGCAAAAGTTATACCAGCGAATTC 58.120 37.500 0.00 0.00 0.00 2.17
526 528 4.728608 GCAAAAGTTATACCAGCGAATTCG 59.271 41.667 23.34 23.34 43.27 3.34
527 529 5.672819 GCAAAAGTTATACCAGCGAATTCGT 60.673 40.000 27.24 12.64 42.22 3.85
528 530 6.455913 GCAAAAGTTATACCAGCGAATTCGTA 60.456 38.462 27.24 13.25 42.22 3.43
529 531 7.627340 CAAAAGTTATACCAGCGAATTCGTAT 58.373 34.615 27.24 18.68 42.22 3.06
530 532 7.781548 AAAGTTATACCAGCGAATTCGTATT 57.218 32.000 27.24 12.01 42.22 1.89
531 533 7.404139 AAGTTATACCAGCGAATTCGTATTC 57.596 36.000 27.24 11.90 42.22 1.75
532 534 6.509656 AGTTATACCAGCGAATTCGTATTCA 58.490 36.000 27.24 11.97 40.17 2.57
533 535 6.982141 AGTTATACCAGCGAATTCGTATTCAA 59.018 34.615 27.24 10.80 40.17 2.69
534 536 7.493320 AGTTATACCAGCGAATTCGTATTCAAA 59.507 33.333 27.24 12.20 40.17 2.69
535 537 6.671614 ATACCAGCGAATTCGTATTCAAAA 57.328 33.333 27.24 7.95 40.17 2.44
536 538 4.969816 ACCAGCGAATTCGTATTCAAAAG 58.030 39.130 27.24 9.85 40.17 2.27
537 539 4.693566 ACCAGCGAATTCGTATTCAAAAGA 59.306 37.500 27.24 0.00 40.17 2.52
538 540 5.180492 ACCAGCGAATTCGTATTCAAAAGAA 59.820 36.000 27.24 0.00 40.17 2.52
539 541 5.734498 CCAGCGAATTCGTATTCAAAAGAAG 59.266 40.000 27.24 3.73 40.17 2.85
540 542 6.307155 CAGCGAATTCGTATTCAAAAGAAGT 58.693 36.000 27.24 0.00 40.17 3.01
541 543 6.797033 CAGCGAATTCGTATTCAAAAGAAGTT 59.203 34.615 27.24 0.00 40.17 2.66
542 544 7.323656 CAGCGAATTCGTATTCAAAAGAAGTTT 59.676 33.333 27.24 0.00 40.17 2.66
543 545 7.860872 AGCGAATTCGTATTCAAAAGAAGTTTT 59.139 29.630 27.24 0.00 40.17 2.43
544 546 8.147793 GCGAATTCGTATTCAAAAGAAGTTTTC 58.852 33.333 27.24 1.72 40.17 2.29
545 547 9.165014 CGAATTCGTATTCAAAAGAAGTTTTCA 57.835 29.630 19.67 0.00 40.17 2.69
568 570 9.561069 TTCAACTATATAATTTCTTCTCCTGCC 57.439 33.333 0.00 0.00 0.00 4.85
569 571 8.713971 TCAACTATATAATTTCTTCTCCTGCCA 58.286 33.333 0.00 0.00 0.00 4.92
570 572 8.778358 CAACTATATAATTTCTTCTCCTGCCAC 58.222 37.037 0.00 0.00 0.00 5.01
571 573 8.034313 ACTATATAATTTCTTCTCCTGCCACA 57.966 34.615 0.00 0.00 0.00 4.17
572 574 8.153550 ACTATATAATTTCTTCTCCTGCCACAG 58.846 37.037 0.00 0.00 0.00 3.66
573 575 3.515602 AATTTCTTCTCCTGCCACAGT 57.484 42.857 0.00 0.00 0.00 3.55
574 576 3.515602 ATTTCTTCTCCTGCCACAGTT 57.484 42.857 0.00 0.00 0.00 3.16
575 577 2.260844 TTCTTCTCCTGCCACAGTTG 57.739 50.000 0.00 0.00 0.00 3.16
577 579 0.109342 CTTCTCCTGCCACAGTTGGT 59.891 55.000 0.00 0.00 45.98 3.67
578 580 0.108585 TTCTCCTGCCACAGTTGGTC 59.891 55.000 0.00 0.00 45.98 4.02
579 581 0.764369 TCTCCTGCCACAGTTGGTCT 60.764 55.000 0.00 0.00 45.98 3.85
580 582 0.321122 CTCCTGCCACAGTTGGTCTC 60.321 60.000 0.00 0.00 45.98 3.36
581 583 1.669115 CCTGCCACAGTTGGTCTCG 60.669 63.158 0.00 0.00 45.98 4.04
582 584 1.069765 CTGCCACAGTTGGTCTCGT 59.930 57.895 0.00 0.00 45.98 4.18
583 585 0.532862 CTGCCACAGTTGGTCTCGTT 60.533 55.000 0.00 0.00 45.98 3.85
584 586 0.813610 TGCCACAGTTGGTCTCGTTG 60.814 55.000 0.00 0.00 45.98 4.10
585 587 1.507141 GCCACAGTTGGTCTCGTTGG 61.507 60.000 0.00 0.00 45.98 3.77
586 588 0.179056 CCACAGTTGGTCTCGTTGGT 60.179 55.000 0.00 0.00 38.23 3.67
587 589 1.663695 CACAGTTGGTCTCGTTGGTT 58.336 50.000 0.00 0.00 0.00 3.67
588 590 2.484065 CCACAGTTGGTCTCGTTGGTTA 60.484 50.000 0.00 0.00 38.23 2.85
589 591 3.199677 CACAGTTGGTCTCGTTGGTTAA 58.800 45.455 0.00 0.00 0.00 2.01
590 592 3.623960 CACAGTTGGTCTCGTTGGTTAAA 59.376 43.478 0.00 0.00 0.00 1.52
591 593 4.274950 CACAGTTGGTCTCGTTGGTTAAAT 59.725 41.667 0.00 0.00 0.00 1.40
592 594 4.885325 ACAGTTGGTCTCGTTGGTTAAATT 59.115 37.500 0.00 0.00 0.00 1.82
593 595 5.358725 ACAGTTGGTCTCGTTGGTTAAATTT 59.641 36.000 0.00 0.00 0.00 1.82
594 596 6.543100 ACAGTTGGTCTCGTTGGTTAAATTTA 59.457 34.615 0.00 0.00 0.00 1.40
595 597 7.229907 ACAGTTGGTCTCGTTGGTTAAATTTAT 59.770 33.333 0.00 0.00 0.00 1.40
596 598 7.537306 CAGTTGGTCTCGTTGGTTAAATTTATG 59.463 37.037 0.00 0.00 0.00 1.90
597 599 7.446013 AGTTGGTCTCGTTGGTTAAATTTATGA 59.554 33.333 0.00 0.00 0.00 2.15
598 600 7.931578 TGGTCTCGTTGGTTAAATTTATGAT 57.068 32.000 0.00 0.00 0.00 2.45
599 601 7.981142 TGGTCTCGTTGGTTAAATTTATGATC 58.019 34.615 0.00 0.00 0.00 2.92
600 602 7.608376 TGGTCTCGTTGGTTAAATTTATGATCA 59.392 33.333 0.00 0.00 0.00 2.92
601 603 8.455682 GGTCTCGTTGGTTAAATTTATGATCAA 58.544 33.333 0.00 0.00 0.00 2.57
602 604 9.834628 GTCTCGTTGGTTAAATTTATGATCAAA 57.165 29.630 0.00 0.00 0.00 2.69
604 606 9.840427 CTCGTTGGTTAAATTTATGATCAAAGT 57.160 29.630 0.00 0.00 0.00 2.66
609 611 9.921637 TGGTTAAATTTATGATCAAAGTTGGAC 57.078 29.630 0.00 0.67 29.44 4.02
610 612 9.366216 GGTTAAATTTATGATCAAAGTTGGACC 57.634 33.333 0.00 5.86 31.86 4.46
613 615 6.683974 ATTTATGATCAAAGTTGGACCTCG 57.316 37.500 0.00 0.00 0.00 4.63
614 616 2.472695 TGATCAAAGTTGGACCTCGG 57.527 50.000 0.00 0.00 0.00 4.63
615 617 1.003118 TGATCAAAGTTGGACCTCGGG 59.997 52.381 0.00 0.00 0.00 5.14
616 618 1.278127 GATCAAAGTTGGACCTCGGGA 59.722 52.381 0.00 0.00 0.00 5.14
617 619 1.133363 TCAAAGTTGGACCTCGGGAA 58.867 50.000 0.00 0.00 0.00 3.97
618 620 1.071699 TCAAAGTTGGACCTCGGGAAG 59.928 52.381 0.00 0.00 0.00 3.46
619 621 0.250770 AAAGTTGGACCTCGGGAAGC 60.251 55.000 0.00 0.00 0.00 3.86
620 622 2.434359 GTTGGACCTCGGGAAGCG 60.434 66.667 0.00 0.00 0.00 4.68
621 623 4.388499 TTGGACCTCGGGAAGCGC 62.388 66.667 0.00 0.00 0.00 5.92
636 638 3.637714 CGCGGGCGCACTATATTT 58.362 55.556 8.62 0.00 42.06 1.40
637 639 1.938861 CGCGGGCGCACTATATTTT 59.061 52.632 8.62 0.00 42.06 1.82
638 640 0.384230 CGCGGGCGCACTATATTTTG 60.384 55.000 8.62 0.00 42.06 2.44
639 641 0.040425 GCGGGCGCACTATATTTTGG 60.040 55.000 8.62 0.00 41.49 3.28
640 642 1.588674 CGGGCGCACTATATTTTGGA 58.411 50.000 8.62 0.00 0.00 3.53
641 643 1.944024 CGGGCGCACTATATTTTGGAA 59.056 47.619 8.62 0.00 0.00 3.53
642 644 2.552315 CGGGCGCACTATATTTTGGAAT 59.448 45.455 8.62 0.00 0.00 3.01
643 645 3.609175 CGGGCGCACTATATTTTGGAATG 60.609 47.826 8.62 0.00 0.00 2.67
644 646 3.305335 GGGCGCACTATATTTTGGAATGG 60.305 47.826 10.83 0.00 0.00 3.16
645 647 3.568007 GGCGCACTATATTTTGGAATGGA 59.432 43.478 10.83 0.00 0.00 3.41
646 648 4.320494 GGCGCACTATATTTTGGAATGGAG 60.320 45.833 10.83 0.00 0.00 3.86
647 649 4.320494 GCGCACTATATTTTGGAATGGAGG 60.320 45.833 0.30 0.00 0.00 4.30
648 650 4.216257 CGCACTATATTTTGGAATGGAGGG 59.784 45.833 0.00 0.00 0.00 4.30
649 651 5.385198 GCACTATATTTTGGAATGGAGGGA 58.615 41.667 0.00 0.00 0.00 4.20
745 750 4.895668 ATCAAGGCAAACACCATTGATT 57.104 36.364 0.00 0.00 35.69 2.57
873 878 2.906182 TAGCCCAACAGCTCGCATCG 62.906 60.000 0.00 0.00 43.67 3.84
1013 1018 2.439409 TCAGGTGATGCAGATGTTTGG 58.561 47.619 0.00 0.00 0.00 3.28
1242 1247 1.212935 CAAGGGAGGTTTCGGATGGAT 59.787 52.381 0.00 0.00 0.00 3.41
1266 1274 4.038402 CCCAATATGAAAGACAAGGCCATC 59.962 45.833 5.01 0.00 0.00 3.51
1998 2017 3.967332 AAATGTGATGGGAGCCAAAAG 57.033 42.857 0.00 0.00 36.95 2.27
2071 2090 2.949644 GTTAACAAAGTCCACCTGCTGT 59.050 45.455 0.00 0.00 0.00 4.40
2383 2414 1.969208 CAGATCATCCTGCTAGGCTGA 59.031 52.381 9.98 9.98 43.78 4.26
2533 2573 0.960364 GCGATCAAGCCCTCCAACAA 60.960 55.000 0.00 0.00 0.00 2.83
2652 2702 6.818644 GCCACATCCGTACATATTGATATCTT 59.181 38.462 3.98 0.00 0.00 2.40
2833 2910 6.699575 AAGATATTTCTTTGGGATGAACCG 57.300 37.500 0.00 0.00 39.18 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
417 419 5.012328 AGCACTCTATTTTAGAACGGAGG 57.988 43.478 0.00 0.00 33.75 4.30
418 420 5.520649 GGAAGCACTCTATTTTAGAACGGAG 59.479 44.000 0.00 0.00 33.75 4.63
419 421 5.187186 AGGAAGCACTCTATTTTAGAACGGA 59.813 40.000 0.00 0.00 33.75 4.69
420 422 5.420409 AGGAAGCACTCTATTTTAGAACGG 58.580 41.667 0.00 0.00 33.75 4.44
421 423 6.334202 AGAGGAAGCACTCTATTTTAGAACG 58.666 40.000 4.07 0.00 45.62 3.95
433 435 1.757699 ACGGGAATAGAGGAAGCACTC 59.242 52.381 0.00 0.00 37.77 3.51
434 436 1.482593 CACGGGAATAGAGGAAGCACT 59.517 52.381 0.00 0.00 0.00 4.40
435 437 1.941325 CACGGGAATAGAGGAAGCAC 58.059 55.000 0.00 0.00 0.00 4.40
436 438 0.178068 GCACGGGAATAGAGGAAGCA 59.822 55.000 0.00 0.00 0.00 3.91
437 439 0.466124 AGCACGGGAATAGAGGAAGC 59.534 55.000 0.00 0.00 0.00 3.86
438 440 2.990066 AAGCACGGGAATAGAGGAAG 57.010 50.000 0.00 0.00 0.00 3.46
439 441 4.224370 AGTTAAAGCACGGGAATAGAGGAA 59.776 41.667 0.00 0.00 0.00 3.36
440 442 3.773119 AGTTAAAGCACGGGAATAGAGGA 59.227 43.478 0.00 0.00 0.00 3.71
441 443 4.138487 AGTTAAAGCACGGGAATAGAGG 57.862 45.455 0.00 0.00 0.00 3.69
442 444 5.642063 TCAAAGTTAAAGCACGGGAATAGAG 59.358 40.000 0.00 0.00 0.00 2.43
443 445 5.410439 GTCAAAGTTAAAGCACGGGAATAGA 59.590 40.000 0.00 0.00 0.00 1.98
444 446 5.391629 GGTCAAAGTTAAAGCACGGGAATAG 60.392 44.000 0.00 0.00 0.00 1.73
445 447 4.456566 GGTCAAAGTTAAAGCACGGGAATA 59.543 41.667 0.00 0.00 0.00 1.75
446 448 3.254903 GGTCAAAGTTAAAGCACGGGAAT 59.745 43.478 0.00 0.00 0.00 3.01
447 449 2.619646 GGTCAAAGTTAAAGCACGGGAA 59.380 45.455 0.00 0.00 0.00 3.97
448 450 2.223745 GGTCAAAGTTAAAGCACGGGA 58.776 47.619 0.00 0.00 0.00 5.14
449 451 1.950909 TGGTCAAAGTTAAAGCACGGG 59.049 47.619 0.00 0.00 0.00 5.28
450 452 3.915437 ATGGTCAAAGTTAAAGCACGG 57.085 42.857 0.00 0.00 0.00 4.94
451 453 7.867445 AATTTATGGTCAAAGTTAAAGCACG 57.133 32.000 0.00 0.00 0.00 5.34
464 466 9.489084 CGGTCTCATTAGATAAATTTATGGTCA 57.511 33.333 15.39 0.00 33.30 4.02
465 467 9.706691 TCGGTCTCATTAGATAAATTTATGGTC 57.293 33.333 15.39 2.51 33.30 4.02
466 468 9.490379 GTCGGTCTCATTAGATAAATTTATGGT 57.510 33.333 15.39 5.34 33.30 3.55
467 469 9.712305 AGTCGGTCTCATTAGATAAATTTATGG 57.288 33.333 15.39 0.84 33.30 2.74
469 471 9.209175 GCAGTCGGTCTCATTAGATAAATTTAT 57.791 33.333 10.51 10.51 33.30 1.40
470 472 7.381408 CGCAGTCGGTCTCATTAGATAAATTTA 59.619 37.037 0.00 0.00 33.30 1.40
471 473 6.201044 CGCAGTCGGTCTCATTAGATAAATTT 59.799 38.462 0.00 0.00 33.30 1.82
472 474 5.692204 CGCAGTCGGTCTCATTAGATAAATT 59.308 40.000 0.00 0.00 33.30 1.82
473 475 5.223382 CGCAGTCGGTCTCATTAGATAAAT 58.777 41.667 0.00 0.00 33.30 1.40
474 476 4.607955 CGCAGTCGGTCTCATTAGATAAA 58.392 43.478 0.00 0.00 33.30 1.40
475 477 4.224715 CGCAGTCGGTCTCATTAGATAA 57.775 45.455 0.00 0.00 33.30 1.75
476 478 3.898517 CGCAGTCGGTCTCATTAGATA 57.101 47.619 0.00 0.00 33.30 1.98
477 479 2.783828 CGCAGTCGGTCTCATTAGAT 57.216 50.000 0.00 0.00 33.30 1.98
491 493 4.947147 TTTTGCTCCCGCCGCAGT 62.947 61.111 0.00 0.00 38.80 4.40
492 494 4.107051 CTTTTGCTCCCGCCGCAG 62.107 66.667 0.00 0.00 38.80 5.18
493 495 4.887932 TATAACTTTTGCTCCCGCCGCA 62.888 50.000 0.00 0.00 35.22 5.69
494 496 1.654023 ATAACTTTTGCTCCCGCCGC 61.654 55.000 0.00 0.00 34.43 6.53
495 497 1.329599 GTATAACTTTTGCTCCCGCCG 59.670 52.381 0.00 0.00 34.43 6.46
496 498 1.674441 GGTATAACTTTTGCTCCCGCC 59.326 52.381 0.00 0.00 34.43 6.13
497 499 2.354821 CTGGTATAACTTTTGCTCCCGC 59.645 50.000 0.00 0.00 0.00 6.13
498 500 2.354821 GCTGGTATAACTTTTGCTCCCG 59.645 50.000 0.00 0.00 0.00 5.14
499 501 2.354821 CGCTGGTATAACTTTTGCTCCC 59.645 50.000 0.00 0.00 0.00 4.30
500 502 3.267483 TCGCTGGTATAACTTTTGCTCC 58.733 45.455 0.00 0.00 0.00 4.70
501 503 4.939509 TTCGCTGGTATAACTTTTGCTC 57.060 40.909 0.00 0.00 0.00 4.26
502 504 5.447279 CGAATTCGCTGGTATAACTTTTGCT 60.447 40.000 15.93 0.00 0.00 3.91
503 505 4.728608 CGAATTCGCTGGTATAACTTTTGC 59.271 41.667 15.93 0.00 0.00 3.68
504 506 5.864986 ACGAATTCGCTGGTATAACTTTTG 58.135 37.500 27.03 0.00 44.43 2.44
505 507 7.781548 ATACGAATTCGCTGGTATAACTTTT 57.218 32.000 27.03 5.48 44.43 2.27
506 508 7.493320 TGAATACGAATTCGCTGGTATAACTTT 59.507 33.333 27.03 5.92 43.84 2.66
507 509 6.982141 TGAATACGAATTCGCTGGTATAACTT 59.018 34.615 27.03 6.12 43.84 2.66
508 510 6.509656 TGAATACGAATTCGCTGGTATAACT 58.490 36.000 27.03 6.64 43.84 2.24
509 511 6.758593 TGAATACGAATTCGCTGGTATAAC 57.241 37.500 27.03 14.11 43.84 1.89
510 512 7.773864 TTTGAATACGAATTCGCTGGTATAA 57.226 32.000 27.03 11.24 43.84 0.98
511 513 7.707464 TCTTTTGAATACGAATTCGCTGGTATA 59.293 33.333 27.03 11.52 43.84 1.47
512 514 6.537301 TCTTTTGAATACGAATTCGCTGGTAT 59.463 34.615 27.03 14.30 43.84 2.73
513 515 5.870433 TCTTTTGAATACGAATTCGCTGGTA 59.130 36.000 27.03 12.61 43.84 3.25
514 516 4.693566 TCTTTTGAATACGAATTCGCTGGT 59.306 37.500 27.03 10.70 43.84 4.00
515 517 5.216566 TCTTTTGAATACGAATTCGCTGG 57.783 39.130 27.03 1.98 43.84 4.85
516 518 6.307155 ACTTCTTTTGAATACGAATTCGCTG 58.693 36.000 27.03 2.36 43.84 5.18
517 519 6.481954 ACTTCTTTTGAATACGAATTCGCT 57.518 33.333 27.03 16.31 43.84 4.93
518 520 7.548673 AAACTTCTTTTGAATACGAATTCGC 57.451 32.000 27.03 11.66 43.84 4.70
519 521 9.165014 TGAAAACTTCTTTTGAATACGAATTCG 57.835 29.630 25.64 25.64 43.84 3.34
542 544 9.561069 GGCAGGAGAAGAAATTATATAGTTGAA 57.439 33.333 0.00 0.00 0.00 2.69
543 545 8.713971 TGGCAGGAGAAGAAATTATATAGTTGA 58.286 33.333 0.00 0.00 0.00 3.18
544 546 8.778358 GTGGCAGGAGAAGAAATTATATAGTTG 58.222 37.037 0.00 0.00 0.00 3.16
545 547 8.494433 TGTGGCAGGAGAAGAAATTATATAGTT 58.506 33.333 0.00 0.00 0.00 2.24
546 548 8.034313 TGTGGCAGGAGAAGAAATTATATAGT 57.966 34.615 0.00 0.00 0.00 2.12
547 549 8.153550 ACTGTGGCAGGAGAAGAAATTATATAG 58.846 37.037 0.00 0.00 35.51 1.31
548 550 8.034313 ACTGTGGCAGGAGAAGAAATTATATA 57.966 34.615 0.00 0.00 35.51 0.86
549 551 6.904626 ACTGTGGCAGGAGAAGAAATTATAT 58.095 36.000 0.00 0.00 35.51 0.86
550 552 6.313519 ACTGTGGCAGGAGAAGAAATTATA 57.686 37.500 0.00 0.00 35.51 0.98
551 553 5.184892 ACTGTGGCAGGAGAAGAAATTAT 57.815 39.130 0.00 0.00 35.51 1.28
552 554 4.640771 ACTGTGGCAGGAGAAGAAATTA 57.359 40.909 0.00 0.00 35.51 1.40
553 555 3.515602 ACTGTGGCAGGAGAAGAAATT 57.484 42.857 0.00 0.00 35.51 1.82
554 556 3.152341 CAACTGTGGCAGGAGAAGAAAT 58.848 45.455 0.00 0.00 35.51 2.17
555 557 2.575532 CAACTGTGGCAGGAGAAGAAA 58.424 47.619 0.00 0.00 35.51 2.52
556 558 1.202806 CCAACTGTGGCAGGAGAAGAA 60.203 52.381 0.00 0.00 38.35 2.52
557 559 0.397941 CCAACTGTGGCAGGAGAAGA 59.602 55.000 0.00 0.00 38.35 2.87
558 560 2.938354 CCAACTGTGGCAGGAGAAG 58.062 57.895 0.00 0.00 38.35 2.85
568 570 1.663695 AACCAACGAGACCAACTGTG 58.336 50.000 0.00 0.00 0.00 3.66
569 571 3.547054 TTAACCAACGAGACCAACTGT 57.453 42.857 0.00 0.00 0.00 3.55
570 572 5.432885 AATTTAACCAACGAGACCAACTG 57.567 39.130 0.00 0.00 0.00 3.16
571 573 7.446013 TCATAAATTTAACCAACGAGACCAACT 59.554 33.333 1.21 0.00 0.00 3.16
572 574 7.586747 TCATAAATTTAACCAACGAGACCAAC 58.413 34.615 1.21 0.00 0.00 3.77
573 575 7.747155 TCATAAATTTAACCAACGAGACCAA 57.253 32.000 1.21 0.00 0.00 3.67
574 576 7.608376 TGATCATAAATTTAACCAACGAGACCA 59.392 33.333 1.21 0.00 0.00 4.02
575 577 7.981142 TGATCATAAATTTAACCAACGAGACC 58.019 34.615 1.21 0.00 0.00 3.85
576 578 9.834628 TTTGATCATAAATTTAACCAACGAGAC 57.165 29.630 1.21 0.00 0.00 3.36
578 580 9.840427 ACTTTGATCATAAATTTAACCAACGAG 57.160 29.630 1.21 3.35 0.00 4.18
583 585 9.921637 GTCCAACTTTGATCATAAATTTAACCA 57.078 29.630 1.21 0.00 0.00 3.67
584 586 9.366216 GGTCCAACTTTGATCATAAATTTAACC 57.634 33.333 1.21 0.00 0.00 2.85
587 589 8.673711 CGAGGTCCAACTTTGATCATAAATTTA 58.326 33.333 0.00 0.00 0.00 1.40
588 590 7.362920 CCGAGGTCCAACTTTGATCATAAATTT 60.363 37.037 0.00 0.00 0.00 1.82
589 591 6.095440 CCGAGGTCCAACTTTGATCATAAATT 59.905 38.462 0.00 0.00 0.00 1.82
590 592 5.590259 CCGAGGTCCAACTTTGATCATAAAT 59.410 40.000 0.00 0.00 0.00 1.40
591 593 4.941263 CCGAGGTCCAACTTTGATCATAAA 59.059 41.667 0.00 0.00 0.00 1.40
592 594 4.513442 CCGAGGTCCAACTTTGATCATAA 58.487 43.478 0.00 0.00 0.00 1.90
593 595 3.118408 CCCGAGGTCCAACTTTGATCATA 60.118 47.826 0.00 0.00 0.00 2.15
594 596 2.356125 CCCGAGGTCCAACTTTGATCAT 60.356 50.000 0.00 0.00 0.00 2.45
595 597 1.003118 CCCGAGGTCCAACTTTGATCA 59.997 52.381 0.00 0.00 0.00 2.92
596 598 1.278127 TCCCGAGGTCCAACTTTGATC 59.722 52.381 0.00 0.00 0.00 2.92
597 599 1.358152 TCCCGAGGTCCAACTTTGAT 58.642 50.000 0.00 0.00 0.00 2.57
598 600 1.071699 CTTCCCGAGGTCCAACTTTGA 59.928 52.381 0.00 0.00 0.00 2.69
599 601 1.523758 CTTCCCGAGGTCCAACTTTG 58.476 55.000 0.00 0.00 0.00 2.77
600 602 0.250770 GCTTCCCGAGGTCCAACTTT 60.251 55.000 0.00 0.00 0.00 2.66
601 603 1.375326 GCTTCCCGAGGTCCAACTT 59.625 57.895 0.00 0.00 0.00 2.66
602 604 2.943978 CGCTTCCCGAGGTCCAACT 61.944 63.158 0.00 0.00 40.02 3.16
603 605 2.434359 CGCTTCCCGAGGTCCAAC 60.434 66.667 0.00 0.00 40.02 3.77
604 606 4.388499 GCGCTTCCCGAGGTCCAA 62.388 66.667 0.00 0.00 40.02 3.53
619 621 0.384230 CAAAATATAGTGCGCCCGCG 60.384 55.000 4.18 4.36 45.51 6.46
620 622 0.040425 CCAAAATATAGTGCGCCCGC 60.040 55.000 4.18 5.60 42.35 6.13
621 623 1.588674 TCCAAAATATAGTGCGCCCG 58.411 50.000 4.18 0.00 0.00 6.13
622 624 3.305335 CCATTCCAAAATATAGTGCGCCC 60.305 47.826 4.18 0.00 0.00 6.13
623 625 3.568007 TCCATTCCAAAATATAGTGCGCC 59.432 43.478 4.18 0.00 0.00 6.53
624 626 4.320494 CCTCCATTCCAAAATATAGTGCGC 60.320 45.833 0.00 0.00 0.00 6.09
625 627 4.216257 CCCTCCATTCCAAAATATAGTGCG 59.784 45.833 0.00 0.00 0.00 5.34
626 628 5.385198 TCCCTCCATTCCAAAATATAGTGC 58.615 41.667 0.00 0.00 0.00 4.40
627 629 6.605119 ACTCCCTCCATTCCAAAATATAGTG 58.395 40.000 0.00 0.00 0.00 2.74
628 630 6.848562 ACTCCCTCCATTCCAAAATATAGT 57.151 37.500 0.00 0.00 0.00 2.12
629 631 7.880195 CAGTACTCCCTCCATTCCAAAATATAG 59.120 40.741 0.00 0.00 0.00 1.31
630 632 7.691791 GCAGTACTCCCTCCATTCCAAAATATA 60.692 40.741 0.00 0.00 0.00 0.86
631 633 6.605119 CAGTACTCCCTCCATTCCAAAATAT 58.395 40.000 0.00 0.00 0.00 1.28
632 634 5.631481 GCAGTACTCCCTCCATTCCAAAATA 60.631 44.000 0.00 0.00 0.00 1.40
633 635 4.860022 CAGTACTCCCTCCATTCCAAAAT 58.140 43.478 0.00 0.00 0.00 1.82
634 636 3.561313 GCAGTACTCCCTCCATTCCAAAA 60.561 47.826 0.00 0.00 0.00 2.44
635 637 2.026262 GCAGTACTCCCTCCATTCCAAA 60.026 50.000 0.00 0.00 0.00 3.28
636 638 1.559682 GCAGTACTCCCTCCATTCCAA 59.440 52.381 0.00 0.00 0.00 3.53
637 639 1.204146 GCAGTACTCCCTCCATTCCA 58.796 55.000 0.00 0.00 0.00 3.53
638 640 1.501582 AGCAGTACTCCCTCCATTCC 58.498 55.000 0.00 0.00 0.00 3.01
639 641 3.301274 AGTAGCAGTACTCCCTCCATTC 58.699 50.000 0.00 0.00 34.00 2.67
640 642 3.406512 AGTAGCAGTACTCCCTCCATT 57.593 47.619 0.00 0.00 34.00 3.16
641 643 4.140900 ACATAGTAGCAGTACTCCCTCCAT 60.141 45.833 0.00 0.00 40.23 3.41
642 644 3.204606 ACATAGTAGCAGTACTCCCTCCA 59.795 47.826 0.00 0.00 40.23 3.86
643 645 3.834938 ACATAGTAGCAGTACTCCCTCC 58.165 50.000 0.00 0.00 40.23 4.30
644 646 6.005198 ACATACATAGTAGCAGTACTCCCTC 58.995 44.000 0.00 0.00 40.23 4.30
645 647 5.954757 ACATACATAGTAGCAGTACTCCCT 58.045 41.667 0.00 0.00 40.23 4.20
646 648 7.380431 CTACATACATAGTAGCAGTACTCCC 57.620 44.000 0.00 0.00 40.23 4.30
745 750 3.513912 TCGAGAATTCCTTCAACAGCCTA 59.486 43.478 0.65 0.00 33.56 3.93
873 878 4.637091 CCCCATTGCCATTTCTTTTCATTC 59.363 41.667 0.00 0.00 0.00 2.67
984 989 1.634973 TGCATCACCTGATTGGGAAGA 59.365 47.619 0.00 0.00 41.11 2.87
1013 1018 0.107945 ATCCTCCTCGTCTTGCTTGC 60.108 55.000 0.00 0.00 0.00 4.01
1242 1247 3.011144 TGGCCTTGTCTTTCATATTGGGA 59.989 43.478 3.32 0.00 0.00 4.37
1308 1316 4.153117 CAGAGATCTTGTGGGTTTTTCTCG 59.847 45.833 0.00 0.00 34.70 4.04
1998 2017 3.352648 TGTAAATGGCTAAAGTCCCAGC 58.647 45.455 0.00 0.00 34.01 4.85
2383 2414 3.201290 CAATATTGCACGGAGCTTCTCT 58.799 45.455 1.74 0.00 45.94 3.10
2533 2573 8.244113 CCACTGTTAAACTTTTCTTCTTTCTGT 58.756 33.333 0.00 0.00 0.00 3.41
2652 2702 0.764890 ACCAACAGTAGCTGCAGGAA 59.235 50.000 17.12 0.00 34.37 3.36


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

AutoCloner maintained by Alex Coulton.