Multiple sequence alignment - TraesCS7B01G167700

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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 TraesCS7B01G167700 chr7B 100.000 3563 0 0 1 3563 233028711 233025149 0.000000e+00 6580.0
1 TraesCS7B01G167700 chr7B 82.906 117 14 5 3165 3276 233025434 233025319 2.260000e-17 100.0
2 TraesCS7B01G167700 chr7A 96.049 2126 44 17 697 2793 274663242 274661128 0.000000e+00 3424.0
3 TraesCS7B01G167700 chr7A 90.932 397 31 5 3172 3563 274642171 274641775 2.440000e-146 529.0
4 TraesCS7B01G167700 chr7A 93.506 154 9 1 2848 3000 274660931 274660778 9.950000e-56 228.0
5 TraesCS7B01G167700 chr7A 86.517 178 13 1 3009 3186 274644192 274644026 6.070000e-43 185.0
6 TraesCS7B01G167700 chr7A 82.051 117 16 4 3165 3276 274642064 274641948 1.050000e-15 95.3
7 TraesCS7B01G167700 chr7D 97.283 1951 49 1 758 2704 255059514 255057564 0.000000e+00 3306.0
8 TraesCS7B01G167700 chr7D 91.837 539 41 2 1 536 480813141 480812603 0.000000e+00 749.0
9 TraesCS7B01G167700 chr7D 88.091 571 58 9 2997 3563 255056435 255055871 0.000000e+00 669.0
10 TraesCS7B01G167700 chr7D 84.099 283 21 6 2701 2959 255057213 255056931 5.900000e-63 252.0
11 TraesCS7B01G167700 chr7D 100.000 44 0 0 2949 2992 255056505 255056462 8.200000e-12 82.4
12 TraesCS7B01G167700 chr5D 81.053 1367 245 11 1109 2471 412076936 412078292 0.000000e+00 1077.0
13 TraesCS7B01G167700 chr5D 91.837 539 41 1 1 536 99381004 99380466 0.000000e+00 749.0
14 TraesCS7B01G167700 chr5D 90.286 525 48 2 15 536 438833747 438834271 0.000000e+00 684.0
15 TraesCS7B01G167700 chr5A 81.040 1366 247 9 1109 2471 523815637 523816993 0.000000e+00 1077.0
16 TraesCS7B01G167700 chr5A 92.022 539 40 1 1 536 667035062 667035600 0.000000e+00 754.0
17 TraesCS7B01G167700 chr5B 80.629 1368 249 13 1109 2471 495019849 495021205 0.000000e+00 1044.0
18 TraesCS7B01G167700 chr6A 91.095 539 45 1 1 536 593382098 593381560 0.000000e+00 726.0
19 TraesCS7B01G167700 chr6A 75.234 214 53 0 1121 1334 476000196 476000409 6.290000e-18 102.0
20 TraesCS7B01G167700 chr3A 89.425 539 47 3 1 536 61332985 61332454 0.000000e+00 671.0
21 TraesCS7B01G167700 chr3A 88.865 467 49 1 67 530 12703953 12703487 3.990000e-159 571.0
22 TraesCS7B01G167700 chr3A 87.257 463 38 7 17 475 114716226 114715781 3.170000e-140 508.0
23 TraesCS7B01G167700 chr6B 71.846 547 131 19 1850 2386 484100174 484099641 6.200000e-28 135.0
24 TraesCS7B01G167700 chr6B 78.912 147 27 4 1190 1334 484100810 484100666 2.930000e-16 97.1
25 TraesCS7B01G167700 chr6D 94.253 87 5 0 2 88 54546816 54546730 2.230000e-27 134.0
26 TraesCS7B01G167700 chr6D 75.463 216 49 4 1121 1334 336366526 336366739 6.290000e-18 102.0
27 TraesCS7B01G167700 chr4B 96.203 79 3 0 458 536 65934820 65934742 2.890000e-26 130.0
28 TraesCS7B01G167700 chr3B 94.915 59 3 0 1 59 92342161 92342219 3.790000e-15 93.5
29 TraesCS7B01G167700 chr1B 100.000 33 0 0 3376 3408 512809113 512809145 1.070000e-05 62.1
30 TraesCS7B01G167700 chr4A 88.235 51 4 2 3376 3424 620397130 620397080 3.840000e-05 60.2


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 TraesCS7B01G167700 chr7B 233025149 233028711 3562 True 3340.000000 6580 91.45300 1 3563 2 chr7B.!!$R1 3562
1 TraesCS7B01G167700 chr7A 274660778 274663242 2464 True 1826.000000 3424 94.77750 697 3000 2 chr7A.!!$R2 2303
2 TraesCS7B01G167700 chr7A 274641775 274644192 2417 True 269.766667 529 86.50000 3009 3563 3 chr7A.!!$R1 554
3 TraesCS7B01G167700 chr7D 255055871 255059514 3643 True 1077.350000 3306 92.36825 758 3563 4 chr7D.!!$R2 2805
4 TraesCS7B01G167700 chr7D 480812603 480813141 538 True 749.000000 749 91.83700 1 536 1 chr7D.!!$R1 535
5 TraesCS7B01G167700 chr5D 412076936 412078292 1356 False 1077.000000 1077 81.05300 1109 2471 1 chr5D.!!$F1 1362
6 TraesCS7B01G167700 chr5D 99380466 99381004 538 True 749.000000 749 91.83700 1 536 1 chr5D.!!$R1 535
7 TraesCS7B01G167700 chr5D 438833747 438834271 524 False 684.000000 684 90.28600 15 536 1 chr5D.!!$F2 521
8 TraesCS7B01G167700 chr5A 523815637 523816993 1356 False 1077.000000 1077 81.04000 1109 2471 1 chr5A.!!$F1 1362
9 TraesCS7B01G167700 chr5A 667035062 667035600 538 False 754.000000 754 92.02200 1 536 1 chr5A.!!$F2 535
10 TraesCS7B01G167700 chr5B 495019849 495021205 1356 False 1044.000000 1044 80.62900 1109 2471 1 chr5B.!!$F1 1362
11 TraesCS7B01G167700 chr6A 593381560 593382098 538 True 726.000000 726 91.09500 1 536 1 chr6A.!!$R1 535
12 TraesCS7B01G167700 chr3A 61332454 61332985 531 True 671.000000 671 89.42500 1 536 1 chr3A.!!$R2 535

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
664 668 0.183492 CCGGGATGGATGGACAATGT 59.817 55.0 0.0 0.0 42.00 2.71 F
675 679 0.394352 GGACAATGTCCCCAAGCGAT 60.394 55.0 21.3 0.0 46.19 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 1869 0.548031 CACCACCACTCCAGGCATAT 59.452 55.000 0.0 0.0 0.0 1.78 R
2721 3110 6.149129 GGGACCAATATAAAAGCAAAGGAG 57.851 41.667 0.0 0.0 0.0 3.69 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
28 29 8.237267 CCAACATCTAGCGAAGTAGAAAATTTT 58.763 33.333 2.28 2.28 32.72 1.82
61 62 4.570369 TGTGCATCAACATTCATAGTACGG 59.430 41.667 0.00 0.00 0.00 4.02
144 145 5.425217 TGATTGCACTATACCTTCCTTCAGA 59.575 40.000 0.00 0.00 0.00 3.27
170 171 1.906574 TCTTTATCTCCGCCACCACTT 59.093 47.619 0.00 0.00 0.00 3.16
171 172 2.304761 TCTTTATCTCCGCCACCACTTT 59.695 45.455 0.00 0.00 0.00 2.66
172 173 2.396590 TTATCTCCGCCACCACTTTC 57.603 50.000 0.00 0.00 0.00 2.62
197 201 7.541783 TCTTATCACATGCAATAACAACTTTGC 59.458 33.333 0.00 0.88 46.53 3.68
258 262 1.237285 GCGACTGCCTCCAATGTTGT 61.237 55.000 0.00 0.00 33.98 3.32
301 305 3.737559 ACCATAGCTGATGAACCCAAA 57.262 42.857 0.00 0.00 37.82 3.28
320 324 5.303589 CCCAAAAAGAGGCATATGTGATCAT 59.696 40.000 0.00 0.00 38.00 2.45
328 332 3.319972 GGCATATGTGATCATGGCAAACT 59.680 43.478 13.92 0.00 44.67 2.66
332 336 6.459985 GCATATGTGATCATGGCAAACTGTAA 60.460 38.462 0.00 0.00 36.44 2.41
354 358 2.076863 GGATGCGCCACTATTACCATC 58.923 52.381 4.18 0.00 36.34 3.51
356 360 3.403038 GATGCGCCACTATTACCATCTT 58.597 45.455 4.18 0.00 0.00 2.40
421 425 1.659098 GGTGATGTCCATTTCGTCGTC 59.341 52.381 0.00 0.00 0.00 4.20
486 490 4.503296 GCAGGACTCAGTTTTCAAGGACTA 60.503 45.833 0.00 0.00 0.00 2.59
497 501 6.371825 AGTTTTCAAGGACTACAATTCGGATC 59.628 38.462 0.00 0.00 0.00 3.36
502 506 5.878406 AGGACTACAATTCGGATCTGAAT 57.122 39.130 21.82 21.82 40.22 2.57
536 540 2.450992 TGAGTGGCATGTGGACTCA 58.549 52.632 15.44 15.44 42.96 3.41
537 541 0.986527 TGAGTGGCATGTGGACTCAT 59.013 50.000 15.44 0.00 40.88 2.90
538 542 1.352017 TGAGTGGCATGTGGACTCATT 59.648 47.619 15.44 0.00 40.88 2.57
539 543 1.741706 GAGTGGCATGTGGACTCATTG 59.258 52.381 13.06 0.00 36.83 2.82
540 544 0.813184 GTGGCATGTGGACTCATTGG 59.187 55.000 0.00 0.00 0.00 3.16
541 545 0.697658 TGGCATGTGGACTCATTGGA 59.302 50.000 0.00 0.00 0.00 3.53
542 546 1.340308 TGGCATGTGGACTCATTGGAG 60.340 52.381 0.00 0.00 46.96 3.86
543 547 1.065199 GGCATGTGGACTCATTGGAGA 60.065 52.381 0.00 0.00 44.26 3.71
544 548 2.618816 GGCATGTGGACTCATTGGAGAA 60.619 50.000 0.00 0.00 44.26 2.87
545 549 3.285484 GCATGTGGACTCATTGGAGAAT 58.715 45.455 0.00 0.00 44.26 2.40
546 550 3.314635 GCATGTGGACTCATTGGAGAATC 59.685 47.826 0.00 0.00 44.26 2.52
560 564 3.369835 GAGAATCCAAACTGTTACGCG 57.630 47.619 3.53 3.53 0.00 6.01
561 565 2.073816 AGAATCCAAACTGTTACGCGG 58.926 47.619 12.47 0.00 0.00 6.46
562 566 2.070783 GAATCCAAACTGTTACGCGGA 58.929 47.619 12.47 0.00 0.00 5.54
563 567 2.396590 ATCCAAACTGTTACGCGGAT 57.603 45.000 12.47 1.05 0.00 4.18
564 568 3.530265 ATCCAAACTGTTACGCGGATA 57.470 42.857 12.47 0.00 31.51 2.59
565 569 3.316071 TCCAAACTGTTACGCGGATAA 57.684 42.857 12.47 0.00 0.00 1.75
566 570 3.661944 TCCAAACTGTTACGCGGATAAA 58.338 40.909 12.47 0.00 0.00 1.40
567 571 3.432933 TCCAAACTGTTACGCGGATAAAC 59.567 43.478 12.47 9.88 0.00 2.01
568 572 3.434299 CCAAACTGTTACGCGGATAAACT 59.566 43.478 12.47 0.00 0.00 2.66
569 573 4.626604 CCAAACTGTTACGCGGATAAACTA 59.373 41.667 12.47 0.00 0.00 2.24
570 574 5.292589 CCAAACTGTTACGCGGATAAACTAT 59.707 40.000 12.47 0.00 0.00 2.12
571 575 5.961395 AACTGTTACGCGGATAAACTATG 57.039 39.130 12.47 6.78 0.00 2.23
572 576 5.252969 ACTGTTACGCGGATAAACTATGA 57.747 39.130 12.47 0.00 0.00 2.15
573 577 5.279384 ACTGTTACGCGGATAAACTATGAG 58.721 41.667 12.47 5.43 0.00 2.90
574 578 5.066893 ACTGTTACGCGGATAAACTATGAGA 59.933 40.000 12.47 0.00 0.00 3.27
575 579 5.893687 TGTTACGCGGATAAACTATGAGAA 58.106 37.500 12.47 0.00 0.00 2.87
576 580 6.331845 TGTTACGCGGATAAACTATGAGAAA 58.668 36.000 12.47 0.00 0.00 2.52
577 581 6.812656 TGTTACGCGGATAAACTATGAGAAAA 59.187 34.615 12.47 0.00 0.00 2.29
578 582 7.331440 TGTTACGCGGATAAACTATGAGAAAAA 59.669 33.333 12.47 0.00 0.00 1.94
579 583 6.103222 ACGCGGATAAACTATGAGAAAAAC 57.897 37.500 12.47 0.00 0.00 2.43
580 584 5.640357 ACGCGGATAAACTATGAGAAAAACA 59.360 36.000 12.47 0.00 0.00 2.83
581 585 6.148150 ACGCGGATAAACTATGAGAAAAACAA 59.852 34.615 12.47 0.00 0.00 2.83
582 586 7.018826 CGCGGATAAACTATGAGAAAAACAAA 58.981 34.615 0.00 0.00 0.00 2.83
583 587 7.535940 CGCGGATAAACTATGAGAAAAACAAAA 59.464 33.333 0.00 0.00 0.00 2.44
584 588 9.187455 GCGGATAAACTATGAGAAAAACAAAAA 57.813 29.630 0.00 0.00 0.00 1.94
615 619 7.873739 ACAAAATAGAAATAACACAGCAAGC 57.126 32.000 0.00 0.00 0.00 4.01
616 620 6.868339 ACAAAATAGAAATAACACAGCAAGCC 59.132 34.615 0.00 0.00 0.00 4.35
617 621 6.588719 AAATAGAAATAACACAGCAAGCCA 57.411 33.333 0.00 0.00 0.00 4.75
618 622 3.923017 AGAAATAACACAGCAAGCCAC 57.077 42.857 0.00 0.00 0.00 5.01
619 623 3.221771 AGAAATAACACAGCAAGCCACA 58.778 40.909 0.00 0.00 0.00 4.17
620 624 3.636300 AGAAATAACACAGCAAGCCACAA 59.364 39.130 0.00 0.00 0.00 3.33
621 625 4.099266 AGAAATAACACAGCAAGCCACAAA 59.901 37.500 0.00 0.00 0.00 2.83
622 626 2.861462 TAACACAGCAAGCCACAAAC 57.139 45.000 0.00 0.00 0.00 2.93
623 627 0.894141 AACACAGCAAGCCACAAACA 59.106 45.000 0.00 0.00 0.00 2.83
624 628 1.113788 ACACAGCAAGCCACAAACAT 58.886 45.000 0.00 0.00 0.00 2.71
625 629 2.305928 ACACAGCAAGCCACAAACATA 58.694 42.857 0.00 0.00 0.00 2.29
626 630 2.892852 ACACAGCAAGCCACAAACATAT 59.107 40.909 0.00 0.00 0.00 1.78
627 631 4.078537 ACACAGCAAGCCACAAACATATA 58.921 39.130 0.00 0.00 0.00 0.86
628 632 4.156556 ACACAGCAAGCCACAAACATATAG 59.843 41.667 0.00 0.00 0.00 1.31
629 633 3.129287 ACAGCAAGCCACAAACATATAGC 59.871 43.478 0.00 0.00 0.00 2.97
630 634 2.689983 AGCAAGCCACAAACATATAGCC 59.310 45.455 0.00 0.00 0.00 3.93
631 635 2.223805 GCAAGCCACAAACATATAGCCC 60.224 50.000 0.00 0.00 0.00 5.19
632 636 3.023119 CAAGCCACAAACATATAGCCCA 58.977 45.455 0.00 0.00 0.00 5.36
633 637 2.654863 AGCCACAAACATATAGCCCAC 58.345 47.619 0.00 0.00 0.00 4.61
634 638 2.025416 AGCCACAAACATATAGCCCACA 60.025 45.455 0.00 0.00 0.00 4.17
635 639 2.958355 GCCACAAACATATAGCCCACAT 59.042 45.455 0.00 0.00 0.00 3.21
636 640 4.141274 AGCCACAAACATATAGCCCACATA 60.141 41.667 0.00 0.00 0.00 2.29
637 641 4.582656 GCCACAAACATATAGCCCACATAA 59.417 41.667 0.00 0.00 0.00 1.90
638 642 5.068460 GCCACAAACATATAGCCCACATAAA 59.932 40.000 0.00 0.00 0.00 1.40
639 643 6.406400 GCCACAAACATATAGCCCACATAAAA 60.406 38.462 0.00 0.00 0.00 1.52
640 644 7.551585 CCACAAACATATAGCCCACATAAAAA 58.448 34.615 0.00 0.00 0.00 1.94
656 660 2.900547 AAAAAGGCCGGGATGGATG 58.099 52.632 2.18 0.00 42.00 3.51
657 661 0.687427 AAAAAGGCCGGGATGGATGG 60.687 55.000 2.18 0.00 42.00 3.51
658 662 1.580066 AAAAGGCCGGGATGGATGGA 61.580 55.000 2.18 0.00 42.00 3.41
659 663 2.284515 AAAGGCCGGGATGGATGGAC 62.285 60.000 2.18 0.00 42.00 4.02
660 664 3.488569 GGCCGGGATGGATGGACA 61.489 66.667 2.18 0.00 42.00 4.02
661 665 2.595095 GCCGGGATGGATGGACAA 59.405 61.111 2.18 0.00 42.00 3.18
662 666 1.151450 GCCGGGATGGATGGACAAT 59.849 57.895 2.18 0.00 42.00 2.71
663 667 1.174712 GCCGGGATGGATGGACAATG 61.175 60.000 2.18 0.00 42.00 2.82
664 668 0.183492 CCGGGATGGATGGACAATGT 59.817 55.000 0.00 0.00 42.00 2.71
665 669 1.597742 CGGGATGGATGGACAATGTC 58.402 55.000 4.51 4.51 0.00 3.06
673 677 3.590824 GGACAATGTCCCCAAGCG 58.409 61.111 21.30 0.00 46.19 4.68
674 678 1.002624 GGACAATGTCCCCAAGCGA 60.003 57.895 21.30 0.00 46.19 4.93
675 679 0.394352 GGACAATGTCCCCAAGCGAT 60.394 55.000 21.30 0.00 46.19 4.58
676 680 1.134220 GGACAATGTCCCCAAGCGATA 60.134 52.381 21.30 0.00 46.19 2.92
677 681 2.213499 GACAATGTCCCCAAGCGATAG 58.787 52.381 1.10 0.00 0.00 2.08
689 693 4.368391 CGATAGCCCACCATCTGC 57.632 61.111 0.00 0.00 0.00 4.26
690 694 1.750930 CGATAGCCCACCATCTGCT 59.249 57.895 0.00 0.00 39.10 4.24
691 695 0.969149 CGATAGCCCACCATCTGCTA 59.031 55.000 0.00 0.00 41.43 3.49
692 696 1.344438 CGATAGCCCACCATCTGCTAA 59.656 52.381 0.00 0.00 40.65 3.09
693 697 2.611473 CGATAGCCCACCATCTGCTAAG 60.611 54.545 0.00 0.00 40.65 2.18
694 698 2.174685 TAGCCCACCATCTGCTAAGA 57.825 50.000 0.00 0.00 34.82 2.10
695 699 1.516110 AGCCCACCATCTGCTAAGAT 58.484 50.000 0.00 0.00 44.35 2.40
703 707 6.115446 CCACCATCTGCTAAGATAGAAACAA 58.885 40.000 0.00 0.00 41.43 2.83
719 723 4.898861 AGAAACAAGCATTACCCCTCAAAA 59.101 37.500 0.00 0.00 0.00 2.44
725 729 6.126911 ACAAGCATTACCCCTCAAAAGAAAAA 60.127 34.615 0.00 0.00 0.00 1.94
772 788 7.672239 ACAGGTTAGTAAAATTCCATGGCTAAA 59.328 33.333 6.96 0.00 0.00 1.85
783 799 1.789464 CATGGCTAAATCTCGCTCGAC 59.211 52.381 0.00 0.00 0.00 4.20
786 802 1.482278 GCTAAATCTCGCTCGACTGG 58.518 55.000 0.00 0.00 0.00 4.00
792 808 0.456221 TCTCGCTCGACTGGGATTTC 59.544 55.000 0.00 0.00 0.00 2.17
929 946 2.653115 GCAAGCAAAGCCCTGACC 59.347 61.111 0.00 0.00 0.00 4.02
1090 1107 2.126850 GGCCAAAGAAAGCGCGAC 60.127 61.111 12.10 0.04 0.00 5.19
1548 1571 2.753043 ATCCGCGTGTACCTCCGT 60.753 61.111 4.92 0.00 0.00 4.69
1627 1650 1.588239 TCCCATCAACTGCATCCTCT 58.412 50.000 0.00 0.00 0.00 3.69
1818 1841 3.140814 GAATGGGGCCGCTTGGTC 61.141 66.667 21.80 6.50 36.29 4.02
1846 1869 1.284297 CGTTCACAGCTGCATGTCGA 61.284 55.000 15.27 0.00 0.00 4.20
2520 2543 2.037871 TGCAGACGCAGACAGTGTA 58.962 52.632 0.00 0.00 45.36 2.90
2751 3141 6.001460 TGCTTTTATATTGGTCCCCGATAAG 58.999 40.000 0.00 0.00 33.99 1.73
2784 3174 2.728846 CGGCAGATCGAACAATTGGTTG 60.729 50.000 10.83 7.48 40.63 3.77
2793 3183 1.981256 ACAATTGGTTGGAGCGAACT 58.019 45.000 10.83 0.00 39.70 3.01
2794 3184 1.608590 ACAATTGGTTGGAGCGAACTG 59.391 47.619 10.83 0.00 39.70 3.16
2817 3313 2.416296 CGTTCGCTACAATACTCCCACA 60.416 50.000 0.00 0.00 0.00 4.17
2920 3452 2.005370 ATGCCATTAGCCCATGAAGG 57.995 50.000 0.00 0.00 42.71 3.46
3036 4032 8.597167 TCTAGGAAATCCATACCACATGATAAG 58.403 37.037 0.00 0.00 38.89 1.73
3141 4137 3.130633 CGTGATGTCCAAACTGACTTCA 58.869 45.455 5.86 5.86 43.23 3.02
3228 6093 8.622572 ACCCATTGGTCCAAATATAAGAAAAT 57.377 30.769 8.75 0.00 43.06 1.82
3342 6209 9.639601 CCCATTGGTCTAAAAGAATTAAGAAAC 57.360 33.333 1.20 0.00 0.00 2.78
3457 6324 9.941325 ATGAAAATACAGTTAAATTTGCCATGA 57.059 25.926 0.00 0.00 0.00 3.07
3462 6329 8.761575 ATACAGTTAAATTTGCCATGACAAAG 57.238 30.769 12.80 0.47 42.45 2.77
3475 6342 9.436957 TTGCCATGACAAAGTTAAAAGTAAAAA 57.563 25.926 0.00 0.00 0.00 1.94
3508 6376 9.807649 GTATGCTTGATGTAAATTTTCCTTGAT 57.192 29.630 0.00 0.00 0.00 2.57
3547 6415 4.099266 GCCATGGCAGTGGATGTAAATTTA 59.901 41.667 32.08 0.00 42.02 1.40
3554 6422 6.040842 GGCAGTGGATGTAAATTTACCATGAT 59.959 38.462 22.47 11.27 33.19 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.699749 ACAATTTAGCAAAATTTTCTACTTCGC 58.300 29.630 0.00 0.00 41.50 4.70
28 29 4.581077 TGTTGATGCACACAATTTAGCA 57.419 36.364 10.57 0.00 41.73 3.49
61 62 6.535274 AGCTGTGATTTCATTTTTGAAAGC 57.465 33.333 9.17 9.17 42.49 3.51
91 92 0.108804 TTAACGCTCGGGCAAGAGAG 60.109 55.000 8.62 11.38 42.52 3.20
144 145 4.593206 TGGTGGCGGAGATAAAGAATAGAT 59.407 41.667 0.00 0.00 0.00 1.98
170 171 9.409312 CAAAGTTGTTATTGCATGTGATAAGAA 57.591 29.630 0.00 2.15 0.00 2.52
171 172 8.969121 CAAAGTTGTTATTGCATGTGATAAGA 57.031 30.769 0.00 0.00 0.00 2.10
197 201 1.374252 CGTTGGACTTGTCCCTCGG 60.374 63.158 16.23 1.04 0.00 4.63
243 247 1.308069 CCCGACAACATTGGAGGCAG 61.308 60.000 0.00 0.00 32.66 4.85
258 262 1.548081 TACCGACATTTCAGACCCGA 58.452 50.000 0.00 0.00 0.00 5.14
301 305 3.825014 GCCATGATCACATATGCCTCTTT 59.175 43.478 1.58 0.00 35.09 2.52
320 324 0.878416 GCATCCGTTACAGTTTGCCA 59.122 50.000 0.00 0.00 0.00 4.92
328 332 0.462375 ATAGTGGCGCATCCGTTACA 59.538 50.000 10.83 0.00 37.80 2.41
332 336 0.249741 GGTAATAGTGGCGCATCCGT 60.250 55.000 10.83 0.00 37.80 4.69
354 358 1.593196 TGACGGAGGTCTTGCAAAAG 58.407 50.000 0.00 0.00 43.79 2.27
356 360 1.134220 AGTTGACGGAGGTCTTGCAAA 60.134 47.619 0.00 0.00 43.79 3.68
403 407 1.548719 AGGACGACGAAATGGACATCA 59.451 47.619 0.00 0.00 0.00 3.07
405 409 2.233922 AGAAGGACGACGAAATGGACAT 59.766 45.455 0.00 0.00 0.00 3.06
421 425 2.190578 GGGATGCGGGTGAGAAGG 59.809 66.667 0.00 0.00 0.00 3.46
486 490 6.276847 GTCACTAGATTCAGATCCGAATTGT 58.723 40.000 5.65 3.63 35.74 2.71
497 501 3.510388 TGGCTTCGTCACTAGATTCAG 57.490 47.619 0.00 0.00 0.00 3.02
502 506 2.164422 CACTCATGGCTTCGTCACTAGA 59.836 50.000 0.00 0.00 0.00 2.43
538 542 3.071479 GCGTAACAGTTTGGATTCTCCA 58.929 45.455 0.00 0.00 46.61 3.86
539 543 2.093783 CGCGTAACAGTTTGGATTCTCC 59.906 50.000 0.00 0.00 36.96 3.71
540 544 2.093783 CCGCGTAACAGTTTGGATTCTC 59.906 50.000 4.92 0.00 0.00 2.87
541 545 2.073816 CCGCGTAACAGTTTGGATTCT 58.926 47.619 4.92 0.00 0.00 2.40
542 546 2.070783 TCCGCGTAACAGTTTGGATTC 58.929 47.619 4.92 0.00 0.00 2.52
543 547 2.172851 TCCGCGTAACAGTTTGGATT 57.827 45.000 4.92 0.00 0.00 3.01
544 548 2.396590 ATCCGCGTAACAGTTTGGAT 57.603 45.000 4.92 0.00 0.00 3.41
545 549 3.316071 TTATCCGCGTAACAGTTTGGA 57.684 42.857 4.92 0.00 0.00 3.53
546 550 3.434299 AGTTTATCCGCGTAACAGTTTGG 59.566 43.478 4.92 0.00 0.00 3.28
547 551 4.657075 AGTTTATCCGCGTAACAGTTTG 57.343 40.909 4.92 0.00 0.00 2.93
548 552 6.101332 TCATAGTTTATCCGCGTAACAGTTT 58.899 36.000 4.92 0.00 0.00 2.66
549 553 5.653507 TCATAGTTTATCCGCGTAACAGTT 58.346 37.500 4.92 0.00 0.00 3.16
550 554 5.066893 TCTCATAGTTTATCCGCGTAACAGT 59.933 40.000 4.92 0.00 0.00 3.55
551 555 5.516996 TCTCATAGTTTATCCGCGTAACAG 58.483 41.667 4.92 0.00 0.00 3.16
552 556 5.503662 TCTCATAGTTTATCCGCGTAACA 57.496 39.130 4.92 0.00 0.00 2.41
553 557 6.817270 TTTCTCATAGTTTATCCGCGTAAC 57.183 37.500 4.92 3.96 0.00 2.50
554 558 7.331440 TGTTTTTCTCATAGTTTATCCGCGTAA 59.669 33.333 4.92 0.00 0.00 3.18
555 559 6.812656 TGTTTTTCTCATAGTTTATCCGCGTA 59.187 34.615 4.92 0.00 0.00 4.42
556 560 5.640357 TGTTTTTCTCATAGTTTATCCGCGT 59.360 36.000 4.92 0.00 0.00 6.01
557 561 6.102006 TGTTTTTCTCATAGTTTATCCGCG 57.898 37.500 0.00 0.00 0.00 6.46
558 562 8.736751 TTTTGTTTTTCTCATAGTTTATCCGC 57.263 30.769 0.00 0.00 0.00 5.54
589 593 8.764287 GCTTGCTGTGTTATTTCTATTTTGTTT 58.236 29.630 0.00 0.00 0.00 2.83
590 594 7.384932 GGCTTGCTGTGTTATTTCTATTTTGTT 59.615 33.333 0.00 0.00 0.00 2.83
591 595 6.868339 GGCTTGCTGTGTTATTTCTATTTTGT 59.132 34.615 0.00 0.00 0.00 2.83
592 596 6.867816 TGGCTTGCTGTGTTATTTCTATTTTG 59.132 34.615 0.00 0.00 0.00 2.44
593 597 6.868339 GTGGCTTGCTGTGTTATTTCTATTTT 59.132 34.615 0.00 0.00 0.00 1.82
594 598 6.015519 TGTGGCTTGCTGTGTTATTTCTATTT 60.016 34.615 0.00 0.00 0.00 1.40
595 599 5.476599 TGTGGCTTGCTGTGTTATTTCTATT 59.523 36.000 0.00 0.00 0.00 1.73
596 600 5.009631 TGTGGCTTGCTGTGTTATTTCTAT 58.990 37.500 0.00 0.00 0.00 1.98
597 601 4.393834 TGTGGCTTGCTGTGTTATTTCTA 58.606 39.130 0.00 0.00 0.00 2.10
598 602 3.221771 TGTGGCTTGCTGTGTTATTTCT 58.778 40.909 0.00 0.00 0.00 2.52
599 603 3.641437 TGTGGCTTGCTGTGTTATTTC 57.359 42.857 0.00 0.00 0.00 2.17
600 604 4.119136 GTTTGTGGCTTGCTGTGTTATTT 58.881 39.130 0.00 0.00 0.00 1.40
601 605 3.131933 TGTTTGTGGCTTGCTGTGTTATT 59.868 39.130 0.00 0.00 0.00 1.40
602 606 2.692557 TGTTTGTGGCTTGCTGTGTTAT 59.307 40.909 0.00 0.00 0.00 1.89
603 607 2.095461 TGTTTGTGGCTTGCTGTGTTA 58.905 42.857 0.00 0.00 0.00 2.41
604 608 0.894141 TGTTTGTGGCTTGCTGTGTT 59.106 45.000 0.00 0.00 0.00 3.32
605 609 1.113788 ATGTTTGTGGCTTGCTGTGT 58.886 45.000 0.00 0.00 0.00 3.72
606 610 3.581024 ATATGTTTGTGGCTTGCTGTG 57.419 42.857 0.00 0.00 0.00 3.66
607 611 3.129287 GCTATATGTTTGTGGCTTGCTGT 59.871 43.478 0.00 0.00 0.00 4.40
608 612 3.489738 GGCTATATGTTTGTGGCTTGCTG 60.490 47.826 0.00 0.00 0.00 4.41
609 613 2.689983 GGCTATATGTTTGTGGCTTGCT 59.310 45.455 0.00 0.00 0.00 3.91
610 614 2.223805 GGGCTATATGTTTGTGGCTTGC 60.224 50.000 0.00 0.00 0.00 4.01
611 615 3.023119 TGGGCTATATGTTTGTGGCTTG 58.977 45.455 0.00 0.00 0.00 4.01
612 616 3.023832 GTGGGCTATATGTTTGTGGCTT 58.976 45.455 0.00 0.00 0.00 4.35
613 617 2.025416 TGTGGGCTATATGTTTGTGGCT 60.025 45.455 0.00 0.00 0.00 4.75
614 618 2.374184 TGTGGGCTATATGTTTGTGGC 58.626 47.619 0.00 0.00 0.00 5.01
615 619 6.707440 TTTATGTGGGCTATATGTTTGTGG 57.293 37.500 0.00 0.00 0.00 4.17
638 642 0.687427 CCATCCATCCCGGCCTTTTT 60.687 55.000 0.00 0.00 33.14 1.94
639 643 1.076044 CCATCCATCCCGGCCTTTT 60.076 57.895 0.00 0.00 33.14 2.27
640 644 2.006415 TCCATCCATCCCGGCCTTT 61.006 57.895 0.00 0.00 33.14 3.11
641 645 2.368192 TCCATCCATCCCGGCCTT 60.368 61.111 0.00 0.00 33.14 4.35
642 646 3.171388 GTCCATCCATCCCGGCCT 61.171 66.667 0.00 0.00 33.14 5.19
643 647 2.357593 ATTGTCCATCCATCCCGGCC 62.358 60.000 0.00 0.00 33.14 6.13
644 648 1.151450 ATTGTCCATCCATCCCGGC 59.849 57.895 0.00 0.00 33.14 6.13
645 649 0.183492 ACATTGTCCATCCATCCCGG 59.817 55.000 0.00 0.00 0.00 5.73
646 650 1.597742 GACATTGTCCATCCATCCCG 58.402 55.000 5.44 0.00 0.00 5.14
657 661 2.213499 CTATCGCTTGGGGACATTGTC 58.787 52.381 8.34 8.34 42.32 3.18
658 662 1.747206 GCTATCGCTTGGGGACATTGT 60.747 52.381 0.00 0.00 42.32 2.71
659 663 0.947244 GCTATCGCTTGGGGACATTG 59.053 55.000 0.00 0.00 42.32 2.82
660 664 0.179018 GGCTATCGCTTGGGGACATT 60.179 55.000 0.00 0.00 42.32 2.71
661 665 1.451936 GGCTATCGCTTGGGGACAT 59.548 57.895 0.00 0.00 42.32 3.06
662 666 2.742116 GGGCTATCGCTTGGGGACA 61.742 63.158 0.00 0.00 39.83 4.02
663 667 2.111251 GGGCTATCGCTTGGGGAC 59.889 66.667 0.00 0.00 36.09 4.46
664 668 2.366301 TGGGCTATCGCTTGGGGA 60.366 61.111 0.00 0.00 36.09 4.81
665 669 2.203209 GTGGGCTATCGCTTGGGG 60.203 66.667 0.00 0.00 36.09 4.96
666 670 2.203209 GGTGGGCTATCGCTTGGG 60.203 66.667 0.00 0.00 36.09 4.12
667 671 0.886490 GATGGTGGGCTATCGCTTGG 60.886 60.000 0.00 0.00 36.09 3.61
668 672 0.107456 AGATGGTGGGCTATCGCTTG 59.893 55.000 0.00 0.00 37.62 4.01
669 673 0.107456 CAGATGGTGGGCTATCGCTT 59.893 55.000 0.00 0.00 37.62 4.68
670 674 1.750930 CAGATGGTGGGCTATCGCT 59.249 57.895 0.00 0.00 37.62 4.93
671 675 1.963338 GCAGATGGTGGGCTATCGC 60.963 63.158 0.00 0.00 37.62 4.58
672 676 0.969149 TAGCAGATGGTGGGCTATCG 59.031 55.000 0.00 0.00 37.62 2.92
673 677 2.634940 TCTTAGCAGATGGTGGGCTATC 59.365 50.000 0.00 0.00 39.63 2.08
674 678 2.694397 TCTTAGCAGATGGTGGGCTAT 58.306 47.619 0.00 0.00 39.63 2.97
675 679 2.174685 TCTTAGCAGATGGTGGGCTA 57.825 50.000 0.00 0.00 39.01 3.93
676 680 1.516110 ATCTTAGCAGATGGTGGGCT 58.484 50.000 0.00 0.00 38.44 5.19
677 681 2.634940 TCTATCTTAGCAGATGGTGGGC 59.365 50.000 0.00 0.00 40.28 5.36
678 682 4.963318 TTCTATCTTAGCAGATGGTGGG 57.037 45.455 0.00 0.00 40.28 4.61
679 683 5.674525 TGTTTCTATCTTAGCAGATGGTGG 58.325 41.667 0.00 0.00 40.28 4.61
680 684 6.238320 GCTTGTTTCTATCTTAGCAGATGGTG 60.238 42.308 0.00 0.00 40.28 4.17
681 685 5.819901 GCTTGTTTCTATCTTAGCAGATGGT 59.180 40.000 0.00 0.00 40.28 3.55
682 686 5.819379 TGCTTGTTTCTATCTTAGCAGATGG 59.181 40.000 0.00 0.00 40.28 3.51
683 687 6.915544 TGCTTGTTTCTATCTTAGCAGATG 57.084 37.500 0.00 0.00 40.28 2.90
684 688 9.050601 GTAATGCTTGTTTCTATCTTAGCAGAT 57.949 33.333 0.00 0.00 41.35 2.90
685 689 7.495934 GGTAATGCTTGTTTCTATCTTAGCAGA 59.504 37.037 0.00 0.00 41.35 4.26
686 690 7.254932 GGGTAATGCTTGTTTCTATCTTAGCAG 60.255 40.741 0.00 0.00 41.35 4.24
687 691 6.542370 GGGTAATGCTTGTTTCTATCTTAGCA 59.458 38.462 0.00 0.00 42.14 3.49
688 692 6.017026 GGGGTAATGCTTGTTTCTATCTTAGC 60.017 42.308 0.00 0.00 0.00 3.09
689 693 7.283329 AGGGGTAATGCTTGTTTCTATCTTAG 58.717 38.462 0.00 0.00 0.00 2.18
690 694 7.092623 TGAGGGGTAATGCTTGTTTCTATCTTA 60.093 37.037 0.00 0.00 0.00 2.10
691 695 6.079712 AGGGGTAATGCTTGTTTCTATCTT 57.920 37.500 0.00 0.00 0.00 2.40
692 696 5.191722 TGAGGGGTAATGCTTGTTTCTATCT 59.808 40.000 0.00 0.00 0.00 1.98
693 697 5.437060 TGAGGGGTAATGCTTGTTTCTATC 58.563 41.667 0.00 0.00 0.00 2.08
694 698 5.450818 TGAGGGGTAATGCTTGTTTCTAT 57.549 39.130 0.00 0.00 0.00 1.98
695 699 4.919774 TGAGGGGTAATGCTTGTTTCTA 57.080 40.909 0.00 0.00 0.00 2.10
725 729 4.039973 TGTGGGTCATCGAGTAGTTTCTTT 59.960 41.667 0.00 0.00 0.00 2.52
754 770 5.915196 GCGAGATTTAGCCATGGAATTTTAC 59.085 40.000 18.40 0.00 0.00 2.01
756 772 4.646492 AGCGAGATTTAGCCATGGAATTTT 59.354 37.500 18.40 0.00 0.00 1.82
763 779 1.789464 GTCGAGCGAGATTTAGCCATG 59.211 52.381 0.00 0.00 0.00 3.66
772 788 1.067821 GAAATCCCAGTCGAGCGAGAT 59.932 52.381 0.00 0.00 0.00 2.75
783 799 1.444836 TACGGTTTGCGAAATCCCAG 58.555 50.000 0.00 0.00 0.00 4.45
786 802 5.575019 ACAATATTACGGTTTGCGAAATCC 58.425 37.500 0.00 0.00 0.00 3.01
792 808 3.303526 GGCCTACAATATTACGGTTTGCG 60.304 47.826 0.00 0.00 0.00 4.85
929 946 0.875040 CGTGCCAGATGCTAGCTCAG 60.875 60.000 17.23 7.79 42.00 3.35
1369 1392 2.780094 CGACCAGGAGCAGCGAGAT 61.780 63.158 0.00 0.00 0.00 2.75
1818 1841 1.739562 GCTGTGAACGGAGAGCCTG 60.740 63.158 0.00 0.00 0.00 4.85
1846 1869 0.548031 CACCACCACTCCAGGCATAT 59.452 55.000 0.00 0.00 0.00 1.78
2721 3110 6.149129 GGGACCAATATAAAAGCAAAGGAG 57.851 41.667 0.00 0.00 0.00 3.69
2776 3166 0.598065 GCAGTTCGCTCCAACCAATT 59.402 50.000 0.00 0.00 37.77 2.32
2794 3184 1.206523 GGAGTATTGTAGCGAACGGC 58.793 55.000 0.00 0.00 44.05 5.68
2858 3390 1.607178 CATTTGGCTGGCCCACTGA 60.607 57.895 9.28 0.00 45.34 3.41
2904 3436 3.234234 ACATCCTTCATGGGCTAATGG 57.766 47.619 0.00 0.00 36.72 3.16
2931 3468 4.877251 AGCACACAACATTGCAATTCTTTT 59.123 33.333 9.83 0.00 41.48 2.27
2935 3472 2.733026 GGAGCACACAACATTGCAATTC 59.267 45.455 9.83 1.16 41.48 2.17
3007 4002 8.685257 TCATGTGGTATGGATTTCCTAGATAT 57.315 34.615 0.00 0.00 36.82 1.63
3026 4022 4.735578 GCATGGCAACCTTCTTATCATGTG 60.736 45.833 0.00 0.00 34.68 3.21
3030 4026 3.054139 AGAGCATGGCAACCTTCTTATCA 60.054 43.478 0.00 0.00 0.00 2.15
3036 4032 2.012673 CACTAGAGCATGGCAACCTTC 58.987 52.381 0.00 0.00 0.00 3.46
3102 4098 2.161609 CACGGCAAATACTGAACCTTCC 59.838 50.000 0.00 0.00 0.00 3.46
3141 4137 9.991388 CAAATTTTTCACACTCAATTTTGTCAT 57.009 25.926 0.00 0.00 28.44 3.06
3232 6098 8.775527 TGAACTATTTTTGTACGTAGCATTTCA 58.224 29.630 0.00 0.00 0.00 2.69
3316 6182 9.639601 GTTTCTTAATTCTTTTAGACCAATGGG 57.360 33.333 3.55 0.00 41.29 4.00
3477 6344 9.754382 GGAAAATTTACATCAAGCATACATGAT 57.246 29.630 0.00 0.00 34.63 2.45


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

AutoCloner maintained by Alex Coulton.