Multiple sequence alignment - TraesCS1B01G293800

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 TraesCS1B01G293800 chr1B 100.000 3299 0 0 1 3299 511450743 511454041 0.000000e+00 6093.0
1 TraesCS1B01G293800 chr1D 91.688 2767 89 44 581 3299 381313541 381316214 0.000000e+00 3705.0
2 TraesCS1B01G293800 chr1D 90.909 462 27 10 1 456 381313097 381313549 1.010000e-169 606.0
3 TraesCS1B01G293800 chr1A 89.311 2816 153 65 569 3299 481932486 481935238 0.000000e+00 3397.0
4 TraesCS1B01G293800 chr1A 89.588 413 23 9 52 456 481932106 481932506 1.060000e-139 507.0
5 TraesCS1B01G293800 chr1A 100.000 29 0 0 2853 2881 496855518 496855490 2.000000e-03 54.7
6 TraesCS1B01G293800 chr3B 85.471 998 128 14 1060 2050 617268777 617267790 0.000000e+00 1024.0
7 TraesCS1B01G293800 chr3D 84.403 1013 135 17 1052 2051 463811418 463810416 0.000000e+00 974.0
8 TraesCS1B01G293800 chr3A 84.323 1027 128 22 1052 2051 606830532 606829512 0.000000e+00 974.0
9 TraesCS1B01G293800 chr3A 100.000 28 0 0 2854 2881 15341214 15341241 6.000000e-03 52.8
10 TraesCS1B01G293800 chr4D 79.870 770 118 18 1287 2050 42238308 42237570 2.250000e-146 529.0
11 TraesCS1B01G293800 chr4D 100.000 62 0 0 1123 1184 228102956 228102895 7.480000e-22 115.0
12 TraesCS1B01G293800 chr4D 98.387 62 1 0 1123 1184 41791145 41791084 3.480000e-20 110.0
13 TraesCS1B01G293800 chr4D 98.387 62 1 0 1123 1184 41798805 41798744 3.480000e-20 110.0
14 TraesCS1B01G293800 chr4A 78.886 772 122 21 1287 2050 597458292 597457554 4.950000e-133 484.0
15 TraesCS1B01G293800 chr4A 78.682 774 127 19 1287 2053 597590707 597589965 6.400000e-132 481.0
16 TraesCS1B01G293800 chr4A 99.194 124 1 0 457 580 142800818 142800941 1.190000e-54 224.0
17 TraesCS1B01G293800 chr4A 83.453 139 23 0 1287 1425 597617490 597617352 2.670000e-26 130.0
18 TraesCS1B01G293800 chr5A 97.710 131 3 0 457 587 608862350 608862220 3.310000e-55 226.0
19 TraesCS1B01G293800 chr5A 97.638 127 3 0 456 582 673731821 673731695 5.540000e-53 219.0
20 TraesCS1B01G293800 chr6B 95.070 142 5 2 450 590 184353132 184353272 4.280000e-54 222.0
21 TraesCS1B01G293800 chr2B 98.400 125 2 0 457 581 49318699 49318575 1.540000e-53 220.0
22 TraesCS1B01G293800 chrUn 96.923 130 3 1 455 584 50587057 50586929 1.990000e-52 217.0
23 TraesCS1B01G293800 chrUn 96.923 130 3 1 455 584 278339140 278339268 1.990000e-52 217.0
24 TraesCS1B01G293800 chrUn 96.923 130 3 1 455 584 278346417 278346545 1.990000e-52 217.0
25 TraesCS1B01G293800 chr2A 96.923 130 3 1 453 582 739923513 739923641 1.990000e-52 217.0
26 TraesCS1B01G293800 chr7D 100.000 61 0 0 1123 1183 334651341 334651281 2.690000e-21 113.0


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 TraesCS1B01G293800 chr1B 511450743 511454041 3298 False 6093.0 6093 100.0000 1 3299 1 chr1B.!!$F1 3298
1 TraesCS1B01G293800 chr1D 381313097 381316214 3117 False 2155.5 3705 91.2985 1 3299 2 chr1D.!!$F1 3298
2 TraesCS1B01G293800 chr1A 481932106 481935238 3132 False 1952.0 3397 89.4495 52 3299 2 chr1A.!!$F1 3247
3 TraesCS1B01G293800 chr3B 617267790 617268777 987 True 1024.0 1024 85.4710 1060 2050 1 chr3B.!!$R1 990
4 TraesCS1B01G293800 chr3D 463810416 463811418 1002 True 974.0 974 84.4030 1052 2051 1 chr3D.!!$R1 999
5 TraesCS1B01G293800 chr3A 606829512 606830532 1020 True 974.0 974 84.3230 1052 2051 1 chr3A.!!$R1 999
6 TraesCS1B01G293800 chr4D 42237570 42238308 738 True 529.0 529 79.8700 1287 2050 1 chr4D.!!$R3 763
7 TraesCS1B01G293800 chr4A 597457554 597458292 738 True 484.0 484 78.8860 1287 2050 1 chr4A.!!$R1 763
8 TraesCS1B01G293800 chr4A 597589965 597590707 742 True 481.0 481 78.6820 1287 2053 1 chr4A.!!$R2 766

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
572 586 0.17915 CTGCAGTACGTCAGAGGAGC 60.179 60.0 5.25 0.0 32.26 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 2524 0.105401 TCCCCCACTTTTCAAACCCC 60.105 55.0 0.0 0.0 0.0 4.95 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
22 23 1.909700 TTTGAATGGCTGGTCTGGTC 58.090 50.000 0.00 0.00 0.00 4.02
23 24 1.067295 TTGAATGGCTGGTCTGGTCT 58.933 50.000 0.00 0.00 0.00 3.85
46 47 2.190578 CCCGGGAGCATTGGAGAC 59.809 66.667 18.48 0.00 0.00 3.36
76 77 4.154918 AGAAACATTCTTTCCATCACGCTC 59.845 41.667 0.00 0.00 36.36 5.03
104 109 5.913514 CGGTTCCAATACAACTCTATACGAG 59.086 44.000 0.00 0.00 45.56 4.18
105 110 6.238566 CGGTTCCAATACAACTCTATACGAGA 60.239 42.308 0.00 0.00 42.62 4.04
107 112 7.808856 GGTTCCAATACAACTCTATACGAGATC 59.191 40.741 0.00 0.00 42.62 2.75
108 113 8.569641 GTTCCAATACAACTCTATACGAGATCT 58.430 37.037 0.00 0.00 42.62 2.75
215 220 2.700897 CCTCCCTCAATCATTCTACGGT 59.299 50.000 0.00 0.00 0.00 4.83
348 357 4.137543 GACCCGCAAAAGATTCTATCCAT 58.862 43.478 0.00 0.00 0.00 3.41
352 361 4.756642 CCGCAAAAGATTCTATCCATGCTA 59.243 41.667 0.00 0.00 33.26 3.49
473 487 3.462678 GGACTCGGCTCCCCTGAC 61.463 72.222 0.00 0.00 0.00 3.51
474 488 3.827898 GACTCGGCTCCCCTGACG 61.828 72.222 0.00 0.00 40.31 4.35
475 489 4.680537 ACTCGGCTCCCCTGACGT 62.681 66.667 0.00 0.00 39.83 4.34
476 490 2.439701 CTCGGCTCCCCTGACGTA 60.440 66.667 0.00 0.00 39.83 3.57
477 491 2.753043 TCGGCTCCCCTGACGTAC 60.753 66.667 0.00 0.00 39.83 3.67
478 492 2.754658 CGGCTCCCCTGACGTACT 60.755 66.667 0.00 0.00 33.11 2.73
479 493 2.893398 GGCTCCCCTGACGTACTG 59.107 66.667 0.00 0.00 0.00 2.74
480 494 2.184579 GCTCCCCTGACGTACTGC 59.815 66.667 0.00 0.00 0.00 4.40
481 495 2.646175 GCTCCCCTGACGTACTGCA 61.646 63.158 0.00 0.00 0.00 4.41
482 496 1.513158 CTCCCCTGACGTACTGCAG 59.487 63.158 13.48 13.48 0.00 4.41
485 499 2.125512 CCTGACGTACTGCAGGGC 60.126 66.667 19.93 9.18 46.24 5.19
486 500 2.507102 CTGACGTACTGCAGGGCG 60.507 66.667 23.98 23.98 0.00 6.13
487 501 4.735132 TGACGTACTGCAGGGCGC 62.735 66.667 25.03 19.20 42.89 6.53
502 516 3.414700 CGCAGTTGGGTCGCTGAC 61.415 66.667 0.00 0.79 34.87 3.51
503 517 2.280797 GCAGTTGGGTCGCTGACA 60.281 61.111 10.14 0.00 34.87 3.58
504 518 2.320587 GCAGTTGGGTCGCTGACAG 61.321 63.158 0.00 0.00 34.87 3.51
505 519 1.669115 CAGTTGGGTCGCTGACAGG 60.669 63.158 4.26 0.00 34.87 4.00
506 520 2.140792 AGTTGGGTCGCTGACAGGT 61.141 57.895 4.26 0.00 33.68 4.00
507 521 1.961277 GTTGGGTCGCTGACAGGTG 60.961 63.158 4.26 0.00 33.68 4.00
508 522 3.177194 TTGGGTCGCTGACAGGTGG 62.177 63.158 4.26 0.00 33.68 4.61
509 523 4.394712 GGGTCGCTGACAGGTGGG 62.395 72.222 4.26 0.00 33.68 4.61
513 527 4.641645 CGCTGACAGGTGGGCCAA 62.642 66.667 8.40 0.00 37.19 4.52
514 528 2.985847 GCTGACAGGTGGGCCAAC 60.986 66.667 15.52 15.52 37.19 3.77
515 529 2.839098 CTGACAGGTGGGCCAACT 59.161 61.111 21.01 21.01 37.19 3.16
516 530 1.151450 CTGACAGGTGGGCCAACTT 59.849 57.895 24.60 13.86 37.19 2.66
517 531 1.152777 TGACAGGTGGGCCAACTTG 60.153 57.895 24.60 20.50 37.19 3.16
518 532 2.521708 ACAGGTGGGCCAACTTGC 60.522 61.111 24.60 0.90 37.19 4.01
519 533 2.203538 CAGGTGGGCCAACTTGCT 60.204 61.111 24.60 0.00 37.19 3.91
520 534 1.833934 CAGGTGGGCCAACTTGCTT 60.834 57.895 24.60 0.00 37.19 3.91
521 535 1.075301 AGGTGGGCCAACTTGCTTT 60.075 52.632 21.01 0.00 37.19 3.51
522 536 1.115326 AGGTGGGCCAACTTGCTTTC 61.115 55.000 21.01 0.00 37.19 2.62
523 537 1.007387 GTGGGCCAACTTGCTTTCG 60.007 57.895 8.40 0.00 0.00 3.46
524 538 2.199652 TGGGCCAACTTGCTTTCGG 61.200 57.895 2.13 0.00 0.00 4.30
525 539 2.650778 GGCCAACTTGCTTTCGGG 59.349 61.111 0.00 0.00 0.00 5.14
526 540 2.049156 GCCAACTTGCTTTCGGGC 60.049 61.111 0.00 0.00 0.00 6.13
527 541 2.650778 CCAACTTGCTTTCGGGCC 59.349 61.111 0.00 0.00 0.00 5.80
528 542 2.650778 CAACTTGCTTTCGGGCCC 59.349 61.111 13.57 13.57 0.00 5.80
529 543 2.197324 AACTTGCTTTCGGGCCCA 59.803 55.556 24.92 6.15 0.00 5.36
530 544 2.200337 AACTTGCTTTCGGGCCCAC 61.200 57.895 24.92 5.64 0.00 4.61
531 545 3.373565 CTTGCTTTCGGGCCCACC 61.374 66.667 24.92 4.81 0.00 4.61
532 546 3.868200 CTTGCTTTCGGGCCCACCT 62.868 63.158 24.92 0.00 36.97 4.00
533 547 4.659172 TGCTTTCGGGCCCACCTG 62.659 66.667 24.92 10.12 44.63 4.00
534 548 4.660938 GCTTTCGGGCCCACCTGT 62.661 66.667 24.92 0.00 43.58 4.00
535 549 2.359975 CTTTCGGGCCCACCTGTC 60.360 66.667 24.92 0.00 43.58 3.51
536 550 3.172106 TTTCGGGCCCACCTGTCA 61.172 61.111 24.92 0.00 43.58 3.58
537 551 2.690653 CTTTCGGGCCCACCTGTCAA 62.691 60.000 24.92 1.80 43.58 3.18
538 552 2.075355 TTTCGGGCCCACCTGTCAAT 62.075 55.000 24.92 0.00 43.58 2.57
539 553 2.751436 CGGGCCCACCTGTCAATG 60.751 66.667 24.92 0.00 37.57 2.82
540 554 2.362889 GGGCCCACCTGTCAATGG 60.363 66.667 19.95 0.00 35.85 3.16
541 555 3.070576 GGCCCACCTGTCAATGGC 61.071 66.667 0.00 0.00 41.42 4.40
542 556 3.070576 GCCCACCTGTCAATGGCC 61.071 66.667 0.00 0.00 36.07 5.36
543 557 2.362889 CCCACCTGTCAATGGCCC 60.363 66.667 0.00 0.00 34.37 5.80
544 558 2.440147 CCACCTGTCAATGGCCCA 59.560 61.111 0.00 0.00 0.00 5.36
545 559 1.228831 CCACCTGTCAATGGCCCAA 60.229 57.895 0.00 0.00 0.00 4.12
546 560 1.535204 CCACCTGTCAATGGCCCAAC 61.535 60.000 0.00 0.00 0.00 3.77
547 561 0.540365 CACCTGTCAATGGCCCAACT 60.540 55.000 0.00 0.00 0.00 3.16
548 562 0.540365 ACCTGTCAATGGCCCAACTG 60.540 55.000 0.00 0.00 0.00 3.16
549 563 1.588082 CTGTCAATGGCCCAACTGC 59.412 57.895 0.00 0.00 0.00 4.40
550 564 2.203972 CTGTCAATGGCCCAACTGCG 62.204 60.000 0.00 0.00 0.00 5.18
551 565 3.372730 TCAATGGCCCAACTGCGC 61.373 61.111 0.00 0.00 0.00 6.09
552 566 4.440127 CAATGGCCCAACTGCGCC 62.440 66.667 4.18 0.00 45.92 6.53
565 579 4.735132 GCGCCCTGCAGTACGTCA 62.735 66.667 21.94 0.00 45.45 4.35
566 580 2.507102 CGCCCTGCAGTACGTCAG 60.507 66.667 13.81 9.54 0.00 3.51
567 581 2.970639 GCCCTGCAGTACGTCAGA 59.029 61.111 13.81 0.00 32.26 3.27
568 582 1.153745 GCCCTGCAGTACGTCAGAG 60.154 63.158 13.81 6.74 32.26 3.35
569 583 1.513158 CCCTGCAGTACGTCAGAGG 59.487 63.158 13.81 12.06 32.26 3.69
570 584 0.965866 CCCTGCAGTACGTCAGAGGA 60.966 60.000 13.81 0.00 32.26 3.71
571 585 0.453793 CCTGCAGTACGTCAGAGGAG 59.546 60.000 13.81 0.00 32.26 3.69
572 586 0.179150 CTGCAGTACGTCAGAGGAGC 60.179 60.000 5.25 0.00 32.26 4.70
573 587 1.139947 GCAGTACGTCAGAGGAGCC 59.860 63.158 0.00 0.00 0.00 4.70
574 588 1.316706 GCAGTACGTCAGAGGAGCCT 61.317 60.000 0.00 0.00 0.00 4.58
575 589 0.736053 CAGTACGTCAGAGGAGCCTC 59.264 60.000 8.50 8.50 43.03 4.70
576 590 0.745128 AGTACGTCAGAGGAGCCTCG 60.745 60.000 10.69 6.49 46.90 4.63
577 591 1.025647 GTACGTCAGAGGAGCCTCGT 61.026 60.000 10.69 8.30 46.90 4.18
578 592 0.743701 TACGTCAGAGGAGCCTCGTC 60.744 60.000 10.69 6.30 46.90 4.20
579 593 2.766400 CGTCAGAGGAGCCTCGTCC 61.766 68.421 10.64 2.33 46.90 4.79
580 594 2.043852 TCAGAGGAGCCTCGTCCC 60.044 66.667 10.64 0.00 46.90 4.46
581 595 3.522731 CAGAGGAGCCTCGTCCCG 61.523 72.222 10.64 0.00 46.90 5.14
671 685 0.969894 GCAGTGTAGTCCAGTCCAGT 59.030 55.000 0.00 0.00 0.00 4.00
672 686 1.344763 GCAGTGTAGTCCAGTCCAGTT 59.655 52.381 0.00 0.00 0.00 3.16
673 687 2.610727 GCAGTGTAGTCCAGTCCAGTTC 60.611 54.545 0.00 0.00 0.00 3.01
674 688 2.894126 CAGTGTAGTCCAGTCCAGTTCT 59.106 50.000 0.00 0.00 0.00 3.01
675 689 3.322254 CAGTGTAGTCCAGTCCAGTTCTT 59.678 47.826 0.00 0.00 0.00 2.52
676 690 3.574826 AGTGTAGTCCAGTCCAGTTCTTC 59.425 47.826 0.00 0.00 0.00 2.87
677 691 3.574826 GTGTAGTCCAGTCCAGTTCTTCT 59.425 47.826 0.00 0.00 0.00 2.85
678 692 3.827302 TGTAGTCCAGTCCAGTTCTTCTC 59.173 47.826 0.00 0.00 0.00 2.87
679 693 2.252714 AGTCCAGTCCAGTTCTTCTCC 58.747 52.381 0.00 0.00 0.00 3.71
786 812 1.043022 CAAAGGCTTTGCACTTCCCT 58.957 50.000 25.46 0.00 33.36 4.20
876 912 2.550830 AGCGCCGAGGAAATATTCAT 57.449 45.000 2.29 0.00 0.00 2.57
906 948 3.842923 CTCGGCTCGGCTCACCAT 61.843 66.667 0.00 0.00 34.57 3.55
1042 1091 1.669760 CGCCGGCTGGTTGTTCTTA 60.670 57.895 26.68 0.00 37.67 2.10
1614 1693 2.047274 AACATCACCCGCGTCCTG 60.047 61.111 4.92 0.00 0.00 3.86
2242 2321 3.777925 CGTCGTCGGCAAAGGCAG 61.778 66.667 0.00 0.00 43.71 4.85
2254 2333 1.123246 AAAGGCAGCAGCAATTGGGT 61.123 50.000 7.72 0.00 44.61 4.51
2278 2357 5.820423 TGGTGGTGTATAGCATTGTTGTATC 59.180 40.000 0.00 0.00 36.58 2.24
2306 2394 0.605589 CCTCTGGTATGAGATCCGGC 59.394 60.000 0.00 0.00 36.23 6.13
2397 2486 8.190784 ACAATTGTTTCTTCTTTGTTACTCCTG 58.809 33.333 4.92 0.00 0.00 3.86
2432 2524 6.698380 ACTAGGAGTTAACCTGTACACAATG 58.302 40.000 0.88 0.00 40.81 2.82
2445 2537 4.712337 TGTACACAATGGGGTTTGAAAAGT 59.288 37.500 0.00 0.00 0.00 2.66
2473 2572 2.060050 AGGTAGATGACTCGAGGTGG 57.940 55.000 18.41 0.00 0.00 4.61
2499 2598 0.595567 TTGAGCTGCAAAGCAAAGCG 60.596 50.000 1.02 0.00 38.41 4.68
2502 2601 2.027897 CTGCAAAGCAAAGCGGCA 59.972 55.556 1.45 6.05 38.41 5.69
2510 2609 2.531522 AGCAAAGCGGCATTCTTTTT 57.468 40.000 1.45 0.00 35.83 1.94
2620 2719 2.615747 GGTTCTACCAGGGCTGTTTCTC 60.616 54.545 0.00 0.00 38.42 2.87
2631 2735 1.284982 CTGTTTCTCCGTGGACGCAG 61.285 60.000 0.00 0.00 38.18 5.18
2632 2736 2.357034 TTTCTCCGTGGACGCAGC 60.357 61.111 0.00 0.00 38.18 5.25
2633 2737 4.717629 TTCTCCGTGGACGCAGCG 62.718 66.667 14.82 14.82 38.18 5.18
2682 2791 2.058675 ACGGAAGTGAGTGGGGAAG 58.941 57.895 0.00 0.00 46.97 3.46
2683 2792 1.296715 CGGAAGTGAGTGGGGAAGG 59.703 63.158 0.00 0.00 0.00 3.46
2685 2794 1.685820 GAAGTGAGTGGGGAAGGGG 59.314 63.158 0.00 0.00 0.00 4.79
2687 2796 4.048470 GTGAGTGGGGAAGGGGGC 62.048 72.222 0.00 0.00 0.00 5.80
2688 2797 4.285790 TGAGTGGGGAAGGGGGCT 62.286 66.667 0.00 0.00 0.00 5.19
2689 2798 2.941583 GAGTGGGGAAGGGGGCTT 60.942 66.667 0.00 0.00 0.00 4.35
2690 2799 3.268032 AGTGGGGAAGGGGGCTTG 61.268 66.667 0.00 0.00 0.00 4.01
2734 2857 2.363147 GTGAGGGGAGAGGCGAGT 60.363 66.667 0.00 0.00 0.00 4.18
2853 2981 2.981977 TTTTCGGCTTGCGTCCGTCT 62.982 55.000 10.23 0.00 46.49 4.18
2939 3068 2.752238 CGCTCTCGTCTCCACCCT 60.752 66.667 0.00 0.00 0.00 4.34
2978 3107 0.464036 ACGACTTGCTTGTGGTCTCA 59.536 50.000 0.00 0.00 0.00 3.27
3013 3142 1.337823 GGTAGCAGTTCAGAGCGGAAA 60.338 52.381 0.00 0.00 35.48 3.13
3063 3196 3.118038 CCTTATCCTCATTTCGGGGACAA 60.118 47.826 0.00 0.00 31.48 3.18
3064 3197 2.717639 ATCCTCATTTCGGGGACAAG 57.282 50.000 0.00 0.00 31.48 3.16
3065 3198 0.035439 TCCTCATTTCGGGGACAAGC 60.035 55.000 0.00 0.00 0.00 4.01
3078 3211 4.505217 CAAGCCGCGTCGCACATC 62.505 66.667 18.75 2.53 0.00 3.06
3091 3224 1.995646 GCACATCCACATGCGCATCA 61.996 55.000 22.51 5.03 37.89 3.07
3145 3278 1.454111 GAGCTCGAGCCCACCTCTA 60.454 63.158 32.94 0.00 43.38 2.43
3146 3279 1.452145 GAGCTCGAGCCCACCTCTAG 61.452 65.000 32.94 0.00 43.38 2.43
3147 3280 1.755008 GCTCGAGCCCACCTCTAGT 60.755 63.158 27.22 0.00 38.49 2.57
3148 3281 2.010582 GCTCGAGCCCACCTCTAGTG 62.011 65.000 27.22 0.00 46.83 2.74
3176 3315 2.734893 GACCCGATCGATCTCCCTT 58.265 57.895 22.43 3.00 0.00 3.95
3177 3316 0.315568 GACCCGATCGATCTCCCTTG 59.684 60.000 22.43 6.32 0.00 3.61
3197 3339 4.148825 ATCGTCACCAGGCGAGGC 62.149 66.667 0.00 0.00 40.56 4.70
3218 3361 1.226030 TGCAGAGAAGACGACGACGA 61.226 55.000 15.32 0.00 42.66 4.20
3222 3365 0.862283 GAGAAGACGACGACGATGCC 60.862 60.000 15.32 0.68 42.66 4.40
3223 3366 1.872679 GAAGACGACGACGATGCCC 60.873 63.158 15.32 0.00 42.66 5.36
3224 3367 2.537792 GAAGACGACGACGATGCCCA 62.538 60.000 15.32 0.00 42.66 5.36
3225 3368 2.814183 AAGACGACGACGATGCCCAC 62.814 60.000 15.32 0.00 42.66 4.61
3226 3369 4.771356 ACGACGACGATGCCCACG 62.771 66.667 15.32 0.00 42.66 4.94
3281 3427 1.423921 GGGACTGGAAACCCTTCTTCA 59.576 52.381 0.00 0.00 42.56 3.02
3284 3430 2.106684 GACTGGAAACCCTTCTTCAGGT 59.893 50.000 0.00 0.00 42.02 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.571653 TGTTTCTCATCGGGTCTCCAAT 59.428 45.455 0.00 0.00 0.00 3.16
39 40 1.974957 TGTTTCTCATCGGGTCTCCAA 59.025 47.619 0.00 0.00 0.00 3.53
46 47 4.009675 TGGAAAGAATGTTTCTCATCGGG 58.990 43.478 2.91 0.00 39.61 5.14
76 77 3.782046 AGAGTTGTATTGGAACCGATCG 58.218 45.455 8.51 8.51 0.00 3.69
283 288 1.370587 GACGAGGCGAGTACTCTGCT 61.371 60.000 27.01 18.18 32.83 4.24
348 357 9.211485 GGTAAGTTTATAAAGACAAGTGTAGCA 57.789 33.333 0.00 0.00 0.00 3.49
400 409 2.897207 GGGCCGGGTTTAATTGCC 59.103 61.111 2.18 0.00 41.42 4.52
456 470 3.462678 GTCAGGGGAGCCGAGTCC 61.463 72.222 0.00 0.00 35.64 3.85
457 471 3.827898 CGTCAGGGGAGCCGAGTC 61.828 72.222 0.00 0.00 0.00 3.36
458 472 3.278072 TACGTCAGGGGAGCCGAGT 62.278 63.158 0.00 0.00 0.00 4.18
459 473 2.439701 TACGTCAGGGGAGCCGAG 60.440 66.667 0.00 0.00 0.00 4.63
460 474 2.753043 GTACGTCAGGGGAGCCGA 60.753 66.667 0.00 0.00 0.00 5.54
461 475 2.754658 AGTACGTCAGGGGAGCCG 60.755 66.667 0.00 0.00 0.00 5.52
462 476 2.893398 CAGTACGTCAGGGGAGCC 59.107 66.667 0.00 0.00 0.00 4.70
463 477 2.184579 GCAGTACGTCAGGGGAGC 59.815 66.667 0.00 0.00 0.00 4.70
464 478 1.513158 CTGCAGTACGTCAGGGGAG 59.487 63.158 5.25 0.00 0.00 4.30
465 479 1.982395 CCTGCAGTACGTCAGGGGA 60.982 63.158 21.58 0.00 44.64 4.81
466 480 2.579201 CCTGCAGTACGTCAGGGG 59.421 66.667 21.58 5.35 44.64 4.79
469 483 2.507102 CGCCCTGCAGTACGTCAG 60.507 66.667 13.81 9.54 0.00 3.51
470 484 4.735132 GCGCCCTGCAGTACGTCA 62.735 66.667 21.94 0.00 45.45 4.35
485 499 3.414700 GTCAGCGACCCAACTGCG 61.415 66.667 0.00 0.00 33.80 5.18
486 500 2.280797 TGTCAGCGACCCAACTGC 60.281 61.111 6.30 0.00 33.80 4.40
487 501 1.669115 CCTGTCAGCGACCCAACTG 60.669 63.158 0.00 0.00 35.15 3.16
488 502 2.140792 ACCTGTCAGCGACCCAACT 61.141 57.895 0.00 0.00 0.00 3.16
489 503 1.961277 CACCTGTCAGCGACCCAAC 60.961 63.158 0.00 0.00 0.00 3.77
490 504 2.425592 CACCTGTCAGCGACCCAA 59.574 61.111 0.00 0.00 0.00 4.12
491 505 3.625897 CCACCTGTCAGCGACCCA 61.626 66.667 0.00 0.00 0.00 4.51
492 506 4.394712 CCCACCTGTCAGCGACCC 62.395 72.222 0.00 0.00 0.00 4.46
496 510 4.641645 TTGGCCCACCTGTCAGCG 62.642 66.667 0.00 0.00 36.63 5.18
497 511 2.983725 AAGTTGGCCCACCTGTCAGC 62.984 60.000 2.72 0.00 36.63 4.26
498 512 1.151450 AAGTTGGCCCACCTGTCAG 59.849 57.895 2.72 0.00 36.63 3.51
499 513 1.152777 CAAGTTGGCCCACCTGTCA 60.153 57.895 2.72 0.00 36.63 3.58
500 514 2.564721 GCAAGTTGGCCCACCTGTC 61.565 63.158 2.72 0.00 36.63 3.51
501 515 2.521708 GCAAGTTGGCCCACCTGT 60.522 61.111 2.72 0.00 36.63 4.00
502 516 1.402107 AAAGCAAGTTGGCCCACCTG 61.402 55.000 2.72 1.84 36.63 4.00
503 517 1.075301 AAAGCAAGTTGGCCCACCT 60.075 52.632 2.72 0.00 36.63 4.00
504 518 1.367471 GAAAGCAAGTTGGCCCACC 59.633 57.895 2.72 0.00 0.00 4.61
505 519 1.007387 CGAAAGCAAGTTGGCCCAC 60.007 57.895 0.00 0.00 0.00 4.61
506 520 2.199652 CCGAAAGCAAGTTGGCCCA 61.200 57.895 0.00 0.00 0.00 5.36
507 521 2.650778 CCGAAAGCAAGTTGGCCC 59.349 61.111 0.00 0.00 0.00 5.80
508 522 2.650778 CCCGAAAGCAAGTTGGCC 59.349 61.111 4.75 0.00 0.00 5.36
509 523 2.049156 GCCCGAAAGCAAGTTGGC 60.049 61.111 4.75 0.00 0.00 4.52
510 524 2.650778 GGCCCGAAAGCAAGTTGG 59.349 61.111 4.75 0.00 0.00 3.77
511 525 2.199652 TGGGCCCGAAAGCAAGTTG 61.200 57.895 19.37 0.00 0.00 3.16
512 526 2.197324 TGGGCCCGAAAGCAAGTT 59.803 55.556 19.37 0.00 0.00 2.66
513 527 2.597510 GTGGGCCCGAAAGCAAGT 60.598 61.111 19.37 0.00 0.00 3.16
514 528 3.373565 GGTGGGCCCGAAAGCAAG 61.374 66.667 19.37 0.00 0.00 4.01
515 529 3.897122 AGGTGGGCCCGAAAGCAA 61.897 61.111 19.37 0.00 38.74 3.91
516 530 4.659172 CAGGTGGGCCCGAAAGCA 62.659 66.667 19.37 0.00 38.74 3.91
517 531 4.660938 ACAGGTGGGCCCGAAAGC 62.661 66.667 19.37 9.80 38.74 3.51
518 532 2.359975 GACAGGTGGGCCCGAAAG 60.360 66.667 19.37 10.07 38.74 2.62
519 533 2.075355 ATTGACAGGTGGGCCCGAAA 62.075 55.000 19.37 0.00 38.74 3.46
520 534 2.534396 ATTGACAGGTGGGCCCGAA 61.534 57.895 19.37 0.00 38.74 4.30
521 535 2.933287 ATTGACAGGTGGGCCCGA 60.933 61.111 19.37 3.06 38.74 5.14
522 536 2.751436 CATTGACAGGTGGGCCCG 60.751 66.667 19.37 4.81 38.74 6.13
523 537 2.362889 CCATTGACAGGTGGGCCC 60.363 66.667 17.59 17.59 34.57 5.80
524 538 3.070576 GCCATTGACAGGTGGGCC 61.071 66.667 0.00 0.00 38.70 5.80
526 540 2.362889 GGGCCATTGACAGGTGGG 60.363 66.667 4.39 0.00 36.00 4.61
527 541 1.228831 TTGGGCCATTGACAGGTGG 60.229 57.895 7.26 4.93 38.55 4.61
528 542 0.540365 AGTTGGGCCATTGACAGGTG 60.540 55.000 7.26 0.00 0.00 4.00
529 543 0.540365 CAGTTGGGCCATTGACAGGT 60.540 55.000 7.26 0.00 0.00 4.00
530 544 1.880819 GCAGTTGGGCCATTGACAGG 61.881 60.000 19.35 8.07 0.00 4.00
531 545 1.588082 GCAGTTGGGCCATTGACAG 59.412 57.895 19.35 8.50 0.00 3.51
532 546 2.267351 CGCAGTTGGGCCATTGACA 61.267 57.895 19.35 0.00 0.00 3.58
533 547 2.568090 CGCAGTTGGGCCATTGAC 59.432 61.111 19.35 10.35 0.00 3.18
534 548 3.372730 GCGCAGTTGGGCCATTGA 61.373 61.111 19.35 0.00 46.68 2.57
548 562 4.735132 TGACGTACTGCAGGGCGC 62.735 66.667 25.03 19.20 42.89 6.53
549 563 2.507102 CTGACGTACTGCAGGGCG 60.507 66.667 23.98 23.98 0.00 6.13
550 564 1.153745 CTCTGACGTACTGCAGGGC 60.154 63.158 19.93 9.18 33.05 5.19
551 565 0.965866 TCCTCTGACGTACTGCAGGG 60.966 60.000 19.93 9.39 33.05 4.45
552 566 0.453793 CTCCTCTGACGTACTGCAGG 59.546 60.000 19.93 2.38 33.05 4.85
553 567 0.179150 GCTCCTCTGACGTACTGCAG 60.179 60.000 13.48 13.48 0.00 4.41
554 568 1.595993 GGCTCCTCTGACGTACTGCA 61.596 60.000 0.00 0.00 0.00 4.41
555 569 1.139947 GGCTCCTCTGACGTACTGC 59.860 63.158 0.00 0.00 0.00 4.40
556 570 0.736053 GAGGCTCCTCTGACGTACTG 59.264 60.000 2.15 0.00 39.80 2.74
557 571 0.745128 CGAGGCTCCTCTGACGTACT 60.745 60.000 9.32 0.00 40.69 2.73
558 572 1.025647 ACGAGGCTCCTCTGACGTAC 61.026 60.000 9.32 0.00 40.69 3.67
559 573 0.743701 GACGAGGCTCCTCTGACGTA 60.744 60.000 9.32 0.00 40.69 3.57
560 574 2.034376 ACGAGGCTCCTCTGACGT 59.966 61.111 9.32 4.69 40.69 4.34
561 575 2.766400 GGACGAGGCTCCTCTGACG 61.766 68.421 9.32 4.08 40.69 4.35
562 576 2.419739 GGGACGAGGCTCCTCTGAC 61.420 68.421 9.32 7.69 40.69 3.51
563 577 2.043852 GGGACGAGGCTCCTCTGA 60.044 66.667 9.32 0.00 40.69 3.27
583 597 4.263572 TAATGATGGCGCCCCCGG 62.264 66.667 26.77 0.00 35.87 5.73
584 598 2.978010 GTAATGATGGCGCCCCCG 60.978 66.667 26.77 0.00 35.87 5.73
585 599 2.978010 CGTAATGATGGCGCCCCC 60.978 66.667 26.77 16.34 0.00 5.40
586 600 2.978010 CCGTAATGATGGCGCCCC 60.978 66.667 26.77 16.75 0.00 5.80
587 601 2.978010 CCCGTAATGATGGCGCCC 60.978 66.667 26.77 10.34 0.00 6.13
588 602 3.660111 GCCCGTAATGATGGCGCC 61.660 66.667 22.73 22.73 35.08 6.53
589 603 3.660111 GGCCCGTAATGATGGCGC 61.660 66.667 0.00 0.00 46.31 6.53
671 685 0.972983 CCAGCGAGGAGGGAGAAGAA 60.973 60.000 0.00 0.00 41.22 2.52
672 686 1.380515 CCAGCGAGGAGGGAGAAGA 60.381 63.158 0.00 0.00 41.22 2.87
673 687 1.380515 TCCAGCGAGGAGGGAGAAG 60.381 63.158 0.00 0.00 43.07 2.85
674 688 2.770827 TCCAGCGAGGAGGGAGAA 59.229 61.111 0.00 0.00 43.07 2.87
695 709 0.534412 CTGGAGTGGAGTGTAGCAGG 59.466 60.000 0.00 0.00 0.00 4.85
786 812 1.227823 CTGGTTGGGTTCAGTGCGA 60.228 57.895 0.00 0.00 0.00 5.10
876 912 3.003173 CCGAGCCCCAGAGTGGAA 61.003 66.667 0.00 0.00 40.96 3.53
1035 1084 0.322098 CGGCCACCACCATAAGAACA 60.322 55.000 2.24 0.00 0.00 3.18
1038 1087 2.675242 CCCGGCCACCACCATAAGA 61.675 63.158 2.24 0.00 0.00 2.10
2189 2268 1.069090 GCAGTGTCGTTCCTGGTCA 59.931 57.895 0.00 0.00 0.00 4.02
2191 2270 2.029073 CGCAGTGTCGTTCCTGGT 59.971 61.111 0.00 0.00 0.00 4.00
2230 2309 4.953010 TGCTGCTGCCTTTGCCGA 62.953 61.111 13.47 0.00 38.71 5.54
2242 2321 2.209315 ACCACCACCCAATTGCTGC 61.209 57.895 0.00 0.00 0.00 5.25
2254 2333 4.027674 ACAACAATGCTATACACCACCA 57.972 40.909 0.00 0.00 0.00 4.17
2278 2357 2.034878 TCATACCAGAGGCAGCAGTAG 58.965 52.381 0.00 0.00 0.00 2.57
2306 2394 0.456221 AATGGACGACTAGCTCACCG 59.544 55.000 0.00 0.00 0.00 4.94
2417 2509 4.141228 TCAAACCCCATTGTGTACAGGTTA 60.141 41.667 13.54 0.00 36.61 2.85
2432 2524 0.105401 TCCCCCACTTTTCAAACCCC 60.105 55.000 0.00 0.00 0.00 4.95
2445 2537 1.651770 AGTCATCTACCTTCTCCCCCA 59.348 52.381 0.00 0.00 0.00 4.96
2473 2572 3.134021 GCTTTGCAGCTCAATCTTCTC 57.866 47.619 0.00 0.00 43.51 2.87
2502 2601 1.467342 GACGCGGGCAGTAAAAAGAAT 59.533 47.619 12.47 0.00 0.00 2.40
2609 2708 1.671379 GTCCACGGAGAAACAGCCC 60.671 63.158 0.00 0.00 0.00 5.19
2610 2709 2.027625 CGTCCACGGAGAAACAGCC 61.028 63.158 0.00 0.00 35.37 4.85
2633 2737 0.794473 GCAAAATGGAAGCAGCTTGC 59.206 50.000 19.31 19.31 45.46 4.01
2634 2738 2.066262 CAGCAAAATGGAAGCAGCTTG 58.934 47.619 13.91 0.00 0.00 4.01
2635 2739 1.965643 TCAGCAAAATGGAAGCAGCTT 59.034 42.857 7.60 7.60 0.00 3.74
2636 2740 1.624336 TCAGCAAAATGGAAGCAGCT 58.376 45.000 0.00 0.00 0.00 4.24
2637 2741 2.443887 TTCAGCAAAATGGAAGCAGC 57.556 45.000 0.00 0.00 0.00 5.25
2638 2742 3.176708 CGATTCAGCAAAATGGAAGCAG 58.823 45.455 0.00 0.00 0.00 4.24
2639 2743 2.094597 CCGATTCAGCAAAATGGAAGCA 60.095 45.455 0.00 0.00 0.00 3.91
2640 2744 2.533266 CCGATTCAGCAAAATGGAAGC 58.467 47.619 0.00 0.00 0.00 3.86
2641 2745 2.736400 GCCCGATTCAGCAAAATGGAAG 60.736 50.000 0.00 0.00 0.00 3.46
2643 2747 0.817013 GCCCGATTCAGCAAAATGGA 59.183 50.000 0.00 0.00 0.00 3.41
2673 2782 3.268032 CAAGCCCCCTTCCCCACT 61.268 66.667 0.00 0.00 0.00 4.00
2734 2857 2.530661 CACCCCACCTACCACCCA 60.531 66.667 0.00 0.00 0.00 4.51
2817 2945 1.772182 AAAGGCGATCGAATCTAGCG 58.228 50.000 21.57 0.00 0.00 4.26
2925 3054 2.750637 GCGAGGGTGGAGACGAGA 60.751 66.667 0.00 0.00 0.00 4.04
3025 3154 3.056328 GGCCGGGTGAGAAGTTGC 61.056 66.667 2.18 0.00 0.00 4.17
3102 3235 3.695606 TGTCAGGCACGAGGAGGC 61.696 66.667 0.00 0.00 0.00 4.70
3146 3279 1.658686 ATCGGGTCGAGTGAGCTCAC 61.659 60.000 34.82 34.82 46.77 3.51
3147 3280 1.377366 GATCGGGTCGAGTGAGCTCA 61.377 60.000 13.74 13.74 41.71 4.26
3148 3281 1.357334 GATCGGGTCGAGTGAGCTC 59.643 63.158 6.82 6.82 42.30 4.09
3149 3282 3.515611 GATCGGGTCGAGTGAGCT 58.484 61.111 0.00 0.00 42.30 4.09
3176 3315 2.212900 CTCGCCTGGTGACGATGTCA 62.213 60.000 5.70 0.00 40.50 3.58
3177 3316 1.517257 CTCGCCTGGTGACGATGTC 60.517 63.158 5.70 0.00 37.72 3.06
3197 3339 1.263776 GTCGTCGTCTTCTCTGCATG 58.736 55.000 0.00 0.00 0.00 4.06
3218 3361 4.457496 CTCTCGTGGCGTGGGCAT 62.457 66.667 0.00 0.00 40.92 4.40


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

AutoCloner maintained by Alex Coulton.