Multiple sequence alignment - TraesCS3D01G370500

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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 TraesCS3D01G370500 chr3D 100.000 2411 0 0 1 2411 484338779 484341189 0.000000e+00 4453
1 TraesCS3D01G370500 chr3D 85.714 147 17 4 2264 2408 602199378 602199522 4.150000e-33 152
2 TraesCS3D01G370500 chr3B 87.507 1801 148 39 666 2411 647169360 647171138 0.000000e+00 2008
3 TraesCS3D01G370500 chr3B 90.074 272 22 3 2130 2401 290615134 290615400 4.930000e-92 348
4 TraesCS3D01G370500 chr3B 81.794 379 33 12 675 1018 647134946 647134569 3.920000e-73 285
5 TraesCS3D01G370500 chr3A 87.808 1747 128 40 740 2411 627269174 627270910 0.000000e+00 1967
6 TraesCS3D01G370500 chr3A 85.135 148 20 2 2264 2410 730940278 730940132 1.490000e-32 150
7 TraesCS3D01G370500 chr6D 90.317 568 50 4 1 566 149809861 149809297 0.000000e+00 739
8 TraesCS3D01G370500 chr6D 94.840 407 21 0 1001 1407 47812384 47812790 9.400000e-179 636
9 TraesCS3D01G370500 chr6D 90.991 222 20 0 2188 2409 294698274 294698053 1.400000e-77 300
10 TraesCS3D01G370500 chr4D 90.300 567 51 3 1 566 414680180 414680743 0.000000e+00 739
11 TraesCS3D01G370500 chr4D 90.381 551 51 2 1 550 62520105 62519556 0.000000e+00 723
12 TraesCS3D01G370500 chr4D 89.223 566 60 1 1 566 450403920 450403356 0.000000e+00 706
13 TraesCS3D01G370500 chr4D 94.231 416 24 0 992 1407 444177282 444177697 9.400000e-179 636
14 TraesCS3D01G370500 chr5B 90.317 568 48 4 1 566 268636812 268637374 0.000000e+00 737
15 TraesCS3D01G370500 chr1D 89.753 566 54 4 1 566 53239930 53239369 0.000000e+00 721
16 TraesCS3D01G370500 chr1D 93.765 417 24 2 1001 1417 369925926 369925512 2.040000e-175 625
17 TraesCS3D01G370500 chr1D 94.444 72 4 0 2188 2259 390213818 390213889 7.050000e-21 111
18 TraesCS3D01G370500 chr4A 89.242 567 57 3 1 566 319790230 319789667 0.000000e+00 706
19 TraesCS3D01G370500 chr4A 94.840 407 21 0 1001 1407 23611217 23610811 9.400000e-179 636
20 TraesCS3D01G370500 chr5A 89.146 562 58 2 3 563 84812693 84813252 0.000000e+00 697
21 TraesCS3D01G370500 chr7D 88.693 566 62 2 1 566 309719877 309720440 0.000000e+00 689
22 TraesCS3D01G370500 chr1A 94.245 417 22 2 1001 1417 468599195 468598781 9.400000e-179 636
23 TraesCS3D01G370500 chr6A 94.595 407 22 0 1001 1407 67142086 67141680 4.370000e-177 630
24 TraesCS3D01G370500 chr6A 91.135 282 20 3 2129 2409 251475484 251475207 6.290000e-101 377
25 TraesCS3D01G370500 chr6A 89.643 280 24 3 2130 2409 252021073 252021347 3.810000e-93 351
26 TraesCS3D01G370500 chr1B 91.991 437 31 4 981 1417 492369064 492368632 5.700000e-171 610
27 TraesCS3D01G370500 chr5D 91.786 280 18 3 2130 2409 79988055 79988329 3.760000e-103 385
28 TraesCS3D01G370500 chr7B 91.111 225 20 0 2185 2409 601441486 601441710 3.010000e-79 305
29 TraesCS3D01G370500 chr4B 89.655 232 23 1 2179 2409 397269108 397268877 6.520000e-76 294
30 TraesCS3D01G370500 chr7A 90.345 145 9 3 2130 2274 397430736 397430597 4.090000e-43 185
31 TraesCS3D01G370500 chr7A 87.857 140 17 0 2270 2409 397428945 397428806 5.330000e-37 165
32 TraesCS3D01G370500 chr7A 88.043 92 10 1 2169 2259 178609969 178609878 9.110000e-20 108


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 TraesCS3D01G370500 chr3D 484338779 484341189 2410 False 4453 4453 100.000 1 2411 1 chr3D.!!$F1 2410
1 TraesCS3D01G370500 chr3B 647169360 647171138 1778 False 2008 2008 87.507 666 2411 1 chr3B.!!$F2 1745
2 TraesCS3D01G370500 chr3A 627269174 627270910 1736 False 1967 1967 87.808 740 2411 1 chr3A.!!$F1 1671
3 TraesCS3D01G370500 chr6D 149809297 149809861 564 True 739 739 90.317 1 566 1 chr6D.!!$R1 565
4 TraesCS3D01G370500 chr4D 414680180 414680743 563 False 739 739 90.300 1 566 1 chr4D.!!$F1 565
5 TraesCS3D01G370500 chr4D 62519556 62520105 549 True 723 723 90.381 1 550 1 chr4D.!!$R1 549
6 TraesCS3D01G370500 chr4D 450403356 450403920 564 True 706 706 89.223 1 566 1 chr4D.!!$R2 565
7 TraesCS3D01G370500 chr5B 268636812 268637374 562 False 737 737 90.317 1 566 1 chr5B.!!$F1 565
8 TraesCS3D01G370500 chr1D 53239369 53239930 561 True 721 721 89.753 1 566 1 chr1D.!!$R1 565
9 TraesCS3D01G370500 chr4A 319789667 319790230 563 True 706 706 89.242 1 566 1 chr4A.!!$R2 565
10 TraesCS3D01G370500 chr5A 84812693 84813252 559 False 697 697 89.146 3 563 1 chr5A.!!$F1 560
11 TraesCS3D01G370500 chr7D 309719877 309720440 563 False 689 689 88.693 1 566 1 chr7D.!!$F1 565

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
568 572 0.252742 AACAACGAGAGGGGGAGGAT 60.253 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1672 0.027586 AAGAAAGCAACACACGTCGC 59.972 50.0 0.0 0.0 0.0 5.19 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
194 198 9.612066 AACCACAATAATTTTTCATCAAGTGTT 57.388 25.926 0.00 0.00 0.00 3.32
242 246 4.494199 GGCCGTAGTCAAATTCGATTCAAG 60.494 45.833 0.00 0.00 0.00 3.02
326 330 1.270625 TGGAACCGGTCTCATGAACAC 60.271 52.381 8.04 0.00 0.00 3.32
327 331 1.270625 GGAACCGGTCTCATGAACACA 60.271 52.381 8.04 0.00 0.00 3.72
343 347 2.504367 ACACAGTCATGTAAGGTTGGC 58.496 47.619 0.00 0.00 37.65 4.52
349 353 2.235761 ATGTAAGGTTGGCCCGGGT 61.236 57.895 24.63 1.77 38.74 5.28
483 487 4.932789 GCTCGGATGCCACTGTTA 57.067 55.556 0.00 0.00 0.00 2.41
536 540 5.690997 TCTACGATCACGCAAGATCTATT 57.309 39.130 12.06 1.83 41.74 1.73
540 544 6.073327 ACGATCACGCAAGATCTATTTAGA 57.927 37.500 12.06 0.00 41.74 2.10
550 554 8.929746 CGCAAGATCTATTTAGAAGATGCATAA 58.070 33.333 0.00 0.00 37.60 1.90
567 571 0.410663 TAACAACGAGAGGGGGAGGA 59.589 55.000 0.00 0.00 0.00 3.71
568 572 0.252742 AACAACGAGAGGGGGAGGAT 60.253 55.000 0.00 0.00 0.00 3.24
569 573 0.688087 ACAACGAGAGGGGGAGGATC 60.688 60.000 0.00 0.00 0.00 3.36
570 574 0.397816 CAACGAGAGGGGGAGGATCT 60.398 60.000 0.00 0.00 33.73 2.75
571 575 1.133450 CAACGAGAGGGGGAGGATCTA 60.133 57.143 0.00 0.00 33.73 1.98
572 576 1.462426 ACGAGAGGGGGAGGATCTAT 58.538 55.000 0.00 0.00 33.73 1.98
573 577 1.356398 ACGAGAGGGGGAGGATCTATC 59.644 57.143 0.00 0.00 33.73 2.08
574 578 1.638589 CGAGAGGGGGAGGATCTATCT 59.361 57.143 0.00 0.00 33.73 1.98
575 579 2.847449 CGAGAGGGGGAGGATCTATCTA 59.153 54.545 0.00 0.00 33.73 1.98
576 580 3.118038 CGAGAGGGGGAGGATCTATCTAG 60.118 56.522 0.00 0.00 33.73 2.43
577 581 3.204382 GAGAGGGGGAGGATCTATCTAGG 59.796 56.522 0.00 0.00 33.73 3.02
578 582 2.930405 GAGGGGGAGGATCTATCTAGGT 59.070 54.545 0.00 0.00 33.73 3.08
579 583 3.338519 GAGGGGGAGGATCTATCTAGGTT 59.661 52.174 0.00 0.00 33.73 3.50
580 584 3.740889 AGGGGGAGGATCTATCTAGGTTT 59.259 47.826 0.00 0.00 33.73 3.27
581 585 4.175065 AGGGGGAGGATCTATCTAGGTTTT 59.825 45.833 0.00 0.00 33.73 2.43
582 586 4.914581 GGGGGAGGATCTATCTAGGTTTTT 59.085 45.833 0.00 0.00 33.73 1.94
604 608 5.734855 TTTTAAATATGACGCTGAGAGGC 57.265 39.130 0.00 0.00 0.00 4.70
605 609 4.672587 TTAAATATGACGCTGAGAGGCT 57.327 40.909 0.00 0.00 0.00 4.58
606 610 3.550437 AAATATGACGCTGAGAGGCTT 57.450 42.857 0.00 0.00 0.00 4.35
607 611 2.522836 ATATGACGCTGAGAGGCTTG 57.477 50.000 0.00 0.00 0.00 4.01
608 612 1.474330 TATGACGCTGAGAGGCTTGA 58.526 50.000 0.00 0.00 0.00 3.02
609 613 0.610174 ATGACGCTGAGAGGCTTGAA 59.390 50.000 0.00 0.00 0.00 2.69
610 614 0.392706 TGACGCTGAGAGGCTTGAAA 59.607 50.000 0.00 0.00 0.00 2.69
611 615 1.202639 TGACGCTGAGAGGCTTGAAAA 60.203 47.619 0.00 0.00 0.00 2.29
612 616 1.195674 GACGCTGAGAGGCTTGAAAAC 59.804 52.381 0.00 0.00 0.00 2.43
613 617 1.202698 ACGCTGAGAGGCTTGAAAACT 60.203 47.619 0.00 0.00 0.00 2.66
614 618 1.462670 CGCTGAGAGGCTTGAAAACTC 59.537 52.381 0.00 0.00 0.00 3.01
615 619 2.777094 GCTGAGAGGCTTGAAAACTCT 58.223 47.619 0.00 0.00 43.81 3.24
619 623 2.777094 AGAGGCTTGAAAACTCTCAGC 58.223 47.619 0.00 0.00 36.96 4.26
620 624 1.462670 GAGGCTTGAAAACTCTCAGCG 59.537 52.381 0.00 0.00 0.00 5.18
621 625 1.202698 AGGCTTGAAAACTCTCAGCGT 60.203 47.619 0.00 0.00 0.00 5.07
622 626 1.604278 GGCTTGAAAACTCTCAGCGTT 59.396 47.619 0.00 0.00 0.00 4.84
623 627 2.603173 GGCTTGAAAACTCTCAGCGTTG 60.603 50.000 0.00 0.00 0.00 4.10
624 628 2.603173 GCTTGAAAACTCTCAGCGTTGG 60.603 50.000 0.00 0.00 0.00 3.77
625 629 1.593196 TGAAAACTCTCAGCGTTGGG 58.407 50.000 0.00 0.00 0.00 4.12
626 630 1.140052 TGAAAACTCTCAGCGTTGGGA 59.860 47.619 0.62 0.62 31.52 4.37
627 631 2.218603 GAAAACTCTCAGCGTTGGGAA 58.781 47.619 2.64 0.00 32.16 3.97
628 632 2.341846 AAACTCTCAGCGTTGGGAAA 57.658 45.000 2.64 0.00 32.16 3.13
629 633 2.341846 AACTCTCAGCGTTGGGAAAA 57.658 45.000 2.64 0.00 32.16 2.29
630 634 2.341846 ACTCTCAGCGTTGGGAAAAA 57.658 45.000 2.64 0.00 32.16 1.94
631 635 2.222027 ACTCTCAGCGTTGGGAAAAAG 58.778 47.619 2.64 0.00 32.16 2.27
632 636 2.222027 CTCTCAGCGTTGGGAAAAAGT 58.778 47.619 2.64 0.00 32.16 2.66
633 637 2.218603 TCTCAGCGTTGGGAAAAAGTC 58.781 47.619 0.00 0.00 28.50 3.01
634 638 2.158813 TCTCAGCGTTGGGAAAAAGTCT 60.159 45.455 0.00 0.00 28.50 3.24
635 639 1.946768 TCAGCGTTGGGAAAAAGTCTG 59.053 47.619 0.00 0.00 0.00 3.51
636 640 1.001378 CAGCGTTGGGAAAAAGTCTGG 60.001 52.381 0.00 0.00 0.00 3.86
637 641 1.133915 AGCGTTGGGAAAAAGTCTGGA 60.134 47.619 0.00 0.00 0.00 3.86
638 642 1.001706 GCGTTGGGAAAAAGTCTGGAC 60.002 52.381 0.00 0.00 0.00 4.02
639 643 1.607148 CGTTGGGAAAAAGTCTGGACC 59.393 52.381 0.00 0.00 0.00 4.46
640 644 1.961394 GTTGGGAAAAAGTCTGGACCC 59.039 52.381 0.00 0.00 37.99 4.46
641 645 1.227249 TGGGAAAAAGTCTGGACCCA 58.773 50.000 0.00 0.00 43.96 4.51
642 646 1.133606 TGGGAAAAAGTCTGGACCCAC 60.134 52.381 0.00 0.00 41.76 4.61
643 647 1.617322 GGAAAAAGTCTGGACCCACC 58.383 55.000 0.00 0.00 39.54 4.61
644 648 1.145119 GGAAAAAGTCTGGACCCACCT 59.855 52.381 0.00 0.00 39.86 4.00
645 649 2.230660 GAAAAAGTCTGGACCCACCTG 58.769 52.381 0.00 0.00 39.86 4.00
646 650 1.222567 AAAAGTCTGGACCCACCTGT 58.777 50.000 0.00 0.00 39.86 4.00
647 651 0.765510 AAAGTCTGGACCCACCTGTC 59.234 55.000 0.00 0.00 39.86 3.51
648 652 1.472662 AAGTCTGGACCCACCTGTCG 61.473 60.000 0.00 0.00 39.86 4.35
649 653 3.311110 TCTGGACCCACCTGTCGC 61.311 66.667 0.00 0.00 39.86 5.19
650 654 3.314331 CTGGACCCACCTGTCGCT 61.314 66.667 0.00 0.00 39.86 4.93
651 655 3.302347 CTGGACCCACCTGTCGCTC 62.302 68.421 0.00 0.00 39.86 5.03
652 656 2.997897 GGACCCACCTGTCGCTCT 60.998 66.667 0.00 0.00 36.07 4.09
653 657 1.681327 GGACCCACCTGTCGCTCTA 60.681 63.158 0.00 0.00 36.07 2.43
654 658 1.043673 GGACCCACCTGTCGCTCTAT 61.044 60.000 0.00 0.00 36.07 1.98
655 659 1.688772 GACCCACCTGTCGCTCTATA 58.311 55.000 0.00 0.00 0.00 1.31
656 660 1.609555 GACCCACCTGTCGCTCTATAG 59.390 57.143 0.00 0.00 0.00 1.31
657 661 1.214673 ACCCACCTGTCGCTCTATAGA 59.785 52.381 1.69 1.69 0.00 1.98
658 662 2.307768 CCCACCTGTCGCTCTATAGAA 58.692 52.381 3.57 0.00 0.00 2.10
659 663 2.693591 CCCACCTGTCGCTCTATAGAAA 59.306 50.000 3.57 0.00 0.00 2.52
660 664 3.491104 CCCACCTGTCGCTCTATAGAAAC 60.491 52.174 3.57 3.64 0.00 2.78
661 665 3.364062 CACCTGTCGCTCTATAGAAACG 58.636 50.000 15.39 15.39 0.00 3.60
662 666 2.223525 ACCTGTCGCTCTATAGAAACGC 60.224 50.000 16.31 10.19 0.00 4.84
663 667 2.033550 CCTGTCGCTCTATAGAAACGCT 59.966 50.000 16.31 0.00 0.00 5.07
664 668 3.250280 CCTGTCGCTCTATAGAAACGCTA 59.750 47.826 16.31 9.09 0.00 4.26
671 675 2.292569 TCTATAGAAACGCTAGCCCACG 59.707 50.000 9.66 0.00 31.33 4.94
686 690 4.681978 ACGGCCAGACCAGCGAAC 62.682 66.667 2.24 0.00 39.03 3.95
730 734 0.801067 GATCCGCGTGACACTACACC 60.801 60.000 4.92 0.00 37.48 4.16
731 735 2.221906 ATCCGCGTGACACTACACCC 62.222 60.000 4.92 0.00 37.48 4.61
732 736 2.803670 CGCGTGACACTACACCCG 60.804 66.667 3.68 0.00 37.48 5.28
738 746 1.443872 GACACTACACCCGCTCACG 60.444 63.158 0.00 0.00 39.67 4.35
934 980 0.698886 CCCCATCCTCTCCATCCCAA 60.699 60.000 0.00 0.00 0.00 4.12
960 1023 2.101640 AATCCCCCAAGCAAACAACT 57.898 45.000 0.00 0.00 0.00 3.16
1200 1263 3.207669 CTGATCCGCAAGCTGCCC 61.208 66.667 0.00 0.00 41.12 5.36
1500 1564 5.529800 GTGGTGTAGTTAACATGTTCCTGTT 59.470 40.000 15.85 0.55 41.10 3.16
1507 1571 2.550830 ACATGTTCCTGTTCGCTCTT 57.449 45.000 0.00 0.00 0.00 2.85
1576 1640 7.226128 TCAATGAAGAGTGCAGTTATCATCATC 59.774 37.037 18.06 0.29 32.03 2.92
1617 1681 3.887777 TTTTTCTGTGCGACGTGTG 57.112 47.368 0.00 0.00 0.00 3.82
1618 1682 1.080298 TTTTTCTGTGCGACGTGTGT 58.920 45.000 0.00 0.00 0.00 3.72
1661 1743 2.602217 CGTTGTCTAGCTTGTTTGTGCC 60.602 50.000 0.00 0.00 0.00 5.01
1672 1754 0.593128 GTTTGTGCCGTGAAGCAGAT 59.407 50.000 0.00 0.00 45.14 2.90
1678 1773 1.712081 CCGTGAAGCAGATGAAGCG 59.288 57.895 0.00 0.00 37.01 4.68
1688 1783 7.374491 GTGAAGCAGATGAAGCGTAATAATTTC 59.626 37.037 0.00 0.00 37.01 2.17
1689 1784 7.280876 TGAAGCAGATGAAGCGTAATAATTTCT 59.719 33.333 0.00 0.00 37.01 2.52
1694 1789 9.208022 CAGATGAAGCGTAATAATTTCTATCCA 57.792 33.333 0.00 0.00 0.00 3.41
1696 1791 9.979270 GATGAAGCGTAATAATTTCTATCCATG 57.021 33.333 0.00 0.00 0.00 3.66
1727 1823 0.732571 CCGTCATTGGATTGTTCCCG 59.267 55.000 0.00 0.00 41.83 5.14
1729 1825 2.623535 CGTCATTGGATTGTTCCCGTA 58.376 47.619 0.00 0.00 41.83 4.02
1741 1840 3.581755 TGTTCCCGTATTCTTTCACTCG 58.418 45.455 0.00 0.00 0.00 4.18
1743 1842 4.240096 GTTCCCGTATTCTTTCACTCGAA 58.760 43.478 0.00 0.00 0.00 3.71
1746 1845 4.868171 TCCCGTATTCTTTCACTCGAATTG 59.132 41.667 0.00 0.00 32.53 2.32
1766 1865 6.859715 ATTGATTTTTCGATCTTTCGCTTG 57.140 33.333 0.00 0.00 45.10 4.01
1767 1866 4.722194 TGATTTTTCGATCTTTCGCTTGG 58.278 39.130 0.00 0.00 45.10 3.61
1780 1879 1.202879 TCGCTTGGGTTTTCTGATGGT 60.203 47.619 0.00 0.00 0.00 3.55
1817 1916 1.201343 GAAGAACAGTATCGCCGCTC 58.799 55.000 0.00 0.00 0.00 5.03
1849 1949 2.107366 TCATGGATAAGCTCACCGTGA 58.893 47.619 18.42 18.42 44.22 4.35
1852 1952 3.627395 TGGATAAGCTCACCGTGATTT 57.373 42.857 0.62 3.00 0.00 2.17
1853 1953 3.270027 TGGATAAGCTCACCGTGATTTG 58.730 45.455 0.62 0.00 0.00 2.32
1855 1955 3.531538 GATAAGCTCACCGTGATTTGGA 58.468 45.455 0.62 0.00 0.00 3.53
1856 1956 2.270352 AAGCTCACCGTGATTTGGAA 57.730 45.000 0.62 0.00 0.00 3.53
1857 1957 2.496899 AGCTCACCGTGATTTGGAAT 57.503 45.000 0.62 0.00 0.00 3.01
1859 1959 2.489329 AGCTCACCGTGATTTGGAATTG 59.511 45.455 0.62 0.00 0.00 2.32
1860 1960 2.228822 GCTCACCGTGATTTGGAATTGT 59.771 45.455 0.62 0.00 0.00 2.71
1861 1961 3.825308 CTCACCGTGATTTGGAATTGTG 58.175 45.455 0.62 0.00 0.00 3.33
1862 1962 3.218453 TCACCGTGATTTGGAATTGTGT 58.782 40.909 0.00 0.00 0.00 3.72
1864 1964 3.735240 CACCGTGATTTGGAATTGTGTTG 59.265 43.478 0.00 0.00 0.00 3.33
1867 1967 4.808364 CCGTGATTTGGAATTGTGTTGTTT 59.192 37.500 0.00 0.00 0.00 2.83
1868 1968 5.051106 CCGTGATTTGGAATTGTGTTGTTTC 60.051 40.000 0.00 0.00 0.00 2.78
1869 1969 5.051106 CGTGATTTGGAATTGTGTTGTTTCC 60.051 40.000 0.00 0.00 39.50 3.13
1875 1985 8.655651 TTTGGAATTGTGTTGTTTCCTATTTC 57.344 30.769 0.00 0.00 39.72 2.17
1923 2033 2.427410 GTGCTCCGCGTTTGCTTG 60.427 61.111 4.92 0.00 39.65 4.01
1935 2045 0.459489 TTTGCTTGTTTGCCGCTTCT 59.541 45.000 0.00 0.00 0.00 2.85
1941 2052 1.007387 GTTTGCCGCTTCTGTTGGG 60.007 57.895 0.00 0.00 0.00 4.12
1942 2053 2.855514 TTTGCCGCTTCTGTTGGGC 61.856 57.895 0.00 0.00 45.76 5.36
1945 2056 3.423154 CCGCTTCTGTTGGGCGTC 61.423 66.667 0.00 0.00 46.23 5.19
1975 2086 8.281212 GAAGGAATCCAATAGTAGCTGAAAAA 57.719 34.615 0.61 0.00 0.00 1.94
1989 2100 2.677573 GAAAAACAACGCTGGCCGCT 62.678 55.000 15.78 2.80 41.76 5.52
1990 2101 1.448922 AAAAACAACGCTGGCCGCTA 61.449 50.000 15.78 0.00 41.76 4.26
1992 2103 2.125202 AAACAACGCTGGCCGCTAAC 62.125 55.000 15.78 0.00 41.76 2.34
1993 2104 3.047280 CAACGCTGGCCGCTAACA 61.047 61.111 15.78 0.00 41.76 2.41
1994 2105 2.281208 AACGCTGGCCGCTAACAA 60.281 55.556 15.78 0.00 41.76 2.83
1995 2106 2.613506 AACGCTGGCCGCTAACAAC 61.614 57.895 15.78 0.00 41.76 3.32
1996 2107 3.799755 CGCTGGCCGCTAACAACC 61.800 66.667 15.78 0.00 36.13 3.77
2019 2130 1.926511 GCCCGCTGTCATTGACTTGG 61.927 60.000 17.26 14.61 33.15 3.61
2020 2131 0.321564 CCCGCTGTCATTGACTTGGA 60.322 55.000 17.26 0.00 33.15 3.53
2036 2147 3.300765 GAGACGTCGTGGGGGTGT 61.301 66.667 10.46 0.00 0.00 4.16
2059 2170 2.093447 ACCGAATCCAGCAAAGTAGGAG 60.093 50.000 0.00 0.00 34.40 3.69
2070 2181 2.123382 GTAGGAGACGGGAGGGGG 60.123 72.222 0.00 0.00 0.00 5.40
2115 2227 1.405526 CGATCTCACGTCCAAACCCAT 60.406 52.381 0.00 0.00 0.00 4.00
2162 2274 2.958576 GGATCTAGCGAGCCTCGG 59.041 66.667 16.95 0.00 42.48 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.265165 AGACATGATGTGATATATGTTGATGC 57.735 34.615 1.23 0.00 34.18 3.91
204 208 0.107848 CGGCCGGTCCTTATTGAAGT 60.108 55.000 20.10 0.00 0.00 3.01
211 215 0.611618 TTGACTACGGCCGGTCCTTA 60.612 55.000 31.76 11.40 0.00 2.69
242 246 4.275196 GGGTGTCTGTTTCTCCAACTTTAC 59.725 45.833 0.00 0.00 36.21 2.01
326 330 1.463674 GGGCCAACCTTACATGACTG 58.536 55.000 4.39 0.00 35.85 3.51
327 331 0.035439 CGGGCCAACCTTACATGACT 60.035 55.000 4.39 0.00 36.97 3.41
343 347 3.323758 TTGGATGAAGCGACCCGGG 62.324 63.158 22.25 22.25 0.00 5.73
349 353 2.276201 CGGTATTGTTGGATGAAGCGA 58.724 47.619 0.00 0.00 0.00 4.93
483 487 4.025360 TGAAATTGCATGCTATGTTCCCT 58.975 39.130 20.33 0.00 0.00 4.20
514 518 5.690997 AATAGATCTTGCGTGATCGTAGA 57.309 39.130 0.00 0.00 45.35 2.59
536 540 6.042777 CCTCTCGTTGTTATGCATCTTCTAA 58.957 40.000 0.19 0.00 0.00 2.10
540 544 3.535561 CCCTCTCGTTGTTATGCATCTT 58.464 45.455 0.19 0.00 0.00 2.40
550 554 0.688087 GATCCTCCCCCTCTCGTTGT 60.688 60.000 0.00 0.00 0.00 3.32
581 585 5.880332 AGCCTCTCAGCGTCATATTTAAAAA 59.120 36.000 0.00 0.00 38.01 1.94
582 586 5.428253 AGCCTCTCAGCGTCATATTTAAAA 58.572 37.500 0.00 0.00 38.01 1.52
583 587 5.023533 AGCCTCTCAGCGTCATATTTAAA 57.976 39.130 0.00 0.00 38.01 1.52
584 588 4.672587 AGCCTCTCAGCGTCATATTTAA 57.327 40.909 0.00 0.00 38.01 1.52
585 589 4.099419 TCAAGCCTCTCAGCGTCATATTTA 59.901 41.667 0.00 0.00 38.01 1.40
586 590 3.118629 TCAAGCCTCTCAGCGTCATATTT 60.119 43.478 0.00 0.00 38.01 1.40
587 591 2.432146 TCAAGCCTCTCAGCGTCATATT 59.568 45.455 0.00 0.00 38.01 1.28
588 592 2.034878 TCAAGCCTCTCAGCGTCATAT 58.965 47.619 0.00 0.00 38.01 1.78
589 593 1.474330 TCAAGCCTCTCAGCGTCATA 58.526 50.000 0.00 0.00 38.01 2.15
590 594 0.610174 TTCAAGCCTCTCAGCGTCAT 59.390 50.000 0.00 0.00 38.01 3.06
591 595 0.392706 TTTCAAGCCTCTCAGCGTCA 59.607 50.000 0.00 0.00 38.01 4.35
592 596 1.195674 GTTTTCAAGCCTCTCAGCGTC 59.804 52.381 0.00 0.00 38.01 5.19
593 597 1.202698 AGTTTTCAAGCCTCTCAGCGT 60.203 47.619 0.00 0.00 38.01 5.07
594 598 1.462670 GAGTTTTCAAGCCTCTCAGCG 59.537 52.381 0.00 0.00 38.01 5.18
595 599 2.741517 GAGAGTTTTCAAGCCTCTCAGC 59.258 50.000 10.23 0.00 46.72 4.26
599 603 2.777094 GCTGAGAGTTTTCAAGCCTCT 58.223 47.619 0.00 0.00 38.25 3.69
600 604 1.462670 CGCTGAGAGTTTTCAAGCCTC 59.537 52.381 0.00 0.00 33.87 4.70
601 605 1.202698 ACGCTGAGAGTTTTCAAGCCT 60.203 47.619 0.00 0.00 33.87 4.58
602 606 1.230324 ACGCTGAGAGTTTTCAAGCC 58.770 50.000 0.00 0.00 33.87 4.35
603 607 2.603173 CCAACGCTGAGAGTTTTCAAGC 60.603 50.000 0.00 0.00 34.00 4.01
604 608 2.031682 CCCAACGCTGAGAGTTTTCAAG 60.032 50.000 0.00 0.00 0.00 3.02
605 609 1.946768 CCCAACGCTGAGAGTTTTCAA 59.053 47.619 0.00 0.00 0.00 2.69
606 610 1.140052 TCCCAACGCTGAGAGTTTTCA 59.860 47.619 0.00 0.00 0.00 2.69
607 611 1.878953 TCCCAACGCTGAGAGTTTTC 58.121 50.000 0.00 0.00 0.00 2.29
608 612 2.341846 TTCCCAACGCTGAGAGTTTT 57.658 45.000 0.00 0.00 0.00 2.43
609 613 2.341846 TTTCCCAACGCTGAGAGTTT 57.658 45.000 0.00 0.00 0.00 2.66
610 614 2.341846 TTTTCCCAACGCTGAGAGTT 57.658 45.000 0.00 0.00 0.00 3.01
611 615 2.222027 CTTTTTCCCAACGCTGAGAGT 58.778 47.619 0.00 0.00 0.00 3.24
612 616 2.222027 ACTTTTTCCCAACGCTGAGAG 58.778 47.619 0.00 0.00 0.00 3.20
613 617 2.158813 AGACTTTTTCCCAACGCTGAGA 60.159 45.455 0.00 0.00 0.00 3.27
614 618 2.031682 CAGACTTTTTCCCAACGCTGAG 60.032 50.000 0.00 0.00 0.00 3.35
615 619 1.946768 CAGACTTTTTCCCAACGCTGA 59.053 47.619 0.00 0.00 0.00 4.26
616 620 1.001378 CCAGACTTTTTCCCAACGCTG 60.001 52.381 0.00 0.00 0.00 5.18
617 621 1.133915 TCCAGACTTTTTCCCAACGCT 60.134 47.619 0.00 0.00 0.00 5.07
618 622 1.001706 GTCCAGACTTTTTCCCAACGC 60.002 52.381 0.00 0.00 0.00 4.84
619 623 1.607148 GGTCCAGACTTTTTCCCAACG 59.393 52.381 0.00 0.00 0.00 4.10
620 624 1.961394 GGGTCCAGACTTTTTCCCAAC 59.039 52.381 0.00 0.00 35.43 3.77
621 625 1.571457 TGGGTCCAGACTTTTTCCCAA 59.429 47.619 0.00 0.00 41.38 4.12
622 626 1.133606 GTGGGTCCAGACTTTTTCCCA 60.134 52.381 0.00 0.00 41.96 4.37
623 627 1.617322 GTGGGTCCAGACTTTTTCCC 58.383 55.000 0.00 0.00 35.85 3.97
624 628 1.145119 AGGTGGGTCCAGACTTTTTCC 59.855 52.381 0.00 0.00 39.02 3.13
625 629 2.230660 CAGGTGGGTCCAGACTTTTTC 58.769 52.381 0.00 0.00 39.02 2.29
626 630 1.569072 ACAGGTGGGTCCAGACTTTTT 59.431 47.619 0.00 0.00 39.02 1.94
627 631 1.143073 GACAGGTGGGTCCAGACTTTT 59.857 52.381 0.00 0.00 39.02 2.27
628 632 0.765510 GACAGGTGGGTCCAGACTTT 59.234 55.000 0.00 0.00 39.02 2.66
629 633 1.472662 CGACAGGTGGGTCCAGACTT 61.473 60.000 0.00 0.00 39.02 3.01
630 634 1.908793 CGACAGGTGGGTCCAGACT 60.909 63.158 0.00 0.00 39.02 3.24
631 635 2.657237 CGACAGGTGGGTCCAGAC 59.343 66.667 0.00 0.00 39.02 3.51
632 636 3.311110 GCGACAGGTGGGTCCAGA 61.311 66.667 0.00 0.00 39.02 3.86
633 637 3.302347 GAGCGACAGGTGGGTCCAG 62.302 68.421 2.71 0.00 39.02 3.86
634 638 2.435120 TAGAGCGACAGGTGGGTCCA 62.435 60.000 9.51 0.00 36.65 4.02
635 639 1.043673 ATAGAGCGACAGGTGGGTCC 61.044 60.000 9.51 0.00 36.65 4.46
636 640 1.609555 CTATAGAGCGACAGGTGGGTC 59.390 57.143 5.63 5.63 36.31 4.46
637 641 1.214673 TCTATAGAGCGACAGGTGGGT 59.785 52.381 0.00 0.00 0.00 4.51
638 642 1.982660 TCTATAGAGCGACAGGTGGG 58.017 55.000 0.00 0.00 0.00 4.61
639 643 3.707793 GTTTCTATAGAGCGACAGGTGG 58.292 50.000 2.02 0.00 0.00 4.61
640 644 3.364062 CGTTTCTATAGAGCGACAGGTG 58.636 50.000 18.19 0.00 0.00 4.00
641 645 2.223525 GCGTTTCTATAGAGCGACAGGT 60.224 50.000 23.85 0.00 0.00 4.00
642 646 2.033550 AGCGTTTCTATAGAGCGACAGG 59.966 50.000 23.85 7.65 0.00 4.00
643 647 3.341857 AGCGTTTCTATAGAGCGACAG 57.658 47.619 23.85 12.75 0.00 3.51
644 648 3.303857 GCTAGCGTTTCTATAGAGCGACA 60.304 47.826 23.85 13.58 0.00 4.35
645 649 3.227948 GCTAGCGTTTCTATAGAGCGAC 58.772 50.000 23.85 17.14 0.00 5.19
646 650 2.225963 GGCTAGCGTTTCTATAGAGCGA 59.774 50.000 23.85 11.98 0.00 4.93
647 651 2.586900 GGCTAGCGTTTCTATAGAGCG 58.413 52.381 18.52 18.52 0.00 5.03
648 652 2.296471 TGGGCTAGCGTTTCTATAGAGC 59.704 50.000 9.00 3.52 0.00 4.09
649 653 3.609644 CGTGGGCTAGCGTTTCTATAGAG 60.610 52.174 9.00 0.00 0.00 2.43
650 654 2.292569 CGTGGGCTAGCGTTTCTATAGA 59.707 50.000 9.00 0.00 0.00 1.98
651 655 2.607282 CCGTGGGCTAGCGTTTCTATAG 60.607 54.545 9.00 0.00 0.00 1.31
652 656 1.338973 CCGTGGGCTAGCGTTTCTATA 59.661 52.381 9.00 0.00 0.00 1.31
653 657 0.104304 CCGTGGGCTAGCGTTTCTAT 59.896 55.000 9.00 0.00 0.00 1.98
654 658 1.514087 CCGTGGGCTAGCGTTTCTA 59.486 57.895 9.00 0.00 0.00 2.10
655 659 2.264794 CCGTGGGCTAGCGTTTCT 59.735 61.111 9.00 0.00 0.00 2.52
656 660 3.497031 GCCGTGGGCTAGCGTTTC 61.497 66.667 9.00 0.00 46.69 2.78
671 675 4.373116 TCGTTCGCTGGTCTGGCC 62.373 66.667 0.00 0.00 37.90 5.36
673 677 0.108615 ATTCTCGTTCGCTGGTCTGG 60.109 55.000 0.00 0.00 0.00 3.86
678 682 0.867753 CCTCGATTCTCGTTCGCTGG 60.868 60.000 0.00 0.00 41.35 4.85
683 687 0.102663 GGGTCCCTCGATTCTCGTTC 59.897 60.000 0.00 0.00 41.35 3.95
686 690 2.034607 GAGGGTCCCTCGATTCTCG 58.965 63.158 22.53 0.00 41.08 4.04
738 746 1.607801 GGTTTCTCATTGGCTGGGGC 61.608 60.000 0.00 0.00 37.82 5.80
801 809 0.902531 GAGATTGGTTCTCGGGGTGA 59.097 55.000 0.00 0.00 41.51 4.02
852 860 2.224161 CGAGTGGAGGGAAGATGGATTC 60.224 54.545 0.00 0.00 0.00 2.52
934 980 1.388133 GCTTGGGGGATTTGGGAGT 59.612 57.895 0.00 0.00 0.00 3.85
960 1023 3.081409 GGGGAGGCTGCTTCGGTA 61.081 66.667 5.84 0.00 0.00 4.02
983 1046 3.344137 ATTGCTGCGGGGTAGGGTG 62.344 63.158 0.00 0.00 0.00 4.61
984 1047 3.015145 ATTGCTGCGGGGTAGGGT 61.015 61.111 0.00 0.00 0.00 4.34
1011 1074 2.048222 TTCCTCGCCGTCTGCTTG 60.048 61.111 0.00 0.00 38.05 4.01
1218 1281 1.139734 GAAGTCCTGCGCGATCTCA 59.860 57.895 12.10 0.00 0.00 3.27
1500 1564 1.487482 CAAGACAACGACAAGAGCGA 58.513 50.000 0.00 0.00 0.00 4.93
1507 1571 3.052455 ACATATGGCAAGACAACGACA 57.948 42.857 7.80 0.00 0.00 4.35
1603 1667 2.521771 GCAACACACGTCGCACAGA 61.522 57.895 0.00 0.00 0.00 3.41
1604 1668 2.035617 AAGCAACACACGTCGCACAG 62.036 55.000 0.00 0.00 0.00 3.66
1605 1669 1.640210 AAAGCAACACACGTCGCACA 61.640 50.000 0.00 0.00 0.00 4.57
1606 1670 0.923911 GAAAGCAACACACGTCGCAC 60.924 55.000 0.00 0.00 0.00 5.34
1607 1671 1.087202 AGAAAGCAACACACGTCGCA 61.087 50.000 0.00 0.00 0.00 5.10
1608 1672 0.027586 AAGAAAGCAACACACGTCGC 59.972 50.000 0.00 0.00 0.00 5.19
1610 1674 2.825086 ACAAGAAAGCAACACACGTC 57.175 45.000 0.00 0.00 0.00 4.34
1611 1675 2.747446 AGAACAAGAAAGCAACACACGT 59.253 40.909 0.00 0.00 0.00 4.49
1612 1676 3.405170 AGAACAAGAAAGCAACACACG 57.595 42.857 0.00 0.00 0.00 4.49
1613 1677 4.732784 TGAAGAACAAGAAAGCAACACAC 58.267 39.130 0.00 0.00 0.00 3.82
1615 1679 4.986622 ACTGAAGAACAAGAAAGCAACAC 58.013 39.130 0.00 0.00 0.00 3.32
1616 1680 5.643379 AACTGAAGAACAAGAAAGCAACA 57.357 34.783 0.00 0.00 0.00 3.33
1617 1681 5.228012 CGAAACTGAAGAACAAGAAAGCAAC 59.772 40.000 0.00 0.00 0.00 4.17
1618 1682 5.106317 ACGAAACTGAAGAACAAGAAAGCAA 60.106 36.000 0.00 0.00 0.00 3.91
1661 1743 1.629013 TACGCTTCATCTGCTTCACG 58.371 50.000 0.00 0.00 0.00 4.35
1672 1754 8.154203 TCCATGGATAGAAATTATTACGCTTCA 58.846 33.333 11.44 0.00 0.00 3.02
1688 1783 4.467795 ACGGGATGTCTAATCCATGGATAG 59.532 45.833 27.54 21.80 39.93 2.08
1689 1784 4.425772 ACGGGATGTCTAATCCATGGATA 58.574 43.478 27.54 12.13 39.93 2.59
1703 1798 2.806945 ACAATCCAATGACGGGATGT 57.193 45.000 0.00 0.00 44.30 3.06
1757 1856 3.568538 CATCAGAAAACCCAAGCGAAAG 58.431 45.455 0.00 0.00 0.00 2.62
1761 1860 1.068333 CACCATCAGAAAACCCAAGCG 60.068 52.381 0.00 0.00 0.00 4.68
1762 1861 1.337167 GCACCATCAGAAAACCCAAGC 60.337 52.381 0.00 0.00 0.00 4.01
1766 1865 0.244721 GCAGCACCATCAGAAAACCC 59.755 55.000 0.00 0.00 0.00 4.11
1767 1866 1.068055 CAGCAGCACCATCAGAAAACC 60.068 52.381 0.00 0.00 0.00 3.27
1780 1879 0.906775 TCATCTCCATCACAGCAGCA 59.093 50.000 0.00 0.00 0.00 4.41
1849 1949 9.271828 GAAATAGGAAACAACACAATTCCAAAT 57.728 29.630 6.55 0.00 44.08 2.32
1852 1952 7.595819 AGAAATAGGAAACAACACAATTCCA 57.404 32.000 6.55 0.00 44.08 3.53
1853 1953 7.598869 GGAAGAAATAGGAAACAACACAATTCC 59.401 37.037 0.00 0.00 42.38 3.01
1855 1955 7.441836 GGGAAGAAATAGGAAACAACACAATT 58.558 34.615 0.00 0.00 0.00 2.32
1856 1956 6.014584 GGGGAAGAAATAGGAAACAACACAAT 60.015 38.462 0.00 0.00 0.00 2.71
1857 1957 5.303333 GGGGAAGAAATAGGAAACAACACAA 59.697 40.000 0.00 0.00 0.00 3.33
1859 1959 4.830600 TGGGGAAGAAATAGGAAACAACAC 59.169 41.667 0.00 0.00 0.00 3.32
1860 1960 5.068215 TGGGGAAGAAATAGGAAACAACA 57.932 39.130 0.00 0.00 0.00 3.33
1861 1961 5.321927 TCTGGGGAAGAAATAGGAAACAAC 58.678 41.667 0.00 0.00 29.54 3.32
1862 1962 5.592587 TCTGGGGAAGAAATAGGAAACAA 57.407 39.130 0.00 0.00 29.54 2.83
1864 1964 7.039011 ACAAAATCTGGGGAAGAAATAGGAAAC 60.039 37.037 0.00 0.00 38.79 2.78
1867 1967 6.152638 ACAAAATCTGGGGAAGAAATAGGA 57.847 37.500 0.00 0.00 38.79 2.94
1868 1968 6.857437 AACAAAATCTGGGGAAGAAATAGG 57.143 37.500 0.00 0.00 38.79 2.57
1869 1969 7.603784 CCAAAACAAAATCTGGGGAAGAAATAG 59.396 37.037 0.00 0.00 38.79 1.73
1875 1985 4.953940 TCCAAAACAAAATCTGGGGAAG 57.046 40.909 0.00 0.00 0.00 3.46
1921 2031 0.102120 CCAACAGAAGCGGCAAACAA 59.898 50.000 1.45 0.00 0.00 2.83
1923 2033 1.007387 CCCAACAGAAGCGGCAAAC 60.007 57.895 1.45 0.00 0.00 2.93
1941 2052 3.262686 GATTCCTTCCGCCGACGC 61.263 66.667 0.00 0.00 38.22 5.19
1942 2053 2.585247 GGATTCCTTCCGCCGACG 60.585 66.667 0.00 0.00 33.93 5.12
1989 2100 3.253838 AGCGGGCCAGGGTTGTTA 61.254 61.111 4.39 0.00 0.00 2.41
1990 2101 4.974721 CAGCGGGCCAGGGTTGTT 62.975 66.667 4.39 0.00 0.00 2.83
1995 2106 4.431131 AATGACAGCGGGCCAGGG 62.431 66.667 4.39 0.00 0.00 4.45
1996 2107 3.136123 CAATGACAGCGGGCCAGG 61.136 66.667 4.39 0.00 0.00 4.45
2019 2130 3.300765 ACACCCCCACGACGTCTC 61.301 66.667 14.70 0.00 0.00 3.36
2020 2131 3.612681 CACACCCCCACGACGTCT 61.613 66.667 14.70 0.00 0.00 4.18
2036 2147 2.354704 CCTACTTTGCTGGATTCGGTCA 60.355 50.000 0.00 0.00 0.00 4.02
2102 2213 0.034477 GGATGGATGGGTTTGGACGT 60.034 55.000 0.00 0.00 0.00 4.34
2115 2227 4.041762 GGCGGTGGGTTGGATGGA 62.042 66.667 0.00 0.00 0.00 3.41
2162 2274 0.665972 GATCTTCATCTCCGCTCCGC 60.666 60.000 0.00 0.00 0.00 5.54
2385 2497 1.668151 GTCACCTTCGTGCTGGACC 60.668 63.158 0.00 0.00 40.04 4.46


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

AutoCloner maintained by Alex Coulton.