Multiple sequence alignment - TraesCS2A01G026800

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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 TraesCS2A01G026800 chr2A 100.000 3343 0 0 1 3343 12317520 12314178 0.000000e+00 6174
1 TraesCS2A01G026800 chr2D 94.090 1726 68 12 1642 3343 11824238 11822523 0.000000e+00 2591
2 TraesCS2A01G026800 chr2D 92.842 922 51 5 711 1626 11825135 11824223 0.000000e+00 1323
3 TraesCS2A01G026800 chr2D 90.492 610 41 11 2 601 451011865 451012467 0.000000e+00 789
4 TraesCS2A01G026800 chr2D 78.019 323 51 17 2969 3286 11822129 11821822 5.700000e-43 185
5 TraesCS2A01G026800 chr2B 89.382 923 54 7 711 1633 18198146 18197268 0.000000e+00 1122
6 TraesCS2A01G026800 chr2B 91.240 742 52 5 1661 2401 18197270 18196541 0.000000e+00 998
7 TraesCS2A01G026800 chr2B 90.188 744 62 8 1713 2453 18194472 18193737 0.000000e+00 959
8 TraesCS2A01G026800 chr2B 88.076 369 30 9 2421 2781 18196552 18196190 3.080000e-115 425
9 TraesCS2A01G026800 chr2B 79.767 514 79 17 1010 1509 17838128 17837626 1.910000e-92 350
10 TraesCS2A01G026800 chr6D 91.514 601 42 5 2 599 23078967 23079561 0.000000e+00 819
11 TraesCS2A01G026800 chr5D 91.060 604 46 6 2 602 546898673 546898075 0.000000e+00 809
12 TraesCS2A01G026800 chr5D 90.312 609 47 7 2 604 428663657 428663055 0.000000e+00 787
13 TraesCS2A01G026800 chr5D 90.547 603 46 7 3 599 458628276 458628873 0.000000e+00 787
14 TraesCS2A01G026800 chr5D 89.951 607 51 8 2 605 225854793 225854194 0.000000e+00 774
15 TraesCS2A01G026800 chr5D 89.967 608 47 7 2 602 531902750 531902150 0.000000e+00 773
16 TraesCS2A01G026800 chr1D 90.312 609 43 7 2 601 364717048 364716447 0.000000e+00 784
17 TraesCS2A01G026800 chr3D 90.115 607 46 7 2 599 561086885 561087486 0.000000e+00 776
18 TraesCS2A01G026800 chr3D 78.906 512 86 16 1006 1509 564919129 564919626 8.940000e-86 327
19 TraesCS2A01G026800 chr1A 79.297 512 80 18 1011 1509 12355215 12355713 5.340000e-88 335
20 TraesCS2A01G026800 chr3B 77.821 514 88 15 1006 1509 752439358 752439855 9.070000e-76 294
21 TraesCS2A01G026800 chr7A 93.860 114 7 0 599 712 164426621 164426508 4.430000e-39 172
22 TraesCS2A01G026800 chr7D 92.982 114 8 0 599 712 477408937 477409050 2.060000e-37 167
23 TraesCS2A01G026800 chr4B 92.174 115 9 0 599 713 82415103 82415217 2.670000e-36 163
24 TraesCS2A01G026800 chr5B 89.231 130 12 2 599 726 699388810 699388681 9.600000e-36 161
25 TraesCS2A01G026800 chr4A 91.964 112 9 0 599 710 742140159 742140048 1.240000e-34 158
26 TraesCS2A01G026800 chr6B 90.678 118 10 1 599 715 140848522 140848639 4.470000e-34 156
27 TraesCS2A01G026800 chr7B 89.565 115 9 2 601 713 747329078 747329191 3.480000e-30 143


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 TraesCS2A01G026800 chr2A 12314178 12317520 3342 True 6174.000000 6174 100.0000 1 3343 1 chr2A.!!$R1 3342
1 TraesCS2A01G026800 chr2D 11821822 11825135 3313 True 1366.333333 2591 88.3170 711 3343 3 chr2D.!!$R1 2632
2 TraesCS2A01G026800 chr2D 451011865 451012467 602 False 789.000000 789 90.4920 2 601 1 chr2D.!!$F1 599
3 TraesCS2A01G026800 chr2B 18193737 18198146 4409 True 876.000000 1122 89.7215 711 2781 4 chr2B.!!$R2 2070
4 TraesCS2A01G026800 chr2B 17837626 17838128 502 True 350.000000 350 79.7670 1010 1509 1 chr2B.!!$R1 499
5 TraesCS2A01G026800 chr6D 23078967 23079561 594 False 819.000000 819 91.5140 2 599 1 chr6D.!!$F1 597
6 TraesCS2A01G026800 chr5D 546898075 546898673 598 True 809.000000 809 91.0600 2 602 1 chr5D.!!$R4 600
7 TraesCS2A01G026800 chr5D 428663055 428663657 602 True 787.000000 787 90.3120 2 604 1 chr5D.!!$R2 602
8 TraesCS2A01G026800 chr5D 458628276 458628873 597 False 787.000000 787 90.5470 3 599 1 chr5D.!!$F1 596
9 TraesCS2A01G026800 chr5D 225854194 225854793 599 True 774.000000 774 89.9510 2 605 1 chr5D.!!$R1 603
10 TraesCS2A01G026800 chr5D 531902150 531902750 600 True 773.000000 773 89.9670 2 602 1 chr5D.!!$R3 600
11 TraesCS2A01G026800 chr1D 364716447 364717048 601 True 784.000000 784 90.3120 2 601 1 chr1D.!!$R1 599
12 TraesCS2A01G026800 chr3D 561086885 561087486 601 False 776.000000 776 90.1150 2 599 1 chr3D.!!$F1 597

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
607 624 0.107459 GGAGCTGGCCTAAGGTTGAG 60.107 60.0 3.32 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 2429 0.584396 TGTCTAACAAAAGCCACGCG 59.416 50.0 3.53 3.53 0.0 6.01 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
46 47 3.831651 GCTAGAGGAGGAGCCACTA 57.168 57.895 0.00 0.00 38.61 2.74
144 146 1.461091 AACCGGACGAGCTCAAGACA 61.461 55.000 15.40 0.00 0.00 3.41
149 151 2.085320 GGACGAGCTCAAGACAGACTA 58.915 52.381 15.40 0.00 0.00 2.59
187 189 4.776647 GGCGGGTGCGCAAATCAC 62.777 66.667 14.00 0.00 44.10 3.06
189 191 4.459331 CGGGTGCGCAAATCACGG 62.459 66.667 14.00 0.92 35.39 4.94
190 192 3.361977 GGGTGCGCAAATCACGGT 61.362 61.111 14.00 0.00 35.39 4.83
192 194 2.126888 GTGCGCAAATCACGGTGG 60.127 61.111 14.00 0.00 0.00 4.61
444 456 1.227853 GTGCTGTCCGTTTCACCCT 60.228 57.895 0.00 0.00 0.00 4.34
454 466 2.359531 CCGTTTCACCCTAAAAGCAACA 59.640 45.455 0.00 0.00 0.00 3.33
489 501 1.202604 GGATGGGTCGAAAGCGGATAA 60.203 52.381 0.00 0.00 38.28 1.75
516 529 1.358759 CAAAAGTCCGTTTGCGCCT 59.641 52.632 4.18 0.00 36.67 5.52
551 565 2.102925 TCTGGTTCGTCCGTTTTACCTT 59.897 45.455 0.00 0.00 39.52 3.50
582 596 3.849951 CGGACAGGATGGGGTCGG 61.850 72.222 0.00 0.00 43.62 4.79
605 622 0.257039 ATGGAGCTGGCCTAAGGTTG 59.743 55.000 3.32 0.00 0.00 3.77
606 623 0.840288 TGGAGCTGGCCTAAGGTTGA 60.840 55.000 3.32 0.00 0.00 3.18
607 624 0.107459 GGAGCTGGCCTAAGGTTGAG 60.107 60.000 3.32 0.00 0.00 3.02
608 625 0.905357 GAGCTGGCCTAAGGTTGAGA 59.095 55.000 3.32 0.00 0.00 3.27
609 626 1.279271 GAGCTGGCCTAAGGTTGAGAA 59.721 52.381 3.32 0.00 0.00 2.87
610 627 1.705186 AGCTGGCCTAAGGTTGAGAAA 59.295 47.619 3.32 0.00 0.00 2.52
611 628 2.087646 GCTGGCCTAAGGTTGAGAAAG 58.912 52.381 3.32 0.00 0.00 2.62
612 629 2.290323 GCTGGCCTAAGGTTGAGAAAGA 60.290 50.000 3.32 0.00 0.00 2.52
613 630 3.810743 GCTGGCCTAAGGTTGAGAAAGAA 60.811 47.826 3.32 0.00 0.00 2.52
614 631 4.398319 CTGGCCTAAGGTTGAGAAAGAAA 58.602 43.478 3.32 0.00 0.00 2.52
615 632 4.798882 TGGCCTAAGGTTGAGAAAGAAAA 58.201 39.130 3.32 0.00 0.00 2.29
616 633 4.827284 TGGCCTAAGGTTGAGAAAGAAAAG 59.173 41.667 3.32 0.00 0.00 2.27
617 634 5.070685 GGCCTAAGGTTGAGAAAGAAAAGA 58.929 41.667 0.00 0.00 0.00 2.52
618 635 5.535030 GGCCTAAGGTTGAGAAAGAAAAGAA 59.465 40.000 0.00 0.00 0.00 2.52
619 636 6.294231 GGCCTAAGGTTGAGAAAGAAAAGAAG 60.294 42.308 0.00 0.00 0.00 2.85
620 637 6.486993 GCCTAAGGTTGAGAAAGAAAAGAAGA 59.513 38.462 0.00 0.00 0.00 2.87
621 638 7.175816 GCCTAAGGTTGAGAAAGAAAAGAAGAT 59.824 37.037 0.00 0.00 0.00 2.40
622 639 9.726438 CCTAAGGTTGAGAAAGAAAAGAAGATA 57.274 33.333 0.00 0.00 0.00 1.98
624 641 8.628630 AAGGTTGAGAAAGAAAAGAAGATAGG 57.371 34.615 0.00 0.00 0.00 2.57
625 642 6.657117 AGGTTGAGAAAGAAAAGAAGATAGGC 59.343 38.462 0.00 0.00 0.00 3.93
626 643 6.657117 GGTTGAGAAAGAAAAGAAGATAGGCT 59.343 38.462 0.00 0.00 0.00 4.58
627 644 7.175816 GGTTGAGAAAGAAAAGAAGATAGGCTT 59.824 37.037 0.00 0.00 40.25 4.35
628 645 7.678947 TGAGAAAGAAAAGAAGATAGGCTTG 57.321 36.000 0.00 0.00 36.83 4.01
629 646 6.656693 TGAGAAAGAAAAGAAGATAGGCTTGG 59.343 38.462 0.00 0.00 36.83 3.61
630 647 6.547402 AGAAAGAAAAGAAGATAGGCTTGGT 58.453 36.000 0.00 0.00 36.83 3.67
631 648 6.432472 AGAAAGAAAAGAAGATAGGCTTGGTG 59.568 38.462 0.00 0.00 36.83 4.17
632 649 5.248380 AGAAAAGAAGATAGGCTTGGTGT 57.752 39.130 0.00 0.00 36.83 4.16
633 650 6.374417 AGAAAAGAAGATAGGCTTGGTGTA 57.626 37.500 0.00 0.00 36.83 2.90
634 651 6.963322 AGAAAAGAAGATAGGCTTGGTGTAT 58.037 36.000 0.00 0.00 36.83 2.29
635 652 7.051000 AGAAAAGAAGATAGGCTTGGTGTATC 58.949 38.462 0.00 0.00 36.83 2.24
636 653 4.965200 AGAAGATAGGCTTGGTGTATCC 57.035 45.455 0.00 0.00 36.83 2.59
637 654 4.561752 AGAAGATAGGCTTGGTGTATCCT 58.438 43.478 0.00 0.00 36.83 3.24
638 655 4.591072 AGAAGATAGGCTTGGTGTATCCTC 59.409 45.833 0.00 0.00 36.83 3.71
639 656 3.928754 AGATAGGCTTGGTGTATCCTCA 58.071 45.455 0.00 0.00 37.07 3.86
640 657 3.900601 AGATAGGCTTGGTGTATCCTCAG 59.099 47.826 0.00 0.00 37.07 3.35
641 658 0.543749 AGGCTTGGTGTATCCTCAGC 59.456 55.000 0.00 0.00 40.30 4.26
642 659 0.811616 GGCTTGGTGTATCCTCAGCG 60.812 60.000 0.00 0.00 41.24 5.18
643 660 1.432270 GCTTGGTGTATCCTCAGCGC 61.432 60.000 0.00 0.00 38.47 5.92
644 661 0.811616 CTTGGTGTATCCTCAGCGCC 60.812 60.000 2.29 0.00 38.47 6.53
645 662 1.549243 TTGGTGTATCCTCAGCGCCA 61.549 55.000 2.29 0.00 40.53 5.69
646 663 1.521681 GGTGTATCCTCAGCGCCAC 60.522 63.158 2.29 1.60 33.35 5.01
647 664 1.878522 GTGTATCCTCAGCGCCACG 60.879 63.158 2.29 0.00 0.00 4.94
648 665 2.348104 TGTATCCTCAGCGCCACGT 61.348 57.895 2.29 0.00 0.00 4.49
649 666 1.878522 GTATCCTCAGCGCCACGTG 60.879 63.158 9.08 9.08 0.00 4.49
650 667 2.348104 TATCCTCAGCGCCACGTGT 61.348 57.895 15.65 0.00 0.00 4.49
651 668 1.033202 TATCCTCAGCGCCACGTGTA 61.033 55.000 15.65 0.00 0.00 2.90
652 669 2.284798 ATCCTCAGCGCCACGTGTAG 62.285 60.000 15.65 8.95 0.00 2.74
653 670 3.181967 CTCAGCGCCACGTGTAGC 61.182 66.667 20.41 20.41 0.00 3.58
654 671 3.914605 CTCAGCGCCACGTGTAGCA 62.915 63.158 26.68 11.92 0.00 3.49
655 672 3.777925 CAGCGCCACGTGTAGCAC 61.778 66.667 26.68 14.09 0.00 4.40
664 681 4.187056 GTGTAGCACGGAGAAGGC 57.813 61.111 0.00 0.00 0.00 4.35
665 682 1.805945 GTGTAGCACGGAGAAGGCG 60.806 63.158 0.00 0.00 0.00 5.52
666 683 2.202756 GTAGCACGGAGAAGGCGG 60.203 66.667 0.00 0.00 0.00 6.13
667 684 4.143333 TAGCACGGAGAAGGCGGC 62.143 66.667 0.00 0.00 0.00 6.53
685 702 2.968697 GGACGCGGACGGTGTTTT 60.969 61.111 12.47 0.00 46.04 2.43
686 703 2.547798 GACGCGGACGGTGTTTTC 59.452 61.111 12.47 0.00 46.04 2.29
687 704 2.202905 ACGCGGACGGTGTTTTCA 60.203 55.556 12.47 0.00 46.04 2.69
688 705 2.154427 GACGCGGACGGTGTTTTCAG 62.154 60.000 12.47 0.00 46.04 3.02
689 706 2.251371 GCGGACGGTGTTTTCAGC 59.749 61.111 0.00 0.00 43.90 4.26
690 707 2.943653 CGGACGGTGTTTTCAGCC 59.056 61.111 0.00 0.00 44.42 4.85
691 708 2.943653 GGACGGTGTTTTCAGCCG 59.056 61.111 0.00 0.00 44.42 5.52
692 709 2.613506 GGACGGTGTTTTCAGCCGG 61.614 63.158 0.00 0.00 44.42 6.13
693 710 1.890510 GACGGTGTTTTCAGCCGGT 60.891 57.895 1.90 0.00 44.42 5.28
694 711 1.441732 GACGGTGTTTTCAGCCGGTT 61.442 55.000 1.90 0.00 44.42 4.44
695 712 1.008995 CGGTGTTTTCAGCCGGTTG 60.009 57.895 12.81 12.81 44.42 3.77
696 713 1.440938 CGGTGTTTTCAGCCGGTTGA 61.441 55.000 17.98 17.98 44.42 3.18
697 714 0.741915 GGTGTTTTCAGCCGGTTGAA 59.258 50.000 27.56 27.56 41.83 2.69
698 715 1.269051 GGTGTTTTCAGCCGGTTGAAG 60.269 52.381 29.03 0.53 41.83 3.02
699 716 1.028905 TGTTTTCAGCCGGTTGAAGG 58.971 50.000 29.03 0.15 38.25 3.46
700 717 1.029681 GTTTTCAGCCGGTTGAAGGT 58.970 50.000 29.03 0.00 38.25 3.50
701 718 2.223745 GTTTTCAGCCGGTTGAAGGTA 58.776 47.619 29.03 15.54 38.25 3.08
702 719 2.619646 GTTTTCAGCCGGTTGAAGGTAA 59.380 45.455 29.03 19.98 38.25 2.85
703 720 2.178912 TTCAGCCGGTTGAAGGTAAG 57.821 50.000 27.56 0.00 32.39 2.34
704 721 1.053424 TCAGCCGGTTGAAGGTAAGT 58.947 50.000 19.64 0.00 0.00 2.24
705 722 1.418637 TCAGCCGGTTGAAGGTAAGTT 59.581 47.619 19.64 0.00 0.00 2.66
706 723 2.158726 TCAGCCGGTTGAAGGTAAGTTT 60.159 45.455 19.64 0.00 0.00 2.66
707 724 2.621526 CAGCCGGTTGAAGGTAAGTTTT 59.378 45.455 13.89 0.00 0.00 2.43
708 725 3.067601 CAGCCGGTTGAAGGTAAGTTTTT 59.932 43.478 13.89 0.00 0.00 1.94
709 726 3.317149 AGCCGGTTGAAGGTAAGTTTTTC 59.683 43.478 1.90 0.00 0.00 2.29
856 873 1.267121 CTTTCTTCTCCTCCCCGTCA 58.733 55.000 0.00 0.00 0.00 4.35
872 889 0.725784 GTCACTGTCGCGGCAAAATG 60.726 55.000 16.92 13.84 0.00 2.32
907 924 3.596066 AAGCGCGCTCACCAGTCAT 62.596 57.895 36.57 12.91 0.00 3.06
915 932 1.135139 GCTCACCAGTCATCGCTAAGA 59.865 52.381 0.00 0.00 0.00 2.10
916 933 2.223923 GCTCACCAGTCATCGCTAAGAT 60.224 50.000 0.00 0.00 41.01 2.40
1008 1030 2.282110 CCACCAACCATGTCGGCA 60.282 61.111 0.00 0.00 39.03 5.69
1063 1085 4.341502 CCACCTTTGCCGGCGTTG 62.342 66.667 23.90 13.60 0.00 4.10
1116 1138 3.264897 CGCATCTTCCGCTTCCCG 61.265 66.667 0.00 0.00 0.00 5.14
1297 1322 2.043450 CTCCTGAGGTCGGCTCCT 60.043 66.667 0.00 0.00 40.97 3.69
1377 1402 4.849329 CGGCTCTACACCCGCGAC 62.849 72.222 8.23 0.00 37.85 5.19
1410 1435 3.064820 CCGTCAAGTACAACTGCAACTTT 59.935 43.478 0.00 0.00 31.21 2.66
1420 1445 0.317269 CTGCAACTTTGACCTGCACG 60.317 55.000 0.00 0.00 41.01 5.34
1458 1483 2.117156 GCGCGACACCCTCTACCTA 61.117 63.158 12.10 0.00 0.00 3.08
1547 1572 5.186198 CCGAGACTCCACTCCATTAATTTT 58.814 41.667 0.00 0.00 33.83 1.82
1548 1573 6.070424 ACCGAGACTCCACTCCATTAATTTTA 60.070 38.462 0.00 0.00 33.83 1.52
1549 1574 6.480320 CCGAGACTCCACTCCATTAATTTTAG 59.520 42.308 0.00 0.00 33.83 1.85
1550 1575 6.018669 CGAGACTCCACTCCATTAATTTTAGC 60.019 42.308 0.00 0.00 33.83 3.09
1651 1676 4.545823 TTTTTGAAGCTTGTCCACGTAG 57.454 40.909 2.10 0.00 0.00 3.51
1653 1678 4.325028 TTTGAAGCTTGTCCACGTAGTA 57.675 40.909 2.10 0.00 41.61 1.82
1654 1679 3.570926 TGAAGCTTGTCCACGTAGTAG 57.429 47.619 2.10 0.00 41.61 2.57
1655 1680 2.889045 TGAAGCTTGTCCACGTAGTAGT 59.111 45.455 2.10 0.00 41.61 2.73
1656 1681 3.057736 TGAAGCTTGTCCACGTAGTAGTC 60.058 47.826 2.10 0.00 41.61 2.59
1657 1682 2.511659 AGCTTGTCCACGTAGTAGTCA 58.488 47.619 0.00 0.00 41.61 3.41
1658 1683 2.488545 AGCTTGTCCACGTAGTAGTCAG 59.511 50.000 0.00 0.00 41.61 3.51
1659 1684 2.864968 CTTGTCCACGTAGTAGTCAGC 58.135 52.381 0.00 0.00 41.61 4.26
1897 1922 2.032681 GGCTTCCTCACGGTGCTT 59.967 61.111 2.51 0.00 33.63 3.91
1969 1994 4.612412 GTCACGCCAACACCGGGA 62.612 66.667 6.32 0.00 35.48 5.14
1999 2024 1.667724 GTCAATGTGGGCGATCTCTTG 59.332 52.381 0.00 0.00 0.00 3.02
2011 2036 3.858877 GCGATCTCTTGCAGGTACCTATG 60.859 52.174 15.80 5.31 0.00 2.23
2049 2075 7.821652 TGGTCACGCTAAAATCATTAAAATCA 58.178 30.769 0.00 0.00 0.00 2.57
2091 2117 4.383552 GGCATACATGTGTCTTTCCTCTCT 60.384 45.833 9.11 0.00 0.00 3.10
2147 2173 0.174389 AGCACAGAGTCATCGCGAAT 59.826 50.000 15.24 0.00 0.00 3.34
2189 2215 0.313672 TCGCATGTTTCCCAAGCAAC 59.686 50.000 0.00 0.00 37.63 4.17
2236 2262 2.249413 ATCAAGGAGCTGCTGTCGGG 62.249 60.000 9.14 0.00 0.00 5.14
2300 2326 1.846782 GTCGCGCACTATTACTCTGTG 59.153 52.381 8.75 0.00 35.08 3.66
2347 2373 9.940166 CATCAATGATTTTCGTCTATGAAATCA 57.060 29.630 11.65 11.65 37.66 2.57
2365 2391 8.977267 TGAAATCATTGGAAAAATCCTTTGTT 57.023 26.923 0.00 0.00 0.00 2.83
2375 2401 8.364142 TGGAAAAATCCTTTGTTATGATTTCGT 58.636 29.630 0.00 0.00 37.64 3.85
2403 2429 3.451141 TGGACAACAAATTCCAAGTGC 57.549 42.857 0.00 0.00 39.04 4.40
2406 2432 0.777631 CAACAAATTCCAAGTGCGCG 59.222 50.000 0.00 0.00 0.00 6.86
2409 2435 1.003262 CAAATTCCAAGTGCGCGTGG 61.003 55.000 24.23 24.23 44.11 4.94
2435 2461 7.093945 GCTTTTGTTAGACATATTCCAAGGGAA 60.094 37.037 0.00 0.00 46.39 3.97
2480 2506 6.052360 TCGCTACCATGTGCTAAATCATTTA 58.948 36.000 0.00 0.00 0.00 1.40
2519 2545 2.335316 TAACCTGAACGTGCACCTTT 57.665 45.000 12.15 4.47 0.00 3.11
2677 2707 2.030412 ATCACACTTGCGCCGTGA 59.970 55.556 27.03 22.27 43.35 4.35
2738 2771 3.231160 CGGTAATTCCAACAAAACTCGC 58.769 45.455 0.00 0.00 35.57 5.03
2793 2826 1.887320 CAGTGCAGCGCAGTTTATTC 58.113 50.000 11.47 0.00 40.54 1.75
2858 2891 0.306840 GCATGTCCATCGCACATCAG 59.693 55.000 0.00 0.00 31.83 2.90
2958 2991 2.284190 GGACTAGCTCACTTTCATGGC 58.716 52.381 0.00 0.00 0.00 4.40
3033 3066 2.155065 AGGAACTGGTTCAGGGTGG 58.845 57.895 14.25 0.00 41.20 4.61
3091 3124 4.528596 GGAGACCCTAGCATATACACATGT 59.471 45.833 0.00 0.00 0.00 3.21
3098 3131 8.260818 ACCCTAGCATATACACATGTTATGATC 58.739 37.037 16.70 3.85 0.00 2.92
3214 3247 0.599204 AGAGTAAACGTGTGCACCGG 60.599 55.000 24.76 15.43 0.00 5.28
3269 3302 4.204799 AGAAGTCACCCTTGTTAACCAAC 58.795 43.478 2.48 0.00 32.03 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.993264 GCAAGGCCACATGCAGGT 60.993 61.111 19.61 0.00 43.89 4.00
126 128 1.867919 CTGTCTTGAGCTCGTCCGGT 61.868 60.000 9.64 0.00 0.00 5.28
131 133 3.060736 TCTAGTCTGTCTTGAGCTCGT 57.939 47.619 9.64 0.00 0.00 4.18
144 146 1.694696 GATTTGGGGCGGATCTAGTCT 59.305 52.381 0.00 0.00 0.00 3.24
149 151 2.510906 CGGATTTGGGGCGGATCT 59.489 61.111 0.00 0.00 0.00 2.75
187 189 4.317444 TACCCAACCACGCCACCG 62.317 66.667 0.00 0.00 41.14 4.94
189 191 3.053896 GCTACCCAACCACGCCAC 61.054 66.667 0.00 0.00 0.00 5.01
190 192 3.246112 AGCTACCCAACCACGCCA 61.246 61.111 0.00 0.00 0.00 5.69
192 194 2.813908 CGAGCTACCCAACCACGC 60.814 66.667 0.00 0.00 0.00 5.34
218 221 3.021263 GCCCAGCCCCTTTCCCTA 61.021 66.667 0.00 0.00 0.00 3.53
242 245 2.659897 GCTATGCAGCTCGGACGG 60.660 66.667 0.00 0.00 44.93 4.79
278 287 3.764466 CACTCTTCCCTCGCCGCT 61.764 66.667 0.00 0.00 0.00 5.52
444 456 4.675671 CGACCCAAGTTTGTGTTGCTTTTA 60.676 41.667 0.00 0.00 0.00 1.52
454 466 0.251165 CATCCCCGACCCAAGTTTGT 60.251 55.000 0.00 0.00 0.00 2.83
465 477 3.026431 GCTTTCGACCCATCCCCGA 62.026 63.158 0.00 0.00 0.00 5.14
582 596 3.106986 TTAGGCCAGCTCCATCGCC 62.107 63.158 5.01 0.00 41.96 5.54
592 609 3.703001 TCTTTCTCAACCTTAGGCCAG 57.297 47.619 5.01 0.00 0.00 4.85
605 622 6.657117 ACCAAGCCTATCTTCTTTTCTTTCTC 59.343 38.462 0.00 0.00 31.27 2.87
606 623 6.432472 CACCAAGCCTATCTTCTTTTCTTTCT 59.568 38.462 0.00 0.00 31.27 2.52
607 624 6.207614 ACACCAAGCCTATCTTCTTTTCTTTC 59.792 38.462 0.00 0.00 31.27 2.62
608 625 6.071320 ACACCAAGCCTATCTTCTTTTCTTT 58.929 36.000 0.00 0.00 31.27 2.52
609 626 5.635120 ACACCAAGCCTATCTTCTTTTCTT 58.365 37.500 0.00 0.00 31.27 2.52
610 627 5.248380 ACACCAAGCCTATCTTCTTTTCT 57.752 39.130 0.00 0.00 31.27 2.52
611 628 6.261158 GGATACACCAAGCCTATCTTCTTTTC 59.739 42.308 0.00 0.00 38.79 2.29
612 629 6.069381 AGGATACACCAAGCCTATCTTCTTTT 60.069 38.462 0.00 0.00 42.04 2.27
613 630 5.430089 AGGATACACCAAGCCTATCTTCTTT 59.570 40.000 0.00 0.00 42.04 2.52
614 631 4.971924 AGGATACACCAAGCCTATCTTCTT 59.028 41.667 0.00 0.00 42.04 2.52
615 632 4.561752 AGGATACACCAAGCCTATCTTCT 58.438 43.478 0.00 0.00 42.04 2.85
616 633 4.345257 TGAGGATACACCAAGCCTATCTTC 59.655 45.833 0.00 0.00 42.04 2.87
617 634 4.298626 TGAGGATACACCAAGCCTATCTT 58.701 43.478 0.00 0.00 42.04 2.40
618 635 3.900601 CTGAGGATACACCAAGCCTATCT 59.099 47.826 0.00 0.00 42.04 1.98
619 636 3.556004 GCTGAGGATACACCAAGCCTATC 60.556 52.174 0.00 0.00 41.64 2.08
620 637 2.370189 GCTGAGGATACACCAAGCCTAT 59.630 50.000 0.00 0.00 41.64 2.57
621 638 1.762957 GCTGAGGATACACCAAGCCTA 59.237 52.381 0.00 0.00 41.64 3.93
622 639 0.543749 GCTGAGGATACACCAAGCCT 59.456 55.000 0.00 0.00 41.64 4.58
623 640 0.811616 CGCTGAGGATACACCAAGCC 60.812 60.000 0.00 0.00 43.32 4.35
624 641 1.432270 GCGCTGAGGATACACCAAGC 61.432 60.000 0.00 0.00 43.02 4.01
625 642 0.811616 GGCGCTGAGGATACACCAAG 60.812 60.000 7.64 0.00 42.04 3.61
626 643 1.220749 GGCGCTGAGGATACACCAA 59.779 57.895 7.64 0.00 42.04 3.67
627 644 1.987306 TGGCGCTGAGGATACACCA 60.987 57.895 7.64 0.00 42.04 4.17
628 645 1.521681 GTGGCGCTGAGGATACACC 60.522 63.158 7.64 0.00 41.41 4.16
629 646 1.878522 CGTGGCGCTGAGGATACAC 60.879 63.158 7.64 2.93 41.41 2.90
630 647 2.348104 ACGTGGCGCTGAGGATACA 61.348 57.895 7.64 0.00 41.41 2.29
631 648 1.878522 CACGTGGCGCTGAGGATAC 60.879 63.158 7.95 0.00 0.00 2.24
632 649 1.033202 TACACGTGGCGCTGAGGATA 61.033 55.000 21.57 0.00 0.00 2.59
633 650 2.284798 CTACACGTGGCGCTGAGGAT 62.285 60.000 21.57 0.00 0.00 3.24
634 651 2.986979 TACACGTGGCGCTGAGGA 60.987 61.111 21.57 0.00 0.00 3.71
635 652 2.507102 CTACACGTGGCGCTGAGG 60.507 66.667 21.57 2.49 0.00 3.86
636 653 3.181967 GCTACACGTGGCGCTGAG 61.182 66.667 21.57 7.85 0.00 3.35
637 654 3.984749 TGCTACACGTGGCGCTGA 61.985 61.111 24.91 9.28 40.17 4.26
638 655 3.777925 GTGCTACACGTGGCGCTG 61.778 66.667 24.91 0.00 43.02 5.18
647 664 1.805945 CGCCTTCTCCGTGCTACAC 60.806 63.158 0.00 0.00 0.00 2.90
648 665 2.571757 CGCCTTCTCCGTGCTACA 59.428 61.111 0.00 0.00 0.00 2.74
649 666 2.202756 CCGCCTTCTCCGTGCTAC 60.203 66.667 0.00 0.00 0.00 3.58
650 667 4.143333 GCCGCCTTCTCCGTGCTA 62.143 66.667 0.00 0.00 0.00 3.49
668 685 2.946752 GAAAACACCGTCCGCGTCC 61.947 63.158 4.92 0.00 36.15 4.79
669 686 2.154427 CTGAAAACACCGTCCGCGTC 62.154 60.000 4.92 0.00 36.15 5.19
670 687 2.202905 TGAAAACACCGTCCGCGT 60.203 55.556 4.92 0.00 36.15 6.01
671 688 2.549282 CTGAAAACACCGTCCGCG 59.451 61.111 0.00 0.00 37.95 6.46
672 689 2.251371 GCTGAAAACACCGTCCGC 59.749 61.111 0.00 0.00 0.00 5.54
673 690 2.943653 GGCTGAAAACACCGTCCG 59.056 61.111 0.00 0.00 0.00 4.79
674 691 2.613506 CCGGCTGAAAACACCGTCC 61.614 63.158 0.00 0.00 45.49 4.79
675 692 1.441732 AACCGGCTGAAAACACCGTC 61.442 55.000 0.00 0.00 45.49 4.79
676 693 1.452470 AACCGGCTGAAAACACCGT 60.452 52.632 0.00 0.00 45.49 4.83
677 694 1.008995 CAACCGGCTGAAAACACCG 60.009 57.895 0.00 0.00 46.50 4.94
678 695 0.741915 TTCAACCGGCTGAAAACACC 59.258 50.000 17.76 0.00 32.39 4.16
679 696 1.269051 CCTTCAACCGGCTGAAAACAC 60.269 52.381 20.18 0.00 34.96 3.32
680 697 1.028905 CCTTCAACCGGCTGAAAACA 58.971 50.000 20.18 0.00 34.96 2.83
681 698 1.029681 ACCTTCAACCGGCTGAAAAC 58.970 50.000 20.18 0.00 34.96 2.43
682 699 2.642154 TACCTTCAACCGGCTGAAAA 57.358 45.000 20.18 7.20 34.96 2.29
683 700 2.158726 ACTTACCTTCAACCGGCTGAAA 60.159 45.455 20.18 4.15 34.96 2.69
684 701 1.418637 ACTTACCTTCAACCGGCTGAA 59.581 47.619 18.82 18.82 34.22 3.02
685 702 1.053424 ACTTACCTTCAACCGGCTGA 58.947 50.000 2.67 2.67 0.00 4.26
686 703 1.892209 AACTTACCTTCAACCGGCTG 58.108 50.000 0.00 0.00 0.00 4.85
687 704 2.651382 AAACTTACCTTCAACCGGCT 57.349 45.000 0.00 0.00 0.00 5.52
688 705 3.551454 GGAAAAACTTACCTTCAACCGGC 60.551 47.826 0.00 0.00 0.00 6.13
689 706 3.005050 GGGAAAAACTTACCTTCAACCGG 59.995 47.826 0.00 0.00 0.00 5.28
690 707 3.633065 TGGGAAAAACTTACCTTCAACCG 59.367 43.478 0.00 0.00 0.00 4.44
691 708 5.601583 TTGGGAAAAACTTACCTTCAACC 57.398 39.130 0.00 0.00 0.00 3.77
692 709 6.533723 CAGTTTGGGAAAAACTTACCTTCAAC 59.466 38.462 0.82 0.00 38.32 3.18
693 710 6.437793 TCAGTTTGGGAAAAACTTACCTTCAA 59.562 34.615 0.82 0.00 38.32 2.69
694 711 5.952947 TCAGTTTGGGAAAAACTTACCTTCA 59.047 36.000 0.82 0.00 38.32 3.02
695 712 6.459670 TCAGTTTGGGAAAAACTTACCTTC 57.540 37.500 0.82 0.00 38.32 3.46
696 713 6.860790 TTCAGTTTGGGAAAAACTTACCTT 57.139 33.333 0.82 0.00 38.32 3.50
697 714 6.685368 GCATTCAGTTTGGGAAAAACTTACCT 60.685 38.462 0.82 0.00 38.32 3.08
698 715 5.465390 GCATTCAGTTTGGGAAAAACTTACC 59.535 40.000 0.82 0.00 38.32 2.85
699 716 6.045955 TGCATTCAGTTTGGGAAAAACTTAC 58.954 36.000 0.82 0.00 38.32 2.34
700 717 6.227298 TGCATTCAGTTTGGGAAAAACTTA 57.773 33.333 0.82 0.00 38.32 2.24
701 718 5.096443 TGCATTCAGTTTGGGAAAAACTT 57.904 34.783 0.82 0.00 38.32 2.66
702 719 4.751767 TGCATTCAGTTTGGGAAAAACT 57.248 36.364 0.00 0.00 40.80 2.66
703 720 5.118510 CGTATGCATTCAGTTTGGGAAAAAC 59.881 40.000 3.54 0.00 0.00 2.43
704 721 5.221342 ACGTATGCATTCAGTTTGGGAAAAA 60.221 36.000 3.54 0.00 0.00 1.94
705 722 4.279671 ACGTATGCATTCAGTTTGGGAAAA 59.720 37.500 3.54 0.00 0.00 2.29
706 723 3.823873 ACGTATGCATTCAGTTTGGGAAA 59.176 39.130 3.54 0.00 0.00 3.13
707 724 3.190327 CACGTATGCATTCAGTTTGGGAA 59.810 43.478 3.54 0.00 0.00 3.97
708 725 2.746904 CACGTATGCATTCAGTTTGGGA 59.253 45.455 3.54 0.00 0.00 4.37
709 726 3.135414 CACGTATGCATTCAGTTTGGG 57.865 47.619 3.54 0.00 0.00 4.12
830 847 2.438614 GGAGAAGAAAGGCCCGGC 60.439 66.667 0.00 0.00 0.00 6.13
831 848 1.222113 GAGGAGAAGAAAGGCCCGG 59.778 63.158 0.00 0.00 0.00 5.73
856 873 1.163420 TGACATTTTGCCGCGACAGT 61.163 50.000 8.23 0.00 0.00 3.55
907 924 4.099419 TGTTCTTATCTGCCATCTTAGCGA 59.901 41.667 0.00 0.00 0.00 4.93
915 932 2.766263 TCGGACTGTTCTTATCTGCCAT 59.234 45.455 0.00 0.00 0.00 4.40
916 933 2.094182 GTCGGACTGTTCTTATCTGCCA 60.094 50.000 0.00 0.00 0.00 4.92
1169 1194 1.152631 TCGATCACCGGGATGGCTA 60.153 57.895 6.32 0.00 43.94 3.93
1239 1264 2.529389 AAGAACCCCCACTCCGCT 60.529 61.111 0.00 0.00 0.00 5.52
1410 1435 1.285950 CTTCGACTCGTGCAGGTCA 59.714 57.895 6.26 0.00 33.19 4.02
1420 1445 0.951040 CAGTTGGCCACCTTCGACTC 60.951 60.000 3.88 0.00 0.00 3.36
1550 1575 1.604185 GGGCATTGTCGAGCTAGCTAG 60.604 57.143 19.38 18.55 0.00 3.42
1632 1657 3.188159 ACTACGTGGACAAGCTTCAAA 57.812 42.857 5.70 0.00 0.00 2.69
1633 1658 2.902705 ACTACGTGGACAAGCTTCAA 57.097 45.000 5.70 0.00 0.00 2.69
1634 1659 2.889045 ACTACTACGTGGACAAGCTTCA 59.111 45.455 5.70 0.00 0.00 3.02
1635 1660 3.057736 TGACTACTACGTGGACAAGCTTC 60.058 47.826 5.70 0.00 0.00 3.86
1636 1661 2.889045 TGACTACTACGTGGACAAGCTT 59.111 45.455 5.70 0.00 0.00 3.74
1638 1663 2.864968 CTGACTACTACGTGGACAAGC 58.135 52.381 5.70 0.00 0.00 4.01
1639 1664 2.488545 AGCTGACTACTACGTGGACAAG 59.511 50.000 5.70 2.59 0.00 3.16
1640 1665 2.511659 AGCTGACTACTACGTGGACAA 58.488 47.619 5.70 0.00 0.00 3.18
1641 1666 2.195741 AGCTGACTACTACGTGGACA 57.804 50.000 5.70 0.00 0.00 4.02
1642 1667 3.057736 TCAAAGCTGACTACTACGTGGAC 60.058 47.826 5.70 0.00 0.00 4.02
1643 1668 3.151554 TCAAAGCTGACTACTACGTGGA 58.848 45.455 5.70 0.00 0.00 4.02
1644 1669 3.570926 TCAAAGCTGACTACTACGTGG 57.429 47.619 0.00 0.00 0.00 4.94
1655 1680 4.925054 GCATGCATTTTTAGTCAAAGCTGA 59.075 37.500 14.21 0.00 0.00 4.26
1656 1681 4.687018 TGCATGCATTTTTAGTCAAAGCTG 59.313 37.500 18.46 0.00 0.00 4.24
1657 1682 4.885413 TGCATGCATTTTTAGTCAAAGCT 58.115 34.783 18.46 0.00 0.00 3.74
1658 1683 4.687483 ACTGCATGCATTTTTAGTCAAAGC 59.313 37.500 22.97 0.00 0.00 3.51
1659 1684 5.921976 TCACTGCATGCATTTTTAGTCAAAG 59.078 36.000 22.97 7.02 0.00 2.77
1927 1952 4.268687 CACTGGTTCTCGTGGAGC 57.731 61.111 0.00 0.00 0.00 4.70
1941 1966 2.279918 GCGTGACGTCAACCCACT 60.280 61.111 21.95 0.00 0.00 4.00
1948 1973 2.586635 GGTGTTGGCGTGACGTCA 60.587 61.111 15.76 15.76 40.58 4.35
1969 1994 1.078709 CCACATTGACGATGAACGCT 58.921 50.000 9.78 0.00 46.94 5.07
1999 2024 3.134458 GTGAAGATGCATAGGTACCTGC 58.866 50.000 25.33 20.80 37.91 4.85
2011 2036 2.855180 CGTGACCAATTGTGAAGATGC 58.145 47.619 4.43 0.00 0.00 3.91
2049 2075 4.168922 GCCTTTAGCATTTTACGGTTGT 57.831 40.909 0.00 0.00 42.97 3.32
2091 2117 6.299922 ACCTGTCATTCGAGATCATCTAGTA 58.700 40.000 0.00 0.00 0.00 1.82
2147 2173 0.968901 AGACCCTCGGTGCATCGTTA 60.969 55.000 20.53 0.00 35.25 3.18
2189 2215 4.081420 CCATATATCCTCTCCGAACTTGGG 60.081 50.000 0.00 0.00 0.00 4.12
2236 2262 0.675837 GTACAAGGGCGGGTTCTTCC 60.676 60.000 0.00 0.00 0.00 3.46
2249 2275 1.402984 GCGAGTGTCTCCCTGTACAAG 60.403 57.143 0.00 0.00 0.00 3.16
2349 2375 8.364142 ACGAAATCATAACAAAGGATTTTTCCA 58.636 29.630 0.00 0.00 45.89 3.53
2350 2376 8.757164 ACGAAATCATAACAAAGGATTTTTCC 57.243 30.769 0.00 0.00 45.89 3.13
2364 2390 9.781834 GTTGTCCAATTATTGACGAAATCATAA 57.218 29.630 6.50 0.00 37.11 1.90
2365 2391 8.951243 TGTTGTCCAATTATTGACGAAATCATA 58.049 29.630 6.50 0.00 37.11 2.15
2366 2392 7.825681 TGTTGTCCAATTATTGACGAAATCAT 58.174 30.769 6.50 0.00 37.11 2.45
2403 2429 0.584396 TGTCTAACAAAAGCCACGCG 59.416 50.000 3.53 3.53 0.00 6.01
2406 2432 6.509418 TGGAATATGTCTAACAAAAGCCAC 57.491 37.500 0.00 0.00 0.00 5.01
2409 2435 6.377146 TCCCTTGGAATATGTCTAACAAAAGC 59.623 38.462 0.00 0.00 0.00 3.51
2435 2461 6.818644 AGCGAACATATCTGAATACACAAAGT 59.181 34.615 0.00 0.00 0.00 2.66
2480 2506 6.037726 GGTTATTGGTCAACTTCGTTTTGTT 58.962 36.000 0.00 0.00 0.00 2.83
2586 2612 1.946063 TAGCTAGTTCCCGGCCCTCT 61.946 60.000 0.00 0.00 0.00 3.69
2701 2731 0.816421 ACCGTTGTTGTTAAGCCGCT 60.816 50.000 0.00 0.00 0.00 5.52
2758 2791 1.039856 ACTGCGCCTTTGTCCATTTT 58.960 45.000 4.18 0.00 0.00 1.82
2793 2826 1.949525 CCAGGGCTCGTCATAAAATGG 59.050 52.381 0.00 0.00 0.00 3.16
2858 2891 9.204570 AGTTAGTGTGTATGACTTAATGTTCAC 57.795 33.333 0.00 0.00 0.00 3.18
2947 2980 0.027194 CTCATCGCGCCATGAAAGTG 59.973 55.000 18.37 3.53 32.24 3.16
2958 2991 2.524034 CTGGATAGCATACTCATCGCG 58.476 52.381 0.00 0.00 0.00 5.87
3014 3047 0.250901 CCACCCTGAACCAGTTCCTG 60.251 60.000 8.01 1.67 38.77 3.86
3033 3066 0.698818 ATTCCCCAGGTGGAGTGTTC 59.301 55.000 0.00 0.00 35.37 3.18
3042 3075 2.044946 GCAGCGAATTCCCCAGGT 60.045 61.111 0.00 0.00 0.00 4.00
3067 3100 3.154710 TGTGTATATGCTAGGGTCTCCG 58.845 50.000 0.00 0.00 38.33 4.63
3214 3247 0.670854 GGACTTCGTCTCCAAGGTGC 60.671 60.000 0.00 0.00 32.47 5.01
3218 3251 1.403514 GCTGAGGACTTCGTCTCCAAG 60.404 57.143 1.00 0.00 32.47 3.61
3269 3302 2.182030 GTGCTCTTCTCCGACGGG 59.818 66.667 15.25 4.97 0.00 5.28


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

AutoCloner maintained by Alex Coulton.