Multiple sequence alignment - TraesCS2D01G543100

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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 TraesCS2D01G543100 chr2D 100.000 2579 0 0 1 2579 621141763 621139185 0.000000e+00 4763.0
1 TraesCS2D01G543100 chr2D 90.284 1266 100 14 802 2054 621265637 621264382 0.000000e+00 1635.0
2 TraesCS2D01G543100 chr2D 85.071 1266 152 22 802 2054 621313634 621312393 0.000000e+00 1256.0
3 TraesCS2D01G543100 chr2D 93.465 505 11 3 181 684 621310747 621310264 0.000000e+00 730.0
4 TraesCS2D01G543100 chr2D 95.902 122 3 2 1 121 621310870 621310750 2.020000e-46 196.0
5 TraesCS2D01G543100 chr2D 76.923 338 57 14 2256 2578 605383638 605383969 3.410000e-39 172.0
6 TraesCS2D01G543100 chr2D 92.308 91 7 0 707 797 453546495 453546585 2.080000e-26 130.0
7 TraesCS2D01G543100 chrUn 93.192 1792 104 10 802 2579 342645017 342643230 0.000000e+00 2617.0
8 TraesCS2D01G543100 chrUn 92.634 1792 104 13 802 2579 343020567 343018790 0.000000e+00 2553.0
9 TraesCS2D01G543100 chrUn 89.374 1374 135 8 846 2210 338975313 338976684 0.000000e+00 1718.0
10 TraesCS2D01G543100 chrUn 89.374 1374 135 8 846 2210 342893166 342894537 0.000000e+00 1718.0
11 TraesCS2D01G543100 chrUn 92.752 952 55 7 1638 2579 440176042 440176989 0.000000e+00 1363.0
12 TraesCS2D01G543100 chrUn 100.000 34 0 0 676 709 342645050 342645017 2.140000e-06 63.9
13 TraesCS2D01G543100 chrUn 100.000 34 0 0 676 709 343020600 343020567 2.140000e-06 63.9
14 TraesCS2D01G543100 chr2B 93.196 1793 102 12 802 2579 762071964 762070177 0.000000e+00 2617.0
15 TraesCS2D01G543100 chr2B 79.281 473 46 31 1 446 80953535 80953982 1.510000e-72 283.0
16 TraesCS2D01G543100 chr2B 92.632 95 7 0 703 797 462945866 462945960 1.240000e-28 137.0
17 TraesCS2D01G543100 chr2B 100.000 34 0 0 676 709 762071997 762071964 2.140000e-06 63.9
18 TraesCS2D01G543100 chr2A 92.329 1460 103 6 1127 2579 753041810 753040353 0.000000e+00 2067.0
19 TraesCS2D01G543100 chr2A 94.369 1101 60 2 802 1901 753053405 753052306 0.000000e+00 1688.0
20 TraesCS2D01G543100 chr2A 84.634 1217 158 18 853 2054 753004608 753003406 0.000000e+00 1184.0
21 TraesCS2D01G543100 chr2A 87.528 449 34 6 2138 2579 753052304 753051871 1.380000e-137 499.0
22 TraesCS2D01G543100 chr2A 80.420 715 62 44 1 675 373419171 373419847 8.350000e-130 473.0
23 TraesCS2D01G543100 chr2A 76.312 705 90 50 1 679 413340175 413339522 3.220000e-79 305.0
24 TraesCS2D01G543100 chr2A 93.103 58 3 1 2218 2274 387110090 387110033 1.640000e-12 84.2
25 TraesCS2D01G543100 chr2A 100.000 34 0 0 676 709 753053438 753053405 2.140000e-06 63.9
26 TraesCS2D01G543100 chr4D 94.985 678 30 4 1 675 477503464 477502788 0.000000e+00 1061.0
27 TraesCS2D01G543100 chr4D 80.259 309 32 15 2225 2532 493338191 493338471 3.360000e-49 206.0
28 TraesCS2D01G543100 chr4A 92.972 683 36 3 1 675 630750562 630751240 0.000000e+00 985.0
29 TraesCS2D01G543100 chr1A 92.398 684 36 8 1 675 388184196 388184872 0.000000e+00 961.0
30 TraesCS2D01G543100 chr4B 92.695 616 39 5 7 619 25964434 25965046 0.000000e+00 883.0
31 TraesCS2D01G543100 chr5A 90.089 676 59 6 1 674 266990705 266991374 0.000000e+00 870.0
32 TraesCS2D01G543100 chr5A 81.143 350 57 7 2224 2567 672842611 672842957 3.270000e-69 272.0
33 TraesCS2D01G543100 chr5A 77.818 275 45 13 2303 2565 626108417 626108147 3.440000e-34 156.0
34 TraesCS2D01G543100 chr1B 78.542 480 66 29 1 460 14517219 14517681 5.430000e-72 281.0
35 TraesCS2D01G543100 chr1B 85.517 145 15 3 538 681 654703952 654703813 2.070000e-31 147.0
36 TraesCS2D01G543100 chr5B 81.303 353 54 9 2231 2573 491113829 491114179 2.530000e-70 276.0
37 TraesCS2D01G543100 chr7B 82.569 327 40 12 1 319 729607948 729608265 3.270000e-69 272.0
38 TraesCS2D01G543100 chr7B 82.263 327 41 12 1 319 729601165 729601482 1.520000e-67 267.0
39 TraesCS2D01G543100 chr7B 93.478 92 6 0 706 797 11170319 11170410 1.240000e-28 137.0
40 TraesCS2D01G543100 chr7B 85.401 137 11 6 550 685 626437604 626437476 1.610000e-27 134.0
41 TraesCS2D01G543100 chr7B 90.698 86 7 1 1 85 729632047 729632132 2.100000e-21 113.0
42 TraesCS2D01G543100 chr3A 87.143 140 9 4 538 675 154734800 154734668 1.600000e-32 150.0
43 TraesCS2D01G543100 chr3B 92.157 102 5 2 707 805 177503872 177503771 9.620000e-30 141.0
44 TraesCS2D01G543100 chr5D 93.548 93 6 0 707 799 328501286 328501378 3.460000e-29 139.0
45 TraesCS2D01G543100 chr5D 92.553 94 7 0 704 797 364234731 364234824 4.480000e-28 135.0
46 TraesCS2D01G543100 chr5D 95.294 85 4 0 713 797 443776613 443776529 4.480000e-28 135.0
47 TraesCS2D01G543100 chr6D 93.478 92 6 0 706 797 425085960 425086051 1.240000e-28 137.0
48 TraesCS2D01G543100 chr7A 94.118 85 3 2 705 788 63718066 63718149 7.490000e-26 128.0


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 TraesCS2D01G543100 chr2D 621139185 621141763 2578 True 4763.000000 4763 100.000000 1 2579 1 chr2D.!!$R1 2578
1 TraesCS2D01G543100 chr2D 621264382 621265637 1255 True 1635.000000 1635 90.284000 802 2054 1 chr2D.!!$R2 1252
2 TraesCS2D01G543100 chr2D 621310264 621313634 3370 True 727.333333 1256 91.479333 1 2054 3 chr2D.!!$R3 2053
3 TraesCS2D01G543100 chrUn 338975313 338976684 1371 False 1718.000000 1718 89.374000 846 2210 1 chrUn.!!$F1 1364
4 TraesCS2D01G543100 chrUn 342893166 342894537 1371 False 1718.000000 1718 89.374000 846 2210 1 chrUn.!!$F2 1364
5 TraesCS2D01G543100 chrUn 440176042 440176989 947 False 1363.000000 1363 92.752000 1638 2579 1 chrUn.!!$F3 941
6 TraesCS2D01G543100 chrUn 342643230 342645050 1820 True 1340.450000 2617 96.596000 676 2579 2 chrUn.!!$R1 1903
7 TraesCS2D01G543100 chrUn 343018790 343020600 1810 True 1308.450000 2553 96.317000 676 2579 2 chrUn.!!$R2 1903
8 TraesCS2D01G543100 chr2B 762070177 762071997 1820 True 1340.450000 2617 96.598000 676 2579 2 chr2B.!!$R1 1903
9 TraesCS2D01G543100 chr2A 753040353 753041810 1457 True 2067.000000 2067 92.329000 1127 2579 1 chr2A.!!$R4 1452
10 TraesCS2D01G543100 chr2A 753003406 753004608 1202 True 1184.000000 1184 84.634000 853 2054 1 chr2A.!!$R3 1201
11 TraesCS2D01G543100 chr2A 753051871 753053438 1567 True 750.300000 1688 93.965667 676 2579 3 chr2A.!!$R5 1903
12 TraesCS2D01G543100 chr2A 373419171 373419847 676 False 473.000000 473 80.420000 1 675 1 chr2A.!!$F1 674
13 TraesCS2D01G543100 chr2A 413339522 413340175 653 True 305.000000 305 76.312000 1 679 1 chr2A.!!$R2 678
14 TraesCS2D01G543100 chr4D 477502788 477503464 676 True 1061.000000 1061 94.985000 1 675 1 chr4D.!!$R1 674
15 TraesCS2D01G543100 chr4A 630750562 630751240 678 False 985.000000 985 92.972000 1 675 1 chr4A.!!$F1 674
16 TraesCS2D01G543100 chr1A 388184196 388184872 676 False 961.000000 961 92.398000 1 675 1 chr1A.!!$F1 674
17 TraesCS2D01G543100 chr4B 25964434 25965046 612 False 883.000000 883 92.695000 7 619 1 chr4B.!!$F1 612
18 TraesCS2D01G543100 chr5A 266990705 266991374 669 False 870.000000 870 90.089000 1 674 1 chr5A.!!$F1 673

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
627 721 0.031817 ATCTGGCCCAAAATCCCAGG 60.032 55.0 0.0 0.0 44.87 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 3168 0.977108 AGGAGGAAGAGGAGCAGCAG 60.977 60.0 0.0 0.0 0.0 4.24 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
18 19 1.907739 TCCGGCCCTCTTCATTCTG 59.092 57.895 0.00 0.00 0.00 3.02
476 549 3.822192 CCGGATGGCGTCGAGACA 61.822 66.667 0.00 0.00 45.56 3.41
509 602 3.321648 TGCAGACCCGCAGTGGAT 61.322 61.111 0.00 0.00 42.00 3.41
568 662 2.091541 CGGTATGTGTTTTGGGCTGAT 58.908 47.619 0.00 0.00 0.00 2.90
569 663 2.491693 CGGTATGTGTTTTGGGCTGATT 59.508 45.455 0.00 0.00 0.00 2.57
570 664 3.056891 CGGTATGTGTTTTGGGCTGATTT 60.057 43.478 0.00 0.00 0.00 2.17
571 665 4.560513 CGGTATGTGTTTTGGGCTGATTTT 60.561 41.667 0.00 0.00 0.00 1.82
572 666 5.304778 GGTATGTGTTTTGGGCTGATTTTT 58.695 37.500 0.00 0.00 0.00 1.94
593 687 5.456548 TTTTCTGTCCCGGTTAAAAATCC 57.543 39.130 0.00 0.00 0.00 3.01
594 688 3.791953 TCTGTCCCGGTTAAAAATCCA 57.208 42.857 0.00 0.00 0.00 3.41
595 689 4.310022 TCTGTCCCGGTTAAAAATCCAT 57.690 40.909 0.00 0.00 0.00 3.41
596 690 5.438698 TCTGTCCCGGTTAAAAATCCATA 57.561 39.130 0.00 0.00 0.00 2.74
597 691 5.433526 TCTGTCCCGGTTAAAAATCCATAG 58.566 41.667 0.00 0.00 0.00 2.23
598 692 4.528920 TGTCCCGGTTAAAAATCCATAGG 58.471 43.478 0.00 0.00 0.00 2.57
599 693 4.018233 TGTCCCGGTTAAAAATCCATAGGT 60.018 41.667 0.00 0.00 0.00 3.08
600 694 5.191323 TGTCCCGGTTAAAAATCCATAGGTA 59.809 40.000 0.00 0.00 0.00 3.08
601 695 6.126420 TGTCCCGGTTAAAAATCCATAGGTAT 60.126 38.462 0.00 0.00 0.00 2.73
602 696 7.072202 TGTCCCGGTTAAAAATCCATAGGTATA 59.928 37.037 0.00 0.00 0.00 1.47
603 697 8.105197 GTCCCGGTTAAAAATCCATAGGTATAT 58.895 37.037 0.00 0.00 0.00 0.86
604 698 9.336462 TCCCGGTTAAAAATCCATAGGTATATA 57.664 33.333 0.00 0.00 0.00 0.86
605 699 9.962809 CCCGGTTAAAAATCCATAGGTATATAA 57.037 33.333 0.00 0.00 0.00 0.98
616 710 8.506196 TCCATAGGTATATAATAATCTGGCCC 57.494 38.462 0.00 0.00 0.00 5.80
617 711 8.077512 TCCATAGGTATATAATAATCTGGCCCA 58.922 37.037 0.00 0.00 0.00 5.36
618 712 8.723365 CCATAGGTATATAATAATCTGGCCCAA 58.277 37.037 0.00 0.00 0.00 4.12
622 716 9.700831 AGGTATATAATAATCTGGCCCAAAATC 57.299 33.333 0.00 0.00 0.00 2.17
623 717 8.914011 GGTATATAATAATCTGGCCCAAAATCC 58.086 37.037 0.00 0.00 0.00 3.01
624 718 7.978099 ATATAATAATCTGGCCCAAAATCCC 57.022 36.000 0.00 0.00 0.00 3.85
625 719 3.704545 ATAATCTGGCCCAAAATCCCA 57.295 42.857 0.00 0.00 0.00 4.37
626 720 1.870064 AATCTGGCCCAAAATCCCAG 58.130 50.000 0.00 0.00 45.88 4.45
627 721 0.031817 ATCTGGCCCAAAATCCCAGG 60.032 55.000 0.00 0.00 44.87 4.45
628 722 1.686800 CTGGCCCAAAATCCCAGGG 60.687 63.158 0.00 0.00 45.68 4.45
629 723 2.449777 GGCCCAAAATCCCAGGGT 59.550 61.111 5.01 0.00 44.69 4.34
630 724 1.989508 GGCCCAAAATCCCAGGGTG 60.990 63.158 5.01 0.00 44.69 4.61
631 725 1.989508 GCCCAAAATCCCAGGGTGG 60.990 63.158 5.01 5.55 44.69 4.61
662 756 2.933287 CACCCTGGCCACCCTGTA 60.933 66.667 0.00 0.00 0.00 2.74
663 757 2.610859 ACCCTGGCCACCCTGTAG 60.611 66.667 0.00 0.00 0.00 2.74
664 758 4.115199 CCCTGGCCACCCTGTAGC 62.115 72.222 0.00 0.00 0.00 3.58
665 759 3.011517 CCTGGCCACCCTGTAGCT 61.012 66.667 0.00 0.00 0.00 3.32
666 760 2.586792 CTGGCCACCCTGTAGCTC 59.413 66.667 0.00 0.00 0.00 4.09
667 761 3.009115 TGGCCACCCTGTAGCTCC 61.009 66.667 0.00 0.00 0.00 4.70
668 762 4.162690 GGCCACCCTGTAGCTCCG 62.163 72.222 0.00 0.00 0.00 4.63
669 763 4.840005 GCCACCCTGTAGCTCCGC 62.840 72.222 0.00 0.00 0.00 5.54
670 764 4.162690 CCACCCTGTAGCTCCGCC 62.163 72.222 0.00 0.00 0.00 6.13
671 765 4.162690 CACCCTGTAGCTCCGCCC 62.163 72.222 0.00 0.00 0.00 6.13
674 768 3.854669 CCTGTAGCTCCGCCCCTG 61.855 72.222 0.00 0.00 0.00 4.45
709 803 3.679389 CTTGCTTGTGTTCCCATCTACT 58.321 45.455 0.00 0.00 0.00 2.57
710 804 3.788227 TGCTTGTGTTCCCATCTACTT 57.212 42.857 0.00 0.00 0.00 2.24
711 805 3.674997 TGCTTGTGTTCCCATCTACTTC 58.325 45.455 0.00 0.00 0.00 3.01
712 806 3.010420 GCTTGTGTTCCCATCTACTTCC 58.990 50.000 0.00 0.00 0.00 3.46
713 807 3.307762 GCTTGTGTTCCCATCTACTTCCT 60.308 47.826 0.00 0.00 0.00 3.36
714 808 4.508662 CTTGTGTTCCCATCTACTTCCTC 58.491 47.826 0.00 0.00 0.00 3.71
715 809 2.838202 TGTGTTCCCATCTACTTCCTCC 59.162 50.000 0.00 0.00 0.00 4.30
716 810 2.108168 TGTTCCCATCTACTTCCTCCG 58.892 52.381 0.00 0.00 0.00 4.63
717 811 2.108970 GTTCCCATCTACTTCCTCCGT 58.891 52.381 0.00 0.00 0.00 4.69
718 812 2.500504 GTTCCCATCTACTTCCTCCGTT 59.499 50.000 0.00 0.00 0.00 4.44
719 813 2.829023 TCCCATCTACTTCCTCCGTTT 58.171 47.619 0.00 0.00 0.00 3.60
720 814 2.764572 TCCCATCTACTTCCTCCGTTTC 59.235 50.000 0.00 0.00 0.00 2.78
721 815 2.500098 CCCATCTACTTCCTCCGTTTCA 59.500 50.000 0.00 0.00 0.00 2.69
722 816 3.055385 CCCATCTACTTCCTCCGTTTCAA 60.055 47.826 0.00 0.00 0.00 2.69
723 817 4.564821 CCCATCTACTTCCTCCGTTTCAAA 60.565 45.833 0.00 0.00 0.00 2.69
724 818 5.001232 CCATCTACTTCCTCCGTTTCAAAA 58.999 41.667 0.00 0.00 0.00 2.44
725 819 5.648092 CCATCTACTTCCTCCGTTTCAAAAT 59.352 40.000 0.00 0.00 0.00 1.82
726 820 6.821665 CCATCTACTTCCTCCGTTTCAAAATA 59.178 38.462 0.00 0.00 0.00 1.40
727 821 7.011482 CCATCTACTTCCTCCGTTTCAAAATAG 59.989 40.741 0.00 0.00 0.00 1.73
728 822 7.235935 TCTACTTCCTCCGTTTCAAAATAGA 57.764 36.000 0.00 0.00 0.00 1.98
729 823 7.848128 TCTACTTCCTCCGTTTCAAAATAGAT 58.152 34.615 0.00 0.00 0.00 1.98
730 824 6.743575 ACTTCCTCCGTTTCAAAATAGATG 57.256 37.500 0.00 0.00 0.00 2.90
731 825 6.472887 ACTTCCTCCGTTTCAAAATAGATGA 58.527 36.000 0.00 0.00 0.00 2.92
732 826 6.371825 ACTTCCTCCGTTTCAAAATAGATGAC 59.628 38.462 0.00 0.00 0.00 3.06
733 827 5.183228 TCCTCCGTTTCAAAATAGATGACC 58.817 41.667 0.00 0.00 0.00 4.02
734 828 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
735 829 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
736 830 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
737 831 5.949354 TCCGTTTCAAAATAGATGACCCAAT 59.051 36.000 0.00 0.00 0.00 3.16
738 832 6.435904 TCCGTTTCAAAATAGATGACCCAATT 59.564 34.615 0.00 0.00 0.00 2.32
739 833 7.039363 TCCGTTTCAAAATAGATGACCCAATTT 60.039 33.333 0.00 0.00 0.00 1.82
740 834 7.602265 CCGTTTCAAAATAGATGACCCAATTTT 59.398 33.333 0.00 0.00 33.07 1.82
741 835 9.632807 CGTTTCAAAATAGATGACCCAATTTTA 57.367 29.630 0.00 0.00 31.97 1.52
793 887 8.970691 AAAATTGAGTCATCTATTTTGGAACG 57.029 30.769 11.47 0.00 44.08 3.95
794 888 6.683974 ATTGAGTCATCTATTTTGGAACGG 57.316 37.500 0.00 0.00 0.00 4.44
795 889 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
796 890 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
797 891 5.186992 TGAGTCATCTATTTTGGAACGGAGA 59.813 40.000 0.00 0.00 0.00 3.71
798 892 5.665459 AGTCATCTATTTTGGAACGGAGAG 58.335 41.667 0.00 0.00 0.00 3.20
799 893 5.187967 AGTCATCTATTTTGGAACGGAGAGT 59.812 40.000 0.00 0.00 0.00 3.24
800 894 5.292101 GTCATCTATTTTGGAACGGAGAGTG 59.708 44.000 0.00 0.00 0.00 3.51
817 911 3.002656 AGAGTGCACAACATTCAAAGTCG 59.997 43.478 21.04 0.00 37.47 4.18
844 943 1.153823 GCAGGTACACGCACTCGAT 60.154 57.895 0.00 0.00 39.41 3.59
1003 1116 1.132643 CTGCAAGCTCTGCTTCCATTC 59.867 52.381 17.72 0.00 46.77 2.67
1011 1124 0.322456 CTGCTTCCATTCCCAACCGA 60.322 55.000 0.00 0.00 0.00 4.69
1036 1152 2.165998 GCTGCAAGGAGAACCATTCTT 58.834 47.619 0.00 0.00 40.87 2.52
1037 1153 2.163211 GCTGCAAGGAGAACCATTCTTC 59.837 50.000 0.00 0.00 40.87 2.87
1077 1193 4.056125 CCTGAGCACGGCGTCTGA 62.056 66.667 10.85 3.92 0.00 3.27
1083 1199 3.414700 CACGGCGTCTGAGGCAAC 61.415 66.667 22.08 6.60 36.37 4.17
1204 1322 1.157513 TACTCCCCTCAGGCACACA 59.842 57.895 0.00 0.00 34.51 3.72
1217 1335 2.022129 CACACAACGTCCTCGAGGC 61.022 63.158 27.39 19.70 40.62 4.70
1289 1407 1.133025 CAACTCCGGGAATGATGTTGC 59.867 52.381 11.64 0.00 0.00 4.17
1292 1410 2.158900 ACTCCGGGAATGATGTTGCTAG 60.159 50.000 0.00 0.00 0.00 3.42
1569 1689 6.183360 GCAGGCACATGTGTACTTTATGTATT 60.183 38.462 26.01 0.00 33.57 1.89
1881 2008 4.016444 GTGAAGAACAATTAGGATGGCCA 58.984 43.478 8.56 8.56 36.29 5.36
2072 2210 2.513753 TGTTATGTTCTTGTGGCTGGG 58.486 47.619 0.00 0.00 0.00 4.45
2073 2211 1.202348 GTTATGTTCTTGTGGCTGGGC 59.798 52.381 0.00 0.00 0.00 5.36
2167 2305 1.067213 ACATGCGGCATTGGGTAAAAC 60.067 47.619 13.81 0.00 0.00 2.43
2173 2311 3.016736 CGGCATTGGGTAAAACTGATCT 58.983 45.455 0.00 0.00 0.00 2.75
2250 3168 2.046285 CACCTCCATTGGAACCGGC 61.046 63.158 6.88 0.00 0.00 6.13
2318 3977 2.685017 TGGCGAGTCTGGAGGCAT 60.685 61.111 0.00 0.00 35.49 4.40
2321 3980 2.898738 CGAGTCTGGAGGCATGCT 59.101 61.111 18.92 3.20 0.00 3.79
2322 3981 1.521010 CGAGTCTGGAGGCATGCTG 60.521 63.158 18.92 3.45 0.00 4.41
2360 4045 2.439104 GCCTCGCCCAGATCTCCTT 61.439 63.158 0.00 0.00 0.00 3.36
2423 4119 2.169769 TCGTCTTCTTTTATCGGGCCAT 59.830 45.455 4.39 0.00 0.00 4.40
2477 4173 2.427453 GGAGAGAAATGTGCTCGGACTA 59.573 50.000 0.00 0.00 37.46 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 9.093970 CATGCATAATTTTCACATCATTTCTGT 57.906 29.630 0.00 0.00 0.00 3.41
101 103 8.861033 TTTTTGCACTATGCTATCATGAATTC 57.139 30.769 0.00 0.00 45.31 2.17
500 576 1.226802 CCTCGTCTCATCCACTGCG 60.227 63.158 0.00 0.00 0.00 5.18
509 602 3.311110 GGCCACACCCTCGTCTCA 61.311 66.667 0.00 0.00 0.00 3.27
570 664 5.363005 TGGATTTTTAACCGGGACAGAAAAA 59.637 36.000 6.32 10.88 34.51 1.94
571 665 4.894114 TGGATTTTTAACCGGGACAGAAAA 59.106 37.500 6.32 6.19 0.00 2.29
572 666 4.471548 TGGATTTTTAACCGGGACAGAAA 58.528 39.130 6.32 0.25 0.00 2.52
573 667 4.101645 TGGATTTTTAACCGGGACAGAA 57.898 40.909 6.32 0.00 0.00 3.02
574 668 3.791953 TGGATTTTTAACCGGGACAGA 57.208 42.857 6.32 0.00 0.00 3.41
575 669 4.578928 CCTATGGATTTTTAACCGGGACAG 59.421 45.833 6.32 0.00 0.00 3.51
576 670 4.018233 ACCTATGGATTTTTAACCGGGACA 60.018 41.667 6.32 0.00 0.00 4.02
577 671 4.529897 ACCTATGGATTTTTAACCGGGAC 58.470 43.478 6.32 0.00 0.00 4.46
578 672 4.866327 ACCTATGGATTTTTAACCGGGA 57.134 40.909 6.32 0.00 0.00 5.14
579 673 9.962809 TTATATACCTATGGATTTTTAACCGGG 57.037 33.333 6.32 0.00 0.00 5.73
590 684 9.117223 GGGCCAGATTATTATATACCTATGGAT 57.883 37.037 4.39 0.00 0.00 3.41
591 685 8.077512 TGGGCCAGATTATTATATACCTATGGA 58.922 37.037 0.00 0.00 0.00 3.41
592 686 8.275187 TGGGCCAGATTATTATATACCTATGG 57.725 38.462 0.00 0.00 0.00 2.74
596 690 9.700831 GATTTTGGGCCAGATTATTATATACCT 57.299 33.333 6.23 0.00 0.00 3.08
597 691 8.914011 GGATTTTGGGCCAGATTATTATATACC 58.086 37.037 6.23 0.00 0.00 2.73
598 692 8.914011 GGGATTTTGGGCCAGATTATTATATAC 58.086 37.037 6.23 0.00 0.00 1.47
599 693 8.628281 TGGGATTTTGGGCCAGATTATTATATA 58.372 33.333 6.23 0.00 0.00 0.86
600 694 7.486473 TGGGATTTTGGGCCAGATTATTATAT 58.514 34.615 6.23 0.00 0.00 0.86
601 695 6.868826 TGGGATTTTGGGCCAGATTATTATA 58.131 36.000 6.23 0.00 0.00 0.98
602 696 5.725490 TGGGATTTTGGGCCAGATTATTAT 58.275 37.500 6.23 0.00 0.00 1.28
603 697 5.147032 CTGGGATTTTGGGCCAGATTATTA 58.853 41.667 6.23 0.00 0.00 0.98
604 698 3.969312 CTGGGATTTTGGGCCAGATTATT 59.031 43.478 6.23 0.00 0.00 1.40
605 699 3.580039 CTGGGATTTTGGGCCAGATTAT 58.420 45.455 6.23 0.00 0.00 1.28
606 700 2.359143 CCTGGGATTTTGGGCCAGATTA 60.359 50.000 6.23 0.00 0.00 1.75
607 701 1.623279 CCTGGGATTTTGGGCCAGATT 60.623 52.381 6.23 0.00 0.00 2.40
608 702 0.031817 CCTGGGATTTTGGGCCAGAT 60.032 55.000 6.23 5.12 0.00 2.90
609 703 1.387737 CCTGGGATTTTGGGCCAGA 59.612 57.895 6.23 0.00 0.00 3.86
610 704 1.686800 CCCTGGGATTTTGGGCCAG 60.687 63.158 7.01 0.00 33.88 4.85
611 705 2.449312 CCCTGGGATTTTGGGCCA 59.551 61.111 7.01 0.00 33.88 5.36
612 706 1.989508 CACCCTGGGATTTTGGGCC 60.990 63.158 22.23 0.00 44.56 5.80
613 707 1.989508 CCACCCTGGGATTTTGGGC 60.990 63.158 22.23 0.00 44.56 5.36
614 708 4.459199 CCACCCTGGGATTTTGGG 57.541 61.111 22.23 6.82 46.07 4.12
645 739 2.933287 TACAGGGTGGCCAGGGTG 60.933 66.667 5.11 6.08 0.00 4.61
646 740 2.610859 CTACAGGGTGGCCAGGGT 60.611 66.667 5.11 4.53 0.00 4.34
647 741 4.115199 GCTACAGGGTGGCCAGGG 62.115 72.222 5.11 0.00 33.94 4.45
648 742 3.011517 AGCTACAGGGTGGCCAGG 61.012 66.667 5.11 0.00 40.93 4.45
649 743 2.586792 GAGCTACAGGGTGGCCAG 59.413 66.667 5.11 0.00 40.93 4.85
650 744 3.009115 GGAGCTACAGGGTGGCCA 61.009 66.667 0.00 0.00 40.93 5.36
651 745 4.162690 CGGAGCTACAGGGTGGCC 62.163 72.222 0.00 0.00 40.93 5.36
669 763 4.488136 TACGCATGCAGCCAGGGG 62.488 66.667 19.57 0.50 41.38 4.79
670 764 2.898840 CTACGCATGCAGCCAGGG 60.899 66.667 19.57 1.32 41.38 4.45
671 765 3.580193 GCTACGCATGCAGCCAGG 61.580 66.667 19.57 2.13 41.38 4.45
672 766 2.110967 AAGCTACGCATGCAGCCAG 61.111 57.895 22.48 12.14 41.38 4.85
673 767 2.046023 AAGCTACGCATGCAGCCA 60.046 55.556 22.48 2.34 41.38 4.75
674 768 2.406401 CAAGCTACGCATGCAGCC 59.594 61.111 22.48 8.40 41.38 4.85
709 803 5.646360 GGTCATCTATTTTGAAACGGAGGAA 59.354 40.000 0.00 0.00 0.00 3.36
710 804 5.183228 GGTCATCTATTTTGAAACGGAGGA 58.817 41.667 0.00 0.00 0.00 3.71
711 805 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
712 806 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
713 807 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
714 808 5.637006 TTGGGTCATCTATTTTGAAACGG 57.363 39.130 0.00 0.00 0.00 4.44
715 809 8.532977 AAAATTGGGTCATCTATTTTGAAACG 57.467 30.769 0.00 0.00 31.14 3.60
768 862 8.028938 CCGTTCCAAAATAGATGACTCAATTTT 58.971 33.333 0.00 0.00 33.07 1.82
769 863 7.393234 TCCGTTCCAAAATAGATGACTCAATTT 59.607 33.333 0.00 0.00 0.00 1.82
770 864 6.884295 TCCGTTCCAAAATAGATGACTCAATT 59.116 34.615 0.00 0.00 0.00 2.32
771 865 6.414732 TCCGTTCCAAAATAGATGACTCAAT 58.585 36.000 0.00 0.00 0.00 2.57
772 866 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
773 867 5.186992 TCTCCGTTCCAAAATAGATGACTCA 59.813 40.000 0.00 0.00 0.00 3.41
774 868 5.661458 TCTCCGTTCCAAAATAGATGACTC 58.339 41.667 0.00 0.00 0.00 3.36
775 869 5.187967 ACTCTCCGTTCCAAAATAGATGACT 59.812 40.000 0.00 0.00 0.00 3.41
776 870 5.292101 CACTCTCCGTTCCAAAATAGATGAC 59.708 44.000 0.00 0.00 0.00 3.06
777 871 5.419542 CACTCTCCGTTCCAAAATAGATGA 58.580 41.667 0.00 0.00 0.00 2.92
778 872 4.034510 GCACTCTCCGTTCCAAAATAGATG 59.965 45.833 0.00 0.00 0.00 2.90
779 873 4.192317 GCACTCTCCGTTCCAAAATAGAT 58.808 43.478 0.00 0.00 0.00 1.98
780 874 3.007506 TGCACTCTCCGTTCCAAAATAGA 59.992 43.478 0.00 0.00 0.00 1.98
781 875 3.125316 GTGCACTCTCCGTTCCAAAATAG 59.875 47.826 10.32 0.00 0.00 1.73
782 876 3.071479 GTGCACTCTCCGTTCCAAAATA 58.929 45.455 10.32 0.00 0.00 1.40
783 877 1.880027 GTGCACTCTCCGTTCCAAAAT 59.120 47.619 10.32 0.00 0.00 1.82
784 878 1.305201 GTGCACTCTCCGTTCCAAAA 58.695 50.000 10.32 0.00 0.00 2.44
785 879 0.179234 TGTGCACTCTCCGTTCCAAA 59.821 50.000 19.41 0.00 0.00 3.28
786 880 0.179234 TTGTGCACTCTCCGTTCCAA 59.821 50.000 19.41 0.00 0.00 3.53
787 881 0.531974 GTTGTGCACTCTCCGTTCCA 60.532 55.000 19.41 0.00 0.00 3.53
788 882 0.531974 TGTTGTGCACTCTCCGTTCC 60.532 55.000 19.41 0.00 0.00 3.62
789 883 1.512926 ATGTTGTGCACTCTCCGTTC 58.487 50.000 19.41 0.49 0.00 3.95
790 884 1.873591 GAATGTTGTGCACTCTCCGTT 59.126 47.619 19.41 10.11 0.00 4.44
791 885 1.202639 TGAATGTTGTGCACTCTCCGT 60.203 47.619 19.41 1.62 0.00 4.69
792 886 1.511850 TGAATGTTGTGCACTCTCCG 58.488 50.000 19.41 0.00 0.00 4.63
793 887 3.316308 ACTTTGAATGTTGTGCACTCTCC 59.684 43.478 19.41 3.64 0.00 3.71
794 888 4.531332 GACTTTGAATGTTGTGCACTCTC 58.469 43.478 19.41 8.80 0.00 3.20
795 889 3.002656 CGACTTTGAATGTTGTGCACTCT 59.997 43.478 19.41 0.00 0.00 3.24
796 890 3.002246 TCGACTTTGAATGTTGTGCACTC 59.998 43.478 19.41 11.68 0.00 3.51
797 891 2.942376 TCGACTTTGAATGTTGTGCACT 59.058 40.909 19.41 0.00 0.00 4.40
798 892 3.332761 TCGACTTTGAATGTTGTGCAC 57.667 42.857 10.75 10.75 0.00 4.57
799 893 4.362932 TTTCGACTTTGAATGTTGTGCA 57.637 36.364 0.00 0.00 0.00 4.57
800 894 5.458452 TGATTTTCGACTTTGAATGTTGTGC 59.542 36.000 0.00 0.00 0.00 4.57
817 911 2.225491 TGCGTGTACCTGCTTGATTTTC 59.775 45.455 7.78 0.00 0.00 2.29
851 950 0.586802 GAGAAACGTGTGAGGTTGGC 59.413 55.000 0.00 0.00 0.00 4.52
1003 1116 1.814772 TTGCAGCCATTTCGGTTGGG 61.815 55.000 0.00 0.00 45.79 4.12
1011 1124 1.260544 GGTTCTCCTTGCAGCCATTT 58.739 50.000 0.00 0.00 0.00 2.32
1077 1193 1.072505 CCCACGTTGTAGGTTGCCT 59.927 57.895 0.00 0.00 37.71 4.75
1083 1199 2.813908 GCTCGCCCACGTTGTAGG 60.814 66.667 0.00 0.00 41.18 3.18
1217 1335 0.811616 GTCATAGTCGGCCTTGCTGG 60.812 60.000 0.00 0.00 35.34 4.85
1265 1383 1.672881 CATCATTCCCGGAGTTGAAGC 59.327 52.381 0.73 0.00 0.00 3.86
1289 1407 4.514577 CGGTGGCGGTGAGGCTAG 62.515 72.222 0.00 0.00 46.88 3.42
1627 1747 1.135402 GCAAAGCCCAAATACGTCCAG 60.135 52.381 0.00 0.00 0.00 3.86
1648 1769 9.933723 AAATCCTCCAAAATGAATCAGTAAAAG 57.066 29.630 0.00 0.00 0.00 2.27
1881 2008 2.582436 CAGTATGTTCGGGGCGGT 59.418 61.111 0.00 0.00 0.00 5.68
2167 2305 4.940483 TGACCTATCCCTGGATAGATCAG 58.060 47.826 27.43 16.31 46.94 2.90
2173 2311 2.551270 GCCATGACCTATCCCTGGATA 58.449 52.381 5.79 5.79 36.17 2.59
2250 3168 0.977108 AGGAGGAAGAGGAGCAGCAG 60.977 60.000 0.00 0.00 0.00 4.24
2310 3969 1.149854 CATAGCCAGCATGCCTCCA 59.850 57.895 15.66 0.00 31.97 3.86
2318 3977 2.111669 CCCGCATCATAGCCAGCA 59.888 61.111 0.00 0.00 0.00 4.41
2321 3980 4.624364 CCGCCCGCATCATAGCCA 62.624 66.667 0.00 0.00 0.00 4.75
2482 4178 1.515020 CTCTTCTGCCCTCTCCGTG 59.485 63.158 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.