Multiple sequence alignment - TraesCS6A01G235600

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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 TraesCS6A01G235600 chr6A 100.000 3325 0 0 1 3325 445303406 445306730 0.000000e+00 6141
1 TraesCS6A01G235600 chr6A 93.671 79 5 0 1 79 445286249 445286171 5.830000e-23 119
2 TraesCS6A01G235600 chr6D 93.319 1856 77 19 830 2661 308590496 308592328 0.000000e+00 2697
3 TraesCS6A01G235600 chr6D 90.370 675 39 16 2661 3318 308593399 308594064 0.000000e+00 863
4 TraesCS6A01G235600 chr6D 91.643 359 23 7 54 410 308589539 308589892 1.070000e-134 490
5 TraesCS6A01G235600 chr6D 83.738 412 31 16 402 804 308590032 308590416 1.130000e-94 357
6 TraesCS6A01G235600 chr6B 93.364 1763 75 17 829 2589 475730697 475732419 0.000000e+00 2569
7 TraesCS6A01G235600 chr6B 86.924 673 41 20 88 749 475730000 475730636 0.000000e+00 712
8 TraesCS6A01G235600 chr6B 91.202 466 32 6 2856 3320 475814387 475814844 2.820000e-175 625
9 TraesCS6A01G235600 chr6B 92.391 184 14 0 2674 2857 475814110 475814293 2.540000e-66 263


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 TraesCS6A01G235600 chr6A 445303406 445306730 3324 False 6141.00 6141 100.0000 1 3325 1 chr6A.!!$F1 3324
1 TraesCS6A01G235600 chr6D 308589539 308594064 4525 False 1101.75 2697 89.7675 54 3318 4 chr6D.!!$F1 3264
2 TraesCS6A01G235600 chr6B 475730000 475732419 2419 False 1640.50 2569 90.1440 88 2589 2 chr6B.!!$F1 2501
3 TraesCS6A01G235600 chr6B 475814110 475814844 734 False 444.00 625 91.7965 2674 3320 2 chr6B.!!$F2 646

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
589 746 0.035056 CCCCAAGCTGTACTCCAAGG 60.035 60.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 2682 0.107165 AAGCTGGGCCGATCCTTTAC 60.107 55.0 0.0 0.0 34.39 2.01 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
20 21 3.211803 GGGCGTTAAATTTGTGGAGTC 57.788 47.619 0.00 0.00 0.00 3.36
21 22 2.094906 GGGCGTTAAATTTGTGGAGTCC 60.095 50.000 0.73 0.73 0.00 3.85
22 23 2.817844 GGCGTTAAATTTGTGGAGTCCT 59.182 45.455 11.33 0.00 0.00 3.85
23 24 3.119955 GGCGTTAAATTTGTGGAGTCCTC 60.120 47.826 11.33 7.59 0.00 3.71
24 25 3.500680 GCGTTAAATTTGTGGAGTCCTCA 59.499 43.478 11.33 10.57 0.00 3.86
25 26 4.378459 GCGTTAAATTTGTGGAGTCCTCAG 60.378 45.833 13.39 1.96 0.00 3.35
26 27 4.755123 CGTTAAATTTGTGGAGTCCTCAGT 59.245 41.667 13.39 4.98 0.00 3.41
27 28 5.929992 CGTTAAATTTGTGGAGTCCTCAGTA 59.070 40.000 13.39 7.19 0.00 2.74
28 29 6.425721 CGTTAAATTTGTGGAGTCCTCAGTAA 59.574 38.462 13.39 7.32 0.00 2.24
29 30 7.570691 CGTTAAATTTGTGGAGTCCTCAGTAAC 60.571 40.741 13.39 16.40 0.00 2.50
30 31 4.974645 ATTTGTGGAGTCCTCAGTAACA 57.025 40.909 13.39 3.98 0.00 2.41
31 32 4.974645 TTTGTGGAGTCCTCAGTAACAT 57.025 40.909 13.39 0.00 0.00 2.71
32 33 4.974645 TTGTGGAGTCCTCAGTAACATT 57.025 40.909 13.39 0.00 0.00 2.71
33 34 4.974645 TGTGGAGTCCTCAGTAACATTT 57.025 40.909 11.33 0.00 0.00 2.32
34 35 5.304686 TGTGGAGTCCTCAGTAACATTTT 57.695 39.130 11.33 0.00 0.00 1.82
35 36 5.063204 TGTGGAGTCCTCAGTAACATTTTG 58.937 41.667 11.33 0.00 0.00 2.44
36 37 5.063880 GTGGAGTCCTCAGTAACATTTTGT 58.936 41.667 11.33 0.00 0.00 2.83
37 38 6.183361 TGTGGAGTCCTCAGTAACATTTTGTA 60.183 38.462 11.33 0.00 0.00 2.41
38 39 6.708949 GTGGAGTCCTCAGTAACATTTTGTAA 59.291 38.462 11.33 0.00 0.00 2.41
39 40 6.934645 TGGAGTCCTCAGTAACATTTTGTAAG 59.065 38.462 11.33 0.00 0.00 2.34
40 41 6.935208 GGAGTCCTCAGTAACATTTTGTAAGT 59.065 38.462 0.41 0.00 0.00 2.24
41 42 7.444487 GGAGTCCTCAGTAACATTTTGTAAGTT 59.556 37.037 0.41 0.00 0.00 2.66
42 43 8.747538 AGTCCTCAGTAACATTTTGTAAGTTT 57.252 30.769 0.00 0.00 0.00 2.66
43 44 9.185680 AGTCCTCAGTAACATTTTGTAAGTTTT 57.814 29.630 0.00 0.00 0.00 2.43
44 45 9.233232 GTCCTCAGTAACATTTTGTAAGTTTTG 57.767 33.333 0.00 0.00 0.00 2.44
45 46 9.179909 TCCTCAGTAACATTTTGTAAGTTTTGA 57.820 29.630 0.00 0.00 0.00 2.69
46 47 9.796120 CCTCAGTAACATTTTGTAAGTTTTGAA 57.204 29.630 0.00 0.00 0.00 2.69
65 66 8.608844 TTTTGAACTAAAACACCACATTTTGT 57.391 26.923 0.00 0.00 33.48 2.83
66 67 8.499162 TTTTGAACTAAAACACCACATTTTGTG 58.501 29.630 0.62 0.62 39.32 3.33
67 68 5.578727 TGAACTAAAACACCACATTTTGTGC 59.421 36.000 2.09 0.00 46.51 4.57
68 69 5.078411 ACTAAAACACCACATTTTGTGCA 57.922 34.783 2.09 0.00 46.51 4.57
69 70 5.482908 ACTAAAACACCACATTTTGTGCAA 58.517 33.333 2.09 0.00 46.51 4.08
70 71 4.943142 AAAACACCACATTTTGTGCAAG 57.057 36.364 2.09 0.00 46.51 4.01
72 73 3.608316 ACACCACATTTTGTGCAAGTT 57.392 38.095 2.09 0.00 46.51 2.66
74 75 3.683822 ACACCACATTTTGTGCAAGTTTG 59.316 39.130 2.09 0.00 46.51 2.93
77 78 3.063725 CCACATTTTGTGCAAGTTTGTGG 59.936 43.478 17.42 17.42 46.51 4.17
78 79 3.931468 CACATTTTGTGCAAGTTTGTGGA 59.069 39.130 9.13 0.00 41.89 4.02
79 80 4.033129 CACATTTTGTGCAAGTTTGTGGAG 59.967 41.667 9.13 0.00 41.89 3.86
81 82 3.502191 TTTGTGCAAGTTTGTGGAGTC 57.498 42.857 0.00 0.00 0.00 3.36
82 83 1.388547 TGTGCAAGTTTGTGGAGTCC 58.611 50.000 0.73 0.73 0.00 3.85
83 84 1.064758 TGTGCAAGTTTGTGGAGTCCT 60.065 47.619 11.33 0.00 0.00 3.85
85 86 1.211703 TGCAAGTTTGTGGAGTCCTCA 59.788 47.619 11.33 10.57 0.00 3.86
86 87 1.876156 GCAAGTTTGTGGAGTCCTCAG 59.124 52.381 13.39 3.93 0.00 3.35
90 91 0.397941 TTTGTGGAGTCCTCAGCCTG 59.602 55.000 13.39 0.00 0.00 4.85
126 127 1.450134 GCTGGGATCACGATGCACA 60.450 57.895 0.00 0.00 0.00 4.57
236 237 2.475466 GCCACCATGTGATCTGCCG 61.475 63.158 0.00 0.00 35.23 5.69
260 261 0.248215 CCGTTTCGATACGTACGGCT 60.248 55.000 23.47 5.83 43.63 5.52
261 262 1.107720 CGTTTCGATACGTACGGCTC 58.892 55.000 21.06 14.03 36.80 4.70
370 371 2.905996 TTCCCCGGCTTGTCTGCAT 61.906 57.895 0.00 0.00 34.04 3.96
373 374 2.753966 CCCGGCTTGTCTGCATTCG 61.754 63.158 0.00 0.00 34.04 3.34
422 571 9.793252 CTCAAAATTTTCTATTAGATGGGTGTG 57.207 33.333 0.00 0.00 0.00 3.82
447 596 3.865745 CGTACTTCAGATTTGGGCTGTAG 59.134 47.826 0.00 0.00 36.98 2.74
467 616 2.677524 TGTCGTACGGGGACAGGG 60.678 66.667 16.52 0.00 39.36 4.45
510 660 5.030874 GCCGTGGCAAATGTTACTATATC 57.969 43.478 5.89 0.00 41.49 1.63
511 661 4.513692 GCCGTGGCAAATGTTACTATATCA 59.486 41.667 5.89 0.00 41.49 2.15
559 716 4.729868 AGCCAAATTGAAGTAGGACTGTT 58.270 39.130 0.00 0.00 0.00 3.16
560 717 5.876357 AGCCAAATTGAAGTAGGACTGTTA 58.124 37.500 0.00 0.00 0.00 2.41
561 718 6.485171 AGCCAAATTGAAGTAGGACTGTTAT 58.515 36.000 0.00 0.00 0.00 1.89
562 719 6.948309 AGCCAAATTGAAGTAGGACTGTTATT 59.052 34.615 0.00 0.00 0.00 1.40
563 720 7.029563 GCCAAATTGAAGTAGGACTGTTATTG 58.970 38.462 0.00 0.00 0.00 1.90
564 721 7.094377 GCCAAATTGAAGTAGGACTGTTATTGA 60.094 37.037 0.00 0.00 0.00 2.57
565 722 8.792633 CCAAATTGAAGTAGGACTGTTATTGAA 58.207 33.333 0.00 0.00 0.00 2.69
571 728 9.010029 TGAAGTAGGACTGTTATTGAAAAATCC 57.990 33.333 0.00 0.00 0.00 3.01
572 729 7.939784 AGTAGGACTGTTATTGAAAAATCCC 57.060 36.000 0.00 0.00 0.00 3.85
573 730 6.890268 AGTAGGACTGTTATTGAAAAATCCCC 59.110 38.462 0.00 0.00 0.00 4.81
574 731 5.650283 AGGACTGTTATTGAAAAATCCCCA 58.350 37.500 0.00 0.00 0.00 4.96
575 732 6.081356 AGGACTGTTATTGAAAAATCCCCAA 58.919 36.000 0.00 0.00 0.00 4.12
576 733 6.211384 AGGACTGTTATTGAAAAATCCCCAAG 59.789 38.462 0.00 0.00 0.00 3.61
577 734 5.793817 ACTGTTATTGAAAAATCCCCAAGC 58.206 37.500 0.00 0.00 0.00 4.01
578 735 5.543790 ACTGTTATTGAAAAATCCCCAAGCT 59.456 36.000 0.00 0.00 0.00 3.74
579 736 5.792741 TGTTATTGAAAAATCCCCAAGCTG 58.207 37.500 0.00 0.00 0.00 4.24
580 737 5.306678 TGTTATTGAAAAATCCCCAAGCTGT 59.693 36.000 0.00 0.00 0.00 4.40
581 738 6.495181 TGTTATTGAAAAATCCCCAAGCTGTA 59.505 34.615 0.00 0.00 0.00 2.74
582 739 4.864704 TTGAAAAATCCCCAAGCTGTAC 57.135 40.909 0.00 0.00 0.00 2.90
583 740 4.112634 TGAAAAATCCCCAAGCTGTACT 57.887 40.909 0.00 0.00 0.00 2.73
584 741 4.079253 TGAAAAATCCCCAAGCTGTACTC 58.921 43.478 0.00 0.00 0.00 2.59
585 742 2.808906 AAATCCCCAAGCTGTACTCC 57.191 50.000 0.00 0.00 0.00 3.85
586 743 1.668826 AATCCCCAAGCTGTACTCCA 58.331 50.000 0.00 0.00 0.00 3.86
587 744 1.668826 ATCCCCAAGCTGTACTCCAA 58.331 50.000 0.00 0.00 0.00 3.53
588 745 0.984230 TCCCCAAGCTGTACTCCAAG 59.016 55.000 0.00 0.00 0.00 3.61
589 746 0.035056 CCCCAAGCTGTACTCCAAGG 60.035 60.000 0.00 0.00 0.00 3.61
590 747 0.678048 CCCAAGCTGTACTCCAAGGC 60.678 60.000 0.00 0.00 0.00 4.35
607 764 3.281332 GCCCCAGCCTGTATGAAAA 57.719 52.632 0.00 0.00 0.00 2.29
612 783 3.099141 CCCAGCCTGTATGAAAATGGTT 58.901 45.455 0.00 0.00 0.00 3.67
615 786 4.142315 CCAGCCTGTATGAAAATGGTTCTG 60.142 45.833 0.00 0.00 0.00 3.02
628 799 1.014564 GGTTCTGGTAGCACGCACTC 61.015 60.000 0.00 0.00 0.00 3.51
637 808 3.027170 GCACGCACTCATTGGACCG 62.027 63.158 0.00 0.00 0.00 4.79
663 834 6.107901 CCAAAATGGTTGAAAATGGGTAGA 57.892 37.500 0.00 0.00 31.35 2.59
703 881 2.222886 GACACCTGAGCTATCTCGCTA 58.777 52.381 0.00 0.00 42.26 4.26
793 971 2.409064 TAACCTCTGGTGGTCTTCCA 57.591 50.000 0.00 0.00 39.83 3.53
804 982 3.347216 GTGGTCTTCCAACATGTATGCT 58.653 45.455 0.00 0.00 46.15 3.79
814 1029 8.588290 TTCCAACATGTATGCTTAATTTAGGT 57.412 30.769 0.00 0.00 0.00 3.08
933 1170 3.767673 CCTATAAATAGCCCTCACCGCTA 59.232 47.826 0.00 0.00 42.74 4.26
941 1178 0.537188 CCCTCACCGCTACATGACTT 59.463 55.000 0.00 0.00 0.00 3.01
943 1180 1.002366 CTCACCGCTACATGACTTGC 58.998 55.000 0.00 0.00 0.00 4.01
969 1206 1.067821 CTCATCCCGCTCTCCAGTAAC 59.932 57.143 0.00 0.00 0.00 2.50
1165 1402 4.814294 CCCCGGACGCGAAGAAGG 62.814 72.222 15.93 8.52 0.00 3.46
1424 1669 1.251527 GGAACCGTCTCTCTCAGCCA 61.252 60.000 0.00 0.00 0.00 4.75
1425 1670 0.820871 GAACCGTCTCTCTCAGCCAT 59.179 55.000 0.00 0.00 0.00 4.40
1426 1671 2.025155 GAACCGTCTCTCTCAGCCATA 58.975 52.381 0.00 0.00 0.00 2.74
1427 1672 1.686355 ACCGTCTCTCTCAGCCATAG 58.314 55.000 0.00 0.00 0.00 2.23
1428 1673 0.958091 CCGTCTCTCTCAGCCATAGG 59.042 60.000 0.00 0.00 0.00 2.57
1429 1674 0.958091 CGTCTCTCTCAGCCATAGGG 59.042 60.000 0.00 0.00 37.18 3.53
1450 1698 1.756538 CCATACCAGCCCATTTTGGAC 59.243 52.381 0.00 0.00 40.96 4.02
1451 1699 2.624029 CCATACCAGCCCATTTTGGACT 60.624 50.000 0.00 0.00 40.96 3.85
1452 1700 3.372566 CCATACCAGCCCATTTTGGACTA 60.373 47.826 0.00 0.00 40.96 2.59
1453 1701 2.514458 ACCAGCCCATTTTGGACTAG 57.486 50.000 0.00 0.00 40.96 2.57
1533 1781 2.546494 AACAACTCGCACAGCCTGC 61.546 57.895 0.00 0.00 43.21 4.85
1647 1895 1.745264 GGCTCCATCTCCCTCTTCG 59.255 63.158 0.00 0.00 0.00 3.79
1753 2001 3.473647 CGCCATCCCTCTCCTGCA 61.474 66.667 0.00 0.00 0.00 4.41
1769 2017 2.187946 CAGAGGTCCATCGGGCAC 59.812 66.667 0.00 0.00 0.00 5.01
2015 2263 2.108976 ATGGATGCCGCCTACACG 59.891 61.111 0.00 0.00 0.00 4.49
2042 2290 2.872001 GCAGCTCTGTCGTCGTCG 60.872 66.667 0.00 0.00 38.55 5.12
2072 2320 1.284982 CTGACGAGGAGTGTTTGCCG 61.285 60.000 0.00 0.00 0.00 5.69
2220 2468 1.602323 GTCGGGCATGTTTGGGTCA 60.602 57.895 0.00 0.00 0.00 4.02
2309 2557 1.066303 CATCTCCGTCCAGAGTGCTAC 59.934 57.143 0.00 0.00 35.28 3.58
2331 2579 3.492011 CGCAGATGATTTGTGATCGATCA 59.508 43.478 23.99 23.99 0.00 2.92
2382 2631 2.183300 CTCGGCGATTTCCCGTCA 59.817 61.111 11.27 0.00 45.71 4.35
2399 2648 4.227134 ATGCCGCCCTGCTACGAG 62.227 66.667 0.00 0.00 0.00 4.18
2401 2650 4.874977 GCCGCCCTGCTACGAGTC 62.875 72.222 0.00 0.00 0.00 3.36
2402 2651 3.141488 CCGCCCTGCTACGAGTCT 61.141 66.667 0.00 0.00 0.00 3.24
2403 2652 1.822613 CCGCCCTGCTACGAGTCTA 60.823 63.158 0.00 0.00 0.00 2.59
2404 2653 1.355916 CGCCCTGCTACGAGTCTAC 59.644 63.158 0.00 0.00 0.00 2.59
2405 2654 1.355916 GCCCTGCTACGAGTCTACG 59.644 63.158 0.00 0.00 39.31 3.51
2406 2655 1.094073 GCCCTGCTACGAGTCTACGA 61.094 60.000 0.00 0.00 37.03 3.43
2431 2680 0.877743 GGAGACCTGCTGCTGTTTTC 59.122 55.000 0.00 0.00 31.32 2.29
2433 2682 1.534595 GAGACCTGCTGCTGTTTTCTG 59.465 52.381 0.00 0.00 0.00 3.02
2435 2684 2.104792 AGACCTGCTGCTGTTTTCTGTA 59.895 45.455 0.00 0.00 0.00 2.74
2486 2737 8.943909 AACATGTTGGTTCGGTTTTTATTTTA 57.056 26.923 11.07 0.00 0.00 1.52
2497 2757 8.834749 TCGGTTTTTATTTTATTTTTGAGGGG 57.165 30.769 0.00 0.00 0.00 4.79
2498 2758 8.430431 TCGGTTTTTATTTTATTTTTGAGGGGT 58.570 29.630 0.00 0.00 0.00 4.95
2515 2775 7.852971 TGAGGGGTAACAAGTTTTATATTCG 57.147 36.000 0.00 0.00 39.74 3.34
2516 2776 7.622713 TGAGGGGTAACAAGTTTTATATTCGA 58.377 34.615 0.00 0.00 39.74 3.71
2527 2787 6.567050 AGTTTTATATTCGACGTAAGCCAGA 58.433 36.000 0.00 0.00 45.62 3.86
2540 2800 2.918712 AGCCAGAAATACATCTCGGG 57.081 50.000 0.00 0.00 0.00 5.14
2551 2811 1.128200 CATCTCGGGTCATGGGGTTA 58.872 55.000 0.00 0.00 0.00 2.85
2570 2830 0.465460 AACCAAGCCACACATGACGT 60.465 50.000 0.00 0.00 0.00 4.34
2573 2833 1.667830 AAGCCACACATGACGTCCG 60.668 57.895 14.12 6.83 0.00 4.79
2576 2836 2.027073 CCACACATGACGTCCGTGG 61.027 63.158 28.44 25.03 41.06 4.94
2589 2849 0.245539 TCCGTGGCCTAAAGAACGAG 59.754 55.000 12.21 3.49 38.27 4.18
2598 2858 3.250040 GCCTAAAGAACGAGCAAACTTGA 59.750 43.478 0.00 0.00 0.00 3.02
2611 2871 6.597832 AGCAAACTTGACTAGACTATGAGT 57.402 37.500 0.00 0.00 0.00 3.41
2666 3997 9.191995 CAAACATAAAATGACAAGTAAGGGTTC 57.808 33.333 0.00 0.00 0.00 3.62
2706 4037 2.877168 GGCCTCAACATCTCATCATGTC 59.123 50.000 0.00 0.00 35.87 3.06
2742 4073 7.888021 TGTCCTTCCATATATTTGTTGTTGAGT 59.112 33.333 0.00 0.00 0.00 3.41
2749 4080 7.166307 CCATATATTTGTTGTTGAGTCATTGCG 59.834 37.037 0.00 0.00 0.00 4.85
2755 4086 1.003003 TGTTGAGTCATTGCGGATCCA 59.997 47.619 13.41 0.00 0.00 3.41
2834 4178 8.090250 TCTTTGTGTGTATATGTTGGTGTTAC 57.910 34.615 0.00 0.00 0.00 2.50
2867 4305 7.632861 CATCCTTGTCATATATATGTTGGGGA 58.367 38.462 19.78 20.30 35.26 4.81
2876 4314 3.959495 ATATGTTGGGGAAGTGCTCAT 57.041 42.857 0.00 0.00 0.00 2.90
2877 4315 2.610438 ATGTTGGGGAAGTGCTCATT 57.390 45.000 0.00 0.00 0.00 2.57
2878 4316 1.619654 TGTTGGGGAAGTGCTCATTG 58.380 50.000 0.00 0.00 0.00 2.82
2879 4317 1.133513 TGTTGGGGAAGTGCTCATTGT 60.134 47.619 0.00 0.00 0.00 2.71
2880 4318 1.270550 GTTGGGGAAGTGCTCATTGTG 59.729 52.381 0.00 0.00 0.00 3.33
2889 4327 5.449862 GGAAGTGCTCATTGTGTTGTGTTTA 60.450 40.000 0.00 0.00 0.00 2.01
2975 4414 3.365969 GCTCGGTCAATTTTCCATCGTTT 60.366 43.478 0.00 0.00 0.00 3.60
2995 4434 0.739462 CGGGCTGCTACGATTGTTGA 60.739 55.000 10.80 0.00 0.00 3.18
3045 4484 7.979786 AAAAGAAGGATATCACTGGAGAGTA 57.020 36.000 4.83 0.00 0.00 2.59
3077 4516 5.181811 CCAGCTTGTGTGAATTTCTGACATA 59.818 40.000 0.00 0.00 0.00 2.29
3082 4521 7.862372 GCTTGTGTGAATTTCTGACATAAAGAA 59.138 33.333 13.60 0.00 31.85 2.52
3129 4568 3.669939 AATTTGGCCTACATGCTAGGT 57.330 42.857 17.38 1.53 37.06 3.08
3146 4585 7.049799 TGCTAGGTTATGAAGCTTTGTTTTT 57.950 32.000 0.00 0.00 40.27 1.94
3160 4599 6.038271 AGCTTTGTTTTTATGTCGTCTTGAGT 59.962 34.615 0.00 0.00 0.00 3.41
3195 4634 7.935210 TCACCTTTTACTCTTTATTTTCGTCCT 59.065 33.333 0.00 0.00 0.00 3.85
3196 4635 8.228464 CACCTTTTACTCTTTATTTTCGTCCTC 58.772 37.037 0.00 0.00 0.00 3.71
3257 4696 3.414700 GCGTGTTCTCGGCCACAG 61.415 66.667 2.24 0.00 0.00 3.66
3283 4722 5.455525 GTGTTCAACGATCTTTCAAAACCTG 59.544 40.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.094906 GGACTCCACAAATTTAACGCCC 60.095 50.000 0.00 0.00 0.00 6.13
1 2 2.817844 AGGACTCCACAAATTTAACGCC 59.182 45.455 0.00 0.00 0.00 5.68
2 3 3.500680 TGAGGACTCCACAAATTTAACGC 59.499 43.478 0.00 0.00 0.00 4.84
3 4 4.755123 ACTGAGGACTCCACAAATTTAACG 59.245 41.667 0.00 0.00 0.00 3.18
4 5 7.227910 TGTTACTGAGGACTCCACAAATTTAAC 59.772 37.037 0.00 4.17 0.00 2.01
5 6 7.284074 TGTTACTGAGGACTCCACAAATTTAA 58.716 34.615 0.00 0.00 0.00 1.52
6 7 6.833041 TGTTACTGAGGACTCCACAAATTTA 58.167 36.000 0.00 0.00 0.00 1.40
7 8 5.690865 TGTTACTGAGGACTCCACAAATTT 58.309 37.500 0.00 0.00 0.00 1.82
8 9 5.304686 TGTTACTGAGGACTCCACAAATT 57.695 39.130 0.00 0.00 0.00 1.82
9 10 4.974645 TGTTACTGAGGACTCCACAAAT 57.025 40.909 0.00 0.00 0.00 2.32
10 11 4.974645 ATGTTACTGAGGACTCCACAAA 57.025 40.909 0.00 0.00 0.00 2.83
11 12 4.974645 AATGTTACTGAGGACTCCACAA 57.025 40.909 0.00 0.00 0.00 3.33
12 13 4.974645 AAATGTTACTGAGGACTCCACA 57.025 40.909 0.00 0.00 0.00 4.17
13 14 5.063880 ACAAAATGTTACTGAGGACTCCAC 58.936 41.667 0.00 0.00 0.00 4.02
14 15 5.304686 ACAAAATGTTACTGAGGACTCCA 57.695 39.130 0.00 0.00 0.00 3.86
15 16 6.935208 ACTTACAAAATGTTACTGAGGACTCC 59.065 38.462 0.00 0.00 0.00 3.85
16 17 7.964604 ACTTACAAAATGTTACTGAGGACTC 57.035 36.000 0.00 0.00 0.00 3.36
17 18 8.747538 AAACTTACAAAATGTTACTGAGGACT 57.252 30.769 0.00 0.00 0.00 3.85
18 19 9.233232 CAAAACTTACAAAATGTTACTGAGGAC 57.767 33.333 0.00 0.00 0.00 3.85
19 20 9.179909 TCAAAACTTACAAAATGTTACTGAGGA 57.820 29.630 0.00 0.00 0.00 3.71
20 21 9.796120 TTCAAAACTTACAAAATGTTACTGAGG 57.204 29.630 0.00 0.00 0.00 3.86
40 41 8.499162 CACAAAATGTGGTGTTTTAGTTCAAAA 58.501 29.630 2.56 0.00 44.27 2.44
41 42 8.023050 CACAAAATGTGGTGTTTTAGTTCAAA 57.977 30.769 2.56 0.00 44.27 2.69
42 43 7.588143 CACAAAATGTGGTGTTTTAGTTCAA 57.412 32.000 2.56 0.00 44.27 2.69
65 66 1.211703 TGAGGACTCCACAAACTTGCA 59.788 47.619 0.00 0.00 0.00 4.08
66 67 1.876156 CTGAGGACTCCACAAACTTGC 59.124 52.381 0.00 0.00 0.00 4.01
67 68 1.876156 GCTGAGGACTCCACAAACTTG 59.124 52.381 0.00 0.00 0.00 3.16
68 69 1.202818 GGCTGAGGACTCCACAAACTT 60.203 52.381 0.00 0.00 0.00 2.66
69 70 0.398318 GGCTGAGGACTCCACAAACT 59.602 55.000 0.00 0.00 0.00 2.66
70 71 0.398318 AGGCTGAGGACTCCACAAAC 59.602 55.000 0.00 0.00 0.00 2.93
72 73 1.483595 CCAGGCTGAGGACTCCACAA 61.484 60.000 17.94 0.00 0.00 3.33
74 75 2.664081 CCCAGGCTGAGGACTCCAC 61.664 68.421 17.94 0.00 0.00 4.02
77 78 1.194781 TGTTCCCAGGCTGAGGACTC 61.195 60.000 17.94 15.20 0.00 3.36
78 79 1.152030 TGTTCCCAGGCTGAGGACT 60.152 57.895 17.94 0.00 0.00 3.85
79 80 1.003233 GTGTTCCCAGGCTGAGGAC 60.003 63.158 17.94 8.59 0.00 3.85
81 82 1.002868 CTGTGTTCCCAGGCTGAGG 60.003 63.158 17.94 15.52 0.00 3.86
82 83 1.002868 CCTGTGTTCCCAGGCTGAG 60.003 63.158 17.94 1.68 45.19 3.35
83 84 3.160585 CCTGTGTTCCCAGGCTGA 58.839 61.111 17.94 0.00 45.19 4.26
90 91 3.901797 CTCACGGCCCTGTGTTCCC 62.902 68.421 10.17 0.00 40.74 3.97
126 127 4.706962 GCTTATCACCTTCCATGGAACTTT 59.293 41.667 23.63 7.46 0.00 2.66
260 261 3.706373 GGAACAGCTGGGCTCCGA 61.706 66.667 19.93 0.00 36.40 4.55
261 262 3.710722 AGGAACAGCTGGGCTCCG 61.711 66.667 19.93 0.00 36.40 4.63
356 357 2.753966 CCGAATGCAGACAAGCCGG 61.754 63.158 0.00 0.00 32.50 6.13
357 358 2.753966 CCCGAATGCAGACAAGCCG 61.754 63.158 0.00 0.00 0.00 5.52
370 371 2.937873 GCAACAGCTATTACACCCCGAA 60.938 50.000 0.00 0.00 0.00 4.30
373 374 2.289565 GAGCAACAGCTATTACACCCC 58.710 52.381 0.00 0.00 39.10 4.95
395 396 8.971073 ACACCCATCTAATAGAAAATTTTGAGG 58.029 33.333 8.47 0.00 0.00 3.86
422 571 3.125316 CAGCCCAAATCTGAAGTACGAAC 59.875 47.826 0.00 0.00 33.54 3.95
447 596 1.080974 CTGTCCCCGTACGACACAC 60.081 63.158 18.76 8.15 35.35 3.82
467 616 3.554692 CACGACGGGAAGATGCGC 61.555 66.667 0.00 0.00 0.00 6.09
504 654 2.731451 CACATGGCCGTCGTTGATATAG 59.269 50.000 0.00 0.00 0.00 1.31
509 659 1.958715 CACACATGGCCGTCGTTGA 60.959 57.895 0.00 0.00 0.00 3.18
510 660 1.781025 AACACACATGGCCGTCGTTG 61.781 55.000 0.00 0.00 0.00 4.10
511 661 1.098712 AAACACACATGGCCGTCGTT 61.099 50.000 0.00 0.00 0.00 3.85
559 716 6.252995 AGTACAGCTTGGGGATTTTTCAATA 58.747 36.000 0.00 0.00 0.00 1.90
560 717 5.086621 AGTACAGCTTGGGGATTTTTCAAT 58.913 37.500 0.00 0.00 0.00 2.57
561 718 4.479158 AGTACAGCTTGGGGATTTTTCAA 58.521 39.130 0.00 0.00 0.00 2.69
562 719 4.079253 GAGTACAGCTTGGGGATTTTTCA 58.921 43.478 0.00 0.00 0.00 2.69
563 720 3.444034 GGAGTACAGCTTGGGGATTTTTC 59.556 47.826 0.00 0.00 0.00 2.29
564 721 3.181423 TGGAGTACAGCTTGGGGATTTTT 60.181 43.478 0.00 0.00 0.00 1.94
565 722 2.378547 TGGAGTACAGCTTGGGGATTTT 59.621 45.455 0.00 0.00 0.00 1.82
566 723 1.992557 TGGAGTACAGCTTGGGGATTT 59.007 47.619 0.00 0.00 0.00 2.17
567 724 1.668826 TGGAGTACAGCTTGGGGATT 58.331 50.000 0.00 0.00 0.00 3.01
568 725 1.561542 CTTGGAGTACAGCTTGGGGAT 59.438 52.381 0.00 0.00 0.00 3.85
569 726 0.984230 CTTGGAGTACAGCTTGGGGA 59.016 55.000 0.00 0.00 0.00 4.81
570 727 0.035056 CCTTGGAGTACAGCTTGGGG 60.035 60.000 0.00 0.00 0.00 4.96
571 728 0.678048 GCCTTGGAGTACAGCTTGGG 60.678 60.000 0.00 0.00 0.00 4.12
572 729 0.678048 GGCCTTGGAGTACAGCTTGG 60.678 60.000 0.00 0.00 0.00 3.61
573 730 0.678048 GGGCCTTGGAGTACAGCTTG 60.678 60.000 0.84 0.00 0.00 4.01
574 731 1.685820 GGGCCTTGGAGTACAGCTT 59.314 57.895 0.84 0.00 0.00 3.74
575 732 2.301738 GGGGCCTTGGAGTACAGCT 61.302 63.158 0.84 0.00 0.00 4.24
576 733 2.272471 GGGGCCTTGGAGTACAGC 59.728 66.667 0.84 0.00 0.00 4.40
577 734 1.604378 CTGGGGCCTTGGAGTACAG 59.396 63.158 0.84 0.00 0.00 2.74
578 735 2.602676 GCTGGGGCCTTGGAGTACA 61.603 63.158 0.84 0.00 0.00 2.90
579 736 2.272471 GCTGGGGCCTTGGAGTAC 59.728 66.667 0.84 0.00 0.00 2.73
589 746 1.410153 CATTTTCATACAGGCTGGGGC 59.590 52.381 20.34 0.00 37.82 5.80
590 747 2.034124 CCATTTTCATACAGGCTGGGG 58.966 52.381 20.34 7.70 0.00 4.96
606 763 0.036164 TGCGTGCTACCAGAACCATT 59.964 50.000 0.00 0.00 0.00 3.16
607 764 0.673644 GTGCGTGCTACCAGAACCAT 60.674 55.000 0.00 0.00 0.00 3.55
612 783 0.608130 AATGAGTGCGTGCTACCAGA 59.392 50.000 0.00 0.00 0.00 3.86
615 786 0.391130 TCCAATGAGTGCGTGCTACC 60.391 55.000 0.00 0.00 0.00 3.18
628 799 1.204467 CCATTTTGGTCCGGTCCAATG 59.796 52.381 29.81 24.76 45.30 2.82
660 831 4.729227 TGTATCGAGCACCAAACATCTA 57.271 40.909 0.00 0.00 0.00 1.98
663 834 3.623060 GTCATGTATCGAGCACCAAACAT 59.377 43.478 0.00 0.00 0.00 2.71
752 930 8.811378 GGTTATTTCCGACAGTTAGTGTAATAC 58.189 37.037 0.00 0.00 40.56 1.89
753 931 8.752187 AGGTTATTTCCGACAGTTAGTGTAATA 58.248 33.333 0.00 0.00 40.56 0.98
755 933 6.996509 AGGTTATTTCCGACAGTTAGTGTAA 58.003 36.000 0.00 0.00 40.56 2.41
758 936 5.577164 CAGAGGTTATTTCCGACAGTTAGTG 59.423 44.000 0.00 0.00 0.00 2.74
759 937 5.337330 CCAGAGGTTATTTCCGACAGTTAGT 60.337 44.000 0.00 0.00 0.00 2.24
760 938 5.109903 CCAGAGGTTATTTCCGACAGTTAG 58.890 45.833 0.00 0.00 0.00 2.34
761 939 4.529377 ACCAGAGGTTATTTCCGACAGTTA 59.471 41.667 0.00 0.00 27.29 2.24
762 940 3.326880 ACCAGAGGTTATTTCCGACAGTT 59.673 43.478 0.00 0.00 27.29 3.16
763 941 2.904434 ACCAGAGGTTATTTCCGACAGT 59.096 45.455 0.00 0.00 27.29 3.55
764 942 3.262420 CACCAGAGGTTATTTCCGACAG 58.738 50.000 0.00 0.00 31.02 3.51
765 943 2.027561 CCACCAGAGGTTATTTCCGACA 60.028 50.000 0.00 0.00 31.02 4.35
766 944 2.027469 ACCACCAGAGGTTATTTCCGAC 60.027 50.000 0.00 0.00 39.34 4.79
767 945 2.235402 GACCACCAGAGGTTATTTCCGA 59.765 50.000 0.00 0.00 43.38 4.55
768 946 2.236395 AGACCACCAGAGGTTATTTCCG 59.764 50.000 0.00 0.00 43.38 4.30
814 1029 7.658167 TCCGTGTTTCACTAATTTGATGTAAGA 59.342 33.333 0.00 0.00 31.34 2.10
818 1033 6.817765 ATCCGTGTTTCACTAATTTGATGT 57.182 33.333 0.00 0.00 31.34 3.06
825 1040 6.655003 ACAGAATCAATCCGTGTTTCACTAAT 59.345 34.615 0.00 0.00 38.09 1.73
826 1041 5.995282 ACAGAATCAATCCGTGTTTCACTAA 59.005 36.000 0.00 0.00 38.09 2.24
827 1042 5.547465 ACAGAATCAATCCGTGTTTCACTA 58.453 37.500 0.00 0.00 38.09 2.74
933 1170 0.036105 TGAGGCGATGCAAGTCATGT 60.036 50.000 0.00 0.00 35.05 3.21
941 1178 4.916293 GCGGGATGAGGCGATGCA 62.916 66.667 0.00 0.00 0.00 3.96
943 1180 2.356793 GAGCGGGATGAGGCGATG 60.357 66.667 0.00 0.00 0.00 3.84
969 1206 0.032678 AGGAGTGCAGAGAACGTGTG 59.967 55.000 0.00 0.00 0.00 3.82
1071 1308 3.823330 GCGATGGGAGTCGACGGT 61.823 66.667 10.46 0.00 44.06 4.83
1311 1548 3.723235 CTGTGGATCCACTCGGCGG 62.723 68.421 37.92 18.26 46.30 6.13
1429 1674 0.465287 CCAAAATGGGCTGGTATGGC 59.535 55.000 0.00 0.00 32.67 4.40
1438 1683 4.522789 TCAGTTTTCTAGTCCAAAATGGGC 59.477 41.667 10.28 0.00 44.07 5.36
1450 1698 3.988517 GGACCGAACAGTCAGTTTTCTAG 59.011 47.826 0.00 0.00 41.51 2.43
1451 1699 3.385433 TGGACCGAACAGTCAGTTTTCTA 59.615 43.478 0.00 0.00 41.51 2.10
1452 1700 2.169769 TGGACCGAACAGTCAGTTTTCT 59.830 45.455 0.00 0.00 41.51 2.52
1453 1701 2.557317 TGGACCGAACAGTCAGTTTTC 58.443 47.619 0.00 0.00 41.51 2.29
1753 2001 3.461773 CGTGCCCGATGGACCTCT 61.462 66.667 0.00 0.00 35.63 3.69
2015 2263 2.049063 AGAGCTGCAACGTCCGTC 60.049 61.111 1.02 0.00 0.00 4.79
2233 2481 3.955101 CTCCGACTAGAGCGCCGG 61.955 72.222 13.42 13.42 43.02 6.13
2309 2557 3.492011 TGATCGATCACAAATCATCTGCG 59.508 43.478 23.99 0.00 0.00 5.18
2331 2579 1.043816 ACGCATCTGCAGGCTATAGT 58.956 50.000 15.13 4.35 42.21 2.12
2382 2631 4.227134 CTCGTAGCAGGGCGGCAT 62.227 66.667 12.47 0.00 35.83 4.40
2400 2649 2.160205 CAGGTCTCCAACAGTCGTAGA 58.840 52.381 0.00 0.00 0.00 2.59
2401 2650 1.402984 GCAGGTCTCCAACAGTCGTAG 60.403 57.143 0.00 0.00 0.00 3.51
2402 2651 0.601558 GCAGGTCTCCAACAGTCGTA 59.398 55.000 0.00 0.00 0.00 3.43
2403 2652 1.115930 AGCAGGTCTCCAACAGTCGT 61.116 55.000 0.00 0.00 0.00 4.34
2404 2653 0.668706 CAGCAGGTCTCCAACAGTCG 60.669 60.000 0.00 0.00 0.00 4.18
2405 2654 0.952984 GCAGCAGGTCTCCAACAGTC 60.953 60.000 0.00 0.00 0.00 3.51
2406 2655 1.072159 GCAGCAGGTCTCCAACAGT 59.928 57.895 0.00 0.00 0.00 3.55
2431 2680 0.815615 GCTGGGCCGATCCTTTACAG 60.816 60.000 0.00 0.00 34.39 2.74
2433 2682 0.107165 AAGCTGGGCCGATCCTTTAC 60.107 55.000 0.00 0.00 34.39 2.01
2435 2684 0.251787 AAAAGCTGGGCCGATCCTTT 60.252 50.000 0.00 2.10 34.39 3.11
2493 2753 6.536224 CGTCGAATATAAAACTTGTTACCCCT 59.464 38.462 0.00 0.00 0.00 4.79
2497 2757 9.401445 GCTTACGTCGAATATAAAACTTGTTAC 57.599 33.333 0.00 0.00 0.00 2.50
2498 2758 8.594687 GGCTTACGTCGAATATAAAACTTGTTA 58.405 33.333 0.00 0.00 0.00 2.41
2500 2760 6.591062 TGGCTTACGTCGAATATAAAACTTGT 59.409 34.615 0.00 0.00 0.00 3.16
2515 2775 4.441415 CGAGATGTATTTCTGGCTTACGTC 59.559 45.833 0.00 0.00 33.84 4.34
2516 2776 4.360563 CGAGATGTATTTCTGGCTTACGT 58.639 43.478 0.00 0.00 0.00 3.57
2527 2787 2.106511 CCCCATGACCCGAGATGTATTT 59.893 50.000 0.00 0.00 0.00 1.40
2540 2800 1.182667 GGCTTGGTTAACCCCATGAC 58.817 55.000 21.97 7.68 33.60 3.06
2551 2811 0.465460 ACGTCATGTGTGGCTTGGTT 60.465 50.000 0.00 0.00 0.00 3.67
2570 2830 0.245539 CTCGTTCTTTAGGCCACGGA 59.754 55.000 5.01 0.00 33.39 4.69
2573 2833 1.519408 TTGCTCGTTCTTTAGGCCAC 58.481 50.000 5.01 0.00 0.00 5.01
2576 2836 3.250040 TCAAGTTTGCTCGTTCTTTAGGC 59.750 43.478 0.00 0.00 0.00 3.93
2589 2849 7.410942 CGAAACTCATAGTCTAGTCAAGTTTGC 60.411 40.741 12.66 7.10 36.06 3.68
2598 2858 6.660722 CGAATAGCGAAACTCATAGTCTAGT 58.339 40.000 0.00 0.00 44.57 2.57
2624 2884 9.706691 TTTTATGTTTGAAAGTCGAGATACTCT 57.293 29.630 0.00 0.00 0.00 3.24
2633 2893 8.560576 ACTTGTCATTTTATGTTTGAAAGTCG 57.439 30.769 0.00 0.00 0.00 4.18
2666 3997 3.697747 TACGGGTGCAGGGTTCCG 61.698 66.667 9.73 9.73 46.95 4.30
2706 4037 2.536761 TGGAAGGACAACTGGTTACG 57.463 50.000 0.00 0.00 0.00 3.18
2742 4073 3.049708 GATCAGATGGATCCGCAATGA 57.950 47.619 7.39 9.07 45.58 2.57
2834 4178 6.812879 ATATATGACAAGGATGCACACATG 57.187 37.500 0.00 0.00 36.35 3.21
2867 4305 4.454728 AAACACAACACAATGAGCACTT 57.545 36.364 0.00 0.00 0.00 3.16
2947 4385 3.260884 TGGAAAATTGACCGAGCTCTACT 59.739 43.478 12.85 0.00 0.00 2.57
2959 4397 2.094957 GCCCGAAACGATGGAAAATTGA 60.095 45.455 0.00 0.00 0.00 2.57
2961 4399 2.094752 CAGCCCGAAACGATGGAAAATT 60.095 45.455 0.00 0.00 0.00 1.82
2975 4414 0.739462 CAACAATCGTAGCAGCCCGA 60.739 55.000 7.19 7.19 37.51 5.14
2995 4434 6.655078 AATAATGAGGCAACAACAACTCTT 57.345 33.333 0.00 0.00 41.41 2.85
3032 4471 3.456277 GGGACCAATTACTCTCCAGTGAT 59.544 47.826 0.00 0.00 33.62 3.06
3045 4484 1.133513 TCACACAAGCTGGGACCAATT 60.134 47.619 0.00 0.00 0.00 2.32
3077 4516 9.367160 TCCATCTTTCCAGATAAACTTTTCTTT 57.633 29.630 0.00 0.00 37.71 2.52
3082 4521 6.153510 GCCTTCCATCTTTCCAGATAAACTTT 59.846 38.462 0.00 0.00 37.71 2.66
3091 4530 4.813750 AATTTGCCTTCCATCTTTCCAG 57.186 40.909 0.00 0.00 0.00 3.86
3129 4568 8.564574 AGACGACATAAAAACAAAGCTTCATAA 58.435 29.630 0.00 0.00 0.00 1.90
3146 4585 5.707242 AACAGAAGACTCAAGACGACATA 57.293 39.130 0.00 0.00 0.00 2.29
3160 4599 9.847224 ATAAAGAGTAAAAGGTGAAACAGAAGA 57.153 29.630 0.00 0.00 39.98 2.87
3195 4634 0.308684 ACTTCGTTGCGTAGTGTCGA 59.691 50.000 0.35 0.00 36.26 4.20
3196 4635 1.903139 CTACTTCGTTGCGTAGTGTCG 59.097 52.381 10.25 0.00 37.94 4.35
3246 4685 1.069090 GAACACACTGTGGCCGAGA 59.931 57.895 13.77 0.00 37.94 4.04
3257 4696 5.229260 GGTTTTGAAAGATCGTTGAACACAC 59.771 40.000 10.74 1.89 0.00 3.82
3283 4722 4.995124 TCTACAAACTGGACTAATCTCGC 58.005 43.478 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.