Multiple sequence alignment - TraesCS3B01G276200

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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 TraesCS3B01G276200 chr3B 100.000 3785 0 0 1 3785 446168005 446171789 0.000000e+00 6990.0
1 TraesCS3B01G276200 chr3D 93.564 2626 140 19 716 3333 346639533 346642137 0.000000e+00 3886.0
2 TraesCS3B01G276200 chr3D 90.805 174 12 3 3454 3627 346642377 346642546 2.940000e-56 230.0
3 TraesCS3B01G276200 chr3A 93.082 2631 151 18 716 3333 457088853 457086241 0.000000e+00 3821.0
4 TraesCS3B01G276200 chr3A 89.254 335 29 5 3454 3785 457086158 457085828 2.720000e-111 412.0
5 TraesCS3B01G276200 chr3A 79.487 156 25 5 3579 3730 466477948 466478100 1.860000e-18 104.0
6 TraesCS3B01G276200 chr2A 93.231 650 34 2 1 640 760108294 760108943 0.000000e+00 948.0
7 TraesCS3B01G276200 chr2A 75.926 486 103 10 166 639 67964077 67964560 1.760000e-58 237.0
8 TraesCS3B01G276200 chr1B 92.473 651 38 3 1 641 493733735 493734384 0.000000e+00 920.0
9 TraesCS3B01G276200 chr1D 87.403 643 66 7 11 640 366691028 366690388 0.000000e+00 725.0
10 TraesCS3B01G276200 chr7D 87.097 651 69 10 2 639 478217175 478217823 0.000000e+00 723.0
11 TraesCS3B01G276200 chr5D 80.215 652 110 11 3 640 351952983 351952337 4.430000e-129 472.0
12 TraesCS3B01G276200 chr2D 80.903 487 79 6 170 645 75695576 75695093 4.620000e-99 372.0
13 TraesCS3B01G276200 chr6D 80.263 456 67 16 199 643 22093457 22093900 4.720000e-84 322.0
14 TraesCS3B01G276200 chr4D 86.697 218 23 6 425 639 87031769 87031983 1.760000e-58 237.0
15 TraesCS3B01G276200 chr7A 80.503 159 24 5 3579 3733 709984639 709984484 8.590000e-22 115.0
16 TraesCS3B01G276200 chr4A 80.503 159 24 5 3579 3733 542490041 542489886 8.590000e-22 115.0
17 TraesCS3B01G276200 chr1A 80.769 156 23 5 3579 3730 307482742 307482894 8.590000e-22 115.0
18 TraesCS3B01G276200 chr2B 79.433 141 23 4 3594 3730 699117815 699117677 1.120000e-15 95.3


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 TraesCS3B01G276200 chr3B 446168005 446171789 3784 False 6990.0 6990 100.0000 1 3785 1 chr3B.!!$F1 3784
1 TraesCS3B01G276200 chr3D 346639533 346642546 3013 False 2058.0 3886 92.1845 716 3627 2 chr3D.!!$F1 2911
2 TraesCS3B01G276200 chr3A 457085828 457088853 3025 True 2116.5 3821 91.1680 716 3785 2 chr3A.!!$R1 3069
3 TraesCS3B01G276200 chr2A 760108294 760108943 649 False 948.0 948 93.2310 1 640 1 chr2A.!!$F2 639
4 TraesCS3B01G276200 chr1B 493733735 493734384 649 False 920.0 920 92.4730 1 641 1 chr1B.!!$F1 640
5 TraesCS3B01G276200 chr1D 366690388 366691028 640 True 725.0 725 87.4030 11 640 1 chr1D.!!$R1 629
6 TraesCS3B01G276200 chr7D 478217175 478217823 648 False 723.0 723 87.0970 2 639 1 chr7D.!!$F1 637
7 TraesCS3B01G276200 chr5D 351952337 351952983 646 True 472.0 472 80.2150 3 640 1 chr5D.!!$R1 637

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
672 684 0.031585 GGAGAAAACCAAACACGCCC 59.968 55.0 0.0 0.0 0.0 6.13 F
2385 2407 0.034337 TGTGGGAGGCGTACAAGTTC 59.966 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 2518 0.107456 AGTTGTCAGGCTCCACTGTG 59.893 55.0 0.0 0.0 39.48 3.66 R
3447 3671 0.186873 CCCCTGCCCAGCATAATCTT 59.813 55.0 0.0 0.0 38.13 2.40 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
70 71 7.011389 CGATGTGCTTCATTAAGAGGTATTTGA 59.989 37.037 0.00 0.00 36.83 2.69
86 87 7.856415 AGGTATTTGAAAGAGCTAGAGATTGT 58.144 34.615 2.06 0.00 0.00 2.71
288 290 2.030823 GCTGTTGTTTTTGAAGGCTTGC 59.969 45.455 3.46 0.00 0.00 4.01
373 375 4.808414 ATCTGAACGACTTGGAGATTGA 57.192 40.909 0.00 0.00 0.00 2.57
654 666 2.523168 AAAAACCAGGCCCGGTGG 60.523 61.111 12.64 10.02 39.95 4.61
655 667 3.076217 AAAAACCAGGCCCGGTGGA 62.076 57.895 12.64 0.00 39.95 4.02
656 668 2.994643 AAAAACCAGGCCCGGTGGAG 62.995 60.000 12.64 0.00 39.95 3.86
657 669 4.974438 AACCAGGCCCGGTGGAGA 62.974 66.667 12.64 0.00 39.95 3.71
658 670 4.974438 ACCAGGCCCGGTGGAGAA 62.974 66.667 10.77 0.00 38.07 2.87
659 671 3.646715 CCAGGCCCGGTGGAGAAA 61.647 66.667 3.32 0.00 37.23 2.52
660 672 2.434331 CAGGCCCGGTGGAGAAAA 59.566 61.111 0.00 0.00 0.00 2.29
661 673 1.971695 CAGGCCCGGTGGAGAAAAC 60.972 63.158 0.00 0.00 0.00 2.43
662 674 2.675423 GGCCCGGTGGAGAAAACC 60.675 66.667 0.00 0.00 0.00 3.27
663 675 2.114411 GCCCGGTGGAGAAAACCA 59.886 61.111 0.00 0.00 37.57 3.67
664 676 1.529713 GCCCGGTGGAGAAAACCAA 60.530 57.895 0.00 0.00 41.87 3.67
665 677 1.110518 GCCCGGTGGAGAAAACCAAA 61.111 55.000 0.00 0.00 41.87 3.28
666 678 0.671796 CCCGGTGGAGAAAACCAAAC 59.328 55.000 0.00 0.00 41.87 2.93
667 679 1.394618 CCGGTGGAGAAAACCAAACA 58.605 50.000 0.00 0.00 41.87 2.83
668 680 1.066454 CCGGTGGAGAAAACCAAACAC 59.934 52.381 0.00 0.00 41.87 3.32
669 681 1.268335 CGGTGGAGAAAACCAAACACG 60.268 52.381 0.00 0.00 41.87 4.49
670 682 1.535226 GGTGGAGAAAACCAAACACGC 60.535 52.381 0.00 0.00 41.87 5.34
671 683 0.741915 TGGAGAAAACCAAACACGCC 59.258 50.000 0.00 0.00 36.96 5.68
672 684 0.031585 GGAGAAAACCAAACACGCCC 59.968 55.000 0.00 0.00 0.00 6.13
673 685 0.031585 GAGAAAACCAAACACGCCCC 59.968 55.000 0.00 0.00 0.00 5.80
674 686 0.396556 AGAAAACCAAACACGCCCCT 60.397 50.000 0.00 0.00 0.00 4.79
675 687 1.133730 AGAAAACCAAACACGCCCCTA 60.134 47.619 0.00 0.00 0.00 3.53
676 688 1.268625 GAAAACCAAACACGCCCCTAG 59.731 52.381 0.00 0.00 0.00 3.02
677 689 1.176619 AAACCAAACACGCCCCTAGC 61.177 55.000 0.00 0.00 38.52 3.42
678 690 2.033448 CCAAACACGCCCCTAGCA 59.967 61.111 0.00 0.00 44.04 3.49
679 691 1.602323 CCAAACACGCCCCTAGCAA 60.602 57.895 0.00 0.00 44.04 3.91
680 692 0.965363 CCAAACACGCCCCTAGCAAT 60.965 55.000 0.00 0.00 44.04 3.56
681 693 1.680555 CCAAACACGCCCCTAGCAATA 60.681 52.381 0.00 0.00 44.04 1.90
682 694 1.670811 CAAACACGCCCCTAGCAATAG 59.329 52.381 0.00 0.00 44.04 1.73
683 695 0.463833 AACACGCCCCTAGCAATAGC 60.464 55.000 0.00 0.00 44.04 2.97
684 696 1.146041 CACGCCCCTAGCAATAGCA 59.854 57.895 0.00 0.00 45.49 3.49
685 697 0.882042 CACGCCCCTAGCAATAGCAG 60.882 60.000 0.00 0.00 45.49 4.24
686 698 1.338136 ACGCCCCTAGCAATAGCAGT 61.338 55.000 0.00 0.00 45.49 4.40
687 699 0.601311 CGCCCCTAGCAATAGCAGTC 60.601 60.000 0.00 0.00 45.49 3.51
688 700 0.761802 GCCCCTAGCAATAGCAGTCT 59.238 55.000 0.00 0.00 45.49 3.24
689 701 1.971357 GCCCCTAGCAATAGCAGTCTA 59.029 52.381 0.00 0.00 45.49 2.59
690 702 2.028567 GCCCCTAGCAATAGCAGTCTAG 60.029 54.545 0.00 0.00 45.49 2.43
691 703 2.028567 CCCCTAGCAATAGCAGTCTAGC 60.029 54.545 0.00 0.00 45.49 3.42
692 704 2.630098 CCCTAGCAATAGCAGTCTAGCA 59.370 50.000 0.00 0.00 45.49 3.49
693 705 3.305950 CCCTAGCAATAGCAGTCTAGCAG 60.306 52.174 0.00 0.00 45.49 4.24
694 706 3.320541 CCTAGCAATAGCAGTCTAGCAGT 59.679 47.826 0.00 0.00 45.49 4.40
695 707 3.902881 AGCAATAGCAGTCTAGCAGTT 57.097 42.857 0.00 0.00 45.49 3.16
696 708 4.213564 AGCAATAGCAGTCTAGCAGTTT 57.786 40.909 0.00 0.00 45.49 2.66
697 709 4.187694 AGCAATAGCAGTCTAGCAGTTTC 58.812 43.478 0.00 0.00 45.49 2.78
698 710 4.081198 AGCAATAGCAGTCTAGCAGTTTCT 60.081 41.667 0.00 0.00 45.49 2.52
699 711 4.269844 GCAATAGCAGTCTAGCAGTTTCTC 59.730 45.833 0.00 0.00 41.58 2.87
700 712 5.414360 CAATAGCAGTCTAGCAGTTTCTCA 58.586 41.667 0.00 0.00 36.85 3.27
701 713 5.667539 ATAGCAGTCTAGCAGTTTCTCAA 57.332 39.130 0.00 0.00 36.85 3.02
702 714 4.342862 AGCAGTCTAGCAGTTTCTCAAA 57.657 40.909 0.00 0.00 36.85 2.69
703 715 4.708177 AGCAGTCTAGCAGTTTCTCAAAA 58.292 39.130 0.00 0.00 36.85 2.44
704 716 5.126067 AGCAGTCTAGCAGTTTCTCAAAAA 58.874 37.500 0.00 0.00 36.85 1.94
947 969 2.590575 AAACACCCACGCTGACCG 60.591 61.111 0.00 0.00 44.21 4.79
973 995 2.679996 GCCGCCCACCCAAATCTT 60.680 61.111 0.00 0.00 0.00 2.40
1067 1089 4.473520 CGCCACCATCTCCCGCTT 62.474 66.667 0.00 0.00 0.00 4.68
1161 1183 2.284995 AGCTCCTCCCACCAGGAC 60.285 66.667 0.00 0.00 40.93 3.85
1190 1212 2.028130 AGCCTTCTCGTCGATTCATCT 58.972 47.619 0.00 0.00 0.00 2.90
1356 1378 4.870636 TGGTGGATTTCTATGCCAAGAAT 58.129 39.130 0.00 0.00 35.48 2.40
1401 1423 0.389817 TCTTTGACGAGATGCCGGTG 60.390 55.000 1.90 0.00 0.00 4.94
1443 1465 4.119862 ACTGTTTGATCACCGGATATTCG 58.880 43.478 9.46 0.00 32.67 3.34
1446 1468 5.179533 TGTTTGATCACCGGATATTCGAAA 58.820 37.500 9.46 0.00 32.67 3.46
1460 1482 2.401583 TCGAAATCTGGTGATGTGGG 57.598 50.000 0.00 0.00 32.44 4.61
1472 1494 0.181350 GATGTGGGTAAGGCCAGGAG 59.819 60.000 5.01 0.00 39.65 3.69
1565 1587 2.310538 GGAATTCCGGGAAGCATTGAT 58.689 47.619 15.72 0.00 0.00 2.57
1752 1774 6.315144 TGATGGAAATGTATGTAAAGTGTCGG 59.685 38.462 0.00 0.00 0.00 4.79
1784 1806 1.068417 CACGTCGGGAGTTTGACCA 59.932 57.895 0.00 0.00 0.00 4.02
1863 1885 0.107945 GCAGGCCACTCGAATCTCTT 60.108 55.000 5.01 0.00 0.00 2.85
1886 1908 3.064900 ACTGTTTGAGAGGATGAAGGC 57.935 47.619 0.00 0.00 0.00 4.35
2067 2089 2.676121 TGCGGGCATGTTGGAAGG 60.676 61.111 0.00 0.00 0.00 3.46
2075 2097 2.543797 ATGTTGGAAGGGCCCGGAA 61.544 57.895 18.44 4.81 34.97 4.30
2112 2134 2.962421 GGAACAAAAAGGGGTCATCACA 59.038 45.455 0.00 0.00 0.00 3.58
2151 2173 1.339291 GGCCTAGCAATGAATGGCTTC 59.661 52.381 0.00 0.00 42.84 3.86
2170 2192 1.940334 GCAGAAGATGCGATCAGCC 59.060 57.895 7.00 0.00 46.99 4.85
2193 2215 6.738453 GCCTGTATGAAAATATGGCGGAAAAT 60.738 38.462 0.00 0.00 0.00 1.82
2196 2218 5.867903 ATGAAAATATGGCGGAAAATGGA 57.132 34.783 0.00 0.00 0.00 3.41
2208 2230 2.460669 GAAAATGGAGTCCAGCCCAAT 58.539 47.619 18.69 0.00 36.75 3.16
2223 2245 2.555199 CCCAATGAGATCACCTTCGTC 58.445 52.381 0.00 0.00 0.00 4.20
2328 2350 1.757306 CCCTCAAGTGGAGCACTGT 59.243 57.895 0.00 0.00 44.62 3.55
2385 2407 0.034337 TGTGGGAGGCGTACAAGTTC 59.966 55.000 0.00 0.00 0.00 3.01
2415 2437 0.462225 TGGAAGTCGAACCAAACGCA 60.462 50.000 5.03 0.00 32.93 5.24
2430 2452 1.807165 CGCAGTGATCTGGACCACG 60.807 63.158 0.00 0.00 41.57 4.94
2439 2461 3.231889 CTGGACCACGCTGCTCAGT 62.232 63.158 0.00 0.00 0.00 3.41
2450 2472 3.887783 GCTCAGTTCCTGCAGAGC 58.112 61.111 17.39 11.66 45.50 4.09
2469 2491 1.471119 CCCATGCTGATGTTGAGCTT 58.529 50.000 0.00 0.00 37.35 3.74
2472 2494 1.201414 CATGCTGATGTTGAGCTTGCA 59.799 47.619 0.00 0.00 35.55 4.08
2497 2519 4.441695 CCGCGAGCAAGCTCCTCA 62.442 66.667 8.23 0.00 39.77 3.86
2500 2522 2.099431 GCGAGCAAGCTCCTCACAG 61.099 63.158 15.81 2.65 39.77 3.66
2508 2530 4.126908 CTCCTCACAGTGGAGCCT 57.873 61.111 0.00 0.00 43.67 4.58
2544 2566 4.142790 TCTACGTCCTCCTGTCCAATATC 58.857 47.826 0.00 0.00 0.00 1.63
2643 2665 4.019321 TCTGCCTACAGTTGGATAAAGCTT 60.019 41.667 5.05 0.00 44.77 3.74
2652 2674 5.183713 CAGTTGGATAAAGCTTGATGGTGAA 59.816 40.000 0.00 0.00 0.00 3.18
2688 2710 0.767998 TGCAAGACACATACCACCCA 59.232 50.000 0.00 0.00 0.00 4.51
2690 2712 2.235016 GCAAGACACATACCACCCAAA 58.765 47.619 0.00 0.00 0.00 3.28
2706 2728 5.393461 CCACCCAAAATCAGCTGAGATTTAC 60.393 44.000 22.96 0.00 44.96 2.01
2713 2735 2.486592 TCAGCTGAGATTTACGACGTCA 59.513 45.455 13.74 0.00 0.00 4.35
2734 2756 4.660938 ACGGCTTGGGGTTGCTCC 62.661 66.667 0.00 0.00 0.00 4.70
2736 2758 2.966732 CGGCTTGGGGTTGCTCCTA 61.967 63.158 0.00 0.00 36.25 2.94
2742 2764 2.187163 GGGTTGCTCCTAGACCGC 59.813 66.667 0.00 0.00 34.22 5.68
2757 2779 4.193334 CGCGCCGACTCTGATCCA 62.193 66.667 0.00 0.00 0.00 3.41
2787 2809 3.471680 AGTTTCAGAGCTCTGTTGAACC 58.528 45.455 36.32 20.23 44.12 3.62
2797 2819 7.592903 CAGAGCTCTGTTGAACCTTTATTTTTC 59.407 37.037 31.71 0.00 39.09 2.29
2799 2821 7.781056 AGCTCTGTTGAACCTTTATTTTTCAA 58.219 30.769 0.00 0.00 37.00 2.69
2849 2871 6.211184 AGGAACACAAAGCATTCCATTGATTA 59.789 34.615 5.13 0.00 43.75 1.75
2851 2873 6.839124 ACACAAAGCATTCCATTGATTAGA 57.161 33.333 0.00 0.00 0.00 2.10
2859 2881 3.459232 TCCATTGATTAGACGAGCTGG 57.541 47.619 0.00 0.00 0.00 4.85
2863 2885 4.437239 CATTGATTAGACGAGCTGGACTT 58.563 43.478 6.00 0.00 0.00 3.01
2876 2898 0.535780 TGGACTTGCCAGCAGACAAG 60.536 55.000 3.61 3.61 46.91 3.16
2890 2912 7.467623 CCAGCAGACAAGTTCTTTTACATATC 58.532 38.462 0.00 0.00 28.96 1.63
2925 2948 7.982761 ATCAAGCCAAATCTGATAGATTCTC 57.017 36.000 4.68 0.00 43.67 2.87
2926 2949 6.892485 TCAAGCCAAATCTGATAGATTCTCA 58.108 36.000 4.68 0.00 43.67 3.27
2927 2950 7.341030 TCAAGCCAAATCTGATAGATTCTCAA 58.659 34.615 4.68 0.00 43.67 3.02
2928 2951 7.997223 TCAAGCCAAATCTGATAGATTCTCAAT 59.003 33.333 4.68 0.00 43.67 2.57
2929 2952 8.630917 CAAGCCAAATCTGATAGATTCTCAATT 58.369 33.333 4.68 0.00 43.67 2.32
2930 2953 8.393671 AGCCAAATCTGATAGATTCTCAATTC 57.606 34.615 4.68 0.00 43.67 2.17
2931 2954 7.447853 AGCCAAATCTGATAGATTCTCAATTCC 59.552 37.037 4.68 0.00 43.67 3.01
2932 2955 7.230108 GCCAAATCTGATAGATTCTCAATTCCA 59.770 37.037 4.68 0.00 43.67 3.53
2933 2956 9.298250 CCAAATCTGATAGATTCTCAATTCCAT 57.702 33.333 4.68 0.00 43.67 3.41
2981 3005 7.230510 AGAGTGTGCAGAAATATTACAAAACCA 59.769 33.333 0.00 0.00 0.00 3.67
2991 3015 7.524717 AATATTACAAAACCAGTGAGCAAGT 57.475 32.000 0.00 0.00 0.00 3.16
2993 3017 3.782889 ACAAAACCAGTGAGCAAGTTC 57.217 42.857 0.00 0.00 0.00 3.01
3002 3026 4.246458 CAGTGAGCAAGTTCCTACCTTAC 58.754 47.826 0.00 0.00 0.00 2.34
3005 3029 3.251571 GAGCAAGTTCCTACCTTACACG 58.748 50.000 0.00 0.00 0.00 4.49
3024 3048 2.816087 ACGACTGAAAAGCTGATTGCAT 59.184 40.909 0.00 0.00 45.94 3.96
3030 3054 5.142061 TGAAAAGCTGATTGCATCACATT 57.858 34.783 0.00 0.00 45.94 2.71
3111 3136 4.813697 GCAGTCATATCCCTTCTCTTTGAC 59.186 45.833 0.00 0.00 33.84 3.18
3117 3142 6.613271 TCATATCCCTTCTCTTTGACTAGCTT 59.387 38.462 0.00 0.00 0.00 3.74
3118 3143 4.810191 TCCCTTCTCTTTGACTAGCTTC 57.190 45.455 0.00 0.00 0.00 3.86
3131 3156 6.861065 TGACTAGCTTCGTTTCTTTCAAAT 57.139 33.333 0.00 0.00 0.00 2.32
3139 3164 8.134895 AGCTTCGTTTCTTTCAAATCACAATAA 58.865 29.630 0.00 0.00 0.00 1.40
3140 3165 8.207906 GCTTCGTTTCTTTCAAATCACAATAAC 58.792 33.333 0.00 0.00 0.00 1.89
3143 3171 7.646130 TCGTTTCTTTCAAATCACAATAACCAC 59.354 33.333 0.00 0.00 0.00 4.16
3171 3199 8.470002 AGAATATAAACTTCCAGACATTTTGCC 58.530 33.333 0.00 0.00 0.00 4.52
3172 3200 7.961326 ATATAAACTTCCAGACATTTTGCCT 57.039 32.000 0.00 0.00 0.00 4.75
3173 3201 4.326504 AAACTTCCAGACATTTTGCCTG 57.673 40.909 0.00 0.00 0.00 4.85
3200 3228 9.434420 CTCTATTTTCAGAATATCCTCCATCAC 57.566 37.037 0.00 0.00 0.00 3.06
3201 3229 9.163894 TCTATTTTCAGAATATCCTCCATCACT 57.836 33.333 0.00 0.00 0.00 3.41
3230 3258 4.943093 GGCATTTGGGCAATTGATAAGTTT 59.057 37.500 10.34 0.00 42.77 2.66
3234 3262 7.495279 GCATTTGGGCAATTGATAAGTTTCATA 59.505 33.333 10.34 0.00 0.00 2.15
3235 3263 9.550406 CATTTGGGCAATTGATAAGTTTCATAT 57.450 29.630 10.34 0.00 0.00 1.78
3276 3305 6.861572 GCAGTTCTCCAAATAACCTTACAAAC 59.138 38.462 0.00 0.00 0.00 2.93
3293 3322 3.068165 ACAAACTTGCACTTTAGGAAGCC 59.932 43.478 0.00 0.00 40.18 4.35
3300 3361 2.354821 GCACTTTAGGAAGCCATAACCG 59.645 50.000 0.00 0.00 36.29 4.44
3309 3370 3.192633 GGAAGCCATAACCGTGACAAATT 59.807 43.478 0.00 0.00 0.00 1.82
3316 3377 3.518634 AACCGTGACAAATTTGCACTT 57.481 38.095 27.54 19.48 34.96 3.16
3334 3395 4.379918 GCACTTTAGAAAGCAATGACCTCC 60.380 45.833 1.86 0.00 39.63 4.30
3336 3397 2.024176 TAGAAAGCAATGACCTCCGC 57.976 50.000 0.00 0.00 0.00 5.54
3341 3402 2.464459 GCAATGACCTCCGCCTTCG 61.464 63.158 0.00 0.00 0.00 3.79
3353 3577 4.178540 CTCCGCCTTCGTCTAATTAACAA 58.821 43.478 0.00 0.00 0.00 2.83
3362 3586 8.342634 CCTTCGTCTAATTAACAACATATTGGG 58.657 37.037 0.00 0.00 40.42 4.12
3366 3590 8.779303 CGTCTAATTAACAACATATTGGGCATA 58.221 33.333 0.00 0.00 40.42 3.14
3369 3593 9.897744 CTAATTAACAACATATTGGGCATAGTG 57.102 33.333 0.00 0.00 40.42 2.74
3374 3598 6.841601 ACAACATATTGGGCATAGTGTATCT 58.158 36.000 0.00 0.00 40.42 1.98
3375 3599 6.712095 ACAACATATTGGGCATAGTGTATCTG 59.288 38.462 0.00 0.00 40.42 2.90
3377 3601 5.013495 ACATATTGGGCATAGTGTATCTGCT 59.987 40.000 0.00 0.00 36.18 4.24
3378 3602 6.213397 ACATATTGGGCATAGTGTATCTGCTA 59.787 38.462 0.00 0.00 36.18 3.49
3379 3603 4.336889 TTGGGCATAGTGTATCTGCTAC 57.663 45.455 0.00 0.00 36.18 3.58
3380 3604 3.304829 TGGGCATAGTGTATCTGCTACA 58.695 45.455 0.00 0.00 38.02 2.74
3381 3605 3.709141 TGGGCATAGTGTATCTGCTACAA 59.291 43.478 0.00 0.00 41.93 2.41
3382 3606 4.347876 TGGGCATAGTGTATCTGCTACAAT 59.652 41.667 0.00 0.00 41.93 2.71
3383 3607 5.163205 TGGGCATAGTGTATCTGCTACAATT 60.163 40.000 0.00 0.00 41.93 2.32
3384 3608 5.409826 GGGCATAGTGTATCTGCTACAATTC 59.590 44.000 0.00 0.00 41.93 2.17
3385 3609 5.409826 GGCATAGTGTATCTGCTACAATTCC 59.590 44.000 0.00 0.00 41.93 3.01
3386 3610 6.226787 GCATAGTGTATCTGCTACAATTCCT 58.773 40.000 0.00 0.00 41.93 3.36
3387 3611 6.367422 GCATAGTGTATCTGCTACAATTCCTC 59.633 42.308 0.00 0.00 41.93 3.71
3388 3612 7.665690 CATAGTGTATCTGCTACAATTCCTCT 58.334 38.462 0.00 0.00 41.93 3.69
3389 3613 6.552445 AGTGTATCTGCTACAATTCCTCTT 57.448 37.500 0.00 0.00 41.93 2.85
3390 3614 6.951971 AGTGTATCTGCTACAATTCCTCTTT 58.048 36.000 0.00 0.00 41.93 2.52
3391 3615 7.398024 AGTGTATCTGCTACAATTCCTCTTTT 58.602 34.615 0.00 0.00 41.93 2.27
3392 3616 7.550906 AGTGTATCTGCTACAATTCCTCTTTTC 59.449 37.037 0.00 0.00 41.93 2.29
3393 3617 6.823689 TGTATCTGCTACAATTCCTCTTTTCC 59.176 38.462 0.00 0.00 37.40 3.13
3394 3618 4.253685 TCTGCTACAATTCCTCTTTTCCG 58.746 43.478 0.00 0.00 0.00 4.30
3395 3619 2.747446 TGCTACAATTCCTCTTTTCCGC 59.253 45.455 0.00 0.00 0.00 5.54
3396 3620 2.747446 GCTACAATTCCTCTTTTCCGCA 59.253 45.455 0.00 0.00 0.00 5.69
3397 3621 3.181506 GCTACAATTCCTCTTTTCCGCAG 60.182 47.826 0.00 0.00 0.00 5.18
3398 3622 2.863809 ACAATTCCTCTTTTCCGCAGT 58.136 42.857 0.00 0.00 0.00 4.40
3399 3623 3.222603 ACAATTCCTCTTTTCCGCAGTT 58.777 40.909 0.00 0.00 0.00 3.16
3400 3624 3.636764 ACAATTCCTCTTTTCCGCAGTTT 59.363 39.130 0.00 0.00 0.00 2.66
3401 3625 4.229876 CAATTCCTCTTTTCCGCAGTTTC 58.770 43.478 0.00 0.00 0.00 2.78
3402 3626 2.631160 TCCTCTTTTCCGCAGTTTCA 57.369 45.000 0.00 0.00 0.00 2.69
3403 3627 3.140325 TCCTCTTTTCCGCAGTTTCAT 57.860 42.857 0.00 0.00 0.00 2.57
3404 3628 3.486383 TCCTCTTTTCCGCAGTTTCATT 58.514 40.909 0.00 0.00 0.00 2.57
3405 3629 3.502211 TCCTCTTTTCCGCAGTTTCATTC 59.498 43.478 0.00 0.00 0.00 2.67
3406 3630 3.503748 CCTCTTTTCCGCAGTTTCATTCT 59.496 43.478 0.00 0.00 0.00 2.40
3407 3631 4.022849 CCTCTTTTCCGCAGTTTCATTCTT 60.023 41.667 0.00 0.00 0.00 2.52
3408 3632 5.181245 CCTCTTTTCCGCAGTTTCATTCTTA 59.819 40.000 0.00 0.00 0.00 2.10
3409 3633 6.241207 TCTTTTCCGCAGTTTCATTCTTAG 57.759 37.500 0.00 0.00 0.00 2.18
3410 3634 5.995282 TCTTTTCCGCAGTTTCATTCTTAGA 59.005 36.000 0.00 0.00 0.00 2.10
3411 3635 5.607119 TTTCCGCAGTTTCATTCTTAGAC 57.393 39.130 0.00 0.00 0.00 2.59
3412 3636 3.250744 TCCGCAGTTTCATTCTTAGACG 58.749 45.455 0.00 0.00 0.00 4.18
3413 3637 2.993899 CCGCAGTTTCATTCTTAGACGT 59.006 45.455 0.00 0.00 0.00 4.34
3414 3638 4.082625 TCCGCAGTTTCATTCTTAGACGTA 60.083 41.667 0.00 0.00 0.00 3.57
3415 3639 4.031426 CCGCAGTTTCATTCTTAGACGTAC 59.969 45.833 0.00 0.00 0.00 3.67
3416 3640 4.258899 CGCAGTTTCATTCTTAGACGTACG 60.259 45.833 15.01 15.01 0.00 3.67
3417 3641 4.490479 GCAGTTTCATTCTTAGACGTACGC 60.490 45.833 16.72 8.42 0.00 4.42
3418 3642 4.857588 CAGTTTCATTCTTAGACGTACGCT 59.142 41.667 16.72 15.57 0.00 5.07
3419 3643 6.025896 CAGTTTCATTCTTAGACGTACGCTA 58.974 40.000 16.72 14.53 0.00 4.26
3420 3644 6.691818 CAGTTTCATTCTTAGACGTACGCTAT 59.308 38.462 16.72 3.79 0.00 2.97
3421 3645 7.220300 CAGTTTCATTCTTAGACGTACGCTATT 59.780 37.037 16.72 0.00 0.00 1.73
3422 3646 8.400947 AGTTTCATTCTTAGACGTACGCTATTA 58.599 33.333 16.72 6.35 0.00 0.98
3423 3647 8.467574 GTTTCATTCTTAGACGTACGCTATTAC 58.532 37.037 16.72 0.30 0.00 1.89
3431 3655 3.609103 CGTACGCTATTACGGGTTAGT 57.391 47.619 0.52 0.00 40.97 2.24
3432 3656 3.291585 CGTACGCTATTACGGGTTAGTG 58.708 50.000 0.52 0.00 40.97 2.74
3433 3657 2.877043 ACGCTATTACGGGTTAGTGG 57.123 50.000 0.00 0.00 37.37 4.00
3434 3658 2.102578 ACGCTATTACGGGTTAGTGGT 58.897 47.619 0.00 0.00 37.37 4.16
3435 3659 2.099756 ACGCTATTACGGGTTAGTGGTC 59.900 50.000 0.00 0.00 37.37 4.02
3436 3660 2.099592 CGCTATTACGGGTTAGTGGTCA 59.900 50.000 0.00 0.00 0.00 4.02
3437 3661 3.243636 CGCTATTACGGGTTAGTGGTCAT 60.244 47.826 0.00 0.00 0.00 3.06
3438 3662 4.022935 CGCTATTACGGGTTAGTGGTCATA 60.023 45.833 0.00 0.00 0.00 2.15
3439 3663 5.507817 CGCTATTACGGGTTAGTGGTCATAA 60.508 44.000 0.00 0.00 0.00 1.90
3440 3664 6.282930 GCTATTACGGGTTAGTGGTCATAAA 58.717 40.000 0.00 0.00 0.00 1.40
3441 3665 6.762661 GCTATTACGGGTTAGTGGTCATAAAA 59.237 38.462 0.00 0.00 0.00 1.52
3442 3666 7.042254 GCTATTACGGGTTAGTGGTCATAAAAG 60.042 40.741 0.00 0.00 0.00 2.27
3443 3667 3.946606 ACGGGTTAGTGGTCATAAAAGG 58.053 45.455 0.00 0.00 0.00 3.11
3444 3668 3.328637 ACGGGTTAGTGGTCATAAAAGGT 59.671 43.478 0.00 0.00 0.00 3.50
3445 3669 3.687698 CGGGTTAGTGGTCATAAAAGGTG 59.312 47.826 0.00 0.00 0.00 4.00
3446 3670 4.563993 CGGGTTAGTGGTCATAAAAGGTGA 60.564 45.833 0.00 0.00 0.00 4.02
3447 3671 5.318630 GGGTTAGTGGTCATAAAAGGTGAA 58.681 41.667 0.00 0.00 0.00 3.18
3448 3672 5.771165 GGGTTAGTGGTCATAAAAGGTGAAA 59.229 40.000 0.00 0.00 0.00 2.69
3449 3673 6.072119 GGGTTAGTGGTCATAAAAGGTGAAAG 60.072 42.308 0.00 0.00 0.00 2.62
3450 3674 6.713450 GGTTAGTGGTCATAAAAGGTGAAAGA 59.287 38.462 0.00 0.00 0.00 2.52
3451 3675 7.393515 GGTTAGTGGTCATAAAAGGTGAAAGAT 59.606 37.037 0.00 0.00 0.00 2.40
3452 3676 8.793592 GTTAGTGGTCATAAAAGGTGAAAGATT 58.206 33.333 0.00 0.00 0.00 2.40
3460 3684 5.665916 AAAAGGTGAAAGATTATGCTGGG 57.334 39.130 0.00 0.00 0.00 4.45
3468 3692 0.771127 GATTATGCTGGGCAGGGGTA 59.229 55.000 0.00 0.00 43.65 3.69
3469 3693 1.144913 GATTATGCTGGGCAGGGGTAA 59.855 52.381 0.00 0.00 43.65 2.85
3480 3704 1.886542 GCAGGGGTAAAAAGTCCACAG 59.113 52.381 0.00 0.00 0.00 3.66
3495 3719 6.635030 AGTCCACAGTTTCTTCCAAAATAC 57.365 37.500 0.00 0.00 0.00 1.89
3499 3723 5.147162 CACAGTTTCTTCCAAAATACGCTC 58.853 41.667 0.00 0.00 0.00 5.03
3500 3724 5.049405 CACAGTTTCTTCCAAAATACGCTCT 60.049 40.000 0.00 0.00 0.00 4.09
3502 3726 4.695928 AGTTTCTTCCAAAATACGCTCTCC 59.304 41.667 0.00 0.00 0.00 3.71
3526 3750 6.128172 CCCTTTGAACACTATCACTTGATGAC 60.128 42.308 1.77 0.00 41.24 3.06
3536 3760 4.456280 TCACTTGATGACGAAGCTACAT 57.544 40.909 0.00 0.00 29.99 2.29
3555 3779 2.320587 CGTGTGCAGAGTTCCTGGC 61.321 63.158 0.00 0.00 43.13 4.85
3610 3834 2.435805 TCCTGGATCGGAATTTGGAGAG 59.564 50.000 0.00 0.00 0.00 3.20
3627 3851 4.772100 TGGAGAGTGACATGTACATCTTCA 59.228 41.667 5.07 8.87 0.00 3.02
3629 3853 6.070596 TGGAGAGTGACATGTACATCTTCATT 60.071 38.462 16.27 13.28 0.00 2.57
3630 3854 7.124147 TGGAGAGTGACATGTACATCTTCATTA 59.876 37.037 16.27 0.13 0.00 1.90
3631 3855 7.981789 GGAGAGTGACATGTACATCTTCATTAA 59.018 37.037 16.27 0.00 0.00 1.40
3636 3863 9.760660 GTGACATGTACATCTTCATTAAAAGTC 57.239 33.333 16.27 11.73 0.00 3.01
3659 3886 1.419374 CGGAGCTGTTGTATATCCGC 58.581 55.000 0.00 0.00 45.47 5.54
3679 3906 2.457598 CTGTGCTAGAGGTAGGGTCAA 58.542 52.381 0.00 0.00 0.00 3.18
3689 3916 5.032846 AGAGGTAGGGTCAATCAAATCTGA 58.967 41.667 0.00 0.00 35.56 3.27
3714 3941 3.385755 CCTTAGCAAAAATATGGCTGCCT 59.614 43.478 21.03 8.02 38.55 4.75
3722 3949 1.688772 ATATGGCTGCCTTTGCTGAG 58.311 50.000 21.03 0.00 38.61 3.35
3731 3958 2.813754 TGCCTTTGCTGAGATGTTACAC 59.186 45.455 0.00 0.00 38.71 2.90
3734 3961 3.438087 CCTTTGCTGAGATGTTACACTGG 59.562 47.826 0.00 0.00 0.00 4.00
3745 3972 4.727507 TGTTACACTGGTTTTGTGCAAT 57.272 36.364 0.00 0.00 38.86 3.56
3771 3998 2.625823 CCGCGCAACCCACATTCTT 61.626 57.895 8.75 0.00 0.00 2.52
3775 4002 0.243636 CGCAACCCACATTCTTTCCC 59.756 55.000 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.443329 TGGAATTCATTGTCGTGAATGGG 59.557 43.478 7.93 0.00 45.49 4.00
70 71 5.703130 GGACAACAACAATCTCTAGCTCTTT 59.297 40.000 0.00 0.00 0.00 2.52
86 87 0.453793 CTGTGGCAAACGGACAACAA 59.546 50.000 0.00 0.00 35.15 2.83
157 159 6.681120 GCAATTCATCTTTGCTGCATTACCTA 60.681 38.462 1.84 0.00 44.71 3.08
182 184 3.393800 CAAAGTAGATAGCCCACCATCG 58.606 50.000 0.00 0.00 0.00 3.84
288 290 1.227089 CCAGACTTGCCGGATCGAG 60.227 63.158 5.05 0.00 0.00 4.04
340 342 3.994392 GTCGTTCAGATTTAGGTCTTGCA 59.006 43.478 0.00 0.00 0.00 4.08
343 345 5.011738 TCCAAGTCGTTCAGATTTAGGTCTT 59.988 40.000 0.00 0.00 0.00 3.01
373 375 6.127054 TGAGATTACTTCCTGACAATCCGAAT 60.127 38.462 0.00 0.00 0.00 3.34
419 430 1.300465 CTCCCTGATGATCGGTGCG 60.300 63.158 0.00 0.00 0.00 5.34
476 488 8.420374 AATTATTTTCTCTATGCTCGAAACGA 57.580 30.769 0.00 0.00 0.00 3.85
642 654 3.204467 TTTTCTCCACCGGGCCTGG 62.204 63.158 30.26 30.26 0.00 4.45
643 655 1.971695 GTTTTCTCCACCGGGCCTG 60.972 63.158 6.32 3.88 0.00 4.85
644 656 2.434774 GTTTTCTCCACCGGGCCT 59.565 61.111 6.32 0.00 0.00 5.19
645 657 2.675423 GGTTTTCTCCACCGGGCC 60.675 66.667 6.32 0.00 0.00 5.80
646 658 1.110518 TTTGGTTTTCTCCACCGGGC 61.111 55.000 6.32 0.00 37.07 6.13
647 659 0.671796 GTTTGGTTTTCTCCACCGGG 59.328 55.000 6.32 0.00 37.07 5.73
648 660 1.066454 GTGTTTGGTTTTCTCCACCGG 59.934 52.381 0.00 0.00 37.07 5.28
649 661 1.268335 CGTGTTTGGTTTTCTCCACCG 60.268 52.381 0.00 0.00 37.07 4.94
650 662 1.535226 GCGTGTTTGGTTTTCTCCACC 60.535 52.381 0.00 0.00 37.20 4.61
651 663 1.535226 GGCGTGTTTGGTTTTCTCCAC 60.535 52.381 0.00 0.00 37.20 4.02
652 664 0.741915 GGCGTGTTTGGTTTTCTCCA 59.258 50.000 0.00 0.00 35.49 3.86
653 665 0.031585 GGGCGTGTTTGGTTTTCTCC 59.968 55.000 0.00 0.00 0.00 3.71
654 666 0.031585 GGGGCGTGTTTGGTTTTCTC 59.968 55.000 0.00 0.00 0.00 2.87
655 667 0.396556 AGGGGCGTGTTTGGTTTTCT 60.397 50.000 0.00 0.00 0.00 2.52
656 668 1.268625 CTAGGGGCGTGTTTGGTTTTC 59.731 52.381 0.00 0.00 0.00 2.29
657 669 1.324383 CTAGGGGCGTGTTTGGTTTT 58.676 50.000 0.00 0.00 0.00 2.43
658 670 1.176619 GCTAGGGGCGTGTTTGGTTT 61.177 55.000 0.00 0.00 0.00 3.27
659 671 1.602605 GCTAGGGGCGTGTTTGGTT 60.603 57.895 0.00 0.00 0.00 3.67
660 672 2.033602 GCTAGGGGCGTGTTTGGT 59.966 61.111 0.00 0.00 0.00 3.67
661 673 0.965363 ATTGCTAGGGGCGTGTTTGG 60.965 55.000 0.00 0.00 45.43 3.28
662 674 1.670811 CTATTGCTAGGGGCGTGTTTG 59.329 52.381 0.00 0.00 45.43 2.93
663 675 2.017113 GCTATTGCTAGGGGCGTGTTT 61.017 52.381 0.00 0.00 45.43 2.83
664 676 0.463833 GCTATTGCTAGGGGCGTGTT 60.464 55.000 0.00 0.00 45.43 3.32
665 677 1.146263 GCTATTGCTAGGGGCGTGT 59.854 57.895 0.00 0.00 45.43 4.49
666 678 0.882042 CTGCTATTGCTAGGGGCGTG 60.882 60.000 0.00 0.00 45.43 5.34
667 679 1.338136 ACTGCTATTGCTAGGGGCGT 61.338 55.000 0.00 0.00 45.43 5.68
668 680 0.601311 GACTGCTATTGCTAGGGGCG 60.601 60.000 0.00 0.00 45.43 6.13
669 681 0.761802 AGACTGCTATTGCTAGGGGC 59.238 55.000 0.00 0.00 40.48 5.80
670 682 2.028567 GCTAGACTGCTATTGCTAGGGG 60.029 54.545 0.00 0.00 40.48 4.79
671 683 2.630098 TGCTAGACTGCTATTGCTAGGG 59.370 50.000 0.00 0.00 40.48 3.53
672 684 3.320541 ACTGCTAGACTGCTATTGCTAGG 59.679 47.826 0.00 0.00 40.48 3.02
673 685 4.582701 ACTGCTAGACTGCTATTGCTAG 57.417 45.455 0.00 0.00 40.48 3.42
674 686 5.127845 AGAAACTGCTAGACTGCTATTGCTA 59.872 40.000 0.00 0.00 40.48 3.49
675 687 3.902881 AACTGCTAGACTGCTATTGCT 57.097 42.857 0.00 0.00 40.48 3.91
676 688 4.187694 AGAAACTGCTAGACTGCTATTGC 58.812 43.478 0.00 0.00 40.20 3.56
677 689 5.414360 TGAGAAACTGCTAGACTGCTATTG 58.586 41.667 0.00 0.00 0.00 1.90
678 690 5.667539 TGAGAAACTGCTAGACTGCTATT 57.332 39.130 0.00 0.00 0.00 1.73
679 691 5.667539 TTGAGAAACTGCTAGACTGCTAT 57.332 39.130 0.00 0.00 0.00 2.97
680 692 5.468540 TTTGAGAAACTGCTAGACTGCTA 57.531 39.130 0.00 0.00 0.00 3.49
681 693 4.342862 TTTGAGAAACTGCTAGACTGCT 57.657 40.909 0.00 0.00 0.00 4.24
682 694 5.424121 TTTTTGAGAAACTGCTAGACTGC 57.576 39.130 0.00 0.00 0.00 4.40
710 722 4.008074 TGCTGCTAGACTGCTAGTTTTT 57.992 40.909 0.00 0.00 44.84 1.94
711 723 3.685139 TGCTGCTAGACTGCTAGTTTT 57.315 42.857 0.00 0.00 44.84 2.43
712 724 3.244215 TGTTGCTGCTAGACTGCTAGTTT 60.244 43.478 0.00 0.00 44.84 2.66
713 725 2.300152 TGTTGCTGCTAGACTGCTAGTT 59.700 45.455 0.00 0.00 44.84 2.24
714 726 1.895798 TGTTGCTGCTAGACTGCTAGT 59.104 47.619 0.00 0.00 44.84 2.57
826 838 0.530650 CAGAGTGCAGTTGTGGTCGT 60.531 55.000 0.00 0.00 0.00 4.34
831 843 1.779025 AAGCGCAGAGTGCAGTTGTG 61.779 55.000 11.47 4.37 45.36 3.33
1066 1088 2.876879 CGAACAGGTTGCGTGCGAA 61.877 57.895 0.00 0.00 37.63 4.70
1067 1089 3.334751 CGAACAGGTTGCGTGCGA 61.335 61.111 0.00 0.00 37.63 5.10
1111 1133 0.322975 GAGAGGAAGGTGCTGCAGAA 59.677 55.000 20.43 2.96 0.00 3.02
1161 1183 1.261238 ACGAGAAGGCTTGGAGGAGG 61.261 60.000 3.46 0.00 0.00 4.30
1283 1305 2.401766 CCACGGACAAGAGCATGGC 61.402 63.158 0.00 0.00 0.00 4.40
1401 1423 5.162075 CAGTTTATCGGTATCGGATCCTTC 58.838 45.833 10.75 0.00 36.95 3.46
1443 1465 3.947834 CCTTACCCACATCACCAGATTTC 59.052 47.826 0.00 0.00 30.20 2.17
1446 1468 1.212935 GCCTTACCCACATCACCAGAT 59.787 52.381 0.00 0.00 33.87 2.90
1472 1494 3.555168 CCTCTCCATACCGTCAAATAGCC 60.555 52.174 0.00 0.00 0.00 3.93
1565 1587 2.743664 CTCAGCATCCGATCAAACAACA 59.256 45.455 0.00 0.00 0.00 3.33
1752 1774 3.017314 CGTGCGTCGTCGATAGCC 61.017 66.667 18.59 11.33 39.71 3.93
1764 1786 2.355363 TCAAACTCCCGACGTGCG 60.355 61.111 0.00 0.00 40.47 5.34
1784 1806 3.627123 CACGACATCTCTCTCTGACATCT 59.373 47.826 0.00 0.00 0.00 2.90
1791 1813 1.408340 CATGCCACGACATCTCTCTCT 59.592 52.381 0.00 0.00 0.00 3.10
1792 1814 1.537776 CCATGCCACGACATCTCTCTC 60.538 57.143 0.00 0.00 0.00 3.20
1863 1885 4.645535 CCTTCATCCTCTCAAACAGTTCA 58.354 43.478 0.00 0.00 0.00 3.18
1886 1908 0.247185 ATTTGGCCTGCAATCGGTTG 59.753 50.000 3.38 3.38 38.39 3.77
1899 1921 3.715628 ACAAGTGTCACTTCATTTGGC 57.284 42.857 15.48 0.00 36.03 4.52
2067 2089 2.115291 GCTGAAGACATTCCGGGCC 61.115 63.158 0.00 0.00 34.28 5.80
2075 2097 0.911769 TTCCATCCGGCTGAAGACAT 59.088 50.000 6.92 0.00 0.00 3.06
2163 2185 5.391310 CGCCATATTTTCATACAGGCTGATC 60.391 44.000 23.66 0.00 37.30 2.92
2170 2192 6.642131 CCATTTTCCGCCATATTTTCATACAG 59.358 38.462 0.00 0.00 0.00 2.74
2181 2203 1.562008 TGGACTCCATTTTCCGCCATA 59.438 47.619 0.00 0.00 34.24 2.74
2193 2215 0.547471 TCTCATTGGGCTGGACTCCA 60.547 55.000 0.00 0.00 0.00 3.86
2196 2218 1.211457 GTGATCTCATTGGGCTGGACT 59.789 52.381 0.00 0.00 0.00 3.85
2208 2230 1.136774 CGCGACGAAGGTGATCTCA 59.863 57.895 0.00 0.00 0.00 3.27
2328 2350 0.181114 GGAGGTCCACTATGCATGCA 59.819 55.000 25.04 25.04 35.64 3.96
2404 2426 1.197721 CCAGATCACTGCGTTTGGTTC 59.802 52.381 0.00 0.00 42.25 3.62
2415 2437 1.593787 CAGCGTGGTCCAGATCACT 59.406 57.895 9.26 0.00 40.19 3.41
2439 2461 2.044650 GCATGGGCTCTGCAGGAA 60.045 61.111 15.13 0.00 39.46 3.36
2450 2472 1.134367 CAAGCTCAACATCAGCATGGG 59.866 52.381 0.00 0.00 39.56 4.00
2496 2518 0.107456 AGTTGTCAGGCTCCACTGTG 59.893 55.000 0.00 0.00 39.48 3.66
2497 2519 0.394565 GAGTTGTCAGGCTCCACTGT 59.605 55.000 0.00 0.00 39.48 3.55
2508 2530 3.192844 GGACGTAGATTGAGGAGTTGTCA 59.807 47.826 0.00 0.00 0.00 3.58
2643 2665 2.346766 ACTTGTGCACTTCACCATCA 57.653 45.000 19.41 0.00 45.03 3.07
2652 2674 3.100545 CACCAGGAACTTGTGCACT 57.899 52.632 19.41 0.00 44.92 4.40
2688 2710 4.929808 ACGTCGTAAATCTCAGCTGATTTT 59.070 37.500 18.63 20.52 42.06 1.82
2690 2712 4.106197 GACGTCGTAAATCTCAGCTGATT 58.894 43.478 18.63 11.60 38.19 2.57
2734 2756 3.203412 AGAGTCGGCGCGGTCTAG 61.203 66.667 14.07 0.00 0.00 2.43
2742 2764 1.064946 GTCTGGATCAGAGTCGGCG 59.935 63.158 0.00 0.00 41.46 6.46
2757 2779 2.495669 GAGCTCTGAAACTAGCAGGTCT 59.504 50.000 6.43 0.00 41.32 3.85
2820 2842 2.627699 GGAATGCTTTGTGTTCCTTCCA 59.372 45.455 0.00 0.00 38.65 3.53
2821 2843 2.627699 TGGAATGCTTTGTGTTCCTTCC 59.372 45.455 5.14 0.00 41.52 3.46
2849 2871 2.210013 TGGCAAGTCCAGCTCGTCT 61.210 57.895 0.00 0.00 40.72 4.18
2863 2885 2.057137 AAAGAACTTGTCTGCTGGCA 57.943 45.000 0.00 0.00 36.40 4.92
2890 2912 5.420104 AGATTTGGCTTGATACCTTTCCAAG 59.580 40.000 0.00 0.00 40.00 3.61
2937 2960 8.404000 GCACACTCTTTAGCTACTTATAGTGTA 58.596 37.037 18.58 0.00 43.14 2.90
2940 2963 7.339721 TCTGCACACTCTTTAGCTACTTATAGT 59.660 37.037 0.00 0.00 0.00 2.12
2942 2965 7.640597 TCTGCACACTCTTTAGCTACTTATA 57.359 36.000 0.00 0.00 0.00 0.98
2956 2979 7.367285 TGGTTTTGTAATATTTCTGCACACTC 58.633 34.615 0.00 0.00 0.00 3.51
2958 2981 7.114811 CACTGGTTTTGTAATATTTCTGCACAC 59.885 37.037 0.00 0.00 0.00 3.82
2978 3002 1.348036 GGTAGGAACTTGCTCACTGGT 59.652 52.381 0.00 0.00 41.75 4.00
2981 3005 3.901844 TGTAAGGTAGGAACTTGCTCACT 59.098 43.478 0.00 0.00 41.75 3.41
2991 3015 5.534207 TTTTCAGTCGTGTAAGGTAGGAA 57.466 39.130 0.00 0.00 0.00 3.36
2993 3017 3.678548 GCTTTTCAGTCGTGTAAGGTAGG 59.321 47.826 0.00 0.00 0.00 3.18
3002 3026 2.031769 TGCAATCAGCTTTTCAGTCGTG 60.032 45.455 0.00 0.00 45.94 4.35
3094 3119 6.239176 CGAAGCTAGTCAAAGAGAAGGGATAT 60.239 42.308 0.00 0.00 0.00 1.63
3099 3124 4.181309 ACGAAGCTAGTCAAAGAGAAGG 57.819 45.455 0.00 0.00 0.00 3.46
3111 3136 6.658831 TGTGATTTGAAAGAAACGAAGCTAG 58.341 36.000 0.00 0.00 0.00 3.42
3117 3142 7.646130 GTGGTTATTGTGATTTGAAAGAAACGA 59.354 33.333 0.00 0.00 0.00 3.85
3118 3143 7.433719 TGTGGTTATTGTGATTTGAAAGAAACG 59.566 33.333 0.00 0.00 0.00 3.60
3139 3164 7.458397 TGTCTGGAAGTTTATATTCTTGTGGT 58.542 34.615 0.00 0.00 33.76 4.16
3140 3165 7.921786 TGTCTGGAAGTTTATATTCTTGTGG 57.078 36.000 0.00 0.00 33.76 4.17
3171 3199 7.448420 TGGAGGATATTCTGAAAATAGAGCAG 58.552 38.462 0.00 0.00 0.00 4.24
3172 3200 7.379059 TGGAGGATATTCTGAAAATAGAGCA 57.621 36.000 0.00 0.00 0.00 4.26
3173 3201 8.099537 TGATGGAGGATATTCTGAAAATAGAGC 58.900 37.037 0.00 0.00 0.00 4.09
3200 3228 1.186917 TTGCCCAAATGCCACCTCAG 61.187 55.000 0.00 0.00 0.00 3.35
3201 3229 0.544833 ATTGCCCAAATGCCACCTCA 60.545 50.000 0.00 0.00 0.00 3.86
3205 3233 2.406596 ATCAATTGCCCAAATGCCAC 57.593 45.000 0.00 0.00 0.00 5.01
3207 3235 4.141233 ACTTATCAATTGCCCAAATGCC 57.859 40.909 0.00 0.00 0.00 4.40
3263 3291 7.722285 TCCTAAAGTGCAAGTTTGTAAGGTTAT 59.278 33.333 5.71 0.00 40.30 1.89
3276 3305 4.142381 GGTTATGGCTTCCTAAAGTGCAAG 60.142 45.833 0.00 0.00 34.79 4.01
3293 3322 4.545610 AGTGCAAATTTGTCACGGTTATG 58.454 39.130 25.85 1.81 38.94 1.90
3300 3361 6.255453 TGCTTTCTAAAGTGCAAATTTGTCAC 59.745 34.615 25.39 25.39 33.75 3.67
3316 3377 2.356135 GCGGAGGTCATTGCTTTCTAA 58.644 47.619 0.00 0.00 0.00 2.10
3334 3395 4.914312 TGTTGTTAATTAGACGAAGGCG 57.086 40.909 0.00 0.00 44.79 5.52
3336 3397 8.342634 CCCAATATGTTGTTAATTAGACGAAGG 58.657 37.037 1.26 0.00 33.36 3.46
3353 3577 5.013495 AGCAGATACACTATGCCCAATATGT 59.987 40.000 0.00 0.00 40.89 2.29
3362 3586 6.226787 AGGAATTGTAGCAGATACACTATGC 58.773 40.000 0.00 0.00 44.14 3.14
3366 3590 6.552445 AAGAGGAATTGTAGCAGATACACT 57.448 37.500 0.00 0.00 44.14 3.55
3369 3593 6.018669 CGGAAAAGAGGAATTGTAGCAGATAC 60.019 42.308 0.00 0.00 34.72 2.24
3374 3598 2.747446 GCGGAAAAGAGGAATTGTAGCA 59.253 45.455 0.00 0.00 0.00 3.49
3375 3599 2.747446 TGCGGAAAAGAGGAATTGTAGC 59.253 45.455 0.00 0.00 0.00 3.58
3377 3601 4.015872 ACTGCGGAAAAGAGGAATTGTA 57.984 40.909 0.00 0.00 0.00 2.41
3378 3602 2.863809 ACTGCGGAAAAGAGGAATTGT 58.136 42.857 0.00 0.00 0.00 2.71
3379 3603 3.923017 AACTGCGGAAAAGAGGAATTG 57.077 42.857 0.00 0.00 0.00 2.32
3380 3604 3.888930 TGAAACTGCGGAAAAGAGGAATT 59.111 39.130 0.00 0.00 0.00 2.17
3381 3605 3.486383 TGAAACTGCGGAAAAGAGGAAT 58.514 40.909 0.00 0.00 0.00 3.01
3382 3606 2.925724 TGAAACTGCGGAAAAGAGGAA 58.074 42.857 0.00 0.00 0.00 3.36
3383 3607 2.631160 TGAAACTGCGGAAAAGAGGA 57.369 45.000 0.00 0.00 0.00 3.71
3384 3608 3.503748 AGAATGAAACTGCGGAAAAGAGG 59.496 43.478 0.00 0.00 0.00 3.69
3385 3609 4.756084 AGAATGAAACTGCGGAAAAGAG 57.244 40.909 0.00 0.00 0.00 2.85
3386 3610 5.995282 TCTAAGAATGAAACTGCGGAAAAGA 59.005 36.000 0.00 0.00 0.00 2.52
3387 3611 6.080406 GTCTAAGAATGAAACTGCGGAAAAG 58.920 40.000 0.00 0.00 0.00 2.27
3388 3612 5.333798 CGTCTAAGAATGAAACTGCGGAAAA 60.334 40.000 0.00 0.00 0.00 2.29
3389 3613 4.151689 CGTCTAAGAATGAAACTGCGGAAA 59.848 41.667 0.00 0.00 0.00 3.13
3390 3614 3.678072 CGTCTAAGAATGAAACTGCGGAA 59.322 43.478 0.00 0.00 0.00 4.30
3391 3615 3.250744 CGTCTAAGAATGAAACTGCGGA 58.749 45.455 0.00 0.00 0.00 5.54
3392 3616 2.993899 ACGTCTAAGAATGAAACTGCGG 59.006 45.455 0.00 0.00 0.00 5.69
3393 3617 4.258899 CGTACGTCTAAGAATGAAACTGCG 60.259 45.833 7.22 0.00 0.00 5.18
3394 3618 4.490479 GCGTACGTCTAAGAATGAAACTGC 60.490 45.833 17.90 0.00 0.00 4.40
3395 3619 4.857588 AGCGTACGTCTAAGAATGAAACTG 59.142 41.667 17.90 0.00 0.00 3.16
3396 3620 5.056894 AGCGTACGTCTAAGAATGAAACT 57.943 39.130 17.90 0.00 0.00 2.66
3397 3621 7.447243 AATAGCGTACGTCTAAGAATGAAAC 57.553 36.000 17.90 0.00 0.00 2.78
3398 3622 7.374228 CGTAATAGCGTACGTCTAAGAATGAAA 59.626 37.037 17.90 0.00 41.51 2.69
3399 3623 6.847792 CGTAATAGCGTACGTCTAAGAATGAA 59.152 38.462 17.90 0.00 41.51 2.57
3400 3624 6.357980 CGTAATAGCGTACGTCTAAGAATGA 58.642 40.000 17.90 0.00 41.51 2.57
3401 3625 5.562998 CCGTAATAGCGTACGTCTAAGAATG 59.437 44.000 17.90 12.04 44.24 2.67
3402 3626 5.334414 CCCGTAATAGCGTACGTCTAAGAAT 60.334 44.000 17.90 9.14 44.24 2.40
3403 3627 4.024893 CCCGTAATAGCGTACGTCTAAGAA 60.025 45.833 17.90 6.15 44.24 2.52
3404 3628 3.494626 CCCGTAATAGCGTACGTCTAAGA 59.505 47.826 17.90 8.12 44.24 2.10
3405 3629 3.248602 ACCCGTAATAGCGTACGTCTAAG 59.751 47.826 17.90 10.87 44.24 2.18
3406 3630 3.202906 ACCCGTAATAGCGTACGTCTAA 58.797 45.455 17.90 2.55 44.24 2.10
3407 3631 2.833794 ACCCGTAATAGCGTACGTCTA 58.166 47.619 17.90 17.68 44.24 2.59
3408 3632 1.668419 ACCCGTAATAGCGTACGTCT 58.332 50.000 17.90 16.10 44.24 4.18
3409 3633 2.475200 AACCCGTAATAGCGTACGTC 57.525 50.000 17.90 9.31 44.24 4.34
3410 3634 2.943033 ACTAACCCGTAATAGCGTACGT 59.057 45.455 17.90 6.37 44.24 3.57
3411 3635 3.291585 CACTAACCCGTAATAGCGTACG 58.708 50.000 11.84 11.84 45.10 3.67
3412 3636 3.066760 ACCACTAACCCGTAATAGCGTAC 59.933 47.826 0.00 0.00 0.00 3.67
3413 3637 3.287222 ACCACTAACCCGTAATAGCGTA 58.713 45.455 0.00 0.00 0.00 4.42
3414 3638 2.099756 GACCACTAACCCGTAATAGCGT 59.900 50.000 0.00 0.00 0.00 5.07
3415 3639 2.099592 TGACCACTAACCCGTAATAGCG 59.900 50.000 0.00 0.00 0.00 4.26
3416 3640 3.806625 TGACCACTAACCCGTAATAGC 57.193 47.619 0.00 0.00 0.00 2.97
3417 3641 7.440255 CCTTTTATGACCACTAACCCGTAATAG 59.560 40.741 0.00 0.00 0.00 1.73
3418 3642 7.092935 ACCTTTTATGACCACTAACCCGTAATA 60.093 37.037 0.00 0.00 0.00 0.98
3419 3643 6.117488 CCTTTTATGACCACTAACCCGTAAT 58.883 40.000 0.00 0.00 0.00 1.89
3420 3644 5.012975 ACCTTTTATGACCACTAACCCGTAA 59.987 40.000 0.00 0.00 0.00 3.18
3421 3645 4.531732 ACCTTTTATGACCACTAACCCGTA 59.468 41.667 0.00 0.00 0.00 4.02
3422 3646 3.328637 ACCTTTTATGACCACTAACCCGT 59.671 43.478 0.00 0.00 0.00 5.28
3423 3647 3.687698 CACCTTTTATGACCACTAACCCG 59.312 47.826 0.00 0.00 0.00 5.28
3424 3648 4.913784 TCACCTTTTATGACCACTAACCC 58.086 43.478 0.00 0.00 0.00 4.11
3425 3649 6.713450 TCTTTCACCTTTTATGACCACTAACC 59.287 38.462 0.00 0.00 0.00 2.85
3426 3650 7.739498 TCTTTCACCTTTTATGACCACTAAC 57.261 36.000 0.00 0.00 0.00 2.34
3427 3651 8.934023 AATCTTTCACCTTTTATGACCACTAA 57.066 30.769 0.00 0.00 0.00 2.24
3429 3653 8.960591 CATAATCTTTCACCTTTTATGACCACT 58.039 33.333 0.00 0.00 33.93 4.00
3430 3654 7.702348 GCATAATCTTTCACCTTTTATGACCAC 59.298 37.037 0.00 0.00 33.93 4.16
3431 3655 7.615365 AGCATAATCTTTCACCTTTTATGACCA 59.385 33.333 0.00 0.00 33.93 4.02
3432 3656 7.917505 CAGCATAATCTTTCACCTTTTATGACC 59.082 37.037 0.00 0.00 33.93 4.02
3433 3657 7.917505 CCAGCATAATCTTTCACCTTTTATGAC 59.082 37.037 0.00 0.00 33.93 3.06
3434 3658 7.068593 CCCAGCATAATCTTTCACCTTTTATGA 59.931 37.037 0.00 0.00 33.93 2.15
3435 3659 7.205297 CCCAGCATAATCTTTCACCTTTTATG 58.795 38.462 0.00 0.00 34.76 1.90
3436 3660 6.183360 GCCCAGCATAATCTTTCACCTTTTAT 60.183 38.462 0.00 0.00 0.00 1.40
3437 3661 5.127031 GCCCAGCATAATCTTTCACCTTTTA 59.873 40.000 0.00 0.00 0.00 1.52
3438 3662 4.081476 GCCCAGCATAATCTTTCACCTTTT 60.081 41.667 0.00 0.00 0.00 2.27
3439 3663 3.448660 GCCCAGCATAATCTTTCACCTTT 59.551 43.478 0.00 0.00 0.00 3.11
3440 3664 3.026694 GCCCAGCATAATCTTTCACCTT 58.973 45.455 0.00 0.00 0.00 3.50
3441 3665 2.025037 TGCCCAGCATAATCTTTCACCT 60.025 45.455 0.00 0.00 31.71 4.00
3442 3666 2.360165 CTGCCCAGCATAATCTTTCACC 59.640 50.000 0.00 0.00 38.13 4.02
3443 3667 2.360165 CCTGCCCAGCATAATCTTTCAC 59.640 50.000 0.00 0.00 38.13 3.18
3444 3668 2.658285 CCTGCCCAGCATAATCTTTCA 58.342 47.619 0.00 0.00 38.13 2.69
3445 3669 1.959282 CCCTGCCCAGCATAATCTTTC 59.041 52.381 0.00 0.00 38.13 2.62
3446 3670 1.412074 CCCCTGCCCAGCATAATCTTT 60.412 52.381 0.00 0.00 38.13 2.52
3447 3671 0.186873 CCCCTGCCCAGCATAATCTT 59.813 55.000 0.00 0.00 38.13 2.40
3448 3672 0.995675 ACCCCTGCCCAGCATAATCT 60.996 55.000 0.00 0.00 38.13 2.40
3449 3673 0.771127 TACCCCTGCCCAGCATAATC 59.229 55.000 0.00 0.00 38.13 1.75
3450 3674 1.231018 TTACCCCTGCCCAGCATAAT 58.769 50.000 0.00 0.00 38.13 1.28
3451 3675 1.003646 TTTACCCCTGCCCAGCATAA 58.996 50.000 0.00 0.00 38.13 1.90
3452 3676 1.003646 TTTTACCCCTGCCCAGCATA 58.996 50.000 0.00 0.00 38.13 3.14
3460 3684 1.886542 CTGTGGACTTTTTACCCCTGC 59.113 52.381 0.00 0.00 0.00 4.85
3468 3692 5.993748 TTGGAAGAAACTGTGGACTTTTT 57.006 34.783 0.00 0.00 0.00 1.94
3469 3693 5.993748 TTTGGAAGAAACTGTGGACTTTT 57.006 34.783 0.00 0.00 0.00 2.27
3480 3704 4.142665 GGGAGAGCGTATTTTGGAAGAAAC 60.143 45.833 0.00 0.00 0.00 2.78
3495 3719 2.743636 TAGTGTTCAAAGGGAGAGCG 57.256 50.000 0.00 0.00 0.00 5.03
3499 3723 5.551233 TCAAGTGATAGTGTTCAAAGGGAG 58.449 41.667 0.00 0.00 0.00 4.30
3500 3724 5.560722 TCAAGTGATAGTGTTCAAAGGGA 57.439 39.130 0.00 0.00 0.00 4.20
3502 3726 6.401474 CGTCATCAAGTGATAGTGTTCAAAGG 60.401 42.308 0.00 0.00 39.48 3.11
3526 3750 0.642291 CTGCACACGATGTAGCTTCG 59.358 55.000 4.77 4.77 42.20 3.79
3536 3760 1.367471 CCAGGAACTCTGCACACGA 59.633 57.895 0.00 0.00 42.05 4.35
3541 3765 1.073722 CCAAGCCAGGAACTCTGCA 59.926 57.895 0.00 0.00 42.05 4.41
3610 3834 9.760660 GACTTTTAATGAAGATGTACATGTCAC 57.239 33.333 14.43 8.01 0.00 3.67
3627 3851 4.124851 ACAGCTCCGATCGACTTTTAAT 57.875 40.909 18.66 0.00 0.00 1.40
3629 3853 3.250744 CAACAGCTCCGATCGACTTTTA 58.749 45.455 18.66 0.00 0.00 1.52
3630 3854 2.069273 CAACAGCTCCGATCGACTTTT 58.931 47.619 18.66 7.45 0.00 2.27
3631 3855 1.000955 ACAACAGCTCCGATCGACTTT 59.999 47.619 18.66 1.01 0.00 2.66
3636 3863 3.502920 GGATATACAACAGCTCCGATCG 58.497 50.000 8.51 8.51 0.00 3.69
3658 3885 0.747852 GACCCTACCTCTAGCACAGC 59.252 60.000 0.00 0.00 0.00 4.40
3659 3886 2.145397 TGACCCTACCTCTAGCACAG 57.855 55.000 0.00 0.00 0.00 3.66
3689 3916 5.178061 GCAGCCATATTTTTGCTAAGGTTT 58.822 37.500 0.00 0.00 33.16 3.27
3714 3941 4.085357 ACCAGTGTAACATCTCAGCAAA 57.915 40.909 0.00 0.00 41.43 3.68
3722 3949 4.300189 TGCACAAAACCAGTGTAACATC 57.700 40.909 0.00 0.00 41.43 3.06
3757 3984 0.608130 GGGGAAAGAATGTGGGTTGC 59.392 55.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.