Multiple sequence alignment - TraesCS1B01G107900

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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 TraesCS1B01G107900 chr1B 100.000 2917 0 0 1 2917 120039365 120042281 0.000000e+00 5387
1 TraesCS1B01G107900 chr1B 95.225 356 17 0 2559 2914 94551046 94551401 5.460000e-157 564
2 TraesCS1B01G107900 chr1B 95.211 355 15 1 2562 2916 583428604 583428252 7.060000e-156 560
3 TraesCS1B01G107900 chr1A 96.691 1813 52 7 434 2244 77272808 77274614 0.000000e+00 3009
4 TraesCS1B01G107900 chr1A 96.520 431 14 1 1 431 77272315 77272744 0.000000e+00 712
5 TraesCS1B01G107900 chr1A 97.010 301 6 2 2265 2563 77274828 77275127 1.210000e-138 503
6 TraesCS1B01G107900 chr5A 94.766 363 17 2 2554 2916 509637610 509637970 5.460000e-157 564
7 TraesCS1B01G107900 chr5D 94.693 358 18 1 2559 2916 16150272 16149916 3.280000e-154 555
8 TraesCS1B01G107900 chr7B 94.413 358 17 3 2559 2916 634577144 634577498 5.500000e-152 547
9 TraesCS1B01G107900 chr2D 94.857 350 18 0 2568 2917 72485574 72485923 5.500000e-152 547
10 TraesCS1B01G107900 chr1D 94.366 355 20 0 2562 2916 431627473 431627119 1.980000e-151 545
11 TraesCS1B01G107900 chr6D 94.118 357 20 1 2560 2916 82637360 82637715 2.560000e-150 542
12 TraesCS1B01G107900 chr6D 93.425 365 20 4 2552 2916 462263399 462263039 3.310000e-149 538


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 TraesCS1B01G107900 chr1B 120039365 120042281 2916 False 5387 5387 100.000000 1 2917 1 chr1B.!!$F2 2916
1 TraesCS1B01G107900 chr1A 77272315 77275127 2812 False 1408 3009 96.740333 1 2563 3 chr1A.!!$F1 2562

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
867 930 0.676736 CCTCCTCTTCTGTATCCCGC 59.323 60.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2753 3012 0.029035 CGGAGCGTCGTATGTAGCTT 59.971 55.0 0.0 0.0 40.39 3.74 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
47 48 3.018856 TGCAAAATACATCCAGCTCCTG 58.981 45.455 0.00 0.00 0.00 3.86
210 211 7.116948 GGATGATTGATAGTCATTACTGGTTCG 59.883 40.741 0.00 0.00 36.49 3.95
254 255 5.460091 GCAAAGACAAGTTTTGAACATCTCC 59.540 40.000 2.18 0.00 37.65 3.71
308 309 7.039784 AGCATAAACAAGCCATTAGACTTGAAA 60.040 33.333 9.54 0.00 44.89 2.69
325 326 7.227512 AGACTTGAAACCTTGAACATCTAGTTG 59.772 37.037 0.00 0.00 41.51 3.16
355 356 6.698008 AATGTGAAAGATCTGTTTGTCACA 57.302 33.333 19.88 19.88 40.41 3.58
405 406 7.501225 AGTTAAAGTAGTGCATTGTAGGTTTGT 59.499 33.333 0.00 0.00 0.00 2.83
431 432 5.687166 ATACTCCGTCCCAAAATAAGTGA 57.313 39.130 0.00 0.00 0.00 3.41
432 433 3.939066 ACTCCGTCCCAAAATAAGTGAG 58.061 45.455 0.00 0.00 0.00 3.51
477 539 9.468532 GATGTCAAATCATTATTTTAAGCCCTC 57.531 33.333 0.00 0.00 32.87 4.30
485 547 7.555087 TCATTATTTTAAGCCCTCAATTGTGG 58.445 34.615 17.88 17.88 0.00 4.17
500 562 7.406031 TCAATTGTGGGTAAAGTTAAACACA 57.594 32.000 5.13 0.00 37.09 3.72
505 567 7.934855 TGTGGGTAAAGTTAAACACAGTTAA 57.065 32.000 0.00 0.00 34.31 2.01
524 586 6.537301 CAGTTAACTGGTTTGAGTGAGTGTTA 59.463 38.462 25.19 0.00 40.20 2.41
525 587 7.065324 CAGTTAACTGGTTTGAGTGAGTGTTAA 59.935 37.037 25.19 0.00 40.20 2.01
610 673 6.206634 TCTGCTTTAATATGGGCCGATTTAAG 59.793 38.462 18.30 18.30 0.00 1.85
671 734 8.516234 TGCTGTGTAGTGTCTTTTCTTTTTAAA 58.484 29.630 0.00 0.00 0.00 1.52
716 779 4.301072 TGTACTTCTGGCCTTAGCATTT 57.699 40.909 3.32 0.00 42.56 2.32
725 788 4.357325 TGGCCTTAGCATTTATTTTGGGA 58.643 39.130 3.32 0.00 42.56 4.37
726 789 4.780021 TGGCCTTAGCATTTATTTTGGGAA 59.220 37.500 3.32 0.00 42.56 3.97
727 790 5.428131 TGGCCTTAGCATTTATTTTGGGAAT 59.572 36.000 3.32 0.00 42.56 3.01
791 854 8.462143 TGACTTTTTATTTACTGTCTCGCTAG 57.538 34.615 0.00 0.00 0.00 3.42
867 930 0.676736 CCTCCTCTTCTGTATCCCGC 59.323 60.000 0.00 0.00 0.00 6.13
974 1038 9.844790 ACCAAACTGTAAACTGTACTTAAAAAC 57.155 29.630 0.00 0.00 0.00 2.43
975 1039 9.843334 CCAAACTGTAAACTGTACTTAAAAACA 57.157 29.630 0.00 0.00 0.00 2.83
1020 1084 3.446570 GCTGCTCCGCCAAATGCT 61.447 61.111 0.00 0.00 38.05 3.79
1144 1208 8.582657 AGCTCTTATGAACAAAGTAGAGACTA 57.417 34.615 0.00 0.00 33.58 2.59
1179 1243 0.533032 GAGCTGCGGAGTTAGACCTT 59.467 55.000 5.62 0.00 0.00 3.50
1197 1261 2.574322 CTTCGAGGACAAAATTGCACG 58.426 47.619 0.00 0.00 0.00 5.34
1294 1358 1.535896 GTTCAGAACCCCTTTCGCTTC 59.464 52.381 1.29 0.00 39.47 3.86
1308 1372 2.493035 TCGCTTCAAGATGCTTGTTCA 58.507 42.857 7.02 0.00 0.00 3.18
1411 1475 1.001706 CAGCTTCCATGATTGGCATCG 60.002 52.381 0.00 0.00 43.29 3.84
1450 1514 5.592054 TGCTTCTTCTTCATGTATACCGAG 58.408 41.667 0.00 0.00 0.00 4.63
1491 1555 3.433615 GCAGAAGATGTACCAACAGTCAC 59.566 47.826 0.00 0.00 39.49 3.67
1638 1702 3.013921 TGACTTGGAACTTGTGAACACC 58.986 45.455 2.46 0.00 0.00 4.16
1746 1810 6.407299 GGAGAATAATTGGATTGTTGCATGGT 60.407 38.462 0.00 0.00 0.00 3.55
1795 1859 1.895798 TCTCCCATGCTGATATCGGAC 59.104 52.381 16.04 7.30 0.00 4.79
1954 2018 0.178873 TACAGCCCTTGTTCCCTCCT 60.179 55.000 0.00 0.00 41.29 3.69
1957 2021 1.204113 AGCCCTTGTTCCCTCCTGAG 61.204 60.000 0.00 0.00 0.00 3.35
1961 2025 1.274712 CTTGTTCCCTCCTGAGCTCT 58.725 55.000 16.19 0.00 0.00 4.09
1963 2027 2.623418 TGTTCCCTCCTGAGCTCTTA 57.377 50.000 16.19 0.00 0.00 2.10
1981 2045 5.471456 GCTCTTATTGTTATCCCATCCACAG 59.529 44.000 0.00 0.00 0.00 3.66
2000 2064 1.962822 TTGCTGCTCGAACTGCTGG 60.963 57.895 16.98 2.70 35.70 4.85
2010 2074 2.869801 TCGAACTGCTGGTAAACAACAG 59.130 45.455 0.00 0.00 46.33 3.16
2011 2075 2.032030 CGAACTGCTGGTAAACAACAGG 60.032 50.000 2.95 0.00 45.43 4.00
2132 2196 7.451255 TGGAACAGTAAGAATGGATTGATTGTT 59.549 33.333 0.00 0.00 0.00 2.83
2153 2217 7.288810 TGTTTGGTTTTCTGCTTCAGATTAT 57.711 32.000 0.00 0.00 40.39 1.28
2230 2294 6.839124 TGCCATTCAGAATACTGTGATTTT 57.161 33.333 0.00 0.00 43.81 1.82
2244 2308 5.982516 ACTGTGATTTTATTCTGCGCAAAAA 59.017 32.000 17.30 17.30 0.00 1.94
2337 2594 2.111972 ACTCTCTTGTCCCCTCACCTTA 59.888 50.000 0.00 0.00 0.00 2.69
2360 2617 8.721019 TTAAGAGTTTAGTTTCCTTTTCGTGA 57.279 30.769 0.00 0.00 0.00 4.35
2539 2798 8.667463 GCAACTACTTGTAAAATATAACGGGAA 58.333 33.333 0.00 0.00 0.00 3.97
2563 2822 8.449423 AATATGGGATACAGCCAGAGTTATTA 57.551 34.615 0.00 0.00 39.74 0.98
2564 2823 5.546621 TGGGATACAGCCAGAGTTATTAC 57.453 43.478 0.00 0.00 39.74 1.89
2565 2824 4.347000 TGGGATACAGCCAGAGTTATTACC 59.653 45.833 0.00 0.00 39.74 2.85
2566 2825 4.557205 GGATACAGCCAGAGTTATTACCG 58.443 47.826 0.00 0.00 0.00 4.02
2567 2826 4.280174 GGATACAGCCAGAGTTATTACCGA 59.720 45.833 0.00 0.00 0.00 4.69
2568 2827 5.221382 GGATACAGCCAGAGTTATTACCGAA 60.221 44.000 0.00 0.00 0.00 4.30
2569 2828 4.546829 ACAGCCAGAGTTATTACCGAAA 57.453 40.909 0.00 0.00 0.00 3.46
2570 2829 4.901868 ACAGCCAGAGTTATTACCGAAAA 58.098 39.130 0.00 0.00 0.00 2.29
2571 2830 5.310451 ACAGCCAGAGTTATTACCGAAAAA 58.690 37.500 0.00 0.00 0.00 1.94
2572 2831 5.411669 ACAGCCAGAGTTATTACCGAAAAAG 59.588 40.000 0.00 0.00 0.00 2.27
2573 2832 4.941873 AGCCAGAGTTATTACCGAAAAAGG 59.058 41.667 0.00 0.00 37.30 3.11
2574 2833 4.438336 GCCAGAGTTATTACCGAAAAAGGC 60.438 45.833 0.00 0.00 33.69 4.35
2575 2834 4.941873 CCAGAGTTATTACCGAAAAAGGCT 59.058 41.667 0.00 0.00 33.69 4.58
2576 2835 5.414765 CCAGAGTTATTACCGAAAAAGGCTT 59.585 40.000 0.00 0.00 33.69 4.35
2577 2836 6.072119 CCAGAGTTATTACCGAAAAAGGCTTT 60.072 38.462 6.68 6.68 33.69 3.51
2578 2837 7.021790 CAGAGTTATTACCGAAAAAGGCTTTC 58.978 38.462 13.76 0.41 33.69 2.62
2580 2839 2.691984 TTACCGAAAAAGGCTTTCGC 57.308 45.000 13.76 7.41 46.89 4.70
2590 2849 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
2591 2850 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
2592 2851 1.235724 GCTTTCGCCCCGCTTTATAT 58.764 50.000 0.00 0.00 0.00 0.86
2593 2852 2.419667 GCTTTCGCCCCGCTTTATATA 58.580 47.619 0.00 0.00 0.00 0.86
2594 2853 3.007635 GCTTTCGCCCCGCTTTATATAT 58.992 45.455 0.00 0.00 0.00 0.86
2595 2854 4.186159 GCTTTCGCCCCGCTTTATATATA 58.814 43.478 0.00 0.00 0.00 0.86
2596 2855 4.632688 GCTTTCGCCCCGCTTTATATATAA 59.367 41.667 0.81 0.81 0.00 0.98
2597 2856 5.122711 GCTTTCGCCCCGCTTTATATATAAA 59.877 40.000 15.47 15.47 0.00 1.40
2614 2873 8.978874 ATATATAAAGCACAGATCACCAACAA 57.021 30.769 0.00 0.00 0.00 2.83
2615 2874 3.715628 AAAGCACAGATCACCAACAAC 57.284 42.857 0.00 0.00 0.00 3.32
2616 2875 1.609208 AGCACAGATCACCAACAACC 58.391 50.000 0.00 0.00 0.00 3.77
2617 2876 0.598065 GCACAGATCACCAACAACCC 59.402 55.000 0.00 0.00 0.00 4.11
2618 2877 1.979855 CACAGATCACCAACAACCCA 58.020 50.000 0.00 0.00 0.00 4.51
2619 2878 1.881973 CACAGATCACCAACAACCCAG 59.118 52.381 0.00 0.00 0.00 4.45
2620 2879 1.494721 ACAGATCACCAACAACCCAGT 59.505 47.619 0.00 0.00 0.00 4.00
2621 2880 2.708861 ACAGATCACCAACAACCCAGTA 59.291 45.455 0.00 0.00 0.00 2.74
2622 2881 3.074412 CAGATCACCAACAACCCAGTAC 58.926 50.000 0.00 0.00 0.00 2.73
2623 2882 2.708861 AGATCACCAACAACCCAGTACA 59.291 45.455 0.00 0.00 0.00 2.90
2624 2883 2.631160 TCACCAACAACCCAGTACAG 57.369 50.000 0.00 0.00 0.00 2.74
2625 2884 0.951558 CACCAACAACCCAGTACAGC 59.048 55.000 0.00 0.00 0.00 4.40
2626 2885 0.548989 ACCAACAACCCAGTACAGCA 59.451 50.000 0.00 0.00 0.00 4.41
2627 2886 0.951558 CCAACAACCCAGTACAGCAC 59.048 55.000 0.00 0.00 0.00 4.40
2628 2887 1.674359 CAACAACCCAGTACAGCACA 58.326 50.000 0.00 0.00 0.00 4.57
2629 2888 1.333619 CAACAACCCAGTACAGCACAC 59.666 52.381 0.00 0.00 0.00 3.82
2630 2889 0.531974 ACAACCCAGTACAGCACACG 60.532 55.000 0.00 0.00 0.00 4.49
2631 2890 1.597027 AACCCAGTACAGCACACGC 60.597 57.895 0.00 0.00 38.99 5.34
2632 2891 2.742372 CCCAGTACAGCACACGCC 60.742 66.667 0.00 0.00 39.83 5.68
2633 2892 2.030412 CCAGTACAGCACACGCCA 59.970 61.111 0.00 0.00 39.83 5.69
2634 2893 2.317609 CCAGTACAGCACACGCCAC 61.318 63.158 0.00 0.00 39.83 5.01
2635 2894 2.030562 AGTACAGCACACGCCACC 59.969 61.111 0.00 0.00 39.83 4.61
2636 2895 2.280524 GTACAGCACACGCCACCA 60.281 61.111 0.00 0.00 39.83 4.17
2637 2896 1.890041 GTACAGCACACGCCACCAA 60.890 57.895 0.00 0.00 39.83 3.67
2638 2897 1.890041 TACAGCACACGCCACCAAC 60.890 57.895 0.00 0.00 39.83 3.77
2639 2898 2.595009 TACAGCACACGCCACCAACA 62.595 55.000 0.00 0.00 39.83 3.33
2640 2899 3.209097 AGCACACGCCACCAACAC 61.209 61.111 0.00 0.00 39.83 3.32
2641 2900 3.513438 GCACACGCCACCAACACA 61.513 61.111 0.00 0.00 0.00 3.72
2642 2901 2.407210 CACACGCCACCAACACAC 59.593 61.111 0.00 0.00 0.00 3.82
2643 2902 2.045829 ACACGCCACCAACACACA 60.046 55.556 0.00 0.00 0.00 3.72
2644 2903 2.403378 ACACGCCACCAACACACAC 61.403 57.895 0.00 0.00 0.00 3.82
2645 2904 3.199190 ACGCCACCAACACACACG 61.199 61.111 0.00 0.00 0.00 4.49
2646 2905 4.605967 CGCCACCAACACACACGC 62.606 66.667 0.00 0.00 0.00 5.34
2647 2906 3.513438 GCCACCAACACACACGCA 61.513 61.111 0.00 0.00 0.00 5.24
2648 2907 2.407210 CCACCAACACACACGCAC 59.593 61.111 0.00 0.00 0.00 5.34
2649 2908 2.402572 CCACCAACACACACGCACA 61.403 57.895 0.00 0.00 0.00 4.57
2650 2909 1.226267 CACCAACACACACGCACAC 60.226 57.895 0.00 0.00 0.00 3.82
2651 2910 1.672682 ACCAACACACACGCACACA 60.673 52.632 0.00 0.00 0.00 3.72
2652 2911 1.226267 CCAACACACACGCACACAC 60.226 57.895 0.00 0.00 0.00 3.82
2653 2912 1.226267 CAACACACACGCACACACC 60.226 57.895 0.00 0.00 0.00 4.16
2654 2913 2.403378 AACACACACGCACACACCC 61.403 57.895 0.00 0.00 0.00 4.61
2655 2914 2.821810 CACACACGCACACACCCA 60.822 61.111 0.00 0.00 0.00 4.51
2656 2915 2.045829 ACACACGCACACACCCAA 60.046 55.556 0.00 0.00 0.00 4.12
2657 2916 2.112198 ACACACGCACACACCCAAG 61.112 57.895 0.00 0.00 0.00 3.61
2658 2917 2.515991 ACACGCACACACCCAAGG 60.516 61.111 0.00 0.00 0.00 3.61
2659 2918 3.964875 CACGCACACACCCAAGGC 61.965 66.667 0.00 0.00 0.00 4.35
2660 2919 4.497984 ACGCACACACCCAAGGCA 62.498 61.111 0.00 0.00 0.00 4.75
2661 2920 3.663176 CGCACACACCCAAGGCAG 61.663 66.667 0.00 0.00 0.00 4.85
2662 2921 3.297620 GCACACACCCAAGGCAGG 61.298 66.667 0.00 0.00 0.00 4.85
2663 2922 2.515398 CACACACCCAAGGCAGGA 59.485 61.111 0.00 0.00 0.00 3.86
2664 2923 1.075482 CACACACCCAAGGCAGGAT 59.925 57.895 0.00 0.00 0.00 3.24
2665 2924 0.327924 CACACACCCAAGGCAGGATA 59.672 55.000 0.00 0.00 0.00 2.59
2666 2925 0.328258 ACACACCCAAGGCAGGATAC 59.672 55.000 0.00 0.00 0.00 2.24
2667 2926 0.327924 CACACCCAAGGCAGGATACA 59.672 55.000 0.00 0.00 41.41 2.29
2668 2927 1.072266 ACACCCAAGGCAGGATACAA 58.928 50.000 0.00 0.00 41.41 2.41
2669 2928 1.427368 ACACCCAAGGCAGGATACAAA 59.573 47.619 0.00 0.00 41.41 2.83
2670 2929 2.094675 CACCCAAGGCAGGATACAAAG 58.905 52.381 0.00 0.00 41.41 2.77
2671 2930 1.005924 ACCCAAGGCAGGATACAAAGG 59.994 52.381 0.00 0.00 41.41 3.11
2672 2931 1.106285 CCAAGGCAGGATACAAAGGC 58.894 55.000 0.00 0.00 41.41 4.35
2673 2932 0.734889 CAAGGCAGGATACAAAGGCG 59.265 55.000 0.00 0.00 41.41 5.52
2674 2933 1.032114 AAGGCAGGATACAAAGGCGC 61.032 55.000 0.00 0.00 41.41 6.53
2675 2934 1.452108 GGCAGGATACAAAGGCGCT 60.452 57.895 7.64 0.00 41.41 5.92
2676 2935 1.718757 GGCAGGATACAAAGGCGCTG 61.719 60.000 7.64 0.00 41.41 5.18
2677 2936 0.744414 GCAGGATACAAAGGCGCTGA 60.744 55.000 7.64 0.00 41.41 4.26
2678 2937 1.293924 CAGGATACAAAGGCGCTGAG 58.706 55.000 7.64 0.00 41.41 3.35
2679 2938 0.462759 AGGATACAAAGGCGCTGAGC 60.463 55.000 7.64 0.00 43.13 4.26
2680 2939 3.121327 AGGATACAAAGGCGCTGAGCA 62.121 52.381 7.64 0.00 45.24 4.26
2691 2950 4.146058 CTGAGCACAGCAACACCA 57.854 55.556 0.00 0.00 37.33 4.17
2692 2951 1.650912 CTGAGCACAGCAACACCAC 59.349 57.895 0.00 0.00 37.33 4.16
2693 2952 1.789078 CTGAGCACAGCAACACCACC 61.789 60.000 0.00 0.00 37.33 4.61
2694 2953 2.519302 AGCACAGCAACACCACCC 60.519 61.111 0.00 0.00 0.00 4.61
2695 2954 3.605664 GCACAGCAACACCACCCC 61.606 66.667 0.00 0.00 0.00 4.95
2696 2955 2.195683 CACAGCAACACCACCCCT 59.804 61.111 0.00 0.00 0.00 4.79
2697 2956 1.454104 CACAGCAACACCACCCCTA 59.546 57.895 0.00 0.00 0.00 3.53
2698 2957 0.606401 CACAGCAACACCACCCCTAG 60.606 60.000 0.00 0.00 0.00 3.02
2699 2958 1.675641 CAGCAACACCACCCCTAGC 60.676 63.158 0.00 0.00 0.00 3.42
2700 2959 2.153401 AGCAACACCACCCCTAGCA 61.153 57.895 0.00 0.00 0.00 3.49
2701 2960 1.971695 GCAACACCACCCCTAGCAC 60.972 63.158 0.00 0.00 0.00 4.40
2702 2961 1.761174 CAACACCACCCCTAGCACT 59.239 57.895 0.00 0.00 0.00 4.40
2703 2962 0.981183 CAACACCACCCCTAGCACTA 59.019 55.000 0.00 0.00 0.00 2.74
2704 2963 0.981943 AACACCACCCCTAGCACTAC 59.018 55.000 0.00 0.00 0.00 2.73
2705 2964 0.178915 ACACCACCCCTAGCACTACA 60.179 55.000 0.00 0.00 0.00 2.74
2706 2965 0.981183 CACCACCCCTAGCACTACAA 59.019 55.000 0.00 0.00 0.00 2.41
2707 2966 1.066143 CACCACCCCTAGCACTACAAG 60.066 57.143 0.00 0.00 0.00 3.16
2708 2967 1.203262 ACCACCCCTAGCACTACAAGA 60.203 52.381 0.00 0.00 0.00 3.02
2709 2968 1.482593 CCACCCCTAGCACTACAAGAG 59.517 57.143 0.00 0.00 0.00 2.85
2710 2969 1.134670 CACCCCTAGCACTACAAGAGC 60.135 57.143 0.00 0.00 31.73 4.09
2711 2970 0.466124 CCCCTAGCACTACAAGAGCC 59.534 60.000 0.00 0.00 31.96 4.70
2712 2971 1.195115 CCCTAGCACTACAAGAGCCA 58.805 55.000 0.00 0.00 31.96 4.75
2713 2972 1.134670 CCCTAGCACTACAAGAGCCAC 60.135 57.143 0.00 0.00 31.96 5.01
2714 2973 1.134670 CCTAGCACTACAAGAGCCACC 60.135 57.143 0.00 0.00 31.96 4.61
2715 2974 0.530744 TAGCACTACAAGAGCCACCG 59.469 55.000 0.00 0.00 31.96 4.94
2716 2975 1.741770 GCACTACAAGAGCCACCGG 60.742 63.158 0.00 0.00 0.00 5.28
2717 2976 1.079127 CACTACAAGAGCCACCGGG 60.079 63.158 6.32 0.00 37.18 5.73
2718 2977 2.291043 ACTACAAGAGCCACCGGGG 61.291 63.158 6.32 0.00 40.85 5.73
2719 2978 3.006728 TACAAGAGCCACCGGGGG 61.007 66.667 22.08 22.08 37.04 5.40
2727 2986 2.361992 CCACCGGGGGCCTTAAAC 60.362 66.667 11.58 0.00 0.00 2.01
2728 2987 2.748647 CACCGGGGGCCTTAAACG 60.749 66.667 6.32 0.04 0.00 3.60
2729 2988 3.251509 ACCGGGGGCCTTAAACGT 61.252 61.111 6.32 0.00 0.00 3.99
2730 2989 2.748647 CCGGGGGCCTTAAACGTG 60.749 66.667 0.84 0.00 0.00 4.49
2731 2990 2.348243 CGGGGGCCTTAAACGTGA 59.652 61.111 0.84 0.00 0.00 4.35
2732 2991 1.302671 CGGGGGCCTTAAACGTGAA 60.303 57.895 0.84 0.00 0.00 3.18
2733 2992 1.579964 CGGGGGCCTTAAACGTGAAC 61.580 60.000 0.84 0.00 0.00 3.18
2734 2993 0.537828 GGGGGCCTTAAACGTGAACA 60.538 55.000 0.84 0.00 0.00 3.18
2735 2994 0.594602 GGGGCCTTAAACGTGAACAC 59.405 55.000 0.84 0.00 0.00 3.32
2752 3011 3.862124 CGCCACCGTGAAGAGAAG 58.138 61.111 0.00 0.00 0.00 2.85
2753 3012 1.289066 CGCCACCGTGAAGAGAAGA 59.711 57.895 0.00 0.00 0.00 2.87
2754 3013 0.319555 CGCCACCGTGAAGAGAAGAA 60.320 55.000 0.00 0.00 0.00 2.52
2755 3014 1.433534 GCCACCGTGAAGAGAAGAAG 58.566 55.000 0.00 0.00 0.00 2.85
2756 3015 1.433534 CCACCGTGAAGAGAAGAAGC 58.566 55.000 0.00 0.00 0.00 3.86
2757 3016 1.001406 CCACCGTGAAGAGAAGAAGCT 59.999 52.381 0.00 0.00 0.00 3.74
2758 3017 2.231478 CCACCGTGAAGAGAAGAAGCTA 59.769 50.000 0.00 0.00 0.00 3.32
2759 3018 3.246619 CACCGTGAAGAGAAGAAGCTAC 58.753 50.000 0.00 0.00 0.00 3.58
2760 3019 2.891580 ACCGTGAAGAGAAGAAGCTACA 59.108 45.455 0.00 0.00 0.00 2.74
2761 3020 3.511934 ACCGTGAAGAGAAGAAGCTACAT 59.488 43.478 0.00 0.00 0.00 2.29
2762 3021 4.705507 ACCGTGAAGAGAAGAAGCTACATA 59.294 41.667 0.00 0.00 0.00 2.29
2763 3022 5.038033 CCGTGAAGAGAAGAAGCTACATAC 58.962 45.833 0.00 0.00 0.00 2.39
2764 3023 4.731000 CGTGAAGAGAAGAAGCTACATACG 59.269 45.833 0.00 0.00 0.00 3.06
2765 3024 5.447413 CGTGAAGAGAAGAAGCTACATACGA 60.447 44.000 0.00 0.00 0.00 3.43
2766 3025 5.740099 GTGAAGAGAAGAAGCTACATACGAC 59.260 44.000 0.00 0.00 0.00 4.34
2767 3026 4.539509 AGAGAAGAAGCTACATACGACG 57.460 45.455 0.00 0.00 0.00 5.12
2768 3027 3.037324 GAGAAGAAGCTACATACGACGC 58.963 50.000 0.00 0.00 0.00 5.19
2769 3028 2.683867 AGAAGAAGCTACATACGACGCT 59.316 45.455 0.00 0.00 0.00 5.07
2770 3029 2.759538 AGAAGCTACATACGACGCTC 57.240 50.000 0.00 0.00 31.30 5.03
2771 3030 1.334243 AGAAGCTACATACGACGCTCC 59.666 52.381 0.00 0.00 31.30 4.70
2772 3031 0.029035 AAGCTACATACGACGCTCCG 59.971 55.000 0.00 0.00 31.30 4.63
2773 3032 1.094073 AGCTACATACGACGCTCCGT 61.094 55.000 0.00 5.62 45.10 4.69
2774 3033 0.928908 GCTACATACGACGCTCCGTG 60.929 60.000 9.95 0.00 41.37 4.94
2775 3034 0.316772 CTACATACGACGCTCCGTGG 60.317 60.000 9.95 0.00 41.37 4.94
2776 3035 1.717791 TACATACGACGCTCCGTGGG 61.718 60.000 9.95 5.16 41.37 4.61
2777 3036 4.203076 ATACGACGCTCCGTGGGC 62.203 66.667 9.95 0.00 41.37 5.36
2788 3047 4.335647 CGTGGGCTCCAAGGCAGT 62.336 66.667 2.81 0.00 43.44 4.40
2789 3048 2.674380 GTGGGCTCCAAGGCAGTG 60.674 66.667 2.81 0.00 43.44 3.66
2790 3049 4.666253 TGGGCTCCAAGGCAGTGC 62.666 66.667 6.55 6.55 43.44 4.40
2801 3060 3.359002 GCAGTGCCAACAGGAAGG 58.641 61.111 2.85 0.00 0.00 3.46
2802 3061 1.529244 GCAGTGCCAACAGGAAGGT 60.529 57.895 2.85 0.00 0.00 3.50
2803 3062 1.109323 GCAGTGCCAACAGGAAGGTT 61.109 55.000 2.85 0.00 0.00 3.50
2804 3063 1.817740 GCAGTGCCAACAGGAAGGTTA 60.818 52.381 2.85 0.00 0.00 2.85
2805 3064 1.880027 CAGTGCCAACAGGAAGGTTAC 59.120 52.381 0.00 0.00 0.00 2.50
2806 3065 0.872388 GTGCCAACAGGAAGGTTACG 59.128 55.000 0.00 0.00 0.00 3.18
2807 3066 0.759959 TGCCAACAGGAAGGTTACGA 59.240 50.000 0.00 0.00 0.00 3.43
2808 3067 1.154197 GCCAACAGGAAGGTTACGAC 58.846 55.000 0.00 0.00 0.00 4.34
2809 3068 1.541670 GCCAACAGGAAGGTTACGACA 60.542 52.381 0.00 0.00 0.00 4.35
2810 3069 2.140717 CCAACAGGAAGGTTACGACAC 58.859 52.381 0.00 0.00 0.00 3.67
2811 3070 2.224209 CCAACAGGAAGGTTACGACACT 60.224 50.000 0.00 0.00 0.00 3.55
2812 3071 2.800544 CAACAGGAAGGTTACGACACTG 59.199 50.000 0.00 0.00 0.00 3.66
2813 3072 2.313317 ACAGGAAGGTTACGACACTGA 58.687 47.619 0.00 0.00 0.00 3.41
2814 3073 2.696707 ACAGGAAGGTTACGACACTGAA 59.303 45.455 0.00 0.00 0.00 3.02
2815 3074 3.243771 ACAGGAAGGTTACGACACTGAAG 60.244 47.826 0.00 0.00 0.00 3.02
2816 3075 2.067013 GGAAGGTTACGACACTGAAGC 58.933 52.381 0.00 0.00 0.00 3.86
2817 3076 1.719780 GAAGGTTACGACACTGAAGCG 59.280 52.381 0.00 0.00 0.00 4.68
2818 3077 0.666577 AGGTTACGACACTGAAGCGC 60.667 55.000 0.00 0.00 0.00 5.92
2819 3078 1.623973 GGTTACGACACTGAAGCGCC 61.624 60.000 2.29 0.00 0.00 6.53
2820 3079 1.731613 TTACGACACTGAAGCGCCG 60.732 57.895 2.29 0.00 0.00 6.46
2841 3100 4.547367 CCGCCCGACCCAAGGATC 62.547 72.222 0.00 0.00 0.00 3.36
2842 3101 3.781307 CGCCCGACCCAAGGATCA 61.781 66.667 0.00 0.00 0.00 2.92
2843 3102 2.190578 GCCCGACCCAAGGATCAG 59.809 66.667 0.00 0.00 0.00 2.90
2844 3103 2.911143 CCCGACCCAAGGATCAGG 59.089 66.667 0.00 0.00 0.00 3.86
2850 3109 3.596362 CCCAAGGATCAGGGTTTCC 57.404 57.895 8.55 0.00 40.34 3.13
2851 3110 0.033109 CCCAAGGATCAGGGTTTCCC 60.033 60.000 8.55 0.00 45.90 3.97
2860 3119 3.974293 GGGTTTCCCCCGGAGCAA 61.974 66.667 0.73 0.00 45.80 3.91
2861 3120 2.675423 GGTTTCCCCCGGAGCAAC 60.675 66.667 0.73 0.01 31.21 4.17
2862 3121 2.114411 GTTTCCCCCGGAGCAACA 59.886 61.111 0.73 0.00 31.21 3.33
2863 3122 2.114411 TTTCCCCCGGAGCAACAC 59.886 61.111 0.73 0.00 31.21 3.32
2864 3123 3.835790 TTTCCCCCGGAGCAACACG 62.836 63.158 0.73 0.00 31.21 4.49
2871 3130 4.980805 GGAGCAACACGACGGGCA 62.981 66.667 0.00 0.00 0.00 5.36
2872 3131 3.414700 GAGCAACACGACGGGCAG 61.415 66.667 0.00 0.00 0.00 4.85
2880 3139 4.838486 CGACGGGCAGCGAGAGTC 62.838 72.222 0.00 0.00 0.00 3.36
2881 3140 4.838486 GACGGGCAGCGAGAGTCG 62.838 72.222 0.00 0.00 43.89 4.18
2900 3159 3.169198 GGCGACGCCTTCAAGAAG 58.831 61.111 31.30 2.83 46.69 2.85
2910 3169 2.464157 CTTCAAGAAGGGAACGAGCT 57.536 50.000 1.86 0.00 34.87 4.09
2911 3170 2.772287 CTTCAAGAAGGGAACGAGCTT 58.228 47.619 1.86 0.00 34.87 3.74
2912 3171 2.457366 TCAAGAAGGGAACGAGCTTC 57.543 50.000 0.00 0.00 0.00 3.86
2913 3172 1.071605 CAAGAAGGGAACGAGCTTCG 58.928 55.000 0.00 0.00 46.93 3.79
2914 3173 0.670854 AAGAAGGGAACGAGCTTCGC 60.671 55.000 5.63 0.00 45.12 4.70
2915 3174 2.047179 AAGGGAACGAGCTTCGCC 60.047 61.111 5.63 1.00 45.12 5.54
2916 3175 2.781595 GAAGGGAACGAGCTTCGCCA 62.782 60.000 5.63 0.00 45.12 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.156293 AGCTGGATGTATTTTGCACACA 58.844 40.909 0.00 0.00 0.00 3.72
47 48 6.258727 CACACATAGGGAATGAATGACAGTAC 59.741 42.308 0.00 0.00 39.07 2.73
127 128 7.831753 TGTAGGTCTCTGATCTTAGAACTTTG 58.168 38.462 17.15 0.00 40.29 2.77
138 139 5.767665 TGCTTATCTCTGTAGGTCTCTGATC 59.232 44.000 0.00 0.00 0.00 2.92
210 211 3.565905 CTTCCAACAAAGCATGAGGAC 57.434 47.619 0.00 0.00 36.80 3.85
233 234 6.966534 ATGGAGATGTTCAAAACTTGTCTT 57.033 33.333 3.88 0.00 31.90 3.01
254 255 6.484643 ACAACAGATCCGGAGATTGATTAATG 59.515 38.462 20.44 12.37 30.90 1.90
308 309 5.564550 AGATTGCAACTAGATGTTCAAGGT 58.435 37.500 0.00 0.00 36.63 3.50
325 326 8.025445 ACAAACAGATCTTTCACATTAGATTGC 58.975 33.333 0.00 0.00 31.46 3.56
355 356 4.579753 CCACAAATGGGCAAAATCAGTTTT 59.420 37.500 0.00 0.00 43.04 2.43
431 432 8.055181 TGACATCTAATTCCTTAAAGGCATTCT 58.945 33.333 0.00 0.00 33.34 2.40
432 433 8.225603 TGACATCTAATTCCTTAAAGGCATTC 57.774 34.615 0.00 0.00 33.34 2.67
477 539 7.262048 ACTGTGTTTAACTTTACCCACAATTG 58.738 34.615 3.24 3.24 32.96 2.32
485 547 7.988737 ACCAGTTAACTGTGTTTAACTTTACC 58.011 34.615 29.05 0.00 45.85 2.85
500 562 5.099042 ACACTCACTCAAACCAGTTAACT 57.901 39.130 1.12 1.12 0.00 2.24
505 567 5.497474 ACTTTAACACTCACTCAAACCAGT 58.503 37.500 0.00 0.00 0.00 4.00
591 653 5.626142 TCAGCTTAAATCGGCCCATATTAA 58.374 37.500 0.00 0.00 0.00 1.40
610 673 7.087007 TGATCAAGAACGACATCTATATCAGC 58.913 38.462 0.00 0.00 31.89 4.26
974 1038 6.512342 AGCAATGAGAAAAAGAGAAGGATG 57.488 37.500 0.00 0.00 0.00 3.51
975 1039 7.628234 TCTAGCAATGAGAAAAAGAGAAGGAT 58.372 34.615 0.00 0.00 0.00 3.24
976 1040 7.009179 TCTAGCAATGAGAAAAAGAGAAGGA 57.991 36.000 0.00 0.00 0.00 3.36
978 1042 7.679164 GCCATCTAGCAATGAGAAAAAGAGAAG 60.679 40.741 0.00 0.00 0.00 2.85
981 1045 5.589452 AGCCATCTAGCAATGAGAAAAAGAG 59.411 40.000 0.00 0.00 34.23 2.85
1020 1084 4.208460 CACTTCTGTAACTCGCTCGAAAAA 59.792 41.667 0.00 0.00 0.00 1.94
1064 1128 9.915629 GTCCGATAGTGATGAAAAATATAGAGT 57.084 33.333 0.00 0.00 0.00 3.24
1118 1182 7.543756 AGTCTCTACTTTGTTCATAAGAGCTC 58.456 38.462 5.27 5.27 32.38 4.09
1179 1243 0.871722 CCGTGCAATTTTGTCCTCGA 59.128 50.000 0.00 0.00 0.00 4.04
1197 1261 1.218316 CTCCTCCACTACAACGCCC 59.782 63.158 0.00 0.00 0.00 6.13
1369 1433 4.695455 TGGTGCATAAACTCTTGCTCTTAC 59.305 41.667 0.00 0.00 39.60 2.34
1411 1475 3.434984 AGAAGCAAGTCTTTCTCGCAATC 59.565 43.478 0.00 0.00 34.56 2.67
1426 1490 5.972935 TCGGTATACATGAAGAAGAAGCAA 58.027 37.500 5.01 0.00 0.00 3.91
1450 1514 6.639632 TCTGCCCAAATTCTTAATATCTGC 57.360 37.500 0.00 0.00 0.00 4.26
1491 1555 2.239654 TGGACTAAGAATCAAGCCCTGG 59.760 50.000 0.00 0.00 0.00 4.45
1638 1702 4.000325 TGAGGTTCATTGTGTATCCAACG 59.000 43.478 0.00 0.00 0.00 4.10
1671 1735 5.182001 TGAGCTTCCTTTTTCACTTGCTATC 59.818 40.000 0.00 0.00 0.00 2.08
1746 1810 2.312390 GTAAACTGCCCTCCAAAACCA 58.688 47.619 0.00 0.00 0.00 3.67
1795 1859 1.126846 GTGATGTCGCCTCAGAAAACG 59.873 52.381 0.00 0.00 0.00 3.60
1954 2018 5.369404 TGGATGGGATAACAATAAGAGCTCA 59.631 40.000 17.77 0.00 0.00 4.26
1957 2021 5.376625 TGTGGATGGGATAACAATAAGAGC 58.623 41.667 0.00 0.00 0.00 4.09
1961 2025 5.359576 GCAACTGTGGATGGGATAACAATAA 59.640 40.000 0.00 0.00 0.00 1.40
1963 2027 3.701040 GCAACTGTGGATGGGATAACAAT 59.299 43.478 0.00 0.00 0.00 2.71
1981 2045 1.206072 CAGCAGTTCGAGCAGCAAC 59.794 57.895 18.20 0.00 0.00 4.17
2000 2064 3.547746 TGAACCTGACCCTGTTGTTTAC 58.452 45.455 0.00 0.00 0.00 2.01
2010 2074 2.359900 CAGCACTAATGAACCTGACCC 58.640 52.381 0.00 0.00 0.00 4.46
2011 2075 1.740025 GCAGCACTAATGAACCTGACC 59.260 52.381 0.00 0.00 0.00 4.02
2132 2196 8.641541 AGAAAATAATCTGAAGCAGAAAACCAA 58.358 29.630 0.78 0.00 44.04 3.67
2153 2217 8.952278 AGTGTTCACAACTACAATAACAGAAAA 58.048 29.630 5.74 0.00 0.00 2.29
2176 2240 9.294030 GAGGCAAATTTTGAATTACTATCAGTG 57.706 33.333 13.26 0.00 0.00 3.66
2251 2315 9.832445 AGACATGAAGTAAATTATGGTATTCGT 57.168 29.630 0.00 0.00 0.00 3.85
2257 2321 8.978874 TGCATAGACATGAAGTAAATTATGGT 57.021 30.769 0.00 0.00 33.67 3.55
2258 2322 9.888878 CTTGCATAGACATGAAGTAAATTATGG 57.111 33.333 0.00 0.00 33.67 2.74
2259 2323 9.390795 GCTTGCATAGACATGAAGTAAATTATG 57.609 33.333 0.00 0.00 33.67 1.90
2260 2324 8.571336 GGCTTGCATAGACATGAAGTAAATTAT 58.429 33.333 0.00 0.00 33.67 1.28
2262 2326 6.604795 AGGCTTGCATAGACATGAAGTAAATT 59.395 34.615 0.00 0.00 32.58 1.82
2263 2327 6.125029 AGGCTTGCATAGACATGAAGTAAAT 58.875 36.000 0.00 0.00 32.58 1.40
2272 2529 4.708421 ACATTTTGAGGCTTGCATAGACAT 59.292 37.500 4.83 0.00 32.58 3.06
2337 2594 7.715686 AGATCACGAAAAGGAAACTAAACTCTT 59.284 33.333 0.00 0.00 42.68 2.85
2360 2617 6.058183 GGAATCACCATTTACTAGCACAGAT 58.942 40.000 0.00 0.00 38.79 2.90
2453 2712 7.957484 CACAGATCAACTTAGGTCATAAAAACG 59.043 37.037 0.00 0.00 0.00 3.60
2539 2798 6.959606 AATAACTCTGGCTGTATCCCATAT 57.040 37.500 0.00 0.00 0.00 1.78
2574 2833 6.730960 TTTATATATAAAGCGGGGCGAAAG 57.269 37.500 12.90 0.00 0.00 2.62
2575 2834 6.730960 CTTTATATATAAAGCGGGGCGAAA 57.269 37.500 25.10 1.66 41.69 3.46
2589 2848 8.840321 GTTGTTGGTGATCTGTGCTTTATATAT 58.160 33.333 0.00 0.00 0.00 0.86
2590 2849 7.282224 GGTTGTTGGTGATCTGTGCTTTATATA 59.718 37.037 0.00 0.00 0.00 0.86
2591 2850 6.095440 GGTTGTTGGTGATCTGTGCTTTATAT 59.905 38.462 0.00 0.00 0.00 0.86
2592 2851 5.414454 GGTTGTTGGTGATCTGTGCTTTATA 59.586 40.000 0.00 0.00 0.00 0.98
2593 2852 4.218417 GGTTGTTGGTGATCTGTGCTTTAT 59.782 41.667 0.00 0.00 0.00 1.40
2594 2853 3.568007 GGTTGTTGGTGATCTGTGCTTTA 59.432 43.478 0.00 0.00 0.00 1.85
2595 2854 2.362077 GGTTGTTGGTGATCTGTGCTTT 59.638 45.455 0.00 0.00 0.00 3.51
2596 2855 1.956477 GGTTGTTGGTGATCTGTGCTT 59.044 47.619 0.00 0.00 0.00 3.91
2597 2856 1.609208 GGTTGTTGGTGATCTGTGCT 58.391 50.000 0.00 0.00 0.00 4.40
2598 2857 0.598065 GGGTTGTTGGTGATCTGTGC 59.402 55.000 0.00 0.00 0.00 4.57
2599 2858 1.881973 CTGGGTTGTTGGTGATCTGTG 59.118 52.381 0.00 0.00 0.00 3.66
2600 2859 1.494721 ACTGGGTTGTTGGTGATCTGT 59.505 47.619 0.00 0.00 0.00 3.41
2601 2860 2.276732 ACTGGGTTGTTGGTGATCTG 57.723 50.000 0.00 0.00 0.00 2.90
2602 2861 2.708861 TGTACTGGGTTGTTGGTGATCT 59.291 45.455 0.00 0.00 0.00 2.75
2603 2862 3.074412 CTGTACTGGGTTGTTGGTGATC 58.926 50.000 0.00 0.00 0.00 2.92
2604 2863 2.814097 GCTGTACTGGGTTGTTGGTGAT 60.814 50.000 1.65 0.00 0.00 3.06
2605 2864 1.476110 GCTGTACTGGGTTGTTGGTGA 60.476 52.381 1.65 0.00 0.00 4.02
2606 2865 0.951558 GCTGTACTGGGTTGTTGGTG 59.048 55.000 1.65 0.00 0.00 4.17
2607 2866 0.548989 TGCTGTACTGGGTTGTTGGT 59.451 50.000 1.65 0.00 0.00 3.67
2608 2867 0.951558 GTGCTGTACTGGGTTGTTGG 59.048 55.000 1.65 0.00 0.00 3.77
2609 2868 1.333619 GTGTGCTGTACTGGGTTGTTG 59.666 52.381 1.65 0.00 0.00 3.33
2610 2869 1.675552 GTGTGCTGTACTGGGTTGTT 58.324 50.000 1.65 0.00 0.00 2.83
2611 2870 0.531974 CGTGTGCTGTACTGGGTTGT 60.532 55.000 1.65 0.00 0.00 3.32
2612 2871 1.841663 GCGTGTGCTGTACTGGGTTG 61.842 60.000 1.65 0.00 38.39 3.77
2613 2872 1.597027 GCGTGTGCTGTACTGGGTT 60.597 57.895 1.65 0.00 38.39 4.11
2614 2873 2.030562 GCGTGTGCTGTACTGGGT 59.969 61.111 1.65 0.00 38.39 4.51
2615 2874 2.742372 GGCGTGTGCTGTACTGGG 60.742 66.667 1.65 0.00 42.25 4.45
2616 2875 2.030412 TGGCGTGTGCTGTACTGG 59.970 61.111 1.65 0.00 42.25 4.00
2617 2876 2.317609 GGTGGCGTGTGCTGTACTG 61.318 63.158 0.00 0.00 42.25 2.74
2618 2877 2.030562 GGTGGCGTGTGCTGTACT 59.969 61.111 0.00 0.00 42.25 2.73
2619 2878 1.890041 TTGGTGGCGTGTGCTGTAC 60.890 57.895 0.00 0.00 42.25 2.90
2620 2879 1.890041 GTTGGTGGCGTGTGCTGTA 60.890 57.895 0.00 0.00 42.25 2.74
2621 2880 3.209097 GTTGGTGGCGTGTGCTGT 61.209 61.111 0.00 0.00 42.25 4.40
2622 2881 3.208383 TGTTGGTGGCGTGTGCTG 61.208 61.111 0.00 0.00 42.25 4.41
2623 2882 3.209097 GTGTTGGTGGCGTGTGCT 61.209 61.111 0.00 0.00 42.25 4.40
2624 2883 3.513438 TGTGTTGGTGGCGTGTGC 61.513 61.111 0.00 0.00 41.71 4.57
2625 2884 2.402572 TGTGTGTTGGTGGCGTGTG 61.403 57.895 0.00 0.00 0.00 3.82
2626 2885 2.045829 TGTGTGTTGGTGGCGTGT 60.046 55.556 0.00 0.00 0.00 4.49
2627 2886 2.407210 GTGTGTGTTGGTGGCGTG 59.593 61.111 0.00 0.00 0.00 5.34
2628 2887 3.199190 CGTGTGTGTTGGTGGCGT 61.199 61.111 0.00 0.00 0.00 5.68
2629 2888 4.605967 GCGTGTGTGTTGGTGGCG 62.606 66.667 0.00 0.00 0.00 5.69
2630 2889 3.513438 TGCGTGTGTGTTGGTGGC 61.513 61.111 0.00 0.00 0.00 5.01
2631 2890 2.402572 TGTGCGTGTGTGTTGGTGG 61.403 57.895 0.00 0.00 0.00 4.61
2632 2891 1.226267 GTGTGCGTGTGTGTTGGTG 60.226 57.895 0.00 0.00 0.00 4.17
2633 2892 1.672682 TGTGTGCGTGTGTGTTGGT 60.673 52.632 0.00 0.00 0.00 3.67
2634 2893 1.226267 GTGTGTGCGTGTGTGTTGG 60.226 57.895 0.00 0.00 0.00 3.77
2635 2894 1.226267 GGTGTGTGCGTGTGTGTTG 60.226 57.895 0.00 0.00 0.00 3.33
2636 2895 2.403378 GGGTGTGTGCGTGTGTGTT 61.403 57.895 0.00 0.00 0.00 3.32
2637 2896 2.822255 GGGTGTGTGCGTGTGTGT 60.822 61.111 0.00 0.00 0.00 3.72
2638 2897 2.321668 CTTGGGTGTGTGCGTGTGTG 62.322 60.000 0.00 0.00 0.00 3.82
2639 2898 2.045829 TTGGGTGTGTGCGTGTGT 60.046 55.556 0.00 0.00 0.00 3.72
2640 2899 2.715005 CTTGGGTGTGTGCGTGTG 59.285 61.111 0.00 0.00 0.00 3.82
2641 2900 2.515991 CCTTGGGTGTGTGCGTGT 60.516 61.111 0.00 0.00 0.00 4.49
2642 2901 3.964875 GCCTTGGGTGTGTGCGTG 61.965 66.667 0.00 0.00 0.00 5.34
2643 2902 4.497984 TGCCTTGGGTGTGTGCGT 62.498 61.111 0.00 0.00 0.00 5.24
2644 2903 3.663176 CTGCCTTGGGTGTGTGCG 61.663 66.667 0.00 0.00 0.00 5.34
2645 2904 3.297620 CCTGCCTTGGGTGTGTGC 61.298 66.667 0.00 0.00 0.00 4.57
2646 2905 0.327924 TATCCTGCCTTGGGTGTGTG 59.672 55.000 0.00 0.00 0.00 3.82
2647 2906 0.328258 GTATCCTGCCTTGGGTGTGT 59.672 55.000 0.00 0.00 0.00 3.72
2648 2907 0.327924 TGTATCCTGCCTTGGGTGTG 59.672 55.000 0.00 0.00 0.00 3.82
2649 2908 1.072266 TTGTATCCTGCCTTGGGTGT 58.928 50.000 0.00 0.00 0.00 4.16
2650 2909 2.094675 CTTTGTATCCTGCCTTGGGTG 58.905 52.381 0.00 0.00 0.00 4.61
2651 2910 1.005924 CCTTTGTATCCTGCCTTGGGT 59.994 52.381 0.00 0.00 0.00 4.51
2652 2911 1.767759 CCTTTGTATCCTGCCTTGGG 58.232 55.000 0.00 0.00 0.00 4.12
2653 2912 1.106285 GCCTTTGTATCCTGCCTTGG 58.894 55.000 0.00 0.00 0.00 3.61
2654 2913 0.734889 CGCCTTTGTATCCTGCCTTG 59.265 55.000 0.00 0.00 0.00 3.61
2655 2914 1.032114 GCGCCTTTGTATCCTGCCTT 61.032 55.000 0.00 0.00 0.00 4.35
2656 2915 1.452108 GCGCCTTTGTATCCTGCCT 60.452 57.895 0.00 0.00 0.00 4.75
2657 2916 1.452108 AGCGCCTTTGTATCCTGCC 60.452 57.895 2.29 0.00 0.00 4.85
2658 2917 0.744414 TCAGCGCCTTTGTATCCTGC 60.744 55.000 2.29 0.00 0.00 4.85
2659 2918 1.293924 CTCAGCGCCTTTGTATCCTG 58.706 55.000 2.29 0.00 0.00 3.86
2660 2919 0.462759 GCTCAGCGCCTTTGTATCCT 60.463 55.000 2.29 0.00 0.00 3.24
2661 2920 0.744414 TGCTCAGCGCCTTTGTATCC 60.744 55.000 2.29 0.00 38.05 2.59
2662 2921 0.375106 GTGCTCAGCGCCTTTGTATC 59.625 55.000 2.29 0.00 38.05 2.24
2663 2922 0.321564 TGTGCTCAGCGCCTTTGTAT 60.322 50.000 7.99 0.00 38.39 2.29
2664 2923 0.950555 CTGTGCTCAGCGCCTTTGTA 60.951 55.000 7.99 0.00 38.39 2.41
2665 2924 2.203195 TGTGCTCAGCGCCTTTGT 60.203 55.556 7.99 0.00 38.39 2.83
2666 2925 2.559840 CTGTGCTCAGCGCCTTTG 59.440 61.111 7.99 0.00 38.39 2.77
2674 2933 1.650912 GTGGTGTTGCTGTGCTCAG 59.349 57.895 11.44 11.44 43.87 3.35
2675 2934 1.823470 GGTGGTGTTGCTGTGCTCA 60.823 57.895 0.00 0.00 0.00 4.26
2676 2935 2.555547 GGGTGGTGTTGCTGTGCTC 61.556 63.158 0.00 0.00 0.00 4.26
2677 2936 2.519302 GGGTGGTGTTGCTGTGCT 60.519 61.111 0.00 0.00 0.00 4.40
2678 2937 2.690653 TAGGGGTGGTGTTGCTGTGC 62.691 60.000 0.00 0.00 0.00 4.57
2679 2938 0.606401 CTAGGGGTGGTGTTGCTGTG 60.606 60.000 0.00 0.00 0.00 3.66
2680 2939 1.761174 CTAGGGGTGGTGTTGCTGT 59.239 57.895 0.00 0.00 0.00 4.40
2681 2940 1.675641 GCTAGGGGTGGTGTTGCTG 60.676 63.158 0.00 0.00 0.00 4.41
2682 2941 2.153401 TGCTAGGGGTGGTGTTGCT 61.153 57.895 0.00 0.00 0.00 3.91
2683 2942 1.971695 GTGCTAGGGGTGGTGTTGC 60.972 63.158 0.00 0.00 0.00 4.17
2684 2943 0.981183 TAGTGCTAGGGGTGGTGTTG 59.019 55.000 0.00 0.00 0.00 3.33
2685 2944 0.981943 GTAGTGCTAGGGGTGGTGTT 59.018 55.000 0.00 0.00 0.00 3.32
2686 2945 0.178915 TGTAGTGCTAGGGGTGGTGT 60.179 55.000 0.00 0.00 0.00 4.16
2687 2946 0.981183 TTGTAGTGCTAGGGGTGGTG 59.019 55.000 0.00 0.00 0.00 4.17
2688 2947 1.203262 TCTTGTAGTGCTAGGGGTGGT 60.203 52.381 0.00 0.00 0.00 4.16
2689 2948 1.482593 CTCTTGTAGTGCTAGGGGTGG 59.517 57.143 0.00 0.00 0.00 4.61
2690 2949 1.134670 GCTCTTGTAGTGCTAGGGGTG 60.135 57.143 0.00 0.00 32.42 4.61
2691 2950 1.196012 GCTCTTGTAGTGCTAGGGGT 58.804 55.000 0.00 0.00 32.42 4.95
2692 2951 0.466124 GGCTCTTGTAGTGCTAGGGG 59.534 60.000 0.00 0.00 35.27 4.79
2693 2952 1.134670 GTGGCTCTTGTAGTGCTAGGG 60.135 57.143 0.00 0.00 35.27 3.53
2694 2953 1.134670 GGTGGCTCTTGTAGTGCTAGG 60.135 57.143 0.00 0.00 35.27 3.02
2695 2954 1.469940 CGGTGGCTCTTGTAGTGCTAG 60.470 57.143 0.00 0.00 35.27 3.42
2696 2955 0.530744 CGGTGGCTCTTGTAGTGCTA 59.469 55.000 0.00 0.00 35.27 3.49
2697 2956 1.293498 CGGTGGCTCTTGTAGTGCT 59.707 57.895 0.00 0.00 35.27 4.40
2698 2957 1.741770 CCGGTGGCTCTTGTAGTGC 60.742 63.158 0.00 0.00 34.23 4.40
2699 2958 1.079127 CCCGGTGGCTCTTGTAGTG 60.079 63.158 0.00 0.00 0.00 2.74
2700 2959 2.291043 CCCCGGTGGCTCTTGTAGT 61.291 63.158 0.00 0.00 0.00 2.73
2701 2960 2.584608 CCCCGGTGGCTCTTGTAG 59.415 66.667 0.00 0.00 0.00 2.74
2702 2961 3.006728 CCCCCGGTGGCTCTTGTA 61.007 66.667 0.00 0.00 0.00 2.41
2710 2969 2.361992 GTTTAAGGCCCCCGGTGG 60.362 66.667 0.00 0.00 0.00 4.61
2711 2970 2.748647 CGTTTAAGGCCCCCGGTG 60.749 66.667 0.00 0.00 0.00 4.94
2712 2971 3.251509 ACGTTTAAGGCCCCCGGT 61.252 61.111 0.00 0.00 0.00 5.28
2713 2972 2.748647 CACGTTTAAGGCCCCCGG 60.749 66.667 0.00 0.00 0.00 5.73
2714 2973 1.302671 TTCACGTTTAAGGCCCCCG 60.303 57.895 0.00 0.00 0.00 5.73
2715 2974 0.537828 TGTTCACGTTTAAGGCCCCC 60.538 55.000 0.00 0.00 0.00 5.40
2716 2975 0.594602 GTGTTCACGTTTAAGGCCCC 59.405 55.000 0.00 0.00 0.00 5.80
2717 2976 0.236449 CGTGTTCACGTTTAAGGCCC 59.764 55.000 15.81 0.00 0.00 5.80
2718 2977 0.385098 GCGTGTTCACGTTTAAGGCC 60.385 55.000 22.85 0.00 35.26 5.19
2719 2978 0.385098 GGCGTGTTCACGTTTAAGGC 60.385 55.000 22.85 7.48 35.26 4.35
2720 2979 0.938713 TGGCGTGTTCACGTTTAAGG 59.061 50.000 22.85 0.00 35.26 2.69
2721 2980 1.333435 GGTGGCGTGTTCACGTTTAAG 60.333 52.381 22.85 0.00 36.09 1.85
2722 2981 0.656785 GGTGGCGTGTTCACGTTTAA 59.343 50.000 22.85 7.11 36.09 1.52
2723 2982 1.489070 CGGTGGCGTGTTCACGTTTA 61.489 55.000 22.85 9.77 36.09 2.01
2724 2983 2.815298 CGGTGGCGTGTTCACGTTT 61.815 57.895 22.85 0.00 36.09 3.60
2725 2984 3.266376 CGGTGGCGTGTTCACGTT 61.266 61.111 22.85 0.00 36.09 3.99
2726 2985 4.517815 ACGGTGGCGTGTTCACGT 62.518 61.111 22.85 3.14 36.09 4.49
2727 2986 3.995669 CACGGTGGCGTGTTCACG 61.996 66.667 19.03 19.03 36.09 4.35
2728 2987 2.101209 CTTCACGGTGGCGTGTTCAC 62.101 60.000 8.50 0.00 40.41 3.18
2729 2988 1.885388 CTTCACGGTGGCGTGTTCA 60.885 57.895 8.50 0.00 40.41 3.18
2730 2989 1.557443 CTCTTCACGGTGGCGTGTTC 61.557 60.000 8.50 0.00 40.41 3.18
2731 2990 1.594293 CTCTTCACGGTGGCGTGTT 60.594 57.895 8.50 0.00 40.41 3.32
2732 2991 2.023414 TTCTCTTCACGGTGGCGTGT 62.023 55.000 8.50 0.00 40.41 4.49
2733 2992 1.284982 CTTCTCTTCACGGTGGCGTG 61.285 60.000 8.50 0.00 40.84 5.34
2734 2993 1.006102 CTTCTCTTCACGGTGGCGT 60.006 57.895 8.50 0.00 0.00 5.68
2735 2994 0.319555 TTCTTCTCTTCACGGTGGCG 60.320 55.000 8.50 0.00 0.00 5.69
2736 2995 1.433534 CTTCTTCTCTTCACGGTGGC 58.566 55.000 8.50 0.00 0.00 5.01
2737 2996 1.001406 AGCTTCTTCTCTTCACGGTGG 59.999 52.381 8.50 0.00 0.00 4.61
2738 2997 2.447244 AGCTTCTTCTCTTCACGGTG 57.553 50.000 0.56 0.56 0.00 4.94
2739 2998 2.891580 TGTAGCTTCTTCTCTTCACGGT 59.108 45.455 0.00 0.00 0.00 4.83
2740 2999 3.577649 TGTAGCTTCTTCTCTTCACGG 57.422 47.619 0.00 0.00 0.00 4.94
2741 3000 4.731000 CGTATGTAGCTTCTTCTCTTCACG 59.269 45.833 0.00 0.00 0.00 4.35
2742 3001 5.740099 GTCGTATGTAGCTTCTTCTCTTCAC 59.260 44.000 0.00 0.00 0.00 3.18
2743 3002 5.447413 CGTCGTATGTAGCTTCTTCTCTTCA 60.447 44.000 0.00 0.00 0.00 3.02
2744 3003 4.965158 CGTCGTATGTAGCTTCTTCTCTTC 59.035 45.833 0.00 0.00 0.00 2.87
2745 3004 4.731193 GCGTCGTATGTAGCTTCTTCTCTT 60.731 45.833 0.00 0.00 0.00 2.85
2746 3005 3.242804 GCGTCGTATGTAGCTTCTTCTCT 60.243 47.826 0.00 0.00 0.00 3.10
2747 3006 3.037324 GCGTCGTATGTAGCTTCTTCTC 58.963 50.000 0.00 0.00 0.00 2.87
2748 3007 2.683867 AGCGTCGTATGTAGCTTCTTCT 59.316 45.455 0.00 0.00 36.41 2.85
2749 3008 3.037324 GAGCGTCGTATGTAGCTTCTTC 58.963 50.000 0.00 0.00 40.39 2.87
2750 3009 2.223525 GGAGCGTCGTATGTAGCTTCTT 60.224 50.000 0.00 0.00 40.39 2.52
2751 3010 1.334243 GGAGCGTCGTATGTAGCTTCT 59.666 52.381 0.00 0.00 40.39 2.85
2752 3011 1.756367 GGAGCGTCGTATGTAGCTTC 58.244 55.000 0.00 3.44 40.39 3.86
2753 3012 0.029035 CGGAGCGTCGTATGTAGCTT 59.971 55.000 0.00 0.00 40.39 3.74
2754 3013 1.094073 ACGGAGCGTCGTATGTAGCT 61.094 55.000 5.63 6.62 41.98 3.32
2755 3014 0.928908 CACGGAGCGTCGTATGTAGC 60.929 60.000 7.03 0.00 41.86 3.58
2756 3015 0.316772 CCACGGAGCGTCGTATGTAG 60.317 60.000 7.03 0.00 41.86 2.74
2757 3016 1.717791 CCCACGGAGCGTCGTATGTA 61.718 60.000 7.03 0.00 41.86 2.29
2758 3017 2.488355 CCACGGAGCGTCGTATGT 59.512 61.111 7.03 0.00 41.86 2.29
2759 3018 2.278596 CCCACGGAGCGTCGTATG 60.279 66.667 7.03 2.77 41.86 2.39
2760 3019 4.203076 GCCCACGGAGCGTCGTAT 62.203 66.667 7.03 0.00 41.86 3.06
2767 3026 4.785453 CCTTGGAGCCCACGGAGC 62.785 72.222 10.18 0.00 44.56 4.70
2768 3027 4.785453 GCCTTGGAGCCCACGGAG 62.785 72.222 17.45 3.50 44.56 4.63
2771 3030 4.335647 ACTGCCTTGGAGCCCACG 62.336 66.667 0.00 0.00 30.78 4.94
2772 3031 2.674380 CACTGCCTTGGAGCCCAC 60.674 66.667 0.00 0.00 30.78 4.61
2773 3032 4.666253 GCACTGCCTTGGAGCCCA 62.666 66.667 0.00 0.00 0.00 5.36
2784 3043 1.109323 AACCTTCCTGTTGGCACTGC 61.109 55.000 0.00 0.00 0.00 4.40
2785 3044 1.880027 GTAACCTTCCTGTTGGCACTG 59.120 52.381 0.00 0.00 0.00 3.66
2786 3045 1.542547 CGTAACCTTCCTGTTGGCACT 60.543 52.381 0.00 0.00 0.00 4.40
2787 3046 0.872388 CGTAACCTTCCTGTTGGCAC 59.128 55.000 0.00 0.00 0.00 5.01
2788 3047 0.759959 TCGTAACCTTCCTGTTGGCA 59.240 50.000 0.00 0.00 0.00 4.92
2789 3048 1.154197 GTCGTAACCTTCCTGTTGGC 58.846 55.000 0.00 0.00 0.00 4.52
2790 3049 2.140717 GTGTCGTAACCTTCCTGTTGG 58.859 52.381 0.00 0.00 0.00 3.77
2791 3050 2.800544 CAGTGTCGTAACCTTCCTGTTG 59.199 50.000 0.00 0.00 0.00 3.33
2792 3051 2.696707 TCAGTGTCGTAACCTTCCTGTT 59.303 45.455 0.00 0.00 0.00 3.16
2793 3052 2.313317 TCAGTGTCGTAACCTTCCTGT 58.687 47.619 0.00 0.00 0.00 4.00
2794 3053 3.318017 CTTCAGTGTCGTAACCTTCCTG 58.682 50.000 0.00 0.00 0.00 3.86
2795 3054 2.288886 GCTTCAGTGTCGTAACCTTCCT 60.289 50.000 0.00 0.00 0.00 3.36
2796 3055 2.067013 GCTTCAGTGTCGTAACCTTCC 58.933 52.381 0.00 0.00 0.00 3.46
2797 3056 1.719780 CGCTTCAGTGTCGTAACCTTC 59.280 52.381 0.00 0.00 0.00 3.46
2798 3057 1.779569 CGCTTCAGTGTCGTAACCTT 58.220 50.000 0.00 0.00 0.00 3.50
2799 3058 0.666577 GCGCTTCAGTGTCGTAACCT 60.667 55.000 0.00 0.00 0.00 3.50
2800 3059 1.623973 GGCGCTTCAGTGTCGTAACC 61.624 60.000 7.64 0.00 0.00 2.85
2801 3060 1.779683 GGCGCTTCAGTGTCGTAAC 59.220 57.895 7.64 0.00 0.00 2.50
2802 3061 4.255126 GGCGCTTCAGTGTCGTAA 57.745 55.556 7.64 0.00 0.00 3.18
2824 3083 4.547367 GATCCTTGGGTCGGGCGG 62.547 72.222 0.00 0.00 0.00 6.13
2825 3084 3.740128 CTGATCCTTGGGTCGGGCG 62.740 68.421 0.83 0.00 0.00 6.13
2826 3085 2.190578 CTGATCCTTGGGTCGGGC 59.809 66.667 0.83 0.00 0.00 6.13
2827 3086 2.746375 CCCTGATCCTTGGGTCGGG 61.746 68.421 18.62 18.62 40.01 5.14
2828 3087 2.911143 CCCTGATCCTTGGGTCGG 59.089 66.667 1.81 1.81 38.65 4.79
2845 3104 2.114411 TGTTGCTCCGGGGGAAAC 59.886 61.111 11.00 11.15 0.00 2.78
2846 3105 2.114411 GTGTTGCTCCGGGGGAAA 59.886 61.111 11.00 0.00 0.00 3.13
2847 3106 4.323477 CGTGTTGCTCCGGGGGAA 62.323 66.667 3.12 3.12 0.00 3.97
2854 3113 4.980805 TGCCCGTCGTGTTGCTCC 62.981 66.667 0.00 0.00 0.00 4.70
2855 3114 3.414700 CTGCCCGTCGTGTTGCTC 61.415 66.667 0.00 0.00 0.00 4.26
2863 3122 4.838486 GACTCTCGCTGCCCGTCG 62.838 72.222 0.00 0.00 38.35 5.12
2864 3123 4.838486 CGACTCTCGCTGCCCGTC 62.838 72.222 0.00 0.00 38.35 4.79
2884 3143 2.391389 CCCTTCTTGAAGGCGTCGC 61.391 63.158 20.71 9.22 38.63 5.19
2885 3144 0.320421 TTCCCTTCTTGAAGGCGTCG 60.320 55.000 20.71 9.66 38.63 5.12
2886 3145 1.157585 GTTCCCTTCTTGAAGGCGTC 58.842 55.000 20.71 10.58 38.63 5.19
2887 3146 0.602905 CGTTCCCTTCTTGAAGGCGT 60.603 55.000 20.71 0.00 38.63 5.68
2888 3147 0.320421 TCGTTCCCTTCTTGAAGGCG 60.320 55.000 20.71 18.28 38.63 5.52
2889 3148 1.443802 CTCGTTCCCTTCTTGAAGGC 58.556 55.000 20.71 9.02 38.63 4.35
2890 3149 1.002544 AGCTCGTTCCCTTCTTGAAGG 59.997 52.381 19.53 19.53 39.68 3.46
2891 3150 2.464157 AGCTCGTTCCCTTCTTGAAG 57.536 50.000 3.55 3.55 0.00 3.02
2892 3151 2.767505 GAAGCTCGTTCCCTTCTTGAA 58.232 47.619 0.00 0.00 35.67 2.69
2893 3152 1.336887 CGAAGCTCGTTCCCTTCTTGA 60.337 52.381 0.00 0.00 36.25 3.02
2894 3153 1.071605 CGAAGCTCGTTCCCTTCTTG 58.928 55.000 0.00 0.00 36.25 3.02
2895 3154 3.516578 CGAAGCTCGTTCCCTTCTT 57.483 52.632 0.00 0.00 36.25 2.52


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

AutoCloner maintained by Alex Coulton.