Multiple sequence alignment - TraesCS7B01G458000

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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 TraesCS7B01G458000 chr7B 100.000 2960 0 0 1 2960 716841580 716844539 0 5430
1 TraesCS7B01G458000 chr7B 99.185 2578 20 1 1 2577 716881821 716884398 0 4643
2 TraesCS7B01G458000 chr7B 99.732 373 1 0 2588 2960 716843254 716843626 0 684
3 TraesCS7B01G458000 chr7A 98.991 2578 23 3 1 2577 60276273 60273698 0 4614
4 TraesCS7B01G458000 chr7A 98.875 2578 27 2 1 2577 120844192 120846768 0 4599
5 TraesCS7B01G458000 chr7D 98.952 2577 23 1 1 2577 381976796 381979368 0 4606
6 TraesCS7B01G458000 chr7D 98.836 2577 26 1 1 2577 203496965 203494393 0 4590
7 TraesCS7B01G458000 chr7D 98.720 2578 28 2 1 2577 381916944 381914371 0 4573
8 TraesCS7B01G458000 chr7D 99.732 373 1 0 2588 2960 203495295 203494923 0 684
9 TraesCS7B01G458000 chr7D 99.732 373 1 0 2588 2960 381978466 381978838 0 684
10 TraesCS7B01G458000 chr7D 99.464 373 2 0 2588 2960 381915274 381914902 0 678
11 TraesCS7B01G458000 chr6D 98.952 2577 22 2 1 2577 124514490 124511919 0 4604
12 TraesCS7B01G458000 chr6D 100.000 373 0 0 2588 2960 124512820 124512448 0 689
13 TraesCS7B01G458000 chr6D 99.731 372 1 0 2589 2960 283227234 283227605 0 682
14 TraesCS7B01G458000 chr1B 98.836 2577 28 2 1 2577 672557173 672559747 0 4591
15 TraesCS7B01G458000 chr1B 99.464 373 2 0 2588 2960 672558845 672559217 0 678
16 TraesCS7B01G458000 chr2B 98.758 2577 31 1 1 2577 391079892 391082467 0 4580
17 TraesCS7B01G458000 chr2B 99.732 373 1 0 2588 2960 391081565 391081937 0 684
18 TraesCS7B01G458000 chr4D 99.464 373 2 0 2588 2960 123299011 123298639 0 678
19 TraesCS7B01G458000 chr4D 99.464 373 2 0 2588 2960 123330765 123330393 0 678


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 TraesCS7B01G458000 chr7B 716841580 716844539 2959 False 3057.0 5430 99.866 1 2960 2 chr7B.!!$F2 2959
1 TraesCS7B01G458000 chr7B 716881821 716884398 2577 False 4643.0 4643 99.185 1 2577 1 chr7B.!!$F1 2576
2 TraesCS7B01G458000 chr7A 60273698 60276273 2575 True 4614.0 4614 98.991 1 2577 1 chr7A.!!$R1 2576
3 TraesCS7B01G458000 chr7A 120844192 120846768 2576 False 4599.0 4599 98.875 1 2577 1 chr7A.!!$F1 2576
4 TraesCS7B01G458000 chr7D 381976796 381979368 2572 False 2645.0 4606 99.342 1 2960 2 chr7D.!!$F1 2959
5 TraesCS7B01G458000 chr7D 203494393 203496965 2572 True 2637.0 4590 99.284 1 2960 2 chr7D.!!$R1 2959
6 TraesCS7B01G458000 chr7D 381914371 381916944 2573 True 2625.5 4573 99.092 1 2960 2 chr7D.!!$R2 2959
7 TraesCS7B01G458000 chr6D 124511919 124514490 2571 True 2646.5 4604 99.476 1 2960 2 chr6D.!!$R1 2959
8 TraesCS7B01G458000 chr1B 672557173 672559747 2574 False 2634.5 4591 99.150 1 2960 2 chr1B.!!$F1 2959
9 TraesCS7B01G458000 chr2B 391079892 391082467 2575 False 2632.0 4580 99.245 1 2960 2 chr2B.!!$F1 2959

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
376 377 4.201851 GCGTGAGTTATACCGAGTACTCAA 60.202 45.833 22.37 7.77 45.94 3.02 F
1104 1109 6.793505 AAGGAGTTCTGGAACGATTACTAT 57.206 37.500 7.67 0.00 45.50 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1524 4.911514 TTGTAGAAACCTTGCTTGTTCC 57.088 40.909 0.0 0.0 0.0 3.62 R
2775 2784 0.105246 TGGTTGCCAATCCAAGGGTT 60.105 50.000 0.0 0.0 0.0 4.11 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
376 377 4.201851 GCGTGAGTTATACCGAGTACTCAA 60.202 45.833 22.37 7.77 45.94 3.02
1104 1109 6.793505 AAGGAGTTCTGGAACGATTACTAT 57.206 37.500 7.67 0.00 45.50 2.12
1218 1224 7.785033 AGAAGAATCAAAATGGTGTGTTTTCT 58.215 30.769 0.00 0.00 0.00 2.52
1518 1524 7.596749 AGATCAACTTAATTCAACTGTACGG 57.403 36.000 0.00 0.00 0.00 4.02
1948 1954 2.815503 GGTTACTTATGCAAACCCACGT 59.184 45.455 6.03 0.00 37.31 4.49
2096 2103 9.045223 GTTTGAAATAAACAAAAGGCTCTTGAT 57.955 29.630 7.72 0.00 38.63 2.57
2612 2621 8.348983 GAAATACTTGCTCCAATTCATGATTG 57.651 34.615 0.00 3.71 43.89 2.67
2613 2622 7.649533 AATACTTGCTCCAATTCATGATTGA 57.350 32.000 15.30 2.85 46.59 2.57
2614 2623 5.988310 ACTTGCTCCAATTCATGATTGAA 57.012 34.783 15.30 0.00 46.59 2.69
2615 2624 6.349243 ACTTGCTCCAATTCATGATTGAAA 57.651 33.333 15.30 6.28 46.59 2.69
2616 2625 6.395629 ACTTGCTCCAATTCATGATTGAAAG 58.604 36.000 15.30 13.12 46.59 2.62
2617 2626 6.209986 ACTTGCTCCAATTCATGATTGAAAGA 59.790 34.615 15.30 7.04 46.59 2.52
2618 2627 6.593268 TGCTCCAATTCATGATTGAAAGAA 57.407 33.333 15.30 7.57 46.59 2.52
2619 2628 6.995364 TGCTCCAATTCATGATTGAAAGAAA 58.005 32.000 15.30 6.09 46.59 2.52
2620 2629 7.617225 TGCTCCAATTCATGATTGAAAGAAAT 58.383 30.769 15.30 0.00 46.59 2.17
2621 2630 7.547722 TGCTCCAATTCATGATTGAAAGAAATG 59.452 33.333 15.30 0.00 46.59 2.32
2622 2631 7.548075 GCTCCAATTCATGATTGAAAGAAATGT 59.452 33.333 15.30 0.00 46.59 2.71
2623 2632 9.431887 CTCCAATTCATGATTGAAAGAAATGTT 57.568 29.630 15.30 0.00 46.59 2.71
2624 2633 9.426837 TCCAATTCATGATTGAAAGAAATGTTC 57.573 29.630 15.30 0.00 46.59 3.18
2625 2634 9.431887 CCAATTCATGATTGAAAGAAATGTTCT 57.568 29.630 15.30 0.00 46.59 3.01
2646 2655 9.035890 TGTTCTACATATATCAACAGATAGGGG 57.964 37.037 0.00 0.00 0.00 4.79
2647 2656 9.256228 GTTCTACATATATCAACAGATAGGGGA 57.744 37.037 0.00 0.00 0.00 4.81
2648 2657 9.480861 TTCTACATATATCAACAGATAGGGGAG 57.519 37.037 0.00 0.00 0.00 4.30
2649 2658 8.624670 TCTACATATATCAACAGATAGGGGAGT 58.375 37.037 0.00 0.00 0.00 3.85
2650 2659 9.922477 CTACATATATCAACAGATAGGGGAGTA 57.078 37.037 0.00 0.00 0.00 2.59
2652 2661 9.036980 ACATATATCAACAGATAGGGGAGTAAC 57.963 37.037 0.00 0.00 0.00 2.50
2653 2662 9.035890 CATATATCAACAGATAGGGGAGTAACA 57.964 37.037 0.00 0.00 0.00 2.41
2654 2663 7.931015 ATATCAACAGATAGGGGAGTAACAA 57.069 36.000 0.00 0.00 0.00 2.83
2655 2664 6.636454 ATCAACAGATAGGGGAGTAACAAA 57.364 37.500 0.00 0.00 0.00 2.83
2656 2665 6.442541 TCAACAGATAGGGGAGTAACAAAA 57.557 37.500 0.00 0.00 0.00 2.44
2657 2666 6.472887 TCAACAGATAGGGGAGTAACAAAAG 58.527 40.000 0.00 0.00 0.00 2.27
2658 2667 6.271391 TCAACAGATAGGGGAGTAACAAAAGA 59.729 38.462 0.00 0.00 0.00 2.52
2659 2668 6.697641 ACAGATAGGGGAGTAACAAAAGAA 57.302 37.500 0.00 0.00 0.00 2.52
2660 2669 6.712276 ACAGATAGGGGAGTAACAAAAGAAG 58.288 40.000 0.00 0.00 0.00 2.85
2661 2670 6.500751 ACAGATAGGGGAGTAACAAAAGAAGA 59.499 38.462 0.00 0.00 0.00 2.87
2662 2671 7.182930 ACAGATAGGGGAGTAACAAAAGAAGAT 59.817 37.037 0.00 0.00 0.00 2.40
2663 2672 7.713073 CAGATAGGGGAGTAACAAAAGAAGATC 59.287 40.741 0.00 0.00 0.00 2.75
2664 2673 5.180810 AGGGGAGTAACAAAAGAAGATCC 57.819 43.478 0.00 0.00 0.00 3.36
2665 2674 4.601857 AGGGGAGTAACAAAAGAAGATCCA 59.398 41.667 0.00 0.00 0.00 3.41
2666 2675 4.944317 GGGGAGTAACAAAAGAAGATCCAG 59.056 45.833 0.00 0.00 0.00 3.86
2667 2676 5.515008 GGGGAGTAACAAAAGAAGATCCAGT 60.515 44.000 0.00 0.00 0.00 4.00
2668 2677 5.412904 GGGAGTAACAAAAGAAGATCCAGTG 59.587 44.000 0.00 0.00 0.00 3.66
2669 2678 5.106515 GGAGTAACAAAAGAAGATCCAGTGC 60.107 44.000 0.00 0.00 0.00 4.40
2670 2679 5.625150 AGTAACAAAAGAAGATCCAGTGCT 58.375 37.500 0.00 0.00 0.00 4.40
2671 2680 4.843220 AACAAAAGAAGATCCAGTGCTG 57.157 40.909 0.00 0.00 0.00 4.41
2684 2693 4.756084 CCAGTGCTGGTTCTTAAGAAAG 57.244 45.455 19.30 14.72 45.53 2.62
2685 2694 3.503748 CCAGTGCTGGTTCTTAAGAAAGG 59.496 47.826 19.30 12.73 45.53 3.11
2686 2695 4.137543 CAGTGCTGGTTCTTAAGAAAGGT 58.862 43.478 19.30 0.00 35.58 3.50
2687 2696 4.214332 CAGTGCTGGTTCTTAAGAAAGGTC 59.786 45.833 19.30 7.19 35.58 3.85
2688 2697 4.134563 GTGCTGGTTCTTAAGAAAGGTCA 58.865 43.478 19.30 13.47 35.58 4.02
2689 2698 4.578928 GTGCTGGTTCTTAAGAAAGGTCAA 59.421 41.667 19.30 0.28 35.58 3.18
2690 2699 4.821805 TGCTGGTTCTTAAGAAAGGTCAAG 59.178 41.667 19.30 10.80 35.58 3.02
2691 2700 4.216472 GCTGGTTCTTAAGAAAGGTCAAGG 59.784 45.833 19.30 6.71 35.58 3.61
2692 2701 4.725490 TGGTTCTTAAGAAAGGTCAAGGG 58.275 43.478 19.30 0.00 35.58 3.95
2693 2702 4.167307 TGGTTCTTAAGAAAGGTCAAGGGT 59.833 41.667 19.30 0.00 35.58 4.34
2694 2703 5.370289 TGGTTCTTAAGAAAGGTCAAGGGTA 59.630 40.000 19.30 0.00 35.58 3.69
2695 2704 6.045106 TGGTTCTTAAGAAAGGTCAAGGGTAT 59.955 38.462 19.30 0.00 35.58 2.73
2696 2705 7.238096 TGGTTCTTAAGAAAGGTCAAGGGTATA 59.762 37.037 19.30 0.00 35.58 1.47
2697 2706 8.272889 GGTTCTTAAGAAAGGTCAAGGGTATAT 58.727 37.037 19.30 0.00 35.58 0.86
2700 2709 9.947189 TCTTAAGAAAGGTCAAGGGTATATAGA 57.053 33.333 1.68 0.00 33.22 1.98
2702 2711 9.947189 TTAAGAAAGGTCAAGGGTATATAGAGA 57.053 33.333 0.00 0.00 0.00 3.10
2703 2712 8.855804 AAGAAAGGTCAAGGGTATATAGAGAA 57.144 34.615 0.00 0.00 0.00 2.87
2704 2713 9.453830 AAGAAAGGTCAAGGGTATATAGAGAAT 57.546 33.333 0.00 0.00 0.00 2.40
2705 2714 9.453830 AGAAAGGTCAAGGGTATATAGAGAATT 57.546 33.333 0.00 0.00 0.00 2.17
2706 2715 9.713713 GAAAGGTCAAGGGTATATAGAGAATTC 57.286 37.037 0.00 0.00 0.00 2.17
2707 2716 9.453830 AAAGGTCAAGGGTATATAGAGAATTCT 57.546 33.333 7.95 7.95 37.46 2.40
2708 2717 9.453830 AAGGTCAAGGGTATATAGAGAATTCTT 57.546 33.333 9.87 2.63 34.79 2.52
2709 2718 8.875168 AGGTCAAGGGTATATAGAGAATTCTTG 58.125 37.037 9.87 0.00 34.79 3.02
2710 2719 8.652290 GGTCAAGGGTATATAGAGAATTCTTGT 58.348 37.037 9.87 2.99 34.79 3.16
2723 2732 8.565896 AGAGAATTCTTGTTATGTTATGTGCA 57.434 30.769 9.87 0.00 0.00 4.57
2724 2733 9.013229 AGAGAATTCTTGTTATGTTATGTGCAA 57.987 29.630 9.87 0.00 0.00 4.08
2725 2734 9.793252 GAGAATTCTTGTTATGTTATGTGCAAT 57.207 29.630 9.87 0.00 0.00 3.56
2729 2738 9.926158 ATTCTTGTTATGTTATGTGCAATTTGA 57.074 25.926 0.00 0.00 0.00 2.69
2730 2739 9.755804 TTCTTGTTATGTTATGTGCAATTTGAA 57.244 25.926 0.00 0.00 0.00 2.69
2731 2740 9.190858 TCTTGTTATGTTATGTGCAATTTGAAC 57.809 29.630 0.09 0.09 0.00 3.18
2732 2741 8.877808 TTGTTATGTTATGTGCAATTTGAACA 57.122 26.923 12.58 12.58 40.82 3.18
2741 2750 6.709145 TGTGCAATTTGAACATAAATCTGC 57.291 33.333 6.08 0.00 29.08 4.26
2742 2751 6.457355 TGTGCAATTTGAACATAAATCTGCT 58.543 32.000 6.08 0.00 36.35 4.24
2743 2752 6.587226 TGTGCAATTTGAACATAAATCTGCTC 59.413 34.615 6.08 0.00 36.35 4.26
2744 2753 6.035327 GTGCAATTTGAACATAAATCTGCTCC 59.965 38.462 2.43 0.00 36.35 4.70
2745 2754 5.521372 GCAATTTGAACATAAATCTGCTCCC 59.479 40.000 0.00 0.00 34.71 4.30
2746 2755 6.628844 GCAATTTGAACATAAATCTGCTCCCT 60.629 38.462 0.00 0.00 34.71 4.20
2747 2756 7.416664 GCAATTTGAACATAAATCTGCTCCCTA 60.417 37.037 0.00 0.00 34.71 3.53
2748 2757 8.636213 CAATTTGAACATAAATCTGCTCCCTAT 58.364 33.333 0.00 0.00 30.33 2.57
2749 2758 7.807977 TTTGAACATAAATCTGCTCCCTATC 57.192 36.000 0.00 0.00 0.00 2.08
2750 2759 6.499106 TGAACATAAATCTGCTCCCTATCA 57.501 37.500 0.00 0.00 0.00 2.15
2751 2760 6.899089 TGAACATAAATCTGCTCCCTATCAA 58.101 36.000 0.00 0.00 0.00 2.57
2752 2761 7.345691 TGAACATAAATCTGCTCCCTATCAAA 58.654 34.615 0.00 0.00 0.00 2.69
2753 2762 7.283127 TGAACATAAATCTGCTCCCTATCAAAC 59.717 37.037 0.00 0.00 0.00 2.93
2754 2763 6.904626 ACATAAATCTGCTCCCTATCAAACT 58.095 36.000 0.00 0.00 0.00 2.66
2755 2764 6.995091 ACATAAATCTGCTCCCTATCAAACTC 59.005 38.462 0.00 0.00 0.00 3.01
2756 2765 5.441718 AAATCTGCTCCCTATCAAACTCA 57.558 39.130 0.00 0.00 0.00 3.41
2757 2766 5.441718 AATCTGCTCCCTATCAAACTCAA 57.558 39.130 0.00 0.00 0.00 3.02
2758 2767 5.643421 ATCTGCTCCCTATCAAACTCAAT 57.357 39.130 0.00 0.00 0.00 2.57
2759 2768 5.028549 TCTGCTCCCTATCAAACTCAATC 57.971 43.478 0.00 0.00 0.00 2.67
2760 2769 4.718774 TCTGCTCCCTATCAAACTCAATCT 59.281 41.667 0.00 0.00 0.00 2.40
2761 2770 5.190528 TCTGCTCCCTATCAAACTCAATCTT 59.809 40.000 0.00 0.00 0.00 2.40
2762 2771 5.431765 TGCTCCCTATCAAACTCAATCTTC 58.568 41.667 0.00 0.00 0.00 2.87
2763 2772 4.819088 GCTCCCTATCAAACTCAATCTTCC 59.181 45.833 0.00 0.00 0.00 3.46
2764 2773 5.023533 TCCCTATCAAACTCAATCTTCCG 57.976 43.478 0.00 0.00 0.00 4.30
2765 2774 4.714802 TCCCTATCAAACTCAATCTTCCGA 59.285 41.667 0.00 0.00 0.00 4.55
2766 2775 5.366768 TCCCTATCAAACTCAATCTTCCGAT 59.633 40.000 0.00 0.00 0.00 4.18
2767 2776 5.468072 CCCTATCAAACTCAATCTTCCGATG 59.532 44.000 0.00 0.00 0.00 3.84
2768 2777 4.889832 ATCAAACTCAATCTTCCGATGC 57.110 40.909 0.00 0.00 0.00 3.91
2769 2778 3.942829 TCAAACTCAATCTTCCGATGCT 58.057 40.909 0.00 0.00 0.00 3.79
2770 2779 4.326826 TCAAACTCAATCTTCCGATGCTT 58.673 39.130 0.00 0.00 0.00 3.91
2771 2780 4.761739 TCAAACTCAATCTTCCGATGCTTT 59.238 37.500 0.00 0.00 0.00 3.51
2772 2781 4.691860 AACTCAATCTTCCGATGCTTTG 57.308 40.909 0.00 0.00 0.00 2.77
2773 2782 2.421424 ACTCAATCTTCCGATGCTTTGC 59.579 45.455 0.00 0.00 0.00 3.68
2774 2783 2.421073 CTCAATCTTCCGATGCTTTGCA 59.579 45.455 0.00 0.00 44.86 4.08
2775 2784 2.819019 TCAATCTTCCGATGCTTTGCAA 59.181 40.909 0.00 0.00 43.62 4.08
2776 2785 3.255395 TCAATCTTCCGATGCTTTGCAAA 59.745 39.130 12.14 12.14 43.62 3.68
2777 2786 2.704725 TCTTCCGATGCTTTGCAAAC 57.295 45.000 8.05 6.31 43.62 2.93
2778 2787 1.269448 TCTTCCGATGCTTTGCAAACC 59.731 47.619 8.05 2.13 43.62 3.27
2779 2788 0.316841 TTCCGATGCTTTGCAAACCC 59.683 50.000 8.05 2.94 43.62 4.11
2780 2789 0.539438 TCCGATGCTTTGCAAACCCT 60.539 50.000 8.05 0.00 43.62 4.34
2781 2790 0.318120 CCGATGCTTTGCAAACCCTT 59.682 50.000 8.05 0.66 43.62 3.95
2782 2791 1.421382 CGATGCTTTGCAAACCCTTG 58.579 50.000 8.05 0.00 43.62 3.61
2783 2792 1.799544 GATGCTTTGCAAACCCTTGG 58.200 50.000 8.05 0.00 43.62 3.61
2784 2793 1.344114 GATGCTTTGCAAACCCTTGGA 59.656 47.619 8.05 0.00 43.62 3.53
2785 2794 1.422531 TGCTTTGCAAACCCTTGGAT 58.577 45.000 8.05 0.00 34.76 3.41
2786 2795 1.767681 TGCTTTGCAAACCCTTGGATT 59.232 42.857 8.05 0.00 34.76 3.01
2787 2796 2.145536 GCTTTGCAAACCCTTGGATTG 58.854 47.619 8.05 0.00 38.30 2.67
2788 2797 2.769893 CTTTGCAAACCCTTGGATTGG 58.230 47.619 8.05 0.00 36.24 3.16
2789 2798 0.396060 TTGCAAACCCTTGGATTGGC 59.604 50.000 0.00 0.00 36.24 4.52
2790 2799 0.762082 TGCAAACCCTTGGATTGGCA 60.762 50.000 0.00 0.00 36.24 4.92
2791 2800 0.396060 GCAAACCCTTGGATTGGCAA 59.604 50.000 0.68 0.68 36.24 4.52
2792 2801 1.877680 GCAAACCCTTGGATTGGCAAC 60.878 52.381 0.00 0.00 36.24 4.17
2793 2802 1.055849 AAACCCTTGGATTGGCAACC 58.944 50.000 0.00 6.99 0.00 3.77
2794 2803 0.105246 AACCCTTGGATTGGCAACCA 60.105 50.000 14.79 14.79 0.00 3.67
2795 2804 0.542702 ACCCTTGGATTGGCAACCAG 60.543 55.000 17.05 11.09 37.48 4.00
2796 2805 1.593265 CCTTGGATTGGCAACCAGC 59.407 57.895 17.05 3.05 44.65 4.85
2805 2814 2.045536 GCAACCAGCAGAGAGGGG 60.046 66.667 0.00 0.00 44.79 4.79
2806 2815 2.673523 CAACCAGCAGAGAGGGGG 59.326 66.667 0.00 0.00 0.00 5.40
2807 2816 2.208349 AACCAGCAGAGAGGGGGT 59.792 61.111 0.00 0.00 0.00 4.95
2808 2817 1.920835 AACCAGCAGAGAGGGGGTC 60.921 63.158 0.00 0.00 0.00 4.46
2809 2818 2.040278 CCAGCAGAGAGGGGGTCT 59.960 66.667 0.00 0.00 38.71 3.85
2810 2819 2.365586 CCAGCAGAGAGGGGGTCTG 61.366 68.421 0.00 0.00 43.77 3.51
2811 2820 1.305633 CAGCAGAGAGGGGGTCTGA 60.306 63.158 4.28 0.00 43.65 3.27
2812 2821 0.690411 CAGCAGAGAGGGGGTCTGAT 60.690 60.000 4.28 0.00 43.65 2.90
2813 2822 0.398381 AGCAGAGAGGGGGTCTGATC 60.398 60.000 4.28 0.00 43.65 2.92
2814 2823 1.406860 GCAGAGAGGGGGTCTGATCC 61.407 65.000 0.00 0.00 43.65 3.36
2815 2824 0.264359 CAGAGAGGGGGTCTGATCCT 59.736 60.000 6.95 2.00 43.65 3.24
2816 2825 0.264359 AGAGAGGGGGTCTGATCCTG 59.736 60.000 6.95 0.00 34.71 3.86
2817 2826 0.263172 GAGAGGGGGTCTGATCCTGA 59.737 60.000 6.95 0.00 34.71 3.86
2818 2827 0.948050 AGAGGGGGTCTGATCCTGAT 59.052 55.000 6.95 0.00 32.57 2.90
2819 2828 2.110899 GAGAGGGGGTCTGATCCTGATA 59.889 54.545 6.95 0.00 34.71 2.15
2820 2829 2.158234 AGAGGGGGTCTGATCCTGATAC 60.158 54.545 6.95 0.00 32.57 2.24
2821 2830 1.580658 AGGGGGTCTGATCCTGATACA 59.419 52.381 6.95 0.00 0.00 2.29
2822 2831 2.183210 AGGGGGTCTGATCCTGATACAT 59.817 50.000 6.95 0.00 0.00 2.29
2823 2832 2.982488 GGGGGTCTGATCCTGATACATT 59.018 50.000 6.95 0.00 0.00 2.71
2824 2833 4.140447 AGGGGGTCTGATCCTGATACATTA 60.140 45.833 6.95 0.00 0.00 1.90
2825 2834 4.785376 GGGGGTCTGATCCTGATACATTAT 59.215 45.833 6.95 0.00 0.00 1.28
2826 2835 5.104735 GGGGGTCTGATCCTGATACATTATC 60.105 48.000 6.95 0.00 35.74 1.75
2827 2836 5.394663 GGGGTCTGATCCTGATACATTATCG 60.395 48.000 6.95 0.00 38.02 2.92
2828 2837 5.394663 GGGTCTGATCCTGATACATTATCGG 60.395 48.000 0.00 0.00 40.49 4.18
2829 2838 5.419155 GGTCTGATCCTGATACATTATCGGA 59.581 44.000 3.92 6.46 42.85 4.55
2830 2839 6.097554 GGTCTGATCCTGATACATTATCGGAT 59.902 42.308 14.24 14.24 44.00 4.18
2834 2843 7.340122 GATCCTGATACATTATCGGATCTGA 57.660 40.000 23.00 6.72 46.83 3.27
2835 2844 7.911130 ATCCTGATACATTATCGGATCTGAT 57.089 36.000 20.64 20.64 42.85 2.90
2836 2845 9.072375 GATCCTGATACATTATCGGATCTGATA 57.928 37.037 18.56 18.56 46.83 2.15
2837 2846 8.457238 TCCTGATACATTATCGGATCTGATAG 57.543 38.462 20.82 14.42 42.85 2.08
2838 2847 7.503902 TCCTGATACATTATCGGATCTGATAGG 59.496 40.741 20.82 17.91 42.85 2.57
2839 2848 7.503902 CCTGATACATTATCGGATCTGATAGGA 59.496 40.741 20.82 10.42 42.85 2.94
2840 2849 8.457238 TGATACATTATCGGATCTGATAGGAG 57.543 38.462 20.82 16.90 38.02 3.69
2841 2850 7.503902 TGATACATTATCGGATCTGATAGGAGG 59.496 40.741 20.82 13.34 38.02 4.30
2842 2851 5.584913 ACATTATCGGATCTGATAGGAGGT 58.415 41.667 20.82 13.89 32.70 3.85
2843 2852 6.019748 ACATTATCGGATCTGATAGGAGGTT 58.980 40.000 20.82 0.37 32.70 3.50
2844 2853 7.182760 ACATTATCGGATCTGATAGGAGGTTA 58.817 38.462 20.82 8.02 32.70 2.85
2845 2854 7.122948 ACATTATCGGATCTGATAGGAGGTTAC 59.877 40.741 20.82 0.00 32.70 2.50
2846 2855 4.726035 TCGGATCTGATAGGAGGTTACT 57.274 45.455 0.00 0.00 0.00 2.24
2847 2856 5.063017 TCGGATCTGATAGGAGGTTACTT 57.937 43.478 0.00 0.00 0.00 2.24
2848 2857 6.196918 TCGGATCTGATAGGAGGTTACTTA 57.803 41.667 0.00 0.00 0.00 2.24
2849 2858 6.791371 TCGGATCTGATAGGAGGTTACTTAT 58.209 40.000 0.00 0.00 0.00 1.73
2850 2859 6.659668 TCGGATCTGATAGGAGGTTACTTATG 59.340 42.308 0.00 0.00 0.00 1.90
2851 2860 6.626181 CGGATCTGATAGGAGGTTACTTATGC 60.626 46.154 0.00 0.00 0.00 3.14
2852 2861 6.211584 GGATCTGATAGGAGGTTACTTATGCA 59.788 42.308 0.00 0.00 0.00 3.96
2853 2862 7.256332 GGATCTGATAGGAGGTTACTTATGCAA 60.256 40.741 0.00 0.00 0.00 4.08
2854 2863 7.432148 TCTGATAGGAGGTTACTTATGCAAA 57.568 36.000 0.00 0.00 0.00 3.68
2855 2864 7.272978 TCTGATAGGAGGTTACTTATGCAAAC 58.727 38.462 0.00 0.00 0.00 2.93
2856 2865 6.354130 TGATAGGAGGTTACTTATGCAAACC 58.646 40.000 8.89 8.89 42.48 3.27
2857 2866 3.964411 AGGAGGTTACTTATGCAAACCC 58.036 45.455 12.60 5.67 43.04 4.11
2858 2867 3.332485 AGGAGGTTACTTATGCAAACCCA 59.668 43.478 12.60 0.00 43.04 4.51
2859 2868 3.442625 GGAGGTTACTTATGCAAACCCAC 59.557 47.826 12.60 8.09 43.04 4.61
2860 2869 3.078837 AGGTTACTTATGCAAACCCACG 58.921 45.455 12.60 0.00 43.04 4.94
2861 2870 2.162809 GGTTACTTATGCAAACCCACGG 59.837 50.000 6.03 0.00 37.31 4.94
2862 2871 2.116827 TACTTATGCAAACCCACGGG 57.883 50.000 0.00 0.00 42.03 5.28
2877 2886 3.441101 CCACGGGGGATATCTAGAATCA 58.559 50.000 0.00 0.00 40.01 2.57
2878 2887 3.195825 CCACGGGGGATATCTAGAATCAC 59.804 52.174 0.00 2.72 40.01 3.06
2879 2888 4.090090 CACGGGGGATATCTAGAATCACT 58.910 47.826 13.43 0.00 0.00 3.41
2880 2889 4.528596 CACGGGGGATATCTAGAATCACTT 59.471 45.833 13.43 0.00 0.00 3.16
2881 2890 5.012148 CACGGGGGATATCTAGAATCACTTT 59.988 44.000 13.43 0.00 0.00 2.66
2882 2891 5.246429 ACGGGGGATATCTAGAATCACTTTC 59.754 44.000 13.43 6.47 34.31 2.62
2883 2892 5.622460 CGGGGGATATCTAGAATCACTTTCG 60.622 48.000 13.43 11.63 39.46 3.46
2884 2893 5.337652 GGGGGATATCTAGAATCACTTTCGG 60.338 48.000 13.43 0.00 39.46 4.30
2885 2894 5.172205 GGGATATCTAGAATCACTTTCGGC 58.828 45.833 2.05 0.00 39.46 5.54
2886 2895 5.046950 GGGATATCTAGAATCACTTTCGGCT 60.047 44.000 2.05 0.00 39.46 5.52
2887 2896 6.153000 GGGATATCTAGAATCACTTTCGGCTA 59.847 42.308 2.05 0.00 39.46 3.93
2888 2897 7.147811 GGGATATCTAGAATCACTTTCGGCTAT 60.148 40.741 2.05 0.00 39.46 2.97
2889 2898 8.254508 GGATATCTAGAATCACTTTCGGCTATT 58.745 37.037 2.05 0.00 39.46 1.73
2892 2901 8.819643 ATCTAGAATCACTTTCGGCTATTAAC 57.180 34.615 0.00 0.00 39.46 2.01
2893 2902 8.008513 TCTAGAATCACTTTCGGCTATTAACT 57.991 34.615 0.00 0.00 39.46 2.24
2894 2903 8.475639 TCTAGAATCACTTTCGGCTATTAACTT 58.524 33.333 0.00 0.00 39.46 2.66
2895 2904 7.541122 AGAATCACTTTCGGCTATTAACTTC 57.459 36.000 0.00 0.00 39.46 3.01
2896 2905 6.539103 AGAATCACTTTCGGCTATTAACTTCC 59.461 38.462 0.00 0.00 39.46 3.46
2897 2906 4.510571 TCACTTTCGGCTATTAACTTCCC 58.489 43.478 0.00 0.00 0.00 3.97
2898 2907 4.020039 TCACTTTCGGCTATTAACTTCCCA 60.020 41.667 0.00 0.00 0.00 4.37
2899 2908 4.881850 CACTTTCGGCTATTAACTTCCCAT 59.118 41.667 0.00 0.00 0.00 4.00
2900 2909 4.881850 ACTTTCGGCTATTAACTTCCCATG 59.118 41.667 0.00 0.00 0.00 3.66
2901 2910 4.764050 TTCGGCTATTAACTTCCCATGA 57.236 40.909 0.00 0.00 0.00 3.07
2902 2911 4.067972 TCGGCTATTAACTTCCCATGAC 57.932 45.455 0.00 0.00 0.00 3.06
2903 2912 3.709653 TCGGCTATTAACTTCCCATGACT 59.290 43.478 0.00 0.00 0.00 3.41
2904 2913 4.163458 TCGGCTATTAACTTCCCATGACTT 59.837 41.667 0.00 0.00 0.00 3.01
2905 2914 5.364446 TCGGCTATTAACTTCCCATGACTTA 59.636 40.000 0.00 0.00 0.00 2.24
2906 2915 6.053005 CGGCTATTAACTTCCCATGACTTAA 58.947 40.000 0.00 0.00 0.00 1.85
2907 2916 6.540914 CGGCTATTAACTTCCCATGACTTAAA 59.459 38.462 0.00 0.00 0.00 1.52
2908 2917 7.466860 CGGCTATTAACTTCCCATGACTTAAAC 60.467 40.741 0.00 0.00 0.00 2.01
2909 2918 7.201794 GGCTATTAACTTCCCATGACTTAAACC 60.202 40.741 0.00 0.00 0.00 3.27
2910 2919 7.338449 GCTATTAACTTCCCATGACTTAAACCA 59.662 37.037 0.00 0.00 0.00 3.67
2911 2920 6.887626 TTAACTTCCCATGACTTAAACCAC 57.112 37.500 0.00 0.00 0.00 4.16
2912 2921 4.724279 ACTTCCCATGACTTAAACCACT 57.276 40.909 0.00 0.00 0.00 4.00
2913 2922 5.061721 ACTTCCCATGACTTAAACCACTT 57.938 39.130 0.00 0.00 0.00 3.16
2914 2923 5.070685 ACTTCCCATGACTTAAACCACTTC 58.929 41.667 0.00 0.00 0.00 3.01
2915 2924 4.993705 TCCCATGACTTAAACCACTTCT 57.006 40.909 0.00 0.00 0.00 2.85
2916 2925 6.043938 ACTTCCCATGACTTAAACCACTTCTA 59.956 38.462 0.00 0.00 0.00 2.10
2917 2926 6.636454 TCCCATGACTTAAACCACTTCTAT 57.364 37.500 0.00 0.00 0.00 1.98
2918 2927 7.743116 TCCCATGACTTAAACCACTTCTATA 57.257 36.000 0.00 0.00 0.00 1.31
2919 2928 8.331931 TCCCATGACTTAAACCACTTCTATAT 57.668 34.615 0.00 0.00 0.00 0.86
2920 2929 9.442062 TCCCATGACTTAAACCACTTCTATATA 57.558 33.333 0.00 0.00 0.00 0.86
2955 2964 6.882610 AAAAGAATACAAGCAGATGTGTGA 57.117 33.333 0.00 0.00 34.75 3.58
2956 2965 7.458409 AAAAGAATACAAGCAGATGTGTGAT 57.542 32.000 0.00 0.00 34.75 3.06
2957 2966 8.565896 AAAAGAATACAAGCAGATGTGTGATA 57.434 30.769 0.00 0.00 34.75 2.15
2958 2967 8.743085 AAAGAATACAAGCAGATGTGTGATAT 57.257 30.769 0.00 0.00 34.75 1.63
2959 2968 8.743085 AAGAATACAAGCAGATGTGTGATATT 57.257 30.769 0.00 0.00 34.75 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1104 1109 4.842574 TGTCAATATCCAACAGCTTAGCA 58.157 39.130 7.07 0.00 0.00 3.49
1335 1341 8.211629 CCCTTTAGATATTGCTTAGTGTTAGGT 58.788 37.037 0.00 0.00 0.00 3.08
1342 1348 5.828328 GGCAACCCTTTAGATATTGCTTAGT 59.172 40.000 7.15 0.00 44.03 2.24
1518 1524 4.911514 TTGTAGAAACCTTGCTTGTTCC 57.088 40.909 0.00 0.00 0.00 3.62
1948 1954 5.279506 GCCGAAAGTGATTCTAGATATCCCA 60.280 44.000 0.00 0.00 35.79 4.37
2096 2103 8.335532 ACATTGACGATTCTTTTCCAGAAATA 57.664 30.769 0.00 0.00 45.06 1.40
2587 2596 8.192774 TCAATCATGAATTGGAGCAAGTATTTC 58.807 33.333 0.00 0.00 44.19 2.17
2588 2597 8.070034 TCAATCATGAATTGGAGCAAGTATTT 57.930 30.769 0.00 0.00 44.19 1.40
2589 2598 7.649533 TCAATCATGAATTGGAGCAAGTATT 57.350 32.000 0.00 0.00 44.19 1.89
2590 2599 7.649533 TTCAATCATGAATTGGAGCAAGTAT 57.350 32.000 0.00 0.00 44.19 2.12
2591 2600 7.394077 TCTTTCAATCATGAATTGGAGCAAGTA 59.606 33.333 0.00 0.00 44.70 2.24
2592 2601 5.988310 TTCAATCATGAATTGGAGCAAGT 57.012 34.783 0.00 0.00 44.19 3.16
2593 2602 6.627243 TCTTTCAATCATGAATTGGAGCAAG 58.373 36.000 0.00 6.60 44.70 4.01
2594 2603 6.593268 TCTTTCAATCATGAATTGGAGCAA 57.407 33.333 0.00 0.00 44.70 3.91
2595 2604 6.593268 TTCTTTCAATCATGAATTGGAGCA 57.407 33.333 0.00 0.00 44.70 4.26
2596 2605 7.548075 ACATTTCTTTCAATCATGAATTGGAGC 59.452 33.333 0.00 0.00 44.70 4.70
2597 2606 8.997621 ACATTTCTTTCAATCATGAATTGGAG 57.002 30.769 0.00 7.42 44.70 3.86
2598 2607 9.426837 GAACATTTCTTTCAATCATGAATTGGA 57.573 29.630 0.00 0.00 44.70 3.53
2599 2608 9.431887 AGAACATTTCTTTCAATCATGAATTGG 57.568 29.630 0.00 0.00 44.70 3.16
2620 2629 9.035890 CCCCTATCTGTTGATATATGTAGAACA 57.964 37.037 0.00 0.00 34.95 3.18
2621 2630 9.256228 TCCCCTATCTGTTGATATATGTAGAAC 57.744 37.037 0.00 0.00 34.95 3.01
2622 2631 9.480861 CTCCCCTATCTGTTGATATATGTAGAA 57.519 37.037 0.00 0.00 34.95 2.10
2623 2632 8.624670 ACTCCCCTATCTGTTGATATATGTAGA 58.375 37.037 0.00 0.00 34.95 2.59
2624 2633 8.830915 ACTCCCCTATCTGTTGATATATGTAG 57.169 38.462 0.00 0.00 34.95 2.74
2626 2635 9.036980 GTTACTCCCCTATCTGTTGATATATGT 57.963 37.037 0.00 0.00 34.95 2.29
2627 2636 9.035890 TGTTACTCCCCTATCTGTTGATATATG 57.964 37.037 0.00 0.00 34.95 1.78
2628 2637 9.615660 TTGTTACTCCCCTATCTGTTGATATAT 57.384 33.333 0.00 0.00 34.95 0.86
2629 2638 9.442062 TTTGTTACTCCCCTATCTGTTGATATA 57.558 33.333 0.00 0.00 34.95 0.86
2630 2639 7.931015 TTGTTACTCCCCTATCTGTTGATAT 57.069 36.000 0.00 0.00 34.95 1.63
2631 2640 7.743116 TTTGTTACTCCCCTATCTGTTGATA 57.257 36.000 0.00 0.00 34.32 2.15
2632 2641 6.636454 TTTGTTACTCCCCTATCTGTTGAT 57.364 37.500 0.00 0.00 36.74 2.57
2633 2642 6.271391 TCTTTTGTTACTCCCCTATCTGTTGA 59.729 38.462 0.00 0.00 0.00 3.18
2634 2643 6.472887 TCTTTTGTTACTCCCCTATCTGTTG 58.527 40.000 0.00 0.00 0.00 3.33
2635 2644 6.697641 TCTTTTGTTACTCCCCTATCTGTT 57.302 37.500 0.00 0.00 0.00 3.16
2636 2645 6.500751 TCTTCTTTTGTTACTCCCCTATCTGT 59.499 38.462 0.00 0.00 0.00 3.41
2637 2646 6.947464 TCTTCTTTTGTTACTCCCCTATCTG 58.053 40.000 0.00 0.00 0.00 2.90
2638 2647 7.147461 GGATCTTCTTTTGTTACTCCCCTATCT 60.147 40.741 0.00 0.00 0.00 1.98
2639 2648 6.993308 GGATCTTCTTTTGTTACTCCCCTATC 59.007 42.308 0.00 0.00 0.00 2.08
2640 2649 6.447084 TGGATCTTCTTTTGTTACTCCCCTAT 59.553 38.462 0.00 0.00 0.00 2.57
2641 2650 5.788533 TGGATCTTCTTTTGTTACTCCCCTA 59.211 40.000 0.00 0.00 0.00 3.53
2642 2651 4.601857 TGGATCTTCTTTTGTTACTCCCCT 59.398 41.667 0.00 0.00 0.00 4.79
2643 2652 4.918588 TGGATCTTCTTTTGTTACTCCCC 58.081 43.478 0.00 0.00 0.00 4.81
2644 2653 5.412904 CACTGGATCTTCTTTTGTTACTCCC 59.587 44.000 0.00 0.00 0.00 4.30
2645 2654 5.106515 GCACTGGATCTTCTTTTGTTACTCC 60.107 44.000 0.00 0.00 0.00 3.85
2646 2655 5.703130 AGCACTGGATCTTCTTTTGTTACTC 59.297 40.000 0.00 0.00 0.00 2.59
2647 2656 5.471456 CAGCACTGGATCTTCTTTTGTTACT 59.529 40.000 0.00 0.00 0.00 2.24
2648 2657 5.693814 CAGCACTGGATCTTCTTTTGTTAC 58.306 41.667 0.00 0.00 0.00 2.50
2649 2658 5.947228 CAGCACTGGATCTTCTTTTGTTA 57.053 39.130 0.00 0.00 0.00 2.41
2650 2659 4.843220 CAGCACTGGATCTTCTTTTGTT 57.157 40.909 0.00 0.00 0.00 2.83
2661 2670 5.006386 CTTTCTTAAGAACCAGCACTGGAT 58.994 41.667 23.30 11.69 42.45 3.41
2662 2671 4.389374 CTTTCTTAAGAACCAGCACTGGA 58.611 43.478 23.30 0.00 42.45 3.86
2663 2672 3.503748 CCTTTCTTAAGAACCAGCACTGG 59.496 47.826 17.51 15.23 44.00 4.00
2664 2673 4.137543 ACCTTTCTTAAGAACCAGCACTG 58.862 43.478 17.51 3.94 33.13 3.66
2665 2674 4.141482 TGACCTTTCTTAAGAACCAGCACT 60.141 41.667 17.51 0.00 33.13 4.40
2666 2675 4.134563 TGACCTTTCTTAAGAACCAGCAC 58.865 43.478 17.51 9.90 33.13 4.40
2667 2676 4.431416 TGACCTTTCTTAAGAACCAGCA 57.569 40.909 17.51 10.80 33.13 4.41
2668 2677 4.216472 CCTTGACCTTTCTTAAGAACCAGC 59.784 45.833 17.51 8.52 33.13 4.85
2669 2678 4.762251 CCCTTGACCTTTCTTAAGAACCAG 59.238 45.833 17.51 12.79 33.13 4.00
2670 2679 4.167307 ACCCTTGACCTTTCTTAAGAACCA 59.833 41.667 17.51 10.25 33.13 3.67
2671 2680 4.726583 ACCCTTGACCTTTCTTAAGAACC 58.273 43.478 17.51 7.99 33.13 3.62
2674 2683 9.947189 TCTATATACCCTTGACCTTTCTTAAGA 57.053 33.333 0.00 0.00 32.92 2.10
2676 2685 9.947189 TCTCTATATACCCTTGACCTTTCTTAA 57.053 33.333 0.00 0.00 0.00 1.85
2677 2686 9.947189 TTCTCTATATACCCTTGACCTTTCTTA 57.053 33.333 0.00 0.00 0.00 2.10
2678 2687 8.855804 TTCTCTATATACCCTTGACCTTTCTT 57.144 34.615 0.00 0.00 0.00 2.52
2679 2688 9.453830 AATTCTCTATATACCCTTGACCTTTCT 57.546 33.333 0.00 0.00 0.00 2.52
2680 2689 9.713713 GAATTCTCTATATACCCTTGACCTTTC 57.286 37.037 0.00 0.00 0.00 2.62
2681 2690 9.453830 AGAATTCTCTATATACCCTTGACCTTT 57.546 33.333 0.88 0.00 0.00 3.11
2682 2691 9.453830 AAGAATTCTCTATATACCCTTGACCTT 57.546 33.333 8.78 0.00 0.00 3.50
2683 2692 8.875168 CAAGAATTCTCTATATACCCTTGACCT 58.125 37.037 8.78 0.00 32.61 3.85
2684 2693 8.652290 ACAAGAATTCTCTATATACCCTTGACC 58.348 37.037 8.78 0.00 34.37 4.02
2697 2706 9.665719 TGCACATAACATAACAAGAATTCTCTA 57.334 29.630 8.78 1.59 0.00 2.43
2698 2707 8.565896 TGCACATAACATAACAAGAATTCTCT 57.434 30.769 8.78 0.00 0.00 3.10
2699 2708 9.793252 ATTGCACATAACATAACAAGAATTCTC 57.207 29.630 8.78 0.00 0.00 2.87
2703 2712 9.926158 TCAAATTGCACATAACATAACAAGAAT 57.074 25.926 0.00 0.00 0.00 2.40
2704 2713 9.755804 TTCAAATTGCACATAACATAACAAGAA 57.244 25.926 0.00 0.00 0.00 2.52
2705 2714 9.190858 GTTCAAATTGCACATAACATAACAAGA 57.809 29.630 0.00 0.00 0.00 3.02
2706 2715 8.976471 TGTTCAAATTGCACATAACATAACAAG 58.024 29.630 0.00 0.00 0.00 3.16
2707 2716 8.877808 TGTTCAAATTGCACATAACATAACAA 57.122 26.923 0.00 0.00 0.00 2.83
2713 2722 9.926158 AGATTTATGTTCAAATTGCACATAACA 57.074 25.926 23.59 17.05 42.83 2.41
2715 2724 8.871862 GCAGATTTATGTTCAAATTGCACATAA 58.128 29.630 21.20 21.20 41.96 1.90
2716 2725 8.252417 AGCAGATTTATGTTCAAATTGCACATA 58.748 29.630 13.02 13.02 35.86 2.29
2717 2726 7.101054 AGCAGATTTATGTTCAAATTGCACAT 58.899 30.769 14.88 14.88 37.87 3.21
2718 2727 6.457355 AGCAGATTTATGTTCAAATTGCACA 58.543 32.000 0.36 0.36 36.04 4.57
2719 2728 6.035327 GGAGCAGATTTATGTTCAAATTGCAC 59.965 38.462 0.00 0.00 36.04 4.57
2720 2729 6.101332 GGAGCAGATTTATGTTCAAATTGCA 58.899 36.000 13.20 0.00 36.04 4.08
2721 2730 5.521372 GGGAGCAGATTTATGTTCAAATTGC 59.479 40.000 0.00 0.00 35.04 3.56
2722 2731 6.870769 AGGGAGCAGATTTATGTTCAAATTG 58.129 36.000 0.00 0.00 32.55 2.32
2723 2732 8.773033 ATAGGGAGCAGATTTATGTTCAAATT 57.227 30.769 0.00 0.00 32.55 1.82
2724 2733 8.000709 TGATAGGGAGCAGATTTATGTTCAAAT 58.999 33.333 0.00 0.00 32.55 2.32
2725 2734 7.345691 TGATAGGGAGCAGATTTATGTTCAAA 58.654 34.615 0.00 0.00 32.55 2.69
2726 2735 6.899089 TGATAGGGAGCAGATTTATGTTCAA 58.101 36.000 0.00 0.00 32.55 2.69
2727 2736 6.499106 TGATAGGGAGCAGATTTATGTTCA 57.501 37.500 0.00 0.00 32.55 3.18
2728 2737 7.500559 AGTTTGATAGGGAGCAGATTTATGTTC 59.499 37.037 0.00 0.00 0.00 3.18
2729 2738 7.349598 AGTTTGATAGGGAGCAGATTTATGTT 58.650 34.615 0.00 0.00 0.00 2.71
2730 2739 6.904626 AGTTTGATAGGGAGCAGATTTATGT 58.095 36.000 0.00 0.00 0.00 2.29
2731 2740 6.994496 TGAGTTTGATAGGGAGCAGATTTATG 59.006 38.462 0.00 0.00 0.00 1.90
2732 2741 7.141758 TGAGTTTGATAGGGAGCAGATTTAT 57.858 36.000 0.00 0.00 0.00 1.40
2733 2742 6.560003 TGAGTTTGATAGGGAGCAGATTTA 57.440 37.500 0.00 0.00 0.00 1.40
2734 2743 5.441718 TGAGTTTGATAGGGAGCAGATTT 57.558 39.130 0.00 0.00 0.00 2.17
2735 2744 5.441718 TTGAGTTTGATAGGGAGCAGATT 57.558 39.130 0.00 0.00 0.00 2.40
2736 2745 5.369110 AGATTGAGTTTGATAGGGAGCAGAT 59.631 40.000 0.00 0.00 0.00 2.90
2737 2746 4.718774 AGATTGAGTTTGATAGGGAGCAGA 59.281 41.667 0.00 0.00 0.00 4.26
2738 2747 5.033589 AGATTGAGTTTGATAGGGAGCAG 57.966 43.478 0.00 0.00 0.00 4.24
2739 2748 5.431765 GAAGATTGAGTTTGATAGGGAGCA 58.568 41.667 0.00 0.00 0.00 4.26
2740 2749 4.819088 GGAAGATTGAGTTTGATAGGGAGC 59.181 45.833 0.00 0.00 0.00 4.70
2741 2750 5.053145 CGGAAGATTGAGTTTGATAGGGAG 58.947 45.833 0.00 0.00 0.00 4.30
2742 2751 4.714802 TCGGAAGATTGAGTTTGATAGGGA 59.285 41.667 0.00 0.00 33.31 4.20
2743 2752 5.023533 TCGGAAGATTGAGTTTGATAGGG 57.976 43.478 0.00 0.00 33.31 3.53
2758 2767 3.971346 GGGTTTGCAAAGCATCGGAAGA 61.971 50.000 34.69 0.00 38.76 2.87
2759 2768 1.669795 GGGTTTGCAAAGCATCGGAAG 60.670 52.381 34.69 0.00 38.76 3.46
2760 2769 0.316841 GGGTTTGCAAAGCATCGGAA 59.683 50.000 34.69 0.45 38.76 4.30
2761 2770 0.539438 AGGGTTTGCAAAGCATCGGA 60.539 50.000 34.69 1.22 38.76 4.55
2762 2771 0.318120 AAGGGTTTGCAAAGCATCGG 59.682 50.000 34.69 0.00 38.76 4.18
2763 2772 1.421382 CAAGGGTTTGCAAAGCATCG 58.579 50.000 34.69 19.93 38.76 3.84
2764 2773 1.344114 TCCAAGGGTTTGCAAAGCATC 59.656 47.619 34.69 22.12 38.76 3.91
2765 2774 1.422531 TCCAAGGGTTTGCAAAGCAT 58.577 45.000 34.69 28.81 38.76 3.79
2766 2775 1.422531 ATCCAAGGGTTTGCAAAGCA 58.577 45.000 34.69 19.36 38.11 3.91
2767 2776 2.145536 CAATCCAAGGGTTTGCAAAGC 58.854 47.619 28.80 28.80 35.75 3.51
2768 2777 2.769893 CCAATCCAAGGGTTTGCAAAG 58.230 47.619 13.26 0.00 32.72 2.77
2769 2778 1.202746 GCCAATCCAAGGGTTTGCAAA 60.203 47.619 8.05 8.05 32.72 3.68
2770 2779 0.396060 GCCAATCCAAGGGTTTGCAA 59.604 50.000 0.00 0.00 32.72 4.08
2771 2780 0.762082 TGCCAATCCAAGGGTTTGCA 60.762 50.000 6.75 6.75 32.72 4.08
2772 2781 0.396060 TTGCCAATCCAAGGGTTTGC 59.604 50.000 1.44 1.44 32.72 3.68
2773 2782 1.270785 GGTTGCCAATCCAAGGGTTTG 60.271 52.381 0.00 0.00 33.56 2.93
2774 2783 1.055849 GGTTGCCAATCCAAGGGTTT 58.944 50.000 0.00 0.00 0.00 3.27
2775 2784 0.105246 TGGTTGCCAATCCAAGGGTT 60.105 50.000 0.00 0.00 0.00 4.11
2776 2785 0.542702 CTGGTTGCCAATCCAAGGGT 60.543 55.000 1.42 0.00 30.80 4.34
2777 2786 1.891722 GCTGGTTGCCAATCCAAGGG 61.892 60.000 1.42 0.00 30.80 3.95
2778 2787 1.186917 TGCTGGTTGCCAATCCAAGG 61.187 55.000 1.42 0.00 42.00 3.61
2779 2788 0.245539 CTGCTGGTTGCCAATCCAAG 59.754 55.000 1.42 0.00 42.00 3.61
2780 2789 0.178967 TCTGCTGGTTGCCAATCCAA 60.179 50.000 1.42 0.00 42.00 3.53
2781 2790 0.609957 CTCTGCTGGTTGCCAATCCA 60.610 55.000 0.00 0.00 42.00 3.41
2782 2791 0.322816 TCTCTGCTGGTTGCCAATCC 60.323 55.000 0.00 0.00 42.00 3.01
2783 2792 1.093159 CTCTCTGCTGGTTGCCAATC 58.907 55.000 0.00 0.00 42.00 2.67
2784 2793 0.323178 CCTCTCTGCTGGTTGCCAAT 60.323 55.000 0.00 0.00 42.00 3.16
2785 2794 1.073722 CCTCTCTGCTGGTTGCCAA 59.926 57.895 0.00 0.00 42.00 4.52
2786 2795 2.752358 CCTCTCTGCTGGTTGCCA 59.248 61.111 0.00 0.00 42.00 4.92
2787 2796 2.045536 CCCTCTCTGCTGGTTGCC 60.046 66.667 0.00 0.00 42.00 4.52
2788 2797 2.045536 CCCCTCTCTGCTGGTTGC 60.046 66.667 0.00 0.00 43.25 4.17
2789 2798 2.190488 GACCCCCTCTCTGCTGGTTG 62.190 65.000 0.00 0.00 0.00 3.77
2790 2799 1.920835 GACCCCCTCTCTGCTGGTT 60.921 63.158 0.00 0.00 0.00 3.67
2791 2800 2.284995 GACCCCCTCTCTGCTGGT 60.285 66.667 0.00 0.00 0.00 4.00
2792 2801 2.040278 AGACCCCCTCTCTGCTGG 59.960 66.667 0.00 0.00 0.00 4.85
2793 2802 0.690411 ATCAGACCCCCTCTCTGCTG 60.690 60.000 0.00 0.00 35.95 4.41
2794 2803 0.398381 GATCAGACCCCCTCTCTGCT 60.398 60.000 0.00 0.00 35.95 4.24
2795 2804 1.406860 GGATCAGACCCCCTCTCTGC 61.407 65.000 0.00 0.00 35.95 4.26
2796 2805 0.264359 AGGATCAGACCCCCTCTCTG 59.736 60.000 0.00 0.00 37.14 3.35
2797 2806 0.264359 CAGGATCAGACCCCCTCTCT 59.736 60.000 0.00 0.00 0.00 3.10
2798 2807 0.263172 TCAGGATCAGACCCCCTCTC 59.737 60.000 0.00 0.00 0.00 3.20
2799 2808 0.948050 ATCAGGATCAGACCCCCTCT 59.052 55.000 0.00 0.00 0.00 3.69
2800 2809 2.252714 GTATCAGGATCAGACCCCCTC 58.747 57.143 0.00 0.00 0.00 4.30
2801 2810 1.580658 TGTATCAGGATCAGACCCCCT 59.419 52.381 0.00 0.00 0.00 4.79
2802 2811 2.103153 TGTATCAGGATCAGACCCCC 57.897 55.000 0.00 0.00 0.00 5.40
2803 2812 5.394663 CGATAATGTATCAGGATCAGACCCC 60.395 48.000 0.00 0.00 34.87 4.95
2804 2813 5.394663 CCGATAATGTATCAGGATCAGACCC 60.395 48.000 0.00 0.00 34.87 4.46
2805 2814 5.419155 TCCGATAATGTATCAGGATCAGACC 59.581 44.000 0.00 0.00 34.95 3.85
2806 2815 6.516739 TCCGATAATGTATCAGGATCAGAC 57.483 41.667 0.00 0.00 34.95 3.51
2811 2820 7.911130 ATCAGATCCGATAATGTATCAGGAT 57.089 36.000 15.36 15.36 44.00 3.24
2812 2821 7.503902 CCTATCAGATCCGATAATGTATCAGGA 59.496 40.741 0.47 9.63 39.94 3.86
2813 2822 7.503902 TCCTATCAGATCCGATAATGTATCAGG 59.496 40.741 0.47 0.00 34.87 3.86
2814 2823 8.457238 TCCTATCAGATCCGATAATGTATCAG 57.543 38.462 0.47 0.00 34.87 2.90
2815 2824 7.503902 CCTCCTATCAGATCCGATAATGTATCA 59.496 40.741 0.47 0.00 34.87 2.15
2816 2825 7.504238 ACCTCCTATCAGATCCGATAATGTATC 59.496 40.741 0.47 0.00 0.00 2.24
2817 2826 7.358263 ACCTCCTATCAGATCCGATAATGTAT 58.642 38.462 0.47 0.00 0.00 2.29
2818 2827 6.732487 ACCTCCTATCAGATCCGATAATGTA 58.268 40.000 0.47 0.00 0.00 2.29
2819 2828 5.584913 ACCTCCTATCAGATCCGATAATGT 58.415 41.667 0.47 0.00 0.00 2.71
2820 2829 6.537453 AACCTCCTATCAGATCCGATAATG 57.463 41.667 0.47 0.00 0.00 1.90
2821 2830 7.415086 AGTAACCTCCTATCAGATCCGATAAT 58.585 38.462 0.47 0.00 0.00 1.28
2822 2831 6.791371 AGTAACCTCCTATCAGATCCGATAA 58.209 40.000 0.47 0.00 0.00 1.75
2823 2832 6.390048 AGTAACCTCCTATCAGATCCGATA 57.610 41.667 0.00 0.00 0.00 2.92
2824 2833 5.263872 AGTAACCTCCTATCAGATCCGAT 57.736 43.478 0.00 0.00 0.00 4.18
2825 2834 4.726035 AGTAACCTCCTATCAGATCCGA 57.274 45.455 0.00 0.00 0.00 4.55
2826 2835 6.626181 GCATAAGTAACCTCCTATCAGATCCG 60.626 46.154 0.00 0.00 0.00 4.18
2827 2836 6.211584 TGCATAAGTAACCTCCTATCAGATCC 59.788 42.308 0.00 0.00 0.00 3.36
2828 2837 7.233389 TGCATAAGTAACCTCCTATCAGATC 57.767 40.000 0.00 0.00 0.00 2.75
2829 2838 7.618019 TTGCATAAGTAACCTCCTATCAGAT 57.382 36.000 0.00 0.00 0.00 2.90
2830 2839 7.272978 GTTTGCATAAGTAACCTCCTATCAGA 58.727 38.462 0.00 0.00 0.00 3.27
2831 2840 6.483640 GGTTTGCATAAGTAACCTCCTATCAG 59.516 42.308 9.55 0.00 38.58 2.90
2832 2841 6.354130 GGTTTGCATAAGTAACCTCCTATCA 58.646 40.000 9.55 0.00 38.58 2.15
2833 2842 5.763698 GGGTTTGCATAAGTAACCTCCTATC 59.236 44.000 15.13 0.00 40.86 2.08
2834 2843 5.192923 TGGGTTTGCATAAGTAACCTCCTAT 59.807 40.000 15.13 0.00 40.86 2.57
2835 2844 4.536888 TGGGTTTGCATAAGTAACCTCCTA 59.463 41.667 15.13 0.42 40.86 2.94
2836 2845 3.332485 TGGGTTTGCATAAGTAACCTCCT 59.668 43.478 15.13 0.00 40.86 3.69
2837 2846 3.442625 GTGGGTTTGCATAAGTAACCTCC 59.557 47.826 15.13 4.65 40.86 4.30
2838 2847 3.126343 CGTGGGTTTGCATAAGTAACCTC 59.874 47.826 15.13 7.65 40.86 3.85
2839 2848 3.078837 CGTGGGTTTGCATAAGTAACCT 58.921 45.455 15.13 0.00 40.86 3.50
2840 2849 2.162809 CCGTGGGTTTGCATAAGTAACC 59.837 50.000 8.48 8.48 40.44 2.85
2841 2850 2.162809 CCCGTGGGTTTGCATAAGTAAC 59.837 50.000 0.00 0.00 0.00 2.50
2842 2851 2.438411 CCCGTGGGTTTGCATAAGTAA 58.562 47.619 0.00 0.00 0.00 2.24
2843 2852 1.340211 CCCCGTGGGTTTGCATAAGTA 60.340 52.381 3.83 0.00 38.25 2.24
2844 2853 0.610785 CCCCGTGGGTTTGCATAAGT 60.611 55.000 3.83 0.00 38.25 2.24
2845 2854 2.188912 CCCCGTGGGTTTGCATAAG 58.811 57.895 3.83 0.00 38.25 1.73
2846 2855 4.425099 CCCCGTGGGTTTGCATAA 57.575 55.556 3.83 0.00 38.25 1.90
2856 2865 3.195825 GTGATTCTAGATATCCCCCGTGG 59.804 52.174 0.00 0.00 0.00 4.94
2857 2866 4.090090 AGTGATTCTAGATATCCCCCGTG 58.910 47.826 0.00 0.00 0.00 4.94
2858 2867 4.405756 AGTGATTCTAGATATCCCCCGT 57.594 45.455 0.00 0.00 0.00 5.28
2859 2868 5.622460 CGAAAGTGATTCTAGATATCCCCCG 60.622 48.000 0.00 0.00 35.79 5.73
2860 2869 5.337652 CCGAAAGTGATTCTAGATATCCCCC 60.338 48.000 0.00 0.00 35.79 5.40
2861 2870 5.725362 CCGAAAGTGATTCTAGATATCCCC 58.275 45.833 0.00 0.00 35.79 4.81
2862 2871 5.046950 AGCCGAAAGTGATTCTAGATATCCC 60.047 44.000 0.00 0.00 35.79 3.85
2863 2872 6.031751 AGCCGAAAGTGATTCTAGATATCC 57.968 41.667 0.00 0.00 35.79 2.59
2866 2875 9.909644 GTTAATAGCCGAAAGTGATTCTAGATA 57.090 33.333 0.00 0.00 35.79 1.98
2867 2876 8.643324 AGTTAATAGCCGAAAGTGATTCTAGAT 58.357 33.333 0.00 0.00 35.79 1.98
2868 2877 8.008513 AGTTAATAGCCGAAAGTGATTCTAGA 57.991 34.615 0.00 0.00 35.79 2.43
2869 2878 8.649973 AAGTTAATAGCCGAAAGTGATTCTAG 57.350 34.615 0.00 0.00 35.79 2.43
2870 2879 7.709613 GGAAGTTAATAGCCGAAAGTGATTCTA 59.290 37.037 0.00 0.00 35.79 2.10
2871 2880 6.539103 GGAAGTTAATAGCCGAAAGTGATTCT 59.461 38.462 0.00 0.00 35.79 2.40
2872 2881 6.238402 GGGAAGTTAATAGCCGAAAGTGATTC 60.238 42.308 0.00 0.00 34.52 2.52
2873 2882 5.589050 GGGAAGTTAATAGCCGAAAGTGATT 59.411 40.000 0.00 0.00 0.00 2.57
2874 2883 5.123936 GGGAAGTTAATAGCCGAAAGTGAT 58.876 41.667 0.00 0.00 0.00 3.06
2875 2884 4.020039 TGGGAAGTTAATAGCCGAAAGTGA 60.020 41.667 0.00 0.00 0.00 3.41
2876 2885 4.258543 TGGGAAGTTAATAGCCGAAAGTG 58.741 43.478 0.00 0.00 0.00 3.16
2877 2886 4.563140 TGGGAAGTTAATAGCCGAAAGT 57.437 40.909 0.00 0.00 0.00 2.66
2878 2887 5.007724 GTCATGGGAAGTTAATAGCCGAAAG 59.992 44.000 0.00 0.00 0.00 2.62
2879 2888 4.879545 GTCATGGGAAGTTAATAGCCGAAA 59.120 41.667 0.00 0.00 0.00 3.46
2880 2889 4.163458 AGTCATGGGAAGTTAATAGCCGAA 59.837 41.667 0.00 0.00 0.00 4.30
2881 2890 3.709653 AGTCATGGGAAGTTAATAGCCGA 59.290 43.478 0.00 0.00 0.00 5.54
2882 2891 4.073293 AGTCATGGGAAGTTAATAGCCG 57.927 45.455 0.00 0.00 0.00 5.52
2883 2892 7.201794 GGTTTAAGTCATGGGAAGTTAATAGCC 60.202 40.741 0.00 0.00 0.00 3.93
2884 2893 7.338449 TGGTTTAAGTCATGGGAAGTTAATAGC 59.662 37.037 0.00 0.00 0.00 2.97
2885 2894 8.674607 GTGGTTTAAGTCATGGGAAGTTAATAG 58.325 37.037 0.00 0.00 0.00 1.73
2886 2895 8.387813 AGTGGTTTAAGTCATGGGAAGTTAATA 58.612 33.333 0.00 0.00 0.00 0.98
2887 2896 7.238710 AGTGGTTTAAGTCATGGGAAGTTAAT 58.761 34.615 0.00 0.00 0.00 1.40
2888 2897 6.607019 AGTGGTTTAAGTCATGGGAAGTTAA 58.393 36.000 0.00 0.00 0.00 2.01
2889 2898 6.195600 AGTGGTTTAAGTCATGGGAAGTTA 57.804 37.500 0.00 0.00 0.00 2.24
2890 2899 5.061721 AGTGGTTTAAGTCATGGGAAGTT 57.938 39.130 0.00 0.00 0.00 2.66
2891 2900 4.724279 AGTGGTTTAAGTCATGGGAAGT 57.276 40.909 0.00 0.00 0.00 3.01
2892 2901 5.316987 AGAAGTGGTTTAAGTCATGGGAAG 58.683 41.667 0.00 0.00 0.00 3.46
2893 2902 5.319043 AGAAGTGGTTTAAGTCATGGGAA 57.681 39.130 0.00 0.00 0.00 3.97
2894 2903 4.993705 AGAAGTGGTTTAAGTCATGGGA 57.006 40.909 0.00 0.00 0.00 4.37
2931 2940 7.275888 TCACACATCTGCTTGTATTCTTTTT 57.724 32.000 0.00 0.00 0.00 1.94
2932 2941 6.882610 TCACACATCTGCTTGTATTCTTTT 57.117 33.333 0.00 0.00 0.00 2.27
2933 2942 8.743085 ATATCACACATCTGCTTGTATTCTTT 57.257 30.769 0.00 0.00 0.00 2.52
2934 2943 8.743085 AATATCACACATCTGCTTGTATTCTT 57.257 30.769 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.