Multiple sequence alignment - TraesCS5B01G080700

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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 TraesCS5B01G080700 chr5B 100.000 3041 0 0 1 3041 98847266 98844226 0.000000e+00 5616
1 TraesCS5B01G080700 chr5B 84.045 1686 233 19 990 2667 5067241 5065584 0.000000e+00 1591
2 TraesCS5B01G080700 chr5B 84.827 1562 226 9 1013 2565 5072940 5071381 0.000000e+00 1561
3 TraesCS5B01G080700 chr5B 96.474 397 10 4 2649 3041 281571155 281570759 0.000000e+00 652
4 TraesCS5B01G080700 chr5D 97.320 1679 40 2 990 2667 93862968 93861294 0.000000e+00 2846
5 TraesCS5B01G080700 chr5D 85.166 1564 222 7 1012 2565 3632897 3634460 0.000000e+00 1594
6 TraesCS5B01G080700 chr5A 96.431 1681 48 2 988 2667 87417788 87416119 0.000000e+00 2761
7 TraesCS5B01G080700 chr3A 96.559 988 33 1 1 988 687004784 687005770 0.000000e+00 1635
8 TraesCS5B01G080700 chr3A 96.588 381 12 1 2661 3041 676074014 676073635 5.530000e-177 630
9 TraesCS5B01G080700 chr2B 96.255 988 36 1 1 988 584817016 584818002 0.000000e+00 1618
10 TraesCS5B01G080700 chr2B 95.248 989 41 3 1 988 511153386 511154369 0.000000e+00 1561
11 TraesCS5B01G080700 chr2B 80.851 705 102 21 1 697 46328648 46327969 9.660000e-145 523
12 TraesCS5B01G080700 chr2B 83.333 408 54 8 1 401 52975526 52975926 6.200000e-97 364
13 TraesCS5B01G080700 chr7D 85.112 1518 216 2 991 2507 610421509 610420001 0.000000e+00 1543
14 TraesCS5B01G080700 chr7A 84.391 1576 236 2 991 2565 700300301 700301867 0.000000e+00 1539
15 TraesCS5B01G080700 chr7A 84.327 1576 237 2 991 2565 700338119 700339685 0.000000e+00 1533
16 TraesCS5B01G080700 chr7A 97.082 377 10 1 2666 3041 571789114 571789490 4.280000e-178 634
17 TraesCS5B01G080700 chr7B 84.288 1553 232 5 993 2543 698682805 698684347 0.000000e+00 1506
18 TraesCS5B01G080700 chr7B 96.654 807 26 1 182 988 707260962 707260157 0.000000e+00 1339
19 TraesCS5B01G080700 chr7B 87.879 858 90 8 143 989 2757277 2756423 0.000000e+00 996
20 TraesCS5B01G080700 chr7B 96.364 385 12 2 2659 3041 664046779 664047163 1.540000e-177 632
21 TraesCS5B01G080700 chr2A 92.605 906 58 5 89 988 765675703 765676605 0.000000e+00 1293
22 TraesCS5B01G080700 chr2A 97.872 376 7 1 2666 3041 157450147 157450521 0.000000e+00 649
23 TraesCS5B01G080700 chr2A 96.345 383 13 1 2657 3039 18195186 18195567 1.990000e-176 628
24 TraesCS5B01G080700 chr1B 86.987 999 116 12 1 989 20748815 20749809 0.000000e+00 1112
25 TraesCS5B01G080700 chr1B 86.563 707 82 12 1 697 627705289 627705992 0.000000e+00 767
26 TraesCS5B01G080700 chr1B 96.891 386 10 2 2657 3041 295769577 295769193 0.000000e+00 645
27 TraesCS5B01G080700 chr6B 97.326 374 10 0 2668 3041 589922179 589922552 1.190000e-178 636
28 TraesCS5B01G080700 chr6B 88.302 265 30 1 1 264 707819981 707819717 1.760000e-82 316
29 TraesCS5B01G080700 chr4B 96.364 385 10 4 2660 3041 28681506 28681889 5.530000e-177 630
30 TraesCS5B01G080700 chr4B 87.908 306 36 1 684 989 29631074 29631378 2.880000e-95 359
31 TraesCS5B01G080700 chrUn 87.908 306 36 1 684 989 413062211 413061907 2.880000e-95 359


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 TraesCS5B01G080700 chr5B 98844226 98847266 3040 True 5616 5616 100.000 1 3041 1 chr5B.!!$R3 3040
1 TraesCS5B01G080700 chr5B 5065584 5067241 1657 True 1591 1591 84.045 990 2667 1 chr5B.!!$R1 1677
2 TraesCS5B01G080700 chr5B 5071381 5072940 1559 True 1561 1561 84.827 1013 2565 1 chr5B.!!$R2 1552
3 TraesCS5B01G080700 chr5D 93861294 93862968 1674 True 2846 2846 97.320 990 2667 1 chr5D.!!$R1 1677
4 TraesCS5B01G080700 chr5D 3632897 3634460 1563 False 1594 1594 85.166 1012 2565 1 chr5D.!!$F1 1553
5 TraesCS5B01G080700 chr5A 87416119 87417788 1669 True 2761 2761 96.431 988 2667 1 chr5A.!!$R1 1679
6 TraesCS5B01G080700 chr3A 687004784 687005770 986 False 1635 1635 96.559 1 988 1 chr3A.!!$F1 987
7 TraesCS5B01G080700 chr2B 584817016 584818002 986 False 1618 1618 96.255 1 988 1 chr2B.!!$F3 987
8 TraesCS5B01G080700 chr2B 511153386 511154369 983 False 1561 1561 95.248 1 988 1 chr2B.!!$F2 987
9 TraesCS5B01G080700 chr2B 46327969 46328648 679 True 523 523 80.851 1 697 1 chr2B.!!$R1 696
10 TraesCS5B01G080700 chr7D 610420001 610421509 1508 True 1543 1543 85.112 991 2507 1 chr7D.!!$R1 1516
11 TraesCS5B01G080700 chr7A 700300301 700301867 1566 False 1539 1539 84.391 991 2565 1 chr7A.!!$F2 1574
12 TraesCS5B01G080700 chr7A 700338119 700339685 1566 False 1533 1533 84.327 991 2565 1 chr7A.!!$F3 1574
13 TraesCS5B01G080700 chr7B 698682805 698684347 1542 False 1506 1506 84.288 993 2543 1 chr7B.!!$F2 1550
14 TraesCS5B01G080700 chr7B 707260157 707260962 805 True 1339 1339 96.654 182 988 1 chr7B.!!$R2 806
15 TraesCS5B01G080700 chr7B 2756423 2757277 854 True 996 996 87.879 143 989 1 chr7B.!!$R1 846
16 TraesCS5B01G080700 chr2A 765675703 765676605 902 False 1293 1293 92.605 89 988 1 chr2A.!!$F3 899
17 TraesCS5B01G080700 chr1B 20748815 20749809 994 False 1112 1112 86.987 1 989 1 chr1B.!!$F1 988
18 TraesCS5B01G080700 chr1B 627705289 627705992 703 False 767 767 86.563 1 697 1 chr1B.!!$F2 696

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
333 340 0.250727 GCCAAGCACTGGGTGTAGAA 60.251 55.0 6.95 0.0 46.54 2.10 F
733 742 0.322816 ACCGTCAGCTACCTCCGTTA 60.323 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1558 1.341482 TGGCTTTGTTGGTGAACAGGA 60.341 47.619 0.0 0.0 43.03 3.86 R
2712 2762 0.392863 TGAATGGTGATGGAGGCGTG 60.393 55.000 0.0 0.0 0.00 5.34 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
17 18 2.741985 TGCGGGTCATGTTGCTCG 60.742 61.111 0.00 0.00 0.00 5.03
98 101 1.027792 GCATTTTTCGGACCCGCCTA 61.028 55.000 3.13 0.00 39.59 3.93
140 143 3.000727 GCACTGCTATGGTTTCTACGTT 58.999 45.455 0.00 0.00 0.00 3.99
272 279 3.404773 GCCCAGCCACCTACTTCT 58.595 61.111 0.00 0.00 0.00 2.85
333 340 0.250727 GCCAAGCACTGGGTGTAGAA 60.251 55.000 6.95 0.00 46.54 2.10
637 646 6.466885 ACTGTATAAGCCGAGTGTTATCTT 57.533 37.500 0.00 0.00 0.00 2.40
642 651 3.028094 AGCCGAGTGTTATCTTAGGGA 57.972 47.619 0.00 0.00 0.00 4.20
706 715 2.297597 ACACGGCTTATAGGATGCTCTC 59.702 50.000 0.00 0.00 0.00 3.20
733 742 0.322816 ACCGTCAGCTACCTCCGTTA 60.323 55.000 0.00 0.00 0.00 3.18
798 807 5.360591 CCGAGTGCTTTTTCCTGTAGATAT 58.639 41.667 0.00 0.00 0.00 1.63
801 810 4.811557 AGTGCTTTTTCCTGTAGATATCGC 59.188 41.667 0.00 0.00 0.00 4.58
930 947 2.321719 TGCATATAAGCCGAGTACCCA 58.678 47.619 0.00 0.00 0.00 4.51
966 985 3.412386 GCTTATAGCCTAACACATGGGG 58.588 50.000 0.00 0.00 34.48 4.96
975 994 2.074729 AACACATGGGGAAACGGAAA 57.925 45.000 0.00 0.00 0.00 3.13
980 999 3.006323 CACATGGGGAAACGGAAATTTCA 59.994 43.478 19.49 0.00 39.85 2.69
1059 1078 3.058160 GCTGTGGCGAGCACCATT 61.058 61.111 3.60 0.00 43.01 3.16
1095 1114 1.224592 GCAGAACCACATCCCGGAT 59.775 57.895 0.73 0.00 0.00 4.18
1386 1405 1.377725 CTCCAAGCAGCGACCCAAT 60.378 57.895 0.00 0.00 0.00 3.16
1986 2006 1.945354 GCGACAAGGACTCCGATGGA 61.945 60.000 8.32 0.00 0.00 3.41
2141 2162 1.301293 CAAGGAGAAGCTGGACCCC 59.699 63.158 0.00 0.00 0.00 4.95
2237 2258 2.359900 GCCAAGAACTACCTGGATGTG 58.640 52.381 0.00 0.00 0.00 3.21
2240 2261 3.338249 CAAGAACTACCTGGATGTGGTG 58.662 50.000 0.00 0.00 38.42 4.17
2325 2346 1.606531 GCAGAGAACCTGATGCCCT 59.393 57.895 0.00 0.00 45.78 5.19
2406 2427 1.667830 CAGGCCAAAGAAGACGCGA 60.668 57.895 15.93 0.00 0.00 5.87
2583 2633 5.822204 ACAAGATACAGGAGTAGAGTGAGT 58.178 41.667 0.00 0.00 32.86 3.41
2584 2634 5.650266 ACAAGATACAGGAGTAGAGTGAGTG 59.350 44.000 0.00 0.00 32.86 3.51
2585 2635 5.702065 AGATACAGGAGTAGAGTGAGTGA 57.298 43.478 0.00 0.00 32.86 3.41
2586 2636 5.680619 AGATACAGGAGTAGAGTGAGTGAG 58.319 45.833 0.00 0.00 32.86 3.51
2592 2642 3.194542 GGAGTAGAGTGAGTGAGCATGTT 59.805 47.826 0.00 0.00 0.00 2.71
2637 2687 4.256920 AGATGCAGTGTTGGTTCAGATAC 58.743 43.478 0.00 0.00 0.00 2.24
2670 2720 8.786826 ATCACTCAACTGAAATAAAATACGGA 57.213 30.769 0.00 0.00 0.00 4.69
2671 2721 8.610248 TCACTCAACTGAAATAAAATACGGAA 57.390 30.769 0.00 0.00 0.00 4.30
2672 2722 9.058174 TCACTCAACTGAAATAAAATACGGAAA 57.942 29.630 0.00 0.00 0.00 3.13
2673 2723 9.840427 CACTCAACTGAAATAAAATACGGAAAT 57.160 29.630 0.00 0.00 0.00 2.17
2674 2724 9.840427 ACTCAACTGAAATAAAATACGGAAATG 57.160 29.630 0.00 0.00 0.00 2.32
2675 2725 9.840427 CTCAACTGAAATAAAATACGGAAATGT 57.160 29.630 0.00 0.00 0.00 2.71
2681 2731 9.063739 TGAAATAAAATACGGAAATGTTAACGC 57.936 29.630 0.26 0.00 0.00 4.84
2682 2732 7.974243 AATAAAATACGGAAATGTTAACGCC 57.026 32.000 0.26 0.00 0.00 5.68
2683 2733 4.359971 AAATACGGAAATGTTAACGCCC 57.640 40.909 0.26 0.00 0.00 6.13
2684 2734 2.469274 TACGGAAATGTTAACGCCCA 57.531 45.000 0.26 0.00 0.00 5.36
2685 2735 0.876399 ACGGAAATGTTAACGCCCAC 59.124 50.000 0.26 0.00 0.00 4.61
2686 2736 0.875728 CGGAAATGTTAACGCCCACA 59.124 50.000 0.26 0.00 0.00 4.17
2687 2737 1.400500 CGGAAATGTTAACGCCCACAC 60.400 52.381 0.26 0.00 0.00 3.82
2688 2738 1.400500 GGAAATGTTAACGCCCACACG 60.400 52.381 0.26 0.00 39.50 4.49
2700 2750 2.024022 CACACGTGTGGGCGTTTG 59.976 61.111 35.65 12.14 43.83 2.93
2701 2751 3.883180 ACACGTGTGGGCGTTTGC 61.883 61.111 22.71 0.00 43.83 3.68
2702 2752 3.882013 CACGTGTGGGCGTTTGCA 61.882 61.111 7.58 0.00 43.83 4.08
2711 2761 4.036804 GCGTTTGCACATCGCCCA 62.037 61.111 15.37 0.00 43.41 5.36
2712 2762 2.126888 CGTTTGCACATCGCCCAC 60.127 61.111 0.00 0.00 41.33 4.61
2713 2763 2.902419 CGTTTGCACATCGCCCACA 61.902 57.895 0.00 0.00 41.33 4.17
2714 2764 1.371635 GTTTGCACATCGCCCACAC 60.372 57.895 0.00 0.00 41.33 3.82
2715 2765 2.902419 TTTGCACATCGCCCACACG 61.902 57.895 0.00 0.00 41.33 4.49
2719 2769 4.760047 ACATCGCCCACACGCCTC 62.760 66.667 0.00 0.00 0.00 4.70
2724 2774 4.408821 GCCCACACGCCTCCATCA 62.409 66.667 0.00 0.00 0.00 3.07
2725 2775 2.436646 CCCACACGCCTCCATCAC 60.437 66.667 0.00 0.00 0.00 3.06
2726 2776 2.436646 CCACACGCCTCCATCACC 60.437 66.667 0.00 0.00 0.00 4.02
2727 2777 2.347114 CACACGCCTCCATCACCA 59.653 61.111 0.00 0.00 0.00 4.17
2728 2778 1.078214 CACACGCCTCCATCACCAT 60.078 57.895 0.00 0.00 0.00 3.55
2729 2779 0.677731 CACACGCCTCCATCACCATT 60.678 55.000 0.00 0.00 0.00 3.16
2730 2780 0.392998 ACACGCCTCCATCACCATTC 60.393 55.000 0.00 0.00 0.00 2.67
2731 2781 0.392863 CACGCCTCCATCACCATTCA 60.393 55.000 0.00 0.00 0.00 2.57
2732 2782 0.548031 ACGCCTCCATCACCATTCAT 59.452 50.000 0.00 0.00 0.00 2.57
2733 2783 1.064463 ACGCCTCCATCACCATTCATT 60.064 47.619 0.00 0.00 0.00 2.57
2734 2784 2.026641 CGCCTCCATCACCATTCATTT 58.973 47.619 0.00 0.00 0.00 2.32
2735 2785 2.428171 CGCCTCCATCACCATTCATTTT 59.572 45.455 0.00 0.00 0.00 1.82
2736 2786 3.735820 CGCCTCCATCACCATTCATTTTG 60.736 47.826 0.00 0.00 0.00 2.44
2737 2787 3.788937 CCTCCATCACCATTCATTTTGC 58.211 45.455 0.00 0.00 0.00 3.68
2738 2788 3.431207 CCTCCATCACCATTCATTTTGCC 60.431 47.826 0.00 0.00 0.00 4.52
2739 2789 3.171528 TCCATCACCATTCATTTTGCCA 58.828 40.909 0.00 0.00 0.00 4.92
2740 2790 3.055963 TCCATCACCATTCATTTTGCCAC 60.056 43.478 0.00 0.00 0.00 5.01
2741 2791 2.721274 TCACCATTCATTTTGCCACG 57.279 45.000 0.00 0.00 0.00 4.94
2742 2792 1.959985 TCACCATTCATTTTGCCACGT 59.040 42.857 0.00 0.00 0.00 4.49
2743 2793 3.149981 TCACCATTCATTTTGCCACGTA 58.850 40.909 0.00 0.00 0.00 3.57
2744 2794 3.761218 TCACCATTCATTTTGCCACGTAT 59.239 39.130 0.00 0.00 0.00 3.06
2745 2795 3.858812 CACCATTCATTTTGCCACGTATG 59.141 43.478 0.00 0.00 0.00 2.39
2746 2796 3.761218 ACCATTCATTTTGCCACGTATGA 59.239 39.130 0.00 0.00 0.00 2.15
2747 2797 4.219507 ACCATTCATTTTGCCACGTATGAA 59.780 37.500 10.64 10.64 40.21 2.57
2748 2798 5.105392 ACCATTCATTTTGCCACGTATGAAT 60.105 36.000 13.63 13.63 44.35 2.57
2749 2799 6.096141 ACCATTCATTTTGCCACGTATGAATA 59.904 34.615 17.28 0.00 42.66 1.75
2750 2800 6.638063 CCATTCATTTTGCCACGTATGAATAG 59.362 38.462 17.28 9.83 42.66 1.73
2751 2801 6.993786 TTCATTTTGCCACGTATGAATAGA 57.006 33.333 5.31 0.00 33.41 1.98
2752 2802 7.566760 TTCATTTTGCCACGTATGAATAGAT 57.433 32.000 5.31 0.00 33.41 1.98
2753 2803 6.958255 TCATTTTGCCACGTATGAATAGATG 58.042 36.000 0.00 0.00 0.00 2.90
2754 2804 6.765512 TCATTTTGCCACGTATGAATAGATGA 59.234 34.615 0.00 0.00 0.00 2.92
2755 2805 5.984233 TTTGCCACGTATGAATAGATGAC 57.016 39.130 0.00 0.00 0.00 3.06
2756 2806 4.664150 TGCCACGTATGAATAGATGACA 57.336 40.909 0.00 0.00 0.00 3.58
2757 2807 5.213891 TGCCACGTATGAATAGATGACAT 57.786 39.130 0.00 0.00 0.00 3.06
2758 2808 5.230182 TGCCACGTATGAATAGATGACATC 58.770 41.667 7.39 7.39 0.00 3.06
2759 2809 5.221422 TGCCACGTATGAATAGATGACATCA 60.221 40.000 17.57 4.35 0.00 3.07
2760 2810 5.347093 GCCACGTATGAATAGATGACATCAG 59.653 44.000 17.57 0.66 0.00 2.90
2761 2811 5.347093 CCACGTATGAATAGATGACATCAGC 59.653 44.000 17.57 4.42 0.00 4.26
2762 2812 5.922544 CACGTATGAATAGATGACATCAGCA 59.077 40.000 17.57 9.50 34.14 4.41
2763 2813 6.089150 CACGTATGAATAGATGACATCAGCAG 59.911 42.308 17.57 2.12 34.14 4.24
2764 2814 6.015940 ACGTATGAATAGATGACATCAGCAGA 60.016 38.462 17.57 4.54 34.14 4.26
2765 2815 6.865205 CGTATGAATAGATGACATCAGCAGAA 59.135 38.462 17.57 0.00 34.14 3.02
2766 2816 7.383300 CGTATGAATAGATGACATCAGCAGAAA 59.617 37.037 17.57 0.00 34.14 2.52
2767 2817 9.217278 GTATGAATAGATGACATCAGCAGAAAT 57.783 33.333 17.57 5.11 34.14 2.17
2768 2818 8.693120 ATGAATAGATGACATCAGCAGAAATT 57.307 30.769 17.57 5.45 34.14 1.82
2769 2819 8.515695 TGAATAGATGACATCAGCAGAAATTT 57.484 30.769 17.57 0.00 34.14 1.82
2770 2820 8.963725 TGAATAGATGACATCAGCAGAAATTTT 58.036 29.630 17.57 0.00 34.14 1.82
2771 2821 9.798994 GAATAGATGACATCAGCAGAAATTTTT 57.201 29.630 17.57 0.00 34.14 1.94
2793 2843 6.986904 TTTTGGTTTTCGGCTTAAAAATGT 57.013 29.167 0.00 0.00 30.53 2.71
2794 2844 6.986904 TTTGGTTTTCGGCTTAAAAATGTT 57.013 29.167 0.00 0.00 30.53 2.71
2795 2845 5.975410 TGGTTTTCGGCTTAAAAATGTTG 57.025 34.783 0.00 0.00 30.53 3.33
2796 2846 5.420409 TGGTTTTCGGCTTAAAAATGTTGT 58.580 33.333 0.00 0.00 30.53 3.32
2797 2847 6.570692 TGGTTTTCGGCTTAAAAATGTTGTA 58.429 32.000 0.00 0.00 30.53 2.41
2798 2848 7.210873 TGGTTTTCGGCTTAAAAATGTTGTAT 58.789 30.769 0.00 0.00 30.53 2.29
2799 2849 7.382759 TGGTTTTCGGCTTAAAAATGTTGTATC 59.617 33.333 0.00 0.00 30.53 2.24
2800 2850 7.597369 GGTTTTCGGCTTAAAAATGTTGTATCT 59.403 33.333 0.00 0.00 30.53 1.98
2801 2851 8.635983 GTTTTCGGCTTAAAAATGTTGTATCTC 58.364 33.333 0.00 0.00 30.53 2.75
2802 2852 6.431198 TCGGCTTAAAAATGTTGTATCTCC 57.569 37.500 0.00 0.00 0.00 3.71
2803 2853 6.177610 TCGGCTTAAAAATGTTGTATCTCCT 58.822 36.000 0.00 0.00 0.00 3.69
2804 2854 7.332557 TCGGCTTAAAAATGTTGTATCTCCTA 58.667 34.615 0.00 0.00 0.00 2.94
2805 2855 7.494625 TCGGCTTAAAAATGTTGTATCTCCTAG 59.505 37.037 0.00 0.00 0.00 3.02
2806 2856 7.494625 CGGCTTAAAAATGTTGTATCTCCTAGA 59.505 37.037 0.00 0.00 0.00 2.43
2807 2857 9.343539 GGCTTAAAAATGTTGTATCTCCTAGAT 57.656 33.333 0.00 0.00 38.70 1.98
2833 2883 7.528481 AAAAAGCGAACTAAAAATCCGTTTT 57.472 28.000 0.00 0.00 42.24 2.43
2834 2884 6.742999 AAAGCGAACTAAAAATCCGTTTTC 57.257 33.333 0.00 0.00 40.07 2.29
2835 2885 5.427036 AGCGAACTAAAAATCCGTTTTCA 57.573 34.783 0.00 0.00 40.07 2.69
2836 2886 5.209977 AGCGAACTAAAAATCCGTTTTCAC 58.790 37.500 0.00 0.00 40.07 3.18
2837 2887 4.380678 GCGAACTAAAAATCCGTTTTCACC 59.619 41.667 0.00 0.00 40.07 4.02
2838 2888 5.512473 CGAACTAAAAATCCGTTTTCACCA 58.488 37.500 0.00 0.00 40.07 4.17
2839 2889 6.146898 CGAACTAAAAATCCGTTTTCACCAT 58.853 36.000 0.00 0.00 40.07 3.55
2840 2890 6.639279 CGAACTAAAAATCCGTTTTCACCATT 59.361 34.615 0.00 0.00 40.07 3.16
2841 2891 7.804129 CGAACTAAAAATCCGTTTTCACCATTA 59.196 33.333 0.00 0.00 40.07 1.90
2842 2892 9.465985 GAACTAAAAATCCGTTTTCACCATTAA 57.534 29.630 0.00 0.00 40.07 1.40
2843 2893 9.819267 AACTAAAAATCCGTTTTCACCATTAAA 57.181 25.926 0.00 0.00 40.07 1.52
2844 2894 9.990360 ACTAAAAATCCGTTTTCACCATTAAAT 57.010 25.926 0.00 0.00 40.07 1.40
2846 2896 7.899178 AAAATCCGTTTTCACCATTAAATCC 57.101 32.000 0.00 0.00 32.14 3.01
2847 2897 4.688511 TCCGTTTTCACCATTAAATCCG 57.311 40.909 0.00 0.00 0.00 4.18
2848 2898 4.073549 TCCGTTTTCACCATTAAATCCGT 58.926 39.130 0.00 0.00 0.00 4.69
2849 2899 4.154556 TCCGTTTTCACCATTAAATCCGTC 59.845 41.667 0.00 0.00 0.00 4.79
2850 2900 4.155280 CCGTTTTCACCATTAAATCCGTCT 59.845 41.667 0.00 0.00 0.00 4.18
2851 2901 5.321516 CGTTTTCACCATTAAATCCGTCTC 58.678 41.667 0.00 0.00 0.00 3.36
2852 2902 5.106869 CGTTTTCACCATTAAATCCGTCTCA 60.107 40.000 0.00 0.00 0.00 3.27
2853 2903 6.566942 CGTTTTCACCATTAAATCCGTCTCAA 60.567 38.462 0.00 0.00 0.00 3.02
2854 2904 5.873179 TTCACCATTAAATCCGTCTCAAC 57.127 39.130 0.00 0.00 0.00 3.18
2871 2921 7.271936 GTCTCAACGAGATCTTCAAAACTAG 57.728 40.000 0.00 0.00 40.98 2.57
2872 2922 7.085116 GTCTCAACGAGATCTTCAAAACTAGA 58.915 38.462 0.00 0.00 40.98 2.43
2873 2923 7.061326 GTCTCAACGAGATCTTCAAAACTAGAC 59.939 40.741 0.00 0.27 40.98 2.59
2874 2924 6.157211 TCAACGAGATCTTCAAAACTAGACC 58.843 40.000 0.00 0.00 0.00 3.85
2875 2925 5.074584 ACGAGATCTTCAAAACTAGACCC 57.925 43.478 0.00 0.00 0.00 4.46
2876 2926 4.081586 ACGAGATCTTCAAAACTAGACCCC 60.082 45.833 0.00 0.00 0.00 4.95
2877 2927 4.081642 CGAGATCTTCAAAACTAGACCCCA 60.082 45.833 0.00 0.00 0.00 4.96
2878 2928 5.395768 CGAGATCTTCAAAACTAGACCCCAT 60.396 44.000 0.00 0.00 0.00 4.00
2879 2929 5.749462 AGATCTTCAAAACTAGACCCCATG 58.251 41.667 0.00 0.00 0.00 3.66
2880 2930 4.993705 TCTTCAAAACTAGACCCCATGT 57.006 40.909 0.00 0.00 0.00 3.21
2881 2931 5.319043 TCTTCAAAACTAGACCCCATGTT 57.681 39.130 0.00 0.00 0.00 2.71
2882 2932 5.070001 TCTTCAAAACTAGACCCCATGTTG 58.930 41.667 0.00 0.00 0.00 3.33
2883 2933 4.715534 TCAAAACTAGACCCCATGTTGA 57.284 40.909 0.00 0.00 0.00 3.18
2884 2934 5.255397 TCAAAACTAGACCCCATGTTGAT 57.745 39.130 0.00 0.00 0.00 2.57
2885 2935 6.381498 TCAAAACTAGACCCCATGTTGATA 57.619 37.500 0.00 0.00 0.00 2.15
2886 2936 6.969043 TCAAAACTAGACCCCATGTTGATAT 58.031 36.000 0.00 0.00 0.00 1.63
2887 2937 6.828273 TCAAAACTAGACCCCATGTTGATATG 59.172 38.462 0.00 0.00 0.00 1.78
2888 2938 5.975988 AACTAGACCCCATGTTGATATGT 57.024 39.130 0.00 0.00 0.00 2.29
2889 2939 5.975988 ACTAGACCCCATGTTGATATGTT 57.024 39.130 0.00 0.00 0.00 2.71
2890 2940 6.327386 ACTAGACCCCATGTTGATATGTTT 57.673 37.500 0.00 0.00 0.00 2.83
2891 2941 6.357367 ACTAGACCCCATGTTGATATGTTTC 58.643 40.000 0.00 0.00 0.00 2.78
2892 2942 4.199310 AGACCCCATGTTGATATGTTTCG 58.801 43.478 0.00 0.00 0.00 3.46
2893 2943 4.080582 AGACCCCATGTTGATATGTTTCGA 60.081 41.667 0.00 0.00 0.00 3.71
2894 2944 3.945285 ACCCCATGTTGATATGTTTCGAC 59.055 43.478 0.00 0.00 0.00 4.20
2895 2945 3.002246 CCCCATGTTGATATGTTTCGACG 59.998 47.826 0.00 0.00 33.42 5.12
2896 2946 3.868661 CCCATGTTGATATGTTTCGACGA 59.131 43.478 0.00 0.00 33.42 4.20
2897 2947 4.331443 CCCATGTTGATATGTTTCGACGAA 59.669 41.667 6.10 6.10 33.42 3.85
2898 2948 5.163804 CCCATGTTGATATGTTTCGACGAAA 60.164 40.000 18.66 18.66 33.42 3.46
2899 2949 6.458206 CCCATGTTGATATGTTTCGACGAAAT 60.458 38.462 24.48 13.13 33.97 2.17
2900 2950 6.966632 CCATGTTGATATGTTTCGACGAAATT 59.033 34.615 24.48 17.31 33.97 1.82
2901 2951 7.484641 CCATGTTGATATGTTTCGACGAAATTT 59.515 33.333 24.48 16.99 33.97 1.82
2902 2952 8.849490 CATGTTGATATGTTTCGACGAAATTTT 58.151 29.630 24.48 14.82 33.97 1.82
2903 2953 8.789881 TGTTGATATGTTTCGACGAAATTTTT 57.210 26.923 24.48 11.42 33.97 1.94
2921 2971 2.307934 TTTTTGCCAGAAGTTGCCAC 57.692 45.000 0.00 0.00 0.00 5.01
2922 2972 1.189752 TTTTGCCAGAAGTTGCCACA 58.810 45.000 0.00 0.00 0.00 4.17
2923 2973 1.189752 TTTGCCAGAAGTTGCCACAA 58.810 45.000 0.00 0.00 0.00 3.33
2924 2974 1.412079 TTGCCAGAAGTTGCCACAAT 58.588 45.000 0.00 0.00 0.00 2.71
2925 2975 0.675083 TGCCAGAAGTTGCCACAATG 59.325 50.000 0.00 0.00 0.00 2.82
2926 2976 0.675633 GCCAGAAGTTGCCACAATGT 59.324 50.000 0.00 0.00 0.00 2.71
2927 2977 1.069049 GCCAGAAGTTGCCACAATGTT 59.931 47.619 0.00 0.00 0.00 2.71
2928 2978 2.483538 GCCAGAAGTTGCCACAATGTTT 60.484 45.455 0.00 0.00 0.00 2.83
2929 2979 3.243704 GCCAGAAGTTGCCACAATGTTTA 60.244 43.478 0.00 0.00 0.00 2.01
2930 2980 4.298332 CCAGAAGTTGCCACAATGTTTAC 58.702 43.478 0.00 0.00 0.00 2.01
2931 2981 4.202101 CCAGAAGTTGCCACAATGTTTACA 60.202 41.667 0.00 0.00 0.00 2.41
2932 2982 4.739716 CAGAAGTTGCCACAATGTTTACAC 59.260 41.667 0.00 0.00 0.00 2.90
2933 2983 4.644685 AGAAGTTGCCACAATGTTTACACT 59.355 37.500 0.00 0.00 0.00 3.55
2934 2984 4.305989 AGTTGCCACAATGTTTACACTG 57.694 40.909 0.00 0.00 0.00 3.66
2935 2985 2.791383 TGCCACAATGTTTACACTGC 57.209 45.000 0.00 0.00 0.00 4.40
2936 2986 2.027385 TGCCACAATGTTTACACTGCA 58.973 42.857 0.00 0.00 0.00 4.41
2937 2987 2.034432 TGCCACAATGTTTACACTGCAG 59.966 45.455 13.48 13.48 0.00 4.41
2938 2988 2.034558 GCCACAATGTTTACACTGCAGT 59.965 45.455 15.25 15.25 0.00 4.40
2939 2989 3.490761 GCCACAATGTTTACACTGCAGTT 60.491 43.478 18.94 11.49 0.00 3.16
2940 2990 4.043750 CCACAATGTTTACACTGCAGTTG 58.956 43.478 18.94 15.15 0.00 3.16
2941 2991 3.486841 CACAATGTTTACACTGCAGTTGC 59.513 43.478 18.94 6.29 42.50 4.17
2942 2992 3.052036 CAATGTTTACACTGCAGTTGCC 58.948 45.455 18.94 4.24 41.18 4.52
2943 2993 1.756430 TGTTTACACTGCAGTTGCCA 58.244 45.000 18.94 6.98 41.18 4.92
2944 2994 2.305928 TGTTTACACTGCAGTTGCCAT 58.694 42.857 18.94 3.07 41.18 4.40
2945 2995 3.481453 TGTTTACACTGCAGTTGCCATA 58.519 40.909 18.94 2.04 41.18 2.74
2946 2996 3.501828 TGTTTACACTGCAGTTGCCATAG 59.498 43.478 18.94 6.59 41.18 2.23
2947 2997 2.401583 TACACTGCAGTTGCCATAGG 57.598 50.000 18.94 5.76 41.18 2.57
2948 2998 0.322816 ACACTGCAGTTGCCATAGGG 60.323 55.000 18.94 4.96 41.18 3.53
2964 3014 5.891451 CCATAGGGCTTAAACTAAAGTTGC 58.109 41.667 0.00 0.00 38.44 4.17
2965 3015 5.163550 CCATAGGGCTTAAACTAAAGTTGCC 60.164 44.000 12.13 12.13 41.29 4.52
2966 3016 3.839778 AGGGCTTAAACTAAAGTTGCCA 58.160 40.909 18.84 0.00 42.80 4.92
2967 3017 4.416516 AGGGCTTAAACTAAAGTTGCCAT 58.583 39.130 18.84 12.34 42.80 4.40
2968 3018 4.220602 AGGGCTTAAACTAAAGTTGCCATG 59.779 41.667 18.84 0.00 42.80 3.66
2969 3019 4.021456 GGGCTTAAACTAAAGTTGCCATGT 60.021 41.667 18.84 0.00 42.80 3.21
2970 3020 4.923281 GGCTTAAACTAAAGTTGCCATGTG 59.077 41.667 14.54 0.00 41.51 3.21
2971 3021 4.923281 GCTTAAACTAAAGTTGCCATGTGG 59.077 41.667 0.00 0.00 38.44 4.17
2987 3037 6.949578 CCATGTGGCAATTTTAGTTTGTAG 57.050 37.500 0.00 0.00 0.00 2.74
2988 3038 6.686630 CCATGTGGCAATTTTAGTTTGTAGA 58.313 36.000 0.00 0.00 0.00 2.59
2989 3039 7.322664 CCATGTGGCAATTTTAGTTTGTAGAT 58.677 34.615 0.00 0.00 0.00 1.98
2990 3040 7.489113 CCATGTGGCAATTTTAGTTTGTAGATC 59.511 37.037 0.00 0.00 0.00 2.75
2991 3041 7.517614 TGTGGCAATTTTAGTTTGTAGATCA 57.482 32.000 0.00 0.00 0.00 2.92
2992 3042 8.121305 TGTGGCAATTTTAGTTTGTAGATCAT 57.879 30.769 0.00 0.00 0.00 2.45
2993 3043 8.028354 TGTGGCAATTTTAGTTTGTAGATCATG 58.972 33.333 0.00 0.00 0.00 3.07
2994 3044 7.489113 GTGGCAATTTTAGTTTGTAGATCATGG 59.511 37.037 0.00 0.00 0.00 3.66
2995 3045 6.476706 GGCAATTTTAGTTTGTAGATCATGGC 59.523 38.462 0.00 0.00 0.00 4.40
2996 3046 7.035004 GCAATTTTAGTTTGTAGATCATGGCA 58.965 34.615 0.00 0.00 0.00 4.92
2997 3047 7.545265 GCAATTTTAGTTTGTAGATCATGGCAA 59.455 33.333 0.00 0.00 0.00 4.52
2998 3048 9.590451 CAATTTTAGTTTGTAGATCATGGCAAT 57.410 29.630 0.00 0.00 0.00 3.56
3001 3051 9.995003 TTTTAGTTTGTAGATCATGGCAATTTT 57.005 25.926 0.00 0.00 0.00 1.82
3004 3054 8.353423 AGTTTGTAGATCATGGCAATTTTAGT 57.647 30.769 0.00 0.00 0.00 2.24
3005 3055 9.461312 AGTTTGTAGATCATGGCAATTTTAGTA 57.539 29.630 0.00 0.00 0.00 1.82
3017 3067 8.945481 TGGCAATTTTAGTATTTTGATGATGG 57.055 30.769 0.00 0.00 0.00 3.51
3018 3068 7.495279 TGGCAATTTTAGTATTTTGATGATGGC 59.505 33.333 0.00 0.00 0.00 4.40
3019 3069 7.495279 GGCAATTTTAGTATTTTGATGATGGCA 59.505 33.333 0.00 0.00 0.00 4.92
3020 3070 8.881743 GCAATTTTAGTATTTTGATGATGGCAA 58.118 29.630 0.00 0.00 0.00 4.52
3024 3074 9.638239 TTTTAGTATTTTGATGATGGCAACTTC 57.362 29.630 0.00 0.00 41.00 3.01
3035 3085 6.012658 TGATGGCAACTTCAGTAATTTGAC 57.987 37.500 0.00 0.00 44.96 3.18
3036 3086 4.846779 TGGCAACTTCAGTAATTTGACC 57.153 40.909 0.00 0.00 33.44 4.02
3037 3087 4.211125 TGGCAACTTCAGTAATTTGACCA 58.789 39.130 0.00 0.00 33.44 4.02
3038 3088 4.832266 TGGCAACTTCAGTAATTTGACCAT 59.168 37.500 0.00 0.00 33.44 3.55
3039 3089 5.163513 GGCAACTTCAGTAATTTGACCATG 58.836 41.667 0.00 0.00 29.24 3.66
3040 3090 5.048083 GGCAACTTCAGTAATTTGACCATGA 60.048 40.000 0.00 0.00 29.24 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.628032 GCATAAGAAGTTCTAGGCCAACC 59.372 47.826 5.01 0.00 0.00 3.77
78 81 2.631580 GGCGGGTCCGAAAAATGCA 61.632 57.895 14.15 0.00 42.83 3.96
333 340 7.715657 TGCAAAAGTCACTACTGAAAATTCAT 58.284 30.769 0.00 0.00 35.62 2.57
607 615 7.286215 ACACTCGGCTTATACAGTACATAAT 57.714 36.000 0.00 0.00 0.00 1.28
637 646 5.142639 ACAGTATATAAGCCGTGTTCCCTA 58.857 41.667 0.00 0.00 0.00 3.53
681 690 1.128200 ATCCTATAAGCCGTGTGCCA 58.872 50.000 0.00 0.00 42.71 4.92
733 742 2.586258 GACATCTGCCACGTGTCTAT 57.414 50.000 15.65 0.00 39.24 1.98
798 807 0.248907 GGCTTATAGTGAGCACGCGA 60.249 55.000 15.93 0.00 41.89 5.87
801 810 1.600663 CCTCGGCTTATAGTGAGCACG 60.601 57.143 0.00 0.49 41.89 5.34
827 836 7.495934 GCCATCTATAAGCTGAGTGTAGAAAAA 59.504 37.037 0.00 0.00 0.00 1.94
966 985 6.664515 TCACACTACATGAAATTTCCGTTTC 58.335 36.000 15.48 0.00 38.32 2.78
975 994 4.836825 CTGGACCTCACACTACATGAAAT 58.163 43.478 0.00 0.00 0.00 2.17
980 999 0.905357 GGCTGGACCTCACACTACAT 59.095 55.000 0.00 0.00 34.51 2.29
1059 1078 1.638070 TGCACCATGGACCATAGGAAA 59.362 47.619 21.47 9.74 0.00 3.13
1386 1405 3.505680 GGTACAAACTGATGACATTGGCA 59.494 43.478 0.00 0.00 0.00 4.92
1513 1533 2.569059 CTGGCGGTTCTTGATGATGAT 58.431 47.619 0.00 0.00 0.00 2.45
1538 1558 1.341482 TGGCTTTGTTGGTGAACAGGA 60.341 47.619 0.00 0.00 43.03 3.86
1586 1606 4.864334 CATGGCTCCAGGCGGTCC 62.864 72.222 0.00 0.56 44.42 4.46
1589 1609 2.203070 GTACATGGCTCCAGGCGG 60.203 66.667 0.00 0.00 44.42 6.13
1863 1883 2.729467 CGTCGTCTCGATGAAGAGCTTT 60.729 50.000 5.58 0.00 44.49 3.51
1986 2006 3.002038 TGGTACTTGGGTTTGTCGTTT 57.998 42.857 0.00 0.00 0.00 3.60
2211 2232 2.431057 CCAGGTAGTTCTTGGCGAGTAT 59.569 50.000 0.77 0.00 36.52 2.12
2325 2346 4.887655 GTCCCTCTTTTTCTTCTTGGACAA 59.112 41.667 0.00 0.00 40.52 3.18
2592 2642 0.530744 GGTCACGGAGCATGTAGTGA 59.469 55.000 9.45 9.45 40.77 3.41
2667 2717 0.875728 TGTGGGCGTTAACATTTCCG 59.124 50.000 6.39 0.00 0.00 4.30
2668 2718 1.400500 CGTGTGGGCGTTAACATTTCC 60.400 52.381 6.39 1.91 0.00 3.13
2669 2719 1.264826 ACGTGTGGGCGTTAACATTTC 59.735 47.619 6.39 0.00 43.04 2.17
2670 2720 1.002251 CACGTGTGGGCGTTAACATTT 60.002 47.619 7.58 0.00 43.83 2.32
2671 2721 0.589223 CACGTGTGGGCGTTAACATT 59.411 50.000 7.58 0.00 43.83 2.71
2672 2722 0.533308 ACACGTGTGGGCGTTAACAT 60.533 50.000 22.71 0.00 43.83 2.71
2673 2723 1.153409 ACACGTGTGGGCGTTAACA 60.153 52.632 22.71 0.00 43.83 2.41
2674 2724 1.277440 CACACGTGTGGGCGTTAAC 59.723 57.895 35.65 0.00 43.83 2.01
2675 2725 3.720531 CACACGTGTGGGCGTTAA 58.279 55.556 35.65 0.00 43.83 2.01
2687 2737 3.192954 ATGTGCAAACGCCCACACG 62.193 57.895 0.00 0.00 43.89 4.49
2688 2738 1.371635 GATGTGCAAACGCCCACAC 60.372 57.895 0.00 0.00 43.89 3.82
2689 2739 2.902419 CGATGTGCAAACGCCCACA 61.902 57.895 0.00 0.00 45.01 4.17
2690 2740 2.126888 CGATGTGCAAACGCCCAC 60.127 61.111 0.00 0.00 0.00 4.61
2691 2741 4.036804 GCGATGTGCAAACGCCCA 62.037 61.111 18.18 0.00 45.35 5.36
2707 2757 4.408821 TGATGGAGGCGTGTGGGC 62.409 66.667 0.00 0.00 42.69 5.36
2708 2758 2.436646 GTGATGGAGGCGTGTGGG 60.437 66.667 0.00 0.00 0.00 4.61
2709 2759 2.436646 GGTGATGGAGGCGTGTGG 60.437 66.667 0.00 0.00 0.00 4.17
2710 2760 0.677731 AATGGTGATGGAGGCGTGTG 60.678 55.000 0.00 0.00 0.00 3.82
2711 2761 0.392998 GAATGGTGATGGAGGCGTGT 60.393 55.000 0.00 0.00 0.00 4.49
2712 2762 0.392863 TGAATGGTGATGGAGGCGTG 60.393 55.000 0.00 0.00 0.00 5.34
2713 2763 0.548031 ATGAATGGTGATGGAGGCGT 59.452 50.000 0.00 0.00 0.00 5.68
2714 2764 1.683943 AATGAATGGTGATGGAGGCG 58.316 50.000 0.00 0.00 0.00 5.52
2715 2765 3.788937 CAAAATGAATGGTGATGGAGGC 58.211 45.455 0.00 0.00 0.00 4.70
2716 2766 3.431207 GGCAAAATGAATGGTGATGGAGG 60.431 47.826 0.00 0.00 0.00 4.30
2717 2767 3.196039 TGGCAAAATGAATGGTGATGGAG 59.804 43.478 0.00 0.00 0.00 3.86
2718 2768 3.055963 GTGGCAAAATGAATGGTGATGGA 60.056 43.478 0.00 0.00 0.00 3.41
2719 2769 3.264104 GTGGCAAAATGAATGGTGATGG 58.736 45.455 0.00 0.00 0.00 3.51
2720 2770 2.924926 CGTGGCAAAATGAATGGTGATG 59.075 45.455 0.00 0.00 0.00 3.07
2721 2771 2.562298 ACGTGGCAAAATGAATGGTGAT 59.438 40.909 0.00 0.00 0.00 3.06
2722 2772 1.959985 ACGTGGCAAAATGAATGGTGA 59.040 42.857 0.00 0.00 0.00 4.02
2723 2773 2.437200 ACGTGGCAAAATGAATGGTG 57.563 45.000 0.00 0.00 0.00 4.17
2724 2774 3.761218 TCATACGTGGCAAAATGAATGGT 59.239 39.130 0.00 0.00 0.00 3.55
2725 2775 4.368874 TCATACGTGGCAAAATGAATGG 57.631 40.909 0.00 0.00 0.00 3.16
2726 2776 7.416817 TCTATTCATACGTGGCAAAATGAATG 58.583 34.615 26.97 20.55 44.59 2.67
2727 2777 7.566760 TCTATTCATACGTGGCAAAATGAAT 57.433 32.000 24.50 24.50 45.93 2.57
2728 2778 6.993786 TCTATTCATACGTGGCAAAATGAA 57.006 33.333 17.48 17.48 41.24 2.57
2729 2779 6.765512 TCATCTATTCATACGTGGCAAAATGA 59.234 34.615 0.00 0.00 0.00 2.57
2730 2780 6.852853 GTCATCTATTCATACGTGGCAAAATG 59.147 38.462 0.00 0.00 0.00 2.32
2731 2781 6.542005 TGTCATCTATTCATACGTGGCAAAAT 59.458 34.615 0.00 0.00 0.00 1.82
2732 2782 5.877564 TGTCATCTATTCATACGTGGCAAAA 59.122 36.000 0.00 0.00 0.00 2.44
2733 2783 5.423886 TGTCATCTATTCATACGTGGCAAA 58.576 37.500 0.00 0.00 0.00 3.68
2734 2784 5.017294 TGTCATCTATTCATACGTGGCAA 57.983 39.130 0.00 0.00 0.00 4.52
2735 2785 4.664150 TGTCATCTATTCATACGTGGCA 57.336 40.909 0.00 0.00 0.00 4.92
2736 2786 5.230182 TGATGTCATCTATTCATACGTGGC 58.770 41.667 13.90 0.00 0.00 5.01
2737 2787 5.347093 GCTGATGTCATCTATTCATACGTGG 59.653 44.000 13.90 0.00 0.00 4.94
2738 2788 5.922544 TGCTGATGTCATCTATTCATACGTG 59.077 40.000 13.90 0.00 0.00 4.49
2739 2789 6.015940 TCTGCTGATGTCATCTATTCATACGT 60.016 38.462 13.90 0.00 0.00 3.57
2740 2790 6.385033 TCTGCTGATGTCATCTATTCATACG 58.615 40.000 13.90 0.00 0.00 3.06
2741 2791 8.599055 TTTCTGCTGATGTCATCTATTCATAC 57.401 34.615 13.90 0.00 0.00 2.39
2742 2792 9.788889 AATTTCTGCTGATGTCATCTATTCATA 57.211 29.630 13.90 0.00 0.00 2.15
2743 2793 8.693120 AATTTCTGCTGATGTCATCTATTCAT 57.307 30.769 13.90 0.00 0.00 2.57
2744 2794 8.515695 AAATTTCTGCTGATGTCATCTATTCA 57.484 30.769 13.90 5.77 0.00 2.57
2745 2795 9.798994 AAAAATTTCTGCTGATGTCATCTATTC 57.201 29.630 13.90 1.79 0.00 1.75
2769 2819 7.379098 ACATTTTTAAGCCGAAAACCAAAAA 57.621 28.000 0.00 0.00 31.65 1.94
2770 2820 6.986904 ACATTTTTAAGCCGAAAACCAAAA 57.013 29.167 0.00 0.00 0.00 2.44
2771 2821 6.371825 ACAACATTTTTAAGCCGAAAACCAAA 59.628 30.769 0.00 0.00 0.00 3.28
2772 2822 5.875359 ACAACATTTTTAAGCCGAAAACCAA 59.125 32.000 0.00 0.00 0.00 3.67
2773 2823 5.420409 ACAACATTTTTAAGCCGAAAACCA 58.580 33.333 0.00 0.00 0.00 3.67
2774 2824 5.977171 ACAACATTTTTAAGCCGAAAACC 57.023 34.783 0.00 0.00 0.00 3.27
2775 2825 8.515473 AGATACAACATTTTTAAGCCGAAAAC 57.485 30.769 0.00 0.00 0.00 2.43
2776 2826 7.810759 GGAGATACAACATTTTTAAGCCGAAAA 59.189 33.333 0.00 0.00 0.00 2.29
2777 2827 7.175990 AGGAGATACAACATTTTTAAGCCGAAA 59.824 33.333 0.00 0.00 0.00 3.46
2778 2828 6.657541 AGGAGATACAACATTTTTAAGCCGAA 59.342 34.615 0.00 0.00 0.00 4.30
2779 2829 6.177610 AGGAGATACAACATTTTTAAGCCGA 58.822 36.000 0.00 0.00 0.00 5.54
2780 2830 6.436843 AGGAGATACAACATTTTTAAGCCG 57.563 37.500 0.00 0.00 0.00 5.52
2781 2831 8.732746 TCTAGGAGATACAACATTTTTAAGCC 57.267 34.615 0.00 0.00 0.00 4.35
2809 2859 7.275999 TGAAAACGGATTTTTAGTTCGCTTTTT 59.724 29.630 0.00 0.00 38.17 1.94
2810 2860 6.752815 TGAAAACGGATTTTTAGTTCGCTTTT 59.247 30.769 0.00 0.00 38.17 2.27
2811 2861 6.197655 GTGAAAACGGATTTTTAGTTCGCTTT 59.802 34.615 0.00 0.00 38.17 3.51
2812 2862 5.684184 GTGAAAACGGATTTTTAGTTCGCTT 59.316 36.000 0.00 0.00 38.17 4.68
2813 2863 5.209977 GTGAAAACGGATTTTTAGTTCGCT 58.790 37.500 0.00 0.00 38.17 4.93
2814 2864 4.380678 GGTGAAAACGGATTTTTAGTTCGC 59.619 41.667 0.00 0.00 38.17 4.70
2815 2865 5.512473 TGGTGAAAACGGATTTTTAGTTCG 58.488 37.500 0.00 0.00 38.17 3.95
2816 2866 7.940178 AATGGTGAAAACGGATTTTTAGTTC 57.060 32.000 0.00 0.00 38.17 3.01
2817 2867 9.819267 TTTAATGGTGAAAACGGATTTTTAGTT 57.181 25.926 0.00 0.00 38.17 2.24
2818 2868 9.990360 ATTTAATGGTGAAAACGGATTTTTAGT 57.010 25.926 0.00 0.00 38.17 2.24
2820 2870 9.425577 GGATTTAATGGTGAAAACGGATTTTTA 57.574 29.630 0.00 0.00 38.17 1.52
2821 2871 7.117092 CGGATTTAATGGTGAAAACGGATTTTT 59.883 33.333 0.00 0.00 38.17 1.94
2822 2872 6.588373 CGGATTTAATGGTGAAAACGGATTTT 59.412 34.615 0.00 0.00 40.83 1.82
2823 2873 6.096695 CGGATTTAATGGTGAAAACGGATTT 58.903 36.000 0.00 0.00 0.00 2.17
2824 2874 5.184287 ACGGATTTAATGGTGAAAACGGATT 59.816 36.000 0.00 0.00 0.00 3.01
2825 2875 4.703093 ACGGATTTAATGGTGAAAACGGAT 59.297 37.500 0.00 0.00 0.00 4.18
2826 2876 4.073549 ACGGATTTAATGGTGAAAACGGA 58.926 39.130 0.00 0.00 0.00 4.69
2827 2877 4.155280 AGACGGATTTAATGGTGAAAACGG 59.845 41.667 0.00 0.00 0.00 4.44
2828 2878 5.106869 TGAGACGGATTTAATGGTGAAAACG 60.107 40.000 0.00 0.00 0.00 3.60
2829 2879 6.249035 TGAGACGGATTTAATGGTGAAAAC 57.751 37.500 0.00 0.00 0.00 2.43
2830 2880 6.566942 CGTTGAGACGGATTTAATGGTGAAAA 60.567 38.462 0.00 0.00 45.32 2.29
2831 2881 5.106869 CGTTGAGACGGATTTAATGGTGAAA 60.107 40.000 0.00 0.00 45.32 2.69
2832 2882 4.390603 CGTTGAGACGGATTTAATGGTGAA 59.609 41.667 0.00 0.00 45.32 3.18
2833 2883 3.930229 CGTTGAGACGGATTTAATGGTGA 59.070 43.478 0.00 0.00 45.32 4.02
2834 2884 4.258935 CGTTGAGACGGATTTAATGGTG 57.741 45.455 0.00 0.00 45.32 4.17
2847 2897 7.061326 GTCTAGTTTTGAAGATCTCGTTGAGAC 59.939 40.741 0.00 0.00 41.76 3.36
2848 2898 7.085116 GTCTAGTTTTGAAGATCTCGTTGAGA 58.915 38.462 0.00 0.00 43.20 3.27
2849 2899 6.309251 GGTCTAGTTTTGAAGATCTCGTTGAG 59.691 42.308 0.00 0.00 0.00 3.02
2850 2900 6.157211 GGTCTAGTTTTGAAGATCTCGTTGA 58.843 40.000 0.00 0.00 0.00 3.18
2851 2901 5.348997 GGGTCTAGTTTTGAAGATCTCGTTG 59.651 44.000 0.00 0.00 0.00 4.10
2852 2902 5.480205 GGGTCTAGTTTTGAAGATCTCGTT 58.520 41.667 0.00 0.00 0.00 3.85
2853 2903 4.081586 GGGGTCTAGTTTTGAAGATCTCGT 60.082 45.833 0.00 0.00 0.00 4.18
2854 2904 4.081642 TGGGGTCTAGTTTTGAAGATCTCG 60.082 45.833 0.00 0.00 0.00 4.04
2855 2905 5.422214 TGGGGTCTAGTTTTGAAGATCTC 57.578 43.478 0.00 0.00 0.00 2.75
2856 2906 5.251700 ACATGGGGTCTAGTTTTGAAGATCT 59.748 40.000 0.00 0.00 0.00 2.75
2857 2907 5.501156 ACATGGGGTCTAGTTTTGAAGATC 58.499 41.667 0.00 0.00 0.00 2.75
2858 2908 5.520748 ACATGGGGTCTAGTTTTGAAGAT 57.479 39.130 0.00 0.00 0.00 2.40
2859 2909 4.993705 ACATGGGGTCTAGTTTTGAAGA 57.006 40.909 0.00 0.00 0.00 2.87
2860 2910 5.070001 TCAACATGGGGTCTAGTTTTGAAG 58.930 41.667 0.00 0.00 0.00 3.02
2861 2911 5.055265 TCAACATGGGGTCTAGTTTTGAA 57.945 39.130 0.00 0.00 0.00 2.69
2862 2912 4.715534 TCAACATGGGGTCTAGTTTTGA 57.284 40.909 0.00 0.00 0.00 2.69
2863 2913 6.603201 ACATATCAACATGGGGTCTAGTTTTG 59.397 38.462 0.00 0.00 0.00 2.44
2864 2914 6.731467 ACATATCAACATGGGGTCTAGTTTT 58.269 36.000 0.00 0.00 0.00 2.43
2865 2915 6.327386 ACATATCAACATGGGGTCTAGTTT 57.673 37.500 0.00 0.00 0.00 2.66
2866 2916 5.975988 ACATATCAACATGGGGTCTAGTT 57.024 39.130 0.00 0.00 0.00 2.24
2867 2917 5.975988 AACATATCAACATGGGGTCTAGT 57.024 39.130 0.00 0.00 0.00 2.57
2868 2918 5.466728 CGAAACATATCAACATGGGGTCTAG 59.533 44.000 0.00 0.00 0.00 2.43
2869 2919 5.129650 TCGAAACATATCAACATGGGGTCTA 59.870 40.000 0.00 0.00 0.00 2.59
2870 2920 4.080582 TCGAAACATATCAACATGGGGTCT 60.081 41.667 0.00 0.00 0.00 3.85
2871 2921 4.035208 GTCGAAACATATCAACATGGGGTC 59.965 45.833 0.00 0.00 0.00 4.46
2872 2922 3.945285 GTCGAAACATATCAACATGGGGT 59.055 43.478 0.00 0.00 0.00 4.95
2873 2923 3.002246 CGTCGAAACATATCAACATGGGG 59.998 47.826 0.00 0.00 0.00 4.96
2874 2924 3.868661 TCGTCGAAACATATCAACATGGG 59.131 43.478 0.00 0.00 0.00 4.00
2875 2925 5.463499 TTCGTCGAAACATATCAACATGG 57.537 39.130 4.91 0.00 0.00 3.66
2876 2926 7.953305 AATTTCGTCGAAACATATCAACATG 57.047 32.000 21.91 0.00 34.23 3.21
2877 2927 8.964420 AAAATTTCGTCGAAACATATCAACAT 57.036 26.923 21.91 0.12 34.23 2.71
2878 2928 8.789881 AAAAATTTCGTCGAAACATATCAACA 57.210 26.923 21.91 0.00 34.23 3.33
2908 2958 3.457610 AAACATTGTGGCAACTTCTGG 57.542 42.857 0.00 0.00 37.61 3.86
2909 2959 4.739716 GTGTAAACATTGTGGCAACTTCTG 59.260 41.667 0.00 0.00 37.61 3.02
2910 2960 4.644685 AGTGTAAACATTGTGGCAACTTCT 59.355 37.500 0.00 0.00 37.61 2.85
2911 2961 4.739716 CAGTGTAAACATTGTGGCAACTTC 59.260 41.667 0.00 0.00 37.61 3.01
2912 2962 4.681744 CAGTGTAAACATTGTGGCAACTT 58.318 39.130 0.00 0.00 37.61 2.66
2913 2963 3.490761 GCAGTGTAAACATTGTGGCAACT 60.491 43.478 7.35 0.00 36.18 3.16
2914 2964 2.794350 GCAGTGTAAACATTGTGGCAAC 59.206 45.455 7.35 0.00 36.18 4.17
2915 2965 2.428530 TGCAGTGTAAACATTGTGGCAA 59.571 40.909 7.35 0.00 36.18 4.52
2916 2966 2.027385 TGCAGTGTAAACATTGTGGCA 58.973 42.857 7.35 0.00 36.18 4.92
2917 2967 2.034558 ACTGCAGTGTAAACATTGTGGC 59.965 45.455 20.97 0.00 36.18 5.01
2918 2968 3.988379 ACTGCAGTGTAAACATTGTGG 57.012 42.857 20.97 3.85 36.18 4.17
2919 2969 3.486841 GCAACTGCAGTGTAAACATTGTG 59.513 43.478 22.49 11.72 41.59 3.33
2920 2970 3.490761 GGCAACTGCAGTGTAAACATTGT 60.491 43.478 22.49 0.00 44.36 2.71
2921 2971 3.052036 GGCAACTGCAGTGTAAACATTG 58.948 45.455 22.49 13.25 44.36 2.82
2922 2972 2.692557 TGGCAACTGCAGTGTAAACATT 59.307 40.909 22.49 0.00 44.36 2.71
2923 2973 2.305928 TGGCAACTGCAGTGTAAACAT 58.694 42.857 22.49 0.00 44.36 2.71
2924 2974 1.756430 TGGCAACTGCAGTGTAAACA 58.244 45.000 22.49 12.56 44.36 2.83
2925 2975 3.119849 CCTATGGCAACTGCAGTGTAAAC 60.120 47.826 22.49 10.01 44.36 2.01
2926 2976 3.081061 CCTATGGCAACTGCAGTGTAAA 58.919 45.455 22.49 7.60 44.36 2.01
2927 2977 2.617788 CCCTATGGCAACTGCAGTGTAA 60.618 50.000 22.49 7.20 44.36 2.41
2928 2978 1.065491 CCCTATGGCAACTGCAGTGTA 60.065 52.381 22.49 7.59 44.36 2.90
2929 2979 0.322816 CCCTATGGCAACTGCAGTGT 60.323 55.000 22.49 7.95 44.36 3.55
2930 2980 2.485677 CCCTATGGCAACTGCAGTG 58.514 57.895 22.49 15.42 44.36 3.66
2941 2991 5.163550 GGCAACTTTAGTTTAAGCCCTATGG 60.164 44.000 9.98 0.00 38.15 2.74
2942 2992 5.417580 TGGCAACTTTAGTTTAAGCCCTATG 59.582 40.000 15.69 0.00 41.31 2.23
2943 2993 5.576128 TGGCAACTTTAGTTTAAGCCCTAT 58.424 37.500 15.69 0.00 41.31 2.57
2944 2994 4.988029 TGGCAACTTTAGTTTAAGCCCTA 58.012 39.130 15.69 1.20 41.31 3.53
2945 2995 3.839778 TGGCAACTTTAGTTTAAGCCCT 58.160 40.909 15.69 0.00 41.31 5.19
2946 2996 4.021456 ACATGGCAACTTTAGTTTAAGCCC 60.021 41.667 15.69 4.15 41.31 5.19
2947 2997 4.923281 CACATGGCAACTTTAGTTTAAGCC 59.077 41.667 12.91 12.91 41.94 4.35
2948 2998 4.923281 CCACATGGCAACTTTAGTTTAAGC 59.077 41.667 0.00 0.00 35.83 3.09
2964 3014 6.686630 TCTACAAACTAAAATTGCCACATGG 58.313 36.000 0.00 0.00 38.53 3.66
2965 3015 8.028354 TGATCTACAAACTAAAATTGCCACATG 58.972 33.333 0.00 0.00 0.00 3.21
2966 3016 8.121305 TGATCTACAAACTAAAATTGCCACAT 57.879 30.769 0.00 0.00 0.00 3.21
2967 3017 7.517614 TGATCTACAAACTAAAATTGCCACA 57.482 32.000 0.00 0.00 0.00 4.17
2968 3018 7.489113 CCATGATCTACAAACTAAAATTGCCAC 59.511 37.037 0.00 0.00 0.00 5.01
2969 3019 7.546358 CCATGATCTACAAACTAAAATTGCCA 58.454 34.615 0.00 0.00 0.00 4.92
2970 3020 6.476706 GCCATGATCTACAAACTAAAATTGCC 59.523 38.462 0.00 0.00 0.00 4.52
2971 3021 7.035004 TGCCATGATCTACAAACTAAAATTGC 58.965 34.615 0.00 0.00 0.00 3.56
2972 3022 8.984891 TTGCCATGATCTACAAACTAAAATTG 57.015 30.769 0.00 0.00 0.00 2.32
2975 3025 9.995003 AAAATTGCCATGATCTACAAACTAAAA 57.005 25.926 0.00 0.00 0.00 1.52
2978 3028 9.461312 ACTAAAATTGCCATGATCTACAAACTA 57.539 29.630 0.00 0.00 0.00 2.24
2979 3029 8.353423 ACTAAAATTGCCATGATCTACAAACT 57.647 30.769 0.00 0.00 0.00 2.66
2991 3041 9.550406 CCATCATCAAAATACTAAAATTGCCAT 57.450 29.630 0.00 0.00 0.00 4.40
2992 3042 7.495279 GCCATCATCAAAATACTAAAATTGCCA 59.505 33.333 0.00 0.00 0.00 4.92
2993 3043 7.495279 TGCCATCATCAAAATACTAAAATTGCC 59.505 33.333 0.00 0.00 0.00 4.52
2994 3044 8.422973 TGCCATCATCAAAATACTAAAATTGC 57.577 30.769 0.00 0.00 0.00 3.56
2998 3048 9.638239 GAAGTTGCCATCATCAAAATACTAAAA 57.362 29.630 0.00 0.00 0.00 1.52
2999 3049 8.801299 TGAAGTTGCCATCATCAAAATACTAAA 58.199 29.630 0.00 0.00 0.00 1.85
3000 3050 8.347004 TGAAGTTGCCATCATCAAAATACTAA 57.653 30.769 0.00 0.00 0.00 2.24
3001 3051 7.611467 ACTGAAGTTGCCATCATCAAAATACTA 59.389 33.333 0.00 0.00 0.00 1.82
3002 3052 6.435277 ACTGAAGTTGCCATCATCAAAATACT 59.565 34.615 0.00 0.00 0.00 2.12
3003 3053 6.624423 ACTGAAGTTGCCATCATCAAAATAC 58.376 36.000 0.00 0.00 0.00 1.89
3004 3054 6.839124 ACTGAAGTTGCCATCATCAAAATA 57.161 33.333 0.00 0.00 0.00 1.40
3005 3055 5.733620 ACTGAAGTTGCCATCATCAAAAT 57.266 34.783 0.00 0.00 0.00 1.82
3006 3056 6.647334 TTACTGAAGTTGCCATCATCAAAA 57.353 33.333 0.00 0.00 0.00 2.44
3007 3057 6.839124 ATTACTGAAGTTGCCATCATCAAA 57.161 33.333 0.00 0.00 0.00 2.69
3008 3058 6.839124 AATTACTGAAGTTGCCATCATCAA 57.161 33.333 0.00 0.00 0.00 2.57
3009 3059 6.433716 TCAAATTACTGAAGTTGCCATCATCA 59.566 34.615 0.00 0.00 39.82 3.07
3010 3060 6.749118 GTCAAATTACTGAAGTTGCCATCATC 59.251 38.462 0.00 0.00 39.82 2.92
3011 3061 6.350445 GGTCAAATTACTGAAGTTGCCATCAT 60.350 38.462 0.00 0.00 39.82 2.45
3012 3062 5.048083 GGTCAAATTACTGAAGTTGCCATCA 60.048 40.000 0.00 0.00 39.82 3.07
3013 3063 5.048083 TGGTCAAATTACTGAAGTTGCCATC 60.048 40.000 8.74 0.00 39.56 3.51
3014 3064 4.832266 TGGTCAAATTACTGAAGTTGCCAT 59.168 37.500 8.74 0.00 39.56 4.40
3015 3065 4.211125 TGGTCAAATTACTGAAGTTGCCA 58.789 39.130 8.74 8.74 40.82 4.92
3016 3066 4.846779 TGGTCAAATTACTGAAGTTGCC 57.153 40.909 0.00 0.00 39.82 4.52
3017 3067 6.012658 TCATGGTCAAATTACTGAAGTTGC 57.987 37.500 0.00 0.00 39.82 4.17


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

AutoCloner maintained by Alex Coulton.