Multiple sequence alignment - TraesCS6D01G213400

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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 TraesCS6D01G213400 chr6D 100.000 3287 0 0 1 3287 303440863 303444149 0.000000e+00 6071.0
1 TraesCS6D01G213400 chr6D 89.583 96 8 2 2659 2753 242999407 242999501 1.600000e-23 121.0
2 TraesCS6D01G213400 chr6B 96.364 2695 51 21 1 2660 469065853 469068535 0.000000e+00 4390.0
3 TraesCS6D01G213400 chr6B 91.379 58 3 2 3071 3127 469069890 469069946 9.780000e-11 78.7
4 TraesCS6D01G213400 chr6A 96.151 1481 35 11 32 1493 411895554 411897031 0.000000e+00 2399.0
5 TraesCS6D01G213400 chr6A 93.844 796 38 6 1873 2660 411897037 411897829 0.000000e+00 1188.0
6 TraesCS6D01G213400 chr6A 94.792 192 8 1 2972 3161 411899135 411899326 6.900000e-77 298.0
7 TraesCS6D01G213400 chr6A 95.876 97 4 0 2884 2980 411897826 411897922 1.220000e-34 158.0
8 TraesCS6D01G213400 chr5A 94.359 195 2 1 2658 2843 612999714 612999908 1.150000e-74 291.0
9 TraesCS6D01G213400 chr5D 92.818 181 4 1 2672 2843 317779873 317780053 1.510000e-63 254.0
10 TraesCS6D01G213400 chr7B 87.179 195 15 5 2659 2843 700853036 700853230 2.570000e-51 213.0
11 TraesCS6D01G213400 chr2D 86.802 197 15 7 2657 2843 544209963 544210158 3.320000e-50 209.0
12 TraesCS6D01G213400 chr2B 86.802 197 15 7 2657 2843 767705806 767705611 3.320000e-50 209.0
13 TraesCS6D01G213400 chr2B 85.279 197 18 7 2657 2843 767738675 767738480 3.350000e-45 193.0
14 TraesCS6D01G213400 chr4A 86.154 195 19 3 2657 2843 697818075 697818269 1.550000e-48 204.0
15 TraesCS6D01G213400 chr5B 85.641 195 17 7 2659 2843 29217569 29217762 9.310000e-46 195.0


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 TraesCS6D01G213400 chr6D 303440863 303444149 3286 False 6071.00 6071 100.00000 1 3287 1 chr6D.!!$F2 3286
1 TraesCS6D01G213400 chr6B 469065853 469069946 4093 False 2234.35 4390 93.87150 1 3127 2 chr6B.!!$F1 3126
2 TraesCS6D01G213400 chr6A 411895554 411899326 3772 False 1010.75 2399 95.16575 32 3161 4 chr6A.!!$F1 3129

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
236 241 0.754957 CCAAAACCCTGTGGCTGTGA 60.755 55.0 0.00 0.00 33.59 3.58 F
1494 1518 0.250467 CTGCCAGGTGTGCACTTACT 60.250 55.0 19.41 10.38 34.46 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1583 1.347707 AGGACCACTACCATGTGTGTG 59.652 52.381 0.0 6.24 36.30 3.82 R
2803 2852 0.030638 CAAACAACTGCCCCGAACAG 59.969 55.000 0.0 0.00 41.08 3.16 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
179 184 3.141398 GCAGGTGAGACTGTCATTTTCA 58.859 45.455 10.88 1.97 40.59 2.69
236 241 0.754957 CCAAAACCCTGTGGCTGTGA 60.755 55.000 0.00 0.00 33.59 3.58
260 265 8.647796 TGAGGTCAACTAATCTAAACTTTCTGA 58.352 33.333 0.00 0.00 0.00 3.27
394 399 6.101650 TGTCAAACAGCGGATAGATGATAT 57.898 37.500 0.00 0.00 38.85 1.63
434 439 5.840693 AGAGGGTTGAAAGAATGGTCATTTT 59.159 36.000 0.00 0.00 0.00 1.82
593 599 9.011095 AGAAGCCCAAGTTTATTACTTAGTTTC 57.989 33.333 0.00 0.00 45.29 2.78
647 653 5.340360 CCCCTATCTCATTTCCCAAGTTTCT 60.340 44.000 0.00 0.00 0.00 2.52
1443 1467 2.139917 ACTTGAAAATACAGCGCACGA 58.860 42.857 11.47 0.00 0.00 4.35
1493 1517 1.237285 CCTGCCAGGTGTGCACTTAC 61.237 60.000 19.41 8.68 34.46 2.34
1494 1518 0.250467 CTGCCAGGTGTGCACTTACT 60.250 55.000 19.41 10.38 34.46 2.24
1495 1519 1.001974 CTGCCAGGTGTGCACTTACTA 59.998 52.381 19.41 0.00 34.46 1.82
1496 1520 1.418264 TGCCAGGTGTGCACTTACTAA 59.582 47.619 19.41 0.00 32.85 2.24
1497 1521 2.076863 GCCAGGTGTGCACTTACTAAG 58.923 52.381 19.41 9.06 0.00 2.18
1538 1562 7.201565 GCACACCTATGAGTCAATCTTAGAAAC 60.202 40.741 0.00 0.00 37.70 2.78
1559 1583 9.099454 AGAAACAAATACGATCTATTTCTCACC 57.901 33.333 0.00 0.00 31.03 4.02
1597 1621 5.163216 TGGTCCTTTTCTTTTGGCAATCATT 60.163 36.000 0.00 0.00 0.00 2.57
1607 1631 3.719268 TGGCAATCATTGTAGTGGTCT 57.281 42.857 0.00 0.00 0.00 3.85
1608 1632 4.032960 TGGCAATCATTGTAGTGGTCTT 57.967 40.909 0.00 0.00 0.00 3.01
1611 1635 5.414454 TGGCAATCATTGTAGTGGTCTTAAC 59.586 40.000 0.00 0.00 0.00 2.01
1615 1639 7.521529 CAATCATTGTAGTGGTCTTAACTGTG 58.478 38.462 0.00 0.00 0.00 3.66
1710 1734 1.149101 AACCAGTGTCCATGGGAAGT 58.851 50.000 13.02 0.05 42.48 3.01
1729 1753 8.752766 GGGAAGTTAAACTGCTTTAAATTACC 57.247 34.615 13.63 13.63 46.27 2.85
1761 1785 7.793927 TGGCATGTTTATGTCATATTTACGA 57.206 32.000 0.00 0.00 43.59 3.43
1794 1818 7.384387 GGTTCCACTGTTAGTAAGTTCTAACTG 59.616 40.741 18.99 18.99 45.59 3.16
1834 1858 8.275015 TGAGAATAGTACTCTTGACTCTTGAG 57.725 38.462 0.00 0.00 35.66 3.02
1835 1859 8.103935 TGAGAATAGTACTCTTGACTCTTGAGA 58.896 37.037 0.00 0.00 35.66 3.27
1851 1883 6.852664 CTCTTGAGAGTTAGAGAACCTTCTC 58.147 44.000 6.92 6.92 43.64 2.87
1903 1935 7.855375 ACCAATTAGATCTTCAAGATGTCTCA 58.145 34.615 4.06 0.00 34.53 3.27
1971 2008 7.927048 TCTTCACTCAGATCATGCAATAAATG 58.073 34.615 0.00 0.00 0.00 2.32
2026 2068 0.179156 GCGGCAAACTGGTCATGATG 60.179 55.000 0.00 0.00 0.00 3.07
2035 2077 6.308766 GCAAACTGGTCATGATGAAAACATAC 59.691 38.462 0.00 0.00 0.00 2.39
2118 2160 5.010282 AGAAGTGGTCTGTTCAGTTTGTTT 58.990 37.500 0.00 0.00 34.29 2.83
2124 2166 7.033185 GTGGTCTGTTCAGTTTGTTTGTTTAT 58.967 34.615 0.00 0.00 0.00 1.40
2161 2203 7.978414 TGTTTGATGCTTTTGACATAAAACTGA 59.022 29.630 14.62 0.00 44.29 3.41
2398 2445 1.938585 AGGAAAGGATGGAGTCGTGA 58.061 50.000 0.00 0.00 0.00 4.35
2524 2571 1.800586 CATGGTCCAAATATCTCCGCG 59.199 52.381 0.00 0.00 0.00 6.46
2617 2666 9.944663 TGTTTCTGATTTTAATTATATGTCCGC 57.055 29.630 0.00 0.00 0.00 5.54
2631 2680 2.259204 CCGCGTTTACCTGACGGA 59.741 61.111 4.92 0.00 46.71 4.69
2660 2709 6.183360 CGTTGCCAAATTTCATGGAATTTAGG 60.183 38.462 21.69 22.62 40.56 2.69
2662 2711 4.576053 GCCAAATTTCATGGAATTTAGGCC 59.424 41.667 31.20 21.99 41.27 5.19
2663 2712 5.125356 CCAAATTTCATGGAATTTAGGCCC 58.875 41.667 21.69 0.00 40.56 5.80
2664 2713 5.125356 CAAATTTCATGGAATTTAGGCCCC 58.875 41.667 21.69 0.00 37.17 5.80
2665 2714 2.065899 TTCATGGAATTTAGGCCCCG 57.934 50.000 0.00 0.00 0.00 5.73
2666 2715 0.923358 TCATGGAATTTAGGCCCCGT 59.077 50.000 0.00 0.00 0.00 5.28
2667 2716 1.286553 TCATGGAATTTAGGCCCCGTT 59.713 47.619 0.00 0.00 0.00 4.44
2668 2717 1.681264 CATGGAATTTAGGCCCCGTTC 59.319 52.381 0.00 0.00 0.00 3.95
2669 2718 0.393267 TGGAATTTAGGCCCCGTTCG 60.393 55.000 0.00 0.00 0.00 3.95
2670 2719 1.099295 GGAATTTAGGCCCCGTTCGG 61.099 60.000 0.00 4.08 0.00 4.30
2682 2731 4.821589 GTTCGGGAGCTCGCCTGG 62.822 72.222 23.61 11.05 34.94 4.45
2706 2755 3.485431 CGCAGCCAGCTTCTCGTG 61.485 66.667 0.00 0.00 42.61 4.35
2707 2756 3.123620 GCAGCCAGCTTCTCGTGG 61.124 66.667 0.00 0.00 41.15 4.94
2708 2757 2.435586 CAGCCAGCTTCTCGTGGG 60.436 66.667 0.00 0.00 34.06 4.61
2709 2758 2.604686 AGCCAGCTTCTCGTGGGA 60.605 61.111 0.00 0.00 34.06 4.37
2710 2759 2.125350 GCCAGCTTCTCGTGGGAG 60.125 66.667 0.00 0.00 41.89 4.30
2711 2760 2.125350 CCAGCTTCTCGTGGGAGC 60.125 66.667 3.82 3.82 40.26 4.70
2712 2761 2.125350 CAGCTTCTCGTGGGAGCC 60.125 66.667 7.58 0.00 40.26 4.70
2713 2762 2.604686 AGCTTCTCGTGGGAGCCA 60.605 61.111 7.58 0.00 40.26 4.75
2714 2763 2.125350 GCTTCTCGTGGGAGCCAG 60.125 66.667 1.04 0.00 40.26 4.85
2715 2764 2.125350 CTTCTCGTGGGAGCCAGC 60.125 66.667 0.00 0.00 40.26 4.85
2716 2765 3.997064 CTTCTCGTGGGAGCCAGCG 62.997 68.421 0.00 0.00 40.26 5.18
2728 2777 2.894387 CCAGCGCTAGCCAGCTTC 60.894 66.667 10.99 0.00 46.26 3.86
2729 2778 2.894387 CAGCGCTAGCCAGCTTCC 60.894 66.667 10.99 0.00 46.26 3.46
2730 2779 4.168291 AGCGCTAGCCAGCTTCCC 62.168 66.667 8.99 0.00 46.26 3.97
2731 2780 4.473520 GCGCTAGCCAGCTTCCCA 62.474 66.667 9.66 0.00 46.26 4.37
2732 2781 2.512515 CGCTAGCCAGCTTCCCAC 60.513 66.667 9.66 0.00 46.26 4.61
2733 2782 2.512515 GCTAGCCAGCTTCCCACG 60.513 66.667 2.29 0.00 44.93 4.94
2734 2783 2.187946 CTAGCCAGCTTCCCACGG 59.812 66.667 0.00 0.00 0.00 4.94
2735 2784 3.391665 CTAGCCAGCTTCCCACGGG 62.392 68.421 0.00 0.00 0.00 5.28
2736 2785 3.916438 TAGCCAGCTTCCCACGGGA 62.916 63.158 0.00 0.00 43.52 5.14
2737 2786 4.785453 GCCAGCTTCCCACGGGAG 62.785 72.222 4.68 1.35 46.06 4.30
2738 2787 4.785453 CCAGCTTCCCACGGGAGC 62.785 72.222 15.00 15.00 46.06 4.70
2739 2788 4.785453 CAGCTTCCCACGGGAGCC 62.785 72.222 17.68 8.76 46.06 4.70
2741 2790 4.785453 GCTTCCCACGGGAGCCAG 62.785 72.222 4.68 1.36 46.06 4.85
2742 2791 4.101448 CTTCCCACGGGAGCCAGG 62.101 72.222 4.68 0.00 46.06 4.45
2743 2792 4.649705 TTCCCACGGGAGCCAGGA 62.650 66.667 4.68 0.00 46.06 3.86
2762 2811 3.041940 CGTTCGGCGCTCCAAGTT 61.042 61.111 7.64 0.00 0.00 2.66
2763 2812 2.861006 GTTCGGCGCTCCAAGTTC 59.139 61.111 7.64 0.00 0.00 3.01
2764 2813 1.668151 GTTCGGCGCTCCAAGTTCT 60.668 57.895 7.64 0.00 0.00 3.01
2765 2814 1.667830 TTCGGCGCTCCAAGTTCTG 60.668 57.895 7.64 0.00 0.00 3.02
2766 2815 3.793144 CGGCGCTCCAAGTTCTGC 61.793 66.667 7.64 0.00 0.00 4.26
2767 2816 2.359230 GGCGCTCCAAGTTCTGCT 60.359 61.111 7.64 0.00 0.00 4.24
2768 2817 2.684843 GGCGCTCCAAGTTCTGCTG 61.685 63.158 7.64 0.00 0.00 4.41
2769 2818 2.866028 CGCTCCAAGTTCTGCTGC 59.134 61.111 0.00 0.00 0.00 5.25
2770 2819 1.962822 CGCTCCAAGTTCTGCTGCA 60.963 57.895 0.88 0.88 0.00 4.41
2771 2820 1.303799 CGCTCCAAGTTCTGCTGCAT 61.304 55.000 1.31 0.00 0.00 3.96
2772 2821 0.170561 GCTCCAAGTTCTGCTGCATG 59.829 55.000 1.31 0.00 0.00 4.06
2773 2822 0.809385 CTCCAAGTTCTGCTGCATGG 59.191 55.000 11.98 11.98 0.00 3.66
2774 2823 0.609957 TCCAAGTTCTGCTGCATGGG 60.610 55.000 16.72 3.97 0.00 4.00
2775 2824 1.214589 CAAGTTCTGCTGCATGGGC 59.785 57.895 1.31 0.00 41.68 5.36
2776 2825 1.076192 AAGTTCTGCTGCATGGGCT 59.924 52.632 1.31 0.00 41.91 5.19
2777 2826 1.248785 AAGTTCTGCTGCATGGGCTG 61.249 55.000 1.31 0.00 41.91 4.85
2778 2827 2.361992 TTCTGCTGCATGGGCTGG 60.362 61.111 1.31 0.00 41.91 4.85
2802 2851 3.409384 AGGAAGGGAGCCTGAAGC 58.591 61.111 0.00 0.00 44.25 3.86
2803 2852 2.273776 GGAAGGGAGCCTGAAGCC 59.726 66.667 0.00 0.00 45.47 4.35
2804 2853 2.304831 GGAAGGGAGCCTGAAGCCT 61.305 63.158 0.00 0.00 45.47 4.58
2805 2854 1.077858 GAAGGGAGCCTGAAGCCTG 60.078 63.158 0.00 0.00 45.47 4.85
2806 2855 1.846712 GAAGGGAGCCTGAAGCCTGT 61.847 60.000 0.00 0.00 45.47 4.00
2807 2856 1.430369 AAGGGAGCCTGAAGCCTGTT 61.430 55.000 0.00 0.00 45.47 3.16
2808 2857 1.377856 GGGAGCCTGAAGCCTGTTC 60.378 63.158 0.00 0.00 45.47 3.18
2809 2858 1.743252 GGAGCCTGAAGCCTGTTCG 60.743 63.158 0.00 0.00 45.47 3.95
2810 2859 1.743252 GAGCCTGAAGCCTGTTCGG 60.743 63.158 0.00 0.00 45.47 4.30
2811 2860 2.747855 GCCTGAAGCCTGTTCGGG 60.748 66.667 8.08 8.08 45.56 5.14
2812 2861 2.045926 CCTGAAGCCTGTTCGGGG 60.046 66.667 4.88 0.00 40.46 5.73
2819 2868 2.113139 CCTGTTCGGGGCAGTTGT 59.887 61.111 0.00 0.00 32.41 3.32
2820 2869 1.528309 CCTGTTCGGGGCAGTTGTT 60.528 57.895 0.00 0.00 32.41 2.83
2821 2870 1.106944 CCTGTTCGGGGCAGTTGTTT 61.107 55.000 0.00 0.00 32.41 2.83
2822 2871 0.030638 CTGTTCGGGGCAGTTGTTTG 59.969 55.000 0.00 0.00 0.00 2.93
2823 2872 0.394488 TGTTCGGGGCAGTTGTTTGA 60.394 50.000 0.00 0.00 0.00 2.69
2824 2873 0.958822 GTTCGGGGCAGTTGTTTGAT 59.041 50.000 0.00 0.00 0.00 2.57
2825 2874 0.958091 TTCGGGGCAGTTGTTTGATG 59.042 50.000 0.00 0.00 0.00 3.07
2826 2875 0.893270 TCGGGGCAGTTGTTTGATGG 60.893 55.000 0.00 0.00 0.00 3.51
2827 2876 1.293179 GGGGCAGTTGTTTGATGGC 59.707 57.895 0.00 0.00 38.68 4.40
2828 2877 4.994744 GGCAGTTGTTTGATGGCC 57.005 55.556 0.00 0.00 33.69 5.36
2829 2878 1.293179 GGCAGTTGTTTGATGGCCC 59.707 57.895 0.00 0.00 35.42 5.80
2830 2879 1.080569 GCAGTTGTTTGATGGCCCG 60.081 57.895 0.00 0.00 0.00 6.13
2831 2880 1.523154 GCAGTTGTTTGATGGCCCGA 61.523 55.000 0.00 0.00 0.00 5.14
2832 2881 1.176527 CAGTTGTTTGATGGCCCGAT 58.823 50.000 0.00 0.00 0.00 4.18
2833 2882 1.545582 CAGTTGTTTGATGGCCCGATT 59.454 47.619 0.00 0.00 0.00 3.34
2834 2883 2.029110 CAGTTGTTTGATGGCCCGATTT 60.029 45.455 0.00 0.00 0.00 2.17
2835 2884 2.632512 AGTTGTTTGATGGCCCGATTTT 59.367 40.909 0.00 0.00 0.00 1.82
2836 2885 2.736192 GTTGTTTGATGGCCCGATTTTG 59.264 45.455 0.00 0.00 0.00 2.44
2837 2886 1.967066 TGTTTGATGGCCCGATTTTGT 59.033 42.857 0.00 0.00 0.00 2.83
2838 2887 2.288702 TGTTTGATGGCCCGATTTTGTG 60.289 45.455 0.00 0.00 0.00 3.33
2839 2888 0.894141 TTGATGGCCCGATTTTGTGG 59.106 50.000 0.00 0.00 0.00 4.17
2846 2895 2.466867 CCGATTTTGTGGGGAGACG 58.533 57.895 0.00 0.00 0.00 4.18
2847 2896 1.644786 CCGATTTTGTGGGGAGACGC 61.645 60.000 0.00 0.00 44.99 5.19
2848 2897 0.673644 CGATTTTGTGGGGAGACGCT 60.674 55.000 0.00 0.00 45.02 5.07
2849 2898 0.804989 GATTTTGTGGGGAGACGCTG 59.195 55.000 0.00 0.00 45.02 5.18
2850 2899 0.400213 ATTTTGTGGGGAGACGCTGA 59.600 50.000 0.00 0.00 45.02 4.26
2851 2900 0.181587 TTTTGTGGGGAGACGCTGAA 59.818 50.000 0.00 0.00 45.02 3.02
2852 2901 0.250295 TTTGTGGGGAGACGCTGAAG 60.250 55.000 0.00 0.00 45.02 3.02
2853 2902 2.435059 GTGGGGAGACGCTGAAGC 60.435 66.667 0.00 0.00 45.02 3.86
2854 2903 2.604686 TGGGGAGACGCTGAAGCT 60.605 61.111 0.10 0.00 45.02 3.74
2855 2904 2.125350 GGGGAGACGCTGAAGCTG 60.125 66.667 0.10 0.00 40.76 4.24
2856 2905 2.125350 GGGAGACGCTGAAGCTGG 60.125 66.667 0.10 0.00 39.32 4.85
2857 2906 2.817396 GGAGACGCTGAAGCTGGC 60.817 66.667 0.10 0.00 39.32 4.85
2858 2907 2.264166 GAGACGCTGAAGCTGGCT 59.736 61.111 0.10 1.60 39.32 4.75
2859 2908 2.047465 AGACGCTGAAGCTGGCTG 60.047 61.111 0.10 0.00 39.32 4.85
2860 2909 3.797546 GACGCTGAAGCTGGCTGC 61.798 66.667 8.47 8.47 43.29 5.25
2861 2910 4.631247 ACGCTGAAGCTGGCTGCA 62.631 61.111 18.84 3.03 45.94 4.41
2864 2913 2.350134 CTGAAGCTGGCTGCAGGA 59.650 61.111 19.87 0.45 44.15 3.86
2865 2914 1.745864 CTGAAGCTGGCTGCAGGAG 60.746 63.158 19.87 6.64 44.15 3.69
2866 2915 2.181445 CTGAAGCTGGCTGCAGGAGA 62.181 60.000 19.87 0.00 44.15 3.71
2867 2916 1.744741 GAAGCTGGCTGCAGGAGAC 60.745 63.158 17.12 0.00 45.94 3.36
2868 2917 3.602513 AAGCTGGCTGCAGGAGACG 62.603 63.158 17.12 0.00 45.94 4.18
2869 2918 4.074526 GCTGGCTGCAGGAGACGA 62.075 66.667 17.12 0.00 42.31 4.20
2870 2919 2.898738 CTGGCTGCAGGAGACGAT 59.101 61.111 17.12 0.00 28.23 3.73
2871 2920 1.227205 CTGGCTGCAGGAGACGATC 60.227 63.158 17.12 0.00 28.23 3.69
2879 2928 2.412112 GGAGACGATCCGAACGGG 59.588 66.667 13.29 0.19 38.67 5.28
2880 2929 2.278661 GAGACGATCCGAACGGGC 60.279 66.667 13.29 5.36 34.94 6.13
2881 2930 3.769875 GAGACGATCCGAACGGGCC 62.770 68.421 13.29 0.00 34.94 5.80
2882 2931 4.886121 GACGATCCGAACGGGCCC 62.886 72.222 13.57 13.57 34.94 5.80
2884 2933 4.157120 CGATCCGAACGGGCCCTT 62.157 66.667 22.43 7.92 34.94 3.95
2885 2934 2.788640 CGATCCGAACGGGCCCTTA 61.789 63.158 22.43 0.00 34.94 2.69
2886 2935 1.069258 GATCCGAACGGGCCCTTAG 59.931 63.158 22.43 13.03 34.94 2.18
2887 2936 2.990830 GATCCGAACGGGCCCTTAGC 62.991 65.000 22.43 5.55 42.60 3.09
2939 2991 0.247460 CAGGTTGCTCCAGTCGATGA 59.753 55.000 0.00 0.00 39.02 2.92
2983 4450 6.861572 GCCAATTTGACCTCTTAAAACACTAC 59.138 38.462 0.00 0.00 0.00 2.73
3028 4495 1.709147 GCGGGCACACTAGCAATGAG 61.709 60.000 0.00 0.00 35.83 2.90
3052 4559 2.237643 TGTAGCAAAGCTTTGGCATCA 58.762 42.857 34.02 23.97 40.44 3.07
3067 4576 4.980590 TGGCATCAATTTTGATACGTGTC 58.019 39.130 5.21 5.21 45.62 3.67
3127 4647 1.967597 GCGCTTAGGGTTCTTCACGC 61.968 60.000 0.00 0.00 38.67 5.34
3161 4681 2.716017 CGGCCAGAGGAGTGGAGAC 61.716 68.421 2.24 0.00 40.44 3.36
3162 4682 2.363172 GGCCAGAGGAGTGGAGACC 61.363 68.421 0.00 0.00 40.44 3.85
3163 4683 2.363172 GCCAGAGGAGTGGAGACCC 61.363 68.421 0.00 0.00 40.44 4.46
3164 4684 2.055042 CCAGAGGAGTGGAGACCCG 61.055 68.421 0.00 0.00 40.44 5.28
3165 4685 2.363147 AGAGGAGTGGAGACCCGC 60.363 66.667 0.00 0.00 43.25 6.13
3166 4686 3.462678 GAGGAGTGGAGACCCGCC 61.463 72.222 0.00 0.00 43.97 6.13
3169 4689 3.003763 GAGTGGAGACCCGCCCTT 61.004 66.667 0.00 0.00 43.97 3.95
3170 4690 2.529389 AGTGGAGACCCGCCCTTT 60.529 61.111 0.00 0.00 43.97 3.11
3171 4691 2.046217 GTGGAGACCCGCCCTTTC 60.046 66.667 0.00 0.00 36.97 2.62
3172 4692 2.203938 TGGAGACCCGCCCTTTCT 60.204 61.111 0.00 0.00 34.29 2.52
3173 4693 2.269241 GGAGACCCGCCCTTTCTG 59.731 66.667 0.00 0.00 0.00 3.02
3174 4694 2.291043 GGAGACCCGCCCTTTCTGA 61.291 63.158 0.00 0.00 0.00 3.27
3175 4695 1.079057 GAGACCCGCCCTTTCTGAC 60.079 63.158 0.00 0.00 0.00 3.51
3176 4696 2.046217 GACCCGCCCTTTCTGACC 60.046 66.667 0.00 0.00 0.00 4.02
3177 4697 2.852075 ACCCGCCCTTTCTGACCA 60.852 61.111 0.00 0.00 0.00 4.02
3178 4698 2.045926 CCCGCCCTTTCTGACCAG 60.046 66.667 0.00 0.00 0.00 4.00
3179 4699 2.592993 CCCGCCCTTTCTGACCAGA 61.593 63.158 0.00 0.00 35.27 3.86
3180 4700 1.078848 CCGCCCTTTCTGACCAGAG 60.079 63.158 0.00 0.00 38.88 3.35
3181 4701 1.078848 CGCCCTTTCTGACCAGAGG 60.079 63.158 0.00 0.33 38.88 3.69
3182 4702 1.544825 CGCCCTTTCTGACCAGAGGA 61.545 60.000 7.68 0.00 38.88 3.71
3183 4703 0.251634 GCCCTTTCTGACCAGAGGAG 59.748 60.000 7.68 6.71 38.88 3.69
3184 4704 1.650528 CCCTTTCTGACCAGAGGAGT 58.349 55.000 6.82 0.00 38.88 3.85
3185 4705 1.277557 CCCTTTCTGACCAGAGGAGTG 59.722 57.143 6.82 0.00 38.88 3.51
3186 4706 1.277557 CCTTTCTGACCAGAGGAGTGG 59.722 57.143 0.00 0.00 44.01 4.00
3187 4707 2.251818 CTTTCTGACCAGAGGAGTGGA 58.748 52.381 0.00 0.00 40.44 4.02
3188 4708 1.930251 TTCTGACCAGAGGAGTGGAG 58.070 55.000 0.00 0.00 40.44 3.86
3189 4709 1.076438 TCTGACCAGAGGAGTGGAGA 58.924 55.000 0.00 0.00 40.44 3.71
3190 4710 1.181786 CTGACCAGAGGAGTGGAGAC 58.818 60.000 0.00 0.00 40.44 3.36
3191 4711 0.251832 TGACCAGAGGAGTGGAGACC 60.252 60.000 0.00 0.00 40.44 3.85
3192 4712 0.040499 GACCAGAGGAGTGGAGACCT 59.960 60.000 0.00 0.00 40.44 3.85
3193 4713 0.252012 ACCAGAGGAGTGGAGACCTG 60.252 60.000 0.00 0.00 40.44 4.00
3194 4714 1.612395 CCAGAGGAGTGGAGACCTGC 61.612 65.000 0.00 0.00 40.44 4.85
3195 4715 1.305718 AGAGGAGTGGAGACCTGCC 60.306 63.158 0.00 0.00 36.57 4.85
3196 4716 2.284995 AGGAGTGGAGACCTGCCC 60.285 66.667 0.00 0.00 34.99 5.36
3197 4717 2.284995 GGAGTGGAGACCTGCCCT 60.285 66.667 0.00 0.00 0.00 5.19
3198 4718 1.920835 GGAGTGGAGACCTGCCCTT 60.921 63.158 0.00 0.00 0.00 3.95
3199 4719 1.492993 GGAGTGGAGACCTGCCCTTT 61.493 60.000 0.00 0.00 0.00 3.11
3200 4720 0.035915 GAGTGGAGACCTGCCCTTTC 60.036 60.000 0.00 0.00 0.00 2.62
3201 4721 0.474660 AGTGGAGACCTGCCCTTTCT 60.475 55.000 0.00 0.00 0.00 2.52
3202 4722 0.402121 GTGGAGACCTGCCCTTTCTT 59.598 55.000 0.00 0.00 0.00 2.52
3203 4723 1.149101 TGGAGACCTGCCCTTTCTTT 58.851 50.000 0.00 0.00 0.00 2.52
3204 4724 1.202927 TGGAGACCTGCCCTTTCTTTG 60.203 52.381 0.00 0.00 0.00 2.77
3205 4725 1.202940 GGAGACCTGCCCTTTCTTTGT 60.203 52.381 0.00 0.00 0.00 2.83
3206 4726 2.587522 GAGACCTGCCCTTTCTTTGTT 58.412 47.619 0.00 0.00 0.00 2.83
3207 4727 2.554462 GAGACCTGCCCTTTCTTTGTTC 59.446 50.000 0.00 0.00 0.00 3.18
3208 4728 2.175715 AGACCTGCCCTTTCTTTGTTCT 59.824 45.455 0.00 0.00 0.00 3.01
3209 4729 2.959030 GACCTGCCCTTTCTTTGTTCTT 59.041 45.455 0.00 0.00 0.00 2.52
3210 4730 2.695147 ACCTGCCCTTTCTTTGTTCTTG 59.305 45.455 0.00 0.00 0.00 3.02
3211 4731 2.036346 CCTGCCCTTTCTTTGTTCTTGG 59.964 50.000 0.00 0.00 0.00 3.61
3212 4732 2.958355 CTGCCCTTTCTTTGTTCTTGGA 59.042 45.455 0.00 0.00 0.00 3.53
3213 4733 3.575687 CTGCCCTTTCTTTGTTCTTGGAT 59.424 43.478 0.00 0.00 0.00 3.41
3214 4734 3.966665 TGCCCTTTCTTTGTTCTTGGATT 59.033 39.130 0.00 0.00 0.00 3.01
3215 4735 4.408596 TGCCCTTTCTTTGTTCTTGGATTT 59.591 37.500 0.00 0.00 0.00 2.17
3216 4736 5.600484 TGCCCTTTCTTTGTTCTTGGATTTA 59.400 36.000 0.00 0.00 0.00 1.40
3217 4737 6.098982 TGCCCTTTCTTTGTTCTTGGATTTAA 59.901 34.615 0.00 0.00 0.00 1.52
3218 4738 7.161404 GCCCTTTCTTTGTTCTTGGATTTAAT 58.839 34.615 0.00 0.00 0.00 1.40
3219 4739 8.311109 GCCCTTTCTTTGTTCTTGGATTTAATA 58.689 33.333 0.00 0.00 0.00 0.98
3220 4740 9.860898 CCCTTTCTTTGTTCTTGGATTTAATAG 57.139 33.333 0.00 0.00 0.00 1.73
3221 4741 9.860898 CCTTTCTTTGTTCTTGGATTTAATAGG 57.139 33.333 0.00 0.00 0.00 2.57
3234 4754 9.952030 TTGGATTTAATAGGAATTTGTTTTCCC 57.048 29.630 0.00 0.00 45.32 3.97
3235 4755 9.332713 TGGATTTAATAGGAATTTGTTTTCCCT 57.667 29.630 0.00 0.00 45.32 4.20
3238 4758 9.958180 ATTTAATAGGAATTTGTTTTCCCTTGG 57.042 29.630 0.00 0.00 45.32 3.61
3239 4759 8.499288 TTAATAGGAATTTGTTTTCCCTTGGT 57.501 30.769 0.00 0.00 45.32 3.67
3240 4760 7.387265 AATAGGAATTTGTTTTCCCTTGGTT 57.613 32.000 0.00 0.00 45.32 3.67
3241 4761 5.708736 AGGAATTTGTTTTCCCTTGGTTT 57.291 34.783 0.00 0.00 45.32 3.27
3242 4762 6.073447 AGGAATTTGTTTTCCCTTGGTTTT 57.927 33.333 0.00 0.00 45.32 2.43
3243 4763 6.489603 AGGAATTTGTTTTCCCTTGGTTTTT 58.510 32.000 0.00 0.00 45.32 1.94
3244 4764 6.601613 AGGAATTTGTTTTCCCTTGGTTTTTC 59.398 34.615 0.00 0.00 45.32 2.29
3245 4765 6.601613 GGAATTTGTTTTCCCTTGGTTTTTCT 59.398 34.615 0.00 0.00 39.46 2.52
3246 4766 7.201696 GGAATTTGTTTTCCCTTGGTTTTTCTC 60.202 37.037 0.00 0.00 39.46 2.87
3247 4767 6.367374 TTTGTTTTCCCTTGGTTTTTCTCT 57.633 33.333 0.00 0.00 0.00 3.10
3248 4768 5.592104 TGTTTTCCCTTGGTTTTTCTCTC 57.408 39.130 0.00 0.00 0.00 3.20
3249 4769 4.404394 TGTTTTCCCTTGGTTTTTCTCTCC 59.596 41.667 0.00 0.00 0.00 3.71
3250 4770 4.536295 TTTCCCTTGGTTTTTCTCTCCT 57.464 40.909 0.00 0.00 0.00 3.69
3251 4771 3.508845 TCCCTTGGTTTTTCTCTCCTG 57.491 47.619 0.00 0.00 0.00 3.86
3252 4772 2.108250 TCCCTTGGTTTTTCTCTCCTGG 59.892 50.000 0.00 0.00 0.00 4.45
3253 4773 1.889170 CCTTGGTTTTTCTCTCCTGGC 59.111 52.381 0.00 0.00 0.00 4.85
3254 4774 2.586425 CTTGGTTTTTCTCTCCTGGCA 58.414 47.619 0.00 0.00 0.00 4.92
3255 4775 2.276732 TGGTTTTTCTCTCCTGGCAG 57.723 50.000 7.75 7.75 0.00 4.85
3256 4776 0.884514 GGTTTTTCTCTCCTGGCAGC 59.115 55.000 9.56 0.00 0.00 5.25
3257 4777 1.609208 GTTTTTCTCTCCTGGCAGCA 58.391 50.000 9.56 0.00 0.00 4.41
3258 4778 2.165998 GTTTTTCTCTCCTGGCAGCAT 58.834 47.619 9.56 0.00 0.00 3.79
3259 4779 1.830279 TTTTCTCTCCTGGCAGCATG 58.170 50.000 9.56 0.99 40.87 4.06
3260 4780 0.034767 TTTCTCTCCTGGCAGCATGG 60.035 55.000 9.56 0.00 35.86 3.66
3261 4781 1.918467 TTCTCTCCTGGCAGCATGGG 61.918 60.000 9.56 0.88 35.86 4.00
3262 4782 2.611800 TCTCCTGGCAGCATGGGT 60.612 61.111 9.56 0.00 35.86 4.51
3263 4783 2.124403 CTCCTGGCAGCATGGGTC 60.124 66.667 9.56 0.00 35.86 4.46
3264 4784 4.100084 TCCTGGCAGCATGGGTCG 62.100 66.667 9.56 0.00 35.86 4.79
3265 4785 4.100084 CCTGGCAGCATGGGTCGA 62.100 66.667 9.56 0.00 35.86 4.20
3266 4786 2.821366 CTGGCAGCATGGGTCGAC 60.821 66.667 7.13 7.13 35.86 4.20
3267 4787 3.610619 CTGGCAGCATGGGTCGACA 62.611 63.158 18.91 0.00 35.86 4.35
3268 4788 2.359850 GGCAGCATGGGTCGACAA 60.360 61.111 18.91 5.15 35.86 3.18
3269 4789 2.401766 GGCAGCATGGGTCGACAAG 61.402 63.158 18.91 4.68 35.86 3.16
3270 4790 1.375908 GCAGCATGGGTCGACAAGA 60.376 57.895 18.91 0.00 35.86 3.02
3271 4791 1.364626 GCAGCATGGGTCGACAAGAG 61.365 60.000 18.91 5.43 35.86 2.85
3272 4792 1.078848 AGCATGGGTCGACAAGAGC 60.079 57.895 18.91 15.15 46.08 4.09
3278 4798 2.533318 GGTCGACAAGAGCCTGTTG 58.467 57.895 18.91 0.00 41.28 3.33
3279 4799 0.033504 GGTCGACAAGAGCCTGTTGA 59.966 55.000 18.91 0.00 41.28 3.18
3280 4800 3.588277 TCGACAAGAGCCTGTTGAC 57.412 52.632 8.78 1.08 35.25 3.18
3281 4801 1.040646 TCGACAAGAGCCTGTTGACT 58.959 50.000 8.78 0.00 35.25 3.41
3282 4802 1.000163 TCGACAAGAGCCTGTTGACTC 60.000 52.381 8.78 0.00 35.25 3.36
3283 4803 1.000283 CGACAAGAGCCTGTTGACTCT 60.000 52.381 8.78 0.00 45.13 3.24
3284 4804 2.682836 GACAAGAGCCTGTTGACTCTC 58.317 52.381 8.78 0.00 42.41 3.20
3285 4805 2.298729 GACAAGAGCCTGTTGACTCTCT 59.701 50.000 8.78 0.00 42.41 3.10
3286 4806 2.703007 ACAAGAGCCTGTTGACTCTCTT 59.297 45.455 8.78 0.00 42.41 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.196695 AGCAAGTCAAAAGGAGAAGAGTTT 58.803 37.500 0.00 0.00 0.00 2.66
21 22 4.085357 TGCTAAGCAAGTCAAAAGGAGA 57.915 40.909 0.00 0.00 34.76 3.71
179 184 7.432059 CACTGTCTGTATGACTATGACATCAT 58.568 38.462 0.00 0.00 45.54 2.45
236 241 8.429641 TGTCAGAAAGTTTAGATTAGTTGACCT 58.570 33.333 0.00 0.00 32.45 3.85
306 311 3.713826 TGGATTCAGTACTGTTTCCCC 57.286 47.619 28.40 20.69 34.29 4.81
434 439 9.362151 GTATTTATCACCCATGAATTCCCTAAA 57.638 33.333 2.27 0.00 38.69 1.85
585 591 7.381678 GTGCCAATATAGACTACGGAAACTAAG 59.618 40.741 0.00 0.00 0.00 2.18
593 599 4.585955 AGTGTGCCAATATAGACTACGG 57.414 45.455 0.00 0.00 0.00 4.02
647 653 0.178891 AGAGGGCAAGGAGAAGGTCA 60.179 55.000 0.00 0.00 0.00 4.02
1538 1562 7.277760 TGTGTGGTGAGAAATAGATCGTATTTG 59.722 37.037 12.16 0.00 0.00 2.32
1559 1583 1.347707 AGGACCACTACCATGTGTGTG 59.652 52.381 0.00 6.24 36.30 3.82
1597 1621 6.964807 TCTTACACAGTTAAGACCACTACA 57.035 37.500 0.00 0.00 0.00 2.74
1729 1753 5.295950 TGACATAAACATGCCAAAACAAGG 58.704 37.500 0.00 0.00 0.00 3.61
1851 1883 3.407424 TGATATGGGAAATCGAGGCTG 57.593 47.619 0.00 0.00 0.00 4.85
1903 1935 2.357009 GGCACAAGAATGATCTGCGATT 59.643 45.455 0.00 0.00 35.59 3.34
1971 2008 3.239026 CGATCTGAACAAAATGCAATCGC 59.761 43.478 0.00 0.00 39.24 4.58
2035 2077 8.616076 ACTCAACTACAGAAGTTTGAGATTTTG 58.384 33.333 15.27 0.00 46.61 2.44
2051 2093 1.872237 GCACGCAAGGACTCAACTACA 60.872 52.381 0.00 0.00 46.39 2.74
2118 2160 5.950883 TCAAACACGTCCACAAAATAAACA 58.049 33.333 0.00 0.00 0.00 2.83
2124 2166 2.425312 AGCATCAAACACGTCCACAAAA 59.575 40.909 0.00 0.00 0.00 2.44
2524 2571 2.175878 TCTCTTGCTCTGCTTCAACC 57.824 50.000 0.00 0.00 0.00 3.77
2631 2680 4.892433 TCCATGAAATTTGGCAACGATTT 58.108 34.783 9.10 9.10 37.56 2.17
2665 2714 4.821589 CCAGGCGAGCTCCCGAAC 62.822 72.222 8.47 0.00 0.00 3.95
2690 2739 3.123620 CCACGAGAAGCTGGCTGC 61.124 66.667 8.47 8.47 43.29 5.25
2691 2740 2.435586 CCCACGAGAAGCTGGCTG 60.436 66.667 0.00 0.00 0.00 4.85
2692 2741 2.604686 TCCCACGAGAAGCTGGCT 60.605 61.111 0.00 0.00 0.00 4.75
2693 2742 2.125350 CTCCCACGAGAAGCTGGC 60.125 66.667 0.00 0.00 38.52 4.85
2694 2743 2.125350 GCTCCCACGAGAAGCTGG 60.125 66.667 0.00 0.00 38.52 4.85
2695 2744 2.125350 GGCTCCCACGAGAAGCTG 60.125 66.667 0.00 0.00 38.52 4.24
2696 2745 2.604686 TGGCTCCCACGAGAAGCT 60.605 61.111 0.00 0.00 38.52 3.74
2697 2746 2.125350 CTGGCTCCCACGAGAAGC 60.125 66.667 0.00 0.00 38.52 3.86
2698 2747 2.125350 GCTGGCTCCCACGAGAAG 60.125 66.667 0.00 0.00 38.52 2.85
2699 2748 4.069232 CGCTGGCTCCCACGAGAA 62.069 66.667 0.00 0.00 38.52 2.87
2717 2766 2.187946 CCGTGGGAAGCTGGCTAG 59.812 66.667 0.00 0.00 0.00 3.42
2718 2767 3.399181 CCCGTGGGAAGCTGGCTA 61.399 66.667 0.00 0.00 37.50 3.93
2720 2769 4.785453 CTCCCGTGGGAAGCTGGC 62.785 72.222 9.34 0.00 44.66 4.85
2721 2770 4.785453 GCTCCCGTGGGAAGCTGG 62.785 72.222 9.34 0.00 44.66 4.85
2722 2771 4.785453 GGCTCCCGTGGGAAGCTG 62.785 72.222 21.06 8.03 44.66 4.24
2724 2773 4.785453 CTGGCTCCCGTGGGAAGC 62.785 72.222 9.34 13.70 44.66 3.86
2725 2774 4.101448 CCTGGCTCCCGTGGGAAG 62.101 72.222 9.34 3.65 44.66 3.46
2726 2775 4.649705 TCCTGGCTCCCGTGGGAA 62.650 66.667 9.34 0.00 44.66 3.97
2732 2781 4.821589 GAACGCTCCTGGCTCCCG 62.822 72.222 0.00 0.00 39.13 5.14
2733 2782 4.821589 CGAACGCTCCTGGCTCCC 62.822 72.222 0.00 0.00 39.13 4.30
2734 2783 4.821589 CCGAACGCTCCTGGCTCC 62.822 72.222 0.00 0.00 39.13 4.70
2746 2795 1.668151 AGAACTTGGAGCGCCGAAC 60.668 57.895 2.29 0.00 36.79 3.95
2747 2796 1.667830 CAGAACTTGGAGCGCCGAA 60.668 57.895 2.29 0.00 36.79 4.30
2748 2797 2.048222 CAGAACTTGGAGCGCCGA 60.048 61.111 2.29 0.00 36.79 5.54
2749 2798 3.793144 GCAGAACTTGGAGCGCCG 61.793 66.667 2.29 0.00 36.79 6.46
2750 2799 2.359230 AGCAGAACTTGGAGCGCC 60.359 61.111 2.29 0.00 0.00 6.53
2751 2800 2.866028 CAGCAGAACTTGGAGCGC 59.134 61.111 0.00 0.00 0.00 5.92
2752 2801 1.303799 ATGCAGCAGAACTTGGAGCG 61.304 55.000 0.00 0.00 0.00 5.03
2753 2802 0.170561 CATGCAGCAGAACTTGGAGC 59.829 55.000 0.00 0.00 0.00 4.70
2754 2803 0.809385 CCATGCAGCAGAACTTGGAG 59.191 55.000 6.14 0.00 33.96 3.86
2755 2804 0.609957 CCCATGCAGCAGAACTTGGA 60.610 55.000 12.82 0.00 33.96 3.53
2756 2805 1.888018 CCCATGCAGCAGAACTTGG 59.112 57.895 0.00 2.79 0.00 3.61
2757 2806 1.214589 GCCCATGCAGCAGAACTTG 59.785 57.895 0.00 0.00 37.47 3.16
2758 2807 1.076192 AGCCCATGCAGCAGAACTT 59.924 52.632 0.00 0.00 41.13 2.66
2759 2808 1.677966 CAGCCCATGCAGCAGAACT 60.678 57.895 0.00 0.00 41.13 3.01
2760 2809 2.707849 CCAGCCCATGCAGCAGAAC 61.708 63.158 0.00 0.00 41.13 3.01
2761 2810 2.361992 CCAGCCCATGCAGCAGAA 60.362 61.111 0.00 0.00 41.13 3.02
2785 2834 2.304831 GGCTTCAGGCTCCCTTCCT 61.305 63.158 0.00 0.00 41.46 3.36
2786 2835 2.273776 GGCTTCAGGCTCCCTTCC 59.726 66.667 0.00 0.00 41.46 3.46
2794 2843 2.747855 CCCGAACAGGCTTCAGGC 60.748 66.667 0.00 0.00 39.21 4.85
2795 2844 2.045926 CCCCGAACAGGCTTCAGG 60.046 66.667 0.00 0.00 39.21 3.86
2802 2851 1.106944 AAACAACTGCCCCGAACAGG 61.107 55.000 4.67 0.00 39.55 4.00
2803 2852 0.030638 CAAACAACTGCCCCGAACAG 59.969 55.000 0.00 0.00 41.08 3.16
2804 2853 0.394488 TCAAACAACTGCCCCGAACA 60.394 50.000 0.00 0.00 0.00 3.18
2805 2854 0.958822 ATCAAACAACTGCCCCGAAC 59.041 50.000 0.00 0.00 0.00 3.95
2806 2855 0.958091 CATCAAACAACTGCCCCGAA 59.042 50.000 0.00 0.00 0.00 4.30
2807 2856 0.893270 CCATCAAACAACTGCCCCGA 60.893 55.000 0.00 0.00 0.00 5.14
2808 2857 1.586028 CCATCAAACAACTGCCCCG 59.414 57.895 0.00 0.00 0.00 5.73
2809 2858 1.293179 GCCATCAAACAACTGCCCC 59.707 57.895 0.00 0.00 0.00 5.80
2810 2859 1.293179 GGCCATCAAACAACTGCCC 59.707 57.895 0.00 0.00 32.74 5.36
2811 2860 1.293179 GGGCCATCAAACAACTGCC 59.707 57.895 4.39 0.00 38.16 4.85
2812 2861 1.080569 CGGGCCATCAAACAACTGC 60.081 57.895 4.39 0.00 0.00 4.40
2813 2862 1.176527 ATCGGGCCATCAAACAACTG 58.823 50.000 4.39 0.00 0.00 3.16
2814 2863 1.923356 AATCGGGCCATCAAACAACT 58.077 45.000 4.39 0.00 0.00 3.16
2815 2864 2.736192 CAAAATCGGGCCATCAAACAAC 59.264 45.455 4.39 0.00 0.00 3.32
2816 2865 2.366916 ACAAAATCGGGCCATCAAACAA 59.633 40.909 4.39 0.00 0.00 2.83
2817 2866 1.967066 ACAAAATCGGGCCATCAAACA 59.033 42.857 4.39 0.00 0.00 2.83
2818 2867 2.336667 CACAAAATCGGGCCATCAAAC 58.663 47.619 4.39 0.00 0.00 2.93
2819 2868 1.274728 CCACAAAATCGGGCCATCAAA 59.725 47.619 4.39 0.00 0.00 2.69
2820 2869 0.894141 CCACAAAATCGGGCCATCAA 59.106 50.000 4.39 0.00 0.00 2.57
2821 2870 0.969917 CCCACAAAATCGGGCCATCA 60.970 55.000 4.39 0.00 35.09 3.07
2822 2871 1.675720 CCCCACAAAATCGGGCCATC 61.676 60.000 4.39 0.00 41.57 3.51
2823 2872 1.685421 CCCCACAAAATCGGGCCAT 60.685 57.895 4.39 0.00 41.57 4.40
2824 2873 2.283532 CCCCACAAAATCGGGCCA 60.284 61.111 4.39 0.00 41.57 5.36
2825 2874 2.036572 TCCCCACAAAATCGGGCC 59.963 61.111 0.00 0.00 41.57 5.80
2826 2875 1.001393 TCTCCCCACAAAATCGGGC 60.001 57.895 0.00 0.00 41.57 6.13
2827 2876 1.024579 CGTCTCCCCACAAAATCGGG 61.025 60.000 0.00 0.00 42.67 5.14
2828 2877 1.644786 GCGTCTCCCCACAAAATCGG 61.645 60.000 0.00 0.00 0.00 4.18
2829 2878 0.673644 AGCGTCTCCCCACAAAATCG 60.674 55.000 0.00 0.00 0.00 3.34
2830 2879 0.804989 CAGCGTCTCCCCACAAAATC 59.195 55.000 0.00 0.00 0.00 2.17
2831 2880 0.400213 TCAGCGTCTCCCCACAAAAT 59.600 50.000 0.00 0.00 0.00 1.82
2832 2881 0.181587 TTCAGCGTCTCCCCACAAAA 59.818 50.000 0.00 0.00 0.00 2.44
2833 2882 0.250295 CTTCAGCGTCTCCCCACAAA 60.250 55.000 0.00 0.00 0.00 2.83
2834 2883 1.371183 CTTCAGCGTCTCCCCACAA 59.629 57.895 0.00 0.00 0.00 3.33
2835 2884 3.059982 CTTCAGCGTCTCCCCACA 58.940 61.111 0.00 0.00 0.00 4.17
2836 2885 2.435059 GCTTCAGCGTCTCCCCAC 60.435 66.667 0.00 0.00 0.00 4.61
2846 2895 3.441290 CCTGCAGCCAGCTTCAGC 61.441 66.667 13.01 3.85 45.94 4.26
2847 2896 1.745864 CTCCTGCAGCCAGCTTCAG 60.746 63.158 8.66 11.72 45.94 3.02
2848 2897 2.219164 TCTCCTGCAGCCAGCTTCA 61.219 57.895 8.66 0.00 45.94 3.02
2849 2898 1.744741 GTCTCCTGCAGCCAGCTTC 60.745 63.158 8.66 0.00 45.94 3.86
2850 2899 2.350514 GTCTCCTGCAGCCAGCTT 59.649 61.111 8.66 0.00 45.94 3.74
2851 2900 4.079850 CGTCTCCTGCAGCCAGCT 62.080 66.667 8.66 0.00 45.94 4.24
2852 2901 3.382803 ATCGTCTCCTGCAGCCAGC 62.383 63.158 8.66 2.26 45.96 4.85
2853 2902 1.227205 GATCGTCTCCTGCAGCCAG 60.227 63.158 8.66 6.37 38.85 4.85
2854 2903 2.725312 GGATCGTCTCCTGCAGCCA 61.725 63.158 8.66 0.00 41.29 4.75
2855 2904 2.107953 GGATCGTCTCCTGCAGCC 59.892 66.667 8.66 0.00 41.29 4.85
2856 2905 2.279120 CGGATCGTCTCCTGCAGC 60.279 66.667 8.66 0.00 42.47 5.25
2857 2906 0.526524 GTTCGGATCGTCTCCTGCAG 60.527 60.000 6.78 6.78 42.47 4.41
2858 2907 1.511305 GTTCGGATCGTCTCCTGCA 59.489 57.895 5.48 0.00 42.47 4.41
2859 2908 1.586564 CGTTCGGATCGTCTCCTGC 60.587 63.158 0.42 0.00 42.47 4.85
2860 2909 1.064296 CCGTTCGGATCGTCTCCTG 59.936 63.158 5.19 0.71 42.47 3.86
2861 2910 2.119655 CCCGTTCGGATCGTCTCCT 61.120 63.158 13.08 0.00 42.47 3.69
2862 2911 2.412112 CCCGTTCGGATCGTCTCC 59.588 66.667 13.08 0.00 41.07 3.71
2863 2912 2.278661 GCCCGTTCGGATCGTCTC 60.279 66.667 13.08 0.00 0.00 3.36
2864 2913 3.834799 GGCCCGTTCGGATCGTCT 61.835 66.667 13.08 0.00 0.00 4.18
2865 2914 4.886121 GGGCCCGTTCGGATCGTC 62.886 72.222 5.69 0.00 0.00 4.20
2867 2916 2.694829 CTAAGGGCCCGTTCGGATCG 62.695 65.000 17.88 1.56 0.00 3.69
2868 2917 1.069258 CTAAGGGCCCGTTCGGATC 59.931 63.158 17.88 4.12 0.00 3.36
2869 2918 3.103091 GCTAAGGGCCCGTTCGGAT 62.103 63.158 17.88 0.00 34.27 4.18
2870 2919 3.777910 GCTAAGGGCCCGTTCGGA 61.778 66.667 17.88 0.00 34.27 4.55
2880 2929 4.864334 CCTGGCGCTGGCTAAGGG 62.864 72.222 7.64 0.63 38.52 3.95
2881 2930 4.864334 CCCTGGCGCTGGCTAAGG 62.864 72.222 7.64 5.15 40.51 2.69
2882 2931 1.758440 TATCCCTGGCGCTGGCTAAG 61.758 60.000 7.64 0.00 39.81 2.18
2883 2932 1.341913 TTATCCCTGGCGCTGGCTAA 61.342 55.000 7.64 5.41 39.81 3.09
2884 2933 1.127567 ATTATCCCTGGCGCTGGCTA 61.128 55.000 7.64 0.00 39.81 3.93
2885 2934 1.127567 TATTATCCCTGGCGCTGGCT 61.128 55.000 7.64 0.00 39.81 4.75
2886 2935 0.250727 TTATTATCCCTGGCGCTGGC 60.251 55.000 7.64 0.00 38.90 4.85
2887 2936 2.290260 TGATTATTATCCCTGGCGCTGG 60.290 50.000 7.64 10.33 0.00 4.85
2888 2937 3.057969 TGATTATTATCCCTGGCGCTG 57.942 47.619 7.64 0.00 0.00 5.18
2889 2938 4.307032 AATGATTATTATCCCTGGCGCT 57.693 40.909 7.64 0.00 0.00 5.92
2890 2939 4.458989 TCAAATGATTATTATCCCTGGCGC 59.541 41.667 0.00 0.00 0.00 6.53
2891 2940 6.375174 TGATCAAATGATTATTATCCCTGGCG 59.625 38.462 0.00 0.00 34.37 5.69
2892 2941 7.707624 TGATCAAATGATTATTATCCCTGGC 57.292 36.000 0.00 0.00 34.37 4.85
2934 2986 1.337071 ACCAGTACCGCAGTATCATCG 59.663 52.381 0.00 0.00 0.00 3.84
2935 2987 3.381949 GAACCAGTACCGCAGTATCATC 58.618 50.000 0.00 0.00 0.00 2.92
2939 2991 0.458669 CCGAACCAGTACCGCAGTAT 59.541 55.000 0.00 0.00 0.00 2.12
2983 4450 0.452987 CATTCATTCCTGGTGGCACG 59.547 55.000 12.17 0.00 0.00 5.34
3028 4495 1.728425 GCCAAAGCTTTGCTACATTGC 59.272 47.619 29.93 22.03 38.25 3.56
3127 4647 3.261951 CGCCTACGATGCCGGTTG 61.262 66.667 1.90 0.00 43.93 3.77
3161 4681 2.045926 CTGGTCAGAAAGGGCGGG 60.046 66.667 0.00 0.00 0.00 6.13
3162 4682 1.078848 CTCTGGTCAGAAAGGGCGG 60.079 63.158 2.13 0.00 36.94 6.13
3163 4683 1.078848 CCTCTGGTCAGAAAGGGCG 60.079 63.158 2.13 0.00 36.94 6.13
3164 4684 0.251634 CTCCTCTGGTCAGAAAGGGC 59.748 60.000 2.13 0.00 36.94 5.19
3165 4685 1.277557 CACTCCTCTGGTCAGAAAGGG 59.722 57.143 2.13 0.94 36.94 3.95
3166 4686 1.277557 CCACTCCTCTGGTCAGAAAGG 59.722 57.143 2.13 1.61 36.94 3.11
3167 4687 2.233431 CTCCACTCCTCTGGTCAGAAAG 59.767 54.545 2.13 5.55 36.94 2.62
3168 4688 2.158310 TCTCCACTCCTCTGGTCAGAAA 60.158 50.000 2.13 0.00 36.94 2.52
3169 4689 1.429299 TCTCCACTCCTCTGGTCAGAA 59.571 52.381 2.13 0.00 36.94 3.02
3170 4690 1.076438 TCTCCACTCCTCTGGTCAGA 58.924 55.000 0.45 0.45 35.85 3.27
3171 4691 1.181786 GTCTCCACTCCTCTGGTCAG 58.818 60.000 0.00 0.00 32.50 3.51
3172 4692 0.251832 GGTCTCCACTCCTCTGGTCA 60.252 60.000 0.00 0.00 32.50 4.02
3173 4693 0.040499 AGGTCTCCACTCCTCTGGTC 59.960 60.000 0.00 0.00 32.50 4.02
3174 4694 0.252012 CAGGTCTCCACTCCTCTGGT 60.252 60.000 0.00 0.00 32.50 4.00
3175 4695 1.612395 GCAGGTCTCCACTCCTCTGG 61.612 65.000 0.00 0.00 30.91 3.86
3176 4696 1.612395 GGCAGGTCTCCACTCCTCTG 61.612 65.000 0.00 0.00 30.91 3.35
3177 4697 1.305718 GGCAGGTCTCCACTCCTCT 60.306 63.158 0.00 0.00 30.91 3.69
3178 4698 2.363172 GGGCAGGTCTCCACTCCTC 61.363 68.421 0.00 0.00 30.91 3.71
3179 4699 2.284995 GGGCAGGTCTCCACTCCT 60.285 66.667 0.00 0.00 33.96 3.69
3180 4700 1.492993 AAAGGGCAGGTCTCCACTCC 61.493 60.000 0.00 0.00 0.00 3.85
3181 4701 0.035915 GAAAGGGCAGGTCTCCACTC 60.036 60.000 0.00 0.00 0.00 3.51
3182 4702 0.474660 AGAAAGGGCAGGTCTCCACT 60.475 55.000 0.00 0.00 0.00 4.00
3183 4703 0.402121 AAGAAAGGGCAGGTCTCCAC 59.598 55.000 0.00 0.00 0.00 4.02
3184 4704 1.149101 AAAGAAAGGGCAGGTCTCCA 58.851 50.000 0.00 0.00 0.00 3.86
3185 4705 1.202940 ACAAAGAAAGGGCAGGTCTCC 60.203 52.381 0.00 0.00 0.00 3.71
3186 4706 2.278332 ACAAAGAAAGGGCAGGTCTC 57.722 50.000 0.00 0.00 0.00 3.36
3187 4707 2.175715 AGAACAAAGAAAGGGCAGGTCT 59.824 45.455 0.00 0.00 0.00 3.85
3188 4708 2.587522 AGAACAAAGAAAGGGCAGGTC 58.412 47.619 0.00 0.00 0.00 3.85
3189 4709 2.695147 CAAGAACAAAGAAAGGGCAGGT 59.305 45.455 0.00 0.00 0.00 4.00
3190 4710 2.036346 CCAAGAACAAAGAAAGGGCAGG 59.964 50.000 0.00 0.00 0.00 4.85
3191 4711 2.958355 TCCAAGAACAAAGAAAGGGCAG 59.042 45.455 0.00 0.00 0.00 4.85
3192 4712 3.025322 TCCAAGAACAAAGAAAGGGCA 57.975 42.857 0.00 0.00 0.00 5.36
3193 4713 4.607293 AATCCAAGAACAAAGAAAGGGC 57.393 40.909 0.00 0.00 0.00 5.19
3194 4714 9.860898 CTATTAAATCCAAGAACAAAGAAAGGG 57.139 33.333 0.00 0.00 0.00 3.95
3195 4715 9.860898 CCTATTAAATCCAAGAACAAAGAAAGG 57.139 33.333 0.00 0.00 0.00 3.11
3208 4728 9.952030 GGGAAAACAAATTCCTATTAAATCCAA 57.048 29.630 6.08 0.00 46.66 3.53
3209 4729 9.332713 AGGGAAAACAAATTCCTATTAAATCCA 57.667 29.630 6.08 0.00 46.66 3.41
3212 4732 9.958180 CCAAGGGAAAACAAATTCCTATTAAAT 57.042 29.630 6.08 0.00 46.66 1.40
3213 4733 8.939932 ACCAAGGGAAAACAAATTCCTATTAAA 58.060 29.630 6.08 0.00 46.66 1.52
3214 4734 8.499288 ACCAAGGGAAAACAAATTCCTATTAA 57.501 30.769 6.08 0.00 46.66 1.40
3215 4735 8.499288 AACCAAGGGAAAACAAATTCCTATTA 57.501 30.769 6.08 0.00 46.66 0.98
3216 4736 7.387265 AACCAAGGGAAAACAAATTCCTATT 57.613 32.000 6.08 0.03 46.66 1.73
3217 4737 7.387265 AAACCAAGGGAAAACAAATTCCTAT 57.613 32.000 6.08 0.00 46.66 2.57
3218 4738 6.816616 AAACCAAGGGAAAACAAATTCCTA 57.183 33.333 6.08 0.00 46.66 2.94
3219 4739 5.708736 AAACCAAGGGAAAACAAATTCCT 57.291 34.783 6.08 0.00 46.66 3.36
3220 4740 6.601613 AGAAAAACCAAGGGAAAACAAATTCC 59.398 34.615 0.00 0.00 46.74 3.01
3221 4741 7.552687 AGAGAAAAACCAAGGGAAAACAAATTC 59.447 33.333 0.00 0.00 0.00 2.17
3222 4742 7.402054 AGAGAAAAACCAAGGGAAAACAAATT 58.598 30.769 0.00 0.00 0.00 1.82
3223 4743 6.957631 AGAGAAAAACCAAGGGAAAACAAAT 58.042 32.000 0.00 0.00 0.00 2.32
3224 4744 6.367374 AGAGAAAAACCAAGGGAAAACAAA 57.633 33.333 0.00 0.00 0.00 2.83
3225 4745 5.105106 GGAGAGAAAAACCAAGGGAAAACAA 60.105 40.000 0.00 0.00 0.00 2.83
3226 4746 4.404394 GGAGAGAAAAACCAAGGGAAAACA 59.596 41.667 0.00 0.00 0.00 2.83
3227 4747 4.649674 AGGAGAGAAAAACCAAGGGAAAAC 59.350 41.667 0.00 0.00 0.00 2.43
3228 4748 4.649218 CAGGAGAGAAAAACCAAGGGAAAA 59.351 41.667 0.00 0.00 0.00 2.29
3229 4749 4.215109 CAGGAGAGAAAAACCAAGGGAAA 58.785 43.478 0.00 0.00 0.00 3.13
3230 4750 3.436470 CCAGGAGAGAAAAACCAAGGGAA 60.436 47.826 0.00 0.00 0.00 3.97
3231 4751 2.108250 CCAGGAGAGAAAAACCAAGGGA 59.892 50.000 0.00 0.00 0.00 4.20
3232 4752 2.519013 CCAGGAGAGAAAAACCAAGGG 58.481 52.381 0.00 0.00 0.00 3.95
3233 4753 1.889170 GCCAGGAGAGAAAAACCAAGG 59.111 52.381 0.00 0.00 0.00 3.61
3234 4754 2.555757 CTGCCAGGAGAGAAAAACCAAG 59.444 50.000 0.00 0.00 0.00 3.61
3235 4755 2.586425 CTGCCAGGAGAGAAAAACCAA 58.414 47.619 0.00 0.00 0.00 3.67
3236 4756 1.819305 GCTGCCAGGAGAGAAAAACCA 60.819 52.381 0.00 0.00 0.00 3.67
3237 4757 0.884514 GCTGCCAGGAGAGAAAAACC 59.115 55.000 0.00 0.00 0.00 3.27
3238 4758 1.609208 TGCTGCCAGGAGAGAAAAAC 58.391 50.000 0.00 0.00 0.00 2.43
3239 4759 2.165167 CATGCTGCCAGGAGAGAAAAA 58.835 47.619 0.00 0.00 0.00 1.94
3240 4760 1.615116 CCATGCTGCCAGGAGAGAAAA 60.615 52.381 0.00 0.00 0.00 2.29
3241 4761 0.034767 CCATGCTGCCAGGAGAGAAA 60.035 55.000 0.00 0.00 0.00 2.52
3242 4762 1.605992 CCATGCTGCCAGGAGAGAA 59.394 57.895 0.00 0.00 0.00 2.87
3243 4763 2.372890 CCCATGCTGCCAGGAGAGA 61.373 63.158 8.81 0.00 0.00 3.10
3244 4764 2.192443 CCCATGCTGCCAGGAGAG 59.808 66.667 8.81 0.00 0.00 3.20
3245 4765 2.611800 ACCCATGCTGCCAGGAGA 60.612 61.111 8.81 0.00 0.00 3.71
3246 4766 2.124403 GACCCATGCTGCCAGGAG 60.124 66.667 8.81 2.69 0.00 3.69
3247 4767 4.100084 CGACCCATGCTGCCAGGA 62.100 66.667 8.81 0.00 0.00 3.86
3248 4768 4.100084 TCGACCCATGCTGCCAGG 62.100 66.667 0.00 0.00 0.00 4.45
3249 4769 2.821366 GTCGACCCATGCTGCCAG 60.821 66.667 3.51 0.00 0.00 4.85
3250 4770 3.189376 TTGTCGACCCATGCTGCCA 62.189 57.895 14.12 0.00 0.00 4.92
3251 4771 2.359850 TTGTCGACCCATGCTGCC 60.360 61.111 14.12 0.00 0.00 4.85
3252 4772 1.364626 CTCTTGTCGACCCATGCTGC 61.365 60.000 14.12 0.00 0.00 5.25
3253 4773 1.364626 GCTCTTGTCGACCCATGCTG 61.365 60.000 14.12 0.00 0.00 4.41
3254 4774 1.078848 GCTCTTGTCGACCCATGCT 60.079 57.895 14.12 0.00 0.00 3.79
3255 4775 2.109126 GGCTCTTGTCGACCCATGC 61.109 63.158 14.12 12.08 0.00 4.06
3256 4776 0.742281 CAGGCTCTTGTCGACCCATG 60.742 60.000 14.12 2.26 0.00 3.66
3257 4777 1.194781 ACAGGCTCTTGTCGACCCAT 61.195 55.000 14.12 0.00 0.00 4.00
3258 4778 1.407656 AACAGGCTCTTGTCGACCCA 61.408 55.000 14.12 0.00 0.00 4.51
3259 4779 0.951040 CAACAGGCTCTTGTCGACCC 60.951 60.000 14.12 6.38 0.00 4.46
3260 4780 0.033504 TCAACAGGCTCTTGTCGACC 59.966 55.000 14.12 0.00 0.00 4.79
3261 4781 1.140816 GTCAACAGGCTCTTGTCGAC 58.859 55.000 9.11 9.11 28.90 4.20
3262 4782 1.000163 GAGTCAACAGGCTCTTGTCGA 60.000 52.381 2.38 0.00 0.00 4.20
3263 4783 1.000283 AGAGTCAACAGGCTCTTGTCG 60.000 52.381 2.38 0.00 38.81 4.35
3264 4784 2.298729 AGAGAGTCAACAGGCTCTTGTC 59.701 50.000 0.73 0.00 41.63 3.18
3265 4785 2.324541 AGAGAGTCAACAGGCTCTTGT 58.675 47.619 0.73 0.00 41.63 3.16
3266 4786 3.399440 AAGAGAGTCAACAGGCTCTTG 57.601 47.619 0.00 0.00 43.79 3.02


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

AutoCloner maintained by Alex Coulton.