Multiple sequence alignment - TraesCS2D01G257200

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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 TraesCS2D01G257200 chr2D 100.000 2198 0 0 1 2198 313027178 313024981 0.000000e+00 4060.0
1 TraesCS2D01G257200 chr2D 95.636 275 12 0 1729 2003 423857933 423857659 2.000000e-120 442.0
2 TraesCS2D01G257200 chr2D 94.946 277 12 2 1729 2003 645448000 645448276 1.210000e-117 433.0
3 TraesCS2D01G257200 chr6D 91.676 853 60 11 882 1730 27396237 27397082 0.000000e+00 1171.0
4 TraesCS2D01G257200 chr6D 88.343 875 90 10 865 1730 63799376 63798505 0.000000e+00 1040.0
5 TraesCS2D01G257200 chr6A 90.711 872 77 4 862 1730 605135866 605136736 0.000000e+00 1158.0
6 TraesCS2D01G257200 chr6A 94.946 277 12 2 1729 2003 435593513 435593789 1.210000e-117 433.0
7 TraesCS2D01G257200 chr4D 91.283 803 62 7 932 1730 170689757 170690555 0.000000e+00 1088.0
8 TraesCS2D01G257200 chr1B 92.136 763 51 8 973 1731 151086033 151086790 0.000000e+00 1068.0
9 TraesCS2D01G257200 chr1B 88.462 806 80 9 930 1730 488773528 488772731 0.000000e+00 961.0
10 TraesCS2D01G257200 chr1B 86.499 874 96 21 865 1730 672368476 672369335 0.000000e+00 941.0
11 TraesCS2D01G257200 chr4A 87.671 876 104 4 858 1730 75923535 75924409 0.000000e+00 1016.0
12 TraesCS2D01G257200 chr4A 95.290 276 12 1 1729 2003 600683612 600683337 9.320000e-119 436.0
13 TraesCS2D01G257200 chr3D 88.645 819 74 12 923 1730 587538786 587539596 0.000000e+00 979.0
14 TraesCS2D01G257200 chr3D 85.779 886 76 17 865 1730 166939682 166938827 0.000000e+00 893.0
15 TraesCS2D01G257200 chr2B 87.972 848 65 15 1 819 380307688 380306849 0.000000e+00 966.0
16 TraesCS2D01G257200 chr2B 80.571 875 94 35 865 1689 799441464 799440616 2.410000e-169 604.0
17 TraesCS2D01G257200 chr2B 94.565 92 5 0 865 956 52406099 52406190 2.270000e-30 143.0
18 TraesCS2D01G257200 chr2A 94.685 508 22 3 1 507 424167374 424167877 0.000000e+00 784.0
19 TraesCS2D01G257200 chr2A 92.151 344 21 5 1667 2004 16492311 16491968 4.240000e-132 481.0
20 TraesCS2D01G257200 chr2A 89.730 185 18 1 2014 2198 424169239 424169422 3.650000e-58 235.0
21 TraesCS2D01G257200 chr3A 95.290 276 11 2 1729 2003 444720545 444720819 9.320000e-119 436.0
22 TraesCS2D01G257200 chr7D 94.928 276 14 0 1729 2004 90836634 90836359 1.210000e-117 433.0
23 TraesCS2D01G257200 chr5B 94.946 277 12 2 1729 2004 477961119 477961394 1.210000e-117 433.0
24 TraesCS2D01G257200 chr1A 94.928 276 14 0 1729 2004 369326582 369326307 1.210000e-117 433.0
25 TraesCS2D01G257200 chr1A 90.000 50 5 0 707 756 568649043 568648994 5.070000e-07 65.8


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 TraesCS2D01G257200 chr2D 313024981 313027178 2197 True 4060.0 4060 100.0000 1 2198 1 chr2D.!!$R1 2197
1 TraesCS2D01G257200 chr6D 27396237 27397082 845 False 1171.0 1171 91.6760 882 1730 1 chr6D.!!$F1 848
2 TraesCS2D01G257200 chr6D 63798505 63799376 871 True 1040.0 1040 88.3430 865 1730 1 chr6D.!!$R1 865
3 TraesCS2D01G257200 chr6A 605135866 605136736 870 False 1158.0 1158 90.7110 862 1730 1 chr6A.!!$F2 868
4 TraesCS2D01G257200 chr4D 170689757 170690555 798 False 1088.0 1088 91.2830 932 1730 1 chr4D.!!$F1 798
5 TraesCS2D01G257200 chr1B 151086033 151086790 757 False 1068.0 1068 92.1360 973 1731 1 chr1B.!!$F1 758
6 TraesCS2D01G257200 chr1B 488772731 488773528 797 True 961.0 961 88.4620 930 1730 1 chr1B.!!$R1 800
7 TraesCS2D01G257200 chr1B 672368476 672369335 859 False 941.0 941 86.4990 865 1730 1 chr1B.!!$F2 865
8 TraesCS2D01G257200 chr4A 75923535 75924409 874 False 1016.0 1016 87.6710 858 1730 1 chr4A.!!$F1 872
9 TraesCS2D01G257200 chr3D 587538786 587539596 810 False 979.0 979 88.6450 923 1730 1 chr3D.!!$F1 807
10 TraesCS2D01G257200 chr3D 166938827 166939682 855 True 893.0 893 85.7790 865 1730 1 chr3D.!!$R1 865
11 TraesCS2D01G257200 chr2B 380306849 380307688 839 True 966.0 966 87.9720 1 819 1 chr2B.!!$R1 818
12 TraesCS2D01G257200 chr2B 799440616 799441464 848 True 604.0 604 80.5710 865 1689 1 chr2B.!!$R2 824
13 TraesCS2D01G257200 chr2A 424167374 424169422 2048 False 509.5 784 92.2075 1 2198 2 chr2A.!!$F1 2197

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
858 1914 0.248539 GACATACGTCTGGAGCGACC 60.249 60.0 5.87 0.0 39.22 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 3076 0.03716 TGAGATATGCATGCGGCCAT 59.963 50.0 14.09 3.14 43.89 4.4 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
45 46 2.604046 AGCTAGCCAAACCATAGTCG 57.396 50.000 12.13 0.00 0.00 4.18
105 106 4.662179 ACATCACATCCAATCTGGGACTAT 59.338 41.667 0.00 0.00 40.44 2.12
268 279 3.859411 TGAAACACAACACTTGGAACC 57.141 42.857 0.00 0.00 34.12 3.62
406 436 1.098050 GGGACGAGCAAGCAATCAAT 58.902 50.000 0.00 0.00 0.00 2.57
442 472 1.463056 GATTTCATGAACGCGTGGTGA 59.537 47.619 14.98 14.92 0.00 4.02
580 1635 7.920738 ACATTTCAATTTTAGCGATAGAGACC 58.079 34.615 0.00 0.00 39.76 3.85
599 1654 2.025605 ACCAACACCTCTCATCATGCAT 60.026 45.455 0.00 0.00 0.00 3.96
626 1681 7.547370 GCACTAGAGTAAAAACTGATGTCATCT 59.453 37.037 13.90 0.00 0.00 2.90
675 1730 9.548208 TTTAAAATGTTTTGTTGCTTAAACTGC 57.452 25.926 1.16 0.00 39.70 4.40
695 1750 4.082845 TGCCGGTCTGATTTAAAATCCAA 58.917 39.130 1.90 0.00 0.00 3.53
697 1752 5.163561 TGCCGGTCTGATTTAAAATCCAATC 60.164 40.000 1.90 0.00 0.00 2.67
729 1784 4.452753 GTCGCGACGAGACATTCA 57.547 55.556 25.19 0.00 36.23 2.57
740 1795 6.030849 CGACGAGACATTCAAAACTAGATCT 58.969 40.000 0.00 0.00 0.00 2.75
791 1847 5.013568 TCAAGACAAAAGTTACGAGGACA 57.986 39.130 0.00 0.00 0.00 4.02
792 1848 4.807304 TCAAGACAAAAGTTACGAGGACAC 59.193 41.667 0.00 0.00 0.00 3.67
794 1850 4.369182 AGACAAAAGTTACGAGGACACTG 58.631 43.478 0.00 0.00 0.00 3.66
795 1851 4.098960 AGACAAAAGTTACGAGGACACTGA 59.901 41.667 0.00 0.00 0.00 3.41
796 1852 4.957296 ACAAAAGTTACGAGGACACTGAT 58.043 39.130 0.00 0.00 0.00 2.90
810 1866 7.201794 CGAGGACACTGATAATGTAAGTTAGGA 60.202 40.741 0.00 0.00 0.00 2.94
819 1875 8.642432 TGATAATGTAAGTTAGGACATCTCCAG 58.358 37.037 0.00 0.00 39.39 3.86
822 1878 3.618690 AAGTTAGGACATCTCCAGCAC 57.381 47.619 0.00 0.00 39.39 4.40
825 1881 0.826715 TAGGACATCTCCAGCACTGC 59.173 55.000 0.00 0.00 39.39 4.40
835 1891 0.901580 CCAGCACTGCCCCTCAAAAT 60.902 55.000 0.00 0.00 0.00 1.82
845 1901 1.676006 CCCCTCAAAATGCCGACATAC 59.324 52.381 0.00 0.00 34.62 2.39
848 1904 2.030457 CCTCAAAATGCCGACATACGTC 59.970 50.000 0.00 0.00 40.78 4.34
849 1905 2.930040 CTCAAAATGCCGACATACGTCT 59.070 45.455 0.00 0.00 40.23 4.18
850 1906 2.670905 TCAAAATGCCGACATACGTCTG 59.329 45.455 0.00 0.00 40.23 3.51
851 1907 1.651987 AAATGCCGACATACGTCTGG 58.348 50.000 5.87 0.00 40.23 3.86
852 1908 0.821517 AATGCCGACATACGTCTGGA 59.178 50.000 5.87 0.00 40.23 3.86
853 1909 0.385751 ATGCCGACATACGTCTGGAG 59.614 55.000 5.87 0.00 40.23 3.86
854 1910 1.589196 GCCGACATACGTCTGGAGC 60.589 63.158 5.87 1.63 40.23 4.70
855 1911 1.298413 CCGACATACGTCTGGAGCG 60.298 63.158 5.87 6.11 40.23 5.03
856 1912 1.712018 CCGACATACGTCTGGAGCGA 61.712 60.000 5.87 0.00 40.23 4.93
857 1913 0.589229 CGACATACGTCTGGAGCGAC 60.589 60.000 5.87 0.00 40.23 5.19
858 1914 0.248539 GACATACGTCTGGAGCGACC 60.249 60.000 5.87 0.00 39.22 4.79
859 1915 1.065928 CATACGTCTGGAGCGACCC 59.934 63.158 0.00 0.00 38.00 4.46
860 1916 2.125961 ATACGTCTGGAGCGACCCC 61.126 63.158 0.00 0.00 38.00 4.95
863 1919 3.319198 GTCTGGAGCGACCCCCAA 61.319 66.667 0.00 0.00 38.00 4.12
958 2014 4.671590 TCGTCCCACCTCCTCGCA 62.672 66.667 0.00 0.00 0.00 5.10
959 2015 3.691342 CGTCCCACCTCCTCGCAA 61.691 66.667 0.00 0.00 0.00 4.85
1122 2193 1.987855 GGTGGATCTGGTGTCCCGA 60.988 63.158 0.00 0.00 34.76 5.14
1125 2196 1.987855 GGATCTGGTGTCCCGACCA 60.988 63.158 0.00 0.00 44.09 4.02
1196 2298 4.865761 GCCGGTGCGCACGATCTA 62.866 66.667 32.35 0.00 0.00 1.98
1325 2428 2.267961 GCGAAATCCCTGACCGGT 59.732 61.111 6.92 6.92 0.00 5.28
1371 2501 2.895424 CGTTCCCCTCCTTGCAGGT 61.895 63.158 0.00 0.00 36.53 4.00
1418 2549 0.860901 ACCTTCCCCTAGGTCTCCCT 60.861 60.000 8.29 0.00 45.44 4.20
1604 2735 1.593296 GACTCGCGTAGGTGGAGGTT 61.593 60.000 5.77 0.00 32.11 3.50
1668 2799 3.003113 GCTCGCGTAGGTGGAGGTT 62.003 63.158 5.77 0.00 0.00 3.50
1671 2802 1.005394 CGCGTAGGTGGAGGTTGTT 60.005 57.895 0.00 0.00 0.00 2.83
1701 2832 4.891727 GATGGCGTCGATGGCGGT 62.892 66.667 24.19 16.24 38.28 5.68
1736 2868 4.392138 GGTTGTACCTTAATCTGTGAGTGC 59.608 45.833 0.00 0.00 34.73 4.40
1737 2869 3.845178 TGTACCTTAATCTGTGAGTGCG 58.155 45.455 0.00 0.00 0.00 5.34
1738 2870 3.257375 TGTACCTTAATCTGTGAGTGCGT 59.743 43.478 0.00 0.00 0.00 5.24
1739 2871 2.960819 ACCTTAATCTGTGAGTGCGTC 58.039 47.619 0.00 0.00 0.00 5.19
1740 2872 1.920574 CCTTAATCTGTGAGTGCGTCG 59.079 52.381 0.00 0.00 0.00 5.12
1741 2873 1.321743 CTTAATCTGTGAGTGCGTCGC 59.678 52.381 11.10 11.10 36.09 5.19
1742 2874 0.242555 TAATCTGTGAGTGCGTCGCA 59.757 50.000 17.58 17.58 43.66 5.10
1751 2883 4.893601 TGCGTCGCACCGGTTTGA 62.894 61.111 17.58 1.99 31.71 2.69
1752 2884 4.072088 GCGTCGCACCGGTTTGAG 62.072 66.667 13.44 0.00 0.00 3.02
1753 2885 4.072088 CGTCGCACCGGTTTGAGC 62.072 66.667 2.97 3.98 0.00 4.26
1754 2886 3.723348 GTCGCACCGGTTTGAGCC 61.723 66.667 2.97 0.00 0.00 4.70
1762 2894 3.647771 GGTTTGAGCCCCGGACCT 61.648 66.667 0.73 0.00 0.00 3.85
1763 2895 2.359975 GTTTGAGCCCCGGACCTG 60.360 66.667 0.73 0.00 0.00 4.00
1764 2896 3.646715 TTTGAGCCCCGGACCTGG 61.647 66.667 0.73 0.00 0.00 4.45
1770 2902 4.181010 CCCCGGACCTGGCAGATG 62.181 72.222 17.94 2.11 0.00 2.90
1771 2903 4.181010 CCCGGACCTGGCAGATGG 62.181 72.222 17.94 11.34 0.00 3.51
1772 2904 4.864334 CCGGACCTGGCAGATGGC 62.864 72.222 17.94 1.25 43.74 4.40
1773 2905 3.790437 CGGACCTGGCAGATGGCT 61.790 66.667 17.94 0.00 44.01 4.75
1774 2906 2.191641 GGACCTGGCAGATGGCTC 59.808 66.667 17.94 2.03 44.01 4.70
1775 2907 2.202987 GACCTGGCAGATGGCTCG 60.203 66.667 17.94 0.00 44.01 5.03
1776 2908 3.746949 GACCTGGCAGATGGCTCGG 62.747 68.421 17.94 10.14 44.01 4.63
1777 2909 3.790437 CCTGGCAGATGGCTCGGT 61.790 66.667 17.94 0.00 44.01 4.69
1778 2910 2.202987 CTGGCAGATGGCTCGGTC 60.203 66.667 9.42 0.00 44.01 4.79
1779 2911 4.147449 TGGCAGATGGCTCGGTCG 62.147 66.667 7.95 0.00 44.01 4.79
1780 2912 4.899239 GGCAGATGGCTCGGTCGG 62.899 72.222 0.00 0.00 44.01 4.79
1781 2913 4.899239 GCAGATGGCTCGGTCGGG 62.899 72.222 0.00 0.00 40.25 5.14
1782 2914 4.227134 CAGATGGCTCGGTCGGGG 62.227 72.222 0.00 0.00 0.00 5.73
1800 2932 3.478540 GCCTCCGGCTTTAGATGTT 57.521 52.632 0.00 0.00 46.69 2.71
1801 2933 2.614829 GCCTCCGGCTTTAGATGTTA 57.385 50.000 0.00 0.00 46.69 2.41
1802 2934 2.484889 GCCTCCGGCTTTAGATGTTAG 58.515 52.381 0.00 0.00 46.69 2.34
1803 2935 2.807108 GCCTCCGGCTTTAGATGTTAGG 60.807 54.545 0.00 0.00 46.69 2.69
1804 2936 2.484889 CTCCGGCTTTAGATGTTAGGC 58.515 52.381 0.00 0.00 0.00 3.93
1805 2937 2.103263 CTCCGGCTTTAGATGTTAGGCT 59.897 50.000 0.00 0.00 32.77 4.58
1806 2938 2.504175 TCCGGCTTTAGATGTTAGGCTT 59.496 45.455 0.00 0.00 32.77 4.35
1807 2939 3.707611 TCCGGCTTTAGATGTTAGGCTTA 59.292 43.478 0.00 0.00 32.77 3.09
1808 2940 4.058817 CCGGCTTTAGATGTTAGGCTTAG 58.941 47.826 0.00 0.00 32.77 2.18
1809 2941 4.058817 CGGCTTTAGATGTTAGGCTTAGG 58.941 47.826 0.00 0.00 32.77 2.69
1810 2942 4.443034 CGGCTTTAGATGTTAGGCTTAGGT 60.443 45.833 0.00 0.00 32.77 3.08
1811 2943 4.816925 GGCTTTAGATGTTAGGCTTAGGTG 59.183 45.833 0.00 0.00 0.00 4.00
1812 2944 5.396436 GGCTTTAGATGTTAGGCTTAGGTGA 60.396 44.000 0.00 0.00 0.00 4.02
1813 2945 5.755861 GCTTTAGATGTTAGGCTTAGGTGAG 59.244 44.000 0.00 0.00 0.00 3.51
1814 2946 6.407074 GCTTTAGATGTTAGGCTTAGGTGAGA 60.407 42.308 0.00 0.00 0.00 3.27
1815 2947 6.716934 TTAGATGTTAGGCTTAGGTGAGAG 57.283 41.667 0.00 0.00 0.00 3.20
1816 2948 3.964031 AGATGTTAGGCTTAGGTGAGAGG 59.036 47.826 0.00 0.00 0.00 3.69
1817 2949 3.185880 TGTTAGGCTTAGGTGAGAGGT 57.814 47.619 0.00 0.00 0.00 3.85
1818 2950 3.097614 TGTTAGGCTTAGGTGAGAGGTC 58.902 50.000 0.00 0.00 0.00 3.85
1819 2951 3.245658 TGTTAGGCTTAGGTGAGAGGTCT 60.246 47.826 0.00 0.00 0.00 3.85
1820 2952 1.859302 AGGCTTAGGTGAGAGGTCTG 58.141 55.000 0.00 0.00 0.00 3.51
1821 2953 0.827368 GGCTTAGGTGAGAGGTCTGG 59.173 60.000 0.00 0.00 0.00 3.86
1822 2954 0.827368 GCTTAGGTGAGAGGTCTGGG 59.173 60.000 0.00 0.00 0.00 4.45
1823 2955 1.897647 GCTTAGGTGAGAGGTCTGGGT 60.898 57.143 0.00 0.00 0.00 4.51
1824 2956 2.623502 GCTTAGGTGAGAGGTCTGGGTA 60.624 54.545 0.00 0.00 0.00 3.69
1825 2957 3.917300 CTTAGGTGAGAGGTCTGGGTAT 58.083 50.000 0.00 0.00 0.00 2.73
1826 2958 2.166907 AGGTGAGAGGTCTGGGTATG 57.833 55.000 0.00 0.00 0.00 2.39
1827 2959 1.362932 AGGTGAGAGGTCTGGGTATGT 59.637 52.381 0.00 0.00 0.00 2.29
1828 2960 1.482593 GGTGAGAGGTCTGGGTATGTG 59.517 57.143 0.00 0.00 0.00 3.21
1829 2961 1.482593 GTGAGAGGTCTGGGTATGTGG 59.517 57.143 0.00 0.00 0.00 4.17
1830 2962 0.466124 GAGAGGTCTGGGTATGTGGC 59.534 60.000 0.00 0.00 0.00 5.01
1831 2963 0.983378 AGAGGTCTGGGTATGTGGCC 60.983 60.000 0.00 0.00 0.00 5.36
1832 2964 1.984288 GAGGTCTGGGTATGTGGCCC 61.984 65.000 0.00 0.00 46.26 5.80
1837 2969 2.683475 GGGTATGTGGCCCAGCTT 59.317 61.111 0.00 0.00 45.40 3.74
1838 2970 1.754234 GGGTATGTGGCCCAGCTTG 60.754 63.158 0.00 0.00 45.40 4.01
1839 2971 2.418083 GGTATGTGGCCCAGCTTGC 61.418 63.158 0.00 0.00 0.00 4.01
1840 2972 1.678635 GTATGTGGCCCAGCTTGCA 60.679 57.895 0.00 0.00 0.00 4.08
1841 2973 1.678635 TATGTGGCCCAGCTTGCAC 60.679 57.895 0.00 4.56 0.00 4.57
1847 2979 2.677875 CCCAGCTTGCACCCCTTC 60.678 66.667 0.00 0.00 0.00 3.46
1848 2980 2.115910 CCAGCTTGCACCCCTTCA 59.884 61.111 0.00 0.00 0.00 3.02
1849 2981 1.304713 CCAGCTTGCACCCCTTCAT 60.305 57.895 0.00 0.00 0.00 2.57
1850 2982 1.318158 CCAGCTTGCACCCCTTCATC 61.318 60.000 0.00 0.00 0.00 2.92
1851 2983 0.609957 CAGCTTGCACCCCTTCATCA 60.610 55.000 0.00 0.00 0.00 3.07
1852 2984 0.333993 AGCTTGCACCCCTTCATCAT 59.666 50.000 0.00 0.00 0.00 2.45
1853 2985 1.188863 GCTTGCACCCCTTCATCATT 58.811 50.000 0.00 0.00 0.00 2.57
1854 2986 1.551883 GCTTGCACCCCTTCATCATTT 59.448 47.619 0.00 0.00 0.00 2.32
1855 2987 2.675889 GCTTGCACCCCTTCATCATTTG 60.676 50.000 0.00 0.00 0.00 2.32
1856 2988 1.559368 TGCACCCCTTCATCATTTGG 58.441 50.000 0.00 0.00 0.00 3.28
1857 2989 1.076841 TGCACCCCTTCATCATTTGGA 59.923 47.619 0.00 0.00 0.00 3.53
1858 2990 2.292389 TGCACCCCTTCATCATTTGGAT 60.292 45.455 0.00 0.00 36.39 3.41
1859 2991 3.053019 TGCACCCCTTCATCATTTGGATA 60.053 43.478 0.00 0.00 33.95 2.59
1860 2992 3.571401 GCACCCCTTCATCATTTGGATAG 59.429 47.826 0.00 0.00 33.95 2.08
1861 2993 4.689705 GCACCCCTTCATCATTTGGATAGA 60.690 45.833 0.00 0.00 33.95 1.98
1862 2994 5.448654 CACCCCTTCATCATTTGGATAGAA 58.551 41.667 0.00 0.00 33.95 2.10
1863 2995 5.533903 CACCCCTTCATCATTTGGATAGAAG 59.466 44.000 0.00 0.00 38.94 2.85
1864 2996 5.194537 ACCCCTTCATCATTTGGATAGAAGT 59.805 40.000 0.00 0.00 38.31 3.01
1865 2997 6.389869 ACCCCTTCATCATTTGGATAGAAGTA 59.610 38.462 0.00 0.00 38.31 2.24
1866 2998 6.939163 CCCCTTCATCATTTGGATAGAAGTAG 59.061 42.308 0.00 0.00 38.31 2.57
1867 2999 6.429385 CCCTTCATCATTTGGATAGAAGTAGC 59.571 42.308 0.00 0.00 38.31 3.58
1868 3000 6.146837 CCTTCATCATTTGGATAGAAGTAGCG 59.853 42.308 0.00 0.00 38.31 4.26
1869 3001 5.541845 TCATCATTTGGATAGAAGTAGCGG 58.458 41.667 0.00 0.00 33.95 5.52
1870 3002 3.728845 TCATTTGGATAGAAGTAGCGGC 58.271 45.455 0.00 0.00 0.00 6.53
1871 3003 3.133901 TCATTTGGATAGAAGTAGCGGCA 59.866 43.478 1.45 0.00 0.00 5.69
1872 3004 2.890808 TTGGATAGAAGTAGCGGCAG 57.109 50.000 1.45 0.00 0.00 4.85
1873 3005 2.067365 TGGATAGAAGTAGCGGCAGA 57.933 50.000 1.45 0.00 0.00 4.26
1874 3006 2.598565 TGGATAGAAGTAGCGGCAGAT 58.401 47.619 1.45 0.00 0.00 2.90
1875 3007 2.297315 TGGATAGAAGTAGCGGCAGATG 59.703 50.000 1.45 0.00 0.00 2.90
1876 3008 2.297597 GGATAGAAGTAGCGGCAGATGT 59.702 50.000 1.45 0.00 0.00 3.06
1877 3009 3.243907 GGATAGAAGTAGCGGCAGATGTT 60.244 47.826 1.45 0.00 0.00 2.71
1878 3010 2.015736 AGAAGTAGCGGCAGATGTTG 57.984 50.000 1.45 0.00 0.00 3.33
1897 3029 2.711711 CCAAGATGGCGGATTCAGG 58.288 57.895 0.00 0.00 0.00 3.86
1898 3030 0.107017 CCAAGATGGCGGATTCAGGT 60.107 55.000 0.00 0.00 0.00 4.00
1899 3031 1.140852 CCAAGATGGCGGATTCAGGTA 59.859 52.381 0.00 0.00 0.00 3.08
1900 3032 2.224621 CCAAGATGGCGGATTCAGGTAT 60.225 50.000 0.00 0.00 0.00 2.73
1901 3033 3.007940 CCAAGATGGCGGATTCAGGTATA 59.992 47.826 0.00 0.00 0.00 1.47
1902 3034 4.323792 CCAAGATGGCGGATTCAGGTATAT 60.324 45.833 0.00 0.00 0.00 0.86
1903 3035 5.248640 CAAGATGGCGGATTCAGGTATATT 58.751 41.667 0.00 0.00 0.00 1.28
1904 3036 4.836825 AGATGGCGGATTCAGGTATATTG 58.163 43.478 0.00 0.00 0.00 1.90
1905 3037 4.287067 AGATGGCGGATTCAGGTATATTGT 59.713 41.667 0.00 0.00 0.00 2.71
1906 3038 4.431416 TGGCGGATTCAGGTATATTGTT 57.569 40.909 0.00 0.00 0.00 2.83
1907 3039 4.133820 TGGCGGATTCAGGTATATTGTTG 58.866 43.478 0.00 0.00 0.00 3.33
1908 3040 4.134563 GGCGGATTCAGGTATATTGTTGT 58.865 43.478 0.00 0.00 0.00 3.32
1909 3041 4.578928 GGCGGATTCAGGTATATTGTTGTT 59.421 41.667 0.00 0.00 0.00 2.83
1910 3042 5.277828 GGCGGATTCAGGTATATTGTTGTTC 60.278 44.000 0.00 0.00 0.00 3.18
1911 3043 5.527582 GCGGATTCAGGTATATTGTTGTTCT 59.472 40.000 0.00 0.00 0.00 3.01
1912 3044 6.704493 GCGGATTCAGGTATATTGTTGTTCTA 59.296 38.462 0.00 0.00 0.00 2.10
1913 3045 7.307219 GCGGATTCAGGTATATTGTTGTTCTAC 60.307 40.741 0.00 0.00 0.00 2.59
1914 3046 7.926555 CGGATTCAGGTATATTGTTGTTCTACT 59.073 37.037 0.00 0.00 0.00 2.57
1915 3047 9.614792 GGATTCAGGTATATTGTTGTTCTACTT 57.385 33.333 0.00 0.00 0.00 2.24
1918 3050 9.787435 TTCAGGTATATTGTTGTTCTACTTTGT 57.213 29.630 0.00 0.00 0.00 2.83
1925 3057 6.930667 TTGTTGTTCTACTTTGTAAGGTCC 57.069 37.500 0.00 0.00 0.00 4.46
1926 3058 6.243216 TGTTGTTCTACTTTGTAAGGTCCT 57.757 37.500 0.00 0.00 0.00 3.85
1927 3059 6.285990 TGTTGTTCTACTTTGTAAGGTCCTC 58.714 40.000 0.00 0.00 0.00 3.71
1928 3060 5.130292 TGTTCTACTTTGTAAGGTCCTCG 57.870 43.478 0.00 0.00 0.00 4.63
1929 3061 4.828939 TGTTCTACTTTGTAAGGTCCTCGA 59.171 41.667 0.00 0.00 0.00 4.04
1930 3062 5.048224 TGTTCTACTTTGTAAGGTCCTCGAG 60.048 44.000 5.13 5.13 0.00 4.04
1931 3063 4.914983 TCTACTTTGTAAGGTCCTCGAGA 58.085 43.478 15.71 0.00 0.00 4.04
1932 3064 5.319453 TCTACTTTGTAAGGTCCTCGAGAA 58.681 41.667 15.71 0.00 0.00 2.87
1933 3065 5.950549 TCTACTTTGTAAGGTCCTCGAGAAT 59.049 40.000 15.71 0.00 0.00 2.40
1934 3066 7.114754 TCTACTTTGTAAGGTCCTCGAGAATA 58.885 38.462 15.71 0.00 0.00 1.75
1935 3067 6.600882 ACTTTGTAAGGTCCTCGAGAATAA 57.399 37.500 15.71 0.00 0.00 1.40
1936 3068 7.184067 ACTTTGTAAGGTCCTCGAGAATAAT 57.816 36.000 15.71 0.00 0.00 1.28
1937 3069 7.621796 ACTTTGTAAGGTCCTCGAGAATAATT 58.378 34.615 15.71 4.65 0.00 1.40
1938 3070 8.755977 ACTTTGTAAGGTCCTCGAGAATAATTA 58.244 33.333 15.71 3.67 0.00 1.40
1939 3071 9.595823 CTTTGTAAGGTCCTCGAGAATAATTAA 57.404 33.333 15.71 0.00 0.00 1.40
1948 3080 9.827411 GTCCTCGAGAATAATTAATAAAATGGC 57.173 33.333 15.71 0.00 0.00 4.40
1949 3081 9.010029 TCCTCGAGAATAATTAATAAAATGGCC 57.990 33.333 15.71 0.00 0.00 5.36
1950 3082 7.962918 CCTCGAGAATAATTAATAAAATGGCCG 59.037 37.037 15.71 0.00 0.00 6.13
1951 3083 7.302524 TCGAGAATAATTAATAAAATGGCCGC 58.697 34.615 0.00 0.00 0.00 6.53
1952 3084 7.041030 TCGAGAATAATTAATAAAATGGCCGCA 60.041 33.333 0.00 0.00 0.00 5.69
1953 3085 7.754924 CGAGAATAATTAATAAAATGGCCGCAT 59.245 33.333 0.00 0.00 0.00 4.73
1954 3086 8.761575 AGAATAATTAATAAAATGGCCGCATG 57.238 30.769 0.00 0.00 0.00 4.06
1955 3087 6.966435 ATAATTAATAAAATGGCCGCATGC 57.034 33.333 7.91 7.91 40.16 4.06
1956 3088 3.808466 TTAATAAAATGGCCGCATGCA 57.192 38.095 19.57 0.00 43.89 3.96
1957 3089 2.914695 AATAAAATGGCCGCATGCAT 57.085 40.000 19.57 0.00 43.89 3.96
1958 3090 5.459536 TTAATAAAATGGCCGCATGCATA 57.540 34.783 19.57 0.19 43.89 3.14
1959 3091 4.540359 AATAAAATGGCCGCATGCATAT 57.460 36.364 19.57 2.82 43.89 1.78
1960 3092 2.443887 AAAATGGCCGCATGCATATC 57.556 45.000 19.57 4.47 43.89 1.63
1961 3093 1.624336 AAATGGCCGCATGCATATCT 58.376 45.000 19.57 0.00 43.89 1.98
1962 3094 1.171308 AATGGCCGCATGCATATCTC 58.829 50.000 19.57 1.17 43.89 2.75
1963 3095 0.037160 ATGGCCGCATGCATATCTCA 59.963 50.000 19.57 7.02 43.89 3.27
1964 3096 0.604511 TGGCCGCATGCATATCTCAG 60.605 55.000 19.57 0.00 43.89 3.35
1965 3097 0.321034 GGCCGCATGCATATCTCAGA 60.321 55.000 19.57 0.00 43.89 3.27
1966 3098 1.678123 GGCCGCATGCATATCTCAGAT 60.678 52.381 19.57 0.00 43.89 2.90
1967 3099 1.397343 GCCGCATGCATATCTCAGATG 59.603 52.381 19.57 0.00 40.77 2.90
1975 3107 2.975266 CATATCTCAGATGCAGAGGCC 58.025 52.381 0.00 0.00 40.13 5.19
1976 3108 0.964700 TATCTCAGATGCAGAGGCCG 59.035 55.000 0.00 0.00 40.13 6.13
1977 3109 1.756408 ATCTCAGATGCAGAGGCCGG 61.756 60.000 0.00 0.00 40.13 6.13
1978 3110 3.457625 CTCAGATGCAGAGGCCGGG 62.458 68.421 2.18 0.00 40.13 5.73
1979 3111 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
1985 3117 3.866582 CAGAGGCCGGGGGTCATC 61.867 72.222 2.18 0.00 0.00 2.92
1995 3127 2.709992 GGGGTCATCCTCCTTTCCA 58.290 57.895 0.00 0.00 35.33 3.53
1996 3128 0.999712 GGGGTCATCCTCCTTTCCAA 59.000 55.000 0.00 0.00 35.33 3.53
1997 3129 1.357761 GGGGTCATCCTCCTTTCCAAA 59.642 52.381 0.00 0.00 35.33 3.28
1998 3130 2.225267 GGGGTCATCCTCCTTTCCAAAA 60.225 50.000 0.00 0.00 35.33 2.44
1999 3131 3.506398 GGGTCATCCTCCTTTCCAAAAA 58.494 45.455 0.00 0.00 0.00 1.94
2015 3147 4.442018 AAAAACGTCCGGAGCGAA 57.558 50.000 26.02 0.00 0.00 4.70
2016 3148 1.936658 AAAAACGTCCGGAGCGAAC 59.063 52.632 26.02 6.78 0.00 3.95
2017 3149 0.531311 AAAAACGTCCGGAGCGAACT 60.531 50.000 26.02 11.78 0.00 3.01
2018 3150 1.219522 AAAACGTCCGGAGCGAACTG 61.220 55.000 26.02 6.90 0.00 3.16
2019 3151 2.359570 AAACGTCCGGAGCGAACTGT 62.360 55.000 26.02 7.43 0.00 3.55
2020 3152 2.504244 CGTCCGGAGCGAACTGTC 60.504 66.667 17.91 0.00 0.00 3.51
2059 3191 7.492344 GCCAAAATGTGAACCCTTATTTATCTG 59.508 37.037 0.00 0.00 0.00 2.90
2065 3197 4.080807 TGAACCCTTATTTATCTGCGGACA 60.081 41.667 0.00 0.00 0.00 4.02
2067 3199 3.199071 ACCCTTATTTATCTGCGGACACA 59.801 43.478 0.00 0.00 0.00 3.72
2087 3219 0.391130 TCCGCTTGTCTGAATTCCCG 60.391 55.000 2.27 0.00 0.00 5.14
2092 3224 2.682856 GCTTGTCTGAATTCCCGCATAA 59.317 45.455 2.27 0.00 0.00 1.90
2108 3240 2.223572 GCATAATGAGGGAGTTTTGCGG 60.224 50.000 0.00 0.00 0.00 5.69
2110 3242 0.112412 AATGAGGGAGTTTTGCGGGT 59.888 50.000 0.00 0.00 0.00 5.28
2137 3269 0.105039 CCTCCGCAACATAGGACTCC 59.895 60.000 0.00 0.00 31.64 3.85
2168 3300 0.614697 CCAACTCAAATCCCCCACCC 60.615 60.000 0.00 0.00 0.00 4.61
2172 3304 1.621205 TCAAATCCCCCACCCGGAT 60.621 57.895 0.73 0.00 42.12 4.18
2191 3323 4.752101 CGGATCACTTTTCTTTCACTCTGT 59.248 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.104451 AGAGGGAGATGTGATGTGATGC 59.896 50.000 0.00 0.00 0.00 3.91
105 106 1.405105 GGCGCCATTTGCATCTTTCTA 59.595 47.619 24.80 0.00 41.33 2.10
268 279 5.950883 TGAAGTATTAGTCAGAGACAACCG 58.049 41.667 0.00 0.00 34.60 4.44
342 354 4.403752 CACAGGTGAGACCATTGATCTCTA 59.596 45.833 9.46 0.00 41.95 2.43
442 472 1.593196 CGTCCCCACGCAATTCATAT 58.407 50.000 0.00 0.00 39.69 1.78
553 1608 9.214953 GTCTCTATCGCTAAAATTGAAATGTTG 57.785 33.333 0.00 0.00 0.00 3.33
580 1635 2.223502 GCATGCATGATGAGAGGTGTTG 60.224 50.000 30.64 0.00 33.31 3.33
599 1654 6.521162 TGACATCAGTTTTTACTCTAGTGCA 58.479 36.000 0.00 0.00 0.00 4.57
673 1728 3.691575 TGGATTTTAAATCAGACCGGCA 58.308 40.909 17.92 3.77 0.00 5.69
675 1730 6.699575 AGATTGGATTTTAAATCAGACCGG 57.300 37.500 17.92 0.00 35.63 5.28
695 1750 2.290641 GCGACGGATTTAATGGCAAGAT 59.709 45.455 0.00 0.00 0.00 2.40
697 1752 1.594518 CGCGACGGATTTAATGGCAAG 60.595 52.381 0.00 0.00 0.00 4.01
762 1818 8.129211 CCTCGTAACTTTTGTCTTGAGAAAAAT 58.871 33.333 7.03 0.00 31.87 1.82
771 1827 4.809426 CAGTGTCCTCGTAACTTTTGTCTT 59.191 41.667 0.00 0.00 0.00 3.01
772 1828 4.098960 TCAGTGTCCTCGTAACTTTTGTCT 59.901 41.667 0.00 0.00 0.00 3.41
775 1831 7.117812 ACATTATCAGTGTCCTCGTAACTTTTG 59.882 37.037 0.00 0.00 0.00 2.44
783 1839 5.916661 ACTTACATTATCAGTGTCCTCGT 57.083 39.130 0.00 0.00 0.00 4.18
785 1841 7.921745 GTCCTAACTTACATTATCAGTGTCCTC 59.078 40.741 0.00 0.00 0.00 3.71
791 1847 8.643324 GGAGATGTCCTAACTTACATTATCAGT 58.357 37.037 0.54 0.00 40.17 3.41
792 1848 8.642432 TGGAGATGTCCTAACTTACATTATCAG 58.358 37.037 10.72 0.00 44.30 2.90
794 1850 7.600752 GCTGGAGATGTCCTAACTTACATTATC 59.399 40.741 10.72 0.00 44.30 1.75
795 1851 7.071196 TGCTGGAGATGTCCTAACTTACATTAT 59.929 37.037 10.72 0.00 44.30 1.28
796 1852 6.382859 TGCTGGAGATGTCCTAACTTACATTA 59.617 38.462 10.72 0.00 44.30 1.90
810 1866 2.673523 GGGCAGTGCTGGAGATGT 59.326 61.111 16.11 0.00 0.00 3.06
819 1875 1.079612 GCATTTTGAGGGGCAGTGC 60.080 57.895 6.55 6.55 0.00 4.40
822 1878 1.678635 TCGGCATTTTGAGGGGCAG 60.679 57.895 0.00 0.00 0.00 4.85
825 1881 1.676006 GTATGTCGGCATTTTGAGGGG 59.324 52.381 8.30 0.00 36.58 4.79
848 1904 3.316573 GAGTTGGGGGTCGCTCCAG 62.317 68.421 0.00 0.00 38.11 3.86
849 1905 3.319198 GAGTTGGGGGTCGCTCCA 61.319 66.667 0.00 0.00 38.11 3.86
850 1906 3.003763 AGAGTTGGGGGTCGCTCC 61.004 66.667 0.00 0.00 0.00 4.70
851 1907 2.579738 GAGAGTTGGGGGTCGCTC 59.420 66.667 0.00 0.00 0.00 5.03
852 1908 3.382832 CGAGAGTTGGGGGTCGCT 61.383 66.667 0.00 0.00 0.00 4.93
854 1910 4.796231 CGCGAGAGTTGGGGGTCG 62.796 72.222 0.00 0.00 35.51 4.79
855 1911 3.379445 TCGCGAGAGTTGGGGGTC 61.379 66.667 3.71 0.00 34.84 4.46
856 1912 3.692406 GTCGCGAGAGTTGGGGGT 61.692 66.667 10.24 0.00 43.49 4.95
857 1913 4.452733 GGTCGCGAGAGTTGGGGG 62.453 72.222 10.24 0.00 43.49 5.40
858 1914 4.452733 GGGTCGCGAGAGTTGGGG 62.453 72.222 10.24 0.00 43.49 4.96
859 1915 4.452733 GGGGTCGCGAGAGTTGGG 62.453 72.222 10.24 0.00 43.49 4.12
860 1916 4.452733 GGGGGTCGCGAGAGTTGG 62.453 72.222 10.24 0.00 43.49 3.77
1189 2291 2.913060 GGGGAGGCGCTAGATCGT 60.913 66.667 7.64 0.00 0.00 3.73
1252 2354 2.207924 AGAACCGGCGACCAAGAGT 61.208 57.895 9.30 0.00 0.00 3.24
1371 2501 3.574396 GAGGAGATCAATCCATACCGACA 59.426 47.826 3.98 0.00 42.26 4.35
1418 2549 3.306472 ACAAAGTTAGGGCTTTCACCA 57.694 42.857 0.00 0.00 36.64 4.17
1541 2672 0.904865 CCATGCTAGGATAGGGCCGA 60.905 60.000 0.00 0.00 39.70 5.54
1668 2799 0.306228 CATCACGACGCCAAACAACA 59.694 50.000 0.00 0.00 0.00 3.33
1671 2802 2.612567 GCCATCACGACGCCAAACA 61.613 57.895 0.00 0.00 0.00 2.83
1734 2866 4.893601 TCAAACCGGTGCGACGCA 62.894 61.111 20.50 20.50 35.60 5.24
1735 2867 4.072088 CTCAAACCGGTGCGACGC 62.072 66.667 8.52 14.19 0.00 5.19
1736 2868 4.072088 GCTCAAACCGGTGCGACG 62.072 66.667 8.52 3.44 0.00 5.12
1737 2869 3.723348 GGCTCAAACCGGTGCGAC 61.723 66.667 8.52 2.92 0.00 5.19
1745 2877 3.647771 AGGTCCGGGGCTCAAACC 61.648 66.667 0.00 0.00 0.00 3.27
1746 2878 2.359975 CAGGTCCGGGGCTCAAAC 60.360 66.667 0.00 0.00 0.00 2.93
1747 2879 3.646715 CCAGGTCCGGGGCTCAAA 61.647 66.667 0.00 0.00 0.00 2.69
1753 2885 4.181010 CATCTGCCAGGTCCGGGG 62.181 72.222 10.37 4.20 0.00 5.73
1754 2886 4.181010 CCATCTGCCAGGTCCGGG 62.181 72.222 0.00 3.19 0.00 5.73
1755 2887 4.864334 GCCATCTGCCAGGTCCGG 62.864 72.222 0.00 0.00 0.00 5.14
1756 2888 3.746949 GAGCCATCTGCCAGGTCCG 62.747 68.421 0.00 0.00 42.71 4.79
1757 2889 2.191641 GAGCCATCTGCCAGGTCC 59.808 66.667 0.00 0.00 42.71 4.46
1758 2890 2.202987 CGAGCCATCTGCCAGGTC 60.203 66.667 0.00 0.00 42.71 3.85
1759 2891 3.790437 CCGAGCCATCTGCCAGGT 61.790 66.667 0.00 0.00 42.71 4.00
1760 2892 3.746949 GACCGAGCCATCTGCCAGG 62.747 68.421 0.00 0.00 42.71 4.45
1761 2893 2.202987 GACCGAGCCATCTGCCAG 60.203 66.667 0.00 0.00 42.71 4.85
1762 2894 4.147449 CGACCGAGCCATCTGCCA 62.147 66.667 0.00 0.00 42.71 4.92
1763 2895 4.899239 CCGACCGAGCCATCTGCC 62.899 72.222 0.00 0.00 42.71 4.85
1764 2896 4.899239 CCCGACCGAGCCATCTGC 62.899 72.222 0.00 0.00 41.71 4.26
1765 2897 4.227134 CCCCGACCGAGCCATCTG 62.227 72.222 0.00 0.00 0.00 2.90
1784 2916 2.103263 AGCCTAACATCTAAAGCCGGAG 59.897 50.000 5.05 0.00 0.00 4.63
1785 2917 2.116238 AGCCTAACATCTAAAGCCGGA 58.884 47.619 5.05 0.00 0.00 5.14
1786 2918 2.622064 AGCCTAACATCTAAAGCCGG 57.378 50.000 0.00 0.00 0.00 6.13
1787 2919 4.058817 CCTAAGCCTAACATCTAAAGCCG 58.941 47.826 0.00 0.00 0.00 5.52
1788 2920 4.816925 CACCTAAGCCTAACATCTAAAGCC 59.183 45.833 0.00 0.00 0.00 4.35
1789 2921 5.671493 TCACCTAAGCCTAACATCTAAAGC 58.329 41.667 0.00 0.00 0.00 3.51
1790 2922 7.113658 TCTCACCTAAGCCTAACATCTAAAG 57.886 40.000 0.00 0.00 0.00 1.85
1791 2923 6.098409 CCTCTCACCTAAGCCTAACATCTAAA 59.902 42.308 0.00 0.00 0.00 1.85
1792 2924 5.598830 CCTCTCACCTAAGCCTAACATCTAA 59.401 44.000 0.00 0.00 0.00 2.10
1793 2925 5.141182 CCTCTCACCTAAGCCTAACATCTA 58.859 45.833 0.00 0.00 0.00 1.98
1794 2926 3.964031 CCTCTCACCTAAGCCTAACATCT 59.036 47.826 0.00 0.00 0.00 2.90
1795 2927 3.707102 ACCTCTCACCTAAGCCTAACATC 59.293 47.826 0.00 0.00 0.00 3.06
1796 2928 3.707102 GACCTCTCACCTAAGCCTAACAT 59.293 47.826 0.00 0.00 0.00 2.71
1797 2929 3.097614 GACCTCTCACCTAAGCCTAACA 58.902 50.000 0.00 0.00 0.00 2.41
1798 2930 3.131400 CAGACCTCTCACCTAAGCCTAAC 59.869 52.174 0.00 0.00 0.00 2.34
1799 2931 3.366396 CAGACCTCTCACCTAAGCCTAA 58.634 50.000 0.00 0.00 0.00 2.69
1800 2932 2.358300 CCAGACCTCTCACCTAAGCCTA 60.358 54.545 0.00 0.00 0.00 3.93
1801 2933 1.621072 CCAGACCTCTCACCTAAGCCT 60.621 57.143 0.00 0.00 0.00 4.58
1802 2934 0.827368 CCAGACCTCTCACCTAAGCC 59.173 60.000 0.00 0.00 0.00 4.35
1803 2935 0.827368 CCCAGACCTCTCACCTAAGC 59.173 60.000 0.00 0.00 0.00 3.09
1804 2936 2.239681 ACCCAGACCTCTCACCTAAG 57.760 55.000 0.00 0.00 0.00 2.18
1805 2937 3.012502 ACATACCCAGACCTCTCACCTAA 59.987 47.826 0.00 0.00 0.00 2.69
1806 2938 2.585900 ACATACCCAGACCTCTCACCTA 59.414 50.000 0.00 0.00 0.00 3.08
1807 2939 1.362932 ACATACCCAGACCTCTCACCT 59.637 52.381 0.00 0.00 0.00 4.00
1808 2940 1.482593 CACATACCCAGACCTCTCACC 59.517 57.143 0.00 0.00 0.00 4.02
1809 2941 1.482593 CCACATACCCAGACCTCTCAC 59.517 57.143 0.00 0.00 0.00 3.51
1810 2942 1.866015 CCACATACCCAGACCTCTCA 58.134 55.000 0.00 0.00 0.00 3.27
1811 2943 0.466124 GCCACATACCCAGACCTCTC 59.534 60.000 0.00 0.00 0.00 3.20
1812 2944 0.983378 GGCCACATACCCAGACCTCT 60.983 60.000 0.00 0.00 0.00 3.69
1813 2945 1.527370 GGCCACATACCCAGACCTC 59.473 63.158 0.00 0.00 0.00 3.85
1814 2946 3.741325 GGCCACATACCCAGACCT 58.259 61.111 0.00 0.00 0.00 3.85
1821 2953 2.418083 GCAAGCTGGGCCACATACC 61.418 63.158 0.00 0.00 0.00 2.73
1822 2954 1.678635 TGCAAGCTGGGCCACATAC 60.679 57.895 0.00 0.00 0.00 2.39
1823 2955 1.678635 GTGCAAGCTGGGCCACATA 60.679 57.895 0.00 0.00 0.00 2.29
1824 2956 2.993264 GTGCAAGCTGGGCCACAT 60.993 61.111 0.00 0.00 0.00 3.21
1830 2962 2.677875 GAAGGGGTGCAAGCTGGG 60.678 66.667 0.00 0.00 0.00 4.45
1831 2963 1.304713 ATGAAGGGGTGCAAGCTGG 60.305 57.895 0.00 0.00 0.00 4.85
1832 2964 0.609957 TGATGAAGGGGTGCAAGCTG 60.610 55.000 0.00 0.00 0.00 4.24
1833 2965 0.333993 ATGATGAAGGGGTGCAAGCT 59.666 50.000 0.00 0.00 0.00 3.74
1834 2966 1.188863 AATGATGAAGGGGTGCAAGC 58.811 50.000 0.00 0.00 0.00 4.01
1835 2967 2.093869 CCAAATGATGAAGGGGTGCAAG 60.094 50.000 0.00 0.00 0.00 4.01
1836 2968 1.901159 CCAAATGATGAAGGGGTGCAA 59.099 47.619 0.00 0.00 0.00 4.08
1837 2969 1.076841 TCCAAATGATGAAGGGGTGCA 59.923 47.619 0.00 0.00 0.00 4.57
1838 2970 1.851304 TCCAAATGATGAAGGGGTGC 58.149 50.000 0.00 0.00 0.00 5.01
1839 2971 5.052693 TCTATCCAAATGATGAAGGGGTG 57.947 43.478 0.00 0.00 34.76 4.61
1840 2972 5.194537 ACTTCTATCCAAATGATGAAGGGGT 59.805 40.000 0.00 0.00 39.87 4.95
1841 2973 5.699143 ACTTCTATCCAAATGATGAAGGGG 58.301 41.667 0.00 0.00 39.87 4.79
1842 2974 6.429385 GCTACTTCTATCCAAATGATGAAGGG 59.571 42.308 0.00 0.00 39.87 3.95
1843 2975 6.146837 CGCTACTTCTATCCAAATGATGAAGG 59.853 42.308 0.00 0.00 39.87 3.46
1844 2976 6.146837 CCGCTACTTCTATCCAAATGATGAAG 59.853 42.308 0.00 0.00 40.55 3.02
1845 2977 5.991606 CCGCTACTTCTATCCAAATGATGAA 59.008 40.000 0.00 0.00 34.76 2.57
1846 2978 5.541845 CCGCTACTTCTATCCAAATGATGA 58.458 41.667 0.00 0.00 34.76 2.92
1847 2979 4.153117 GCCGCTACTTCTATCCAAATGATG 59.847 45.833 0.00 0.00 34.76 3.07
1848 2980 4.202357 TGCCGCTACTTCTATCCAAATGAT 60.202 41.667 0.00 0.00 37.49 2.45
1849 2981 3.133901 TGCCGCTACTTCTATCCAAATGA 59.866 43.478 0.00 0.00 0.00 2.57
1850 2982 3.466836 TGCCGCTACTTCTATCCAAATG 58.533 45.455 0.00 0.00 0.00 2.32
1851 2983 3.388024 TCTGCCGCTACTTCTATCCAAAT 59.612 43.478 0.00 0.00 0.00 2.32
1852 2984 2.764010 TCTGCCGCTACTTCTATCCAAA 59.236 45.455 0.00 0.00 0.00 3.28
1853 2985 2.384828 TCTGCCGCTACTTCTATCCAA 58.615 47.619 0.00 0.00 0.00 3.53
1854 2986 2.067365 TCTGCCGCTACTTCTATCCA 57.933 50.000 0.00 0.00 0.00 3.41
1855 2987 2.297597 ACATCTGCCGCTACTTCTATCC 59.702 50.000 0.00 0.00 0.00 2.59
1856 2988 3.651803 ACATCTGCCGCTACTTCTATC 57.348 47.619 0.00 0.00 0.00 2.08
1857 2989 3.722147 CAACATCTGCCGCTACTTCTAT 58.278 45.455 0.00 0.00 0.00 1.98
1858 2990 2.738643 GCAACATCTGCCGCTACTTCTA 60.739 50.000 0.00 0.00 46.13 2.10
1859 2991 2.009042 GCAACATCTGCCGCTACTTCT 61.009 52.381 0.00 0.00 46.13 2.85
1860 2992 0.375106 GCAACATCTGCCGCTACTTC 59.625 55.000 0.00 0.00 46.13 3.01
1861 2993 2.471255 GCAACATCTGCCGCTACTT 58.529 52.632 0.00 0.00 46.13 2.24
1862 2994 4.208632 GCAACATCTGCCGCTACT 57.791 55.556 0.00 0.00 46.13 2.57
1879 3011 0.107017 ACCTGAATCCGCCATCTTGG 60.107 55.000 0.00 0.00 41.55 3.61
1880 3012 2.620251 TACCTGAATCCGCCATCTTG 57.380 50.000 0.00 0.00 0.00 3.02
1881 3013 5.221925 ACAATATACCTGAATCCGCCATCTT 60.222 40.000 0.00 0.00 0.00 2.40
1882 3014 4.287067 ACAATATACCTGAATCCGCCATCT 59.713 41.667 0.00 0.00 0.00 2.90
1883 3015 4.579869 ACAATATACCTGAATCCGCCATC 58.420 43.478 0.00 0.00 0.00 3.51
1884 3016 4.640771 ACAATATACCTGAATCCGCCAT 57.359 40.909 0.00 0.00 0.00 4.40
1885 3017 4.133820 CAACAATATACCTGAATCCGCCA 58.866 43.478 0.00 0.00 0.00 5.69
1886 3018 4.134563 ACAACAATATACCTGAATCCGCC 58.865 43.478 0.00 0.00 0.00 6.13
1887 3019 5.527582 AGAACAACAATATACCTGAATCCGC 59.472 40.000 0.00 0.00 0.00 5.54
1888 3020 7.926555 AGTAGAACAACAATATACCTGAATCCG 59.073 37.037 0.00 0.00 0.00 4.18
1889 3021 9.614792 AAGTAGAACAACAATATACCTGAATCC 57.385 33.333 0.00 0.00 0.00 3.01
1892 3024 9.787435 ACAAAGTAGAACAACAATATACCTGAA 57.213 29.630 0.00 0.00 0.00 3.02
1899 3031 9.227777 GGACCTTACAAAGTAGAACAACAATAT 57.772 33.333 0.00 0.00 0.00 1.28
1900 3032 8.434392 AGGACCTTACAAAGTAGAACAACAATA 58.566 33.333 0.00 0.00 0.00 1.90
1901 3033 7.287810 AGGACCTTACAAAGTAGAACAACAAT 58.712 34.615 0.00 0.00 0.00 2.71
1902 3034 6.655930 AGGACCTTACAAAGTAGAACAACAA 58.344 36.000 0.00 0.00 0.00 2.83
1903 3035 6.243216 AGGACCTTACAAAGTAGAACAACA 57.757 37.500 0.00 0.00 0.00 3.33
1904 3036 5.404667 CGAGGACCTTACAAAGTAGAACAAC 59.595 44.000 0.00 0.00 0.00 3.32
1905 3037 5.302568 TCGAGGACCTTACAAAGTAGAACAA 59.697 40.000 0.00 0.00 0.00 2.83
1906 3038 4.828939 TCGAGGACCTTACAAAGTAGAACA 59.171 41.667 0.00 0.00 0.00 3.18
1907 3039 5.182760 TCTCGAGGACCTTACAAAGTAGAAC 59.817 44.000 13.56 0.00 0.00 3.01
1908 3040 5.319453 TCTCGAGGACCTTACAAAGTAGAA 58.681 41.667 13.56 0.00 0.00 2.10
1909 3041 4.914983 TCTCGAGGACCTTACAAAGTAGA 58.085 43.478 13.56 0.00 0.00 2.59
1910 3042 5.640189 TTCTCGAGGACCTTACAAAGTAG 57.360 43.478 13.56 0.00 0.00 2.57
1911 3043 7.707624 TTATTCTCGAGGACCTTACAAAGTA 57.292 36.000 13.56 0.00 0.00 2.24
1912 3044 6.600882 TTATTCTCGAGGACCTTACAAAGT 57.399 37.500 13.56 0.00 0.00 2.66
1913 3045 9.595823 TTAATTATTCTCGAGGACCTTACAAAG 57.404 33.333 13.56 0.00 0.00 2.77
1922 3054 9.827411 GCCATTTTATTAATTATTCTCGAGGAC 57.173 33.333 13.56 0.00 0.00 3.85
1923 3055 9.010029 GGCCATTTTATTAATTATTCTCGAGGA 57.990 33.333 13.56 3.44 0.00 3.71
1924 3056 7.962918 CGGCCATTTTATTAATTATTCTCGAGG 59.037 37.037 13.56 0.00 0.00 4.63
1925 3057 7.481798 GCGGCCATTTTATTAATTATTCTCGAG 59.518 37.037 5.93 5.93 0.00 4.04
1926 3058 7.041030 TGCGGCCATTTTATTAATTATTCTCGA 60.041 33.333 2.24 0.00 0.00 4.04
1927 3059 7.081349 TGCGGCCATTTTATTAATTATTCTCG 58.919 34.615 2.24 0.00 0.00 4.04
1928 3060 8.863049 CATGCGGCCATTTTATTAATTATTCTC 58.137 33.333 2.24 0.00 0.00 2.87
1929 3061 7.331687 GCATGCGGCCATTTTATTAATTATTCT 59.668 33.333 0.00 0.00 36.11 2.40
1930 3062 7.117523 TGCATGCGGCCATTTTATTAATTATTC 59.882 33.333 14.09 0.00 43.89 1.75
1931 3063 6.933521 TGCATGCGGCCATTTTATTAATTATT 59.066 30.769 14.09 0.00 43.89 1.40
1932 3064 6.462500 TGCATGCGGCCATTTTATTAATTAT 58.538 32.000 14.09 0.00 43.89 1.28
1933 3065 5.847304 TGCATGCGGCCATTTTATTAATTA 58.153 33.333 14.09 0.00 43.89 1.40
1934 3066 4.701765 TGCATGCGGCCATTTTATTAATT 58.298 34.783 14.09 0.00 43.89 1.40
1935 3067 4.333913 TGCATGCGGCCATTTTATTAAT 57.666 36.364 14.09 0.00 43.89 1.40
1936 3068 3.808466 TGCATGCGGCCATTTTATTAA 57.192 38.095 14.09 0.00 43.89 1.40
1937 3069 5.418524 AGATATGCATGCGGCCATTTTATTA 59.581 36.000 14.09 0.00 43.89 0.98
1938 3070 2.914695 ATGCATGCGGCCATTTTATT 57.085 40.000 14.09 0.00 43.89 1.40
1939 3071 3.765511 AGATATGCATGCGGCCATTTTAT 59.234 39.130 14.09 0.00 43.89 1.40
1940 3072 3.156293 AGATATGCATGCGGCCATTTTA 58.844 40.909 14.09 0.00 43.89 1.52
1941 3073 1.965643 AGATATGCATGCGGCCATTTT 59.034 42.857 14.09 0.00 43.89 1.82
1942 3074 1.542915 GAGATATGCATGCGGCCATTT 59.457 47.619 14.09 0.00 43.89 2.32
1943 3075 1.171308 GAGATATGCATGCGGCCATT 58.829 50.000 14.09 0.00 43.89 3.16
1944 3076 0.037160 TGAGATATGCATGCGGCCAT 59.963 50.000 14.09 3.14 43.89 4.40
1945 3077 0.604511 CTGAGATATGCATGCGGCCA 60.605 55.000 14.09 4.22 43.89 5.36
1946 3078 0.321034 TCTGAGATATGCATGCGGCC 60.321 55.000 14.09 0.00 43.89 6.13
1947 3079 1.397343 CATCTGAGATATGCATGCGGC 59.603 52.381 14.09 1.90 45.13 6.53
1955 3087 2.674462 CGGCCTCTGCATCTGAGATATG 60.674 54.545 0.00 0.00 40.13 1.78
1956 3088 1.549620 CGGCCTCTGCATCTGAGATAT 59.450 52.381 0.00 0.00 40.13 1.63
1957 3089 0.964700 CGGCCTCTGCATCTGAGATA 59.035 55.000 0.00 0.00 40.13 1.98
1958 3090 1.747145 CGGCCTCTGCATCTGAGAT 59.253 57.895 0.00 0.00 40.13 2.75
1959 3091 2.429767 CCGGCCTCTGCATCTGAGA 61.430 63.158 0.00 0.00 40.13 3.27
1960 3092 2.108566 CCGGCCTCTGCATCTGAG 59.891 66.667 0.00 0.00 40.13 3.35
1961 3093 3.473647 CCCGGCCTCTGCATCTGA 61.474 66.667 0.00 0.00 40.13 3.27
1962 3094 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
1968 3100 3.866582 GATGACCCCCGGCCTCTG 61.867 72.222 0.00 0.00 0.00 3.35
1974 3106 1.984288 GAAAGGAGGATGACCCCCGG 61.984 65.000 0.00 0.00 36.73 5.73
1975 3107 1.527370 GAAAGGAGGATGACCCCCG 59.473 63.158 0.00 0.00 36.73 5.73
1976 3108 0.919289 TGGAAAGGAGGATGACCCCC 60.919 60.000 0.00 0.00 36.73 5.40
1977 3109 0.999712 TTGGAAAGGAGGATGACCCC 59.000 55.000 0.00 0.00 36.73 4.95
1978 3110 2.899303 TTTGGAAAGGAGGATGACCC 57.101 50.000 0.00 0.00 36.73 4.46
1998 3130 0.531311 AGTTCGCTCCGGACGTTTTT 60.531 50.000 20.62 7.55 40.73 1.94
1999 3131 1.068585 AGTTCGCTCCGGACGTTTT 59.931 52.632 20.62 8.87 40.73 2.43
2000 3132 1.663702 CAGTTCGCTCCGGACGTTT 60.664 57.895 20.62 9.13 40.73 3.60
2001 3133 2.049433 CAGTTCGCTCCGGACGTT 60.049 61.111 20.62 9.39 40.73 3.99
2002 3134 3.264866 GACAGTTCGCTCCGGACGT 62.265 63.158 20.62 0.00 40.73 4.34
2003 3135 2.504244 GACAGTTCGCTCCGGACG 60.504 66.667 17.01 17.01 40.73 4.79
2004 3136 1.444553 CTGACAGTTCGCTCCGGAC 60.445 63.158 0.00 0.00 35.29 4.79
2005 3137 1.176619 TTCTGACAGTTCGCTCCGGA 61.177 55.000 2.93 2.93 0.00 5.14
2006 3138 1.009389 GTTCTGACAGTTCGCTCCGG 61.009 60.000 1.59 0.00 0.00 5.14
2007 3139 1.337817 CGTTCTGACAGTTCGCTCCG 61.338 60.000 1.59 0.00 0.00 4.63
2008 3140 0.318784 ACGTTCTGACAGTTCGCTCC 60.319 55.000 16.91 0.00 0.00 4.70
2009 3141 2.243407 CTACGTTCTGACAGTTCGCTC 58.757 52.381 16.91 0.00 0.00 5.03
2010 3142 1.607628 ACTACGTTCTGACAGTTCGCT 59.392 47.619 16.91 10.02 0.00 4.93
2011 3143 2.047679 ACTACGTTCTGACAGTTCGC 57.952 50.000 16.91 1.78 0.00 4.70
2012 3144 3.361724 GCAAACTACGTTCTGACAGTTCG 60.362 47.826 15.94 15.94 31.06 3.95
2013 3145 3.059800 GGCAAACTACGTTCTGACAGTTC 60.060 47.826 1.59 0.00 31.06 3.01
2014 3146 2.870411 GGCAAACTACGTTCTGACAGTT 59.130 45.455 1.59 0.00 32.73 3.16
2015 3147 2.159014 TGGCAAACTACGTTCTGACAGT 60.159 45.455 1.59 0.00 0.00 3.55
2016 3148 2.479837 TGGCAAACTACGTTCTGACAG 58.520 47.619 0.00 0.00 0.00 3.51
2017 3149 2.605837 TGGCAAACTACGTTCTGACA 57.394 45.000 0.00 0.00 0.00 3.58
2018 3150 3.955771 TTTGGCAAACTACGTTCTGAC 57.044 42.857 8.93 0.00 0.00 3.51
2019 3151 4.336993 ACATTTTGGCAAACTACGTTCTGA 59.663 37.500 13.10 0.00 0.00 3.27
2020 3152 4.440758 CACATTTTGGCAAACTACGTTCTG 59.559 41.667 13.10 3.38 0.00 3.02
2037 3169 6.183360 CCGCAGATAAATAAGGGTTCACATTT 60.183 38.462 0.00 0.00 0.00 2.32
2065 3197 2.359900 GGAATTCAGACAAGCGGATGT 58.640 47.619 7.93 0.00 35.90 3.06
2067 3199 1.743772 CGGGAATTCAGACAAGCGGAT 60.744 52.381 7.93 0.00 0.00 4.18
2087 3219 2.223572 CCGCAAAACTCCCTCATTATGC 60.224 50.000 0.00 0.00 0.00 3.14
2092 3224 0.988832 TACCCGCAAAACTCCCTCAT 59.011 50.000 0.00 0.00 0.00 2.90
2123 3255 1.641577 GTGTCGGAGTCCTATGTTGC 58.358 55.000 7.77 0.00 0.00 4.17
2125 3257 1.192428 GGGTGTCGGAGTCCTATGTT 58.808 55.000 7.77 0.00 0.00 2.71
2127 3259 1.033574 GAGGGTGTCGGAGTCCTATG 58.966 60.000 7.77 0.00 0.00 2.23
2128 3260 0.465824 CGAGGGTGTCGGAGTCCTAT 60.466 60.000 7.77 0.00 45.58 2.57
2130 3262 2.361357 CGAGGGTGTCGGAGTCCT 60.361 66.667 7.77 0.00 45.58 3.85
2168 3300 4.752101 ACAGAGTGAAAGAAAAGTGATCCG 59.248 41.667 0.00 0.00 0.00 4.18
2172 3304 4.164221 AGGGACAGAGTGAAAGAAAAGTGA 59.836 41.667 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.