Multiple sequence alignment - TraesCS6D01G015600

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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 TraesCS6D01G015600 chr6D 100.000 2850 0 0 1 2850 6352979 6355828 0.000000e+00 5264.0
1 TraesCS6D01G015600 chr6D 88.749 2062 225 5 1 2061 6371383 6373438 0.000000e+00 2516.0
2 TraesCS6D01G015600 chr6D 86.110 1879 240 16 194 2067 6426508 6428370 0.000000e+00 2004.0
3 TraesCS6D01G015600 chr6D 85.805 1881 243 15 1 1864 6497498 6499371 0.000000e+00 1973.0
4 TraesCS6D01G015600 chr6D 86.732 1334 142 18 729 2061 6465693 6466992 0.000000e+00 1450.0
5 TraesCS6D01G015600 chr6D 81.086 1565 282 14 215 1772 7033393 7034950 0.000000e+00 1238.0
6 TraesCS6D01G015600 chr6D 89.338 619 55 7 2230 2845 6326821 6327431 0.000000e+00 767.0
7 TraesCS6D01G015600 chr6D 89.437 568 60 0 1 568 6443077 6443644 0.000000e+00 717.0
8 TraesCS6D01G015600 chr6D 86.667 180 22 2 1 179 6426521 6426699 6.230000e-47 198.0
9 TraesCS6D01G015600 chr6D 94.737 38 1 1 1 37 6443005 6443042 1.100000e-04 58.4
10 TraesCS6D01G015600 chr6A 88.555 2062 232 4 1 2061 5917707 5919765 0.000000e+00 2497.0
11 TraesCS6D01G015600 chr6A 89.598 1865 192 2 198 2061 5901924 5903787 0.000000e+00 2368.0
12 TraesCS6D01G015600 chr6A 86.111 1872 240 15 194 2061 5940875 5942730 0.000000e+00 1999.0
13 TraesCS6D01G015600 chr6A 83.036 224 34 4 1 222 5940888 5941109 1.730000e-47 200.0
14 TraesCS6D01G015600 chr6A 91.743 109 7 2 2730 2837 29373502 29373395 1.770000e-32 150.0
15 TraesCS6D01G015600 chr6A 94.737 38 1 1 1 37 5917635 5917672 1.100000e-04 58.4
16 TraesCS6D01G015600 chr6B 85.152 1879 253 16 1 1864 11793478 11795345 0.000000e+00 1901.0
17 TraesCS6D01G015600 chr6B 92.333 1226 89 4 642 1864 11599598 11600821 0.000000e+00 1738.0
18 TraesCS6D01G015600 chr6B 85.812 437 58 4 1625 2060 11795645 11796078 7.190000e-126 460.0
19 TraesCS6D01G015600 chr6B 92.893 197 14 0 1 197 11593756 11593952 1.290000e-73 287.0
20 TraesCS6D01G015600 chr6B 85.938 128 16 2 2724 2850 52448289 52448415 4.950000e-28 135.0
21 TraesCS6D01G015600 chr6B 87.671 73 8 1 2576 2648 687003597 687003526 1.820000e-12 84.2
22 TraesCS6D01G015600 chr5A 93.878 49 3 0 2579 2627 680699203 680699251 1.100000e-09 75.0
23 TraesCS6D01G015600 chr7B 81.928 83 10 5 2732 2811 99640012 99639932 6.590000e-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 TraesCS6D01G015600 chr6D 6352979 6355828 2849 False 5264.0 5264 100.0000 1 2850 1 chr6D.!!$F2 2849
1 TraesCS6D01G015600 chr6D 6371383 6373438 2055 False 2516.0 2516 88.7490 1 2061 1 chr6D.!!$F3 2060
2 TraesCS6D01G015600 chr6D 6497498 6499371 1873 False 1973.0 1973 85.8050 1 1864 1 chr6D.!!$F5 1863
3 TraesCS6D01G015600 chr6D 6465693 6466992 1299 False 1450.0 1450 86.7320 729 2061 1 chr6D.!!$F4 1332
4 TraesCS6D01G015600 chr6D 7033393 7034950 1557 False 1238.0 1238 81.0860 215 1772 1 chr6D.!!$F6 1557
5 TraesCS6D01G015600 chr6D 6426508 6428370 1862 False 1101.0 2004 86.3885 1 2067 2 chr6D.!!$F7 2066
6 TraesCS6D01G015600 chr6D 6326821 6327431 610 False 767.0 767 89.3380 2230 2845 1 chr6D.!!$F1 615
7 TraesCS6D01G015600 chr6D 6443005 6443644 639 False 387.7 717 92.0870 1 568 2 chr6D.!!$F8 567
8 TraesCS6D01G015600 chr6A 5901924 5903787 1863 False 2368.0 2368 89.5980 198 2061 1 chr6A.!!$F1 1863
9 TraesCS6D01G015600 chr6A 5917635 5919765 2130 False 1277.7 2497 91.6460 1 2061 2 chr6A.!!$F2 2060
10 TraesCS6D01G015600 chr6A 5940875 5942730 1855 False 1099.5 1999 84.5735 1 2061 2 chr6A.!!$F3 2060
11 TraesCS6D01G015600 chr6B 11599598 11600821 1223 False 1738.0 1738 92.3330 642 1864 1 chr6B.!!$F2 1222
12 TraesCS6D01G015600 chr6B 11793478 11796078 2600 False 1180.5 1901 85.4820 1 2060 2 chr6B.!!$F4 2059

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
183 265 0.038618 GTTGGGGAATTGCACCGAAC 60.039 55.0 0.0 3.74 46.01 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 2789 0.10104 TATACGTGGTTCGCGGGAAG 59.899 55.0 15.99 6.41 41.96 3.46 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
45 118 1.341080 AGGGTTGGGAAATTGCACTG 58.659 50.000 0.00 0.00 0.00 3.66
180 262 0.607620 AATGTTGGGGAATTGCACCG 59.392 50.000 0.00 0.00 46.01 4.94
183 265 0.038618 GTTGGGGAATTGCACCGAAC 60.039 55.000 0.00 3.74 46.01 3.95
203 285 9.193806 ACCGAACTATATTACCTTACTCTTTCA 57.806 33.333 0.00 0.00 0.00 2.69
262 344 4.395231 GGGGAATTACACTAGTTTGCAGTC 59.605 45.833 0.00 0.00 0.00 3.51
290 372 3.596214 TCTTTCGAGCAACCATCTTACC 58.404 45.455 0.00 0.00 0.00 2.85
314 396 3.990369 ACCTATACTGCTAGGGACAACA 58.010 45.455 8.31 0.00 42.29 3.33
429 511 6.879458 GCACCTTTCTCTTTCTAAGAACCATA 59.121 38.462 0.00 0.00 37.02 2.74
441 523 5.958380 TCTAAGAACCATATCACTGGACACT 59.042 40.000 0.00 0.00 39.73 3.55
492 574 1.534235 ACTGGACTCGACCTTGGCT 60.534 57.895 0.00 0.00 0.00 4.75
530 612 2.289072 CGTGATCACAGAGGAACACCTT 60.289 50.000 24.93 0.00 37.30 3.50
546 628 6.764560 GGAACACCTTGTTACTCTAAAGAACA 59.235 38.462 0.00 0.00 41.28 3.18
560 642 7.824779 ACTCTAAAGAACATAAACCATCTGGAC 59.175 37.037 2.55 0.00 38.94 4.02
654 736 4.946160 TCCTCCAATAAATTCACTGGGT 57.054 40.909 1.12 0.00 0.00 4.51
656 738 5.751586 TCCTCCAATAAATTCACTGGGTAC 58.248 41.667 1.12 0.00 0.00 3.34
666 748 4.715534 TTCACTGGGTACATTCCTGAAA 57.284 40.909 0.00 0.00 0.00 2.69
849 931 7.893124 AGTTTAGCATTCATGGATCTTTCAT 57.107 32.000 0.00 0.00 0.00 2.57
899 981 7.415765 CCATCATGGATCGGAGACTTAGTATAC 60.416 44.444 0.00 0.00 42.51 1.47
960 1042 7.238486 GGAGATATTCCAGTGACTATCACAT 57.762 40.000 11.33 0.00 44.87 3.21
1290 1372 2.821378 TCATGCAACCAATTGAGTGGAG 59.179 45.455 7.12 0.00 41.65 3.86
1466 1548 0.818040 GACGCCAACTTGACACCCTT 60.818 55.000 0.00 0.00 0.00 3.95
1576 1658 4.335315 AGAGCACGACAATCAACAGAAAAA 59.665 37.500 0.00 0.00 0.00 1.94
1634 1716 0.887836 GACTTGGGTCCGGGTTTGTC 60.888 60.000 0.00 0.00 36.53 3.18
1820 2443 6.839124 ACAAGATAATGCAAATCTGGTGAA 57.161 33.333 17.45 0.00 36.47 3.18
1844 2468 4.803098 TCTTTCACCCTAGTACTGAAGC 57.197 45.455 5.39 0.00 0.00 3.86
1866 2490 4.567959 GCATGAAATAAATGAAGGTGCCAC 59.432 41.667 0.00 0.00 0.00 5.01
1867 2491 4.433186 TGAAATAAATGAAGGTGCCACG 57.567 40.909 0.00 0.00 0.00 4.94
1904 2528 8.119226 GCTTGTGCTAGTATATGTTCTTTTCTG 58.881 37.037 0.00 0.00 36.03 3.02
2053 2677 5.944049 TCGTAATCTGTAAGCGAATGTTC 57.056 39.130 0.00 0.00 0.00 3.18
2061 2685 3.740832 TGTAAGCGAATGTTCTGTGAGTG 59.259 43.478 0.00 0.00 0.00 3.51
2062 2686 1.800805 AGCGAATGTTCTGTGAGTGG 58.199 50.000 0.00 0.00 0.00 4.00
2063 2687 0.166814 GCGAATGTTCTGTGAGTGGC 59.833 55.000 0.00 0.00 0.00 5.01
2064 2688 1.800805 CGAATGTTCTGTGAGTGGCT 58.199 50.000 0.00 0.00 0.00 4.75
2065 2689 2.930887 GCGAATGTTCTGTGAGTGGCTA 60.931 50.000 0.00 0.00 0.00 3.93
2066 2690 2.926200 CGAATGTTCTGTGAGTGGCTAG 59.074 50.000 0.00 0.00 0.00 3.42
2067 2691 2.393271 ATGTTCTGTGAGTGGCTAGC 57.607 50.000 6.04 6.04 0.00 3.42
2068 2692 1.047801 TGTTCTGTGAGTGGCTAGCA 58.952 50.000 18.24 0.00 0.00 3.49
2069 2693 1.001293 TGTTCTGTGAGTGGCTAGCAG 59.999 52.381 18.24 3.16 0.00 4.24
2070 2694 1.001406 GTTCTGTGAGTGGCTAGCAGT 59.999 52.381 18.24 5.63 0.00 4.40
2071 2695 0.605083 TCTGTGAGTGGCTAGCAGTG 59.395 55.000 18.24 0.00 0.00 3.66
2072 2696 0.605083 CTGTGAGTGGCTAGCAGTGA 59.395 55.000 18.24 0.00 0.00 3.41
2073 2697 0.605083 TGTGAGTGGCTAGCAGTGAG 59.395 55.000 18.24 0.00 0.00 3.51
2074 2698 0.108424 GTGAGTGGCTAGCAGTGAGG 60.108 60.000 18.24 0.00 0.00 3.86
2075 2699 1.260538 TGAGTGGCTAGCAGTGAGGG 61.261 60.000 18.24 0.00 0.00 4.30
2076 2700 0.972983 GAGTGGCTAGCAGTGAGGGA 60.973 60.000 18.24 0.00 0.00 4.20
2077 2701 0.545309 AGTGGCTAGCAGTGAGGGAA 60.545 55.000 18.24 0.00 0.00 3.97
2078 2702 0.391793 GTGGCTAGCAGTGAGGGAAC 60.392 60.000 18.24 0.00 0.00 3.62
2080 2704 1.273041 TGGCTAGCAGTGAGGGAACTA 60.273 52.381 18.24 0.00 44.43 2.24
2081 2705 1.831736 GGCTAGCAGTGAGGGAACTAA 59.168 52.381 18.24 0.00 44.43 2.24
2082 2706 2.236395 GGCTAGCAGTGAGGGAACTAAA 59.764 50.000 18.24 0.00 44.43 1.85
2083 2707 3.307480 GGCTAGCAGTGAGGGAACTAAAA 60.307 47.826 18.24 0.00 44.43 1.52
2084 2708 3.935828 GCTAGCAGTGAGGGAACTAAAAG 59.064 47.826 10.63 0.00 44.43 2.27
2085 2709 2.784347 AGCAGTGAGGGAACTAAAAGC 58.216 47.619 0.00 0.00 44.43 3.51
2086 2710 1.813178 GCAGTGAGGGAACTAAAAGCC 59.187 52.381 0.00 0.00 44.43 4.35
2087 2711 2.814097 GCAGTGAGGGAACTAAAAGCCA 60.814 50.000 0.00 0.00 44.43 4.75
2088 2712 3.690460 CAGTGAGGGAACTAAAAGCCAT 58.310 45.455 0.00 0.00 44.43 4.40
2089 2713 4.082125 CAGTGAGGGAACTAAAAGCCATT 58.918 43.478 0.00 0.00 44.43 3.16
2090 2714 5.253330 CAGTGAGGGAACTAAAAGCCATTA 58.747 41.667 0.00 0.00 44.43 1.90
2091 2715 5.888161 CAGTGAGGGAACTAAAAGCCATTAT 59.112 40.000 0.00 0.00 44.43 1.28
2092 2716 7.054124 CAGTGAGGGAACTAAAAGCCATTATA 58.946 38.462 0.00 0.00 44.43 0.98
2093 2717 7.556275 CAGTGAGGGAACTAAAAGCCATTATAA 59.444 37.037 0.00 0.00 44.43 0.98
2094 2718 7.556635 AGTGAGGGAACTAAAAGCCATTATAAC 59.443 37.037 0.00 0.00 44.43 1.89
2095 2719 7.338449 GTGAGGGAACTAAAAGCCATTATAACA 59.662 37.037 0.00 0.00 44.43 2.41
2096 2720 7.891183 TGAGGGAACTAAAAGCCATTATAACAA 59.109 33.333 0.00 0.00 44.43 2.83
2097 2721 8.658840 AGGGAACTAAAAGCCATTATAACAAA 57.341 30.769 0.00 0.00 40.61 2.83
2098 2722 9.095700 AGGGAACTAAAAGCCATTATAACAAAA 57.904 29.630 0.00 0.00 40.61 2.44
2099 2723 9.146984 GGGAACTAAAAGCCATTATAACAAAAC 57.853 33.333 0.00 0.00 0.00 2.43
2100 2724 8.856247 GGAACTAAAAGCCATTATAACAAAACG 58.144 33.333 0.00 0.00 0.00 3.60
2101 2725 9.615295 GAACTAAAAGCCATTATAACAAAACGA 57.385 29.630 0.00 0.00 0.00 3.85
2102 2726 9.968870 AACTAAAAGCCATTATAACAAAACGAA 57.031 25.926 0.00 0.00 0.00 3.85
2107 2731 9.705290 AAAGCCATTATAACAAAACGAATTTCT 57.295 25.926 0.00 0.00 0.00 2.52
2108 2732 8.687824 AGCCATTATAACAAAACGAATTTCTG 57.312 30.769 0.00 0.00 0.00 3.02
2109 2733 7.759433 AGCCATTATAACAAAACGAATTTCTGG 59.241 33.333 0.00 0.00 0.00 3.86
2110 2734 7.464045 GCCATTATAACAAAACGAATTTCTGGC 60.464 37.037 0.00 0.00 0.00 4.85
2111 2735 7.253618 CCATTATAACAAAACGAATTTCTGGCG 60.254 37.037 0.00 0.00 0.00 5.69
2112 2736 2.415697 ACAAAACGAATTTCTGGCGG 57.584 45.000 0.00 0.00 0.00 6.13
2113 2737 1.000717 ACAAAACGAATTTCTGGCGGG 60.001 47.619 0.00 0.00 0.00 6.13
2114 2738 1.268352 CAAAACGAATTTCTGGCGGGA 59.732 47.619 0.00 0.00 0.00 5.14
2115 2739 1.611519 AAACGAATTTCTGGCGGGAA 58.388 45.000 0.00 0.00 0.00 3.97
2116 2740 1.611519 AACGAATTTCTGGCGGGAAA 58.388 45.000 7.66 7.66 39.16 3.13
2117 2741 1.165270 ACGAATTTCTGGCGGGAAAG 58.835 50.000 10.31 0.36 38.38 2.62
2118 2742 1.271163 ACGAATTTCTGGCGGGAAAGA 60.271 47.619 10.31 0.00 38.38 2.52
2119 2743 1.810151 CGAATTTCTGGCGGGAAAGAA 59.190 47.619 10.31 0.00 38.38 2.52
2120 2744 2.227865 CGAATTTCTGGCGGGAAAGAAA 59.772 45.455 10.31 5.72 44.25 2.52
2121 2745 3.305064 CGAATTTCTGGCGGGAAAGAAAA 60.305 43.478 10.31 0.00 43.57 2.29
2122 2746 3.660501 ATTTCTGGCGGGAAAGAAAAC 57.339 42.857 10.31 0.00 43.57 2.43
2123 2747 1.324383 TTCTGGCGGGAAAGAAAACC 58.676 50.000 0.00 0.00 29.59 3.27
2124 2748 0.183971 TCTGGCGGGAAAGAAAACCA 59.816 50.000 0.00 0.00 0.00 3.67
2125 2749 1.036707 CTGGCGGGAAAGAAAACCAA 58.963 50.000 0.00 0.00 0.00 3.67
2126 2750 1.410882 CTGGCGGGAAAGAAAACCAAA 59.589 47.619 0.00 0.00 0.00 3.28
2127 2751 2.037121 CTGGCGGGAAAGAAAACCAAAT 59.963 45.455 0.00 0.00 0.00 2.32
2128 2752 2.436173 TGGCGGGAAAGAAAACCAAATT 59.564 40.909 0.00 0.00 0.00 1.82
2129 2753 3.118223 TGGCGGGAAAGAAAACCAAATTT 60.118 39.130 0.00 0.00 0.00 1.82
2130 2754 4.101119 TGGCGGGAAAGAAAACCAAATTTA 59.899 37.500 0.00 0.00 0.00 1.40
2131 2755 5.057819 GGCGGGAAAGAAAACCAAATTTAA 58.942 37.500 0.00 0.00 0.00 1.52
2132 2756 5.178623 GGCGGGAAAGAAAACCAAATTTAAG 59.821 40.000 0.00 0.00 0.00 1.85
2133 2757 5.178623 GCGGGAAAGAAAACCAAATTTAAGG 59.821 40.000 0.00 0.00 0.00 2.69
2134 2758 5.178623 CGGGAAAGAAAACCAAATTTAAGGC 59.821 40.000 0.00 0.00 0.00 4.35
2135 2759 5.178623 GGGAAAGAAAACCAAATTTAAGGCG 59.821 40.000 0.00 0.00 0.00 5.52
2136 2760 5.178623 GGAAAGAAAACCAAATTTAAGGCGG 59.821 40.000 0.00 0.00 0.00 6.13
2137 2761 4.265904 AGAAAACCAAATTTAAGGCGGG 57.734 40.909 0.00 0.00 0.00 6.13
2138 2762 3.898741 AGAAAACCAAATTTAAGGCGGGA 59.101 39.130 0.00 0.00 0.00 5.14
2139 2763 4.345547 AGAAAACCAAATTTAAGGCGGGAA 59.654 37.500 0.00 0.00 0.00 3.97
2140 2764 4.691326 AAACCAAATTTAAGGCGGGAAA 57.309 36.364 0.00 0.00 0.00 3.13
2141 2765 4.691326 AACCAAATTTAAGGCGGGAAAA 57.309 36.364 0.00 0.00 0.00 2.29
2142 2766 3.997762 ACCAAATTTAAGGCGGGAAAAC 58.002 40.909 0.00 0.00 0.00 2.43
2143 2767 2.990514 CCAAATTTAAGGCGGGAAAACG 59.009 45.455 0.00 0.00 0.00 3.60
2144 2768 3.305471 CCAAATTTAAGGCGGGAAAACGA 60.305 43.478 0.00 0.00 35.47 3.85
2145 2769 4.299978 CAAATTTAAGGCGGGAAAACGAA 58.700 39.130 0.00 0.00 35.47 3.85
2146 2770 4.587584 AATTTAAGGCGGGAAAACGAAA 57.412 36.364 0.00 0.00 35.47 3.46
2147 2771 4.794278 ATTTAAGGCGGGAAAACGAAAT 57.206 36.364 0.00 0.00 35.47 2.17
2148 2772 4.587584 TTTAAGGCGGGAAAACGAAATT 57.412 36.364 0.00 0.00 35.47 1.82
2149 2773 2.432206 AAGGCGGGAAAACGAAATTG 57.568 45.000 0.00 0.00 35.47 2.32
2150 2774 0.601057 AGGCGGGAAAACGAAATTGG 59.399 50.000 0.00 0.00 35.47 3.16
2151 2775 0.389296 GGCGGGAAAACGAAATTGGG 60.389 55.000 0.00 0.00 35.47 4.12
2152 2776 1.011968 GCGGGAAAACGAAATTGGGC 61.012 55.000 0.00 0.00 35.47 5.36
2153 2777 0.731174 CGGGAAAACGAAATTGGGCG 60.731 55.000 0.00 0.00 35.47 6.13
2154 2778 0.599060 GGGAAAACGAAATTGGGCGA 59.401 50.000 0.00 0.00 0.00 5.54
2155 2779 1.402325 GGGAAAACGAAATTGGGCGAG 60.402 52.381 0.00 0.00 0.00 5.03
2156 2780 1.336877 GAAAACGAAATTGGGCGAGC 58.663 50.000 0.00 0.00 0.00 5.03
2157 2781 0.671251 AAAACGAAATTGGGCGAGCA 59.329 45.000 0.00 0.00 0.00 4.26
2158 2782 0.240945 AAACGAAATTGGGCGAGCAG 59.759 50.000 0.00 0.00 0.00 4.24
2159 2783 1.586154 AACGAAATTGGGCGAGCAGG 61.586 55.000 0.00 0.00 0.00 4.85
2160 2784 2.040544 CGAAATTGGGCGAGCAGGT 61.041 57.895 0.00 0.00 0.00 4.00
2161 2785 1.508088 GAAATTGGGCGAGCAGGTG 59.492 57.895 0.00 0.00 0.00 4.00
2162 2786 1.937546 GAAATTGGGCGAGCAGGTGG 61.938 60.000 0.00 0.00 0.00 4.61
2163 2787 2.424842 AAATTGGGCGAGCAGGTGGA 62.425 55.000 0.00 0.00 0.00 4.02
2164 2788 2.424842 AATTGGGCGAGCAGGTGGAA 62.425 55.000 0.00 0.00 0.00 3.53
2165 2789 3.842925 TTGGGCGAGCAGGTGGAAC 62.843 63.158 0.00 0.00 0.00 3.62
2166 2790 4.021925 GGGCGAGCAGGTGGAACT 62.022 66.667 0.00 0.00 36.74 3.01
2167 2791 2.032681 GGCGAGCAGGTGGAACTT 59.967 61.111 0.00 0.00 36.74 2.66
2168 2792 2.035442 GGCGAGCAGGTGGAACTTC 61.035 63.158 0.00 0.00 36.74 3.01
2169 2793 2.035442 GCGAGCAGGTGGAACTTCC 61.035 63.158 0.20 0.20 36.74 3.46
2170 2794 1.376037 CGAGCAGGTGGAACTTCCC 60.376 63.158 5.30 0.00 35.03 3.97
2171 2795 1.376037 GAGCAGGTGGAACTTCCCG 60.376 63.158 5.30 0.00 35.03 5.14
2172 2796 3.056328 GCAGGTGGAACTTCCCGC 61.056 66.667 5.30 0.00 35.03 6.13
2173 2797 2.742372 CAGGTGGAACTTCCCGCG 60.742 66.667 0.00 0.00 37.58 6.46
2174 2798 2.920912 AGGTGGAACTTCCCGCGA 60.921 61.111 8.23 0.00 37.58 5.87
2175 2799 2.031465 GGTGGAACTTCCCGCGAA 59.969 61.111 8.23 0.00 37.58 4.70
2176 2800 2.322830 GGTGGAACTTCCCGCGAAC 61.323 63.158 8.23 0.00 37.58 3.95
2177 2801 2.031465 TGGAACTTCCCGCGAACC 59.969 61.111 8.23 0.30 35.03 3.62
2178 2802 2.031465 GGAACTTCCCGCGAACCA 59.969 61.111 8.23 0.00 0.00 3.67
2179 2803 2.322830 GGAACTTCCCGCGAACCAC 61.323 63.158 8.23 0.00 0.00 4.16
2180 2804 2.663852 AACTTCCCGCGAACCACG 60.664 61.111 8.23 0.00 45.66 4.94
2181 2805 3.450043 AACTTCCCGCGAACCACGT 62.450 57.895 8.23 0.00 44.60 4.49
2182 2806 2.086251 AACTTCCCGCGAACCACGTA 62.086 55.000 8.23 0.00 44.60 3.57
2183 2807 1.153706 CTTCCCGCGAACCACGTAT 60.154 57.895 8.23 0.00 44.60 3.06
2184 2808 0.101040 CTTCCCGCGAACCACGTATA 59.899 55.000 8.23 0.00 44.60 1.47
2185 2809 0.101040 TTCCCGCGAACCACGTATAG 59.899 55.000 8.23 0.00 44.60 1.31
2186 2810 0.747644 TCCCGCGAACCACGTATAGA 60.748 55.000 8.23 0.00 44.60 1.98
2187 2811 0.101040 CCCGCGAACCACGTATAGAA 59.899 55.000 8.23 0.00 44.60 2.10
2188 2812 1.474017 CCGCGAACCACGTATAGAAG 58.526 55.000 8.23 0.00 44.60 2.85
2189 2813 1.202222 CCGCGAACCACGTATAGAAGT 60.202 52.381 8.23 0.00 44.60 3.01
2190 2814 1.844357 CGCGAACCACGTATAGAAGTG 59.156 52.381 0.00 0.00 44.60 3.16
2197 2821 2.793933 CACGTATAGAAGTGGGTGACG 58.206 52.381 0.00 0.00 34.93 4.35
2198 2822 1.133790 ACGTATAGAAGTGGGTGACGC 59.866 52.381 0.00 0.00 32.28 5.19
2199 2823 1.535437 CGTATAGAAGTGGGTGACGCC 60.535 57.143 0.00 0.00 0.00 5.68
2200 2824 1.755380 GTATAGAAGTGGGTGACGCCT 59.245 52.381 4.75 0.00 37.43 5.52
2201 2825 2.154567 ATAGAAGTGGGTGACGCCTA 57.845 50.000 4.75 0.00 37.43 3.93
2202 2826 1.471119 TAGAAGTGGGTGACGCCTAG 58.529 55.000 4.75 0.00 37.43 3.02
2203 2827 0.251653 AGAAGTGGGTGACGCCTAGA 60.252 55.000 4.75 0.00 37.43 2.43
2204 2828 0.173708 GAAGTGGGTGACGCCTAGAG 59.826 60.000 4.75 0.00 37.43 2.43
2205 2829 0.542232 AAGTGGGTGACGCCTAGAGT 60.542 55.000 4.75 0.00 37.43 3.24
2206 2830 0.542232 AGTGGGTGACGCCTAGAGTT 60.542 55.000 4.75 0.00 37.43 3.01
2207 2831 1.180029 GTGGGTGACGCCTAGAGTTA 58.820 55.000 4.75 0.00 37.43 2.24
2208 2832 1.547372 GTGGGTGACGCCTAGAGTTAA 59.453 52.381 4.75 0.00 37.43 2.01
2209 2833 2.167900 GTGGGTGACGCCTAGAGTTAAT 59.832 50.000 4.75 0.00 37.43 1.40
2210 2834 3.382546 GTGGGTGACGCCTAGAGTTAATA 59.617 47.826 4.75 0.00 37.43 0.98
2211 2835 4.025360 TGGGTGACGCCTAGAGTTAATAA 58.975 43.478 4.75 0.00 37.43 1.40
2212 2836 4.652421 TGGGTGACGCCTAGAGTTAATAAT 59.348 41.667 4.75 0.00 37.43 1.28
2213 2837 5.834742 TGGGTGACGCCTAGAGTTAATAATA 59.165 40.000 4.75 0.00 37.43 0.98
2214 2838 6.155136 GGGTGACGCCTAGAGTTAATAATAC 58.845 44.000 4.75 0.00 37.43 1.89
2215 2839 6.239120 GGGTGACGCCTAGAGTTAATAATACA 60.239 42.308 4.75 0.00 37.43 2.29
2216 2840 6.862090 GGTGACGCCTAGAGTTAATAATACAG 59.138 42.308 0.00 0.00 0.00 2.74
2217 2841 6.862090 GTGACGCCTAGAGTTAATAATACAGG 59.138 42.308 0.00 0.00 0.00 4.00
2218 2842 5.780984 ACGCCTAGAGTTAATAATACAGGC 58.219 41.667 0.00 0.00 43.09 4.85
2220 2844 5.169295 GCCTAGAGTTAATAATACAGGCGG 58.831 45.833 0.00 0.00 38.11 6.13
2221 2845 5.279356 GCCTAGAGTTAATAATACAGGCGGT 60.279 44.000 0.00 0.00 38.11 5.68
2222 2846 6.740681 GCCTAGAGTTAATAATACAGGCGGTT 60.741 42.308 0.00 0.00 38.11 4.44
2223 2847 7.215085 CCTAGAGTTAATAATACAGGCGGTTT 58.785 38.462 0.00 0.00 0.00 3.27
2224 2848 6.920569 AGAGTTAATAATACAGGCGGTTTG 57.079 37.500 0.00 0.00 0.00 2.93
2225 2849 6.646267 AGAGTTAATAATACAGGCGGTTTGA 58.354 36.000 0.00 0.00 0.00 2.69
2226 2850 7.107542 AGAGTTAATAATACAGGCGGTTTGAA 58.892 34.615 0.00 0.00 0.00 2.69
2227 2851 7.280205 AGAGTTAATAATACAGGCGGTTTGAAG 59.720 37.037 0.00 0.00 0.00 3.02
2228 2852 6.882678 AGTTAATAATACAGGCGGTTTGAAGT 59.117 34.615 0.00 0.00 0.00 3.01
2260 2884 6.208797 AGCCCCACTTAAACACTTTATTTCTC 59.791 38.462 0.00 0.00 0.00 2.87
2309 2934 4.000325 GCAAAACAAAACAACAGGGAAGT 59.000 39.130 0.00 0.00 0.00 3.01
2314 2939 5.262588 ACAAAACAACAGGGAAGTGATTC 57.737 39.130 0.00 0.00 0.00 2.52
2315 2940 4.709397 ACAAAACAACAGGGAAGTGATTCA 59.291 37.500 0.00 0.00 0.00 2.57
2323 2948 1.606668 GGGAAGTGATTCAAACGCACA 59.393 47.619 0.00 0.00 35.08 4.57
2336 2961 2.576083 CGCACAACGCAACAACATT 58.424 47.368 0.00 0.00 42.60 2.71
2360 2985 0.179062 CTCAGCACCCCATGTAGAGC 60.179 60.000 0.00 0.00 0.00 4.09
2366 2991 0.912486 ACCCCATGTAGAGCAGAACC 59.088 55.000 0.00 0.00 0.00 3.62
2382 3007 2.187946 CCACCAGGTCATCGCTCC 59.812 66.667 0.00 0.00 0.00 4.70
2399 3024 2.813754 GCTCCACATGTGTTCAAAGCTA 59.186 45.455 23.79 0.00 0.00 3.32
2418 3043 7.683437 AAGCTAGTTTCCGCTTTATTTAACT 57.317 32.000 0.00 0.00 43.43 2.24
2419 3044 8.782339 AAGCTAGTTTCCGCTTTATTTAACTA 57.218 30.769 0.00 0.00 43.43 2.24
2491 3116 1.153041 AAGGGCCATTTACTGGGGGT 61.153 55.000 6.18 0.00 46.06 4.95
2492 3117 1.381191 GGGCCATTTACTGGGGGTG 60.381 63.158 4.39 0.00 46.06 4.61
2506 3131 2.576191 TGGGGGTGAAGAAATTCTCGAT 59.424 45.455 0.00 0.00 0.00 3.59
2510 3135 4.575236 GGGGTGAAGAAATTCTCGATAACC 59.425 45.833 0.00 0.57 0.00 2.85
2518 3143 2.925578 TTCTCGATAACCGCTCGAAA 57.074 45.000 0.00 0.00 43.85 3.46
2519 3144 3.431922 TTCTCGATAACCGCTCGAAAT 57.568 42.857 0.00 0.00 43.85 2.17
2521 3146 2.356695 TCTCGATAACCGCTCGAAATCA 59.643 45.455 0.00 0.00 43.85 2.57
2522 3147 2.456989 TCGATAACCGCTCGAAATCAC 58.543 47.619 0.00 0.00 41.79 3.06
2654 3279 4.131088 GAGGCCGGTCGTCAGGAC 62.131 72.222 1.90 0.00 45.31 3.85
2689 3316 2.928396 ACGCCTAGGGGTGCAAGT 60.928 61.111 29.21 4.56 46.37 3.16
2690 3317 2.351276 CGCCTAGGGGTGCAAGTT 59.649 61.111 17.58 0.00 36.23 2.66
2702 3329 1.108727 TGCAAGTTGAAGCACCCCTG 61.109 55.000 7.16 0.00 35.51 4.45
2727 3354 3.195698 GATCAGTTGCGACCGGCC 61.196 66.667 0.00 0.00 42.61 6.13
2769 3396 1.579429 CCTTTGTAAGGCACCGCAC 59.421 57.895 0.00 0.00 42.78 5.34
2776 3403 1.136305 GTAAGGCACCGCACTGAGATA 59.864 52.381 0.00 0.00 0.00 1.98
2785 3412 3.638627 ACCGCACTGAGATAAGATCATCA 59.361 43.478 0.00 0.00 0.00 3.07
2797 3424 8.783833 AGATAAGATCATCATTGTAAATCCCG 57.216 34.615 0.00 0.00 0.00 5.14
2833 3460 9.950496 AACTCTCATTATACAGTGAAGATTTGT 57.050 29.630 0.00 0.00 0.00 2.83
2838 3465 6.509418 TTATACAGTGAAGATTTGTTGGCC 57.491 37.500 0.00 0.00 0.00 5.36
2845 3472 0.893727 AGATTTGTTGGCCGGTGTCC 60.894 55.000 1.90 0.00 0.00 4.02
2847 3474 2.969300 ATTTGTTGGCCGGTGTCCGT 62.969 55.000 1.90 0.00 46.80 4.69
2848 3475 4.920112 TGTTGGCCGGTGTCCGTG 62.920 66.667 1.90 0.70 46.80 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 118 8.443953 AGATTGTTATTGGAGAGATAAACAGC 57.556 34.615 0.00 0.00 0.00 4.40
173 255 7.069085 AGAGTAAGGTAATATAGTTCGGTGCAA 59.931 37.037 0.00 0.00 0.00 4.08
203 285 4.635699 ATCTCCGGTAAGAAGGTTGTTT 57.364 40.909 0.00 0.00 0.00 2.83
290 372 3.220110 TGTCCCTAGCAGTATAGGTTCG 58.780 50.000 0.00 0.00 40.77 3.95
386 468 3.568538 GTGCCTCAAACTAGTGCAATTG 58.431 45.455 6.42 0.00 33.11 2.32
441 523 4.293494 AGCAGACTGATCTTAGATGGGAA 58.707 43.478 6.65 0.00 30.42 3.97
492 574 5.303333 TGATCACGCCATCTAGGTTATTGTA 59.697 40.000 0.00 0.00 40.61 2.41
546 628 6.957631 TGTGTGATAAGTCCAGATGGTTTAT 58.042 36.000 0.00 5.19 36.34 1.40
551 633 4.836825 AGTTGTGTGATAAGTCCAGATGG 58.163 43.478 0.00 0.00 0.00 3.51
560 642 5.641209 CCCTGAGAAAGAGTTGTGTGATAAG 59.359 44.000 0.00 0.00 0.00 1.73
600 682 6.732896 TTCTACTAATCCCTTAGCTCCAAG 57.267 41.667 0.00 0.00 38.33 3.61
611 693 9.713713 GAGGATAAAGTCAATTCTACTAATCCC 57.286 37.037 17.90 11.53 38.86 3.85
644 726 4.927267 TTCAGGAATGTACCCAGTGAAT 57.073 40.909 0.00 0.00 0.00 2.57
654 736 7.499321 ACGTACAAATTGTTTCAGGAATGTA 57.501 32.000 3.17 0.00 0.00 2.29
656 738 6.915300 TCAACGTACAAATTGTTTCAGGAATG 59.085 34.615 3.17 0.00 0.00 2.67
666 748 4.457466 AGGTTCCTCAACGTACAAATTGT 58.543 39.130 3.43 3.43 32.68 2.71
960 1042 3.451178 AGTTGGCGAAGGAGCTTAAGATA 59.549 43.478 6.67 0.00 37.29 1.98
970 1052 2.870435 GCTAAACTCAGTTGGCGAAGGA 60.870 50.000 0.00 0.00 0.00 3.36
1101 1183 5.966742 ACTTCTCTAAATTTGCCCACTTC 57.033 39.130 0.00 0.00 0.00 3.01
1226 1308 3.845781 TTGAGAGAGGTTATGCCATCC 57.154 47.619 0.00 0.00 40.61 3.51
1290 1372 5.689835 AGCTCCAATCTTCCTAGGAATTTC 58.310 41.667 24.48 9.39 33.28 2.17
1466 1548 6.670464 TGTATATGGACTGGTTCTCCAAGTAA 59.330 38.462 0.00 0.00 43.81 2.24
1576 1658 2.026822 ACAGGCTCGGAAACATTCTGAT 60.027 45.455 2.32 0.00 43.68 2.90
1730 1812 3.430931 CCAAGTAACAACCACAAACACG 58.569 45.455 0.00 0.00 0.00 4.49
1820 2443 5.279556 GCTTCAGTACTAGGGTGAAAGAACT 60.280 44.000 0.00 0.00 30.00 3.01
1835 2458 8.462016 ACCTTCATTTATTTCATGCTTCAGTAC 58.538 33.333 0.00 0.00 0.00 2.73
1844 2468 4.799949 CGTGGCACCTTCATTTATTTCATG 59.200 41.667 12.86 0.00 0.00 3.07
1866 2490 0.456653 GCACAAGCTACCAAATGCCG 60.457 55.000 0.00 0.00 37.91 5.69
1867 2491 3.423848 GCACAAGCTACCAAATGCC 57.576 52.632 0.00 0.00 37.91 4.40
1904 2528 4.882671 TCGTATTACAAGTCTACCGGAC 57.117 45.455 9.46 0.00 44.80 4.79
2053 2677 0.605083 TCACTGCTAGCCACTCACAG 59.395 55.000 13.29 3.16 0.00 3.66
2061 2685 1.486211 TAGTTCCCTCACTGCTAGCC 58.514 55.000 13.29 0.00 0.00 3.93
2062 2686 3.611766 TTTAGTTCCCTCACTGCTAGC 57.388 47.619 8.10 8.10 0.00 3.42
2063 2687 3.935828 GCTTTTAGTTCCCTCACTGCTAG 59.064 47.826 0.00 0.00 0.00 3.42
2064 2688 3.307480 GGCTTTTAGTTCCCTCACTGCTA 60.307 47.826 0.00 0.00 0.00 3.49
2065 2689 2.553247 GGCTTTTAGTTCCCTCACTGCT 60.553 50.000 0.00 0.00 0.00 4.24
2066 2690 1.813178 GGCTTTTAGTTCCCTCACTGC 59.187 52.381 0.00 0.00 0.00 4.40
2067 2691 3.140325 TGGCTTTTAGTTCCCTCACTG 57.860 47.619 0.00 0.00 0.00 3.66
2068 2692 4.388577 AATGGCTTTTAGTTCCCTCACT 57.611 40.909 0.00 0.00 0.00 3.41
2069 2693 7.338449 TGTTATAATGGCTTTTAGTTCCCTCAC 59.662 37.037 0.00 0.00 0.00 3.51
2070 2694 7.406916 TGTTATAATGGCTTTTAGTTCCCTCA 58.593 34.615 0.00 0.00 0.00 3.86
2071 2695 7.875327 TGTTATAATGGCTTTTAGTTCCCTC 57.125 36.000 0.00 0.00 0.00 4.30
2072 2696 8.658840 TTTGTTATAATGGCTTTTAGTTCCCT 57.341 30.769 0.00 0.00 0.00 4.20
2073 2697 9.146984 GTTTTGTTATAATGGCTTTTAGTTCCC 57.853 33.333 0.00 0.00 0.00 3.97
2074 2698 8.856247 CGTTTTGTTATAATGGCTTTTAGTTCC 58.144 33.333 0.00 0.00 0.00 3.62
2075 2699 9.615295 TCGTTTTGTTATAATGGCTTTTAGTTC 57.385 29.630 0.00 0.00 0.00 3.01
2076 2700 9.968870 TTCGTTTTGTTATAATGGCTTTTAGTT 57.031 25.926 0.00 0.00 0.00 2.24
2081 2705 9.705290 AGAAATTCGTTTTGTTATAATGGCTTT 57.295 25.926 0.00 0.00 0.00 3.51
2082 2706 9.139174 CAGAAATTCGTTTTGTTATAATGGCTT 57.861 29.630 0.00 0.00 0.00 4.35
2083 2707 7.759433 CCAGAAATTCGTTTTGTTATAATGGCT 59.241 33.333 0.00 0.00 0.00 4.75
2084 2708 7.464045 GCCAGAAATTCGTTTTGTTATAATGGC 60.464 37.037 0.00 0.00 0.00 4.40
2085 2709 7.253618 CGCCAGAAATTCGTTTTGTTATAATGG 60.254 37.037 0.00 0.00 0.00 3.16
2086 2710 7.253618 CCGCCAGAAATTCGTTTTGTTATAATG 60.254 37.037 0.00 0.00 0.00 1.90
2087 2711 6.750039 CCGCCAGAAATTCGTTTTGTTATAAT 59.250 34.615 0.00 0.00 0.00 1.28
2088 2712 6.087522 CCGCCAGAAATTCGTTTTGTTATAA 58.912 36.000 0.00 0.00 0.00 0.98
2089 2713 5.392165 CCCGCCAGAAATTCGTTTTGTTATA 60.392 40.000 0.00 0.00 0.00 0.98
2090 2714 4.481463 CCGCCAGAAATTCGTTTTGTTAT 58.519 39.130 0.00 0.00 0.00 1.89
2091 2715 3.304794 CCCGCCAGAAATTCGTTTTGTTA 60.305 43.478 0.00 0.00 0.00 2.41
2092 2716 2.544903 CCCGCCAGAAATTCGTTTTGTT 60.545 45.455 0.00 0.00 0.00 2.83
2093 2717 1.000717 CCCGCCAGAAATTCGTTTTGT 60.001 47.619 0.00 0.00 0.00 2.83
2094 2718 1.268352 TCCCGCCAGAAATTCGTTTTG 59.732 47.619 0.00 0.00 0.00 2.44
2095 2719 1.611519 TCCCGCCAGAAATTCGTTTT 58.388 45.000 0.00 0.00 0.00 2.43
2096 2720 1.611519 TTCCCGCCAGAAATTCGTTT 58.388 45.000 0.00 0.00 0.00 3.60
2097 2721 1.539827 CTTTCCCGCCAGAAATTCGTT 59.460 47.619 0.00 0.00 35.30 3.85
2098 2722 1.165270 CTTTCCCGCCAGAAATTCGT 58.835 50.000 0.00 0.00 35.30 3.85
2099 2723 1.448985 TCTTTCCCGCCAGAAATTCG 58.551 50.000 0.00 0.00 35.30 3.34
2100 2724 3.934457 TTTCTTTCCCGCCAGAAATTC 57.066 42.857 0.00 0.00 34.71 2.17
2101 2725 3.244078 GGTTTTCTTTCCCGCCAGAAATT 60.244 43.478 0.00 0.00 38.51 1.82
2102 2726 2.299013 GGTTTTCTTTCCCGCCAGAAAT 59.701 45.455 0.00 0.00 38.51 2.17
2103 2727 1.684450 GGTTTTCTTTCCCGCCAGAAA 59.316 47.619 0.00 0.00 37.26 2.52
2104 2728 1.324383 GGTTTTCTTTCCCGCCAGAA 58.676 50.000 0.00 0.00 0.00 3.02
2105 2729 0.183971 TGGTTTTCTTTCCCGCCAGA 59.816 50.000 0.00 0.00 0.00 3.86
2106 2730 1.036707 TTGGTTTTCTTTCCCGCCAG 58.963 50.000 0.00 0.00 0.00 4.85
2107 2731 1.486211 TTTGGTTTTCTTTCCCGCCA 58.514 45.000 0.00 0.00 0.00 5.69
2108 2732 2.831685 ATTTGGTTTTCTTTCCCGCC 57.168 45.000 0.00 0.00 0.00 6.13
2109 2733 5.178623 CCTTAAATTTGGTTTTCTTTCCCGC 59.821 40.000 0.00 0.00 0.00 6.13
2110 2734 5.178623 GCCTTAAATTTGGTTTTCTTTCCCG 59.821 40.000 0.00 0.00 0.00 5.14
2111 2735 5.178623 CGCCTTAAATTTGGTTTTCTTTCCC 59.821 40.000 0.00 0.00 0.00 3.97
2112 2736 5.178623 CCGCCTTAAATTTGGTTTTCTTTCC 59.821 40.000 0.00 0.00 0.00 3.13
2113 2737 5.178623 CCCGCCTTAAATTTGGTTTTCTTTC 59.821 40.000 0.00 0.00 0.00 2.62
2114 2738 5.060506 CCCGCCTTAAATTTGGTTTTCTTT 58.939 37.500 0.00 0.00 0.00 2.52
2115 2739 4.345547 TCCCGCCTTAAATTTGGTTTTCTT 59.654 37.500 0.00 0.00 0.00 2.52
2116 2740 3.898741 TCCCGCCTTAAATTTGGTTTTCT 59.101 39.130 0.00 0.00 0.00 2.52
2117 2741 4.260139 TCCCGCCTTAAATTTGGTTTTC 57.740 40.909 0.00 0.00 0.00 2.29
2118 2742 4.691326 TTCCCGCCTTAAATTTGGTTTT 57.309 36.364 0.00 0.00 0.00 2.43
2119 2743 4.691326 TTTCCCGCCTTAAATTTGGTTT 57.309 36.364 0.00 0.00 0.00 3.27
2120 2744 4.382291 GTTTTCCCGCCTTAAATTTGGTT 58.618 39.130 0.00 0.00 0.00 3.67
2121 2745 3.553302 CGTTTTCCCGCCTTAAATTTGGT 60.553 43.478 0.00 0.00 0.00 3.67
2122 2746 2.990514 CGTTTTCCCGCCTTAAATTTGG 59.009 45.455 0.00 0.00 0.00 3.28
2123 2747 3.903360 TCGTTTTCCCGCCTTAAATTTG 58.097 40.909 0.00 0.00 0.00 2.32
2124 2748 4.587584 TTCGTTTTCCCGCCTTAAATTT 57.412 36.364 0.00 0.00 0.00 1.82
2125 2749 4.587584 TTTCGTTTTCCCGCCTTAAATT 57.412 36.364 0.00 0.00 0.00 1.82
2126 2750 4.794278 ATTTCGTTTTCCCGCCTTAAAT 57.206 36.364 0.00 0.00 0.00 1.40
2127 2751 4.299978 CAATTTCGTTTTCCCGCCTTAAA 58.700 39.130 0.00 0.00 0.00 1.52
2128 2752 3.305471 CCAATTTCGTTTTCCCGCCTTAA 60.305 43.478 0.00 0.00 0.00 1.85
2129 2753 2.229302 CCAATTTCGTTTTCCCGCCTTA 59.771 45.455 0.00 0.00 0.00 2.69
2130 2754 1.000394 CCAATTTCGTTTTCCCGCCTT 60.000 47.619 0.00 0.00 0.00 4.35
2131 2755 0.601057 CCAATTTCGTTTTCCCGCCT 59.399 50.000 0.00 0.00 0.00 5.52
2132 2756 0.389296 CCCAATTTCGTTTTCCCGCC 60.389 55.000 0.00 0.00 0.00 6.13
2133 2757 1.011968 GCCCAATTTCGTTTTCCCGC 61.012 55.000 0.00 0.00 0.00 6.13
2134 2758 0.731174 CGCCCAATTTCGTTTTCCCG 60.731 55.000 0.00 0.00 0.00 5.14
2135 2759 0.599060 TCGCCCAATTTCGTTTTCCC 59.401 50.000 0.00 0.00 0.00 3.97
2136 2760 1.977188 CTCGCCCAATTTCGTTTTCC 58.023 50.000 0.00 0.00 0.00 3.13
2137 2761 1.335506 TGCTCGCCCAATTTCGTTTTC 60.336 47.619 0.00 0.00 0.00 2.29
2138 2762 0.671251 TGCTCGCCCAATTTCGTTTT 59.329 45.000 0.00 0.00 0.00 2.43
2139 2763 0.240945 CTGCTCGCCCAATTTCGTTT 59.759 50.000 0.00 0.00 0.00 3.60
2140 2764 1.586154 CCTGCTCGCCCAATTTCGTT 61.586 55.000 0.00 0.00 0.00 3.85
2141 2765 2.040544 CCTGCTCGCCCAATTTCGT 61.041 57.895 0.00 0.00 0.00 3.85
2142 2766 2.040544 ACCTGCTCGCCCAATTTCG 61.041 57.895 0.00 0.00 0.00 3.46
2143 2767 1.508088 CACCTGCTCGCCCAATTTC 59.492 57.895 0.00 0.00 0.00 2.17
2144 2768 1.978617 CCACCTGCTCGCCCAATTT 60.979 57.895 0.00 0.00 0.00 1.82
2145 2769 2.361610 CCACCTGCTCGCCCAATT 60.362 61.111 0.00 0.00 0.00 2.32
2146 2770 2.905996 TTCCACCTGCTCGCCCAAT 61.906 57.895 0.00 0.00 0.00 3.16
2147 2771 3.565214 TTCCACCTGCTCGCCCAA 61.565 61.111 0.00 0.00 0.00 4.12
2148 2772 4.329545 GTTCCACCTGCTCGCCCA 62.330 66.667 0.00 0.00 0.00 5.36
2149 2773 3.553095 AAGTTCCACCTGCTCGCCC 62.553 63.158 0.00 0.00 0.00 6.13
2150 2774 2.032681 AAGTTCCACCTGCTCGCC 59.967 61.111 0.00 0.00 0.00 5.54
2151 2775 2.035442 GGAAGTTCCACCTGCTCGC 61.035 63.158 17.44 0.00 36.28 5.03
2152 2776 1.376037 GGGAAGTTCCACCTGCTCG 60.376 63.158 23.33 0.00 38.64 5.03
2153 2777 1.376037 CGGGAAGTTCCACCTGCTC 60.376 63.158 23.33 3.26 38.64 4.26
2154 2778 2.750350 CGGGAAGTTCCACCTGCT 59.250 61.111 23.33 0.00 38.64 4.24
2156 2780 2.725203 TTCGCGGGAAGTTCCACCTG 62.725 60.000 23.33 10.69 38.64 4.00
2157 2781 2.513259 TTCGCGGGAAGTTCCACCT 61.513 57.895 23.33 0.00 38.64 4.00
2158 2782 2.031465 TTCGCGGGAAGTTCCACC 59.969 61.111 23.33 11.93 38.64 4.61
2159 2783 2.322830 GGTTCGCGGGAAGTTCCAC 61.323 63.158 23.33 13.42 38.64 4.02
2160 2784 2.031465 GGTTCGCGGGAAGTTCCA 59.969 61.111 23.33 0.00 38.64 3.53
2161 2785 2.031465 TGGTTCGCGGGAAGTTCC 59.969 61.111 15.99 13.99 35.23 3.62
2162 2786 2.664436 CGTGGTTCGCGGGAAGTTC 61.664 63.158 15.99 8.89 33.47 3.01
2163 2787 2.086251 TACGTGGTTCGCGGGAAGTT 62.086 55.000 15.99 1.12 41.96 2.66
2164 2788 1.880819 ATACGTGGTTCGCGGGAAGT 61.881 55.000 15.99 12.06 41.96 3.01
2165 2789 0.101040 TATACGTGGTTCGCGGGAAG 59.899 55.000 15.99 6.41 41.96 3.46
2166 2790 0.101040 CTATACGTGGTTCGCGGGAA 59.899 55.000 11.32 11.32 41.96 3.97
2167 2791 0.747644 TCTATACGTGGTTCGCGGGA 60.748 55.000 6.13 0.00 41.96 5.14
2168 2792 0.101040 TTCTATACGTGGTTCGCGGG 59.899 55.000 6.13 0.00 41.96 6.13
2169 2793 1.202222 ACTTCTATACGTGGTTCGCGG 60.202 52.381 6.13 0.00 41.96 6.46
2170 2794 1.844357 CACTTCTATACGTGGTTCGCG 59.156 52.381 0.00 0.00 44.19 5.87
2171 2795 2.190981 CCACTTCTATACGTGGTTCGC 58.809 52.381 0.00 0.00 44.38 4.70
2177 2801 2.793933 CGTCACCCACTTCTATACGTG 58.206 52.381 0.00 0.00 0.00 4.49
2178 2802 1.133790 GCGTCACCCACTTCTATACGT 59.866 52.381 0.00 0.00 0.00 3.57
2179 2803 1.535437 GGCGTCACCCACTTCTATACG 60.535 57.143 0.00 0.00 0.00 3.06
2180 2804 1.755380 AGGCGTCACCCACTTCTATAC 59.245 52.381 0.00 0.00 40.58 1.47
2181 2805 2.154567 AGGCGTCACCCACTTCTATA 57.845 50.000 0.00 0.00 40.58 1.31
2182 2806 2.032620 CTAGGCGTCACCCACTTCTAT 58.967 52.381 0.00 0.00 40.58 1.98
2183 2807 1.005097 TCTAGGCGTCACCCACTTCTA 59.995 52.381 0.00 0.00 40.58 2.10
2184 2808 0.251653 TCTAGGCGTCACCCACTTCT 60.252 55.000 0.00 0.00 40.58 2.85
2185 2809 0.173708 CTCTAGGCGTCACCCACTTC 59.826 60.000 0.00 0.00 40.58 3.01
2186 2810 0.542232 ACTCTAGGCGTCACCCACTT 60.542 55.000 0.00 0.00 40.58 3.16
2187 2811 0.542232 AACTCTAGGCGTCACCCACT 60.542 55.000 0.00 0.00 40.58 4.00
2188 2812 1.180029 TAACTCTAGGCGTCACCCAC 58.820 55.000 0.00 0.00 40.58 4.61
2189 2813 1.927487 TTAACTCTAGGCGTCACCCA 58.073 50.000 0.00 0.00 40.58 4.51
2190 2814 4.660789 TTATTAACTCTAGGCGTCACCC 57.339 45.455 0.00 0.00 40.58 4.61
2191 2815 6.742109 TGTATTATTAACTCTAGGCGTCACC 58.258 40.000 0.00 0.00 39.61 4.02
2192 2816 6.862090 CCTGTATTATTAACTCTAGGCGTCAC 59.138 42.308 0.00 0.00 0.00 3.67
2193 2817 6.516194 GCCTGTATTATTAACTCTAGGCGTCA 60.516 42.308 0.00 0.00 39.89 4.35
2194 2818 5.862860 GCCTGTATTATTAACTCTAGGCGTC 59.137 44.000 0.00 0.00 39.89 5.19
2195 2819 5.780984 GCCTGTATTATTAACTCTAGGCGT 58.219 41.667 0.00 0.00 39.89 5.68
2197 2821 5.169295 CCGCCTGTATTATTAACTCTAGGC 58.831 45.833 0.00 0.00 44.47 3.93
2198 2822 6.342338 ACCGCCTGTATTATTAACTCTAGG 57.658 41.667 0.00 0.00 0.00 3.02
2199 2823 7.924412 TCAAACCGCCTGTATTATTAACTCTAG 59.076 37.037 0.00 0.00 0.00 2.43
2200 2824 7.784037 TCAAACCGCCTGTATTATTAACTCTA 58.216 34.615 0.00 0.00 0.00 2.43
2201 2825 6.646267 TCAAACCGCCTGTATTATTAACTCT 58.354 36.000 0.00 0.00 0.00 3.24
2202 2826 6.913873 TCAAACCGCCTGTATTATTAACTC 57.086 37.500 0.00 0.00 0.00 3.01
2203 2827 6.882678 ACTTCAAACCGCCTGTATTATTAACT 59.117 34.615 0.00 0.00 0.00 2.24
2204 2828 6.964934 CACTTCAAACCGCCTGTATTATTAAC 59.035 38.462 0.00 0.00 0.00 2.01
2205 2829 6.094325 CCACTTCAAACCGCCTGTATTATTAA 59.906 38.462 0.00 0.00 0.00 1.40
2206 2830 5.587043 CCACTTCAAACCGCCTGTATTATTA 59.413 40.000 0.00 0.00 0.00 0.98
2207 2831 4.398044 CCACTTCAAACCGCCTGTATTATT 59.602 41.667 0.00 0.00 0.00 1.40
2208 2832 3.945285 CCACTTCAAACCGCCTGTATTAT 59.055 43.478 0.00 0.00 0.00 1.28
2209 2833 3.244630 ACCACTTCAAACCGCCTGTATTA 60.245 43.478 0.00 0.00 0.00 0.98
2210 2834 2.159382 CCACTTCAAACCGCCTGTATT 58.841 47.619 0.00 0.00 0.00 1.89
2211 2835 1.073284 ACCACTTCAAACCGCCTGTAT 59.927 47.619 0.00 0.00 0.00 2.29
2212 2836 0.470766 ACCACTTCAAACCGCCTGTA 59.529 50.000 0.00 0.00 0.00 2.74
2213 2837 0.395173 AACCACTTCAAACCGCCTGT 60.395 50.000 0.00 0.00 0.00 4.00
2214 2838 0.744281 AAACCACTTCAAACCGCCTG 59.256 50.000 0.00 0.00 0.00 4.85
2215 2839 0.744281 CAAACCACTTCAAACCGCCT 59.256 50.000 0.00 0.00 0.00 5.52
2216 2840 0.741915 TCAAACCACTTCAAACCGCC 59.258 50.000 0.00 0.00 0.00 6.13
2217 2841 1.864029 GCTCAAACCACTTCAAACCGC 60.864 52.381 0.00 0.00 0.00 5.68
2218 2842 1.269051 GGCTCAAACCACTTCAAACCG 60.269 52.381 0.00 0.00 0.00 4.44
2219 2843 1.068588 GGGCTCAAACCACTTCAAACC 59.931 52.381 0.00 0.00 0.00 3.27
2220 2844 1.068588 GGGGCTCAAACCACTTCAAAC 59.931 52.381 0.00 0.00 0.00 2.93
2221 2845 1.342474 TGGGGCTCAAACCACTTCAAA 60.342 47.619 0.00 0.00 32.68 2.69
2222 2846 0.260230 TGGGGCTCAAACCACTTCAA 59.740 50.000 0.00 0.00 32.68 2.69
2223 2847 1.926657 TGGGGCTCAAACCACTTCA 59.073 52.632 0.00 0.00 32.68 3.02
2224 2848 4.920828 TGGGGCTCAAACCACTTC 57.079 55.556 0.00 0.00 32.68 3.01
2228 2852 2.312390 GTTTAAGTGGGGCTCAAACCA 58.688 47.619 0.00 0.00 0.00 3.67
2275 2899 3.735237 TTGTTTTGCCTAATTCCGCAA 57.265 38.095 7.76 7.76 42.99 4.85
2293 2917 5.261209 TGAATCACTTCCCTGTTGTTTTG 57.739 39.130 0.00 0.00 0.00 2.44
2309 2934 3.156401 GCGTTGTGCGTTTGAATCA 57.844 47.368 0.00 0.00 43.66 2.57
2323 2948 3.138304 TGAGCTAGAATGTTGTTGCGTT 58.862 40.909 0.00 0.00 0.00 4.84
2336 2961 0.618680 ACATGGGGTGCTGAGCTAGA 60.619 55.000 5.83 0.00 0.00 2.43
2366 2991 1.448540 GTGGAGCGATGACCTGGTG 60.449 63.158 2.82 0.00 0.00 4.17
2382 3007 5.215160 GGAAACTAGCTTTGAACACATGTG 58.785 41.667 24.25 24.25 0.00 3.21
2480 3105 5.321927 GAGAATTTCTTCACCCCCAGTAAA 58.678 41.667 0.00 0.00 33.56 2.01
2485 3110 1.982226 TCGAGAATTTCTTCACCCCCA 59.018 47.619 0.00 0.00 33.56 4.96
2491 3116 4.755411 AGCGGTTATCGAGAATTTCTTCA 58.245 39.130 0.00 0.00 42.43 3.02
2492 3117 4.085517 CGAGCGGTTATCGAGAATTTCTTC 60.086 45.833 0.00 0.00 42.76 2.87
2506 3131 2.350899 TTCGTGATTTCGAGCGGTTA 57.649 45.000 0.00 0.00 40.86 2.85
2533 3158 5.619981 GCCTGCTCTAGTGTTTTGGTTATTG 60.620 44.000 0.00 0.00 0.00 1.90
2534 3159 4.459337 GCCTGCTCTAGTGTTTTGGTTATT 59.541 41.667 0.00 0.00 0.00 1.40
2535 3160 4.010349 GCCTGCTCTAGTGTTTTGGTTAT 58.990 43.478 0.00 0.00 0.00 1.89
2563 3188 4.355543 AAACATAACAAGCACTATGGCG 57.644 40.909 0.00 0.00 39.27 5.69
2566 3191 7.537715 TGGATCAAAACATAACAAGCACTATG 58.462 34.615 0.00 0.00 0.00 2.23
2617 3242 1.016130 CGCTCCGCATTGTCAGAAGT 61.016 55.000 0.00 0.00 0.00 3.01
2663 3288 4.162690 CCTAGGCGTCCCTGGCAC 62.163 72.222 0.00 0.00 42.90 5.01
2670 3295 3.682292 CTTGCACCCCTAGGCGTCC 62.682 68.421 2.05 0.00 36.11 4.79
2689 3316 0.546122 ATATCGCAGGGGTGCTTCAA 59.454 50.000 0.00 0.00 0.00 2.69
2690 3317 0.179048 CATATCGCAGGGGTGCTTCA 60.179 55.000 0.00 0.00 0.00 3.02
2702 3329 1.457303 GTCGCAACTGATCCATATCGC 59.543 52.381 0.00 0.00 34.60 4.58
2705 3332 1.270305 CCGGTCGCAACTGATCCATAT 60.270 52.381 0.00 0.00 33.20 1.78
2708 3335 2.264480 CCGGTCGCAACTGATCCA 59.736 61.111 0.00 0.00 33.20 3.41
2709 3336 3.195698 GCCGGTCGCAACTGATCC 61.196 66.667 1.90 0.00 37.47 3.36
2761 3388 2.131183 GATCTTATCTCAGTGCGGTGC 58.869 52.381 0.00 0.00 0.00 5.01
2765 3392 5.695363 ACAATGATGATCTTATCTCAGTGCG 59.305 40.000 12.42 0.00 36.71 5.34
2776 3403 4.520492 GCCGGGATTTACAATGATGATCTT 59.480 41.667 2.18 0.00 0.00 2.40
2785 3412 5.923733 TTACAAATGCCGGGATTTACAAT 57.076 34.783 30.37 18.96 0.00 2.71
2797 3424 8.893727 ACTGTATAATGAGAGTTTACAAATGCC 58.106 33.333 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.