Multiple sequence alignment - TraesCS7B01G166100

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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 TraesCS7B01G166100 chr7B 100.000 4864 0 0 1 4864 228921629 228916766 0.000000e+00 8983.0
1 TraesCS7B01G166100 chr7B 94.521 73 4 0 2825 2897 34609758 34609686 3.980000e-21 113.0
2 TraesCS7B01G166100 chr7B 95.588 68 3 0 4098 4165 228917456 228917389 5.150000e-20 110.0
3 TraesCS7B01G166100 chr7B 95.588 68 3 0 4174 4241 228917532 228917465 5.150000e-20 110.0
4 TraesCS7B01G166100 chr7A 93.216 1990 101 16 2902 4864 268864027 268866009 0.000000e+00 2896.0
5 TraesCS7B01G166100 chr7A 88.090 1696 122 35 60 1722 268861415 268863063 0.000000e+00 1940.0
6 TraesCS7B01G166100 chr7A 93.115 886 52 5 1949 2829 268863124 268864005 0.000000e+00 1290.0
7 TraesCS7B01G166100 chr7A 78.422 431 50 26 1918 2346 122344115 122343726 1.750000e-59 241.0
8 TraesCS7B01G166100 chr7A 82.917 240 33 4 2109 2346 74139940 74140173 4.930000e-50 209.0
9 TraesCS7B01G166100 chr7A 93.846 130 7 1 1898 2026 74139776 74139905 1.380000e-45 195.0
10 TraesCS7B01G166100 chr7A 95.775 71 3 0 4171 4241 268865234 268865304 1.110000e-21 115.0
11 TraesCS7B01G166100 chr7A 94.444 72 4 0 4094 4165 268865309 268865380 1.430000e-20 111.0
12 TraesCS7B01G166100 chr7D 91.622 1874 107 25 3028 4864 252242512 252240652 0.000000e+00 2545.0
13 TraesCS7B01G166100 chr7D 90.442 1810 85 27 1 1771 252245110 252243350 0.000000e+00 2303.0
14 TraesCS7B01G166100 chr7D 89.139 488 45 4 2347 2829 252243182 252242698 6.970000e-168 601.0
15 TraesCS7B01G166100 chr7D 90.345 145 14 0 2194 2338 561701247 561701103 1.790000e-44 191.0
16 TraesCS7B01G166100 chr7D 88.000 150 12 3 2902 3045 252242679 252242530 6.470000e-39 172.0
17 TraesCS7B01G166100 chr7D 94.444 72 4 0 4094 4165 252241345 252241274 1.430000e-20 111.0
18 TraesCS7B01G166100 chr3B 81.425 463 60 16 1896 2346 710386825 710387273 5.990000e-94 355.0
19 TraesCS7B01G166100 chr3B 90.476 126 11 1 1904 2029 808854686 808854562 1.080000e-36 165.0
20 TraesCS7B01G166100 chr3B 92.308 78 6 0 2825 2902 308390936 308391013 1.430000e-20 111.0
21 TraesCS7B01G166100 chr6A 85.804 317 26 14 1901 2199 23894945 23895260 7.860000e-83 318.0
22 TraesCS7B01G166100 chr5D 79.574 470 45 23 1901 2346 379542908 379543350 6.160000e-74 289.0
23 TraesCS7B01G166100 chr5D 77.253 466 74 18 1099 1539 405398873 405398415 1.350000e-60 244.0
24 TraesCS7B01G166100 chr5D 92.208 77 6 0 2826 2902 560242933 560243009 5.150000e-20 110.0
25 TraesCS7B01G166100 chr5D 87.500 88 9 2 2816 2902 313637472 313637558 3.100000e-17 100.0
26 TraesCS7B01G166100 chr1D 85.448 268 34 5 2081 2347 445587646 445587383 1.720000e-69 274.0
27 TraesCS7B01G166100 chr1D 100.000 29 0 0 2070 2098 365898666 365898694 2.000000e-03 54.7
28 TraesCS7B01G166100 chr5B 77.468 466 73 18 1099 1539 486368914 486368456 2.910000e-62 250.0
29 TraesCS7B01G166100 chr5B 94.366 71 4 0 1901 1971 391160040 391160110 5.150000e-20 110.0
30 TraesCS7B01G166100 chr5B 80.000 120 11 8 2035 2154 576056940 576056834 5.220000e-10 76.8
31 TraesCS7B01G166100 chr1B 82.375 261 31 14 2097 2346 633965517 633965773 3.810000e-51 213.0
32 TraesCS7B01G166100 chr2B 90.909 154 14 0 2193 2346 748585985 748585832 1.770000e-49 207.0
33 TraesCS7B01G166100 chr2B 88.608 158 14 4 2192 2348 617928798 617928952 6.430000e-44 189.0
34 TraesCS7B01G166100 chr2B 94.366 71 4 0 2827 2897 456339450 456339380 5.150000e-20 110.0
35 TraesCS7B01G166100 chr2B 93.333 45 3 0 2053 2097 793516492 793516536 3.140000e-07 67.6
36 TraesCS7B01G166100 chr2D 89.744 156 15 1 2192 2346 607078447 607078292 1.070000e-46 198.0
37 TraesCS7B01G166100 chr2D 91.566 83 7 0 2820 2902 444766886 444766968 1.110000e-21 115.0
38 TraesCS7B01G166100 chr4D 90.541 148 11 3 2192 2338 51607909 51607764 4.970000e-45 193.0
39 TraesCS7B01G166100 chr6D 88.971 136 15 0 1901 2036 9853487 9853622 8.370000e-38 169.0
40 TraesCS7B01G166100 chr3A 94.366 71 4 0 2827 2897 642924939 642924869 5.150000e-20 110.0
41 TraesCS7B01G166100 chr4A 91.139 79 7 0 2824 2902 152742131 152742053 1.850000e-19 108.0
42 TraesCS7B01G166100 chr5A 89.024 82 9 0 2821 2902 64655820 64655901 8.610000e-18 102.0
43 TraesCS7B01G166100 chr3D 85.366 82 9 3 2080 2160 584129415 584129336 1.120000e-11 82.4


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 TraesCS7B01G166100 chr7B 228916766 228921629 4863 True 8983.0 8983 100.0000 1 4864 1 chr7B.!!$R2 4863
1 TraesCS7B01G166100 chr7A 268861415 268866009 4594 False 1270.4 2896 92.9280 60 4864 5 chr7A.!!$F2 4804
2 TraesCS7B01G166100 chr7D 252240652 252245110 4458 True 1146.4 2545 90.7294 1 4864 5 chr7D.!!$R2 4863

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
718 766 0.109504 GGAAAATAGGCGCACGCAAA 60.110 50.0 17.69 4.13 44.11 3.68 F
1016 1076 1.194781 AACATGAGCAGGTCTCCGGT 61.195 55.0 0.00 0.00 41.18 5.28 F
1917 2078 0.044092 TGGGGAATGGCTAGGAGTCA 59.956 55.0 0.00 0.00 32.55 3.41 F
1995 2156 0.100503 GATGGAAAATGAACGGCCCG 59.899 55.0 0.00 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2059 0.044092 TGACTCCTAGCCATTCCCCA 59.956 55.0 0.00 0.00 0.00 4.96 R
2893 3064 0.179076 ACGCATGATCCGATGCTTCA 60.179 50.0 14.16 0.00 45.60 3.02 R
3500 3749 0.027716 GTGCATCATTCAGAGCTGCG 59.972 55.0 0.00 0.00 35.48 5.18 R
3939 4188 0.031449 GGCTCGGCTCTGACAGATAC 59.969 60.0 5.42 1.29 0.00 2.24 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
60 61 9.635520 CCGTACTAATCCTACAAGGTTAATATG 57.364 37.037 0.00 0.00 36.53 1.78
69 70 9.442062 TCCTACAAGGTTAATATGATCCAGTTA 57.558 33.333 0.00 0.00 36.53 2.24
209 224 7.743104 AGAATCGCAACATAAGTTCTTTACAG 58.257 34.615 0.00 0.00 35.28 2.74
210 225 5.277601 TCGCAACATAAGTTCTTTACAGC 57.722 39.130 0.00 0.00 35.28 4.40
288 308 9.455847 GTAGCATAAACTTGATGGAAATCAATC 57.544 33.333 1.85 0.00 39.52 2.67
293 313 7.605410 AAACTTGATGGAAATCAATCAATGC 57.395 32.000 12.45 0.00 39.52 3.56
375 399 6.439599 TGTATTTTTGTGTGGAATTGGTACG 58.560 36.000 0.00 0.00 0.00 3.67
380 405 4.555348 TGTGTGGAATTGGTACGTTTTC 57.445 40.909 0.00 0.00 0.00 2.29
479 505 3.915437 AACGTTTATGAGTTGCCCTTG 57.085 42.857 0.00 0.00 0.00 3.61
496 537 0.109781 TTGTACCGTCCGTTACTCGC 60.110 55.000 0.00 0.00 38.35 5.03
524 565 7.226720 CCAAAACGTGTATGAGGATAAGCTTAT 59.773 37.037 18.92 18.92 0.00 1.73
588 630 5.581126 ATTTTGCACTGTTTCACTCTCAA 57.419 34.783 0.00 0.00 0.00 3.02
597 639 4.277476 TGTTTCACTCTCAACCACCAAAT 58.723 39.130 0.00 0.00 0.00 2.32
679 727 0.393537 CCTGCGATTTTCCAGGCTCT 60.394 55.000 0.00 0.00 41.86 4.09
680 728 1.012841 CTGCGATTTTCCAGGCTCTC 58.987 55.000 0.00 0.00 0.00 3.20
716 764 2.745785 CGGAAAATAGGCGCACGCA 61.746 57.895 17.69 0.00 44.11 5.24
718 766 0.109504 GGAAAATAGGCGCACGCAAA 60.110 50.000 17.69 4.13 44.11 3.68
758 806 1.568504 ACAGAACGAATAGGCCAGGA 58.431 50.000 5.01 0.00 0.00 3.86
768 816 4.202305 CGAATAGGCCAGGAATTCTCTTCT 60.202 45.833 5.01 0.55 0.00 2.85
775 823 5.252547 GCCAGGAATTCTCTTCTTTCTCTT 58.747 41.667 5.23 0.00 0.00 2.85
776 824 5.123661 GCCAGGAATTCTCTTCTTTCTCTTG 59.876 44.000 5.23 0.00 0.00 3.02
868 928 7.936847 TGTTTAGATCTTCTCCTTTTTGCAGTA 59.063 33.333 0.00 0.00 0.00 2.74
871 931 3.399330 TCTTCTCCTTTTTGCAGTACCG 58.601 45.455 0.00 0.00 0.00 4.02
920 980 4.916041 TTCCTGACCACATTCTCTCAAT 57.084 40.909 0.00 0.00 0.00 2.57
933 993 6.316390 ACATTCTCTCAATTCCGTAATCCAAC 59.684 38.462 0.00 0.00 0.00 3.77
1016 1076 1.194781 AACATGAGCAGGTCTCCGGT 61.195 55.000 0.00 0.00 41.18 5.28
1117 1180 1.826054 CCTCCGGAGAGCGACATCT 60.826 63.158 33.39 0.00 38.96 2.90
1137 1200 3.402681 CACATGCCGGACTCCCCT 61.403 66.667 5.05 0.00 0.00 4.79
1507 1570 1.835483 CGCAAAGCTCGCAGAACTGT 61.835 55.000 8.63 0.00 31.01 3.55
1548 1611 3.384789 AGGCAAAAAGGTTTGGTCTCTTC 59.615 43.478 1.72 0.00 43.73 2.87
1574 1637 3.941483 TCTCTTCTTGCGAAATTCCATCC 59.059 43.478 0.00 0.00 0.00 3.51
1578 1641 3.601435 TCTTGCGAAATTCCATCCGTAA 58.399 40.909 0.00 0.00 0.00 3.18
1607 1670 7.943079 ATCCACTGTTCATCACAATTTGATA 57.057 32.000 2.79 0.00 43.68 2.15
1608 1671 7.757941 TCCACTGTTCATCACAATTTGATAA 57.242 32.000 2.79 0.00 43.68 1.75
1609 1672 7.819644 TCCACTGTTCATCACAATTTGATAAG 58.180 34.615 2.79 0.00 43.68 1.73
1610 1673 7.448161 TCCACTGTTCATCACAATTTGATAAGT 59.552 33.333 2.79 0.00 43.68 2.24
1611 1674 8.729756 CCACTGTTCATCACAATTTGATAAGTA 58.270 33.333 2.79 0.00 43.68 2.24
1612 1675 9.546909 CACTGTTCATCACAATTTGATAAGTAC 57.453 33.333 2.79 0.00 43.68 2.73
1613 1676 9.507329 ACTGTTCATCACAATTTGATAAGTACT 57.493 29.630 2.79 0.00 43.68 2.73
1653 1721 6.698380 TCCCAGGCTATTTCTTATCGAATAC 58.302 40.000 0.00 0.00 0.00 1.89
1701 1769 5.003096 AGAATGAAAGGGGTCTGAAATGT 57.997 39.130 0.00 0.00 0.00 2.71
1789 1902 7.924103 AAATTAAAACTGATTGAACGTGACC 57.076 32.000 0.00 0.00 0.00 4.02
1792 1905 5.924475 AAAACTGATTGAACGTGACCTAG 57.076 39.130 0.00 0.00 0.00 3.02
1793 1906 4.866508 AACTGATTGAACGTGACCTAGA 57.133 40.909 0.00 0.00 0.00 2.43
1794 1907 4.442375 ACTGATTGAACGTGACCTAGAG 57.558 45.455 0.00 0.00 0.00 2.43
1796 1909 4.281182 ACTGATTGAACGTGACCTAGAGTT 59.719 41.667 0.00 0.00 0.00 3.01
1797 1910 5.475909 ACTGATTGAACGTGACCTAGAGTTA 59.524 40.000 0.00 0.00 0.00 2.24
1798 1911 6.015688 ACTGATTGAACGTGACCTAGAGTTAA 60.016 38.462 0.00 0.00 0.00 2.01
1799 1912 6.154445 TGATTGAACGTGACCTAGAGTTAAC 58.846 40.000 0.00 0.00 0.00 2.01
1800 1913 5.518848 TTGAACGTGACCTAGAGTTAACA 57.481 39.130 8.61 0.00 0.00 2.41
1801 1914 5.717078 TGAACGTGACCTAGAGTTAACAT 57.283 39.130 8.61 0.00 0.00 2.71
1803 1916 6.518493 TGAACGTGACCTAGAGTTAACATTT 58.482 36.000 8.61 0.00 0.00 2.32
1804 1917 7.660112 TGAACGTGACCTAGAGTTAACATTTA 58.340 34.615 8.61 0.00 0.00 1.40
1805 1918 8.308931 TGAACGTGACCTAGAGTTAACATTTAT 58.691 33.333 8.61 0.00 0.00 1.40
1806 1919 8.699283 AACGTGACCTAGAGTTAACATTTATC 57.301 34.615 8.61 0.00 0.00 1.75
1807 1920 7.833786 ACGTGACCTAGAGTTAACATTTATCA 58.166 34.615 8.61 1.75 0.00 2.15
1809 1922 8.755941 CGTGACCTAGAGTTAACATTTATCATG 58.244 37.037 8.61 6.09 0.00 3.07
1816 1929 8.771920 AGAGTTAACATTTATCATGAACACGA 57.228 30.769 8.61 0.00 0.00 4.35
1817 1930 9.214957 AGAGTTAACATTTATCATGAACACGAA 57.785 29.630 8.61 0.00 0.00 3.85
1832 1993 1.929230 ACGAAACGTGTGTGATGTGA 58.071 45.000 0.00 0.00 39.18 3.58
1839 2000 1.272490 CGTGTGTGATGTGACCCTACT 59.728 52.381 0.00 0.00 0.00 2.57
1846 2007 2.426024 TGATGTGACCCTACTAACGAGC 59.574 50.000 0.00 0.00 0.00 5.03
1850 2011 1.816835 TGACCCTACTAACGAGCACTG 59.183 52.381 0.00 0.00 0.00 3.66
1855 2016 3.119101 CCCTACTAACGAGCACTGACAAT 60.119 47.826 0.00 0.00 0.00 2.71
1858 2019 5.515626 CCTACTAACGAGCACTGACAATTAC 59.484 44.000 0.00 0.00 0.00 1.89
1914 2075 2.826674 TTTTGGGGAATGGCTAGGAG 57.173 50.000 0.00 0.00 0.00 3.69
1915 2076 1.681229 TTTGGGGAATGGCTAGGAGT 58.319 50.000 0.00 0.00 0.00 3.85
1916 2077 1.213296 TTGGGGAATGGCTAGGAGTC 58.787 55.000 0.00 0.00 0.00 3.36
1917 2078 0.044092 TGGGGAATGGCTAGGAGTCA 59.956 55.000 0.00 0.00 32.55 3.41
1918 2079 1.213296 GGGGAATGGCTAGGAGTCAA 58.787 55.000 0.00 0.00 31.33 3.18
1919 2080 1.777272 GGGGAATGGCTAGGAGTCAAT 59.223 52.381 0.00 0.00 31.33 2.57
1920 2081 2.224646 GGGGAATGGCTAGGAGTCAATC 60.225 54.545 0.00 0.00 31.33 2.67
1921 2082 2.548920 GGGAATGGCTAGGAGTCAATCG 60.549 54.545 0.00 0.00 30.74 3.34
1922 2083 2.365617 GGAATGGCTAGGAGTCAATCGA 59.634 50.000 0.00 0.00 30.74 3.59
1923 2084 3.385577 GAATGGCTAGGAGTCAATCGAC 58.614 50.000 0.00 0.00 42.95 4.20
1939 2100 7.723270 GTCAATCGACTGAAATTTTGATTTGG 58.277 34.615 0.00 0.00 39.22 3.28
1940 2101 6.867816 TCAATCGACTGAAATTTTGATTTGGG 59.132 34.615 0.00 0.00 0.00 4.12
1941 2102 5.782893 TCGACTGAAATTTTGATTTGGGT 57.217 34.783 0.00 0.00 0.00 4.51
1942 2103 5.768317 TCGACTGAAATTTTGATTTGGGTC 58.232 37.500 0.00 0.00 0.00 4.46
1943 2104 5.300539 TCGACTGAAATTTTGATTTGGGTCA 59.699 36.000 0.00 0.00 0.00 4.02
1944 2105 5.630680 CGACTGAAATTTTGATTTGGGTCAG 59.369 40.000 0.00 0.00 0.00 3.51
1945 2106 6.484364 ACTGAAATTTTGATTTGGGTCAGT 57.516 33.333 0.00 0.00 0.00 3.41
1946 2107 6.515832 ACTGAAATTTTGATTTGGGTCAGTC 58.484 36.000 0.00 0.00 30.08 3.51
1947 2108 6.098124 ACTGAAATTTTGATTTGGGTCAGTCA 59.902 34.615 0.00 0.00 30.08 3.41
1948 2109 6.882656 TGAAATTTTGATTTGGGTCAGTCAA 58.117 32.000 0.00 0.00 0.00 3.18
1949 2110 7.507829 TGAAATTTTGATTTGGGTCAGTCAAT 58.492 30.769 0.00 0.00 31.39 2.57
1950 2111 7.992033 TGAAATTTTGATTTGGGTCAGTCAATT 59.008 29.630 0.00 0.00 31.39 2.32
1951 2112 8.750515 AAATTTTGATTTGGGTCAGTCAATTT 57.249 26.923 0.00 0.00 31.39 1.82
1952 2113 7.733402 ATTTTGATTTGGGTCAGTCAATTTG 57.267 32.000 0.00 0.00 31.39 2.32
1953 2114 4.870123 TGATTTGGGTCAGTCAATTTGG 57.130 40.909 0.00 0.00 0.00 3.28
1954 2115 3.006752 TGATTTGGGTCAGTCAATTTGGC 59.993 43.478 0.00 0.00 0.00 4.52
1968 2129 2.673775 TTTGGCCTGGATCAGTTTGA 57.326 45.000 3.32 0.00 0.00 2.69
1972 2133 0.449388 GCCTGGATCAGTTTGAAGCG 59.551 55.000 0.00 0.00 0.00 4.68
1995 2156 0.100503 GATGGAAAATGAACGGCCCG 59.899 55.000 0.00 0.00 0.00 6.13
1996 2157 1.319614 ATGGAAAATGAACGGCCCGG 61.320 55.000 8.57 0.00 0.00 5.73
2015 2176 3.553096 CCGGATTATGTCTTCTTCCTCCG 60.553 52.174 0.00 0.00 42.97 4.63
2018 2179 4.141914 GGATTATGTCTTCTTCCTCCGTGT 60.142 45.833 0.00 0.00 0.00 4.49
2035 2196 3.236816 CGTGTGTTTTCCAGATTGCATC 58.763 45.455 0.00 0.00 0.00 3.91
2047 2213 1.492176 GATTGCATCTTCCTCCTCCCA 59.508 52.381 0.00 0.00 0.00 4.37
2056 2222 2.997315 CTCCTCCCACCGACTGCA 60.997 66.667 0.00 0.00 0.00 4.41
2132 2298 4.308458 CCACCGCCGGTCTTGTCA 62.308 66.667 5.41 0.00 31.02 3.58
2162 2328 3.851184 ATCCCTCTAGCCCCGCCT 61.851 66.667 0.00 0.00 0.00 5.52
2164 2330 4.860881 CCCTCTAGCCCCGCCTGA 62.861 72.222 0.00 0.00 0.00 3.86
2167 2333 1.152735 CTCTAGCCCCGCCTGAGTA 60.153 63.158 0.00 0.00 0.00 2.59
2169 2335 1.455959 CTAGCCCCGCCTGAGTACT 60.456 63.158 0.00 0.00 0.00 2.73
2228 2394 7.443477 GGACCCTGAACCTTAAGATAGATAAC 58.557 42.308 3.36 0.00 0.00 1.89
2232 2398 6.267014 CCTGAACCTTAAGATAGATAACGGGA 59.733 42.308 3.36 0.00 0.00 5.14
2233 2399 7.038941 CCTGAACCTTAAGATAGATAACGGGAT 60.039 40.741 3.36 0.00 0.00 3.85
2242 2408 1.000955 AGATAACGGGATGATGACGGC 59.999 52.381 0.00 0.00 0.00 5.68
2261 2427 1.681486 CGAGCCCCTTCCTTCTCTCC 61.681 65.000 0.00 0.00 0.00 3.71
2263 2429 1.686110 GCCCCTTCCTTCTCTCCGA 60.686 63.158 0.00 0.00 0.00 4.55
2264 2430 1.051556 GCCCCTTCCTTCTCTCCGAT 61.052 60.000 0.00 0.00 0.00 4.18
2284 2450 3.205522 AGGCCCTTCCTTCTCCTTT 57.794 52.632 0.00 0.00 44.75 3.11
2287 2453 1.356059 GGCCCTTCCTTCTCCTTTCTT 59.644 52.381 0.00 0.00 0.00 2.52
2314 2480 3.328382 AAATCGACTGACCCGAATTCA 57.672 42.857 6.22 0.00 39.62 2.57
2352 2518 5.468746 TGACATGTAGCTAAACTGGTGTTTC 59.531 40.000 0.00 0.00 44.35 2.78
2385 2551 4.478206 TCTCTCGGATGAAAATGCTTCT 57.522 40.909 0.00 0.00 0.00 2.85
2430 2596 3.190079 CACGATGTGATCCGAAGAACAT 58.810 45.455 0.00 0.00 35.23 2.71
2436 2602 3.058293 TGTGATCCGAAGAACATGCAAAC 60.058 43.478 0.00 0.00 0.00 2.93
2491 2661 4.766375 AGTCCTTCTGTTCGAAAAGTTCA 58.234 39.130 14.96 0.24 0.00 3.18
2648 2818 4.422840 CAGAAGCAACAACATTGTCAACA 58.577 39.130 0.00 0.00 41.31 3.33
2660 2830 0.815213 TGTCAACACAGCTGGCACTC 60.815 55.000 19.93 4.51 0.00 3.51
2782 2952 2.163613 GGCACCTGTAATGCTGGTTTAC 59.836 50.000 0.00 0.00 45.59 2.01
2793 2963 1.335496 GCTGGTTTACACGGCAAGAAA 59.665 47.619 0.00 0.00 0.00 2.52
2836 3007 8.967664 TCTAACAGAAGAATACTACTCTCTCC 57.032 38.462 0.00 0.00 0.00 3.71
2837 3008 6.687081 AACAGAAGAATACTACTCTCTCCG 57.313 41.667 0.00 0.00 0.00 4.63
2839 3010 6.181908 ACAGAAGAATACTACTCTCTCCGTT 58.818 40.000 0.00 0.00 0.00 4.44
2840 3011 6.316890 ACAGAAGAATACTACTCTCTCCGTTC 59.683 42.308 0.00 0.00 0.00 3.95
2841 3012 6.316640 CAGAAGAATACTACTCTCTCCGTTCA 59.683 42.308 0.00 0.00 0.00 3.18
2842 3013 6.316890 AGAAGAATACTACTCTCTCCGTTCAC 59.683 42.308 0.00 0.00 0.00 3.18
2845 3016 6.660094 AGAATACTACTCTCTCCGTTCACTTT 59.340 38.462 0.00 0.00 0.00 2.66
2846 3017 6.837471 ATACTACTCTCTCCGTTCACTTTT 57.163 37.500 0.00 0.00 0.00 2.27
2849 3020 7.934855 ACTACTCTCTCCGTTCACTTTTATA 57.065 36.000 0.00 0.00 0.00 0.98
2850 3021 8.345724 ACTACTCTCTCCGTTCACTTTTATAA 57.654 34.615 0.00 0.00 0.00 0.98
2851 3022 8.460428 ACTACTCTCTCCGTTCACTTTTATAAG 58.540 37.037 0.00 0.00 37.40 1.73
2852 3023 7.229581 ACTCTCTCCGTTCACTTTTATAAGT 57.770 36.000 0.00 0.00 45.40 2.24
2853 3024 7.314393 ACTCTCTCCGTTCACTTTTATAAGTC 58.686 38.462 0.00 0.00 42.67 3.01
2854 3025 6.320171 TCTCTCCGTTCACTTTTATAAGTCG 58.680 40.000 0.00 0.00 42.67 4.18
2855 3026 6.017400 TCTCCGTTCACTTTTATAAGTCGT 57.983 37.500 0.00 0.00 42.67 4.34
2856 3027 6.449698 TCTCCGTTCACTTTTATAAGTCGTT 58.550 36.000 0.00 0.00 42.67 3.85
2857 3028 6.925165 TCTCCGTTCACTTTTATAAGTCGTTT 59.075 34.615 0.00 0.00 42.67 3.60
2858 3029 7.109006 TCCGTTCACTTTTATAAGTCGTTTC 57.891 36.000 0.00 0.00 42.67 2.78
2859 3030 6.700960 TCCGTTCACTTTTATAAGTCGTTTCA 59.299 34.615 0.00 0.00 42.67 2.69
2860 3031 7.007697 CCGTTCACTTTTATAAGTCGTTTCAG 58.992 38.462 0.00 0.00 42.67 3.02
2861 3032 7.095940 CCGTTCACTTTTATAAGTCGTTTCAGA 60.096 37.037 0.00 0.00 42.67 3.27
2862 3033 7.734726 CGTTCACTTTTATAAGTCGTTTCAGAC 59.265 37.037 0.00 0.00 42.67 3.51
2863 3034 8.545420 GTTCACTTTTATAAGTCGTTTCAGACA 58.455 33.333 0.00 0.00 42.67 3.41
2864 3035 8.651391 TCACTTTTATAAGTCGTTTCAGACAA 57.349 30.769 0.00 0.00 42.67 3.18
2865 3036 8.761497 TCACTTTTATAAGTCGTTTCAGACAAG 58.239 33.333 0.00 0.00 42.67 3.16
2866 3037 8.548721 CACTTTTATAAGTCGTTTCAGACAAGT 58.451 33.333 0.00 0.00 42.67 3.16
2867 3038 8.548721 ACTTTTATAAGTCGTTTCAGACAAGTG 58.451 33.333 0.00 0.00 40.60 3.16
2868 3039 8.651391 TTTTATAAGTCGTTTCAGACAAGTGA 57.349 30.769 0.00 0.00 43.24 3.41
2869 3040 8.651391 TTTATAAGTCGTTTCAGACAAGTGAA 57.349 30.769 0.00 0.00 43.24 3.18
2870 3041 8.651391 TTATAAGTCGTTTCAGACAAGTGAAA 57.349 30.769 0.00 0.00 42.79 2.69
2871 3042 7.730364 ATAAGTCGTTTCAGACAAGTGAAAT 57.270 32.000 2.59 0.00 45.71 2.17
2872 3043 5.659048 AGTCGTTTCAGACAAGTGAAATC 57.341 39.130 2.59 0.00 45.71 2.17
2873 3044 4.209288 AGTCGTTTCAGACAAGTGAAATCG 59.791 41.667 2.59 8.09 45.71 3.34
2874 3045 4.208460 GTCGTTTCAGACAAGTGAAATCGA 59.792 41.667 14.33 14.33 45.71 3.59
2875 3046 4.444388 TCGTTTCAGACAAGTGAAATCGAG 59.556 41.667 14.33 4.88 45.71 4.04
2876 3047 4.458708 GTTTCAGACAAGTGAAATCGAGC 58.541 43.478 2.59 0.00 45.71 5.03
2877 3048 3.667497 TCAGACAAGTGAAATCGAGCT 57.333 42.857 0.00 0.00 0.00 4.09
2878 3049 3.320626 TCAGACAAGTGAAATCGAGCTG 58.679 45.455 0.00 0.00 0.00 4.24
2879 3050 3.062763 CAGACAAGTGAAATCGAGCTGT 58.937 45.455 0.00 0.00 0.00 4.40
2880 3051 3.496130 CAGACAAGTGAAATCGAGCTGTT 59.504 43.478 0.00 0.00 0.00 3.16
2881 3052 4.024556 CAGACAAGTGAAATCGAGCTGTTT 60.025 41.667 0.00 0.00 0.00 2.83
2882 3053 4.576463 AGACAAGTGAAATCGAGCTGTTTT 59.424 37.500 0.00 0.00 0.00 2.43
2883 3054 5.758296 AGACAAGTGAAATCGAGCTGTTTTA 59.242 36.000 0.00 0.00 0.00 1.52
2884 3055 5.748592 ACAAGTGAAATCGAGCTGTTTTAC 58.251 37.500 0.00 0.00 0.00 2.01
2885 3056 5.295787 ACAAGTGAAATCGAGCTGTTTTACA 59.704 36.000 0.00 0.00 0.00 2.41
2886 3057 5.344207 AGTGAAATCGAGCTGTTTTACAC 57.656 39.130 0.00 0.00 0.00 2.90
2887 3058 4.814234 AGTGAAATCGAGCTGTTTTACACA 59.186 37.500 0.00 0.00 0.00 3.72
2888 3059 4.904154 GTGAAATCGAGCTGTTTTACACAC 59.096 41.667 0.00 0.00 0.00 3.82
2889 3060 4.814234 TGAAATCGAGCTGTTTTACACACT 59.186 37.500 0.00 0.00 0.00 3.55
2890 3061 4.732285 AATCGAGCTGTTTTACACACTG 57.268 40.909 0.00 0.00 0.00 3.66
2891 3062 3.173668 TCGAGCTGTTTTACACACTGT 57.826 42.857 0.00 0.00 0.00 3.55
2892 3063 3.120792 TCGAGCTGTTTTACACACTGTC 58.879 45.455 0.00 0.00 0.00 3.51
2893 3064 3.123804 CGAGCTGTTTTACACACTGTCT 58.876 45.455 0.00 0.00 0.00 3.41
2894 3065 3.060272 CGAGCTGTTTTACACACTGTCTG 60.060 47.826 0.00 0.00 0.00 3.51
2895 3066 4.119862 GAGCTGTTTTACACACTGTCTGA 58.880 43.478 0.00 0.00 0.00 3.27
2896 3067 4.513442 AGCTGTTTTACACACTGTCTGAA 58.487 39.130 0.00 0.00 0.00 3.02
2897 3068 4.572389 AGCTGTTTTACACACTGTCTGAAG 59.428 41.667 0.00 0.00 0.00 3.02
2898 3069 4.786609 GCTGTTTTACACACTGTCTGAAGC 60.787 45.833 0.00 0.00 0.00 3.86
2899 3070 4.257731 TGTTTTACACACTGTCTGAAGCA 58.742 39.130 0.00 0.00 0.00 3.91
2900 3071 4.881273 TGTTTTACACACTGTCTGAAGCAT 59.119 37.500 0.00 0.00 0.00 3.79
2922 3094 1.205893 GGATCATGCGTATCCTCTCCC 59.794 57.143 4.95 0.00 39.93 4.30
2923 3095 1.895798 GATCATGCGTATCCTCTCCCA 59.104 52.381 0.00 0.00 0.00 4.37
2952 3128 9.941664 GATTTCATGTAGTTTTCACTATCATGG 57.058 33.333 16.41 0.00 40.69 3.66
3145 3361 5.496556 TGACTGAGGGTGTGTTAATTATGG 58.503 41.667 0.00 0.00 0.00 2.74
3425 3674 4.577246 GAGGGGCGCTCTAGCACG 62.577 72.222 22.89 0.40 42.53 5.34
3487 3736 5.622448 GGTTTTTCGTCGAAAACTTACCATC 59.378 40.000 30.28 16.60 44.77 3.51
3500 3749 2.099141 TACCATCTGCTGCTGTTGTC 57.901 50.000 14.00 0.00 0.00 3.18
3515 3764 2.005451 GTTGTCGCAGCTCTGAATGAT 58.995 47.619 0.29 0.00 0.00 2.45
3575 3824 2.112898 CCAGATGGGCAATGCTGTC 58.887 57.895 4.82 1.09 0.00 3.51
3720 3969 4.569180 AGCACCAGCAGCCGTTGT 62.569 61.111 0.00 0.00 45.49 3.32
3881 4130 1.327303 GATCGAGCTCCTGTCTGGAT 58.673 55.000 8.47 2.78 45.16 3.41
3904 4153 6.636454 TTACAGGAATTTCACAGGGATACT 57.364 37.500 0.00 0.00 0.00 2.12
3921 4170 4.941873 GGATACTGTGAAACGAAAATCCCT 59.058 41.667 0.00 0.00 42.39 4.20
3939 4188 1.032014 CTACCGGGCAAAATCCATGG 58.968 55.000 4.97 4.97 0.00 3.66
3955 4204 1.683385 CATGGTATCTGTCAGAGCCGA 59.317 52.381 8.82 5.16 0.00 5.54
3957 4206 0.031449 GGTATCTGTCAGAGCCGAGC 59.969 60.000 8.82 0.19 0.00 5.03
3958 4207 0.031449 GTATCTGTCAGAGCCGAGCC 59.969 60.000 8.82 0.00 0.00 4.70
3974 4223 1.304134 GCCGATTCAGGGGGTTGTT 60.304 57.895 0.00 0.00 0.00 2.83
3978 4227 0.614697 GATTCAGGGGGTTGTTGGGG 60.615 60.000 0.00 0.00 0.00 4.96
3979 4228 1.376249 ATTCAGGGGGTTGTTGGGGT 61.376 55.000 0.00 0.00 0.00 4.95
4003 4252 4.040047 TCACCCAAGTGTAGATGGATCAT 58.960 43.478 0.00 0.00 44.83 2.45
4020 4269 5.723405 TGGATCATCAGCAAGTATATAGCCT 59.277 40.000 0.00 0.00 0.00 4.58
4021 4270 6.897413 TGGATCATCAGCAAGTATATAGCCTA 59.103 38.462 0.00 0.00 0.00 3.93
4042 4291 6.363065 CCTATATATACAGGGTTCGAGGCTA 58.637 44.000 0.00 0.00 0.00 3.93
4053 4302 3.057033 GGTTCGAGGCTACTCAAGTTACA 60.057 47.826 0.00 0.00 44.17 2.41
4064 4313 5.599999 ACTCAAGTTACAGTCAGTTGTCT 57.400 39.130 2.83 0.00 32.56 3.41
4096 4346 8.028938 TCCTTCTGAAGAAAAGTTTTGTTCTTG 58.971 33.333 28.31 22.41 42.67 3.02
4101 4351 5.738619 AGAAAAGTTTTGTTCTTGTGGGT 57.261 34.783 5.36 0.00 29.67 4.51
4169 4419 6.271488 TGCAGATTCTTCGGATTTGAAAAT 57.729 33.333 0.00 0.00 0.00 1.82
4242 4492 2.582052 TGCAGATTCTTCGGGTTTGTT 58.418 42.857 0.00 0.00 0.00 2.83
4247 4497 5.106317 GCAGATTCTTCGGGTTTGTTGATAA 60.106 40.000 0.00 0.00 0.00 1.75
4341 4591 7.448777 TGGCCTTTGTATGTACAGATTGTTTTA 59.551 33.333 3.32 0.00 37.52 1.52
4427 4677 1.328279 TGTCCTCTCTGCGTTCTTCA 58.672 50.000 0.00 0.00 0.00 3.02
4463 4713 6.169419 TGCGTATTTAGCAGCATATTCATC 57.831 37.500 0.00 0.00 40.01 2.92
4484 4734 6.705825 TCATCGAAGAAACAAAGACAATCTGA 59.294 34.615 0.00 0.00 43.58 3.27
4492 4742 5.490139 ACAAAGACAATCTGACAAGTGTG 57.510 39.130 0.00 0.00 0.00 3.82
4538 4788 8.530269 AAAGACTCACCAATTTAGTACGTTAG 57.470 34.615 0.00 0.00 0.00 2.34
4546 4799 6.591448 ACCAATTTAGTACGTTAGTAGTTGGC 59.409 38.462 15.05 0.00 37.63 4.52
4578 4831 4.098807 ACAAACCACATGTTTTGGGACTAC 59.901 41.667 21.30 0.00 44.80 2.73
4619 4872 4.229876 GTCTTGCAAGAAAAAGGGAATCG 58.770 43.478 29.99 0.00 36.68 3.34
4641 4894 8.018529 ATCGCAGATCCCTCAAAAAGGAAAAG 62.019 42.308 0.00 0.00 45.99 2.27
4719 4974 3.318839 TGAGTGCTCCATGTTCCTTTTTG 59.681 43.478 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.330074 CGTGTACATCCTTTCAATGACTCC 59.670 45.833 0.00 0.00 0.00 3.85
60 61 9.657419 ATTTTGGTCAAATTTGATAACTGGATC 57.343 29.630 23.05 7.51 39.73 3.36
288 308 4.385447 CAGTTTTTAATGGACACGGCATTG 59.615 41.667 0.00 0.00 0.00 2.82
293 313 4.621034 GCATTCAGTTTTTAATGGACACGG 59.379 41.667 0.00 0.00 34.37 4.94
420 445 4.661222 TGCACATGTGGAAAGGATTAAGA 58.339 39.130 26.55 0.00 0.00 2.10
451 477 5.286082 GGCAACTCATAAACGTTTAGCATTG 59.714 40.000 23.78 22.20 0.00 2.82
479 505 1.226407 GGCGAGTAACGGACGGTAC 60.226 63.158 11.68 11.68 42.83 3.34
496 537 2.483014 TCCTCATACACGTTTTGGGG 57.517 50.000 2.27 2.27 31.90 4.96
524 565 4.438145 CGCAAACACGTTTTACTTGCAATA 59.562 37.500 0.00 0.00 41.92 1.90
588 630 1.560505 GAGATTGGGCATTTGGTGGT 58.439 50.000 0.00 0.00 0.00 4.16
597 639 1.788229 TATCTCGTGGAGATTGGGCA 58.212 50.000 12.86 0.00 45.86 5.36
679 727 1.537348 CGGACGACAAACAGTGAAGGA 60.537 52.381 0.00 0.00 0.00 3.36
680 728 0.859232 CGGACGACAAACAGTGAAGG 59.141 55.000 0.00 0.00 0.00 3.46
716 764 1.838112 TCGGCTTGCAGATTGGATTT 58.162 45.000 0.00 0.00 0.00 2.17
718 766 1.134007 TCATCGGCTTGCAGATTGGAT 60.134 47.619 5.56 0.00 0.00 3.41
758 806 7.495934 TCAAACGACAAGAGAAAGAAGAGAATT 59.504 33.333 0.00 0.00 0.00 2.17
768 816 5.008613 CCTTGGATTCAAACGACAAGAGAAA 59.991 40.000 0.00 0.00 40.60 2.52
775 823 2.226330 CCACCTTGGATTCAAACGACA 58.774 47.619 0.00 0.00 40.96 4.35
776 824 2.227194 ACCACCTTGGATTCAAACGAC 58.773 47.619 0.00 0.00 40.96 4.34
854 914 1.804748 GGACGGTACTGCAAAAAGGAG 59.195 52.381 0.23 0.00 42.18 3.69
868 928 0.107557 AACGTTGAGGTTTGGACGGT 60.108 50.000 0.00 0.00 39.63 4.83
871 931 2.540157 CGGAAAACGTTGAGGTTTGGAC 60.540 50.000 0.00 0.00 40.40 4.02
920 980 3.731089 ACGTTCTTGTTGGATTACGGAA 58.269 40.909 0.00 0.00 33.66 4.30
954 1014 4.764050 TTAGAATATCCCTCCACGCAAA 57.236 40.909 0.00 0.00 0.00 3.68
970 1030 4.080299 GGCTCCAAGAATCTCCCTTTAGAA 60.080 45.833 0.00 0.00 0.00 2.10
1374 1437 0.966875 TGGAATGGCTGTGGTGATGC 60.967 55.000 0.00 0.00 0.00 3.91
1507 1570 4.034269 CCTTCTTAGGGTCGACAAGCGA 62.034 54.545 18.91 3.87 41.54 4.93
1521 1584 4.959839 AGACCAAACCTTTTTGCCTTCTTA 59.040 37.500 0.00 0.00 40.84 2.10
1574 1637 6.756542 TGTGATGAACAGTGGATAATCTTACG 59.243 38.462 0.00 0.00 33.78 3.18
1578 1641 8.464404 CAAATTGTGATGAACAGTGGATAATCT 58.536 33.333 0.00 0.00 40.74 2.40
1653 1721 8.893219 TTCTTCATCCATATAACAGCTGTAAG 57.107 34.615 22.01 15.24 0.00 2.34
1771 1884 5.209818 TCTAGGTCACGTTCAATCAGTTT 57.790 39.130 0.00 0.00 0.00 2.66
1772 1885 4.281182 ACTCTAGGTCACGTTCAATCAGTT 59.719 41.667 0.00 0.00 0.00 3.16
1773 1886 3.827302 ACTCTAGGTCACGTTCAATCAGT 59.173 43.478 0.00 0.00 0.00 3.41
1775 1888 4.866508 AACTCTAGGTCACGTTCAATCA 57.133 40.909 0.00 0.00 0.00 2.57
1776 1889 6.154445 TGTTAACTCTAGGTCACGTTCAATC 58.846 40.000 7.22 0.00 0.00 2.67
1777 1890 6.092955 TGTTAACTCTAGGTCACGTTCAAT 57.907 37.500 7.22 0.00 0.00 2.57
1778 1891 5.518848 TGTTAACTCTAGGTCACGTTCAA 57.481 39.130 7.22 0.00 0.00 2.69
1779 1892 5.717078 ATGTTAACTCTAGGTCACGTTCA 57.283 39.130 7.22 0.00 0.00 3.18
1780 1893 8.699283 ATAAATGTTAACTCTAGGTCACGTTC 57.301 34.615 7.22 0.00 0.00 3.95
1783 1896 8.755941 CATGATAAATGTTAACTCTAGGTCACG 58.244 37.037 7.22 0.00 0.00 4.35
1792 1905 9.820229 TTTCGTGTTCATGATAAATGTTAACTC 57.180 29.630 7.22 0.00 0.00 3.01
1793 1906 9.607285 GTTTCGTGTTCATGATAAATGTTAACT 57.393 29.630 7.22 0.00 0.00 2.24
1794 1907 8.563949 CGTTTCGTGTTCATGATAAATGTTAAC 58.436 33.333 0.00 0.00 0.00 2.01
1796 1909 7.798801 ACGTTTCGTGTTCATGATAAATGTTA 58.201 30.769 0.00 0.00 39.18 2.41
1797 1910 6.664515 ACGTTTCGTGTTCATGATAAATGTT 58.335 32.000 0.00 0.00 39.18 2.71
1798 1911 6.236017 ACGTTTCGTGTTCATGATAAATGT 57.764 33.333 0.00 2.25 39.18 2.71
1813 1926 1.591158 GTCACATCACACACGTTTCGT 59.409 47.619 0.00 0.00 42.36 3.85
1814 1927 1.070843 GGTCACATCACACACGTTTCG 60.071 52.381 0.00 0.00 0.00 3.46
1815 1928 1.263217 GGGTCACATCACACACGTTTC 59.737 52.381 0.00 0.00 0.00 2.78
1816 1929 1.134220 AGGGTCACATCACACACGTTT 60.134 47.619 0.00 0.00 0.00 3.60
1817 1930 0.468226 AGGGTCACATCACACACGTT 59.532 50.000 0.00 0.00 0.00 3.99
1824 1985 3.734293 GCTCGTTAGTAGGGTCACATCAC 60.734 52.174 0.00 0.00 0.00 3.06
1832 1993 1.817447 GTCAGTGCTCGTTAGTAGGGT 59.183 52.381 0.00 0.00 0.00 4.34
1839 2000 6.795098 AATTGTAATTGTCAGTGCTCGTTA 57.205 33.333 0.00 0.00 0.00 3.18
1894 2055 2.381961 ACTCCTAGCCATTCCCCAAAAA 59.618 45.455 0.00 0.00 0.00 1.94
1895 2056 2.000048 ACTCCTAGCCATTCCCCAAAA 59.000 47.619 0.00 0.00 0.00 2.44
1896 2057 1.564348 GACTCCTAGCCATTCCCCAAA 59.436 52.381 0.00 0.00 0.00 3.28
1897 2058 1.213296 GACTCCTAGCCATTCCCCAA 58.787 55.000 0.00 0.00 0.00 4.12
1898 2059 0.044092 TGACTCCTAGCCATTCCCCA 59.956 55.000 0.00 0.00 0.00 4.96
1899 2060 1.213296 TTGACTCCTAGCCATTCCCC 58.787 55.000 0.00 0.00 0.00 4.81
1900 2061 2.548920 CGATTGACTCCTAGCCATTCCC 60.549 54.545 0.00 0.00 0.00 3.97
1901 2062 2.365617 TCGATTGACTCCTAGCCATTCC 59.634 50.000 0.00 0.00 0.00 3.01
1902 2063 3.385577 GTCGATTGACTCCTAGCCATTC 58.614 50.000 5.79 0.00 42.08 2.67
1903 2064 3.460857 GTCGATTGACTCCTAGCCATT 57.539 47.619 5.79 0.00 42.08 3.16
1912 2073 8.633408 CAAATCAAAATTTCAGTCGATTGACTC 58.367 33.333 13.01 0.00 42.08 3.36
1913 2074 7.596248 CCAAATCAAAATTTCAGTCGATTGACT 59.404 33.333 10.49 10.02 43.46 3.41
1914 2075 7.148755 CCCAAATCAAAATTTCAGTCGATTGAC 60.149 37.037 10.49 4.78 37.93 3.18
1915 2076 6.867816 CCCAAATCAAAATTTCAGTCGATTGA 59.132 34.615 6.51 6.51 32.69 2.57
1916 2077 6.646240 ACCCAAATCAAAATTTCAGTCGATTG 59.354 34.615 0.68 0.68 32.69 2.67
1917 2078 6.758254 ACCCAAATCAAAATTTCAGTCGATT 58.242 32.000 0.00 0.00 32.69 3.34
1918 2079 6.015519 TGACCCAAATCAAAATTTCAGTCGAT 60.016 34.615 0.00 0.00 37.05 3.59
1919 2080 5.300539 TGACCCAAATCAAAATTTCAGTCGA 59.699 36.000 0.00 0.00 37.05 4.20
1920 2081 5.527951 TGACCCAAATCAAAATTTCAGTCG 58.472 37.500 0.00 0.00 37.05 4.18
1921 2082 6.515832 ACTGACCCAAATCAAAATTTCAGTC 58.484 36.000 0.00 0.00 33.98 3.51
1922 2083 6.098124 TGACTGACCCAAATCAAAATTTCAGT 59.902 34.615 0.67 0.67 38.19 3.41
1923 2084 6.514947 TGACTGACCCAAATCAAAATTTCAG 58.485 36.000 0.00 0.00 32.69 3.02
1924 2085 6.477053 TGACTGACCCAAATCAAAATTTCA 57.523 33.333 0.00 0.00 32.69 2.69
1925 2086 7.967890 ATTGACTGACCCAAATCAAAATTTC 57.032 32.000 0.00 0.00 34.88 2.17
1926 2087 8.623030 CAAATTGACTGACCCAAATCAAAATTT 58.377 29.630 0.00 0.00 34.88 1.82
1927 2088 7.229106 CCAAATTGACTGACCCAAATCAAAATT 59.771 33.333 0.00 0.00 34.88 1.82
1928 2089 6.711645 CCAAATTGACTGACCCAAATCAAAAT 59.288 34.615 0.00 0.00 34.88 1.82
1929 2090 6.054295 CCAAATTGACTGACCCAAATCAAAA 58.946 36.000 0.00 0.00 34.88 2.44
1930 2091 5.609423 CCAAATTGACTGACCCAAATCAAA 58.391 37.500 0.00 0.00 34.88 2.69
1931 2092 4.502950 GCCAAATTGACTGACCCAAATCAA 60.503 41.667 0.00 0.00 35.64 2.57
1932 2093 3.006752 GCCAAATTGACTGACCCAAATCA 59.993 43.478 0.00 0.00 0.00 2.57
1933 2094 3.588955 GCCAAATTGACTGACCCAAATC 58.411 45.455 0.00 0.00 0.00 2.17
1934 2095 2.302733 GGCCAAATTGACTGACCCAAAT 59.697 45.455 0.00 0.00 0.00 2.32
1935 2096 1.691434 GGCCAAATTGACTGACCCAAA 59.309 47.619 0.00 0.00 0.00 3.28
1936 2097 1.133199 AGGCCAAATTGACTGACCCAA 60.133 47.619 5.01 0.00 0.00 4.12
1937 2098 0.482446 AGGCCAAATTGACTGACCCA 59.518 50.000 5.01 0.00 0.00 4.51
1938 2099 0.890683 CAGGCCAAATTGACTGACCC 59.109 55.000 5.01 0.00 32.86 4.46
1939 2100 0.890683 CCAGGCCAAATTGACTGACC 59.109 55.000 5.01 1.44 32.86 4.02
1940 2101 1.909700 TCCAGGCCAAATTGACTGAC 58.090 50.000 5.01 0.00 32.86 3.51
1941 2102 2.041485 TGATCCAGGCCAAATTGACTGA 59.959 45.455 5.01 6.02 32.86 3.41
1942 2103 2.426024 CTGATCCAGGCCAAATTGACTG 59.574 50.000 5.01 9.59 0.00 3.51
1943 2104 2.042162 ACTGATCCAGGCCAAATTGACT 59.958 45.455 5.01 0.00 35.51 3.41
1944 2105 2.450476 ACTGATCCAGGCCAAATTGAC 58.550 47.619 5.01 0.00 35.51 3.18
1945 2106 2.905415 ACTGATCCAGGCCAAATTGA 57.095 45.000 5.01 0.00 35.51 2.57
1946 2107 3.258872 TCAAACTGATCCAGGCCAAATTG 59.741 43.478 5.01 0.00 35.51 2.32
1947 2108 3.509442 TCAAACTGATCCAGGCCAAATT 58.491 40.909 5.01 0.00 35.51 1.82
1948 2109 3.173953 TCAAACTGATCCAGGCCAAAT 57.826 42.857 5.01 0.00 35.51 2.32
1949 2110 2.673775 TCAAACTGATCCAGGCCAAA 57.326 45.000 5.01 0.00 35.51 3.28
1950 2111 2.517959 CTTCAAACTGATCCAGGCCAA 58.482 47.619 5.01 0.00 35.51 4.52
1951 2112 1.887956 GCTTCAAACTGATCCAGGCCA 60.888 52.381 5.01 0.00 35.51 5.36
1952 2113 0.813821 GCTTCAAACTGATCCAGGCC 59.186 55.000 0.00 0.00 35.51 5.19
1953 2114 0.449388 CGCTTCAAACTGATCCAGGC 59.551 55.000 0.00 0.00 35.51 4.85
1954 2115 1.813513 ACGCTTCAAACTGATCCAGG 58.186 50.000 0.00 0.00 35.51 4.45
1968 2129 4.142687 CCGTTCATTTTCCATCTAACGCTT 60.143 41.667 0.00 0.00 38.60 4.68
1972 2133 3.181490 GGGCCGTTCATTTTCCATCTAAC 60.181 47.826 0.00 0.00 0.00 2.34
1995 2156 4.141914 ACACGGAGGAAGAAGACATAATCC 60.142 45.833 0.00 0.00 0.00 3.01
1996 2157 4.806247 CACACGGAGGAAGAAGACATAATC 59.194 45.833 0.00 0.00 0.00 1.75
2035 2196 1.305381 AGTCGGTGGGAGGAGGAAG 60.305 63.158 0.00 0.00 0.00 3.46
2116 2282 3.041940 GTGACAAGACCGGCGGTG 61.042 66.667 39.41 24.85 35.25 4.94
2204 2370 7.146648 CGTTATCTATCTTAAGGTTCAGGGTC 58.853 42.308 1.85 0.00 0.00 4.46
2215 2381 7.362660 CCGTCATCATCCCGTTATCTATCTTAA 60.363 40.741 0.00 0.00 0.00 1.85
2228 2394 2.355126 CTCGCCGTCATCATCCCG 60.355 66.667 0.00 0.00 0.00 5.14
2232 2398 4.241555 GGGGCTCGCCGTCATCAT 62.242 66.667 1.24 0.00 36.85 2.45
2242 2408 1.681486 GGAGAGAAGGAAGGGGCTCG 61.681 65.000 0.00 0.00 32.80 5.03
2284 2450 4.695455 GGGTCAGTCGATTTTGAATGAAGA 59.305 41.667 0.00 0.00 43.64 2.87
2287 2453 3.000041 CGGGTCAGTCGATTTTGAATGA 59.000 45.455 0.00 0.00 40.31 2.57
2352 2518 5.907207 TCATCCGAGAGATTTTGACCTTAG 58.093 41.667 0.00 0.00 30.59 2.18
2385 2551 9.321562 GTGTGTTTAGCTTATACTTATGGCTAA 57.678 33.333 0.00 0.00 41.65 3.09
2408 2574 2.029380 TGTTCTTCGGATCACATCGTGT 60.029 45.455 0.00 0.00 34.79 4.49
2430 2596 5.279256 GCCATTTTCTAGGTAAAGGTTTGCA 60.279 40.000 0.00 0.00 0.00 4.08
2436 2602 7.362660 GGTTAGTTGCCATTTTCTAGGTAAAGG 60.363 40.741 0.00 0.00 31.25 3.11
2648 2818 0.251354 CATGTAGGAGTGCCAGCTGT 59.749 55.000 13.81 0.00 36.29 4.40
2660 2830 2.505819 AGGGGCAGTTCTTACATGTAGG 59.494 50.000 8.64 8.64 0.00 3.18
2776 2946 5.180680 AGTTCTATTTCTTGCCGTGTAAACC 59.819 40.000 0.00 0.00 0.00 3.27
2782 2952 7.033791 TCTAGTTAGTTCTATTTCTTGCCGTG 58.966 38.462 0.00 0.00 0.00 4.94
2829 3000 6.469595 CGACTTATAAAAGTGAACGGAGAGAG 59.530 42.308 0.00 0.00 46.09 3.20
2832 3003 6.017400 ACGACTTATAAAAGTGAACGGAGA 57.983 37.500 0.00 0.00 46.09 3.71
2834 3005 6.700960 TGAAACGACTTATAAAAGTGAACGGA 59.299 34.615 0.00 0.00 46.09 4.69
2835 3006 6.879962 TGAAACGACTTATAAAAGTGAACGG 58.120 36.000 0.00 0.00 46.09 4.44
2836 3007 7.734726 GTCTGAAACGACTTATAAAAGTGAACG 59.265 37.037 0.00 0.00 46.09 3.95
2837 3008 8.545420 TGTCTGAAACGACTTATAAAAGTGAAC 58.455 33.333 0.00 0.00 46.09 3.18
2839 3010 8.651391 TTGTCTGAAACGACTTATAAAAGTGA 57.349 30.769 0.00 0.00 46.09 3.41
2840 3011 8.548721 ACTTGTCTGAAACGACTTATAAAAGTG 58.451 33.333 0.00 0.00 46.09 3.16
2842 3013 8.761497 TCACTTGTCTGAAACGACTTATAAAAG 58.239 33.333 0.00 0.00 38.77 2.27
2845 3016 8.651391 TTTCACTTGTCTGAAACGACTTATAA 57.349 30.769 0.00 0.00 35.63 0.98
2846 3017 8.827177 ATTTCACTTGTCTGAAACGACTTATA 57.173 30.769 0.00 0.00 41.76 0.98
2849 3020 5.276868 CGATTTCACTTGTCTGAAACGACTT 60.277 40.000 0.00 0.00 41.76 3.01
2850 3021 4.209288 CGATTTCACTTGTCTGAAACGACT 59.791 41.667 0.00 0.00 41.76 4.18
2851 3022 4.208460 TCGATTTCACTTGTCTGAAACGAC 59.792 41.667 11.65 0.00 41.76 4.34
2852 3023 4.364860 TCGATTTCACTTGTCTGAAACGA 58.635 39.130 11.65 11.65 41.76 3.85
2853 3024 4.692135 CTCGATTTCACTTGTCTGAAACG 58.308 43.478 0.00 4.21 41.76 3.60
2854 3025 4.212214 AGCTCGATTTCACTTGTCTGAAAC 59.788 41.667 0.00 0.00 41.76 2.78
2855 3026 4.212004 CAGCTCGATTTCACTTGTCTGAAA 59.788 41.667 0.00 0.00 42.83 2.69
2856 3027 3.742882 CAGCTCGATTTCACTTGTCTGAA 59.257 43.478 0.00 0.00 0.00 3.02
2857 3028 3.243873 ACAGCTCGATTTCACTTGTCTGA 60.244 43.478 0.00 0.00 0.00 3.27
2858 3029 3.062763 ACAGCTCGATTTCACTTGTCTG 58.937 45.455 0.00 0.00 0.00 3.51
2859 3030 3.393089 ACAGCTCGATTTCACTTGTCT 57.607 42.857 0.00 0.00 0.00 3.41
2860 3031 4.474226 AAACAGCTCGATTTCACTTGTC 57.526 40.909 0.00 0.00 0.00 3.18
2861 3032 4.900635 AAAACAGCTCGATTTCACTTGT 57.099 36.364 0.00 0.00 0.00 3.16
2862 3033 5.621228 GTGTAAAACAGCTCGATTTCACTTG 59.379 40.000 0.00 0.00 0.00 3.16
2863 3034 5.295787 TGTGTAAAACAGCTCGATTTCACTT 59.704 36.000 10.76 0.00 33.78 3.16
2864 3035 4.814234 TGTGTAAAACAGCTCGATTTCACT 59.186 37.500 10.76 0.00 33.78 3.41
2865 3036 4.904154 GTGTGTAAAACAGCTCGATTTCAC 59.096 41.667 0.00 0.00 40.26 3.18
2866 3037 4.814234 AGTGTGTAAAACAGCTCGATTTCA 59.186 37.500 0.00 0.00 40.26 2.69
2867 3038 5.140177 CAGTGTGTAAAACAGCTCGATTTC 58.860 41.667 0.00 0.00 40.26 2.17
2868 3039 4.574828 ACAGTGTGTAAAACAGCTCGATTT 59.425 37.500 0.00 0.00 40.26 2.17
2869 3040 4.127171 ACAGTGTGTAAAACAGCTCGATT 58.873 39.130 0.00 0.00 40.26 3.34
2870 3041 3.728845 ACAGTGTGTAAAACAGCTCGAT 58.271 40.909 0.00 0.00 40.26 3.59
2871 3042 3.120792 GACAGTGTGTAAAACAGCTCGA 58.879 45.455 0.00 0.00 40.26 4.04
2872 3043 3.060272 CAGACAGTGTGTAAAACAGCTCG 60.060 47.826 0.00 0.00 40.26 5.03
2873 3044 4.119862 TCAGACAGTGTGTAAAACAGCTC 58.880 43.478 0.00 0.00 40.26 4.09
2874 3045 4.137116 TCAGACAGTGTGTAAAACAGCT 57.863 40.909 0.00 0.00 40.26 4.24
2875 3046 4.786609 GCTTCAGACAGTGTGTAAAACAGC 60.787 45.833 0.00 0.00 40.26 4.40
2876 3047 4.332543 TGCTTCAGACAGTGTGTAAAACAG 59.667 41.667 0.00 0.00 40.26 3.16
2877 3048 4.257731 TGCTTCAGACAGTGTGTAAAACA 58.742 39.130 0.00 0.00 36.04 2.83
2878 3049 4.875544 TGCTTCAGACAGTGTGTAAAAC 57.124 40.909 0.00 0.00 0.00 2.43
2879 3050 4.211164 CGATGCTTCAGACAGTGTGTAAAA 59.789 41.667 0.00 0.00 0.00 1.52
2880 3051 3.740832 CGATGCTTCAGACAGTGTGTAAA 59.259 43.478 0.00 0.00 0.00 2.01
2881 3052 3.317150 CGATGCTTCAGACAGTGTGTAA 58.683 45.455 0.00 0.00 0.00 2.41
2882 3053 2.352715 CCGATGCTTCAGACAGTGTGTA 60.353 50.000 0.00 0.00 0.00 2.90
2883 3054 1.606480 CCGATGCTTCAGACAGTGTGT 60.606 52.381 0.00 0.00 0.00 3.72
2884 3055 1.073964 CCGATGCTTCAGACAGTGTG 58.926 55.000 0.00 0.00 0.00 3.82
2885 3056 0.969149 TCCGATGCTTCAGACAGTGT 59.031 50.000 0.00 0.00 0.00 3.55
2886 3057 2.200067 GATCCGATGCTTCAGACAGTG 58.800 52.381 0.08 0.00 0.00 3.66
2887 3058 1.827344 TGATCCGATGCTTCAGACAGT 59.173 47.619 0.08 0.00 0.00 3.55
2888 3059 2.591571 TGATCCGATGCTTCAGACAG 57.408 50.000 0.08 0.00 0.00 3.51
2889 3060 2.830104 CATGATCCGATGCTTCAGACA 58.170 47.619 0.08 0.00 0.00 3.41
2890 3061 1.530293 GCATGATCCGATGCTTCAGAC 59.470 52.381 10.06 0.00 44.57 3.51
2891 3062 1.870993 CGCATGATCCGATGCTTCAGA 60.871 52.381 14.16 0.00 45.60 3.27
2892 3063 0.511653 CGCATGATCCGATGCTTCAG 59.488 55.000 14.16 0.00 45.60 3.02
2893 3064 0.179076 ACGCATGATCCGATGCTTCA 60.179 50.000 14.16 0.00 45.60 3.02
2894 3065 1.783284 TACGCATGATCCGATGCTTC 58.217 50.000 14.16 0.00 45.60 3.86
2895 3066 2.341257 GATACGCATGATCCGATGCTT 58.659 47.619 14.16 8.76 45.60 3.91
2896 3067 1.404717 GGATACGCATGATCCGATGCT 60.405 52.381 14.16 6.05 45.60 3.79
2897 3068 1.002366 GGATACGCATGATCCGATGC 58.998 55.000 7.74 7.74 44.54 3.91
2898 3069 2.165234 AGAGGATACGCATGATCCGATG 59.835 50.000 0.00 0.00 46.49 3.84
2899 3070 2.425312 GAGAGGATACGCATGATCCGAT 59.575 50.000 0.00 0.00 46.49 4.18
2900 3071 1.813178 GAGAGGATACGCATGATCCGA 59.187 52.381 0.00 0.00 46.49 4.55
2951 3127 3.989817 GACATGCTTGGACAATTTTCACC 59.010 43.478 4.44 0.00 0.00 4.02
2952 3128 4.619973 TGACATGCTTGGACAATTTTCAC 58.380 39.130 4.44 0.00 0.00 3.18
3145 3361 3.455327 GGAACAAGGTTAGCTATCGACC 58.545 50.000 5.10 5.10 0.00 4.79
3363 3600 3.689649 CACCTTTTAATCACCTTCTCCCG 59.310 47.826 0.00 0.00 0.00 5.14
3500 3749 0.027716 GTGCATCATTCAGAGCTGCG 59.972 55.000 0.00 0.00 35.48 5.18
3515 3764 1.162698 GCAGCTCAGATTTCAGTGCA 58.837 50.000 0.00 0.00 0.00 4.57
3560 3809 2.484062 CCCGACAGCATTGCCCATC 61.484 63.158 4.70 0.00 0.00 3.51
3569 3818 1.224315 CATCATTCCCCCGACAGCA 59.776 57.895 0.00 0.00 0.00 4.41
3570 3819 0.107214 TTCATCATTCCCCCGACAGC 60.107 55.000 0.00 0.00 0.00 4.40
3572 3821 1.285280 AGTTCATCATTCCCCCGACA 58.715 50.000 0.00 0.00 0.00 4.35
3575 3824 2.418368 TCAAGTTCATCATTCCCCCG 57.582 50.000 0.00 0.00 0.00 5.73
3621 3870 0.332972 ATTGGCTGGTTTCCTCCTCC 59.667 55.000 0.00 0.00 0.00 4.30
3622 3871 1.272147 ACATTGGCTGGTTTCCTCCTC 60.272 52.381 0.00 0.00 0.00 3.71
3623 3872 0.779997 ACATTGGCTGGTTTCCTCCT 59.220 50.000 0.00 0.00 0.00 3.69
3629 3878 1.786937 TGTGGAACATTGGCTGGTTT 58.213 45.000 0.00 0.00 45.67 3.27
3680 3929 0.381089 GGTGAATCTGCTGCATCTGC 59.619 55.000 1.31 0.00 42.50 4.26
3881 4130 6.414732 CAGTATCCCTGTGAAATTCCTGTAA 58.585 40.000 0.00 0.00 36.37 2.41
3904 4153 3.068560 CGGTAGGGATTTTCGTTTCACA 58.931 45.455 0.00 0.00 0.00 3.58
3921 4170 0.333312 ACCATGGATTTTGCCCGGTA 59.667 50.000 21.47 0.00 32.60 4.02
3934 4183 1.269988 CGGCTCTGACAGATACCATGG 60.270 57.143 11.19 11.19 0.00 3.66
3939 4188 0.031449 GGCTCGGCTCTGACAGATAC 59.969 60.000 5.42 1.29 0.00 2.24
3955 4204 1.789576 AACAACCCCCTGAATCGGCT 61.790 55.000 0.00 0.00 0.00 5.52
3957 4206 0.965363 CCAACAACCCCCTGAATCGG 60.965 60.000 0.00 0.00 0.00 4.18
3958 4207 0.965363 CCCAACAACCCCCTGAATCG 60.965 60.000 0.00 0.00 0.00 3.34
3978 4227 5.070446 TGATCCATCTACACTTGGGTGATAC 59.930 44.000 3.06 0.00 45.61 2.24
3979 4228 5.215845 TGATCCATCTACACTTGGGTGATA 58.784 41.667 3.06 0.00 45.61 2.15
3997 4246 6.232581 AGGCTATATACTTGCTGATGATCC 57.767 41.667 0.00 0.00 0.00 3.36
4020 4269 6.966751 AGTAGCCTCGAACCCTGTATATATA 58.033 40.000 0.00 0.00 0.00 0.86
4021 4270 5.828871 AGTAGCCTCGAACCCTGTATATAT 58.171 41.667 0.00 0.00 0.00 0.86
4028 4277 0.895530 TTGAGTAGCCTCGAACCCTG 59.104 55.000 0.00 0.00 40.85 4.45
4036 4285 4.218852 ACTGACTGTAACTTGAGTAGCCTC 59.781 45.833 0.00 0.00 38.27 4.70
4042 4291 5.599999 AGACAACTGACTGTAACTTGAGT 57.400 39.130 0.00 0.00 0.00 3.41
4053 4302 5.242838 CAGAAGGAAGACTAGACAACTGACT 59.757 44.000 0.00 0.00 0.00 3.41
4088 4338 3.201266 ACCTGTAGAACCCACAAGAACAA 59.799 43.478 0.00 0.00 0.00 2.83
4096 4346 1.375523 CCGCACCTGTAGAACCCAC 60.376 63.158 0.00 0.00 0.00 4.61
4101 4351 2.224426 ACAAACATCCGCACCTGTAGAA 60.224 45.455 0.00 0.00 0.00 2.10
4169 4419 0.690762 GCACCTGTAGACCCCAGAAA 59.309 55.000 0.00 0.00 31.38 2.52
4242 4492 9.322773 CTTCTTAATCAGATTGACAGCTTATCA 57.677 33.333 5.85 0.00 0.00 2.15
4247 4497 5.585445 CAGCTTCTTAATCAGATTGACAGCT 59.415 40.000 5.85 9.78 0.00 4.24
4341 4591 1.055849 GGCCCCAGACCAAAACAAAT 58.944 50.000 0.00 0.00 0.00 2.32
4427 4677 9.236691 CTGCTAAATACGCATCATTTTGTATTT 57.763 29.630 12.21 12.21 44.89 1.40
4463 4713 6.048073 TGTCAGATTGTCTTTGTTTCTTCG 57.952 37.500 0.00 0.00 0.00 3.79
4511 4761 8.891671 AACGTACTAAATTGGTGAGTCTTTTA 57.108 30.769 0.00 0.00 0.00 1.52
4527 4777 9.357652 CAATTAAGCCAACTACTAACGTACTAA 57.642 33.333 0.00 0.00 0.00 2.24
4528 4778 7.489113 GCAATTAAGCCAACTACTAACGTACTA 59.511 37.037 0.00 0.00 0.00 1.82
4538 4788 4.684242 GGTTTGTGCAATTAAGCCAACTAC 59.316 41.667 0.00 0.00 0.00 2.73
4619 4872 4.814147 CTTTTCCTTTTTGAGGGATCTGC 58.186 43.478 0.00 0.00 46.31 4.26
4641 4894 5.539582 TCAATAAATACACGGTTCTGTGC 57.460 39.130 11.14 0.00 43.74 4.57
4719 4974 0.674895 AGTGTCAGATTTGCTCGCCC 60.675 55.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.