Multiple sequence alignment - TraesCS2A01G392300

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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 TraesCS2A01G392300 chr2A 100.000 6133 0 0 1 6133 642574854 642568722 0.000000e+00 11326.0
1 TraesCS2A01G392300 chr2B 93.906 4283 167 39 1770 6016 584116149 584111925 0.000000e+00 6377.0
2 TraesCS2A01G392300 chr2B 94.383 1086 43 6 1 1070 584117837 584116754 0.000000e+00 1652.0
3 TraesCS2A01G392300 chr2B 89.620 973 83 13 3147 4119 734355396 734356350 0.000000e+00 1221.0
4 TraesCS2A01G392300 chr2B 94.071 506 24 4 1057 1557 584116736 584116232 0.000000e+00 763.0
5 TraesCS2A01G392300 chr2B 84.343 198 18 3 2235 2424 734354923 734355115 1.360000e-41 182.0
6 TraesCS2A01G392300 chr2B 91.597 119 9 1 6016 6133 584111794 584111676 4.920000e-36 163.0
7 TraesCS2A01G392300 chr2B 85.057 87 7 6 1562 1647 411139536 411139455 3.940000e-12 84.2
8 TraesCS2A01G392300 chr2D 94.583 2640 93 15 3408 6016 498028855 498026235 0.000000e+00 4037.0
9 TraesCS2A01G392300 chr2D 91.527 1133 53 16 2211 3324 498029958 498028850 0.000000e+00 1520.0
10 TraesCS2A01G392300 chr2D 89.301 1187 56 30 1 1126 498032645 498031469 0.000000e+00 1423.0
11 TraesCS2A01G392300 chr2D 91.152 486 25 7 1620 2104 498030786 498030318 1.440000e-180 643.0
12 TraesCS2A01G392300 chr2D 92.670 191 8 4 1145 1330 498031232 498031043 2.820000e-68 270.0
13 TraesCS2A01G392300 chr2D 87.200 250 9 5 1318 1562 498031014 498030783 4.710000e-66 263.0
14 TraesCS2A01G392300 chr2D 90.083 121 8 3 6016 6133 498026074 498025955 2.960000e-33 154.0
15 TraesCS2A01G392300 chr2D 82.692 104 17 1 6024 6126 88053646 88053749 2.350000e-14 91.6
16 TraesCS2A01G392300 chr2D 81.915 94 15 2 6040 6132 62035456 62035548 1.830000e-10 78.7
17 TraesCS2A01G392300 chr1B 90.246 1179 93 17 3150 4326 117783295 117782137 0.000000e+00 1520.0
18 TraesCS2A01G392300 chr1B 86.364 198 15 2 2235 2424 117783772 117783579 8.060000e-49 206.0
19 TraesCS2A01G392300 chr3B 90.076 1179 95 17 3150 4326 16704871 16703713 0.000000e+00 1509.0
20 TraesCS2A01G392300 chr3B 84.343 198 19 2 2235 2424 16705348 16705155 3.780000e-42 183.0
21 TraesCS2A01G392300 chr1D 89.487 1189 96 18 3147 4326 18772943 18771775 0.000000e+00 1476.0
22 TraesCS2A01G392300 chr1D 83.505 194 21 6 2235 2424 18773410 18773224 2.940000e-38 171.0
23 TraesCS2A01G392300 chr6B 89.492 1180 99 19 3150 4326 16554896 16553739 0.000000e+00 1469.0
24 TraesCS2A01G392300 chr3A 89.900 1000 83 11 3333 4323 523893841 523894831 0.000000e+00 1271.0
25 TraesCS2A01G392300 chr3D 92.453 53 3 1 5917 5969 143003782 143003731 2.370000e-09 75.0
26 TraesCS2A01G392300 chr5B 97.619 42 1 0 1577 1618 412805699 412805740 8.530000e-09 73.1
27 TraesCS2A01G392300 chr5B 91.667 48 4 0 1571 1618 462751235 462751282 3.970000e-07 67.6
28 TraesCS2A01G392300 chr7B 88.889 54 5 1 1564 1617 686143811 686143759 1.430000e-06 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 TraesCS2A01G392300 chr2A 642568722 642574854 6132 True 11326.000000 11326 100.000000 1 6133 1 chr2A.!!$R1 6132
1 TraesCS2A01G392300 chr2B 584111676 584117837 6161 True 2238.750000 6377 93.489250 1 6133 4 chr2B.!!$R2 6132
2 TraesCS2A01G392300 chr2B 734354923 734356350 1427 False 701.500000 1221 86.981500 2235 4119 2 chr2B.!!$F1 1884
3 TraesCS2A01G392300 chr2D 498025955 498032645 6690 True 1187.142857 4037 90.930857 1 6133 7 chr2D.!!$R1 6132
4 TraesCS2A01G392300 chr1B 117782137 117783772 1635 True 863.000000 1520 88.305000 2235 4326 2 chr1B.!!$R1 2091
5 TraesCS2A01G392300 chr3B 16703713 16705348 1635 True 846.000000 1509 87.209500 2235 4326 2 chr3B.!!$R1 2091
6 TraesCS2A01G392300 chr1D 18771775 18773410 1635 True 823.500000 1476 86.496000 2235 4326 2 chr1D.!!$R1 2091
7 TraesCS2A01G392300 chr6B 16553739 16554896 1157 True 1469.000000 1469 89.492000 3150 4326 1 chr6B.!!$R1 1176
8 TraesCS2A01G392300 chr3A 523893841 523894831 990 False 1271.000000 1271 89.900000 3333 4323 1 chr3A.!!$F1 990

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
617 637 1.945819 GCAGGCTTCGGTTTCATCAGA 60.946 52.381 0.00 0.0 0.0 3.27 F
1885 2259 0.033366 GGGCATGTGGGTTGTTTGTC 59.967 55.000 0.00 0.0 0.0 3.18 F
2555 3219 0.108992 TTACAGCGGATGTCGTGTCC 60.109 55.000 0.45 0.0 42.7 4.02 F
2831 3530 0.617935 TCTCCGGAATTGGCATGTCA 59.382 50.000 5.23 0.0 0.0 3.58 F
3018 3720 1.500474 ATGATCCGTGGATGGTGTCT 58.500 50.000 6.03 0.0 34.6 3.41 F
4313 5026 2.292267 ACTGTGAGACTGGTTTTGCTG 58.708 47.619 0.00 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2476 0.099968 TCTTATCTCCCGTCGCGTTG 59.900 55.000 5.77 0.00 0.00 4.10 R
2816 3515 1.473677 ACATGTGACATGCCAATTCCG 59.526 47.619 24.32 0.00 0.00 4.30 R
3366 4070 2.117156 GGTGCGCTGCAGGATCATT 61.117 57.895 17.12 0.00 40.08 2.57 R
4758 5474 1.202604 CCGCCCGTAATAAGATGGTGT 60.203 52.381 0.00 0.00 0.00 4.16 R
4978 5698 2.448453 AGAAGGGACTCTGTACGAAGG 58.552 52.381 0.00 0.00 38.49 3.46 R
5950 6701 0.521242 CGCACGTGCATAAAGGCTTC 60.521 55.000 37.03 6.34 42.21 3.86 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
31 32 3.469008 TTCTCTCAAAGAAAGCGGACA 57.531 42.857 0.00 0.00 41.10 4.02
94 95 2.540931 CAGTGCAACACCAATTTTCAGC 59.459 45.455 0.00 0.00 41.43 4.26
343 344 6.213195 GGATTAATCTGGTGATGGAGAGAGAT 59.787 42.308 14.95 0.00 32.44 2.75
352 353 5.512232 GGTGATGGAGAGAGATTATGGAACC 60.512 48.000 0.00 0.00 0.00 3.62
355 356 4.483950 TGGAGAGAGATTATGGAACCGAT 58.516 43.478 0.00 0.00 0.00 4.18
379 380 2.283529 GCTCAGGGAGGTTCGGACA 61.284 63.158 0.00 0.00 0.00 4.02
617 637 1.945819 GCAGGCTTCGGTTTCATCAGA 60.946 52.381 0.00 0.00 0.00 3.27
619 639 2.417933 CAGGCTTCGGTTTCATCAGAAG 59.582 50.000 0.00 0.21 40.62 2.85
621 641 2.615493 GGCTTCGGTTTCATCAGAAGGA 60.615 50.000 6.25 0.00 39.04 3.36
636 656 4.281688 TCAGAAGGAAAAATGGGCTGAAAG 59.718 41.667 0.00 0.00 0.00 2.62
651 671 4.899048 CTGAAAGAGAGCCCAGGAAGGC 62.899 59.091 0.00 0.00 46.57 4.35
701 721 7.093245 TGCATGGCCATATTTTATGCATAGAAT 60.093 33.333 20.30 21.99 46.31 2.40
704 724 9.705103 ATGGCCATATTTTATGCATAGAATAGT 57.295 29.630 25.30 15.48 0.00 2.12
872 893 9.868389 GTATAACCGTATACAAAAATGTTAGCC 57.132 33.333 3.32 0.00 41.21 3.93
974 1032 2.900122 TGTTTGCTTAGCTTGATCGC 57.100 45.000 5.60 0.00 0.00 4.58
1012 1072 1.407851 CCTGGACCATGGTCATGACTG 60.408 57.143 38.83 25.72 46.20 3.51
1030 1090 1.411977 CTGGTGGAGCAGATGTAGGAG 59.588 57.143 0.00 0.00 0.00 3.69
1032 1092 0.105778 GTGGAGCAGATGTAGGAGGC 59.894 60.000 0.00 0.00 0.00 4.70
1157 1466 9.060347 TGATAAAGAAGAGATGCATATGGTTTC 57.940 33.333 0.00 0.24 0.00 2.78
1224 1538 6.265577 AGTACCATTCGCATTGCTTTATTTC 58.734 36.000 7.12 0.00 0.00 2.17
1235 1549 5.743026 TTGCTTTATTTCGCCGAATATCA 57.257 34.783 0.00 0.00 0.00 2.15
1236 1550 5.090652 TGCTTTATTTCGCCGAATATCAC 57.909 39.130 0.00 0.00 0.00 3.06
1360 1721 7.506114 AGATGTTCAAAGTTTACACAGTAGGA 58.494 34.615 5.53 0.00 0.00 2.94
1383 1744 3.546020 GGGAATTATCGTGTTGATGTGCG 60.546 47.826 0.00 0.00 37.99 5.34
1384 1745 2.737467 ATTATCGTGTTGATGTGCGC 57.263 45.000 0.00 0.00 37.99 6.09
1386 1747 2.570442 TATCGTGTTGATGTGCGCTA 57.430 45.000 9.73 0.00 37.99 4.26
1422 1783 3.200165 GCTCTACCCCATTCTAAACTGGT 59.800 47.826 0.00 0.00 0.00 4.00
1471 1832 2.079049 GCAAGGTAAGCGTTCTCGG 58.921 57.895 0.00 0.00 37.56 4.63
1489 1850 1.367471 GCCACGGGATGATCGATGA 59.633 57.895 0.54 0.00 0.00 2.92
1558 1920 3.151554 CCCCCGTTACTTTTGCTAACTT 58.848 45.455 0.00 0.00 0.00 2.66
1560 1922 3.566742 CCCCGTTACTTTTGCTAACTTGT 59.433 43.478 0.00 0.00 0.00 3.16
1561 1923 4.756135 CCCCGTTACTTTTGCTAACTTGTA 59.244 41.667 0.00 0.00 0.00 2.41
1562 1924 5.413523 CCCCGTTACTTTTGCTAACTTGTAT 59.586 40.000 0.00 0.00 0.00 2.29
1563 1925 6.072342 CCCCGTTACTTTTGCTAACTTGTATT 60.072 38.462 0.00 0.00 0.00 1.89
1564 1926 7.019418 CCCGTTACTTTTGCTAACTTGTATTC 58.981 38.462 0.00 0.00 0.00 1.75
1565 1927 7.019418 CCGTTACTTTTGCTAACTTGTATTCC 58.981 38.462 0.00 0.00 0.00 3.01
1566 1928 7.019418 CGTTACTTTTGCTAACTTGTATTCCC 58.981 38.462 0.00 0.00 0.00 3.97
1567 1929 7.094933 CGTTACTTTTGCTAACTTGTATTCCCT 60.095 37.037 0.00 0.00 0.00 4.20
1568 1930 8.573885 GTTACTTTTGCTAACTTGTATTCCCTT 58.426 33.333 0.00 0.00 0.00 3.95
1569 1931 7.597288 ACTTTTGCTAACTTGTATTCCCTTT 57.403 32.000 0.00 0.00 0.00 3.11
1570 1932 7.433680 ACTTTTGCTAACTTGTATTCCCTTTG 58.566 34.615 0.00 0.00 0.00 2.77
1571 1933 6.969993 TTTGCTAACTTGTATTCCCTTTGT 57.030 33.333 0.00 0.00 0.00 2.83
1572 1934 6.569179 TTGCTAACTTGTATTCCCTTTGTC 57.431 37.500 0.00 0.00 0.00 3.18
1573 1935 5.876357 TGCTAACTTGTATTCCCTTTGTCT 58.124 37.500 0.00 0.00 0.00 3.41
1574 1936 5.705441 TGCTAACTTGTATTCCCTTTGTCTG 59.295 40.000 0.00 0.00 0.00 3.51
1575 1937 5.123979 GCTAACTTGTATTCCCTTTGTCTGG 59.876 44.000 0.00 0.00 0.00 3.86
1576 1938 4.993705 ACTTGTATTCCCTTTGTCTGGA 57.006 40.909 0.00 0.00 0.00 3.86
1577 1939 5.319043 ACTTGTATTCCCTTTGTCTGGAA 57.681 39.130 0.00 0.00 44.34 3.53
1578 1940 5.701224 ACTTGTATTCCCTTTGTCTGGAAA 58.299 37.500 0.00 0.00 43.50 3.13
1579 1941 6.314917 ACTTGTATTCCCTTTGTCTGGAAAT 58.685 36.000 0.00 0.00 43.50 2.17
1580 1942 7.466804 ACTTGTATTCCCTTTGTCTGGAAATA 58.533 34.615 0.00 0.00 43.50 1.40
1581 1943 7.393515 ACTTGTATTCCCTTTGTCTGGAAATAC 59.606 37.037 0.00 0.00 43.50 1.89
1582 1944 7.027874 TGTATTCCCTTTGTCTGGAAATACT 57.972 36.000 0.00 0.00 43.50 2.12
1583 1945 7.466804 TGTATTCCCTTTGTCTGGAAATACTT 58.533 34.615 0.00 0.00 43.50 2.24
1584 1946 6.840780 ATTCCCTTTGTCTGGAAATACTTG 57.159 37.500 0.00 0.00 43.50 3.16
1585 1947 5.319043 TCCCTTTGTCTGGAAATACTTGT 57.681 39.130 0.00 0.00 0.00 3.16
1586 1948 5.313712 TCCCTTTGTCTGGAAATACTTGTC 58.686 41.667 0.00 0.00 0.00 3.18
1587 1949 5.070001 CCCTTTGTCTGGAAATACTTGTCA 58.930 41.667 0.00 0.00 0.00 3.58
1588 1950 5.711976 CCCTTTGTCTGGAAATACTTGTCAT 59.288 40.000 0.00 0.00 0.00 3.06
1589 1951 6.209391 CCCTTTGTCTGGAAATACTTGTCATT 59.791 38.462 0.00 0.00 0.00 2.57
1590 1952 7.393234 CCCTTTGTCTGGAAATACTTGTCATTA 59.607 37.037 0.00 0.00 0.00 1.90
1591 1953 8.792633 CCTTTGTCTGGAAATACTTGTCATTAA 58.207 33.333 0.00 0.00 0.00 1.40
1596 1958 9.573133 GTCTGGAAATACTTGTCATTAAAATGG 57.427 33.333 3.00 0.00 37.03 3.16
1597 1959 9.527157 TCTGGAAATACTTGTCATTAAAATGGA 57.473 29.630 3.00 0.00 37.03 3.41
1633 1995 9.810545 ATGTATCTAGAGAGTAGCTTGTTTTTC 57.189 33.333 0.00 0.00 0.00 2.29
1646 2008 9.406828 GTAGCTTGTTTTTCGAGGATAATTTTT 57.593 29.630 0.00 0.00 0.00 1.94
1648 2010 7.384932 AGCTTGTTTTTCGAGGATAATTTTTGG 59.615 33.333 0.00 0.00 0.00 3.28
1697 2059 2.437359 GGCGCTCCAGCTGTTCAT 60.437 61.111 13.81 0.00 39.32 2.57
1698 2060 2.042831 GGCGCTCCAGCTGTTCATT 61.043 57.895 13.81 0.00 39.32 2.57
1699 2061 1.589716 GGCGCTCCAGCTGTTCATTT 61.590 55.000 13.81 0.00 39.32 2.32
1700 2062 0.179179 GCGCTCCAGCTGTTCATTTC 60.179 55.000 13.81 0.00 39.32 2.17
1701 2063 1.446907 CGCTCCAGCTGTTCATTTCT 58.553 50.000 13.81 0.00 39.32 2.52
1702 2064 1.808945 CGCTCCAGCTGTTCATTTCTT 59.191 47.619 13.81 0.00 39.32 2.52
1703 2065 2.227388 CGCTCCAGCTGTTCATTTCTTT 59.773 45.455 13.81 0.00 39.32 2.52
1704 2066 3.304928 CGCTCCAGCTGTTCATTTCTTTT 60.305 43.478 13.81 0.00 39.32 2.27
1705 2067 4.625028 GCTCCAGCTGTTCATTTCTTTTT 58.375 39.130 13.81 0.00 38.21 1.94
1709 2071 7.224557 GCTCCAGCTGTTCATTTCTTTTTAAAA 59.775 33.333 13.81 0.00 38.21 1.52
1730 2092 1.731720 AAATCAGCAAGCTCGACTCC 58.268 50.000 0.00 0.00 0.00 3.85
1736 2098 3.002791 CAGCAAGCTCGACTCCAAATAA 58.997 45.455 0.00 0.00 0.00 1.40
1793 2167 0.747644 TGCAGACATACGGCCAATGG 60.748 55.000 17.10 0.00 38.85 3.16
1795 2169 1.815408 GCAGACATACGGCCAATGGAT 60.815 52.381 17.10 4.73 33.80 3.41
1819 2193 5.048083 TGGAGCGAAAATGTAGCAGAAATTT 60.048 36.000 0.00 0.00 0.00 1.82
1824 2198 5.566627 CGAAAATGTAGCAGAAATTTGGGGT 60.567 40.000 0.00 0.00 0.00 4.95
1835 2209 6.520272 CAGAAATTTGGGGTGTTTTGTGATA 58.480 36.000 0.00 0.00 0.00 2.15
1836 2210 6.646240 CAGAAATTTGGGGTGTTTTGTGATAG 59.354 38.462 0.00 0.00 0.00 2.08
1837 2211 4.535526 ATTTGGGGTGTTTTGTGATAGC 57.464 40.909 0.00 0.00 0.00 2.97
1838 2212 1.529226 TGGGGTGTTTTGTGATAGCG 58.471 50.000 0.00 0.00 0.00 4.26
1839 2213 0.808755 GGGGTGTTTTGTGATAGCGG 59.191 55.000 0.00 0.00 0.00 5.52
1855 2229 0.237498 GCGGTTAGCGCTCTGTTTTT 59.763 50.000 21.72 0.00 35.41 1.94
1856 2230 1.724973 GCGGTTAGCGCTCTGTTTTTC 60.725 52.381 21.72 0.00 35.41 2.29
1868 2242 3.817647 CTCTGTTTTTCTCTTCCTGTGGG 59.182 47.826 0.00 0.00 0.00 4.61
1869 2243 2.294512 CTGTTTTTCTCTTCCTGTGGGC 59.705 50.000 0.00 0.00 0.00 5.36
1885 2259 0.033366 GGGCATGTGGGTTGTTTGTC 59.967 55.000 0.00 0.00 0.00 3.18
1886 2260 0.749649 GGCATGTGGGTTGTTTGTCA 59.250 50.000 0.00 0.00 0.00 3.58
1887 2261 1.137872 GGCATGTGGGTTGTTTGTCAA 59.862 47.619 0.00 0.00 0.00 3.18
1888 2262 2.419297 GGCATGTGGGTTGTTTGTCAAA 60.419 45.455 0.00 0.00 37.81 2.69
1889 2263 3.265791 GCATGTGGGTTGTTTGTCAAAA 58.734 40.909 0.00 0.00 37.81 2.44
1890 2264 3.309410 GCATGTGGGTTGTTTGTCAAAAG 59.691 43.478 0.00 0.00 37.81 2.27
1891 2265 4.753233 CATGTGGGTTGTTTGTCAAAAGA 58.247 39.130 0.00 0.00 37.81 2.52
1921 2296 7.590279 ACACACGAGGAAATTAATTTTGGTAG 58.410 34.615 14.45 8.34 0.00 3.18
1981 2356 4.192317 GTCAGATCTGGCTAAAAACGGAT 58.808 43.478 20.20 0.00 35.49 4.18
1988 2363 2.417239 TGGCTAAAAACGGATAGCAACG 59.583 45.455 7.06 0.00 44.99 4.10
2122 2512 1.283181 CGCGACGGGAGATAAGAGG 59.717 63.158 0.00 0.00 0.00 3.69
2344 2994 2.613576 GAAGAGGGAGGAGGGAGGGG 62.614 70.000 0.00 0.00 0.00 4.79
2345 2995 4.179599 GAGGGAGGAGGGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
2346 2996 4.761304 AGGGAGGAGGGAGGGGGA 62.761 72.222 0.00 0.00 0.00 4.81
2349 2999 4.862823 GAGGAGGGAGGGGGACGG 62.863 77.778 0.00 0.00 0.00 4.79
2485 3140 2.201022 GCCGCTCCGATCCCTCTTA 61.201 63.158 0.00 0.00 0.00 2.10
2523 3178 3.186047 GACGAACGTCCATGGGCG 61.186 66.667 35.98 35.98 39.08 6.13
2555 3219 0.108992 TTACAGCGGATGTCGTGTCC 60.109 55.000 0.45 0.00 42.70 4.02
2677 3341 1.393539 CGGTGCTCGGTATTTGTTGAG 59.606 52.381 0.00 0.00 34.75 3.02
2702 3366 1.882198 AATCACGCGATTGCTTTTCG 58.118 45.000 15.93 0.14 40.45 3.46
2722 3386 5.739752 TCGAACATGAATGCAAAGGATAG 57.260 39.130 0.00 0.00 0.00 2.08
2731 3395 2.564771 TGCAAAGGATAGCTGGAATCG 58.435 47.619 0.00 0.00 0.00 3.34
2786 3455 4.682787 TGTGCTTAGATTACGACAGGATG 58.317 43.478 0.00 0.00 46.00 3.51
2816 3515 3.010420 GGTCCAACAAATACTGCTCTCC 58.990 50.000 0.00 0.00 0.00 3.71
2831 3530 0.617935 TCTCCGGAATTGGCATGTCA 59.382 50.000 5.23 0.00 0.00 3.58
2837 3536 2.732912 CGGAATTGGCATGTCACATGTG 60.733 50.000 20.18 20.18 0.00 3.21
2874 3573 7.822822 GGACTTTGAACTTAGAAGCTACCATTA 59.177 37.037 0.00 0.00 0.00 1.90
3015 3717 1.694150 AGGTATGATCCGTGGATGGTG 59.306 52.381 6.03 0.00 34.60 4.17
3018 3720 1.500474 ATGATCCGTGGATGGTGTCT 58.500 50.000 6.03 0.00 34.60 3.41
3129 3831 7.556275 GGGTATTCCTGTTAAAATCTCATGACA 59.444 37.037 0.00 0.00 0.00 3.58
3222 3926 3.797865 GCTGTGCTCTCATGTTTGCTTTT 60.798 43.478 0.00 0.00 0.00 2.27
3366 4070 5.538053 TCTGGCATGAGTAAATTGACCAAAA 59.462 36.000 0.00 0.00 0.00 2.44
3367 4071 6.041409 TCTGGCATGAGTAAATTGACCAAAAA 59.959 34.615 0.00 0.00 0.00 1.94
3368 4072 6.767456 TGGCATGAGTAAATTGACCAAAAAT 58.233 32.000 0.00 0.00 0.00 1.82
3369 4073 6.649973 TGGCATGAGTAAATTGACCAAAAATG 59.350 34.615 0.00 0.00 0.00 2.32
3370 4074 6.873076 GGCATGAGTAAATTGACCAAAAATGA 59.127 34.615 0.00 0.00 0.00 2.57
3371 4075 7.550196 GGCATGAGTAAATTGACCAAAAATGAT 59.450 33.333 0.00 0.00 0.00 2.45
3674 4386 4.561213 GCACATGCCCTTTACGAAATAAAC 59.439 41.667 0.00 0.00 34.31 2.01
3680 4392 9.360093 CATGCCCTTTACGAAATAAACAATTTA 57.640 29.630 0.00 0.00 37.93 1.40
3796 4508 7.726033 AGAACTATCCAGTGAGTACAAATCT 57.274 36.000 0.00 0.00 34.36 2.40
3803 4515 6.387465 TCCAGTGAGTACAAATCTCTTTACG 58.613 40.000 0.00 0.00 33.59 3.18
3836 4548 4.462508 TCAGATTCATCGCTGTTTCTCT 57.537 40.909 0.00 0.00 33.90 3.10
3941 4654 3.659183 ATTCAGCTAGCAATGGAACCT 57.341 42.857 18.83 0.00 0.00 3.50
3951 4664 2.489722 GCAATGGAACCTTGTCTCCTTC 59.510 50.000 0.00 0.00 32.51 3.46
4251 4964 6.233434 TCTGTGCTTCTTGATTAGTTGATGT 58.767 36.000 0.00 0.00 0.00 3.06
4277 4990 7.578458 TTTACTTCTATGTAACCTTCCCCTT 57.422 36.000 0.00 0.00 32.84 3.95
4300 5013 5.841810 TGGGCAAATTTTCTAAACTGTGAG 58.158 37.500 0.00 0.00 0.00 3.51
4313 5026 2.292267 ACTGTGAGACTGGTTTTGCTG 58.708 47.619 0.00 0.00 0.00 4.41
4466 5180 8.173542 TGAAATCTTACATGGCTACTATACGA 57.826 34.615 0.00 0.00 0.00 3.43
4682 5398 3.119708 GCAGTTGAAGACTTGGCCATAAG 60.120 47.826 6.09 4.08 36.10 1.73
4856 5576 3.186409 TCTTTTCTGCAGAAAACGATCGG 59.814 43.478 38.40 29.46 45.76 4.18
4978 5698 5.007430 CAGTATGCATTCTCCTTGTCACATC 59.993 44.000 3.54 0.00 0.00 3.06
5051 5771 5.350365 GCAGACTGTTATTAAATCCACACGA 59.650 40.000 3.99 0.00 0.00 4.35
5179 5899 4.689345 GCCACGTGTAGTAAAGTTCTTGAT 59.311 41.667 15.65 0.00 0.00 2.57
5344 6064 2.615465 TTGGGCCATGCTAGTGCCT 61.615 57.895 7.26 0.00 44.71 4.75
5401 6121 2.159226 CGGAGTCTTCGTGCTAGGAAAT 60.159 50.000 0.00 0.00 0.00 2.17
5402 6122 3.066342 CGGAGTCTTCGTGCTAGGAAATA 59.934 47.826 0.00 0.00 0.00 1.40
5403 6123 4.361420 GGAGTCTTCGTGCTAGGAAATAC 58.639 47.826 0.00 0.00 0.00 1.89
5481 6201 6.016860 TGCATAAATGATATTGGTGCACTCTC 60.017 38.462 17.98 7.18 36.33 3.20
5634 6360 6.288941 TGACGTGTTTAGGAGGAATTATGA 57.711 37.500 0.00 0.00 0.00 2.15
5679 6405 3.686726 GGAAAACGAAGCAGTCATGATCT 59.313 43.478 0.00 0.00 0.00 2.75
5681 6407 5.351465 GGAAAACGAAGCAGTCATGATCTAA 59.649 40.000 0.00 0.00 0.00 2.10
5683 6409 7.224753 GGAAAACGAAGCAGTCATGATCTAATA 59.775 37.037 0.00 0.00 0.00 0.98
5695 6421 6.369065 GTCATGATCTAATAAAAGGTAGCCGG 59.631 42.308 0.00 0.00 0.00 6.13
5706 6432 1.173913 GGTAGCCGGCACTTTTTGAT 58.826 50.000 31.54 6.76 0.00 2.57
5777 6503 5.824624 TGTCATTCAATATTTCAGAGCCTCC 59.175 40.000 0.00 0.00 0.00 4.30
5779 6505 6.204495 GTCATTCAATATTTCAGAGCCTCCTC 59.796 42.308 0.00 0.00 38.42 3.71
5819 6567 5.305644 TCCAGCTCTGTTCTAAAAGTTCTCT 59.694 40.000 0.00 0.00 0.00 3.10
5820 6568 6.493802 TCCAGCTCTGTTCTAAAAGTTCTCTA 59.506 38.462 0.00 0.00 0.00 2.43
5889 6640 2.545952 GGCACATAGATCACCGAACGAT 60.546 50.000 0.00 0.00 0.00 3.73
5890 6641 2.726760 GCACATAGATCACCGAACGATC 59.273 50.000 0.00 0.00 39.71 3.69
5891 6642 3.795488 GCACATAGATCACCGAACGATCA 60.795 47.826 10.13 0.10 41.49 2.92
5895 6646 5.473846 ACATAGATCACCGAACGATCACTAT 59.526 40.000 10.13 0.00 41.49 2.12
5911 6662 7.445707 ACGATCACTATTGCTACTAGAATGAGA 59.554 37.037 0.00 0.00 0.00 3.27
5928 6679 3.659089 GACGCTTGGAGCCGGCTTA 62.659 63.158 33.34 20.53 38.18 3.09
5937 6688 4.164843 TGGAGCCGGCTTAGATTTTATT 57.835 40.909 33.34 2.41 0.00 1.40
5948 6699 6.961554 GGCTTAGATTTTATTGTTGACAGTCG 59.038 38.462 0.00 0.00 0.00 4.18
5950 6701 7.900352 GCTTAGATTTTATTGTTGACAGTCGAG 59.100 37.037 0.00 0.00 0.00 4.04
5958 6709 2.158957 TGTTGACAGTCGAGAAGCCTTT 60.159 45.455 0.00 0.00 0.00 3.11
5967 6718 1.061131 CGAGAAGCCTTTATGCACGTG 59.939 52.381 12.28 12.28 0.00 4.49
5968 6719 0.804989 AGAAGCCTTTATGCACGTGC 59.195 50.000 33.11 33.11 42.50 5.34
5982 6735 3.036084 GTGCGTGACGTGTCCCTG 61.036 66.667 6.91 0.00 0.00 4.45
6013 6766 1.573829 TTTGGAGCCGCATTCGTCAC 61.574 55.000 0.00 0.00 0.00 3.67
6033 6840 4.022935 TCACTGCATCAGACACCAAATTTC 60.023 41.667 0.29 0.00 35.18 2.17
6061 6977 3.700038 ACGACGAGAAATCCTAACCTCAT 59.300 43.478 0.00 0.00 0.00 2.90
6064 6980 3.700038 ACGAGAAATCCTAACCTCATCGT 59.300 43.478 0.00 0.00 36.18 3.73
6126 7043 5.008331 ACTACGTCTAGATGGACAAACTCA 58.992 41.667 16.30 0.00 36.12 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.887152 GCCTGTCAGTTCTGATGGTTTT 59.113 45.455 18.33 0.00 0.00 2.43
94 95 6.091441 CACCCTCTATTTCTTTCACTTTCTCG 59.909 42.308 0.00 0.00 0.00 4.04
343 344 1.843851 AGCTTCCCATCGGTTCCATAA 59.156 47.619 0.00 0.00 0.00 1.90
352 353 1.445095 CTCCCTGAGCTTCCCATCG 59.555 63.158 0.00 0.00 0.00 3.84
355 356 1.151810 AACCTCCCTGAGCTTCCCA 60.152 57.895 0.00 0.00 0.00 4.37
379 380 3.181476 ACCTGCGCTTGATTTCAGTTTTT 60.181 39.130 9.73 0.00 0.00 1.94
413 414 5.945784 TGATTTCTTTGAACTATGGTGGGAG 59.054 40.000 0.00 0.00 0.00 4.30
617 637 4.482990 TCTCTTTCAGCCCATTTTTCCTT 58.517 39.130 0.00 0.00 0.00 3.36
619 639 3.367806 GCTCTCTTTCAGCCCATTTTTCC 60.368 47.826 0.00 0.00 0.00 3.13
621 641 3.949842 GCTCTCTTTCAGCCCATTTTT 57.050 42.857 0.00 0.00 0.00 1.94
651 671 0.099436 GCAAGCAAATGCCTAGGTCG 59.901 55.000 11.31 0.00 43.38 4.79
802 822 9.595823 GTAGTTCAGGCTATTTTATACTCACAA 57.404 33.333 0.00 0.00 0.00 3.33
880 901 2.290705 GGGTTACCTTGCACATGGTAGT 60.291 50.000 13.31 0.00 40.67 2.73
882 905 1.004979 GGGGTTACCTTGCACATGGTA 59.995 52.381 10.49 10.49 39.30 3.25
884 907 2.578683 GGGGTTACCTTGCACATGG 58.421 57.895 0.00 1.22 36.80 3.66
943 978 7.413475 AGCTAAGCAAACATTATATCGACAG 57.587 36.000 0.00 0.00 0.00 3.51
946 981 8.607441 ATCAAGCTAAGCAAACATTATATCGA 57.393 30.769 0.00 0.00 0.00 3.59
974 1032 1.679898 GTCCACCCCTGTTCTCCAG 59.320 63.158 0.00 0.00 41.15 3.86
1012 1072 0.755686 CCTCCTACATCTGCTCCACC 59.244 60.000 0.00 0.00 0.00 4.61
1030 1090 1.953231 GCATCTTCCAAAGCTGGGCC 61.953 60.000 0.00 0.00 43.71 5.80
1032 1092 1.067354 GTTGCATCTTCCAAAGCTGGG 60.067 52.381 0.00 0.00 43.71 4.45
1074 1165 5.105752 AGTAGCAATGTTCTTCATCGTCTC 58.894 41.667 0.00 0.00 35.48 3.36
1157 1466 8.066595 CCTTTCTAGCATCAATCTTTAATCACG 58.933 37.037 0.00 0.00 0.00 4.35
1224 1538 2.028476 TCCCCATTAGTGATATTCGGCG 60.028 50.000 0.00 0.00 0.00 6.46
1235 1549 4.687219 GCAAGCACTAGATTCCCCATTAGT 60.687 45.833 0.00 0.00 0.00 2.24
1236 1550 3.817647 GCAAGCACTAGATTCCCCATTAG 59.182 47.826 0.00 0.00 0.00 1.73
1360 1721 3.627577 GCACATCAACACGATAATTCCCT 59.372 43.478 0.00 0.00 31.20 4.20
1395 1756 1.883084 GAATGGGGTAGAGCGCACG 60.883 63.158 11.47 0.00 0.00 5.34
1471 1832 0.946221 GTCATCGATCATCCCGTGGC 60.946 60.000 0.00 0.00 0.00 5.01
1489 1850 3.639561 ACGGCAAGAAATTAAAAGGTGGT 59.360 39.130 0.00 0.00 0.00 4.16
1560 1922 7.466804 ACAAGTATTTCCAGACAAAGGGAATA 58.533 34.615 0.00 0.00 42.44 1.75
1561 1923 6.314917 ACAAGTATTTCCAGACAAAGGGAAT 58.685 36.000 0.00 0.00 42.44 3.01
1562 1924 5.701224 ACAAGTATTTCCAGACAAAGGGAA 58.299 37.500 0.00 0.00 41.27 3.97
1563 1925 5.163141 TGACAAGTATTTCCAGACAAAGGGA 60.163 40.000 0.00 0.00 0.00 4.20
1564 1926 5.070001 TGACAAGTATTTCCAGACAAAGGG 58.930 41.667 0.00 0.00 0.00 3.95
1565 1927 6.824305 ATGACAAGTATTTCCAGACAAAGG 57.176 37.500 0.00 0.00 0.00 3.11
1570 1932 9.573133 CCATTTTAATGACAAGTATTTCCAGAC 57.427 33.333 4.07 0.00 38.70 3.51
1571 1933 9.527157 TCCATTTTAATGACAAGTATTTCCAGA 57.473 29.630 4.07 0.00 38.70 3.86
1601 1963 9.719355 CAAGCTACTCTCTAGATACATCTTCTA 57.281 37.037 0.00 0.00 38.32 2.10
1602 1964 8.217799 ACAAGCTACTCTCTAGATACATCTTCT 58.782 37.037 0.00 0.00 38.32 2.85
1603 1965 8.391075 ACAAGCTACTCTCTAGATACATCTTC 57.609 38.462 0.00 0.00 38.32 2.87
1604 1966 8.760980 AACAAGCTACTCTCTAGATACATCTT 57.239 34.615 0.00 0.00 38.32 2.40
1605 1967 8.760980 AAACAAGCTACTCTCTAGATACATCT 57.239 34.615 0.00 0.00 40.86 2.90
1606 1968 9.810545 AAAAACAAGCTACTCTCTAGATACATC 57.189 33.333 0.00 0.00 0.00 3.06
1607 1969 9.810545 GAAAAACAAGCTACTCTCTAGATACAT 57.189 33.333 0.00 0.00 0.00 2.29
1608 1970 7.968956 CGAAAAACAAGCTACTCTCTAGATACA 59.031 37.037 0.00 0.00 0.00 2.29
1609 1971 8.182881 TCGAAAAACAAGCTACTCTCTAGATAC 58.817 37.037 0.00 0.00 0.00 2.24
1610 1972 8.277490 TCGAAAAACAAGCTACTCTCTAGATA 57.723 34.615 0.00 0.00 0.00 1.98
1611 1973 7.159322 TCGAAAAACAAGCTACTCTCTAGAT 57.841 36.000 0.00 0.00 0.00 1.98
1612 1974 6.349445 CCTCGAAAAACAAGCTACTCTCTAGA 60.349 42.308 0.00 0.00 0.00 2.43
1613 1975 5.802956 CCTCGAAAAACAAGCTACTCTCTAG 59.197 44.000 0.00 0.00 0.00 2.43
1614 1976 5.475909 TCCTCGAAAAACAAGCTACTCTCTA 59.524 40.000 0.00 0.00 0.00 2.43
1615 1977 4.281182 TCCTCGAAAAACAAGCTACTCTCT 59.719 41.667 0.00 0.00 0.00 3.10
1616 1978 4.557205 TCCTCGAAAAACAAGCTACTCTC 58.443 43.478 0.00 0.00 0.00 3.20
1617 1979 4.602340 TCCTCGAAAAACAAGCTACTCT 57.398 40.909 0.00 0.00 0.00 3.24
1618 1980 6.963049 TTATCCTCGAAAAACAAGCTACTC 57.037 37.500 0.00 0.00 0.00 2.59
1633 1995 5.992217 AGCTAGCTACCAAAAATTATCCTCG 59.008 40.000 17.69 0.00 0.00 4.63
1646 2008 3.418047 GGAAACCAAAAGCTAGCTACCA 58.582 45.455 19.70 0.00 0.00 3.25
1709 2071 2.485814 GGAGTCGAGCTTGCTGATTTTT 59.514 45.455 0.00 0.00 0.00 1.94
1759 2121 7.538334 CGTATGTCTGCAGAAAATTGAAATCAA 59.462 33.333 20.19 0.00 40.51 2.57
1793 2167 3.198068 TCTGCTACATTTTCGCTCCATC 58.802 45.455 0.00 0.00 0.00 3.51
1795 2169 2.760634 TCTGCTACATTTTCGCTCCA 57.239 45.000 0.00 0.00 0.00 3.86
1819 2193 1.529226 CGCTATCACAAAACACCCCA 58.471 50.000 0.00 0.00 0.00 4.96
1824 2198 2.413796 CGCTAACCGCTATCACAAAACA 59.586 45.455 0.00 0.00 36.13 2.83
1837 2211 1.798813 AGAAAAACAGAGCGCTAACCG 59.201 47.619 11.50 0.86 40.75 4.44
1838 2212 3.067833 AGAGAAAAACAGAGCGCTAACC 58.932 45.455 11.50 0.00 0.00 2.85
1839 2213 4.377533 GGAAGAGAAAAACAGAGCGCTAAC 60.378 45.833 11.50 0.00 0.00 2.34
1855 2229 0.325933 CACATGCCCACAGGAAGAGA 59.674 55.000 0.00 0.00 33.47 3.10
1856 2230 0.679002 CCACATGCCCACAGGAAGAG 60.679 60.000 0.00 0.00 33.47 2.85
1868 2242 2.593346 TTGACAAACAACCCACATGC 57.407 45.000 0.00 0.00 33.18 4.06
1869 2243 4.753233 TCTTTTGACAAACAACCCACATG 58.247 39.130 0.00 0.00 38.29 3.21
1897 2271 6.526674 GCTACCAAAATTAATTTCCTCGTGTG 59.473 38.462 13.68 6.70 0.00 3.82
1921 2296 1.270550 CAATTAGCCCATGATTCCCGC 59.729 52.381 0.00 0.00 0.00 6.13
1981 2356 2.260434 GCTCGTGTCCCGTTGCTA 59.740 61.111 0.00 0.00 37.94 3.49
1988 2363 1.146358 GATAGTTGCGCTCGTGTCCC 61.146 60.000 9.73 0.00 0.00 4.46
2099 2474 2.894240 TTATCTCCCGTCGCGTTGGC 62.894 60.000 5.77 0.00 0.00 4.52
2101 2476 0.099968 TCTTATCTCCCGTCGCGTTG 59.900 55.000 5.77 0.00 0.00 4.10
2122 2512 2.791868 GGCGGCCTCTTCTCTCCTC 61.792 68.421 12.87 0.00 0.00 3.71
2316 2951 0.398381 CCTCCCTCTTCCTCCTCCTG 60.398 65.000 0.00 0.00 0.00 3.86
2467 3117 2.148558 CTAAGAGGGATCGGAGCGGC 62.149 65.000 0.00 0.00 0.00 6.53
2474 3124 3.452474 CTGAACAAGCTAAGAGGGATCG 58.548 50.000 0.00 0.00 0.00 3.69
2481 3136 4.804261 GCCTCTTTCCTGAACAAGCTAAGA 60.804 45.833 0.00 0.00 0.00 2.10
2483 3138 3.073062 AGCCTCTTTCCTGAACAAGCTAA 59.927 43.478 0.00 0.00 0.00 3.09
2485 3140 1.423161 AGCCTCTTTCCTGAACAAGCT 59.577 47.619 0.00 0.00 0.00 3.74
2527 3182 4.319911 CGACATCCGCTGTAAAAGGAAAAA 60.320 41.667 0.00 0.00 38.54 1.94
2537 3192 1.509463 GGACACGACATCCGCTGTA 59.491 57.895 0.00 0.00 43.32 2.74
2538 3193 2.261671 GGACACGACATCCGCTGT 59.738 61.111 0.00 0.00 43.32 4.40
2677 3341 2.470821 AGCAATCGCGTGATTACTACC 58.529 47.619 22.88 9.80 42.94 3.18
2702 3366 5.279384 CAGCTATCCTTTGCATTCATGTTC 58.721 41.667 0.00 0.00 0.00 3.18
2745 3409 4.086524 GCACAAATACAATGAAACACGACG 59.913 41.667 0.00 0.00 0.00 5.12
2786 3455 7.067008 AGCAGTATTTGTTGGACCATTGTATAC 59.933 37.037 0.00 0.00 0.00 1.47
2816 3515 1.473677 ACATGTGACATGCCAATTCCG 59.526 47.619 24.32 0.00 0.00 4.30
3124 3826 7.934855 ATAATCAGAGAACAAAGCTTGTCAT 57.065 32.000 0.00 0.00 44.59 3.06
3129 3831 7.066766 CAGCCTTATAATCAGAGAACAAAGCTT 59.933 37.037 0.00 0.00 0.00 3.74
3366 4070 2.117156 GGTGCGCTGCAGGATCATT 61.117 57.895 17.12 0.00 40.08 2.57
3367 4071 2.515523 GGTGCGCTGCAGGATCAT 60.516 61.111 17.12 0.00 40.08 2.45
3368 4072 3.963687 CTGGTGCGCTGCAGGATCA 62.964 63.158 17.12 0.00 40.08 2.92
3369 4073 3.200593 CTGGTGCGCTGCAGGATC 61.201 66.667 17.12 0.00 40.08 3.36
3680 4392 9.196139 TGATTCCGGATCCAAAATTTAACTAAT 57.804 29.630 13.41 0.00 33.60 1.73
3796 4508 5.543714 TCTGAACCAGCATTTACGTAAAGA 58.456 37.500 23.78 10.23 0.00 2.52
3803 4515 5.505286 CGATGAATCTGAACCAGCATTTAC 58.495 41.667 0.00 0.00 0.00 2.01
3836 4548 6.855763 AATCATTGAAACCTAGCAATTGGA 57.144 33.333 7.72 0.00 32.74 3.53
3941 4654 5.505654 GCTGTTCAATTTTCGAAGGAGACAA 60.506 40.000 0.00 0.00 0.00 3.18
3951 4664 6.789262 AGGATCATTAGCTGTTCAATTTTCG 58.211 36.000 0.00 0.00 0.00 3.46
4042 4755 8.044060 TGAGATGAATGAAAGGTCAAACATAC 57.956 34.615 0.00 0.00 37.30 2.39
4051 4764 4.643784 GCCTCATTGAGATGAATGAAAGGT 59.356 41.667 15.36 0.00 40.89 3.50
4251 4964 8.865244 AGGGGAAGGTTACATAGAAGTAAATA 57.135 34.615 0.00 0.00 35.88 1.40
4277 4990 5.596361 TCTCACAGTTTAGAAAATTTGCCCA 59.404 36.000 0.00 0.00 0.00 5.36
4300 5013 2.292103 TTGCAACAGCAAAACCAGTC 57.708 45.000 0.00 0.00 44.65 3.51
4313 5026 4.689812 TGTGCCATTGTTGATATTTGCAAC 59.310 37.500 0.00 0.00 44.40 4.17
4464 5178 5.897377 ATTATTCTGGGACAAAAGGTTCG 57.103 39.130 0.00 0.00 38.70 3.95
4466 5180 6.994421 ACAATTATTCTGGGACAAAAGGTT 57.006 33.333 0.00 0.00 38.70 3.50
4758 5474 1.202604 CCGCCCGTAATAAGATGGTGT 60.203 52.381 0.00 0.00 0.00 4.16
4856 5576 9.237846 GTTATGCAGTAAAGAATATCAAAAGCC 57.762 33.333 0.00 0.00 0.00 4.35
4883 5603 5.067674 CCATTTCCGATCCATCAGCTTAAAA 59.932 40.000 0.00 0.00 0.00 1.52
4978 5698 2.448453 AGAAGGGACTCTGTACGAAGG 58.552 52.381 0.00 0.00 38.49 3.46
5025 5745 6.348132 CGTGTGGATTTAATAACAGTCTGCAA 60.348 38.462 0.00 0.00 0.00 4.08
5051 5771 1.889454 CTCTCTCTCAAGCTGGCGT 59.111 57.895 0.00 0.00 0.00 5.68
5116 5836 1.467342 GTTGCTAACGGGCGAGAAAAT 59.533 47.619 0.00 0.00 34.52 1.82
5179 5899 6.653020 ACATTCCACTCATTAGAAGCATGTA 58.347 36.000 0.00 0.00 0.00 2.29
5192 5912 3.455910 CCCTGATTCCTACATTCCACTCA 59.544 47.826 0.00 0.00 0.00 3.41
5344 6064 5.471556 TGTTTCCGAAAGTACATCCTACA 57.528 39.130 0.00 0.00 0.00 2.74
5401 6121 7.880195 AGGAGTTTCAGAACTTACTACGTAGTA 59.120 37.037 27.51 27.51 45.88 1.82
5402 6122 6.714356 AGGAGTTTCAGAACTTACTACGTAGT 59.286 38.462 29.62 29.62 45.88 2.73
5403 6123 7.094890 TGAGGAGTTTCAGAACTTACTACGTAG 60.095 40.741 20.97 20.97 45.88 3.51
5481 6201 2.776330 ACGTGTGTTTAGTGCAAAACG 58.224 42.857 8.96 2.72 41.33 3.60
5577 6301 5.382616 ACCCGACCTCTTATTTTTGAAGTT 58.617 37.500 0.00 0.00 0.00 2.66
5578 6302 4.981812 ACCCGACCTCTTATTTTTGAAGT 58.018 39.130 0.00 0.00 0.00 3.01
5661 6387 8.492673 TTTTATTAGATCATGACTGCTTCGTT 57.507 30.769 0.00 0.00 0.00 3.85
5679 6405 3.918294 AGTGCCGGCTACCTTTTATTA 57.082 42.857 29.70 0.00 0.00 0.98
5681 6407 2.801077 AAGTGCCGGCTACCTTTTAT 57.199 45.000 29.70 4.29 0.00 1.40
5683 6409 1.699730 AAAAGTGCCGGCTACCTTTT 58.300 45.000 29.67 29.67 0.00 2.27
5695 6421 5.074430 CAAAGTCTGCAATCAAAAAGTGC 57.926 39.130 0.00 0.00 38.78 4.40
5819 6567 9.719355 TGTTGCTTGAGATGTTTTATACTTCTA 57.281 29.630 0.00 0.00 40.32 2.10
5820 6568 8.621532 TGTTGCTTGAGATGTTTTATACTTCT 57.378 30.769 0.00 0.00 42.24 2.85
5862 6610 2.804527 CGGTGATCTATGTGCCTCAATG 59.195 50.000 0.00 0.00 0.00 2.82
5889 6640 6.513556 GCGTCTCATTCTAGTAGCAATAGTGA 60.514 42.308 0.00 0.00 0.00 3.41
5890 6641 5.627367 GCGTCTCATTCTAGTAGCAATAGTG 59.373 44.000 0.00 0.00 0.00 2.74
5891 6642 5.533154 AGCGTCTCATTCTAGTAGCAATAGT 59.467 40.000 0.00 0.00 0.00 2.12
5895 6646 4.424626 CAAGCGTCTCATTCTAGTAGCAA 58.575 43.478 0.00 0.00 0.00 3.91
5911 6662 3.665675 CTAAGCCGGCTCCAAGCGT 62.666 63.158 32.93 15.33 43.62 5.07
5928 6679 7.360438 GCTTCTCGACTGTCAACAATAAAATCT 60.360 37.037 8.73 0.00 0.00 2.40
5937 6688 1.040646 AGGCTTCTCGACTGTCAACA 58.959 50.000 8.73 0.00 0.00 3.33
5948 6699 1.202076 GCACGTGCATAAAGGCTTCTC 60.202 52.381 34.52 0.00 41.59 2.87
5950 6701 0.521242 CGCACGTGCATAAAGGCTTC 60.521 55.000 37.03 6.34 42.21 3.86
5967 6718 2.430921 CTCAGGGACACGTCACGC 60.431 66.667 0.00 0.00 38.25 5.34
5968 6719 2.258591 CCTCAGGGACACGTCACG 59.741 66.667 0.00 0.00 38.25 4.35
5977 6730 0.614979 AAAGCGCTAGTCCTCAGGGA 60.615 55.000 12.05 0.00 39.70 4.20
5982 6735 0.808060 GCTCCAAAGCGCTAGTCCTC 60.808 60.000 12.05 0.00 39.10 3.71
6013 6766 3.495193 CGAAATTTGGTGTCTGATGCAG 58.505 45.455 0.00 0.00 0.00 4.41
6033 6840 1.331138 AGGATTTCTCGTCGTCTAGCG 59.669 52.381 0.00 0.83 43.01 4.26
6047 6854 3.112263 TGGGACGATGAGGTTAGGATTT 58.888 45.455 0.00 0.00 0.00 2.17
6064 6980 1.186200 CTCATGTCGTCTCCTTGGGA 58.814 55.000 0.00 0.00 0.00 4.37
6080 6996 1.030488 CGGAGCTTCGGGTAGACTCA 61.030 60.000 6.48 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.