Multiple sequence alignment - TraesCS2D01G343200

Loading Multiple Alignment...

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 TraesCS2D01G343200 chr2D 100.000 6325 0 0 1 6325 439562259 439568583 0.000000e+00 11681.0
1 TraesCS2D01G343200 chr2D 96.711 152 4 1 1708 1859 518050831 518050981 1.050000e-62 252.0
2 TraesCS2D01G343200 chr2D 96.026 151 5 1 1707 1857 3120789 3120938 1.760000e-60 244.0
3 TraesCS2D01G343200 chr2B 97.547 4485 50 14 1856 6325 517596846 517601285 0.000000e+00 7618.0
4 TraesCS2D01G343200 chr2B 94.647 1644 48 18 1 1619 517595221 517596849 0.000000e+00 2512.0
5 TraesCS2D01G343200 chr2B 92.929 99 7 0 1618 1716 206464790 206464692 1.840000e-30 145.0
6 TraesCS2D01G343200 chr2B 92.079 101 8 0 1616 1716 23591661 23591561 6.610000e-30 143.0
7 TraesCS2D01G343200 chr2B 88.889 108 12 0 1609 1716 115388319 115388426 3.980000e-27 134.0
8 TraesCS2D01G343200 chr2A 94.559 4117 134 38 1856 5910 549293713 549289625 0.000000e+00 6279.0
9 TraesCS2D01G343200 chr2A 96.929 1107 15 12 527 1619 549294811 549293710 0.000000e+00 1838.0
10 TraesCS2D01G343200 chr2A 92.537 536 33 1 1 529 549295599 549295064 0.000000e+00 761.0
11 TraesCS2D01G343200 chr2A 92.905 296 7 3 6042 6325 549289431 549289138 9.810000e-113 418.0
12 TraesCS2D01G343200 chr3B 87.651 664 51 13 1 633 40870233 40869570 0.000000e+00 743.0
13 TraesCS2D01G343200 chr3B 96.026 151 5 1 1707 1857 194141514 194141365 1.760000e-60 244.0
14 TraesCS2D01G343200 chr3B 93.478 138 9 0 5133 5270 528176328 528176191 8.310000e-49 206.0
15 TraesCS2D01G343200 chr7D 96.732 153 4 1 1707 1859 527303393 527303544 2.930000e-63 254.0
16 TraesCS2D01G343200 chr7D 96.078 153 5 1 1707 1859 526878413 526878564 1.360000e-61 248.0
17 TraesCS2D01G343200 chr7D 94.771 153 7 1 1707 1859 527046235 527046386 2.950000e-58 237.0
18 TraesCS2D01G343200 chr7D 92.593 108 6 2 1611 1716 527046107 527046214 3.050000e-33 154.0
19 TraesCS2D01G343200 chr7D 97.297 37 0 1 5985 6021 513211167 513211202 1.900000e-05 62.1
20 TraesCS2D01G343200 chr3D 96.026 151 5 1 1707 1857 570543878 570544027 1.760000e-60 244.0
21 TraesCS2D01G343200 chr3D 89.308 159 15 2 5113 5270 76231151 76230994 1.390000e-46 198.0
22 TraesCS2D01G343200 chr3D 88.679 159 16 2 5113 5270 73853081 73853238 6.470000e-45 193.0
23 TraesCS2D01G343200 chr3D 86.290 124 13 4 3477 3600 613071481 613071362 1.430000e-26 132.0
24 TraesCS2D01G343200 chr1D 96.000 150 5 1 1707 1856 55459666 55459814 6.340000e-60 243.0
25 TraesCS2D01G343200 chr1B 95.364 151 6 1 1707 1857 619483646 619483497 8.200000e-59 239.0
26 TraesCS2D01G343200 chr1B 93.814 97 6 0 1620 1716 578780973 578780877 5.110000e-31 147.0
27 TraesCS2D01G343200 chr1B 92.157 102 8 0 1615 1716 507624402 507624301 1.840000e-30 145.0
28 TraesCS2D01G343200 chr1B 94.737 38 2 0 5984 6021 456977426 456977463 6.850000e-05 60.2
29 TraesCS2D01G343200 chr1B 81.944 72 5 4 5985 6048 602347615 602347544 3.000000e-03 54.7
30 TraesCS2D01G343200 chr5B 83.600 250 26 9 1621 1856 658979430 658979182 2.970000e-53 220.0
31 TraesCS2D01G343200 chr5B 89.542 153 16 0 5118 5270 403708732 403708580 1.800000e-45 195.0
32 TraesCS2D01G343200 chr5B 88.679 159 17 1 5112 5270 328105893 328105736 6.470000e-45 193.0
33 TraesCS2D01G343200 chr5B 91.262 103 8 1 1614 1716 373358262 373358161 8.550000e-29 139.0
34 TraesCS2D01G343200 chr5B 97.297 37 1 0 5985 6021 375576635 375576671 5.290000e-06 63.9
35 TraesCS2D01G343200 chr5B 100.000 28 0 0 6021 6048 578372298 578372271 1.100000e-02 52.8
36 TraesCS2D01G343200 chr7B 89.375 160 15 2 5113 5270 505937474 505937315 3.870000e-47 200.0
37 TraesCS2D01G343200 chr7B 97.368 38 1 0 5984 6021 435128379 435128342 1.470000e-06 65.8
38 TraesCS2D01G343200 chr7B 93.023 43 2 1 6008 6049 128344171 128344129 1.900000e-05 62.1
39 TraesCS2D01G343200 chr6B 92.199 141 11 0 5130 5270 209587529 209587389 3.870000e-47 200.0
40 TraesCS2D01G343200 chr6B 91.837 98 8 0 1619 1716 14999468 14999565 3.080000e-28 137.0
41 TraesCS2D01G343200 chr6B 100.000 38 0 0 5984 6021 485061277 485061240 3.160000e-08 71.3
42 TraesCS2D01G343200 chr6A 100.000 37 0 0 5984 6020 61420480 61420444 1.140000e-07 69.4
43 TraesCS2D01G343200 chr5D 100.000 35 0 0 5984 6018 240087185 240087219 1.470000e-06 65.8
44 TraesCS2D01G343200 chr4B 100.000 34 0 0 5985 6018 3890809 3890842 5.290000e-06 63.9


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 TraesCS2D01G343200 chr2D 439562259 439568583 6324 False 11681 11681 100.0000 1 6325 1 chr2D.!!$F2 6324
1 TraesCS2D01G343200 chr2B 517595221 517601285 6064 False 5065 7618 96.0970 1 6325 2 chr2B.!!$F2 6324
2 TraesCS2D01G343200 chr2A 549289138 549295599 6461 True 2324 6279 94.2325 1 6325 4 chr2A.!!$R1 6324
3 TraesCS2D01G343200 chr3B 40869570 40870233 663 True 743 743 87.6510 1 633 1 chr3B.!!$R1 632

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
183 185 0.542333 TCCCACCAACTGTTCGTCAA 59.458 50.000 0.00 0.00 0.00 3.18 F
1640 1947 0.038310 GGCTGTTTGGTTCTAGGCCT 59.962 55.000 11.78 11.78 35.73 5.19 F
1823 2130 0.405585 AACCATAGGTGTGGCAAGCT 59.594 50.000 0.00 0.00 43.27 3.74 F
1824 2131 0.405585 ACCATAGGTGTGGCAAGCTT 59.594 50.000 0.00 0.00 43.27 3.74 F
3312 3658 0.886490 CTGGCGAGTGAGTTTTGCCT 60.886 55.000 2.99 0.00 44.12 4.75 F
4117 4479 3.466836 CTGCTGTCCAACTGTTCAGTTA 58.533 45.455 16.23 1.62 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2154 0.036306 CGAGGTTGTAAGGGGCTGTT 59.964 55.000 0.0 0.0 0.0 3.16 R
3312 3658 0.116342 TAGGCTGAGGGTCACTTGGA 59.884 55.000 0.0 0.0 0.0 3.53 R
3641 3997 3.006537 TGCAACAGAGGTCCTACAAGTAC 59.993 47.826 0.0 0.0 0.0 2.73 R
4117 4479 7.710475 CCAGTTAAACACCAAATTCAGTTCATT 59.290 33.333 0.0 0.0 0.0 2.57 R
5003 5369 0.529833 CACACAAACACAGGTTGCCA 59.470 50.000 0.0 0.0 37.3 4.92 R
5965 6388 1.073964 CGTGTCAGTCTGCCTCATTG 58.926 55.000 0.0 0.0 0.0 2.82 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
95 97 2.902608 TCCACCATGGACTCAACTAGT 58.097 47.619 21.47 0.00 42.67 2.57
183 185 0.542333 TCCCACCAACTGTTCGTCAA 59.458 50.000 0.00 0.00 0.00 3.18
241 243 3.073062 TCAGCTAGTGCCTTCCTTCTTTT 59.927 43.478 0.00 0.00 40.80 2.27
284 286 9.075519 CATGCGTACAAATTAAGATTCAACATT 57.924 29.630 0.00 0.00 0.00 2.71
289 291 9.516314 GTACAAATTAAGATTCAACATTAGGCC 57.484 33.333 0.00 0.00 0.00 5.19
307 309 1.582968 CGCATGCCAGCAAAAGACT 59.417 52.632 13.15 0.00 0.00 3.24
314 316 1.871772 CAGCAAAAGACTGGAGCCG 59.128 57.895 0.00 0.00 0.00 5.52
315 317 1.968540 AGCAAAAGACTGGAGCCGC 60.969 57.895 0.00 0.00 0.00 6.53
316 318 1.968540 GCAAAAGACTGGAGCCGCT 60.969 57.895 0.00 0.00 0.00 5.52
350 355 0.745486 TGAAGTCGCTGATGCCATGG 60.745 55.000 7.63 7.63 35.36 3.66
567 839 5.106436 CGGTTTTGTAGATTTTAGGGTCACC 60.106 44.000 0.00 0.00 0.00 4.02
698 997 1.939980 AAGAAAGAGTAGGCGAGGGT 58.060 50.000 0.00 0.00 0.00 4.34
789 1094 2.415843 GCTACGCTGGCCATACGA 59.584 61.111 28.95 14.76 0.00 3.43
802 1107 1.760875 ATACGAGTCATGGCCGGGT 60.761 57.895 2.18 2.53 0.00 5.28
976 1283 4.995058 TCCCAGACCCCACCACCC 62.995 72.222 0.00 0.00 0.00 4.61
1317 1624 2.039613 CCTCAAGGAGTTCAAGAAGGCT 59.960 50.000 0.00 0.00 37.39 4.58
1534 1841 1.143813 AGGTATGATGCTCCCCCTTG 58.856 55.000 0.00 0.00 0.00 3.61
1619 1926 6.839033 TCGTCACAGTAGTATGACAACTTAG 58.161 40.000 9.55 0.00 44.54 2.18
1620 1927 6.028368 CGTCACAGTAGTATGACAACTTAGG 58.972 44.000 9.55 0.00 44.54 2.69
1621 1928 6.331061 GTCACAGTAGTATGACAACTTAGGG 58.669 44.000 4.05 0.00 43.89 3.53
1622 1929 5.421056 TCACAGTAGTATGACAACTTAGGGG 59.579 44.000 0.00 0.00 0.00 4.79
1623 1930 4.161754 ACAGTAGTATGACAACTTAGGGGC 59.838 45.833 0.00 0.00 0.00 5.80
1624 1931 4.406003 CAGTAGTATGACAACTTAGGGGCT 59.594 45.833 0.00 0.00 0.00 5.19
1625 1932 3.914426 AGTATGACAACTTAGGGGCTG 57.086 47.619 0.00 0.00 0.00 4.85
1626 1933 3.182152 AGTATGACAACTTAGGGGCTGT 58.818 45.455 0.00 0.00 0.00 4.40
1627 1934 3.587506 AGTATGACAACTTAGGGGCTGTT 59.412 43.478 0.00 0.00 0.00 3.16
1628 1935 3.525800 ATGACAACTTAGGGGCTGTTT 57.474 42.857 0.00 0.00 0.00 2.83
1629 1936 2.582052 TGACAACTTAGGGGCTGTTTG 58.418 47.619 0.00 0.00 0.00 2.93
1630 1937 1.886542 GACAACTTAGGGGCTGTTTGG 59.113 52.381 0.00 0.00 0.00 3.28
1631 1938 1.216930 ACAACTTAGGGGCTGTTTGGT 59.783 47.619 0.00 0.00 0.00 3.67
1632 1939 2.316108 CAACTTAGGGGCTGTTTGGTT 58.684 47.619 0.00 0.00 0.00 3.67
1633 1940 2.287977 ACTTAGGGGCTGTTTGGTTC 57.712 50.000 0.00 0.00 0.00 3.62
1634 1941 1.780919 ACTTAGGGGCTGTTTGGTTCT 59.219 47.619 0.00 0.00 0.00 3.01
1635 1942 2.983898 ACTTAGGGGCTGTTTGGTTCTA 59.016 45.455 0.00 0.00 0.00 2.10
1636 1943 3.009143 ACTTAGGGGCTGTTTGGTTCTAG 59.991 47.826 0.00 0.00 0.00 2.43
1637 1944 0.698818 AGGGGCTGTTTGGTTCTAGG 59.301 55.000 0.00 0.00 0.00 3.02
1638 1945 0.965866 GGGGCTGTTTGGTTCTAGGC 60.966 60.000 0.00 0.00 35.24 3.93
1639 1946 0.965866 GGGCTGTTTGGTTCTAGGCC 60.966 60.000 0.00 0.00 46.53 5.19
1640 1947 0.038310 GGCTGTTTGGTTCTAGGCCT 59.962 55.000 11.78 11.78 35.73 5.19
1641 1948 1.280998 GGCTGTTTGGTTCTAGGCCTA 59.719 52.381 13.09 13.09 35.73 3.93
1642 1949 2.633488 GCTGTTTGGTTCTAGGCCTAG 58.367 52.381 30.94 30.94 34.56 3.02
1643 1950 2.236395 GCTGTTTGGTTCTAGGCCTAGA 59.764 50.000 34.33 34.33 40.17 2.43
1644 1951 3.307480 GCTGTTTGGTTCTAGGCCTAGAA 60.307 47.826 39.83 39.83 46.51 2.10
1664 1971 3.207265 AGTGCCACACTTTGTCATACA 57.793 42.857 0.00 0.00 42.59 2.29
1665 1972 3.550820 AGTGCCACACTTTGTCATACAA 58.449 40.909 0.00 0.00 42.59 2.41
1666 1973 4.144297 AGTGCCACACTTTGTCATACAAT 58.856 39.130 0.00 0.00 42.59 2.71
1667 1974 5.312895 AGTGCCACACTTTGTCATACAATA 58.687 37.500 0.00 0.00 42.59 1.90
1668 1975 5.945784 AGTGCCACACTTTGTCATACAATAT 59.054 36.000 0.00 0.00 42.59 1.28
1669 1976 6.434028 AGTGCCACACTTTGTCATACAATATT 59.566 34.615 0.00 0.00 42.59 1.28
1670 1977 6.527722 GTGCCACACTTTGTCATACAATATTG 59.472 38.462 14.01 14.01 38.00 1.90
1671 1978 5.516339 GCCACACTTTGTCATACAATATTGC 59.484 40.000 15.48 0.00 38.00 3.56
1672 1979 6.035843 CCACACTTTGTCATACAATATTGCC 58.964 40.000 15.48 0.00 38.00 4.52
1673 1980 6.350027 CCACACTTTGTCATACAATATTGCCA 60.350 38.462 15.48 4.14 38.00 4.92
1674 1981 7.089538 CACACTTTGTCATACAATATTGCCAA 58.910 34.615 15.48 7.89 38.00 4.52
1675 1982 7.598118 CACACTTTGTCATACAATATTGCCAAA 59.402 33.333 15.48 13.81 38.00 3.28
1676 1983 7.598493 ACACTTTGTCATACAATATTGCCAAAC 59.402 33.333 15.48 9.46 38.00 2.93
1677 1984 7.814107 CACTTTGTCATACAATATTGCCAAACT 59.186 33.333 15.48 0.00 38.00 2.66
1678 1985 8.367156 ACTTTGTCATACAATATTGCCAAACTT 58.633 29.630 15.48 0.00 38.00 2.66
1679 1986 8.531622 TTTGTCATACAATATTGCCAAACTTG 57.468 30.769 15.48 3.56 38.00 3.16
1680 1987 7.459795 TGTCATACAATATTGCCAAACTTGA 57.540 32.000 15.48 5.62 0.00 3.02
1681 1988 7.312154 TGTCATACAATATTGCCAAACTTGAC 58.688 34.615 15.48 15.51 0.00 3.18
1682 1989 7.176515 TGTCATACAATATTGCCAAACTTGACT 59.823 33.333 15.48 0.00 32.09 3.41
1683 1990 8.673711 GTCATACAATATTGCCAAACTTGACTA 58.326 33.333 15.48 0.00 0.00 2.59
1684 1991 9.237187 TCATACAATATTGCCAAACTTGACTAA 57.763 29.630 15.48 0.00 0.00 2.24
1685 1992 9.507280 CATACAATATTGCCAAACTTGACTAAG 57.493 33.333 15.48 0.00 39.86 2.18
1686 1993 6.924111 ACAATATTGCCAAACTTGACTAAGG 58.076 36.000 15.48 0.00 38.26 2.69
1687 1994 6.493458 ACAATATTGCCAAACTTGACTAAGGT 59.507 34.615 15.48 0.00 38.26 3.50
1688 1995 7.015195 ACAATATTGCCAAACTTGACTAAGGTT 59.985 33.333 15.48 0.00 44.49 3.50
1689 1996 8.519526 CAATATTGCCAAACTTGACTAAGGTTA 58.480 33.333 1.74 0.00 41.80 2.85
1690 1997 6.575162 ATTGCCAAACTTGACTAAGGTTAG 57.425 37.500 0.00 0.00 41.80 2.34
1691 1998 5.043737 TGCCAAACTTGACTAAGGTTAGT 57.956 39.130 1.92 1.92 41.80 2.24
1692 1999 5.442391 TGCCAAACTTGACTAAGGTTAGTT 58.558 37.500 3.93 0.00 41.80 2.24
1693 2000 5.889289 TGCCAAACTTGACTAAGGTTAGTTT 59.111 36.000 3.93 0.00 41.80 2.66
1694 2001 6.378848 TGCCAAACTTGACTAAGGTTAGTTTT 59.621 34.615 3.93 0.00 41.80 2.43
1695 2002 7.093684 TGCCAAACTTGACTAAGGTTAGTTTTT 60.094 33.333 3.93 0.66 41.80 1.94
1696 2003 7.434307 GCCAAACTTGACTAAGGTTAGTTTTTC 59.566 37.037 3.93 0.00 41.80 2.29
1697 2004 8.463607 CCAAACTTGACTAAGGTTAGTTTTTCA 58.536 33.333 3.93 0.00 41.80 2.69
1698 2005 9.849166 CAAACTTGACTAAGGTTAGTTTTTCAA 57.151 29.630 3.93 3.50 41.80 2.69
1707 2014 9.399403 CTAAGGTTAGTTTTTCAAAATGAGAGC 57.601 33.333 0.00 0.00 0.00 4.09
1708 2015 6.749139 AGGTTAGTTTTTCAAAATGAGAGCC 58.251 36.000 0.00 0.00 0.00 4.70
1709 2016 6.323739 AGGTTAGTTTTTCAAAATGAGAGCCA 59.676 34.615 0.00 0.00 0.00 4.75
1710 2017 6.420903 GGTTAGTTTTTCAAAATGAGAGCCAC 59.579 38.462 0.00 0.00 0.00 5.01
1711 2018 5.596836 AGTTTTTCAAAATGAGAGCCACA 57.403 34.783 0.00 0.00 0.00 4.17
1712 2019 5.976458 AGTTTTTCAAAATGAGAGCCACAA 58.024 33.333 0.00 0.00 0.00 3.33
1713 2020 6.044682 AGTTTTTCAAAATGAGAGCCACAAG 58.955 36.000 0.00 0.00 0.00 3.16
1714 2021 5.596836 TTTTCAAAATGAGAGCCACAAGT 57.403 34.783 0.00 0.00 0.00 3.16
1715 2022 5.596836 TTTCAAAATGAGAGCCACAAGTT 57.403 34.783 0.00 0.00 0.00 2.66
1716 2023 5.596836 TTCAAAATGAGAGCCACAAGTTT 57.403 34.783 0.00 0.00 0.00 2.66
1717 2024 5.596836 TCAAAATGAGAGCCACAAGTTTT 57.403 34.783 0.00 0.00 0.00 2.43
1718 2025 5.976458 TCAAAATGAGAGCCACAAGTTTTT 58.024 33.333 0.00 0.00 0.00 1.94
1719 2026 5.811613 TCAAAATGAGAGCCACAAGTTTTTG 59.188 36.000 0.00 0.00 40.24 2.44
1733 2040 6.862209 ACAAGTTTTTGTGTGTATGTGATGT 58.138 32.000 0.00 0.00 45.54 3.06
1734 2041 6.751425 ACAAGTTTTTGTGTGTATGTGATGTG 59.249 34.615 0.00 0.00 45.54 3.21
1735 2042 5.830912 AGTTTTTGTGTGTATGTGATGTGG 58.169 37.500 0.00 0.00 0.00 4.17
1736 2043 4.844998 TTTTGTGTGTATGTGATGTGGG 57.155 40.909 0.00 0.00 0.00 4.61
1737 2044 3.778954 TTGTGTGTATGTGATGTGGGA 57.221 42.857 0.00 0.00 0.00 4.37
1738 2045 3.052455 TGTGTGTATGTGATGTGGGAC 57.948 47.619 0.00 0.00 0.00 4.46
1739 2046 2.290008 TGTGTGTATGTGATGTGGGACC 60.290 50.000 0.00 0.00 0.00 4.46
1740 2047 1.981495 TGTGTATGTGATGTGGGACCA 59.019 47.619 0.00 0.00 0.00 4.02
1741 2048 2.575735 TGTGTATGTGATGTGGGACCAT 59.424 45.455 0.00 0.00 0.00 3.55
1742 2049 3.777522 TGTGTATGTGATGTGGGACCATA 59.222 43.478 0.00 0.00 0.00 2.74
1743 2050 4.141733 TGTGTATGTGATGTGGGACCATAG 60.142 45.833 0.00 0.00 0.00 2.23
1744 2051 4.037222 TGTATGTGATGTGGGACCATAGT 58.963 43.478 0.00 0.00 0.00 2.12
1745 2052 3.565764 ATGTGATGTGGGACCATAGTG 57.434 47.619 0.00 0.00 0.00 2.74
1746 2053 2.265367 TGTGATGTGGGACCATAGTGT 58.735 47.619 0.00 0.00 0.00 3.55
1747 2054 2.027285 TGTGATGTGGGACCATAGTGTG 60.027 50.000 0.00 0.00 0.00 3.82
1757 2064 2.418368 CCATAGTGTGGCTTGCCTAA 57.582 50.000 13.18 0.00 42.12 2.69
1758 2065 2.292267 CCATAGTGTGGCTTGCCTAAG 58.708 52.381 13.18 0.00 42.12 2.18
1759 2066 2.092968 CCATAGTGTGGCTTGCCTAAGA 60.093 50.000 13.18 0.00 42.12 2.10
1760 2067 3.434167 CCATAGTGTGGCTTGCCTAAGAT 60.434 47.826 13.18 0.00 42.12 2.40
1761 2068 2.119801 AGTGTGGCTTGCCTAAGATG 57.880 50.000 13.18 0.00 35.92 2.90
1762 2069 1.352352 AGTGTGGCTTGCCTAAGATGT 59.648 47.619 13.18 0.00 35.92 3.06
1763 2070 1.470098 GTGTGGCTTGCCTAAGATGTG 59.530 52.381 13.18 0.00 35.92 3.21
1764 2071 1.098050 GTGGCTTGCCTAAGATGTGG 58.902 55.000 13.18 0.00 35.92 4.17
1772 2079 1.745653 GCCTAAGATGTGGCTTGAACC 59.254 52.381 0.00 0.00 45.26 3.62
1773 2080 2.879756 GCCTAAGATGTGGCTTGAACCA 60.880 50.000 0.00 0.00 45.26 3.67
1774 2081 3.420893 CCTAAGATGTGGCTTGAACCAA 58.579 45.455 0.00 0.00 42.70 3.67
1775 2082 3.826157 CCTAAGATGTGGCTTGAACCAAA 59.174 43.478 0.00 0.00 42.70 3.28
1776 2083 3.733443 AAGATGTGGCTTGAACCAAAC 57.267 42.857 0.00 0.00 42.70 2.93
1777 2084 2.665165 AGATGTGGCTTGAACCAAACA 58.335 42.857 0.00 0.00 42.70 2.83
1778 2085 2.362077 AGATGTGGCTTGAACCAAACAC 59.638 45.455 0.00 0.00 42.70 3.32
1779 2086 1.550327 TGTGGCTTGAACCAAACACA 58.450 45.000 10.68 10.68 42.70 3.72
1780 2087 1.203523 TGTGGCTTGAACCAAACACAC 59.796 47.619 10.68 0.00 42.70 3.82
1781 2088 0.453793 TGGCTTGAACCAAACACACG 59.546 50.000 0.00 0.00 36.55 4.49
1782 2089 0.869880 GGCTTGAACCAAACACACGC 60.870 55.000 0.00 0.00 0.00 5.34
1783 2090 0.869880 GCTTGAACCAAACACACGCC 60.870 55.000 0.00 0.00 0.00 5.68
1784 2091 0.738389 CTTGAACCAAACACACGCCT 59.262 50.000 0.00 0.00 0.00 5.52
1785 2092 1.944024 CTTGAACCAAACACACGCCTA 59.056 47.619 0.00 0.00 0.00 3.93
1786 2093 2.039818 TGAACCAAACACACGCCTAA 57.960 45.000 0.00 0.00 0.00 2.69
1787 2094 1.944024 TGAACCAAACACACGCCTAAG 59.056 47.619 0.00 0.00 0.00 2.18
1788 2095 1.944709 GAACCAAACACACGCCTAAGT 59.055 47.619 0.00 0.00 0.00 2.24
1789 2096 2.047002 ACCAAACACACGCCTAAGTT 57.953 45.000 0.00 0.00 0.00 2.66
1790 2097 1.673920 ACCAAACACACGCCTAAGTTG 59.326 47.619 0.00 0.00 0.00 3.16
1791 2098 1.001815 CCAAACACACGCCTAAGTTGG 60.002 52.381 0.00 0.00 0.00 3.77
1792 2099 1.673920 CAAACACACGCCTAAGTTGGT 59.326 47.619 0.00 0.00 0.00 3.67
1793 2100 1.589803 AACACACGCCTAAGTTGGTC 58.410 50.000 0.00 0.00 0.00 4.02
1794 2101 0.466543 ACACACGCCTAAGTTGGTCA 59.533 50.000 0.00 0.00 0.00 4.02
1795 2102 1.134340 ACACACGCCTAAGTTGGTCAA 60.134 47.619 0.00 0.00 0.00 3.18
1796 2103 1.944024 CACACGCCTAAGTTGGTCAAA 59.056 47.619 0.00 0.00 0.00 2.69
1797 2104 1.944709 ACACGCCTAAGTTGGTCAAAC 59.055 47.619 0.00 0.00 39.24 2.93
1807 2114 3.364889 GTTGGTCAAACTTGCCTAACC 57.635 47.619 5.07 0.00 35.75 2.85
1808 2115 2.691011 GTTGGTCAAACTTGCCTAACCA 59.309 45.455 0.00 0.00 35.75 3.67
1809 2116 3.237268 TGGTCAAACTTGCCTAACCAT 57.763 42.857 0.00 0.00 32.08 3.55
1810 2117 4.374689 TGGTCAAACTTGCCTAACCATA 57.625 40.909 0.00 0.00 32.08 2.74
1811 2118 4.331968 TGGTCAAACTTGCCTAACCATAG 58.668 43.478 0.00 0.00 32.08 2.23
1812 2119 8.232087 GTTGGTCAAACTTGCCTAACCATAGG 62.232 46.154 2.59 0.00 42.34 2.57
1820 2127 2.799126 CCTAACCATAGGTGTGGCAA 57.201 50.000 0.00 0.00 43.32 4.52
1821 2128 2.643551 CCTAACCATAGGTGTGGCAAG 58.356 52.381 0.00 0.00 43.32 4.01
1822 2129 2.017049 CTAACCATAGGTGTGGCAAGC 58.983 52.381 0.00 0.00 43.27 4.01
1823 2130 0.405585 AACCATAGGTGTGGCAAGCT 59.594 50.000 0.00 0.00 43.27 3.74
1824 2131 0.405585 ACCATAGGTGTGGCAAGCTT 59.594 50.000 0.00 0.00 43.27 3.74
1825 2132 1.203050 ACCATAGGTGTGGCAAGCTTT 60.203 47.619 0.00 0.00 43.27 3.51
1826 2133 1.203052 CCATAGGTGTGGCAAGCTTTG 59.797 52.381 0.00 8.64 31.43 2.77
1827 2134 1.203052 CATAGGTGTGGCAAGCTTTGG 59.797 52.381 0.00 0.00 0.00 3.28
1837 2144 3.097877 GCAAGCTTTGGCAAACTTAGT 57.902 42.857 19.88 4.41 41.70 2.24
1838 2145 3.457234 GCAAGCTTTGGCAAACTTAGTT 58.543 40.909 19.88 4.37 41.70 2.24
1839 2146 3.871006 GCAAGCTTTGGCAAACTTAGTTT 59.129 39.130 19.88 4.30 41.70 2.66
1840 2147 4.025730 GCAAGCTTTGGCAAACTTAGTTTC 60.026 41.667 19.88 3.48 41.70 2.78
1841 2148 5.108517 CAAGCTTTGGCAAACTTAGTTTCA 58.891 37.500 19.88 1.35 41.70 2.69
1842 2149 5.337578 AGCTTTGGCAAACTTAGTTTCAA 57.662 34.783 8.93 7.52 41.70 2.69
1843 2150 5.729510 AGCTTTGGCAAACTTAGTTTCAAA 58.270 33.333 17.65 17.65 41.70 2.69
1844 2151 5.580691 AGCTTTGGCAAACTTAGTTTCAAAC 59.419 36.000 15.86 13.48 41.70 2.93
1845 2152 5.220586 GCTTTGGCAAACTTAGTTTCAAACC 60.221 40.000 15.86 12.04 33.10 3.27
1846 2153 5.407407 TTGGCAAACTTAGTTTCAAACCA 57.593 34.783 7.45 10.15 33.10 3.67
1847 2154 5.407407 TGGCAAACTTAGTTTCAAACCAA 57.593 34.783 7.45 0.00 33.10 3.67
1848 2155 5.794894 TGGCAAACTTAGTTTCAAACCAAA 58.205 33.333 7.45 0.00 33.10 3.28
1849 2156 5.639931 TGGCAAACTTAGTTTCAAACCAAAC 59.360 36.000 7.45 0.00 33.10 2.93
1850 2157 5.639931 GGCAAACTTAGTTTCAAACCAAACA 59.360 36.000 7.45 0.00 38.53 2.83
1851 2158 6.183360 GGCAAACTTAGTTTCAAACCAAACAG 60.183 38.462 7.45 0.00 38.53 3.16
1852 2159 6.672118 GCAAACTTAGTTTCAAACCAAACAGC 60.672 38.462 7.45 0.47 38.53 4.40
1853 2160 5.006153 ACTTAGTTTCAAACCAAACAGCC 57.994 39.130 0.00 0.00 38.53 4.85
1854 2161 2.979814 AGTTTCAAACCAAACAGCCC 57.020 45.000 0.00 0.00 38.53 5.19
1855 2162 1.484653 AGTTTCAAACCAAACAGCCCC 59.515 47.619 0.00 0.00 38.53 5.80
1856 2163 1.484653 GTTTCAAACCAAACAGCCCCT 59.515 47.619 0.00 0.00 36.44 4.79
1857 2164 1.872773 TTCAAACCAAACAGCCCCTT 58.127 45.000 0.00 0.00 0.00 3.95
1858 2165 2.757894 TCAAACCAAACAGCCCCTTA 57.242 45.000 0.00 0.00 0.00 2.69
1880 2187 4.710324 ACAACCTCGAGTTTTGACCATAA 58.290 39.130 23.75 0.00 36.18 1.90
1887 2194 7.176690 ACCTCGAGTTTTGACCATAAATCAATT 59.823 33.333 12.31 0.00 36.02 2.32
1889 2196 6.806249 TCGAGTTTTGACCATAAATCAATTGC 59.194 34.615 0.00 0.00 36.02 3.56
2115 2423 2.111043 AGCTCGGGGTTGTGTGTG 59.889 61.111 0.00 0.00 0.00 3.82
3289 3635 7.463961 TTGTAACTGGAAAAGGTGTTGTAAA 57.536 32.000 0.00 0.00 0.00 2.01
3301 3647 1.165270 GTTGTAAATGCCTGGCGAGT 58.835 50.000 14.98 3.55 0.00 4.18
3312 3658 0.886490 CTGGCGAGTGAGTTTTGCCT 60.886 55.000 2.99 0.00 44.12 4.75
3894 4251 4.536090 TGAAGACAAGGGATTAGTGGTGAT 59.464 41.667 0.00 0.00 0.00 3.06
4117 4479 3.466836 CTGCTGTCCAACTGTTCAGTTA 58.533 45.455 16.23 1.62 0.00 2.24
4190 4552 7.554118 TGTGAATATCCTGCTCCTTTAAGAAAG 59.446 37.037 0.00 0.00 38.24 2.62
5003 5369 4.714802 GGCCCCACTAAAATGAACCTATTT 59.285 41.667 0.00 0.00 31.87 1.40
5020 5387 2.376808 TTTGGCAACCTGTGTTTGTG 57.623 45.000 0.00 0.00 30.42 3.33
5223 5590 8.574737 AGACTAAAACGTGTCTATATACATCCC 58.425 37.037 4.58 0.00 41.19 3.85
5561 5929 3.739167 TTTGTCCGACAAAGGGCG 58.261 55.556 20.42 0.00 42.55 6.13
5646 6036 0.460109 GCCCATGTTTTGGCCGAATC 60.460 55.000 6.16 6.54 44.97 2.52
5758 6150 3.746492 GTGAACATAGTTCGAAGCCAGTT 59.254 43.478 0.00 1.68 0.00 3.16
5882 6277 4.041198 TCTGTAAGGTTTCCCGAGTTTCAT 59.959 41.667 0.00 0.00 35.12 2.57
5965 6388 5.117592 GCTTCATGCTGTTGTTTACATGTTC 59.882 40.000 2.30 0.00 40.57 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 88 2.344950 CCTCAGCAGCAACTAGTTGAG 58.655 52.381 34.43 25.83 42.93 3.02
90 92 0.689623 AAGCCTCAGCAGCAACTAGT 59.310 50.000 0.00 0.00 43.56 2.57
93 95 0.888285 GACAAGCCTCAGCAGCAACT 60.888 55.000 0.00 0.00 43.56 3.16
95 97 1.601759 GGACAAGCCTCAGCAGCAA 60.602 57.895 0.00 0.00 43.56 3.91
134 136 3.474570 GGGCCTCTCGCTCACCAT 61.475 66.667 0.84 0.00 38.16 3.55
183 185 6.820656 AGCAGATTGAATCGAACTATCAAAGT 59.179 34.615 15.11 1.86 41.49 2.66
241 243 5.250200 ACGCATGGTAGAAAATTTAGGACA 58.750 37.500 0.00 0.00 0.00 4.02
289 291 0.731514 CAGTCTTTTGCTGGCATGCG 60.732 55.000 12.44 0.00 35.36 4.73
298 300 1.968540 AGCGGCTCCAGTCTTTTGC 60.969 57.895 0.00 0.00 0.00 3.68
443 455 4.758165 CACTTTTCTTTTACCCTTCGGCTA 59.242 41.667 0.00 0.00 0.00 3.93
567 839 0.178068 CGGACACATAACCCCCTGAG 59.822 60.000 0.00 0.00 0.00 3.35
698 997 4.688770 GGTCCAAACCCACAACCA 57.311 55.556 0.00 0.00 39.93 3.67
1534 1841 4.857645 CAAGGCTGTCTTAGTCAGAAGGAC 60.858 50.000 10.44 0.00 39.16 3.85
1619 1926 0.965866 GCCTAGAACCAAACAGCCCC 60.966 60.000 0.00 0.00 0.00 5.80
1620 1927 0.965866 GGCCTAGAACCAAACAGCCC 60.966 60.000 0.00 0.00 32.68 5.19
1621 1928 0.038310 AGGCCTAGAACCAAACAGCC 59.962 55.000 1.29 0.00 39.25 4.85
1622 1929 2.236395 TCTAGGCCTAGAACCAAACAGC 59.764 50.000 35.52 0.00 39.08 4.40
1623 1930 4.020128 ACTTCTAGGCCTAGAACCAAACAG 60.020 45.833 39.83 31.67 44.58 3.16
1624 1931 3.908103 ACTTCTAGGCCTAGAACCAAACA 59.092 43.478 39.83 24.33 44.58 2.83
1625 1932 4.254492 CACTTCTAGGCCTAGAACCAAAC 58.746 47.826 39.83 0.00 44.58 2.93
1626 1933 3.307480 GCACTTCTAGGCCTAGAACCAAA 60.307 47.826 39.83 25.58 44.58 3.28
1627 1934 2.236395 GCACTTCTAGGCCTAGAACCAA 59.764 50.000 39.83 25.90 44.58 3.67
1628 1935 1.831736 GCACTTCTAGGCCTAGAACCA 59.168 52.381 39.83 26.22 44.58 3.67
1629 1936 1.139256 GGCACTTCTAGGCCTAGAACC 59.861 57.143 39.83 34.73 44.58 3.62
1630 1937 2.605837 GGCACTTCTAGGCCTAGAAC 57.394 55.000 39.83 31.40 44.58 3.01
1636 1943 1.679898 AGTGTGGCACTTCTAGGCC 59.320 57.895 19.83 0.00 42.59 5.19
1647 1954 5.516339 GCAATATTGTATGACAAAGTGTGGC 59.484 40.000 16.61 0.00 41.96 5.01
1648 1955 6.035843 GGCAATATTGTATGACAAAGTGTGG 58.964 40.000 16.61 0.00 41.96 4.17
1649 1956 6.619744 TGGCAATATTGTATGACAAAGTGTG 58.380 36.000 16.61 0.00 41.96 3.82
1650 1957 6.832520 TGGCAATATTGTATGACAAAGTGT 57.167 33.333 16.61 0.00 41.96 3.55
1655 1962 7.812191 GTCAAGTTTGGCAATATTGTATGACAA 59.188 33.333 16.61 3.33 42.61 3.18
1656 1963 7.176515 AGTCAAGTTTGGCAATATTGTATGACA 59.823 33.333 16.61 0.00 35.85 3.58
1657 1964 7.538575 AGTCAAGTTTGGCAATATTGTATGAC 58.461 34.615 16.61 16.84 34.61 3.06
1658 1965 7.701539 AGTCAAGTTTGGCAATATTGTATGA 57.298 32.000 16.61 8.10 34.61 2.15
1659 1966 9.507280 CTTAGTCAAGTTTGGCAATATTGTATG 57.493 33.333 16.61 6.21 34.61 2.39
1660 1967 8.686334 CCTTAGTCAAGTTTGGCAATATTGTAT 58.314 33.333 16.61 13.20 34.61 2.29
1661 1968 7.668052 ACCTTAGTCAAGTTTGGCAATATTGTA 59.332 33.333 16.61 4.10 34.61 2.41
1662 1969 6.493458 ACCTTAGTCAAGTTTGGCAATATTGT 59.507 34.615 16.61 8.26 34.61 2.71
1663 1970 6.924111 ACCTTAGTCAAGTTTGGCAATATTG 58.076 36.000 11.27 11.27 34.61 1.90
1664 1971 7.539034 AACCTTAGTCAAGTTTGGCAATATT 57.461 32.000 0.00 0.00 34.61 1.28
1665 1972 7.888546 ACTAACCTTAGTCAAGTTTGGCAATAT 59.111 33.333 0.00 0.00 39.72 1.28
1666 1973 7.228590 ACTAACCTTAGTCAAGTTTGGCAATA 58.771 34.615 0.00 0.00 39.72 1.90
1667 1974 6.068670 ACTAACCTTAGTCAAGTTTGGCAAT 58.931 36.000 0.00 0.00 39.72 3.56
1668 1975 5.442391 ACTAACCTTAGTCAAGTTTGGCAA 58.558 37.500 0.00 0.00 39.72 4.52
1669 1976 5.043737 ACTAACCTTAGTCAAGTTTGGCA 57.956 39.130 0.00 0.00 39.72 4.92
1670 1977 6.387041 AAACTAACCTTAGTCAAGTTTGGC 57.613 37.500 0.00 0.00 42.86 4.52
1671 1978 8.463607 TGAAAAACTAACCTTAGTCAAGTTTGG 58.536 33.333 0.00 0.00 42.86 3.28
1672 1979 9.849166 TTGAAAAACTAACCTTAGTCAAGTTTG 57.151 29.630 0.00 0.00 42.86 2.93
1681 1988 9.399403 GCTCTCATTTTGAAAAACTAACCTTAG 57.601 33.333 0.00 0.00 36.82 2.18
1682 1989 8.357402 GGCTCTCATTTTGAAAAACTAACCTTA 58.643 33.333 0.00 0.00 0.00 2.69
1683 1990 7.147742 TGGCTCTCATTTTGAAAAACTAACCTT 60.148 33.333 0.00 0.00 0.00 3.50
1684 1991 6.323739 TGGCTCTCATTTTGAAAAACTAACCT 59.676 34.615 0.00 0.00 0.00 3.50
1685 1992 6.420903 GTGGCTCTCATTTTGAAAAACTAACC 59.579 38.462 0.00 0.00 0.00 2.85
1686 1993 6.978080 TGTGGCTCTCATTTTGAAAAACTAAC 59.022 34.615 0.00 0.00 0.00 2.34
1687 1994 7.106439 TGTGGCTCTCATTTTGAAAAACTAA 57.894 32.000 0.00 0.00 0.00 2.24
1688 1995 6.707440 TGTGGCTCTCATTTTGAAAAACTA 57.293 33.333 0.00 0.00 0.00 2.24
1689 1996 5.596836 TGTGGCTCTCATTTTGAAAAACT 57.403 34.783 0.00 0.00 0.00 2.66
1690 1997 5.812127 ACTTGTGGCTCTCATTTTGAAAAAC 59.188 36.000 0.00 0.00 0.00 2.43
1691 1998 5.976458 ACTTGTGGCTCTCATTTTGAAAAA 58.024 33.333 0.00 0.00 0.00 1.94
1692 1999 5.596836 ACTTGTGGCTCTCATTTTGAAAA 57.403 34.783 0.00 0.00 0.00 2.29
1693 2000 5.596836 AACTTGTGGCTCTCATTTTGAAA 57.403 34.783 0.00 0.00 0.00 2.69
1694 2001 5.596836 AAACTTGTGGCTCTCATTTTGAA 57.403 34.783 0.00 0.00 0.00 2.69
1695 2002 5.596836 AAAACTTGTGGCTCTCATTTTGA 57.403 34.783 0.00 0.00 0.00 2.69
1696 2003 5.581874 ACAAAAACTTGTGGCTCTCATTTTG 59.418 36.000 0.00 0.00 40.49 2.44
1697 2004 5.581874 CACAAAAACTTGTGGCTCTCATTTT 59.418 36.000 9.62 0.00 46.26 1.82
1698 2005 5.111293 CACAAAAACTTGTGGCTCTCATTT 58.889 37.500 9.62 0.00 46.26 2.32
1699 2006 4.685924 CACAAAAACTTGTGGCTCTCATT 58.314 39.130 9.62 0.00 46.26 2.57
1700 2007 4.311816 CACAAAAACTTGTGGCTCTCAT 57.688 40.909 9.62 0.00 46.26 2.90
1701 2008 3.781079 CACAAAAACTTGTGGCTCTCA 57.219 42.857 9.62 0.00 46.26 3.27
1709 2016 6.751425 CACATCACATACACACAAAAACTTGT 59.249 34.615 0.00 0.00 35.14 3.16
1710 2017 6.198778 CCACATCACATACACACAAAAACTTG 59.801 38.462 0.00 0.00 0.00 3.16
1711 2018 6.272318 CCACATCACATACACACAAAAACTT 58.728 36.000 0.00 0.00 0.00 2.66
1712 2019 5.221224 CCCACATCACATACACACAAAAACT 60.221 40.000 0.00 0.00 0.00 2.66
1713 2020 4.981674 CCCACATCACATACACACAAAAAC 59.018 41.667 0.00 0.00 0.00 2.43
1714 2021 4.889995 TCCCACATCACATACACACAAAAA 59.110 37.500 0.00 0.00 0.00 1.94
1715 2022 4.277174 GTCCCACATCACATACACACAAAA 59.723 41.667 0.00 0.00 0.00 2.44
1716 2023 3.818210 GTCCCACATCACATACACACAAA 59.182 43.478 0.00 0.00 0.00 2.83
1717 2024 3.407698 GTCCCACATCACATACACACAA 58.592 45.455 0.00 0.00 0.00 3.33
1718 2025 2.290008 GGTCCCACATCACATACACACA 60.290 50.000 0.00 0.00 0.00 3.72
1719 2026 2.290008 TGGTCCCACATCACATACACAC 60.290 50.000 0.00 0.00 0.00 3.82
1720 2027 1.981495 TGGTCCCACATCACATACACA 59.019 47.619 0.00 0.00 0.00 3.72
1721 2028 2.779755 TGGTCCCACATCACATACAC 57.220 50.000 0.00 0.00 0.00 2.90
1722 2029 4.037222 ACTATGGTCCCACATCACATACA 58.963 43.478 0.00 0.00 32.39 2.29
1723 2030 4.141711 ACACTATGGTCCCACATCACATAC 60.142 45.833 0.00 0.00 32.39 2.39
1724 2031 4.037222 ACACTATGGTCCCACATCACATA 58.963 43.478 0.00 0.00 32.39 2.29
1725 2032 2.846206 ACACTATGGTCCCACATCACAT 59.154 45.455 0.00 0.00 32.39 3.21
1726 2033 2.027285 CACACTATGGTCCCACATCACA 60.027 50.000 0.00 0.00 32.39 3.58
1727 2034 2.632377 CACACTATGGTCCCACATCAC 58.368 52.381 0.00 0.00 32.39 3.06
1728 2035 1.559219 CCACACTATGGTCCCACATCA 59.441 52.381 0.00 0.00 44.46 3.07
1729 2036 2.332063 CCACACTATGGTCCCACATC 57.668 55.000 0.00 0.00 44.46 3.06
1739 2046 3.266510 TCTTAGGCAAGCCACACTATG 57.733 47.619 14.40 0.00 38.92 2.23
1740 2047 3.200825 ACATCTTAGGCAAGCCACACTAT 59.799 43.478 14.40 0.00 38.92 2.12
1741 2048 2.571653 ACATCTTAGGCAAGCCACACTA 59.428 45.455 14.40 0.00 38.92 2.74
1742 2049 1.352352 ACATCTTAGGCAAGCCACACT 59.648 47.619 14.40 0.00 38.92 3.55
1743 2050 1.470098 CACATCTTAGGCAAGCCACAC 59.530 52.381 14.40 0.00 38.92 3.82
1744 2051 1.614051 CCACATCTTAGGCAAGCCACA 60.614 52.381 14.40 0.00 38.92 4.17
1745 2052 1.098050 CCACATCTTAGGCAAGCCAC 58.902 55.000 14.40 0.00 38.92 5.01
1746 2053 3.575506 CCACATCTTAGGCAAGCCA 57.424 52.632 14.40 0.00 38.92 4.75
1753 2060 3.071874 TGGTTCAAGCCACATCTTAGG 57.928 47.619 0.00 0.00 32.81 2.69
1754 2061 4.278170 TGTTTGGTTCAAGCCACATCTTAG 59.722 41.667 0.00 0.00 38.42 2.18
1755 2062 4.037446 GTGTTTGGTTCAAGCCACATCTTA 59.963 41.667 0.00 0.00 38.42 2.10
1756 2063 3.030291 TGTTTGGTTCAAGCCACATCTT 58.970 40.909 0.00 0.00 38.42 2.40
1757 2064 2.362077 GTGTTTGGTTCAAGCCACATCT 59.638 45.455 0.00 0.00 38.42 2.90
1758 2065 2.100584 TGTGTTTGGTTCAAGCCACATC 59.899 45.455 9.54 0.00 38.42 3.06
1759 2066 2.106566 TGTGTTTGGTTCAAGCCACAT 58.893 42.857 9.54 0.00 38.42 3.21
1760 2067 1.203523 GTGTGTTTGGTTCAAGCCACA 59.796 47.619 9.54 9.54 38.42 4.17
1761 2068 1.797348 CGTGTGTTTGGTTCAAGCCAC 60.797 52.381 0.00 0.00 38.42 5.01
1762 2069 0.453793 CGTGTGTTTGGTTCAAGCCA 59.546 50.000 0.00 0.00 36.62 4.75
1763 2070 0.869880 GCGTGTGTTTGGTTCAAGCC 60.870 55.000 0.00 0.00 32.34 4.35
1764 2071 0.869880 GGCGTGTGTTTGGTTCAAGC 60.870 55.000 0.00 0.00 36.26 4.01
1765 2072 0.738389 AGGCGTGTGTTTGGTTCAAG 59.262 50.000 0.00 0.00 0.00 3.02
1766 2073 2.039818 TAGGCGTGTGTTTGGTTCAA 57.960 45.000 0.00 0.00 0.00 2.69
1767 2074 1.944024 CTTAGGCGTGTGTTTGGTTCA 59.056 47.619 0.00 0.00 0.00 3.18
1768 2075 1.944709 ACTTAGGCGTGTGTTTGGTTC 59.055 47.619 0.00 0.00 0.00 3.62
1769 2076 2.047002 ACTTAGGCGTGTGTTTGGTT 57.953 45.000 0.00 0.00 0.00 3.67
1770 2077 1.673920 CAACTTAGGCGTGTGTTTGGT 59.326 47.619 0.00 0.00 0.00 3.67
1771 2078 1.001815 CCAACTTAGGCGTGTGTTTGG 60.002 52.381 0.00 0.00 0.00 3.28
1772 2079 1.673920 ACCAACTTAGGCGTGTGTTTG 59.326 47.619 0.00 0.00 0.00 2.93
1773 2080 1.944709 GACCAACTTAGGCGTGTGTTT 59.055 47.619 0.00 0.00 0.00 2.83
1774 2081 1.134340 TGACCAACTTAGGCGTGTGTT 60.134 47.619 0.00 0.00 0.00 3.32
1775 2082 0.466543 TGACCAACTTAGGCGTGTGT 59.533 50.000 0.00 0.00 0.00 3.72
1776 2083 1.588674 TTGACCAACTTAGGCGTGTG 58.411 50.000 0.00 0.00 0.00 3.82
1777 2084 1.944709 GTTTGACCAACTTAGGCGTGT 59.055 47.619 0.00 0.00 31.92 4.49
1778 2085 2.218603 AGTTTGACCAACTTAGGCGTG 58.781 47.619 0.00 0.00 43.89 5.34
1779 2086 2.632987 AGTTTGACCAACTTAGGCGT 57.367 45.000 0.00 0.00 43.89 5.68
1787 2094 2.691011 TGGTTAGGCAAGTTTGACCAAC 59.309 45.455 1.06 1.06 36.67 3.77
1788 2095 3.019799 TGGTTAGGCAAGTTTGACCAA 57.980 42.857 0.00 0.00 36.67 3.67
1789 2096 2.738587 TGGTTAGGCAAGTTTGACCA 57.261 45.000 0.00 0.00 36.67 4.02
1790 2097 3.694566 CCTATGGTTAGGCAAGTTTGACC 59.305 47.826 0.00 0.00 38.75 4.02
1791 2098 4.965119 CCTATGGTTAGGCAAGTTTGAC 57.035 45.455 0.00 0.00 38.75 3.18
1802 2109 2.017049 GCTTGCCACACCTATGGTTAG 58.983 52.381 0.00 0.00 42.28 2.34
1803 2110 1.633432 AGCTTGCCACACCTATGGTTA 59.367 47.619 0.00 0.00 42.28 2.85
1804 2111 0.405585 AGCTTGCCACACCTATGGTT 59.594 50.000 0.00 0.00 42.28 3.67
1805 2112 0.405585 AAGCTTGCCACACCTATGGT 59.594 50.000 0.00 0.00 42.28 3.55
1806 2113 1.203052 CAAAGCTTGCCACACCTATGG 59.797 52.381 0.00 0.00 43.26 2.74
1807 2114 1.203052 CCAAAGCTTGCCACACCTATG 59.797 52.381 0.00 0.00 0.00 2.23
1808 2115 1.549203 CCAAAGCTTGCCACACCTAT 58.451 50.000 0.00 0.00 0.00 2.57
1809 2116 1.178534 GCCAAAGCTTGCCACACCTA 61.179 55.000 0.00 0.00 35.50 3.08
1810 2117 2.501602 GCCAAAGCTTGCCACACCT 61.502 57.895 0.00 0.00 35.50 4.00
1811 2118 2.029518 GCCAAAGCTTGCCACACC 59.970 61.111 0.00 0.00 35.50 4.16
1812 2119 0.461693 TTTGCCAAAGCTTGCCACAC 60.462 50.000 0.00 0.00 40.80 3.82
1813 2120 0.461693 GTTTGCCAAAGCTTGCCACA 60.462 50.000 0.00 0.00 40.80 4.17
1814 2121 0.179076 AGTTTGCCAAAGCTTGCCAC 60.179 50.000 0.00 0.00 40.80 5.01
1815 2122 0.540923 AAGTTTGCCAAAGCTTGCCA 59.459 45.000 0.00 0.00 35.72 4.92
1816 2123 2.224042 ACTAAGTTTGCCAAAGCTTGCC 60.224 45.455 0.00 0.00 37.41 4.52
1817 2124 3.097877 ACTAAGTTTGCCAAAGCTTGC 57.902 42.857 0.00 0.00 37.41 4.01
1818 2125 5.108517 TGAAACTAAGTTTGCCAAAGCTTG 58.891 37.500 0.00 0.00 37.41 4.01
1819 2126 5.337578 TGAAACTAAGTTTGCCAAAGCTT 57.662 34.783 0.00 0.00 39.76 3.74
1820 2127 5.337578 TTGAAACTAAGTTTGCCAAAGCT 57.662 34.783 0.00 0.00 40.80 3.74
1821 2128 5.220586 GGTTTGAAACTAAGTTTGCCAAAGC 60.221 40.000 8.09 2.18 38.81 3.51
1822 2129 5.872070 TGGTTTGAAACTAAGTTTGCCAAAG 59.128 36.000 8.09 0.00 35.77 2.77
1823 2130 5.794894 TGGTTTGAAACTAAGTTTGCCAAA 58.205 33.333 8.09 0.00 35.77 3.28
1824 2131 5.407407 TGGTTTGAAACTAAGTTTGCCAA 57.593 34.783 8.09 0.00 35.77 4.52
1825 2132 5.407407 TTGGTTTGAAACTAAGTTTGCCA 57.593 34.783 8.09 0.00 35.77 4.92
1826 2133 5.639931 TGTTTGGTTTGAAACTAAGTTTGCC 59.360 36.000 8.09 0.00 35.77 4.52
1827 2134 6.672118 GCTGTTTGGTTTGAAACTAAGTTTGC 60.672 38.462 8.09 7.62 35.77 3.68
1828 2135 6.183360 GGCTGTTTGGTTTGAAACTAAGTTTG 60.183 38.462 8.09 2.09 35.77 2.93
1829 2136 5.872617 GGCTGTTTGGTTTGAAACTAAGTTT 59.127 36.000 8.09 0.00 38.54 2.66
1830 2137 5.416083 GGCTGTTTGGTTTGAAACTAAGTT 58.584 37.500 8.09 0.00 36.86 2.66
1831 2138 4.142026 GGGCTGTTTGGTTTGAAACTAAGT 60.142 41.667 8.09 0.00 36.86 2.24
1832 2139 4.368315 GGGCTGTTTGGTTTGAAACTAAG 58.632 43.478 8.09 0.00 36.86 2.18
1833 2140 3.133183 GGGGCTGTTTGGTTTGAAACTAA 59.867 43.478 8.09 5.33 36.86 2.24
1834 2141 2.696187 GGGGCTGTTTGGTTTGAAACTA 59.304 45.455 8.09 0.00 36.86 2.24
1835 2142 1.484653 GGGGCTGTTTGGTTTGAAACT 59.515 47.619 8.09 0.00 36.86 2.66
1836 2143 1.484653 AGGGGCTGTTTGGTTTGAAAC 59.515 47.619 0.00 0.00 36.53 2.78
1837 2144 1.872773 AGGGGCTGTTTGGTTTGAAA 58.127 45.000 0.00 0.00 0.00 2.69
1838 2145 1.872773 AAGGGGCTGTTTGGTTTGAA 58.127 45.000 0.00 0.00 0.00 2.69
1839 2146 2.312390 GTAAGGGGCTGTTTGGTTTGA 58.688 47.619 0.00 0.00 0.00 2.69
1840 2147 2.035632 TGTAAGGGGCTGTTTGGTTTG 58.964 47.619 0.00 0.00 0.00 2.93
1841 2148 2.432874 GTTGTAAGGGGCTGTTTGGTTT 59.567 45.455 0.00 0.00 0.00 3.27
1842 2149 2.036387 GTTGTAAGGGGCTGTTTGGTT 58.964 47.619 0.00 0.00 0.00 3.67
1843 2150 1.699730 GTTGTAAGGGGCTGTTTGGT 58.300 50.000 0.00 0.00 0.00 3.67
1844 2151 0.966179 GGTTGTAAGGGGCTGTTTGG 59.034 55.000 0.00 0.00 0.00 3.28
1845 2152 1.886542 GAGGTTGTAAGGGGCTGTTTG 59.113 52.381 0.00 0.00 0.00 2.93
1846 2153 1.544759 CGAGGTTGTAAGGGGCTGTTT 60.545 52.381 0.00 0.00 0.00 2.83
1847 2154 0.036306 CGAGGTTGTAAGGGGCTGTT 59.964 55.000 0.00 0.00 0.00 3.16
1848 2155 0.834687 TCGAGGTTGTAAGGGGCTGT 60.835 55.000 0.00 0.00 0.00 4.40
1849 2156 0.108138 CTCGAGGTTGTAAGGGGCTG 60.108 60.000 3.91 0.00 0.00 4.85
1850 2157 0.544595 ACTCGAGGTTGTAAGGGGCT 60.545 55.000 18.41 0.00 0.00 5.19
1851 2158 0.323957 AACTCGAGGTTGTAAGGGGC 59.676 55.000 18.41 0.00 36.70 5.80
1852 2159 2.812011 CAAAACTCGAGGTTGTAAGGGG 59.188 50.000 18.15 0.00 38.29 4.79
1853 2160 3.497262 GTCAAAACTCGAGGTTGTAAGGG 59.503 47.826 18.15 2.91 38.29 3.95
1854 2161 3.497262 GGTCAAAACTCGAGGTTGTAAGG 59.503 47.826 18.15 4.71 38.29 2.69
1855 2162 4.124238 TGGTCAAAACTCGAGGTTGTAAG 58.876 43.478 18.15 7.63 38.29 2.34
1856 2163 4.139859 TGGTCAAAACTCGAGGTTGTAA 57.860 40.909 18.15 2.17 38.29 2.41
1857 2164 3.823281 TGGTCAAAACTCGAGGTTGTA 57.177 42.857 18.15 4.96 38.29 2.41
1858 2165 2.702592 TGGTCAAAACTCGAGGTTGT 57.297 45.000 18.15 4.23 38.29 3.32
1880 2187 9.060347 CACTGATGTATACCTAAGCAATTGATT 57.940 33.333 14.20 14.20 0.00 2.57
1887 2194 9.899661 AAATTTACACTGATGTATACCTAAGCA 57.100 29.630 0.00 0.00 41.02 3.91
2115 2423 2.028020 GCTATCTAGTATGCACCCACCC 60.028 54.545 0.00 0.00 0.00 4.61
2616 2924 8.821147 TTACAACTAGCGAGTAATGAGAAAAA 57.179 30.769 0.00 0.00 33.58 1.94
2617 2925 8.706035 GTTTACAACTAGCGAGTAATGAGAAAA 58.294 33.333 0.00 0.00 33.58 2.29
2618 2926 8.086522 AGTTTACAACTAGCGAGTAATGAGAAA 58.913 33.333 0.00 0.74 40.69 2.52
2619 2927 7.600065 AGTTTACAACTAGCGAGTAATGAGAA 58.400 34.615 0.00 0.00 40.69 2.87
3282 3628 1.135689 CACTCGCCAGGCATTTACAAC 60.136 52.381 13.30 0.00 0.00 3.32
3289 3635 0.250901 AAAACTCACTCGCCAGGCAT 60.251 50.000 13.30 0.00 0.00 4.40
3301 3647 2.297701 GTCACTTGGAGGCAAAACTCA 58.702 47.619 0.00 0.00 39.27 3.41
3312 3658 0.116342 TAGGCTGAGGGTCACTTGGA 59.884 55.000 0.00 0.00 0.00 3.53
3641 3997 3.006537 TGCAACAGAGGTCCTACAAGTAC 59.993 47.826 0.00 0.00 0.00 2.73
4117 4479 7.710475 CCAGTTAAACACCAAATTCAGTTCATT 59.290 33.333 0.00 0.00 0.00 2.57
4159 4521 5.894298 AGGAGCAGGATATTCACATAACA 57.106 39.130 0.00 0.00 0.00 2.41
5003 5369 0.529833 CACACAAACACAGGTTGCCA 59.470 50.000 0.00 0.00 37.30 4.92
5020 5387 7.381948 TGAGACAATTTCAATAACAATGTGCAC 59.618 33.333 10.75 10.75 0.00 4.57
5168 5535 6.372381 TGTTCACTCATTTCAGTCCATATGTG 59.628 38.462 1.24 0.00 0.00 3.21
5561 5929 6.435292 AACCAACATACCCCAGATATAGAC 57.565 41.667 0.00 0.00 0.00 2.59
5646 6036 1.543802 TCATAGCCCAAAAACTTGCCG 59.456 47.619 0.00 0.00 0.00 5.69
5758 6150 3.398318 TTACAGTCAGGGATGCCTAGA 57.602 47.619 5.01 3.21 0.00 2.43
5965 6388 1.073964 CGTGTCAGTCTGCCTCATTG 58.926 55.000 0.00 0.00 0.00 2.82
6040 6497 7.722285 TGTTAGTTTTGCCAAATAACTACTCCT 59.278 33.333 12.44 0.00 34.93 3.69


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

AutoCloner maintained by Alex Coulton.