Multiple sequence alignment - TraesCS6B01G459800

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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 TraesCS6B01G459800 chr6B 100.000 2429 0 0 1 2429 713946661 713949089 0.000000e+00 4486.0
1 TraesCS6B01G459800 chr6B 95.482 1638 64 5 1 1637 713461486 713463114 0.000000e+00 2606.0
2 TraesCS6B01G459800 chr6B 93.354 1640 105 3 1 1637 713826128 713827766 0.000000e+00 2422.0
3 TraesCS6B01G459800 chr6B 92.796 1638 109 4 1 1637 713909285 713910914 0.000000e+00 2362.0
4 TraesCS6B01G459800 chr6B 92.002 1638 118 7 1 1637 713358694 713360319 0.000000e+00 2287.0
5 TraesCS6B01G459800 chr6B 91.778 1642 120 9 1 1637 713680349 713681980 0.000000e+00 2270.0
6 TraesCS6B01G459800 chr6B 91.489 1645 120 12 3 1637 713499546 713501180 0.000000e+00 2244.0
7 TraesCS6B01G459800 chr6B 90.075 1592 136 7 2 1591 713771528 713773099 0.000000e+00 2045.0
8 TraesCS6B01G459800 chr6B 97.753 178 3 1 1639 1816 559355018 559355194 3.030000e-79 305.0
9 TraesCS6B01G459800 chr6B 97.619 84 1 1 2254 2337 713953870 713953952 2.520000e-30 143.0
10 TraesCS6B01G459800 chr6B 93.750 64 2 1 1820 1881 713827759 713827822 7.150000e-16 95.3
11 TraesCS6B01G459800 chr6A 92.931 1641 104 5 1 1637 613974830 613976462 0.000000e+00 2377.0
12 TraesCS6B01G459800 chr6A 96.354 192 5 2 1639 1829 70570996 70570806 5.040000e-82 315.0
13 TraesCS6B01G459800 chr6A 97.268 183 4 1 1639 1821 326797733 326797552 2.350000e-80 309.0
14 TraesCS6B01G459800 chr6D 91.783 1643 119 9 1 1637 467859466 467861098 0.000000e+00 2272.0
15 TraesCS6B01G459800 chr2A 86.047 559 37 17 1882 2429 223510338 223509810 1.630000e-156 562.0
16 TraesCS6B01G459800 chr2A 93.367 196 9 4 1629 1822 15369361 15369554 1.100000e-73 287.0
17 TraesCS6B01G459800 chr2A 94.536 183 9 1 1639 1820 14573000 14572818 5.110000e-72 281.0
18 TraesCS6B01G459800 chr2A 94.536 183 7 3 1639 1820 15815005 15814825 1.840000e-71 279.0
19 TraesCS6B01G459800 chr2A 93.443 183 10 2 1639 1820 15364183 15364364 1.110000e-68 270.0
20 TraesCS6B01G459800 chr7A 91.144 271 13 9 1882 2146 1494011 1494276 8.260000e-95 357.0
21 TraesCS6B01G459800 chr7A 82.222 225 28 7 2206 2428 711373036 711373250 1.480000e-42 183.0
22 TraesCS6B01G459800 chr5A 97.790 181 4 0 1639 1819 659880935 659881115 1.810000e-81 313.0
23 TraesCS6B01G459800 chr2B 94.819 193 6 4 1637 1829 511131676 511131488 5.080000e-77 298.0
24 TraesCS6B01G459800 chr2B 88.000 200 16 4 2232 2429 655823454 655823261 1.880000e-56 230.0
25 TraesCS6B01G459800 chr2B 79.701 335 37 18 2096 2424 663910036 663910345 1.890000e-51 213.0
26 TraesCS6B01G459800 chr2B 77.273 242 24 18 2096 2331 663914116 663914332 1.970000e-21 113.0
27 TraesCS6B01G459800 chr4D 77.023 309 28 28 1881 2149 455910387 455910692 1.170000e-28 137.0
28 TraesCS6B01G459800 chr4D 90.426 94 4 3 1882 1970 455914075 455914168 4.240000e-23 119.0
29 TraesCS6B01G459800 chr4D 93.182 44 3 0 1770 1813 423890258 423890301 5.610000e-07 65.8
30 TraesCS6B01G459800 chr3D 88.889 99 7 2 1884 1978 418482631 418482729 4.240000e-23 119.0
31 TraesCS6B01G459800 chr3D 87.156 109 7 5 2083 2186 21450640 21450534 1.530000e-22 117.0
32 TraesCS6B01G459800 chr3D 91.379 58 5 0 1771 1828 587765797 587765740 2.000000e-11 80.5
33 TraesCS6B01G459800 chr3D 92.308 52 4 0 1771 1822 8307788 8307737 9.310000e-10 75.0
34 TraesCS6B01G459800 chrUn 77.273 242 24 18 2096 2331 477876018 477875802 1.970000e-21 113.0
35 TraesCS6B01G459800 chr5D 93.243 74 2 3 2083 2153 164620796 164620723 3.300000e-19 106.0
36 TraesCS6B01G459800 chr3B 87.368 95 7 5 2095 2188 754957775 754957865 1.190000e-18 104.0
37 TraesCS6B01G459800 chr3B 86.170 94 10 3 2095 2188 754961786 754961876 5.530000e-17 99.0
38 TraesCS6B01G459800 chr7B 100.000 49 0 0 2096 2144 66171787 66171835 9.250000e-15 91.6
39 TraesCS6B01G459800 chr7B 75.000 272 31 25 1907 2144 509602355 509602623 9.250000e-15 91.6
40 TraesCS6B01G459800 chr7B 100.000 30 0 0 1907 1936 509605139 509605110 3.370000e-04 56.5
41 TraesCS6B01G459800 chr2D 97.674 43 1 0 1771 1813 361422374 361422416 9.310000e-10 75.0
42 TraesCS6B01G459800 chr7D 86.441 59 7 1 1771 1828 631359517 631359575 2.020000e-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 TraesCS6B01G459800 chr6B 713946661 713949089 2428 False 4486.00 4486 100.000 1 2429 1 chr6B.!!$F8 2428
1 TraesCS6B01G459800 chr6B 713461486 713463114 1628 False 2606.00 2606 95.482 1 1637 1 chr6B.!!$F3 1636
2 TraesCS6B01G459800 chr6B 713909285 713910914 1629 False 2362.00 2362 92.796 1 1637 1 chr6B.!!$F7 1636
3 TraesCS6B01G459800 chr6B 713358694 713360319 1625 False 2287.00 2287 92.002 1 1637 1 chr6B.!!$F2 1636
4 TraesCS6B01G459800 chr6B 713680349 713681980 1631 False 2270.00 2270 91.778 1 1637 1 chr6B.!!$F5 1636
5 TraesCS6B01G459800 chr6B 713499546 713501180 1634 False 2244.00 2244 91.489 3 1637 1 chr6B.!!$F4 1634
6 TraesCS6B01G459800 chr6B 713771528 713773099 1571 False 2045.00 2045 90.075 2 1591 1 chr6B.!!$F6 1589
7 TraesCS6B01G459800 chr6B 713826128 713827822 1694 False 1258.65 2422 93.552 1 1881 2 chr6B.!!$F10 1880
8 TraesCS6B01G459800 chr6A 613974830 613976462 1632 False 2377.00 2377 92.931 1 1637 1 chr6A.!!$F1 1636
9 TraesCS6B01G459800 chr6D 467859466 467861098 1632 False 2272.00 2272 91.783 1 1637 1 chr6D.!!$F1 1636
10 TraesCS6B01G459800 chr2A 223509810 223510338 528 True 562.00 562 86.047 1882 2429 1 chr2A.!!$R3 547

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
91 92 2.095869 CACATCAGCAAAGAGACACAGC 60.096 50.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 1672 0.110328 TTCGCGAAGTCTCAGTCGAC 60.11 55.0 19.38 7.7 39.64 4.2 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
50 51 6.003326 TGCACTCATGGAAAAGAGTTTGATA 58.997 36.000 0.00 0.00 42.87 2.15
91 92 2.095869 CACATCAGCAAAGAGACACAGC 60.096 50.000 0.00 0.00 0.00 4.40
331 346 4.870021 AATCAAGGGCTACTCTTGGAAT 57.130 40.909 7.33 0.00 41.23 3.01
332 347 3.914426 TCAAGGGCTACTCTTGGAATC 57.086 47.619 7.33 0.00 41.23 2.52
586 601 3.417069 TTCATCGGAATGTGGTCAAGT 57.583 42.857 0.00 0.00 34.32 3.16
840 855 4.022589 GGCAACTTTACTACCAAGGTTTCC 60.023 45.833 0.00 0.00 0.00 3.13
1125 1140 2.039879 TCCCCAAGTTGTAGAAGAAGCC 59.960 50.000 1.45 0.00 0.00 4.35
1200 1215 4.658901 ACCAAAGGAAGAGAAAGACCTACA 59.341 41.667 0.00 0.00 32.06 2.74
1249 1264 9.959721 TGCAACTCCTAAAAACTAGAAGATTAT 57.040 29.630 0.00 0.00 0.00 1.28
1434 1449 1.446099 CTTGCCACGCTAGCGAAGA 60.446 57.895 41.33 19.65 42.83 2.87
1640 1656 6.732154 CAAGTCATTGTGATTAAGCTATGGG 58.268 40.000 0.00 0.00 0.00 4.00
1641 1657 6.006275 AGTCATTGTGATTAAGCTATGGGT 57.994 37.500 0.00 0.00 0.00 4.51
1642 1658 6.426587 AGTCATTGTGATTAAGCTATGGGTT 58.573 36.000 0.00 0.00 37.00 4.11
1643 1659 6.891908 AGTCATTGTGATTAAGCTATGGGTTT 59.108 34.615 0.00 0.00 34.76 3.27
1644 1660 6.974622 GTCATTGTGATTAAGCTATGGGTTTG 59.025 38.462 0.00 0.00 34.76 2.93
1645 1661 6.663093 TCATTGTGATTAAGCTATGGGTTTGT 59.337 34.615 0.00 0.00 34.76 2.83
1646 1662 6.509418 TTGTGATTAAGCTATGGGTTTGTC 57.491 37.500 0.00 0.00 34.76 3.18
1647 1663 5.815581 TGTGATTAAGCTATGGGTTTGTCT 58.184 37.500 0.00 0.00 34.76 3.41
1648 1664 6.953101 TGTGATTAAGCTATGGGTTTGTCTA 58.047 36.000 0.00 0.00 34.76 2.59
1649 1665 7.047891 TGTGATTAAGCTATGGGTTTGTCTAG 58.952 38.462 0.00 0.00 34.76 2.43
1650 1666 6.483640 GTGATTAAGCTATGGGTTTGTCTAGG 59.516 42.308 0.00 0.00 34.76 3.02
1651 1667 6.157994 TGATTAAGCTATGGGTTTGTCTAGGT 59.842 38.462 0.00 0.00 34.76 3.08
1652 1668 4.489306 AAGCTATGGGTTTGTCTAGGTC 57.511 45.455 0.00 0.00 0.00 3.85
1653 1669 3.725634 AGCTATGGGTTTGTCTAGGTCT 58.274 45.455 0.00 0.00 0.00 3.85
1654 1670 4.104831 AGCTATGGGTTTGTCTAGGTCTT 58.895 43.478 0.00 0.00 0.00 3.01
1655 1671 5.278061 AGCTATGGGTTTGTCTAGGTCTTA 58.722 41.667 0.00 0.00 0.00 2.10
1656 1672 5.364157 AGCTATGGGTTTGTCTAGGTCTTAG 59.636 44.000 0.00 0.00 0.00 2.18
1657 1673 5.128991 GCTATGGGTTTGTCTAGGTCTTAGT 59.871 44.000 0.00 0.00 0.00 2.24
1658 1674 5.678955 ATGGGTTTGTCTAGGTCTTAGTC 57.321 43.478 0.00 0.00 0.00 2.59
1659 1675 3.508793 TGGGTTTGTCTAGGTCTTAGTCG 59.491 47.826 0.00 0.00 0.00 4.18
1660 1676 3.760684 GGGTTTGTCTAGGTCTTAGTCGA 59.239 47.826 0.00 0.00 0.00 4.20
1661 1677 4.380339 GGGTTTGTCTAGGTCTTAGTCGAC 60.380 50.000 7.70 7.70 0.00 4.20
1662 1678 4.458642 GGTTTGTCTAGGTCTTAGTCGACT 59.541 45.833 23.66 23.66 34.38 4.18
1663 1679 5.392286 GTTTGTCTAGGTCTTAGTCGACTG 58.608 45.833 28.12 12.46 34.38 3.51
1664 1680 4.548451 TGTCTAGGTCTTAGTCGACTGA 57.452 45.455 28.12 19.13 34.38 3.41
1665 1681 4.505808 TGTCTAGGTCTTAGTCGACTGAG 58.494 47.826 26.80 26.80 34.38 3.35
1666 1682 4.222366 TGTCTAGGTCTTAGTCGACTGAGA 59.778 45.833 30.05 30.05 36.42 3.27
1673 1689 4.044024 GTCGACTGAGACTTCGCG 57.956 61.111 8.70 0.00 38.09 5.87
1674 1690 1.496393 GTCGACTGAGACTTCGCGA 59.504 57.895 3.71 3.71 38.09 5.87
1675 1691 0.110328 GTCGACTGAGACTTCGCGAA 60.110 55.000 22.01 22.01 38.09 4.70
1676 1692 0.166161 TCGACTGAGACTTCGCGAAG 59.834 55.000 39.55 39.55 43.79 3.79
1685 1701 3.775065 CTTCGCGAAGTCTCAGTCA 57.225 52.632 34.97 5.14 33.87 3.41
1686 1702 2.051879 CTTCGCGAAGTCTCAGTCAA 57.948 50.000 34.97 4.60 33.87 3.18
1687 1703 1.982223 CTTCGCGAAGTCTCAGTCAAG 59.018 52.381 34.97 10.93 33.87 3.02
1688 1704 0.387367 TCGCGAAGTCTCAGTCAAGC 60.387 55.000 6.20 0.00 0.00 4.01
1689 1705 0.664466 CGCGAAGTCTCAGTCAAGCA 60.664 55.000 0.00 0.00 0.00 3.91
1690 1706 1.502231 GCGAAGTCTCAGTCAAGCAA 58.498 50.000 0.00 0.00 0.00 3.91
1691 1707 2.072298 GCGAAGTCTCAGTCAAGCAAT 58.928 47.619 0.00 0.00 0.00 3.56
1692 1708 2.159734 GCGAAGTCTCAGTCAAGCAATG 60.160 50.000 0.00 0.00 0.00 2.82
1693 1709 3.062763 CGAAGTCTCAGTCAAGCAATGT 58.937 45.455 0.00 0.00 0.00 2.71
1694 1710 4.237724 CGAAGTCTCAGTCAAGCAATGTA 58.762 43.478 0.00 0.00 0.00 2.29
1695 1711 4.325741 CGAAGTCTCAGTCAAGCAATGTAG 59.674 45.833 0.00 0.00 0.00 2.74
1696 1712 4.881019 AGTCTCAGTCAAGCAATGTAGT 57.119 40.909 0.00 0.00 0.00 2.73
1697 1713 5.984695 AGTCTCAGTCAAGCAATGTAGTA 57.015 39.130 0.00 0.00 0.00 1.82
1698 1714 6.537453 AGTCTCAGTCAAGCAATGTAGTAT 57.463 37.500 0.00 0.00 0.00 2.12
1699 1715 6.336566 AGTCTCAGTCAAGCAATGTAGTATG 58.663 40.000 0.00 0.00 0.00 2.39
1700 1716 5.006165 GTCTCAGTCAAGCAATGTAGTATGC 59.994 44.000 0.00 0.00 42.87 3.14
1701 1717 4.831107 TCAGTCAAGCAATGTAGTATGCA 58.169 39.130 0.00 0.00 44.95 3.96
1702 1718 5.244755 TCAGTCAAGCAATGTAGTATGCAA 58.755 37.500 0.00 0.00 44.95 4.08
1703 1719 5.352293 TCAGTCAAGCAATGTAGTATGCAAG 59.648 40.000 0.00 0.00 44.95 4.01
1704 1720 5.352293 CAGTCAAGCAATGTAGTATGCAAGA 59.648 40.000 0.00 0.00 44.95 3.02
1705 1721 5.939883 AGTCAAGCAATGTAGTATGCAAGAA 59.060 36.000 0.00 0.00 44.95 2.52
1706 1722 6.093219 AGTCAAGCAATGTAGTATGCAAGAAG 59.907 38.462 0.00 0.00 44.95 2.85
1707 1723 6.092670 GTCAAGCAATGTAGTATGCAAGAAGA 59.907 38.462 0.00 0.00 44.95 2.87
1708 1724 6.654582 TCAAGCAATGTAGTATGCAAGAAGAA 59.345 34.615 0.00 0.00 44.95 2.52
1709 1725 7.174772 TCAAGCAATGTAGTATGCAAGAAGAAA 59.825 33.333 0.00 0.00 44.95 2.52
1710 1726 7.452880 AGCAATGTAGTATGCAAGAAGAAAA 57.547 32.000 0.00 0.00 44.95 2.29
1711 1727 7.533426 AGCAATGTAGTATGCAAGAAGAAAAG 58.467 34.615 0.00 0.00 44.95 2.27
1712 1728 7.391554 AGCAATGTAGTATGCAAGAAGAAAAGA 59.608 33.333 0.00 0.00 44.95 2.52
1713 1729 8.023128 GCAATGTAGTATGCAAGAAGAAAAGAA 58.977 33.333 0.00 0.00 42.12 2.52
1714 1730 9.897744 CAATGTAGTATGCAAGAAGAAAAGAAA 57.102 29.630 0.00 0.00 31.62 2.52
1716 1732 9.899226 ATGTAGTATGCAAGAAGAAAAGAAAAC 57.101 29.630 0.00 0.00 31.62 2.43
1717 1733 9.120538 TGTAGTATGCAAGAAGAAAAGAAAACT 57.879 29.630 0.00 0.00 0.00 2.66
1718 1734 9.387123 GTAGTATGCAAGAAGAAAAGAAAACTG 57.613 33.333 0.00 0.00 0.00 3.16
1719 1735 8.225603 AGTATGCAAGAAGAAAAGAAAACTGA 57.774 30.769 0.00 0.00 0.00 3.41
1720 1736 8.686334 AGTATGCAAGAAGAAAAGAAAACTGAA 58.314 29.630 0.00 0.00 0.00 3.02
1721 1737 9.301153 GTATGCAAGAAGAAAAGAAAACTGAAA 57.699 29.630 0.00 0.00 0.00 2.69
1722 1738 8.776376 ATGCAAGAAGAAAAGAAAACTGAAAA 57.224 26.923 0.00 0.00 0.00 2.29
1723 1739 8.600449 TGCAAGAAGAAAAGAAAACTGAAAAA 57.400 26.923 0.00 0.00 0.00 1.94
1749 1765 9.615295 AAAAATTGTTTGCATAAATCTCAATGC 57.385 25.926 0.44 0.44 46.92 3.56
1758 1774 7.390918 GCATAAATCTCAATGCAAGATCAAC 57.609 36.000 0.00 0.00 46.19 3.18
1759 1775 6.976349 GCATAAATCTCAATGCAAGATCAACA 59.024 34.615 0.00 0.00 46.19 3.33
1760 1776 7.167635 GCATAAATCTCAATGCAAGATCAACAG 59.832 37.037 0.00 0.00 46.19 3.16
1761 1777 6.829229 AAATCTCAATGCAAGATCAACAGA 57.171 33.333 0.00 0.00 32.29 3.41
1762 1778 7.406031 AAATCTCAATGCAAGATCAACAGAT 57.594 32.000 0.00 0.00 32.29 2.90
1763 1779 7.406031 AATCTCAATGCAAGATCAACAGATT 57.594 32.000 0.00 0.00 32.29 2.40
1764 1780 6.190954 TCTCAATGCAAGATCAACAGATTG 57.809 37.500 0.00 0.00 37.14 2.67
1765 1781 5.708697 TCTCAATGCAAGATCAACAGATTGT 59.291 36.000 0.00 0.00 37.11 2.71
1766 1782 6.880529 TCTCAATGCAAGATCAACAGATTGTA 59.119 34.615 0.00 0.00 37.11 2.41
1767 1783 7.065443 TCTCAATGCAAGATCAACAGATTGTAG 59.935 37.037 0.00 0.00 37.11 2.74
1768 1784 6.656270 TCAATGCAAGATCAACAGATTGTAGT 59.344 34.615 0.00 0.00 37.11 2.73
1769 1785 7.823799 TCAATGCAAGATCAACAGATTGTAGTA 59.176 33.333 0.00 0.00 37.11 1.82
1770 1786 8.618677 CAATGCAAGATCAACAGATTGTAGTAT 58.381 33.333 0.00 0.00 37.11 2.12
1771 1787 7.776933 TGCAAGATCAACAGATTGTAGTATC 57.223 36.000 0.00 0.00 37.11 2.24
1772 1788 6.476706 TGCAAGATCAACAGATTGTAGTATCG 59.523 38.462 0.00 0.00 37.11 2.92
1773 1789 6.697455 GCAAGATCAACAGATTGTAGTATCGA 59.303 38.462 0.00 0.00 37.11 3.59
1774 1790 7.306283 GCAAGATCAACAGATTGTAGTATCGAC 60.306 40.741 0.00 0.00 37.11 4.20
1775 1791 7.575414 AGATCAACAGATTGTAGTATCGACT 57.425 36.000 0.00 0.00 37.11 4.18
1776 1792 7.421599 AGATCAACAGATTGTAGTATCGACTG 58.578 38.462 0.00 0.00 37.11 3.51
1777 1793 6.753107 TCAACAGATTGTAGTATCGACTGA 57.247 37.500 0.00 0.00 37.11 3.41
1778 1794 6.786207 TCAACAGATTGTAGTATCGACTGAG 58.214 40.000 0.00 0.00 37.11 3.35
1779 1795 6.598064 TCAACAGATTGTAGTATCGACTGAGA 59.402 38.462 0.00 0.00 37.11 3.27
1780 1796 6.366315 ACAGATTGTAGTATCGACTGAGAC 57.634 41.667 0.00 0.00 36.28 3.36
1782 1798 6.600032 ACAGATTGTAGTATCGACTGAGACTT 59.400 38.462 0.00 0.00 43.97 3.01
1783 1799 7.129622 CAGATTGTAGTATCGACTGAGACTTC 58.870 42.308 0.00 0.00 43.97 3.01
1784 1800 5.466432 TTGTAGTATCGACTGAGACTTCG 57.534 43.478 0.00 0.00 43.97 3.79
1785 1801 3.309138 TGTAGTATCGACTGAGACTTCGC 59.691 47.826 0.00 0.00 43.97 4.70
1786 1802 1.328069 AGTATCGACTGAGACTTCGCG 59.672 52.381 0.00 0.00 43.97 5.87
1787 1803 1.326852 GTATCGACTGAGACTTCGCGA 59.673 52.381 3.71 3.71 33.52 5.87
1788 1804 0.803117 ATCGACTGAGACTTCGCGAA 59.197 50.000 22.01 22.01 35.15 4.70
1789 1805 0.166161 TCGACTGAGACTTCGCGAAG 59.834 55.000 39.55 39.55 43.79 3.79
1798 1814 2.631303 CTTCGCGAAGTCTCAGTCG 58.369 57.895 34.97 12.16 40.24 4.18
1799 1815 0.166161 CTTCGCGAAGTCTCAGTCGA 59.834 55.000 34.97 4.60 39.64 4.20
1800 1816 0.803117 TTCGCGAAGTCTCAGTCGAT 59.197 50.000 19.38 0.00 39.64 3.59
1801 1817 0.803117 TCGCGAAGTCTCAGTCGATT 59.197 50.000 6.20 0.00 39.64 3.34
1802 1818 0.910513 CGCGAAGTCTCAGTCGATTG 59.089 55.000 0.00 0.68 39.64 2.67
1803 1819 1.465856 CGCGAAGTCTCAGTCGATTGA 60.466 52.381 10.44 10.44 39.64 2.57
1804 1820 2.792890 CGCGAAGTCTCAGTCGATTGAT 60.793 50.000 11.34 0.00 39.64 2.57
1805 1821 3.182967 GCGAAGTCTCAGTCGATTGATT 58.817 45.455 11.34 3.05 39.64 2.57
1806 1822 3.614616 GCGAAGTCTCAGTCGATTGATTT 59.385 43.478 11.34 6.62 39.64 2.17
1807 1823 4.092091 GCGAAGTCTCAGTCGATTGATTTT 59.908 41.667 11.34 6.29 39.64 1.82
1808 1824 5.389935 GCGAAGTCTCAGTCGATTGATTTTT 60.390 40.000 11.34 5.96 39.64 1.94
1809 1825 6.183360 GCGAAGTCTCAGTCGATTGATTTTTA 60.183 38.462 11.34 0.00 39.64 1.52
1810 1826 7.387180 CGAAGTCTCAGTCGATTGATTTTTAG 58.613 38.462 11.34 0.00 39.64 1.85
1811 1827 6.654793 AGTCTCAGTCGATTGATTTTTAGC 57.345 37.500 11.34 0.00 0.00 3.09
1812 1828 6.166279 AGTCTCAGTCGATTGATTTTTAGCA 58.834 36.000 11.34 0.00 0.00 3.49
1813 1829 6.650807 AGTCTCAGTCGATTGATTTTTAGCAA 59.349 34.615 11.34 0.00 0.00 3.91
1814 1830 7.173218 AGTCTCAGTCGATTGATTTTTAGCAAA 59.827 33.333 11.34 0.00 0.00 3.68
1815 1831 7.479916 GTCTCAGTCGATTGATTTTTAGCAAAG 59.520 37.037 11.34 0.00 0.00 2.77
1816 1832 6.086222 TCAGTCGATTGATTTTTAGCAAAGC 58.914 36.000 6.51 0.00 0.00 3.51
1817 1833 5.287035 CAGTCGATTGATTTTTAGCAAAGCC 59.713 40.000 0.86 0.00 0.00 4.35
1818 1834 4.262976 GTCGATTGATTTTTAGCAAAGCCG 59.737 41.667 0.00 0.00 0.00 5.52
1819 1835 4.083003 TCGATTGATTTTTAGCAAAGCCGT 60.083 37.500 0.00 0.00 0.00 5.68
1820 1836 4.621034 CGATTGATTTTTAGCAAAGCCGTT 59.379 37.500 0.00 0.00 0.00 4.44
1821 1837 5.797934 CGATTGATTTTTAGCAAAGCCGTTA 59.202 36.000 0.00 0.00 0.00 3.18
1822 1838 6.306837 CGATTGATTTTTAGCAAAGCCGTTAA 59.693 34.615 0.00 0.00 0.00 2.01
1823 1839 7.461416 CGATTGATTTTTAGCAAAGCCGTTAAG 60.461 37.037 0.00 0.00 0.00 1.85
1824 1840 4.920927 TGATTTTTAGCAAAGCCGTTAAGC 59.079 37.500 0.00 0.00 0.00 3.09
1826 1842 5.692613 TTTTTAGCAAAGCCGTTAAGCTA 57.307 34.783 0.00 0.00 44.11 3.32
1827 1843 5.890424 TTTTAGCAAAGCCGTTAAGCTAT 57.110 34.783 0.00 0.00 44.11 2.97
1857 1873 9.169592 GCTGGATAAAGGTATTTTACAGTGTTA 57.830 33.333 0.00 0.00 34.22 2.41
1881 1899 2.813907 ACTGCTACTCATGTCTCACCT 58.186 47.619 0.00 0.00 0.00 4.00
1882 1900 2.495270 ACTGCTACTCATGTCTCACCTG 59.505 50.000 0.00 0.00 0.00 4.00
1883 1901 2.495270 CTGCTACTCATGTCTCACCTGT 59.505 50.000 0.00 0.00 0.00 4.00
1884 1902 2.899900 TGCTACTCATGTCTCACCTGTT 59.100 45.455 0.00 0.00 0.00 3.16
1885 1903 3.257393 GCTACTCATGTCTCACCTGTTG 58.743 50.000 0.00 0.00 0.00 3.33
1886 1904 2.847327 ACTCATGTCTCACCTGTTGG 57.153 50.000 0.00 0.00 39.83 3.77
1890 1908 3.885297 CTCATGTCTCACCTGTTGGTTTT 59.115 43.478 0.00 0.00 46.05 2.43
1891 1909 3.631686 TCATGTCTCACCTGTTGGTTTTG 59.368 43.478 0.00 0.00 46.05 2.44
1895 1913 2.093394 TCTCACCTGTTGGTTTTGTCGA 60.093 45.455 0.00 0.00 46.05 4.20
1917 1938 2.743183 CGGATCAAATCACCAGGACCTC 60.743 54.545 0.00 0.00 0.00 3.85
1936 1957 2.863740 CTCTGCACACTCACGTACAAAA 59.136 45.455 0.00 0.00 0.00 2.44
1957 1978 1.246737 AACCAAGCAAGCTGCCTAGC 61.247 55.000 0.00 0.00 46.52 3.42
2002 2025 3.181503 CGTGTGTATAGCCACGTACTTCT 60.182 47.826 13.37 0.00 46.87 2.85
2062 2086 1.738350 TCGATCGATCTAGGCGGATTC 59.262 52.381 22.43 0.00 0.00 2.52
2086 2111 4.084223 TCTCGTAACTTGCGAATGGAAAAC 60.084 41.667 3.50 0.00 37.93 2.43
2087 2112 3.810941 TCGTAACTTGCGAATGGAAAACT 59.189 39.130 0.00 0.00 35.28 2.66
2088 2113 3.906008 CGTAACTTGCGAATGGAAAACTG 59.094 43.478 0.00 0.00 0.00 3.16
2089 2114 4.319190 CGTAACTTGCGAATGGAAAACTGA 60.319 41.667 0.00 0.00 0.00 3.41
2090 2115 4.853924 AACTTGCGAATGGAAAACTGAT 57.146 36.364 0.00 0.00 0.00 2.90
2091 2116 4.425577 ACTTGCGAATGGAAAACTGATC 57.574 40.909 0.00 0.00 0.00 2.92
2092 2117 3.120199 ACTTGCGAATGGAAAACTGATCG 60.120 43.478 0.00 0.00 0.00 3.69
2093 2118 2.694213 TGCGAATGGAAAACTGATCGA 58.306 42.857 0.00 0.00 32.38 3.59
2094 2119 3.270027 TGCGAATGGAAAACTGATCGAT 58.730 40.909 0.00 0.00 32.38 3.59
2095 2120 3.689161 TGCGAATGGAAAACTGATCGATT 59.311 39.130 0.00 0.00 32.38 3.34
2096 2121 4.155826 TGCGAATGGAAAACTGATCGATTT 59.844 37.500 0.00 0.00 32.38 2.17
2097 2122 5.095490 GCGAATGGAAAACTGATCGATTTT 58.905 37.500 0.00 6.47 32.38 1.82
2098 2123 5.003778 GCGAATGGAAAACTGATCGATTTTG 59.996 40.000 10.53 0.00 32.38 2.44
2099 2124 6.314018 CGAATGGAAAACTGATCGATTTTGA 58.686 36.000 10.53 0.28 32.38 2.69
2104 2129 5.393461 GGAAAACTGATCGATTTTGATGGCT 60.393 40.000 10.53 0.00 0.00 4.75
2126 2151 3.423154 GCCCGTGTCGAGCCTTTG 61.423 66.667 0.00 0.00 0.00 2.77
2127 2152 3.423154 CCCGTGTCGAGCCTTTGC 61.423 66.667 0.00 0.00 37.95 3.68
2146 2171 6.703165 CCTTTGCTTTGTATTGCTTTTCTCTT 59.297 34.615 0.00 0.00 0.00 2.85
2147 2172 7.225341 CCTTTGCTTTGTATTGCTTTTCTCTTT 59.775 33.333 0.00 0.00 0.00 2.52
2149 2174 7.698836 TGCTTTGTATTGCTTTTCTCTTTTC 57.301 32.000 0.00 0.00 0.00 2.29
2152 2177 8.271487 GCTTTGTATTGCTTTTCTCTTTTCTTG 58.729 33.333 0.00 0.00 0.00 3.02
2155 2180 7.995289 TGTATTGCTTTTCTCTTTTCTTGTGA 58.005 30.769 0.00 0.00 0.00 3.58
2180 2205 0.032416 AGGGGTAGGAGTACACGCAT 60.032 55.000 0.00 0.00 32.71 4.73
2181 2206 1.216175 AGGGGTAGGAGTACACGCATA 59.784 52.381 0.00 0.00 32.71 3.14
2182 2207 2.158355 AGGGGTAGGAGTACACGCATAT 60.158 50.000 0.00 0.00 32.71 1.78
2183 2208 3.074985 AGGGGTAGGAGTACACGCATATA 59.925 47.826 0.00 0.00 32.71 0.86
2184 2209 4.021916 GGGGTAGGAGTACACGCATATAT 58.978 47.826 0.00 0.00 32.71 0.86
2185 2210 5.044624 AGGGGTAGGAGTACACGCATATATA 60.045 44.000 0.00 0.00 32.71 0.86
2186 2211 5.832060 GGGGTAGGAGTACACGCATATATAT 59.168 44.000 0.00 0.00 32.71 0.86
2187 2212 7.000472 GGGGTAGGAGTACACGCATATATATA 59.000 42.308 0.00 0.00 32.71 0.86
2188 2213 7.668886 GGGGTAGGAGTACACGCATATATATAT 59.331 40.741 0.00 0.00 32.71 0.86
2189 2214 9.730705 GGGTAGGAGTACACGCATATATATATA 57.269 37.037 4.90 4.92 0.00 0.86
2238 2263 3.873910 TGAACATAGCCTAGGAGCAAAC 58.126 45.455 14.75 0.00 34.23 2.93
2254 2279 2.480932 GCAAACCTAGTCGGCTACTACC 60.481 54.545 0.00 0.00 39.80 3.18
2262 2287 1.674962 GTCGGCTACTACCTGTACCTG 59.325 57.143 0.00 0.00 0.00 4.00
2337 2362 4.065088 GTGTTTAGCTCTCACATTCACCA 58.935 43.478 0.00 0.00 33.04 4.17
2339 2364 3.334583 TTAGCTCTCACATTCACCACC 57.665 47.619 0.00 0.00 0.00 4.61
2347 2372 3.482436 TCACATTCACCACCCTAAACAC 58.518 45.455 0.00 0.00 0.00 3.32
2365 2390 3.735029 GACGTCCTCGGTGCGACT 61.735 66.667 3.51 0.00 41.85 4.18
2370 2395 1.982395 TCCTCGGTGCGACTTGGAT 60.982 57.895 0.00 0.00 0.00 3.41
2386 2411 0.749454 GGATCCCAAATGCGACTGCT 60.749 55.000 0.00 0.00 43.34 4.24
2398 2423 1.846782 GCGACTGCTGTTACTCGTATG 59.153 52.381 0.00 0.00 38.39 2.39
2416 2441 5.064707 TCGTATGCTTTACTCTTGGCATTTC 59.935 40.000 4.65 0.00 41.80 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 5.060506 TGTGACACATCTCCGTTTTATTGT 58.939 37.500 3.56 0.00 0.00 2.71
91 92 7.747155 TCGATATGACTTACCTAAGAGAAGG 57.253 40.000 0.00 0.00 42.82 3.46
331 346 8.755028 TGTGGCACTTTAGTCTAATATTAGTGA 58.245 33.333 19.83 6.13 34.87 3.41
332 347 8.942338 TGTGGCACTTTAGTCTAATATTAGTG 57.058 34.615 19.83 13.32 35.75 2.74
346 361 7.575414 TCTTTGTTTTATCTGTGGCACTTTA 57.425 32.000 19.83 4.37 0.00 1.85
840 855 0.600255 ACCTCGAAGCACCAAAGTCG 60.600 55.000 0.00 0.00 34.85 4.18
1030 1045 6.025749 AGCCAAGCTTTGTTTTATACCTTC 57.974 37.500 0.00 0.00 33.89 3.46
1125 1140 7.960738 GCAATTTCATCAATTTCATTCTGGTTG 59.039 33.333 0.00 0.00 32.24 3.77
1200 1215 6.739565 GCAACTTCATTTCCACCTCTTTCATT 60.740 38.462 0.00 0.00 0.00 2.57
1434 1449 3.882444 CAGATGATCATCCCACTGTGTT 58.118 45.455 28.23 7.22 38.58 3.32
1626 1642 6.157994 ACCTAGACAAACCCATAGCTTAATCA 59.842 38.462 0.00 0.00 0.00 2.57
1637 1653 3.508793 CGACTAAGACCTAGACAAACCCA 59.491 47.826 0.00 0.00 0.00 4.51
1638 1654 3.760684 TCGACTAAGACCTAGACAAACCC 59.239 47.826 0.00 0.00 0.00 4.11
1639 1655 4.458642 AGTCGACTAAGACCTAGACAAACC 59.541 45.833 18.46 0.00 41.83 3.27
1640 1656 5.180868 TCAGTCGACTAAGACCTAGACAAAC 59.819 44.000 19.57 0.00 41.83 2.93
1641 1657 5.311265 TCAGTCGACTAAGACCTAGACAAA 58.689 41.667 19.57 0.00 41.83 2.83
1642 1658 4.903054 TCAGTCGACTAAGACCTAGACAA 58.097 43.478 19.57 0.00 41.83 3.18
1643 1659 4.222366 TCTCAGTCGACTAAGACCTAGACA 59.778 45.833 19.57 0.00 41.83 3.41
1644 1660 4.567959 GTCTCAGTCGACTAAGACCTAGAC 59.432 50.000 31.01 21.66 41.65 2.59
1645 1661 4.467082 AGTCTCAGTCGACTAAGACCTAGA 59.533 45.833 35.12 18.43 41.23 2.43
1646 1662 4.761975 AGTCTCAGTCGACTAAGACCTAG 58.238 47.826 35.12 15.46 41.23 3.02
1647 1663 4.822685 AGTCTCAGTCGACTAAGACCTA 57.177 45.455 35.12 7.90 41.23 3.08
1648 1664 3.706600 AGTCTCAGTCGACTAAGACCT 57.293 47.619 35.12 23.42 41.23 3.85
1649 1665 3.181518 CGAAGTCTCAGTCGACTAAGACC 60.182 52.174 35.12 23.74 41.23 3.85
1650 1666 3.725600 GCGAAGTCTCAGTCGACTAAGAC 60.726 52.174 33.03 33.03 43.14 3.01
1651 1667 2.415857 GCGAAGTCTCAGTCGACTAAGA 59.584 50.000 19.57 17.01 43.14 2.10
1652 1668 2.776330 GCGAAGTCTCAGTCGACTAAG 58.224 52.381 19.57 14.47 43.14 2.18
1653 1669 1.128136 CGCGAAGTCTCAGTCGACTAA 59.872 52.381 19.57 1.94 43.14 2.24
1654 1670 0.720027 CGCGAAGTCTCAGTCGACTA 59.280 55.000 19.57 0.00 43.14 2.59
1655 1671 0.949588 TCGCGAAGTCTCAGTCGACT 60.950 55.000 13.58 13.58 45.73 4.18
1656 1672 0.110328 TTCGCGAAGTCTCAGTCGAC 60.110 55.000 19.38 7.70 39.64 4.20
1657 1673 0.166161 CTTCGCGAAGTCTCAGTCGA 59.834 55.000 34.97 4.60 39.64 4.20
1658 1674 2.631303 CTTCGCGAAGTCTCAGTCG 58.369 57.895 34.97 12.16 40.24 4.18
1667 1683 1.982223 CTTGACTGAGACTTCGCGAAG 59.018 52.381 39.55 39.55 43.79 3.79
1668 1684 1.930817 GCTTGACTGAGACTTCGCGAA 60.931 52.381 22.01 22.01 0.00 4.70
1669 1685 0.387367 GCTTGACTGAGACTTCGCGA 60.387 55.000 3.71 3.71 0.00 5.87
1670 1686 0.664466 TGCTTGACTGAGACTTCGCG 60.664 55.000 0.00 0.00 0.00 5.87
1671 1687 1.502231 TTGCTTGACTGAGACTTCGC 58.498 50.000 0.00 0.00 0.00 4.70
1672 1688 3.062763 ACATTGCTTGACTGAGACTTCG 58.937 45.455 0.00 0.00 0.00 3.79
1673 1689 5.233988 ACTACATTGCTTGACTGAGACTTC 58.766 41.667 0.00 0.00 0.00 3.01
1674 1690 5.220710 ACTACATTGCTTGACTGAGACTT 57.779 39.130 0.00 0.00 0.00 3.01
1675 1691 4.881019 ACTACATTGCTTGACTGAGACT 57.119 40.909 0.00 0.00 0.00 3.24
1676 1692 5.006165 GCATACTACATTGCTTGACTGAGAC 59.994 44.000 0.00 0.00 35.95 3.36
1677 1693 5.111989 GCATACTACATTGCTTGACTGAGA 58.888 41.667 0.00 0.00 35.95 3.27
1678 1694 4.872124 TGCATACTACATTGCTTGACTGAG 59.128 41.667 0.00 0.00 39.60 3.35
1679 1695 4.831107 TGCATACTACATTGCTTGACTGA 58.169 39.130 0.00 0.00 39.60 3.41
1680 1696 5.352293 TCTTGCATACTACATTGCTTGACTG 59.648 40.000 0.00 0.00 39.60 3.51
1681 1697 5.491070 TCTTGCATACTACATTGCTTGACT 58.509 37.500 0.00 0.00 39.60 3.41
1682 1698 5.801350 TCTTGCATACTACATTGCTTGAC 57.199 39.130 0.00 0.00 39.60 3.18
1683 1699 6.172630 TCTTCTTGCATACTACATTGCTTGA 58.827 36.000 0.00 0.00 39.60 3.02
1684 1700 6.426980 TCTTCTTGCATACTACATTGCTTG 57.573 37.500 0.00 0.00 39.60 4.01
1685 1701 7.452880 TTTCTTCTTGCATACTACATTGCTT 57.547 32.000 0.00 0.00 39.60 3.91
1686 1702 7.391554 TCTTTTCTTCTTGCATACTACATTGCT 59.608 33.333 0.00 0.00 39.60 3.91
1687 1703 7.530010 TCTTTTCTTCTTGCATACTACATTGC 58.470 34.615 0.00 0.00 39.33 3.56
1688 1704 9.897744 TTTCTTTTCTTCTTGCATACTACATTG 57.102 29.630 0.00 0.00 0.00 2.82
1690 1706 9.899226 GTTTTCTTTTCTTCTTGCATACTACAT 57.101 29.630 0.00 0.00 0.00 2.29
1691 1707 9.120538 AGTTTTCTTTTCTTCTTGCATACTACA 57.879 29.630 0.00 0.00 0.00 2.74
1692 1708 9.387123 CAGTTTTCTTTTCTTCTTGCATACTAC 57.613 33.333 0.00 0.00 0.00 2.73
1693 1709 9.337396 TCAGTTTTCTTTTCTTCTTGCATACTA 57.663 29.630 0.00 0.00 0.00 1.82
1694 1710 8.225603 TCAGTTTTCTTTTCTTCTTGCATACT 57.774 30.769 0.00 0.00 0.00 2.12
1695 1711 8.856490 TTCAGTTTTCTTTTCTTCTTGCATAC 57.144 30.769 0.00 0.00 0.00 2.39
1696 1712 9.868277 TTTTCAGTTTTCTTTTCTTCTTGCATA 57.132 25.926 0.00 0.00 0.00 3.14
1697 1713 8.776376 TTTTCAGTTTTCTTTTCTTCTTGCAT 57.224 26.923 0.00 0.00 0.00 3.96
1698 1714 8.600449 TTTTTCAGTTTTCTTTTCTTCTTGCA 57.400 26.923 0.00 0.00 0.00 4.08
1723 1739 9.615295 GCATTGAGATTTATGCAAACAATTTTT 57.385 25.926 0.00 0.00 44.99 1.94
1734 1750 6.976349 TGTTGATCTTGCATTGAGATTTATGC 59.024 34.615 1.03 0.00 45.66 3.14
1735 1751 8.403236 TCTGTTGATCTTGCATTGAGATTTATG 58.597 33.333 1.03 0.00 34.13 1.90
1736 1752 8.515695 TCTGTTGATCTTGCATTGAGATTTAT 57.484 30.769 1.03 0.00 34.13 1.40
1737 1753 7.926674 TCTGTTGATCTTGCATTGAGATTTA 57.073 32.000 1.03 0.00 34.13 1.40
1738 1754 6.829229 TCTGTTGATCTTGCATTGAGATTT 57.171 33.333 1.03 0.00 34.13 2.17
1739 1755 7.093902 ACAATCTGTTGATCTTGCATTGAGATT 60.094 33.333 1.03 0.00 38.71 2.40
1740 1756 6.377429 ACAATCTGTTGATCTTGCATTGAGAT 59.623 34.615 0.00 0.00 38.71 2.75
1741 1757 5.708697 ACAATCTGTTGATCTTGCATTGAGA 59.291 36.000 10.16 0.00 38.71 3.27
1742 1758 5.950883 ACAATCTGTTGATCTTGCATTGAG 58.049 37.500 10.16 0.00 38.71 3.02
1743 1759 5.970317 ACAATCTGTTGATCTTGCATTGA 57.030 34.783 10.16 0.00 38.71 2.57
1744 1760 6.849502 ACTACAATCTGTTGATCTTGCATTG 58.150 36.000 0.00 0.00 38.71 2.82
1745 1761 8.743085 ATACTACAATCTGTTGATCTTGCATT 57.257 30.769 0.00 0.00 38.71 3.56
1746 1762 7.170489 CGATACTACAATCTGTTGATCTTGCAT 59.830 37.037 0.00 0.00 38.71 3.96
1747 1763 6.476706 CGATACTACAATCTGTTGATCTTGCA 59.523 38.462 0.00 0.00 38.71 4.08
1748 1764 6.697455 TCGATACTACAATCTGTTGATCTTGC 59.303 38.462 0.00 0.00 38.71 4.01
1749 1765 7.918033 AGTCGATACTACAATCTGTTGATCTTG 59.082 37.037 0.00 0.00 38.71 3.02
1750 1766 7.918033 CAGTCGATACTACAATCTGTTGATCTT 59.082 37.037 0.00 0.00 34.62 2.40
1751 1767 7.283354 TCAGTCGATACTACAATCTGTTGATCT 59.717 37.037 0.00 0.00 34.62 2.75
1752 1768 7.418408 TCAGTCGATACTACAATCTGTTGATC 58.582 38.462 0.00 0.00 34.62 2.92
1753 1769 7.283354 TCTCAGTCGATACTACAATCTGTTGAT 59.717 37.037 0.00 0.00 34.62 2.57
1754 1770 6.598064 TCTCAGTCGATACTACAATCTGTTGA 59.402 38.462 0.00 0.00 34.62 3.18
1755 1771 6.689241 GTCTCAGTCGATACTACAATCTGTTG 59.311 42.308 0.00 0.00 36.13 3.33
1756 1772 6.600032 AGTCTCAGTCGATACTACAATCTGTT 59.400 38.462 0.00 0.00 33.48 3.16
1757 1773 6.116806 AGTCTCAGTCGATACTACAATCTGT 58.883 40.000 0.00 0.00 33.48 3.41
1758 1774 6.612247 AGTCTCAGTCGATACTACAATCTG 57.388 41.667 0.00 0.00 33.48 2.90
1759 1775 6.018588 CGAAGTCTCAGTCGATACTACAATCT 60.019 42.308 0.00 0.00 39.64 2.40
1760 1776 6.130723 CGAAGTCTCAGTCGATACTACAATC 58.869 44.000 0.00 0.00 39.64 2.67
1761 1777 5.504337 GCGAAGTCTCAGTCGATACTACAAT 60.504 44.000 0.00 0.00 39.64 2.71
1762 1778 4.201792 GCGAAGTCTCAGTCGATACTACAA 60.202 45.833 0.00 0.00 39.64 2.41
1763 1779 3.309138 GCGAAGTCTCAGTCGATACTACA 59.691 47.826 0.00 0.00 39.64 2.74
1764 1780 3.602038 CGCGAAGTCTCAGTCGATACTAC 60.602 52.174 0.00 0.00 39.64 2.73
1765 1781 2.538861 CGCGAAGTCTCAGTCGATACTA 59.461 50.000 0.00 0.00 39.64 1.82
1766 1782 1.328069 CGCGAAGTCTCAGTCGATACT 59.672 52.381 0.00 0.00 39.64 2.12
1767 1783 1.326852 TCGCGAAGTCTCAGTCGATAC 59.673 52.381 6.20 0.00 39.64 2.24
1768 1784 1.648504 TCGCGAAGTCTCAGTCGATA 58.351 50.000 6.20 0.00 39.64 2.92
1769 1785 0.803117 TTCGCGAAGTCTCAGTCGAT 59.197 50.000 19.38 0.00 39.64 3.59
1770 1786 0.166161 CTTCGCGAAGTCTCAGTCGA 59.834 55.000 34.97 4.60 39.64 4.20
1771 1787 2.631303 CTTCGCGAAGTCTCAGTCG 58.369 57.895 34.97 12.16 40.24 4.18
1780 1796 0.166161 TCGACTGAGACTTCGCGAAG 59.834 55.000 39.55 39.55 43.79 3.79
1781 1797 0.803117 ATCGACTGAGACTTCGCGAA 59.197 50.000 22.01 22.01 35.15 4.70
1782 1798 0.803117 AATCGACTGAGACTTCGCGA 59.197 50.000 3.71 3.71 35.15 5.87
1783 1799 0.910513 CAATCGACTGAGACTTCGCG 59.089 55.000 0.00 0.00 35.15 5.87
1784 1800 2.264109 TCAATCGACTGAGACTTCGC 57.736 50.000 0.00 0.00 35.15 4.70
1785 1801 5.769967 AAAATCAATCGACTGAGACTTCG 57.230 39.130 1.98 0.00 36.55 3.79
1786 1802 7.148573 TGCTAAAAATCAATCGACTGAGACTTC 60.149 37.037 1.98 0.00 0.00 3.01
1787 1803 6.650807 TGCTAAAAATCAATCGACTGAGACTT 59.349 34.615 1.98 0.00 0.00 3.01
1788 1804 6.166279 TGCTAAAAATCAATCGACTGAGACT 58.834 36.000 1.98 0.00 0.00 3.24
1789 1805 6.408858 TGCTAAAAATCAATCGACTGAGAC 57.591 37.500 1.98 0.00 0.00 3.36
1790 1806 7.433708 TTTGCTAAAAATCAATCGACTGAGA 57.566 32.000 1.98 0.00 0.00 3.27
1791 1807 6.250104 GCTTTGCTAAAAATCAATCGACTGAG 59.750 38.462 1.98 0.00 0.00 3.35
1792 1808 6.086222 GCTTTGCTAAAAATCAATCGACTGA 58.914 36.000 0.00 0.00 0.00 3.41
1793 1809 5.287035 GGCTTTGCTAAAAATCAATCGACTG 59.713 40.000 0.00 0.00 0.00 3.51
1794 1810 5.402398 GGCTTTGCTAAAAATCAATCGACT 58.598 37.500 0.00 0.00 0.00 4.18
1795 1811 4.262976 CGGCTTTGCTAAAAATCAATCGAC 59.737 41.667 0.00 0.00 0.00 4.20
1796 1812 4.083003 ACGGCTTTGCTAAAAATCAATCGA 60.083 37.500 0.00 0.00 0.00 3.59
1797 1813 4.165779 ACGGCTTTGCTAAAAATCAATCG 58.834 39.130 0.00 0.00 0.00 3.34
1798 1814 7.575332 TTAACGGCTTTGCTAAAAATCAATC 57.425 32.000 0.00 0.00 0.00 2.67
1799 1815 6.090763 GCTTAACGGCTTTGCTAAAAATCAAT 59.909 34.615 0.00 0.00 0.00 2.57
1800 1816 5.404066 GCTTAACGGCTTTGCTAAAAATCAA 59.596 36.000 0.00 0.00 0.00 2.57
1801 1817 4.920927 GCTTAACGGCTTTGCTAAAAATCA 59.079 37.500 0.00 0.00 0.00 2.57
1802 1818 5.161358 AGCTTAACGGCTTTGCTAAAAATC 58.839 37.500 0.00 0.00 39.86 2.17
1803 1819 5.134202 AGCTTAACGGCTTTGCTAAAAAT 57.866 34.783 0.00 0.00 39.86 1.82
1804 1820 4.577834 AGCTTAACGGCTTTGCTAAAAA 57.422 36.364 0.00 0.00 39.86 1.94
1805 1821 5.392595 CCATAGCTTAACGGCTTTGCTAAAA 60.393 40.000 0.00 0.00 42.97 1.52
1806 1822 4.095782 CCATAGCTTAACGGCTTTGCTAAA 59.904 41.667 0.00 0.00 42.97 1.85
1807 1823 3.625764 CCATAGCTTAACGGCTTTGCTAA 59.374 43.478 0.00 0.00 42.97 3.09
1808 1824 3.202906 CCATAGCTTAACGGCTTTGCTA 58.797 45.455 0.00 0.00 42.97 3.49
1809 1825 2.017049 CCATAGCTTAACGGCTTTGCT 58.983 47.619 0.00 0.00 42.97 3.91
1810 1826 1.743394 ACCATAGCTTAACGGCTTTGC 59.257 47.619 0.00 0.00 42.97 3.68
1811 1827 2.477863 GCACCATAGCTTAACGGCTTTG 60.478 50.000 0.00 0.00 42.97 2.77
1812 1828 1.743394 GCACCATAGCTTAACGGCTTT 59.257 47.619 0.00 0.00 42.97 3.51
1813 1829 1.065418 AGCACCATAGCTTAACGGCTT 60.065 47.619 0.00 0.00 43.70 4.35
1814 1830 0.541863 AGCACCATAGCTTAACGGCT 59.458 50.000 0.00 0.00 43.70 5.52
1815 1831 0.657840 CAGCACCATAGCTTAACGGC 59.342 55.000 0.00 0.00 43.70 5.68
1816 1832 1.134521 TCCAGCACCATAGCTTAACGG 60.135 52.381 0.00 0.00 43.70 4.44
1817 1833 2.309528 TCCAGCACCATAGCTTAACG 57.690 50.000 0.00 0.00 43.70 3.18
1818 1834 5.239525 CCTTTATCCAGCACCATAGCTTAAC 59.760 44.000 0.00 0.00 43.70 2.01
1819 1835 5.104109 ACCTTTATCCAGCACCATAGCTTAA 60.104 40.000 0.00 0.00 43.70 1.85
1820 1836 4.412199 ACCTTTATCCAGCACCATAGCTTA 59.588 41.667 0.00 0.00 43.70 3.09
1821 1837 3.203040 ACCTTTATCCAGCACCATAGCTT 59.797 43.478 0.00 0.00 43.70 3.74
1823 1839 3.214696 ACCTTTATCCAGCACCATAGC 57.785 47.619 0.00 0.00 0.00 2.97
1824 1840 7.823745 AAAATACCTTTATCCAGCACCATAG 57.176 36.000 0.00 0.00 0.00 2.23
1825 1841 8.275758 TGTAAAATACCTTTATCCAGCACCATA 58.724 33.333 0.00 0.00 32.14 2.74
1826 1842 7.122715 TGTAAAATACCTTTATCCAGCACCAT 58.877 34.615 0.00 0.00 32.14 3.55
1827 1843 6.486056 TGTAAAATACCTTTATCCAGCACCA 58.514 36.000 0.00 0.00 32.14 4.17
1881 1899 1.868498 GATCCGTCGACAAAACCAACA 59.132 47.619 17.16 0.00 0.00 3.33
1882 1900 1.868498 TGATCCGTCGACAAAACCAAC 59.132 47.619 17.16 0.00 0.00 3.77
1883 1901 2.242047 TGATCCGTCGACAAAACCAA 57.758 45.000 17.16 0.00 0.00 3.67
1884 1902 2.242047 TTGATCCGTCGACAAAACCA 57.758 45.000 17.16 3.56 0.00 3.67
1885 1903 3.187637 TGATTTGATCCGTCGACAAAACC 59.812 43.478 17.16 5.54 37.14 3.27
1886 1904 4.148891 GTGATTTGATCCGTCGACAAAAC 58.851 43.478 17.16 7.47 37.14 2.43
1890 1908 1.273886 TGGTGATTTGATCCGTCGACA 59.726 47.619 17.16 0.00 0.00 4.35
1891 1909 1.927174 CTGGTGATTTGATCCGTCGAC 59.073 52.381 5.18 5.18 0.00 4.20
1895 1913 1.065418 GGTCCTGGTGATTTGATCCGT 60.065 52.381 0.00 0.00 0.00 4.69
1936 1957 0.178992 TAGGCAGCTTGCTTGGTTGT 60.179 50.000 7.85 0.00 44.28 3.32
1972 1993 2.821378 TGGCTATACACACGTACACTGT 59.179 45.455 0.00 0.00 0.00 3.55
2002 2025 1.369692 CAAGCCACCCTCACGTACA 59.630 57.895 0.00 0.00 0.00 2.90
2010 2033 0.549169 TTACTAGCCCAAGCCACCCT 60.549 55.000 0.00 0.00 41.25 4.34
2011 2034 0.393944 GTTACTAGCCCAAGCCACCC 60.394 60.000 0.00 0.00 41.25 4.61
2012 2035 0.743345 CGTTACTAGCCCAAGCCACC 60.743 60.000 0.00 0.00 41.25 4.61
2043 2066 1.740585 AGAATCCGCCTAGATCGATCG 59.259 52.381 19.33 9.36 0.00 3.69
2044 2067 3.013921 AGAGAATCCGCCTAGATCGATC 58.986 50.000 17.91 17.91 33.66 3.69
2053 2077 1.765230 AGTTACGAGAGAATCCGCCT 58.235 50.000 0.00 0.00 33.66 5.52
2062 2086 2.876091 TCCATTCGCAAGTTACGAGAG 58.124 47.619 0.00 0.00 41.18 3.20
2086 2111 5.755813 CCTTTAGCCATCAAAATCGATCAG 58.244 41.667 0.00 0.00 0.00 2.90
2087 2112 4.036734 GCCTTTAGCCATCAAAATCGATCA 59.963 41.667 0.00 0.00 34.35 2.92
2088 2113 4.540824 GCCTTTAGCCATCAAAATCGATC 58.459 43.478 0.00 0.00 34.35 3.69
2089 2114 4.574599 GCCTTTAGCCATCAAAATCGAT 57.425 40.909 0.00 0.00 34.35 3.59
2126 2151 7.936950 AGAAAAGAGAAAAGCAATACAAAGC 57.063 32.000 0.00 0.00 0.00 3.51
2127 2152 9.305925 ACAAGAAAAGAGAAAAGCAATACAAAG 57.694 29.630 0.00 0.00 0.00 2.77
2128 2153 9.086336 CACAAGAAAAGAGAAAAGCAATACAAA 57.914 29.630 0.00 0.00 0.00 2.83
2130 2155 7.995289 TCACAAGAAAAGAGAAAAGCAATACA 58.005 30.769 0.00 0.00 0.00 2.29
2131 2156 9.468532 AATCACAAGAAAAGAGAAAAGCAATAC 57.531 29.630 0.00 0.00 0.00 1.89
2133 2158 9.468532 GTAATCACAAGAAAAGAGAAAAGCAAT 57.531 29.630 0.00 0.00 0.00 3.56
2134 2159 8.465999 TGTAATCACAAGAAAAGAGAAAAGCAA 58.534 29.630 0.00 0.00 0.00 3.91
2135 2160 7.995289 TGTAATCACAAGAAAAGAGAAAAGCA 58.005 30.769 0.00 0.00 0.00 3.91
2136 2161 8.856490 TTGTAATCACAAGAAAAGAGAAAAGC 57.144 30.769 0.00 0.00 39.75 3.51
2152 2177 4.713321 TGTACTCCTACCCCTTGTAATCAC 59.287 45.833 0.00 0.00 0.00 3.06
2155 2180 3.703052 CGTGTACTCCTACCCCTTGTAAT 59.297 47.826 0.00 0.00 0.00 1.89
2215 2240 1.414181 TGCTCCTAGGCTATGTTCAGC 59.586 52.381 2.96 5.87 41.02 4.26
2238 2263 2.345124 ACAGGTAGTAGCCGACTAGG 57.655 55.000 0.00 0.00 41.47 3.02
2262 2287 5.704515 TGTATTAGCATCCGAGTAGTACTCC 59.295 44.000 21.92 9.51 42.12 3.85
2337 2362 0.600057 GAGGACGTCGTGTTTAGGGT 59.400 55.000 16.63 0.00 0.00 4.34
2339 2364 3.011513 CGAGGACGTCGTGTTTAGG 57.988 57.895 16.63 0.00 44.20 2.69
2358 2383 1.133025 CATTTGGGATCCAAGTCGCAC 59.867 52.381 15.23 0.00 44.84 5.34
2362 2387 1.401905 GTCGCATTTGGGATCCAAGTC 59.598 52.381 15.23 0.00 44.84 3.01
2365 2390 1.462616 CAGTCGCATTTGGGATCCAA 58.537 50.000 15.23 0.00 42.29 3.53
2370 2395 0.537143 AACAGCAGTCGCATTTGGGA 60.537 50.000 0.00 0.00 42.27 4.37
2386 2411 6.097356 CCAAGAGTAAAGCATACGAGTAACA 58.903 40.000 0.00 0.00 0.00 2.41
2398 2423 5.107337 GCAAAAGAAATGCCAAGAGTAAAGC 60.107 40.000 0.00 0.00 37.85 3.51


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

AutoCloner maintained by Alex Coulton.