Multiple sequence alignment - TraesCS6B01G079100

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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 TraesCS6B01G079100 chr6B 100.000 2480 0 0 1 2480 55690967 55693446 0.000000e+00 4580.0
1 TraesCS6B01G079100 chr6B 96.875 736 19 1 851 1582 658660263 658659528 0.000000e+00 1229.0
2 TraesCS6B01G079100 chr6B 86.916 107 7 3 1746 1850 613614127 613614026 2.020000e-21 113.0
3 TraesCS6B01G079100 chr5D 96.009 852 31 3 1 850 515097149 515096299 0.000000e+00 1382.0
4 TraesCS6B01G079100 chr5D 87.534 369 46 0 1037 1405 61857692 61858060 6.340000e-116 427.0
5 TraesCS6B01G079100 chr5D 87.543 289 26 4 1120 1407 61849456 61849735 2.380000e-85 326.0
6 TraesCS6B01G079100 chr3D 95.780 853 34 2 1 851 569838161 569837309 0.000000e+00 1375.0
7 TraesCS6B01G079100 chr3D 85.659 258 36 1 1037 1293 568344661 568344404 1.130000e-68 270.0
8 TraesCS6B01G079100 chr7D 95.540 852 36 2 1 850 636817192 636818043 0.000000e+00 1362.0
9 TraesCS6B01G079100 chr2A 95.417 851 36 3 3 851 17214027 17213178 0.000000e+00 1352.0
10 TraesCS6B01G079100 chr2A 95.316 854 36 3 1 851 104997121 104997973 0.000000e+00 1352.0
11 TraesCS6B01G079100 chr2A 95.210 856 36 4 1 852 98602177 98603031 0.000000e+00 1349.0
12 TraesCS6B01G079100 chr2A 94.614 854 41 5 1 850 720558646 720557794 0.000000e+00 1317.0
13 TraesCS6B01G079100 chr1A 95.316 854 33 5 3 851 575874759 575873908 0.000000e+00 1349.0
14 TraesCS6B01G079100 chr4A 94.988 858 38 4 1 854 641518370 641519226 0.000000e+00 1341.0
15 TraesCS6B01G079100 chr4A 93.377 755 44 4 860 1610 741807351 741808103 0.000000e+00 1112.0
16 TraesCS6B01G079100 chr4A 94.972 179 7 2 1431 1609 294253721 294253897 1.880000e-71 279.0
17 TraesCS6B01G079100 chr4A 87.736 106 8 2 1746 1850 676923077 676923178 4.330000e-23 119.0
18 TraesCS6B01G079100 chr7B 96.475 766 20 4 851 1609 593284430 593285195 0.000000e+00 1258.0
19 TraesCS6B01G079100 chr7B 84.865 370 56 0 1038 1407 725264210 725264579 8.380000e-100 374.0
20 TraesCS6B01G079100 chr3B 93.590 624 39 1 1857 2480 561636822 561637444 0.000000e+00 929.0
21 TraesCS6B01G079100 chr2B 93.269 624 42 0 1857 2480 800553232 800553855 0.000000e+00 920.0
22 TraesCS6B01G079100 chr2B 82.508 606 106 0 1857 2462 165255396 165254791 1.310000e-147 532.0
23 TraesCS6B01G079100 chr2B 92.973 185 12 1 1425 1609 794657839 794658022 4.070000e-68 268.0
24 TraesCS6B01G079100 chr2B 92.778 180 13 0 2301 2480 636488324 636488145 6.800000e-66 261.0
25 TraesCS6B01G079100 chr2B 100.000 31 0 0 2290 2320 636488339 636488369 9.580000e-05 58.4
26 TraesCS6B01G079100 chr1B 87.900 562 44 15 853 1410 687721492 687720951 7.480000e-180 640.0
27 TraesCS6B01G079100 chr1D 87.114 551 55 13 865 1410 494474820 494474281 5.860000e-171 610.0
28 TraesCS6B01G079100 chrUn 81.022 137 21 5 1475 1609 195765349 195765482 1.210000e-18 104.0
29 TraesCS6B01G079100 chrUn 81.022 137 21 5 1475 1609 195766473 195766606 1.210000e-18 104.0
30 TraesCS6B01G079100 chrUn 81.022 137 21 5 1475 1609 195767035 195767168 1.210000e-18 104.0
31 TraesCS6B01G079100 chrUn 81.022 137 21 5 1475 1609 195767597 195767730 1.210000e-18 104.0


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 TraesCS6B01G079100 chr6B 55690967 55693446 2479 False 4580 4580 100.000 1 2480 1 chr6B.!!$F1 2479
1 TraesCS6B01G079100 chr6B 658659528 658660263 735 True 1229 1229 96.875 851 1582 1 chr6B.!!$R2 731
2 TraesCS6B01G079100 chr5D 515096299 515097149 850 True 1382 1382 96.009 1 850 1 chr5D.!!$R1 849
3 TraesCS6B01G079100 chr3D 569837309 569838161 852 True 1375 1375 95.780 1 851 1 chr3D.!!$R2 850
4 TraesCS6B01G079100 chr7D 636817192 636818043 851 False 1362 1362 95.540 1 850 1 chr7D.!!$F1 849
5 TraesCS6B01G079100 chr2A 17213178 17214027 849 True 1352 1352 95.417 3 851 1 chr2A.!!$R1 848
6 TraesCS6B01G079100 chr2A 104997121 104997973 852 False 1352 1352 95.316 1 851 1 chr2A.!!$F2 850
7 TraesCS6B01G079100 chr2A 98602177 98603031 854 False 1349 1349 95.210 1 852 1 chr2A.!!$F1 851
8 TraesCS6B01G079100 chr2A 720557794 720558646 852 True 1317 1317 94.614 1 850 1 chr2A.!!$R2 849
9 TraesCS6B01G079100 chr1A 575873908 575874759 851 True 1349 1349 95.316 3 851 1 chr1A.!!$R1 848
10 TraesCS6B01G079100 chr4A 641518370 641519226 856 False 1341 1341 94.988 1 854 1 chr4A.!!$F2 853
11 TraesCS6B01G079100 chr4A 741807351 741808103 752 False 1112 1112 93.377 860 1610 1 chr4A.!!$F4 750
12 TraesCS6B01G079100 chr7B 593284430 593285195 765 False 1258 1258 96.475 851 1609 1 chr7B.!!$F1 758
13 TraesCS6B01G079100 chr3B 561636822 561637444 622 False 929 929 93.590 1857 2480 1 chr3B.!!$F1 623
14 TraesCS6B01G079100 chr2B 800553232 800553855 623 False 920 920 93.269 1857 2480 1 chr2B.!!$F3 623
15 TraesCS6B01G079100 chr2B 165254791 165255396 605 True 532 532 82.508 1857 2462 1 chr2B.!!$R1 605
16 TraesCS6B01G079100 chr1B 687720951 687721492 541 True 640 640 87.900 853 1410 1 chr1B.!!$R1 557
17 TraesCS6B01G079100 chr1D 494474281 494474820 539 True 610 610 87.114 865 1410 1 chr1D.!!$R1 545

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
876 884 0.318441 CTATGGACATGGATCGCCGT 59.682 55.0 0.0 0.0 36.79 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 1896 0.033796 CCATGAAGTGTGCCCTGGAT 60.034 55.0 0.0 0.0 0.0 3.41 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
40 41 0.403271 AGTTCTTGCATGCTCCCACT 59.597 50.000 20.33 12.67 0.00 4.00
44 45 2.318908 TCTTGCATGCTCCCACTTTTT 58.681 42.857 20.33 0.00 0.00 1.94
64 65 2.497138 TCACATTGGACAGCAGTGAAG 58.503 47.619 0.00 0.00 36.39 3.02
153 154 2.303890 TGGTGAGTGCATTCTCTGATGT 59.696 45.455 10.82 0.00 35.68 3.06
261 263 5.178623 CACGGAAACAAGCTACTGTATCAAA 59.821 40.000 0.00 0.00 0.00 2.69
283 285 8.097038 TCAAAATCAAGTACAGAAGCTGAGTAT 58.903 33.333 0.82 0.00 35.18 2.12
337 339 6.325028 TGATATGGGTTCAAACCTTGTTGAAA 59.675 34.615 11.52 0.00 46.28 2.69
389 391 4.452795 CACGGTTGTGGTGTGATAACATTA 59.547 41.667 0.00 0.00 42.59 1.90
397 399 4.153296 TGGTGTGATAACATTAGTGCAACG 59.847 41.667 0.00 0.00 45.86 4.10
538 540 2.622942 TCAAGTTGCAGATGGTTTCACC 59.377 45.455 0.00 0.00 39.22 4.02
554 556 3.737559 TCACCAAAGCCTTATCATGGT 57.262 42.857 0.00 0.00 44.95 3.55
682 689 1.134640 ACTCTTGGTGTTGCGTGTGTA 60.135 47.619 0.00 0.00 0.00 2.90
684 691 2.139917 TCTTGGTGTTGCGTGTGTATC 58.860 47.619 0.00 0.00 0.00 2.24
813 821 7.039270 CCTATGGCTATATATAACACGCAACA 58.961 38.462 4.62 0.00 0.00 3.33
827 835 1.671742 CAACACGTCCCTGCTAGGT 59.328 57.895 0.00 0.00 31.93 3.08
832 840 2.304092 CACGTCCCTGCTAGGTATACA 58.696 52.381 5.01 0.00 31.93 2.29
858 866 5.752650 TCAAGCCATCTTTCAGAATCATCT 58.247 37.500 0.00 0.00 35.88 2.90
876 884 0.318441 CTATGGACATGGATCGCCGT 59.682 55.000 0.00 0.00 36.79 5.68
980 1020 2.472695 AGCAACCGAGTCATAGCAAA 57.527 45.000 0.00 0.00 0.00 3.68
1029 1079 1.058270 CCAATCGATCGATCATTCGCG 59.942 52.381 29.48 10.62 45.10 5.87
1177 1230 2.605601 TGCTGCTCCTCCTGCTGA 60.606 61.111 0.00 0.00 0.00 4.26
1419 1475 1.566231 CTCCCCACCCTTTTCATAGCT 59.434 52.381 0.00 0.00 0.00 3.32
1623 1683 3.315140 TGACCCCGCGTCATCCAA 61.315 61.111 4.92 0.00 46.80 3.53
1624 1684 2.046700 GACCCCGCGTCATCCAAA 60.047 61.111 4.92 0.00 41.54 3.28
1625 1685 2.046314 ACCCCGCGTCATCCAAAG 60.046 61.111 4.92 0.00 0.00 2.77
1626 1686 2.267642 CCCCGCGTCATCCAAAGA 59.732 61.111 4.92 0.00 0.00 2.52
1627 1687 1.376683 CCCCGCGTCATCCAAAGAA 60.377 57.895 4.92 0.00 0.00 2.52
1628 1688 1.369091 CCCCGCGTCATCCAAAGAAG 61.369 60.000 4.92 0.00 0.00 2.85
1629 1689 1.425428 CCGCGTCATCCAAAGAAGC 59.575 57.895 4.92 0.00 37.18 3.86
1630 1690 1.425428 CGCGTCATCCAAAGAAGCC 59.575 57.895 0.00 0.00 37.22 4.35
1631 1691 1.298157 CGCGTCATCCAAAGAAGCCA 61.298 55.000 0.00 0.00 37.22 4.75
1632 1692 0.449388 GCGTCATCCAAAGAAGCCAG 59.551 55.000 0.00 0.00 34.99 4.85
1633 1693 0.449388 CGTCATCCAAAGAAGCCAGC 59.551 55.000 0.00 0.00 0.00 4.85
1634 1694 1.538047 GTCATCCAAAGAAGCCAGCA 58.462 50.000 0.00 0.00 0.00 4.41
1635 1695 1.200948 GTCATCCAAAGAAGCCAGCAC 59.799 52.381 0.00 0.00 0.00 4.40
1636 1696 0.169672 CATCCAAAGAAGCCAGCACG 59.830 55.000 0.00 0.00 0.00 5.34
1637 1697 1.589716 ATCCAAAGAAGCCAGCACGC 61.590 55.000 0.00 0.00 0.00 5.34
1638 1698 2.256461 CAAAGAAGCCAGCACGCC 59.744 61.111 0.00 0.00 0.00 5.68
1639 1699 2.203337 AAAGAAGCCAGCACGCCA 60.203 55.556 0.00 0.00 0.00 5.69
1640 1700 2.555547 AAAGAAGCCAGCACGCCAC 61.556 57.895 0.00 0.00 0.00 5.01
1641 1701 3.772853 AAGAAGCCAGCACGCCACA 62.773 57.895 0.00 0.00 0.00 4.17
1642 1702 3.730761 GAAGCCAGCACGCCACAG 61.731 66.667 0.00 0.00 0.00 3.66
1653 1713 3.353836 GCCACAGCGCGGAAGAAA 61.354 61.111 16.26 0.00 0.00 2.52
1654 1714 2.690778 GCCACAGCGCGGAAGAAAT 61.691 57.895 16.26 0.00 0.00 2.17
1655 1715 1.425428 CCACAGCGCGGAAGAAATC 59.575 57.895 16.26 0.00 0.00 2.17
1656 1716 1.021390 CCACAGCGCGGAAGAAATCT 61.021 55.000 16.26 0.00 0.00 2.40
1657 1717 0.095935 CACAGCGCGGAAGAAATCTG 59.904 55.000 16.26 6.39 37.49 2.90
1658 1718 0.320771 ACAGCGCGGAAGAAATCTGT 60.321 50.000 16.26 7.11 36.73 3.41
1659 1719 0.798776 CAGCGCGGAAGAAATCTGTT 59.201 50.000 8.83 0.00 36.73 3.16
1660 1720 0.798776 AGCGCGGAAGAAATCTGTTG 59.201 50.000 8.83 0.00 36.73 3.33
1661 1721 0.794605 GCGCGGAAGAAATCTGTTGC 60.795 55.000 8.83 0.00 36.73 4.17
1662 1722 0.519175 CGCGGAAGAAATCTGTTGCG 60.519 55.000 0.00 8.38 41.70 4.85
1663 1723 0.517316 GCGGAAGAAATCTGTTGCGT 59.483 50.000 0.00 0.00 41.00 5.24
1664 1724 1.725931 GCGGAAGAAATCTGTTGCGTG 60.726 52.381 0.00 0.00 41.00 5.34
1665 1725 1.531149 CGGAAGAAATCTGTTGCGTGT 59.469 47.619 0.00 0.00 35.35 4.49
1666 1726 2.032030 CGGAAGAAATCTGTTGCGTGTT 60.032 45.455 0.00 0.00 35.35 3.32
1667 1727 3.185594 CGGAAGAAATCTGTTGCGTGTTA 59.814 43.478 0.00 0.00 35.35 2.41
1668 1728 4.142902 CGGAAGAAATCTGTTGCGTGTTAT 60.143 41.667 0.00 0.00 35.35 1.89
1669 1729 5.324697 GGAAGAAATCTGTTGCGTGTTATC 58.675 41.667 0.00 0.00 0.00 1.75
1670 1730 5.106712 GGAAGAAATCTGTTGCGTGTTATCA 60.107 40.000 0.00 0.00 0.00 2.15
1671 1731 5.940192 AGAAATCTGTTGCGTGTTATCAA 57.060 34.783 0.00 0.00 0.00 2.57
1672 1732 6.312399 AGAAATCTGTTGCGTGTTATCAAA 57.688 33.333 0.00 0.00 0.00 2.69
1673 1733 6.734137 AGAAATCTGTTGCGTGTTATCAAAA 58.266 32.000 0.00 0.00 0.00 2.44
1674 1734 7.199766 AGAAATCTGTTGCGTGTTATCAAAAA 58.800 30.769 0.00 0.00 0.00 1.94
1675 1735 7.867403 AGAAATCTGTTGCGTGTTATCAAAAAT 59.133 29.630 0.00 0.00 0.00 1.82
1676 1736 7.566858 AATCTGTTGCGTGTTATCAAAAATC 57.433 32.000 0.00 0.00 0.00 2.17
1677 1737 6.066054 TCTGTTGCGTGTTATCAAAAATCA 57.934 33.333 0.00 0.00 0.00 2.57
1678 1738 6.499172 TCTGTTGCGTGTTATCAAAAATCAA 58.501 32.000 0.00 0.00 0.00 2.57
1679 1739 6.975197 TCTGTTGCGTGTTATCAAAAATCAAA 59.025 30.769 0.00 0.00 0.00 2.69
1680 1740 7.489435 TCTGTTGCGTGTTATCAAAAATCAAAA 59.511 29.630 0.00 0.00 0.00 2.44
1681 1741 7.963981 TGTTGCGTGTTATCAAAAATCAAAAA 58.036 26.923 0.00 0.00 0.00 1.94
1682 1742 8.113062 TGTTGCGTGTTATCAAAAATCAAAAAG 58.887 29.630 0.00 0.00 0.00 2.27
1683 1743 7.993821 TGCGTGTTATCAAAAATCAAAAAGA 57.006 28.000 0.00 0.00 0.00 2.52
1684 1744 8.586570 TGCGTGTTATCAAAAATCAAAAAGAT 57.413 26.923 0.00 0.00 39.09 2.40
1686 1746 9.305110 GCGTGTTATCAAAAATCAAAAAGATTG 57.695 29.630 0.00 0.00 46.09 2.67
1699 1759 8.812513 ATCAAAAAGATTGTATGAGATGGTCA 57.187 30.769 0.00 0.00 34.35 4.02
1700 1760 8.634335 TCAAAAAGATTGTATGAGATGGTCAA 57.366 30.769 0.00 0.00 39.19 3.18
1701 1761 9.246670 TCAAAAAGATTGTATGAGATGGTCAAT 57.753 29.630 0.00 0.00 39.19 2.57
1705 1765 9.512588 AAAGATTGTATGAGATGGTCAATATCC 57.487 33.333 0.00 0.00 39.19 2.59
1706 1766 8.211030 AGATTGTATGAGATGGTCAATATCCA 57.789 34.615 0.00 0.00 39.19 3.41
1707 1767 8.833734 AGATTGTATGAGATGGTCAATATCCAT 58.166 33.333 0.00 0.00 46.78 3.41
1708 1768 9.458727 GATTGTATGAGATGGTCAATATCCATT 57.541 33.333 0.00 0.00 44.52 3.16
1709 1769 9.818270 ATTGTATGAGATGGTCAATATCCATTT 57.182 29.630 0.00 0.00 44.52 2.32
1710 1770 9.645128 TTGTATGAGATGGTCAATATCCATTTT 57.355 29.630 0.00 0.00 44.52 1.82
1711 1771 9.288576 TGTATGAGATGGTCAATATCCATTTTC 57.711 33.333 0.00 0.00 44.52 2.29
1712 1772 9.288576 GTATGAGATGGTCAATATCCATTTTCA 57.711 33.333 12.06 12.06 44.52 2.69
1713 1773 8.771521 ATGAGATGGTCAATATCCATTTTCAA 57.228 30.769 13.02 3.36 44.52 2.69
1714 1774 8.592529 TGAGATGGTCAATATCCATTTTCAAA 57.407 30.769 0.00 0.00 44.52 2.69
1715 1775 9.033711 TGAGATGGTCAATATCCATTTTCAAAA 57.966 29.630 0.00 0.00 44.52 2.44
1716 1776 9.874205 GAGATGGTCAATATCCATTTTCAAAAA 57.126 29.630 0.00 0.00 44.52 1.94
1717 1777 9.880157 AGATGGTCAATATCCATTTTCAAAAAG 57.120 29.630 0.00 0.00 44.52 2.27
1718 1778 7.903995 TGGTCAATATCCATTTTCAAAAAGC 57.096 32.000 0.00 0.00 0.00 3.51
1719 1779 6.878389 TGGTCAATATCCATTTTCAAAAAGCC 59.122 34.615 0.00 0.00 0.00 4.35
1720 1780 6.316140 GGTCAATATCCATTTTCAAAAAGCCC 59.684 38.462 0.00 0.00 0.00 5.19
1721 1781 6.316140 GTCAATATCCATTTTCAAAAAGCCCC 59.684 38.462 0.00 0.00 0.00 5.80
1722 1782 6.013032 TCAATATCCATTTTCAAAAAGCCCCA 60.013 34.615 0.00 0.00 0.00 4.96
1723 1783 4.720775 ATCCATTTTCAAAAAGCCCCAA 57.279 36.364 0.00 0.00 0.00 4.12
1724 1784 4.510167 TCCATTTTCAAAAAGCCCCAAA 57.490 36.364 0.00 0.00 0.00 3.28
1725 1785 5.059134 TCCATTTTCAAAAAGCCCCAAAT 57.941 34.783 0.00 0.00 0.00 2.32
1726 1786 6.192970 TCCATTTTCAAAAAGCCCCAAATA 57.807 33.333 0.00 0.00 0.00 1.40
1727 1787 6.605119 TCCATTTTCAAAAAGCCCCAAATAA 58.395 32.000 0.00 0.00 0.00 1.40
1728 1788 7.062957 TCCATTTTCAAAAAGCCCCAAATAAA 58.937 30.769 0.00 0.00 0.00 1.40
1729 1789 7.561356 TCCATTTTCAAAAAGCCCCAAATAAAA 59.439 29.630 0.00 0.00 0.00 1.52
1730 1790 8.200120 CCATTTTCAAAAAGCCCCAAATAAAAA 58.800 29.630 0.00 0.00 0.00 1.94
1745 1805 3.042560 AAAAACCAGCAGCTCGCC 58.957 55.556 0.00 0.00 44.04 5.54
1746 1806 1.827789 AAAAACCAGCAGCTCGCCA 60.828 52.632 0.00 0.00 44.04 5.69
1747 1807 1.181098 AAAAACCAGCAGCTCGCCAT 61.181 50.000 0.00 0.00 44.04 4.40
1748 1808 1.589716 AAAACCAGCAGCTCGCCATC 61.590 55.000 0.00 0.00 44.04 3.51
1749 1809 2.753009 AAACCAGCAGCTCGCCATCA 62.753 55.000 0.00 0.00 44.04 3.07
1750 1810 2.203167 CCAGCAGCTCGCCATCAT 60.203 61.111 0.00 0.00 44.04 2.45
1751 1811 2.252346 CCAGCAGCTCGCCATCATC 61.252 63.158 0.00 0.00 44.04 2.92
1752 1812 1.523032 CAGCAGCTCGCCATCATCA 60.523 57.895 0.00 0.00 44.04 3.07
1753 1813 1.523258 AGCAGCTCGCCATCATCAC 60.523 57.895 0.00 0.00 44.04 3.06
1754 1814 1.816679 GCAGCTCGCCATCATCACA 60.817 57.895 0.00 0.00 32.94 3.58
1755 1815 1.371337 GCAGCTCGCCATCATCACAA 61.371 55.000 0.00 0.00 32.94 3.33
1756 1816 1.306148 CAGCTCGCCATCATCACAAT 58.694 50.000 0.00 0.00 0.00 2.71
1757 1817 1.674441 CAGCTCGCCATCATCACAATT 59.326 47.619 0.00 0.00 0.00 2.32
1758 1818 2.098607 CAGCTCGCCATCATCACAATTT 59.901 45.455 0.00 0.00 0.00 1.82
1759 1819 2.098607 AGCTCGCCATCATCACAATTTG 59.901 45.455 0.00 0.00 0.00 2.32
1760 1820 2.097954 GCTCGCCATCATCACAATTTGA 59.902 45.455 2.79 0.00 39.11 2.69
1761 1821 3.427909 GCTCGCCATCATCACAATTTGAA 60.428 43.478 2.79 0.00 37.92 2.69
1762 1822 4.735578 GCTCGCCATCATCACAATTTGAAT 60.736 41.667 2.79 0.00 37.92 2.57
1763 1823 4.674475 TCGCCATCATCACAATTTGAATG 58.326 39.130 2.79 6.77 37.92 2.67
1764 1824 4.158209 TCGCCATCATCACAATTTGAATGT 59.842 37.500 2.79 0.00 37.92 2.71
1765 1825 4.865925 CGCCATCATCACAATTTGAATGTT 59.134 37.500 2.79 0.00 37.92 2.71
1766 1826 5.005012 CGCCATCATCACAATTTGAATGTTC 59.995 40.000 2.79 0.00 37.92 3.18
1767 1827 5.870433 GCCATCATCACAATTTGAATGTTCA 59.130 36.000 2.79 0.00 37.92 3.18
1768 1828 6.035650 GCCATCATCACAATTTGAATGTTCAG 59.964 38.462 2.79 0.88 37.92 3.02
1769 1829 6.533723 CCATCATCACAATTTGAATGTTCAGG 59.466 38.462 2.79 4.87 37.92 3.86
1770 1830 6.653526 TCATCACAATTTGAATGTTCAGGT 57.346 33.333 2.79 0.00 37.92 4.00
1771 1831 6.680810 TCATCACAATTTGAATGTTCAGGTC 58.319 36.000 2.79 0.00 37.92 3.85
1772 1832 6.264970 TCATCACAATTTGAATGTTCAGGTCA 59.735 34.615 2.79 0.00 37.92 4.02
1773 1833 6.075762 TCACAATTTGAATGTTCAGGTCAG 57.924 37.500 2.79 0.00 38.61 3.51
1774 1834 4.682860 CACAATTTGAATGTTCAGGTCAGC 59.317 41.667 2.79 0.00 38.61 4.26
1775 1835 4.341806 ACAATTTGAATGTTCAGGTCAGCA 59.658 37.500 2.79 0.00 38.61 4.41
1776 1836 5.163426 ACAATTTGAATGTTCAGGTCAGCAA 60.163 36.000 2.79 0.00 38.61 3.91
1777 1837 4.572985 TTTGAATGTTCAGGTCAGCAAG 57.427 40.909 0.00 0.00 38.61 4.01
1778 1838 3.213206 TGAATGTTCAGGTCAGCAAGT 57.787 42.857 0.00 0.00 32.50 3.16
1779 1839 3.554934 TGAATGTTCAGGTCAGCAAGTT 58.445 40.909 0.00 0.00 32.50 2.66
1780 1840 4.713553 TGAATGTTCAGGTCAGCAAGTTA 58.286 39.130 0.00 0.00 32.50 2.24
1781 1841 4.756642 TGAATGTTCAGGTCAGCAAGTTAG 59.243 41.667 0.00 0.00 32.50 2.34
1782 1842 3.126001 TGTTCAGGTCAGCAAGTTAGG 57.874 47.619 0.00 0.00 0.00 2.69
1783 1843 2.438021 TGTTCAGGTCAGCAAGTTAGGT 59.562 45.455 0.00 0.00 0.00 3.08
1784 1844 2.808543 GTTCAGGTCAGCAAGTTAGGTG 59.191 50.000 0.00 0.00 38.31 4.00
1785 1845 2.047061 TCAGGTCAGCAAGTTAGGTGT 58.953 47.619 0.00 0.00 38.15 4.16
1786 1846 2.037251 TCAGGTCAGCAAGTTAGGTGTC 59.963 50.000 0.00 0.00 38.15 3.67
1787 1847 2.047061 AGGTCAGCAAGTTAGGTGTCA 58.953 47.619 0.00 0.00 38.15 3.58
1788 1848 2.438021 AGGTCAGCAAGTTAGGTGTCAA 59.562 45.455 0.00 0.00 38.15 3.18
1789 1849 2.808543 GGTCAGCAAGTTAGGTGTCAAG 59.191 50.000 0.00 0.00 38.15 3.02
1790 1850 3.494398 GGTCAGCAAGTTAGGTGTCAAGA 60.494 47.826 0.00 0.00 38.15 3.02
1791 1851 3.743396 GTCAGCAAGTTAGGTGTCAAGAG 59.257 47.826 0.00 0.00 38.15 2.85
1792 1852 3.388024 TCAGCAAGTTAGGTGTCAAGAGT 59.612 43.478 0.00 0.00 38.15 3.24
1793 1853 3.743396 CAGCAAGTTAGGTGTCAAGAGTC 59.257 47.826 0.00 0.00 32.59 3.36
1794 1854 3.067833 GCAAGTTAGGTGTCAAGAGTCC 58.932 50.000 0.00 0.00 0.00 3.85
1795 1855 3.665190 CAAGTTAGGTGTCAAGAGTCCC 58.335 50.000 0.00 0.00 0.00 4.46
1796 1856 2.972348 AGTTAGGTGTCAAGAGTCCCA 58.028 47.619 0.00 0.00 0.00 4.37
1797 1857 3.314693 AGTTAGGTGTCAAGAGTCCCAA 58.685 45.455 0.00 0.00 0.00 4.12
1798 1858 3.910627 AGTTAGGTGTCAAGAGTCCCAAT 59.089 43.478 0.00 0.00 0.00 3.16
1799 1859 4.351111 AGTTAGGTGTCAAGAGTCCCAATT 59.649 41.667 0.00 0.00 0.00 2.32
1800 1860 5.546499 AGTTAGGTGTCAAGAGTCCCAATTA 59.454 40.000 0.00 0.00 0.00 1.40
1801 1861 4.559862 AGGTGTCAAGAGTCCCAATTAG 57.440 45.455 0.00 0.00 0.00 1.73
1802 1862 3.910627 AGGTGTCAAGAGTCCCAATTAGT 59.089 43.478 0.00 0.00 0.00 2.24
1803 1863 5.091552 AGGTGTCAAGAGTCCCAATTAGTA 58.908 41.667 0.00 0.00 0.00 1.82
1804 1864 5.187967 AGGTGTCAAGAGTCCCAATTAGTAG 59.812 44.000 0.00 0.00 0.00 2.57
1805 1865 4.870991 GTGTCAAGAGTCCCAATTAGTAGC 59.129 45.833 0.00 0.00 0.00 3.58
1806 1866 4.530553 TGTCAAGAGTCCCAATTAGTAGCA 59.469 41.667 0.00 0.00 0.00 3.49
1807 1867 4.870991 GTCAAGAGTCCCAATTAGTAGCAC 59.129 45.833 0.00 0.00 0.00 4.40
1808 1868 4.777896 TCAAGAGTCCCAATTAGTAGCACT 59.222 41.667 0.00 0.00 0.00 4.40
1809 1869 5.105310 TCAAGAGTCCCAATTAGTAGCACTC 60.105 44.000 0.00 0.00 0.00 3.51
1810 1870 3.707102 AGAGTCCCAATTAGTAGCACTCC 59.293 47.826 0.00 0.00 31.02 3.85
1811 1871 2.772515 AGTCCCAATTAGTAGCACTCCC 59.227 50.000 0.00 0.00 0.00 4.30
1812 1872 2.504175 GTCCCAATTAGTAGCACTCCCA 59.496 50.000 0.00 0.00 0.00 4.37
1813 1873 3.136626 GTCCCAATTAGTAGCACTCCCAT 59.863 47.826 0.00 0.00 0.00 4.00
1814 1874 3.136443 TCCCAATTAGTAGCACTCCCATG 59.864 47.826 0.00 0.00 0.00 3.66
1815 1875 3.480470 CCAATTAGTAGCACTCCCATGG 58.520 50.000 4.14 4.14 0.00 3.66
1816 1876 3.117888 CCAATTAGTAGCACTCCCATGGT 60.118 47.826 11.73 0.00 0.00 3.55
1817 1877 3.845781 ATTAGTAGCACTCCCATGGTG 57.154 47.619 11.73 3.49 37.70 4.17
1818 1878 2.543037 TAGTAGCACTCCCATGGTGA 57.457 50.000 11.73 6.87 36.89 4.02
1819 1879 1.198713 AGTAGCACTCCCATGGTGAG 58.801 55.000 21.90 21.90 36.89 3.51
1820 1880 0.905357 GTAGCACTCCCATGGTGAGT 59.095 55.000 22.93 22.93 43.70 3.41
1821 1881 2.108168 GTAGCACTCCCATGGTGAGTA 58.892 52.381 26.08 14.40 41.02 2.59
1822 1882 0.905357 AGCACTCCCATGGTGAGTAC 59.095 55.000 26.08 22.36 41.02 2.73
1823 1883 0.905357 GCACTCCCATGGTGAGTACT 59.095 55.000 26.08 0.00 41.02 2.73
1824 1884 2.108168 GCACTCCCATGGTGAGTACTA 58.892 52.381 26.08 0.00 41.02 1.82
1825 1885 2.500098 GCACTCCCATGGTGAGTACTAA 59.500 50.000 26.08 0.00 41.02 2.24
1826 1886 3.134804 GCACTCCCATGGTGAGTACTAAT 59.865 47.826 26.08 8.52 41.02 1.73
1827 1887 4.384208 GCACTCCCATGGTGAGTACTAATT 60.384 45.833 26.08 7.97 41.02 1.40
1828 1888 5.745227 CACTCCCATGGTGAGTACTAATTT 58.255 41.667 26.08 7.42 41.02 1.82
1829 1889 5.586243 CACTCCCATGGTGAGTACTAATTTG 59.414 44.000 26.08 13.58 41.02 2.32
1830 1890 5.110814 TCCCATGGTGAGTACTAATTTGG 57.889 43.478 11.73 0.00 0.00 3.28
1831 1891 4.538490 TCCCATGGTGAGTACTAATTTGGT 59.462 41.667 11.73 0.00 0.00 3.67
1832 1892 5.014755 TCCCATGGTGAGTACTAATTTGGTT 59.985 40.000 11.73 0.00 0.00 3.67
1833 1893 5.357032 CCCATGGTGAGTACTAATTTGGTTC 59.643 44.000 11.73 0.00 0.00 3.62
1834 1894 5.064707 CCATGGTGAGTACTAATTTGGTTCG 59.935 44.000 2.57 0.00 0.00 3.95
1835 1895 5.471556 TGGTGAGTACTAATTTGGTTCGA 57.528 39.130 0.00 0.00 0.00 3.71
1836 1896 5.856156 TGGTGAGTACTAATTTGGTTCGAA 58.144 37.500 0.00 0.00 0.00 3.71
1837 1897 6.469410 TGGTGAGTACTAATTTGGTTCGAAT 58.531 36.000 0.00 0.00 0.00 3.34
1838 1898 6.592607 TGGTGAGTACTAATTTGGTTCGAATC 59.407 38.462 0.00 0.00 0.00 2.52
1839 1899 6.036844 GGTGAGTACTAATTTGGTTCGAATCC 59.963 42.308 5.84 7.81 0.00 3.01
1840 1900 6.592607 GTGAGTACTAATTTGGTTCGAATCCA 59.407 38.462 5.84 10.38 0.00 3.41
1841 1901 6.816640 TGAGTACTAATTTGGTTCGAATCCAG 59.183 38.462 5.84 4.17 36.28 3.86
1842 1902 6.113411 AGTACTAATTTGGTTCGAATCCAGG 58.887 40.000 5.84 5.50 36.28 4.45
1843 1903 4.270008 ACTAATTTGGTTCGAATCCAGGG 58.730 43.478 5.84 5.78 36.28 4.45
1844 1904 1.474330 ATTTGGTTCGAATCCAGGGC 58.526 50.000 5.84 0.00 36.28 5.19
1845 1905 0.111446 TTTGGTTCGAATCCAGGGCA 59.889 50.000 5.84 0.00 36.28 5.36
1846 1906 0.608035 TTGGTTCGAATCCAGGGCAC 60.608 55.000 5.84 0.00 36.28 5.01
1847 1907 1.002624 GGTTCGAATCCAGGGCACA 60.003 57.895 0.00 0.00 0.00 4.57
1848 1908 1.305930 GGTTCGAATCCAGGGCACAC 61.306 60.000 0.00 0.00 0.00 3.82
1849 1909 0.321653 GTTCGAATCCAGGGCACACT 60.322 55.000 0.00 0.00 0.00 3.55
1850 1910 0.400213 TTCGAATCCAGGGCACACTT 59.600 50.000 0.00 0.00 0.00 3.16
1851 1911 0.036388 TCGAATCCAGGGCACACTTC 60.036 55.000 0.00 0.00 0.00 3.01
1852 1912 0.321564 CGAATCCAGGGCACACTTCA 60.322 55.000 0.00 0.00 0.00 3.02
1853 1913 1.679944 CGAATCCAGGGCACACTTCAT 60.680 52.381 0.00 0.00 0.00 2.57
1854 1914 1.747355 GAATCCAGGGCACACTTCATG 59.253 52.381 0.00 0.00 0.00 3.07
1855 1915 0.033796 ATCCAGGGCACACTTCATGG 60.034 55.000 0.00 0.00 0.00 3.66
1879 1939 4.037923 CACCCTTGTTAATTCTGTGCTTGT 59.962 41.667 0.00 0.00 0.00 3.16
1955 2015 3.180984 GCTGGAGCGAATACTACGG 57.819 57.895 0.00 0.00 0.00 4.02
1973 2033 1.673477 GGGCTTTCTTTGGCAAGGG 59.327 57.895 9.63 2.89 0.00 3.95
1983 2043 0.762418 TTGGCAAGGGAAGAACTCGA 59.238 50.000 0.00 0.00 0.00 4.04
1990 2050 4.065088 CAAGGGAAGAACTCGACAAATGA 58.935 43.478 0.00 0.00 0.00 2.57
2004 2064 3.489355 ACAAATGATGGACACTGCTTGA 58.511 40.909 0.00 0.00 0.00 3.02
2046 2106 3.850173 TCTACCAAAGCTTAATGGAGGGT 59.150 43.478 21.51 12.37 39.12 4.34
2063 2123 1.341209 GGGTTTGGCCTCAGAAACTTG 59.659 52.381 14.15 0.00 37.43 3.16
2436 2496 1.009829 GAATCTAACTGCCACAGCCG 58.990 55.000 0.00 0.00 38.69 5.52
2458 2518 2.295885 CAGAGAATTGCAGGCCCTAAG 58.704 52.381 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.698539 TCACTGCTGTCCAATGTGAAAAA 59.301 39.130 0.00 0.00 35.15 1.94
44 45 2.104622 TCTTCACTGCTGTCCAATGTGA 59.895 45.455 0.00 0.00 36.10 3.58
261 263 9.593134 CTTTATACTCAGCTTCTGTACTTGATT 57.407 33.333 0.00 0.00 32.61 2.57
304 306 5.127682 GGTTTGAACCCATATCAATTCTGCT 59.872 40.000 1.32 0.00 43.43 4.24
389 391 3.801114 TGCTGATAGATACGTTGCACT 57.199 42.857 0.00 0.00 0.00 4.40
397 399 7.280876 TGAAACACTGGATTTGCTGATAGATAC 59.719 37.037 0.00 0.00 0.00 2.24
538 540 3.194116 ACTTGCACCATGATAAGGCTTTG 59.806 43.478 4.45 0.00 0.00 2.77
554 556 6.112734 TGTTCTTGAACTCTTCTAACTTGCA 58.887 36.000 13.65 0.00 0.00 4.08
682 689 8.047310 CCTAACTACCAGATTACAAAGTTGGAT 58.953 37.037 0.00 0.00 29.87 3.41
684 691 7.166167 ACCTAACTACCAGATTACAAAGTTGG 58.834 38.462 0.00 0.00 35.07 3.77
813 821 2.091994 AGTGTATACCTAGCAGGGACGT 60.092 50.000 0.00 0.00 40.58 4.34
827 835 6.946340 TCTGAAAGATGGCTTGAAGTGTATA 58.054 36.000 0.00 0.00 38.67 1.47
832 840 5.319453 TGATTCTGAAAGATGGCTTGAAGT 58.681 37.500 0.00 0.00 46.36 3.01
858 866 0.317160 GACGGCGATCCATGTCCATA 59.683 55.000 16.62 0.00 0.00 2.74
980 1020 5.771469 TCATTCATTCATTCAAGTTTGCGT 58.229 33.333 0.00 0.00 0.00 5.24
1419 1475 0.955428 GCGCACAGATTCCAGTTCCA 60.955 55.000 0.30 0.00 0.00 3.53
1610 1670 1.982073 GCTTCTTTGGATGACGCGGG 61.982 60.000 12.47 0.00 0.00 6.13
1611 1671 1.425428 GCTTCTTTGGATGACGCGG 59.575 57.895 12.47 0.00 0.00 6.46
1612 1672 1.298157 TGGCTTCTTTGGATGACGCG 61.298 55.000 3.53 3.53 30.76 6.01
1613 1673 0.449388 CTGGCTTCTTTGGATGACGC 59.551 55.000 0.00 0.00 0.00 5.19
1614 1674 0.449388 GCTGGCTTCTTTGGATGACG 59.551 55.000 0.00 0.00 0.00 4.35
1615 1675 1.200948 GTGCTGGCTTCTTTGGATGAC 59.799 52.381 0.00 0.00 0.00 3.06
1616 1676 1.538047 GTGCTGGCTTCTTTGGATGA 58.462 50.000 0.00 0.00 0.00 2.92
1617 1677 0.169672 CGTGCTGGCTTCTTTGGATG 59.830 55.000 0.00 0.00 0.00 3.51
1618 1678 1.589716 GCGTGCTGGCTTCTTTGGAT 61.590 55.000 0.00 0.00 0.00 3.41
1619 1679 2.260869 GCGTGCTGGCTTCTTTGGA 61.261 57.895 0.00 0.00 0.00 3.53
1620 1680 2.256461 GCGTGCTGGCTTCTTTGG 59.744 61.111 0.00 0.00 0.00 3.28
1621 1681 2.256461 GGCGTGCTGGCTTCTTTG 59.744 61.111 0.00 0.00 40.72 2.77
1622 1682 2.203337 TGGCGTGCTGGCTTCTTT 60.203 55.556 4.85 0.00 45.14 2.52
1623 1683 2.980233 GTGGCGTGCTGGCTTCTT 60.980 61.111 4.85 0.00 45.14 2.52
1624 1684 4.254709 TGTGGCGTGCTGGCTTCT 62.255 61.111 4.85 0.00 45.14 2.85
1625 1685 3.730761 CTGTGGCGTGCTGGCTTC 61.731 66.667 4.85 0.04 45.14 3.86
1636 1696 2.583685 GATTTCTTCCGCGCTGTGGC 62.584 60.000 5.56 0.00 32.51 5.01
1637 1697 1.021390 AGATTTCTTCCGCGCTGTGG 61.021 55.000 5.56 0.00 33.99 4.17
1638 1698 0.095935 CAGATTTCTTCCGCGCTGTG 59.904 55.000 5.56 0.00 0.00 3.66
1639 1699 0.320771 ACAGATTTCTTCCGCGCTGT 60.321 50.000 5.56 2.84 0.00 4.40
1640 1700 0.798776 AACAGATTTCTTCCGCGCTG 59.201 50.000 5.56 0.00 0.00 5.18
1641 1701 0.798776 CAACAGATTTCTTCCGCGCT 59.201 50.000 5.56 0.00 0.00 5.92
1642 1702 0.794605 GCAACAGATTTCTTCCGCGC 60.795 55.000 0.00 0.00 0.00 6.86
1643 1703 0.519175 CGCAACAGATTTCTTCCGCG 60.519 55.000 0.00 0.00 35.14 6.46
1644 1704 0.517316 ACGCAACAGATTTCTTCCGC 59.483 50.000 0.00 0.00 0.00 5.54
1645 1705 1.531149 ACACGCAACAGATTTCTTCCG 59.469 47.619 0.00 0.00 0.00 4.30
1646 1706 3.626028 AACACGCAACAGATTTCTTCC 57.374 42.857 0.00 0.00 0.00 3.46
1647 1707 5.927030 TGATAACACGCAACAGATTTCTTC 58.073 37.500 0.00 0.00 0.00 2.87
1648 1708 5.940192 TGATAACACGCAACAGATTTCTT 57.060 34.783 0.00 0.00 0.00 2.52
1649 1709 5.940192 TTGATAACACGCAACAGATTTCT 57.060 34.783 0.00 0.00 0.00 2.52
1650 1710 6.984740 TTTTGATAACACGCAACAGATTTC 57.015 33.333 0.00 0.00 0.00 2.17
1651 1711 7.651304 TGATTTTTGATAACACGCAACAGATTT 59.349 29.630 0.00 0.00 0.00 2.17
1652 1712 7.144661 TGATTTTTGATAACACGCAACAGATT 58.855 30.769 0.00 0.00 0.00 2.40
1653 1713 6.676950 TGATTTTTGATAACACGCAACAGAT 58.323 32.000 0.00 0.00 0.00 2.90
1654 1714 6.066054 TGATTTTTGATAACACGCAACAGA 57.934 33.333 0.00 0.00 0.00 3.41
1655 1715 6.746104 TTGATTTTTGATAACACGCAACAG 57.254 33.333 0.00 0.00 0.00 3.16
1656 1716 7.525688 TTTTGATTTTTGATAACACGCAACA 57.474 28.000 0.00 0.00 0.00 3.33
1657 1717 8.324567 TCTTTTTGATTTTTGATAACACGCAAC 58.675 29.630 0.00 0.00 0.00 4.17
1658 1718 8.412608 TCTTTTTGATTTTTGATAACACGCAA 57.587 26.923 0.00 0.00 0.00 4.85
1659 1719 7.993821 TCTTTTTGATTTTTGATAACACGCA 57.006 28.000 0.00 0.00 0.00 5.24
1660 1720 9.305110 CAATCTTTTTGATTTTTGATAACACGC 57.695 29.630 0.00 0.00 43.00 5.34
1673 1733 9.246670 TGACCATCTCATACAATCTTTTTGATT 57.753 29.630 0.00 0.00 45.52 2.57
1674 1734 8.812513 TGACCATCTCATACAATCTTTTTGAT 57.187 30.769 0.00 0.00 36.89 2.57
1675 1735 8.634335 TTGACCATCTCATACAATCTTTTTGA 57.366 30.769 0.00 0.00 0.00 2.69
1679 1739 9.512588 GGATATTGACCATCTCATACAATCTTT 57.487 33.333 0.00 0.00 33.99 2.52
1680 1740 8.663167 TGGATATTGACCATCTCATACAATCTT 58.337 33.333 0.00 0.00 33.99 2.40
1681 1741 8.211030 TGGATATTGACCATCTCATACAATCT 57.789 34.615 0.00 0.00 33.99 2.40
1682 1742 9.458727 AATGGATATTGACCATCTCATACAATC 57.541 33.333 0.00 0.00 45.89 2.67
1683 1743 9.818270 AAATGGATATTGACCATCTCATACAAT 57.182 29.630 0.00 0.00 45.89 2.71
1684 1744 9.645128 AAAATGGATATTGACCATCTCATACAA 57.355 29.630 0.00 0.00 45.89 2.41
1685 1745 9.288576 GAAAATGGATATTGACCATCTCATACA 57.711 33.333 0.00 0.00 45.89 2.29
1686 1746 9.288576 TGAAAATGGATATTGACCATCTCATAC 57.711 33.333 0.00 0.00 45.89 2.39
1687 1747 9.865152 TTGAAAATGGATATTGACCATCTCATA 57.135 29.630 0.00 0.00 45.89 2.15
1688 1748 8.771521 TTGAAAATGGATATTGACCATCTCAT 57.228 30.769 0.00 0.00 45.89 2.90
1689 1749 8.592529 TTTGAAAATGGATATTGACCATCTCA 57.407 30.769 0.00 0.00 45.89 3.27
1690 1750 9.874205 TTTTTGAAAATGGATATTGACCATCTC 57.126 29.630 0.00 0.00 45.89 2.75
1691 1751 9.880157 CTTTTTGAAAATGGATATTGACCATCT 57.120 29.630 0.00 0.00 45.89 2.90
1692 1752 8.606602 GCTTTTTGAAAATGGATATTGACCATC 58.393 33.333 0.00 0.00 45.89 3.51
1694 1754 6.878389 GGCTTTTTGAAAATGGATATTGACCA 59.122 34.615 5.82 0.00 41.83 4.02
1695 1755 6.316140 GGGCTTTTTGAAAATGGATATTGACC 59.684 38.462 5.82 0.00 0.00 4.02
1696 1756 6.316140 GGGGCTTTTTGAAAATGGATATTGAC 59.684 38.462 5.82 0.00 0.00 3.18
1697 1757 6.013032 TGGGGCTTTTTGAAAATGGATATTGA 60.013 34.615 5.82 0.00 0.00 2.57
1698 1758 6.179040 TGGGGCTTTTTGAAAATGGATATTG 58.821 36.000 5.82 0.00 0.00 1.90
1699 1759 6.385766 TGGGGCTTTTTGAAAATGGATATT 57.614 33.333 5.82 0.00 0.00 1.28
1700 1760 6.385766 TTGGGGCTTTTTGAAAATGGATAT 57.614 33.333 5.82 0.00 0.00 1.63
1701 1761 5.832539 TTGGGGCTTTTTGAAAATGGATA 57.167 34.783 5.82 0.00 0.00 2.59
1702 1762 4.720775 TTGGGGCTTTTTGAAAATGGAT 57.279 36.364 5.82 0.00 0.00 3.41
1703 1763 4.510167 TTTGGGGCTTTTTGAAAATGGA 57.490 36.364 5.82 0.00 0.00 3.41
1704 1764 6.890979 TTATTTGGGGCTTTTTGAAAATGG 57.109 33.333 5.82 0.00 0.00 3.16
1728 1788 1.181098 ATGGCGAGCTGCTGGTTTTT 61.181 50.000 7.01 0.00 45.43 1.94
1729 1789 1.589716 GATGGCGAGCTGCTGGTTTT 61.590 55.000 7.01 0.00 45.43 2.43
1730 1790 2.034687 ATGGCGAGCTGCTGGTTT 59.965 55.556 7.01 0.00 45.43 3.27
1731 1791 2.437359 GATGGCGAGCTGCTGGTT 60.437 61.111 7.01 0.00 45.43 3.67
1732 1792 2.937379 GATGATGGCGAGCTGCTGGT 62.937 60.000 7.01 0.00 45.43 4.00
1733 1793 2.203167 ATGATGGCGAGCTGCTGG 60.203 61.111 7.01 7.21 45.43 4.85
1734 1794 1.523032 TGATGATGGCGAGCTGCTG 60.523 57.895 7.01 0.28 45.43 4.41
1735 1795 1.523258 GTGATGATGGCGAGCTGCT 60.523 57.895 0.00 0.00 45.43 4.24
1736 1796 1.371337 TTGTGATGATGGCGAGCTGC 61.371 55.000 0.00 0.00 45.38 5.25
1737 1797 1.306148 ATTGTGATGATGGCGAGCTG 58.694 50.000 0.00 0.00 0.00 4.24
1738 1798 2.048444 AATTGTGATGATGGCGAGCT 57.952 45.000 0.00 0.00 0.00 4.09
1739 1799 2.097954 TCAAATTGTGATGATGGCGAGC 59.902 45.455 0.00 0.00 0.00 5.03
1740 1800 4.359971 TTCAAATTGTGATGATGGCGAG 57.640 40.909 0.00 0.00 35.70 5.03
1741 1801 4.158209 ACATTCAAATTGTGATGATGGCGA 59.842 37.500 15.08 0.00 35.70 5.54
1742 1802 4.426416 ACATTCAAATTGTGATGATGGCG 58.574 39.130 15.08 0.00 35.70 5.69
1743 1803 5.870433 TGAACATTCAAATTGTGATGATGGC 59.130 36.000 15.08 0.00 35.70 4.40
1744 1804 6.533723 CCTGAACATTCAAATTGTGATGATGG 59.466 38.462 15.08 9.22 36.64 3.51
1745 1805 7.094631 ACCTGAACATTCAAATTGTGATGATG 58.905 34.615 15.08 6.74 36.64 3.07
1746 1806 7.039574 TGACCTGAACATTCAAATTGTGATGAT 60.040 33.333 15.08 6.77 36.64 2.45
1747 1807 6.264970 TGACCTGAACATTCAAATTGTGATGA 59.735 34.615 15.08 0.00 36.64 2.92
1748 1808 6.448852 TGACCTGAACATTCAAATTGTGATG 58.551 36.000 9.34 9.34 36.64 3.07
1749 1809 6.653526 TGACCTGAACATTCAAATTGTGAT 57.346 33.333 0.00 0.00 36.64 3.06
1750 1810 5.507817 GCTGACCTGAACATTCAAATTGTGA 60.508 40.000 0.00 0.00 36.64 3.58
1751 1811 4.682860 GCTGACCTGAACATTCAAATTGTG 59.317 41.667 0.00 0.00 36.64 3.33
1752 1812 4.341806 TGCTGACCTGAACATTCAAATTGT 59.658 37.500 0.00 0.00 36.64 2.71
1753 1813 4.873817 TGCTGACCTGAACATTCAAATTG 58.126 39.130 0.00 0.00 36.64 2.32
1754 1814 5.069516 ACTTGCTGACCTGAACATTCAAATT 59.930 36.000 0.00 0.00 36.64 1.82
1755 1815 4.586001 ACTTGCTGACCTGAACATTCAAAT 59.414 37.500 0.00 0.00 36.64 2.32
1756 1816 3.953612 ACTTGCTGACCTGAACATTCAAA 59.046 39.130 0.00 0.00 36.64 2.69
1757 1817 3.554934 ACTTGCTGACCTGAACATTCAA 58.445 40.909 0.00 0.00 36.64 2.69
1758 1818 3.213206 ACTTGCTGACCTGAACATTCA 57.787 42.857 0.00 0.00 35.57 2.57
1759 1819 4.154918 CCTAACTTGCTGACCTGAACATTC 59.845 45.833 0.00 0.00 0.00 2.67
1760 1820 4.074970 CCTAACTTGCTGACCTGAACATT 58.925 43.478 0.00 0.00 0.00 2.71
1761 1821 3.073062 ACCTAACTTGCTGACCTGAACAT 59.927 43.478 0.00 0.00 0.00 2.71
1762 1822 2.438021 ACCTAACTTGCTGACCTGAACA 59.562 45.455 0.00 0.00 0.00 3.18
1763 1823 2.808543 CACCTAACTTGCTGACCTGAAC 59.191 50.000 0.00 0.00 0.00 3.18
1764 1824 2.438021 ACACCTAACTTGCTGACCTGAA 59.562 45.455 0.00 0.00 0.00 3.02
1765 1825 2.037251 GACACCTAACTTGCTGACCTGA 59.963 50.000 0.00 0.00 0.00 3.86
1766 1826 2.224281 TGACACCTAACTTGCTGACCTG 60.224 50.000 0.00 0.00 0.00 4.00
1767 1827 2.047061 TGACACCTAACTTGCTGACCT 58.953 47.619 0.00 0.00 0.00 3.85
1768 1828 2.543777 TGACACCTAACTTGCTGACC 57.456 50.000 0.00 0.00 0.00 4.02
1769 1829 3.728845 TCTTGACACCTAACTTGCTGAC 58.271 45.455 0.00 0.00 0.00 3.51
1770 1830 3.388024 ACTCTTGACACCTAACTTGCTGA 59.612 43.478 0.00 0.00 0.00 4.26
1771 1831 3.733337 ACTCTTGACACCTAACTTGCTG 58.267 45.455 0.00 0.00 0.00 4.41
1772 1832 3.244249 GGACTCTTGACACCTAACTTGCT 60.244 47.826 0.00 0.00 0.00 3.91
1773 1833 3.067833 GGACTCTTGACACCTAACTTGC 58.932 50.000 0.00 0.00 0.00 4.01
1774 1834 3.071023 TGGGACTCTTGACACCTAACTTG 59.929 47.826 0.00 0.00 0.00 3.16
1775 1835 3.314693 TGGGACTCTTGACACCTAACTT 58.685 45.455 0.00 0.00 0.00 2.66
1776 1836 2.972348 TGGGACTCTTGACACCTAACT 58.028 47.619 0.00 0.00 0.00 2.24
1777 1837 3.764237 TTGGGACTCTTGACACCTAAC 57.236 47.619 0.00 0.00 0.00 2.34
1778 1838 4.993705 AATTGGGACTCTTGACACCTAA 57.006 40.909 0.00 0.00 0.00 2.69
1779 1839 5.091552 ACTAATTGGGACTCTTGACACCTA 58.908 41.667 0.00 0.00 0.00 3.08
1780 1840 3.910627 ACTAATTGGGACTCTTGACACCT 59.089 43.478 0.00 0.00 0.00 4.00
1781 1841 4.287766 ACTAATTGGGACTCTTGACACC 57.712 45.455 0.00 0.00 0.00 4.16
1782 1842 4.870991 GCTACTAATTGGGACTCTTGACAC 59.129 45.833 0.00 0.00 0.00 3.67
1783 1843 4.530553 TGCTACTAATTGGGACTCTTGACA 59.469 41.667 0.00 0.00 0.00 3.58
1784 1844 4.870991 GTGCTACTAATTGGGACTCTTGAC 59.129 45.833 0.00 0.00 0.00 3.18
1785 1845 4.777896 AGTGCTACTAATTGGGACTCTTGA 59.222 41.667 0.00 0.00 0.00 3.02
1786 1846 5.091261 AGTGCTACTAATTGGGACTCTTG 57.909 43.478 0.00 0.00 0.00 3.02
1787 1847 4.162509 GGAGTGCTACTAATTGGGACTCTT 59.837 45.833 16.65 0.00 44.16 2.85
1788 1848 3.707102 GGAGTGCTACTAATTGGGACTCT 59.293 47.826 16.65 4.29 44.16 3.24
1789 1849 3.181464 GGGAGTGCTACTAATTGGGACTC 60.181 52.174 12.19 12.19 44.05 3.36
1790 1850 2.772515 GGGAGTGCTACTAATTGGGACT 59.227 50.000 0.00 0.00 34.52 3.85
1791 1851 2.504175 TGGGAGTGCTACTAATTGGGAC 59.496 50.000 0.00 0.00 0.00 4.46
1792 1852 2.840511 TGGGAGTGCTACTAATTGGGA 58.159 47.619 0.00 0.00 0.00 4.37
1793 1853 3.480470 CATGGGAGTGCTACTAATTGGG 58.520 50.000 0.00 0.00 0.00 4.12
1794 1854 3.117888 ACCATGGGAGTGCTACTAATTGG 60.118 47.826 18.09 0.00 0.00 3.16
1795 1855 3.879295 CACCATGGGAGTGCTACTAATTG 59.121 47.826 18.09 0.00 0.00 2.32
1796 1856 3.780294 TCACCATGGGAGTGCTACTAATT 59.220 43.478 18.09 0.00 35.14 1.40
1797 1857 3.384168 TCACCATGGGAGTGCTACTAAT 58.616 45.455 18.09 0.00 35.14 1.73
1798 1858 2.766263 CTCACCATGGGAGTGCTACTAA 59.234 50.000 18.09 0.00 35.14 2.24
1799 1859 2.292257 ACTCACCATGGGAGTGCTACTA 60.292 50.000 26.02 0.00 43.65 1.82
1800 1860 1.198713 CTCACCATGGGAGTGCTACT 58.801 55.000 18.09 0.00 35.14 2.57
1801 1861 0.905357 ACTCACCATGGGAGTGCTAC 59.095 55.000 26.02 0.00 43.65 3.58
1802 1862 2.108168 GTACTCACCATGGGAGTGCTA 58.892 52.381 30.76 17.49 44.86 3.49
1803 1863 0.905357 GTACTCACCATGGGAGTGCT 59.095 55.000 30.76 16.35 44.86 4.40
1804 1864 0.905357 AGTACTCACCATGGGAGTGC 59.095 55.000 30.76 29.44 44.86 4.40
1805 1865 5.359194 AATTAGTACTCACCATGGGAGTG 57.641 43.478 30.76 20.27 44.86 3.51
1806 1866 5.339200 CCAAATTAGTACTCACCATGGGAGT 60.339 44.000 28.09 28.09 46.71 3.85
1807 1867 5.126067 CCAAATTAGTACTCACCATGGGAG 58.874 45.833 21.90 21.90 38.36 4.30
1808 1868 4.538490 ACCAAATTAGTACTCACCATGGGA 59.462 41.667 18.09 9.65 0.00 4.37
1809 1869 4.855340 ACCAAATTAGTACTCACCATGGG 58.145 43.478 18.09 5.22 0.00 4.00
1810 1870 5.064707 CGAACCAAATTAGTACTCACCATGG 59.935 44.000 11.19 11.19 0.00 3.66
1811 1871 5.872617 TCGAACCAAATTAGTACTCACCATG 59.127 40.000 0.00 0.00 0.00 3.66
1812 1872 6.045072 TCGAACCAAATTAGTACTCACCAT 57.955 37.500 0.00 0.00 0.00 3.55
1813 1873 5.471556 TCGAACCAAATTAGTACTCACCA 57.528 39.130 0.00 0.00 0.00 4.17
1814 1874 6.036844 GGATTCGAACCAAATTAGTACTCACC 59.963 42.308 0.00 0.00 0.00 4.02
1815 1875 6.592607 TGGATTCGAACCAAATTAGTACTCAC 59.407 38.462 14.54 0.00 34.25 3.51
1816 1876 6.703319 TGGATTCGAACCAAATTAGTACTCA 58.297 36.000 14.54 0.00 34.25 3.41
1817 1877 6.258068 CCTGGATTCGAACCAAATTAGTACTC 59.742 42.308 16.68 0.66 36.95 2.59
1818 1878 6.113411 CCTGGATTCGAACCAAATTAGTACT 58.887 40.000 16.68 0.00 36.95 2.73
1819 1879 5.296035 CCCTGGATTCGAACCAAATTAGTAC 59.704 44.000 16.68 0.00 36.95 2.73
1820 1880 5.433526 CCCTGGATTCGAACCAAATTAGTA 58.566 41.667 16.68 0.00 36.95 1.82
1821 1881 4.270008 CCCTGGATTCGAACCAAATTAGT 58.730 43.478 16.68 0.00 36.95 2.24
1822 1882 3.066760 GCCCTGGATTCGAACCAAATTAG 59.933 47.826 16.68 7.87 36.95 1.73
1823 1883 3.020984 GCCCTGGATTCGAACCAAATTA 58.979 45.455 16.68 0.00 36.95 1.40
1824 1884 1.824852 GCCCTGGATTCGAACCAAATT 59.175 47.619 16.68 0.00 36.95 1.82
1825 1885 1.272425 TGCCCTGGATTCGAACCAAAT 60.272 47.619 16.68 0.00 36.95 2.32
1826 1886 0.111446 TGCCCTGGATTCGAACCAAA 59.889 50.000 16.68 4.82 36.95 3.28
1827 1887 0.608035 GTGCCCTGGATTCGAACCAA 60.608 55.000 16.68 0.00 36.95 3.67
1828 1888 1.002624 GTGCCCTGGATTCGAACCA 60.003 57.895 15.60 15.60 35.96 3.67
1829 1889 1.002624 TGTGCCCTGGATTCGAACC 60.003 57.895 0.00 4.86 0.00 3.62
1830 1890 0.321653 AGTGTGCCCTGGATTCGAAC 60.322 55.000 0.00 0.00 0.00 3.95
1831 1891 0.400213 AAGTGTGCCCTGGATTCGAA 59.600 50.000 0.00 0.00 0.00 3.71
1832 1892 0.036388 GAAGTGTGCCCTGGATTCGA 60.036 55.000 0.00 0.00 0.00 3.71
1833 1893 0.321564 TGAAGTGTGCCCTGGATTCG 60.322 55.000 0.00 0.00 0.00 3.34
1834 1894 1.747355 CATGAAGTGTGCCCTGGATTC 59.253 52.381 0.00 0.00 0.00 2.52
1835 1895 1.617804 CCATGAAGTGTGCCCTGGATT 60.618 52.381 0.00 0.00 0.00 3.01
1836 1896 0.033796 CCATGAAGTGTGCCCTGGAT 60.034 55.000 0.00 0.00 0.00 3.41
1837 1897 1.379916 CCATGAAGTGTGCCCTGGA 59.620 57.895 0.00 0.00 0.00 3.86
1838 1898 2.345760 GCCATGAAGTGTGCCCTGG 61.346 63.158 0.00 0.00 0.00 4.45
1839 1899 1.604308 TGCCATGAAGTGTGCCCTG 60.604 57.895 0.00 0.00 0.00 4.45
1840 1900 1.604593 GTGCCATGAAGTGTGCCCT 60.605 57.895 0.00 0.00 0.00 5.19
1841 1901 2.639327 GGTGCCATGAAGTGTGCCC 61.639 63.158 0.00 0.00 0.00 5.36
1842 1902 2.639327 GGGTGCCATGAAGTGTGCC 61.639 63.158 0.00 0.00 0.00 5.01
1843 1903 1.181098 AAGGGTGCCATGAAGTGTGC 61.181 55.000 0.00 0.00 0.00 4.57
1844 1904 0.599558 CAAGGGTGCCATGAAGTGTG 59.400 55.000 0.00 0.00 0.00 3.82
1845 1905 0.185901 ACAAGGGTGCCATGAAGTGT 59.814 50.000 0.00 0.00 0.00 3.55
1846 1906 1.331214 AACAAGGGTGCCATGAAGTG 58.669 50.000 0.00 0.00 0.00 3.16
1847 1907 2.969821 TAACAAGGGTGCCATGAAGT 57.030 45.000 0.00 0.00 0.00 3.01
1848 1908 4.463891 AGAATTAACAAGGGTGCCATGAAG 59.536 41.667 0.00 0.00 0.00 3.02
1849 1909 4.220382 CAGAATTAACAAGGGTGCCATGAA 59.780 41.667 0.00 0.00 0.00 2.57
1850 1910 3.763360 CAGAATTAACAAGGGTGCCATGA 59.237 43.478 0.00 0.00 0.00 3.07
1851 1911 3.511146 ACAGAATTAACAAGGGTGCCATG 59.489 43.478 0.00 0.00 0.00 3.66
1852 1912 3.511146 CACAGAATTAACAAGGGTGCCAT 59.489 43.478 0.00 0.00 0.00 4.40
1853 1913 2.890311 CACAGAATTAACAAGGGTGCCA 59.110 45.455 0.00 0.00 0.00 4.92
1854 1914 2.352715 GCACAGAATTAACAAGGGTGCC 60.353 50.000 0.00 0.00 43.05 5.01
1855 1915 2.946564 GCACAGAATTAACAAGGGTGC 58.053 47.619 0.00 0.00 42.54 5.01
1879 1939 4.141181 CCATGAAGTAATTGGGGATGGAGA 60.141 45.833 0.00 0.00 32.20 3.71
1955 2015 0.831711 TCCCTTGCCAAAGAAAGCCC 60.832 55.000 0.00 0.00 35.19 5.19
1973 2033 4.690748 TGTCCATCATTTGTCGAGTTCTTC 59.309 41.667 0.00 0.00 0.00 2.87
1983 2043 3.489355 TCAAGCAGTGTCCATCATTTGT 58.511 40.909 0.00 0.00 0.00 2.83
2004 2064 3.055094 AGAGTGACAAAATCCCACGCTAT 60.055 43.478 0.00 0.00 38.75 2.97
2046 2106 4.277476 TCTTTCAAGTTTCTGAGGCCAAA 58.723 39.130 5.01 0.00 0.00 3.28
2063 2123 4.619973 TCATTGCCATGTTGTGTTCTTTC 58.380 39.130 0.00 0.00 0.00 2.62
2214 2274 1.522668 TGCTGTATGGTTGACTGCAC 58.477 50.000 3.59 0.00 43.96 4.57
2241 2301 3.482436 CCAAAGTGCACCTGGTAGTTTA 58.518 45.455 22.06 0.00 33.64 2.01
2436 2496 2.421399 GGGCCTGCAATTCTCTGGC 61.421 63.158 0.84 13.54 44.64 4.85
2458 2518 2.240612 GATGCCGTCCAAAGCGTCAC 62.241 60.000 0.00 0.00 43.17 3.67


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

AutoCloner maintained by Alex Coulton.