Multiple sequence alignment - TraesCS3A01G475100

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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 TraesCS3A01G475100 chr3A 100.000 2462 0 0 1 2462 706442778 706445239 0.000000e+00 4547.0
1 TraesCS3A01G475100 chr3A 97.968 689 12 1 1 687 679478130 679478818 0.000000e+00 1194.0
2 TraesCS3A01G475100 chr3A 91.603 786 60 3 771 1555 706543247 706544027 0.000000e+00 1081.0
3 TraesCS3A01G475100 chr3A 91.980 399 21 3 1928 2323 706544027 706544417 1.290000e-152 549.0
4 TraesCS3A01G475100 chr3A 88.491 391 36 8 1545 1929 725451958 725451571 4.800000e-127 464.0
5 TraesCS3A01G475100 chr3A 99.213 127 0 1 563 689 706438195 706438320 6.850000e-56 228.0
6 TraesCS3A01G475100 chr3A 97.561 123 3 0 567 689 679473554 679473676 6.900000e-51 211.0
7 TraesCS3A01G475100 chr3A 81.148 244 36 6 1100 1335 706545770 706546011 1.160000e-43 187.0
8 TraesCS3A01G475100 chr3A 94.898 98 4 1 2353 2449 706544417 706544514 4.240000e-33 152.0
9 TraesCS3A01G475100 chr3A 97.222 36 1 0 701 736 742195319 742195354 7.350000e-06 62.1
10 TraesCS3A01G475100 chr3D 96.774 868 22 2 688 1555 572426393 572425532 0.000000e+00 1443.0
11 TraesCS3A01G475100 chr3D 93.084 535 15 1 1928 2462 572425532 572425020 0.000000e+00 763.0
12 TraesCS3A01G475100 chr3D 85.507 138 20 0 688 825 595209891 595209754 7.100000e-31 145.0
13 TraesCS3A01G475100 chr3B 93.070 837 47 6 723 1555 761494389 761495218 0.000000e+00 1214.0
14 TraesCS3A01G475100 chr3B 92.658 395 26 3 1928 2321 761495218 761495610 1.280000e-157 566.0
15 TraesCS3A01G475100 chr3B 84.259 540 80 5 1016 1554 761761940 761762475 2.810000e-144 521.0
16 TraesCS3A01G475100 chr3B 89.460 389 34 4 1547 1930 594928491 594928105 3.680000e-133 484.0
17 TraesCS3A01G475100 chr3B 78.740 508 91 11 1037 1540 760590226 760589732 8.490000e-85 324.0
18 TraesCS3A01G475100 chr3B 78.914 479 83 15 1016 1489 760578699 760578234 2.380000e-80 309.0
19 TraesCS3A01G475100 chr3B 76.965 547 102 20 1011 1553 760548517 760547991 8.610000e-75 291.0
20 TraesCS3A01G475100 chr3B 77.547 481 89 11 1016 1493 760597690 760597226 3.120000e-69 272.0
21 TraesCS3A01G475100 chr3B 76.618 479 91 12 1016 1488 760606382 760605919 6.800000e-61 244.0
22 TraesCS3A01G475100 chr3B 95.699 93 4 0 2356 2448 761495611 761495703 1.530000e-32 150.0
23 TraesCS3A01G475100 chr5D 93.419 699 36 2 1 690 446280973 446280276 0.000000e+00 1027.0
24 TraesCS3A01G475100 chr5D 77.465 142 18 6 684 825 11315786 11315659 3.400000e-09 73.1
25 TraesCS3A01G475100 chr2A 97.024 504 15 0 186 689 705285926 705286429 0.000000e+00 848.0
26 TraesCS3A01G475100 chr2A 99.200 125 1 0 1 125 705285806 705285930 2.460000e-55 226.0
27 TraesCS3A01G475100 chr2A 97.561 123 3 0 567 689 705281227 705281349 6.900000e-51 211.0
28 TraesCS3A01G475100 chr7D 89.896 386 30 6 1551 1931 496720569 496720950 2.850000e-134 488.0
29 TraesCS3A01G475100 chr7D 89.501 381 30 6 1554 1929 556776446 556776821 7.970000e-130 473.0
30 TraesCS3A01G475100 chr7D 88.550 393 30 12 1542 1929 47118247 47118629 1.720000e-126 462.0
31 TraesCS3A01G475100 chr5A 88.946 389 38 4 1545 1929 287582778 287583165 2.220000e-130 475.0
32 TraesCS3A01G475100 chr6D 88.491 391 37 5 1539 1924 27459168 27458781 1.330000e-127 466.0
33 TraesCS3A01G475100 chr6D 82.653 98 15 1 693 790 288169530 288169625 4.360000e-13 86.1
34 TraesCS3A01G475100 chr4D 88.860 386 33 7 1551 1931 60170511 60170891 1.330000e-127 466.0
35 TraesCS3A01G475100 chr6B 88.265 392 41 4 1543 1930 640627229 640626839 4.800000e-127 464.0
36 TraesCS3A01G475100 chr6B 84.173 139 22 0 688 826 554022289 554022427 4.270000e-28 135.0
37 TraesCS3A01G475100 chr1B 88.321 137 16 0 690 826 380628763 380628899 5.450000e-37 165.0
38 TraesCS3A01G475100 chr1D 83.607 122 20 0 688 809 424483355 424483476 5.560000e-22 115.0
39 TraesCS3A01G475100 chr7A 81.967 122 20 2 705 826 728280368 728280487 4.330000e-18 102.0


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 TraesCS3A01G475100 chr3A 706442778 706445239 2461 False 4547.000000 4547 100.00000 1 2462 1 chr3A.!!$F4 2461
1 TraesCS3A01G475100 chr3A 679478130 679478818 688 False 1194.000000 1194 97.96800 1 687 1 chr3A.!!$F2 686
2 TraesCS3A01G475100 chr3A 706543247 706546011 2764 False 492.250000 1081 89.90725 771 2449 4 chr3A.!!$F6 1678
3 TraesCS3A01G475100 chr3D 572425020 572426393 1373 True 1103.000000 1443 94.92900 688 2462 2 chr3D.!!$R2 1774
4 TraesCS3A01G475100 chr3B 761494389 761495703 1314 False 643.333333 1214 93.80900 723 2448 3 chr3B.!!$F2 1725
5 TraesCS3A01G475100 chr3B 761761940 761762475 535 False 521.000000 521 84.25900 1016 1554 1 chr3B.!!$F1 538
6 TraesCS3A01G475100 chr3B 760547991 760548517 526 True 291.000000 291 76.96500 1011 1553 1 chr3B.!!$R2 542
7 TraesCS3A01G475100 chr5D 446280276 446280973 697 True 1027.000000 1027 93.41900 1 690 1 chr5D.!!$R2 689
8 TraesCS3A01G475100 chr2A 705285806 705286429 623 False 537.000000 848 98.11200 1 689 2 chr2A.!!$F2 688

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
291 301 0.107945 CCCTTCTCTGCCTTCTTCCG 60.108 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 1864 0.038166 TCACCTCATCAAAGGCCCAC 59.962 55.0 0.0 0.0 40.34 4.61 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
137 147 4.737578 AGACTCACCTTGTAGTACTGGAA 58.262 43.478 5.39 0.00 0.00 3.53
291 301 0.107945 CCCTTCTCTGCCTTCTTCCG 60.108 60.000 0.00 0.00 0.00 4.30
395 405 3.947173 GCAGCTGCTCCTCTCCTA 58.053 61.111 31.33 0.00 38.21 2.94
404 414 0.882927 CTCCTCTCCTACTCCGCTCG 60.883 65.000 0.00 0.00 0.00 5.03
593 603 6.464222 AGAGTTGTGTCGAAATTTCTGGATA 58.536 36.000 15.92 2.95 0.00 2.59
636 646 9.629878 GCTACAGAGTAGGGTACATATATGTAT 57.370 37.037 24.67 13.87 44.25 2.29
690 702 0.944386 CACACACAGCCCAACACTAC 59.056 55.000 0.00 0.00 0.00 2.73
691 703 0.837272 ACACACAGCCCAACACTACT 59.163 50.000 0.00 0.00 0.00 2.57
765 777 3.171388 ATGGGCGCCCCTAAGAGG 61.171 66.667 41.75 0.00 45.70 3.69
812 824 1.000283 CATCCGTCACTCCTAGGCATC 60.000 57.143 2.96 0.00 0.00 3.91
889 901 6.938030 AGTCGTATTATTTGTGGGTTTCTTCA 59.062 34.615 0.00 0.00 0.00 3.02
971 983 8.276325 CGTACATATAACCAGCAGATTCTTTTC 58.724 37.037 0.00 0.00 0.00 2.29
985 997 7.649306 GCAGATTCTTTTCATGTACAAACAACT 59.351 33.333 0.00 0.00 39.58 3.16
995 1007 7.995289 TCATGTACAAACAACTGATTCTTGTT 58.005 30.769 0.00 0.00 42.41 2.83
996 1008 9.114952 TCATGTACAAACAACTGATTCTTGTTA 57.885 29.630 0.00 0.00 40.24 2.41
997 1009 9.897744 CATGTACAAACAACTGATTCTTGTTAT 57.102 29.630 0.00 1.21 40.24 1.89
1035 1047 7.897575 ACGATTTTCCAGATATCAGCTAATC 57.102 36.000 5.32 6.53 0.00 1.75
1151 1163 4.403432 ACTTATGTCTGCCATCCAAAATGG 59.597 41.667 0.00 0.00 41.99 3.16
1193 1205 5.813717 TCAGAACGCATGATCATCAAATTC 58.186 37.500 4.86 7.67 0.00 2.17
1465 1478 2.156917 TGTTCAAGCATGCCTGAAGAG 58.843 47.619 27.86 5.74 0.00 2.85
1476 1489 2.302733 TGCCTGAAGAGCTACACATCAA 59.697 45.455 0.00 0.00 0.00 2.57
1576 1590 3.030652 GGAATACCCCGCGCATTG 58.969 61.111 8.75 0.00 0.00 2.82
1577 1591 2.331451 GAATACCCCGCGCATTGC 59.669 61.111 8.75 0.00 41.47 3.56
1578 1592 2.124320 AATACCCCGCGCATTGCT 60.124 55.556 8.75 0.00 43.27 3.91
1579 1593 2.392613 GAATACCCCGCGCATTGCTG 62.393 60.000 8.75 1.74 43.27 4.41
1588 1602 2.650196 GCATTGCTGCGGAAACCA 59.350 55.556 0.16 0.00 38.92 3.67
1589 1603 1.216178 GCATTGCTGCGGAAACCAT 59.784 52.632 0.16 0.00 38.92 3.55
1590 1604 0.390209 GCATTGCTGCGGAAACCATT 60.390 50.000 0.16 0.00 38.92 3.16
1591 1605 1.352114 CATTGCTGCGGAAACCATTG 58.648 50.000 0.00 0.00 0.00 2.82
1592 1606 0.390209 ATTGCTGCGGAAACCATTGC 60.390 50.000 0.00 0.00 0.00 3.56
1593 1607 1.742324 TTGCTGCGGAAACCATTGCA 61.742 50.000 0.00 0.00 35.75 4.08
1594 1608 1.006337 GCTGCGGAAACCATTGCAA 60.006 52.632 0.00 0.00 36.82 4.08
1595 1609 0.390209 GCTGCGGAAACCATTGCAAT 60.390 50.000 5.99 5.99 36.82 3.56
1596 1610 1.135141 GCTGCGGAAACCATTGCAATA 60.135 47.619 12.53 0.00 36.82 1.90
1597 1611 2.481795 GCTGCGGAAACCATTGCAATAT 60.482 45.455 12.53 0.00 36.82 1.28
1598 1612 3.243367 GCTGCGGAAACCATTGCAATATA 60.243 43.478 12.53 0.00 36.82 0.86
1599 1613 4.559300 GCTGCGGAAACCATTGCAATATAT 60.559 41.667 12.53 0.00 36.82 0.86
1600 1614 5.528043 TGCGGAAACCATTGCAATATATT 57.472 34.783 12.53 7.02 33.80 1.28
1601 1615 5.911752 TGCGGAAACCATTGCAATATATTT 58.088 33.333 12.53 12.32 33.80 1.40
1602 1616 5.982516 TGCGGAAACCATTGCAATATATTTC 59.017 36.000 22.23 22.23 33.80 2.17
1603 1617 5.982516 GCGGAAACCATTGCAATATATTTCA 59.017 36.000 26.88 0.00 0.00 2.69
1604 1618 6.144402 GCGGAAACCATTGCAATATATTTCAG 59.856 38.462 26.88 25.01 0.00 3.02
1605 1619 7.202526 CGGAAACCATTGCAATATATTTCAGT 58.797 34.615 26.88 10.74 0.00 3.41
1606 1620 7.167968 CGGAAACCATTGCAATATATTTCAGTG 59.832 37.037 26.88 11.80 0.00 3.66
1607 1621 8.196771 GGAAACCATTGCAATATATTTCAGTGA 58.803 33.333 26.88 0.00 0.00 3.41
1608 1622 9.754382 GAAACCATTGCAATATATTTCAGTGAT 57.246 29.630 23.88 2.57 0.00 3.06
1611 1625 9.537192 ACCATTGCAATATATTTCAGTGATTTG 57.463 29.630 17.86 7.30 0.00 2.32
1612 1626 9.752961 CCATTGCAATATATTTCAGTGATTTGA 57.247 29.630 17.86 0.00 0.00 2.69
1623 1637 8.922058 ATTTCAGTGATTTGATTGTATGAAGC 57.078 30.769 0.00 0.00 0.00 3.86
1624 1638 7.692460 TTCAGTGATTTGATTGTATGAAGCT 57.308 32.000 0.00 0.00 0.00 3.74
1625 1639 7.692460 TCAGTGATTTGATTGTATGAAGCTT 57.308 32.000 0.00 0.00 0.00 3.74
1626 1640 8.114331 TCAGTGATTTGATTGTATGAAGCTTT 57.886 30.769 0.00 0.00 0.00 3.51
1627 1641 8.239314 TCAGTGATTTGATTGTATGAAGCTTTC 58.761 33.333 0.00 0.00 0.00 2.62
1628 1642 8.024865 CAGTGATTTGATTGTATGAAGCTTTCA 58.975 33.333 0.00 0.27 45.01 2.69
1629 1643 8.242053 AGTGATTTGATTGTATGAAGCTTTCAG 58.758 33.333 0.00 0.00 43.98 3.02
1630 1644 7.008992 GTGATTTGATTGTATGAAGCTTTCAGC 59.991 37.037 0.00 0.00 43.98 4.26
1703 1717 9.607988 ATTGTATTTGATTATTGTGTAGTCGGA 57.392 29.630 0.00 0.00 0.00 4.55
1704 1718 9.438228 TTGTATTTGATTATTGTGTAGTCGGAA 57.562 29.630 0.00 0.00 0.00 4.30
1705 1719 9.438228 TGTATTTGATTATTGTGTAGTCGGAAA 57.562 29.630 0.00 0.00 0.00 3.13
1765 1779 4.933505 TTTTTCATGCATGTTGAGTGGA 57.066 36.364 25.43 1.24 0.00 4.02
1766 1780 3.921119 TTTCATGCATGTTGAGTGGAC 57.079 42.857 25.43 0.00 0.00 4.02
1767 1781 2.865119 TCATGCATGTTGAGTGGACT 57.135 45.000 25.43 0.00 0.00 3.85
1768 1782 3.144657 TCATGCATGTTGAGTGGACTT 57.855 42.857 25.43 0.00 0.00 3.01
1769 1783 3.489355 TCATGCATGTTGAGTGGACTTT 58.511 40.909 25.43 0.00 0.00 2.66
1770 1784 3.890756 TCATGCATGTTGAGTGGACTTTT 59.109 39.130 25.43 0.00 0.00 2.27
1771 1785 3.713858 TGCATGTTGAGTGGACTTTTG 57.286 42.857 0.00 0.00 0.00 2.44
1772 1786 3.286353 TGCATGTTGAGTGGACTTTTGA 58.714 40.909 0.00 0.00 0.00 2.69
1773 1787 3.890756 TGCATGTTGAGTGGACTTTTGAT 59.109 39.130 0.00 0.00 0.00 2.57
1774 1788 4.232221 GCATGTTGAGTGGACTTTTGATG 58.768 43.478 0.00 0.00 0.00 3.07
1775 1789 4.022935 GCATGTTGAGTGGACTTTTGATGA 60.023 41.667 0.00 0.00 0.00 2.92
1776 1790 5.696822 CATGTTGAGTGGACTTTTGATGAG 58.303 41.667 0.00 0.00 0.00 2.90
1777 1791 4.136796 TGTTGAGTGGACTTTTGATGAGG 58.863 43.478 0.00 0.00 0.00 3.86
1778 1792 4.137543 GTTGAGTGGACTTTTGATGAGGT 58.862 43.478 0.00 0.00 0.00 3.85
1779 1793 3.743521 TGAGTGGACTTTTGATGAGGTG 58.256 45.455 0.00 0.00 0.00 4.00
1780 1794 2.485814 GAGTGGACTTTTGATGAGGTGC 59.514 50.000 0.00 0.00 0.00 5.01
1781 1795 1.541588 GTGGACTTTTGATGAGGTGCC 59.458 52.381 0.00 0.00 0.00 5.01
1782 1796 1.144708 TGGACTTTTGATGAGGTGCCA 59.855 47.619 0.00 0.00 0.00 4.92
1783 1797 2.225091 TGGACTTTTGATGAGGTGCCAT 60.225 45.455 0.00 0.00 0.00 4.40
1784 1798 2.165030 GGACTTTTGATGAGGTGCCATG 59.835 50.000 0.00 0.00 0.00 3.66
1785 1799 2.821969 GACTTTTGATGAGGTGCCATGT 59.178 45.455 0.00 0.00 0.00 3.21
1786 1800 2.559668 ACTTTTGATGAGGTGCCATGTG 59.440 45.455 0.00 0.00 0.00 3.21
1787 1801 2.291209 TTTGATGAGGTGCCATGTGT 57.709 45.000 0.00 0.00 0.00 3.72
1788 1802 1.536940 TTGATGAGGTGCCATGTGTG 58.463 50.000 0.00 0.00 0.00 3.82
1800 1814 3.631145 CCATGTGTGGTGAAGTGAAAG 57.369 47.619 0.00 0.00 40.83 2.62
1801 1815 2.294233 CCATGTGTGGTGAAGTGAAAGG 59.706 50.000 0.00 0.00 40.83 3.11
1802 1816 2.799126 TGTGTGGTGAAGTGAAAGGT 57.201 45.000 0.00 0.00 0.00 3.50
1803 1817 2.364632 TGTGTGGTGAAGTGAAAGGTG 58.635 47.619 0.00 0.00 0.00 4.00
1804 1818 2.290641 TGTGTGGTGAAGTGAAAGGTGT 60.291 45.455 0.00 0.00 0.00 4.16
1805 1819 2.097466 GTGTGGTGAAGTGAAAGGTGTG 59.903 50.000 0.00 0.00 0.00 3.82
1806 1820 1.065551 GTGGTGAAGTGAAAGGTGTGC 59.934 52.381 0.00 0.00 0.00 4.57
1807 1821 1.340502 TGGTGAAGTGAAAGGTGTGCA 60.341 47.619 0.00 0.00 0.00 4.57
1808 1822 1.956477 GGTGAAGTGAAAGGTGTGCAT 59.044 47.619 0.00 0.00 0.00 3.96
1809 1823 2.287788 GGTGAAGTGAAAGGTGTGCATG 60.288 50.000 0.00 0.00 0.00 4.06
1810 1824 2.618241 GTGAAGTGAAAGGTGTGCATGA 59.382 45.455 0.00 0.00 0.00 3.07
1811 1825 2.880268 TGAAGTGAAAGGTGTGCATGAG 59.120 45.455 0.00 0.00 0.00 2.90
1812 1826 2.936919 AGTGAAAGGTGTGCATGAGA 57.063 45.000 0.00 0.00 0.00 3.27
1813 1827 3.430042 AGTGAAAGGTGTGCATGAGAT 57.570 42.857 0.00 0.00 0.00 2.75
1814 1828 3.341823 AGTGAAAGGTGTGCATGAGATC 58.658 45.455 0.00 0.00 0.00 2.75
1815 1829 3.076621 GTGAAAGGTGTGCATGAGATCA 58.923 45.455 0.00 0.00 0.00 2.92
1816 1830 3.503363 GTGAAAGGTGTGCATGAGATCAA 59.497 43.478 0.00 0.00 0.00 2.57
1817 1831 4.157289 GTGAAAGGTGTGCATGAGATCAAT 59.843 41.667 0.00 0.00 0.00 2.57
1818 1832 4.768448 TGAAAGGTGTGCATGAGATCAATT 59.232 37.500 0.00 0.00 0.00 2.32
1819 1833 5.945191 TGAAAGGTGTGCATGAGATCAATTA 59.055 36.000 0.00 0.00 0.00 1.40
1820 1834 6.433716 TGAAAGGTGTGCATGAGATCAATTAA 59.566 34.615 0.00 0.00 0.00 1.40
1821 1835 7.123098 TGAAAGGTGTGCATGAGATCAATTAAT 59.877 33.333 0.00 0.00 0.00 1.40
1822 1836 8.523915 AAAGGTGTGCATGAGATCAATTAATA 57.476 30.769 0.00 0.00 0.00 0.98
1823 1837 8.523915 AAGGTGTGCATGAGATCAATTAATAA 57.476 30.769 0.00 0.00 0.00 1.40
1824 1838 8.701908 AGGTGTGCATGAGATCAATTAATAAT 57.298 30.769 0.00 0.00 0.00 1.28
1825 1839 8.573885 AGGTGTGCATGAGATCAATTAATAATG 58.426 33.333 0.00 0.00 0.00 1.90
1826 1840 8.570488 GGTGTGCATGAGATCAATTAATAATGA 58.430 33.333 0.00 0.00 0.00 2.57
1827 1841 9.955208 GTGTGCATGAGATCAATTAATAATGAA 57.045 29.630 0.00 0.00 0.00 2.57
1850 1864 4.741321 AAAATTCCCATGCATGTAGTGG 57.259 40.909 24.58 17.99 0.00 4.00
1851 1865 3.386932 AATTCCCATGCATGTAGTGGT 57.613 42.857 24.58 3.29 0.00 4.16
1852 1866 2.127271 TTCCCATGCATGTAGTGGTG 57.873 50.000 24.58 7.82 0.00 4.17
1853 1867 0.255604 TCCCATGCATGTAGTGGTGG 59.744 55.000 24.58 16.27 0.00 4.61
1854 1868 0.752743 CCCATGCATGTAGTGGTGGG 60.753 60.000 24.58 14.27 40.22 4.61
1855 1869 1.386525 CCATGCATGTAGTGGTGGGC 61.387 60.000 24.58 0.00 0.00 5.36
1856 1870 1.076777 ATGCATGTAGTGGTGGGCC 60.077 57.895 0.00 0.00 0.00 5.80
1857 1871 1.574526 ATGCATGTAGTGGTGGGCCT 61.575 55.000 4.53 0.00 35.27 5.19
1858 1872 1.000896 GCATGTAGTGGTGGGCCTT 60.001 57.895 4.53 0.00 35.27 4.35
1859 1873 0.611896 GCATGTAGTGGTGGGCCTTT 60.612 55.000 4.53 0.00 35.27 3.11
1860 1874 1.176527 CATGTAGTGGTGGGCCTTTG 58.823 55.000 4.53 0.00 35.27 2.77
1861 1875 1.072266 ATGTAGTGGTGGGCCTTTGA 58.928 50.000 4.53 0.00 35.27 2.69
1862 1876 1.072266 TGTAGTGGTGGGCCTTTGAT 58.928 50.000 4.53 0.00 35.27 2.57
1863 1877 1.271871 TGTAGTGGTGGGCCTTTGATG 60.272 52.381 4.53 0.00 35.27 3.07
1864 1878 1.004277 GTAGTGGTGGGCCTTTGATGA 59.996 52.381 4.53 0.00 35.27 2.92
1865 1879 0.038744 AGTGGTGGGCCTTTGATGAG 59.961 55.000 4.53 0.00 35.27 2.90
1866 1880 0.967380 GTGGTGGGCCTTTGATGAGG 60.967 60.000 4.53 0.00 39.93 3.86
1867 1881 1.384191 GGTGGGCCTTTGATGAGGT 59.616 57.895 4.53 0.00 39.11 3.85
1868 1882 0.967380 GGTGGGCCTTTGATGAGGTG 60.967 60.000 4.53 0.00 39.11 4.00
1869 1883 0.038166 GTGGGCCTTTGATGAGGTGA 59.962 55.000 4.53 0.00 39.11 4.02
1870 1884 0.038166 TGGGCCTTTGATGAGGTGAC 59.962 55.000 4.53 0.00 39.11 3.67
1871 1885 0.038166 GGGCCTTTGATGAGGTGACA 59.962 55.000 0.84 0.00 39.11 3.58
1872 1886 1.341383 GGGCCTTTGATGAGGTGACAT 60.341 52.381 0.84 0.00 39.11 3.06
1873 1887 1.747355 GGCCTTTGATGAGGTGACATG 59.253 52.381 0.00 0.00 39.11 3.21
1874 1888 2.440409 GCCTTTGATGAGGTGACATGT 58.560 47.619 0.00 0.00 39.11 3.21
1875 1889 2.163010 GCCTTTGATGAGGTGACATGTG 59.837 50.000 1.15 0.00 39.11 3.21
1876 1890 3.415212 CCTTTGATGAGGTGACATGTGT 58.585 45.455 1.15 0.00 31.89 3.72
1877 1891 3.189910 CCTTTGATGAGGTGACATGTGTG 59.810 47.826 1.15 0.00 31.89 3.82
1878 1892 1.812235 TGATGAGGTGACATGTGTGC 58.188 50.000 1.15 0.00 0.00 4.57
1879 1893 1.072015 TGATGAGGTGACATGTGTGCA 59.928 47.619 1.15 0.00 0.00 4.57
1880 1894 2.290450 TGATGAGGTGACATGTGTGCAT 60.290 45.455 1.15 0.00 35.32 3.96
1895 1909 6.682423 TGTGTGCATGTTGAGATAAATAGG 57.318 37.500 0.00 0.00 0.00 2.57
1896 1910 6.413892 TGTGTGCATGTTGAGATAAATAGGA 58.586 36.000 0.00 0.00 0.00 2.94
1897 1911 7.056006 TGTGTGCATGTTGAGATAAATAGGAT 58.944 34.615 0.00 0.00 0.00 3.24
1898 1912 8.210265 TGTGTGCATGTTGAGATAAATAGGATA 58.790 33.333 0.00 0.00 0.00 2.59
1899 1913 8.715998 GTGTGCATGTTGAGATAAATAGGATAG 58.284 37.037 0.00 0.00 0.00 2.08
1900 1914 8.432013 TGTGCATGTTGAGATAAATAGGATAGT 58.568 33.333 0.00 0.00 0.00 2.12
1901 1915 8.715998 GTGCATGTTGAGATAAATAGGATAGTG 58.284 37.037 0.00 0.00 0.00 2.74
1902 1916 7.879677 TGCATGTTGAGATAAATAGGATAGTGG 59.120 37.037 0.00 0.00 0.00 4.00
1903 1917 7.335422 GCATGTTGAGATAAATAGGATAGTGGG 59.665 40.741 0.00 0.00 0.00 4.61
1904 1918 7.316393 TGTTGAGATAAATAGGATAGTGGGG 57.684 40.000 0.00 0.00 0.00 4.96
1905 1919 7.079700 TGTTGAGATAAATAGGATAGTGGGGA 58.920 38.462 0.00 0.00 0.00 4.81
1906 1920 7.739444 TGTTGAGATAAATAGGATAGTGGGGAT 59.261 37.037 0.00 0.00 0.00 3.85
1907 1921 7.979786 TGAGATAAATAGGATAGTGGGGATC 57.020 40.000 0.00 0.00 0.00 3.36
1908 1922 7.487338 TGAGATAAATAGGATAGTGGGGATCA 58.513 38.462 0.00 0.00 0.00 2.92
1909 1923 7.961431 TGAGATAAATAGGATAGTGGGGATCAA 59.039 37.037 0.00 0.00 0.00 2.57
1910 1924 8.152023 AGATAAATAGGATAGTGGGGATCAAC 57.848 38.462 0.00 0.00 0.00 3.18
1911 1925 7.964293 AGATAAATAGGATAGTGGGGATCAACT 59.036 37.037 0.00 0.00 0.00 3.16
1912 1926 6.848562 AAATAGGATAGTGGGGATCAACTT 57.151 37.500 0.00 0.00 0.00 2.66
1913 1927 6.441088 AATAGGATAGTGGGGATCAACTTC 57.559 41.667 0.00 0.00 0.00 3.01
1914 1928 4.014273 AGGATAGTGGGGATCAACTTCT 57.986 45.455 0.00 0.00 0.00 2.85
1915 1929 4.375313 AGGATAGTGGGGATCAACTTCTT 58.625 43.478 0.00 0.00 0.00 2.52
1916 1930 5.538877 AGGATAGTGGGGATCAACTTCTTA 58.461 41.667 0.00 0.00 0.00 2.10
1917 1931 6.153924 AGGATAGTGGGGATCAACTTCTTAT 58.846 40.000 0.00 0.00 0.00 1.73
1918 1932 6.043706 AGGATAGTGGGGATCAACTTCTTATG 59.956 42.308 0.00 0.00 0.00 1.90
1919 1933 6.183361 GGATAGTGGGGATCAACTTCTTATGT 60.183 42.308 0.00 0.00 0.00 2.29
1920 1934 7.016268 GGATAGTGGGGATCAACTTCTTATGTA 59.984 40.741 0.00 0.00 0.00 2.29
1921 1935 6.831664 AGTGGGGATCAACTTCTTATGTAT 57.168 37.500 0.00 0.00 0.00 2.29
1922 1936 7.931015 AGTGGGGATCAACTTCTTATGTATA 57.069 36.000 0.00 0.00 0.00 1.47
1923 1937 8.511748 AGTGGGGATCAACTTCTTATGTATAT 57.488 34.615 0.00 0.00 0.00 0.86
1924 1938 9.615660 AGTGGGGATCAACTTCTTATGTATATA 57.384 33.333 0.00 0.00 0.00 0.86
2030 2044 6.352516 AGGATTGAGTAGATTGATGTCAACC 58.647 40.000 0.00 0.00 38.86 3.77
2156 2171 6.923508 TGCATAGGTGTCGAATTCTTACATAG 59.076 38.462 12.07 4.68 0.00 2.23
2323 2340 5.512788 GCATTTGTGTGTATGCTTATGTCAC 59.487 40.000 0.00 0.00 42.91 3.67
2328 2345 4.636249 TGTGTATGCTTATGTCACACACA 58.364 39.130 3.48 3.48 43.22 3.72
2329 2346 4.450757 TGTGTATGCTTATGTCACACACAC 59.549 41.667 3.48 0.00 43.22 3.82
2330 2347 4.450757 GTGTATGCTTATGTCACACACACA 59.549 41.667 0.00 0.00 38.04 3.72
2331 2348 4.450757 TGTATGCTTATGTCACACACACAC 59.549 41.667 0.00 0.00 38.04 3.82
2332 2349 2.911484 TGCTTATGTCACACACACACA 58.089 42.857 0.00 0.00 38.04 3.72
2333 2350 2.611751 TGCTTATGTCACACACACACAC 59.388 45.455 0.00 0.00 38.04 3.82
2334 2351 2.611751 GCTTATGTCACACACACACACA 59.388 45.455 0.00 0.00 38.04 3.72
2335 2352 3.546020 GCTTATGTCACACACACACACAC 60.546 47.826 0.00 0.00 38.04 3.82
2336 2353 2.106477 ATGTCACACACACACACACA 57.894 45.000 0.00 0.00 38.04 3.72
2337 2354 1.152510 TGTCACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
2338 2355 1.152510 GTCACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
2339 2356 1.136085 GTCACACACACACACACACAC 60.136 52.381 0.00 0.00 0.00 3.82
2340 2357 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2341 2358 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2342 2359 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2343 2360 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2344 2361 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2345 2362 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2346 2363 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2347 2364 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2348 2365 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2349 2366 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 2.080693 CTGCGGTTTGCCTGTGTATTA 58.919 47.619 0.00 0.00 45.60 0.98
137 147 1.676006 GTACCTTGCTGTGCTTGTTGT 59.324 47.619 0.00 0.00 0.00 3.32
291 301 1.357991 GACAGAAGAAGGCAGCTCGC 61.358 60.000 0.00 0.00 41.28 5.03
395 405 3.063084 GGTGGTCTCGAGCGGAGT 61.063 66.667 7.81 0.00 43.60 3.85
404 414 1.590147 CCGTACTGGTGGTGGTCTC 59.410 63.158 0.00 0.00 0.00 3.36
528 538 3.323622 CTGCTGTAGCCCCCATCA 58.676 61.111 0.80 0.00 41.18 3.07
579 589 4.816925 GGGAGAAGGTATCCAGAAATTTCG 59.183 45.833 12.42 7.63 38.70 3.46
593 603 0.327000 AGCTAGCCATGGGAGAAGGT 60.327 55.000 15.13 0.00 0.00 3.50
812 824 0.251354 AGCATCACACTACTGCAGGG 59.749 55.000 19.93 12.82 38.37 4.45
889 901 2.222445 GCTTGGACATAACAACGACGTT 59.778 45.455 7.57 7.57 0.00 3.99
950 962 8.757982 ACATGAAAAGAATCTGCTGGTTATAT 57.242 30.769 0.00 0.00 0.00 0.86
953 965 6.939730 TGTACATGAAAAGAATCTGCTGGTTA 59.060 34.615 0.00 0.00 0.00 2.85
971 983 9.897744 ATAACAAGAATCAGTTGTTTGTACATG 57.102 29.630 6.53 0.00 43.97 3.21
998 1010 9.832445 ATCTGGAAAATCGTAAGTTGTACATAT 57.168 29.630 0.00 0.00 39.48 1.78
1151 1163 7.222999 CGTTCTGATTTGAGATTCCTTACCTAC 59.777 40.741 0.00 0.00 0.00 3.18
1465 1478 6.955963 CGTCTTCTGTAAAATTGATGTGTAGC 59.044 38.462 0.00 0.00 0.00 3.58
1476 1489 2.744202 CTGCAGGCGTCTTCTGTAAAAT 59.256 45.455 5.57 0.00 34.89 1.82
1559 1573 3.030652 CAATGCGCGGGGTATTCC 58.969 61.111 8.83 0.00 0.00 3.01
1560 1574 2.331451 GCAATGCGCGGGGTATTC 59.669 61.111 8.83 0.00 0.00 1.75
1571 1585 0.390209 AATGGTTTCCGCAGCAATGC 60.390 50.000 0.00 0.00 0.00 3.56
1572 1586 1.352114 CAATGGTTTCCGCAGCAATG 58.648 50.000 0.00 0.00 0.00 2.82
1573 1587 0.390209 GCAATGGTTTCCGCAGCAAT 60.390 50.000 0.00 0.00 0.00 3.56
1574 1588 1.006337 GCAATGGTTTCCGCAGCAA 60.006 52.632 0.00 0.00 0.00 3.91
1575 1589 1.742324 TTGCAATGGTTTCCGCAGCA 61.742 50.000 0.00 0.00 35.47 4.41
1576 1590 0.390209 ATTGCAATGGTTTCCGCAGC 60.390 50.000 12.09 0.00 35.47 5.25
1577 1591 2.937469 TATTGCAATGGTTTCCGCAG 57.063 45.000 22.27 0.00 35.47 5.18
1578 1592 5.528043 AATATATTGCAATGGTTTCCGCA 57.472 34.783 22.27 0.00 0.00 5.69
1579 1593 5.982516 TGAAATATATTGCAATGGTTTCCGC 59.017 36.000 25.99 14.01 0.00 5.54
1580 1594 7.167968 CACTGAAATATATTGCAATGGTTTCCG 59.832 37.037 25.99 23.70 0.00 4.30
1581 1595 8.196771 TCACTGAAATATATTGCAATGGTTTCC 58.803 33.333 25.99 16.67 0.00 3.13
1582 1596 9.754382 ATCACTGAAATATATTGCAATGGTTTC 57.246 29.630 22.27 23.53 0.00 2.78
1585 1599 9.537192 CAAATCACTGAAATATATTGCAATGGT 57.463 29.630 22.27 12.60 0.00 3.55
1586 1600 9.752961 TCAAATCACTGAAATATATTGCAATGG 57.247 29.630 22.27 2.98 0.00 3.16
1598 1612 8.746530 AGCTTCATACAATCAAATCACTGAAAT 58.253 29.630 0.00 0.00 0.00 2.17
1599 1613 8.114331 AGCTTCATACAATCAAATCACTGAAA 57.886 30.769 0.00 0.00 0.00 2.69
1600 1614 7.692460 AGCTTCATACAATCAAATCACTGAA 57.308 32.000 0.00 0.00 0.00 3.02
1601 1615 7.692460 AAGCTTCATACAATCAAATCACTGA 57.308 32.000 0.00 0.00 0.00 3.41
1602 1616 8.024865 TGAAAGCTTCATACAATCAAATCACTG 58.975 33.333 0.00 0.00 34.08 3.66
1603 1617 8.114331 TGAAAGCTTCATACAATCAAATCACT 57.886 30.769 0.00 0.00 34.08 3.41
1604 1618 8.390854 CTGAAAGCTTCATACAATCAAATCAC 57.609 34.615 0.00 0.00 39.30 3.06
1677 1691 9.607988 TCCGACTACACAATAATCAAATACAAT 57.392 29.630 0.00 0.00 0.00 2.71
1678 1692 9.438228 TTCCGACTACACAATAATCAAATACAA 57.562 29.630 0.00 0.00 0.00 2.41
1679 1693 9.438228 TTTCCGACTACACAATAATCAAATACA 57.562 29.630 0.00 0.00 0.00 2.29
1744 1758 4.341806 AGTCCACTCAACATGCATGAAAAA 59.658 37.500 32.75 13.51 0.00 1.94
1745 1759 3.890756 AGTCCACTCAACATGCATGAAAA 59.109 39.130 32.75 15.21 0.00 2.29
1746 1760 3.489355 AGTCCACTCAACATGCATGAAA 58.511 40.909 32.75 15.55 0.00 2.69
1747 1761 3.144657 AGTCCACTCAACATGCATGAA 57.855 42.857 32.75 15.89 0.00 2.57
1748 1762 2.865119 AGTCCACTCAACATGCATGA 57.135 45.000 32.75 11.15 0.00 3.07
1749 1763 3.928727 AAAGTCCACTCAACATGCATG 57.071 42.857 25.09 25.09 0.00 4.06
1750 1764 3.890756 TCAAAAGTCCACTCAACATGCAT 59.109 39.130 0.00 0.00 0.00 3.96
1751 1765 3.286353 TCAAAAGTCCACTCAACATGCA 58.714 40.909 0.00 0.00 0.00 3.96
1752 1766 3.988379 TCAAAAGTCCACTCAACATGC 57.012 42.857 0.00 0.00 0.00 4.06
1753 1767 5.335426 CCTCATCAAAAGTCCACTCAACATG 60.335 44.000 0.00 0.00 0.00 3.21
1754 1768 4.763793 CCTCATCAAAAGTCCACTCAACAT 59.236 41.667 0.00 0.00 0.00 2.71
1755 1769 4.136796 CCTCATCAAAAGTCCACTCAACA 58.863 43.478 0.00 0.00 0.00 3.33
1756 1770 4.023707 CACCTCATCAAAAGTCCACTCAAC 60.024 45.833 0.00 0.00 0.00 3.18
1757 1771 4.136796 CACCTCATCAAAAGTCCACTCAA 58.863 43.478 0.00 0.00 0.00 3.02
1758 1772 3.743521 CACCTCATCAAAAGTCCACTCA 58.256 45.455 0.00 0.00 0.00 3.41
1759 1773 2.485814 GCACCTCATCAAAAGTCCACTC 59.514 50.000 0.00 0.00 0.00 3.51
1760 1774 2.508526 GCACCTCATCAAAAGTCCACT 58.491 47.619 0.00 0.00 0.00 4.00
1761 1775 1.541588 GGCACCTCATCAAAAGTCCAC 59.458 52.381 0.00 0.00 0.00 4.02
1762 1776 1.144708 TGGCACCTCATCAAAAGTCCA 59.855 47.619 0.00 0.00 0.00 4.02
1763 1777 1.909700 TGGCACCTCATCAAAAGTCC 58.090 50.000 0.00 0.00 0.00 3.85
1764 1778 2.821969 ACATGGCACCTCATCAAAAGTC 59.178 45.455 0.00 0.00 0.00 3.01
1765 1779 2.559668 CACATGGCACCTCATCAAAAGT 59.440 45.455 0.00 0.00 0.00 2.66
1766 1780 2.559668 ACACATGGCACCTCATCAAAAG 59.440 45.455 0.00 0.00 0.00 2.27
1767 1781 2.296752 CACACATGGCACCTCATCAAAA 59.703 45.455 0.00 0.00 0.00 2.44
1768 1782 1.887854 CACACATGGCACCTCATCAAA 59.112 47.619 0.00 0.00 0.00 2.69
1769 1783 1.536940 CACACATGGCACCTCATCAA 58.463 50.000 0.00 0.00 0.00 2.57
1770 1784 0.322726 CCACACATGGCACCTCATCA 60.323 55.000 0.00 0.00 39.82 3.07
1771 1785 2.485677 CCACACATGGCACCTCATC 58.514 57.895 0.00 0.00 39.82 2.92
1772 1786 4.749323 CCACACATGGCACCTCAT 57.251 55.556 0.00 0.00 39.82 2.90
1781 1795 2.951642 ACCTTTCACTTCACCACACATG 59.048 45.455 0.00 0.00 0.00 3.21
1782 1796 2.951642 CACCTTTCACTTCACCACACAT 59.048 45.455 0.00 0.00 0.00 3.21
1783 1797 2.290641 ACACCTTTCACTTCACCACACA 60.291 45.455 0.00 0.00 0.00 3.72
1784 1798 2.097466 CACACCTTTCACTTCACCACAC 59.903 50.000 0.00 0.00 0.00 3.82
1785 1799 2.364632 CACACCTTTCACTTCACCACA 58.635 47.619 0.00 0.00 0.00 4.17
1786 1800 1.065551 GCACACCTTTCACTTCACCAC 59.934 52.381 0.00 0.00 0.00 4.16
1787 1801 1.340502 TGCACACCTTTCACTTCACCA 60.341 47.619 0.00 0.00 0.00 4.17
1788 1802 1.388547 TGCACACCTTTCACTTCACC 58.611 50.000 0.00 0.00 0.00 4.02
1789 1803 2.618241 TCATGCACACCTTTCACTTCAC 59.382 45.455 0.00 0.00 0.00 3.18
1790 1804 2.880268 CTCATGCACACCTTTCACTTCA 59.120 45.455 0.00 0.00 0.00 3.02
1791 1805 3.141398 TCTCATGCACACCTTTCACTTC 58.859 45.455 0.00 0.00 0.00 3.01
1792 1806 3.213206 TCTCATGCACACCTTTCACTT 57.787 42.857 0.00 0.00 0.00 3.16
1793 1807 2.936919 TCTCATGCACACCTTTCACT 57.063 45.000 0.00 0.00 0.00 3.41
1794 1808 3.076621 TGATCTCATGCACACCTTTCAC 58.923 45.455 0.00 0.00 0.00 3.18
1795 1809 3.421919 TGATCTCATGCACACCTTTCA 57.578 42.857 0.00 0.00 0.00 2.69
1796 1810 4.978083 ATTGATCTCATGCACACCTTTC 57.022 40.909 0.00 0.00 0.00 2.62
1797 1811 6.839124 TTAATTGATCTCATGCACACCTTT 57.161 33.333 0.00 0.00 0.00 3.11
1798 1812 8.523915 TTATTAATTGATCTCATGCACACCTT 57.476 30.769 0.00 0.00 0.00 3.50
1799 1813 8.573885 CATTATTAATTGATCTCATGCACACCT 58.426 33.333 0.00 0.00 0.00 4.00
1800 1814 8.570488 TCATTATTAATTGATCTCATGCACACC 58.430 33.333 0.00 0.00 0.00 4.16
1801 1815 9.955208 TTCATTATTAATTGATCTCATGCACAC 57.045 29.630 0.00 0.00 0.00 3.82
1828 1842 4.531732 ACCACTACATGCATGGGAATTTTT 59.468 37.500 29.41 9.36 37.86 1.94
1829 1843 4.081531 CACCACTACATGCATGGGAATTTT 60.082 41.667 29.41 10.09 37.86 1.82
1830 1844 3.448301 CACCACTACATGCATGGGAATTT 59.552 43.478 29.41 10.82 37.86 1.82
1831 1845 3.025978 CACCACTACATGCATGGGAATT 58.974 45.455 29.41 11.55 37.86 2.17
1832 1846 2.658285 CACCACTACATGCATGGGAAT 58.342 47.619 29.41 11.93 37.86 3.01
1833 1847 1.340893 CCACCACTACATGCATGGGAA 60.341 52.381 29.41 14.03 37.86 3.97
1834 1848 0.255604 CCACCACTACATGCATGGGA 59.744 55.000 29.41 16.32 37.86 4.37
1835 1849 0.752743 CCCACCACTACATGCATGGG 60.753 60.000 29.41 22.06 43.31 4.00
1836 1850 1.386525 GCCCACCACTACATGCATGG 61.387 60.000 29.41 16.32 39.57 3.66
1837 1851 1.386525 GGCCCACCACTACATGCATG 61.387 60.000 25.09 25.09 35.26 4.06
1838 1852 1.076777 GGCCCACCACTACATGCAT 60.077 57.895 0.00 0.00 35.26 3.96
1839 1853 1.788518 AAGGCCCACCACTACATGCA 61.789 55.000 0.00 0.00 39.06 3.96
1840 1854 0.611896 AAAGGCCCACCACTACATGC 60.612 55.000 0.00 0.00 39.06 4.06
1841 1855 1.176527 CAAAGGCCCACCACTACATG 58.823 55.000 0.00 0.00 39.06 3.21
1842 1856 1.072266 TCAAAGGCCCACCACTACAT 58.928 50.000 0.00 0.00 39.06 2.29
1843 1857 1.072266 ATCAAAGGCCCACCACTACA 58.928 50.000 0.00 0.00 39.06 2.74
1844 1858 1.004277 TCATCAAAGGCCCACCACTAC 59.996 52.381 0.00 0.00 39.06 2.73
1845 1859 1.281867 CTCATCAAAGGCCCACCACTA 59.718 52.381 0.00 0.00 39.06 2.74
1846 1860 0.038744 CTCATCAAAGGCCCACCACT 59.961 55.000 0.00 0.00 39.06 4.00
1847 1861 0.967380 CCTCATCAAAGGCCCACCAC 60.967 60.000 0.00 0.00 39.06 4.16
1848 1862 1.383799 CCTCATCAAAGGCCCACCA 59.616 57.895 0.00 0.00 39.06 4.17
1849 1863 0.967380 CACCTCATCAAAGGCCCACC 60.967 60.000 0.00 0.00 40.34 4.61
1850 1864 0.038166 TCACCTCATCAAAGGCCCAC 59.962 55.000 0.00 0.00 40.34 4.61
1851 1865 0.038166 GTCACCTCATCAAAGGCCCA 59.962 55.000 0.00 0.00 40.34 5.36
1852 1866 0.038166 TGTCACCTCATCAAAGGCCC 59.962 55.000 0.00 0.00 40.34 5.80
1853 1867 1.747355 CATGTCACCTCATCAAAGGCC 59.253 52.381 0.00 0.00 40.34 5.19
1854 1868 2.163010 CACATGTCACCTCATCAAAGGC 59.837 50.000 0.00 0.00 40.34 4.35
1855 1869 3.189910 CACACATGTCACCTCATCAAAGG 59.810 47.826 0.00 0.00 42.55 3.11
1856 1870 3.365666 GCACACATGTCACCTCATCAAAG 60.366 47.826 0.00 0.00 0.00 2.77
1857 1871 2.553602 GCACACATGTCACCTCATCAAA 59.446 45.455 0.00 0.00 0.00 2.69
1858 1872 2.153645 GCACACATGTCACCTCATCAA 58.846 47.619 0.00 0.00 0.00 2.57
1859 1873 1.072015 TGCACACATGTCACCTCATCA 59.928 47.619 0.00 0.00 0.00 3.07
1860 1874 1.812235 TGCACACATGTCACCTCATC 58.188 50.000 0.00 0.00 0.00 2.92
1861 1875 2.502142 ATGCACACATGTCACCTCAT 57.498 45.000 0.00 0.00 34.35 2.90
1871 1885 7.056006 TCCTATTTATCTCAACATGCACACAT 58.944 34.615 0.00 0.00 36.79 3.21
1872 1886 6.413892 TCCTATTTATCTCAACATGCACACA 58.586 36.000 0.00 0.00 0.00 3.72
1873 1887 6.925610 TCCTATTTATCTCAACATGCACAC 57.074 37.500 0.00 0.00 0.00 3.82
1874 1888 8.432013 ACTATCCTATTTATCTCAACATGCACA 58.568 33.333 0.00 0.00 0.00 4.57
1875 1889 8.715998 CACTATCCTATTTATCTCAACATGCAC 58.284 37.037 0.00 0.00 0.00 4.57
1876 1890 7.879677 CCACTATCCTATTTATCTCAACATGCA 59.120 37.037 0.00 0.00 0.00 3.96
1877 1891 7.335422 CCCACTATCCTATTTATCTCAACATGC 59.665 40.741 0.00 0.00 0.00 4.06
1878 1892 7.826252 CCCCACTATCCTATTTATCTCAACATG 59.174 40.741 0.00 0.00 0.00 3.21
1879 1893 7.739444 TCCCCACTATCCTATTTATCTCAACAT 59.261 37.037 0.00 0.00 0.00 2.71
1880 1894 7.079700 TCCCCACTATCCTATTTATCTCAACA 58.920 38.462 0.00 0.00 0.00 3.33
1881 1895 7.554959 TCCCCACTATCCTATTTATCTCAAC 57.445 40.000 0.00 0.00 0.00 3.18
1882 1896 7.961431 TGATCCCCACTATCCTATTTATCTCAA 59.039 37.037 0.00 0.00 0.00 3.02
1883 1897 7.487338 TGATCCCCACTATCCTATTTATCTCA 58.513 38.462 0.00 0.00 0.00 3.27
1884 1898 7.979786 TGATCCCCACTATCCTATTTATCTC 57.020 40.000 0.00 0.00 0.00 2.75
1885 1899 7.964293 AGTTGATCCCCACTATCCTATTTATCT 59.036 37.037 0.00 0.00 0.00 1.98
1886 1900 8.152023 AGTTGATCCCCACTATCCTATTTATC 57.848 38.462 0.00 0.00 0.00 1.75
1887 1901 8.525729 AAGTTGATCCCCACTATCCTATTTAT 57.474 34.615 0.00 0.00 0.00 1.40
1888 1902 7.794683 AGAAGTTGATCCCCACTATCCTATTTA 59.205 37.037 0.00 0.00 0.00 1.40
1889 1903 6.621514 AGAAGTTGATCCCCACTATCCTATTT 59.378 38.462 0.00 0.00 0.00 1.40
1890 1904 6.153924 AGAAGTTGATCCCCACTATCCTATT 58.846 40.000 0.00 0.00 0.00 1.73
1891 1905 5.731924 AGAAGTTGATCCCCACTATCCTAT 58.268 41.667 0.00 0.00 0.00 2.57
1892 1906 5.157770 AGAAGTTGATCCCCACTATCCTA 57.842 43.478 0.00 0.00 0.00 2.94
1893 1907 4.014273 AGAAGTTGATCCCCACTATCCT 57.986 45.455 0.00 0.00 0.00 3.24
1894 1908 4.779993 AAGAAGTTGATCCCCACTATCC 57.220 45.455 0.00 0.00 0.00 2.59
1895 1909 6.831976 ACATAAGAAGTTGATCCCCACTATC 58.168 40.000 0.00 0.00 0.00 2.08
1896 1910 6.831664 ACATAAGAAGTTGATCCCCACTAT 57.168 37.500 0.00 0.00 0.00 2.12
1897 1911 7.931015 ATACATAAGAAGTTGATCCCCACTA 57.069 36.000 0.00 0.00 0.00 2.74
1898 1912 6.831664 ATACATAAGAAGTTGATCCCCACT 57.168 37.500 0.00 0.00 0.00 4.00
1916 1930 7.978414 CCGCTGACTTCAGAATCATATATACAT 59.022 37.037 10.54 0.00 46.59 2.29
1917 1931 7.039714 ACCGCTGACTTCAGAATCATATATACA 60.040 37.037 10.54 0.00 46.59 2.29
1918 1932 7.274468 CACCGCTGACTTCAGAATCATATATAC 59.726 40.741 10.54 0.00 46.59 1.47
1919 1933 7.315890 CACCGCTGACTTCAGAATCATATATA 58.684 38.462 10.54 0.00 46.59 0.86
1920 1934 6.162079 CACCGCTGACTTCAGAATCATATAT 58.838 40.000 10.54 0.00 46.59 0.86
1921 1935 5.509670 CCACCGCTGACTTCAGAATCATATA 60.510 44.000 10.54 0.00 46.59 0.86
1922 1936 4.375272 CACCGCTGACTTCAGAATCATAT 58.625 43.478 10.54 0.00 46.59 1.78
1923 1937 3.430790 CCACCGCTGACTTCAGAATCATA 60.431 47.826 10.54 0.00 46.59 2.15
1924 1938 2.625737 CACCGCTGACTTCAGAATCAT 58.374 47.619 10.54 0.00 46.59 2.45
1925 1939 1.338105 CCACCGCTGACTTCAGAATCA 60.338 52.381 10.54 0.00 46.59 2.57
1926 1940 1.338200 ACCACCGCTGACTTCAGAATC 60.338 52.381 10.54 0.00 46.59 2.52
1927 1941 0.687354 ACCACCGCTGACTTCAGAAT 59.313 50.000 10.54 0.00 46.59 2.40
1935 1949 1.204941 AGACTAATGACCACCGCTGAC 59.795 52.381 0.00 0.00 0.00 3.51
2030 2044 2.819608 CACAGTGGGGTCAATTTGGTAG 59.180 50.000 0.00 0.00 0.00 3.18
2212 2227 0.465705 TAAGAGGCCAGCATCTTCCG 59.534 55.000 21.44 0.00 42.41 4.30
2323 2340 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2325 2342 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2327 2344 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2328 2345 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2329 2346 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2330 2347 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2331 2348 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2332 2349 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
2333 2350 5.861222 ATATATGTGTGTGTGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.