Multiple sequence alignment - TraesCS1D01G188400

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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 TraesCS1D01G188400 chr1D 100.000 2111 0 0 1 2111 260891852 260893962 0.000000e+00 3899.0
1 TraesCS1D01G188400 chr1D 95.510 1559 54 7 1 1554 254416810 254418357 0.000000e+00 2477.0
2 TraesCS1D01G188400 chr1D 95.315 1558 68 4 1 1554 51878328 51876772 0.000000e+00 2468.0
3 TraesCS1D01G188400 chr6D 95.833 1560 54 8 1 1554 45511826 45510272 0.000000e+00 2510.0
4 TraesCS1D01G188400 chr5D 95.524 1564 59 9 1 1554 503287045 503288607 0.000000e+00 2490.0
5 TraesCS1D01G188400 chr5D 95.571 1558 60 9 1 1554 120799617 120801169 0.000000e+00 2486.0
6 TraesCS1D01G188400 chr5D 95.256 1560 58 9 1 1554 6181201 6179652 0.000000e+00 2457.0
7 TraesCS1D01G188400 chr5D 94.291 1559 77 12 1 1554 167071679 167073230 0.000000e+00 2375.0
8 TraesCS1D01G188400 chr5D 96.019 1055 34 7 508 1554 512416234 512415180 0.000000e+00 1709.0
9 TraesCS1D01G188400 chr1A 95.202 1563 54 10 1 1554 554458212 554459762 0.000000e+00 2451.0
10 TraesCS1D01G188400 chr2A 94.843 1144 42 8 418 1554 334595896 334594763 0.000000e+00 1770.0
11 TraesCS1D01G188400 chr4A 93.571 1151 70 4 1 1150 310730854 310729707 0.000000e+00 1712.0
12 TraesCS1D01G188400 chr6A 84.091 132 12 7 1931 2055 74821898 74821769 3.680000e-23 119.0
13 TraesCS1D01G188400 chr1B 100.000 31 0 0 1779 1809 338432767 338432737 8.140000e-05 58.4


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 TraesCS1D01G188400 chr1D 260891852 260893962 2110 False 3899 3899 100.000 1 2111 1 chr1D.!!$F2 2110
1 TraesCS1D01G188400 chr1D 254416810 254418357 1547 False 2477 2477 95.510 1 1554 1 chr1D.!!$F1 1553
2 TraesCS1D01G188400 chr1D 51876772 51878328 1556 True 2468 2468 95.315 1 1554 1 chr1D.!!$R1 1553
3 TraesCS1D01G188400 chr6D 45510272 45511826 1554 True 2510 2510 95.833 1 1554 1 chr6D.!!$R1 1553
4 TraesCS1D01G188400 chr5D 503287045 503288607 1562 False 2490 2490 95.524 1 1554 1 chr5D.!!$F3 1553
5 TraesCS1D01G188400 chr5D 120799617 120801169 1552 False 2486 2486 95.571 1 1554 1 chr5D.!!$F1 1553
6 TraesCS1D01G188400 chr5D 6179652 6181201 1549 True 2457 2457 95.256 1 1554 1 chr5D.!!$R1 1553
7 TraesCS1D01G188400 chr5D 167071679 167073230 1551 False 2375 2375 94.291 1 1554 1 chr5D.!!$F2 1553
8 TraesCS1D01G188400 chr5D 512415180 512416234 1054 True 1709 1709 96.019 508 1554 1 chr5D.!!$R2 1046
9 TraesCS1D01G188400 chr1A 554458212 554459762 1550 False 2451 2451 95.202 1 1554 1 chr1A.!!$F1 1553
10 TraesCS1D01G188400 chr2A 334594763 334595896 1133 True 1770 1770 94.843 418 1554 1 chr2A.!!$R1 1136
11 TraesCS1D01G188400 chr4A 310729707 310730854 1147 True 1712 1712 93.571 1 1150 1 chr4A.!!$R1 1149

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
295 297 2.093973 AGAGTGCGAATACAAGGAGGTG 60.094 50.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 1911 0.035739 ACCGGTATTGTTGGAACGCT 59.964 50.0 4.49 0.0 0.0 5.07 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
99 100 6.744082 GGTTTTATGCGACACTAATAAACACC 59.256 38.462 0.00 0.00 0.00 4.16
295 297 2.093973 AGAGTGCGAATACAAGGAGGTG 60.094 50.000 0.00 0.00 0.00 4.00
331 333 6.150318 GGAAAGTCCGAAGAAAAAGGATTTC 58.850 40.000 0.00 0.00 37.28 2.17
339 341 7.335924 TCCGAAGAAAAAGGATTTCGAATATGT 59.664 33.333 0.00 0.00 43.60 2.29
506 510 3.380320 GCCAAATTACCCGAAGCTTATGT 59.620 43.478 0.00 0.00 0.00 2.29
746 754 7.432148 TCTTCTACATTGAATGGGTAGCTAA 57.568 36.000 10.27 0.00 35.58 3.09
779 787 2.119495 GGATCAGCCTTTCTACTCCCA 58.881 52.381 0.00 0.00 0.00 4.37
841 859 7.290714 CACAATACCTAACCACCTAACCCTATA 59.709 40.741 0.00 0.00 0.00 1.31
964 987 2.287368 CGTGTGGTAAGGAAAAACTGGC 60.287 50.000 0.00 0.00 0.00 4.85
1087 1112 7.028131 AGGATTCTTATCTAATGACCCAGGAT 58.972 38.462 0.00 0.00 0.00 3.24
1118 1143 3.434299 GGACGCGAGGAGTAAAAATTCAA 59.566 43.478 15.93 0.00 0.00 2.69
1175 1205 3.778075 TCTATGAGAAAATCCGGGGTCAA 59.222 43.478 0.00 0.00 0.00 3.18
1213 1243 4.344104 GAAAGTCCCAAATGATCCAAGGA 58.656 43.478 0.00 0.00 0.00 3.36
1308 1339 0.976641 TCAGCCATCTCTCCACGTTT 59.023 50.000 0.00 0.00 0.00 3.60
1501 1535 7.873719 TCTTTCTAAAAATCGATATTGGCCA 57.126 32.000 0.00 0.00 0.00 5.36
1541 1575 3.350219 TTCTCTTTAGCGGGCATTTCT 57.650 42.857 0.00 0.00 0.00 2.52
1554 1588 5.568825 GCGGGCATTTCTATATAGGACTTGA 60.569 44.000 9.89 0.00 0.00 3.02
1555 1589 6.464222 CGGGCATTTCTATATAGGACTTGAA 58.536 40.000 9.89 0.00 0.00 2.69
1556 1590 7.106239 CGGGCATTTCTATATAGGACTTGAAT 58.894 38.462 9.89 0.00 0.00 2.57
1557 1591 8.258007 CGGGCATTTCTATATAGGACTTGAATA 58.742 37.037 9.89 0.00 0.00 1.75
1558 1592 9.959721 GGGCATTTCTATATAGGACTTGAATAA 57.040 33.333 9.89 0.00 0.00 1.40
1572 1606 9.533831 AGGACTTGAATAAATAGTTCACCAATT 57.466 29.630 0.00 0.00 35.47 2.32
1573 1607 9.573133 GGACTTGAATAAATAGTTCACCAATTG 57.427 33.333 0.00 0.00 35.47 2.32
1574 1608 9.573133 GACTTGAATAAATAGTTCACCAATTGG 57.427 33.333 23.31 23.31 35.47 3.16
1575 1609 8.531146 ACTTGAATAAATAGTTCACCAATTGGG 58.469 33.333 27.89 16.62 44.81 4.12
1576 1610 8.657387 TTGAATAAATAGTTCACCAATTGGGA 57.343 30.769 27.89 18.56 41.15 4.37
1577 1611 8.657387 TGAATAAATAGTTCACCAATTGGGAA 57.343 30.769 27.89 22.70 41.15 3.97
1578 1612 9.094578 TGAATAAATAGTTCACCAATTGGGAAA 57.905 29.630 27.89 17.88 41.15 3.13
1579 1613 9.936759 GAATAAATAGTTCACCAATTGGGAAAA 57.063 29.630 27.89 15.48 41.15 2.29
1581 1615 9.942850 ATAAATAGTTCACCAATTGGGAAAAAG 57.057 29.630 27.89 10.51 41.15 2.27
1582 1616 6.994421 ATAGTTCACCAATTGGGAAAAAGT 57.006 33.333 27.89 18.64 41.15 2.66
1583 1617 5.692115 AGTTCACCAATTGGGAAAAAGTT 57.308 34.783 27.89 1.53 41.15 2.66
1584 1618 5.427378 AGTTCACCAATTGGGAAAAAGTTG 58.573 37.500 27.89 14.32 41.15 3.16
1585 1619 5.188751 AGTTCACCAATTGGGAAAAAGTTGA 59.811 36.000 27.89 16.33 41.15 3.18
1586 1620 5.017294 TCACCAATTGGGAAAAAGTTGAC 57.983 39.130 27.89 0.00 41.15 3.18
1587 1621 4.714308 TCACCAATTGGGAAAAAGTTGACT 59.286 37.500 27.89 0.00 41.15 3.41
1588 1622 4.810491 CACCAATTGGGAAAAAGTTGACTG 59.190 41.667 27.89 8.77 41.15 3.51
1589 1623 4.141733 ACCAATTGGGAAAAAGTTGACTGG 60.142 41.667 27.89 0.00 41.15 4.00
1590 1624 4.100808 CCAATTGGGAAAAAGTTGACTGGA 59.899 41.667 17.36 0.00 40.01 3.86
1591 1625 5.221702 CCAATTGGGAAAAAGTTGACTGGAT 60.222 40.000 17.36 0.00 40.01 3.41
1592 1626 6.290605 CAATTGGGAAAAAGTTGACTGGATT 58.709 36.000 0.00 0.00 0.00 3.01
1593 1627 5.948742 TTGGGAAAAAGTTGACTGGATTT 57.051 34.783 0.00 0.00 0.00 2.17
1594 1628 5.275067 TGGGAAAAAGTTGACTGGATTTG 57.725 39.130 0.00 0.00 0.00 2.32
1595 1629 4.714308 TGGGAAAAAGTTGACTGGATTTGT 59.286 37.500 0.00 0.00 0.00 2.83
1596 1630 5.188751 TGGGAAAAAGTTGACTGGATTTGTT 59.811 36.000 0.00 0.00 0.00 2.83
1597 1631 6.112734 GGGAAAAAGTTGACTGGATTTGTTT 58.887 36.000 0.00 0.00 0.00 2.83
1598 1632 6.597672 GGGAAAAAGTTGACTGGATTTGTTTT 59.402 34.615 0.00 0.00 0.00 2.43
1599 1633 7.120579 GGGAAAAAGTTGACTGGATTTGTTTTT 59.879 33.333 0.00 0.00 0.00 1.94
1600 1634 8.175069 GGAAAAAGTTGACTGGATTTGTTTTTC 58.825 33.333 0.00 0.00 39.91 2.29
1601 1635 8.614469 AAAAAGTTGACTGGATTTGTTTTTCA 57.386 26.923 0.00 0.00 0.00 2.69
1602 1636 8.614469 AAAAGTTGACTGGATTTGTTTTTCAA 57.386 26.923 0.00 0.00 0.00 2.69
1604 1638 8.614469 AAGTTGACTGGATTTGTTTTTCAAAA 57.386 26.923 0.00 0.00 46.97 2.44
1605 1639 8.614469 AGTTGACTGGATTTGTTTTTCAAAAA 57.386 26.923 0.00 0.00 46.97 1.94
1644 1678 9.421399 AGAAAAAGAAAGGAATAAGGAACAAGA 57.579 29.630 0.00 0.00 0.00 3.02
1699 1733 9.665264 AAAATAATAAAAAGGATCTCGCGAATC 57.335 29.630 11.33 15.38 0.00 2.52
1700 1734 7.962964 ATAATAAAAAGGATCTCGCGAATCA 57.037 32.000 23.27 8.58 0.00 2.57
1701 1735 5.659048 ATAAAAAGGATCTCGCGAATCAC 57.341 39.130 23.27 16.10 0.00 3.06
1702 1736 2.672961 AAAGGATCTCGCGAATCACA 57.327 45.000 23.27 4.34 0.00 3.58
1703 1737 1.927895 AAGGATCTCGCGAATCACAC 58.072 50.000 23.27 12.36 0.00 3.82
1704 1738 0.103208 AGGATCTCGCGAATCACACC 59.897 55.000 23.27 15.57 0.00 4.16
1705 1739 0.179111 GGATCTCGCGAATCACACCA 60.179 55.000 23.27 0.00 0.00 4.17
1706 1740 1.203928 GATCTCGCGAATCACACCAG 58.796 55.000 11.33 0.00 0.00 4.00
1707 1741 0.817654 ATCTCGCGAATCACACCAGA 59.182 50.000 11.33 0.00 0.00 3.86
1708 1742 0.817654 TCTCGCGAATCACACCAGAT 59.182 50.000 11.33 0.00 0.00 2.90
1709 1743 2.021457 TCTCGCGAATCACACCAGATA 58.979 47.619 11.33 0.00 0.00 1.98
1710 1744 2.033424 TCTCGCGAATCACACCAGATAG 59.967 50.000 11.33 0.00 0.00 2.08
1711 1745 1.749063 TCGCGAATCACACCAGATAGT 59.251 47.619 6.20 0.00 0.00 2.12
1712 1746 2.165641 TCGCGAATCACACCAGATAGTT 59.834 45.455 6.20 0.00 0.00 2.24
1713 1747 2.282555 CGCGAATCACACCAGATAGTTG 59.717 50.000 0.00 0.00 0.00 3.16
1714 1748 3.262420 GCGAATCACACCAGATAGTTGT 58.738 45.455 0.00 0.00 0.00 3.32
1715 1749 3.307242 GCGAATCACACCAGATAGTTGTC 59.693 47.826 0.00 0.00 0.00 3.18
1716 1750 3.547868 CGAATCACACCAGATAGTTGTCG 59.452 47.826 0.00 0.00 0.00 4.35
1717 1751 4.495422 GAATCACACCAGATAGTTGTCGT 58.505 43.478 0.00 0.00 0.00 4.34
1718 1752 5.647589 GAATCACACCAGATAGTTGTCGTA 58.352 41.667 0.00 0.00 0.00 3.43
1719 1753 4.696899 TCACACCAGATAGTTGTCGTAG 57.303 45.455 0.00 0.00 0.00 3.51
1720 1754 4.077108 TCACACCAGATAGTTGTCGTAGT 58.923 43.478 0.00 0.00 0.00 2.73
1721 1755 4.521639 TCACACCAGATAGTTGTCGTAGTT 59.478 41.667 0.00 0.00 0.00 2.24
1722 1756 4.621460 CACACCAGATAGTTGTCGTAGTTG 59.379 45.833 0.00 0.00 0.00 3.16
1723 1757 4.521639 ACACCAGATAGTTGTCGTAGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
1724 1758 4.857588 CACCAGATAGTTGTCGTAGTTGAC 59.142 45.833 0.00 0.00 39.37 3.18
1725 1759 4.765856 ACCAGATAGTTGTCGTAGTTGACT 59.234 41.667 0.00 0.00 39.64 3.41
1726 1760 5.942236 ACCAGATAGTTGTCGTAGTTGACTA 59.058 40.000 0.00 0.00 39.64 2.59
1727 1761 6.128063 ACCAGATAGTTGTCGTAGTTGACTAC 60.128 42.308 10.55 10.55 44.00 2.73
1728 1762 6.256686 CAGATAGTTGTCGTAGTTGACTACC 58.743 44.000 13.98 3.87 44.46 3.18
1729 1763 5.942236 AGATAGTTGTCGTAGTTGACTACCA 59.058 40.000 13.98 6.08 44.46 3.25
1730 1764 6.602406 AGATAGTTGTCGTAGTTGACTACCAT 59.398 38.462 13.98 0.00 44.46 3.55
1731 1765 5.056894 AGTTGTCGTAGTTGACTACCATC 57.943 43.478 13.98 7.67 44.46 3.51
1732 1766 3.752412 TGTCGTAGTTGACTACCATCG 57.248 47.619 13.98 4.62 44.46 3.84
1733 1767 2.159476 TGTCGTAGTTGACTACCATCGC 60.159 50.000 13.98 3.27 44.46 4.58
1734 1768 2.097142 GTCGTAGTTGACTACCATCGCT 59.903 50.000 13.98 0.00 44.46 4.93
1735 1769 3.310774 GTCGTAGTTGACTACCATCGCTA 59.689 47.826 13.98 0.00 44.46 4.26
1736 1770 3.940852 TCGTAGTTGACTACCATCGCTAA 59.059 43.478 13.98 0.00 44.46 3.09
1737 1771 4.033684 CGTAGTTGACTACCATCGCTAAC 58.966 47.826 13.98 0.00 44.46 2.34
1738 1772 4.437794 CGTAGTTGACTACCATCGCTAACA 60.438 45.833 13.98 0.00 44.46 2.41
1739 1773 4.737855 AGTTGACTACCATCGCTAACAT 57.262 40.909 0.00 0.00 0.00 2.71
1740 1774 4.433615 AGTTGACTACCATCGCTAACATG 58.566 43.478 0.00 0.00 0.00 3.21
1741 1775 4.159693 AGTTGACTACCATCGCTAACATGA 59.840 41.667 0.00 0.00 0.00 3.07
1742 1776 4.729227 TGACTACCATCGCTAACATGAA 57.271 40.909 0.00 0.00 0.00 2.57
1743 1777 5.079689 TGACTACCATCGCTAACATGAAA 57.920 39.130 0.00 0.00 0.00 2.69
1744 1778 4.868171 TGACTACCATCGCTAACATGAAAC 59.132 41.667 0.00 0.00 0.00 2.78
1745 1779 3.863424 ACTACCATCGCTAACATGAAACG 59.137 43.478 0.00 0.00 0.00 3.60
1746 1780 2.006888 ACCATCGCTAACATGAAACGG 58.993 47.619 0.00 0.00 0.00 4.44
1747 1781 1.330521 CCATCGCTAACATGAAACGGG 59.669 52.381 0.00 0.00 0.00 5.28
1748 1782 1.330521 CATCGCTAACATGAAACGGGG 59.669 52.381 0.00 0.00 0.00 5.73
1749 1783 0.609151 TCGCTAACATGAAACGGGGA 59.391 50.000 0.00 0.00 0.00 4.81
1750 1784 1.006832 CGCTAACATGAAACGGGGAG 58.993 55.000 0.00 0.00 0.00 4.30
1751 1785 1.379527 GCTAACATGAAACGGGGAGG 58.620 55.000 0.00 0.00 0.00 4.30
1752 1786 2.017113 GCTAACATGAAACGGGGAGGG 61.017 57.143 0.00 0.00 0.00 4.30
1753 1787 0.621609 TAACATGAAACGGGGAGGGG 59.378 55.000 0.00 0.00 0.00 4.79
1754 1788 2.150014 AACATGAAACGGGGAGGGGG 62.150 60.000 0.00 0.00 0.00 5.40
1755 1789 3.739613 ATGAAACGGGGAGGGGGC 61.740 66.667 0.00 0.00 0.00 5.80
1757 1791 3.974293 GAAACGGGGAGGGGGCAA 61.974 66.667 0.00 0.00 0.00 4.52
1758 1792 3.938637 GAAACGGGGAGGGGGCAAG 62.939 68.421 0.00 0.00 0.00 4.01
1768 1802 4.699522 GGGGCAAGGTCGCGAGTT 62.700 66.667 10.24 2.78 0.00 3.01
1769 1803 3.119096 GGGCAAGGTCGCGAGTTC 61.119 66.667 10.24 1.89 0.00 3.01
1770 1804 3.479269 GGCAAGGTCGCGAGTTCG 61.479 66.667 10.24 0.00 43.27 3.95
1771 1805 2.430244 GCAAGGTCGCGAGTTCGA 60.430 61.111 10.24 0.00 43.02 3.71
1772 1806 2.437343 GCAAGGTCGCGAGTTCGAG 61.437 63.158 10.24 1.94 43.02 4.04
1773 1807 1.081376 CAAGGTCGCGAGTTCGAGT 60.081 57.895 10.24 0.00 43.02 4.18
1774 1808 1.066114 CAAGGTCGCGAGTTCGAGTC 61.066 60.000 10.24 0.00 43.02 3.36
1775 1809 1.235948 AAGGTCGCGAGTTCGAGTCT 61.236 55.000 10.24 2.48 43.02 3.24
1776 1810 1.226073 GGTCGCGAGTTCGAGTCTC 60.226 63.158 10.24 8.89 43.02 3.36
1777 1811 1.496393 GTCGCGAGTTCGAGTCTCA 59.504 57.895 10.24 0.00 43.02 3.27
1778 1812 0.519586 GTCGCGAGTTCGAGTCTCAG 60.520 60.000 10.24 10.90 43.02 3.35
1779 1813 1.226156 CGCGAGTTCGAGTCTCAGG 60.226 63.158 0.00 6.57 43.02 3.86
1780 1814 1.636570 CGCGAGTTCGAGTCTCAGGA 61.637 60.000 0.00 0.00 43.02 3.86
1781 1815 0.522180 GCGAGTTCGAGTCTCAGGAA 59.478 55.000 16.12 0.00 43.02 3.36
1782 1816 1.068472 GCGAGTTCGAGTCTCAGGAAA 60.068 52.381 16.12 0.00 43.02 3.13
1783 1817 2.607282 GCGAGTTCGAGTCTCAGGAAAA 60.607 50.000 16.12 0.00 43.02 2.29
1784 1818 2.981140 CGAGTTCGAGTCTCAGGAAAAC 59.019 50.000 16.12 0.00 43.02 2.43
1785 1819 3.304794 CGAGTTCGAGTCTCAGGAAAACT 60.305 47.826 16.12 1.69 43.02 2.66
1786 1820 4.231439 GAGTTCGAGTCTCAGGAAAACTC 58.769 47.826 12.65 6.91 35.77 3.01
1787 1821 3.892588 AGTTCGAGTCTCAGGAAAACTCT 59.107 43.478 0.00 0.00 37.79 3.24
1788 1822 5.071370 AGTTCGAGTCTCAGGAAAACTCTA 58.929 41.667 0.00 0.00 37.79 2.43
1789 1823 5.712917 AGTTCGAGTCTCAGGAAAACTCTAT 59.287 40.000 0.00 0.00 37.79 1.98
1790 1824 6.209788 AGTTCGAGTCTCAGGAAAACTCTATT 59.790 38.462 0.00 0.00 37.79 1.73
1791 1825 6.591750 TCGAGTCTCAGGAAAACTCTATTT 57.408 37.500 0.00 0.00 37.79 1.40
1792 1826 6.390721 TCGAGTCTCAGGAAAACTCTATTTG 58.609 40.000 0.00 0.00 37.79 2.32
1793 1827 5.062809 CGAGTCTCAGGAAAACTCTATTTGC 59.937 44.000 0.00 0.00 37.79 3.68
1794 1828 5.249420 AGTCTCAGGAAAACTCTATTTGCC 58.751 41.667 0.00 0.00 31.70 4.52
1795 1829 4.093556 GTCTCAGGAAAACTCTATTTGCCG 59.906 45.833 0.00 0.00 31.70 5.69
1796 1830 2.747446 TCAGGAAAACTCTATTTGCCGC 59.253 45.455 0.00 0.00 31.70 6.53
1797 1831 2.749621 CAGGAAAACTCTATTTGCCGCT 59.250 45.455 0.00 0.00 31.70 5.52
1798 1832 3.010420 AGGAAAACTCTATTTGCCGCTC 58.990 45.455 0.00 0.00 31.70 5.03
1799 1833 3.010420 GGAAAACTCTATTTGCCGCTCT 58.990 45.455 0.00 0.00 0.00 4.09
1800 1834 3.064134 GGAAAACTCTATTTGCCGCTCTC 59.936 47.826 0.00 0.00 0.00 3.20
1801 1835 3.618690 AAACTCTATTTGCCGCTCTCT 57.381 42.857 0.00 0.00 0.00 3.10
1802 1836 2.593346 ACTCTATTTGCCGCTCTCTG 57.407 50.000 0.00 0.00 0.00 3.35
1803 1837 1.216122 CTCTATTTGCCGCTCTCTGC 58.784 55.000 0.00 0.00 38.57 4.26
1820 1854 2.033448 CGGCAAGCAGTTGGGGTA 59.967 61.111 0.00 0.00 33.87 3.69
1821 1855 2.332654 CGGCAAGCAGTTGGGGTAC 61.333 63.158 0.00 0.00 33.87 3.34
1833 1867 3.078836 GGGTACCGCACAGGGCTA 61.079 66.667 5.65 0.00 46.96 3.93
1834 1868 2.440817 GGGTACCGCACAGGGCTAT 61.441 63.158 5.65 0.00 46.96 2.97
1835 1869 1.069258 GGTACCGCACAGGGCTATC 59.931 63.158 0.00 0.00 46.96 2.08
1836 1870 1.299926 GTACCGCACAGGGCTATCG 60.300 63.158 0.00 0.00 46.96 2.92
1837 1871 1.454295 TACCGCACAGGGCTATCGA 60.454 57.895 0.00 0.00 46.96 3.59
1838 1872 1.452953 TACCGCACAGGGCTATCGAG 61.453 60.000 0.00 0.00 46.96 4.04
1847 1881 2.699916 AGGGCTATCGAGCAAGCTCTC 61.700 57.143 18.82 5.97 46.74 3.20
1853 1887 4.443266 GAGCAAGCTCTCGCGGGT 62.443 66.667 14.52 0.00 42.32 5.28
1854 1888 4.749310 AGCAAGCTCTCGCGGGTG 62.749 66.667 5.57 4.24 42.32 4.61
1876 1910 2.361865 GGTTGGGCCGGCATGTTA 60.362 61.111 30.85 5.96 0.00 2.41
1877 1911 1.979693 GGTTGGGCCGGCATGTTAA 60.980 57.895 30.85 12.21 0.00 2.01
1878 1912 1.510844 GTTGGGCCGGCATGTTAAG 59.489 57.895 30.85 0.00 0.00 1.85
1879 1913 2.347322 TTGGGCCGGCATGTTAAGC 61.347 57.895 30.85 7.76 0.00 3.09
1880 1914 3.887868 GGGCCGGCATGTTAAGCG 61.888 66.667 30.85 0.00 0.00 4.68
1881 1915 3.131478 GGCCGGCATGTTAAGCGT 61.131 61.111 30.85 0.00 0.00 5.07
1882 1916 2.696759 GGCCGGCATGTTAAGCGTT 61.697 57.895 30.85 0.00 0.00 4.84
1883 1917 1.226295 GCCGGCATGTTAAGCGTTC 60.226 57.895 24.80 0.00 0.00 3.95
1884 1918 1.427819 CCGGCATGTTAAGCGTTCC 59.572 57.895 0.00 0.00 0.00 3.62
1885 1919 1.302383 CCGGCATGTTAAGCGTTCCA 61.302 55.000 0.00 0.00 0.00 3.53
1886 1920 0.519519 CGGCATGTTAAGCGTTCCAA 59.480 50.000 0.00 0.00 0.00 3.53
1887 1921 1.727857 CGGCATGTTAAGCGTTCCAAC 60.728 52.381 0.00 0.00 0.00 3.77
1888 1922 1.268352 GGCATGTTAAGCGTTCCAACA 59.732 47.619 0.00 2.65 36.66 3.33
1889 1923 2.287909 GGCATGTTAAGCGTTCCAACAA 60.288 45.455 4.03 0.00 35.91 2.83
1890 1924 3.574614 GCATGTTAAGCGTTCCAACAAT 58.425 40.909 4.03 0.00 35.91 2.71
1891 1925 4.380023 GGCATGTTAAGCGTTCCAACAATA 60.380 41.667 4.03 0.00 35.91 1.90
1892 1926 4.557301 GCATGTTAAGCGTTCCAACAATAC 59.443 41.667 4.03 0.00 35.91 1.89
1893 1927 4.752661 TGTTAAGCGTTCCAACAATACC 57.247 40.909 0.00 0.00 0.00 2.73
1894 1928 3.186817 TGTTAAGCGTTCCAACAATACCG 59.813 43.478 0.00 0.00 0.00 4.02
1895 1929 1.161843 AAGCGTTCCAACAATACCGG 58.838 50.000 0.00 0.00 0.00 5.28
1896 1930 0.035739 AGCGTTCCAACAATACCGGT 59.964 50.000 13.98 13.98 0.00 5.28
1897 1931 0.876399 GCGTTCCAACAATACCGGTT 59.124 50.000 15.04 0.00 0.00 4.44
1898 1932 1.267533 GCGTTCCAACAATACCGGTTT 59.732 47.619 15.04 0.14 0.00 3.27
1899 1933 2.287728 GCGTTCCAACAATACCGGTTTT 60.288 45.455 15.04 8.90 0.00 2.43
1900 1934 3.301706 CGTTCCAACAATACCGGTTTTG 58.698 45.455 29.19 29.19 0.00 2.44
1901 1935 3.644823 GTTCCAACAATACCGGTTTTGG 58.355 45.455 32.29 26.93 38.48 3.28
1902 1936 2.240279 TCCAACAATACCGGTTTTGGG 58.760 47.619 32.29 25.84 37.82 4.12
1903 1937 2.158505 TCCAACAATACCGGTTTTGGGA 60.159 45.455 32.29 27.22 37.82 4.37
1904 1938 2.628657 CCAACAATACCGGTTTTGGGAA 59.371 45.455 32.29 8.03 34.26 3.97
1905 1939 3.553302 CCAACAATACCGGTTTTGGGAAC 60.553 47.826 32.29 0.00 34.26 3.62
1921 1955 3.821421 GGAACCTTCTATGGACGTCAT 57.179 47.619 18.91 11.34 39.78 3.06
1922 1956 4.931661 GGAACCTTCTATGGACGTCATA 57.068 45.455 18.91 11.86 37.30 2.15
1927 1961 3.794690 CTATGGACGTCATAGCCGG 57.205 57.895 18.91 0.00 45.94 6.13
1928 1962 0.388649 CTATGGACGTCATAGCCGGC 60.389 60.000 21.89 21.89 45.94 6.13
1931 1965 2.499685 GACGTCATAGCCGGCCTT 59.500 61.111 26.15 8.44 0.00 4.35
1932 1966 1.153429 GACGTCATAGCCGGCCTTT 60.153 57.895 26.15 7.52 0.00 3.11
1933 1967 0.743345 GACGTCATAGCCGGCCTTTT 60.743 55.000 26.15 7.06 0.00 2.27
1934 1968 0.322187 ACGTCATAGCCGGCCTTTTT 60.322 50.000 26.15 6.59 0.00 1.94
1966 2000 3.957591 GGAACCTTCTAGAACGTTCCT 57.042 47.619 35.32 14.51 45.11 3.36
1968 2002 5.397142 GGAACCTTCTAGAACGTTCCTAA 57.603 43.478 35.32 14.54 45.11 2.69
1969 2003 5.975282 GGAACCTTCTAGAACGTTCCTAAT 58.025 41.667 35.32 13.43 45.11 1.73
1970 2004 6.041511 GGAACCTTCTAGAACGTTCCTAATC 58.958 44.000 35.32 21.29 45.11 1.75
1971 2005 5.595257 ACCTTCTAGAACGTTCCTAATCC 57.405 43.478 24.22 0.00 0.00 3.01
1972 2006 5.270794 ACCTTCTAGAACGTTCCTAATCCT 58.729 41.667 24.22 6.92 0.00 3.24
1973 2007 5.720520 ACCTTCTAGAACGTTCCTAATCCTT 59.279 40.000 24.22 6.18 0.00 3.36
1974 2008 6.212993 ACCTTCTAGAACGTTCCTAATCCTTT 59.787 38.462 24.22 5.45 0.00 3.11
1975 2009 7.104290 CCTTCTAGAACGTTCCTAATCCTTTT 58.896 38.462 24.22 4.71 0.00 2.27
1976 2010 7.606839 CCTTCTAGAACGTTCCTAATCCTTTTT 59.393 37.037 24.22 4.19 0.00 1.94
2081 2115 9.737844 ATCTTCTTGCTCTTTTATCTCTTCTTT 57.262 29.630 0.00 0.00 0.00 2.52
2082 2116 9.566432 TCTTCTTGCTCTTTTATCTCTTCTTTT 57.434 29.630 0.00 0.00 0.00 2.27
2083 2117 9.824534 CTTCTTGCTCTTTTATCTCTTCTTTTC 57.175 33.333 0.00 0.00 0.00 2.29
2084 2118 9.566432 TTCTTGCTCTTTTATCTCTTCTTTTCT 57.434 29.630 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.400975 TAAGGCAGCGGGTTTTGGTA 59.599 50.000 0.00 0.00 0.00 3.25
156 157 7.043059 GCATGTGTAGAATACTAGCAAGAGAAC 60.043 40.741 0.00 0.00 43.54 3.01
295 297 3.119424 TCGGACTTTCCCAAACACAAAAC 60.119 43.478 0.00 0.00 31.13 2.43
331 333 6.599638 AGGGAAAGAAGGAAAAGACATATTCG 59.400 38.462 0.00 0.00 0.00 3.34
378 381 9.120538 TCATTCTTGTAGAGTAAATAATTGGGC 57.879 33.333 0.00 0.00 0.00 5.36
616 621 7.557724 TGAACACATCATTCAATTTGGCATAT 58.442 30.769 0.00 0.00 33.16 1.78
746 754 5.945144 AGGCTGATCCAAATTTATTGCTT 57.055 34.783 0.00 0.00 37.29 3.91
779 787 0.254178 CCTGCTCAACCTAGGTGCAT 59.746 55.000 21.88 2.32 33.02 3.96
1062 1087 6.393897 TCCTGGGTCATTAGATAAGAATCCT 58.606 40.000 0.00 0.00 31.98 3.24
1087 1112 2.721167 CCTCGCGTCCAGGATTCCA 61.721 63.158 5.77 0.00 31.91 3.53
1213 1243 1.134670 CGAATCCCTCTCTTTCCGCTT 60.135 52.381 0.00 0.00 0.00 4.68
1275 1305 1.592223 GCTGAGTGGACTAAGCGGT 59.408 57.895 0.16 0.00 40.40 5.68
1308 1339 1.332375 CACGGAAACCTTTCGCTTTGA 59.668 47.619 0.00 0.00 38.06 2.69
1555 1589 9.942850 CTTTTTCCCAATTGGTGAACTATTTAT 57.057 29.630 22.91 0.00 34.77 1.40
1556 1590 8.929487 ACTTTTTCCCAATTGGTGAACTATTTA 58.071 29.630 22.91 7.39 34.77 1.40
1557 1591 7.801104 ACTTTTTCCCAATTGGTGAACTATTT 58.199 30.769 22.91 6.87 34.77 1.40
1558 1592 7.373617 ACTTTTTCCCAATTGGTGAACTATT 57.626 32.000 22.91 8.02 34.77 1.73
1559 1593 6.994421 ACTTTTTCCCAATTGGTGAACTAT 57.006 33.333 22.91 8.71 34.77 2.12
1560 1594 6.381420 TCAACTTTTTCCCAATTGGTGAACTA 59.619 34.615 22.91 12.61 34.77 2.24
1561 1595 5.188751 TCAACTTTTTCCCAATTGGTGAACT 59.811 36.000 22.91 6.25 34.77 3.01
1562 1596 5.293324 GTCAACTTTTTCCCAATTGGTGAAC 59.707 40.000 22.91 8.54 34.77 3.18
1563 1597 5.188751 AGTCAACTTTTTCCCAATTGGTGAA 59.811 36.000 22.91 20.56 34.77 3.18
1564 1598 4.714308 AGTCAACTTTTTCCCAATTGGTGA 59.286 37.500 22.91 16.20 34.77 4.02
1565 1599 4.810491 CAGTCAACTTTTTCCCAATTGGTG 59.190 41.667 22.91 14.20 34.77 4.17
1566 1600 4.141733 CCAGTCAACTTTTTCCCAATTGGT 60.142 41.667 22.91 0.00 34.77 3.67
1567 1601 4.100808 TCCAGTCAACTTTTTCCCAATTGG 59.899 41.667 18.21 18.21 0.00 3.16
1568 1602 5.275067 TCCAGTCAACTTTTTCCCAATTG 57.725 39.130 0.00 0.00 0.00 2.32
1569 1603 6.499106 AATCCAGTCAACTTTTTCCCAATT 57.501 33.333 0.00 0.00 0.00 2.32
1570 1604 6.126796 ACAAATCCAGTCAACTTTTTCCCAAT 60.127 34.615 0.00 0.00 0.00 3.16
1571 1605 5.188751 ACAAATCCAGTCAACTTTTTCCCAA 59.811 36.000 0.00 0.00 0.00 4.12
1572 1606 4.714308 ACAAATCCAGTCAACTTTTTCCCA 59.286 37.500 0.00 0.00 0.00 4.37
1573 1607 5.276461 ACAAATCCAGTCAACTTTTTCCC 57.724 39.130 0.00 0.00 0.00 3.97
1574 1608 7.609760 AAAACAAATCCAGTCAACTTTTTCC 57.390 32.000 0.00 0.00 0.00 3.13
1575 1609 8.716909 TGAAAAACAAATCCAGTCAACTTTTTC 58.283 29.630 0.00 0.00 37.09 2.29
1576 1610 8.614469 TGAAAAACAAATCCAGTCAACTTTTT 57.386 26.923 0.00 0.00 0.00 1.94
1577 1611 8.614469 TTGAAAAACAAATCCAGTCAACTTTT 57.386 26.923 0.00 0.00 35.39 2.27
1578 1612 8.614469 TTTGAAAAACAAATCCAGTCAACTTT 57.386 26.923 0.00 0.00 42.57 2.66
1579 1613 8.614469 TTTTGAAAAACAAATCCAGTCAACTT 57.386 26.923 0.00 0.00 45.99 2.66
1580 1614 8.614469 TTTTTGAAAAACAAATCCAGTCAACT 57.386 26.923 0.00 0.00 45.99 3.16
1618 1652 9.421399 TCTTGTTCCTTATTCCTTTCTTTTTCT 57.579 29.630 0.00 0.00 0.00 2.52
1673 1707 9.665264 GATTCGCGAGATCCTTTTTATTATTTT 57.335 29.630 9.59 0.00 41.60 1.82
1674 1708 8.836413 TGATTCGCGAGATCCTTTTTATTATTT 58.164 29.630 20.77 0.00 41.60 1.40
1675 1709 8.283291 GTGATTCGCGAGATCCTTTTTATTATT 58.717 33.333 20.77 0.00 41.60 1.40
1676 1710 7.441157 TGTGATTCGCGAGATCCTTTTTATTAT 59.559 33.333 20.77 4.75 41.60 1.28
1677 1711 6.759356 TGTGATTCGCGAGATCCTTTTTATTA 59.241 34.615 20.77 0.28 41.60 0.98
1678 1712 5.584649 TGTGATTCGCGAGATCCTTTTTATT 59.415 36.000 20.77 0.00 41.60 1.40
1679 1713 5.006746 GTGTGATTCGCGAGATCCTTTTTAT 59.993 40.000 20.77 5.75 41.60 1.40
1680 1714 4.328983 GTGTGATTCGCGAGATCCTTTTTA 59.671 41.667 20.77 1.32 41.60 1.52
1681 1715 3.125316 GTGTGATTCGCGAGATCCTTTTT 59.875 43.478 20.77 0.00 41.60 1.94
1682 1716 2.673368 GTGTGATTCGCGAGATCCTTTT 59.327 45.455 20.77 0.00 41.60 2.27
1683 1717 2.271800 GTGTGATTCGCGAGATCCTTT 58.728 47.619 20.77 0.83 41.60 3.11
1684 1718 1.471676 GGTGTGATTCGCGAGATCCTT 60.472 52.381 20.77 2.30 41.60 3.36
1685 1719 0.103208 GGTGTGATTCGCGAGATCCT 59.897 55.000 20.77 3.65 41.60 3.24
1686 1720 0.179111 TGGTGTGATTCGCGAGATCC 60.179 55.000 20.77 14.47 41.60 3.36
1687 1721 1.202302 TCTGGTGTGATTCGCGAGATC 60.202 52.381 9.59 15.41 41.60 2.75
1688 1722 0.817654 TCTGGTGTGATTCGCGAGAT 59.182 50.000 9.59 6.18 41.60 2.75
1689 1723 0.817654 ATCTGGTGTGATTCGCGAGA 59.182 50.000 9.59 0.00 43.33 4.04
1690 1724 2.223595 ACTATCTGGTGTGATTCGCGAG 60.224 50.000 9.59 0.00 34.48 5.03
1691 1725 1.749063 ACTATCTGGTGTGATTCGCGA 59.251 47.619 3.71 3.71 0.00 5.87
1692 1726 2.209838 ACTATCTGGTGTGATTCGCG 57.790 50.000 0.00 0.00 0.00 5.87
1693 1727 3.262420 ACAACTATCTGGTGTGATTCGC 58.738 45.455 0.00 0.00 46.28 4.70
1701 1735 4.857588 GTCAACTACGACAACTATCTGGTG 59.142 45.833 0.00 0.00 39.79 4.17
1702 1736 4.765856 AGTCAACTACGACAACTATCTGGT 59.234 41.667 0.00 0.00 38.43 4.00
1703 1737 5.312120 AGTCAACTACGACAACTATCTGG 57.688 43.478 0.00 0.00 38.43 3.86
1716 1750 4.990257 TGTTAGCGATGGTAGTCAACTAC 58.010 43.478 11.13 11.13 46.09 2.73
1717 1751 5.358725 TCATGTTAGCGATGGTAGTCAACTA 59.641 40.000 0.00 0.00 0.00 2.24
1718 1752 4.159693 TCATGTTAGCGATGGTAGTCAACT 59.840 41.667 0.00 0.00 0.00 3.16
1719 1753 4.430007 TCATGTTAGCGATGGTAGTCAAC 58.570 43.478 0.00 0.00 0.00 3.18
1720 1754 4.729227 TCATGTTAGCGATGGTAGTCAA 57.271 40.909 0.00 0.00 0.00 3.18
1721 1755 4.729227 TTCATGTTAGCGATGGTAGTCA 57.271 40.909 0.00 0.00 0.00 3.41
1722 1756 4.026804 CGTTTCATGTTAGCGATGGTAGTC 60.027 45.833 0.00 0.00 0.00 2.59
1723 1757 3.863424 CGTTTCATGTTAGCGATGGTAGT 59.137 43.478 0.00 0.00 0.00 2.73
1724 1758 3.245284 CCGTTTCATGTTAGCGATGGTAG 59.755 47.826 7.99 0.00 0.00 3.18
1725 1759 3.191669 CCGTTTCATGTTAGCGATGGTA 58.808 45.455 7.99 0.00 0.00 3.25
1726 1760 2.006888 CCGTTTCATGTTAGCGATGGT 58.993 47.619 7.99 0.00 0.00 3.55
1727 1761 1.330521 CCCGTTTCATGTTAGCGATGG 59.669 52.381 7.99 0.32 0.00 3.51
1728 1762 1.330521 CCCCGTTTCATGTTAGCGATG 59.669 52.381 7.99 0.00 0.00 3.84
1729 1763 1.208535 TCCCCGTTTCATGTTAGCGAT 59.791 47.619 7.99 0.00 0.00 4.58
1730 1764 0.609151 TCCCCGTTTCATGTTAGCGA 59.391 50.000 7.99 0.00 0.00 4.93
1731 1765 1.006832 CTCCCCGTTTCATGTTAGCG 58.993 55.000 0.00 0.00 0.00 4.26
1732 1766 1.379527 CCTCCCCGTTTCATGTTAGC 58.620 55.000 0.00 0.00 0.00 3.09
1733 1767 1.408266 CCCCTCCCCGTTTCATGTTAG 60.408 57.143 0.00 0.00 0.00 2.34
1734 1768 0.621609 CCCCTCCCCGTTTCATGTTA 59.378 55.000 0.00 0.00 0.00 2.41
1735 1769 1.382629 CCCCTCCCCGTTTCATGTT 59.617 57.895 0.00 0.00 0.00 2.71
1736 1770 2.612493 CCCCCTCCCCGTTTCATGT 61.612 63.158 0.00 0.00 0.00 3.21
1737 1771 2.275418 CCCCCTCCCCGTTTCATG 59.725 66.667 0.00 0.00 0.00 3.07
1738 1772 3.739613 GCCCCCTCCCCGTTTCAT 61.740 66.667 0.00 0.00 0.00 2.57
1740 1774 3.938637 CTTGCCCCCTCCCCGTTTC 62.939 68.421 0.00 0.00 0.00 2.78
1741 1775 3.979497 CTTGCCCCCTCCCCGTTT 61.979 66.667 0.00 0.00 0.00 3.60
1751 1785 4.699522 AACTCGCGACCTTGCCCC 62.700 66.667 3.71 0.00 0.00 5.80
1752 1786 3.119096 GAACTCGCGACCTTGCCC 61.119 66.667 3.71 0.00 0.00 5.36
1753 1787 3.479269 CGAACTCGCGACCTTGCC 61.479 66.667 3.71 0.00 0.00 4.52
1754 1788 2.430244 TCGAACTCGCGACCTTGC 60.430 61.111 3.71 0.00 39.60 4.01
1755 1789 1.066114 GACTCGAACTCGCGACCTTG 61.066 60.000 3.71 0.00 39.60 3.61
1756 1790 1.209640 GACTCGAACTCGCGACCTT 59.790 57.895 3.71 0.00 39.60 3.50
1757 1791 1.637478 GAGACTCGAACTCGCGACCT 61.637 60.000 3.71 0.00 39.60 3.85
1758 1792 1.226073 GAGACTCGAACTCGCGACC 60.226 63.158 3.71 0.00 39.60 4.79
1759 1793 0.519586 CTGAGACTCGAACTCGCGAC 60.520 60.000 3.71 0.00 39.60 5.19
1760 1794 1.636570 CCTGAGACTCGAACTCGCGA 61.637 60.000 9.26 9.26 39.60 5.87
1761 1795 1.226156 CCTGAGACTCGAACTCGCG 60.226 63.158 0.00 0.00 39.60 5.87
1762 1796 0.522180 TTCCTGAGACTCGAACTCGC 59.478 55.000 12.47 1.79 39.60 5.03
1763 1797 2.981140 GTTTTCCTGAGACTCGAACTCG 59.019 50.000 12.47 0.00 37.22 4.18
1764 1798 4.022676 AGAGTTTTCCTGAGACTCGAACTC 60.023 45.833 18.09 18.09 43.43 3.01
1765 1799 3.892588 AGAGTTTTCCTGAGACTCGAACT 59.107 43.478 0.00 3.37 43.43 3.01
1766 1800 4.245845 AGAGTTTTCCTGAGACTCGAAC 57.754 45.455 0.00 0.00 43.43 3.95
1767 1801 6.591750 AATAGAGTTTTCCTGAGACTCGAA 57.408 37.500 0.00 0.00 43.43 3.71
1768 1802 6.390721 CAAATAGAGTTTTCCTGAGACTCGA 58.609 40.000 0.00 0.00 43.43 4.04
1769 1803 5.062809 GCAAATAGAGTTTTCCTGAGACTCG 59.937 44.000 0.00 0.00 43.43 4.18
1770 1804 5.352846 GGCAAATAGAGTTTTCCTGAGACTC 59.647 44.000 0.00 0.00 39.99 3.36
1771 1805 5.249420 GGCAAATAGAGTTTTCCTGAGACT 58.751 41.667 0.00 0.00 0.00 3.24
1772 1806 4.093556 CGGCAAATAGAGTTTTCCTGAGAC 59.906 45.833 0.00 0.00 0.00 3.36
1773 1807 4.253685 CGGCAAATAGAGTTTTCCTGAGA 58.746 43.478 0.00 0.00 0.00 3.27
1774 1808 3.181506 GCGGCAAATAGAGTTTTCCTGAG 60.182 47.826 0.00 0.00 0.00 3.35
1775 1809 2.747446 GCGGCAAATAGAGTTTTCCTGA 59.253 45.455 0.00 0.00 0.00 3.86
1776 1810 2.749621 AGCGGCAAATAGAGTTTTCCTG 59.250 45.455 1.45 0.00 0.00 3.86
1777 1811 3.010420 GAGCGGCAAATAGAGTTTTCCT 58.990 45.455 1.45 0.00 0.00 3.36
1778 1812 3.010420 AGAGCGGCAAATAGAGTTTTCC 58.990 45.455 1.45 0.00 0.00 3.13
1779 1813 3.935828 AGAGAGCGGCAAATAGAGTTTTC 59.064 43.478 1.45 0.00 0.00 2.29
1780 1814 3.686726 CAGAGAGCGGCAAATAGAGTTTT 59.313 43.478 1.45 0.00 0.00 2.43
1781 1815 3.265791 CAGAGAGCGGCAAATAGAGTTT 58.734 45.455 1.45 0.00 0.00 2.66
1782 1816 2.898705 CAGAGAGCGGCAAATAGAGTT 58.101 47.619 1.45 0.00 0.00 3.01
1783 1817 1.472376 GCAGAGAGCGGCAAATAGAGT 60.472 52.381 1.45 0.00 35.17 3.24
1784 1818 1.216122 GCAGAGAGCGGCAAATAGAG 58.784 55.000 1.45 0.00 35.17 2.43
1785 1819 3.369381 GCAGAGAGCGGCAAATAGA 57.631 52.632 1.45 0.00 35.17 1.98
1803 1837 2.033448 TACCCCAACTGCTTGCCG 59.967 61.111 0.00 0.00 0.00 5.69
1804 1838 1.977009 GGTACCCCAACTGCTTGCC 60.977 63.158 0.00 0.00 0.00 4.52
1805 1839 2.332654 CGGTACCCCAACTGCTTGC 61.333 63.158 6.25 0.00 0.00 4.01
1806 1840 2.332654 GCGGTACCCCAACTGCTTG 61.333 63.158 6.25 0.00 46.27 4.01
1807 1841 2.033602 GCGGTACCCCAACTGCTT 59.966 61.111 6.25 0.00 46.27 3.91
1810 1844 1.671054 CTGTGCGGTACCCCAACTG 60.671 63.158 6.25 2.79 0.00 3.16
1811 1845 2.747686 CTGTGCGGTACCCCAACT 59.252 61.111 6.25 0.00 0.00 3.16
1812 1846 2.359478 CCTGTGCGGTACCCCAAC 60.359 66.667 6.25 2.77 0.00 3.77
1813 1847 3.642503 CCCTGTGCGGTACCCCAA 61.643 66.667 6.25 0.00 0.00 4.12
1859 1893 1.944234 CTTAACATGCCGGCCCAACC 61.944 60.000 26.77 0.00 0.00 3.77
1860 1894 1.510844 CTTAACATGCCGGCCCAAC 59.489 57.895 26.77 0.00 0.00 3.77
1861 1895 2.347322 GCTTAACATGCCGGCCCAA 61.347 57.895 26.77 5.45 0.00 4.12
1862 1896 2.753849 GCTTAACATGCCGGCCCA 60.754 61.111 26.77 6.41 0.00 5.36
1863 1897 3.887868 CGCTTAACATGCCGGCCC 61.888 66.667 26.77 0.00 0.00 5.80
1864 1898 2.592623 GAACGCTTAACATGCCGGCC 62.593 60.000 26.77 6.44 0.00 6.13
1865 1899 1.226295 GAACGCTTAACATGCCGGC 60.226 57.895 22.73 22.73 0.00 6.13
1866 1900 1.302383 TGGAACGCTTAACATGCCGG 61.302 55.000 0.00 0.00 0.00 6.13
1867 1901 0.519519 TTGGAACGCTTAACATGCCG 59.480 50.000 0.00 0.00 0.00 5.69
1868 1902 1.268352 TGTTGGAACGCTTAACATGCC 59.732 47.619 0.00 0.00 30.06 4.40
1869 1903 2.697431 TGTTGGAACGCTTAACATGC 57.303 45.000 0.00 0.00 30.06 4.06
1870 1904 5.092781 GGTATTGTTGGAACGCTTAACATG 58.907 41.667 0.00 0.00 34.63 3.21
1871 1905 4.142773 CGGTATTGTTGGAACGCTTAACAT 60.143 41.667 0.00 0.00 34.63 2.71
1872 1906 3.186817 CGGTATTGTTGGAACGCTTAACA 59.813 43.478 0.00 0.00 32.93 2.41
1873 1907 3.425227 CCGGTATTGTTGGAACGCTTAAC 60.425 47.826 0.00 0.00 0.00 2.01
1874 1908 2.743126 CCGGTATTGTTGGAACGCTTAA 59.257 45.455 0.00 0.00 0.00 1.85
1875 1909 2.289569 ACCGGTATTGTTGGAACGCTTA 60.290 45.455 4.49 0.00 0.00 3.09
1876 1910 1.161843 CCGGTATTGTTGGAACGCTT 58.838 50.000 0.00 0.00 0.00 4.68
1877 1911 0.035739 ACCGGTATTGTTGGAACGCT 59.964 50.000 4.49 0.00 0.00 5.07
1878 1912 0.876399 AACCGGTATTGTTGGAACGC 59.124 50.000 8.00 0.00 0.00 4.84
1879 1913 3.301706 CAAAACCGGTATTGTTGGAACG 58.698 45.455 8.00 0.00 0.00 3.95
1880 1914 3.553302 CCCAAAACCGGTATTGTTGGAAC 60.553 47.826 27.99 0.00 41.05 3.62
1881 1915 2.628657 CCCAAAACCGGTATTGTTGGAA 59.371 45.455 27.99 0.00 41.05 3.53
1882 1916 2.158505 TCCCAAAACCGGTATTGTTGGA 60.159 45.455 27.99 18.53 41.05 3.53
1883 1917 2.240279 TCCCAAAACCGGTATTGTTGG 58.760 47.619 22.99 22.99 38.77 3.77
1884 1918 3.553302 GGTTCCCAAAACCGGTATTGTTG 60.553 47.826 8.00 10.29 0.00 3.33
1885 1919 2.629137 GGTTCCCAAAACCGGTATTGTT 59.371 45.455 8.00 0.00 0.00 2.83
1886 1920 2.158430 AGGTTCCCAAAACCGGTATTGT 60.158 45.455 8.00 0.00 44.82 2.71
1887 1921 2.521126 AGGTTCCCAAAACCGGTATTG 58.479 47.619 8.00 0.00 44.82 1.90
1888 1922 2.984435 AGGTTCCCAAAACCGGTATT 57.016 45.000 8.00 1.22 44.82 1.89
1889 1923 2.377531 AGAAGGTTCCCAAAACCGGTAT 59.622 45.455 8.00 0.00 44.82 2.73
1890 1924 1.776063 AGAAGGTTCCCAAAACCGGTA 59.224 47.619 8.00 0.00 44.82 4.02
1891 1925 0.554305 AGAAGGTTCCCAAAACCGGT 59.446 50.000 0.00 0.00 44.82 5.28
1892 1926 2.572209 TAGAAGGTTCCCAAAACCGG 57.428 50.000 0.00 0.00 44.82 5.28
1893 1927 2.752903 CCATAGAAGGTTCCCAAAACCG 59.247 50.000 1.52 0.00 44.82 4.44
1894 1928 3.762288 GTCCATAGAAGGTTCCCAAAACC 59.238 47.826 0.00 0.00 40.58 3.27
1895 1929 3.439129 CGTCCATAGAAGGTTCCCAAAAC 59.561 47.826 0.00 0.00 0.00 2.43
1896 1930 3.073356 ACGTCCATAGAAGGTTCCCAAAA 59.927 43.478 0.00 0.00 0.00 2.44
1897 1931 2.640826 ACGTCCATAGAAGGTTCCCAAA 59.359 45.455 0.00 0.00 0.00 3.28
1898 1932 2.235402 GACGTCCATAGAAGGTTCCCAA 59.765 50.000 3.51 0.00 0.00 4.12
1899 1933 1.829222 GACGTCCATAGAAGGTTCCCA 59.171 52.381 3.51 0.00 0.00 4.37
1900 1934 1.829222 TGACGTCCATAGAAGGTTCCC 59.171 52.381 14.12 0.00 0.00 3.97
1901 1935 3.821421 ATGACGTCCATAGAAGGTTCC 57.179 47.619 14.12 0.00 32.72 3.62
1910 1944 1.663739 GCCGGCTATGACGTCCATA 59.336 57.895 22.15 9.87 36.71 2.74
1911 1945 2.421739 GCCGGCTATGACGTCCAT 59.578 61.111 22.15 9.22 39.25 3.41
1912 1946 3.845259 GGCCGGCTATGACGTCCA 61.845 66.667 28.56 1.26 28.54 4.02
1913 1947 2.588856 AAAGGCCGGCTATGACGTCC 62.589 60.000 28.56 5.83 28.54 4.79
1914 1948 0.743345 AAAAGGCCGGCTATGACGTC 60.743 55.000 28.56 9.11 28.54 4.34
1915 1949 0.322187 AAAAAGGCCGGCTATGACGT 60.322 50.000 28.56 4.01 28.54 4.34
1916 1950 2.477880 AAAAAGGCCGGCTATGACG 58.522 52.632 28.56 0.00 0.00 4.35
1932 1966 1.112950 GGTTCCCACAACCCGAAAAA 58.887 50.000 0.00 0.00 34.26 1.94
1933 1967 0.259356 AGGTTCCCACAACCCGAAAA 59.741 50.000 0.00 0.00 41.18 2.29
1934 1968 0.259356 AAGGTTCCCACAACCCGAAA 59.741 50.000 0.00 0.00 41.18 3.46
1935 1969 0.179012 GAAGGTTCCCACAACCCGAA 60.179 55.000 0.00 0.00 41.18 4.30
1936 1970 1.057851 AGAAGGTTCCCACAACCCGA 61.058 55.000 0.00 0.00 41.18 5.14
1937 1971 0.688487 TAGAAGGTTCCCACAACCCG 59.312 55.000 0.00 0.00 41.18 5.28
1938 1972 1.982958 TCTAGAAGGTTCCCACAACCC 59.017 52.381 0.00 0.00 41.18 4.11
1939 1973 3.409570 GTTCTAGAAGGTTCCCACAACC 58.590 50.000 5.12 0.00 40.58 3.77
1940 1974 3.064931 CGTTCTAGAAGGTTCCCACAAC 58.935 50.000 15.51 0.00 0.00 3.32
1941 1975 2.701951 ACGTTCTAGAAGGTTCCCACAA 59.298 45.455 22.01 0.00 36.14 3.33
1942 1976 2.322658 ACGTTCTAGAAGGTTCCCACA 58.677 47.619 22.01 0.00 36.14 4.17
1943 1977 3.397849 AACGTTCTAGAAGGTTCCCAC 57.602 47.619 29.03 7.20 43.35 4.61
1949 1983 5.270794 AGGATTAGGAACGTTCTAGAAGGT 58.729 41.667 26.32 22.01 40.65 3.50
1950 1984 5.855740 AGGATTAGGAACGTTCTAGAAGG 57.144 43.478 26.32 20.77 0.00 3.46
1951 1985 8.549338 AAAAAGGATTAGGAACGTTCTAGAAG 57.451 34.615 26.32 3.05 0.00 2.85
2055 2089 9.737844 AAAGAAGAGATAAAAGAGCAAGAAGAT 57.262 29.630 0.00 0.00 0.00 2.40
2056 2090 9.566432 AAAAGAAGAGATAAAAGAGCAAGAAGA 57.434 29.630 0.00 0.00 0.00 2.87
2057 2091 9.824534 GAAAAGAAGAGATAAAAGAGCAAGAAG 57.175 33.333 0.00 0.00 0.00 2.85
2058 2092 9.566432 AGAAAAGAAGAGATAAAAGAGCAAGAA 57.434 29.630 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.