Multiple sequence alignment - TraesCS7A01G196800

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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 TraesCS7A01G196800 chr7A 100.000 2456 0 0 1 2456 156552540 156550085 0.000000e+00 4536.0
1 TraesCS7A01G196800 chr5A 98.164 1634 27 3 1 1632 576598765 576600397 0.000000e+00 2848.0
2 TraesCS7A01G196800 chr1A 96.632 1633 50 5 1 1631 371516013 371514384 0.000000e+00 2706.0
3 TraesCS7A01G196800 chr1A 84.551 479 59 10 1978 2453 496141951 496142417 6.190000e-126 460.0
4 TraesCS7A01G196800 chr5D 95.944 863 28 4 725 1581 543750747 543751608 0.000000e+00 1393.0
5 TraesCS7A01G196800 chr5D 96.858 732 15 4 1 725 543749958 543750688 0.000000e+00 1218.0
6 TraesCS7A01G196800 chr5D 84.615 247 28 3 785 1031 421858751 421858515 1.140000e-58 237.0
7 TraesCS7A01G196800 chr3B 93.947 793 38 8 852 1638 389747598 389746810 0.000000e+00 1190.0
8 TraesCS7A01G196800 chr3B 95.257 738 27 4 1 731 389765633 389764897 0.000000e+00 1162.0
9 TraesCS7A01G196800 chr3B 96.721 61 2 0 723 783 389764846 389764786 4.320000e-18 102.0
10 TraesCS7A01G196800 chr3A 84.674 1057 100 35 1 1031 486443473 486444493 0.000000e+00 998.0
11 TraesCS7A01G196800 chr4D 84.216 1058 100 40 1 1031 479969609 479968592 0.000000e+00 966.0
12 TraesCS7A01G196800 chr4A 90.150 731 58 9 1 725 646110484 646109762 0.000000e+00 939.0
13 TraesCS7A01G196800 chr4A 93.528 309 18 2 723 1031 646109704 646109398 2.230000e-125 459.0
14 TraesCS7A01G196800 chr4A 86.829 205 13 5 827 1031 647833952 647834142 1.480000e-52 217.0
15 TraesCS7A01G196800 chr1D 88.514 740 67 13 1 731 211711126 211710396 0.000000e+00 880.0
16 TraesCS7A01G196800 chr1D 87.618 743 70 17 1 731 487590251 487589519 0.000000e+00 843.0
17 TraesCS7A01G196800 chr1D 85.208 480 54 12 1978 2453 399393348 399393814 6.140000e-131 477.0
18 TraesCS7A01G196800 chr1D 82.942 469 57 16 1992 2453 399413809 399414261 3.800000e-108 401.0
19 TraesCS7A01G196800 chr3D 88.011 734 66 18 1 725 562640379 562641099 0.000000e+00 848.0
20 TraesCS7A01G196800 chr3D 85.020 247 19 5 785 1031 51087955 51087727 4.080000e-58 235.0
21 TraesCS7A01G196800 chr7B 96.640 506 13 2 1952 2456 116754772 116754270 0.000000e+00 837.0
22 TraesCS7A01G196800 chr7B 83.158 475 66 8 1980 2453 45051026 45051487 2.920000e-114 422.0
23 TraesCS7A01G196800 chr7B 100.000 43 0 0 1879 1921 116754814 116754772 2.020000e-11 80.5
24 TraesCS7A01G196800 chr7D 87.432 740 73 15 1 731 192365615 192364887 0.000000e+00 833.0
25 TraesCS7A01G196800 chr7D 94.677 526 25 2 1933 2456 154934346 154934870 0.000000e+00 813.0
26 TraesCS7A01G196800 chr7D 88.261 230 15 6 1690 1914 154926233 154926455 5.210000e-67 265.0
27 TraesCS7A01G196800 chr1B 85.595 479 54 10 1978 2453 535797980 535798446 2.840000e-134 488.0
28 TraesCS7A01G196800 chr1B 82.599 431 54 13 1978 2402 535908198 535908613 6.460000e-96 361.0
29 TraesCS7A01G196800 chr1B 83.806 247 30 3 785 1031 37721469 37721233 2.460000e-55 226.0
30 TraesCS7A01G196800 chr6A 85.020 247 27 3 785 1031 22740184 22739948 2.440000e-60 243.0


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 TraesCS7A01G196800 chr7A 156550085 156552540 2455 True 4536.00 4536 100.000 1 2456 1 chr7A.!!$R1 2455
1 TraesCS7A01G196800 chr5A 576598765 576600397 1632 False 2848.00 2848 98.164 1 1632 1 chr5A.!!$F1 1631
2 TraesCS7A01G196800 chr1A 371514384 371516013 1629 True 2706.00 2706 96.632 1 1631 1 chr1A.!!$R1 1630
3 TraesCS7A01G196800 chr5D 543749958 543751608 1650 False 1305.50 1393 96.401 1 1581 2 chr5D.!!$F1 1580
4 TraesCS7A01G196800 chr3B 389746810 389747598 788 True 1190.00 1190 93.947 852 1638 1 chr3B.!!$R1 786
5 TraesCS7A01G196800 chr3B 389764786 389765633 847 True 632.00 1162 95.989 1 783 2 chr3B.!!$R2 782
6 TraesCS7A01G196800 chr3A 486443473 486444493 1020 False 998.00 998 84.674 1 1031 1 chr3A.!!$F1 1030
7 TraesCS7A01G196800 chr4D 479968592 479969609 1017 True 966.00 966 84.216 1 1031 1 chr4D.!!$R1 1030
8 TraesCS7A01G196800 chr4A 646109398 646110484 1086 True 699.00 939 91.839 1 1031 2 chr4A.!!$R1 1030
9 TraesCS7A01G196800 chr1D 211710396 211711126 730 True 880.00 880 88.514 1 731 1 chr1D.!!$R1 730
10 TraesCS7A01G196800 chr1D 487589519 487590251 732 True 843.00 843 87.618 1 731 1 chr1D.!!$R2 730
11 TraesCS7A01G196800 chr3D 562640379 562641099 720 False 848.00 848 88.011 1 725 1 chr3D.!!$F1 724
12 TraesCS7A01G196800 chr7B 116754270 116754814 544 True 458.75 837 98.320 1879 2456 2 chr7B.!!$R1 577
13 TraesCS7A01G196800 chr7D 192364887 192365615 728 True 833.00 833 87.432 1 731 1 chr7D.!!$R1 730
14 TraesCS7A01G196800 chr7D 154934346 154934870 524 False 813.00 813 94.677 1933 2456 1 chr7D.!!$F2 523

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
1091 1169 0.171231 CTCATCTCCGTCTCGCAACA 59.829 55.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2037 0.796927 GCGACCACTTTCTAAGCACC 59.203 55.0 0.0 0.0 0.0 5.01 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
1091 1169 0.171231 CTCATCTCCGTCTCGCAACA 59.829 55.000 0.00 0.00 0.00 3.33
1552 1637 3.698040 CTGGCCTGACATGCTTTAAGATT 59.302 43.478 3.32 0.00 0.00 2.40
1624 1709 2.298411 GGCACGTTCGGGACTTATTA 57.702 50.000 0.00 0.00 0.00 0.98
1628 1713 4.095334 GGCACGTTCGGGACTTATTAATTT 59.905 41.667 0.00 0.00 0.00 1.82
1632 1717 5.639082 ACGTTCGGGACTTATTAATTTCGTT 59.361 36.000 0.00 0.00 0.00 3.85
1650 1735 6.578163 TTCGTTATTTTTAGGGGTTTGAGG 57.422 37.500 0.00 0.00 0.00 3.86
1651 1736 5.011586 TCGTTATTTTTAGGGGTTTGAGGG 58.988 41.667 0.00 0.00 0.00 4.30
1652 1737 4.768448 CGTTATTTTTAGGGGTTTGAGGGT 59.232 41.667 0.00 0.00 0.00 4.34
1653 1738 5.244402 CGTTATTTTTAGGGGTTTGAGGGTT 59.756 40.000 0.00 0.00 0.00 4.11
1654 1739 6.433716 CGTTATTTTTAGGGGTTTGAGGGTTA 59.566 38.462 0.00 0.00 0.00 2.85
1655 1740 7.362315 CGTTATTTTTAGGGGTTTGAGGGTTAG 60.362 40.741 0.00 0.00 0.00 2.34
1656 1741 5.406570 TTTTTAGGGGTTTGAGGGTTAGT 57.593 39.130 0.00 0.00 0.00 2.24
1657 1742 4.376225 TTTAGGGGTTTGAGGGTTAGTG 57.624 45.455 0.00 0.00 0.00 2.74
1658 1743 1.829138 AGGGGTTTGAGGGTTAGTGT 58.171 50.000 0.00 0.00 0.00 3.55
1659 1744 2.141067 AGGGGTTTGAGGGTTAGTGTT 58.859 47.619 0.00 0.00 0.00 3.32
1660 1745 2.107726 AGGGGTTTGAGGGTTAGTGTTC 59.892 50.000 0.00 0.00 0.00 3.18
1661 1746 2.107726 GGGGTTTGAGGGTTAGTGTTCT 59.892 50.000 0.00 0.00 0.00 3.01
1662 1747 3.328637 GGGGTTTGAGGGTTAGTGTTCTA 59.671 47.826 0.00 0.00 0.00 2.10
1663 1748 4.321718 GGGTTTGAGGGTTAGTGTTCTAC 58.678 47.826 0.00 0.00 0.00 2.59
1664 1749 4.041321 GGGTTTGAGGGTTAGTGTTCTACT 59.959 45.833 0.00 0.00 43.56 2.57
1665 1750 5.246883 GGGTTTGAGGGTTAGTGTTCTACTA 59.753 44.000 0.00 0.00 40.89 1.82
1666 1751 6.396450 GGTTTGAGGGTTAGTGTTCTACTAG 58.604 44.000 0.00 0.00 42.57 2.57
1667 1752 6.210185 GGTTTGAGGGTTAGTGTTCTACTAGA 59.790 42.308 0.00 0.00 42.57 2.43
1668 1753 6.830873 TTGAGGGTTAGTGTTCTACTAGAC 57.169 41.667 0.00 0.00 42.57 2.59
1669 1754 6.137104 TGAGGGTTAGTGTTCTACTAGACT 57.863 41.667 0.00 0.00 42.57 3.24
1670 1755 6.550163 TGAGGGTTAGTGTTCTACTAGACTT 58.450 40.000 0.00 0.00 42.57 3.01
1671 1756 6.433404 TGAGGGTTAGTGTTCTACTAGACTTG 59.567 42.308 0.00 0.00 42.57 3.16
1672 1757 5.185442 AGGGTTAGTGTTCTACTAGACTTGC 59.815 44.000 0.00 0.00 42.57 4.01
1673 1758 5.185442 GGGTTAGTGTTCTACTAGACTTGCT 59.815 44.000 0.00 0.00 42.57 3.91
1674 1759 6.324042 GGTTAGTGTTCTACTAGACTTGCTC 58.676 44.000 0.00 0.00 42.57 4.26
1675 1760 6.151480 GGTTAGTGTTCTACTAGACTTGCTCT 59.849 42.308 0.00 0.00 42.57 4.09
1676 1761 7.336427 GGTTAGTGTTCTACTAGACTTGCTCTA 59.664 40.741 0.00 0.00 42.57 2.43
1677 1762 8.728833 GTTAGTGTTCTACTAGACTTGCTCTAA 58.271 37.037 0.00 0.00 42.57 2.10
1678 1763 7.762588 AGTGTTCTACTAGACTTGCTCTAAA 57.237 36.000 0.00 0.00 38.04 1.85
1679 1764 7.822658 AGTGTTCTACTAGACTTGCTCTAAAG 58.177 38.462 0.00 0.00 38.04 1.85
1680 1765 7.666388 AGTGTTCTACTAGACTTGCTCTAAAGA 59.334 37.037 0.00 0.00 38.04 2.52
1681 1766 7.751793 GTGTTCTACTAGACTTGCTCTAAAGAC 59.248 40.741 0.00 0.00 30.58 3.01
1682 1767 7.666388 TGTTCTACTAGACTTGCTCTAAAGACT 59.334 37.037 0.00 0.00 36.41 3.24
1683 1768 9.165035 GTTCTACTAGACTTGCTCTAAAGACTA 57.835 37.037 0.00 0.00 34.67 2.59
1684 1769 8.721019 TCTACTAGACTTGCTCTAAAGACTAC 57.279 38.462 0.00 0.00 34.67 2.73
1685 1770 8.542080 TCTACTAGACTTGCTCTAAAGACTACT 58.458 37.037 0.00 0.00 34.67 2.57
1686 1771 7.619964 ACTAGACTTGCTCTAAAGACTACTC 57.380 40.000 0.00 0.00 34.67 2.59
1687 1772 5.907866 AGACTTGCTCTAAAGACTACTCC 57.092 43.478 0.00 0.00 31.74 3.85
1688 1773 5.576128 AGACTTGCTCTAAAGACTACTCCT 58.424 41.667 0.00 0.00 31.74 3.69
1689 1774 6.014012 AGACTTGCTCTAAAGACTACTCCTT 58.986 40.000 0.00 0.00 31.74 3.36
1690 1775 6.031751 ACTTGCTCTAAAGACTACTCCTTG 57.968 41.667 0.00 0.00 0.00 3.61
1691 1776 5.775701 ACTTGCTCTAAAGACTACTCCTTGA 59.224 40.000 0.00 0.00 0.00 3.02
1692 1777 5.646577 TGCTCTAAAGACTACTCCTTGAC 57.353 43.478 0.00 0.00 0.00 3.18
1693 1778 4.463186 TGCTCTAAAGACTACTCCTTGACC 59.537 45.833 0.00 0.00 0.00 4.02
1694 1779 4.142116 GCTCTAAAGACTACTCCTTGACCC 60.142 50.000 0.00 0.00 0.00 4.46
1695 1780 5.265989 CTCTAAAGACTACTCCTTGACCCT 58.734 45.833 0.00 0.00 0.00 4.34
1696 1781 6.398655 TCTAAAGACTACTCCTTGACCCTA 57.601 41.667 0.00 0.00 0.00 3.53
1697 1782 6.982899 TCTAAAGACTACTCCTTGACCCTAT 58.017 40.000 0.00 0.00 0.00 2.57
1698 1783 7.061688 TCTAAAGACTACTCCTTGACCCTATC 58.938 42.308 0.00 0.00 0.00 2.08
1699 1784 4.187506 AGACTACTCCTTGACCCTATCC 57.812 50.000 0.00 0.00 0.00 2.59
1700 1785 3.117054 AGACTACTCCTTGACCCTATCCC 60.117 52.174 0.00 0.00 0.00 3.85
1701 1786 2.866454 ACTACTCCTTGACCCTATCCCT 59.134 50.000 0.00 0.00 0.00 4.20
1702 1787 2.972153 ACTCCTTGACCCTATCCCTT 57.028 50.000 0.00 0.00 0.00 3.95
1703 1788 3.222394 ACTCCTTGACCCTATCCCTTT 57.778 47.619 0.00 0.00 0.00 3.11
1704 1789 3.542604 ACTCCTTGACCCTATCCCTTTT 58.457 45.455 0.00 0.00 0.00 2.27
1705 1790 3.923425 ACTCCTTGACCCTATCCCTTTTT 59.077 43.478 0.00 0.00 0.00 1.94
1706 1791 4.263949 ACTCCTTGACCCTATCCCTTTTTG 60.264 45.833 0.00 0.00 0.00 2.44
1707 1792 3.011257 TCCTTGACCCTATCCCTTTTTGG 59.989 47.826 0.00 0.00 0.00 3.28
1708 1793 2.525105 TGACCCTATCCCTTTTTGGC 57.475 50.000 0.00 0.00 0.00 4.52
1709 1794 1.006639 TGACCCTATCCCTTTTTGGCC 59.993 52.381 0.00 0.00 0.00 5.36
1710 1795 1.006639 GACCCTATCCCTTTTTGGCCA 59.993 52.381 0.00 0.00 0.00 5.36
1711 1796 1.435168 ACCCTATCCCTTTTTGGCCAA 59.565 47.619 16.05 16.05 0.00 4.52
1712 1797 2.158081 ACCCTATCCCTTTTTGGCCAAA 60.158 45.455 27.13 27.13 0.00 3.28
1713 1798 2.909662 CCCTATCCCTTTTTGGCCAAAA 59.090 45.455 34.56 34.56 38.40 2.44
1714 1799 3.307410 CCCTATCCCTTTTTGGCCAAAAC 60.307 47.826 37.24 0.00 39.70 2.43
1715 1800 3.326297 CCTATCCCTTTTTGGCCAAAACA 59.674 43.478 37.24 26.57 39.70 2.83
1716 1801 2.700722 TCCCTTTTTGGCCAAAACAC 57.299 45.000 37.24 0.00 39.70 3.32
1717 1802 1.210722 TCCCTTTTTGGCCAAAACACC 59.789 47.619 37.24 0.00 39.70 4.16
1718 1803 1.065126 CCCTTTTTGGCCAAAACACCA 60.065 47.619 37.24 24.03 39.70 4.17
1719 1804 2.619074 CCCTTTTTGGCCAAAACACCAA 60.619 45.455 37.24 23.69 44.11 3.67
1728 1813 7.736447 TTGGCCAAAACACCAAAATTATTAG 57.264 32.000 17.98 0.00 42.87 1.73
1729 1814 7.067496 TGGCCAAAACACCAAAATTATTAGA 57.933 32.000 0.61 0.00 31.46 2.10
1730 1815 7.158021 TGGCCAAAACACCAAAATTATTAGAG 58.842 34.615 0.61 0.00 31.46 2.43
1731 1816 7.015682 TGGCCAAAACACCAAAATTATTAGAGA 59.984 33.333 0.61 0.00 31.46 3.10
1732 1817 7.545615 GGCCAAAACACCAAAATTATTAGAGAG 59.454 37.037 0.00 0.00 0.00 3.20
1733 1818 8.088365 GCCAAAACACCAAAATTATTAGAGAGT 58.912 33.333 0.00 0.00 0.00 3.24
1734 1819 9.410556 CCAAAACACCAAAATTATTAGAGAGTG 57.589 33.333 0.00 0.00 0.00 3.51
1735 1820 9.410556 CAAAACACCAAAATTATTAGAGAGTGG 57.589 33.333 0.00 0.00 0.00 4.00
1736 1821 8.706322 AAACACCAAAATTATTAGAGAGTGGT 57.294 30.769 0.00 0.00 38.65 4.16
1739 1824 6.790319 ACCAAAATTATTAGAGAGTGGTGGT 58.210 36.000 0.00 0.00 36.77 4.16
1740 1825 6.659242 ACCAAAATTATTAGAGAGTGGTGGTG 59.341 38.462 0.00 0.00 36.77 4.17
1741 1826 6.404734 CCAAAATTATTAGAGAGTGGTGGTGC 60.405 42.308 0.00 0.00 0.00 5.01
1742 1827 3.520290 TTATTAGAGAGTGGTGGTGCG 57.480 47.619 0.00 0.00 0.00 5.34
1743 1828 1.267121 ATTAGAGAGTGGTGGTGCGT 58.733 50.000 0.00 0.00 0.00 5.24
1744 1829 1.045407 TTAGAGAGTGGTGGTGCGTT 58.955 50.000 0.00 0.00 0.00 4.84
1745 1830 0.601558 TAGAGAGTGGTGGTGCGTTC 59.398 55.000 0.00 0.00 0.00 3.95
1746 1831 1.115930 AGAGAGTGGTGGTGCGTTCT 61.116 55.000 0.00 0.00 0.00 3.01
1747 1832 0.601558 GAGAGTGGTGGTGCGTTCTA 59.398 55.000 0.00 0.00 0.00 2.10
1748 1833 1.204941 GAGAGTGGTGGTGCGTTCTAT 59.795 52.381 0.00 0.00 0.00 1.98
1749 1834 1.066858 AGAGTGGTGGTGCGTTCTATG 60.067 52.381 0.00 0.00 0.00 2.23
1750 1835 0.973632 AGTGGTGGTGCGTTCTATGA 59.026 50.000 0.00 0.00 0.00 2.15
1751 1836 1.076332 GTGGTGGTGCGTTCTATGAC 58.924 55.000 0.00 0.00 0.00 3.06
1752 1837 0.682292 TGGTGGTGCGTTCTATGACA 59.318 50.000 0.00 0.00 0.00 3.58
1753 1838 1.277842 TGGTGGTGCGTTCTATGACAT 59.722 47.619 0.00 0.00 0.00 3.06
1754 1839 2.498078 TGGTGGTGCGTTCTATGACATA 59.502 45.455 0.00 0.00 0.00 2.29
1755 1840 3.133901 TGGTGGTGCGTTCTATGACATAT 59.866 43.478 0.00 0.00 0.00 1.78
1756 1841 3.741344 GGTGGTGCGTTCTATGACATATC 59.259 47.826 0.00 0.00 0.00 1.63
1757 1842 4.368315 GTGGTGCGTTCTATGACATATCA 58.632 43.478 0.00 0.00 39.83 2.15
1758 1843 4.209288 GTGGTGCGTTCTATGACATATCAC 59.791 45.833 0.00 0.83 37.79 3.06
1759 1844 4.142049 TGGTGCGTTCTATGACATATCACA 60.142 41.667 0.00 0.00 37.79 3.58
1760 1845 4.808895 GGTGCGTTCTATGACATATCACAA 59.191 41.667 0.00 0.00 37.79 3.33
1761 1846 5.293324 GGTGCGTTCTATGACATATCACAAA 59.707 40.000 0.00 0.00 37.79 2.83
1762 1847 6.183360 GGTGCGTTCTATGACATATCACAAAA 60.183 38.462 0.00 0.00 37.79 2.44
1763 1848 6.682863 GTGCGTTCTATGACATATCACAAAAC 59.317 38.462 0.00 0.00 37.79 2.43
1764 1849 6.183360 TGCGTTCTATGACATATCACAAAACC 60.183 38.462 0.00 0.00 37.79 3.27
1765 1850 6.715464 CGTTCTATGACATATCACAAAACCC 58.285 40.000 0.00 0.00 37.79 4.11
1766 1851 6.315144 CGTTCTATGACATATCACAAAACCCA 59.685 38.462 0.00 0.00 37.79 4.51
1767 1852 7.472543 GTTCTATGACATATCACAAAACCCAC 58.527 38.462 0.00 0.00 37.79 4.61
1768 1853 6.119536 TCTATGACATATCACAAAACCCACC 58.880 40.000 0.00 0.00 37.79 4.61
1769 1854 3.426615 TGACATATCACAAAACCCACCC 58.573 45.455 0.00 0.00 0.00 4.61
1770 1855 3.181428 TGACATATCACAAAACCCACCCA 60.181 43.478 0.00 0.00 0.00 4.51
1771 1856 3.161866 ACATATCACAAAACCCACCCAC 58.838 45.455 0.00 0.00 0.00 4.61
1772 1857 3.181423 ACATATCACAAAACCCACCCACT 60.181 43.478 0.00 0.00 0.00 4.00
1773 1858 1.703411 ATCACAAAACCCACCCACTG 58.297 50.000 0.00 0.00 0.00 3.66
1774 1859 0.626382 TCACAAAACCCACCCACTGA 59.374 50.000 0.00 0.00 0.00 3.41
1775 1860 1.216678 TCACAAAACCCACCCACTGAT 59.783 47.619 0.00 0.00 0.00 2.90
1776 1861 2.443632 TCACAAAACCCACCCACTGATA 59.556 45.455 0.00 0.00 0.00 2.15
1777 1862 2.556622 CACAAAACCCACCCACTGATAC 59.443 50.000 0.00 0.00 0.00 2.24
1778 1863 2.175931 ACAAAACCCACCCACTGATACA 59.824 45.455 0.00 0.00 0.00 2.29
1779 1864 3.181423 ACAAAACCCACCCACTGATACAT 60.181 43.478 0.00 0.00 0.00 2.29
1780 1865 4.043561 ACAAAACCCACCCACTGATACATA 59.956 41.667 0.00 0.00 0.00 2.29
1781 1866 3.926058 AACCCACCCACTGATACATAC 57.074 47.619 0.00 0.00 0.00 2.39
1782 1867 3.130734 ACCCACCCACTGATACATACT 57.869 47.619 0.00 0.00 0.00 2.12
1783 1868 3.039011 ACCCACCCACTGATACATACTC 58.961 50.000 0.00 0.00 0.00 2.59
1784 1869 2.368875 CCCACCCACTGATACATACTCC 59.631 54.545 0.00 0.00 0.00 3.85
1785 1870 2.035961 CCACCCACTGATACATACTCCG 59.964 54.545 0.00 0.00 0.00 4.63
1786 1871 2.693591 CACCCACTGATACATACTCCGT 59.306 50.000 0.00 0.00 0.00 4.69
1787 1872 3.887110 CACCCACTGATACATACTCCGTA 59.113 47.826 0.00 0.00 0.00 4.02
1788 1873 4.523173 CACCCACTGATACATACTCCGTAT 59.477 45.833 0.00 0.00 32.24 3.06
1790 1875 4.082190 CCCACTGATACATACTCCGTATGG 60.082 50.000 15.91 0.00 46.98 2.74
1791 1876 4.523173 CCACTGATACATACTCCGTATGGT 59.477 45.833 15.91 6.46 46.98 3.55
1792 1877 5.335740 CCACTGATACATACTCCGTATGGTC 60.336 48.000 15.91 13.42 46.98 4.02
1793 1878 4.765856 ACTGATACATACTCCGTATGGTCC 59.234 45.833 15.91 6.81 46.98 4.46
1794 1879 3.754850 TGATACATACTCCGTATGGTCCG 59.245 47.826 15.91 0.00 46.98 4.79
1795 1880 2.062971 ACATACTCCGTATGGTCCGT 57.937 50.000 15.91 0.16 46.98 4.69
1796 1881 1.679680 ACATACTCCGTATGGTCCGTG 59.320 52.381 15.91 0.00 46.98 4.94
1797 1882 1.951602 CATACTCCGTATGGTCCGTGA 59.048 52.381 0.00 0.00 41.30 4.35
1798 1883 2.127271 TACTCCGTATGGTCCGTGAA 57.873 50.000 0.00 0.00 36.30 3.18
1799 1884 0.815734 ACTCCGTATGGTCCGTGAAG 59.184 55.000 0.00 0.00 36.30 3.02
1800 1885 0.527817 CTCCGTATGGTCCGTGAAGC 60.528 60.000 0.00 0.00 36.30 3.86
1801 1886 0.968901 TCCGTATGGTCCGTGAAGCT 60.969 55.000 0.00 0.00 36.30 3.74
1802 1887 0.108329 CCGTATGGTCCGTGAAGCTT 60.108 55.000 0.00 0.00 0.00 3.74
1803 1888 1.278238 CGTATGGTCCGTGAAGCTTC 58.722 55.000 19.89 19.89 0.00 3.86
1804 1889 1.135083 CGTATGGTCCGTGAAGCTTCT 60.135 52.381 26.09 6.90 0.00 2.85
1805 1890 2.098607 CGTATGGTCCGTGAAGCTTCTA 59.901 50.000 26.09 10.83 0.00 2.10
1806 1891 2.674796 ATGGTCCGTGAAGCTTCTAC 57.325 50.000 26.09 19.81 0.00 2.59
1807 1892 1.334160 TGGTCCGTGAAGCTTCTACA 58.666 50.000 26.09 13.01 0.00 2.74
1808 1893 1.000506 TGGTCCGTGAAGCTTCTACAC 59.999 52.381 26.09 16.01 0.00 2.90
1809 1894 1.272769 GGTCCGTGAAGCTTCTACACT 59.727 52.381 26.09 0.00 33.13 3.55
1810 1895 2.490903 GGTCCGTGAAGCTTCTACACTA 59.509 50.000 26.09 2.80 33.13 2.74
1811 1896 3.500014 GTCCGTGAAGCTTCTACACTAC 58.500 50.000 26.09 14.06 33.13 2.73
1812 1897 3.057736 GTCCGTGAAGCTTCTACACTACA 60.058 47.826 26.09 1.96 33.13 2.74
1813 1898 3.057736 TCCGTGAAGCTTCTACACTACAC 60.058 47.826 26.09 13.27 33.13 2.90
1814 1899 3.057456 CCGTGAAGCTTCTACACTACACT 60.057 47.826 26.09 0.00 33.13 3.55
1815 1900 4.547532 CGTGAAGCTTCTACACTACACTT 58.452 43.478 26.09 0.00 33.13 3.16
1816 1901 4.383052 CGTGAAGCTTCTACACTACACTTG 59.617 45.833 26.09 4.74 33.13 3.16
1817 1902 4.150804 GTGAAGCTTCTACACTACACTTGC 59.849 45.833 26.09 0.00 0.00 4.01
1818 1903 2.947852 AGCTTCTACACTACACTTGCG 58.052 47.619 0.00 0.00 0.00 4.85
1819 1904 2.296471 AGCTTCTACACTACACTTGCGT 59.704 45.455 0.00 0.00 0.00 5.24
1820 1905 3.504906 AGCTTCTACACTACACTTGCGTA 59.495 43.478 0.00 0.00 0.00 4.42
1821 1906 3.607209 GCTTCTACACTACACTTGCGTAC 59.393 47.826 0.00 0.00 0.00 3.67
1822 1907 4.615452 GCTTCTACACTACACTTGCGTACT 60.615 45.833 0.00 0.00 0.00 2.73
1823 1908 4.414999 TCTACACTACACTTGCGTACTG 57.585 45.455 0.00 0.00 0.00 2.74
1824 1909 1.779569 ACACTACACTTGCGTACTGC 58.220 50.000 3.22 3.22 46.70 4.40
1825 1910 1.340248 ACACTACACTTGCGTACTGCT 59.660 47.619 10.27 0.00 46.63 4.24
1826 1911 1.986378 CACTACACTTGCGTACTGCTC 59.014 52.381 10.27 0.00 46.63 4.26
1827 1912 1.260206 CTACACTTGCGTACTGCTCG 58.740 55.000 10.27 4.91 46.63 5.03
1828 1913 0.109458 TACACTTGCGTACTGCTCGG 60.109 55.000 10.27 4.38 46.63 4.63
1829 1914 2.094659 CACTTGCGTACTGCTCGGG 61.095 63.158 10.27 0.00 46.63 5.14
1830 1915 2.261671 CTTGCGTACTGCTCGGGT 59.738 61.111 10.27 0.00 46.63 5.28
1831 1916 2.048597 TTGCGTACTGCTCGGGTG 60.049 61.111 10.27 0.00 46.63 4.61
1832 1917 4.735132 TGCGTACTGCTCGGGTGC 62.735 66.667 10.27 0.00 46.63 5.01
1834 1919 4.111016 CGTACTGCTCGGGTGCGA 62.111 66.667 0.00 0.00 43.35 5.10
1835 1920 2.494918 GTACTGCTCGGGTGCGAT 59.505 61.111 0.00 0.00 35.36 4.58
1836 1921 1.589196 GTACTGCTCGGGTGCGATC 60.589 63.158 0.00 0.00 35.36 3.69
1837 1922 1.753078 TACTGCTCGGGTGCGATCT 60.753 57.895 0.00 0.00 35.36 2.75
1838 1923 1.320344 TACTGCTCGGGTGCGATCTT 61.320 55.000 0.00 0.00 35.36 2.40
1839 1924 1.448540 CTGCTCGGGTGCGATCTTT 60.449 57.895 0.00 0.00 35.36 2.52
1840 1925 0.179111 CTGCTCGGGTGCGATCTTTA 60.179 55.000 0.00 0.00 35.36 1.85
1841 1926 0.179111 TGCTCGGGTGCGATCTTTAG 60.179 55.000 0.00 0.00 35.36 1.85
1842 1927 0.179108 GCTCGGGTGCGATCTTTAGT 60.179 55.000 0.00 0.00 0.00 2.24
1843 1928 1.841450 CTCGGGTGCGATCTTTAGTC 58.159 55.000 0.00 0.00 0.00 2.59
1844 1929 1.134367 CTCGGGTGCGATCTTTAGTCA 59.866 52.381 0.00 0.00 0.00 3.41
1845 1930 1.546923 TCGGGTGCGATCTTTAGTCAA 59.453 47.619 0.00 0.00 0.00 3.18
1846 1931 1.659098 CGGGTGCGATCTTTAGTCAAC 59.341 52.381 0.00 0.00 0.00 3.18
1847 1932 2.674177 CGGGTGCGATCTTTAGTCAACT 60.674 50.000 0.00 0.00 0.00 3.16
1848 1933 3.428452 CGGGTGCGATCTTTAGTCAACTA 60.428 47.826 0.00 0.00 0.00 2.24
1849 1934 3.864003 GGGTGCGATCTTTAGTCAACTAC 59.136 47.826 0.00 0.00 0.00 2.73
1850 1935 3.864003 GGTGCGATCTTTAGTCAACTACC 59.136 47.826 0.00 0.00 0.00 3.18
1851 1936 4.491676 GTGCGATCTTTAGTCAACTACCA 58.508 43.478 0.00 0.00 0.00 3.25
1852 1937 4.563184 GTGCGATCTTTAGTCAACTACCAG 59.437 45.833 0.00 0.00 0.00 4.00
1853 1938 3.552294 GCGATCTTTAGTCAACTACCAGC 59.448 47.826 0.00 0.00 0.00 4.85
1854 1939 4.744570 CGATCTTTAGTCAACTACCAGCA 58.255 43.478 0.00 0.00 0.00 4.41
1855 1940 4.800993 CGATCTTTAGTCAACTACCAGCAG 59.199 45.833 0.00 0.00 0.00 4.24
1856 1941 5.393135 CGATCTTTAGTCAACTACCAGCAGA 60.393 44.000 0.00 0.00 0.00 4.26
1857 1942 5.135508 TCTTTAGTCAACTACCAGCAGAC 57.864 43.478 0.00 0.00 0.00 3.51
1858 1943 3.955650 TTAGTCAACTACCAGCAGACC 57.044 47.619 0.00 0.00 0.00 3.85
1859 1944 2.016905 AGTCAACTACCAGCAGACCT 57.983 50.000 0.00 0.00 0.00 3.85
1860 1945 2.330216 AGTCAACTACCAGCAGACCTT 58.670 47.619 0.00 0.00 0.00 3.50
1861 1946 2.037772 AGTCAACTACCAGCAGACCTTG 59.962 50.000 0.00 0.00 0.00 3.61
1872 1957 1.707632 CAGACCTTGCAGAGAAGTCG 58.292 55.000 0.00 0.00 0.00 4.18
1873 1958 0.037790 AGACCTTGCAGAGAAGTCGC 60.038 55.000 0.00 0.00 0.00 5.19
1874 1959 1.004440 ACCTTGCAGAGAAGTCGCC 60.004 57.895 0.00 0.00 0.00 5.54
1875 1960 2.097038 CCTTGCAGAGAAGTCGCCG 61.097 63.158 0.00 0.00 0.00 6.46
1876 1961 2.734673 CTTGCAGAGAAGTCGCCGC 61.735 63.158 0.00 0.00 0.00 6.53
1877 1962 3.513768 TTGCAGAGAAGTCGCCGCA 62.514 57.895 0.00 0.00 0.00 5.69
1921 2006 2.158623 GCATCCATCCAACCTGATACCA 60.159 50.000 0.00 0.00 0.00 3.25
1922 2007 3.688126 GCATCCATCCAACCTGATACCAA 60.688 47.826 0.00 0.00 0.00 3.67
1923 2008 3.931907 TCCATCCAACCTGATACCAAG 57.068 47.619 0.00 0.00 0.00 3.61
1925 2010 2.423373 CCATCCAACCTGATACCAAGGG 60.423 54.545 0.00 0.00 0.00 3.95
1926 2011 0.623723 TCCAACCTGATACCAAGGGC 59.376 55.000 0.00 0.00 0.00 5.19
1927 2012 0.625849 CCAACCTGATACCAAGGGCT 59.374 55.000 0.00 0.00 0.00 5.19
1928 2013 1.683011 CCAACCTGATACCAAGGGCTG 60.683 57.143 0.00 0.00 0.00 4.85
1946 2031 2.501610 GGAGCCTGGGATCGTCAC 59.498 66.667 0.00 0.00 0.00 3.67
1951 2036 1.065928 CCTGGGATCGTCACGTAGC 59.934 63.158 0.00 0.00 0.00 3.58
1952 2037 1.298413 CTGGGATCGTCACGTAGCG 60.298 63.158 0.00 4.80 0.00 4.26
2157 2244 0.752009 CCACCGATCTCTCCTCCGAA 60.752 60.000 0.00 0.00 0.00 4.30
2382 2469 3.612247 CTCCTTGGTCACCAGGCCG 62.612 68.421 0.00 0.00 33.81 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 200 5.804473 TGATGGCAAATTTAGTTTACGCATG 59.196 36.000 0.00 0.00 0.00 4.06
243 249 5.994250 TCTTATCTTCTTGCCATGTAAGCT 58.006 37.500 0.00 0.00 0.00 3.74
987 1065 2.019408 CGACATGGTCACGAACGCA 61.019 57.895 0.00 0.00 32.09 5.24
1075 1153 1.478510 AGATTGTTGCGAGACGGAGAT 59.521 47.619 0.00 0.00 0.00 2.75
1091 1169 0.539051 CTCTGTCCTTGCCGGAGATT 59.461 55.000 5.05 0.00 44.20 2.40
1332 1416 4.797743 TGAGATATCGATCAGATAGGGGG 58.202 47.826 0.00 0.00 44.30 5.40
1333 1417 5.445069 ACTGAGATATCGATCAGATAGGGG 58.555 45.833 22.34 2.63 44.68 4.79
1507 1592 3.875134 ACACGTCATCTCCTTTTTCGTTT 59.125 39.130 0.00 0.00 0.00 3.60
1552 1637 4.055360 CTGACCGTTAGATGACAACACAA 58.945 43.478 0.00 0.00 0.00 3.33
1624 1709 8.092068 CCTCAAACCCCTAAAAATAACGAAATT 58.908 33.333 0.00 0.00 0.00 1.82
1628 1713 5.011586 CCCTCAAACCCCTAAAAATAACGA 58.988 41.667 0.00 0.00 0.00 3.85
1632 1717 6.949463 CACTAACCCTCAAACCCCTAAAAATA 59.051 38.462 0.00 0.00 0.00 1.40
1638 1723 2.994355 ACACTAACCCTCAAACCCCTA 58.006 47.619 0.00 0.00 0.00 3.53
1639 1724 1.829138 ACACTAACCCTCAAACCCCT 58.171 50.000 0.00 0.00 0.00 4.79
1640 1725 2.107726 AGAACACTAACCCTCAAACCCC 59.892 50.000 0.00 0.00 0.00 4.95
1641 1726 3.503800 AGAACACTAACCCTCAAACCC 57.496 47.619 0.00 0.00 0.00 4.11
1642 1727 5.224821 AGTAGAACACTAACCCTCAAACC 57.775 43.478 0.00 0.00 34.98 3.27
1643 1728 7.039853 AGTCTAGTAGAACACTAACCCTCAAAC 60.040 40.741 0.17 0.00 39.28 2.93
1644 1729 7.008941 AGTCTAGTAGAACACTAACCCTCAAA 58.991 38.462 0.17 0.00 39.28 2.69
1645 1730 6.550163 AGTCTAGTAGAACACTAACCCTCAA 58.450 40.000 0.17 0.00 39.28 3.02
1646 1731 6.137104 AGTCTAGTAGAACACTAACCCTCA 57.863 41.667 0.17 0.00 39.28 3.86
1647 1732 6.625520 GCAAGTCTAGTAGAACACTAACCCTC 60.626 46.154 0.17 0.00 39.28 4.30
1648 1733 5.185442 GCAAGTCTAGTAGAACACTAACCCT 59.815 44.000 0.17 0.00 39.28 4.34
1649 1734 5.185442 AGCAAGTCTAGTAGAACACTAACCC 59.815 44.000 0.17 0.00 39.28 4.11
1650 1735 6.151480 AGAGCAAGTCTAGTAGAACACTAACC 59.849 42.308 0.17 0.00 39.28 2.85
1651 1736 7.148355 AGAGCAAGTCTAGTAGAACACTAAC 57.852 40.000 0.17 0.00 39.28 2.34
1652 1737 8.859236 TTAGAGCAAGTCTAGTAGAACACTAA 57.141 34.615 0.17 4.51 39.28 2.24
1653 1738 8.859236 TTTAGAGCAAGTCTAGTAGAACACTA 57.141 34.615 0.17 0.00 39.05 2.74
1654 1739 7.666388 TCTTTAGAGCAAGTCTAGTAGAACACT 59.334 37.037 0.17 0.00 39.05 3.55
1655 1740 7.751793 GTCTTTAGAGCAAGTCTAGTAGAACAC 59.248 40.741 0.17 0.00 39.05 3.32
1656 1741 7.666388 AGTCTTTAGAGCAAGTCTAGTAGAACA 59.334 37.037 0.17 0.00 39.05 3.18
1657 1742 8.047413 AGTCTTTAGAGCAAGTCTAGTAGAAC 57.953 38.462 0.17 0.00 39.05 3.01
1658 1743 9.165035 GTAGTCTTTAGAGCAAGTCTAGTAGAA 57.835 37.037 0.17 0.00 39.05 2.10
1659 1744 8.542080 AGTAGTCTTTAGAGCAAGTCTAGTAGA 58.458 37.037 0.00 0.00 39.05 2.59
1660 1745 8.726870 AGTAGTCTTTAGAGCAAGTCTAGTAG 57.273 38.462 0.00 0.00 39.05 2.57
1661 1746 7.769970 GGAGTAGTCTTTAGAGCAAGTCTAGTA 59.230 40.741 0.00 0.00 39.05 1.82
1662 1747 6.600427 GGAGTAGTCTTTAGAGCAAGTCTAGT 59.400 42.308 0.00 0.00 39.05 2.57
1663 1748 6.826741 AGGAGTAGTCTTTAGAGCAAGTCTAG 59.173 42.308 0.00 0.00 39.05 2.43
1664 1749 6.723339 AGGAGTAGTCTTTAGAGCAAGTCTA 58.277 40.000 0.00 0.00 36.64 2.59
1665 1750 5.576128 AGGAGTAGTCTTTAGAGCAAGTCT 58.424 41.667 0.00 0.00 39.59 3.24
1666 1751 5.907866 AGGAGTAGTCTTTAGAGCAAGTC 57.092 43.478 0.00 0.00 0.00 3.01
1667 1752 5.775701 TCAAGGAGTAGTCTTTAGAGCAAGT 59.224 40.000 0.00 0.00 0.00 3.16
1668 1753 6.096695 GTCAAGGAGTAGTCTTTAGAGCAAG 58.903 44.000 0.00 0.00 0.00 4.01
1669 1754 5.047235 GGTCAAGGAGTAGTCTTTAGAGCAA 60.047 44.000 13.79 0.00 0.00 3.91
1670 1755 4.463186 GGTCAAGGAGTAGTCTTTAGAGCA 59.537 45.833 13.79 0.00 0.00 4.26
1671 1756 4.142116 GGGTCAAGGAGTAGTCTTTAGAGC 60.142 50.000 11.83 11.83 0.00 4.09
1672 1757 5.265989 AGGGTCAAGGAGTAGTCTTTAGAG 58.734 45.833 0.00 0.00 0.00 2.43
1673 1758 5.272405 AGGGTCAAGGAGTAGTCTTTAGA 57.728 43.478 0.00 0.00 0.00 2.10
1674 1759 6.265876 GGATAGGGTCAAGGAGTAGTCTTTAG 59.734 46.154 0.00 0.00 0.00 1.85
1675 1760 6.134754 GGATAGGGTCAAGGAGTAGTCTTTA 58.865 44.000 0.00 0.00 0.00 1.85
1676 1761 4.963628 GGATAGGGTCAAGGAGTAGTCTTT 59.036 45.833 0.00 0.00 0.00 2.52
1677 1762 4.548669 GGATAGGGTCAAGGAGTAGTCTT 58.451 47.826 0.00 0.00 0.00 3.01
1678 1763 3.117054 GGGATAGGGTCAAGGAGTAGTCT 60.117 52.174 0.00 0.00 0.00 3.24
1679 1764 3.117054 AGGGATAGGGTCAAGGAGTAGTC 60.117 52.174 0.00 0.00 0.00 2.59
1680 1765 2.866454 AGGGATAGGGTCAAGGAGTAGT 59.134 50.000 0.00 0.00 0.00 2.73
1681 1766 3.621682 AGGGATAGGGTCAAGGAGTAG 57.378 52.381 0.00 0.00 0.00 2.57
1682 1767 4.363546 AAAGGGATAGGGTCAAGGAGTA 57.636 45.455 0.00 0.00 0.00 2.59
1683 1768 2.972153 AAGGGATAGGGTCAAGGAGT 57.028 50.000 0.00 0.00 0.00 3.85
1684 1769 4.273318 CAAAAAGGGATAGGGTCAAGGAG 58.727 47.826 0.00 0.00 0.00 3.69
1685 1770 3.011257 CCAAAAAGGGATAGGGTCAAGGA 59.989 47.826 0.00 0.00 0.00 3.36
1686 1771 3.365472 CCAAAAAGGGATAGGGTCAAGG 58.635 50.000 0.00 0.00 0.00 3.61
1687 1772 2.760650 GCCAAAAAGGGATAGGGTCAAG 59.239 50.000 0.00 0.00 38.09 3.02
1688 1773 2.558800 GGCCAAAAAGGGATAGGGTCAA 60.559 50.000 0.00 0.00 38.09 3.18
1689 1774 1.006639 GGCCAAAAAGGGATAGGGTCA 59.993 52.381 0.00 0.00 38.09 4.02
1690 1775 1.006639 TGGCCAAAAAGGGATAGGGTC 59.993 52.381 0.61 0.00 38.09 4.46
1691 1776 1.089123 TGGCCAAAAAGGGATAGGGT 58.911 50.000 0.61 0.00 38.09 4.34
1692 1777 2.246091 TTGGCCAAAAAGGGATAGGG 57.754 50.000 17.98 0.00 38.09 3.53
1693 1778 3.326297 TGTTTTGGCCAAAAAGGGATAGG 59.674 43.478 38.37 0.00 41.37 2.57
1694 1779 4.314961 GTGTTTTGGCCAAAAAGGGATAG 58.685 43.478 38.37 0.00 41.37 2.08
1695 1780 3.071747 GGTGTTTTGGCCAAAAAGGGATA 59.928 43.478 38.37 17.75 41.37 2.59
1696 1781 2.158682 GGTGTTTTGGCCAAAAAGGGAT 60.159 45.455 38.37 0.00 41.37 3.85
1697 1782 1.210722 GGTGTTTTGGCCAAAAAGGGA 59.789 47.619 38.37 22.46 41.37 4.20
1698 1783 1.065126 TGGTGTTTTGGCCAAAAAGGG 60.065 47.619 38.37 0.00 41.37 3.95
1699 1784 2.409948 TGGTGTTTTGGCCAAAAAGG 57.590 45.000 38.37 0.00 41.37 3.11
1704 1789 7.509546 TCTAATAATTTTGGTGTTTTGGCCAA 58.490 30.769 16.05 16.05 42.38 4.52
1705 1790 7.015682 TCTCTAATAATTTTGGTGTTTTGGCCA 59.984 33.333 0.00 0.00 0.00 5.36
1706 1791 7.382898 TCTCTAATAATTTTGGTGTTTTGGCC 58.617 34.615 0.00 0.00 0.00 5.36
1707 1792 8.088365 ACTCTCTAATAATTTTGGTGTTTTGGC 58.912 33.333 0.00 0.00 0.00 4.52
1708 1793 9.410556 CACTCTCTAATAATTTTGGTGTTTTGG 57.589 33.333 0.00 0.00 0.00 3.28
1709 1794 9.410556 CCACTCTCTAATAATTTTGGTGTTTTG 57.589 33.333 0.00 0.00 0.00 2.44
1710 1795 9.143155 ACCACTCTCTAATAATTTTGGTGTTTT 57.857 29.630 0.00 0.00 34.78 2.43
1711 1796 8.576442 CACCACTCTCTAATAATTTTGGTGTTT 58.424 33.333 8.90 0.00 45.10 2.83
1712 1797 8.110860 CACCACTCTCTAATAATTTTGGTGTT 57.889 34.615 8.90 0.00 45.10 3.32
1713 1798 7.687941 CACCACTCTCTAATAATTTTGGTGT 57.312 36.000 8.90 0.00 45.10 4.16
1715 1800 6.659242 CACCACCACTCTCTAATAATTTTGGT 59.341 38.462 0.00 0.00 36.53 3.67
1716 1801 6.404734 GCACCACCACTCTCTAATAATTTTGG 60.405 42.308 0.00 0.00 0.00 3.28
1717 1802 6.555315 GCACCACCACTCTCTAATAATTTTG 58.445 40.000 0.00 0.00 0.00 2.44
1718 1803 5.354234 CGCACCACCACTCTCTAATAATTTT 59.646 40.000 0.00 0.00 0.00 1.82
1719 1804 4.876107 CGCACCACCACTCTCTAATAATTT 59.124 41.667 0.00 0.00 0.00 1.82
1720 1805 4.081087 ACGCACCACCACTCTCTAATAATT 60.081 41.667 0.00 0.00 0.00 1.40
1721 1806 3.451178 ACGCACCACCACTCTCTAATAAT 59.549 43.478 0.00 0.00 0.00 1.28
1722 1807 2.829720 ACGCACCACCACTCTCTAATAA 59.170 45.455 0.00 0.00 0.00 1.40
1723 1808 2.453521 ACGCACCACCACTCTCTAATA 58.546 47.619 0.00 0.00 0.00 0.98
1724 1809 1.267121 ACGCACCACCACTCTCTAAT 58.733 50.000 0.00 0.00 0.00 1.73
1725 1810 1.000506 GAACGCACCACCACTCTCTAA 59.999 52.381 0.00 0.00 0.00 2.10
1726 1811 0.601558 GAACGCACCACCACTCTCTA 59.398 55.000 0.00 0.00 0.00 2.43
1727 1812 1.115930 AGAACGCACCACCACTCTCT 61.116 55.000 0.00 0.00 0.00 3.10
1728 1813 0.601558 TAGAACGCACCACCACTCTC 59.398 55.000 0.00 0.00 0.00 3.20
1729 1814 1.066858 CATAGAACGCACCACCACTCT 60.067 52.381 0.00 0.00 0.00 3.24
1730 1815 1.067142 TCATAGAACGCACCACCACTC 60.067 52.381 0.00 0.00 0.00 3.51
1731 1816 0.973632 TCATAGAACGCACCACCACT 59.026 50.000 0.00 0.00 0.00 4.00
1732 1817 1.076332 GTCATAGAACGCACCACCAC 58.924 55.000 0.00 0.00 0.00 4.16
1733 1818 0.682292 TGTCATAGAACGCACCACCA 59.318 50.000 0.00 0.00 0.00 4.17
1734 1819 2.024176 ATGTCATAGAACGCACCACC 57.976 50.000 0.00 0.00 0.00 4.61
1735 1820 4.209288 GTGATATGTCATAGAACGCACCAC 59.791 45.833 0.00 0.00 36.60 4.16
1736 1821 4.142049 TGTGATATGTCATAGAACGCACCA 60.142 41.667 0.00 0.00 36.60 4.17
1737 1822 4.368315 TGTGATATGTCATAGAACGCACC 58.632 43.478 0.00 0.00 36.60 5.01
1738 1823 5.966636 TTGTGATATGTCATAGAACGCAC 57.033 39.130 0.00 0.00 36.60 5.34
1739 1824 6.183360 GGTTTTGTGATATGTCATAGAACGCA 60.183 38.462 13.44 3.39 39.73 5.24
1740 1825 6.192360 GGTTTTGTGATATGTCATAGAACGC 58.808 40.000 13.44 6.16 39.73 4.84
1741 1826 6.315144 TGGGTTTTGTGATATGTCATAGAACG 59.685 38.462 13.44 0.00 39.73 3.95
1742 1827 7.415206 GGTGGGTTTTGTGATATGTCATAGAAC 60.415 40.741 12.08 12.08 38.79 3.01
1743 1828 6.601613 GGTGGGTTTTGTGATATGTCATAGAA 59.398 38.462 0.00 0.00 36.60 2.10
1744 1829 6.119536 GGTGGGTTTTGTGATATGTCATAGA 58.880 40.000 0.00 0.00 36.60 1.98
1745 1830 5.299279 GGGTGGGTTTTGTGATATGTCATAG 59.701 44.000 0.00 0.00 36.60 2.23
1746 1831 5.197451 GGGTGGGTTTTGTGATATGTCATA 58.803 41.667 0.00 0.00 36.60 2.15
1747 1832 4.023291 GGGTGGGTTTTGTGATATGTCAT 58.977 43.478 0.00 0.00 36.60 3.06
1748 1833 3.181428 TGGGTGGGTTTTGTGATATGTCA 60.181 43.478 0.00 0.00 0.00 3.58
1749 1834 3.192633 GTGGGTGGGTTTTGTGATATGTC 59.807 47.826 0.00 0.00 0.00 3.06
1750 1835 3.161866 GTGGGTGGGTTTTGTGATATGT 58.838 45.455 0.00 0.00 0.00 2.29
1751 1836 3.193267 CAGTGGGTGGGTTTTGTGATATG 59.807 47.826 0.00 0.00 0.00 1.78
1752 1837 3.075283 TCAGTGGGTGGGTTTTGTGATAT 59.925 43.478 0.00 0.00 0.00 1.63
1753 1838 2.443632 TCAGTGGGTGGGTTTTGTGATA 59.556 45.455 0.00 0.00 0.00 2.15
1754 1839 1.216678 TCAGTGGGTGGGTTTTGTGAT 59.783 47.619 0.00 0.00 0.00 3.06
1755 1840 0.626382 TCAGTGGGTGGGTTTTGTGA 59.374 50.000 0.00 0.00 0.00 3.58
1756 1841 1.703411 ATCAGTGGGTGGGTTTTGTG 58.297 50.000 0.00 0.00 0.00 3.33
1757 1842 2.175931 TGTATCAGTGGGTGGGTTTTGT 59.824 45.455 0.00 0.00 0.00 2.83
1758 1843 2.870175 TGTATCAGTGGGTGGGTTTTG 58.130 47.619 0.00 0.00 0.00 2.44
1759 1844 3.825908 ATGTATCAGTGGGTGGGTTTT 57.174 42.857 0.00 0.00 0.00 2.43
1760 1845 3.850173 AGTATGTATCAGTGGGTGGGTTT 59.150 43.478 0.00 0.00 0.00 3.27
1761 1846 3.454812 GAGTATGTATCAGTGGGTGGGTT 59.545 47.826 0.00 0.00 0.00 4.11
1762 1847 3.039011 GAGTATGTATCAGTGGGTGGGT 58.961 50.000 0.00 0.00 0.00 4.51
1763 1848 2.368875 GGAGTATGTATCAGTGGGTGGG 59.631 54.545 0.00 0.00 0.00 4.61
1764 1849 2.035961 CGGAGTATGTATCAGTGGGTGG 59.964 54.545 0.00 0.00 0.00 4.61
1765 1850 2.693591 ACGGAGTATGTATCAGTGGGTG 59.306 50.000 0.00 0.00 41.94 4.61
1766 1851 3.028094 ACGGAGTATGTATCAGTGGGT 57.972 47.619 0.00 0.00 41.94 4.51
1781 1866 0.527817 GCTTCACGGACCATACGGAG 60.528 60.000 0.00 0.00 35.59 4.63
1782 1867 0.968901 AGCTTCACGGACCATACGGA 60.969 55.000 0.00 0.00 35.59 4.69
1783 1868 0.108329 AAGCTTCACGGACCATACGG 60.108 55.000 0.00 0.00 38.77 4.02
1784 1869 1.135083 AGAAGCTTCACGGACCATACG 60.135 52.381 27.57 0.00 37.36 3.06
1785 1870 2.674796 AGAAGCTTCACGGACCATAC 57.325 50.000 27.57 0.00 0.00 2.39
1786 1871 3.093814 TGTAGAAGCTTCACGGACCATA 58.906 45.455 27.57 6.47 0.00 2.74
1787 1872 1.899814 TGTAGAAGCTTCACGGACCAT 59.100 47.619 27.57 7.48 0.00 3.55
1788 1873 1.000506 GTGTAGAAGCTTCACGGACCA 59.999 52.381 27.57 11.46 0.00 4.02
1789 1874 1.272769 AGTGTAGAAGCTTCACGGACC 59.727 52.381 27.57 10.37 36.97 4.46
1790 1875 2.726832 AGTGTAGAAGCTTCACGGAC 57.273 50.000 27.57 18.49 36.97 4.79
1791 1876 3.057736 GTGTAGTGTAGAAGCTTCACGGA 60.058 47.826 27.57 9.27 36.97 4.69
1792 1877 3.057456 AGTGTAGTGTAGAAGCTTCACGG 60.057 47.826 27.57 0.00 36.97 4.94
1793 1878 4.162096 AGTGTAGTGTAGAAGCTTCACG 57.838 45.455 27.57 0.00 36.97 4.35
1794 1879 4.150804 GCAAGTGTAGTGTAGAAGCTTCAC 59.849 45.833 27.57 21.53 34.59 3.18
1795 1880 4.307432 GCAAGTGTAGTGTAGAAGCTTCA 58.693 43.478 27.57 11.42 0.00 3.02
1796 1881 3.365220 CGCAAGTGTAGTGTAGAAGCTTC 59.635 47.826 19.11 19.11 0.00 3.86
1797 1882 3.318017 CGCAAGTGTAGTGTAGAAGCTT 58.682 45.455 0.00 0.00 0.00 3.74
1798 1883 2.947852 CGCAAGTGTAGTGTAGAAGCT 58.052 47.619 0.00 0.00 0.00 3.74
1813 1898 2.094659 CACCCGAGCAGTACGCAAG 61.095 63.158 11.30 5.39 46.13 4.01
1814 1899 2.048597 CACCCGAGCAGTACGCAA 60.049 61.111 11.30 0.00 46.13 4.85
1815 1900 4.735132 GCACCCGAGCAGTACGCA 62.735 66.667 11.30 0.00 46.13 5.24
1817 1902 4.111016 TCGCACCCGAGCAGTACG 62.111 66.667 0.00 0.00 38.82 3.67
1826 1911 1.659098 GTTGACTAAAGATCGCACCCG 59.341 52.381 0.00 0.00 0.00 5.28
1827 1912 2.973945 AGTTGACTAAAGATCGCACCC 58.026 47.619 0.00 0.00 0.00 4.61
1828 1913 3.864003 GGTAGTTGACTAAAGATCGCACC 59.136 47.826 0.00 0.00 0.00 5.01
1829 1914 4.491676 TGGTAGTTGACTAAAGATCGCAC 58.508 43.478 0.00 0.00 0.00 5.34
1830 1915 4.744570 CTGGTAGTTGACTAAAGATCGCA 58.255 43.478 0.00 0.00 0.00 5.10
1831 1916 3.552294 GCTGGTAGTTGACTAAAGATCGC 59.448 47.826 6.39 0.00 0.00 4.58
1832 1917 4.744570 TGCTGGTAGTTGACTAAAGATCG 58.255 43.478 6.39 0.00 0.00 3.69
1833 1918 5.808030 GTCTGCTGGTAGTTGACTAAAGATC 59.192 44.000 6.39 0.00 0.00 2.75
1834 1919 5.337652 GGTCTGCTGGTAGTTGACTAAAGAT 60.338 44.000 6.39 0.00 0.00 2.40
1835 1920 4.021368 GGTCTGCTGGTAGTTGACTAAAGA 60.021 45.833 6.39 0.00 0.00 2.52
1836 1921 4.021016 AGGTCTGCTGGTAGTTGACTAAAG 60.021 45.833 0.00 0.00 0.00 1.85
1837 1922 3.901844 AGGTCTGCTGGTAGTTGACTAAA 59.098 43.478 0.00 0.00 0.00 1.85
1838 1923 3.507411 AGGTCTGCTGGTAGTTGACTAA 58.493 45.455 0.00 0.00 0.00 2.24
1839 1924 3.170991 AGGTCTGCTGGTAGTTGACTA 57.829 47.619 0.00 0.00 0.00 2.59
1840 1925 2.016905 AGGTCTGCTGGTAGTTGACT 57.983 50.000 0.00 0.00 0.00 3.41
1841 1926 2.417719 CAAGGTCTGCTGGTAGTTGAC 58.582 52.381 0.00 0.00 0.00 3.18
1842 1927 2.839486 CAAGGTCTGCTGGTAGTTGA 57.161 50.000 0.00 0.00 0.00 3.18
1853 1938 1.707632 CGACTTCTCTGCAAGGTCTG 58.292 55.000 0.00 0.00 0.00 3.51
1854 1939 0.037790 GCGACTTCTCTGCAAGGTCT 60.038 55.000 0.00 0.00 0.00 3.85
1855 1940 1.016653 GGCGACTTCTCTGCAAGGTC 61.017 60.000 0.00 0.00 0.00 3.85
1856 1941 1.004440 GGCGACTTCTCTGCAAGGT 60.004 57.895 0.00 0.00 0.00 3.50
1857 1942 2.097038 CGGCGACTTCTCTGCAAGG 61.097 63.158 0.00 0.00 0.00 3.61
1858 1943 2.734673 GCGGCGACTTCTCTGCAAG 61.735 63.158 12.98 0.00 33.43 4.01
1859 1944 2.738521 GCGGCGACTTCTCTGCAA 60.739 61.111 12.98 0.00 33.43 4.08
1860 1945 3.300934 ATGCGGCGACTTCTCTGCA 62.301 57.895 12.98 5.24 45.57 4.41
1861 1946 2.510238 ATGCGGCGACTTCTCTGC 60.510 61.111 12.98 0.00 33.80 4.26
1862 1947 2.169789 CCATGCGGCGACTTCTCTG 61.170 63.158 12.98 0.00 0.00 3.35
1863 1948 2.185350 CCATGCGGCGACTTCTCT 59.815 61.111 12.98 0.00 0.00 3.10
1873 1958 2.969238 GATCGTGGAGCCATGCGG 60.969 66.667 3.81 0.00 33.28 5.69
1874 1959 2.969238 GGATCGTGGAGCCATGCG 60.969 66.667 3.81 0.00 38.12 4.73
1875 1960 2.190313 TGGATCGTGGAGCCATGC 59.810 61.111 0.00 0.00 43.58 4.06
1925 2010 4.247380 CGATCCCAGGCTCCCAGC 62.247 72.222 0.00 0.00 41.46 4.85
1926 2011 2.765807 ACGATCCCAGGCTCCCAG 60.766 66.667 0.00 0.00 0.00 4.45
1927 2012 2.764128 GACGATCCCAGGCTCCCA 60.764 66.667 0.00 0.00 0.00 4.37
1928 2013 2.764128 TGACGATCCCAGGCTCCC 60.764 66.667 0.00 0.00 0.00 4.30
1929 2014 2.501610 GTGACGATCCCAGGCTCC 59.498 66.667 0.00 0.00 0.00 4.70
1930 2015 1.381928 TACGTGACGATCCCAGGCTC 61.382 60.000 13.70 0.00 0.00 4.70
1931 2016 1.379443 TACGTGACGATCCCAGGCT 60.379 57.895 13.70 0.00 0.00 4.58
1932 2017 1.065928 CTACGTGACGATCCCAGGC 59.934 63.158 13.70 0.00 0.00 4.85
1933 2018 1.065928 GCTACGTGACGATCCCAGG 59.934 63.158 13.70 0.00 0.00 4.45
1934 2019 1.298413 CGCTACGTGACGATCCCAG 60.298 63.158 13.70 1.57 0.00 4.45
1935 2020 2.767445 CCGCTACGTGACGATCCCA 61.767 63.158 13.70 0.00 0.00 4.37
1936 2021 2.025727 CCGCTACGTGACGATCCC 59.974 66.667 13.70 0.00 0.00 3.85
1937 2022 1.585521 CACCGCTACGTGACGATCC 60.586 63.158 13.70 0.00 35.68 3.36
1946 2031 1.654105 CACTTTCTAAGCACCGCTACG 59.346 52.381 0.00 0.00 38.25 3.51
1951 2036 1.068474 CGACCACTTTCTAAGCACCG 58.932 55.000 0.00 0.00 0.00 4.94
1952 2037 0.796927 GCGACCACTTTCTAAGCACC 59.203 55.000 0.00 0.00 0.00 5.01
2145 2232 1.144093 GAGGAGGATTCGGAGGAGAGA 59.856 57.143 0.00 0.00 0.00 3.10
2157 2244 1.765657 GAGCTGGCAGGAGGAGGAT 60.766 63.158 17.64 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.