Multiple sequence alignment - TraesCS2B01G223300

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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 TraesCS2B01G223300 chr2B 100.000 2342 0 0 1 2342 212938500 212936159 0.000000e+00 4325.0
1 TraesCS2B01G223300 chr2B 95.122 41 2 0 1649 1689 667782261 667782221 5.400000e-07 65.8
2 TraesCS2B01G223300 chr2D 90.918 1046 38 18 645 1650 155552623 155551595 0.000000e+00 1352.0
3 TraesCS2B01G223300 chr2D 91.753 388 13 7 1965 2342 155514204 155513826 2.670000e-144 521.0
4 TraesCS2B01G223300 chr2A 85.993 1078 61 49 646 1647 144614712 144615775 0.000000e+00 1072.0
5 TraesCS2B01G223300 chr2A 93.078 549 20 9 1803 2342 144651843 144652382 0.000000e+00 787.0
6 TraesCS2B01G223300 chr2A 88.481 599 51 12 11 602 735780505 735781092 0.000000e+00 708.0
7 TraesCS2B01G223300 chr7A 89.447 597 49 11 11 602 14177658 14178245 0.000000e+00 741.0
8 TraesCS2B01G223300 chr7A 92.195 410 30 2 199 607 80533119 80533527 1.560000e-161 579.0
9 TraesCS2B01G223300 chr5A 89.280 597 50 9 11 602 535652611 535653198 0.000000e+00 736.0
10 TraesCS2B01G223300 chr5A 87.563 595 48 13 13 602 206804078 206803505 0.000000e+00 665.0
11 TraesCS2B01G223300 chr5A 89.339 469 39 7 138 602 2093994 2094455 1.560000e-161 579.0
12 TraesCS2B01G223300 chr5A 82.072 608 82 21 11 602 615324016 615324612 5.810000e-136 494.0
13 TraesCS2B01G223300 chr5B 89.226 594 52 9 11 599 479636934 479637520 0.000000e+00 732.0
14 TraesCS2B01G223300 chr5B 100.000 36 0 0 1654 1689 600488562 600488527 1.500000e-07 67.6
15 TraesCS2B01G223300 chr5B 100.000 35 0 0 1655 1689 492602020 492601986 5.400000e-07 65.8
16 TraesCS2B01G223300 chr3A 88.610 597 54 10 11 602 163100405 163099818 0.000000e+00 713.0
17 TraesCS2B01G223300 chr3A 97.500 40 1 0 1650 1689 227368667 227368706 4.180000e-08 69.4
18 TraesCS2B01G223300 chr3A 100.000 36 0 0 1654 1689 696373520 696373485 1.500000e-07 67.6
19 TraesCS2B01G223300 chr3A 100.000 35 0 0 1655 1689 69643770 69643804 5.400000e-07 65.8
20 TraesCS2B01G223300 chr3A 100.000 35 0 0 1655 1689 663575324 663575358 5.400000e-07 65.8
21 TraesCS2B01G223300 chr4A 87.521 601 61 12 11 605 5739534 5740126 0.000000e+00 682.0
22 TraesCS2B01G223300 chr4B 90.000 60 1 5 1657 1715 64610920 64610865 3.230000e-09 73.1
23 TraesCS2B01G223300 chr4B 95.122 41 2 0 1649 1689 607645144 607645184 5.400000e-07 65.8
24 TraesCS2B01G223300 chr7D 100.000 29 0 0 611 639 621266760 621266732 1.000000e-03 54.7
25 TraesCS2B01G223300 chr6B 100.000 29 0 0 611 639 290212320 290212292 1.000000e-03 54.7


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 TraesCS2B01G223300 chr2B 212936159 212938500 2341 True 4325 4325 100.000 1 2342 1 chr2B.!!$R1 2341
1 TraesCS2B01G223300 chr2D 155551595 155552623 1028 True 1352 1352 90.918 645 1650 1 chr2D.!!$R2 1005
2 TraesCS2B01G223300 chr2A 144614712 144615775 1063 False 1072 1072 85.993 646 1647 1 chr2A.!!$F1 1001
3 TraesCS2B01G223300 chr2A 144651843 144652382 539 False 787 787 93.078 1803 2342 1 chr2A.!!$F2 539
4 TraesCS2B01G223300 chr2A 735780505 735781092 587 False 708 708 88.481 11 602 1 chr2A.!!$F3 591
5 TraesCS2B01G223300 chr7A 14177658 14178245 587 False 741 741 89.447 11 602 1 chr7A.!!$F1 591
6 TraesCS2B01G223300 chr5A 535652611 535653198 587 False 736 736 89.280 11 602 1 chr5A.!!$F2 591
7 TraesCS2B01G223300 chr5A 206803505 206804078 573 True 665 665 87.563 13 602 1 chr5A.!!$R1 589
8 TraesCS2B01G223300 chr5A 615324016 615324612 596 False 494 494 82.072 11 602 1 chr5A.!!$F3 591
9 TraesCS2B01G223300 chr5B 479636934 479637520 586 False 732 732 89.226 11 599 1 chr5B.!!$F1 588
10 TraesCS2B01G223300 chr3A 163099818 163100405 587 True 713 713 88.610 11 602 1 chr3A.!!$R1 591
11 TraesCS2B01G223300 chr4A 5739534 5740126 592 False 682 682 87.521 11 605 1 chr4A.!!$F1 594

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
992 1017 1.062873 GATCGCTAGCTAGCTTCGCG 61.063 60.0 35.67 35.67 46.85 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 2350 1.007842 GGAGGAGGAGGAGGAAGAAGT 59.992 57.143 0.0 0.0 0.0 3.01 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
34 35 4.675190 ATTCTCGCTCATGACAAAGTTG 57.325 40.909 0.00 0.00 0.00 3.16
134 138 7.562454 TTTTCAGTGTCCAGTTTTTACTAGG 57.438 36.000 0.00 0.00 0.00 3.02
158 163 4.083271 CGAACCTGGGACAAAAAGAGAATC 60.083 45.833 0.00 0.00 38.70 2.52
195 200 6.202954 ACTGCGTCTAATATAAAATCAGGTGC 59.797 38.462 0.00 0.00 0.00 5.01
212 221 5.191722 TCAGGTGCACTTATAGGAAGGAATT 59.808 40.000 17.98 0.00 0.00 2.17
224 233 2.492088 GGAAGGAATTTGTAGTGGGTGC 59.508 50.000 0.00 0.00 0.00 5.01
297 306 5.980715 CCCTGCGTGTGTACTTTTTATTTTT 59.019 36.000 0.00 0.00 0.00 1.94
430 443 2.987821 GCTGTTTCGGTCTCTAACAGTC 59.012 50.000 13.69 5.06 46.48 3.51
464 477 3.798650 GCGTGCCACATAAGCGCA 61.799 61.111 11.47 0.00 46.23 6.09
624 641 9.936759 ACCTTATTTCTTTTTGACTTTTCAACA 57.063 25.926 0.00 0.00 41.64 3.33
643 660 9.834628 TTTCAACAAAGTTAAAAGTACAGACAG 57.165 29.630 0.00 0.00 0.00 3.51
678 695 5.329035 ACATTCATTAGAAACACATGGGC 57.671 39.130 0.00 0.00 37.29 5.36
731 748 2.053865 CCCTGATGGCGCCAAATGT 61.054 57.895 36.33 18.31 0.00 2.71
811 828 1.803922 GCCGCGGCCAATAAACAAC 60.804 57.895 39.89 7.10 34.56 3.32
823 840 5.621329 GCCAATAAACAACGCACCTAATCTT 60.621 40.000 0.00 0.00 0.00 2.40
960 985 1.338200 CCACACTTGGCTACTCACCTC 60.338 57.143 0.00 0.00 35.56 3.85
962 987 1.896465 ACACTTGGCTACTCACCTCTC 59.104 52.381 0.00 0.00 0.00 3.20
992 1017 1.062873 GATCGCTAGCTAGCTTCGCG 61.063 60.000 35.67 35.67 46.85 5.87
994 1019 3.390823 GCTAGCTAGCTTCGCGCG 61.391 66.667 33.71 26.76 45.62 6.86
1407 1480 4.435436 CTAGCGTGCGTGGCTGGA 62.435 66.667 6.26 0.00 41.00 3.86
1411 1484 4.435436 CGTGCGTGGCTGGAGCTA 62.435 66.667 0.00 0.00 41.70 3.32
1494 1594 1.995376 AGTTTTGGTGCCGGATCTTT 58.005 45.000 5.05 0.00 0.00 2.52
1495 1595 1.886542 AGTTTTGGTGCCGGATCTTTC 59.113 47.619 5.05 0.00 0.00 2.62
1496 1596 1.886542 GTTTTGGTGCCGGATCTTTCT 59.113 47.619 5.05 0.00 0.00 2.52
1497 1597 2.286365 TTTGGTGCCGGATCTTTCTT 57.714 45.000 5.05 0.00 0.00 2.52
1515 1615 4.448537 TCTTGTGTTCTTTGGTTGGTTG 57.551 40.909 0.00 0.00 0.00 3.77
1581 1682 2.046023 TTGGCTGATGCGTCCTGG 60.046 61.111 2.83 0.00 40.82 4.45
1600 1701 4.093408 CCTGGCATACGTATATTCATGTGC 59.907 45.833 7.96 6.37 0.00 4.57
1614 1715 6.589830 ATTCATGTGCTGTAATAAGACGAC 57.410 37.500 0.00 0.00 0.00 4.34
1628 1729 2.688507 AGACGACCTGCTACATGTTTG 58.311 47.619 2.30 0.00 0.00 2.93
1634 1735 4.575885 GACCTGCTACATGTTTGGAAGTA 58.424 43.478 2.30 0.00 0.00 2.24
1650 1751 7.908827 TTGGAAGTATAAATTCACTGCGTTA 57.091 32.000 2.38 0.00 0.00 3.18
1651 1752 7.298507 TGGAAGTATAAATTCACTGCGTTAC 57.701 36.000 2.38 0.00 0.00 2.50
1652 1753 6.035220 TGGAAGTATAAATTCACTGCGTTACG 59.965 38.462 0.00 0.00 0.00 3.18
1653 1754 6.035327 GGAAGTATAAATTCACTGCGTTACGT 59.965 38.462 6.63 0.00 0.00 3.57
1654 1755 7.220683 GGAAGTATAAATTCACTGCGTTACGTA 59.779 37.037 6.63 0.00 0.00 3.57
1655 1756 7.441878 AGTATAAATTCACTGCGTTACGTAC 57.558 36.000 6.63 0.00 0.00 3.67
1656 1757 7.253422 AGTATAAATTCACTGCGTTACGTACT 58.747 34.615 6.63 0.00 0.00 2.73
1657 1758 8.397906 AGTATAAATTCACTGCGTTACGTACTA 58.602 33.333 6.63 0.00 0.00 1.82
1658 1759 5.752098 AAATTCACTGCGTTACGTACTAC 57.248 39.130 6.63 0.00 0.00 2.73
1659 1760 4.691860 ATTCACTGCGTTACGTACTACT 57.308 40.909 6.63 0.00 0.00 2.57
1660 1761 3.729526 TCACTGCGTTACGTACTACTC 57.270 47.619 6.63 0.00 0.00 2.59
1661 1762 2.416547 TCACTGCGTTACGTACTACTCC 59.583 50.000 6.63 0.00 0.00 3.85
1662 1763 1.740025 ACTGCGTTACGTACTACTCCC 59.260 52.381 6.63 0.00 0.00 4.30
1663 1764 2.012673 CTGCGTTACGTACTACTCCCT 58.987 52.381 6.63 0.00 0.00 4.20
1664 1765 2.009774 TGCGTTACGTACTACTCCCTC 58.990 52.381 6.63 0.00 0.00 4.30
1665 1766 2.284190 GCGTTACGTACTACTCCCTCT 58.716 52.381 6.63 0.00 0.00 3.69
1666 1767 2.031437 GCGTTACGTACTACTCCCTCTG 59.969 54.545 6.63 0.00 0.00 3.35
1667 1768 3.265791 CGTTACGTACTACTCCCTCTGT 58.734 50.000 0.00 0.00 0.00 3.41
1668 1769 4.433615 CGTTACGTACTACTCCCTCTGTA 58.566 47.826 0.00 0.00 0.00 2.74
1669 1770 4.268884 CGTTACGTACTACTCCCTCTGTAC 59.731 50.000 0.00 0.00 33.89 2.90
1670 1771 3.274095 ACGTACTACTCCCTCTGTACC 57.726 52.381 0.00 0.00 33.73 3.34
1671 1772 2.208431 CGTACTACTCCCTCTGTACCG 58.792 57.143 0.00 0.00 33.73 4.02
1672 1773 2.159043 CGTACTACTCCCTCTGTACCGA 60.159 54.545 0.00 0.00 33.73 4.69
1673 1774 3.679917 CGTACTACTCCCTCTGTACCGAA 60.680 52.174 0.00 0.00 33.73 4.30
1674 1775 3.446442 ACTACTCCCTCTGTACCGAAA 57.554 47.619 0.00 0.00 0.00 3.46
1675 1776 3.978610 ACTACTCCCTCTGTACCGAAAT 58.021 45.455 0.00 0.00 0.00 2.17
1676 1777 5.121380 ACTACTCCCTCTGTACCGAAATA 57.879 43.478 0.00 0.00 0.00 1.40
1677 1778 5.131784 ACTACTCCCTCTGTACCGAAATAG 58.868 45.833 0.00 0.00 0.00 1.73
1678 1779 3.978610 ACTCCCTCTGTACCGAAATAGT 58.021 45.455 0.00 0.00 0.00 2.12
1679 1780 4.351127 ACTCCCTCTGTACCGAAATAGTT 58.649 43.478 0.00 0.00 0.00 2.24
1680 1781 4.159879 ACTCCCTCTGTACCGAAATAGTTG 59.840 45.833 0.00 0.00 0.00 3.16
1681 1782 4.091549 TCCCTCTGTACCGAAATAGTTGT 58.908 43.478 0.00 0.00 0.00 3.32
1682 1783 4.159135 TCCCTCTGTACCGAAATAGTTGTC 59.841 45.833 0.00 0.00 0.00 3.18
1683 1784 4.103357 CCTCTGTACCGAAATAGTTGTCG 58.897 47.826 0.00 0.00 37.01 4.35
1684 1785 3.504863 TCTGTACCGAAATAGTTGTCGC 58.495 45.455 0.00 0.00 35.93 5.19
1685 1786 3.192001 TCTGTACCGAAATAGTTGTCGCT 59.808 43.478 0.00 0.00 35.93 4.93
1686 1787 3.247442 TGTACCGAAATAGTTGTCGCTG 58.753 45.455 0.00 0.00 35.93 5.18
1687 1788 1.722011 ACCGAAATAGTTGTCGCTGG 58.278 50.000 0.00 0.00 35.93 4.85
1688 1789 1.274167 ACCGAAATAGTTGTCGCTGGA 59.726 47.619 0.00 0.00 35.93 3.86
1689 1790 1.659098 CCGAAATAGTTGTCGCTGGAC 59.341 52.381 0.00 0.00 43.71 4.02
1690 1791 2.607187 CGAAATAGTTGTCGCTGGACT 58.393 47.619 0.00 0.00 43.79 3.85
1691 1792 2.599082 CGAAATAGTTGTCGCTGGACTC 59.401 50.000 0.00 0.00 43.79 3.36
1692 1793 2.279582 AATAGTTGTCGCTGGACTCG 57.720 50.000 0.00 0.00 43.79 4.18
1693 1794 0.456221 ATAGTTGTCGCTGGACTCGG 59.544 55.000 0.00 0.00 43.79 4.63
1694 1795 0.892358 TAGTTGTCGCTGGACTCGGT 60.892 55.000 0.00 0.00 43.79 4.69
1695 1796 0.892358 AGTTGTCGCTGGACTCGGTA 60.892 55.000 0.00 0.00 43.79 4.02
1696 1797 0.731855 GTTGTCGCTGGACTCGGTAC 60.732 60.000 0.00 0.00 43.79 3.34
1697 1798 1.174078 TTGTCGCTGGACTCGGTACA 61.174 55.000 0.00 0.00 43.79 2.90
1698 1799 1.136984 GTCGCTGGACTCGGTACAG 59.863 63.158 10.85 10.85 46.49 2.74
1699 1800 1.002990 TCGCTGGACTCGGTACAGA 60.003 57.895 17.42 0.00 46.68 3.41
1700 1801 1.025113 TCGCTGGACTCGGTACAGAG 61.025 60.000 19.82 19.82 46.68 3.35
1701 1802 1.810532 GCTGGACTCGGTACAGAGG 59.189 63.158 24.12 9.67 46.68 3.69
1702 1803 1.668101 GCTGGACTCGGTACAGAGGG 61.668 65.000 24.12 13.22 46.68 4.30
1703 1804 0.034380 CTGGACTCGGTACAGAGGGA 60.034 60.000 24.12 8.80 46.68 4.20
1704 1805 0.034380 TGGACTCGGTACAGAGGGAG 60.034 60.000 24.12 10.70 42.31 4.30
1705 1806 0.034283 GGACTCGGTACAGAGGGAGT 60.034 60.000 24.12 13.41 42.31 3.85
1706 1807 1.211457 GGACTCGGTACAGAGGGAGTA 59.789 57.143 24.12 0.00 42.31 2.59
1707 1808 2.563702 GACTCGGTACAGAGGGAGTAG 58.436 57.143 24.12 1.80 42.31 2.57
1708 1809 1.914798 ACTCGGTACAGAGGGAGTAGT 59.085 52.381 24.12 2.41 42.31 2.73
1709 1810 3.110705 ACTCGGTACAGAGGGAGTAGTA 58.889 50.000 24.12 0.00 42.31 1.82
1710 1811 3.118445 ACTCGGTACAGAGGGAGTAGTAC 60.118 52.174 24.12 0.00 42.31 2.73
1711 1812 2.840038 TCGGTACAGAGGGAGTAGTACA 59.160 50.000 2.52 0.00 38.78 2.90
1712 1813 3.264193 TCGGTACAGAGGGAGTAGTACAA 59.736 47.826 2.52 0.00 38.78 2.41
1713 1814 4.080129 TCGGTACAGAGGGAGTAGTACAAT 60.080 45.833 2.52 0.00 38.78 2.71
1714 1815 4.036498 CGGTACAGAGGGAGTAGTACAATG 59.964 50.000 2.52 0.00 38.78 2.82
1715 1816 4.341520 GGTACAGAGGGAGTAGTACAATGG 59.658 50.000 2.52 0.00 38.78 3.16
1716 1817 4.062490 ACAGAGGGAGTAGTACAATGGT 57.938 45.455 2.52 0.00 0.00 3.55
1717 1818 4.426704 ACAGAGGGAGTAGTACAATGGTT 58.573 43.478 2.52 0.00 0.00 3.67
1718 1819 4.223032 ACAGAGGGAGTAGTACAATGGTTG 59.777 45.833 2.52 0.00 0.00 3.77
1720 1821 4.844655 AGAGGGAGTAGTACAATGGTTGTT 59.155 41.667 2.52 0.00 42.22 2.83
1721 1822 5.309806 AGAGGGAGTAGTACAATGGTTGTTT 59.690 40.000 2.52 0.00 42.22 2.83
1722 1823 5.557866 AGGGAGTAGTACAATGGTTGTTTC 58.442 41.667 2.52 0.00 42.22 2.78
1723 1824 5.072600 AGGGAGTAGTACAATGGTTGTTTCA 59.927 40.000 2.52 0.00 42.22 2.69
1724 1825 5.180680 GGGAGTAGTACAATGGTTGTTTCAC 59.819 44.000 2.52 0.00 42.22 3.18
1725 1826 5.180680 GGAGTAGTACAATGGTTGTTTCACC 59.819 44.000 2.52 0.00 42.22 4.02
1726 1827 4.753107 AGTAGTACAATGGTTGTTTCACCG 59.247 41.667 2.52 0.00 42.22 4.94
1727 1828 2.882137 AGTACAATGGTTGTTTCACCGG 59.118 45.455 0.00 0.00 42.22 5.28
1728 1829 1.770294 ACAATGGTTGTTTCACCGGT 58.230 45.000 0.00 0.00 42.22 5.28
1729 1830 2.933573 ACAATGGTTGTTTCACCGGTA 58.066 42.857 6.87 0.00 42.22 4.02
1730 1831 3.492337 ACAATGGTTGTTTCACCGGTAT 58.508 40.909 6.87 0.00 42.22 2.73
1731 1832 4.653868 ACAATGGTTGTTTCACCGGTATA 58.346 39.130 6.87 0.00 42.22 1.47
1732 1833 5.071370 ACAATGGTTGTTTCACCGGTATAA 58.929 37.500 6.87 1.20 42.22 0.98
1733 1834 5.535406 ACAATGGTTGTTTCACCGGTATAAA 59.465 36.000 6.87 8.63 42.22 1.40
1734 1835 6.209788 ACAATGGTTGTTTCACCGGTATAAAT 59.790 34.615 6.87 0.00 42.22 1.40
1735 1836 5.630661 TGGTTGTTTCACCGGTATAAATG 57.369 39.130 6.87 0.00 40.09 2.32
1736 1837 4.082679 TGGTTGTTTCACCGGTATAAATGC 60.083 41.667 6.87 5.76 40.09 3.56
1737 1838 4.157105 GGTTGTTTCACCGGTATAAATGCT 59.843 41.667 6.87 0.00 0.00 3.79
1738 1839 5.329493 GTTGTTTCACCGGTATAAATGCTC 58.671 41.667 6.87 0.09 0.00 4.26
1739 1840 3.619483 TGTTTCACCGGTATAAATGCTCG 59.381 43.478 6.87 0.00 0.00 5.03
1740 1841 1.860676 TCACCGGTATAAATGCTCGC 58.139 50.000 6.87 0.00 0.00 5.03
1741 1842 0.865769 CACCGGTATAAATGCTCGCC 59.134 55.000 6.87 0.00 0.00 5.54
1742 1843 0.756903 ACCGGTATAAATGCTCGCCT 59.243 50.000 4.49 0.00 0.00 5.52
1743 1844 1.148310 CCGGTATAAATGCTCGCCTG 58.852 55.000 0.00 0.00 0.00 4.85
1744 1845 1.270094 CCGGTATAAATGCTCGCCTGA 60.270 52.381 0.00 0.00 0.00 3.86
1745 1846 2.612972 CCGGTATAAATGCTCGCCTGAT 60.613 50.000 0.00 0.00 0.00 2.90
1746 1847 2.668457 CGGTATAAATGCTCGCCTGATC 59.332 50.000 0.00 0.00 0.00 2.92
1747 1848 3.003480 GGTATAAATGCTCGCCTGATCC 58.997 50.000 0.00 0.00 0.00 3.36
1748 1849 2.936919 ATAAATGCTCGCCTGATCCA 57.063 45.000 0.00 0.00 0.00 3.41
1749 1850 2.936919 TAAATGCTCGCCTGATCCAT 57.063 45.000 0.00 0.00 0.00 3.41
1750 1851 1.315690 AAATGCTCGCCTGATCCATG 58.684 50.000 0.00 0.00 0.00 3.66
1751 1852 1.170919 AATGCTCGCCTGATCCATGC 61.171 55.000 0.00 0.00 0.00 4.06
1752 1853 2.976903 GCTCGCCTGATCCATGCC 60.977 66.667 0.00 0.00 0.00 4.40
1753 1854 2.664185 CTCGCCTGATCCATGCCG 60.664 66.667 0.00 0.00 0.00 5.69
1754 1855 3.451556 CTCGCCTGATCCATGCCGT 62.452 63.158 0.00 0.00 0.00 5.68
1755 1856 3.274586 CGCCTGATCCATGCCGTG 61.275 66.667 0.00 0.00 0.00 4.94
1768 1869 3.740397 CCGTGGACGCGTGGTAGA 61.740 66.667 20.70 0.00 38.18 2.59
1769 1870 2.202440 CGTGGACGCGTGGTAGAG 60.202 66.667 20.70 0.00 0.00 2.43
1770 1871 2.181021 GTGGACGCGTGGTAGAGG 59.819 66.667 20.70 0.00 0.00 3.69
1771 1872 2.034532 TGGACGCGTGGTAGAGGA 59.965 61.111 20.70 0.00 0.00 3.71
1772 1873 2.044555 TGGACGCGTGGTAGAGGAG 61.045 63.158 20.70 0.00 0.00 3.69
1773 1874 1.748122 GGACGCGTGGTAGAGGAGA 60.748 63.158 20.70 0.00 0.00 3.71
1774 1875 1.428620 GACGCGTGGTAGAGGAGAC 59.571 63.158 20.70 0.00 0.00 3.36
1775 1876 2.307137 GACGCGTGGTAGAGGAGACG 62.307 65.000 20.70 0.00 34.93 4.18
1776 1877 2.799371 GCGTGGTAGAGGAGACGG 59.201 66.667 0.00 0.00 32.45 4.79
1777 1878 2.772691 GCGTGGTAGAGGAGACGGG 61.773 68.421 0.00 0.00 32.45 5.28
1778 1879 1.077930 CGTGGTAGAGGAGACGGGA 60.078 63.158 0.00 0.00 0.00 5.14
1779 1880 0.679002 CGTGGTAGAGGAGACGGGAA 60.679 60.000 0.00 0.00 0.00 3.97
1780 1881 1.553706 GTGGTAGAGGAGACGGGAAA 58.446 55.000 0.00 0.00 0.00 3.13
1781 1882 1.897802 GTGGTAGAGGAGACGGGAAAA 59.102 52.381 0.00 0.00 0.00 2.29
1782 1883 1.897802 TGGTAGAGGAGACGGGAAAAC 59.102 52.381 0.00 0.00 0.00 2.43
1783 1884 1.897802 GGTAGAGGAGACGGGAAAACA 59.102 52.381 0.00 0.00 0.00 2.83
1784 1885 2.094130 GGTAGAGGAGACGGGAAAACAG 60.094 54.545 0.00 0.00 0.00 3.16
1785 1886 2.011122 AGAGGAGACGGGAAAACAGA 57.989 50.000 0.00 0.00 0.00 3.41
1786 1887 2.326428 AGAGGAGACGGGAAAACAGAA 58.674 47.619 0.00 0.00 0.00 3.02
1787 1888 2.907042 AGAGGAGACGGGAAAACAGAAT 59.093 45.455 0.00 0.00 0.00 2.40
1788 1889 3.003480 GAGGAGACGGGAAAACAGAATG 58.997 50.000 0.00 0.00 46.00 2.67
1789 1890 1.468914 GGAGACGGGAAAACAGAATGC 59.531 52.381 0.00 0.00 42.53 3.56
1790 1891 2.427506 GAGACGGGAAAACAGAATGCT 58.572 47.619 0.00 0.00 42.53 3.79
1791 1892 2.814336 GAGACGGGAAAACAGAATGCTT 59.186 45.455 0.00 0.00 42.53 3.91
1792 1893 2.554032 AGACGGGAAAACAGAATGCTTG 59.446 45.455 0.00 0.00 42.53 4.01
1793 1894 2.293399 GACGGGAAAACAGAATGCTTGT 59.707 45.455 0.00 0.00 42.53 3.16
1794 1895 2.034558 ACGGGAAAACAGAATGCTTGTG 59.965 45.455 0.00 0.00 42.53 3.33
1795 1896 2.293122 CGGGAAAACAGAATGCTTGTGA 59.707 45.455 1.15 0.00 42.53 3.58
1796 1897 3.057315 CGGGAAAACAGAATGCTTGTGAT 60.057 43.478 1.15 0.00 42.53 3.06
1797 1898 4.488879 GGGAAAACAGAATGCTTGTGATC 58.511 43.478 1.15 0.00 42.53 2.92
1798 1899 4.022068 GGGAAAACAGAATGCTTGTGATCA 60.022 41.667 0.00 0.00 42.53 2.92
1799 1900 4.919754 GGAAAACAGAATGCTTGTGATCAC 59.080 41.667 19.27 19.27 42.53 3.06
1800 1901 5.278660 GGAAAACAGAATGCTTGTGATCACT 60.279 40.000 25.55 5.03 42.53 3.41
1801 1902 4.761235 AACAGAATGCTTGTGATCACTG 57.239 40.909 25.55 18.51 42.53 3.66
1815 1916 3.129113 TGATCACTGAATTTTCCGCATGG 59.871 43.478 0.00 0.00 0.00 3.66
1850 1951 4.578898 CGGCCGCCGCATAGTACA 62.579 66.667 20.79 0.00 41.17 2.90
1855 1956 0.179121 CCGCCGCATAGTACACTCAA 60.179 55.000 0.00 0.00 0.00 3.02
1907 2008 1.587547 GAGGAGGAATTGATGCCGTC 58.412 55.000 0.00 0.00 0.00 4.79
1912 2013 2.009774 AGGAATTGATGCCGTCTTTCG 58.990 47.619 0.00 0.00 39.52 3.46
1923 2024 1.359848 CGTCTTTCGGAGTTGGATGG 58.640 55.000 0.00 0.00 35.71 3.51
1924 2025 1.067142 CGTCTTTCGGAGTTGGATGGA 60.067 52.381 0.00 0.00 35.71 3.41
1925 2026 2.611971 CGTCTTTCGGAGTTGGATGGAA 60.612 50.000 0.00 0.00 35.71 3.53
1926 2027 3.408634 GTCTTTCGGAGTTGGATGGAAA 58.591 45.455 0.00 0.00 0.00 3.13
1927 2028 3.188667 GTCTTTCGGAGTTGGATGGAAAC 59.811 47.826 0.00 0.00 0.00 2.78
1928 2029 2.194201 TTCGGAGTTGGATGGAAACC 57.806 50.000 0.00 0.00 0.00 3.27
1929 2030 1.358152 TCGGAGTTGGATGGAAACCT 58.642 50.000 0.00 0.00 0.00 3.50
1930 2031 1.702957 TCGGAGTTGGATGGAAACCTT 59.297 47.619 0.00 0.00 0.00 3.50
1931 2032 2.084546 CGGAGTTGGATGGAAACCTTC 58.915 52.381 0.00 0.00 0.00 3.46
1955 2056 2.686816 CCGGTCAAACACGATGGCC 61.687 63.158 0.00 0.00 39.23 5.36
1987 2093 1.230635 GCACCAAGACGCACTCACAT 61.231 55.000 0.00 0.00 0.00 3.21
1997 2103 1.337728 CGCACTCACATACCAGGTTCA 60.338 52.381 0.00 0.00 0.00 3.18
2006 2112 4.943705 CACATACCAGGTTCACTTGCTAAT 59.056 41.667 0.00 0.00 0.00 1.73
2033 2139 1.218316 CAGCGGTACCAGTTCCTCC 59.782 63.158 13.54 0.00 0.00 4.30
2046 2152 4.830765 CCTCCGAATTCGCCGCCA 62.831 66.667 22.36 2.34 38.18 5.69
2072 2179 6.749036 AATAGAAGTAATCCGATTCCTGGT 57.251 37.500 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.000727 AGCGAGAATTTTAGTTCGGGTG 58.999 45.455 0.00 0.00 33.89 4.61
1 2 3.259902 GAGCGAGAATTTTAGTTCGGGT 58.740 45.455 0.00 0.00 33.89 5.28
2 3 3.259064 TGAGCGAGAATTTTAGTTCGGG 58.741 45.455 0.00 0.00 33.89 5.14
3 4 4.566759 TCATGAGCGAGAATTTTAGTTCGG 59.433 41.667 0.00 0.00 33.89 4.30
4 5 5.062183 TGTCATGAGCGAGAATTTTAGTTCG 59.938 40.000 0.00 0.00 36.23 3.95
5 6 6.408858 TGTCATGAGCGAGAATTTTAGTTC 57.591 37.500 0.00 0.00 0.00 3.01
6 7 6.801539 TTGTCATGAGCGAGAATTTTAGTT 57.198 33.333 0.00 0.00 0.00 2.24
7 8 6.428159 ACTTTGTCATGAGCGAGAATTTTAGT 59.572 34.615 0.00 0.00 0.00 2.24
8 9 6.835914 ACTTTGTCATGAGCGAGAATTTTAG 58.164 36.000 0.00 0.00 0.00 1.85
9 10 6.801539 ACTTTGTCATGAGCGAGAATTTTA 57.198 33.333 0.00 0.00 0.00 1.52
34 35 9.830294 GTAAAATGTTTAACCCATACTGTACAC 57.170 33.333 0.00 0.00 0.00 2.90
90 94 7.221828 GAAAAATCTCACCTTTTTCACACAC 57.778 36.000 13.51 0.00 45.43 3.82
134 138 1.266989 CTCTTTTTGTCCCAGGTTCGC 59.733 52.381 0.00 0.00 0.00 4.70
146 150 9.500785 AGTTCTTCTTCCTAGATTCTCTTTTTG 57.499 33.333 0.00 0.00 0.00 2.44
195 200 7.499232 CCCACTACAAATTCCTTCCTATAAGTG 59.501 40.741 0.00 0.00 0.00 3.16
212 221 0.548989 AACCACTGCACCCACTACAA 59.451 50.000 0.00 0.00 0.00 2.41
464 477 7.170489 CACTTTGCTCATATTCAGACGTATCAT 59.830 37.037 0.00 0.00 0.00 2.45
617 634 9.834628 CTGTCTGTACTTTTAACTTTGTTGAAA 57.165 29.630 0.00 0.00 0.00 2.69
618 635 9.221933 TCTGTCTGTACTTTTAACTTTGTTGAA 57.778 29.630 0.00 0.00 0.00 2.69
619 636 8.780846 TCTGTCTGTACTTTTAACTTTGTTGA 57.219 30.769 0.00 0.00 0.00 3.18
620 637 8.665685 ACTCTGTCTGTACTTTTAACTTTGTTG 58.334 33.333 0.00 0.00 0.00 3.33
621 638 8.788325 ACTCTGTCTGTACTTTTAACTTTGTT 57.212 30.769 0.00 0.00 0.00 2.83
622 639 9.310716 GTACTCTGTCTGTACTTTTAACTTTGT 57.689 33.333 0.00 0.00 37.76 2.83
623 640 9.530633 AGTACTCTGTCTGTACTTTTAACTTTG 57.469 33.333 0.00 0.00 45.60 2.77
634 651 9.694137 AATGTTTTAAGAGTACTCTGTCTGTAC 57.306 33.333 25.83 17.65 40.36 2.90
635 652 9.909644 GAATGTTTTAAGAGTACTCTGTCTGTA 57.090 33.333 25.83 11.30 40.36 2.74
636 653 8.421784 TGAATGTTTTAAGAGTACTCTGTCTGT 58.578 33.333 25.83 12.33 40.36 3.41
637 654 8.818141 TGAATGTTTTAAGAGTACTCTGTCTG 57.182 34.615 25.83 0.00 40.36 3.51
664 681 1.346395 ACGTGAGCCCATGTGTTTCTA 59.654 47.619 0.00 0.00 40.77 2.10
731 748 4.931002 CCGAACGTCCTTGTTTTTATCCTA 59.069 41.667 0.00 0.00 30.75 2.94
811 828 0.466189 ATGGCCCAAGATTAGGTGCG 60.466 55.000 0.00 0.00 0.00 5.34
879 896 7.283625 AGATCCAGAGACGGATATATAATGC 57.716 40.000 0.00 0.00 46.13 3.56
960 985 1.107114 AGCGATCACAGTACAGGGAG 58.893 55.000 0.00 0.00 0.00 4.30
962 987 1.269309 GCTAGCGATCACAGTACAGGG 60.269 57.143 0.00 0.00 0.00 4.45
994 1019 2.757099 CAGGCTGGCCATGGGAAC 60.757 66.667 15.13 0.00 38.92 3.62
1039 1087 2.428569 GAAGTCGTCGTCGCTGCA 60.429 61.111 0.00 0.00 36.96 4.41
1040 1088 1.801913 ATGAAGTCGTCGTCGCTGC 60.802 57.895 0.00 0.00 36.96 5.25
1042 1090 1.801913 GCATGAAGTCGTCGTCGCT 60.802 57.895 0.00 0.00 36.96 4.93
1043 1091 2.689766 GCATGAAGTCGTCGTCGC 59.310 61.111 0.00 0.00 36.96 5.19
1044 1092 2.497092 CGGCATGAAGTCGTCGTCG 61.497 63.158 0.00 0.00 41.32 5.12
1343 1403 1.231296 ATCTGATCGCTCGCTCGCTA 61.231 55.000 0.00 0.00 0.00 4.26
1462 1536 3.564225 CACCAAAACTAGACCTCCACAAC 59.436 47.826 0.00 0.00 0.00 3.32
1494 1594 3.829601 ACAACCAACCAAAGAACACAAGA 59.170 39.130 0.00 0.00 0.00 3.02
1495 1595 4.186856 ACAACCAACCAAAGAACACAAG 57.813 40.909 0.00 0.00 0.00 3.16
1496 1596 4.608948 AACAACCAACCAAAGAACACAA 57.391 36.364 0.00 0.00 0.00 3.33
1497 1597 5.923733 ATAACAACCAACCAAAGAACACA 57.076 34.783 0.00 0.00 0.00 3.72
1515 1615 8.186821 CCATCTCAATTCTCAACCAAGAATAAC 58.813 37.037 0.00 0.00 43.53 1.89
1581 1682 5.845985 ACAGCACATGAATATACGTATGC 57.154 39.130 18.37 11.48 0.00 3.14
1585 1686 9.193133 GTCTTATTACAGCACATGAATATACGT 57.807 33.333 0.00 0.00 0.00 3.57
1586 1687 8.365938 CGTCTTATTACAGCACATGAATATACG 58.634 37.037 0.00 2.39 0.00 3.06
1587 1688 9.406828 TCGTCTTATTACAGCACATGAATATAC 57.593 33.333 0.00 0.00 0.00 1.47
1588 1689 9.406828 GTCGTCTTATTACAGCACATGAATATA 57.593 33.333 0.00 0.00 0.00 0.86
1600 1701 5.244785 TGTAGCAGGTCGTCTTATTACAG 57.755 43.478 0.00 0.00 0.00 2.74
1614 1715 7.624360 TTTATACTTCCAAACATGTAGCAGG 57.376 36.000 0.00 0.00 0.00 4.85
1628 1729 6.035327 ACGTAACGCAGTGAATTTATACTTCC 59.965 38.462 0.00 0.00 45.00 3.46
1634 1735 7.253422 AGTAGTACGTAACGCAGTGAATTTAT 58.747 34.615 0.00 0.00 45.00 1.40
1650 1751 2.419297 CGGTACAGAGGGAGTAGTACGT 60.419 54.545 0.00 0.00 38.12 3.57
1651 1752 2.159043 TCGGTACAGAGGGAGTAGTACG 60.159 54.545 0.00 0.00 38.12 3.67
1652 1753 3.550437 TCGGTACAGAGGGAGTAGTAC 57.450 52.381 0.00 0.00 36.88 2.73
1653 1754 4.574674 TTTCGGTACAGAGGGAGTAGTA 57.425 45.455 0.00 0.00 0.00 1.82
1654 1755 3.446442 TTTCGGTACAGAGGGAGTAGT 57.554 47.619 0.00 0.00 0.00 2.73
1655 1756 5.131784 ACTATTTCGGTACAGAGGGAGTAG 58.868 45.833 0.00 0.00 0.00 2.57
1656 1757 5.121380 ACTATTTCGGTACAGAGGGAGTA 57.879 43.478 0.00 0.00 0.00 2.59
1657 1758 3.978610 ACTATTTCGGTACAGAGGGAGT 58.021 45.455 0.00 0.00 0.00 3.85
1658 1759 4.159879 ACAACTATTTCGGTACAGAGGGAG 59.840 45.833 0.00 0.00 0.00 4.30
1659 1760 4.091549 ACAACTATTTCGGTACAGAGGGA 58.908 43.478 0.00 0.00 0.00 4.20
1660 1761 4.430908 GACAACTATTTCGGTACAGAGGG 58.569 47.826 0.00 0.00 0.00 4.30
1661 1762 4.103357 CGACAACTATTTCGGTACAGAGG 58.897 47.826 0.00 0.00 0.00 3.69
1662 1763 3.546670 GCGACAACTATTTCGGTACAGAG 59.453 47.826 0.00 0.00 35.73 3.35
1663 1764 3.192001 AGCGACAACTATTTCGGTACAGA 59.808 43.478 0.00 0.00 43.71 3.41
1664 1765 3.303495 CAGCGACAACTATTTCGGTACAG 59.697 47.826 0.00 0.00 43.70 2.74
1665 1766 3.247442 CAGCGACAACTATTTCGGTACA 58.753 45.455 0.00 0.00 43.70 2.90
1666 1767 2.601763 CCAGCGACAACTATTTCGGTAC 59.398 50.000 0.00 0.00 43.70 3.34
1667 1768 2.492881 TCCAGCGACAACTATTTCGGTA 59.507 45.455 0.00 0.00 43.70 4.02
1668 1769 1.274167 TCCAGCGACAACTATTTCGGT 59.726 47.619 0.00 0.00 46.29 4.69
1669 1770 1.659098 GTCCAGCGACAACTATTTCGG 59.341 52.381 0.00 0.00 38.99 4.30
1670 1771 2.599082 GAGTCCAGCGACAACTATTTCG 59.401 50.000 0.00 0.00 41.87 3.46
1671 1772 2.599082 CGAGTCCAGCGACAACTATTTC 59.401 50.000 0.00 0.00 41.87 2.17
1672 1773 2.607187 CGAGTCCAGCGACAACTATTT 58.393 47.619 0.00 0.00 41.87 1.40
1673 1774 1.135083 CCGAGTCCAGCGACAACTATT 60.135 52.381 0.00 0.00 41.87 1.73
1674 1775 0.456221 CCGAGTCCAGCGACAACTAT 59.544 55.000 0.00 0.00 41.87 2.12
1675 1776 0.892358 ACCGAGTCCAGCGACAACTA 60.892 55.000 0.00 0.00 41.87 2.24
1676 1777 0.892358 TACCGAGTCCAGCGACAACT 60.892 55.000 0.00 0.00 41.87 3.16
1677 1778 0.731855 GTACCGAGTCCAGCGACAAC 60.732 60.000 0.00 0.00 41.87 3.32
1678 1779 1.174078 TGTACCGAGTCCAGCGACAA 61.174 55.000 0.00 0.00 41.87 3.18
1679 1780 1.583495 CTGTACCGAGTCCAGCGACA 61.583 60.000 0.00 0.00 41.87 4.35
1680 1781 1.136984 CTGTACCGAGTCCAGCGAC 59.863 63.158 0.00 0.00 39.50 5.19
1681 1782 1.002990 TCTGTACCGAGTCCAGCGA 60.003 57.895 0.00 0.00 0.00 4.93
1682 1783 1.429825 CTCTGTACCGAGTCCAGCG 59.570 63.158 6.16 0.00 0.00 5.18
1683 1784 1.668101 CCCTCTGTACCGAGTCCAGC 61.668 65.000 12.61 0.00 0.00 4.85
1684 1785 0.034380 TCCCTCTGTACCGAGTCCAG 60.034 60.000 12.61 0.00 0.00 3.86
1685 1786 0.034380 CTCCCTCTGTACCGAGTCCA 60.034 60.000 12.61 0.00 0.00 4.02
1686 1787 0.034283 ACTCCCTCTGTACCGAGTCC 60.034 60.000 12.61 0.00 29.62 3.85
1687 1788 2.093021 ACTACTCCCTCTGTACCGAGTC 60.093 54.545 12.61 0.00 36.91 3.36
1688 1789 1.914798 ACTACTCCCTCTGTACCGAGT 59.085 52.381 12.61 7.47 38.97 4.18
1689 1790 2.713863 ACTACTCCCTCTGTACCGAG 57.286 55.000 7.29 7.29 0.00 4.63
1690 1791 2.840038 TGTACTACTCCCTCTGTACCGA 59.160 50.000 0.00 0.00 35.68 4.69
1691 1792 3.272574 TGTACTACTCCCTCTGTACCG 57.727 52.381 0.00 0.00 35.68 4.02
1692 1793 4.341520 CCATTGTACTACTCCCTCTGTACC 59.658 50.000 0.00 0.00 35.68 3.34
1693 1794 4.954826 ACCATTGTACTACTCCCTCTGTAC 59.045 45.833 0.00 0.00 36.69 2.90
1694 1795 5.202746 ACCATTGTACTACTCCCTCTGTA 57.797 43.478 0.00 0.00 0.00 2.74
1695 1796 4.062490 ACCATTGTACTACTCCCTCTGT 57.938 45.455 0.00 0.00 0.00 3.41
1696 1797 4.223032 ACAACCATTGTACTACTCCCTCTG 59.777 45.833 0.00 0.00 43.27 3.35
1697 1798 4.426704 ACAACCATTGTACTACTCCCTCT 58.573 43.478 0.00 0.00 43.27 3.69
1698 1799 4.820894 ACAACCATTGTACTACTCCCTC 57.179 45.455 0.00 0.00 43.27 4.30
1699 1800 5.072600 TGAAACAACCATTGTACTACTCCCT 59.927 40.000 0.00 0.00 44.59 4.20
1700 1801 5.180680 GTGAAACAACCATTGTACTACTCCC 59.819 44.000 0.00 0.00 44.59 4.30
1701 1802 5.180680 GGTGAAACAACCATTGTACTACTCC 59.819 44.000 0.00 0.00 44.59 3.85
1702 1803 5.107220 CGGTGAAACAACCATTGTACTACTC 60.107 44.000 0.00 0.00 44.59 2.59
1703 1804 4.753107 CGGTGAAACAACCATTGTACTACT 59.247 41.667 0.00 0.00 44.59 2.57
1704 1805 4.083696 CCGGTGAAACAACCATTGTACTAC 60.084 45.833 0.00 0.00 44.59 2.73
1705 1806 4.066490 CCGGTGAAACAACCATTGTACTA 58.934 43.478 0.00 0.00 44.59 1.82
1706 1807 2.882137 CCGGTGAAACAACCATTGTACT 59.118 45.455 0.00 0.00 44.59 2.73
1707 1808 2.619646 ACCGGTGAAACAACCATTGTAC 59.380 45.455 6.12 0.00 44.59 2.90
1708 1809 2.933573 ACCGGTGAAACAACCATTGTA 58.066 42.857 6.12 0.00 44.59 2.41
1710 1811 5.630661 TTATACCGGTGAAACAACCATTG 57.369 39.130 19.93 0.00 40.53 2.82
1711 1812 6.626302 CATTTATACCGGTGAAACAACCATT 58.374 36.000 19.93 0.00 40.53 3.16
1712 1813 5.393678 GCATTTATACCGGTGAAACAACCAT 60.394 40.000 19.93 0.98 40.53 3.55
1713 1814 4.082679 GCATTTATACCGGTGAAACAACCA 60.083 41.667 19.93 0.00 40.53 3.67
1714 1815 4.157105 AGCATTTATACCGGTGAAACAACC 59.843 41.667 19.93 6.96 39.98 3.77
1715 1816 5.305139 AGCATTTATACCGGTGAAACAAC 57.695 39.130 19.93 10.20 39.98 3.32
1716 1817 4.093703 CGAGCATTTATACCGGTGAAACAA 59.906 41.667 19.93 3.03 39.98 2.83
1717 1818 3.619483 CGAGCATTTATACCGGTGAAACA 59.381 43.478 19.93 0.00 39.98 2.83
1718 1819 3.545426 GCGAGCATTTATACCGGTGAAAC 60.545 47.826 19.93 6.81 0.00 2.78
1719 1820 2.610374 GCGAGCATTTATACCGGTGAAA 59.390 45.455 19.93 17.63 0.00 2.69
1720 1821 2.206750 GCGAGCATTTATACCGGTGAA 58.793 47.619 19.93 8.68 0.00 3.18
1721 1822 1.539496 GGCGAGCATTTATACCGGTGA 60.539 52.381 19.93 1.17 0.00 4.02
1722 1823 0.865769 GGCGAGCATTTATACCGGTG 59.134 55.000 19.93 0.00 0.00 4.94
1723 1824 0.756903 AGGCGAGCATTTATACCGGT 59.243 50.000 13.98 13.98 0.00 5.28
1724 1825 1.148310 CAGGCGAGCATTTATACCGG 58.852 55.000 0.00 0.00 0.00 5.28
1725 1826 2.148916 TCAGGCGAGCATTTATACCG 57.851 50.000 0.00 0.00 0.00 4.02
1726 1827 3.003480 GGATCAGGCGAGCATTTATACC 58.997 50.000 0.00 0.00 0.00 2.73
1727 1828 3.664107 TGGATCAGGCGAGCATTTATAC 58.336 45.455 0.00 0.00 0.00 1.47
1728 1829 4.256110 CATGGATCAGGCGAGCATTTATA 58.744 43.478 0.00 0.00 0.00 0.98
1729 1830 2.936919 TGGATCAGGCGAGCATTTAT 57.063 45.000 0.00 0.00 0.00 1.40
1730 1831 2.497138 CATGGATCAGGCGAGCATTTA 58.503 47.619 0.00 0.00 0.00 1.40
1731 1832 1.315690 CATGGATCAGGCGAGCATTT 58.684 50.000 0.00 0.00 0.00 2.32
1732 1833 1.170919 GCATGGATCAGGCGAGCATT 61.171 55.000 0.00 0.00 30.03 3.56
1733 1834 1.600076 GCATGGATCAGGCGAGCAT 60.600 57.895 0.00 0.00 30.03 3.79
1734 1835 2.203112 GCATGGATCAGGCGAGCA 60.203 61.111 0.00 0.00 30.03 4.26
1735 1836 2.976903 GGCATGGATCAGGCGAGC 60.977 66.667 0.00 0.00 42.38 5.03
1751 1852 3.678717 CTCTACCACGCGTCCACGG 62.679 68.421 9.86 10.85 40.23 4.94
1752 1853 2.202440 CTCTACCACGCGTCCACG 60.202 66.667 9.86 0.00 43.27 4.94
1753 1854 2.181021 CCTCTACCACGCGTCCAC 59.819 66.667 9.86 0.00 0.00 4.02
1754 1855 2.034532 TCCTCTACCACGCGTCCA 59.965 61.111 9.86 0.00 0.00 4.02
1755 1856 1.748122 TCTCCTCTACCACGCGTCC 60.748 63.158 9.86 0.00 0.00 4.79
1756 1857 1.428620 GTCTCCTCTACCACGCGTC 59.571 63.158 9.86 0.00 0.00 5.19
1757 1858 2.396955 CGTCTCCTCTACCACGCGT 61.397 63.158 5.58 5.58 0.00 6.01
1758 1859 2.403987 CGTCTCCTCTACCACGCG 59.596 66.667 3.53 3.53 0.00 6.01
1759 1860 2.772691 CCCGTCTCCTCTACCACGC 61.773 68.421 0.00 0.00 0.00 5.34
1760 1861 0.679002 TTCCCGTCTCCTCTACCACG 60.679 60.000 0.00 0.00 0.00 4.94
1761 1862 1.553706 TTTCCCGTCTCCTCTACCAC 58.446 55.000 0.00 0.00 0.00 4.16
1762 1863 1.897802 GTTTTCCCGTCTCCTCTACCA 59.102 52.381 0.00 0.00 0.00 3.25
1763 1864 1.897802 TGTTTTCCCGTCTCCTCTACC 59.102 52.381 0.00 0.00 0.00 3.18
1764 1865 2.824341 TCTGTTTTCCCGTCTCCTCTAC 59.176 50.000 0.00 0.00 0.00 2.59
1765 1866 3.165087 TCTGTTTTCCCGTCTCCTCTA 57.835 47.619 0.00 0.00 0.00 2.43
1766 1867 2.011122 TCTGTTTTCCCGTCTCCTCT 57.989 50.000 0.00 0.00 0.00 3.69
1767 1868 2.833631 TTCTGTTTTCCCGTCTCCTC 57.166 50.000 0.00 0.00 0.00 3.71
1768 1869 2.876079 GCATTCTGTTTTCCCGTCTCCT 60.876 50.000 0.00 0.00 0.00 3.69
1769 1870 1.468914 GCATTCTGTTTTCCCGTCTCC 59.531 52.381 0.00 0.00 0.00 3.71
1770 1871 2.427506 AGCATTCTGTTTTCCCGTCTC 58.572 47.619 0.00 0.00 0.00 3.36
1771 1872 2.554032 CAAGCATTCTGTTTTCCCGTCT 59.446 45.455 0.00 0.00 0.00 4.18
1772 1873 2.293399 ACAAGCATTCTGTTTTCCCGTC 59.707 45.455 0.00 0.00 0.00 4.79
1773 1874 2.034558 CACAAGCATTCTGTTTTCCCGT 59.965 45.455 0.00 0.00 0.00 5.28
1774 1875 2.293122 TCACAAGCATTCTGTTTTCCCG 59.707 45.455 0.00 0.00 0.00 5.14
1775 1876 4.022068 TGATCACAAGCATTCTGTTTTCCC 60.022 41.667 0.00 0.00 0.00 3.97
1776 1877 4.919754 GTGATCACAAGCATTCTGTTTTCC 59.080 41.667 21.07 0.00 0.00 3.13
1777 1878 5.628193 CAGTGATCACAAGCATTCTGTTTTC 59.372 40.000 27.02 0.00 0.00 2.29
1778 1879 5.300034 TCAGTGATCACAAGCATTCTGTTTT 59.700 36.000 27.02 0.00 0.00 2.43
1779 1880 4.823442 TCAGTGATCACAAGCATTCTGTTT 59.177 37.500 27.02 0.00 0.00 2.83
1780 1881 4.392047 TCAGTGATCACAAGCATTCTGTT 58.608 39.130 27.02 0.00 0.00 3.16
1781 1882 4.011966 TCAGTGATCACAAGCATTCTGT 57.988 40.909 27.02 0.00 0.00 3.41
1782 1883 5.562506 ATTCAGTGATCACAAGCATTCTG 57.437 39.130 27.02 13.87 0.00 3.02
1783 1884 6.585695 AAATTCAGTGATCACAAGCATTCT 57.414 33.333 27.02 1.19 0.00 2.40
1784 1885 6.309737 GGAAAATTCAGTGATCACAAGCATTC 59.690 38.462 27.02 20.27 0.00 2.67
1785 1886 6.161381 GGAAAATTCAGTGATCACAAGCATT 58.839 36.000 27.02 16.99 0.00 3.56
1786 1887 5.620654 CGGAAAATTCAGTGATCACAAGCAT 60.621 40.000 27.02 12.30 0.00 3.79
1787 1888 4.320421 CGGAAAATTCAGTGATCACAAGCA 60.320 41.667 27.02 10.53 0.00 3.91
1788 1889 4.161333 CGGAAAATTCAGTGATCACAAGC 58.839 43.478 27.02 0.33 0.00 4.01
1789 1890 4.161333 GCGGAAAATTCAGTGATCACAAG 58.839 43.478 27.02 18.48 0.00 3.16
1790 1891 3.567585 TGCGGAAAATTCAGTGATCACAA 59.432 39.130 27.02 14.24 0.00 3.33
1791 1892 3.145286 TGCGGAAAATTCAGTGATCACA 58.855 40.909 27.02 7.74 0.00 3.58
1792 1893 3.829886 TGCGGAAAATTCAGTGATCAC 57.170 42.857 18.47 18.47 0.00 3.06
1793 1894 3.129113 CCATGCGGAAAATTCAGTGATCA 59.871 43.478 0.00 0.00 0.00 2.92
1794 1895 3.378112 TCCATGCGGAAAATTCAGTGATC 59.622 43.478 0.00 0.00 38.83 2.92
1795 1896 3.355378 TCCATGCGGAAAATTCAGTGAT 58.645 40.909 0.00 0.00 38.83 3.06
1796 1897 2.789213 TCCATGCGGAAAATTCAGTGA 58.211 42.857 0.00 0.00 38.83 3.41
1815 1916 4.495184 CGGCCGACCATAATTTACACTTTC 60.495 45.833 24.07 0.00 34.57 2.62
1845 1946 5.971202 CGCAAAAACAATTCTTGAGTGTACT 59.029 36.000 0.00 0.00 35.09 2.73
1850 1951 3.383185 TCCCGCAAAAACAATTCTTGAGT 59.617 39.130 0.00 0.00 0.00 3.41
1855 1956 3.120041 CGTTTCCCGCAAAAACAATTCT 58.880 40.909 6.45 0.00 36.60 2.40
1888 1989 1.139853 AGACGGCATCAATTCCTCCTC 59.860 52.381 0.00 0.00 0.00 3.71
1907 2008 2.488153 GGTTTCCATCCAACTCCGAAAG 59.512 50.000 0.00 0.00 0.00 2.62
1912 2013 2.084546 CGAAGGTTTCCATCCAACTCC 58.915 52.381 0.00 0.00 0.00 3.85
1916 2017 2.882137 GTCAACGAAGGTTTCCATCCAA 59.118 45.455 0.00 0.00 32.98 3.53
1917 2018 2.500229 GTCAACGAAGGTTTCCATCCA 58.500 47.619 0.00 0.00 32.98 3.41
1987 2093 4.751060 CGTATTAGCAAGTGAACCTGGTA 58.249 43.478 0.00 0.00 0.00 3.25
1997 2103 2.159517 GCTGCAAAGCGTATTAGCAAGT 60.160 45.455 0.00 0.00 40.15 3.16
2021 2127 1.134907 GCGAATTCGGAGGAACTGGTA 60.135 52.381 27.78 0.00 38.46 3.25
2033 2139 2.108700 CTATTTTTGGCGGCGAATTCG 58.891 47.619 23.34 23.34 43.27 3.34
2046 2152 8.053355 ACCAGGAATCGGATTACTTCTATTTTT 58.947 33.333 12.83 0.00 28.64 1.94
2072 2179 5.350504 TTGTTTTCTGGAAATGCTTTGGA 57.649 34.783 0.00 0.00 0.00 3.53
2243 2350 1.007842 GGAGGAGGAGGAGGAAGAAGT 59.992 57.143 0.00 0.00 0.00 3.01
2290 2397 1.403687 GGAGCAACCCTAGATCCGCT 61.404 60.000 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.