Multiple sequence alignment - TraesCS5A01G277700

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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 TraesCS5A01G277700 chr5A 100.000 2035 0 0 1 2035 487672970 487670936 0.000000e+00 3759
1 TraesCS5A01G277700 chr5A 100.000 121 0 0 2423 2543 487670548 487670428 9.160000e-55 224
2 TraesCS5A01G277700 chr7A 96.517 1579 53 2 1 1577 605172135 605173713 0.000000e+00 2610
3 TraesCS5A01G277700 chr2D 95.503 1579 69 2 1 1577 20082577 20080999 0.000000e+00 2521
4 TraesCS5A01G277700 chr6A 95.244 1577 72 3 1 1574 33587899 33586323 0.000000e+00 2494
5 TraesCS5A01G277700 chr5B 95.181 1577 74 2 1 1575 278794387 278792811 0.000000e+00 2490
6 TraesCS5A01G277700 chr6B 94.487 1578 80 6 1 1575 192049784 192051357 0.000000e+00 2425
7 TraesCS5A01G277700 chr2B 94.652 1496 77 3 80 1573 24750018 24751512 0.000000e+00 2316
8 TraesCS5A01G277700 chr1A 92.780 1482 94 10 96 1574 548406031 548407502 0.000000e+00 2132
9 TraesCS5A01G277700 chr7B 90.341 1584 132 15 1 1575 711073881 711075452 0.000000e+00 2058
10 TraesCS5A01G277700 chr4A 93.807 1211 72 3 368 1576 589731053 589732262 0.000000e+00 1818
11 TraesCS5A01G277700 chr5D 82.713 457 49 15 1589 2035 385695747 385695311 1.850000e-101 379


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 TraesCS5A01G277700 chr5A 487670428 487672970 2542 True 1991.5 3759 100.000 1 2543 2 chr5A.!!$R1 2542
1 TraesCS5A01G277700 chr7A 605172135 605173713 1578 False 2610.0 2610 96.517 1 1577 1 chr7A.!!$F1 1576
2 TraesCS5A01G277700 chr2D 20080999 20082577 1578 True 2521.0 2521 95.503 1 1577 1 chr2D.!!$R1 1576
3 TraesCS5A01G277700 chr6A 33586323 33587899 1576 True 2494.0 2494 95.244 1 1574 1 chr6A.!!$R1 1573
4 TraesCS5A01G277700 chr5B 278792811 278794387 1576 True 2490.0 2490 95.181 1 1575 1 chr5B.!!$R1 1574
5 TraesCS5A01G277700 chr6B 192049784 192051357 1573 False 2425.0 2425 94.487 1 1575 1 chr6B.!!$F1 1574
6 TraesCS5A01G277700 chr2B 24750018 24751512 1494 False 2316.0 2316 94.652 80 1573 1 chr2B.!!$F1 1493
7 TraesCS5A01G277700 chr1A 548406031 548407502 1471 False 2132.0 2132 92.780 96 1574 1 chr1A.!!$F1 1478
8 TraesCS5A01G277700 chr7B 711073881 711075452 1571 False 2058.0 2058 90.341 1 1575 1 chr7B.!!$F1 1574
9 TraesCS5A01G277700 chr4A 589731053 589732262 1209 False 1818.0 1818 93.807 368 1576 1 chr4A.!!$F1 1208

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
720 724 1.017177 CCTAAGGCGCGTGCTTTGTA 61.017 55.0 26.26 8.25 41.01 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1603 1613 0.026803 GGAGATTGCATGCGACGAAC 59.973 55.0 10.57 2.61 0.0 3.95 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
154 155 5.502079 TGGTCTGGAACTGTTAAAACAAGA 58.498 37.500 0.00 0.00 38.66 3.02
257 259 3.831715 ACAGCTAAAAAGCATCGAACC 57.168 42.857 0.00 0.00 37.25 3.62
259 261 3.568007 ACAGCTAAAAAGCATCGAACCAA 59.432 39.130 0.00 0.00 37.25 3.67
260 262 4.161333 CAGCTAAAAAGCATCGAACCAAG 58.839 43.478 0.00 0.00 37.25 3.61
366 368 5.808366 TGCCGAAGAGATCCTAAACATAT 57.192 39.130 0.00 0.00 0.00 1.78
532 535 1.149148 GAAAGAAGACTGTGGGACGC 58.851 55.000 0.00 0.00 40.62 5.19
636 639 2.628178 AGAGTGACTCACCATCAAACGA 59.372 45.455 15.86 0.00 34.49 3.85
671 675 8.990163 TGTGTACTATATGTGGAGTTCAGATA 57.010 34.615 0.00 0.00 36.28 1.98
719 723 2.325082 CCTAAGGCGCGTGCTTTGT 61.325 57.895 26.26 5.53 41.01 2.83
720 724 1.017177 CCTAAGGCGCGTGCTTTGTA 61.017 55.000 26.26 8.25 41.01 2.41
847 852 5.028375 GCGAGCAAGTGTTATTTATGTTCC 58.972 41.667 0.00 0.00 0.00 3.62
848 853 5.391523 GCGAGCAAGTGTTATTTATGTTCCA 60.392 40.000 0.00 0.00 0.00 3.53
862 867 1.908619 TGTTCCAGAGAGCTTGGCATA 59.091 47.619 0.00 0.00 0.00 3.14
899 904 7.616528 TGATTTTTGGAAGAGGGAAAGAATT 57.383 32.000 0.00 0.00 0.00 2.17
901 910 7.289782 TGATTTTTGGAAGAGGGAAAGAATTGA 59.710 33.333 0.00 0.00 0.00 2.57
921 931 6.741992 TTGATGAATGCGTCTGTTATCTTT 57.258 33.333 0.00 0.00 0.00 2.52
967 977 1.143183 ACTTCCAACGCTCGTGTGT 59.857 52.632 0.00 0.00 38.76 3.72
988 998 1.859302 AGTGGACCAAAGCACCAAAA 58.141 45.000 0.00 0.00 35.40 2.44
1032 1042 3.623510 GGGAGATTCTTAGTCCGCAAAAG 59.376 47.826 0.00 0.00 0.00 2.27
1033 1043 3.064134 GGAGATTCTTAGTCCGCAAAAGC 59.936 47.826 0.00 0.00 0.00 3.51
1164 1174 4.078336 AGGAATCATCTGGGAGAAGTCCTA 60.078 45.833 0.00 0.00 43.36 2.94
1353 1363 9.225682 AGGTCTCCTTATGTGGATCTAAAAATA 57.774 33.333 0.00 0.00 35.30 1.40
1354 1364 9.847224 GGTCTCCTTATGTGGATCTAAAAATAA 57.153 33.333 0.00 0.00 35.30 1.40
1502 1512 2.042404 TTTGTTCCGCCCTACGTGGT 62.042 55.000 0.00 0.00 43.26 4.16
1524 1534 8.953990 GTGGTTAATTATGTAATGAACGATTGC 58.046 33.333 6.82 0.00 37.73 3.56
1611 1621 2.928295 TTTTAACCTTCGTTCGTCGC 57.072 45.000 0.00 0.00 39.67 5.19
1612 1622 1.850377 TTTAACCTTCGTTCGTCGCA 58.150 45.000 0.00 0.00 39.67 5.10
1613 1623 2.068837 TTAACCTTCGTTCGTCGCAT 57.931 45.000 0.00 0.00 39.67 4.73
1614 1624 1.342555 TAACCTTCGTTCGTCGCATG 58.657 50.000 0.00 0.00 39.67 4.06
1615 1625 1.897398 AACCTTCGTTCGTCGCATGC 61.897 55.000 7.91 7.91 39.67 4.06
1616 1626 2.379634 CCTTCGTTCGTCGCATGCA 61.380 57.895 19.57 1.73 39.67 3.96
1617 1627 1.491127 CTTCGTTCGTCGCATGCAA 59.509 52.632 19.57 0.00 39.67 4.08
1618 1628 0.095245 CTTCGTTCGTCGCATGCAAT 59.905 50.000 19.57 0.00 39.67 3.56
1619 1629 0.094558 TTCGTTCGTCGCATGCAATC 59.905 50.000 19.57 6.11 39.67 2.67
1620 1630 0.735978 TCGTTCGTCGCATGCAATCT 60.736 50.000 19.57 0.00 39.67 2.40
1621 1631 0.314578 CGTTCGTCGCATGCAATCTC 60.315 55.000 19.57 2.27 0.00 2.75
1622 1632 0.026803 GTTCGTCGCATGCAATCTCC 59.973 55.000 19.57 0.00 0.00 3.71
1623 1633 0.390998 TTCGTCGCATGCAATCTCCA 60.391 50.000 19.57 0.00 0.00 3.86
1624 1634 0.390998 TCGTCGCATGCAATCTCCAA 60.391 50.000 19.57 0.00 0.00 3.53
1625 1635 0.659427 CGTCGCATGCAATCTCCAAT 59.341 50.000 19.57 0.00 0.00 3.16
1626 1636 1.866601 CGTCGCATGCAATCTCCAATA 59.133 47.619 19.57 0.00 0.00 1.90
1627 1637 2.481568 CGTCGCATGCAATCTCCAATAT 59.518 45.455 19.57 0.00 0.00 1.28
1628 1638 3.666111 CGTCGCATGCAATCTCCAATATG 60.666 47.826 19.57 0.00 0.00 1.78
1629 1639 3.251729 GTCGCATGCAATCTCCAATATGT 59.748 43.478 19.57 0.00 0.00 2.29
1630 1640 3.884693 TCGCATGCAATCTCCAATATGTT 59.115 39.130 19.57 0.00 0.00 2.71
1631 1641 3.978855 CGCATGCAATCTCCAATATGTTG 59.021 43.478 19.57 0.00 35.05 3.33
1642 1652 2.646930 CAATATGTTGGAGCTGGCTCA 58.353 47.619 21.75 7.57 44.40 4.26
1643 1653 2.617308 CAATATGTTGGAGCTGGCTCAG 59.383 50.000 21.75 0.00 44.40 3.35
1644 1654 0.543277 TATGTTGGAGCTGGCTCAGG 59.457 55.000 21.75 0.00 44.40 3.86
1645 1655 2.749441 GTTGGAGCTGGCTCAGGC 60.749 66.667 21.75 7.48 44.40 4.85
1646 1656 4.399395 TTGGAGCTGGCTCAGGCG 62.399 66.667 21.75 0.00 44.40 5.52
1661 1671 2.102161 GCGCACGGCCCATTTTAG 59.898 61.111 0.30 0.00 34.80 1.85
1662 1672 2.696759 GCGCACGGCCCATTTTAGT 61.697 57.895 0.30 0.00 34.80 2.24
1663 1673 1.880186 CGCACGGCCCATTTTAGTT 59.120 52.632 0.00 0.00 0.00 2.24
1664 1674 1.088306 CGCACGGCCCATTTTAGTTA 58.912 50.000 0.00 0.00 0.00 2.24
1665 1675 1.673920 CGCACGGCCCATTTTAGTTAT 59.326 47.619 0.00 0.00 0.00 1.89
1666 1676 2.873472 CGCACGGCCCATTTTAGTTATA 59.127 45.455 0.00 0.00 0.00 0.98
1667 1677 3.500680 CGCACGGCCCATTTTAGTTATAT 59.499 43.478 0.00 0.00 0.00 0.86
1668 1678 4.023536 CGCACGGCCCATTTTAGTTATATT 60.024 41.667 0.00 0.00 0.00 1.28
1669 1679 5.506649 CGCACGGCCCATTTTAGTTATATTT 60.507 40.000 0.00 0.00 0.00 1.40
1670 1680 5.689961 GCACGGCCCATTTTAGTTATATTTG 59.310 40.000 0.00 0.00 0.00 2.32
1671 1681 6.212955 CACGGCCCATTTTAGTTATATTTGG 58.787 40.000 0.00 0.00 0.00 3.28
1672 1682 6.039941 CACGGCCCATTTTAGTTATATTTGGA 59.960 38.462 0.00 0.00 0.00 3.53
1673 1683 6.040054 ACGGCCCATTTTAGTTATATTTGGAC 59.960 38.462 0.00 0.00 0.00 4.02
1674 1684 6.443792 GGCCCATTTTAGTTATATTTGGACG 58.556 40.000 0.00 0.00 0.00 4.79
1675 1685 5.918576 GCCCATTTTAGTTATATTTGGACGC 59.081 40.000 0.00 0.00 0.00 5.19
1676 1686 6.443792 CCCATTTTAGTTATATTTGGACGCC 58.556 40.000 0.00 0.00 0.00 5.68
1677 1687 6.039941 CCCATTTTAGTTATATTTGGACGCCA 59.960 38.462 0.00 0.00 0.00 5.69
1678 1688 6.915843 CCATTTTAGTTATATTTGGACGCCAC 59.084 38.462 0.00 0.00 30.78 5.01
1679 1689 7.201785 CCATTTTAGTTATATTTGGACGCCACT 60.202 37.037 0.00 0.00 30.78 4.00
1680 1690 8.832521 CATTTTAGTTATATTTGGACGCCACTA 58.167 33.333 0.00 0.00 30.78 2.74
1681 1691 8.789825 TTTTAGTTATATTTGGACGCCACTAA 57.210 30.769 0.00 0.03 30.78 2.24
1682 1692 8.789825 TTTAGTTATATTTGGACGCCACTAAA 57.210 30.769 0.00 5.25 30.78 1.85
1683 1693 6.673154 AGTTATATTTGGACGCCACTAAAC 57.327 37.500 0.00 1.10 30.78 2.01
1684 1694 6.174760 AGTTATATTTGGACGCCACTAAACA 58.825 36.000 0.00 0.00 30.78 2.83
1685 1695 6.315393 AGTTATATTTGGACGCCACTAAACAG 59.685 38.462 0.00 0.00 30.78 3.16
1686 1696 0.948678 TTTGGACGCCACTAAACAGC 59.051 50.000 0.00 0.00 30.78 4.40
1687 1697 0.179043 TTGGACGCCACTAAACAGCA 60.179 50.000 0.00 0.00 30.78 4.41
1688 1698 0.179043 TGGACGCCACTAAACAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
1689 1699 0.948678 GGACGCCACTAAACAGCAAA 59.051 50.000 0.00 0.00 0.00 3.68
1690 1700 1.334689 GGACGCCACTAAACAGCAAAC 60.335 52.381 0.00 0.00 0.00 2.93
1691 1701 0.666374 ACGCCACTAAACAGCAAACC 59.334 50.000 0.00 0.00 0.00 3.27
1692 1702 0.951558 CGCCACTAAACAGCAAACCT 59.048 50.000 0.00 0.00 0.00 3.50
1693 1703 2.147958 CGCCACTAAACAGCAAACCTA 58.852 47.619 0.00 0.00 0.00 3.08
1694 1704 2.550606 CGCCACTAAACAGCAAACCTAA 59.449 45.455 0.00 0.00 0.00 2.69
1695 1705 3.364964 CGCCACTAAACAGCAAACCTAAG 60.365 47.826 0.00 0.00 0.00 2.18
1696 1706 3.057526 GCCACTAAACAGCAAACCTAAGG 60.058 47.826 0.00 0.00 0.00 2.69
1697 1707 4.142038 CCACTAAACAGCAAACCTAAGGT 58.858 43.478 0.00 0.00 37.65 3.50
1720 1730 2.652313 TTGGCAATCCAAGGGAACG 58.348 52.632 0.00 0.00 46.89 3.95
1721 1731 1.531739 TTGGCAATCCAAGGGAACGC 61.532 55.000 0.00 0.00 46.89 4.84
1722 1732 2.710902 GGCAATCCAAGGGAACGCC 61.711 63.158 11.20 11.20 42.83 5.68
1732 1742 2.186125 GGAACGCCCTTAGGACCG 59.814 66.667 0.00 4.73 33.47 4.79
1733 1743 2.653087 GGAACGCCCTTAGGACCGT 61.653 63.158 10.27 10.27 33.47 4.83
1734 1744 1.153686 GAACGCCCTTAGGACCGTC 60.154 63.158 14.97 7.41 31.62 4.79
1735 1745 1.880819 GAACGCCCTTAGGACCGTCA 61.881 60.000 14.97 0.00 31.62 4.35
1736 1746 1.885163 AACGCCCTTAGGACCGTCAG 61.885 60.000 14.97 0.00 31.62 3.51
1737 1747 2.050350 CGCCCTTAGGACCGTCAGA 61.050 63.158 0.00 0.00 33.47 3.27
1738 1748 1.392710 CGCCCTTAGGACCGTCAGAT 61.393 60.000 0.00 0.00 33.47 2.90
1739 1749 0.389757 GCCCTTAGGACCGTCAGATC 59.610 60.000 0.00 0.00 33.47 2.75
1740 1750 2.030045 GCCCTTAGGACCGTCAGATCT 61.030 57.143 0.00 0.00 33.47 2.75
1741 1751 1.957877 CCCTTAGGACCGTCAGATCTC 59.042 57.143 0.00 0.00 33.47 2.75
1742 1752 1.604755 CCTTAGGACCGTCAGATCTCG 59.395 57.143 0.00 0.00 0.00 4.04
1743 1753 2.562635 CTTAGGACCGTCAGATCTCGA 58.437 52.381 5.45 0.00 0.00 4.04
1744 1754 2.932855 TAGGACCGTCAGATCTCGAT 57.067 50.000 5.45 0.00 0.00 3.59
1745 1755 2.060050 AGGACCGTCAGATCTCGATT 57.940 50.000 5.45 0.00 0.00 3.34
1746 1756 1.678627 AGGACCGTCAGATCTCGATTG 59.321 52.381 5.45 0.63 0.00 2.67
1747 1757 1.676529 GGACCGTCAGATCTCGATTGA 59.323 52.381 5.45 0.00 0.00 2.57
1748 1758 2.099263 GGACCGTCAGATCTCGATTGAA 59.901 50.000 5.45 0.00 0.00 2.69
1749 1759 3.109619 GACCGTCAGATCTCGATTGAAC 58.890 50.000 5.45 0.00 0.00 3.18
1750 1760 2.492088 ACCGTCAGATCTCGATTGAACA 59.508 45.455 5.45 0.00 0.00 3.18
1751 1761 2.854777 CCGTCAGATCTCGATTGAACAC 59.145 50.000 5.45 0.00 0.00 3.32
1752 1762 3.501950 CGTCAGATCTCGATTGAACACA 58.498 45.455 0.00 0.00 0.00 3.72
1753 1763 4.108336 CGTCAGATCTCGATTGAACACAT 58.892 43.478 0.00 0.00 0.00 3.21
1754 1764 4.027050 CGTCAGATCTCGATTGAACACATG 60.027 45.833 0.00 0.00 0.00 3.21
1755 1765 4.269603 GTCAGATCTCGATTGAACACATGG 59.730 45.833 0.00 0.00 0.00 3.66
1756 1766 3.002042 CAGATCTCGATTGAACACATGGC 59.998 47.826 0.00 0.00 0.00 4.40
1757 1767 2.470983 TCTCGATTGAACACATGGCA 57.529 45.000 0.00 0.00 0.00 4.92
1758 1768 2.777094 TCTCGATTGAACACATGGCAA 58.223 42.857 0.00 0.00 0.00 4.52
1759 1769 3.346315 TCTCGATTGAACACATGGCAAT 58.654 40.909 0.00 1.43 35.14 3.56
1760 1770 3.758023 TCTCGATTGAACACATGGCAATT 59.242 39.130 0.00 0.00 32.80 2.32
1761 1771 4.940654 TCTCGATTGAACACATGGCAATTA 59.059 37.500 0.00 0.00 32.80 1.40
1762 1772 4.980590 TCGATTGAACACATGGCAATTAC 58.019 39.130 0.00 0.00 32.80 1.89
1763 1773 4.699735 TCGATTGAACACATGGCAATTACT 59.300 37.500 0.00 0.00 32.80 2.24
1764 1774 5.877564 TCGATTGAACACATGGCAATTACTA 59.122 36.000 0.00 0.00 32.80 1.82
1765 1775 6.542005 TCGATTGAACACATGGCAATTACTAT 59.458 34.615 0.00 0.00 32.80 2.12
1766 1776 6.634035 CGATTGAACACATGGCAATTACTATG 59.366 38.462 0.00 0.71 32.80 2.23
1767 1777 5.247507 TGAACACATGGCAATTACTATGC 57.752 39.130 2.11 0.00 43.08 3.14
1768 1778 3.969117 ACACATGGCAATTACTATGCG 57.031 42.857 2.11 0.00 44.75 4.73
1769 1779 2.033299 ACACATGGCAATTACTATGCGC 59.967 45.455 0.00 0.00 44.75 6.09
1770 1780 2.033174 CACATGGCAATTACTATGCGCA 59.967 45.455 14.96 14.96 44.75 6.09
1771 1781 2.687425 ACATGGCAATTACTATGCGCAA 59.313 40.909 17.11 0.00 44.75 4.85
1772 1782 3.318839 ACATGGCAATTACTATGCGCAAT 59.681 39.130 17.11 5.69 44.75 3.56
1773 1783 3.352554 TGGCAATTACTATGCGCAATG 57.647 42.857 17.11 13.20 44.75 2.82
1774 1784 2.687425 TGGCAATTACTATGCGCAATGT 59.313 40.909 17.11 18.75 44.75 2.71
1775 1785 3.243035 TGGCAATTACTATGCGCAATGTC 60.243 43.478 17.11 7.32 44.75 3.06
1776 1786 2.966708 GCAATTACTATGCGCAATGTCG 59.033 45.455 17.11 3.52 33.57 4.35
1786 1796 2.532531 CGCAATGTCGCAATTTCTCT 57.467 45.000 0.00 0.00 0.00 3.10
1787 1797 3.656651 CGCAATGTCGCAATTTCTCTA 57.343 42.857 0.00 0.00 0.00 2.43
1788 1798 3.345714 CGCAATGTCGCAATTTCTCTAC 58.654 45.455 0.00 0.00 0.00 2.59
1789 1799 3.685058 GCAATGTCGCAATTTCTCTACC 58.315 45.455 0.00 0.00 0.00 3.18
1790 1800 3.126858 GCAATGTCGCAATTTCTCTACCA 59.873 43.478 0.00 0.00 0.00 3.25
1791 1801 4.201950 GCAATGTCGCAATTTCTCTACCAT 60.202 41.667 0.00 0.00 0.00 3.55
1792 1802 5.677091 GCAATGTCGCAATTTCTCTACCATT 60.677 40.000 0.00 0.00 0.00 3.16
1793 1803 6.324819 CAATGTCGCAATTTCTCTACCATTT 58.675 36.000 0.00 0.00 0.00 2.32
1794 1804 5.957842 TGTCGCAATTTCTCTACCATTTT 57.042 34.783 0.00 0.00 0.00 1.82
1795 1805 6.325919 TGTCGCAATTTCTCTACCATTTTT 57.674 33.333 0.00 0.00 0.00 1.94
1878 1888 4.870123 TTTTTCACATGACAATCCTGGG 57.130 40.909 0.00 0.00 0.00 4.45
1879 1889 1.838112 TTCACATGACAATCCTGGGC 58.162 50.000 0.00 0.00 0.00 5.36
1880 1890 0.994247 TCACATGACAATCCTGGGCT 59.006 50.000 0.00 0.00 0.00 5.19
1881 1891 1.355381 TCACATGACAATCCTGGGCTT 59.645 47.619 0.00 0.00 0.00 4.35
1882 1892 1.747355 CACATGACAATCCTGGGCTTC 59.253 52.381 0.00 0.00 0.00 3.86
1883 1893 1.637553 ACATGACAATCCTGGGCTTCT 59.362 47.619 0.00 0.00 0.00 2.85
1884 1894 2.295885 CATGACAATCCTGGGCTTCTC 58.704 52.381 0.00 0.00 0.00 2.87
1885 1895 1.661463 TGACAATCCTGGGCTTCTCT 58.339 50.000 0.00 0.00 0.00 3.10
1886 1896 1.556911 TGACAATCCTGGGCTTCTCTC 59.443 52.381 0.00 0.00 0.00 3.20
1887 1897 0.539051 ACAATCCTGGGCTTCTCTCG 59.461 55.000 0.00 0.00 0.00 4.04
1888 1898 0.179062 CAATCCTGGGCTTCTCTCGG 60.179 60.000 0.00 0.00 0.00 4.63
1889 1899 0.325671 AATCCTGGGCTTCTCTCGGA 60.326 55.000 0.00 0.00 0.00 4.55
1890 1900 0.325671 ATCCTGGGCTTCTCTCGGAA 60.326 55.000 0.00 0.00 0.00 4.30
1891 1901 0.544357 TCCTGGGCTTCTCTCGGAAA 60.544 55.000 0.00 0.00 33.07 3.13
1892 1902 0.543749 CCTGGGCTTCTCTCGGAAAT 59.456 55.000 0.00 0.00 33.07 2.17
1893 1903 1.474143 CCTGGGCTTCTCTCGGAAATC 60.474 57.143 0.00 0.00 33.07 2.17
1894 1904 1.208052 CTGGGCTTCTCTCGGAAATCA 59.792 52.381 0.00 0.00 33.07 2.57
1895 1905 1.839994 TGGGCTTCTCTCGGAAATCAT 59.160 47.619 0.00 0.00 33.07 2.45
1896 1906 3.038280 TGGGCTTCTCTCGGAAATCATA 58.962 45.455 0.00 0.00 33.07 2.15
1897 1907 3.181465 TGGGCTTCTCTCGGAAATCATAC 60.181 47.826 0.00 0.00 33.07 2.39
1898 1908 3.181465 GGGCTTCTCTCGGAAATCATACA 60.181 47.826 0.00 0.00 33.07 2.29
1899 1909 4.442706 GGCTTCTCTCGGAAATCATACAA 58.557 43.478 0.00 0.00 33.07 2.41
1900 1910 4.876107 GGCTTCTCTCGGAAATCATACAAA 59.124 41.667 0.00 0.00 33.07 2.83
1901 1911 5.529060 GGCTTCTCTCGGAAATCATACAAAT 59.471 40.000 0.00 0.00 33.07 2.32
1902 1912 6.293135 GGCTTCTCTCGGAAATCATACAAATC 60.293 42.308 0.00 0.00 33.07 2.17
1903 1913 6.481644 GCTTCTCTCGGAAATCATACAAATCT 59.518 38.462 0.00 0.00 33.07 2.40
1904 1914 7.518052 GCTTCTCTCGGAAATCATACAAATCTG 60.518 40.741 0.00 0.00 33.07 2.90
1905 1915 7.112452 TCTCTCGGAAATCATACAAATCTGA 57.888 36.000 0.00 0.00 0.00 3.27
1906 1916 6.980978 TCTCTCGGAAATCATACAAATCTGAC 59.019 38.462 0.00 0.00 0.00 3.51
1907 1917 6.049149 TCTCGGAAATCATACAAATCTGACC 58.951 40.000 0.00 0.00 0.00 4.02
1908 1918 5.989477 TCGGAAATCATACAAATCTGACCT 58.011 37.500 0.00 0.00 0.00 3.85
1909 1919 6.049149 TCGGAAATCATACAAATCTGACCTC 58.951 40.000 0.00 0.00 0.00 3.85
1910 1920 5.817296 CGGAAATCATACAAATCTGACCTCA 59.183 40.000 0.00 0.00 0.00 3.86
1911 1921 6.018425 CGGAAATCATACAAATCTGACCTCAG 60.018 42.308 0.00 0.00 45.08 3.35
1912 1922 6.825721 GGAAATCATACAAATCTGACCTCAGT 59.174 38.462 2.25 0.00 44.12 3.41
1913 1923 7.337942 GGAAATCATACAAATCTGACCTCAGTT 59.662 37.037 2.25 0.00 44.12 3.16
1914 1924 8.641498 AAATCATACAAATCTGACCTCAGTTT 57.359 30.769 2.25 0.00 44.12 2.66
1915 1925 8.641498 AATCATACAAATCTGACCTCAGTTTT 57.359 30.769 2.25 4.24 43.03 2.43
1916 1926 8.641498 ATCATACAAATCTGACCTCAGTTTTT 57.359 30.769 8.14 5.02 41.38 1.94
1944 1954 9.703892 AATATGCTGTGTATTTAGTTGCAAAAA 57.296 25.926 0.00 0.00 32.66 1.94
2500 2510 2.869101 TGGAACGACCATGGATTCAA 57.131 45.000 21.47 9.80 44.64 2.69
2501 2511 3.147553 TGGAACGACCATGGATTCAAA 57.852 42.857 21.47 8.39 44.64 2.69
2502 2512 3.696045 TGGAACGACCATGGATTCAAAT 58.304 40.909 21.47 0.00 44.64 2.32
2503 2513 4.849518 TGGAACGACCATGGATTCAAATA 58.150 39.130 21.47 4.59 44.64 1.40
2504 2514 5.445069 TGGAACGACCATGGATTCAAATAT 58.555 37.500 21.47 0.00 44.64 1.28
2505 2515 6.596621 TGGAACGACCATGGATTCAAATATA 58.403 36.000 21.47 0.90 44.64 0.86
2506 2516 7.057264 TGGAACGACCATGGATTCAAATATAA 58.943 34.615 21.47 0.00 44.64 0.98
2507 2517 7.228507 TGGAACGACCATGGATTCAAATATAAG 59.771 37.037 21.47 0.00 44.64 1.73
2508 2518 7.444183 GGAACGACCATGGATTCAAATATAAGA 59.556 37.037 21.47 0.00 38.79 2.10
2509 2519 8.746052 AACGACCATGGATTCAAATATAAGAA 57.254 30.769 21.47 0.00 0.00 2.52
2510 2520 8.924511 ACGACCATGGATTCAAATATAAGAAT 57.075 30.769 21.47 3.04 37.19 2.40
2511 2521 9.354673 ACGACCATGGATTCAAATATAAGAATT 57.645 29.630 21.47 0.00 34.79 2.17
2539 2549 8.628630 TGTGTTACAAATGGATTCTTCATACA 57.371 30.769 0.00 0.00 0.00 2.29
2540 2550 9.241919 TGTGTTACAAATGGATTCTTCATACAT 57.758 29.630 0.00 0.00 38.20 2.29
2541 2551 9.507280 GTGTTACAAATGGATTCTTCATACATG 57.493 33.333 0.00 0.00 35.00 3.21
2542 2552 9.241919 TGTTACAAATGGATTCTTCATACATGT 57.758 29.630 2.69 2.69 35.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.800544 CACACAACGACTCTGGGTAAAG 59.199 50.000 0.00 0.00 0.00 1.85
154 155 2.091830 TCGACCACTCTCCATATGACCT 60.092 50.000 3.65 0.00 0.00 3.85
257 259 1.202687 TCTGACACCCACTTCAGCTTG 60.203 52.381 0.00 0.00 39.36 4.01
259 261 1.131638 TTCTGACACCCACTTCAGCT 58.868 50.000 0.00 0.00 39.36 4.24
260 262 2.191128 ATTCTGACACCCACTTCAGC 57.809 50.000 0.00 0.00 39.36 4.26
366 368 1.351076 TCTCCCACAGACTGAATGCA 58.649 50.000 10.08 0.00 0.00 3.96
532 535 4.571176 GCGGAACCTTAGTCTTCCAAATAG 59.429 45.833 6.70 0.00 36.47 1.73
636 639 8.170730 TCCACATATAGTACACATACTGGAGAT 58.829 37.037 0.00 0.00 41.92 2.75
719 723 2.038426 CACACATCCCCAAGGCGATATA 59.962 50.000 0.00 0.00 0.00 0.86
720 724 1.140312 ACACATCCCCAAGGCGATAT 58.860 50.000 0.00 0.00 0.00 1.63
847 852 2.367894 TCCTCATATGCCAAGCTCTCTG 59.632 50.000 0.00 0.00 0.00 3.35
848 853 2.687297 TCCTCATATGCCAAGCTCTCT 58.313 47.619 0.00 0.00 0.00 3.10
862 867 6.588719 TCCAAAAATCAAATCGTTCCTCAT 57.411 33.333 0.00 0.00 0.00 2.90
899 904 5.643348 ACAAAGATAACAGACGCATTCATCA 59.357 36.000 0.00 0.00 0.00 3.07
901 910 5.163723 CCACAAAGATAACAGACGCATTCAT 60.164 40.000 0.00 0.00 0.00 2.57
921 931 9.396022 GAGAAAGTCTTCCAATAATTATCCACA 57.604 33.333 0.00 0.00 31.28 4.17
967 977 2.738587 TTGGTGCTTTGGTCCACTTA 57.261 45.000 0.00 0.00 32.68 2.24
988 998 2.287194 CCCCATCACCCCCTTCCT 60.287 66.667 0.00 0.00 0.00 3.36
1032 1042 2.409378 CCAAACAGCACGATCATTTTGC 59.591 45.455 0.00 0.00 36.45 3.68
1033 1043 3.899734 TCCAAACAGCACGATCATTTTG 58.100 40.909 0.00 0.00 0.00 2.44
1063 1073 9.436957 AACATTTATCTTAATATACTCCCGCTG 57.563 33.333 0.00 0.00 0.00 5.18
1099 1109 3.523547 CAGATCTCAAGCTCTCCACAAG 58.476 50.000 0.00 0.00 0.00 3.16
1164 1174 6.472887 TCGAATAAAATCCCAAGAAGACACT 58.527 36.000 0.00 0.00 0.00 3.55
1235 1245 6.595716 GTGAAGAGAAATACCAATGTACAGCT 59.404 38.462 0.33 0.00 0.00 4.24
1591 1601 2.606725 TGCGACGAACGAAGGTTAAAAA 59.393 40.909 0.00 0.00 45.77 1.94
1592 1602 2.200067 TGCGACGAACGAAGGTTAAAA 58.800 42.857 0.00 0.00 45.77 1.52
1593 1603 1.850377 TGCGACGAACGAAGGTTAAA 58.150 45.000 0.00 0.00 45.77 1.52
1594 1604 1.722464 CATGCGACGAACGAAGGTTAA 59.278 47.619 0.00 0.00 45.77 2.01
1595 1605 1.342555 CATGCGACGAACGAAGGTTA 58.657 50.000 0.00 0.00 45.77 2.85
1596 1606 1.897398 GCATGCGACGAACGAAGGTT 61.897 55.000 0.00 0.00 45.77 3.50
1597 1607 2.380410 GCATGCGACGAACGAAGGT 61.380 57.895 0.00 0.00 45.77 3.50
1598 1608 1.896339 TTGCATGCGACGAACGAAGG 61.896 55.000 14.09 3.46 45.77 3.46
1599 1609 0.095245 ATTGCATGCGACGAACGAAG 59.905 50.000 10.57 0.00 45.77 3.79
1600 1610 0.094558 GATTGCATGCGACGAACGAA 59.905 50.000 10.57 0.00 45.77 3.85
1601 1611 0.735978 AGATTGCATGCGACGAACGA 60.736 50.000 10.57 0.00 45.77 3.85
1602 1612 0.314578 GAGATTGCATGCGACGAACG 60.315 55.000 10.57 0.00 45.66 3.95
1603 1613 0.026803 GGAGATTGCATGCGACGAAC 59.973 55.000 10.57 2.61 0.00 3.95
1604 1614 0.390998 TGGAGATTGCATGCGACGAA 60.391 50.000 10.57 0.00 0.00 3.85
1605 1615 0.390998 TTGGAGATTGCATGCGACGA 60.391 50.000 10.57 0.00 0.00 4.20
1606 1616 0.659427 ATTGGAGATTGCATGCGACG 59.341 50.000 10.57 0.00 0.00 5.12
1607 1617 3.251729 ACATATTGGAGATTGCATGCGAC 59.748 43.478 10.57 5.09 0.00 5.19
1608 1618 3.479489 ACATATTGGAGATTGCATGCGA 58.521 40.909 10.79 10.79 0.00 5.10
1609 1619 3.909776 ACATATTGGAGATTGCATGCG 57.090 42.857 14.09 0.00 0.00 4.73
1622 1632 2.617308 CTGAGCCAGCTCCAACATATTG 59.383 50.000 16.69 0.00 42.09 1.90
1623 1633 2.422519 CCTGAGCCAGCTCCAACATATT 60.423 50.000 16.69 0.00 42.09 1.28
1624 1634 1.142465 CCTGAGCCAGCTCCAACATAT 59.858 52.381 16.69 0.00 42.09 1.78
1625 1635 0.543277 CCTGAGCCAGCTCCAACATA 59.457 55.000 16.69 0.00 42.09 2.29
1626 1636 1.302285 CCTGAGCCAGCTCCAACAT 59.698 57.895 16.69 0.00 42.09 2.71
1627 1637 2.752358 CCTGAGCCAGCTCCAACA 59.248 61.111 16.69 0.00 42.09 3.33
1628 1638 2.749441 GCCTGAGCCAGCTCCAAC 60.749 66.667 16.69 2.52 42.09 3.77
1629 1639 4.399395 CGCCTGAGCCAGCTCCAA 62.399 66.667 16.69 0.00 42.09 3.53
1644 1654 2.102161 CTAAAATGGGCCGTGCGC 59.898 61.111 0.00 0.00 41.94 6.09
1645 1655 1.088306 TAACTAAAATGGGCCGTGCG 58.912 50.000 0.00 0.00 0.00 5.34
1646 1656 5.447624 AATATAACTAAAATGGGCCGTGC 57.552 39.130 0.00 0.00 0.00 5.34
1647 1657 6.039941 TCCAAATATAACTAAAATGGGCCGTG 59.960 38.462 0.00 0.00 0.00 4.94
1648 1658 6.040054 GTCCAAATATAACTAAAATGGGCCGT 59.960 38.462 0.00 0.00 0.00 5.68
1649 1659 6.443792 GTCCAAATATAACTAAAATGGGCCG 58.556 40.000 0.00 0.00 0.00 6.13
1650 1660 6.443792 CGTCCAAATATAACTAAAATGGGCC 58.556 40.000 0.00 0.00 0.00 5.80
1651 1661 5.918576 GCGTCCAAATATAACTAAAATGGGC 59.081 40.000 0.00 0.00 0.00 5.36
1652 1662 6.039941 TGGCGTCCAAATATAACTAAAATGGG 59.960 38.462 0.00 0.00 0.00 4.00
1653 1663 6.915843 GTGGCGTCCAAATATAACTAAAATGG 59.084 38.462 0.00 0.00 34.18 3.16
1654 1664 7.703328 AGTGGCGTCCAAATATAACTAAAATG 58.297 34.615 0.00 0.00 34.18 2.32
1655 1665 7.875327 AGTGGCGTCCAAATATAACTAAAAT 57.125 32.000 0.00 0.00 34.18 1.82
1656 1666 8.789825 TTAGTGGCGTCCAAATATAACTAAAA 57.210 30.769 0.00 0.00 34.18 1.52
1657 1667 8.667463 GTTTAGTGGCGTCCAAATATAACTAAA 58.333 33.333 0.00 1.19 34.18 1.85
1658 1668 7.823310 TGTTTAGTGGCGTCCAAATATAACTAA 59.177 33.333 0.00 0.00 34.18 2.24
1659 1669 7.329499 TGTTTAGTGGCGTCCAAATATAACTA 58.671 34.615 0.00 0.00 34.18 2.24
1660 1670 6.174760 TGTTTAGTGGCGTCCAAATATAACT 58.825 36.000 0.00 0.00 34.18 2.24
1661 1671 6.425577 TGTTTAGTGGCGTCCAAATATAAC 57.574 37.500 0.00 3.16 34.18 1.89
1662 1672 5.065474 GCTGTTTAGTGGCGTCCAAATATAA 59.935 40.000 0.00 0.00 34.18 0.98
1663 1673 4.573201 GCTGTTTAGTGGCGTCCAAATATA 59.427 41.667 0.00 0.00 34.18 0.86
1664 1674 3.377172 GCTGTTTAGTGGCGTCCAAATAT 59.623 43.478 0.00 0.00 34.18 1.28
1665 1675 2.745281 GCTGTTTAGTGGCGTCCAAATA 59.255 45.455 0.00 0.00 34.18 1.40
1666 1676 1.539827 GCTGTTTAGTGGCGTCCAAAT 59.460 47.619 0.00 0.00 34.18 2.32
1667 1677 0.948678 GCTGTTTAGTGGCGTCCAAA 59.051 50.000 0.00 0.00 34.18 3.28
1668 1678 0.179043 TGCTGTTTAGTGGCGTCCAA 60.179 50.000 0.00 0.00 34.18 3.53
1669 1679 0.179043 TTGCTGTTTAGTGGCGTCCA 60.179 50.000 0.00 0.00 0.00 4.02
1670 1680 0.948678 TTTGCTGTTTAGTGGCGTCC 59.051 50.000 0.00 0.00 0.00 4.79
1671 1681 1.334689 GGTTTGCTGTTTAGTGGCGTC 60.335 52.381 0.00 0.00 0.00 5.19
1672 1682 0.666374 GGTTTGCTGTTTAGTGGCGT 59.334 50.000 0.00 0.00 0.00 5.68
1673 1683 0.951558 AGGTTTGCTGTTTAGTGGCG 59.048 50.000 0.00 0.00 0.00 5.69
1674 1684 3.057526 CCTTAGGTTTGCTGTTTAGTGGC 60.058 47.826 0.00 0.00 0.00 5.01
1675 1685 4.142038 ACCTTAGGTTTGCTGTTTAGTGG 58.858 43.478 0.00 0.00 27.29 4.00
1676 1686 5.767816 AACCTTAGGTTTGCTGTTTAGTG 57.232 39.130 11.39 0.00 44.33 2.74
1703 1713 1.976474 GCGTTCCCTTGGATTGCCA 60.976 57.895 0.00 0.00 44.17 4.92
1704 1714 2.710902 GGCGTTCCCTTGGATTGCC 61.711 63.158 9.52 9.52 42.29 4.52
1705 1715 2.885113 GGCGTTCCCTTGGATTGC 59.115 61.111 0.00 0.00 33.36 3.56
1715 1725 2.186125 CGGTCCTAAGGGCGTTCC 59.814 66.667 0.00 0.00 0.00 3.62
1716 1726 1.153686 GACGGTCCTAAGGGCGTTC 60.154 63.158 0.00 0.00 32.90 3.95
1717 1727 1.885163 CTGACGGTCCTAAGGGCGTT 61.885 60.000 5.55 0.00 32.90 4.84
1718 1728 2.283388 TGACGGTCCTAAGGGCGT 60.283 61.111 5.55 0.00 34.83 5.68
1719 1729 1.392710 ATCTGACGGTCCTAAGGGCG 61.393 60.000 5.55 0.00 0.00 6.13
1720 1730 0.389757 GATCTGACGGTCCTAAGGGC 59.610 60.000 5.55 0.00 0.00 5.19
1721 1731 1.957877 GAGATCTGACGGTCCTAAGGG 59.042 57.143 0.00 0.00 0.00 3.95
1722 1732 1.604755 CGAGATCTGACGGTCCTAAGG 59.395 57.143 0.00 0.00 0.00 2.69
1723 1733 2.562635 TCGAGATCTGACGGTCCTAAG 58.437 52.381 0.00 0.00 0.00 2.18
1724 1734 2.704464 TCGAGATCTGACGGTCCTAA 57.296 50.000 0.00 0.00 0.00 2.69
1725 1735 2.879026 CAATCGAGATCTGACGGTCCTA 59.121 50.000 0.00 0.00 0.00 2.94
1726 1736 1.678627 CAATCGAGATCTGACGGTCCT 59.321 52.381 0.00 0.00 0.00 3.85
1727 1737 1.676529 TCAATCGAGATCTGACGGTCC 59.323 52.381 0.00 0.00 0.00 4.46
1728 1738 3.109619 GTTCAATCGAGATCTGACGGTC 58.890 50.000 0.00 0.00 0.00 4.79
1729 1739 2.492088 TGTTCAATCGAGATCTGACGGT 59.508 45.455 0.00 0.00 0.00 4.83
1730 1740 2.854777 GTGTTCAATCGAGATCTGACGG 59.145 50.000 0.00 0.00 0.00 4.79
1731 1741 3.501950 TGTGTTCAATCGAGATCTGACG 58.498 45.455 0.00 0.00 0.00 4.35
1732 1742 4.269603 CCATGTGTTCAATCGAGATCTGAC 59.730 45.833 0.00 0.00 0.00 3.51
1733 1743 4.436332 CCATGTGTTCAATCGAGATCTGA 58.564 43.478 0.00 0.00 0.00 3.27
1734 1744 3.002042 GCCATGTGTTCAATCGAGATCTG 59.998 47.826 0.00 0.00 0.00 2.90
1735 1745 3.201290 GCCATGTGTTCAATCGAGATCT 58.799 45.455 0.00 0.00 0.00 2.75
1736 1746 2.938451 TGCCATGTGTTCAATCGAGATC 59.062 45.455 0.00 0.00 0.00 2.75
1737 1747 2.989909 TGCCATGTGTTCAATCGAGAT 58.010 42.857 0.00 0.00 0.00 2.75
1738 1748 2.470983 TGCCATGTGTTCAATCGAGA 57.529 45.000 0.00 0.00 0.00 4.04
1739 1749 3.770263 ATTGCCATGTGTTCAATCGAG 57.230 42.857 0.00 0.00 0.00 4.04
1740 1750 4.699735 AGTAATTGCCATGTGTTCAATCGA 59.300 37.500 0.00 0.00 30.84 3.59
1741 1751 4.985413 AGTAATTGCCATGTGTTCAATCG 58.015 39.130 0.00 0.00 30.84 3.34
1742 1752 6.418819 GCATAGTAATTGCCATGTGTTCAATC 59.581 38.462 4.15 0.00 33.95 2.67
1743 1753 6.275335 GCATAGTAATTGCCATGTGTTCAAT 58.725 36.000 4.15 0.00 33.95 2.57
1744 1754 5.649557 GCATAGTAATTGCCATGTGTTCAA 58.350 37.500 4.15 0.00 33.95 2.69
1745 1755 4.201901 CGCATAGTAATTGCCATGTGTTCA 60.202 41.667 7.21 0.00 36.75 3.18
1746 1756 4.282068 CGCATAGTAATTGCCATGTGTTC 58.718 43.478 7.21 0.00 36.75 3.18
1747 1757 3.489059 GCGCATAGTAATTGCCATGTGTT 60.489 43.478 14.62 0.00 36.75 3.32
1748 1758 2.033299 GCGCATAGTAATTGCCATGTGT 59.967 45.455 14.62 0.00 36.75 3.72
1749 1759 2.033174 TGCGCATAGTAATTGCCATGTG 59.967 45.455 5.66 10.29 36.75 3.21
1750 1760 2.296792 TGCGCATAGTAATTGCCATGT 58.703 42.857 5.66 0.00 36.75 3.21
1751 1761 3.352554 TTGCGCATAGTAATTGCCATG 57.647 42.857 12.75 0.00 36.75 3.66
1752 1762 3.318839 ACATTGCGCATAGTAATTGCCAT 59.681 39.130 12.75 0.00 36.75 4.40
1753 1763 2.687425 ACATTGCGCATAGTAATTGCCA 59.313 40.909 12.75 0.00 36.75 4.92
1754 1764 3.300009 GACATTGCGCATAGTAATTGCC 58.700 45.455 12.75 0.00 36.75 4.52
1755 1765 2.966708 CGACATTGCGCATAGTAATTGC 59.033 45.455 12.75 0.00 32.74 3.56
1767 1777 2.532531 AGAGAAATTGCGACATTGCG 57.467 45.000 0.00 0.00 37.81 4.85
1768 1778 3.126858 TGGTAGAGAAATTGCGACATTGC 59.873 43.478 0.00 0.00 0.00 3.56
1769 1779 4.944962 TGGTAGAGAAATTGCGACATTG 57.055 40.909 0.00 0.00 0.00 2.82
1770 1780 6.515272 AAATGGTAGAGAAATTGCGACATT 57.485 33.333 0.00 0.00 0.00 2.71
1771 1781 6.515272 AAAATGGTAGAGAAATTGCGACAT 57.485 33.333 0.00 0.00 0.00 3.06
1772 1782 5.957842 AAAATGGTAGAGAAATTGCGACA 57.042 34.783 0.00 0.00 0.00 4.35
1857 1867 3.006752 GCCCAGGATTGTCATGTGAAAAA 59.993 43.478 0.00 0.00 0.00 1.94
1858 1868 2.562298 GCCCAGGATTGTCATGTGAAAA 59.438 45.455 0.00 0.00 0.00 2.29
1859 1869 2.170166 GCCCAGGATTGTCATGTGAAA 58.830 47.619 0.00 0.00 0.00 2.69
1860 1870 1.355381 AGCCCAGGATTGTCATGTGAA 59.645 47.619 0.00 0.00 0.00 3.18
1861 1871 0.994247 AGCCCAGGATTGTCATGTGA 59.006 50.000 0.00 0.00 0.00 3.58
1862 1872 1.747355 GAAGCCCAGGATTGTCATGTG 59.253 52.381 0.00 0.00 0.00 3.21
1863 1873 1.637553 AGAAGCCCAGGATTGTCATGT 59.362 47.619 0.00 0.00 0.00 3.21
1864 1874 2.092538 AGAGAAGCCCAGGATTGTCATG 60.093 50.000 13.52 0.00 36.46 3.07
1865 1875 2.172293 GAGAGAAGCCCAGGATTGTCAT 59.828 50.000 13.52 0.13 36.46 3.06
1866 1876 1.556911 GAGAGAAGCCCAGGATTGTCA 59.443 52.381 13.52 0.00 36.46 3.58
1867 1877 1.472376 CGAGAGAAGCCCAGGATTGTC 60.472 57.143 3.77 3.77 34.62 3.18
1868 1878 0.539051 CGAGAGAAGCCCAGGATTGT 59.461 55.000 0.00 0.00 0.00 2.71
1869 1879 0.179062 CCGAGAGAAGCCCAGGATTG 60.179 60.000 0.00 0.00 0.00 2.67
1870 1880 0.325671 TCCGAGAGAAGCCCAGGATT 60.326 55.000 0.00 0.00 0.00 3.01
1871 1881 0.325671 TTCCGAGAGAAGCCCAGGAT 60.326 55.000 0.00 0.00 0.00 3.24
1872 1882 0.544357 TTTCCGAGAGAAGCCCAGGA 60.544 55.000 0.00 0.00 35.40 3.86
1873 1883 0.543749 ATTTCCGAGAGAAGCCCAGG 59.456 55.000 0.00 0.00 35.40 4.45
1874 1884 1.208052 TGATTTCCGAGAGAAGCCCAG 59.792 52.381 0.00 0.00 35.40 4.45
1875 1885 1.275666 TGATTTCCGAGAGAAGCCCA 58.724 50.000 0.00 0.00 35.40 5.36
1876 1886 2.629336 ATGATTTCCGAGAGAAGCCC 57.371 50.000 0.00 0.00 35.40 5.19
1877 1887 4.060038 TGTATGATTTCCGAGAGAAGCC 57.940 45.455 0.00 0.00 35.40 4.35
1878 1888 6.481644 AGATTTGTATGATTTCCGAGAGAAGC 59.518 38.462 0.00 0.00 35.40 3.86
1879 1889 7.708322 TCAGATTTGTATGATTTCCGAGAGAAG 59.292 37.037 0.00 0.00 35.40 2.85
1880 1890 7.492669 GTCAGATTTGTATGATTTCCGAGAGAA 59.507 37.037 0.00 0.00 0.00 2.87
1881 1891 6.980978 GTCAGATTTGTATGATTTCCGAGAGA 59.019 38.462 0.00 0.00 0.00 3.10
1882 1892 6.201806 GGTCAGATTTGTATGATTTCCGAGAG 59.798 42.308 0.00 0.00 0.00 3.20
1883 1893 6.049149 GGTCAGATTTGTATGATTTCCGAGA 58.951 40.000 0.00 0.00 0.00 4.04
1884 1894 6.051717 AGGTCAGATTTGTATGATTTCCGAG 58.948 40.000 0.00 0.00 0.00 4.63
1885 1895 5.989477 AGGTCAGATTTGTATGATTTCCGA 58.011 37.500 0.00 0.00 0.00 4.55
1886 1896 5.817296 TGAGGTCAGATTTGTATGATTTCCG 59.183 40.000 0.00 0.00 0.00 4.30
1887 1897 6.825721 ACTGAGGTCAGATTTGTATGATTTCC 59.174 38.462 13.99 0.00 46.59 3.13
1888 1898 7.856145 ACTGAGGTCAGATTTGTATGATTTC 57.144 36.000 13.99 0.00 46.59 2.17
1889 1899 8.641498 AAACTGAGGTCAGATTTGTATGATTT 57.359 30.769 13.99 0.00 46.59 2.17
1890 1900 8.641498 AAAACTGAGGTCAGATTTGTATGATT 57.359 30.769 13.99 0.00 43.98 2.57
1891 1901 8.641498 AAAAACTGAGGTCAGATTTGTATGAT 57.359 30.769 13.99 0.00 44.58 2.45
1918 1928 9.703892 TTTTTGCAACTAAATACACAGCATATT 57.296 25.926 0.00 0.00 0.00 1.28
2465 2475 9.567776 TGGTCGTTCCAAATACATGAATATATT 57.432 29.630 0.00 0.00 44.12 1.28
2482 2492 7.444183 TCTTATATTTGAATCCATGGTCGTTCC 59.556 37.037 12.58 0.00 0.00 3.62
2483 2493 8.378172 TCTTATATTTGAATCCATGGTCGTTC 57.622 34.615 12.58 14.54 0.00 3.95
2484 2494 8.746052 TTCTTATATTTGAATCCATGGTCGTT 57.254 30.769 12.58 5.57 0.00 3.85
2485 2495 8.924511 ATTCTTATATTTGAATCCATGGTCGT 57.075 30.769 12.58 0.00 0.00 4.34
2513 2523 9.241919 TGTATGAAGAATCCATTTGTAACACAT 57.758 29.630 0.00 0.00 0.00 3.21
2514 2524 8.628630 TGTATGAAGAATCCATTTGTAACACA 57.371 30.769 0.00 0.00 0.00 3.72
2515 2525 9.507280 CATGTATGAAGAATCCATTTGTAACAC 57.493 33.333 0.00 0.00 0.00 3.32
2516 2526 9.241919 ACATGTATGAAGAATCCATTTGTAACA 57.758 29.630 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.