Multiple sequence alignment - TraesCS2D01G552900

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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 TraesCS2D01G552900 chr2D 100.000 3825 0 0 1 3825 627917361 627921185 0.000000e+00 7064.0
1 TraesCS2D01G552900 chr2A 95.960 1213 45 4 2542 3751 758396335 758397546 0.000000e+00 1965.0
2 TraesCS2D01G552900 chr2A 86.630 1638 84 51 1 1601 758393734 758395273 0.000000e+00 1687.0
3 TraesCS2D01G552900 chr2A 96.154 702 27 0 1809 2510 758395636 758396337 0.000000e+00 1147.0
4 TraesCS2D01G552900 chr2A 91.473 129 10 1 3568 3695 758686782 758686654 3.930000e-40 176.0
5 TraesCS2D01G552900 chr2A 84.259 108 13 2 1809 1916 758395281 758395384 6.760000e-18 102.0
6 TraesCS2D01G552900 chr2A 96.226 53 2 0 3773 3825 758397544 758397596 1.890000e-13 87.9
7 TraesCS2D01G552900 chr2B 95.229 1090 49 3 2665 3751 770679795 770680884 0.000000e+00 1722.0
8 TraesCS2D01G552900 chr2B 85.860 1669 104 60 1 1604 770676815 770678416 0.000000e+00 1653.0
9 TraesCS2D01G552900 chr2B 95.925 859 33 2 1809 2666 770678776 770679633 0.000000e+00 1391.0
10 TraesCS2D01G552900 chr2B 88.778 499 24 7 53 551 748203008 748202542 1.980000e-162 582.0
11 TraesCS2D01G552900 chr2B 85.844 551 28 12 1 551 748356455 748355955 1.210000e-149 540.0


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 TraesCS2D01G552900 chr2D 627917361 627921185 3824 False 7064.000000 7064 100.0000 1 3825 1 chr2D.!!$F1 3824
1 TraesCS2D01G552900 chr2A 758393734 758397596 3862 False 997.780000 1965 91.8458 1 3825 5 chr2A.!!$F1 3824
2 TraesCS2D01G552900 chr2B 770676815 770680884 4069 False 1588.666667 1722 92.3380 1 3751 3 chr2B.!!$F1 3750
3 TraesCS2D01G552900 chr2B 748355955 748356455 500 True 540.000000 540 85.8440 1 551 1 chr2B.!!$R2 550

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
688 702 0.107165 GGTATCCACCCCTGTGCTTC 60.107 60.0 0.0 0.0 41.35 3.86 F
1200 1275 0.690762 TAAGCCCACACTGTCCCTTC 59.309 55.0 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1668 0.689623 AGTCCAAGTTGCCTCAGAGG 59.310 55.000 12.81 12.81 38.8 3.69 R
3115 3714 1.737236 CACAGCTGCCGCATAAGTTAA 59.263 47.619 15.27 0.00 39.1 2.01 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
256 257 2.838225 CCCGTATCTCCACCGCCT 60.838 66.667 0.00 0.00 0.00 5.52
336 337 3.847602 CAGGCGAGGGAGCAGGAG 61.848 72.222 0.00 0.00 39.27 3.69
391 392 4.023792 CCGTCGCCATGTAAGTACAGTATA 60.024 45.833 0.00 0.00 39.92 1.47
419 420 0.321653 GAACGGCTTGGACAGTGGAT 60.322 55.000 0.00 0.00 0.00 3.41
459 468 5.400066 ACATATAGGGTGGTTTTTGCAAC 57.600 39.130 0.00 0.00 0.00 4.17
632 646 3.154473 CCGGCGAATCCCTCTCCA 61.154 66.667 9.30 0.00 0.00 3.86
633 647 2.731571 CCGGCGAATCCCTCTCCAA 61.732 63.158 9.30 0.00 0.00 3.53
687 701 1.999346 GGTATCCACCCCTGTGCTT 59.001 57.895 0.00 0.00 41.35 3.91
688 702 0.107165 GGTATCCACCCCTGTGCTTC 60.107 60.000 0.00 0.00 41.35 3.86
689 703 0.912486 GTATCCACCCCTGTGCTTCT 59.088 55.000 0.00 0.00 41.35 2.85
790 806 2.158959 GTGATCGGTTCGACTGCGG 61.159 63.158 0.00 0.00 39.18 5.69
792 808 2.126071 ATCGGTTCGACTGCGGTG 60.126 61.111 0.80 0.00 39.18 4.94
915 961 1.468914 GTTTGATGAAACGCCTCTCCC 59.531 52.381 0.00 0.00 32.49 4.30
1040 1106 4.673375 CAAGGGCTGGCAGCAGGT 62.673 66.667 37.49 20.29 44.75 4.00
1053 1119 2.912624 GCAGGTGGCTGTTGCAGTC 61.913 63.158 0.00 0.00 41.91 3.51
1101 1167 3.295093 TCCGAAGAGAGCTGATCTGATT 58.705 45.455 0.00 0.00 38.84 2.57
1200 1275 0.690762 TAAGCCCACACTGTCCCTTC 59.309 55.000 0.00 0.00 0.00 3.46
1201 1276 1.062488 AAGCCCACACTGTCCCTTCT 61.062 55.000 0.00 0.00 0.00 2.85
1202 1277 1.003233 GCCCACACTGTCCCTTCTC 60.003 63.158 0.00 0.00 0.00 2.87
1203 1278 1.484444 GCCCACACTGTCCCTTCTCT 61.484 60.000 0.00 0.00 0.00 3.10
1204 1279 1.059913 CCCACACTGTCCCTTCTCTT 58.940 55.000 0.00 0.00 0.00 2.85
1208 1283 3.772025 CCACACTGTCCCTTCTCTTATCT 59.228 47.826 0.00 0.00 0.00 1.98
1247 1322 2.548875 TGTTTGGACATTTGTTGCTGC 58.451 42.857 0.00 0.00 0.00 5.25
1398 1476 5.589855 TCACCCATGCTATTGTTGTAGAATG 59.410 40.000 0.00 0.00 37.44 2.67
1400 1478 5.590259 ACCCATGCTATTGTTGTAGAATGTC 59.410 40.000 2.22 0.00 36.41 3.06
1402 1480 6.992123 CCCATGCTATTGTTGTAGAATGTCTA 59.008 38.462 2.22 0.00 36.41 2.59
1429 1507 8.622948 TTTTCCCTGTTTATGTTGTTTGTTTT 57.377 26.923 0.00 0.00 0.00 2.43
1430 1508 7.602517 TTCCCTGTTTATGTTGTTTGTTTTG 57.397 32.000 0.00 0.00 0.00 2.44
1435 1513 7.710475 CCTGTTTATGTTGTTTGTTTTGGAGAT 59.290 33.333 0.00 0.00 0.00 2.75
1494 1572 7.148018 ACAGGGTTATATGAAGCATTTGTTCTG 60.148 37.037 0.00 0.00 0.00 3.02
1500 1578 4.524316 TGAAGCATTTGTTCTGGATTGG 57.476 40.909 0.00 0.00 0.00 3.16
1517 1595 4.038642 GGATTGGTTCCTTTTGTTGCTGTA 59.961 41.667 0.00 0.00 41.78 2.74
1525 1603 6.403866 TCCTTTTGTTGCTGTATTGTTCAT 57.596 33.333 0.00 0.00 0.00 2.57
1534 1612 7.392953 TGTTGCTGTATTGTTCATTGGATTCTA 59.607 33.333 0.00 0.00 0.00 2.10
1578 1656 7.133891 AGTTTCTGAACAACTTGAATATCCG 57.866 36.000 0.00 0.00 38.26 4.18
1624 1702 2.309613 TGGACTGGCCATGAATAATGC 58.690 47.619 5.51 0.00 43.33 3.56
1625 1703 2.091720 TGGACTGGCCATGAATAATGCT 60.092 45.455 5.51 0.00 43.33 3.79
1626 1704 3.138098 TGGACTGGCCATGAATAATGCTA 59.862 43.478 5.51 0.00 43.33 3.49
1627 1705 4.202599 TGGACTGGCCATGAATAATGCTAT 60.203 41.667 5.51 0.00 43.33 2.97
1628 1706 4.157289 GGACTGGCCATGAATAATGCTATG 59.843 45.833 5.51 0.00 34.67 2.23
1629 1707 3.508793 ACTGGCCATGAATAATGCTATGC 59.491 43.478 5.51 0.00 34.67 3.14
1630 1708 3.498334 TGGCCATGAATAATGCTATGCA 58.502 40.909 0.00 0.00 44.86 3.96
1631 1709 3.508402 TGGCCATGAATAATGCTATGCAG 59.492 43.478 0.00 0.00 43.65 4.41
1632 1710 3.760151 GGCCATGAATAATGCTATGCAGA 59.240 43.478 0.00 0.00 43.65 4.26
1633 1711 4.219070 GGCCATGAATAATGCTATGCAGAA 59.781 41.667 0.00 0.00 43.65 3.02
1634 1712 5.399858 GCCATGAATAATGCTATGCAGAAG 58.600 41.667 0.00 0.00 43.65 2.85
1635 1713 5.182570 GCCATGAATAATGCTATGCAGAAGA 59.817 40.000 0.00 0.00 43.65 2.87
1636 1714 6.623114 GCCATGAATAATGCTATGCAGAAGAG 60.623 42.308 0.00 0.00 43.65 2.85
1637 1715 6.127980 CCATGAATAATGCTATGCAGAAGAGG 60.128 42.308 0.00 0.00 43.65 3.69
1638 1716 6.178607 TGAATAATGCTATGCAGAAGAGGA 57.821 37.500 3.11 0.00 43.65 3.71
1639 1717 6.228995 TGAATAATGCTATGCAGAAGAGGAG 58.771 40.000 3.11 0.00 43.65 3.69
1640 1718 2.547299 ATGCTATGCAGAAGAGGAGC 57.453 50.000 3.11 0.00 43.65 4.70
1641 1719 1.197812 TGCTATGCAGAAGAGGAGCA 58.802 50.000 3.11 0.00 43.14 4.26
1642 1720 1.556451 TGCTATGCAGAAGAGGAGCAA 59.444 47.619 3.11 0.00 42.15 3.91
1643 1721 1.939255 GCTATGCAGAAGAGGAGCAAC 59.061 52.381 3.11 0.00 42.15 4.17
1644 1722 2.419851 GCTATGCAGAAGAGGAGCAACT 60.420 50.000 3.11 0.00 42.15 3.16
1645 1723 2.110901 ATGCAGAAGAGGAGCAACTG 57.889 50.000 0.00 0.00 42.15 3.16
1646 1724 1.051008 TGCAGAAGAGGAGCAACTGA 58.949 50.000 0.00 0.00 34.97 3.41
1647 1725 1.001746 TGCAGAAGAGGAGCAACTGAG 59.998 52.381 0.00 0.00 34.97 3.35
1648 1726 1.001860 GCAGAAGAGGAGCAACTGAGT 59.998 52.381 0.00 0.00 0.00 3.41
1649 1727 2.549778 GCAGAAGAGGAGCAACTGAGTT 60.550 50.000 0.00 0.00 0.00 3.01
1650 1728 3.737850 CAGAAGAGGAGCAACTGAGTTT 58.262 45.455 0.00 0.00 0.00 2.66
1651 1729 3.497640 CAGAAGAGGAGCAACTGAGTTTG 59.502 47.826 0.00 0.00 0.00 2.93
1652 1730 2.557920 AGAGGAGCAACTGAGTTTGG 57.442 50.000 0.00 0.00 0.00 3.28
1653 1731 1.771255 AGAGGAGCAACTGAGTTTGGT 59.229 47.619 0.00 0.00 39.89 3.67
1654 1732 2.972713 AGAGGAGCAACTGAGTTTGGTA 59.027 45.455 0.00 0.00 37.33 3.25
1655 1733 3.584848 AGAGGAGCAACTGAGTTTGGTAT 59.415 43.478 0.00 0.00 37.33 2.73
1656 1734 3.935828 GAGGAGCAACTGAGTTTGGTATC 59.064 47.826 0.00 0.00 37.33 2.24
1657 1735 3.010420 GGAGCAACTGAGTTTGGTATCC 58.990 50.000 0.00 0.00 37.33 2.59
1658 1736 3.010420 GAGCAACTGAGTTTGGTATCCC 58.990 50.000 0.00 0.00 37.33 3.85
1659 1737 2.644798 AGCAACTGAGTTTGGTATCCCT 59.355 45.455 0.00 0.00 35.45 4.20
1660 1738 3.074538 AGCAACTGAGTTTGGTATCCCTT 59.925 43.478 0.00 0.00 35.45 3.95
1661 1739 3.826729 GCAACTGAGTTTGGTATCCCTTT 59.173 43.478 0.00 0.00 0.00 3.11
1662 1740 4.280929 GCAACTGAGTTTGGTATCCCTTTT 59.719 41.667 0.00 0.00 0.00 2.27
1663 1741 5.475564 GCAACTGAGTTTGGTATCCCTTTTA 59.524 40.000 0.00 0.00 0.00 1.52
1664 1742 6.349363 GCAACTGAGTTTGGTATCCCTTTTAG 60.349 42.308 0.00 0.00 0.00 1.85
1665 1743 6.449830 ACTGAGTTTGGTATCCCTTTTAGT 57.550 37.500 0.00 0.00 0.00 2.24
1666 1744 6.849151 ACTGAGTTTGGTATCCCTTTTAGTT 58.151 36.000 0.00 0.00 0.00 2.24
1667 1745 7.295340 ACTGAGTTTGGTATCCCTTTTAGTTT 58.705 34.615 0.00 0.00 0.00 2.66
1668 1746 7.230712 ACTGAGTTTGGTATCCCTTTTAGTTTG 59.769 37.037 0.00 0.00 0.00 2.93
1669 1747 7.064229 TGAGTTTGGTATCCCTTTTAGTTTGT 58.936 34.615 0.00 0.00 0.00 2.83
1670 1748 7.229907 TGAGTTTGGTATCCCTTTTAGTTTGTC 59.770 37.037 0.00 0.00 0.00 3.18
1671 1749 7.295340 AGTTTGGTATCCCTTTTAGTTTGTCT 58.705 34.615 0.00 0.00 0.00 3.41
1672 1750 8.442374 AGTTTGGTATCCCTTTTAGTTTGTCTA 58.558 33.333 0.00 0.00 0.00 2.59
1673 1751 8.509690 GTTTGGTATCCCTTTTAGTTTGTCTAC 58.490 37.037 0.00 0.00 0.00 2.59
1674 1752 6.714278 TGGTATCCCTTTTAGTTTGTCTACC 58.286 40.000 0.00 0.00 0.00 3.18
1675 1753 6.272792 TGGTATCCCTTTTAGTTTGTCTACCA 59.727 38.462 0.00 0.00 34.17 3.25
1676 1754 6.596888 GGTATCCCTTTTAGTTTGTCTACCAC 59.403 42.308 0.00 0.00 0.00 4.16
1677 1755 5.633655 TCCCTTTTAGTTTGTCTACCACA 57.366 39.130 0.00 0.00 0.00 4.17
1678 1756 5.370679 TCCCTTTTAGTTTGTCTACCACAC 58.629 41.667 0.00 0.00 33.41 3.82
1679 1757 5.104444 TCCCTTTTAGTTTGTCTACCACACA 60.104 40.000 0.00 0.00 33.41 3.72
1680 1758 5.591067 CCCTTTTAGTTTGTCTACCACACAA 59.409 40.000 0.00 0.00 33.41 3.33
1681 1759 6.459161 CCCTTTTAGTTTGTCTACCACACAAC 60.459 42.308 0.00 0.00 33.42 3.32
1682 1760 6.094325 CCTTTTAGTTTGTCTACCACACAACA 59.906 38.462 0.00 0.00 33.42 3.33
1683 1761 6.425577 TTTAGTTTGTCTACCACACAACAC 57.574 37.500 0.00 0.00 33.42 3.32
1684 1762 3.945346 AGTTTGTCTACCACACAACACA 58.055 40.909 0.00 0.00 33.42 3.72
1685 1763 4.523083 AGTTTGTCTACCACACAACACAT 58.477 39.130 0.00 0.00 33.42 3.21
1686 1764 4.335315 AGTTTGTCTACCACACAACACATG 59.665 41.667 0.00 0.00 33.42 3.21
1687 1765 3.552132 TGTCTACCACACAACACATGT 57.448 42.857 0.00 0.00 45.34 3.21
1688 1766 3.879998 TGTCTACCACACAACACATGTT 58.120 40.909 0.00 0.00 41.46 2.71
1689 1767 3.874543 TGTCTACCACACAACACATGTTC 59.125 43.478 0.00 0.00 41.46 3.18
1690 1768 3.874543 GTCTACCACACAACACATGTTCA 59.125 43.478 0.00 0.00 41.46 3.18
1691 1769 4.024893 GTCTACCACACAACACATGTTCAG 60.025 45.833 0.00 0.00 41.46 3.02
1692 1770 2.722094 ACCACACAACACATGTTCAGT 58.278 42.857 0.00 0.00 41.46 3.41
1693 1771 3.088532 ACCACACAACACATGTTCAGTT 58.911 40.909 0.00 0.00 41.46 3.16
1694 1772 3.509575 ACCACACAACACATGTTCAGTTT 59.490 39.130 0.00 0.00 41.46 2.66
1695 1773 4.104776 CCACACAACACATGTTCAGTTTC 58.895 43.478 0.00 0.00 41.46 2.78
1696 1774 4.380339 CCACACAACACATGTTCAGTTTCA 60.380 41.667 0.00 0.00 41.46 2.69
1697 1775 5.342433 CACACAACACATGTTCAGTTTCAT 58.658 37.500 0.00 0.00 41.46 2.57
1698 1776 5.806502 CACACAACACATGTTCAGTTTCATT 59.193 36.000 0.00 0.00 41.46 2.57
1699 1777 6.310956 CACACAACACATGTTCAGTTTCATTT 59.689 34.615 0.00 0.00 41.46 2.32
1700 1778 6.873076 ACACAACACATGTTCAGTTTCATTTT 59.127 30.769 0.00 0.00 41.46 1.82
1701 1779 7.063308 ACACAACACATGTTCAGTTTCATTTTC 59.937 33.333 0.00 0.00 41.46 2.29
1702 1780 6.534793 ACAACACATGTTCAGTTTCATTTTCC 59.465 34.615 0.00 0.00 40.06 3.13
1703 1781 5.280945 ACACATGTTCAGTTTCATTTTCCG 58.719 37.500 0.00 0.00 0.00 4.30
1704 1782 5.163561 ACACATGTTCAGTTTCATTTTCCGT 60.164 36.000 0.00 0.00 0.00 4.69
1705 1783 6.038825 ACACATGTTCAGTTTCATTTTCCGTA 59.961 34.615 0.00 0.00 0.00 4.02
1706 1784 6.359617 CACATGTTCAGTTTCATTTTCCGTAC 59.640 38.462 0.00 0.00 0.00 3.67
1707 1785 6.262273 ACATGTTCAGTTTCATTTTCCGTACT 59.738 34.615 0.00 0.00 0.00 2.73
1708 1786 6.687081 TGTTCAGTTTCATTTTCCGTACTT 57.313 33.333 0.00 0.00 0.00 2.24
1709 1787 6.491394 TGTTCAGTTTCATTTTCCGTACTTG 58.509 36.000 0.00 0.00 0.00 3.16
1710 1788 5.682943 TCAGTTTCATTTTCCGTACTTGG 57.317 39.130 0.00 0.00 0.00 3.61
1711 1789 4.023536 TCAGTTTCATTTTCCGTACTTGGC 60.024 41.667 0.00 0.00 0.00 4.52
1712 1790 3.886505 AGTTTCATTTTCCGTACTTGGCA 59.113 39.130 0.00 0.00 0.00 4.92
1713 1791 4.023193 AGTTTCATTTTCCGTACTTGGCAG 60.023 41.667 0.00 0.00 0.00 4.85
1714 1792 3.134574 TCATTTTCCGTACTTGGCAGT 57.865 42.857 0.00 0.00 36.99 4.40
1715 1793 3.482436 TCATTTTCCGTACTTGGCAGTT 58.518 40.909 0.00 0.00 34.06 3.16
1716 1794 3.886505 TCATTTTCCGTACTTGGCAGTTT 59.113 39.130 0.00 0.00 34.06 2.66
1717 1795 4.339814 TCATTTTCCGTACTTGGCAGTTTT 59.660 37.500 0.00 0.00 34.06 2.43
1718 1796 4.722361 TTTTCCGTACTTGGCAGTTTTT 57.278 36.364 0.00 0.00 34.06 1.94
1719 1797 3.974871 TTCCGTACTTGGCAGTTTTTC 57.025 42.857 0.00 0.00 34.06 2.29
1720 1798 3.202829 TCCGTACTTGGCAGTTTTTCT 57.797 42.857 0.00 0.00 34.06 2.52
1721 1799 2.875933 TCCGTACTTGGCAGTTTTTCTG 59.124 45.455 0.00 0.00 46.12 3.02
1734 1812 6.639671 CAGTTTTTCTGCTGCTACTACTAG 57.360 41.667 0.00 0.00 37.36 2.57
1735 1813 5.062809 CAGTTTTTCTGCTGCTACTACTAGC 59.937 44.000 0.00 0.00 40.43 3.42
1736 1814 7.286017 CAGTTTTTCTGCTGCTACTACTAGCA 61.286 42.308 0.00 4.33 43.67 3.49
1737 1815 8.689068 CAGTTTTTCTGCTGCTACTACTAGCAA 61.689 40.741 0.00 0.00 45.73 3.91
1747 1825 6.385649 GCTACTACTAGCAAGATGTTCTCT 57.614 41.667 0.00 0.00 44.45 3.10
1748 1826 6.205784 GCTACTACTAGCAAGATGTTCTCTG 58.794 44.000 0.00 0.00 44.45 3.35
1749 1827 5.004922 ACTACTAGCAAGATGTTCTCTGC 57.995 43.478 0.00 0.00 33.29 4.26
1750 1828 3.969287 ACTAGCAAGATGTTCTCTGCA 57.031 42.857 11.48 0.00 34.92 4.41
1751 1829 4.484537 ACTAGCAAGATGTTCTCTGCAT 57.515 40.909 11.48 0.00 34.92 3.96
1752 1830 4.440880 ACTAGCAAGATGTTCTCTGCATC 58.559 43.478 11.48 0.00 42.08 3.91
1753 1831 2.641305 AGCAAGATGTTCTCTGCATCC 58.359 47.619 11.48 0.00 42.58 3.51
1754 1832 2.239150 AGCAAGATGTTCTCTGCATCCT 59.761 45.455 11.48 0.00 42.58 3.24
1755 1833 3.453717 AGCAAGATGTTCTCTGCATCCTA 59.546 43.478 11.48 0.00 42.58 2.94
1756 1834 3.559242 GCAAGATGTTCTCTGCATCCTAC 59.441 47.826 0.00 0.00 42.58 3.18
1757 1835 4.763073 CAAGATGTTCTCTGCATCCTACA 58.237 43.478 0.00 0.00 42.58 2.74
1758 1836 5.366460 CAAGATGTTCTCTGCATCCTACAT 58.634 41.667 4.85 4.85 42.58 2.29
1759 1837 6.519382 CAAGATGTTCTCTGCATCCTACATA 58.481 40.000 0.00 0.00 42.58 2.29
1760 1838 6.931790 AGATGTTCTCTGCATCCTACATAT 57.068 37.500 0.00 0.00 42.58 1.78
1761 1839 6.934056 AGATGTTCTCTGCATCCTACATATC 58.066 40.000 0.00 0.00 42.58 1.63
1762 1840 6.496218 AGATGTTCTCTGCATCCTACATATCA 59.504 38.462 0.00 0.00 42.58 2.15
1763 1841 6.484364 TGTTCTCTGCATCCTACATATCAA 57.516 37.500 0.00 0.00 0.00 2.57
1764 1842 6.888105 TGTTCTCTGCATCCTACATATCAAA 58.112 36.000 0.00 0.00 0.00 2.69
1765 1843 6.988580 TGTTCTCTGCATCCTACATATCAAAG 59.011 38.462 0.00 0.00 0.00 2.77
1766 1844 6.737720 TCTCTGCATCCTACATATCAAAGT 57.262 37.500 0.00 0.00 0.00 2.66
1767 1845 7.129457 TCTCTGCATCCTACATATCAAAGTT 57.871 36.000 0.00 0.00 0.00 2.66
1768 1846 7.212976 TCTCTGCATCCTACATATCAAAGTTC 58.787 38.462 0.00 0.00 0.00 3.01
1769 1847 6.888105 TCTGCATCCTACATATCAAAGTTCA 58.112 36.000 0.00 0.00 0.00 3.18
1770 1848 6.763135 TCTGCATCCTACATATCAAAGTTCAC 59.237 38.462 0.00 0.00 0.00 3.18
1771 1849 6.653020 TGCATCCTACATATCAAAGTTCACT 58.347 36.000 0.00 0.00 0.00 3.41
1772 1850 6.763135 TGCATCCTACATATCAAAGTTCACTC 59.237 38.462 0.00 0.00 0.00 3.51
1773 1851 6.989169 GCATCCTACATATCAAAGTTCACTCT 59.011 38.462 0.00 0.00 0.00 3.24
1774 1852 7.497249 GCATCCTACATATCAAAGTTCACTCTT 59.503 37.037 0.00 0.00 0.00 2.85
1775 1853 9.388506 CATCCTACATATCAAAGTTCACTCTTT 57.611 33.333 0.00 0.00 38.04 2.52
1776 1854 9.606631 ATCCTACATATCAAAGTTCACTCTTTC 57.393 33.333 0.00 0.00 35.77 2.62
1777 1855 8.593679 TCCTACATATCAAAGTTCACTCTTTCA 58.406 33.333 0.00 0.00 35.77 2.69
1778 1856 9.388506 CCTACATATCAAAGTTCACTCTTTCAT 57.611 33.333 0.00 0.00 35.77 2.57
1781 1859 9.512588 ACATATCAAAGTTCACTCTTTCATTCT 57.487 29.630 0.00 0.00 35.77 2.40
1782 1860 9.985318 CATATCAAAGTTCACTCTTTCATTCTC 57.015 33.333 0.00 0.00 35.77 2.87
1783 1861 6.530913 TCAAAGTTCACTCTTTCATTCTCG 57.469 37.500 0.00 0.00 35.77 4.04
1784 1862 6.280643 TCAAAGTTCACTCTTTCATTCTCGA 58.719 36.000 0.00 0.00 35.77 4.04
1785 1863 6.761242 TCAAAGTTCACTCTTTCATTCTCGAA 59.239 34.615 0.00 0.00 35.77 3.71
1786 1864 7.279981 TCAAAGTTCACTCTTTCATTCTCGAAA 59.720 33.333 0.00 0.00 35.77 3.46
1800 1878 3.528009 CTCGAAAGGAGAAGTTTGTGC 57.472 47.619 0.00 0.00 46.23 4.57
1801 1879 3.134458 CTCGAAAGGAGAAGTTTGTGCT 58.866 45.455 0.00 0.00 46.23 4.40
1802 1880 3.541632 TCGAAAGGAGAAGTTTGTGCTT 58.458 40.909 0.00 0.00 33.66 3.91
1803 1881 3.945285 TCGAAAGGAGAAGTTTGTGCTTT 59.055 39.130 7.96 7.96 43.01 3.51
1804 1882 4.398044 TCGAAAGGAGAAGTTTGTGCTTTT 59.602 37.500 9.28 0.00 41.03 2.27
1805 1883 4.500477 CGAAAGGAGAAGTTTGTGCTTTTG 59.500 41.667 9.28 8.73 41.03 2.44
1806 1884 5.650543 GAAAGGAGAAGTTTGTGCTTTTGA 58.349 37.500 9.28 0.00 41.03 2.69
1807 1885 5.859205 AAGGAGAAGTTTGTGCTTTTGAT 57.141 34.783 0.00 0.00 27.79 2.57
1824 1902 7.934665 TGCTTTTGATACTGTCTTTTACCAGTA 59.065 33.333 2.36 2.36 45.40 2.74
1825 1903 8.228464 GCTTTTGATACTGTCTTTTACCAGTAC 58.772 37.037 1.94 0.00 44.46 2.73
1827 1905 5.957798 TGATACTGTCTTTTACCAGTACGG 58.042 41.667 1.94 2.71 44.46 4.02
1828 1906 3.036075 ACTGTCTTTTACCAGTACGGC 57.964 47.619 4.00 0.00 40.03 5.68
1829 1907 2.366266 ACTGTCTTTTACCAGTACGGCA 59.634 45.455 4.00 0.00 40.03 5.69
1837 1915 1.975660 ACCAGTACGGCACAATTTGT 58.024 45.000 0.00 0.00 39.03 2.83
1894 2328 5.312079 CATTCATCTATGGACTTCCTTCCC 58.688 45.833 0.00 0.00 34.33 3.97
1911 2345 5.659971 TCCTTCCCGTCTAACTAAAATAGCT 59.340 40.000 0.00 0.00 0.00 3.32
1997 2431 1.873591 GACATGCCTGAGAACACGTTT 59.126 47.619 0.00 0.00 0.00 3.60
2394 2828 0.976073 GAGGAACTGGGGGATCGTGA 60.976 60.000 0.00 0.00 41.55 4.35
2528 2962 8.442632 TCTTTGTGAGAATGATACCATGAATC 57.557 34.615 0.00 0.00 32.36 2.52
2536 2970 2.158914 TGATACCATGAATCGTGCTGCT 60.159 45.455 0.00 0.00 0.00 4.24
2598 3032 6.482308 GGATGTTGCTTCGTAAGGTAATATGT 59.518 38.462 0.00 0.00 38.47 2.29
2712 3310 4.298103 ACACTTCTGATGGCTGAATCTT 57.702 40.909 0.00 0.00 32.53 2.40
2720 3318 2.189594 TGGCTGAATCTTGGTGTCAG 57.810 50.000 0.00 0.00 41.44 3.51
2726 3324 5.525378 GGCTGAATCTTGGTGTCAGTATAAG 59.475 44.000 0.00 0.00 40.76 1.73
2790 3388 7.106439 TGAAGCAAGGAGAAAAATGTTGTTA 57.894 32.000 0.00 0.00 0.00 2.41
2941 3540 3.281727 ACAACCTTGCTCAAACTCAGA 57.718 42.857 0.00 0.00 0.00 3.27
2947 3546 0.035317 TGCTCAAACTCAGATGGCGT 59.965 50.000 0.00 0.00 0.00 5.68
2949 3548 1.941209 GCTCAAACTCAGATGGCGTGA 60.941 52.381 0.00 0.00 0.00 4.35
3106 3705 5.108187 ACACATCAGAATATGGACAGCTT 57.892 39.130 0.00 0.00 0.00 3.74
3115 3714 7.016957 TCAGAATATGGACAGCTTAATGAGGAT 59.983 37.037 0.00 0.00 0.00 3.24
3129 3731 3.552132 TGAGGATTAACTTATGCGGCA 57.448 42.857 4.58 4.58 0.00 5.69
3171 3773 0.595310 GCATTCTAGACTCGCCCGAC 60.595 60.000 0.00 0.00 0.00 4.79
3564 4166 9.112725 CAAACATGTAAGATGGATGACAGATAA 57.887 33.333 0.00 0.00 0.00 1.75
3669 4271 3.005554 CACAATCTTCACAAGGCGATCT 58.994 45.455 0.00 0.00 0.00 2.75
3697 4299 6.741992 ATCTGTCAAAGCGTGAATAATCAA 57.258 33.333 0.00 0.00 38.23 2.57
3730 4332 2.108601 ACCAGGAACGGAATGGGTTAAA 59.891 45.455 0.00 0.00 38.48 1.52
3750 4352 7.601130 GGTTAAAAGGTGTCTTTGTCAGTTTTT 59.399 33.333 0.00 0.00 41.92 1.94
3769 4371 5.882076 TTTTTAAGGGGGTGGTAGGTAAT 57.118 39.130 0.00 0.00 0.00 1.89
3770 4372 6.984355 TTTTTAAGGGGGTGGTAGGTAATA 57.016 37.500 0.00 0.00 0.00 0.98
3771 4373 5.974156 TTTAAGGGGGTGGTAGGTAATAC 57.026 43.478 0.00 0.00 0.00 1.89
3772 4374 3.809219 AAGGGGGTGGTAGGTAATACT 57.191 47.619 0.00 0.00 34.56 2.12
3773 4375 3.809219 AGGGGGTGGTAGGTAATACTT 57.191 47.619 0.00 0.00 34.56 2.24
3807 4409 7.359595 TGTTGGTGAATTATGACGAAAGAAAG 58.640 34.615 0.00 0.00 0.00 2.62
3821 4423 4.738252 CGAAAGAAAGTGGTTTTGTAAGGC 59.262 41.667 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
370 371 6.732154 TCTTATACTGTACTTACATGGCGAC 58.268 40.000 0.00 0.00 35.36 5.19
372 373 7.368059 TCATCTTATACTGTACTTACATGGCG 58.632 38.462 0.00 0.00 35.36 5.69
373 374 9.144747 CATCATCTTATACTGTACTTACATGGC 57.855 37.037 0.00 0.00 35.36 4.40
374 375 9.645059 CCATCATCTTATACTGTACTTACATGG 57.355 37.037 0.00 0.00 35.36 3.66
391 392 1.281867 TCCAAGCCGTTCCATCATCTT 59.718 47.619 0.00 0.00 0.00 2.40
419 420 7.611467 CCTATATGTATTTATTTGCCAGCCTCA 59.389 37.037 0.00 0.00 0.00 3.86
459 468 0.318699 TCGACTCGACCTGTGCAAAG 60.319 55.000 0.00 0.00 0.00 2.77
606 620 3.392595 GATTCGCCGGAGTCGTCGT 62.393 63.158 5.05 0.00 38.92 4.34
652 666 1.220749 CCTTGCGGGAAATCTCGGA 59.779 57.895 4.68 0.00 37.23 4.55
657 671 1.947456 GTGGATACCTTGCGGGAAATC 59.053 52.381 2.42 5.21 38.76 2.17
687 701 1.556911 GGAGCCAAGAGGAATGTGAGA 59.443 52.381 0.00 0.00 36.89 3.27
688 702 1.407989 GGGAGCCAAGAGGAATGTGAG 60.408 57.143 0.00 0.00 36.89 3.51
689 703 0.620556 GGGAGCCAAGAGGAATGTGA 59.379 55.000 0.00 0.00 36.89 3.58
736 750 0.455815 TCATCACACTCGACATCCCG 59.544 55.000 0.00 0.00 0.00 5.14
867 913 2.740826 CGTGATCCCAAACGCCGT 60.741 61.111 0.00 0.00 32.40 5.68
915 961 4.034858 CAGCCACATAGTTAAGCAGTGATG 59.965 45.833 0.00 0.00 32.14 3.07
1040 1106 1.891919 GAACCGACTGCAACAGCCA 60.892 57.895 0.00 0.00 34.37 4.75
1193 1268 5.304871 ACCCGATTAAGATAAGAGAAGGGAC 59.695 44.000 0.00 0.00 38.49 4.46
1200 1275 4.747108 CAGCACACCCGATTAAGATAAGAG 59.253 45.833 0.00 0.00 0.00 2.85
1201 1276 4.161565 ACAGCACACCCGATTAAGATAAGA 59.838 41.667 0.00 0.00 0.00 2.10
1202 1277 4.442706 ACAGCACACCCGATTAAGATAAG 58.557 43.478 0.00 0.00 0.00 1.73
1203 1278 4.481368 ACAGCACACCCGATTAAGATAA 57.519 40.909 0.00 0.00 0.00 1.75
1204 1279 4.481368 AACAGCACACCCGATTAAGATA 57.519 40.909 0.00 0.00 0.00 1.98
1208 1283 3.945346 ACATAACAGCACACCCGATTAA 58.055 40.909 0.00 0.00 0.00 1.40
1247 1322 5.934781 AGGCTCTAAAATGATGGTCTAAGG 58.065 41.667 0.00 0.00 0.00 2.69
1304 1382 5.512788 GTGTTTCAATAATCGAGCAACCATG 59.487 40.000 0.00 0.00 0.00 3.66
1398 1476 9.758651 AAACAACATAAACAGGGAAAAATAGAC 57.241 29.630 0.00 0.00 0.00 2.59
1400 1478 9.541143 ACAAACAACATAAACAGGGAAAAATAG 57.459 29.630 0.00 0.00 0.00 1.73
1402 1480 8.800370 AACAAACAACATAAACAGGGAAAAAT 57.200 26.923 0.00 0.00 0.00 1.82
1420 1498 8.877864 ATTATGTCCTATCTCCAAAACAAACA 57.122 30.769 0.00 0.00 0.00 2.83
1456 1534 8.902540 TCATATAACCCTGTGTTCATATTCAC 57.097 34.615 0.00 0.00 38.42 3.18
1500 1578 6.039616 TGAACAATACAGCAACAAAAGGAAC 58.960 36.000 0.00 0.00 0.00 3.62
1555 1633 6.899114 ACGGATATTCAAGTTGTTCAGAAAC 58.101 36.000 2.11 0.00 35.85 2.78
1578 1656 6.599638 AGTTGCCTCAGAGGATTAATAACAAC 59.400 38.462 21.89 19.42 37.67 3.32
1588 1666 1.280421 GTCCAAGTTGCCTCAGAGGAT 59.720 52.381 21.89 0.00 37.67 3.24
1590 1668 0.689623 AGTCCAAGTTGCCTCAGAGG 59.310 55.000 12.81 12.81 38.80 3.69
1591 1669 1.610102 CCAGTCCAAGTTGCCTCAGAG 60.610 57.143 0.00 0.00 0.00 3.35
1605 1683 2.590821 AGCATTATTCATGGCCAGTCC 58.409 47.619 13.05 0.00 32.81 3.85
1606 1684 4.380233 GCATAGCATTATTCATGGCCAGTC 60.380 45.833 13.05 0.00 32.81 3.51
1607 1685 3.508793 GCATAGCATTATTCATGGCCAGT 59.491 43.478 13.05 0.00 32.81 4.00
1608 1686 3.508402 TGCATAGCATTATTCATGGCCAG 59.492 43.478 13.05 3.43 31.71 4.85
1609 1687 3.498334 TGCATAGCATTATTCATGGCCA 58.502 40.909 8.56 8.56 31.71 5.36
1610 1688 3.760151 TCTGCATAGCATTATTCATGGCC 59.240 43.478 0.00 0.00 38.13 5.36
1611 1689 5.182570 TCTTCTGCATAGCATTATTCATGGC 59.817 40.000 0.00 0.00 38.13 4.40
1612 1690 6.127980 CCTCTTCTGCATAGCATTATTCATGG 60.128 42.308 0.00 0.00 38.13 3.66
1613 1691 6.653740 TCCTCTTCTGCATAGCATTATTCATG 59.346 38.462 0.00 0.00 38.13 3.07
1614 1692 6.776744 TCCTCTTCTGCATAGCATTATTCAT 58.223 36.000 0.00 0.00 38.13 2.57
1615 1693 6.178607 TCCTCTTCTGCATAGCATTATTCA 57.821 37.500 0.00 0.00 38.13 2.57
1616 1694 5.122082 GCTCCTCTTCTGCATAGCATTATTC 59.878 44.000 0.00 0.00 38.13 1.75
1617 1695 5.002516 GCTCCTCTTCTGCATAGCATTATT 58.997 41.667 0.00 0.00 38.13 1.40
1618 1696 4.041321 TGCTCCTCTTCTGCATAGCATTAT 59.959 41.667 0.00 0.00 38.13 1.28
1619 1697 3.389002 TGCTCCTCTTCTGCATAGCATTA 59.611 43.478 0.00 0.00 38.13 1.90
1620 1698 2.172082 TGCTCCTCTTCTGCATAGCATT 59.828 45.455 0.00 0.00 38.13 3.56
1621 1699 1.767088 TGCTCCTCTTCTGCATAGCAT 59.233 47.619 0.00 0.00 38.13 3.79
1622 1700 1.197812 TGCTCCTCTTCTGCATAGCA 58.802 50.000 0.00 0.00 37.62 3.49
1623 1701 1.939255 GTTGCTCCTCTTCTGCATAGC 59.061 52.381 0.00 0.00 36.55 2.97
1624 1702 3.118847 TCAGTTGCTCCTCTTCTGCATAG 60.119 47.826 0.00 0.00 36.55 2.23
1625 1703 2.833943 TCAGTTGCTCCTCTTCTGCATA 59.166 45.455 0.00 0.00 36.55 3.14
1626 1704 1.627329 TCAGTTGCTCCTCTTCTGCAT 59.373 47.619 0.00 0.00 36.55 3.96
1627 1705 1.001746 CTCAGTTGCTCCTCTTCTGCA 59.998 52.381 0.00 0.00 34.69 4.41
1628 1706 1.001860 ACTCAGTTGCTCCTCTTCTGC 59.998 52.381 0.00 0.00 0.00 4.26
1629 1707 3.399440 AACTCAGTTGCTCCTCTTCTG 57.601 47.619 0.00 0.00 0.00 3.02
1630 1708 3.495806 CCAAACTCAGTTGCTCCTCTTCT 60.496 47.826 0.00 0.00 0.00 2.85
1631 1709 2.810852 CCAAACTCAGTTGCTCCTCTTC 59.189 50.000 0.00 0.00 0.00 2.87
1632 1710 2.173569 ACCAAACTCAGTTGCTCCTCTT 59.826 45.455 0.00 0.00 0.00 2.85
1633 1711 1.771255 ACCAAACTCAGTTGCTCCTCT 59.229 47.619 0.00 0.00 0.00 3.69
1634 1712 2.262423 ACCAAACTCAGTTGCTCCTC 57.738 50.000 0.00 0.00 0.00 3.71
1635 1713 3.307762 GGATACCAAACTCAGTTGCTCCT 60.308 47.826 0.00 0.00 0.00 3.69
1636 1714 3.010420 GGATACCAAACTCAGTTGCTCC 58.990 50.000 0.00 0.00 0.00 4.70
1647 1725 8.509690 GTAGACAAACTAAAAGGGATACCAAAC 58.490 37.037 0.00 0.00 46.52 2.93
1648 1726 7.666804 GGTAGACAAACTAAAAGGGATACCAAA 59.333 37.037 0.00 0.00 46.52 3.28
1649 1727 7.170277 GGTAGACAAACTAAAAGGGATACCAA 58.830 38.462 0.00 0.00 46.52 3.67
1650 1728 6.272792 TGGTAGACAAACTAAAAGGGATACCA 59.727 38.462 0.00 0.00 46.52 3.25
1651 1729 6.596888 GTGGTAGACAAACTAAAAGGGATACC 59.403 42.308 0.00 0.00 45.24 2.73
1652 1730 7.118825 GTGTGGTAGACAAACTAAAAGGGATAC 59.881 40.741 0.00 0.00 35.91 2.24
1653 1731 7.163441 GTGTGGTAGACAAACTAAAAGGGATA 58.837 38.462 0.00 0.00 35.91 2.59
1654 1732 6.002082 GTGTGGTAGACAAACTAAAAGGGAT 58.998 40.000 0.00 0.00 35.91 3.85
1655 1733 5.104444 TGTGTGGTAGACAAACTAAAAGGGA 60.104 40.000 0.00 0.00 38.20 4.20
1656 1734 5.127491 TGTGTGGTAGACAAACTAAAAGGG 58.873 41.667 0.00 0.00 38.20 3.95
1657 1735 6.094325 TGTTGTGTGGTAGACAAACTAAAAGG 59.906 38.462 0.00 0.00 38.20 3.11
1658 1736 6.964934 GTGTTGTGTGGTAGACAAACTAAAAG 59.035 38.462 0.00 0.00 38.20 2.27
1659 1737 6.430308 TGTGTTGTGTGGTAGACAAACTAAAA 59.570 34.615 0.00 0.00 38.20 1.52
1660 1738 5.938710 TGTGTTGTGTGGTAGACAAACTAAA 59.061 36.000 0.00 0.00 38.20 1.85
1661 1739 5.489249 TGTGTTGTGTGGTAGACAAACTAA 58.511 37.500 0.00 0.00 38.20 2.24
1662 1740 5.087391 TGTGTTGTGTGGTAGACAAACTA 57.913 39.130 0.00 0.00 38.20 2.24
1663 1741 3.945346 TGTGTTGTGTGGTAGACAAACT 58.055 40.909 0.00 0.00 38.20 2.66
1664 1742 4.095782 ACATGTGTTGTGTGGTAGACAAAC 59.904 41.667 0.00 0.00 37.11 2.93
1665 1743 4.265893 ACATGTGTTGTGTGGTAGACAAA 58.734 39.130 0.00 0.00 37.11 2.83
1666 1744 3.879998 ACATGTGTTGTGTGGTAGACAA 58.120 40.909 0.00 0.00 37.11 3.18
1667 1745 3.552132 ACATGTGTTGTGTGGTAGACA 57.448 42.857 0.00 0.00 37.11 3.41
1668 1746 3.874543 TGAACATGTGTTGTGTGGTAGAC 59.125 43.478 0.00 0.00 38.99 2.59
1669 1747 4.126437 CTGAACATGTGTTGTGTGGTAGA 58.874 43.478 0.00 0.00 38.99 2.59
1670 1748 3.876914 ACTGAACATGTGTTGTGTGGTAG 59.123 43.478 0.00 0.00 38.99 3.18
1671 1749 3.879998 ACTGAACATGTGTTGTGTGGTA 58.120 40.909 0.00 0.00 38.99 3.25
1672 1750 2.722094 ACTGAACATGTGTTGTGTGGT 58.278 42.857 0.00 0.00 38.99 4.16
1673 1751 3.781079 AACTGAACATGTGTTGTGTGG 57.219 42.857 0.00 0.00 38.99 4.17
1674 1752 4.731720 TGAAACTGAACATGTGTTGTGTG 58.268 39.130 0.00 0.00 38.99 3.82
1675 1753 5.581126 ATGAAACTGAACATGTGTTGTGT 57.419 34.783 0.00 0.00 38.99 3.72
1676 1754 6.890663 AAATGAAACTGAACATGTGTTGTG 57.109 33.333 0.00 0.00 38.99 3.33
1677 1755 6.534793 GGAAAATGAAACTGAACATGTGTTGT 59.465 34.615 0.00 0.00 41.53 3.32
1678 1756 6.291743 CGGAAAATGAAACTGAACATGTGTTG 60.292 38.462 0.00 0.00 38.56 3.33
1679 1757 5.748152 CGGAAAATGAAACTGAACATGTGTT 59.252 36.000 0.00 0.00 41.64 3.32
1680 1758 5.163561 ACGGAAAATGAAACTGAACATGTGT 60.164 36.000 0.00 0.00 0.00 3.72
1681 1759 5.280945 ACGGAAAATGAAACTGAACATGTG 58.719 37.500 0.00 0.00 0.00 3.21
1682 1760 5.514274 ACGGAAAATGAAACTGAACATGT 57.486 34.783 0.00 0.00 0.00 3.21
1683 1761 6.668323 AGTACGGAAAATGAAACTGAACATG 58.332 36.000 0.00 0.00 0.00 3.21
1684 1762 6.877611 AGTACGGAAAATGAAACTGAACAT 57.122 33.333 0.00 0.00 0.00 2.71
1685 1763 6.459024 CCAAGTACGGAAAATGAAACTGAACA 60.459 38.462 0.00 0.00 0.00 3.18
1686 1764 5.912955 CCAAGTACGGAAAATGAAACTGAAC 59.087 40.000 0.00 0.00 0.00 3.18
1687 1765 5.506649 GCCAAGTACGGAAAATGAAACTGAA 60.507 40.000 0.00 0.00 0.00 3.02
1688 1766 4.023536 GCCAAGTACGGAAAATGAAACTGA 60.024 41.667 0.00 0.00 0.00 3.41
1689 1767 4.226761 GCCAAGTACGGAAAATGAAACTG 58.773 43.478 0.00 0.00 0.00 3.16
1690 1768 3.886505 TGCCAAGTACGGAAAATGAAACT 59.113 39.130 0.00 0.00 0.00 2.66
1691 1769 4.226761 CTGCCAAGTACGGAAAATGAAAC 58.773 43.478 0.00 0.00 0.00 2.78
1692 1770 3.886505 ACTGCCAAGTACGGAAAATGAAA 59.113 39.130 0.00 0.00 33.79 2.69
1693 1771 3.482436 ACTGCCAAGTACGGAAAATGAA 58.518 40.909 0.00 0.00 33.79 2.57
1694 1772 3.134574 ACTGCCAAGTACGGAAAATGA 57.865 42.857 0.00 0.00 33.79 2.57
1695 1773 3.915437 AACTGCCAAGTACGGAAAATG 57.085 42.857 0.00 0.00 34.77 2.32
1696 1774 4.929819 AAAACTGCCAAGTACGGAAAAT 57.070 36.364 0.00 0.00 34.77 1.82
1697 1775 4.399934 AGAAAAACTGCCAAGTACGGAAAA 59.600 37.500 0.00 0.00 34.77 2.29
1698 1776 3.949113 AGAAAAACTGCCAAGTACGGAAA 59.051 39.130 0.00 0.00 34.77 3.13
1699 1777 3.314080 CAGAAAAACTGCCAAGTACGGAA 59.686 43.478 0.00 0.00 39.86 4.30
1700 1778 2.875933 CAGAAAAACTGCCAAGTACGGA 59.124 45.455 0.00 0.00 39.86 4.69
1701 1779 3.268013 CAGAAAAACTGCCAAGTACGG 57.732 47.619 0.00 0.00 39.86 4.02
1724 1802 6.205784 CAGAGAACATCTTGCTAGTAGTAGC 58.794 44.000 20.71 20.71 43.72 3.58
1725 1803 6.183360 TGCAGAGAACATCTTGCTAGTAGTAG 60.183 42.308 0.00 0.00 35.47 2.57
1726 1804 5.652452 TGCAGAGAACATCTTGCTAGTAGTA 59.348 40.000 0.00 0.00 35.47 1.82
1727 1805 4.464244 TGCAGAGAACATCTTGCTAGTAGT 59.536 41.667 0.00 0.00 35.47 2.73
1728 1806 5.003692 TGCAGAGAACATCTTGCTAGTAG 57.996 43.478 12.38 0.00 35.47 2.57
1729 1807 5.452496 GGATGCAGAGAACATCTTGCTAGTA 60.452 44.000 0.00 0.00 42.88 1.82
1730 1808 3.969287 TGCAGAGAACATCTTGCTAGT 57.031 42.857 12.38 0.00 35.47 2.57
1731 1809 3.808726 GGATGCAGAGAACATCTTGCTAG 59.191 47.826 0.00 0.00 42.88 3.42
1732 1810 3.453717 AGGATGCAGAGAACATCTTGCTA 59.546 43.478 0.00 0.00 42.88 3.49
1733 1811 2.239150 AGGATGCAGAGAACATCTTGCT 59.761 45.455 0.00 0.00 42.88 3.91
1734 1812 2.641305 AGGATGCAGAGAACATCTTGC 58.359 47.619 0.00 7.25 42.88 4.01
1735 1813 4.763073 TGTAGGATGCAGAGAACATCTTG 58.237 43.478 0.00 0.00 42.88 3.02
1736 1814 5.627182 ATGTAGGATGCAGAGAACATCTT 57.373 39.130 0.00 0.00 42.88 2.40
1737 1815 6.496218 TGATATGTAGGATGCAGAGAACATCT 59.504 38.462 9.89 2.81 42.88 2.90
1738 1816 6.695429 TGATATGTAGGATGCAGAGAACATC 58.305 40.000 9.89 0.00 42.62 3.06
1739 1817 6.676990 TGATATGTAGGATGCAGAGAACAT 57.323 37.500 10.99 10.99 31.11 2.71
1740 1818 6.484364 TTGATATGTAGGATGCAGAGAACA 57.516 37.500 0.00 0.00 31.11 3.18
1741 1819 6.989169 ACTTTGATATGTAGGATGCAGAGAAC 59.011 38.462 0.00 0.00 31.11 3.01
1742 1820 7.129457 ACTTTGATATGTAGGATGCAGAGAA 57.871 36.000 0.00 0.00 31.11 2.87
1743 1821 6.737720 ACTTTGATATGTAGGATGCAGAGA 57.262 37.500 0.00 0.00 31.11 3.10
1744 1822 6.988580 TGAACTTTGATATGTAGGATGCAGAG 59.011 38.462 0.00 0.00 31.11 3.35
1745 1823 6.763135 GTGAACTTTGATATGTAGGATGCAGA 59.237 38.462 0.00 0.00 31.11 4.26
1746 1824 6.765036 AGTGAACTTTGATATGTAGGATGCAG 59.235 38.462 0.00 0.00 31.11 4.41
1747 1825 6.653020 AGTGAACTTTGATATGTAGGATGCA 58.347 36.000 0.00 0.00 33.12 3.96
1748 1826 6.989169 AGAGTGAACTTTGATATGTAGGATGC 59.011 38.462 0.00 0.00 0.00 3.91
1749 1827 8.954950 AAGAGTGAACTTTGATATGTAGGATG 57.045 34.615 0.00 0.00 0.00 3.51
1750 1828 9.606631 GAAAGAGTGAACTTTGATATGTAGGAT 57.393 33.333 0.00 0.00 39.71 3.24
1751 1829 8.593679 TGAAAGAGTGAACTTTGATATGTAGGA 58.406 33.333 0.00 0.00 39.71 2.94
1752 1830 8.777865 TGAAAGAGTGAACTTTGATATGTAGG 57.222 34.615 0.00 0.00 39.71 3.18
1755 1833 9.512588 AGAATGAAAGAGTGAACTTTGATATGT 57.487 29.630 0.00 0.00 39.71 2.29
1756 1834 9.985318 GAGAATGAAAGAGTGAACTTTGATATG 57.015 33.333 0.00 0.00 39.71 1.78
1757 1835 8.877779 CGAGAATGAAAGAGTGAACTTTGATAT 58.122 33.333 0.00 0.00 39.71 1.63
1758 1836 8.088365 TCGAGAATGAAAGAGTGAACTTTGATA 58.912 33.333 0.00 0.00 39.71 2.15
1759 1837 6.931281 TCGAGAATGAAAGAGTGAACTTTGAT 59.069 34.615 0.00 0.00 39.71 2.57
1760 1838 6.280643 TCGAGAATGAAAGAGTGAACTTTGA 58.719 36.000 0.00 0.00 39.71 2.69
1761 1839 6.530913 TCGAGAATGAAAGAGTGAACTTTG 57.469 37.500 0.00 0.00 39.71 2.77
1762 1840 7.553881 TTTCGAGAATGAAAGAGTGAACTTT 57.446 32.000 0.00 0.00 41.86 2.66
1779 1857 3.131396 GCACAAACTTCTCCTTTCGAGA 58.869 45.455 0.00 0.00 46.29 4.04
1780 1858 3.134458 AGCACAAACTTCTCCTTTCGAG 58.866 45.455 0.00 0.00 40.30 4.04
1781 1859 3.194005 AGCACAAACTTCTCCTTTCGA 57.806 42.857 0.00 0.00 0.00 3.71
1782 1860 3.971032 AAGCACAAACTTCTCCTTTCG 57.029 42.857 0.00 0.00 0.00 3.46
1783 1861 5.650543 TCAAAAGCACAAACTTCTCCTTTC 58.349 37.500 0.00 0.00 0.00 2.62
1784 1862 5.659440 TCAAAAGCACAAACTTCTCCTTT 57.341 34.783 0.00 0.00 0.00 3.11
1785 1863 5.859205 ATCAAAAGCACAAACTTCTCCTT 57.141 34.783 0.00 0.00 0.00 3.36
1786 1864 6.016777 CAGTATCAAAAGCACAAACTTCTCCT 60.017 38.462 0.00 0.00 0.00 3.69
1787 1865 6.145535 CAGTATCAAAAGCACAAACTTCTCC 58.854 40.000 0.00 0.00 0.00 3.71
1788 1866 6.729187 ACAGTATCAAAAGCACAAACTTCTC 58.271 36.000 0.00 0.00 0.00 2.87
1789 1867 6.543831 AGACAGTATCAAAAGCACAAACTTCT 59.456 34.615 0.00 0.00 0.00 2.85
1790 1868 6.729187 AGACAGTATCAAAAGCACAAACTTC 58.271 36.000 0.00 0.00 0.00 3.01
1791 1869 6.699575 AGACAGTATCAAAAGCACAAACTT 57.300 33.333 0.00 0.00 0.00 2.66
1792 1870 6.699575 AAGACAGTATCAAAAGCACAAACT 57.300 33.333 0.00 0.00 0.00 2.66
1793 1871 7.755582 AAAAGACAGTATCAAAAGCACAAAC 57.244 32.000 0.00 0.00 0.00 2.93
1794 1872 7.918562 GGTAAAAGACAGTATCAAAAGCACAAA 59.081 33.333 0.00 0.00 0.00 2.83
1795 1873 7.067615 TGGTAAAAGACAGTATCAAAAGCACAA 59.932 33.333 0.00 0.00 0.00 3.33
1796 1874 6.544197 TGGTAAAAGACAGTATCAAAAGCACA 59.456 34.615 0.00 0.00 0.00 4.57
1797 1875 6.966021 TGGTAAAAGACAGTATCAAAAGCAC 58.034 36.000 0.00 0.00 0.00 4.40
1798 1876 6.770785 ACTGGTAAAAGACAGTATCAAAAGCA 59.229 34.615 0.00 0.00 45.45 3.91
1799 1877 7.203255 ACTGGTAAAAGACAGTATCAAAAGC 57.797 36.000 0.00 0.00 45.45 3.51
1807 1885 3.573538 TGCCGTACTGGTAAAAGACAGTA 59.426 43.478 0.00 0.00 45.45 2.74
1829 1907 6.867816 CAGTTTGCCATGTATACACAAATTGT 59.132 34.615 21.91 0.00 42.84 2.71
1837 1915 7.334858 TGTATCTTCAGTTTGCCATGTATACA 58.665 34.615 8.27 8.27 0.00 2.29
1838 1916 7.495934 ACTGTATCTTCAGTTTGCCATGTATAC 59.504 37.037 0.00 0.00 44.92 1.47
1875 2309 2.700897 ACGGGAAGGAAGTCCATAGATG 59.299 50.000 0.00 0.00 39.70 2.90
1876 2310 2.966516 GACGGGAAGGAAGTCCATAGAT 59.033 50.000 0.00 0.00 39.70 1.98
1880 2314 2.500504 GTTAGACGGGAAGGAAGTCCAT 59.499 50.000 0.00 0.00 39.70 3.41
1889 2323 6.817140 ACAAGCTATTTTAGTTAGACGGGAAG 59.183 38.462 0.00 0.00 0.00 3.46
1894 2328 7.829378 AGGAACAAGCTATTTTAGTTAGACG 57.171 36.000 0.00 0.00 0.00 4.18
1997 2431 1.222661 CTGAGCATAGGCAGCACCA 59.777 57.895 0.67 0.00 44.61 4.17
2394 2828 2.597340 CTTGGGATCCGGGCATGT 59.403 61.111 5.45 0.00 0.00 3.21
2528 2962 4.093408 ACTTGTTAACATATCAGCAGCACG 59.907 41.667 9.56 0.00 0.00 5.34
2567 3001 2.254546 ACGAAGCAACATCCAACAGA 57.745 45.000 0.00 0.00 0.00 3.41
2686 3284 7.743749 AGATTCAGCCATCAGAAGTGTAATAT 58.256 34.615 0.00 0.00 0.00 1.28
2712 3310 4.030216 TCAGCCATCTTATACTGACACCA 58.970 43.478 0.00 0.00 34.35 4.17
2720 3318 8.526978 TGTATCTGAGATTCAGCCATCTTATAC 58.473 37.037 0.00 3.89 43.95 1.47
2726 3324 4.202295 TGGTGTATCTGAGATTCAGCCATC 60.202 45.833 22.55 4.09 43.95 3.51
2770 3368 7.532682 TTGTTAACAACATTTTTCTCCTTGC 57.467 32.000 17.01 0.00 41.79 4.01
2813 3411 7.475771 TGAGCAATTTTATTTTTGGTGTGAC 57.524 32.000 0.00 0.00 33.99 3.67
2941 3540 5.446143 TTTCTGTAAATTTGTCACGCCAT 57.554 34.783 0.00 0.00 0.00 4.40
2947 3546 5.988561 GCATGGGTTTTCTGTAAATTTGTCA 59.011 36.000 0.00 0.00 0.00 3.58
2949 3548 5.304778 GGCATGGGTTTTCTGTAAATTTGT 58.695 37.500 0.00 0.00 0.00 2.83
3106 3705 5.616270 TGCCGCATAAGTTAATCCTCATTA 58.384 37.500 0.00 0.00 0.00 1.90
3115 3714 1.737236 CACAGCTGCCGCATAAGTTAA 59.263 47.619 15.27 0.00 39.10 2.01
3264 3866 1.612676 ATTGCTGCCATGCGTATCAT 58.387 45.000 0.00 0.00 35.31 2.45
3507 4109 2.271800 CTTCTGTAGGCCGATTGTGTC 58.728 52.381 0.00 0.00 0.00 3.67
3564 4166 3.256704 TCTCCATTTCACTACCCTGGTT 58.743 45.455 0.00 0.00 0.00 3.67
3704 4306 3.158676 CCCATTCCGTTCCTGGTTAAAA 58.841 45.455 0.00 0.00 0.00 1.52
3750 4352 5.239275 AGTATTACCTACCACCCCCTTAA 57.761 43.478 0.00 0.00 0.00 1.85
3751 4353 4.924608 AGTATTACCTACCACCCCCTTA 57.075 45.455 0.00 0.00 0.00 2.69
3752 4354 3.809219 AGTATTACCTACCACCCCCTT 57.191 47.619 0.00 0.00 0.00 3.95
3753 4355 3.809219 AAGTATTACCTACCACCCCCT 57.191 47.619 0.00 0.00 0.00 4.79
3754 4356 3.781965 TGAAAGTATTACCTACCACCCCC 59.218 47.826 0.00 0.00 0.00 5.40
3755 4357 4.225717 TGTGAAAGTATTACCTACCACCCC 59.774 45.833 0.00 0.00 0.00 4.95
3756 4358 5.425196 TGTGAAAGTATTACCTACCACCC 57.575 43.478 0.00 0.00 0.00 4.61
3757 4359 7.933215 ATTTGTGAAAGTATTACCTACCACC 57.067 36.000 0.00 0.00 0.00 4.61
3758 4360 8.789762 ACAATTTGTGAAAGTATTACCTACCAC 58.210 33.333 0.15 0.00 0.00 4.16
3759 4361 8.927675 ACAATTTGTGAAAGTATTACCTACCA 57.072 30.769 0.15 0.00 0.00 3.25
3760 4362 9.620660 CAACAATTTGTGAAAGTATTACCTACC 57.379 33.333 2.13 0.00 0.00 3.18
3761 4363 9.620660 CCAACAATTTGTGAAAGTATTACCTAC 57.379 33.333 2.13 0.00 0.00 3.18
3762 4364 9.357161 ACCAACAATTTGTGAAAGTATTACCTA 57.643 29.630 2.13 0.00 0.00 3.08
3763 4365 8.141268 CACCAACAATTTGTGAAAGTATTACCT 58.859 33.333 2.13 0.00 0.00 3.08
3764 4366 8.138712 TCACCAACAATTTGTGAAAGTATTACC 58.861 33.333 2.13 0.00 0.00 2.85
3765 4367 9.522804 TTCACCAACAATTTGTGAAAGTATTAC 57.477 29.630 2.13 0.00 33.54 1.89
3767 4369 9.612066 AATTCACCAACAATTTGTGAAAGTATT 57.388 25.926 10.99 1.17 36.85 1.89
3770 4372 9.044150 CATAATTCACCAACAATTTGTGAAAGT 57.956 29.630 10.99 6.40 36.85 2.66
3771 4373 9.258826 TCATAATTCACCAACAATTTGTGAAAG 57.741 29.630 10.99 4.38 36.85 2.62
3772 4374 9.039870 GTCATAATTCACCAACAATTTGTGAAA 57.960 29.630 10.99 0.00 36.85 2.69
3773 4375 7.380870 CGTCATAATTCACCAACAATTTGTGAA 59.619 33.333 2.13 9.76 37.26 3.18


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

AutoCloner maintained by Alex Coulton.