Multiple sequence alignment - TraesCS2A01G111100

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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 TraesCS2A01G111100 chr2A 100.000 2375 0 0 1 2375 62379681 62382055 0.000000e+00 4386.0
1 TraesCS2A01G111100 chr2A 89.623 106 10 1 1922 2026 62381272 62381377 1.480000e-27 134.0
2 TraesCS2A01G111100 chr2A 89.623 106 10 1 1592 1697 62381602 62381706 1.480000e-27 134.0
3 TraesCS2A01G111100 chr2D 92.525 1632 70 24 1 1623 62051319 62052907 0.000000e+00 2290.0
4 TraesCS2A01G111100 chr2D 75.263 380 52 30 1824 2170 62052823 62053193 2.460000e-30 143.0
5 TraesCS2A01G111100 chr2B 91.162 1652 73 35 1 1623 97413869 97415476 0.000000e+00 2174.0
6 TraesCS2A01G111100 chr2B 92.793 777 49 5 829 1598 97424375 97425151 0.000000e+00 1118.0
7 TraesCS2A01G111100 chr2B 86.800 500 48 10 1824 2318 97425084 97425570 2.080000e-150 542.0
8 TraesCS2A01G111100 chr2B 77.526 485 58 35 1824 2278 97415392 97415855 6.560000e-61 244.0
9 TraesCS2A01G111100 chr2B 95.000 80 2 2 1717 1796 97415328 97415405 8.910000e-25 124.0
10 TraesCS2A01G111100 chr2B 95.000 60 3 0 777 836 97417013 97417072 6.990000e-16 95.3


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 TraesCS2A01G111100 chr2A 62379681 62382055 2374 False 1551.333333 4386 93.0820 1 2375 3 chr2A.!!$F1 2374
1 TraesCS2A01G111100 chr2D 62051319 62053193 1874 False 1216.500000 2290 83.8940 1 2170 2 chr2D.!!$F1 2169
2 TraesCS2A01G111100 chr2B 97424375 97425570 1195 False 830.000000 1118 89.7965 829 2318 2 chr2B.!!$F2 1489
3 TraesCS2A01G111100 chr2B 97413869 97417072 3203 False 659.325000 2174 89.6720 1 2278 4 chr2B.!!$F1 2277

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
27 28 0.239082 TGCTGCTCTGAATTTGCACG 59.761 50.0 0.0 0.0 32.91 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 1740 1.004927 CGCCGATTACAACTAAGCAGC 60.005 52.381 0.0 0.0 0.0 5.25 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
27 28 0.239082 TGCTGCTCTGAATTTGCACG 59.761 50.000 0.00 0.00 32.91 5.34
36 40 1.001924 TGAATTTGCACGCGACATTGT 60.002 42.857 15.93 0.00 0.00 2.71
41 45 0.590682 TGCACGCGACATTGTCAATT 59.409 45.000 15.93 0.00 32.09 2.32
152 158 2.555199 CCTCTTCCCTCATAAAGCACG 58.445 52.381 0.00 0.00 0.00 5.34
200 206 2.747460 CGTACGTCGTCCCTCCCA 60.747 66.667 7.22 0.00 34.52 4.37
394 403 1.228245 GTGAAGAGGCCAACCAGCA 60.228 57.895 5.01 0.00 39.06 4.41
421 430 2.202676 GGCTCGCTCTCGGAACAG 60.203 66.667 0.00 0.00 36.13 3.16
470 480 4.953868 AGCAACCGCGTACGTGCA 62.954 61.111 24.65 0.00 42.08 4.57
517 527 3.039988 CACGACGTGTCTCCACCT 58.960 61.111 19.77 0.00 38.41 4.00
663 677 5.164061 CCCGTGTACTACAATGTAAAACGTC 60.164 44.000 6.95 0.97 35.14 4.34
775 789 0.245539 TGCCTTGTGGTAGCTACGAC 59.754 55.000 26.73 26.73 35.77 4.34
827 841 1.532090 GGTATCGTCTCGCTGTCACTG 60.532 57.143 0.00 0.00 0.00 3.66
945 959 2.017559 GAGGGAGCCAACGAGCGTAT 62.018 60.000 0.00 0.00 38.01 3.06
959 973 2.016961 CGTATCGCCATTTGCAGCT 58.983 52.632 0.00 0.00 41.33 4.24
960 974 1.217001 CGTATCGCCATTTGCAGCTA 58.783 50.000 0.00 0.00 41.33 3.32
1231 1255 2.427325 CTATCGGCTCGTCGACGTCC 62.427 65.000 34.40 31.13 46.75 4.79
1387 1414 3.724914 GAGTAGCTGGCGTGGGCTC 62.725 68.421 0.00 0.00 39.65 4.70
1408 1435 2.202797 CTGGTGAGATCGGGCGTG 60.203 66.667 0.00 0.00 0.00 5.34
1529 1562 7.900352 CGAAGAATTTTTAGAAGGTTCTGATCG 59.100 37.037 2.32 0.00 38.19 3.69
1532 1565 9.372369 AGAATTTTTAGAAGGTTCTGATCGTAG 57.628 33.333 2.32 0.00 38.19 3.51
1533 1566 8.494016 AATTTTTAGAAGGTTCTGATCGTAGG 57.506 34.615 2.32 0.00 38.19 3.18
1534 1567 4.650754 TTAGAAGGTTCTGATCGTAGGC 57.349 45.455 2.32 0.00 38.19 3.93
1535 1568 2.457598 AGAAGGTTCTGATCGTAGGCA 58.542 47.619 0.00 0.00 35.89 4.75
1536 1569 3.034635 AGAAGGTTCTGATCGTAGGCAT 58.965 45.455 0.00 0.00 35.89 4.40
1537 1570 2.898729 AGGTTCTGATCGTAGGCATG 57.101 50.000 0.00 0.00 0.00 4.06
1538 1571 2.111384 AGGTTCTGATCGTAGGCATGT 58.889 47.619 0.00 0.00 0.00 3.21
1539 1572 2.501723 AGGTTCTGATCGTAGGCATGTT 59.498 45.455 0.00 0.00 0.00 2.71
1540 1573 3.055094 AGGTTCTGATCGTAGGCATGTTT 60.055 43.478 0.00 0.00 0.00 2.83
1541 1574 3.689649 GGTTCTGATCGTAGGCATGTTTT 59.310 43.478 0.00 0.00 0.00 2.43
1542 1575 4.201822 GGTTCTGATCGTAGGCATGTTTTC 60.202 45.833 0.00 0.00 0.00 2.29
1543 1576 4.471904 TCTGATCGTAGGCATGTTTTCT 57.528 40.909 0.00 0.00 0.00 2.52
1544 1577 5.592104 TCTGATCGTAGGCATGTTTTCTA 57.408 39.130 0.00 0.00 0.00 2.10
1545 1578 5.348986 TCTGATCGTAGGCATGTTTTCTAC 58.651 41.667 0.00 1.67 0.00 2.59
1546 1579 4.439057 TGATCGTAGGCATGTTTTCTACC 58.561 43.478 0.00 0.00 32.14 3.18
1547 1580 3.965379 TCGTAGGCATGTTTTCTACCA 57.035 42.857 0.00 0.00 32.14 3.25
1548 1581 3.857052 TCGTAGGCATGTTTTCTACCAG 58.143 45.455 0.00 0.00 32.14 4.00
1549 1582 3.512329 TCGTAGGCATGTTTTCTACCAGA 59.488 43.478 0.00 0.00 32.14 3.86
1550 1583 3.865745 CGTAGGCATGTTTTCTACCAGAG 59.134 47.826 0.00 0.00 32.14 3.35
1551 1584 4.620803 CGTAGGCATGTTTTCTACCAGAGT 60.621 45.833 0.00 0.00 32.14 3.24
1552 1585 4.373156 AGGCATGTTTTCTACCAGAGTT 57.627 40.909 0.00 0.00 0.00 3.01
1553 1586 4.074970 AGGCATGTTTTCTACCAGAGTTG 58.925 43.478 0.00 0.00 0.00 3.16
1554 1587 3.821033 GGCATGTTTTCTACCAGAGTTGT 59.179 43.478 0.00 0.00 0.00 3.32
1555 1588 4.278419 GGCATGTTTTCTACCAGAGTTGTT 59.722 41.667 0.00 0.00 0.00 2.83
1556 1589 5.215160 GCATGTTTTCTACCAGAGTTGTTG 58.785 41.667 0.00 0.00 0.00 3.33
1557 1590 5.762045 CATGTTTTCTACCAGAGTTGTTGG 58.238 41.667 0.00 0.00 41.60 3.77
1558 1591 5.105567 TGTTTTCTACCAGAGTTGTTGGA 57.894 39.130 0.00 0.00 39.08 3.53
1559 1592 5.690865 TGTTTTCTACCAGAGTTGTTGGAT 58.309 37.500 0.00 0.00 39.08 3.41
1560 1593 6.126409 TGTTTTCTACCAGAGTTGTTGGATT 58.874 36.000 0.00 0.00 39.08 3.01
1561 1594 6.262273 TGTTTTCTACCAGAGTTGTTGGATTC 59.738 38.462 0.00 0.00 39.08 2.52
1562 1595 5.560722 TTCTACCAGAGTTGTTGGATTCA 57.439 39.130 0.00 0.00 39.08 2.57
1563 1596 5.762179 TCTACCAGAGTTGTTGGATTCAT 57.238 39.130 0.00 0.00 39.08 2.57
1564 1597 6.867519 TCTACCAGAGTTGTTGGATTCATA 57.132 37.500 0.00 0.00 39.08 2.15
1565 1598 6.878317 TCTACCAGAGTTGTTGGATTCATAG 58.122 40.000 0.00 0.00 39.08 2.23
1566 1599 4.848357 ACCAGAGTTGTTGGATTCATAGG 58.152 43.478 0.00 0.00 39.08 2.57
1567 1600 4.536090 ACCAGAGTTGTTGGATTCATAGGA 59.464 41.667 0.00 0.00 39.08 2.94
1568 1601 5.192522 ACCAGAGTTGTTGGATTCATAGGAT 59.807 40.000 0.00 0.00 39.08 3.24
1569 1602 6.125029 CCAGAGTTGTTGGATTCATAGGATT 58.875 40.000 0.00 0.00 37.96 3.01
1570 1603 6.039047 CCAGAGTTGTTGGATTCATAGGATTG 59.961 42.308 0.00 0.00 37.96 2.67
1571 1604 5.591877 AGAGTTGTTGGATTCATAGGATTGC 59.408 40.000 0.00 0.00 0.00 3.56
1572 1605 5.263599 AGTTGTTGGATTCATAGGATTGCA 58.736 37.500 0.00 0.00 0.00 4.08
1573 1606 5.716228 AGTTGTTGGATTCATAGGATTGCAA 59.284 36.000 0.00 0.00 33.97 4.08
1574 1607 6.211184 AGTTGTTGGATTCATAGGATTGCAAA 59.789 34.615 1.71 0.00 36.78 3.68
1575 1608 5.964758 TGTTGGATTCATAGGATTGCAAAC 58.035 37.500 1.71 0.00 36.78 2.93
1576 1609 5.105392 TGTTGGATTCATAGGATTGCAAACC 60.105 40.000 17.54 17.54 36.78 3.27
1577 1610 3.631686 TGGATTCATAGGATTGCAAACCG 59.368 43.478 18.91 6.46 0.00 4.44
1578 1611 3.632145 GGATTCATAGGATTGCAAACCGT 59.368 43.478 18.91 10.01 0.00 4.83
1579 1612 4.819630 GGATTCATAGGATTGCAAACCGTA 59.180 41.667 18.91 12.30 0.00 4.02
1580 1613 5.277828 GGATTCATAGGATTGCAAACCGTAC 60.278 44.000 18.91 8.31 0.00 3.67
1581 1614 4.209307 TCATAGGATTGCAAACCGTACA 57.791 40.909 18.91 7.34 0.00 2.90
1582 1615 4.580868 TCATAGGATTGCAAACCGTACAA 58.419 39.130 18.91 5.39 0.00 2.41
1583 1616 5.189928 TCATAGGATTGCAAACCGTACAAT 58.810 37.500 18.91 4.33 36.74 2.71
1584 1617 5.650266 TCATAGGATTGCAAACCGTACAATT 59.350 36.000 18.91 3.64 34.28 2.32
1585 1618 4.864704 AGGATTGCAAACCGTACAATTT 57.135 36.364 18.91 0.00 34.28 1.82
1586 1619 5.208463 AGGATTGCAAACCGTACAATTTT 57.792 34.783 18.91 0.00 34.28 1.82
1587 1620 5.606505 AGGATTGCAAACCGTACAATTTTT 58.393 33.333 18.91 0.00 34.28 1.94
1626 1659 9.953697 AAGATTTATTTGTACGTTTTGTAGCAA 57.046 25.926 0.00 0.00 32.51 3.91
1627 1660 9.953697 AGATTTATTTGTACGTTTTGTAGCAAA 57.046 25.926 0.00 0.00 37.88 3.68
1633 1666 9.909043 ATTTGTACGTTTTGTAGCAAATTTTTC 57.091 25.926 0.00 0.00 39.26 2.29
1634 1667 7.452630 TGTACGTTTTGTAGCAAATTTTTCC 57.547 32.000 0.00 0.00 32.51 3.13
1635 1668 7.033791 TGTACGTTTTGTAGCAAATTTTTCCA 58.966 30.769 0.00 0.00 32.51 3.53
1636 1669 7.707035 TGTACGTTTTGTAGCAAATTTTTCCAT 59.293 29.630 0.00 0.00 32.51 3.41
1637 1670 7.172654 ACGTTTTGTAGCAAATTTTTCCATC 57.827 32.000 0.00 0.00 0.00 3.51
1638 1671 6.201997 ACGTTTTGTAGCAAATTTTTCCATCC 59.798 34.615 0.00 0.00 0.00 3.51
1639 1672 6.201806 CGTTTTGTAGCAAATTTTTCCATCCA 59.798 34.615 0.00 0.00 0.00 3.41
1640 1673 7.351981 GTTTTGTAGCAAATTTTTCCATCCAC 58.648 34.615 0.00 0.00 0.00 4.02
1641 1674 5.146010 TGTAGCAAATTTTTCCATCCACC 57.854 39.130 0.00 0.00 0.00 4.61
1642 1675 4.837860 TGTAGCAAATTTTTCCATCCACCT 59.162 37.500 0.00 0.00 0.00 4.00
1643 1676 4.980339 AGCAAATTTTTCCATCCACCTT 57.020 36.364 0.00 0.00 0.00 3.50
1644 1677 6.495181 TGTAGCAAATTTTTCCATCCACCTTA 59.505 34.615 0.00 0.00 0.00 2.69
1645 1678 6.432403 AGCAAATTTTTCCATCCACCTTAA 57.568 33.333 0.00 0.00 0.00 1.85
1646 1679 6.230472 AGCAAATTTTTCCATCCACCTTAAC 58.770 36.000 0.00 0.00 0.00 2.01
1647 1680 5.411361 GCAAATTTTTCCATCCACCTTAACC 59.589 40.000 0.00 0.00 0.00 2.85
1648 1681 6.744056 GCAAATTTTTCCATCCACCTTAACCT 60.744 38.462 0.00 0.00 0.00 3.50
1649 1682 6.605471 AATTTTTCCATCCACCTTAACCTC 57.395 37.500 0.00 0.00 0.00 3.85
1650 1683 5.333566 TTTTTCCATCCACCTTAACCTCT 57.666 39.130 0.00 0.00 0.00 3.69
1651 1684 5.333566 TTTTCCATCCACCTTAACCTCTT 57.666 39.130 0.00 0.00 0.00 2.85
1652 1685 4.301072 TTCCATCCACCTTAACCTCTTG 57.699 45.455 0.00 0.00 0.00 3.02
1653 1686 3.526899 TCCATCCACCTTAACCTCTTGA 58.473 45.455 0.00 0.00 0.00 3.02
1654 1687 3.913799 TCCATCCACCTTAACCTCTTGAA 59.086 43.478 0.00 0.00 0.00 2.69
1655 1688 4.352595 TCCATCCACCTTAACCTCTTGAAA 59.647 41.667 0.00 0.00 0.00 2.69
1656 1689 5.076873 CCATCCACCTTAACCTCTTGAAAA 58.923 41.667 0.00 0.00 0.00 2.29
1657 1690 5.048013 CCATCCACCTTAACCTCTTGAAAAC 60.048 44.000 0.00 0.00 0.00 2.43
1658 1691 4.131596 TCCACCTTAACCTCTTGAAAACG 58.868 43.478 0.00 0.00 0.00 3.60
1659 1692 4.131596 CCACCTTAACCTCTTGAAAACGA 58.868 43.478 0.00 0.00 0.00 3.85
1660 1693 4.577283 CCACCTTAACCTCTTGAAAACGAA 59.423 41.667 0.00 0.00 0.00 3.85
1661 1694 5.240844 CCACCTTAACCTCTTGAAAACGAAT 59.759 40.000 0.00 0.00 0.00 3.34
1662 1695 6.238925 CCACCTTAACCTCTTGAAAACGAATT 60.239 38.462 0.00 0.00 0.00 2.17
1663 1696 6.856426 CACCTTAACCTCTTGAAAACGAATTC 59.144 38.462 0.00 0.00 0.00 2.17
1664 1697 6.771267 ACCTTAACCTCTTGAAAACGAATTCT 59.229 34.615 3.52 0.00 0.00 2.40
1665 1698 7.935210 ACCTTAACCTCTTGAAAACGAATTCTA 59.065 33.333 3.52 0.00 0.00 2.10
1666 1699 8.228464 CCTTAACCTCTTGAAAACGAATTCTAC 58.772 37.037 3.52 0.00 0.00 2.59
1667 1700 8.665643 TTAACCTCTTGAAAACGAATTCTACA 57.334 30.769 3.52 0.00 0.00 2.74
1668 1701 7.745620 AACCTCTTGAAAACGAATTCTACAT 57.254 32.000 3.52 0.00 0.00 2.29
1669 1702 7.365840 ACCTCTTGAAAACGAATTCTACATC 57.634 36.000 3.52 0.00 0.00 3.06
1670 1703 7.162082 ACCTCTTGAAAACGAATTCTACATCT 58.838 34.615 3.52 0.00 0.00 2.90
1671 1704 7.332182 ACCTCTTGAAAACGAATTCTACATCTC 59.668 37.037 3.52 0.00 0.00 2.75
1672 1705 7.547370 CCTCTTGAAAACGAATTCTACATCTCT 59.453 37.037 3.52 0.00 0.00 3.10
1673 1706 8.467402 TCTTGAAAACGAATTCTACATCTCTC 57.533 34.615 3.52 0.00 0.00 3.20
1674 1707 8.088365 TCTTGAAAACGAATTCTACATCTCTCA 58.912 33.333 3.52 0.00 0.00 3.27
1675 1708 8.777865 TTGAAAACGAATTCTACATCTCTCAT 57.222 30.769 3.52 0.00 0.00 2.90
1676 1709 8.189709 TGAAAACGAATTCTACATCTCTCATG 57.810 34.615 3.52 0.00 0.00 3.07
1677 1710 7.819415 TGAAAACGAATTCTACATCTCTCATGT 59.181 33.333 3.52 0.00 36.13 3.21
1678 1711 9.302345 GAAAACGAATTCTACATCTCTCATGTA 57.698 33.333 3.52 0.00 33.76 2.29
1679 1712 8.635877 AAACGAATTCTACATCTCTCATGTAC 57.364 34.615 3.52 0.00 33.76 2.90
1680 1713 6.431278 ACGAATTCTACATCTCTCATGTACG 58.569 40.000 3.52 0.00 33.76 3.67
1681 1714 5.340932 CGAATTCTACATCTCTCATGTACGC 59.659 44.000 3.52 0.00 33.76 4.42
1682 1715 5.774498 ATTCTACATCTCTCATGTACGCA 57.226 39.130 0.00 0.00 33.76 5.24
1683 1716 5.576447 TTCTACATCTCTCATGTACGCAA 57.424 39.130 0.00 0.00 33.76 4.85
1684 1717 5.774498 TCTACATCTCTCATGTACGCAAT 57.226 39.130 0.00 0.00 33.76 3.56
1685 1718 5.763088 TCTACATCTCTCATGTACGCAATC 58.237 41.667 0.00 0.00 33.76 2.67
1686 1719 4.391405 ACATCTCTCATGTACGCAATCA 57.609 40.909 0.00 0.00 0.00 2.57
1687 1720 4.758688 ACATCTCTCATGTACGCAATCAA 58.241 39.130 0.00 0.00 0.00 2.57
1688 1721 5.178061 ACATCTCTCATGTACGCAATCAAA 58.822 37.500 0.00 0.00 0.00 2.69
1689 1722 5.063944 ACATCTCTCATGTACGCAATCAAAC 59.936 40.000 0.00 0.00 0.00 2.93
1690 1723 4.565022 TCTCTCATGTACGCAATCAAACA 58.435 39.130 0.00 0.00 0.00 2.83
1691 1724 4.627035 TCTCTCATGTACGCAATCAAACAG 59.373 41.667 0.00 0.00 0.00 3.16
1692 1725 3.125146 TCTCATGTACGCAATCAAACAGC 59.875 43.478 0.00 0.00 0.00 4.40
1693 1726 2.161410 TCATGTACGCAATCAAACAGCC 59.839 45.455 0.00 0.00 0.00 4.85
1694 1727 1.598882 TGTACGCAATCAAACAGCCA 58.401 45.000 0.00 0.00 0.00 4.75
1695 1728 2.158559 TGTACGCAATCAAACAGCCAT 58.841 42.857 0.00 0.00 0.00 4.40
1696 1729 2.556189 TGTACGCAATCAAACAGCCATT 59.444 40.909 0.00 0.00 0.00 3.16
1697 1730 3.753797 TGTACGCAATCAAACAGCCATTA 59.246 39.130 0.00 0.00 0.00 1.90
1698 1731 4.397730 TGTACGCAATCAAACAGCCATTAT 59.602 37.500 0.00 0.00 0.00 1.28
1699 1732 3.772932 ACGCAATCAAACAGCCATTATG 58.227 40.909 0.00 0.00 0.00 1.90
1700 1733 2.536803 CGCAATCAAACAGCCATTATGC 59.463 45.455 0.00 0.00 0.00 3.14
1701 1734 3.523547 GCAATCAAACAGCCATTATGCA 58.476 40.909 0.00 0.00 0.00 3.96
1702 1735 4.124238 GCAATCAAACAGCCATTATGCAT 58.876 39.130 3.79 3.79 0.00 3.96
1703 1736 4.025229 GCAATCAAACAGCCATTATGCATG 60.025 41.667 10.16 0.00 0.00 4.06
1704 1737 3.167921 TCAAACAGCCATTATGCATGC 57.832 42.857 11.82 11.82 0.00 4.06
1705 1738 2.159071 TCAAACAGCCATTATGCATGCC 60.159 45.455 16.68 0.00 0.00 4.40
1706 1739 1.784358 AACAGCCATTATGCATGCCT 58.216 45.000 16.68 8.18 0.00 4.75
1707 1740 1.037493 ACAGCCATTATGCATGCCTG 58.963 50.000 16.68 15.07 42.95 4.85
1708 1741 2.968143 ACAGCCATTATGCATGCCTGC 61.968 52.381 16.68 7.06 41.31 4.85
1716 1749 3.915575 GCATGCCTGCTGCTTAGT 58.084 55.556 6.36 0.00 45.32 2.24
1717 1750 2.187073 GCATGCCTGCTGCTTAGTT 58.813 52.632 6.36 0.00 45.32 2.24
1718 1751 0.179145 GCATGCCTGCTGCTTAGTTG 60.179 55.000 6.36 0.00 45.32 3.16
1719 1752 1.171308 CATGCCTGCTGCTTAGTTGT 58.829 50.000 0.00 0.00 42.00 3.32
1720 1753 2.358957 CATGCCTGCTGCTTAGTTGTA 58.641 47.619 0.00 0.00 42.00 2.41
1721 1754 2.559698 TGCCTGCTGCTTAGTTGTAA 57.440 45.000 0.00 0.00 42.00 2.41
1722 1755 3.071874 TGCCTGCTGCTTAGTTGTAAT 57.928 42.857 0.00 0.00 42.00 1.89
1723 1756 3.009723 TGCCTGCTGCTTAGTTGTAATC 58.990 45.455 0.00 0.00 42.00 1.75
1724 1757 2.030946 GCCTGCTGCTTAGTTGTAATCG 59.969 50.000 0.00 0.00 36.87 3.34
1725 1758 2.609459 CCTGCTGCTTAGTTGTAATCGG 59.391 50.000 0.00 0.00 0.00 4.18
1726 1759 2.006888 TGCTGCTTAGTTGTAATCGGC 58.993 47.619 0.00 0.00 37.23 5.54
1727 1760 1.004927 GCTGCTTAGTTGTAATCGGCG 60.005 52.381 0.00 0.00 29.40 6.46
1728 1761 1.593006 CTGCTTAGTTGTAATCGGCGG 59.407 52.381 7.21 0.00 0.00 6.13
1729 1762 1.205179 TGCTTAGTTGTAATCGGCGGA 59.795 47.619 7.21 0.00 0.00 5.54
1730 1763 2.273557 GCTTAGTTGTAATCGGCGGAA 58.726 47.619 7.21 0.00 0.00 4.30
1731 1764 2.674357 GCTTAGTTGTAATCGGCGGAAA 59.326 45.455 7.21 0.00 0.00 3.13
1732 1765 3.311596 GCTTAGTTGTAATCGGCGGAAAT 59.688 43.478 7.21 0.00 0.00 2.17
1733 1766 4.508861 GCTTAGTTGTAATCGGCGGAAATA 59.491 41.667 7.21 0.00 0.00 1.40
1734 1767 5.006941 GCTTAGTTGTAATCGGCGGAAATAA 59.993 40.000 7.21 2.25 0.00 1.40
1735 1768 4.870221 AGTTGTAATCGGCGGAAATAAC 57.130 40.909 7.21 8.01 0.00 1.89
1736 1769 4.255301 AGTTGTAATCGGCGGAAATAACA 58.745 39.130 7.21 0.61 0.00 2.41
1737 1770 4.879545 AGTTGTAATCGGCGGAAATAACAT 59.120 37.500 7.21 0.00 0.00 2.71
1738 1771 5.355910 AGTTGTAATCGGCGGAAATAACATT 59.644 36.000 7.21 0.00 0.00 2.71
1739 1772 5.163302 TGTAATCGGCGGAAATAACATTG 57.837 39.130 7.21 0.00 0.00 2.82
1740 1773 4.876679 TGTAATCGGCGGAAATAACATTGA 59.123 37.500 7.21 0.00 0.00 2.57
1741 1774 4.552166 AATCGGCGGAAATAACATTGAG 57.448 40.909 7.21 0.00 0.00 3.02
1742 1775 1.668751 TCGGCGGAAATAACATTGAGC 59.331 47.619 7.21 0.00 0.00 4.26
1743 1776 1.268539 CGGCGGAAATAACATTGAGCC 60.269 52.381 0.00 0.00 39.89 4.70
1744 1777 2.024414 GGCGGAAATAACATTGAGCCT 58.976 47.619 0.00 0.00 40.12 4.58
1745 1778 2.033424 GGCGGAAATAACATTGAGCCTC 59.967 50.000 0.00 0.00 40.12 4.70
1746 1779 2.945668 GCGGAAATAACATTGAGCCTCT 59.054 45.455 0.00 0.00 0.00 3.69
1747 1780 3.378427 GCGGAAATAACATTGAGCCTCTT 59.622 43.478 0.00 0.00 0.00 2.85
1748 1781 4.142381 GCGGAAATAACATTGAGCCTCTTT 60.142 41.667 0.00 0.00 0.00 2.52
1749 1782 5.335127 CGGAAATAACATTGAGCCTCTTTG 58.665 41.667 0.00 0.00 0.00 2.77
1750 1783 5.123820 CGGAAATAACATTGAGCCTCTTTGA 59.876 40.000 0.00 0.00 0.00 2.69
1751 1784 6.183360 CGGAAATAACATTGAGCCTCTTTGAT 60.183 38.462 0.00 0.00 0.00 2.57
1752 1785 7.550712 GGAAATAACATTGAGCCTCTTTGATT 58.449 34.615 0.00 0.00 0.00 2.57
1753 1786 7.704047 GGAAATAACATTGAGCCTCTTTGATTC 59.296 37.037 0.00 0.00 0.00 2.52
1754 1787 7.707624 AATAACATTGAGCCTCTTTGATTCA 57.292 32.000 0.00 0.00 0.00 2.57
1755 1788 7.707624 ATAACATTGAGCCTCTTTGATTCAA 57.292 32.000 0.00 0.00 32.90 2.69
1756 1789 6.409524 AACATTGAGCCTCTTTGATTCAAA 57.590 33.333 11.19 11.19 32.21 2.69
1773 1806 9.981114 TTGATTCAAAGAATTTTTAGAGGGTTC 57.019 29.630 0.00 0.00 35.03 3.62
1774 1807 9.367160 TGATTCAAAGAATTTTTAGAGGGTTCT 57.633 29.630 0.00 0.00 35.03 3.01
1784 1817 9.922477 AATTTTTAGAGGGTTCTAATCCTTAGG 57.078 33.333 0.00 0.00 43.53 2.69
1785 1818 6.496144 TTTAGAGGGTTCTAATCCTTAGGC 57.504 41.667 0.00 0.00 43.53 3.93
1786 1819 4.008916 AGAGGGTTCTAATCCTTAGGCA 57.991 45.455 0.00 0.00 40.40 4.75
1787 1820 4.571951 AGAGGGTTCTAATCCTTAGGCAT 58.428 43.478 0.00 0.00 40.40 4.40
1788 1821 4.349342 AGAGGGTTCTAATCCTTAGGCATG 59.651 45.833 0.00 0.00 40.40 4.06
1789 1822 4.047883 AGGGTTCTAATCCTTAGGCATGT 58.952 43.478 0.00 0.00 35.49 3.21
1790 1823 4.137543 GGGTTCTAATCCTTAGGCATGTG 58.862 47.826 0.00 0.00 34.00 3.21
1791 1824 4.385310 GGGTTCTAATCCTTAGGCATGTGT 60.385 45.833 0.00 0.00 34.00 3.72
1792 1825 5.193679 GGTTCTAATCCTTAGGCATGTGTT 58.806 41.667 0.00 0.00 34.00 3.32
1793 1826 5.652452 GGTTCTAATCCTTAGGCATGTGTTT 59.348 40.000 0.00 0.00 34.00 2.83
1794 1827 6.183360 GGTTCTAATCCTTAGGCATGTGTTTC 60.183 42.308 0.00 0.00 34.00 2.78
1795 1828 6.313519 TCTAATCCTTAGGCATGTGTTTCT 57.686 37.500 0.00 0.00 34.00 2.52
1796 1829 6.721318 TCTAATCCTTAGGCATGTGTTTCTT 58.279 36.000 0.00 0.00 34.00 2.52
1797 1830 7.175104 TCTAATCCTTAGGCATGTGTTTCTTT 58.825 34.615 0.00 0.00 34.00 2.52
1798 1831 6.670695 AATCCTTAGGCATGTGTTTCTTTT 57.329 33.333 0.00 0.00 0.00 2.27
1799 1832 5.705609 TCCTTAGGCATGTGTTTCTTTTC 57.294 39.130 0.00 0.00 0.00 2.29
1800 1833 5.385198 TCCTTAGGCATGTGTTTCTTTTCT 58.615 37.500 0.00 0.00 0.00 2.52
1801 1834 5.833131 TCCTTAGGCATGTGTTTCTTTTCTT 59.167 36.000 0.00 0.00 0.00 2.52
1802 1835 6.323739 TCCTTAGGCATGTGTTTCTTTTCTTT 59.676 34.615 0.00 0.00 0.00 2.52
1803 1836 6.642540 CCTTAGGCATGTGTTTCTTTTCTTTC 59.357 38.462 0.00 0.00 0.00 2.62
1804 1837 5.859205 AGGCATGTGTTTCTTTTCTTTCT 57.141 34.783 0.00 0.00 0.00 2.52
1805 1838 6.225981 AGGCATGTGTTTCTTTTCTTTCTT 57.774 33.333 0.00 0.00 0.00 2.52
1806 1839 6.643388 AGGCATGTGTTTCTTTTCTTTCTTT 58.357 32.000 0.00 0.00 0.00 2.52
1807 1840 6.758416 AGGCATGTGTTTCTTTTCTTTCTTTC 59.242 34.615 0.00 0.00 0.00 2.62
1808 1841 6.758416 GGCATGTGTTTCTTTTCTTTCTTTCT 59.242 34.615 0.00 0.00 0.00 2.52
1809 1842 7.278646 GGCATGTGTTTCTTTTCTTTCTTTCTT 59.721 33.333 0.00 0.00 0.00 2.52
1810 1843 8.659491 GCATGTGTTTCTTTTCTTTCTTTCTTT 58.341 29.630 0.00 0.00 0.00 2.52
1869 1902 6.189859 TCTTGGATTCATAGGATTGCAAACT 58.810 36.000 1.71 7.78 35.34 2.66
1875 1908 8.725148 GGATTCATAGGATTGCAAACTATACAG 58.275 37.037 20.20 12.27 0.00 2.74
1876 1909 8.627208 ATTCATAGGATTGCAAACTATACAGG 57.373 34.615 20.20 12.02 0.00 4.00
1903 1936 9.562583 TTGTTACAAGATTTATTATTTGTCGGC 57.437 29.630 0.00 0.00 35.55 5.54
1992 2079 6.636850 CACCTTAACCTCTTGAAAACGAATTG 59.363 38.462 0.00 0.00 0.00 2.32
1999 2086 5.050634 CCTCTTGAAAACGAATTGTACGTCA 60.051 40.000 0.00 0.00 43.16 4.35
2002 2089 6.848800 TCTTGAAAACGAATTGTACGTCATTG 59.151 34.615 0.00 0.00 43.16 2.82
2033 2120 5.162794 CAATCAAACAGCCATTCATTTCGA 58.837 37.500 0.00 0.00 0.00 3.71
2037 2124 4.361451 AACAGCCATTCATTTCGATGTC 57.639 40.909 0.00 0.00 0.00 3.06
2040 2127 2.357009 AGCCATTCATTTCGATGTCTGC 59.643 45.455 0.00 0.00 0.00 4.26
2057 2152 1.236616 TGCGTGCACATCAAAGAGGG 61.237 55.000 18.64 0.00 0.00 4.30
2118 2223 0.813210 GTGGTAGCTGCTCTGATGGC 60.813 60.000 4.91 0.00 0.00 4.40
2119 2224 1.266867 TGGTAGCTGCTCTGATGGCA 61.267 55.000 4.91 0.00 38.10 4.92
2166 2274 9.533253 CATGTATTTCTTGTTTATTTCCCCATC 57.467 33.333 0.00 0.00 0.00 3.51
2185 2293 1.052287 CGAACGAAAGCAATGTTGGC 58.948 50.000 0.00 0.00 0.00 4.52
2199 2307 4.686191 ATGTTGGCAAGAATCCAAACAA 57.314 36.364 0.00 0.00 44.36 2.83
2200 2308 4.686191 TGTTGGCAAGAATCCAAACAAT 57.314 36.364 0.00 0.00 44.36 2.71
2204 2312 3.006752 TGGCAAGAATCCAAACAATGACC 59.993 43.478 0.00 0.00 0.00 4.02
2206 2314 3.259123 GCAAGAATCCAAACAATGACCCT 59.741 43.478 0.00 0.00 0.00 4.34
2207 2315 4.262592 GCAAGAATCCAAACAATGACCCTT 60.263 41.667 0.00 0.00 0.00 3.95
2238 2346 7.217200 TCTTCTTGTTACTGACTGCTTGTTAT 58.783 34.615 0.00 0.00 0.00 1.89
2297 3197 1.486726 TGAGCTAGCCTCTTAAAGCCC 59.513 52.381 12.13 0.00 41.35 5.19
2303 3203 1.282653 GCCTCTTAAAGCCCTCCCCT 61.283 60.000 0.00 0.00 0.00 4.79
2313 3213 0.394488 GCCCTCCCCTAAACTCTTGC 60.394 60.000 0.00 0.00 0.00 4.01
2318 3218 4.325030 CCCTCCCCTAAACTCTTGCATTTA 60.325 45.833 0.00 0.00 0.00 1.40
2351 3259 6.880822 TTAACTAAATGTCGATGAAGACCG 57.119 37.500 0.00 0.00 40.26 4.79
2353 3261 5.263968 ACTAAATGTCGATGAAGACCGAT 57.736 39.130 0.00 0.00 40.26 4.18
2356 3264 3.801114 ATGTCGATGAAGACCGATCAA 57.199 42.857 0.00 0.00 40.26 2.57
2358 3266 3.250744 TGTCGATGAAGACCGATCAAAC 58.749 45.455 0.00 0.00 40.26 2.93
2359 3267 3.250744 GTCGATGAAGACCGATCAAACA 58.749 45.455 0.00 0.00 37.14 2.83
2360 3268 3.060895 GTCGATGAAGACCGATCAAACAC 59.939 47.826 0.00 0.00 37.14 3.32
2361 3269 3.056821 TCGATGAAGACCGATCAAACACT 60.057 43.478 0.00 0.00 0.00 3.55
2362 3270 4.157105 TCGATGAAGACCGATCAAACACTA 59.843 41.667 0.00 0.00 0.00 2.74
2363 3271 4.265556 CGATGAAGACCGATCAAACACTAC 59.734 45.833 0.00 0.00 0.00 2.73
2364 3272 4.594123 TGAAGACCGATCAAACACTACA 57.406 40.909 0.00 0.00 0.00 2.74
2365 3273 5.147330 TGAAGACCGATCAAACACTACAT 57.853 39.130 0.00 0.00 0.00 2.29
2367 3275 3.861840 AGACCGATCAAACACTACATGG 58.138 45.455 0.00 0.00 0.00 3.66
2368 3276 3.260884 AGACCGATCAAACACTACATGGT 59.739 43.478 0.00 0.00 0.00 3.55
2369 3277 3.596214 ACCGATCAAACACTACATGGTC 58.404 45.455 0.00 0.00 0.00 4.02
2370 3278 2.936498 CCGATCAAACACTACATGGTCC 59.064 50.000 0.00 0.00 0.00 4.46
2371 3279 3.369471 CCGATCAAACACTACATGGTCCT 60.369 47.826 0.00 0.00 0.00 3.85
2372 3280 3.865745 CGATCAAACACTACATGGTCCTC 59.134 47.826 0.00 0.00 0.00 3.71
2373 3281 3.695830 TCAAACACTACATGGTCCTCC 57.304 47.619 0.00 0.00 0.00 4.30
2374 3282 3.248024 TCAAACACTACATGGTCCTCCT 58.752 45.455 0.00 0.00 34.23 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 40 1.275010 TCTGGCTACTGTGCGAATTGA 59.725 47.619 0.00 0.00 0.00 2.57
41 45 1.409064 CCTATTCTGGCTACTGTGCGA 59.591 52.381 0.00 0.00 0.00 5.10
65 69 1.618074 GCTGGGATTTTCTCAGGCCTT 60.618 52.381 0.00 0.00 45.03 4.35
73 77 1.208165 ACGAGGGGCTGGGATTTTCT 61.208 55.000 0.00 0.00 0.00 2.52
185 191 2.747460 CGTGGGAGGGACGACGTA 60.747 66.667 0.00 0.00 39.21 3.57
517 527 2.679837 CGCAGGAAGAAGGTACGTAGTA 59.320 50.000 0.00 0.00 45.11 1.82
590 604 5.171516 CACACACATAGAATATGACGACGAC 59.828 44.000 0.00 0.00 0.00 4.34
827 841 1.052287 GCGCGCATTGTATATTTGGC 58.948 50.000 29.10 0.00 0.00 4.52
928 942 1.591863 GATACGCTCGTTGGCTCCC 60.592 63.158 0.00 0.00 0.00 4.30
929 943 1.944676 CGATACGCTCGTTGGCTCC 60.945 63.158 0.00 0.00 42.56 4.70
1387 1414 2.503061 CCCGATCTCACCAGCCAG 59.497 66.667 0.00 0.00 0.00 4.85
1392 1419 4.451150 GCACGCCCGATCTCACCA 62.451 66.667 0.00 0.00 0.00 4.17
1467 1496 7.865385 GGCTCAATGTTATTTTTGCCGATTATA 59.135 33.333 0.00 0.00 0.00 0.98
1468 1497 6.701400 GGCTCAATGTTATTTTTGCCGATTAT 59.299 34.615 0.00 0.00 0.00 1.28
1518 1551 2.111384 ACATGCCTACGATCAGAACCT 58.889 47.619 0.00 0.00 0.00 3.50
1529 1562 4.833390 ACTCTGGTAGAAAACATGCCTAC 58.167 43.478 0.00 0.00 33.79 3.18
1532 1565 3.821033 ACAACTCTGGTAGAAAACATGCC 59.179 43.478 0.00 0.00 0.00 4.40
1533 1566 5.215160 CAACAACTCTGGTAGAAAACATGC 58.785 41.667 0.00 0.00 0.00 4.06
1534 1567 5.530915 TCCAACAACTCTGGTAGAAAACATG 59.469 40.000 0.00 0.00 35.30 3.21
1535 1568 5.690865 TCCAACAACTCTGGTAGAAAACAT 58.309 37.500 0.00 0.00 35.30 2.71
1536 1569 5.105567 TCCAACAACTCTGGTAGAAAACA 57.894 39.130 0.00 0.00 35.30 2.83
1537 1570 6.262273 TGAATCCAACAACTCTGGTAGAAAAC 59.738 38.462 0.00 0.00 35.30 2.43
1538 1571 6.361433 TGAATCCAACAACTCTGGTAGAAAA 58.639 36.000 0.00 0.00 35.30 2.29
1539 1572 5.935945 TGAATCCAACAACTCTGGTAGAAA 58.064 37.500 0.00 0.00 35.30 2.52
1540 1573 5.560722 TGAATCCAACAACTCTGGTAGAA 57.439 39.130 0.00 0.00 35.30 2.10
1541 1574 5.762179 ATGAATCCAACAACTCTGGTAGA 57.238 39.130 0.00 0.00 35.30 2.59
1542 1575 6.051717 CCTATGAATCCAACAACTCTGGTAG 58.948 44.000 0.00 0.00 35.30 3.18
1543 1576 5.724370 TCCTATGAATCCAACAACTCTGGTA 59.276 40.000 0.00 0.00 35.30 3.25
1544 1577 4.536090 TCCTATGAATCCAACAACTCTGGT 59.464 41.667 0.00 0.00 35.30 4.00
1545 1578 5.102953 TCCTATGAATCCAACAACTCTGG 57.897 43.478 0.00 0.00 35.05 3.86
1546 1579 6.459298 GCAATCCTATGAATCCAACAACTCTG 60.459 42.308 0.00 0.00 0.00 3.35
1547 1580 5.591877 GCAATCCTATGAATCCAACAACTCT 59.408 40.000 0.00 0.00 0.00 3.24
1548 1581 5.357878 TGCAATCCTATGAATCCAACAACTC 59.642 40.000 0.00 0.00 0.00 3.01
1549 1582 5.263599 TGCAATCCTATGAATCCAACAACT 58.736 37.500 0.00 0.00 0.00 3.16
1550 1583 5.581126 TGCAATCCTATGAATCCAACAAC 57.419 39.130 0.00 0.00 0.00 3.32
1551 1584 6.397272 GTTTGCAATCCTATGAATCCAACAA 58.603 36.000 0.00 0.00 0.00 2.83
1552 1585 5.105392 GGTTTGCAATCCTATGAATCCAACA 60.105 40.000 17.69 0.00 0.00 3.33
1553 1586 5.351458 GGTTTGCAATCCTATGAATCCAAC 58.649 41.667 17.69 0.00 0.00 3.77
1554 1587 4.097741 CGGTTTGCAATCCTATGAATCCAA 59.902 41.667 21.35 0.00 0.00 3.53
1555 1588 3.631686 CGGTTTGCAATCCTATGAATCCA 59.368 43.478 21.35 0.00 0.00 3.41
1556 1589 3.632145 ACGGTTTGCAATCCTATGAATCC 59.368 43.478 21.35 0.00 0.00 3.01
1557 1590 4.900635 ACGGTTTGCAATCCTATGAATC 57.099 40.909 21.35 0.00 0.00 2.52
1558 1591 5.189928 TGTACGGTTTGCAATCCTATGAAT 58.810 37.500 21.35 5.59 0.00 2.57
1559 1592 4.580868 TGTACGGTTTGCAATCCTATGAA 58.419 39.130 21.35 3.99 0.00 2.57
1560 1593 4.209307 TGTACGGTTTGCAATCCTATGA 57.791 40.909 21.35 4.27 0.00 2.15
1561 1594 4.955925 TTGTACGGTTTGCAATCCTATG 57.044 40.909 21.35 10.67 0.00 2.23
1562 1595 6.524101 AAATTGTACGGTTTGCAATCCTAT 57.476 33.333 21.35 13.22 39.41 2.57
1563 1596 5.968528 AAATTGTACGGTTTGCAATCCTA 57.031 34.783 21.35 11.60 39.41 2.94
1564 1597 4.864704 AAATTGTACGGTTTGCAATCCT 57.135 36.364 21.35 12.42 39.41 3.24
1565 1598 5.915812 AAAAATTGTACGGTTTGCAATCC 57.084 34.783 15.43 15.43 39.41 3.01
1600 1633 9.953697 TTGCTACAAAACGTACAAATAAATCTT 57.046 25.926 0.00 0.00 0.00 2.40
1601 1634 9.953697 TTTGCTACAAAACGTACAAATAAATCT 57.046 25.926 0.00 0.00 31.75 2.40
1607 1640 9.909043 GAAAAATTTGCTACAAAACGTACAAAT 57.091 25.926 0.00 0.00 40.08 2.32
1608 1641 8.381387 GGAAAAATTTGCTACAAAACGTACAAA 58.619 29.630 0.00 0.00 36.47 2.83
1609 1642 7.544566 TGGAAAAATTTGCTACAAAACGTACAA 59.455 29.630 0.00 0.00 0.00 2.41
1610 1643 7.033791 TGGAAAAATTTGCTACAAAACGTACA 58.966 30.769 0.00 0.00 0.00 2.90
1611 1644 7.452630 TGGAAAAATTTGCTACAAAACGTAC 57.547 32.000 0.00 0.00 0.00 3.67
1612 1645 7.382759 GGATGGAAAAATTTGCTACAAAACGTA 59.617 33.333 0.00 0.00 0.00 3.57
1613 1646 6.201997 GGATGGAAAAATTTGCTACAAAACGT 59.798 34.615 0.00 0.00 0.00 3.99
1614 1647 6.201806 TGGATGGAAAAATTTGCTACAAAACG 59.798 34.615 0.00 0.00 0.00 3.60
1615 1648 7.351981 GTGGATGGAAAAATTTGCTACAAAAC 58.648 34.615 0.00 0.00 0.00 2.43
1616 1649 6.484977 GGTGGATGGAAAAATTTGCTACAAAA 59.515 34.615 0.00 0.00 0.00 2.44
1617 1650 5.994668 GGTGGATGGAAAAATTTGCTACAAA 59.005 36.000 0.00 0.00 0.00 2.83
1618 1651 5.306678 AGGTGGATGGAAAAATTTGCTACAA 59.693 36.000 0.00 0.00 0.00 2.41
1619 1652 4.837860 AGGTGGATGGAAAAATTTGCTACA 59.162 37.500 0.00 0.00 0.00 2.74
1620 1653 5.405935 AGGTGGATGGAAAAATTTGCTAC 57.594 39.130 0.00 0.00 0.00 3.58
1621 1654 7.382898 GTTAAGGTGGATGGAAAAATTTGCTA 58.617 34.615 0.00 0.00 0.00 3.49
1622 1655 4.980339 AAGGTGGATGGAAAAATTTGCT 57.020 36.364 0.00 0.00 0.00 3.91
1623 1656 5.411361 GGTTAAGGTGGATGGAAAAATTTGC 59.589 40.000 0.00 0.00 0.00 3.68
1624 1657 6.768483 AGGTTAAGGTGGATGGAAAAATTTG 58.232 36.000 0.00 0.00 0.00 2.32
1625 1658 6.787458 AGAGGTTAAGGTGGATGGAAAAATTT 59.213 34.615 0.00 0.00 0.00 1.82
1626 1659 6.322931 AGAGGTTAAGGTGGATGGAAAAATT 58.677 36.000 0.00 0.00 0.00 1.82
1627 1660 5.903923 AGAGGTTAAGGTGGATGGAAAAAT 58.096 37.500 0.00 0.00 0.00 1.82
1628 1661 5.333566 AGAGGTTAAGGTGGATGGAAAAA 57.666 39.130 0.00 0.00 0.00 1.94
1629 1662 5.076873 CAAGAGGTTAAGGTGGATGGAAAA 58.923 41.667 0.00 0.00 0.00 2.29
1630 1663 4.352595 TCAAGAGGTTAAGGTGGATGGAAA 59.647 41.667 0.00 0.00 0.00 3.13
1631 1664 3.913799 TCAAGAGGTTAAGGTGGATGGAA 59.086 43.478 0.00 0.00 0.00 3.53
1632 1665 3.526899 TCAAGAGGTTAAGGTGGATGGA 58.473 45.455 0.00 0.00 0.00 3.41
1633 1666 4.301072 TTCAAGAGGTTAAGGTGGATGG 57.699 45.455 0.00 0.00 0.00 3.51
1634 1667 5.334879 CGTTTTCAAGAGGTTAAGGTGGATG 60.335 44.000 0.00 0.00 0.00 3.51
1635 1668 4.760204 CGTTTTCAAGAGGTTAAGGTGGAT 59.240 41.667 0.00 0.00 0.00 3.41
1636 1669 4.131596 CGTTTTCAAGAGGTTAAGGTGGA 58.868 43.478 0.00 0.00 0.00 4.02
1637 1670 4.131596 TCGTTTTCAAGAGGTTAAGGTGG 58.868 43.478 0.00 0.00 0.00 4.61
1638 1671 5.744666 TTCGTTTTCAAGAGGTTAAGGTG 57.255 39.130 0.00 0.00 0.00 4.00
1639 1672 6.771267 AGAATTCGTTTTCAAGAGGTTAAGGT 59.229 34.615 0.00 0.00 0.00 3.50
1640 1673 7.203255 AGAATTCGTTTTCAAGAGGTTAAGG 57.797 36.000 0.00 0.00 0.00 2.69
1641 1674 8.770828 TGTAGAATTCGTTTTCAAGAGGTTAAG 58.229 33.333 0.00 0.00 0.00 1.85
1642 1675 8.665643 TGTAGAATTCGTTTTCAAGAGGTTAA 57.334 30.769 0.00 0.00 0.00 2.01
1643 1676 8.842358 ATGTAGAATTCGTTTTCAAGAGGTTA 57.158 30.769 0.00 0.00 0.00 2.85
1644 1677 7.661847 AGATGTAGAATTCGTTTTCAAGAGGTT 59.338 33.333 0.00 0.00 0.00 3.50
1645 1678 7.162082 AGATGTAGAATTCGTTTTCAAGAGGT 58.838 34.615 0.00 0.00 0.00 3.85
1646 1679 7.547370 AGAGATGTAGAATTCGTTTTCAAGAGG 59.453 37.037 0.00 0.00 0.00 3.69
1647 1680 8.472683 AGAGATGTAGAATTCGTTTTCAAGAG 57.527 34.615 0.00 0.00 0.00 2.85
1648 1681 8.088365 TGAGAGATGTAGAATTCGTTTTCAAGA 58.912 33.333 0.00 0.00 0.00 3.02
1649 1682 8.244494 TGAGAGATGTAGAATTCGTTTTCAAG 57.756 34.615 0.00 0.00 0.00 3.02
1650 1683 8.659491 CATGAGAGATGTAGAATTCGTTTTCAA 58.341 33.333 0.00 0.00 0.00 2.69
1651 1684 7.819415 ACATGAGAGATGTAGAATTCGTTTTCA 59.181 33.333 0.00 0.00 0.00 2.69
1652 1685 8.190888 ACATGAGAGATGTAGAATTCGTTTTC 57.809 34.615 0.00 0.00 0.00 2.29
1653 1686 9.088512 GTACATGAGAGATGTAGAATTCGTTTT 57.911 33.333 0.00 0.00 35.43 2.43
1654 1687 7.432545 CGTACATGAGAGATGTAGAATTCGTTT 59.567 37.037 0.00 0.00 35.43 3.60
1655 1688 6.913132 CGTACATGAGAGATGTAGAATTCGTT 59.087 38.462 0.00 0.00 35.43 3.85
1656 1689 6.431278 CGTACATGAGAGATGTAGAATTCGT 58.569 40.000 0.00 0.00 35.43 3.85
1657 1690 5.340932 GCGTACATGAGAGATGTAGAATTCG 59.659 44.000 0.00 0.00 35.43 3.34
1658 1691 6.209361 TGCGTACATGAGAGATGTAGAATTC 58.791 40.000 0.00 0.00 35.43 2.17
1659 1692 6.149129 TGCGTACATGAGAGATGTAGAATT 57.851 37.500 0.00 0.00 35.43 2.17
1660 1693 5.774498 TGCGTACATGAGAGATGTAGAAT 57.226 39.130 0.00 0.00 35.43 2.40
1661 1694 5.576447 TTGCGTACATGAGAGATGTAGAA 57.424 39.130 0.00 0.00 35.43 2.10
1662 1695 5.299279 TGATTGCGTACATGAGAGATGTAGA 59.701 40.000 0.00 0.00 35.43 2.59
1663 1696 5.523369 TGATTGCGTACATGAGAGATGTAG 58.477 41.667 0.00 0.00 35.43 2.74
1664 1697 5.514274 TGATTGCGTACATGAGAGATGTA 57.486 39.130 0.00 0.00 33.76 2.29
1665 1698 4.391405 TGATTGCGTACATGAGAGATGT 57.609 40.909 0.00 0.00 36.13 3.06
1666 1699 5.063817 TGTTTGATTGCGTACATGAGAGATG 59.936 40.000 0.00 0.00 0.00 2.90
1667 1700 5.178061 TGTTTGATTGCGTACATGAGAGAT 58.822 37.500 0.00 0.00 0.00 2.75
1668 1701 4.565022 TGTTTGATTGCGTACATGAGAGA 58.435 39.130 0.00 0.00 0.00 3.10
1669 1702 4.726021 GCTGTTTGATTGCGTACATGAGAG 60.726 45.833 0.00 0.00 0.00 3.20
1670 1703 3.125146 GCTGTTTGATTGCGTACATGAGA 59.875 43.478 0.00 0.00 0.00 3.27
1671 1704 3.419915 GCTGTTTGATTGCGTACATGAG 58.580 45.455 0.00 0.00 0.00 2.90
1672 1705 2.161410 GGCTGTTTGATTGCGTACATGA 59.839 45.455 0.00 0.00 0.00 3.07
1673 1706 2.095314 TGGCTGTTTGATTGCGTACATG 60.095 45.455 0.00 0.00 0.00 3.21
1674 1707 2.158559 TGGCTGTTTGATTGCGTACAT 58.841 42.857 0.00 0.00 0.00 2.29
1675 1708 1.598882 TGGCTGTTTGATTGCGTACA 58.401 45.000 0.00 0.00 0.00 2.90
1676 1709 2.919666 ATGGCTGTTTGATTGCGTAC 57.080 45.000 0.00 0.00 0.00 3.67
1677 1710 4.733230 GCATAATGGCTGTTTGATTGCGTA 60.733 41.667 0.00 0.00 0.00 4.42
1678 1711 3.772932 CATAATGGCTGTTTGATTGCGT 58.227 40.909 0.00 0.00 0.00 5.24
1679 1712 2.536803 GCATAATGGCTGTTTGATTGCG 59.463 45.455 0.00 0.00 0.00 4.85
1680 1713 3.523547 TGCATAATGGCTGTTTGATTGC 58.476 40.909 0.00 0.00 34.04 3.56
1681 1714 4.025229 GCATGCATAATGGCTGTTTGATTG 60.025 41.667 14.21 0.00 36.71 2.67
1682 1715 4.124238 GCATGCATAATGGCTGTTTGATT 58.876 39.130 14.21 0.00 36.71 2.57
1683 1716 3.724374 GCATGCATAATGGCTGTTTGAT 58.276 40.909 14.21 0.00 36.71 2.57
1684 1717 3.167921 GCATGCATAATGGCTGTTTGA 57.832 42.857 14.21 0.00 36.71 2.69
1703 1736 2.030946 CGATTACAACTAAGCAGCAGGC 59.969 50.000 0.00 0.00 45.30 4.85
1704 1737 2.609459 CCGATTACAACTAAGCAGCAGG 59.391 50.000 0.00 0.00 0.00 4.85
1705 1738 2.030946 GCCGATTACAACTAAGCAGCAG 59.969 50.000 0.00 0.00 0.00 4.24
1706 1739 2.006888 GCCGATTACAACTAAGCAGCA 58.993 47.619 0.00 0.00 0.00 4.41
1707 1740 1.004927 CGCCGATTACAACTAAGCAGC 60.005 52.381 0.00 0.00 0.00 5.25
1708 1741 1.593006 CCGCCGATTACAACTAAGCAG 59.407 52.381 0.00 0.00 0.00 4.24
1709 1742 1.205179 TCCGCCGATTACAACTAAGCA 59.795 47.619 0.00 0.00 0.00 3.91
1710 1743 1.930567 TCCGCCGATTACAACTAAGC 58.069 50.000 0.00 0.00 0.00 3.09
1711 1744 6.036300 TGTTATTTCCGCCGATTACAACTAAG 59.964 38.462 0.00 0.00 0.00 2.18
1712 1745 5.873712 TGTTATTTCCGCCGATTACAACTAA 59.126 36.000 0.00 0.00 0.00 2.24
1713 1746 5.417811 TGTTATTTCCGCCGATTACAACTA 58.582 37.500 0.00 0.00 0.00 2.24
1714 1747 4.255301 TGTTATTTCCGCCGATTACAACT 58.745 39.130 0.00 0.00 0.00 3.16
1715 1748 4.603231 TGTTATTTCCGCCGATTACAAC 57.397 40.909 0.00 0.00 0.00 3.32
1716 1749 5.354513 TCAATGTTATTTCCGCCGATTACAA 59.645 36.000 0.00 0.00 0.00 2.41
1717 1750 4.876679 TCAATGTTATTTCCGCCGATTACA 59.123 37.500 0.00 0.00 0.00 2.41
1718 1751 5.412526 TCAATGTTATTTCCGCCGATTAC 57.587 39.130 0.00 0.00 0.00 1.89
1719 1752 4.024387 GCTCAATGTTATTTCCGCCGATTA 60.024 41.667 0.00 0.00 0.00 1.75
1720 1753 3.243068 GCTCAATGTTATTTCCGCCGATT 60.243 43.478 0.00 0.00 0.00 3.34
1721 1754 2.290641 GCTCAATGTTATTTCCGCCGAT 59.709 45.455 0.00 0.00 0.00 4.18
1722 1755 1.668751 GCTCAATGTTATTTCCGCCGA 59.331 47.619 0.00 0.00 0.00 5.54
1723 1756 1.268539 GGCTCAATGTTATTTCCGCCG 60.269 52.381 0.00 0.00 0.00 6.46
1724 1757 2.024414 AGGCTCAATGTTATTTCCGCC 58.976 47.619 0.00 0.00 36.58 6.13
1725 1758 2.945668 AGAGGCTCAATGTTATTTCCGC 59.054 45.455 18.26 0.00 0.00 5.54
1726 1759 5.123820 TCAAAGAGGCTCAATGTTATTTCCG 59.876 40.000 18.26 0.00 0.00 4.30
1727 1760 6.515272 TCAAAGAGGCTCAATGTTATTTCC 57.485 37.500 18.26 0.00 0.00 3.13
1728 1761 8.246180 TGAATCAAAGAGGCTCAATGTTATTTC 58.754 33.333 18.26 14.90 0.00 2.17
1729 1762 8.125978 TGAATCAAAGAGGCTCAATGTTATTT 57.874 30.769 18.26 3.53 0.00 1.40
1730 1763 7.707624 TGAATCAAAGAGGCTCAATGTTATT 57.292 32.000 18.26 10.84 0.00 1.40
1731 1764 7.707624 TTGAATCAAAGAGGCTCAATGTTAT 57.292 32.000 18.26 2.99 0.00 1.89
1732 1765 7.523293 TTTGAATCAAAGAGGCTCAATGTTA 57.477 32.000 18.26 0.64 0.00 2.41
1733 1766 6.409524 TTTGAATCAAAGAGGCTCAATGTT 57.590 33.333 18.26 11.03 0.00 2.71
1747 1780 9.981114 GAACCCTCTAAAAATTCTTTGAATCAA 57.019 29.630 0.00 0.00 0.00 2.57
1748 1781 9.367160 AGAACCCTCTAAAAATTCTTTGAATCA 57.633 29.630 0.00 0.00 0.00 2.57
1774 1807 7.669722 AGAAAAGAAACACATGCCTAAGGATTA 59.330 33.333 0.00 0.00 0.00 1.75
1775 1808 6.494835 AGAAAAGAAACACATGCCTAAGGATT 59.505 34.615 0.00 0.00 0.00 3.01
1776 1809 6.012745 AGAAAAGAAACACATGCCTAAGGAT 58.987 36.000 0.00 0.00 0.00 3.24
1777 1810 5.385198 AGAAAAGAAACACATGCCTAAGGA 58.615 37.500 0.00 0.00 0.00 3.36
1778 1811 5.712152 AGAAAAGAAACACATGCCTAAGG 57.288 39.130 0.00 0.00 0.00 2.69
1779 1812 7.428826 AGAAAGAAAAGAAACACATGCCTAAG 58.571 34.615 0.00 0.00 0.00 2.18
1780 1813 7.346751 AGAAAGAAAAGAAACACATGCCTAA 57.653 32.000 0.00 0.00 0.00 2.69
1781 1814 6.959639 AGAAAGAAAAGAAACACATGCCTA 57.040 33.333 0.00 0.00 0.00 3.93
1782 1815 5.859205 AGAAAGAAAAGAAACACATGCCT 57.141 34.783 0.00 0.00 0.00 4.75
1783 1816 6.758416 AGAAAGAAAGAAAAGAAACACATGCC 59.242 34.615 0.00 0.00 0.00 4.40
1784 1817 7.761651 AGAAAGAAAGAAAAGAAACACATGC 57.238 32.000 0.00 0.00 0.00 4.06
1879 1912 9.783256 AAGCCGACAAATAATAAATCTTGTAAC 57.217 29.630 0.00 0.00 32.31 2.50
1920 1953 9.802039 ACCTACAAAGAAATCTTATAACAACCA 57.198 29.630 0.00 0.00 34.61 3.67
1945 1981 8.040727 AGGTGGATGGAAATTTTGCTATAAAAC 58.959 33.333 2.25 0.00 0.00 2.43
1949 1985 8.691797 GTTAAGGTGGATGGAAATTTTGCTATA 58.308 33.333 2.25 0.00 0.00 1.31
1950 1986 7.364673 GGTTAAGGTGGATGGAAATTTTGCTAT 60.365 37.037 2.25 0.00 0.00 2.97
1992 2079 5.113383 TGATTGGGTACATCAATGACGTAC 58.887 41.667 10.75 10.75 35.26 3.67
1999 2086 4.160252 GGCTGTTTGATTGGGTACATCAAT 59.840 41.667 11.79 11.79 37.52 2.57
2002 2089 3.088532 TGGCTGTTTGATTGGGTACATC 58.911 45.455 0.00 0.00 0.00 3.06
2009 2096 4.327898 CGAAATGAATGGCTGTTTGATTGG 59.672 41.667 0.00 0.00 0.00 3.16
2033 2120 1.198408 CTTTGATGTGCACGCAGACAT 59.802 47.619 13.13 0.00 35.46 3.06
2037 2124 0.167470 CCTCTTTGATGTGCACGCAG 59.833 55.000 13.13 3.41 0.00 5.18
2040 2127 1.503542 GCCCTCTTTGATGTGCACG 59.496 57.895 13.13 0.00 0.00 5.34
2057 2152 1.153958 GCATCTGGCGAACAAAGGC 60.154 57.895 0.00 0.00 0.00 4.35
2070 2170 8.761575 AAATTAATTGATGTTTCAACGCATCT 57.238 26.923 0.39 0.00 44.36 2.90
2160 2268 1.094785 ATTGCTTTCGTTCGATGGGG 58.905 50.000 0.00 0.00 0.00 4.96
2166 2274 1.052287 GCCAACATTGCTTTCGTTCG 58.948 50.000 0.00 0.00 0.00 3.95
2185 2293 5.473066 AAGGGTCATTGTTTGGATTCTTG 57.527 39.130 0.00 0.00 0.00 3.02
2214 2322 5.741388 AACAAGCAGTCAGTAACAAGAAG 57.259 39.130 0.00 0.00 0.00 2.85
2215 2323 7.217200 AGATAACAAGCAGTCAGTAACAAGAA 58.783 34.615 0.00 0.00 0.00 2.52
2217 2325 6.870965 AGAGATAACAAGCAGTCAGTAACAAG 59.129 38.462 0.00 0.00 0.00 3.16
2220 2328 5.062809 GCAGAGATAACAAGCAGTCAGTAAC 59.937 44.000 0.00 0.00 0.00 2.50
2297 3197 6.202954 CGTATAAATGCAAGAGTTTAGGGGAG 59.797 42.308 0.00 0.00 0.00 4.30
2329 3237 6.198650 TCGGTCTTCATCGACATTTAGTTA 57.801 37.500 0.00 0.00 35.63 2.24
2337 3245 3.250744 GTTTGATCGGTCTTCATCGACA 58.749 45.455 0.00 0.00 38.25 4.35
2338 3246 3.060895 GTGTTTGATCGGTCTTCATCGAC 59.939 47.826 0.00 0.00 38.25 4.20
2345 3253 4.253685 CCATGTAGTGTTTGATCGGTCTT 58.746 43.478 0.00 0.00 0.00 3.01
2346 3254 3.260884 ACCATGTAGTGTTTGATCGGTCT 59.739 43.478 0.00 0.00 0.00 3.85
2347 3255 3.596214 ACCATGTAGTGTTTGATCGGTC 58.404 45.455 0.00 0.00 0.00 4.79
2349 3257 2.936498 GGACCATGTAGTGTTTGATCGG 59.064 50.000 0.00 0.00 0.00 4.18
2350 3258 3.861840 AGGACCATGTAGTGTTTGATCG 58.138 45.455 0.00 0.00 0.00 3.69
2351 3259 4.080863 AGGAGGACCATGTAGTGTTTGATC 60.081 45.833 0.00 0.00 38.94 2.92
2353 3261 3.248024 AGGAGGACCATGTAGTGTTTGA 58.752 45.455 0.00 0.00 38.94 2.69


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

AutoCloner maintained by Alex Coulton.