Multiple sequence alignment - TraesCS1D01G209100

Loading Multiple Alignment...

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 TraesCS1D01G209100 chr1D 100.000 2498 0 0 1 2498 295185822 295188319 0.000000e+00 4614.0
1 TraesCS1D01G209100 chr1B 95.872 1526 43 12 1 1516 396595949 396597464 0.000000e+00 2451.0
2 TraesCS1D01G209100 chr1B 78.182 330 51 17 2156 2478 681726407 681726722 9.120000e-45 191.0
3 TraesCS1D01G209100 chr1B 83.051 118 20 0 2219 2336 667660131 667660014 9.450000e-20 108.0
4 TraesCS1D01G209100 chr1B 83.333 108 18 0 1784 1891 573066804 573066697 1.580000e-17 100.0
5 TraesCS1D01G209100 chr1A 94.572 1566 54 11 1 1538 368363294 368364856 0.000000e+00 2392.0
6 TraesCS1D01G209100 chr1A 77.374 358 58 15 2148 2498 399827610 399827269 9.120000e-45 191.0
7 TraesCS1D01G209100 chr1A 87.770 139 16 1 1784 1922 554093783 554093920 7.150000e-36 161.0
8 TraesCS1D01G209100 chr1A 75.170 294 60 12 2210 2497 575681239 575680953 2.610000e-25 126.0
9 TraesCS1D01G209100 chr7A 77.181 745 134 16 1780 2498 592200608 592199874 3.870000e-108 401.0
10 TraesCS1D01G209100 chr7A 74.359 468 82 26 1917 2359 17688925 17689379 5.530000e-37 165.0
11 TraesCS1D01G209100 chr7A 84.000 125 17 2 1787 1910 509954597 509954475 1.570000e-22 117.0
12 TraesCS1D01G209100 chr4D 76.445 692 108 30 1849 2498 85001077 85000399 8.620000e-85 324.0
13 TraesCS1D01G209100 chr6A 78.692 474 75 17 1987 2443 11236871 11237335 2.430000e-75 292.0
14 TraesCS1D01G209100 chr6D 79.211 279 55 3 2222 2498 454924373 454924650 9.120000e-45 191.0
15 TraesCS1D01G209100 chr6D 78.882 161 28 4 2167 2321 384442629 384442469 1.220000e-18 104.0
16 TraesCS1D01G209100 chr5B 90.000 90 9 0 1790 1879 82243814 82243725 1.570000e-22 117.0
17 TraesCS1D01G209100 chr5B 81.818 110 20 0 2219 2328 36619508 36619617 2.650000e-15 93.5
18 TraesCS1D01G209100 chr2D 86.239 109 14 1 1783 1890 541549254 541549362 1.570000e-22 117.0
19 TraesCS1D01G209100 chr7D 89.011 91 10 0 1800 1890 45152702 45152612 2.030000e-21 113.0
20 TraesCS1D01G209100 chr5D 85.437 103 14 1 2219 2321 70522659 70522558 3.400000e-19 106.0
21 TraesCS1D01G209100 chr3D 84.615 104 16 0 1787 1890 1883944 1884047 1.220000e-18 104.0
22 TraesCS1D01G209100 chr5A 83.333 108 17 1 1783 1889 428994211 428994104 5.690000e-17 99.0
23 TraesCS1D01G209100 chr4A 77.049 122 27 1 1784 1905 38668362 38668242 4.460000e-08 69.4


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 TraesCS1D01G209100 chr1D 295185822 295188319 2497 False 4614 4614 100.000 1 2498 1 chr1D.!!$F1 2497
1 TraesCS1D01G209100 chr1B 396595949 396597464 1515 False 2451 2451 95.872 1 1516 1 chr1B.!!$F1 1515
2 TraesCS1D01G209100 chr1A 368363294 368364856 1562 False 2392 2392 94.572 1 1538 1 chr1A.!!$F1 1537
3 TraesCS1D01G209100 chr7A 592199874 592200608 734 True 401 401 77.181 1780 2498 1 chr7A.!!$R2 718
4 TraesCS1D01G209100 chr4D 85000399 85001077 678 True 324 324 76.445 1849 2498 1 chr4D.!!$R1 649

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
294 296 0.332972 GGGCTTCCTTCCCAGACAAT 59.667 55.0 0.0 0.0 43.37 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 1710 0.041535 AGGAAATGCAATCTGCCCCA 59.958 50.0 0.0 0.0 44.23 4.96 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
213 214 1.723220 GCACGAACTTCCCCTACTTC 58.277 55.000 0.00 0.00 0.00 3.01
294 296 0.332972 GGGCTTCCTTCCCAGACAAT 59.667 55.000 0.00 0.00 43.37 2.71
396 409 3.809832 AGCACGCTGGATTATCAACATAC 59.190 43.478 0.00 0.00 0.00 2.39
411 424 1.519455 ATACGAGCGCCTCAACAGC 60.519 57.895 2.29 0.00 0.00 4.40
538 564 0.596600 CTCGGGCAACATACGCGTAT 60.597 55.000 25.54 25.54 43.20 3.06
539 565 0.667453 TCGGGCAACATACGCGTATA 59.333 50.000 29.79 7.97 43.20 1.47
590 617 0.459585 GCCGATTTCTGCCTACACGA 60.460 55.000 0.00 0.00 0.00 4.35
665 692 1.158466 TCCAGCAGGGAAGAGGACA 59.842 57.895 0.00 0.00 44.80 4.02
1510 1545 3.102097 GCTGACCGCCATGCTTAC 58.898 61.111 0.00 0.00 0.00 2.34
1533 1571 6.609237 CATGGAGTATGTGTTCGATGAAAT 57.391 37.500 0.00 0.00 33.10 2.17
1538 1576 6.111768 AGTATGTGTTCGATGAAATGCTTC 57.888 37.500 0.00 0.00 0.00 3.86
1539 1577 3.454042 TGTGTTCGATGAAATGCTTCG 57.546 42.857 0.00 0.00 43.30 3.79
1544 1582 2.959516 TCGATGAAATGCTTCGACTGT 58.040 42.857 0.00 0.00 44.91 3.55
1545 1583 4.104696 TCGATGAAATGCTTCGACTGTA 57.895 40.909 0.00 0.00 44.91 2.74
1546 1584 4.682787 TCGATGAAATGCTTCGACTGTAT 58.317 39.130 0.00 0.00 44.91 2.29
1547 1585 4.740205 TCGATGAAATGCTTCGACTGTATC 59.260 41.667 0.00 0.00 44.91 2.24
1563 1601 5.468592 ACTGTATCGATCAATGATCTCTGC 58.531 41.667 19.62 11.08 36.96 4.26
1564 1602 5.010415 ACTGTATCGATCAATGATCTCTGCA 59.990 40.000 19.62 14.35 36.96 4.41
1565 1603 6.034161 TGTATCGATCAATGATCTCTGCAT 57.966 37.500 19.62 7.44 36.96 3.96
1566 1604 5.867716 TGTATCGATCAATGATCTCTGCATG 59.132 40.000 19.62 4.05 36.96 4.06
1567 1605 4.595762 TCGATCAATGATCTCTGCATGA 57.404 40.909 19.62 6.22 36.96 3.07
1568 1606 4.304939 TCGATCAATGATCTCTGCATGAC 58.695 43.478 19.62 0.00 36.96 3.06
1569 1607 4.038883 TCGATCAATGATCTCTGCATGACT 59.961 41.667 19.62 0.00 36.96 3.41
1570 1608 4.150804 CGATCAATGATCTCTGCATGACTG 59.849 45.833 19.62 0.00 36.96 3.51
1571 1609 4.482952 TCAATGATCTCTGCATGACTGT 57.517 40.909 0.00 0.00 0.00 3.55
1572 1610 5.603170 TCAATGATCTCTGCATGACTGTA 57.397 39.130 0.00 0.00 0.00 2.74
1573 1611 5.981174 TCAATGATCTCTGCATGACTGTAA 58.019 37.500 0.00 0.00 0.00 2.41
1574 1612 6.408869 TCAATGATCTCTGCATGACTGTAAA 58.591 36.000 0.00 0.00 0.00 2.01
1575 1613 6.537660 TCAATGATCTCTGCATGACTGTAAAG 59.462 38.462 0.00 0.00 0.00 1.85
1576 1614 4.186926 TGATCTCTGCATGACTGTAAAGC 58.813 43.478 0.00 0.00 0.00 3.51
1577 1615 3.969287 TCTCTGCATGACTGTAAAGCT 57.031 42.857 0.00 0.00 0.00 3.74
1578 1616 3.854666 TCTCTGCATGACTGTAAAGCTC 58.145 45.455 0.00 0.00 0.00 4.09
1579 1617 3.513119 TCTCTGCATGACTGTAAAGCTCT 59.487 43.478 0.00 0.00 0.00 4.09
1580 1618 3.854666 TCTGCATGACTGTAAAGCTCTC 58.145 45.455 0.00 0.00 0.00 3.20
1581 1619 3.513119 TCTGCATGACTGTAAAGCTCTCT 59.487 43.478 0.00 0.00 0.00 3.10
1582 1620 4.020751 TCTGCATGACTGTAAAGCTCTCTT 60.021 41.667 0.00 0.00 0.00 2.85
1583 1621 4.645535 TGCATGACTGTAAAGCTCTCTTT 58.354 39.130 0.00 0.00 44.22 2.52
1584 1622 4.692625 TGCATGACTGTAAAGCTCTCTTTC 59.307 41.667 0.00 0.00 41.34 2.62
1585 1623 4.934602 GCATGACTGTAAAGCTCTCTTTCT 59.065 41.667 0.00 0.00 41.34 2.52
1586 1624 5.163874 GCATGACTGTAAAGCTCTCTTTCTG 60.164 44.000 0.00 0.00 41.34 3.02
1587 1625 4.310769 TGACTGTAAAGCTCTCTTTCTGC 58.689 43.478 0.00 0.00 41.34 4.26
1588 1626 3.669536 ACTGTAAAGCTCTCTTTCTGCC 58.330 45.455 0.00 0.00 41.34 4.85
1589 1627 3.071602 ACTGTAAAGCTCTCTTTCTGCCA 59.928 43.478 0.00 0.00 41.34 4.92
1590 1628 3.668447 TGTAAAGCTCTCTTTCTGCCAG 58.332 45.455 0.00 0.00 41.34 4.85
1591 1629 3.324846 TGTAAAGCTCTCTTTCTGCCAGA 59.675 43.478 0.00 0.00 41.34 3.86
1592 1630 3.717452 AAAGCTCTCTTTCTGCCAGAT 57.283 42.857 0.00 0.00 38.03 2.90
1593 1631 3.717452 AAGCTCTCTTTCTGCCAGATT 57.283 42.857 0.00 0.00 0.00 2.40
1594 1632 2.988570 AGCTCTCTTTCTGCCAGATTG 58.011 47.619 0.00 0.00 0.00 2.67
1595 1633 1.401199 GCTCTCTTTCTGCCAGATTGC 59.599 52.381 0.00 0.00 0.00 3.56
1596 1634 2.708051 CTCTCTTTCTGCCAGATTGCA 58.292 47.619 0.00 0.00 39.37 4.08
1604 1642 1.985473 TGCCAGATTGCAGTCAAACT 58.015 45.000 12.16 0.00 35.98 2.66
1605 1643 2.309613 TGCCAGATTGCAGTCAAACTT 58.690 42.857 12.16 0.00 33.72 2.66
1606 1644 2.694628 TGCCAGATTGCAGTCAAACTTT 59.305 40.909 12.16 0.00 33.72 2.66
1607 1645 3.243501 TGCCAGATTGCAGTCAAACTTTC 60.244 43.478 12.16 0.00 33.72 2.62
1608 1646 3.243501 GCCAGATTGCAGTCAAACTTTCA 60.244 43.478 12.16 0.00 33.72 2.69
1609 1647 4.293415 CCAGATTGCAGTCAAACTTTCAC 58.707 43.478 12.16 0.00 33.72 3.18
1610 1648 4.202040 CCAGATTGCAGTCAAACTTTCACA 60.202 41.667 12.16 0.00 33.72 3.58
1611 1649 5.342433 CAGATTGCAGTCAAACTTTCACAA 58.658 37.500 12.16 0.00 33.72 3.33
1612 1650 5.457799 CAGATTGCAGTCAAACTTTCACAAG 59.542 40.000 12.16 0.00 33.72 3.16
1613 1651 4.782019 TTGCAGTCAAACTTTCACAAGT 57.218 36.364 0.00 0.00 45.89 3.16
1657 1695 9.754382 CCAAAAGGTTATTATCTGATCAAATGG 57.246 33.333 0.00 0.00 0.00 3.16
1662 1700 9.927081 AGGTTATTATCTGATCAAATGGTTTCT 57.073 29.630 0.00 0.00 0.00 2.52
1667 1705 8.648557 TTATCTGATCAAATGGTTTCTCTACG 57.351 34.615 0.00 0.00 0.00 3.51
1668 1706 6.037786 TCTGATCAAATGGTTTCTCTACGT 57.962 37.500 0.00 0.00 0.00 3.57
1669 1707 7.165460 TCTGATCAAATGGTTTCTCTACGTA 57.835 36.000 0.00 0.00 0.00 3.57
1670 1708 7.782049 TCTGATCAAATGGTTTCTCTACGTAT 58.218 34.615 0.00 0.00 0.00 3.06
1671 1709 8.258007 TCTGATCAAATGGTTTCTCTACGTATT 58.742 33.333 0.00 0.00 0.00 1.89
1672 1710 8.786826 TGATCAAATGGTTTCTCTACGTATTT 57.213 30.769 0.00 0.00 0.00 1.40
1673 1711 8.664798 TGATCAAATGGTTTCTCTACGTATTTG 58.335 33.333 0.00 2.06 36.11 2.32
1674 1712 7.372451 TCAAATGGTTTCTCTACGTATTTGG 57.628 36.000 12.28 0.00 35.83 3.28
1675 1713 6.373216 TCAAATGGTTTCTCTACGTATTTGGG 59.627 38.462 12.28 0.00 35.83 4.12
1676 1714 4.210724 TGGTTTCTCTACGTATTTGGGG 57.789 45.455 0.00 0.00 0.00 4.96
1677 1715 2.941064 GGTTTCTCTACGTATTTGGGGC 59.059 50.000 0.00 0.00 0.00 5.80
1678 1716 3.602483 GTTTCTCTACGTATTTGGGGCA 58.398 45.455 0.00 0.00 0.00 5.36
1679 1717 3.536956 TTCTCTACGTATTTGGGGCAG 57.463 47.619 0.00 0.00 0.00 4.85
1680 1718 2.742348 TCTCTACGTATTTGGGGCAGA 58.258 47.619 0.00 0.00 0.00 4.26
1681 1719 3.305720 TCTCTACGTATTTGGGGCAGAT 58.694 45.455 0.00 0.00 0.00 2.90
1682 1720 3.709653 TCTCTACGTATTTGGGGCAGATT 59.290 43.478 0.00 0.00 0.00 2.40
1683 1721 3.804036 TCTACGTATTTGGGGCAGATTG 58.196 45.455 0.00 0.00 0.00 2.67
1684 1722 1.102978 ACGTATTTGGGGCAGATTGC 58.897 50.000 0.00 0.00 44.08 3.56
1700 1738 2.951269 TGCATTTCCTCTGCACTGG 58.049 52.632 0.00 0.00 44.30 4.00
1701 1739 0.401356 TGCATTTCCTCTGCACTGGA 59.599 50.000 0.00 0.00 44.30 3.86
1702 1740 1.005097 TGCATTTCCTCTGCACTGGAT 59.995 47.619 4.01 0.00 44.30 3.41
1703 1741 2.097825 GCATTTCCTCTGCACTGGATT 58.902 47.619 4.01 0.00 39.46 3.01
1704 1742 2.494870 GCATTTCCTCTGCACTGGATTT 59.505 45.455 4.01 0.00 39.46 2.17
1705 1743 3.675228 GCATTTCCTCTGCACTGGATTTG 60.675 47.826 4.01 6.28 39.46 2.32
1706 1744 1.538047 TTCCTCTGCACTGGATTTGC 58.462 50.000 4.01 0.00 40.63 3.68
1707 1745 0.694771 TCCTCTGCACTGGATTTGCT 59.305 50.000 0.00 0.00 40.86 3.91
1708 1746 1.093159 CCTCTGCACTGGATTTGCTC 58.907 55.000 0.00 0.00 40.86 4.26
1709 1747 1.612462 CCTCTGCACTGGATTTGCTCA 60.612 52.381 0.00 0.00 40.86 4.26
1710 1748 1.467734 CTCTGCACTGGATTTGCTCAC 59.532 52.381 0.00 0.00 40.86 3.51
1711 1749 1.202794 TCTGCACTGGATTTGCTCACA 60.203 47.619 0.00 0.00 40.86 3.58
1712 1750 0.953727 TGCACTGGATTTGCTCACAC 59.046 50.000 0.00 0.00 40.86 3.82
1713 1751 0.110056 GCACTGGATTTGCTCACACG 60.110 55.000 0.00 0.00 37.00 4.49
1714 1752 1.229428 CACTGGATTTGCTCACACGT 58.771 50.000 0.00 0.00 0.00 4.49
1715 1753 1.603802 CACTGGATTTGCTCACACGTT 59.396 47.619 0.00 0.00 0.00 3.99
1716 1754 1.873591 ACTGGATTTGCTCACACGTTC 59.126 47.619 0.00 0.00 0.00 3.95
1717 1755 0.865111 TGGATTTGCTCACACGTTCG 59.135 50.000 0.00 0.00 0.00 3.95
1718 1756 0.865769 GGATTTGCTCACACGTTCGT 59.134 50.000 0.00 0.00 0.00 3.85
1719 1757 2.063266 GGATTTGCTCACACGTTCGTA 58.937 47.619 0.00 0.00 0.00 3.43
1720 1758 2.159881 GGATTTGCTCACACGTTCGTAC 60.160 50.000 0.00 0.00 0.00 3.67
1730 1768 3.388059 CGTTCGTACGGTCATCACA 57.612 52.632 16.52 0.00 43.94 3.58
1731 1769 1.688793 CGTTCGTACGGTCATCACAA 58.311 50.000 16.52 0.00 43.94 3.33
1732 1770 2.052891 CGTTCGTACGGTCATCACAAA 58.947 47.619 16.52 0.00 43.94 2.83
1733 1771 2.160065 CGTTCGTACGGTCATCACAAAC 60.160 50.000 16.52 7.93 43.94 2.93
1734 1772 2.796031 GTTCGTACGGTCATCACAAACA 59.204 45.455 16.52 0.00 0.00 2.83
1735 1773 3.306917 TCGTACGGTCATCACAAACAT 57.693 42.857 16.52 0.00 0.00 2.71
1736 1774 4.437772 TCGTACGGTCATCACAAACATA 57.562 40.909 16.52 0.00 0.00 2.29
1737 1775 4.168014 TCGTACGGTCATCACAAACATAC 58.832 43.478 16.52 0.00 0.00 2.39
1738 1776 4.082625 TCGTACGGTCATCACAAACATACT 60.083 41.667 16.52 0.00 0.00 2.12
1739 1777 5.123661 TCGTACGGTCATCACAAACATACTA 59.876 40.000 16.52 0.00 0.00 1.82
1740 1778 5.801444 CGTACGGTCATCACAAACATACTAA 59.199 40.000 7.57 0.00 0.00 2.24
1741 1779 6.237384 CGTACGGTCATCACAAACATACTAAC 60.237 42.308 7.57 0.00 0.00 2.34
1742 1780 5.790593 ACGGTCATCACAAACATACTAACT 58.209 37.500 0.00 0.00 0.00 2.24
1743 1781 6.228258 ACGGTCATCACAAACATACTAACTT 58.772 36.000 0.00 0.00 0.00 2.66
1744 1782 6.708949 ACGGTCATCACAAACATACTAACTTT 59.291 34.615 0.00 0.00 0.00 2.66
1745 1783 7.015289 CGGTCATCACAAACATACTAACTTTG 58.985 38.462 0.00 0.00 0.00 2.77
1746 1784 7.305474 GGTCATCACAAACATACTAACTTTGG 58.695 38.462 0.00 0.00 30.52 3.28
1747 1785 7.305474 GTCATCACAAACATACTAACTTTGGG 58.695 38.462 0.00 0.00 30.79 4.12
1748 1786 6.432783 TCATCACAAACATACTAACTTTGGGG 59.567 38.462 0.00 0.00 30.57 4.96
1749 1787 4.521256 TCACAAACATACTAACTTTGGGGC 59.479 41.667 0.00 0.00 30.57 5.80
1750 1788 3.830178 ACAAACATACTAACTTTGGGGCC 59.170 43.478 0.00 0.00 30.52 5.80
1751 1789 3.818295 AACATACTAACTTTGGGGCCA 57.182 42.857 4.39 0.00 0.00 5.36
1752 1790 3.081710 ACATACTAACTTTGGGGCCAC 57.918 47.619 4.39 0.00 0.00 5.01
1753 1791 2.647802 ACATACTAACTTTGGGGCCACT 59.352 45.455 6.53 0.00 0.00 4.00
1754 1792 3.279434 CATACTAACTTTGGGGCCACTC 58.721 50.000 6.53 0.00 0.00 3.51
1755 1793 1.446016 ACTAACTTTGGGGCCACTCT 58.554 50.000 6.53 0.00 0.00 3.24
1756 1794 2.627933 ACTAACTTTGGGGCCACTCTA 58.372 47.619 6.53 0.00 0.00 2.43
1757 1795 2.983898 ACTAACTTTGGGGCCACTCTAA 59.016 45.455 6.53 0.00 0.00 2.10
1758 1796 3.591977 ACTAACTTTGGGGCCACTCTAAT 59.408 43.478 6.53 0.00 0.00 1.73
1759 1797 3.542969 AACTTTGGGGCCACTCTAATT 57.457 42.857 6.53 0.00 0.00 1.40
1760 1798 4.668138 AACTTTGGGGCCACTCTAATTA 57.332 40.909 6.53 0.00 0.00 1.40
1761 1799 4.668138 ACTTTGGGGCCACTCTAATTAA 57.332 40.909 6.53 0.00 0.00 1.40
1762 1800 5.206905 ACTTTGGGGCCACTCTAATTAAT 57.793 39.130 6.53 0.00 0.00 1.40
1763 1801 5.201243 ACTTTGGGGCCACTCTAATTAATC 58.799 41.667 6.53 0.00 0.00 1.75
1764 1802 3.876309 TGGGGCCACTCTAATTAATCC 57.124 47.619 6.53 0.00 0.00 3.01
1765 1803 2.445525 TGGGGCCACTCTAATTAATCCC 59.554 50.000 6.53 0.00 0.00 3.85
1766 1804 2.225041 GGGGCCACTCTAATTAATCCCC 60.225 54.545 4.39 7.64 44.53 4.81
1767 1805 2.716969 GGGCCACTCTAATTAATCCCCT 59.283 50.000 4.39 0.00 0.00 4.79
1768 1806 3.914435 GGGCCACTCTAATTAATCCCCTA 59.086 47.826 4.39 0.00 0.00 3.53
1769 1807 4.540502 GGGCCACTCTAATTAATCCCCTAT 59.459 45.833 4.39 0.00 0.00 2.57
1770 1808 5.729718 GGGCCACTCTAATTAATCCCCTATA 59.270 44.000 4.39 0.00 0.00 1.31
1771 1809 6.390165 GGGCCACTCTAATTAATCCCCTATAT 59.610 42.308 4.39 0.00 0.00 0.86
1772 1810 7.571357 GGGCCACTCTAATTAATCCCCTATATA 59.429 40.741 4.39 0.00 0.00 0.86
1773 1811 9.172060 GGCCACTCTAATTAATCCCCTATATAT 57.828 37.037 0.00 0.00 0.00 0.86
1790 1828 8.451245 CCCTATATATAACCGAGAACCCCTATA 58.549 40.741 0.00 0.00 0.00 1.31
1798 1836 9.947189 ATAACCGAGAACCCCTATATATAATGA 57.053 33.333 0.00 0.00 0.00 2.57
1805 1843 9.453830 AGAACCCCTATATATAATGAAGGATCC 57.546 37.037 2.48 2.48 0.00 3.36
1810 1848 6.208797 CCTATATATAATGAAGGATCCGGCGA 59.791 42.308 9.30 0.00 0.00 5.54
1817 1855 1.931841 GAAGGATCCGGCGAAGTAAAC 59.068 52.381 9.30 0.00 0.00 2.01
1826 1864 2.353011 CGGCGAAGTAAACCCTTAGTGA 60.353 50.000 0.00 0.00 0.00 3.41
1858 1896 9.920946 TTTTACTCTATTAAGATTTGGCTGGAT 57.079 29.630 0.00 0.00 0.00 3.41
1881 1919 8.283699 GATCTAGCCGATCCCCTATATATAAC 57.716 42.308 2.91 0.00 42.24 1.89
1882 1920 7.157947 TCTAGCCGATCCCCTATATATAACA 57.842 40.000 0.00 0.00 0.00 2.41
1883 1921 7.589081 TCTAGCCGATCCCCTATATATAACAA 58.411 38.462 0.00 0.00 0.00 2.83
1887 1925 7.842743 AGCCGATCCCCTATATATAACAAAGTA 59.157 37.037 0.00 0.00 0.00 2.24
1915 1953 8.845413 AAATCAAAATTGCATAAGTTAAGCCA 57.155 26.923 7.59 0.00 0.00 4.75
1924 1962 6.991938 TGCATAAGTTAAGCCAAGTTTCAAT 58.008 32.000 7.59 0.00 31.99 2.57
1925 1963 7.090173 TGCATAAGTTAAGCCAAGTTTCAATC 58.910 34.615 7.59 0.00 31.99 2.67
1926 1964 7.090173 GCATAAGTTAAGCCAAGTTTCAATCA 58.910 34.615 0.00 0.00 31.99 2.57
1930 1979 7.770801 AGTTAAGCCAAGTTTCAATCAAAAC 57.229 32.000 0.00 0.00 39.03 2.43
1964 2013 4.301072 AAGCATAAGTTCAACCTAGGCA 57.699 40.909 9.30 0.00 0.00 4.75
1965 2014 4.301072 AGCATAAGTTCAACCTAGGCAA 57.699 40.909 9.30 0.00 0.00 4.52
1975 2024 6.493458 AGTTCAACCTAGGCAAACATATTGTT 59.507 34.615 9.30 0.00 43.41 2.83
1988 2037 4.950050 ACATATTGTTTTGGCAACCGAAA 58.050 34.783 0.00 0.00 34.80 3.46
1989 2038 5.546526 ACATATTGTTTTGGCAACCGAAAT 58.453 33.333 0.00 0.79 38.89 2.17
1990 2039 6.692486 ACATATTGTTTTGGCAACCGAAATA 58.308 32.000 0.00 3.09 38.89 1.40
1991 2040 7.155328 ACATATTGTTTTGGCAACCGAAATAA 58.845 30.769 0.00 9.96 40.49 1.40
1992 2041 7.657761 ACATATTGTTTTGGCAACCGAAATAAA 59.342 29.630 11.18 6.34 39.94 1.40
1996 2045 5.817816 TGTTTTGGCAACCGAAATAAAACAT 59.182 32.000 0.00 0.00 40.77 2.71
2052 2117 3.689872 TCCTTGCCATAGTAGAGGTCT 57.310 47.619 0.00 0.00 0.00 3.85
2065 2130 5.265191 AGTAGAGGTCTAGTCAATCTTGCA 58.735 41.667 0.00 0.00 0.00 4.08
2068 2133 4.713814 AGAGGTCTAGTCAATCTTGCATCA 59.286 41.667 0.00 0.00 0.00 3.07
2090 2155 2.044352 GCTACCGCCCATTGGGTT 60.044 61.111 22.82 10.28 46.51 4.11
2098 2163 4.418328 CCATTGGGTTCGGGCCGA 62.418 66.667 27.46 27.46 0.00 5.54
2150 2238 4.052229 CCACTCCTCCGCGTCGTT 62.052 66.667 4.92 0.00 0.00 3.85
2153 2241 2.049433 CTCCTCCGCGTCGTTGTT 60.049 61.111 4.92 0.00 0.00 2.83
2154 2242 2.355363 TCCTCCGCGTCGTTGTTG 60.355 61.111 4.92 0.00 0.00 3.33
2175 2284 3.121030 CCGCCTTGCTCCTCGTTG 61.121 66.667 0.00 0.00 0.00 4.10
2186 2295 1.763968 TCCTCGTTGTCGGAGATGAT 58.236 50.000 0.00 0.00 40.67 2.45
2207 2316 3.308705 GACCTCCCCGTTGACCGT 61.309 66.667 0.00 0.00 33.66 4.83
2214 2323 4.052229 CCGTTGACCGTCCGCTCT 62.052 66.667 0.00 0.00 33.66 4.09
2217 2326 3.611674 TTGACCGTCCGCTCTGCA 61.612 61.111 0.00 0.00 0.00 4.41
2223 2332 1.424493 CCGTCCGCTCTGCAAAGATC 61.424 60.000 0.00 0.00 0.00 2.75
2226 2335 2.319032 CGCTCTGCAAAGATCGCG 59.681 61.111 0.00 0.00 34.50 5.87
2283 2392 1.327690 GGTCCGCCATGTACTCCTCA 61.328 60.000 0.00 0.00 34.09 3.86
2353 2465 3.245346 TCACCGCATCCACCACCA 61.245 61.111 0.00 0.00 0.00 4.17
2354 2466 3.055719 CACCGCATCCACCACCAC 61.056 66.667 0.00 0.00 0.00 4.16
2383 2495 4.176752 GGGATGAGGTGGACGGGC 62.177 72.222 0.00 0.00 0.00 6.13
2385 2497 2.746375 GGATGAGGTGGACGGGCAT 61.746 63.158 0.00 0.00 0.00 4.40
2387 2499 2.978452 GATGAGGTGGACGGGCATCG 62.978 65.000 0.00 0.00 45.88 3.84
2409 2521 1.304052 CCCACGGGAAATTGAGCCA 60.304 57.895 0.00 0.00 37.50 4.75
2415 2527 1.579429 GGAAATTGAGCCACGCGTT 59.421 52.632 10.22 0.00 0.00 4.84
2454 2567 1.138859 CTGCCACGGTCATATTCCAGA 59.861 52.381 0.00 0.00 0.00 3.86
2483 2597 0.320073 TTCGTCATGTGGAACGACCC 60.320 55.000 6.85 0.00 42.39 4.46
2484 2598 2.092291 CGTCATGTGGAACGACCCG 61.092 63.158 0.00 0.00 42.39 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 214 2.472059 CGTGAATGGTCATGGCGGG 61.472 63.158 0.00 0.00 37.16 6.13
278 280 3.610911 GTGGTATTGTCTGGGAAGGAAG 58.389 50.000 0.00 0.00 0.00 3.46
294 296 2.437002 GGCGCGAATTGGGTGGTA 60.437 61.111 12.10 0.00 0.00 3.25
341 346 0.535335 GACGGTTCATGGCTGTAGGA 59.465 55.000 0.00 0.00 0.00 2.94
396 409 3.184683 GAGCTGTTGAGGCGCTCG 61.185 66.667 7.64 0.00 40.48 5.03
411 424 4.864334 GAGCATGGCCCGGTGGAG 62.864 72.222 0.00 0.00 0.00 3.86
461 475 1.613610 GCCCCTAGGGTTTCTTCCC 59.386 63.158 26.66 0.66 46.51 3.97
463 477 1.223763 CCGCCCCTAGGGTTTCTTC 59.776 63.158 26.66 7.14 46.51 2.87
538 564 4.181578 GAGATTTCGTGCCTTTAGCTGTA 58.818 43.478 0.00 0.00 44.23 2.74
539 565 3.003480 GAGATTTCGTGCCTTTAGCTGT 58.997 45.455 0.00 0.00 44.23 4.40
590 617 0.881118 CACCTGCACCTAATTTGCGT 59.119 50.000 0.00 0.00 43.34 5.24
665 692 3.006644 GGACTCGTAGGGTTTCTTCAGTT 59.993 47.826 0.00 0.00 0.00 3.16
759 786 4.029520 CAACCCAATCCCAATCCAACATA 58.970 43.478 0.00 0.00 0.00 2.29
1056 1091 2.125673 ACGATGGTGCAGTACGGC 60.126 61.111 11.37 11.37 0.00 5.68
1233 1268 1.214853 GAAGAGGACGACGGGGAAC 59.785 63.158 0.00 0.00 0.00 3.62
1457 1492 4.436998 GCGTCCTGAGGGTGTCGG 62.437 72.222 0.00 0.00 0.00 4.79
1510 1545 6.424683 CATTTCATCGAACACATACTCCATG 58.575 40.000 0.00 0.00 40.78 3.66
1539 1577 5.572511 GCAGAGATCATTGATCGATACAGTC 59.427 44.000 18.52 10.30 43.17 3.51
1540 1578 5.010415 TGCAGAGATCATTGATCGATACAGT 59.990 40.000 18.52 2.07 43.17 3.55
1541 1579 5.467705 TGCAGAGATCATTGATCGATACAG 58.532 41.667 18.52 10.75 43.17 2.74
1542 1580 5.458041 TGCAGAGATCATTGATCGATACA 57.542 39.130 18.52 13.68 43.17 2.29
1543 1581 6.034790 GTCATGCAGAGATCATTGATCGATAC 59.965 42.308 18.52 11.67 43.17 2.24
1544 1582 6.071503 AGTCATGCAGAGATCATTGATCGATA 60.072 38.462 18.52 7.51 43.17 2.92
1545 1583 4.930405 GTCATGCAGAGATCATTGATCGAT 59.070 41.667 18.52 0.00 43.17 3.59
1546 1584 4.038883 AGTCATGCAGAGATCATTGATCGA 59.961 41.667 18.52 7.35 43.17 3.59
1547 1585 4.150804 CAGTCATGCAGAGATCATTGATCG 59.849 45.833 18.52 8.02 43.17 3.69
1548 1586 5.057819 ACAGTCATGCAGAGATCATTGATC 58.942 41.667 17.26 17.26 39.17 2.92
1549 1587 5.037383 ACAGTCATGCAGAGATCATTGAT 57.963 39.130 0.00 0.00 0.00 2.57
1550 1588 4.482952 ACAGTCATGCAGAGATCATTGA 57.517 40.909 0.00 0.00 0.00 2.57
1551 1589 6.673154 TTTACAGTCATGCAGAGATCATTG 57.327 37.500 0.00 0.00 0.00 2.82
1552 1590 5.296283 GCTTTACAGTCATGCAGAGATCATT 59.704 40.000 0.00 0.00 0.00 2.57
1553 1591 4.815308 GCTTTACAGTCATGCAGAGATCAT 59.185 41.667 0.00 0.00 0.00 2.45
1554 1592 4.081254 AGCTTTACAGTCATGCAGAGATCA 60.081 41.667 0.00 0.00 0.00 2.92
1555 1593 4.440880 AGCTTTACAGTCATGCAGAGATC 58.559 43.478 0.00 0.00 0.00 2.75
1556 1594 4.161942 AGAGCTTTACAGTCATGCAGAGAT 59.838 41.667 0.00 0.00 0.00 2.75
1557 1595 3.513119 AGAGCTTTACAGTCATGCAGAGA 59.487 43.478 0.00 0.00 0.00 3.10
1558 1596 3.859443 AGAGCTTTACAGTCATGCAGAG 58.141 45.455 0.00 0.00 0.00 3.35
1559 1597 3.513119 AGAGAGCTTTACAGTCATGCAGA 59.487 43.478 0.00 0.00 0.00 4.26
1560 1598 3.859443 AGAGAGCTTTACAGTCATGCAG 58.141 45.455 0.00 0.00 0.00 4.41
1561 1599 3.969287 AGAGAGCTTTACAGTCATGCA 57.031 42.857 0.00 0.00 0.00 3.96
1562 1600 4.934602 AGAAAGAGAGCTTTACAGTCATGC 59.065 41.667 0.00 0.00 44.10 4.06
1563 1601 5.163874 GCAGAAAGAGAGCTTTACAGTCATG 60.164 44.000 0.00 0.00 44.10 3.07
1564 1602 4.934602 GCAGAAAGAGAGCTTTACAGTCAT 59.065 41.667 0.00 0.00 44.10 3.06
1565 1603 4.310769 GCAGAAAGAGAGCTTTACAGTCA 58.689 43.478 0.00 0.00 44.10 3.41
1566 1604 3.682377 GGCAGAAAGAGAGCTTTACAGTC 59.318 47.826 0.00 0.00 44.10 3.51
1567 1605 3.071602 TGGCAGAAAGAGAGCTTTACAGT 59.928 43.478 0.00 0.00 44.10 3.55
1568 1606 3.668447 TGGCAGAAAGAGAGCTTTACAG 58.332 45.455 0.00 0.00 44.10 2.74
1569 1607 3.324846 TCTGGCAGAAAGAGAGCTTTACA 59.675 43.478 16.28 0.00 44.10 2.41
1570 1608 3.931578 TCTGGCAGAAAGAGAGCTTTAC 58.068 45.455 16.28 0.00 44.10 2.01
1571 1609 4.833478 ATCTGGCAGAAAGAGAGCTTTA 57.167 40.909 22.84 0.00 44.10 1.85
1572 1610 3.717452 ATCTGGCAGAAAGAGAGCTTT 57.283 42.857 22.84 0.00 46.62 3.51
1573 1611 3.345414 CAATCTGGCAGAAAGAGAGCTT 58.655 45.455 22.84 5.55 35.37 3.74
1574 1612 2.940527 GCAATCTGGCAGAAAGAGAGCT 60.941 50.000 22.84 0.00 0.00 4.09
1575 1613 1.401199 GCAATCTGGCAGAAAGAGAGC 59.599 52.381 22.84 14.54 0.00 4.09
1576 1614 2.708051 TGCAATCTGGCAGAAAGAGAG 58.292 47.619 22.84 8.81 39.25 3.20
1577 1615 2.865119 TGCAATCTGGCAGAAAGAGA 57.135 45.000 22.84 1.83 39.25 3.10
1585 1623 1.985473 AGTTTGACTGCAATCTGGCA 58.015 45.000 0.00 0.00 42.53 4.92
1586 1624 3.243501 TGAAAGTTTGACTGCAATCTGGC 60.244 43.478 0.00 0.00 34.99 4.85
1587 1625 4.202040 TGTGAAAGTTTGACTGCAATCTGG 60.202 41.667 6.76 0.00 34.99 3.86
1588 1626 4.923893 TGTGAAAGTTTGACTGCAATCTG 58.076 39.130 6.76 0.00 34.99 2.90
1589 1627 5.126061 ACTTGTGAAAGTTTGACTGCAATCT 59.874 36.000 6.76 0.00 35.99 2.40
1590 1628 5.343249 ACTTGTGAAAGTTTGACTGCAATC 58.657 37.500 6.76 0.00 33.25 2.67
1591 1629 5.329035 ACTTGTGAAAGTTTGACTGCAAT 57.671 34.783 6.76 0.00 33.25 3.56
1592 1630 4.782019 ACTTGTGAAAGTTTGACTGCAA 57.218 36.364 6.76 0.00 0.00 4.08
1593 1631 4.782019 AACTTGTGAAAGTTTGACTGCA 57.218 36.364 6.76 0.00 39.81 4.41
1594 1632 9.118236 GATAATAACTTGTGAAAGTTTGACTGC 57.882 33.333 8.97 0.00 42.48 4.40
1636 1674 9.927081 AGAAACCATTTGATCAGATAATAACCT 57.073 29.630 0.00 0.00 0.00 3.50
1641 1679 9.265901 CGTAGAGAAACCATTTGATCAGATAAT 57.734 33.333 0.00 0.00 0.00 1.28
1642 1680 8.258007 ACGTAGAGAAACCATTTGATCAGATAA 58.742 33.333 0.00 0.00 0.00 1.75
1643 1681 7.782049 ACGTAGAGAAACCATTTGATCAGATA 58.218 34.615 0.00 0.00 0.00 1.98
1644 1682 6.644347 ACGTAGAGAAACCATTTGATCAGAT 58.356 36.000 0.00 0.00 0.00 2.90
1645 1683 6.037786 ACGTAGAGAAACCATTTGATCAGA 57.962 37.500 0.00 0.00 0.00 3.27
1646 1684 8.425577 AATACGTAGAGAAACCATTTGATCAG 57.574 34.615 0.08 0.00 0.00 2.90
1647 1685 8.664798 CAAATACGTAGAGAAACCATTTGATCA 58.335 33.333 0.08 0.00 33.89 2.92
1648 1686 8.122952 CCAAATACGTAGAGAAACCATTTGATC 58.877 37.037 13.49 0.00 33.89 2.92
1649 1687 7.067008 CCCAAATACGTAGAGAAACCATTTGAT 59.933 37.037 13.49 0.00 33.89 2.57
1650 1688 6.373216 CCCAAATACGTAGAGAAACCATTTGA 59.627 38.462 13.49 0.00 33.89 2.69
1651 1689 6.404293 CCCCAAATACGTAGAGAAACCATTTG 60.404 42.308 0.08 4.69 32.90 2.32
1652 1690 5.650703 CCCCAAATACGTAGAGAAACCATTT 59.349 40.000 0.08 0.00 0.00 2.32
1653 1691 5.190677 CCCCAAATACGTAGAGAAACCATT 58.809 41.667 0.08 0.00 0.00 3.16
1654 1692 4.777463 CCCCAAATACGTAGAGAAACCAT 58.223 43.478 0.08 0.00 0.00 3.55
1655 1693 3.620472 GCCCCAAATACGTAGAGAAACCA 60.620 47.826 0.08 0.00 0.00 3.67
1656 1694 2.941064 GCCCCAAATACGTAGAGAAACC 59.059 50.000 0.08 0.00 0.00 3.27
1657 1695 3.602483 TGCCCCAAATACGTAGAGAAAC 58.398 45.455 0.08 0.00 0.00 2.78
1658 1696 3.516300 TCTGCCCCAAATACGTAGAGAAA 59.484 43.478 0.08 0.00 0.00 2.52
1659 1697 3.101437 TCTGCCCCAAATACGTAGAGAA 58.899 45.455 0.08 0.00 0.00 2.87
1660 1698 2.742348 TCTGCCCCAAATACGTAGAGA 58.258 47.619 0.08 0.00 0.00 3.10
1661 1699 3.753294 ATCTGCCCCAAATACGTAGAG 57.247 47.619 0.08 0.00 0.00 2.43
1662 1700 3.804036 CAATCTGCCCCAAATACGTAGA 58.196 45.455 0.08 0.00 0.00 2.59
1663 1701 2.290641 GCAATCTGCCCCAAATACGTAG 59.709 50.000 0.08 0.00 37.42 3.51
1664 1702 2.294074 GCAATCTGCCCCAAATACGTA 58.706 47.619 0.00 0.00 37.42 3.57
1665 1703 1.102978 GCAATCTGCCCCAAATACGT 58.897 50.000 0.00 0.00 37.42 3.57
1666 1704 1.102154 TGCAATCTGCCCCAAATACG 58.898 50.000 0.00 0.00 44.23 3.06
1667 1705 3.825143 AATGCAATCTGCCCCAAATAC 57.175 42.857 0.00 0.00 44.23 1.89
1668 1706 3.134442 GGAAATGCAATCTGCCCCAAATA 59.866 43.478 0.00 0.00 44.23 1.40
1669 1707 2.092807 GGAAATGCAATCTGCCCCAAAT 60.093 45.455 0.00 0.00 44.23 2.32
1670 1708 1.278699 GGAAATGCAATCTGCCCCAAA 59.721 47.619 0.00 0.00 44.23 3.28
1671 1709 0.903942 GGAAATGCAATCTGCCCCAA 59.096 50.000 0.00 0.00 44.23 4.12
1672 1710 0.041535 AGGAAATGCAATCTGCCCCA 59.958 50.000 0.00 0.00 44.23 4.96
1673 1711 0.749049 GAGGAAATGCAATCTGCCCC 59.251 55.000 0.00 0.00 44.23 5.80
1674 1712 1.407979 CAGAGGAAATGCAATCTGCCC 59.592 52.381 0.00 0.00 44.23 5.36
1675 1713 2.865343 CAGAGGAAATGCAATCTGCC 57.135 50.000 0.00 0.00 44.23 4.85
1683 1721 1.760192 ATCCAGTGCAGAGGAAATGC 58.240 50.000 10.82 0.00 44.11 3.56
1684 1722 3.675228 GCAAATCCAGTGCAGAGGAAATG 60.675 47.826 10.82 12.67 41.80 2.32
1685 1723 2.494870 GCAAATCCAGTGCAGAGGAAAT 59.505 45.455 10.82 1.48 41.80 2.17
1686 1724 1.888512 GCAAATCCAGTGCAGAGGAAA 59.111 47.619 10.82 0.00 41.80 3.13
1687 1725 1.074405 AGCAAATCCAGTGCAGAGGAA 59.926 47.619 10.82 0.00 44.74 3.36
1688 1726 0.694771 AGCAAATCCAGTGCAGAGGA 59.305 50.000 9.33 9.33 44.74 3.71
1689 1727 1.093159 GAGCAAATCCAGTGCAGAGG 58.907 55.000 0.00 0.00 44.74 3.69
1690 1728 1.467734 GTGAGCAAATCCAGTGCAGAG 59.532 52.381 0.00 0.00 44.74 3.35
1691 1729 1.202794 TGTGAGCAAATCCAGTGCAGA 60.203 47.619 0.00 0.00 44.74 4.26
1692 1730 1.068748 GTGTGAGCAAATCCAGTGCAG 60.069 52.381 0.00 0.00 44.74 4.41
1693 1731 0.953727 GTGTGAGCAAATCCAGTGCA 59.046 50.000 0.00 0.00 44.74 4.57
1694 1732 0.110056 CGTGTGAGCAAATCCAGTGC 60.110 55.000 0.00 0.00 42.55 4.40
1695 1733 1.229428 ACGTGTGAGCAAATCCAGTG 58.771 50.000 0.00 0.00 0.00 3.66
1696 1734 1.873591 GAACGTGTGAGCAAATCCAGT 59.126 47.619 0.00 0.00 0.00 4.00
1697 1735 1.136252 CGAACGTGTGAGCAAATCCAG 60.136 52.381 0.00 0.00 0.00 3.86
1698 1736 0.865111 CGAACGTGTGAGCAAATCCA 59.135 50.000 0.00 0.00 0.00 3.41
1699 1737 0.865769 ACGAACGTGTGAGCAAATCC 59.134 50.000 0.00 0.00 0.00 3.01
1700 1738 2.470140 CGTACGAACGTGTGAGCAAATC 60.470 50.000 10.44 0.00 44.21 2.17
1701 1739 1.454276 CGTACGAACGTGTGAGCAAAT 59.546 47.619 10.44 0.00 44.21 2.32
1702 1740 0.847670 CGTACGAACGTGTGAGCAAA 59.152 50.000 10.44 0.00 44.21 3.68
1703 1741 2.497804 CGTACGAACGTGTGAGCAA 58.502 52.632 10.44 0.00 44.21 3.91
1704 1742 4.215330 CGTACGAACGTGTGAGCA 57.785 55.556 10.44 0.00 44.21 4.26
1713 1751 2.796031 TGTTTGTGATGACCGTACGAAC 59.204 45.455 18.76 10.10 38.56 3.95
1714 1752 3.095102 TGTTTGTGATGACCGTACGAA 57.905 42.857 18.76 1.90 0.00 3.85
1715 1753 2.797074 TGTTTGTGATGACCGTACGA 57.203 45.000 18.76 0.00 0.00 3.43
1716 1754 4.171005 AGTATGTTTGTGATGACCGTACG 58.829 43.478 8.69 8.69 0.00 3.67
1717 1755 6.810182 AGTTAGTATGTTTGTGATGACCGTAC 59.190 38.462 0.00 0.00 0.00 3.67
1718 1756 6.927416 AGTTAGTATGTTTGTGATGACCGTA 58.073 36.000 0.00 0.00 0.00 4.02
1719 1757 5.790593 AGTTAGTATGTTTGTGATGACCGT 58.209 37.500 0.00 0.00 0.00 4.83
1720 1758 6.721571 AAGTTAGTATGTTTGTGATGACCG 57.278 37.500 0.00 0.00 0.00 4.79
1721 1759 7.305474 CCAAAGTTAGTATGTTTGTGATGACC 58.695 38.462 0.00 0.00 30.60 4.02
1722 1760 7.305474 CCCAAAGTTAGTATGTTTGTGATGAC 58.695 38.462 0.00 0.00 30.60 3.06
1723 1761 6.432783 CCCCAAAGTTAGTATGTTTGTGATGA 59.567 38.462 0.00 0.00 30.60 2.92
1724 1762 6.620678 CCCCAAAGTTAGTATGTTTGTGATG 58.379 40.000 0.00 0.00 30.60 3.07
1725 1763 5.185056 GCCCCAAAGTTAGTATGTTTGTGAT 59.815 40.000 0.00 0.00 30.60 3.06
1726 1764 4.521256 GCCCCAAAGTTAGTATGTTTGTGA 59.479 41.667 0.00 0.00 30.60 3.58
1727 1765 4.321675 GGCCCCAAAGTTAGTATGTTTGTG 60.322 45.833 0.00 0.00 30.60 3.33
1728 1766 3.830178 GGCCCCAAAGTTAGTATGTTTGT 59.170 43.478 0.00 0.00 30.60 2.83
1729 1767 3.829601 TGGCCCCAAAGTTAGTATGTTTG 59.170 43.478 0.00 0.00 0.00 2.93
1730 1768 3.830178 GTGGCCCCAAAGTTAGTATGTTT 59.170 43.478 0.00 0.00 0.00 2.83
1731 1769 3.075432 AGTGGCCCCAAAGTTAGTATGTT 59.925 43.478 0.00 0.00 0.00 2.71
1732 1770 2.647802 AGTGGCCCCAAAGTTAGTATGT 59.352 45.455 0.00 0.00 0.00 2.29
1733 1771 3.054361 AGAGTGGCCCCAAAGTTAGTATG 60.054 47.826 0.00 0.00 0.00 2.39
1734 1772 3.190439 AGAGTGGCCCCAAAGTTAGTAT 58.810 45.455 0.00 0.00 0.00 2.12
1735 1773 2.627933 AGAGTGGCCCCAAAGTTAGTA 58.372 47.619 0.00 0.00 0.00 1.82
1736 1774 1.446016 AGAGTGGCCCCAAAGTTAGT 58.554 50.000 0.00 0.00 0.00 2.24
1737 1775 3.713826 TTAGAGTGGCCCCAAAGTTAG 57.286 47.619 0.00 0.00 0.00 2.34
1738 1776 4.668138 AATTAGAGTGGCCCCAAAGTTA 57.332 40.909 0.00 0.00 0.00 2.24
1739 1777 3.542969 AATTAGAGTGGCCCCAAAGTT 57.457 42.857 0.00 0.00 0.00 2.66
1740 1778 4.668138 TTAATTAGAGTGGCCCCAAAGT 57.332 40.909 0.00 0.00 0.00 2.66
1741 1779 4.584743 GGATTAATTAGAGTGGCCCCAAAG 59.415 45.833 0.00 0.00 0.00 2.77
1742 1780 4.542697 GGATTAATTAGAGTGGCCCCAAA 58.457 43.478 0.00 0.00 0.00 3.28
1743 1781 3.117284 GGGATTAATTAGAGTGGCCCCAA 60.117 47.826 0.00 0.00 0.00 4.12
1744 1782 2.445525 GGGATTAATTAGAGTGGCCCCA 59.554 50.000 0.00 0.00 0.00 4.96
1745 1783 2.225041 GGGGATTAATTAGAGTGGCCCC 60.225 54.545 0.00 7.64 46.37 5.80
1746 1784 2.716969 AGGGGATTAATTAGAGTGGCCC 59.283 50.000 0.00 0.00 0.00 5.80
1747 1785 5.780958 ATAGGGGATTAATTAGAGTGGCC 57.219 43.478 0.00 0.00 0.00 5.36
1758 1796 9.205513 GGTTCTCGGTTATATATAGGGGATTAA 57.794 37.037 0.00 0.00 0.00 1.40
1759 1797 7.786464 GGGTTCTCGGTTATATATAGGGGATTA 59.214 40.741 0.00 0.00 0.00 1.75
1760 1798 6.614496 GGGTTCTCGGTTATATATAGGGGATT 59.386 42.308 0.00 0.00 0.00 3.01
1761 1799 6.141790 GGGTTCTCGGTTATATATAGGGGAT 58.858 44.000 0.00 0.00 0.00 3.85
1762 1800 5.522641 GGGTTCTCGGTTATATATAGGGGA 58.477 45.833 0.00 0.00 0.00 4.81
1763 1801 4.652881 GGGGTTCTCGGTTATATATAGGGG 59.347 50.000 0.00 0.00 0.00 4.79
1764 1802 5.526434 AGGGGTTCTCGGTTATATATAGGG 58.474 45.833 0.00 0.00 0.00 3.53
1772 1810 9.947189 TCATTATATATAGGGGTTCTCGGTTAT 57.053 33.333 0.00 0.00 0.00 1.89
1773 1811 9.772605 TTCATTATATATAGGGGTTCTCGGTTA 57.227 33.333 0.00 0.00 0.00 2.85
1774 1812 8.674925 TTCATTATATATAGGGGTTCTCGGTT 57.325 34.615 0.00 0.00 0.00 4.44
1775 1813 7.344871 CCTTCATTATATATAGGGGTTCTCGGT 59.655 40.741 0.00 0.00 0.00 4.69
1776 1814 7.563924 TCCTTCATTATATATAGGGGTTCTCGG 59.436 40.741 0.00 0.00 0.00 4.63
1777 1815 8.534954 TCCTTCATTATATATAGGGGTTCTCG 57.465 38.462 0.00 0.00 0.00 4.04
1782 1820 6.787957 CCGGATCCTTCATTATATATAGGGGT 59.212 42.308 10.75 0.00 0.00 4.95
1790 1828 4.223032 ACTTCGCCGGATCCTTCATTATAT 59.777 41.667 5.05 0.00 0.00 0.86
1791 1829 3.576982 ACTTCGCCGGATCCTTCATTATA 59.423 43.478 5.05 0.00 0.00 0.98
1792 1830 2.368875 ACTTCGCCGGATCCTTCATTAT 59.631 45.455 5.05 0.00 0.00 1.28
1793 1831 1.760613 ACTTCGCCGGATCCTTCATTA 59.239 47.619 5.05 0.00 0.00 1.90
1795 1833 1.410004 TACTTCGCCGGATCCTTCAT 58.590 50.000 5.05 0.00 0.00 2.57
1796 1834 1.187974 TTACTTCGCCGGATCCTTCA 58.812 50.000 5.05 0.00 0.00 3.02
1798 1836 1.406477 GGTTTACTTCGCCGGATCCTT 60.406 52.381 5.05 0.00 0.00 3.36
1805 1843 1.997606 CACTAAGGGTTTACTTCGCCG 59.002 52.381 0.00 0.00 32.02 6.46
1858 1896 7.157947 TGTTATATATAGGGGATCGGCTAGA 57.842 40.000 0.00 0.00 0.00 2.43
1894 1932 7.656707 ACTTGGCTTAACTTATGCAATTTTG 57.343 32.000 8.49 0.00 0.00 2.44
1898 1936 6.991938 TGAAACTTGGCTTAACTTATGCAAT 58.008 32.000 8.49 0.00 0.00 3.56
1940 1989 6.242396 TGCCTAGGTTGAACTTATGCTTAAA 58.758 36.000 11.31 0.00 0.00 1.52
1945 1994 4.217550 TGTTTGCCTAGGTTGAACTTATGC 59.782 41.667 11.31 7.57 0.00 3.14
1965 2014 4.592485 TCGGTTGCCAAAACAATATGTT 57.408 36.364 0.00 0.00 43.41 2.71
1975 2024 8.608844 ATTTATGTTTTATTTCGGTTGCCAAA 57.391 26.923 0.00 0.00 0.00 3.28
2012 2061 8.338986 GCAAGGATGAAGATTAGTTTAGCTTAC 58.661 37.037 0.00 0.00 0.00 2.34
2016 2066 5.590259 TGGCAAGGATGAAGATTAGTTTAGC 59.410 40.000 0.00 0.00 0.00 3.09
2112 2177 1.219124 GCGCATCTTCCCTGACTCA 59.781 57.895 0.30 0.00 0.00 3.41
2150 2238 4.927782 AGCAAGGCGGCGACAACA 62.928 61.111 18.30 0.00 39.27 3.33
2174 2283 2.625314 GAGGTCATCATCATCTCCGACA 59.375 50.000 0.00 0.00 0.00 4.35
2175 2284 2.029470 GGAGGTCATCATCATCTCCGAC 60.029 54.545 0.00 0.00 35.30 4.79
2186 2295 1.550130 GGTCAACGGGGAGGTCATCA 61.550 60.000 0.00 0.00 0.00 3.07
2214 2323 3.853330 GAGCGCGCGATCTTTGCA 61.853 61.111 37.74 0.00 0.00 4.08
2338 2449 4.344865 GGTGGTGGTGGATGCGGT 62.345 66.667 0.00 0.00 0.00 5.68
2363 2475 4.530857 CGTCCACCTCATCCCGCC 62.531 72.222 0.00 0.00 0.00 6.13
2392 2504 1.883021 GTGGCTCAATTTCCCGTGG 59.117 57.895 0.00 0.00 0.00 4.94
2395 2507 2.485122 GCGTGGCTCAATTTCCCG 59.515 61.111 0.00 0.00 0.00 5.14
2396 2508 1.862602 AACGCGTGGCTCAATTTCCC 61.863 55.000 14.98 0.00 0.00 3.97
2401 2513 2.255252 GCAAACGCGTGGCTCAAT 59.745 55.556 23.94 0.00 0.00 2.57
2422 2534 1.745489 GTGGCAGGTCCGATTCCAC 60.745 63.158 8.43 8.43 40.13 4.02
2465 2578 1.290955 GGGTCGTTCCACATGACGA 59.709 57.895 0.00 0.62 45.01 4.20
2470 2583 1.261938 TGGATCGGGTCGTTCCACAT 61.262 55.000 13.91 0.00 46.42 3.21


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

AutoCloner maintained by Alex Coulton.