Multiple sequence alignment - TraesCS1A01G433700

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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 TraesCS1A01G433700 chr1A 100.000 2372 0 0 1 2372 584780039 584777668 0.000000e+00 4381.0
1 TraesCS1A01G433700 chr1A 96.507 1231 36 5 334 1564 168442037 168443260 0.000000e+00 2028.0
2 TraesCS1A01G433700 chr1A 87.631 477 40 11 1577 2039 348728304 348727833 9.650000e-149 536.0
3 TraesCS1A01G433700 chr1A 81.250 304 35 12 2024 2323 67699532 67699817 2.370000e-55 226.0
4 TraesCS1A01G433700 chr3B 98.281 1571 22 3 1 1566 201523605 201522035 0.000000e+00 2747.0
5 TraesCS1A01G433700 chr3B 82.295 305 41 9 2042 2342 794881969 794882264 3.910000e-63 252.0
6 TraesCS1A01G433700 chr3A 97.643 1570 31 4 1 1566 672913412 672914979 0.000000e+00 2689.0
7 TraesCS1A01G433700 chr3A 83.221 298 37 8 2075 2368 731785288 731785576 6.500000e-66 261.0
8 TraesCS1A01G433700 chr2D 97.527 1577 25 7 1 1566 272797299 272798872 0.000000e+00 2684.0
9 TraesCS1A01G433700 chr2D 87.368 475 46 7 1577 2039 576459992 576459520 1.250000e-147 532.0
10 TraesCS1A01G433700 chr2D 85.744 477 51 13 1577 2039 608382172 608381699 2.740000e-134 488.0
11 TraesCS1A01G433700 chr4D 97.263 1571 37 4 1 1566 19925394 19923825 0.000000e+00 2658.0
12 TraesCS1A01G433700 chr6A 97.256 1567 36 4 1 1566 271186368 271184808 0.000000e+00 2649.0
13 TraesCS1A01G433700 chr6A 85.501 469 59 6 1577 2039 178074109 178073644 4.590000e-132 481.0
14 TraesCS1A01G433700 chr6A 82.692 312 45 7 2063 2369 468256077 468256384 3.890000e-68 268.0
15 TraesCS1A01G433700 chr2B 96.883 1572 42 4 1 1566 369624641 369623071 0.000000e+00 2625.0
16 TraesCS1A01G433700 chr7B 96.842 1520 32 5 57 1566 559141856 559140343 0.000000e+00 2527.0
17 TraesCS1A01G433700 chr7B 94.366 142 3 1 1409 1545 586987895 586987754 1.850000e-51 213.0
18 TraesCS1A01G433700 chr7A 95.350 1570 60 7 1 1566 352185209 352186769 0.000000e+00 2483.0
19 TraesCS1A01G433700 chr7A 80.737 597 71 25 1795 2368 642555924 642556499 2.180000e-115 425.0
20 TraesCS1A01G433700 chr7A 97.414 232 6 0 203 434 92690965 92691196 1.710000e-106 396.0
21 TraesCS1A01G433700 chr7A 97.368 38 1 0 1 38 591407526 591407563 5.470000e-07 65.8
22 TraesCS1A01G433700 chr3D 86.694 481 46 13 1577 2039 475867127 475866647 3.490000e-143 518.0
23 TraesCS1A01G433700 chr3D 88.811 429 35 11 1573 1992 327510531 327510955 4.520000e-142 514.0
24 TraesCS1A01G433700 chr7D 85.684 475 54 9 1577 2039 14555512 14555040 2.740000e-134 488.0
25 TraesCS1A01G433700 chr7D 81.742 356 48 13 2022 2372 554409834 554410177 4.990000e-72 281.0
26 TraesCS1A01G433700 chr7D 80.926 367 46 15 2022 2372 136297462 136297820 3.890000e-68 268.0
27 TraesCS1A01G433700 chr5D 85.294 476 55 8 1577 2039 374701152 374700679 5.930000e-131 477.0
28 TraesCS1A01G433700 chr5D 84.956 226 21 8 2022 2243 85464223 85464439 1.430000e-52 217.0
29 TraesCS1A01G433700 chr4A 85.031 481 55 13 1579 2044 649158642 649158164 7.670000e-130 473.0
30 TraesCS1A01G433700 chr4A 87.059 170 17 5 2201 2370 549870035 549870199 1.120000e-43 187.0
31 TraesCS1A01G433700 chr6D 81.389 360 45 13 1897 2242 418309422 418309071 8.350000e-70 274.0
32 TraesCS1A01G433700 chr6D 84.884 172 18 8 2201 2372 422032279 422032442 1.460000e-37 167.0
33 TraesCS1A01G433700 chr2A 90.476 63 6 0 1 63 715346528 715346466 1.510000e-12 84.2


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 TraesCS1A01G433700 chr1A 584777668 584780039 2371 True 4381 4381 100.000 1 2372 1 chr1A.!!$R2 2371
1 TraesCS1A01G433700 chr1A 168442037 168443260 1223 False 2028 2028 96.507 334 1564 1 chr1A.!!$F2 1230
2 TraesCS1A01G433700 chr3B 201522035 201523605 1570 True 2747 2747 98.281 1 1566 1 chr3B.!!$R1 1565
3 TraesCS1A01G433700 chr3A 672913412 672914979 1567 False 2689 2689 97.643 1 1566 1 chr3A.!!$F1 1565
4 TraesCS1A01G433700 chr2D 272797299 272798872 1573 False 2684 2684 97.527 1 1566 1 chr2D.!!$F1 1565
5 TraesCS1A01G433700 chr4D 19923825 19925394 1569 True 2658 2658 97.263 1 1566 1 chr4D.!!$R1 1565
6 TraesCS1A01G433700 chr6A 271184808 271186368 1560 True 2649 2649 97.256 1 1566 1 chr6A.!!$R2 1565
7 TraesCS1A01G433700 chr2B 369623071 369624641 1570 True 2625 2625 96.883 1 1566 1 chr2B.!!$R1 1565
8 TraesCS1A01G433700 chr7B 559140343 559141856 1513 True 2527 2527 96.842 57 1566 1 chr7B.!!$R1 1509
9 TraesCS1A01G433700 chr7A 352185209 352186769 1560 False 2483 2483 95.350 1 1566 1 chr7A.!!$F2 1565
10 TraesCS1A01G433700 chr7A 642555924 642556499 575 False 425 425 80.737 1795 2368 1 chr7A.!!$F4 573

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
655 670 2.032894 AGCAATAACACGATATGCACGC 60.033 45.455 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 1718 0.036306 GTGCCTCTCGGAAAGGGAAA 59.964 55.0 0.0 0.0 35.86 3.13 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
655 670 2.032894 AGCAATAACACGATATGCACGC 60.033 45.455 0.00 0.00 0.00 5.34
688 703 9.287373 GGAAAAATATGGGTACGTATATTTCCA 57.713 33.333 18.47 9.55 37.59 3.53
722 737 2.370849 ACACTAAGACCCACGGAAACAT 59.629 45.455 0.00 0.00 0.00 2.71
1116 1141 6.944557 CGATATGCTCGTATTGGTGATTTA 57.055 37.500 0.00 0.00 42.56 1.40
1566 1597 9.599322 CTATAAGAAATGCGGACATGAATAAAC 57.401 33.333 0.00 0.00 36.36 2.01
1567 1598 6.515272 AAGAAATGCGGACATGAATAAACT 57.485 33.333 0.00 0.00 36.36 2.66
1568 1599 7.624360 AAGAAATGCGGACATGAATAAACTA 57.376 32.000 0.00 0.00 36.36 2.24
1569 1600 7.251704 AGAAATGCGGACATGAATAAACTAG 57.748 36.000 0.00 0.00 36.36 2.57
1570 1601 7.047891 AGAAATGCGGACATGAATAAACTAGA 58.952 34.615 0.00 0.00 36.36 2.43
1571 1602 7.716998 AGAAATGCGGACATGAATAAACTAGAT 59.283 33.333 0.00 0.00 36.36 1.98
1572 1603 8.902540 AAATGCGGACATGAATAAACTAGATA 57.097 30.769 0.00 0.00 36.36 1.98
1573 1604 7.891183 ATGCGGACATGAATAAACTAGATAC 57.109 36.000 0.00 0.00 34.35 2.24
1574 1605 6.220930 TGCGGACATGAATAAACTAGATACC 58.779 40.000 0.00 0.00 0.00 2.73
1575 1606 6.183360 TGCGGACATGAATAAACTAGATACCA 60.183 38.462 0.00 0.00 0.00 3.25
1576 1607 6.874134 GCGGACATGAATAAACTAGATACCAT 59.126 38.462 0.00 0.00 0.00 3.55
1577 1608 7.148573 GCGGACATGAATAAACTAGATACCATG 60.149 40.741 0.00 9.11 36.97 3.66
1578 1609 7.331934 CGGACATGAATAAACTAGATACCATGG 59.668 40.741 11.19 11.19 35.70 3.66
1579 1610 8.375506 GGACATGAATAAACTAGATACCATGGA 58.624 37.037 21.47 2.01 35.70 3.41
1580 1611 9.950496 GACATGAATAAACTAGATACCATGGAT 57.050 33.333 21.47 7.62 35.70 3.41
1586 1617 9.712305 AATAAACTAGATACCATGGATTTCTCG 57.288 33.333 21.47 14.47 0.00 4.04
1587 1618 5.140747 ACTAGATACCATGGATTTCTCGC 57.859 43.478 21.47 0.00 0.00 5.03
1588 1619 3.032017 AGATACCATGGATTTCTCGCG 57.968 47.619 21.47 0.00 0.00 5.87
1589 1620 2.365617 AGATACCATGGATTTCTCGCGT 59.634 45.455 21.47 0.00 0.00 6.01
1590 1621 2.684001 TACCATGGATTTCTCGCGTT 57.316 45.000 21.47 0.00 0.00 4.84
1591 1622 1.086696 ACCATGGATTTCTCGCGTTG 58.913 50.000 21.47 0.00 0.00 4.10
1592 1623 1.338674 ACCATGGATTTCTCGCGTTGA 60.339 47.619 21.47 2.87 0.00 3.18
1593 1624 1.328680 CCATGGATTTCTCGCGTTGAG 59.671 52.381 5.56 0.00 46.72 3.02
1604 1635 3.788434 TCGCGTTGAGATCTTCAAAAC 57.212 42.857 5.77 0.00 46.85 2.43
1605 1636 3.390135 TCGCGTTGAGATCTTCAAAACT 58.610 40.909 5.77 0.00 46.85 2.66
1606 1637 4.552355 TCGCGTTGAGATCTTCAAAACTA 58.448 39.130 5.77 0.00 46.85 2.24
1607 1638 4.621460 TCGCGTTGAGATCTTCAAAACTAG 59.379 41.667 5.77 0.00 46.85 2.57
1608 1639 4.621460 CGCGTTGAGATCTTCAAAACTAGA 59.379 41.667 0.00 0.00 46.85 2.43
1609 1640 5.289675 CGCGTTGAGATCTTCAAAACTAGAT 59.710 40.000 0.00 0.00 46.85 1.98
1610 1641 6.472486 CGCGTTGAGATCTTCAAAACTAGATA 59.528 38.462 0.00 0.00 46.85 1.98
1611 1642 7.513814 CGCGTTGAGATCTTCAAAACTAGATAC 60.514 40.741 0.00 0.00 46.85 2.24
1612 1643 7.254151 GCGTTGAGATCTTCAAAACTAGATACC 60.254 40.741 0.00 0.00 46.85 2.73
1613 1644 7.759886 CGTTGAGATCTTCAAAACTAGATACCA 59.240 37.037 0.00 0.00 46.85 3.25
1614 1645 9.606631 GTTGAGATCTTCAAAACTAGATACCAT 57.393 33.333 0.00 0.00 46.85 3.55
1615 1646 9.605275 TTGAGATCTTCAAAACTAGATACCATG 57.395 33.333 0.00 0.00 42.69 3.66
1616 1647 8.762645 TGAGATCTTCAAAACTAGATACCATGT 58.237 33.333 0.00 0.00 31.34 3.21
1617 1648 9.255304 GAGATCTTCAAAACTAGATACCATGTC 57.745 37.037 0.00 0.00 0.00 3.06
1618 1649 7.923344 AGATCTTCAAAACTAGATACCATGTCG 59.077 37.037 0.00 0.00 0.00 4.35
1619 1650 7.165460 TCTTCAAAACTAGATACCATGTCGA 57.835 36.000 0.00 0.00 0.00 4.20
1620 1651 7.782049 TCTTCAAAACTAGATACCATGTCGAT 58.218 34.615 0.00 0.00 0.00 3.59
1621 1652 8.909923 TCTTCAAAACTAGATACCATGTCGATA 58.090 33.333 0.00 0.00 0.00 2.92
1622 1653 9.186323 CTTCAAAACTAGATACCATGTCGATAG 57.814 37.037 0.00 0.00 0.00 2.08
1623 1654 7.658261 TCAAAACTAGATACCATGTCGATAGG 58.342 38.462 0.00 0.00 0.00 2.57
1624 1655 7.287005 TCAAAACTAGATACCATGTCGATAGGT 59.713 37.037 10.58 10.58 39.41 3.08
1625 1656 7.598759 AAACTAGATACCATGTCGATAGGTT 57.401 36.000 10.95 0.00 36.87 3.50
1626 1657 7.598759 AACTAGATACCATGTCGATAGGTTT 57.401 36.000 10.95 4.54 36.87 3.27
1627 1658 7.598759 ACTAGATACCATGTCGATAGGTTTT 57.401 36.000 10.95 1.53 36.87 2.43
1628 1659 7.434492 ACTAGATACCATGTCGATAGGTTTTG 58.566 38.462 10.95 0.00 36.87 2.44
1629 1660 5.611374 AGATACCATGTCGATAGGTTTTGG 58.389 41.667 10.95 4.69 36.87 3.28
1630 1661 2.365582 ACCATGTCGATAGGTTTTGGC 58.634 47.619 0.00 0.00 29.58 4.52
1631 1662 2.290641 ACCATGTCGATAGGTTTTGGCA 60.291 45.455 0.00 0.00 29.58 4.92
1632 1663 2.752354 CCATGTCGATAGGTTTTGGCAA 59.248 45.455 0.00 0.00 0.00 4.52
1633 1664 3.192422 CCATGTCGATAGGTTTTGGCAAA 59.808 43.478 8.93 8.93 0.00 3.68
1634 1665 3.907894 TGTCGATAGGTTTTGGCAAAC 57.092 42.857 13.10 7.98 41.57 2.93
1635 1666 3.482436 TGTCGATAGGTTTTGGCAAACT 58.518 40.909 13.10 10.11 41.92 2.66
1636 1667 3.886505 TGTCGATAGGTTTTGGCAAACTT 59.113 39.130 13.10 7.21 41.92 2.66
1637 1668 4.339814 TGTCGATAGGTTTTGGCAAACTTT 59.660 37.500 13.10 2.76 41.92 2.66
1638 1669 5.163499 TGTCGATAGGTTTTGGCAAACTTTT 60.163 36.000 13.10 1.65 41.92 2.27
1639 1670 5.751509 GTCGATAGGTTTTGGCAAACTTTTT 59.248 36.000 13.10 0.00 41.92 1.94
1657 1688 1.910688 TTTTCACGAAAAACACCGGC 58.089 45.000 0.00 0.00 37.35 6.13
1658 1689 0.100861 TTTCACGAAAAACACCGGCC 59.899 50.000 0.00 0.00 0.00 6.13
1659 1690 2.049475 TTCACGAAAAACACCGGCCG 62.049 55.000 21.04 21.04 0.00 6.13
1660 1691 2.203042 ACGAAAAACACCGGCCGA 60.203 55.556 30.73 0.00 0.00 5.54
1661 1692 1.818785 ACGAAAAACACCGGCCGAA 60.819 52.632 30.73 0.00 0.00 4.30
1662 1693 1.355916 CGAAAAACACCGGCCGAAA 59.644 52.632 30.73 0.00 0.00 3.46
1663 1694 0.248539 CGAAAAACACCGGCCGAAAA 60.249 50.000 30.73 0.00 0.00 2.29
1664 1695 1.798079 CGAAAAACACCGGCCGAAAAA 60.798 47.619 30.73 0.00 0.00 1.94
1730 1761 1.795768 GTGCCTCTCACGAAATCACA 58.204 50.000 0.00 0.00 35.76 3.58
1731 1762 2.143122 GTGCCTCTCACGAAATCACAA 58.857 47.619 0.00 0.00 35.76 3.33
1732 1763 2.096218 GTGCCTCTCACGAAATCACAAC 60.096 50.000 0.00 0.00 35.76 3.32
1733 1764 1.464997 GCCTCTCACGAAATCACAACC 59.535 52.381 0.00 0.00 0.00 3.77
1734 1765 1.726791 CCTCTCACGAAATCACAACCG 59.273 52.381 0.00 0.00 0.00 4.44
1735 1766 2.404215 CTCTCACGAAATCACAACCGT 58.596 47.619 0.00 0.00 35.46 4.83
1738 1769 2.294479 CACGAAATCACAACCGTGTC 57.706 50.000 0.00 0.00 44.88 3.67
1739 1770 1.864711 CACGAAATCACAACCGTGTCT 59.135 47.619 0.00 0.00 44.88 3.41
1740 1771 2.096909 CACGAAATCACAACCGTGTCTC 60.097 50.000 0.00 0.00 44.88 3.36
1741 1772 2.223971 ACGAAATCACAACCGTGTCTCT 60.224 45.455 0.00 0.00 44.02 3.10
1742 1773 2.408704 CGAAATCACAACCGTGTCTCTC 59.591 50.000 0.00 0.00 44.02 3.20
1743 1774 2.065993 AATCACAACCGTGTCTCTCG 57.934 50.000 0.00 0.00 44.02 4.04
1744 1775 0.388649 ATCACAACCGTGTCTCTCGC 60.389 55.000 0.00 0.00 44.02 5.03
1745 1776 1.299850 CACAACCGTGTCTCTCGCA 60.300 57.895 0.00 0.00 38.41 5.10
1746 1777 1.007271 ACAACCGTGTCTCTCGCAG 60.007 57.895 0.00 0.00 29.49 5.18
1747 1778 1.285950 CAACCGTGTCTCTCGCAGA 59.714 57.895 0.00 0.00 0.00 4.26
1748 1779 0.318699 CAACCGTGTCTCTCGCAGAA 60.319 55.000 0.00 0.00 34.09 3.02
1749 1780 0.039074 AACCGTGTCTCTCGCAGAAG 60.039 55.000 0.00 0.00 34.09 2.85
1750 1781 1.803519 CCGTGTCTCTCGCAGAAGC 60.804 63.158 0.00 0.00 34.09 3.86
1751 1782 1.081175 CGTGTCTCTCGCAGAAGCA 60.081 57.895 0.00 0.00 42.27 3.91
1752 1783 0.664466 CGTGTCTCTCGCAGAAGCAA 60.664 55.000 0.00 0.00 42.27 3.91
1753 1784 1.502231 GTGTCTCTCGCAGAAGCAAA 58.498 50.000 0.00 0.00 42.27 3.68
1754 1785 1.867233 GTGTCTCTCGCAGAAGCAAAA 59.133 47.619 0.00 0.00 42.27 2.44
1755 1786 1.867233 TGTCTCTCGCAGAAGCAAAAC 59.133 47.619 0.00 0.00 42.27 2.43
1756 1787 1.195674 GTCTCTCGCAGAAGCAAAACC 59.804 52.381 0.00 0.00 42.27 3.27
1757 1788 0.164647 CTCTCGCAGAAGCAAAACCG 59.835 55.000 0.00 0.00 42.27 4.44
1758 1789 0.531974 TCTCGCAGAAGCAAAACCGT 60.532 50.000 0.00 0.00 42.27 4.83
1759 1790 0.384725 CTCGCAGAAGCAAAACCGTG 60.385 55.000 0.00 0.00 42.27 4.94
1760 1791 0.812014 TCGCAGAAGCAAAACCGTGA 60.812 50.000 0.00 0.00 42.27 4.35
1761 1792 0.657368 CGCAGAAGCAAAACCGTGAC 60.657 55.000 0.00 0.00 42.27 3.67
1762 1793 0.663153 GCAGAAGCAAAACCGTGACT 59.337 50.000 0.00 0.00 41.58 3.41
1763 1794 1.334149 GCAGAAGCAAAACCGTGACTC 60.334 52.381 0.00 0.00 41.58 3.36
1764 1795 2.213499 CAGAAGCAAAACCGTGACTCT 58.787 47.619 0.00 0.00 0.00 3.24
1765 1796 2.221981 CAGAAGCAAAACCGTGACTCTC 59.778 50.000 0.00 0.00 0.00 3.20
1766 1797 1.192534 GAAGCAAAACCGTGACTCTCG 59.807 52.381 0.00 0.00 0.00 4.04
1767 1798 0.104304 AGCAAAACCGTGACTCTCGT 59.896 50.000 0.24 0.00 0.00 4.18
1768 1799 0.232303 GCAAAACCGTGACTCTCGTG 59.768 55.000 0.24 0.00 0.00 4.35
1769 1800 0.859232 CAAAACCGTGACTCTCGTGG 59.141 55.000 0.24 0.00 0.00 4.94
1770 1801 0.748450 AAAACCGTGACTCTCGTGGA 59.252 50.000 0.24 0.00 0.00 4.02
1771 1802 0.748450 AAACCGTGACTCTCGTGGAA 59.252 50.000 0.24 0.00 0.00 3.53
1772 1803 0.314302 AACCGTGACTCTCGTGGAAG 59.686 55.000 0.24 0.00 0.00 3.46
1773 1804 1.213013 CCGTGACTCTCGTGGAAGG 59.787 63.158 0.24 0.00 0.00 3.46
1774 1805 1.241990 CCGTGACTCTCGTGGAAGGA 61.242 60.000 0.24 0.00 0.00 3.36
1775 1806 0.596577 CGTGACTCTCGTGGAAGGAA 59.403 55.000 0.00 0.00 0.00 3.36
1776 1807 1.000607 CGTGACTCTCGTGGAAGGAAA 60.001 52.381 0.00 0.00 0.00 3.13
1777 1808 2.545113 CGTGACTCTCGTGGAAGGAAAA 60.545 50.000 0.00 0.00 0.00 2.29
1778 1809 3.463944 GTGACTCTCGTGGAAGGAAAAA 58.536 45.455 0.00 0.00 0.00 1.94
1877 1909 2.440539 AGCAAAATCGTGACTCTCGT 57.559 45.000 0.76 0.00 0.00 4.18
1878 1910 2.061773 AGCAAAATCGTGACTCTCGTG 58.938 47.619 0.76 0.00 0.00 4.35
1883 1915 2.638556 ATCGTGACTCTCGTGAAAGG 57.361 50.000 0.76 0.00 0.00 3.11
1933 1973 4.988716 ACGGCCGTGACTCTCCCA 62.989 66.667 33.75 0.00 0.00 4.37
1940 1980 1.593196 CGTGACTCTCCCAAAAGCAA 58.407 50.000 0.00 0.00 0.00 3.91
1942 1982 2.357637 CGTGACTCTCCCAAAAGCAAAA 59.642 45.455 0.00 0.00 0.00 2.44
1943 1983 3.706698 GTGACTCTCCCAAAAGCAAAAC 58.293 45.455 0.00 0.00 0.00 2.43
1953 1993 1.111277 AAAGCAAAACCGTGCCTCTT 58.889 45.000 0.00 0.00 46.14 2.85
1984 2024 0.600255 ACCGTGACTCTTGCGAAAGG 60.600 55.000 2.54 0.00 0.00 3.11
2023 2072 0.741915 GTTTCCAAAAGACACGGCCA 59.258 50.000 2.24 0.00 0.00 5.36
2031 2080 0.247736 AAGACACGGCCATGACTCTC 59.752 55.000 5.45 0.00 0.00 3.20
2033 2082 2.214181 GACACGGCCATGACTCTCGT 62.214 60.000 5.45 0.00 34.19 4.18
2108 2157 1.487482 CGTGACTCTCGTGAAAGCAA 58.513 50.000 0.00 0.00 0.00 3.91
2111 2160 3.602491 CGTGACTCTCGTGAAAGCAAAAG 60.602 47.826 0.00 0.00 0.00 2.27
2112 2161 3.309954 GTGACTCTCGTGAAAGCAAAAGT 59.690 43.478 0.00 0.00 0.00 2.66
2116 2165 2.111756 CTCGTGAAAGCAAAAGTGTGC 58.888 47.619 0.00 0.00 45.28 4.57
2119 2168 2.735126 CGTGAAAGCAAAAGTGTGCCTT 60.735 45.455 0.00 0.00 46.14 4.35
2122 2171 2.208326 AAGCAAAAGTGTGCCTTTCG 57.792 45.000 0.00 0.00 46.14 3.46
2135 2184 1.269257 GCCTTTCGCAGAAGCAAAACT 60.269 47.619 0.00 0.00 45.90 2.66
2136 2185 2.388121 CCTTTCGCAGAAGCAAAACTG 58.612 47.619 0.00 0.00 45.90 3.16
2145 2194 3.873361 CAGAAGCAAAACTGTGACTCTCA 59.127 43.478 0.00 0.00 0.00 3.27
2228 2281 3.067106 GGAAGCAAAATCGTGACTCTCA 58.933 45.455 0.00 0.00 0.00 3.27
2229 2282 3.686726 GGAAGCAAAATCGTGACTCTCAT 59.313 43.478 0.00 0.00 0.00 2.90
2231 2284 3.930336 AGCAAAATCGTGACTCTCATGA 58.070 40.909 0.00 0.00 45.40 3.07
2232 2285 4.318332 AGCAAAATCGTGACTCTCATGAA 58.682 39.130 0.00 0.00 44.60 2.57
2233 2286 4.756642 AGCAAAATCGTGACTCTCATGAAA 59.243 37.500 0.00 0.00 44.60 2.69
2234 2287 5.084722 GCAAAATCGTGACTCTCATGAAAG 58.915 41.667 0.00 0.00 44.60 2.62
2235 2288 5.106948 GCAAAATCGTGACTCTCATGAAAGA 60.107 40.000 2.24 0.00 44.60 2.52
2236 2289 6.566564 GCAAAATCGTGACTCTCATGAAAGAA 60.567 38.462 2.24 0.00 44.60 2.52
2237 2290 7.355017 CAAAATCGTGACTCTCATGAAAGAAA 58.645 34.615 2.24 0.00 44.60 2.52
2308 2361 0.613777 AAGCTAAGGAAGACCGGTGG 59.386 55.000 14.63 0.00 41.83 4.61
2314 2367 0.109913 AGGAAGACCGGTGGAAAACC 59.890 55.000 14.63 6.78 46.60 3.27
2368 2421 0.453782 AAATAGCCGAAAACGCGTGC 60.454 50.000 14.98 12.13 0.00 5.34
2369 2422 2.557265 AATAGCCGAAAACGCGTGCG 62.557 55.000 14.98 17.33 46.03 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
395 401 1.552348 GCTCCTCGCGAATGGAATCG 61.552 60.000 16.83 7.89 45.41 3.34
655 670 2.452505 ACCCATATTTTTCCACCACGG 58.547 47.619 0.00 0.00 0.00 4.94
688 703 4.502087 GGTCTTAGTGTAACCGGTTTGTCT 60.502 45.833 27.64 21.10 37.80 3.41
722 737 1.632018 CCCTTTCCCGAGCCCATACA 61.632 60.000 0.00 0.00 0.00 2.29
1114 1139 6.580791 GCGTCTTTGATTACAGCAACAATTAA 59.419 34.615 0.00 0.00 0.00 1.40
1116 1141 4.917415 GCGTCTTTGATTACAGCAACAATT 59.083 37.500 0.00 0.00 0.00 2.32
1566 1597 4.169508 CGCGAGAAATCCATGGTATCTAG 58.830 47.826 12.58 14.08 0.00 2.43
1567 1598 3.572682 ACGCGAGAAATCCATGGTATCTA 59.427 43.478 15.93 0.00 0.00 1.98
1568 1599 2.365617 ACGCGAGAAATCCATGGTATCT 59.634 45.455 15.93 13.40 0.00 1.98
1569 1600 2.755650 ACGCGAGAAATCCATGGTATC 58.244 47.619 15.93 8.72 0.00 2.24
1570 1601 2.872245 CAACGCGAGAAATCCATGGTAT 59.128 45.455 15.93 0.98 0.00 2.73
1571 1602 2.093921 TCAACGCGAGAAATCCATGGTA 60.094 45.455 15.93 0.00 0.00 3.25
1572 1603 1.086696 CAACGCGAGAAATCCATGGT 58.913 50.000 15.93 0.00 0.00 3.55
1573 1604 1.328680 CTCAACGCGAGAAATCCATGG 59.671 52.381 15.93 4.97 45.45 3.66
1574 1605 2.726555 CTCAACGCGAGAAATCCATG 57.273 50.000 15.93 0.00 45.45 3.66
1583 1614 3.430218 AGTTTTGAAGATCTCAACGCGAG 59.570 43.478 15.93 4.76 43.90 5.03
1584 1615 3.390135 AGTTTTGAAGATCTCAACGCGA 58.610 40.909 15.93 0.00 43.90 5.87
1585 1616 3.795561 AGTTTTGAAGATCTCAACGCG 57.204 42.857 3.53 3.53 43.90 6.01
1586 1617 6.654793 ATCTAGTTTTGAAGATCTCAACGC 57.345 37.500 0.00 0.00 43.90 4.84
1587 1618 7.759886 TGGTATCTAGTTTTGAAGATCTCAACG 59.240 37.037 0.00 0.00 43.90 4.10
1588 1619 9.606631 ATGGTATCTAGTTTTGAAGATCTCAAC 57.393 33.333 0.00 0.00 43.90 3.18
1589 1620 9.605275 CATGGTATCTAGTTTTGAAGATCTCAA 57.395 33.333 0.00 0.00 42.48 3.02
1590 1621 8.762645 ACATGGTATCTAGTTTTGAAGATCTCA 58.237 33.333 0.00 0.00 0.00 3.27
1591 1622 9.255304 GACATGGTATCTAGTTTTGAAGATCTC 57.745 37.037 0.00 0.00 0.00 2.75
1592 1623 7.923344 CGACATGGTATCTAGTTTTGAAGATCT 59.077 37.037 0.00 0.00 0.00 2.75
1593 1624 7.921214 TCGACATGGTATCTAGTTTTGAAGATC 59.079 37.037 0.00 0.00 0.00 2.75
1594 1625 7.782049 TCGACATGGTATCTAGTTTTGAAGAT 58.218 34.615 0.00 0.00 0.00 2.40
1595 1626 7.165460 TCGACATGGTATCTAGTTTTGAAGA 57.835 36.000 0.00 0.00 0.00 2.87
1596 1627 9.186323 CTATCGACATGGTATCTAGTTTTGAAG 57.814 37.037 0.00 0.00 0.00 3.02
1597 1628 8.141909 CCTATCGACATGGTATCTAGTTTTGAA 58.858 37.037 0.00 0.00 0.00 2.69
1598 1629 7.287005 ACCTATCGACATGGTATCTAGTTTTGA 59.713 37.037 0.00 0.00 31.50 2.69
1599 1630 7.434492 ACCTATCGACATGGTATCTAGTTTTG 58.566 38.462 0.00 0.00 31.50 2.44
1600 1631 7.598759 ACCTATCGACATGGTATCTAGTTTT 57.401 36.000 0.00 0.00 31.50 2.43
1601 1632 7.598759 AACCTATCGACATGGTATCTAGTTT 57.401 36.000 6.30 0.00 33.17 2.66
1602 1633 7.598759 AAACCTATCGACATGGTATCTAGTT 57.401 36.000 6.30 0.00 33.17 2.24
1603 1634 7.434492 CAAAACCTATCGACATGGTATCTAGT 58.566 38.462 6.30 0.00 33.17 2.57
1604 1635 6.868864 CCAAAACCTATCGACATGGTATCTAG 59.131 42.308 6.30 0.00 33.17 2.43
1605 1636 6.740401 GCCAAAACCTATCGACATGGTATCTA 60.740 42.308 6.30 0.00 33.17 1.98
1606 1637 5.611374 CCAAAACCTATCGACATGGTATCT 58.389 41.667 6.30 0.00 33.17 1.98
1607 1638 4.213482 GCCAAAACCTATCGACATGGTATC 59.787 45.833 6.30 0.00 33.17 2.24
1608 1639 4.134563 GCCAAAACCTATCGACATGGTAT 58.865 43.478 6.30 0.00 33.17 2.73
1609 1640 3.055021 TGCCAAAACCTATCGACATGGTA 60.055 43.478 6.30 0.00 33.17 3.25
1610 1641 2.290641 TGCCAAAACCTATCGACATGGT 60.291 45.455 0.00 0.00 35.29 3.55
1611 1642 2.364632 TGCCAAAACCTATCGACATGG 58.635 47.619 0.00 0.00 0.00 3.66
1612 1643 4.082787 AGTTTGCCAAAACCTATCGACATG 60.083 41.667 0.00 0.00 45.75 3.21
1613 1644 4.079253 AGTTTGCCAAAACCTATCGACAT 58.921 39.130 0.00 0.00 45.75 3.06
1614 1645 3.482436 AGTTTGCCAAAACCTATCGACA 58.518 40.909 0.00 0.00 45.75 4.35
1615 1646 4.499037 AAGTTTGCCAAAACCTATCGAC 57.501 40.909 0.00 0.00 45.75 4.20
1616 1647 5.523438 AAAAGTTTGCCAAAACCTATCGA 57.477 34.783 0.00 0.00 45.75 3.59
1637 1668 2.260481 GCCGGTGTTTTTCGTGAAAAA 58.740 42.857 14.67 14.67 44.98 1.94
1638 1669 1.469423 GGCCGGTGTTTTTCGTGAAAA 60.469 47.619 1.90 3.74 38.40 2.29
1639 1670 0.100861 GGCCGGTGTTTTTCGTGAAA 59.899 50.000 1.90 0.00 0.00 2.69
1640 1671 1.728672 GGCCGGTGTTTTTCGTGAA 59.271 52.632 1.90 0.00 0.00 3.18
1641 1672 2.535788 CGGCCGGTGTTTTTCGTGA 61.536 57.895 20.10 0.00 0.00 4.35
1642 1673 2.049475 TTCGGCCGGTGTTTTTCGTG 62.049 55.000 27.83 0.00 0.00 4.35
1643 1674 1.375098 TTTCGGCCGGTGTTTTTCGT 61.375 50.000 27.83 0.00 0.00 3.85
1644 1675 0.248539 TTTTCGGCCGGTGTTTTTCG 60.249 50.000 27.83 0.00 0.00 3.46
1645 1676 1.923899 TTTTTCGGCCGGTGTTTTTC 58.076 45.000 27.83 0.00 0.00 2.29
1661 1692 1.152922 TGCTCCCGGTTCGGTTTTT 60.153 52.632 0.00 0.00 46.80 1.94
1662 1693 1.895231 GTGCTCCCGGTTCGGTTTT 60.895 57.895 0.00 0.00 46.80 2.43
1663 1694 2.281276 GTGCTCCCGGTTCGGTTT 60.281 61.111 0.00 0.00 46.80 3.27
1664 1695 4.675029 CGTGCTCCCGGTTCGGTT 62.675 66.667 0.00 0.00 46.80 4.44
1668 1699 3.837570 AAACCCGTGCTCCCGGTTC 62.838 63.158 0.00 0.00 46.66 3.62
1669 1700 2.914756 AAAAACCCGTGCTCCCGGTT 62.915 55.000 0.00 4.62 46.66 4.44
1670 1701 3.424780 AAAAACCCGTGCTCCCGGT 62.425 57.895 0.00 0.00 46.66 5.28
1685 1716 1.144093 TGCCTCTCGGAAAGGGAAAAA 59.856 47.619 0.00 0.00 34.26 1.94
1686 1717 0.768622 TGCCTCTCGGAAAGGGAAAA 59.231 50.000 0.00 0.00 34.26 2.29
1687 1718 0.036306 GTGCCTCTCGGAAAGGGAAA 59.964 55.000 0.00 0.00 35.86 3.13
1688 1719 1.677552 GTGCCTCTCGGAAAGGGAA 59.322 57.895 0.00 0.00 35.86 3.97
1689 1720 2.646175 CGTGCCTCTCGGAAAGGGA 61.646 63.158 0.00 0.00 34.26 4.20
1690 1721 2.125512 CGTGCCTCTCGGAAAGGG 60.126 66.667 0.00 0.00 34.26 3.95
1691 1722 2.815647 GCGTGCCTCTCGGAAAGG 60.816 66.667 0.00 0.00 36.95 3.11
1692 1723 2.815647 GGCGTGCCTCTCGGAAAG 60.816 66.667 2.98 0.00 0.00 2.62
1693 1724 4.388499 GGGCGTGCCTCTCGGAAA 62.388 66.667 11.25 0.00 36.10 3.13
1711 1742 1.795768 TGTGATTTCGTGAGAGGCAC 58.204 50.000 0.00 0.00 43.69 5.01
1712 1743 2.143122 GTTGTGATTTCGTGAGAGGCA 58.857 47.619 0.00 0.00 43.69 4.75
1713 1744 1.464997 GGTTGTGATTTCGTGAGAGGC 59.535 52.381 0.00 0.00 43.69 4.70
1714 1745 1.726791 CGGTTGTGATTTCGTGAGAGG 59.273 52.381 0.00 0.00 43.69 3.69
1715 1746 2.404215 ACGGTTGTGATTTCGTGAGAG 58.596 47.619 0.00 0.00 43.69 3.20
1716 1747 2.519377 ACGGTTGTGATTTCGTGAGA 57.481 45.000 0.00 0.00 34.40 3.27
1728 1759 1.007271 CTGCGAGAGACACGGTTGT 60.007 57.895 0.00 0.00 39.32 3.32
1729 1760 0.318699 TTCTGCGAGAGACACGGTTG 60.319 55.000 0.00 0.00 0.00 3.77
1730 1761 0.039074 CTTCTGCGAGAGACACGGTT 60.039 55.000 0.00 0.00 0.00 4.44
1731 1762 1.581954 CTTCTGCGAGAGACACGGT 59.418 57.895 0.00 0.00 0.00 4.83
1732 1763 1.803519 GCTTCTGCGAGAGACACGG 60.804 63.158 0.00 0.00 0.00 4.94
1733 1764 0.664466 TTGCTTCTGCGAGAGACACG 60.664 55.000 0.00 0.00 43.34 4.49
1734 1765 1.502231 TTTGCTTCTGCGAGAGACAC 58.498 50.000 0.00 0.00 43.34 3.67
1735 1766 1.867233 GTTTTGCTTCTGCGAGAGACA 59.133 47.619 0.00 0.00 43.34 3.41
1736 1767 1.195674 GGTTTTGCTTCTGCGAGAGAC 59.804 52.381 0.00 0.00 43.34 3.36
1737 1768 1.512926 GGTTTTGCTTCTGCGAGAGA 58.487 50.000 0.00 0.00 43.34 3.10
1738 1769 0.164647 CGGTTTTGCTTCTGCGAGAG 59.835 55.000 0.00 0.00 43.34 3.20
1739 1770 0.531974 ACGGTTTTGCTTCTGCGAGA 60.532 50.000 0.00 0.00 43.34 4.04
1740 1771 0.384725 CACGGTTTTGCTTCTGCGAG 60.385 55.000 0.00 0.00 43.34 5.03
1741 1772 0.812014 TCACGGTTTTGCTTCTGCGA 60.812 50.000 0.00 0.00 43.34 5.10
1742 1773 0.657368 GTCACGGTTTTGCTTCTGCG 60.657 55.000 0.00 0.00 43.34 5.18
1743 1774 0.663153 AGTCACGGTTTTGCTTCTGC 59.337 50.000 0.00 0.00 40.20 4.26
1744 1775 2.213499 AGAGTCACGGTTTTGCTTCTG 58.787 47.619 0.00 0.00 0.00 3.02
1745 1776 2.484889 GAGAGTCACGGTTTTGCTTCT 58.515 47.619 0.00 0.00 0.00 2.85
1746 1777 1.192534 CGAGAGTCACGGTTTTGCTTC 59.807 52.381 1.62 0.00 0.00 3.86
1747 1778 1.217882 CGAGAGTCACGGTTTTGCTT 58.782 50.000 1.62 0.00 0.00 3.91
1748 1779 0.104304 ACGAGAGTCACGGTTTTGCT 59.896 50.000 14.49 0.00 44.19 3.91
1749 1780 2.601562 ACGAGAGTCACGGTTTTGC 58.398 52.632 14.49 0.00 44.19 3.68
1801 1832 1.578206 GGCTGTGCCTCCTCGAAAAC 61.578 60.000 0.73 0.00 46.69 2.43
1814 1845 2.163390 CGCGAGAGTCATGGCTGTG 61.163 63.158 3.48 0.00 0.00 3.66
1815 1846 1.877576 TTCGCGAGAGTCATGGCTGT 61.878 55.000 3.48 0.00 43.69 4.40
1816 1847 0.737367 TTTCGCGAGAGTCATGGCTG 60.737 55.000 3.48 0.00 43.69 4.85
1817 1848 0.459237 CTTTCGCGAGAGTCATGGCT 60.459 55.000 17.92 0.00 43.69 4.75
1820 1851 0.368227 GTGCTTTCGCGAGAGTCATG 59.632 55.000 25.34 7.32 43.69 3.07
1821 1852 0.038251 TGTGCTTTCGCGAGAGTCAT 60.038 50.000 25.34 0.00 43.69 3.06
1829 1861 4.368808 CACGGGTGTGCTTTCGCG 62.369 66.667 0.00 0.00 39.67 5.87
1931 1971 0.179086 AGGCACGGTTTTGCTTTTGG 60.179 50.000 0.00 0.00 42.56 3.28
1933 1973 1.111277 AGAGGCACGGTTTTGCTTTT 58.889 45.000 0.00 0.00 42.56 2.27
1940 1980 2.951475 TTCCGCAAGAGGCACGGTTT 62.951 55.000 0.00 0.00 46.92 3.27
1942 1982 3.883744 CTTCCGCAAGAGGCACGGT 62.884 63.158 0.00 0.00 46.92 4.83
1960 2000 0.657368 CGCAAGAGTCACGGTTTTGC 60.657 55.000 3.16 3.16 40.40 3.68
2004 2053 0.741915 TGGCCGTGTCTTTTGGAAAC 59.258 50.000 0.00 0.00 0.00 2.78
2009 2058 1.197721 GAGTCATGGCCGTGTCTTTTG 59.802 52.381 23.08 0.00 0.00 2.44
2011 2060 0.687354 AGAGTCATGGCCGTGTCTTT 59.313 50.000 23.08 16.19 0.00 2.52
2012 2061 0.247736 GAGAGTCATGGCCGTGTCTT 59.752 55.000 23.08 14.11 0.00 3.01
2067 2116 0.941542 CGTGCCTCTTGGAAACGAAA 59.058 50.000 0.00 0.00 43.27 3.46
2068 2117 0.882927 CCGTGCCTCTTGGAAACGAA 60.883 55.000 10.74 0.00 43.27 3.85
2069 2118 1.301401 CCGTGCCTCTTGGAAACGA 60.301 57.895 10.74 0.00 43.27 3.85
2070 2119 2.966309 GCCGTGCCTCTTGGAAACG 61.966 63.158 0.00 0.00 41.54 3.60
2119 2168 2.013400 TCACAGTTTTGCTTCTGCGAA 58.987 42.857 0.00 0.00 43.34 4.70
2122 2171 2.615912 AGAGTCACAGTTTTGCTTCTGC 59.384 45.455 0.00 0.00 40.20 4.26
2180 2229 0.319555 TGTCGTGCCTCTCGGAAAAG 60.320 55.000 0.00 0.00 0.00 2.27
2181 2230 0.599204 GTGTCGTGCCTCTCGGAAAA 60.599 55.000 0.00 0.00 0.00 2.29
2207 2260 3.067106 TGAGAGTCACGATTTTGCTTCC 58.933 45.455 0.00 0.00 0.00 3.46
2208 2261 4.389992 TCATGAGAGTCACGATTTTGCTTC 59.610 41.667 0.00 0.00 0.00 3.86
2286 2339 3.307199 CCACCGGTCTTCCTTAGCTTTTA 60.307 47.826 2.59 0.00 0.00 1.52
2346 2399 3.088552 CACGCGTTTTCGGCTATTTTAG 58.911 45.455 10.22 0.00 44.29 1.85
2347 2400 2.725452 GCACGCGTTTTCGGCTATTTTA 60.725 45.455 10.22 0.00 44.29 1.52
2348 2401 1.958417 CACGCGTTTTCGGCTATTTT 58.042 45.000 10.22 0.00 44.29 1.82


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

AutoCloner maintained by Alex Coulton.