Multiple sequence alignment - TraesCS3A01G269500

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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 TraesCS3A01G269500 chr3A 100.000 3610 0 0 1 3610 496035795 496039404 0.000000e+00 6667.0
1 TraesCS3A01G269500 chr3A 95.122 82 3 1 1734 1814 655987823 655987904 1.050000e-25 128.0
2 TraesCS3A01G269500 chr3A 80.488 123 19 5 85 204 727823866 727823986 4.960000e-14 89.8
3 TraesCS3A01G269500 chr3D 91.188 1793 70 28 1 1735 374011257 374013019 0.000000e+00 2355.0
4 TraesCS3A01G269500 chr3D 96.360 1401 35 8 2213 3610 374013446 374014833 0.000000e+00 2290.0
5 TraesCS3A01G269500 chr3D 89.670 455 29 7 1810 2262 374013016 374013454 6.770000e-157 564.0
6 TraesCS3A01G269500 chr3D 86.735 98 12 1 58 154 559605317 559605414 1.370000e-19 108.0
7 TraesCS3A01G269500 chr3D 86.842 76 9 1 3437 3511 64194770 64194845 2.310000e-12 84.2
8 TraesCS3A01G269500 chr3D 81.053 95 12 4 3440 3534 477907443 477907355 1.800000e-08 71.3
9 TraesCS3A01G269500 chr3B 88.796 1794 102 49 1 1732 487767062 487768818 0.000000e+00 2108.0
10 TraesCS3A01G269500 chr3B 97.447 1136 23 3 2213 3346 487769247 487770378 0.000000e+00 1932.0
11 TraesCS3A01G269500 chr3B 88.839 448 31 8 1817 2262 487768825 487769255 1.910000e-147 532.0
12 TraesCS3A01G269500 chr3B 91.786 280 14 5 3334 3610 487773293 487773566 7.310000e-102 381.0
13 TraesCS3A01G269500 chr3B 95.122 82 3 1 1734 1814 101907404 101907485 1.050000e-25 128.0
14 TraesCS3A01G269500 chr3B 81.053 95 12 4 3440 3534 637089781 637089693 1.800000e-08 71.3
15 TraesCS3A01G269500 chr4D 84.000 150 20 4 57 204 374625185 374625038 1.350000e-29 141.0
16 TraesCS3A01G269500 chr6B 96.341 82 2 1 1734 1814 18747325 18747406 2.260000e-27 134.0
17 TraesCS3A01G269500 chr5D 96.341 82 2 1 1734 1814 6262164 6262245 2.260000e-27 134.0
18 TraesCS3A01G269500 chr5D 95.122 82 3 1 1734 1814 6164173 6164254 1.050000e-25 128.0
19 TraesCS3A01G269500 chr5D 94.286 35 1 1 1 34 322006491 322006457 7.000000e-03 52.8
20 TraesCS3A01G269500 chr1D 96.341 82 1 2 1734 1814 51859293 51859373 2.260000e-27 134.0
21 TraesCS3A01G269500 chr1D 80.000 100 14 4 3436 3534 101285143 101285237 6.470000e-08 69.4
22 TraesCS3A01G269500 chrUn 95.122 82 3 1 1734 1814 414538301 414538382 1.050000e-25 128.0
23 TraesCS3A01G269500 chrUn 79.856 139 19 8 51 187 1085878 1086009 3.840000e-15 93.5
24 TraesCS3A01G269500 chr7A 95.122 82 3 1 1734 1814 571440897 571440816 1.050000e-25 128.0
25 TraesCS3A01G269500 chr7A 78.899 109 12 9 3427 3534 618200747 618200845 3.010000e-06 63.9
26 TraesCS3A01G269500 chr2D 95.122 82 3 1 1734 1814 135988268 135988187 1.050000e-25 128.0
27 TraesCS3A01G269500 chr2D 80.247 162 28 4 45 204 548739773 548739614 6.330000e-23 119.0
28 TraesCS3A01G269500 chr6D 83.212 137 22 1 57 192 1432379 1432515 1.360000e-24 124.0
29 TraesCS3A01G269500 chr7D 79.730 148 27 3 59 204 190143709 190143855 1.770000e-18 104.0
30 TraesCS3A01G269500 chr7D 85.185 81 11 1 439 518 457437638 457437558 8.310000e-12 82.4
31 TraesCS3A01G269500 chr7D 83.721 86 9 3 3450 3535 236641973 236642053 3.870000e-10 76.8
32 TraesCS3A01G269500 chr7D 90.909 55 5 0 1 55 603904923 603904869 1.390000e-09 75.0
33 TraesCS3A01G269500 chr6A 78.632 117 21 4 77 190 192832162 192832047 1.390000e-09 75.0
34 TraesCS3A01G269500 chr1A 80.198 101 12 6 3436 3534 104216552 104216458 6.470000e-08 69.4
35 TraesCS3A01G269500 chr5A 85.714 63 8 1 454 515 558344905 558344967 8.370000e-07 65.8


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 TraesCS3A01G269500 chr3A 496035795 496039404 3609 False 6667.000000 6667 100.000 1 3610 1 chr3A.!!$F1 3609
1 TraesCS3A01G269500 chr3D 374011257 374014833 3576 False 1736.333333 2355 92.406 1 3610 3 chr3D.!!$F3 3609
2 TraesCS3A01G269500 chr3B 487767062 487773566 6504 False 1238.250000 2108 91.717 1 3610 4 chr3B.!!$F2 3609

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
88 99 0.808755 ACAAACGCCGATTGAATCCC 59.191 50.0 14.22 0.0 0.0 3.85 F
1765 1830 0.397564 AAATGTTGCAAAGCCTGGGG 59.602 50.0 0.00 0.0 0.0 4.96 F
1772 1837 0.467804 GCAAAGCCTGGGGTGAAAAA 59.532 50.0 0.00 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2022 0.101399 CGGACGAGATCCTTGTCAGG 59.899 60.000 14.29 4.24 46.69 3.86 R
2567 2677 0.028242 CGTCTTCTGGATCGTCGGAG 59.972 60.000 0.00 0.00 0.00 4.63 R
2682 2795 2.178984 ACAAGGAAGGAAAACCCCATGA 59.821 45.455 0.00 0.00 34.66 3.07 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
49 60 7.936847 AGGATCAAACTTGTAGTTACATGAACA 59.063 33.333 0.00 0.00 37.47 3.18
78 89 2.549282 CACCGAAGACAAACGCCG 59.451 61.111 0.00 0.00 0.00 6.46
88 99 0.808755 ACAAACGCCGATTGAATCCC 59.191 50.000 14.22 0.00 0.00 3.85
145 156 3.643320 TCCGAAGATGCTAGAATCACCAT 59.357 43.478 13.47 0.00 0.00 3.55
154 166 1.887707 GAATCACCATCGGACGGGC 60.888 63.158 0.00 0.00 0.00 6.13
214 226 5.565592 TGTCGTCGCCTCTACTAATTTTA 57.434 39.130 0.00 0.00 0.00 1.52
244 256 7.809238 TGATTCCAAATGATACCAAGAGATCT 58.191 34.615 0.00 0.00 0.00 2.75
366 400 2.916111 CGACAAATCTGACGTTTTGGG 58.084 47.619 13.40 3.38 37.19 4.12
432 466 4.014406 AGGTGGATAATCCCGACAAAAAC 58.986 43.478 0.00 0.00 35.03 2.43
433 467 4.014406 GGTGGATAATCCCGACAAAAACT 58.986 43.478 0.00 0.00 35.03 2.66
441 475 4.610605 TCCCGACAAAAACTGAGTATGA 57.389 40.909 0.00 0.00 0.00 2.15
442 476 4.963373 TCCCGACAAAAACTGAGTATGAA 58.037 39.130 0.00 0.00 0.00 2.57
522 579 9.421806 CCATGCTTAAAAATCTGACATTTGTAA 57.578 29.630 0.00 0.00 0.00 2.41
625 682 7.103641 TGCAAATTACTCTCCTAAGTAACCAG 58.896 38.462 0.00 0.00 42.78 4.00
724 781 8.463930 TCCTGGATTTTTATTTCAAGCGATAT 57.536 30.769 0.00 0.00 0.00 1.63
1038 1097 3.661648 GACAGCATGGGGTGGGGT 61.662 66.667 0.00 0.00 46.66 4.95
1045 1104 2.147387 ATGGGGTGGGGTAGATCGC 61.147 63.158 0.00 0.00 0.00 4.58
1290 1349 5.988561 TGAAGCGAACATATGTGTATATGCA 59.011 36.000 9.63 0.00 46.60 3.96
1513 1572 5.529581 TCTTTTCCCCTTCATGTTGTTTC 57.470 39.130 0.00 0.00 0.00 2.78
1560 1619 9.939802 AAGAAAAACTTGATATAGGTACTCGTT 57.060 29.630 0.00 0.00 37.38 3.85
1596 1656 6.852420 ATGTGGAAGCAGTAGAAGTAAGTA 57.148 37.500 0.00 0.00 0.00 2.24
1597 1657 6.022163 TGTGGAAGCAGTAGAAGTAAGTAC 57.978 41.667 0.00 0.00 0.00 2.73
1606 1666 7.612244 AGCAGTAGAAGTAAGTACTGATCTTCA 59.388 37.037 23.93 14.21 46.17 3.02
1608 1668 9.944663 CAGTAGAAGTAAGTACTGATCTTCATC 57.055 37.037 23.93 18.57 46.17 2.92
1622 1682 4.732285 TCTTCATCTTTTGCGAGTGAAC 57.268 40.909 0.00 0.00 0.00 3.18
1625 1685 4.472691 TCATCTTTTGCGAGTGAACAAG 57.527 40.909 0.00 0.00 0.00 3.16
1626 1686 3.876914 TCATCTTTTGCGAGTGAACAAGT 59.123 39.130 0.00 0.00 0.00 3.16
1628 1688 4.789095 TCTTTTGCGAGTGAACAAGTAC 57.211 40.909 0.00 0.00 0.00 2.73
1629 1689 4.439057 TCTTTTGCGAGTGAACAAGTACT 58.561 39.130 0.00 0.00 0.00 2.73
1630 1690 4.270084 TCTTTTGCGAGTGAACAAGTACTG 59.730 41.667 0.00 0.00 0.00 2.74
1631 1691 3.446310 TTGCGAGTGAACAAGTACTGA 57.554 42.857 0.00 0.00 0.00 3.41
1632 1692 3.660501 TGCGAGTGAACAAGTACTGAT 57.339 42.857 0.00 0.00 0.00 2.90
1633 1693 4.776795 TGCGAGTGAACAAGTACTGATA 57.223 40.909 0.00 0.00 0.00 2.15
1634 1694 5.324784 TGCGAGTGAACAAGTACTGATAT 57.675 39.130 0.00 0.00 0.00 1.63
1635 1695 5.720202 TGCGAGTGAACAAGTACTGATATT 58.280 37.500 0.00 0.00 0.00 1.28
1636 1696 5.805486 TGCGAGTGAACAAGTACTGATATTC 59.195 40.000 0.00 0.00 0.00 1.75
1637 1697 6.037098 GCGAGTGAACAAGTACTGATATTCT 58.963 40.000 0.00 0.00 0.00 2.40
1638 1698 6.531948 GCGAGTGAACAAGTACTGATATTCTT 59.468 38.462 0.00 0.00 0.00 2.52
1639 1699 7.063544 GCGAGTGAACAAGTACTGATATTCTTT 59.936 37.037 0.00 0.00 0.00 2.52
1640 1700 8.926710 CGAGTGAACAAGTACTGATATTCTTTT 58.073 33.333 0.00 0.00 0.00 2.27
1642 1702 9.778741 AGTGAACAAGTACTGATATTCTTTTCA 57.221 29.630 0.00 0.00 0.00 2.69
1643 1703 9.813080 GTGAACAAGTACTGATATTCTTTTCAC 57.187 33.333 0.00 0.62 34.82 3.18
1644 1704 8.999431 TGAACAAGTACTGATATTCTTTTCACC 58.001 33.333 0.00 0.00 0.00 4.02
1645 1705 8.918202 AACAAGTACTGATATTCTTTTCACCA 57.082 30.769 0.00 0.00 0.00 4.17
1668 1728 7.976175 ACCAAAGTGAGATTTTGAGTTTTCTTC 59.024 33.333 0.00 0.00 37.65 2.87
1691 1756 7.633361 TCGTGATAAACAGTGAAGAAACTAC 57.367 36.000 0.00 0.00 0.00 2.73
1742 1807 6.780457 ATGAACAATCATTCTTTCCCGATT 57.220 33.333 0.00 0.00 43.89 3.34
1743 1808 6.588719 TGAACAATCATTCTTTCCCGATTT 57.411 33.333 0.00 0.00 0.00 2.17
1744 1809 6.991938 TGAACAATCATTCTTTCCCGATTTT 58.008 32.000 0.00 0.00 0.00 1.82
1745 1810 6.867816 TGAACAATCATTCTTTCCCGATTTTG 59.132 34.615 0.00 0.00 0.00 2.44
1746 1811 6.588719 ACAATCATTCTTTCCCGATTTTGA 57.411 33.333 0.00 0.00 0.00 2.69
1747 1812 6.991938 ACAATCATTCTTTCCCGATTTTGAA 58.008 32.000 0.00 0.00 0.00 2.69
1748 1813 7.441017 ACAATCATTCTTTCCCGATTTTGAAA 58.559 30.769 0.00 0.00 0.00 2.69
1749 1814 8.096414 ACAATCATTCTTTCCCGATTTTGAAAT 58.904 29.630 0.00 0.00 30.67 2.17
1750 1815 8.385111 CAATCATTCTTTCCCGATTTTGAAATG 58.615 33.333 0.00 0.00 30.67 2.32
1751 1816 6.991938 TCATTCTTTCCCGATTTTGAAATGT 58.008 32.000 0.00 0.00 30.67 2.71
1752 1817 7.441017 TCATTCTTTCCCGATTTTGAAATGTT 58.559 30.769 0.00 0.00 30.67 2.71
1753 1818 7.384660 TCATTCTTTCCCGATTTTGAAATGTTG 59.615 33.333 0.00 0.00 30.67 3.33
1754 1819 4.987912 TCTTTCCCGATTTTGAAATGTTGC 59.012 37.500 0.00 0.00 30.67 4.17
1755 1820 4.327982 TTCCCGATTTTGAAATGTTGCA 57.672 36.364 0.00 0.00 0.00 4.08
1756 1821 4.327982 TCCCGATTTTGAAATGTTGCAA 57.672 36.364 0.00 0.00 0.00 4.08
1757 1822 4.697514 TCCCGATTTTGAAATGTTGCAAA 58.302 34.783 0.00 0.00 32.63 3.68
1758 1823 4.749099 TCCCGATTTTGAAATGTTGCAAAG 59.251 37.500 0.00 0.00 35.64 2.77
1759 1824 4.456914 CCGATTTTGAAATGTTGCAAAGC 58.543 39.130 0.00 0.00 35.64 3.51
1760 1825 4.456914 CGATTTTGAAATGTTGCAAAGCC 58.543 39.130 0.00 0.00 35.64 4.35
1761 1826 4.211794 CGATTTTGAAATGTTGCAAAGCCT 59.788 37.500 0.00 0.00 35.64 4.58
1762 1827 4.879104 TTTTGAAATGTTGCAAAGCCTG 57.121 36.364 0.00 0.00 35.64 4.85
1763 1828 2.529780 TGAAATGTTGCAAAGCCTGG 57.470 45.000 0.00 0.00 0.00 4.45
1764 1829 1.070445 TGAAATGTTGCAAAGCCTGGG 59.930 47.619 0.00 0.00 0.00 4.45
1765 1830 0.397564 AAATGTTGCAAAGCCTGGGG 59.602 50.000 0.00 0.00 0.00 4.96
1766 1831 0.763986 AATGTTGCAAAGCCTGGGGT 60.764 50.000 0.00 0.00 0.00 4.95
1767 1832 1.474332 ATGTTGCAAAGCCTGGGGTG 61.474 55.000 0.00 0.00 0.00 4.61
1768 1833 1.832167 GTTGCAAAGCCTGGGGTGA 60.832 57.895 0.00 0.00 0.00 4.02
1769 1834 1.075674 TTGCAAAGCCTGGGGTGAA 60.076 52.632 0.00 0.00 0.00 3.18
1770 1835 0.689080 TTGCAAAGCCTGGGGTGAAA 60.689 50.000 0.00 0.00 0.00 2.69
1771 1836 0.689080 TGCAAAGCCTGGGGTGAAAA 60.689 50.000 0.00 0.00 0.00 2.29
1772 1837 0.467804 GCAAAGCCTGGGGTGAAAAA 59.532 50.000 0.00 0.00 0.00 1.94
1791 1856 3.833559 AAAGGGGAGAAATGATGTGGT 57.166 42.857 0.00 0.00 0.00 4.16
1792 1857 3.833559 AAGGGGAGAAATGATGTGGTT 57.166 42.857 0.00 0.00 0.00 3.67
1793 1858 4.946160 AAGGGGAGAAATGATGTGGTTA 57.054 40.909 0.00 0.00 0.00 2.85
1794 1859 4.236527 AGGGGAGAAATGATGTGGTTAC 57.763 45.455 0.00 0.00 0.00 2.50
1795 1860 3.591527 AGGGGAGAAATGATGTGGTTACA 59.408 43.478 0.00 0.00 41.89 2.41
1796 1861 3.947834 GGGGAGAAATGATGTGGTTACAG 59.052 47.826 0.00 0.00 40.79 2.74
1797 1862 3.947834 GGGAGAAATGATGTGGTTACAGG 59.052 47.826 0.00 0.00 40.79 4.00
1798 1863 4.324254 GGGAGAAATGATGTGGTTACAGGA 60.324 45.833 0.00 0.00 40.79 3.86
1799 1864 5.440610 GGAGAAATGATGTGGTTACAGGAT 58.559 41.667 0.00 0.00 40.79 3.24
1800 1865 5.297776 GGAGAAATGATGTGGTTACAGGATG 59.702 44.000 0.00 0.00 40.79 3.51
1801 1866 4.641989 AGAAATGATGTGGTTACAGGATGC 59.358 41.667 0.00 0.00 42.53 3.91
1802 1867 3.650281 ATGATGTGGTTACAGGATGCA 57.350 42.857 0.00 0.00 42.53 3.96
1803 1868 3.431673 TGATGTGGTTACAGGATGCAA 57.568 42.857 0.00 0.00 42.53 4.08
1804 1869 3.966979 TGATGTGGTTACAGGATGCAAT 58.033 40.909 0.00 0.00 42.53 3.56
1805 1870 4.343231 TGATGTGGTTACAGGATGCAATT 58.657 39.130 0.00 0.00 42.53 2.32
1806 1871 4.771577 TGATGTGGTTACAGGATGCAATTT 59.228 37.500 0.00 0.00 42.53 1.82
1807 1872 4.782019 TGTGGTTACAGGATGCAATTTC 57.218 40.909 0.00 0.00 42.53 2.17
1808 1873 3.509575 TGTGGTTACAGGATGCAATTTCC 59.490 43.478 0.00 0.00 42.53 3.13
1809 1874 3.763897 GTGGTTACAGGATGCAATTTCCT 59.236 43.478 1.25 1.25 44.60 3.36
1810 1875 4.016444 TGGTTACAGGATGCAATTTCCTC 58.984 43.478 4.28 0.00 41.78 3.71
1811 1876 4.263905 TGGTTACAGGATGCAATTTCCTCT 60.264 41.667 4.28 0.00 41.78 3.69
1812 1877 4.706962 GGTTACAGGATGCAATTTCCTCTT 59.293 41.667 4.28 0.00 41.78 2.85
1813 1878 5.163612 GGTTACAGGATGCAATTTCCTCTTC 60.164 44.000 4.28 0.00 41.78 2.87
1814 1879 4.038271 ACAGGATGCAATTTCCTCTTCA 57.962 40.909 4.28 0.00 41.78 3.02
1815 1880 4.015084 ACAGGATGCAATTTCCTCTTCAG 58.985 43.478 4.28 0.00 41.78 3.02
1823 1888 9.428097 GATGCAATTTCCTCTTCAGTTAATTTT 57.572 29.630 0.00 0.00 0.00 1.82
1851 1916 3.389983 TGTTTCCAGTTAGGTGTGCTAGT 59.610 43.478 0.00 0.00 39.02 2.57
1855 1920 3.258372 TCCAGTTAGGTGTGCTAGTTCTG 59.742 47.826 0.00 0.00 39.02 3.02
1858 1923 1.938585 TAGGTGTGCTAGTTCTGCCT 58.061 50.000 0.00 0.00 0.00 4.75
1867 1932 3.071602 TGCTAGTTCTGCCTGTTCTCTTT 59.928 43.478 0.00 0.00 0.00 2.52
1875 1940 4.101585 TCTGCCTGTTCTCTTTCTTCTTCA 59.898 41.667 0.00 0.00 0.00 3.02
1882 1947 5.749109 TGTTCTCTTTCTTCTTCACTCGTTC 59.251 40.000 0.00 0.00 0.00 3.95
1891 1956 8.433421 TTCTTCTTCACTCGTTCTTAATTTGT 57.567 30.769 0.00 0.00 0.00 2.83
1892 1957 9.537192 TTCTTCTTCACTCGTTCTTAATTTGTA 57.463 29.630 0.00 0.00 0.00 2.41
1893 1958 8.975439 TCTTCTTCACTCGTTCTTAATTTGTAC 58.025 33.333 0.00 0.00 0.00 2.90
1894 1959 8.882415 TTCTTCACTCGTTCTTAATTTGTACT 57.118 30.769 0.00 0.00 0.00 2.73
1895 1960 9.970395 TTCTTCACTCGTTCTTAATTTGTACTA 57.030 29.630 0.00 0.00 0.00 1.82
1896 1961 9.403110 TCTTCACTCGTTCTTAATTTGTACTAC 57.597 33.333 0.00 0.00 0.00 2.73
1897 1962 9.408069 CTTCACTCGTTCTTAATTTGTACTACT 57.592 33.333 0.00 0.00 0.00 2.57
1899 1964 9.831737 TCACTCGTTCTTAATTTGTACTACTAC 57.168 33.333 0.00 0.00 0.00 2.73
1930 1995 8.715191 ATTTTCTCCTTGATCATAGATATCGC 57.285 34.615 0.00 0.00 0.00 4.58
1957 2022 7.792383 TTATCGCGTTATCTAAGCAGTTATC 57.208 36.000 5.77 0.00 0.00 1.75
2028 2095 7.968246 ACATGATTAAACTTTCTCTGATCACG 58.032 34.615 0.00 0.00 0.00 4.35
2031 2098 7.151976 TGATTAAACTTTCTCTGATCACGTCA 58.848 34.615 0.00 0.00 35.05 4.35
2033 2100 7.962964 TTAAACTTTCTCTGATCACGTCATT 57.037 32.000 0.00 0.00 35.97 2.57
2034 2101 6.867662 AAACTTTCTCTGATCACGTCATTT 57.132 33.333 0.00 0.00 35.97 2.32
2035 2102 5.852738 ACTTTCTCTGATCACGTCATTTG 57.147 39.130 0.00 0.00 35.97 2.32
2036 2103 5.300752 ACTTTCTCTGATCACGTCATTTGT 58.699 37.500 0.00 0.00 35.97 2.83
2037 2104 5.760253 ACTTTCTCTGATCACGTCATTTGTT 59.240 36.000 0.00 0.00 35.97 2.83
2038 2105 6.260936 ACTTTCTCTGATCACGTCATTTGTTT 59.739 34.615 0.00 0.00 35.97 2.83
2039 2106 7.441157 ACTTTCTCTGATCACGTCATTTGTTTA 59.559 33.333 0.00 0.00 35.97 2.01
2090 2157 5.295431 TCTTGTTTGTTCTTCCATATGCG 57.705 39.130 0.00 0.00 0.00 4.73
2120 2187 7.812648 AGCTACATATCAAGATCTCTTACGAC 58.187 38.462 0.00 0.00 34.28 4.34
2126 2193 8.729756 CATATCAAGATCTCTTACGACATCTCT 58.270 37.037 0.00 0.00 34.28 3.10
2130 2197 3.006112 TCTCTTACGACATCTCTGGCT 57.994 47.619 0.00 0.00 0.00 4.75
2139 2206 3.186001 CGACATCTCTGGCTTTATCATGC 59.814 47.826 0.00 0.00 0.00 4.06
2144 2211 3.054875 TCTCTGGCTTTATCATGCACAGT 60.055 43.478 0.00 0.00 32.93 3.55
2146 2213 4.842574 TCTGGCTTTATCATGCACAGTTA 58.157 39.130 0.00 0.00 32.93 2.24
2170 2237 4.244802 GCGGAGAGAGGAGACGCG 62.245 72.222 3.53 3.53 40.84 6.01
2176 2243 1.082627 GAGAGGAGACGCGCGATAC 60.083 63.158 39.36 24.76 34.13 2.24
2200 2267 2.168521 TGAATTCCAGACTCCCATCGTC 59.831 50.000 2.27 0.00 0.00 4.20
2221 2329 2.838736 AGGTACTGCACACAACTTCAG 58.161 47.619 0.00 0.00 37.18 3.02
2224 2332 3.741344 GGTACTGCACACAACTTCAGTAG 59.259 47.826 0.00 0.00 41.13 2.57
2254 2362 6.316890 TGAATTTACCCGGAATAACAAGCTAC 59.683 38.462 0.73 0.00 0.00 3.58
2303 2411 1.216064 TATGCCTGCCAACCAGATCT 58.784 50.000 0.00 0.00 44.64 2.75
2314 2422 0.694771 ACCAGATCTCCAAGCAGCAA 59.305 50.000 0.00 0.00 0.00 3.91
2392 2500 3.568007 GCACCAGAGGTATGTCTCTCTAG 59.432 52.174 0.00 0.00 41.76 2.43
2438 2548 3.189287 ACGAGTTGAATGGCTGATCAAAC 59.811 43.478 0.00 0.00 37.31 2.93
2468 2578 9.988350 ATTATACACTGCGAAGTTATCTTTTTG 57.012 29.630 0.00 0.00 33.64 2.44
2567 2677 2.789893 GGCTGATTCGACGAGTATGAAC 59.210 50.000 0.00 0.00 0.00 3.18
2627 2740 6.541641 AGCTATGATCCACAAATGTTCTTCTC 59.458 38.462 0.00 0.00 0.00 2.87
2628 2741 6.238593 GCTATGATCCACAAATGTTCTTCTCC 60.239 42.308 0.00 0.00 0.00 3.71
2629 2742 5.246981 TGATCCACAAATGTTCTTCTCCT 57.753 39.130 0.00 0.00 0.00 3.69
2682 2795 4.065789 CGACAGTTCCTTTCTTTAGCCTT 58.934 43.478 0.00 0.00 0.00 4.35
3039 3153 1.267806 ACTTGCATCGCAGACCTTTTG 59.732 47.619 0.00 0.00 42.51 2.44
3051 3167 5.278266 CGCAGACCTTTTGTTTTATCCAGAA 60.278 40.000 0.00 0.00 0.00 3.02
3127 3243 6.811665 TGCACAGCTGTATTTTGTACTACTAG 59.188 38.462 21.20 1.97 0.00 2.57
3212 3328 7.779326 ACAGAAGATCTATGATCTCTCTGTGAA 59.221 37.037 28.64 0.00 40.55 3.18
3332 3448 8.574251 AATTACAGGTAGTATTTTGTCATGCA 57.426 30.769 0.00 0.00 31.53 3.96
3380 6419 9.902684 GATATATCCATGAGATTTGATCCTTGT 57.097 33.333 0.81 0.00 36.33 3.16
3398 6437 4.807834 CCTTGTCGACGTCTCTGTATAGTA 59.192 45.833 14.70 0.00 0.00 1.82
3399 6438 5.466058 CCTTGTCGACGTCTCTGTATAGTAT 59.534 44.000 14.70 0.00 0.00 2.12
3497 6539 5.196341 GGCCATTTTATAGCCTACCAAAC 57.804 43.478 0.00 0.00 43.62 2.93
3498 6540 4.038763 GGCCATTTTATAGCCTACCAAACC 59.961 45.833 0.00 0.00 43.62 3.27
3504 6546 2.754946 TAGCCTACCAAACCGTCTTG 57.245 50.000 0.00 0.00 0.00 3.02
3557 6599 5.926542 GGAAAAAGCAAACTGATAAAGGGTC 59.073 40.000 0.00 0.00 0.00 4.46
3558 6600 6.462347 GGAAAAAGCAAACTGATAAAGGGTCA 60.462 38.462 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.547967 TCATGTAACTACAAGTTTGATCCTTC 57.452 34.615 0.00 0.00 39.51 3.46
49 60 2.028020 GTCTTCGGTGGATCCTGTCTTT 60.028 50.000 14.23 0.00 0.00 2.52
78 89 3.134458 GTGGATCTCACGGGATTCAATC 58.866 50.000 0.00 0.00 33.53 2.67
88 99 1.313091 TGTCTCCGGTGGATCTCACG 61.313 60.000 0.00 3.22 46.96 4.35
117 128 3.151958 TAGCATCTTCGGAGGGCGC 62.152 63.158 0.00 0.00 34.66 6.53
145 156 2.992689 TGCTTAGTGCCCGTCCGA 60.993 61.111 0.00 0.00 42.00 4.55
154 166 7.657336 TGGAATAAAGTTTTTCCTGCTTAGTG 58.343 34.615 20.56 0.00 41.65 2.74
214 226 8.365060 TCTTGGTATCATTTGGAATCAACAAT 57.635 30.769 0.00 0.00 31.78 2.71
263 275 2.798976 TTTTGCTACGTACGTGAGGT 57.201 45.000 30.25 5.82 0.00 3.85
384 418 3.025978 TGAAGGAAATTGCTATGCAGGG 58.974 45.455 0.00 0.00 40.61 4.45
386 420 3.129813 TGCTGAAGGAAATTGCTATGCAG 59.870 43.478 0.00 6.34 40.61 4.41
452 486 6.034898 GGTAAATTATGTTGTCACAAGCATGC 59.965 38.462 10.51 10.51 36.16 4.06
599 656 7.455058 TGGTTACTTAGGAGAGTAATTTGCAA 58.545 34.615 0.00 0.00 42.31 4.08
625 682 3.091545 TCTTTGCCATCAATTGTCTCCC 58.908 45.455 5.13 0.00 31.33 4.30
724 781 1.074926 ACCATGTGCCCCAAAACCA 60.075 52.632 0.00 0.00 0.00 3.67
810 867 2.625314 GACTTGCTCTCCCAAGCTTTTT 59.375 45.455 0.00 0.00 44.66 1.94
1038 1097 2.912542 CTGGAGCCGGGCGATCTA 60.913 66.667 14.39 3.65 0.00 1.98
1290 1349 7.278424 GCAAGCAAATCCATACACACAAAATAT 59.722 33.333 0.00 0.00 0.00 1.28
1476 1535 0.541863 AAAGATGACAGCCTACCCCG 59.458 55.000 0.00 0.00 0.00 5.73
1590 1650 7.275779 TCGCAAAAGATGAAGATCAGTACTTAC 59.724 37.037 0.00 0.00 0.00 2.34
1591 1651 7.320399 TCGCAAAAGATGAAGATCAGTACTTA 58.680 34.615 0.00 0.00 0.00 2.24
1596 1656 4.391216 CACTCGCAAAAGATGAAGATCAGT 59.609 41.667 0.00 0.00 0.00 3.41
1597 1657 4.628766 TCACTCGCAAAAGATGAAGATCAG 59.371 41.667 0.00 0.00 0.00 2.90
1606 1666 5.050091 CAGTACTTGTTCACTCGCAAAAGAT 60.050 40.000 0.00 0.00 0.00 2.40
1608 1668 4.270084 TCAGTACTTGTTCACTCGCAAAAG 59.730 41.667 0.00 0.00 0.00 2.27
1641 1701 7.260603 AGAAAACTCAAAATCTCACTTTGGTG 58.739 34.615 0.00 0.00 44.23 4.17
1642 1702 7.410120 AGAAAACTCAAAATCTCACTTTGGT 57.590 32.000 0.00 0.00 35.03 3.67
1643 1703 7.166473 CGAAGAAAACTCAAAATCTCACTTTGG 59.834 37.037 0.00 0.00 35.03 3.28
1644 1704 7.698130 ACGAAGAAAACTCAAAATCTCACTTTG 59.302 33.333 0.00 0.00 35.51 2.77
1645 1705 7.698130 CACGAAGAAAACTCAAAATCTCACTTT 59.302 33.333 0.00 0.00 0.00 2.66
1661 1721 7.780008 TCTTCACTGTTTATCACGAAGAAAA 57.220 32.000 0.00 0.00 36.95 2.29
1664 1724 6.984474 AGTTTCTTCACTGTTTATCACGAAGA 59.016 34.615 0.00 0.00 37.54 2.87
1665 1725 7.178712 AGTTTCTTCACTGTTTATCACGAAG 57.821 36.000 0.00 0.00 34.43 3.79
1668 1728 7.639162 AGTAGTTTCTTCACTGTTTATCACG 57.361 36.000 0.00 0.00 0.00 4.35
1723 1788 6.588719 TCAAAATCGGGAAAGAATGATTGT 57.411 33.333 0.00 0.00 31.79 2.71
1735 1800 4.327982 TTGCAACATTTCAAAATCGGGA 57.672 36.364 0.00 0.00 0.00 5.14
1736 1801 4.611130 GCTTTGCAACATTTCAAAATCGGG 60.611 41.667 0.00 0.00 32.55 5.14
1737 1802 4.456914 GCTTTGCAACATTTCAAAATCGG 58.543 39.130 0.00 0.00 32.55 4.18
1738 1803 4.211794 AGGCTTTGCAACATTTCAAAATCG 59.788 37.500 0.00 0.00 32.55 3.34
1739 1804 5.445845 CAGGCTTTGCAACATTTCAAAATC 58.554 37.500 0.00 0.00 32.55 2.17
1740 1805 4.276431 CCAGGCTTTGCAACATTTCAAAAT 59.724 37.500 0.00 0.00 32.55 1.82
1741 1806 3.626670 CCAGGCTTTGCAACATTTCAAAA 59.373 39.130 0.00 0.00 32.55 2.44
1742 1807 3.204526 CCAGGCTTTGCAACATTTCAAA 58.795 40.909 0.00 0.00 0.00 2.69
1743 1808 2.485124 CCCAGGCTTTGCAACATTTCAA 60.485 45.455 0.00 0.00 0.00 2.69
1744 1809 1.070445 CCCAGGCTTTGCAACATTTCA 59.930 47.619 0.00 0.00 0.00 2.69
1745 1810 1.608801 CCCCAGGCTTTGCAACATTTC 60.609 52.381 0.00 0.00 0.00 2.17
1746 1811 0.397564 CCCCAGGCTTTGCAACATTT 59.602 50.000 0.00 0.00 0.00 2.32
1747 1812 0.763986 ACCCCAGGCTTTGCAACATT 60.764 50.000 0.00 0.00 0.00 2.71
1748 1813 1.152269 ACCCCAGGCTTTGCAACAT 60.152 52.632 0.00 0.00 0.00 2.71
1749 1814 2.132996 CACCCCAGGCTTTGCAACA 61.133 57.895 0.00 0.00 0.00 3.33
1750 1815 1.398958 TTCACCCCAGGCTTTGCAAC 61.399 55.000 0.00 0.00 0.00 4.17
1751 1816 0.689080 TTTCACCCCAGGCTTTGCAA 60.689 50.000 0.00 0.00 0.00 4.08
1752 1817 0.689080 TTTTCACCCCAGGCTTTGCA 60.689 50.000 0.00 0.00 0.00 4.08
1753 1818 0.467804 TTTTTCACCCCAGGCTTTGC 59.532 50.000 0.00 0.00 0.00 3.68
1769 1834 4.492646 ACCACATCATTTCTCCCCTTTTT 58.507 39.130 0.00 0.00 0.00 1.94
1770 1835 4.132122 ACCACATCATTTCTCCCCTTTT 57.868 40.909 0.00 0.00 0.00 2.27
1771 1836 3.833559 ACCACATCATTTCTCCCCTTT 57.166 42.857 0.00 0.00 0.00 3.11
1772 1837 3.833559 AACCACATCATTTCTCCCCTT 57.166 42.857 0.00 0.00 0.00 3.95
1773 1838 3.591527 TGTAACCACATCATTTCTCCCCT 59.408 43.478 0.00 0.00 0.00 4.79
1774 1839 3.947834 CTGTAACCACATCATTTCTCCCC 59.052 47.826 0.00 0.00 33.14 4.81
1775 1840 3.947834 CCTGTAACCACATCATTTCTCCC 59.052 47.826 0.00 0.00 33.14 4.30
1776 1841 4.843728 TCCTGTAACCACATCATTTCTCC 58.156 43.478 0.00 0.00 33.14 3.71
1777 1842 5.220931 GCATCCTGTAACCACATCATTTCTC 60.221 44.000 0.00 0.00 33.14 2.87
1778 1843 4.641989 GCATCCTGTAACCACATCATTTCT 59.358 41.667 0.00 0.00 33.14 2.52
1779 1844 4.398988 TGCATCCTGTAACCACATCATTTC 59.601 41.667 0.00 0.00 33.14 2.17
1780 1845 4.343231 TGCATCCTGTAACCACATCATTT 58.657 39.130 0.00 0.00 33.14 2.32
1781 1846 3.966979 TGCATCCTGTAACCACATCATT 58.033 40.909 0.00 0.00 33.14 2.57
1782 1847 3.650281 TGCATCCTGTAACCACATCAT 57.350 42.857 0.00 0.00 33.14 2.45
1783 1848 3.431673 TTGCATCCTGTAACCACATCA 57.568 42.857 0.00 0.00 33.14 3.07
1784 1849 4.989279 AATTGCATCCTGTAACCACATC 57.011 40.909 0.00 0.00 33.14 3.06
1785 1850 4.160252 GGAAATTGCATCCTGTAACCACAT 59.840 41.667 0.00 0.00 33.14 3.21
1786 1851 3.509575 GGAAATTGCATCCTGTAACCACA 59.490 43.478 0.00 0.00 33.98 4.17
1787 1852 3.763897 AGGAAATTGCATCCTGTAACCAC 59.236 43.478 6.55 0.00 45.60 4.16
1788 1853 4.046286 AGGAAATTGCATCCTGTAACCA 57.954 40.909 6.55 0.00 45.60 3.67
1796 1861 6.515272 TTAACTGAAGAGGAAATTGCATCC 57.485 37.500 0.00 0.00 37.22 3.51
1797 1862 8.992835 AAATTAACTGAAGAGGAAATTGCATC 57.007 30.769 0.00 0.00 0.00 3.91
1799 1864 9.912634 CTAAAATTAACTGAAGAGGAAATTGCA 57.087 29.630 0.00 0.00 0.00 4.08
1823 1888 5.472137 GCACACCTAACTGGAAACAAATCTA 59.528 40.000 0.00 0.00 42.06 1.98
1851 1916 4.696479 AGAAGAAAGAGAACAGGCAGAA 57.304 40.909 0.00 0.00 0.00 3.02
1855 1920 4.384940 AGTGAAGAAGAAAGAGAACAGGC 58.615 43.478 0.00 0.00 0.00 4.85
1858 1923 5.263968 ACGAGTGAAGAAGAAAGAGAACA 57.736 39.130 0.00 0.00 0.00 3.18
1867 1932 8.975439 GTACAAATTAAGAACGAGTGAAGAAGA 58.025 33.333 0.00 0.00 0.00 2.87
1930 1995 4.923871 ACTGCTTAGATAACGCGATAATGG 59.076 41.667 15.93 0.00 0.00 3.16
1957 2022 0.101399 CGGACGAGATCCTTGTCAGG 59.899 60.000 14.29 4.24 46.69 3.86
2009 2074 7.962964 AATGACGTGATCAGAGAAAGTTTAA 57.037 32.000 0.00 0.00 41.91 1.52
2010 2075 7.441157 ACAAATGACGTGATCAGAGAAAGTTTA 59.559 33.333 0.00 0.00 41.91 2.01
2024 2091 9.986833 CTGATGATAATTAAACAAATGACGTGA 57.013 29.630 0.00 0.00 0.00 4.35
2025 2092 8.736742 GCTGATGATAATTAAACAAATGACGTG 58.263 33.333 0.00 0.00 0.00 4.49
2026 2093 8.677300 AGCTGATGATAATTAAACAAATGACGT 58.323 29.630 0.00 0.00 0.00 4.34
2033 2100 7.484641 GCACGAAAGCTGATGATAATTAAACAA 59.515 33.333 0.00 0.00 0.00 2.83
2034 2101 6.966632 GCACGAAAGCTGATGATAATTAAACA 59.033 34.615 0.00 0.00 0.00 2.83
2035 2102 7.189512 AGCACGAAAGCTGATGATAATTAAAC 58.810 34.615 0.00 0.00 44.66 2.01
2036 2103 7.320443 AGCACGAAAGCTGATGATAATTAAA 57.680 32.000 0.00 0.00 44.66 1.52
2037 2104 6.925610 AGCACGAAAGCTGATGATAATTAA 57.074 33.333 0.00 0.00 44.66 1.40
2090 2157 4.804108 AGATCTTGATATGTAGCTCACGC 58.196 43.478 0.00 0.00 0.00 5.34
2120 2187 3.881089 TGTGCATGATAAAGCCAGAGATG 59.119 43.478 0.00 0.00 0.00 2.90
2126 2193 3.378112 GCTAACTGTGCATGATAAAGCCA 59.622 43.478 0.00 0.00 0.00 4.75
2139 2206 3.055591 CTCTCCGCATATGCTAACTGTG 58.944 50.000 24.56 7.74 39.32 3.66
2144 2211 2.822561 CTCCTCTCTCCGCATATGCTAA 59.177 50.000 24.56 11.77 39.32 3.09
2146 2213 1.202989 TCTCCTCTCTCCGCATATGCT 60.203 52.381 24.56 0.00 39.32 3.79
2154 2221 4.244802 GCGCGTCTCCTCTCTCCG 62.245 72.222 8.43 0.00 0.00 4.63
2170 2237 1.859080 GTCTGGAATTCACCGTATCGC 59.141 52.381 7.93 0.00 0.00 4.58
2176 2243 0.613260 TGGGAGTCTGGAATTCACCG 59.387 55.000 7.93 0.00 0.00 4.94
2200 2267 2.545526 CTGAAGTTGTGTGCAGTACCTG 59.454 50.000 0.00 0.00 34.12 4.00
2218 2326 4.081309 CCGGGTAAATTCAAGGACTACTGA 60.081 45.833 0.00 0.00 0.00 3.41
2221 2329 4.476628 TCCGGGTAAATTCAAGGACTAC 57.523 45.455 0.00 0.00 0.00 2.73
2224 2332 5.648960 TGTTATTCCGGGTAAATTCAAGGAC 59.351 40.000 0.00 0.00 0.00 3.85
2254 2362 2.221169 TGCAGTTGTTAGTTGGAGCTG 58.779 47.619 0.00 0.00 0.00 4.24
2303 2411 3.676049 CGTAGATAGTGTTGCTGCTTGGA 60.676 47.826 0.00 0.00 0.00 3.53
2314 2422 0.324923 TGGTGGCCCGTAGATAGTGT 60.325 55.000 0.00 0.00 0.00 3.55
2392 2500 3.747854 TCTGTCTCCATGATCTGCATC 57.252 47.619 0.00 0.00 34.15 3.91
2438 2548 4.864916 AACTTCGCAGTGTATAATGCTG 57.135 40.909 10.18 4.23 45.17 4.41
2514 2624 1.222936 CATGGTGCCCTCTCAGACC 59.777 63.158 0.00 0.00 0.00 3.85
2567 2677 0.028242 CGTCTTCTGGATCGTCGGAG 59.972 60.000 0.00 0.00 0.00 4.63
2613 2723 6.289064 ACGTAAGAAGGAGAAGAACATTTGT 58.711 36.000 0.00 0.00 43.62 2.83
2627 2740 4.642885 AGAGGAGAGATGAACGTAAGAAGG 59.357 45.833 0.00 0.00 43.62 3.46
2628 2741 5.355630 TCAGAGGAGAGATGAACGTAAGAAG 59.644 44.000 0.00 0.00 43.62 2.85
2629 2742 5.254115 TCAGAGGAGAGATGAACGTAAGAA 58.746 41.667 0.00 0.00 43.62 2.52
2682 2795 2.178984 ACAAGGAAGGAAAACCCCATGA 59.821 45.455 0.00 0.00 34.66 3.07
3039 3153 5.415701 TCCATCTTGTGCTTCTGGATAAAAC 59.584 40.000 0.00 0.00 31.19 2.43
3127 3243 3.242870 GCTTACACAGGCTGCATTACATC 60.243 47.826 15.89 0.00 0.00 3.06
3212 3328 3.578282 TCACCAGACACTGACATACACAT 59.422 43.478 0.00 0.00 32.44 3.21
3328 3444 4.581824 CCTGGTATAACTGAAAGCATGCAT 59.418 41.667 21.98 4.57 37.60 3.96
3332 3448 4.227300 TCCACCTGGTATAACTGAAAGCAT 59.773 41.667 0.00 0.00 34.75 3.79
3380 6419 6.507023 TGTACATACTATACAGAGACGTCGA 58.493 40.000 10.46 0.00 0.00 4.20
3452 6493 8.238631 GGCCTACAAAAACGTCTTATATTTTGA 58.761 33.333 21.46 9.08 42.48 2.69
3512 6554 6.795144 TCCAAAGTATTACCTCCGTATCAA 57.205 37.500 0.00 0.00 0.00 2.57
3513 6555 6.795144 TTCCAAAGTATTACCTCCGTATCA 57.205 37.500 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.