Multiple sequence alignment - TraesCS7D01G273300

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 TraesCS7D01G273300 chr7D 100.000 2219 0 0 1 2219 263953397 263951179 0.000000e+00 4098.0
1 TraesCS7D01G273300 chr7D 80.334 778 130 14 561 1326 263958966 263958200 3.200000e-158 568.0
2 TraesCS7D01G273300 chr7D 97.015 134 4 0 1609 1742 263951723 263951590 2.220000e-55 226.0
3 TraesCS7D01G273300 chr7D 97.015 134 4 0 1675 1808 263951789 263951656 2.220000e-55 226.0
4 TraesCS7D01G273300 chr7D 100.000 68 0 0 1609 1676 263951657 263951590 2.310000e-25 126.0
5 TraesCS7D01G273300 chr7D 100.000 68 0 0 1741 1808 263951789 263951722 2.310000e-25 126.0
6 TraesCS7D01G273300 chr7A 91.382 1346 78 20 184 1513 287208306 287206983 0.000000e+00 1808.0
7 TraesCS7D01G273300 chr7A 90.239 461 35 3 1741 2200 287193350 287192899 5.280000e-166 593.0
8 TraesCS7D01G273300 chr7A 80.359 779 129 17 561 1326 287215491 287214724 8.890000e-159 569.0
9 TraesCS7D01G273300 chr7A 94.400 125 3 3 1531 1655 287193424 287193304 2.910000e-44 189.0
10 TraesCS7D01G273300 chr7B 79.719 784 130 17 561 1326 244270102 244269330 6.970000e-150 540.0
11 TraesCS7D01G273300 chr7B 92.192 333 15 4 1010 1342 244218841 244218520 5.580000e-126 460.0
12 TraesCS7D01G273300 chr7B 91.830 306 21 3 716 1018 244219172 244218868 7.320000e-115 424.0
13 TraesCS7D01G273300 chr7B 87.283 346 23 8 1882 2219 244211078 244210746 2.080000e-100 375.0
14 TraesCS7D01G273300 chr7B 85.650 223 20 5 1 211 244219627 244219405 7.970000e-55 224.0
15 TraesCS7D01G273300 chr7B 93.478 138 5 1 235 372 244219305 244219172 3.740000e-48 202.0
16 TraesCS7D01G273300 chr5A 84.821 112 17 0 2076 2187 590458159 590458270 1.800000e-21 113.0
17 TraesCS7D01G273300 chr1D 83.740 123 12 5 2076 2196 76796757 76796641 2.330000e-20 110.0
18 TraesCS7D01G273300 chr1B 95.122 41 2 0 1544 1584 250420950 250420910 5.110000e-07 65.8
19 TraesCS7D01G273300 chr1A 95.122 41 2 0 1544 1584 171459215 171459255 5.110000e-07 65.8
20 TraesCS7D01G273300 chr5D 77.165 127 18 6 938 1056 434679116 434678993 1.840000e-06 63.9
21 TraesCS7D01G273300 chr5B 88.636 44 5 0 980 1023 527606446 527606489 1.000000e-03 54.7


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 TraesCS7D01G273300 chr7D 263951179 263953397 2218 True 960.4 4098 98.8060 1 2219 5 chr7D.!!$R2 2218
1 TraesCS7D01G273300 chr7D 263958200 263958966 766 True 568.0 568 80.3340 561 1326 1 chr7D.!!$R1 765
2 TraesCS7D01G273300 chr7A 287206983 287208306 1323 True 1808.0 1808 91.3820 184 1513 1 chr7A.!!$R1 1329
3 TraesCS7D01G273300 chr7A 287214724 287215491 767 True 569.0 569 80.3590 561 1326 1 chr7A.!!$R2 765
4 TraesCS7D01G273300 chr7A 287192899 287193424 525 True 391.0 593 92.3195 1531 2200 2 chr7A.!!$R3 669
5 TraesCS7D01G273300 chr7B 244269330 244270102 772 True 540.0 540 79.7190 561 1326 1 chr7B.!!$R2 765
6 TraesCS7D01G273300 chr7B 244218520 244219627 1107 True 327.5 460 90.7875 1 1342 4 chr7B.!!$R3 1341

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
142 155 0.453793 CACTCTCTCGCGGTGATTCT 59.546 55.0 6.13 0.0 33.32 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2154 0.249155 GTTCGACGGTGAACCAGTCA 60.249 55.0 18.11 8.01 41.88 3.41 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
73 74 4.431524 CTGGGGTGGCCCTCCCTA 62.432 72.222 25.86 21.16 44.66 3.53
79 80 4.172232 TGGCCCTCCCTATCGCCT 62.172 66.667 0.00 0.00 42.15 5.52
87 88 3.996124 CCTATCGCCTGCGGGAGG 61.996 72.222 18.31 11.72 46.13 4.30
99 111 4.845307 GGGAGGGGAAGGGGGAGG 62.845 77.778 0.00 0.00 0.00 4.30
142 155 0.453793 CACTCTCTCGCGGTGATTCT 59.546 55.000 6.13 0.00 33.32 2.40
164 177 7.385778 TCTTCAAAAGAAAAAGAACTTCGGA 57.614 32.000 0.00 0.00 33.83 4.55
196 209 1.687297 GACCCCCTAAAGAGGCCTCG 61.687 65.000 26.95 12.63 42.21 4.63
219 232 9.140286 CTCGAGTAATGTTCTAATTTGTCTTGA 57.860 33.333 3.62 0.00 0.00 3.02
229 242 7.750229 TCTAATTTGTCTTGACAGCTCAAAT 57.250 32.000 3.61 2.40 35.92 2.32
230 243 7.587629 TCTAATTTGTCTTGACAGCTCAAATG 58.412 34.615 7.75 0.00 35.92 2.32
293 382 0.965363 GAATTGGTGGCCGTGATGGT 60.965 55.000 0.00 0.00 41.21 3.55
294 383 0.965363 AATTGGTGGCCGTGATGGTC 60.965 55.000 0.00 0.00 45.24 4.02
311 400 2.184322 CCGTCCATCCACACCTCG 59.816 66.667 0.00 0.00 0.00 4.63
422 511 9.678260 AGCTTGTTATGTCAGATCTAGAAAATT 57.322 29.630 0.00 0.00 0.00 1.82
436 525 3.356290 AGAAAATTCTACAATGGCGCCT 58.644 40.909 29.70 9.99 35.34 5.52
438 527 1.392589 AATTCTACAATGGCGCCTGG 58.607 50.000 29.70 18.89 0.00 4.45
439 528 0.546122 ATTCTACAATGGCGCCTGGA 59.454 50.000 29.70 14.80 0.00 3.86
472 563 8.818141 TTACTTCTGTGTCAAAATACTCTCAG 57.182 34.615 0.00 0.00 0.00 3.35
498 589 3.261897 ACAGATATGGCCAGCTACATACC 59.738 47.826 13.05 0.00 32.87 2.73
527 618 5.354234 CAGTAAAGATGTCCCACCATGTAAC 59.646 44.000 0.00 0.00 0.00 2.50
558 649 2.076100 CAGTGCACTAAATCTTGCGGA 58.924 47.619 21.20 0.00 41.96 5.54
559 650 2.483877 CAGTGCACTAAATCTTGCGGAA 59.516 45.455 21.20 0.00 41.96 4.30
605 696 2.229784 GAGTTCAAATGCCTTGTCCCTG 59.770 50.000 0.00 0.00 36.34 4.45
649 740 4.485163 GTTGTGGAACCAAAGATGCATAC 58.515 43.478 0.00 0.00 34.36 2.39
664 755 0.474184 CATACCCTCCCATCACACCC 59.526 60.000 0.00 0.00 0.00 4.61
666 757 3.797353 CCCTCCCATCACACCCGG 61.797 72.222 0.00 0.00 0.00 5.73
672 763 1.377202 CCATCACACCCGGTTCCTG 60.377 63.158 0.00 0.00 0.00 3.86
751 852 5.163311 TGACCATTTCTTCTCAGAGTCACAA 60.163 40.000 0.00 0.00 29.72 3.33
861 962 2.034221 GGGCGAAGAAGGGCAACT 59.966 61.111 0.00 0.00 0.00 3.16
932 1035 3.467803 GCCACTGTGTTGTCTACTCTTT 58.532 45.455 7.08 0.00 0.00 2.52
973 1076 2.125673 CCTTGGTGTACCTCCGCG 60.126 66.667 0.00 0.00 36.82 6.46
1087 1225 4.943093 TGATGGAGTATGTGATGTGTTTGG 59.057 41.667 0.00 0.00 0.00 3.28
1144 1282 5.508825 GCACTCCTCAGTTCCATAGTGATAG 60.509 48.000 0.00 0.00 37.18 2.08
1161 1299 1.715019 TAGCTTGCCACCACCCAAGT 61.715 55.000 0.00 0.00 40.34 3.16
1170 1308 2.618045 CCACCACCCAAGTAGAATGGTC 60.618 54.545 0.00 0.00 41.79 4.02
1229 1367 2.674747 GCAGCTCCTGAAGAGTGAAGAG 60.675 54.545 0.00 0.00 45.21 2.85
1230 1368 2.562298 CAGCTCCTGAAGAGTGAAGAGT 59.438 50.000 0.00 0.00 45.21 3.24
1242 1380 4.282195 AGAGTGAAGAGTTTAGACCCACAG 59.718 45.833 0.00 0.00 0.00 3.66
1287 1428 0.670546 CCAACTGTACACCTGGAGCG 60.671 60.000 11.58 0.00 0.00 5.03
1361 1502 9.918630 AAATCACATCTTGAATAGAAACAAAGG 57.081 29.630 0.00 0.00 37.92 3.11
1364 1505 8.567948 TCACATCTTGAATAGAAACAAAGGAAC 58.432 33.333 0.00 0.00 36.22 3.62
1389 1530 6.093495 CCGAGCTTTCCATCAAAATAGTAACA 59.907 38.462 0.00 0.00 0.00 2.41
1393 1534 9.515226 AGCTTTCCATCAAAATAGTAACAACTA 57.485 29.630 0.00 0.00 0.00 2.24
1407 1548 4.772886 AACAACTACTCAACCACTTCCT 57.227 40.909 0.00 0.00 0.00 3.36
1421 1562 4.105697 ACCACTTCCTTAGATTCCACCAAA 59.894 41.667 0.00 0.00 0.00 3.28
1422 1563 4.702131 CCACTTCCTTAGATTCCACCAAAG 59.298 45.833 0.00 0.00 0.00 2.77
1430 1571 8.531982 TCCTTAGATTCCACCAAAGATATATCG 58.468 37.037 7.08 0.00 0.00 2.92
1454 1607 6.253727 CGTGTATGCACCAAACAAAAGTAAAA 59.746 34.615 8.45 0.00 42.39 1.52
1458 1611 6.900568 TGCACCAAACAAAAGTAAAATCAG 57.099 33.333 0.00 0.00 0.00 2.90
1496 1649 1.478105 GCCTCTTAACCATTTGCAGGG 59.522 52.381 0.00 0.00 0.00 4.45
1498 1651 1.478105 CTCTTAACCATTTGCAGGGGC 59.522 52.381 6.16 0.00 41.68 5.80
1517 1670 1.328986 GCAGTTGCCTCTTAATCGAGC 59.671 52.381 0.00 0.00 34.31 5.03
1518 1671 2.898705 CAGTTGCCTCTTAATCGAGCT 58.101 47.619 0.00 0.00 0.00 4.09
1519 1672 3.265791 CAGTTGCCTCTTAATCGAGCTT 58.734 45.455 0.00 0.00 0.00 3.74
1520 1673 3.686726 CAGTTGCCTCTTAATCGAGCTTT 59.313 43.478 0.00 0.00 0.00 3.51
1521 1674 4.154918 CAGTTGCCTCTTAATCGAGCTTTT 59.845 41.667 0.00 0.00 0.00 2.27
1522 1675 4.154918 AGTTGCCTCTTAATCGAGCTTTTG 59.845 41.667 0.00 0.00 0.00 2.44
1523 1676 3.674997 TGCCTCTTAATCGAGCTTTTGT 58.325 40.909 0.00 0.00 0.00 2.83
1524 1677 4.072131 TGCCTCTTAATCGAGCTTTTGTT 58.928 39.130 0.00 0.00 0.00 2.83
1525 1678 4.083324 TGCCTCTTAATCGAGCTTTTGTTG 60.083 41.667 0.00 0.00 0.00 3.33
1526 1679 4.154195 GCCTCTTAATCGAGCTTTTGTTGA 59.846 41.667 0.00 0.00 0.00 3.18
1527 1680 5.163713 GCCTCTTAATCGAGCTTTTGTTGAT 60.164 40.000 0.00 0.00 0.00 2.57
1528 1681 6.037172 GCCTCTTAATCGAGCTTTTGTTGATA 59.963 38.462 0.00 0.00 0.00 2.15
1529 1682 7.414098 GCCTCTTAATCGAGCTTTTGTTGATAA 60.414 37.037 0.00 0.00 0.00 1.75
1530 1683 8.450964 CCTCTTAATCGAGCTTTTGTTGATAAA 58.549 33.333 0.00 0.00 0.00 1.40
1531 1684 9.267096 CTCTTAATCGAGCTTTTGTTGATAAAC 57.733 33.333 0.00 0.00 0.00 2.01
1532 1685 8.234546 TCTTAATCGAGCTTTTGTTGATAAACC 58.765 33.333 0.00 0.00 0.00 3.27
1533 1686 6.575162 AATCGAGCTTTTGTTGATAAACCT 57.425 33.333 0.00 0.00 0.00 3.50
1534 1687 7.681939 AATCGAGCTTTTGTTGATAAACCTA 57.318 32.000 0.00 0.00 0.00 3.08
1535 1688 6.476243 TCGAGCTTTTGTTGATAAACCTAC 57.524 37.500 0.00 0.00 0.00 3.18
1536 1689 5.992829 TCGAGCTTTTGTTGATAAACCTACA 59.007 36.000 0.00 0.00 0.00 2.74
1537 1690 6.483974 TCGAGCTTTTGTTGATAAACCTACAA 59.516 34.615 0.00 0.00 0.00 2.41
1538 1691 7.012515 TCGAGCTTTTGTTGATAAACCTACAAA 59.987 33.333 0.00 0.00 38.35 2.83
1539 1692 7.323656 CGAGCTTTTGTTGATAAACCTACAAAG 59.676 37.037 0.00 0.00 40.38 2.77
1568 1721 4.911390 ACTCCCTCCAGTTCACAAATAAG 58.089 43.478 0.00 0.00 0.00 1.73
1581 1734 8.352942 AGTTCACAAATAAGTGATCTTTTGGAC 58.647 33.333 0.00 0.00 46.90 4.02
1657 1810 8.653036 ACCTAAGAAGATTATAGTATTCGGCT 57.347 34.615 0.00 0.00 0.00 5.52
1658 1811 9.750783 ACCTAAGAAGATTATAGTATTCGGCTA 57.249 33.333 0.00 0.00 0.00 3.93
1662 1815 9.790389 AAGAAGATTATAGTATTCGGCTATTCG 57.210 33.333 0.00 0.00 32.15 3.34
1663 1816 7.916450 AGAAGATTATAGTATTCGGCTATTCGC 59.084 37.037 0.00 0.00 38.13 4.70
1674 1827 1.927895 GCTATTCGCCCATCCTATCG 58.072 55.000 0.00 0.00 0.00 2.92
1675 1828 1.476891 GCTATTCGCCCATCCTATCGA 59.523 52.381 0.00 0.00 0.00 3.59
1676 1829 2.735762 GCTATTCGCCCATCCTATCGAC 60.736 54.545 0.00 0.00 0.00 4.20
1677 1830 0.608640 ATTCGCCCATCCTATCGACC 59.391 55.000 0.00 0.00 0.00 4.79
1678 1831 0.757561 TTCGCCCATCCTATCGACCA 60.758 55.000 0.00 0.00 0.00 4.02
1679 1832 0.541998 TCGCCCATCCTATCGACCAT 60.542 55.000 0.00 0.00 0.00 3.55
1680 1833 0.321671 CGCCCATCCTATCGACCATT 59.678 55.000 0.00 0.00 0.00 3.16
1681 1834 1.548719 CGCCCATCCTATCGACCATTA 59.451 52.381 0.00 0.00 0.00 1.90
1682 1835 2.417379 CGCCCATCCTATCGACCATTAG 60.417 54.545 0.00 0.00 0.00 1.73
1683 1836 2.567615 GCCCATCCTATCGACCATTAGT 59.432 50.000 0.00 0.00 0.00 2.24
1684 1837 3.008049 GCCCATCCTATCGACCATTAGTT 59.992 47.826 0.00 0.00 0.00 2.24
1685 1838 4.505039 GCCCATCCTATCGACCATTAGTTT 60.505 45.833 0.00 0.00 0.00 2.66
1686 1839 4.997395 CCCATCCTATCGACCATTAGTTTG 59.003 45.833 0.00 0.00 0.00 2.93
1687 1840 5.454755 CCCATCCTATCGACCATTAGTTTGT 60.455 44.000 0.00 0.00 0.00 2.83
1688 1841 6.239487 CCCATCCTATCGACCATTAGTTTGTA 60.239 42.308 0.00 0.00 0.00 2.41
1689 1842 7.386851 CCATCCTATCGACCATTAGTTTGTAT 58.613 38.462 0.00 0.00 0.00 2.29
1690 1843 8.528643 CCATCCTATCGACCATTAGTTTGTATA 58.471 37.037 0.00 0.00 0.00 1.47
1723 1876 8.734593 ACCTAAGAAGATTATAGGATTCAGCT 57.265 34.615 5.14 0.00 38.81 4.24
1724 1877 9.830186 ACCTAAGAAGATTATAGGATTCAGCTA 57.170 33.333 5.14 0.00 38.81 3.32
1728 1881 9.868277 AAGAAGATTATAGGATTCAGCTATTCG 57.132 33.333 0.00 0.00 0.00 3.34
1729 1882 7.978975 AGAAGATTATAGGATTCAGCTATTCGC 59.021 37.037 0.00 0.00 39.57 4.70
1730 1883 6.578023 AGATTATAGGATTCAGCTATTCGCC 58.422 40.000 0.00 0.00 40.39 5.54
1731 1884 3.618690 ATAGGATTCAGCTATTCGCCC 57.381 47.619 0.00 0.00 40.39 6.13
1732 1885 1.131638 AGGATTCAGCTATTCGCCCA 58.868 50.000 0.00 0.00 40.39 5.36
1733 1886 1.701847 AGGATTCAGCTATTCGCCCAT 59.298 47.619 0.00 0.00 40.39 4.00
1734 1887 2.079925 GGATTCAGCTATTCGCCCATC 58.920 52.381 0.00 0.00 40.39 3.51
1735 1888 2.079925 GATTCAGCTATTCGCCCATCC 58.920 52.381 0.00 0.00 40.39 3.51
1736 1889 1.131638 TTCAGCTATTCGCCCATCCT 58.868 50.000 0.00 0.00 40.39 3.24
1737 1890 2.009681 TCAGCTATTCGCCCATCCTA 57.990 50.000 0.00 0.00 40.39 2.94
1738 1891 2.540383 TCAGCTATTCGCCCATCCTAT 58.460 47.619 0.00 0.00 40.39 2.57
1739 1892 2.497675 TCAGCTATTCGCCCATCCTATC 59.502 50.000 0.00 0.00 40.39 2.08
1740 1893 1.478510 AGCTATTCGCCCATCCTATCG 59.521 52.381 0.00 0.00 40.39 2.92
1741 1894 1.476891 GCTATTCGCCCATCCTATCGA 59.523 52.381 0.00 0.00 0.00 3.59
1742 1895 2.735762 GCTATTCGCCCATCCTATCGAC 60.736 54.545 0.00 0.00 0.00 4.20
1743 1896 0.608640 ATTCGCCCATCCTATCGACC 59.391 55.000 0.00 0.00 0.00 4.79
1744 1897 0.757561 TTCGCCCATCCTATCGACCA 60.758 55.000 0.00 0.00 0.00 4.02
1745 1898 0.541998 TCGCCCATCCTATCGACCAT 60.542 55.000 0.00 0.00 0.00 3.55
1746 1899 0.321671 CGCCCATCCTATCGACCATT 59.678 55.000 0.00 0.00 0.00 3.16
1747 1900 1.548719 CGCCCATCCTATCGACCATTA 59.451 52.381 0.00 0.00 0.00 1.90
1748 1901 2.417379 CGCCCATCCTATCGACCATTAG 60.417 54.545 0.00 0.00 0.00 1.73
1749 1902 2.567615 GCCCATCCTATCGACCATTAGT 59.432 50.000 0.00 0.00 0.00 2.24
1750 1903 3.008049 GCCCATCCTATCGACCATTAGTT 59.992 47.826 0.00 0.00 0.00 2.24
1751 1904 4.505039 GCCCATCCTATCGACCATTAGTTT 60.505 45.833 0.00 0.00 0.00 2.66
1752 1905 4.997395 CCCATCCTATCGACCATTAGTTTG 59.003 45.833 0.00 0.00 0.00 2.93
1753 1906 5.454755 CCCATCCTATCGACCATTAGTTTGT 60.455 44.000 0.00 0.00 0.00 2.83
1754 1907 6.239487 CCCATCCTATCGACCATTAGTTTGTA 60.239 42.308 0.00 0.00 0.00 2.41
1755 1908 7.386851 CCATCCTATCGACCATTAGTTTGTAT 58.613 38.462 0.00 0.00 0.00 2.29
1756 1909 8.528643 CCATCCTATCGACCATTAGTTTGTATA 58.471 37.037 0.00 0.00 0.00 1.47
1789 1942 8.653036 ACCTAAGAAGATTATAGTATTCGGCT 57.347 34.615 0.00 0.00 0.00 5.52
1790 1943 9.750783 ACCTAAGAAGATTATAGTATTCGGCTA 57.249 33.333 0.00 0.00 0.00 3.93
1794 1947 9.790389 AAGAAGATTATAGTATTCGGCTATTCG 57.210 33.333 0.00 0.00 32.15 3.34
1876 2029 5.458015 CAATATCATGCAGTTGTATGCCAG 58.542 41.667 5.46 0.00 45.91 4.85
1890 2043 5.419542 TGTATGCCAGACTGAAACAGATAC 58.580 41.667 3.32 1.47 35.18 2.24
1894 2047 3.428999 GCCAGACTGAAACAGATACGCTA 60.429 47.826 3.32 0.00 35.18 4.26
1900 2053 9.119329 CAGACTGAAACAGATACGCTATAATAC 57.881 37.037 0.00 0.00 35.18 1.89
1908 2061 7.076362 ACAGATACGCTATAATACTGTTCACG 58.924 38.462 0.00 0.00 34.21 4.35
1921 2074 2.288666 TGTTCACGCTTTTCAGCTTCT 58.711 42.857 0.00 0.00 44.85 2.85
1922 2075 2.032054 TGTTCACGCTTTTCAGCTTCTG 59.968 45.455 0.00 0.00 44.85 3.02
1924 2077 0.386478 CACGCTTTTCAGCTTCTGCC 60.386 55.000 0.00 0.00 44.85 4.85
1944 2097 2.290260 CCAAGAGGTGGTACATGAGCAA 60.290 50.000 0.00 0.00 44.52 3.91
1951 2104 5.043189 GGTGGTACATGAGCAACTAAAAC 57.957 43.478 0.00 0.00 44.52 2.43
1960 2113 6.490040 ACATGAGCAACTAAAACATTGTAGGT 59.510 34.615 0.00 0.00 0.00 3.08
2000 2154 2.834549 ACTCCTGAGTGATCGGTTGATT 59.165 45.455 0.00 0.00 40.75 2.57
2006 2160 2.932614 GAGTGATCGGTTGATTGACTGG 59.067 50.000 0.00 0.00 34.09 4.00
2015 2169 2.163818 TGATTGACTGGTTCACCGTC 57.836 50.000 11.68 11.68 39.43 4.79
2016 2170 1.068474 GATTGACTGGTTCACCGTCG 58.932 55.000 12.98 0.00 40.15 5.12
2024 2178 3.914117 TTCACCGTCGAACCGCCA 61.914 61.111 0.00 0.00 0.00 5.69
2033 2187 3.195698 GAACCGCCAGCTAAGCCG 61.196 66.667 2.51 0.00 0.00 5.52
2039 2193 1.452108 GCCAGCTAAGCCGGTTCAT 60.452 57.895 1.90 0.00 0.00 2.57
2046 2200 2.643551 CTAAGCCGGTTCATTGTGGAT 58.356 47.619 1.90 0.00 0.00 3.41
2062 2216 8.423349 TCATTGTGGATGAAGAAAAGTCAAATT 58.577 29.630 0.00 0.00 41.73 1.82
2079 2233 7.405769 AGTCAAATTTAAATTTTGTTGGTGCG 58.594 30.769 20.92 8.85 36.52 5.34
2104 2258 3.938334 GCCACGGCCATTTGAAATATTTT 59.062 39.130 2.24 0.00 34.56 1.82
2200 2354 8.429641 GGGTAATAATTGAGATCCACTTCACTA 58.570 37.037 0.00 0.00 0.00 2.74
2201 2355 9.482627 GGTAATAATTGAGATCCACTTCACTAG 57.517 37.037 0.00 0.00 0.00 2.57
2202 2356 8.983724 GTAATAATTGAGATCCACTTCACTAGC 58.016 37.037 0.00 0.00 0.00 3.42
2203 2357 5.426689 AATTGAGATCCACTTCACTAGCA 57.573 39.130 0.00 0.00 0.00 3.49
2204 2358 4.890158 TTGAGATCCACTTCACTAGCAA 57.110 40.909 0.00 0.00 0.00 3.91
2205 2359 5.426689 TTGAGATCCACTTCACTAGCAAT 57.573 39.130 0.00 0.00 0.00 3.56
2206 2360 4.763073 TGAGATCCACTTCACTAGCAATG 58.237 43.478 0.00 0.00 0.00 2.82
2207 2361 4.223700 TGAGATCCACTTCACTAGCAATGT 59.776 41.667 0.00 0.00 0.00 2.71
2208 2362 5.422012 TGAGATCCACTTCACTAGCAATGTA 59.578 40.000 0.00 0.00 0.00 2.29
2209 2363 6.070824 TGAGATCCACTTCACTAGCAATGTAA 60.071 38.462 0.00 0.00 0.00 2.41
2210 2364 6.344500 AGATCCACTTCACTAGCAATGTAAG 58.656 40.000 0.00 0.00 0.00 2.34
2211 2365 5.483685 TCCACTTCACTAGCAATGTAAGT 57.516 39.130 0.00 0.00 0.00 2.24
2212 2366 5.865085 TCCACTTCACTAGCAATGTAAGTT 58.135 37.500 0.00 0.00 0.00 2.66
2213 2367 5.700832 TCCACTTCACTAGCAATGTAAGTTG 59.299 40.000 0.00 0.00 0.00 3.16
2214 2368 5.700832 CCACTTCACTAGCAATGTAAGTTGA 59.299 40.000 0.00 0.00 0.00 3.18
2215 2369 6.372659 CCACTTCACTAGCAATGTAAGTTGAT 59.627 38.462 0.00 0.00 0.00 2.57
2216 2370 7.549134 CCACTTCACTAGCAATGTAAGTTGATA 59.451 37.037 0.00 0.00 0.00 2.15
2217 2371 8.935844 CACTTCACTAGCAATGTAAGTTGATAA 58.064 33.333 0.00 0.00 30.50 1.75
2218 2372 9.502091 ACTTCACTAGCAATGTAAGTTGATAAA 57.498 29.630 0.00 0.00 30.50 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.012721 ACCTCCTCCCCTCGCCTT 62.013 66.667 0.00 0.00 0.00 4.35
13 14 4.787280 CACCTCCTCCCCTCGCCT 62.787 72.222 0.00 0.00 0.00 5.52
33 34 2.188161 GCCGGTCTCTACCTCTCCG 61.188 68.421 1.90 0.00 44.35 4.63
61 62 3.942439 GGCGATAGGGAGGGCCAC 61.942 72.222 6.18 0.00 44.91 5.01
122 134 0.526524 GAATCACCGCGAGAGAGTGG 60.527 60.000 8.23 0.00 46.65 4.00
124 136 1.133407 GAAGAATCACCGCGAGAGAGT 59.867 52.381 8.23 0.46 0.00 3.24
142 155 6.152154 ACCTCCGAAGTTCTTTTTCTTTTGAA 59.848 34.615 0.56 0.00 36.52 2.69
154 167 0.832135 TGGCTGACCTCCGAAGTTCT 60.832 55.000 0.56 0.00 36.63 3.01
219 232 4.763793 AGATGCTTTACACATTTGAGCTGT 59.236 37.500 0.00 0.00 34.56 4.40
229 242 3.138884 TGGCTTCAGATGCTTTACACA 57.861 42.857 8.14 0.00 0.00 3.72
230 243 3.441572 ACATGGCTTCAGATGCTTTACAC 59.558 43.478 8.14 0.00 0.00 2.90
293 382 2.348104 CGAGGTGTGGATGGACGGA 61.348 63.158 0.00 0.00 0.00 4.69
294 383 2.184322 CGAGGTGTGGATGGACGG 59.816 66.667 0.00 0.00 0.00 4.79
311 400 0.329596 AGGGTGGGAAAGAGATGTGC 59.670 55.000 0.00 0.00 0.00 4.57
422 511 0.546122 ATTCCAGGCGCCATTGTAGA 59.454 50.000 31.54 12.49 0.00 2.59
498 589 2.749621 GTGGGACATCTTTACTGGCTTG 59.250 50.000 0.00 0.00 44.52 4.01
527 618 2.315925 AGTGCACTGGACCATTATCG 57.684 50.000 20.97 0.00 0.00 2.92
558 649 7.148018 CCCTTGTTGAGATGTTGCTATATGTTT 60.148 37.037 0.00 0.00 0.00 2.83
559 650 6.319658 CCCTTGTTGAGATGTTGCTATATGTT 59.680 38.462 0.00 0.00 0.00 2.71
605 696 4.702131 ACCATCAAAGATAGCAAGTTGTCC 59.298 41.667 4.48 0.00 0.00 4.02
649 740 3.797353 CCGGGTGTGATGGGAGGG 61.797 72.222 0.00 0.00 0.00 4.30
664 755 4.188462 TGAGCATGTATTTACAGGAACCG 58.812 43.478 6.57 0.00 40.13 4.44
666 757 5.506317 GCCATGAGCATGTATTTACAGGAAC 60.506 44.000 6.57 0.81 40.13 3.62
861 962 3.901844 GGTGTATCTCCTTGCCCACTATA 59.098 47.826 0.00 0.00 0.00 1.31
949 1052 2.197465 GAGGTACACCAAGGGGATCTT 58.803 52.381 0.00 0.00 38.89 2.40
973 1076 2.301583 AGAGTTCCTGGAAGACTCTTGC 59.698 50.000 20.42 3.40 45.77 4.01
1087 1225 5.153950 TCCTTTGAAGCTTCTCTCCTAAC 57.846 43.478 26.09 0.00 0.00 2.34
1144 1282 1.228429 TACTTGGGTGGTGGCAAGC 60.228 57.895 0.00 0.00 0.00 4.01
1161 1299 3.430790 CGCTGAGTGATTGGACCATTCTA 60.431 47.826 15.58 2.31 0.00 2.10
1170 1308 2.672961 TAAGTCCGCTGAGTGATTGG 57.327 50.000 0.00 0.00 0.00 3.16
1229 1367 4.499188 GGTGAAAAAGCTGTGGGTCTAAAC 60.499 45.833 0.00 0.00 0.00 2.01
1230 1368 3.634910 GGTGAAAAAGCTGTGGGTCTAAA 59.365 43.478 0.00 0.00 0.00 1.85
1287 1428 0.716666 AAAACGTTGCACAAAACCGC 59.283 45.000 0.00 0.00 0.00 5.68
1347 1488 4.695928 AGCTCGGTTCCTTTGTTTCTATTC 59.304 41.667 0.00 0.00 0.00 1.75
1360 1501 1.821216 TTGATGGAAAGCTCGGTTCC 58.179 50.000 8.49 8.49 44.19 3.62
1361 1502 3.915437 TTTTGATGGAAAGCTCGGTTC 57.085 42.857 0.00 0.00 0.00 3.62
1364 1505 6.093495 TGTTACTATTTTGATGGAAAGCTCGG 59.907 38.462 0.00 0.00 0.00 4.63
1389 1530 6.936968 ATCTAAGGAAGTGGTTGAGTAGTT 57.063 37.500 0.00 0.00 0.00 2.24
1393 1534 4.597507 TGGAATCTAAGGAAGTGGTTGAGT 59.402 41.667 0.00 0.00 0.00 3.41
1399 1540 4.301072 TTGGTGGAATCTAAGGAAGTGG 57.699 45.455 0.00 0.00 0.00 4.00
1407 1548 8.647796 ACACGATATATCTTTGGTGGAATCTAA 58.352 33.333 17.45 0.00 0.00 2.10
1430 1571 7.527084 TTTTACTTTTGTTTGGTGCATACAC 57.473 32.000 0.00 0.00 46.66 2.90
1454 1607 5.069781 GGCTCACTAGACCATTAGTTCTGAT 59.930 44.000 0.00 0.00 31.64 2.90
1458 1611 4.647399 AGAGGCTCACTAGACCATTAGTTC 59.353 45.833 18.26 0.00 31.64 3.01
1470 1623 4.261801 GCAAATGGTTAAGAGGCTCACTA 58.738 43.478 18.26 4.56 0.00 2.74
1506 1659 8.234546 GGTTTATCAACAAAAGCTCGATTAAGA 58.765 33.333 0.00 0.00 34.15 2.10
1513 1666 6.236017 TGTAGGTTTATCAACAAAAGCTCG 57.764 37.500 3.78 0.00 42.12 5.03
1514 1667 7.595130 CCTTTGTAGGTTTATCAACAAAAGCTC 59.405 37.037 3.78 0.00 42.12 4.09
1515 1668 7.286775 TCCTTTGTAGGTTTATCAACAAAAGCT 59.713 33.333 5.70 5.70 44.43 3.74
1516 1669 7.430441 TCCTTTGTAGGTTTATCAACAAAAGC 58.570 34.615 0.00 0.00 40.28 3.51
1519 1672 9.802039 AGTATCCTTTGTAGGTTTATCAACAAA 57.198 29.630 0.00 0.00 42.60 2.83
1521 1674 9.880157 GTAGTATCCTTTGTAGGTTTATCAACA 57.120 33.333 0.00 0.00 42.60 3.33
1524 1677 8.921205 GGAGTAGTATCCTTTGTAGGTTTATCA 58.079 37.037 0.00 0.00 42.60 2.15
1525 1678 8.366401 GGGAGTAGTATCCTTTGTAGGTTTATC 58.634 40.741 0.00 0.00 42.60 1.75
1526 1679 8.072480 AGGGAGTAGTATCCTTTGTAGGTTTAT 58.928 37.037 0.00 0.00 42.60 1.40
1527 1680 7.425003 AGGGAGTAGTATCCTTTGTAGGTTTA 58.575 38.462 0.00 0.00 42.60 2.01
1528 1681 6.269974 AGGGAGTAGTATCCTTTGTAGGTTT 58.730 40.000 0.00 0.00 42.60 3.27
1529 1682 5.851418 AGGGAGTAGTATCCTTTGTAGGTT 58.149 41.667 0.00 0.00 42.60 3.50
1530 1683 5.456779 GAGGGAGTAGTATCCTTTGTAGGT 58.543 45.833 0.00 0.00 42.60 3.08
1531 1684 4.833938 GGAGGGAGTAGTATCCTTTGTAGG 59.166 50.000 0.00 0.00 43.46 3.18
1532 1685 5.455872 TGGAGGGAGTAGTATCCTTTGTAG 58.544 45.833 0.00 0.00 39.50 2.74
1533 1686 5.043582 ACTGGAGGGAGTAGTATCCTTTGTA 60.044 44.000 0.00 0.00 39.50 2.41
1534 1687 4.264895 ACTGGAGGGAGTAGTATCCTTTGT 60.265 45.833 0.00 0.00 39.50 2.83
1535 1688 4.290942 ACTGGAGGGAGTAGTATCCTTTG 58.709 47.826 0.00 0.00 39.50 2.77
1536 1689 4.628661 ACTGGAGGGAGTAGTATCCTTT 57.371 45.455 0.00 0.00 39.50 3.11
1537 1690 4.016479 TGAACTGGAGGGAGTAGTATCCTT 60.016 45.833 0.00 0.00 39.50 3.36
1538 1691 3.532232 TGAACTGGAGGGAGTAGTATCCT 59.468 47.826 0.00 0.00 39.50 3.24
1539 1692 3.637694 GTGAACTGGAGGGAGTAGTATCC 59.362 52.174 0.00 0.00 38.76 2.59
1540 1693 4.279145 TGTGAACTGGAGGGAGTAGTATC 58.721 47.826 0.00 0.00 0.00 2.24
1541 1694 4.332683 TGTGAACTGGAGGGAGTAGTAT 57.667 45.455 0.00 0.00 0.00 2.12
1542 1695 3.820195 TGTGAACTGGAGGGAGTAGTA 57.180 47.619 0.00 0.00 0.00 1.82
1543 1696 2.696526 TGTGAACTGGAGGGAGTAGT 57.303 50.000 0.00 0.00 0.00 2.73
1544 1697 4.559862 ATTTGTGAACTGGAGGGAGTAG 57.440 45.455 0.00 0.00 0.00 2.57
1568 1721 5.416952 AGACCATCAATGTCCAAAAGATCAC 59.583 40.000 0.00 0.00 0.00 3.06
1656 1809 2.159226 GGTCGATAGGATGGGCGAATAG 60.159 54.545 0.00 0.00 34.29 1.73
1657 1810 1.822990 GGTCGATAGGATGGGCGAATA 59.177 52.381 0.00 0.00 34.29 1.75
1658 1811 0.608640 GGTCGATAGGATGGGCGAAT 59.391 55.000 0.00 0.00 34.29 3.34
1659 1812 0.757561 TGGTCGATAGGATGGGCGAA 60.758 55.000 0.00 0.00 34.29 4.70
1660 1813 0.541998 ATGGTCGATAGGATGGGCGA 60.542 55.000 0.00 0.00 0.00 5.54
1661 1814 0.321671 AATGGTCGATAGGATGGGCG 59.678 55.000 0.00 0.00 0.00 6.13
1662 1815 2.567615 ACTAATGGTCGATAGGATGGGC 59.432 50.000 0.00 0.00 0.00 5.36
1663 1816 4.891992 AACTAATGGTCGATAGGATGGG 57.108 45.455 0.00 0.00 0.00 4.00
1664 1817 5.611374 ACAAACTAATGGTCGATAGGATGG 58.389 41.667 0.00 0.00 0.00 3.51
1697 1850 9.830186 AGCTGAATCCTATAATCTTCTTAGGTA 57.170 33.333 0.00 0.00 35.13 3.08
1698 1851 8.734593 AGCTGAATCCTATAATCTTCTTAGGT 57.265 34.615 0.00 0.00 35.13 3.08
1702 1855 9.868277 CGAATAGCTGAATCCTATAATCTTCTT 57.132 33.333 0.00 0.00 0.00 2.52
1703 1856 7.978975 GCGAATAGCTGAATCCTATAATCTTCT 59.021 37.037 0.00 0.00 44.04 2.85
1704 1857 8.125728 GCGAATAGCTGAATCCTATAATCTTC 57.874 38.462 0.00 0.00 44.04 2.87
1712 1865 8.961611 TAGGATGGGCGAATAGCTGAATCCTA 62.962 46.154 14.66 14.66 46.89 2.94
1722 1875 2.159226 GGTCGATAGGATGGGCGAATAG 60.159 54.545 0.00 0.00 34.29 1.73
1723 1876 1.822990 GGTCGATAGGATGGGCGAATA 59.177 52.381 0.00 0.00 34.29 1.75
1724 1877 0.608640 GGTCGATAGGATGGGCGAAT 59.391 55.000 0.00 0.00 34.29 3.34
1725 1878 0.757561 TGGTCGATAGGATGGGCGAA 60.758 55.000 0.00 0.00 34.29 4.70
1726 1879 0.541998 ATGGTCGATAGGATGGGCGA 60.542 55.000 0.00 0.00 0.00 5.54
1727 1880 0.321671 AATGGTCGATAGGATGGGCG 59.678 55.000 0.00 0.00 0.00 6.13
1728 1881 2.567615 ACTAATGGTCGATAGGATGGGC 59.432 50.000 0.00 0.00 0.00 5.36
1729 1882 4.891992 AACTAATGGTCGATAGGATGGG 57.108 45.455 0.00 0.00 0.00 4.00
1730 1883 5.611374 ACAAACTAATGGTCGATAGGATGG 58.389 41.667 0.00 0.00 0.00 3.51
1763 1916 9.750783 AGCCGAATACTATAATCTTCTTAGGTA 57.249 33.333 0.00 0.00 0.00 3.08
1764 1917 8.653036 AGCCGAATACTATAATCTTCTTAGGT 57.347 34.615 0.00 0.00 0.00 3.08
1768 1921 9.790389 CGAATAGCCGAATACTATAATCTTCTT 57.210 33.333 0.00 0.00 30.14 2.52
1769 1922 7.916450 GCGAATAGCCGAATACTATAATCTTCT 59.084 37.037 0.00 0.00 40.81 2.85
1770 1923 8.052313 GCGAATAGCCGAATACTATAATCTTC 57.948 38.462 0.00 0.00 40.81 2.87
1771 1924 7.988904 GCGAATAGCCGAATACTATAATCTT 57.011 36.000 0.00 0.00 40.81 2.40
1788 1941 3.017442 TCTCGATAGGATGGGCGAATAG 58.983 50.000 0.00 0.00 31.89 1.73
1789 1942 3.081710 TCTCGATAGGATGGGCGAATA 57.918 47.619 0.00 0.00 31.89 1.75
1790 1943 1.924731 TCTCGATAGGATGGGCGAAT 58.075 50.000 0.00 0.00 31.89 3.34
1791 1944 1.699730 TTCTCGATAGGATGGGCGAA 58.300 50.000 0.00 0.00 31.89 4.70
1792 1945 1.924731 ATTCTCGATAGGATGGGCGA 58.075 50.000 0.00 0.00 0.00 5.54
1793 1946 2.755655 AGTATTCTCGATAGGATGGGCG 59.244 50.000 0.00 0.00 0.00 6.13
1794 1947 3.764434 TCAGTATTCTCGATAGGATGGGC 59.236 47.826 0.00 0.00 0.00 5.36
1876 2029 9.119329 CAGTATTATAGCGTATCTGTTTCAGTC 57.881 37.037 0.00 0.00 32.61 3.51
1890 2043 5.637104 AAAGCGTGAACAGTATTATAGCG 57.363 39.130 0.00 0.00 0.00 4.26
1894 2047 5.643777 AGCTGAAAAGCGTGAACAGTATTAT 59.356 36.000 0.00 0.00 40.27 1.28
1900 2053 2.289002 AGAAGCTGAAAAGCGTGAACAG 59.711 45.455 0.00 0.00 40.27 3.16
1908 2061 1.610522 TCTTGGCAGAAGCTGAAAAGC 59.389 47.619 0.00 0.00 41.70 3.51
1924 2077 2.744202 GTTGCTCATGTACCACCTCTTG 59.256 50.000 0.00 0.00 0.00 3.02
1934 2087 7.663905 ACCTACAATGTTTTAGTTGCTCATGTA 59.336 33.333 0.00 0.00 0.00 2.29
1941 2094 7.198306 ACTACACCTACAATGTTTTAGTTGC 57.802 36.000 0.00 0.00 0.00 4.17
1944 2097 8.967664 TTGAACTACACCTACAATGTTTTAGT 57.032 30.769 0.00 0.00 0.00 2.24
1951 2104 6.142817 GCAACTTTGAACTACACCTACAATG 58.857 40.000 0.00 0.00 0.00 2.82
1960 2113 4.127171 GAGTCCTGCAACTTTGAACTACA 58.873 43.478 0.00 0.00 0.00 2.74
2000 2154 0.249155 GTTCGACGGTGAACCAGTCA 60.249 55.000 18.11 8.01 41.88 3.41
2006 2160 3.408851 GGCGGTTCGACGGTGAAC 61.409 66.667 12.12 12.12 45.91 3.18
2015 2169 3.195698 GGCTTAGCTGGCGGTTCG 61.196 66.667 3.59 0.00 0.00 3.95
2024 2178 1.453155 CACAATGAACCGGCTTAGCT 58.547 50.000 0.00 0.00 0.00 3.32
2033 2187 6.089249 ACTTTTCTTCATCCACAATGAACC 57.911 37.500 0.00 0.00 46.96 3.62
2052 2206 9.566530 GCACCAACAAAATTTAAATTTGACTTT 57.433 25.926 23.34 12.80 39.56 2.66
2056 2210 7.308782 ACGCACCAACAAAATTTAAATTTGA 57.691 28.000 23.34 0.00 39.56 2.69
2062 2216 3.309954 GGCAACGCACCAACAAAATTTAA 59.690 39.130 0.00 0.00 0.00 1.52
2064 2218 1.668237 GGCAACGCACCAACAAAATTT 59.332 42.857 0.00 0.00 0.00 1.82
2079 2233 0.249657 TTTCAAATGGCCGTGGCAAC 60.250 50.000 13.76 0.00 42.43 4.17
2173 2327 7.054124 GTGAAGTGGATCTCAATTATTACCCA 58.946 38.462 0.00 0.00 33.43 4.51
2176 2330 8.983724 GCTAGTGAAGTGGATCTCAATTATTAC 58.016 37.037 0.00 0.00 33.43 1.89


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

AutoCloner maintained by Alex Coulton.