Multiple sequence alignment - TraesCS2A01G043900

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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 TraesCS2A01G043900 chr2A 100.000 2231 0 0 1 2231 17503112 17500882 0.000000e+00 4120
1 TraesCS2A01G043900 chr2A 93.032 1550 103 4 1 1548 17534176 17532630 0.000000e+00 2259
2 TraesCS2A01G043900 chr2A 89.666 1645 142 10 1 1626 17598697 17597062 0.000000e+00 2071
3 TraesCS2A01G043900 chr2A 90.316 1549 140 6 1 1548 17474955 17473416 0.000000e+00 2021
4 TraesCS2A01G043900 chr2A 89.533 1414 147 1 2 1415 17549508 17548096 0.000000e+00 1790
5 TraesCS2A01G043900 chr2A 90.024 822 79 3 1 821 17425298 17424479 0.000000e+00 1061
6 TraesCS2A01G043900 chr2A 87.772 597 48 4 1653 2231 17473263 17472674 0.000000e+00 675
7 TraesCS2A01G043900 chr2A 86.811 599 50 9 1653 2231 17547851 17547262 1.870000e-180 641
8 TraesCS2A01G043900 chr2A 86.622 598 55 7 1653 2231 17539847 17539256 2.420000e-179 638
9 TraesCS2A01G043900 chr2A 86.455 598 54 7 1653 2231 17532492 17531903 4.040000e-177 630
10 TraesCS2A01G043900 chr2A 79.585 867 92 32 1308 2157 17418556 17417758 1.950000e-150 542
11 TraesCS2A01G043900 chr2A 87.032 347 38 4 1287 1633 17559176 17558837 3.480000e-103 385
12 TraesCS2A01G043900 chr2A 91.597 119 10 0 1649 1767 17558767 17558649 4.930000e-37 165
13 TraesCS2A01G043900 chr2A 80.000 230 24 6 1762 1973 17558315 17558090 1.380000e-32 150
14 TraesCS2A01G043900 chr2A 81.507 146 16 7 1653 1797 17411473 17411338 2.340000e-20 110
15 TraesCS2A01G043900 chr2B 89.330 1790 176 6 1 1782 27544796 27543014 0.000000e+00 2233
16 TraesCS2A01G043900 chr2B 84.629 1646 190 34 1 1621 27617214 27615607 0.000000e+00 1580
17 TraesCS2A01G043900 chr2B 87.359 973 117 6 9 979 27582193 27581225 0.000000e+00 1110
18 TraesCS2A01G043900 chr2B 87.600 250 15 8 1853 2088 27543014 27542767 2.180000e-70 276
19 TraesCS2A01G043900 chr2B 89.241 158 11 4 2078 2231 27539597 27539442 2.260000e-45 193
20 TraesCS2A01G043900 chr2D 87.650 1247 146 3 1 1239 15506543 15505297 0.000000e+00 1443
21 TraesCS2A01G043900 chr2D 80.964 1660 259 37 1 1627 15472236 15470601 0.000000e+00 1262
22 TraesCS2A01G043900 chr2D 86.358 755 76 8 872 1606 15458327 15457580 0.000000e+00 798
23 TraesCS2A01G043900 chr2D 78.708 418 46 28 1653 2032 15470526 15470114 2.860000e-59 239
24 TraesCS2A01G043900 chr2D 80.282 213 29 9 1419 1621 15505169 15504960 4.960000e-32 148


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 TraesCS2A01G043900 chr2A 17500882 17503112 2230 True 4120.000000 4120 100.000000 1 2231 1 chr2A.!!$R4 2230
1 TraesCS2A01G043900 chr2A 17597062 17598697 1635 True 2071.000000 2071 89.666000 1 1626 1 chr2A.!!$R6 1625
2 TraesCS2A01G043900 chr2A 17531903 17534176 2273 True 1444.500000 2259 89.743500 1 2231 2 chr2A.!!$R8 2230
3 TraesCS2A01G043900 chr2A 17472674 17474955 2281 True 1348.000000 2021 89.044000 1 2231 2 chr2A.!!$R7 2230
4 TraesCS2A01G043900 chr2A 17547262 17549508 2246 True 1215.500000 1790 88.172000 2 2231 2 chr2A.!!$R9 2229
5 TraesCS2A01G043900 chr2A 17424479 17425298 819 True 1061.000000 1061 90.024000 1 821 1 chr2A.!!$R3 820
6 TraesCS2A01G043900 chr2A 17539256 17539847 591 True 638.000000 638 86.622000 1653 2231 1 chr2A.!!$R5 578
7 TraesCS2A01G043900 chr2A 17417758 17418556 798 True 542.000000 542 79.585000 1308 2157 1 chr2A.!!$R2 849
8 TraesCS2A01G043900 chr2A 17558090 17559176 1086 True 233.333333 385 86.209667 1287 1973 3 chr2A.!!$R10 686
9 TraesCS2A01G043900 chr2B 27615607 27617214 1607 True 1580.000000 1580 84.629000 1 1621 1 chr2B.!!$R2 1620
10 TraesCS2A01G043900 chr2B 27581225 27582193 968 True 1110.000000 1110 87.359000 9 979 1 chr2B.!!$R1 970
11 TraesCS2A01G043900 chr2B 27539442 27544796 5354 True 900.666667 2233 88.723667 1 2231 3 chr2B.!!$R3 2230
12 TraesCS2A01G043900 chr2D 15457580 15458327 747 True 798.000000 798 86.358000 872 1606 1 chr2D.!!$R1 734
13 TraesCS2A01G043900 chr2D 15504960 15506543 1583 True 795.500000 1443 83.966000 1 1621 2 chr2D.!!$R3 1620
14 TraesCS2A01G043900 chr2D 15470114 15472236 2122 True 750.500000 1262 79.836000 1 2032 2 chr2D.!!$R2 2031

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
617 630 0.54851 GAGAGGTGCCCCAAGCTATT 59.451 55.0 0.0 0.0 44.23 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 5906 0.324275 ACACTTGTTGGTGGTTGCCT 60.324 50.0 0.0 0.0 41.09 4.75 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
105 106 5.787953 TGCATCTTTTGACTTCAATTGGA 57.212 34.783 5.42 0.00 35.55 3.53
245 249 1.166531 GCCGTGAAGTTGCTCAAGGT 61.167 55.000 7.33 0.00 44.22 3.50
320 330 2.923121 AGAAGAACTGCAAGCTGTCAA 58.077 42.857 5.05 0.00 37.60 3.18
424 437 4.224594 TGCAAGATGAAGAGAAGATGGAGT 59.775 41.667 0.00 0.00 0.00 3.85
433 446 1.137872 AGAAGATGGAGTGTGGATCGC 59.862 52.381 0.00 0.00 0.00 4.58
468 481 3.128242 ACAACACTCGGAGGATTAGTACG 59.872 47.826 10.23 0.00 0.00 3.67
565 578 1.766494 CATTCCATGCCCACAAGCTA 58.234 50.000 0.00 0.00 0.00 3.32
617 630 0.548510 GAGAGGTGCCCCAAGCTATT 59.451 55.000 0.00 0.00 44.23 1.73
622 635 1.768870 GGTGCCCCAAGCTATTCTCTA 59.231 52.381 0.00 0.00 44.23 2.43
725 738 2.353704 CGTGCTACATCTGGAACTGGAA 60.354 50.000 0.00 0.00 0.00 3.53
867 880 1.326852 GAGACGCTCGAGATCGTGTAA 59.673 52.381 20.41 0.00 39.22 2.41
1245 1264 1.282157 AGGTGAGCTATGTTTGGTCCC 59.718 52.381 0.00 0.00 0.00 4.46
1276 1295 9.085645 TCCTTTCATCAGTAACTTACTTAGTGA 57.914 33.333 0.00 2.15 45.14 3.41
1311 1331 8.193438 ACTTACGTTTACCATTCTATCTGTACC 58.807 37.037 0.00 0.00 0.00 3.34
1518 1584 1.742761 TGCCTTACTTGATGCTGCTC 58.257 50.000 0.00 0.00 0.00 4.26
1519 1585 1.280133 TGCCTTACTTGATGCTGCTCT 59.720 47.619 0.00 0.00 0.00 4.09
1521 1589 2.869192 GCCTTACTTGATGCTGCTCTAC 59.131 50.000 0.00 0.00 0.00 2.59
1523 1591 4.202161 GCCTTACTTGATGCTGCTCTACTA 60.202 45.833 0.00 0.00 0.00 1.82
1537 1613 4.106197 GCTCTACTAGTCCGTGTGAAATG 58.894 47.826 0.00 0.00 0.00 2.32
1542 1618 0.944386 AGTCCGTGTGAAATGTGCAC 59.056 50.000 10.75 10.75 36.81 4.57
1561 1639 2.756207 CACCTGCAAATCCATGATGTGA 59.244 45.455 0.00 0.00 29.25 3.58
1606 1692 2.035530 TTTGCTTTGGTTTGGCTTGG 57.964 45.000 0.00 0.00 0.00 3.61
1607 1693 0.463474 TTGCTTTGGTTTGGCTTGGC 60.463 50.000 0.00 0.00 0.00 4.52
1608 1694 1.336632 TGCTTTGGTTTGGCTTGGCT 61.337 50.000 0.00 0.00 0.00 4.75
1609 1695 0.179048 GCTTTGGTTTGGCTTGGCTT 60.179 50.000 0.00 0.00 0.00 4.35
1610 1696 1.585297 CTTTGGTTTGGCTTGGCTTG 58.415 50.000 0.00 0.00 0.00 4.01
1611 1697 1.138661 CTTTGGTTTGGCTTGGCTTGA 59.861 47.619 0.00 0.00 0.00 3.02
1612 1698 1.422531 TTGGTTTGGCTTGGCTTGAT 58.577 45.000 0.00 0.00 0.00 2.57
1613 1699 1.422531 TGGTTTGGCTTGGCTTGATT 58.577 45.000 0.00 0.00 0.00 2.57
1614 1700 1.767681 TGGTTTGGCTTGGCTTGATTT 59.232 42.857 0.00 0.00 0.00 2.17
1615 1701 2.145536 GGTTTGGCTTGGCTTGATTTG 58.854 47.619 0.00 0.00 0.00 2.32
1616 1702 1.532437 GTTTGGCTTGGCTTGATTTGC 59.468 47.619 0.00 0.00 0.00 3.68
1617 1703 1.050204 TTGGCTTGGCTTGATTTGCT 58.950 45.000 0.00 0.00 0.00 3.91
1618 1704 1.050204 TGGCTTGGCTTGATTTGCTT 58.950 45.000 0.00 0.00 0.00 3.91
1619 1705 1.417145 TGGCTTGGCTTGATTTGCTTT 59.583 42.857 0.00 0.00 0.00 3.51
1620 1706 1.802365 GGCTTGGCTTGATTTGCTTTG 59.198 47.619 0.00 0.00 0.00 2.77
1621 1707 1.802365 GCTTGGCTTGATTTGCTTTGG 59.198 47.619 0.00 0.00 0.00 3.28
1622 1708 2.807837 GCTTGGCTTGATTTGCTTTGGT 60.808 45.455 0.00 0.00 0.00 3.67
1623 1709 3.469739 CTTGGCTTGATTTGCTTTGGTT 58.530 40.909 0.00 0.00 0.00 3.67
1732 1902 2.663075 CCTGCCTGCTCCTGCTGTA 61.663 63.158 0.00 0.00 40.48 2.74
1752 1922 0.317020 GCTCTCCGTTTGTGTGTTGC 60.317 55.000 0.00 0.00 0.00 4.17
1753 1923 1.013596 CTCTCCGTTTGTGTGTTGCA 58.986 50.000 0.00 0.00 0.00 4.08
1804 2313 6.561737 TTACTGTAATGCGAAACAATTCCA 57.438 33.333 0.00 0.00 31.52 3.53
1843 2358 5.625921 TGGTGATTTGTGTGTGTGATATG 57.374 39.130 0.00 0.00 0.00 1.78
1847 2362 7.392953 TGGTGATTTGTGTGTGTGATATGTAAT 59.607 33.333 0.00 0.00 0.00 1.89
1848 2363 8.888716 GGTGATTTGTGTGTGTGATATGTAATA 58.111 33.333 0.00 0.00 0.00 0.98
1857 2372 7.332182 TGTGTGTGATATGTAATAAACTGCGAA 59.668 33.333 0.00 0.00 29.06 4.70
1915 2448 7.883391 TTGTAAAATCCTTGACTGGTTGTTA 57.117 32.000 0.00 0.00 0.00 2.41
2045 2603 5.477607 TTTGGCTTACACTAGCAAGACTA 57.522 39.130 6.71 0.00 43.02 2.59
2091 5829 6.228616 AGTAAGTAGAAGCAGAATCCCTTC 57.771 41.667 3.86 3.86 38.14 3.46
2104 5846 6.376581 GCAGAATCCCTTCTATTTATCCATGG 59.623 42.308 4.97 4.97 39.78 3.66
2117 5859 2.885135 TCCATGGCACTGAAATGAGT 57.115 45.000 6.96 0.00 0.00 3.41
2159 5906 1.188871 TACCATGCGACACCTCCACA 61.189 55.000 0.00 0.00 0.00 4.17
2173 5920 1.756172 CCACAGGCAACCACCAACA 60.756 57.895 0.00 0.00 37.17 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 3.909732 CCTAATGGTGAAGCCCCAAATA 58.090 45.455 0.00 0.00 35.14 1.40
245 249 2.763710 TGCTGCTGGCTCCCGATA 60.764 61.111 0.00 0.00 42.39 2.92
264 268 8.955388 TCACTTGCATATAAGTATTGAGCAAAA 58.045 29.630 0.00 0.00 38.78 2.44
424 437 1.262417 TGTTCCTGTAGCGATCCACA 58.738 50.000 0.00 0.00 0.00 4.17
433 446 3.245284 CGAGTGTTGTGTTGTTCCTGTAG 59.755 47.826 0.00 0.00 0.00 2.74
468 481 1.168714 CAGGGGCTAAAGCAACACTC 58.831 55.000 4.07 0.00 44.36 3.51
565 578 2.437359 GAGCCAGCGCCAATCTGT 60.437 61.111 2.29 0.00 34.57 3.41
617 630 2.119495 GGGGAGTGGCAAAGATAGAGA 58.881 52.381 0.00 0.00 0.00 3.10
622 635 0.779997 AGTTGGGGAGTGGCAAAGAT 59.220 50.000 0.00 0.00 0.00 2.40
725 738 5.249780 TCCACTTGGTTGGTATGTTGTAT 57.750 39.130 0.00 0.00 37.93 2.29
867 880 3.843027 AGACTTCCTTCAGATCACCACAT 59.157 43.478 0.00 0.00 0.00 3.21
1157 1170 0.830648 TGGTTCATAGAGCGAAGGGG 59.169 55.000 0.00 0.00 0.00 4.79
1245 1264 7.607250 AGTAAGTTACTGATGAAAGGAGACAG 58.393 38.462 14.82 0.00 37.69 3.51
1518 1584 3.612860 GCACATTTCACACGGACTAGTAG 59.387 47.826 0.00 0.00 0.00 2.57
1519 1585 3.006003 TGCACATTTCACACGGACTAGTA 59.994 43.478 0.00 0.00 0.00 1.82
1521 1589 2.157668 GTGCACATTTCACACGGACTAG 59.842 50.000 13.17 0.00 34.73 2.57
1523 1591 0.944386 GTGCACATTTCACACGGACT 59.056 50.000 13.17 0.00 34.73 3.85
1542 1618 2.223409 CGTCACATCATGGATTTGCAGG 60.223 50.000 0.00 0.00 0.00 4.85
1548 1624 1.382522 GCACCGTCACATCATGGATT 58.617 50.000 0.00 0.00 0.00 3.01
1549 1625 0.811219 CGCACCGTCACATCATGGAT 60.811 55.000 0.00 0.00 0.00 3.41
1550 1626 1.447663 CGCACCGTCACATCATGGA 60.448 57.895 0.00 0.00 0.00 3.41
1561 1639 1.300697 GAACTGGAAGACGCACCGT 60.301 57.895 0.00 0.00 45.10 4.83
1606 1692 3.205338 ACCAAACCAAAGCAAATCAAGC 58.795 40.909 0.00 0.00 0.00 4.01
1607 1693 5.448904 CCAAACCAAACCAAAGCAAATCAAG 60.449 40.000 0.00 0.00 0.00 3.02
1608 1694 4.397417 CCAAACCAAACCAAAGCAAATCAA 59.603 37.500 0.00 0.00 0.00 2.57
1609 1695 3.944015 CCAAACCAAACCAAAGCAAATCA 59.056 39.130 0.00 0.00 0.00 2.57
1610 1696 3.243035 GCCAAACCAAACCAAAGCAAATC 60.243 43.478 0.00 0.00 0.00 2.17
1611 1697 2.687425 GCCAAACCAAACCAAAGCAAAT 59.313 40.909 0.00 0.00 0.00 2.32
1612 1698 2.087646 GCCAAACCAAACCAAAGCAAA 58.912 42.857 0.00 0.00 0.00 3.68
1613 1699 1.280421 AGCCAAACCAAACCAAAGCAA 59.720 42.857 0.00 0.00 0.00 3.91
1614 1700 0.908198 AGCCAAACCAAACCAAAGCA 59.092 45.000 0.00 0.00 0.00 3.91
1615 1701 1.670295 CAAGCCAAACCAAACCAAAGC 59.330 47.619 0.00 0.00 0.00 3.51
1616 1702 3.258971 TCAAGCCAAACCAAACCAAAG 57.741 42.857 0.00 0.00 0.00 2.77
1617 1703 3.922171 ATCAAGCCAAACCAAACCAAA 57.078 38.095 0.00 0.00 0.00 3.28
1618 1704 3.739519 CGAATCAAGCCAAACCAAACCAA 60.740 43.478 0.00 0.00 0.00 3.67
1619 1705 2.223923 CGAATCAAGCCAAACCAAACCA 60.224 45.455 0.00 0.00 0.00 3.67
1620 1706 2.403259 CGAATCAAGCCAAACCAAACC 58.597 47.619 0.00 0.00 0.00 3.27
1621 1707 2.223947 ACCGAATCAAGCCAAACCAAAC 60.224 45.455 0.00 0.00 0.00 2.93
1622 1708 2.035632 ACCGAATCAAGCCAAACCAAA 58.964 42.857 0.00 0.00 0.00 3.28
1623 1709 1.698506 ACCGAATCAAGCCAAACCAA 58.301 45.000 0.00 0.00 0.00 3.67
1732 1902 1.299541 CAACACACAAACGGAGAGCT 58.700 50.000 0.00 0.00 0.00 4.09
1752 1922 4.142752 CCATAGCTGACAAATCACACACTG 60.143 45.833 0.00 0.00 0.00 3.66
1753 1923 4.005650 CCATAGCTGACAAATCACACACT 58.994 43.478 0.00 0.00 0.00 3.55
1847 2362 9.907576 CAAAACAAAACATAAATTCGCAGTTTA 57.092 25.926 0.00 0.00 32.62 2.01
1848 2363 7.427895 GCAAAACAAAACATAAATTCGCAGTTT 59.572 29.630 0.00 0.00 34.19 2.66
1849 2364 6.904543 GCAAAACAAAACATAAATTCGCAGTT 59.095 30.769 0.00 0.00 0.00 3.16
1852 2367 5.427082 CGCAAAACAAAACATAAATTCGCA 58.573 33.333 0.00 0.00 0.00 5.10
1857 2372 6.423302 TGATCAGCGCAAAACAAAACATAAAT 59.577 30.769 11.47 0.00 0.00 1.40
2021 2579 5.316987 AGTCTTGCTAGTGTAAGCCAAATT 58.683 37.500 0.00 0.00 42.05 1.82
2091 5829 7.230108 ACTCATTTCAGTGCCATGGATAAATAG 59.770 37.037 18.40 11.86 0.00 1.73
2128 5871 4.094294 TGTCGCATGGTAGCTAATTGAAAC 59.906 41.667 0.00 0.00 0.00 2.78
2159 5906 0.324275 ACACTTGTTGGTGGTTGCCT 60.324 50.000 0.00 0.00 41.09 4.75
2173 5920 3.791973 TGAAATGCGGTGAAAACACTT 57.208 38.095 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.