Multiple sequence alignment - TraesCS5A01G474800

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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 TraesCS5A01G474800 chr5A 100.000 2333 0 0 1 2333 650465005 650467337 0.000000e+00 4309
1 TraesCS5A01G474800 chr5A 85.131 686 86 13 1655 2333 581733900 581734576 0.000000e+00 688
2 TraesCS5A01G474800 chr5A 91.795 390 23 7 1257 1642 663167831 663167447 3.410000e-148 534
3 TraesCS5A01G474800 chr5A 93.778 225 10 1 2109 2333 650474529 650474749 3.710000e-88 335
4 TraesCS5A01G474800 chr1A 93.659 1656 100 4 1 1655 351875791 351877442 0.000000e+00 2471
5 TraesCS5A01G474800 chr2A 94.581 1587 83 3 70 1655 15885460 15887044 0.000000e+00 2451
6 TraesCS5A01G474800 chr2A 85.749 1670 220 16 3 1668 592001361 592003016 0.000000e+00 1749
7 TraesCS5A01G474800 chr2A 92.979 584 33 6 1078 1655 662943052 662942471 0.000000e+00 845
8 TraesCS5A01G474800 chr3A 93.422 1657 102 5 1 1655 688363387 688361736 0.000000e+00 2449
9 TraesCS5A01G474800 chr3D 88.065 1659 186 9 4 1659 136729489 136727840 0.000000e+00 1956
10 TraesCS5A01G474800 chr6A 85.085 1656 235 10 3 1655 503934369 503936015 0.000000e+00 1679
11 TraesCS5A01G474800 chr4D 85.048 1652 229 12 3 1650 82938985 82937348 0.000000e+00 1666
12 TraesCS5A01G474800 chr5B 84.597 1662 240 14 3 1661 485732444 485730796 0.000000e+00 1637
13 TraesCS5A01G474800 chr5B 84.489 1644 235 14 16 1654 641251424 641249796 0.000000e+00 1605
14 TraesCS5A01G474800 chr7B 91.556 675 50 6 1655 2324 627638993 627639665 0.000000e+00 924
15 TraesCS5A01G474800 chr7B 91.420 676 48 8 1655 2324 150550065 150550736 0.000000e+00 918
16 TraesCS5A01G474800 chr1B 91.556 675 50 6 1655 2324 218959876 218960548 0.000000e+00 924
17 TraesCS5A01G474800 chr2B 91.420 676 48 8 1655 2324 485163524 485162853 0.000000e+00 918
18 TraesCS5A01G474800 chrUn 95.864 411 15 2 1245 1655 322729897 322730305 0.000000e+00 664
19 TraesCS5A01G474800 chr7A 95.864 411 15 2 1245 1655 37344830 37345238 0.000000e+00 664
20 TraesCS5A01G474800 chr4B 88.558 437 46 3 1898 2333 86687439 86687006 5.710000e-146 527
21 TraesCS5A01G474800 chr4A 87.179 468 50 6 1867 2333 497690023 497690481 7.390000e-145 523
22 TraesCS5A01G474800 chr3B 86.966 468 51 6 1867 2333 520462785 520462327 3.440000e-143 518


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 TraesCS5A01G474800 chr5A 650465005 650467337 2332 False 4309 4309 100.000 1 2333 1 chr5A.!!$F2 2332
1 TraesCS5A01G474800 chr5A 581733900 581734576 676 False 688 688 85.131 1655 2333 1 chr5A.!!$F1 678
2 TraesCS5A01G474800 chr1A 351875791 351877442 1651 False 2471 2471 93.659 1 1655 1 chr1A.!!$F1 1654
3 TraesCS5A01G474800 chr2A 15885460 15887044 1584 False 2451 2451 94.581 70 1655 1 chr2A.!!$F1 1585
4 TraesCS5A01G474800 chr2A 592001361 592003016 1655 False 1749 1749 85.749 3 1668 1 chr2A.!!$F2 1665
5 TraesCS5A01G474800 chr2A 662942471 662943052 581 True 845 845 92.979 1078 1655 1 chr2A.!!$R1 577
6 TraesCS5A01G474800 chr3A 688361736 688363387 1651 True 2449 2449 93.422 1 1655 1 chr3A.!!$R1 1654
7 TraesCS5A01G474800 chr3D 136727840 136729489 1649 True 1956 1956 88.065 4 1659 1 chr3D.!!$R1 1655
8 TraesCS5A01G474800 chr6A 503934369 503936015 1646 False 1679 1679 85.085 3 1655 1 chr6A.!!$F1 1652
9 TraesCS5A01G474800 chr4D 82937348 82938985 1637 True 1666 1666 85.048 3 1650 1 chr4D.!!$R1 1647
10 TraesCS5A01G474800 chr5B 485730796 485732444 1648 True 1637 1637 84.597 3 1661 1 chr5B.!!$R1 1658
11 TraesCS5A01G474800 chr5B 641249796 641251424 1628 True 1605 1605 84.489 16 1654 1 chr5B.!!$R2 1638
12 TraesCS5A01G474800 chr7B 627638993 627639665 672 False 924 924 91.556 1655 2324 1 chr7B.!!$F2 669
13 TraesCS5A01G474800 chr7B 150550065 150550736 671 False 918 918 91.420 1655 2324 1 chr7B.!!$F1 669
14 TraesCS5A01G474800 chr1B 218959876 218960548 672 False 924 924 91.556 1655 2324 1 chr1B.!!$F1 669
15 TraesCS5A01G474800 chr2B 485162853 485163524 671 True 918 918 91.420 1655 2324 1 chr2B.!!$R1 669

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
909 918 0.107165 GAGGGTGGAAGGGAAATCCG 60.107 60.0 0.0 0.0 39.98 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2124 0.107703 GAGGAATGGATGACGGTGCA 60.108 55.0 0.0 0.0 0.0 4.57 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
119 120 9.624373 TTGCATTTTATTATATGGCCATGTTTT 57.376 25.926 29.04 14.34 0.00 2.43
195 201 2.161609 GGCACGTGACCCAGAATAAAAG 59.838 50.000 22.23 0.00 0.00 2.27
240 246 8.243426 GTGGACTAGAATATGCAGATCTAAGAG 58.757 40.741 0.00 0.00 0.00 2.85
439 446 7.286775 GGAAGGCCATTATGAAGGTAAAACATA 59.713 37.037 5.01 0.00 0.00 2.29
801 810 5.128919 GCTGGATGTGACTTTAGATGGATT 58.871 41.667 0.00 0.00 0.00 3.01
859 868 0.819259 GTGGCAGCTGTTTCAGGACA 60.819 55.000 16.64 0.00 31.21 4.02
909 918 0.107165 GAGGGTGGAAGGGAAATCCG 60.107 60.000 0.00 0.00 39.98 4.18
1024 1033 1.302949 GGCACTGCCTTGTATCCCA 59.697 57.895 13.28 0.00 46.69 4.37
1170 1179 5.531659 TGAGTTTAAACCGCTTACAAATCCA 59.468 36.000 14.72 0.00 0.00 3.41
1219 1229 0.921896 AATGTGCTACTGGGCAGGAT 59.078 50.000 0.00 0.00 43.25 3.24
1329 1339 3.197790 CAAGATGAGGCGGCGTGG 61.198 66.667 9.37 0.00 0.00 4.94
1359 1370 2.627515 GAGATGCTGCTCCATGGTTA 57.372 50.000 12.58 0.00 0.00 2.85
1363 1374 4.088634 AGATGCTGCTCCATGGTTAAAAA 58.911 39.130 12.58 0.00 0.00 1.94
1610 1628 4.365514 TCTTTGGACTGCTGTATTTCCA 57.634 40.909 0.00 0.00 36.31 3.53
1681 1699 7.178805 TGTTTGAATCATGATTTGGATTCTCCA 59.821 33.333 21.57 9.13 46.61 3.86
1794 1815 7.451731 TCCCCTCATATTCAAGTTACTCAAT 57.548 36.000 0.00 0.00 0.00 2.57
1813 1834 8.814038 ACTCAATAATAAATATCATGGCCCTC 57.186 34.615 0.00 0.00 0.00 4.30
1838 1859 6.458751 CGATTTGGTTGCAGTAGAAGCATAAT 60.459 38.462 0.00 0.00 42.33 1.28
1861 1882 4.756564 TGATTCACCTCTGCCTATATCCT 58.243 43.478 0.00 0.00 0.00 3.24
1865 1886 5.074746 TCACCTCTGCCTATATCCTAACA 57.925 43.478 0.00 0.00 0.00 2.41
1866 1887 5.080337 TCACCTCTGCCTATATCCTAACAG 58.920 45.833 0.00 0.00 0.00 3.16
1872 1893 4.747583 TGCCTATATCCTAACAGTGGCTA 58.252 43.478 0.00 0.00 39.77 3.93
1909 1930 8.972127 TCACCTTGATTCATATATACTAGCCTC 58.028 37.037 0.00 0.00 0.00 4.70
2012 2035 6.375455 ACTTCAAAACCATGGATGTGATCTAC 59.625 38.462 21.47 0.00 0.00 2.59
2019 2042 8.497910 AACCATGGATGTGATCTACTATAAGT 57.502 34.615 21.47 0.00 0.00 2.24
2060 2083 0.108585 AGGTTCCTCACGTTGTGCAT 59.891 50.000 0.00 0.00 32.98 3.96
2061 2084 1.346395 AGGTTCCTCACGTTGTGCATA 59.654 47.619 0.00 0.00 32.98 3.14
2083 2106 2.367202 ATGAAGGATGTCGGGCCGT 61.367 57.895 27.32 6.51 0.00 5.68
2096 2119 2.115291 GGCCGTTCAGATGCCTTCC 61.115 63.158 0.00 0.00 42.01 3.46
2100 2123 1.339055 CCGTTCAGATGCCTTCCTCAA 60.339 52.381 0.00 0.00 0.00 3.02
2101 2124 2.636830 CGTTCAGATGCCTTCCTCAAT 58.363 47.619 0.00 0.00 0.00 2.57
2104 2127 1.282738 TCAGATGCCTTCCTCAATGCA 59.717 47.619 0.00 0.00 37.52 3.96
2114 2137 0.392863 CCTCAATGCACCGTCATCCA 60.393 55.000 0.00 0.00 0.00 3.41
2115 2138 1.671979 CTCAATGCACCGTCATCCAT 58.328 50.000 0.00 0.00 0.00 3.41
2158 2181 2.076863 GACATTTCGGTGTTGAGGAGG 58.923 52.381 0.00 0.00 31.16 4.30
2161 2184 3.244911 ACATTTCGGTGTTGAGGAGGAAT 60.245 43.478 0.00 0.00 0.00 3.01
2183 2206 5.833406 TTATTTCATCGCACATGTGGATT 57.167 34.783 26.55 13.80 0.00 3.01
2240 2264 1.523758 AAGTAGGTGAAGGCTTTGCG 58.476 50.000 0.00 0.00 0.00 4.85
2302 2326 9.908747 TTATTCCTCGGTTTATTTTGATCCTAA 57.091 29.630 0.00 0.00 0.00 2.69
2307 2331 7.259290 TCGGTTTATTTTGATCCTAAGCATC 57.741 36.000 0.00 0.00 0.00 3.91
2315 2339 4.679373 TGATCCTAAGCATCAGAAGGAC 57.321 45.455 0.00 0.00 40.83 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 9.010029 CCTAGCAAGTATAGTTTTGGAAAGAAA 57.990 33.333 0.00 0.00 0.00 2.52
124 130 8.325787 TCAATCCTAGCAAGTATAGTTTTGGAA 58.674 33.333 0.00 0.00 0.00 3.53
195 201 5.177696 GTCCACTTGACAAGATAATATCGCC 59.822 44.000 21.95 0.00 43.85 5.54
240 246 1.282382 TTACACCCAGCCCTCCTTAC 58.718 55.000 0.00 0.00 0.00 2.34
390 397 5.935789 CCAACATGGAGAATCATTGCTTTTT 59.064 36.000 0.00 0.00 40.96 1.94
439 446 5.222007 CCACTCTTCTCCCTGCCATATAAAT 60.222 44.000 0.00 0.00 0.00 1.40
762 771 3.303938 TCCAGCAATGTTCCTTTCCAAA 58.696 40.909 0.00 0.00 0.00 3.28
801 810 2.551270 AGAGGTATTCTGGCACTCCAA 58.449 47.619 0.00 0.00 42.91 3.53
859 868 3.752665 TCACTTCTCTCGTTAGGACAGT 58.247 45.455 0.00 0.00 0.00 3.55
909 918 3.559655 GCCCACCACAAAAAGAACATTTC 59.440 43.478 0.00 0.00 0.00 2.17
1024 1033 7.927629 CCATACATAAGCTTGCCAAATGTTATT 59.072 33.333 15.12 1.74 33.15 1.40
1329 1339 1.584175 CAGCATCTCCAGCAGATCAC 58.416 55.000 0.00 0.00 40.20 3.06
1471 1487 5.709164 ACGACACCTAATCACAGTAACTAGT 59.291 40.000 0.00 0.00 0.00 2.57
1610 1628 5.363580 CCCCTTTCCATTACTGCAACATAAT 59.636 40.000 0.00 0.00 0.00 1.28
1717 1735 9.693739 ATCATTATACCCATGAACAAAGTAACA 57.306 29.630 0.00 0.00 34.31 2.41
1794 1815 7.339212 CCAAATCGAGGGCCATGATATTTATTA 59.661 37.037 6.18 0.00 0.00 0.98
1813 1834 2.483877 TGCTTCTACTGCAACCAAATCG 59.516 45.455 0.00 0.00 37.51 3.34
1838 1859 5.158141 AGGATATAGGCAGAGGTGAATCAA 58.842 41.667 0.00 0.00 0.00 2.57
1846 1867 4.221703 CCACTGTTAGGATATAGGCAGAGG 59.778 50.000 0.00 0.00 0.00 3.69
1872 1893 2.198827 TCAAGGTGATTGGCGTTGAT 57.801 45.000 0.00 0.00 39.54 2.57
1909 1930 6.204359 CAAAGGAGACAAAGATTCACAACTG 58.796 40.000 0.00 0.00 0.00 3.16
1955 1977 7.398618 TCCACATGATCAAGGGCTTTTATTTTA 59.601 33.333 0.00 0.00 0.00 1.52
2019 2042 8.434589 ACCTCAATGGAAAATCAAGGAATAAA 57.565 30.769 0.00 0.00 39.71 1.40
2060 2083 2.301870 GGCCCGACATCCTTCATGTATA 59.698 50.000 0.00 0.00 46.53 1.47
2061 2084 1.072331 GGCCCGACATCCTTCATGTAT 59.928 52.381 0.00 0.00 46.53 2.29
2083 2106 2.291089 TGCATTGAGGAAGGCATCTGAA 60.291 45.455 0.00 0.00 43.67 3.02
2096 2119 1.671979 ATGGATGACGGTGCATTGAG 58.328 50.000 0.00 0.00 0.00 3.02
2100 2123 0.548031 AGGAATGGATGACGGTGCAT 59.452 50.000 0.00 0.00 0.00 3.96
2101 2124 0.107703 GAGGAATGGATGACGGTGCA 60.108 55.000 0.00 0.00 0.00 4.57
2104 2127 1.123928 GAGGAGGAATGGATGACGGT 58.876 55.000 0.00 0.00 0.00 4.83
2114 2137 2.700897 CGATGTTGGGTAGAGGAGGAAT 59.299 50.000 0.00 0.00 0.00 3.01
2115 2138 2.108168 CGATGTTGGGTAGAGGAGGAA 58.892 52.381 0.00 0.00 0.00 3.36
2158 2181 5.820131 TCCACATGTGCGATGAAATAATTC 58.180 37.500 20.81 0.00 36.04 2.17
2161 2184 5.833406 AATCCACATGTGCGATGAAATAA 57.167 34.783 20.81 0.00 0.00 1.40
2183 2206 6.484288 TCTAGAATCCAAGGAATCAAGCAAA 58.516 36.000 6.92 0.00 0.00 3.68
2240 2264 3.141398 TGCCCGATTAATCTGCATCTTC 58.859 45.455 19.62 1.79 30.64 2.87


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

AutoCloner maintained by Alex Coulton.