Multiple sequence alignment - TraesCS7D01G387900

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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 TraesCS7D01G387900 chr7D 100.000 2287 0 0 1 2287 501629521 501631807 0.000000e+00 4224
1 TraesCS7D01G387900 chr7D 93.390 590 26 6 1709 2287 501830447 501831034 0.000000e+00 861
2 TraesCS7D01G387900 chr7D 85.137 619 36 26 1709 2287 501530449 501529847 1.180000e-162 582
3 TraesCS7D01G387900 chr5D 93.481 1718 84 8 2 1717 353957356 353959047 0.000000e+00 2527
4 TraesCS7D01G387900 chr4D 93.267 1708 78 11 1 1705 345354879 345356552 0.000000e+00 2483
5 TraesCS7D01G387900 chr4D 93.144 1692 100 11 22 1708 460669983 460668303 0.000000e+00 2468
6 TraesCS7D01G387900 chr1D 94.234 1613 85 6 95 1705 467504894 467506500 0.000000e+00 2457
7 TraesCS7D01G387900 chr3D 92.636 1711 87 8 1 1709 124068659 124066986 0.000000e+00 2425
8 TraesCS7D01G387900 chr7A 91.503 1730 112 15 1 1704 25850554 25852274 0.000000e+00 2348
9 TraesCS7D01G387900 chr7A 87.352 506 42 11 1708 2206 569122329 569122819 5.520000e-156 560
10 TraesCS7D01G387900 chr7A 81.711 596 44 22 1723 2287 568116748 568116187 9.700000e-119 436
11 TraesCS7D01G387900 chr7A 86.686 338 26 10 1709 2041 568702846 568703169 7.770000e-95 357
12 TraesCS7D01G387900 chr7A 87.500 168 15 3 2126 2287 568488990 568488823 3.000000e-44 189
13 TraesCS7D01G387900 chr7A 79.195 298 32 18 1760 2040 568489939 568489655 1.810000e-41 180
14 TraesCS7D01G387900 chr5A 90.771 1712 130 12 1 1705 312260204 312258514 0.000000e+00 2261
15 TraesCS7D01G387900 chr3A 91.296 1620 132 8 95 1709 145634067 145635682 0.000000e+00 2202
16 TraesCS7D01G387900 chr3A 93.135 1413 92 4 1 1410 598875362 598873952 0.000000e+00 2067
17 TraesCS7D01G387900 chr6D 94.082 1318 71 4 1 1317 56319564 56320875 0.000000e+00 1995
18 TraesCS7D01G387900 chr6D 93.483 890 56 2 1 890 11696573 11695686 0.000000e+00 1321
19 TraesCS7D01G387900 chr7B 88.060 603 37 15 1709 2287 531153736 531153145 0.000000e+00 682
20 TraesCS7D01G387900 chr7B 86.882 587 43 16 1709 2287 531434972 531435532 5.360000e-176 627


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 TraesCS7D01G387900 chr7D 501629521 501631807 2286 False 4224 4224 100.000 1 2287 1 chr7D.!!$F1 2286
1 TraesCS7D01G387900 chr7D 501830447 501831034 587 False 861 861 93.390 1709 2287 1 chr7D.!!$F2 578
2 TraesCS7D01G387900 chr7D 501529847 501530449 602 True 582 582 85.137 1709 2287 1 chr7D.!!$R1 578
3 TraesCS7D01G387900 chr5D 353957356 353959047 1691 False 2527 2527 93.481 2 1717 1 chr5D.!!$F1 1715
4 TraesCS7D01G387900 chr4D 345354879 345356552 1673 False 2483 2483 93.267 1 1705 1 chr4D.!!$F1 1704
5 TraesCS7D01G387900 chr4D 460668303 460669983 1680 True 2468 2468 93.144 22 1708 1 chr4D.!!$R1 1686
6 TraesCS7D01G387900 chr1D 467504894 467506500 1606 False 2457 2457 94.234 95 1705 1 chr1D.!!$F1 1610
7 TraesCS7D01G387900 chr3D 124066986 124068659 1673 True 2425 2425 92.636 1 1709 1 chr3D.!!$R1 1708
8 TraesCS7D01G387900 chr7A 25850554 25852274 1720 False 2348 2348 91.503 1 1704 1 chr7A.!!$F1 1703
9 TraesCS7D01G387900 chr7A 568116187 568116748 561 True 436 436 81.711 1723 2287 1 chr7A.!!$R1 564
10 TraesCS7D01G387900 chr5A 312258514 312260204 1690 True 2261 2261 90.771 1 1705 1 chr5A.!!$R1 1704
11 TraesCS7D01G387900 chr3A 145634067 145635682 1615 False 2202 2202 91.296 95 1709 1 chr3A.!!$F1 1614
12 TraesCS7D01G387900 chr3A 598873952 598875362 1410 True 2067 2067 93.135 1 1410 1 chr3A.!!$R1 1409
13 TraesCS7D01G387900 chr6D 56319564 56320875 1311 False 1995 1995 94.082 1 1317 1 chr6D.!!$F1 1316
14 TraesCS7D01G387900 chr6D 11695686 11696573 887 True 1321 1321 93.483 1 890 1 chr6D.!!$R1 889
15 TraesCS7D01G387900 chr7B 531153145 531153736 591 True 682 682 88.060 1709 2287 1 chr7B.!!$R1 578
16 TraesCS7D01G387900 chr7B 531434972 531435532 560 False 627 627 86.882 1709 2287 1 chr7B.!!$F1 578

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
304 305 0.037326 ATCATGACAACTGCCGTCGT 60.037 50.0 0.0 0.0 36.11 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1595 0.106521 GGTGTTTGGTTGCCTGCATT 59.893 50.0 0.0 0.0 0.0 3.56 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
80 81 1.589196 GATCTGCCAGGTACGACGC 60.589 63.158 0.00 0.00 0.00 5.19
139 140 2.950990 TCTTCCTCCTCCTTAGGCTT 57.049 50.000 0.00 0.00 43.31 4.35
222 223 1.222113 GGAGCCCAGTAGGTCTTGC 59.778 63.158 0.00 0.00 38.26 4.01
227 228 1.278127 GCCCAGTAGGTCTTGCACTTA 59.722 52.381 0.00 0.00 38.26 2.24
242 243 3.644265 TGCACTTACACCACTTCTTCCTA 59.356 43.478 0.00 0.00 0.00 2.94
287 288 0.595095 GATTCATGGCCCAGCGAATC 59.405 55.000 17.95 17.95 37.62 2.52
291 292 0.820482 CATGGCCCAGCGAATCATGA 60.820 55.000 0.00 0.00 37.87 3.07
300 301 0.247814 GCGAATCATGACAACTGCCG 60.248 55.000 0.00 0.00 0.00 5.69
304 305 0.037326 ATCATGACAACTGCCGTCGT 60.037 50.000 0.00 0.00 36.11 4.34
489 490 2.386935 GCCCTCCAGCCAATACCCT 61.387 63.158 0.00 0.00 0.00 4.34
562 563 2.368875 GGAGGAAGGTTGACAGTGAGAA 59.631 50.000 0.00 0.00 0.00 2.87
674 686 4.500499 ACTCCATGCTCTTCAATTAGCT 57.500 40.909 0.00 0.00 39.53 3.32
722 757 2.169352 ACTCTGTGTTGTGCTTGACTCT 59.831 45.455 0.00 0.00 0.00 3.24
824 859 2.359354 CACCCAATGCCCGACGAA 60.359 61.111 0.00 0.00 0.00 3.85
866 902 2.125633 GAAGACCCGAAGACGCCC 60.126 66.667 0.00 0.00 38.29 6.13
896 932 2.502492 CGACGAGGGCATGGAGGAT 61.502 63.158 0.00 0.00 0.00 3.24
897 933 1.369321 GACGAGGGCATGGAGGATC 59.631 63.158 0.00 0.00 0.00 3.36
940 976 3.361281 ACTACGACCACTACCATCAGA 57.639 47.619 0.00 0.00 0.00 3.27
1133 1170 2.276740 GGATCAGGGTTGGGCCAG 59.723 66.667 6.23 0.00 39.65 4.85
1196 1234 0.324738 TCAAGCTCCTCACTCCCGAT 60.325 55.000 0.00 0.00 0.00 4.18
1251 1289 0.176910 TGAGGTCGTCAACAAGTGCA 59.823 50.000 0.00 0.00 29.64 4.57
1328 1367 3.128938 AGCGTACTATCGAGTCTGCTTTT 59.871 43.478 0.00 0.00 41.19 2.27
1441 1498 1.741706 GTGCTTATGATGTGTGCTGCT 59.258 47.619 0.00 0.00 0.00 4.24
1483 1541 5.248477 TCATCAACTAGCCAAAGAGGTTACT 59.752 40.000 0.00 0.00 40.61 2.24
1493 1551 4.039973 CCAAAGAGGTTACTACACACCAGA 59.960 45.833 0.00 0.00 35.25 3.86
1536 1595 2.964209 TGCCTTGGGTTTGTCCATAAA 58.036 42.857 0.00 0.00 36.58 1.40
1561 1620 1.519719 GCAACCAAACACCAGGCAA 59.480 52.632 0.00 0.00 0.00 4.52
1565 1624 1.494960 ACCAAACACCAGGCAATGTT 58.505 45.000 0.00 0.00 40.76 2.71
1573 1632 0.963962 CCAGGCAATGTTGTTCTGCT 59.036 50.000 10.52 0.00 36.32 4.24
1633 1692 1.404391 CAGATGGTGCATTTGAGGCTC 59.596 52.381 7.79 7.79 28.98 4.70
1640 1699 2.028748 GTGCATTTGAGGCTCCATTTGT 60.029 45.455 12.86 0.00 0.00 2.83
1645 1704 5.300286 GCATTTGAGGCTCCATTTGTATAGT 59.700 40.000 12.86 0.00 0.00 2.12
1721 1780 1.154225 CGTCCTTGGTTTCATGCGC 60.154 57.895 0.00 0.00 0.00 6.09
1768 1832 4.318332 AGTGCTCGATCTTTGACAAATCA 58.682 39.130 0.05 0.00 0.00 2.57
1843 1925 4.373116 GGCGAGCACTCCACGGAA 62.373 66.667 0.00 0.00 0.00 4.30
1872 1963 2.647529 TCACGACATACACATTCGCT 57.352 45.000 0.00 0.00 36.18 4.93
1993 2103 4.770874 CCATTCCGCCCCGTCGTT 62.771 66.667 0.00 0.00 0.00 3.85
2006 2121 2.022129 GTCGTTGGTGTGCTCTCGG 61.022 63.158 0.00 0.00 0.00 4.63
2042 2160 1.000394 TGACGTGATATATGTGCGGGG 60.000 52.381 0.00 0.00 0.00 5.73
2093 2224 1.145945 TGGTGGCTTTGGTTGGTGATA 59.854 47.619 0.00 0.00 0.00 2.15
2237 2375 0.230515 CATGTCGATCGATGTTGCGG 59.769 55.000 22.50 3.50 0.00 5.69
2241 2379 1.518352 CGATCGATGTTGCGGGTCA 60.518 57.895 10.26 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 4.444838 CGGCGGTCATCGGTGGAA 62.445 66.667 0.00 0.00 39.69 3.53
222 223 5.794894 ACATAGGAAGAAGTGGTGTAAGTG 58.205 41.667 0.00 0.00 0.00 3.16
227 228 5.246307 GCTAAACATAGGAAGAAGTGGTGT 58.754 41.667 0.00 0.00 0.00 4.16
242 243 0.806868 TCTCCGACGACGCTAAACAT 59.193 50.000 0.64 0.00 38.29 2.71
287 288 1.492873 CACGACGGCAGTTGTCATG 59.507 57.895 6.93 0.00 42.86 3.07
489 490 1.428718 AACGCCAACCCCTTCCCTTA 61.429 55.000 0.00 0.00 0.00 2.69
562 563 1.132168 ACTTACCCACCCCCTCTCTTT 60.132 52.381 0.00 0.00 0.00 2.52
674 686 5.744171 TGGCTAATTGAAGAGCAGTTCATA 58.256 37.500 4.54 0.00 40.64 2.15
722 757 4.122046 CCTCGATCTGCACACAATTCATA 58.878 43.478 0.00 0.00 0.00 2.15
866 902 3.791928 CTCGTCGTCGCCATCCTCG 62.792 68.421 0.00 0.00 36.96 4.63
940 976 0.779997 AAGTGAGTTGGGCCATCCTT 59.220 50.000 7.26 6.09 36.20 3.36
1133 1170 0.175760 TCTGATGAACGGCTGGTAGC 59.824 55.000 0.00 0.00 41.46 3.58
1196 1234 6.900390 GTCGAAGATGATGACCTTGAGGGTA 61.900 48.000 1.54 0.00 45.00 3.69
1251 1289 2.048127 GGCTTCGTCGTGCTTCCT 60.048 61.111 11.32 0.00 0.00 3.36
1273 1311 2.050350 CGACCCTACTCCTTGGCGA 61.050 63.158 0.00 0.00 0.00 5.54
1328 1367 6.430308 TCAACGCCTAAACCATAAACATGTTA 59.570 34.615 12.39 0.87 0.00 2.41
1441 1498 2.708861 ATGAGGTTACCACCACACTTCA 59.291 45.455 3.51 0.00 45.38 3.02
1462 1519 5.541101 TGTAGTAACCTCTTTGGCTAGTTGA 59.459 40.000 0.00 0.00 40.22 3.18
1483 1541 2.036089 TGTATGCAACGTCTGGTGTGTA 59.964 45.455 0.00 0.00 0.00 2.90
1536 1595 0.106521 GGTGTTTGGTTGCCTGCATT 59.893 50.000 0.00 0.00 0.00 3.56
1633 1692 5.532406 CCATCCAACCTGACTATACAAATGG 59.468 44.000 0.00 0.00 0.00 3.16
1640 1699 6.636454 ACTTTTCCATCCAACCTGACTATA 57.364 37.500 0.00 0.00 0.00 1.31
1645 1704 5.827797 GCATATACTTTTCCATCCAACCTGA 59.172 40.000 0.00 0.00 0.00 3.86
1721 1780 3.479269 GCCGGCTCTTTCGACGTG 61.479 66.667 22.15 0.00 0.00 4.49
1768 1832 0.600255 CGTGAGGGCGACACTTCTTT 60.600 55.000 0.00 0.00 36.29 2.52
1843 1925 9.935682 GAATGTGTATGTCGTGATCATTTATTT 57.064 29.630 0.00 0.00 0.00 1.40
1993 2103 2.338620 CGAACCGAGAGCACACCA 59.661 61.111 0.00 0.00 0.00 4.17
2032 2150 1.377987 GGCTTCAACCCCGCACATA 60.378 57.895 0.00 0.00 0.00 2.29
2042 2160 1.070758 TGAGAGTGGTCAGGCTTCAAC 59.929 52.381 0.00 0.00 0.00 3.18
2093 2224 1.086696 GCACACAACCTACGCATCAT 58.913 50.000 0.00 0.00 0.00 2.45
2237 2375 3.432051 CTGGGCCGAGATCGTGACC 62.432 68.421 9.58 8.22 37.94 4.02
2241 2379 2.123251 ATCCTGGGCCGAGATCGT 60.123 61.111 17.59 0.00 37.74 3.73


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

AutoCloner maintained by Alex Coulton.