Multiple sequence alignment - TraesCS6D01G146200

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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 TraesCS6D01G146200 chr6D 100.000 2675 0 0 1 2675 116954190 116951516 0.000000e+00 4940
1 TraesCS6D01G146200 chr6B 92.185 2751 100 48 1 2675 207156742 207154031 0.000000e+00 3783
2 TraesCS6D01G146200 chr6A 91.399 2395 105 44 1 2324 145135489 145133125 0.000000e+00 3188
3 TraesCS6D01G146200 chr6A 93.514 370 13 4 2309 2673 145133111 145132748 8.420000e-150 540
4 TraesCS6D01G146200 chr7B 78.014 282 42 16 1098 1370 646210283 646210013 2.760000e-35 159
5 TraesCS6D01G146200 chr7A 80.569 211 31 7 1098 1300 671483724 671483516 1.280000e-33 154
6 TraesCS6D01G146200 chr7D 77.305 282 44 16 1098 1370 579961746 579961476 5.970000e-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 TraesCS6D01G146200 chr6D 116951516 116954190 2674 True 4940 4940 100.0000 1 2675 1 chr6D.!!$R1 2674
1 TraesCS6D01G146200 chr6B 207154031 207156742 2711 True 3783 3783 92.1850 1 2675 1 chr6B.!!$R1 2674
2 TraesCS6D01G146200 chr6A 145132748 145135489 2741 True 1864 3188 92.4565 1 2673 2 chr6A.!!$R1 2672

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
388 424 1.327764 CGGCTAAATCTTTGCGTCTCC 59.672 52.381 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2486 1.445238 GCTGAGATCGATAGCCCGC 60.445 63.158 7.32 0.66 0.0 6.13 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
41 42 4.031765 GTGTAGTGTAGACATGCACATTCG 59.968 45.833 0.00 0.00 43.79 3.34
244 275 1.884579 GCCACGATATTCCCTCGTCTA 59.115 52.381 0.00 0.00 45.63 2.59
245 276 2.351544 GCCACGATATTCCCTCGTCTAC 60.352 54.545 0.00 0.00 45.63 2.59
386 422 1.369625 CCGGCTAAATCTTTGCGTCT 58.630 50.000 0.00 0.00 0.00 4.18
388 424 1.327764 CGGCTAAATCTTTGCGTCTCC 59.672 52.381 0.00 0.00 0.00 3.71
414 450 2.554462 TCTCGTTCACAAGAGACAGAGG 59.446 50.000 0.00 0.00 38.46 3.69
437 473 4.134187 CACGCGCGTGCTCGATTT 62.134 61.111 44.73 14.43 39.39 2.17
446 482 3.430862 GCTCGATTTGGCACGCCA 61.431 61.111 6.67 6.67 45.63 5.69
463 503 2.203015 ACAAGTGGACGTGCGCTT 60.203 55.556 27.39 27.39 0.00 4.68
465 505 3.036084 AAGTGGACGTGCGCTTCG 61.036 61.111 27.39 19.87 0.00 3.79
518 558 4.776322 TGACCGGCGGCCATGAAG 62.776 66.667 28.71 1.43 0.00 3.02
837 900 4.760047 CCAGAAGGCGACCCCACG 62.760 72.222 0.00 0.00 35.39 4.94
1248 1312 0.034863 ACACCGACACCACCAACTTT 60.035 50.000 0.00 0.00 0.00 2.66
1479 1549 2.820479 CAGCAGCAGAGCCAGCTC 60.820 66.667 11.78 11.78 41.14 4.09
1735 1809 7.719871 TTAAGGTACACTTAATCAGAGAGCT 57.280 36.000 10.65 0.00 44.55 4.09
1738 1812 6.664714 AGGTACACTTAATCAGAGAGCTAGA 58.335 40.000 0.00 0.00 0.00 2.43
1754 1845 3.766591 AGCTAGAGAGAACAGCAAGCTTA 59.233 43.478 0.00 0.00 35.39 3.09
1866 1969 7.841282 AGGCTAGCTGATTAAGACAGTAATA 57.159 36.000 15.72 5.05 37.64 0.98
1868 1971 8.145122 AGGCTAGCTGATTAAGACAGTAATAAC 58.855 37.037 15.72 0.00 37.64 1.89
1889 1992 6.862469 AACTAGTTGTAATAGTAGCCACCA 57.138 37.500 7.48 0.00 33.15 4.17
1970 2076 5.857822 ATAGTTTTAGCTTTCGGTGTGTC 57.142 39.130 0.00 0.00 0.00 3.67
2060 2171 0.762418 TCTCGGAAGCAAAGTTGGGA 59.238 50.000 0.00 0.00 0.00 4.37
2264 2382 4.933330 TCTGACTAACATATTCGAGTGCC 58.067 43.478 0.00 0.00 0.00 5.01
2457 2608 0.668535 GGCAGGTCAAAGTCACAACC 59.331 55.000 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.045142 TCCCACTTGGACGACGAC 58.955 61.111 0.00 0.00 38.61 4.34
244 275 0.899019 GGGCGAAGGAAGAAGAGAGT 59.101 55.000 0.00 0.00 0.00 3.24
245 276 0.176910 GGGGCGAAGGAAGAAGAGAG 59.823 60.000 0.00 0.00 0.00 3.20
289 325 5.471456 ACATGCGTTCTTTTCATCTTCTCTT 59.529 36.000 0.00 0.00 0.00 2.85
290 326 4.999950 ACATGCGTTCTTTTCATCTTCTCT 59.000 37.500 0.00 0.00 0.00 3.10
291 327 5.288543 ACATGCGTTCTTTTCATCTTCTC 57.711 39.130 0.00 0.00 0.00 2.87
292 328 5.009010 ACAACATGCGTTCTTTTCATCTTCT 59.991 36.000 0.00 0.00 31.13 2.85
293 329 5.116074 CACAACATGCGTTCTTTTCATCTTC 59.884 40.000 0.00 0.00 31.13 2.87
386 422 0.530744 CTTGTGAACGAGATCCGGGA 59.469 55.000 0.00 0.00 43.93 5.14
388 424 1.472878 TCTCTTGTGAACGAGATCCGG 59.527 52.381 0.00 0.00 43.93 5.14
437 473 4.182433 TCCACTTGTGGCGTGCCA 62.182 61.111 10.06 10.06 45.02 4.92
446 482 2.203015 AAGCGCACGTCCACTTGT 60.203 55.556 11.47 0.00 0.00 3.16
518 558 4.210304 CTCGCCGCAAGCTAACGC 62.210 66.667 2.89 0.00 40.39 4.84
542 595 4.052229 CGGAAGCACGACCGTCCT 62.052 66.667 0.00 0.00 43.53 3.85
648 703 2.372172 CCTCCCCTACTCTCTCTCTCTC 59.628 59.091 0.00 0.00 0.00 3.20
649 704 2.294263 ACCTCCCCTACTCTCTCTCTCT 60.294 54.545 0.00 0.00 0.00 3.10
949 1013 2.567985 GGAGGAGTAGAGTTCTCGAGG 58.432 57.143 13.56 0.00 33.26 4.63
1391 1455 3.642778 AACGACATCACGGCCGAGG 62.643 63.158 35.90 23.43 37.61 4.63
1735 1809 3.766591 AGCTAAGCTTGCTGTTCTCTCTA 59.233 43.478 18.58 0.00 39.56 2.43
1866 1969 6.211986 TGTGGTGGCTACTATTACAACTAGTT 59.788 38.462 1.12 1.12 31.96 2.24
1868 1971 6.040878 GTGTGGTGGCTACTATTACAACTAG 58.959 44.000 0.00 0.00 0.00 2.57
1888 1991 3.206150 AGCTGAACCTGTAAAGTGTGTG 58.794 45.455 0.00 0.00 0.00 3.82
1889 1992 3.560636 AGCTGAACCTGTAAAGTGTGT 57.439 42.857 0.00 0.00 0.00 3.72
2060 2171 1.747325 GCATGGTGGTGGTTGCAGTT 61.747 55.000 0.00 0.00 35.22 3.16
2264 2382 2.624636 GGTAAGGAACACGGTACATGG 58.375 52.381 0.00 0.00 0.00 3.66
2324 2470 3.521995 CGCAGGTCAGTCATCAGTT 57.478 52.632 0.00 0.00 0.00 3.16
2340 2486 1.445238 GCTGAGATCGATAGCCCGC 60.445 63.158 7.32 0.66 0.00 6.13
2392 2539 0.614697 TCAATCGAGCTCCCAGTGGA 60.615 55.000 11.95 0.00 38.75 4.02
2397 2544 0.904649 ATGTGTCAATCGAGCTCCCA 59.095 50.000 8.47 0.00 0.00 4.37
2398 2545 1.293924 CATGTGTCAATCGAGCTCCC 58.706 55.000 8.47 0.00 0.00 4.30
2472 2623 1.328279 GGGTTGGACTTTTCCCAGTG 58.672 55.000 0.00 0.00 42.01 3.66


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

AutoCloner maintained by Alex Coulton.