Multiple sequence alignment - TraesCS6B01G232500

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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 TraesCS6B01G232500 chr6B 100.000 2600 0 0 1 2600 388129948 388127349 0 4802
1 TraesCS6B01G232500 chrUn 97.889 2605 50 3 1 2600 223706934 223704330 0 4501
2 TraesCS6B01G232500 chr1B 97.849 2603 53 3 1 2600 683734142 683731540 0 4494
3 TraesCS6B01G232500 chr1B 97.391 2606 60 5 1 2600 583536771 583534168 0 4429
4 TraesCS6B01G232500 chr2A 97.812 2605 51 4 1 2600 605912877 605910274 0 4490
5 TraesCS6B01G232500 chr2A 97.310 2602 68 2 1 2600 563256642 563259243 0 4416
6 TraesCS6B01G232500 chr7B 97.734 2604 55 3 1 2600 698140160 698142763 0 4479
7 TraesCS6B01G232500 chr5B 97.463 2602 63 3 1 2600 713082218 713079618 0 4436
8 TraesCS6B01G232500 chr3B 97.390 2605 62 4 1 2600 92142924 92145527 0 4429
9 TraesCS6B01G232500 chr3B 97.199 2606 64 6 1 2600 92261856 92264458 0 4399


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 TraesCS6B01G232500 chr6B 388127349 388129948 2599 True 4802 4802 100.000 1 2600 1 chr6B.!!$R1 2599
1 TraesCS6B01G232500 chrUn 223704330 223706934 2604 True 4501 4501 97.889 1 2600 1 chrUn.!!$R1 2599
2 TraesCS6B01G232500 chr1B 683731540 683734142 2602 True 4494 4494 97.849 1 2600 1 chr1B.!!$R2 2599
3 TraesCS6B01G232500 chr1B 583534168 583536771 2603 True 4429 4429 97.391 1 2600 1 chr1B.!!$R1 2599
4 TraesCS6B01G232500 chr2A 605910274 605912877 2603 True 4490 4490 97.812 1 2600 1 chr2A.!!$R1 2599
5 TraesCS6B01G232500 chr2A 563256642 563259243 2601 False 4416 4416 97.310 1 2600 1 chr2A.!!$F1 2599
6 TraesCS6B01G232500 chr7B 698140160 698142763 2603 False 4479 4479 97.734 1 2600 1 chr7B.!!$F1 2599
7 TraesCS6B01G232500 chr5B 713079618 713082218 2600 True 4436 4436 97.463 1 2600 1 chr5B.!!$R1 2599
8 TraesCS6B01G232500 chr3B 92142924 92145527 2603 False 4429 4429 97.390 1 2600 1 chr3B.!!$F1 2599
9 TraesCS6B01G232500 chr3B 92261856 92264458 2602 False 4399 4399 97.199 1 2600 1 chr3B.!!$F2 2599

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
291 292 1.553248 CGGATAACAACAGAGTGGGGA 59.447 52.381 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2069 1.068472 CACGACCTCTCTTTGCGTACT 60.068 52.381 0.0 0.0 33.45 2.73 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
32 33 1.599047 CCACGAGAGCCCAATCACT 59.401 57.895 0.00 0.00 0.00 3.41
53 54 3.258971 AGAGGCTCATACAGAAAGCAC 57.741 47.619 18.26 0.00 37.78 4.40
147 148 6.422100 CCAATCTTCTCGATCGAACATATTGT 59.578 38.462 25.30 8.28 0.00 2.71
159 160 9.416794 GATCGAACATATTGTCATCAATACTCT 57.583 33.333 0.00 0.00 45.45 3.24
291 292 1.553248 CGGATAACAACAGAGTGGGGA 59.447 52.381 0.00 0.00 0.00 4.81
366 367 6.403200 GCTCATATTGGTGACGTTATTGTTGT 60.403 38.462 0.00 0.00 0.00 3.32
429 430 4.576879 TCAGACAGAAGTAAGACGAGCTA 58.423 43.478 0.00 0.00 0.00 3.32
462 463 6.074676 ACGTACATGTAAAGAACTCAAACGTC 60.075 38.462 7.25 0.00 33.22 4.34
547 548 1.798223 CTCGAGTTTTTGGTGCGATCA 59.202 47.619 3.62 0.00 0.00 2.92
566 567 4.451629 TCACTCGGGAATTGAGACTTAC 57.548 45.455 0.00 0.00 36.93 2.34
895 896 3.695060 TCCTGGTCTTCGAACTAGTCATC 59.305 47.826 0.00 0.00 0.00 2.92
931 932 5.190330 ACATAGGTACCCTTTTTCGGTATGT 59.810 40.000 8.74 9.76 38.14 2.29
958 959 5.141568 GCGAACACTTTCATTTTTAGCGTA 58.858 37.500 0.00 0.00 0.00 4.42
1045 1046 7.723616 TCTTCTTTTTCATTACTTCCATGGTCA 59.276 33.333 12.58 0.00 0.00 4.02
1051 1052 1.595311 TACTTCCATGGTCATGCCCT 58.405 50.000 12.58 0.00 37.49 5.19
1107 1108 2.159226 CGTCAGTAGAGATGTTCCCACC 60.159 54.545 0.00 0.00 0.00 4.61
1206 1207 6.131972 AGGAAATTCATACGATCCATGGAT 57.868 37.500 27.66 27.66 37.59 3.41
1311 1312 5.622770 ATGCTTTATTTCGTTTCGTTCCT 57.377 34.783 0.00 0.00 0.00 3.36
1391 1392 3.259064 GCGGTCTGCTCTGTTTACAATA 58.741 45.455 0.00 0.00 41.73 1.90
1397 1398 6.426937 GGTCTGCTCTGTTTACAATACTTTCA 59.573 38.462 0.00 0.00 0.00 2.69
1570 1571 1.065997 TGGGCCTATAGCTTTCCCCC 61.066 60.000 4.53 0.00 43.05 5.40
1598 1607 1.067364 TCGTCGAGTGGTGCTTGTTTA 59.933 47.619 0.00 0.00 0.00 2.01
1775 1785 0.179084 CGACCCGATGGCTTATGTGT 60.179 55.000 0.00 0.00 33.59 3.72
1790 1800 3.093172 TGTGACCTGTGGCCCACA 61.093 61.111 17.22 17.22 42.45 4.17
1916 1926 6.669154 AGGAAGATGGCTTATTCCAAAATTCA 59.331 34.615 23.60 0.00 44.11 2.57
2549 2560 3.193267 GCATACATTTTCTTGCTGGGTCA 59.807 43.478 0.00 0.00 32.41 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.026744 AGTGCTTTCTGTATGAGCCTCTA 58.973 43.478 0.00 0.00 35.59 2.43
53 54 3.087031 CAATATTGGGCTATGGGCTGAG 58.913 50.000 7.62 0.00 41.46 3.35
147 148 4.889409 GGCCATGGAAAAGAGTATTGATGA 59.111 41.667 18.40 0.00 0.00 2.92
159 160 0.894141 CCGTGAATGGCCATGGAAAA 59.106 50.000 21.63 0.00 44.12 2.29
366 367 3.255642 GGGCACTGCTTCTTTGATTACAA 59.744 43.478 0.00 0.00 0.00 2.41
462 463 8.905103 TCATATCGTATTATCATACCGTTGTG 57.095 34.615 0.00 0.00 32.79 3.33
547 548 3.087031 TCGTAAGTCTCAATTCCCGAGT 58.913 45.455 0.00 0.00 39.48 4.18
566 567 8.244494 TCATGAGACTCTTTTAGTGAAATTCG 57.756 34.615 3.68 0.00 39.07 3.34
745 746 5.615925 AGTAGATGCTATTCGAACCCTTT 57.384 39.130 0.00 0.00 0.00 3.11
895 896 1.750193 ACCTATGTTGCCGACCATTG 58.250 50.000 0.00 0.00 0.00 2.82
931 932 5.231147 GCTAAAAATGAAAGTGTTCGCAACA 59.769 36.000 0.00 0.00 39.52 3.33
1107 1108 1.089920 CATTGGAAGAAGAGGCACCG 58.910 55.000 0.00 0.00 0.00 4.94
1197 1198 4.891756 CCACTTTTTGCTCTATCCATGGAT 59.108 41.667 29.66 29.66 38.54 3.41
1206 1207 3.882888 CCAACACTCCACTTTTTGCTCTA 59.117 43.478 0.00 0.00 0.00 2.43
1391 1392 8.308207 GTGGTAAAGAGAAGAGAGTATGAAAGT 58.692 37.037 0.00 0.00 0.00 2.66
1397 1398 4.201930 CGCGTGGTAAAGAGAAGAGAGTAT 60.202 45.833 0.00 0.00 0.00 2.12
1775 1785 3.884774 GGTGTGGGCCACAGGTCA 61.885 66.667 38.36 15.05 45.43 4.02
1790 1800 6.064717 GCCCTGAACAAATAGAATATGAGGT 58.935 40.000 0.00 0.00 0.00 3.85
1795 1805 4.398319 CCCGCCCTGAACAAATAGAATAT 58.602 43.478 0.00 0.00 0.00 1.28
1916 1926 4.956075 CCAAAGTTCCTTACCCTTATGCAT 59.044 41.667 3.79 3.79 0.00 3.96
2059 2069 1.068472 CACGACCTCTCTTTGCGTACT 60.068 52.381 0.00 0.00 33.45 2.73
2294 2305 0.107848 CCCCACGTCCGCTTTTATCT 60.108 55.000 0.00 0.00 0.00 1.98
2418 2429 8.613060 AATAGAATCTAATATGTGCAGTGGTG 57.387 34.615 0.00 0.00 0.00 4.17
2421 2432 8.877779 GGCTAATAGAATCTAATATGTGCAGTG 58.122 37.037 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.