Multiple sequence alignment - TraesCS3B01G187900

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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 TraesCS3B01G187900 chr3B 100.000 2471 0 0 1 2471 201535252 201532782 0 4564
1 TraesCS3B01G187900 chr5D 98.826 2471 27 1 1 2471 503226441 503223973 0 4401
2 TraesCS3B01G187900 chr5D 98.544 2472 33 2 1 2471 503270103 503272572 0 4362
3 TraesCS3B01G187900 chr5D 98.422 2472 37 2 1 2471 503236758 503234288 0 4348
4 TraesCS3B01G187900 chr3A 98.624 2471 31 2 1 2471 66009400 66011867 0 4372
5 TraesCS3B01G187900 chr1D 98.180 2472 44 1 1 2471 254386863 254389334 0 4314
6 TraesCS3B01G187900 chrUn 98.098 2471 43 2 1 2471 216510385 216512851 0 4300
7 TraesCS3B01G187900 chrUn 98.098 2471 43 2 1 2471 286272998 286270532 0 4300
8 TraesCS3B01G187900 chr4D 97.977 2472 44 4 1 2471 177441220 177443686 0 4283
9 TraesCS3B01G187900 chr1B 97.855 2471 47 4 1 2471 633745676 633748140 0 4265


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 TraesCS3B01G187900 chr3B 201532782 201535252 2470 True 4564 4564 100.000 1 2471 1 chr3B.!!$R1 2470
1 TraesCS3B01G187900 chr5D 503223973 503226441 2468 True 4401 4401 98.826 1 2471 1 chr5D.!!$R1 2470
2 TraesCS3B01G187900 chr5D 503270103 503272572 2469 False 4362 4362 98.544 1 2471 1 chr5D.!!$F1 2470
3 TraesCS3B01G187900 chr5D 503234288 503236758 2470 True 4348 4348 98.422 1 2471 1 chr5D.!!$R2 2470
4 TraesCS3B01G187900 chr3A 66009400 66011867 2467 False 4372 4372 98.624 1 2471 1 chr3A.!!$F1 2470
5 TraesCS3B01G187900 chr1D 254386863 254389334 2471 False 4314 4314 98.180 1 2471 1 chr1D.!!$F1 2470
6 TraesCS3B01G187900 chrUn 216510385 216512851 2466 False 4300 4300 98.098 1 2471 1 chrUn.!!$F1 2470
7 TraesCS3B01G187900 chrUn 286270532 286272998 2466 True 4300 4300 98.098 1 2471 1 chrUn.!!$R1 2470
8 TraesCS3B01G187900 chr4D 177441220 177443686 2466 False 4283 4283 97.977 1 2471 1 chr4D.!!$F1 2470
9 TraesCS3B01G187900 chr1B 633745676 633748140 2464 False 4265 4265 97.855 1 2471 1 chr1B.!!$F1 2470

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
104 105 5.313712 AGGTGAAAATCTCATGTACGGTTT 58.686 37.5 0.0 0.0 36.14 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 1910 2.15924 TCAGAGGTTGAATCGGTCATCG 60.159 50.0 0.0 0.0 35.7 3.84 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
104 105 5.313712 AGGTGAAAATCTCATGTACGGTTT 58.686 37.500 0.00 0.0 36.14 3.27
342 343 5.511545 GCATTATTCGAGGAACCCTAGATGT 60.512 44.000 0.00 0.0 35.34 3.06
457 458 5.643777 GCTAGAAACATGTGAAGTGTATGGT 59.356 40.000 0.00 0.0 0.00 3.55
644 646 6.702723 TCGAAATACCTCGACTTTTTCAGAAA 59.297 34.615 0.00 0.0 42.69 2.52
1234 1237 9.853177 CTCCCAATATAGGAGTAAAAACAAGAT 57.147 33.333 11.89 0.0 45.05 2.40
1398 1401 2.085343 ATGCTGCCAAAGGGAGTGGT 62.085 55.000 6.44 0.0 43.30 4.16
1674 1677 8.632906 AGAATCTTATGGAAATAGCATGGAAG 57.367 34.615 0.00 0.0 0.00 3.46
1685 1688 7.285401 GGAAATAGCATGGAAGAAGGTTTGATA 59.715 37.037 0.00 0.0 0.00 2.15
1709 1712 6.003950 ACTATTCATGGGGATTCCGTAAATG 58.996 40.000 0.00 0.0 38.76 2.32
1906 1910 7.981789 CCTAATTTTTGGCCTAATTCTTCTTCC 59.018 37.037 3.32 0.0 0.00 3.46
1912 1916 3.810386 GGCCTAATTCTTCTTCCGATGAC 59.190 47.826 0.00 0.0 0.00 3.06
2000 2004 3.012934 AGCATAACGGCCCTATTGTTT 57.987 42.857 0.00 0.0 0.00 2.83
2389 2393 2.025887 GGCTATATGGTTCATCTGGGGG 60.026 54.545 0.00 0.0 0.00 5.40
2414 2421 4.637977 GGGAGATCGAGCTTCAAGAAATTT 59.362 41.667 11.82 0.0 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 3.975312 TCACCCTTACTGTCCCTTTACAA 59.025 43.478 0.0 0.0 0.00 2.41
342 343 3.644823 TGACGATTCTTTACTGCGACAA 58.355 40.909 0.0 0.0 0.00 3.18
644 646 3.695830 TTGCTATTTGACTCGGACCTT 57.304 42.857 0.0 0.0 0.00 3.50
748 750 1.204786 TCCTTTTCCCGCCAGGATCA 61.205 55.000 0.0 0.0 46.94 2.92
755 757 1.076014 TTTCCCTCCTTTTCCCGCC 59.924 57.895 0.0 0.0 0.00 6.13
1674 1677 6.601332 TCCCCATGAATAGTATCAAACCTTC 58.399 40.000 0.0 0.0 32.06 3.46
1685 1688 5.640158 TTTACGGAATCCCCATGAATAGT 57.360 39.130 0.0 0.0 34.14 2.12
1709 1712 6.836577 TTGTTTCGATTTTTGAAATGGGAC 57.163 33.333 0.0 0.0 37.62 4.46
1906 1910 2.159240 TCAGAGGTTGAATCGGTCATCG 60.159 50.000 0.0 0.0 35.70 3.84
1912 1916 5.412594 TCTTTTTGATCAGAGGTTGAATCGG 59.587 40.000 0.0 0.0 39.77 4.18
2000 2004 7.841282 AATTATAGGTTCTTCTCTCCATCGA 57.159 36.000 0.0 0.0 0.00 3.59
2289 2293 8.941995 TTCATAGTAGCCTCATTAGACTGTAT 57.058 34.615 0.0 0.0 0.00 2.29
2389 2393 0.105778 CTTGAAGCTCGATCTCCCCC 59.894 60.000 0.0 0.0 0.00 5.40
2390 2394 1.115467 TCTTGAAGCTCGATCTCCCC 58.885 55.000 0.0 0.0 0.00 4.81
2414 2421 7.731882 TTTGTGTATTGATAAGACCGTTCAA 57.268 32.000 0.0 0.0 34.18 2.69


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

AutoCloner maintained by Alex Coulton.