Multiple sequence alignment - TraesCS6A01G267900

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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 TraesCS6A01G267900 chr6A 100.000 3233 0 0 1 3233 494425300 494428532 0 5971
1 TraesCS6A01G267900 chr6A 96.786 3236 100 4 1 3233 554915088 554918322 0 5397
2 TraesCS6A01G267900 chr3A 97.681 3234 72 3 1 3233 745750330 745753561 0 5553
3 TraesCS6A01G267900 chr3A 97.186 3234 83 5 1 3233 711578029 711574803 0 5461
4 TraesCS6A01G267900 chr2A 97.279 3234 83 4 1 3233 733070589 733073818 0 5480
5 TraesCS6A01G267900 chr2A 96.969 3233 89 4 1 3233 58510412 58507189 0 5419
6 TraesCS6A01G267900 chr1A 97.250 3236 83 6 1 3233 21073548 21070316 0 5478
7 TraesCS6A01G267900 chr1A 96.419 3239 106 8 1 3233 365631558 365634792 0 5330
8 TraesCS6A01G267900 chr7A 96.293 3237 108 8 1 3233 675357138 675353910 0 5302
9 TraesCS6A01G267900 chr5A 96.232 3238 113 8 1 3233 33905187 33908420 0 5295


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 TraesCS6A01G267900 chr6A 494425300 494428532 3232 False 5971 5971 100.000 1 3233 1 chr6A.!!$F1 3232
1 TraesCS6A01G267900 chr6A 554915088 554918322 3234 False 5397 5397 96.786 1 3233 1 chr6A.!!$F2 3232
2 TraesCS6A01G267900 chr3A 745750330 745753561 3231 False 5553 5553 97.681 1 3233 1 chr3A.!!$F1 3232
3 TraesCS6A01G267900 chr3A 711574803 711578029 3226 True 5461 5461 97.186 1 3233 1 chr3A.!!$R1 3232
4 TraesCS6A01G267900 chr2A 733070589 733073818 3229 False 5480 5480 97.279 1 3233 1 chr2A.!!$F1 3232
5 TraesCS6A01G267900 chr2A 58507189 58510412 3223 True 5419 5419 96.969 1 3233 1 chr2A.!!$R1 3232
6 TraesCS6A01G267900 chr1A 21070316 21073548 3232 True 5478 5478 97.250 1 3233 1 chr1A.!!$R1 3232
7 TraesCS6A01G267900 chr1A 365631558 365634792 3234 False 5330 5330 96.419 1 3233 1 chr1A.!!$F1 3232
8 TraesCS6A01G267900 chr7A 675353910 675357138 3228 True 5302 5302 96.293 1 3233 1 chr7A.!!$R1 3232
9 TraesCS6A01G267900 chr5A 33905187 33908420 3233 False 5295 5295 96.232 1 3233 1 chr5A.!!$F1 3232

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
384 389 3.020274 TGTAGTGCAACAGGAAAAGCAA 58.980 40.909 0.0 0.0 41.43 3.91 F
1068 1079 2.440627 TGATATGGATCAGCAGCAACCT 59.559 45.455 0.0 0.0 37.15 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1406 1417 0.682209 ACCCATCCGTAGTGCGTAGT 60.682 55.0 0.0 0.0 39.32 2.73 R
2441 2454 0.180406 ACCGTCCACCCAGAATATGC 59.820 55.0 0.0 0.0 0.00 3.14 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
384 389 3.020274 TGTAGTGCAACAGGAAAAGCAA 58.980 40.909 0.00 0.00 41.43 3.91
643 648 6.455360 TGTGCAGAAAAATCTGAAAAGAGT 57.545 33.333 9.89 0.00 39.99 3.24
650 655 8.193438 CAGAAAAATCTGAAAAGAGTTCCTTGT 58.807 33.333 0.00 0.00 39.99 3.16
835 843 6.604735 AAAGATTATGCTACGGTCATGTTC 57.395 37.500 0.00 0.00 0.00 3.18
1068 1079 2.440627 TGATATGGATCAGCAGCAACCT 59.559 45.455 0.00 0.00 37.15 3.50
1091 1102 6.322201 CCTAGCATACAACAAGGAAATTGGAT 59.678 38.462 0.00 0.00 43.68 3.41
1406 1417 7.446931 TCAAATTGCTAAGGATCACTACAACAA 59.553 33.333 0.00 0.00 0.00 2.83
1718 1729 3.300009 CGAAAATGTTGGTGAAGCTGAC 58.700 45.455 0.00 0.00 0.00 3.51
1871 1882 9.102757 CATCTTGTATAACTGCAACTTGACTAT 57.897 33.333 0.00 0.00 0.00 2.12
2003 2014 1.541588 GTGTCCAACTTCCCATGCTTC 59.458 52.381 0.00 0.00 0.00 3.86
2115 2126 5.862678 TTTTAAAAAGGTGCAGCTAGGTT 57.137 34.783 20.51 15.15 0.00 3.50
2230 2243 8.367156 ACTGTTTGTTTTTGTATTATGCAGGAT 58.633 29.630 0.00 0.00 0.00 3.24
2460 2473 0.180406 GCATATTCTGGGTGGACGGT 59.820 55.000 0.00 0.00 0.00 4.83
2569 2582 3.211045 GCGCCCTTCATAGGAATAAACA 58.789 45.455 0.00 0.00 45.05 2.83
2680 2693 2.106511 GCTATGGATGGCAAACCTCCTA 59.893 50.000 13.62 0.00 35.44 2.94
2720 2733 0.745845 GATGGTGCGATGAGGCAGTT 60.746 55.000 0.00 0.00 44.93 3.16
2990 3003 3.386486 CGTGCTACTTCAAACACAGGTA 58.614 45.455 0.00 0.00 33.23 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 135 4.463891 CAGTTGGCCAGGATACATTTTCTT 59.536 41.667 5.11 0.00 41.41 2.52
384 389 6.267471 TCATTAGCCATGGACAAAAGTTCTTT 59.733 34.615 18.40 0.00 33.07 2.52
643 648 3.007473 AGGTTTCCGTTTCACAAGGAA 57.993 42.857 0.00 0.00 41.76 3.36
650 655 8.479689 TGTAATGATCTATAGGTTTCCGTTTCA 58.520 33.333 0.00 0.00 0.00 2.69
1068 1079 8.271458 TCTATCCAATTTCCTTGTTGTATGCTA 58.729 33.333 0.00 0.00 32.61 3.49
1091 1102 8.525316 TGTAGTAAACAGATCGACCATTTTCTA 58.475 33.333 0.00 0.00 33.01 2.10
1406 1417 0.682209 ACCCATCCGTAGTGCGTAGT 60.682 55.000 0.00 0.00 39.32 2.73
1584 1595 5.770919 TCTTCTTCCATCTCCTCATCACTA 58.229 41.667 0.00 0.00 0.00 2.74
1669 1680 5.474532 TGCATTCAGTCTGCTTTATTGTCTT 59.525 36.000 0.00 0.00 40.34 3.01
1718 1729 2.429058 CCTCCCATCGCCCATCTG 59.571 66.667 0.00 0.00 0.00 2.90
1871 1882 6.445786 AGGGATATAGAAAAACACCACACCTA 59.554 38.462 0.00 0.00 0.00 3.08
2003 2014 7.383102 AGAAGCACCAAAAGTGATATACAAG 57.617 36.000 0.00 0.00 46.71 3.16
2088 2099 3.862845 AGCTGCACCTTTTTAAAAACACG 59.137 39.130 9.31 0.85 0.00 4.49
2115 2126 5.066375 CAGAACATAATCGCAGGAAATGGAA 59.934 40.000 0.00 0.00 0.00 3.53
2230 2243 4.208746 TCTGCCATTACATGCATCATTCA 58.791 39.130 0.00 0.00 36.79 2.57
2441 2454 0.180406 ACCGTCCACCCAGAATATGC 59.820 55.000 0.00 0.00 0.00 3.14
2448 2461 0.391263 GAGCTAAACCGTCCACCCAG 60.391 60.000 0.00 0.00 0.00 4.45
2569 2582 2.429610 GCATGAAAGATTGGCCATGTCT 59.570 45.455 6.09 11.12 38.78 3.41
2680 2693 3.007940 TCCTGATCGGTGATGAAGTTGTT 59.992 43.478 0.00 0.00 0.00 2.83
2720 2733 7.147391 TGGTGGTTGGAAAGATGCTCTATATTA 60.147 37.037 0.00 0.00 0.00 0.98
2990 3003 0.494095 AGACTGGAGGAAGGGGAAGT 59.506 55.000 0.00 0.00 0.00 3.01
3129 3143 5.048782 GTGTTCTGTCCTGTAATCATTGCAA 60.049 40.000 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.