Multiple sequence alignment - TraesCS3A01G431200

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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 TraesCS3A01G431200 chr3A 100.000 3018 0 0 1 3018 672911757 672908740 0.000000e+00 5574
1 TraesCS3A01G431200 chrUn 98.377 3020 43 6 1 3018 93411379 93408364 0.000000e+00 5301
2 TraesCS3A01G431200 chrUn 98.236 2948 49 3 72 3018 216520280 216517335 0.000000e+00 5153
3 TraesCS3A01G431200 chr5D 98.377 3019 46 3 1 3018 503216470 503219486 0.000000e+00 5301
4 TraesCS3A01G431200 chr5D 97.978 2720 50 5 301 3018 6187492 6190208 0.000000e+00 4713
5 TraesCS3A01G431200 chr5D 97.977 2719 51 4 301 3018 503279673 503276958 0.000000e+00 4713
6 TraesCS3A01G431200 chr3B 98.245 3020 48 5 1 3018 201525276 201528292 0.000000e+00 5278
7 TraesCS3A01G431200 chr3B 96.634 505 16 1 1 505 395369454 395369957 0.000000e+00 837
8 TraesCS3A01G431200 chr3B 95.735 211 9 0 1 211 416932673 416932463 1.040000e-89 340
9 TraesCS3A01G431200 chr6D 98.338 2949 45 4 72 3018 168253248 168256194 0.000000e+00 5171
10 TraesCS3A01G431200 chr5A 97.084 3018 83 5 1 3016 619264622 619267636 0.000000e+00 5081
11 TraesCS3A01G431200 chr3D 98.235 2719 41 6 301 3018 589280989 589278277 0.000000e+00 4748
12 TraesCS3A01G431200 chr2A 98.671 301 4 0 1 301 726910783 726910483 4.430000e-148 534


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 TraesCS3A01G431200 chr3A 672908740 672911757 3017 True 5574 5574 100.000 1 3018 1 chr3A.!!$R1 3017
1 TraesCS3A01G431200 chrUn 93408364 93411379 3015 True 5301 5301 98.377 1 3018 1 chrUn.!!$R1 3017
2 TraesCS3A01G431200 chrUn 216517335 216520280 2945 True 5153 5153 98.236 72 3018 1 chrUn.!!$R2 2946
3 TraesCS3A01G431200 chr5D 503216470 503219486 3016 False 5301 5301 98.377 1 3018 1 chr5D.!!$F2 3017
4 TraesCS3A01G431200 chr5D 6187492 6190208 2716 False 4713 4713 97.978 301 3018 1 chr5D.!!$F1 2717
5 TraesCS3A01G431200 chr5D 503276958 503279673 2715 True 4713 4713 97.977 301 3018 1 chr5D.!!$R1 2717
6 TraesCS3A01G431200 chr3B 201525276 201528292 3016 False 5278 5278 98.245 1 3018 1 chr3B.!!$F1 3017
7 TraesCS3A01G431200 chr3B 395369454 395369957 503 False 837 837 96.634 1 505 1 chr3B.!!$F2 504
8 TraesCS3A01G431200 chr6D 168253248 168256194 2946 False 5171 5171 98.338 72 3018 1 chr6D.!!$F1 2946
9 TraesCS3A01G431200 chr5A 619264622 619267636 3014 False 5081 5081 97.084 1 3016 1 chr5A.!!$F1 3015
10 TraesCS3A01G431200 chr3D 589278277 589280989 2712 True 4748 4748 98.235 301 3018 1 chr3D.!!$R1 2717

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
93 94 3.893813 AGTTTCCTCGTAGTAACACCAGT 59.106 43.478 0.00 0.00 0.00 4.00 F
1107 1114 2.091775 ACACTTAGATCCGGCTCTACCT 60.092 50.000 14.52 0.18 35.61 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1739 0.817654 AGCGCCCCTTATTTCAAAGC 59.182 50.0 2.29 0.00 0.00 3.51 R
2272 2279 1.846712 TTGATCCATGGACGGCACCA 61.847 55.0 18.99 5.68 44.41 4.17 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
88 89 7.218228 TCATAACAGTTTCCTCGTAGTAACA 57.782 36.000 0.00 0.00 0.00 2.41
93 94 3.893813 AGTTTCCTCGTAGTAACACCAGT 59.106 43.478 0.00 0.00 0.00 4.00
185 186 6.104665 TCTCTCGAACTTAAGTAGACGATCA 58.895 40.000 22.74 15.53 36.40 2.92
288 289 9.990868 AACTTGTCATAAATAAGGTTATTCCCT 57.009 29.630 0.00 0.00 36.75 4.20
616 620 5.972935 TGATGAGCTACAAAAGGATTCGTA 58.027 37.500 0.00 0.00 0.00 3.43
646 650 3.929610 GTGTCACAGCTGATTACTCCTTC 59.070 47.826 23.35 0.00 0.00 3.46
686 691 6.845908 AGTGGCATTCTATGTCCAATATCTT 58.154 36.000 0.00 0.00 37.89 2.40
891 897 8.403236 GCAATTTTCCATATTCCTAGTTACGTT 58.597 33.333 0.00 0.00 0.00 3.99
1107 1114 2.091775 ACACTTAGATCCGGCTCTACCT 60.092 50.000 14.52 0.18 35.61 3.08
1679 1686 5.503002 GGGGTCTTAATTACCACTGCTTAA 58.497 41.667 8.85 0.00 37.44 1.85
1732 1739 1.108776 TGAATAACCCGTCCTCCTCG 58.891 55.000 0.00 0.00 0.00 4.63
1741 1748 1.676014 CCGTCCTCCTCGCTTTGAAAT 60.676 52.381 0.00 0.00 0.00 2.17
1856 1863 2.812591 CTGAACTCAATCACTTGCTGCT 59.187 45.455 0.00 0.00 32.11 4.24
1936 1943 5.100259 GTGATCGATTTCTAGGTTTCGTCA 58.900 41.667 0.00 8.49 33.52 4.35
2272 2279 5.562635 TGGAATTACGACCTTTACCACAAT 58.437 37.500 0.00 0.00 0.00 2.71
2437 2447 5.291905 AGAAGTGGAATAGAATAACCCGG 57.708 43.478 0.00 0.00 0.00 5.73
2509 2520 9.508721 AATAGGTCCTATTCTTCTACCTTTTCT 57.491 33.333 17.17 0.00 40.89 2.52
2715 2726 5.953571 TCCTATGCTCTGAGTTCCAGTATA 58.046 41.667 6.53 0.00 43.38 1.47
2817 2828 2.830923 AGATTCCATGGATAGAGAGCCG 59.169 50.000 17.06 0.00 31.83 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 3.322254 AGTTCTTGACGAGATTCACTGGT 59.678 43.478 0.00 0.00 40.12 4.00
93 94 5.463392 CACAAAGAGTTCTTGACGAGATTCA 59.537 40.000 0.00 0.00 36.12 2.57
288 289 9.528489 AGATTCAAAATAAAGTAAAGGTAGGCA 57.472 29.630 0.00 0.00 0.00 4.75
623 627 2.899900 AGGAGTAATCAGCTGTGACACA 59.100 45.455 14.67 8.26 34.75 3.72
646 650 6.849588 ATGCCACTCTTTAAAAAGCAAAAG 57.150 33.333 0.00 0.00 35.99 2.27
686 691 3.898482 TCTGACCTCCATACTTCGATCA 58.102 45.455 0.00 0.00 0.00 2.92
749 754 0.832135 TCCGCCCCTTATCCAGCTAG 60.832 60.000 0.00 0.00 0.00 3.42
891 897 3.281341 TCTTCGTCGCCGTAAGTAAAA 57.719 42.857 0.00 0.00 35.01 1.52
932 938 9.689501 TTGGAAGAAGAACTAGTAAAAGGAAAA 57.310 29.630 0.00 0.00 0.00 2.29
942 948 2.037251 TGCGCTTGGAAGAAGAACTAGT 59.963 45.455 9.73 0.00 0.00 2.57
1496 1503 3.452755 TCATAACATGAGCGATTCGGT 57.547 42.857 11.02 11.02 41.33 4.69
1679 1686 3.565307 TGGTCAGAGGCAAATTGAAAGT 58.435 40.909 0.00 0.00 0.00 2.66
1732 1739 0.817654 AGCGCCCCTTATTTCAAAGC 59.182 50.000 2.29 0.00 0.00 3.51
1741 1748 3.319441 GAACCGGAAGCGCCCCTTA 62.319 63.158 9.46 0.00 32.78 2.69
1963 1970 6.205853 AGTGCGGTTTGAACTATTGATTTACA 59.794 34.615 0.00 0.00 33.30 2.41
2272 2279 1.846712 TTGATCCATGGACGGCACCA 61.847 55.000 18.99 5.68 44.41 4.17
2437 2447 6.201044 CAGACGTATGATCATTACCCTTCAAC 59.799 42.308 14.65 1.44 0.00 3.18
2509 2520 4.466827 TGTGAATAGCCATCGACTACCTA 58.533 43.478 0.00 0.00 0.00 3.08
2817 2828 7.013369 GGAACATTCCATAAGTCTATTGGAACC 59.987 40.741 15.27 10.18 46.76 3.62
2902 2913 4.382901 GCATCCATGGCTGAATGGTTAAAA 60.383 41.667 19.76 0.00 46.24 1.52


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

AutoCloner maintained by Alex Coulton.