Multiple sequence alignment - TraesCS6A01G019200

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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 TraesCS6A01G019200 chr6A 100.000 3177 0 0 1 3177 9184748 9187924 0.000000e+00 5867
1 TraesCS6A01G019200 chr6A 91.048 458 36 5 2685 3139 123776983 123776528 5.820000e-172 614
2 TraesCS6A01G019200 chr5A 97.814 2699 43 6 3 2693 439808559 439811249 0.000000e+00 4643
3 TraesCS6A01G019200 chr5A 97.978 1484 18 4 1212 2693 22978690 22977217 0.000000e+00 2564
4 TraesCS6A01G019200 chr5A 96.904 969 28 2 1 969 390557177 390558143 0.000000e+00 1622
5 TraesCS6A01G019200 chr3A 97.736 2694 56 4 2 2693 583077387 583080077 0.000000e+00 4632
6 TraesCS6A01G019200 chr4B 94.952 2694 121 7 1 2693 215062193 215059514 0.000000e+00 4207
7 TraesCS6A01G019200 chr4B 93.801 2694 127 6 1 2693 215014174 215011520 0.000000e+00 4013
8 TraesCS6A01G019200 chr7A 98.014 2064 29 4 632 2693 31808966 31811019 0.000000e+00 3574
9 TraesCS6A01G019200 chr7A 97.784 722 16 0 1 722 31808382 31809103 0.000000e+00 1245
10 TraesCS6A01G019200 chr6B 98.014 2064 29 4 632 2693 532352178 532354231 0.000000e+00 3574
11 TraesCS6A01G019200 chr6B 97.922 722 15 0 1 722 532351594 532352315 0.000000e+00 1251
12 TraesCS6A01G019200 chr2A 96.027 2064 60 11 632 2693 180213945 180211902 0.000000e+00 3338
13 TraesCS6A01G019200 chr2A 98.092 786 14 1 1 786 180214529 180213745 0.000000e+00 1367
14 TraesCS6A01G019200 chr2A 98.616 289 3 1 2406 2693 758963835 758964123 7.860000e-141 510
15 TraesCS6A01G019200 chr1B 97.732 1499 19 6 1199 2693 150371937 150370450 0.000000e+00 2566
16 TraesCS6A01G019200 chr2B 95.073 893 44 0 107 999 124292954 124293846 0.000000e+00 1406
17 TraesCS6A01G019200 chr2B 90.020 501 36 10 2685 3177 258682587 258682093 1.240000e-178 636
18 TraesCS6A01G019200 chrUn 90.619 501 37 8 2685 3176 271777793 271778292 0.000000e+00 656
19 TraesCS6A01G019200 chrUn 90.619 501 37 8 2685 3176 271780279 271780778 0.000000e+00 656
20 TraesCS6A01G019200 chrUn 90.619 501 37 8 2685 3176 271783501 271784000 0.000000e+00 656
21 TraesCS6A01G019200 chr3B 90.389 489 39 8 2685 3167 438912362 438912848 1.240000e-178 636
22 TraesCS6A01G019200 chr3B 87.832 452 49 6 981 1428 782172458 782172009 2.810000e-145 525
23 TraesCS6A01G019200 chr1A 89.400 500 41 9 2685 3177 264362958 264363452 1.250000e-173 619
24 TraesCS6A01G019200 chr4D 88.732 497 48 7 2685 3177 418420520 418421012 4.530000e-168 601
25 TraesCS6A01G019200 chr4D 88.554 498 49 8 2685 3177 416220576 416220082 5.870000e-167 597


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 TraesCS6A01G019200 chr6A 9184748 9187924 3176 False 5867.0 5867 100.0000 1 3177 1 chr6A.!!$F1 3176
1 TraesCS6A01G019200 chr5A 439808559 439811249 2690 False 4643.0 4643 97.8140 3 2693 1 chr5A.!!$F2 2690
2 TraesCS6A01G019200 chr5A 22977217 22978690 1473 True 2564.0 2564 97.9780 1212 2693 1 chr5A.!!$R1 1481
3 TraesCS6A01G019200 chr5A 390557177 390558143 966 False 1622.0 1622 96.9040 1 969 1 chr5A.!!$F1 968
4 TraesCS6A01G019200 chr3A 583077387 583080077 2690 False 4632.0 4632 97.7360 2 2693 1 chr3A.!!$F1 2691
5 TraesCS6A01G019200 chr4B 215059514 215062193 2679 True 4207.0 4207 94.9520 1 2693 1 chr4B.!!$R2 2692
6 TraesCS6A01G019200 chr4B 215011520 215014174 2654 True 4013.0 4013 93.8010 1 2693 1 chr4B.!!$R1 2692
7 TraesCS6A01G019200 chr7A 31808382 31811019 2637 False 2409.5 3574 97.8990 1 2693 2 chr7A.!!$F1 2692
8 TraesCS6A01G019200 chr6B 532351594 532354231 2637 False 2412.5 3574 97.9680 1 2693 2 chr6B.!!$F1 2692
9 TraesCS6A01G019200 chr2A 180211902 180214529 2627 True 2352.5 3338 97.0595 1 2693 2 chr2A.!!$R1 2692
10 TraesCS6A01G019200 chr1B 150370450 150371937 1487 True 2566.0 2566 97.7320 1199 2693 1 chr1B.!!$R1 1494
11 TraesCS6A01G019200 chr2B 124292954 124293846 892 False 1406.0 1406 95.0730 107 999 1 chr2B.!!$F1 892
12 TraesCS6A01G019200 chrUn 271777793 271784000 6207 False 656.0 656 90.6190 2685 3176 3 chrUn.!!$F1 491

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
439 440 1.344438 GGATGAGGCGACATGGTATGA 59.656 52.381 0.00 0.0 0.00 2.15 F
489 490 3.638627 TCGTGATCAAGAGGCTGACATAT 59.361 43.478 7.29 0.0 0.00 1.78 F
723 778 4.202556 TGAGGGAACATTTGAAGGATGTGA 60.203 41.667 0.00 0.0 37.76 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 1776 2.827921 TCAGCTTCATCACTGTCTGCTA 59.172 45.455 0.0 0.0 35.37 3.49 R
1959 2016 7.013655 GCTTCCAAAGATTTGCATAAGGATCTA 59.986 37.037 0.0 0.0 36.86 1.98 R
2710 2783 0.252197 AACTACCCGGCATGACTTCC 59.748 55.000 0.0 0.0 0.00 3.46 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
405 406 9.438163 ACAATTGGATATTAGAAAATGGTCCAT 57.562 29.630 10.83 0.00 39.21 3.41
439 440 1.344438 GGATGAGGCGACATGGTATGA 59.656 52.381 0.00 0.00 0.00 2.15
451 452 5.542779 GACATGGTATGACAATCTCCCTAC 58.457 45.833 0.00 0.00 0.00 3.18
489 490 3.638627 TCGTGATCAAGAGGCTGACATAT 59.361 43.478 7.29 0.00 0.00 1.78
604 659 9.331282 AGCTTAGTATCTTTGATGTATTTCCAC 57.669 33.333 0.00 0.00 0.00 4.02
723 778 4.202556 TGAGGGAACATTTGAAGGATGTGA 60.203 41.667 0.00 0.00 37.76 3.58
1146 1202 5.343307 AACCTGCAACTTTCAAGTTCAAT 57.657 34.783 1.76 0.00 45.65 2.57
1343 1400 5.431765 TCTGAGTCAGAAAAGCAAAGACTT 58.568 37.500 20.65 0.00 39.47 3.01
1422 1479 5.140454 TGAGTGGATAGCTGCTATTGTCTA 58.860 41.667 22.09 7.13 0.00 2.59
1423 1480 5.777223 TGAGTGGATAGCTGCTATTGTCTAT 59.223 40.000 22.09 7.91 0.00 1.98
1719 1776 6.218522 AGGGAACTTGAGGGAAATCTAATTCT 59.781 38.462 0.00 0.00 37.44 2.40
2505 2577 5.915758 GCGTATGTGTGTTGGTTAATTCAAA 59.084 36.000 0.00 0.00 0.00 2.69
2506 2578 6.418226 GCGTATGTGTGTTGGTTAATTCAAAA 59.582 34.615 0.00 0.00 0.00 2.44
2507 2579 7.115663 GCGTATGTGTGTTGGTTAATTCAAAAT 59.884 33.333 0.00 0.00 0.00 1.82
2508 2580 8.973378 CGTATGTGTGTTGGTTAATTCAAAATT 58.027 29.630 0.00 0.00 0.00 1.82
2699 2772 5.047566 TGGCAAGTACTATTGGTATGCAT 57.952 39.130 13.77 3.79 37.85 3.96
2722 2795 4.693283 TGTAATCTAAGGAAGTCATGCCG 58.307 43.478 0.00 0.00 0.00 5.69
2937 5497 9.939802 TGATATGAGATTCTATCCAACATGAAG 57.060 33.333 0.00 0.00 0.00 3.02
2941 5501 5.374921 AGATTCTATCCAACATGAAGCTGG 58.625 41.667 0.00 0.44 34.49 4.85
2942 5502 4.574674 TTCTATCCAACATGAAGCTGGT 57.425 40.909 0.00 0.00 34.95 4.00
2952 5512 3.503748 ACATGAAGCTGGTGAGTTTAAGC 59.496 43.478 0.00 0.00 35.86 3.09
2956 5516 1.699634 AGCTGGTGAGTTTAAGCTGGA 59.300 47.619 0.00 0.00 44.14 3.86
2960 5520 2.884639 TGGTGAGTTTAAGCTGGAAAGC 59.115 45.455 0.00 0.00 0.00 3.51
2973 5533 4.892345 AGCTGGAAAGCTTTTCTCTTCTTT 59.108 37.500 18.32 0.00 43.52 2.52
2999 5559 7.581213 TTCCAAGAGCTAAGTTGAATTGAAA 57.419 32.000 4.83 0.00 0.00 2.69
3021 5581 9.581289 TGAAAAACTTATCTAAGGTTGATGGAA 57.419 29.630 1.17 0.00 42.04 3.53
3024 5584 7.573968 AACTTATCTAAGGTTGATGGAATGC 57.426 36.000 2.29 0.00 37.62 3.56
3028 5588 2.610438 AAGGTTGATGGAATGCTGGT 57.390 45.000 0.00 0.00 0.00 4.00
3127 5692 8.514330 AAATGCCGACTAAACTAATCCATTTA 57.486 30.769 0.00 0.00 31.07 1.40
3128 5693 8.691661 AATGCCGACTAAACTAATCCATTTAT 57.308 30.769 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
300 301 5.182001 GCCTTTGAGTAAGAATCTTGAAGCA 59.818 40.000 5.64 0.00 35.80 3.91
405 406 4.996758 CGCCTCATCCACAACATAATCATA 59.003 41.667 0.00 0.00 0.00 2.15
439 440 3.288964 CCAGTACTCGTAGGGAGATTGT 58.711 50.000 0.00 0.00 46.23 2.71
451 452 2.183555 GAACCCGCCCAGTACTCG 59.816 66.667 0.00 0.00 0.00 4.18
489 490 2.113774 CTTGGCAGCCCACTCACA 59.886 61.111 9.64 0.00 41.97 3.58
508 509 6.032094 CACATTTGCTGAGCGATTAAATCTT 58.968 36.000 0.00 0.00 0.00 2.40
604 659 4.156556 ACATCCTTCAAATGTTCCATCACG 59.843 41.667 0.00 0.00 33.62 4.35
723 778 6.238731 CGCATGGAAATACATCAAAGGTACAT 60.239 38.462 0.00 0.00 0.00 2.29
1146 1202 4.428209 CACATTGCAAGTGGTGTTGTTTA 58.572 39.130 16.32 0.00 33.43 2.01
1199 1255 1.949525 CCACTTGGGTTTGAGTGACAG 59.050 52.381 5.15 0.00 44.65 3.51
1232 1288 2.622452 CCCCACTTCTCCTTGCATTGAT 60.622 50.000 0.00 0.00 0.00 2.57
1385 1442 9.638176 AGCTATCCACTCATTTTAAAATCAGAT 57.362 29.630 17.52 13.11 0.00 2.90
1719 1776 2.827921 TCAGCTTCATCACTGTCTGCTA 59.172 45.455 0.00 0.00 35.37 3.49
1959 2016 7.013655 GCTTCCAAAGATTTGCATAAGGATCTA 59.986 37.037 0.00 0.00 36.86 1.98
2676 2749 5.047566 TGCATACCAATAGTACTTGCCAT 57.952 39.130 0.00 0.00 36.51 4.40
2699 2772 5.116180 CGGCATGACTTCCTTAGATTACAA 58.884 41.667 0.00 0.00 0.00 2.41
2710 2783 0.252197 AACTACCCGGCATGACTTCC 59.748 55.000 0.00 0.00 0.00 3.46
2937 5497 2.185004 TCCAGCTTAAACTCACCAGC 57.815 50.000 0.00 0.00 0.00 4.85
2973 5533 7.581213 TCAATTCAACTTAGCTCTTGGAAAA 57.419 32.000 0.00 0.00 0.00 2.29
2999 5559 7.836183 AGCATTCCATCAACCTTAGATAAGTTT 59.164 33.333 0.00 0.00 0.00 2.66
3007 5567 3.624777 ACCAGCATTCCATCAACCTTAG 58.375 45.455 0.00 0.00 0.00 2.18
3021 5581 5.927281 ATTTCTTTGAGCAATACCAGCAT 57.073 34.783 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.