Multiple sequence alignment - TraesCS3A01G430100

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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 TraesCS3A01G430100 chr3A 100.000 2531 0 0 1 2531 672878433 672875903 0.000000 4674.0
1 TraesCS3A01G430100 chr2D 97.502 2522 28 7 1 2498 630270292 630272802 0.000000 4276.0
2 TraesCS3A01G430100 chr2D 97.426 2525 27 8 1 2498 33933815 33936328 0.000000 4268.0
3 TraesCS3A01G430100 chr3B 96.845 2504 52 9 1 2498 201560775 201558293 0.000000 4161.0
4 TraesCS3A01G430100 chr5B 96.243 2502 70 10 1 2498 432876723 432879204 0.000000 4078.0
5 TraesCS3A01G430100 chr5B 97.326 1907 40 7 589 2488 413608022 413609924 0.000000 3229.0
6 TraesCS3A01G430100 chr4A 95.244 2502 91 9 1 2498 310762405 310764882 0.000000 3936.0
7 TraesCS3A01G430100 chr4D 96.250 2320 77 7 182 2498 245648863 245651175 0.000000 3794.0
8 TraesCS3A01G430100 chr5D 96.894 2125 58 8 1 2121 432292719 432290599 0.000000 3552.0
9 TraesCS3A01G430100 chr1B 97.510 2048 48 3 1 2046 633728865 633726819 0.000000 3496.0
10 TraesCS3A01G430100 chr1A 96.086 1482 44 8 1010 2488 371922144 371923614 0.000000 2403.0
11 TraesCS3A01G430100 chr1A 94.291 1016 49 5 1 1012 371831413 371832423 0.000000 1546.0
12 TraesCS3A01G430100 chr1A 100.000 33 0 0 2499 2531 14239715 14239683 0.000008 62.1
13 TraesCS3A01G430100 chr3D 92.971 882 27 10 1609 2488 182097139 182097987 0.000000 1253.0
14 TraesCS3A01G430100 chr3D 100.000 32 0 0 2500 2531 581005672 581005641 0.000027 60.2
15 TraesCS3A01G430100 chr5A 97.125 487 7 4 2014 2498 482027372 482026891 0.000000 815.0
16 TraesCS3A01G430100 chrUn 96.741 491 8 4 2012 2498 451362689 451363175 0.000000 811.0
17 TraesCS3A01G430100 chrUn 100.000 32 0 0 2500 2531 197539606 197539575 0.000027 60.2
18 TraesCS3A01G430100 chrUn 100.000 32 0 0 2500 2531 200115349 200115380 0.000027 60.2
19 TraesCS3A01G430100 chrUn 100.000 32 0 0 2500 2531 221381657 221381688 0.000027 60.2
20 TraesCS3A01G430100 chrUn 100.000 32 0 0 2500 2531 228687480 228687511 0.000027 60.2
21 TraesCS3A01G430100 chr2A 100.000 33 0 0 2499 2531 757259490 757259522 0.000008 62.1
22 TraesCS3A01G430100 chr6A 100.000 32 0 0 2500 2531 19317390 19317421 0.000027 60.2
23 TraesCS3A01G430100 chr6A 100.000 32 0 0 2500 2531 24464824 24464793 0.000027 60.2


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 TraesCS3A01G430100 chr3A 672875903 672878433 2530 True 4674 4674 100.000 1 2531 1 chr3A.!!$R1 2530
1 TraesCS3A01G430100 chr2D 630270292 630272802 2510 False 4276 4276 97.502 1 2498 1 chr2D.!!$F2 2497
2 TraesCS3A01G430100 chr2D 33933815 33936328 2513 False 4268 4268 97.426 1 2498 1 chr2D.!!$F1 2497
3 TraesCS3A01G430100 chr3B 201558293 201560775 2482 True 4161 4161 96.845 1 2498 1 chr3B.!!$R1 2497
4 TraesCS3A01G430100 chr5B 432876723 432879204 2481 False 4078 4078 96.243 1 2498 1 chr5B.!!$F2 2497
5 TraesCS3A01G430100 chr5B 413608022 413609924 1902 False 3229 3229 97.326 589 2488 1 chr5B.!!$F1 1899
6 TraesCS3A01G430100 chr4A 310762405 310764882 2477 False 3936 3936 95.244 1 2498 1 chr4A.!!$F1 2497
7 TraesCS3A01G430100 chr4D 245648863 245651175 2312 False 3794 3794 96.250 182 2498 1 chr4D.!!$F1 2316
8 TraesCS3A01G430100 chr5D 432290599 432292719 2120 True 3552 3552 96.894 1 2121 1 chr5D.!!$R1 2120
9 TraesCS3A01G430100 chr1B 633726819 633728865 2046 True 3496 3496 97.510 1 2046 1 chr1B.!!$R1 2045
10 TraesCS3A01G430100 chr1A 371922144 371923614 1470 False 2403 2403 96.086 1010 2488 1 chr1A.!!$F2 1478
11 TraesCS3A01G430100 chr1A 371831413 371832423 1010 False 1546 1546 94.291 1 1012 1 chr1A.!!$F1 1011
12 TraesCS3A01G430100 chr3D 182097139 182097987 848 False 1253 1253 92.971 1609 2488 1 chr3D.!!$F1 879

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
412 415 2.223144 GCTTGTGAAGTATGTGTTCGCA 59.777 45.455 0.0 0.0 41.5 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 1944 4.385358 AGGGCTATAACAAAAATTGCGG 57.615 40.909 0.0 0.0 0.0 5.69 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
412 415 2.223144 GCTTGTGAAGTATGTGTTCGCA 59.777 45.455 0.00 0.00 41.50 5.10
606 609 9.730705 ACCTATGATCGTCATGAATTGAATTAT 57.269 29.630 0.00 0.00 37.70 1.28
641 644 2.674796 AGTCGGTTAGCAATCTCCAC 57.325 50.000 0.00 0.00 0.00 4.02
682 685 9.065871 CAATTCAAACAATTAGGAATTCGTCTC 57.934 33.333 3.47 0.00 37.75 3.36
735 738 9.020813 TCGAATTCAAGAACGATTACTGATTAG 57.979 33.333 6.22 0.00 0.00 1.73
1112 1126 5.514659 CCAACCCCATTTATTCTGCCTTTTT 60.515 40.000 0.00 0.00 0.00 1.94
1926 1944 7.931275 AGTCGCCAATTAAAAGGAGATATTTC 58.069 34.615 6.33 0.00 36.14 2.17
1951 1969 4.934602 GCAATTTTTGTTATAGCCCTTGCA 59.065 37.500 0.00 0.00 41.13 4.08
2022 2040 6.802348 CGTAATAGGAAATCCACTCGTATCAG 59.198 42.308 1.67 0.00 38.89 2.90
2434 2495 5.092554 TGGATAAACCATTGCTTCGTCTA 57.907 39.130 0.00 0.00 44.64 2.59
2503 2564 6.300354 ACCAGATCTATAAATTTTTCGGCG 57.700 37.500 0.00 0.00 0.00 6.46
2504 2565 6.053005 ACCAGATCTATAAATTTTTCGGCGA 58.947 36.000 4.99 4.99 0.00 5.54
2505 2566 6.540914 ACCAGATCTATAAATTTTTCGGCGAA 59.459 34.615 19.83 19.83 0.00 4.70
2506 2567 7.072030 CCAGATCTATAAATTTTTCGGCGAAG 58.928 38.462 22.52 7.76 0.00 3.79
2507 2568 7.072030 CAGATCTATAAATTTTTCGGCGAAGG 58.928 38.462 22.52 6.01 0.00 3.46
2508 2569 5.744666 TCTATAAATTTTTCGGCGAAGGG 57.255 39.130 22.52 6.49 0.00 3.95
2509 2570 2.640346 TAAATTTTTCGGCGAAGGGC 57.360 45.000 22.52 0.00 42.51 5.19
2510 2571 0.676736 AAATTTTTCGGCGAAGGGCA 59.323 45.000 22.52 4.91 46.16 5.36
2511 2572 0.243636 AATTTTTCGGCGAAGGGCAG 59.756 50.000 22.52 0.00 46.16 4.85
2512 2573 2.212900 ATTTTTCGGCGAAGGGCAGC 62.213 55.000 22.52 0.00 46.16 5.25
2529 2590 3.131240 CAGCCGCACTGGTTTATAAAC 57.869 47.619 18.30 18.30 43.19 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
412 415 6.014840 ACAACGGGTAAATCTATCGGACATAT 60.015 38.462 0.00 0.00 0.00 1.78
606 609 7.966204 GCTAACCGACTTAAAGCAATTTGATTA 59.034 33.333 0.00 0.00 33.38 1.75
641 644 7.377398 TGTTTGAATTGTGTAATCTCCCATTG 58.623 34.615 0.00 0.00 0.00 2.82
1112 1126 4.469657 ACAAACAAGAACTAATCCCAGCA 58.530 39.130 0.00 0.00 0.00 4.41
1179 1196 6.007076 TCCCACATAAATAAGAAGTTGTGCA 58.993 36.000 0.00 0.00 34.57 4.57
1926 1944 4.385358 AGGGCTATAACAAAAATTGCGG 57.615 40.909 0.00 0.00 0.00 5.69
2337 2398 9.220767 GAAGAGAGCCAAGAGACTTTAATTTTA 57.779 33.333 0.00 0.00 0.00 1.52
2488 2549 3.695060 TGCCCTTCGCCGAAAAATTTATA 59.305 39.130 0.00 0.00 36.24 0.98
2490 2551 1.887198 TGCCCTTCGCCGAAAAATTTA 59.113 42.857 0.00 0.00 36.24 1.40
2507 2568 0.746563 TATAAACCAGTGCGGCTGCC 60.747 55.000 16.57 9.11 43.71 4.85
2508 2569 1.091537 TTATAAACCAGTGCGGCTGC 58.908 50.000 11.65 11.65 43.71 5.25
2509 2570 3.131240 GTTTATAAACCAGTGCGGCTG 57.869 47.619 16.14 1.55 44.63 4.85


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

AutoCloner maintained by Alex Coulton.