Multiple sequence alignment - TraesCS6A01G261300

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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 TraesCS6A01G261300 chr6A 100.000 2512 0 0 1 2512 484784654 484782143 0 4639
1 TraesCS6A01G261300 chr6A 95.671 2518 90 12 2 2512 176534601 176532096 0 4028
2 TraesCS6A01G261300 chr6A 95.765 614 17 4 1899 2512 357524783 357524179 0 981
3 TraesCS6A01G261300 chr4A 96.387 2519 77 11 2 2512 45631394 45633906 0 4135
4 TraesCS6A01G261300 chr4A 95.277 614 19 4 1899 2512 246821249 246820646 0 965
5 TraesCS6A01G261300 chr7D 96.104 2541 63 22 2 2512 421675282 421677816 0 4111
6 TraesCS6A01G261300 chr6D 95.861 2537 73 19 2 2512 451600149 451597619 0 4074
7 TraesCS6A01G261300 chr6D 95.317 2541 72 22 2 2512 397854472 397851949 0 3989
8 TraesCS6A01G261300 chr2A 95.832 2519 90 15 2 2512 677262022 677264533 0 4056
9 TraesCS6A01G261300 chr2A 95.277 614 20 4 1899 2512 596740876 596740272 0 965
10 TraesCS6A01G261300 chr1A 95.393 2518 85 11 2 2512 519376703 519374210 0 3978
11 TraesCS6A01G261300 chr1A 95.440 614 19 4 1899 2512 517445084 517444480 0 970
12 TraesCS6A01G261300 chr5A 95.316 2519 94 14 2 2512 13143403 13140901 0 3976
13 TraesCS6A01G261300 chr5D 95.630 2380 70 20 2 2354 58009617 58007245 0 3788


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 TraesCS6A01G261300 chr6A 484782143 484784654 2511 True 4639 4639 100.000 1 2512 1 chr6A.!!$R3 2511
1 TraesCS6A01G261300 chr6A 176532096 176534601 2505 True 4028 4028 95.671 2 2512 1 chr6A.!!$R1 2510
2 TraesCS6A01G261300 chr6A 357524179 357524783 604 True 981 981 95.765 1899 2512 1 chr6A.!!$R2 613
3 TraesCS6A01G261300 chr4A 45631394 45633906 2512 False 4135 4135 96.387 2 2512 1 chr4A.!!$F1 2510
4 TraesCS6A01G261300 chr4A 246820646 246821249 603 True 965 965 95.277 1899 2512 1 chr4A.!!$R1 613
5 TraesCS6A01G261300 chr7D 421675282 421677816 2534 False 4111 4111 96.104 2 2512 1 chr7D.!!$F1 2510
6 TraesCS6A01G261300 chr6D 451597619 451600149 2530 True 4074 4074 95.861 2 2512 1 chr6D.!!$R2 2510
7 TraesCS6A01G261300 chr6D 397851949 397854472 2523 True 3989 3989 95.317 2 2512 1 chr6D.!!$R1 2510
8 TraesCS6A01G261300 chr2A 677262022 677264533 2511 False 4056 4056 95.832 2 2512 1 chr2A.!!$F1 2510
9 TraesCS6A01G261300 chr2A 596740272 596740876 604 True 965 965 95.277 1899 2512 1 chr2A.!!$R1 613
10 TraesCS6A01G261300 chr1A 519374210 519376703 2493 True 3978 3978 95.393 2 2512 1 chr1A.!!$R2 2510
11 TraesCS6A01G261300 chr1A 517444480 517445084 604 True 970 970 95.440 1899 2512 1 chr1A.!!$R1 613
12 TraesCS6A01G261300 chr5A 13140901 13143403 2502 True 3976 3976 95.316 2 2512 1 chr5A.!!$R1 2510
13 TraesCS6A01G261300 chr5D 58007245 58009617 2372 True 3788 3788 95.630 2 2354 1 chr5D.!!$R1 2352

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
873 932 1.483827 AGCAGATCGAGCAATTCCTCA 59.516 47.619 2.38 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 1932 0.54153 TTTGTGGGCCTATTGCAGCA 60.542 50.0 4.53 0.0 43.89 4.41 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
177 219 3.904965 CCTAAACCCTCTCTCCCTATTCC 59.095 52.174 0.00 0.00 0.00 3.01
257 301 8.472007 TGAAAATGACCTACACCAAGTTTATT 57.528 30.769 0.00 0.00 0.00 1.40
521 580 8.893563 TTTGAAATCAGGTCAAACCCTAATAT 57.106 30.769 0.00 0.00 39.46 1.28
531 590 4.227754 TCAAACCCTAATATCCCCGTTGAA 59.772 41.667 0.00 0.00 0.00 2.69
546 605 2.639065 GTTGAATCGCTCATAACCCCA 58.361 47.619 0.00 0.00 32.78 4.96
616 675 3.213402 CGCCAAACACCACCCGTT 61.213 61.111 0.00 0.00 0.00 4.44
822 881 9.942526 AAATCATCAATATAACTTCCCCTTCTT 57.057 29.630 0.00 0.00 0.00 2.52
873 932 1.483827 AGCAGATCGAGCAATTCCTCA 59.516 47.619 2.38 0.00 0.00 3.86
997 1056 1.980052 CCGGTGTATGGTCCAGTGT 59.020 57.895 0.00 0.00 0.00 3.55
1278 1338 1.115326 GCTTCAAGGGTTGGGCTTGT 61.115 55.000 0.00 0.00 0.00 3.16
1317 1377 1.328680 CAATCCGCGAGTTCAATCTGG 59.671 52.381 8.23 0.00 0.00 3.86
1327 1387 2.170166 GTTCAATCTGGCCCATGACAA 58.830 47.619 0.00 0.00 0.00 3.18
1482 1542 6.556874 AGCTTTAGGAATACTTGCTCTAGGAT 59.443 38.462 0.00 0.00 31.99 3.24
1540 1600 1.264288 GTCTACTGTTGTTGCCACTGC 59.736 52.381 0.00 0.00 38.26 4.40
1823 1883 2.875087 TTTGTCCTCGAGTTCGTCAA 57.125 45.000 12.31 3.90 40.80 3.18
1830 1890 1.318785 CTCGAGTTCGTCAATTCTGCG 59.681 52.381 3.62 0.00 40.80 5.18
1867 1932 0.753111 GCGGGCCCAAAGAGAATCAT 60.753 55.000 24.92 0.00 37.82 2.45
1911 1976 2.683211 AATGAGGCCCAGAAACAAGT 57.317 45.000 0.00 0.00 0.00 3.16
2016 2082 8.377034 CCAATCTCTTCTATCTCATTGAGGAAT 58.623 37.037 13.59 3.75 0.00 3.01
2207 2314 8.515414 ACTAAAGCCAAACATCTCAAAGTATTC 58.485 33.333 0.00 0.00 0.00 1.75
2246 2353 7.510549 TCTGAAAACCAAAGTATTCTTGGAG 57.489 36.000 8.54 0.00 33.79 3.86
2279 2386 3.567478 ACAGAGCTCTCAAACCAAAGT 57.433 42.857 14.96 2.14 0.00 2.66
2388 2495 4.082949 GCCAATTAGCCGTGTCTAAACTTT 60.083 41.667 0.00 0.00 32.86 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 6.166982 AGAAGGATCTGAACTTACCTTTTCG 58.833 40.000 0.00 0.0 40.42 3.46
67 69 8.261522 AGTGAATAAGAAGGATCTGAACTTACC 58.738 37.037 0.00 0.0 35.59 2.85
177 219 2.131972 TGAACATGTTCGGAGTTCGTG 58.868 47.619 28.55 2.1 43.36 4.35
505 564 2.709397 CGGGGATATTAGGGTTTGACCT 59.291 50.000 0.00 0.0 44.75 3.85
521 580 1.116308 TATGAGCGATTCAACGGGGA 58.884 50.000 0.00 0.0 39.77 4.81
531 590 1.496060 TCTGTGGGGTTATGAGCGAT 58.504 50.000 0.00 0.0 0.00 4.58
546 605 2.683211 AGGGTTTGGAGCATTTCTGT 57.317 45.000 0.00 0.0 0.00 3.41
592 651 2.055042 TGGTGTTTGGCGCTTGGTT 61.055 52.632 7.64 0.0 0.00 3.67
616 675 0.764890 GCATGCCTACCCCACATCTA 59.235 55.000 6.36 0.0 0.00 1.98
779 838 7.160049 TGATGATTTGCCACATTGTATTTTGT 58.840 30.769 0.00 0.0 0.00 2.83
822 881 4.039603 TGTCTGTCAGATGGAGAAGAGA 57.960 45.455 5.68 0.0 0.00 3.10
873 932 3.307762 CGAGAAGATGGGGGAAAGAAACT 60.308 47.826 0.00 0.0 0.00 2.66
1278 1338 0.106719 GCATTCCCCCTCGAATCCAA 60.107 55.000 0.00 0.0 29.85 3.53
1317 1377 3.129913 GAGCGGCATTGTCATGGGC 62.130 63.158 1.45 0.0 0.00 5.36
1540 1600 7.550551 TGAGATAAACAGACTTGGATTGCTAAG 59.449 37.037 0.00 0.0 38.45 2.18
1867 1932 0.541530 TTTGTGGGCCTATTGCAGCA 60.542 50.000 4.53 0.0 43.89 4.41
1926 1991 8.106247 AGAATAAAGCAATCGTTCCTAAACAA 57.894 30.769 0.00 0.0 34.93 2.83
2388 2495 9.653287 TTGTTATGTTTGTATTTTGTTTGTCCA 57.347 25.926 0.00 0.0 0.00 4.02


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

AutoCloner maintained by Alex Coulton.