Multiple sequence alignment - TraesCS6A01G249000

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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 TraesCS6A01G249000 chr6A 100.000 2512 0 0 1 2512 461947764 461950275 0 4639
1 TraesCS6A01G249000 chr6A 96.746 2520 69 10 1 2512 468224298 468226812 0 4187
2 TraesCS6A01G249000 chr5A 96.829 2523 65 14 1 2512 639808005 639810523 0 4202
3 TraesCS6A01G249000 chr5A 96.818 2514 67 12 7 2512 580225350 580222842 0 4187
4 TraesCS6A01G249000 chr1A 96.792 2525 64 15 1 2512 257591382 257588862 0 4198
5 TraesCS6A01G249000 chr3A 96.460 2514 76 10 7 2512 480296072 480298580 0 4137
6 TraesCS6A01G249000 chr3A 96.458 2513 75 12 7 2512 654166983 654169488 0 4135
7 TraesCS6A01G249000 chr3A 93.992 2430 125 18 7 2421 191743856 191746279 0 3659
8 TraesCS6A01G249000 chr3A 96.808 2005 56 8 512 2512 542252760 542254760 0 3341
9 TraesCS6A01G249000 chr3A 95.931 2015 71 10 1 2009 679383985 679381976 0 3256
10 TraesCS6A01G249000 chr3A 95.712 513 13 4 2007 2512 679375529 679375019 0 817


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 TraesCS6A01G249000 chr6A 461947764 461950275 2511 False 4639 4639 100.000 1 2512 1 chr6A.!!$F1 2511
1 TraesCS6A01G249000 chr6A 468224298 468226812 2514 False 4187 4187 96.746 1 2512 1 chr6A.!!$F2 2511
2 TraesCS6A01G249000 chr5A 639808005 639810523 2518 False 4202 4202 96.829 1 2512 1 chr5A.!!$F1 2511
3 TraesCS6A01G249000 chr5A 580222842 580225350 2508 True 4187 4187 96.818 7 2512 1 chr5A.!!$R1 2505
4 TraesCS6A01G249000 chr1A 257588862 257591382 2520 True 4198 4198 96.792 1 2512 1 chr1A.!!$R1 2511
5 TraesCS6A01G249000 chr3A 480296072 480298580 2508 False 4137 4137 96.460 7 2512 1 chr3A.!!$F2 2505
6 TraesCS6A01G249000 chr3A 654166983 654169488 2505 False 4135 4135 96.458 7 2512 1 chr3A.!!$F4 2505
7 TraesCS6A01G249000 chr3A 191743856 191746279 2423 False 3659 3659 93.992 7 2421 1 chr3A.!!$F1 2414
8 TraesCS6A01G249000 chr3A 542252760 542254760 2000 False 3341 3341 96.808 512 2512 1 chr3A.!!$F3 2000
9 TraesCS6A01G249000 chr3A 679381976 679383985 2009 True 3256 3256 95.931 1 2009 1 chr3A.!!$R2 2008
10 TraesCS6A01G249000 chr3A 679375019 679375529 510 True 817 817 95.712 2007 2512 1 chr3A.!!$R1 505

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
626 643 0.473694 ACCACCTGTCAGATGTGGGA 60.474 55.0 24.06 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2222 2253 1.53895 GCTTTGGTTTGAGAGCTCTGG 59.461 52.381 23.91 0.94 32.54 3.86 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
104 105 6.712547 CCTTCTTACTCACTCCAAAATGAAGT 59.287 38.462 0.00 0.0 0.00 3.01
411 424 5.986004 AAATGCGCCTATACTGAGTTTAC 57.014 39.130 4.18 0.0 0.00 2.01
626 643 0.473694 ACCACCTGTCAGATGTGGGA 60.474 55.000 24.06 0.0 0.00 4.37
629 646 1.280133 CACCTGTCAGATGTGGGACAT 59.720 52.381 0.00 0.0 44.52 3.06
673 690 1.630369 TCCTGATTGGCTACTGCACTT 59.370 47.619 0.00 0.0 41.91 3.16
802 821 6.262720 ACTGCAAAATACAATGTGGCAAATTT 59.737 30.769 0.00 0.0 0.00 1.82
948 968 1.788229 TCCTCTTGGGCGATATGTCA 58.212 50.000 0.00 0.0 34.39 3.58
966 986 3.547787 AACCTCCTCGTCAGCCCCT 62.548 63.158 0.00 0.0 0.00 4.79
992 1012 2.987125 GTGGCCGGTGTATGGTCT 59.013 61.111 1.90 0.0 30.50 3.85
1098 1118 1.491563 GCGCGAGTTCGTCAAATGT 59.508 52.632 12.10 0.0 42.22 2.71
1129 1149 1.052617 GGAGGGGCAGGTTAGATCTC 58.947 60.000 0.00 0.0 0.00 2.75
1144 1164 6.273825 GTTAGATCTCAGTTTTCCTCGCATA 58.726 40.000 0.00 0.0 0.00 3.14
1189 1210 8.477419 AAAAACTGTCAGATTTGGATTTAGGA 57.523 30.769 6.91 0.0 0.00 2.94
1272 1293 2.274542 TCCATAGGCTTCAAGGGTCAA 58.725 47.619 0.00 0.0 0.00 3.18
1325 1346 1.002069 AGTCCAATCTGCCCCATGAA 58.998 50.000 0.00 0.0 0.00 2.57
2244 2275 1.143684 AGAGCTCTCAAACCAAAGCCA 59.856 47.619 11.45 0.0 35.32 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.356433 TCATATCTAAAACGTGTTATTTGACGA 57.644 29.630 0.00 0.00 38.94 4.20
152 157 0.326713 AGGGAGAGAGGGTTTAGGGC 60.327 60.000 0.00 0.00 0.00 5.19
613 630 0.691904 TGCATGTCCCACATCTGACA 59.308 50.000 0.00 0.00 44.86 3.58
626 643 2.827051 GCGGATCGTGCATGCATGT 61.827 57.895 33.08 22.71 34.75 3.21
692 710 4.411869 TCATATGTAAAGTGGGGCAGATCA 59.588 41.667 1.90 0.00 0.00 2.92
802 821 7.316841 AGAGGAGAAGGGGAAGATATATTGAA 58.683 38.462 0.00 0.00 0.00 2.69
811 830 2.292587 GGAGAAGAGGAGAAGGGGAAGA 60.293 54.545 0.00 0.00 0.00 2.87
948 968 3.003763 GGGGCTGACGAGGAGGTT 61.004 66.667 0.00 0.00 0.00 3.50
1098 1118 3.393970 CCCTCCGGCTTGCTCTCA 61.394 66.667 0.00 0.00 0.00 3.27
1129 1149 6.758886 AGAGATAAAGTATGCGAGGAAAACTG 59.241 38.462 0.00 0.00 0.00 3.16
1189 1210 7.277760 TCACGATCTGAAAACGAAATCATGTAT 59.722 33.333 8.66 0.00 0.00 2.29
1256 1277 1.362224 AGCTTGACCCTTGAAGCCTA 58.638 50.000 0.00 0.00 44.79 3.93
1272 1293 1.222936 CCCTCGAATCCAGCAAGCT 59.777 57.895 0.00 0.00 0.00 3.74
1366 1387 2.521126 TCAGTTCGACATCTACCACCA 58.479 47.619 0.00 0.00 0.00 4.17
1391 1412 8.688747 AGTTCTTGTTCATCTTCTTCAATTCT 57.311 30.769 0.00 0.00 0.00 2.40
1436 1457 6.388435 GCTATCAGATTGGATTGCTTCTTT 57.612 37.500 0.00 0.00 41.03 2.52
2222 2253 1.538950 GCTTTGGTTTGAGAGCTCTGG 59.461 52.381 23.91 0.94 32.54 3.86
2470 2510 2.434336 TGTGTTGCCCGAGCTATCTATT 59.566 45.455 0.00 0.00 40.80 1.73


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

AutoCloner maintained by Alex Coulton.