Multiple sequence alignment - TraesCS5B01G106800

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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 TraesCS5B01G106800 chr5B 100.000 3298 0 0 1 3298 144814704 144818001 0.000000e+00 6091.0
1 TraesCS5B01G106800 chr5B 92.323 495 32 4 7 500 529536720 529536231 0.000000e+00 699.0
2 TraesCS5B01G106800 chr5B 86.510 341 23 9 509 828 614977904 614977566 1.600000e-93 353.0
3 TraesCS5B01G106800 chr5B 92.537 134 5 1 510 643 416380874 416381002 1.710000e-43 187.0
4 TraesCS5B01G106800 chr5B 100.000 99 0 0 3517 3615 144818220 144818318 2.220000e-42 183.0
5 TraesCS5B01G106800 chr5A 94.041 1913 68 22 822 2711 156224808 156226697 0.000000e+00 2859.0
6 TraesCS5B01G106800 chr5D 94.794 1844 51 19 815 2632 133536456 133538280 0.000000e+00 2832.0
7 TraesCS5B01G106800 chr5D 91.400 500 37 3 1 500 380088621 380088128 0.000000e+00 680.0
8 TraesCS5B01G106800 chr5D 91.398 279 19 4 2792 3067 133539267 133539543 9.470000e-101 377.0
9 TraesCS5B01G106800 chr5D 80.473 338 36 4 511 820 361578250 361578585 7.810000e-57 231.0
10 TraesCS5B01G106800 chr5D 93.000 100 6 1 3517 3615 133539695 133539794 1.050000e-30 145.0
11 TraesCS5B01G106800 chr5D 96.154 78 3 0 2738 2815 133538324 133538401 1.050000e-25 128.0
12 TraesCS5B01G106800 chr6B 92.400 500 32 2 1 500 481436745 481436252 0.000000e+00 708.0
13 TraesCS5B01G106800 chr7D 92.540 496 31 2 4 499 504248469 504248958 0.000000e+00 706.0
14 TraesCS5B01G106800 chr2B 92.137 496 30 4 4 499 96626732 96627218 0.000000e+00 691.0
15 TraesCS5B01G106800 chr2B 91.734 496 36 1 4 499 104049783 104049293 0.000000e+00 684.0
16 TraesCS5B01G106800 chr3D 91.784 499 31 6 4 499 517006214 517006705 0.000000e+00 686.0
17 TraesCS5B01G106800 chr7B 91.583 499 37 1 1 499 559006657 559007150 0.000000e+00 684.0
18 TraesCS5B01G106800 chr4D 91.734 496 34 3 4 499 25383967 25384455 0.000000e+00 682.0
19 TraesCS5B01G106800 chr4B 81.232 341 33 16 509 820 44469026 44469364 2.790000e-61 246.0
20 TraesCS5B01G106800 chr4B 80.938 341 34 16 509 820 44658265 44658603 1.300000e-59 241.0
21 TraesCS5B01G106800 chr1D 90.426 188 15 3 637 823 437475215 437475030 1.000000e-60 244.0
22 TraesCS5B01G106800 chr1D 95.041 121 6 0 523 643 437475358 437475238 1.320000e-44 191.0
23 TraesCS5B01G106800 chr3A 88.462 182 19 2 636 817 475737624 475737803 6.080000e-53 219.0
24 TraesCS5B01G106800 chr4A 100.000 34 0 0 3580 3613 400582971 400583004 3.010000e-06 63.9


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 TraesCS5B01G106800 chr5B 144814704 144818318 3614 False 3137.0 6091 100.0000 1 3615 2 chr5B.!!$F2 3614
1 TraesCS5B01G106800 chr5A 156224808 156226697 1889 False 2859.0 2859 94.0410 822 2711 1 chr5A.!!$F1 1889
2 TraesCS5B01G106800 chr5D 133536456 133539794 3338 False 870.5 2832 93.8365 815 3615 4 chr5D.!!$F2 2800


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
234 235 0.030908 CACCTACTCCGCCTCGATTC 59.969 60.0 0.00 0.0 0.0 2.52 F
1589 1596 0.029300 GCGCTGCAGAGTTTGTTTCA 59.971 50.0 20.43 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2041 0.962356 ACGCCTGCTGGAAGAATTGG 60.962 55.0 14.77 0.0 34.07 3.16 R
3074 3991 0.319469 TCACAATGTCTCTTGCGCGA 60.319 50.0 12.10 0.0 0.00 5.87 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)



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AutoCloner maintained by Alex Coulton.