Multiple sequence alignment - TraesCS6A01G226900

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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 TraesCS6A01G226900 chr6A 100.000 2454 0 0 1 2454 427195580 427193127 0.000000e+00 4532
1 TraesCS6A01G226900 chr6A 93.447 412 23 3 112 520 531028179 531027769 2.090000e-170 608
2 TraesCS6A01G226900 chr6D 89.074 1986 100 50 521 2454 293493576 293495496 0.000000e+00 2357
3 TraesCS6A01G226900 chr6D 93.478 414 23 4 109 520 178795927 178796338 1.610000e-171 612
4 TraesCS6A01G226900 chr6D 88.496 113 2 4 1 111 293493480 293493583 2.560000e-25 126
5 TraesCS6A01G226900 chr6B 89.266 1444 72 30 1049 2454 458007242 458008640 0.000000e+00 1731
6 TraesCS6A01G226900 chr6B 86.000 450 39 12 521 966 458006499 458006928 6.180000e-126 460
7 TraesCS6A01G226900 chr3D 94.712 416 18 4 107 520 43798013 43797600 0.000000e+00 643
8 TraesCS6A01G226900 chr3D 93.947 413 20 4 113 523 445107450 445107041 9.640000e-174 619
9 TraesCS6A01G226900 chr3D 93.917 411 21 4 112 520 570039119 570039527 3.470000e-173 617
10 TraesCS6A01G226900 chr1D 94.189 413 17 6 113 520 427487169 427487579 7.450000e-175 623
11 TraesCS6A01G226900 chr3A 94.146 410 19 5 113 520 86609511 86609105 9.640000e-174 619
12 TraesCS6A01G226900 chr3A 93.253 415 23 5 110 520 110335795 110335382 7.500000e-170 606
13 TraesCS6A01G226900 chr5D 93.705 413 22 3 112 520 332222411 332221999 1.250000e-172 616


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 TraesCS6A01G226900 chr6A 427193127 427195580 2453 True 4532.0 4532 100.000 1 2454 1 chr6A.!!$R1 2453
1 TraesCS6A01G226900 chr6D 293493480 293495496 2016 False 1241.5 2357 88.785 1 2454 2 chr6D.!!$F2 2453
2 TraesCS6A01G226900 chr6B 458006499 458008640 2141 False 1095.5 1731 87.633 521 2454 2 chr6B.!!$F1 1933


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
129 132 0.319469 TTGAGTGCGACGAATCTGCA 60.319 50.0 0.0 0.0 33.79 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1980 0.250467 ACGGATTTGCACTGCACTCT 60.25 50.0 2.26 0.0 38.71 3.24 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.