Multiple sequence alignment - TraesCS3B01G420400

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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 TraesCS3B01G420400 chr3B 100.000 2580 0 0 1 2580 657348219 657345640 0.000000e+00 4765
1 TraesCS3B01G420400 chr3A 88.505 1592 104 38 146 1711 637289497 637291035 0.000000e+00 1853
2 TraesCS3B01G420400 chr3D 89.937 1431 102 20 325 1735 497374093 497372685 0.000000e+00 1807
3 TraesCS3B01G420400 chr3D 89.198 324 31 4 11 331 497376501 497376179 4.000000e-108 401
4 TraesCS3B01G420400 chr4A 98.137 805 14 1 1777 2580 742251240 742250436 0.000000e+00 1402
5 TraesCS3B01G420400 chr4B 97.888 805 16 1 1777 2580 662026130 662025326 0.000000e+00 1391
6 TraesCS3B01G420400 chr2B 97.519 806 18 2 1777 2580 25664072 25664877 0.000000e+00 1376
7 TraesCS3B01G420400 chr2B 97.516 805 17 3 1777 2580 23320890 23320088 0.000000e+00 1373
8 TraesCS3B01G420400 chr2B 95.782 806 31 3 1777 2580 93633125 93633929 0.000000e+00 1297
9 TraesCS3B01G420400 chr1A 95.539 807 34 2 1776 2580 534238510 534237704 0.000000e+00 1290
10 TraesCS3B01G420400 chr7B 95.533 806 34 2 1777 2580 96900910 96900105 0.000000e+00 1288
11 TraesCS3B01G420400 chr5B 94.913 806 39 2 1777 2580 492095809 492095004 0.000000e+00 1260
12 TraesCS3B01G420400 chr5A 94.907 805 40 1 1777 2580 708587674 708586870 0.000000e+00 1258


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 TraesCS3B01G420400 chr3B 657345640 657348219 2579 True 4765 4765 100.0000 1 2580 1 chr3B.!!$R1 2579
1 TraesCS3B01G420400 chr3A 637289497 637291035 1538 False 1853 1853 88.5050 146 1711 1 chr3A.!!$F1 1565
2 TraesCS3B01G420400 chr3D 497372685 497376501 3816 True 1104 1807 89.5675 11 1735 2 chr3D.!!$R1 1724
3 TraesCS3B01G420400 chr4A 742250436 742251240 804 True 1402 1402 98.1370 1777 2580 1 chr4A.!!$R1 803
4 TraesCS3B01G420400 chr4B 662025326 662026130 804 True 1391 1391 97.8880 1777 2580 1 chr4B.!!$R1 803
5 TraesCS3B01G420400 chr2B 25664072 25664877 805 False 1376 1376 97.5190 1777 2580 1 chr2B.!!$F1 803
6 TraesCS3B01G420400 chr2B 23320088 23320890 802 True 1373 1373 97.5160 1777 2580 1 chr2B.!!$R1 803
7 TraesCS3B01G420400 chr2B 93633125 93633929 804 False 1297 1297 95.7820 1777 2580 1 chr2B.!!$F2 803
8 TraesCS3B01G420400 chr1A 534237704 534238510 806 True 1290 1290 95.5390 1776 2580 1 chr1A.!!$R1 804
9 TraesCS3B01G420400 chr7B 96900105 96900910 805 True 1288 1288 95.5330 1777 2580 1 chr7B.!!$R1 803
10 TraesCS3B01G420400 chr5B 492095004 492095809 805 True 1260 1260 94.9130 1777 2580 1 chr5B.!!$R1 803
11 TraesCS3B01G420400 chr5A 708586870 708587674 804 True 1258 1258 94.9070 1777 2580 1 chr5A.!!$R1 803


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
767 2880 0.03601 ATCTCCGCCAACTGAAGGTG 60.036 55.0 0.0 0.0 36.41 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2366 4504 0.389948 AACGACGATGCCTCCAGAAC 60.39 55.0 0.0 0.0 0.0 3.01 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.