Multiple sequence alignment - TraesCS5B01G099200

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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 TraesCS5B01G099200 chr5B 100.000 8033 0 0 1 8033 132278640 132286672 0.000000e+00 14835.0
1 TraesCS5B01G099200 chr5B 97.126 2818 33 8 1514 4306 132278747 132281541 0.000000e+00 4711.0
2 TraesCS5B01G099200 chr5B 97.126 2818 33 8 108 2902 132280153 132282945 0.000000e+00 4711.0
3 TraesCS5B01G099200 chr5B 95.927 1424 20 2 2903 4306 132278747 132280152 0.000000e+00 2274.0
4 TraesCS5B01G099200 chr5B 95.927 1424 20 2 108 1513 132281542 132282945 0.000000e+00 2274.0
5 TraesCS5B01G099200 chr5B 100.000 50 0 0 7452 7501 132286036 132286085 8.580000e-15 93.5
6 TraesCS5B01G099200 chr5B 100.000 50 0 0 7397 7446 132286091 132286140 8.580000e-15 93.5
7 TraesCS5B01G099200 chr5A 95.264 1858 64 12 5614 7449 129597816 129599671 0.000000e+00 2922.0
8 TraesCS5B01G099200 chr5A 93.777 1141 60 8 3617 4751 129596671 129597806 0.000000e+00 1703.0
9 TraesCS5B01G099200 chr5A 94.653 692 33 4 2213 2902 129596671 129597360 0.000000e+00 1070.0
10 TraesCS5B01G099200 chr5A 94.509 692 34 4 824 1513 129596671 129597360 0.000000e+00 1064.0
11 TraesCS5B01G099200 chr5A 98.459 584 7 2 7452 8033 129599619 129600202 0.000000e+00 1027.0
12 TraesCS5B01G099200 chr5A 88.318 856 48 9 1 826 129594485 129595318 0.000000e+00 979.0
13 TraesCS5B01G099200 chr5A 92.287 376 26 3 3150 3525 129594888 129595260 1.530000e-146 531.0
14 TraesCS5B01G099200 chr5A 91.979 374 23 4 1759 2127 129594888 129595259 1.200000e-142 518.0
15 TraesCS5B01G099200 chr5A 94.094 254 8 4 2903 3150 129594592 129594844 5.880000e-101 379.0
16 TraesCS5B01G099200 chr5A 92.857 252 11 4 1514 1759 129594592 129594842 7.670000e-95 359.0
17 TraesCS5B01G099200 chr5A 98.246 57 1 0 2159 2215 129595262 129595318 5.130000e-17 100.0
18 TraesCS5B01G099200 chr5D 94.054 1934 56 28 5572 7449 119482842 119484772 0.000000e+00 2880.0
19 TraesCS5B01G099200 chr5D 95.130 1273 54 6 3547 4815 119481577 119482845 0.000000e+00 2001.0
20 TraesCS5B01G099200 chr5D 97.372 761 19 1 2143 2902 119481577 119482337 0.000000e+00 1293.0
21 TraesCS5B01G099200 chr5D 97.240 761 20 1 754 1513 119481577 119482337 0.000000e+00 1288.0
22 TraesCS5B01G099200 chr5D 93.191 749 36 7 1 743 119457234 119457973 0.000000e+00 1086.0
23 TraesCS5B01G099200 chr5D 98.630 584 6 2 7452 8033 119484720 119485303 0.000000e+00 1033.0
24 TraesCS5B01G099200 chr5D 93.218 634 25 5 2903 3518 119457340 119457973 0.000000e+00 917.0
25 TraesCS5B01G099200 chr5D 92.429 634 25 5 1514 2124 119457340 119457973 0.000000e+00 883.0
26 TraesCS5B01G099200 chr2D 95.257 759 34 2 4812 5570 558787864 558788620 0.000000e+00 1201.0
27 TraesCS5B01G099200 chr2D 94.709 756 40 0 4815 5570 534926663 534927418 0.000000e+00 1175.0
28 TraesCS5B01G099200 chr2D 84.758 269 34 6 6385 6649 500812024 500811759 6.180000e-66 263.0
29 TraesCS5B01G099200 chr2B 95.257 759 34 2 4815 5572 756570426 756569669 0.000000e+00 1201.0
30 TraesCS5B01G099200 chr1D 95.238 756 36 0 4815 5570 233886414 233887169 0.000000e+00 1197.0
31 TraesCS5B01G099200 chr1D 94.716 757 37 3 4815 5570 270634337 270635091 0.000000e+00 1173.0
32 TraesCS5B01G099200 chr4B 94.974 756 36 2 4815 5570 5172768 5173521 0.000000e+00 1184.0
33 TraesCS5B01G099200 chr3D 94.862 759 37 1 4812 5570 445110571 445109815 0.000000e+00 1184.0
34 TraesCS5B01G099200 chr3D 94.293 771 38 4 4804 5570 20702635 20703403 0.000000e+00 1175.0
35 TraesCS5B01G099200 chr6A 94.828 754 36 2 4817 5570 419774086 419773336 0.000000e+00 1173.0
36 TraesCS5B01G099200 chr3A 82.528 269 35 5 6391 6649 25031877 25032143 8.110000e-55 226.0


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 TraesCS5B01G099200 chr5B 132278640 132286672 8032 False 14835.000000 14835 100.000000 1 8033 1 chr5B.!!$F1 8032
1 TraesCS5B01G099200 chr5B 132278747 132286140 7393 False 2359.500000 4711 97.684333 108 7501 6 chr5B.!!$F2 7393
2 TraesCS5B01G099200 chr5A 129594485 129600202 5717 False 968.363636 2922 94.040273 1 8033 11 chr5A.!!$F1 8032
3 TraesCS5B01G099200 chr5D 119481577 119485303 3726 False 1699.000000 2880 96.485200 754 8033 5 chr5D.!!$F2 7279
4 TraesCS5B01G099200 chr5D 119457234 119457973 739 False 962.000000 1086 92.946000 1 3518 3 chr5D.!!$F1 3517
5 TraesCS5B01G099200 chr2D 558787864 558788620 756 False 1201.000000 1201 95.257000 4812 5570 1 chr2D.!!$F2 758
6 TraesCS5B01G099200 chr2D 534926663 534927418 755 False 1175.000000 1175 94.709000 4815 5570 1 chr2D.!!$F1 755
7 TraesCS5B01G099200 chr2B 756569669 756570426 757 True 1201.000000 1201 95.257000 4815 5572 1 chr2B.!!$R1 757
8 TraesCS5B01G099200 chr1D 233886414 233887169 755 False 1197.000000 1197 95.238000 4815 5570 1 chr1D.!!$F1 755
9 TraesCS5B01G099200 chr1D 270634337 270635091 754 False 1173.000000 1173 94.716000 4815 5570 1 chr1D.!!$F2 755
10 TraesCS5B01G099200 chr4B 5172768 5173521 753 False 1184.000000 1184 94.974000 4815 5570 1 chr4B.!!$F1 755
11 TraesCS5B01G099200 chr3D 445109815 445110571 756 True 1184.000000 1184 94.862000 4812 5570 1 chr3D.!!$R1 758
12 TraesCS5B01G099200 chr3D 20702635 20703403 768 False 1175.000000 1175 94.293000 4804 5570 1 chr3D.!!$F1 766
13 TraesCS5B01G099200 chr6A 419773336 419774086 750 True 1173.000000 1173 94.828000 4817 5570 1 chr6A.!!$R1 753


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
25 26 0.179048 CATATTCACGCCCAGCCTCA 60.179 55.0 0.00 0.0 0.00 3.86 F
2079 3481 2.242196 GGGAAGATGTGAGGGAAATCCA 59.758 50.0 1.22 0.0 38.24 3.41 F
2326 3728 0.033504 TCGTGACAAAGCTGACCTCC 59.966 55.0 0.00 0.0 0.00 4.30 F
3010 4412 0.032017 GCCACCTCTCCTCCTTCCTA 60.032 60.0 0.00 0.0 0.00 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 3486 2.555757 GTTGCCTGAATTGTTCTCAGCT 59.444 45.455 0.00 0.00 39.23 4.24 R
2991 4393 0.032017 TAGGAAGGAGGAGAGGTGGC 60.032 60.000 0.00 0.00 0.00 5.01 R
3416 4818 0.036732 TTCCTTGCGAGGTCAATGCT 59.963 50.000 19.96 0.00 43.97 3.79 R
7501 10325 8.319881 ACAGGAGAGATCAATATATTGTCCATG 58.680 37.037 23.68 20.48 38.84 3.66 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.