Multiple sequence alignment - TraesCS2A01G259300

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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 TraesCS2A01G259300 chr2A 100.000 2716 0 0 1 2716 407124441 407127156 0.000000e+00 5016.0
1 TraesCS2A01G259300 chr2A 99.595 2717 9 1 1 2715 406995942 406998658 0.000000e+00 4955.0
2 TraesCS2A01G259300 chr2A 86.704 895 97 18 847 1730 73183551 73182668 0.000000e+00 974.0
3 TraesCS2A01G259300 chr2A 85.532 940 90 17 844 1778 73179956 73179058 0.000000e+00 941.0
4 TraesCS2A01G259300 chr2A 88.567 726 69 8 996 1717 406964297 406963582 0.000000e+00 869.0
5 TraesCS2A01G259300 chr2A 88.567 726 69 8 996 1717 407092473 407091758 0.000000e+00 869.0
6 TraesCS2A01G259300 chr2A 85.414 665 92 5 1 662 203229513 203230175 0.000000e+00 686.0
7 TraesCS2A01G259300 chr2A 100.000 41 0 0 1772 1812 406997687 406997727 2.900000e-10 76.8
8 TraesCS2A01G259300 chr2A 100.000 41 0 0 1744 1784 406997715 406997755 2.900000e-10 76.8
9 TraesCS2A01G259300 chr2A 100.000 41 0 0 1772 1812 407126184 407126224 2.900000e-10 76.8
10 TraesCS2A01G259300 chr2A 100.000 41 0 0 1744 1784 407126212 407126252 2.900000e-10 76.8
11 TraesCS2A01G259300 chr2D 95.351 1054 36 8 735 1784 323517319 323516275 0.000000e+00 1663.0
12 TraesCS2A01G259300 chr2D 85.320 1124 107 34 671 1764 73820435 73819340 0.000000e+00 1109.0
13 TraesCS2A01G259300 chr2D 86.149 1018 100 21 775 1778 73592377 73591387 0.000000e+00 1061.0
14 TraesCS2A01G259300 chr2D 88.874 737 70 8 983 1717 323561355 323562081 0.000000e+00 896.0
15 TraesCS2A01G259300 chr2D 83.994 681 102 4 1 677 323520940 323520263 0.000000e+00 647.0
16 TraesCS2A01G259300 chr2D 88.109 513 51 3 1875 2387 323516244 323515742 3.870000e-168 601.0
17 TraesCS2A01G259300 chr2D 94.444 72 4 0 673 744 323517566 323517495 7.950000e-21 111.0
18 TraesCS2A01G259300 chr2B 84.729 1146 111 40 668 1773 111669755 111668634 0.000000e+00 1088.0
19 TraesCS2A01G259300 chr2B 89.540 631 45 8 671 1298 391496143 391495531 0.000000e+00 780.0
20 TraesCS2A01G259300 chr2B 78.571 518 74 19 1876 2382 391492941 391492450 9.450000e-80 307.0
21 TraesCS2A01G259300 chr1B 85.460 674 93 5 1 671 339360872 339361543 0.000000e+00 697.0
22 TraesCS2A01G259300 chr1B 84.697 660 95 4 1 658 434563300 434562645 0.000000e+00 654.0
23 TraesCS2A01G259300 chr4D 84.695 673 99 4 1 671 309942570 309943240 0.000000e+00 669.0
24 TraesCS2A01G259300 chr1D 84.435 681 98 8 1 677 447464813 447464137 0.000000e+00 664.0
25 TraesCS2A01G259300 chr1D 84.273 674 100 6 1 671 417913500 417912830 0.000000e+00 652.0
26 TraesCS2A01G259300 chr3A 84.000 675 101 7 1 671 59949382 59950053 2.280000e-180 641.0
27 TraesCS2A01G259300 chr6A 98.485 330 5 0 2387 2716 169321079 169321408 1.400000e-162 582.0
28 TraesCS2A01G259300 chr6A 98.176 329 6 0 2388 2716 96001469 96001141 2.350000e-160 575.0
29 TraesCS2A01G259300 chr6A 98.176 329 6 0 2388 2716 415911780 415912108 2.350000e-160 575.0
30 TraesCS2A01G259300 chr1A 98.485 330 5 0 2387 2716 277182535 277182864 1.400000e-162 582.0
31 TraesCS2A01G259300 chr1A 98.485 330 5 0 2387 2716 277190632 277190961 1.400000e-162 582.0
32 TraesCS2A01G259300 chr1A 98.182 330 6 0 2387 2716 273340417 273340088 6.520000e-161 577.0
33 TraesCS2A01G259300 chr4A 98.187 331 5 1 2387 2716 13085331 13085001 6.520000e-161 577.0
34 TraesCS2A01G259300 chr4A 98.182 330 6 0 2387 2716 577574860 577574531 6.520000e-161 577.0


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 TraesCS2A01G259300 chr2A 407124441 407127156 2715 False 1723.200000 5016 100.0000 1 2716 3 chr2A.!!$F3 2715
1 TraesCS2A01G259300 chr2A 406995942 406998658 2716 False 1702.866667 4955 99.8650 1 2715 3 chr2A.!!$F2 2714
2 TraesCS2A01G259300 chr2A 73179058 73183551 4493 True 957.500000 974 86.1180 844 1778 2 chr2A.!!$R3 934
3 TraesCS2A01G259300 chr2A 406963582 406964297 715 True 869.000000 869 88.5670 996 1717 1 chr2A.!!$R1 721
4 TraesCS2A01G259300 chr2A 407091758 407092473 715 True 869.000000 869 88.5670 996 1717 1 chr2A.!!$R2 721
5 TraesCS2A01G259300 chr2A 203229513 203230175 662 False 686.000000 686 85.4140 1 662 1 chr2A.!!$F1 661
6 TraesCS2A01G259300 chr2D 73819340 73820435 1095 True 1109.000000 1109 85.3200 671 1764 1 chr2D.!!$R2 1093
7 TraesCS2A01G259300 chr2D 73591387 73592377 990 True 1061.000000 1061 86.1490 775 1778 1 chr2D.!!$R1 1003
8 TraesCS2A01G259300 chr2D 323561355 323562081 726 False 896.000000 896 88.8740 983 1717 1 chr2D.!!$F1 734
9 TraesCS2A01G259300 chr2D 323515742 323520940 5198 True 755.500000 1663 90.4745 1 2387 4 chr2D.!!$R3 2386
10 TraesCS2A01G259300 chr2B 111668634 111669755 1121 True 1088.000000 1088 84.7290 668 1773 1 chr2B.!!$R1 1105
11 TraesCS2A01G259300 chr2B 391492450 391496143 3693 True 543.500000 780 84.0555 671 2382 2 chr2B.!!$R2 1711
12 TraesCS2A01G259300 chr1B 339360872 339361543 671 False 697.000000 697 85.4600 1 671 1 chr1B.!!$F1 670
13 TraesCS2A01G259300 chr1B 434562645 434563300 655 True 654.000000 654 84.6970 1 658 1 chr1B.!!$R1 657
14 TraesCS2A01G259300 chr4D 309942570 309943240 670 False 669.000000 669 84.6950 1 671 1 chr4D.!!$F1 670
15 TraesCS2A01G259300 chr1D 447464137 447464813 676 True 664.000000 664 84.4350 1 677 1 chr1D.!!$R2 676
16 TraesCS2A01G259300 chr1D 417912830 417913500 670 True 652.000000 652 84.2730 1 671 1 chr1D.!!$R1 670
17 TraesCS2A01G259300 chr3A 59949382 59950053 671 False 641.000000 641 84.0000 1 671 1 chr3A.!!$F1 670

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
1584 6634 1.918293 ATGGACGAGGTCAAGGGCA 60.918 57.895 0.0 0.0 33.68 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2458 11094 7.896811 TGTAGAGTTGTGTTGTGATATCTTCT 58.103 34.615 3.98 0.0 0.0 2.85 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
1584 6634 1.918293 ATGGACGAGGTCAAGGGCA 60.918 57.895 0.0 0.0 33.68 5.36
1604 6654 2.365635 AGCCCATACGGAGCTGGT 60.366 61.111 0.0 0.0 37.41 4.00
2458 11094 2.215942 TCAAGATCAGGGACTCACGA 57.784 50.000 0.0 0.0 34.60 4.35
2715 11351 4.794439 TCGTCAGCGGGCATCACG 62.794 66.667 0.0 0.0 38.89 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1584 6634 2.765807 AGCTCCGTATGGGCTGCT 60.766 61.111 14.12 12.0 39.42 4.24
2458 11094 7.896811 TGTAGAGTTGTGTTGTGATATCTTCT 58.103 34.615 3.98 0.0 0.00 2.85


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

AutoCloner maintained by Alex Coulton.