Multiple sequence alignment - TraesCS6A01G106000

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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 TraesCS6A01G106000 chr6A 100.000 3310 0 0 318 3627 74109128 74105819 0.000000e+00 6113.0
1 TraesCS6A01G106000 chr6A 98.519 135 1 1 3493 3626 577839669 577839535 1.680000e-58 237.0
2 TraesCS6A01G106000 chr6A 100.000 104 0 0 1 104 74109445 74109342 3.700000e-45 193.0
3 TraesCS6A01G106000 chr7D 91.347 1514 73 27 318 1791 101556964 101558459 0.000000e+00 2017.0
4 TraesCS6A01G106000 chr7D 92.384 1405 49 19 2151 3502 101558448 101559847 0.000000e+00 1949.0
5 TraesCS6A01G106000 chr7D 92.308 117 9 0 1202 1318 101557799 101557915 2.240000e-37 167.0
6 TraesCS6A01G106000 chr7D 95.146 103 3 2 1 103 101556810 101556910 1.040000e-35 161.0
7 TraesCS6A01G106000 chr7B 85.877 1494 113 42 318 1776 58716089 58717519 0.000000e+00 1500.0
8 TraesCS6A01G106000 chr7B 93.839 422 22 2 3078 3499 58720399 58720816 1.840000e-177 632.0
9 TraesCS6A01G106000 chr7B 97.275 367 9 1 1791 2156 48114852 48115218 3.980000e-174 621.0
10 TraesCS6A01G106000 chr7B 96.730 367 11 1 1791 2156 579488788 579488422 8.610000e-171 610.0
11 TraesCS6A01G106000 chr7B 86.833 281 29 4 2501 2780 58717826 58718099 1.270000e-79 307.0
12 TraesCS6A01G106000 chr7B 98.519 135 1 1 3494 3627 65668987 65669121 1.680000e-58 237.0
13 TraesCS6A01G106000 chr7B 88.194 144 14 3 2903 3044 97375033 97375175 6.230000e-38 169.0
14 TraesCS6A01G106000 chr7B 89.916 119 12 0 1199 1317 58716894 58717012 1.740000e-33 154.0
15 TraesCS6A01G106000 chr7B 79.612 103 19 1 3168 3268 58545254 58545356 5.020000e-09 73.1
16 TraesCS6A01G106000 chr7A 84.795 1026 77 35 319 1314 105243674 105244650 0.000000e+00 957.0
17 TraesCS6A01G106000 chr7A 89.846 650 57 6 1132 1775 105244513 105245159 0.000000e+00 826.0
18 TraesCS6A01G106000 chr7A 88.000 450 26 7 3078 3502 105264855 105265301 1.160000e-139 507.0
19 TraesCS6A01G106000 chr7A 87.087 333 25 11 2501 2826 105247384 105247705 9.570000e-96 361.0
20 TraesCS6A01G106000 chr7A 97.794 136 3 0 3492 3627 724225137 724225002 6.050000e-58 235.0
21 TraesCS6A01G106000 chr5B 97.011 368 10 1 1790 2156 446984662 446985029 5.150000e-173 617.0
22 TraesCS6A01G106000 chr5B 98.519 135 1 1 3493 3627 127860646 127860513 1.680000e-58 237.0
23 TraesCS6A01G106000 chr5B 85.976 164 17 4 2903 3062 216348872 216348711 1.730000e-38 171.0
24 TraesCS6A01G106000 chr5B 84.091 88 13 1 2820 2906 696611500 696611587 2.320000e-12 84.2
25 TraesCS6A01G106000 chr5A 97.003 367 10 1 1791 2156 548850036 548850402 1.850000e-172 616.0
26 TraesCS6A01G106000 chr5A 87.356 87 10 1 2820 2905 528368698 528368612 8.290000e-17 99.0
27 TraesCS6A01G106000 chr3A 97.003 367 10 1 1791 2156 140958008 140958374 1.850000e-172 616.0
28 TraesCS6A01G106000 chr3B 96.995 366 10 1 1792 2156 567172915 567172550 6.660000e-172 614.0
29 TraesCS6A01G106000 chr6B 96.739 368 10 2 1791 2156 584057371 584057004 2.390000e-171 612.0
30 TraesCS6A01G106000 chr6B 96.730 367 11 1 1791 2156 275927400 275927766 8.610000e-171 610.0
31 TraesCS6A01G106000 chr6B 97.101 138 3 1 3491 3627 646649020 646649157 7.830000e-57 231.0
32 TraesCS6A01G106000 chr4B 96.739 368 11 1 1790 2156 452699133 452699500 2.390000e-171 612.0
33 TraesCS6A01G106000 chr4B 97.794 136 3 0 3492 3627 664108290 664108425 6.050000e-58 235.0
34 TraesCS6A01G106000 chr1A 98.529 136 2 0 3492 3627 4557987 4558122 1.300000e-59 241.0
35 TraesCS6A01G106000 chr1A 85.714 161 17 4 2903 3059 407254118 407254276 8.060000e-37 165.0
36 TraesCS6A01G106000 chr4A 98.519 135 0 2 3493 3627 616146320 616146188 1.680000e-58 237.0
37 TraesCS6A01G106000 chr4A 97.778 135 3 0 3493 3627 618818217 618818083 2.180000e-57 233.0
38 TraesCS6A01G106000 chr6D 90.604 149 11 3 2903 3048 422936423 422936571 1.030000e-45 195.0
39 TraesCS6A01G106000 chr2B 88.356 146 14 3 2903 3046 172978981 172979125 4.810000e-39 172.0
40 TraesCS6A01G106000 chr2D 88.194 144 15 1 2903 3044 74951200 74951057 1.730000e-38 171.0
41 TraesCS6A01G106000 chr2D 88.276 145 12 4 2905 3045 547680226 547680369 6.230000e-38 169.0
42 TraesCS6A01G106000 chr3D 87.671 146 16 2 2903 3046 395050159 395050304 6.230000e-38 169.0
43 TraesCS6A01G106000 chr3D 84.615 91 10 3 2821 2907 593227316 593227226 1.790000e-13 87.9
44 TraesCS6A01G106000 chrUn 84.091 88 13 1 2820 2906 333321178 333321265 2.320000e-12 84.2
45 TraesCS6A01G106000 chrUn 84.091 88 13 1 2820 2906 363221951 363221864 2.320000e-12 84.2
46 TraesCS6A01G106000 chrUn 84.091 88 13 1 2820 2906 402875549 402875462 2.320000e-12 84.2
47 TraesCS6A01G106000 chrUn 84.091 88 13 1 2820 2906 452611230 452611143 2.320000e-12 84.2
48 TraesCS6A01G106000 chrUn 84.091 88 13 1 2820 2906 475148765 475148852 2.320000e-12 84.2


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 TraesCS6A01G106000 chr6A 74105819 74109445 3626 True 3153.000000 6113 100.000000 1 3627 2 chr6A.!!$R2 3626
1 TraesCS6A01G106000 chr7D 101556810 101559847 3037 False 1073.500000 2017 92.796250 1 3502 4 chr7D.!!$F1 3501
2 TraesCS6A01G106000 chr7B 58716089 58720816 4727 False 648.250000 1500 89.116250 318 3499 4 chr7B.!!$F5 3181
3 TraesCS6A01G106000 chr7A 105243674 105247705 4031 False 714.666667 957 87.242667 319 2826 3 chr7A.!!$F2 2507


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
728 747 0.319900 CACTAGTGCGTGTCTTGCCT 60.32 55.0 10.54 0.0 0.0 4.75 F
1856 1953 0.250467 GGCAGCATCACGGATACCAT 60.25 55.0 0.00 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2061 0.040425 GCTGTCGTTTGCGGACATTT 60.040 50.0 0.00 0.00 38.89 2.32 R
3583 7953 0.179073 ATTCCCCGCAAGATCTGACG 60.179 55.0 9.99 9.99 43.02 4.35 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.