Multiple sequence alignment - TraesCS5D01G418100

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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 TraesCS5D01G418100 chr5D 100.000 2869 0 0 1 2869 480156389 480153521 0.000000e+00 5299
1 TraesCS5D01G418100 chr5D 92.055 365 23 4 2508 2869 543496019 543495658 2.550000e-140 508
2 TraesCS5D01G418100 chr5D 81.646 158 22 6 1008 1160 371872966 371872811 1.080000e-24 124
3 TraesCS5D01G418100 chr5B 89.365 1213 72 34 738 1945 588157031 588155871 0.000000e+00 1472
4 TraesCS5D01G418100 chr5B 91.525 413 34 1 2055 2467 206080197 206079786 4.150000e-158 568
5 TraesCS5D01G418100 chr5B 89.423 416 40 4 2054 2467 372565078 372565491 3.280000e-144 521
6 TraesCS5D01G418100 chr5B 89.209 417 44 1 2051 2466 368701159 368701575 1.180000e-143 520
7 TraesCS5D01G418100 chr5B 85.185 270 24 5 295 562 345977218 345977473 2.190000e-66 263
8 TraesCS5D01G418100 chr5B 76.334 431 87 12 1403 1827 441811578 441811157 1.730000e-52 217
9 TraesCS5D01G418100 chr5A 94.428 664 31 2 1388 2051 598637757 598637100 0.000000e+00 1016
10 TraesCS5D01G418100 chr5A 88.325 197 11 6 675 859 598637949 598637753 2.880000e-55 226
11 TraesCS5D01G418100 chr5A 79.375 160 24 7 1008 1160 475310746 475310589 1.410000e-18 104
12 TraesCS5D01G418100 chr2B 91.630 681 51 6 1 676 664414870 664414191 0.000000e+00 937
13 TraesCS5D01G418100 chr2B 91.262 412 36 0 2055 2466 720851553 720851964 1.930000e-156 562
14 TraesCS5D01G418100 chr2B 91.081 370 24 7 2508 2869 5158842 5159210 2.570000e-135 492
15 TraesCS5D01G418100 chr1A 91.298 678 46 7 1 675 477119924 477120591 0.000000e+00 913
16 TraesCS5D01G418100 chr6B 90.896 681 53 7 1 676 210779837 210780513 0.000000e+00 905
17 TraesCS5D01G418100 chr3D 92.190 589 41 5 1 585 66901902 66901315 0.000000e+00 828
18 TraesCS5D01G418100 chr3D 91.967 361 26 2 2508 2866 438060327 438059968 1.190000e-138 503
19 TraesCS5D01G418100 chr3D 81.140 456 69 11 1403 1845 92783755 92784206 1.640000e-92 350
20 TraesCS5D01G418100 chr3D 80.702 456 71 11 1403 1845 92750230 92749779 3.540000e-89 339
21 TraesCS5D01G418100 chr3D 90.816 98 8 1 583 679 66900935 66900838 2.320000e-26 130
22 TraesCS5D01G418100 chr3B 88.416 682 66 9 1 677 169264372 169265045 0.000000e+00 809
23 TraesCS5D01G418100 chr3B 91.283 413 35 1 2055 2467 366972324 366971913 1.930000e-156 562
24 TraesCS5D01G418100 chr3B 90.884 362 28 5 2510 2869 420305099 420304741 5.560000e-132 481
25 TraesCS5D01G418100 chr3B 80.338 473 82 7 1403 1865 144070200 144070671 5.880000e-92 348
26 TraesCS5D01G418100 chr3B 80.127 473 83 7 1403 1865 144057775 144057304 2.740000e-90 342
27 TraesCS5D01G418100 chr3B 87.879 264 29 3 314 574 631524287 631524550 9.990000e-80 307
28 TraesCS5D01G418100 chr3A 88.253 681 59 12 1 676 41224179 41223515 0.000000e+00 795
29 TraesCS5D01G418100 chr3A 92.033 364 25 4 2508 2869 720854605 720854966 2.550000e-140 508
30 TraesCS5D01G418100 chr3A 90.634 363 31 3 2508 2869 549911369 549911729 2.000000e-131 479
31 TraesCS5D01G418100 chr4D 91.546 414 35 0 2054 2467 105926441 105926028 3.210000e-159 571
32 TraesCS5D01G418100 chr4D 90.503 358 32 2 2514 2869 441078508 441078865 3.350000e-129 472
33 TraesCS5D01G418100 chr2D 93.600 375 18 2 2098 2467 351374981 351375354 3.230000e-154 555
34 TraesCS5D01G418100 chr2D 77.907 430 77 14 1403 1826 15966853 15967270 4.750000e-63 252
35 TraesCS5D01G418100 chr1B 89.976 419 41 1 2049 2467 280989536 280989953 9.040000e-150 540
36 TraesCS5D01G418100 chr1B 79.233 443 70 19 1403 1837 101591228 101590800 3.620000e-74 289
37 TraesCS5D01G418100 chr1B 80.879 387 51 19 1461 1837 101519772 101520145 1.680000e-72 283
38 TraesCS5D01G418100 chr6A 89.831 413 42 0 2055 2467 461140282 461140694 5.440000e-147 531
39 TraesCS5D01G418100 chr4A 90.909 363 30 3 2508 2869 675598225 675598585 4.300000e-133 484
40 TraesCS5D01G418100 chr4B 89.894 376 31 4 2497 2868 546822505 546822877 7.190000e-131 477
41 TraesCS5D01G418100 chr4B 80.338 473 82 7 1403 1865 50399960 50399489 5.880000e-92 348
42 TraesCS5D01G418100 chr4B 80.338 473 82 7 1403 1865 50443679 50444150 5.880000e-92 348
43 TraesCS5D01G418100 chr4B 88.095 168 17 1 989 1156 50400346 50400182 2.260000e-46 196
44 TraesCS5D01G418100 chr4B 87.719 171 18 1 986 1156 50443282 50443449 2.260000e-46 196
45 TraesCS5D01G418100 chr1D 80.435 414 61 17 1403 1809 63544066 63544466 6.010000e-77 298
46 TraesCS5D01G418100 chr2A 77.427 412 75 14 1403 1808 17857632 17858031 2.220000e-56 230
47 TraesCS5D01G418100 chr7D 88.571 105 12 0 1008 1112 148160791 148160895 8.340000e-26 128
48 TraesCS5D01G418100 chr7B 88.571 105 12 0 1008 1112 111317291 111317395 8.340000e-26 128


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 TraesCS5D01G418100 chr5D 480153521 480156389 2868 True 5299 5299 100.0000 1 2869 1 chr5D.!!$R2 2868
1 TraesCS5D01G418100 chr5B 588155871 588157031 1160 True 1472 1472 89.3650 738 1945 1 chr5B.!!$R3 1207
2 TraesCS5D01G418100 chr5A 598637100 598637949 849 True 621 1016 91.3765 675 2051 2 chr5A.!!$R2 1376
3 TraesCS5D01G418100 chr2B 664414191 664414870 679 True 937 937 91.6300 1 676 1 chr2B.!!$R1 675
4 TraesCS5D01G418100 chr1A 477119924 477120591 667 False 913 913 91.2980 1 675 1 chr1A.!!$F1 674
5 TraesCS5D01G418100 chr6B 210779837 210780513 676 False 905 905 90.8960 1 676 1 chr6B.!!$F1 675
6 TraesCS5D01G418100 chr3D 66900838 66901902 1064 True 479 828 91.5030 1 679 2 chr3D.!!$R3 678
7 TraesCS5D01G418100 chr3B 169264372 169265045 673 False 809 809 88.4160 1 677 1 chr3B.!!$F2 676
8 TraesCS5D01G418100 chr3A 41223515 41224179 664 True 795 795 88.2530 1 676 1 chr3A.!!$R1 675
9 TraesCS5D01G418100 chr4B 50399489 50400346 857 True 272 348 84.2165 989 1865 2 chr4B.!!$R1 876
10 TraesCS5D01G418100 chr4B 50443282 50444150 868 False 272 348 84.0285 986 1865 2 chr4B.!!$F2 879


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
918 1334 0.032615 AGCCTGCCTCACTACTAGCT 60.033 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 2853 0.038166 ATCTCGGTTGGTGCAATGGT 59.962 50.0 0.0 0.0 0.0 3.55 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.