Multiple sequence alignment - TraesCS3B01G423100

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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 TraesCS3B01G423100 chr3B 100.000 2339 0 0 1 2339 660332195 660334533 0.000000e+00 4320
1 TraesCS3B01G423100 chr3D 95.441 2347 84 9 1 2339 499597675 499600006 0.000000e+00 3720
2 TraesCS3B01G423100 chr3D 94.216 1141 53 6 1 1135 225357596 225358729 0.000000e+00 1729
3 TraesCS3B01G423100 chr3D 84.971 1364 188 13 3 1359 300565481 300566834 0.000000e+00 1367
4 TraesCS3B01G423100 chr3D 87.054 224 18 4 1472 1684 499594000 499593777 2.320000e-60 243
5 TraesCS3B01G423100 chr5D 93.933 1368 74 6 2 1362 117351130 117352495 0.000000e+00 2058
6 TraesCS3B01G423100 chr6D 93.050 1367 85 7 3 1362 158872462 158871099 0.000000e+00 1989
7 TraesCS3B01G423100 chr6D 85.777 1364 186 7 3 1362 48683473 48682114 0.000000e+00 1437
8 TraesCS3B01G423100 chr2B 91.387 1370 104 11 3 1362 361567414 361568779 0.000000e+00 1864
9 TraesCS3B01G423100 chr2B 83.871 124 19 1 1561 1684 182845744 182845866 1.470000e-22 117
10 TraesCS3B01G423100 chr1D 86.404 1368 171 12 3 1362 216023919 216022559 0.000000e+00 1482
11 TraesCS3B01G423100 chr2D 85.359 1366 185 15 3 1362 574398710 574397354 0.000000e+00 1400
12 TraesCS3B01G423100 chr6B 91.768 656 42 3 1685 2339 295781466 295782110 0.000000e+00 902
13 TraesCS3B01G423100 chr7B 91.077 650 48 1 1690 2339 679174035 679173396 0.000000e+00 870
14 TraesCS3B01G423100 chr5B 90.382 655 52 2 1685 2339 139195378 139194735 0.000000e+00 850
15 TraesCS3B01G423100 chr5B 84.545 110 15 2 1577 1685 549123676 549123568 8.840000e-20 108
16 TraesCS3B01G423100 chr5B 80.420 143 23 5 1543 1684 549165412 549165550 1.140000e-18 104
17 TraesCS3B01G423100 chr3A 86.350 652 74 7 1688 2339 375744129 375743493 0.000000e+00 697
18 TraesCS3B01G423100 chr3A 83.019 159 26 1 1822 1979 511997834 511997676 2.420000e-30 143
19 TraesCS3B01G423100 chr7D 86.239 109 15 0 1577 1685 638400294 638400402 4.080000e-23 119
20 TraesCS3B01G423100 chr7D 82.069 145 18 8 1543 1684 459895472 459895611 1.470000e-22 117
21 TraesCS3B01G423100 chr6A 78.431 204 27 10 1496 1686 92886745 92886546 1.470000e-22 117
22 TraesCS3B01G423100 chr7A 83.065 124 20 1 1561 1684 617979749 617979627 6.830000e-21 111


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 TraesCS3B01G423100 chr3B 660332195 660334533 2338 False 4320 4320 100.000 1 2339 1 chr3B.!!$F1 2338
1 TraesCS3B01G423100 chr3D 499597675 499600006 2331 False 3720 3720 95.441 1 2339 1 chr3D.!!$F3 2338
2 TraesCS3B01G423100 chr3D 225357596 225358729 1133 False 1729 1729 94.216 1 1135 1 chr3D.!!$F1 1134
3 TraesCS3B01G423100 chr3D 300565481 300566834 1353 False 1367 1367 84.971 3 1359 1 chr3D.!!$F2 1356
4 TraesCS3B01G423100 chr5D 117351130 117352495 1365 False 2058 2058 93.933 2 1362 1 chr5D.!!$F1 1360
5 TraesCS3B01G423100 chr6D 158871099 158872462 1363 True 1989 1989 93.050 3 1362 1 chr6D.!!$R2 1359
6 TraesCS3B01G423100 chr6D 48682114 48683473 1359 True 1437 1437 85.777 3 1362 1 chr6D.!!$R1 1359
7 TraesCS3B01G423100 chr2B 361567414 361568779 1365 False 1864 1864 91.387 3 1362 1 chr2B.!!$F2 1359
8 TraesCS3B01G423100 chr1D 216022559 216023919 1360 True 1482 1482 86.404 3 1362 1 chr1D.!!$R1 1359
9 TraesCS3B01G423100 chr2D 574397354 574398710 1356 True 1400 1400 85.359 3 1362 1 chr2D.!!$R1 1359
10 TraesCS3B01G423100 chr6B 295781466 295782110 644 False 902 902 91.768 1685 2339 1 chr6B.!!$F1 654
11 TraesCS3B01G423100 chr7B 679173396 679174035 639 True 870 870 91.077 1690 2339 1 chr7B.!!$R1 649
12 TraesCS3B01G423100 chr5B 139194735 139195378 643 True 850 850 90.382 1685 2339 1 chr5B.!!$R1 654
13 TraesCS3B01G423100 chr3A 375743493 375744129 636 True 697 697 86.350 1688 2339 1 chr3A.!!$R1 651


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
953 962 1.193323 AGAGATGACAGAGGCAGGTG 58.807 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 2320 1.456892 ATATGGTGGTCCTCGGCGA 60.457 57.895 10.14 10.14 34.23 5.54 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.