Multiple sequence alignment - TraesCS5B01G009200

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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 TraesCS5B01G009200 chr5B 100.000 2633 0 0 1 2633 9297720 9300352 0.000000e+00 4863
1 TraesCS5B01G009200 chr5B 93.009 329 19 4 362 686 691456895 691456567 6.590000e-131 477
2 TraesCS5B01G009200 chr5B 91.014 345 26 3 363 702 57619186 57619530 6.640000e-126 460
3 TraesCS5B01G009200 chr5D 88.803 1545 86 40 1090 2620 9290951 9292422 0.000000e+00 1814
4 TraesCS5B01G009200 chr5D 85.172 580 40 20 688 1252 9290490 9291038 1.060000e-153 553
5 TraesCS5B01G009200 chr5D 89.493 276 16 5 89 363 9290226 9290489 1.170000e-88 337
6 TraesCS5B01G009200 chr5A 87.063 1546 98 47 1090 2620 7487295 7488753 0.000000e+00 1653
7 TraesCS5B01G009200 chr5A 82.696 601 37 24 685 1252 7486816 7487382 3.070000e-129 472
8 TraesCS5B01G009200 chr5A 86.301 292 16 12 89 365 7486535 7486817 1.980000e-76 296
9 TraesCS5B01G009200 chr3D 93.293 328 18 2 364 687 7429105 7428778 5.100000e-132 481
10 TraesCS5B01G009200 chr2A 92.966 327 19 2 364 686 301240561 301240235 8.530000e-130 473
11 TraesCS5B01G009200 chr7D 92.705 329 20 4 364 688 100765780 100765452 3.070000e-129 472
12 TraesCS5B01G009200 chr7D 92.470 332 20 4 361 687 522870432 522870763 1.100000e-128 470
13 TraesCS5B01G009200 chr1B 92.515 334 18 6 359 686 640026964 640027296 3.070000e-129 472
14 TraesCS5B01G009200 chr6D 92.683 328 20 4 363 686 304698233 304697906 1.100000e-128 470
15 TraesCS5B01G009200 chr7A 92.121 330 22 2 362 687 400048377 400048048 1.850000e-126 462


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 TraesCS5B01G009200 chr5B 9297720 9300352 2632 False 4863.000000 4863 100.000000 1 2633 1 chr5B.!!$F1 2632
1 TraesCS5B01G009200 chr5D 9290226 9292422 2196 False 901.333333 1814 87.822667 89 2620 3 chr5D.!!$F1 2531
2 TraesCS5B01G009200 chr5A 7486535 7488753 2218 False 807.000000 1653 85.353333 89 2620 3 chr5A.!!$F1 2531


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
299 311 0.031178 CTGGTTCACAGCAGGCAAAC 59.969 55.0 0.0 0.0 43.72 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2004 0.042967 GAAATCGGCGATGTTCGAGC 60.043 55.0 24.73 1.1 43.74 5.03 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.