Multiple sequence alignment - TraesCS4B01G316200

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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 TraesCS4B01G316200 chr4B 100.000 2867 0 0 1 2867 605694239 605691373 0.000000e+00 5295
1 TraesCS4B01G316200 chr4B 81.250 304 53 4 1137 1438 605682888 605683189 2.850000e-60 243
2 TraesCS4B01G316200 chr4D 95.045 2886 93 19 1 2867 479000351 478997497 0.000000e+00 4492
3 TraesCS4B01G316200 chr4D 84.328 268 34 6 1156 1419 382738013 382738276 3.670000e-64 255
4 TraesCS4B01G316200 chr4D 79.245 265 40 14 1154 1412 52763827 52764082 1.370000e-38 171
5 TraesCS4B01G316200 chr4A 90.824 2899 157 41 53 2867 685382574 685379701 0.000000e+00 3779
6 TraesCS4B01G316200 chr4A 82.566 304 49 4 1137 1438 685372125 685372426 6.090000e-67 265
7 TraesCS4B01G316200 chr4A 84.586 266 37 4 1156 1419 64956723 64956986 7.880000e-66 261
8 TraesCS4B01G316200 chr4A 100.000 57 0 0 2 58 685402995 685402939 3.910000e-19 106
9 TraesCS4B01G316200 chr6D 87.132 272 33 2 1150 1420 462273020 462272750 9.980000e-80 307
10 TraesCS4B01G316200 chr6A 87.085 271 35 0 1150 1420 609107553 609107283 9.980000e-80 307
11 TraesCS4B01G316200 chr6B 86.765 272 34 2 1150 1420 704751360 704751630 4.640000e-78 302
12 TraesCS4B01G316200 chr3D 75.000 260 41 22 1143 1392 511726697 511726452 6.540000e-17 99
13 TraesCS4B01G316200 chr3A 75.000 260 41 22 1143 1392 647755513 647755268 6.540000e-17 99


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 TraesCS4B01G316200 chr4B 605691373 605694239 2866 True 5295 5295 100.000 1 2867 1 chr4B.!!$R1 2866
1 TraesCS4B01G316200 chr4D 478997497 479000351 2854 True 4492 4492 95.045 1 2867 1 chr4D.!!$R1 2866
2 TraesCS4B01G316200 chr4A 685379701 685382574 2873 True 3779 3779 90.824 53 2867 1 chr4A.!!$R1 2814


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
985 1020 1.208293 CTCTTTCCCCCTTCCTCTTCG 59.792 57.143 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2404 2459 1.566703 ACTGGAGGAGCTAGCTAGTCA 59.433 52.381 19.38 12.56 0.0 3.41 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.