Multiple sequence alignment - TraesCS4A01G103300

Loading Multiple Alignment...

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 TraesCS4A01G103300 chr4A 100.000 2609 0 0 1 2609 116478679 116476071 0.000000e+00 4819
1 TraesCS4A01G103300 chr4B 88.774 2699 131 52 1 2609 428963931 428966547 0.000000e+00 3147
2 TraesCS4A01G103300 chr4B 82.793 401 44 17 482 862 115554268 115554663 4.160000e-88 335
3 TraesCS4A01G103300 chr4D 90.763 1808 69 42 864 2608 348795723 348797495 0.000000e+00 2324
4 TraesCS4A01G103300 chr2A 85.337 341 36 12 533 863 110894267 110893931 8.940000e-90 340
5 TraesCS4A01G103300 chr3B 88.930 271 30 0 2 272 201848226 201848496 4.160000e-88 335
6 TraesCS4A01G103300 chr5B 83.117 385 42 17 484 857 569886747 569887119 1.940000e-86 329
7 TraesCS4A01G103300 chr6B 84.795 342 35 12 533 862 701604915 701605251 6.960000e-86 327
8 TraesCS4A01G103300 chr2B 82.687 387 49 13 487 862 388944315 388944694 6.960000e-86 327
9 TraesCS4A01G103300 chr2B 84.706 340 33 14 532 862 789967529 789967200 3.240000e-84 322
10 TraesCS4A01G103300 chr7A 89.764 254 24 2 20 272 721178158 721178410 9.010000e-85 324
11 TraesCS4A01G103300 chr3D 89.494 257 26 1 16 272 554148897 554148642 9.010000e-85 324
12 TraesCS4A01G103300 chr3A 84.848 330 41 6 534 858 565557670 565557995 9.010000e-85 324
13 TraesCS4A01G103300 chr7B 87.823 271 32 1 2 272 412092538 412092269 1.510000e-82 316
14 TraesCS4A01G103300 chr7B 86.842 190 21 3 31 219 520415202 520415388 2.630000e-50 209
15 TraesCS4A01G103300 chr5D 93.810 210 13 0 1264 1473 480618649 480618440 1.510000e-82 316
16 TraesCS4A01G103300 chr5D 82.955 264 23 8 2 265 508988991 508988750 4.370000e-53 219
17 TraesCS4A01G103300 chr2D 82.005 389 43 23 487 858 642102079 642102457 3.260000e-79 305
18 TraesCS4A01G103300 chr2D 81.912 387 45 21 487 858 598330538 598330914 1.170000e-78 303
19 TraesCS4A01G103300 chr5A 87.795 254 31 0 11 264 241136317 241136064 5.460000e-77 298
20 TraesCS4A01G103300 chr6A 91.566 166 14 0 107 272 611906813 611906648 2.020000e-56 230
21 TraesCS4A01G103300 chr6A 88.554 166 19 0 107 272 125265110 125264945 4.400000e-48 202


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 TraesCS4A01G103300 chr4A 116476071 116478679 2608 True 4819 4819 100.000 1 2609 1 chr4A.!!$R1 2608
1 TraesCS4A01G103300 chr4B 428963931 428966547 2616 False 3147 3147 88.774 1 2609 1 chr4B.!!$F2 2608
2 TraesCS4A01G103300 chr4D 348795723 348797495 1772 False 2324 2324 90.763 864 2608 1 chr4D.!!$F1 1744


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
234 235 0.106769 TGTTGCTCCTTGTGCCTTCA 60.107 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1716 0.03601 AGCACTGCTCGGCAACTTAT 60.036 50.0 0.0 0.0 38.41 1.73 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)



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.