Multiple sequence alignment - TraesCS6B01G188000

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 TraesCS6B01G188000 chr6B 100.000 2899 0 0 524 3422 216468144 216471042 0.000000e+00 5354.0
1 TraesCS6B01G188000 chr6B 100.000 185 0 0 1 185 216467621 216467805 3.270000e-90 342.0
2 TraesCS6B01G188000 chr6A 92.892 2856 129 38 566 3380 162033443 162036265 0.000000e+00 4082.0
3 TraesCS6B01G188000 chr6D 95.616 2395 60 16 524 2897 122730071 122732441 0.000000e+00 3799.0
4 TraesCS6B01G188000 chr6D 82.963 405 42 14 3031 3414 122733451 122733849 1.180000e-89 340.0
5 TraesCS6B01G188000 chr6D 92.000 100 3 4 1 97 197879377 197879280 5.960000e-28 135.0
6 TraesCS6B01G188000 chr6D 88.350 103 8 4 1 100 270717639 270717538 1.670000e-23 121.0
7 TraesCS6B01G188000 chrUn 100.000 419 0 0 1355 1773 476947789 476948207 0.000000e+00 774.0
8 TraesCS6B01G188000 chr4B 90.625 96 5 3 1 94 277534600 277534693 1.290000e-24 124.0
9 TraesCS6B01G188000 chr2D 89.899 99 7 2 1 97 158104755 158104658 1.290000e-24 124.0
10 TraesCS6B01G188000 chr2D 88.889 99 7 3 2 98 223964111 223964207 6.000000e-23 119.0
11 TraesCS6B01G188000 chr1D 89.899 99 7 2 1 97 262868765 262868862 1.290000e-24 124.0
12 TraesCS6B01G188000 chr1D 75.102 245 51 7 2055 2294 37437993 37437754 4.670000e-19 106.0
13 TraesCS6B01G188000 chr5D 89.000 100 8 3 1 98 206828838 206828936 1.670000e-23 121.0
14 TraesCS6B01G188000 chr4A 89.000 100 8 2 1 98 312685602 312685504 1.670000e-23 121.0
15 TraesCS6B01G188000 chr7A 88.889 99 8 2 1 97 246704101 246704198 6.000000e-23 119.0
16 TraesCS6B01G188000 chr1B 75.102 245 51 7 2055 2294 57023673 57023434 4.670000e-19 106.0
17 TraesCS6B01G188000 chr1A 93.750 48 3 0 2055 2102 36620554 36620507 4.740000e-09 73.1


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 TraesCS6B01G188000 chr6B 216467621 216471042 3421 False 2848.0 5354 100.0000 1 3422 2 chr6B.!!$F1 3421
1 TraesCS6B01G188000 chr6A 162033443 162036265 2822 False 4082.0 4082 92.8920 566 3380 1 chr6A.!!$F1 2814
2 TraesCS6B01G188000 chr6D 122730071 122733849 3778 False 2069.5 3799 89.2895 524 3414 2 chr6D.!!$F1 2890


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
80 81 0.035458 ACTTTCTCTTGGGTCTGCGG 59.965 55.0 0.0 0.0 0.00 5.69 F
182 183 0.035458 CTTCCTGTCACACCCCTGAC 59.965 60.0 0.0 0.0 40.98 3.51 F
801 812 0.323957 ACATTGCAGAGCAGAGCAGA 59.676 50.0 0.0 0.0 42.39 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1387 0.454957 CGTAGTTCACCCCGTACGTG 60.455 60.000 15.21 6.26 34.84 4.49 R
1896 1930 1.065928 CTCCGGGTCGCTCATGTAC 59.934 63.158 0.00 0.00 0.00 2.90 R
2475 2509 2.067013 GGCGAGTTGTGGTCTTCTAAC 58.933 52.381 0.00 0.00 0.00 2.34 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.