Multiple sequence alignment - TraesCS6A01G271300

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 TraesCS6A01G271300 chr6A 100.000 3949 0 0 1 3949 498005924 498009872 0.000000e+00 7293
1 TraesCS6A01G271300 chr6A 88.166 169 20 0 3764 3932 498011470 498011302 6.690000e-48 202
2 TraesCS6A01G271300 chr6B 89.270 3700 160 98 125 3744 536002629 536006171 0.000000e+00 4414
3 TraesCS6A01G271300 chr6D 93.677 2151 61 30 819 2949 346098579 346100674 0.000000e+00 3149
4 TraesCS6A01G271300 chr6D 91.889 826 37 12 2950 3764 346100703 346101509 0.000000e+00 1127
5 TraesCS6A01G271300 chr6D 91.176 408 25 5 125 528 346097901 346098301 9.650000e-151 544
6 TraesCS6A01G271300 chr6D 92.797 236 7 7 533 766 346098336 346098563 2.270000e-87 333
7 TraesCS6A01G271300 chr1A 97.354 189 5 0 3761 3949 516588871 516588683 4.920000e-84 322
8 TraesCS6A01G271300 chr1A 94.574 129 7 0 1 129 132482496 132482368 2.410000e-47 200
9 TraesCS6A01G271300 chr1A 94.444 126 7 0 1 126 558036562 558036437 1.120000e-45 195
10 TraesCS6A01G271300 chr2B 96.392 194 6 1 3756 3949 162518581 162518773 6.370000e-83 318
11 TraesCS6A01G271300 chr2B 92.806 139 8 2 1 139 78102494 78102630 2.410000e-47 200
12 TraesCS6A01G271300 chrUn 91.304 184 16 0 3765 3948 27335789 27335972 6.550000e-63 252
13 TraesCS6A01G271300 chr3A 90.270 185 18 0 3764 3948 707353373 707353189 3.940000e-60 243
14 TraesCS6A01G271300 chr3A 86.413 184 21 3 3761 3943 648496483 648496303 8.660000e-47 198
15 TraesCS6A01G271300 chr7A 94.574 129 7 0 1 129 215187797 215187669 2.410000e-47 200
16 TraesCS6A01G271300 chr7A 95.238 126 6 0 1 126 674113520 674113645 2.410000e-47 200
17 TraesCS6A01G271300 chr4A 94.574 129 7 0 1 129 17247916 17247788 2.410000e-47 200
18 TraesCS6A01G271300 chr5A 93.939 132 7 1 1 132 1838768 1838638 8.660000e-47 198
19 TraesCS6A01G271300 chr5D 85.638 188 26 1 3757 3944 565740475 565740661 3.110000e-46 196
20 TraesCS6A01G271300 chr2D 92.593 135 10 0 1 135 366061251 366061117 1.120000e-45 195
21 TraesCS6A01G271300 chr2D 93.798 129 8 0 1 129 529693164 529693292 1.120000e-45 195
22 TraesCS6A01G271300 chr5B 85.185 189 27 1 3761 3949 380957353 380957540 4.030000e-45 193
23 TraesCS6A01G271300 chr2A 86.188 181 21 4 3759 3937 14927982 14928160 4.030000e-45 193


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 TraesCS6A01G271300 chr6A 498005924 498009872 3948 False 7293.00 7293 100.00000 1 3949 1 chr6A.!!$F1 3948
1 TraesCS6A01G271300 chr6B 536002629 536006171 3542 False 4414.00 4414 89.27000 125 3744 1 chr6B.!!$F1 3619
2 TraesCS6A01G271300 chr6D 346097901 346101509 3608 False 1288.25 3149 92.38475 125 3764 4 chr6D.!!$F1 3639


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
138 139 0.107654 CAGGCCTAAAGACGGGAAGG 60.108 60.0 3.98 0.00 0.00 3.46 F
338 343 0.110373 AAGCGTAAAAAGAAGCGGCG 60.110 50.0 0.51 0.51 34.34 6.46 F
920 963 0.178935 CCCATCTCCTCTCCTCTCCC 60.179 65.0 0.00 0.00 0.00 4.30 F
2081 2128 0.037975 ACCGTAAGTCGCCGTCATTT 60.038 50.0 0.00 0.00 38.35 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1233 1280 0.035439 AGATGGGCCCGTACTTGTTG 60.035 55.0 19.13 0.00 0.00 3.33 R
2080 2127 0.038166 GGGTCAGCTGGGTTCATGAA 59.962 55.0 15.13 3.38 0.00 2.57 R
2473 2528 0.250338 AGGTGAGTTGCGAGTTTCCC 60.250 55.0 0.00 0.00 0.00 3.97 R
3369 3472 0.034616 GCCTGTCAGTCTGCTGTCTT 59.965 55.0 0.00 0.00 43.05 3.01 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.