Multiple sequence alignment - TraesCS6B01G246200

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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 TraesCS6B01G246200 chr6B 100.000 4772 0 0 1 4772 438917401 438912630 0.000000e+00 8813.0
1 TraesCS6B01G246200 chr6A 93.994 4695 153 41 64 4689 398637533 398642167 0.000000e+00 6988.0
2 TraesCS6B01G246200 chr6A 93.333 60 4 0 4713 4772 398974442 398974501 6.580000e-14 89.8
3 TraesCS6B01G246200 chr6D 94.190 2599 77 21 25 2583 277023781 277021217 0.000000e+00 3895.0
4 TraesCS6B01G246200 chr6D 94.991 2196 84 9 2586 4772 277021131 277018953 0.000000e+00 3422.0
5 TraesCS6B01G246200 chr3B 81.921 177 24 8 2212 2385 413032621 413032450 4.980000e-30 143.0
6 TraesCS6B01G246200 chr5B 76.639 244 33 13 2161 2389 281627779 281627545 3.900000e-21 113.0
7 TraesCS6B01G246200 chr5B 86.667 75 6 4 3124 3195 11043577 11043504 3.960000e-11 80.5
8 TraesCS6B01G246200 chr7D 86.000 100 12 2 2212 2310 598431028 598431126 6.530000e-19 106.0


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 TraesCS6B01G246200 chr6B 438912630 438917401 4771 True 8813.0 8813 100.0000 1 4772 1 chr6B.!!$R1 4771
1 TraesCS6B01G246200 chr6A 398637533 398642167 4634 False 6988.0 6988 93.9940 64 4689 1 chr6A.!!$F1 4625
2 TraesCS6B01G246200 chr6D 277018953 277023781 4828 True 3658.5 3895 94.5905 25 4772 2 chr6D.!!$R1 4747


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
547 572 0.104120 CCATCCATCTGGTTCGCGTA 59.896 55.000 5.77 0.00 36.34 4.42 F
725 751 1.202200 TGCCTTTTCGAAACAACGTGG 60.202 47.619 10.79 7.35 34.70 4.94 F
1123 1172 1.531149 CTGTTGTAAGCGTGTTCCTGG 59.469 52.381 0.00 0.00 0.00 4.45 F
2450 2513 0.250727 TACACCCCTTGCAGCACTTC 60.251 55.000 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2407 0.610509 TAAGGCGCCCATGCTTTTCA 60.611 50.000 26.15 0.0 35.6 2.69 R
2434 2497 1.529244 GTGAAGTGCTGCAAGGGGT 60.529 57.895 2.77 0.0 0.0 4.95 R
3078 3226 4.329545 GGCTGCCGGTTCACTCCA 62.330 66.667 1.35 0.0 0.0 3.86 R
4033 4183 0.029300 CAAACCCGCACAGTTCACAG 59.971 55.000 0.00 0.0 0.0 3.66 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.