Multiple sequence alignment - TraesCS6A01G252200

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 TraesCS6A01G252200 chr6A 100.000 2264 0 0 1 2264 466678913 466681176 0.000000e+00 4181
1 TraesCS6A01G252200 chr5A 98.455 2266 31 4 1 2264 591473726 591475989 0.000000e+00 3988
2 TraesCS6A01G252200 chr1B 98.453 2262 31 4 1 2260 649301320 649299061 0.000000e+00 3980
3 TraesCS6A01G252200 chr7A 98.276 2262 35 4 1 2260 497719530 497717271 0.000000e+00 3958
4 TraesCS6A01G252200 chr5B 98.258 2182 34 4 1 2180 297110492 297112671 0.000000e+00 3816
5 TraesCS6A01G252200 chr5B 99.126 1946 16 1 1 1945 351469616 351467671 0.000000e+00 3498
6 TraesCS6A01G252200 chr5B 99.126 1946 16 1 1 1945 433002513 433000568 0.000000e+00 3498
7 TraesCS6A01G252200 chr5B 99.126 1945 17 0 1 1945 471294933 471292989 0.000000e+00 3498
8 TraesCS6A01G252200 chr5B 98.028 355 7 0 1910 2264 433000567 433000213 3.190000e-173 617
9 TraesCS6A01G252200 chr5B 97.183 355 10 0 1910 2264 471292988 471292634 3.220000e-168 601
10 TraesCS6A01G252200 chr2A 99.177 1945 16 0 1 1945 148615284 148613340 0.000000e+00 3504
11 TraesCS6A01G252200 chr2A 99.228 1942 15 0 1 1942 728933672 728935613 0.000000e+00 3504
12 TraesCS6A01G252200 chr2A 97.746 355 8 0 1910 2264 728935735 728936089 1.490000e-171 612
13 TraesCS6A01G252200 chr3B 87.311 528 55 10 1738 2262 16122670 16122152 5.380000e-166 593
14 TraesCS6A01G252200 chr2B 86.338 527 58 11 1738 2262 563915374 563914860 1.520000e-156 562


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 TraesCS6A01G252200 chr6A 466678913 466681176 2263 False 4181.0 4181 100.0000 1 2264 1 chr6A.!!$F1 2263
1 TraesCS6A01G252200 chr5A 591473726 591475989 2263 False 3988.0 3988 98.4550 1 2264 1 chr5A.!!$F1 2263
2 TraesCS6A01G252200 chr1B 649299061 649301320 2259 True 3980.0 3980 98.4530 1 2260 1 chr1B.!!$R1 2259
3 TraesCS6A01G252200 chr7A 497717271 497719530 2259 True 3958.0 3958 98.2760 1 2260 1 chr7A.!!$R1 2259
4 TraesCS6A01G252200 chr5B 297110492 297112671 2179 False 3816.0 3816 98.2580 1 2180 1 chr5B.!!$F1 2179
5 TraesCS6A01G252200 chr5B 351467671 351469616 1945 True 3498.0 3498 99.1260 1 1945 1 chr5B.!!$R1 1944
6 TraesCS6A01G252200 chr5B 433000213 433002513 2300 True 2057.5 3498 98.5770 1 2264 2 chr5B.!!$R2 2263
7 TraesCS6A01G252200 chr5B 471292634 471294933 2299 True 2049.5 3498 98.1545 1 2264 2 chr5B.!!$R3 2263
8 TraesCS6A01G252200 chr2A 148613340 148615284 1944 True 3504.0 3504 99.1770 1 1945 1 chr2A.!!$R1 1944
9 TraesCS6A01G252200 chr2A 728933672 728936089 2417 False 2058.0 3504 98.4870 1 2264 2 chr2A.!!$F1 2263
10 TraesCS6A01G252200 chr3B 16122152 16122670 518 True 593.0 593 87.3110 1738 2262 1 chr3B.!!$R1 524
11 TraesCS6A01G252200 chr2B 563914860 563915374 514 True 562.0 562 86.3380 1738 2262 1 chr2B.!!$R1 524


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
786 789 0.622136 TAGAGGTGGTGGTCGAGCTA 59.378 55.0 16.64 0.0 30.83 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1660 1.795525 CGACAGTTCATCATCGACGCT 60.796 52.381 0.0 0.0 36.7 5.07 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
459 460 1.344393 TGGATGACCTGGCTGGATACT 60.344 52.381 18.12 0.0 39.71 2.12
460 461 2.090775 TGGATGACCTGGCTGGATACTA 60.091 50.000 18.12 1.2 39.71 1.82
785 788 0.681564 CTAGAGGTGGTGGTCGAGCT 60.682 60.000 16.64 0.0 33.17 4.09
786 789 0.622136 TAGAGGTGGTGGTCGAGCTA 59.378 55.000 16.64 0.0 30.83 3.32
900 903 8.047911 TCGGTTATTTGTTTAATCCAGATGGTA 58.952 33.333 0.00 0.0 36.34 3.25
1427 1430 1.066143 CAGATTGGTTACGGAGGCAGT 60.066 52.381 0.00 0.0 0.00 4.40
1657 1660 2.380064 AGACAAATGGAAAGGCACCA 57.620 45.000 0.00 0.0 41.83 4.17
1782 1785 6.546972 TTATGTGCAAACTATGTTCGTCAA 57.453 33.333 0.00 0.0 0.00 3.18
2190 2229 1.656441 CGTCTGGCTTGCTTTGCTT 59.344 52.632 0.00 0.0 0.00 3.91
2244 2401 2.927856 TGGACACCCAGACGCCAT 60.928 61.111 0.00 0.0 37.58 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
459 460 5.659463 GCTACCAAATTGTTTCATGCCATA 58.341 37.500 0.00 0.00 0.00 2.74
460 461 4.506758 GCTACCAAATTGTTTCATGCCAT 58.493 39.130 0.00 0.00 0.00 4.40
785 788 1.550524 CCACCTCTAGCACTTGTGCTA 59.449 52.381 27.11 27.11 44.28 3.49
1427 1430 3.157881 CATAGGACTCCTCGAATAGGCA 58.842 50.000 0.00 0.00 46.10 4.75
1657 1660 1.795525 CGACAGTTCATCATCGACGCT 60.796 52.381 0.00 0.00 36.70 5.07
1782 1785 6.810911 ACAAAGCATATCAACTAGTCTCGAT 58.189 36.000 0.00 1.77 0.00 3.59
2149 2188 2.501610 GACCCTGGCGTCTGGATC 59.498 66.667 15.35 2.20 34.32 3.36
2190 2229 3.519973 CTGTCTGGTCACCTGCGCA 62.520 63.158 10.98 10.98 0.00 6.09
2244 2401 2.842462 ACCAGACGCCAGTGACCA 60.842 61.111 0.00 0.00 0.00 4.02



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

AutoCloner maintained by Alex Coulton.