Multiple sequence alignment - TraesCS2B01G331800

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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 TraesCS2B01G331800 chr2B 100.000 2372 0 0 1 2372 474921131 474923502 0 4381
1 TraesCS2B01G331800 chr3A 98.314 2373 35 2 1 2372 66004933 66002565 0 4156
2 TraesCS2B01G331800 chr6D 98.230 2373 37 2 1 2372 389245622 389243254 0 4145
3 TraesCS2B01G331800 chr5D 98.146 2373 39 2 1 2372 503264576 503262208 0 4133
4 TraesCS2B01G331800 chr5D 98.062 2373 41 2 1 2372 503245472 503247840 0 4122
5 TraesCS2B01G331800 chr2D 98.146 2373 39 2 1 2372 591984809 591987177 0 4133
6 TraesCS2B01G331800 chr2A 98.104 2373 40 2 1 2372 726906255 726903887 0 4128
7 TraesCS2B01G331800 chr3D 98.062 2373 40 3 1 2372 589263326 589260959 0 4122
8 TraesCS2B01G331800 chr7B 97.893 2373 45 2 1 2372 663099225 663096857 0 4100
9 TraesCS2B01G331800 chr3B 97.767 2373 46 3 1 2372 201539722 201542088 0 4082


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 TraesCS2B01G331800 chr2B 474921131 474923502 2371 False 4381 4381 100.000 1 2372 1 chr2B.!!$F1 2371
1 TraesCS2B01G331800 chr3A 66002565 66004933 2368 True 4156 4156 98.314 1 2372 1 chr3A.!!$R1 2371
2 TraesCS2B01G331800 chr6D 389243254 389245622 2368 True 4145 4145 98.230 1 2372 1 chr6D.!!$R1 2371
3 TraesCS2B01G331800 chr5D 503262208 503264576 2368 True 4133 4133 98.146 1 2372 1 chr5D.!!$R1 2371
4 TraesCS2B01G331800 chr5D 503245472 503247840 2368 False 4122 4122 98.062 1 2372 1 chr5D.!!$F1 2371
5 TraesCS2B01G331800 chr2D 591984809 591987177 2368 False 4133 4133 98.146 1 2372 1 chr2D.!!$F1 2371
6 TraesCS2B01G331800 chr2A 726903887 726906255 2368 True 4128 4128 98.104 1 2372 1 chr2A.!!$R1 2371
7 TraesCS2B01G331800 chr3D 589260959 589263326 2367 True 4122 4122 98.062 1 2372 1 chr3D.!!$R1 2371
8 TraesCS2B01G331800 chr7B 663096857 663099225 2368 True 4100 4100 97.893 1 2372 1 chr7B.!!$R1 2371
9 TraesCS2B01G331800 chr3B 201539722 201542088 2366 False 4082 4082 97.767 1 2372 1 chr3B.!!$F1 2371

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
750 752 0.89553 AAGATCAAAGAGTCGGGCGA 59.104 50.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2021 0.318955 GCTGTGCCTCAACGCATTTT 60.319 50.0 0.0 0.0 41.7 1.82 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
266 268 1.541310 TACCTGAACCGGTGGCTCAG 61.541 60.000 22.65 22.65 43.32 3.35
336 338 5.308237 ACTCTACTGAGACAAAAAGATGGGT 59.692 40.000 0.00 0.00 42.73 4.51
441 443 3.064412 TCTCCTAGGCTTCCCTCATCTA 58.936 50.000 2.96 0.00 41.75 1.98
511 513 3.682999 GCACTATCTCCCTTCAACCCTTC 60.683 52.174 0.00 0.00 0.00 3.46
604 606 4.974438 ACCCCAAGGACGCCCTCA 62.974 66.667 0.00 0.00 43.48 3.86
620 622 3.625897 CAGCGTCCAGGGGTCACA 61.626 66.667 0.00 0.00 0.00 3.58
750 752 0.895530 AAGATCAAAGAGTCGGGCGA 59.104 50.000 0.00 0.00 0.00 5.54
910 912 3.058914 ACGATGAAAGTTGTAAGCTGTGC 60.059 43.478 0.00 0.00 0.00 4.57
913 915 3.540617 TGAAAGTTGTAAGCTGTGCTCA 58.459 40.909 0.00 0.00 38.25 4.26
914 916 3.561310 TGAAAGTTGTAAGCTGTGCTCAG 59.439 43.478 11.44 11.44 38.25 3.35
915 917 2.175878 AGTTGTAAGCTGTGCTCAGG 57.824 50.000 16.98 0.02 38.25 3.86
916 918 1.160137 GTTGTAAGCTGTGCTCAGGG 58.840 55.000 16.98 0.00 38.25 4.45
964 966 2.569059 CTCTATGGTAGAACCCGTCGA 58.431 52.381 0.00 0.00 37.50 4.20
1176 1178 4.131596 GGCATAGCCTTAACGTTAATGGA 58.868 43.478 26.88 15.20 46.69 3.41
1413 1415 1.108776 AAGCGATTCCCGTAGTAGCA 58.891 50.000 0.00 0.00 41.15 3.49
1779 1781 1.611673 CCTGTTGAAGAATGAGCCGGT 60.612 52.381 1.90 0.00 0.00 5.28
1812 1814 0.766131 TGGCTTGGTTAAGGGAACGA 59.234 50.000 0.00 0.00 39.12 3.85
1899 1901 3.246301 CCTGGGTGATCTATCCATGACT 58.754 50.000 0.00 0.00 0.00 3.41
1938 1940 4.345257 TGAAACTAAGCAGAGGTCTGAACT 59.655 41.667 11.29 0.00 46.59 3.01
1958 1960 6.767423 TGAACTGACTGATGTTGAAGAATCAA 59.233 34.615 0.00 0.00 43.18 2.57
2019 2021 1.571457 AGAGCTAGCTGGTTCTCCCTA 59.429 52.381 24.99 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.037441 TCGCCCCTACGATCCAAA 57.963 55.556 0.00 0.0 37.09 3.28
266 268 7.120873 GTCCTCTTCCCCATTACTTAGAAAAAC 59.879 40.741 0.00 0.0 0.00 2.43
336 338 5.012768 CCTACCTCCTCTACCTTTTTGACAA 59.987 44.000 0.00 0.0 0.00 3.18
441 443 1.238896 TCCTCTTCCCCAGGGATCCT 61.239 60.000 12.58 0.0 44.74 3.24
511 513 2.415168 TCCTTTTGCTACATTTCGCTCG 59.585 45.455 0.00 0.0 0.00 5.03
604 606 3.314331 CTGTGACCCCTGGACGCT 61.314 66.667 0.00 0.0 0.00 5.07
620 622 0.335361 ACAGGGTCTATGGTCGGTCT 59.665 55.000 0.00 0.0 0.00 3.85
774 776 4.263331 GGAATCCAGTTACAGGAGAACCAA 60.263 45.833 2.43 0.0 38.83 3.67
831 833 4.096382 TCTCAAAACAAAAGGTGCTGAGTC 59.904 41.667 0.00 0.0 38.89 3.36
886 888 5.163854 GCACAGCTTACAACTTTCATCGTAT 60.164 40.000 0.00 0.0 0.00 3.06
1069 1071 4.211794 CGAACTGCTGAATTGGCAAAATTT 59.788 37.500 3.01 0.0 39.30 1.82
1176 1178 3.139211 AGCCTTTCCTCTTTTGAACCTCT 59.861 43.478 0.00 0.0 0.00 3.69
1413 1415 2.512515 GCTCCCATTTCGCTCGCT 60.513 61.111 0.00 0.0 0.00 4.93
1779 1781 1.065926 CAAGCCACTGCCTATGAGTCA 60.066 52.381 0.00 0.0 38.69 3.41
1812 1814 2.924101 TACGGCTCCGGTGGGTTT 60.924 61.111 13.31 0.0 44.69 3.27
1899 1901 5.441718 AGTTTCATCCAAGCTTCATCCTA 57.558 39.130 0.00 0.0 0.00 2.94
1958 1960 1.278127 CCCTAACCACAACTCATCCGT 59.722 52.381 0.00 0.0 0.00 4.69
2019 2021 0.318955 GCTGTGCCTCAACGCATTTT 60.319 50.000 0.00 0.0 41.70 1.82


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

AutoCloner maintained by Alex Coulton.