Multiple sequence alignment - TraesCS2A01G361000

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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 TraesCS2A01G361000 chr2A 100.000 2762 0 0 1 2762 605130740 605127979 0.000000e+00 5101
1 TraesCS2A01G361000 chr2A 87.245 1913 205 20 859 2762 605188637 605186755 0.000000e+00 2145
2 TraesCS2A01G361000 chr2A 88.248 1804 189 13 970 2762 605398590 605400381 0.000000e+00 2135
3 TraesCS2A01G361000 chr3A 98.588 2763 38 1 1 2762 727468524 727471286 0.000000e+00 4885
4 TraesCS2A01G361000 chr3A 87.815 1863 201 16 911 2760 727397545 727399394 0.000000e+00 2159
5 TraesCS2A01G361000 chr3B 94.711 2212 105 7 553 2762 804237378 804239579 0.000000e+00 3426
6 TraesCS2A01G361000 chr3B 87.577 1940 217 19 837 2762 804129992 804131921 0.000000e+00 2226
7 TraesCS2A01G361000 chr3B 89.220 872 90 4 1892 2762 804228291 804229159 0.000000e+00 1086
8 TraesCS2A01G361000 chr3B 86.437 988 117 10 865 1838 804167822 804168806 0.000000e+00 1066
9 TraesCS2A01G361000 chr3B 86.813 910 115 5 1857 2762 804170642 804171550 0.000000e+00 1011
10 TraesCS2A01G361000 chr3B 85.366 984 118 18 873 1838 804214233 804215208 0.000000e+00 996
11 TraesCS2A01G361000 chr3D 94.940 1996 85 4 776 2762 597486582 597488570 0.000000e+00 3112
12 TraesCS2A01G361000 chr3D 88.022 910 103 6 1857 2762 597480260 597481167 0.000000e+00 1072
13 TraesCS2A01G361000 chr3D 86.507 919 118 6 903 1818 597407601 597408516 0.000000e+00 1005
14 TraesCS2A01G361000 chr3D 93.182 220 14 1 1 220 597486271 597486489 3.430000e-84 322
15 TraesCS2A01G361000 chr3D 98.851 87 1 0 252 338 597486484 597486570 3.680000e-34 156


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 TraesCS2A01G361000 chr2A 605127979 605130740 2761 True 5101.000000 5101 100.000000 1 2762 1 chr2A.!!$R1 2761
1 TraesCS2A01G361000 chr2A 605186755 605188637 1882 True 2145.000000 2145 87.245000 859 2762 1 chr2A.!!$R2 1903
2 TraesCS2A01G361000 chr2A 605398590 605400381 1791 False 2135.000000 2135 88.248000 970 2762 1 chr2A.!!$F1 1792
3 TraesCS2A01G361000 chr3A 727468524 727471286 2762 False 4885.000000 4885 98.588000 1 2762 1 chr3A.!!$F2 2761
4 TraesCS2A01G361000 chr3A 727397545 727399394 1849 False 2159.000000 2159 87.815000 911 2760 1 chr3A.!!$F1 1849
5 TraesCS2A01G361000 chr3B 804237378 804239579 2201 False 3426.000000 3426 94.711000 553 2762 1 chr3B.!!$F4 2209
6 TraesCS2A01G361000 chr3B 804129992 804131921 1929 False 2226.000000 2226 87.577000 837 2762 1 chr3B.!!$F1 1925
7 TraesCS2A01G361000 chr3B 804228291 804229159 868 False 1086.000000 1086 89.220000 1892 2762 1 chr3B.!!$F3 870
8 TraesCS2A01G361000 chr3B 804167822 804171550 3728 False 1038.500000 1066 86.625000 865 2762 2 chr3B.!!$F5 1897
9 TraesCS2A01G361000 chr3B 804214233 804215208 975 False 996.000000 996 85.366000 873 1838 1 chr3B.!!$F2 965
10 TraesCS2A01G361000 chr3D 597486271 597488570 2299 False 1196.666667 3112 95.657667 1 2762 3 chr3D.!!$F3 2761
11 TraesCS2A01G361000 chr3D 597480260 597481167 907 False 1072.000000 1072 88.022000 1857 2762 1 chr3D.!!$F2 905
12 TraesCS2A01G361000 chr3D 597407601 597408516 915 False 1005.000000 1005 86.507000 903 1818 1 chr3D.!!$F1 915

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
101 102 0.383949 CCGACCACCAACCAACAAAG 59.616 55.000 0.0 0.0 0.00 2.77 F
1310 1343 4.142038 ACTGGTTTTATCCAAGACACCAC 58.858 43.478 0.0 0.0 37.01 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 1393 2.350772 GCACAAGTTTCTTGATGTCCCG 60.351 50.0 15.04 0.0 0.0 5.14 R
2218 4119 2.830923 ACATCTCTGAGTTGACCTGGAG 59.169 50.0 19.66 0.0 0.0 3.86 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
101 102 0.383949 CCGACCACCAACCAACAAAG 59.616 55.000 0.00 0.00 0.00 2.77
909 915 4.953940 TGTTTCTTGGCCTTTTTGCTAT 57.046 36.364 3.32 0.00 0.00 2.97
1268 1301 4.145876 TCGATGACTTCATGTGCAAAAC 57.854 40.909 0.00 0.00 36.57 2.43
1310 1343 4.142038 ACTGGTTTTATCCAAGACACCAC 58.858 43.478 0.00 0.00 37.01 4.16
1360 1393 0.105593 TCAGATCGCTGGGCAGATTC 59.894 55.000 0.00 0.00 42.53 2.52
1759 1800 6.513180 TGTGAGTTAAATGTTCTTCTCGACT 58.487 36.000 0.00 0.00 0.00 4.18
2136 4037 2.011222 GTTGTTTTGGTCACCACGAGA 58.989 47.619 0.00 0.00 30.78 4.04
2137 4038 1.948104 TGTTTTGGTCACCACGAGAG 58.052 50.000 0.00 0.00 30.78 3.20
2218 4119 6.318396 AGGATATTTTGCTCTGAAGAAGCTTC 59.682 38.462 19.11 19.11 0.00 3.86
2274 4175 3.054728 TCTCAAGAAGTGTGGTGGTTTGA 60.055 43.478 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
909 915 5.018809 AGCCTGCTGAATGAAGGAAATTTA 58.981 37.500 0.00 0.0 44.79 1.40
1310 1343 3.548818 CCTTGAAGTTTTGAGGCGTTGAG 60.549 47.826 0.00 0.0 0.00 3.02
1360 1393 2.350772 GCACAAGTTTCTTGATGTCCCG 60.351 50.000 15.04 0.0 0.00 5.14
2098 3999 4.415150 ATGCCCCAGCCACAGTCG 62.415 66.667 0.00 0.0 38.69 4.18
2136 4037 8.606830 ACTAAGAGGTTCCATTTCAAGAATACT 58.393 33.333 0.00 0.0 0.00 2.12
2137 4038 8.669243 CACTAAGAGGTTCCATTTCAAGAATAC 58.331 37.037 0.00 0.0 0.00 1.89
2151 4052 6.334102 TGAGTCTTCTTCACTAAGAGGTTC 57.666 41.667 0.00 0.0 42.60 3.62
2218 4119 2.830923 ACATCTCTGAGTTGACCTGGAG 59.169 50.000 19.66 0.0 0.00 3.86
2274 4175 5.829391 TGGATATGCTAATGATTGCAAGTGT 59.171 36.000 4.94 0.0 42.74 3.55


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

AutoCloner maintained by Alex Coulton.