Multiple sequence alignment - TraesCS6A01G348500

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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 TraesCS6A01G348500 chr6A 100.000 5977 0 0 1 5977 581287842 581293818 0.000000e+00 10964.0
1 TraesCS6A01G348500 chr6A 99.514 5973 27 1 5 5977 581330461 581336431 0.000000e+00 10794.0
2 TraesCS6A01G348500 chr6A 95.139 144 7 0 3477 3620 605554512 605554369 1.680000e-55 228.0
3 TraesCS6A01G348500 chr2A 92.018 1303 96 4 1 1299 22919988 22921286 0.000000e+00 1823.0
4 TraesCS6A01G348500 chr2A 91.635 1303 100 5 1 1299 23210453 23209156 0.000000e+00 1794.0
5 TraesCS6A01G348500 chr2A 91.558 1303 100 6 1 1299 23095799 23097095 0.000000e+00 1788.0
6 TraesCS6A01G348500 chr2A 91.411 1304 102 6 1 1299 22693891 22692593 0.000000e+00 1779.0
7 TraesCS6A01G348500 chr2A 91.251 1303 105 5 1 1299 23011013 23012310 0.000000e+00 1766.0
8 TraesCS6A01G348500 chrUn 91.865 1303 97 6 1 1299 183448173 183446876 0.000000e+00 1810.0
9 TraesCS6A01G348500 chrUn 91.334 1304 103 6 1 1299 224376293 224374995 0.000000e+00 1773.0
10 TraesCS6A01G348500 chrUn 91.328 1303 104 5 1 1299 237056893 237055596 0.000000e+00 1772.0
11 TraesCS6A01G348500 chrUn 91.174 1303 104 5 1 1299 154027888 154026593 0.000000e+00 1759.0
12 TraesCS6A01G348500 chr7D 91.328 1303 103 9 1 1299 563660157 563661453 0.000000e+00 1772.0
13 TraesCS6A01G348500 chr3B 88.386 663 50 11 2478 3131 421235043 421235687 0.000000e+00 774.0
14 TraesCS6A01G348500 chr3B 88.462 52 4 2 3212 3263 809601814 809601765 1.800000e-05 62.1
15 TraesCS6A01G348500 chr1D 79.605 456 68 12 2479 2926 40224617 40224179 7.530000e-79 305.0
16 TraesCS6A01G348500 chr1D 88.199 161 16 1 1365 1525 58817982 58818139 7.910000e-44 189.0
17 TraesCS6A01G348500 chr1D 100.000 40 0 0 1299 1338 58817943 58817982 2.310000e-09 75.0
18 TraesCS6A01G348500 chr5D 87.124 233 24 1 1299 1525 547632074 547631842 5.940000e-65 259.0
19 TraesCS6A01G348500 chr6B 95.833 144 6 0 3477 3620 699195014 699194871 3.600000e-57 233.0
20 TraesCS6A01G348500 chr4A 89.560 182 19 0 1305 1486 692268049 692268230 1.300000e-56 231.0
21 TraesCS6A01G348500 chr6D 95.139 144 7 0 3477 3620 459831587 459831444 1.680000e-55 228.0
22 TraesCS6A01G348500 chr1A 84.375 192 22 6 2478 2665 283852112 283851925 1.320000e-41 182.0
23 TraesCS6A01G348500 chr1A 73.162 272 51 16 5683 5944 138233500 138233759 1.790000e-10 78.7
24 TraesCS6A01G348500 chr5A 75.926 270 39 19 5683 5943 507962311 507962059 1.360000e-21 115.0
25 TraesCS6A01G348500 chr3D 82.051 78 5 4 3192 3262 602325101 602325026 2.330000e-04 58.4
26 TraesCS6A01G348500 chr3A 89.130 46 3 2 3212 3257 732057352 732057309 8.370000e-04 56.5


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 TraesCS6A01G348500 chr6A 581287842 581293818 5976 False 10964 10964 100.000 1 5977 1 chr6A.!!$F1 5976
1 TraesCS6A01G348500 chr6A 581330461 581336431 5970 False 10794 10794 99.514 5 5977 1 chr6A.!!$F2 5972
2 TraesCS6A01G348500 chr2A 22919988 22921286 1298 False 1823 1823 92.018 1 1299 1 chr2A.!!$F1 1298
3 TraesCS6A01G348500 chr2A 23209156 23210453 1297 True 1794 1794 91.635 1 1299 1 chr2A.!!$R2 1298
4 TraesCS6A01G348500 chr2A 23095799 23097095 1296 False 1788 1788 91.558 1 1299 1 chr2A.!!$F3 1298
5 TraesCS6A01G348500 chr2A 22692593 22693891 1298 True 1779 1779 91.411 1 1299 1 chr2A.!!$R1 1298
6 TraesCS6A01G348500 chr2A 23011013 23012310 1297 False 1766 1766 91.251 1 1299 1 chr2A.!!$F2 1298
7 TraesCS6A01G348500 chrUn 183446876 183448173 1297 True 1810 1810 91.865 1 1299 1 chrUn.!!$R2 1298
8 TraesCS6A01G348500 chrUn 224374995 224376293 1298 True 1773 1773 91.334 1 1299 1 chrUn.!!$R3 1298
9 TraesCS6A01G348500 chrUn 237055596 237056893 1297 True 1772 1772 91.328 1 1299 1 chrUn.!!$R4 1298
10 TraesCS6A01G348500 chrUn 154026593 154027888 1295 True 1759 1759 91.174 1 1299 1 chrUn.!!$R1 1298
11 TraesCS6A01G348500 chr7D 563660157 563661453 1296 False 1772 1772 91.328 1 1299 1 chr7D.!!$F1 1298
12 TraesCS6A01G348500 chr3B 421235043 421235687 644 False 774 774 88.386 2478 3131 1 chr3B.!!$F1 653

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
308 312 1.007271 CACGAGAGACAGCGTTGGT 60.007 57.895 3.74 0.0 38.92 3.67 F
852 857 1.957177 GTCGAGGTGATGCTCCATCTA 59.043 52.381 6.74 0.0 41.06 1.98 F
4309 4327 3.071874 TGCTTAAGAGGGTTGTCATGG 57.928 47.619 6.67 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1136 1142 8.337532 GCATGTAATCTATATAATGCAATGCGA 58.662 33.333 0.0 0.0 40.05 5.10 R
4309 4327 0.038159 CGGTAGGATGGGCTCGAATC 60.038 60.000 0.0 0.0 0.00 2.52 R
5857 5875 4.163078 CACCTTCTCTCTCTCTCTCTCTCT 59.837 50.000 0.0 0.0 0.00 3.10 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
39 40 5.123227 GGGACAAAATCTTCATCATACCGA 58.877 41.667 0.00 0.00 0.00 4.69
119 120 2.970639 CGAAGAAGAGGGGCGACA 59.029 61.111 0.00 0.00 0.00 4.35
169 170 2.425668 GCTGGTTTGTTGGTGTAGTTGT 59.574 45.455 0.00 0.00 0.00 3.32
211 215 2.575993 CGCCAGAGCTGCTGTAGT 59.424 61.111 7.01 0.00 43.33 2.73
308 312 1.007271 CACGAGAGACAGCGTTGGT 60.007 57.895 3.74 0.00 38.92 3.67
568 573 3.763897 AGCCATGGTCATGTTACCTTTTC 59.236 43.478 14.67 0.00 40.44 2.29
852 857 1.957177 GTCGAGGTGATGCTCCATCTA 59.043 52.381 6.74 0.00 41.06 1.98
4309 4327 3.071874 TGCTTAAGAGGGTTGTCATGG 57.928 47.619 6.67 0.00 0.00 3.66
4352 4370 6.239317 CGACAGGATCCTAATATCAACAAGGA 60.239 42.308 15.67 0.00 42.17 3.36
4422 4440 6.343716 TGCACATTTTTGATCAAGTACCAT 57.656 33.333 8.41 0.00 0.00 3.55
4510 4528 0.323999 TCTAAGGCGCACTGACCCTA 60.324 55.000 10.83 0.00 0.00 3.53
5664 5682 0.958822 GCCCAACGGACACATTTTCT 59.041 50.000 0.00 0.00 0.00 2.52
5830 5848 3.277715 GGGAGAAATGGAGCTTGAGAAG 58.722 50.000 0.00 0.00 0.00 2.85
5856 5874 3.614092 AGGCATACAAGGTCATTGAGTG 58.386 45.455 3.86 3.61 41.83 3.51
5857 5875 3.264193 AGGCATACAAGGTCATTGAGTGA 59.736 43.478 3.86 0.00 41.83 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.433343 TGAAGTCATGGATTGTTGGCAT 58.567 40.909 0.00 0.00 0.00 4.40
119 120 1.678101 GCTTCAACAACAACTCTGGCT 59.322 47.619 0.00 0.00 0.00 4.75
187 188 4.519437 CAGCTCTGGCGGCGATGA 62.519 66.667 12.98 3.71 44.37 2.92
308 312 2.304761 ACCAACCTTCGCCAATCTTCTA 59.695 45.455 0.00 0.00 0.00 2.10
345 349 1.243342 TGAGTTTTGATGCCCGCCTG 61.243 55.000 0.00 0.00 0.00 4.85
568 573 3.181499 GCATCAAGCTGACCAATCTTCAG 60.181 47.826 0.00 0.00 43.01 3.02
852 857 0.254178 ACCGCAGATCAAAGGAGCAT 59.746 50.000 7.26 0.00 0.00 3.79
1028 1034 3.752665 TCCATCGAGAGTATGTCTACCC 58.247 50.000 0.00 0.00 34.71 3.69
1136 1142 8.337532 GCATGTAATCTATATAATGCAATGCGA 58.662 33.333 0.00 0.00 40.05 5.10
4309 4327 0.038159 CGGTAGGATGGGCTCGAATC 60.038 60.000 0.00 0.00 0.00 2.52
4352 4370 2.345244 CAAGGAGGTGACGCAGCT 59.655 61.111 10.57 10.57 45.28 4.24
4422 4440 3.769300 TGATTAGAGGAACTGTAGCTGCA 59.231 43.478 3.90 3.90 41.55 4.41
4510 4528 4.802039 CGTCATTACTGTGTTATACGCCTT 59.198 41.667 0.00 0.00 0.00 4.35
5566 5584 8.531146 CAATTTATAAGGTTTTGTGGTGGATCT 58.469 33.333 0.00 0.00 0.00 2.75
5830 5848 4.947388 TCAATGACCTTGTATGCCTTTACC 59.053 41.667 0.00 0.00 36.20 2.85
5856 5874 4.407296 ACCTTCTCTCTCTCTCTCTCTCTC 59.593 50.000 0.00 0.00 0.00 3.20
5857 5875 4.163078 CACCTTCTCTCTCTCTCTCTCTCT 59.837 50.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.