Multiple sequence alignment - TraesCS6D01G254600

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 TraesCS6D01G254600 chr6D 100.000 2473 0 0 1 2473 359439057 359436585 0 4567
1 TraesCS6D01G254600 chr6D 95.115 1863 83 5 3 1858 11364955 11366816 0 2929
2 TraesCS6D01G254600 chr6D 94.654 1852 79 9 13 1858 388966432 388968269 0 2854
3 TraesCS6D01G254600 chr6D 94.382 623 29 6 1853 2473 339384762 339384144 0 952
4 TraesCS6D01G254600 chr6D 94.231 624 29 6 1853 2473 359428810 359428191 0 946
5 TraesCS6D01G254600 chr2D 95.655 1864 71 8 1 1858 349010866 349009007 0 2985
6 TraesCS6D01G254600 chr2D 95.496 1865 72 10 1 1858 60191051 60189192 0 2968
7 TraesCS6D01G254600 chr2D 94.061 623 33 4 1853 2473 102029284 102028664 0 942
8 TraesCS6D01G254600 chr7D 95.381 1862 81 4 1 1858 460639781 460637921 0 2957
9 TraesCS6D01G254600 chr7D 95.062 1863 81 8 1 1858 536395134 536396990 0 2920
10 TraesCS6D01G254600 chr4D 94.895 1861 92 2 1 1858 462137804 462135944 0 2907
11 TraesCS6D01G254600 chr4D 94.222 623 32 4 1853 2473 509015967 509015347 0 948
12 TraesCS6D01G254600 chr4D 94.071 624 31 6 1853 2473 416466281 416466901 0 942
13 TraesCS6D01G254600 chr5D 94.895 1861 89 4 1 1858 432505714 432507571 0 2905
14 TraesCS6D01G254600 chrUn 94.895 1861 86 8 1 1858 26613996 26612142 0 2902
15 TraesCS6D01G254600 chr1D 94.543 623 30 4 1853 2473 360451141 360450521 0 959
16 TraesCS6D01G254600 chr1D 94.061 623 33 4 1853 2473 222320272 222320892 0 942
17 TraesCS6D01G254600 chr3D 94.525 621 29 5 1853 2471 350678466 350679083 0 953
18 TraesCS6D01G254600 chr3D 94.061 623 33 4 1853 2473 415692617 415691997 0 942


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 TraesCS6D01G254600 chr6D 359436585 359439057 2472 True 4567 4567 100.000 1 2473 1 chr6D.!!$R3 2472
1 TraesCS6D01G254600 chr6D 11364955 11366816 1861 False 2929 2929 95.115 3 1858 1 chr6D.!!$F1 1855
2 TraesCS6D01G254600 chr6D 388966432 388968269 1837 False 2854 2854 94.654 13 1858 1 chr6D.!!$F2 1845
3 TraesCS6D01G254600 chr6D 339384144 339384762 618 True 952 952 94.382 1853 2473 1 chr6D.!!$R1 620
4 TraesCS6D01G254600 chr6D 359428191 359428810 619 True 946 946 94.231 1853 2473 1 chr6D.!!$R2 620
5 TraesCS6D01G254600 chr2D 349009007 349010866 1859 True 2985 2985 95.655 1 1858 1 chr2D.!!$R3 1857
6 TraesCS6D01G254600 chr2D 60189192 60191051 1859 True 2968 2968 95.496 1 1858 1 chr2D.!!$R1 1857
7 TraesCS6D01G254600 chr2D 102028664 102029284 620 True 942 942 94.061 1853 2473 1 chr2D.!!$R2 620
8 TraesCS6D01G254600 chr7D 460637921 460639781 1860 True 2957 2957 95.381 1 1858 1 chr7D.!!$R1 1857
9 TraesCS6D01G254600 chr7D 536395134 536396990 1856 False 2920 2920 95.062 1 1858 1 chr7D.!!$F1 1857
10 TraesCS6D01G254600 chr4D 462135944 462137804 1860 True 2907 2907 94.895 1 1858 1 chr4D.!!$R1 1857
11 TraesCS6D01G254600 chr4D 509015347 509015967 620 True 948 948 94.222 1853 2473 1 chr4D.!!$R2 620
12 TraesCS6D01G254600 chr4D 416466281 416466901 620 False 942 942 94.071 1853 2473 1 chr4D.!!$F1 620
13 TraesCS6D01G254600 chr5D 432505714 432507571 1857 False 2905 2905 94.895 1 1858 1 chr5D.!!$F1 1857
14 TraesCS6D01G254600 chrUn 26612142 26613996 1854 True 2902 2902 94.895 1 1858 1 chrUn.!!$R1 1857
15 TraesCS6D01G254600 chr1D 360450521 360451141 620 True 959 959 94.543 1853 2473 1 chr1D.!!$R1 620
16 TraesCS6D01G254600 chr1D 222320272 222320892 620 False 942 942 94.061 1853 2473 1 chr1D.!!$F1 620
17 TraesCS6D01G254600 chr3D 350678466 350679083 617 False 953 953 94.525 1853 2471 1 chr3D.!!$F1 618
18 TraesCS6D01G254600 chr3D 415691997 415692617 620 True 942 942 94.061 1853 2473 1 chr3D.!!$R1 620

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
407 410 0.447801 GCGACATTGCCGTTTGATCT 59.552 50.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 1950 0.178861 TGGCCCTCCTTTCCTTCTCT 60.179 55.0 0.0 0.0 0.0 3.1 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
70 71 1.076632 CTACAGAGTCGGGCTCCCT 60.077 63.158 5.89 0.00 45.21 4.20
312 315 2.126228 CCGAACGCCTTCGCTACA 60.126 61.111 11.72 0.00 46.72 2.74
402 405 2.975799 ACCGCGACATTGCCGTTT 60.976 55.556 8.23 0.00 0.00 3.60
407 410 0.447801 GCGACATTGCCGTTTGATCT 59.552 50.000 0.00 0.00 0.00 2.75
514 517 4.418392 TCGTTTGCTCTCGTTAGGTATTC 58.582 43.478 0.00 0.00 0.00 1.75
877 885 0.824109 CCAGACGTGGCCATCTTCTA 59.176 55.000 9.72 0.00 36.89 2.10
961 969 2.546494 GCTGCGTGTTGCTTCCTGT 61.546 57.895 0.00 0.00 46.63 4.00
1053 1061 4.505039 GCGGAGGGATTGTTAATGGAGTAT 60.505 45.833 0.00 0.00 0.00 2.12
1092 1100 1.610673 GGTGTGGAGAGGCAGGAGA 60.611 63.158 0.00 0.00 0.00 3.71
1215 1229 3.072476 ACCCGGAGATCTCAGTTCAAAAA 59.928 43.478 23.85 0.00 0.00 1.94
1256 1271 5.043762 AGGGGTGATTTCCTTCAATAGGTA 58.956 41.667 0.00 0.00 45.03 3.08
1325 1340 8.950007 ATTAGGAAAGTTAGGATTTTTGGACA 57.050 30.769 0.00 0.00 0.00 4.02
1623 1640 9.722056 GAGTCGATTGATTTGCATAATTTAAGT 57.278 29.630 0.00 0.00 0.00 2.24
1658 1675 7.765360 TCCGTGATTTGTTATACGTTAGGAAAT 59.235 33.333 0.00 0.00 34.96 2.17
1700 1717 6.472887 AGTGGAGAGAAAAATAAACCGATGA 58.527 36.000 0.00 0.00 0.00 2.92
1822 1844 2.496111 ACCAGCGAAAATAAACCACGA 58.504 42.857 0.00 0.00 0.00 4.35
1888 1911 2.439880 CCAAGTAGGATTCCCCTCCTTC 59.560 54.545 0.00 0.00 43.33 3.46
1927 1950 3.596046 AGAGAAGGAAAGAGAGGGAGAGA 59.404 47.826 0.00 0.00 0.00 3.10
2016 2042 1.519719 CTCTTGGCCCTTCTCCTCG 59.480 63.158 0.00 0.00 0.00 4.63
2069 2095 2.279918 CCCGGCGAATTCCCGTAG 60.280 66.667 24.50 16.08 44.13 3.51
2075 2101 0.102481 GCGAATTCCCGTAGCTCTCA 59.898 55.000 0.00 0.00 0.00 3.27
2076 2102 1.841450 CGAATTCCCGTAGCTCTCAC 58.159 55.000 0.00 0.00 0.00 3.51
2167 2193 6.639563 TGATCTTTATGTCTCGACCATTTCA 58.360 36.000 0.00 0.00 0.00 2.69
2174 2200 3.320826 TGTCTCGACCATTTCAAGACTCA 59.679 43.478 0.00 0.00 0.00 3.41
2206 2232 0.558220 TGATCTCATCCGGGACTCCT 59.442 55.000 0.00 0.00 0.00 3.69
2228 2254 7.284074 TCCTAACAACCTTCAGTACATCAAAA 58.716 34.615 0.00 0.00 0.00 2.44
2297 2323 4.718961 CCCTATGGGTTTGAGAACTATGG 58.281 47.826 0.00 0.00 38.25 2.74
2317 2343 2.688446 GGAGACATGACCGAGACACATA 59.312 50.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 2.109799 CCCTTCGATGCCAGCGAT 59.890 61.111 5.66 0.00 37.64 4.58
205 208 1.006571 GGCGTCTGACTTCGTCCAA 60.007 57.895 6.21 0.00 0.00 3.53
277 280 2.881389 AGCTCCTCGACAAGCTCG 59.119 61.111 10.32 0.00 45.57 5.03
312 315 2.284798 ATCTCGTTGGCGCAGACGAT 62.285 55.000 29.05 17.62 41.59 3.73
576 579 1.076549 ATGTGCCACGGGGTCAATT 59.923 52.632 5.12 0.00 36.17 2.32
598 601 2.745308 ATGGGCGTGCATAGGAGCA 61.745 57.895 0.00 0.00 43.35 4.26
632 636 3.036084 CGTGTGCGCGGAAGAAGT 61.036 61.111 8.83 0.00 0.00 3.01
862 870 0.389391 CCGATAGAAGATGGCCACGT 59.611 55.000 8.16 0.00 39.76 4.49
1053 1061 1.984570 CTCCGCCACCTCCTTCTCA 60.985 63.158 0.00 0.00 0.00 3.27
1092 1100 3.717294 GGTGACACCGCCCCAGAT 61.717 66.667 9.33 0.00 36.97 2.90
1215 1229 4.289672 ACCCCTCCATCGATATTAGCATTT 59.710 41.667 0.00 0.00 0.00 2.32
1300 1315 8.950007 TGTCCAAAAATCCTAACTTTCCTAAT 57.050 30.769 0.00 0.00 0.00 1.73
1322 1337 4.646492 ACCCCATTTGCATAGAAATCTGTC 59.354 41.667 0.00 0.00 0.00 3.51
1325 1340 6.625532 AAAACCCCATTTGCATAGAAATCT 57.374 33.333 0.00 0.00 0.00 2.40
1623 1640 9.454585 CGTATAACAAATCACGGATCTAACTTA 57.545 33.333 0.00 0.00 0.00 2.24
1658 1675 7.741785 TCTCCACTCTTTATTACAACCAGAAA 58.258 34.615 0.00 0.00 0.00 2.52
1819 1841 3.255149 ACGAGTTGGTGAATAGTCTTCGT 59.745 43.478 0.00 0.00 0.00 3.85
1822 1844 3.576982 TGGACGAGTTGGTGAATAGTCTT 59.423 43.478 0.00 0.00 0.00 3.01
1927 1950 0.178861 TGGCCCTCCTTTCCTTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
2016 2042 2.426842 ATTGGGCTTTAGTGGAGAGC 57.573 50.000 0.00 0.00 35.71 4.09
2069 2095 2.342910 TTTTCGGAGTACGTGAGAGC 57.657 50.000 0.00 0.00 44.69 4.09
2075 2101 2.491693 TCGGGTATTTTTCGGAGTACGT 59.508 45.455 0.00 0.00 44.69 3.57
2076 2102 3.149436 TCGGGTATTTTTCGGAGTACG 57.851 47.619 0.00 0.00 46.11 3.67
2174 2200 2.024414 TGAGATCACGGACATGACGAT 58.976 47.619 18.41 3.21 34.93 3.73
2206 2232 7.337184 TGTGTTTTGATGTACTGAAGGTTGTTA 59.663 33.333 0.00 0.00 0.00 2.41
2228 2254 9.594478 TGACGATTTGTATTATGAGTTATGTGT 57.406 29.630 0.00 0.00 0.00 3.72
2297 2323 2.949451 ATGTGTCTCGGTCATGTCTC 57.051 50.000 0.00 0.00 0.00 3.36
2317 2343 4.758165 CCGCTATTGGTTATTTTACCGGAT 59.242 41.667 9.46 0.00 41.28 4.18
2324 2350 4.401202 CCAGGTTCCGCTATTGGTTATTTT 59.599 41.667 0.00 0.00 0.00 1.82
2325 2351 3.951680 CCAGGTTCCGCTATTGGTTATTT 59.048 43.478 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.