Multiple sequence alignment - TraesCS2A01G517700

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 TraesCS2A01G517700 chr2A 100.000 2201 0 0 1 2201 740873041 740875241 0.000000e+00 4065
1 TraesCS2A01G517700 chr2B 94.049 1882 92 10 327 2201 742892510 742894378 0.000000e+00 2837
2 TraesCS2A01G517700 chr2B 96.691 272 7 1 1 272 742892230 742892499 3.330000e-123 451
3 TraesCS2A01G517700 chr2D 95.074 1624 56 8 1 1608 608978617 608980232 0.000000e+00 2534
4 TraesCS2A01G517700 chr2D 91.333 600 45 6 1604 2201 608980333 608980927 0.000000e+00 813


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 TraesCS2A01G517700 chr2A 740873041 740875241 2200 False 4065.0 4065 100.0000 1 2201 1 chr2A.!!$F1 2200
1 TraesCS2A01G517700 chr2B 742892230 742894378 2148 False 1644.0 2837 95.3700 1 2201 2 chr2B.!!$F1 2200
2 TraesCS2A01G517700 chr2D 608978617 608980927 2310 False 1673.5 2534 93.2035 1 2201 2 chr2D.!!$F1 2200

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
746 767 1.071471 CGGGTTCTTGTGGCACTCT 59.929 57.895 19.83 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2166 2.60356 GGTCACTCGGATAAAAGAAGCG 59.396 50.0 0.0 0.0 0.0 4.68 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
34 35 8.259194 GCATCGTATTGTTGTATTGCATTTAAC 58.741 33.333 0.00 0.0 0.00 2.01
39 40 9.724839 GTATTGTTGTATTGCATTTAACCGTAT 57.275 29.630 0.00 0.0 0.00 3.06
88 89 6.372659 TGCCAAAGTGCTAAAAATTGTTTCAA 59.627 30.769 0.00 0.0 0.00 2.69
232 233 2.288763 GGGAAGGCATCGATTCTCTCTC 60.289 54.545 0.00 0.0 0.00 3.20
233 234 2.606795 GGAAGGCATCGATTCTCTCTCG 60.607 54.545 0.00 0.0 37.47 4.04
272 273 2.141517 GATGTGAATGGGAGAGCATCG 58.858 52.381 0.00 0.0 42.67 3.84
281 285 2.125512 AGAGCATCGGTTGGCGAC 60.126 61.111 0.00 0.0 42.67 5.19
299 303 1.322538 ACGATTCATGCAAAGCCCCC 61.323 55.000 0.00 0.0 0.00 5.40
327 338 6.869695 ACAAAAATGATTCATGCATAGCAGA 58.130 32.000 0.00 0.0 43.65 4.26
374 390 1.923204 GACACGCAAAACACATGCAAA 59.077 42.857 0.00 0.0 44.01 3.68
728 749 2.766229 GGGTGCCTCCTCTCCCTC 60.766 72.222 0.00 0.0 36.94 4.30
746 767 1.071471 CGGGTTCTTGTGGCACTCT 59.929 57.895 19.83 0.0 0.00 3.24
789 810 1.372087 GACCTGCATCTCCTTTGGCG 61.372 60.000 0.00 0.0 0.00 5.69
814 835 3.007973 GCTCGGCCGGTCTCTCTTT 62.008 63.158 27.83 0.0 0.00 2.52
897 918 1.584724 CTGAGGGTGGTGGTATTCCT 58.415 55.000 0.00 0.0 34.23 3.36
929 950 3.480133 GGCGGCTGAGGGTGGTAT 61.480 66.667 0.00 0.0 0.00 2.73
948 969 4.988598 CCGGTTGCTGCTCGGTGT 62.989 66.667 16.90 0.0 39.04 4.16
969 990 1.207791 CTGCTGAGGGTGGTATTCCT 58.792 55.000 0.00 0.0 35.82 3.36
1545 1567 0.251341 ACTGGTGGCAATCAAGGTCC 60.251 55.000 0.00 0.0 0.00 4.46
1591 1613 2.874086 TGTGTTGACAGAAGCATCAGTG 59.126 45.455 0.00 0.0 0.00 3.66
1637 1764 4.463891 CCCCAAAATCAGTGCATACTTTCT 59.536 41.667 0.00 0.0 34.07 2.52
1837 1965 2.225117 CCTCTTTGGTCCATGGGAAACT 60.225 50.000 13.02 0.0 31.38 2.66
1839 1967 4.325344 CCTCTTTGGTCCATGGGAAACTAT 60.325 45.833 13.02 0.0 31.38 2.12
1911 2039 6.509199 GCGAATATGAAGTGACAGAAGATGTG 60.509 42.308 0.00 0.0 44.17 3.21
1975 2103 8.174757 ACTATTTTTCACTAGGTGGGGTTTAAT 58.825 33.333 0.00 0.0 33.87 1.40
1985 2113 6.713731 AGGTGGGGTTTAATCTCTTCTTAA 57.286 37.500 0.00 0.0 0.00 1.85
2052 2180 2.888594 TGGTCTCGCTTCTTTTATCCG 58.111 47.619 0.00 0.0 0.00 4.18
2054 2182 3.117046 GGTCTCGCTTCTTTTATCCGAG 58.883 50.000 0.00 0.0 44.76 4.63
2065 2193 6.555463 TCTTTTATCCGAGTGACCCTAAAT 57.445 37.500 0.00 0.0 0.00 1.40
2066 2194 6.954232 TCTTTTATCCGAGTGACCCTAAATT 58.046 36.000 0.00 0.0 0.00 1.82
2067 2195 7.399634 TCTTTTATCCGAGTGACCCTAAATTT 58.600 34.615 0.00 0.0 0.00 1.82
2068 2196 7.886446 TCTTTTATCCGAGTGACCCTAAATTTT 59.114 33.333 0.00 0.0 0.00 1.82
2069 2197 8.411991 TTTTATCCGAGTGACCCTAAATTTTT 57.588 30.769 0.00 0.0 0.00 1.94
2166 2294 5.324409 AGTCAGAAAATGGGAAGCAACATA 58.676 37.500 0.00 0.0 0.00 2.29
2167 2295 5.183904 AGTCAGAAAATGGGAAGCAACATAC 59.816 40.000 0.00 0.0 0.00 2.39
2168 2296 5.048083 GTCAGAAAATGGGAAGCAACATACA 60.048 40.000 0.00 0.0 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.742188 GGTTAAATGCAATACAACAATACGATG 58.258 33.333 0.00 0.00 0.00 3.84
10 11 7.642194 CGGTTAAATGCAATACAACAATACGAT 59.358 33.333 0.00 0.00 0.00 3.73
19 20 9.862371 AAATTCATACGGTTAAATGCAATACAA 57.138 25.926 0.00 0.00 0.00 2.41
39 40 7.384660 GCAAATAAATGGTGTGTGAGAAATTCA 59.615 33.333 0.00 0.00 0.00 2.57
88 89 5.531287 GTGTCTCCTTTTCAACATAGTGGTT 59.469 40.000 0.00 0.00 0.00 3.67
272 273 1.062525 GCATGAATCGTCGCCAACC 59.937 57.895 0.00 0.00 0.00 3.77
281 285 1.438814 GGGGGCTTTGCATGAATCG 59.561 57.895 0.00 0.00 0.00 3.34
299 303 6.643770 GCTATGCATGAATCATTTTTGTAGGG 59.356 38.462 10.16 0.00 0.00 3.53
327 338 6.486320 TGATTACCAATGATTCGTGTATGCAT 59.514 34.615 3.79 3.79 0.00 3.96
695 716 2.341543 CCGATGGGAGAGATGCCG 59.658 66.667 0.00 0.00 34.06 5.69
728 749 1.071471 AGAGTGCCACAAGAACCCG 59.929 57.895 0.00 0.00 0.00 5.28
767 788 1.457346 CAAAGGAGATGCAGGTCCAC 58.543 55.000 17.27 0.00 35.02 4.02
789 810 3.991536 GACCGGCCGAGCTTGAGAC 62.992 68.421 30.73 4.13 0.00 3.36
814 835 4.144727 GGGAGGAGGAGAGGCCGA 62.145 72.222 0.00 0.00 43.43 5.54
948 969 0.253044 GAATACCACCCTCAGCAGCA 59.747 55.000 0.00 0.00 0.00 4.41
969 990 4.648626 GCCCACTGAGCAGCCACA 62.649 66.667 0.00 0.00 0.00 4.17
1545 1567 8.310382 CAGATCTCCACTATAATCTTAAGGGTG 58.690 40.741 1.85 3.36 0.00 4.61
1591 1613 9.053840 GGGGCTTCATTAGTAACTATTTACTTC 57.946 37.037 10.40 0.00 44.77 3.01
1616 1743 9.643693 AAATTAGAAAGTATGCACTGATTTTGG 57.356 29.630 0.00 0.00 34.36 3.28
1795 1922 6.613271 AGAGGTCATAACATCTCAACCATACT 59.387 38.462 0.00 0.00 42.67 2.12
1873 2001 8.993121 CACTTCATATTCGCCTACAGAAATTAT 58.007 33.333 0.00 0.00 0.00 1.28
1911 2039 4.535526 AATTTGTATTTGTGCCTCCCAC 57.464 40.909 0.00 0.00 44.90 4.61
2024 2152 6.817765 AAAAGAAGCGAGACCATCAATTTA 57.182 33.333 0.00 0.00 0.00 1.40
2038 2166 2.603560 GGTCACTCGGATAAAAGAAGCG 59.396 50.000 0.00 0.00 0.00 4.68
2069 2197 5.391950 GCATGATTTCTGCTCGTAGGAAAAA 60.392 40.000 0.00 0.00 36.68 1.94
2070 2198 4.094887 GCATGATTTCTGCTCGTAGGAAAA 59.905 41.667 0.00 0.00 36.68 2.29
2076 2204 5.369685 TTTTTGCATGATTTCTGCTCGTA 57.630 34.783 0.00 0.00 40.34 3.43


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

AutoCloner maintained by Alex Coulton.