Multiple sequence alignment - TraesCS3A01G267600

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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 TraesCS3A01G267600 chr3A 100.000 2279 0 0 1 2279 492735569 492737847 0.000000e+00 4209
1 TraesCS3A01G267600 chr3D 96.452 2283 73 6 1 2279 371868811 371871089 0.000000e+00 3760
2 TraesCS3A01G267600 chr3B 95.113 2292 82 13 1 2279 482783391 482785665 0.000000e+00 3585
3 TraesCS3A01G267600 chr1B 78.579 929 173 19 870 1788 638782832 638783744 7.010000e-165 590
4 TraesCS3A01G267600 chr1B 78.335 937 173 22 870 1791 638820932 638821853 1.520000e-161 579
5 TraesCS3A01G267600 chr1D 77.908 937 177 22 870 1791 463325447 463326368 7.110000e-155 556
6 TraesCS3A01G267600 chr1A 77.801 937 178 22 870 1791 555522152 555523073 3.310000e-153 551
7 TraesCS3A01G267600 chr1A 77.326 935 174 30 870 1788 555484043 555484955 3.360000e-143 518


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 TraesCS3A01G267600 chr3A 492735569 492737847 2278 False 4209 4209 100.000 1 2279 1 chr3A.!!$F1 2278
1 TraesCS3A01G267600 chr3D 371868811 371871089 2278 False 3760 3760 96.452 1 2279 1 chr3D.!!$F1 2278
2 TraesCS3A01G267600 chr3B 482783391 482785665 2274 False 3585 3585 95.113 1 2279 1 chr3B.!!$F1 2278
3 TraesCS3A01G267600 chr1B 638782832 638783744 912 False 590 590 78.579 870 1788 1 chr1B.!!$F1 918
4 TraesCS3A01G267600 chr1B 638820932 638821853 921 False 579 579 78.335 870 1791 1 chr1B.!!$F2 921
5 TraesCS3A01G267600 chr1D 463325447 463326368 921 False 556 556 77.908 870 1791 1 chr1D.!!$F1 921
6 TraesCS3A01G267600 chr1A 555522152 555523073 921 False 551 551 77.801 870 1791 1 chr1A.!!$F2 921
7 TraesCS3A01G267600 chr1A 555484043 555484955 912 False 518 518 77.326 870 1788 1 chr1A.!!$F1 918

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
335 336 0.244721 GGCAACATTTGGAGCAGTCC 59.755 55.0 0.0 0.0 44.24 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2070 1.116308 CCCCCGTCACAAAAAGGTTT 58.884 50.0 0.0 0.0 0.0 3.27 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
96 97 9.964303 TGTGTATTCAATTGCCATGATTTATAC 57.036 29.630 0.00 0.00 0.00 1.47
101 102 6.804677 TCAATTGCCATGATTTATACCACAC 58.195 36.000 0.00 0.00 0.00 3.82
103 104 3.210227 TGCCATGATTTATACCACACCG 58.790 45.455 0.00 0.00 0.00 4.94
250 251 2.150390 CGGTCACATTCCACAATGACA 58.850 47.619 5.66 0.00 41.97 3.58
301 302 2.816672 TGCCAGATAAATTGTTGACGCA 59.183 40.909 0.00 0.00 0.00 5.24
320 321 3.452474 GCATGTACACAAAACAAGGCAA 58.548 40.909 0.00 0.00 33.75 4.52
335 336 0.244721 GGCAACATTTGGAGCAGTCC 59.755 55.000 0.00 0.00 44.24 3.85
365 366 8.625651 CGAGGAATATTTCTCTCTTCTGTTAGA 58.374 37.037 19.48 0.00 0.00 2.10
384 385 3.571590 AGAAGATCACCGATTAGGCTCT 58.428 45.455 0.00 0.00 46.52 4.09
385 386 4.730966 AGAAGATCACCGATTAGGCTCTA 58.269 43.478 0.00 0.00 46.52 2.43
443 447 6.247229 TGTTACCATCACATAAGGTAGCAT 57.753 37.500 0.00 0.00 41.95 3.79
449 453 5.413833 CCATCACATAAGGTAGCATTCCATC 59.586 44.000 0.00 0.00 0.00 3.51
519 523 4.486125 AACCTTTCAAACAAGCAACCAT 57.514 36.364 0.00 0.00 0.00 3.55
721 729 2.021723 GCCCATGTTCCGGATGCTAAA 61.022 52.381 4.15 0.00 0.00 1.85
738 746 9.080915 GGATGCTAAAGCTCTAAAAATGAAAAG 57.919 33.333 3.26 0.00 42.66 2.27
768 776 0.458260 AAACGGTTTCAACTGCACCC 59.542 50.000 0.00 0.00 38.89 4.61
775 783 3.260100 CAACTGCACCCCCTCCCT 61.260 66.667 0.00 0.00 0.00 4.20
915 923 1.072015 GAGAATCCCCAGATGCAGAGG 59.928 57.143 0.00 0.00 29.07 3.69
1581 1589 1.524002 CATGAGCACCCCGATGACT 59.476 57.895 0.00 0.00 0.00 3.41
1812 1829 2.925170 AACAGCAGCCTCCTCCGT 60.925 61.111 0.00 0.00 0.00 4.69
1923 1940 3.249091 CGAGTGAGATGGACTTGACTTG 58.751 50.000 0.00 0.00 0.00 3.16
1932 1949 3.741476 CTTGACTTGGCGCTGGGC 61.741 66.667 7.64 8.35 42.51 5.36
1994 2016 5.855045 AGTATTTAAGCGAGATAAGTGGGG 58.145 41.667 0.00 0.00 0.00 4.96
2003 2025 1.133792 AGATAAGTGGGGGATTTGCGG 60.134 52.381 0.00 0.00 0.00 5.69
2044 2070 2.457598 AGAGTGCGGAGGAGATTTACA 58.542 47.619 0.00 0.00 0.00 2.41
2171 2197 8.154649 ACACAAATTCGAATATATGTCCTTCC 57.845 34.615 11.83 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.411318 ACAATTCAACAAAGCTTGAAGTTTAG 57.589 30.769 0.00 0.00 42.13 1.85
70 71 9.964303 GTATAAATCATGGCAATTGAATACACA 57.036 29.630 10.34 0.00 0.00 3.72
80 81 4.278170 CGGTGTGGTATAAATCATGGCAAT 59.722 41.667 0.00 0.00 0.00 3.56
96 97 1.216710 GCCTCTTCTCTCGGTGTGG 59.783 63.158 0.00 0.00 0.00 4.17
101 102 3.632604 TGTAATGTAGCCTCTTCTCTCGG 59.367 47.826 0.00 0.00 0.00 4.63
103 104 6.874134 TGTTTTGTAATGTAGCCTCTTCTCTC 59.126 38.462 0.00 0.00 0.00 3.20
232 233 4.539870 CTTGTGTCATTGTGGAATGTGAC 58.460 43.478 0.00 0.00 40.09 3.67
283 284 6.465781 GTGTACATGCGTCAACAATTTATCTG 59.534 38.462 0.00 0.00 0.00 2.90
301 302 4.727507 TGTTGCCTTGTTTTGTGTACAT 57.272 36.364 0.00 0.00 0.00 2.29
320 321 0.610232 GGCTGGACTGCTCCAAATGT 60.610 55.000 0.00 0.00 46.63 2.71
335 336 4.599047 AGAGAGAAATATTCCTCGGCTG 57.401 45.455 0.00 0.00 34.34 4.85
339 340 8.625651 TCTAACAGAAGAGAGAAATATTCCTCG 58.374 37.037 0.00 0.00 34.34 4.63
365 366 5.221541 CCTTTAGAGCCTAATCGGTGATCTT 60.222 44.000 0.00 0.00 34.25 2.40
366 367 4.282195 CCTTTAGAGCCTAATCGGTGATCT 59.718 45.833 0.00 0.00 34.25 2.75
384 385 7.411486 TCTTCACAAAATGTTGGTTCCTTTA 57.589 32.000 0.00 0.00 39.22 1.85
385 386 6.293004 TCTTCACAAAATGTTGGTTCCTTT 57.707 33.333 0.00 0.00 39.22 3.11
443 447 4.933134 TGGAAGGATGTTTGATGATGGAA 58.067 39.130 0.00 0.00 0.00 3.53
449 453 5.314923 ACGAAATGGAAGGATGTTTGATG 57.685 39.130 0.00 0.00 0.00 3.07
504 508 3.196469 TGGTTTGATGGTTGCTTGTTTGA 59.804 39.130 0.00 0.00 0.00 2.69
519 523 2.955660 GAGGTTGGTGATTGTGGTTTGA 59.044 45.455 0.00 0.00 0.00 2.69
642 646 9.606631 AGTCTAATTGCACCTATTTCTAAGAAG 57.393 33.333 0.00 0.00 0.00 2.85
662 670 9.702253 ATCTCAAAGGAAGTACATCTAGTCTAA 57.298 33.333 0.00 0.00 0.00 2.10
721 729 9.746457 ATCTAACCTCTTTTCATTTTTAGAGCT 57.254 29.630 0.00 0.00 34.23 4.09
738 746 5.469084 AGTTGAAACCGTTTGATCTAACCTC 59.531 40.000 13.34 6.75 0.00 3.85
768 776 2.663196 GACGTTGGTGAGGGAGGG 59.337 66.667 0.00 0.00 0.00 4.30
775 783 1.885388 CAAGTGGCGACGTTGGTGA 60.885 57.895 4.64 0.00 0.00 4.02
1581 1589 2.047750 TTGCTCATGGCGTGCGTA 60.048 55.556 0.65 0.00 45.43 4.42
1932 1949 1.992277 CCTCCTCACCTCACCCCAG 60.992 68.421 0.00 0.00 0.00 4.45
1940 1957 1.229984 CCCCTTTCCCTCCTCACCT 60.230 63.158 0.00 0.00 0.00 4.00
1994 2016 2.234300 TCGTAATCTCCCGCAAATCC 57.766 50.000 0.00 0.00 0.00 3.01
2030 2052 5.959618 AAAAGGTTTGTAAATCTCCTCCG 57.040 39.130 0.00 0.00 0.00 4.63
2044 2070 1.116308 CCCCCGTCACAAAAAGGTTT 58.884 50.000 0.00 0.00 0.00 3.27
2058 2084 3.568430 GCTTCCATTATTTTACTCCCCCG 59.432 47.826 0.00 0.00 0.00 5.73
2171 2197 8.732746 ATACTACTAGTTTGCATTAACAAGGG 57.267 34.615 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.