Multiple sequence alignment - TraesCS3B01G364100

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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 TraesCS3B01G364100 chr3B 100.000 2285 0 0 1 2285 575769422 575767138 0 4220
1 TraesCS3B01G364100 chr3B 96.763 2286 71 3 1 2285 483372317 483374600 0 3808
2 TraesCS3B01G364100 chr1A 97.375 2286 59 1 1 2285 238155129 238152844 0 3888
3 TraesCS3B01G364100 chr1A 97.288 2286 61 1 1 2285 238109744 238107459 0 3877
4 TraesCS3B01G364100 chr5A 97.200 2286 63 1 1 2285 16577919 16575634 0 3866
5 TraesCS3B01G364100 chr7A 96.982 2286 68 1 1 2285 60329009 60326724 0 3838
6 TraesCS3B01G364100 chr6B 96.982 2286 64 3 1 2285 596657305 596655024 0 3834
7 TraesCS3B01G364100 chr7D 96.938 2286 66 2 1 2285 579015579 579017861 0 3831


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 TraesCS3B01G364100 chr3B 575767138 575769422 2284 True 4220 4220 100.000 1 2285 1 chr3B.!!$R1 2284
1 TraesCS3B01G364100 chr3B 483372317 483374600 2283 False 3808 3808 96.763 1 2285 1 chr3B.!!$F1 2284
2 TraesCS3B01G364100 chr1A 238152844 238155129 2285 True 3888 3888 97.375 1 2285 1 chr1A.!!$R2 2284
3 TraesCS3B01G364100 chr1A 238107459 238109744 2285 True 3877 3877 97.288 1 2285 1 chr1A.!!$R1 2284
4 TraesCS3B01G364100 chr5A 16575634 16577919 2285 True 3866 3866 97.200 1 2285 1 chr5A.!!$R1 2284
5 TraesCS3B01G364100 chr7A 60326724 60329009 2285 True 3838 3838 96.982 1 2285 1 chr7A.!!$R1 2284
6 TraesCS3B01G364100 chr6B 596655024 596657305 2281 True 3834 3834 96.982 1 2285 1 chr6B.!!$R1 2284
7 TraesCS3B01G364100 chr7D 579015579 579017861 2282 False 3831 3831 96.938 1 2285 1 chr7D.!!$F1 2284

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
84 85 0.956902 GTTCCCCGCCGAGCTTTTTA 60.957 55.0 0.0 0.0 0.0 1.52 F
1005 1006 0.478072 AGTGGGCTTTGGTGATGTCA 59.522 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1272 1.233019 GCCATCATGGACCAAGATCG 58.767 55.0 8.30 4.66 40.96 3.69 R
1830 1834 1.675007 AAGGGAAAGGGAGCTAGCTT 58.325 50.0 20.42 1.21 0.00 3.74 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
60 61 6.092955 TGTAATGGTTTAGAAGAGTCACGT 57.907 37.500 0.00 0.00 0.00 4.49
76 77 4.011517 GTTCCTGTTCCCCGCCGA 62.012 66.667 0.00 0.00 0.00 5.54
84 85 0.956902 GTTCCCCGCCGAGCTTTTTA 60.957 55.000 0.00 0.00 0.00 1.52
139 140 2.208349 AGGCAGGTGAGGAAGGGT 59.792 61.111 0.00 0.00 0.00 4.34
143 144 2.121963 AGGTGAGGAAGGGTGGCA 60.122 61.111 0.00 0.00 0.00 4.92
175 176 2.163509 CTGTCTTCTCTCTTGGTCGGA 58.836 52.381 0.00 0.00 0.00 4.55
274 275 1.700042 GGATGGGGTCTCGCTTGGAT 61.700 60.000 0.00 0.00 0.00 3.41
312 313 7.669304 CCATAGATCTGGATAGAGTCTTTCTCA 59.331 40.741 5.18 6.20 40.89 3.27
361 362 2.483714 GGCTTATGCAGTGGATCTTCGA 60.484 50.000 0.00 0.00 41.91 3.71
485 486 2.735151 GGGTTCGAATCCCATTTCCTT 58.265 47.619 17.16 0.00 44.05 3.36
525 526 1.567504 CGGGCGAAATTACGTGAGAT 58.432 50.000 0.00 0.00 35.59 2.75
536 537 7.513196 CGAAATTACGTGAGATAAAGAACCTCG 60.513 40.741 0.00 0.00 0.00 4.63
780 781 3.445450 TGGTTAGAGCAAAACAAGCAACA 59.555 39.130 0.00 0.00 0.00 3.33
908 909 3.500343 CCTGGAAATCCTTCAGTGGTTT 58.500 45.455 0.44 0.00 36.82 3.27
962 963 4.441695 CTCCGCGAGCAAGGAGCA 62.442 66.667 8.23 0.00 46.23 4.26
1005 1006 0.478072 AGTGGGCTTTGGTGATGTCA 59.522 50.000 0.00 0.00 0.00 3.58
1168 1169 2.143122 GTGATGCCAGAAGTCGTTTCA 58.857 47.619 5.49 0.00 38.31 2.69
1265 1268 7.506261 GGAGTACCTCCTAACAAGATTGATCTA 59.494 40.741 2.98 0.00 46.41 1.98
1290 1293 1.144503 GATCTTGGTCCATGATGGCCT 59.855 52.381 21.76 1.73 37.47 5.19
1359 1363 1.687123 CTTCGGATCGGGAGTAACCAT 59.313 52.381 0.30 0.00 41.20 3.55
1403 1407 4.014273 AGGACATAGGAAAGAGGGATGT 57.986 45.455 0.00 0.00 33.52 3.06
1464 1468 2.183300 GCGCACGGACCATACTCA 59.817 61.111 0.30 0.00 0.00 3.41
1484 1488 1.207791 AGCTTCGGATCAATGTCCCT 58.792 50.000 0.00 0.00 34.67 4.20
1586 1590 3.329743 GGTTGAGCAATCGACATGATG 57.670 47.619 0.00 0.00 37.39 3.07
1609 1613 0.035152 TTGCTCACATTCCAGGCGAT 60.035 50.000 0.00 0.00 0.00 4.58
1685 1689 0.400213 TTCGCCAGGTGTGAAATCCT 59.600 50.000 0.00 0.00 40.41 3.24
1695 1699 5.696724 CAGGTGTGAAATCCTATCGTATTCC 59.303 44.000 0.00 0.00 32.26 3.01
1723 1727 2.833338 CAAGGATTTGCTGGGAATTCCA 59.167 45.455 25.67 11.08 44.79 3.53
1830 1834 4.683766 TTTTTGGGGGTGATATGGAAGA 57.316 40.909 0.00 0.00 0.00 2.87
1854 1858 5.166407 AGCTAGCTCCCTTTCCCTTATTAT 58.834 41.667 12.68 0.00 0.00 1.28
1932 1936 6.712276 AGAAAAGAAATCTTCTACGGGTGAT 58.288 36.000 0.00 0.00 39.61 3.06
1937 1941 3.897657 ATCTTCTACGGGTGATAGGGA 57.102 47.619 0.00 0.00 0.00 4.20
2145 2149 9.142014 TCTTCCTCATTCTTATTTTGGTTTTCA 57.858 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 3.702048 CTCGGCGGGGAACAGGAA 61.702 66.667 7.21 0.00 0.00 3.36
76 77 5.619533 CGTCTAGTCGAGAAGGTAAAAAGCT 60.620 44.000 3.09 0.00 35.37 3.74
139 140 3.329889 AGGGTCAAGCCGATGCCA 61.330 61.111 0.00 0.00 38.69 4.92
143 144 0.250513 GAAGACAGGGTCAAGCCGAT 59.749 55.000 0.00 0.00 38.44 4.18
175 176 4.162320 TGAATGAGAAACTTAGCCTCCGAT 59.838 41.667 0.00 0.00 0.00 4.18
245 246 3.173151 GAGACCCCATCCAAACCAAATT 58.827 45.455 0.00 0.00 0.00 1.82
274 275 2.544721 GATCTATGGATCTCCCCAGCA 58.455 52.381 11.58 0.00 43.55 4.41
312 313 4.613167 CGCACGTACTCTTCTTTACTGAGT 60.613 45.833 0.00 0.00 42.74 3.41
346 347 0.321346 TTGCTCGAAGATCCACTGCA 59.679 50.000 0.00 0.00 33.89 4.41
361 362 3.808218 ATGTGCCGGGTTGGTTGCT 62.808 57.895 2.18 0.00 41.21 3.91
485 486 1.210931 CGTTCTACTTCCGTGCCGA 59.789 57.895 0.00 0.00 0.00 5.54
525 526 4.469945 ACTCCATCAATCCGAGGTTCTTTA 59.530 41.667 0.00 0.00 0.00 1.85
536 537 1.595382 CGGCGGACTCCATCAATCC 60.595 63.158 0.00 0.00 0.00 3.01
562 563 5.241949 GCTCCTAGTCACTAAGCAGCTATTA 59.758 44.000 0.00 0.00 33.21 0.98
666 667 1.337260 GCTTGCTCAAGAACCGAGAGA 60.337 52.381 13.33 0.00 40.79 3.10
780 781 0.173481 TCGCGCTAGTTGCTCAATCT 59.827 50.000 5.56 0.00 40.11 2.40
908 909 1.827344 AGACGCTCAGATGTGGATTCA 59.173 47.619 0.00 0.00 0.00 2.57
962 963 1.747367 CTCTCGCTCTCCTCGTGGT 60.747 63.158 2.99 0.00 34.23 4.16
965 966 1.363145 CGTTCTCTCGCTCTCCTCGT 61.363 60.000 0.00 0.00 0.00 4.18
1265 1268 4.139786 CCATCATGGACCAAGATCGAAAT 58.860 43.478 9.27 0.00 40.96 2.17
1269 1272 1.233019 GCCATCATGGACCAAGATCG 58.767 55.000 8.30 4.66 40.96 3.69
1359 1363 2.615391 CCCCCTTTGCCCTTTCTAAAA 58.385 47.619 0.00 0.00 0.00 1.52
1424 1428 4.994852 CCGTTTTTCTTCTCTACCATGACA 59.005 41.667 0.00 0.00 0.00 3.58
1458 1462 5.028549 ACATTGATCCGAAGCTTGAGTAT 57.971 39.130 2.10 0.00 0.00 2.12
1464 1468 1.561542 AGGGACATTGATCCGAAGCTT 59.438 47.619 0.00 0.00 39.97 3.74
1484 1488 3.470709 GCATGCATACTCCTTGCTTCTA 58.529 45.455 14.21 0.00 40.77 2.10
1586 1590 2.223340 CGCCTGGAATGTGAGCAAATAC 60.223 50.000 0.00 0.00 0.00 1.89
1609 1613 3.342377 TGTTCCTGCGAATTATGACCA 57.658 42.857 0.00 0.00 0.00 4.02
1685 1689 4.800023 TCCTTGACTCCTGGAATACGATA 58.200 43.478 0.00 0.00 0.00 2.92
1695 1699 2.089980 CCAGCAAATCCTTGACTCCTG 58.910 52.381 0.00 0.00 34.14 3.86
1723 1727 7.899648 TTTAGATCTTCCCTTTCTACGATCT 57.100 36.000 0.00 0.00 40.29 2.75
1819 1823 3.580458 GGGAGCTAGCTTCTTCCATATCA 59.420 47.826 22.47 0.00 0.00 2.15
1830 1834 1.675007 AAGGGAAAGGGAGCTAGCTT 58.325 50.000 20.42 1.21 0.00 3.74
1924 1928 3.152400 GGCGTCCCTATCACCCGT 61.152 66.667 0.00 0.00 0.00 5.28
1982 1986 4.963276 TCAGTTACAATAGCACAATGCC 57.037 40.909 0.00 0.00 46.52 4.40
2023 2027 5.419542 CCTGTAGTGATTTCAGAATTCGGA 58.580 41.667 4.00 4.00 0.00 4.55
2145 2149 2.807967 CGCGAACCAACATCCATGATAT 59.192 45.455 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.