Multiple sequence alignment - TraesCS3B01G301400

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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 TraesCS3B01G301400 chr3B 100.000 2300 0 0 1 2300 483372316 483374615 0 4248
1 TraesCS3B01G301400 chr1A 98.610 2302 30 2 1 2300 238109745 238107444 0 4072
2 TraesCS3B01G301400 chr1A 98.523 2302 32 2 1 2300 238155130 238152829 0 4061
3 TraesCS3B01G301400 chr5A 98.523 2302 32 2 1 2300 16577920 16575619 0 4061
4 TraesCS3B01G301400 chr6B 98.436 2302 30 4 1 2300 596657306 596655009 0 4047
5 TraesCS3B01G301400 chr7D 98.393 2302 32 3 1 2300 579015578 579017876 0 4041
6 TraesCS3B01G301400 chr7A 98.349 2302 36 2 1 2300 60329010 60326709 0 4039


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 TraesCS3B01G301400 chr3B 483372316 483374615 2299 False 4248 4248 100.000 1 2300 1 chr3B.!!$F1 2299
1 TraesCS3B01G301400 chr1A 238107444 238109745 2301 True 4072 4072 98.610 1 2300 1 chr1A.!!$R1 2299
2 TraesCS3B01G301400 chr1A 238152829 238155130 2301 True 4061 4061 98.523 1 2300 1 chr1A.!!$R2 2299
3 TraesCS3B01G301400 chr5A 16575619 16577920 2301 True 4061 4061 98.523 1 2300 1 chr5A.!!$R1 2299
4 TraesCS3B01G301400 chr6B 596655009 596657306 2297 True 4047 4047 98.436 1 2300 1 chr6B.!!$R1 2299
5 TraesCS3B01G301400 chr7D 579015578 579017876 2298 False 4041 4041 98.393 1 2300 1 chr7D.!!$F1 2299
6 TraesCS3B01G301400 chr7A 60326709 60329010 2301 True 4039 4039 98.349 1 2300 1 chr7A.!!$R1 2299

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
392 393 1.024271 CGGCACATCCAATTCCGATT 58.976 50.0 0.0 0.0 42.43 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2158 1.169661 AAAGCGCGAACCAACATCCA 61.17 50.0 12.1 0.0 0.0 3.41 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
32 33 4.499183 GTCATGACGAGAATGGACTTCTT 58.501 43.478 10.69 0.00 44.42 2.52
206 207 4.378874 GCTAAGTTTCTCATTCAGTGGTGC 60.379 45.833 0.00 0.00 0.00 5.01
392 393 1.024271 CGGCACATCCAATTCCGATT 58.976 50.000 0.00 0.00 42.43 3.34
449 450 6.208644 GCATTGGTTTGCTAAATCGACATAT 58.791 36.000 0.00 0.00 39.57 1.78
551 552 4.360889 AGAACCTCAGATTGATGGAGTCT 58.639 43.478 0.00 0.00 0.00 3.24
1122 1124 3.947834 CCTATCCAGAAAAATTGTCGGCT 59.052 43.478 0.00 0.00 0.00 5.52
1298 1302 5.136068 TGGTCCATGATGGCCTTTTATTA 57.864 39.130 20.41 2.06 37.47 0.98
1610 1614 0.955428 TGCTCACATTCCAGGCGAAC 60.955 55.000 0.00 0.00 31.79 3.95
1734 1738 2.101917 TGGGAATTCCGGATCGTAGAAC 59.898 50.000 18.30 0.46 38.34 3.01
2098 2105 5.517924 ACAATGTGTCCCCATGATCATTTA 58.482 37.500 5.16 0.00 32.21 1.40
2099 2106 5.360714 ACAATGTGTCCCCATGATCATTTAC 59.639 40.000 5.16 2.77 32.21 2.01
2100 2107 4.860802 TGTGTCCCCATGATCATTTACT 57.139 40.909 5.16 0.00 0.00 2.24
2101 2108 5.191727 TGTGTCCCCATGATCATTTACTT 57.808 39.130 5.16 0.00 0.00 2.24
2102 2109 6.320434 TGTGTCCCCATGATCATTTACTTA 57.680 37.500 5.16 0.00 0.00 2.24
2104 2111 6.119536 GTGTCCCCATGATCATTTACTTACA 58.880 40.000 5.16 3.63 0.00 2.41
2105 2112 6.260936 GTGTCCCCATGATCATTTACTTACAG 59.739 42.308 5.16 0.00 0.00 2.74
2106 2113 6.157820 TGTCCCCATGATCATTTACTTACAGA 59.842 38.462 5.16 0.00 0.00 3.41
2232 2239 7.437713 AGGATTGTTCATGGAACTACTATCA 57.562 36.000 10.14 0.00 42.39 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.116747 AGAAGTCCATTCTCGTCATGAC 57.883 45.455 16.21 16.21 45.50 3.06
32 33 6.931838 ACTCTTCTAAACCATTACATGACGA 58.068 36.000 0.00 0.00 0.00 4.20
206 207 2.159517 GCCTTGCTTTCTATGAACACCG 60.160 50.000 0.00 0.00 0.00 4.94
392 393 3.585289 TCAGCCATACCTCCAAGTTGTTA 59.415 43.478 1.45 0.00 0.00 2.41
449 450 7.119709 TCGAACCCATGATACAATCTTCTTA 57.880 36.000 0.00 0.00 0.00 2.10
551 552 1.132453 CAGCTATTCTGTCCGACGACA 59.868 52.381 0.00 0.00 46.91 4.35
594 595 2.306847 GCACCAAGAACAAGAAAGGGA 58.693 47.619 0.00 0.00 0.00 4.20
820 822 1.946768 CAGTCCAGCAAGAAAACGGAA 59.053 47.619 0.00 0.00 0.00 4.30
1044 1046 5.221661 ACCGAGTGGAATCAAAGAAACTAGT 60.222 40.000 0.00 0.00 39.21 2.57
1122 1124 2.419021 GGGATCGGAACCACATTCGTAA 60.419 50.000 6.63 0.00 38.31 3.18
1298 1302 8.206867 TCATAGAGAGATCCAATCGTCAAAATT 58.793 33.333 0.00 0.00 0.00 1.82
1610 1614 4.271049 AGAATGTTCCTGCGAATTATGACG 59.729 41.667 0.00 0.00 0.00 4.35
1734 1738 4.641396 TGCACCATATTTAGATCTTCCCG 58.359 43.478 0.00 0.00 0.00 5.14
1964 1968 1.202568 GCTTTTTGTGGCTTCCTGCTT 60.203 47.619 0.00 0.00 42.39 3.91
2098 2105 9.152595 GGAAGAAAAAGATATCGTTCTGTAAGT 57.847 33.333 15.66 4.76 33.76 2.24
2099 2106 9.372369 AGGAAGAAAAAGATATCGTTCTGTAAG 57.628 33.333 15.66 0.00 30.85 2.34
2100 2107 9.367444 GAGGAAGAAAAAGATATCGTTCTGTAA 57.633 33.333 15.66 0.00 30.85 2.41
2101 2108 8.528643 TGAGGAAGAAAAAGATATCGTTCTGTA 58.471 33.333 15.66 4.00 30.85 2.74
2102 2109 7.386851 TGAGGAAGAAAAAGATATCGTTCTGT 58.613 34.615 15.66 9.11 30.85 3.41
2104 2111 9.103861 GAATGAGGAAGAAAAAGATATCGTTCT 57.896 33.333 4.30 8.54 31.74 3.01
2105 2112 9.103861 AGAATGAGGAAGAAAAAGATATCGTTC 57.896 33.333 4.30 6.55 33.62 3.95
2106 2113 9.454859 AAGAATGAGGAAGAAAAAGATATCGTT 57.545 29.630 0.00 0.00 0.00 3.85
2151 2158 1.169661 AAAGCGCGAACCAACATCCA 61.170 50.000 12.10 0.00 0.00 3.41
2232 2239 8.977412 ACTTGGAAATATGGTCCGAATAATTTT 58.023 29.630 2.15 0.00 38.06 1.82


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

AutoCloner maintained by Alex Coulton.