Multiple sequence alignment - TraesCS2A01G380500

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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 TraesCS2A01G380500 chr2A 100.000 5100 0 0 1 5100 623945410 623940311 0 9419
1 TraesCS2A01G380500 chr2D 97.652 5111 98 11 1 5100 481055602 481050503 0 8754
2 TraesCS2A01G380500 chr2B 96.641 5121 130 22 1 5100 564236620 564231521 0 8466


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 TraesCS2A01G380500 chr2A 623940311 623945410 5099 True 9419 9419 100.000 1 5100 1 chr2A.!!$R1 5099
1 TraesCS2A01G380500 chr2D 481050503 481055602 5099 True 8754 8754 97.652 1 5100 1 chr2D.!!$R1 5099
2 TraesCS2A01G380500 chr2B 564231521 564236620 5099 True 8466 8466 96.641 1 5100 1 chr2B.!!$R1 5099

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
742 745 1.056660 ACTCGACCAAACATGGACCT 58.943 50.0 1.10 0.0 0.00 3.85 F
1303 1307 0.591170 ATGTGGCACAACGCTTACAC 59.409 50.0 25.95 0.0 44.16 2.90 F
2331 2349 2.092103 GCCACATGGTATCCTTAACCCA 60.092 50.0 0.00 0.0 36.06 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 2611 0.755686 TTGGCTTGACGGGCATTTTT 59.244 45.000 0.00 0.0 41.29 1.94 R
2642 2660 2.036387 TGTCACTTCCTCACCGAAGAA 58.964 47.619 5.39 0.0 41.57 2.52 R
4309 4332 0.618458 GGGTATGTCACAGGAAGGCA 59.382 55.000 0.00 0.0 0.00 4.75 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
171 172 4.090761 TCATTTGAGAGCCACTTGAACT 57.909 40.909 0.00 0.00 0.00 3.01
271 272 6.760298 GGTACAAATAAGCCAGTAGTTAGGTC 59.240 42.308 0.00 0.00 0.00 3.85
273 274 5.186409 ACAAATAAGCCAGTAGTTAGGTCGA 59.814 40.000 0.00 0.00 0.00 4.20
343 344 3.609853 TCTTCTAATGTTTGCGCTCCAT 58.390 40.909 9.73 5.01 0.00 3.41
483 484 6.476378 AGGTGCTAGTTTATTGAGATGTTGT 58.524 36.000 0.00 0.00 0.00 3.32
484 485 6.942576 AGGTGCTAGTTTATTGAGATGTTGTT 59.057 34.615 0.00 0.00 0.00 2.83
485 486 7.023575 GGTGCTAGTTTATTGAGATGTTGTTG 58.976 38.462 0.00 0.00 0.00 3.33
514 515 4.958509 AGCTTGGATCTATGTGACATCTG 58.041 43.478 0.00 0.00 0.00 2.90
656 658 5.713792 AGGACGAACATAGATGGTCATAG 57.286 43.478 8.24 0.00 44.65 2.23
735 738 4.069304 CTCCCAAATAACTCGACCAAACA 58.931 43.478 0.00 0.00 0.00 2.83
742 745 1.056660 ACTCGACCAAACATGGACCT 58.943 50.000 1.10 0.00 0.00 3.85
787 790 8.908903 TGTACATCAAGACAAATTAAGTTGGTT 58.091 29.630 18.88 9.57 32.50 3.67
809 812 7.877097 TGGTTTTCCATTTCACATGAAAATAGG 59.123 33.333 10.90 12.46 46.22 2.57
860 863 2.305635 AGGACACTATCACACCATTGCA 59.694 45.455 0.00 0.00 0.00 4.08
903 906 7.665690 TCACAAAAGCAATTAATTCAGGCTAA 58.334 30.769 10.84 0.00 33.80 3.09
1187 1190 2.696707 ACCAAAGGCCATGCATGAATAG 59.303 45.455 28.31 12.10 0.00 1.73
1303 1307 0.591170 ATGTGGCACAACGCTTACAC 59.409 50.000 25.95 0.00 44.16 2.90
1439 1443 3.501349 CAGGTAAGGGCTGCTCTATCTA 58.499 50.000 0.60 0.00 0.00 1.98
1465 1469 4.502962 ACCATTTTTCATAAACCATGCCG 58.497 39.130 0.00 0.00 34.35 5.69
1643 1648 3.824133 CACCCCATTTATGATCAGAGCA 58.176 45.455 0.09 0.00 0.00 4.26
1688 1693 6.046593 TGGCACATGCACTATACTAAAGTAC 58.953 40.000 6.15 0.00 44.36 2.73
1827 1832 5.617609 TCAAACGATGAAAAGCTAATCACG 58.382 37.500 15.37 15.37 34.30 4.35
1964 1969 4.748701 TGGTCTTACTTCTTGGAGTAGGT 58.251 43.478 0.00 0.00 33.91 3.08
2102 2107 4.681744 GTTGACATTCCAAAAACTGCAGA 58.318 39.130 23.35 0.00 0.00 4.26
2266 2284 8.358582 AGATTCTTTCTGAATTAGGTTGCATT 57.641 30.769 0.00 0.00 44.70 3.56
2267 2285 8.810041 AGATTCTTTCTGAATTAGGTTGCATTT 58.190 29.630 0.00 0.00 44.70 2.32
2331 2349 2.092103 GCCACATGGTATCCTTAACCCA 60.092 50.000 0.00 0.00 36.06 4.51
2383 2401 3.983741 ACAGAAGAAACTGAAGGTCTCG 58.016 45.455 0.00 0.00 40.63 4.04
2593 2611 9.996554 TCACTGTGAGATCTTAACATTCTTTTA 57.003 29.630 6.36 0.00 0.00 1.52
2622 2640 3.365969 CCCGTCAAGCCAACTATTTTGTC 60.366 47.826 0.00 0.00 0.00 3.18
2642 2660 4.338964 TGTCGAAATTCATAATGCATGGCT 59.661 37.500 0.00 0.00 35.16 4.75
2852 2874 0.409484 ACCCAGTGATTTGAAGGGGG 59.591 55.000 0.00 0.00 43.96 5.40
3204 3227 3.133901 TCCTATCTTGCTTGATTGCGGTA 59.866 43.478 0.00 0.00 35.36 4.02
3484 3507 9.116080 TCCAACCTGGTATCATATCTAAATCAT 57.884 33.333 0.00 0.00 39.03 2.45
3602 3625 4.638421 AGAGTCAAATTTCCACGTCAAACA 59.362 37.500 0.00 0.00 0.00 2.83
3788 3811 6.578919 GCACATTAGCTGACAAAAGTAAACTC 59.421 38.462 0.00 0.00 0.00 3.01
3923 3946 9.793252 AAGCATAGTTTTTATGATGAATGTGTC 57.207 29.630 0.00 0.00 0.00 3.67
4309 4332 6.187727 TCTGAAGGTTTACTGGTGAAGATT 57.812 37.500 0.00 0.00 0.00 2.40
4724 4747 7.475137 TTTTACTATTTACTGCAGGGCAAAT 57.525 32.000 19.93 20.09 38.41 2.32
4901 4924 7.883311 CCGAATCCTTAACCCTATGATGTAAAT 59.117 37.037 0.00 0.00 0.00 1.40
4902 4925 8.721478 CGAATCCTTAACCCTATGATGTAAATG 58.279 37.037 0.00 0.00 0.00 2.32
4911 4934 4.456911 CCTATGATGTAAATGCGCATTCCT 59.543 41.667 33.93 22.45 0.00 3.36
4944 4967 8.236586 CAGCTTTATGTTGCAACTGTAAATCTA 58.763 33.333 28.61 7.02 0.00 1.98
5072 5095 3.239449 ACATGTGTCTCTGTTACTCCCA 58.761 45.455 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.659111 AATGGTCACAATACATGCCATG 57.341 40.909 2.40 2.40 35.50 3.66
38 39 7.168219 TCCTAAGCAACATGTTAGATGAGTTT 58.832 34.615 11.53 4.85 0.00 2.66
41 42 6.820656 ACTTCCTAAGCAACATGTTAGATGAG 59.179 38.462 11.53 7.15 0.00 2.90
171 172 7.752518 TGGTGGGTACAATAATCTAAAGGTA 57.247 36.000 0.00 0.00 0.00 3.08
254 255 3.960571 ACTCGACCTAACTACTGGCTTA 58.039 45.455 0.00 0.00 0.00 3.09
271 272 7.036669 GACTGTAGTCTATACGTCATACTCG 57.963 44.000 4.81 0.00 41.65 4.18
593 595 0.698238 TTAGCTGGCCCAAGTCACAT 59.302 50.000 0.00 0.00 0.00 3.21
735 738 7.543755 AGATAATAGGAGAAGAGAAGGTCCAT 58.456 38.462 0.00 0.00 0.00 3.41
787 790 8.313292 CCTTCCTATTTTCATGTGAAATGGAAA 58.687 33.333 22.85 0.00 42.83 3.13
798 801 6.878923 TGTGACTACACCTTCCTATTTTCATG 59.121 38.462 0.00 0.00 45.40 3.07
860 863 7.581213 TTTGTGAGACCATACAATTTCTGTT 57.419 32.000 0.00 0.00 39.64 3.16
903 906 3.578716 ACACACTGAACATAGCCTACTGT 59.421 43.478 0.00 0.00 0.00 3.55
1439 1443 6.351796 GGCATGGTTTATGAAAAATGGTACCT 60.352 38.462 14.36 0.00 39.21 3.08
1465 1469 9.846248 AGAACATACTGAATTCAAAATACTTGC 57.154 29.630 9.88 0.00 0.00 4.01
1600 1605 3.821033 GCAATTTACAGTGGTTGACTCCT 59.179 43.478 0.00 0.00 29.75 3.69
1643 1648 8.844244 GTGCCATCATCTATCTTGTATCTTTTT 58.156 33.333 0.00 0.00 0.00 1.94
1772 1777 7.141363 AGTTGATGCTTGTAAAAGAACACATC 58.859 34.615 0.00 0.87 35.23 3.06
1858 1863 9.528489 GATAAAAATAAATACCATAGGCCCAGA 57.472 33.333 0.00 0.00 0.00 3.86
1964 1969 4.755123 TCGAGATCTGTAACTGATGCGATA 59.245 41.667 0.00 0.00 0.00 2.92
2306 2324 4.141574 GGTTAAGGATACCATGTGGCTACA 60.142 45.833 4.99 4.99 39.32 2.74
2331 2349 5.581126 TGTGAGCTTCATTCAAAGTTGTT 57.419 34.783 0.00 0.00 0.00 2.83
2383 2401 0.790814 GGTACAGAAGCTGCGTTGAC 59.209 55.000 7.81 0.00 34.37 3.18
2593 2611 0.755686 TTGGCTTGACGGGCATTTTT 59.244 45.000 0.00 0.00 41.29 1.94
2622 2640 5.526115 AGAAGCCATGCATTATGAATTTCG 58.474 37.500 0.00 0.00 39.21 3.46
2642 2660 2.036387 TGTCACTTCCTCACCGAAGAA 58.964 47.619 5.39 0.00 41.57 2.52
3204 3227 7.716998 ACAAGAAATGTACTGAAGTTCACAGAT 59.283 33.333 0.08 0.00 41.63 2.90
3602 3625 9.683069 CAGAAAATTCAACTGCTACTACATTTT 57.317 29.630 0.00 0.00 0.00 1.82
3741 3764 4.261572 GCATAAAAGTTTCTGTCCTGCACA 60.262 41.667 0.00 0.00 0.00 4.57
3788 3811 5.947228 AGCATGGTATTATCAATTGTCCG 57.053 39.130 5.13 0.00 0.00 4.79
3908 3931 8.183536 CCAATTTTCTCGACACATTCATCATAA 58.816 33.333 0.00 0.00 0.00 1.90
3923 3946 3.253188 TGGAAGAGTTGCCAATTTTCTCG 59.747 43.478 0.00 0.00 0.00 4.04
4309 4332 0.618458 GGGTATGTCACAGGAAGGCA 59.382 55.000 0.00 0.00 0.00 4.75
4724 4747 6.192044 GGATTTTAATAAAGGACTGTGGGGA 58.808 40.000 0.00 0.00 0.00 4.81
4901 4924 2.564504 AGCTGATCTATAGGAATGCGCA 59.435 45.455 14.96 14.96 0.00 6.09
4902 4925 3.244033 AGCTGATCTATAGGAATGCGC 57.756 47.619 0.00 0.00 0.00 6.09
4911 4934 7.770433 ACAGTTGCAACATAAAGCTGATCTATA 59.230 33.333 30.11 0.00 0.00 1.31
4944 4967 7.177568 CACCAGCAGTCTATCAGGTATTACTAT 59.822 40.741 0.00 0.00 0.00 2.12
5072 5095 9.630098 GACAACAATTACAGAATGAATTCACAT 57.370 29.630 11.07 2.44 39.69 3.21


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

AutoCloner maintained by Alex Coulton.