Multiple sequence alignment - TraesCS5D01G322100

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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 TraesCS5D01G322100 chr5D 100.000 2354 0 0 1 2354 413971884 413974237 0 4348
1 TraesCS5D01G322100 chr5D 96.314 2360 80 7 1 2354 143712366 143710008 0 3869
2 TraesCS5D01G322100 chr5D 96.015 2359 87 7 1 2354 474621903 474619547 0 3829
3 TraesCS5D01G322100 chr1D 96.776 2357 71 5 1 2352 215669659 215667303 0 3927
4 TraesCS5D01G322100 chr3D 96.482 2359 78 5 1 2354 178331722 178334080 0 3892
5 TraesCS5D01G322100 chr7D 96.594 2349 65 10 11 2354 444824827 444822489 0 3880
6 TraesCS5D01G322100 chr2D 96.309 2357 78 7 1 2352 123945600 123947952 0 3862
7 TraesCS5D01G322100 chr2D 96.020 2362 82 9 1 2354 344137019 344139376 0 3831
8 TraesCS5D01G322100 chr4D 96.230 2361 81 8 1 2354 395867677 395870036 0 3860


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 TraesCS5D01G322100 chr5D 413971884 413974237 2353 False 4348 4348 100.000 1 2354 1 chr5D.!!$F1 2353
1 TraesCS5D01G322100 chr5D 143710008 143712366 2358 True 3869 3869 96.314 1 2354 1 chr5D.!!$R1 2353
2 TraesCS5D01G322100 chr5D 474619547 474621903 2356 True 3829 3829 96.015 1 2354 1 chr5D.!!$R2 2353
3 TraesCS5D01G322100 chr1D 215667303 215669659 2356 True 3927 3927 96.776 1 2352 1 chr1D.!!$R1 2351
4 TraesCS5D01G322100 chr3D 178331722 178334080 2358 False 3892 3892 96.482 1 2354 1 chr3D.!!$F1 2353
5 TraesCS5D01G322100 chr7D 444822489 444824827 2338 True 3880 3880 96.594 11 2354 1 chr7D.!!$R1 2343
6 TraesCS5D01G322100 chr2D 123945600 123947952 2352 False 3862 3862 96.309 1 2352 1 chr2D.!!$F1 2351
7 TraesCS5D01G322100 chr2D 344137019 344139376 2357 False 3831 3831 96.020 1 2354 1 chr2D.!!$F2 2353
8 TraesCS5D01G322100 chr4D 395867677 395870036 2359 False 3860 3860 96.230 1 2354 1 chr4D.!!$F1 2353

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
751 760 0.905357 AGCTTATGGTCGGAGCACTT 59.095 50.0 12.67 0.0 38.85 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1851 0.190815 ACCCTGCCATTCCCAAAGTT 59.809 50.0 0.0 0.0 0.0 2.66 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
114 118 5.051153 GGATCTAGGGTTTCGTGAGATTTC 58.949 45.833 0.00 0.00 41.60 2.17
115 119 5.395324 GGATCTAGGGTTTCGTGAGATTTCA 60.395 44.000 0.00 0.00 41.60 2.69
116 120 5.677319 TCTAGGGTTTCGTGAGATTTCAT 57.323 39.130 0.00 0.00 41.60 2.57
156 161 3.005367 TCTGTCACTTCGTCATTGTGCTA 59.995 43.478 0.00 0.00 0.00 3.49
629 637 5.927030 ACAAACATGAAGTTAGTGTATGCG 58.073 37.500 0.00 0.00 40.26 4.73
655 664 9.677567 GGCACTGTATTTATTTTGTATATGTGG 57.322 33.333 0.00 0.00 0.00 4.17
687 696 7.986889 ACTATATGTATGTGTGAACTGCATTGA 59.013 33.333 0.00 0.00 0.00 2.57
751 760 0.905357 AGCTTATGGTCGGAGCACTT 59.095 50.000 12.67 0.00 38.85 3.16
902 911 9.941325 TCAATTGATTAACCATTATTTTGCAGT 57.059 25.926 3.38 0.00 0.00 4.40
961 970 3.245284 CGTTTTGTCTGAGACACAATCGT 59.755 43.478 15.94 0.00 42.60 3.73
1014 1023 2.355716 GGATTGGATGGTCTCGGAACAA 60.356 50.000 0.00 0.00 31.09 2.83
1108 1117 1.568597 AGGAGAAGCAGAGGAGAGCTA 59.431 52.381 0.00 0.00 40.90 3.32
1111 1120 2.757868 GAGAAGCAGAGGAGAGCTACAA 59.242 50.000 0.00 0.00 40.90 2.41
1645 1657 5.092259 AGATGATGCTGAGGGAGATGATTA 58.908 41.667 0.00 0.00 0.00 1.75
1672 1684 5.793026 TTTAACAAGACCGTACGTTTGTT 57.207 34.783 28.94 28.94 43.72 2.83
1693 1705 1.402787 CTTCCCACTGTTTGCAAGGT 58.597 50.000 0.00 0.00 0.00 3.50
1753 1765 3.809832 CGGGATGCTAGATTTGGTGTTAG 59.190 47.826 0.00 0.00 0.00 2.34
1764 1776 4.647424 TTTGGTGTTAGCTTTGAACTGG 57.353 40.909 0.00 0.00 0.00 4.00
1786 1798 4.286910 GCAGTAAAGAAAAATGTGTCGCA 58.713 39.130 0.00 0.00 0.00 5.10
1839 1851 1.852309 ACCCTGCCACCATGATAATGA 59.148 47.619 0.00 0.00 0.00 2.57
2074 2087 1.267806 CATGTGACTGTTGACCTTGCC 59.732 52.381 0.00 0.00 0.00 4.52
2121 2134 1.074775 AGAATTTGCTGTGCCCCGA 59.925 52.632 0.00 0.00 0.00 5.14
2124 2137 3.574074 ATTTGCTGTGCCCCGAGCT 62.574 57.895 0.00 0.00 44.23 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 8.491331 AAATTACACAAGCAAAACAGAAACAT 57.509 26.923 0.00 0.0 0.00 2.71
13 14 6.254589 CGGAAAAATTACACAAGCAAAACAGA 59.745 34.615 0.00 0.0 0.00 3.41
45 47 5.057149 ACTCCAAATCGAGATAAAATCGGG 58.943 41.667 0.00 0.0 40.54 5.14
114 118 9.791820 TGACAGATATAAGCAACAAAATCAATG 57.208 29.630 0.00 0.0 0.00 2.82
115 119 9.793252 GTGACAGATATAAGCAACAAAATCAAT 57.207 29.630 0.00 0.0 0.00 2.57
116 120 9.013229 AGTGACAGATATAAGCAACAAAATCAA 57.987 29.630 0.00 0.0 0.00 2.57
366 374 4.481368 ACCGCAATCACCTACTTGATTA 57.519 40.909 0.00 0.0 43.08 1.75
629 637 9.677567 CCACATATACAAAATAAATACAGTGCC 57.322 33.333 0.00 0.0 0.00 5.01
655 664 8.982685 CAGTTCACACATACATATAGTGGAATC 58.017 37.037 0.00 0.0 37.58 2.52
657 666 6.761242 GCAGTTCACACATACATATAGTGGAA 59.239 38.462 0.00 0.0 37.58 3.53
742 751 6.851222 AGACATATAAAATGAAGTGCTCCG 57.149 37.500 0.00 0.0 0.00 4.63
886 895 6.013812 ACATTACCCACTGCAAAATAATGGTT 60.014 34.615 14.97 0.0 35.35 3.67
902 911 1.423541 AGCTCACACCAACATTACCCA 59.576 47.619 0.00 0.0 0.00 4.51
961 970 4.412843 TCCTGTGTACCATCAACAGACTA 58.587 43.478 10.91 0.0 0.00 2.59
979 988 4.286297 TCCAATCCTGTGTAACTTCCTG 57.714 45.455 0.00 0.0 38.04 3.86
1108 1117 1.757423 GCACCCTTGGCACCATTTGT 61.757 55.000 0.00 0.0 0.00 2.83
1645 1657 4.737054 ACGTACGGTCTTGTTAAATCGAT 58.263 39.130 21.06 0.0 0.00 3.59
1672 1684 0.746063 CTTGCAAACAGTGGGAAGCA 59.254 50.000 0.00 0.0 0.00 3.91
1693 1705 1.682854 CCTCTTTCAACAAGGCAGCAA 59.317 47.619 0.00 0.0 0.00 3.91
1753 1765 4.568152 TTCTTTACTGCCAGTTCAAAGC 57.432 40.909 13.07 0.0 28.69 3.51
1764 1776 4.146443 GTGCGACACATTTTTCTTTACTGC 59.854 41.667 5.30 0.0 34.08 4.40
1839 1851 0.190815 ACCCTGCCATTCCCAAAGTT 59.809 50.000 0.00 0.0 0.00 2.66
1999 2012 4.074970 CAAGCAAGTCCTTGACACCTATT 58.925 43.478 11.12 0.0 43.79 1.73
2096 2109 3.019564 GGCACAGCAAATTCTGGTAGAT 58.980 45.455 0.00 0.0 38.36 1.98
2121 2134 0.751643 ACCCAAACGAACTGCAAGCT 60.752 50.000 0.00 0.0 37.60 3.74
2124 2137 2.158871 ACTCTACCCAAACGAACTGCAA 60.159 45.455 0.00 0.0 0.00 4.08


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

AutoCloner maintained by Alex Coulton.