Multiple sequence alignment - TraesCS2B01G331600

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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 TraesCS2B01G331600 chr2B 100.000 2177 0 0 1 2177 474918684 474916508 0 4021
1 TraesCS2B01G331600 chr6D 98.300 2177 37 0 1 2177 389254923 389252747 0 3816
2 TraesCS2B01G331600 chr5D 98.254 2177 37 1 1 2177 503238780 503236605 0 3808
3 TraesCS2B01G331600 chr5D 98.339 2167 35 1 11 2177 503243019 503240854 0 3801
4 TraesCS2B01G331600 chr3A 98.254 2177 37 1 1 2177 66007378 66009553 0 3808
5 TraesCS2B01G331600 chr3A 97.565 2177 53 0 1 2177 672899767 672901943 0 3727
6 TraesCS2B01G331600 chrUn 98.026 2178 39 2 1 2177 216508364 216510538 0 3781
7 TraesCS2B01G331600 chr3B 97.749 2177 48 1 1 2177 201537274 201535099 0 3747
8 TraesCS2B01G331600 chr2A 97.382 2177 57 0 1 2177 335845066 335842890 0 3705
9 TraesCS2B01G331600 chr1B 97.198 2177 55 1 1 2177 633743659 633745829 0 3677


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 TraesCS2B01G331600 chr2B 474916508 474918684 2176 True 4021.0 4021 100.0000 1 2177 1 chr2B.!!$R1 2176
1 TraesCS2B01G331600 chr6D 389252747 389254923 2176 True 3816.0 3816 98.3000 1 2177 1 chr6D.!!$R1 2176
2 TraesCS2B01G331600 chr5D 503236605 503243019 6414 True 3804.5 3808 98.2965 1 2177 2 chr5D.!!$R1 2176
3 TraesCS2B01G331600 chr3A 66007378 66009553 2175 False 3808.0 3808 98.2540 1 2177 1 chr3A.!!$F1 2176
4 TraesCS2B01G331600 chr3A 672899767 672901943 2176 False 3727.0 3727 97.5650 1 2177 1 chr3A.!!$F2 2176
5 TraesCS2B01G331600 chrUn 216508364 216510538 2174 False 3781.0 3781 98.0260 1 2177 1 chrUn.!!$F1 2176
6 TraesCS2B01G331600 chr3B 201535099 201537274 2175 True 3747.0 3747 97.7490 1 2177 1 chr3B.!!$R1 2176
7 TraesCS2B01G331600 chr2A 335842890 335845066 2176 True 3705.0 3705 97.3820 1 2177 1 chr2A.!!$R1 2176
8 TraesCS2B01G331600 chr1B 633743659 633745829 2170 False 3677.0 3677 97.1980 1 2177 1 chr1B.!!$F1 2176

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
311 312 1.303317 ACGTCAATCCCACAAGCCC 60.303 57.895 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 6293 1.595993 TTCGAGAGTCTCCGCCCTTG 61.596 60.0 14.61 0.0 0.0 3.61 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
52 53 3.893813 AGGTTCTTACGTGTTACTCACCT 59.106 43.478 0.00 0.00 43.51 4.00
57 58 4.338964 TCTTACGTGTTACTCACCTGTTCA 59.661 41.667 0.00 0.00 43.51 3.18
311 312 1.303317 ACGTCAATCCCACAAGCCC 60.303 57.895 0.00 0.00 0.00 5.19
383 384 3.434940 ACTCACATTGGGTTTAGGGAC 57.565 47.619 0.00 0.00 0.00 4.46
414 415 2.547855 CGAACTGATGACTTCCACCACA 60.548 50.000 0.00 0.00 0.00 4.17
462 463 2.561378 ATCCCTTCCCCGTCCCATCA 62.561 60.000 0.00 0.00 0.00 3.07
489 490 8.759782 AGAAAGAGAATTAACGAATCCTAAGGA 58.240 33.333 0.00 0.00 35.55 3.36
649 650 5.811613 CCATCGCACATGGTTTCATAAAATT 59.188 36.000 0.00 0.00 34.56 1.82
714 715 5.411977 AGAAGATCTTGTTCAGCATGTTCTG 59.588 40.000 14.00 0.00 37.40 3.02
797 799 4.474651 ACCAAGTCAAGATGATATGGGTCA 59.525 41.667 14.76 0.00 38.50 4.02
833 835 3.694072 CGCCAAAGATCTTACCATTTCCA 59.306 43.478 8.75 0.00 0.00 3.53
1496 5746 4.447138 TCCCTTCAACACAACATAGGTT 57.553 40.909 0.00 0.00 37.87 3.50
1619 5869 4.081752 CCCGTCAATTTTGGATCCAATTCA 60.082 41.667 27.53 14.99 35.70 2.57
1665 5915 6.925165 CGGGAAGAAATTGGAATGGAATAATG 59.075 38.462 0.00 0.00 0.00 1.90
1746 5997 6.462342 AGGGATAGAGGAAGAGGGAAAAATA 58.538 40.000 0.00 0.00 0.00 1.40
1815 6066 3.011032 AGAAGAGCCCAGATTCCAAATGT 59.989 43.478 0.00 0.00 0.00 2.71
1821 6072 4.706962 AGCCCAGATTCCAAATGTAGAAAC 59.293 41.667 0.00 0.00 0.00 2.78
2099 6353 0.984230 AAGAATTGACCGAGGAGCCA 59.016 50.000 0.00 0.00 0.00 4.75
2159 6413 5.046520 GGACAGTAAGGGTGACTTATCTGTT 60.047 44.000 16.09 7.18 44.54 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.004862 TGGTGTTTCCAGTGGTGAACA 59.995 47.619 21.79 21.79 41.93 3.18
105 106 3.067985 TCAGGATGAACGCTGGCA 58.932 55.556 0.00 0.00 45.97 4.92
311 312 1.202651 AGCGAACGGGAATGGATAAGG 60.203 52.381 0.00 0.00 0.00 2.69
383 384 2.606725 GTCATCAGTTCGAGCCTGATTG 59.393 50.000 20.77 16.85 45.12 2.67
414 415 1.204941 GCGGTAGAGTGTCACCTTGAT 59.795 52.381 0.00 0.00 32.29 2.57
462 463 9.384764 CCTTAGGATTCGTTAATTCTCTTTCTT 57.615 33.333 0.00 0.00 32.81 2.52
489 490 2.230660 CTTGAGTTTCTCGCCCCTTTT 58.769 47.619 0.00 0.00 32.35 2.27
649 650 7.473027 GATTTAGATCGGGAAAATCGTACAA 57.527 36.000 0.00 0.00 31.93 2.41
714 715 5.450274 GGTTCTTCTCCTACCAGTATCGAAC 60.450 48.000 0.00 0.00 32.12 3.95
797 799 2.034221 GGCGCAAGAAGAAGGGGT 59.966 61.111 10.83 0.00 43.02 4.95
833 835 3.076032 AGAAATGTAGCCCCAGTTCCTTT 59.924 43.478 9.09 0.00 39.56 3.11
1419 5669 2.224209 CGGTAGCAATAGAACGGGGAAT 60.224 50.000 0.00 0.00 0.00 3.01
1453 5703 7.773224 AGGGATATCTATATGATCCGATCGATC 59.227 40.741 18.66 15.68 46.70 3.69
1496 5746 3.875727 AGTCGTCCGAGATCTTTTCGATA 59.124 43.478 0.00 0.00 40.36 2.92
1619 5869 4.280929 CCGAAACTTCCCAAGAAAAATCCT 59.719 41.667 0.00 0.00 0.00 3.24
1665 5915 8.426881 GAACCTTTTCCTCTGTATGAATCTAC 57.573 38.462 0.00 0.00 0.00 2.59
1691 5941 3.242739 GGTACAGCGTTTGCATCAATAGG 60.243 47.826 0.00 0.00 46.23 2.57
1815 6066 4.947645 TCCTTTTCGAGTTTCCGTTTCTA 58.052 39.130 0.00 0.00 0.00 2.10
1821 6072 2.973945 AGGATCCTTTTCGAGTTTCCG 58.026 47.619 9.02 0.00 32.49 4.30
2039 6293 1.595993 TTCGAGAGTCTCCGCCCTTG 61.596 60.000 14.61 0.00 0.00 3.61
2099 6353 6.931281 CCGTACATGAGATTTTCACCTCATAT 59.069 38.462 0.00 0.00 45.39 1.78


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

AutoCloner maintained by Alex Coulton.