Multiple sequence alignment - TraesCS6D01G158800

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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 TraesCS6D01G158800 chr6D 100.000 2211 0 0 1 2211 135459564 135461774 0 4084
1 TraesCS6D01G158800 chr3B 97.746 2218 42 3 1 2211 101916062 101913846 0 3812
2 TraesCS6D01G158800 chr3D 97.694 2212 49 2 1 2211 589272074 589274284 0 3801
3 TraesCS6D01G158800 chrUn 97.694 2212 48 2 1 2211 216513723 216515932 0 3799
4 TraesCS6D01G158800 chrUn 97.694 2212 48 2 1 2211 286269660 286267451 0 3799
5 TraesCS6D01G158800 chr5D 97.606 2214 50 2 1 2211 503223102 503220889 0 3792
6 TraesCS6D01G158800 chr5D 97.244 2213 58 3 1 2211 6193822 6191611 0 3746
7 TraesCS6D01G158800 chr3A 97.377 2211 57 1 1 2211 672905130 672907339 0 3760
8 TraesCS6D01G158800 chr3A 97.241 2211 60 1 1 2211 594894745 594896954 0 3744
9 TraesCS6D01G158800 chr1D 97.285 2210 59 1 1 2209 254393230 254395439 0 3747


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 TraesCS6D01G158800 chr6D 135459564 135461774 2210 False 4084 4084 100.000 1 2211 1 chr6D.!!$F1 2210
1 TraesCS6D01G158800 chr3B 101913846 101916062 2216 True 3812 3812 97.746 1 2211 1 chr3B.!!$R1 2210
2 TraesCS6D01G158800 chr3D 589272074 589274284 2210 False 3801 3801 97.694 1 2211 1 chr3D.!!$F1 2210
3 TraesCS6D01G158800 chrUn 216513723 216515932 2209 False 3799 3799 97.694 1 2211 1 chrUn.!!$F1 2210
4 TraesCS6D01G158800 chrUn 286267451 286269660 2209 True 3799 3799 97.694 1 2211 1 chrUn.!!$R1 2210
5 TraesCS6D01G158800 chr5D 503220889 503223102 2213 True 3792 3792 97.606 1 2211 1 chr5D.!!$R2 2210
6 TraesCS6D01G158800 chr5D 6191611 6193822 2211 True 3746 3746 97.244 1 2211 1 chr5D.!!$R1 2210
7 TraesCS6D01G158800 chr3A 672905130 672907339 2209 False 3760 3760 97.377 1 2211 1 chr3A.!!$F2 2210
8 TraesCS6D01G158800 chr3A 594894745 594896954 2209 False 3744 3744 97.241 1 2211 1 chr3A.!!$F1 2210
9 TraesCS6D01G158800 chr1D 254393230 254395439 2209 False 3747 3747 97.285 1 2209 1 chr1D.!!$F1 2208

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
107 108 2.731217 ACTCAAACAAGCATGAAACGC 58.269 42.857 0.0 0.0 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1380 3.070576 GCGCCAGGCCCAGATTTT 61.071 61.111 5.63 0.0 34.8 1.82 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
84 85 2.999185 TTTGGGGAATCTCCTTGCTT 57.001 45.000 0.00 0.0 36.57 3.91
107 108 2.731217 ACTCAAACAAGCATGAAACGC 58.269 42.857 0.00 0.0 0.00 4.84
132 133 3.557054 GCTTGCATATTCGTCCATAGGGA 60.557 47.826 0.00 0.0 42.29 4.20
265 266 7.121907 TGCTTGCATTGTATTATTTGGTCTACA 59.878 33.333 0.00 0.0 0.00 2.74
391 393 2.737252 CACTAGCAGGTTTCTTCGGAAC 59.263 50.000 0.00 0.0 33.18 3.62
481 483 7.612677 ACGAGTGTTCTTTCCATCTACTATTT 58.387 34.615 0.00 0.0 0.00 1.40
784 786 5.169295 GGCGCTAGGGTTATGAACTTATAG 58.831 45.833 7.64 0.0 0.00 1.31
799 801 8.459911 TGAACTTATAGTCATGGAATCGACTA 57.540 34.615 0.00 0.0 45.99 2.59
839 842 5.104941 AGTTCATTCCATATCGAACCAGACA 60.105 40.000 0.00 0.0 38.80 3.41
845 848 3.461061 CATATCGAACCAGACAGTGCAT 58.539 45.455 0.00 0.0 0.00 3.96
979 982 6.988580 CAGACCTGCTTTTGACATATCTATCA 59.011 38.462 0.00 0.0 0.00 2.15
1039 1042 7.128976 GCTTCTATTGAATCGAGAAATTGGAC 58.871 38.462 0.00 0.0 0.00 4.02
1042 1045 4.685169 TTGAATCGAGAAATTGGACTGC 57.315 40.909 0.00 0.0 0.00 4.40
1443 1446 5.284582 ACCATCTCCCTGAGAAAAGTAGAT 58.715 41.667 0.00 0.0 42.27 1.98
1520 1524 6.224584 CCTCGAAGGAGATAATAAAGAACCC 58.775 44.000 0.00 0.0 43.27 4.11
1732 1738 6.817765 AAGTAGCGATCAAATCAAGGAAAA 57.182 33.333 0.00 0.0 0.00 2.29
1733 1739 6.428385 AGTAGCGATCAAATCAAGGAAAAG 57.572 37.500 0.00 0.0 0.00 2.27
1782 1793 6.294899 CCAAATCATGATCTTCACCAACTTGT 60.295 38.462 9.06 0.0 0.00 3.16
1844 1855 3.173953 ACCATGAAAAGCAAGATCCCA 57.826 42.857 0.00 0.0 0.00 4.37
1872 1883 4.101119 AGAAAACAGAAACCGAGGAAGAGA 59.899 41.667 0.00 0.0 0.00 3.10
1976 1987 6.767524 TGCCGACCAAAAATTCTATATGTT 57.232 33.333 0.00 0.0 0.00 2.71
2052 2065 3.119495 CCGATTTGTCAAAGGGATTGGAC 60.119 47.826 11.10 0.0 39.62 4.02
2134 2147 6.127591 CGGATCGGGTGAATTAGAGAATAGAT 60.128 42.308 0.00 0.0 0.00 1.98
2155 2168 0.521735 GAGGTCCGTTGGCATTTCAC 59.478 55.000 0.00 0.0 0.00 3.18
2158 2171 1.605165 TCCGTTGGCATTTCACCCC 60.605 57.895 0.00 0.0 0.00 4.95
2189 2202 1.874129 TCAGGGCCTATCCGAAAGAA 58.126 50.000 5.28 0.0 34.94 2.52
2193 2206 3.954258 CAGGGCCTATCCGAAAGAAAATT 59.046 43.478 5.28 0.0 34.94 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 4.737765 GCGTTTCATGCTTGTTTGAGTAAA 59.262 37.500 0.00 0.0 0.00 2.01
107 108 3.909776 ATGGACGAATATGCAAGCATG 57.090 42.857 17.26 3.4 37.82 4.06
265 266 5.301045 TCTCGAATGTTATCAGTTCCGGTAT 59.699 40.000 0.00 0.0 0.00 2.73
391 393 6.453943 CATCCACACCAGAATAGATAGAGTG 58.546 44.000 0.00 0.0 0.00 3.51
784 786 6.018589 TGATGATCTAGTCGATTCCATGAC 57.981 41.667 0.00 0.0 35.33 3.06
828 830 3.195610 AGAATATGCACTGTCTGGTTCGA 59.804 43.478 0.00 0.0 0.00 3.71
863 866 3.904800 TTCCATAGGCTCGAATGAACA 57.095 42.857 0.00 0.0 0.00 3.18
865 868 5.551233 CCTATTTCCATAGGCTCGAATGAA 58.449 41.667 0.00 0.0 44.71 2.57
1003 1006 6.127897 CGATTCAATAGAAGCCCAAAGAAGTT 60.128 38.462 0.00 0.0 36.84 2.66
1006 1009 5.496556 TCGATTCAATAGAAGCCCAAAGAA 58.503 37.500 0.00 0.0 36.84 2.52
1039 1042 7.884816 AATCAAAAAGATGAAAGATGTGCAG 57.115 32.000 0.00 0.0 36.96 4.41
1377 1380 3.070576 GCGCCAGGCCCAGATTTT 61.071 61.111 5.63 0.0 34.80 1.82
1520 1524 3.812053 GCAGTAGGATACCATCTGCTTTG 59.188 47.826 20.35 0.0 44.47 2.77
1782 1793 5.163893 GCGATTTTCACGAGAGAACCAAATA 60.164 40.000 0.00 0.0 0.00 1.40
1813 1824 6.053632 TGCTTTTCATGGTTCTCATCTCTA 57.946 37.500 0.00 0.0 32.92 2.43
1844 1855 7.501225 TCTTCCTCGGTTTCTGTTTTCTTATTT 59.499 33.333 0.00 0.0 0.00 1.40
1872 1883 5.990668 ACTAGTCTTCACTCTTGTGGTTTT 58.009 37.500 0.00 0.0 43.94 2.43
2134 2147 1.626321 TGAAATGCCAACGGACCTCTA 59.374 47.619 0.00 0.0 0.00 2.43


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

AutoCloner maintained by Alex Coulton.