Multiple sequence alignment - TraesCS1B01G458600

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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 TraesCS1B01G458600 chr1B 100.000 2744 0 0 1 2744 672540211 672542954 0 5068
1 TraesCS1B01G458600 chr6B 98.762 2746 31 3 1 2744 596602871 596600127 0 4879
2 TraesCS1B01G458600 chr6B 98.477 2167 30 2 580 2744 715991505 715989340 0 3816
3 TraesCS1B01G458600 chrUn 98.580 2747 33 6 1 2744 171007273 171010016 0 4852
4 TraesCS1B01G458600 chr7A 98.544 2747 35 4 1 2744 638508678 638505934 0 4846
5 TraesCS1B01G458600 chr7A 98.507 2746 35 5 1 2744 708244614 708247355 0 4839
6 TraesCS1B01G458600 chr5B 97.999 2748 50 4 1 2744 567278982 567281728 0 4765
7 TraesCS1B01G458600 chr4B 97.814 2745 53 6 1 2744 495566953 495569691 0 4730
8 TraesCS1B01G458600 chr2B 97.744 2748 55 5 1 2744 391226256 391223512 0 4724
9 TraesCS1B01G458600 chr2B 97.705 2745 60 3 1 2744 391143792 391146534 0 4717
10 TraesCS1B01G458600 chr2B 97.693 1127 24 2 1 1126 357227775 357228900 0 1936


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 TraesCS1B01G458600 chr1B 672540211 672542954 2743 False 5068 5068 100.000 1 2744 1 chr1B.!!$F1 2743
1 TraesCS1B01G458600 chr6B 596600127 596602871 2744 True 4879 4879 98.762 1 2744 1 chr6B.!!$R1 2743
2 TraesCS1B01G458600 chr6B 715989340 715991505 2165 True 3816 3816 98.477 580 2744 1 chr6B.!!$R2 2164
3 TraesCS1B01G458600 chrUn 171007273 171010016 2743 False 4852 4852 98.580 1 2744 1 chrUn.!!$F1 2743
4 TraesCS1B01G458600 chr7A 638505934 638508678 2744 True 4846 4846 98.544 1 2744 1 chr7A.!!$R1 2743
5 TraesCS1B01G458600 chr7A 708244614 708247355 2741 False 4839 4839 98.507 1 2744 1 chr7A.!!$F1 2743
6 TraesCS1B01G458600 chr5B 567278982 567281728 2746 False 4765 4765 97.999 1 2744 1 chr5B.!!$F1 2743
7 TraesCS1B01G458600 chr4B 495566953 495569691 2738 False 4730 4730 97.814 1 2744 1 chr4B.!!$F1 2743
8 TraesCS1B01G458600 chr2B 391223512 391226256 2744 True 4724 4724 97.744 1 2744 1 chr2B.!!$R1 2743
9 TraesCS1B01G458600 chr2B 391143792 391146534 2742 False 4717 4717 97.705 1 2744 1 chr2B.!!$F2 2743
10 TraesCS1B01G458600 chr2B 357227775 357228900 1125 False 1936 1936 97.693 1 1126 1 chr2B.!!$F1 1125

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
821 829 0.696143 TCCATTTCATAGGCGGGGGA 60.696 55.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2168 0.808755 CTTTTTCATCGGTTCCGGGG 59.191 55.0 11.37 4.34 0.0 5.73 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
296 298 1.145119 GGGAAAGTGAACTCCTGGGTT 59.855 52.381 0.00 0.0 31.88 4.11
741 749 3.598019 TTCTTTCAAGAATGCATGGCC 57.402 42.857 0.00 0.0 39.95 5.36
817 825 3.081804 GGGTTATCCATTTCATAGGCGG 58.918 50.000 0.00 0.0 35.00 6.13
821 829 0.696143 TCCATTTCATAGGCGGGGGA 60.696 55.000 0.00 0.0 0.00 4.81
965 973 7.122650 TCGGCTTGGAAGAAGAAAATGAAATAT 59.877 33.333 0.00 0.0 0.00 1.28
1038 1046 4.687483 CCAGCATTCAAGTTCCATTTCAAC 59.313 41.667 0.00 0.0 0.00 3.18
1747 1756 6.697395 ACCTTTAAAATGTGGATTTAGTGCC 58.303 36.000 0.00 0.0 31.18 5.01
1838 1847 6.240292 GGGGAGATCCTATTCATGGTAAACAT 60.240 42.308 0.00 0.0 36.82 2.71
1999 2010 4.689345 CGAATTGGTAGGTTTCTCGAAGTT 59.311 41.667 0.00 0.0 0.00 2.66
2120 2131 5.108517 CAGTGCATACCTCTCTTTCTCTTC 58.891 45.833 0.00 0.0 0.00 2.87
2136 2147 5.614324 TCTCTTCTGAGTTTTTCTGGTCA 57.386 39.130 0.00 0.0 40.98 4.02
2157 2168 1.740025 CGCAAGATCTTTGGTCTTCCC 59.260 52.381 4.86 0.0 43.02 3.97
2391 2403 6.500041 AGAGTGTAGTTCGAGCATTCTATTC 58.500 40.000 1.01 0.0 29.45 1.75
2704 2716 3.364549 CACCCAATAGGCCAGATTTTCA 58.635 45.455 5.01 0.0 40.58 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
567 569 0.108377 TTCGCAATAGCAGCTCCGAA 60.108 50.000 0.00 7.09 42.27 4.30
741 749 2.168521 TGTTGAAGCGGAATAGGAGGAG 59.831 50.000 0.00 0.00 0.00 3.69
817 825 2.614013 TTGCTTCTCCCCCTCCCC 60.614 66.667 0.00 0.00 0.00 4.81
821 829 3.721706 CGGCTTGCTTCTCCCCCT 61.722 66.667 0.00 0.00 0.00 4.79
1038 1046 1.063649 CATGGTACGTCGTCCTCCG 59.936 63.158 0.00 0.00 38.13 4.63
1239 1248 7.106890 TCATAACCACGAATAGGAATGAAACA 58.893 34.615 0.00 0.00 32.88 2.83
1747 1756 5.012893 GCCAGGGAAATCCTTATATTCTGG 58.987 45.833 11.93 11.93 45.47 3.86
1999 2010 9.720769 CTATTTCCTGAGAAACCTACTAAAACA 57.279 33.333 0.00 0.00 44.57 2.83
2120 2131 1.939934 TGCGTGACCAGAAAAACTCAG 59.060 47.619 0.00 0.00 0.00 3.35
2136 2147 2.427506 GGAAGACCAAAGATCTTGCGT 58.572 47.619 9.17 8.05 36.53 5.24
2157 2168 0.808755 CTTTTTCATCGGTTCCGGGG 59.191 55.000 11.37 4.34 0.00 5.73
2391 2403 1.759994 GTATCACGGATCGAGCACAG 58.240 55.000 1.84 0.00 0.00 3.66
2487 2499 2.158900 CCCGAGTGCAACCAGATAAGAT 60.159 50.000 0.00 0.00 37.80 2.40
2556 2568 6.949715 ACCCTCATTGCATGTTTTCAAATAT 58.050 32.000 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.