Multiple sequence alignment - TraesCS3B01G188200

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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 TraesCS3B01G188200 chr3B 100.000 2309 0 0 1 2309 201538068 201540376 0 4265
1 TraesCS3B01G188200 chr7B 98.874 2309 25 1 1 2309 663100878 663098571 0 4119
2 TraesCS3B01G188200 chr3D 98.787 2309 24 2 1 2309 589264976 589262672 0 4106
3 TraesCS3B01G188200 chr3A 98.744 2309 27 1 1 2309 66006585 66004279 0 4102
4 TraesCS3B01G188200 chr3A 98.094 2309 42 2 1 2309 695638935 695641241 0 4019
5 TraesCS3B01G188200 chr2A 98.744 2309 28 1 1 2309 726907908 726905601 0 4102
6 TraesCS3B01G188200 chr2A 97.707 2311 49 3 1 2309 335845859 335848167 0 3971
7 TraesCS3B01G188200 chr2B 98.224 2309 40 1 1 2309 474919477 474921784 0 4036


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 TraesCS3B01G188200 chr3B 201538068 201540376 2308 False 4265 4265 100.000 1 2309 1 chr3B.!!$F1 2308
1 TraesCS3B01G188200 chr7B 663098571 663100878 2307 True 4119 4119 98.874 1 2309 1 chr7B.!!$R1 2308
2 TraesCS3B01G188200 chr3D 589262672 589264976 2304 True 4106 4106 98.787 1 2309 1 chr3D.!!$R1 2308
3 TraesCS3B01G188200 chr3A 66004279 66006585 2306 True 4102 4102 98.744 1 2309 1 chr3A.!!$R1 2308
4 TraesCS3B01G188200 chr3A 695638935 695641241 2306 False 4019 4019 98.094 1 2309 1 chr3A.!!$F1 2308
5 TraesCS3B01G188200 chr2A 726905601 726907908 2307 True 4102 4102 98.744 1 2309 1 chr2A.!!$R1 2308
6 TraesCS3B01G188200 chr2A 335845859 335848167 2308 False 3971 3971 97.707 1 2309 1 chr2A.!!$F1 2308
7 TraesCS3B01G188200 chr2B 474919477 474921784 2307 False 4036 4036 98.224 1 2309 1 chr2B.!!$F1 2308

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
321 322 0.03601 CCTCAGTTCGGATTGCAGGT 60.036 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1711 0.734253 CTTGAACCAGAGACCTCGCG 60.734 60.0 0.0 0.0 34.09 5.87 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
180 181 2.047560 GACCGCCGGTGTTAAGCT 60.048 61.111 16.53 0.00 35.25 3.74
321 322 0.036010 CCTCAGTTCGGATTGCAGGT 60.036 55.000 0.00 0.00 0.00 4.00
616 617 2.159296 ACACTTCTTCACGCCCAAAAAC 60.159 45.455 0.00 0.00 0.00 2.43
655 656 7.344612 TCTGAGCTAAACTTGGATATGGAAGTA 59.655 37.037 0.00 0.00 32.03 2.24
759 760 3.055580 TTTTTGGCGTCCCCATGC 58.944 55.556 0.00 0.00 44.89 4.06
817 818 4.106341 AGGAAAGGGATGGAGTTTTTCTCA 59.894 41.667 0.00 0.00 44.40 3.27
882 883 3.892588 GGCTATTAGCTCAGTGGTAGAGT 59.107 47.826 15.02 0.00 41.99 3.24
891 892 3.075005 TGGTAGAGTGCGCCCCTC 61.075 66.667 14.47 14.47 0.00 4.30
902 903 1.724582 GCGCCCCTCATAATTGCGTT 61.725 55.000 0.00 0.00 46.39 4.84
1077 1078 2.303022 GAGGATAGATGGGGCGATTCAA 59.697 50.000 0.00 0.00 0.00 2.69
1258 1265 3.572255 GGAAAATGGAGCACCTAACAACA 59.428 43.478 0.71 0.00 37.04 3.33
1704 1711 1.003866 GGGCGATGATTTACTTCACGC 60.004 52.381 0.00 0.00 41.28 5.34
2205 2213 2.929043 AGGAAGGAAAATCCATGGACCT 59.071 45.455 18.99 16.33 39.61 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 181 1.062581 CCTCATCCTCTCCTTCCTCCA 60.063 57.143 0.00 0.00 0.00 3.86
616 617 1.080995 GCTCAGACGTAGCTGCCTTG 61.081 60.000 0.00 0.00 37.01 3.61
655 656 7.387122 GTCTTACTTCACCCTAAACGAAAGAAT 59.613 37.037 0.00 0.00 0.00 2.40
817 818 1.971695 GGCCTGCTACGCCAAAAGT 60.972 57.895 0.00 0.00 46.27 2.66
882 883 2.186160 CGCAATTATGAGGGGCGCA 61.186 57.895 10.83 0.00 41.27 6.09
891 892 4.043750 CCAGGCACAATAACGCAATTATG 58.956 43.478 0.00 0.00 33.53 1.90
902 903 0.035152 CTCACAGCCCAGGCACAATA 60.035 55.000 12.03 0.00 44.88 1.90
1077 1078 6.619464 AGTTAGATCTACATGGGATCTCACT 58.381 40.000 25.37 25.37 44.33 3.41
1258 1265 4.696479 AGTTCTTGGTCTGTGAAGATGT 57.304 40.909 0.00 0.00 0.00 3.06
1704 1711 0.734253 CTTGAACCAGAGACCTCGCG 60.734 60.000 0.00 0.00 34.09 5.87
2205 2213 0.917333 GGGGTGGAGACAATGGGGTA 60.917 60.000 0.00 0.00 46.06 3.69


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

AutoCloner maintained by Alex Coulton.