Multiple sequence alignment - TraesCS6D01G375200

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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 TraesCS6D01G375200 chr6D 100.000 2270 0 0 1 2270 458917728 458919997 0 4193
1 TraesCS6D01G375200 chr2B 98.416 2273 29 2 1 2270 449208701 449210969 0 3991
2 TraesCS6D01G375200 chr2B 98.108 2273 35 3 1 2270 234530533 234532800 0 3952
3 TraesCS6D01G375200 chr3A 98.328 2273 30 3 1 2270 495091913 495094180 0 3980
4 TraesCS6D01G375200 chr3B 98.240 2273 33 2 1 2270 6000139 6002407 0 3969
5 TraesCS6D01G375200 chr7A 98.064 2273 36 3 1 2270 60220138 60222405 0 3947
6 TraesCS6D01G375200 chr1B 97.536 2273 48 3 1 2270 619184704 619186971 0 3880


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 TraesCS6D01G375200 chr6D 458917728 458919997 2269 False 4193 4193 100.000 1 2270 1 chr6D.!!$F1 2269
1 TraesCS6D01G375200 chr2B 449208701 449210969 2268 False 3991 3991 98.416 1 2270 1 chr2B.!!$F2 2269
2 TraesCS6D01G375200 chr2B 234530533 234532800 2267 False 3952 3952 98.108 1 2270 1 chr2B.!!$F1 2269
3 TraesCS6D01G375200 chr3A 495091913 495094180 2267 False 3980 3980 98.328 1 2270 1 chr3A.!!$F1 2269
4 TraesCS6D01G375200 chr3B 6000139 6002407 2268 False 3969 3969 98.240 1 2270 1 chr3B.!!$F1 2269
5 TraesCS6D01G375200 chr7A 60220138 60222405 2267 False 3947 3947 98.064 1 2270 1 chr7A.!!$F1 2269
6 TraesCS6D01G375200 chr1B 619184704 619186971 2267 False 3880 3880 97.536 1 2270 1 chr1B.!!$F1 2269

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
817 818 3.065925 CGGCAAGAGAAAGATGGAATTCC 59.934 47.826 18.17 18.17 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1692 3.244457 GGGCGCTAGGGTTATGAACTTAT 60.244 47.826 7.64 0.0 0.0 1.73 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
607 608 3.371063 GCCGACTCCAGTCCGACA 61.371 66.667 0.40 0.00 41.86 4.35
651 652 3.073650 AGCTCCTGAACAGACTCCAAAAT 59.926 43.478 3.19 0.00 0.00 1.82
814 815 3.634397 TCGGCAAGAGAAAGATGGAAT 57.366 42.857 0.00 0.00 0.00 3.01
815 816 3.955471 TCGGCAAGAGAAAGATGGAATT 58.045 40.909 0.00 0.00 0.00 2.17
816 817 3.941483 TCGGCAAGAGAAAGATGGAATTC 59.059 43.478 0.00 0.00 0.00 2.17
817 818 3.065925 CGGCAAGAGAAAGATGGAATTCC 59.934 47.826 18.17 18.17 0.00 3.01
965 966 7.954835 TGAATTTCTCTGACATTCCATGTTTT 58.045 30.769 0.00 0.00 45.03 2.43
1184 1188 2.034687 AGTGGCAGCTGCGGAATT 59.965 55.556 31.19 14.01 43.26 2.17
1186 1190 1.181098 AGTGGCAGCTGCGGAATTTT 61.181 50.000 31.19 10.26 43.26 1.82
1571 1575 5.952347 AAGGACGTAGGGATTTCTATGTT 57.048 39.130 0.00 0.00 38.98 2.71
1572 1576 5.952347 AGGACGTAGGGATTTCTATGTTT 57.048 39.130 0.00 0.00 38.98 2.83
1573 1577 6.309389 AGGACGTAGGGATTTCTATGTTTT 57.691 37.500 0.00 0.00 38.98 2.43
1658 1662 5.996644 TGGTTCGGTATGGAATGAACTTAT 58.003 37.500 4.23 0.00 40.34 1.73
1688 1692 5.705609 TGATCGAGTCGATTCCATGATTA 57.294 39.130 27.65 0.00 47.00 1.75
2034 2038 4.110482 CGTAAGGAGTCCTATTGAAACCG 58.890 47.826 13.43 2.55 31.13 4.44
2140 2144 5.046231 GGGATAAGAGACATAGGGCTAAAGG 60.046 48.000 0.00 0.00 0.00 3.11
2201 2205 7.171508 GCATAATCTCGAATGTTATCAGTTCCA 59.828 37.037 0.00 0.00 0.00 3.53
2205 2209 7.348080 TCTCGAATGTTATCAGTTCCAGTAT 57.652 36.000 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 4.803098 AAAGACCTATATCGGATTCGGG 57.197 45.455 0.00 0.00 36.95 5.14
121 122 9.615295 GTCGAGTATGAAGAAAAGACCTATATC 57.385 37.037 0.00 0.00 0.00 1.63
607 608 4.569180 CAGCGCCCGGGGATTGAT 62.569 66.667 25.28 0.48 0.00 2.57
699 700 5.607592 AGTACTATAGCCTCACTAGTCCTCA 59.392 44.000 0.00 0.00 33.29 3.86
816 817 7.954666 TTGATTTCCTTCCTTATACCAAAGG 57.045 36.000 0.00 0.00 46.35 3.11
817 818 7.968405 CGTTTGATTTCCTTCCTTATACCAAAG 59.032 37.037 0.00 0.00 0.00 2.77
965 966 9.767228 TGAAATATTTTATAGGATCCGTTTCGA 57.233 29.630 5.98 0.00 0.00 3.71
1256 1260 7.309133 CCTGCAGTTATGTTTAACCTTGAATGA 60.309 37.037 13.81 0.00 38.81 2.57
1278 1282 5.705905 ACTTTGTATTTGGTAACTCTCCTGC 59.294 40.000 0.00 0.00 37.61 4.85
1658 1662 5.473504 TGGAATCGACTCGATCATCAGATTA 59.526 40.000 14.25 0.00 46.30 1.75
1688 1692 3.244457 GGGCGCTAGGGTTATGAACTTAT 60.244 47.826 7.64 0.00 0.00 1.73
2201 2205 9.845740 TGCATTGTATTATTTGGTCTACATACT 57.154 29.630 0.00 0.00 0.00 2.12
2205 2209 7.121907 TGCTTGCATTGTATTATTTGGTCTACA 59.878 33.333 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.