Multiple sequence alignment - TraesCS7B01G396400

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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 TraesCS7B01G396400 chr7B 100.000 2177 0 0 1 2177 663101670 663103846 0.000000e+00 4021
1 TraesCS7B01G396400 chr7B 98.771 1953 10 2 1 1939 662724159 662722207 0.000000e+00 3461
2 TraesCS7B01G396400 chr6D 98.859 2191 11 2 1 2177 389254924 389252734 0.000000e+00 3895
3 TraesCS7B01G396400 chr6D 98.744 2070 12 2 1 2056 389250129 389248060 0.000000e+00 3666
4 TraesCS7B01G396400 chr3A 98.768 2191 12 3 1 2177 66007377 66009566 0.000000e+00 3882
5 TraesCS7B01G396400 chr5D 98.722 2191 13 3 1 2177 503238781 503236592 0.000000e+00 3877
6 TraesCS7B01G396400 chr5D 98.676 2191 11 4 1 2177 503243027 503240841 0.000000e+00 3869
7 TraesCS7B01G396400 chr5D 98.462 1951 13 3 1 1937 503229000 503227053 0.000000e+00 3421
8 TraesCS7B01G396400 chr5D 97.484 795 7 1 1396 2177 503227069 503226275 0.000000e+00 1345
9 TraesCS7B01G396400 chr5D 97.358 795 8 1 1396 2177 503269475 503270269 0.000000e+00 1339
10 TraesCS7B01G396400 chrUn 98.403 2192 17 4 1 2177 216508363 216510551 0.000000e+00 3838
11 TraesCS7B01G396400 chrUn 98.258 1435 12 1 756 2177 397077306 397078740 0.000000e+00 2499
12 TraesCS7B01G396400 chr3D 98.602 2075 14 3 1 2061 589265768 589267841 0.000000e+00 3657
13 TraesCS7B01G396400 chr4A 95.181 2179 70 8 1 2177 310786276 310788421 0.000000e+00 3410
14 TraesCS7B01G396400 chr6A 97.961 981 6 2 1210 2177 608869208 608870187 0.000000e+00 1688
15 TraesCS7B01G396400 chr7D 92.179 358 20 4 1591 1948 202053379 202053030 1.160000e-137 499


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 TraesCS7B01G396400 chr7B 663101670 663103846 2176 False 4021.0 4021 100.0000 1 2177 1 chr7B.!!$F1 2176
1 TraesCS7B01G396400 chr7B 662722207 662724159 1952 True 3461.0 3461 98.7710 1 1939 1 chr7B.!!$R1 1938
2 TraesCS7B01G396400 chr6D 389248060 389254924 6864 True 3780.5 3895 98.8015 1 2177 2 chr6D.!!$R1 2176
3 TraesCS7B01G396400 chr3A 66007377 66009566 2189 False 3882.0 3882 98.7680 1 2177 1 chr3A.!!$F1 2176
4 TraesCS7B01G396400 chr5D 503236592 503243027 6435 True 3873.0 3877 98.6990 1 2177 2 chr5D.!!$R2 2176
5 TraesCS7B01G396400 chr5D 503226275 503229000 2725 True 2383.0 3421 97.9730 1 2177 2 chr5D.!!$R1 2176
6 TraesCS7B01G396400 chr5D 503269475 503270269 794 False 1339.0 1339 97.3580 1396 2177 1 chr5D.!!$F1 781
7 TraesCS7B01G396400 chrUn 216508363 216510551 2188 False 3838.0 3838 98.4030 1 2177 1 chrUn.!!$F1 2176
8 TraesCS7B01G396400 chrUn 397077306 397078740 1434 False 2499.0 2499 98.2580 756 2177 1 chrUn.!!$F2 1421
9 TraesCS7B01G396400 chr3D 589265768 589267841 2073 False 3657.0 3657 98.6020 1 2061 1 chr3D.!!$F1 2060
10 TraesCS7B01G396400 chr4A 310786276 310788421 2145 False 3410.0 3410 95.1810 1 2177 1 chr4A.!!$F1 2176
11 TraesCS7B01G396400 chr6A 608869208 608870187 979 False 1688.0 1688 97.9610 1210 2177 1 chr6A.!!$F1 967


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
934 5186 8.25175 CTCGAAACATGAGGACAAATTACTTA 57.748 34.615 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 6824 1.229209 TCCGCCCTTCTTCCACTCT 60.229 57.895 0.0 0.0 0.0 3.24 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
934 5186 8.251750 CTCGAAACATGAGGACAAATTACTTA 57.748 34.615 0.00 0.0 0.00 2.24
1439 5694 3.262405 ACTTTCCCCGTTCTATTGCTACA 59.738 43.478 0.00 0.0 0.00 2.74
2017 6824 3.760684 GGTCTTAGTTAGTCTTCGGGACA 59.239 47.826 10.91 0.0 46.72 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
934 5186 9.014297 CCTTTTTCTTGTATGTGTTCCTAAGAT 57.986 33.333 0.0 0.0 0.0 2.40
1439 5694 0.464036 TCGATTGCATAAGACCCGCT 59.536 50.000 0.0 0.0 0.0 5.52
2017 6824 1.229209 TCCGCCCTTCTTCCACTCT 60.229 57.895 0.0 0.0 0.0 3.24



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

AutoCloner maintained by Alex Coulton.