Multiple sequence alignment - TraesCS2B01G146600

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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 TraesCS2B01G146600 chr2B 100.000 2439 0 0 1 2439 112842637 112840199 0 4505
1 TraesCS2B01G146600 chr5A 98.569 2446 25 7 1 2439 19247241 19249683 0 4314
2 TraesCS2B01G146600 chr7D 98.525 2441 31 4 1 2439 381925603 381923166 0 4303
3 TraesCS2B01G146600 chr7D 98.322 2443 30 7 1 2439 382051681 382049246 0 4274
4 TraesCS2B01G146600 chr7D 98.240 2443 33 8 1 2439 203501601 203499165 0 4265
5 TraesCS2B01G146600 chr7B 98.362 2442 32 5 1 2439 716877179 716879615 0 4281


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 TraesCS2B01G146600 chr2B 112840199 112842637 2438 True 4505 4505 100.000 1 2439 1 chr2B.!!$R1 2438
1 TraesCS2B01G146600 chr5A 19247241 19249683 2442 False 4314 4314 98.569 1 2439 1 chr5A.!!$F1 2438
2 TraesCS2B01G146600 chr7D 381923166 381925603 2437 True 4303 4303 98.525 1 2439 1 chr7D.!!$R2 2438
3 TraesCS2B01G146600 chr7D 382049246 382051681 2435 True 4274 4274 98.322 1 2439 1 chr7D.!!$R3 2438
4 TraesCS2B01G146600 chr7D 203499165 203501601 2436 True 4265 4265 98.240 1 2439 1 chr7D.!!$R1 2438
5 TraesCS2B01G146600 chr7B 716877179 716879615 2436 False 4281 4281 98.362 1 2439 1 chr7B.!!$F1 2438

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
26 27 0.749818 TGCACGGAAAACTGCCTTCA 60.75 50.0 0.0 0.0 31.97 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1801 0.550914 AGGATCCGTCTGCTCTCTCT 59.449 55.0 5.98 0.0 0.0 3.1 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
26 27 0.749818 TGCACGGAAAACTGCCTTCA 60.750 50.000 0.00 0.00 31.97 3.02
43 44 3.328050 CCTTCAGTCTCCCAACCTTACTT 59.672 47.826 0.00 0.00 0.00 2.24
654 655 8.317679 GCCCACATATATAGAGTCAAAAGAGAT 58.682 37.037 0.00 0.00 0.00 2.75
735 736 2.031508 CCACAAGTTGTTAATTCGCCGT 60.032 45.455 5.57 0.00 0.00 5.68
846 847 2.953648 TGTTCACGTAACTCCACTCTCA 59.046 45.455 0.00 0.00 38.99 3.27
916 917 2.621998 GCCTAGCAGAGACGTGGTTATA 59.378 50.000 0.00 0.00 0.00 0.98
1089 1090 1.056700 GGAAGGCTGCTATCCCCTCA 61.057 60.000 11.57 0.00 0.00 3.86
1187 1189 1.351153 CTTCGTCGAGCCTTTCCTTC 58.649 55.000 0.00 0.00 0.00 3.46
1272 1274 0.179073 CCGGGTGAACATAGGCTCAG 60.179 60.000 0.00 0.00 0.00 3.35
1377 1381 2.879372 TGCTTTCCTGTGTTGCACA 58.121 47.368 1.88 1.88 42.45 4.57
1592 1596 2.012673 GCAGAAGCAGAAACGATCCAT 58.987 47.619 0.00 0.00 41.58 3.41
1640 1644 7.329962 CCCAAAAACGAACTCTGTTTACTTTTT 59.670 33.333 0.00 0.00 38.52 1.94
1724 1728 8.783833 ATGTATCTATTTTGGAATCATCTCCG 57.216 34.615 0.00 0.00 38.44 4.63
1792 1800 8.489990 TTGCATCAAAGAAAATAGAGAGAGAG 57.510 34.615 0.00 0.00 0.00 3.20
1793 1801 7.845037 TGCATCAAAGAAAATAGAGAGAGAGA 58.155 34.615 0.00 0.00 0.00 3.10
1805 1813 3.133721 AGAGAGAGAGAGAGAGAGCAGAC 59.866 52.174 0.00 0.00 0.00 3.51
1815 1823 3.585289 AGAGAGAGCAGACGGATCCTATA 59.415 47.826 10.75 0.00 30.22 1.31
1842 1850 7.255836 CCCTATAACGAACACTCATTCCTATCA 60.256 40.741 0.00 0.00 0.00 2.15
1871 1879 8.088365 TGATAGAAAAGAAAGATCTTCGTCACA 58.912 33.333 8.78 2.66 45.19 3.58
2108 2121 1.831736 GTACTTCTGGAGGGCAAGCTA 59.168 52.381 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.200165 GCCATAAGTAAGGTTGGGAGACT 59.800 47.826 0.00 0.00 0.00 3.24
77 78 2.447443 CAGTGGGAGTAGTGACTAGCA 58.553 52.381 0.00 0.00 35.45 3.49
654 655 1.133450 CCCTCTCCCTCGGACTCAATA 60.133 57.143 0.00 0.00 0.00 1.90
735 736 2.703007 CCCTTTTGTGTGAATTCCCCAA 59.297 45.455 2.27 0.45 0.00 4.12
916 917 7.684529 ACTACAAAAGAGAGAATCCACTTCAT 58.315 34.615 0.00 0.00 36.24 2.57
1027 1028 5.878669 ACGTTCTAATAAAGAATTCCGGCTT 59.121 36.000 0.65 0.00 45.84 4.35
1089 1090 3.703001 TCATCGAAAAGGAAGAAGGCT 57.297 42.857 0.00 0.00 0.00 4.58
1187 1189 2.439507 AGGTGCATATCCCTTACCACTG 59.560 50.000 0.00 0.00 33.88 3.66
1272 1274 1.216990 AGGACCCCTCCAATCATGTC 58.783 55.000 0.00 0.00 39.39 3.06
1592 1596 2.270850 CCGAAGCCCCGAATGGAA 59.729 61.111 0.00 0.00 37.49 3.53
1792 1800 0.951558 GGATCCGTCTGCTCTCTCTC 59.048 60.000 0.00 0.00 0.00 3.20
1793 1801 0.550914 AGGATCCGTCTGCTCTCTCT 59.449 55.000 5.98 0.00 0.00 3.10
1805 1813 5.649395 TGTTCGTTATAGGGTATAGGATCCG 59.351 44.000 5.98 0.00 0.00 4.18
1815 1823 4.715297 AGGAATGAGTGTTCGTTATAGGGT 59.285 41.667 0.00 0.00 32.73 4.34
2016 2029 7.521669 AGAAGCCTGCCTATTGACTAATATTT 58.478 34.615 0.00 0.00 0.00 1.40
2235 2248 2.173356 GGGTTAGGGTATAGGCCGTTTT 59.827 50.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.