Multiple sequence alignment - TraesCS4B01G276900

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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 TraesCS4B01G276900 chr4B 100.000 3797 0 0 1 3797 558577472 558581268 0.000000e+00 7012
1 TraesCS4B01G276900 chr4B 83.019 530 78 11 3261 3781 340553986 340553460 1.600000e-128 470
2 TraesCS4B01G276900 chr4D 97.625 3790 72 10 14 3797 446427392 446431169 0.000000e+00 6484
3 TraesCS4B01G276900 chr4D 89.544 373 28 6 3433 3797 85665190 85665559 2.670000e-126 462
4 TraesCS4B01G276900 chr4D 84.109 258 25 9 3060 3312 85600593 85600839 6.340000e-58 235
5 TraesCS4B01G276900 chr4D 86.029 136 18 1 3313 3448 85627507 85627641 1.100000e-30 145
6 TraesCS4B01G276900 chr4A 95.327 3809 137 16 1 3788 21066313 21062525 0.000000e+00 6010
7 TraesCS4B01G276900 chr4A 91.982 1322 80 12 1 1307 21074702 21073392 0.000000e+00 1831
8 TraesCS4B01G276900 chr4A 98.701 77 1 0 1294 1370 21069349 21069273 1.840000e-28 137


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 TraesCS4B01G276900 chr4B 558577472 558581268 3796 False 7012.0 7012 100.000 1 3797 1 chr4B.!!$F1 3796
1 TraesCS4B01G276900 chr4B 340553460 340553986 526 True 470.0 470 83.019 3261 3781 1 chr4B.!!$R1 520
2 TraesCS4B01G276900 chr4D 446427392 446431169 3777 False 6484.0 6484 97.625 14 3797 1 chr4D.!!$F4 3783
3 TraesCS4B01G276900 chr4A 21062525 21069349 6824 True 3073.5 6010 97.014 1 3788 2 chr4A.!!$R2 3787
4 TraesCS4B01G276900 chr4A 21073392 21074702 1310 True 1831.0 1831 91.982 1 1307 1 chr4A.!!$R1 1306

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
318 3356 1.599542 GCACCTTACTGATCGGCATTC 59.400 52.381 0.0 0.0 0.0 2.67 F
1269 4322 1.843851 TCTGGTGAACTTGTCCTTGGT 59.156 47.619 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 5114 0.892814 GGCTCAATCCAGGGCTATGC 60.893 60.000 0.0 0.0 0.0 3.14 R
2841 5895 1.816835 TCTACCACTGCTACCTGTTCG 59.183 52.381 0.0 0.0 0.0 3.95 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
243 3281 4.020218 CCCACTGATCTCCACAGTTTCTAA 60.020 45.833 0.00 0.00 44.69 2.10
318 3356 1.599542 GCACCTTACTGATCGGCATTC 59.400 52.381 0.00 0.00 0.00 2.67
324 3362 4.692625 CCTTACTGATCGGCATTCCTATTG 59.307 45.833 0.00 0.00 0.00 1.90
325 3363 5.511373 CCTTACTGATCGGCATTCCTATTGA 60.511 44.000 0.00 0.00 0.00 2.57
328 3366 6.114187 ACTGATCGGCATTCCTATTGATAA 57.886 37.500 0.00 0.00 0.00 1.75
787 3837 2.949142 TCGCTTTTACATCGTAGCACA 58.051 42.857 0.00 0.00 33.29 4.57
837 3887 3.277142 TGCATCAGATGTGCATCTCTT 57.723 42.857 12.18 0.56 46.76 2.85
891 3943 2.136229 GGGATTACCGGCGTAGGGT 61.136 63.158 6.01 0.00 41.62 4.34
943 3996 9.744468 TCTTGTTTTGCTTTCTCCTTTTTATAC 57.256 29.630 0.00 0.00 0.00 1.47
1269 4322 1.843851 TCTGGTGAACTTGTCCTTGGT 59.156 47.619 0.00 0.00 0.00 3.67
1416 4469 2.890371 GCATTTGCTGGGGCTGAG 59.110 61.111 0.00 0.00 39.59 3.35
1485 4538 8.212259 AGTTATTCTTCCTAGCATCCATGTAT 57.788 34.615 0.00 0.00 0.00 2.29
1635 4688 4.884164 GCAGCAGGATTTAGGACTATTGTT 59.116 41.667 0.00 0.00 0.00 2.83
1815 4868 3.006430 CACCCGGTTTGGCTAAGATTTTT 59.994 43.478 0.00 0.00 35.87 1.94
2238 5291 1.812571 GAAAATGGCAGTGTCGATGGT 59.187 47.619 0.00 0.00 0.00 3.55
2622 5675 3.383505 TGTCACCTATGGACAACTATCCG 59.616 47.826 0.00 0.00 41.96 4.18
2841 5895 3.426292 GGGCAGATCGTTTTTCTAGTTGC 60.426 47.826 0.00 0.00 0.00 4.17
3347 6403 0.035317 TCATGTCGCTTGCCTTGTCT 59.965 50.000 0.00 0.00 0.00 3.41
3406 6464 4.338682 CCGAGGCTTCAGTAACACTACTAT 59.661 45.833 0.00 0.00 36.14 2.12
3744 6808 3.510459 TCTCATTCTTCAGGACTGGTGA 58.490 45.455 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
250 3288 1.153168 GTGTGCCGGGTATGCATCT 60.153 57.895 0.19 0.00 41.46 2.90
252 3290 2.124320 GGTGTGCCGGGTATGCAT 60.124 61.111 2.18 3.79 41.46 3.96
264 3302 3.056962 CGGATCTAGATCTGGATGGTGTG 60.057 52.174 27.62 7.14 39.85 3.82
328 3366 9.150348 GGTTGCTGCATATTTTATTACTTTGTT 57.850 29.630 1.84 0.00 0.00 2.83
362 3400 6.313658 TCTGAATGTTTGGTATCAGAACATCG 59.686 38.462 13.42 8.18 43.79 3.84
787 3837 5.104402 TGGTCAGATTGTGTGGTGATATCAT 60.104 40.000 9.02 0.00 0.00 2.45
837 3887 1.677633 TCATCGTGACTGGGAGCGA 60.678 57.895 0.00 0.00 37.76 4.93
874 3924 1.068585 CACCCTACGCCGGTAATCC 59.931 63.158 1.90 0.00 30.42 3.01
943 3996 3.500982 CCACATGAACAAAATAGCCACG 58.499 45.455 0.00 0.00 0.00 4.94
1269 4322 1.002624 GCAAGATCCGTCACCCCAA 60.003 57.895 0.00 0.00 0.00 4.12
1416 4469 1.619827 CTGAGAGCATCATCCTCCTCC 59.380 57.143 0.00 0.00 37.28 4.30
1485 4538 3.724508 ACATGACGTGGAAATGCAAAA 57.275 38.095 0.00 0.00 0.00 2.44
1635 4688 2.040278 ACCAGCTTCAAATGGCAGTAGA 59.960 45.455 0.00 0.00 40.45 2.59
1815 4868 3.624777 GCTCAGATTCAAATCCTTCCCA 58.375 45.455 0.00 0.00 36.04 4.37
2061 5114 0.892814 GGCTCAATCCAGGGCTATGC 60.893 60.000 0.00 0.00 0.00 3.14
2238 5291 1.953686 GCCACTTGCTCCTTACACAAA 59.046 47.619 0.00 0.00 36.87 2.83
2622 5675 9.638239 TCAAAAGCTTGGAACACATTATTTATC 57.362 29.630 0.00 0.00 39.29 1.75
2841 5895 1.816835 TCTACCACTGCTACCTGTTCG 59.183 52.381 0.00 0.00 0.00 3.95
3535 6595 1.401552 CAACCACTCACCAATATGGCG 59.598 52.381 0.00 0.00 42.67 5.69
3553 6613 8.477984 GCATTTATTGCCTTTTGTCTTATCAA 57.522 30.769 0.00 0.00 46.15 2.57


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

AutoCloner maintained by Alex Coulton.