Multiple sequence alignment - TraesCS7D01G238700

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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 TraesCS7D01G238700 chr7D 100.000 2483 0 0 1 2483 203515035 203512553 0 4586
1 TraesCS7D01G238700 chr7D 99.034 2485 21 2 1 2483 381958719 381961202 0 4453
2 TraesCS7D01G238700 chr7D 98.954 2485 23 2 1 2483 382065120 382062637 0 4442
3 TraesCS7D01G238700 chr7D 98.833 2486 24 4 1 2483 626682793 626685276 0 4425
4 TraesCS7D01G238700 chr6D 99.034 2485 21 2 1 2483 124532564 124530081 0 4453
5 TraesCS7D01G238700 chr1D 98.954 2485 22 3 1 2483 141316693 141319175 0 4442
6 TraesCS7D01G238700 chrUn 98.834 2488 23 5 1 2483 189407526 189405040 0 4429
7 TraesCS7D01G238700 chr7B 98.833 2486 25 3 1 2483 644463886 644461402 0 4427
8 TraesCS7D01G238700 chr3A 98.551 2485 33 2 1 2483 633107698 633105215 0 4386
9 TraesCS7D01G238700 chr1B 98.513 2489 30 4 1 2483 668808717 668811204 0 4385


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 TraesCS7D01G238700 chr7D 203512553 203515035 2482 True 4586 4586 100.000 1 2483 1 chr7D.!!$R1 2482
1 TraesCS7D01G238700 chr7D 381958719 381961202 2483 False 4453 4453 99.034 1 2483 1 chr7D.!!$F1 2482
2 TraesCS7D01G238700 chr7D 382062637 382065120 2483 True 4442 4442 98.954 1 2483 1 chr7D.!!$R2 2482
3 TraesCS7D01G238700 chr7D 626682793 626685276 2483 False 4425 4425 98.833 1 2483 1 chr7D.!!$F2 2482
4 TraesCS7D01G238700 chr6D 124530081 124532564 2483 True 4453 4453 99.034 1 2483 1 chr6D.!!$R1 2482
5 TraesCS7D01G238700 chr1D 141316693 141319175 2482 False 4442 4442 98.954 1 2483 1 chr1D.!!$F1 2482
6 TraesCS7D01G238700 chrUn 189405040 189407526 2486 True 4429 4429 98.834 1 2483 1 chrUn.!!$R1 2482
7 TraesCS7D01G238700 chr7B 644461402 644463886 2484 True 4427 4427 98.833 1 2483 1 chr7B.!!$R1 2482
8 TraesCS7D01G238700 chr3A 633105215 633107698 2483 True 4386 4386 98.551 1 2483 1 chr3A.!!$R1 2482
9 TraesCS7D01G238700 chr1B 668808717 668811204 2487 False 4385 4385 98.513 1 2483 1 chr1B.!!$F1 2482


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
326 327 1.195115 TGAACGGGAGCTAGCAATCT 58.805 50.000 18.83 0.0 0.0 2.40 F
895 896 1.196808 GCAGCGTTCCATTCTTTTCGA 59.803 47.619 0.00 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1148 1149 3.317603 TCGATGAACAGCAGATTGACA 57.682 42.857 0.0 0.0 0.0 3.58 R
2376 2385 5.899547 TCCTTCATCTTCTTATGAGTAGCCA 59.100 40.000 0.0 0.0 37.2 4.75 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
326 327 1.195115 TGAACGGGAGCTAGCAATCT 58.805 50.000 18.83 0.00 0.00 2.40
464 465 1.261619 CCGAGGCATAAAAGACGCATC 59.738 52.381 0.00 0.00 33.34 3.91
834 835 5.556915 TGTTTGAATGATCGGGTAAAGAGT 58.443 37.500 0.00 0.00 0.00 3.24
895 896 1.196808 GCAGCGTTCCATTCTTTTCGA 59.803 47.619 0.00 0.00 0.00 3.71
1105 1106 3.064207 CGAACAAAAGGATCGGAACTCA 58.936 45.455 0.00 0.00 38.05 3.41
1148 1149 1.544691 CAAAGCAATGCCAAGAGCTCT 59.455 47.619 11.45 11.45 44.23 4.09
1373 1374 3.394274 TCAGAATCAACAAGGGTTCTCCA 59.606 43.478 0.00 0.00 38.24 3.86
1605 1610 3.963374 TGATTAGACCATGTCCCTGAGAG 59.037 47.826 0.00 0.00 32.18 3.20
1721 1728 2.512485 CACCAAAATGCAAGTGCTGA 57.488 45.000 4.69 0.00 42.66 4.26
2106 2114 3.330701 ACTCTTTCCTATCCACTTTGCCA 59.669 43.478 0.00 0.00 0.00 4.92
2183 2191 7.386851 CACAGTTTCTTAAGGATCCTGTAAGA 58.613 38.462 26.23 26.23 35.16 2.10
2376 2385 2.203998 CTGAGGACCCCCTGTGGT 60.204 66.667 0.00 0.00 44.53 4.16
2436 2445 4.721274 TGATCACCCCTCTGATTTGTGATA 59.279 41.667 12.91 4.00 44.33 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
254 255 5.480422 AGATTTTTATGGCGGTTCTTCCTTT 59.520 36.000 0.00 0.0 0.00 3.11
326 327 3.073356 AGGAACCTTTTCAATACGGTCCA 59.927 43.478 0.00 0.0 32.80 4.02
834 835 4.220821 GTCGGATCCCATATAAGAAGCTCA 59.779 45.833 6.06 0.0 0.00 4.26
1105 1106 7.079451 TGTTTTTCTCTCCTTTCCTATCAGT 57.921 36.000 0.00 0.0 0.00 3.41
1148 1149 3.317603 TCGATGAACAGCAGATTGACA 57.682 42.857 0.00 0.0 0.00 3.58
1373 1374 3.463944 CAGTTGTACACTCCCTTCGTTT 58.536 45.455 0.00 0.0 30.92 3.60
2106 2114 7.458170 TGAGTTATCTTTTAGTTCTCTCCCCTT 59.542 37.037 0.00 0.0 0.00 3.95
2183 2191 9.740710 AGCTAAATGACAATCTTAACCTACTTT 57.259 29.630 0.00 0.0 0.00 2.66
2376 2385 5.899547 TCCTTCATCTTCTTATGAGTAGCCA 59.100 40.000 0.00 0.0 37.20 4.75
2446 2455 6.125719 AGTCTGAGAGAAGGCTTTTTCTTTT 58.874 36.000 14.05 0.0 37.53 2.27



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

AutoCloner maintained by Alex Coulton.