Multiple sequence alignment - TraesCS5D01G098600

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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 TraesCS5D01G098600 chr5D 100.000 2435 0 0 1 2435 110330764 110333198 0 4497
1 TraesCS5D01G098600 chr5D 93.724 2438 144 6 1 2435 417561069 417558638 0 3646
2 TraesCS5D01G098600 chr4D 95.365 2438 109 3 1 2435 286382977 286380541 0 3873
3 TraesCS5D01G098600 chr6D 94.584 2437 125 6 1 2435 48390206 48392637 0 3762
4 TraesCS5D01G098600 chr6D 94.108 2444 120 15 4 2435 329718446 329716015 0 3694
5 TraesCS5D01G098600 chr5A 93.730 2440 139 8 1 2435 681179502 681177072 0 3646
6 TraesCS5D01G098600 chr5A 93.689 2440 140 9 1 2435 681108652 681106222 0 3640
7 TraesCS5D01G098600 chr7D 93.440 2439 148 9 1 2435 155166553 155164123 0 3607
8 TraesCS5D01G098600 chr7A 93.404 2441 151 8 1 2435 350165427 350162991 0 3607
9 TraesCS5D01G098600 chr6A 93.246 2443 156 7 1 2435 203811716 203814157 0 3589


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 TraesCS5D01G098600 chr5D 110330764 110333198 2434 False 4497 4497 100.000 1 2435 1 chr5D.!!$F1 2434
1 TraesCS5D01G098600 chr5D 417558638 417561069 2431 True 3646 3646 93.724 1 2435 1 chr5D.!!$R1 2434
2 TraesCS5D01G098600 chr4D 286380541 286382977 2436 True 3873 3873 95.365 1 2435 1 chr4D.!!$R1 2434
3 TraesCS5D01G098600 chr6D 48390206 48392637 2431 False 3762 3762 94.584 1 2435 1 chr6D.!!$F1 2434
4 TraesCS5D01G098600 chr6D 329716015 329718446 2431 True 3694 3694 94.108 4 2435 1 chr6D.!!$R1 2431
5 TraesCS5D01G098600 chr5A 681177072 681179502 2430 True 3646 3646 93.730 1 2435 1 chr5A.!!$R2 2434
6 TraesCS5D01G098600 chr5A 681106222 681108652 2430 True 3640 3640 93.689 1 2435 1 chr5A.!!$R1 2434
7 TraesCS5D01G098600 chr7D 155164123 155166553 2430 True 3607 3607 93.440 1 2435 1 chr7D.!!$R1 2434
8 TraesCS5D01G098600 chr7A 350162991 350165427 2436 True 3607 3607 93.404 1 2435 1 chr7A.!!$R1 2434
9 TraesCS5D01G098600 chr6A 203811716 203814157 2441 False 3589 3589 93.246 1 2435 1 chr6A.!!$F1 2434

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
773 796 1.358725 ATGCGCAACGTGCTAATCGT 61.359 50.0 17.11 0.0 42.25 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 1761 0.601558 TAGCCTGCGTCTCTTTTCGT 59.398 50.0 0.0 0.0 0.0 3.85 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
380 385 2.287547 GCGTTTGATGCCTTCAACTCAA 60.288 45.455 0.00 0.00 43.99 3.02
430 435 2.270205 CTTGCCAGAGCCACGGAT 59.730 61.111 0.00 0.00 38.69 4.18
773 796 1.358725 ATGCGCAACGTGCTAATCGT 61.359 50.000 17.11 0.00 42.25 3.73
1013 1036 1.897423 CAGGTATGCTGACGGGTCA 59.103 57.895 1.05 1.05 38.06 4.02
1073 1096 1.013005 CCAGAGCTCTCACAACTGCG 61.013 60.000 14.96 0.00 0.00 5.18
1290 1313 0.035439 CTAACCACATGGCCGAGGTT 60.035 55.000 20.20 20.20 45.63 3.50
1635 1661 5.484290 ACAGACAAGTACCCAACTAGCTATT 59.516 40.000 0.00 0.00 37.50 1.73
1698 1724 4.174704 AGTTCCGTTAAGGGTTCCTTTT 57.825 40.909 13.68 0.00 41.69 2.27
1715 1741 1.847798 TTTCCTGGGTACGCATGCCT 61.848 55.000 13.58 2.75 0.00 4.75
1735 1761 4.188462 CCTTAATGTGCATGTCCGAACTA 58.812 43.478 0.00 0.00 0.00 2.24
1763 1789 3.060602 GAGACGCAGGCTATAAACATCC 58.939 50.000 0.00 0.00 0.00 3.51
1951 1977 3.007614 ACGTAGGGCATAAACACAAGAGT 59.992 43.478 0.00 0.00 0.00 3.24
2038 2065 5.940192 TGTGGAAGAATAACACATGTGTC 57.060 39.130 30.64 18.29 44.13 3.67
2135 2163 3.123621 GCGTCAAGATTGTGTAGTCAAGG 59.876 47.826 0.00 0.00 0.00 3.61
2140 2168 3.668447 AGATTGTGTAGTCAAGGCACAG 58.332 45.455 0.00 0.00 42.91 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
380 385 1.428219 CACGGATGTACGCGTCTCT 59.572 57.895 18.63 0.00 37.37 3.10
430 435 8.938801 TTACCCGTATATCCTTTACATACTGA 57.061 34.615 0.00 0.00 0.00 3.41
619 626 1.518302 GCCTTCTCGGACTCCTTCC 59.482 63.158 0.00 0.00 41.75 3.46
713 721 4.502777 GGAGTCATCTGCAGCATCTATTGA 60.503 45.833 9.47 0.52 32.20 2.57
1013 1036 1.535202 GGCATCTCCTCCTCGGGAT 60.535 63.158 0.00 0.00 34.56 3.85
1073 1096 2.251642 ACCTGCCGAACTTGTTCGC 61.252 57.895 24.91 20.45 42.62 4.70
1113 1136 1.002624 GGAGACGGATGGCCACAAA 60.003 57.895 8.16 0.00 0.00 2.83
1140 1163 2.631012 CTACAAGCTCCCCCATGCCC 62.631 65.000 0.00 0.00 0.00 5.36
1290 1313 4.590553 TCAGGCCCCACAGGTCCA 62.591 66.667 0.00 0.00 43.64 4.02
1351 1374 2.325583 TGGGAATACTTTGCGGCTAG 57.674 50.000 0.00 1.17 0.00 3.42
1549 1574 4.202493 ACCCCGGTTTTTACATAACTGAGT 60.202 41.667 0.00 0.00 34.50 3.41
1649 1675 6.729100 TCTCCCTGGAAGATGTTTCTTACTAA 59.271 38.462 0.00 0.00 42.50 2.24
1698 1724 0.978667 TAAGGCATGCGTACCCAGGA 60.979 55.000 14.17 0.00 0.00 3.86
1715 1741 3.615056 CGTAGTTCGGACATGCACATTAA 59.385 43.478 0.00 0.00 35.71 1.40
1735 1761 0.601558 TAGCCTGCGTCTCTTTTCGT 59.398 50.000 0.00 0.00 0.00 3.85
1763 1789 9.765795 TTTTATTTATTTTAATACATGCCCCCG 57.234 29.630 0.00 0.00 0.00 5.73
1848 1874 2.651455 CCGGATGTGTACCTCAGACTA 58.349 52.381 0.00 0.00 0.00 2.59
1951 1977 2.115910 CCAAGCTGGGTTGCCTGA 59.884 61.111 0.00 0.00 32.67 3.86
2135 2163 3.288809 CCTCAAAAGGCTAAACTGTGC 57.711 47.619 0.00 0.00 35.37 4.57
2221 2258 2.297698 TGTTCGTCTCCTTACCTCCA 57.702 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.