Multiple sequence alignment - TraesCS6D01G197100

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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 TraesCS6D01G197100 chr6D 100.000 3333 0 0 573 3905 273924798 273921466 0.000000e+00 6156
1 TraesCS6D01G197100 chr6D 100.000 231 0 0 1 231 273925370 273925140 1.000000e-115 427
2 TraesCS6D01G197100 chr6A 97.901 3335 46 4 573 3905 392196030 392192718 0.000000e+00 5749
3 TraesCS6D01G197100 chr6A 98.701 231 3 0 1 231 392196380 392196150 1.010000e-110 411
4 TraesCS6D01G197100 chr6B 93.460 3318 152 26 573 3866 435834709 435831433 0.000000e+00 4865
5 TraesCS6D01G197100 chr6B 92.704 233 15 1 1 231 435835060 435834828 6.250000e-88 335
6 TraesCS6D01G197100 chr5B 89.873 79 8 0 2001 2079 19791257 19791179 6.900000e-18 102


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 TraesCS6D01G197100 chr6D 273921466 273925370 3904 True 3291.5 6156 100.000 1 3905 2 chr6D.!!$R1 3904
1 TraesCS6D01G197100 chr6A 392192718 392196380 3662 True 3080.0 5749 98.301 1 3905 2 chr6A.!!$R1 3904
2 TraesCS6D01G197100 chr6B 435831433 435835060 3627 True 2600.0 4865 93.082 1 3866 2 chr6B.!!$R1 3865

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
36 37 5.073144 TCCAGGGGTATCAAGATTATTGTCC 59.927 44.000 0.0 0.0 0.0 4.02 F
1577 1584 1.271379 CCTTTGCATGCAGACACACAT 59.729 47.619 21.5 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1335 2.260844 AATGGTGACCTGACACACTG 57.739 50.0 2.11 0.0 41.88 3.66 R
2992 3012 1.286501 ACATTACGCTGCACCATACG 58.713 50.0 0.00 0.0 0.00 3.06 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
36 37 5.073144 TCCAGGGGTATCAAGATTATTGTCC 59.927 44.000 0.00 0.00 0.00 4.02
1577 1584 1.271379 CCTTTGCATGCAGACACACAT 59.729 47.619 21.50 0.00 0.00 3.21
1589 1596 5.468409 TGCAGACACACATTAAAATCGAAGA 59.532 36.000 0.00 0.00 45.75 2.87
1662 1669 6.323203 ACTTCCAGCAATGCATGTTATATC 57.677 37.500 8.35 0.00 0.00 1.63
1791 1810 3.853671 GCATTAAACAATTGGACAGCTCG 59.146 43.478 10.83 0.00 0.00 5.03
1977 1996 6.884295 AGCTCCAGTTTATATGCTTGTAACAA 59.116 34.615 0.00 0.00 0.00 2.83
2210 2229 2.658807 GGTTGTTCCCTTCCTTCTGT 57.341 50.000 0.00 0.00 0.00 3.41
2911 2931 5.358160 AGACGATACATCAGATGACAACTGA 59.642 40.000 17.81 16.70 46.17 3.41
2987 3007 4.335647 CAAGCGCTCCAGGTGGGT 62.336 66.667 12.06 0.00 38.11 4.51
2992 3012 2.985847 GCTCCAGGTGGGTGTTGC 60.986 66.667 0.00 0.00 38.11 4.17
3136 3156 6.560253 TGATGAGGAAAGCTTAAAGTTGAC 57.440 37.500 0.00 0.00 0.00 3.18
3178 3200 9.528018 GAGTAAAGATCTCTCATGTTTCCTAAG 57.472 37.037 0.00 0.00 0.00 2.18
3251 3273 0.746659 AAGGCAGTGCAGTGAAAACC 59.253 50.000 25.76 15.86 0.00 3.27
3333 3357 6.293626 CGACCTCCAATGATTAATCCAATGAC 60.294 42.308 12.90 0.00 0.00 3.06
3362 3386 3.262660 TGCTGATGACCTCACTGAGAATT 59.737 43.478 7.69 0.00 0.00 2.17
3708 3733 5.695851 CCATGACATGGTAAGATAAAGGC 57.304 43.478 24.15 0.00 45.54 4.35
3738 3763 3.452474 TGTTTCCAATTTTCAAGGTGCG 58.548 40.909 0.00 0.00 0.00 5.34
3775 3800 6.405953 GCAGCTTCTCTGTTATACCAGAACTA 60.406 42.308 1.33 0.00 44.66 2.24
3795 3820 0.441533 GCATCACACTTCTCACAGCG 59.558 55.000 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 144 0.719465 GTAAGCATGGTGTTCCGTCG 59.281 55.000 0.00 0.00 36.30 5.12
1247 1250 5.118050 GGTTAAACGTTAAATGCAGAAAGCC 59.882 40.000 0.00 0.00 44.83 4.35
1330 1335 2.260844 AATGGTGACCTGACACACTG 57.739 50.000 2.11 0.00 41.88 3.66
1511 1518 4.034048 AGCGAAAACATGTCGAATACCATC 59.966 41.667 9.39 0.00 41.02 3.51
1517 1524 3.994392 ACACTAGCGAAAACATGTCGAAT 59.006 39.130 9.39 0.35 41.02 3.34
1589 1596 5.535030 TGCGAGTCTAGACCAATGTGTATAT 59.465 40.000 19.38 0.00 0.00 0.86
1662 1669 6.257411 CAGCAAAGTACATGGATCTTCACTAG 59.743 42.308 0.00 0.00 0.00 2.57
1791 1810 8.515414 GCTTGTATAATTTGATGGTTAGGATCC 58.485 37.037 2.48 2.48 0.00 3.36
1977 1996 3.719924 TGGTAAGTTTGTCATCGTTCGT 58.280 40.909 0.00 0.00 0.00 3.85
2134 2153 1.211703 TCACCAACCTGTGTGACATGT 59.788 47.619 0.00 0.00 36.62 3.21
2207 2226 8.789881 TTTAAATCGTGGAAACAAATACACAG 57.210 30.769 0.00 0.00 46.06 3.66
2210 2229 9.751542 AACATTTAAATCGTGGAAACAAATACA 57.248 25.926 0.00 0.00 46.06 2.29
2286 2306 2.029290 ACGAACTAGGTGTGGACATCAC 60.029 50.000 0.00 0.00 46.23 3.06
2573 2593 6.098838 TCAGTGTAGAATCTCAATGGTGCTAT 59.901 38.462 9.12 0.00 31.83 2.97
2790 2810 5.765182 TGAGAAGTCCCTTGAGTTGAAATTC 59.235 40.000 0.00 0.00 34.24 2.17
2911 2931 3.944015 GCAGAGTTGGAATGCAGTTATCT 59.056 43.478 0.00 0.00 39.75 1.98
2987 3007 2.676029 CGCTGCACCATACGCAACA 61.676 57.895 0.00 0.00 39.30 3.33
2992 3012 1.286501 ACATTACGCTGCACCATACG 58.713 50.000 0.00 0.00 0.00 3.06
3136 3156 6.513180 TCTTTACTCTCATTGCCCTAATACG 58.487 40.000 0.00 0.00 0.00 3.06
3178 3200 4.875544 TTGGCGTCAAATCTAATAGTGC 57.124 40.909 0.00 0.00 0.00 4.40
3251 3273 4.077184 TGGCTGCGGGACCTTACG 62.077 66.667 0.00 0.00 0.00 3.18
3280 3302 4.640789 AAAGACTCCTAGCACTATGACG 57.359 45.455 0.00 0.00 0.00 4.35
3333 3357 4.210746 CAGTGAGGTCATCAGCATAAATCG 59.789 45.833 0.00 0.00 39.07 3.34
3362 3386 3.246350 TGGGGAGAGGGTTCTGAATTCTA 60.246 47.826 7.05 0.00 32.53 2.10
3708 3733 6.182039 TGAAAATTGGAAACAGATAGCTCG 57.818 37.500 0.00 0.00 44.54 5.03
3775 3800 1.805869 GCTGTGAGAAGTGTGATGCT 58.194 50.000 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.