Multiple sequence alignment - TraesCS3B01G329500

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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 TraesCS3B01G329500 chr3B 100.000 2276 0 0 1 2276 532591013 532588738 0 4204
1 TraesCS3B01G329500 chr3B 94.262 2283 121 8 1 2276 441031158 441028879 0 3482
2 TraesCS3B01G329500 chr7B 95.092 2282 103 8 2 2276 35584175 35581896 0 3585
3 TraesCS3B01G329500 chr7B 94.748 2285 106 9 1 2276 115033330 115031051 0 3542
4 TraesCS3B01G329500 chr5B 95.004 2282 104 9 1 2276 122800521 122802798 0 3574
5 TraesCS3B01G329500 chr1B 94.956 2280 108 7 1 2276 518058719 518056443 0 3567
6 TraesCS3B01G329500 chr6B 94.479 2282 118 7 1 2276 568678613 568676334 0 3509
7 TraesCS3B01G329500 chr6B 94.316 2287 115 12 1 2276 593121552 593123834 0 3489
8 TraesCS3B01G329500 chr2B 94.218 2283 123 6 1 2276 747922158 747919878 0 3476
9 TraesCS3B01G329500 chr2B 94.182 1461 81 4 1 1458 752245794 752244335 0 2224
10 TraesCS3B01G329500 chr2B 95.292 977 45 1 1300 2276 43034788 43035763 0 1548


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 TraesCS3B01G329500 chr3B 532588738 532591013 2275 True 4204 4204 100.000 1 2276 1 chr3B.!!$R2 2275
1 TraesCS3B01G329500 chr3B 441028879 441031158 2279 True 3482 3482 94.262 1 2276 1 chr3B.!!$R1 2275
2 TraesCS3B01G329500 chr7B 35581896 35584175 2279 True 3585 3585 95.092 2 2276 1 chr7B.!!$R1 2274
3 TraesCS3B01G329500 chr7B 115031051 115033330 2279 True 3542 3542 94.748 1 2276 1 chr7B.!!$R2 2275
4 TraesCS3B01G329500 chr5B 122800521 122802798 2277 False 3574 3574 95.004 1 2276 1 chr5B.!!$F1 2275
5 TraesCS3B01G329500 chr1B 518056443 518058719 2276 True 3567 3567 94.956 1 2276 1 chr1B.!!$R1 2275
6 TraesCS3B01G329500 chr6B 568676334 568678613 2279 True 3509 3509 94.479 1 2276 1 chr6B.!!$R1 2275
7 TraesCS3B01G329500 chr6B 593121552 593123834 2282 False 3489 3489 94.316 1 2276 1 chr6B.!!$F1 2275
8 TraesCS3B01G329500 chr2B 747919878 747922158 2280 True 3476 3476 94.218 1 2276 1 chr2B.!!$R1 2275
9 TraesCS3B01G329500 chr2B 752244335 752245794 1459 True 2224 2224 94.182 1 1458 1 chr2B.!!$R2 1457
10 TraesCS3B01G329500 chr2B 43034788 43035763 975 False 1548 1548 95.292 1300 2276 1 chr2B.!!$F1 976

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
757 759 0.887387 GCTACCCCACAACGAAGCAA 60.887 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1785 0.192566 ATGGGAATAGTAGGGGGCGA 59.807 55.0 0.0 0.0 0.0 5.54 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
88 89 1.511768 GACTGTACGTGGAGAGCCC 59.488 63.158 0.00 0.00 0.00 5.19
122 123 2.662596 GAGGTCCATGGTCGCACA 59.337 61.111 12.58 0.00 0.00 4.57
202 203 2.104331 ACCGGCTGTATCTTCGCG 59.896 61.111 0.00 0.00 0.00 5.87
263 265 2.743718 CGTTGACAGCTGGGACCT 59.256 61.111 19.93 0.00 0.00 3.85
443 445 2.184322 CACCGCGGATGTGCTACT 59.816 61.111 35.90 1.64 0.00 2.57
484 486 3.012959 AGTTTCCCACTCCTCTCCATCTA 59.987 47.826 0.00 0.00 0.00 1.98
656 658 3.050166 GCATGCAATGGAACGCGGA 62.050 57.895 14.21 0.00 46.86 5.54
678 680 1.420138 AGGTCAACGTGGTCAAGGAAT 59.580 47.619 0.00 0.00 0.00 3.01
757 759 0.887387 GCTACCCCACAACGAAGCAA 60.887 55.000 0.00 0.00 0.00 3.91
900 903 1.529244 GCTCTTGGGTGCTTGGTGT 60.529 57.895 0.00 0.00 0.00 4.16
956 959 1.202698 GGAAGCCCTATCAATGCGAGT 60.203 52.381 0.00 0.00 0.00 4.18
1071 1075 3.047877 CGTTCGGTTGTGGCTCCC 61.048 66.667 0.00 0.00 0.00 4.30
1235 1240 5.075344 AGACCCCTAGATTTTTGGTAACCAA 59.925 40.000 0.00 0.00 42.29 3.67
1408 1419 2.672996 CGTTTGCCCCCTGACTGG 60.673 66.667 0.00 0.00 0.00 4.00
1675 1695 3.555168 CCGTAGTGCTTCTTCAACCTCTT 60.555 47.826 0.00 0.00 0.00 2.85
1764 1785 3.842923 CTGCCGCGGAGGACTCAT 61.843 66.667 33.48 0.00 45.00 2.90
1783 1804 0.192566 TCGCCCCCTACTATTCCCAT 59.807 55.000 0.00 0.00 0.00 4.00
1858 1880 1.814586 CTCGTACTCCTCTCCGCGT 60.815 63.158 4.92 0.00 0.00 6.01
2072 2098 1.344763 AGTAAGTCGCTTTGTCAGGCT 59.655 47.619 0.00 0.00 0.00 4.58
2133 2159 1.678970 GGCTGGCCGAGAAAATGGT 60.679 57.895 0.00 0.00 0.00 3.55
2183 2209 9.021863 GTACATTTTTAAAACACATCAAACCGA 57.978 29.630 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 236 3.496130 CAGCTGTCAACGGGATGAATATC 59.504 47.826 5.25 0.00 0.00 1.63
347 349 0.981183 AACATCCAACGGTCCAGCTA 59.019 50.000 0.00 0.00 0.00 3.32
441 443 4.988598 CTGGTTCGGGTGCGCAGT 62.989 66.667 12.22 0.00 0.00 4.40
484 486 2.524394 ACAGGGCAGTGGAGTCGT 60.524 61.111 0.00 0.00 0.00 4.34
595 597 1.221523 TCCCCACTATCAGCCTCTCAT 59.778 52.381 0.00 0.00 0.00 2.90
634 636 0.458889 GCGTTCCATTGCATGCATGT 60.459 50.000 26.79 10.91 0.00 3.21
656 658 0.393077 CCTTGACCACGTTGACCTCT 59.607 55.000 0.00 0.00 0.00 3.69
757 759 0.615331 CCATGACCTGGTAGCACAGT 59.385 55.000 0.00 0.00 40.49 3.55
1319 1327 4.792068 TGGAGGAATCATTATTTTCCGCT 58.208 39.130 5.61 0.00 44.99 5.52
1675 1695 1.004560 CGGCTGGAGCAAGAAGACA 60.005 57.895 0.20 0.00 44.36 3.41
1764 1785 0.192566 ATGGGAATAGTAGGGGGCGA 59.807 55.000 0.00 0.00 0.00 5.54
1808 1830 4.996434 GCTGCGGTGTGAGGCTGT 62.996 66.667 0.00 0.00 0.00 4.40
2072 2098 2.433604 TGAAAGATTTGCAGCCCAACAA 59.566 40.909 0.00 0.00 31.97 2.83
2133 2159 5.715439 ACCCATTTCTCATTACTGATGGA 57.285 39.130 2.80 0.00 31.95 3.41
2241 2270 2.270352 TCCAACAAATTCTCCACGCT 57.730 45.000 0.00 0.00 0.00 5.07


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

AutoCloner maintained by Alex Coulton.