Multiple sequence alignment - TraesCS4B01G145900

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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 TraesCS4B01G145900 chr4B 100.000 2636 0 0 1 2636 209082023 209079388 0 4868
1 TraesCS4B01G145900 chr7B 98.371 2639 40 3 1 2636 644462934 644465572 0 4632
2 TraesCS4B01G145900 chrUn 98.333 2639 41 3 1 2636 189406574 189409212 0 4626
3 TraesCS4B01G145900 chrUn 98.067 2638 49 2 1 2636 251410021 251407384 0 4588
4 TraesCS4B01G145900 chr1B 98.256 2638 44 2 1 2636 668809669 668807032 0 4615
5 TraesCS4B01G145900 chr1B 98.067 2639 47 4 1 2636 638705174 638702537 0 4588
6 TraesCS4B01G145900 chr1B 97.878 2639 53 3 1 2636 672474652 672477290 0 4560
7 TraesCS4B01G145900 chr3A 97.954 2639 50 4 1 2636 633106746 633109383 0 4571
8 TraesCS4B01G145900 chr7D 97.953 2638 50 4 1 2636 626683745 626681110 0 4569
9 TraesCS4B01G145900 chr6D 97.955 2640 47 5 1 2636 124531612 124534248 0 4569


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 TraesCS4B01G145900 chr4B 209079388 209082023 2635 True 4868 4868 100.000 1 2636 1 chr4B.!!$R1 2635
1 TraesCS4B01G145900 chr7B 644462934 644465572 2638 False 4632 4632 98.371 1 2636 1 chr7B.!!$F1 2635
2 TraesCS4B01G145900 chrUn 189406574 189409212 2638 False 4626 4626 98.333 1 2636 1 chrUn.!!$F1 2635
3 TraesCS4B01G145900 chrUn 251407384 251410021 2637 True 4588 4588 98.067 1 2636 1 chrUn.!!$R1 2635
4 TraesCS4B01G145900 chr1B 668807032 668809669 2637 True 4615 4615 98.256 1 2636 1 chr1B.!!$R2 2635
5 TraesCS4B01G145900 chr1B 638702537 638705174 2637 True 4588 4588 98.067 1 2636 1 chr1B.!!$R1 2635
6 TraesCS4B01G145900 chr1B 672474652 672477290 2638 False 4560 4560 97.878 1 2636 1 chr1B.!!$F1 2635
7 TraesCS4B01G145900 chr3A 633106746 633109383 2637 False 4571 4571 97.954 1 2636 1 chr3A.!!$F1 2635
8 TraesCS4B01G145900 chr7D 626681110 626683745 2635 True 4569 4569 97.953 1 2636 1 chr7D.!!$R1 2635
9 TraesCS4B01G145900 chr6D 124531612 124534248 2636 False 4569 4569 97.955 1 2636 1 chr6D.!!$F1 2635

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
75 76 0.793104 GCGGAAAAGAATGGAACGCG 60.793 55.0 3.53 3.53 36.14 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 1935 2.630158 AGAGCGCGTACTCTTCTTCTA 58.37 47.619 8.43 0.0 44.76 2.1 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
75 76 0.793104 GCGGAAAAGAATGGAACGCG 60.793 55.000 3.53 3.53 36.14 6.01
257 258 1.141019 GGAGCGCTAATGGACACGA 59.859 57.895 11.50 0.00 0.00 4.35
296 297 2.727798 CGTGTCGTTCGTAATGGAAAGT 59.272 45.455 0.00 0.00 0.00 2.66
334 335 2.593436 CTTTGTTGGACCGCCGGT 60.593 61.111 9.43 9.43 39.44 5.28
381 382 4.703093 GGACCAGGAACCAATTCGAATTTA 59.297 41.667 20.56 0.00 35.48 1.40
394 395 7.377928 CCAATTCGAATTTAGATCTTGACATGC 59.622 37.037 20.56 0.00 0.00 4.06
474 475 2.520968 GGGTGGCTGGTGGTTTCT 59.479 61.111 0.00 0.00 0.00 2.52
522 523 1.410004 CCTCGGGTATTAGCCACAGA 58.590 55.000 12.21 1.05 34.89 3.41
656 658 2.296471 CTCCCGTTCATAGTTCCGCTAT 59.704 50.000 0.00 0.00 40.86 2.97
706 708 5.123936 GGCGGTTCTTCCTTCTAATTACAT 58.876 41.667 0.00 0.00 0.00 2.29
919 921 2.267642 CTGCCGGATTTCGTCCCA 59.732 61.111 5.05 0.00 44.77 4.37
1094 1096 5.389935 CCTCACAATCTTCAGTTTTACGCTC 60.390 44.000 0.00 0.00 0.00 5.03
1436 1438 5.006386 AGAACTGAAGAAGATTTGGCGAAT 58.994 37.500 0.00 0.00 0.00 3.34
1829 1832 0.185901 TGGGCCAGCAAGAAGACTTT 59.814 50.000 0.00 0.00 33.70 2.66
1932 1935 2.093447 GTGGATTTGGATGGAGTCTCGT 60.093 50.000 0.00 0.00 0.00 4.18
1950 1953 1.062294 CGTAGAAGAAGAGTACGCGCT 59.938 52.381 5.73 0.00 33.78 5.92
1992 1995 1.000171 GTCCTTTTTCTGCTTGCTGGG 60.000 52.381 0.00 0.00 0.00 4.45
2023 2026 3.732048 TTACTGAATCCCCCTTCCAAC 57.268 47.619 0.00 0.00 0.00 3.77
2036 2039 2.491825 CCTTCCAACCACCAACCCAATA 60.492 50.000 0.00 0.00 0.00 1.90
2385 2390 2.362397 TCTAGTGCGGATCCAATCAGAC 59.638 50.000 13.41 0.00 0.00 3.51
2618 2624 0.107703 TTCGCTTCAGGCCATAGTGG 60.108 55.000 5.01 0.00 41.55 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 0.456142 GCCGCGTTCCATTCTTTTCC 60.456 55.000 4.92 0.00 0.00 3.13
86 87 2.498941 GGGATCCGACGCATCCAGA 61.499 63.158 19.26 0.00 41.68 3.86
257 258 3.080121 CTTCGCCTGCTCCCTCCT 61.080 66.667 0.00 0.00 0.00 3.69
296 297 2.490903 GAGGCGAAGTAGTGGTGTCTTA 59.509 50.000 0.00 0.00 0.00 2.10
349 350 0.321996 GTTCCTGGTCCTGGTCAGAC 59.678 60.000 14.11 6.25 33.11 3.51
381 382 1.003580 ACAACCGGCATGTCAAGATCT 59.996 47.619 0.00 0.00 0.00 2.75
474 475 1.208535 ACGCATTTTCTACGGGATCCA 59.791 47.619 15.23 0.00 0.00 3.41
522 523 8.095169 GGGGTAGAATTACTGAATGAATACGAT 58.905 37.037 0.00 0.00 0.00 3.73
656 658 6.446781 AAAATCTTCCTCGTGTATCGTCTA 57.553 37.500 0.00 0.00 40.80 2.59
706 708 8.250143 TGGTAAAAGAGAGTCATAGATATGCA 57.750 34.615 0.00 0.00 33.76 3.96
723 725 3.944015 CCTCCTGCTTCATCTGGTAAAAG 59.056 47.826 0.00 0.00 0.00 2.27
775 777 0.584876 GTACTTCGCACCACAACCAC 59.415 55.000 0.00 0.00 0.00 4.16
785 787 1.497991 GTGCACAAGAGTACTTCGCA 58.502 50.000 13.17 0.00 38.45 5.10
871 873 1.210478 GCTCTGAATAACCAGCCCAGA 59.790 52.381 0.00 0.00 34.28 3.86
1094 1096 4.455877 AGAACATTTCTTCCCTTAAGCGTG 59.544 41.667 0.00 0.00 36.36 5.34
1370 1372 4.520492 TGAATCTTTGTGGAAGAAGAAGCC 59.480 41.667 0.00 0.00 46.90 4.35
1436 1438 7.669089 ATAAACCCTTTGACCTTTTTCTTCA 57.331 32.000 0.00 0.00 0.00 3.02
1829 1832 3.024547 CCATTCTTCGTCTCCCTAGTCA 58.975 50.000 0.00 0.00 0.00 3.41
1932 1935 2.630158 AGAGCGCGTACTCTTCTTCTA 58.370 47.619 8.43 0.00 44.76 2.10
1950 1953 4.143333 GTCTTGGGGCGCGCTAGA 62.143 66.667 32.29 23.23 0.00 2.43
2023 2026 2.965147 GGAATGGATATTGGGTTGGTGG 59.035 50.000 0.00 0.00 0.00 4.61
2146 2149 2.193087 ATAAGCAAGCGGGTTCGGGT 62.193 55.000 0.00 0.00 38.39 5.28
2385 2390 4.016444 TGTCAGGCCTTGGCTTTATAAAG 58.984 43.478 19.08 19.08 35.88 1.85


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

AutoCloner maintained by Alex Coulton.