Multiple sequence alignment - TraesCS1B01G110100

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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 TraesCS1B01G110100 chr1B 100.000 2499 0 0 1 2499 122762735 122765233 0 4615
1 TraesCS1B01G110100 chr1B 98.043 2504 41 4 1 2497 615477352 615479854 0 4346
2 TraesCS1B01G110100 chr1B 97.804 2505 48 4 1 2499 618190611 618188108 0 4314
3 TraesCS1B01G110100 chr7B 97.803 2503 48 3 1 2497 678101136 678103637 0 4311
4 TraesCS1B01G110100 chr7B 97.365 2505 59 4 1 2499 134328268 134325765 0 4253
5 TraesCS1B01G110100 chr3B 95.458 2510 97 11 1 2499 542641339 542638836 0 3988
6 TraesCS1B01G110100 chr3B 95.449 2505 95 8 1 2494 28345344 28347840 0 3976
7 TraesCS1B01G110100 chr3B 95.291 2506 96 11 1 2494 81550056 81547561 0 3954
8 TraesCS1B01G110100 chr4B 95.373 2507 88 10 1 2499 82274453 82271967 0 3962
9 TraesCS1B01G110100 chr5B 95.320 2500 91 11 1 2494 351452199 351449720 0 3945
10 TraesCS1B01G110100 chr5B 94.551 2514 98 17 1 2493 415773880 415771385 0 3847


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 TraesCS1B01G110100 chr1B 122762735 122765233 2498 False 4615 4615 100.000 1 2499 1 chr1B.!!$F1 2498
1 TraesCS1B01G110100 chr1B 615477352 615479854 2502 False 4346 4346 98.043 1 2497 1 chr1B.!!$F2 2496
2 TraesCS1B01G110100 chr1B 618188108 618190611 2503 True 4314 4314 97.804 1 2499 1 chr1B.!!$R1 2498
3 TraesCS1B01G110100 chr7B 678101136 678103637 2501 False 4311 4311 97.803 1 2497 1 chr7B.!!$F1 2496
4 TraesCS1B01G110100 chr7B 134325765 134328268 2503 True 4253 4253 97.365 1 2499 1 chr7B.!!$R1 2498
5 TraesCS1B01G110100 chr3B 542638836 542641339 2503 True 3988 3988 95.458 1 2499 1 chr3B.!!$R2 2498
6 TraesCS1B01G110100 chr3B 28345344 28347840 2496 False 3976 3976 95.449 1 2494 1 chr3B.!!$F1 2493
7 TraesCS1B01G110100 chr3B 81547561 81550056 2495 True 3954 3954 95.291 1 2494 1 chr3B.!!$R1 2493
8 TraesCS1B01G110100 chr4B 82271967 82274453 2486 True 3962 3962 95.373 1 2499 1 chr4B.!!$R1 2498
9 TraesCS1B01G110100 chr5B 351449720 351452199 2479 True 3945 3945 95.320 1 2494 1 chr5B.!!$R1 2493
10 TraesCS1B01G110100 chr5B 415771385 415773880 2495 True 3847 3847 94.551 1 2493 1 chr5B.!!$R2 2492

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
712 714 0.610232 CCTGGGAGTGGCCTTTTGAG 60.61 60.0 3.32 0.0 36.66 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 1865 0.511653 GTTGGACGAGCGGAAGAAAC 59.488 55.0 0.0 0.0 0.0 2.78 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
204 205 1.136110 CGACAAAGGGTTGCAGGTTTT 59.864 47.619 0.00 0.00 38.39 2.43
558 560 7.824672 TGCATGTGATTGTTCAATGTGTATAA 58.175 30.769 2.63 0.00 32.48 0.98
559 561 7.969508 TGCATGTGATTGTTCAATGTGTATAAG 59.030 33.333 2.63 0.00 32.48 1.73
712 714 0.610232 CCTGGGAGTGGCCTTTTGAG 60.610 60.000 3.32 0.00 36.66 3.02
815 817 3.565764 AGGCATACATAAGCAAGCTCA 57.434 42.857 0.00 0.00 0.00 4.26
1202 1206 1.550524 TCATGCTTTGTAGGACGAGCT 59.449 47.619 0.00 0.00 33.04 4.09
1496 1502 1.216064 TTATGGCCCTCTGCATGACT 58.784 50.000 0.00 0.00 43.89 3.41
1668 1674 4.630111 CGGTCTCGTTAGGAGTACTCTAT 58.370 47.826 21.88 13.49 43.60 1.98
1762 1774 0.250467 TGCCTCTGCAGAAGGTTGTC 60.250 55.000 24.26 13.55 44.23 3.18
1790 1802 1.717194 CCGAACACTAGCCGCTTTAA 58.283 50.000 0.00 0.00 0.00 1.52
1853 1865 6.051074 TGTGCTCAGTATAGAATGGATGTTG 58.949 40.000 0.00 0.00 0.00 3.33
1871 1883 0.105224 TGTTTCTTCCGCTCGTCCAA 59.895 50.000 0.00 0.00 0.00 3.53
2000 2033 1.065418 CGGACTATTTGGAGCTTGGGT 60.065 52.381 0.00 0.00 0.00 4.51
2002 2035 2.026262 GGACTATTTGGAGCTTGGGTCA 60.026 50.000 0.00 0.00 0.00 4.02
2036 2069 0.106769 TGCTCCACAGCCAACTCAAA 60.107 50.000 0.00 0.00 46.26 2.69
2064 2097 3.223661 CTTCTCAAGAAGCACGCCT 57.776 52.632 6.82 0.00 44.10 5.52
2152 2185 0.326264 AGATGCCTGCGAAAAGAGGT 59.674 50.000 0.00 0.00 0.00 3.85
2348 2381 7.383300 TCGTTGCTCTAATGTCTCATTGATATG 59.617 37.037 5.40 0.00 0.00 1.78
2349 2382 7.383300 CGTTGCTCTAATGTCTCATTGATATGA 59.617 37.037 5.40 0.00 38.45 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
547 549 6.748658 CCAACTGCACATTCTTATACACATTG 59.251 38.462 0.00 0.00 0.00 2.82
558 560 0.396435 TCCGTCCAACTGCACATTCT 59.604 50.000 0.00 0.00 0.00 2.40
559 561 0.798776 CTCCGTCCAACTGCACATTC 59.201 55.000 0.00 0.00 0.00 2.67
712 714 1.536662 ATACCGCTCCTCATCCCCC 60.537 63.158 0.00 0.00 0.00 5.40
815 817 4.725490 ACCTGGTTGTAAGTAAGCATGTT 58.275 39.130 0.00 0.00 37.42 2.71
1202 1206 2.757314 TGACATTCTTGTTGTGTTGCCA 59.243 40.909 0.00 0.00 35.79 4.92
1467 1473 1.981495 GAGGGCCATAATCTAGGTGCT 59.019 52.381 6.18 0.00 0.00 4.40
1496 1502 5.316167 AGAGACAAAAATGCATACCACTCA 58.684 37.500 0.00 0.00 0.00 3.41
1632 1638 2.083002 GAGACCGTCCGTTTCTCTACT 58.917 52.381 0.00 0.00 34.16 2.57
1668 1674 9.623000 GTTCATATTAAAAAGGCCTCTAACCTA 57.377 33.333 5.23 0.00 36.14 3.08
1790 1802 1.918262 TGAACCTCCATGGCAAGAGAT 59.082 47.619 16.92 7.43 40.22 2.75
1853 1865 0.511653 GTTGGACGAGCGGAAGAAAC 59.488 55.000 0.00 0.00 0.00 2.78
1871 1883 1.664965 GACGTGCTTGGCTCGAAGT 60.665 57.895 18.24 0.00 46.28 3.01
2000 2033 1.415289 AGCATCTTCCATCTGCGATGA 59.585 47.619 16.69 0.00 40.78 2.92
2002 2035 1.270732 GGAGCATCTTCCATCTGCGAT 60.271 52.381 0.00 0.00 40.78 4.58
2036 2069 4.270245 CTTCTTGAGAAGGCTGAGAAGT 57.730 45.455 11.99 0.00 45.79 3.01
2064 2097 4.021229 TCGGATGTTCCTTGAGCTAACTA 58.979 43.478 0.00 0.00 33.30 2.24
2132 2165 1.012841 CCTCTTTTCGCAGGCATCTC 58.987 55.000 0.00 0.00 0.00 2.75
2152 2185 5.871524 GCATCAGTCATCACTTCACTTCTTA 59.128 40.000 0.00 0.00 0.00 2.10
2306 2339 4.943705 AGCAACGAACTTAACATGATCCAT 59.056 37.500 0.00 0.00 0.00 3.41
2348 2381 3.855689 AATGCCAAGTACAGCAACATC 57.144 42.857 8.97 0.00 43.36 3.06
2349 2382 5.920193 ATAAATGCCAAGTACAGCAACAT 57.080 34.783 8.97 0.00 43.36 2.71


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

AutoCloner maintained by Alex Coulton.