Multiple sequence alignment - TraesCS1A01G098500

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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 TraesCS1A01G098500 chr1A 100.000 2723 0 0 1 2723 94773998 94776720 0 5029
1 TraesCS1A01G098500 chrUn 98.202 2725 42 3 1 2723 189394040 189396759 0 4754
2 TraesCS1A01G098500 chr5B 98.127 2723 46 1 1 2723 679660398 679663115 0 4741
3 TraesCS1A01G098500 chr7B 98.090 2723 47 1 1 2723 743087700 743090417 0 4735
4 TraesCS1A01G098500 chr7D 98.018 2725 47 3 1 2723 203554845 203552126 0 4726
5 TraesCS1A01G098500 chr5A 98.017 2723 49 1 1 2723 16601422 16598705 0 4724
6 TraesCS1A01G098500 chr5A 97.797 2724 54 2 1 2723 300074480 300077198 0 4693
7 TraesCS1A01G098500 chr6A 97.943 2723 51 2 1 2723 289130131 289132848 0 4713
8 TraesCS1A01G098500 chr4A 97.686 2723 62 1 2 2723 67586033 67583311 0 4678
9 TraesCS1A01G098500 chr3A 97.686 2723 58 2 1 2723 653824607 653821890 0 4674


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 TraesCS1A01G098500 chr1A 94773998 94776720 2722 False 5029 5029 100.000 1 2723 1 chr1A.!!$F1 2722
1 TraesCS1A01G098500 chrUn 189394040 189396759 2719 False 4754 4754 98.202 1 2723 1 chrUn.!!$F1 2722
2 TraesCS1A01G098500 chr5B 679660398 679663115 2717 False 4741 4741 98.127 1 2723 1 chr5B.!!$F1 2722
3 TraesCS1A01G098500 chr7B 743087700 743090417 2717 False 4735 4735 98.090 1 2723 1 chr7B.!!$F1 2722
4 TraesCS1A01G098500 chr7D 203552126 203554845 2719 True 4726 4726 98.018 1 2723 1 chr7D.!!$R1 2722
5 TraesCS1A01G098500 chr5A 16598705 16601422 2717 True 4724 4724 98.017 1 2723 1 chr5A.!!$R1 2722
6 TraesCS1A01G098500 chr5A 300074480 300077198 2718 False 4693 4693 97.797 1 2723 1 chr5A.!!$F1 2722
7 TraesCS1A01G098500 chr6A 289130131 289132848 2717 False 4713 4713 97.943 1 2723 1 chr6A.!!$F1 2722
8 TraesCS1A01G098500 chr4A 67583311 67586033 2722 True 4678 4678 97.686 2 2723 1 chr4A.!!$R1 2721
9 TraesCS1A01G098500 chr3A 653821890 653824607 2717 True 4674 4674 97.686 1 2723 1 chr3A.!!$R1 2722

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
576 582 0.606673 GGTGGCCGAGAAGCTTCTTT 60.607 55.000 29.02 9.31 37.73 2.52 F
802 808 1.726352 AGTTAGGGGTAAGAGGGGACA 59.274 52.381 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1416 0.965866 TGAAAACACGGTGCACCCAA 60.966 50.000 29.95 3.95 0.0 4.12 R
2487 2497 1.218047 CGTTCATCCCTTCGCTCCA 59.782 57.895 0.00 0.00 0.0 3.86 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
64 65 8.359875 TCTCTCACAAGACAGAGAAAGATTAT 57.640 34.615 0.00 0.00 41.82 1.28
289 295 6.420903 CGATGGCGATGTAAGATAGAAAGAAA 59.579 38.462 0.00 0.00 40.82 2.52
428 434 4.035792 CGTGGGTGAATCAAGTACAACAAA 59.964 41.667 0.00 0.00 0.00 2.83
576 582 0.606673 GGTGGCCGAGAAGCTTCTTT 60.607 55.000 29.02 9.31 37.73 2.52
649 655 2.965831 CCTACGGAGGGAGAAATCATCA 59.034 50.000 5.47 0.00 39.48 3.07
728 734 5.876460 TGACTAAGGAGGCCGTAAAAATTAC 59.124 40.000 0.00 0.00 0.00 1.89
802 808 1.726352 AGTTAGGGGTAAGAGGGGACA 59.274 52.381 0.00 0.00 0.00 4.02
1056 1063 3.375610 TGTCAAAGACAAAAAGCTACGCA 59.624 39.130 0.00 0.00 39.78 5.24
1120 1127 6.935208 GGCTATTCATTTAAGTCTTCGGGTAT 59.065 38.462 0.00 0.00 0.00 2.73
1379 1387 2.156098 GGTGTGGGATGCTCGTTTAAA 58.844 47.619 0.00 0.00 0.00 1.52
1384 1392 5.353123 GTGTGGGATGCTCGTTTAAATTCTA 59.647 40.000 0.00 0.00 0.00 2.10
1418 1426 3.692690 TCCTTATTTACTTGGGTGCACC 58.307 45.455 28.57 28.57 40.81 5.01
1462 1470 3.741388 CGAACCGGCTCCTATTTCAATCT 60.741 47.826 0.00 0.00 0.00 2.40
1544 1552 0.034186 CAACCTGGGAGCATTAGCCA 60.034 55.000 0.00 0.00 43.56 4.75
1619 1627 4.164981 TCTAACTTTGCCTTCTCTACCCA 58.835 43.478 0.00 0.00 0.00 4.51
1752 1760 8.568794 GCTCTCAAATAAAAACCTAGTTCACTT 58.431 33.333 0.00 0.00 0.00 3.16
2136 2145 7.691993 ATCTAGAAATAGGTAAAGGAAGGCA 57.308 36.000 0.00 0.00 0.00 4.75
2207 2217 9.645059 TCTAAATTGAAAACATGAACACAAACA 57.355 25.926 0.00 0.00 0.00 2.83
2298 2308 6.018343 GGAGATGGATCGAATTCAGTCTTTTC 60.018 42.308 6.22 2.51 0.00 2.29
2304 2314 5.689383 TCGAATTCAGTCTTTTCCCTTTG 57.311 39.130 6.22 0.00 0.00 2.77
2389 2399 1.479709 ACCTCTTGAGCGCTATCTGT 58.520 50.000 11.50 0.00 0.00 3.41
2487 2497 2.354805 GCCAAGTACTCGACCAATCCTT 60.355 50.000 0.00 0.00 0.00 3.36
2543 2553 3.421919 TCATTGAGGTCAGCATCACAA 57.578 42.857 0.00 0.00 34.95 3.33
2548 2558 3.819368 TGAGGTCAGCATCACAAGAAAA 58.181 40.909 0.00 0.00 29.72 2.29
2645 2655 1.477295 CTCGTCTTCTCCTTGGTACCC 59.523 57.143 10.07 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 4.436113 TGGATTGGATTGGATGAATCGA 57.564 40.909 0.00 0.00 41.45 3.59
289 295 1.689582 CCGAAGCCCTAACTCCCCT 60.690 63.158 0.00 0.00 0.00 4.79
428 434 1.356124 ACCACAAGCTCTGACCTGAT 58.644 50.000 0.00 0.00 0.00 2.90
576 582 2.203625 GCTTTTGGGGGCACTGGA 60.204 61.111 0.00 0.00 0.00 3.86
649 655 5.709594 CCTTTCAGGGGATGAGGATATTTT 58.290 41.667 0.00 0.00 39.68 1.82
802 808 3.071167 GGATTGACTTTCTATACGGGCCT 59.929 47.826 0.84 0.00 0.00 5.19
1056 1063 4.848357 ACCGAGATCCAATGAGAATTTGT 58.152 39.130 0.00 0.00 0.00 2.83
1120 1127 3.496692 CCTTGTTGAAGATCTGGTGGTGA 60.497 47.826 0.00 0.00 0.00 4.02
1213 1220 6.195600 TGGGAACAAGGAACTGTTTATAGT 57.804 37.500 0.00 0.00 40.86 2.12
1357 1365 2.764637 AAACGAGCATCCCACACCCC 62.765 60.000 0.00 0.00 0.00 4.95
1408 1416 0.965866 TGAAAACACGGTGCACCCAA 60.966 50.000 29.95 3.95 0.00 4.12
1418 1426 3.769536 ACAGGAAGCTTTTGAAAACACG 58.230 40.909 16.11 0.00 0.00 4.49
1462 1470 1.328279 ATATCGATCGGTCCAGCACA 58.672 50.000 16.41 0.00 0.00 4.57
1544 1552 7.577303 AGGAACATGTATTGATGTACCAGATT 58.423 34.615 0.00 0.00 35.43 2.40
1605 1613 4.298626 ACAAGATATGGGTAGAGAAGGCA 58.701 43.478 0.00 0.00 0.00 4.75
1606 1614 4.965200 ACAAGATATGGGTAGAGAAGGC 57.035 45.455 0.00 0.00 0.00 4.35
1619 1627 5.120208 CGTGTTTCCAGAACGAACAAGATAT 59.880 40.000 0.00 0.00 39.64 1.63
1857 1865 2.039084 TCTTTCCCTCCTCTGTTTCTGC 59.961 50.000 0.00 0.00 0.00 4.26
2298 2308 5.922544 GTGTTGAAGATCATCAAACAAAGGG 59.077 40.000 14.54 0.00 40.76 3.95
2487 2497 1.218047 CGTTCATCCCTTCGCTCCA 59.782 57.895 0.00 0.00 0.00 3.86
2543 2553 5.763204 TCGAATGGAAGTGCTAAAGTTTTCT 59.237 36.000 0.00 0.00 0.00 2.52
2548 2558 6.260936 CCAATATCGAATGGAAGTGCTAAAGT 59.739 38.462 9.06 0.00 39.12 2.66


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

AutoCloner maintained by Alex Coulton.