Multiple sequence alignment - TraesCS6D01G261800

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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 TraesCS6D01G261800 chr6D 100.000 2753 0 0 1 2753 370000192 369997440 0 5084
1 TraesCS6D01G261800 chr6D 98.491 530 7 1 1 529 430466077 430465548 0 933
2 TraesCS6D01G261800 chr7D 98.509 2214 30 3 543 2753 579030455 579032668 0 3903
3 TraesCS6D01G261800 chr1A 98.419 2214 32 3 543 2753 112004185 112001972 0 3892
4 TraesCS6D01G261800 chrUn 98.328 2213 35 2 543 2753 86478776 86480988 0 3880
5 TraesCS6D01G261800 chrUn 98.193 2214 37 3 543 2753 186190693 186188480 0 3864
6 TraesCS6D01G261800 chrUn 98.677 529 7 0 1 529 45133681 45133153 0 939
7 TraesCS6D01G261800 chr7B 98.192 2212 38 2 543 2752 743006786 743008997 0 3862
8 TraesCS6D01G261800 chr7B 98.299 529 9 0 1 529 742965789 742966317 0 928
9 TraesCS6D01G261800 chr2D 98.147 2213 39 2 543 2753 200914988 200917200 0 3858
10 TraesCS6D01G261800 chr1D 97.967 2214 40 5 543 2753 212467145 212464934 0 3834
11 TraesCS6D01G261800 chr7A 97.785 2212 46 3 543 2752 211292997 211295207 0 3810
12 TraesCS6D01G261800 chr4B 97.695 2213 47 4 543 2753 209270586 209268376 0 3801
13 TraesCS6D01G261800 chr3D 98.488 529 8 0 1 529 202624773 202624245 0 933
14 TraesCS6D01G261800 chr3B 98.299 529 9 0 1 529 92225920 92225392 0 928
15 TraesCS6D01G261800 chr3B 98.299 529 9 0 1 529 92238498 92239026 0 928
16 TraesCS6D01G261800 chr3B 98.299 529 9 0 1 529 201583054 201582526 0 928
17 TraesCS6D01G261800 chr2B 98.299 529 9 0 1 529 449202298 449201770 0 928
18 TraesCS6D01G261800 chr4D 98.110 529 9 1 1 529 97362526 97363053 0 920


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 TraesCS6D01G261800 chr6D 369997440 370000192 2752 True 5084 5084 100.000 1 2753 1 chr6D.!!$R1 2752
1 TraesCS6D01G261800 chr6D 430465548 430466077 529 True 933 933 98.491 1 529 1 chr6D.!!$R2 528
2 TraesCS6D01G261800 chr7D 579030455 579032668 2213 False 3903 3903 98.509 543 2753 1 chr7D.!!$F1 2210
3 TraesCS6D01G261800 chr1A 112001972 112004185 2213 True 3892 3892 98.419 543 2753 1 chr1A.!!$R1 2210
4 TraesCS6D01G261800 chrUn 86478776 86480988 2212 False 3880 3880 98.328 543 2753 1 chrUn.!!$F1 2210
5 TraesCS6D01G261800 chrUn 186188480 186190693 2213 True 3864 3864 98.193 543 2753 1 chrUn.!!$R2 2210
6 TraesCS6D01G261800 chrUn 45133153 45133681 528 True 939 939 98.677 1 529 1 chrUn.!!$R1 528
7 TraesCS6D01G261800 chr7B 743006786 743008997 2211 False 3862 3862 98.192 543 2752 1 chr7B.!!$F2 2209
8 TraesCS6D01G261800 chr7B 742965789 742966317 528 False 928 928 98.299 1 529 1 chr7B.!!$F1 528
9 TraesCS6D01G261800 chr2D 200914988 200917200 2212 False 3858 3858 98.147 543 2753 1 chr2D.!!$F1 2210
10 TraesCS6D01G261800 chr1D 212464934 212467145 2211 True 3834 3834 97.967 543 2753 1 chr1D.!!$R1 2210
11 TraesCS6D01G261800 chr7A 211292997 211295207 2210 False 3810 3810 97.785 543 2752 1 chr7A.!!$F1 2209
12 TraesCS6D01G261800 chr4B 209268376 209270586 2210 True 3801 3801 97.695 543 2753 1 chr4B.!!$R1 2210
13 TraesCS6D01G261800 chr3D 202624245 202624773 528 True 933 933 98.488 1 529 1 chr3D.!!$R1 528
14 TraesCS6D01G261800 chr3B 92225392 92225920 528 True 928 928 98.299 1 529 1 chr3B.!!$R1 528
15 TraesCS6D01G261800 chr3B 92238498 92239026 528 False 928 928 98.299 1 529 1 chr3B.!!$F1 528
16 TraesCS6D01G261800 chr3B 201582526 201583054 528 True 928 928 98.299 1 529 1 chr3B.!!$R2 528
17 TraesCS6D01G261800 chr2B 449201770 449202298 528 True 928 928 98.299 1 529 1 chr2B.!!$R1 528
18 TraesCS6D01G261800 chr4D 97362526 97363053 527 False 920 920 98.110 1 529 1 chr4D.!!$F1 528

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
710 712 1.621317 TCTTCAACATGCGTGGACCTA 59.379 47.619 11.36 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 1961 0.53109 CCACAAGAACGAACGACCCA 60.531 55.0 0.14 0.0 0.0 4.51 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
211 212 3.655486 TCGCCTTATTTCGTTTGACTCA 58.345 40.909 0.00 0.00 0.00 3.41
233 234 4.744795 TGGAGCTGAGAAATCTACTTCC 57.255 45.455 0.00 0.00 0.00 3.46
280 281 3.515602 AAGAACAAGCAAGGGATGAGT 57.484 42.857 0.00 0.00 0.00 3.41
397 399 2.562738 GTTGTGCTTTTTCCCCTATGCT 59.437 45.455 0.00 0.00 0.00 3.79
510 512 2.572290 CATCTGAGGCTGCATCAATCA 58.428 47.619 18.18 5.66 0.00 2.57
529 531 4.054780 TCAAGGATACACGACATAAGGC 57.945 45.455 0.00 0.00 41.41 4.35
530 532 2.794910 CAAGGATACACGACATAAGGCG 59.205 50.000 0.00 0.00 41.41 5.52
531 533 2.304092 AGGATACACGACATAAGGCGA 58.696 47.619 0.00 0.00 41.41 5.54
532 534 2.691526 AGGATACACGACATAAGGCGAA 59.308 45.455 0.00 0.00 41.41 4.70
533 535 3.131577 AGGATACACGACATAAGGCGAAA 59.868 43.478 0.00 0.00 41.41 3.46
534 536 4.056050 GGATACACGACATAAGGCGAAAT 58.944 43.478 0.00 0.00 0.00 2.17
535 537 5.010314 AGGATACACGACATAAGGCGAAATA 59.990 40.000 0.00 0.00 41.41 1.40
536 538 5.867716 GGATACACGACATAAGGCGAAATAT 59.132 40.000 0.00 0.00 0.00 1.28
537 539 7.031372 GGATACACGACATAAGGCGAAATATA 58.969 38.462 0.00 0.00 0.00 0.86
538 540 7.220300 GGATACACGACATAAGGCGAAATATAG 59.780 40.741 0.00 0.00 0.00 1.31
539 541 5.227908 ACACGACATAAGGCGAAATATAGG 58.772 41.667 0.00 0.00 0.00 2.57
540 542 4.091509 CACGACATAAGGCGAAATATAGGC 59.908 45.833 0.00 0.00 0.00 3.93
541 543 4.021368 ACGACATAAGGCGAAATATAGGCT 60.021 41.667 0.00 0.00 45.54 4.58
710 712 1.621317 TCTTCAACATGCGTGGACCTA 59.379 47.619 11.36 0.00 0.00 3.08
728 730 6.782494 TGGACCTAGAATGACTATGCATAGAA 59.218 38.462 34.86 23.58 34.50 2.10
1051 1054 4.998051 TCTTGGATTTCTAGTTTGGGCTT 58.002 39.130 0.00 0.00 0.00 4.35
1088 1091 2.169561 TGGGCTTAGACGTTGATATGCA 59.830 45.455 12.83 0.00 0.00 3.96
1271 1274 1.003696 AGTTCTAGCAAACTCTGGGCC 59.996 52.381 0.00 0.00 34.37 5.80
1955 1961 3.833070 ACCTAAGTCAGTTCGAACCTGAT 59.167 43.478 24.22 14.31 0.00 2.90
1969 1975 0.246635 CCTGATGGGTCGTTCGTTCT 59.753 55.000 0.00 0.00 0.00 3.01
2012 2018 8.359060 CTTACTCAGGATTTCTTTATCTTCGG 57.641 38.462 0.00 0.00 0.00 4.30
2064 2070 3.629398 GGGAAGTGTCTCCATTTATGCTG 59.371 47.826 0.00 0.00 37.20 4.41
2074 2080 4.985538 TCCATTTATGCTGATAGAACCCC 58.014 43.478 0.00 0.00 0.00 4.95
2075 2081 4.415179 TCCATTTATGCTGATAGAACCCCA 59.585 41.667 0.00 0.00 0.00 4.96
2076 2082 4.763793 CCATTTATGCTGATAGAACCCCAG 59.236 45.833 0.00 0.00 0.00 4.45
2094 2100 5.045432 ACCCCAGAAAAAGAATATACCGTCA 60.045 40.000 0.00 0.00 0.00 4.35
2282 2288 0.827089 TCGTTACGGTGGTTGAGGGA 60.827 55.000 4.53 0.00 0.00 4.20
2305 2311 2.297315 CCTGCCGTTCAGAGATGCTATA 59.703 50.000 3.77 0.00 45.72 1.31
2379 2386 1.206132 TCATACAGACGCAACCCGATT 59.794 47.619 0.00 0.00 41.02 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 212 4.718774 TGGAAGTAGATTTCTCAGCTCCAT 59.281 41.667 0.00 0.00 0.00 3.41
233 234 3.513515 ACTAGCACTCTTTCCCTCTCTTG 59.486 47.826 0.00 0.00 0.00 3.02
280 281 2.435938 GGATTTCGCTCCCGTGCA 60.436 61.111 0.00 0.00 35.54 4.57
407 409 2.103263 GGCCAATCCTACTCCACTAGTG 59.897 54.545 16.34 16.34 39.39 2.74
510 512 2.691526 TCGCCTTATGTCGTGTATCCTT 59.308 45.455 0.00 0.00 0.00 3.36
529 531 2.808543 GCCCACTTCAGCCTATATTTCG 59.191 50.000 0.00 0.00 0.00 3.46
530 532 3.817647 CTGCCCACTTCAGCCTATATTTC 59.182 47.826 0.00 0.00 0.00 2.17
531 533 3.825328 CTGCCCACTTCAGCCTATATTT 58.175 45.455 0.00 0.00 0.00 1.40
532 534 3.498774 CTGCCCACTTCAGCCTATATT 57.501 47.619 0.00 0.00 0.00 1.28
710 712 8.200024 AGTGGTATTCTATGCATAGTCATTCT 57.800 34.615 28.51 17.32 0.00 2.40
749 751 6.552445 AAGTAGGAATGCTGTCACTAGAAT 57.448 37.500 0.00 0.00 0.00 2.40
1051 1054 8.148351 GTCTAAGCCCACAGTAAACATATGATA 58.852 37.037 10.38 0.00 0.00 2.15
1088 1091 1.450312 GCTGCGGTGAAGTAGGCAT 60.450 57.895 0.00 0.00 34.49 4.40
1207 1210 6.074648 TGGTGAACAAAAAGATGAACCCTAT 58.925 36.000 0.00 0.00 0.00 2.57
1271 1274 9.486497 AATAAGTATCATGTAGAGCAATGTCTG 57.514 33.333 0.00 0.00 0.00 3.51
1450 1453 2.673775 TGCATGGGAAAGAAGGTCAA 57.326 45.000 0.00 0.00 0.00 3.18
1700 1703 4.380843 TCTCCAAAAGTATGAAAGGCCA 57.619 40.909 5.01 0.00 0.00 5.36
1955 1961 0.531090 CCACAAGAACGAACGACCCA 60.531 55.000 0.14 0.00 0.00 4.51
2012 2018 2.939103 GACATATGAATATGCCTCGCCC 59.061 50.000 10.38 0.00 42.98 6.13
2064 2070 9.286170 GGTATATTCTTTTTCTGGGGTTCTATC 57.714 37.037 0.00 0.00 0.00 2.08
2094 2100 3.644966 TCGCATCCTTGGTCCTTAAAT 57.355 42.857 0.00 0.00 0.00 1.40
2282 2288 0.674895 GCATCTCTGAACGGCAGGTT 60.675 55.000 7.56 0.00 44.98 3.50
2305 2311 5.827326 ACTTGGCTAACTTTCCTACTCTT 57.173 39.130 0.00 0.00 0.00 2.85
2415 2422 2.109834 TGGAAATGGGAAAGGCAGAGAA 59.890 45.455 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.