Multiple sequence alignment - TraesCS6B01G121500

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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 TraesCS6B01G121500 chr6B 100.000 2549 0 0 1 2549 116268575 116271123 0.000000e+00 4708
1 TraesCS6B01G121500 chr6B 98.586 1980 24 3 572 2549 660437743 660435766 0.000000e+00 3498
2 TraesCS6B01G121500 chr7A 98.342 1990 29 3 563 2549 701581932 701583920 0.000000e+00 3489
3 TraesCS6B01G121500 chr6A 98.628 1968 24 3 572 2537 617222869 617220903 0.000000e+00 3482
4 TraesCS6B01G121500 chr6A 95.622 571 18 3 1 571 102116987 102117550 0.000000e+00 909
5 TraesCS6B01G121500 chr3B 98.434 1980 27 3 572 2549 379294093 379296070 0.000000e+00 3482
6 TraesCS6B01G121500 chr1A 98.383 1979 29 3 572 2549 22791529 22793505 0.000000e+00 3474
7 TraesCS6B01G121500 chr7B 98.285 1983 30 4 569 2549 692881449 692883429 0.000000e+00 3470
8 TraesCS6B01G121500 chr7B 98.285 1983 29 3 571 2549 552932144 552930163 0.000000e+00 3469
9 TraesCS6B01G121500 chr5A 98.285 1982 31 3 570 2549 459744879 459746859 0.000000e+00 3469
10 TraesCS6B01G121500 chr3A 98.239 1987 28 5 567 2549 722406051 722404068 0.000000e+00 3469
11 TraesCS6B01G121500 chr5B 99.124 571 5 0 1 571 641795209 641794639 0.000000e+00 1027
12 TraesCS6B01G121500 chr1B 99.124 571 5 0 1 571 84964099 84963529 0.000000e+00 1027
13 TraesCS6B01G121500 chr4D 92.205 449 30 5 1 446 213704658 213705104 4.630000e-177 630


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 TraesCS6B01G121500 chr6B 116268575 116271123 2548 False 4708 4708 100.000 1 2549 1 chr6B.!!$F1 2548
1 TraesCS6B01G121500 chr6B 660435766 660437743 1977 True 3498 3498 98.586 572 2549 1 chr6B.!!$R1 1977
2 TraesCS6B01G121500 chr7A 701581932 701583920 1988 False 3489 3489 98.342 563 2549 1 chr7A.!!$F1 1986
3 TraesCS6B01G121500 chr6A 617220903 617222869 1966 True 3482 3482 98.628 572 2537 1 chr6A.!!$R1 1965
4 TraesCS6B01G121500 chr6A 102116987 102117550 563 False 909 909 95.622 1 571 1 chr6A.!!$F1 570
5 TraesCS6B01G121500 chr3B 379294093 379296070 1977 False 3482 3482 98.434 572 2549 1 chr3B.!!$F1 1977
6 TraesCS6B01G121500 chr1A 22791529 22793505 1976 False 3474 3474 98.383 572 2549 1 chr1A.!!$F1 1977
7 TraesCS6B01G121500 chr7B 692881449 692883429 1980 False 3470 3470 98.285 569 2549 1 chr7B.!!$F1 1980
8 TraesCS6B01G121500 chr7B 552930163 552932144 1981 True 3469 3469 98.285 571 2549 1 chr7B.!!$R1 1978
9 TraesCS6B01G121500 chr5A 459744879 459746859 1980 False 3469 3469 98.285 570 2549 1 chr5A.!!$F1 1979
10 TraesCS6B01G121500 chr3A 722404068 722406051 1983 True 3469 3469 98.239 567 2549 1 chr3A.!!$R1 1982
11 TraesCS6B01G121500 chr5B 641794639 641795209 570 True 1027 1027 99.124 1 571 1 chr5B.!!$R1 570
12 TraesCS6B01G121500 chr1B 84963529 84964099 570 True 1027 1027 99.124 1 571 1 chr1B.!!$R1 570

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
841 844 2.043992 TGGCGGGTGTGCTATATAAGT 58.956 47.619 0.0 0.0 34.52 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 2444 3.248888 AGTGCCACTCTAACCCTAAACT 58.751 45.455 0.0 0.0 0.0 2.66 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
72 73 2.955342 TGGCCCCGTTTTAACTAACT 57.045 45.000 0.00 0.00 0.00 2.24
350 353 9.669353 GCCACAGTTCAAAGAAATATATATGTG 57.331 33.333 0.00 0.00 34.44 3.21
505 508 2.096980 CCGACGATAGCTAGTTGTGTGA 59.903 50.000 0.00 0.00 42.67 3.58
572 575 9.561069 AATGTAGGTAGAGCAATACAAAATAGG 57.439 33.333 1.41 0.00 32.31 2.57
573 576 7.506114 TGTAGGTAGAGCAATACAAAATAGGG 58.494 38.462 1.41 0.00 0.00 3.53
574 577 6.576778 AGGTAGAGCAATACAAAATAGGGT 57.423 37.500 1.41 0.00 0.00 4.34
575 578 6.970191 AGGTAGAGCAATACAAAATAGGGTT 58.030 36.000 1.41 0.00 0.00 4.11
576 579 7.410991 AGGTAGAGCAATACAAAATAGGGTTT 58.589 34.615 1.41 0.00 0.00 3.27
841 844 2.043992 TGGCGGGTGTGCTATATAAGT 58.956 47.619 0.00 0.00 34.52 2.24
850 853 3.323691 TGTGCTATATAAGTGGGCGACAT 59.676 43.478 1.61 0.00 0.00 3.06
1133 1138 1.275291 GACACCGAGGAACCAGAATCA 59.725 52.381 0.00 0.00 0.00 2.57
1248 1253 1.200716 GTGTTCATGCAGGTGACATGG 59.799 52.381 11.97 0.00 44.09 3.66
1270 1275 3.140325 TCTTTCTTTGGGTCGATGCTT 57.860 42.857 0.00 0.00 0.00 3.91
2245 2255 4.383118 GCTAGGACAGATGGCAAGACTTTA 60.383 45.833 0.00 0.00 0.00 1.85
2382 2397 3.975479 TTTTGGAGGGTTGGAAGGTTA 57.025 42.857 0.00 0.00 0.00 2.85
2429 2444 3.569194 TTTTGGTCAGAGTGGCACTTA 57.431 42.857 22.98 7.89 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
350 353 8.464770 TGTCTTGCATGATTTTGCTTTTATAC 57.535 30.769 5.49 0.00 43.18 1.47
351 354 8.924691 GTTGTCTTGCATGATTTTGCTTTTATA 58.075 29.630 5.49 0.00 43.18 0.98
505 508 6.021596 GCGTCTGTCGATATTGTTTCATTTT 58.978 36.000 0.00 0.00 42.86 1.82
571 574 5.423931 TGAGGGCAAAAGGATAATTAAACCC 59.576 40.000 7.99 0.00 0.00 4.11
572 575 6.154534 ACTGAGGGCAAAAGGATAATTAAACC 59.845 38.462 0.00 0.00 0.00 3.27
573 576 7.035612 CACTGAGGGCAAAAGGATAATTAAAC 58.964 38.462 0.00 0.00 0.00 2.01
574 577 6.154363 CCACTGAGGGCAAAAGGATAATTAAA 59.846 38.462 0.00 0.00 0.00 1.52
575 578 5.656416 CCACTGAGGGCAAAAGGATAATTAA 59.344 40.000 0.00 0.00 0.00 1.40
576 579 5.200483 CCACTGAGGGCAAAAGGATAATTA 58.800 41.667 0.00 0.00 0.00 1.40
914 919 0.980231 CCCTCCACAGCTAGCTTCCT 60.980 60.000 16.46 0.00 0.00 3.36
1248 1253 2.814336 AGCATCGACCCAAAGAAAGAAC 59.186 45.455 0.00 0.00 0.00 3.01
1270 1275 3.009363 TCATTCATCAGAGTCTTGGCCAA 59.991 43.478 19.25 19.25 0.00 4.52
1359 1364 1.071385 CCATCCATCTCTTCTTCCGGG 59.929 57.143 0.00 0.00 0.00 5.73
1681 1687 9.981114 TCAAAAGTTTCTGAATTCCTAATTTCC 57.019 29.630 2.27 0.00 0.00 3.13
1964 1970 7.026631 TGAATTGGATTAATTAACAGCTCCG 57.973 36.000 0.00 0.00 39.06 4.63
2245 2255 4.090027 ACCTTCCTTCCCTACCTATGTT 57.910 45.455 0.00 0.00 0.00 2.71
2382 2397 6.398234 TGTGGTAGTGCAACATACATTTTT 57.602 33.333 0.00 0.00 41.43 1.94
2429 2444 3.248888 AGTGCCACTCTAACCCTAAACT 58.751 45.455 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.