Multiple sequence alignment - TraesCS3B01G240400

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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 TraesCS3B01G240400 chr3B 100.000 2549 0 0 1 2549 379293521 379296069 0 4708
1 TraesCS3B01G240400 chr6B 98.939 1980 19 2 571 2549 660437745 660435767 0 3539
2 TraesCS3B01G240400 chr6B 94.580 572 31 0 1 572 476222199 476221628 0 885
3 TraesCS3B01G240400 chr6B 94.056 572 34 0 1 572 185126182 185125611 0 869
4 TraesCS3B01G240400 chr6A 98.888 1978 18 3 563 2538 617222878 617220903 0 3528
5 TraesCS3B01G240400 chr6A 94.231 572 33 0 1 572 179718402 179718973 0 874
6 TraesCS3B01G240400 chr7A 98.642 1988 25 1 564 2549 701581932 701583919 0 3520
7 TraesCS3B01G240400 chr7B 98.737 1980 22 2 573 2549 552932143 552930164 0 3515
8 TraesCS3B01G240400 chr7B 98.734 1975 23 2 573 2546 692881452 692883425 0 3507
9 TraesCS3B01G240400 chr7B 98.536 1981 27 1 571 2549 1776633 1774653 0 3496
10 TraesCS3B01G240400 chr5A 98.686 1979 23 2 573 2549 459744881 459746858 0 3507
11 TraesCS3B01G240400 chr1A 98.686 1979 23 3 572 2549 22791528 22793504 0 3507
12 TraesCS3B01G240400 chr2B 98.486 1982 26 3 571 2549 4739874 4741854 0 3491
13 TraesCS3B01G240400 chr2B 94.580 572 31 0 1 572 406174916 406175487 0 885
14 TraesCS3B01G240400 chr2B 94.231 572 33 0 1 572 85442352 85442923 0 874
15 TraesCS3B01G240400 chr2B 94.241 573 32 1 1 572 182844993 182845565 0 874
16 TraesCS3B01G240400 chr2B 94.231 572 33 0 1 572 202008308 202007737 0 874
17 TraesCS3B01G240400 chr4B 94.251 574 31 1 1 572 175803674 175803101 0 876
18 TraesCS3B01G240400 chr3D 94.231 572 32 1 1 572 602771877 602771307 0 872


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 TraesCS3B01G240400 chr3B 379293521 379296069 2548 False 4708 4708 100.000 1 2549 1 chr3B.!!$F1 2548
1 TraesCS3B01G240400 chr6B 660435767 660437745 1978 True 3539 3539 98.939 571 2549 1 chr6B.!!$R3 1978
2 TraesCS3B01G240400 chr6B 476221628 476222199 571 True 885 885 94.580 1 572 1 chr6B.!!$R2 571
3 TraesCS3B01G240400 chr6B 185125611 185126182 571 True 869 869 94.056 1 572 1 chr6B.!!$R1 571
4 TraesCS3B01G240400 chr6A 617220903 617222878 1975 True 3528 3528 98.888 563 2538 1 chr6A.!!$R1 1975
5 TraesCS3B01G240400 chr6A 179718402 179718973 571 False 874 874 94.231 1 572 1 chr6A.!!$F1 571
6 TraesCS3B01G240400 chr7A 701581932 701583919 1987 False 3520 3520 98.642 564 2549 1 chr7A.!!$F1 1985
7 TraesCS3B01G240400 chr7B 552930164 552932143 1979 True 3515 3515 98.737 573 2549 1 chr7B.!!$R2 1976
8 TraesCS3B01G240400 chr7B 692881452 692883425 1973 False 3507 3507 98.734 573 2546 1 chr7B.!!$F1 1973
9 TraesCS3B01G240400 chr7B 1774653 1776633 1980 True 3496 3496 98.536 571 2549 1 chr7B.!!$R1 1978
10 TraesCS3B01G240400 chr5A 459744881 459746858 1977 False 3507 3507 98.686 573 2549 1 chr5A.!!$F1 1976
11 TraesCS3B01G240400 chr1A 22791528 22793504 1976 False 3507 3507 98.686 572 2549 1 chr1A.!!$F1 1977
12 TraesCS3B01G240400 chr2B 4739874 4741854 1980 False 3491 3491 98.486 571 2549 1 chr2B.!!$F1 1978
13 TraesCS3B01G240400 chr2B 406174916 406175487 571 False 885 885 94.580 1 572 1 chr2B.!!$F4 571
14 TraesCS3B01G240400 chr2B 85442352 85442923 571 False 874 874 94.231 1 572 1 chr2B.!!$F2 571
15 TraesCS3B01G240400 chr2B 182844993 182845565 572 False 874 874 94.241 1 572 1 chr2B.!!$F3 571
16 TraesCS3B01G240400 chr2B 202007737 202008308 571 True 874 874 94.231 1 572 1 chr2B.!!$R1 571
17 TraesCS3B01G240400 chr4B 175803101 175803674 573 True 876 876 94.251 1 572 1 chr4B.!!$R1 571
18 TraesCS3B01G240400 chr3D 602771307 602771877 570 True 872 872 94.231 1 572 1 chr3D.!!$R1 571

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
274 278 0.902984 GGGGTTTGTAAGGGCAAGGG 60.903 60.000 0.0 0.0 0.00 3.95 F
325 329 2.147387 AGGCAAGTCCTTCGTGGGT 61.147 57.895 0.0 0.0 44.75 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1380 1386 0.319383 CTCTGTCAGTGCGTGCTTCT 60.319 55.000 0.00 0.0 0.00 2.85 R
1778 1784 1.003355 GCCTGCACTTGGCTCTACA 60.003 57.895 8.16 0.0 46.38 2.74 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
73 75 3.447742 CCAAGTTGCTTTCCACTCAAAC 58.552 45.455 0.00 0.00 0.00 2.93
117 121 8.602328 CAAATATGTGAGAGAGAGTTGAATGTC 58.398 37.037 0.00 0.00 0.00 3.06
138 142 2.289694 CGGGGAGACTGTCATTTGAAGT 60.290 50.000 10.88 0.00 0.00 3.01
191 195 7.112779 CACCATCTATTACCTTTTGGAGAGTT 58.887 38.462 0.00 0.00 44.07 3.01
257 261 2.065899 TTGTGGAGTTGAACCAAGGG 57.934 50.000 0.00 0.00 39.22 3.95
274 278 0.902984 GGGGTTTGTAAGGGCAAGGG 60.903 60.000 0.00 0.00 0.00 3.95
325 329 2.147387 AGGCAAGTCCTTCGTGGGT 61.147 57.895 0.00 0.00 44.75 4.51
460 464 4.283467 TGGATGTATGATAGCACCACCTAC 59.717 45.833 0.00 0.00 0.00 3.18
1230 1236 5.815581 AGCAATGGGTTGATCTGTTTAGTA 58.184 37.500 0.00 0.00 37.53 1.82
1380 1386 2.042464 CCGGAAGAAGAGATGGATGGA 58.958 52.381 0.00 0.00 0.00 3.41
1563 1569 7.654923 GGAAAGGCATGAATTATGAAGGAATTC 59.345 37.037 0.00 0.00 41.63 2.17
1778 1784 2.800250 CTCTTGGGCCAAATTCAGAGT 58.200 47.619 21.28 0.00 0.00 3.24
1908 1915 7.433425 GGCAGTAAATCATAATGCTGAAACTTC 59.567 37.037 7.67 0.00 38.42 3.01
1985 1992 8.825667 TTTTTGGAGCTGTTAATTAATCCAAC 57.174 30.769 22.21 5.95 44.27 3.77
2419 2434 4.022416 GCACTACCACATGATTTTGGTCAA 60.022 41.667 8.88 0.00 42.86 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 75 2.734755 TGGCTATGGTGGAAAGATGG 57.265 50.000 0.00 0.00 0.00 3.51
117 121 2.289694 ACTTCAAATGACAGTCTCCCCG 60.290 50.000 1.31 0.00 0.00 5.73
138 142 4.890158 TGATGAACTCCTTGCTCTTGTA 57.110 40.909 0.00 0.00 0.00 2.41
191 195 4.466370 CACCTAACCAATCTAGGAGACACA 59.534 45.833 2.94 0.00 38.63 3.72
257 261 0.113580 TCCCCTTGCCCTTACAAACC 59.886 55.000 0.00 0.00 0.00 3.27
274 278 1.404391 TCTTCACGAAGTAGGCGATCC 59.596 52.381 6.68 0.00 41.61 3.36
325 329 2.906389 GTCTATCCCACCATGGCTATCA 59.094 50.000 13.04 0.00 35.79 2.15
460 464 1.613437 AGATTTTTGGCGTGGTTCTGG 59.387 47.619 0.00 0.00 0.00 3.86
549 553 6.769822 CCCAAGAGTATATGAGCAACAGAAAT 59.230 38.462 0.00 0.00 0.00 2.17
866 870 4.056125 CCGCCGTGCTCTCTGTCA 62.056 66.667 0.00 0.00 0.00 3.58
1230 1236 2.139323 AGCATGTCACCTGCATGAAT 57.861 45.000 7.87 0.00 44.60 2.57
1380 1386 0.319383 CTCTGTCAGTGCGTGCTTCT 60.319 55.000 0.00 0.00 0.00 2.85
1778 1784 1.003355 GCCTGCACTTGGCTCTACA 60.003 57.895 8.16 0.00 46.38 2.74
1908 1915 7.645340 CGGAATAATTCAATTAGCTTCCACAAG 59.355 37.037 17.30 3.54 35.25 3.16
1985 1992 9.619316 TTTGATTTAAATCACGGTGTATTTGAG 57.381 29.630 26.69 0.00 44.54 3.02
2419 2434 1.216930 ACCCTAAACCAAGTGCCACTT 59.783 47.619 3.74 3.74 39.39 3.16


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

AutoCloner maintained by Alex Coulton.