Multiple sequence alignment - TraesCS3B01G473900

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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 TraesCS3B01G473900 chr3B 100.000 2549 0 0 1 2549 723100961 723103509 0 4708
1 TraesCS3B01G473900 chr3B 94.972 1989 82 6 568 2549 804661031 804663008 0 3103
2 TraesCS3B01G473900 chr1B 96.123 1986 71 6 567 2549 575860357 575858375 0 3236
3 TraesCS3B01G473900 chr2B 96.067 1983 74 4 568 2549 666075774 666073795 0 3227
4 TraesCS3B01G473900 chr5B 95.869 1985 72 6 569 2549 518021938 518019960 0 3203
5 TraesCS3B01G473900 chr4B 95.670 1986 78 7 567 2549 656538185 656536205 0 3184
6 TraesCS3B01G473900 chr4B 94.238 1996 96 9 558 2546 585994898 585996881 0 3031
7 TraesCS3B01G473900 chr7B 95.519 1986 74 8 569 2549 503449501 503451476 0 3160
8 TraesCS3B01G473900 chr2D 94.578 1992 90 8 569 2549 64508698 64510682 0 3064
9 TraesCS3B01G473900 chr2D 94.728 569 28 2 1 568 498145037 498145604 0 883
10 TraesCS3B01G473900 chrUn 93.841 1997 99 11 569 2549 60558711 60560699 0 2985
11 TraesCS3B01G473900 chr4D 95.079 569 26 2 1 568 133750354 133749787 0 894
12 TraesCS3B01G473900 chr4D 94.912 570 26 3 1 568 437672179 437672747 0 889
13 TraesCS3B01G473900 chr7D 94.912 570 26 3 1 568 118917594 118917026 0 889
14 TraesCS3B01G473900 chr7D 95.204 563 25 2 1 562 541615283 541615844 0 889
15 TraesCS3B01G473900 chr5D 94.755 572 25 3 1 568 285094393 285093823 0 885
16 TraesCS3B01G473900 chr3D 94.737 570 27 3 1 568 451936674 451937242 0 883
17 TraesCS3B01G473900 chr3D 94.737 570 24 6 1 568 379641507 379640942 0 881
18 TraesCS3B01G473900 chr1D 94.728 569 27 3 1 568 488985561 488984995 0 881


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 TraesCS3B01G473900 chr3B 723100961 723103509 2548 False 4708 4708 100.000 1 2549 1 chr3B.!!$F1 2548
1 TraesCS3B01G473900 chr3B 804661031 804663008 1977 False 3103 3103 94.972 568 2549 1 chr3B.!!$F2 1981
2 TraesCS3B01G473900 chr1B 575858375 575860357 1982 True 3236 3236 96.123 567 2549 1 chr1B.!!$R1 1982
3 TraesCS3B01G473900 chr2B 666073795 666075774 1979 True 3227 3227 96.067 568 2549 1 chr2B.!!$R1 1981
4 TraesCS3B01G473900 chr5B 518019960 518021938 1978 True 3203 3203 95.869 569 2549 1 chr5B.!!$R1 1980
5 TraesCS3B01G473900 chr4B 656536205 656538185 1980 True 3184 3184 95.670 567 2549 1 chr4B.!!$R1 1982
6 TraesCS3B01G473900 chr4B 585994898 585996881 1983 False 3031 3031 94.238 558 2546 1 chr4B.!!$F1 1988
7 TraesCS3B01G473900 chr7B 503449501 503451476 1975 False 3160 3160 95.519 569 2549 1 chr7B.!!$F1 1980
8 TraesCS3B01G473900 chr2D 64508698 64510682 1984 False 3064 3064 94.578 569 2549 1 chr2D.!!$F1 1980
9 TraesCS3B01G473900 chr2D 498145037 498145604 567 False 883 883 94.728 1 568 1 chr2D.!!$F2 567
10 TraesCS3B01G473900 chrUn 60558711 60560699 1988 False 2985 2985 93.841 569 2549 1 chrUn.!!$F1 1980
11 TraesCS3B01G473900 chr4D 133749787 133750354 567 True 894 894 95.079 1 568 1 chr4D.!!$R1 567
12 TraesCS3B01G473900 chr4D 437672179 437672747 568 False 889 889 94.912 1 568 1 chr4D.!!$F1 567
13 TraesCS3B01G473900 chr7D 118917026 118917594 568 True 889 889 94.912 1 568 1 chr7D.!!$R1 567
14 TraesCS3B01G473900 chr7D 541615283 541615844 561 False 889 889 95.204 1 562 1 chr7D.!!$F1 561
15 TraesCS3B01G473900 chr5D 285093823 285094393 570 True 885 885 94.755 1 568 1 chr5D.!!$R1 567
16 TraesCS3B01G473900 chr3D 451936674 451937242 568 False 883 883 94.737 1 568 1 chr3D.!!$F1 567
17 TraesCS3B01G473900 chr3D 379640942 379641507 565 True 881 881 94.737 1 568 1 chr3D.!!$R1 567
18 TraesCS3B01G473900 chr1D 488984995 488985561 566 True 881 881 94.728 1 568 1 chr1D.!!$R1 567

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
55 56 0.264657 ACCTTGTTTGGGCCTTTCCT 59.735 50.000 4.53 0.0 34.39 3.36 F
878 888 1.005630 GCAACAGAGAGCACGACCT 60.006 57.895 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1046 1058 1.003476 ACATGCATCTCCACACGCA 60.003 52.632 0.0 0.0 39.01 5.24 R
2244 2269 4.682778 AGTGCCACTCTAACACTAAACA 57.317 40.909 0.0 0.0 42.65 2.83 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
36 37 8.020819 CAGTGACTTCAAAAAGTTGTACAGAAA 58.979 33.333 0.00 0.0 45.80 2.52
55 56 0.264657 ACCTTGTTTGGGCCTTTCCT 59.735 50.000 4.53 0.0 34.39 3.36
164 166 4.417506 CGACAGTTGTACACAATATCCGA 58.582 43.478 0.00 0.0 38.24 4.55
173 175 7.160547 TGTACACAATATCCGAGTCAACTTA 57.839 36.000 0.00 0.0 0.00 2.24
230 235 5.234466 AGGAGGTATGCATTAGGCTTAAG 57.766 43.478 3.54 0.0 45.15 1.85
377 384 8.635877 TTTTAATTTCATTACTTGTTGTGCGT 57.364 26.923 0.00 0.0 0.00 5.24
562 571 7.597288 AGCTAGAAAATGGGTTGTACTTTTT 57.403 32.000 0.00 0.0 0.00 1.94
878 888 1.005630 GCAACAGAGAGCACGACCT 60.006 57.895 0.00 0.0 0.00 3.85
889 899 3.542676 ACGACCTTGACCACGGCA 61.543 61.111 0.00 0.0 0.00 5.69
938 950 1.741770 CTAGTTGTGGAGGGTGCGC 60.742 63.158 0.00 0.0 0.00 6.09
1133 1147 1.001974 CACACCGAGGAACCAGAATCA 59.998 52.381 0.00 0.0 0.00 2.57
1234 1248 1.459592 GGTTGATCTGTTCCGTGTTCG 59.540 52.381 0.00 0.0 0.00 3.95
1281 1297 1.817099 CGATGCTCTGGCCAAGACC 60.817 63.158 7.01 0.0 37.74 3.85
1282 1298 1.452833 GATGCTCTGGCCAAGACCC 60.453 63.158 7.01 0.0 37.74 4.46
1440 1456 6.943899 AGGATCTTGAAGAAGAAGGTTAGT 57.056 37.500 0.00 0.0 41.64 2.24
2244 2269 5.869649 AATTTTGGTTAGAGTGGCACTTT 57.130 34.783 22.98 19.0 0.00 2.66
2426 2457 9.598517 GAAGAAATTATATGTTTGGGCATGAAA 57.401 29.630 0.00 0.0 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.264657 AGGAAAGGCCCAAACAAGGT 59.735 50.000 0.00 0.00 37.37 3.50
55 56 2.741985 CCCACATTCAGCGACGCA 60.742 61.111 23.70 0.79 0.00 5.24
89 90 6.814506 AGGCCTATGTAGTATAGTACAACG 57.185 41.667 21.35 15.22 36.51 4.10
164 166 4.444449 GGGGCGGAGAATAATAAGTTGACT 60.444 45.833 0.00 0.00 0.00 3.41
173 175 1.071471 CAGCGGGGCGGAGAATAAT 59.929 57.895 0.00 0.00 0.00 1.28
377 384 8.994429 ACGTTAAAATCCAATGAAATATTGCA 57.006 26.923 0.00 0.00 0.00 4.08
449 456 8.039603 TGATGGGATCCGAAATATTTTTATCG 57.960 34.615 5.45 1.26 35.19 2.92
507 516 9.619316 CAACGATTAATAATTTCAACCAACTGA 57.381 29.630 0.00 0.00 0.00 3.41
562 571 7.093245 GGGCAAAAGGATAATTAACCCTTGTTA 60.093 37.037 17.93 0.00 39.97 2.41
738 748 5.590259 GTCTGAATAAAATTGGCTGCCTCTA 59.410 40.000 21.03 5.70 0.00 2.43
779 789 1.741770 CTCTCTTTTGGGTCCCGCG 60.742 63.158 2.65 0.00 0.00 6.46
790 800 2.497675 TCTATGCTCAACGGCTCTCTTT 59.502 45.455 0.00 0.00 0.00 2.52
791 801 2.100584 CTCTATGCTCAACGGCTCTCTT 59.899 50.000 0.00 0.00 0.00 2.85
850 860 1.069823 CTCTCTGTTGCTGTGGTCACT 59.930 52.381 2.66 0.00 0.00 3.41
862 872 1.040646 TCAAGGTCGTGCTCTCTGTT 58.959 50.000 0.00 0.00 0.00 3.16
878 888 1.301716 GCTCTCTTGCCGTGGTCAA 60.302 57.895 0.00 0.00 0.00 3.18
889 899 1.504446 GTCGTGCTCTCGCTCTCTT 59.496 57.895 0.00 0.00 36.97 2.85
938 950 0.392193 CACAGCTAGCTTCCCACCAG 60.392 60.000 16.46 3.46 0.00 4.00
1046 1058 1.003476 ACATGCATCTCCACACGCA 60.003 52.632 0.00 0.00 39.01 5.24
1234 1248 1.242076 AAGAAGCATGTCACCTGCAC 58.758 50.000 7.87 1.46 42.15 4.57
1281 1297 6.677431 GCTCTTCTTGCAGTTCATTTATCAGG 60.677 42.308 0.00 0.00 0.00 3.86
1282 1298 6.128090 TGCTCTTCTTGCAGTTCATTTATCAG 60.128 38.462 0.00 0.00 35.31 2.90
1422 1438 7.657761 TCAAGCTTACTAACCTTCTTCTTCAAG 59.342 37.037 0.00 0.00 0.00 3.02
1800 1818 4.981806 ATCACGGTGTATTTGAATTGGG 57.018 40.909 8.17 0.00 0.00 4.12
2244 2269 4.682778 AGTGCCACTCTAACACTAAACA 57.317 40.909 0.00 0.00 42.65 2.83


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

AutoCloner maintained by Alex Coulton.