Multiple sequence alignment - TraesCS6A01G286800

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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 TraesCS6A01G286800 chr6A 100.000 6305 0 0 1 6305 519204403 519210707 0.000000e+00 11644.0
1 TraesCS6A01G286800 chr6A 83.044 519 53 18 5793 6305 449360351 449360840 7.500000e-119 438.0
2 TraesCS6A01G286800 chr6A 79.110 517 58 30 5793 6305 15495352 15494882 1.710000e-80 311.0
3 TraesCS6A01G286800 chr6A 87.500 80 5 4 643 721 488319604 488319679 3.130000e-13 87.9
4 TraesCS6A01G286800 chr6B 94.592 3661 155 23 2053 5682 563996882 564000530 0.000000e+00 5624.0
5 TraesCS6A01G286800 chr6B 95.323 1176 42 6 888 2053 563995662 563996834 0.000000e+00 1855.0
6 TraesCS6A01G286800 chr6B 85.268 448 42 12 3 446 563994830 563995257 2.090000e-119 440.0
7 TraesCS6A01G286800 chr6B 95.833 48 2 0 853 900 563995597 563995644 1.880000e-10 78.7
8 TraesCS6A01G286800 chr6D 94.674 3624 131 26 2100 5682 377544325 377547927 0.000000e+00 5566.0
9 TraesCS6A01G286800 chr6D 93.833 1200 45 8 853 2030 377543132 377544324 0.000000e+00 1779.0
10 TraesCS6A01G286800 chr6D 91.680 649 42 8 1 646 377541137 377541776 0.000000e+00 889.0
11 TraesCS6A01G286800 chr6D 96.209 211 8 0 646 856 377542856 377543066 4.680000e-91 346.0
12 TraesCS6A01G286800 chr6D 97.917 48 0 1 2007 2053 84938453 84938500 1.460000e-11 82.4
13 TraesCS6A01G286800 chr6D 100.000 43 0 0 2011 2053 84938543 84938501 5.240000e-11 80.5
14 TraesCS6A01G286800 chr6D 92.683 41 2 1 695 735 13960331 13960370 2.460000e-04 58.4
15 TraesCS6A01G286800 chr7D 89.362 517 34 12 5793 6305 349949988 349949489 1.150000e-176 630.0
16 TraesCS6A01G286800 chr7D 88.072 503 38 13 5793 6290 499718858 499719343 1.520000e-160 577.0
17 TraesCS6A01G286800 chr7D 92.135 89 6 1 509 597 602187239 602187326 2.390000e-24 124.0
18 TraesCS6A01G286800 chr7D 92.941 85 5 1 513 597 556311132 556311049 8.580000e-24 122.0
19 TraesCS6A01G286800 chr7D 98.039 51 1 0 2027 2077 611705822 611705772 8.710000e-14 89.8
20 TraesCS6A01G286800 chr1D 89.189 518 38 13 5791 6303 320980036 320980540 1.150000e-176 630.0
21 TraesCS6A01G286800 chr1D 86.260 524 43 17 5793 6305 361098999 361099504 5.560000e-150 542.0
22 TraesCS6A01G286800 chr1D 97.297 37 1 0 620 656 465819 465855 5.280000e-06 63.9
23 TraesCS6A01G286800 chr3D 88.247 519 43 11 5791 6305 16130929 16130425 6.990000e-169 604.0
24 TraesCS6A01G286800 chr3D 88.395 517 40 10 5793 6305 580085878 580086378 6.990000e-169 604.0
25 TraesCS6A01G286800 chr3D 87.984 516 46 11 5793 6305 556936763 556937265 4.210000e-166 595.0
26 TraesCS6A01G286800 chr3D 94.340 53 2 1 2011 2062 607096386 607096438 5.240000e-11 80.5
27 TraesCS6A01G286800 chr5D 87.500 520 36 16 5793 6305 325474803 325474306 1.970000e-159 573.0
28 TraesCS6A01G286800 chr4D 87.449 494 44 13 5789 6276 473846274 473845793 2.570000e-153 553.0
29 TraesCS6A01G286800 chr1A 82.852 519 57 18 5787 6296 570121314 570121809 2.700000e-118 436.0
30 TraesCS6A01G286800 chr1A 94.444 90 3 2 506 595 513118099 513118186 3.070000e-28 137.0
31 TraesCS6A01G286800 chr4B 86.634 202 12 10 1816 2012 493764672 493764863 6.410000e-50 209.0
32 TraesCS6A01G286800 chr2A 96.471 85 2 1 511 595 431044670 431044587 8.520000e-29 139.0
33 TraesCS6A01G286800 chr2A 93.103 87 5 1 509 595 714336274 714336359 6.640000e-25 126.0
34 TraesCS6A01G286800 chr7A 92.391 92 5 2 504 595 709389662 709389751 5.130000e-26 130.0
35 TraesCS6A01G286800 chr7A 76.866 134 24 6 604 733 680345935 680345805 1.130000e-07 69.4
36 TraesCS6A01G286800 chr5B 95.062 81 3 1 516 596 13704884 13704963 6.640000e-25 126.0
37 TraesCS6A01G286800 chr2B 93.103 87 5 1 509 595 1266746 1266831 6.640000e-25 126.0
38 TraesCS6A01G286800 chr2B 97.872 47 1 0 2007 2053 749661560 749661606 1.460000e-11 82.4
39 TraesCS6A01G286800 chr2D 92.000 75 3 3 2004 2076 631034908 631034835 1.120000e-17 102.0
40 TraesCS6A01G286800 chrUn 79.839 124 15 9 618 737 71287551 71287434 1.460000e-11 82.4
41 TraesCS6A01G286800 chrUn 92.683 41 2 1 695 735 402795637 402795598 2.460000e-04 58.4
42 TraesCS6A01G286800 chr3B 94.340 53 2 1 2011 2062 816606481 816606533 5.240000e-11 80.5


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 TraesCS6A01G286800 chr6A 519204403 519210707 6304 False 11644.000 11644 100.000 1 6305 1 chr6A.!!$F3 6304
1 TraesCS6A01G286800 chr6B 563994830 564000530 5700 False 1999.425 5624 92.754 3 5682 4 chr6B.!!$F1 5679
2 TraesCS6A01G286800 chr6D 377541137 377547927 6790 False 2145.000 5566 94.099 1 5682 4 chr6D.!!$F3 5681
3 TraesCS6A01G286800 chr1D 320980036 320980540 504 False 630.000 630 89.189 5791 6303 1 chr1D.!!$F2 512
4 TraesCS6A01G286800 chr1D 361098999 361099504 505 False 542.000 542 86.260 5793 6305 1 chr1D.!!$F3 512
5 TraesCS6A01G286800 chr3D 16130425 16130929 504 True 604.000 604 88.247 5791 6305 1 chr3D.!!$R1 514
6 TraesCS6A01G286800 chr3D 580085878 580086378 500 False 604.000 604 88.395 5793 6305 1 chr3D.!!$F2 512
7 TraesCS6A01G286800 chr3D 556936763 556937265 502 False 595.000 595 87.984 5793 6305 1 chr3D.!!$F1 512


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
173 176 0.896923 TTGGCATGGGAAATGAGTGC 59.103 50.000 0.00 0.0 35.17 4.40 F
867 2035 1.278637 CGTTCGTCACAACAAGCCC 59.721 57.895 0.00 0.0 0.00 5.19 F
1668 2889 0.179012 CCCCACGGTTACTGTTGGTT 60.179 55.000 12.58 0.0 0.00 3.67 F
1812 3033 1.094785 ACGGGCAATTTCAAGGATCG 58.905 50.000 0.00 0.0 0.00 3.69 F
2794 4081 1.069022 CACAGCAAGTCCCACATTTCG 60.069 52.381 0.00 0.0 0.00 3.46 F
4002 5303 0.037326 GGTGCTGACATCCTCGTTGA 60.037 55.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1493 2714 0.253113 TCATCACATCCCCCACCTCA 60.253 55.000 0.00 0.0 0.00 3.86 R
1963 3184 0.618458 TCTCGGGGAACAAATCTGGG 59.382 55.000 0.00 0.0 0.00 4.45 R
2654 3939 2.441750 AGGAACTAGTGCAACCTTTCCA 59.558 45.455 16.62 0.0 40.27 3.53 R
3087 4375 2.768527 TGGATGAGGAGTGATGGACTTC 59.231 50.000 0.00 0.0 33.83 3.01 R
4182 5485 2.035321 TCGTTGCCCTTTTGGACAAATC 59.965 45.455 0.00 0.0 44.07 2.17 R
5732 7050 0.033504 ACTGGACACGAAGCACGAAT 59.966 50.000 10.05 0.0 45.77 3.34 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)



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AutoCloner maintained by Alex Coulton.