Multiple sequence alignment - TraesCS6B01G115300

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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 TraesCS6B01G115300 chr6B 100.000 3563 0 0 1 3563 100716452 100720014 0.000000e+00 6580
1 TraesCS6B01G115300 chr6B 99.263 1493 11 0 1456 2948 100760932 100762424 0.000000e+00 2697
2 TraesCS6B01G115300 chr6B 97.814 1464 10 2 1 1462 100751103 100752546 0.000000e+00 2507
3 TraesCS6B01G115300 chr6B 99.160 476 3 1 3088 3563 100762794 100763268 0.000000e+00 856
4 TraesCS6B01G115300 chr6B 83.995 881 118 19 1 864 485534712 485533838 0.000000e+00 824
5 TraesCS6B01G115300 chr6B 87.016 439 35 9 3026 3458 100893149 100893571 3.220000e-130 475
6 TraesCS6B01G115300 chr6B 91.710 193 12 3 2804 2994 100892629 100892819 7.580000e-67 265
7 TraesCS6B01G115300 chr6B 90.667 75 6 1 2741 2815 100890834 100890907 8.140000e-17 99
8 TraesCS6B01G115300 chr1A 93.243 2738 139 14 1 2737 18495811 18493119 0.000000e+00 3989
9 TraesCS6B01G115300 chr1A 92.915 2738 139 15 1 2737 518796083 518793400 0.000000e+00 3930
10 TraesCS6B01G115300 chr3A 93.202 2736 136 19 1 2734 416041434 416044121 0.000000e+00 3976
11 TraesCS6B01G115300 chr3A 81.217 756 117 21 766 1512 104460211 104460950 1.430000e-163 586
12 TraesCS6B01G115300 chr3A 86.316 190 20 5 704 889 104460243 104460430 6.030000e-48 202
13 TraesCS6B01G115300 chr3A 90.816 98 8 1 704 801 104460306 104460402 2.890000e-26 130
14 TraesCS6B01G115300 chr3D 93.875 1943 91 9 1 1941 432089804 432091720 0.000000e+00 2904
15 TraesCS6B01G115300 chr3D 84.300 293 21 11 567 857 87942951 87943220 2.730000e-66 263
16 TraesCS6B01G115300 chr3D 80.676 207 35 4 766 970 432090486 432090689 4.760000e-34 156
17 TraesCS6B01G115300 chr6D 93.674 1897 115 5 844 2737 156259401 156261295 0.000000e+00 2833
18 TraesCS6B01G115300 chr6D 92.412 1924 89 20 844 2737 156256446 156254550 0.000000e+00 2691
19 TraesCS6B01G115300 chr6A 94.617 1579 81 3 1160 2737 607382809 607384384 0.000000e+00 2442
20 TraesCS6B01G115300 chr6A 89.730 779 38 11 386 1164 607379313 607380049 0.000000e+00 957
21 TraesCS6B01G115300 chr4D 94.705 1152 56 4 1587 2737 304695349 304696496 0.000000e+00 1784
22 TraesCS6B01G115300 chr2D 87.310 1576 168 15 1140 2710 579218877 579217329 0.000000e+00 1773
23 TraesCS6B01G115300 chr2D 84.114 875 116 19 1 858 642016001 642016869 0.000000e+00 824
24 TraesCS6B01G115300 chr5B 84.114 875 116 19 1 858 565833030 565833898 0.000000e+00 824
25 TraesCS6B01G115300 chr5B 84.114 875 116 19 1 858 565905634 565906502 0.000000e+00 824
26 TraesCS6B01G115300 chr2A 85.238 210 26 5 2526 2734 294769012 294769217 1.000000e-50 211


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 TraesCS6B01G115300 chr6B 100716452 100720014 3562 False 6580.000000 6580 100.000000 1 3563 1 chr6B.!!$F1 3562
1 TraesCS6B01G115300 chr6B 100751103 100752546 1443 False 2507.000000 2507 97.814000 1 1462 1 chr6B.!!$F2 1461
2 TraesCS6B01G115300 chr6B 100760932 100763268 2336 False 1776.500000 2697 99.211500 1456 3563 2 chr6B.!!$F3 2107
3 TraesCS6B01G115300 chr6B 485533838 485534712 874 True 824.000000 824 83.995000 1 864 1 chr6B.!!$R1 863
4 TraesCS6B01G115300 chr6B 100890834 100893571 2737 False 279.666667 475 89.797667 2741 3458 3 chr6B.!!$F4 717
5 TraesCS6B01G115300 chr1A 18493119 18495811 2692 True 3989.000000 3989 93.243000 1 2737 1 chr1A.!!$R1 2736
6 TraesCS6B01G115300 chr1A 518793400 518796083 2683 True 3930.000000 3930 92.915000 1 2737 1 chr1A.!!$R2 2736
7 TraesCS6B01G115300 chr3A 416041434 416044121 2687 False 3976.000000 3976 93.202000 1 2734 1 chr3A.!!$F1 2733
8 TraesCS6B01G115300 chr3A 104460211 104460950 739 False 306.000000 586 86.116333 704 1512 3 chr3A.!!$F2 808
9 TraesCS6B01G115300 chr3D 432089804 432091720 1916 False 1530.000000 2904 87.275500 1 1941 2 chr3D.!!$F2 1940
10 TraesCS6B01G115300 chr6D 156259401 156261295 1894 False 2833.000000 2833 93.674000 844 2737 1 chr6D.!!$F1 1893
11 TraesCS6B01G115300 chr6D 156254550 156256446 1896 True 2691.000000 2691 92.412000 844 2737 1 chr6D.!!$R1 1893
12 TraesCS6B01G115300 chr6A 607379313 607384384 5071 False 1699.500000 2442 92.173500 386 2737 2 chr6A.!!$F1 2351
13 TraesCS6B01G115300 chr4D 304695349 304696496 1147 False 1784.000000 1784 94.705000 1587 2737 1 chr4D.!!$F1 1150
14 TraesCS6B01G115300 chr2D 579217329 579218877 1548 True 1773.000000 1773 87.310000 1140 2710 1 chr2D.!!$R1 1570
15 TraesCS6B01G115300 chr2D 642016001 642016869 868 False 824.000000 824 84.114000 1 858 1 chr2D.!!$F1 857
16 TraesCS6B01G115300 chr5B 565833030 565833898 868 False 824.000000 824 84.114000 1 858 1 chr5B.!!$F1 857
17 TraesCS6B01G115300 chr5B 565905634 565906502 868 False 824.000000 824 84.114000 1 858 1 chr5B.!!$F2 857

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
535 536 1.815003 GCTGGTCAAATGTGGGAAGAG 59.185 52.381 0.0 0.0 0.0 2.85 F
1608 4419 5.716703 AGTTGCCCAAATGAGCTTTTATAGT 59.283 36.000 0.0 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 4419 7.28104 AGAACTCATTTCAGCAAGAATTTCA 57.719 32.0 0.0 0.0 36.57 2.69 R
3024 7635 0.24928 AAAACCTTTTTCTGGGCGCG 60.249 50.0 0.0 0.0 0.00 6.86 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 8.821686 AGATACATGTTGTCAATGGGATTTTA 57.178 30.769 2.30 0.00 0.00 1.52
377 378 5.459536 TGTTGTGGCTTGTTGCATTATTA 57.540 34.783 0.00 0.00 45.15 0.98
535 536 1.815003 GCTGGTCAAATGTGGGAAGAG 59.185 52.381 0.00 0.00 0.00 2.85
1608 4419 5.716703 AGTTGCCCAAATGAGCTTTTATAGT 59.283 36.000 0.00 0.00 0.00 2.12
2717 5564 3.290948 TGCCCATATCCACCTTAACAC 57.709 47.619 0.00 0.00 0.00 3.32
2948 7527 2.615912 GAGCTCAAATCCAGTGCCATAC 59.384 50.000 9.40 0.00 0.00 2.39
2952 7531 4.214971 GCTCAAATCCAGTGCCATACTATG 59.785 45.833 0.00 0.00 37.60 2.23
3040 7919 3.670377 GCGCGCCCAGAAAAAGGT 61.670 61.111 23.24 0.00 0.00 3.50
3044 7923 1.497991 GCGCCCAGAAAAAGGTTTTC 58.502 50.000 0.00 5.50 0.00 2.29
3046 7925 1.497991 GCCCAGAAAAAGGTTTTCGC 58.502 50.000 7.59 2.99 33.86 4.70
3071 7950 3.643792 ACTACTCTCAGCACTTTCCAAGT 59.356 43.478 0.00 0.00 44.06 3.16
3476 8360 1.373435 CTACCAGGCAACCGGAACA 59.627 57.895 9.46 0.00 37.17 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 221 4.779993 AAGGTTGAACAACTCCTTCTCT 57.220 40.909 15.60 2.13 40.94 3.10
377 378 6.274436 ACCCCATCATTTAAAACCCAATTCTT 59.726 34.615 0.00 0.00 0.00 2.52
1608 4419 7.281040 AGAACTCATTTCAGCAAGAATTTCA 57.719 32.000 0.00 0.00 36.57 2.69
2717 5564 3.502123 TTGTGTTTGGTTAGAGGGAGG 57.498 47.619 0.00 0.00 0.00 4.30
2948 7527 3.093057 AGGTAAGATAGCCTCGCCATAG 58.907 50.000 0.00 0.00 0.00 2.23
2974 7553 3.507162 TGATTCAGAAAGCACCCTCAA 57.493 42.857 0.00 0.00 0.00 3.02
2979 7558 3.119352 GGGTCATTGATTCAGAAAGCACC 60.119 47.826 0.00 0.00 28.70 5.01
3022 7633 4.759096 CCTTTTTCTGGGCGCGCG 62.759 66.667 28.44 28.44 0.00 6.86
3023 7634 2.693250 AAACCTTTTTCTGGGCGCGC 62.693 55.000 25.94 25.94 0.00 6.86
3024 7635 0.249280 AAAACCTTTTTCTGGGCGCG 60.249 50.000 0.00 0.00 0.00 6.86
3032 7911 5.699915 AGAGTAGTAGGCGAAAACCTTTTTC 59.300 40.000 1.93 1.93 41.50 2.29
3040 7919 2.823747 TGCTGAGAGTAGTAGGCGAAAA 59.176 45.455 0.00 0.00 0.00 2.29
3044 7923 1.384525 AGTGCTGAGAGTAGTAGGCG 58.615 55.000 0.00 0.00 0.00 5.52
3046 7925 3.764434 TGGAAAGTGCTGAGAGTAGTAGG 59.236 47.826 0.00 0.00 0.00 3.18
3476 8360 2.585869 CGCGAACGTTGCACACTCT 61.586 57.895 5.00 0.00 33.53 3.24


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

AutoCloner maintained by Alex Coulton.