Multiple sequence alignment - TraesCS6A01G051200

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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 TraesCS6A01G051200 chr6A 100.000 3488 0 0 1 3488 26716967 26720454 0.000000e+00 6442.0
1 TraesCS6A01G051200 chr6A 89.796 1568 145 11 964 2525 26734196 26735754 0.000000e+00 1995.0
2 TraesCS6A01G051200 chr6A 84.000 100 10 6 3333 3428 40221021 40220924 1.330000e-14 91.6
3 TraesCS6A01G051200 chr6B 93.490 1782 101 7 854 2634 46092710 46094477 0.000000e+00 2634.0
4 TraesCS6A01G051200 chr6B 92.265 1603 116 6 1036 2638 46072335 46073929 0.000000e+00 2266.0
5 TraesCS6A01G051200 chr6B 89.954 1533 151 1 993 2522 45983437 45984969 0.000000e+00 1975.0
6 TraesCS6A01G051200 chr6B 87.753 1682 171 22 855 2525 46390063 46391720 0.000000e+00 1932.0
7 TraesCS6A01G051200 chr6B 90.185 540 50 3 2162 2701 46081997 46082533 0.000000e+00 701.0
8 TraesCS6A01G051200 chr6B 91.019 412 37 0 1036 1447 46026758 46027169 1.090000e-154 556.0
9 TraesCS6A01G051200 chr6B 85.287 435 37 16 3060 3488 46082541 46082954 1.160000e-114 424.0
10 TraesCS6A01G051200 chr6B 89.492 295 26 5 3061 3354 46094589 46094879 5.500000e-98 368.0
11 TraesCS6A01G051200 chr6B 88.535 157 11 2 2020 2169 46074173 46074329 2.140000e-42 183.0
12 TraesCS6A01G051200 chr6B 88.889 144 9 1 609 752 46092577 46092713 1.660000e-38 171.0
13 TraesCS6A01G051200 chrUn 88.705 1629 151 17 907 2525 95385239 95386844 0.000000e+00 1958.0
14 TraesCS6A01G051200 chrUn 83.051 118 15 5 747 861 63620316 63620201 6.160000e-18 102.0
15 TraesCS6A01G051200 chr7D 95.183 602 28 1 1 601 126541078 126540477 0.000000e+00 950.0
16 TraesCS6A01G051200 chr7D 90.741 108 10 0 749 856 60693479 60693372 1.010000e-30 145.0
17 TraesCS6A01G051200 chr7D 81.416 113 18 3 749 859 35050741 35050630 4.800000e-14 89.8
18 TraesCS6A01G051200 chr4A 94.527 603 30 3 1 601 613656512 613655911 0.000000e+00 928.0
19 TraesCS6A01G051200 chr4A 93.023 602 41 1 1 601 163647651 163648252 0.000000e+00 878.0
20 TraesCS6A01G051200 chr1D 94.020 602 31 3 1 601 426614652 426614055 0.000000e+00 907.0
21 TraesCS6A01G051200 chr1D 89.560 364 38 0 2698 3061 343523090 343523453 2.450000e-126 462.0
22 TraesCS6A01G051200 chr1D 89.160 369 35 2 2694 3061 210582789 210583153 4.100000e-124 455.0
23 TraesCS6A01G051200 chr1D 88.770 374 38 2 2694 3066 419639054 419639424 4.100000e-124 455.0
24 TraesCS6A01G051200 chr1A 93.688 602 37 1 1 601 519996863 519997464 0.000000e+00 900.0
25 TraesCS6A01G051200 chr3A 93.909 591 35 1 12 601 237408597 237408007 0.000000e+00 891.0
26 TraesCS6A01G051200 chr3A 89.835 364 35 2 2699 3061 432235463 432235825 1.900000e-127 466.0
27 TraesCS6A01G051200 chr3A 88.235 119 12 2 749 866 511066845 511066728 1.310000e-29 141.0
28 TraesCS6A01G051200 chr2A 93.570 591 37 1 12 601 519857072 519857662 0.000000e+00 880.0
29 TraesCS6A01G051200 chr2A 92.691 602 43 1 1 601 112868395 112868996 0.000000e+00 867.0
30 TraesCS6A01G051200 chr2A 88.889 108 11 1 749 855 590983403 590983510 7.860000e-27 132.0
31 TraesCS6A01G051200 chr5A 92.751 607 42 2 1 605 565257038 565257644 0.000000e+00 876.0
32 TraesCS6A01G051200 chr5A 90.826 109 8 2 748 855 621222428 621222321 1.010000e-30 145.0
33 TraesCS6A01G051200 chr5A 82.667 75 9 3 3362 3436 665442783 665442853 2.910000e-06 63.9
34 TraesCS6A01G051200 chr6D 90.164 366 35 1 2697 3061 464399673 464399308 3.150000e-130 475.0
35 TraesCS6A01G051200 chr6D 89.617 366 34 2 2697 3061 449666017 449665655 2.450000e-126 462.0
36 TraesCS6A01G051200 chr4D 89.160 369 39 1 2694 3061 102158699 102159067 3.170000e-125 459.0
37 TraesCS6A01G051200 chr4B 89.589 365 33 4 2698 3061 135874156 135874516 3.170000e-125 459.0
38 TraesCS6A01G051200 chr2D 89.160 369 34 4 2697 3064 113605541 113605178 4.100000e-124 455.0
39 TraesCS6A01G051200 chr5B 84.259 108 16 1 749 855 426512663 426512770 1.710000e-18 104.0


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 TraesCS6A01G051200 chr6A 26716967 26720454 3487 False 6442.000000 6442 100.000000 1 3488 1 chr6A.!!$F1 3487
1 TraesCS6A01G051200 chr6A 26734196 26735754 1558 False 1995.000000 1995 89.796000 964 2525 1 chr6A.!!$F2 1561
2 TraesCS6A01G051200 chr6B 45983437 45984969 1532 False 1975.000000 1975 89.954000 993 2522 1 chr6B.!!$F1 1529
3 TraesCS6A01G051200 chr6B 46390063 46391720 1657 False 1932.000000 1932 87.753000 855 2525 1 chr6B.!!$F3 1670
4 TraesCS6A01G051200 chr6B 46072335 46074329 1994 False 1224.500000 2266 90.400000 1036 2638 2 chr6B.!!$F4 1602
5 TraesCS6A01G051200 chr6B 46092577 46094879 2302 False 1057.666667 2634 90.623667 609 3354 3 chr6B.!!$F6 2745
6 TraesCS6A01G051200 chr6B 46081997 46082954 957 False 562.500000 701 87.736000 2162 3488 2 chr6B.!!$F5 1326
7 TraesCS6A01G051200 chrUn 95385239 95386844 1605 False 1958.000000 1958 88.705000 907 2525 1 chrUn.!!$F1 1618
8 TraesCS6A01G051200 chr7D 126540477 126541078 601 True 950.000000 950 95.183000 1 601 1 chr7D.!!$R3 600
9 TraesCS6A01G051200 chr4A 613655911 613656512 601 True 928.000000 928 94.527000 1 601 1 chr4A.!!$R1 600
10 TraesCS6A01G051200 chr4A 163647651 163648252 601 False 878.000000 878 93.023000 1 601 1 chr4A.!!$F1 600
11 TraesCS6A01G051200 chr1D 426614055 426614652 597 True 907.000000 907 94.020000 1 601 1 chr1D.!!$R1 600
12 TraesCS6A01G051200 chr1A 519996863 519997464 601 False 900.000000 900 93.688000 1 601 1 chr1A.!!$F1 600
13 TraesCS6A01G051200 chr3A 237408007 237408597 590 True 891.000000 891 93.909000 12 601 1 chr3A.!!$R1 589
14 TraesCS6A01G051200 chr2A 519857072 519857662 590 False 880.000000 880 93.570000 12 601 1 chr2A.!!$F2 589
15 TraesCS6A01G051200 chr2A 112868395 112868996 601 False 867.000000 867 92.691000 1 601 1 chr2A.!!$F1 600
16 TraesCS6A01G051200 chr5A 565257038 565257644 606 False 876.000000 876 92.751000 1 605 1 chr5A.!!$F1 604


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
729 731 0.038343 TTGTCCGGCCGTAGTACAAC 60.038 55.0 26.12 10.4 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2675 2821 0.111061 TCCACTCAAGGCACATTGCT 59.889 50.0 0.0 0.0 44.28 3.91 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.