Multiple sequence alignment - TraesCS5D01G453800

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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 TraesCS5D01G453800 chr5D 100.000 3830 0 0 1 3830 501094735 501098564 0.000000e+00 7073.0
1 TraesCS5D01G453800 chr5A 90.237 2827 118 52 694 3421 626121322 626118555 0.000000e+00 3546.0
2 TraesCS5D01G453800 chr5A 81.299 385 30 19 219 589 626127373 626127017 1.360000e-69 274.0
3 TraesCS5D01G453800 chr5A 84.416 77 6 5 16 87 155603354 155603279 1.910000e-08 71.3
4 TraesCS5D01G453800 chr5B 94.180 2182 76 21 694 2831 622604064 622606238 0.000000e+00 3278.0
5 TraesCS5D01G453800 chr5B 85.106 517 42 15 1 490 622585986 622586494 2.660000e-136 496.0
6 TraesCS5D01G453800 chr5B 80.366 601 40 37 2837 3409 622606273 622606823 6.000000e-103 385.0
7 TraesCS5D01G453800 chr5B 92.727 55 4 0 501 555 622586583 622586637 3.170000e-11 80.5
8 TraesCS5D01G453800 chr3A 83.852 836 108 22 1061 1890 609688722 609687908 0.000000e+00 771.0
9 TraesCS5D01G453800 chr3A 82.827 757 121 4 2038 2787 609687760 609687006 0.000000e+00 669.0
10 TraesCS5D01G453800 chr3B 82.994 835 117 15 1061 1890 620455897 620455083 0.000000e+00 732.0
11 TraesCS5D01G453800 chr3B 82.034 757 127 4 2038 2787 620454935 620454181 1.500000e-178 636.0
12 TraesCS5D01G453800 chr3D 82.895 836 116 22 1061 1890 466680074 466679260 0.000000e+00 726.0
13 TraesCS5D01G453800 chr3D 82.540 756 125 5 2038 2787 466679112 466678358 0.000000e+00 658.0
14 TraesCS5D01G453800 chr7D 83.747 726 111 5 2051 2770 591813571 591812847 0.000000e+00 680.0
15 TraesCS5D01G453800 chr7B 83.426 718 110 6 2051 2762 671703011 671703725 0.000000e+00 658.0
16 TraesCS5D01G453800 chr7B 83.108 740 100 19 1138 1870 671702160 671702881 0.000000e+00 651.0
17 TraesCS5D01G453800 chr7A 82.953 745 94 27 1138 1871 727276739 727277461 3.230000e-180 641.0
18 TraesCS5D01G453800 chr7A 82.845 717 119 4 2051 2765 726605085 726604371 1.160000e-179 640.0
19 TraesCS5D01G453800 chr7A 82.048 713 124 4 2052 2762 727277588 727278298 4.230000e-169 604.0
20 TraesCS5D01G453800 chr4B 80.590 814 124 20 1078 1874 20001277 20002073 7.080000e-167 597.0
21 TraesCS5D01G453800 chr4A 80.242 825 120 27 1070 1874 593289929 593289128 7.130000e-162 580.0
22 TraesCS5D01G453800 chr6D 87.747 253 24 2 3553 3805 467790328 467790573 4.840000e-74 289.0
23 TraesCS5D01G453800 chr1D 82.353 68 12 0 9 76 198740141 198740074 4.130000e-05 60.2
24 TraesCS5D01G453800 chr2D 96.970 33 1 0 17 49 636480251 636480219 5.350000e-04 56.5


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 TraesCS5D01G453800 chr5D 501094735 501098564 3829 False 7073.00 7073 100.0000 1 3830 1 chr5D.!!$F1 3829
1 TraesCS5D01G453800 chr5A 626118555 626121322 2767 True 3546.00 3546 90.2370 694 3421 1 chr5A.!!$R2 2727
2 TraesCS5D01G453800 chr5B 622604064 622606823 2759 False 1831.50 3278 87.2730 694 3409 2 chr5B.!!$F2 2715
3 TraesCS5D01G453800 chr5B 622585986 622586637 651 False 288.25 496 88.9165 1 555 2 chr5B.!!$F1 554
4 TraesCS5D01G453800 chr3A 609687006 609688722 1716 True 720.00 771 83.3395 1061 2787 2 chr3A.!!$R1 1726
5 TraesCS5D01G453800 chr3B 620454181 620455897 1716 True 684.00 732 82.5140 1061 2787 2 chr3B.!!$R1 1726
6 TraesCS5D01G453800 chr3D 466678358 466680074 1716 True 692.00 726 82.7175 1061 2787 2 chr3D.!!$R1 1726
7 TraesCS5D01G453800 chr7D 591812847 591813571 724 True 680.00 680 83.7470 2051 2770 1 chr7D.!!$R1 719
8 TraesCS5D01G453800 chr7B 671702160 671703725 1565 False 654.50 658 83.2670 1138 2762 2 chr7B.!!$F1 1624
9 TraesCS5D01G453800 chr7A 726604371 726605085 714 True 640.00 640 82.8450 2051 2765 1 chr7A.!!$R1 714
10 TraesCS5D01G453800 chr7A 727276739 727278298 1559 False 622.50 641 82.5005 1138 2762 2 chr7A.!!$F1 1624
11 TraesCS5D01G453800 chr4B 20001277 20002073 796 False 597.00 597 80.5900 1078 1874 1 chr4B.!!$F1 796
12 TraesCS5D01G453800 chr4A 593289128 593289929 801 True 580.00 580 80.2420 1070 1874 1 chr4A.!!$R1 804


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
276 307 0.111061 AGGAACACCAGCAAGCATCA 59.889 50.0 0.00 0.00 0.0 3.07 F
1987 2176 0.529119 AAAAACAGAGGACGCGACGT 60.529 50.0 15.93 8.78 45.1 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2214 2.126463 CTGCTCGAAGACGGCGAA 60.126 61.111 16.62 0.0 37.32 4.70 R
3790 4113 0.032952 GGCCTAAGTGTGTCGTGTCA 59.967 55.000 0.00 0.0 0.00 3.58 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.