Multiple sequence alignment - TraesCS5D01G542900

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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 TraesCS5D01G542900 chr5D 100.000 2479 0 0 1 2479 553422987 553420509 0.000000e+00 4578.0
1 TraesCS5D01G542900 chr5D 90.445 1057 62 16 950 1989 553002684 553001650 0.000000e+00 1356.0
2 TraesCS5D01G542900 chr5D 94.970 656 23 4 1 647 553003714 553003060 0.000000e+00 1020.0
3 TraesCS5D01G542900 chr5D 92.508 307 20 3 1758 2063 553420928 553420624 1.050000e-118 436.0
4 TraesCS5D01G542900 chr5D 92.508 307 20 3 2060 2364 553421230 553420925 1.050000e-118 436.0
5 TraesCS5D01G542900 chr5D 93.960 149 4 2 693 836 553003064 553002916 1.150000e-53 220.0
6 TraesCS5D01G542900 chr5D 74.603 441 76 24 950 1360 553462894 553463328 7.100000e-36 161.0
7 TraesCS5D01G542900 chr5D 75.703 391 51 21 1001 1364 553010143 553009770 3.300000e-34 156.0
8 TraesCS5D01G542900 chr5D 95.506 89 4 0 862 950 553002854 553002766 2.570000e-30 143.0
9 TraesCS5D01G542900 chr5D 94.937 79 4 0 2286 2364 553001531 553001453 9.310000e-25 124.0
10 TraesCS5D01G542900 chr5D 87.037 108 12 2 2372 2477 443339408 443339515 1.200000e-23 121.0
11 TraesCS5D01G542900 chr5D 75.824 273 44 12 1106 1364 553464880 553464616 4.330000e-23 119.0
12 TraesCS5D01G542900 chr5D 88.542 96 10 1 2383 2477 443333680 443333775 5.600000e-22 115.0
13 TraesCS5D01G542900 chr5D 91.250 80 7 0 1985 2064 553001531 553001452 2.610000e-20 110.0
14 TraesCS5D01G542900 chr5D 80.380 158 17 5 1101 1247 553468250 553468096 9.380000e-20 108.0
15 TraesCS5D01G542900 chr4A 76.607 389 49 19 1003 1364 615117654 615118027 2.530000e-40 176.0
16 TraesCS5D01G542900 chr3D 92.079 101 6 2 2378 2477 586302375 586302276 9.240000e-30 141.0
17 TraesCS5D01G542900 chr3D 90.625 96 8 1 2381 2475 357730262 357730357 2.590000e-25 126.0
18 TraesCS5D01G542900 chrUn 92.708 96 6 1 2383 2477 22759827 22759732 1.200000e-28 137.0
19 TraesCS5D01G542900 chr5B 91.837 98 7 1 2381 2477 462116205 462116302 4.300000e-28 135.0
20 TraesCS5D01G542900 chr5B 76.793 237 34 10 1001 1228 697493443 697493667 2.020000e-21 113.0
21 TraesCS5D01G542900 chr5B 82.946 129 13 4 1106 1228 697349242 697349367 9.380000e-20 108.0
22 TraesCS5D01G542900 chr2D 91.667 96 7 1 2383 2477 381559879 381559974 5.560000e-27 132.0
23 TraesCS5D01G542900 chr2D 95.122 41 2 0 862 902 45565535 45565575 5.720000e-07 65.8
24 TraesCS5D01G542900 chr1B 88.235 102 10 2 2378 2477 589076047 589076148 1.200000e-23 121.0
25 TraesCS5D01G542900 chr3B 87.755 98 11 1 2381 2477 685819007 685819104 2.020000e-21 113.0
26 TraesCS5D01G542900 chr6A 95.652 46 2 0 862 907 100300455 100300500 9.510000e-10 75.0
27 TraesCS5D01G542900 chr6A 97.561 41 1 0 862 902 100300554 100300514 1.230000e-08 71.3
28 TraesCS5D01G542900 chr2A 97.674 43 1 0 860 902 715416534 715416576 9.510000e-10 75.0
29 TraesCS5D01G542900 chr4D 97.561 41 1 0 862 902 465124193 465124153 1.230000e-08 71.3
30 TraesCS5D01G542900 chr4B 97.561 41 1 0 862 902 581904239 581904279 1.230000e-08 71.3
31 TraesCS5D01G542900 chr7D 95.349 43 2 0 862 904 100233211 100233169 4.420000e-08 69.4
32 TraesCS5D01G542900 chr2B 95.238 42 2 0 861 902 184776815 184776856 1.590000e-07 67.6
33 TraesCS5D01G542900 chr7B 97.297 37 1 0 125 161 701866902 701866938 2.060000e-06 63.9


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 TraesCS5D01G542900 chr5D 553420509 553422987 2478 True 1816.666667 4578 95.005333 1 2479 3 chr5D.!!$R3 2478
1 TraesCS5D01G542900 chr5D 553001452 553003714 2262 True 495.500000 1356 93.511333 1 2364 6 chr5D.!!$R2 2363


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
945 995 0.17895 TCCAGCACCTCTGTCAGTCT 60.179 55.0 0.0 0.0 41.25 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2201 0.112218 TTGGAGTGGGGACATGTTGG 59.888 55.0 0.0 0.0 46.14 3.77 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.