Multiple sequence alignment - TraesCS3D01G000900

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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 TraesCS3D01G000900 chr3D 100.000 2371 0 0 1 2371 509226 506856 0.000000e+00 4379.0
1 TraesCS3D01G000900 chr3D 96.774 155 4 1 2218 2371 214070508 214070662 8.410000e-65 257.0
2 TraesCS3D01G000900 chr3D 78.704 324 47 7 1891 2212 352780571 352780268 1.860000e-46 196.0
3 TraesCS3D01G000900 chr3B 91.509 1060 44 12 787 1800 6088724 6089783 0.000000e+00 1417.0
4 TraesCS3D01G000900 chr3B 92.177 294 22 1 60 353 6088095 6088387 4.710000e-112 414.0
5 TraesCS3D01G000900 chr3B 97.608 209 5 0 551 759 6088519 6088727 2.240000e-95 359.0
6 TraesCS3D01G000900 chr2B 82.423 421 48 10 1803 2222 159101435 159101830 6.270000e-91 344.0
7 TraesCS3D01G000900 chr2B 82.185 421 49 10 1803 2222 159100844 159101239 2.920000e-89 339.0
8 TraesCS3D01G000900 chr3A 84.503 342 43 8 1800 2136 689781409 689781745 1.760000e-86 329.0
9 TraesCS3D01G000900 chr3A 85.139 323 44 4 1800 2120 689657584 689657904 6.320000e-86 327.0
10 TraesCS3D01G000900 chr3A 84.830 323 45 4 1800 2120 689651548 689651868 2.940000e-84 322.0
11 TraesCS3D01G000900 chr3A 83.692 325 45 7 1800 2120 689578034 689578354 1.380000e-77 300.0
12 TraesCS3D01G000900 chr3A 82.334 317 34 5 202 506 650043043 650043349 3.020000e-64 255.0
13 TraesCS3D01G000900 chr3A 78.689 305 43 11 205 506 73631963 73631678 1.450000e-42 183.0
14 TraesCS3D01G000900 chr3A 78.599 257 33 4 250 506 73619210 73618976 1.470000e-32 150.0
15 TraesCS3D01G000900 chr3A 84.416 77 12 0 430 506 73630374 73630298 2.530000e-10 76.8
16 TraesCS3D01G000900 chr2A 80.378 423 65 6 1805 2225 670699439 670699033 2.960000e-79 305.0
17 TraesCS3D01G000900 chr2A 84.080 201 31 1 307 506 45133584 45133784 2.400000e-45 193.0
18 TraesCS3D01G000900 chr2A 81.333 150 23 3 361 510 27997936 27998080 1.490000e-22 117.0
19 TraesCS3D01G000900 chr6A 79.907 428 70 12 1803 2226 483545345 483545760 1.380000e-77 300.0
20 TraesCS3D01G000900 chr6A 77.811 338 52 9 1891 2226 611204096 611204412 1.120000e-43 187.0
21 TraesCS3D01G000900 chr5D 98.026 152 1 2 2221 2371 400022905 400022755 1.810000e-66 263.0
22 TraesCS3D01G000900 chr5D 98.649 148 1 1 2225 2371 26175191 26175044 6.500000e-66 261.0
23 TraesCS3D01G000900 chr5D 78.972 214 25 9 309 506 110353791 110353582 6.880000e-26 128.0
24 TraesCS3D01G000900 chr5D 87.013 77 8 2 2163 2238 504022493 504022568 4.200000e-13 86.1
25 TraesCS3D01G000900 chr2D 97.419 155 1 3 2220 2371 195711271 195711425 6.500000e-66 261.0
26 TraesCS3D01G000900 chr2D 98.013 151 2 1 2222 2371 363818370 363818520 6.500000e-66 261.0
27 TraesCS3D01G000900 chr2D 97.386 153 3 1 2220 2371 197850767 197850919 2.340000e-65 259.0
28 TraesCS3D01G000900 chr2D 96.795 156 3 2 2218 2371 441790756 441790601 2.340000e-65 259.0
29 TraesCS3D01G000900 chr2D 88.750 80 8 1 2147 2226 622224002 622223924 1.940000e-16 97.1
30 TraesCS3D01G000900 chr1A 81.009 337 57 6 1803 2136 548233941 548234273 6.500000e-66 261.0
31 TraesCS3D01G000900 chr1A 75.265 283 56 11 235 506 516590461 516590182 3.200000e-24 122.0
32 TraesCS3D01G000900 chr6D 96.815 157 2 2 2216 2371 25702528 25702682 2.340000e-65 259.0
33 TraesCS3D01G000900 chr6D 95.152 165 4 4 2208 2371 271274402 271274563 8.410000e-65 257.0
34 TraesCS3D01G000900 chr6D 81.081 259 30 9 235 480 354104337 354104085 3.110000e-44 189.0
35 TraesCS3D01G000900 chr6B 77.442 430 72 14 1801 2226 643788683 643788275 1.420000e-57 233.0
36 TraesCS3D01G000900 chr7A 82.014 278 38 7 201 472 278452692 278452421 2.370000e-55 226.0
37 TraesCS3D01G000900 chr4B 78.161 348 48 19 1893 2236 558724182 558723859 1.860000e-46 196.0
38 TraesCS3D01G000900 chr4B 86.667 105 9 1 235 339 24915141 24915042 6.930000e-21 111.0
39 TraesCS3D01G000900 chr5A 77.850 307 50 12 209 506 410871251 410870954 8.710000e-40 174.0
40 TraesCS3D01G000900 chr5A 85.714 77 9 2 2163 2238 631806562 631806637 1.950000e-11 80.5
41 TraesCS3D01G000900 chr5A 84.810 79 10 2 2163 2240 52853916 52853993 7.030000e-11 78.7
42 TraesCS3D01G000900 chr4D 81.951 205 19 6 308 506 14938969 14939161 8.770000e-35 158.0
43 TraesCS3D01G000900 chr4D 81.061 132 19 6 307 434 433111473 433111602 1.500000e-17 100.0
44 TraesCS3D01G000900 chr4D 86.667 75 8 2 2163 2236 421890665 421890592 5.430000e-12 82.4
45 TraesCS3D01G000900 chr7D 79.235 183 21 11 339 506 370864935 370865115 6.930000e-21 111.0
46 TraesCS3D01G000900 chr4A 79.630 162 22 5 353 506 471841068 471841226 3.220000e-19 106.0


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 TraesCS3D01G000900 chr3D 506856 509226 2370 True 4379.0 4379 100.000000 1 2371 1 chr3D.!!$R1 2370
1 TraesCS3D01G000900 chr3B 6088095 6089783 1688 False 730.0 1417 93.764667 60 1800 3 chr3B.!!$F1 1740
2 TraesCS3D01G000900 chr2B 159100844 159101830 986 False 341.5 344 82.304000 1803 2222 2 chr2B.!!$F1 419


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
759 760 0.03601 CAGGAGGTTGAATCGGCACT 60.036 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 2879 0.108186 TGCATCTTGGTGAGCGTAGG 60.108 55.0 0.0 0.0 0.0 3.18 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.