Multiple sequence alignment - TraesCS5A01G418600

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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 TraesCS5A01G418600 chr5A 100.000 2775 0 0 1 2775 606525205 606527979 0.000000e+00 5125.0
1 TraesCS5A01G418600 chr5A 85.939 1017 69 32 957 1958 606460719 606461676 0.000000e+00 1018.0
2 TraesCS5A01G418600 chr5A 85.020 741 72 19 2025 2736 606461675 606462405 0.000000e+00 717.0
3 TraesCS5A01G418600 chr5A 78.131 503 77 19 1087 1559 606306986 606307485 3.500000e-74 289.0
4 TraesCS5A01G418600 chr5A 93.197 147 10 0 664 810 606460558 606460704 1.670000e-52 217.0
5 TraesCS5A01G418600 chr5A 92.742 124 7 2 370 492 606460050 606460172 7.900000e-41 178.0
6 TraesCS5A01G418600 chr5A 93.396 106 3 4 390 492 606486636 606486740 1.330000e-33 154.0
7 TraesCS5A01G418600 chr5A 77.340 203 32 10 808 1003 606306740 606306935 1.050000e-19 108.0
8 TraesCS5A01G418600 chr5D 89.462 1860 143 28 951 2775 485268063 485269904 0.000000e+00 2300.0
9 TraesCS5A01G418600 chr5D 94.138 1177 57 7 753 1925 485294140 485295308 0.000000e+00 1781.0
10 TraesCS5A01G418600 chr5D 88.902 847 59 8 664 1497 485266841 485267665 0.000000e+00 1011.0
11 TraesCS5A01G418600 chr5D 74.154 650 112 33 808 1437 484973762 484974375 4.650000e-53 219.0
12 TraesCS5A01G418600 chr5D 92.143 140 10 1 353 492 485163196 485163334 2.180000e-46 196.0
13 TraesCS5A01G418600 chr5B 88.075 1174 93 26 664 1812 596903856 596905007 0.000000e+00 1349.0
14 TraesCS5A01G418600 chr5B 91.950 323 14 5 519 838 596880339 596880652 2.540000e-120 442.0
15 TraesCS5A01G418600 chr5B 91.200 250 19 3 2016 2264 596905186 596905433 1.230000e-88 337.0
16 TraesCS5A01G418600 chr5B 77.886 615 73 25 1093 1662 596439068 596438472 9.590000e-85 324.0
17 TraesCS5A01G418600 chr5B 90.503 179 14 3 38 214 596901223 596901400 1.660000e-57 233.0
18 TraesCS5A01G418600 chr5B 92.157 51 4 0 1277 1327 596438731 596438681 3.830000e-09 73.1
19 TraesCS5A01G418600 chr5B 95.455 44 2 0 449 492 596901554 596901597 1.380000e-08 71.3
20 TraesCS5A01G418600 chr6A 89.516 124 8 4 2300 2421 582923881 582923761 4.790000e-33 152.0
21 TraesCS5A01G418600 chr3B 89.431 123 10 3 2300 2421 49677506 49677386 4.790000e-33 152.0
22 TraesCS5A01G418600 chr6B 89.256 121 11 2 2302 2421 534229398 534229279 1.720000e-32 150.0
23 TraesCS5A01G418600 chr1D 89.256 121 9 4 2300 2417 108102211 108102330 6.190000e-32 148.0
24 TraesCS5A01G418600 chr1D 81.609 87 12 4 252 334 50915208 50915294 4.960000e-08 69.4
25 TraesCS5A01G418600 chr1A 88.710 124 10 4 2297 2418 111124571 111124692 6.190000e-32 148.0
26 TraesCS5A01G418600 chr7B 88.000 125 11 4 2300 2421 548112877 548113000 8.010000e-31 145.0
27 TraesCS5A01G418600 chr6D 87.903 124 12 3 213 334 174403688 174403810 2.880000e-30 143.0
28 TraesCS5A01G418600 chr6D 80.682 88 11 6 252 334 123059412 123059326 2.310000e-06 63.9
29 TraesCS5A01G418600 chr3D 87.903 124 12 3 213 334 468635783 468635905 2.880000e-30 143.0
30 TraesCS5A01G418600 chr2D 87.805 123 10 5 2302 2421 590031415 590031535 3.730000e-29 139.0
31 TraesCS5A01G418600 chr2D 87.097 124 13 3 213 334 614638521 614638399 1.340000e-28 137.0
32 TraesCS5A01G418600 chr7A 86.777 121 14 2 2302 2421 439487520 439487401 1.730000e-27 134.0
33 TraesCS5A01G418600 chr1B 81.897 116 14 6 222 334 278705222 278705111 1.060000e-14 91.6
34 TraesCS5A01G418600 chr4B 87.302 63 5 3 275 334 561171038 561170976 4.960000e-08 69.4
35 TraesCS5A01G418600 chr4D 82.895 76 11 2 252 325 103256451 103256376 1.780000e-07 67.6


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 TraesCS5A01G418600 chr5A 606525205 606527979 2774 False 5125.000 5125 100.00000 1 2775 1 chr5A.!!$F2 2774
1 TraesCS5A01G418600 chr5A 606460050 606462405 2355 False 532.500 1018 89.22450 370 2736 4 chr5A.!!$F4 2366
2 TraesCS5A01G418600 chr5D 485294140 485295308 1168 False 1781.000 1781 94.13800 753 1925 1 chr5D.!!$F3 1172
3 TraesCS5A01G418600 chr5D 485266841 485269904 3063 False 1655.500 2300 89.18200 664 2775 2 chr5D.!!$F4 2111
4 TraesCS5A01G418600 chr5D 484973762 484974375 613 False 219.000 219 74.15400 808 1437 1 chr5D.!!$F1 629
5 TraesCS5A01G418600 chr5B 596901223 596905433 4210 False 497.575 1349 91.30825 38 2264 4 chr5B.!!$F2 2226


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
248 251 0.025001 CGACGCTTTCACTTATGCCG 59.975 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 5467 0.322997 CGCCCCACTCCATTGGTTAA 60.323 55.0 1.86 0.0 34.44 2.01 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.