Multiple sequence alignment - TraesCS6B01G286000

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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 TraesCS6B01G286000 chr6B 100.000 3835 0 0 1 3835 515072534 515068700 0.000000e+00 7083.0
1 TraesCS6B01G286000 chr6B 85.279 197 25 3 364 560 11571600 11571792 2.340000e-47 200.0
2 TraesCS6B01G286000 chr6B 79.928 279 40 13 47 314 334468634 334468361 1.410000e-44 191.0
3 TraesCS6B01G286000 chr6B 84.466 103 7 6 216 314 550784038 550784135 4.080000e-15 93.5
4 TraesCS6B01G286000 chr6B 86.747 83 8 3 10 91 176771078 176770998 5.280000e-14 89.8
5 TraesCS6B01G286000 chr6D 93.360 1988 86 29 1 1954 311542065 311544040 0.000000e+00 2898.0
6 TraesCS6B01G286000 chr6D 90.212 756 48 14 3084 3830 311545152 311545890 0.000000e+00 963.0
7 TraesCS6B01G286000 chr6D 89.961 259 19 2 2114 2370 311544210 311544463 1.030000e-85 327.0
8 TraesCS6B01G286000 chr6D 81.111 360 47 14 216 557 427121118 427121474 6.320000e-68 268.0
9 TraesCS6B01G286000 chr6D 86.161 224 23 3 2460 2682 311544520 311544736 6.410000e-58 235.0
10 TraesCS6B01G286000 chr6D 83.744 203 28 4 360 557 448560300 448560502 1.820000e-43 187.0
11 TraesCS6B01G286000 chr6A 90.879 1831 79 32 885 2699 448217208 448218966 0.000000e+00 2375.0
12 TraesCS6B01G286000 chr6A 91.508 1048 49 18 2807 3835 448218993 448220019 0.000000e+00 1406.0
13 TraesCS6B01G286000 chr4D 82.335 334 42 15 1 323 307806539 307806866 1.360000e-69 274.0
14 TraesCS6B01G286000 chr7A 83.045 289 37 9 1 287 716249890 716249612 6.360000e-63 252.0
15 TraesCS6B01G286000 chr5D 82.642 265 34 10 1 258 520584040 520584299 1.390000e-54 224.0
16 TraesCS6B01G286000 chr2B 78.652 356 59 11 216 556 39783670 39784023 1.790000e-53 220.0
17 TraesCS6B01G286000 chr2B 85.167 209 27 3 357 563 165113725 165113519 1.080000e-50 211.0
18 TraesCS6B01G286000 chr2B 75.726 379 47 23 216 554 798806901 798807274 8.580000e-32 148.0
19 TraesCS6B01G286000 chr2B 89.011 91 6 4 228 314 668006148 668006058 4.050000e-20 110.0
20 TraesCS6B01G286000 chr3B 85.047 214 26 6 357 564 712526328 712526115 3.000000e-51 213.0
21 TraesCS6B01G286000 chr3B 89.412 85 7 2 7 91 133444640 133444558 5.240000e-19 106.0
22 TraesCS6B01G286000 chr2D 84.793 217 27 6 90 301 555225489 555225274 3.000000e-51 213.0
23 TraesCS6B01G286000 chr2D 80.836 287 42 12 30 307 609634136 609634418 3.000000e-51 213.0
24 TraesCS6B01G286000 chr7D 84.804 204 24 7 56 258 65621130 65620933 8.400000e-47 198.0
25 TraesCS6B01G286000 chr7D 84.577 201 29 2 360 558 575575736 575575936 8.400000e-47 198.0
26 TraesCS6B01G286000 chr5B 84.615 195 28 2 364 556 470406504 470406310 3.910000e-45 193.0
27 TraesCS6B01G286000 chr2A 80.784 255 35 12 9 258 13078533 13078778 1.820000e-43 187.0
28 TraesCS6B01G286000 chr7B 91.954 87 6 1 4 90 579829010 579828925 1.870000e-23 121.0


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 TraesCS6B01G286000 chr6B 515068700 515072534 3834 True 7083.00 7083 100.0000 1 3835 1 chr6B.!!$R3 3834
1 TraesCS6B01G286000 chr6D 311542065 311545890 3825 False 1105.75 2898 89.9235 1 3830 4 chr6D.!!$F3 3829
2 TraesCS6B01G286000 chr6A 448217208 448220019 2811 False 1890.50 2375 91.1935 885 3835 2 chr6A.!!$F1 2950


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
395 422 0.031043 CCCAAAACGTCGAAAACCCC 59.969 55.000 0.00 0.00 0.00 4.95 F
1173 1201 1.226603 GTCCAAGTACGAGCGCGAT 60.227 57.895 19.05 1.23 41.64 4.58 F
1260 1288 1.626654 CCTACAACAGCTTCACCGCG 61.627 60.000 0.00 0.00 34.40 6.46 F
2783 2883 0.252103 AGGAAGAGGAGGTTACCGCA 60.252 55.000 7.54 0.00 34.73 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 2214 0.037326 TCCAGTTGCATCTGACGACC 60.037 55.000 23.46 0.0 37.61 4.79 R
2551 2645 0.030908 CTCCCGAATAGTCTGTCGCC 59.969 60.000 2.97 0.0 35.93 5.54 R
2788 2888 0.038343 TTAACTGTGCCCGACGGTAC 60.038 55.000 13.94 12.0 43.96 3.34 R
3687 3915 3.057033 GGAAGCATCTTGACAACAGCATT 60.057 43.478 5.02 0.0 0.00 3.56 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.