Multiple sequence alignment - TraesCS6A01G017700

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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 TraesCS6A01G017700 chr6A 100.000 2507 0 0 1 2507 8711903 8714409 0.000000e+00 4630.0
1 TraesCS6A01G017700 chr6A 87.598 2032 163 30 48 2029 8624821 8622829 0.000000e+00 2274.0
2 TraesCS6A01G017700 chr6A 79.260 1244 215 36 313 1532 35581638 35580414 0.000000e+00 828.0
3 TraesCS6A01G017700 chr6A 79.823 679 126 10 860 1532 9572511 9573184 3.750000e-133 484.0
4 TraesCS6A01G017700 chr6A 88.750 80 9 0 1892 1971 30558758 30558679 5.710000e-17 99.0
5 TraesCS6A01G017700 chr6A 97.674 43 0 1 2268 2310 8614460 8614419 3.460000e-09 73.1
6 TraesCS6A01G017700 chr6D 90.285 1791 134 19 263 2029 8147284 8145510 0.000000e+00 2307.0
7 TraesCS6A01G017700 chr6D 87.956 1727 152 33 339 2030 8249774 8251479 0.000000e+00 1986.0
8 TraesCS6A01G017700 chr6D 80.597 1474 224 41 90 1532 8245222 8246664 0.000000e+00 1081.0
9 TraesCS6A01G017700 chr6D 79.607 1221 213 28 330 1532 8967563 8968765 0.000000e+00 843.0
10 TraesCS6A01G017700 chr6D 78.820 1237 215 37 321 1532 7885716 7886930 0.000000e+00 789.0
11 TraesCS6A01G017700 chr6D 78.679 1196 214 32 339 1514 8552807 8551633 0.000000e+00 758.0
12 TraesCS6A01G017700 chr6D 90.704 398 19 2 2041 2438 8258319 8258698 4.780000e-142 514.0
13 TraesCS6A01G017700 chr6D 79.937 633 119 8 883 1511 14518180 14518808 2.270000e-125 459.0
14 TraesCS6A01G017700 chr6B 87.517 1514 126 24 194 1681 15115836 15114360 0.000000e+00 1690.0
15 TraesCS6A01G017700 chr6B 89.593 1230 115 9 313 1532 21458671 21459897 0.000000e+00 1550.0
16 TraesCS6A01G017700 chr6B 77.787 1202 230 32 329 1509 15744098 15742913 0.000000e+00 706.0
17 TraesCS6A01G017700 chr6B 77.750 1200 220 37 339 1514 52981060 52979884 0.000000e+00 693.0
18 TraesCS6A01G017700 chr6B 92.949 312 19 3 1719 2029 15114362 15114053 3.800000e-123 451.0
19 TraesCS6A01G017700 chr6B 84.677 124 13 3 1904 2025 15297699 15297580 4.380000e-23 119.0
20 TraesCS6A01G017700 chr7D 79.043 1212 215 31 331 1525 161390632 161391821 0.000000e+00 795.0
21 TraesCS6A01G017700 chr4D 84.024 169 18 5 2102 2263 3235175 3235341 1.200000e-33 154.0
22 TraesCS6A01G017700 chr4B 79.803 203 24 9 2102 2297 2686693 2686501 5.630000e-27 132.0
23 TraesCS6A01G017700 chr4A 84.211 133 18 2 2117 2246 602337332 602337200 2.620000e-25 126.0
24 TraesCS6A01G017700 chr4A 92.958 71 5 0 2436 2506 318044418 318044488 1.230000e-18 104.0
25 TraesCS6A01G017700 chr1A 95.588 68 3 0 2440 2507 57407736 57407803 2.640000e-20 110.0
26 TraesCS6A01G017700 chr1A 91.045 67 6 0 2440 2506 475411191 475411125 9.550000e-15 91.6
27 TraesCS6A01G017700 chr1A 94.737 57 3 0 2450 2506 475313288 475313232 3.430000e-14 89.8
28 TraesCS6A01G017700 chr7A 91.304 69 4 1 2440 2506 681522554 681522622 2.660000e-15 93.5
29 TraesCS6A01G017700 chr2A 89.706 68 7 0 2440 2507 371013052 371012985 1.240000e-13 87.9
30 TraesCS6A01G017700 chr5A 88.406 69 7 1 2440 2507 700597523 700597591 5.750000e-12 82.4
31 TraesCS6A01G017700 chr3B 85.714 70 6 4 2440 2507 766825698 766825631 1.240000e-08 71.3
32 TraesCS6A01G017700 chr3A 84.211 76 7 5 2435 2507 233696349 233696276 4.470000e-08 69.4


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 TraesCS6A01G017700 chr6A 8711903 8714409 2506 False 4630.0 4630 100.0000 1 2507 1 chr6A.!!$F1 2506
1 TraesCS6A01G017700 chr6A 8622829 8624821 1992 True 2274.0 2274 87.5980 48 2029 1 chr6A.!!$R2 1981
2 TraesCS6A01G017700 chr6A 35580414 35581638 1224 True 828.0 828 79.2600 313 1532 1 chr6A.!!$R4 1219
3 TraesCS6A01G017700 chr6A 9572511 9573184 673 False 484.0 484 79.8230 860 1532 1 chr6A.!!$F2 672
4 TraesCS6A01G017700 chr6D 8145510 8147284 1774 True 2307.0 2307 90.2850 263 2029 1 chr6D.!!$R1 1766
5 TraesCS6A01G017700 chr6D 8245222 8251479 6257 False 1533.5 1986 84.2765 90 2030 2 chr6D.!!$F5 1940
6 TraesCS6A01G017700 chr6D 8967563 8968765 1202 False 843.0 843 79.6070 330 1532 1 chr6D.!!$F3 1202
7 TraesCS6A01G017700 chr6D 7885716 7886930 1214 False 789.0 789 78.8200 321 1532 1 chr6D.!!$F1 1211
8 TraesCS6A01G017700 chr6D 8551633 8552807 1174 True 758.0 758 78.6790 339 1514 1 chr6D.!!$R2 1175
9 TraesCS6A01G017700 chr6D 14518180 14518808 628 False 459.0 459 79.9370 883 1511 1 chr6D.!!$F4 628
10 TraesCS6A01G017700 chr6B 21458671 21459897 1226 False 1550.0 1550 89.5930 313 1532 1 chr6B.!!$F1 1219
11 TraesCS6A01G017700 chr6B 15114053 15115836 1783 True 1070.5 1690 90.2330 194 2029 2 chr6B.!!$R4 1835
12 TraesCS6A01G017700 chr6B 15742913 15744098 1185 True 706.0 706 77.7870 329 1509 1 chr6B.!!$R2 1180
13 TraesCS6A01G017700 chr6B 52979884 52981060 1176 True 693.0 693 77.7500 339 1514 1 chr6B.!!$R3 1175
14 TraesCS6A01G017700 chr7D 161390632 161391821 1189 False 795.0 795 79.0430 331 1525 1 chr7D.!!$F1 1194


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
21 22 0.305922 GCGGATCCAAATGAAGAGCG 59.694 55.0 13.41 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 6273 1.066573 CAACTGGCCAACAACAAACCA 60.067 47.619 7.01 0.0 0.0 3.67 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.