Multiple sequence alignment - TraesCS1A01G328100

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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 TraesCS1A01G328100 chr1A 100.000 2732 0 0 1 2732 517397066 517399797 0.000000e+00 5046.0
1 TraesCS1A01G328100 chr1D 88.058 1231 45 43 820 2031 421021252 421022399 0.000000e+00 1365.0
2 TraesCS1A01G328100 chr1D 83.667 649 38 29 2103 2731 421022555 421023155 1.430000e-152 549.0
3 TraesCS1A01G328100 chr1D 77.891 294 44 16 49 329 321677183 321676898 2.180000e-36 163.0
4 TraesCS1A01G328100 chr1D 97.872 47 1 0 1 47 421021181 421021227 6.270000e-12 82.4
5 TraesCS1A01G328100 chr1B 88.832 1164 55 32 895 2028 570023176 570024294 0.000000e+00 1360.0
6 TraesCS1A01G328100 chr1B 92.308 312 12 4 2103 2402 570024500 570024811 1.500000e-117 433.0
7 TraesCS1A01G328100 chr1B 84.170 259 33 6 538 791 502239316 502239571 7.560000e-61 244.0
8 TraesCS1A01G328100 chr1B 86.977 215 19 3 2526 2731 570025061 570025275 1.640000e-57 233.0
9 TraesCS1A01G328100 chr3B 86.517 356 41 7 438 790 555075190 555075541 4.270000e-103 385.0
10 TraesCS1A01G328100 chr3B 90.110 91 8 1 174 264 555065257 555065346 1.720000e-22 117.0
11 TraesCS1A01G328100 chr3B 81.699 153 16 8 281 432 555075095 555075236 1.720000e-22 117.0
12 TraesCS1A01G328100 chr7D 84.341 364 42 11 432 790 543586240 543586593 2.610000e-90 342.0
13 TraesCS1A01G328100 chr4D 81.910 398 50 9 49 425 152692730 152693126 1.580000e-82 316.0
14 TraesCS1A01G328100 chr4A 90.598 234 20 1 191 424 468762051 468762282 2.640000e-80 309.0
15 TraesCS1A01G328100 chr4A 88.172 93 9 2 174 266 468761963 468762053 2.880000e-20 110.0
16 TraesCS1A01G328100 chr6B 81.440 361 48 8 432 790 141626315 141625972 7.450000e-71 278.0
17 TraesCS1A01G328100 chr6B 79.775 178 31 5 610 785 180937480 180937306 1.030000e-24 124.0
18 TraesCS1A01G328100 chr6B 77.838 185 35 5 609 790 542915857 542916038 2.880000e-20 110.0
19 TraesCS1A01G328100 chr3D 80.930 215 34 6 564 775 263987618 263987828 2.180000e-36 163.0
20 TraesCS1A01G328100 chr2D 80.220 182 31 4 612 791 625130159 625129981 6.140000e-27 132.0
21 TraesCS1A01G328100 chr4B 73.418 237 52 10 557 788 504827864 504828094 8.110000e-11 78.7


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 TraesCS1A01G328100 chr1A 517397066 517399797 2731 False 5046.000000 5046 100.000000 1 2732 1 chr1A.!!$F1 2731
1 TraesCS1A01G328100 chr1D 421021181 421023155 1974 False 665.466667 1365 89.865667 1 2731 3 chr1D.!!$F1 2730
2 TraesCS1A01G328100 chr1B 570023176 570025275 2099 False 675.333333 1360 89.372333 895 2731 3 chr1B.!!$F2 1836


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
667 668 0.03254 CATACCCGTACCCGCCTAAC 59.967 60.0 0.0 0.0 0.0 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1936 0.036577 GTGCAGTGCAGTGGAGATCT 60.037 55.0 20.42 0.0 40.08 2.75 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.