Multiple sequence alignment - TraesCS3A01G170000

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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 TraesCS3A01G170000 chr3A 100.000 2771 0 0 1 2771 178131215 178133985 0.000000e+00 5118.0
1 TraesCS3A01G170000 chr3A 86.550 171 18 5 2148 2317 582283208 582283374 1.700000e-42 183.0
2 TraesCS3A01G170000 chr3D 93.268 1946 106 9 22 1945 152557678 152555736 0.000000e+00 2844.0
3 TraesCS3A01G170000 chr3D 89.078 412 27 3 2021 2414 152555740 152555329 1.920000e-136 496.0
4 TraesCS3A01G170000 chr3D 86.740 362 21 8 2435 2771 152555333 152554974 7.240000e-101 377.0
5 TraesCS3A01G170000 chr3D 89.677 155 15 1 2155 2309 288550611 288550458 2.180000e-46 196.0
6 TraesCS3A01G170000 chr3B 95.891 1728 54 11 230 1949 223038039 223036321 0.000000e+00 2782.0
7 TraesCS3A01G170000 chr3B 93.077 780 30 8 2009 2771 223036229 223035457 0.000000e+00 1120.0
8 TraesCS3A01G170000 chr3B 87.264 212 20 5 30 235 223038299 223038089 4.610000e-58 235.0
9 TraesCS3A01G170000 chr3B 93.182 88 6 0 1936 2023 394954547 394954634 2.240000e-26 130.0
10 TraesCS3A01G170000 chr3B 87.059 85 11 0 1938 2022 25057610 25057526 2.270000e-16 97.1
11 TraesCS3A01G170000 chr4D 89.744 156 15 1 2155 2310 74079351 74079505 6.050000e-47 198.0
12 TraesCS3A01G170000 chr7D 89.744 156 13 3 2155 2309 454079077 454079230 2.180000e-46 196.0
13 TraesCS3A01G170000 chr7D 84.270 89 14 0 1935 2023 613328367 613328455 1.370000e-13 87.9
14 TraesCS3A01G170000 chr7D 97.222 36 1 0 2735 2770 535728030 535727995 8.290000e-06 62.1
15 TraesCS3A01G170000 chr5B 89.677 155 14 2 2155 2309 299602375 299602223 2.180000e-46 196.0
16 TraesCS3A01G170000 chr5B 83.516 91 13 2 1934 2023 472940440 472940351 1.770000e-12 84.2
17 TraesCS3A01G170000 chr1D 89.677 155 15 1 2155 2309 193504383 193504536 2.180000e-46 196.0
18 TraesCS3A01G170000 chr1D 89.888 89 8 1 1935 2023 464733131 464733218 2.260000e-21 113.0
19 TraesCS3A01G170000 chr5A 86.207 174 16 8 2138 2309 86662004 86662171 6.100000e-42 182.0
20 TraesCS3A01G170000 chr4A 88.636 88 9 1 1935 2022 585459851 585459937 3.770000e-19 106.0
21 TraesCS3A01G170000 chr4A 86.364 88 12 0 1935 2022 739709959 739709872 2.270000e-16 97.1
22 TraesCS3A01G170000 chr4A 86.364 88 12 0 1935 2022 742105451 742105364 2.270000e-16 97.1
23 TraesCS3A01G170000 chr4A 84.444 90 12 1 1935 2022 739785051 739785140 1.370000e-13 87.9
24 TraesCS3A01G170000 chr4B 77.778 135 29 1 1614 1747 529570475 529570341 6.360000e-12 82.4
25 TraesCS3A01G170000 chr7B 97.297 37 1 0 2735 2771 577563655 577563619 2.300000e-06 63.9


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 TraesCS3A01G170000 chr3A 178131215 178133985 2770 False 5118 5118 100.000000 1 2771 1 chr3A.!!$F1 2770
1 TraesCS3A01G170000 chr3D 152554974 152557678 2704 True 1239 2844 89.695333 22 2771 3 chr3D.!!$R2 2749
2 TraesCS3A01G170000 chr3B 223035457 223038299 2842 True 1379 2782 92.077333 30 2771 3 chr3B.!!$R2 2741


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
78 82 0.932955 TGGTTGGCATCCATATGGGT 59.067 50.0 21.78 12.51 38.11 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2089 0.033306 GAAGGTACTCCCTCCGTCCT 60.033 60.0 0.0 0.0 45.47 3.85 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.