Multiple sequence alignment - TraesCS2D01G380400

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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 TraesCS2D01G380400 chr2D 100.000 5965 0 0 1 5965 484851818 484857782 0.000000e+00 11016
1 TraesCS2D01G380400 chr2D 94.200 500 17 1 499 986 397963570 397964069 0.000000e+00 752
2 TraesCS2D01G380400 chr2D 94.000 500 15 7 498 986 6219498 6219993 0.000000e+00 743
3 TraesCS2D01G380400 chr2A 96.974 3404 63 14 2571 5965 628734418 628737790 0.000000e+00 5679
4 TraesCS2D01G380400 chr2A 97.482 1549 34 4 987 2532 628730513 628732059 0.000000e+00 2639
5 TraesCS2D01G380400 chr2A 92.368 511 27 3 1 500 628730010 628730519 0.000000e+00 717
6 TraesCS2D01G380400 chr2A 91.195 477 41 1 508 984 191972393 191971918 0.000000e+00 647
7 TraesCS2D01G380400 chr2B 92.843 1956 101 20 4014 5965 569498184 569500104 0.000000e+00 2800
8 TraesCS2D01G380400 chr2B 98.673 226 3 0 3798 4023 569497443 569497668 9.310000e-108 401
9 TraesCS2D01G380400 chr5D 96.192 499 8 3 499 986 11172007 11172505 0.000000e+00 806
10 TraesCS2D01G380400 chr5D 94.200 500 18 1 498 986 401034411 401034910 0.000000e+00 752
11 TraesCS2D01G380400 chr5D 94.355 496 17 1 502 986 529172861 529173356 0.000000e+00 750
12 TraesCS2D01G380400 chr6D 95.372 497 12 3 501 986 305074224 305074720 0.000000e+00 780
13 TraesCS2D01G380400 chr3D 94.779 498 15 1 500 986 533412852 533413349 0.000000e+00 765
14 TraesCS2D01G380400 chr3D 93.750 496 19 7 502 986 596278581 596279075 0.000000e+00 734
15 TraesCS2D01G380400 chr3D 91.734 496 29 7 502 986 612613101 612612607 0.000000e+00 678
16 TraesCS2D01G380400 chr7D 94.212 501 18 1 500 989 500789271 500788771 0.000000e+00 754
17 TraesCS2D01G380400 chr1D 93.988 499 18 1 500 986 75927935 75927437 0.000000e+00 745
18 TraesCS2D01G380400 chr3A 92.540 496 26 1 502 986 187438710 187438215 0.000000e+00 701
19 TraesCS2D01G380400 chr6B 94.667 75 3 1 500 574 13832028 13831955 1.360000e-21 115


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 TraesCS2D01G380400 chr2D 484851818 484857782 5964 False 11016.000000 11016 100.000 1 5965 1 chr2D.!!$F3 5964
1 TraesCS2D01G380400 chr2A 628730010 628737790 7780 False 3011.666667 5679 95.608 1 5965 3 chr2A.!!$F1 5964
2 TraesCS2D01G380400 chr2B 569497443 569500104 2661 False 1600.500000 2800 95.758 3798 5965 2 chr2B.!!$F1 2167
3 TraesCS2D01G380400 chr7D 500788771 500789271 500 True 754.000000 754 94.212 500 989 1 chr7D.!!$R1 489


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
205 206 0.846693 AGGGGCCATCATGTACCTTC 59.153 55.000 4.39 0.0 0.00 3.46 F
1004 1027 0.462759 GTGGCTGACCCTAGCATGAC 60.463 60.000 0.00 0.0 45.46 3.06 F
1840 1863 1.597937 GCTTTTGTCCAGAAGTGCGTG 60.598 52.381 0.33 0.0 0.00 5.34 F
2541 2567 0.036164 ATAAGCACGTCACCAGGCAA 59.964 50.000 0.00 0.0 0.00 4.52 F
2546 2572 0.036388 CACGTCACCAGGCAACCTAT 60.036 55.000 0.00 0.0 29.64 2.57 F
2548 2574 0.249120 CGTCACCAGGCAACCTATCA 59.751 55.000 0.00 0.0 29.64 2.15 F
3647 5993 0.932955 AGAGGGCTCCATCAGAGAGA 59.067 55.000 3.28 0.0 46.50 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 1368 1.160137 ATCTCAAGAACACGCTTGCC 58.840 50.000 0.00 0.00 43.78 4.52 R
2453 2479 1.452110 TGTTCATTGCCGGACTGATG 58.548 50.000 5.05 2.81 0.00 3.07 R
3647 5993 0.179009 TTCTTGCTGCTTGCCACTCT 60.179 50.000 0.00 0.00 42.00 3.24 R
4520 7391 2.373169 ACTCTTGCTTTCCACCTCATCA 59.627 45.455 0.00 0.00 0.00 3.07 R
4523 7394 2.806745 CGAACTCTTGCTTTCCACCTCA 60.807 50.000 0.00 0.00 0.00 3.86 R
4559 7430 2.361757 CCTCCTGCATCTCTGAGTACTG 59.638 54.545 0.00 2.90 0.00 2.74 R
5559 8439 0.178992 CTTCCTTGGGAGGTGTTGCA 60.179 55.000 0.00 0.00 43.97 4.08 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.