Multiple sequence alignment - TraesCS3D01G490400

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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 TraesCS3D01G490400 chr3D 100.000 3089 0 0 1 3089 584449339 584446251 0.000000e+00 5705
1 TraesCS3D01G490400 chr3D 77.184 767 125 33 1032 1754 584456828 584456068 4.800000e-108 401
2 TraesCS3D01G490400 chr3D 78.974 585 92 21 1103 1664 584130001 584130577 1.350000e-98 370
3 TraesCS3D01G490400 chrUn 93.605 2236 101 20 861 3089 45489206 45487006 0.000000e+00 3299
4 TraesCS3D01G490400 chrUn 96.284 619 19 1 1 615 45490120 45489502 0.000000e+00 1013
5 TraesCS3D01G490400 chrUn 80.880 523 93 5 1234 1754 45482937 45482420 3.710000e-109 405
6 TraesCS3D01G490400 chrUn 96.392 194 7 0 630 823 45489404 45489211 1.380000e-83 320
7 TraesCS3D01G490400 chr3B 86.910 1398 123 23 1022 2368 781483449 781482061 0.000000e+00 1513
8 TraesCS3D01G490400 chr3B 95.238 336 14 2 630 963 781483790 781483455 5.870000e-147 531
9 TraesCS3D01G490400 chr3B 79.059 659 116 19 1103 1754 781494671 781494028 1.700000e-117 433
10 TraesCS3D01G490400 chr3B 76.757 740 126 25 1032 1730 781356275 781357009 3.760000e-99 372
11 TraesCS3D01G490400 chr3B 89.825 285 24 3 1905 2187 781475452 781475171 8.140000e-96 361
12 TraesCS3D01G490400 chr3B 97.531 162 4 0 1 162 781484261 781484100 8.440000e-71 278


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 TraesCS3D01G490400 chr3D 584446251 584449339 3088 True 5705 5705 100.000000 1 3089 1 chr3D.!!$R1 3088
1 TraesCS3D01G490400 chr3D 584456068 584456828 760 True 401 401 77.184000 1032 1754 1 chr3D.!!$R2 722
2 TraesCS3D01G490400 chr3D 584130001 584130577 576 False 370 370 78.974000 1103 1664 1 chr3D.!!$F1 561
3 TraesCS3D01G490400 chrUn 45487006 45490120 3114 True 1544 3299 95.427000 1 3089 3 chrUn.!!$R2 3088
4 TraesCS3D01G490400 chrUn 45482420 45482937 517 True 405 405 80.880000 1234 1754 1 chrUn.!!$R1 520
5 TraesCS3D01G490400 chr3B 781482061 781484261 2200 True 774 1513 93.226333 1 2368 3 chr3B.!!$R3 2367
6 TraesCS3D01G490400 chr3B 781494028 781494671 643 True 433 433 79.059000 1103 1754 1 chr3B.!!$R2 651
7 TraesCS3D01G490400 chr3B 781356275 781357009 734 False 372 372 76.757000 1032 1730 1 chr3B.!!$F1 698


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
546 754 1.202770 ACTTCAGCCACCACTGGTAAC 60.203 52.381 0.0 0.0 40.17 2.50 F
1514 1865 0.530744 CTCCCTCGACGTTGGATTCA 59.469 55.000 2.2 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 2019 0.035056 AGTGTACAATGCCTCAGCCC 60.035 55.0 0.0 0.0 38.69 5.19 R
2502 2868 0.249238 GAGGCGGTCTATGCTGTCAG 60.249 60.0 0.0 0.0 0.00 3.51 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.