Multiple sequence alignment - TraesCS3A01G450500

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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 TraesCS3A01G450500 chr3A 100.000 2889 0 0 1 2889 689110923 689113811 0.000000e+00 5336.0
1 TraesCS3A01G450500 chr3D 90.441 2176 108 32 1 2108 552781387 552783530 0.000000e+00 2774.0
2 TraesCS3A01G450500 chr3D 93.103 783 34 8 2108 2889 552783616 552784379 0.000000e+00 1129.0
3 TraesCS3A01G450500 chr3B 90.009 2162 110 37 2 2108 733627638 733629748 0.000000e+00 2699.0
4 TraesCS3A01G450500 chr3B 92.112 786 50 9 2108 2889 733629828 733630605 0.000000e+00 1098.0
5 TraesCS3A01G450500 chr3B 85.859 495 52 2 996 1490 733574030 733574506 7.140000e-141 510.0
6 TraesCS3A01G450500 chr3B 97.059 34 1 0 767 800 733573780 733573813 1.120000e-04 58.4
7 TraesCS3A01G450500 chr7D 84.524 756 89 17 997 1731 573898063 573898811 0.000000e+00 723.0
8 TraesCS3A01G450500 chr1D 81.930 891 114 21 996 1857 395559591 395558719 0.000000e+00 710.0
9 TraesCS3A01G450500 chr1D 85.393 267 23 10 590 844 460183315 460183053 2.210000e-66 263.0
10 TraesCS3A01G450500 chr1A 81.646 899 110 26 996 1861 489601197 489600321 0.000000e+00 695.0
11 TraesCS3A01G450500 chr7B 83.905 758 87 20 996 1731 632684676 632685420 0.000000e+00 691.0
12 TraesCS3A01G450500 chr7B 80.567 247 39 8 2647 2887 19954953 19954710 6.360000e-42 182.0
13 TraesCS3A01G450500 chr1B 80.832 913 109 28 996 1861 526348897 526348004 0.000000e+00 656.0
14 TraesCS3A01G450500 chr2B 77.996 509 89 13 996 1492 759274380 759273883 6.050000e-77 298.0
15 TraesCS3A01G450500 chr5D 87.435 191 12 7 2195 2382 67965704 67965523 2.920000e-50 209.0
16 TraesCS3A01G450500 chr4B 78.109 201 29 8 483 675 48905134 48904941 2.350000e-21 113.0
17 TraesCS3A01G450500 chr4D 75.124 201 33 10 483 675 34062939 34062748 8.580000e-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 TraesCS3A01G450500 chr3A 689110923 689113811 2888 False 5336.0 5336 100.0000 1 2889 1 chr3A.!!$F1 2888
1 TraesCS3A01G450500 chr3D 552781387 552784379 2992 False 1951.5 2774 91.7720 1 2889 2 chr3D.!!$F1 2888
2 TraesCS3A01G450500 chr3B 733627638 733630605 2967 False 1898.5 2699 91.0605 2 2889 2 chr3B.!!$F2 2887
3 TraesCS3A01G450500 chr3B 733573780 733574506 726 False 284.2 510 91.4590 767 1490 2 chr3B.!!$F1 723
4 TraesCS3A01G450500 chr7D 573898063 573898811 748 False 723.0 723 84.5240 997 1731 1 chr7D.!!$F1 734
5 TraesCS3A01G450500 chr1D 395558719 395559591 872 True 710.0 710 81.9300 996 1857 1 chr1D.!!$R1 861
6 TraesCS3A01G450500 chr1A 489600321 489601197 876 True 695.0 695 81.6460 996 1861 1 chr1A.!!$R1 865
7 TraesCS3A01G450500 chr7B 632684676 632685420 744 False 691.0 691 83.9050 996 1731 1 chr7B.!!$F1 735
8 TraesCS3A01G450500 chr1B 526348004 526348897 893 True 656.0 656 80.8320 996 1861 1 chr1B.!!$R1 865


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
430 433 0.035439 GTGGCGAATGGAGAAAGGGA 60.035 55.0 0.0 0.0 0.0 4.20 F
961 1028 0.468400 TCCGGAAAACCCCAACCTTG 60.468 55.0 0.0 0.0 0.0 3.61 F
993 1065 0.969894 CTCCAAGAACTCACCTCCGT 59.030 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 1994 0.905337 GGTCAGCTGAGGTAGTGGGT 60.905 60.000 18.89 0.00 0.00 4.51 R
1843 2003 1.277273 TCTGTTGATGGGTCAGCTGAG 59.723 52.381 18.89 0.82 38.15 3.35 R
2602 2857 2.027837 TGCATGTCAGCATCACACTACT 60.028 45.455 0.00 0.00 40.11 2.57 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.