Multiple sequence alignment - TraesCS3A01G092400

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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 TraesCS3A01G092400 chr3A 100.000 4006 0 0 1 4006 57961372 57957367 0.000000e+00 7398.0
1 TraesCS3A01G092400 chr3B 95.077 3169 75 20 892 4006 72935457 72938598 0.000000e+00 4913.0
2 TraesCS3A01G092400 chr3B 88.449 909 52 13 1 869 72934572 72935467 0.000000e+00 1048.0
3 TraesCS3A01G092400 chr3D 94.029 3182 98 25 892 4006 46554080 46557236 0.000000e+00 4739.0
4 TraesCS3A01G092400 chr3D 87.015 670 34 15 1 657 46553218 46553847 0.000000e+00 706.0
5 TraesCS3A01G092400 chr3D 94.170 223 7 4 653 872 46553874 46554093 6.420000e-88 335.0
6 TraesCS3A01G092400 chr3D 87.086 302 32 6 2527 2822 369413408 369413708 6.420000e-88 335.0
7 TraesCS3A01G092400 chr7B 89.869 306 27 2 2521 2822 13823711 13823406 1.350000e-104 390.0
8 TraesCS3A01G092400 chr7B 86.688 308 34 5 2522 2823 616539803 616540109 6.420000e-88 335.0
9 TraesCS3A01G092400 chr7B 92.216 167 13 0 1012 1178 147586614 147586448 1.860000e-58 237.0
10 TraesCS3A01G092400 chr5D 89.542 306 27 3 2522 2822 115401775 115401470 2.260000e-102 383.0
11 TraesCS3A01G092400 chr5B 89.542 306 27 3 2522 2822 126598771 126598466 2.260000e-102 383.0
12 TraesCS3A01G092400 chr5A 88.925 307 28 3 2522 2822 121412055 121411749 1.360000e-99 374.0
13 TraesCS3A01G092400 chr4D 85.759 316 36 9 2517 2826 421335522 421335210 3.860000e-85 326.0
14 TraesCS3A01G092400 chr2D 90.950 221 18 1 1012 1232 196365211 196365429 3.030000e-76 296.0
15 TraesCS3A01G092400 chr6A 91.617 167 14 0 1012 1178 576945102 576944936 8.660000e-57 231.0
16 TraesCS3A01G092400 chrUn 91.018 167 15 0 1012 1178 50316819 50316653 4.030000e-55 226.0
17 TraesCS3A01G092400 chrUn 91.018 167 15 0 1012 1178 307457563 307457397 4.030000e-55 226.0
18 TraesCS3A01G092400 chr6B 83.333 228 32 5 281 504 157774322 157774547 5.250000e-49 206.0
19 TraesCS3A01G092400 chr7A 80.435 92 13 5 281 370 25858208 25858120 9.290000e-07 65.8


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 TraesCS3A01G092400 chr3A 57957367 57961372 4005 True 7398.000000 7398 100.000 1 4006 1 chr3A.!!$R1 4005
1 TraesCS3A01G092400 chr3B 72934572 72938598 4026 False 2980.500000 4913 91.763 1 4006 2 chr3B.!!$F1 4005
2 TraesCS3A01G092400 chr3D 46553218 46557236 4018 False 1926.666667 4739 91.738 1 4006 3 chr3D.!!$F2 4005


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
72 76 0.323360 GGTTCAGGGGTTAGCATGCA 60.323 55.000 21.98 2.77 0.0 3.96 F
469 487 1.341156 CCCCACACCTCATCTCTCCC 61.341 65.000 0.00 0.00 0.0 4.30 F
482 500 1.653918 TCTCTCCCCCTCTTCCATTCT 59.346 52.381 0.00 0.00 0.0 2.40 F
2015 2095 2.072298 GCAAATCGAGAGCTTCACAGT 58.928 47.619 0.00 0.00 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1917 1.467734 CAGTGCAGACTTTCAGCATCC 59.532 52.381 0.0 0.0 40.92 3.51 R
2082 2163 0.179009 AACATGTGCCAGTGCTCAGT 60.179 50.000 0.0 0.0 43.52 3.41 R
2093 2174 4.516698 CACCAGATAATCCCTAACATGTGC 59.483 45.833 0.0 0.0 0.00 4.57 R
3005 3100 1.377856 GCTTGGGTTCCTCAGCCTC 60.378 63.158 0.0 0.0 44.37 4.70 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.