Multiple sequence alignment - TraesCS5B01G365400

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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 TraesCS5B01G365400 chr5B 100.000 4437 0 0 1 4437 544325672 544330108 0.000000e+00 8194.0
1 TraesCS5B01G365400 chr5B 93.939 99 4 2 3967 4063 650023919 650023821 9.940000e-32 148.0
2 TraesCS5B01G365400 chr5B 94.792 96 4 1 3962 4057 658145688 658145782 9.940000e-32 148.0
3 TraesCS5B01G365400 chr5D 93.408 3216 131 31 223 3408 446397358 446400522 0.000000e+00 4689.0
4 TraesCS5B01G365400 chr5D 85.143 700 47 36 3766 4434 446400522 446401195 0.000000e+00 664.0
5 TraesCS5B01G365400 chr5D 96.629 89 2 1 3967 4054 522112056 522112144 3.580000e-31 147.0
6 TraesCS5B01G365400 chr5A 92.827 2370 124 26 1509 3863 564072360 564074698 0.000000e+00 3393.0
7 TraesCS5B01G365400 chr5A 91.853 1522 81 21 223 1714 564070849 564072357 0.000000e+00 2084.0
8 TraesCS5B01G365400 chr5A 86.458 480 42 14 3966 4434 564075033 564075500 5.120000e-139 505.0
9 TraesCS5B01G365400 chr5A 91.667 48 4 0 1496 1543 564072317 564072364 2.860000e-07 67.6
10 TraesCS5B01G365400 chr3A 85.256 156 17 5 37 189 521573991 521573839 5.940000e-34 156.0
11 TraesCS5B01G365400 chr3A 84.112 107 13 4 91 194 631713118 631713013 2.820000e-17 100.0
12 TraesCS5B01G365400 chr2A 85.161 155 19 3 34 186 16067468 16067620 5.940000e-34 156.0
13 TraesCS5B01G365400 chr7D 94.000 100 2 2 3968 4067 535550405 535550310 9.940000e-32 148.0
14 TraesCS5B01G365400 chr7D 95.604 91 4 0 3964 4054 599463144 599463234 3.580000e-31 147.0
15 TraesCS5B01G365400 chr1D 96.629 89 2 1 3967 4054 342187344 342187432 3.580000e-31 147.0
16 TraesCS5B01G365400 chr7B 98.780 82 0 1 3974 4054 678291170 678291251 1.290000e-30 145.0
17 TraesCS5B01G365400 chr4B 84.507 142 18 3 34 173 545148055 545148194 2.150000e-28 137.0
18 TraesCS5B01G365400 chr2D 89.423 104 9 2 89 190 558190084 558189981 3.600000e-26 130.0
19 TraesCS5B01G365400 chr1A 84.762 105 14 2 34 137 486600129 486600026 2.180000e-18 104.0


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 TraesCS5B01G365400 chr5B 544325672 544330108 4436 False 8194.0 8194 100.00000 1 4437 1 chr5B.!!$F1 4436
1 TraesCS5B01G365400 chr5D 446397358 446401195 3837 False 2676.5 4689 89.27550 223 4434 2 chr5D.!!$F2 4211
2 TraesCS5B01G365400 chr5A 564070849 564075500 4651 False 1512.4 3393 90.70125 223 4434 4 chr5A.!!$F1 4211


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
595 596 0.174845 TGTTAAGCCGAGGATCCGTG 59.825 55.0 5.98 2.41 0.00 4.94 F
806 815 0.175760 TAGCACGAATCCCAGACAGC 59.824 55.0 0.00 0.00 0.00 4.40 F
1317 1344 0.542333 GGTAGGTCCTTCCCTGCTTC 59.458 60.0 3.05 0.00 37.38 3.86 F
3132 3400 0.031178 ACACCGTCACGTCTTACACC 59.969 55.0 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 2660 0.176680 CTCGATGGCCAGCACTAAGT 59.823 55.000 22.95 0.0 0.00 2.24 R
2488 2740 2.740714 GCGTGATCGACAGGGTTGC 61.741 63.158 0.00 0.0 39.71 4.17 R
3137 3405 0.485543 TCGGGTATATCTGCAGGGGA 59.514 55.000 15.13 0.0 0.00 4.81 R
4123 4647 1.627864 CCCGTTTTGAAGGTCCCATT 58.372 50.000 0.00 0.0 0.00 3.16 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.