Multiple sequence alignment - TraesCS3B01G429300

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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 TraesCS3B01G429300 chr3B 100.000 2654 0 0 1 2654 667854954 667857607 0.000000e+00 4902
1 TraesCS3B01G429300 chr3B 93.248 311 19 2 2344 2654 13459089 13458781 8.660000e-125 457
2 TraesCS3B01G429300 chr3B 85.714 455 37 11 2227 2654 64479658 64479205 3.110000e-124 455
3 TraesCS3B01G429300 chr3B 95.376 173 6 1 2061 2233 169427635 169427805 9.360000e-70 274
4 TraesCS3B01G429300 chr3A 94.358 1223 57 7 843 2059 644779948 644781164 0.000000e+00 1866
5 TraesCS3B01G429300 chr3A 87.500 120 15 0 962 1081 644696507 644696626 3.560000e-29 139
6 TraesCS3B01G429300 chr3D 92.242 1289 62 16 788 2059 506160828 506162095 0.000000e+00 1792
7 TraesCS3B01G429300 chr3D 97.126 174 5 0 2060 2233 101562887 101562714 7.180000e-76 294
8 TraesCS3B01G429300 chr1B 84.490 677 82 19 58 722 688402374 688401709 0.000000e+00 647
9 TraesCS3B01G429300 chr1B 89.908 109 11 0 2125 2233 624670308 624670200 9.900000e-30 141
10 TraesCS3B01G429300 chr2B 83.772 684 74 29 58 716 14614132 14614803 4.860000e-172 614
11 TraesCS3B01G429300 chr2B 83.793 617 73 19 112 716 154188809 154188208 6.420000e-156 560
12 TraesCS3B01G429300 chr2B 80.220 728 79 33 4 716 642447867 642448544 1.100000e-133 486
13 TraesCS3B01G429300 chr2B 86.830 448 30 10 2233 2654 690938125 690937681 8.600000e-130 473
14 TraesCS3B01G429300 chr2B 93.569 311 19 1 2344 2654 787544049 787544358 1.860000e-126 462
15 TraesCS3B01G429300 chr2B 93.770 305 18 1 2344 2648 787510538 787510841 8.660000e-125 457
16 TraesCS3B01G429300 chr2B 84.524 336 38 11 1 331 32066799 32066473 1.190000e-83 320
17 TraesCS3B01G429300 chr2B 95.402 174 6 1 2060 2233 411495392 411495563 2.600000e-70 276
18 TraesCS3B01G429300 chr2B 90.984 122 9 2 2229 2349 758929489 758929369 2.110000e-36 163
19 TraesCS3B01G429300 chr2B 90.678 118 9 2 2233 2349 216717862 216717746 3.540000e-34 156
20 TraesCS3B01G429300 chrUn 82.407 756 82 33 1 716 345775541 345774797 1.750000e-171 612
21 TraesCS3B01G429300 chr4B 82.082 759 81 34 1 716 578345666 578346412 4.890000e-167 597
22 TraesCS3B01G429300 chr4B 93.910 312 16 3 2343 2654 113883511 113883819 4.000000e-128 468
23 TraesCS3B01G429300 chr4B 91.597 119 10 0 2231 2349 619599137 619599255 5.880000e-37 165
24 TraesCS3B01G429300 chr6B 83.259 669 87 19 63 716 9021131 9021789 2.280000e-165 592
25 TraesCS3B01G429300 chr6B 82.840 676 83 25 63 716 198914246 198913582 2.290000e-160 575
26 TraesCS3B01G429300 chr6B 95.977 174 7 0 2060 2233 420748390 420748217 1.560000e-72 283
27 TraesCS3B01G429300 chr7B 82.127 677 89 19 63 714 496887906 496887237 3.860000e-153 551
28 TraesCS3B01G429300 chr7B 92.742 124 9 0 2226 2349 630889690 630889813 2.100000e-41 180
29 TraesCS3B01G429300 chr5A 84.965 572 54 25 152 716 322134079 322134625 3.860000e-153 551
30 TraesCS3B01G429300 chr6D 93.291 313 19 2 2343 2654 464142470 464142159 6.690000e-126 460
31 TraesCS3B01G429300 chr6D 87.234 141 12 6 2212 2349 225141924 225142061 3.540000e-34 156
32 TraesCS3B01G429300 chr5B 92.949 312 22 0 2343 2654 30869191 30869502 3.110000e-124 455
33 TraesCS3B01G429300 chr5B 97.701 174 4 0 2060 2233 327703950 327704123 1.540000e-77 300
34 TraesCS3B01G429300 chr2D 92.652 313 22 1 2343 2654 37871703 37872015 1.450000e-122 449
35 TraesCS3B01G429300 chr1D 98.266 173 3 0 2061 2233 490355899 490356071 1.190000e-78 303
36 TraesCS3B01G429300 chr1D 91.453 117 10 0 2233 2349 320981941 320981825 7.600000e-36 161
37 TraesCS3B01G429300 chr5D 91.597 119 9 1 2231 2349 470036865 470036982 2.110000e-36 163
38 TraesCS3B01G429300 chr5D 91.379 116 10 0 2234 2349 294049167 294049052 2.730000e-35 159
39 TraesCS3B01G429300 chr7D 90.083 121 12 0 2229 2349 593423662 593423782 9.830000e-35 158


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 TraesCS3B01G429300 chr3B 667854954 667857607 2653 False 4902 4902 100.000 1 2654 1 chr3B.!!$F2 2653
1 TraesCS3B01G429300 chr3A 644779948 644781164 1216 False 1866 1866 94.358 843 2059 1 chr3A.!!$F2 1216
2 TraesCS3B01G429300 chr3D 506160828 506162095 1267 False 1792 1792 92.242 788 2059 1 chr3D.!!$F1 1271
3 TraesCS3B01G429300 chr1B 688401709 688402374 665 True 647 647 84.490 58 722 1 chr1B.!!$R2 664
4 TraesCS3B01G429300 chr2B 14614132 14614803 671 False 614 614 83.772 58 716 1 chr2B.!!$F1 658
5 TraesCS3B01G429300 chr2B 154188208 154188809 601 True 560 560 83.793 112 716 1 chr2B.!!$R2 604
6 TraesCS3B01G429300 chr2B 642447867 642448544 677 False 486 486 80.220 4 716 1 chr2B.!!$F3 712
7 TraesCS3B01G429300 chrUn 345774797 345775541 744 True 612 612 82.407 1 716 1 chrUn.!!$R1 715
8 TraesCS3B01G429300 chr4B 578345666 578346412 746 False 597 597 82.082 1 716 1 chr4B.!!$F2 715
9 TraesCS3B01G429300 chr6B 9021131 9021789 658 False 592 592 83.259 63 716 1 chr6B.!!$F1 653
10 TraesCS3B01G429300 chr6B 198913582 198914246 664 True 575 575 82.840 63 716 1 chr6B.!!$R1 653
11 TraesCS3B01G429300 chr7B 496887237 496887906 669 True 551 551 82.127 63 714 1 chr7B.!!$R1 651
12 TraesCS3B01G429300 chr5A 322134079 322134625 546 False 551 551 84.965 152 716 1 chr5A.!!$F1 564


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
760 848 0.107831 TGGTACCAATATCGCAGGCC 59.892 55.0 13.6 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2464 2581 0.027194 TATTCGTCGCGAGAACCGAG 59.973 55.0 10.24 0.0 45.01 4.63 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.