Multiple sequence alignment - TraesCS6A01G281700

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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 TraesCS6A01G281700 chr6A 100.000 2971 0 0 1 2971 511526917 511529887 0.000000e+00 5487.0
1 TraesCS6A01G281700 chr6A 88.034 117 4 5 2477 2586 7373596 7373483 2.400000e-26 130.0
2 TraesCS6A01G281700 chr6D 94.727 1574 39 10 908 2473 370689023 370690560 0.000000e+00 2407.0
3 TraesCS6A01G281700 chr6D 96.460 226 8 0 2746 2971 370690845 370691070 1.010000e-99 374.0
4 TraesCS6A01G281700 chr6D 95.714 210 9 0 2539 2748 370690551 370690760 3.670000e-89 339.0
5 TraesCS6A01G281700 chr6D 90.964 166 9 6 753 916 370581681 370581842 4.990000e-53 219.0
6 TraesCS6A01G281700 chr6D 90.909 66 2 4 2543 2608 249956924 249956985 5.280000e-13 86.1
7 TraesCS6A01G281700 chr6D 95.122 41 2 0 2545 2585 32919203 32919243 6.870000e-07 65.8
8 TraesCS6A01G281700 chr6B 95.785 1210 30 5 999 2208 555805027 555806215 0.000000e+00 1932.0
9 TraesCS6A01G281700 chr6B 93.303 433 18 4 1 424 690877724 690877294 1.940000e-176 628.0
10 TraesCS6A01G281700 chr6B 93.000 400 16 4 2584 2971 555806508 555806907 9.240000e-160 573.0
11 TraesCS6A01G281700 chr6B 90.875 263 17 5 2211 2473 555806252 555806507 2.190000e-91 346.0
12 TraesCS6A01G281700 chr6B 88.462 52 5 1 949 999 555804945 555804996 8.890000e-06 62.1
13 TraesCS6A01G281700 chr6B 100.000 28 0 0 2139 2166 555806229 555806256 5.000000e-03 52.8
14 TraesCS6A01G281700 chr2A 92.702 781 43 5 1 771 173513698 173512922 0.000000e+00 1114.0
15 TraesCS6A01G281700 chr2A 92.138 407 27 2 364 768 572845984 572846387 1.190000e-158 569.0
16 TraesCS6A01G281700 chr3D 93.995 433 15 4 1 424 384009782 384010212 0.000000e+00 645.0
17 TraesCS6A01G281700 chr3D 93.187 411 23 2 364 772 384010205 384010612 1.520000e-167 599.0
18 TraesCS6A01G281700 chr3D 86.885 122 12 3 2467 2585 555010894 555010774 1.860000e-27 134.0
19 TraesCS6A01G281700 chr4B 93.533 433 15 6 1 424 2710910 2710482 1.500000e-177 632.0
20 TraesCS6A01G281700 chr4B 92.575 431 20 6 3 424 97791441 97791014 2.530000e-170 608.0
21 TraesCS6A01G281700 chr4B 91.748 412 29 3 364 773 97879642 97879234 4.300000e-158 568.0
22 TraesCS6A01G281700 chr4B 91.707 410 29 3 364 771 2710489 2710083 5.560000e-157 564.0
23 TraesCS6A01G281700 chr4B 91.687 409 29 2 364 770 535069233 535069638 2.000000e-156 562.0
24 TraesCS6A01G281700 chr4B 91.057 123 6 4 2853 2971 625330743 625330622 8.520000e-36 161.0
25 TraesCS6A01G281700 chr5A 93.303 433 17 5 1 424 354275638 354276067 1.940000e-176 628.0
26 TraesCS6A01G281700 chr4D 93.303 433 18 4 1 424 79010223 79010653 1.940000e-176 628.0
27 TraesCS6A01G281700 chr4D 93.269 104 5 1 2482 2585 135171085 135170984 5.130000e-33 152.0
28 TraesCS6A01G281700 chr1A 93.072 433 18 5 1 424 2283303 2282874 9.040000e-175 623.0
29 TraesCS6A01G281700 chr1A 91.847 417 29 4 364 776 2282881 2282466 7.140000e-161 577.0
30 TraesCS6A01G281700 chr5B 92.841 433 19 5 1 424 345812121 345812550 4.210000e-173 617.0
31 TraesCS6A01G281700 chrUn 92.346 405 26 2 365 767 122648353 122648754 3.320000e-159 571.0
32 TraesCS6A01G281700 chrUn 89.655 116 6 2 2476 2585 65138954 65138839 3.090000e-30 143.0
33 TraesCS6A01G281700 chr7A 91.892 407 28 2 364 768 606194815 606195218 5.560000e-157 564.0
34 TraesCS6A01G281700 chr2D 91.964 112 3 2 2477 2586 79387429 79387322 5.130000e-33 152.0
35 TraesCS6A01G281700 chr2D 95.122 41 2 0 2545 2585 422085571 422085611 6.870000e-07 65.8
36 TraesCS6A01G281700 chr5D 91.071 112 7 2 2477 2586 361674424 361674314 6.630000e-32 148.0
37 TraesCS6A01G281700 chr5D 86.179 123 9 7 2853 2968 499710911 499711032 3.110000e-25 126.0
38 TraesCS6A01G281700 chr3B 91.743 109 4 2 2480 2586 636441639 636441534 2.390000e-31 147.0
39 TraesCS6A01G281700 chr7B 89.474 114 7 2 2477 2585 475307981 475308094 3.990000e-29 139.0
40 TraesCS6A01G281700 chr3A 89.381 113 8 3 2477 2586 18825595 18825484 3.990000e-29 139.0
41 TraesCS6A01G281700 chr7D 94.444 54 3 0 2543 2596 101475417 101475470 1.900000e-12 84.2
42 TraesCS6A01G281700 chr2B 97.368 38 1 0 1343 1380 573814522 573814485 6.870000e-07 65.8
43 TraesCS6A01G281700 chr4A 88.679 53 2 4 2548 2600 516208934 516208886 8.890000e-06 62.1


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 TraesCS6A01G281700 chr6A 511526917 511529887 2970 False 5487.00 5487 100.000000 1 2971 1 chr6A.!!$F1 2970
1 TraesCS6A01G281700 chr6D 370689023 370691070 2047 False 1040.00 2407 95.633667 908 2971 3 chr6D.!!$F4 2063
2 TraesCS6A01G281700 chr6B 555804945 555806907 1962 False 593.18 1932 93.624400 949 2971 5 chr6B.!!$F1 2022
3 TraesCS6A01G281700 chr2A 173512922 173513698 776 True 1114.00 1114 92.702000 1 771 1 chr2A.!!$R1 770
4 TraesCS6A01G281700 chr3D 384009782 384010612 830 False 622.00 645 93.591000 1 772 2 chr3D.!!$F1 771
5 TraesCS6A01G281700 chr4B 2710083 2710910 827 True 598.00 632 92.620000 1 771 2 chr4B.!!$R4 770
6 TraesCS6A01G281700 chr1A 2282466 2283303 837 True 600.00 623 92.459500 1 776 2 chr1A.!!$R1 775


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
833 901 0.110688 CGTTGTCATGCCAACTCGTG 60.111 55.0 16.78 0.0 42.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2615 0.338814 ATGGGACGGAGGGAGTAACT 59.661 55.0 0.0 0.0 0.0 2.24 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.