Multiple sequence alignment - TraesCS6B01G407700

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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 TraesCS6B01G407700 chr6B 100.000 3344 0 0 1 3344 682135100 682138443 0.000000e+00 6176.0
1 TraesCS6B01G407700 chr6B 93.823 1117 66 1 981 2094 682312820 682311704 0.000000e+00 1677.0
2 TraesCS6B01G407700 chr6B 96.914 648 18 1 1957 2602 682310376 682309729 0.000000e+00 1085.0
3 TraesCS6B01G407700 chr6B 91.520 684 29 13 293 962 682313978 682313310 0.000000e+00 915.0
4 TraesCS6B01G407700 chr6B 96.774 310 8 2 2 310 539199683 539199375 1.780000e-142 516.0
5 TraesCS6B01G407700 chr6B 85.012 407 39 9 2637 3041 682316696 682316310 8.700000e-106 394.0
6 TraesCS6B01G407700 chr6B 85.000 400 38 10 2637 3034 682121408 682121787 1.460000e-103 387.0
7 TraesCS6B01G407700 chr6B 88.710 62 4 3 432 492 467454404 467454345 4.630000e-09 73.1
8 TraesCS6B01G407700 chr6B 100.000 29 0 0 807 835 682135808 682135836 2.000000e-03 54.7
9 TraesCS6B01G407700 chr6B 100.000 29 0 0 807 835 682313558 682313530 2.000000e-03 54.7
10 TraesCS6B01G407700 chr6B 100.000 28 0 0 777 804 682135712 682135685 6.000000e-03 52.8
11 TraesCS6B01G407700 chr6B 100.000 28 0 0 586 613 682135903 682135876 6.000000e-03 52.8
12 TraesCS6B01G407700 chr6D 93.064 1932 113 10 829 2750 449971479 449973399 0.000000e+00 2806.0
13 TraesCS6B01G407700 chr6D 86.691 2179 241 29 829 2989 449922005 449924152 0.000000e+00 2372.0
14 TraesCS6B01G407700 chr6D 83.591 1554 212 22 971 2516 449993960 449995478 0.000000e+00 1417.0
15 TraesCS6B01G407700 chr6D 92.786 402 22 3 2749 3149 449973560 449973955 2.890000e-160 575.0
16 TraesCS6B01G407700 chr6D 84.131 397 43 10 2638 3034 449920781 449921157 1.900000e-97 366.0
17 TraesCS6B01G407700 chr6D 94.845 194 9 1 3147 3340 463798319 463798511 5.420000e-78 302.0
18 TraesCS6B01G407700 chr6D 86.111 144 16 2 503 646 297668904 297669043 5.780000e-33 152.0
19 TraesCS6B01G407700 chr6D 87.097 62 5 3 432 492 302053833 302053774 2.150000e-07 67.6
20 TraesCS6B01G407700 chr6A 92.746 1668 104 6 826 2487 595497997 595499653 0.000000e+00 2394.0
21 TraesCS6B01G407700 chr6A 89.697 495 29 10 293 774 595493467 595493952 2.210000e-171 612.0
22 TraesCS6B01G407700 chr6A 91.111 270 15 6 2479 2745 595501969 595502232 1.140000e-94 357.0
23 TraesCS6B01G407700 chr6A 83.750 80 11 1 440 517 414872723 414872802 1.290000e-09 75.0
24 TraesCS6B01G407700 chr5B 99.315 292 2 0 1 292 314264333 314264624 2.280000e-146 529.0
25 TraesCS6B01G407700 chr5B 98.983 295 3 0 1 295 522774564 522774270 2.280000e-146 529.0
26 TraesCS6B01G407700 chr5B 95.288 191 9 0 3150 3340 598743000 598742810 1.510000e-78 303.0
27 TraesCS6B01G407700 chr2B 98.339 301 5 0 1 301 11718679 11718979 2.280000e-146 529.0
28 TraesCS6B01G407700 chr2B 98.328 299 4 1 1 298 103747733 103748031 1.060000e-144 523.0
29 TraesCS6B01G407700 chr2B 92.453 106 8 0 3044 3149 493975628 493975523 5.780000e-33 152.0
30 TraesCS6B01G407700 chr1B 98.980 294 3 0 1 294 621301699 621301992 8.220000e-146 527.0
31 TraesCS6B01G407700 chr1B 98.976 293 3 0 1 293 83199523 83199815 2.960000e-145 525.0
32 TraesCS6B01G407700 chr1B 93.171 205 13 1 3137 3340 609703254 609703050 1.950000e-77 300.0
33 TraesCS6B01G407700 chrUn 98.644 295 4 0 1 295 85648053 85648347 1.060000e-144 523.0
34 TraesCS6B01G407700 chrUn 94.845 194 8 2 3150 3342 348131498 348131306 5.420000e-78 302.0
35 TraesCS6B01G407700 chr4B 98.328 299 4 1 1 298 445185204 445184906 1.060000e-144 523.0
36 TraesCS6B01G407700 chr4B 94.845 194 8 2 3150 3342 641640395 641640203 5.420000e-78 302.0
37 TraesCS6B01G407700 chr5D 95.812 191 8 0 3150 3340 537335341 537335151 3.240000e-80 309.0
38 TraesCS6B01G407700 chr5D 83.051 295 36 9 2638 2932 442365692 442365972 4.280000e-64 255.0
39 TraesCS6B01G407700 chr5D 86.885 61 6 2 432 492 217080281 217080339 2.150000e-07 67.6
40 TraesCS6B01G407700 chr5D 92.683 41 0 3 612 651 300756940 300756978 4.660000e-04 56.5
41 TraesCS6B01G407700 chr3A 95.312 192 9 0 3151 3342 482803248 482803057 4.190000e-79 305.0
42 TraesCS6B01G407700 chr3A 89.655 58 4 2 434 489 640841291 640841348 4.630000e-09 73.1
43 TraesCS6B01G407700 chr7D 95.288 191 9 0 3150 3340 225492705 225492515 1.510000e-78 303.0
44 TraesCS6B01G407700 chr7D 94.330 194 11 0 3147 3340 136519045 136518852 7.010000e-77 298.0
45 TraesCS6B01G407700 chr7D 83.390 295 35 9 2638 2932 179698590 179698310 9.200000e-66 261.0
46 TraesCS6B01G407700 chr3D 83.051 295 36 9 2638 2932 50834867 50835147 4.280000e-64 255.0
47 TraesCS6B01G407700 chr1D 83.051 295 36 9 2638 2932 460357381 460357661 4.280000e-64 255.0
48 TraesCS6B01G407700 chr2A 89.720 107 9 2 3045 3149 754471035 754470929 5.820000e-28 135.0
49 TraesCS6B01G407700 chr3B 96.000 50 2 0 440 489 447014902 447014853 7.690000e-12 82.4


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 TraesCS6B01G407700 chr6B 682135100 682138443 3343 False 3115.35 6176 100.0000 1 3344 2 chr6B.!!$F2 3343
1 TraesCS6B01G407700 chr6B 682309729 682316696 6967 True 825.14 1677 93.4538 293 3041 5 chr6B.!!$R4 2748
2 TraesCS6B01G407700 chr6D 449971479 449973955 2476 False 1690.50 2806 92.9250 829 3149 2 chr6D.!!$F5 2320
3 TraesCS6B01G407700 chr6D 449993960 449995478 1518 False 1417.00 1417 83.5910 971 2516 1 chr6D.!!$F2 1545
4 TraesCS6B01G407700 chr6D 449920781 449924152 3371 False 1369.00 2372 85.4110 829 3034 2 chr6D.!!$F4 2205
5 TraesCS6B01G407700 chr6A 595497997 595502232 4235 False 1375.50 2394 91.9285 826 2745 2 chr6A.!!$F3 1919


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
333 2760 0.252696 TGGGCCTACTCCTGTCATGT 60.253 55.0 4.53 0.0 0.0 3.21 F
1774 4695 0.745845 CAAGATCCTTCCCACGCCAG 60.746 60.0 0.00 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 4713 0.105593 TAGTAGGCCGAGTCGACGAT 59.894 55.0 15.64 0.0 35.09 3.73 R
3181 10063 0.037160 GGGACAAAAGGCCCTTACGA 59.963 55.0 0.00 0.0 41.31 3.43 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.