Multiple sequence alignment - TraesCS6B01G111500

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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 TraesCS6B01G111500 chr6B 100.000 5300 0 0 1 5300 93429964 93435263 0.000000e+00 9788.0
1 TraesCS6B01G111500 chr6B 80.526 950 153 20 1 939 558829637 558828709 0.000000e+00 701.0
2 TraesCS6B01G111500 chr6B 80.316 950 155 20 1 939 558747054 558746126 0.000000e+00 689.0
3 TraesCS6B01G111500 chr6B 88.727 479 44 2 2774 3243 683548158 683548635 1.280000e-160 577.0
4 TraesCS6B01G111500 chrUn 95.458 1475 55 6 3828 5300 19246121 19244657 0.000000e+00 2342.0
5 TraesCS6B01G111500 chrUn 88.372 258 24 4 2275 2529 19248149 19247895 6.670000e-79 305.0
6 TraesCS6B01G111500 chrUn 99.225 129 1 0 3680 3808 183131008 183130880 3.190000e-57 233.0
7 TraesCS6B01G111500 chrUn 90.000 180 16 2 2103 2280 19248391 19248212 1.150000e-56 231.0
8 TraesCS6B01G111500 chrUn 96.923 65 2 0 3423 3487 19247093 19247029 5.610000e-20 110.0
9 TraesCS6B01G111500 chrUn 96.552 58 1 1 3597 3654 19246344 19246288 1.570000e-15 95.3
10 TraesCS6B01G111500 chr6A 94.752 1410 57 9 3896 5300 57690187 57691584 0.000000e+00 2178.0
11 TraesCS6B01G111500 chr6A 83.083 266 37 6 2266 2529 57685011 57685270 8.870000e-58 235.0
12 TraesCS6B01G111500 chr6A 96.923 65 2 0 3423 3487 57688132 57688196 5.610000e-20 110.0
13 TraesCS6B01G111500 chr5A 96.680 964 29 3 404 1365 114380262 114379300 0.000000e+00 1600.0
14 TraesCS6B01G111500 chr5A 96.144 389 15 0 1714 2102 114378482 114378094 2.080000e-178 636.0
15 TraesCS6B01G111500 chr5A 95.686 255 11 0 1373 1627 114379108 114378854 1.370000e-110 411.0
16 TraesCS6B01G111500 chr5A 75.726 758 141 30 1 743 545879039 545879768 1.830000e-89 340.0
17 TraesCS6B01G111500 chr5A 79.310 377 61 8 386 759 4092261 4091899 1.140000e-61 248.0
18 TraesCS6B01G111500 chr5A 96.599 147 5 0 2530 2676 423046851 423046705 1.470000e-60 244.0
19 TraesCS6B01G111500 chr5A 96.575 146 4 1 2531 2676 423044194 423044338 1.910000e-59 241.0
20 TraesCS6B01G111500 chr7B 82.583 844 125 12 1 839 11288737 11289563 0.000000e+00 725.0
21 TraesCS6B01G111500 chr7B 78.723 517 94 16 5 512 692920433 692920942 1.100000e-86 331.0
22 TraesCS6B01G111500 chr7B 95.890 146 4 1 2531 2676 2750831 2750974 8.870000e-58 235.0
23 TraesCS6B01G111500 chr7B 71.905 630 144 24 1373 1976 11290202 11290824 9.190000e-33 152.0
24 TraesCS6B01G111500 chr6D 88.130 615 58 5 2677 3280 450354551 450355161 0.000000e+00 717.0
25 TraesCS6B01G111500 chr6D 78.543 755 135 17 1 748 31798615 31797881 6.210000e-129 472.0
26 TraesCS6B01G111500 chr7D 80.717 949 145 26 1 936 504350619 504351542 0.000000e+00 704.0
27 TraesCS6B01G111500 chr7D 74.716 969 181 42 1 939 497949289 497948355 1.800000e-99 374.0
28 TraesCS6B01G111500 chr7D 78.947 152 29 3 1858 2007 497946994 497946844 3.380000e-17 100.0
29 TraesCS6B01G111500 chr7D 72.593 270 68 5 1653 1920 504353913 504354178 3.400000e-12 84.2
30 TraesCS6B01G111500 chr4D 80.243 577 86 15 190 759 87556594 87556039 4.940000e-110 409.0
31 TraesCS6B01G111500 chr3A 79.203 577 91 17 190 759 660898053 660897499 1.800000e-99 374.0
32 TraesCS6B01G111500 chr3A 81.548 336 45 8 450 783 9877510 9877830 1.460000e-65 261.0
33 TraesCS6B01G111500 chr3A 98.496 133 2 0 3676 3808 653508462 653508330 8.870000e-58 235.0
34 TraesCS6B01G111500 chr3A 97.778 135 3 0 3674 3808 481651575 481651441 3.190000e-57 233.0
35 TraesCS6B01G111500 chr3A 77.910 335 68 5 1 332 72224946 72224615 2.500000e-48 204.0
36 TraesCS6B01G111500 chr3A 85.475 179 26 0 586 764 67370881 67371059 2.520000e-43 187.0
37 TraesCS6B01G111500 chr3A 85.475 179 26 0 586 764 67375308 67375486 2.520000e-43 187.0
38 TraesCS6B01G111500 chr3A 85.475 179 26 0 586 764 67379722 67379900 2.520000e-43 187.0
39 TraesCS6B01G111500 chr4B 97.260 146 3 1 2531 2676 183675891 183675747 4.100000e-61 246.0
40 TraesCS6B01G111500 chr4B 95.395 152 7 0 2525 2676 183673231 183673382 5.300000e-60 243.0
41 TraesCS6B01G111500 chr4B 95.890 146 4 1 2531 2676 602889305 602889162 8.870000e-58 235.0
42 TraesCS6B01G111500 chr4B 94.118 153 6 3 2525 2676 602883927 602884077 4.130000e-56 230.0
43 TraesCS6B01G111500 chr2A 96.599 147 4 1 2530 2676 757957939 757958084 5.300000e-60 243.0
44 TraesCS6B01G111500 chr2A 96.575 146 4 1 2531 2676 757960595 757960451 1.910000e-59 241.0
45 TraesCS6B01G111500 chr2A 97.710 131 3 0 3681 3811 43500348 43500218 5.340000e-55 226.0
46 TraesCS6B01G111500 chr7A 99.237 131 1 0 3677 3807 98086655 98086525 2.470000e-58 237.0
47 TraesCS6B01G111500 chr4A 98.519 135 1 1 3678 3811 58534198 58534064 2.470000e-58 237.0
48 TraesCS6B01G111500 chr3B 99.225 129 1 0 3679 3807 523966901 523966773 3.190000e-57 233.0
49 TraesCS6B01G111500 chr1B 98.438 128 2 0 3680 3807 669017179 669017052 5.340000e-55 226.0
50 TraesCS6B01G111500 chr5B 79.429 350 46 13 439 783 18672389 18672717 1.920000e-54 224.0
51 TraesCS6B01G111500 chr1A 96.992 133 4 0 3675 3807 14170196 14170064 1.920000e-54 224.0
52 TraesCS6B01G111500 chr1A 87.151 179 23 0 586 764 590297596 590297774 2.500000e-48 204.0


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 TraesCS6B01G111500 chr6B 93429964 93435263 5299 False 9788.000000 9788 100.0000 1 5300 1 chr6B.!!$F1 5299
1 TraesCS6B01G111500 chr6B 558828709 558829637 928 True 701.000000 701 80.5260 1 939 1 chr6B.!!$R2 938
2 TraesCS6B01G111500 chr6B 558746126 558747054 928 True 689.000000 689 80.3160 1 939 1 chr6B.!!$R1 938
3 TraesCS6B01G111500 chrUn 19244657 19248391 3734 True 616.660000 2342 93.4610 2103 5300 5 chrUn.!!$R2 3197
4 TraesCS6B01G111500 chr6A 57685011 57691584 6573 False 841.000000 2178 91.5860 2266 5300 3 chr6A.!!$F1 3034
5 TraesCS6B01G111500 chr5A 114378094 114380262 2168 True 882.333333 1600 96.1700 404 2102 3 chr5A.!!$R3 1698
6 TraesCS6B01G111500 chr5A 545879039 545879768 729 False 340.000000 340 75.7260 1 743 1 chr5A.!!$F2 742
7 TraesCS6B01G111500 chr7B 11288737 11290824 2087 False 438.500000 725 77.2440 1 1976 2 chr7B.!!$F3 1975
8 TraesCS6B01G111500 chr7B 692920433 692920942 509 False 331.000000 331 78.7230 5 512 1 chr7B.!!$F2 507
9 TraesCS6B01G111500 chr6D 450354551 450355161 610 False 717.000000 717 88.1300 2677 3280 1 chr6D.!!$F1 603
10 TraesCS6B01G111500 chr6D 31797881 31798615 734 True 472.000000 472 78.5430 1 748 1 chr6D.!!$R1 747
11 TraesCS6B01G111500 chr7D 504350619 504354178 3559 False 394.100000 704 76.6550 1 1920 2 chr7D.!!$F1 1919
12 TraesCS6B01G111500 chr7D 497946844 497949289 2445 True 237.000000 374 76.8315 1 2007 2 chr7D.!!$R1 2006
13 TraesCS6B01G111500 chr4D 87556039 87556594 555 True 409.000000 409 80.2430 190 759 1 chr4D.!!$R1 569
14 TraesCS6B01G111500 chr3A 660897499 660898053 554 True 374.000000 374 79.2030 190 759 1 chr3A.!!$R4 569


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
344 365 0.038166 ACCGGCATGATCCAGTGTTT 59.962 50.0 0.0 0.0 0.00 2.83 F
1642 1917 0.030638 GAGACTGAGCAGCGAGGATC 59.969 60.0 0.0 0.0 0.00 3.36 F
2535 4424 0.107848 AGATAGGGTTTTGCGGACGG 60.108 55.0 0.0 0.0 0.00 4.79 F
2673 4627 0.169672 TCGACTAGTACAACGCTGCC 59.830 55.0 0.0 0.0 0.00 4.85 F
2769 4723 0.318441 CAGTTCTCTGGACGAAGCCA 59.682 55.0 0.0 0.0 37.97 4.75 F
3093 5056 0.384309 TAGCGTACAGGATTGGCTCG 59.616 55.0 0.0 0.0 35.28 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 3852 0.025001 CTTTATCACAACGGCTCGCG 59.975 55.000 0.00 0.0 0.00 5.87 R
3575 8345 0.040958 GACAAGTGCAAGAACCTGCG 60.041 55.000 0.00 0.0 45.74 5.18 R
3789 10122 0.329261 TCTACTCCCTCCGTTCCGAA 59.671 55.000 0.00 0.0 0.00 4.30 R
3843 10176 0.521867 CGTGCATGCTGAAATCCACG 60.522 55.000 20.33 13.6 39.75 4.94 R
3848 10181 1.200716 CCTTGACGTGCATGCTGAAAT 59.799 47.619 20.33 0.0 0.00 2.17 R
4374 10728 1.278238 GAACATCTGTTACGGCCTCG 58.722 55.000 0.00 0.0 38.56 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.