Multiple sequence alignment - TraesCS6B01G286700

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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 TraesCS6B01G286700 chr6B 100.000 3071 0 0 1 3071 516489156 516486086 0.000000e+00 5672
1 TraesCS6B01G286700 chr6B 92.099 848 43 9 1 826 668716668 668715823 0.000000e+00 1173
2 TraesCS6B01G286700 chr6A 95.697 2254 71 17 838 3071 482087264 482085017 0.000000e+00 3602
3 TraesCS6B01G286700 chr6D 96.556 2178 48 14 913 3071 342028457 342026288 0.000000e+00 3581
4 TraesCS6B01G286700 chr3B 93.152 847 36 3 1 826 161141491 161142336 0.000000e+00 1223
5 TraesCS6B01G286700 chr3B 92.970 569 34 4 1 564 221751934 221752501 0.000000e+00 824
6 TraesCS6B01G286700 chr3B 91.791 536 41 3 46 581 641672252 641671720 0.000000e+00 743
7 TraesCS6B01G286700 chr3B 86.493 422 33 14 427 826 161140743 161140324 2.810000e-120 442
8 TraesCS6B01G286700 chr3B 85.343 423 37 11 426 826 641672901 641673320 6.130000e-112 414
9 TraesCS6B01G286700 chr3B 90.323 217 20 1 1 216 511385896 511386112 1.800000e-72 283
10 TraesCS6B01G286700 chr7B 92.280 842 41 4 1 821 641594285 641595123 0.000000e+00 1173
11 TraesCS6B01G286700 chr2B 87.797 885 75 18 1 855 717007432 717006551 0.000000e+00 1005
12 TraesCS6B01G286700 chr2B 88.179 736 58 13 115 826 608361419 608360689 0.000000e+00 850
13 TraesCS6B01G286700 chr5B 97.314 484 11 2 1 484 426594785 426595266 0.000000e+00 821
14 TraesCS6B01G286700 chr5B 86.505 289 18 2 559 826 426595268 426595556 6.440000e-77 298
15 TraesCS6B01G286700 chr4A 91.753 485 34 5 115 597 146044625 146044145 0.000000e+00 669
16 TraesCS6B01G286700 chr4A 84.223 412 42 9 437 826 146045194 146045604 2.230000e-101 379
17 TraesCS6B01G286700 chr4B 92.257 452 13 3 396 826 615141976 615142426 3.360000e-174 621
18 TraesCS6B01G286700 chr4D 93.204 103 7 0 724 826 397673461 397673359 5.300000e-33 152
19 TraesCS6B01G286700 chr1D 93.204 103 7 0 724 826 452630148 452630250 5.300000e-33 152
20 TraesCS6B01G286700 chr1D 92.233 103 8 0 724 826 490132450 490132552 2.470000e-31 147
21 TraesCS6B01G286700 chr3D 92.233 103 8 0 724 826 155951209 155951107 2.470000e-31 147


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 TraesCS6B01G286700 chr6B 516486086 516489156 3070 True 5672.0 5672 100.0000 1 3071 1 chr6B.!!$R1 3070
1 TraesCS6B01G286700 chr6B 668715823 668716668 845 True 1173.0 1173 92.0990 1 826 1 chr6B.!!$R2 825
2 TraesCS6B01G286700 chr6A 482085017 482087264 2247 True 3602.0 3602 95.6970 838 3071 1 chr6A.!!$R1 2233
3 TraesCS6B01G286700 chr6D 342026288 342028457 2169 True 3581.0 3581 96.5560 913 3071 1 chr6D.!!$R1 2158
4 TraesCS6B01G286700 chr3B 161141491 161142336 845 False 1223.0 1223 93.1520 1 826 1 chr3B.!!$F1 825
5 TraesCS6B01G286700 chr3B 221751934 221752501 567 False 824.0 824 92.9700 1 564 1 chr3B.!!$F2 563
6 TraesCS6B01G286700 chr3B 641671720 641672252 532 True 743.0 743 91.7910 46 581 1 chr3B.!!$R2 535
7 TraesCS6B01G286700 chr7B 641594285 641595123 838 False 1173.0 1173 92.2800 1 821 1 chr7B.!!$F1 820
8 TraesCS6B01G286700 chr2B 717006551 717007432 881 True 1005.0 1005 87.7970 1 855 1 chr2B.!!$R2 854
9 TraesCS6B01G286700 chr2B 608360689 608361419 730 True 850.0 850 88.1790 115 826 1 chr2B.!!$R1 711
10 TraesCS6B01G286700 chr5B 426594785 426595556 771 False 559.5 821 91.9095 1 826 2 chr5B.!!$F1 825

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
862 899 1.197949 CACGAGACGAGAGCTCTGAAA 59.802 52.381 23.91 0.0 33.86 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 2342 1.613317 CCATACACCTCAGCCGGACA 61.613 60.0 5.05 0.0 0.0 4.02 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
424 426 4.875561 AGAAGTTCTCGCCTCTTTTACT 57.124 40.909 0.00 0.00 0.00 2.24
491 498 3.064987 CTCAGGTCGCCGGTTCGAT 62.065 63.158 7.44 0.00 40.84 3.59
666 676 2.285977 ACACACAAACGAAGGGAGTTC 58.714 47.619 0.00 0.00 0.00 3.01
700 711 2.910479 ACGTCAGCACCCGACAGA 60.910 61.111 0.00 0.00 32.72 3.41
702 713 2.734591 GTCAGCACCCGACAGACA 59.265 61.111 0.00 0.00 33.43 3.41
783 815 7.712205 AGTTGGTACTGACACGTAAAAATTACT 59.288 33.333 0.00 0.00 31.99 2.24
826 858 2.159393 CCAATGCCTCAATTGTGGTACG 60.159 50.000 23.73 15.44 36.06 3.67
856 893 1.917782 GAGTGCACGAGACGAGAGCT 61.918 60.000 12.01 0.00 0.00 4.09
862 899 1.197949 CACGAGACGAGAGCTCTGAAA 59.802 52.381 23.91 0.00 33.86 2.69
867 904 3.153919 AGACGAGAGCTCTGAAACTTCT 58.846 45.455 23.91 11.93 0.00 2.85
868 905 3.572255 AGACGAGAGCTCTGAAACTTCTT 59.428 43.478 23.91 0.00 0.00 2.52
869 906 4.038642 AGACGAGAGCTCTGAAACTTCTTT 59.961 41.667 23.91 0.00 0.00 2.52
935 972 1.799933 AAAACAATCACCCAGGCCAA 58.200 45.000 5.01 0.00 0.00 4.52
965 1002 2.594303 CCAGCGGCACAAGTCCAA 60.594 61.111 1.45 0.00 0.00 3.53
1278 1320 1.531602 GCCCACCAAGCTCCAGTTT 60.532 57.895 0.00 0.00 0.00 2.66
1881 1923 1.005748 TGCAAGACACCTCTGCTCG 60.006 57.895 0.00 0.00 0.00 5.03
2119 2161 9.485206 GTAATGTATGGTTTCACCGTTCTATAT 57.515 33.333 0.00 0.00 42.58 0.86
2216 2258 9.609346 ACATTTAATGTTACCTAAATCTAGCGT 57.391 29.630 4.56 0.00 41.63 5.07
2245 2287 1.867233 CAGTGCTTGAACTTACAGCGT 59.133 47.619 0.00 0.00 0.00 5.07
2465 2507 2.745152 CGTGGTCTTTCCTTGAGTGGTT 60.745 50.000 0.00 0.00 37.07 3.67
2696 2739 0.036765 TCGGTTTCCTCCATTGGACG 60.037 55.000 0.00 3.03 35.58 4.79
2697 2740 0.036765 CGGTTTCCTCCATTGGACGA 60.037 55.000 0.00 0.35 35.58 4.20
2819 2876 2.495669 CACTGGTTGGTGGTGAAAAGTT 59.504 45.455 0.00 0.00 33.95 2.66
2839 2897 6.783708 AGTTAAAACATCAAAGTGGGAACA 57.216 33.333 0.00 0.00 38.70 3.18
2930 2988 4.690748 GTCTCTGTATTACAGTTGCAAGCA 59.309 41.667 20.43 0.00 46.03 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.707161 ACCCATGTTGAACATTTCTTGAAATG 59.293 34.615 25.54 25.54 43.77 2.32
339 341 4.308458 TGCGCGCTGGGTTACTGT 62.308 61.111 33.29 0.00 0.00 3.55
491 498 2.125147 CTGAATCCCGCGCAGGAA 60.125 61.111 17.91 0.00 45.00 3.36
612 621 2.102420 GCCCAATTATTTCGGGGAAAGG 59.898 50.000 3.34 0.00 43.57 3.11
713 724 8.533569 AAAAAGACTAAAACAGGGAATCTGAA 57.466 30.769 0.00 0.00 46.18 3.02
783 815 9.699410 ATTGGAAATAGATTGGTGTCAAGATTA 57.301 29.630 0.00 0.00 36.19 1.75
792 824 4.646040 TGAGGCATTGGAAATAGATTGGTG 59.354 41.667 0.00 0.00 0.00 4.17
802 834 2.971330 ACCACAATTGAGGCATTGGAAA 59.029 40.909 20.41 0.00 32.40 3.13
826 858 1.724623 TCGTGCACTCGAGTAAATTGC 59.275 47.619 19.57 17.36 34.85 3.56
856 893 3.202906 CGGTGTGGAAAGAAGTTTCAGA 58.797 45.455 0.66 0.00 43.52 3.27
862 899 1.228154 GGGCGGTGTGGAAAGAAGT 60.228 57.895 0.00 0.00 0.00 3.01
965 1002 0.538746 GTTCCGTGTGGATTTGGGGT 60.539 55.000 0.00 0.00 45.91 4.95
2119 2161 5.234757 GCAACTGCAAGACATCAATCAAAAA 59.765 36.000 0.00 0.00 41.59 1.94
2216 2258 2.618241 AGTTCAAGCACTGAATTTCGCA 59.382 40.909 4.75 0.00 45.74 5.10
2262 2304 2.108514 CACGCACTGCCGATTGGAT 61.109 57.895 1.98 0.00 37.49 3.41
2300 2342 1.613317 CCATACACCTCAGCCGGACA 61.613 60.000 5.05 0.00 0.00 4.02
2465 2507 3.764434 CCTAAGACTAGACTGAGCAACCA 59.236 47.826 0.00 0.00 0.00 3.67
2502 2544 8.890718 TCAATGCATTGATAGAAAGAAGAGAAG 58.109 33.333 33.08 6.24 41.51 2.85
2696 2739 3.326006 TCCTATGCTTCATGGGACTGATC 59.674 47.826 7.67 0.00 44.56 2.92
2697 2740 3.321039 TCCTATGCTTCATGGGACTGAT 58.679 45.455 7.67 0.00 44.56 2.90
2806 2849 7.547722 ACTTTGATGTTTTAACTTTTCACCACC 59.452 33.333 0.00 0.00 0.00 4.61
2807 2850 8.379902 CACTTTGATGTTTTAACTTTTCACCAC 58.620 33.333 0.00 0.00 0.00 4.16
2808 2851 7.547370 CCACTTTGATGTTTTAACTTTTCACCA 59.453 33.333 0.00 0.00 0.00 4.17
2809 2852 7.011016 CCCACTTTGATGTTTTAACTTTTCACC 59.989 37.037 0.00 0.00 0.00 4.02
2813 2856 8.097662 TGTTCCCACTTTGATGTTTTAACTTTT 58.902 29.630 0.00 0.00 0.00 2.27
2814 2857 7.616313 TGTTCCCACTTTGATGTTTTAACTTT 58.384 30.769 0.00 0.00 0.00 2.66
2815 2858 7.176589 TGTTCCCACTTTGATGTTTTAACTT 57.823 32.000 0.00 0.00 0.00 2.66
2847 2905 6.957631 ACTTTCAGGTATCCATCACATACAA 58.042 36.000 0.00 0.00 0.00 2.41
2930 2988 4.698780 GGCTCCGGTTAACTAACAAAGAAT 59.301 41.667 0.00 0.00 37.92 2.40
3035 3093 6.211587 TGAACCCGTAATCTTTCTTCGATA 57.788 37.500 0.00 0.00 0.00 2.92
3051 3109 2.046892 CAGGTGGAGCTGAACCCG 60.047 66.667 10.21 0.00 37.13 5.28


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.