Multiple sequence alignment - TraesCS2D01G299600

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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 TraesCS2D01G299600 chr2D 100.000 2926 0 0 1 2926 381885881 381882956 0.000000e+00 5404.0
1 TraesCS2D01G299600 chr2B 97.956 2055 35 4 80 2129 452774740 452772688 0.000000e+00 3555.0
2 TraesCS2D01G299600 chr2B 92.724 591 39 4 2337 2925 452660307 452659719 0.000000e+00 850.0
3 TraesCS2D01G299600 chr2B 96.190 210 8 0 2132 2341 452772611 452772402 7.760000e-91 344.0
4 TraesCS2D01G299600 chr2B 85.235 149 17 3 2614 2761 52617894 52617750 6.530000e-32 148.0
5 TraesCS2D01G299600 chr2A 96.396 2109 66 6 27 2129 516297224 516295120 0.000000e+00 3465.0
6 TraesCS2D01G299600 chr2A 94.349 637 23 8 2132 2767 516295045 516294421 0.000000e+00 965.0
7 TraesCS2D01G299600 chr2A 91.837 147 12 0 2779 2925 516282338 516282192 3.820000e-49 206.0
8 TraesCS2D01G299600 chr2A 85.906 149 18 2 2614 2761 34656421 34656275 3.900000e-34 156.0
9 TraesCS2D01G299600 chr3A 94.681 94 3 1 688 781 57262239 57262148 8.450000e-31 145.0
10 TraesCS2D01G299600 chr7B 93.684 95 5 1 683 777 500726045 500725952 1.090000e-29 141.0
11 TraesCS2D01G299600 chr5D 94.565 92 3 1 688 779 128577585 128577674 1.090000e-29 141.0
12 TraesCS2D01G299600 chr5B 92.079 101 6 1 679 779 140965918 140966016 1.090000e-29 141.0
13 TraesCS2D01G299600 chr5B 92.632 95 6 1 682 776 21154100 21154007 5.090000e-28 135.0
14 TraesCS2D01G299600 chr5B 84.375 96 14 1 2614 2708 102644170 102644075 3.100000e-15 93.5
15 TraesCS2D01G299600 chr1D 91.262 103 7 1 675 777 483383034 483382934 3.930000e-29 139.0
16 TraesCS2D01G299600 chr4B 84.892 139 17 3 2614 2751 36799087 36798952 1.410000e-28 137.0
17 TraesCS2D01G299600 chr4B 84.173 139 18 3 2614 2751 36700294 36700159 6.580000e-27 132.0
18 TraesCS2D01G299600 chr4B 84.173 139 18 3 2614 2751 36750166 36750031 6.580000e-27 132.0
19 TraesCS2D01G299600 chr3B 91.000 100 8 1 688 786 429973614 429973515 1.830000e-27 134.0
20 TraesCS2D01G299600 chr7A 83.696 92 14 1 2614 2704 384571444 384571535 5.200000e-13 86.1


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 TraesCS2D01G299600 chr2D 381882956 381885881 2925 True 5404.0 5404 100.0000 1 2926 1 chr2D.!!$R1 2925
1 TraesCS2D01G299600 chr2B 452772402 452774740 2338 True 1949.5 3555 97.0730 80 2341 2 chr2B.!!$R3 2261
2 TraesCS2D01G299600 chr2B 452659719 452660307 588 True 850.0 850 92.7240 2337 2925 1 chr2B.!!$R2 588
3 TraesCS2D01G299600 chr2A 516294421 516297224 2803 True 2215.0 3465 95.3725 27 2767 2 chr2A.!!$R3 2740

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
215 216 1.004745 TCTTCTGAAATGGTGAGCCCC 59.995 52.381 0.00 0.00 0.00 5.80 F
476 479 2.984458 GCGACGAGCTAGTAAACCTAG 58.016 52.381 0.00 0.00 45.17 3.02 F
1251 1259 1.302033 CAGTCAGGCCACTGTGTCC 60.302 63.158 13.82 2.92 45.14 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1259 2.475466 GCGGATGACCAGGCACATG 61.475 63.158 4.66 0.00 35.59 3.21 R
1645 1653 3.438297 ACTCGTACAGGTATGCATGAC 57.562 47.619 10.16 1.48 0.00 3.06 R
2852 2936 0.391263 AAGGCGATGGAACGAACTCC 60.391 55.000 0.00 0.00 35.88 3.85 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
24 25 3.411351 CCGTCACTTGCGGTTCCG 61.411 66.667 6.90 6.90 43.84 4.30
25 26 3.411351 CGTCACTTGCGGTTCCGG 61.411 66.667 13.16 0.00 0.00 5.14
33 34 1.231958 TTGCGGTTCCGGTAAAGCTG 61.232 55.000 13.16 0.00 0.00 4.24
65 66 4.077184 CACCTTCGCGTGCCCCTA 62.077 66.667 5.77 0.00 0.00 3.53
68 69 2.280186 CTTCGCGTGCCCCTATCC 60.280 66.667 5.77 0.00 0.00 2.59
69 70 2.762459 TTCGCGTGCCCCTATCCT 60.762 61.111 5.77 0.00 0.00 3.24
215 216 1.004745 TCTTCTGAAATGGTGAGCCCC 59.995 52.381 0.00 0.00 0.00 5.80
476 479 2.984458 GCGACGAGCTAGTAAACCTAG 58.016 52.381 0.00 0.00 45.17 3.02
1251 1259 1.302033 CAGTCAGGCCACTGTGTCC 60.302 63.158 13.82 2.92 45.14 4.02
1645 1653 2.103094 TGCACTCTAAGGATCGGGAATG 59.897 50.000 0.00 0.00 0.00 2.67
1970 1978 3.811083 AGGAGTAGTAGATGTGGACTCG 58.189 50.000 0.00 0.00 37.91 4.18
1971 1979 2.879646 GGAGTAGTAGATGTGGACTCGG 59.120 54.545 0.00 0.00 37.91 4.63
2173 2255 6.744082 CGTTCGAAAAATAAAATCTGGGGTAC 59.256 38.462 0.00 0.00 0.00 3.34
2215 2298 6.314917 TGATGTAATAGGCTGGTGATCTAGA 58.685 40.000 0.00 0.00 0.00 2.43
2356 2439 9.308000 TCTTTGGAAACCATGTTCTACATTAAT 57.692 29.630 0.00 0.00 36.53 1.40
2479 2562 6.339587 TCCACTACCCAAATCAAATCAAAC 57.660 37.500 0.00 0.00 0.00 2.93
2761 2845 1.002468 GATCGTGTGTGCTGCAGTTTT 60.002 47.619 16.64 0.00 0.00 2.43
2788 2872 4.386867 TCGACAGGTCTGATATTGAACC 57.613 45.455 4.84 0.00 0.00 3.62
2804 2888 9.224267 GATATTGAACCAGTAGAATATGCATGT 57.776 33.333 10.16 0.00 0.00 3.21
2819 2903 1.999048 CATGTTCCATTGCAACGCAT 58.001 45.000 0.00 0.00 38.76 4.73
2821 2905 2.917701 TGTTCCATTGCAACGCATAG 57.082 45.000 0.00 0.00 38.76 2.23
2852 2936 9.998106 TTAGCTAGCTTTATTACTATTGAAGGG 57.002 33.333 24.88 0.00 0.00 3.95
2859 2943 7.041984 GCTTTATTACTATTGAAGGGGAGTTCG 60.042 40.741 0.00 0.00 0.00 3.95
2884 2968 0.690192 TCGCCTTCACTTCCCATCAA 59.310 50.000 0.00 0.00 0.00 2.57
2885 2969 1.089920 CGCCTTCACTTCCCATCAAG 58.910 55.000 0.00 0.00 0.00 3.02
2889 2974 3.321968 GCCTTCACTTCCCATCAAGTTTT 59.678 43.478 0.00 0.00 34.17 2.43
2919 3004 0.609406 GCTGTCCTCCCCTTTGGTTC 60.609 60.000 0.00 0.00 34.77 3.62
2925 3010 1.133167 CCTCCCCTTTGGTTCTTTGGT 60.133 52.381 0.00 0.00 34.77 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.752322 TACCGGAACCGCAAGTGACG 62.752 60.000 9.46 0.00 38.24 4.35
9 10 0.600782 TTACCGGAACCGCAAGTGAC 60.601 55.000 9.46 0.00 38.24 3.67
10 11 0.106335 TTTACCGGAACCGCAAGTGA 59.894 50.000 9.46 0.00 38.24 3.41
11 12 0.515564 CTTTACCGGAACCGCAAGTG 59.484 55.000 9.46 0.00 38.24 3.16
12 13 1.232621 GCTTTACCGGAACCGCAAGT 61.233 55.000 9.46 3.55 38.24 3.16
13 14 0.953960 AGCTTTACCGGAACCGCAAG 60.954 55.000 9.46 9.91 38.24 4.01
14 15 1.071814 AGCTTTACCGGAACCGCAA 59.928 52.632 9.46 1.45 38.24 4.85
15 16 1.669760 CAGCTTTACCGGAACCGCA 60.670 57.895 9.46 0.00 38.24 5.69
16 17 0.743345 ATCAGCTTTACCGGAACCGC 60.743 55.000 9.46 5.35 38.24 5.68
17 18 1.006832 CATCAGCTTTACCGGAACCG 58.993 55.000 9.46 6.25 39.44 4.44
18 19 1.379527 CCATCAGCTTTACCGGAACC 58.620 55.000 9.46 0.00 0.00 3.62
19 20 0.733150 GCCATCAGCTTTACCGGAAC 59.267 55.000 9.46 0.00 38.99 3.62
20 21 3.168773 GCCATCAGCTTTACCGGAA 57.831 52.632 9.46 0.00 38.99 4.30
21 22 4.954933 GCCATCAGCTTTACCGGA 57.045 55.556 9.46 0.00 38.99 5.14
33 34 0.326264 AGGTGTGAGTTGGAGCCATC 59.674 55.000 0.00 0.00 0.00 3.51
74 75 7.604164 ACATGCGAGATAAGAAAAGAGAGAAAA 59.396 33.333 0.00 0.00 0.00 2.29
78 79 5.233902 CCACATGCGAGATAAGAAAAGAGAG 59.766 44.000 0.00 0.00 0.00 3.20
183 184 4.819362 TTTCAGAAGAATGGCGGAGCGT 62.819 50.000 0.00 0.00 44.89 5.07
362 363 1.071699 GCTCACAGTACTTTGGTCCCA 59.928 52.381 9.10 0.00 0.00 4.37
497 500 6.750148 AGGAGTAGTATGCTAATTGCTACAC 58.250 40.000 0.00 0.00 43.37 2.90
1251 1259 2.475466 GCGGATGACCAGGCACATG 61.475 63.158 4.66 0.00 35.59 3.21
1645 1653 3.438297 ACTCGTACAGGTATGCATGAC 57.562 47.619 10.16 1.48 0.00 3.06
2215 2298 5.745312 TTCACATAGGTTCAGATCACACT 57.255 39.130 0.00 0.00 0.00 3.55
2321 2404 6.816136 ACATGGTTTCCAAAGAAAGTTTAGG 58.184 36.000 0.00 0.00 42.60 2.69
2414 2497 7.645058 ATTGATTCGGTTGAGGTTTTGATAT 57.355 32.000 0.00 0.00 0.00 1.63
2508 2591 3.850173 AGTATGGGTAAGGAAGGCAAGAA 59.150 43.478 0.00 0.00 0.00 2.52
2634 2718 2.031245 TGTGTGAATCGTGCACAAATCC 60.031 45.455 18.64 0.00 46.63 3.01
2761 2845 7.107639 TCAATATCAGACCTGTCGAAATACA 57.892 36.000 0.00 0.00 34.09 2.29
2788 2872 7.682501 TTGCAATGGAACATGCATATTCTACTG 60.683 37.037 16.84 12.36 46.14 2.74
2804 2888 0.455410 GGCTATGCGTTGCAATGGAA 59.545 50.000 17.22 6.00 43.62 3.53
2849 2933 1.898154 CGATGGAACGAACTCCCCT 59.102 57.895 0.00 0.00 34.22 4.79
2851 2935 1.814169 GGCGATGGAACGAACTCCC 60.814 63.158 0.00 0.00 34.22 4.30
2852 2936 0.391263 AAGGCGATGGAACGAACTCC 60.391 55.000 0.00 0.00 35.88 3.85
2859 2943 1.087501 GGAAGTGAAGGCGATGGAAC 58.912 55.000 0.00 0.00 0.00 3.62
2889 2974 1.004745 GGAGGACAGCATGGGAGAAAA 59.995 52.381 0.00 0.00 43.62 2.29
2901 2986 1.068121 AGAACCAAAGGGGAGGACAG 58.932 55.000 0.00 0.00 41.15 3.51


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

AutoCloner maintained by Alex Coulton.