Multiple sequence alignment - TraesCS2D01G250400

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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 TraesCS2D01G250400 chr2D 100.000 2543 0 0 1 2543 298838814 298841356 0.000000e+00 4697
1 TraesCS2D01G250400 chr2B 96.894 2157 50 10 1 2155 363486006 363483865 0.000000e+00 3596
2 TraesCS2D01G250400 chr2A 96.429 1288 24 6 895 2176 372373556 372374827 0.000000e+00 2104
3 TraesCS2D01G250400 chr2A 94.910 884 32 6 1 882 372372641 372373513 0.000000e+00 1371
4 TraesCS2D01G250400 chr2A 93.305 463 23 6 2017 2477 372374827 372375283 0.000000e+00 676
5 TraesCS2D01G250400 chr2A 85.908 369 39 11 537 902 770712135 770712493 5.130000e-102 381
6 TraesCS2D01G250400 chr1A 80.212 849 122 23 901 1711 584357656 584356816 1.680000e-166 595
7 TraesCS2D01G250400 chr1D 78.187 1004 141 42 909 1883 486858757 486857803 1.020000e-158 569
8 TraesCS2D01G250400 chr1B 78.122 969 132 45 947 1876 677988035 677987108 2.230000e-150 542
9 TraesCS2D01G250400 chr6B 86.761 355 43 2 537 891 640951530 640951880 2.370000e-105 392
10 TraesCS2D01G250400 chr7A 88.073 327 35 4 537 862 285822567 285822244 3.970000e-103 385
11 TraesCS2D01G250400 chr7D 86.246 349 42 6 557 901 538352178 538352524 8.590000e-100 374
12 TraesCS2D01G250400 chrUn 85.754 358 43 7 537 891 85460403 85460051 3.090000e-99 372
13 TraesCS2D01G250400 chr4D 86.567 335 42 2 551 885 336983257 336982926 1.440000e-97 366
14 TraesCS2D01G250400 chr7B 85.165 364 44 9 537 896 690237888 690238245 5.170000e-97 364


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 TraesCS2D01G250400 chr2D 298838814 298841356 2542 False 4697.000000 4697 100.000000 1 2543 1 chr2D.!!$F1 2542
1 TraesCS2D01G250400 chr2B 363483865 363486006 2141 True 3596.000000 3596 96.894000 1 2155 1 chr2B.!!$R1 2154
2 TraesCS2D01G250400 chr2A 372372641 372375283 2642 False 1383.666667 2104 94.881333 1 2477 3 chr2A.!!$F2 2476
3 TraesCS2D01G250400 chr1A 584356816 584357656 840 True 595.000000 595 80.212000 901 1711 1 chr1A.!!$R1 810
4 TraesCS2D01G250400 chr1D 486857803 486858757 954 True 569.000000 569 78.187000 909 1883 1 chr1D.!!$R1 974
5 TraesCS2D01G250400 chr1B 677987108 677988035 927 True 542.000000 542 78.122000 947 1876 1 chr1B.!!$R1 929

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
266 267 1.476488 ACTTGTTTCCAACAGCACCAC 59.524 47.619 0.0 0.0 43.27 4.16 F
1069 1112 0.760189 AGAGCCCTCCTCAGAGATGC 60.760 60.000 0.0 0.0 43.39 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1524 1593 0.992431 ATCATGGCCTCCTGGAGCTT 60.992 55.0 18.51 1.3 34.57 3.74 R
2282 2541 0.629058 GTGTGGGTGGGGGTGATAAT 59.371 55.0 0.00 0.0 0.00 1.28 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
101 102 4.542697 AGTTTTGGAACTTGTGGGTGTAT 58.457 39.130 0.00 0.00 43.48 2.29
266 267 1.476488 ACTTGTTTCCAACAGCACCAC 59.524 47.619 0.00 0.00 43.27 4.16
734 735 6.800072 AAGACAAATTTGGGGTCTGTAAAA 57.200 33.333 21.74 0.00 40.80 1.52
735 736 6.800072 AGACAAATTTGGGGTCTGTAAAAA 57.200 33.333 21.74 0.00 40.21 1.94
1069 1112 0.760189 AGAGCCCTCCTCAGAGATGC 60.760 60.000 0.00 0.00 43.39 3.91
1113 1156 4.585879 GGGTAACAGGAATGTATGTGTGT 58.414 43.478 0.00 0.00 39.74 3.72
1476 1545 2.303022 TGATGGACTTGACCTGAACCTC 59.697 50.000 0.00 0.00 0.00 3.85
1839 1939 2.835701 TTCAGCTCGACGGATGTGGC 62.836 60.000 0.00 0.00 0.00 5.01
1840 1940 3.071206 AGCTCGACGGATGTGGCT 61.071 61.111 0.00 0.00 0.00 4.75
1841 1941 2.887568 GCTCGACGGATGTGGCTG 60.888 66.667 0.00 0.00 0.00 4.85
1842 1942 2.887568 CTCGACGGATGTGGCTGC 60.888 66.667 0.00 0.00 0.00 5.25
1843 1943 3.647649 CTCGACGGATGTGGCTGCA 62.648 63.158 0.50 0.00 0.00 4.41
1844 1944 3.190849 CGACGGATGTGGCTGCAG 61.191 66.667 10.11 10.11 0.00 4.41
1845 1945 2.265739 GACGGATGTGGCTGCAGA 59.734 61.111 20.43 0.00 0.00 4.26
1846 1946 1.812922 GACGGATGTGGCTGCAGAG 60.813 63.158 20.43 0.00 0.00 3.35
2143 2401 4.920640 TTTCACGAATAAAAACCCAGCA 57.079 36.364 0.00 0.00 0.00 4.41
2256 2514 5.343307 AGTGCAATGAAAGGTCAAGTTTT 57.657 34.783 0.00 0.00 37.30 2.43
2258 2516 6.872920 AGTGCAATGAAAGGTCAAGTTTTTA 58.127 32.000 0.00 0.00 37.30 1.52
2314 2573 2.018542 CCCACACATAACTGGGTACG 57.981 55.000 0.00 0.00 42.21 3.67
2324 2583 1.215647 CTGGGTACGGTCAGCAGAC 59.784 63.158 0.00 0.00 44.21 3.51
2437 2696 1.173913 AACGTGCAGAAAATAGGGGC 58.826 50.000 0.00 0.00 0.00 5.80
2512 2772 9.884636 TGTCATGTAAAAATAGTAGTGCATAGT 57.115 29.630 0.00 0.00 0.00 2.12
2520 2780 8.786826 AAAATAGTAGTGCATAGTAAGTTGCA 57.213 30.769 0.00 0.00 46.03 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 1.268640 GCACCGGCGAGTTTTAAAACA 60.269 47.619 28.03 0.00 41.30 2.83
266 267 6.195165 GCCTCTTTGAGCATAAAAAGATACG 58.805 40.000 0.00 0.00 40.60 3.06
687 688 2.932261 TGCCGAGAGCTACTCAGATAA 58.068 47.619 11.93 0.00 45.14 1.75
734 735 7.773690 AGGAACAGTACATGAACAGTAAACTTT 59.226 33.333 0.00 0.00 0.00 2.66
735 736 7.280356 AGGAACAGTACATGAACAGTAAACTT 58.720 34.615 0.00 0.00 0.00 2.66
736 737 6.827727 AGGAACAGTACATGAACAGTAAACT 58.172 36.000 0.00 0.00 0.00 2.66
737 738 7.117379 GGTAGGAACAGTACATGAACAGTAAAC 59.883 40.741 0.00 0.00 0.00 2.01
1069 1112 3.930504 GGATGCCCCTTGCTTGAG 58.069 61.111 0.00 0.00 42.00 3.02
1398 1463 1.000274 AGGACGCAAGCACCAAATTTC 60.000 47.619 7.74 0.00 45.62 2.17
1476 1545 4.125703 GGATGATCAAAGACTGCTGGTAG 58.874 47.826 0.00 0.00 0.00 3.18
1524 1593 0.992431 ATCATGGCCTCCTGGAGCTT 60.992 55.000 18.51 1.30 34.57 3.74
1839 1939 8.747471 TCAGAATAATAGGATATCACTCTGCAG 58.253 37.037 7.63 7.63 0.00 4.41
1840 1940 8.655935 TCAGAATAATAGGATATCACTCTGCA 57.344 34.615 4.83 0.00 0.00 4.41
1841 1941 9.364989 GTTCAGAATAATAGGATATCACTCTGC 57.635 37.037 4.83 0.00 0.00 4.26
2282 2541 0.629058 GTGTGGGTGGGGGTGATAAT 59.371 55.000 0.00 0.00 0.00 1.28
2314 2573 2.740055 CACTGCCGTCTGCTGACC 60.740 66.667 17.01 5.71 41.11 4.02
2360 2619 2.404186 GGTTCGGCCGATCAAACCC 61.404 63.158 31.56 17.41 36.06 4.11
2486 2746 9.884636 ACTATGCACTACTATTTTTACATGACA 57.115 29.630 0.00 0.00 0.00 3.58
2494 2754 9.226606 TGCAACTTACTATGCACTACTATTTTT 57.773 29.630 0.00 0.00 46.87 1.94
2495 2755 8.786826 TGCAACTTACTATGCACTACTATTTT 57.213 30.769 0.00 0.00 46.87 1.82


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

AutoCloner maintained by Alex Coulton.