Multiple sequence alignment - TraesCS5D01G162000

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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 TraesCS5D01G162000 chr5D 100.000 2780 0 0 1 2780 253176937 253179716 0.000000e+00 5134
1 TraesCS5D01G162000 chr5A 97.363 1934 48 1 847 2780 335672035 335673965 0.000000e+00 3286
2 TraesCS5D01G162000 chr5A 85.764 864 97 13 1 848 548890926 548890073 0.000000e+00 891
3 TraesCS5D01G162000 chr5A 85.665 865 95 15 1 848 548772950 548772098 0.000000e+00 883
4 TraesCS5D01G162000 chr5B 96.363 1622 52 4 847 2464 285499002 285500620 0.000000e+00 2662
5 TraesCS5D01G162000 chr5B 95.307 277 13 0 2504 2780 285500618 285500894 9.140000e-120 440
6 TraesCS5D01G162000 chr2D 94.063 859 38 8 1 847 332556273 332557130 0.000000e+00 1291
7 TraesCS5D01G162000 chr4D 87.717 863 81 15 1 847 98519761 98520614 0.000000e+00 983
8 TraesCS5D01G162000 chr4D 87.413 866 81 18 1 849 478229390 478230244 0.000000e+00 970
9 TraesCS5D01G162000 chr6B 86.674 863 92 17 1 848 57156012 57156866 0.000000e+00 935
10 TraesCS5D01G162000 chr4A 86.674 863 92 19 1 846 102441482 102442338 0.000000e+00 935
11 TraesCS5D01G162000 chr3A 86.079 862 96 18 1 845 595117167 595116313 0.000000e+00 905
12 TraesCS5D01G162000 chr3A 85.930 860 99 19 1 846 703173050 703173901 0.000000e+00 898


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 TraesCS5D01G162000 chr5D 253176937 253179716 2779 False 5134 5134 100.000 1 2780 1 chr5D.!!$F1 2779
1 TraesCS5D01G162000 chr5A 335672035 335673965 1930 False 3286 3286 97.363 847 2780 1 chr5A.!!$F1 1933
2 TraesCS5D01G162000 chr5A 548890073 548890926 853 True 891 891 85.764 1 848 1 chr5A.!!$R2 847
3 TraesCS5D01G162000 chr5A 548772098 548772950 852 True 883 883 85.665 1 848 1 chr5A.!!$R1 847
4 TraesCS5D01G162000 chr5B 285499002 285500894 1892 False 1551 2662 95.835 847 2780 2 chr5B.!!$F1 1933
5 TraesCS5D01G162000 chr2D 332556273 332557130 857 False 1291 1291 94.063 1 847 1 chr2D.!!$F1 846
6 TraesCS5D01G162000 chr4D 98519761 98520614 853 False 983 983 87.717 1 847 1 chr4D.!!$F1 846
7 TraesCS5D01G162000 chr4D 478229390 478230244 854 False 970 970 87.413 1 849 1 chr4D.!!$F2 848
8 TraesCS5D01G162000 chr6B 57156012 57156866 854 False 935 935 86.674 1 848 1 chr6B.!!$F1 847
9 TraesCS5D01G162000 chr4A 102441482 102442338 856 False 935 935 86.674 1 846 1 chr4A.!!$F1 845
10 TraesCS5D01G162000 chr3A 595116313 595117167 854 True 905 905 86.079 1 845 1 chr3A.!!$R1 844
11 TraesCS5D01G162000 chr3A 703173050 703173901 851 False 898 898 85.930 1 846 1 chr3A.!!$F1 845

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
397 421 0.161658 GCGATACGTGGAATCATGCG 59.838 55.0 0.0 0.0 33.32 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 2392 1.268539 GCCACACCAACAGAAGAAACG 60.269 52.381 0.0 0.0 0.0 3.6 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
328 347 7.913297 TGAAAATTAAACAGAAACTTCACTCGG 59.087 33.333 0.00 0.00 0.00 4.63
336 355 6.110707 ACAGAAACTTCACTCGGAAAAAGTA 58.889 36.000 0.00 0.00 34.44 2.24
393 417 2.967362 ACAAAGCGATACGTGGAATCA 58.033 42.857 0.00 0.00 0.00 2.57
397 421 0.161658 GCGATACGTGGAATCATGCG 59.838 55.000 0.00 0.00 33.32 4.73
489 514 4.756084 CCAAGAGGTCTGTGATTCAAAC 57.244 45.455 0.00 0.00 0.00 2.93
516 541 6.295011 CCCTTCATGCCAACTTGTGTTTATAA 60.295 38.462 0.00 0.00 33.52 0.98
803 842 7.492994 TGTTTATTTTTCAAGTTTAGGCACCAC 59.507 33.333 0.00 0.00 0.00 4.16
816 855 1.228215 CACCACACTGACCATGCCA 60.228 57.895 0.00 0.00 0.00 4.92
922 965 1.613317 TTCGTGGCAGATCGGGACAT 61.613 55.000 0.00 0.00 0.00 3.06
1128 1175 3.197106 TGGTCCCCACTTCCTCAAT 57.803 52.632 0.00 0.00 0.00 2.57
1161 1208 0.396695 CCTTCTACCTCGCCCACCTA 60.397 60.000 0.00 0.00 0.00 3.08
1176 1223 2.415843 CTATCCGCCGCCTTCGAA 59.584 61.111 0.00 0.00 38.10 3.71
1439 1486 2.182030 CCTCGGCGTCCTCAACTC 59.818 66.667 6.85 0.00 0.00 3.01
1836 1883 1.956477 CTTGCCTTAGTGTTGCCTGTT 59.044 47.619 0.00 0.00 0.00 3.16
1920 1967 6.792326 AGCTTGTGTAAGTAAAGTTTTGGAC 58.208 36.000 0.00 0.00 36.27 4.02
1932 1979 3.606687 AGTTTTGGACGAGTTTCACAGT 58.393 40.909 0.00 0.00 0.00 3.55
1948 1995 6.525121 TTCACAGTCAAATGTTAGTTCTCG 57.475 37.500 0.00 0.00 0.00 4.04
1950 1997 5.920840 TCACAGTCAAATGTTAGTTCTCGAG 59.079 40.000 5.93 5.93 0.00 4.04
1976 2023 7.650504 GTGTGGTCAATACTTAATACTGCGATA 59.349 37.037 0.00 0.00 0.00 2.92
2002 2049 2.997986 CCGTGCTTATGTTCGTAAGGTT 59.002 45.455 11.98 0.00 33.31 3.50
2003 2050 3.434299 CCGTGCTTATGTTCGTAAGGTTT 59.566 43.478 11.98 0.00 33.31 3.27
2050 2097 6.173339 GTTGGAGTTCATGTCCTCTTTATGA 58.827 40.000 12.09 0.00 34.86 2.15
2291 2338 1.153756 AGTTTGGGGGCAAGACAGG 59.846 57.895 0.00 0.00 0.00 4.00
2345 2392 7.948278 ATTCTGTTCTTCAGTTGTAGTGTAC 57.052 36.000 0.00 0.00 43.97 2.90
2467 2514 6.767902 TGAAGATGCATATACTTCCTTTCACC 59.232 38.462 18.78 0.06 39.14 4.02
2468 2515 6.506538 AGATGCATATACTTCCTTTCACCT 57.493 37.500 0.00 0.00 0.00 4.00
2471 2518 4.473196 TGCATATACTTCCTTTCACCTGGA 59.527 41.667 0.00 0.00 0.00 3.86
2496 2543 7.935338 ACATTTTCAGTGCTGTAAATTTCTG 57.065 32.000 12.10 7.27 38.11 3.02
2636 2683 1.330521 ACAAACACTGTGATGTCGCAC 59.669 47.619 15.86 0.00 36.69 5.34
2679 2726 8.252417 TGTTTGATTGGTATTTGAATGATGAGG 58.748 33.333 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
373 397 2.967362 TGATTCCACGTATCGCTTTGT 58.033 42.857 0.00 0.00 0.00 2.83
482 507 3.173953 TGGCATGAAGGGAGTTTGAAT 57.826 42.857 0.00 0.00 0.00 2.57
489 514 1.542915 CACAAGTTGGCATGAAGGGAG 59.457 52.381 7.96 0.00 0.00 4.30
561 588 1.345176 GCATTAGACGCACGCTGTC 59.655 57.895 6.07 6.07 36.60 3.51
803 842 1.552337 ACTAGTCTGGCATGGTCAGTG 59.448 52.381 0.00 0.00 36.55 3.66
816 855 7.916077 AAATACACTATGCCCTAACTAGTCT 57.084 36.000 0.00 0.00 0.00 3.24
922 965 7.229907 GTGGTTTTCTGATTTACTCCCTACAAA 59.770 37.037 0.00 0.00 0.00 2.83
1128 1175 1.521457 GAAGGCGATGATGCGGTCA 60.521 57.895 0.00 0.00 42.06 4.02
1161 1208 4.530857 CCTTCGAAGGCGGCGGAT 62.531 66.667 30.28 0.00 39.76 4.18
1505 1552 4.435970 TAGGGCCCTCGACGAGCA 62.436 66.667 32.80 4.60 0.00 4.26
1518 1565 4.256180 GCCTGCATCGGGGTAGGG 62.256 72.222 11.87 0.00 40.60 3.53
1920 1967 6.287107 ACTAACATTTGACTGTGAAACTCG 57.713 37.500 0.00 0.00 38.04 4.18
1932 1979 4.988540 CCACACTCGAGAACTAACATTTGA 59.011 41.667 21.68 0.00 0.00 2.69
1948 1995 6.019801 CGCAGTATTAAGTATTGACCACACTC 60.020 42.308 0.00 0.00 0.00 3.51
1950 1997 5.808540 TCGCAGTATTAAGTATTGACCACAC 59.191 40.000 0.00 0.00 0.00 3.82
1976 2023 5.292589 CCTTACGAACATAAGCACGGTTAAT 59.707 40.000 0.00 0.00 31.80 1.40
2002 2049 6.013725 ACAGGTGTGATCCACTATACTTCAAA 60.014 38.462 12.27 0.00 43.94 2.69
2003 2050 5.483937 ACAGGTGTGATCCACTATACTTCAA 59.516 40.000 12.27 0.00 43.94 2.69
2260 2307 1.666888 CCCAAACTGCATTTCGTCAGC 60.667 52.381 0.00 0.00 33.80 4.26
2291 2338 6.545504 TCAACTGTCATAGCTTTGTTCTTC 57.454 37.500 4.00 0.00 0.00 2.87
2345 2392 1.268539 GCCACACCAACAGAAGAAACG 60.269 52.381 0.00 0.00 0.00 3.60
2467 2514 3.996150 ACAGCACTGAAAATGTTCCAG 57.004 42.857 4.31 0.00 32.28 3.86
2468 2515 5.843673 TTTACAGCACTGAAAATGTTCCA 57.156 34.783 4.31 0.00 32.28 3.53
2471 2518 7.042523 GCAGAAATTTACAGCACTGAAAATGTT 60.043 33.333 4.31 0.00 0.00 2.71
2580 2627 7.470935 TCACCTCAATGATCAAAATGAACAT 57.529 32.000 0.00 0.00 40.87 2.71
2679 2726 5.523369 AGAGAATACTTTGCAGCAAACAAC 58.477 37.500 16.93 7.00 0.00 3.32
2728 2775 6.767902 ACAGTAGCCCATTGTATTCATTGTAG 59.232 38.462 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.