Multiple sequence alignment - TraesCS6B01G296600

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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 TraesCS6B01G296600 chr6B 100.000 2126 0 0 1 2126 532336686 532338811 0.000000e+00 3927.0
1 TraesCS6B01G296600 chr6B 97.297 37 1 0 1809 1845 532338461 532338497 1.760000e-06 63.9
2 TraesCS6B01G296600 chr6B 97.297 37 1 0 1776 1812 532338494 532338530 1.760000e-06 63.9
3 TraesCS6B01G296600 chr6A 92.374 1862 84 20 2 1845 495683965 495685786 0.000000e+00 2599.0
4 TraesCS6B01G296600 chr6A 96.078 357 7 4 1776 2126 495685750 495686105 1.830000e-160 575.0
5 TraesCS6B01G296600 chr6A 97.368 38 0 1 1809 1845 495685716 495685753 1.760000e-06 63.9
6 TraesCS6B01G296600 chr6D 90.337 1366 68 11 1 1362 347689274 347687969 0.000000e+00 1733.0
7 TraesCS6B01G296600 chr6D 95.501 689 26 2 1443 2126 347687968 347687280 0.000000e+00 1096.0


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 TraesCS6B01G296600 chr6B 532336686 532338811 2125 False 1351.6 3927 98.198000 1 2126 3 chr6B.!!$F1 2125
1 TraesCS6B01G296600 chr6A 495683965 495686105 2140 False 1079.3 2599 95.273333 2 2126 3 chr6A.!!$F1 2124
2 TraesCS6B01G296600 chr6D 347687280 347689274 1994 True 1414.5 1733 92.919000 1 2126 2 chr6D.!!$R1 2125

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
979 1000 0.534412 CCAGCAGTGATCTTCGGAGT 59.466 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1906 3.001395 TGTTCCGGTAATTTTGTTGCG 57.999 42.857 0.0 0.0 0.0 4.85 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
28 29 4.956075 CAGGATTATACTGGGGTGCTTTTT 59.044 41.667 0.00 0.00 32.38 1.94
59 60 5.394224 TTTTTCGTCCTTCCTTTTGTTGT 57.606 34.783 0.00 0.00 0.00 3.32
161 163 7.437862 TGAGAAAAATCTATGTGTTTTTGTGCC 59.562 33.333 1.08 0.00 37.57 5.01
277 279 2.680841 CAACCCGAGGCGATATTTTGAA 59.319 45.455 0.00 0.00 0.00 2.69
338 340 2.851263 ACCGTTTGAGCCAGTAATGA 57.149 45.000 0.00 0.00 0.00 2.57
351 353 5.530171 AGCCAGTAATGAGATAGCAACATTG 59.470 40.000 11.66 0.00 36.06 2.82
357 359 8.462016 AGTAATGAGATAGCAACATTGTTTTCC 58.538 33.333 11.66 0.00 36.06 3.13
364 366 4.441792 AGCAACATTGTTTTCCAACTTCC 58.558 39.130 0.00 0.00 35.44 3.46
378 380 3.068590 CCAACTTCCATGTTTCAAGCAGT 59.931 43.478 0.00 0.00 0.00 4.40
415 417 1.741327 ATGCCAATTGAGATGCCGGC 61.741 55.000 22.73 22.73 40.02 6.13
483 488 2.945440 GCAATGTCCAGCTCCACCAATA 60.945 50.000 0.00 0.00 0.00 1.90
489 494 6.114187 TGTCCAGCTCCACCAATATTATAG 57.886 41.667 0.00 0.00 0.00 1.31
502 507 9.090103 CACCAATATTATAGACTTCTACCCTGA 57.910 37.037 0.00 0.00 0.00 3.86
551 556 9.595823 TGTGATTTAGGTAAAAGAGTGCTATAC 57.404 33.333 0.00 0.00 0.00 1.47
594 599 6.142139 TGAGAACTATGTTTCATTTTGTGCG 58.858 36.000 0.00 0.00 0.00 5.34
598 603 7.803189 AGAACTATGTTTCATTTTGTGCGTTAG 59.197 33.333 0.00 0.00 0.00 2.34
675 680 8.659925 TCAATTCAAATTTTTGCTGTGTACAT 57.340 26.923 0.00 0.00 38.05 2.29
679 684 6.451393 TCAAATTTTTGCTGTGTACATACCC 58.549 36.000 0.00 0.00 38.05 3.69
807 824 2.799126 TCCAAATGGTTCTATGCCGT 57.201 45.000 0.00 0.00 36.34 5.68
810 827 4.787551 TCCAAATGGTTCTATGCCGTATT 58.212 39.130 0.00 0.00 36.34 1.89
828 845 5.220912 CCGTATTGATGTTCATGCTTCATGT 60.221 40.000 6.68 0.00 41.98 3.21
844 861 7.315142 TGCTTCATGTAAATGATTCTTGTTCC 58.685 34.615 0.00 0.00 0.00 3.62
845 862 7.177216 TGCTTCATGTAAATGATTCTTGTTCCT 59.823 33.333 0.00 0.00 0.00 3.36
846 863 8.031277 GCTTCATGTAAATGATTCTTGTTCCTT 58.969 33.333 0.00 0.00 0.00 3.36
847 864 9.918630 CTTCATGTAAATGATTCTTGTTCCTTT 57.081 29.630 0.00 0.00 0.00 3.11
910 927 1.069973 TGTCATCGAGCGCAAAAAGTG 60.070 47.619 11.47 0.22 0.00 3.16
979 1000 0.534412 CCAGCAGTGATCTTCGGAGT 59.466 55.000 0.00 0.00 0.00 3.85
1246 1267 6.808704 CCTTTCTTTTGTTCTATTGGCTAAGC 59.191 38.462 0.00 0.00 0.00 3.09
1265 1288 7.168804 GGCTAAGCTTTTATCATCTCATTTTGC 59.831 37.037 3.20 0.00 0.00 3.68
1297 1320 0.103755 TCAGCGCATCATCTCCAGAC 59.896 55.000 11.47 0.00 0.00 3.51
1420 1443 5.633830 ACTGTTCTTTCCTGCATGTATTG 57.366 39.130 0.00 0.00 0.00 1.90
1432 1455 4.891260 TGCATGTATTGGCATGTGAAAAA 58.109 34.783 7.71 0.00 45.75 1.94
1615 1638 7.699878 TGCTATATTCTGGGACTCTACTATGA 58.300 38.462 0.00 0.00 0.00 2.15
1631 1654 5.121380 ACTATGATTGCTGTGGGATCTTT 57.879 39.130 0.00 0.00 0.00 2.52
1661 1684 2.624838 ACCAAATCCAAGACAGCACAAG 59.375 45.455 0.00 0.00 0.00 3.16
1849 1906 5.476945 TCCCAAAGGAAAAAGCTTCTATCAC 59.523 40.000 0.00 0.00 40.08 3.06
1868 1925 2.722116 CACGCAACAAAATTACCGGAAC 59.278 45.455 9.46 0.00 0.00 3.62
1893 1950 7.951245 ACAATGGATAGGTAACCCTTTTTGTAA 59.049 33.333 0.00 0.00 42.66 2.41
1965 2023 5.125417 TGCATTTTTCTTAGAGCGCCTTATT 59.875 36.000 2.29 0.00 0.00 1.40
1970 2028 6.569179 TTTCTTAGAGCGCCTTATTTTTGT 57.431 33.333 2.29 0.00 0.00 2.83
2084 2146 7.440198 TCCTATGATCACTCTTGCTATCTTTG 58.560 38.462 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.647399 AGGAAGGACGAAAAATCCAAACAA 59.353 37.500 0.00 0.0 38.86 2.83
43 44 5.774498 AATCAGACAACAAAAGGAAGGAC 57.226 39.130 0.00 0.0 0.00 3.85
45 46 7.510549 TCTAAATCAGACAACAAAAGGAAGG 57.489 36.000 0.00 0.0 0.00 3.46
59 60 6.582295 GCGCAAACAGAAAAATCTAAATCAGA 59.418 34.615 0.30 0.0 37.79 3.27
75 76 0.660300 GAACCTTTCCGCGCAAACAG 60.660 55.000 8.75 0.0 0.00 3.16
76 77 1.357334 GAACCTTTCCGCGCAAACA 59.643 52.632 8.75 0.0 0.00 2.83
77 78 1.371267 GGAACCTTTCCGCGCAAAC 60.371 57.895 8.75 0.0 40.59 2.93
78 79 3.035727 GGAACCTTTCCGCGCAAA 58.964 55.556 8.75 0.0 40.59 3.68
101 103 1.886886 AAAGGCGCCTTTTAACGAGA 58.113 45.000 41.76 0.0 42.93 4.04
161 163 6.309494 CACCTCAATCACAATTTACATTGCAG 59.691 38.462 1.43 0.0 43.39 4.41
261 263 3.493129 TCCGAATTCAAAATATCGCCTCG 59.507 43.478 6.22 0.0 34.13 4.63
277 279 9.035890 TCCATACATATAGAAACATCTCCGAAT 57.964 33.333 0.00 0.0 0.00 3.34
338 340 6.655078 AGTTGGAAAACAATGTTGCTATCT 57.345 33.333 0.00 0.0 41.95 1.98
351 353 5.006649 GCTTGAAACATGGAAGTTGGAAAAC 59.993 40.000 0.00 0.0 0.00 2.43
357 359 4.046462 CACTGCTTGAAACATGGAAGTTG 58.954 43.478 0.00 0.0 0.00 3.16
364 366 4.637534 AGCTATACCACTGCTTGAAACATG 59.362 41.667 0.00 0.0 32.61 3.21
378 380 3.496692 GGCATGGTGATCAAGCTATACCA 60.497 47.826 0.00 0.0 44.66 3.25
415 417 6.011879 GCTATTCATCAATCGCAATAACGAG 58.988 40.000 0.00 0.0 46.69 4.18
452 454 3.382546 AGCTGGACATTGCAAACCATATC 59.617 43.478 18.74 12.9 0.00 1.63
489 494 9.372369 GCATACATTAATATCAGGGTAGAAGTC 57.628 37.037 0.00 0.0 0.00 3.01
540 545 8.663209 AATATCAGAATCAGGTATAGCACTCT 57.337 34.615 4.48 0.0 0.00 3.24
551 556 6.430962 TCTCAGGGAAATATCAGAATCAGG 57.569 41.667 0.00 0.0 0.00 3.86
738 755 7.742089 CGATCTCTATCAGAAAACAACACAAAC 59.258 37.037 0.00 0.0 33.62 2.93
804 821 4.880886 TGAAGCATGAACATCAATACGG 57.119 40.909 0.00 0.0 0.00 4.02
807 824 9.738832 CATTTACATGAAGCATGAACATCAATA 57.261 29.630 13.79 0.0 43.81 1.90
810 827 7.393841 TCATTTACATGAAGCATGAACATCA 57.606 32.000 13.79 0.0 43.81 3.07
848 865 8.367156 CAAAGGAATAAGAATCACCCTCAAAAA 58.633 33.333 0.00 0.0 0.00 1.94
849 866 7.039082 CCAAAGGAATAAGAATCACCCTCAAAA 60.039 37.037 0.00 0.0 0.00 2.44
850 867 6.437162 CCAAAGGAATAAGAATCACCCTCAAA 59.563 38.462 0.00 0.0 0.00 2.69
851 868 5.951747 CCAAAGGAATAAGAATCACCCTCAA 59.048 40.000 0.00 0.0 0.00 3.02
852 869 5.509498 CCAAAGGAATAAGAATCACCCTCA 58.491 41.667 0.00 0.0 0.00 3.86
853 870 4.339530 GCCAAAGGAATAAGAATCACCCTC 59.660 45.833 0.00 0.0 0.00 4.30
854 871 4.264352 TGCCAAAGGAATAAGAATCACCCT 60.264 41.667 0.00 0.0 0.00 4.34
855 872 4.023291 TGCCAAAGGAATAAGAATCACCC 58.977 43.478 0.00 0.0 0.00 4.61
856 873 5.859205 ATGCCAAAGGAATAAGAATCACC 57.141 39.130 0.00 0.0 0.00 4.02
857 874 7.067494 AGTGTATGCCAAAGGAATAAGAATCAC 59.933 37.037 0.00 0.0 0.00 3.06
858 875 7.118723 AGTGTATGCCAAAGGAATAAGAATCA 58.881 34.615 0.00 0.0 0.00 2.57
859 876 7.573968 AGTGTATGCCAAAGGAATAAGAATC 57.426 36.000 0.00 0.0 0.00 2.52
861 878 9.555727 GTATAGTGTATGCCAAAGGAATAAGAA 57.444 33.333 0.00 0.0 0.00 2.52
862 879 8.154856 GGTATAGTGTATGCCAAAGGAATAAGA 58.845 37.037 0.00 0.0 40.26 2.10
863 880 7.936847 TGGTATAGTGTATGCCAAAGGAATAAG 59.063 37.037 1.63 0.0 45.99 1.73
864 881 7.807198 TGGTATAGTGTATGCCAAAGGAATAA 58.193 34.615 1.63 0.0 45.99 1.40
865 882 7.381789 TGGTATAGTGTATGCCAAAGGAATA 57.618 36.000 1.63 0.0 45.99 1.75
866 883 6.260700 TGGTATAGTGTATGCCAAAGGAAT 57.739 37.500 1.63 0.0 45.99 3.01
867 884 5.702065 TGGTATAGTGTATGCCAAAGGAA 57.298 39.130 1.63 0.0 45.99 3.36
910 927 7.946655 TCAGAATGATGTGGTCGATTATAAC 57.053 36.000 0.00 0.0 42.56 1.89
974 995 6.851330 GTCTTTGATGAACACTTTAAACTCCG 59.149 38.462 0.00 0.0 0.00 4.63
979 1000 7.286546 TCCCATGTCTTTGATGAACACTTTAAA 59.713 33.333 0.00 0.0 0.00 1.52
1127 1148 2.029020 TGCTGTCGTTGAGCATAGAACT 60.029 45.455 0.00 0.0 41.56 3.01
1265 1288 6.716898 TGATGCGCTGATAAATAGAGAATG 57.283 37.500 9.73 0.0 0.00 2.67
1420 1443 5.988561 TGGTTGATTTAGTTTTTCACATGCC 59.011 36.000 0.00 0.0 0.00 4.40
1432 1455 9.739276 TGTTTCAAGAGATATGGTTGATTTAGT 57.261 29.630 0.00 0.0 30.50 2.24
1615 1638 3.087031 CTCACAAAGATCCCACAGCAAT 58.913 45.455 0.00 0.0 0.00 3.56
1849 1906 3.001395 TGTTCCGGTAATTTTGTTGCG 57.999 42.857 0.00 0.0 0.00 4.85
1898 1956 7.180229 TCAATACAACTGTTATCCAGAGGAGAA 59.820 37.037 0.00 0.0 44.49 2.87
1935 1993 4.558496 CGCTCTAAGAAAAATGCAAACCCA 60.558 41.667 0.00 0.0 0.00 4.51
1970 2028 9.231297 CCAACTTCCTTAATCAACTTGAATCTA 57.769 33.333 0.00 0.0 0.00 1.98
2084 2146 3.988379 TCATTGTTTCACAGTTCAGGC 57.012 42.857 0.00 0.0 0.00 4.85


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

AutoCloner maintained by Alex Coulton.