Multiple sequence alignment - TraesCS6D01G233100

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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 TraesCS6D01G233100 chr6D 100.000 2189 0 0 1 2189 327205068 327207256 0.000000e+00 4043
1 TraesCS6D01G233100 chr6A 94.823 2067 59 11 157 2189 465933249 465935301 0.000000e+00 3181
2 TraesCS6D01G233100 chr6A 91.447 152 10 1 1 149 465933054 465933205 2.850000e-49 206
3 TraesCS6D01G233100 chr6B 92.650 2068 110 23 155 2189 494428743 494426685 0.000000e+00 2939
4 TraesCS6D01G233100 chr6B 91.503 153 11 2 1 151 494428930 494428778 2.200000e-50 209


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 TraesCS6D01G233100 chr6D 327205068 327207256 2188 False 4043.0 4043 100.0000 1 2189 1 chr6D.!!$F1 2188
1 TraesCS6D01G233100 chr6A 465933054 465935301 2247 False 1693.5 3181 93.1350 1 2189 2 chr6A.!!$F1 2188
2 TraesCS6D01G233100 chr6B 494426685 494428930 2245 True 1574.0 2939 92.0765 1 2189 2 chr6B.!!$R1 2188

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
55 56 0.389426 GCCACAGCAGCAAATCCTTG 60.389 55.0 0.0 0.0 39.53 3.61 F
151 157 1.076332 GCACTGCGTTCCTTAATCGT 58.924 50.0 0.0 0.0 0.00 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1107 1173 1.246056 ACCTTGTGCGCATGATGCTT 61.246 50.000 15.91 0.00 42.25 3.91 R
1501 1568 2.069273 CTAAAACGAGCACAGTCTGGG 58.931 52.381 4.53 0.02 0.00 4.45 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
25 26 1.301716 GCTTGTGCCGACTCTTGGA 60.302 57.895 0.00 0.00 0.00 3.53
27 28 1.151668 CTTGTGCCGACTCTTGGAAG 58.848 55.000 0.00 0.00 0.00 3.46
55 56 0.389426 GCCACAGCAGCAAATCCTTG 60.389 55.000 0.00 0.00 39.53 3.61
85 86 3.427503 CCACCAGTTTGCACGGATAATTC 60.428 47.826 0.00 0.00 0.00 2.17
89 90 5.036737 CCAGTTTGCACGGATAATTCAATC 58.963 41.667 0.00 0.00 0.00 2.67
97 103 9.944663 TTGCACGGATAATTCAATCTAATTTAC 57.055 29.630 0.00 0.00 31.63 2.01
151 157 1.076332 GCACTGCGTTCCTTAATCGT 58.924 50.000 0.00 0.00 0.00 3.73
152 158 1.463444 GCACTGCGTTCCTTAATCGTT 59.537 47.619 0.00 0.00 0.00 3.85
153 159 2.095919 GCACTGCGTTCCTTAATCGTTT 60.096 45.455 0.00 0.00 0.00 3.60
154 160 3.479006 CACTGCGTTCCTTAATCGTTTG 58.521 45.455 0.00 0.00 0.00 2.93
155 161 2.482721 ACTGCGTTCCTTAATCGTTTGG 59.517 45.455 0.00 0.00 0.00 3.28
412 463 7.176690 TGCATCTCACTATTCGGTATCTTATCA 59.823 37.037 0.00 0.00 0.00 2.15
587 638 2.826428 GAGCGCCACTCAGATGATAAA 58.174 47.619 2.29 0.00 45.49 1.40
621 672 4.460382 GGGAAATGACAGAATCTTTGCAGA 59.540 41.667 0.00 0.00 0.00 4.26
626 677 4.206375 TGACAGAATCTTTGCAGACCAAA 58.794 39.130 0.00 0.00 40.97 3.28
885 939 2.554032 CGGAATCCAGACAAAGCAAGTT 59.446 45.455 0.00 0.00 0.00 2.66
898 952 3.151912 AGCAAGTTTTCCAGAGATGCT 57.848 42.857 0.00 0.00 37.80 3.79
905 959 2.592102 TTCCAGAGATGCTTGGCTTT 57.408 45.000 0.00 0.00 0.00 3.51
906 960 3.719268 TTCCAGAGATGCTTGGCTTTA 57.281 42.857 0.00 0.00 0.00 1.85
907 961 3.939740 TCCAGAGATGCTTGGCTTTAT 57.060 42.857 0.00 0.00 0.00 1.40
908 962 5.372343 TTCCAGAGATGCTTGGCTTTATA 57.628 39.130 0.00 0.00 0.00 0.98
909 963 5.573380 TCCAGAGATGCTTGGCTTTATAT 57.427 39.130 0.00 0.00 0.00 0.86
1107 1173 2.350134 CTCCAGCAGCTGAAGGCA 59.650 61.111 24.90 7.27 44.79 4.75
1177 1243 0.461961 GAGGCTGCAGACGATAACCT 59.538 55.000 20.43 12.49 0.00 3.50
1296 1362 0.923358 TGGAGTGGGGTGAACAACTT 59.077 50.000 0.00 0.00 0.00 2.66
1392 1459 8.164058 AGATGGAGATAAATAAAGAAGCAAGC 57.836 34.615 0.00 0.00 0.00 4.01
1447 1514 3.165071 CCAAGTTCCCCAAGCAAATAGT 58.835 45.455 0.00 0.00 0.00 2.12
1531 1598 3.439129 GTGCTCGTTTTAGCCCTTGTAAT 59.561 43.478 0.00 0.00 42.05 1.89
1570 1637 5.708948 TCCTTTTCCTGCAAATATTGAACG 58.291 37.500 0.00 0.00 0.00 3.95
1615 1682 6.583806 CAGAATCAATAGGAAAACACAGCAAC 59.416 38.462 0.00 0.00 0.00 4.17
1616 1683 4.846779 TCAATAGGAAAACACAGCAACC 57.153 40.909 0.00 0.00 0.00 3.77
1777 1866 7.117812 CACACTAACATGATCCTTCGTTAACTT 59.882 37.037 0.00 0.00 0.00 2.66
1807 1896 2.093973 ACGCCGATCTCAAGATTTCACT 60.094 45.455 0.00 0.00 34.37 3.41
1815 1904 8.119226 CCGATCTCAAGATTTCACTATTTTGTC 58.881 37.037 0.00 0.00 34.37 3.18
1859 1950 4.397420 TCAATTAGGCTGAAGCAAAGTGA 58.603 39.130 12.73 12.73 44.36 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.639327 GCTGTGGCATTTCCGGCTT 61.639 57.895 0.00 0.00 37.80 4.35
27 28 3.372730 TGCTGTGGCATTTCCGGC 61.373 61.111 0.00 0.00 44.28 6.13
51 52 2.249844 ACTGGTGGTCGTAAACAAGG 57.750 50.000 0.00 0.00 0.00 3.61
55 56 1.671845 TGCAAACTGGTGGTCGTAAAC 59.328 47.619 0.00 0.00 0.00 2.01
97 103 8.018677 ACGACGAATATGCTCTTATTTATTGG 57.981 34.615 0.00 0.00 0.00 3.16
104 110 4.485024 ACGACGACGAATATGCTCTTAT 57.515 40.909 15.32 0.00 42.66 1.73
151 157 2.855514 GCCGAGGCAAGCAACCAAA 61.856 57.895 9.58 0.00 41.49 3.28
152 158 3.294493 GCCGAGGCAAGCAACCAA 61.294 61.111 9.58 0.00 41.49 3.67
153 159 4.269523 AGCCGAGGCAAGCAACCA 62.270 61.111 17.18 0.00 44.88 3.67
154 160 3.435186 GAGCCGAGGCAAGCAACC 61.435 66.667 17.18 0.00 44.88 3.77
155 161 3.793144 CGAGCCGAGGCAAGCAAC 61.793 66.667 17.18 0.03 44.88 4.17
587 638 7.948034 TTCTGTCATTTCCCGGTTTAATTAT 57.052 32.000 0.00 0.00 0.00 1.28
621 672 3.453424 GTGCAAAAACGAATCCTTTGGT 58.547 40.909 0.00 0.00 31.98 3.67
626 677 0.665835 TGCGTGCAAAAACGAATCCT 59.334 45.000 0.17 0.00 46.49 3.24
628 679 3.911964 ACTAATGCGTGCAAAAACGAATC 59.088 39.130 0.00 0.00 41.03 2.52
629 680 3.896122 ACTAATGCGTGCAAAAACGAAT 58.104 36.364 0.00 0.00 43.82 3.34
632 683 3.805823 AGTACTAATGCGTGCAAAAACG 58.194 40.909 0.00 0.00 46.30 3.60
885 939 2.592102 AAGCCAAGCATCTCTGGAAA 57.408 45.000 0.00 0.00 0.00 3.13
898 952 5.105392 CCAAAGTTGCCTCATATAAAGCCAA 60.105 40.000 0.00 0.00 0.00 4.52
905 959 3.127250 TCCCCCAAAGTTGCCTCATATA 58.873 45.455 0.00 0.00 0.00 0.86
906 960 1.929494 TCCCCCAAAGTTGCCTCATAT 59.071 47.619 0.00 0.00 0.00 1.78
907 961 1.284785 CTCCCCCAAAGTTGCCTCATA 59.715 52.381 0.00 0.00 0.00 2.15
908 962 0.040204 CTCCCCCAAAGTTGCCTCAT 59.960 55.000 0.00 0.00 0.00 2.90
909 963 1.460255 CTCCCCCAAAGTTGCCTCA 59.540 57.895 0.00 0.00 0.00 3.86
919 975 0.758685 CTTTGTGTTGCCTCCCCCAA 60.759 55.000 0.00 0.00 0.00 4.12
920 976 1.152567 CTTTGTGTTGCCTCCCCCA 60.153 57.895 0.00 0.00 0.00 4.96
1107 1173 1.246056 ACCTTGTGCGCATGATGCTT 61.246 50.000 15.91 0.00 42.25 3.91
1392 1459 2.706555 TGCACAAGAGAGTAGTGTCG 57.293 50.000 0.00 0.00 35.75 4.35
1447 1514 7.574217 GCGTTGTAAATTTGACCTCCAGATAAA 60.574 37.037 0.00 0.00 0.00 1.40
1501 1568 2.069273 CTAAAACGAGCACAGTCTGGG 58.931 52.381 4.53 0.02 0.00 4.45
1531 1598 7.174946 CAGGAAAAGGAGACTGCAAAAAGTATA 59.825 37.037 0.00 0.00 42.68 1.47
1698 1787 2.194201 TAGGTTGCACCCACTTTAGC 57.806 50.000 2.00 0.00 39.75 3.09
1777 1866 7.179872 AATCTTGAGATCGGCGTTAGCAAATA 61.180 38.462 6.85 0.55 38.39 1.40
1807 1896 9.965824 GAAAAACAGATGAAAGGAGACAAAATA 57.034 29.630 0.00 0.00 0.00 1.40
1815 1904 8.931385 TTGAAAAGAAAAACAGATGAAAGGAG 57.069 30.769 0.00 0.00 0.00 3.69
1859 1950 4.522789 CACTGGCCCAGTAAGTTATTTGTT 59.477 41.667 17.77 0.00 43.43 2.83


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

AutoCloner maintained by Alex Coulton.