Multiple sequence alignment - TraesCS7D01G177100

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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 TraesCS7D01G177100 chr7D 100.000 1604 0 0 536 2139 129799145 129797542 0.000000e+00 2963.0
1 TraesCS7D01G177100 chr7D 100.000 324 0 0 2547 2870 129797134 129796811 1.470000e-167 599.0
2 TraesCS7D01G177100 chr7D 100.000 44 0 0 1 44 129799680 129799637 6.590000e-12 82.4
3 TraesCS7D01G177100 chr7B 97.387 1569 38 2 537 2103 91212764 91211197 0.000000e+00 2667.0
4 TraesCS7D01G177100 chr7B 95.608 296 11 2 2574 2868 91210540 91210246 9.310000e-130 473.0
5 TraesCS7D01G177100 chr7B 93.182 44 0 2 1 44 91213270 91213230 8.590000e-06 62.1
6 TraesCS7D01G177100 chr7A 97.334 1463 39 0 536 1998 128914807 128913345 0.000000e+00 2486.0
7 TraesCS7D01G177100 chr7A 93.189 323 19 3 2548 2867 128913163 128912841 3.350000e-129 472.0
8 TraesCS7D01G177100 chr7A 97.778 90 1 1 2014 2103 128913354 128913266 1.380000e-33 154.0


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 TraesCS7D01G177100 chr7D 129796811 129799680 2869 True 1214.800000 2963 100.000000 1 2870 3 chr7D.!!$R1 2869
1 TraesCS7D01G177100 chr7B 91210246 91213270 3024 True 1067.366667 2667 95.392333 1 2868 3 chr7B.!!$R1 2867
2 TraesCS7D01G177100 chr7A 128912841 128914807 1966 True 1037.333333 2486 96.100333 536 2867 3 chr7A.!!$R1 2331


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
866 867 4.680237 CTGCCCCAACGTGCTCGA 62.68 66.667 16.04 0.0 40.62 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2608 2796 0.762418 TCTTCAGTTTCCTCGGCCAA 59.238 50.0 2.24 0.0 0.0 4.52 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
866 867 4.680237 CTGCCCCAACGTGCTCGA 62.680 66.667 16.04 0.0 40.62 4.04
1062 1063 1.339727 ACCTATTCGACCTTGTTGGGC 60.340 52.381 0.00 0.0 41.70 5.36
1107 1108 6.431234 AGATGAAGGAAGCGTTTGAACTATTT 59.569 34.615 0.00 0.0 0.00 1.40
1140 1141 0.396435 AGAAAGACCACATCGTGCCA 59.604 50.000 0.00 0.0 31.34 4.92
1162 1163 2.086869 ACCAGCTGACATACAATGTGC 58.913 47.619 17.39 0.0 45.03 4.57
1168 1169 3.624410 GCTGACATACAATGTGCTCATCA 59.376 43.478 1.01 0.0 45.03 3.07
1404 1405 3.810743 GCCTTTGTAGACATGGGAGTGTT 60.811 47.826 0.00 0.0 31.16 3.32
2003 2004 9.220767 GGGATCACTTTCACATAAGATATTACC 57.779 37.037 0.00 0.0 0.00 2.85
2106 2137 1.970917 GATCTGCAACAAGGACGGCG 61.971 60.000 4.80 4.8 0.00 6.46
2129 2160 2.423185 CCTGAGCCAATTTGCGATACAA 59.577 45.455 0.00 0.0 36.13 2.41
2130 2161 3.067180 CCTGAGCCAATTTGCGATACAAT 59.933 43.478 0.00 0.0 38.31 2.71
2132 2163 3.066621 TGAGCCAATTTGCGATACAATCC 59.933 43.478 0.00 0.0 38.31 3.01
2133 2164 3.023119 AGCCAATTTGCGATACAATCCA 58.977 40.909 0.00 0.0 38.31 3.41
2134 2165 3.115554 GCCAATTTGCGATACAATCCAC 58.884 45.455 0.00 0.0 38.31 4.02
2136 2167 4.742417 CCAATTTGCGATACAATCCACAA 58.258 39.130 0.00 0.0 38.31 3.33
2138 2169 3.840890 TTTGCGATACAATCCACAACC 57.159 42.857 0.00 0.0 38.31 3.77
2586 2774 3.357166 TTGATGTTTTTGTGCCCGTAC 57.643 42.857 0.00 0.0 0.00 3.67
2724 2912 3.475566 TTAGCTGACTTGCTGTTCACT 57.524 42.857 0.00 0.0 43.87 3.41
2822 3013 1.266175 CTGTGCACTCTTCAGCCAAAG 59.734 52.381 19.41 0.0 0.00 2.77
2848 3039 8.933807 GTGTTCTCATCCATATATCTGATTGTG 58.066 37.037 0.00 0.0 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
603 604 3.708220 GAGCGCGGAGAAGGTGGAG 62.708 68.421 8.83 0.00 0.00 3.86
723 724 4.467107 GGGAGGAGGCGGAGGAGT 62.467 72.222 0.00 0.00 0.00 3.85
861 862 1.008309 GGCTATGAGGTCGTCGAGC 60.008 63.158 16.47 16.47 36.46 5.03
866 867 1.076923 AGGTCGGCTATGAGGTCGT 60.077 57.895 0.00 0.00 35.67 4.34
894 895 1.078637 GGGGAGGTACTTGTTCCGC 60.079 63.158 0.00 0.67 41.55 5.54
978 979 2.293318 ATCGAGCACCCTGAAGGCA 61.293 57.895 0.00 0.00 40.58 4.75
1107 1108 2.695666 GTCTTTCTCGATCATCCCCTCA 59.304 50.000 0.00 0.00 0.00 3.86
1140 1141 3.603532 CACATTGTATGTCAGCTGGTCT 58.396 45.455 15.13 0.80 42.70 3.85
1162 1163 1.361668 CGGCAGAACCCGTTGATGAG 61.362 60.000 0.00 0.00 43.24 2.90
1372 1373 1.207089 TCTACAAAGGCACCCGATCAG 59.793 52.381 0.00 0.00 0.00 2.90
1404 1405 2.896044 CAGAAGATCGATCCCCTCATCA 59.104 50.000 21.66 0.00 0.00 3.07
1929 1930 5.240844 TCGAGCGATCTTCATACCTGATTTA 59.759 40.000 0.00 0.00 0.00 1.40
2003 2004 6.623486 TGATCATCTTATGTGCAAGTTTTGG 58.377 36.000 0.00 0.00 0.00 3.28
2012 2015 4.024218 GTCAAGCCTGATCATCTTATGTGC 60.024 45.833 0.00 0.00 33.05 4.57
2106 2137 1.098050 ATCGCAAATTGGCTCAGGTC 58.902 50.000 2.72 0.00 0.00 3.85
2546 2577 4.213270 TCAAAGTAGTCAATTTCCTGTGCG 59.787 41.667 0.00 0.00 0.00 5.34
2555 2586 7.224557 GGCACAAAAACATCAAAGTAGTCAATT 59.775 33.333 0.00 0.00 0.00 2.32
2608 2796 0.762418 TCTTCAGTTTCCTCGGCCAA 59.238 50.000 2.24 0.00 0.00 4.52
2724 2912 3.244387 TGGTTTCGGTGATCTGAACATCA 60.244 43.478 0.00 0.00 38.49 3.07
2822 3013 8.933807 CACAATCAGATATATGGATGAGAACAC 58.066 37.037 9.34 0.00 0.00 3.32



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

AutoCloner maintained by Alex Coulton.