Multiple sequence alignment - TraesCS2D01G461700

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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 TraesCS2D01G461700 chr2D 100.000 3237 0 0 1 3237 568090215 568093451 0.000000e+00 5978
1 TraesCS2D01G461700 chr2D 98.724 1959 19 2 1 1953 568104977 568106935 0.000000e+00 3474
2 TraesCS2D01G461700 chr2A 90.882 3016 133 63 296 3237 707567096 707570043 0.000000e+00 3916
3 TraesCS2D01G461700 chr2A 78.878 303 31 10 1 295 707565036 707565313 1.190000e-39 174
4 TraesCS2D01G461700 chr2B 89.031 3045 185 66 1 2970 680596725 680599695 0.000000e+00 3635
5 TraesCS2D01G461700 chrUn 100.000 414 0 0 984 1397 477382456 477382043 0.000000e+00 765


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 TraesCS2D01G461700 chr2D 568090215 568093451 3236 False 5978 5978 100.000 1 3237 1 chr2D.!!$F1 3236
1 TraesCS2D01G461700 chr2D 568104977 568106935 1958 False 3474 3474 98.724 1 1953 1 chr2D.!!$F2 1952
2 TraesCS2D01G461700 chr2A 707565036 707570043 5007 False 2045 3916 84.880 1 3237 2 chr2A.!!$F1 3236
3 TraesCS2D01G461700 chr2B 680596725 680599695 2970 False 3635 3635 89.031 1 2970 1 chr2B.!!$F1 2969

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
84 87 0.236449 CCGTGTACTTTTGGTTCGCC 59.764 55.0 0.0 0.0 37.92 5.54 F
210 218 0.251430 TTGCCCCTTAAACCCCTTCG 60.251 55.0 0.0 0.0 0.00 3.79 F
490 2283 0.531532 CATCAGAGACCCCGATGCAC 60.532 60.0 0.0 0.0 30.96 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 3952 4.949856 AGTAATGCCATTCAACTTTCCGAT 59.050 37.500 0.00 0.00 0.00 4.18 R
2068 3966 7.819415 GCATTATGACTATGAGTAGTAATGCCA 59.181 37.037 22.58 4.48 44.79 4.92 R
2245 4143 1.079543 ATCAGTGGCTCACGCAGAC 60.080 57.895 0.00 0.00 39.64 3.51 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
32 33 8.898761 TGCATTTTCTACTCTAGTTTGTTTTCA 58.101 29.630 0.00 0.00 0.00 2.69
84 87 0.236449 CCGTGTACTTTTGGTTCGCC 59.764 55.000 0.00 0.00 37.92 5.54
210 218 0.251430 TTGCCCCTTAAACCCCTTCG 60.251 55.000 0.00 0.00 0.00 3.79
448 2240 2.537633 AATGATTGACCACATGGGCT 57.462 45.000 5.12 0.00 45.91 5.19
490 2283 0.531532 CATCAGAGACCCCGATGCAC 60.532 60.000 0.00 0.00 30.96 4.57
493 2286 1.043116 CAGAGACCCCGATGCACCTA 61.043 60.000 0.00 0.00 0.00 3.08
1497 3367 8.839343 TGATCGAGTTTATTATGCATCATGTTT 58.161 29.630 0.19 0.00 0.00 2.83
2028 3920 8.642908 ACATGTTTTATGCTGATTGATTCATG 57.357 30.769 0.00 0.00 32.72 3.07
2030 3922 6.869695 TGTTTTATGCTGATTGATTCATGCT 58.130 32.000 0.00 0.00 32.72 3.79
2032 3924 8.468399 TGTTTTATGCTGATTGATTCATGCTTA 58.532 29.630 0.00 0.00 32.72 3.09
2046 3944 9.791820 TGATTCATGCTTATGTCAATTGTTAAG 57.208 29.630 5.13 11.82 0.00 1.85
2047 3945 9.793252 GATTCATGCTTATGTCAATTGTTAAGT 57.207 29.630 18.14 6.03 0.00 2.24
2060 3958 8.928733 GTCAATTGTTAAGTACAGTAATCGGAA 58.071 33.333 5.13 0.00 38.19 4.30
2068 3966 9.715121 TTAAGTACAGTAATCGGAAAGTTGAAT 57.285 29.630 0.00 0.00 0.00 2.57
2080 3978 5.354234 CGGAAAGTTGAATGGCATTACTACT 59.646 40.000 13.65 14.70 0.00 2.57
2081 3979 6.456988 CGGAAAGTTGAATGGCATTACTACTC 60.457 42.308 13.65 12.87 0.00 2.59
2082 3980 6.374333 GGAAAGTTGAATGGCATTACTACTCA 59.626 38.462 13.65 2.70 0.00 3.41
2083 3981 7.067494 GGAAAGTTGAATGGCATTACTACTCAT 59.933 37.037 13.65 10.84 0.00 2.90
2084 3982 9.109393 GAAAGTTGAATGGCATTACTACTCATA 57.891 33.333 13.65 0.00 0.00 2.15
2085 3983 8.668510 AAGTTGAATGGCATTACTACTCATAG 57.331 34.615 13.65 0.00 34.25 2.23
2113 4011 1.810794 GCATGACTGGCTGATGAGAGG 60.811 57.143 0.00 0.00 0.00 3.69
2182 4080 2.437359 GTAGGCAGCAGCAGTGGG 60.437 66.667 2.65 0.00 44.61 4.61
2239 4137 6.127054 CCTCCTACAACTTTATGGAGTGATGA 60.127 42.308 0.00 0.00 41.83 2.92
2240 4138 6.878317 TCCTACAACTTTATGGAGTGATGAG 58.122 40.000 0.00 0.00 28.47 2.90
2241 4139 5.525378 CCTACAACTTTATGGAGTGATGAGC 59.475 44.000 0.00 0.00 28.47 4.26
2242 4140 4.910195 ACAACTTTATGGAGTGATGAGCA 58.090 39.130 0.00 0.00 0.00 4.26
2243 4141 5.503927 ACAACTTTATGGAGTGATGAGCAT 58.496 37.500 0.00 0.00 0.00 3.79
2244 4142 5.587844 ACAACTTTATGGAGTGATGAGCATC 59.412 40.000 3.55 3.55 38.29 3.91
2245 4143 4.375272 ACTTTATGGAGTGATGAGCATCG 58.625 43.478 6.04 0.00 40.63 3.84
2246 4144 4.141846 ACTTTATGGAGTGATGAGCATCGT 60.142 41.667 6.04 0.00 40.63 3.73
2276 4174 5.113446 AGCCACTGATGAAGAGATCAATT 57.887 39.130 0.00 0.00 42.54 2.32
2356 4259 4.130118 GGGGAGTGATGAATGTGATGTAC 58.870 47.826 0.00 0.00 0.00 2.90
2373 4276 7.094677 TGTGATGTACGTAGTTAACTTGCTAGA 60.095 37.037 14.49 0.00 37.78 2.43
2446 4350 1.415659 CTTTCCTCATCTCCGGCATCT 59.584 52.381 0.00 0.00 0.00 2.90
2986 4890 6.262944 TGTTGTATGCTCCTGCTATTTATTGG 59.737 38.462 0.00 0.00 40.48 3.16
3036 4940 4.578928 AGTCGGTTCTAGTTGCACATTTTT 59.421 37.500 0.00 0.00 0.00 1.94
3082 4986 6.695713 GCAACTTCAGTAAAGAAAACGGATTT 59.304 34.615 0.00 0.00 38.44 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.677148 AAAGCATGAAAACAAACTAGAGTAGA 57.323 30.769 0.00 0.00 0.00 2.59
84 87 4.559704 GCTGATACTAGAAGATGGGTTCGG 60.560 50.000 0.00 0.00 0.00 4.30
171 179 7.395489 GGGGCAATAACAAATGATGAGATATCT 59.605 37.037 4.47 4.47 0.00 1.98
448 2240 4.020662 GGGATGTTTGCAATTTTGTAGGGA 60.021 41.667 0.00 0.00 0.00 4.20
490 2283 4.612259 CGTCGGTATGGAGTAATCGTTAGG 60.612 50.000 0.00 0.00 0.00 2.69
493 2286 2.033801 CCGTCGGTATGGAGTAATCGTT 59.966 50.000 2.08 0.00 33.01 3.85
1676 3562 5.109500 TGACATGACCAACCAGCATAATA 57.891 39.130 0.00 0.00 0.00 0.98
2032 3924 8.879759 CCGATTACTGTACTTAACAATTGACAT 58.120 33.333 13.59 0.37 37.74 3.06
2046 3944 6.674760 GCCATTCAACTTTCCGATTACTGTAC 60.675 42.308 0.00 0.00 0.00 2.90
2047 3945 5.353123 GCCATTCAACTTTCCGATTACTGTA 59.647 40.000 0.00 0.00 0.00 2.74
2054 3952 4.949856 AGTAATGCCATTCAACTTTCCGAT 59.050 37.500 0.00 0.00 0.00 4.18
2060 3958 8.267894 ACTATGAGTAGTAATGCCATTCAACTT 58.732 33.333 0.00 0.00 39.36 2.66
2068 3966 7.819415 GCATTATGACTATGAGTAGTAATGCCA 59.181 37.037 22.58 4.48 44.79 4.92
2113 4011 9.722056 GCATTACGGATCAATGGATAATAATTC 57.278 33.333 6.43 0.00 34.58 2.17
2241 4139 2.125952 TGGCTCACGCAGACGATG 60.126 61.111 0.00 0.00 43.93 3.84
2242 4140 2.125912 GTGGCTCACGCAGACGAT 60.126 61.111 0.00 0.00 43.93 3.73
2243 4141 3.295273 AGTGGCTCACGCAGACGA 61.295 61.111 0.00 0.00 43.93 4.20
2245 4143 1.079543 ATCAGTGGCTCACGCAGAC 60.080 57.895 0.00 0.00 39.64 3.51
2246 4144 1.079612 CATCAGTGGCTCACGCAGA 60.080 57.895 0.00 1.71 39.64 4.26
2319 4217 2.225908 ACTCCCCTTGGGTACTTCTCAT 60.226 50.000 4.84 0.00 44.74 2.90
2356 4259 6.946229 AACACATCTAGCAAGTTAACTACG 57.054 37.500 8.92 4.58 0.00 3.51
2684 4588 2.868839 GCACATGCTGGCTTTGAATTGT 60.869 45.455 0.00 0.00 38.21 2.71
3009 4913 3.319972 TGTGCAACTAGAACCGACTTACT 59.680 43.478 0.00 0.00 38.04 2.24
3010 4914 3.645884 TGTGCAACTAGAACCGACTTAC 58.354 45.455 0.00 0.00 38.04 2.34
3011 4915 4.530710 ATGTGCAACTAGAACCGACTTA 57.469 40.909 0.00 0.00 38.04 2.24
3082 4986 0.250858 TGCTAAGCTGCCAAGAAGCA 60.251 50.000 0.00 1.95 43.37 3.91
3173 5077 9.720667 CAATGAATTAATAAAGCAAGATCGACA 57.279 29.630 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.