Multiple sequence alignment - TraesCS1A01G283500

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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 TraesCS1A01G283500 chr1A 100.000 2308 0 0 1 2308 480962068 480959761 0.000000e+00 4263
1 TraesCS1A01G283500 chr1A 96.312 1898 65 2 7 1900 559594938 559593042 0.000000e+00 3112
2 TraesCS1A01G283500 chr1A 96.899 258 8 0 2049 2306 559591319 559591062 1.270000e-117 433
3 TraesCS1A01G283500 chr7A 97.107 1901 54 1 1 1900 643632511 643630611 0.000000e+00 3205
4 TraesCS1A01G283500 chr7A 94.773 2028 86 10 1 2013 192630958 192628936 0.000000e+00 3140
5 TraesCS1A01G283500 chr7A 96.423 1901 64 2 7 1904 130562455 130560556 0.000000e+00 3131
6 TraesCS1A01G283500 chr7A 94.149 2051 102 11 1 2037 38742706 38740660 0.000000e+00 3107
7 TraesCS1A01G283500 chr7A 95.851 1904 75 1 1 1900 699317477 699319380 0.000000e+00 3075
8 TraesCS1A01G283500 chr7A 96.538 260 9 0 2049 2308 130559063 130558804 4.560000e-117 431
9 TraesCS1A01G283500 chr7A 96.538 260 9 0 2049 2308 643611085 643610826 4.560000e-117 431
10 TraesCS1A01G283500 chr7A 95.385 260 12 0 2049 2308 719950688 719950947 4.590000e-112 414
11 TraesCS1A01G283500 chr7A 97.183 142 4 0 1899 2040 16875626 16875767 8.240000e-60 241
12 TraesCS1A01G283500 chr7A 95.683 139 6 0 1899 2037 192629092 192628954 8.300000e-55 224
13 TraesCS1A01G283500 chr7A 94.326 141 6 1 1902 2040 130560593 130560453 4.990000e-52 215
14 TraesCS1A01G283500 chr7A 91.724 145 9 3 1895 2037 134599763 134599620 5.030000e-47 198
15 TraesCS1A01G283500 chr5A 96.640 1905 56 4 1 1900 288263575 288265476 0.000000e+00 3157
16 TraesCS1A01G283500 chr5A 96.053 1900 67 4 1 1895 606694015 606692119 0.000000e+00 3086
17 TraesCS1A01G283500 chr5A 94.245 139 8 0 1899 2037 288265441 288265579 1.800000e-51 213
18 TraesCS1A01G283500 chr5A 91.429 140 10 2 1899 2037 606692149 606692011 8.420000e-45 191
19 TraesCS1A01G283500 chr3A 94.239 2031 94 16 1 2013 635317552 635315527 0.000000e+00 3081
20 TraesCS1A01G283500 chr3A 88.556 367 35 7 1944 2308 22602345 22602706 2.720000e-119 438
21 TraesCS1A01G283500 chr3A 97.794 136 3 0 1902 2037 635315680 635315545 3.830000e-58 235
22 TraesCS1A01G283500 chr2A 97.276 257 7 0 2049 2305 677897560 677897816 9.790000e-119 436
23 TraesCS1A01G283500 chr2A 82.206 281 38 11 1761 2040 677895686 677895955 4.960000e-57 231
24 TraesCS1A01G283500 chr7D 96.457 254 9 0 2055 2308 16797815 16798068 9.860000e-114 420
25 TraesCS1A01G283500 chr6B 95.669 254 11 0 2055 2308 425597874 425597621 2.130000e-110 409
26 TraesCS1A01G283500 chr6A 94.615 260 8 2 2049 2308 79830231 79830484 4.620000e-107 398
27 TraesCS1A01G283500 chr6A 93.103 145 7 1 1899 2040 516294537 516294681 2.320000e-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 TraesCS1A01G283500 chr1A 480959761 480962068 2307 True 4263.0 4263 100.000000 1 2308 1 chr1A.!!$R1 2307
1 TraesCS1A01G283500 chr1A 559591062 559594938 3876 True 1772.5 3112 96.605500 7 2306 2 chr1A.!!$R2 2299
2 TraesCS1A01G283500 chr7A 643630611 643632511 1900 True 3205.0 3205 97.107000 1 1900 1 chr7A.!!$R4 1899
3 TraesCS1A01G283500 chr7A 38740660 38742706 2046 True 3107.0 3107 94.149000 1 2037 1 chr7A.!!$R1 2036
4 TraesCS1A01G283500 chr7A 699317477 699319380 1903 False 3075.0 3075 95.851000 1 1900 1 chr7A.!!$F2 1899
5 TraesCS1A01G283500 chr7A 192628936 192630958 2022 True 1682.0 3140 95.228000 1 2037 2 chr7A.!!$R6 2036
6 TraesCS1A01G283500 chr7A 130558804 130562455 3651 True 1259.0 3131 95.762333 7 2308 3 chr7A.!!$R5 2301
7 TraesCS1A01G283500 chr5A 288263575 288265579 2004 False 1685.0 3157 95.442500 1 2037 2 chr5A.!!$F1 2036
8 TraesCS1A01G283500 chr5A 606692011 606694015 2004 True 1638.5 3086 93.741000 1 2037 2 chr5A.!!$R1 2036
9 TraesCS1A01G283500 chr3A 635315527 635317552 2025 True 1658.0 3081 96.016500 1 2037 2 chr3A.!!$R1 2036
10 TraesCS1A01G283500 chr2A 677895686 677897816 2130 False 333.5 436 89.741000 1761 2305 2 chr2A.!!$F1 544

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
567 568 0.179187 CAAACAAACACCGTGCGTGA 60.179 50.0 8.62 0.0 46.2 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1551 0.033011 TCTTCGCTAGCCTCCTCCTT 60.033 55.0 9.66 0.0 0.0 3.36 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
38 39 5.585390 CATGATGATGATCCATATCGACGA 58.415 41.667 0.00 0.00 34.60 4.20
85 86 4.188462 CAAGTGACAGTGTACACAGGAAA 58.812 43.478 27.06 7.23 39.18 3.13
277 278 7.503549 ACTATGATCTTAATGAGATGTGCACA 58.496 34.615 24.08 24.08 45.17 4.57
289 290 0.670239 TGTGCACACGTGATAGCCAG 60.670 55.000 25.01 3.83 0.00 4.85
513 514 3.055021 TCCCGTGCATCATTTGTAGGTTA 60.055 43.478 0.00 0.00 0.00 2.85
567 568 0.179187 CAAACAAACACCGTGCGTGA 60.179 50.000 8.62 0.00 46.20 4.35
621 622 5.366186 AGTGCAATCAGAGAATAGACCTCAT 59.634 40.000 0.00 0.00 33.25 2.90
700 701 0.550914 AAAGCCTGGTTGGACTCACA 59.449 50.000 0.00 0.00 38.35 3.58
857 862 7.759489 TGACCTATTCTAACAAACTTGCATT 57.241 32.000 0.00 0.00 0.00 3.56
953 958 1.133598 CGATGCCAATGTTGCACTGAT 59.866 47.619 0.00 0.00 42.38 2.90
1148 1154 0.322277 CTTGCCATGGTGCTCAGTCT 60.322 55.000 14.67 0.00 0.00 3.24
1252 1258 1.213926 GGTCCATGAAGAGGAGCCAAT 59.786 52.381 0.00 0.00 45.55 3.16
1280 1286 2.306805 AGAGGAGCCAACACATCATGAA 59.693 45.455 0.00 0.00 0.00 2.57
1415 1421 3.714144 AGTCATAGCTAAGACACCAGGT 58.286 45.455 26.14 6.24 37.23 4.00
1506 1512 6.322201 CCCAACAGGAATGCAAAGATATAAGT 59.678 38.462 0.00 0.00 38.24 2.24
1526 1532 0.107017 CCAACATTGAGGCGGAGGAT 60.107 55.000 0.00 0.00 0.00 3.24
1545 1551 3.181475 GGATGAGGCATACAACGAAGAGA 60.181 47.826 0.00 0.00 0.00 3.10
1750 1758 8.183536 GTGTCTTATGTATGCATGAATTTGTCA 58.816 33.333 10.16 0.00 41.67 3.58
1888 1919 9.950496 ATGTTCTATCTTCTTGTGTGAATAAGT 57.050 29.630 0.00 0.00 0.00 2.24
1889 1920 9.424319 TGTTCTATCTTCTTGTGTGAATAAGTC 57.576 33.333 0.00 0.00 0.00 3.01
1890 1921 8.874816 GTTCTATCTTCTTGTGTGAATAAGTCC 58.125 37.037 0.00 0.00 0.00 3.85
1891 1922 8.134202 TCTATCTTCTTGTGTGAATAAGTCCA 57.866 34.615 0.00 0.00 0.00 4.02
1892 1923 8.593679 TCTATCTTCTTGTGTGAATAAGTCCAA 58.406 33.333 0.00 0.00 0.00 3.53
1893 1924 9.219603 CTATCTTCTTGTGTGAATAAGTCCAAA 57.780 33.333 0.00 0.00 0.00 3.28
1894 1925 7.873719 TCTTCTTGTGTGAATAAGTCCAAAA 57.126 32.000 0.00 0.00 0.00 2.44
1895 1926 8.463930 TCTTCTTGTGTGAATAAGTCCAAAAT 57.536 30.769 0.00 0.00 0.00 1.82
1896 1927 9.567776 TCTTCTTGTGTGAATAAGTCCAAAATA 57.432 29.630 0.00 0.00 0.00 1.40
1900 1931 8.755696 TTGTGTGAATAAGTCCAAAATAATGC 57.244 30.769 0.00 0.00 0.00 3.56
1901 1932 8.121305 TGTGTGAATAAGTCCAAAATAATGCT 57.879 30.769 0.00 0.00 0.00 3.79
1902 1933 9.237187 TGTGTGAATAAGTCCAAAATAATGCTA 57.763 29.630 0.00 0.00 0.00 3.49
1911 1942 8.814038 AGTCCAAAATAATGCTATCTTCTTGT 57.186 30.769 0.00 0.00 0.00 3.16
1912 1943 8.680903 AGTCCAAAATAATGCTATCTTCTTGTG 58.319 33.333 0.00 0.00 0.00 3.33
1913 1944 8.462016 GTCCAAAATAATGCTATCTTCTTGTGT 58.538 33.333 0.00 0.00 0.00 3.72
1914 1945 8.461222 TCCAAAATAATGCTATCTTCTTGTGTG 58.539 33.333 0.00 0.00 0.00 3.82
1915 1946 8.461222 CCAAAATAATGCTATCTTCTTGTGTGA 58.539 33.333 0.00 0.00 0.00 3.58
1916 1947 9.844790 CAAAATAATGCTATCTTCTTGTGTGAA 57.155 29.630 0.00 0.00 0.00 3.18
2004 2080 2.362503 AGACGCCACGATCCCTGA 60.363 61.111 0.00 0.00 0.00 3.86
2040 2116 3.998672 GGGACCAGACGCCACGAA 61.999 66.667 0.00 0.00 0.00 3.85
2041 2117 2.029964 GGACCAGACGCCACGAAA 59.970 61.111 0.00 0.00 0.00 3.46
2042 2118 1.375523 GGACCAGACGCCACGAAAT 60.376 57.895 0.00 0.00 0.00 2.17
2043 2119 0.108520 GGACCAGACGCCACGAAATA 60.109 55.000 0.00 0.00 0.00 1.40
2045 2121 2.277084 GACCAGACGCCACGAAATATT 58.723 47.619 0.00 0.00 0.00 1.28
2047 2123 1.330521 CCAGACGCCACGAAATATTGG 59.669 52.381 0.00 0.00 35.81 3.16
2185 4209 5.408299 TCTCGAATAACAAGTTCACACATGG 59.592 40.000 0.00 0.00 0.00 3.66
2278 4302 1.404035 TCGACATTCCATCATCGACGT 59.596 47.619 0.00 0.00 38.59 4.34
2280 4304 2.794631 CGACATTCCATCATCGACGTCA 60.795 50.000 17.16 3.13 36.70 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.431766 CCCAATAGTAAGCAAGCGTAGGT 60.432 47.826 0.00 0.0 44.60 3.08
277 278 3.159298 CCAAAGCTGGCTATCACGT 57.841 52.632 0.00 0.0 35.39 4.49
513 514 6.678568 ATATCCTGATTGTTCCTTCGATCT 57.321 37.500 0.00 0.0 31.50 2.75
627 628 7.493645 CACACTTGATACTTCTGATATGCTGAA 59.506 37.037 0.00 0.0 33.97 3.02
700 701 0.763223 ACCAACTCCGACCACTCCTT 60.763 55.000 0.00 0.0 0.00 3.36
1252 1258 2.637382 TGTGTTGGCTCCTCTTGATGTA 59.363 45.455 0.00 0.0 0.00 2.29
1280 1286 3.875727 GTGTTGCATCATACTCATGCTCT 59.124 43.478 0.00 0.0 45.90 4.09
1415 1421 8.202461 TCCATGTCTTCTTTCTACCTTTCTTA 57.798 34.615 0.00 0.0 0.00 2.10
1506 1512 1.198094 TCCTCCGCCTCAATGTTGGA 61.198 55.000 0.00 0.0 0.00 3.53
1526 1532 3.368427 CCTTCTCTTCGTTGTATGCCTCA 60.368 47.826 0.00 0.0 0.00 3.86
1545 1551 0.033011 TCTTCGCTAGCCTCCTCCTT 60.033 55.000 9.66 0.0 0.00 3.36
1885 1916 9.247861 ACAAGAAGATAGCATTATTTTGGACTT 57.752 29.630 0.00 0.0 0.00 3.01
1886 1917 8.680903 CACAAGAAGATAGCATTATTTTGGACT 58.319 33.333 0.00 0.0 0.00 3.85
1887 1918 8.462016 ACACAAGAAGATAGCATTATTTTGGAC 58.538 33.333 0.00 0.0 0.00 4.02
1888 1919 8.461222 CACACAAGAAGATAGCATTATTTTGGA 58.539 33.333 0.00 0.0 0.00 3.53
1889 1920 8.461222 TCACACAAGAAGATAGCATTATTTTGG 58.539 33.333 0.00 0.0 0.00 3.28
1890 1921 9.844790 TTCACACAAGAAGATAGCATTATTTTG 57.155 29.630 0.00 0.0 0.00 2.44
1896 1927 9.236006 ACTTATTTCACACAAGAAGATAGCATT 57.764 29.630 0.00 0.0 30.84 3.56
1897 1928 8.798859 ACTTATTTCACACAAGAAGATAGCAT 57.201 30.769 0.00 0.0 30.84 3.79
1898 1929 7.334421 GGACTTATTTCACACAAGAAGATAGCA 59.666 37.037 0.00 0.0 30.84 3.49
1899 1930 7.334421 TGGACTTATTTCACACAAGAAGATAGC 59.666 37.037 0.00 0.0 30.84 2.97
1900 1931 8.777865 TGGACTTATTTCACACAAGAAGATAG 57.222 34.615 0.00 0.0 30.84 2.08
1901 1932 9.567776 TTTGGACTTATTTCACACAAGAAGATA 57.432 29.630 0.00 0.0 30.84 1.98
1902 1933 8.463930 TTTGGACTTATTTCACACAAGAAGAT 57.536 30.769 0.00 0.0 30.84 2.40
1903 1934 7.873719 TTTGGACTTATTTCACACAAGAAGA 57.126 32.000 0.00 0.0 30.84 2.87
1915 1946 8.474831 GCCCTGTACATTATTTTGGACTTATTT 58.525 33.333 0.00 0.0 31.30 1.40
1916 1947 7.069455 GGCCCTGTACATTATTTTGGACTTATT 59.931 37.037 0.00 0.0 31.30 1.40
2004 2080 1.202651 CCCTGACTTCAAACCAGACGT 60.203 52.381 0.00 0.0 0.00 4.34
2040 2116 6.437162 AGTGTGTGCAACCTATTTCCAATATT 59.563 34.615 0.00 0.0 34.36 1.28
2041 2117 5.951747 AGTGTGTGCAACCTATTTCCAATAT 59.048 36.000 0.00 0.0 34.36 1.28
2042 2118 5.321102 AGTGTGTGCAACCTATTTCCAATA 58.679 37.500 0.00 0.0 34.36 1.90
2043 2119 4.151883 AGTGTGTGCAACCTATTTCCAAT 58.848 39.130 0.00 0.0 34.36 3.16
2045 2121 3.222173 AGTGTGTGCAACCTATTTCCA 57.778 42.857 0.00 0.0 34.36 3.53
2047 2123 7.489757 TGTTTAAAAGTGTGTGCAACCTATTTC 59.510 33.333 0.00 0.0 34.36 2.17
2129 4153 7.553760 TGTGATCATGAACTACTTATGTGCAAT 59.446 33.333 0.00 0.0 0.00 3.56
2278 4302 3.228188 AGACAAATGGAAAGGCACTGA 57.772 42.857 0.00 0.0 40.86 3.41


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

AutoCloner maintained by Alex Coulton.