Multiple sequence alignment - TraesCS5D01G457600

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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 TraesCS5D01G457600 chr5D 100.000 4790 0 0 1 4790 503270874 503275663 0.000000e+00 8846
1 TraesCS5D01G457600 chr5D 99.384 2599 15 1 1964 4562 503224253 503221656 0.000000e+00 4710
2 TraesCS5D01G457600 chr5D 99.443 1976 11 0 1 1976 503225671 503223696 0.000000e+00 3589
3 TraesCS5D01G457600 chr5D 98.888 1978 19 2 1 1976 503235987 503234011 0.000000e+00 3528
4 TraesCS5D01G457600 chr3B 99.346 2599 17 0 1964 4562 101917214 101914616 0.000000e+00 4706
5 TraesCS5D01G457600 chr3B 98.501 2601 37 1 1964 4562 201533064 201530464 0.000000e+00 4586
6 TraesCS5D01G457600 chr3B 98.686 1978 24 1 1 1976 201534482 201532505 0.000000e+00 3507
7 TraesCS5D01G457600 chr3B 98.291 234 3 1 4557 4790 101913970 101913738 4.460000e-110 409
8 TraesCS5D01G457600 chr3B 97.863 234 4 1 4557 4790 201529819 201529587 2.080000e-108 403
9 TraesCS5D01G457600 chr3A 98.923 2599 28 0 1964 4562 66011587 66014185 0.000000e+00 4645
10 TraesCS5D01G457600 chr3A 98.846 2599 29 1 1964 4562 164858028 164860625 0.000000e+00 4632
11 TraesCS5D01G457600 chr3A 98.499 2598 39 0 1964 4561 672903978 672906575 0.000000e+00 4582
12 TraesCS5D01G457600 chr3A 99.291 1976 13 1 1 1976 66010170 66012144 0.000000e+00 3570
13 TraesCS5D01G457600 chr3D 98.846 2599 29 1 1964 4562 589270922 589273519 0.000000e+00 4632
14 TraesCS5D01G457600 chr3D 97.863 234 4 1 4557 4790 589274160 589274392 2.080000e-108 403
15 TraesCS5D01G457600 chrUn 98.807 2599 28 2 1964 4562 216512572 216515167 0.000000e+00 4625
16 TraesCS5D01G457600 chrUn 98.807 2599 28 2 1964 4562 286270811 286268216 0.000000e+00 4625
17 TraesCS5D01G457600 chrUn 97.863 234 4 1 4557 4790 421835052 421834820 2.080000e-108 403
18 TraesCS5D01G457600 chrUn 97.436 234 5 1 4557 4790 216515808 216516040 9.660000e-107 398
19 TraesCS5D01G457600 chrUn 97.436 234 5 1 4557 4790 286267575 286267343 9.660000e-107 398
20 TraesCS5D01G457600 chr2B 98.937 1976 21 0 1 1976 449213739 449211764 0.000000e+00 3533
21 TraesCS5D01G457600 chr2B 98.834 1973 20 3 4 1976 474915890 474913921 0.000000e+00 3513
22 TraesCS5D01G457600 chr1A 98.937 1976 21 0 1 1976 278526787 278528762 0.000000e+00 3533
23 TraesCS5D01G457600 chr1A 97.863 234 4 1 4557 4790 554515043 554514811 2.080000e-108 403
24 TraesCS5D01G457600 chr6D 98.836 1976 22 1 1 1976 458922767 458920793 0.000000e+00 3520
25 TraesCS5D01G457600 chr4D 98.685 1977 22 3 1 1976 177441990 177443963 0.000000e+00 3504
26 TraesCS5D01G457600 chr7D 97.863 234 4 1 4557 4790 231588118 231588350 2.080000e-108 403
27 TraesCS5D01G457600 chr2A 97.845 232 4 1 4557 4788 335841423 335841193 2.690000e-107 399


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 TraesCS5D01G457600 chr5D 503270874 503275663 4789 False 8846.0 8846 100.0000 1 4790 1 chr5D.!!$F1 4789
1 TraesCS5D01G457600 chr5D 503221656 503225671 4015 True 4149.5 4710 99.4135 1 4562 2 chr5D.!!$R2 4561
2 TraesCS5D01G457600 chr5D 503234011 503235987 1976 True 3528.0 3528 98.8880 1 1976 1 chr5D.!!$R1 1975
3 TraesCS5D01G457600 chr3B 201529587 201534482 4895 True 2832.0 4586 98.3500 1 4790 3 chr3B.!!$R2 4789
4 TraesCS5D01G457600 chr3B 101913738 101917214 3476 True 2557.5 4706 98.8185 1964 4790 2 chr3B.!!$R1 2826
5 TraesCS5D01G457600 chr3A 164858028 164860625 2597 False 4632.0 4632 98.8460 1964 4562 1 chr3A.!!$F1 2598
6 TraesCS5D01G457600 chr3A 672903978 672906575 2597 False 4582.0 4582 98.4990 1964 4561 1 chr3A.!!$F2 2597
7 TraesCS5D01G457600 chr3A 66010170 66014185 4015 False 4107.5 4645 99.1070 1 4562 2 chr3A.!!$F3 4561
8 TraesCS5D01G457600 chr3D 589270922 589274392 3470 False 2517.5 4632 98.3545 1964 4790 2 chr3D.!!$F1 2826
9 TraesCS5D01G457600 chrUn 216512572 216516040 3468 False 2511.5 4625 98.1215 1964 4790 2 chrUn.!!$F1 2826
10 TraesCS5D01G457600 chrUn 286267343 286270811 3468 True 2511.5 4625 98.1215 1964 4790 2 chrUn.!!$R2 2826
11 TraesCS5D01G457600 chr2B 449211764 449213739 1975 True 3533.0 3533 98.9370 1 1976 1 chr2B.!!$R1 1975
12 TraesCS5D01G457600 chr2B 474913921 474915890 1969 True 3513.0 3513 98.8340 4 1976 1 chr2B.!!$R2 1972
13 TraesCS5D01G457600 chr1A 278526787 278528762 1975 False 3533.0 3533 98.9370 1 1976 1 chr1A.!!$F1 1975
14 TraesCS5D01G457600 chr6D 458920793 458922767 1974 True 3520.0 3520 98.8360 1 1976 1 chr6D.!!$R1 1975
15 TraesCS5D01G457600 chr4D 177441990 177443963 1973 False 3504.0 3504 98.6850 1 1976 1 chr4D.!!$F1 1975

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
672 674 2.363680 CGACTCATAGAATGGCAGAGGT 59.636 50.000 0.0 0.0 0.0 3.85 F
1896 1901 4.322801 CCACTCCGACCAAGATAGAACTTT 60.323 45.833 0.0 0.0 0.0 2.66 F
1960 1965 0.108585 GTGAAGCAGGGTCAGGAACA 59.891 55.000 0.0 0.0 0.0 3.18 F
1961 1966 0.843309 TGAAGCAGGGTCAGGAACAA 59.157 50.000 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 1946 0.108585 TGTTCCTGACCCTGCTTCAC 59.891 55.000 0.00 0.00 0.00 3.18 R
2985 2993 4.261741 GCTTCTTTCTCTCATGCAAAACCA 60.262 41.667 0.00 0.00 0.00 3.67 R
3650 3658 5.409826 GGGGATCTTCTATAATTTCGCACAG 59.590 44.000 0.00 0.00 0.00 3.66 R
3805 3813 9.495382 AGTTAGTAAGAGGGATCTTGAACTAAT 57.505 33.333 12.83 4.64 35.26 1.73 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
514 516 9.853177 AAAGTTCCGATTGAAATAGGATCTAAT 57.147 29.630 13.10 6.17 38.48 1.73
529 531 5.070313 AGGATCTAATCAAGGAAGAGCACTC 59.930 44.000 0.00 0.00 0.00 3.51
672 674 2.363680 CGACTCATAGAATGGCAGAGGT 59.636 50.000 0.00 0.00 0.00 3.85
1499 1502 8.786826 TTCAGTTTATGTTCCTACCTATTGTG 57.213 34.615 0.00 0.00 0.00 3.33
1896 1901 4.322801 CCACTCCGACCAAGATAGAACTTT 60.323 45.833 0.00 0.00 0.00 2.66
1897 1902 5.238583 CACTCCGACCAAGATAGAACTTTT 58.761 41.667 0.00 0.00 0.00 2.27
1898 1903 6.395629 CACTCCGACCAAGATAGAACTTTTA 58.604 40.000 0.00 0.00 0.00 1.52
1899 1904 6.310711 CACTCCGACCAAGATAGAACTTTTAC 59.689 42.308 0.00 0.00 0.00 2.01
1900 1905 5.727434 TCCGACCAAGATAGAACTTTTACC 58.273 41.667 0.00 0.00 0.00 2.85
1901 1906 5.246656 TCCGACCAAGATAGAACTTTTACCA 59.753 40.000 0.00 0.00 0.00 3.25
1902 1907 5.935789 CCGACCAAGATAGAACTTTTACCAA 59.064 40.000 0.00 0.00 0.00 3.67
1903 1908 6.428771 CCGACCAAGATAGAACTTTTACCAAA 59.571 38.462 0.00 0.00 0.00 3.28
1904 1909 7.040961 CCGACCAAGATAGAACTTTTACCAAAA 60.041 37.037 0.00 0.00 0.00 2.44
1924 1929 9.665719 ACCAAAAGTTTATTGTGATCTTTTTGT 57.334 25.926 0.00 0.00 36.58 2.83
1947 1952 8.810652 TGTTCAAATAACAATTAAGGTGAAGC 57.189 30.769 0.00 0.00 0.00 3.86
1948 1953 8.417106 TGTTCAAATAACAATTAAGGTGAAGCA 58.583 29.630 0.00 0.00 0.00 3.91
1949 1954 8.915654 GTTCAAATAACAATTAAGGTGAAGCAG 58.084 33.333 0.00 0.00 0.00 4.24
1950 1955 7.601856 TCAAATAACAATTAAGGTGAAGCAGG 58.398 34.615 0.00 0.00 0.00 4.85
1951 1956 6.530019 AATAACAATTAAGGTGAAGCAGGG 57.470 37.500 0.00 0.00 0.00 4.45
1952 1957 3.525800 ACAATTAAGGTGAAGCAGGGT 57.474 42.857 0.00 0.00 0.00 4.34
1953 1958 3.421844 ACAATTAAGGTGAAGCAGGGTC 58.578 45.455 0.00 0.00 0.00 4.46
1954 1959 3.181434 ACAATTAAGGTGAAGCAGGGTCA 60.181 43.478 0.00 0.00 0.00 4.02
1955 1960 2.859165 TTAAGGTGAAGCAGGGTCAG 57.141 50.000 0.00 0.00 0.00 3.51
1956 1961 0.984230 TAAGGTGAAGCAGGGTCAGG 59.016 55.000 0.00 0.00 0.00 3.86
1957 1962 0.768221 AAGGTGAAGCAGGGTCAGGA 60.768 55.000 0.00 0.00 0.00 3.86
1958 1963 0.768221 AGGTGAAGCAGGGTCAGGAA 60.768 55.000 0.00 0.00 0.00 3.36
1959 1964 0.606673 GGTGAAGCAGGGTCAGGAAC 60.607 60.000 0.00 0.00 0.00 3.62
1960 1965 0.108585 GTGAAGCAGGGTCAGGAACA 59.891 55.000 0.00 0.00 0.00 3.18
1961 1966 0.843309 TGAAGCAGGGTCAGGAACAA 59.157 50.000 0.00 0.00 0.00 2.83
1962 1967 1.425066 TGAAGCAGGGTCAGGAACAAT 59.575 47.619 0.00 0.00 0.00 2.71
1967 1972 2.424956 GCAGGGTCAGGAACAATGAATC 59.575 50.000 0.00 0.00 0.00 2.52
2237 2244 7.060421 TGTATAACTCCCCAGGAATTTCAATC 58.940 38.462 0.00 0.00 0.00 2.67
2814 2821 4.955811 AGTCAGTCATTCACAACCACTA 57.044 40.909 0.00 0.00 0.00 2.74
2901 2909 5.381174 TGGATTCGGTCTTATACATACGG 57.619 43.478 0.00 0.00 0.00 4.02
2985 2993 2.871022 GCGAGATGAAAGTCTCATGCAT 59.129 45.455 0.00 0.00 45.23 3.96
3422 3430 9.322773 CATTCGAGATTATGCAGGATTATACAT 57.677 33.333 0.00 0.00 0.00 2.29
3650 3658 4.521639 ACGAAACCAAGAAATAACCCCTTC 59.478 41.667 0.00 0.00 0.00 3.46
3805 3813 9.364653 CCCTCTTTTAGCTACTAGGTCTATTTA 57.635 37.037 0.00 0.00 0.00 1.40
4581 5240 4.998672 CAGTTCCAAAAACGGGTACTATCA 59.001 41.667 0.00 0.00 34.70 2.15
4624 5283 1.247567 CAGAGGTCCGTTGGCATTTT 58.752 50.000 0.00 0.00 0.00 1.82
4707 5366 4.985538 ATCAGAATAGGACGAACGAACT 57.014 40.909 0.14 1.39 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
514 516 1.293498 GGCGAGTGCTCTTCCTTGA 59.707 57.895 0.00 0.00 42.25 3.02
672 674 6.371548 ACGAAAATGTGCAAGAGCTCTATTTA 59.628 34.615 18.59 3.34 42.74 1.40
1098 1101 6.323739 GGCCAAAAATTAGGATACATTCTGGA 59.676 38.462 0.00 0.00 41.41 3.86
1898 1903 9.665719 ACAAAAAGATCACAATAAACTTTTGGT 57.334 25.926 0.00 0.00 38.81 3.67
1921 1926 9.255304 GCTTCACCTTAATTGTTATTTGAACAA 57.745 29.630 5.41 5.41 43.33 2.83
1922 1927 8.417106 TGCTTCACCTTAATTGTTATTTGAACA 58.583 29.630 0.00 0.00 0.00 3.18
1923 1928 8.810652 TGCTTCACCTTAATTGTTATTTGAAC 57.189 30.769 0.00 0.00 0.00 3.18
1924 1929 8.087750 CCTGCTTCACCTTAATTGTTATTTGAA 58.912 33.333 0.00 0.00 0.00 2.69
1925 1930 7.309744 CCCTGCTTCACCTTAATTGTTATTTGA 60.310 37.037 0.00 0.00 0.00 2.69
1926 1931 6.813152 CCCTGCTTCACCTTAATTGTTATTTG 59.187 38.462 0.00 0.00 0.00 2.32
1927 1932 6.496911 ACCCTGCTTCACCTTAATTGTTATTT 59.503 34.615 0.00 0.00 0.00 1.40
1928 1933 6.016555 ACCCTGCTTCACCTTAATTGTTATT 58.983 36.000 0.00 0.00 0.00 1.40
1929 1934 5.580022 ACCCTGCTTCACCTTAATTGTTAT 58.420 37.500 0.00 0.00 0.00 1.89
1930 1935 4.993028 ACCCTGCTTCACCTTAATTGTTA 58.007 39.130 0.00 0.00 0.00 2.41
1931 1936 3.826729 GACCCTGCTTCACCTTAATTGTT 59.173 43.478 0.00 0.00 0.00 2.83
1932 1937 3.181434 TGACCCTGCTTCACCTTAATTGT 60.181 43.478 0.00 0.00 0.00 2.71
1933 1938 3.420893 TGACCCTGCTTCACCTTAATTG 58.579 45.455 0.00 0.00 0.00 2.32
1934 1939 3.562176 CCTGACCCTGCTTCACCTTAATT 60.562 47.826 0.00 0.00 0.00 1.40
1935 1940 2.025887 CCTGACCCTGCTTCACCTTAAT 60.026 50.000 0.00 0.00 0.00 1.40
1936 1941 1.351017 CCTGACCCTGCTTCACCTTAA 59.649 52.381 0.00 0.00 0.00 1.85
1937 1942 0.984230 CCTGACCCTGCTTCACCTTA 59.016 55.000 0.00 0.00 0.00 2.69
1938 1943 0.768221 TCCTGACCCTGCTTCACCTT 60.768 55.000 0.00 0.00 0.00 3.50
1939 1944 0.768221 TTCCTGACCCTGCTTCACCT 60.768 55.000 0.00 0.00 0.00 4.00
1940 1945 0.606673 GTTCCTGACCCTGCTTCACC 60.607 60.000 0.00 0.00 0.00 4.02
1941 1946 0.108585 TGTTCCTGACCCTGCTTCAC 59.891 55.000 0.00 0.00 0.00 3.18
1942 1947 0.843309 TTGTTCCTGACCCTGCTTCA 59.157 50.000 0.00 0.00 0.00 3.02
1943 1948 1.815003 CATTGTTCCTGACCCTGCTTC 59.185 52.381 0.00 0.00 0.00 3.86
1944 1949 1.425066 TCATTGTTCCTGACCCTGCTT 59.575 47.619 0.00 0.00 0.00 3.91
1945 1950 1.067295 TCATTGTTCCTGACCCTGCT 58.933 50.000 0.00 0.00 0.00 4.24
1946 1951 1.909700 TTCATTGTTCCTGACCCTGC 58.090 50.000 0.00 0.00 0.00 4.85
1947 1952 3.960571 AGATTCATTGTTCCTGACCCTG 58.039 45.455 0.00 0.00 0.00 4.45
1948 1953 4.664688 AAGATTCATTGTTCCTGACCCT 57.335 40.909 0.00 0.00 0.00 4.34
1949 1954 5.728637 AAAAGATTCATTGTTCCTGACCC 57.271 39.130 0.00 0.00 0.00 4.46
1950 1955 8.306761 ACATAAAAAGATTCATTGTTCCTGACC 58.693 33.333 0.00 0.00 0.00 4.02
1951 1956 9.132521 CACATAAAAAGATTCATTGTTCCTGAC 57.867 33.333 0.00 0.00 0.00 3.51
1952 1957 8.306038 CCACATAAAAAGATTCATTGTTCCTGA 58.694 33.333 0.00 0.00 0.00 3.86
1953 1958 8.090214 ACCACATAAAAAGATTCATTGTTCCTG 58.910 33.333 0.00 0.00 0.00 3.86
1954 1959 8.090214 CACCACATAAAAAGATTCATTGTTCCT 58.910 33.333 0.00 0.00 0.00 3.36
1955 1960 7.148590 GCACCACATAAAAAGATTCATTGTTCC 60.149 37.037 0.00 0.00 0.00 3.62
1956 1961 7.599998 AGCACCACATAAAAAGATTCATTGTTC 59.400 33.333 0.00 0.00 0.00 3.18
1957 1962 7.444299 AGCACCACATAAAAAGATTCATTGTT 58.556 30.769 0.00 0.00 0.00 2.83
1958 1963 6.996509 AGCACCACATAAAAAGATTCATTGT 58.003 32.000 0.00 0.00 0.00 2.71
1959 1964 8.863049 GTTAGCACCACATAAAAAGATTCATTG 58.137 33.333 0.00 0.00 0.00 2.82
1960 1965 7.754924 CGTTAGCACCACATAAAAAGATTCATT 59.245 33.333 0.00 0.00 0.00 2.57
1961 1966 7.120579 TCGTTAGCACCACATAAAAAGATTCAT 59.879 33.333 0.00 0.00 0.00 2.57
1962 1967 6.428465 TCGTTAGCACCACATAAAAAGATTCA 59.572 34.615 0.00 0.00 0.00 2.57
1967 1972 8.958175 TTAAATCGTTAGCACCACATAAAAAG 57.042 30.769 0.00 0.00 0.00 2.27
2237 2244 2.677199 ACAGTGATGGATATAAGCGCG 58.323 47.619 0.00 0.00 0.00 6.86
2814 2821 7.121315 CCTTAACTTTTCGAGGAATCCTTCATT 59.879 37.037 2.09 0.00 31.76 2.57
2985 2993 4.261741 GCTTCTTTCTCTCATGCAAAACCA 60.262 41.667 0.00 0.00 0.00 3.67
3650 3658 5.409826 GGGGATCTTCTATAATTTCGCACAG 59.590 44.000 0.00 0.00 0.00 3.66
3805 3813 9.495382 AGTTAGTAAGAGGGATCTTGAACTAAT 57.505 33.333 12.83 4.64 35.26 1.73
4185 4193 8.429641 AGGACACCTTATATGTATCAAAATCGT 58.570 33.333 0.00 0.00 0.00 3.73
4581 5240 6.778069 TGTCTATTCTCTAATTCACCCGATCT 59.222 38.462 0.00 0.00 0.00 2.75
4707 5366 1.407656 AAAGATATCCGCGGAGGCCA 61.408 55.000 33.87 18.19 40.77 5.36


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

AutoCloner maintained by Alex Coulton.