Multiple sequence alignment - TraesCS7D01G143000

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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 TraesCS7D01G143000 chr7D 100.000 2468 0 0 1 2468 91053794 91056261 0.000000e+00 4558.0
1 TraesCS7D01G143000 chr7B 92.272 1967 108 25 1 1943 43950105 43948159 0.000000e+00 2750.0
2 TraesCS7D01G143000 chr7B 90.228 921 37 11 1031 1943 43896940 43896065 0.000000e+00 1153.0
3 TraesCS7D01G143000 chr7B 91.124 507 21 5 1986 2468 43948152 43947646 0.000000e+00 665.0
4 TraesCS7D01G143000 chr7B 90.171 468 23 7 1907 2351 43897406 43896939 2.730000e-164 588.0
5 TraesCS7D01G143000 chr7B 85.225 467 66 3 1000 1464 592357444 592357909 6.170000e-131 477.0
6 TraesCS7D01G143000 chr7B 93.277 119 7 1 2351 2468 43889245 43889127 9.070000e-40 174.0
7 TraesCS7D01G143000 chr7B 100.000 41 0 0 2428 2468 43896065 43896025 2.630000e-10 76.8
8 TraesCS7D01G143000 chr7A 90.293 1978 103 38 1 1930 93063899 93065835 0.000000e+00 2507.0
9 TraesCS7D01G143000 chr7A 85.193 466 67 2 1000 1464 632583791 632584255 6.170000e-131 477.0
10 TraesCS7D01G143000 chr7A 85.813 289 29 8 2187 2468 93066010 93066293 1.860000e-76 296.0
11 TraesCS7D01G143000 chr7A 89.516 124 8 4 2057 2179 93065921 93066040 4.250000e-33 152.0
12 TraesCS7D01G143000 chr1A 94.348 460 26 0 998 1457 364040178 364039719 0.000000e+00 706.0
13 TraesCS7D01G143000 chr1D 92.157 459 36 0 999 1457 291841763 291842221 0.000000e+00 649.0
14 TraesCS7D01G143000 chr1D 91.939 459 37 0 999 1457 291799253 291798795 0.000000e+00 643.0
15 TraesCS7D01G143000 chr1B 91.791 402 33 0 999 1400 392837550 392837951 5.960000e-156 560.0


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 TraesCS7D01G143000 chr7D 91053794 91056261 2467 False 4558.000000 4558 100.000000 1 2468 1 chr7D.!!$F1 2467
1 TraesCS7D01G143000 chr7B 43947646 43950105 2459 True 1707.500000 2750 91.698000 1 2468 2 chr7B.!!$R3 2467
2 TraesCS7D01G143000 chr7B 43896025 43897406 1381 True 605.933333 1153 93.466333 1031 2468 3 chr7B.!!$R2 1437
3 TraesCS7D01G143000 chr7A 93063899 93066293 2394 False 985.000000 2507 88.540667 1 2468 3 chr7A.!!$F2 2467

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
646 661 0.106719 CCATACGGGTTGGGCTCAAT 60.107 55.0 0.27 0.0 35.1 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2060 0.031857 CAAGGGCGCAAACATCAACA 59.968 50.0 10.83 0.0 0.0 3.33 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
93 94 3.691744 CTCCAGAGACAGCGCGTCC 62.692 68.421 22.55 16.04 46.69 4.79
131 132 2.224233 GCATAGCAGCAGAATCAGGAGA 60.224 50.000 0.00 0.00 0.00 3.71
139 140 3.118334 AGCAGAATCAGGAGAACCATCAG 60.118 47.826 0.00 0.00 38.94 2.90
150 151 2.504681 CCATCAGCCGCAAAACGC 60.505 61.111 0.00 0.00 41.76 4.84
171 172 2.100991 GCAATTTCAGCGGCCGAG 59.899 61.111 33.48 21.11 0.00 4.63
230 231 1.756950 CCTGATTCGAGGACGGGGA 60.757 63.158 5.80 0.00 40.21 4.81
398 400 1.681076 GAGCTTACGGTTTGGGGGA 59.319 57.895 0.00 0.00 0.00 4.81
431 433 2.159366 AGTAGCGAGTTCGAGATGGTTG 60.159 50.000 5.60 0.00 43.02 3.77
505 507 2.936032 GGTTGGGCTGGAGGAGGT 60.936 66.667 0.00 0.00 0.00 3.85
593 601 2.352805 GAAGGGGCAGTGGAGGTG 59.647 66.667 0.00 0.00 0.00 4.00
595 603 4.990910 AGGGGCAGTGGAGGTGCT 62.991 66.667 0.00 0.00 40.97 4.40
596 604 4.416738 GGGGCAGTGGAGGTGCTC 62.417 72.222 0.00 0.00 41.02 4.26
597 605 3.325753 GGGCAGTGGAGGTGCTCT 61.326 66.667 0.00 0.00 38.47 4.09
598 606 2.753029 GGCAGTGGAGGTGCTCTT 59.247 61.111 0.00 0.00 40.97 2.85
599 607 1.073897 GGCAGTGGAGGTGCTCTTT 59.926 57.895 0.00 0.00 40.97 2.52
600 608 0.324943 GGCAGTGGAGGTGCTCTTTA 59.675 55.000 0.00 0.00 40.97 1.85
601 609 1.677217 GGCAGTGGAGGTGCTCTTTAG 60.677 57.143 0.00 0.00 40.97 1.85
646 661 0.106719 CCATACGGGTTGGGCTCAAT 60.107 55.000 0.27 0.00 35.10 2.57
740 755 1.602323 TACGTGCTGGGCCCAAAAG 60.602 57.895 28.29 20.89 0.00 2.27
780 795 2.631428 GTTGCAGAGTTCGCGCAA 59.369 55.556 8.75 7.60 43.02 4.85
813 832 0.882042 CGCAGGGATCGGATTCCAAG 60.882 60.000 17.61 10.27 37.53 3.61
898 918 0.982852 ACCCCATCGATCTCAAGCCA 60.983 55.000 0.00 0.00 0.00 4.75
899 919 0.181114 CCCCATCGATCTCAAGCCAA 59.819 55.000 0.00 0.00 0.00 4.52
901 921 1.303309 CCATCGATCTCAAGCCAACC 58.697 55.000 0.00 0.00 0.00 3.77
913 933 2.191128 AGCCAACCAACAAGCTAGAG 57.809 50.000 0.00 0.00 32.73 2.43
929 949 4.019321 AGCTAGAGCCTAGAGAGATCGAAT 60.019 45.833 11.96 0.00 43.38 3.34
931 951 3.334691 AGAGCCTAGAGAGATCGAATCG 58.665 50.000 0.00 0.00 0.00 3.34
932 952 3.007506 AGAGCCTAGAGAGATCGAATCGA 59.992 47.826 8.12 8.12 41.13 3.59
935 955 4.023536 AGCCTAGAGAGATCGAATCGAAAC 60.024 45.833 10.12 7.26 39.99 2.78
936 956 4.261238 GCCTAGAGAGATCGAATCGAAACA 60.261 45.833 10.12 0.00 39.99 2.83
939 959 5.060662 AGAGAGATCGAATCGAAACACAA 57.939 39.130 10.12 0.00 39.99 3.33
941 961 4.810790 AGAGATCGAATCGAAACACAAGT 58.189 39.130 10.12 0.00 39.99 3.16
1179 1212 1.516386 CACGCTCGCCGACTACAAT 60.516 57.895 2.37 0.00 41.02 2.71
1312 1345 1.215647 GTCGACCGCATCAAGGAGT 59.784 57.895 3.51 0.00 0.00 3.85
1416 1449 4.884164 GCAAAGGACTACAATATCAAGGCT 59.116 41.667 0.00 0.00 0.00 4.58
1446 1479 4.135153 CACCTCGTCCTCGCCCTG 62.135 72.222 0.00 0.00 36.96 4.45
1500 1537 3.306571 GGGTTTTACCTACGAGAGCTTGT 60.307 47.826 0.00 0.00 38.64 3.16
1591 1636 3.020984 ACGTAATGGTTTTGGGGCTATG 58.979 45.455 0.00 0.00 0.00 2.23
1593 1638 4.200874 CGTAATGGTTTTGGGGCTATGTA 58.799 43.478 0.00 0.00 0.00 2.29
1646 1691 5.483685 TGAGTCCTTTACATGTAAGCTGT 57.516 39.130 17.36 4.23 0.00 4.40
1946 2023 5.356426 TGAAGATTCAGAACGAACAACTCA 58.644 37.500 0.00 0.00 36.12 3.41
1947 2024 5.463392 TGAAGATTCAGAACGAACAACTCAG 59.537 40.000 0.00 0.00 36.12 3.35
1948 2025 3.743396 AGATTCAGAACGAACAACTCAGC 59.257 43.478 0.00 0.00 36.12 4.26
1949 2026 2.595124 TCAGAACGAACAACTCAGCA 57.405 45.000 0.00 0.00 0.00 4.41
1950 2027 3.111853 TCAGAACGAACAACTCAGCAT 57.888 42.857 0.00 0.00 0.00 3.79
1951 2028 3.466836 TCAGAACGAACAACTCAGCATT 58.533 40.909 0.00 0.00 0.00 3.56
1952 2029 3.494626 TCAGAACGAACAACTCAGCATTC 59.505 43.478 0.00 0.00 0.00 2.67
1953 2030 3.248363 CAGAACGAACAACTCAGCATTCA 59.752 43.478 0.00 0.00 0.00 2.57
1954 2031 3.496130 AGAACGAACAACTCAGCATTCAG 59.504 43.478 0.00 0.00 0.00 3.02
1955 2032 1.532868 ACGAACAACTCAGCATTCAGC 59.467 47.619 0.00 0.00 46.19 4.26
1965 2042 1.440476 GCATTCAGCAATGGAGGCC 59.560 57.895 0.00 0.00 44.79 5.19
1966 2043 1.324740 GCATTCAGCAATGGAGGCCA 61.325 55.000 5.01 0.00 44.79 5.36
1967 2044 1.187974 CATTCAGCAATGGAGGCCAA 58.812 50.000 5.01 0.00 36.95 4.52
1968 2045 1.136305 CATTCAGCAATGGAGGCCAAG 59.864 52.381 5.01 0.00 36.95 3.61
1969 2046 0.112995 TTCAGCAATGGAGGCCAAGT 59.887 50.000 5.01 0.00 36.95 3.16
1970 2047 0.322816 TCAGCAATGGAGGCCAAGTC 60.323 55.000 5.01 0.00 36.95 3.01
1971 2048 1.000396 AGCAATGGAGGCCAAGTCC 60.000 57.895 5.01 3.51 36.95 3.85
1975 2052 2.853542 TGGAGGCCAAGTCCAGCA 60.854 61.111 8.12 0.00 39.28 4.41
1976 2053 2.233566 TGGAGGCCAAGTCCAGCAT 61.234 57.895 8.12 0.00 39.28 3.79
1977 2054 0.913934 TGGAGGCCAAGTCCAGCATA 60.914 55.000 8.12 0.00 39.28 3.14
1978 2055 0.255890 GGAGGCCAAGTCCAGCATAA 59.744 55.000 5.01 0.00 33.84 1.90
1979 2056 1.133668 GGAGGCCAAGTCCAGCATAAT 60.134 52.381 5.01 0.00 33.84 1.28
1980 2057 2.659428 GAGGCCAAGTCCAGCATAATT 58.341 47.619 5.01 0.00 0.00 1.40
1981 2058 2.360165 GAGGCCAAGTCCAGCATAATTG 59.640 50.000 5.01 0.00 0.00 2.32
1982 2059 2.025037 AGGCCAAGTCCAGCATAATTGA 60.025 45.455 5.01 0.00 0.00 2.57
1983 2060 2.961062 GGCCAAGTCCAGCATAATTGAT 59.039 45.455 0.00 0.00 0.00 2.57
1984 2061 3.243636 GGCCAAGTCCAGCATAATTGATG 60.244 47.826 0.00 0.00 39.00 3.07
1995 2072 6.237996 CCAGCATAATTGATGTTGATGTTTGC 60.238 38.462 0.00 0.00 46.72 3.68
1999 2076 0.243365 TGATGTTGATGTTTGCGCCC 59.757 50.000 4.18 0.00 0.00 6.13
2105 2225 5.381174 TCTGAAATGAATGCAAAGTCTGG 57.619 39.130 0.00 0.00 0.00 3.86
2176 2309 1.629353 AGCTATGCATGCTCATAGGCT 59.371 47.619 20.33 15.51 43.70 4.58
2222 2355 4.850822 CTCATGCGCTGAGGTGAT 57.149 55.556 21.81 0.00 46.52 3.06
2344 2487 2.700897 ACACCAGCTCAGACACTAGTTT 59.299 45.455 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 2.265589 TGCTGTGATAGATGGCCATG 57.734 50.000 26.56 7.05 0.00 3.66
131 132 1.285641 CGTTTTGCGGCTGATGGTT 59.714 52.632 0.00 0.00 36.85 3.67
171 172 1.092345 GCCTTCGGCTGTTCTCATCC 61.092 60.000 0.00 0.00 46.69 3.51
191 192 4.166011 GACAGATTGTGCCGCGGC 62.166 66.667 42.35 42.35 42.35 6.53
230 231 2.981909 TCCACGCGTTCCTCTCGT 60.982 61.111 10.22 0.00 38.02 4.18
398 400 1.215647 CGCTACTTCTCCACGCCTT 59.784 57.895 0.00 0.00 0.00 4.35
431 433 2.836944 GGTAACTGGTCGCTCAACC 58.163 57.895 0.00 0.00 39.94 3.77
593 601 2.124109 GGCCCAGCCCTAAAGAGC 60.124 66.667 0.00 0.00 44.06 4.09
628 643 1.308998 GATTGAGCCCAACCCGTATG 58.691 55.000 0.00 0.00 34.72 2.39
631 646 1.002134 CTGATTGAGCCCAACCCGT 60.002 57.895 0.00 0.00 34.72 5.28
646 661 2.239654 CCAAGTTGAGGAATAGGCCTGA 59.760 50.000 17.99 0.00 38.73 3.86
780 795 1.033746 CCTGCGGTGCCATGATTTCT 61.034 55.000 0.00 0.00 0.00 2.52
898 918 3.173965 TCTAGGCTCTAGCTTGTTGGTT 58.826 45.455 0.00 0.00 41.70 3.67
899 919 2.763448 CTCTAGGCTCTAGCTTGTTGGT 59.237 50.000 0.00 0.00 41.70 3.67
901 921 3.951037 TCTCTCTAGGCTCTAGCTTGTTG 59.049 47.826 0.00 0.00 41.70 3.33
913 933 4.223659 GTTTCGATTCGATCTCTCTAGGC 58.776 47.826 9.96 0.00 35.23 3.93
929 949 1.952133 CGCCGGACTTGTGTTTCGA 60.952 57.895 5.05 0.00 0.00 3.71
931 951 0.234884 CTTCGCCGGACTTGTGTTTC 59.765 55.000 5.05 0.00 0.00 2.78
932 952 1.782028 GCTTCGCCGGACTTGTGTTT 61.782 55.000 5.05 0.00 0.00 2.83
935 955 2.357517 AGCTTCGCCGGACTTGTG 60.358 61.111 5.05 0.00 0.00 3.33
936 956 2.048127 GAGCTTCGCCGGACTTGT 60.048 61.111 5.05 0.00 0.00 3.16
1023 1056 1.736645 CGTGATCGTCTTGCCCGTT 60.737 57.895 0.00 0.00 0.00 4.44
1029 1062 0.803768 CCTCCAGCGTGATCGTCTTG 60.804 60.000 0.00 0.00 39.49 3.02
1179 1212 1.285950 CGTCGACTCCTTCTGCACA 59.714 57.895 14.70 0.00 0.00 4.57
1312 1345 2.046864 CCTCCTTCTCCTCGACGCA 61.047 63.158 0.00 0.00 0.00 5.24
1446 1479 4.096003 TAGCAAGCACCGCCCCTC 62.096 66.667 0.00 0.00 0.00 4.30
1458 1491 5.342017 ACCCAGGCATATATCTAGTAGCAA 58.658 41.667 0.00 0.00 0.00 3.91
1558 1599 8.692615 CCAAAACCATTACGTAACAATGTTTAC 58.307 33.333 10.81 0.18 32.55 2.01
1560 1601 6.702282 CCCAAAACCATTACGTAACAATGTTT 59.298 34.615 10.81 13.64 32.55 2.83
1591 1636 7.266922 TCATAAACTTCCAACCACAGTTTAC 57.733 36.000 6.00 0.00 42.78 2.01
1593 1638 6.783708 TTCATAAACTTCCAACCACAGTTT 57.216 33.333 0.00 0.00 42.20 2.66
1943 2020 1.676529 CCTCCATTGCTGAATGCTGAG 59.323 52.381 0.00 0.00 43.37 3.35
1944 2021 1.758936 CCTCCATTGCTGAATGCTGA 58.241 50.000 0.00 0.00 43.37 4.26
1946 2023 1.041447 GGCCTCCATTGCTGAATGCT 61.041 55.000 0.00 0.00 43.37 3.79
1947 2024 1.324740 TGGCCTCCATTGCTGAATGC 61.325 55.000 3.32 0.00 38.14 3.56
1948 2025 1.136305 CTTGGCCTCCATTGCTGAATG 59.864 52.381 3.32 0.00 39.04 2.67
1949 2026 1.272872 ACTTGGCCTCCATTGCTGAAT 60.273 47.619 3.32 0.00 31.53 2.57
1950 2027 0.112995 ACTTGGCCTCCATTGCTGAA 59.887 50.000 3.32 0.00 31.53 3.02
1951 2028 0.322816 GACTTGGCCTCCATTGCTGA 60.323 55.000 3.32 0.00 31.53 4.26
1952 2029 1.318158 GGACTTGGCCTCCATTGCTG 61.318 60.000 3.32 0.00 31.53 4.41
1953 2030 1.000396 GGACTTGGCCTCCATTGCT 60.000 57.895 3.32 0.00 31.53 3.91
1954 2031 1.304381 TGGACTTGGCCTCCATTGC 60.304 57.895 8.12 0.00 32.52 3.56
1955 2032 1.318158 GCTGGACTTGGCCTCCATTG 61.318 60.000 12.37 3.87 37.18 2.82
1956 2033 1.000396 GCTGGACTTGGCCTCCATT 60.000 57.895 12.37 0.00 37.18 3.16
1957 2034 1.578215 ATGCTGGACTTGGCCTCCAT 61.578 55.000 12.37 0.00 37.18 3.41
1958 2035 0.913934 TATGCTGGACTTGGCCTCCA 60.914 55.000 11.51 11.51 36.34 3.86
1959 2036 0.255890 TTATGCTGGACTTGGCCTCC 59.744 55.000 3.32 2.82 0.00 4.30
1960 2037 2.355010 ATTATGCTGGACTTGGCCTC 57.645 50.000 3.32 0.00 0.00 4.70
1961 2038 2.025037 TCAATTATGCTGGACTTGGCCT 60.025 45.455 3.32 0.00 0.00 5.19
1962 2039 2.378038 TCAATTATGCTGGACTTGGCC 58.622 47.619 0.00 0.00 0.00 5.36
1963 2040 3.382546 ACATCAATTATGCTGGACTTGGC 59.617 43.478 0.00 0.00 39.39 4.52
1964 2041 5.125900 TCAACATCAATTATGCTGGACTTGG 59.874 40.000 0.00 0.00 39.39 3.61
1965 2042 6.198650 TCAACATCAATTATGCTGGACTTG 57.801 37.500 0.00 0.00 39.39 3.16
1966 2043 6.379133 ACATCAACATCAATTATGCTGGACTT 59.621 34.615 0.00 0.00 39.39 3.01
1967 2044 5.889853 ACATCAACATCAATTATGCTGGACT 59.110 36.000 0.00 0.00 39.39 3.85
1968 2045 6.140303 ACATCAACATCAATTATGCTGGAC 57.860 37.500 0.00 0.00 39.39 4.02
1969 2046 6.778834 AACATCAACATCAATTATGCTGGA 57.221 33.333 0.00 0.00 39.39 3.86
1970 2047 6.237996 GCAAACATCAACATCAATTATGCTGG 60.238 38.462 0.00 0.00 39.39 4.85
1971 2048 6.507299 CGCAAACATCAACATCAATTATGCTG 60.507 38.462 0.00 0.00 39.39 4.41
1972 2049 5.517411 CGCAAACATCAACATCAATTATGCT 59.483 36.000 0.00 0.00 39.39 3.79
1973 2050 5.720239 CGCAAACATCAACATCAATTATGC 58.280 37.500 0.00 0.00 39.39 3.14
1974 2051 5.276489 GGCGCAAACATCAACATCAATTATG 60.276 40.000 10.83 0.00 41.74 1.90
1975 2052 4.805192 GGCGCAAACATCAACATCAATTAT 59.195 37.500 10.83 0.00 0.00 1.28
1976 2053 4.172505 GGCGCAAACATCAACATCAATTA 58.827 39.130 10.83 0.00 0.00 1.40
1977 2054 2.995258 GGCGCAAACATCAACATCAATT 59.005 40.909 10.83 0.00 0.00 2.32
1978 2055 2.609350 GGCGCAAACATCAACATCAAT 58.391 42.857 10.83 0.00 0.00 2.57
1979 2056 1.336702 GGGCGCAAACATCAACATCAA 60.337 47.619 10.83 0.00 0.00 2.57
1980 2057 0.243365 GGGCGCAAACATCAACATCA 59.757 50.000 10.83 0.00 0.00 3.07
1981 2058 0.527565 AGGGCGCAAACATCAACATC 59.472 50.000 10.83 0.00 0.00 3.06
1982 2059 0.968405 AAGGGCGCAAACATCAACAT 59.032 45.000 10.83 0.00 0.00 2.71
1983 2060 0.031857 CAAGGGCGCAAACATCAACA 59.968 50.000 10.83 0.00 0.00 3.33
1984 2061 0.313672 TCAAGGGCGCAAACATCAAC 59.686 50.000 10.83 0.00 0.00 3.18
1995 2072 1.167851 TTCTCTGCAAATCAAGGGCG 58.832 50.000 0.00 0.00 0.00 6.13
1999 2076 8.528917 TTGAATTTCATTCTCTGCAAATCAAG 57.471 30.769 0.00 0.00 39.96 3.02
2070 2189 7.485810 CATTCATTTCAGAGCATTCAATACCA 58.514 34.615 0.00 0.00 0.00 3.25
2071 2190 6.420008 GCATTCATTTCAGAGCATTCAATACC 59.580 38.462 0.00 0.00 0.00 2.73
2105 2225 6.145535 CAGGTAACAAATTCAGAGCAAAGTC 58.854 40.000 0.00 0.00 41.41 3.01
2400 2553 4.541779 ACGCGCAAAATGAAGTGAAAATA 58.458 34.783 5.73 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.