Multiple sequence alignment - TraesCS5D01G566300

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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 TraesCS5D01G566300 chr5D 100.000 2327 0 0 1 2327 564670386 564672712 0.000000e+00 4298
1 TraesCS5D01G566300 chr6D 97.798 1680 35 2 1 1679 367879771 367878093 0.000000e+00 2896
2 TraesCS5D01G566300 chr6A 95.003 1681 73 7 1 1679 183314290 183312619 0.000000e+00 2628
3 TraesCS5D01G566300 chr6A 94.411 1682 89 5 1 1681 183929704 183931381 0.000000e+00 2580
4 TraesCS5D01G566300 chr6A 89.487 1189 102 17 500 1680 22262078 22263251 0.000000e+00 1482
5 TraesCS5D01G566300 chr7A 94.170 1681 91 7 6 1684 721643425 721641750 0.000000e+00 2555
6 TraesCS5D01G566300 chr7A 90.608 1693 142 12 1 1681 717769091 717767404 0.000000e+00 2230
7 TraesCS5D01G566300 chr1B 90.973 1695 129 20 1 1681 145446317 145444633 0.000000e+00 2261
8 TraesCS5D01G566300 chr5A 90.812 1687 141 13 1 1681 31278727 31280405 0.000000e+00 2244
9 TraesCS5D01G566300 chr2B 83.539 1622 240 22 69 1680 748211381 748212985 0.000000e+00 1491
10 TraesCS5D01G566300 chr5B 87.425 668 51 19 1683 2327 706951667 706952324 0.000000e+00 737
11 TraesCS5D01G566300 chr4A 87.571 531 51 11 1683 2204 607952037 607951513 3.310000e-168 601
12 TraesCS5D01G566300 chr3A 89.180 305 28 4 1385 1684 621497548 621497852 2.180000e-100 375


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 TraesCS5D01G566300 chr5D 564670386 564672712 2326 False 4298 4298 100.000 1 2327 1 chr5D.!!$F1 2326
1 TraesCS5D01G566300 chr6D 367878093 367879771 1678 True 2896 2896 97.798 1 1679 1 chr6D.!!$R1 1678
2 TraesCS5D01G566300 chr6A 183312619 183314290 1671 True 2628 2628 95.003 1 1679 1 chr6A.!!$R1 1678
3 TraesCS5D01G566300 chr6A 183929704 183931381 1677 False 2580 2580 94.411 1 1681 1 chr6A.!!$F2 1680
4 TraesCS5D01G566300 chr6A 22262078 22263251 1173 False 1482 1482 89.487 500 1680 1 chr6A.!!$F1 1180
5 TraesCS5D01G566300 chr7A 721641750 721643425 1675 True 2555 2555 94.170 6 1684 1 chr7A.!!$R2 1678
6 TraesCS5D01G566300 chr7A 717767404 717769091 1687 True 2230 2230 90.608 1 1681 1 chr7A.!!$R1 1680
7 TraesCS5D01G566300 chr1B 145444633 145446317 1684 True 2261 2261 90.973 1 1681 1 chr1B.!!$R1 1680
8 TraesCS5D01G566300 chr5A 31278727 31280405 1678 False 2244 2244 90.812 1 1681 1 chr5A.!!$F1 1680
9 TraesCS5D01G566300 chr2B 748211381 748212985 1604 False 1491 1491 83.539 69 1680 1 chr2B.!!$F1 1611
10 TraesCS5D01G566300 chr5B 706951667 706952324 657 False 737 737 87.425 1683 2327 1 chr5B.!!$F1 644
11 TraesCS5D01G566300 chr4A 607951513 607952037 524 True 601 601 87.571 1683 2204 1 chr4A.!!$R1 521

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
241 242 0.465097 AATCTGCCGCTCCAAGGATG 60.465 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 1887 0.106708 TTTGTCTTGAGGCAGCTCGT 59.893 50.0 0.0 0.0 0.0 4.18 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
174 175 2.474032 GCACCGTAAACGATTCTTCTGC 60.474 50.000 3.65 0.00 43.02 4.26
241 242 0.465097 AATCTGCCGCTCCAAGGATG 60.465 55.000 0.00 0.00 0.00 3.51
402 403 7.172019 GTCTCGGTTAAGACTAAATTTGGTGAA 59.828 37.037 12.36 1.04 42.01 3.18
596 597 6.035112 GTCACGGTTGCAAAGTTTAAAAATGA 59.965 34.615 0.00 0.00 0.00 2.57
656 657 2.267324 GCTGGAGCAGTGGAGGAC 59.733 66.667 0.00 0.00 41.59 3.85
669 670 7.471041 AGCAGTGGAGGACTATGAGTAATATA 58.529 38.462 0.00 0.00 31.73 0.86
808 812 6.926272 GTGTAATTACAAGTGGATTTGGCAAA 59.074 34.615 19.63 16.01 38.04 3.68
901 906 1.118965 TGAGGAGGCGAACTGGTTGA 61.119 55.000 0.00 0.00 0.00 3.18
991 999 2.472029 CTAGGGTCATGTGGAGGACTT 58.528 52.381 0.00 0.00 33.25 3.01
1016 1024 2.282110 CATGTTGGGCACGGACCA 60.282 61.111 0.00 0.00 40.08 4.02
1253 1262 0.955428 GACCGTGAAGCAATGGAGCA 60.955 55.000 0.00 0.00 36.85 4.26
1275 1284 3.849527 TGGAGCTAAGATGCTGAGGATA 58.150 45.455 0.00 0.00 44.17 2.59
1277 1286 4.842948 TGGAGCTAAGATGCTGAGGATAAT 59.157 41.667 0.00 0.00 44.17 1.28
1301 1310 3.611766 GCCTCGAACATGATGCGTATCTA 60.612 47.826 14.76 1.90 34.31 1.98
1490 1511 3.382865 TCAGCCTGTTAATTTTGTGTGCA 59.617 39.130 0.00 0.00 0.00 4.57
1615 1637 0.469144 TCTTTGGTTTCCTGGGTGGC 60.469 55.000 0.00 0.00 35.26 5.01
1710 1733 3.595173 CATACCATGGACAAACGAGACA 58.405 45.455 21.47 0.00 0.00 3.41
1749 1772 0.462581 CGGCAGACTGTACCATGCAT 60.463 55.000 3.99 0.00 40.46 3.96
1772 1795 1.135517 TCGTGATCGATGCAAACGAGA 60.136 47.619 20.24 11.75 46.52 4.04
1778 1801 1.078709 CGATGCAAACGAGACCATGT 58.921 50.000 10.41 0.00 31.90 3.21
1785 1808 3.002791 CAAACGAGACCATGTATGCAGT 58.997 45.455 0.00 0.00 0.00 4.40
1786 1809 2.299993 ACGAGACCATGTATGCAGTG 57.700 50.000 0.00 0.00 0.00 3.66
1789 1812 2.358957 GAGACCATGTATGCAGTGCAA 58.641 47.619 23.90 6.10 43.62 4.08
1858 1887 2.521771 GCGTGTGTGTGCTCGACAA 61.522 57.895 0.00 0.00 35.91 3.18
1902 1944 7.778185 AAAAGGAGTAGACAGTACTACATGT 57.222 36.000 2.69 2.69 43.38 3.21
1903 1945 8.874744 AAAAGGAGTAGACAGTACTACATGTA 57.125 34.615 5.25 5.25 43.38 2.29
1904 1946 8.874744 AAAGGAGTAGACAGTACTACATGTAA 57.125 34.615 7.06 0.00 43.38 2.41
1905 1947 8.508883 AAGGAGTAGACAGTACTACATGTAAG 57.491 38.462 7.06 4.14 43.38 2.34
1906 1948 7.631933 AGGAGTAGACAGTACTACATGTAAGT 58.368 38.462 7.06 9.59 43.38 2.24
1907 1949 8.766476 AGGAGTAGACAGTACTACATGTAAGTA 58.234 37.037 7.06 8.67 43.38 2.24
1908 1950 8.825745 GGAGTAGACAGTACTACATGTAAGTAC 58.174 40.741 23.77 23.77 43.38 2.73
1909 1951 8.729805 AGTAGACAGTACTACATGTAAGTACC 57.270 38.462 25.60 17.54 43.38 3.34
1910 1952 7.772757 AGTAGACAGTACTACATGTAAGTACCC 59.227 40.741 25.60 19.50 43.38 3.69
1911 1953 6.729428 AGACAGTACTACATGTAAGTACCCT 58.271 40.000 25.60 20.57 39.18 4.34
1912 1954 7.865820 AGACAGTACTACATGTAAGTACCCTA 58.134 38.462 25.60 6.47 39.18 3.53
1913 1955 8.501070 AGACAGTACTACATGTAAGTACCCTAT 58.499 37.037 25.60 16.46 39.18 2.57
1914 1956 9.129532 GACAGTACTACATGTAAGTACCCTATT 57.870 37.037 25.60 14.28 39.18 1.73
1915 1957 9.484806 ACAGTACTACATGTAAGTACCCTATTT 57.515 33.333 25.60 13.84 39.18 1.40
2002 2044 1.268692 GCCAATGGATCGACGTACGTA 60.269 52.381 22.87 7.19 43.13 3.57
2069 2111 5.178623 GTGGTTATGTTGAAGTGATCGAACA 59.821 40.000 0.00 0.00 35.24 3.18
2129 2186 0.812014 ACGCACACACGTCCAATCAA 60.812 50.000 0.00 0.00 44.43 2.57
2145 2202 5.812127 TCCAATCAACATCTTCTCATACGTG 59.188 40.000 0.00 0.00 0.00 4.49
2149 2209 6.706055 TCAACATCTTCTCATACGTGTTTC 57.294 37.500 0.00 0.00 0.00 2.78
2164 2224 4.154195 ACGTGTTTCAATGTATCCTTCTGC 59.846 41.667 0.00 0.00 0.00 4.26
2169 2229 4.574674 TCAATGTATCCTTCTGCCACTT 57.425 40.909 0.00 0.00 0.00 3.16
2213 2273 2.783135 CTAGGTCACCAACAAGCATGT 58.217 47.619 0.00 0.00 43.14 3.21
2237 2297 0.179129 CCTGTTGCCCGATTTGCATC 60.179 55.000 0.00 0.00 38.76 3.91
2255 2315 4.949856 TGCATCGATCCACTATGCTAGATA 59.050 41.667 14.41 0.00 44.52 1.98
2291 2351 2.288395 GGTGTGGCTTGTCATGGAAAAG 60.288 50.000 0.00 0.00 30.58 2.27
2293 2353 3.030291 TGTGGCTTGTCATGGAAAAGTT 58.970 40.909 0.00 0.00 30.14 2.66
2294 2354 3.181477 TGTGGCTTGTCATGGAAAAGTTG 60.181 43.478 0.00 0.00 30.14 3.16
2295 2355 2.224018 TGGCTTGTCATGGAAAAGTTGC 60.224 45.455 0.00 0.00 30.14 4.17
2296 2356 2.224018 GGCTTGTCATGGAAAAGTTGCA 60.224 45.455 0.00 0.00 30.14 4.08
2322 2382 0.174845 CACCCGTGCGAGATTAGGAA 59.825 55.000 0.00 0.00 0.00 3.36
2323 2383 0.460311 ACCCGTGCGAGATTAGGAAG 59.540 55.000 0.00 0.00 0.00 3.46
2324 2384 0.744874 CCCGTGCGAGATTAGGAAGA 59.255 55.000 0.00 0.00 0.00 2.87
2325 2385 1.536284 CCCGTGCGAGATTAGGAAGAC 60.536 57.143 0.00 0.00 0.00 3.01
2326 2386 1.134367 CCGTGCGAGATTAGGAAGACA 59.866 52.381 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 0.914644 TTCTCCCCTCATGCTCTTGG 59.085 55.000 0.00 0.00 0.00 3.61
241 242 3.732849 CACCCCCAGGCCTCCTTC 61.733 72.222 0.00 0.00 36.11 3.46
656 657 8.634444 GCCACAGGGATACTATATTACTCATAG 58.366 40.741 0.00 0.00 35.59 2.23
669 670 2.064581 GGTCGGCCACAGGGATACT 61.065 63.158 0.00 0.00 35.59 2.12
808 812 2.507407 TCTTAAGCGGGATTTTGGCT 57.493 45.000 0.00 0.00 39.01 4.75
991 999 0.321021 GTGCCCAACATGCATCCAAA 59.679 50.000 0.00 0.00 41.46 3.28
1016 1024 3.417101 TGCCAAATGTTATTCGGACAGT 58.583 40.909 0.00 0.00 0.00 3.55
1253 1262 2.687297 TCCTCAGCATCTTAGCTCCAT 58.313 47.619 0.00 0.00 44.54 3.41
1275 1284 1.064505 CGCATCATGTTCGAGGCAATT 59.935 47.619 0.00 0.00 42.69 2.32
1277 1286 0.673333 ACGCATCATGTTCGAGGCAA 60.673 50.000 10.01 0.00 42.69 4.52
1490 1511 5.422331 AGTGACACCAACATAGCTACTACAT 59.578 40.000 0.84 0.00 0.00 2.29
1615 1637 4.839796 ACGAAAATACAACAGTTCAACGG 58.160 39.130 0.00 0.00 0.00 4.44
1681 1704 3.720949 TGTCCATGGTATGCGTACTAC 57.279 47.619 12.58 0.00 0.00 2.73
1689 1712 3.595173 TGTCTCGTTTGTCCATGGTATG 58.405 45.455 12.58 2.04 0.00 2.39
1710 1733 4.514577 CGTCGATCAGCGGGGCTT 62.515 66.667 0.00 0.00 36.40 4.35
1772 1795 0.813184 GCTTGCACTGCATACATGGT 59.187 50.000 4.10 0.00 38.76 3.55
1778 1801 1.669049 GCCATGGCTTGCACTGCATA 61.669 55.000 29.98 0.00 38.76 3.14
1785 1808 3.916414 TACTGCGCCATGGCTTGCA 62.916 57.895 33.07 31.26 39.32 4.08
1786 1809 3.133464 TACTGCGCCATGGCTTGC 61.133 61.111 33.07 28.62 39.32 4.01
1789 1812 2.717044 TACGTACTGCGCCATGGCT 61.717 57.895 33.07 17.87 46.11 4.75
1819 1848 0.821711 AGCCAGCTAGCTCTCCTACG 60.822 60.000 16.15 1.10 39.48 3.51
1858 1887 0.106708 TTTGTCTTGAGGCAGCTCGT 59.893 50.000 0.00 0.00 0.00 4.18
1880 1909 8.108364 ACTTACATGTAGTACTGTCTACTCCTT 58.892 37.037 5.39 4.37 40.39 3.36
1884 1913 7.772757 GGGTACTTACATGTAGTACTGTCTACT 59.227 40.741 26.74 4.37 40.39 2.57
1885 1914 7.772757 AGGGTACTTACATGTAGTACTGTCTAC 59.227 40.741 26.74 17.30 38.61 2.59
1886 1915 7.865820 AGGGTACTTACATGTAGTACTGTCTA 58.134 38.462 26.74 6.71 38.61 2.59
1887 1916 6.729428 AGGGTACTTACATGTAGTACTGTCT 58.271 40.000 26.74 21.70 38.61 3.41
1888 1917 8.688747 ATAGGGTACTTACATGTAGTACTGTC 57.311 38.462 26.74 20.69 38.61 3.51
1889 1918 9.484806 AAATAGGGTACTTACATGTAGTACTGT 57.515 33.333 26.74 20.92 38.61 3.55
1900 1942 8.873144 ACACTCTACAAAAATAGGGTACTTACA 58.127 33.333 0.00 0.00 33.35 2.41
1901 1943 9.716531 AACACTCTACAAAAATAGGGTACTTAC 57.283 33.333 0.00 0.00 33.35 2.34
1903 1945 9.063615 CAAACACTCTACAAAAATAGGGTACTT 57.936 33.333 0.00 0.00 33.35 2.24
1904 1946 8.215736 ACAAACACTCTACAAAAATAGGGTACT 58.784 33.333 0.00 0.00 33.35 2.73
1905 1947 8.387190 ACAAACACTCTACAAAAATAGGGTAC 57.613 34.615 0.00 0.00 33.35 3.34
1906 1948 8.983702 AACAAACACTCTACAAAAATAGGGTA 57.016 30.769 0.00 0.00 33.35 3.69
1907 1949 7.891498 AACAAACACTCTACAAAAATAGGGT 57.109 32.000 0.00 0.00 36.23 4.34
1908 1950 8.194769 ACAAACAAACACTCTACAAAAATAGGG 58.805 33.333 0.00 0.00 0.00 3.53
1909 1951 9.019764 CACAAACAAACACTCTACAAAAATAGG 57.980 33.333 0.00 0.00 0.00 2.57
1910 1952 9.567848 ACACAAACAAACACTCTACAAAAATAG 57.432 29.630 0.00 0.00 0.00 1.73
1911 1953 9.347934 CACACAAACAAACACTCTACAAAAATA 57.652 29.630 0.00 0.00 0.00 1.40
1912 1954 7.870445 ACACACAAACAAACACTCTACAAAAAT 59.130 29.630 0.00 0.00 0.00 1.82
1913 1955 7.203910 ACACACAAACAAACACTCTACAAAAA 58.796 30.769 0.00 0.00 0.00 1.94
1914 1956 6.740110 ACACACAAACAAACACTCTACAAAA 58.260 32.000 0.00 0.00 0.00 2.44
1915 1957 6.205853 AGACACACAAACAAACACTCTACAAA 59.794 34.615 0.00 0.00 0.00 2.83
1916 1958 5.703592 AGACACACAAACAAACACTCTACAA 59.296 36.000 0.00 0.00 0.00 2.41
2002 2044 2.023307 AGTAGCCCCTGTGTGTACCTAT 60.023 50.000 0.00 0.00 0.00 2.57
2032 2074 0.680618 TAACCACCACCACTACCGTG 59.319 55.000 0.00 0.00 40.89 4.94
2069 2111 2.083774 CATGTGCAACGACCATACCTT 58.916 47.619 0.00 0.00 42.39 3.50
2080 2137 1.323412 TAACCACCACCATGTGCAAC 58.677 50.000 0.00 0.00 34.85 4.17
2083 2140 2.930455 GCAATTAACCACCACCATGTGC 60.930 50.000 0.00 0.00 34.85 4.57
2129 2186 6.650807 ACATTGAAACACGTATGAGAAGATGT 59.349 34.615 0.91 0.00 0.00 3.06
2145 2202 4.702131 AGTGGCAGAAGGATACATTGAAAC 59.298 41.667 0.00 0.00 41.41 2.78
2149 2209 3.379372 CCAAGTGGCAGAAGGATACATTG 59.621 47.826 0.00 0.00 41.41 2.82
2164 2224 1.259609 ATGAACATGGTGCCAAGTGG 58.740 50.000 0.00 0.00 38.53 4.00
2169 2229 1.268066 ATGCAATGAACATGGTGCCA 58.732 45.000 0.00 0.00 36.12 4.92
2213 2273 2.364632 CAAATCGGGCAACAGGACATA 58.635 47.619 0.00 0.00 39.74 2.29
2237 2297 5.880887 TGGTAGTATCTAGCATAGTGGATCG 59.119 44.000 4.84 0.00 40.38 3.69
2238 2298 7.113437 TCTGGTAGTATCTAGCATAGTGGATC 58.887 42.308 8.71 0.00 40.38 3.36
2245 2305 9.945904 CCGATATATCTGGTAGTATCTAGCATA 57.054 37.037 10.93 3.54 0.00 3.14
2255 2315 3.510360 GCCACACCGATATATCTGGTAGT 59.490 47.826 21.18 18.47 34.17 2.73
2291 2351 0.238289 CACGGGTGAAGACATGCAAC 59.762 55.000 0.00 0.00 0.00 4.17
2293 2353 1.965930 GCACGGGTGAAGACATGCA 60.966 57.895 2.38 0.00 33.27 3.96
2294 2354 2.870372 GCACGGGTGAAGACATGC 59.130 61.111 2.38 0.00 0.00 4.06
2295 2355 1.354337 CTCGCACGGGTGAAGACATG 61.354 60.000 1.02 0.00 32.14 3.21
2296 2356 1.079819 CTCGCACGGGTGAAGACAT 60.080 57.895 1.02 0.00 32.14 3.06
2298 2358 0.389948 AATCTCGCACGGGTGAAGAC 60.390 55.000 1.02 0.00 32.14 3.01
2300 2360 1.560923 CTAATCTCGCACGGGTGAAG 58.439 55.000 1.02 0.00 32.14 3.02
2303 2363 0.174845 TTCCTAATCTCGCACGGGTG 59.825 55.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.