Multiple sequence alignment - TraesCS6D01G318300

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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 TraesCS6D01G318300 chr6D 100.000 2144 0 0 1 2144 426884053 426886196 0.000000e+00 3960.0
1 TraesCS6D01G318300 chr6D 100.000 566 0 0 2505 3070 426886557 426887122 0.000000e+00 1046.0
2 TraesCS6D01G318300 chr6D 90.244 164 13 3 399 560 426884334 426884496 8.620000e-51 211.0
3 TraesCS6D01G318300 chr6D 90.244 164 13 3 282 444 426884451 426884612 8.620000e-51 211.0
4 TraesCS6D01G318300 chr6A 95.285 2121 66 11 2 2109 571639311 571641410 0.000000e+00 3332.0
5 TraesCS6D01G318300 chr6A 93.657 536 32 2 2535 3069 571641654 571642188 0.000000e+00 800.0
6 TraesCS6D01G318300 chr6A 93.210 162 10 1 399 560 571639579 571639739 1.420000e-58 237.0
7 TraesCS6D01G318300 chr6A 89.634 164 14 3 282 444 571639694 571639855 4.010000e-49 206.0
8 TraesCS6D01G318300 chr6A 92.913 127 9 0 1722 1848 571641075 571641201 5.230000e-43 185.0
9 TraesCS6D01G318300 chr6A 93.043 115 8 0 1721 1835 571641132 571641246 5.260000e-38 169.0
10 TraesCS6D01G318300 chr6A 96.154 52 2 0 1897 1948 571641027 571641078 5.450000e-13 86.1
11 TraesCS6D01G318300 chr6B 96.992 1064 28 2 785 1848 642347504 642348563 0.000000e+00 1784.0
12 TraesCS6D01G318300 chr6B 97.942 826 14 3 1 824 642346682 642347506 0.000000e+00 1428.0
13 TraesCS6D01G318300 chr6B 94.561 570 24 6 2505 3070 642349197 642349763 0.000000e+00 874.0
14 TraesCS6D01G318300 chr6B 93.050 259 7 6 1874 2130 642348544 642348793 4.840000e-98 368.0
15 TraesCS6D01G318300 chr6B 89.634 164 14 3 399 560 642346964 642347126 4.010000e-49 206.0
16 TraesCS6D01G318300 chr6B 89.634 164 14 3 282 444 642347081 642347242 4.010000e-49 206.0
17 TraesCS6D01G318300 chr6B 93.043 115 7 1 1721 1835 642348495 642348608 1.890000e-37 167.0
18 TraesCS6D01G318300 chr6B 91.304 69 1 2 1874 1942 642348487 642348550 4.220000e-14 89.8


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 TraesCS6D01G318300 chr6D 426884053 426887122 3069 False 1357.000000 3960 95.122000 1 3070 4 chr6D.!!$F1 3069
1 TraesCS6D01G318300 chr6A 571639311 571642188 2877 False 716.442857 3332 93.413714 2 3069 7 chr6A.!!$F1 3067
2 TraesCS6D01G318300 chr6B 642346682 642349763 3081 False 640.350000 1784 93.270000 1 3070 8 chr6B.!!$F1 3069

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
463 465 1.818674 CCCCAACAGCAAACATACTCC 59.181 52.381 0.00 0.0 0.0 3.85 F
1433 1472 1.875514 TCAAAGAGACACATGCTGCAC 59.124 47.619 3.57 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1934 0.871057 CACACACACACACACACACA 59.129 50.000 0.0 0.0 0.0 3.72 R
2983 3138 1.497278 CATCGCCAGAAACCACACG 59.503 57.895 0.0 0.0 0.0 4.49 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
463 465 1.818674 CCCCAACAGCAAACATACTCC 59.181 52.381 0.00 0.00 0.00 3.85
651 653 7.406031 TGGAATAATCCCTCGATAGATACAC 57.594 40.000 0.00 0.00 45.95 2.90
698 700 2.037121 GGGTTTTCAGTTTCCCACATGG 59.963 50.000 0.00 0.00 39.68 3.66
723 725 9.822185 GGTATTATCAAATGAAGCCTTCAAAAT 57.178 29.630 11.81 5.52 43.95 1.82
1103 1142 1.984066 CCCCTTTACCACGAAAACCA 58.016 50.000 0.00 0.00 0.00 3.67
1423 1462 2.560504 ACACACGCAATCAAAGAGACA 58.439 42.857 0.00 0.00 0.00 3.41
1433 1472 1.875514 TCAAAGAGACACATGCTGCAC 59.124 47.619 3.57 0.00 0.00 4.57
1588 1627 5.300752 GTGATGAAGGAAGAAGACTGTGAA 58.699 41.667 0.00 0.00 0.00 3.18
1751 1790 9.832445 TTTGTGTAATTAAGGTATTTGCCAAAA 57.168 25.926 0.00 0.00 0.00 2.44
1810 1907 8.184304 TGTGTAATTAAGGTATTTGCCAAAGT 57.816 30.769 0.00 0.00 0.00 2.66
1836 1933 6.527057 GTACTGGTACCTTATCAAGTCACT 57.473 41.667 14.36 0.00 0.00 3.41
1837 1934 6.932947 GTACTGGTACCTTATCAAGTCACTT 58.067 40.000 14.36 0.00 0.00 3.16
1838 1935 5.794894 ACTGGTACCTTATCAAGTCACTTG 58.205 41.667 11.69 11.69 42.25 3.16
1839 1936 5.307196 ACTGGTACCTTATCAAGTCACTTGT 59.693 40.000 17.27 7.54 41.66 3.16
1840 1937 5.547465 TGGTACCTTATCAAGTCACTTGTG 58.453 41.667 17.27 6.54 41.66 3.33
1841 1938 5.071250 TGGTACCTTATCAAGTCACTTGTGT 59.929 40.000 17.27 9.94 41.66 3.72
1842 1939 5.408604 GGTACCTTATCAAGTCACTTGTGTG 59.591 44.000 17.27 6.54 41.66 3.82
1843 1940 5.036117 ACCTTATCAAGTCACTTGTGTGT 57.964 39.130 17.27 6.33 44.14 3.72
1844 1941 4.816385 ACCTTATCAAGTCACTTGTGTGTG 59.184 41.667 17.27 7.37 44.14 3.82
1845 1942 4.816385 CCTTATCAAGTCACTTGTGTGTGT 59.184 41.667 17.27 1.44 44.14 3.72
1846 1943 5.277490 CCTTATCAAGTCACTTGTGTGTGTG 60.277 44.000 17.27 3.25 44.14 3.82
1847 1944 3.052455 TCAAGTCACTTGTGTGTGTGT 57.948 42.857 17.27 0.00 44.14 3.72
1848 1945 2.741517 TCAAGTCACTTGTGTGTGTGTG 59.258 45.455 17.27 0.00 44.14 3.82
1849 1946 2.472695 AGTCACTTGTGTGTGTGTGT 57.527 45.000 0.46 0.00 44.14 3.72
1850 1947 2.076100 AGTCACTTGTGTGTGTGTGTG 58.924 47.619 0.46 0.00 44.14 3.82
1851 1948 1.804151 GTCACTTGTGTGTGTGTGTGT 59.196 47.619 0.46 0.00 44.14 3.72
1852 1949 1.803555 TCACTTGTGTGTGTGTGTGTG 59.196 47.619 0.46 0.00 44.14 3.82
1853 1950 1.535028 CACTTGTGTGTGTGTGTGTGT 59.465 47.619 0.00 0.00 39.24 3.72
1854 1951 1.535028 ACTTGTGTGTGTGTGTGTGTG 59.465 47.619 0.00 0.00 0.00 3.82
1855 1952 1.535028 CTTGTGTGTGTGTGTGTGTGT 59.465 47.619 0.00 0.00 0.00 3.72
1856 1953 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1857 1954 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1858 1955 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1859 1956 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1860 1957 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1861 1958 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1862 1959 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
1863 1960 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
1864 1961 2.359214 TGTGTGTGTGTGTGTGTGTTTT 59.641 40.909 0.00 0.00 0.00 2.43
1865 1962 3.181486 TGTGTGTGTGTGTGTGTGTTTTT 60.181 39.130 0.00 0.00 0.00 1.94
1899 1996 9.515020 CAAGTCACTTGTGTTTGTGTAATTAAT 57.485 29.630 9.61 0.00 36.79 1.40
2013 2110 5.401550 TGCTATTATGCAAGCAACAAAGTC 58.598 37.500 8.33 0.00 45.36 3.01
2026 2123 5.127682 AGCAACAAAGTCACATCTTCCTTTT 59.872 36.000 0.00 0.00 0.00 2.27
2027 2124 5.812127 GCAACAAAGTCACATCTTCCTTTTT 59.188 36.000 0.00 0.00 0.00 1.94
2140 2262 6.819397 AAGTAAAGCTGGACAAATTACTCC 57.181 37.500 5.44 0.00 36.17 3.85
2141 2263 6.128138 AGTAAAGCTGGACAAATTACTCCT 57.872 37.500 0.00 0.00 32.84 3.69
2142 2264 6.543735 AGTAAAGCTGGACAAATTACTCCTT 58.456 36.000 0.00 0.00 32.84 3.36
2143 2265 7.004691 AGTAAAGCTGGACAAATTACTCCTTT 58.995 34.615 0.00 0.00 32.84 3.11
2540 2691 8.634335 TCAATCTCAGTATTTGTGGAAATTGA 57.366 30.769 0.00 0.00 33.63 2.57
2638 2789 5.215252 TCAGGAAGAAACTCGAATGAACT 57.785 39.130 0.00 0.00 0.00 3.01
2702 2853 7.027161 GCAAAATCACTCGTGGTACATAATTT 58.973 34.615 0.00 0.00 44.52 1.82
2703 2854 7.008266 GCAAAATCACTCGTGGTACATAATTTG 59.992 37.037 0.00 0.00 44.52 2.32
2774 2925 0.296056 CGCAACGAAGATTCTCTCGC 59.704 55.000 14.18 2.39 0.00 5.03
2785 2936 3.826754 CTCTCGCGCCTGCACCTA 61.827 66.667 0.00 0.00 42.97 3.08
2818 2969 4.394920 CGTGGCAAGTTAACCTATCATGTT 59.605 41.667 0.88 0.00 0.00 2.71
2825 2976 6.374417 AGTTAACCTATCATGTTGTGTCCT 57.626 37.500 0.88 0.00 0.00 3.85
2891 3043 0.606401 GCACTGCTCTGCCTTTACCA 60.606 55.000 0.00 0.00 0.00 3.25
2905 3057 6.862209 TGCCTTTACCATGTGATAATTTGAC 58.138 36.000 0.00 0.00 0.00 3.18
2946 3100 1.888512 GCTCTCCAAGCCATGAAACAA 59.111 47.619 0.00 0.00 45.92 2.83
2972 3126 4.016444 GCATCATTCAGTGGGTTTCCTTA 58.984 43.478 0.00 0.00 0.00 2.69
2981 3136 2.296190 GTGGGTTTCCTTACTTGCAAGG 59.704 50.000 29.18 13.59 45.59 3.61
2983 3138 1.272490 GGTTTCCTTACTTGCAAGGGC 59.728 52.381 29.18 9.09 44.53 5.19
3047 3202 5.290493 AGATAAATATTCCCTGCGTGTCA 57.710 39.130 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
463 465 6.214191 TCCTTTCTCTGCAAGTAGTATCTG 57.786 41.667 0.00 0.00 33.76 2.90
723 725 9.116067 CTGGACTCGGTGGAATTTATTTTTATA 57.884 33.333 0.00 0.00 0.00 0.98
1103 1142 2.431023 CGTAGCCTCTAGCCATGGT 58.569 57.895 14.67 2.69 45.47 3.55
1359 1398 4.262938 CCACAGCATCTATGTCATCCTCAT 60.263 45.833 0.00 0.00 0.00 2.90
1423 1462 1.338484 ACGATCTCTTGTGCAGCATGT 60.338 47.619 0.00 0.00 39.31 3.21
1433 1472 3.742882 TGTTCTGCTTTGACGATCTCTTG 59.257 43.478 0.00 0.00 0.00 3.02
1817 1914 5.071250 ACACAAGTGACTTGATAAGGTACCA 59.929 40.000 30.03 0.00 43.42 3.25
1834 1931 1.535028 CACACACACACACACACAAGT 59.465 47.619 0.00 0.00 0.00 3.16
1835 1932 1.535028 ACACACACACACACACACAAG 59.465 47.619 0.00 0.00 0.00 3.16
1836 1933 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
1837 1934 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1838 1935 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1839 1936 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1840 1937 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1841 1938 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1842 1939 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1843 1940 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
1844 1941 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
1845 1942 3.717400 AAAAACACACACACACACACA 57.283 38.095 0.00 0.00 0.00 3.72
1899 1996 4.156477 ACCAGCTTTGGCAAATACCTTAA 58.844 39.130 13.89 0.00 41.70 1.85
1900 1997 3.773560 ACCAGCTTTGGCAAATACCTTA 58.226 40.909 13.89 0.00 41.70 2.69
1901 1998 2.608623 ACCAGCTTTGGCAAATACCTT 58.391 42.857 13.89 0.00 41.70 3.50
1902 1999 2.309136 ACCAGCTTTGGCAAATACCT 57.691 45.000 13.89 7.53 41.70 3.08
1943 2040 3.564235 TTATTTCAGCTTGCTGCACAG 57.436 42.857 16.91 4.66 45.94 3.66
2026 2123 6.003234 TGCATCGAAAGTCGGAAATAAAAA 57.997 33.333 0.00 0.00 40.88 1.94
2027 2124 5.410132 TCTGCATCGAAAGTCGGAAATAAAA 59.590 36.000 0.00 0.00 40.88 1.52
2114 2236 9.609346 GGAGTAATTTGTCCAGCTTTACTTATA 57.391 33.333 6.26 0.00 34.24 0.98
2607 2758 7.510549 TCGAGTTTCTTCCTGAAATTTCATT 57.489 32.000 20.76 0.00 45.19 2.57
2785 2936 2.048033 TTGCCACGCGTTACCGAT 60.048 55.556 10.22 0.00 35.63 4.18
2798 2949 5.183140 ACACAACATGATAGGTTAACTTGCC 59.817 40.000 5.42 0.00 0.00 4.52
2818 2969 3.582647 ACTGTTACCATGATCAGGACACA 59.417 43.478 9.37 12.41 32.92 3.72
2825 2976 5.716703 TCTCTCTTGACTGTTACCATGATCA 59.283 40.000 0.00 0.00 0.00 2.92
2891 3043 6.772233 TCGGATTCCATGTCAAATTATCACAT 59.228 34.615 3.09 0.00 0.00 3.21
2905 3057 2.036475 CTCCAGGTACTCGGATTCCATG 59.964 54.545 3.09 0.00 34.60 3.66
2946 3100 2.519771 ACCCACTGAATGATGCACAT 57.480 45.000 0.00 0.00 41.45 3.21
2972 3126 2.906897 CCACACGCCCTTGCAAGT 60.907 61.111 24.35 4.39 37.32 3.16
2981 3136 4.025401 CGCCAGAAACCACACGCC 62.025 66.667 0.00 0.00 0.00 5.68
2983 3138 1.497278 CATCGCCAGAAACCACACG 59.503 57.895 0.00 0.00 0.00 4.49
3047 3202 2.301346 CTCTGTGGGCAAGAAGTTGTT 58.699 47.619 0.00 0.00 35.92 2.83


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

AutoCloner maintained by Alex Coulton.