Multiple sequence alignment - TraesCS6B01G087700

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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 TraesCS6B01G087700 chr6B 100.000 1722 0 0 1 1722 63258522 63260243 0.000000e+00 3181
1 TraesCS6B01G087700 chr6B 98.609 1725 20 3 1 1722 63227517 63229240 0.000000e+00 3049
2 TraesCS6B01G087700 chr6B 100.000 602 0 0 1873 2474 63260394 63260995 0.000000e+00 1112
3 TraesCS6B01G087700 chr6B 98.899 454 4 1 2021 2474 63229904 63230356 0.000000e+00 809
4 TraesCS6B01G087700 chr6B 83.429 175 15 10 1558 1721 338379277 338379106 1.530000e-32 150
5 TraesCS6B01G087700 chr6B 84.507 142 13 6 1558 1690 27130091 27129950 5.550000e-27 132
6 TraesCS6B01G087700 chr5D 94.604 1705 72 10 1 1690 365120439 365118740 0.000000e+00 2621
7 TraesCS6B01G087700 chr5D 94.304 1703 81 10 1 1690 12933483 12931784 0.000000e+00 2593
8 TraesCS6B01G087700 chr5D 93.655 1702 86 11 1 1690 454209261 454210952 0.000000e+00 2525
9 TraesCS6B01G087700 chr5D 89.375 160 8 2 1531 1681 454287292 454287451 2.510000e-45 193
10 TraesCS6B01G087700 chr5D 92.373 118 6 2 1874 1988 316894115 316894232 5.470000e-37 165
11 TraesCS6B01G087700 chr1D 94.539 1703 78 8 1 1690 471280900 471282600 0.000000e+00 2615
12 TraesCS6B01G087700 chr1D 94.542 1704 76 11 1 1690 495409691 495407991 0.000000e+00 2615
13 TraesCS6B01G087700 chr1D 94.259 1707 79 9 1 1690 28017872 28019576 0.000000e+00 2591
14 TraesCS6B01G087700 chr1D 88.889 108 12 0 1583 1690 555058 554951 1.540000e-27 134
15 TraesCS6B01G087700 chr3D 94.366 1704 80 8 1 1690 7112519 7114220 0.000000e+00 2601
16 TraesCS6B01G087700 chr3D 94.366 1704 78 10 1 1690 411639466 411637767 0.000000e+00 2599
17 TraesCS6B01G087700 chr3D 92.857 714 40 4 988 1690 581558258 581558971 0.000000e+00 1026
18 TraesCS6B01G087700 chr3D 96.262 107 2 1 1874 1978 578864943 578865049 9.090000e-40 174
19 TraesCS6B01G087700 chr3D 93.277 119 4 3 1874 1989 8302853 8302736 3.270000e-39 172
20 TraesCS6B01G087700 chr2D 94.363 1703 80 9 1 1690 588796858 588795159 0.000000e+00 2599
21 TraesCS6B01G087700 chr1B 93.416 1701 98 8 2 1690 334452532 334450834 0.000000e+00 2508
22 TraesCS6B01G087700 chr1B 96.512 430 14 1 2044 2473 358031231 358031659 0.000000e+00 710
23 TraesCS6B01G087700 chr7D 93.486 1704 76 16 1 1690 548271611 548269929 0.000000e+00 2499
24 TraesCS6B01G087700 chr7D 96.056 431 14 3 2046 2474 114467277 114467706 0.000000e+00 699
25 TraesCS6B01G087700 chr7D 93.103 116 6 1 1874 1987 460638031 460637916 4.230000e-38 169
26 TraesCS6B01G087700 chr7B 93.648 1653 92 6 49 1689 654329221 654330872 0.000000e+00 2459
27 TraesCS6B01G087700 chr7B 96.056 431 16 1 2044 2474 94806119 94806548 0.000000e+00 701
28 TraesCS6B01G087700 chr7B 95.434 438 17 3 2039 2474 154683852 154684288 0.000000e+00 695
29 TraesCS6B01G087700 chr1A 92.547 1704 110 10 1 1690 235651679 235649979 0.000000e+00 2427
30 TraesCS6B01G087700 chr1A 92.506 1708 103 15 1 1690 548953956 548955656 0.000000e+00 2422
31 TraesCS6B01G087700 chr1A 91.525 236 11 3 1458 1690 534402816 534403045 1.430000e-82 316
32 TraesCS6B01G087700 chr2A 92.543 1703 109 9 1 1690 34831007 34832704 0.000000e+00 2425
33 TraesCS6B01G087700 chr2B 87.646 769 37 15 932 1690 56050106 56049386 0.000000e+00 841
34 TraesCS6B01G087700 chr2B 96.296 432 15 1 2043 2474 262903539 262903109 0.000000e+00 708
35 TraesCS6B01G087700 chr5A 96.056 431 16 1 2044 2474 504754267 504754696 0.000000e+00 701
36 TraesCS6B01G087700 chr5A 93.004 243 7 3 1458 1690 184706374 184706132 1.820000e-91 346
37 TraesCS6B01G087700 chr5A 97.170 106 2 1 1874 1978 348174201 348174096 7.030000e-41 178
38 TraesCS6B01G087700 chr4A 95.423 437 18 1 2038 2474 137545885 137546319 0.000000e+00 695
39 TraesCS6B01G087700 chr4B 95.602 432 18 1 2043 2474 409747864 409748294 0.000000e+00 691
40 TraesCS6B01G087700 chr4B 83.099 142 15 6 1558 1690 1744396 1744255 1.200000e-23 121
41 TraesCS6B01G087700 chr7A 94.783 115 3 1 1874 1985 125982199 125982085 2.530000e-40 176
42 TraesCS6B01G087700 chr7A 95.238 105 5 0 1874 1978 136412951 136413055 1.520000e-37 167
43 TraesCS6B01G087700 chr7A 87.324 142 13 4 1874 2011 23699077 23699217 9.160000e-35 158
44 TraesCS6B01G087700 chr6D 94.017 117 6 1 1874 1989 413390953 413391069 2.530000e-40 176


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 TraesCS6B01G087700 chr6B 63258522 63260995 2473 False 2146.5 3181 100.000 1 2474 2 chr6B.!!$F2 2473
1 TraesCS6B01G087700 chr6B 63227517 63230356 2839 False 1929.0 3049 98.754 1 2474 2 chr6B.!!$F1 2473
2 TraesCS6B01G087700 chr5D 365118740 365120439 1699 True 2621.0 2621 94.604 1 1690 1 chr5D.!!$R2 1689
3 TraesCS6B01G087700 chr5D 12931784 12933483 1699 True 2593.0 2593 94.304 1 1690 1 chr5D.!!$R1 1689
4 TraesCS6B01G087700 chr5D 454209261 454210952 1691 False 2525.0 2525 93.655 1 1690 1 chr5D.!!$F2 1689
5 TraesCS6B01G087700 chr1D 471280900 471282600 1700 False 2615.0 2615 94.539 1 1690 1 chr1D.!!$F2 1689
6 TraesCS6B01G087700 chr1D 495407991 495409691 1700 True 2615.0 2615 94.542 1 1690 1 chr1D.!!$R2 1689
7 TraesCS6B01G087700 chr1D 28017872 28019576 1704 False 2591.0 2591 94.259 1 1690 1 chr1D.!!$F1 1689
8 TraesCS6B01G087700 chr3D 7112519 7114220 1701 False 2601.0 2601 94.366 1 1690 1 chr3D.!!$F1 1689
9 TraesCS6B01G087700 chr3D 411637767 411639466 1699 True 2599.0 2599 94.366 1 1690 1 chr3D.!!$R2 1689
10 TraesCS6B01G087700 chr3D 581558258 581558971 713 False 1026.0 1026 92.857 988 1690 1 chr3D.!!$F3 702
11 TraesCS6B01G087700 chr2D 588795159 588796858 1699 True 2599.0 2599 94.363 1 1690 1 chr2D.!!$R1 1689
12 TraesCS6B01G087700 chr1B 334450834 334452532 1698 True 2508.0 2508 93.416 2 1690 1 chr1B.!!$R1 1688
13 TraesCS6B01G087700 chr7D 548269929 548271611 1682 True 2499.0 2499 93.486 1 1690 1 chr7D.!!$R2 1689
14 TraesCS6B01G087700 chr7B 654329221 654330872 1651 False 2459.0 2459 93.648 49 1689 1 chr7B.!!$F3 1640
15 TraesCS6B01G087700 chr1A 235649979 235651679 1700 True 2427.0 2427 92.547 1 1690 1 chr1A.!!$R1 1689
16 TraesCS6B01G087700 chr1A 548953956 548955656 1700 False 2422.0 2422 92.506 1 1690 1 chr1A.!!$F2 1689
17 TraesCS6B01G087700 chr2A 34831007 34832704 1697 False 2425.0 2425 92.543 1 1690 1 chr2A.!!$F1 1689
18 TraesCS6B01G087700 chr2B 56049386 56050106 720 True 841.0 841 87.646 932 1690 1 chr2B.!!$R1 758

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
409 411 2.12531 ATTGCCGTTCGATCCGCA 60.125 55.556 5.55 5.55 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2047 0.389948 AGTTGGTGAATCGTCTCCGC 60.39 55.0 0.0 0.0 39.83 5.54 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
409 411 2.125310 ATTGCCGTTCGATCCGCA 60.125 55.556 5.55 5.55 0.00 5.69
785 807 4.476410 CGCGCCACACTCTCGCTA 62.476 66.667 0.00 0.00 45.87 4.26
1456 1488 2.681344 GGAAGGAAAGTTGTGACGTGTT 59.319 45.455 0.00 0.00 0.00 3.32
1495 1527 9.423061 CCTAAGACAAATTGAACCAATAAAAGG 57.577 33.333 0.00 0.00 32.43 3.11
1901 2005 3.155167 GCGGACTAGGGTGGGAGG 61.155 72.222 0.00 0.00 0.00 4.30
1923 2027 0.898789 GTGGTGGGAGGAGAGACGAA 60.899 60.000 0.00 0.00 0.00 3.85
1924 2028 0.178944 TGGTGGGAGGAGAGACGAAA 60.179 55.000 0.00 0.00 0.00 3.46
1925 2029 0.974383 GGTGGGAGGAGAGACGAAAA 59.026 55.000 0.00 0.00 0.00 2.29
1926 2030 1.346722 GGTGGGAGGAGAGACGAAAAA 59.653 52.381 0.00 0.00 0.00 1.94
1948 2052 3.214066 GCGAAAATAAACCGCGGAG 57.786 52.632 35.90 6.46 39.54 4.63
1949 2053 0.722848 GCGAAAATAAACCGCGGAGA 59.277 50.000 35.90 16.89 39.54 3.71
1950 2054 1.528400 GCGAAAATAAACCGCGGAGAC 60.528 52.381 35.90 12.29 39.54 3.36
1964 2068 1.630148 GGAGACGATTCACCAACTCG 58.370 55.000 0.00 0.00 38.34 4.18
1967 2071 3.509388 ACGATTCACCAACTCGTCC 57.491 52.632 0.00 0.00 41.42 4.79
1968 2072 0.677288 ACGATTCACCAACTCGTCCA 59.323 50.000 0.00 0.00 41.42 4.02
1969 2073 1.275291 ACGATTCACCAACTCGTCCAT 59.725 47.619 0.00 0.00 41.42 3.41
1970 2074 2.289444 ACGATTCACCAACTCGTCCATT 60.289 45.455 0.00 0.00 41.42 3.16
1971 2075 3.056393 ACGATTCACCAACTCGTCCATTA 60.056 43.478 0.00 0.00 41.42 1.90
1972 2076 3.551890 CGATTCACCAACTCGTCCATTAG 59.448 47.826 0.00 0.00 0.00 1.73
1973 2077 3.328382 TTCACCAACTCGTCCATTAGG 57.672 47.619 0.00 0.00 0.00 2.69
1974 2078 2.531771 TCACCAACTCGTCCATTAGGA 58.468 47.619 0.00 0.00 43.21 2.94
1975 2079 2.496070 TCACCAACTCGTCCATTAGGAG 59.504 50.000 0.00 0.00 46.92 3.69
2106 2628 2.047274 CACGCCTCCATCACCGTT 60.047 61.111 0.00 0.00 0.00 4.44
2381 2903 1.979855 TGCAGTGTACATGGCAACTT 58.020 45.000 18.49 0.00 32.54 2.66
2396 2918 3.412386 GCAACTTCCCTAGTGTGATTGT 58.588 45.455 0.00 0.00 37.12 2.71
2400 2922 5.422214 ACTTCCCTAGTGTGATTGTAAGG 57.578 43.478 0.00 0.00 35.19 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1872 1914 3.264104 CCTAGTCCGCGGTTTATTTTCA 58.736 45.455 27.15 0.00 0.00 2.69
1873 1915 2.610833 CCCTAGTCCGCGGTTTATTTTC 59.389 50.000 27.15 6.63 0.00 2.29
1901 2005 2.689034 CTCTCCTCCCACCACCCC 60.689 72.222 0.00 0.00 0.00 4.95
1923 2027 4.559643 CCGCGGTTTATTTTCGCTATTTTT 59.440 37.500 19.50 0.00 46.23 1.94
1924 2028 4.099824 CCGCGGTTTATTTTCGCTATTTT 58.900 39.130 19.50 0.00 46.23 1.82
1925 2029 3.374678 TCCGCGGTTTATTTTCGCTATTT 59.625 39.130 27.15 0.00 46.23 1.40
1926 2030 2.937799 TCCGCGGTTTATTTTCGCTATT 59.062 40.909 27.15 0.00 46.23 1.73
1927 2031 2.542595 CTCCGCGGTTTATTTTCGCTAT 59.457 45.455 27.15 0.00 46.23 2.97
1928 2032 1.928503 CTCCGCGGTTTATTTTCGCTA 59.071 47.619 27.15 0.00 46.23 4.26
1929 2033 0.725117 CTCCGCGGTTTATTTTCGCT 59.275 50.000 27.15 0.00 46.23 4.93
1930 2034 0.722848 TCTCCGCGGTTTATTTTCGC 59.277 50.000 27.15 0.00 45.15 4.70
1931 2035 1.266696 CGTCTCCGCGGTTTATTTTCG 60.267 52.381 27.15 14.89 0.00 3.46
1932 2036 1.994779 TCGTCTCCGCGGTTTATTTTC 59.005 47.619 27.15 7.31 0.00 2.29
1933 2037 2.083167 TCGTCTCCGCGGTTTATTTT 57.917 45.000 27.15 0.00 0.00 1.82
1934 2038 2.304751 ATCGTCTCCGCGGTTTATTT 57.695 45.000 27.15 4.71 0.00 1.40
1935 2039 2.199236 GAATCGTCTCCGCGGTTTATT 58.801 47.619 27.15 17.67 35.12 1.40
1936 2040 1.135527 TGAATCGTCTCCGCGGTTTAT 59.864 47.619 27.15 10.05 35.12 1.40
1937 2041 0.527113 TGAATCGTCTCCGCGGTTTA 59.473 50.000 27.15 9.02 35.12 2.01
1938 2042 1.012486 GTGAATCGTCTCCGCGGTTT 61.012 55.000 27.15 10.21 35.12 3.27
1939 2043 1.445582 GTGAATCGTCTCCGCGGTT 60.446 57.895 27.15 11.07 37.96 4.44
1940 2044 2.181021 GTGAATCGTCTCCGCGGT 59.819 61.111 27.15 2.66 0.00 5.68
1941 2045 2.582498 GGTGAATCGTCTCCGCGG 60.582 66.667 22.12 22.12 0.00 6.46
1942 2046 1.445410 TTGGTGAATCGTCTCCGCG 60.445 57.895 0.00 0.00 39.83 6.46
1943 2047 0.389948 AGTTGGTGAATCGTCTCCGC 60.390 55.000 0.00 0.00 39.83 5.54
1944 2048 1.630148 GAGTTGGTGAATCGTCTCCG 58.370 55.000 0.00 0.00 39.83 4.63
1945 2049 1.067776 ACGAGTTGGTGAATCGTCTCC 60.068 52.381 0.00 0.00 45.92 3.71
1946 2050 2.349297 ACGAGTTGGTGAATCGTCTC 57.651 50.000 0.00 0.00 45.92 3.36
1950 2054 2.010145 ATGGACGAGTTGGTGAATCG 57.990 50.000 0.00 0.00 42.04 3.34
1951 2055 3.871594 CCTAATGGACGAGTTGGTGAATC 59.128 47.826 0.00 0.00 34.57 2.52
1952 2056 3.517901 TCCTAATGGACGAGTTGGTGAAT 59.482 43.478 0.00 0.00 37.46 2.57
1953 2057 2.901192 TCCTAATGGACGAGTTGGTGAA 59.099 45.455 0.00 0.00 37.46 3.18
1954 2058 2.496070 CTCCTAATGGACGAGTTGGTGA 59.504 50.000 0.00 0.00 37.46 4.02
1955 2059 2.233922 ACTCCTAATGGACGAGTTGGTG 59.766 50.000 0.00 0.00 37.46 4.17
1956 2060 2.537143 ACTCCTAATGGACGAGTTGGT 58.463 47.619 0.00 0.00 37.46 3.67
1957 2061 4.939052 ATACTCCTAATGGACGAGTTGG 57.061 45.455 0.00 0.00 37.93 3.77
2106 2628 4.521130 AGATTCGTGCAGAAGTTACTGA 57.479 40.909 0.00 0.00 42.92 3.41
2381 2903 4.942944 TCTCCTTACAATCACACTAGGGA 58.057 43.478 0.00 0.00 0.00 4.20
2396 2918 5.505181 AAAAGAGAGTTGCCATCTCCTTA 57.495 39.130 0.00 0.00 43.53 2.69
2422 2944 1.609580 GCAACTGACATGTCCGGGTAA 60.610 52.381 22.85 2.22 0.00 2.85


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

AutoCloner maintained by Alex Coulton.