Multiple sequence alignment - TraesCS6A01G131200

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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 TraesCS6A01G131200 chr6A 100.000 2609 0 0 1 2609 103759950 103757342 0.000000e+00 4819.0
1 TraesCS6A01G131200 chr6D 93.162 2457 87 32 49 2470 86143854 86141444 0.000000e+00 3531.0
2 TraesCS6A01G131200 chr6D 93.578 109 6 1 2501 2609 86141364 86141257 7.470000e-36 161.0
3 TraesCS6A01G131200 chr6B 91.747 2072 85 32 417 2470 163230635 163228632 0.000000e+00 2800.0
4 TraesCS6A01G131200 chr6B 93.088 434 18 4 1 425 163231090 163230660 2.200000e-175 625.0
5 TraesCS6A01G131200 chr6B 94.495 109 4 2 2501 2609 163228522 163228416 1.610000e-37 167.0
6 TraesCS6A01G131200 chr5A 89.076 357 26 7 50 395 323084410 323084764 5.160000e-117 431.0
7 TraesCS6A01G131200 chr4A 88.385 353 28 5 46 387 113486402 113486752 1.870000e-111 412.0
8 TraesCS6A01G131200 chr7D 81.081 407 53 20 1045 1442 547681359 547680968 1.170000e-78 303.0
9 TraesCS6A01G131200 chr7A 80.988 405 54 17 1045 1442 630869772 630870160 1.520000e-77 300.0
10 TraesCS6A01G131200 chr7B 80.494 405 53 19 1045 1442 590842650 590842265 1.180000e-73 287.0
11 TraesCS6A01G131200 chr2D 83.696 92 11 3 1525 1616 606198801 606198714 1.660000e-12 84.2
12 TraesCS6A01G131200 chr1B 81.522 92 13 2 1525 1616 641140312 641140399 3.600000e-09 73.1


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 TraesCS6A01G131200 chr6A 103757342 103759950 2608 True 4819.000000 4819 100.00 1 2609 1 chr6A.!!$R1 2608
1 TraesCS6A01G131200 chr6D 86141257 86143854 2597 True 1846.000000 3531 93.37 49 2609 2 chr6D.!!$R1 2560
2 TraesCS6A01G131200 chr6B 163228416 163231090 2674 True 1197.333333 2800 93.11 1 2609 3 chr6B.!!$R1 2608

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
763 816 0.026285 GACGCGGTCGATTGGAATTG 59.974 55.0 12.47 0.0 39.41 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2557 0.462047 GCCCACCTATGTTCGACAGG 60.462 60.0 0.0 0.0 35.45 4.0 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
28 29 1.307097 GCAAGCATGAGAGACCCATC 58.693 55.000 0.00 0.00 0.00 3.51
59 60 0.108662 GTTATGCCTGCCCTTTGTGC 60.109 55.000 0.00 0.00 0.00 4.57
68 69 1.006220 CCCTTTGTGCGGGAAAAGC 60.006 57.895 0.00 0.00 44.90 3.51
87 88 4.379374 AGCGATAAACGTGTAACACAAC 57.621 40.909 0.00 0.00 44.60 3.32
97 98 3.061403 CGTGTAACACAACGTTCAGAGAC 60.061 47.826 0.00 0.00 39.14 3.36
149 150 0.387929 TACTGCCGTAGCCTATGCAC 59.612 55.000 0.00 0.00 41.13 4.57
200 201 4.951715 TGGTGGGAGAATTCAAGATGAATG 59.048 41.667 8.44 0.00 45.57 2.67
416 426 2.207590 GCTTAAAATCCCGTCCCGTAG 58.792 52.381 0.00 0.00 0.00 3.51
580 624 0.392998 CCGTCCATCACAGAAAGGGG 60.393 60.000 0.00 0.00 0.00 4.79
581 625 1.026718 CGTCCATCACAGAAAGGGGC 61.027 60.000 0.00 0.00 0.00 5.80
603 650 2.649531 AAAAATCCGTCCACCAGACA 57.350 45.000 0.00 0.00 46.69 3.41
604 651 2.185004 AAAATCCGTCCACCAGACAG 57.815 50.000 0.00 0.00 46.69 3.51
605 652 1.348064 AAATCCGTCCACCAGACAGA 58.652 50.000 0.00 0.00 46.69 3.41
762 815 1.087771 GGACGCGGTCGATTGGAATT 61.088 55.000 12.47 0.00 39.41 2.17
763 816 0.026285 GACGCGGTCGATTGGAATTG 59.974 55.000 12.47 0.00 39.41 2.32
764 817 1.351707 CGCGGTCGATTGGAATTGG 59.648 57.895 0.00 0.00 38.10 3.16
765 818 1.087202 CGCGGTCGATTGGAATTGGA 61.087 55.000 0.00 0.00 38.10 3.53
766 819 1.091537 GCGGTCGATTGGAATTGGAA 58.908 50.000 0.00 0.00 0.00 3.53
767 820 1.676006 GCGGTCGATTGGAATTGGAAT 59.324 47.619 0.00 0.00 0.00 3.01
898 952 3.379445 GTGGAGTCGCCGAGGGAA 61.379 66.667 0.00 0.00 40.66 3.97
899 953 3.068691 TGGAGTCGCCGAGGGAAG 61.069 66.667 0.00 0.00 40.66 3.46
900 954 3.839432 GGAGTCGCCGAGGGAAGG 61.839 72.222 0.00 0.00 0.00 3.46
956 1010 4.838486 CGAGGCGAGCGAGACCAC 62.838 72.222 0.00 0.00 0.00 4.16
957 1011 3.749064 GAGGCGAGCGAGACCACA 61.749 66.667 0.00 0.00 0.00 4.17
958 1012 3.973267 GAGGCGAGCGAGACCACAC 62.973 68.421 0.00 0.00 0.00 3.82
1867 1931 8.248945 AGACTGATAATTTTTGCCATCTTTCTG 58.751 33.333 0.00 0.00 0.00 3.02
1869 1933 8.031277 ACTGATAATTTTTGCCATCTTTCTGTC 58.969 33.333 0.00 0.00 0.00 3.51
1893 1957 5.907866 TCTTACTTGTGTATCATCCACGA 57.092 39.130 0.00 0.00 35.56 4.35
1902 1975 0.745845 ATCATCCACGAGTTGCTGCC 60.746 55.000 0.00 0.00 0.00 4.85
1903 1976 1.376424 CATCCACGAGTTGCTGCCT 60.376 57.895 0.00 0.00 0.00 4.75
1911 1985 1.741732 CGAGTTGCTGCCTCTGCTATT 60.742 52.381 0.00 0.00 38.71 1.73
1915 1989 0.813184 TGCTGCCTCTGCTATTTTGC 59.187 50.000 0.00 0.00 38.71 3.68
1924 1998 7.099764 TGCCTCTGCTATTTTGCTATAGTATC 58.900 38.462 0.84 0.00 38.71 2.24
1939 2016 9.967346 TGCTATAGTATCGATTAATTAGATGCC 57.033 33.333 1.71 7.46 0.00 4.40
1956 2033 5.206587 AGATGCCTAATGGAAGAAAGCAAT 58.793 37.500 0.00 0.00 34.57 3.56
2000 2078 2.627699 TGAACTGGGTCATTTGCTTTCC 59.372 45.455 0.00 0.00 0.00 3.13
2017 2095 0.036732 TCCGAGATTGTTGGCTGCTT 59.963 50.000 0.00 0.00 0.00 3.91
2018 2096 0.169672 CCGAGATTGTTGGCTGCTTG 59.830 55.000 0.00 0.00 0.00 4.01
2023 2101 1.470098 GATTGTTGGCTGCTTGACGAT 59.530 47.619 0.00 1.60 0.00 3.73
2024 2102 0.874390 TTGTTGGCTGCTTGACGATC 59.126 50.000 0.00 0.00 0.00 3.69
2030 2109 0.869454 GCTGCTTGACGATCGAGAGG 60.869 60.000 24.34 8.92 29.08 3.69
2034 2113 2.490509 TGCTTGACGATCGAGAGGTTTA 59.509 45.455 24.34 0.00 29.08 2.01
2037 2116 2.089201 TGACGATCGAGAGGTTTAGCA 58.911 47.619 24.34 1.09 0.00 3.49
2051 2130 4.131596 GGTTTAGCACCTGAAACAGTGTA 58.868 43.478 0.00 0.00 43.29 2.90
2057 2136 5.072741 AGCACCTGAAACAGTGTATGATTT 58.927 37.500 0.00 0.00 0.00 2.17
2073 2157 7.907045 GTGTATGATTTTGCTGTTCTGTATCTG 59.093 37.037 0.00 0.00 0.00 2.90
2132 2216 0.174845 CCTTCCTGCCGACACGATAA 59.825 55.000 0.00 0.00 0.00 1.75
2165 2249 3.318839 TGCACCACAAGATTTTCAAGGAG 59.681 43.478 0.00 0.00 0.00 3.69
2177 2261 8.517062 AGATTTTCAAGGAGTTTGGATCATAG 57.483 34.615 0.00 0.00 37.39 2.23
2182 2266 2.965831 AGGAGTTTGGATCATAGCGCTA 59.034 45.455 21.30 21.30 0.00 4.26
2191 2275 2.713895 TCATAGCGCTACTCTGATGC 57.286 50.000 21.49 0.00 0.00 3.91
2240 2324 5.701290 ACACTAGAAGAAGAACCCAAAATCG 59.299 40.000 0.00 0.00 0.00 3.34
2321 2405 1.844497 TCCTGTCTCTCGAGGTCCATA 59.156 52.381 13.56 0.00 0.00 2.74
2322 2406 2.443632 TCCTGTCTCTCGAGGTCCATAT 59.556 50.000 13.56 0.00 0.00 1.78
2399 2483 2.726821 TCTTTGGGCAAGGATTAGCAG 58.273 47.619 0.00 0.00 32.64 4.24
2411 2495 3.071312 AGGATTAGCAGAAGAGCAGGATG 59.929 47.826 0.00 0.00 40.87 3.51
2428 2512 0.179032 ATGTCGTCAAAGTGGTGCCA 60.179 50.000 0.00 0.00 0.00 4.92
2445 2529 1.369625 CCACACGGTAGAAATGGCTC 58.630 55.000 0.00 0.00 0.00 4.70
2470 2554 6.714278 TGATGATCTTCATTTCTGAGTTCCA 58.286 36.000 7.19 0.00 37.20 3.53
2472 2556 6.955364 ATGATCTTCATTTCTGAGTTCCAGA 58.045 36.000 0.00 0.00 40.84 3.86
2473 2557 6.822676 ATGATCTTCATTTCTGAGTTCCAGAC 59.177 38.462 0.00 0.00 39.35 3.51
2479 2563 1.248486 TCTGAGTTCCAGACCTGTCG 58.752 55.000 0.00 0.00 46.38 4.35
2480 2564 1.202891 TCTGAGTTCCAGACCTGTCGA 60.203 52.381 0.00 0.00 46.38 4.20
2481 2565 1.613925 CTGAGTTCCAGACCTGTCGAA 59.386 52.381 0.00 0.00 45.78 3.71
2483 2567 1.340248 GAGTTCCAGACCTGTCGAACA 59.660 52.381 15.62 0.00 35.57 3.18
2485 2569 3.162666 AGTTCCAGACCTGTCGAACATA 58.837 45.455 15.62 0.00 35.57 2.29
2486 2570 3.193691 AGTTCCAGACCTGTCGAACATAG 59.806 47.826 15.62 0.00 35.57 2.23
2487 2571 2.100197 TCCAGACCTGTCGAACATAGG 58.900 52.381 0.00 0.00 39.38 2.57
2489 2573 2.417379 CCAGACCTGTCGAACATAGGTG 60.417 54.545 14.37 4.18 46.45 4.00
2490 2574 1.825474 AGACCTGTCGAACATAGGTGG 59.175 52.381 14.37 3.62 46.45 4.61
2491 2575 0.902531 ACCTGTCGAACATAGGTGGG 59.097 55.000 10.14 0.94 44.81 4.61
2492 2576 0.462047 CCTGTCGAACATAGGTGGGC 60.462 60.000 0.00 0.00 0.00 5.36
2493 2577 0.806102 CTGTCGAACATAGGTGGGCG 60.806 60.000 0.00 0.00 0.00 6.13
2494 2578 2.171725 GTCGAACATAGGTGGGCGC 61.172 63.158 0.00 0.00 0.00 6.53
2495 2579 2.895372 CGAACATAGGTGGGCGCC 60.895 66.667 21.18 21.18 0.00 6.53
2497 2581 4.483243 AACATAGGTGGGCGCCCG 62.483 66.667 39.00 26.03 39.42 6.13
2518 2680 5.151389 CCGGTTTGGAGAGAAAAATTAACG 58.849 41.667 0.00 0.00 42.00 3.18
2525 2687 4.506217 GAGAGAAAAATTAACGGCGATCG 58.494 43.478 16.62 11.69 45.88 3.69
2597 2759 3.986277 ACAACTACAACGTCCCTACTTG 58.014 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.126488 ACATGCGATGGGTCTCTCAT 58.874 50.000 0.00 0.00 33.60 2.90
28 29 0.526096 GGCATAACCTTGCACATGCG 60.526 55.000 0.00 0.00 43.72 4.73
53 54 1.524848 TATCGCTTTTCCCGCACAAA 58.475 45.000 0.00 0.00 0.00 2.83
59 60 1.461897 ACACGTTTATCGCTTTTCCCG 59.538 47.619 0.00 0.00 44.19 5.14
68 69 4.359041 ACGTTGTGTTACACGTTTATCG 57.641 40.909 11.07 10.50 46.00 2.92
87 88 3.000080 GCCAACGCGTCTCTGAACG 62.000 63.158 14.44 0.00 45.31 3.95
97 98 0.310854 AAAAGGAAAGAGCCAACGCG 59.689 50.000 3.53 3.53 41.18 6.01
149 150 4.994852 TCTATTCCGAACAGTTGTCAAAGG 59.005 41.667 0.00 0.00 0.00 3.11
200 201 3.705072 ACACAAGTCCTACTATAGTGCCC 59.295 47.826 15.90 1.11 32.43 5.36
334 344 1.378514 CATGGTAAGCAGGCGGGTT 60.379 57.895 7.33 7.33 40.94 4.11
345 355 1.790755 GACACAGCGACACATGGTAA 58.209 50.000 0.00 0.00 0.00 2.85
373 383 2.205074 ACGATTCGTGGATGAGATTGC 58.795 47.619 11.56 0.00 39.18 3.56
848 902 0.171455 TTTGTGTGTTTGGTCGGCAC 59.829 50.000 0.00 0.00 0.00 5.01
849 903 0.171455 GTTTGTGTGTTTGGTCGGCA 59.829 50.000 0.00 0.00 0.00 5.69
850 904 0.171455 TGTTTGTGTGTTTGGTCGGC 59.829 50.000 0.00 0.00 0.00 5.54
851 905 2.525055 CTTGTTTGTGTGTTTGGTCGG 58.475 47.619 0.00 0.00 0.00 4.79
852 906 2.525055 CCTTGTTTGTGTGTTTGGTCG 58.475 47.619 0.00 0.00 0.00 4.79
853 907 2.267426 GCCTTGTTTGTGTGTTTGGTC 58.733 47.619 0.00 0.00 0.00 4.02
854 908 1.403514 CGCCTTGTTTGTGTGTTTGGT 60.404 47.619 0.00 0.00 0.00 3.67
1113 1167 0.462759 GCCAGATCGGGGTCTTCTTG 60.463 60.000 14.13 0.00 34.06 3.02
1308 1362 2.745100 ATCGTGCTGCTGTGGCTG 60.745 61.111 0.00 0.00 39.59 4.85
1399 1462 3.532155 GCGGCAGTCCTCCTCGAT 61.532 66.667 0.00 0.00 0.00 3.59
1623 1686 2.815211 TGACGCATCCGAAGCAGC 60.815 61.111 0.00 0.00 38.29 5.25
1624 1687 2.456119 GGTGACGCATCCGAAGCAG 61.456 63.158 0.00 0.00 38.29 4.24
1625 1688 2.434185 GGTGACGCATCCGAAGCA 60.434 61.111 0.00 0.00 38.29 3.91
1867 1931 6.253727 CGTGGATGATACACAAGTAAGAAGAC 59.746 42.308 8.74 0.00 38.74 3.01
1869 1933 6.330278 TCGTGGATGATACACAAGTAAGAAG 58.670 40.000 8.74 0.00 38.74 2.85
1893 1957 2.490903 CAAAATAGCAGAGGCAGCAACT 59.509 45.455 0.00 0.00 44.61 3.16
1895 1959 1.203052 GCAAAATAGCAGAGGCAGCAA 59.797 47.619 0.00 0.00 44.61 3.91
1902 1975 9.579768 AATCGATACTATAGCAAAATAGCAGAG 57.420 33.333 0.00 0.00 33.49 3.35
1924 1998 8.777865 TCTTCCATTAGGCATCTAATTAATCG 57.222 34.615 0.00 0.00 42.51 3.34
1956 2033 8.684386 TCACACAAGTTCATGTAAATTTCCTA 57.316 30.769 0.00 0.00 30.84 2.94
2000 2078 1.135859 GTCAAGCAGCCAACAATCTCG 60.136 52.381 0.00 0.00 0.00 4.04
2017 2095 2.089201 TGCTAAACCTCTCGATCGTCA 58.911 47.619 15.94 1.65 0.00 4.35
2018 2096 2.452105 GTGCTAAACCTCTCGATCGTC 58.548 52.381 15.94 0.00 0.00 4.20
2030 2109 5.468746 TCATACACTGTTTCAGGTGCTAAAC 59.531 40.000 1.90 0.00 35.51 2.01
2034 2113 3.769739 TCATACACTGTTTCAGGTGCT 57.230 42.857 1.90 0.00 35.51 4.40
2037 2116 5.536161 AGCAAAATCATACACTGTTTCAGGT 59.464 36.000 1.90 0.28 35.51 4.00
2042 2121 6.919662 CAGAACAGCAAAATCATACACTGTTT 59.080 34.615 7.54 0.00 45.54 2.83
2045 2124 6.005583 ACAGAACAGCAAAATCATACACTG 57.994 37.500 0.00 0.00 0.00 3.66
2051 2130 6.624423 GCACAGATACAGAACAGCAAAATCAT 60.624 38.462 0.00 0.00 0.00 2.45
2057 2136 3.124578 TGCACAGATACAGAACAGCAA 57.875 42.857 0.00 0.00 0.00 3.91
2132 2216 1.746615 GTGGTGCACATCGATGGCT 60.747 57.895 28.09 6.52 34.08 4.75
2155 2239 5.123820 CGCTATGATCCAAACTCCTTGAAAA 59.876 40.000 0.00 0.00 37.17 2.29
2165 2249 3.738282 CAGAGTAGCGCTATGATCCAAAC 59.262 47.826 21.96 6.74 38.64 2.93
2182 2266 1.753649 AGAGCATACACGCATCAGAGT 59.246 47.619 0.00 0.00 0.00 3.24
2321 2405 5.709164 GCAGAGATTAGCACCATGGATAAAT 59.291 40.000 21.47 11.97 0.00 1.40
2322 2406 5.065914 GCAGAGATTAGCACCATGGATAAA 58.934 41.667 21.47 7.38 0.00 1.40
2399 2483 2.370281 TTGACGACATCCTGCTCTTC 57.630 50.000 0.00 0.00 0.00 2.87
2411 2495 1.092921 TGTGGCACCACTTTGACGAC 61.093 55.000 20.02 0.00 46.30 4.34
2428 2512 1.899814 TCAGAGCCATTTCTACCGTGT 59.100 47.619 0.00 0.00 0.00 4.49
2445 2529 6.822170 TGGAACTCAGAAATGAAGATCATCAG 59.178 38.462 6.79 0.00 35.76 2.90
2470 2554 1.825474 CCACCTATGTTCGACAGGTCT 59.175 52.381 4.62 0.00 40.77 3.85
2472 2556 0.902531 CCCACCTATGTTCGACAGGT 59.097 55.000 2.20 2.20 43.56 4.00
2473 2557 0.462047 GCCCACCTATGTTCGACAGG 60.462 60.000 0.00 0.00 35.45 4.00
2475 2559 1.216977 CGCCCACCTATGTTCGACA 59.783 57.895 0.00 0.00 0.00 4.35
2476 2560 2.171725 GCGCCCACCTATGTTCGAC 61.172 63.158 0.00 0.00 0.00 4.20
2478 2562 2.895372 GGCGCCCACCTATGTTCG 60.895 66.667 18.11 0.00 0.00 3.95
2479 2563 2.516225 GGGCGCCCACCTATGTTC 60.516 66.667 40.73 8.62 35.81 3.18
2480 2564 4.483243 CGGGCGCCCACCTATGTT 62.483 66.667 42.78 0.00 35.37 2.71
2491 2575 3.894547 TTCTCTCCAAACCGGGCGC 62.895 63.158 6.32 0.00 34.36 6.53
2492 2576 0.887387 TTTTCTCTCCAAACCGGGCG 60.887 55.000 6.32 0.00 34.36 6.13
2493 2577 1.324383 TTTTTCTCTCCAAACCGGGC 58.676 50.000 6.32 0.00 34.36 6.13
2494 2578 5.466819 GTTAATTTTTCTCTCCAAACCGGG 58.533 41.667 6.32 0.00 34.36 5.73
2495 2579 5.151389 CGTTAATTTTTCTCTCCAAACCGG 58.849 41.667 0.00 0.00 0.00 5.28
2497 2581 4.921515 GCCGTTAATTTTTCTCTCCAAACC 59.078 41.667 0.00 0.00 0.00 3.27
2498 2582 4.615541 CGCCGTTAATTTTTCTCTCCAAAC 59.384 41.667 0.00 0.00 0.00 2.93
2499 2583 4.515944 TCGCCGTTAATTTTTCTCTCCAAA 59.484 37.500 0.00 0.00 0.00 3.28
2500 2584 4.066490 TCGCCGTTAATTTTTCTCTCCAA 58.934 39.130 0.00 0.00 0.00 3.53
2501 2585 3.666274 TCGCCGTTAATTTTTCTCTCCA 58.334 40.909 0.00 0.00 0.00 3.86
2502 2586 4.550255 CGATCGCCGTTAATTTTTCTCTCC 60.550 45.833 0.26 0.00 0.00 3.71
2503 2587 4.506217 CGATCGCCGTTAATTTTTCTCTC 58.494 43.478 0.26 0.00 0.00 3.20
2504 2588 4.516092 CGATCGCCGTTAATTTTTCTCT 57.484 40.909 0.26 0.00 0.00 3.10
2518 2680 3.251571 CTTAATTAGGGCTACGATCGCC 58.748 50.000 16.60 8.41 46.83 5.54
2525 2687 4.496360 GAGATCGCCTTAATTAGGGCTAC 58.504 47.826 29.55 21.12 45.37 3.58


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

AutoCloner maintained by Alex Coulton.