Multiple sequence alignment - TraesCS1B01G071900

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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 TraesCS1B01G071900 chr1B 100.000 2686 0 0 1 2686 56885076 56882391 0 4961
1 TraesCS1B01G071900 chr1A 92.641 2704 130 33 3 2686 36273084 36270430 0 3827
2 TraesCS1B01G071900 chr1D 92.220 2725 144 37 3 2686 36837649 36834952 0 3795


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 TraesCS1B01G071900 chr1B 56882391 56885076 2685 True 4961 4961 100.000 1 2686 1 chr1B.!!$R1 2685
1 TraesCS1B01G071900 chr1A 36270430 36273084 2654 True 3827 3827 92.641 3 2686 1 chr1A.!!$R1 2683
2 TraesCS1B01G071900 chr1D 36834952 36837649 2697 True 3795 3795 92.220 3 2686 1 chr1D.!!$R1 2683

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
28 29 1.004394 ACCCGATCCTTTTCTGGAACC 59.996 52.381 0.00 0.0 39.85 3.62 F
782 791 1.796459 ACGCGGTTATGTCTGAAACAC 59.204 47.619 12.47 0.0 41.75 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1017 1026 0.108662 TGTAGGTCATCGCTGCAGTG 60.109 55.0 21.43 21.43 0.0 3.66 R
2251 2273 0.037590 CTGACCAACCCCGGAATTCA 59.962 55.0 0.73 0.00 0.0 2.57 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
25 26 1.280998 GGAACCCGATCCTTTTCTGGA 59.719 52.381 0.00 0.00 40.82 3.86
27 28 2.491675 ACCCGATCCTTTTCTGGAAC 57.508 50.000 0.00 0.00 39.85 3.62
28 29 1.004394 ACCCGATCCTTTTCTGGAACC 59.996 52.381 0.00 0.00 39.85 3.62
91 92 3.874392 AGTTGCCAATGAATAACAGCC 57.126 42.857 0.00 0.00 0.00 4.85
400 404 4.022416 CCCGATTCTTGTTTCCAATGTCAA 60.022 41.667 0.00 0.00 0.00 3.18
423 427 5.938438 AGAAAGAGTGAGCAGAAAATCAC 57.062 39.130 0.00 0.00 44.97 3.06
502 506 7.068839 TCCAGTGGCACTTTAAAATACTTGAAA 59.931 33.333 19.43 0.00 0.00 2.69
593 599 6.756542 CAGAACGATCACATTGTTATACCTCA 59.243 38.462 0.00 0.00 37.01 3.86
706 715 4.262463 CCCAAAGAGTGAGCTTACACAGTA 60.262 45.833 11.65 0.00 42.45 2.74
782 791 1.796459 ACGCGGTTATGTCTGAAACAC 59.204 47.619 12.47 0.00 41.75 3.32
799 808 5.651576 TGAAACACTAGCCATGCATTCATTA 59.348 36.000 0.00 0.00 0.00 1.90
1017 1026 2.555220 CGATGCTAACGCCGAATAAC 57.445 50.000 0.00 0.00 34.43 1.89
1034 1043 0.608130 AACACTGCAGCGATGACCTA 59.392 50.000 15.27 0.00 0.00 3.08
1061 1070 3.339141 AGAGAAATTTTCGAGCTCACCC 58.661 45.455 15.40 0.00 34.02 4.61
1223 1232 3.547249 ATCGTCGACCGTTGCACGT 62.547 57.895 10.58 0.00 40.58 4.49
1226 1235 3.902086 TCGACCGTTGCACGTGGA 61.902 61.111 18.88 12.78 40.58 4.02
1239 1248 1.374758 CGTGGAGTGGTGCTCTTCC 60.375 63.158 0.00 0.00 43.62 3.46
1329 1338 2.392662 CTTCAGTGGATAGCTCTGGGA 58.607 52.381 0.00 0.00 0.00 4.37
1330 1339 2.079170 TCAGTGGATAGCTCTGGGAG 57.921 55.000 0.00 0.00 0.00 4.30
1350 1359 5.003804 GGAGTGGTCACTGTACAATCAAAT 58.996 41.667 8.49 0.00 42.66 2.32
1439 1453 7.624549 AGGTTCTATGAGTTCTCAAGCAATTA 58.375 34.615 6.60 0.00 0.00 1.40
1455 1469 9.135189 TCAAGCAATTATAATTAAGCTCATGGT 57.865 29.630 18.32 6.10 29.52 3.55
1456 1470 9.403110 CAAGCAATTATAATTAAGCTCATGGTC 57.597 33.333 18.32 0.79 29.52 4.02
1457 1471 8.696043 AGCAATTATAATTAAGCTCATGGTCA 57.304 30.769 14.27 0.00 0.00 4.02
1458 1472 9.305555 AGCAATTATAATTAAGCTCATGGTCAT 57.694 29.630 14.27 0.00 0.00 3.06
1459 1473 9.350357 GCAATTATAATTAAGCTCATGGTCATG 57.650 33.333 10.34 4.67 40.09 3.07
1460 1474 9.850628 CAATTATAATTAAGCTCATGGTCATGG 57.149 33.333 10.34 3.75 39.24 3.66
1604 1618 2.736826 CCTCCCCGGCTTCTTCCTC 61.737 68.421 0.00 0.00 0.00 3.71
1608 1622 2.689034 CCGGCTTCTTCCTCCCCT 60.689 66.667 0.00 0.00 0.00 4.79
1878 1892 2.052237 GAAACGGCAGCACACGTG 60.052 61.111 15.48 15.48 43.31 4.49
1890 1904 3.345737 ACACGTGTGACTGTGTGAG 57.654 52.632 22.71 0.00 46.87 3.51
1901 1917 4.357947 GTGTGAGTCGCTGCCCGA 62.358 66.667 5.11 0.00 45.15 5.14
1928 1944 1.605165 CGGCCCACTAAAAGCCCAA 60.605 57.895 0.00 0.00 44.13 4.12
1929 1945 1.873270 CGGCCCACTAAAAGCCCAAC 61.873 60.000 0.00 0.00 44.13 3.77
1930 1946 1.541310 GGCCCACTAAAAGCCCAACC 61.541 60.000 0.00 0.00 41.00 3.77
1935 1951 3.165071 CCACTAAAAGCCCAACCAAGAT 58.835 45.455 0.00 0.00 0.00 2.40
1946 1962 3.781307 CCAAGATCCACGGCCCGA 61.781 66.667 11.71 0.00 0.00 5.14
2050 2067 1.418334 CATCCTCCTCCTCATTCGGT 58.582 55.000 0.00 0.00 0.00 4.69
2133 2155 1.649267 GATTCTGCGAAATCCGGCC 59.351 57.895 0.00 0.00 39.04 6.13
2162 2184 1.066605 CCACGATCCGAGGTAATTCGT 59.933 52.381 0.00 0.00 43.18 3.85
2163 2185 2.480759 CCACGATCCGAGGTAATTCGTT 60.481 50.000 0.00 0.00 40.72 3.85
2165 2187 1.521423 CGATCCGAGGTAATTCGTTGC 59.479 52.381 0.00 0.00 38.88 4.17
2166 2188 1.521423 GATCCGAGGTAATTCGTTGCG 59.479 52.381 0.00 0.00 38.88 4.85
2171 2193 3.117794 CGAGGTAATTCGTTGCGGATTA 58.882 45.455 0.00 0.00 36.41 1.75
2172 2194 3.739300 CGAGGTAATTCGTTGCGGATTAT 59.261 43.478 5.68 0.00 39.14 1.28
2240 2262 0.792640 AATCGTGCTTGCTTCGTGAG 59.207 50.000 9.41 0.00 0.00 3.51
2251 2273 2.224281 TGCTTCGTGAGTTTCCTGATGT 60.224 45.455 0.00 0.00 0.00 3.06
2254 2276 3.744238 TCGTGAGTTTCCTGATGTGAA 57.256 42.857 0.00 0.00 0.00 3.18
2258 2280 4.142816 CGTGAGTTTCCTGATGTGAATTCC 60.143 45.833 2.27 0.00 0.00 3.01
2260 2282 3.347216 AGTTTCCTGATGTGAATTCCGG 58.653 45.455 2.27 0.00 0.00 5.14
2262 2284 0.546122 TCCTGATGTGAATTCCGGGG 59.454 55.000 0.00 0.00 0.00 5.73
2263 2285 0.255890 CCTGATGTGAATTCCGGGGT 59.744 55.000 0.00 0.00 0.00 4.95
2271 2293 0.326927 GAATTCCGGGGTTGGTCAGA 59.673 55.000 0.00 0.00 0.00 3.27
2296 2318 3.466714 GGGAGAAGGAGATCCCGAT 57.533 57.895 0.00 0.00 45.63 4.18
2299 2324 1.710816 GAGAAGGAGATCCCGATGGT 58.289 55.000 0.00 0.00 40.87 3.55
2301 2326 0.394565 GAAGGAGATCCCGATGGTGG 59.605 60.000 0.00 0.00 40.87 4.61
2302 2327 1.700042 AAGGAGATCCCGATGGTGGC 61.700 60.000 0.00 0.00 40.87 5.01
2303 2328 2.143419 GGAGATCCCGATGGTGGCT 61.143 63.158 0.00 0.00 0.00 4.75
2336 2361 4.180946 CAGCGACCTCGACCTCGG 62.181 72.222 8.62 0.00 43.02 4.63
2559 2608 1.808945 CTGTGAATTGTGGGTGAGCTC 59.191 52.381 6.82 6.82 0.00 4.09
2614 2663 3.432326 GGATGGTCTGGATGAGTACAACC 60.432 52.174 0.00 0.00 39.06 3.77
2663 2712 1.895707 GCAAGGAGATCGGCCATGG 60.896 63.158 7.63 7.63 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.064825 AAAGGATCGGGTTCCACTGT 58.935 50.000 3.38 0.00 38.32 3.55
1 2 2.084546 GAAAAGGATCGGGTTCCACTG 58.915 52.381 3.38 0.00 38.32 3.66
48 49 6.808008 TTCCTTTATGAGAAGTTCTTGCTG 57.192 37.500 6.88 0.00 0.00 4.41
152 154 2.180432 AGGTAAAACTGTTCTCCCGC 57.820 50.000 0.00 0.00 0.00 6.13
209 212 3.558418 TGTAGAGTTTTGAAGCGGTGAAC 59.442 43.478 0.00 0.00 0.00 3.18
283 286 2.091333 AGGTTGGTTGTCTCCCATGTTT 60.091 45.455 0.00 0.00 0.00 2.83
400 404 5.824624 TGTGATTTTCTGCTCACTCTTTCTT 59.175 36.000 3.56 0.00 41.83 2.52
502 506 7.785033 ACAATCTCTTTGTTTTCATTCTGGTT 58.215 30.769 0.00 0.00 46.51 3.67
706 715 8.215736 AGGGTTAGTAAAAGTAACAATCAGTGT 58.784 33.333 6.90 0.00 44.64 3.55
764 773 3.062234 GCTAGTGTTTCAGACATAACCGC 59.938 47.826 0.00 0.00 41.10 5.68
782 791 5.190992 TGCTTTAATGAATGCATGGCTAG 57.809 39.130 0.00 0.00 39.92 3.42
1017 1026 0.108662 TGTAGGTCATCGCTGCAGTG 60.109 55.000 21.43 21.43 0.00 3.66
1034 1043 5.296780 TGAGCTCGAAAATTTCTCTTGTTGT 59.703 36.000 9.64 0.00 0.00 3.32
1061 1070 3.781079 TTTTCACTGTTTGTGCTGAGG 57.219 42.857 0.00 0.00 45.81 3.86
1226 1235 0.178921 TGGAGAGGAAGAGCACCACT 60.179 55.000 0.00 0.00 0.00 4.00
1231 1240 2.386779 CAGAGATGGAGAGGAAGAGCA 58.613 52.381 0.00 0.00 0.00 4.26
1232 1241 1.069049 GCAGAGATGGAGAGGAAGAGC 59.931 57.143 0.00 0.00 0.00 4.09
1239 1248 4.958509 ACATATGTTGCAGAGATGGAGAG 58.041 43.478 1.41 0.00 0.00 3.20
1290 1299 3.498927 AGCACTGCTCATATTTGTTGC 57.501 42.857 0.00 0.00 30.62 4.17
1329 1338 6.545666 TCAAATTTGATTGTACAGTGACCACT 59.454 34.615 16.91 0.00 35.52 4.00
1330 1339 6.636850 GTCAAATTTGATTGTACAGTGACCAC 59.363 38.462 23.05 2.36 39.73 4.16
1350 1359 4.081406 CTGAACATGAATCCCAGGTCAAA 58.919 43.478 0.00 0.00 39.08 2.69
1439 1453 5.709164 GCTCCATGACCATGAGCTTAATTAT 59.291 40.000 18.39 0.00 41.20 1.28
1455 1469 4.305539 TGGAATCTTTGAAGCTCCATGA 57.694 40.909 0.00 0.00 34.69 3.07
1456 1470 4.381292 GGTTGGAATCTTTGAAGCTCCATG 60.381 45.833 12.35 0.00 37.49 3.66
1457 1471 3.766051 GGTTGGAATCTTTGAAGCTCCAT 59.234 43.478 12.35 0.00 37.49 3.41
1458 1472 3.157087 GGTTGGAATCTTTGAAGCTCCA 58.843 45.455 9.16 9.16 36.54 3.86
1459 1473 3.157087 TGGTTGGAATCTTTGAAGCTCC 58.843 45.455 0.00 5.31 0.00 4.70
1460 1474 4.802999 CTTGGTTGGAATCTTTGAAGCTC 58.197 43.478 0.00 0.00 0.00 4.09
1593 1607 0.995803 AAGAAGGGGAGGAAGAAGCC 59.004 55.000 0.00 0.00 0.00 4.35
1604 1618 4.468689 GACGGCGGGAAGAAGGGG 62.469 72.222 13.24 0.00 0.00 4.79
1881 1895 2.029666 GGCAGCGACTCACACAGT 59.970 61.111 0.00 0.00 38.45 3.55
1882 1896 2.740055 GGGCAGCGACTCACACAG 60.740 66.667 0.00 0.00 0.00 3.66
1884 1898 4.357947 TCGGGCAGCGACTCACAC 62.358 66.667 0.00 0.00 0.00 3.82
1909 1925 2.754254 GGGCTTTTAGTGGGCCGG 60.754 66.667 0.00 0.00 46.10 6.13
1911 1927 1.541310 GGTTGGGCTTTTAGTGGGCC 61.541 60.000 0.00 0.00 46.56 5.80
1928 1944 4.096003 CGGGCCGTGGATCTTGGT 62.096 66.667 19.97 0.00 0.00 3.67
1929 1945 3.323758 TTCGGGCCGTGGATCTTGG 62.324 63.158 27.32 0.00 0.00 3.61
1930 1946 1.815421 CTTCGGGCCGTGGATCTTG 60.815 63.158 27.32 4.51 0.00 3.02
1953 1969 1.663702 CTCACTTTCGGGTTCGCGT 60.664 57.895 5.77 0.00 36.13 6.01
1955 1971 2.677979 GGCTCACTTTCGGGTTCGC 61.678 63.158 0.00 0.00 36.13 4.70
2025 2042 2.468301 TGAGGAGGAGGATGGAGAAG 57.532 55.000 0.00 0.00 0.00 2.85
2026 2043 3.312890 GAATGAGGAGGAGGATGGAGAA 58.687 50.000 0.00 0.00 0.00 2.87
2050 2067 0.606604 GGAACCCTCGAGCACACTAA 59.393 55.000 6.99 0.00 0.00 2.24
2133 2155 1.007271 CGGATCGTGGAGGAATCCG 60.007 63.158 8.44 8.44 46.38 4.18
2166 2188 1.518903 GGCTCCAGCGGCAATAATCC 61.519 60.000 1.45 0.00 43.26 3.01
2240 2262 2.423538 CCCGGAATTCACATCAGGAAAC 59.576 50.000 0.73 0.00 34.50 2.78
2251 2273 0.037590 CTGACCAACCCCGGAATTCA 59.962 55.000 0.73 0.00 0.00 2.57
2254 2276 1.683441 GTCTGACCAACCCCGGAAT 59.317 57.895 0.73 0.00 0.00 3.01
2271 2293 2.688477 GATCTCCTTCTCCCATCTGGT 58.312 52.381 0.00 0.00 34.77 4.00
2467 2516 0.245539 ATAACACACGTCCTGGACCG 59.754 55.000 20.68 17.06 0.00 4.79
2559 2608 1.298563 CACACAGCGGCAACACTTG 60.299 57.895 1.45 0.00 0.00 3.16
2614 2663 4.778143 GCCGCCACCACCACCTAG 62.778 72.222 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.