Multiple sequence alignment - TraesCS5D01G106900

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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 TraesCS5D01G106900 chr5D 100.000 2315 0 0 1 2315 120790186 120787872 0.000000e+00 4276.0
1 TraesCS5D01G106900 chr5A 95.936 1255 32 4 410 1662 131645727 131644490 0.000000e+00 2017.0
2 TraesCS5D01G106900 chr5A 93.731 654 33 7 1666 2315 131644400 131643751 0.000000e+00 974.0
3 TraesCS5D01G106900 chr5A 92.961 412 27 1 1 410 131646218 131645807 1.180000e-167 599.0
4 TraesCS5D01G106900 chr5B 94.526 1224 34 10 410 1618 133894089 133892884 0.000000e+00 1858.0
5 TraesCS5D01G106900 chr5B 93.199 397 19 5 1925 2314 133892499 133892104 5.550000e-161 577.0
6 TraesCS5D01G106900 chr5B 96.414 251 7 1 1 249 133894513 133894263 1.660000e-111 412.0
7 TraesCS5D01G106900 chr5B 93.416 243 10 4 1660 1899 133892732 133892493 2.830000e-94 355.0
8 TraesCS5D01G106900 chr5B 91.667 60 5 0 1603 1662 133892873 133892814 1.470000e-12 84.2


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 TraesCS5D01G106900 chr5D 120787872 120790186 2314 True 4276.000000 4276 100.000000 1 2315 1 chr5D.!!$R1 2314
1 TraesCS5D01G106900 chr5A 131643751 131646218 2467 True 1196.666667 2017 94.209333 1 2315 3 chr5A.!!$R1 2314
2 TraesCS5D01G106900 chr5B 133892104 133894513 2409 True 657.240000 1858 93.844400 1 2314 5 chr5B.!!$R1 2313

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
994 1088 0.101759 GACCGCTGCGAGGTTACATA 59.898 55.0 25.45 0.0 43.01 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2486 1.327303 TGCATGTTGAAGTTGACCCC 58.673 50.0 0.0 0.0 0.0 4.95 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
38 39 3.606065 GACGCTACCGACGCACACT 62.606 63.158 0.00 0.00 38.29 3.55
135 136 2.524699 GCGAACAAAACACACGTTTCTC 59.475 45.455 0.00 0.00 44.65 2.87
205 208 3.860641 TGTGTGATTGACTGTGCGATAT 58.139 40.909 0.00 0.00 0.00 1.63
249 252 3.997021 GAGCATATATGTACTGGTGGCAC 59.003 47.826 9.70 9.70 0.00 5.01
254 257 6.147821 GCATATATGTACTGGTGGCACTTTAG 59.852 42.308 18.45 15.15 0.00 1.85
274 277 8.951243 ACTTTAGATTTCATCTACTCTTTTGGC 58.049 33.333 0.00 0.00 41.33 4.52
305 308 8.837389 GGACTACAATTAAGTTATGCCCTAAAG 58.163 37.037 0.00 0.00 0.00 1.85
330 333 5.925506 AAATGATGATCCATGCTGAAACA 57.074 34.783 0.00 0.00 0.00 2.83
347 350 7.010367 TGCTGAAACAAAAATTTGCAAGTAGAG 59.990 33.333 0.00 0.00 41.79 2.43
349 352 7.327214 TGAAACAAAAATTTGCAAGTAGAGGT 58.673 30.769 0.00 0.00 41.79 3.85
384 387 3.067742 ACCAATATTACGAGTCCAGACCG 59.932 47.826 0.00 7.00 0.00 4.79
457 540 1.227734 GGCCAAATCCATGCATGCC 60.228 57.895 21.69 13.48 0.00 4.40
520 605 2.342279 CTCGCGAGGTCAACCCAA 59.658 61.111 28.40 0.00 36.42 4.12
533 618 4.218852 GGTCAACCCAACAAAATATTCCGA 59.781 41.667 0.00 0.00 0.00 4.55
534 619 5.105513 GGTCAACCCAACAAAATATTCCGAT 60.106 40.000 0.00 0.00 0.00 4.18
535 620 6.095720 GGTCAACCCAACAAAATATTCCGATA 59.904 38.462 0.00 0.00 0.00 2.92
536 621 7.201875 GGTCAACCCAACAAAATATTCCGATAT 60.202 37.037 0.00 0.00 0.00 1.63
537 622 8.842280 GTCAACCCAACAAAATATTCCGATATA 58.158 33.333 0.00 0.00 0.00 0.86
538 623 9.581289 TCAACCCAACAAAATATTCCGATATAT 57.419 29.630 0.00 0.00 0.00 0.86
662 747 3.571401 CACTGCTTCTTGGAAGTTTGGAT 59.429 43.478 8.73 0.00 0.00 3.41
680 765 2.418976 GGATCCAAAACCGTCTAGCAAC 59.581 50.000 6.95 0.00 0.00 4.17
682 767 1.141254 TCCAAAACCGTCTAGCAACCA 59.859 47.619 0.00 0.00 0.00 3.67
767 852 9.645059 CGTGACATCACATATATAGATTCCTTT 57.355 33.333 12.32 0.00 46.75 3.11
797 882 9.944376 ATTACACTGTTAATGATAGTTGTGACT 57.056 29.630 0.00 0.00 39.97 3.41
812 897 1.730064 GTGACTTGTGACACGTGTTGT 59.270 47.619 24.26 15.79 43.10 3.32
994 1088 0.101759 GACCGCTGCGAGGTTACATA 59.898 55.000 25.45 0.00 43.01 2.29
999 1093 2.413796 CGCTGCGAGGTTACATAACAAA 59.586 45.455 18.66 0.00 37.92 2.83
1032 1126 0.529337 TGAAGCTAGCATCTGAGCGC 60.529 55.000 19.79 0.00 43.72 5.92
1165 1259 1.433121 GGGCAAGGAGATGGAGAGAT 58.567 55.000 0.00 0.00 0.00 2.75
1373 1467 3.816994 TCGGAGAGATAAGATGGTCGAA 58.183 45.455 0.00 0.00 0.00 3.71
1636 1760 6.339587 ACATGTAAACGTTTTCATCCCAAT 57.660 33.333 24.78 6.74 0.00 3.16
1655 1779 6.317642 TCCCAATCGTATATTTTGGTGAAGTG 59.682 38.462 9.24 0.00 38.58 3.16
1662 1786 6.092944 CGTATATTTTGGTGAAGTGCAGGTTA 59.907 38.462 0.00 0.00 0.00 2.85
1663 1787 6.909550 ATATTTTGGTGAAGTGCAGGTTAA 57.090 33.333 0.00 0.00 0.00 2.01
1664 1788 4.379339 TTTTGGTGAAGTGCAGGTTAAC 57.621 40.909 0.00 0.00 0.00 2.01
1706 1916 4.459089 GAGTGAGCCACGGCCTCC 62.459 72.222 3.95 0.00 43.17 4.30
1862 2074 3.655615 TTACCACTCCACAACCAAACT 57.344 42.857 0.00 0.00 0.00 2.66
1906 2118 3.726291 AACCGAAACATGTTTTCCTGG 57.274 42.857 24.02 22.45 32.11 4.45
1952 2164 9.443283 CATGTAGATAAGTTTTGCTGCTAATTC 57.557 33.333 0.00 0.00 0.00 2.17
1954 2166 9.177608 TGTAGATAAGTTTTGCTGCTAATTCAT 57.822 29.630 0.00 0.00 0.00 2.57
2123 2336 6.934645 TGTTATAGAACTGGAAAGTGGAACAG 59.065 38.462 1.39 0.00 36.03 3.16
2144 2361 7.372260 ACAGGTCTCTTTGCATATAAGATCT 57.628 36.000 0.00 0.00 31.66 2.75
2268 2486 7.827819 TGTTTCAACTCAGGATTATTAGTCG 57.172 36.000 0.00 0.00 0.00 4.18
2280 2498 5.395990 GGATTATTAGTCGGGGTCAACTTCA 60.396 44.000 0.00 0.00 0.00 3.02
2311 2529 2.437085 TCTCGGCAGAATACTCCTCA 57.563 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.662153 TGTGCGTCGGTAGCGTCA 61.662 61.111 14.79 8.23 37.44 4.35
38 39 5.760743 TCCACACGATTTGTAATCAGTGAAA 59.239 36.000 20.39 9.75 35.67 2.69
71 72 5.649782 AGGCAGGATCATTTGTTTTGTAG 57.350 39.130 0.00 0.00 0.00 2.74
135 136 7.387948 GGCTATTATCCCACACATTAGTAACAG 59.612 40.741 0.00 0.00 0.00 3.16
205 208 0.682532 TGCACACAGTTCAAAGCCCA 60.683 50.000 0.00 0.00 0.00 5.36
274 277 7.973944 GGGCATAACTTAATTGTAGTCCTTTTG 59.026 37.037 0.00 0.00 0.00 2.44
305 308 5.524971 TTCAGCATGGATCATCATTTTCC 57.475 39.130 0.00 0.00 36.16 3.13
330 333 9.740710 ATAGTCTACCTCTACTTGCAAATTTTT 57.259 29.630 0.00 0.00 0.00 1.94
407 410 9.331282 AGCTTGCCTAAAGATTTAATGTACTAG 57.669 33.333 0.00 0.00 38.24 2.57
414 497 7.416326 CCGGTTAAGCTTGCCTAAAGATTTAAT 60.416 37.037 9.86 0.00 41.73 1.40
651 736 2.626266 ACGGTTTTGGATCCAAACTTCC 59.374 45.455 34.50 30.53 44.39 3.46
662 747 1.141254 TGGTTGCTAGACGGTTTTGGA 59.859 47.619 0.00 0.00 0.00 3.53
711 796 3.261897 AGTGACCTTTGACTTCCATCGAT 59.738 43.478 0.00 0.00 0.00 3.59
784 869 4.048504 CGTGTCACAAGTCACAACTATCA 58.951 43.478 3.42 0.00 33.48 2.15
791 876 1.729517 CAACACGTGTCACAAGTCACA 59.270 47.619 23.61 0.00 34.12 3.58
792 877 1.730064 ACAACACGTGTCACAAGTCAC 59.270 47.619 23.61 0.00 34.38 3.67
793 878 2.087501 ACAACACGTGTCACAAGTCA 57.912 45.000 23.61 0.00 34.38 3.41
812 897 3.005684 GTGTTTCCAACATGCCAGATTGA 59.994 43.478 0.00 0.00 44.35 2.57
928 1021 0.110486 GGCTCTTGGAAGGGTGTTGA 59.890 55.000 0.00 0.00 0.00 3.18
994 1088 3.218453 TCATCACACGGTCCATTTTGTT 58.782 40.909 0.00 0.00 0.00 2.83
999 1093 1.003580 AGCTTCATCACACGGTCCATT 59.996 47.619 0.00 0.00 0.00 3.16
1032 1126 3.645975 GTGAACACCACCACGGCG 61.646 66.667 4.80 4.80 39.86 6.46
1165 1259 1.045350 CCGAGCATCTTGAGGAGGGA 61.045 60.000 0.00 0.00 0.00 4.20
1194 1288 3.352338 GAAGACGACCGGCACCGAT 62.352 63.158 11.42 0.00 42.83 4.18
1417 1511 2.417719 CTTCCTTGACACACACTAGGC 58.582 52.381 0.00 0.00 32.13 3.93
1636 1760 4.634004 CCTGCACTTCACCAAAATATACGA 59.366 41.667 0.00 0.00 0.00 3.43
1681 1891 0.878523 CGTGGCTCACTCCGTTTTCA 60.879 55.000 4.21 0.00 31.34 2.69
1706 1916 7.814587 AGATGATATGTACACCACAATGATACG 59.185 37.037 0.00 0.00 41.55 3.06
1776 1986 6.036577 TGGGTCTTGAGCATTTATTTTTCC 57.963 37.500 2.24 0.00 0.00 3.13
1906 2118 1.461127 GTTGGAGACTGCGTTGACATC 59.539 52.381 0.00 0.00 0.00 3.06
2087 2300 6.214615 TCCAGTTCTATAACATGTCTTTGGGA 59.785 38.462 0.00 0.00 38.12 4.37
2144 2361 7.878644 AGTATGAGAACTCACGTGCTATATAGA 59.121 37.037 11.67 0.00 43.11 1.98
2268 2486 1.327303 TGCATGTTGAAGTTGACCCC 58.673 50.000 0.00 0.00 0.00 4.95
2280 2498 1.741706 CTGCCGAGAAGATTGCATGTT 59.258 47.619 0.00 0.00 32.53 2.71


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

AutoCloner maintained by Alex Coulton.