Multiple sequence alignment - TraesCS5A01G179300

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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 TraesCS5A01G179300 chr5A 100.000 2815 0 0 1 2815 377194163 377191349 0 5199
1 TraesCS5A01G179300 chr5A 93.933 890 49 3 1 885 663240149 663239260 0 1339
2 TraesCS5A01G179300 chr5B 94.701 1925 74 11 896 2815 322924149 322922248 0 2964
3 TraesCS5A01G179300 chr5D 94.837 1898 72 9 929 2815 285475516 285473634 0 2939
4 TraesCS5A01G179300 chr3A 93.146 890 55 4 1 885 163175523 163176411 0 1301
5 TraesCS5A01G179300 chr3A 93.042 891 54 6 1 885 555840410 555841298 0 1295
6 TraesCS5A01G179300 chr3A 92.905 888 59 3 1 885 593577212 593576326 0 1288
7 TraesCS5A01G179300 chr2A 93.146 890 52 6 1 885 300132537 300133422 0 1297
8 TraesCS5A01G179300 chr1A 93.049 892 55 4 1 885 90688795 90687904 0 1297
9 TraesCS5A01G179300 chr4A 93.049 892 53 6 1 885 602186346 602185457 0 1295
10 TraesCS5A01G179300 chr4A 93.034 890 56 4 1 885 680414261 680415149 0 1295
11 TraesCS5A01G179300 chr4A 92.921 890 55 5 1 885 685585239 685586125 0 1288


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 TraesCS5A01G179300 chr5A 377191349 377194163 2814 True 5199 5199 100.000 1 2815 1 chr5A.!!$R1 2814
1 TraesCS5A01G179300 chr5A 663239260 663240149 889 True 1339 1339 93.933 1 885 1 chr5A.!!$R2 884
2 TraesCS5A01G179300 chr5B 322922248 322924149 1901 True 2964 2964 94.701 896 2815 1 chr5B.!!$R1 1919
3 TraesCS5A01G179300 chr5D 285473634 285475516 1882 True 2939 2939 94.837 929 2815 1 chr5D.!!$R1 1886
4 TraesCS5A01G179300 chr3A 163175523 163176411 888 False 1301 1301 93.146 1 885 1 chr3A.!!$F1 884
5 TraesCS5A01G179300 chr3A 555840410 555841298 888 False 1295 1295 93.042 1 885 1 chr3A.!!$F2 884
6 TraesCS5A01G179300 chr3A 593576326 593577212 886 True 1288 1288 92.905 1 885 1 chr3A.!!$R1 884
7 TraesCS5A01G179300 chr2A 300132537 300133422 885 False 1297 1297 93.146 1 885 1 chr2A.!!$F1 884
8 TraesCS5A01G179300 chr1A 90687904 90688795 891 True 1297 1297 93.049 1 885 1 chr1A.!!$R1 884
9 TraesCS5A01G179300 chr4A 602185457 602186346 889 True 1295 1295 93.049 1 885 1 chr4A.!!$R1 884
10 TraesCS5A01G179300 chr4A 680414261 680415149 888 False 1295 1295 93.034 1 885 1 chr4A.!!$F1 884
11 TraesCS5A01G179300 chr4A 685585239 685586125 886 False 1288 1288 92.921 1 885 1 chr4A.!!$F2 884

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
65 68 1.039068 CATCCTCGATCTCTGGCACT 58.961 55.000 0.00 0.0 0.00 4.40 F
954 965 1.374758 CGCCTGCGAAGTTCCTCTT 60.375 57.895 5.43 0.0 42.83 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 1230 0.321653 GCTCCATGAAACCGGACTGT 60.322 55.0 9.46 0.0 0.0 3.55 R
2679 2706 0.257328 TGGCAAGGAACAGAACCACA 59.743 50.0 0.00 0.0 0.0 4.17 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
65 68 1.039068 CATCCTCGATCTCTGGCACT 58.961 55.000 0.00 0.00 0.00 4.40
71 74 1.828768 GATCTCTGGCACTGGGGAG 59.171 63.158 0.00 0.00 0.00 4.30
81 84 4.100084 CTGGGGAGCCATGCACGA 62.100 66.667 0.00 0.00 0.00 4.35
412 417 2.026262 GGTCCAAGGCTCATGTTTAGGA 60.026 50.000 0.00 0.00 0.00 2.94
583 588 9.807921 ATGAAGAATTTGAGGTAAAAAGGTAGA 57.192 29.630 0.00 0.00 0.00 2.59
642 647 6.152154 TGTTGGGGCTACTAAATTAGAAAAGC 59.848 38.462 7.06 11.44 0.00 3.51
645 650 6.722129 TGGGGCTACTAAATTAGAAAAGCAAA 59.278 34.615 19.68 8.69 34.04 3.68
772 783 6.503589 TTACGTCCCACAAAGAAAATATGG 57.496 37.500 0.00 0.00 0.00 2.74
788 799 6.751514 AAATATGGACACGACTAAATTGCA 57.248 33.333 0.00 0.00 0.00 4.08
825 836 9.878667 TTATGTTCATTTTGTAGAAGGACGATA 57.121 29.630 0.00 0.00 0.00 2.92
843 854 3.564511 GATACTGCGTTGCAACATGTTT 58.435 40.909 28.01 16.94 38.41 2.83
852 863 6.642540 TGCGTTGCAACATGTTTTTCATAATA 59.357 30.769 28.01 0.00 34.76 0.98
902 913 5.308014 TGTGCATATATGATCCCTTGTGTC 58.692 41.667 17.10 0.00 0.00 3.67
906 917 5.410746 GCATATATGATCCCTTGTGTCTGTG 59.589 44.000 17.10 0.00 0.00 3.66
912 923 5.630121 TGATCCCTTGTGTCTGTGTTAAAT 58.370 37.500 0.00 0.00 0.00 1.40
913 924 6.774673 TGATCCCTTGTGTCTGTGTTAAATA 58.225 36.000 0.00 0.00 0.00 1.40
954 965 1.374758 CGCCTGCGAAGTTCCTCTT 60.375 57.895 5.43 0.00 42.83 2.85
1318 1339 1.066918 GTGGTCGACAACACCGAGT 59.933 57.895 18.41 0.00 36.61 4.18
1378 1399 4.993584 CCTTCGGTTCATCATCCTAATCAG 59.006 45.833 0.00 0.00 0.00 2.90
1416 1437 6.467723 AGCTATTATGCGCTACATTTACAC 57.532 37.500 9.73 0.00 40.38 2.90
1425 1446 5.106515 TGCGCTACATTTACACTGCAATTTA 60.107 36.000 9.73 0.00 0.00 1.40
1426 1447 5.971202 GCGCTACATTTACACTGCAATTTAT 59.029 36.000 0.00 0.00 0.00 1.40
1443 1464 8.524487 TGCAATTTATAACCACGATTTTTACCT 58.476 29.630 0.00 0.00 0.00 3.08
1444 1465 9.016623 GCAATTTATAACCACGATTTTTACCTC 57.983 33.333 0.00 0.00 0.00 3.85
1498 1519 5.884792 ACTTTCTGATTCTGAATGATGGACC 59.115 40.000 19.36 0.00 0.00 4.46
1511 1532 2.241176 TGATGGACCGCCTAAGGATTTT 59.759 45.455 0.00 0.00 34.31 1.82
1518 1539 3.189285 CCGCCTAAGGATTTTTGCATTG 58.811 45.455 0.00 0.00 0.00 2.82
1530 1552 4.519540 TTTTGCATTGCTAGGAAGAACC 57.480 40.909 10.49 0.00 39.35 3.62
1630 1652 5.730550 ACCTATTTGCATCGTTCTGAACTA 58.269 37.500 17.60 8.04 0.00 2.24
1631 1653 6.170506 ACCTATTTGCATCGTTCTGAACTAA 58.829 36.000 17.60 6.92 0.00 2.24
1666 1688 4.279420 GTGAAATTTGGGCTGAAGTTCTCT 59.721 41.667 4.17 0.00 33.59 3.10
1680 1702 1.064357 GTTCTCTACCGCTCTTCTCCG 59.936 57.143 0.00 0.00 0.00 4.63
1748 1770 1.340017 TGGCTGTTCCTCATGCTTACC 60.340 52.381 0.00 0.00 35.26 2.85
1938 1965 9.017669 GTAAGGTATGAATAAACTGTACGACTG 57.982 37.037 0.00 0.00 0.00 3.51
1939 1966 6.040878 AGGTATGAATAAACTGTACGACTGC 58.959 40.000 0.00 0.00 0.00 4.40
1987 2014 3.506067 GGAAACTTGGAGTAACATGTGGG 59.494 47.826 0.00 0.00 0.00 4.61
2223 2250 3.670055 CGCATTCCAGATTTTGTGAACAC 59.330 43.478 0.00 0.00 0.00 3.32
2269 2296 8.531146 ACTTTTGGAATCATTTTCCGTGAATAT 58.469 29.630 0.32 0.00 41.43 1.28
2270 2297 9.369904 CTTTTGGAATCATTTTCCGTGAATATT 57.630 29.630 0.00 0.00 41.43 1.28
2271 2298 8.700722 TTTGGAATCATTTTCCGTGAATATTG 57.299 30.769 0.00 0.00 41.43 1.90
2272 2299 7.403312 TGGAATCATTTTCCGTGAATATTGT 57.597 32.000 0.00 0.00 41.43 2.71
2273 2300 8.512966 TGGAATCATTTTCCGTGAATATTGTA 57.487 30.769 0.00 0.00 41.43 2.41
2274 2301 8.620416 TGGAATCATTTTCCGTGAATATTGTAG 58.380 33.333 0.00 0.00 41.43 2.74
2275 2302 8.076178 GGAATCATTTTCCGTGAATATTGTAGG 58.924 37.037 0.00 0.00 0.00 3.18
2276 2303 6.371809 TCATTTTCCGTGAATATTGTAGGC 57.628 37.500 0.00 0.00 0.00 3.93
2347 2374 4.584874 TCTCAAGGTTTCAGTGTTGTGAA 58.415 39.130 0.00 0.00 34.56 3.18
2350 2377 6.152661 TCTCAAGGTTTCAGTGTTGTGAATTT 59.847 34.615 0.00 0.00 36.34 1.82
2385 2412 3.794475 GCACATTAGCATTGAGTGATGGC 60.794 47.826 0.00 0.00 32.14 4.40
2390 2417 6.321945 ACATTAGCATTGAGTGATGGCAATTA 59.678 34.615 0.00 0.00 32.74 1.40
2679 2706 6.595682 AGCAGTGCACATAAGTAAATCCTAT 58.404 36.000 21.04 0.00 0.00 2.57
2687 2714 7.499232 GCACATAAGTAAATCCTATGTGGTTCT 59.501 37.037 18.20 0.00 44.67 3.01
2727 2754 7.067494 GGGAGCTATATTCTGTTGTTCAAATGT 59.933 37.037 0.00 0.00 0.00 2.71
2739 2766 7.714703 TGTTGTTCAAATGTCTCATGATCAAA 58.285 30.769 0.00 0.00 35.64 2.69
2753 2780 4.207891 TGATCAAAGAACTCTACTGGGC 57.792 45.455 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 74 2.512515 GGAGAGGTCGTGCATGGC 60.513 66.667 5.98 3.41 0.00 4.40
74 77 2.982130 GGTGGAGAGGTCGTGCAT 59.018 61.111 0.00 0.00 0.00 3.96
81 84 3.386237 GCTGCTCGGTGGAGAGGT 61.386 66.667 2.63 0.00 43.27 3.85
433 438 6.494059 AGCCCACAATCCTTTCTTTATTAGT 58.506 36.000 0.00 0.00 0.00 2.24
613 618 6.354130 TCTAATTTAGTAGCCCCAACACATC 58.646 40.000 3.45 0.00 0.00 3.06
657 663 8.054572 TCATGAAGTCCTCATCCATTTTATTCA 58.945 33.333 0.00 0.00 43.28 2.57
754 765 4.457603 CGTGTCCATATTTTCTTTGTGGGA 59.542 41.667 0.00 0.00 0.00 4.37
772 783 3.515071 ACGTTGCAATTTAGTCGTGTC 57.485 42.857 0.59 0.00 0.00 3.67
825 836 5.209749 ATGAAAAACATGTTGCAACGCAGT 61.210 37.500 23.79 18.16 39.67 4.40
843 854 8.433599 TCCCACAGTATCGGATTTATTATGAAA 58.566 33.333 0.00 0.00 0.00 2.69
852 863 4.503714 AATGTCCCACAGTATCGGATTT 57.496 40.909 0.00 0.00 0.00 2.17
885 896 6.560003 AACACAGACACAAGGGATCATATA 57.440 37.500 0.00 0.00 0.00 0.86
886 897 5.441718 AACACAGACACAAGGGATCATAT 57.558 39.130 0.00 0.00 0.00 1.78
887 898 4.908601 AACACAGACACAAGGGATCATA 57.091 40.909 0.00 0.00 0.00 2.15
888 899 3.795688 AACACAGACACAAGGGATCAT 57.204 42.857 0.00 0.00 0.00 2.45
889 900 4.698201 TTAACACAGACACAAGGGATCA 57.302 40.909 0.00 0.00 0.00 2.92
890 901 7.865706 ATATTTAACACAGACACAAGGGATC 57.134 36.000 0.00 0.00 0.00 3.36
891 902 9.747898 TTTATATTTAACACAGACACAAGGGAT 57.252 29.630 0.00 0.00 0.00 3.85
892 903 9.575868 TTTTATATTTAACACAGACACAAGGGA 57.424 29.630 0.00 0.00 0.00 4.20
893 904 9.620660 GTTTTATATTTAACACAGACACAAGGG 57.379 33.333 0.00 0.00 0.00 3.95
894 905 9.620660 GGTTTTATATTTAACACAGACACAAGG 57.379 33.333 0.00 0.00 0.00 3.61
912 923 7.531716 CGGATAAAGCTTGTGTTGGTTTTATA 58.468 34.615 0.00 0.00 36.65 0.98
913 924 6.386654 CGGATAAAGCTTGTGTTGGTTTTAT 58.613 36.000 0.00 0.00 36.65 1.40
1038 1059 2.202756 GAGGATGACACGACGGCC 60.203 66.667 0.00 0.00 0.00 6.13
1209 1230 0.321653 GCTCCATGAAACCGGACTGT 60.322 55.000 9.46 0.00 0.00 3.55
1378 1399 7.689812 CGCATAATAGCTACTGAATGTAATTGC 59.310 37.037 0.00 0.00 36.07 3.56
1416 1437 8.803799 GGTAAAAATCGTGGTTATAAATTGCAG 58.196 33.333 0.00 0.00 0.00 4.41
1470 1491 9.690913 TCCATCATTCAGAATCAGAAAGTAAAT 57.309 29.630 0.00 0.00 0.00 1.40
1498 1519 2.604462 GCAATGCAAAAATCCTTAGGCG 59.396 45.455 0.00 0.00 0.00 5.52
1511 1532 3.084039 CAGGTTCTTCCTAGCAATGCAA 58.916 45.455 8.35 0.00 46.24 4.08
1518 1539 6.995091 ACATAATCAATCAGGTTCTTCCTAGC 59.005 38.462 0.00 0.00 46.24 3.42
1631 1653 9.550406 CAGCCCAAATTTCACATCATAAATTAT 57.450 29.630 0.00 0.00 34.93 1.28
1666 1688 2.415608 CCTGCGGAGAAGAGCGGTA 61.416 63.158 5.10 0.00 38.02 4.02
1680 1702 2.424956 CCAAGATAGACTTTTGCCCTGC 59.575 50.000 0.00 0.00 36.61 4.85
1748 1770 5.591067 TGGTAATTTTATAACTCCAAGGGCG 59.409 40.000 0.00 0.00 0.00 6.13
1933 1960 0.988439 GCGAAGAAGAGAAGCAGTCG 59.012 55.000 0.00 0.00 0.00 4.18
1938 1965 5.109903 TGTAATAAGGCGAAGAAGAGAAGC 58.890 41.667 0.00 0.00 0.00 3.86
1939 1966 7.778470 ATTGTAATAAGGCGAAGAAGAGAAG 57.222 36.000 0.00 0.00 0.00 2.85
1987 2014 6.494842 TCAAGTGAAAAGAAATACACTGTGC 58.505 36.000 7.90 0.00 41.73 4.57
2269 2296 4.617253 TGAAAGAGCTACAAGCCTACAA 57.383 40.909 0.00 0.00 43.77 2.41
2270 2297 4.617253 TTGAAAGAGCTACAAGCCTACA 57.383 40.909 0.00 0.00 43.77 2.74
2271 2298 5.643777 TGAATTGAAAGAGCTACAAGCCTAC 59.356 40.000 0.00 0.00 43.77 3.18
2272 2299 5.804639 TGAATTGAAAGAGCTACAAGCCTA 58.195 37.500 0.00 0.00 43.77 3.93
2273 2300 4.655963 TGAATTGAAAGAGCTACAAGCCT 58.344 39.130 0.00 0.00 43.77 4.58
2274 2301 4.142513 CCTGAATTGAAAGAGCTACAAGCC 60.143 45.833 0.00 0.00 43.77 4.35
2275 2302 4.697352 TCCTGAATTGAAAGAGCTACAAGC 59.303 41.667 0.00 0.00 42.84 4.01
2276 2303 6.998968 ATCCTGAATTGAAAGAGCTACAAG 57.001 37.500 0.00 0.00 0.00 3.16
2350 2377 9.628746 CAATGCTAATGTGCTTATATTATGCAA 57.371 29.630 0.00 0.00 40.00 4.08
2385 2412 9.921637 TTATTAGGAAAAAGCACTTGGTAATTG 57.078 29.630 0.00 0.00 0.00 2.32
2390 2417 6.075315 AGGTTATTAGGAAAAAGCACTTGGT 58.925 36.000 0.00 0.00 0.00 3.67
2610 2637 5.163141 TGACTTCCCCTTCAACAGTTCATTA 60.163 40.000 0.00 0.00 0.00 1.90
2679 2706 0.257328 TGGCAAGGAACAGAACCACA 59.743 50.000 0.00 0.00 0.00 4.17
2727 2754 6.127225 CCCAGTAGAGTTCTTTGATCATGAGA 60.127 42.308 0.09 0.32 0.00 3.27
2739 2766 1.903183 GACCTTGCCCAGTAGAGTTCT 59.097 52.381 0.00 0.00 0.00 3.01
2753 2780 2.408050 CTCTCTGGTTTGTCGACCTTG 58.592 52.381 14.12 0.00 40.47 3.61


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

AutoCloner maintained by Alex Coulton.