Multiple sequence alignment - TraesCS6A01G320900

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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 TraesCS6A01G320900 chr6A 100.000 2825 0 0 1 2825 555486445 555489269 0.000000e+00 5217.0
1 TraesCS6A01G320900 chr6A 98.283 932 12 2 1897 2825 555434110 555433180 0.000000e+00 1629.0
2 TraesCS6A01G320900 chr6A 91.294 827 46 7 1898 2715 52179330 52180139 0.000000e+00 1105.0
3 TraesCS6A01G320900 chr6A 96.923 65 2 0 2761 2825 52181445 52181509 2.980000e-20 110.0
4 TraesCS6A01G320900 chr5A 97.338 1728 34 7 162 1883 60130727 60132448 0.000000e+00 2926.0
5 TraesCS6A01G320900 chr5A 87.943 564 58 6 1288 1851 60246307 60246860 0.000000e+00 656.0
6 TraesCS6A01G320900 chr5A 91.111 135 11 1 741 875 520619067 520618934 6.220000e-42 182.0
7 TraesCS6A01G320900 chr5A 98.039 51 1 0 1 51 60129548 60129598 3.880000e-14 89.8
8 TraesCS6A01G320900 chr7A 98.601 929 11 2 1898 2825 669740640 669741567 0.000000e+00 1642.0
9 TraesCS6A01G320900 chr7A 84.795 855 110 14 985 1826 657431886 657431039 0.000000e+00 841.0
10 TraesCS6A01G320900 chr7A 87.919 149 16 2 738 884 305712261 305712409 1.040000e-39 174.0
11 TraesCS6A01G320900 chr7A 87.671 73 7 2 370 441 657434891 657434820 1.800000e-12 84.2
12 TraesCS6A01G320900 chr4A 98.601 929 10 2 1898 2825 21502905 21503831 0.000000e+00 1640.0
13 TraesCS6A01G320900 chr5D 94.681 1034 52 2 866 1899 69413169 69414199 0.000000e+00 1602.0
14 TraesCS6A01G320900 chr5D 93.987 948 54 3 897 1844 69426614 69427558 0.000000e+00 1432.0
15 TraesCS6A01G320900 chr5D 86.280 707 68 18 50 742 69425879 69426570 0.000000e+00 741.0
16 TraesCS6A01G320900 chr5D 93.485 307 17 2 174 478 69412680 69412985 1.190000e-123 453.0
17 TraesCS6A01G320900 chr5D 92.925 212 9 3 491 702 69412968 69413173 1.270000e-78 303.0
18 TraesCS6A01G320900 chr5D 87.755 98 8 3 89 182 69412563 69412660 8.270000e-21 111.0
19 TraesCS6A01G320900 chr5D 90.244 41 4 0 700 740 521481373 521481333 1.000000e-03 54.7
20 TraesCS6A01G320900 chr5B 93.617 987 55 5 916 1899 75250551 75251532 0.000000e+00 1467.0
21 TraesCS6A01G320900 chr5B 87.243 925 104 11 901 1819 75319204 75320120 0.000000e+00 1042.0
22 TraesCS6A01G320900 chr5B 87.406 667 72 9 901 1562 75685883 75686542 0.000000e+00 756.0
23 TraesCS6A01G320900 chr5B 91.450 269 15 4 181 446 75250103 75250366 2.070000e-96 363.0
24 TraesCS6A01G320900 chr5B 79.198 399 33 33 305 696 75685452 75685807 6.090000e-57 231.0
25 TraesCS6A01G320900 chr5B 78.947 399 34 30 305 696 75318772 75319127 2.830000e-55 226.0
26 TraesCS6A01G320900 chr5B 93.684 95 4 1 1912 2006 511713728 511713820 1.060000e-29 141.0
27 TraesCS6A01G320900 chr5B 94.521 73 1 3 2742 2814 511713813 511713882 2.980000e-20 110.0
28 TraesCS6A01G320900 chrUn 92.537 938 53 6 1898 2825 38482691 38483621 0.000000e+00 1328.0
29 TraesCS6A01G320900 chr2D 90.583 892 49 18 1897 2780 580882666 580881802 0.000000e+00 1149.0
30 TraesCS6A01G320900 chr3A 89.865 888 48 13 1952 2825 531459586 531458727 0.000000e+00 1103.0
31 TraesCS6A01G320900 chr7D 85.548 858 104 13 985 1826 568698160 568699013 0.000000e+00 880.0
32 TraesCS6A01G320900 chr7D 90.769 65 4 2 367 430 568697171 568697234 5.010000e-13 86.1
33 TraesCS6A01G320900 chr3B 91.304 230 12 5 2600 2821 550775571 550775342 9.830000e-80 307.0
34 TraesCS6A01G320900 chr1B 80.602 299 42 11 1933 2222 57780112 57779821 1.700000e-52 217.0
35 TraesCS6A01G320900 chr1B 91.111 135 11 1 744 877 626226880 626227014 6.220000e-42 182.0
36 TraesCS6A01G320900 chr4B 89.262 149 13 3 739 886 17256463 17256317 1.730000e-42 183.0
37 TraesCS6A01G320900 chr4B 89.928 139 13 1 733 870 595726321 595726183 8.040000e-41 178.0
38 TraesCS6A01G320900 chr4B 88.889 144 15 1 726 869 403238098 403238240 2.890000e-40 176.0
39 TraesCS6A01G320900 chr6B 89.437 142 15 0 735 876 207511035 207510894 2.240000e-41 180.0
40 TraesCS6A01G320900 chr1A 89.510 143 13 2 729 870 518716796 518716655 2.240000e-41 180.0
41 TraesCS6A01G320900 chr4D 86.127 173 15 8 2659 2825 352465385 352465216 8.040000e-41 178.0
42 TraesCS6A01G320900 chr7B 88.281 128 15 0 985 1112 624792409 624792282 1.360000e-33 154.0
43 TraesCS6A01G320900 chr7B 87.671 73 7 2 370 441 624793193 624793122 1.800000e-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 TraesCS6A01G320900 chr6A 555486445 555489269 2824 False 5217.00 5217 100.0000 1 2825 1 chr6A.!!$F1 2824
1 TraesCS6A01G320900 chr6A 555433180 555434110 930 True 1629.00 1629 98.2830 1897 2825 1 chr6A.!!$R1 928
2 TraesCS6A01G320900 chr6A 52179330 52181509 2179 False 607.50 1105 94.1085 1898 2825 2 chr6A.!!$F2 927
3 TraesCS6A01G320900 chr5A 60129548 60132448 2900 False 1507.90 2926 97.6885 1 1883 2 chr5A.!!$F2 1882
4 TraesCS6A01G320900 chr5A 60246307 60246860 553 False 656.00 656 87.9430 1288 1851 1 chr5A.!!$F1 563
5 TraesCS6A01G320900 chr7A 669740640 669741567 927 False 1642.00 1642 98.6010 1898 2825 1 chr7A.!!$F2 927
6 TraesCS6A01G320900 chr7A 657431039 657434891 3852 True 462.60 841 86.2330 370 1826 2 chr7A.!!$R1 1456
7 TraesCS6A01G320900 chr4A 21502905 21503831 926 False 1640.00 1640 98.6010 1898 2825 1 chr4A.!!$F1 927
8 TraesCS6A01G320900 chr5D 69425879 69427558 1679 False 1086.50 1432 90.1335 50 1844 2 chr5D.!!$F2 1794
9 TraesCS6A01G320900 chr5D 69412563 69414199 1636 False 617.25 1602 92.2115 89 1899 4 chr5D.!!$F1 1810
10 TraesCS6A01G320900 chr5B 75250103 75251532 1429 False 915.00 1467 92.5335 181 1899 2 chr5B.!!$F1 1718
11 TraesCS6A01G320900 chr5B 75318772 75320120 1348 False 634.00 1042 83.0950 305 1819 2 chr5B.!!$F2 1514
12 TraesCS6A01G320900 chr5B 75685452 75686542 1090 False 493.50 756 83.3020 305 1562 2 chr5B.!!$F3 1257
13 TraesCS6A01G320900 chrUn 38482691 38483621 930 False 1328.00 1328 92.5370 1898 2825 1 chrUn.!!$F1 927
14 TraesCS6A01G320900 chr2D 580881802 580882666 864 True 1149.00 1149 90.5830 1897 2780 1 chr2D.!!$R1 883
15 TraesCS6A01G320900 chr3A 531458727 531459586 859 True 1103.00 1103 89.8650 1952 2825 1 chr3A.!!$R1 873
16 TraesCS6A01G320900 chr7D 568697171 568699013 1842 False 483.05 880 88.1585 367 1826 2 chr7D.!!$F1 1459

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
30 31 1.938861 CGCTAAACACGCCAACTGT 59.061 52.632 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 6011 0.034616 CGCCCCTGATCTCAGATTCC 59.965 60.0 8.78 0.0 46.59 3.01 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
30 31 1.938861 CGCTAAACACGCCAACTGT 59.061 52.632 0.00 0.00 0.00 3.55
74 97 4.044426 GTCTGTGTGTCAATTTGGAAAGC 58.956 43.478 0.00 0.00 0.00 3.51
114 510 7.275999 GTGAGAGCACAAGAAATTAGTAGTACC 59.724 40.741 0.00 0.00 44.51 3.34
151 552 7.000575 TGACTGCGATGCTAGTAAATTTTAC 57.999 36.000 10.68 10.68 0.00 2.01
263 1319 2.767394 TCCCATGCATCCATTTTTCTGG 59.233 45.455 0.00 0.00 37.66 3.86
282 1338 2.224523 TGGTGTGTCCTGGTCATTTCTC 60.225 50.000 0.00 0.00 37.07 2.87
756 4483 2.865343 ATTAGCACTACCTTCGTCCG 57.135 50.000 0.00 0.00 0.00 4.79
786 4513 6.400568 ACTTGTCATCCAAATGCATAAAAGG 58.599 36.000 0.00 0.00 32.58 3.11
864 4591 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
980 5073 8.456471 TCTCGCAAGCTTATATATGTATACGTT 58.544 33.333 2.23 0.00 37.18 3.99
1060 5171 0.526662 CTACGCCGTCAACTTCCTCT 59.473 55.000 0.00 0.00 0.00 3.69
1357 5477 3.555324 TCGTGCAGGCCAAGGTCA 61.555 61.111 5.01 0.00 0.00 4.02
1893 6019 6.312529 ACTATTGACCCGTATAGGAATCTGA 58.687 40.000 0.00 0.00 45.00 3.27
1905 6031 1.043816 GAATCTGAGATCAGGGGCGA 58.956 55.000 9.87 0.00 43.91 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.575236 ACAGATCTCGTTCGATTAGCAGTA 59.425 41.667 0.00 0.00 0.00 2.74
74 97 3.584406 CTCTCACAAGAGTAGGTGTGG 57.416 52.381 4.13 0.00 44.29 4.17
114 510 3.754955 TCGCAGTCATTAGAAGTACGTG 58.245 45.455 0.00 0.00 0.00 4.49
126 522 6.683974 AAAATTTACTAGCATCGCAGTCAT 57.316 33.333 0.00 0.00 0.00 3.06
151 552 1.524355 CATCTCGGTTATTCGCAGCAG 59.476 52.381 0.00 0.00 0.00 4.24
263 1319 3.409026 AGAGAAATGACCAGGACACAC 57.591 47.619 0.00 0.00 0.00 3.82
744 4471 4.110482 CAAGTATTTCCGGACGAAGGTAG 58.890 47.826 1.83 0.00 0.00 3.18
756 4483 5.964758 TGCATTTGGATGACAAGTATTTCC 58.035 37.500 0.00 0.00 40.82 3.13
833 4560 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
864 4591 8.136165 ACATCTCAATTCCAGTTATACGTACTC 58.864 37.037 0.00 0.00 0.00 2.59
980 5073 0.950555 CGCCAGCAGCACTCTACAAA 60.951 55.000 0.00 0.00 44.04 2.83
1060 5171 1.629043 GTAGCGATGGGGATGAGGTA 58.371 55.000 0.00 0.00 0.00 3.08
1357 5477 2.826003 GGGACGGGAACACCTTGGT 61.826 63.158 0.00 0.00 36.97 3.67
1657 5777 1.028330 TAGACGTCGGTTCCGAGCAT 61.028 55.000 14.40 3.06 39.22 3.79
1884 6010 1.433121 GCCCCTGATCTCAGATTCCT 58.567 55.000 8.78 0.00 46.59 3.36
1885 6011 0.034616 CGCCCCTGATCTCAGATTCC 59.965 60.000 8.78 0.00 46.59 3.01


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

AutoCloner maintained by Alex Coulton.