Multiple sequence alignment - TraesCS6B01G220800

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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 TraesCS6B01G220800 chr6B 100.000 2348 0 0 1 2348 315287173 315289520 0.000000e+00 4337.0
1 TraesCS6B01G220800 chr6B 99.012 1720 16 1 1 1719 337862787 337861068 0.000000e+00 3081.0
2 TraesCS6B01G220800 chr6B 97.437 1717 42 2 2 1716 696190942 696192658 0.000000e+00 2926.0
3 TraesCS6B01G220800 chr6B 95.521 1719 75 2 1 1717 129480558 129478840 0.000000e+00 2747.0
4 TraesCS6B01G220800 chr5A 98.778 1719 20 1 1 1719 706702684 706704401 0.000000e+00 3057.0
5 TraesCS6B01G220800 chr4B 98.519 1688 22 3 37 1723 404767222 404768907 0.000000e+00 2976.0
6 TraesCS6B01G220800 chr5B 97.507 1725 39 2 1 1721 176623033 176624757 0.000000e+00 2944.0
7 TraesCS6B01G220800 chr1B 96.711 1733 46 2 1 1722 660662362 660660630 0.000000e+00 2874.0
8 TraesCS6B01G220800 chr3A 95.113 1719 81 3 1 1717 128070850 128069133 0.000000e+00 2706.0
9 TraesCS6B01G220800 chr3B 93.663 1720 108 1 1 1719 41803929 41802210 0.000000e+00 2571.0
10 TraesCS6B01G220800 chr6D 92.429 634 47 1 1716 2348 216864136 216864769 0.000000e+00 904.0
11 TraesCS6B01G220800 chr6A 91.536 638 49 3 1716 2348 273117871 273117234 0.000000e+00 874.0
12 TraesCS6B01G220800 chr7B 93.333 45 2 1 1978 2022 15305060 15305103 5.420000e-07 65.8
13 TraesCS6B01G220800 chr4A 94.444 36 2 0 1988 2023 705806359 705806324 3.260000e-04 56.5


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 TraesCS6B01G220800 chr6B 315287173 315289520 2347 False 4337 4337 100.000 1 2348 1 chr6B.!!$F1 2347
1 TraesCS6B01G220800 chr6B 337861068 337862787 1719 True 3081 3081 99.012 1 1719 1 chr6B.!!$R2 1718
2 TraesCS6B01G220800 chr6B 696190942 696192658 1716 False 2926 2926 97.437 2 1716 1 chr6B.!!$F2 1714
3 TraesCS6B01G220800 chr6B 129478840 129480558 1718 True 2747 2747 95.521 1 1717 1 chr6B.!!$R1 1716
4 TraesCS6B01G220800 chr5A 706702684 706704401 1717 False 3057 3057 98.778 1 1719 1 chr5A.!!$F1 1718
5 TraesCS6B01G220800 chr4B 404767222 404768907 1685 False 2976 2976 98.519 37 1723 1 chr4B.!!$F1 1686
6 TraesCS6B01G220800 chr5B 176623033 176624757 1724 False 2944 2944 97.507 1 1721 1 chr5B.!!$F1 1720
7 TraesCS6B01G220800 chr1B 660660630 660662362 1732 True 2874 2874 96.711 1 1722 1 chr1B.!!$R1 1721
8 TraesCS6B01G220800 chr3A 128069133 128070850 1717 True 2706 2706 95.113 1 1717 1 chr3A.!!$R1 1716
9 TraesCS6B01G220800 chr3B 41802210 41803929 1719 True 2571 2571 93.663 1 1719 1 chr3B.!!$R1 1718
10 TraesCS6B01G220800 chr6D 216864136 216864769 633 False 904 904 92.429 1716 2348 1 chr6D.!!$F1 632
11 TraesCS6B01G220800 chr6A 273117234 273117871 637 True 874 874 91.536 1716 2348 1 chr6A.!!$R1 632

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
595 596 0.972471 TGCCTTCTGCCAGAGATCGA 60.972 55.0 0.0 0.0 40.16 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2074 0.319728 TGAGAGGCTCAGAGTGTTGC 59.68 55.0 18.26 0.0 35.39 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
97 98 1.903294 GCTGAGTCTCTGGCCATCA 59.097 57.895 5.51 5.73 0.00 3.07
295 296 2.240921 TCTTCTCTCTCTAGCCTGCTGA 59.759 50.000 0.97 0.00 0.00 4.26
371 372 3.626930 AGATCCAGTCTCGCTTCTACTT 58.373 45.455 0.00 0.00 28.45 2.24
595 596 0.972471 TGCCTTCTGCCAGAGATCGA 60.972 55.000 0.00 0.00 40.16 3.59
723 724 2.539081 GGCTGGTGACTCCCCCTTT 61.539 63.158 0.00 0.00 34.77 3.11
725 726 2.069165 GCTGGTGACTCCCCCTTTGT 62.069 60.000 0.00 0.00 34.77 2.83
1542 1545 0.679960 GCCCGATTAGCCACCTTGTT 60.680 55.000 0.00 0.00 0.00 2.83
1554 1557 0.466555 ACCTTGTTTTGGGTGCGCTA 60.467 50.000 9.73 0.00 34.16 4.26
1917 1931 6.884280 AGAATTCAGGAACTCGATTGTTTT 57.116 33.333 8.44 0.00 34.60 2.43
2085 2104 1.522580 GCCTCTCAGCCGTTGGATC 60.523 63.158 0.00 0.00 0.00 3.36
2146 2165 4.292208 CGCACGCGCTTCACACAA 62.292 61.111 5.73 0.00 35.30 3.33
2148 2167 2.076628 GCACGCGCTTCACACAATG 61.077 57.895 5.73 0.00 34.30 2.82
2153 2172 1.838913 GCGCTTCACACAATGTTTGT 58.161 45.000 0.00 0.00 46.75 2.83
2199 2218 2.352388 TCCGGCTTTTGTCCTTAATCG 58.648 47.619 0.00 0.00 0.00 3.34
2259 2278 6.149807 GGACCTGAAATGGTAATTAACGTTCA 59.850 38.462 2.82 12.38 41.00 3.18
2272 2291 9.053135 GTAATTAACGTTCATCAATTGCGTTTA 57.947 29.630 20.51 14.53 42.03 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
371 372 1.748244 GCTTATCATGCTCACCAGCCA 60.748 52.381 0.00 0.00 46.26 4.75
595 596 3.710722 CCAGAACTGGGAGCCGCT 61.711 66.667 12.54 0.00 46.81 5.52
1542 1545 0.893270 AACAGCATAGCGCACCCAAA 60.893 50.000 11.47 0.00 46.13 3.28
1554 1557 5.841957 AAAGAAGAGAACAACAACAGCAT 57.158 34.783 0.00 0.00 0.00 3.79
1750 1764 8.840200 AGAGAGTAGTTGGAAGGATACAATAA 57.160 34.615 0.00 0.00 41.41 1.40
1796 1810 8.306761 CCATAGGAGTTTGCTTACTTTTTGATT 58.693 33.333 0.00 0.00 0.00 2.57
1866 1880 8.576442 ACGATTTGGATTAATTTGTCTGTCTTT 58.424 29.630 0.00 0.00 0.00 2.52
1868 1882 7.687941 ACGATTTGGATTAATTTGTCTGTCT 57.312 32.000 0.00 0.00 0.00 3.41
1903 1917 5.342259 GCACAATGGTAAAACAATCGAGTTC 59.658 40.000 0.00 0.00 0.00 3.01
1917 1931 1.077625 GGTTGGGGGCACAATGGTA 59.922 57.895 0.00 0.00 32.24 3.25
2051 2070 1.301716 GGCTCAGAGTGTTGCGGAA 60.302 57.895 0.00 0.00 0.00 4.30
2055 2074 0.319728 TGAGAGGCTCAGAGTGTTGC 59.680 55.000 18.26 0.00 35.39 4.17
2085 2104 5.452777 TGATCTAGATCATACGTTTGAGCG 58.547 41.667 27.93 5.86 42.42 5.03
2097 2116 6.975197 GTGACGACAAGATTTGATCTAGATCA 59.025 38.462 27.93 27.93 45.30 2.92
2118 2137 4.196826 GCGTGCGCGATCTGTGAC 62.197 66.667 26.19 0.00 41.33 3.67
2139 2158 2.235016 GGCCCTACAAACATTGTGTGA 58.765 47.619 13.95 0.00 45.03 3.58
2146 2165 2.046285 GCAGCGGCCCTACAAACAT 61.046 57.895 0.00 0.00 0.00 2.71
2148 2167 2.359975 AGCAGCGGCCCTACAAAC 60.360 61.111 4.82 0.00 42.56 2.93
2153 2172 2.043349 TGTAGAGCAGCGGCCCTA 60.043 61.111 4.82 0.00 42.56 3.53
2181 2200 1.400494 CCCGATTAAGGACAAAAGCCG 59.600 52.381 0.00 0.00 0.00 5.52
2259 2278 3.443329 TCTGCACCATAAACGCAATTGAT 59.557 39.130 10.34 0.00 34.75 2.57
2272 2291 3.379372 GCTGTGTAAATCATCTGCACCAT 59.621 43.478 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.