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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
author bgruening
date Thu, 17 Sep 2015 17:10:07 -0400
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Include kissing hairpins.
Show best local pseudoknots.
Show predicted global structure.

> PKB171 human coronavirus 229E, coronavirus; ribosomal frameshifting; polymerase
CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
Sequence length:  54
Using PKB171 as file identifier

DotKnot is running...
Predicting pseudoknots...
Predicting kissing hairpins...

Detected pseudoknots and kissing hairpins:
1 54 -41.2
CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))


Best 5 pseudoknots and kissing hairpins in terms of energy to length ratio:
1 54 -41.2
CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))
1 46 -26.23
CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGC
((((((((((((...[[[[[)))))))))))).........]]]]]
11 54 -18.12
GUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
(((..((((.....))))....[[[[[[[))).....]]]]]]]
16 37 -7.79
GCUCGACUAGAGCCCUGUAUGG
((((..[[[))))......]]]
11 48 -13.12
GUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAG
(((..((((.....)))).[[[[......)))..]]]]

Best 5 pseudoknots and kissing hairpins in terms of free energy:
1 54 -41.2
CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))
1 46 -26.23
CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGC
((((((((((((...[[[[[)))))))))))).........]]]]]
11 54 -18.12
GUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
(((..((((.....))))....[[[[[[[))).....]]]]]]]
3 54 -16.6
GGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
(((......[[[.((((.....))))))).(((((((.....]]])))))))
2 54 -16.2
GGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
(((...........[[[[[.......)))..(((((((..]]]]].)))))))

Predicted global structure
CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))