miRNA: 3'- cuGACCGGCGCGa-GUC-AAGUuaUCGC- -5'
miRNA: 3'- cUGACCGGCGCGAguCA------AGU---------------UAUCGc -5'
miRNA: 3'- cUGACCGGc--GCGAGUCAAGUUa-UCGC- -5'
miRNA: 3'- -CUGACCGGCGCGAGUCAAGUUAUCGC- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 31935 | 5' | -53.8 | NC_006940.1 | + | 19706 | 0.67 | 0.621429 |
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Target: 5'- -gUUGGCCGCGCgaCGGcUUCG--AGCGa -3' miRNA: 3'- cuGACCGGCGCGa-GUC-AAGUuaUCGC- -5' |
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| 31935 | 5' | -53.8 | NC_006940.1 | + | 25014 | 0.68 | 0.591668 |
|
Target: 5'- cACUGGCCGCGCUguGUgagguuUUAaacauugacgcaagcAUGGCu -3' miRNA: 3'- cUGACCGGCGCGAguCA------AGU---------------UAUCGc -5' |
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| 31935 | 5' | -53.8 | NC_006940.1 | + | 7884 | 0.71 | 0.377479 |
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Target: 5'- aACUGGCUuuuCGCUUAGUUCAAgaGGCGc -3' miRNA: 3'- cUGACCGGc--GCGAGUCAAGUUa-UCGC- -5' |
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| 31935 | 5' | -53.8 | NC_006940.1 | + | 647 | 1.08 | 0.000954 |
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Target: 5'- uGACUGGCCGCGCUCAGUUCAAUAGCGu -3' miRNA: 3'- -CUGACCGGCGCGAGUCAAGUUAUCGC- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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