miRNA: 3'- aaguACCGGCU-----UGUUGa-GCGGGUCGC- -5'
miRNA: 3'- aaguaCCG-GCU-------------UGUUGAGCGGGUCGc -5'
miRNA: 3'- aAGUaCCGGCU-----UGUUG-AGCGGGUCGc -5'
miRNA: 3'- -AAGUACCGGCUUGUUGAGCGGGUCGC- -5'
Results 21 - 24 of 24 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 | |||||||
| 12017 | 3' | -55.8 | NC_003278.1 | + | 21557 | 0.74 | 0.178624 |
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Target: 5'- ---uUGGCCGAgacguGCAAUcaCGCCCAGCGg -3' miRNA: 3'- aaguACCGGCU-----UGUUGa-GCGGGUCGC- -5' |
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| 12017 | 3' | -55.8 | NC_003278.1 | + | 6344 | 0.74 | 0.173154 |
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Target: 5'- ----aGGCgCGAacgccuaugagcuGCAGCUCGCCCAGCu -3' miRNA: 3'- aaguaCCG-GCU-------------UGUUGAGCGGGUCGc -5' |
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| 12017 | 3' | -55.8 | NC_003278.1 | + | 22441 | 0.74 | 0.159446 |
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Target: 5'- cUCAcGGUCGAcggcaACGACaUCGCCCAGCu -3' miRNA: 3'- aAGUaCCGGCU-----UGUUG-AGCGGGUCGc -5' |
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| 12017 | 3' | -55.8 | NC_003278.1 | + | 27448 | 1.06 | 0.000717 |
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Target: 5'- aUUCAUGGCCGAACAACUCGCCCAGCGc -3' miRNA: 3'- -AAGUACCGGCUUGUUGAGCGGGUCGC- -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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