miRNA: 3'- cagCGCGCCuUGUUGUCC---UGCGUuau -5'
miRNA: 3'- caGCGCG--CCUUGUU----------GUCCUGCGUuau -5'
miRNA: 3'- caGCGCGCCUUGUUgu--CCUGCGUUAU- -5'
miRNA: 3'- -CAGCGCGCCUUGUUGUCCUGCGUUAU- -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 | |||||||
| 23522 | 3' | -52.8 | NC_005260.1 | + | 115123 | 0.66 | 0.992093 |
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Target: 5'- --gGUGUGGcGCAACAGGauaGCGCAu-- -3' miRNA: 3'- cagCGCGCCuUGUUGUCC---UGCGUuau -5' |
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| 23522 | 3' | -52.8 | NC_005260.1 | + | 146998 | 0.66 | 0.988332 |
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Target: 5'- -aCGCGCuaGGAGCGAauucccagauCAGGGCGUAu-- -3' miRNA: 3'- caGCGCG--CCUUGUU----------GUCCUGCGUuau -5' |
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| 23522 | 3' | -52.8 | NC_005260.1 | + | 50288 | 0.74 | 0.766806 |
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Target: 5'- -gUGUGUGGAACGAaauuGGACGCGAUGc -3' miRNA: 3'- caGCGCGCCUUGUUgu--CCUGCGUUAU- -5' |
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| 23522 | 3' | -52.8 | NC_005260.1 | + | 134617 | 1.07 | 0.010029 |
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Target: 5'- cGUCGCGCGGAACAACAGGACGCAAUAg -3' miRNA: 3'- -CAGCGCGCCUUGUUGUCCUGCGUUAU- -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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