miRNA: 3'- uuGCGCU-GCUAGCCCU---GCUAa--------UGGCC- -5'
miRNA: 3'- -UUGCGCUG-CUa------GCCCUGCUAa-----------UGGCC- -5'
miRNA: 3'- -UUGCGCUGCU---------------AGCCCUGCUa--AUGGCc -5'
miRNA: 3'- -UUGCGCUGCUAGCCCUGCUAAUGGCC- -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 | |||||||
| 27691 | 5' | -53.5 | NC_005882.1 | + | 8162 | 0.71 | 0.423729 |
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Target: 5'- -uCGCGGcCGGUCGGGAuguCGAUgaucagccgACCGGc -3' miRNA: 3'- uuGCGCU-GCUAGCCCU---GCUAa--------UGGCC- -5' |
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| 27691 | 5' | -53.5 | NC_005882.1 | + | 32206 | 0.74 | 0.299676 |
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Target: 5'- cGGCGCGACuGAgcuggcgCGGGACGAUaucgcgccccagGCCGGc -3' miRNA: 3'- -UUGCGCUG-CUa------GCCCUGCUAa-----------UGGCC- -5' |
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| 27691 | 5' | -53.5 | NC_005882.1 | + | 19715 | 0.79 | 0.146333 |
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Target: 5'- aAAUGCGACGAcugcauccuugugcuUCGGGGCGAgcgUGCCGc -3' miRNA: 3'- -UUGCGCUGCU---------------AGCCCUGCUa--AUGGCc -5' |
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| 27691 | 5' | -53.5 | NC_005882.1 | + | 28605 | 1.08 | 0.001373 |
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Target: 5'- gAACGCGACGAUCGGGACGAUUACCGGc -3' miRNA: 3'- -UUGCGCUGCUAGCCCUGCUAAUGGCC- -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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