miRNA: 3'- aCGCGCgCGGCCAG-------UGCUGAAUaAGU- -5'
miRNA: 3'- -ACgCGCGCGGCCagUGCUGaaUAa---GU- -5'
miRNA: 3'- aCGCG--CGCGgCCAGUGCUGaauaagu -5'
miRNA: 3'- -AC-GCGCGCGGCCAgUGCUGAauaagu -5'
miRNA: 3'- -ACGCGCGCGGCCAGUGCUGAAUAAGU- -5'
Results 1 - 5 of 5 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 | |||||||
| 27350 | 3' | -54.4 | NC_005857.1 | + | 35173 | 0.68 | 0.599478 |
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Target: 5'- cGCGUG-GCCGGUCgcuggcaGCGAUUUG-UCAc -3' miRNA: 3'- aCGCGCgCGGCCAG-------UGCUGAAUaAGU- -5' |
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| 27350 | 3' | -54.4 | NC_005857.1 | + | 1788 | 0.7 | 0.524005 |
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Target: 5'- aUGgGCGCGCUGGaaGCGACggAUggcgCAg -3' miRNA: 3'- -ACgCGCGCGGCCagUGCUGaaUAa---GU- -5' |
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| 27350 | 3' | -54.4 | NC_005857.1 | + | 13104 | 0.7 | 0.492287 |
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Target: 5'- gGCGCagGCGCgGGUCACGAUa------ -3' miRNA: 3'- aCGCG--CGCGgCCAGUGCUGaauaagu -5' |
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| 27350 | 3' | -54.4 | NC_005857.1 | + | 12193 | 0.73 | 0.341247 |
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Target: 5'- cUGaCGCGUGCCGGUgACGGCUc----- -3' miRNA: 3'- -AC-GCGCGCGGCCAgUGCUGAauaagu -5' |
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| 27350 | 3' | -54.4 | NC_005857.1 | + | 26834 | 1.09 | 0.001132 |
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Target: 5'- cUGCGCGCGCCGGUCACGACUUAUUCAa -3' miRNA: 3'- -ACGCGCGCGGCCAGUGCUGAAUAAGU- -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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