miRNA: 3'- gUGCC-CGG-CGCUGCCAGa---GCU---UAUGU- -5'
miRNA: 3'- gUGCC-C-GGCGCUGCCAGagcuUAUGU- -5'
miRNA: 3'- -GUGC-CCG---GCGCUGCCAGaGCU-UAUGu -5'
miRNA: 3'- -GUGCCCGGCGCUGCCAGAGCUUAUGU- -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 | |||||||
| 14711 | 3' | -56.1 | NC_003529.1 | + | 78621 | 0.66 | 0.919579 |
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Target: 5'- aACGGcGCCgGCGGCGGUUauuaCGGcaaAUACAc -3' miRNA: 3'- gUGCC-CGG-CGCUGCCAGa---GCU---UAUGU- -5' |
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| 14711 | 3' | -56.1 | NC_003529.1 | + | 100462 | 0.66 | 0.91388 |
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Target: 5'- aGCGGcGaUCGCGACGGUCgc--GUACAc -3' miRNA: 3'- gUGCC-C-GGCGCUGCCAGagcuUAUGU- -5' |
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| 14711 | 3' | -56.1 | NC_003529.1 | + | 137464 | 0.68 | 0.844603 |
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Target: 5'- cCGCGcGGCaaaCGCGACGGUCgCGAcAUAUu -3' miRNA: 3'- -GUGC-CCG---GCGCUGCCAGaGCU-UAUGu -5' |
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| 14711 | 3' | -56.1 | NC_003529.1 | + | 144596 | 1.08 | 0.003892 |
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Target: 5'- uCACGGGCCGCGACGGUCUCGAAUACAu -3' miRNA: 3'- -GUGCCCGGCGCUGCCAGAGCUUAUGU- -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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