miRNA: 3'- cgcagUGUUACCGCGCUCCu------GAUAUu -5'
miRNA: 3'- -CGCAGUguua-CCG-CGCUCCUGauauu -5'
miRNA: 3'- -CGCAg--UGUUACCG-CGCUCCUGauauu -5'
miRNA: 3'- -CGCAGUGUUACCGCGCUCCUGAUAUU- -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 | |||||||
| 16585 | 3' | -51 | NC_004117.1 | + | 147105 | 0.7 | 0.938581 |
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Target: 5'- ----gGCAAUGGCGCGAGGcaaaucuCUGUAu -3' miRNA: 3'- cgcagUGUUACCGCGCUCCu------GAUAUu -5' |
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| 16585 | 3' | -51 | NC_004117.1 | + | 116684 | 0.7 | 0.916641 |
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Target: 5'- cGCGUCAaagugGGCgGCGGGGACa---- -3' miRNA: 3'- -CGCAGUguua-CCG-CGCUCCUGauauu -5' |
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| 16585 | 3' | -51 | NC_004117.1 | + | 144550 | 0.71 | 0.890584 |
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Target: 5'- uGUGUacaAUAAUGGCgGCGAGGACg---- -3' miRNA: 3'- -CGCAg--UGUUACCG-CGCUCCUGauauu -5' |
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| 16585 | 3' | -51 | NC_004117.1 | + | 37732 | 1.09 | 0.008436 |
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Target: 5'- aGCGUCACAAUGGCGCGAGGACUAUAAu -3' miRNA: 3'- -CGCAGUGUUACCGCGCUCCUGAUAUU- -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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