miRNA: 3'- ucgGGUCgGUGUUG--UCCGAGGAC-AUG- -5'
miRNA: 3'- ucggGUCGg----UGUu--GUCCGAGGACAUG- -5'
miRNA: 3'- -UCGGGUCGGUGUUGUCCGAGGACAUG- -5'
Results 1 - 3 of 3 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 | |||||||
| 33637 | 3' | -57.2 | NC_007610.1 | + | 22760 | 0.66 | 0.812264 |
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Target: 5'- --gCCAGaCAUAGCuaAGGCUCCUGcUGCu -3' miRNA: 3'- ucgGGUCgGUGUUG--UCCGAGGAC-AUG- -5' |
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| 33637 | 3' | -57.2 | NC_007610.1 | + | 71666 | 0.69 | 0.643889 |
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Target: 5'- ---nCAGCaacaaACGuauCAGGCUCCUGUACa -3' miRNA: 3'- ucggGUCGg----UGUu--GUCCGAGGACAUG- -5' |
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| 33637 | 3' | -57.2 | NC_007610.1 | + | 71641 | 1.1 | 0.00131 |
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Target: 5'- uAGCCCAGCCACAACAGGCUCCUGUACa -3' miRNA: 3'- -UCGGGUCGGUGUUGUCCGAGGACAUG- -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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