miRNA: 3'- cuaGGGA----CUCGGcUAGAAGGGa---CUUG- -5'
miRNA: 3'- -CUAGGg-ACUCGGCU--AGAa-GGGACUUg -5'
miRNA: 3'- cuagGGACUCGGcUAGaAGGGACUug -5'
miRNA: 3'- -CUAGGGACUCGGCUAGAAGGGACUUG- -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 | |||||||
| 21874 | 5' | -53.9 | NC_004902.1 | + | 1343 | 0.66 | 0.706843 |
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Target: 5'- --gCCCUuuucGAGCCuGUCUUCCCaaucGGGCa -3' miRNA: 3'- cuaGGGA----CUCGGcUAGAAGGGa---CUUG- -5' |
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| 21874 | 5' | -53.9 | NC_004902.1 | + | 25153 | 0.68 | 0.593551 |
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Target: 5'- aGGUCCagUGAGCCGGguUCUggCCUUGGAa -3' miRNA: 3'- -CUAGGg-ACUCGGCU--AGAa-GGGACUUg -5' |
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| 21874 | 5' | -53.9 | NC_004902.1 | + | 40809 | 0.68 | 0.58224 |
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Target: 5'- ---aCCUGAGCC-AUC-UCCCUGAc- -3' miRNA: 3'- cuagGGACUCGGcUAGaAGGGACUug -5' |
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| 21874 | 5' | -53.9 | NC_004902.1 | + | 1307 | 1.1 | 0.000773 |
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Target: 5'- uGAUCCCUGAGCCGAUCUUCCCUGAACa -3' miRNA: 3'- -CUAGGGACUCGGCUAGAAGGGACUUG- -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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