miRNA: 3'- auaAUGGG-------ACCUCCGUUUU----GCuuCGG- -5'
miRNA: 3'- auaaUGGGaCCUC-CGUUUUGCUUCgg -5'
miRNA: 3'- auaaUGGGaCCUCCGUuuuGCuuCGG- -5'
miRNA: 3'- auaAUGGGACCUCCGUUUUGCUUCGG- -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 | |||||||
| 31697 | 5' | -49.2 | NC_006934.1 | + | 1430 | 0.68 | 0.334992 |
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Target: 5'- --gUACCUcaggauaUGGAGGUGGAGgggcUGggGCCg -3' miRNA: 3'- auaAUGGG-------ACCUCCGUUUU----GCuuCGG- -5' |
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| 31697 | 5' | -49.2 | NC_006934.1 | + | 2270 | 0.69 | 0.307205 |
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Target: 5'- ---cGCCCaGGAGaGUAGAGCGGAGa- -3' miRNA: 3'- auaaUGGGaCCUC-CGUUUUGCUUCgg -5' |
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| 31697 | 5' | -49.2 | NC_006934.1 | + | 4043 | 0.7 | 0.255397 |
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Target: 5'- ---gGCUC-GGAGGCAc--CGggGCCa -3' miRNA: 3'- auaaUGGGaCCUCCGUuuuGCuuCGG- -5' |
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| 31697 | 5' | -49.2 | NC_006934.1 | + | 2994 | 1.06 | 0.000432 |
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Target: 5'- --aUACCCUGGAGGCAAAACGAAGCCu -3' miRNA: 3'- auaAUGGGACCUCCGUUUUGCUUCGG- -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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