miRNA: 3'- -AGAAGGGCUGaCCG-GUaaAGGA-----------AGAG- -5'
miRNA: 3'- agaaGGGCUGa-------CCGGU--AAAGGAAGAg -5'
miRNA: 3'- -AGAAGGGCUGACCGGUAAAGGAAGAG- -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 | |||||||
| 648 | 3' | -51.9 | AC_000017.1 | + | 8037 | 0.68 | 0.625392 |
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Target: 5'- uUCUUCCCGAUcGGCuCGcaUCCUcgcaccgagcgUCUCu -3' miRNA: 3'- -AGAAGGGCUGaCCG-GUaaAGGA-----------AGAG- -5' |
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| 648 | 3' | -51.9 | AC_000017.1 | + | 31593 | 0.7 | 0.532943 |
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Target: 5'- ---gCCCGAUguuugcagGGCCAgcUUUCCUUCUg -3' miRNA: 3'- agaaGGGCUGa-------CCGGU--AAAGGAAGAg -5' |
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| 648 | 3' | -51.9 | AC_000017.1 | + | 24048 | 1.1 | 0.001086 |
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Target: 5'- cUCUUCCCGACUGGCCAUUUCCUUCUCc -3' miRNA: 3'- -AGAAGGGCUGACCGGUAAAGGAAGAG- -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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