miRNA: 3'- cuaCGGCCcUGUUGGCGGGAAGAaca -5'
miRNA: 3'- cuaCGGCCCUGUuGGCGGga-----AGAACa -5'
miRNA: 3'- cUACGGCCCU---GUUGGCGGGA--------AGA----ACA- -5'
miRNA: 3'- -CUACGGCCCUGUUGGCGGGAAGAACA- -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 | |||||||
| 20823 | 5' | -55.8 | NC_004689.1 | + | 52404 | 0.66 | 0.741256 |
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Target: 5'- --aGCCGGuGCAGCUGCCUUUUUc-- -3' miRNA: 3'- cuaCGGCCcUGUUGGCGGGAAGAaca -5' |
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| 20823 | 5' | -55.8 | NC_004689.1 | + | 58671 | 0.68 | 0.634323 |
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Target: 5'- --aGCCGGGACGcCCGUCgaugaugUCUUGg -3' miRNA: 3'- cuaCGGCCCUGUuGGCGGga-----AGAACa -5' |
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| 20823 | 5' | -55.8 | NC_004689.1 | + | 38942 | 0.71 | 0.455942 |
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Target: 5'- cAUGCCGGGAugcCAGCCGCUCUgauacgcgUCUgcguUGUa -3' miRNA: 3'- cUACGGCCCU---GUUGGCGGGA--------AGA----ACA- -5' |
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| 20823 | 5' | -55.8 | NC_004689.1 | + | 57770 | 1.07 | 0.001554 |
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Target: 5'- cGAUGCCGGGACAACCGCCCUUCUUGUu -3' miRNA: 3'- -CUACGGCCCUGUUGGCGGGAAGAACA- -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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