miRNA: 3'- -CGcGUUUCGgUCUGUGaaGCCGC---AGG- -5'
miRNA: 3'- cGCGU-UUCGGucu-----GUGAAGCC-GCAGg -5'
miRNA: 3'- -CgCGUuUCG-GUCUGUGaAGCCGca---GG- -5'
miRNA: 3'- -CGCGUUUCGGUCUGUGAAGCCGCAGG- -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 | |||||||
| 22815 | 3' | -53.3 | NC_005132.1 | + | 5450 | 0.66 | 0.245593 |
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Target: 5'- cGC-CAAGGCaGGAUACgcCGGCGacaUCCg -3' miRNA: 3'- -CGcGUUUCGgUCUGUGaaGCCGC---AGG- -5' |
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| 22815 | 3' | -53.3 | NC_005132.1 | + | 1878 | 0.66 | 0.230934 |
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Target: 5'- aCGCAcGAGCCcacgcacuCGCUUCGGaCGUCa -3' miRNA: 3'- cGCGU-UUCGGucu-----GUGAAGCC-GCAGg -5' |
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| 22815 | 3' | -53.3 | NC_005132.1 | + | 394 | 0.67 | 0.217019 |
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Target: 5'- cGgGCA-AGCuCGGACACgUCGGCagaggCCa -3' miRNA: 3'- -CgCGUuUCG-GUCUGUGaAGCCGca---GG- -5' |
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| 22815 | 3' | -53.3 | NC_005132.1 | + | 3589 | 1.13 | 0.000038 |
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Target: 5'- uGCGCAAAGCCAGACACUUCGGCGUCCc -3' miRNA: 3'- -CGCGUUUCGGUCUGUGAAGCCGCAGG- -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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