miRNA: 3'- aCGGCUGGUCGGccaacCGCUGCUuu -5'
miRNA: 3'- aC-GGCUGGUCGgCcaa-------CCGCUGCUUU- -5'
miRNA: 3'- -ACGGcUGGUCG------GCCAACCG------CUGCUUU- -5'
miRNA: 3'- aCGg---CUGGUCGGCCA---ACCGCUgCUUu -5'
miRNA: 3'- -ACGGCUGGUCGGCCA-AC-CGCUgcuuu -5'
Results 1 - 5 of 5 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 | |||||||
| 20881 | 5' | -58.4 | NC_004689.1 | + | 20159 | 0.66 | 0.58014 |
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Target: 5'- cGCCGACCAGUUuccacGCGACGAc- -3' miRNA: 3'- aCGGCUGGUCGGccaacCGCUGCUuu -5' |
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| 20881 | 5' | -58.4 | NC_004689.1 | + | 22228 | 0.67 | 0.546464 |
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Target: 5'- cGaCCGGCCAGCgGacccuucuucGGCGGCGAAGa -3' miRNA: 3'- aC-GGCUGGUCGgCcaa-------CCGCUGCUUU- -5' |
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| 20881 | 5' | -58.4 | NC_004689.1 | + | 11419 | 0.69 | 0.420057 |
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Target: 5'- aUGCCcACCGGCagaacgCGGUUGGCcugaguGGCGAGAu -3' miRNA: 3'- -ACGGcUGGUCG------GCCAACCG------CUGCUUU- -5' |
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| 20881 | 5' | -58.4 | NC_004689.1 | + | 63492 | 0.69 | 0.401917 |
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Target: 5'- cGCaacgGAUCAGCCGGUcguUGGCGA-GAAu -3' miRNA: 3'- aCGg---CUGGUCGGCCA---ACCGCUgCUUu -5' |
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| 20881 | 5' | -58.4 | NC_004689.1 | + | 37170 | 0.73 | 0.249676 |
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Target: 5'- uUGUCGGCCAGCCGGUcUGaGCGAa---- -3' miRNA: 3'- -ACGGCUGGUCGGCCA-AC-CGCUgcuuu -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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