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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 | |||||||
| 2288 | 5' | -63.4 | NC_001407.1 | + | 3208 | 0.66 | 0.076878 |
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Target: 5'- cCCGUaGGCCUGGuagcagaaCCCagGAuaGCCACCUuGUg -3' miRNA: 3'- -GGCA-CCGGGCC--------GGGa-CU--CGGUGGA-CG- -5' |
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| 2288 | 5' | -63.4 | NC_001407.1 | + | 2096 | 0.66 | 0.074529 |
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Target: 5'- gCCG-GGCCaCGGCCCcgaagaGAGaCCuuuuCCUGg -3' miRNA: 3'- -GGCaCCGG-GCCGGGa-----CUC-GGu---GGACg -5' |
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| 2288 | 5' | -63.4 | NC_001407.1 | + | 7300 | 0.68 | 0.04375 |
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Target: 5'- uCgGUGGCCaCGGuCCCgaagGAGCgGCUgggguUGCg -3' miRNA: 3'- -GgCACCGG-GCC-GGGa---CUCGgUGG-----ACG- -5' |
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| 2288 | 5' | -63.4 | NC_001407.1 | + | 1043 | 0.69 | 0.04239 |
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Target: 5'- ---aGGgCCGGCCCagGAGCCugACCcGCa -3' miRNA: 3'- ggcaCCgGGCCGGGa-CUCGG--UGGaCG- -5' |
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| 2288 | 5' | -63.4 | NC_001407.1 | + | 2075 | 1.11 | 0.000008 |
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Target: 5'- gCCGUGGCCCGGCCCUGAGCCACCUGCc -3' miRNA: 3'- -GGCACCGGGCCGGGACUCGGUGGACG- -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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