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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 | |||||||
| 20780 | 3' | -58.9 | NC_004689.1 | + | 1829 | 0.66 | 0.639736 |
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Target: 5'- gCGGCCUCggcuGCCACCCGUucgGAgGGguacUCGu -3' miRNA: 3'- -GCCGGAG----CGGUGGGCA---CUgCUaa--GGC- -5' |
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| 20780 | 3' | -58.9 | NC_004689.1 | + | 38546 | 0.69 | 0.421365 |
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Target: 5'- aCGGUCUCGUCA-UCGUGGuagccCGGUUCCGc -3' miRNA: 3'- -GCCGGAGCGGUgGGCACU-----GCUAAGGC- -5' |
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| 20780 | 3' | -58.9 | NC_004689.1 | + | 41341 | 0.7 | 0.403645 |
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Target: 5'- cCGGUCUCGCCuGCCUGUGACa------ -3' miRNA: 3'- -GCCGGAGCGG-UGGGCACUGcuaaggc -5' |
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| 20780 | 3' | -58.9 | NC_004689.1 | + | 27301 | 0.7 | 0.374628 |
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Target: 5'- uCGGaaCCUCGCCGaacagaucgagaaCCGUGGCGAUUgCGu -3' miRNA: 3'- -GCC--GGAGCGGUg------------GGCACUGCUAAgGC- -5' |
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| 20780 | 3' | -58.9 | NC_004689.1 | + | 43377 | 0.74 | 0.213676 |
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Target: 5'- gCGGCCUCGUagcaguCGCCCGUGGC--UUCUGg -3' miRNA: 3'- -GCCGGAGCG------GUGGGCACUGcuAAGGC- -5' |
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| 20780 | 3' | -58.9 | NC_004689.1 | + | 20799 | 1.1 | 0.000659 |
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Target: 5'- aCGGCCUCGCCACCCGUGACGAUUCCGg -3' miRNA: 3'- -GCCGGAGCGGUGGGCACUGCUAAGGC- -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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