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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 | |||||||
| 28561 | 3' | -54 | NC_005946.1 | + | 51512 | 0.66 | 0.901206 |
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Target: 5'- cCAUCaGUUaaUGCUCcaGCACCG-GCAGUg -3' miRNA: 3'- -GUAG-CAG--ACGAGucUGUGGCuCGUCG- -5' |
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| 28561 | 3' | -54 | NC_005946.1 | + | 33852 | 0.68 | 0.840555 |
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Target: 5'- cCGUCGUa--CUCGGACACUGucucGCAGUu -3' miRNA: 3'- -GUAGCAgacGAGUCUGUGGCu---CGUCG- -5' |
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| 28561 | 3' | -54 | NC_005946.1 | + | 20895 | 0.69 | 0.776685 |
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Target: 5'- --cUGUCgGcCUCAGACGCCcugGAGCAGg -3' miRNA: 3'- guaGCAGaC-GAGUCUGUGG---CUCGUCg -5' |
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| 28561 | 3' | -54 | NC_005946.1 | + | 672 | 0.69 | 0.766921 |
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Target: 5'- --gCGUCUuuaaaCUUGGACACCcAGCAGCa -3' miRNA: 3'- guaGCAGAc----GAGUCUGUGGcUCGUCG- -5' |
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| 28561 | 3' | -54 | NC_005946.1 | + | 22812 | 0.7 | 0.704934 |
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Target: 5'- gAUCGUucCUGCUCAGAggagaacccguCACCGGGUuccuggugggaucGGCa -3' miRNA: 3'- gUAGCA--GACGAGUCU-----------GUGGCUCG-------------UCG- -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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