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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 | |||||||
| 2360 | 3' | -53.3 | NC_001416.1 | + | 16309 | 0.66 | 0.696201 |
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Target: 5'- cCGCuGUAUUGCCgCGUCugcGGGUUAu-- -3' miRNA: 3'- aGCGuCGUAACGG-GCAG---UCCGAUuaa -5' |
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| 2360 | 3' | -53.3 | NC_001416.1 | + | 3785 | 0.66 | 0.696201 |
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Target: 5'- aCGCcGCAgcGCCgGUCcGGCUGGg- -3' miRNA: 3'- aGCGuCGUaaCGGgCAGuCCGAUUaa -5' |
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| 2360 | 3' | -53.3 | NC_001416.1 | + | 46936 | 0.67 | 0.661927 |
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Target: 5'- cCGCAGagaaGUUcCCCGUCAgGGCUGu-- -3' miRNA: 3'- aGCGUCg---UAAcGGGCAGU-CCGAUuaa -5' |
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| 2360 | 3' | -53.3 | NC_001416.1 | + | 4035 | 0.68 | 0.592866 |
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Target: 5'- uUCGUcGCAU--CCCGUCAGGCg---- -3' miRNA: 3'- -AGCGuCGUAacGGGCAGUCCGauuaa -5' |
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| 2360 | 3' | -53.3 | NC_001416.1 | + | 36403 | 0.68 | 0.581421 |
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Target: 5'- cUC-CGGCcucaucuuUUGCCCG-CAGGCUAAUg -3' miRNA: 3'- -AGcGUCGu-------AACGGGCaGUCCGAUUAa -5' |
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| 2360 | 3' | -53.3 | NC_001416.1 | + | 16746 | 0.7 | 0.492259 |
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Target: 5'- aCGCAGgcCAUUGCCCGUUAcGGUcgUAAUg -3' miRNA: 3'- aGCGUC--GUAACGGGCAGU-CCG--AUUAa -5' |
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| 2360 | 3' | -53.3 | NC_001416.1 | + | 30920 | 1.06 | 0.001758 |
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Target: 5'- uUCGCAGCAUUGCCCGUCAGGCUAAUUc -3' miRNA: 3'- -AGCGUCGUAACGGGCAGUCCGAUUAA- -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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