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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 | |||||||
| 28456 | 3' | -45.5 | NC_005946.1 | + | 45575 | 0.66 | 0.999849 |
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Target: 5'- aCUUUACCg-CCUGGACC-GCCGu--- -3' miRNA: 3'- -GAAAUGGaaGGGCUUGGuUGGUuuua -5' |
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| 28456 | 3' | -45.5 | NC_005946.1 | + | 99978 | 0.66 | 0.999849 |
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Target: 5'- --aUGCCUUCCUccACCAGCUg---- -3' miRNA: 3'- gaaAUGGAAGGGcuUGGUUGGuuuua -5' |
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| 28456 | 3' | -45.5 | NC_005946.1 | + | 45904 | 0.66 | 0.999802 |
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Target: 5'- ----cCCUUUuuGGGCCGGCCAc--- -3' miRNA: 3'- gaaauGGAAGggCUUGGUUGGUuuua -5' |
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| 28456 | 3' | -45.5 | NC_005946.1 | + | 39051 | 0.66 | 0.999743 |
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Target: 5'- ---gACCUUCagGGACCuGACCAGAGg -3' miRNA: 3'- gaaaUGGAAGggCUUGG-UUGGUUUUa -5' |
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| 28456 | 3' | -45.5 | NC_005946.1 | + | 79247 | 0.68 | 0.998421 |
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Target: 5'- -cUUGCUggcCCCGuacACCAGCCAGGGg -3' miRNA: 3'- gaAAUGGaa-GGGCu--UGGUUGGUUUUa -5' |
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| 28456 | 3' | -45.5 | NC_005946.1 | + | 28351 | 0.71 | 0.986572 |
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Target: 5'- ---aACCcugCCCGGGCUAGCCAGGu- -3' miRNA: 3'- gaaaUGGaa-GGGCUUGGUUGGUUUua -5' |
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| 28456 | 3' | -45.5 | NC_005946.1 | + | 67660 | 0.71 | 0.984683 |
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Target: 5'- ---gGCCaUCCgGAGCCcGCCAAAAa -3' miRNA: 3'- gaaaUGGaAGGgCUUGGuUGGUUUUa -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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