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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 | |||||||
| 11222 | 3' | -40.7 | NC_003038.1 | + | 99099 | 0.67 | 1 |
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Target: 5'- --cAGUAGG-AUAu-GGUUCUGGAGCa -3' miRNA: 3'- uuuUCAUCUaUAUuuCCAAGGUCUUG- -5' |
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| 11222 | 3' | -40.7 | NC_003038.1 | + | 52719 | 0.67 | 1 |
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Target: 5'- aGAGGGUGGAgagggugGUGGAGGUggCGGAu- -3' miRNA: 3'- -UUUUCAUCUa------UAUUUCCAagGUCUug -5' |
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| 11222 | 3' | -40.7 | NC_003038.1 | + | 14667 | 0.67 | 1 |
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Target: 5'- aAAAAGaaAGAUAUAGAGGUg-CAGAAg -3' miRNA: 3'- -UUUUCa-UCUAUAUUUCCAagGUCUUg -5' |
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| 11222 | 3' | -40.7 | NC_003038.1 | + | 204529 | 0.66 | 1 |
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Target: 5'- uAGAAGUuaccuuuAGAUGUAAAGGUggUCCAu--- -3' miRNA: 3'- -UUUUCA-------UCUAUAUUUCCA--AGGUcuug -5' |
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| 11222 | 3' | -40.7 | NC_003038.1 | + | 144828 | 0.66 | 1 |
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Target: 5'- cGAAGUcaaAGAUAUuAAGGaa-CAGAACa -3' miRNA: 3'- uUUUCA---UCUAUAuUUCCaagGUCUUG- -5' |
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| 11222 | 3' | -40.7 | NC_003038.1 | + | 44671 | 0.84 | 0.953358 |
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Target: 5'- ----uUAGAUAUAAAGGUUCUGGAACc -3' miRNA: 3'- uuuucAUCUAUAUUUCCAAGGUCUUG- -5' |
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| 11222 | 3' | -40.7 | NC_003038.1 | + | 44421 | 1.09 | 0.121007 |
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Target: 5'- aAAAAGUAGAUAUAAAGGUUCCAGAACc -3' miRNA: 3'- -UUUUCAUCUAUAUUUCCAAGGUCUUG- -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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