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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 27731 | 3' | -39.7 | NC_005884.1 | + | 1368 | 0.66 | 0.999997 |
|
Target: 5'- -gUCCUGACUGGuccuaAUCAGGGUa----- -3' miRNA: 3'- ugAGGAUUGAUC-----UAGUUUCAauuaau -5' |
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| 27731 | 3' | -39.7 | NC_005884.1 | + | 1897 | 1.09 | 0.032993 |
|
Target: 5'- aACUCCUAACUAGAUCAAAGUUAAUUAa -3' miRNA: 3'- -UGAGGAUUGAUCUAGUUUCAAUUAAU- -5' |
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| 27731 | 3' | -39.7 | NC_005884.1 | + | 2003 | 0.75 | 0.974519 |
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Target: 5'- gACUUCUAACUAGGUCAGacuagaaugaccGGUgUAGUUAa -3' miRNA: 3'- -UGAGGAUUGAUCUAGUU------------UCA-AUUAAU- -5' |
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| 27731 | 3' | -39.7 | NC_005884.1 | + | 13112 | 0.66 | 0.999999 |
|
Target: 5'- cACUCCU--CUAGAUCcAGGUcAAUUc -3' miRNA: 3'- -UGAGGAuuGAUCUAGuUUCAaUUAAu -5' |
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| 27731 | 3' | -39.7 | NC_005884.1 | + | 34463 | 0.69 | 0.999842 |
|
Target: 5'- aACUCCUAACUacaaauacucAGAUCAGgugauaGGUUAu--- -3' miRNA: 3'- -UGAGGAUUGA----------UCUAGUU------UCAAUuaau -5' |
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| 27731 | 3' | -39.7 | NC_005884.1 | + | 39868 | 0.73 | 0.992148 |
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Target: 5'- -aUCCc--CUAGAUCAAAGUUAGUa- -3' miRNA: 3'- ugAGGauuGAUCUAGUUUCAAUUAau -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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