miRNA: 3'- uauuaUUUCUAUGG------------UCGAuAGuCCGG- -5'
miRNA: 3'- uAUUAUUUcUA---UGGUCGaUAGUCCGG- -5'
miRNA: 3'- uaUUAUUUCUAUGGUCg--AUAGuc-CGG- -5'
miRNA: 3'- -UAUUAUUUCUAUGGUCGAUAGUCCGG- -5'
Results 1 - 4 of 4 are showing below:
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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 | |||||||
| 8285 | 5' | -44.5 | NC_002032.1 | + | 2538 | 0.66 | 0.885598 |
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Target: 5'- ----gGAAGGUGCCauguuguaguuaAGCUcUCuGGCCc -3' miRNA: 3'- uauuaUUUCUAUGG------------UCGAuAGuCCGG- -5' |
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| 8285 | 5' | -44.5 | NC_002032.1 | + | 8703 | 0.67 | 0.824156 |
|
Target: 5'- uUGAUAGAaGUcaaGCCAGUaGUUAGGCUa -3' miRNA: 3'- uAUUAUUUcUA---UGGUCGaUAGUCCGG- -5' |
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| 8285 | 5' | -44.5 | NC_002032.1 | + | 4061 | 0.73 | 0.499486 |
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Target: 5'- -aGAUGGAGGUACCAGaaaUAUCcauGCCa -3' miRNA: 3'- uaUUAUUUCUAUGGUCg--AUAGuc-CGG- -5' |
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| 8285 | 5' | -44.5 | NC_002032.1 | + | 4050 | 1.13 | 0.000913 |
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Target: 5'- uAUAAUAAAGAUACCAGCUAUCAGGCCa -3' miRNA: 3'- -UAUUAUUUCUAUGGUCGAUAGUCCGG- -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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