miRNA: 3'- -AUAAGGGUUAGUGucUACGACa--------ACCU- -5'
miRNA: 3'- aUAAGGGUUa---GUGUCUACGAca---ACCu -5'
miRNA: 3'- auAAGGGUUAG-UGucuACgACAACCU- -5'
miRNA: 3'- -AUAAGGGUUAGUGUCUACGACAACCU- -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 | |||||||
| 27399 | 5' | -48 | NC_005859.1 | + | 14484 | 0.66 | 0.99838 |
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Target: 5'- uUGUUCCUAGUCGC--GUGCUGauucuuaacUGGAu -3' miRNA: 3'- -AUAAGGGUUAGUGucUACGACa--------ACCU- -5' |
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| 27399 | 5' | -48 | NC_005859.1 | + | 38249 | 0.66 | 0.998037 |
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Target: 5'- cAUUCCCGGcuaaCGCAGGUGCUuucggUGGu -3' miRNA: 3'- aUAAGGGUUa---GUGUCUACGAca---ACCu -5' |
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| 27399 | 5' | -48 | NC_005859.1 | + | 70576 | 0.67 | 0.993517 |
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Target: 5'- -cUUCCCAGUCuGCu--UGgUGUUGGAa -3' miRNA: 3'- auAAGGGUUAG-UGucuACgACAACCU- -5' |
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| 27399 | 5' | -48 | NC_005859.1 | + | 70464 | 1.08 | 0.012943 |
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Target: 5'- gUAUUCCCAAUCACAGAUGCUGUUGGAc -3' miRNA: 3'- -AUAAGGGUUAGUGUCUACGACAACCU- -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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