miRNA: 3'- gaGUUACCu---UCUGCGGa-----ACUGGugCA- -5'
miRNA: 3'- -GAGUu-------ACCUUCUGC-GGaACUGGUGca -5'
miRNA: 3'- gaGUUACCuu--CUGCGGAaCUGGUGCA- -5'
miRNA: 3'- -GAGUUACCUUCUGCGGAACUGGUGCA- -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 | |||||||
| 22461 | 3' | -51.3 | NC_005064.1 | + | 6399 | 0.67 | 0.420624 |
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Target: 5'- -cCAGUGGucagGGACGCUcggccaUGACCugGUc -3' miRNA: 3'- gaGUUACCu---UCUGCGGa-----ACUGGugCA- -5' |
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| 22461 | 3' | -51.3 | NC_005064.1 | + | 3921 | 0.67 | 0.399022 |
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Target: 5'- cCUCGugauggguUGGAAGACGuCCcUGGCCAUu- -3' miRNA: 3'- -GAGUu-------ACCUUCUGC-GGaACUGGUGca -5' |
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| 22461 | 3' | -51.3 | NC_005064.1 | + | 317 | 0.69 | 0.276942 |
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Target: 5'- -gCGGUGGuguuGGCGCCU-GGCUGCGUg -3' miRNA: 3'- gaGUUACCuu--CUGCGGAaCUGGUGCA- -5' |
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| 22461 | 3' | -51.3 | NC_005064.1 | + | 977 | 1.07 | 0.000386 |
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Target: 5'- gCUCAAUGGAAGACGCCUUGACCACGUu -3' miRNA: 3'- -GAGUUACCUUCUGCGGAACUGGUGCA- -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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