miRNA: 3'- aCUUCAG-CCUc--AAAGG---CGUGGCUAGc -5'
miRNA: 3'- -ACU---UCAGCCUCAAagg-CGUGGCUAGc -5'
miRNA: 3'- aCUUCAGCCu-------CAAAGGcGUGGCUagc -5'
miRNA: 3'- -ACUUCAGCCUCAAAGGCGUGGCUAGC- -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 | |||||||
| 21020 | 3' | -51.9 | NC_004735.1 | + | 24615 | 0.68 | 0.942342 |
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Target: 5'- gGAAGUCuGGAaucUUUCCaauGCACUGAUCa -3' miRNA: 3'- aCUUCAG-CCUc--AAAGG---CGUGGCUAGc -5' |
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| 21020 | 3' | -51.9 | NC_004735.1 | + | 92653 | 0.68 | 0.942342 |
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Target: 5'- uUGAgcgGGUUGGGGUUgaaaGCGCUGAUCu -3' miRNA: 3'- -ACU---UCAGCCUCAAagg-CGUGGCUAGc -5' |
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| 21020 | 3' | -51.9 | NC_004735.1 | + | 34090 | 0.7 | 0.903168 |
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Target: 5'- gGAAGUCGGcggggguuGUUUCCuCACCGAa-- -3' miRNA: 3'- aCUUCAGCCu-------CAAAGGcGUGGCUagc -5' |
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| 21020 | 3' | -51.9 | NC_004735.1 | + | 89904 | 1.09 | 0.006741 |
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Target: 5'- aUGAAGUCGGAGUUUCCGCACCGAUCGc -3' miRNA: 3'- -ACUUCAGCCUCAAAGGCGUGGCUAGC- -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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