miRNA: 3'- uaCGGuaCGca--UGAGCUAuGCgUGUG- -5'
miRNA: 3'- uACGGUACGC-------AUGA-GCUaug---CGUGUG- -5'
miRNA: 3'- -UACgGuaCGCAUG--AGCUau-GCGUGUG- -5'
miRNA: 3'- uaCGGUaCGCa---UGAGCUAUg---CGUGUG- -5'
miRNA: 3'- -UACGGUaCGcaUGA-GCUAUGCGUGUG- -5'
Results 1 - 5 of 5 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 | |||||||
| 20759 | 3' | -52.2 | NC_004688.1 | + | 10571 | 0.66 | 0.953031 |
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Target: 5'- -cGCCcgGCagagGCUCGGU-CGgGCACa -3' miRNA: 3'- uaCGGuaCGca--UGAGCUAuGCgUGUG- -5' |
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| 20759 | 3' | -52.2 | NC_004688.1 | + | 105256 | 0.68 | 0.889356 |
|
Target: 5'- cUGCCGUGCGagugaccUACUaCGAggccaaGCGCGCg -3' miRNA: 3'- uACGGUACGC-------AUGA-GCUaug---CGUGUG- -5' |
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| 20759 | 3' | -52.2 | NC_004688.1 | + | 28751 | 0.68 | 0.88276 |
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Target: 5'- cGUGgUcgGCGUGCcaUCGAggcCGCGCGCa -3' miRNA: 3'- -UACgGuaCGCAUG--AGCUau-GCGUGUG- -5' |
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| 20759 | 3' | -52.2 | NC_004688.1 | + | 5183 | 0.71 | 0.757315 |
|
Target: 5'- -cGCCA-GCGagggGCUCGGUAacggGCACGCg -3' miRNA: 3'- uaCGGUaCGCa---UGAGCUAUg---CGUGUG- -5' |
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| 20759 | 3' | -52.2 | NC_004688.1 | + | 37215 | 0.71 | 0.747077 |
|
Target: 5'- gGUGCCA-GCa-GCUcCGGUAUGCACACu -3' miRNA: 3'- -UACGGUaCGcaUGA-GCUAUGCGUGUG- -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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