miRNA: 3'- -GAGUcGUCGauAGGACUCGAA---------UCCGU- -5'
miRNA: 3'- -GAGUCG---------------UCGA--------------UAGGAC-UCGAAUCCGu -5'
miRNA: 3'- -GAGUCGUCGA-UAgGACUCGaau-CCGu -5'
miRNA: 3'- -GAGUCGUCGAUAGGACUCGAAUCCGU- -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 | |||||||
| 15400 | 3' | -53.1 | NC_003907.2 | + | 17848 | 0.69 | 0.541009 |
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Target: 5'- uCUCA-CAGC--UCCUGAGCUUcuucgugcgAGGCGa -3' miRNA: 3'- -GAGUcGUCGauAGGACUCGAA---------UCCGU- -5' |
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| 15400 | 3' | -53.1 | NC_003907.2 | + | 22702 | 0.7 | 0.497803 |
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Target: 5'- cCUCAGCgaaucgacgcuguucGGCUguuaacuuaggcacGUCCUGuAGCUUAGGUu -3' miRNA: 3'- -GAGUCG---------------UCGA--------------UAGGAC-UCGAAUCCGu -5' |
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| 15400 | 3' | -53.1 | NC_003907.2 | + | 7955 | 0.72 | 0.357181 |
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Target: 5'- aCUCGGCGGCUaAUgCUGAGCcuuuGGCu -3' miRNA: 3'- -GAGUCGUCGA-UAgGACUCGaau-CCGu -5' |
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| 15400 | 3' | -53.1 | NC_003907.2 | + | 34849 | 1.09 | 0.000924 |
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Target: 5'- aCUCAGCAGCUAUCCUGAGCUUAGGCAu -3' miRNA: 3'- -GAGUCGUCGAUAGGACUCGAAUCCGU- -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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