miRNA: 3'- -UGGAGA--UGAAGGA-------GGGGUCUaUAAGG- -5'
miRNA: 3'- uGGAGa----UGAAGG--AGGGGUCuaUAAGG- -5'
miRNA: 3'- -UGGAGA--UG-AAGGAGGGGUCUAUaagg -5'
miRNA: 3'- -UGGAGAUGAAGGAGGGGUCUAUAAGG- -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 | |||||||
| 22196 | 3' | -50.4 | NC_004928.1 | + | 73422 | 0.66 | 0.995017 |
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Target: 5'- uACCUUUuaAUUUCCUcucccugCCCUAGA-AUUCCa -3' miRNA: 3'- -UGGAGA--UGAAGGA-------GGGGUCUaUAAGG- -5' |
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| 22196 | 3' | -50.4 | NC_004928.1 | + | 154061 | 0.67 | 0.994295 |
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Target: 5'- uCUUCauauaGCUUCCacUCCCCGGcaGUUCCa -3' miRNA: 3'- uGGAGa----UGAAGG--AGGGGUCuaUAAGG- -5' |
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| 22196 | 3' | -50.4 | NC_004928.1 | + | 122445 | 0.69 | 0.974263 |
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Target: 5'- uGCCUCUuuACgUUCCUCUUCAGGUAa--- -3' miRNA: 3'- -UGGAGA--UG-AAGGAGGGGUCUAUaagg -5' |
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| 22196 | 3' | -50.4 | NC_004928.1 | + | 99031 | 1.13 | 0.00602 |
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Target: 5'- uACCUCUACUUCCUCCCCAGAUAUUCCa -3' miRNA: 3'- -UGGAGAUGAAGGAGGGGUCUAUAAGG- -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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