miRNA: 3'- uUUGAGa------CAUCUau--CCGUCUCG----AGGc -5'
miRNA: 3'- uuUGAGA-CA-----UCUAUCCgUCUCGAGGc -5'
miRNA: 3'- uuUGAGa-CAUCUAUCCGUcUCGAGGc -5'
miRNA: 3'- -UUUGAGACAUCUAUCCGUCUCGAGGC- -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 | |||||||
| 9513 | 3' | -51.5 | NC_002531.1 | + | 13314 | 0.66 | 0.968738 |
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Target: 5'- uGACUCguagacgGUAGAgauuGGCAGGGCuaugUCCu -3' miRNA: 3'- uUUGAGa------CAUCUau--CCGUCUCG----AGGc -5' |
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| 9513 | 3' | -51.5 | NC_002531.1 | + | 4349 | 0.72 | 0.780551 |
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Target: 5'- -uGCUCUaGUgaucaAGGUGGGgAGAGCUCCc -3' miRNA: 3'- uuUGAGA-CA-----UCUAUCCgUCUCGAGGc -5' |
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| 9513 | 3' | -51.5 | NC_002531.1 | + | 83124 | 0.76 | 0.547218 |
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Target: 5'- -cGCUCcgGUAGAUGGGUAuAGCUCCa -3' miRNA: 3'- uuUGAGa-CAUCUAUCCGUcUCGAGGc -5' |
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| 9513 | 3' | -51.5 | NC_002531.1 | + | 122409 | 1.06 | 0.008139 |
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Target: 5'- cAAACUCUGUAGAUAGGCAGAGCUCCGc -3' miRNA: 3'- -UUUGAGACAUCUAUCCGUCUCGAGGC- -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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