miRNA: 3'- gUAGGUCCuuaGCUAaCUGAa-AGAGU- -5'
miRNA: 3'- -GUAGGUCCUUAGCua----ACUGaaa-GAGU- -5'
miRNA: 3'- gUAGGUCCUUAGCUa--ACUGaa------AGAGu -5'
miRNA: 3'- gUAGGUCCU-----------UAGCUAa-----CUGaAAGAGU- -5'
miRNA: 3'- -GUAGGUCCUUAGCUAACUGAAAGAGU- -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 | |||||||
| 31824 | 3' | -45.7 | NC_006938.1 | + | 58670 | 0.66 | 0.998647 |
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Target: 5'- uGUCCAGG---CGGU-GACUggUCUCAc -3' miRNA: 3'- gUAGGUCCuuaGCUAaCUGAa-AGAGU- -5' |
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| 31824 | 3' | -45.7 | NC_006938.1 | + | 55361 | 0.66 | 0.997966 |
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Target: 5'- cUAUCCGGGAGUCGuguagaUGGCaucaCUCGc -3' miRNA: 3'- -GUAGGUCCUUAGCua----ACUGaaa-GAGU- -5' |
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| 31824 | 3' | -45.7 | NC_006938.1 | + | 36165 | 0.7 | 0.972857 |
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Target: 5'- gGUUCGGGAGUCGAgagUGGCgacguagaUCUCc -3' miRNA: 3'- gUAGGUCCUUAGCUa--ACUGaa------AGAGu -5' |
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| 31824 | 3' | -45.7 | NC_006938.1 | + | 12946 | 0.7 | 0.962296 |
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Target: 5'- gGUCCAGGAuuggcccacagGUCGAUgucgucGGCgUUCUCGa -3' miRNA: 3'- gUAGGUCCU-----------UAGCUAa-----CUGaAAGAGU- -5' |
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| 31824 | 3' | -45.7 | NC_006938.1 | + | 20998 | 1.11 | 0.009014 |
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Target: 5'- aCAUCCAGGAAUCGAUUGACUUUCUCAa -3' miRNA: 3'- -GUAGGUCCUUAGCUAACUGAAAGAGU- -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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