miRNA: 3'- -GUGCAAAGGAGaAGGUAGAAgag-UGU- -5'
miRNA: 3'- gUGCAAaGGAGAAGGU-------------AGAAgAGUGU- -5'
miRNA: 3'- -GUGCAa-------AGGAGAAgguAGAAGAGUGU- -5'
miRNA: 3'- -GUGCAAAGGAGAAGGUAGAAGAGUGU- -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 | |||||||
| 14922 | 3' | -47.6 | NC_003663.2 | + | 105752 | 0.66 | 0.999965 |
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Target: 5'- uUACGUUUCUUCgUCCGUCUUgaagGCAa -3' miRNA: 3'- -GUGCAAAGGAGaAGGUAGAAgag-UGU- -5' |
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| 14922 | 3' | -47.6 | NC_003663.2 | + | 186700 | 0.67 | 0.999819 |
|
Target: 5'- gGCGUUaCUUCUUCCAuacacaauaaaucUCUUgUCAUAa -3' miRNA: 3'- gUGCAAaGGAGAAGGU-------------AGAAgAGUGU- -5' |
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| 14922 | 3' | -47.6 | NC_003663.2 | + | 183326 | 0.7 | 0.996321 |
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Target: 5'- aCGCGUacuugaugUCCUCUU---UCUUCUCACAg -3' miRNA: 3'- -GUGCAa-------AGGAGAAgguAGAAGAGUGU- -5' |
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| 14922 | 3' | -47.6 | NC_003663.2 | + | 188743 | 1.1 | 0.025121 |
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Target: 5'- cCACGUUUCCUCUUCCAUCUUCUCACAu -3' miRNA: 3'- -GUGCAAAGGAGAAGGUAGAAGAGUGU- -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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