miRNA: 3'- ccGAGGCCGUaa---GGGCGGUA-CUGCaa -5'
miRNA: 3'- -CCgagGCCGuaaGGGCGGUAC-UGCAa -5'
miRNA: 3'- -CCGAGGCCGuaAGGGC-GGuacuGCAA- -5'
miRNA: 3'- -CCGAGGC-CGU-----AAGG-------------GCGGUACUGCaa -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 | |||||||
| 30669 | 5' | -57.3 | NC_006549.1 | + | 92679 | 0.66 | 0.811585 |
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Target: 5'- -uCUCCGGCAagaccCUCGCCGUaGACGg- -3' miRNA: 3'- ccGAGGCCGUaa---GGGCGGUA-CUGCaa -5' |
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| 30669 | 5' | -57.3 | NC_006549.1 | + | 105296 | 0.67 | 0.802737 |
|
Target: 5'- cGGaaaCGGCuuaCCCGCCAUGcACGUc -3' miRNA: 3'- -CCgagGCCGuaaGGGCGGUAC-UGCAa -5' |
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| 30669 | 5' | -57.3 | NC_006549.1 | + | 121652 | 0.68 | 0.727118 |
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Target: 5'- cGGCUCUGGCcgUCUCGgCCuuauCGUUg -3' miRNA: 3'- -CCGAGGCCGuaAGGGC-GGuacuGCAA- -5' |
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| 30669 | 5' | -57.3 | NC_006549.1 | + | 88723 | 0.68 | 0.706202 |
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Target: 5'- gGGCUCCGcGCGaagccUUCUuuuggccugaaauCGCCGUGGCGa- -3' miRNA: 3'- -CCGAGGC-CGU-----AAGG-------------GCGGUACUGCaa -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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