miRNA: 3'- uauuaCAGU------GGCGGgUA---CUGCAUCAC- -5'
miRNA: 3'- uauuaCAGU--GGCGg-GUACUGCAUCAC- -5'
miRNA: 3'- uauuACAGUGGCGGGU--AC-------UGCAuCAC- -5'
miRNA: 3'- uauuaCAGUGGCGGGU---ACUGC-AUCAC- -5'
miRNA: 3'- -UAUUACAGUGGCGGGUACUGCAUCAC- -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 | |||||||
| 12535 | 5' | -50.7 | NC_003345.1 | + | 21428 | 0.66 | 0.959911 |
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Target: 5'- ----gGUCAucacucCCGCCgGUcacGACGUGGUGg -3' miRNA: 3'- uauuaCAGU------GGCGGgUA---CUGCAUCAC- -5' |
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| 12535 | 5' | -50.7 | NC_003345.1 | + | 36608 | 0.66 | 0.941994 |
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Target: 5'- ----cGUCGuuCCGCaaCGUGAUGUAGUGg -3' miRNA: 3'- uauuaCAGU--GGCGg-GUACUGCAUCAC- -5' |
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| 12535 | 5' | -50.7 | NC_003345.1 | + | 50460 | 0.69 | 0.851832 |
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Target: 5'- ---uUGUCACCGCCCGauUGcucaccuGCGUcGUGg -3' miRNA: 3'- uauuACAGUGGCGGGU--AC-------UGCAuCAC- -5' |
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| 12535 | 5' | -50.7 | NC_003345.1 | + | 21749 | 0.79 | 0.349301 |
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Target: 5'- ----cGUCGCCGCCCGaguUGGCGaUAGUGa -3' miRNA: 3'- uauuaCAGUGGCGGGU---ACUGC-AUCAC- -5' |
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| 12535 | 5' | -50.7 | NC_003345.1 | + | 25716 | 1.08 | 0.004841 |
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Target: 5'- gAUAAUGUCACCGCCCAUGACGUAGUGa -3' miRNA: 3'- -UAUUACAGUGGCGGGUACUGCAUCAC- -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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