miRNA: 3'- gcaCGUUAGCUGCau--UGGCuACAGCU- -5'
miRNA: 3'- -GCACGuuaGCUGCAU------------UGGCUa---CAGCU- -5'
miRNA: 3'- -GCaCGUuAGCUGCAUUGGCua------CAGCU- -5'
miRNA: 3'- gcaCGUUAGCUGCAUUGGCU-----ACaGCU- -5'
miRNA: 3'- -GCACGUUAGCUGCAUUGGCUACAGCU- -5'
Results 21 - 25 of 25 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 | |||||||
| 28022 | 3' | -48.9 | NC_005887.1 | + | 18630 | 0.71 | 0.740341 |
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Target: 5'- --cGCGAUCGGCGgcccGCUGcUGUCGAc -3' miRNA: 3'- gcaCGUUAGCUGCau--UGGCuACAGCU- -5' |
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| 28022 | 3' | -48.9 | NC_005887.1 | + | 41388 | 0.74 | 0.603265 |
|
Target: 5'- cCGUGCg--CGACGUGuucuccgacgauGCCGAgcagGUCGAa -3' miRNA: 3'- -GCACGuuaGCUGCAU------------UGGCUa---CAGCU- -5' |
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| 28022 | 3' | -48.9 | NC_005887.1 | + | 12243 | 0.74 | 0.580261 |
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Target: 5'- aCGgGCGuUCGGCGUAGCCGucgaagcgGUCGAc -3' miRNA: 3'- -GCaCGUuAGCUGCAUUGGCua------CAGCU- -5' |
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| 28022 | 3' | -48.9 | NC_005887.1 | + | 15027 | 0.77 | 0.41819 |
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Target: 5'- --cGCAGUCGACGUGGCCGGacgagUG-CGAg -3' miRNA: 3'- gcaCGUUAGCUGCAUUGGCU-----ACaGCU- -5' |
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| 28022 | 3' | -48.9 | NC_005887.1 | + | 28177 | 1.1 | 0.003527 |
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Target: 5'- gCGUGCAAUCGACGUAACCGAUGUCGAc -3' miRNA: 3'- -GCACGUUAGCUGCAUUGGCUACAGCU- -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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