miRNA: 3'- aGUGg----GCGUCGCUGCUGCUc--UAGa--CU- -5'
miRNA: 3'- agUGGGCGUCgCUgCUGCUCUAGAcu -5'
miRNA: 3'- aGUGGGcGUCGC-UGCUGCUCUa---GACU- -5'
miRNA: 3'- -AGUGGGCGUCGCUGCUGCUCUAGACU- -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 | |||||||
| 6216 | 3' | -55.5 | NC_001844.1 | + | 122069 | 0.66 | 0.908738 |
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Target: 5'- aCGCagguaCGCGGCGGCGGCGGcguGUCgggGAa -3' miRNA: 3'- aGUGg----GCGUCGCUGCUGCUc--UAGa--CU- -5' |
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| 6216 | 3' | -55.5 | NC_001844.1 | + | 97132 | 0.68 | 0.84494 |
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Target: 5'- -uGCCCGCGGaGA-GACGGGGUCUc- -3' miRNA: 3'- agUGGGCGUCgCUgCUGCUCUAGAcu -5' |
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| 6216 | 3' | -55.5 | NC_001844.1 | + | 138716 | 0.71 | 0.707185 |
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Target: 5'- gCACCC-CAGCGuAUGGCGAGAguggUUGGg -3' miRNA: 3'- aGUGGGcGUCGC-UGCUGCUCUa---GACU- -5' |
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| 6216 | 3' | -55.5 | NC_001844.1 | + | 77840 | 1.09 | 0.003105 |
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Target: 5'- cUCACCCGCAGCGACGACGAGAUCUGAg -3' miRNA: 3'- -AGUGGGCGUCGCUGCUGCUCUAGACU- -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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