miRNA: 3'- -UGGGU-CGCUa--CG----------AGCGCUCUUCuaGC- -5'
miRNA: 3'- uGGGUCGCUA-CGagCGCU-CUUCUAGC- -5'
miRNA: 3'- -UGg-GUCGCUaCGAGCGCU-CU-----UCUAGC- -5'
miRNA: 3'- -UGGGUCGCUACGAGCGCUCUUCUAGC- -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 | |||||||
| 5093 | 3' | -54.9 | NC_001793.1 | + | 5396 | 0.67 | 0.140409 |
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Target: 5'- cGCCCAgGUGAaggGCgagcuuuagaUCGCGGGGAGcgCGg -3' miRNA: 3'- -UGGGU-CGCUa--CG----------AGCGCUCUUCuaGC- -5' |
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| 5093 | 3' | -54.9 | NC_001793.1 | + | 184 | 0.7 | 0.082335 |
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Target: 5'- cCCCAGUGAUaGUg-GCGAaGGAGGUCGg -3' miRNA: 3'- uGGGUCGCUA-CGagCGCU-CUUCUAGC- -5' |
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| 5093 | 3' | -54.9 | NC_001793.1 | + | 1621 | 0.71 | 0.0627 |
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Target: 5'- gGCgaCAGCGAgGCUCGCGAcGAcccagGGGUCGa -3' miRNA: 3'- -UGg-GUCGCUaCGAGCGCU-CU-----UCUAGC- -5' |
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| 5093 | 3' | -54.9 | NC_001793.1 | + | 2808 | 1.08 | 0.000051 |
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Target: 5'- gACCCAGCGAUGCUCGCGAGAAGAUCGu -3' miRNA: 3'- -UGGGUCGCUACGAGCGCUCUUCUAGC- -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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