miRNA: 3'- -GAGUg-CGc--UGAGuGgGUGGACGGCCU- -5'
miRNA: 3'- gAGUG----CGCUGAGUgG-GUGGACGGCCu -5'
miRNA: 3'- -GAGuGCGCU---GAGUGGGuGGa--CGGCCu -5'
miRNA: 3'- -GAGUGCGCUGAGUGGGUGGACGGCCU- -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 | |||||||
| 9489 | 3' | -59.3 | NC_002531.1 | + | 122986 | 0.66 | 0.755042 |
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Target: 5'- gCUCAagGCcauGCUC-CgCGCCUGCCGGGc -3' miRNA: 3'- -GAGUg-CGc--UGAGuGgGUGGACGGCCU- -5' |
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| 9489 | 3' | -59.3 | NC_002531.1 | + | 54412 | 0.66 | 0.735967 |
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Target: 5'- uUCACuaggGCGGUUCGgCgCGCCUGCCGGu -3' miRNA: 3'- gAGUG----CGCUGAGUgG-GUGGACGGCCu -5' |
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| 9489 | 3' | -59.3 | NC_002531.1 | + | 36178 | 0.71 | 0.470413 |
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Target: 5'- uCUCuCGCGAaccCUCGCCC-CCgugGCCGGc -3' miRNA: 3'- -GAGuGCGCU---GAGUGGGuGGa--CGGCCu -5' |
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| 9489 | 3' | -59.3 | NC_002531.1 | + | 57089 | 1.09 | 0.001338 |
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Target: 5'- cCUCACGCGACUCACCCACCUGCCGGAg -3' miRNA: 3'- -GAGUGCGCUGAGUGGGUGGACGGCCU- -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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