miRNA: 3'- -UACA----------UGCAAGGUGGG-----------CCUAa---UUUGUA- -5'
miRNA: 3'- -UACaUGCAa----GGUGGG-----------CCUAAUUUGUa -5'
miRNA: 3'- uaCAUGCaa-GGUGGGCCUAAUUUGua -5'
miRNA: 3'- -UACAUGCAAGGUGGGCCUAAUUUGUA- -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 | |||||||
| 18458 | 3' | -48 | NC_004681.1 | + | 37846 | 0.67 | 0.980948 |
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Target: 5'- gGUGUcgccaucgagGCGUUCCACCCugucaaccuucGGGUcgugGAACAUg -3' miRNA: 3'- -UACA----------UGCAAGGUGGG-----------CCUAa---UUUGUA- -5' |
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| 18458 | 3' | -48 | NC_004681.1 | + | 55924 | 0.69 | 0.949637 |
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Target: 5'- cGUGcGCGUgcccgCCACCCuggaacucaagGGAUUGGACAa -3' miRNA: 3'- -UACaUGCAa----GGUGGG-----------CCUAAUUUGUa -5' |
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| 18458 | 3' | -48 | NC_004681.1 | + | 2516 | 0.69 | 0.934173 |
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Target: 5'- -gGUACGaaaUCGCCUGGAUUGAGCu- -3' miRNA: 3'- uaCAUGCaa-GGUGGGCCUAAUUUGua -5' |
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| 18458 | 3' | -48 | NC_004681.1 | + | 40729 | 1.04 | 0.015453 |
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Target: 5'- cAUGUACGUUCCACCCGGAUUAAACAUu -3' miRNA: 3'- -UACAUGCAAGGUGGGCCUAAUUUGUA- -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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