miRNA: 3'- cUG-GGAACUgaAGCGGGUUGAaGCGG- -5'
miRNA: 3'- -CUGggA--ACUGaAGCGGGUu---GAAGCGG- -5'
miRNA: 3'- cUGGGaaCUGAAGCGGGU-----UGA---------AGCGG- -5'
miRNA: 3'- -CUGGGAACUG-AAGCGGGUUGaaGCGg -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 | |||||||
| 22169 | 5' | -53.1 | NC_004927.1 | + | 16063 | 0.67 | 0.858118 |
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Target: 5'- uGCuCCUUGGg-UUGCCUAACUcUGCCg -3' miRNA: 3'- cUG-GGAACUgaAGCGGGUUGAaGCGG- -5' |
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| 22169 | 5' | -53.1 | NC_004927.1 | + | 42485 | 0.67 | 0.858118 |
|
Target: 5'- uGAUuuUugUGACcUCGCCCGucccCUUCGCUa -3' miRNA: 3'- -CUGggA--ACUGaAGCGGGUu---GAAGCGG- -5' |
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| 22169 | 5' | -53.1 | NC_004927.1 | + | 24445 | 0.67 | 0.832412 |
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Target: 5'- cGCCUgcGAUUUCGUCCAguugaGCUaucaucuggUCGCCg -3' miRNA: 3'- cUGGGaaCUGAAGCGGGU-----UGA---------AGCGG- -5' |
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| 22169 | 5' | -53.1 | NC_004927.1 | + | 15239 | 0.81 | 0.184696 |
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Target: 5'- cGACCCUUGACuUUCGCUCGGCggCGUa -3' miRNA: 3'- -CUGGGAACUG-AAGCGGGUUGaaGCGg -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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