miRNA: 3'- -UCgAGUaGUGCCAC-CAGU---------AGCUGGgC- -5'
miRNA: 3'- uCGAgUAGuGCCACC--AGUAGCuGGGC- -5'
miRNA: 3'- uCGAGUAGUGCCAccAGUa---GCUGGGC- -5'
miRNA: 3'- -UCGAGU--AgUGCCACCa-GUAGcUGGGC- -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 | |||||||
| 22104 | 3' | -55.4 | NC_004927.1 | + | 46225 | 0.66 | 0.803475 |
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Target: 5'- gAGgUCG-CGCGGUGcGUCAugcgauacaUCGACCgGa -3' miRNA: 3'- -UCgAGUaGUGCCAC-CAGU---------AGCUGGgC- -5' |
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| 22104 | 3' | -55.4 | NC_004927.1 | + | 15094 | 0.66 | 0.78454 |
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Target: 5'- uGCU-AUCuCGGUGGacUCGUCG-CCCGu -3' miRNA: 3'- uCGAgUAGuGCCACC--AGUAGCuGGGC- -5' |
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| 22104 | 3' | -55.4 | NC_004927.1 | + | 36459 | 0.69 | 0.629185 |
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Target: 5'- cGUUCGUCACGGU--UCGaccaCGGCCCGa -3' miRNA: 3'- uCGAGUAGUGCCAccAGUa---GCUGGGC- -5' |
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| 22104 | 3' | -55.4 | NC_004927.1 | + | 35048 | 0.69 | 0.629185 |
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Target: 5'- aAGCUCAugUgACGGUGGcgCGUC-ACCUGa -3' miRNA: 3'- -UCGAGU--AgUGCCACCa-GUAGcUGGGC- -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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