miRNA: 3'- cUUGCGGCcUCUCG--------UAG---CGGUGGGUU- -5'
miRNA: 3'- cuugCGGCCUcUCGUAGCGG--UGGGUU- -5'
miRNA: 3'- cUUGCGGCCUCuCGUagCGG-UGGGUU- -5'
miRNA: 3'- cUUGCGGCcUCUCGUAGCGGUGG-GUU- -5'
miRNA: 3'- -CUUGCGGCCUCUCGUAGCGGUGGGUU- -5'
Results 1 - 5 of 5 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 | |||||||
| 12303 | 5' | -58.6 | NC_003313.1 | + | 20131 | 0.67 | 0.326208 |
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Target: 5'- cAGCGCCGaAGGGCuugccauuGUCaaaGCCGCCCAGc -3' miRNA: 3'- cUUGCGGCcUCUCG--------UAG---CGGUGGGUU- -5' |
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| 12303 | 5' | -58.6 | NC_003313.1 | + | 10062 | 0.72 | 0.136833 |
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Target: 5'- ---aGCUGGAaGGCAUCGCCacACCCGAg -3' miRNA: 3'- cuugCGGCCUcUCGUAGCGG--UGGGUU- -5' |
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| 12303 | 5' | -58.6 | NC_003313.1 | + | 25408 | 0.73 | 0.121963 |
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Target: 5'- aGACGCCGGAGcGCA--GCCaACCCAAu -3' miRNA: 3'- cUUGCGGCCUCuCGUagCGG-UGGGUU- -5' |
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| 12303 | 5' | -58.6 | NC_003313.1 | + | 20853 | 0.78 | 0.047317 |
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Target: 5'- cAACGCCGcAGAGCAUCGCCGCUgCAAa -3' miRNA: 3'- cUUGCGGCcUCUCGUAGCGGUGG-GUU- -5' |
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| 12303 | 5' | -58.6 | NC_003313.1 | + | 30682 | 1.05 | 0.000371 |
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Target: 5'- gGAACGCCGGAGAGCAUCGCCACCCAAu -3' miRNA: 3'- -CUUGCGGCCUCUCGUAGCGGUGGGUU- -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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