miRNA: 3'- -UCGGa---CGCCGGGCg------AGAGCC-------------CCGCUC- -5'
miRNA: 3'- -UCGGaC-GCCG---GGCGaGAGCC-CCGCUC- -5'
miRNA: 3'- -UCGGAc----GCCGGGCGAGAG------CCCCGCuc -5'
miRNA: 3'- -UCGGACGCCGGGCGAGAGCCCCGCUC- -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 | |||||||
| 22080 | 3' | -65.6 | NC_004927.1 | + | 64306 | 0.66 | 0.321247 |
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Target: 5'- cGGUUgggaGCGGCCCGacuacuaUCUCGGaguggacuacgacGGCGAGc -3' miRNA: 3'- -UCGGa---CGCCGGGCg------AGAGCC-------------CCGCUC- -5' |
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| 22080 | 3' | -65.6 | NC_004927.1 | + | 33845 | 0.66 | 0.293979 |
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Target: 5'- gGGUCgGuCGGCaucCCGUaCUCGGcGGCGAGg -3' miRNA: 3'- -UCGGaC-GCCG---GGCGaGAGCC-CCGCUC- -5' |
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| 22080 | 3' | -65.6 | NC_004927.1 | + | 46179 | 0.71 | 0.137986 |
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Target: 5'- gGGCCUcucacCGGCUCGCUCUCgaacguGGGGCGu- -3' miRNA: 3'- -UCGGAc----GCCGGGCGAGAG------CCCCGCuc -5' |
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| 22080 | 3' | -65.6 | NC_004927.1 | + | 54034 | 1.08 | 0.000192 |
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Target: 5'- cAGCCUGCGGCCCGCUCUCGGGGCGAGg -3' miRNA: 3'- -UCGGACGCCGGGCGAGAGCCCCGCUC- -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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