miRNA: 3'- -CUUGCCGgu---CC----CGGACGGCGgcCACC- -5'
miRNA: 3'- cuugCCGGUCCCGGac-----GGCGGCCa--CC- -5'
miRNA: 3'- cUUGCCGGUCcCGGA-----------CGGCGGCCaCC- -5'
miRNA: 3'- -CUUGCCGGUCCCGGACGGCGGCCACC- -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 | |||||||
| 8861 | 5' | -63.7 | NC_002484.1 | + | 11523 | 0.67 | 0.253541 |
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Target: 5'- aGAGCGGCagcgcGGugauGCCUGCCGCa-GUGGc -3' miRNA: 3'- -CUUGCCGgu---CC----CGGACGGCGgcCACC- -5' |
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| 8861 | 5' | -63.7 | NC_002484.1 | + | 18252 | 0.69 | 0.188035 |
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Target: 5'- ---aGGCCAGGGCCgggaacaUCGCCGGcaaGGg -3' miRNA: 3'- cuugCCGGUCCCGGac-----GGCGGCCa--CC- -5' |
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| 8861 | 5' | -63.7 | NC_002484.1 | + | 3915 | 0.72 | 0.117707 |
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Target: 5'- aAAUGGCCAG-GCCUucgaauacgucGCCGCCGG-GGc -3' miRNA: 3'- cUUGCCGGUCcCGGA-----------CGGCGGCCaCC- -5' |
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| 8861 | 5' | -63.7 | NC_002484.1 | + | 42770 | 1.09 | 0.000154 |
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Target: 5'- gGAACGGCCAGGGCCUGCCGCCGGUGGg -3' miRNA: 3'- -CUUGCCGGUCCCGGACGGCGGCCACC- -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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