miRNA: 3'- gUUGCGa-----UCCAgCCGGUGCUGGGAga -5'
miRNA: 3'- gUUGCGa-UCCaGCCGgUgCU-GGGAGA- -5'
miRNA: 3'- -GUUGCGauccag--CCGGUGCUGGGAGa -5'
miRNA: 3'- -GUUGCGAUCCAGCCGGUGCUGGGAGA- -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 | |||||||
| 31624 | 5' | -57.6 | NC_006879.1 | + | 9842 | 0.66 | 0.438375 |
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Target: 5'- uGAUGCcggccgAGGU-GGUCGCGGCCCUg- -3' miRNA: 3'- gUUGCGa-----UCCAgCCGGUGCUGGGAga -5' |
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| 31624 | 5' | -57.6 | NC_006879.1 | + | 22124 | 0.66 | 0.438375 |
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Target: 5'- gGACGUcgGGGcCGGCgAgGGcCCCUCUa -3' miRNA: 3'- gUUGCGa-UCCaGCCGgUgCU-GGGAGA- -5' |
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| 31624 | 5' | -57.6 | NC_006879.1 | + | 20863 | 0.67 | 0.405538 |
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Target: 5'- gCAGCGCaucgaacgGGCCACGGCCUUCg -3' miRNA: 3'- -GUUGCGauccag--CCGGUGCUGGGAGa -5' |
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| 31624 | 5' | -57.6 | NC_006879.1 | + | 9473 | 1.06 | 0.000488 |
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Target: 5'- gCAACGCUAGGUCGGCCACGACCCUCUc -3' miRNA: 3'- -GUUGCGAUCCAGCCGGUGCUGGGAGA- -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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