miRNA: 3'- -GGCGGa--UAGGAGU----UCCUuuaa------GAGCG- -5'
miRNA: 3'- -GGcGGAUa---GGAgUUCCuuUAAGAGCG- -5'
miRNA: 3'- -GGCGGAUAGGAGUUCCUUUAAGAGCG- -5'
Results 1 - 3 of 3 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 | |||||||
| 3556 | 3' | -48.2 | NC_001628.1 | + | 3501 | 0.65 | 0.328018 |
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Target: 5'- uUCGCCccaGUCCUCGuaagAGGAccacaccgagCUCGCc -3' miRNA: 3'- -GGCGGa--UAGGAGU----UCCUuuaa------GAGCG- -5' |
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| 3556 | 3' | -48.2 | NC_001628.1 | + | 3366 | 0.71 | 0.13743 |
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Target: 5'- gCC-CCUGgaggUCUgGAGGcgGUUCUCGCa -3' miRNA: 3'- -GGcGGAUa---GGAgUUCCuuUAAGAGCG- -5' |
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| 3556 | 3' | -48.2 | NC_001628.1 | + | 2250 | 1.15 | 0.000038 |
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Target: 5'- gCCGCCUAUCCUCAAGGAAAUUCUCGCu -3' miRNA: 3'- -GGCGGAUAGGAGUUCCUUUAAGAGCG- -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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