miRNA: 3'- -GCGCGUGAgGGCUUucaagAGUGGaa -5'
miRNA: 3'- gCGCGUGa-GGGCU---------------UUCAaGAGUGGAA- -5'
miRNA: 3'- gCGCGUGAgGGCU--------UUCAAg-AGUGGAa -5'
miRNA: 3'- -GCGCGUGAGGgCuuUCaAGa--GUGGAA- -5'
miRNA: 3'- -GCGCGUGAGGGCUUUCAAGAGUGGAA- -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 | |||||||
| 17062 | 5' | -53.6 | NC_004333.2 | + | 20737 | 0.66 | 0.767817 |
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Target: 5'- gCGCGCGCUgCCGGAca---UCGCCg- -3' miRNA: 3'- -GCGCGUGAgGGCUUucaagAGUGGaa -5' |
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| 17062 | 5' | -53.6 | NC_004333.2 | + | 23616 | 0.66 | 0.740161 |
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Target: 5'- uGCGCGCgaCCUGGuucaacgcgccguugAAGUcCUCGCCUUg -3' miRNA: 3'- gCGCGUGa-GGGCU---------------UUCAaGAGUGGAA- -5' |
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| 17062 | 5' | -53.6 | NC_004333.2 | + | 41538 | 0.68 | 0.635223 |
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Target: 5'- aGCGCGCUgCCGAgcgcgaucGAGUUgaUUACCUg -3' miRNA: 3'- gCGCGUGAgGGCU--------UUCAAg-AGUGGAa -5' |
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| 17062 | 5' | -53.6 | NC_004333.2 | + | 11943 | 0.69 | 0.589923 |
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Target: 5'- aCGCGCGCUCCaGgcGG-UCgagCGCCUUg -3' miRNA: 3'- -GCGCGUGAGGgCuuUCaAGa--GUGGAA- -5' |
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| 17062 | 5' | -53.6 | NC_004333.2 | + | 19665 | 1.06 | 0.001752 |
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Target: 5'- gCGCGCACUCCCGAAAGUUCUCACCUUg -3' miRNA: 3'- -GCGCGUGAGGGCUUUCAAGAGUGGAA- -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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