miRNA: 3'- -UUGGuCGag----GGACGCGCCG-AgCG--UAG- -5'
miRNA: 3'- -UUGGUCGa--GGGa--CGCGCCGa------GCGUAg -5'
miRNA: 3'- -UUGGUCGaggGAcGCGCCgAGCGUAG- -5'
miRNA: 3'- -UUG-GUCGAGGGACGcGCCGa--GCGUAG- -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 | |||||||
| 8884 | 5' | -60.9 | NC_002484.1 | + | 27375 | 0.66 | 0.356205 |
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Target: 5'- cGACCuGCgccacaCCUGCGCGGCaUgGCugGUCa -3' miRNA: 3'- -UUGGuCGag----GGACGCGCCG-AgCG--UAG- -5' |
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| 8884 | 5' | -60.9 | NC_002484.1 | + | 2734 | 0.67 | 0.31621 |
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Target: 5'- cAGCCGGUcugCCCgcaGCGCGGCgaaucucCGCGUa -3' miRNA: 3'- -UUGGUCGa--GGGa--CGCGCCGa------GCGUAg -5' |
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| 8884 | 5' | -60.9 | NC_002484.1 | + | 16349 | 0.67 | 0.31621 |
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Target: 5'- cGGCCAGCga-CUuCGCGGaUCGCAUCg -3' miRNA: 3'- -UUGGUCGaggGAcGCGCCgAGCGUAG- -5' |
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| 8884 | 5' | -60.9 | NC_002484.1 | + | 26446 | 0.74 | 0.113605 |
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Target: 5'- cGGCuCGGCUUCCUGC-CGGCcggCGCAUCc -3' miRNA: 3'- -UUG-GUCGAGGGACGcGCCGa--GCGUAG- -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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