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miRNA: 3'- -GGGGGAGG------AGAAGGuGGGUU---CAGGUu -5'
miRNA: 3'- -GGGGGAGGAGaagGUGGGUUCagguu -5'
miRNA: 3'- gGGGGAGGAGa---AGG--------------UGGGUUCAGGuu -5'
miRNA: 3'- -GGGGGAGGAGAAGGUGGGUUCAGGUU- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 672 | 5' | -57.4 | AC_000018.1 | + | 26166 | 0.66 | 0.458756 |
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Target: 5'- uCCUCCUCCaaacugUCUUCC-UCCAGgcuGUCCAc -3' miRNA: 3'- -GGGGGAGG------AGAAGGuGGGUU---CAGGUu -5' |
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| 672 | 5' | -57.4 | AC_000018.1 | + | 5793 | 0.68 | 0.321363 |
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Target: 5'- uCCCCCUCCUCca-CAUCCAAGa---- -3' miRNA: 3'- -GGGGGAGGAGaagGUGGGUUCagguu -5' |
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| 672 | 5' | -57.4 | AC_000018.1 | + | 24072 | 0.71 | 0.221293 |
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Target: 5'- gCUCCUCCUCgugcUCCgccggugucacauaGCCCGGGUCCu- -3' miRNA: 3'- gGGGGAGGAGa---AGG--------------UGGGUUCAGGuu -5' |
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| 672 | 5' | -57.4 | AC_000018.1 | + | 14041 | 1.07 | 0.00043 |
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Target: 5'- gCCCCCUCCUCUUCCACCCAAGUCCAAc -3' miRNA: 3'- -GGGGGAGGAGAAGGUGGGUUCAGGUU- -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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