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miRNA: 3'- -CUUUaGGC-------CCGCGACCCCaaa---UACUg -5'
miRNA: 3'- cuuUAGGCCCGCGACC--CCaAAU-ACUG- -5'
miRNA: 3'- -CUUUAGGCCCGCGACCCCAAAUACUG- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 1080 | 3' | -52.4 | NC_000929.1 | + | 20433 | 0.68 | 0.608859 |
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Target: 5'- uGAAAgCCGucagugcGGCGCUGGGGgaaccgGUGAg -3' miRNA: 3'- -CUUUaGGC-------CCGCGACCCCaaa---UACUg -5' |
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| 1080 | 3' | -52.4 | NC_000929.1 | + | 9743 | 0.72 | 0.383428 |
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Target: 5'- --cAUCUGGGCGCUGGccGGaUUGcUGACg -3' miRNA: 3'- cuuUAGGCCCGCGACC--CCaAAU-ACUG- -5' |
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| 1080 | 3' | -52.4 | NC_000929.1 | + | 16976 | 1.1 | 0.00082 |
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Target: 5'- uGAAAUCCGGGCGCUGGGGUUUAUGACg -3' miRNA: 3'- -CUUUAGGCCCGCGACCCCAAAUACUG- -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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