miRNA: 3'- uGGGGCGg-------CAUGUgCCUGa--CCC-GCCG- -5'
miRNA: 3'- -UGGG-GC-GGCAUG------UGCCUGAcCCGCCG- -5'
miRNA: 3'- -UGGGGCGGCA--UGUGCCUGa----CcCGCCG- -5'
miRNA: 3'- -UGGGGCGGCAUGUGCCUGACCCGCCG- -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 | |||||||
| 33209 | 3' | -62.3 | NC_007523.1 | + | 1696 | 0.66 | 0.044002 |
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Target: 5'- cCCCCGUacccaaagGUACGaGGACaggGGGuCGGCg -3' miRNA: 3'- uGGGGCGg-------CAUGUgCCUGa--CCC-GCCG- -5' |
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| 33209 | 3' | -62.3 | NC_007523.1 | + | 129 | 0.71 | 0.013506 |
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Target: 5'- uACCCgCGaCUGUACcaguuaACGGACU-GGCGGCc -3' miRNA: 3'- -UGGG-GC-GGCAUG------UGCCUGAcCCGCCG- -5' |
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| 33209 | 3' | -62.3 | NC_007523.1 | + | 1978 | 0.77 | 0.004543 |
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Target: 5'- gGCCUCGCCGUauGCACGGGCgcgcaGuGCGGCc -3' miRNA: 3'- -UGGGGCGGCA--UGUGCCUGa----CcCGCCG- -5' |
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| 33209 | 3' | -62.3 | NC_007523.1 | + | 470 | 1.11 | 0.000003 |
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Target: 5'- gACCCCGCCGUACACGGACUGGGCGGCa -3' miRNA: 3'- -UGGGGCGGCAUGUGCCUGACCCGCCG- -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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