miRNA: 3'- cgCGGGCc-ACcgCU------------GGGAGCGGGUCG- -5'
miRNA: 3'- cgCGGgCCACCGc-----UGGGA-------------GCGGG-UCG- -5'
miRNA: 3'- -CGCGGGC--CACCGcu-----GGGAGCGGG-----UCG- -5'
miRNA: 3'- cGCGGGCc--ACcgCUGG--GAGCGGguCG- -5'
Results 21 - 24 of 24 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 | |||||||
| 1344 | 5' | -64.2 | NC_001335.1 | + | 38843 | 0.66 | 0.311978 |
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Target: 5'- -gGCCCGuuUGaaGAacucgaugcaguCCCUCGCCCAGCc -3' miRNA: 3'- cgCGGGCc-ACcgCU------------GGGAGCGGGUCG- -5' |
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| 1344 | 5' | -64.2 | NC_001335.1 | + | 51641 | 0.66 | 0.318544 |
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Target: 5'- -gGCCgGGUGGCugucaaGCCCUaaucgcaaauuggUGCCCuAGCu -3' miRNA: 3'- cgCGGgCCACCGc-----UGGGA-------------GCGGG-UCG- -5' |
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| 1344 | 5' | -64.2 | NC_001335.1 | + | 50533 | 0.66 | 0.31928 |
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Target: 5'- cGUGCCCGacGUGGCcgucaugUCUUCGCCCcagucGGCg -3' miRNA: 3'- -CGCGGGC--CACCGcu-----GGGAGCGGG-----UCG- -5' |
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| 1344 | 5' | -64.2 | NC_001335.1 | + | 32516 | 0.66 | 0.31928 |
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Target: 5'- aCGCCCGacuUGuaGACCauCUCGCCguGCu -3' miRNA: 3'- cGCGGGCc--ACcgCUGG--GAGCGGguCG- -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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