miRNA: 3'- -UGUGGUCACC-----UGC----UCCU---CGGGGuCCU- -5'
miRNA: 3'- -UGUGGUCacCUGCUCCUcGGGGuCCU- -5'
miRNA: 3'- uGUGgUCac--CUGCUCCUCGG-GGUCCU- -5'
miRNA: 3'- -UGUGGUCACCUGCUCCUCGGGGUCCU- -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 | |||||||
| 4368 | 3' | -60.1 | NC_001720.1 | + | 27649 | 0.67 | 0.334749 |
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Target: 5'- cACGCCAGUGGugaucACGuuauAGGAaacGCCCUuGGAg -3' miRNA: 3'- -UGUGGUCACC-----UGC----UCCU---CGGGGuCCU- -5' |
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| 4368 | 3' | -60.1 | NC_001720.1 | + | 20774 | 0.68 | 0.282058 |
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Target: 5'- aACGCCAGc-GACGAGGAaUCCCcGGAg -3' miRNA: 3'- -UGUGGUCacCUGCUCCUcGGGGuCCU- -5' |
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| 4368 | 3' | -60.1 | NC_001720.1 | + | 22941 | 0.72 | 0.146313 |
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Target: 5'- cCACgGGgucuGACGAGGGGCCuCCGGGGa -3' miRNA: 3'- uGUGgUCac--CUGCUCCUCGG-GGUCCU- -5' |
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| 4368 | 3' | -60.1 | NC_001720.1 | + | 24174 | 1.07 | 0.000308 |
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Target: 5'- aACACCAGUGGACGAGGAGCCCCAGGAc -3' miRNA: 3'- -UGUGGUCACCUGCUCCUCGGGGUCCU- -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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