miRNA: 3'- uCCUucu-CCG--------------GGUGGACCUCGACCGa -5'
miRNA: 3'- -UCC----UUCUCCGGGuGGa-CCUCGaCCGa -5'
miRNA: 3'- -UCCUUC----------UCCGGgUGGacCUCGACCGA- -5'
miRNA: 3'- -UCCUUCUCCGGGUGGACCUCGACCGA- -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 | |||||||
| 17627 | 5' | -60.8 | NC_004466.2 | + | 44611 | 0.66 | 0.316383 |
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Target: 5'- uGGAucacGGCgauacgcucguccgCUGCCUGGAGCUGGCc -3' miRNA: 3'- uCCUucu-CCG--------------GGUGGACCUCGACCGa -5' |
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| 17627 | 5' | -60.8 | NC_004466.2 | + | 15122 | 0.68 | 0.248053 |
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Target: 5'- aAGGccacAGGAGGCCC-CCagGGAGCcGGUc -3' miRNA: 3'- -UCC----UUCUCCGGGuGGa-CCUCGaCCGa -5' |
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| 17627 | 5' | -60.8 | NC_004466.2 | + | 26482 | 0.68 | 0.248053 |
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Target: 5'- gAGGGAGcaauuccuuaAGGCCaACCcaGAGCUGGCUa -3' miRNA: 3'- -UCCUUC----------UCCGGgUGGacCUCGACCGA- -5' |
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| 17627 | 5' | -60.8 | NC_004466.2 | + | 39182 | 1.08 | 0.000227 |
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Target: 5'- gAGGAAGAGGCCCACCUGGAGCUGGCUg -3' miRNA: 3'- -UCCUUCUCCGGGUGGACCUCGACCGA- -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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