miRNA: 3'- -UUCUCgUGGU----UCUCCGa-----GUGGGGgGa -5'
miRNA: 3'- -UUCUCGUGGUU-CUCCGa--------GUGGG--GGGa -5'
miRNA: 3'- uUCUCGUGGU--UCuCCGAG-----UGGGG-GGa -5'
miRNA: 3'- -UUCUCGUGGUUCUCCGAGUGGGGGGA- -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 | |||||||
| 29237 | 5' | -59.7 | NC_006150.1 | + | 37844 | 0.66 | 0.801108 |
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Target: 5'- aGGGGGgGCCAagcgAGAGGCagccagCGCCCCgCa -3' miRNA: 3'- -UUCUCgUGGU----UCUCCGa-----GUGGGGgGa -5' |
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| 29237 | 5' | -59.7 | NC_006150.1 | + | 150244 | 0.69 | 0.609517 |
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Target: 5'- cGGGAGCGCCAGcGGGGUggcguucggCACCCugCCCg -3' miRNA: 3'- -UUCUCGUGGUU-CUCCGa--------GUGGG--GGGa -5' |
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| 29237 | 5' | -59.7 | NC_006150.1 | + | 38002 | 0.72 | 0.456705 |
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Target: 5'- uAGAGCGCCGucAGuGGCUCaaaguGCCCCaCCa -3' miRNA: 3'- uUCUCGUGGU--UCuCCGAG-----UGGGG-GGa -5' |
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| 29237 | 5' | -59.7 | NC_006150.1 | + | 157064 | 1.05 | 0.00273 |
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Target: 5'- cAAGAGCACCAAGAGGCUCACCCCCCUg -3' miRNA: 3'- -UUCUCGUGGUUCUCCGAGUGGGGGGA- -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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