miRNA: 3'- gcCAGU-------UGGGUUAGCG--UUCAGAuGAU- -5'
miRNA: 3'- gCCAGuuGGGUUAGCGUUCaGA--UGAU- -5'
miRNA: 3'- gCCAgUUGGgUUa--GCGUUCA-GAUGAU- -5'
miRNA: 3'- -GCCAGUUGGGUUAGCGUUCAGAUGAU- -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 | |||||||
| 15406 | 5' | -49.9 | NC_003907.2 | + | 7903 | 0.67 | 0.88296 |
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Target: 5'- -uGUCAucucugcACCCAAUCGCuuGAGUCU-CUGc -3' miRNA: 3'- gcCAGU-------UGGGUUAGCG--UUCAGAuGAU- -5' |
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| 15406 | 5' | -49.9 | NC_003907.2 | + | 5671 | 0.68 | 0.840592 |
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Target: 5'- uGGUCugUCUAGUCGCAGGgCUagACUGg -3' miRNA: 3'- gCCAGuuGGGUUAGCGUUCaGA--UGAU- -5' |
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| 15406 | 5' | -49.9 | NC_003907.2 | + | 22283 | 0.69 | 0.770189 |
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Target: 5'- uGGUgGACCgAAgggUGCAGGUgCUACUAc -3' miRNA: 3'- gCCAgUUGGgUUa--GCGUUCA-GAUGAU- -5' |
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| 15406 | 5' | -49.9 | NC_003907.2 | + | 3231 | 1.08 | 0.003212 |
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Target: 5'- uCGGUCAACCCAAUCGCAAGUCUACUAa -3' miRNA: 3'- -GCCAGUUGGGUUAGCGUUCAGAUGAU- -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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