miRNA: 3'- -GGGgGCGUCGU-----------UUACUUUUU-----AGUUUu -5'
miRNA: 3'- -GGGGGCGu--CGUUUaCUUUUuaGuuuu -5'
miRNA: 3'- -GGGGGCGucGUUUACUUuuUAGUuuu -5'
miRNA: 3'- -GGGggCGUCGUUUACUuu-----UUAGUUUu -5'
miRNA: 3'- -GGGGGCGUCGUUUACUUUUUAGUUUU- -5'
Results 1 - 5 of 5 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 | |||||||
| 7537 | 5' | -44.3 | NC_001954.1 | + | 4850 | 0.66 | 0.794141 |
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Target: 5'- cCCUgCGCAGCGgggggaacguuGGUGAGAAGggcgcUCAGAc -3' miRNA: 3'- -GGGgGCGUCGU-----------UUACUUUUU-----AGUUUu -5' |
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| 7537 | 5' | -44.3 | NC_001954.1 | + | 4873 | 0.66 | 0.781683 |
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Target: 5'- cCCCCCGCugcGCAGG-GAGAAcgCc--- -3' miRNA: 3'- -GGGGGCGu--CGUUUaCUUUUuaGuuuu -5' |
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| 7537 | 5' | -44.3 | NC_001954.1 | + | 1058 | 0.74 | 0.332424 |
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Target: 5'- aCCCCCGC--CAGAUGAAuuAUCAu-- -3' miRNA: 3'- -GGGGGCGucGUUUACUUuuUAGUuuu -5' |
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| 7537 | 5' | -44.3 | NC_001954.1 | + | 544 | 0.75 | 0.293391 |
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Target: 5'- gCCUuuGCAGCAGAUGAugcaaccAGUCAGGc -3' miRNA: 3'- -GGGggCGUCGUUUACUuu-----UUAGUUUu -5' |
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| 7537 | 5' | -44.3 | NC_001954.1 | + | 4215 | 1.09 | 0.001095 |
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Target: 5'- uCCCCCGCAGCAAAUGAAAAAUCAAAAc -3' miRNA: 3'- -GGGGGCGUCGUUUACUUUUUAGUUUU- -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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