miRNA: 3'- -GGGUUCGCUCCcgCGUUUaCUcGUUU- -5'
miRNA: 3'- gGGUUCGCUCCCG-CGuUUAC------------UCGUuu -5'
miRNA: 3'- gGGUUCGCUCCCGCgUUUaCUCGUuu -5'
miRNA: 3'- -GGGUUCGCUCCCGCGUUUACUCGUUU- -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 | |||||||
| 582 | 3' | -53 | AC_000015.1 | + | 27050 | 0.66 | 0.644255 |
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Target: 5'- gCCCGAGCGGGGuuGCGAA-GA-CGAAc -3' miRNA: 3'- -GGGUUCGCUCCcgCGUUUaCUcGUUU- -5' |
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| 582 | 3' | -53 | AC_000015.1 | + | 13044 | 0.67 | 0.609007 |
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Target: 5'- aCCAGGUGGGGGCaGCcAGUGcggguuuaagauGGCAu- -3' miRNA: 3'- gGGUUCGCUCCCG-CGuUUAC------------UCGUuu -5' |
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| 582 | 3' | -53 | AC_000015.1 | + | 9248 | 0.74 | 0.25714 |
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Target: 5'- uUCAGGCGGGGGCGgAGG-GGGCAc- -3' miRNA: 3'- gGGUUCGCUCCCGCgUUUaCUCGUuu -5' |
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| 582 | 3' | -53 | AC_000015.1 | + | 13611 | 1.08 | 0.000831 |
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Target: 5'- aCCCAAGCGAGGGCGCAAAUGAGCAAAc -3' miRNA: 3'- -GGGUUCGCUCCCGCGUUUACUCGUUU- -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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