miRNA: 3'- aACUCCUgaaGU--UUUCCUUCGa----CUAG- -5'
miRNA: 3'- aacUCCUGAAGUU----------UUCCUUCgaCUAG- -5'
miRNA: 3'- -AACUCCUGA---AGUUUUc----CUUCGACUag -5'
miRNA: 3'- -AACUCCUGAAGUUuUCCuuCGAcuag -5'
miRNA: 3'- -AACUCCUGAAGUUUUCCUUCGACUAG- -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 | |||||||
| 18006 | 3' | -47.2 | NC_004665.1 | + | 10736 | 0.66 | 0.932123 |
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Target: 5'- gUGAGGGgc-CAccAGAGGAAGCgaaggGAUCa -3' miRNA: 3'- aACUCCUgaaGU--UUUCCUUCGa----CUAG- -5' |
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| 18006 | 3' | -47.2 | NC_004665.1 | + | 28206 | 0.68 | 0.897327 |
|
Target: 5'- --cAGGACUUCGAgaacauccgcAAGGAAGg-GAUCg -3' miRNA: 3'- aacUCCUGAAGUU----------UUCCUUCgaCUAG- -5' |
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| 18006 | 3' | -47.2 | NC_004665.1 | + | 12440 | 0.69 | 0.844754 |
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Target: 5'- uUUGGGGACUacaUCAAGGcccucGAAGCUGAg- -3' miRNA: 3'- -AACUCCUGA---AGUUUUc----CUUCGACUag -5' |
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| 18006 | 3' | -47.2 | NC_004665.1 | + | 28994 | 0.72 | 0.700757 |
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Target: 5'- cUUGAGGACUUCAAuGGGguGCUc--- -3' miRNA: 3'- -AACUCCUGAAGUUuUCCuuCGAcuag -5' |
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| 18006 | 3' | -47.2 | NC_004665.1 | + | 7158 | 1.09 | 0.003045 |
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Target: 5'- aUUGAGGACUUCAAAAGGAAGCUGAUCg -3' miRNA: 3'- -AACUCCUGAAGUUUUCCUUCGACUAG- -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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