miRNA: 3'- uauaCACCUCGA-------------UGGUugGCGUUUGc -5'
miRNA: 3'- uauacACCUCGA-----------UGGUUGGCGuUUGc -5'
miRNA: 3'- -UAUACACCUCGAUGGUUGGCGUUUGC- -5'
miRNA: 3'- uauacACCU----CGAUGG-UUGGCGUUUGC- -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 |
| Predicted miRNA align pattern | |||||||
| 748 | 3' | -49.9 | AC_000020.1 | + | 11924 | 0.69 | 0.62009 |
|
Target: 5'- ---aGUGGGGCUcaaguuuuccugcAUCAugCGCAAGCu -3' miRNA: 3'- uauaCACCUCGA-------------UGGUugGCGUUUGc -5' |
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| 748 | 3' | -49.9 | AC_000020.1 | + | 16665 | 0.68 | 0.728685 |
|
Target: 5'- ----uUGGAGCUaaagcccucugACCAGCCGCcAGCc -3' miRNA: 3'- uauacACCUCGA-----------UGGUUGGCGuUUGc -5' |
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| 748 | 3' | -49.9 | AC_000020.1 | + | 24259 | 1.08 | 0.001671 |
|
Target: 5'- uAUAUGUGGAGCUACCAACCGCAAACGg -3' miRNA: 3'- -UAUACACCUCGAUGGUUGGCGUUUGC- -5' |
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| 748 | 3' | -49.9 | AC_000020.1 | + | 25593 | 0.66 | 0.795713 |
|
Target: 5'- ----aUGGAgacuGCUACCaAACUGCAAAUGa -3' miRNA: 3'- uauacACCU----CGAUGG-UUGGCGUUUGC- -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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