miRNA: 3'- -UAGCUAUGGGGUUGac-----ACCUu-CGCUg -5'
miRNA: 3'- uAGCU----AUGGGGUUGaCACCuuCgCUG- -5'
miRNA: 3'- uAGCuauGGGGUUGaCA---CCUUCGCUg -5'
miRNA: 3'- uaGCUA---UGGGGUUGaCACCUUCGCUG- -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 | |||||||
| 32349 | 3' | -52.8 | NC_007024.1 | + | 24805 | 0.66 | 0.796632 |
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Target: 5'- cGUCGGUGCCUCAGCggcuacuUGGAucGCGGu -3' miRNA: 3'- -UAGCUAUGGGGUUGac-----ACCUu-CGCUg -5' |
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| 32349 | 3' | -52.8 | NC_007024.1 | + | 29741 | 0.66 | 0.796632 |
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Target: 5'- cUCGAugccUACCCCAAUaGUGGucGgGAUc -3' miRNA: 3'- uAGCU----AUGGGGUUGaCACCuuCgCUG- -5' |
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| 32349 | 3' | -52.8 | NC_007024.1 | + | 2203 | 0.67 | 0.776346 |
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Target: 5'- cUCGuucCCCCAGCaGUcccGGAGGCGAg -3' miRNA: 3'- uAGCuauGGGGUUGaCA---CCUUCGCUg -5' |
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| 32349 | 3' | -52.8 | NC_007024.1 | + | 14859 | 0.69 | 0.633516 |
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Target: 5'- -gUGGUacgGCCUUAGCaGUGGAAGUGGCg -3' miRNA: 3'- uaGCUA---UGGGGUUGaCACCUUCGCUG- -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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