miRNA: 3'- caaUCCCuUGGa------UCCAa--UGGGCGUCg -5'
miRNA: 3'- caaUC-CCUUGGAUCCAAu-GGGCGU----CG- -5'
miRNA: 3'- cAAUCC-CUU-----GGAUCCaa--UGGGCGUCG- -5'
miRNA: 3'- caaUCCCUUGGa------UCCAa-UGGGCGUCg -5'
miRNA: 3'- -CAAUCCCUUGGAUCCAAUGGGCGUCG- -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 | |||||||
| 5025 | 3' | -52.1 | NC_001734.1 | + | 14088 | 0.66 | 0.723534 |
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Target: 5'- --aAGGGcGCCgucguccAGGUcgaGCCCGCGGg -3' miRNA: 3'- caaUCCCuUGGa------UCCAa--UGGGCGUCg -5' |
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| 5025 | 3' | -52.1 | NC_001734.1 | + | 11830 | 0.66 | 0.700528 |
|
Target: 5'- --cAGuGGGGCUUAGGUUuuCCUGCAucauGCg -3' miRNA: 3'- caaUC-CCUUGGAUCCAAu-GGGCGU----CG- -5' |
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| 5025 | 3' | -52.1 | NC_001734.1 | + | 24175 | 0.7 | 0.459101 |
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Target: 5'- uUUGGGuGGAguaauCCUGGGaggcGCCUGCAGCa -3' miRNA: 3'- cAAUCC-CUU-----GGAUCCaa--UGGGCGUCG- -5' |
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| 5025 | 3' | -52.1 | NC_001734.1 | + | 9795 | 0.73 | 0.324362 |
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Target: 5'- --gGGGGAGCUgcaccagAGGUgcACCCGCGGg -3' miRNA: 3'- caaUCCCUUGGa------UCCAa-UGGGCGUCg -5' |
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| 5025 | 3' | -52.1 | NC_001734.1 | + | 11230 | 1.12 | 0.00058 |
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Target: 5'- gGUUAGGGAACCUAGGUUACCCGCAGCu -3' miRNA: 3'- -CAAUCCCUUGGAUCCAAUGGGCGUCG- -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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