miRNA: 3'- ucuuCGa--GCUCGGGCCGCa---GCu-UGGC- -5'
miRNA: 3'- uCuuCGa----GCUCG---------GGCCGCaGCUUGGC- -5'
miRNA: 3'- uCUUCgAGCUCGGg--CCGCa--GCUUGGC- -5'
miRNA: 3'- ucuucGAGCUCGGGCCGCaGCU----UGGC- -5'
miRNA: 3'- -UCUUCGAGCUCGGGCCGCAGCUUGGC- -5'
Results 21 - 25 of 25 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 | |||||||
| 24280 | 3' | -58 | NC_005263.2 | + | 31516 | 0.69 | 0.356027 |
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Target: 5'- ---cGCgcgCGAGCCCGGCGaacgCGucGCCGc -3' miRNA: 3'- ucuuCGa--GCUCGGGCCGCa---GCu-UGGC- -5' |
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| 24280 | 3' | -58 | NC_005263.2 | + | 39697 | 0.7 | 0.315965 |
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Target: 5'- uGggGCgagcgCGAGCuggaaauggCCGGCG-CGGGCCGc -3' miRNA: 3'- uCuuCGa----GCUCG---------GGCCGCaGCUUGGC- -5' |
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| 24280 | 3' | -58 | NC_005263.2 | + | 5864 | 0.71 | 0.265744 |
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Target: 5'- cGAAG-UCGAGCCgcaGGCGguaCGGGCCGa -3' miRNA: 3'- uCUUCgAGCUCGGg--CCGCa--GCUUGGC- -5' |
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| 24280 | 3' | -58 | NC_005263.2 | + | 45462 | 0.75 | 0.157375 |
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Target: 5'- ----cCUCGAGCCCGGCG-CGAacguGCCGa -3' miRNA: 3'- ucuucGAGCUCGGGCCGCaGCU----UGGC- -5' |
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| 24280 | 3' | -58 | NC_005263.2 | + | 19573 | 1.09 | 0.000512 |
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Target: 5'- aAGAAGCUCGAGCCCGGCGUCGAACCGa -3' miRNA: 3'- -UCUUCGAGCUCGGGCCGCAGCUUGGC- -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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