miRNA: 3'- guguuaaCCG----UGGCCCCUa---------ACGGGGg -5'
miRNA: 3'- gUGUUaa-CCgUGGCC-CCUaACGGG-GG- -5'
miRNA: 3'- guGUUA--ACCGUGGCCc---CUaa---CGGGGG- -5'
miRNA: 3'- guGUUaaCCGUG-GCCCcuAACGGGGG- -5'
miRNA: 3'- -GUGUUAACCGUGGCCCCUAACGGGGG- -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 | |||||||
| 8828 | 3' | -56 | NC_002484.1 | + | 51803 | 0.66 | 0.699169 |
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Target: 5'- ------aGGCgcagGCCGGGGAgcacacgcgcUGCCCCa -3' miRNA: 3'- guguuaaCCG----UGGCCCCUa---------ACGGGGg -5' |
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| 8828 | 3' | -56 | NC_002484.1 | + | 33524 | 0.67 | 0.611895 |
|
Target: 5'- gGCAGgcgGGgAUCGGuGGGaUGCCCuCCa -3' miRNA: 3'- gUGUUaa-CCgUGGCC-CCUaACGGG-GG- -5' |
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| 8828 | 3' | -56 | NC_002484.1 | + | 907 | 0.68 | 0.568354 |
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Target: 5'- -uCGGUggUGGCGCCGGaguaGAccucgGCCCCCg -3' miRNA: 3'- guGUUA--ACCGUGGCCc---CUaa---CGGGGG- -5' |
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| 8828 | 3' | -56 | NC_002484.1 | + | 52094 | 0.68 | 0.546859 |
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Target: 5'- -cCAGgcGGUGCuCGGGccUUGCCCCCu -3' miRNA: 3'- guGUUaaCCGUG-GCCCcuAACGGGGG- -5' |
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| 8828 | 3' | -56 | NC_002484.1 | + | 20803 | 1.11 | 0.000621 |
|
Target: 5'- aCACAAUUGGCACCGGGGAUUGCCCCCc -3' miRNA: 3'- -GUGUUAACCGUGGCCCCUAACGGGGG- -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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