miRNA: 3'- -GugGCCac------UGAAGUa---GCCGCUGUAGu -5'
miRNA: 3'- -GUGgCC--ACUGaaGUAGCCGCUGUAGu -5'
miRNA: 3'- -GUGGCCACUga-AgUaGCCGCUGUAGu -5'
miRNA: 3'- guggCCACUGa---AGUaGCCGCUGUAGU- -5'
miRNA: 3'- -GUGGCCACUGAAGUAGCCGCUGUAGU- -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 | |||||||
| 9791 | 3' | -53.1 | NC_002593.1 | + | 51798 | 0.67 | 0.918143 |
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Target: 5'- uCugCGGggcgaguaGCUUCGagagCGGCGACGUCu -3' miRNA: 3'- -GugGCCac------UGAAGUa---GCCGCUGUAGu -5' |
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| 9791 | 3' | -53.1 | NC_002593.1 | + | 70018 | 0.67 | 0.912057 |
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Target: 5'- gUAUgGGccUGACcgCGUCGGCGGCGUUu -3' miRNA: 3'- -GUGgCC--ACUGaaGUAGCCGCUGUAGu -5' |
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| 9791 | 3' | -53.1 | NC_002593.1 | + | 51760 | 0.7 | 0.773055 |
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Target: 5'- uCAUCGGUGAacgUgAaCGGCGGCGUCu -3' miRNA: 3'- -GUGGCCACUga-AgUaGCCGCUGUAGu -5' |
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| 9791 | 3' | -53.1 | NC_002593.1 | + | 18031 | 0.73 | 0.627371 |
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Target: 5'- ---gGGUGGCgaccUCAcCGGCGACAUCAu -3' miRNA: 3'- guggCCACUGa---AGUaGCCGCUGUAGU- -5' |
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| 9791 | 3' | -53.1 | NC_002593.1 | + | 18062 | 1.08 | 0.003932 |
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Target: 5'- gCACCGGUGACUUCAUCGGCGACAUCAu -3' miRNA: 3'- -GUGGCCACUGAAGUAGCCGCUGUAGU- -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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