miRNA: 3'- gACCCGGa--GUCGuaGUCGU--------UCAUGUu -5'
miRNA: 3'- gACCCGGa-GUCG--------------UAGUCGUUCAUGUU- -5'
miRNA: 3'- -GACCCGGa---GUCGua-GUCGUUCaUGUU- -5'
miRNA: 3'- gaCCCGGaGUCGU---AGUCGUUCAUGuu -5'
Results 21 - 24 of 24 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 | |||||||
| 23759 | 5' | -53.9 | NC_005261.1 | + | 136914 | 0.72 | 0.626391 |
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Target: 5'- gUGGGCCgcgCGGCcgCGGCGcaugugguGGUACAu -3' miRNA: 3'- gACCCGGa--GUCGuaGUCGU--------UCAUGUu -5' |
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| 23759 | 5' | -53.9 | NC_005261.1 | + | 101287 | 0.72 | 0.623171 |
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Target: 5'- aUGGGCCcgCGGUcgucgaugcgcgccGUUAGCGGGUGCGAg -3' miRNA: 3'- gACCCGGa-GUCG--------------UAGUCGUUCAUGUU- -5' |
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| 23759 | 5' | -53.9 | NC_005261.1 | + | 90112 | 0.73 | 0.551858 |
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Target: 5'- gCUGGGCCgacgCGGCccgCGGCGAGgGCGAg -3' miRNA: 3'- -GACCCGGa---GUCGua-GUCGUUCaUGUU- -5' |
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| 23759 | 5' | -53.9 | NC_005261.1 | + | 89851 | 0.75 | 0.431933 |
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Target: 5'- -aGGGCCgCGGCGucaUCGGCGAGUACu- -3' miRNA: 3'- gaCCCGGaGUCGU---AGUCGUUCAUGuu -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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