miRNA: 3'- -CUCCAGgUCU----AGUu---GGAGGUCCCCGu -5'
miRNA: 3'- -CUCCA---------------GGUCU---------------AGUUGGAGG---------------UCCCCGU- -5'
miRNA: 3'- -CUCCAGGUCUAGUUGGAGGUCCCCGU- -5'
Results 1 - 3 of 3 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 | |||||||
| 4216 | 5' | -57.6 | NC_001683.1 | + | 3614 | 0.67 | 0.102919 |
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Target: 5'- gGAGGUUgAGAcuccUCGuugcCCUCUGGGGGUg -3' miRNA: 3'- -CUCCAGgUCU----AGUu---GGAGGUCCCCGu -5' |
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| 4216 | 5' | -57.6 | NC_001683.1 | + | 3559 | 0.71 | 0.049725 |
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Target: 5'- gGAGGUguaggggagacacccCCAGAgggcaacgaggagucUCAACCUCCuccaggggaaggggaAGGGGCAg -3' miRNA: 3'- -CUCCA---------------GGUCU---------------AGUUGGAGG---------------UCCCCGU- -5' |
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| 4216 | 5' | -57.6 | NC_001683.1 | + | 3529 | 1.08 | 2.8e-05 |
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Target: 5'- gGAGGUCCAGAUCAACCUCCAGGGGCAa -3' miRNA: 3'- -CUCCAGGUCUAGUUGGAGGUCCCCGU- -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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