miRNA: 3'- gUAGUCGCGCCG---GUGCCa--UCUaacaa -5'
miRNA: 3'- guaGUCGCGCCGGUG-------------CCAUCuaACaa -5'
miRNA: 3'- -GUAGUc-GCGCCGGUGCCa----UCuaACAa -5'
miRNA: 3'- guAGUCGCGCCG-GuGCCAUCUaacaa -5'
miRNA: 3'- -GUAGUCGCGCCGGUGCCAUCUAACAA- -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 | |||||||
| 2651 | 3' | -54.2 | NC_001491.2 | + | 132710 | 0.66 | 0.940821 |
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Target: 5'- gGUCAGCGCGGUccuCACGGaaaAGAa---- -3' miRNA: 3'- gUAGUCGCGCCG---GUGCCa--UCUaacaa -5' |
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| 2651 | 3' | -54.2 | NC_001491.2 | + | 108848 | 0.66 | 0.924779 |
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Target: 5'- --cCAGCGCGGCUGCcacacuuugugggGGUGGggUGa- -3' miRNA: 3'- guaGUCGCGCCGGUG-------------CCAUCuaACaa -5' |
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| 2651 | 3' | -54.2 | NC_001491.2 | + | 64234 | 0.69 | 0.832879 |
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Target: 5'- gCGUCAaaCGCGGCCACGGgcggcGGcgUGUc -3' miRNA: 3'- -GUAGUc-GCGCCGGUGCCa----UCuaACAa -5' |
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| 2651 | 3' | -54.2 | NC_001491.2 | + | 10274 | 0.7 | 0.749182 |
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Target: 5'- -cUCGGCGCGGCgC-CGGUGGAg---- -3' miRNA: 3'- guAGUCGCGCCG-GuGCCAUCUaacaa -5' |
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| 2651 | 3' | -54.2 | NC_001491.2 | + | 100519 | 1.05 | 0.006019 |
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Target: 5'- uCAUCAGCGCGGCCACGGUAGAUUGUUg -3' miRNA: 3'- -GUAGUCGCGCCGGUGCCAUCUAACAA- -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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