miRNA: 3'- gGGCGGCGG----CAGCA----UAACUgucGUGG- -5'
miRNA: 3'- gGgCggCGGCAGCAuAACuGUCGUGG- -5'
miRNA: 3'- gGGCGGCGGCaGCAuaacuGUCGUGG- -5'
miRNA: 3'- ggGCGGCGGCAGCAUAAcu----GUCgUGG- -5'
miRNA: 3'- -GGGCGGCGGCAGCAUAACUgUCGUGG- -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 | |||||||
| 27244 | 5' | -55.3 | NC_005833.1 | + | 14723 | 0.66 | 0.700434 |
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Target: 5'- gCCGCCGCCcccuGUCGUucuuGUUGAaucCGCUa -3' miRNA: 3'- gGGCGGCGG----CAGCA----UAACUgucGUGG- -5' |
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| 27244 | 5' | -55.3 | NC_005833.1 | + | 15036 | 0.66 | 0.689664 |
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Target: 5'- aUgGuuGCCGUCGUcUUGcUGGCAUCg -3' miRNA: 3'- gGgCggCGGCAGCAuAACuGUCGUGG- -5' |
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| 27244 | 5' | -55.3 | NC_005833.1 | + | 34102 | 0.67 | 0.65707 |
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Target: 5'- aCCGCUGCCG-CGUcuu--UAGCGCUa -3' miRNA: 3'- gGGCGGCGGCaGCAuaacuGUCGUGG- -5' |
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| 27244 | 5' | -55.3 | NC_005833.1 | + | 45515 | 0.68 | 0.602419 |
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Target: 5'- -gCGCCGCCGUCGUGUUacccuuCGG-AUCg -3' miRNA: 3'- ggGCGGCGGCAGCAUAAcu----GUCgUGG- -5' |
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| 27244 | 5' | -55.3 | NC_005833.1 | + | 24904 | 1.01 | 0.003869 |
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Target: 5'- uCCCGCCGCCGUCGUAUUGA-AGCACCg -3' miRNA: 3'- -GGGCGGCGGCAGCAUAACUgUCGUGG- -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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