miRNA: 3'- aCUUUGG-------------AAUAGC-AGuaauAGUCCCU- -5'
miRNA: 3'- aCUUUGGAAUa--GCaGUAAUa----GUCCCU- -5'
miRNA: 3'- aCUUUGGaaUAGCAguAAUAGUCCCU- -5'
miRNA: 3'- aCUUUGGaAUAGCAGUaaua--GUCCCU- -5'
miRNA: 3'- -ACUUUGGAAUAGCAGUAAUAGUCCCU- -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 | |||||||
| 21002 | 3' | -44.3 | NC_004735.1 | + | 121050 | 0.66 | 0.999995 |
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Target: 5'- cGAAGCCaaucccggagauaUUGUCGaUCcucuUCAGGGAg -3' miRNA: 3'- aCUUUGG-------------AAUAGC-AGuaauAGUCCCU- -5' |
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| 21002 | 3' | -44.3 | NC_004735.1 | + | 59858 | 0.68 | 0.999952 |
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Target: 5'- gGAAGCCUUAaugCG-CGUUAaggaaCGGGGAa -3' miRNA: 3'- aCUUUGGAAUa--GCaGUAAUa----GUCCCU- -5' |
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| 21002 | 3' | -44.3 | NC_004735.1 | + | 117615 | 0.7 | 0.998984 |
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Target: 5'- cGAAACC--AUUGUgcUUAUCAGGGGc -3' miRNA: 3'- aCUUUGGaaUAGCAguAAUAGUCCCU- -5' |
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| 21002 | 3' | -44.3 | NC_004735.1 | + | 10540 | 0.75 | 0.976151 |
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Target: 5'- aGGAACCcUGUCGUCAagaaugUAGGGAg -3' miRNA: 3'- aCUUUGGaAUAGCAGUaaua--GUCCCU- -5' |
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| 21002 | 3' | -44.3 | NC_004735.1 | + | 10346 | 1.11 | 0.026657 |
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Target: 5'- gUGAAACCUUAUCGUCAUUAUCAGGGAu -3' miRNA: 3'- -ACUUUGGAAUAGCAGUAAUAGUCCCU- -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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