miRNA: 3'- -CUUCUCCCUCUUAGCAGGACCCCGAG- -5'
miRNA: 3'- cUUCUCCCUCU---UAGcagGACCCCGag -5'
miRNA: 3'- -CuuCUCCCUCuuaGCAGGaCCCC-GAG- -5'
miRNA: 3'- cuUCUCCCUCUua-----GCAGGa--CCC----CGAG- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
|
Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 4347 | 3' | -56.1 | NC_001720.1 | + | 19546 | 1.08 | 0.000642 |
|
Target: 5'- gGAAGAGGGAGAAUCGUCCUGGGGCUCc -3' miRNA: 3'- -CUUCUCCCUCUUAGCAGGACCCCGAG- -5' |
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| 4347 | 3' | -56.1 | NC_001720.1 | + | 17615 | 0.7 | 0.355775 |
|
Target: 5'- uGAGAGGGGGAgccAUCaa-CUGGGGCa- -3' miRNA: 3'- cUUCUCCCUCU---UAGcagGACCCCGag -5' |
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| 4347 | 3' | -56.1 | NC_001720.1 | + | 9953 | 0.69 | 0.410232 |
|
Target: 5'- cGggGAGGGAG---CGUUC-GGGGuCUCg -3' miRNA: 3'- -CuuCUCCCUCuuaGCAGGaCCCC-GAG- -5' |
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| 4347 | 3' | -56.1 | NC_001720.1 | + | 38400 | 0.68 | 0.459377 |
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Target: 5'- -uAGGGGGAGAuagaucgCGUCCaagGGGaggaGCUCa -3' miRNA: 3'- cuUCUCCCUCUua-----GCAGGa--CCC----CGAG- -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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