miRNA: 3'- -GGGGGGGGUGUAAUGUCGUUCAGGAA- -5'
miRNA: 3'- -GGGGGGGGUGUA------AUGUCG-----UUCAGGAA- -5'
miRNA: 3'- -GGGGGGGGugUaaugucGUUCAGGAa -5'
miRNA: 3'- gGGGGGGGUGuaauGUCGUUCAGGAa -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 | |||||||
| 2458 | 5' | -55 | NC_001436.1 | + | 1741 | 1.06 | 9.5e-05 |
|
Target: 5'- uCCCCCCCCACAUUACAGCAAGUCCUUc -3' miRNA: 3'- -GGGGGGGGUGUAAUGUCGUUCAGGAA- -5' |
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| 2458 | 5' | -55 | NC_001436.1 | + | 802 | 0.71 | 0.07954 |
|
Target: 5'- cCCCUCCCUAUGUugagccUACAGCcccccAAGUCCUUc -3' miRNA: 3'- -GGGGGGGGUGUA------AUGUCG-----UUCAGGAA- -5' |
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| 2458 | 5' | -55 | NC_001436.1 | + | 6070 | 0.67 | 0.179968 |
|
Target: 5'- aCCCCCCCUugAaaau--CGAGUCCUg -3' miRNA: 3'- -GGGGGGGGugUaaugucGUUCAGGAa -5' |
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| 2458 | 5' | -55 | NC_001436.1 | + | 6857 | 0.66 | 0.18573 |
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Target: 5'- aUUCCUCCAC----CAGCAGGUCCUc -3' miRNA: 3'- gGGGGGGGUGuaauGUCGUUCAGGAa -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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