miRNA: 3'- ugGCCUGCCGCAGUUCCuag---UCCagu -5'
miRNA: 3'- -UGGCC-----UGCCGc-AGUUCCU--AGU-CCAGU- -5'
miRNA: 3'- -UGG-----CCUGCCGCAGuUCcUAGu-CCAGU- -5'
miRNA: 3'- -UGGCC------UGC-CGCa--GUUCCUa-----GUCCAGU- -5'
miRNA: 3'- -UGGCCUGCCGCAGUUCCUAGUCCAGU- -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 | |||||||
| 27686 | 3' | -56.6 | NC_005882.1 | + | 7707 | 0.67 | 0.445434 |
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Target: 5'- -gCGGGCGGCGUCGAGGcuacggAGGa-- -3' miRNA: 3'- ugGCCUGCCGCAGUUCCuag---UCCagu -5' |
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| 27686 | 3' | -56.6 | NC_005882.1 | + | 21533 | 0.68 | 0.435531 |
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Target: 5'- cGCCGGuuccgACGGUcaUCAAGGAugUCAcGGUCAa -3' miRNA: 3'- -UGGCC-----UGCCGc-AGUUCCU--AGU-CCAGU- -5' |
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| 27686 | 3' | -56.6 | NC_005882.1 | + | 16205 | 0.68 | 0.435531 |
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Target: 5'- aGCCguacaGGACGGCGUCcAGcAUCucGGUCAc -3' miRNA: 3'- -UGG-----CCUGCCGCAGuUCcUAGu-CCAGU- -5' |
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| 27686 | 3' | -56.6 | NC_005882.1 | + | 18823 | 0.68 | 0.416113 |
|
Target: 5'- cGCCGGcgugauACGcGCGaugCAGGGAgcgcagCAGGUCGa -3' miRNA: 3'- -UGGCC------UGC-CGCa--GUUCCUa-----GUCCAGU- -5' |
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| 27686 | 3' | -56.6 | NC_005882.1 | + | 27734 | 1.08 | 0.000516 |
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Target: 5'- cACCGGACGGCGUCAAGGAUCAGGUCAa -3' miRNA: 3'- -UGGCCUGCCGCAGUUCCUAGUCCAGU- -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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