miRNA: 3'- gGAUCCUCUAG-AGGugCUgC---------AUCAGG- -5'
miRNA: 3'- -GGAUCCUCUAGAGG-UGCu--GCaUCagg -5'
miRNA: 3'- -GGAUCCUCUAG-----AGGUGCUGcAUcAGG- -5'
miRNA: 3'- -GgAUCCUCU---------------AGAGGUGCUGCAUCagg -5'
miRNA: 3'- -GGAUCCUCUAGAGGUGCUGCAUCAGG- -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 | |||||||
| 11215 | 3' | -51.2 | NC_003038.1 | + | 12260 | 0.66 | 0.998962 |
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Target: 5'- aUUAGGAGGUCaUUUugGAgGagguuuauaUAGUCCa -3' miRNA: 3'- gGAUCCUCUAG-AGGugCUgC---------AUCAGG- -5' |
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| 11215 | 3' | -51.2 | NC_003038.1 | + | 43136 | 0.67 | 0.994556 |
|
Target: 5'- gCUUAGGAGAUCUCCuACGuuuCGgAGa-- -3' miRNA: 3'- -GGAUCCUCUAGAGG-UGCu--GCaUCagg -5' |
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| 11215 | 3' | -51.2 | NC_003038.1 | + | 96962 | 0.7 | 0.968126 |
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Target: 5'- gUCUAGGAGAUCuaucuUCUACGGC-UAuUCCa -3' miRNA: 3'- -GGAUCCUCUAG-----AGGUGCUGcAUcAGG- -5' |
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| 11215 | 3' | -51.2 | NC_003038.1 | + | 43367 | 0.76 | 0.772565 |
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Target: 5'- aCgUAGGAGAucuccuaagcgacgaUCUCCGCGACGUAGn-- -3' miRNA: 3'- -GgAUCCUCU---------------AGAGGUGCUGCAUCagg -5' |
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| 11215 | 3' | -51.2 | NC_003038.1 | + | 43328 | 1.14 | 0.0069 |
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Target: 5'- uCCUAGGAGAUCUCCACGACGUAGUCCu -3' miRNA: 3'- -GGAUCCUCUAGAGGUGCUGCAUCAGG- -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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