miRNA: 3'- -GCAGCGGCa---CGc-------------UAGUCGCCUCCauu -5'
miRNA: 3'- -GCAGC----GGCACGcUAGUCGCCu---CCAUU- -5'
miRNA: 3'- -GCa--GCGG----CACGcUAGUCGCCuCCAUU- -5'
miRNA: 3'- -GCAGCGGCAC-------------GCUAGUCGcC------------UCCAUU- -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
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| Predicted miRNA align pattern | |||||||
| 20869 | 3' | -57.2 | NC_004689.1 | + | 53230 | 0.66 | 0.674849 |
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Target: 5'- uCGUCGUCGgucgGCucggcagccgguucGUCAGCGGAGGc-- -3' miRNA: 3'- -GCAGCGGCa---CGc-------------UAGUCGCCUCCauu -5' |
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| 20869 | 3' | -57.2 | NC_004689.1 | + | 12023 | 0.67 | 0.60632 |
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Target: 5'- gCGUUGagguCCGUGCcAUCGGCGGuggcGGUGAc -3' miRNA: 3'- -GCAGC----GGCACGcUAGUCGCCu---CCAUU- -5' |
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| 20869 | 3' | -57.2 | NC_004689.1 | + | 11625 | 0.68 | 0.563773 |
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Target: 5'- cCGgugCGCCcuguGUGCcGUCAGCGGcGGUGGu -3' miRNA: 3'- -GCa--GCGG----CACGcUAGUCGCCuCCAUU- -5' |
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| 20869 | 3' | -57.2 | NC_004689.1 | + | 29100 | 0.68 | 0.552199 |
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Target: 5'- aCGUCGCCGUGgacgacuggcacaCGAUCAGCcGugagcauguuguAGGUGAg -3' miRNA: 3'- -GCAGCGGCAC-------------GCUAGUCGcC------------UCCAUU- -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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