miRNA: 3'- -CGCGUAGa-----GAGGCGGa---UUUGU------CGGau -5'
miRNA: 3'- cGCGUAGAGAggCGGau----UUGuCGGau -5'
miRNA: 3'- -CGCGUAGAGa--GGCGGAUUuguCGGau -5'
miRNA: 3'- -CGCGUAGAGAGGCGGAUUUGUCGGAU- -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 | |||||||
| 3515 | 3' | -53.6 | NC_001623.1 | + | 109529 | 0.66 | 0.938258 |
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Target: 5'- uGCGCGUUgcagugCUCCGCCgcaaAGGCAgaaugcGCCg- -3' miRNA: 3'- -CGCGUAGa-----GAGGCGGa---UUUGU------CGGau -5' |
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| 3515 | 3' | -53.6 | NC_001623.1 | + | 21249 | 0.67 | 0.910169 |
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Target: 5'- cUGCAUCUCUuuGCCguacuuGAC-GCCg- -3' miRNA: 3'- cGCGUAGAGAggCGGau----UUGuCGGau -5' |
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| 3515 | 3' | -53.6 | NC_001623.1 | + | 18092 | 0.72 | 0.63647 |
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Target: 5'- aGCGCAUUUCgaaCCGCCUAGu--GCCg- -3' miRNA: 3'- -CGCGUAGAGa--GGCGGAUUuguCGGau -5' |
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| 3515 | 3' | -53.6 | NC_001623.1 | + | 122420 | 1.09 | 0.003386 |
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Target: 5'- cGCGCAUCUCUCCGCCUAAACAGCCUAu -3' miRNA: 3'- -CGCGUAGAGAGGCGGAUUUGUCGGAU- -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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