miRNA: 3'- aCGCGa--GACG-----ACAUGUa------GUGUCG-AGU- -5'
miRNA: 3'- aCGCGAGACGa-----CAUgUAGU----GUCGAGU- -5'
miRNA: 3'- -ACGCGA-GACGACaUGua---GUGUCGAGu -5'
miRNA: 3'- -ACGCGAGACGACAUGUAGUGUCGAGU- -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 | |||||||
| 1254 | 3' | -53.2 | NC_001317.1 | + | 8601 | 0.66 | 0.624889 |
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Target: 5'- gGCGCaggCUGUucgggUGUGCAgccgacgCACAGCaUCAg -3' miRNA: 3'- aCGCGa--GACG-----ACAUGUa------GUGUCG-AGU- -5' |
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| 1254 | 3' | -53.2 | NC_001317.1 | + | 14366 | 0.68 | 0.485965 |
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Target: 5'- gGCGCUCUGCacauugGUA-AUCAguacCGGCUCGu -3' miRNA: 3'- aCGCGAGACGa-----CAUgUAGU----GUCGAGU- -5' |
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| 1254 | 3' | -53.2 | NC_001317.1 | + | 9355 | 0.7 | 0.354209 |
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Target: 5'- aUGCGCUgCUGCUG-ACugguaCGCAGCUUu -3' miRNA: 3'- -ACGCGA-GACGACaUGua---GUGUCGAGu -5' |
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| 1254 | 3' | -53.2 | NC_001317.1 | + | 1061 | 1.09 | 0.000621 |
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Target: 5'- cUGCGCUCUGCUGUACAUCACAGCUCAc -3' miRNA: 3'- -ACGCGAGACGACAUGUAGUGUCGAGU- -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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