miRNA: 3'- gCUGGCGGAGA-GAGCG--------------UGGCCGUuGU- -5'
miRNA: 3'- gCUGgcGGAGAGAGCGUG---GCCGUUgu -5'
miRNA: 3'- -GCUGGCGgaGAGAGCGugGCCguUGu -5'
miRNA: 3'- -GCU--GGCGGAgAGAGCGuGG-CCGUUGU- -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 | |||||||
| 22137 | 5' | -58.5 | NC_004927.1 | + | 5583 | 0.66 | 0.641672 |
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Target: 5'- aGACCGCUUCUgCUUGCucgaacuccgauucAUCGGCGuCGg -3' miRNA: 3'- gCUGGCGGAGA-GAGCG--------------UGGCCGUuGU- -5' |
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| 22137 | 5' | -58.5 | NC_004927.1 | + | 71241 | 0.66 | 0.623791 |
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Target: 5'- gGAUauUCUCUCUCGCACggaCGGCAGa- -3' miRNA: 3'- gCUGgcGGAGAGAGCGUG---GCCGUUgu -5' |
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| 22137 | 5' | -58.5 | NC_004927.1 | + | 69469 | 0.67 | 0.581866 |
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Target: 5'- aCGACUGCgaCUCUCGCuaCGGguGCu -3' miRNA: 3'- -GCUGGCGgaGAGAGCGugGCCguUGu -5' |
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| 22137 | 5' | -58.5 | NC_004927.1 | + | 67822 | 0.68 | 0.510212 |
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Target: 5'- aCGAacCCGUCUaUCUCGCuCCgGGCGGCGg -3' miRNA: 3'- -GCU--GGCGGAgAGAGCGuGG-CCGUUGU- -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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