miRNA: 3'- aaaGCGGCUUGCGGGUC-----CCGGUCuua -5'
miRNA: 3'- aaaGCGGC--------UUGCGGG--UCCCGGUCuua -5'
miRNA: 3'- aaAGCGgCUugCGGguCCCgGUCUUa -5'
miRNA: 3'- -AAAGCGGCUUGCGGGUCCCGGUCUUA- -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 | |||||||
| 21230 | 5' | -58.2 | NC_004778.3 | + | 110113 | 0.66 | 0.731734 |
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Target: 5'- --gCGCCGAGCGCUUGGgcaccGGCCGGu-- -3' miRNA: 3'- aaaGCGGCUUGCGGGUC-----CCGGUCuua -5' |
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| 21230 | 5' | -58.2 | NC_004778.3 | + | 35826 | 0.68 | 0.608142 |
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Target: 5'- --gCGCCGcaccaacaAGCGCCUugGGGGCCAGu-- -3' miRNA: 3'- aaaGCGGC--------UUGCGGG--UCCCGGUCuua -5' |
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| 21230 | 5' | -58.2 | NC_004778.3 | + | 49182 | 0.7 | 0.486784 |
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Target: 5'- -cUCGUgGAugGCCguGGGgCAGAAg -3' miRNA: 3'- aaAGCGgCUugCGGguCCCgGUCUUa -5' |
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| 21230 | 5' | -58.2 | NC_004778.3 | + | 63608 | 1.02 | 0.003254 |
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Target: 5'- cUUUCGCCGAACGCCCAGGGCCAGAAUu -3' miRNA: 3'- -AAAGCGGCUUGCGGGUCCCGGUCUUA- -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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