miRNA: 3'- -GGUGu-CGGU-GAGGC-ACGCUuGCCAGU- -5'
miRNA: 3'- -GGUGUCGGUGa-GGCa-CGCu-------UG-CCAGU- -5'
miRNA: 3'- -GGuGUCGGUGAGgCACGCUUGC--CAGu -5'
miRNA: 3'- -GGUGUCGGUGAGGCACGCUUGCCAGU- -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 | |||||||
| 16923 | 5' | -55.9 | NC_004313.1 | + | 9474 | 0.66 | 0.634284 |
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Target: 5'- aCCAUuuGCCAgCUCUGaUGUGA-UGGUCAu -3' miRNA: 3'- -GGUGu-CGGU-GAGGC-ACGCUuGCCAGU- -5' |
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| 16923 | 5' | -55.9 | NC_004313.1 | + | 8153 | 0.66 | 0.634284 |
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Target: 5'- cUCACAGCCACcgCCGcaGCGucaucaccGCuGGUCAc -3' miRNA: 3'- -GGUGUCGGUGa-GGCa-CGCu-------UG-CCAGU- -5' |
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| 16923 | 5' | -55.9 | NC_004313.1 | + | 13597 | 0.69 | 0.451909 |
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Target: 5'- gCC-CGGCCAUUCgGUGUGGACGuuGUUg -3' miRNA: 3'- -GGuGUCGGUGAGgCACGCUUGC--CAGu -5' |
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| 16923 | 5' | -55.9 | NC_004313.1 | + | 14562 | 1.1 | 0.000505 |
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Target: 5'- aCCACAGCCACUCCGUGCGAACGGUCAc -3' miRNA: 3'- -GGUGUCGGUGAGGCACGCUUGCCAGU- -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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