miRNA: 3'- gGCGgCGCgGACCAa-----CCUCUGUUaau -5'
miRNA: 3'- -GGCGGCGCgGaCCaaCCUCUGuuaau -5'
miRNA: 3'- gGCGGCG-------------CGGACCa--ACCUCUGUUaau -5'
miRNA: 3'- -GGCGGCGCGGACCAACCUCUGUUAAU- -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 | |||||||
| 33222 | 5' | -54.6 | NC_007523.1 | + | 2186 | 0.66 | 0.127972 |
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Target: 5'- gCGCgGCG-CUGGUguaaugGGAGGCGGc-- -3' miRNA: 3'- gGCGgCGCgGACCAa-----CCUCUGUUaau -5' |
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| 33222 | 5' | -54.6 | NC_007523.1 | + | 4701 | 0.67 | 0.119552 |
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Target: 5'- cUCGCCGCGgC-GGgaGGAGACu---- -3' miRNA: 3'- -GGCGGCGCgGaCCaaCCUCUGuuaau -5' |
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| 33222 | 5' | -54.6 | NC_007523.1 | + | 2318 | 0.67 | 0.103882 |
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Target: 5'- gCGUCGUcaccaccaucaccGCCUGGgggUGGGGGCGGg-- -3' miRNA: 3'- gGCGGCG-------------CGGACCa--ACCUCUGUUaau -5' |
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| 33222 | 5' | -54.6 | NC_007523.1 | + | 3350 | 1.09 | 2.6e-05 |
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Target: 5'- aCCGCCGCGCCUGGUUGGAGACAAUUAg -3' miRNA: 3'- -GGCGGCGCGGACCAACCUCUGUUAAU- -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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