miRNA: 3'- guuuuaaUAGGCGCG---UCGUG---CACCUc -5'
miRNA: 3'- -GUUUUaaUAGGCGCGUCG------UGcACCUC- -5'
miRNA: 3'- -GUUUUAauaGGCGCGUCGuGCaCCUC- -5'
miRNA: 3'- guuuuaauagGCGCGUCGUGC-ACCUC- -5'
miRNA: 3'- -GUUUUAAuaGGCGCGUCGUGCACCUC- -5'
Results 1 - 5 of 5 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 | |||||||
| 4329 | 5' | -49.1 | NC_001720.1 | + | 8841 | 0.66 | 0.926558 |
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Target: 5'- ------cGUCCGCGUgaaAGCGCcccGUGGAa -3' miRNA: 3'- guuuuaaUAGGCGCG---UCGUG---CACCUc -5' |
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| 4329 | 5' | -49.1 | NC_001720.1 | + | 3752 | 0.69 | 0.791071 |
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Target: 5'- gCGAGAg-GUCCGCGCAGUggauuaGCaUGGGGg -3' miRNA: 3'- -GUUUUaaUAGGCGCGUCG------UGcACCUC- -5' |
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| 4329 | 5' | -49.1 | NC_001720.1 | + | 15930 | 0.72 | 0.667653 |
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Target: 5'- gUAAAGUcgaCCGCGCAGC-CGgGGAGg -3' miRNA: 3'- -GUUUUAauaGGCGCGUCGuGCaCCUC- -5' |
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| 4329 | 5' | -49.1 | NC_001720.1 | + | 26142 | 0.74 | 0.505464 |
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Target: 5'- ---------gCGCGCAGCACGcUGGAGa -3' miRNA: 3'- guuuuaauagGCGCGUCGUGC-ACCUC- -5' |
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| 4329 | 5' | -49.1 | NC_001720.1 | + | 8314 | 0.97 | 0.021367 |
|
Target: 5'- cCAAAAUUuaCCGCGCAGCACGUGGAGg -3' miRNA: 3'- -GUUUUAAuaGGCGCGUCGUGCACCUC- -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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