miRNA: 3'- aAAGUa-CGCGCGGcCUUAGGUCaacu -5'
miRNA: 3'- aaAgUACGCGCGGCCUUAG-------GUCAacu -5'
miRNA: 3'- aaAGUACGCGCGGCC---UUA-GGUCAa--CU- -5'
miRNA: 3'- aaAGUa--CGCGCGGCCUuAGGUCAAcu -5'
miRNA: 3'- -AAAGUACGCGCGGCCUUAGGUCAACU- -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 | |||||||
| 18754 | 5' | -52.4 | NC_004683.1 | + | 41700 | 0.66 | 0.81708 |
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Target: 5'- gUUCGccGCGCGCCcGGAUCCGGc--- -3' miRNA: 3'- aAAGUa-CGCGCGGcCUUAGGUCaacu -5' |
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| 18754 | 5' | -52.4 | NC_004683.1 | + | 46809 | 0.68 | 0.733458 |
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Target: 5'- -gUgGUGCGCGUCGGAAUCggaucguCAGUg-- -3' miRNA: 3'- aaAgUACGCGCGGCCUUAG-------GUCAacu -5' |
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| 18754 | 5' | -52.4 | NC_004683.1 | + | 47090 | 0.77 | 0.246075 |
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Target: 5'- -aUCGUGCGCGCCGGcucGGUaCCGGUgugGAc -3' miRNA: 3'- aaAGUACGCGCGGCC---UUA-GGUCAa--CU- -5' |
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| 18754 | 5' | -52.4 | NC_004683.1 | + | 51250 | 0.78 | 0.233191 |
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Target: 5'- -cUCGgcgGCGCGCCGGA-UCCAGUUc- -3' miRNA: 3'- aaAGUa--CGCGCGGCCUuAGGUCAAcu -5' |
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| 18754 | 5' | -52.4 | NC_004683.1 | + | 1701 | 1.07 | 0.002483 |
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Target: 5'- cUUUCAUGCGCGCCGGAAUCCAGUUGAu -3' miRNA: 3'- -AAAGUACGCGCGGCCUUAGGUCAACU- -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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