miRNA: 3'- aAGCGCUGcaaGGAGGGgGGCCGUaa -5'
miRNA: 3'- aaGCGCUGCAaggaGGGGGGCCGuaa -5'
miRNA: 3'- -AAGCGCUGCaa----GGag-GGGGGCCGuaa -5'
miRNA: 3'- -AAGcGCUGCAAGGAGGgGGGCCGuaa -5'
miRNA: 3'- -AAGCGCUGCAAGGAGGGGGGCCGUAA- -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 | |||||||
| 24955 | 3' | -60.2 | NC_005284.1 | + | 116 | 0.66 | 0.4382 |
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Target: 5'- gUCGCGAUa--CCUCCCaCUGGCAa- -3' miRNA: 3'- aAGCGCUGcaaGGAGGGgGGCCGUaa -5' |
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| 24955 | 3' | -60.2 | NC_005284.1 | + | 15477 | 0.66 | 0.392135 |
|
Target: 5'- -gCGCGACGUag--CCUCCCGGCu-- -3' miRNA: 3'- aaGCGCUGCAaggaGGGGGGCCGuaa -5' |
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| 24955 | 3' | -60.2 | NC_005284.1 | + | 54466 | 0.68 | 0.333178 |
|
Target: 5'- aUUCGCGACGagcgcaCCgcaCCCCCGGUg-- -3' miRNA: 3'- -AAGCGCUGCaa----GGag-GGGGGCCGuaa -5' |
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| 24955 | 3' | -60.2 | NC_005284.1 | + | 39420 | 0.71 | 0.212387 |
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Target: 5'- uUUC-CGACGUUCUUCCgCCCGGUc-- -3' miRNA: 3'- -AAGcGCUGCAAGGAGGgGGGCCGuaa -5' |
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| 24955 | 3' | -60.2 | NC_005284.1 | + | 40980 | 1.03 | 0.00073 |
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Target: 5'- aUUCGCGACGUUCCUCCCCCCGGCAUUg -3' miRNA: 3'- -AAGCGCUGCAAGGAGGGGGGCCGUAA- -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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