miRNA: 3'- gaGGGGGcCGCGa-----AAGCGGUGgCaGC- -5'
miRNA: 3'- -GAGGG-GGCCGCGAaag---CGGugGCaGC- -5'
miRNA: 3'- gagGGGGCCGCGAaaGCGGUGG------------CAGC- -5'
miRNA: 3'- gagGGGGCCGCGAa-AGcGGUGGCAGC- -5'
miRNA: 3'- -GAGGGGGCCGCGAAagcgGUGGCAGC- -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 | |||||||
| 20851 | 5' | -60.9 | NC_004689.1 | + | 60905 | 0.66 | 0.540487 |
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Target: 5'- -gUCCCCaGCGCcaugagUUCGCCACgG-CGa -3' miRNA: 3'- gaGGGGGcCGCGa-----AAGCGGUGgCaGC- -5' |
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| 20851 | 5' | -60.9 | NC_004689.1 | + | 52448 | 0.66 | 0.540487 |
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Target: 5'- gCUUUCaCCGGCGCUggacuaGCCugCG-CGg -3' miRNA: 3'- -GAGGG-GGCCGCGAaag---CGGugGCaGC- -5' |
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| 20851 | 5' | -60.9 | NC_004689.1 | + | 60945 | 0.66 | 0.520534 |
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Target: 5'- --aCUCCGGCGCUggUGCUGCCcagguggcgcguGUCGa -3' miRNA: 3'- gagGGGGCCGCGAaaGCGGUGG------------CAGC- -5' |
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| 20851 | 5' | -60.9 | NC_004689.1 | + | 11542 | 0.68 | 0.40823 |
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Target: 5'- --aCUCCGGUGUUgaUC-CCACCGUCGa -3' miRNA: 3'- gagGGGGCCGCGAa-AGcGGUGGCAGC- -5' |
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| 20851 | 5' | -60.9 | NC_004689.1 | + | 65255 | 0.71 | 0.258471 |
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Target: 5'- aCUUCUCCGGCGCUU----UACCGUCGa -3' miRNA: 3'- -GAGGGGGCCGCGAAagcgGUGGCAGC- -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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