miRNA: 3'- -GGUa-GUUAcUUUUAGCGGGUGCC-----CGC- -5'
miRNA: 3'- -GGUAGU-----------UACUUUUAGCGGg-----UGCCCGc -5'
miRNA: 3'- gguaGUUACUUUUAGCGGGUgCCCGC- -5'
miRNA: 3'- -GGUAGUUACUU--UUAGCG-----GGUGCCCGC- -5'
miRNA: 3'- -GGUAGUUACUUUUAGCGGGUGCCCGC- -5'
Results 21 - 25 of 25 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 | |||||||
| 22728 | 5' | -50.1 | NC_005091.1 | + | 19060 | 0.74 | 0.568948 |
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Target: 5'- cCCAcgCAGU-AAGAUCGCCCACGGugaucGCGa -3' miRNA: 3'- -GGUa-GUUAcUUUUAGCGGGUGCC-----CGC- -5' |
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| 22728 | 5' | -50.1 | NC_005091.1 | + | 7952 | 0.76 | 0.492854 |
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Target: 5'- gCCGUUAcgaggacugacAUGGAAGUCGCCauccaaGCGGGCu -3' miRNA: 3'- -GGUAGU-----------UACUUUUAGCGGg-----UGCCCGc -5' |
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| 22728 | 5' | -50.1 | NC_005091.1 | + | 48628 | 0.76 | 0.471952 |
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Target: 5'- ---cCGAUGAGGAUCGCUCG-GGGCGg -3' miRNA: 3'- gguaGUUACUUUUAGCGGGUgCCCGC- -5' |
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| 22728 | 5' | -50.1 | NC_005091.1 | + | 19166 | 0.79 | 0.357231 |
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Target: 5'- cCCGUCGAUGAAcuGGUCGCgaucaCCGUGGGCGa -3' miRNA: 3'- -GGUAGUUACUU--UUAGCG-----GGUGCCCGC- -5' |
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| 22728 | 5' | -50.1 | NC_005091.1 | + | 51177 | 1.11 | 0.003166 |
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Target: 5'- uCCAUCAAUGAAAAUCGCCCACGGGCGc -3' miRNA: 3'- -GGUAGUUACUUUUAGCGGGUGCCCGC- -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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