miRNA: 3'- aAGGG-GGuCCCGCGGCCG---------------U----UCCCGGC- -5'
miRNA: 3'- aaGGG--GGUC--CCG-------------CGGCCGUUCCCGgC- -5'
miRNA: 3'- aaGGGGGUCCcGCGG---CCGUU--CCCGGc -5'
miRNA: 3'- aagGGGGuCCCGCGGCcGUu-CC-CGGc -5'
Results 21 - 24 of 24 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 | |||||||
| 23109 | 3' | -66.9 | NC_005178.1 | + | 29416 | 0.66 | 0.140529 |
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Target: 5'- aUCCCgCC-GGGCGCUGGCucgguuucacugucgAaggaGGGGCUGc -3' miRNA: 3'- aAGGG-GGuCCCGCGGCCG---------------U----UCCCGGC- -5' |
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| 23109 | 3' | -66.9 | NC_005178.1 | + | 28700 | 0.66 | 0.146273 |
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Target: 5'- -cCCCgaCCAGauGGCggccgacauguggGCCGGCAAGGGCgGc -3' miRNA: 3'- aaGGG--GGUC--CCG-------------CGGCCGUUCCCGgC- -5' |
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| 23109 | 3' | -66.9 | NC_005178.1 | + | 27872 | 0.66 | 0.154674 |
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Target: 5'- -aCCUCCAGGcCGCCcagGGCAAcuGGGUCa -3' miRNA: 3'- aaGGGGGUCCcGCGG---CCGUU--CCCGGc -5' |
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| 23109 | 3' | -66.9 | NC_005178.1 | + | 9417 | 0.66 | 0.154674 |
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Target: 5'- --gCCCCuGGGCGCCGcCAucGGuGCCa -3' miRNA: 3'- aagGGGGuCCCGCGGCcGUu-CC-CGGc -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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