miRNA: 3'- -CGUAGCGG-----GCCGG-GC-UACCU--------UACUac -5'
miRNA: 3'- cgUAGCGG------GCCGGGCuaCC---------------UUACUAC- -5'
miRNA: 3'- -CGU-------AGCGGgCCGGGCUACCuuACUac -5'
miRNA: 3'- -CGUAGCGGGCCGGGCUACCUUACUAC- -5'
Results 1 - 4 of 4 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 | |||||||
| 8498 | 5' | -55.5 | NC_002169.1 | + | 22396 | 0.68 | 0.838332 |
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Target: 5'- gGCGUCGCCauguaCGGCCgCGgAUGGAgcggcgucGUGAg- -3' miRNA: 3'- -CGUAGCGG-----GCCGG-GC-UACCU--------UACUac -5' |
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| 8498 | 5' | -55.5 | NC_002169.1 | + | 123230 | 0.68 | 0.816219 |
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Target: 5'- -uGUCGCCggcaugCGGCCCGcgGGuuuaauuucuggucaGAUGAUGu -3' miRNA: 3'- cgUAGCGG------GCCGGGCuaCC---------------UUACUAC- -5' |
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| 8498 | 5' | -55.5 | NC_002169.1 | + | 36855 | 0.69 | 0.775318 |
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Target: 5'- uGCAguacgauUCGCCgGGCUCGAUGG--UGAa- -3' miRNA: 3'- -CGU-------AGCGGgCCGGGCUACCuuACUac -5' |
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| 8498 | 5' | -55.5 | NC_002169.1 | + | 39374 | 1.1 | 0.002422 |
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Target: 5'- cGCAUCGCCCGGCCCGAUGGAAUGAUGu -3' miRNA: 3'- -CGUAGCGGGCCGGGCUACCUUACUAC- -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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