miRNA: 3'- -UCuaCGGCCA----------ACU--------CGCUGCGGa---GCUU- -5'
miRNA: 3'- -UCuACGGCCAacuCGCuGCGgAGCUu -5'
miRNA: 3'- uCUACGGCCa-----------ACUCGC---------UGCGGAGCUu -5'
miRNA: 3'- -UCUACGGCCAACUCGCUGCGGAGCUU- -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 | |||||||
| 22705 | 3' | -56.9 | NC_005091.1 | + | 35123 | 0.66 | 0.634723 |
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Target: 5'- gAGcgGCCGGUcagcagcuugUGGuacgcgucGCGGCGCCgccgCGAGg -3' miRNA: 3'- -UCuaCGGCCA----------ACU--------CGCUGCGGa---GCUU- -5' |
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| 22705 | 3' | -56.9 | NC_005091.1 | + | 45921 | 0.66 | 0.612796 |
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Target: 5'- gAGuUGCCGGUguuGCGcCGCgUCGAu -3' miRNA: 3'- -UCuACGGCCAacuCGCuGCGgAGCUu -5' |
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| 22705 | 3' | -56.9 | NC_005091.1 | + | 33574 | 0.72 | 0.282657 |
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Target: 5'- cGAUGCCGGccucucgaccuaUGAGCGcgaaaucgcGCGCCUCGGc -3' miRNA: 3'- uCUACGGCCa-----------ACUCGC---------UGCGGAGCUu -5' |
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| 22705 | 3' | -56.9 | NC_005091.1 | + | 33844 | 1.06 | 0.001124 |
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Target: 5'- cAGAUGCCGGUUGAGCGACGCCUCGAAu -3' miRNA: 3'- -UCUACGGCCAACUCGCUGCGGAGCUU- -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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