miRNA: 3'- -GGGUACUGGAa---CGAGCGUCcuc-UGCG- -5'
miRNA: 3'- ggGUACuGGAACGAg-CG-------UCCUCUGCG- -5'
miRNA: 3'- -GGGUACUGGaa----CGAGC-GUCCUCUGCg -5'
miRNA: 3'- -GGGu--ACUGGAACGagCGUCcUCUgCG- -5'
miRNA: 3'- -GGGUACUGGAACGAGCGUCCUCUGCG- -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 | |||||||
| 31548 | 3' | -54.8 | NC_006820.1 | + | 119742 | 0.66 | 0.970606 |
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Target: 5'- aCCUGUGACCUuuugGUUCGUAGccaaACGCu -3' miRNA: 3'- -GGGUACUGGAa---CGAGCGUCcuc-UGCG- -5' |
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| 31548 | 3' | -54.8 | NC_006820.1 | + | 69414 | 0.67 | 0.953435 |
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Target: 5'- -gUAUG-CCUUGCUgaGCaagggccAGGAGGCGCu -3' miRNA: 3'- ggGUACuGGAACGAg-CG-------UCCUCUGCG- -5' |
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| 31548 | 3' | -54.8 | NC_006820.1 | + | 117944 | 0.68 | 0.931539 |
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Target: 5'- aUCCGUGAUUaugaacGCUUGaCAGGGGACGa -3' miRNA: 3'- -GGGUACUGGaa----CGAGC-GUCCUCUGCg -5' |
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| 31548 | 3' | -54.8 | NC_006820.1 | + | 136417 | 0.68 | 0.921013 |
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Target: 5'- uCCCucuUGACCUUGCa-GCAGcAGAaGCa -3' miRNA: 3'- -GGGu--ACUGGAACGagCGUCcUCUgCG- -5' |
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| 31548 | 3' | -54.8 | NC_006820.1 | + | 193277 | 1.14 | 0.002681 |
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Target: 5'- cCCCAUGACCUUGCUCGCAGGAGACGCu -3' miRNA: 3'- -GGGUACUGGAACGAGCGUCCUCUGCG- -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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