miRNA: 3'- ucUGGAAGCGGCAGc--UC-GG-CUCACag -5'
miRNA: 3'- uCUGGA---AGCGGCaGCU-------------CGGCUcACAG- -5'
miRNA: 3'- -UCUGGAAGCG-GCaGCU-CGgC--UCACAG- -5'
miRNA: 3'- -UCUGGAAGCGGCAGCUCGGCUCACAG- -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 | |||||||
| 11952 | 5' | -57 | NC_003278.1 | + | 14635 | 0.66 | 0.516109 |
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Target: 5'- -aACCUUCGCCGUCcccAGuCCuGGGUGg- -3' miRNA: 3'- ucUGGAAGCGGCAGc--UC-GG-CUCACag -5' |
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| 11952 | 5' | -57 | NC_003278.1 | + | 14223 | 0.66 | 0.483393 |
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Target: 5'- cGGCCUcgcUCGCCG-CGAucagcgcugccgcGCCGA-UGUCg -3' miRNA: 3'- uCUGGA---AGCGGCaGCU-------------CGGCUcACAG- -5' |
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| 11952 | 5' | -57 | NC_003278.1 | + | 3643 | 0.71 | 0.26604 |
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Target: 5'- cAGGCCUUCGCgCG-CGAuGCgGuaGGUGUCg -3' miRNA: 3'- -UCUGGAAGCG-GCaGCU-CGgC--UCACAG- -5' |
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| 11952 | 5' | -57 | NC_003278.1 | + | 5315 | 1.08 | 0.000442 |
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Target: 5'- cAGACCUUCGCCGUCGAGCCGAGUGUCc -3' miRNA: 3'- -UCUGGAAGCGGCAGCUCGGCUCACAG- -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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