miRNA: 3'- ucUAGAGAGCauuUCuGAAGCU--UGCG- -5'
miRNA: 3'- -UCUA----GAGAGCaUUUCuGAAGCU-UGCG- -5'
miRNA: 3'- -UCUAG---AGAGcauuuCUGAAGCUUGCG- -5'
miRNA: 3'- -UCUAGAGAGCAUUUCUGAAGCUUGCG- -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 | |||||||
| 3431 | 3' | -45.4 | NC_001598.1 | + | 2916 | 0.66 | 0.92821 |
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Target: 5'- -cGUCUCUCG---AGuCUUCGAuuACGUg -3' miRNA: 3'- ucUAGAGAGCauuUCuGAAGCU--UGCG- -5' |
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| 3431 | 3' | -45.4 | NC_001598.1 | + | 6121 | 0.66 | 0.898734 |
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Target: 5'- cGGAUaucgCUCUCG-AGAG-CUUCGAgACGUu -3' miRNA: 3'- -UCUA----GAGAGCaUUUCuGAAGCU-UGCG- -5' |
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| 3431 | 3' | -45.4 | NC_001598.1 | + | 12955 | 0.69 | 0.76616 |
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Target: 5'- uGGAUUaagUCUCcucu-GGCUUCGGGCGCc -3' miRNA: 3'- -UCUAG---AGAGcauuuCUGAAGCUUGCG- -5' |
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| 3431 | 3' | -45.4 | NC_001598.1 | + | 840 | 1.14 | 0.001154 |
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Target: 5'- gAGAUCUCUCGUAAAGACUUCGAACGCu -3' miRNA: 3'- -UCUAGAGAGCAUUUCUGAAGCUUGCG- -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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