miRNA: 3'- uCCUUGAagUGAGCaUGAGCUGGaag -5'
miRNA: 3'- uccuugaAGU-GAGCAUGAGCUGGAAG- -5'
miRNA: 3'- uCCUU-GAAGUGAGCaUG---AGCUGGAAG- -5'
miRNA: 3'- -UCCUUGAAGUGAGCAUGAGCUGGAAG- -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 | |||||||
| 12159 | 3' | -49.5 | NC_003309.1 | + | 27522 | 0.69 | 0.864629 |
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Target: 5'- uGGAGCU--AUUCGcGCUCGACCa-- -3' miRNA: 3'- uCCUUGAagUGAGCaUGAGCUGGaag -5' |
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| 12159 | 3' | -49.5 | NC_003309.1 | + | 11705 | 0.69 | 0.83811 |
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Target: 5'- ------cUCGcCUCGUAUUCGGCCUUCu -3' miRNA: 3'- uccuugaAGU-GAGCAUGAGCUGGAAG- -5' |
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| 12159 | 3' | -49.5 | NC_003309.1 | + | 31611 | 0.71 | 0.736129 |
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Target: 5'- uGGAGcCUUUGCUCGgGCcggUUGACCUUCg -3' miRNA: 3'- uCCUU-GAAGUGAGCaUG---AGCUGGAAG- -5' |
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| 12159 | 3' | -49.5 | NC_003309.1 | + | 36486 | 1.12 | 0.002574 |
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Target: 5'- gAGGAACUUCACUCGUACUCGACCUUCg -3' miRNA: 3'- -UCCUUGAAGUGAGCAUGAGCUGGAAG- -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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