miRNA: 3'- cacaucagGGGGUGGC---AG-GGGCCGUC- -5'
miRNA: 3'- cACaUCAGGG-GGUGGCaGGgGCCGUC- -5'
miRNA: 3'- cacAUCAGGG--------GGUGGCAGG---------GGCCGUc -5'
miRNA: 3'- -CACAUCAGGGGGUGGCAGGGGCCGUC- -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 | |||||||
| 18541 | 3' | -61.5 | NC_004682.1 | + | 21753 | 0.66 | 0.353023 |
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Target: 5'- -------aCCCCGCCGacaUCuCCCGGCAGg -3' miRNA: 3'- cacaucagGGGGUGGC---AG-GGGCCGUC- -5' |
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| 18541 | 3' | -61.5 | NC_004682.1 | + | 6771 | 0.67 | 0.337027 |
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Target: 5'- uUGgAGUUCCaCCACCGcCUgCGGCGGc -3' miRNA: 3'- cACaUCAGGG-GGUGGCaGGgGCCGUC- -5' |
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| 18541 | 3' | -61.5 | NC_004682.1 | + | 34442 | 0.68 | 0.299379 |
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Target: 5'- --aUGGUCCCcgugggugCCACCGUCCucuucuucaCCGGCAc -3' miRNA: 3'- cacAUCAGGG--------GGUGGCAGG---------GGCCGUc -5' |
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| 18541 | 3' | -61.5 | NC_004682.1 | + | 47205 | 1.09 | 0.000247 |
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Target: 5'- cGUGUAGUCCCCCACCGUCCCCGGCAGg -3' miRNA: 3'- -CACAUCAGGGGGUGGCAGGGGCCGUC- -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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