miRNA: 3'- uaUCGCCGUUg-UCG--UAGC----UGGCGCAU- -5'
miRNA: 3'- -UAUCGCCgUUGUCGUaGC-UGGCgCAU- -5'
miRNA: 3'- uaUCGCCGUUGUCGUAGc------UGG-CGcau -5'
miRNA: 3'- -UAUCGCCGUUGUCGUAGCUGGCGCAU- -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 | |||||||
| 8447 | 5' | -55.5 | NC_002166.1 | + | 895 | 0.66 | 0.566083 |
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Target: 5'- -cAGCGGCAAaaAGCugAUCGgccuGCCGUGUAa -3' miRNA: 3'- uaUCGCCGUUg-UCG--UAGC----UGGCGCAU- -5' |
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| 8447 | 5' | -55.5 | NC_002166.1 | + | 26826 | 0.66 | 0.554819 |
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Target: 5'- gAUAGCGGaAACGGCGaUGuACCGgGUAa -3' miRNA: 3'- -UAUCGCCgUUGUCGUaGC-UGGCgCAU- -5' |
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| 8447 | 5' | -55.5 | NC_002166.1 | + | 8645 | 0.67 | 0.488909 |
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Target: 5'- -cAGCGGCAGCGGCAUCcuccuuuACCuGCu-- -3' miRNA: 3'- uaUCGCCGUUGUCGUAGc------UGG-CGcau -5' |
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| 8447 | 5' | -55.5 | NC_002166.1 | + | 23384 | 1.04 | 0.001057 |
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Target: 5'- aAUAGCGGCAACAGCAUCGACCGCGUAc -3' miRNA: 3'- -UAUCGCCGUUGUCGUAGCUGGCGCAU- -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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