miRNA: 3'- uuUGUCUGc-GGCU----UUAGUAUaa-GCCG- -5'
miRNA: 3'- uuugUCUG-CGGCuuUAGUAUaAGCCG- -5'
miRNA: 3'- -UUUGUCugCgGCUUUaGUAU-----AAGCCG- -5'
miRNA: 3'- -UUUGUCUGCGGCUUUAGUAUAAGCCG- -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 | |||||||
| 16722 | 3' | -46.2 | NC_004167.1 | + | 38738 | 0.67 | 0.974394 |
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Target: 5'- -cGCAGACucCCGGuauuGAUCAUAggcCGGCu -3' miRNA: 3'- uuUGUCUGc-GGCU----UUAGUAUaa-GCCG- -5' |
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| 16722 | 3' | -46.2 | NC_004167.1 | + | 17742 | 0.7 | 0.876898 |
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Target: 5'- ---aAGACuGCCGggGUUGUGcUUGGCg -3' miRNA: 3'- uuugUCUG-CGGCuuUAGUAUaAGCCG- -5' |
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| 16722 | 3' | -46.2 | NC_004167.1 | + | 9974 | 0.71 | 0.859329 |
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Target: 5'- cGAACAGugGgCGAAGcCAUGaaguuUUUGGCg -3' miRNA: 3'- -UUUGUCugCgGCUUUaGUAU-----AAGCCG- -5' |
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| 16722 | 3' | -46.2 | NC_004167.1 | + | 19145 | 1.11 | 0.004301 |
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Target: 5'- aAAACAGACGCCGAAAUCAUAUUCGGCu -3' miRNA: 3'- -UUUGUCUGCGGCUUUAGUAUAAGCCG- -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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