miRNA: 3'- -UCAGG-CCGGCC-AG-GCUC-------------UGAGcuUGG- -5'
miRNA: 3'- -UCAG----GCCGGCCAG-GCUCUGAgCUUgG- -5'
miRNA: 3'- ucagGCCGGCCag-GCUCUGAGCUUGG- -5'
miRNA: 3'- -UCAG-GCC-----GGCCAGGCUCuGAGCUUGG- -5'
miRNA: 3'- -UCAGGCCGGCCAGGCUCUGAGCUUGG- -5'
Results 1 - 5 of 5 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 | |||||||
| 229 | 3' | -58 | AC_000008.1 | + | 33672 | 0.66 | 0.488355 |
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Target: 5'- gGGUCCaGGCCGGcUCuCGGGuuccaugggcucuGCUCcuGCCg -3' miRNA: 3'- -UCAGG-CCGGCC-AG-GCUC-------------UGAGcuUGG- -5' |
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| 229 | 3' | -58 | AC_000008.1 | + | 21836 | 0.77 | 0.097497 |
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Target: 5'- uAGUCaauaCGGCCGGUCgCGAGACUgGGGgCg -3' miRNA: 3'- -UCAG----GCCGGCCAG-GCUCUGAgCUUgG- -5' |
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| 229 | 3' | -58 | AC_000008.1 | + | 25213 | 0.78 | 0.082193 |
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Target: 5'- ---aCGGCCGGauaCGGGGCUCGAACCc -3' miRNA: 3'- ucagGCCGGCCag-GCUCUGAGCUUGG- -5' |
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| 229 | 3' | -58 | AC_000008.1 | + | 10906 | 0.8 | 0.061659 |
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Target: 5'- gAGUCgCGGgacccCCGGUUCGAGuCUCGGACCg -3' miRNA: 3'- -UCAG-GCC-----GGCCAGGCUCuGAGCUUGG- -5' |
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| 229 | 3' | -58 | AC_000008.1 | + | 24956 | 1.12 | 0.000233 |
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Target: 5'- cAGUCCGGCCGGUCCGAGACUCGAACCg -3' miRNA: 3'- -UCAGGCCGGCCAGGCUCUGAGCUUGG- -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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