miRNA: 3'- -GCCGGUu-----CCUGGUCa---CCUUUCCa--AGa -5'
miRNA: 3'- gCCGgUU---------------CCUGGUCACCUU----UCCAAga -5'
miRNA: 3'- -GCCGGUUCCUGGUCACCUUUCCAAGA- -5'
Results 1 - 3 of 3 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 | |||||||
| 17396 | 3' | -53.7 | NC_004421.1 | + | 1879 | 0.67 | 0.2039 |
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Target: 5'- gCGGUCAccugacGGACCAGguucGGAAGGGcagUCg -3' miRNA: 3'- -GCCGGUu-----CCUGGUCa---CCUUUCCa--AGa -5' |
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| 17396 | 3' | -53.7 | NC_004421.1 | + | 7469 | 0.68 | 0.170891 |
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Target: 5'- uGGCgAAuuugaagaagaauuuGGACCAGUGGAGgucuGGGUUg- -3' miRNA: 3'- gCCGgUU---------------CCUGGUCACCUU----UCCAAga -5' |
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| 17396 | 3' | -53.7 | NC_004421.1 | + | 4165 | 1.09 | 0.000086 |
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Target: 5'- aCGGCCAAGGACCAGUGGAAAGGUUCUa -3' miRNA: 3'- -GCCGGUUCCUGGUCACCUUUCCAAGA- -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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