miRNA: 3'- aauuUCGGCGU---UUGGUUUcCGUGGUu -5'
miRNA: 3'- aaUUUC-GGCGU----UUGGUUUCCGUG-GUU- -5'
miRNA: 3'- aaUUUCGgCGU---------UUGGUUUCCGUGguu -5'
miRNA: 3'- -AAUUUCGGCGUUUGGUUUCCGUGGUU- -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 | |||||||
| 12766 | 5' | -49.9 | NC_003379.1 | + | 524 | 0.67 | 0.10229 |
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Target: 5'- ---uAGUCGCAccaGGCCAGA-GCACCAc -3' miRNA: 3'- aauuUCGGCGU---UUGGUUUcCGUGGUu -5' |
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| 12766 | 5' | -49.9 | NC_003379.1 | + | 2585 | 0.67 | 0.087508 |
|
Target: 5'- -cAGAGaUCGCAccaaAACCAAAGGUACgCAGg -3' miRNA: 3'- aaUUUC-GGCGU----UUGGUUUCCGUG-GUU- -5' |
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| 12766 | 5' | -49.9 | NC_003379.1 | + | 2487 | 0.71 | 0.046388 |
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Target: 5'- -aAAGGCgGCAaggaacgggGACCAAAGGCGCa-- -3' miRNA: 3'- aaUUUCGgCGU---------UUGGUUUCCGUGguu -5' |
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| 12766 | 5' | -49.9 | NC_003379.1 | + | 2572 | 1.04 | 0.000048 |
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Target: 5'- uUUAAAGCCGCAAACCAAAGGCACCAAa -3' miRNA: 3'- -AAUUUCGGCGUUUGGUUUCCGUGGUU- -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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