miRNA: 3'- -ACuuCCGUGACg-CGCGCCGGgU---------UCUA- -5'
miRNA: 3'- aCUUC-CGUGACGcg-CGCCGGGUUCua -5'
miRNA: 3'- -ACUUCCGUGACGCGCGCCGGGUUCUA- -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 | |||||||
| 22511 | 3' | -59.1 | NC_005074.1 | + | 1721 | 0.71 | 0.021227 |
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Target: 5'- cUGggGGCGCUGagGCGCGGUCgAuccgugagaGGAUg -3' miRNA: 3'- -ACuuCCGUGACg-CGCGCCGGgU---------UCUA- -5' |
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| 22511 | 3' | -59.1 | NC_005074.1 | + | 2629 | 0.73 | 0.014379 |
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Target: 5'- aGGAGcGCGCUGCcaaGUGGCCCAAGu- -3' miRNA: 3'- aCUUC-CGUGACGcg-CGCCGGGUUCua -5' |
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| 22511 | 3' | -59.1 | NC_005074.1 | + | 2561 | 1.06 | 0.000012 |
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Target: 5'- aUGAAGGCACUGCGCGCGGCCCAAGAUa -3' miRNA: 3'- -ACUUCCGUGACGCGCGCCGGGUUCUA- -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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