miRNA: 3'- -UGCG-------------GGUGUugUga-AGGC-CCUAUAUG- -5'
miRNA: 3'- -UGCGGGUGU----UGUGa----AGGCC-----------CUAUaUG- -5'
miRNA: 3'- -UGCGGGUGU----UGUGa----AGGCC-----------CUAUaUG- -5'
miRNA: 3'- -UGCGGGUGUUGUGAAGgccCUAUAUG- -5'
Results 21 - 24 of 24 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 | |||||||
| 9868 | 3' | -51.8 | NC_002641.1 | + | 145724 | 0.66 | 0.988311 |
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Target: 5'- gGCGCguaccgacggcugCCGCGugGacgUCCGcGGGUGUACa -3' miRNA: 3'- -UGCG-------------GGUGUugUga-AGGC-CCUAUAUG- -5' |
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| 9868 | 3' | -51.8 | NC_002641.1 | + | 147074 | 0.66 | 0.98846 |
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Target: 5'- uACGCCCACAugugACAUggaugUCCGGuguuuuggaccGAUGcGCg -3' miRNA: 3'- -UGCGGGUGU----UGUGa----AGGCC-----------CUAUaUG- -5' |
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| 9868 | 3' | -51.8 | NC_002641.1 | + | 135398 | 0.66 | 0.98846 |
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Target: 5'- uACGCCCACAugugACAUggaugUCCGGuguuuuggaccGAUGcGCg -3' miRNA: 3'- -UGCGGGUGU----UGUGa----AGGCC-----------CUAUaUG- -5' |
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| 9868 | 3' | -51.8 | NC_002641.1 | + | 8669 | 0.66 | 0.98846 |
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Target: 5'- cACGCUCAUGACAUUUCau-GAUGUAUg -3' miRNA: 3'- -UGCGGGUGUUGUGAAGgccCUAUAUG- -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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