miRNA: 3'- -GGU--AGUCGA---GGUCCCGGU--CUGUAggC- -5'
miRNA: 3'- -GGUAGUCGA---GGUcCC-GGUCUGUaGGC- -5'
miRNA: 3'- -GGUAGUCGAGGUCCCGGUCUGUAGGC- -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 | |||||||
| 2121 | 3' | -56.8 | NC_001354.1 | + | 7400 | 0.66 | 0.148731 |
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Target: 5'- aCCGuuUCAGUUguaUCGGGGCCAgaGACGUuuGc -3' miRNA: 3'- -GGU--AGUCGA---GGUCCCGGU--CUGUAggC- -5' |
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| 2121 | 3' | -56.8 | NC_001354.1 | + | 2161 | 0.69 | 0.080361 |
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Target: 5'- uUCAUCAGCUuccCCAuGGuCCAGACA-CCGc -3' miRNA: 3'- -GGUAGUCGA---GGUcCC-GGUCUGUaGGC- -5' |
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| 2121 | 3' | -56.8 | NC_001354.1 | + | 1381 | 1.11 | 0.000024 |
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Target: 5'- gCCAUCAGCUCCAGGGCCAGACAUCCGg -3' miRNA: 3'- -GGUAGUCGAGGUCCCGGUCUGUAGGC- -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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