miRNA: 3'- -AGUCUAGGUgUUCAAUCua-GGCCGag -5'
miRNA: 3'- aGUCuaGGUGUUc---AAUCUAGG-CCGag -5'
miRNA: 3'- -AGuCuaGGUGUUCAAUCU--AGGCCGAG- -5'
miRNA: 3'- -AGUCUAGGUGUUCAAUCUAGGCCGAG- -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 | |||||||
| 22500 | 5' | -50.2 | NC_005069.1 | + | 17666 | 0.66 | 0.897453 |
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Target: 5'- uUCAGGUUCAgGGGUUAGcagCUGGUg- -3' miRNA: 3'- -AGUCUAGGUgUUCAAUCua-GGCCGag -5' |
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| 22500 | 5' | -50.2 | NC_005069.1 | + | 34422 | 0.67 | 0.873977 |
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Target: 5'- cCAGcgCCGCGAcccaUUAGAUCCaGGCg- -3' miRNA: 3'- aGUCuaGGUGUUc---AAUCUAGG-CCGag -5' |
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| 22500 | 5' | -50.2 | NC_005069.1 | + | 7037 | 0.67 | 0.847991 |
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Target: 5'- aUCcGcgCUGCAAGUUGGGuaUCUGGUUCu -3' miRNA: 3'- -AGuCuaGGUGUUCAAUCU--AGGCCGAG- -5' |
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| 22500 | 5' | -50.2 | NC_005069.1 | + | 27862 | 1.11 | 0.001791 |
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Target: 5'- aUCAGAUCCACAAGUUAGAUCCGGCUCu -3' miRNA: 3'- -AGUCUAGGUGUUCAAUCUAGGCCGAG- -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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