miRNA: 3'- aGCCg--CCUUUUGCUUUCGU-------------UUUUAAG- -5'
miRNA: 3'- -AGCCG-CCUUUUGCuuUCGUUUUUaag -5'
miRNA: 3'- -AGCCGCCUUUUGCUUUCGUUUUUAAG- -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 | |||||||
| 3208 | 3' | -42.4 | NC_001506.1 | + | 988 | 0.67 | 0.623866 |
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Target: 5'- cCGGaugGGAGGAUGGGAGCGguuggagagggggAGAGUUUg -3' miRNA: 3'- aGCCg--CCUUUUGCUUUCGU-------------UUUUAAG- -5' |
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| 3208 | 3' | -42.4 | NC_001506.1 | + | 1601 | 0.71 | 0.364512 |
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Target: 5'- gUCGGCuGGGGAAUGguAGUAGGAAa-- -3' miRNA: 3'- -AGCCG-CCUUUUGCuuUCGUUUUUaag -5' |
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| 3208 | 3' | -42.4 | NC_001506.1 | + | 558 | 1.14 | 0.000288 |
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Target: 5'- uUCGGCGGAAAACGAAAGCAAAAAUUCa -3' miRNA: 3'- -AGCCGCCUUUUGCUUUCGUUUUUAAG- -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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