miRNA: 3'- cCUGCuCCU---UCUG-AGcCUGCUCCU-CC- -5'
miRNA: 3'- cCUGCUCCUuCUGA-GCCuGCUCCUCC- -5'
miRNA: 3'- cCUGCUCCUUCUgagCCUgCUCCUCC- -5'
miRNA: 3'- -CCUGCUCCUUCUGAGCCUGCUCCUCC- -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 | |||||||
| 3499 | 3' | -54.6 | NC_001619.1 | + | 3539 | 0.68 | 0.194347 |
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Target: 5'- cGACGuGGAaauGGACaUCaGGCGGGGAuGGa -3' miRNA: 3'- cCUGCuCCU---UCUG-AGcCUGCUCCU-CC- -5' |
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| 3499 | 3' | -54.6 | NC_001619.1 | + | 3347 | 0.77 | 0.041744 |
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Target: 5'- cGACGAGGAcGGCUgCGGcUGGGGGGGu -3' miRNA: 3'- cCUGCUCCUuCUGA-GCCuGCUCCUCC- -5' |
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| 3499 | 3' | -54.6 | NC_001619.1 | + | 625 | 0.79 | 0.029949 |
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Target: 5'- uGACGAGGAGGA---GGAgGAGGAGGa -3' miRNA: 3'- cCUGCUCCUUCUgagCCUgCUCCUCC- -5' |
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| 3499 | 3' | -54.6 | NC_001619.1 | + | 3273 | 1.13 | 5.1e-05 |
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Target: 5'- aGGACGAGGAAGACUCGGACGAGGAGGa -3' miRNA: 3'- -CCUGCUCCUUCUGAGCCUGCUCCUCC- -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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