miRNA: 3'- -ACGUUC--------------CGCCGUC--CGUGU----ACGGgGGG- -5'
miRNA: 3'- aCGU-UCCGCCgu-----CCG-UGUACGGGGGg -5'
miRNA: 3'- -ACGUUCCGCCGUCCGUGUACGGGGGG- -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 | |||||||
| 4212 | 3' | -61.4 | NC_001678.1 | + | 4572 | 0.67 | 0.060547 |
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Target: 5'- uUGCAGGuuugguacagcugcGUGGCAGauGCACGcuuuUGCCgCCCa -3' miRNA: 3'- -ACGUUC--------------CGCCGUC--CGUGU----ACGGgGGG- -5' |
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| 4212 | 3' | -61.4 | NC_001678.1 | + | 4690 | 0.72 | 0.021968 |
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Target: 5'- gGCAcGGGCGGaagaagcGGCuACGUGCCCCUa -3' miRNA: 3'- aCGU-UCCGCCgu-----CCG-UGUACGGGGGg -5' |
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| 4212 | 3' | -61.4 | NC_001678.1 | + | 4560 | 1.1 | 8e-06 |
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Target: 5'- cUGCAAGGCGGCAGGCACAUGCCCCCCc -3' miRNA: 3'- -ACGUUCCGCCGUCCGUGUACGGGGGG- -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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