miRNA: 3'- gaGGCUa----UGGGGGGUU--UUUCUUCGgU- -5'
miRNA: 3'- gaGGC---UAUGGGGGGUuuuu---CUUCGGU- -5'
miRNA: 3'- -GAGGCUAUGGGGGGUUUUUCUUCGGU- -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 | |||||||
| 584 | 5' | -51.6 | AC_000015.1 | + | 2115 | 0.67 | 0.706371 |
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Target: 5'- -gCCGGccuggACCCUCCAGugGAGGAGGCgGa -3' miRNA: 3'- gaGGCUa----UGGGGGGUU--UUUCUUCGgU- -5' |
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| 584 | 5' | -51.6 | AC_000015.1 | + | 25058 | 0.67 | 0.706371 |
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Target: 5'- -aCCGcgaGUGCCCCCCGccgcuauGGAGUCAc -3' miRNA: 3'- gaGGC---UAUGGGGGGUuuuu---CUUCGGU- -5' |
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| 584 | 5' | -51.6 | AC_000015.1 | + | 23163 | 1.1 | 0.001131 |
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Target: 5'- cCUCCGAUACCCCCCAAAAAGAAGCCAa -3' miRNA: 3'- -GAGGCUAUGGGGGGUUUUUCUUCGGU- -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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