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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 12213 | 5' | -59.5 | NC_003309.1 | + | 51511 | 0.66 | 0.461361 |
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Target: 5'- cGGCUUCgGCGCccuGCCGuuccaCGUGAUGUc -3' miRNA: 3'- -CCGGAG-CGCGcu-CGGCuc---GCACUACA- -5' |
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| 12213 | 5' | -59.5 | NC_003309.1 | + | 12079 | 0.66 | 0.461361 |
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Target: 5'- uGCCcuUCGCuacGCGGGCCGccgcGGCGuUGGUGg -3' miRNA: 3'- cCGG--AGCG---CGCUCGGC----UCGC-ACUACa -5' |
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| 12213 | 5' | -59.5 | NC_003309.1 | + | 34439 | 0.67 | 0.412463 |
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Target: 5'- aGGUCgaccguggagaGCGCGAuggcguaguacgGCCGAGCGUGAa-- -3' miRNA: 3'- -CCGGag---------CGCGCU------------CGGCUCGCACUaca -5' |
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| 12213 | 5' | -59.5 | NC_003309.1 | + | 44100 | 0.68 | 0.353595 |
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Target: 5'- uGGCCUUGUGUGAccgauuGCCGGGCGaacgUGcAUGa -3' miRNA: 3'- -CCGGAGCGCGCU------CGGCUCGC----AC-UACa -5' |
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| 12213 | 5' | -59.5 | NC_003309.1 | + | 12576 | 0.7 | 0.278304 |
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Target: 5'- cGGCgauguaCUCGgGCGAGCCaAGCGUGccGUc -3' miRNA: 3'- -CCG------GAGCgCGCUCGGcUCGCACuaCA- -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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