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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 | |||||||
| 12253 | 3' | -54.8 | NC_003309.1 | + | 11248 | 0.66 | 0.736784 |
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Target: 5'- cGCCAGA-CUCCGGUaCGCGGAcUGCg -3' miRNA: 3'- cCGGUUUcGGGGUCA-GUGCUUcACGa -5' |
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| 12253 | 3' | -54.8 | NC_003309.1 | + | 7478 | 0.66 | 0.726088 |
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Target: 5'- cGGCCGucGCcaaCCCGGcgCAuccuucugcCGAAGUGCa -3' miRNA: 3'- -CCGGUuuCG---GGGUCa-GU---------GCUUCACGa -5' |
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| 12253 | 3' | -54.8 | NC_003309.1 | + | 5190 | 0.66 | 0.704419 |
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Target: 5'- cGCCGAAGCCgcgcucgaucgCCAGUUuCGAGGcgaGCUg -3' miRNA: 3'- cCGGUUUCGG-----------GGUCAGuGCUUCa--CGA- -5' |
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| 12253 | 3' | -54.8 | NC_003309.1 | + | 30929 | 0.66 | 0.693471 |
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Target: 5'- aGGCCAucaCgCUGGUCACGGAG-GCg -3' miRNA: 3'- -CCGGUuucGgGGUCAGUGCUUCaCGa -5' |
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| 12253 | 3' | -54.8 | NC_003309.1 | + | 33640 | 0.66 | 0.693471 |
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Target: 5'- aGGCCGgcaucGAGCCCuCAGUCGgcagcCGggGcgacaGCUa -3' miRNA: 3'- -CCGGU-----UUCGGG-GUCAGU-----GCuuCa----CGA- -5' |
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| 12253 | 3' | -54.8 | NC_003309.1 | + | 24764 | 0.69 | 0.517232 |
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Target: 5'- uGGaugCAAAGCCCCGGUCgaGCGAccGGgGCa -3' miRNA: 3'- -CCg--GUUUCGGGGUCAG--UGCU--UCaCGa -5' |
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| 12253 | 3' | -54.8 | NC_003309.1 | + | 49398 | 0.69 | 0.517232 |
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Target: 5'- cGGCCAucGCaCuCCGGaugCGCGAucGGUGCa -3' miRNA: 3'- -CCGGUuuCG-G-GGUCa--GUGCU--UCACGa -5' |
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| 12253 | 3' | -54.8 | NC_003309.1 | + | 32830 | 0.7 | 0.442186 |
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Target: 5'- gGGCCGAAGUCCUgugcggcaacgacgAGUCGCuGGAGaugGCUg -3' miRNA: 3'- -CCGGUUUCGGGG--------------UCAGUG-CUUCa--CGA- -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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