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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 | |||||||
| 28346 | 3' | -59.1 | NC_005946.1 | + | 18785 | 0.66 | 0.760841 |
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Target: 5'- cCCGUCUuugcucagacCCUCuucgucaucgcuaGGGCCaUCUUCGUCAu- -3' miRNA: 3'- -GGCAGA----------GGAG-------------CCCGG-AGAGGCAGUcc -5' |
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| 28346 | 3' | -59.1 | NC_005946.1 | + | 67716 | 0.66 | 0.742889 |
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Target: 5'- aCgGUgaCCUCGGGCUgagggaCGUCGGGc -3' miRNA: 3'- -GgCAgaGGAGCCCGGagag--GCAGUCC- -5' |
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| 28346 | 3' | -59.1 | NC_005946.1 | + | 31241 | 0.66 | 0.742889 |
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Target: 5'- aCgGUCg-CUCGGGUCUCUgucCCGUCGu- -3' miRNA: 3'- -GgCAGagGAGCCCGGAGA---GGCAGUcc -5' |
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| 28346 | 3' | -59.1 | NC_005946.1 | + | 42381 | 0.7 | 0.534759 |
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Target: 5'- uCUGUCUCC-CGGGaccaacgggacCCUUugggCCGUCGGGc -3' miRNA: 3'- -GGCAGAGGaGCCC-----------GGAGa---GGCAGUCC- -5' |
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| 28346 | 3' | -59.1 | NC_005946.1 | + | 68101 | 0.73 | 0.373697 |
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Target: 5'- uCC-UCUCCUUGgccGGCCUCUcugccgccauucCCGUCAGGc -3' miRNA: 3'- -GGcAGAGGAGC---CCGGAGA------------GGCAGUCC- -5' |
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| 28346 | 3' | -59.1 | NC_005946.1 | + | 27810 | 0.73 | 0.350202 |
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Target: 5'- --uUgUCCUCGGGCCUC-CCGUCccucAGGc -3' miRNA: 3'- ggcAgAGGAGCCCGGAGaGGCAG----UCC- -5' |
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| 28346 | 3' | -59.1 | NC_005946.1 | + | 48615 | 0.73 | 0.350202 |
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Target: 5'- gCCGcccUCUCCUC-GGCCUgCUCCucggcaGUCAGGg -3' miRNA: 3'- -GGC---AGAGGAGcCCGGA-GAGG------CAGUCC- -5' |
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| 28346 | 3' | -59.1 | NC_005946.1 | + | 9556 | 1.11 | 0.000921 |
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Target: 5'- aCCGUCUCCUCGGGCCUCUCCGUCAGGc -3' miRNA: 3'- -GGCAGAGGAGCCCGGAGAGGCAGUCC- -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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