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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
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R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 12222 | 3' | -59.9 | NC_003309.1 | + | 5063 | 0.73 | 0.180962 |
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Target: 5'- gGGCGCGgcGG----CCGGUGCCGcGACg -3' miRNA: 3'- -CCGCGCuuCCacaaGGCCGCGGC-CUG- -5' |
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| 12222 | 3' | -59.9 | NC_003309.1 | + | 15428 | 0.8 | 0.059206 |
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Target: 5'- cGCGCGA--GUG-UCCGGCGCCGGAa -3' miRNA: 3'- cCGCGCUucCACaAGGCCGCGGCCUg -5' |
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| 12222 | 3' | -59.9 | NC_003309.1 | + | 18704 | 0.68 | 0.386789 |
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Target: 5'- cGGCGCGGAuacGGccgccGaUCCGGCGgCCGGcCu -3' miRNA: 3'- -CCGCGCUU---CCa----CaAGGCCGC-GGCCuG- -5' |
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| 12222 | 3' | -59.9 | NC_003309.1 | + | 19734 | 0.66 | 0.479489 |
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Target: 5'- cGGUucGCGAAGGUccGUaCCGaGCGCCGa-- -3' miRNA: 3'- -CCG--CGCUUCCA--CAaGGC-CGCGGCcug -5' |
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| 12222 | 3' | -59.9 | NC_003309.1 | + | 37382 | 0.66 | 0.489361 |
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Target: 5'- cGCGUGAgaacgcgcccaAGGUGUUCCagaaguaucGGCG-CGGAg -3' miRNA: 3'- cCGCGCU-----------UCCACAAGG---------CCGCgGCCUg -5' |
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| 12222 | 3' | -59.9 | NC_003309.1 | + | 37602 | 0.67 | 0.441028 |
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Target: 5'- cGGUGUGAAGGUGcaacgcuaCGGCGacgaCCGcGGCg -3' miRNA: 3'- -CCGCGCUUCCACaag-----GCCGC----GGC-CUG- -5' |
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| 12222 | 3' | -59.9 | NC_003309.1 | + | 46673 | 0.69 | 0.306696 |
|
Target: 5'- aGGCGCucAGGUGa-CCGG-GCCGGcGCg -3' miRNA: 3'- -CCGCGcuUCCACaaGGCCgCGGCC-UG- -5' |
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| 12222 | 3' | -59.9 | NC_003309.1 | + | 48036 | 0.74 | 0.150059 |
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Target: 5'- cGGCGUGAAGaGUGg-CCGGUcgaggucGCCGGAUg -3' miRNA: 3'- -CCGCGCUUC-CACaaGGCCG-------CGGCCUG- -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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