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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 | |||||||
| 28023 | 3' | -51.3 | NC_005887.1 | + | 2142 | 0.73 | 0.507216 |
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Target: 5'- uCGUGaagucgcagccgcUCUGGAUCGGCAUGGAcuUC-GGCc -3' miRNA: 3'- -GCAC-------------AGGCCUAGCUGUAUCU--AGaCCG- -5' |
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| 28023 | 3' | -51.3 | NC_005887.1 | + | 22552 | 0.7 | 0.665661 |
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Target: 5'- --cGUCCGcGAUCGACAUGcccgagacgcuGAUgCUGGUc -3' miRNA: 3'- gcaCAGGC-CUAGCUGUAU-----------CUA-GACCG- -5' |
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| 28023 | 3' | -51.3 | NC_005887.1 | + | 35831 | 0.68 | 0.764991 |
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Target: 5'- uCGUGcgCCGcGUCGGCGUAGAUCaucGCc -3' miRNA: 3'- -GCACa-GGCcUAGCUGUAUCUAGac-CG- -5' |
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| 28023 | 3' | -51.3 | NC_005887.1 | + | 40510 | 0.67 | 0.847231 |
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Target: 5'- uCGUGUUCGGcAUccaccacgcggcgcgCGGCAgcgacgacGGUCUGGCg -3' miRNA: 3'- -GCACAGGCC-UA---------------GCUGUau------CUAGACCG- -5' |
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| 28023 | 3' | -51.3 | NC_005887.1 | + | 17149 | 0.66 | 0.869518 |
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Target: 5'- gGUG-CUGG-UCGGCGaAGAUCgcgaGGCg -3' miRNA: 3'- gCACaGGCCuAGCUGUaUCUAGa---CCG- -5' |
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| 28023 | 3' | -51.3 | NC_005887.1 | + | 38170 | 0.66 | 0.884682 |
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Target: 5'- uCG-GUCgCGGucaugucgccgcuGUCGACGaGGAUCUGGa -3' miRNA: 3'- -GCaCAG-GCC-------------UAGCUGUaUCUAGACCg -5' |
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| 28023 | 3' | -51.3 | NC_005887.1 | + | 29362 | 0.68 | 0.799929 |
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Target: 5'- --gGUCCGGGUCGgugccgcgggucgccGCuucGGUCUGGUa -3' miRNA: 3'- gcaCAGGCCUAGC---------------UGuauCUAGACCG- -5' |
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| 28023 | 3' | -51.3 | NC_005887.1 | + | 28077 | 1.13 | 0.001234 |
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Target: 5'- gCGUGUCCGGAUCGACAUAGAUCUGGCu -3' miRNA: 3'- -GCACAGGCCUAGCUGUAUCUAGACCG- -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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