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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 | |||||||
| 12109 | 3' | -52 | NC_003309.1 | + | 48803 | 0.66 | 0.877516 |
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Target: 5'- --cUGaaCGGCGAAUgCGGCUUUcguuugaaGCCCg -3' miRNA: 3'- gcaACaaGCCGCUUA-GUCGGAA--------CGGG- -5' |
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| 12109 | 3' | -52 | NC_003309.1 | + | 49950 | 0.67 | 0.806809 |
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Target: 5'- cCGUcGaUUCGGCGGccgagccgGUCAGU--UGCCCg -3' miRNA: 3'- -GCAaC-AAGCCGCU--------UAGUCGgaACGGG- -5' |
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| 12109 | 3' | -52 | NC_003309.1 | + | 33801 | 0.68 | 0.787014 |
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Target: 5'- uGUUGgcUGGCGggUCAGCUc-GUCg -3' miRNA: 3'- gCAACaaGCCGCuuAGUCGGaaCGGg -5' |
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| 12109 | 3' | -52 | NC_003309.1 | + | 557 | 0.68 | 0.75609 |
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Target: 5'- gGUUGUcgGGUGuuuUCGGCUUUGCgCCg -3' miRNA: 3'- gCAACAagCCGCuu-AGUCGGAACG-GG- -5' |
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| 12109 | 3' | -52 | NC_003309.1 | + | 6539 | 0.69 | 0.702069 |
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Target: 5'- gCGUaucgCGGCGc--CAGCCUUGCUCu -3' miRNA: 3'- -GCAacaaGCCGCuuaGUCGGAACGGG- -5' |
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| 12109 | 3' | -52 | NC_003309.1 | + | 7524 | 1.13 | 0.001243 |
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Target: 5'- gCGUUGUUCGGCGAAUCAGCCUUGCCCu -3' miRNA: 3'- -GCAACAAGCCGCUUAGUCGGAACGGG- -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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