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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 | |||||||
| 27729 | 5' | -52.8 | NC_005884.1 | + | 2372 | 0.66 | 0.730847 |
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Target: 5'- uGCua-CUUGGGCggccuuuaauccUGuCGCCAGCAGACg -3' miRNA: 3'- gUGuaaGAGUCCG------------AC-GCGGUCGUUUG- -5' |
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| 27729 | 5' | -52.8 | NC_005884.1 | + | 2547 | 0.67 | 0.6716 |
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Target: 5'- cCGCAgu-UCAGGUccuauccaacagGCGCCAGCAAGa -3' miRNA: 3'- -GUGUaagAGUCCGa-----------CGCGGUCGUUUg -5' |
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| 27729 | 5' | -52.8 | NC_005884.1 | + | 18114 | 0.67 | 0.650737 |
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Target: 5'- gAgAUUgUCcagAGGCaGCGCCAGCAGGa -3' miRNA: 3'- gUgUAAgAG---UCCGaCGCGGUCGUUUg -5' |
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| 27729 | 5' | -52.8 | NC_005884.1 | + | 612 | 0.68 | 0.597299 |
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Target: 5'- --aAUUCgcucCAGGCUGCGauaagagcgcggcgcUCAGCAAACa -3' miRNA: 3'- gugUAAGa---GUCCGACGC---------------GGUCGUUUG- -5' |
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| 27729 | 5' | -52.8 | NC_005884.1 | + | 517 | 1.09 | 0.001069 |
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Target: 5'- gCACAUUCUCAGGCUGCGCCAGCAAACc -3' miRNA: 3'- -GUGUAAGAGUCCGACGCGGUCGUUUG- -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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