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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 | |||||||
| 28759 | 5' | -45.4 | NC_006146.1 | + | 88258 | 0.66 | 0.999985 |
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Target: 5'- -gCAGGCAAAAUc---CGGCGUGUg- -3' miRNA: 3'- aaGUCCGUUUUGaaauGUCGUACAgu -5' |
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| 28759 | 5' | -45.4 | NC_006146.1 | + | 114156 | 0.66 | 0.999979 |
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Target: 5'- -cCAGGCGcauGCUggcccuggGCAGCAggGUCAc -3' miRNA: 3'- aaGUCCGUuu-UGAaa------UGUCGUa-CAGU- -5' |
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| 28759 | 5' | -45.4 | NC_006146.1 | + | 62020 | 0.67 | 0.999945 |
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Target: 5'- -cCAGGCcAGACUgcacaggaugACAGC-UGUCAc -3' miRNA: 3'- aaGUCCGuUUUGAaa--------UGUCGuACAGU- -5' |
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| 28759 | 5' | -45.4 | NC_006146.1 | + | 101346 | 0.68 | 0.999636 |
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Target: 5'- cUgAGGCAcAACUUuggcuucuacUGCGGCAUGUUc -3' miRNA: 3'- aAgUCCGUuUUGAA----------AUGUCGUACAGu -5' |
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| 28759 | 5' | -45.4 | NC_006146.1 | + | 49669 | 0.69 | 0.999094 |
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Target: 5'- cUCGGGCAGgggGGCUaugGCGGCGUcGUCc -3' miRNA: 3'- aAGUCCGUU---UUGAaa-UGUCGUA-CAGu -5' |
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| 28759 | 5' | -45.4 | NC_006146.1 | + | 155472 | 0.7 | 0.997551 |
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Target: 5'- -cCAGGCAGGACU--GCAGCcgGg-- -3' miRNA: 3'- aaGUCCGUUUUGAaaUGUCGuaCagu -5' |
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| 28759 | 5' | -45.4 | NC_006146.1 | + | 140419 | 1.07 | 0.034525 |
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Target: 5'- gUUCAGGCAAAACUUUACAGCAUGUCAc -3' miRNA: 3'- -AAGUCCGUUUUGAAAUGUCGUACAGU- -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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