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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 | |||||||
| 28428 | 3' | -55.4 | NC_005946.1 | + | 36673 | 0.66 | 0.861075 |
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Target: 5'- -cCUGACGGGcCUGGGCucgGacUCUGUCc -3' miRNA: 3'- gaGACUGUCC-GACCUGua-C--AGACGGc -5' |
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| 28428 | 3' | -55.4 | NC_005946.1 | + | 4360 | 0.68 | 0.772434 |
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Target: 5'- --gUGAgCAGGgaGGACAUGUCUacguuggaggGCCa -3' miRNA: 3'- gagACU-GUCCgaCCUGUACAGA----------CGGc -5' |
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| 28428 | 3' | -55.4 | NC_005946.1 | + | 19619 | 0.68 | 0.732701 |
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Target: 5'- gUCUGAgCAgaccGGCUGccccGACcUGUCUGCCGc -3' miRNA: 3'- gAGACU-GU----CCGAC----CUGuACAGACGGC- -5' |
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| 28428 | 3' | -55.4 | NC_005946.1 | + | 12737 | 0.74 | 0.391069 |
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Target: 5'- ---aGGCAGGCUGGAgcUGUCUGCUc -3' miRNA: 3'- gagaCUGUCCGACCUguACAGACGGc -5' |
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| 28428 | 3' | -55.4 | NC_005946.1 | + | 82539 | 0.78 | 0.243466 |
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Target: 5'- cCUCguccgggGAgAGGCUGGAgGUGUCUGCgGg -3' miRNA: 3'- -GAGa------CUgUCCGACCUgUACAGACGgC- -5' |
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| 28428 | 3' | -55.4 | NC_005946.1 | + | 82626 | 1.1 | 0.001762 |
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Target: 5'- cCUCUGACAGGCUGGACAUGUCUGCCGg -3' miRNA: 3'- -GAGACUGUCCGACCUGUACAGACGGC- -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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