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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 | |||||||
| 11488 | 3' | -52.4 | NC_003085.1 | + | 5628 | 0.66 | 0.814274 |
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Target: 5'- gGACG-GGCUgCUGGAGCgCUCGc--- -3' miRNA: 3'- aCUGCuCCGAaGACUUCG-GAGUagua -5' |
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| 11488 | 3' | -52.4 | NC_003085.1 | + | 337 | 0.66 | 0.813292 |
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Target: 5'- gGACGAGGaCgaCUGAgcaccggGGCCcCGUCAg -3' miRNA: 3'- aCUGCUCC-GaaGACU-------UCGGaGUAGUa -5' |
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| 11488 | 3' | -52.4 | NC_003085.1 | + | 28037 | 0.66 | 0.762877 |
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Target: 5'- gGAUGAGGUcgUUCUGcgcGGCCUCGgacagCAg -3' miRNA: 3'- aCUGCUCCG--AAGACu--UCGGAGUa----GUa -5' |
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| 11488 | 3' | -52.4 | NC_003085.1 | + | 27170 | 0.67 | 0.741197 |
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Target: 5'- cUGAUGAGGUucUUCUGugcGGCCUCccgCAc -3' miRNA: 3'- -ACUGCUCCG--AAGACu--UCGGAGua-GUa -5' |
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| 11488 | 3' | -52.4 | NC_003085.1 | + | 44690 | 0.67 | 0.730169 |
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Target: 5'- gGACGcAGGCUccaaguccucaUCUGA-GCCcgCAUCAg -3' miRNA: 3'- aCUGC-UCCGA-----------AGACUuCGGa-GUAGUa -5' |
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| 11488 | 3' | -52.4 | NC_003085.1 | + | 492 | 0.67 | 0.719033 |
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Target: 5'- gGGCGAGGCUgagggccugcgUUUGGAGCCggUGUCu- -3' miRNA: 3'- aCUGCUCCGA-----------AGACUUCGGa-GUAGua -5' |
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| 11488 | 3' | -52.4 | NC_003085.1 | + | 36213 | 0.93 | 0.019412 |
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Target: 5'- aUGAUGAGGCUUCaGAAGCCUCGUCAg -3' miRNA: 3'- -ACUGCUCCGAAGaCUUCGGAGUAGUa -5' |
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| 11488 | 3' | -52.4 | NC_003085.1 | + | 13247 | 1.05 | 0.002395 |
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Target: 5'- cUGACGAGGCUUCUGAAGCCUCAUCAUc -3' miRNA: 3'- -ACUGCUCCGAAGACUUCGGAGUAGUA- -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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