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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 | |||||||
| 27715 | 3' | -55.5 | NC_005884.1 | + | 34765 | 0.67 | 0.582063 |
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Target: 5'- uUGGgc-GGCUGCuCCAUAgGCCUUUCCa -3' miRNA: 3'- -ACUaauCCGAUGcGGUGU-CGGAGGGG- -5' |
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| 27715 | 3' | -55.5 | NC_005884.1 | + | 526 | 0.67 | 0.582063 |
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Target: 5'- ----cAGGCUGCGCCAgCAaaCCUUCCg -3' miRNA: 3'- acuaaUCCGAUGCGGU-GUc-GGAGGGg -5' |
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| 27715 | 3' | -55.5 | NC_005884.1 | + | 4054 | 0.68 | 0.505568 |
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Target: 5'- ----aAGGCUGCGU--CAGCCUCCa- -3' miRNA: 3'- acuaaUCCGAUGCGguGUCGGAGGgg -5' |
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| 27715 | 3' | -55.5 | NC_005884.1 | + | 1659 | 0.68 | 0.483431 |
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Target: 5'- cUGGUggAGGCUAgGCCAguaacucUAGUCuacuUCCCCa -3' miRNA: 3'- -ACUAa-UCCGAUgCGGU-------GUCGG----AGGGG- -5' |
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| 27715 | 3' | -55.5 | NC_005884.1 | + | 41123 | 0.73 | 0.238918 |
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Target: 5'- cGA-UAGGCUagaauccgGCGCCuggcaAGCUUCCCCa -3' miRNA: 3'- aCUaAUCCGA--------UGCGGug---UCGGAGGGG- -5' |
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| 27715 | 3' | -55.5 | NC_005884.1 | + | 7273 | 1.11 | 0.000444 |
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Target: 5'- aUGAUUAGGCUACGCCACAGCCUCCCCc -3' miRNA: 3'- -ACUAAUCCGAUGCGGUGUCGGAGGGG- -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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