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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 | |||||||
| 31493 | 3' | -47.4 | NC_006657.1 | + | 10581 | 0.66 | 0.850076 |
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Target: 5'- --nUUAUAUaUGGCCAGAUCUaaucCGUUu -3' miRNA: 3'- acuAAUAUAgACCGGUCUAGA----GCAGu -5' |
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| 31493 | 3' | -47.4 | NC_006657.1 | + | 10622 | 0.68 | 0.739596 |
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Target: 5'- ------gAUCUGaCCAGAUCUgGUCAa -3' miRNA: 3'- acuaauaUAGACcGGUCUAGAgCAGU- -5' |
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| 31493 | 3' | -47.4 | NC_006657.1 | + | 10907 | 0.69 | 0.665362 |
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Target: 5'- ------gAUCUGGCCAGAUCU-GUUu -3' miRNA: 3'- acuaauaUAGACCGGUCUAGAgCAGu -5' |
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| 31493 | 3' | -47.4 | NC_006657.1 | + | 10964 | 0.69 | 0.665362 |
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Target: 5'- aGAUUAgAUCUGGCCauauauaaacAGAUCUgGcCAg -3' miRNA: 3'- aCUAAUaUAGACCGG----------UCUAGAgCaGU- -5' |
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| 31493 | 3' | -47.4 | NC_006657.1 | + | 10597 | 0.69 | 0.665362 |
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Target: 5'- ------gAUCUGGCCAGAUCU-GUUu -3' miRNA: 3'- acuaauaUAGACCGGUCUAGAgCAGu -5' |
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| 31493 | 3' | -47.4 | NC_006657.1 | + | 10565 | 0.71 | 0.577068 |
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Target: 5'- ------gAUCUGGCCAGAUCUuuaaauUGUCu -3' miRNA: 3'- acuaauaUAGACCGGUCUAGA------GCAGu -5' |
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| 31493 | 3' | -47.4 | NC_006657.1 | + | 10641 | 1.1 | 0.001387 |
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Target: 5'- cUGAUUAUAUCUGGCCAGAUCUCGUCAg -3' miRNA: 3'- -ACUAAUAUAGACCGGUCUAGAGCAGU- -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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