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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 | |||||||
| 500 | 3' | -57 | AC_000013.1 | + | 14332 | 0.66 | 0.521425 |
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Target: 5'- aGGCgCUCGAGAacaGGC-CUCcucAGGGCGa -3' miRNA: 3'- -CCGgGAGCUCUa--CCGcGAGu--UCUCGU- -5' |
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| 500 | 3' | -57 | AC_000013.1 | + | 7052 | 0.67 | 0.469377 |
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Target: 5'- cGGCCCgaCGGGAUcgGGCaagagccaucuGCUC-AGAGCGu -3' miRNA: 3'- -CCGGGa-GCUCUA--CCG-----------CGAGuUCUCGU- -5' |
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| 500 | 3' | -57 | AC_000013.1 | + | 44293 | 0.68 | 0.449307 |
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Target: 5'- cGUCgCaCGGGGUGGCGCUCgGAGAuGCGg -3' miRNA: 3'- cCGG-GaGCUCUACCGCGAG-UUCU-CGU- -5' |
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| 500 | 3' | -57 | AC_000013.1 | + | 29890 | 0.68 | 0.401305 |
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Target: 5'- uGCCCUUGuAGAUGGCaCUauauuGAGCAg -3' miRNA: 3'- cCGGGAGC-UCUACCGcGAguu--CUCGU- -5' |
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| 500 | 3' | -57 | AC_000013.1 | + | 19328 | 0.69 | 0.356695 |
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Target: 5'- cGGCCgUgcCGAGA--GCGCUCGAGAGaCGa -3' miRNA: 3'- -CCGGgA--GCUCUacCGCGAGUUCUC-GU- -5' |
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| 500 | 3' | -57 | AC_000013.1 | + | 32691 | 0.74 | 0.192466 |
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Target: 5'- uGUCUUCGAGAUGGUGUUCuauuGGAcGCAg -3' miRNA: 3'- cCGGGAGCUCUACCGCGAGu---UCU-CGU- -5' |
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| 500 | 3' | -57 | AC_000013.1 | + | 38245 | 1.1 | 0.000401 |
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Target: 5'- gGGCCCUCGAGAUGGCGCUCAAGAGCAu -3' miRNA: 3'- -CCGGGAGCUCUACCGCGAGUUCUCGU- -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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