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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 | |||||||
| 454 | 3' | -56 | AC_000013.1 | + | 10447 | 0.66 | 0.618835 |
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Target: 5'- gGCCCgGCUUcGUuGCCC-GGCGGUUCc -3' miRNA: 3'- -UGGGaUGAGuUAuCGGGaUCGCCGGG- -5' |
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| 454 | 3' | -56 | AC_000013.1 | + | 18054 | 0.66 | 0.585356 |
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Target: 5'- uACCCUGCUCGGgcugGGUaCC-AGCaGCCg -3' miRNA: 3'- -UGGGAUGAGUUa---UCG-GGaUCGcCGGg -5' |
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| 454 | 3' | -56 | AC_000013.1 | + | 1472 | 0.66 | 0.575371 |
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Target: 5'- aACCCg---CAGUAGCCuCguuaucugccucgagAGCGGCCg -3' miRNA: 3'- -UGGGaugaGUUAUCGG-Ga--------------UCGCCGGg -5' |
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| 454 | 3' | -56 | AC_000013.1 | + | 18515 | 0.66 | 0.574265 |
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Target: 5'- cGCCCU-C-CGAuUAGCUCUAGCuguucGCCCg -3' miRNA: 3'- -UGGGAuGaGUU-AUCGGGAUCGc----CGGG- -5' |
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| 454 | 3' | -56 | AC_000013.1 | + | 5015 | 0.67 | 0.519708 |
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Target: 5'- cACCCUcagaccggacgaGCgggAAUAcGUCCUAGgGGCCCu -3' miRNA: 3'- -UGGGA------------UGag-UUAU-CGGGAUCgCCGGG- -5' |
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| 454 | 3' | -56 | AC_000013.1 | + | 5984 | 1.1 | 0.000463 |
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Target: 5'- aACCCUACUCAAUAGCCCUAGCGGCCCc -3' miRNA: 3'- -UGGGAUGAGUUAUCGGGAUCGCCGGG- -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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