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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 | |||||||
| 474 | 3' | -52.3 | AC_000013.1 | + | 13471 | 0.66 | 0.827657 |
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Target: 5'- gCgUGCuGCGCCGggUACugcgGAGGggugGGAGg -3' miRNA: 3'- -GgAUGcCGCGGCaaAUG----CUCCa---UCUC- -5' |
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| 474 | 3' | -52.3 | AC_000013.1 | + | 6531 | 0.67 | 0.808685 |
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Target: 5'- uCCUaugGCGGUGCgCGgc-GCGAGauuGUGGAGa -3' miRNA: 3'- -GGA---UGCCGCG-GCaaaUGCUC---CAUCUC- -5' |
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| 474 | 3' | -52.3 | AC_000013.1 | + | 28829 | 0.68 | 0.736782 |
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Target: 5'- aCCUcguaaACGGCGCCGUaggGCGAauaaGGAGg -3' miRNA: 3'- -GGA-----UGCCGCGGCAaa-UGCUcca-UCUC- -5' |
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| 474 | 3' | -52.3 | AC_000013.1 | + | 12742 | 0.74 | 0.412978 |
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Target: 5'- gCCUccgacAUGGCGCaCGUUcaucUGCGAGGcAGAGg -3' miRNA: 3'- -GGA-----UGCCGCG-GCAA----AUGCUCCaUCUC- -5' |
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| 474 | 3' | -52.3 | AC_000013.1 | + | 28895 | 1.12 | 0.001131 |
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Target: 5'- cCCUACGGCGCCGUUUACGAGGUAGAGg -3' miRNA: 3'- -GGAUGCCGCGGCAAAUGCUCCAUCUC- -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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