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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 | |||||||
| 31772 | 3' | -52.2 | NC_006938.1 | + | 7557 | 0.66 | 0.912078 |
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Target: 5'- ----cGACGGUgGUCUUGGuGGCGUugaaGGa -3' miRNA: 3'- cacuaCUGCCAgCAGAACU-UCGCG----CC- -5' |
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| 31772 | 3' | -52.2 | NC_006938.1 | + | 4375 | 0.66 | 0.89871 |
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Target: 5'- ----aGACGGUCGUCUggugucGAuucacGCGCGa -3' miRNA: 3'- cacuaCUGCCAGCAGAa-----CUu----CGCGCc -5' |
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| 31772 | 3' | -52.2 | NC_006938.1 | + | 54550 | 0.68 | 0.807254 |
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Target: 5'- aUGGUGGCGG-CGgccugCUUGgcGCGCu- -3' miRNA: 3'- cACUACUGCCaGCa----GAACuuCGCGcc -5' |
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| 31772 | 3' | -52.2 | NC_006938.1 | + | 48143 | 0.68 | 0.797648 |
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Target: 5'- ----cGACGGUCGUUcgGcAGGCGaCGGa -3' miRNA: 3'- cacuaCUGCCAGCAGaaC-UUCGC-GCC- -5' |
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| 31772 | 3' | -52.2 | NC_006938.1 | + | 15146 | 0.69 | 0.767829 |
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Target: 5'- -gGAggGGCGGUCGUCgcuccGGAGC-CGGu -3' miRNA: 3'- caCUa-CUGCCAGCAGaa---CUUCGcGCC- -5' |
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| 31772 | 3' | -52.2 | NC_006938.1 | + | 16960 | 0.7 | 0.71548 |
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Target: 5'- -aGcUGACGGaccuccUCGUCggcagcuggGGAGCGCGGg -3' miRNA: 3'- caCuACUGCC------AGCAGaa-------CUUCGCGCC- -5' |
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| 31772 | 3' | -52.2 | NC_006938.1 | + | 10948 | 1.12 | 0.001874 |
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Target: 5'- gGUGAUGACGGUCGUCUUGAAGCGCGGg -3' miRNA: 3'- -CACUACUGCCAGCAGAACUUCGCGCC- -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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