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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 | |||||||
| 8440 | 5' | -54.8 | NC_002166.1 | + | 11729 | 0.66 | 0.583707 |
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Target: 5'- cUGCagggGCUGaUGAUACCUACcCGCCAGc -3' miRNA: 3'- aAUGg---CGAC-GCUGUGGAUGuGUGGUU- -5' |
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| 8440 | 5' | -54.8 | NC_002166.1 | + | 1601 | 0.68 | 0.472487 |
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Target: 5'- -gGCUGCUGCG-CACC---ACGCCAGg -3' miRNA: 3'- aaUGGCGACGCuGUGGaugUGUGGUU- -5' |
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| 8440 | 5' | -54.8 | NC_002166.1 | + | 16826 | 0.68 | 0.472487 |
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Target: 5'- -gACUGUUGCGACugCUGauacCGCACUGGg -3' miRNA: 3'- aaUGGCGACGCUGugGAU----GUGUGGUU- -5' |
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| 8440 | 5' | -54.8 | NC_002166.1 | + | 33502 | 0.68 | 0.461922 |
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Target: 5'- -aGCUGCUcGCGAUGCCUGcCACguuuGCCAGu -3' miRNA: 3'- aaUGGCGA-CGCUGUGGAU-GUG----UGGUU- -5' |
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| 8440 | 5' | -54.8 | NC_002166.1 | + | 11807 | 0.69 | 0.41107 |
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Target: 5'- -gACgGCUGCGACuauGCCggUACGCGCUAu -3' miRNA: 3'- aaUGgCGACGCUG---UGG--AUGUGUGGUu -5' |
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| 8440 | 5' | -54.8 | NC_002166.1 | + | 16563 | 0.72 | 0.281146 |
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Target: 5'- gUUACCGCUGCGGucaacCAgCUGCGCGCgGu -3' miRNA: 3'- -AAUGGCGACGCU-----GUgGAUGUGUGgUu -5' |
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| 8440 | 5' | -54.8 | NC_002166.1 | + | 11137 | 1.03 | 0.001375 |
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Target: 5'- uUUACCGCUGCGACACCUACACACCAAc -3' miRNA: 3'- -AAUGGCGACGCUGUGGAUGUGUGGUU- -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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