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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 | |||||||
| 28804 | 3' | -54 | NC_006146.1 | + | 94537 | 0.66 | 0.961531 |
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Target: 5'- gCGcCCUCUCgugGCGGucuugaggguggcguGGAgggUGGUGAGGAa -3' miRNA: 3'- -GC-GGAGAGa--CGUC---------------UCU---ACUACUCCUa -5' |
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| 28804 | 3' | -54 | NC_006146.1 | + | 47902 | 0.66 | 0.952313 |
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Target: 5'- gCGCuCUCUCUGgAGAGGgagGAcaGGGAUg -3' miRNA: 3'- -GCG-GAGAGACgUCUCUa--CUacUCCUA- -5' |
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| 28804 | 3' | -54 | NC_006146.1 | + | 66661 | 0.67 | 0.933868 |
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Target: 5'- gGCCUCUggGUagGGGGGUGAUGAcccGGAa -3' miRNA: 3'- gCGGAGAgaCG--UCUCUACUACU---CCUa -5' |
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| 28804 | 3' | -54 | NC_006146.1 | + | 133813 | 0.68 | 0.898763 |
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Target: 5'- uGCCaacugCUCaGgGGAGggGGUGAGGAUg -3' miRNA: 3'- gCGGa----GAGaCgUCUCuaCUACUCCUA- -5' |
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| 28804 | 3' | -54 | NC_006146.1 | + | 165760 | 0.69 | 0.870515 |
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Target: 5'- gGCgUCUC-GCAGGGcgGGUGAGcGAUc -3' miRNA: 3'- gCGgAGAGaCGUCUCuaCUACUC-CUA- -5' |
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| 28804 | 3' | -54 | NC_006146.1 | + | 132849 | 0.69 | 0.870515 |
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Target: 5'- gGCCUCUCaucacaGGAGA-GGUGGGGGUg -3' miRNA: 3'- gCGGAGAGacg---UCUCUaCUACUCCUA- -5' |
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| 28804 | 3' | -54 | NC_006146.1 | + | 65313 | 0.7 | 0.830247 |
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Target: 5'- uGCCUCUUgcgGCcucucGAGuAUGGUGAGGGUc -3' miRNA: 3'- gCGGAGAGa--CGu----CUC-UACUACUCCUA- -5' |
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| 28804 | 3' | -54 | NC_006146.1 | + | 63773 | 0.73 | 0.630645 |
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Target: 5'- aGCCUaUCUGCAcguuggagagguuuGAGAUGAUGAGGc- -3' miRNA: 3'- gCGGAgAGACGU--------------CUCUACUACUCCua -5' |
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| 28804 | 3' | -54 | NC_006146.1 | + | 20177 | 0.73 | 0.623327 |
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Target: 5'- uCGCCUCUUUGCAGAGGgcccccGGGGGc -3' miRNA: 3'- -GCGGAGAGACGUCUCUacua--CUCCUa -5' |
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| 28804 | 3' | -54 | NC_006146.1 | + | 105541 | 1.06 | 0.006185 |
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Target: 5'- uCGCCUCUCUGCAGAGAUGAUGAGGAUg -3' miRNA: 3'- -GCGGAGAGACGUCUCUACUACUCCUA- -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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