miRNA: 3'- -GUCGUUGGg---GGCAGAGC-CCUUC----AGCG- -5'
miRNA: 3'- gUCGUUGG--GGGCAGaGCCCUUCagCG- -5'
miRNA: 3'- -GUCGUUGGGG---GCAGa--------GC-CCUUC--------AGCG- -5'
miRNA: 3'- -GUCGuUGGg--GGCAGAgCCCU--UCAGCg -5'
Results 41 - 44 of 44 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 24760 | 5' | -57.3 | NC_005264.1 | + | 6103 | 0.66 | 0.867324 |
|
Target: 5'- aCGGCGGCCauguCUGUUUUGuGGAAGguguUCGCg -3' miRNA: 3'- -GUCGUUGGg---GGCAGAGC-CCUUC----AGCG- -5' |
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| 24760 | 5' | -57.3 | NC_005264.1 | + | 5075 | 0.71 | 0.600006 |
|
Target: 5'- aGGCGGCCagCCCGUC-CGGGGAGggGUc -3' miRNA: 3'- gUCGUUGG--GGGCAGaGCCCUUCagCG- -5' |
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| 24760 | 5' | -57.3 | NC_005264.1 | + | 3167 | 0.66 | 0.894865 |
|
Target: 5'- aCGGCGACCCUccgCGUCgcgacggcgCGgGGAAGggcuuauuUCGCa -3' miRNA: 3'- -GUCGUUGGGG---GCAGa--------GC-CCUUC--------AGCG- -5' |
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| 24760 | 5' | -57.3 | NC_005264.1 | + | 2768 | 0.69 | 0.757611 |
|
Target: 5'- cCGGC-GCCguaCCGUCUgGGGAguGGUCGg -3' miRNA: 3'- -GUCGuUGGg--GGCAGAgCCCU--UCAGCg -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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