miRNA: 3'- -GCGCUA-CCGCUGGUC-C-UGAGC-CaGCc -5'
miRNA: 3'- -GC-GCUa--CCGCUGgUCCUGAgCCaGCc -5'
miRNA: 3'- gCGCuACCGCUGG-------------UCC----UGAGC-CAGCc -5'
miRNA: 3'- -GCGCU-ACCGcUGGUCCUG-AGCcaGCC- -5'
miRNA: 3'- -GCGCuaCCGC--UGGUCCUGA-GCCagCC- -5'
Results 21 - 25 of 25 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 | |||||||
| 16298 | 5' | -58.3 | NC_004084.1 | + | 5443 | 0.71 | 0.36182 |
|
Target: 5'- uCGCGAUcGGCGACCAGcGcACUCGcGaCGa -3' miRNA: 3'- -GCGCUA-CCGCUGGUC-C-UGAGC-CaGCc -5' |
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| 16298 | 5' | -58.3 | NC_004084.1 | + | 5344 | 0.68 | 0.48882 |
|
Target: 5'- uCGcCGAgcgGGCGGCgAGGACUgGGaCGa -3' miRNA: 3'- -GC-GCUa--CCGCUGgUCCUGAgCCaGCc -5' |
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| 16298 | 5' | -58.3 | NC_004084.1 | + | 5142 | 0.66 | 0.632007 |
|
Target: 5'- gGCG-UGGCGACCgacgucgucccugAGGcagcACUCGaGUCGa -3' miRNA: 3'- gCGCuACCGCUGG-------------UCC----UGAGC-CAGCc -5' |
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| 16298 | 5' | -58.3 | NC_004084.1 | + | 5135 | 0.67 | 0.549333 |
|
Target: 5'- uCGCGGcUGGUcGCCAGGACgUCGccCGGc -3' miRNA: 3'- -GCGCU-ACCGcUGGUCCUG-AGCcaGCC- -5' |
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| 16298 | 5' | -58.3 | NC_004084.1 | + | 3615 | 0.68 | 0.47903 |
|
Target: 5'- uCGCGggGGCGucAUCGGGACUaUGGagGGc -3' miRNA: 3'- -GCGCuaCCGC--UGGUCCUGA-GCCagCC- -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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