miRNA: 3'- gGUCGCG-UACUGUuGCUU-----GAAGCaGC- -5'
miRNA: 3'- -GGUCGCG-------------UACUGUu---GCUUGaaGCAGC- -5'
miRNA: 3'- -GGUCGCGuaCUGUUGCU-----UGaaGCAgc -5'
miRNA: 3'- gGUCGCGua----CUGUUGCuUGAa--GCAGC- -5'
Results 21 - 24 of 24 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 | |||||||
| 11977 | 3' | -49.4 | NC_003278.1 | + | 28560 | 0.67 | 0.878502 |
|
Target: 5'- gCAGCGCgAUGGCGuCGAAgauacCUUCGaCGa -3' miRNA: 3'- gGUCGCG-UACUGUuGCUU-----GAAGCaGC- -5' |
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| 11977 | 3' | -49.4 | NC_003278.1 | + | 28769 | 0.68 | 0.833445 |
|
Target: 5'- aCCAGCGCuggauguucaucgAUGACGcggcCGAGCg-CGUCGc -3' miRNA: 3'- -GGUCGCG-------------UACUGUu---GCUUGaaGCAGC- -5' |
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| 11977 | 3' | -49.4 | NC_003278.1 | + | 30821 | 0.66 | 0.915494 |
|
Target: 5'- cCCAGCGC--GACAGCGGccagaGCggCGUg- -3' miRNA: 3'- -GGUCGCGuaCUGUUGCU-----UGaaGCAgc -5' |
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| 11977 | 3' | -49.4 | NC_003278.1 | + | 34471 | 0.67 | 0.87022 |
|
Target: 5'- aCAGUGCuagcggGGCGGCGuACUccaCGUCGg -3' miRNA: 3'- gGUCGCGua----CUGUUGCuUGAa--GCAGC- -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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