miRNA: 3'- cgaCUUCGGCAGC-CGUA-----GUUACGGCa -5'
miRNA: 3'- -CgACU----UCGGCAGCCGUAGUUaCGGca -5'
miRNA: 3'- cgACUUCGGCAG------CCGuAGuUACGGCa -5'
miRNA: 3'- -CGAC-UUCGGca------GCCGUAGUUACGGCa -5'
miRNA: 3'- -CGACUUCGGCAGCCGUAGUUACGGCA- -5'
Results 1 - 5 of 5 are showing below:
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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 | |||||||
| 13039 | 3' | -54 | NC_003390.1 | + | 6859 | 0.67 | 0.686094 |
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Target: 5'- --gGAGGCCGUUGaGCGUgccggUAAUGCUGg -3' miRNA: 3'- cgaCUUCGGCAGC-CGUA-----GUUACGGCa -5' |
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| 13039 | 3' | -54 | NC_003390.1 | + | 31855 | 0.67 | 0.641207 |
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Target: 5'- gGgUGGaguuGGCCGUUGGUGUCGAgGCCa- -3' miRNA: 3'- -CgACU----UCGGCAGCCGUAGUUaCGGca -5' |
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| 13039 | 3' | -54 | NC_003390.1 | + | 33951 | 0.68 | 0.629936 |
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Target: 5'- -gUGAGGCCGUUcacccgGGC-UCcAUGCCGg -3' miRNA: 3'- cgACUUCGGCAG------CCGuAGuUACGGCa -5' |
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| 13039 | 3' | -54 | NC_003390.1 | + | 3549 | 0.78 | 0.168313 |
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Target: 5'- uGCUGuAGGCCacuacaggUGGCAUCAAUGCCGa -3' miRNA: 3'- -CGAC-UUCGGca------GCCGUAGUUACGGCa -5' |
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| 13039 | 3' | -54 | NC_003390.1 | + | 32440 | 1.09 | 0.001038 |
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Target: 5'- aGCUGAAGCCGUCGGCAUCAAUGCCGUu -3' miRNA: 3'- -CGACUUCGGCAGCCGUAGUUACGGCA- -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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