miRNA: 3'- -CGGUUA----------CGGCGCuuCGUGGGCAAGcc -5'
miRNA: 3'- -CGGuUACGgCGCU-------UCGU-GGGCAaGCC- -5'
miRNA: 3'- -CGGUuaCGGCGCU-----UCGUGGGcaagcc -5'
miRNA: 3'- -CGGUUaCGGCGC-UUCGUGGgcaAGCC- -5'
miRNA: 3'- cGGUUA---CGgCGCUUCGUGgGCa-----AGCC- -5'
Results 41 - 45 of 45 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 | |||||||
| 33087 | 5' | -54.9 | NC_007497.1 | + | 42659 | 0.7 | 0.461706 |
|
Target: 5'- gGCCAGUcggucuacgaGUCGCGggGCAUUCGUUUu- -3' miRNA: 3'- -CGGUUA----------CGGCGCuuCGUGGGCAAGcc -5' |
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| 33087 | 5' | -54.9 | NC_007497.1 | + | 13868 | 0.69 | 0.491326 |
|
Target: 5'- gGCCcAUGCgGCGGccccugcGGCGuCCCGUgCGGc -3' miRNA: 3'- -CGGuUACGgCGCU-------UCGU-GGGCAaGCC- -5' |
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| 33087 | 5' | -54.9 | NC_007497.1 | + | 36025 | 0.68 | 0.556228 |
|
Target: 5'- aGCCGcgGCCGCGGcguucGGCAUCCa----- -3' miRNA: 3'- -CGGUuaCGGCGCU-----UCGUGGGcaagcc -5' |
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| 33087 | 5' | -54.9 | NC_007497.1 | + | 29147 | 0.68 | 0.567129 |
|
Target: 5'- aGCCGAgGCCGUGcGGGCACUg--UCGGu -3' miRNA: 3'- -CGGUUaCGGCGC-UUCGUGGgcaAGCC- -5' |
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| 33087 | 5' | -54.9 | NC_007497.1 | + | 33318 | 0.66 | 0.721153 |
|
Target: 5'- aCCGAUcugGCgGCGAAGCGCaCGaagcugUCGGa -3' miRNA: 3'- cGGUUA---CGgCGCUUCGUGgGCa-----AGCC- -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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