miRNA: 3'- -CCGGU----UGUGCUaaGC-CACG--------------UCGAGUG- -5'
miRNA: 3'- cCGGuugUGCUAA-GCCACGUCGA-GUG- -5'
miRNA: 3'- -CCGGU------UGUGCUAAGCCacg-UCGAgUG- -5'
miRNA: 3'- -CC-GGUUG-UGCUa---AGCCa-----CGUCGaGUG- -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 | |||||||
| 1336 | 3' | -53.2 | NC_001335.1 | + | 42338 | 0.7 | 0.549478 |
|
Target: 5'- cGGCCGaccgGCGCGAgcCGcGUGCgucucggcguccaaGGCUCGCu -3' miRNA: 3'- -CCGGU----UGUGCUaaGC-CACG--------------UCGAGUG- -5' |
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| 1336 | 3' | -53.2 | NC_001335.1 | + | 47059 | 0.68 | 0.664728 |
|
Target: 5'- cGCUu--GCGGUUaCGGUGCGGCUgCGCc -3' miRNA: 3'- cCGGuugUGCUAA-GCCACGUCGA-GUG- -5' |
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| 1336 | 3' | -53.2 | NC_001335.1 | + | 50600 | 0.67 | 0.73101 |
|
Target: 5'- cGGCCAcgucggGCACGGUUCGGcacaAGCU-ACg -3' miRNA: 3'- -CCGGU------UGUGCUAAGCCacg-UCGAgUG- -5' |
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| 1336 | 3' | -53.2 | NC_001335.1 | + | 50738 | 0.66 | 0.783507 |
|
Target: 5'- aGGcCCAGCgACGAgucgUCGGccggggGCGGCgCACc -3' miRNA: 3'- -CC-GGUUG-UGCUa---AGCCa-----CGUCGaGUG- -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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