miRNA: 3'- ccaUGCGGGGCUUGCAa---UCGu----GUUCA- -5'
miRNA: 3'- -CCa-UGCGgGGCUUGCAa------UCGUGUUCa -5'
miRNA: 3'- -CCAUGCGGGGCUUGCAAUCGUGUUCA- -5'
Results 21 - 23 of 23 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 | |||||||
| 24243 | 5' | -51.5 | NC_005263.2 | + | 47561 | 0.72 | 0.551903 |
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Target: 5'- --cGCGCCCUGAACGUgcaaGGCuacguCGAGUc -3' miRNA: 3'- ccaUGCGGGGCUUGCAa---UCGu----GUUCA- -5' |
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| 24243 | 5' | -51.5 | NC_005263.2 | + | 24699 | 0.74 | 0.4353 |
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Target: 5'- cGGcgGCGCgCCGAACGUgccgggcGGCGCAGGc -3' miRNA: 3'- -CCa-UGCGgGGCUUGCAa------UCGUGUUCa -5' |
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| 24243 | 5' | -51.5 | NC_005263.2 | + | 5736 | 1.09 | 0.002063 |
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Target: 5'- gGGUACGCCCCGAACGUUAGCACAAGUc -3' miRNA: 3'- -CCAUGCGGGGCUUGCAAUCGUGUUCA- -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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