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miRNA: 3'- cCCACUGUCa--AGUAGUcg----ACCGU-GUC- -5'
miRNA: 3'- ccCACUG-UCAAGUa-GUCG---ACCGUGuc -5'
miRNA: 3'- -CC-CACUGUCAAG----UAGUCGaCCGUGuc -5'
miRNA: 3'- -CCCACUGUCAAGUAGUCGACCGUGUC- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position |
R_P_ratio#
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P value |
| Predicted miRNA align pattern | |||||||
| 31544 | 5' | -52.5 | NC_006820.1 | + | 23289 | 0.66 | 0.984612 |
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Target: 5'- uGGUGGCAGguaUCAUCGuucugaUGGCAgCAGg -3' miRNA: 3'- cCCACUGUCa--AGUAGUcg----ACCGU-GUC- -5' |
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| 31544 | 5' | -52.5 | NC_006820.1 | + | 108788 | 0.66 | 0.98935 |
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Target: 5'- -aGUGGCaAGUUCAggCAGCaacUGGCACu- -3' miRNA: 3'- ccCACUG-UCAAGUa-GUCG---ACCGUGuc -5' |
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| 31544 | 5' | -52.5 | NC_006820.1 | + | 192455 | 0.66 | 0.986342 |
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Target: 5'- gGGuGUGACAGUUUaaaaAUUGGCaGGCAUg- -3' miRNA: 3'- -CC-CACUGUCAAG----UAGUCGaCCGUGuc -5' |
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| 31544 | 5' | -52.5 | NC_006820.1 | + | 120803 | 1.1 | 0.006215 |
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Target: 5'- gGGGUGACAGUUCAUCAGCUGGCACAGc -3' miRNA: 3'- -CCCACUGUCAAGUAGUCGACCGUGUC- -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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