miRNA: 3'- cCUCCUUGUC---------------CUUC-GGCAugCGgUCa -5'
miRNA: 3'- cCucCUUGUCCuuCGGCA--UGCGGUCA- -5'
miRNA: 3'- ccUCC-UUGUCCUUCGGCaUGCg---GUCa -5'
miRNA: 3'- -CCUCCUUGuCCUUCGGcauGCGGUCa -5'
miRNA: 3'- ccUCCUUGUCC----UUCGGC-AUGCGGUCa -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 | |||||||
| 20856 | 5' | -54.8 | NC_004689.1 | + | 67640 | 0.66 | 0.780697 |
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Target: 5'- aGGGGAACGGugcagcguguccgguGAAGcCCGUugGCgGGg -3' miRNA: 3'- cCUCCUUGUC---------------CUUC-GGCAugCGgUCa -5' |
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| 20856 | 5' | -54.8 | NC_004689.1 | + | 11523 | 0.68 | 0.715303 |
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Target: 5'- cGucGAGCAGGuuGCCGUucAUGUCGGUa -3' miRNA: 3'- cCucCUUGUCCuuCGGCA--UGCGGUCA- -5' |
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| 20856 | 5' | -54.8 | NC_004689.1 | + | 33760 | 0.68 | 0.715303 |
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Target: 5'- -aGGGcAGCAGGAAGCCG-ACGaugaCAGc -3' miRNA: 3'- ccUCC-UUGUCCUUCGGCaUGCg---GUCa -5' |
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| 20856 | 5' | -54.8 | NC_004689.1 | + | 11119 | 0.71 | 0.491508 |
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Target: 5'- cGGGGGAGCcGGAGGCU---UGCCGGa -3' miRNA: 3'- -CCUCCUUGuCCUUCGGcauGCGGUCa -5' |
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| 20856 | 5' | -54.8 | NC_004689.1 | + | 44335 | 0.73 | 0.395635 |
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Target: 5'- -cGGGGACAGGcucaAAGCCGaUGCGUCGGg -3' miRNA: 3'- ccUCCUUGUCC----UUCGGC-AUGCGGUCa -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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