miRNA: 3'- -UUC-UGCG-----ACCUGCUG-CCGUGcuUUAG- -5'
miRNA: 3'- -UUCUGCGACCUGcUG--CCGU------GCUUUAG- -5'
miRNA: 3'- uuCUGCGACCugCuGCCG-------------UGCUUUAG- -5'
miRNA: 3'- uUCUGCGaCCUGCugCCGUGCUUUag -5'
miRNA: 3'- uuCugCG---ACCUGCUGCCGUGCUUUAG- -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 | |||||||
| 20901 | 5' | -53.4 | NC_004689.1 | + | 29105 | 0.68 | 0.752374 |
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Target: 5'- cGAGcACGUcgccgUGGACGACuGGCACacGAUCa -3' miRNA: 3'- -UUC-UGCG-----ACCUGCUG-CCGUGcuUUAG- -5' |
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| 20901 | 5' | -53.4 | NC_004689.1 | + | 26841 | 0.69 | 0.709966 |
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Target: 5'- uAGGAUGCUGGACcGCcuGGCAucaugcUGGAAUCa -3' miRNA: 3'- -UUCUGCGACCUGcUG--CCGU------GCUUUAG- -5' |
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| 20901 | 5' | -53.4 | NC_004689.1 | + | 16810 | 0.69 | 0.708886 |
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Target: 5'- -uGACGCUGGugG-UGGUgaauucaccgucaGCGAAGUUg -3' miRNA: 3'- uuCUGCGACCugCuGCCG-------------UGCUUUAG- -5' |
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| 20901 | 5' | -53.4 | NC_004689.1 | + | 52718 | 0.71 | 0.589089 |
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Target: 5'- uAGACGCcGGGUGugGGCAUGGGAc- -3' miRNA: 3'- uUCUGCGaCCUGCugCCGUGCUUUag -5' |
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| 20901 | 5' | -53.4 | NC_004689.1 | + | 48112 | 0.72 | 0.513575 |
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Target: 5'- -cGugGCcgaUGGAUGAUGGCGUGAGGUCc -3' miRNA: 3'- uuCugCG---ACCUGCUGCCGUGCUUUAG- -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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