miRNA: 3'- -GGG----UACGGu----GCUCugUACCGCuUUGU- -5'
miRNA: 3'- -GGGU-----ACGGUGCUCUGUAc--CGCUUUGU- -5'
miRNA: 3'- -GGGUACGGUGCUCUGUACCGCUUUGU- -5'
Results 1 - 3 of 3 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 | |||||||
| 22501 | 5' | -52.2 | NC_005069.1 | + | 5388 | 0.7 | 0.627204 |
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Target: 5'- aCCUuucaAUGCCucguuUGAGugGUGGCGcAACAg -3' miRNA: 3'- -GGG----UACGGu----GCUCugUACCGCuUUGU- -5' |
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| 22501 | 5' | -52.2 | NC_005069.1 | + | 4028 | 0.75 | 0.339982 |
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Target: 5'- aUCCAuaauuUGCCGCGAGGCAUacuGCGGAAUAc -3' miRNA: 3'- -GGGU-----ACGGUGCUCUGUAc--CGCUUUGU- -5' |
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| 22501 | 5' | -52.2 | NC_005069.1 | + | 41103 | 1.12 | 0.001103 |
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Target: 5'- aCCCAUGCCACGAGACAUGGCGAAACAa -3' miRNA: 3'- -GGGUACGGUGCUCUGUACCGCUUUGU- -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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