miRNA: 3'- -GC-CGCUc--UGCUACUUGAGAA----GGCUUU- -5'
miRNA: 3'- -GCCGCU-CUGCu------------ACUUGag--AAGGCUUU- -5'
miRNA: 3'- gC-CGCUCUGCUACUugAGa---AGGCUUU- -5'
miRNA: 3'- -GCCGCUCUGCUACUUGAGAAGGCUUU- -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# |
P value
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| Predicted miRNA align pattern | |||||||
| 12127 | 5' | -51.1 | NC_003309.1 | + | 34155 | 0.66 | 0.903546 |
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Target: 5'- cCGcGCGAaacGCGAUGAGCUUUUgcaaCCGGAGa -3' miRNA: 3'- -GC-CGCUc--UGCUACUUGAGAA----GGCUUU- -5' |
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| 12127 | 5' | -51.1 | NC_003309.1 | + | 42650 | 0.66 | 0.900731 |
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Target: 5'- cCGGCGAuGGCGuccugucgucguuUGAACgguaUUCCGAAGg -3' miRNA: 3'- -GCCGCU-CUGCu------------ACUUGag--AAGGCUUU- -5' |
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| 12127 | 5' | -51.1 | NC_003309.1 | + | 5358 | 0.69 | 0.770145 |
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Target: 5'- gGcGCGGGAUGGUGAugUUgccgUUCGAGAg -3' miRNA: 3'- gC-CGCUCUGCUACUugAGa---AGGCUUU- -5' |
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| 12127 | 5' | -51.1 | NC_003309.1 | + | 16674 | 1.07 | 0.003518 |
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Target: 5'- aCGGCGAGACGAUGAACUCUUCCGAAAc -3' miRNA: 3'- -GCCGCUCUGCUACUUGAGAAGGCUUU- -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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