miRNA: 3'- uACUGUGU----UCGaauGUAgCCCCG-AUG- -5'
miRNA: 3'- uaCUGUGUUCGa-AUGuaGCCCCGa----UG- -5'
miRNA: 3'- -UACUGUGUUCGa---AUGUa-----GCCCCGAug -5'
miRNA: 3'- uaCUGugUUCGaaUGuaGCC-CCGAUG- -5'
miRNA: 3'- uacugUGUUCGAAUGUAGCCCCGAUG- -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 | |||||||
| 238 | 3' | -51.2 | AC_000008.1 | + | 32218 | 0.66 | 0.770928 |
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Target: 5'- cUGACGCAccccGGCc--CAUgGGGGCaUGCg -3' miRNA: 3'- uACUGUGU----UCGaauGUAgCCCCG-AUG- -5' |
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| 238 | 3' | -51.2 | AC_000008.1 | + | 17870 | 0.66 | 0.770928 |
|
Target: 5'- -gGGCGCGAGCcgUGUcgCGGGGCcagagACg -3' miRNA: 3'- uaCUGUGUUCGa-AUGuaGCCCCGa----UG- -5' |
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| 238 | 3' | -51.2 | AC_000008.1 | + | 16976 | 0.68 | 0.643558 |
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Target: 5'- gGUGGCGCGGGCaaacUGCAccagccCGGGGCUc- -3' miRNA: 3'- -UACUGUGUUCGa---AUGUa-----GCCCCGAug -5' |
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| 238 | 3' | -51.2 | AC_000008.1 | + | 32097 | 0.68 | 0.619704 |
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Target: 5'- -cGGCugAAGCg-GCggCGGaGGCUGCa -3' miRNA: 3'- uaCUGugUUCGaaUGuaGCC-CCGAUG- -5' |
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| 238 | 3' | -51.2 | AC_000008.1 | + | 1000 | 0.91 | 0.022951 |
|
Target: 5'- ----aACAAGCUUACAUCGGGGCUACg -3' miRNA: 3'- uacugUGUUCGAAUGUAGCCCCGAUG- -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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