miRNA: 3'- -GGGCGACGGG--------ACCaCAUgGUCCUUUC- -5'
miRNA: 3'- gGGCGACGGGacCACa--UGGUCCUuuc -5'
miRNA: 3'- -GGGCGACGGGa-CCAc--AUGGU-CCUuuc -5'
miRNA: 3'- -GGgCGACGGGaCCacAUGGUCCUUUC- -5'
miRNA: 3'- -GGGCGACGGGACCACAUGGUCCUUUC- -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 | |||||||
| 270 | 3' | -56.2 | AC_000008.1 | + | 3186 | 0.68 | 0.409095 |
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Target: 5'- aCCCGCUGUUCcuugcauuUGG-GUAaCAGGAGGGg -3' miRNA: 3'- -GGGCGACGGG--------ACCaCAUgGUCCUUUC- -5' |
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| 270 | 3' | -56.2 | AC_000008.1 | + | 23805 | 0.69 | 0.390312 |
|
Target: 5'- gCCGCUGCCC--GUGccaGCCAGGGc-- -3' miRNA: 3'- gGGCGACGGGacCACa--UGGUCCUuuc -5' |
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| 270 | 3' | -56.2 | AC_000008.1 | + | 29314 | 0.69 | 0.381135 |
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Target: 5'- gCCUGCUGCCCggGGUcuuUACCGuGGAc-- -3' miRNA: 3'- -GGGCGACGGGa-CCAc--AUGGU-CCUuuc -5' |
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| 270 | 3' | -56.2 | AC_000008.1 | + | 35037 | 0.73 | 0.205389 |
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Target: 5'- uCCgGCUGCUCgGGc-UGCCGGGAAAGg -3' miRNA: 3'- -GGgCGACGGGaCCacAUGGUCCUUUC- -5' |
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| 270 | 3' | -56.2 | AC_000008.1 | + | 27368 | 1.1 | 0.000403 |
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Target: 5'- gCCCGCUGCCCUGGUGUACCAGGAAAGu -3' miRNA: 3'- -GGGCGACGGGACCACAUGGUCCUUUC- -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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