miRNA: 3'- -GGa---GaGCCUGu--CGGuGgUCGUCGGGG- -5'
miRNA: 3'- -GGa---GaGCCUGu--CGGuGgUCGUCGGGG- -5'
miRNA: 3'- -GGA-GAGCCUg--------UCGgU-GGUCGUCGGGg -5'
miRNA: 3'- -GGAGAGCCUGUCGGUGGUCGUCGGGG- -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 | |||||||
| 2199 | 3' | -59.9 | NC_001401.1 | + | 59 | 0.66 | 0.058321 |
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Target: 5'- cCCgacgCcCGGGCuuuGCC-CgGGCGGCCUCa -3' miRNA: 3'- -GGa---GaGCCUGu--CGGuGgUCGUCGGGG- -5' |
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| 2199 | 3' | -59.9 | NC_001401.1 | + | 4605 | 0.66 | 0.058321 |
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Target: 5'- cCCgacgCcCGGGCuuuGCC-CgGGCGGCCUCa -3' miRNA: 3'- -GGa---GaGCCUGu--CGGuGgUCGUCGGGG- -5' |
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| 2199 | 3' | -59.9 | NC_001401.1 | + | 2664 | 0.69 | 0.027433 |
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Target: 5'- uCCUcCUCGGGaaccggaaaGGCgGgCCAGCAGCCUg -3' miRNA: 3'- -GGA-GAGCCUg--------UCGgU-GGUCGUCGGGg -5' |
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| 2199 | 3' | -59.9 | NC_001401.1 | + | 2759 | 1.12 | 4e-06 |
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Target: 5'- gCCUCUCGGACAGCCACCAGCAGCCCCc -3' miRNA: 3'- -GGAGAGCCUGUCGGUGGUCGUCGGGG- -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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