miRNA: 3'- ggCGCCAG-----CUUGGC----------UCCuuUGGc-UGG- -5'
miRNA: 3'- -GGCG-CCaGCUUGGCU---CCUU--UGGCUGg -5'
miRNA: 3'- ggCGCCaGCUugGCUCCUUUG-GCugG- -5'
miRNA: 3'- -GGcGCCAGcUUGGCuCCUUUGGCuGG- -5'
miRNA: 3'- -GGCGCCAGCUUGGCUCCUUUGGCUGG- -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 | |||||||
| 33213 | 3' | -54.5 | NC_007523.1 | + | 2255 | 0.66 | 0.189459 |
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Target: 5'- -gGCGGUCcaccgGGACCGgcugggggagGGGggGCCacGCCg -3' miRNA: 3'- ggCGCCAG-----CUUGGC----------UCCuuUGGc-UGG- -5' |
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| 33213 | 3' | -54.5 | NC_007523.1 | + | 4172 | 0.68 | 0.120333 |
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Target: 5'- uUCGCuGG-CGAACCGAagcGGGAuaGCUGACg -3' miRNA: 3'- -GGCG-CCaGCUUGGCU---CCUU--UGGCUGg -5' |
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| 33213 | 3' | -54.5 | NC_007523.1 | + | 101 | 0.69 | 0.095314 |
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Target: 5'- -gGCGGcCGAcgCGAGGAAACgCGugCu -3' miRNA: 3'- ggCGCCaGCUugGCUCCUUUG-GCugG- -5' |
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| 33213 | 3' | -54.5 | NC_007523.1 | + | 1364 | 0.72 | 0.06137 |
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Target: 5'- uCCuCGGUUcGACCGcGGAGACCG-CCg -3' miRNA: 3'- -GGcGCCAGcUUGGCuCCUUUGGCuGG- -5' |
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| 33213 | 3' | -54.5 | NC_007523.1 | + | 1386 | 1.13 | 0.000021 |
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Target: 5'- uCCGCGGUCGAACCGAGGAAACCGACCu -3' miRNA: 3'- -GGCGCCAGCUUGGCUCCUUUGGCUGG- -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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