miRNA: 3'- aaaCGCAACUG---GUUAUA-UCGCGG----CCG- -5'
miRNA: 3'- aaACGCAA-----CUGGUUaua--------UCGCGGCCG- -5'
miRNA: 3'- aaaCGCA---AC---UGGUUAUAUCgCGGcCG- -5'
miRNA: 3'- aaaCGCAACug-GUUauaUCGCGgCCG- -5'
Results 21 - 24 of 24 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 | |||||||
| 11282 | 3' | -50.4 | NC_003083.1 | + | 59610 | 0.67 | 0.974795 |
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Target: 5'- --gGUGUUGGCgcgCGAUGUgGGCGCCgucgGGCu -3' miRNA: 3'- aaaCGCAACUG---GUUAUA-UCGCGG----CCG- -5' |
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| 11282 | 3' | -50.4 | NC_003083.1 | + | 61619 | 0.66 | 0.98339 |
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Target: 5'- -gUGCGUUauuagGACCGGcuucugcgacgGGCGCUGGUg -3' miRNA: 3'- aaACGCAA-----CUGGUUaua--------UCGCGGCCG- -5' |
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| 11282 | 3' | -50.4 | NC_003083.1 | + | 93211 | 0.66 | 0.986052 |
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Target: 5'- --cGCGUcuaUGgcuACCGGUAUGGgGCCuGCu -3' miRNA: 3'- aaaCGCA---AC---UGGUUAUAUCgCGGcCG- -5' |
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| 11282 | 3' | -50.4 | NC_003083.1 | + | 73658 | 0.66 | 0.987743 |
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Target: 5'- --gGCGUUGuugCAAcg-GGCGCgGGCg -3' miRNA: 3'- aaaCGCAACug-GUUauaUCGCGgCCG- -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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