miRNA: 3'- -UGCAcGCCCAUCAG----------UCGCUC-CuuAgC- -5'
miRNA: 3'- -UGCAC--GCCCauCAGUCGCUCCUUa---GC- -5'
miRNA: 3'- -UGCACGCCCAUCAGUCGCUCCUUAGC- -5'
Results 1 - 3 of 3 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 | |||||||
| 7344 | 3' | -54.7 | NC_001900.1 | + | 9716 | 0.66 | 0.705129 |
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Target: 5'- gACGUuCGGGUGGUUccgggccgaaGGCGAGuGggUgGa -3' miRNA: 3'- -UGCAcGCCCAUCAG----------UCGCUC-CuuAgC- -5' |
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| 7344 | 3' | -54.7 | NC_001900.1 | + | 29963 | 0.72 | 0.380582 |
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Target: 5'- gACGUGacCGGG--GUCAGCGAGGAAgcacCGa -3' miRNA: 3'- -UGCAC--GCCCauCAGUCGCUCCUUa---GC- -5' |
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| 7344 | 3' | -54.7 | NC_001900.1 | + | 35144 | 1.09 | 0.000982 |
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Target: 5'- cACGUGCGGGUAGUCAGCGAGGAAUCGg -3' miRNA: 3'- -UGCACGCCCAUCAGUCGCUCCUUAGC- -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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