miRNA: 3'- -CGCGG---UGGUCCUCCGUug--GCGGcaac -5'
miRNA: 3'- -CGCGg---UGGUCCU------CCGUUGGCGGCAAC- -5'
miRNA: 3'- -CGCGGUGGUCCUCCGUUGGCGGCAAC- -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 | |||||||
| 9563 | 3' | -59 | NC_002554.1 | + | 2948 | 0.69 | 0.058985 |
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Target: 5'- uGCGUCcauGCCAGGGGGCAcguaCGCCa--- -3' miRNA: 3'- -CGCGG---UGGUCCUCCGUug--GCGGcaac -5' |
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| 9563 | 3' | -59 | NC_002554.1 | + | 2196 | 0.72 | 0.035951 |
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Target: 5'- uGCGCaaugGCUGGGAcgucgaGGUGACCGCUGUUGg -3' miRNA: 3'- -CGCGg---UGGUCCU------CCGUUGGCGGCAAC- -5' |
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| 9563 | 3' | -59 | NC_002554.1 | + | 2275 | 1.1 | 1.8e-05 |
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Target: 5'- aGCGCCACCAGGAGGCAACCGCCGUUGa -3' miRNA: 3'- -CGCGGUGGUCCUCCGUUGGCGGCAAC- -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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