miRNA: 3'- -CCGUCCUggAGc---GGGUCUua--GGGGGU- -5'
miRNA: 3'- -CCGU-CCUGGAG---------------CGGGUCU----UAGGGGGU- -5'
miRNA: 3'- -CCG---------UCCUgGAGCGGGUCUUAG-----GGGGU- -5'
miRNA: 3'- -CCGUCCUGGAGCGGGUCUUAGGGGGU- -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 | |||||||
| 7072 | 5' | -59.9 | NC_001885.1 | + | 184 | 0.66 | 0.101952 |
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Target: 5'- gGGUGGGGuuUCcgauCCCGGAcgagCCCCCAa -3' miRNA: 3'- -CCGUCCUggAGc---GGGUCUua--GGGGGU- -5' |
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| 7072 | 5' | -59.9 | NC_001885.1 | + | 2455 | 0.68 | 0.070246 |
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Target: 5'- gGGCAgGGACCUCcuaaccaaacuaaagGCCCAGAuccaGUUUUCCGc -3' miRNA: 3'- -CCGU-CCUGGAG---------------CGGGUCU----UAGGGGGU- -5' |
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| 7072 | 5' | -59.9 | NC_001885.1 | + | 134 | 0.69 | 0.058946 |
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Target: 5'- gGGUcucacauuuGGGGgCUCGUCCGGGAUCggaaaCCCCAc -3' miRNA: 3'- -CCG---------UCCUgGAGCGGGUCUUAG-----GGGGU- -5' |
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| 7072 | 5' | -59.9 | NC_001885.1 | + | 883 | 1.09 | 0.000017 |
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Target: 5'- uGGCAGGACCUCGCCCAGAAUCCCCCAc -3' miRNA: 3'- -CCGUCCUGGAGCGGGUCUUAGGGGGU- -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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