miRNA: 3'- -UCCCGGUUGc--------GGGUCCU---UUUCC-GGAG- -5'
miRNA: 3'- -UCCCGGUugCGGGUCCuuuuCCGGag -5'
miRNA: 3'- uCCCGGU--UGcGGGUccUUUUCCGGAG- -5'
miRNA: 3'- -UCCCGGUUGCGGGUCCUUUUCCGGAG- -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 | |||||||
| 2302 | 3' | -58.3 | NC_001408.1 | + | 3718 | 0.67 | 0.075075 |
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Target: 5'- aAGGGCUAACaggauccccUCCGGGAgcgGAAGGuCCUCc -3' miRNA: 3'- -UCCCGGUUGc--------GGGUCCU---UUUCC-GGAG- -5' |
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| 2302 | 3' | -58.3 | NC_001408.1 | + | 1034 | 0.68 | 0.063502 |
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Target: 5'- cAGGGCCG--GCCCAGG----GGCCa- -3' miRNA: 3'- -UCCCGGUugCGGGUCCuuuuCCGGag -5' |
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| 2302 | 3' | -58.3 | NC_001408.1 | + | 2084 | 0.68 | 0.061403 |
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Target: 5'- cGGGCCAcgAC-CCCGaaGAGAGGCCUUu -3' miRNA: 3'- uCCCGGU--UGcGGGUccUUUUCCGGAG- -5' |
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| 2302 | 3' | -58.3 | NC_001408.1 | + | 2032 | 1.09 | 1.8e-05 |
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Target: 5'- cAGGGCCAACGCCCAGGAAAAGGCCUCu -3' miRNA: 3'- -UCCCGGUUGCGGGUCCUUUUCCGGAG- -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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