miRNA: 3'- -UCG-----AGCGuaGCCUGCuuaAGCUGGCu -5'
miRNA: 3'- ucGAGCG--UAG----CCUGCUUAAGCUGGcu -5'
miRNA: 3'- -UCGaGCGUAgCCUGCUUaa--------GCUGGCU- -5'
miRNA: 3'- -UCGAGCGUAGCCUGCUUAAGCUGGCU- -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 |
| Predicted miRNA align pattern | |||||||
| 18453 | 5' | -52.7 | NC_004681.1 | + | 21317 | 0.68 | 0.842594 |
|
Target: 5'- aGGCgaccaUCGUcgUGGACGuggUCGACCGc -3' miRNA: 3'- -UCG-----AGCGuaGCCUGCuuaAGCUGGCu -5' |
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| 18453 | 5' | -52.7 | NC_004681.1 | + | 58706 | 0.68 | 0.842594 |
|
Target: 5'- -cCUCGUugAUCcgauGGGCGAAUUCGACCc- -3' miRNA: 3'- ucGAGCG--UAG----CCUGCUUAAGCUGGcu -5' |
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| 18453 | 5' | -52.7 | NC_004681.1 | + | 12066 | 0.68 | 0.851088 |
|
Target: 5'- cGGC-CGCAU-GGACGAGgccgaguacgUGGCCGAg -3' miRNA: 3'- -UCGaGCGUAgCCUGCUUaa--------GCUGGCU- -5' |
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| 18453 | 5' | -52.7 | NC_004681.1 | + | 39580 | 1.09 | 0.002936 |
|
Target: 5'- gAGCUCGCAUCGGACGAAUUCGACCGAc -3' miRNA: 3'- -UCGAGCGUAGCCUGCUUAAGCUGGCU- -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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