miRNA: 3'- -GGGAU-UCCUUGGUGacaa---CCUCuaUG- -5'
miRNA: 3'- -GGgAUUCCu-UGGUGacaACCUCUAUg -5'
miRNA: 3'- gGGAUUCCU----------UGGuGaCAACCUCUAUG- -5'
miRNA: 3'- ggGAUUCCUUGGUGacaa-----CCUCUAUG- -5'
miRNA: 3'- -GGGAUUCCU----------UGGUGACaaCCuCua-UG- -5'
Results 21 - 25 of 25 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 | |||||||
| 13286 | 5' | -48.6 | NC_003409.1 | + | 125925 | 0.67 | 0.99756 |
|
Target: 5'- cCCCUGcAGGAGCCACaacagcaGGAGccACa -3' miRNA: 3'- -GGGAU-UCCUUGGUGacaa---CCUCuaUG- -5' |
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| 13286 | 5' | -48.6 | NC_003409.1 | + | 128542 | 0.69 | 0.987091 |
|
Target: 5'- aCCgUGAGGcuGCCGCg--UGGGGAUAa -3' miRNA: 3'- -GGgAUUCCu-UGGUGacaACCUCUAUg -5' |
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| 13286 | 5' | -48.6 | NC_003409.1 | + | 133003 | 0.75 | 0.842803 |
|
Target: 5'- gCCUGGGGAucugggcgagACC-CcGUUGGAGGUACu -3' miRNA: 3'- gGGAUUCCU----------UGGuGaCAACCUCUAUG- -5' |
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| 13286 | 5' | -48.6 | NC_003409.1 | + | 133240 | 0.66 | 0.998546 |
|
Target: 5'- -gCUGGGGGAUCAUccuucucagGGAGAUGCa -3' miRNA: 3'- ggGAUUCCUUGGUGacaa-----CCUCUAUG- -5' |
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| 13286 | 5' | -48.6 | NC_003409.1 | + | 133868 | 0.67 | 0.997094 |
|
Target: 5'- uCCCUGGGGGcagaccugcuACCGCUGgcGGuGcagGCu -3' miRNA: 3'- -GGGAUUCCU----------UGGUGACaaCCuCua-UG- -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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