miRNA: 3'- -GAGCUCUCggaCGACCAaa-UGC-UCGU- -5'
miRNA: 3'- -GAGCucUCGGa-CGACCAaauGCUCGu -5'
miRNA: 3'- -GAGCU----CUCGGACGa--CCAaauGCUCGU- -5'
miRNA: 3'- gagCUCuCGGA-CGACCAaauGCUCGU- -5'
miRNA: 3'- gAgCUcUCGGa--CGACCaaa-UGCUCGU- -5'
Results 1 - 5 of 5 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 | |||||||
| 7867 | 5' | -53.5 | NC_001973.1 | + | 155174 | 0.66 | 0.964919 |
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Target: 5'- uCUCGAGAG---GCUGGUgcgGCGcAGCGc -3' miRNA: 3'- -GAGCUCUCggaCGACCAaa-UGC-UCGU- -5' |
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| 7867 | 5' | -53.5 | NC_001973.1 | + | 41932 | 0.66 | 0.957783 |
|
Target: 5'- aCUCGucGGCCgcGCUGGUcauCGGGCu -3' miRNA: 3'- -GAGCucUCGGa-CGACCAaauGCUCGu -5' |
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| 7867 | 5' | -53.5 | NC_001973.1 | + | 127857 | 0.67 | 0.940676 |
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Target: 5'- aCUCGAuuucGAGCCUGUccaGGUcgcCGAGCGc -3' miRNA: 3'- -GAGCU----CUCGGACGa--CCAaauGCUCGU- -5' |
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| 7867 | 5' | -53.5 | NC_001973.1 | + | 50831 | 0.67 | 0.935788 |
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Target: 5'- --aGAGcGCCUcGCUGGU---CGAGCAg -3' miRNA: 3'- gagCUCuCGGA-CGACCAaauGCUCGU- -5' |
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| 7867 | 5' | -53.5 | NC_001973.1 | + | 45392 | 0.68 | 0.907613 |
|
Target: 5'- gUgGAcAGCCgcgGCUGGgccgACGAGCAg -3' miRNA: 3'- gAgCUcUCGGa--CGACCaaa-UGCUCGU- -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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