miRNA: 3'- -AGCAGGCGUAGa-------UGCUCuGCaCGuAG- -5'
miRNA: 3'- aGCAgGCGUAga---UGCUCUGcACGUAG- -5'
miRNA: 3'- -AGCAGGCGUAGaUGCucUGCAcGUAG- -5'
miRNA: 3'- -AGcAGGCGUAGa-UGC-UCUGCa--CGUAG- -5'
miRNA: 3'- -AGCAGgCGU----AGAUGCu---CugCACGUag -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 | |||||||
| 23848 | 3' | -52.6 | NC_005261.1 | + | 32610 | 0.69 | 0.891155 |
|
Target: 5'- gUCGUCCGCGUCcucggacgACGAGcCGgGC-UCg -3' miRNA: 3'- -AGCAGGCGUAGa-------UGCUCuGCaCGuAG- -5' |
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| 23848 | 3' | -52.6 | NC_005261.1 | + | 66624 | 0.69 | 0.897931 |
|
Target: 5'- gCGUgCGCAUggccgACGAGACcUGCGUCc -3' miRNA: 3'- aGCAgGCGUAga---UGCUCUGcACGUAG- -5' |
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| 23848 | 3' | -52.6 | NC_005261.1 | + | 93098 | 0.69 | 0.897931 |
|
Target: 5'- cUCGUCCGCAUC-GCGc-GCGU-CGUCg -3' miRNA: 3'- -AGCAGGCGUAGaUGCucUGCAcGUAG- -5' |
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| 23848 | 3' | -52.6 | NC_005261.1 | + | 4819 | 0.69 | 0.904463 |
|
Target: 5'- uUCcUCCGCGUUggGCGcAGGCGgcgGCGUCc -3' miRNA: 3'- -AGcAGGCGUAGa-UGC-UCUGCa--CGUAG- -5' |
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| 23848 | 3' | -52.6 | NC_005261.1 | + | 64035 | 0.66 | 0.975498 |
|
Target: 5'- cUCGUCgGCGcggcUCUGCGccgcGugGUGCGc- -3' miRNA: 3'- -AGCAGgCGU----AGAUGCu---CugCACGUag -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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