miRNA: 3'- gACCGUGUAGCuu------CUGCcGUUCGCGU- -5'
miRNA: 3'- gacCGUGUAGCUU--CUGCCGU--UCGCgu -5'
miRNA: 3'- gaCCGU--GUaGCUUCuGCCGUUCGCGu -5'
miRNA: 3'- -GACCGU-GUAGCuUCUgCCGUUCgCGu -5'
miRNA: 3'- gaCCGUGua----GCUUCUGCCGU--UC-GCGU- -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
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| Predicted miRNA align pattern | |||||||
| 27936 | 5' | -54.6 | NC_005886.2 | + | 17569 | 0.67 | 0.626996 |
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Target: 5'- aUGGCACGUUGcaauccguGACGcCGGGUGCAg -3' miRNA: 3'- gACCGUGUAGCuu------CUGCcGUUCGCGU- -5' |
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| 27936 | 5' | -54.6 | NC_005886.2 | + | 38966 | 0.66 | 0.660806 |
|
Target: 5'- --aGCGCAUCGAAgcGAUGGCGcgAGCGa- -3' miRNA: 3'- gacCGUGUAGCUU--CUGCCGU--UCGCgu -5' |
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| 27936 | 5' | -54.6 | NC_005886.2 | + | 37121 | 0.66 | 0.660806 |
|
Target: 5'- -cGGCGauCGcUGAAG-CGGCAGGCGUg -3' miRNA: 3'- gaCCGU--GUaGCUUCuGCCGUUCGCGu -5' |
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| 27936 | 5' | -54.6 | NC_005886.2 | + | 3857 | 0.66 | 0.683225 |
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Target: 5'- aCUGGCGuCGUUGuGGAaGGCGGGgGCc -3' miRNA: 3'- -GACCGU-GUAGCuUCUgCCGUUCgCGu -5' |
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| 27936 | 5' | -54.6 | NC_005886.2 | + | 43372 | 0.66 | 0.694363 |
|
Target: 5'- -cGGUAUuuuuugCGAAGAUGGCGcaAGuCGCAc -3' miRNA: 3'- gaCCGUGua----GCUUCUGCCGU--UC-GCGU- -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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