miRNA: 3'- uuuuUGCGGGCGUUAGUcuu--UAUUAA- -5'
miRNA: 3'- uuuUugCGGGCGU-------UAGUCUUUaUUAA- -5'
miRNA: 3'- uuUUUGCGGGCGUUA-GUCU--UUAUUaa -5'
miRNA: 3'- uUUUUG---CGGGCGUUAGUCUuuAUUAa -5'
miRNA: 3'- -UUUUUGCGGGCGUUAGUCUUUAUUAA- -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 | |||||||
| 3501 | 3' | -43 | NC_001623.1 | + | 5831 | 0.67 | 0.999993 |
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Target: 5'- ---cACGUCCGCGAUCAaauuuGUAGUUg -3' miRNA: 3'- uuuuUGCGGGCGUUAGUcuu--UAUUAA- -5' |
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| 3501 | 3' | -43 | NC_001623.1 | + | 26106 | 0.68 | 0.999985 |
|
Target: 5'- --uAugGCCCGCAuaauauuAUCGGAAGaAGUUu -3' miRNA: 3'- uuuUugCGGGCGU-------UAGUCUUUaUUAA- -5' |
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| 3501 | 3' | -43 | NC_001623.1 | + | 36151 | 0.69 | 0.999901 |
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Target: 5'- -cGAAUGUCCGCAAUgCAGAuaGGUAAc- -3' miRNA: 3'- uuUUUGCGGGCGUUA-GUCU--UUAUUaa -5' |
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| 3501 | 3' | -43 | NC_001623.1 | + | 17457 | 0.79 | 0.918894 |
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Target: 5'- uGAAGCguuGCCCGCAAUCAGGuuUGAUa -3' miRNA: 3'- uUUUUG---CGGGCGUUAGUCUuuAUUAa -5' |
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| 3501 | 3' | -43 | NC_001623.1 | + | 6026 | 1.03 | 0.083493 |
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Target: 5'- cAAAAACGCCCGCAAUCAGAAAUAAUUc -3' miRNA: 3'- -UUUUUGCGGGCGUUAGUCUUUAUUAA- -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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