miRNA: 3'- -UCUACUCUCGUCGAaggaCgUUCUCC- -5'
miRNA: 3'- ucuACUCUCGUCGa-------AGgaCGUUCUCC- -5'
miRNA: 3'- -UCUACUC--UCG---------------UCGAa--GGACGUUCUCC- -5'
miRNA: 3'- -UCUACUCUCGUCGAAGGACGUUCUCC- -5'
Results 1 - 4 of 4 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 | |||||||
| 3166 | 5' | -52 | NC_001500.1 | + | 1353 | 0.68 | 0.184316 |
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Target: 5'- aGGAUGGGAGCGGUUg---GaGAGGGGg -3' miRNA: 3'- -UCUACUCUCGUCGAaggaCgUUCUCC- -5' |
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| 3166 | 5' | -52 | NC_001500.1 | + | 4328 | 0.68 | 0.161393 |
|
Target: 5'- --uUGAGAGCGGUggggguggUCa-GCAGGAGGu -3' miRNA: 3'- ucuACUCUCGUCGa-------AGgaCGUUCUCC- -5' |
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| 3166 | 5' | -52 | NC_001500.1 | + | 5235 | 0.7 | 0.112608 |
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Target: 5'- aAGGUGGGgcAGUcccagggaccauagaGGCUgcgCCUGUAGGAGGa -3' miRNA: 3'- -UCUACUC--UCG---------------UCGAa--GGACGUUCUCC- -5' |
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| 3166 | 5' | -52 | NC_001500.1 | + | 3604 | 1.12 | 0.000044 |
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Target: 5'- cAGAUGAGAGCAGCUUCCUGCAAGAGGg -3' miRNA: 3'- -UCUACUCUCGUCGAAGGACGUUCUCC- -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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