miRNA: 3'- -CCGGGGC---CAGGUCgC-CUCGG---UCGAGC- -5'
miRNA: 3'- -CCGGg--GCCAGgUCGCCu----CGG-UCGAGC- -5'
miRNA: 3'- -CCGGGGCCAGGUCG---CCUCGGUcgAGc -5'
miRNA: 3'- -CCGGGGCCAGGUCGCCUCGGUCGAGC- -5'
miRNA: 3'- ccGGGGCCaGGuc-GCCUCGGUCG----AGC- -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 7171 | 5' | -63.8 | NC_001900.1 | + | 25820 | 0.68 | 0.211976 |
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Target: 5'- uGGUCCUGugcGUCCAG-GcGAGCCugcAGCUCGg -3' miRNA: 3'- -CCGGGGC---CAGGUCgC-CUCGG---UCGAGC- -5' |
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| 7171 | 5' | -63.8 | NC_001900.1 | + | 45043 | 0.7 | 0.155767 |
|
Target: 5'- cGGCCagaUGGUCaGGCGGuccuuGCCuGGCUCGa -3' miRNA: 3'- -CCGGg--GCCAGgUCGCCu----CGG-UCGAGC- -5' |
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| 7171 | 5' | -63.8 | NC_001900.1 | + | 20235 | 0.7 | 0.143991 |
|
Target: 5'- uGGCUCCGGUCUGGUucgGGGGCCAcgUCa -3' miRNA: 3'- -CCGGGGCCAGGUCG---CCUCGGUcgAGc -5' |
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| 7171 | 5' | -63.8 | NC_001900.1 | + | 40503 | 1.1 | 0.000123 |
|
Target: 5'- uGGCCCCGGUCCAGCGGAGCCAGCUCGa -3' miRNA: 3'- -CCGGGGCCAGGUCGCCUCGGUCGAGC- -5' |
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| 7171 | 5' | -63.8 | NC_001900.1 | + | 18349 | 0.66 | 0.298676 |
|
Target: 5'- -cCCCCGG-CCuuuCGGGGCCGGUggguUCGg -3' miRNA: 3'- ccGGGGCCaGGuc-GCCUCGGUCG----AGC- -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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