miRNA: 3'- -GCAGCACGG------------ACGCCGgc-AGUUCGUac -5'
miRNA: 3'- -GCAGcACGGA-CGCCG-----GCAGUUCGUac -5'
miRNA: 3'- -GCAGC-ACGgaCGCCGGCAGUU-------CGUac -5'
miRNA: 3'- gcAGCACGG--ACGC----CGGCAGuUCGUAc -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 |
| Predicted miRNA align pattern | |||||||
| 12243 | 3' | -57.3 | NC_003309.1 | + | 48089 | 0.67 | 0.541348 |
|
Target: 5'- cCGUCGUGCUcgcacuucguguUGCGGUacuUCGAGCGc- -3' miRNA: 3'- -GCAGCACGG------------ACGCCGgc-AGUUCGUac -5' |
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| 12243 | 3' | -57.3 | NC_003309.1 | + | 39971 | 0.7 | 0.358225 |
|
Target: 5'- cCGUC-UGCCUcGCGGCgcgcuUGUCGAGCAc- -3' miRNA: 3'- -GCAGcACGGA-CGCCG-----GCAGUUCGUac -5' |
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| 12243 | 3' | -57.3 | NC_003309.1 | + | 34524 | 0.67 | 0.540287 |
|
Target: 5'- cCGUCGaUGUggGCGGCCGUCGAaucgauuGCGc- -3' miRNA: 3'- -GCAGC-ACGgaCGCCGGCAGUU-------CGUac -5' |
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| 12243 | 3' | -57.3 | NC_003309.1 | + | 25391 | 0.66 | 0.605991 |
|
Target: 5'- -cUCGUGCCacUGCGuguaGCCGUC-GGCGUc -3' miRNA: 3'- gcAGCACGG--ACGC----CGGCAGuUCGUAc -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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