miRNA: 3'- cuugaUCAGUAGCG-----------UGG--CCGGUUGUc -5'
miRNA: 3'- cUUGAUcAGUAGCGUG--------GCCG-GUUGUC- -5'
miRNA: 3'- cuUGA---UCaGUAGCGUgGCCGGUUGUC- -5'
miRNA: 3'- -CUUGAUC-AGUAGC-GUGGCCGgUUGUc -5'
miRNA: 3'- -CUUGAUCAGUAGCGUGGCCGGUUGUC- -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 | |||||||
| 31935 | 3' | -52.4 | NC_006940.1 | + | 40602 | 0.66 | 0.783268 |
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Target: 5'- ----cAGUCGUCGCcacucucauccGCCcaGGCCAACAu -3' miRNA: 3'- cuugaUCAGUAGCG-----------UGG--CCGGUUGUc -5' |
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| 31935 | 3' | -52.4 | NC_006940.1 | + | 28675 | 0.66 | 0.751328 |
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Target: 5'- cGACUGcUCAUCGCAUaacacuagCGGCgCGAUAGg -3' miRNA: 3'- cUUGAUcAGUAGCGUG--------GCCG-GUUGUC- -5' |
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| 31935 | 3' | -52.4 | NC_006940.1 | + | 19770 | 0.73 | 0.389643 |
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Target: 5'- -cGCUcgaAGcCGUCGCG-CGGCCAACAGa -3' miRNA: 3'- cuUGA---UCaGUAGCGUgGCCGGUUGUC- -5' |
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| 31935 | 3' | -52.4 | NC_006940.1 | + | 29396 | 0.79 | 0.156117 |
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Target: 5'- aGAACUGGuUCAUCGaCGCCGGCgAGCGc -3' miRNA: 3'- -CUUGAUC-AGUAGC-GUGGCCGgUUGUc -5' |
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| 31935 | 3' | -52.4 | NC_006940.1 | + | 613 | 1.08 | 0.00148 |
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Target: 5'- uGAACUAGUCAUCGCACCGGCCAACAGc -3' miRNA: 3'- -CUUGAUCAGUAGCGUGGCCGGUUGUC- -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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