miRNA: 3'- ccucACUGcAGAC----------GACGGCGGCGCCG- -5'
miRNA: 3'- -CCUCACUGCaGacGACGGCGGCG-----CCG- -5'
miRNA: 3'- -CCuCaCUGCAGaCG-ACGGCGGCG-CCG- -5'
miRNA: 3'- -CCUCACUGCA-GACGa---CGGCGGCgCCG- -5'
miRNA: 3'- -CCUCACUGCAGACGACGGCGGCGCCG- -5'
Results 41 - 45 of 45 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 | |||||||
| 11609 | 3' | -59.7 | NC_003085.1 | + | 7897 | 0.73 | 0.168331 |
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Target: 5'- ---cUGAC-UCUGgcucccgcgaCUGCCGCCGCGGCg -3' miRNA: 3'- ccucACUGcAGAC----------GACGGCGGCGCCG- -5' |
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| 11609 | 3' | -59.7 | NC_003085.1 | + | 12774 | 0.73 | 0.168331 |
|
Target: 5'- uGGGGUGAUGcCc-CUGCCGCCGUugucgGGCa -3' miRNA: 3'- -CCUCACUGCaGacGACGGCGGCG-----CCG- -5' |
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| 11609 | 3' | -59.7 | NC_003085.1 | + | 809 | 0.75 | 0.125266 |
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Target: 5'- cGGuG-GACGUCcGCgUGCCGCCGCaGGUc -3' miRNA: 3'- -CCuCaCUGCAGaCG-ACGGCGGCG-CCG- -5' |
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| 11609 | 3' | -59.7 | NC_003085.1 | + | 19312 | 0.82 | 0.035489 |
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Target: 5'- gGGGGUGACGUcCUGCguggGCUGCUGgGGCc -3' miRNA: 3'- -CCUCACUGCA-GACGa---CGGCGGCgCCG- -5' |
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| 11609 | 3' | -59.7 | NC_003085.1 | + | 41540 | 1.13 | 0.000171 |
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Target: 5'- uGGAGUGACGUCUGCUGCCGCCGCGGCg -3' miRNA: 3'- -CCUCACUGCAGACGACGGCGGCGCCG- -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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