miRNA: 3'- cGCGCCGa--C-C-GCCa-CGAGUUUGCGUg -5'
miRNA: 3'- -CGCGcCGACCGcCACGag-UUugCGUg -5'
miRNA: 3'- cgCGCCGACCgCCa--CGAGuuu---GCGUG- -5'
miRNA: 3'- -CGCG--CCGaCCgCCACGAGu-------------UUGCGUG- -5'
miRNA: 3'- -CGCgCCG-ACCGCCACgaguuUGCGug -5'
Results 21 - 25 of 25 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 | |||||||
| 415 | 3' | -58.1 | AC_000011.1 | + | 16562 | 0.66 | 0.425838 |
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Target: 5'- cCGCGGCgccGcGcCGGggGUUCAAGCGCGa -3' miRNA: 3'- cGCGCCGa--C-C-GCCa-CGAGUUUGCGUg -5' |
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| 415 | 3' | -58.1 | AC_000011.1 | + | 6580 | 0.66 | 0.435611 |
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Target: 5'- gGCGC-GCUGGCcGUGCgcgAAugGCAa -3' miRNA: 3'- -CGCGcCGACCGcCACGag-UUugCGUg -5' |
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| 415 | 3' | -58.1 | AC_000011.1 | + | 17277 | 0.66 | 0.435611 |
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Target: 5'- -aGCGGUUGGgGGgagGCUUccugccCGCGCu -3' miRNA: 3'- cgCGCCGACCgCCa--CGAGuuu---GCGUG- -5' |
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| 415 | 3' | -58.1 | AC_000011.1 | + | 15857 | 0.66 | 0.439557 |
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Target: 5'- cGCGCauGGC-GGgGGUGCUCcggugccgccgggcGAUGCGCc -3' miRNA: 3'- -CGCG--CCGaCCgCCACGAGu-------------UUGCGUG- -5' |
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| 415 | 3' | -58.1 | AC_000011.1 | + | 26648 | 0.66 | 0.445513 |
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Target: 5'- uGCGgGGCgUGGCGGUGa----GCGCu- -3' miRNA: 3'- -CGCgCCG-ACCGCCACgaguuUGCGug -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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