miRNA: 3'- -AGUCGGCG--CGGUGgUAaUCugUAGUu -5'
miRNA: 3'- -AGUCGGCGCGgUGGuAAUC-UGUaguu -5'
miRNA: 3'- aGUCGGCGcGGUGGu---AAUCuGUAGUU- -5'
miRNA: 3'- aGUCGGCGcGGUGGu---AAUCuGUAGUU- -5'
miRNA: 3'- -AGUCGGCGCGGUGGUAAUCUGUAGUU- -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 | |||||||
| 678 | 5' | -53.5 | AC_000018.1 | + | 18875 | 0.66 | 0.64071 |
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Target: 5'- aUCAGUCGCugGCUACgGUcGGugGUCAc -3' miRNA: 3'- -AGUCGGCG--CGGUGgUAaUCugUAGUu -5' |
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| 678 | 5' | -53.5 | AC_000018.1 | + | 5327 | 0.66 | 0.605546 |
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Target: 5'- cUCGGCCGCGUgGCCuUUGGcACGg--- -3' miRNA: 3'- -AGUCGGCGCGgUGGuAAUC-UGUaguu -5' |
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| 678 | 5' | -53.5 | AC_000018.1 | + | 35357 | 0.66 | 0.605546 |
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Target: 5'- aCGGCCGCcCCGCCcauuUUAGcCGUUAAc -3' miRNA: 3'- aGUCGGCGcGGUGGu---AAUCuGUAGUU- -5' |
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| 678 | 5' | -53.5 | AC_000018.1 | + | 158 | 0.66 | 0.605546 |
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Target: 5'- aCGGCCGCcCCGCCcauuUUAGcCGUUAAc -3' miRNA: 3'- aGUCGGCGcGGUGGu---AAUCuGUAGUU- -5' |
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| 678 | 5' | -53.5 | AC_000018.1 | + | 27656 | 1.06 | 0.001012 |
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Target: 5'- cUCAGCCGCGCCACCAUUAGACAUCAAu -3' miRNA: 3'- -AGUCGGCGCGGUGGUAAUCUGUAGUU- -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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