miRNA: 3'- -GCGG-ACGCG---UAGGGGCaa--GGCuuaau -5'
miRNA: 3'- gCGGaCGCGUA---GGGGCaAGGCUUAau -5'
miRNA: 3'- gCGGACGCGUag-GGGCAAGg-CUUaau -5'
miRNA: 3'- -GCGGACGCGUAg-GGGCaa-GGCUuaau -5'
miRNA: 3'- -GCGGACGCGUAGGGGCAAGGCUUAAU- -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 | |||||||
| 136 | 3' | -55 | AC_000006.1 | + | 17587 | 0.66 | 0.573416 |
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Target: 5'- cCGCCgUGCGCcgcGUCCCCGcccgCCGc---- -3' miRNA: 3'- -GCGG-ACGCG---UAGGGGCaa--GGCuuaau -5' |
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| 136 | 3' | -55 | AC_000006.1 | + | 10265 | 0.67 | 0.528607 |
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Target: 5'- gGCC-GCGCGUguaCCCCGgUUCGAGUc- -3' miRNA: 3'- gCGGaCGCGUA---GGGGCaAGGCUUAau -5' |
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| 136 | 3' | -55 | AC_000006.1 | + | 10814 | 0.67 | 0.495865 |
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Target: 5'- uGCCUGCGCAaaaCCUGUUCagGGAc-- -3' miRNA: 3'- gCGGACGCGUag-GGGCAAGg-CUUaau -5' |
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| 136 | 3' | -55 | AC_000006.1 | + | 16866 | 0.7 | 0.348892 |
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Target: 5'- gCGCCUGCGCAUggCCCGccgCCGGc--- -3' miRNA: 3'- -GCGGACGCGUAg-GGGCaa-GGCUuaau -5' |
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| 136 | 3' | -55 | AC_000006.1 | + | 16727 | 1.07 | 0.000789 |
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Target: 5'- cCGCCUGCGCAUCCCCGUUCCGAAUUAc -3' miRNA: 3'- -GCGGACGCGUAGGGGCAAGGCUUAAU- -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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