miRNA: 3'- -CGGUCGGUCACa---UgCGGCGGccaaag -5'
miRNA: 3'- -CGGUCGG--UCACaugCGGCG---GCCAaag -5'
miRNA: 3'- -CGGuCGGUCACa--UGCG-GCGGC-CaaAG- -5'
miRNA: 3'- -CGGUCGGUCACAUGCGGCGGCCAAAG- -5'
Results 1 - 4 of 4 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 | |||||||
| 2512 | 3' | -56.9 | NC_001454.1 | + | 13028 | 0.66 | 0.498248 |
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Target: 5'- uGCCGGUCAGUGggcgGgGCUGCCu----- -3' miRNA: 3'- -CGGUCGGUCACa---UgCGGCGGccaaag -5' |
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| 2512 | 3' | -56.9 | NC_001454.1 | + | 33186 | 0.66 | 0.487659 |
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Target: 5'- uGCCAGCCuuAGUGgaaGCCGUgauUGGUa-- -3' miRNA: 3'- -CGGUCGG--UCACaugCGGCG---GCCAaag -5' |
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| 2512 | 3' | -56.9 | NC_001454.1 | + | 13247 | 0.66 | 0.44643 |
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Target: 5'- uGCC-GCCGGUGaugGCGUaCGCCGaGggUCc -3' miRNA: 3'- -CGGuCGGUCACa--UGCG-GCGGC-CaaAG- -5' |
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| 2512 | 3' | -56.9 | NC_001454.1 | + | 20609 | 1.12 | 0.000219 |
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Target: 5'- gGCCAGCCAGUGUACGCCGCCGGUUUCg -3' miRNA: 3'- -CGGUCGGUCACAUGCGGCGGCCAAAG- -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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