miRNA: 3'- -GCGGAUGCGGggGGAGGgCGGagUCC- -5'
miRNA: 3'- -GCGGAUGCGGGgGga----GGGCGGAGU----CC- -5'
miRNA: 3'- gCGGA--------UGCGGgGGGA-GGGCGGAgUCC- -5'
miRNA: 3'- -GCGGAUGCGg-----GGGG--AGGgCGGAGUcc -5'
miRNA: 3'- -GCGGAUGCGGGGGGAGGGCGGAGUCC- -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 | |||||||
| 10651 | 5' | -64.1 | NC_002702.1 | + | 13887 | 0.66 | 0.219099 |
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Target: 5'- gCGUCUACGCCg-CCUCCgGCC--AGGg -3' miRNA: 3'- -GCGGAUGCGGggGGAGGgCGGagUCC- -5' |
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| 10651 | 5' | -64.1 | NC_002702.1 | + | 15209 | 0.66 | 0.213539 |
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Target: 5'- gCGUCUGCGCCUgCgaguagUCCGCCUCAcccuGGa -3' miRNA: 3'- -GCGGAUGCGGGgGga----GGGCGGAGU----CC- -5' |
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| 10651 | 5' | -64.1 | NC_002702.1 | + | 11367 | 0.68 | 0.143782 |
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Target: 5'- gGCCUgcaaauugGCGCUgUCCUcCCCGCCU-AGGg -3' miRNA: 3'- gCGGA--------UGCGGgGGGA-GGGCGGAgUCC- -5' |
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| 10651 | 5' | -64.1 | NC_002702.1 | + | 10350 | 0.73 | 0.062767 |
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Target: 5'- cCGCCUGCGCagccuaCCCCguUCCgGCCUCGu- -3' miRNA: 3'- -GCGGAUGCGg-----GGGG--AGGgCGGAGUcc -5' |
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| 10651 | 5' | -64.1 | NC_002702.1 | + | 15194 | 1.09 | 8.5e-05 |
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Target: 5'- cCGCCUACGCCCCCCUCCCGCCUCAGGc -3' miRNA: 3'- -GCGGAUGCGGGGGGAGGGCGGAGUCC- -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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