miRNA: 3'- -UUGUCagaCUCaGUACUCACG-GUUUg -5'
miRNA: 3'- -UUGUCAGA---CUCAGua---CUC-ACGGUUUG- -5'
miRNA: 3'- -UUGUCA--GACuCaGUACUCACGGUUUG- -5'
miRNA: 3'- -UUGUCAGACUCAGUACUCACGGUUUG- -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 | |||||||
| 12323 | 3' | -49.5 | NC_003324.1 | + | 34196 | 0.66 | 0.945696 |
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Target: 5'- cGACAGg--GAGgCGUGAGUGCgCGAGu -3' miRNA: 3'- -UUGUCagaCUCaGUACUCACG-GUUUg -5' |
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| 12323 | 3' | -49.5 | NC_003324.1 | + | 12210 | 0.68 | 0.845287 |
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Target: 5'- gGACGGUCUcgcGGGUCucgcaGAGaUGCCGAAUg -3' miRNA: 3'- -UUGUCAGA---CUCAGua---CUC-ACGGUUUG- -5' |
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| 12323 | 3' | -49.5 | NC_003324.1 | + | 3935 | 0.72 | 0.650991 |
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Target: 5'- gAGCAGUgaCUGcG-CAUGAGUGCUGAACa -3' miRNA: 3'- -UUGUCA--GACuCaGUACUCACGGUUUG- -5' |
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| 12323 | 3' | -49.5 | NC_003324.1 | + | 4058 | 1.08 | 0.003769 |
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Target: 5'- cAACAGUCUGAGUCAUGAGUGCCAAACu -3' miRNA: 3'- -UUGUCAGACUCAGUACUCACGGUUUG- -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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