miRNA: 3'- -UGC-CCCGC-UGU------------UCGCaG-GCgCGGGGC- -5'
miRNA: 3'- -UGCC-C-CGCUgUUCGCAGGCGCG-GGGC- -5'
miRNA: 3'- -UGcCCCGCUGU----UCG-CAGGCGC-GGGGC- -5'
miRNA: 3'- -UGCCCCGCUGUUCGCAGGCGCGGGGC- -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 | |||||||
| 336 | 3' | -63.8 | AC_000010.1 | + | 8449 | 0.66 | 0.246472 |
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Target: 5'- gGCGaGGGCGcGCGccuggcgguagaGGCGgCuCGgGCCCCGg -3' miRNA: 3'- -UGC-CCCGC-UGU------------UCGCaG-GCgCGGGGC- -5' |
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| 336 | 3' | -63.8 | AC_000010.1 | + | 15779 | 0.66 | 0.228479 |
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Target: 5'- cAUGGaGcGCGG-AAGUGUCCGCGCaCUCGc -3' miRNA: 3'- -UGCC-C-CGCUgUUCGCAGGCGCG-GGGC- -5' |
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| 336 | 3' | -63.8 | AC_000010.1 | + | 5608 | 0.73 | 0.064152 |
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Target: 5'- cGCuGGGUGACAaagaGGCuGUCCGUGuCCCCGu -3' miRNA: 3'- -UGcCCCGCUGU----UCG-CAGGCGC-GGGGC- -5' |
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| 336 | 3' | -63.8 | AC_000010.1 | + | 18005 | 1.08 | 0.000118 |
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Target: 5'- aACGGGGCGACAAGCGUCCGCGCCCCGa -3' miRNA: 3'- -UGCCCCGCUGUUCGCAGGCGCGGGGC- -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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