miRNA: 3'- -UUGCGCCG---------------CCGUggCAGCuUCUGGAC- -5'
miRNA: 3'- -UUGCGCCGCCGUg---GCAGCU--UCUGgac -5'
miRNA: 3'- -UUgCGCCGCCGuGGC-------AGCUUCUGgAC- -5'
miRNA: 3'- -UUGCGCCGCCGUGGCAGCUUCUGGAC- -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 | |||||||
| 8235 | 5' | -59.2 | NC_001981.1 | + | 5026 | 0.67 | 0.060107 |
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Target: 5'- cGGCGCGGCagacucggacugucuGGCA--GUCGcGGGCCUGg -3' miRNA: 3'- -UUGCGCCG---------------CCGUggCAGCuUCUGGAC- -5' |
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| 8235 | 5' | -59.2 | NC_001981.1 | + | 2295 | 0.69 | 0.037994 |
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Target: 5'- aAACGUGGUGGCAacgaCGUCGGccGGACa-- -3' miRNA: 3'- -UUGCGCCGCCGUg---GCAGCU--UCUGgac -5' |
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| 8235 | 5' | -59.2 | NC_001981.1 | + | 4201 | 0.69 | 0.037863 |
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Target: 5'- cGGgGCGGCGGC-CUGgcggggcUCGAAGACgUGg -3' miRNA: 3'- -UUgCGCCGCCGuGGC-------AGCUUCUGgAC- -5' |
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| 8235 | 5' | -59.2 | NC_001981.1 | + | 3118 | 1.05 | 0.000022 |
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Target: 5'- cAACGCGGCGGCACCGUCGAAGACCUGc -3' miRNA: 3'- -UUGCGCCGCCGUGGCAGCUUCUGGAC- -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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