miRNA: 3'- gGCUCGU----CUGC-GCUcUCGGAu-CCAGU- -5'
miRNA: 3'- -GGCUCGUCUGCGc--UCUCG-GA-------------UCCAGU- -5'
miRNA: 3'- ggCUCGuCUGCG--------CUCUCGGAUCCagu -5'
miRNA: 3'- -GGCUCGUCUGCGCUCUCGGAUCCAGU- -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 | |||||||
| 7357 | 3' | -56.7 | NC_001900.1 | + | 39770 | 0.66 | 0.587555 |
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Target: 5'- aCGGGCAccguGACGcCGAuGGCCUcuGGUCGg -3' miRNA: 3'- gGCUCGU----CUGC-GCUcUCGGAu-CCAGU- -5' |
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| 7357 | 3' | -56.7 | NC_001900.1 | + | 27631 | 0.68 | 0.491027 |
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Target: 5'- uUCGAGCAGGCGUagcAGGGCuCUcgggugacguagaGGGUCGc -3' miRNA: 3'- -GGCUCGUCUGCGc--UCUCG-GA-------------UCCAGU- -5' |
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| 7357 | 3' | -56.7 | NC_001900.1 | + | 38514 | 0.68 | 0.471756 |
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Target: 5'- -gGAGCuGGCGUgggguuggGGGAGCCUGGGa-- -3' miRNA: 3'- ggCUCGuCUGCG--------CUCUCGGAUCCagu -5' |
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| 7357 | 3' | -56.7 | NC_001900.1 | + | 41370 | 1.1 | 0.000532 |
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Target: 5'- aCCGAGCAGACGCGAGAGCCUAGGUCAc -3' miRNA: 3'- -GGCUCGUCUGCGCUCUCGGAUCCAGU- -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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