miRNA: 3'- -CUACCCCUAC-CCGa-----CGa---GCAA-GUCGa -5'
miRNA: 3'- cuaCCCCUACCCGac----GAGCAag-----UCGa -5'
miRNA: 3'- cuaCCCCUa-----CCCGA------CGAGCaAGUCGa -5'
miRNA: 3'- cUACCCcuACCCGACgAGCaAGUCGa -5'
miRNA: 3'- -CUACCCCUACCCGACGAGCAAGUCGA- -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 | |||||||
| 18287 | 5' | -56.9 | NC_004681.1 | + | 34614 | 0.66 | 0.666955 |
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Target: 5'- cGAUGGGGAUGcGGCccuuggGUgacaCGUUcCAGCc -3' miRNA: 3'- -CUACCCCUAC-CCGa-----CGa---GCAA-GUCGa -5' |
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| 18287 | 5' | -56.9 | NC_004681.1 | + | 43903 | 0.66 | 0.666955 |
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Target: 5'- --cGGGGGUGGGCgcggacCUCGUggaaggaGGCa -3' miRNA: 3'- cuaCCCCUACCCGac----GAGCAag-----UCGa -5' |
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| 18287 | 5' | -56.9 | NC_004681.1 | + | 16678 | 0.67 | 0.591405 |
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Target: 5'- --cGGGGAcgccggGGGCUuguagcGCUCG-UCGGCa -3' miRNA: 3'- cuaCCCCUa-----CCCGA------CGAGCaAGUCGa -5' |
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| 18287 | 5' | -56.9 | NC_004681.1 | + | 25488 | 0.68 | 0.548762 |
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Target: 5'- cGUGGGacUGGGUUGgUCGcUCAGCg -3' miRNA: 3'- cUACCCcuACCCGACgAGCaAGUCGa -5' |
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| 18287 | 5' | -56.9 | NC_004681.1 | + | 25556 | 1.07 | 0.001167 |
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Target: 5'- cGAUGGGGAUGGGCUGCUCGUUCAGCUu -3' miRNA: 3'- -CUACCCCUACCCGACGAGCAAGUCGA- -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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