miRNA: 3'- -CGuGCGAAGCUGaCCUG---GCGGU--CUGU- -5'
miRNA: 3'- cguGCGAAGcUGAC-------CUGGCGGUCUGU- -5'
miRNA: 3'- -CGugCga--------AGCUGACCUGGCGGuCUGU- -5'
miRNA: 3'- -CG-UGCGAa--GCUGACCuGGCGgUCUGU- -5'
miRNA: 3'- -CGUGCGAAGCUGACCUGGCGGUCUGU- -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 | |||||||
| 8499 | 3' | -56 | NC_002169.1 | + | 125491 | 0.66 | 0.896673 |
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Target: 5'- cGC-CGCUUCGGCcGGACucuCGUCAacGGCGg -3' miRNA: 3'- -CGuGCGAAGCUGaCCUG---GCGGU--CUGU- -5' |
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| 8499 | 3' | -56 | NC_002169.1 | + | 63158 | 0.68 | 0.792728 |
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Target: 5'- --gUGCUUCuACUGcgacgacGGCCGCCGGACGa -3' miRNA: 3'- cguGCGAAGcUGAC-------CUGGCGGUCUGU- -5' |
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| 8499 | 3' | -56 | NC_002169.1 | + | 74999 | 0.7 | 0.676421 |
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Target: 5'- gGCugGaccgucgacaUCGGCUGGACCGUC-GACAu -3' miRNA: 3'- -CGugCga--------AGCUGACCUGGCGGuCUGU- -5' |
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| 8499 | 3' | -56 | NC_002169.1 | + | 106198 | 0.71 | 0.635389 |
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Target: 5'- gGCgACGUUcacCGACUGG-CCGCgAGACAu -3' miRNA: 3'- -CG-UGCGAa--GCUGACCuGGCGgUCUGU- -5' |
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| 8499 | 3' | -56 | NC_002169.1 | + | 41710 | 1.11 | 0.001975 |
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Target: 5'- aGCACGCUUCGACUGGACCGCCAGACAg -3' miRNA: 3'- -CGUGCGAAGCUGACCUGGCGGUCUGU- -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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