miRNA: 3'- -CGgGUCaUUGG--UGGCGGAUGCUGuGG- -5'
miRNA: 3'- -CGGGUC----------AUUgGUGGCGGAUGCuGUGG- -5'
miRNA: 3'- -CGGGUCAU-------------UGGUGgCGGAug-----CUGUGG- -5'
miRNA: 3'- cGGGUCauUGGUGGCGGaUGc-UGUGG- -5'
miRNA: 3'- -CGGGUCAUUGGUGGCGGAUGCUGUGG- -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 | |||||||
| 32998 | 5' | -54.5 | NC_007456.1 | + | 1296 | 0.66 | 0.710253 |
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Target: 5'- aGUgCGG-AACCugACCGUCUACGACcUCa -3' miRNA: 3'- -CGgGUCaUUGG--UGGCGGAUGCUGuGG- -5' |
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| 32998 | 5' | -54.5 | NC_007456.1 | + | 7807 | 0.67 | 0.632273 |
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Target: 5'- uGCUUAGggaacauccuUAAgUACCGCCUACG-CGCUg -3' miRNA: 3'- -CGGGUC----------AUUgGUGGCGGAUGCuGUGG- -5' |
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| 32998 | 5' | -54.5 | NC_007456.1 | + | 14484 | 0.7 | 0.467913 |
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Target: 5'- gGCCCAGUGgaugucaccuucuACCACaGUCUucgcauaGGCACCa -3' miRNA: 3'- -CGGGUCAU-------------UGGUGgCGGAug-----CUGUGG- -5' |
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| 32998 | 5' | -54.5 | NC_007456.1 | + | 9162 | 0.7 | 0.428866 |
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Target: 5'- cCCCAGccACCAUCGCC-ACcaGCACCa -3' miRNA: 3'- cGGGUCauUGGUGGCGGaUGc-UGUGG- -5' |
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| 32998 | 5' | -54.5 | NC_007456.1 | + | 3501 | 1.13 | 0.00047 |
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Target: 5'- gGCCCAGUAACCACCGCCUACGACACCc -3' miRNA: 3'- -CGGGUCAUUGGUGGCGGAUGCUGUGG- -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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