miRNA: 3'- -CUUCGa-------GUGCGaa---GGCGCUCuaUCUC- -5'
miRNA: 3'- -CUUCGAg-UGCG---AAGGCGCUc------UAUCUC- -5'
miRNA: 3'- cuUCGAGUGCGA--------------AGGCGCUCUaucuc -5'
miRNA: 3'- cUUCG---AGUGCGaAGGCGCUCUa---UCUC- -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 | |||||||
| 22182 | 3' | -52.2 | NC_004927.1 | + | 59482 | 0.66 | 0.923115 |
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Target: 5'- cGAGGCcgagaaggUACGCgaaagCCGCGAGcaGGAGa -3' miRNA: 3'- -CUUCGa-------GUGCGaa---GGCGCUCuaUCUC- -5' |
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| 22182 | 3' | -52.2 | NC_004927.1 | + | 67549 | 0.66 | 0.90405 |
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Target: 5'- cGAGGCUgaGCGCccgUUCCGCGAccuguucGUGGAGc -3' miRNA: 3'- -CUUCGAg-UGCG---AAGGCGCUc------UAUCUC- -5' |
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| 22182 | 3' | -52.2 | NC_004927.1 | + | 2444 | 0.73 | 0.566011 |
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Target: 5'- -uAGCUCACGCUggaacucaucggcuUCCGCGAGGg---- -3' miRNA: 3'- cuUCGAGUGCGA--------------AGGCGCUCUaucuc -5' |
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| 22182 | 3' | -52.2 | NC_004927.1 | + | 46817 | 0.77 | 0.343938 |
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Target: 5'- cGAGCgagUCACGC-UCCGCGAGAagugGGAGg -3' miRNA: 3'- cUUCG---AGUGCGaAGGCGCUCUa---UCUC- -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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