miRNA: 3'- -CAgUACUAcCCUCG--CUCUGCCUuCUG- -5'
miRNA: 3'- caguaCUAC----------CCUCGCUCUGCC-UUCUG- -5'
miRNA: 3'- -CAGUa-CUACCcUCGCUCuGCCUUCUG- -5'
miRNA: 3'- -CAGUACUACCCUCGCUCUGCCUUCUG- -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 | |||||||
| 23000 | 5' | -53.2 | NC_005158.1 | + | 108 | 0.66 | 0.067763 |
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Target: 5'- gGUgGUGGUaGGAGUuaGAGACGGAuGAUc -3' miRNA: 3'- -CAgUACUAcCCUCG--CUCUGCCUuCUG- -5' |
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| 23000 | 5' | -53.2 | NC_005158.1 | + | 2231 | 0.68 | 0.042843 |
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Target: 5'- ----cGAUGgcggcggcaaGGAGCGGGACGGuGAGACc -3' miRNA: 3'- caguaCUAC----------CCUCGCUCUGCC-UUCUG- -5' |
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| 23000 | 5' | -53.2 | NC_005158.1 | + | 2158 | 0.73 | 0.016908 |
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Target: 5'- gGUCAggGGUGG-AGUGGGuCGGAAGGCg -3' miRNA: 3'- -CAGUa-CUACCcUCGCUCuGCCUUCUG- -5' |
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| 23000 | 5' | -53.2 | NC_005158.1 | + | 1151 | 1.11 | 7e-06 |
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Target: 5'- aGUCAUGAUGGGAGCGAGACGGAAGACa -3' miRNA: 3'- -CAGUACUACCCUCGCUCUGCCUUCUG- -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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