miRNA: 3'- -CGACUGGaCCGGCUc-------CGCCCa---------GUCAa -5'
miRNA: 3'- -CgACUGGaCCGGCUCCGCCCagucaa -5'
miRNA: 3'- -CGACUGGACCGGCuCCG----------CccAGUCaa -5'
miRNA: 3'- -CGA-CUGG--ACCGGCUCCg---CCCA-GUCAa -5'
miRNA: 3'- -CGACUGGACCGGCUCCGCCCAGUCAA- -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 | |||||||
| 7220 | 5' | -60.4 | NC_001900.1 | + | 5593 | 0.66 | 0.404616 |
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Target: 5'- aGCUGGCC-GGCCGAuccaugacGCGGGgguggucaagCAGUg -3' miRNA: 3'- -CGACUGGaCCGGCUc-------CGCCCa---------GUCAa -5' |
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| 7220 | 5' | -60.4 | NC_001900.1 | + | 45756 | 0.67 | 0.328194 |
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Target: 5'- uGgUGACCgGGUCGAGGUGGGg----- -3' miRNA: 3'- -CgACUGGaCCGGCUCCGCCCagucaa -5' |
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| 7220 | 5' | -60.4 | NC_001900.1 | + | 3443 | 0.69 | 0.243716 |
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Target: 5'- cGCUGGCCUGGCCGuGGCagacgacgaaGuuUCAGg- -3' miRNA: 3'- -CGACUGGACCGGCuCCG----------CccAGUCaa -5' |
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| 7220 | 5' | -60.4 | NC_001900.1 | + | 19680 | 0.7 | 0.203309 |
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Target: 5'- cGCUcGACUgaUGGCCGAGGagauGGGUcCGGUg -3' miRNA: 3'- -CGA-CUGG--ACCGGCUCCg---CCCA-GUCAa -5' |
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| 7220 | 5' | -60.4 | NC_001900.1 | + | 13995 | 1.07 | 0.00031 |
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Target: 5'- cGCUGACCUGGCCGAGGCGGGUCAGUUg -3' miRNA: 3'- -CGACUGGACCGGCUCCGCCCAGUCAA- -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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