miRNA: 3'- -AGUUGUCCUGGUgu-AAAUGuga-AGCU- -5'
miRNA: 3'- -AGUUGuCCUGGUgUAAAUGUGAAGcu -5'
miRNA: 3'- aGUUGUCCUGG---------------UGUaa---AUGUGAAGcu -5'
miRNA: 3'- -AGUUGUCCUGGUgUAaaUGUGA------------AGCU- -5'
miRNA: 3'- -AGUUGUCCUGGUGUAAAUGUGAAGCU- -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 | |||||||
| 31564 | 3' | -45.7 | NC_006820.1 | + | 30856 | 0.66 | 0.999997 |
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Target: 5'- aUUAAUAGGACCAaauUUUACuugaUCGAa -3' miRNA: 3'- -AGUUGUCCUGGUgu-AAAUGuga-AGCU- -5' |
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| 31564 | 3' | -45.7 | NC_006820.1 | + | 186314 | 0.7 | 0.999649 |
|
Target: 5'- uUCAACuGGAUCAaAUUUGCAUUUCc- -3' miRNA: 3'- -AGUUGuCCUGGUgUAAAUGUGAAGcu -5' |
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| 31564 | 3' | -45.7 | NC_006820.1 | + | 126250 | 0.7 | 0.999597 |
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Target: 5'- aCAACAGGACUaucuggaggugggguGCAaacagUACACUUCa- -3' miRNA: 3'- aGUUGUCCUGG---------------UGUaa---AUGUGAAGcu -5' |
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| 31564 | 3' | -45.7 | NC_006820.1 | + | 156976 | 0.7 | 0.999313 |
|
Target: 5'- aUCAACAGGACCAgAUg-AUGCUgauggauaguauUCGAa -3' miRNA: 3'- -AGUUGUCCUGGUgUAaaUGUGA------------AGCU- -5' |
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| 31564 | 3' | -45.7 | NC_006820.1 | + | 156720 | 1.12 | 0.026004 |
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Target: 5'- aUCAACAGGACCACAUUUACACUUCGAa -3' miRNA: 3'- -AGUUGUCCUGGUGUAAAUGUGAAGCU- -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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