miRNA: 3'- cuuCUCuGGCUG-CGAGgGA--AGGUAUG- -5'
miRNA: 3'- -CUUCUCUgGCuGCgAGGGAAGGUa--UG- -5'
miRNA: 3'- -CUUCUcUGGCUGCgaGGGa--AGGUAUG- -5'
miRNA: 3'- -CUUCUCUGGCUGCGAGGGAAGGUAUG- -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 | |||||||
| 490 | 3' | -53.1 | AC_000013.1 | + | 639 | 0.67 | 0.673794 |
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Target: 5'- --uGAGuCCGGCuGCUCgCUcaUCCGUGCu -3' miRNA: 3'- cuuCUCuGGCUG-CGAGgGA--AGGUAUG- -5' |
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| 490 | 3' | -53.1 | AC_000013.1 | + | 28334 | 0.68 | 0.662456 |
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Target: 5'- gGAAGGGAgCGuCGgUCUCUUCCGacgGCg -3' miRNA: 3'- -CUUCUCUgGCuGCgAGGGAAGGUa--UG- -5' |
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| 490 | 3' | -53.1 | AC_000013.1 | + | 26308 | 0.7 | 0.549216 |
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Target: 5'- uGAGGAcGCCGACGaaCCCgucUCCGUAUc -3' miRNA: 3'- -CUUCUcUGGCUGCgaGGGa--AGGUAUG- -5' |
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| 490 | 3' | -53.1 | AC_000013.1 | + | 28268 | 1.1 | 0.00099 |
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Target: 5'- gGAAGAGACCGACGCUCCCUUCCAUACa -3' miRNA: 3'- -CUUCUCUGGCUGCGAGGGAAGGUAUG- -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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