miRNA: 3'- gaAGUACCuCCG---GCAGGGGaGGUGuc -5'
miRNA: 3'- -GAAGUaCCUCCGGCA--------------GGGGAGGUGUc -5'
miRNA: 3'- gaaguaCCUCC-GGCa---GGGGAGGUGUc -5'
miRNA: 3'- gaaGuaCCuCCGGCa------GG-GGAGGugUC- -5'
Results 21 - 24 of 24 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
|
Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 5587 | 3' | -57.7 | NC_001806.1 | + | 148923 | 0.68 | 0.716993 |
|
Target: 5'- -gUCAUGGuGGUcggCGUCCCC-CCGCc- -3' miRNA: 3'- gaAGUACCuCCG---GCAGGGGaGGUGuc -5' |
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| 5587 | 3' | -57.7 | NC_001806.1 | + | 90609 | 0.68 | 0.72386 |
|
Target: 5'- gCUUCAaGGAGGCCGUgugcaucaacaacaCCUUUCUGCAc -3' miRNA: 3'- -GAAGUaCCUCCGGCA--------------GGGGAGGUGUc -5' |
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| 5587 | 3' | -57.7 | NC_001806.1 | + | 64847 | 0.68 | 0.73651 |
|
Target: 5'- -----cGGGGGuCCGaaagCCCCUCCGCGc -3' miRNA: 3'- gaaguaCCUCC-GGCa---GGGGAGGUGUc -5' |
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| 5587 | 3' | -57.7 | NC_001806.1 | + | 66830 | 0.66 | 0.851581 |
|
Target: 5'- --cCcgGGuGGCCGgugugcgCCgCCUCCugGGg -3' miRNA: 3'- gaaGuaCCuCCGGCa------GG-GGAGGugUC- -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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