miRNA: 3'- aCUCG---GAGUUa---GGCCGC-CCuCCUCGG- -5'
miRNA: 3'- aCUCG-------GAGUU---AGGCCGC-CCUCC-----UCGG- -5'
miRNA: 3'- aCUCgGAGuuAGGCCGCCC----------UCCUCGG- -5'
Results 21 - 23 of 23 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 | |||||||
| 28446 | 5' | -59.3 | NC_005946.1 | + | 86954 | 0.72 | 0.358658 |
|
Target: 5'- gGAGCguaCUCGGgaacCUGGCGuGGuGGAGCCa -3' miRNA: 3'- aCUCG---GAGUUa---GGCCGC-CCuCCUCGG- -5' |
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| 28446 | 5' | -59.3 | NC_005946.1 | + | 24934 | 0.73 | 0.319774 |
|
Target: 5'- gGAGCgaucaugCUCAGggcUCCGGCGuGGAGGgugugAGCCg -3' miRNA: 3'- aCUCG-------GAGUU---AGGCCGC-CCUCC-----UCGG- -5' |
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| 28446 | 5' | -59.3 | NC_005946.1 | + | 40136 | 0.76 | 0.18415 |
|
Target: 5'- aGAGgCUC--UCCGGCGGGcauaaacagaGGGGGCCu -3' miRNA: 3'- aCUCgGAGuuAGGCCGCCC----------UCCUCGG- -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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