miRNA: 3'- cUGUGGG---UGUCGCGGuGCG----CCgCGAC- -5'
miRNA: 3'- cUGUGGGUGuc-GCGgUGcgCCGCGAC- -5'
miRNA: 3'- cuGUGGgUgUCGCG-GUGCgcCGCGAC- -5'
miRNA: 3'- -CUGUG-GGUGUCGc---GGUGc--GCCGCGAc -5'
miRNA: 3'- cuGUGGG---UGUCGCGGU----------GCGCCGCGac -5'
Results 21 - 25 of 25 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 | |||||||
| 31840 | 5' | -61.9 | NC_006938.1 | + | 22320 | 0.66 | 0.399771 |
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Target: 5'- uACGCCUgugGCGGUGCCuCGCcggaGGgGCUGa -3' miRNA: 3'- cUGUGGG---UGUCGCGGuGCG----CCgCGAC- -5' |
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| 31840 | 5' | -61.9 | NC_006938.1 | + | 22544 | 0.66 | 0.399771 |
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Target: 5'- aACGCCCACcucCGCgACaaGGUGCUGg -3' miRNA: 3'- cUGUGGGUGuc-GCGgUGcgCCGCGAC- -5' |
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| 31840 | 5' | -61.9 | NC_006938.1 | + | 22290 | 0.66 | 0.417543 |
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Target: 5'- -uCGCCgGgAGCGCuCACGa-GCGCUGg -3' miRNA: 3'- cuGUGGgUgUCGCG-GUGCgcCGCGAC- -5' |
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| 31840 | 5' | -61.9 | NC_006938.1 | + | 24605 | 0.66 | 0.417543 |
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Target: 5'- gGGCACuCCGCAGCacguCUACcucCGGCGCUa -3' miRNA: 3'- -CUGUG-GGUGUCGc---GGUGc--GCCGCGAc -5' |
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| 31840 | 5' | -61.9 | NC_006938.1 | + | 47099 | 0.66 | 0.417543 |
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Target: 5'- -cCGCCCaggGCAGCGUCGuugccacccgUGUGGCGCa- -3' miRNA: 3'- cuGUGGG---UGUCGCGGU----------GCGCCGCGac -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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