miRNA: 3'- -GGCGG-GCu---AAGCCC-CGCCGgccGCAG- -5'
miRNA: 3'- ggCGGGcUAAGc-CCCG-----CCGGCCGCAG- -5'
miRNA: 3'- -GGCGG-------GCUAaGCCCCG--CCGgCCGCaG- -5'
miRNA: 3'- -GgCgGGCUa---AGCCC---------CGCC-------GGCCGCAG- -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
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| Predicted miRNA align pattern | |||||||
| 12488 | 5' | -64.1 | NC_003324.1 | + | 22222 | 0.66 | 0.335562 |
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Target: 5'- gCCGCCgCGcaccUUCGGGaGCGGCaa-CGUCu -3' miRNA: 3'- -GGCGG-GCu---AAGCCC-CGCCGgccGCAG- -5' |
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| 12488 | 5' | -64.1 | NC_003324.1 | + | 4876 | 0.66 | 0.343181 |
|
Target: 5'- -aGCCCuGUUCauGGGCcgucaGGCUGGCGUUa -3' miRNA: 3'- ggCGGGcUAAGc-CCCG-----CCGGCCGCAG- -5' |
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| 12488 | 5' | -64.1 | NC_003324.1 | + | 40257 | 0.65 | 0.357998 |
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Target: 5'- gCCGCCuugcgugCGGUcCGGGGCuuGGCgGGUGcCu -3' miRNA: 3'- -GGCGG-------GCUAaGCCCCG--CCGgCCGCaG- -5' |
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| 12488 | 5' | -64.1 | NC_003324.1 | + | 10244 | 0.65 | 0.357998 |
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Target: 5'- aCgGgCCGAgaggUCGGGcauugucucGCGGauuuguuCCGGCGUCg -3' miRNA: 3'- -GgCgGGCUa---AGCCC---------CGCC-------GGCCGCAG- -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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