miRNA: 3'- -UGCUCCuuC----------UCC-UGCUCCUGUUCcUC- -5'
miRNA: 3'- -UGcUCCU------UCuCCUGCUCCUGUUCCUc -5'
miRNA: 3'- ugCUCCUUCUCCug-CUCCUGU--------UCCUC- -5'
miRNA: 3'- -UGCUCCUUCUCCUGCUCCUGUUCCUC- -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 | |||||||
| 21119 | 3' | -54.2 | NC_004765.1 | + | 3405 | 0.67 | 0.19337 |
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Target: 5'- gACGGGGggGuaauggucccGGGcGCGGGGGCAGGuAGu -3' miRNA: 3'- -UGCUCCuuC----------UCC-UGCUCCUGUUCcUC- -5' |
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| 21119 | 3' | -54.2 | NC_004765.1 | + | 2728 | 0.7 | 0.132102 |
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Target: 5'- uGCuAGGAgacaagGGuGGAUGAGGAUAGGGAu -3' miRNA: 3'- -UGcUCCU------UCuCCUGCUCCUGUUCCUc -5' |
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| 21119 | 3' | -54.2 | NC_004765.1 | + | 4919 | 0.75 | 0.047155 |
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Target: 5'- -gGGGGAGGAGGuugGAGGACAagugaccaGGGAGg -3' miRNA: 3'- ugCUCCUUCUCCug-CUCCUGU--------UCCUC- -5' |
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| 21119 | 3' | -54.2 | NC_004765.1 | + | 3332 | 1.09 | 0.000084 |
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Target: 5'- gACGAGGAAGAGGACGAGGACAAGGAGa -3' miRNA: 3'- -UGCUCCUUCUCCUGCUCCUGUUCCUC- -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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