miRNA: 3'- -CCCAUCUUgCCAUuCU-----CUC-CGg-CGGG- -5'
miRNA: 3'- cccaUCUUGCCA------------UUCUCUCCgGCGGg -5'
miRNA: 3'- cCCAUCUUGCC-------------AUU---------CUCUCCGgCGGG- -5'
miRNA: 3'- -CCCAUCUUGCCAUUCUCUCCGGCGGG- -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 | |||||||
| 9835 | 3' | -54.7 | NC_002617.1 | + | 57 | 0.66 | 0.405422 |
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Target: 5'- cGGGUAGAA-GGUGuGAaucucGAGuGCgaGCCCg -3' miRNA: 3'- -CCCAUCUUgCCAUuCU-----CUC-CGg-CGGG- -5' |
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| 9835 | 3' | -54.7 | NC_002617.1 | + | 1473 | 0.67 | 0.356871 |
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Target: 5'- ---gAGAGCGGUagcaaauagcauGAGGGAGG-CGCCa -3' miRNA: 3'- cccaUCUUGCCA------------UUCUCUCCgGCGGg -5' |
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| 9835 | 3' | -54.7 | NC_002617.1 | + | 6395 | 0.69 | 0.242874 |
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Target: 5'- cGGUAGAACGGagguugugaagucUGGcucgcaauuGAGGGGCgGCCUc -3' miRNA: 3'- cCCAUCUUGCC-------------AUU---------CUCUCCGgCGGG- -5' |
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| 9835 | 3' | -54.7 | NC_002617.1 | + | 6316 | 1.14 | 0.000098 |
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Target: 5'- cGGGUAGAACGGUAAGAGAGGCCGCCCc -3' miRNA: 3'- -CCCAUCUUGCCAUUCUCUCCGGCGGG- -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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