miRNA: 3'- -UCGUGGCGg---CG----------CGUAAGAGUgCGGUC- -5'
miRNA: 3'- ucGUGGCGGCGCGuaa------------GAGugCGGUC- -5'
miRNA: 3'- uCGUGGCGGCG---------------CGUaa------GAGUGCGGUC- -5'
miRNA: 3'- -UCGUGGCGGCGCGUAAGAGUGCGGUC- -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 | |||||||
| 22498 | 5' | -58.5 | NC_005069.1 | + | 4318 | 0.67 | 0.420409 |
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Target: 5'- gAGCACUGCaauuGUuaauuacaauGCAUUCUCA-GCCGGg -3' miRNA: 3'- -UCGUGGCGg---CG----------CGUAAGAGUgCGGUC- -5' |
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| 22498 | 5' | -58.5 | NC_005069.1 | + | 19230 | 0.69 | 0.335172 |
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Target: 5'- -aCGCCGCUGCGCugagugagcaaucagCUUugGCCGGu -3' miRNA: 3'- ucGUGGCGGCGCGuaa------------GAGugCGGUC- -5' |
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| 22498 | 5' | -58.5 | NC_005069.1 | + | 4307 | 0.71 | 0.242463 |
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Target: 5'- cGCACCGCCGCcaguguagaaauccaGUAcgaucucaCUCACGCUAGg -3' miRNA: 3'- uCGUGGCGGCG---------------CGUaa------GAGUGCGGUC- -5' |
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| 22498 | 5' | -58.5 | NC_005069.1 | + | 30358 | 1.07 | 0.000459 |
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Target: 5'- cAGCACCGCCGCGCAUUCUCACGCCAGc -3' miRNA: 3'- -UCGUGGCGGCGCGUAAGAGUGCGGUC- -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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