miRNA: 3'- -UUCGCCAGC--------UCG--------------GACGGCCUAGUgUa -5'
miRNA: 3'- -UUCGC-CAGCUCggACGGCCUAg--UGUA- -5'
miRNA: 3'- -UUCGCCAGCUCGGACGGCCuaGUGUA- -5'
Results 1 - 3 of 3 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 | |||||||
| 2629 | 5' | -58.9 | NC_001491.2 | + | 63054 | 0.66 | 0.73124 |
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Target: 5'- cAGGCGGUCGuuaaucucGGUugggauguucucugCUGCCGGGUCAgGg -3' miRNA: 3'- -UUCGCCAGC--------UCG--------------GACGGCCUAGUgUa -5' |
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| 2629 | 5' | -58.9 | NC_001491.2 | + | 138487 | 0.68 | 0.612615 |
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Target: 5'- gAAGCGuGUCGAGgaUGCCGGAUaugACAUc -3' miRNA: 3'- -UUCGC-CAGCUCggACGGCCUAg--UGUA- -5' |
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| 2629 | 5' | -58.9 | NC_001491.2 | + | 144605 | 0.9 | 0.025003 |
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Target: 5'- aAAGCGGUCGAGCCUGCCGGuaCACAUg -3' miRNA: 3'- -UUCGCCAGCUCGGACGGCCuaGUGUA- -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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