miRNA: 3'- -UGCGUCCACGU-CG---------------UCCGGuauaaUCG- -5'
miRNA: 3'- -UGCGU--CCaCGUCGUC-CGGUaUAaUCG- -5'
miRNA: 3'- -UGCGUCC--------ACGUCGU-CCGGuauaa----UCG- -5'
miRNA: 3'- -UGCGUCCACGUCGUCCGGUAUAAUCG- -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 | |||||||
| 166 | 3' | -53.4 | AC_000007.1 | + | 3502 | 0.69 | 0.447604 |
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Target: 5'- aGCGCGGGUGCAgGCcagcaccaagugaucGGGCCuc---AGCu -3' miRNA: 3'- -UGCGUCCACGU-CG---------------UCCGGuauaaUCG- -5' |
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| 166 | 3' | -53.4 | AC_000007.1 | + | 16251 | 0.69 | 0.44344 |
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Target: 5'- cGCGCGuuGG-GCGGCAGuGCCGgGUcGGCg -3' miRNA: 3'- -UGCGU--CCaCGUCGUC-CGGUaUAaUCG- -5' |
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| 166 | 3' | -53.4 | AC_000007.1 | + | 11374 | 0.71 | 0.361413 |
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Target: 5'- cACGCAGGgcgcgaguUGCGGCAuGGCCugaaccgcgAGCg -3' miRNA: 3'- -UGCGUCC--------ACGUCGU-CCGGuauaa----UCG- -5' |
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| 166 | 3' | -53.4 | AC_000007.1 | + | 10164 | 1.11 | 0.000516 |
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Target: 5'- cACGCAGGUGCAGCAGGCCAUAUUAGCc -3' miRNA: 3'- -UGCGUCCACGUCGUCCGGUAUAAUCG- -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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