miRNA: 3'- gUGUuCGUUugGCUGA---GGGcCGCGGG- -5'
miRNA: 3'- gUGUUCguuuGGCugAGGG---CCGCGGg -5'
miRNA: 3'- -GugUUC----GUUUGGCUGAGGGCC--GCGGG- -5'
miRNA: 3'- -GUGUUCGU--UUG-GCUga-GGGCCGCG-GG- -5'
miRNA: 3'- -GUGUUCGUUUGGCUGAGGGCCGCGGG- -5'
Results 1 - 5 of 5 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 | |||||||
| 15531 | 5' | -56.7 | NC_004001.2 | + | 15366 | 0.66 | 0.505773 |
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Target: 5'- gACGcGCGGugCGACUaugCCCaGUGCCUu -3' miRNA: 3'- gUGUuCGUUugGCUGA---GGGcCGCGGG- -5' |
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| 15531 | 5' | -56.7 | NC_004001.2 | + | 8345 | 0.67 | 0.464025 |
|
Target: 5'- uGCAGGguu-CCGugUCCUuugGGCGCCa -3' miRNA: 3'- gUGUUCguuuGGCugAGGG---CCGCGGg -5' |
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| 15531 | 5' | -56.7 | NC_004001.2 | + | 2168 | 0.7 | 0.317827 |
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Target: 5'- aCugGAGggucCAGGCCGGCUCUCGGguUGUCCu -3' miRNA: 3'- -GugUUC----GUUUGGCUGAGGGCC--GCGGG- -5' |
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| 15531 | 5' | -56.7 | NC_004001.2 | + | 7985 | 0.72 | 0.226691 |
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Target: 5'- gUACAAGCAcaAACaCGAaugCUCGGCGCgCCg -3' miRNA: 3'- -GUGUUCGU--UUG-GCUga-GGGCCGCG-GG- -5' |
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| 15531 | 5' | -56.7 | NC_004001.2 | + | 16931 | 1.11 | 0.000291 |
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Target: 5'- gCACAAGCAAACCGACUCCCGGCGCCCu -3' miRNA: 3'- -GUGUUCGUUUGGCUGAGGGCCGCGGG- -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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