miRNA: 3'- uugCUUgUCGGCG-----CGUAAGCgGACGu -5'
miRNA: 3'- uUGCu-UGUCGGC-GCGUAAGCG----GACGu -5'
miRNA: 3'- -UUGCUU----GUCGGCGCGUa--AGCGgA-CGU- -5'
miRNA: 3'- -UUGCU--UGuCGGCGCGUAa---GCGGACGu -5'
Results 41 - 44 of 44 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 | |||||||
| 24819 | 3' | -56.1 | NC_005284.1 | + | 10756 | 0.66 | 0.614038 |
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Target: 5'- --aGGGgGGCCGCcgaggGCGUUCGgCUGCu -3' miRNA: 3'- uugCUUgUCGGCG-----CGUAAGCgGACGu -5' |
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| 24819 | 3' | -56.1 | NC_005284.1 | + | 35294 | 0.66 | 0.636358 |
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Target: 5'- uGCGcuACAGUCGaCGCGUUCGUgguaCUGCu -3' miRNA: 3'- uUGCu-UGUCGGC-GCGUAAGCG----GACGu -5' |
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| 24819 | 3' | -56.1 | NC_005284.1 | + | 39317 | 0.66 | 0.636358 |
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Target: 5'- cGGCGAGauacCAGUCGCGCAcgaUCGCgUaGCAg -3' miRNA: 3'- -UUGCUU----GUCGGCGCGUa--AGCGgA-CGU- -5' |
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| 24819 | 3' | -56.1 | NC_005284.1 | + | 40278 | 0.66 | 0.636358 |
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Target: 5'- cGGCGAugGCuGCUGCGCGUcggaUGUCUGCu -3' miRNA: 3'- -UUGCU--UGuCGGCGCGUAa---GCGGACGu -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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