miRNA: 3'- cUGaaCUcGGUGUGGCUC---UCugUCGG- -5'
miRNA: 3'- cugaacUCGGuGU--------GGCUCUCUGUCGG- -5'
miRNA: 3'- cugaaCUCGG---UGUGGCUC--UCUgUCGG- -5'
miRNA: 3'- cUGAACUcg-----GUGUGGCUCUCu--GUCGG- -5'
miRNA: 3'- -CUGAACUCGGUGUGGCUCUCUGUCGG- -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
|
Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 12512 | 3' | -54.4 | NC_003345.1 | + | 71026 | 0.66 | 0.811859 |
|
Target: 5'- cGCgaGAaCCGCGCCGAGgauGGugAGCUg -3' miRNA: 3'- cUGaaCUcGGUGUGGCUC---UCugUCGG- -5' |
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| 12512 | 3' | -54.4 | NC_003345.1 | + | 364 | 0.66 | 0.811859 |
|
Target: 5'- -----cGGCC-CAuuagaaucCCGAGAGACGGCCc -3' miRNA: 3'- cugaacUCGGuGU--------GGCUCUCUGUCGG- -5' |
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| 12512 | 3' | -54.4 | NC_003345.1 | + | 22022 | 0.66 | 0.838817 |
|
Target: 5'- ----cGAGUCuuuACACCGAGguAGAgAGCCu -3' miRNA: 3'- cugaaCUCGG---UGUGGCUC--UCUgUCGG- -5' |
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| 12512 | 3' | -54.4 | NC_003345.1 | + | 38537 | 0.66 | 0.838817 |
|
Target: 5'- aACUUGGuaaucgaCGCAUCGAGGGuuuCGGCCa -3' miRNA: 3'- cUGAACUcg-----GUGUGGCUCUCu--GUCGG- -5' |
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| 12512 | 3' | -54.4 | NC_003345.1 | + | 7064 | 1.11 | 0.001209 |
|
Target: 5'- gGACUUGAGCCACACCGAGAGACAGCCu -3' miRNA: 3'- -CUGAACUCGGUGUGGCUCUCUGUCGG- -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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