miRNA: 3'- -GAGGAgCgu-----CGAGUA-GUGGGgGCGGG- -5'
miRNA: 3'- gaGGAGCGuCGaGUaGUGGGGG---CGGG- -5'
miRNA: 3'- -GAGGAGcg--UCgaGUAGUGGGg------GCGGG- -5'
miRNA: 3'- gAGGAGCgU---------CGAgUAGUGGGggCGGG- -5'
miRNA: 3'- -GAGGAGCGUCGAGUAGUGGGGGCGGG- -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 | |||||||
| 90 | 5' | -60.4 | AC_000006.1 | + | 22488 | 0.67 | 0.284842 |
|
Target: 5'- uCUCCUgGaaggucuGCUCGUcCACCUgCGCCUg -3' miRNA: 3'- -GAGGAgCgu-----CGAGUA-GUGGGgGCGGG- -5' |
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| 90 | 5' | -60.4 | AC_000006.1 | + | 12428 | 0.67 | 0.29207 |
|
Target: 5'- -cCCUCGCcGC-CGcCACCUCCucuGCCCa -3' miRNA: 3'- gaGGAGCGuCGaGUaGUGGGGG---CGGG- -5' |
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| 90 | 5' | -60.4 | AC_000006.1 | + | 30942 | 0.66 | 0.338439 |
|
Target: 5'- uCUCCUCcucaAGgaCAUCAUCCagcaccaCGCCCa -3' miRNA: 3'- -GAGGAGcg--UCgaGUAGUGGGg------GCGGG- -5' |
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| 90 | 5' | -60.4 | AC_000006.1 | + | 27401 | 0.66 | 0.346668 |
|
Target: 5'- aUUCUCGgGggacccagaGCUgGUCGCCCuuGCUCg -3' miRNA: 3'- gAGGAGCgU---------CGAgUAGUGGGggCGGG- -5' |
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| 90 | 5' | -60.4 | AC_000006.1 | + | 30389 | 1.1 | 0.000152 |
|
Target: 5'- uCUCCUCGCAGCUCAUCACCCCCGCCCc -3' miRNA: 3'- -GAGGAGCGUCGAGUAGUGGGGGCGGG- -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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