miRNA: 3'- -CGGACGUUCCCGgug--------UCaaAGACGAa -5'
miRNA: 3'- -CGGACGuu------C-CCGG-UGUCAAAGACGAa -5'
miRNA: 3'- -CGGACGUUCCCGGUGUCAAAGACGAA- -5'
Results 1 - 3 of 3 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 | |||||||
| 22790 | 3' | -54.4 | NC_005097.1 | + | 1155 | 0.66 | 0.18056 |
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Target: 5'- uGCCUGUGAGGGCacuuuucuugaAGccUCUGCUg -3' miRNA: 3'- -CGGACGUUCCCGgug--------UCaaAGACGAa -5' |
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| 22790 | 3' | -54.4 | NC_005097.1 | + | 802 | 0.66 | 0.177071 |
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Target: 5'- uGCCUGCcgccguguGcGGCUgGCAGUUUUUGCUg -3' miRNA: 3'- -CGGACGuu------C-CCGG-UGUCAAAGACGAa -5' |
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| 22790 | 3' | -54.4 | NC_005097.1 | + | 387 | 1.07 | 6.7e-05 |
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Target: 5'- uGCCUGCAAGGGCCACAGUUUCUGCUUc -3' miRNA: 3'- -CGGACGUUCCCGGUGUCAAAGACGAA- -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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