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miRNA: 3'- cGGUGGU--ACUGCCUCG--UGUCa--------------CGGCU- -5'
miRNA: 3'- -CGGUGGU------ACUGCC---------UCGUGUCA----CGGCU- -5'
miRNA: 3'- -CgGUGGUA---CUGC-----------CUCGUG---UCACGGCU- -5'
miRNA: 3'- -CGGUGGUaCUGCC----------UCGuGUCACggCU- -5'
Results 21 - 24 of 24 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position |
R_P_ratio#
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P value |
| Predicted miRNA align pattern | |||||||
| 30421 | 3' | -56.6 | NC_006548.1 | + | 23598 | 0.66 | 0.535453 |
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Target: 5'- cCCACCGccUGGCGGGGUcaGCGGgucauccggcccgagGCUGAa -3' miRNA: 3'- cGGUGGU--ACUGCCUCG--UGUCa--------------CGGCU- -5' |
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| 30421 | 3' | -56.6 | NC_006548.1 | + | 27885 | 0.66 | 0.54525 |
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Target: 5'- uGCCAUUGguuuccUGGCGGgugaggugcAGCGCAGUggugGCCGAg -3' miRNA: 3'- -CGGUGGU------ACUGCC---------UCGUGUCA----CGGCU- -5' |
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| 30421 | 3' | -56.6 | NC_006548.1 | + | 36677 | 0.66 | 0.556202 |
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Target: 5'- uGgCACCGUaucGACGcauccccgcgcGAGCACcgcGGUGCCGGc -3' miRNA: 3'- -CgGUGGUA---CUGC-----------CUCGUG---UCACGGCU- -5' |
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| 30421 | 3' | -56.6 | NC_006548.1 | + | 27779 | 0.66 | 0.556202 |
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Target: 5'- cGCCACCA-GGCGGgaauaggcuuGGC-UGGUGuuGAg -3' miRNA: 3'- -CGGUGGUaCUGCC----------UCGuGUCACggCU- -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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