miRNA: 3'- ccAgUGGACC-CCAU--------------AGCUGUAGAG-GU- -5'
miRNA: 3'- -CCAGUGGaCCCCau-----AGCUGUa----GAGGu -5'
miRNA: 3'- -CCAGuGGa--CCCCa-UAGCUGU----------AGAGGU- -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 | |||||||
| 20643 | 5' | -53.7 | NC_004688.1 | + | 58769 | 0.67 | 0.890698 |
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Target: 5'- -uUgGCCUGGuGGUGcccgggcagcuuguUCGGCAUCUCgCAg -3' miRNA: 3'- ccAgUGGACC-CCAU--------------AGCUGUAGAG-GU- -5' |
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| 20643 | 5' | -53.7 | NC_004688.1 | + | 73235 | 0.68 | 0.863428 |
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Target: 5'- cGGUCGCCgGGGGccgccccUCGGCGgugacCUCCc -3' miRNA: 3'- -CCAGUGGaCCCCau-----AGCUGUa----GAGGu -5' |
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| 20643 | 5' | -53.7 | NC_004688.1 | + | 87653 | 0.69 | 0.821842 |
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Target: 5'- aGGUCcCCgagGGGGccGUUGACAagguacuggaUCUCCAg -3' miRNA: 3'- -CCAGuGGa--CCCCa-UAGCUGU----------AGAGGU- -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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