miRNA: 3'- aaAGg--UAGUGU-UCUGUUCGGuguCCC- -5'
miRNA: 3'- aAAGGUAGu-GUUCUgu----UCGGUGUCCc -5'
miRNA: 3'- -AAAGGu-------AGUGUUCUGu---UCGGU----GUCCc -5'
miRNA: 3'- aaaGGUa-------GUGUUCugUUCGgUGUCCC- -5'
miRNA: 3'- -AAAGGUAGUGUUCUGUUCGGUGUCCC- -5'
Results 1 - 5 of 5 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 | |||||||
| 15537 | 3' | -50.3 | NC_004001.2 | + | 13391 | 0.66 | 0.828458 |
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Target: 5'- -cUCaggAUCACAgAGACGAGCCu--GGGa -3' miRNA: 3'- aaAGg--UAGUGU-UCUGUUCGGuguCCC- -5' |
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| 15537 | 3' | -50.3 | NC_004001.2 | + | 17422 | 0.66 | 0.808359 |
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Target: 5'- cUUCCAUCucUAAGAaaacauAGUCACAGGa -3' miRNA: 3'- aAAGGUAGu-GUUCUgu----UCGGUGUCCc -5' |
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| 15537 | 3' | -50.3 | NC_004001.2 | + | 1114 | 0.67 | 0.787391 |
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Target: 5'- uUUUCCugugaaauUCACAAGACuuacAGCCAugucCAGGa -3' miRNA: 3'- -AAAGGu-------AGUGUUCUGu---UCGGU----GUCCc -5' |
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| 15537 | 3' | -50.3 | NC_004001.2 | + | 11579 | 0.67 | 0.743289 |
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Target: 5'- --gCCAgcaggaggCGCGAGuuAAGCgACAGGGa -3' miRNA: 3'- aaaGGUa-------GUGUUCugUUCGgUGUCCC- -5' |
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| 15537 | 3' | -50.3 | NC_004001.2 | + | 34042 | 1.08 | 0.001753 |
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Target: 5'- cUUUCCAUCACAAGACAAGCCACAGGGu -3' miRNA: 3'- -AAAGGUAGUGUUCUGUUCGGUGUCCC- -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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