miRNA: 3'- ucGGCAa---CUCCUCGguUCCCC-GGUGg -5'
miRNA: 3'- uCGGCAa---CucCUCGGuu-CCCCGGuGG- -5'
miRNA: 3'- -UCGGcaa---CUCCUCGGUU-CCCCg--GUGG- -5'
miRNA: 3'- -UCGGca-ACUCC-UCGgUUCCC-CGGUGG- -5'
miRNA: 3'- -UCGGCAACUCCUCGGUUCCCCGGUGG- -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 | |||||||
| 733 | 3' | -59.5 | AC_000020.1 | + | 1880 | 0.66 | 0.334035 |
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Target: 5'- -uCCGUgcucGAGGAGC--AGGGGuCCGCg -3' miRNA: 3'- ucGGCAa---CUCCUCGguUCCCC-GGUGg -5' |
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| 733 | 3' | -59.5 | AC_000020.1 | + | 14205 | 0.67 | 0.279978 |
|
Target: 5'- cGCCGUcaagGccGAGCCcgcGGGGCC-CCu -3' miRNA: 3'- uCGGCAa---CucCUCGGuu-CCCCGGuGG- -5' |
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| 733 | 3' | -59.5 | AC_000020.1 | + | 12088 | 0.69 | 0.203815 |
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Target: 5'- aAGCCcucaggGGGGAGCCAGcGGGGauuCAUCa -3' miRNA: 3'- -UCGGcaa---CUCCUCGGUU-CCCCg--GUGG- -5' |
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| 733 | 3' | -59.5 | AC_000020.1 | + | 14176 | 0.74 | 0.092585 |
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Target: 5'- gGGCCucgUGGGGcAGCaAAGGGcGCCGCCg -3' miRNA: 3'- -UCGGca-ACUCC-UCGgUUCCC-CGGUGG- -5' |
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| 733 | 3' | -59.5 | AC_000020.1 | + | 21598 | 1.12 | 0.000103 |
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Target: 5'- aAGCCGUUGAGGAGCCAAGGGGCCACCa -3' miRNA: 3'- -UCGGCAACUCCUCGGUUCCCCGGUGG- -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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