miRNA: 3'- -CCUCUUACC-----------GCAGa---------GUCCCuAGGCCU- -5'
miRNA: 3'- ccUCuuACCGCaGAGUCcCUAgGCCU- -5'
miRNA: 3'- cCUCUuaCCGCAGagUC-CCUAGGCCu -5'
miRNA: 3'- -CCUCUUACCGCAGAGUCCCUAGGCCU- -5'
Results 1 - 4 of 4 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 | |||||||
| 455 | 5' | -55 | AC_000013.1 | + | 38608 | 0.66 | 0.686193 |
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Target: 5'- uGGAGAGUGGgcggguccuucCGUCcuucggugggCGGGGcUCUGGAu -3' miRNA: 3'- -CCUCUUACC-----------GCAGa---------GUCCCuAGGCCU- -5' |
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| 455 | 5' | -55 | AC_000013.1 | + | 44286 | 0.66 | 0.67519 |
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Target: 5'- -cGGggUGGCG-CUCGGaGAUgCGGGu -3' miRNA: 3'- ccUCuuACCGCaGAGUCcCUAgGCCU- -5' |
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| 455 | 5' | -55 | AC_000013.1 | + | 34978 | 0.74 | 0.251059 |
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Target: 5'- uGAGAcgGGCGUCcgAGaGGAUCCGGu -3' miRNA: 3'- cCUCUuaCCGCAGagUC-CCUAGGCCu -5' |
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| 455 | 5' | -55 | AC_000013.1 | + | 6098 | 1.12 | 0.000612 |
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Target: 5'- aGGAGAAUGGCGUCUCAGGGAUCCGGAg -3' miRNA: 3'- -CCUCUUACCGCAGAGUCCCUAGGCCU- -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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