miRNA: 3'- cgaaCCCUCCU-CGGGGUGU-Cuu-UGGa -5'
miRNA: 3'- cGAACCc-UCCUCGGGGugUCUUUGga -5'
miRNA: 3'- -CGA-ACCCUCC----UCG-GGGUGUCU--------UUGGa -5'
miRNA: 3'- -CGAACCCUCC------UCGGGG----UGUCUUUGGA- -5'
miRNA: 3'- -CGAACCCUCCUCGGGGUGUCUUUGGA- -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 | |||||||
| 602 | 3' | -55.9 | AC_000017.1 | + | 11168 | 0.66 | 0.562937 |
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Target: 5'- ---gGGGAGGGuGCCCUGCAuGucuGCCg -3' miRNA: 3'- cgaaCCCUCCU-CGGGGUGU-Cuu-UGGa -5' |
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| 602 | 3' | -55.9 | AC_000017.1 | + | 7971 | 0.66 | 0.551776 |
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Target: 5'- aCUUGGauGGGGGCCUUugGGAAGCa- -3' miRNA: 3'- cGAACCc-UCCUCGGGGugUCUUUGga -5' |
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| 602 | 3' | -55.9 | AC_000017.1 | + | 12943 | 0.71 | 0.257802 |
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Target: 5'- gGCUgUGGGGGGugcgGGCuCCCACAGGcgacgcgcGACCg -3' miRNA: 3'- -CGA-ACCCUCC----UCG-GGGUGUCU--------UUGGa -5' |
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| 602 | 3' | -55.9 | AC_000017.1 | + | 4068 | 0.81 | 0.051347 |
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Target: 5'- cGCUUGGGAGGggaggaAGCCUUcaggGCAGAAACCUg -3' miRNA: 3'- -CGAACCCUCC------UCGGGG----UGUCUUUGGA- -5' |
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| 602 | 3' | -55.9 | AC_000017.1 | + | 1861 | 1.09 | 0.000463 |
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Target: 5'- uGCUUGGGAGGAGCCCCACAGAAACCUc -3' miRNA: 3'- -CGAACCCUCCUCGGGGUGUCUUUGGA- -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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