miRNA: 3'- -UGAUGuCGGUaGUAuUCGaa-CGCGGA- -5'
miRNA: 3'- -UGAUGUCGGUAGUauUCGaac--------GCGGA- -5'
miRNA: 3'- -UGAUGUCGGUAGUauUCGaac--------GCGGA- -5'
miRNA: 3'- -UGAUGUCG---------GUAGUAUUCGaaCGCGGa -5'
miRNA: 3'- -UGAUGUCGGUAGUAUUCGAACGCGGA- -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 | |||||||
| 676 | 5' | -51.3 | AC_000018.1 | + | 16289 | 0.67 | 0.722523 |
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Target: 5'- cGCUGCuGCCGcCGU-GGCcgcGCGCCUg -3' miRNA: 3'- -UGAUGuCGGUaGUAuUCGaa-CGCGGA- -5' |
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| 676 | 5' | -51.3 | AC_000018.1 | + | 10927 | 0.75 | 0.269083 |
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Target: 5'- gGCUGCAGCCGUCAgcGGCgcgggacagccCGCCUa -3' miRNA: 3'- -UGAUGUCGGUAGUauUCGaac--------GCGGA- -5' |
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| 676 | 5' | -51.3 | AC_000018.1 | + | 11198 | 0.75 | 0.269083 |
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Target: 5'- gGCUGCAGCCGUCAgcGGCgcgggacagccCGCCUa -3' miRNA: 3'- -UGAUGUCGGUAGUauUCGaac--------GCGGA- -5' |
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| 676 | 5' | -51.3 | AC_000018.1 | + | 18865 | 0.75 | 0.257398 |
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Target: 5'- gGCUACGGUcgguggucaCAUCGUGGGUggGCGCCa -3' miRNA: 3'- -UGAUGUCG---------GUAGUAUUCGaaCGCGGa -5' |
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| 676 | 5' | -51.3 | AC_000018.1 | + | 24922 | 1.07 | 0.001451 |
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Target: 5'- cACUACAGCCAUCAUAAGCUUGCGCCUc -3' miRNA: 3'- -UGAUGUCGGUAGUAUUCGAACGCGGA- -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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