miRNA: 3'- -UGCUUuUUUC-------GCGAUCGGguUCUCGG- -5'
miRNA: 3'- uGCUUu-----UUUCGCGAUCGgGU--------UCUCGG- -5'
miRNA: 3'- -UGCUU--------------UUUUCGCGAUCGG---GUUCU--CGG- -5'
miRNA: 3'- -UGCUUUUUUCGCGAUCGGGUUCUCGG- -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 | |||||||
| 27719 | 3' | -49.6 | NC_005884.1 | + | 30086 | 0.66 | 0.919551 |
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Target: 5'- gACGAAuAGAGgaaugacCGCUGGCC--AGGGUCa -3' miRNA: 3'- -UGCUUuUUUC-------GCGAUCGGguUCUCGG- -5' |
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| 27719 | 3' | -49.6 | NC_005884.1 | + | 41761 | 0.67 | 0.884066 |
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Target: 5'- uUGGAuuugcuGGGGCGCUGGCgCAuagucaaaGGAGUCa -3' miRNA: 3'- uGCUUu-----UUUCGCGAUCGgGU--------UCUCGG- -5' |
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| 27719 | 3' | -49.6 | NC_005884.1 | + | 11800 | 0.77 | 0.359563 |
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Target: 5'- cACGAAggagugcaauaaauGAAAGCGCUAGCUcuaCAAGAuuGCCa -3' miRNA: 3'- -UGCUU--------------UUUUCGCGAUCGG---GUUCU--CGG- -5' |
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| 27719 | 3' | -49.6 | NC_005884.1 | + | 11922 | 1.14 | 0.001254 |
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Target: 5'- aACGAAAAAAGCGCUAGCCCAAGAGCCa -3' miRNA: 3'- -UGCUUUUUUCGCGAUCGGGUUCUCGG- -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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