miRNA: 3'- -CCGUCGUg--GGa---GCCGGGgCU-UAGAGc -5'
miRNA: 3'- cCGUCGUGGGAGcCGGGGCU--UAGagc -5'
miRNA: 3'- -CCGUCGugGga--GCCGGGGCUuAGagc -5'
miRNA: 3'- -CCGUCGUGGGAGCCGGGGCUUAGAGC- -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 | |||||||
| 11671 | 5' | -59.4 | NC_003102.1 | + | 72354 | 0.66 | 0.760479 |
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Target: 5'- aGGCAGCGuagCCgaagCGGCCC-GAcAUCUCa -3' miRNA: 3'- -CCGUCGUg--GGa---GCCGGGgCU-UAGAGc -5' |
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| 11671 | 5' | -59.4 | NC_003102.1 | + | 93580 | 0.67 | 0.712785 |
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Target: 5'- cGCGGCGCUCUC-GCCUCGAccGUCg-- -3' miRNA: 3'- cCGUCGUGGGAGcCGGGGCU--UAGagc -5' |
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| 11671 | 5' | -59.4 | NC_003102.1 | + | 133895 | 0.72 | 0.407139 |
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Target: 5'- cGGCGGCugCgacgCGGCCCCGAuUCa-- -3' miRNA: 3'- -CCGUCGugGga--GCCGGGGCUuAGagc -5' |
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| 11671 | 5' | -59.4 | NC_003102.1 | + | 74184 | 1.11 | 0.001008 |
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Target: 5'- cGGCAGCACCCUCGGCCCCGAAUCUCGa -3' miRNA: 3'- -CCGUCGUGGGAGCCGGGGCUUAGAGC- -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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