miRNA: 3'- aCG--CCGGCUUCua----UGaga-ACGACCCC- -5'
miRNA: 3'- aCGcCGGCU---UCUAUgAGAACG--ACCCc -5'
miRNA: 3'- -ACGCCGGCUUCuAUGAGaa-------------CGAC------CCC- -5'
miRNA: 3'- acgCCGG-CUUCUAUGAgaaCGACCCC- -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 | |||||||
| 30825 | 5' | -54.7 | NC_006552.1 | + | 11951 | 0.66 | 0.78891 |
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Target: 5'- cGCuaGGUCGGAGcgcaugGCggugUGCUGGGGa -3' miRNA: 3'- aCG--CCGGCUUCua----UGaga-ACGACCCC- -5' |
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| 30825 | 5' | -54.7 | NC_006552.1 | + | 33854 | 0.66 | 0.769068 |
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Target: 5'- gGCcGCCGAgcgGGAUGgUCUUGUacUGGGc -3' miRNA: 3'- aCGcCGGCU---UCUAUgAGAACG--ACCCc -5' |
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| 30825 | 5' | -54.7 | NC_006552.1 | + | 25551 | 0.7 | 0.572756 |
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Target: 5'- aUGCGGCCGAAG-UACUCgccaccggccaguacGCUGagccgcGGGa -3' miRNA: 3'- -ACGCCGGCUUCuAUGAGaa-------------CGAC------CCC- -5' |
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| 30825 | 5' | -54.7 | NC_006552.1 | + | 59634 | 0.73 | 0.368356 |
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Target: 5'- --gGGCCgGGAGGUGCUg--GCUGGGGa -3' miRNA: 3'- acgCCGG-CUUCUAUGAgaaCGACCCC- -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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