miRNA: 3'- cCGAGAAGC------AGCUaaUGCCGUaGCAg -5'
miRNA: 3'- -CCGAGa--------------AGCA-GCUaAugCCGUAGCag -5'
miRNA: 3'- -CCGAGAAGcaGCUaaUGCCGUAGC-AG- -5'
miRNA: 3'- cCGAGaaGCAGCuaau---GCCGUAGCAg -5'
miRNA: 3'- -CCGAGAAGCAGCUAAUGCCGUAGCAG- -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 | |||||||
| 474 | 5' | -50.3 | AC_000013.1 | + | 15396 | 0.67 | 0.863634 |
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Target: 5'- uGCUCUUCGcucaauUCGA--GCGGCGcCGUa -3' miRNA: 3'- cCGAGAAGC------AGCUaaUGCCGUaGCAg -5' |
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| 474 | 5' | -50.3 | AC_000013.1 | + | 25166 | 0.68 | 0.809412 |
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Target: 5'- uGGCUCcaauccgauuccgagUCGUcCGAaUugGGCAUCGg- -3' miRNA: 3'- -CCGAGa--------------AGCA-GCUaAugCCGUAGCag -5' |
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| 474 | 5' | -50.3 | AC_000013.1 | + | 5080 | 0.69 | 0.788299 |
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Target: 5'- cGGCUUUUC--CGAg-ACGGCAUCGcUCa -3' miRNA: 3'- -CCGAGAAGcaGCUaaUGCCGUAGC-AG- -5' |
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| 474 | 5' | -50.3 | AC_000013.1 | + | 9369 | 0.71 | 0.667731 |
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Target: 5'- cGCUCgaCGUCGuguacguCGGCGUCGUg -3' miRNA: 3'- cCGAGaaGCAGCuaau---GCCGUAGCAg -5' |
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| 474 | 5' | -50.3 | AC_000013.1 | + | 28858 | 1.14 | 0.001309 |
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Target: 5'- cGGCUCUUCGUCGAUUACGGCAUCGUCg -3' miRNA: 3'- -CCGAGAAGCAGCUAAUGCCGUAGCAG- -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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