miRNA: 3'- -CGUUCa-------GCUCCUACAaaugUGUGCCU- -5'
miRNA: 3'- -CGUUCaGCuCCUACaaauGUGUGCCU- -5'
miRNA: 3'- cGUUCAGCUCCUaCAaaUG--UGUGCCU- -5'
miRNA: 3'- -CGUUCAG---CUCCUac-----AAAUGUGUGCCU- -5'
miRNA: 3'- -CGUUCAGCUCCUACAAAUGUGUGCCU- -5'
Results 21 - 25 of 25 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 | |||||||
| 6425 | 5' | -47.6 | NC_001847.1 | + | 84472 | 0.72 | 0.96553 |
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Target: 5'- aGCGGGggggggggCGGGGGUGUgaa-GCGCGGGa -3' miRNA: 3'- -CGUUCa-------GCUCCUACAaaugUGUGCCU- -5' |
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| 6425 | 5' | -47.6 | NC_001847.1 | + | 44683 | 0.72 | 0.96553 |
|
Target: 5'- gGCGAGcCGcGGAUGggc-CGCGCGGAc -3' miRNA: 3'- -CGUUCaGCuCCUACaaauGUGUGCCU- -5' |
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| 6425 | 5' | -47.6 | NC_001847.1 | + | 56391 | 0.73 | 0.949824 |
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Target: 5'- uCGGGUCGGGGAgGUcgGCcgGCGCGGGg -3' miRNA: 3'- cGUUCAGCUCCUaCAaaUG--UGUGCCU- -5' |
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| 6425 | 5' | -47.6 | NC_001847.1 | + | 101864 | 0.78 | 0.750352 |
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Target: 5'- aGCAGGUCgcgGAGGAgcucgccUUUGCGCGCGGAc -3' miRNA: 3'- -CGUUCAG---CUCCUac-----AAAUGUGUGCCU- -5' |
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| 6425 | 5' | -47.6 | NC_001847.1 | + | 76591 | 1.12 | 0.01184 |
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Target: 5'- gGCAAGUCGAGGAUGUUUACACACGGAc -3' miRNA: 3'- -CGUUCAGCUCCUACAAAUGUGUGCCU- -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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