miRNA: 3'- cGCCGUGCCU----UGUGCUGGag---CAA-CGC- -5'
miRNA: 3'- cGCCGUGCC-UUGUG-CUGGaGCaa-CGC- -5'
miRNA: 3'- -CGC-CGUGCC--UUGuGCUGGAGCaaCGc -5'
miRNA: 3'- -CGCcg--UGCCU-------UGUGCUGGAGCaaCGC- -5'
miRNA: 3'- cGCCGuGCCUUGUGCUGgAGCAa--CGC- -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 |
| Predicted miRNA align pattern | |||||||
| 27564 | 5' | -55.2 | NC_005882.1 | + | 26937 | 0.71 | 0.354146 |
|
Target: 5'- uCGGCAUGGGgcggGCGCGGCCggcaaGUUcGCGg -3' miRNA: 3'- cGCCGUGCCU----UGUGCUGGag---CAA-CGC- -5' |
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| 27564 | 5' | -55.2 | NC_005882.1 | + | 27593 | 0.67 | 0.585586 |
|
Target: 5'- cCGGCAUGGcGACGCaGGCCgCGgccGCGg -3' miRNA: 3'- cGCCGUGCC-UUGUG-CUGGaGCaa-CGC- -5' |
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| 27564 | 5' | -55.2 | NC_005882.1 | + | 30210 | 0.67 | 0.596725 |
|
Target: 5'- cGCGcGUACGGcuGAC-CGACCUCG--GCa -3' miRNA: 3'- -CGC-CGUGCC--UUGuGCUGGAGCaaCGc -5' |
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| 27564 | 5' | -55.2 | NC_005882.1 | + | 31106 | 0.67 | 0.551353 |
|
Target: 5'- aGCGaucgACGGAaugacacGCACGACCUCGcaGCGc -3' miRNA: 3'- -CGCcg--UGCCU-------UGUGCUGGAGCaaCGC- -5' |
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| 27564 | 5' | -55.2 | NC_005882.1 | + | 32126 | 0.66 | 0.652689 |
|
Target: 5'- cCGGCcUGGGGCGCGAUaUCGUcccGCGc -3' miRNA: 3'- cGCCGuGCCUUGUGCUGgAGCAa--CGC- -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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