miRNA: 3'- cgGACUCC-------CCCCUaaaCUUGGGGgCc -5'
miRNA: 3'- cGGACuc-----CCCCCUAAACUu------GGGGGCC- -5'
miRNA: 3'- cGGaCUCCC-CCCUaa-ACUUGGGGGCc -5'
miRNA: 3'- -CGGACUCCCCCCUAAACUUGGGGGCC- -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 | |||||||
| 12629 | 5' | -57.5 | NC_003345.1 | + | 3025 | 0.66 | 0.697433 |
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Target: 5'- -aCUGAGGcccuuccGGGGAgucGAACCCCgGa -3' miRNA: 3'- cgGACUCC-------CCCCUaaaCUUGGGGgCc -5' |
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| 12629 | 5' | -57.5 | NC_003345.1 | + | 1902 | 0.68 | 0.573321 |
|
Target: 5'- aCCUGucggaauGGGGGGUUUGGugcuuccCCCUCGGa -3' miRNA: 3'- cGGACuc-----CCCCCUAAACUu------GGGGGCC- -5' |
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| 12629 | 5' | -57.5 | NC_003345.1 | + | 8811 | 0.68 | 0.573321 |
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Target: 5'- uCC-GGGGGuGGGAcgaUGAAUCCCCGa -3' miRNA: 3'- cGGaCUCCC-CCCUaa-ACUUGGGGGCc -5' |
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| 12629 | 5' | -57.5 | NC_003345.1 | + | 40777 | 1.12 | 0.000707 |
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Target: 5'- aGCCUGAGGGGGGAUUUGAACCCCCGGu -3' miRNA: 3'- -CGGACUCCCCCCUAAACUUGGGGGCC- -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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