miRNA: 3'- -UUGCCAGUC---CAGCCc--GCCCaaaAGCc -5'
miRNA: 3'- uugCCAGUCCa--GCCC-GCCCaaaaGCC- -5'
miRNA: 3'- uUGCcAGUcCAGCCCGCCC-------AAAAGCc -5'
miRNA: 3'- -UugCCAGUCCa--GCC-CGCCCAaa-AGCC- -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 | |||||||
| 20748 | 5' | -56.3 | NC_004688.1 | + | 9724 | 0.66 | 0.842314 |
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Target: 5'- cGACGGUCAGuucGUCGGccuCGGGg--UCGa -3' miRNA: 3'- -UUGCCAGUC---CAGCCc--GCCCaaaAGCc -5' |
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| 20748 | 5' | -56.3 | NC_004688.1 | + | 33960 | 0.66 | 0.834022 |
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Target: 5'- --gGGUCAGGcagCGGGuCGGGc---CGGa -3' miRNA: 3'- uugCCAGUCCa--GCCC-GCCCaaaaGCC- -5' |
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| 20748 | 5' | -56.3 | NC_004688.1 | + | 109212 | 0.66 | 0.833182 |
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Target: 5'- cACGaUCAcGUCGGGCGGGcgcauccUUUUCGa -3' miRNA: 3'- uUGCcAGUcCAGCCCGCCC-------AAAAGCc -5' |
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| 20748 | 5' | -56.3 | NC_004688.1 | + | 40944 | 0.73 | 0.441615 |
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Target: 5'- gGugGGUCGGGgacUGGaGCGGGUgacUCGGc -3' miRNA: 3'- -UugCCAGUCCa--GCC-CGCCCAaa-AGCC- -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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