miRNA: 3'- -UACAUCAGc---UUCUAGCGUAA-C-GCGUu -5'
miRNA: 3'- uaCAUCA--------------GCUUCUAGcGUAACGCGUU- -5'
miRNA: 3'- uacaUCAGCUUCuaG-------CGUAACGCGUu -5'
miRNA: 3'- -UACAUCAGCUUCUAGCGUAACGCGUU- -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 | |||||||
| 22542 | 3' | -49.8 | NC_005083.1 | + | 9558 | 0.66 | 0.999233 |
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Target: 5'- cGUGUAGUUuuucAGGGUCGCGUUcGcCGCAu -3' miRNA: 3'- -UACAUCAGc---UUCUAGCGUAA-C-GCGUu -5' |
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| 22542 | 3' | -49.8 | NC_005083.1 | + | 18876 | 0.66 | 0.998528 |
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Target: 5'- -gGUGGUgauguucacauuuaUGAAGAUCaCAUUGUGCAGg -3' miRNA: 3'- uaCAUCA--------------GCUUCUAGcGUAACGCGUU- -5' |
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| 22542 | 3' | -49.8 | NC_005083.1 | + | 109204 | 0.67 | 0.996576 |
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Target: 5'- ---aAGUCGAAGcgCaugaaaaGCGUUGCGCAc -3' miRNA: 3'- uacaUCAGCUUCuaG-------CGUAACGCGUu -5' |
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| 22542 | 3' | -49.8 | NC_005083.1 | + | 42770 | 1.05 | 0.024627 |
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Target: 5'- gAUGUAGUCGAAGAUCGCAUUGCGCAAa -3' miRNA: 3'- -UACAUCAGCUUCUAGCGUAACGCGUU- -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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