miRNA: 3'- -AGGUGAgg-CAAU-GGCG---UGACGCUauu -5'
miRNA: 3'- aGGUGa---GGCA-------------AUGGCGUgACGCUAUU- -5'
miRNA: 3'- -AGGugAggCaAUGGCGuGACGCUAuu -5'
miRNA: 3'- -AGGUGAGGCAAUGGCGUGACGCUAUU- -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 | |||||||
| 8468 | 3' | -52.9 | NC_002167.1 | + | 23009 | 0.66 | 0.74225 |
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Target: 5'- uUCCACUggaGUUAuCCGCaacACUGCGAa-- -3' miRNA: 3'- -AGGUGAgg-CAAU-GGCG---UGACGCUauu -5' |
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| 8468 | 3' | -52.9 | NC_002167.1 | + | 32224 | 0.66 | 0.718893 |
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Target: 5'- aCCACgccgCUGUggcggccgcgaauUAUCGCAgUGCGGUAAc -3' miRNA: 3'- aGGUGa---GGCA-------------AUGGCGUgACGCUAUU- -5' |
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| 8468 | 3' | -52.9 | NC_002167.1 | + | 31602 | 0.67 | 0.662974 |
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Target: 5'- uUCCugUuuG-UGCCGUuCUGCGAUu- -3' miRNA: 3'- -AGGugAggCaAUGGCGuGACGCUAuu -5' |
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| 8468 | 3' | -52.9 | NC_002167.1 | + | 32314 | 1.07 | 0.001461 |
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Target: 5'- uUCCACUCCGUUACCGCACUGCGAUAAu -3' miRNA: 3'- -AGGUGAGGCAAUGGCGUGACGCUAUU- -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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