miRNA: 3'- -CGAaa----GUCuuUGU---------CCUCGAA--AGGGCG- -5'
miRNA: 3'- -CGAAAgUCUU------UGUCCUCGAaa--------GG--GCG- -5'
miRNA: 3'- -CGAAAGUCUUUGU-CCU-CgaaaGGGCG- -5'
miRNA: 3'- -CGAAAGUCUUUGUCCUcGAAAGGGCG- -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 | |||||||
| 25993 | 3' | -48 | NC_005340.1 | + | 6021 | 0.67 | 0.897747 |
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Target: 5'- uGCUcauaggCGGuuGCAuggcgcagcGGGGCUUgcUCCCGCu -3' miRNA: 3'- -CGAaa----GUCuuUGU---------CCUCGAA--AGGGCG- -5' |
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| 25993 | 3' | -48 | NC_005340.1 | + | 25872 | 0.68 | 0.816479 |
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Target: 5'- cGCUUUgAGAAugaaucACAGGAGCUgcacuaauggCCgaCGCa -3' miRNA: 3'- -CGAAAgUCUU------UGUCCUCGAaa--------GG--GCG- -5' |
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| 25993 | 3' | -48 | NC_005340.1 | + | 5015 | 0.69 | 0.773766 |
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Target: 5'- cGUUUUCAGAAACGcGGAuGacg-CCUGCa -3' miRNA: 3'- -CGAAAGUCUUUGU-CCU-CgaaaGGGCG- -5' |
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| 25993 | 3' | -48 | NC_005340.1 | + | 20673 | 1.01 | 0.010581 |
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Target: 5'- gGCUUUCAGAAACAGGA-CUUUCCCGCu -3' miRNA: 3'- -CGAAAGUCUUUGUCCUcGAAAGGGCG- -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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