miRNA: 3'- cGCCU-----------GCGuUAauu-GCGUUgCGCGCG- -5'
miRNA: 3'- cGCCUGCGuuaAUUGCG----UUGCGcGCG- -5'
miRNA: 3'- cgCC---UGCGUUaa--------UUGCG-UUGCGCGCG- -5'
miRNA: 3'- -CGCCUGCGUUAAUUGCGUUGCGCGCG- -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 | |||||||
| 31597 | 3' | -50.9 | NC_006875.1 | + | 2693 | 0.66 | 0.399358 |
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Target: 5'- aCGGGgucguccugccCGCuGUggucCGCAAgGCGCGCg -3' miRNA: 3'- cGCCU-----------GCGuUAauu-GCGUUgCGCGCG- -5' |
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| 31597 | 3' | -50.9 | NC_006875.1 | + | 5104 | 0.66 | 0.37791 |
|
Target: 5'- aUGGACGC---UGGCGCcaccGGCGC-CGCc -3' miRNA: 3'- cGCCUGCGuuaAUUGCG----UUGCGcGCG- -5' |
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| 31597 | 3' | -50.9 | NC_006875.1 | + | 4027 | 0.73 | 0.119169 |
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Target: 5'- -gGGuaaGCGCAGgcuuauuuggGGCGCuGACGCGCGCg -3' miRNA: 3'- cgCC---UGCGUUaa--------UUGCG-UUGCGCGCG- -5' |
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| 31597 | 3' | -50.9 | NC_006875.1 | + | 4091 | 1.15 | 5.9e-05 |
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Target: 5'- uGCGGACGCAAUUAACGCAACGCGCGCg -3' miRNA: 3'- -CGCCUGCGUUAAUUGCGUUGCGCGCG- -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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