miRNA: 3'- cagGCUGU--------CGUAAAAgUgCGGCCCGU- -5'
miRNA: 3'- -CAGGCUGUCGUaaAAGuGCgGCCCGU- -5'
miRNA: 3'- caGGCUGUCGUAaa----AgUGCG-GCCCGu -5'
miRNA: 3'- -CAGGCUGUCGUAAAAGUGCGGCCCGU- -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 | |||||||
| 31627 | 5' | -54.6 | NC_006879.1 | + | 15454 | 0.67 | 0.557935 |
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Target: 5'- --gCGGCGgguacaacGCGUUUUgAgGCCGGGCAc -3' miRNA: 3'- cagGCUGU--------CGUAAAAgUgCGGCCCGU- -5' |
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| 31627 | 5' | -54.6 | NC_006879.1 | + | 16204 | 0.68 | 0.45975 |
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Target: 5'- gGUUCGGCGGCGggUUCcUGaCGGGCGa -3' miRNA: 3'- -CAGGCUGUCGUaaAAGuGCgGCCCGU- -5' |
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| 31627 | 5' | -54.6 | NC_006879.1 | + | 14884 | 0.68 | 0.449391 |
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Target: 5'- -aUCGACAGCGUgguagcUgGCGCuCGGGCc -3' miRNA: 3'- caGGCUGUCGUAaa----AgUGCG-GCCCGu -5' |
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| 31627 | 5' | -54.6 | NC_006879.1 | + | 12581 | 1.08 | 0.000625 |
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Target: 5'- uGUCCGACAGCAUUUUCACGCCGGGCAa -3' miRNA: 3'- -CAGGCUGUCGUAAAAGUGCGGCCCGU- -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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