miRNA: 3'- uGUCCUCCUUCCagg--GGCuuCGcUUC- -5'
miRNA: 3'- ugUCCUCCuUCCAGGG--------------GCuuCGCuuC- -5'
miRNA: 3'- -UGUCCUC-------------CUUCCAGGG--GCUUCgCUUC- -5'
miRNA: 3'- -UGUCCUCCUUCCAGGGGCUUCGCUUC- -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 | |||||||
| 10688 | 5' | -56 | NC_002786.1 | + | 1764 | 0.66 | 0.139876 |
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Target: 5'- uCAGGAGGAGGGagcgaCUGggGCaAAGg -3' miRNA: 3'- uGUCCUCCUUCCagg--GGCuuCGcUUC- -5' |
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| 10688 | 5' | -56 | NC_002786.1 | + | 356 | 0.66 | 0.134058 |
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Target: 5'- -aAGGAGGuGGGUCUCgauggucuuauggaCGggGUGggGu -3' miRNA: 3'- ugUCCUCCuUCCAGGG--------------GCuuCGCuuC- -5' |
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| 10688 | 5' | -56 | NC_002786.1 | + | 987 | 0.67 | 0.11831 |
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Target: 5'- uGCGGGGGaccagccggugacGAAGGUCCUggUGGAGgGAGGc -3' miRNA: 3'- -UGUCCUC-------------CUUCCAGGG--GCUUCgCUUC- -5' |
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| 10688 | 5' | -56 | NC_002786.1 | + | 2011 | 1.09 | 0.00003 |
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Target: 5'- gACAGGAGGAAGGUCCCCGAAGCGAAGg -3' miRNA: 3'- -UGUCCUCCUUCCAGGGGCUUCGCUUC- -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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