miRNA: 3'- gAGGUGGGUCCU-CCaCUGAC-----------ACCCGu -5'
miRNA: 3'- gaGGUGGgUC-CUCCACUGACa--CCCGu -5'
miRNA: 3'- gaGGUGGG-UCcUCCACUGACACC-CGu -5'
miRNA: 3'- -GAGGUGGGUCCUCCACUGACACCCGU- -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 | |||||||
| 7263 | 5' | -59.4 | NC_001900.1 | + | 42400 | 0.68 | 0.320533 |
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Target: 5'- aUCCGCUCAGGAuGGaGACUGaccgcgagaucUGGGUg -3' miRNA: 3'- gAGGUGGGUCCU-CCaCUGAC-----------ACCCGu -5' |
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| 7263 | 5' | -59.4 | NC_001900.1 | + | 2209 | 0.7 | 0.262922 |
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Target: 5'- -gCCACCaAGuGGGGUGGCUGggaGGGCc -3' miRNA: 3'- gaGGUGGgUC-CUCCACUGACa--CCCGu -5' |
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| 7263 | 5' | -59.4 | NC_001900.1 | + | 24867 | 0.71 | 0.214013 |
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Target: 5'- -aCCGCCCgAGaAGGUGGCUGUGGuGUc -3' miRNA: 3'- gaGGUGGG-UCcUCCACUGACACC-CGu -5' |
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| 7263 | 5' | -59.4 | NC_001900.1 | + | 2664 | 1.08 | 0.000394 |
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Target: 5'- gCUCCACCCAGGAGGUGACUGUGGGCAc -3' miRNA: 3'- -GAGGUGGGUCCUCCACUGACACCCGU- -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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