miRNA: 3'- -UGCCuCUcAUCAGGAGgg---UCCGCUGG- -5'
miRNA: 3'- -UGCCUCUc----------AUCAGgAGGGUCCGCuGG- -5'
miRNA: 3'- -UGCCUCUCAUCAGga------GGG------------UCCGCu------GG- -5'
miRNA: 3'- -UGCCUCUCAUCAGGAGGGUCCGCUGG- -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 | |||||||
| 16665 | 3' | -57.7 | NC_004156.1 | + | 84876 | 0.66 | 0.922949 |
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Target: 5'- uACGGuGGaUAGUCUUCaaagaAGGCGAUCg -3' miRNA: 3'- -UGCCuCUcAUCAGGAGgg---UCCGCUGG- -5' |
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| 16665 | 3' | -57.7 | NC_004156.1 | + | 44989 | 0.67 | 0.880878 |
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Target: 5'- aGCGGAGAcacugccgacuUGGUCaUCCUAGGCG-CCu -3' miRNA: 3'- -UGCCUCUc----------AUCAGgAGGGUCCGCuGG- -5' |
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| 16665 | 3' | -57.7 | NC_004156.1 | + | 91903 | 0.69 | 0.804161 |
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Target: 5'- gGCGGAGAGUAGUCaggaggagCCCucuguuccgguuAGGCGcagucguCCg -3' miRNA: 3'- -UGCCUCUCAUCAGga------GGG------------UCCGCu------GG- -5' |
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| 16665 | 3' | -57.7 | NC_004156.1 | + | 44688 | 1.12 | 0.002215 |
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Target: 5'- gACGGAGAGUAGUCCUCCCAGGCGACCg -3' miRNA: 3'- -UGCCUCUCAUCAGGAGGGUCCGCUGG- -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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