miRNA: 3'- aCUGAUgaCUCC-ACCG---AGGUUGUcag -5'
miRNA: 3'- aCUGAuGAcuCCA---CCGAGGUUgUCAG- -5'
miRNA: 3'- aCUGAUGACUC-CA-CCG------AGGUUGU--CAG- -5'
miRNA: 3'- -ACUGAUGACUCCACCGAGGUUGUCAG- -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 | |||||||
| 12552 | 3' | -53 | NC_003345.1 | + | 26010 | 0.67 | 0.819567 |
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Target: 5'- gGACUGgaGAGGaUGGCuucUCCAGCAc-- -3' miRNA: 3'- aCUGAUgaCUCC-ACCG---AGGUUGUcag -5' |
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| 12552 | 3' | -53 | NC_003345.1 | + | 24783 | 0.67 | 0.810184 |
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Target: 5'- cGACUcCUacGGUuacGGCUCCGAgAGUCg -3' miRNA: 3'- aCUGAuGAcuCCA---CCGAGGUUgUCAG- -5' |
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| 12552 | 3' | -53 | NC_003345.1 | + | 23843 | 0.72 | 0.575925 |
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Target: 5'- cGACUGCUGAGcGUcGGCaucgucUCCGGCGucGUCa -3' miRNA: 3'- aCUGAUGACUC-CA-CCG------AGGUUGU--CAG- -5' |
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| 12552 | 3' | -53 | NC_003345.1 | + | 37314 | 1.11 | 0.001653 |
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Target: 5'- gUGACUACUGAGGUGGCUCCAACAGUCg -3' miRNA: 3'- -ACUGAUGACUCCACCGAGGUUGUCAG- -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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