miRNA: 3'- gaCCGgua-----CUUGAGGGUGUUUCCUUc -5'
miRNA: 3'- gACCGGU---ACUUG----AGGGUGuUUCCUUc -5'
miRNA: 3'- gACCGGu--ACU--------UGAGGGUGUUUCCUUc -5'
miRNA: 3'- gACCGGUACU--UGAgGGUGUU-------------UCCUUC- -5'
miRNA: 3'- -GACCGGUACUUGAGGGUGUUUCCUUC- -5'
Results 1 - 5 of 5 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 | |||||||
| 28202 | 5' | -51.1 | NC_005891.1 | + | 12364 | 0.67 | 0.793228 |
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Target: 5'- -cGGCaguccaagGAAUUCCUGCGGAGGAGc -3' miRNA: 3'- gaCCGgua-----CUUGAGGGUGUUUCCUUc -5' |
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| 28202 | 5' | -51.1 | NC_005891.1 | + | 8898 | 0.67 | 0.782769 |
|
Target: 5'- uUGGUCAacgUGAAUacaaUCCCGCuGAGGGAc -3' miRNA: 3'- gACCGGU---ACUUG----AGGGUGuUUCCUUc -5' |
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| 28202 | 5' | -51.1 | NC_005891.1 | + | 28621 | 0.73 | 0.414019 |
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Target: 5'- aUGGCUuguUGAacaggcugACUCCUACAAGGGAAc -3' miRNA: 3'- gACCGGu--ACU--------UGAGGGUGUUUCCUUc -5' |
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| 28202 | 5' | -51.1 | NC_005891.1 | + | 38928 | 0.75 | 0.329775 |
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Target: 5'- gUGGCCAUGGggGCUgCCGCAAcaaccagagccuuAGGAGGc -3' miRNA: 3'- gACCGGUACU--UGAgGGUGUU-------------UCCUUC- -5' |
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| 28202 | 5' | -51.1 | NC_005891.1 | + | 23498 | 1.09 | 0.001584 |
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Target: 5'- aCUGGCCAUGAACUCCCACAAAGGAAGc -3' miRNA: 3'- -GACCGGUACUUGAGGGUGUUUCCUUC- -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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