miRNA: 3'- -CGGGaCCCa----GAGCGGGGGCcu--AGA-GG- -5'
miRNA: 3'- cGGGACCCAGa----GCGGG--GGCCUaGa-GG- -5'
miRNA: 3'- cGGGACCCa------------GAG-----CGGGGGCc--UAGAGG- -5'
miRNA: 3'- -CGGGACCCAGAGCGGGGGCCUAGAGG- -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 | |||||||
| 28397 | 3' | -61.8 | NC_005946.1 | + | 102011 | 0.66 | 0.566716 |
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Target: 5'- aGCUCgGGGgccugCUCGCCUCCGuccuUCUuCCa -3' miRNA: 3'- -CGGGaCCCa----GAGCGGGGGCcu--AGA-GG- -5' |
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| 28397 | 3' | -61.8 | NC_005946.1 | + | 64799 | 0.69 | 0.418461 |
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Target: 5'- cCCCUGGGUCccacgCGCCCgaCUGGAcCggCCg -3' miRNA: 3'- cGGGACCCAGa----GCGGG--GGCCUaGa-GG- -5' |
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| 28397 | 3' | -61.8 | NC_005946.1 | + | 9847 | 0.7 | 0.358255 |
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Target: 5'- aCCCUGGGguagugggggaggCUCcuccuGCCCCCGucuAUCUCCu -3' miRNA: 3'- cGGGACCCa------------GAG-----CGGGGGCc--UAGAGG- -5' |
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| 28397 | 3' | -61.8 | NC_005946.1 | + | 59960 | 1.11 | 0.000447 |
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Target: 5'- gGCCCUGGGUCUCGCCCCCGGAUCUCCc -3' miRNA: 3'- -CGGGACCCAGAGCGGGGGCCUAGAGG- -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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