miRNA: 3'- uaCCG-GCGAC--------CCUUUGUC---------AUAGCUGU- -5'
miRNA: 3'- uACCG----GCGACCCU----UUGUCAUagCUGu -5'
miRNA: 3'- uACCGGCG-ACCCUuUGUC----AUAGCUGU- -5'
miRNA: 3'- -UACCGGCGACCCUUUGUCAUAGCUGU- -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 | |||||||
| 21135 | 5' | -53.6 | NC_004775.1 | + | 1874 | 0.66 | 0.700748 |
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Target: 5'- -cGGCgCGCUGgaugaucaGGAGACGGcugaugaccUGUCGGCGg -3' miRNA: 3'- uaCCG-GCGAC--------CCUUUGUC---------AUAGCUGU- -5' |
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| 21135 | 5' | -53.6 | NC_004775.1 | + | 4025 | 0.67 | 0.597119 |
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Target: 5'- cUGGCuccuCGCUGGGAagugAACGGUGagGAUg -3' miRNA: 3'- uACCG----GCGACCCU----UUGUCAUagCUGu -5' |
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| 21135 | 5' | -53.6 | NC_004775.1 | + | 36983 | 0.8 | 0.092915 |
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Target: 5'- cUGGCCGCaUGGGAuGCAGgauuUAUCGACGa -3' miRNA: 3'- uACCGGCG-ACCCUuUGUC----AUAGCUGU- -5' |
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| 21135 | 5' | -53.6 | NC_004775.1 | + | 30795 | 1.07 | 0.001121 |
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Target: 5'- aAUGGCCGCUGGGAAACAGUAUCGACAa -3' miRNA: 3'- -UACCGGCGACCCUUUGUCAUAGCUGU- -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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