miRNA: 3'- cUGGGCCGgU--UCGACCuu----CUCCGguu -5'
miRNA: 3'- -CUGGG--------CCGGUUCGaCCUuCUCCGGUu -5'
miRNA: 3'- -CUGGGCCGGU-UCGACCuuCUCCGgUu -5'
miRNA: 3'- -CUG-GGCCGGUUCG---ACCUUCUc---CGGUU- -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 | |||||||
| 23407 | 5' | -59.8 | NC_005259.1 | + | 30672 | 0.66 | 0.45918 |
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Target: 5'- cGCCCGGCgAguAGCUGGccaccuGAGGCa-- -3' miRNA: 3'- cUGGGCCGgU--UCGACCuu----CUCCGguu -5' |
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| 23407 | 5' | -59.8 | NC_005259.1 | + | 65689 | 0.69 | 0.31182 |
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Target: 5'- cGGCCCgacgagcgGGCCGAGUaGGAcGAGGUCAc -3' miRNA: 3'- -CUGGG--------CCGGUUCGaCCUuCUCCGGUu -5' |
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| 23407 | 5' | -59.8 | NC_005259.1 | + | 29948 | 0.71 | 0.231268 |
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Target: 5'- cGGCCCGGUCGcGGCUGGu-GGGGCgGg -3' miRNA: 3'- -CUGGGCCGGU-UCGACCuuCUCCGgUu -5' |
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| 23407 | 5' | -59.8 | NC_005259.1 | + | 21091 | 0.72 | 0.2086 |
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Target: 5'- cGACgCUGGCCAAGCucaUGGAAGAaaaaGCCGAg -3' miRNA: 3'- -CUG-GGCCGGUUCG---ACCUUCUc---CGGUU- -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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