miRNA: 3'- uaGCa----CACGAGCGCGGcuUAGuGCUG- -5'
miRNA: 3'- -UAGC---ACA-Cga-GCGCGGCU--------------UAGUGCUG- -5'
miRNA: 3'- uAGCACA------------CGAGCGCGGCuuagUGCUG- -5'
miRNA: 3'- -UAGCAcACGaGCG----CGGCUUAGUGCUG- -5'
Results 21 - 24 of 24 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 | |||||||
| 26019 | 3' | -55 | NC_005342.2 | + | 36097 | 0.66 | 0.666875 |
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Target: 5'- -aCGacaagGUGCUCGCGCCc-GUCuCGGCc -3' miRNA: 3'- uaGCa----CACGAGCGCGGcuUAGuGCUG- -5' |
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| 26019 | 3' | -55 | NC_005342.2 | + | 34993 | 0.66 | 0.674679 |
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Target: 5'- cGUCGauuUGUcGaugCGCGCCGAgcugaucaaccgcuAUCGCGACa -3' miRNA: 3'- -UAGC---ACA-Cga-GCGCGGCU--------------UAGUGCUG- -5' |
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| 26019 | 3' | -55 | NC_005342.2 | + | 4134 | 0.66 | 0.678018 |
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Target: 5'- uUCGUGUacagcgcgccgcGCUCGUGCUGca--GCGGCg -3' miRNA: 3'- uAGCACA------------CGAGCGCGGCuuagUGCUG- -5' |
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| 26019 | 3' | -55 | NC_005342.2 | + | 31572 | 0.65 | 0.700155 |
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Target: 5'- gGUUGUuUGCcUGCaucuGCUGAAUCGCGGCa -3' miRNA: 3'- -UAGCAcACGaGCG----CGGCUUAGUGCUG- -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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