miRNA: 3'- gAAGUuGCCUU---UGCCGCGGU--------CCGUUu -5'
miRNA: 3'- -GAa--GU-UGCCU--UUGCC-GCGGUCCGUuu -5'
miRNA: 3'- gaaGUUGCCUUUGCcgCGGUCCGUuu -5'
miRNA: 3'- gAAGUUGCCUu-------UGCCGCGGU-------CCGUUU- -5'
miRNA: 3'- -GAAGUUGCCUUUGCCGCGGUCCGUUU- -5'
Results 21 - 25 of 25 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 | |||||||
| 22921 | 3' | -53 | NC_005137.2 | + | 39820 | 0.72 | 0.672239 |
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Target: 5'- gUUCAcCGGAAaguGCGGCGCCGcuuagccuGGCAGc -3' miRNA: 3'- gAAGUuGCCUU---UGCCGCGGU--------CCGUUu -5' |
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| 22921 | 3' | -53 | NC_005137.2 | + | 6984 | 0.73 | 0.661587 |
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Target: 5'- gCUgcgCAcACGGAcgAGCGGuCGCCGGGCAc- -3' miRNA: 3'- -GAa--GU-UGCCU--UUGCC-GCGGUCCGUuu -5' |
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| 22921 | 3' | -53 | NC_005137.2 | + | 43224 | 0.75 | 0.544686 |
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Target: 5'- --gCGACGGAAAUGuaGCCGGGCGc- -3' miRNA: 3'- gaaGUUGCCUUUGCcgCGGUCCGUuu -5' |
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| 22921 | 3' | -53 | NC_005137.2 | + | 62997 | 0.75 | 0.533263 |
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Target: 5'- uUUCGGCGGAcccaugguGCGGCGCCGgcgugucGGCAAGc -3' miRNA: 3'- gAAGUUGCCUu-------UGCCGCGGU-------CCGUUU- -5' |
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| 22921 | 3' | -53 | NC_005137.2 | + | 19513 | 1.06 | 0.006453 |
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Target: 5'- uCUUCAACGGAAACGGCGCCAGGCAAAc -3' miRNA: 3'- -GAAGUUGCCUUUGCCGCGGUCCGUUU- -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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