miRNA: 3'- ggAGCAGCCGUGGCCG---CUGCUa-GAGU- -5'
miRNA: 3'- -GGAGCAGCCGUGGC---CGCU---------GCUAGAGu -5'
miRNA: 3'- -GGAGCaGCCGU-----GGC-CGCuGCUAGAGU- -5'
miRNA: 3'- gGAGCAGCCGU---GGCCG---CUGCUAGagu -5'
Results 41 - 44 of 44 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 | |||||||
| 23464 | 3' | -57.4 | NC_005259.1 | + | 58735 | 0.73 | 0.303557 |
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Target: 5'- -gUCGUUGGCACCGGCaccGGCGAagUUCGg -3' miRNA: 3'- ggAGCAGCCGUGGCCG---CUGCUa-GAGU- -5' |
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| 23464 | 3' | -57.4 | NC_005259.1 | + | 67792 | 0.74 | 0.262694 |
|
Target: 5'- aCCUUGUUGGCACCGcguGCGAgcuugagccCGAUCUUg -3' miRNA: 3'- -GGAGCAGCCGUGGC---CGCU---------GCUAGAGu -5' |
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| 23464 | 3' | -57.4 | NC_005259.1 | + | 67042 | 0.75 | 0.243996 |
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Target: 5'- cCCUCGaCGGCGagcacCCGuGCGcCGAUCUCAa -3' miRNA: 3'- -GGAGCaGCCGU-----GGC-CGCuGCUAGAGU- -5' |
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| 23464 | 3' | -57.4 | NC_005259.1 | + | 60551 | 0.75 | 0.232154 |
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Target: 5'- gCUCGUCGGCAugcCCGGUgccGACGGUCa-- -3' miRNA: 3'- gGAGCAGCCGU---GGCCG---CUGCUAGagu -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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