miRNA: 3'- gGAGCGGUcaa-GGCGaa--GCCGGCUGc -5'
miRNA: 3'- -GGAgCGGUCa---AGgCGaaGC-CGGCUGC- -5'
miRNA: 3'- -GGAG-CGGUca-AGgCGAa-GCCGGCUGc -5'
miRNA: 3'- gGAGCGGU----CAAGGCGaAG--------CC-GGCUGc -5'
miRNA: 3'- -GGA-GC-GGUCaagGCGaAGCCGGCUGC- -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 | |||||||
| 22555 | 3' | -57.8 | NC_005091.1 | + | 9283 | 0.66 | 0.610661 |
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Target: 5'- gCUCGCCGcuggCCGCcgacCGGCUGGCc -3' miRNA: 3'- gGAGCGGUcaa-GGCGaa--GCCGGCUGc -5' |
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| 22555 | 3' | -57.8 | NC_005091.1 | + | 50385 | 0.66 | 0.621286 |
|
Target: 5'- aCCU-GCCGGgugaUCgGCcgCGaGCCGACGa -3' miRNA: 3'- -GGAgCGGUCa---AGgCGaaGC-CGGCUGC- -5' |
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| 22555 | 3' | -57.8 | NC_005091.1 | + | 50288 | 0.66 | 0.631919 |
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Target: 5'- gUCUCaGCCAucgUCgGCUcgCGGCCGAUc -3' miRNA: 3'- -GGAG-CGGUca-AGgCGAa-GCCGGCUGc -5' |
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| 22555 | 3' | -57.8 | NC_005091.1 | + | 12195 | 0.66 | 0.653177 |
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Target: 5'- gCUCGCCGugccGUUCCGCaUCaucaagcaGGcCCGGCu -3' miRNA: 3'- gGAGCGGU----CAAGGCGaAG--------CC-GGCUGc -5' |
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| 22555 | 3' | -57.8 | NC_005091.1 | + | 28078 | 0.66 | 0.653177 |
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Target: 5'- aCCUaCGaUCAGgu-CGUgUCGGCCGGCGa -3' miRNA: 3'- -GGA-GC-GGUCaagGCGaAGCCGGCUGC- -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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