miRNA: 3'- gCGC-CCUCGGCAG----UGCCauGUGCCAG- -5'
miRNA: 3'- gcGCCCUCGGCAGUGcca-UGUGCCAg -5'
miRNA: 3'- -GCGCCCUCGgCAGugC---CAu-GUGCCaG- -5'
miRNA: 3'- -GCgCCCUCGGcaguGCCA--UGUGCCAG- -5'
miRNA: 3'- gC-GCCCUCGgCAgU---GCCAUG--UGCCAG- -5'
Results 1 - 5 of 5 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 | |||||||
| 22148 | 3' | -59.2 | NC_004927.1 | + | 75453 | 0.66 | 0.624387 |
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Target: 5'- uGUGuGGGGCCGUUguguACGGc-UAUGGUCg -3' miRNA: 3'- gCGC-CCUCGGCAG----UGCCauGUGCCAG- -5' |
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| 22148 | 3' | -59.2 | NC_004927.1 | + | 31897 | 0.66 | 0.624387 |
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Target: 5'- -uCGGGGGCUGUUACauccGCACGGUg -3' miRNA: 3'- gcGCCCUCGGCAGUGcca-UGUGCCAg -5' |
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| 22148 | 3' | -59.2 | NC_004927.1 | + | 14603 | 0.67 | 0.572657 |
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Target: 5'- uCGUGGGAGCgGUCugGagcGUucCACGG-Cg -3' miRNA: 3'- -GCGCCCUCGgCAGugC---CAu-GUGCCaG- -5' |
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| 22148 | 3' | -59.2 | NC_004927.1 | + | 61736 | 0.67 | 0.54208 |
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Target: 5'- cCGaGGGGGCCuaccCGGUcuACGCGGUCg -3' miRNA: 3'- -GCgCCCUCGGcaguGCCA--UGUGCCAG- -5' |
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| 22148 | 3' | -59.2 | NC_004927.1 | + | 50394 | 0.69 | 0.417789 |
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Target: 5'- uGcCGGGAGCgGUgGuggUGGUGCugGCGGUCa -3' miRNA: 3'- gC-GCCCUCGgCAgU---GCCAUG--UGCCAG- -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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