miRNA: 3'- ucUGCCGUGCAugUGg-----GCAGcUGCGG- -5'
miRNA: 3'- uCUGCCg-UGCa--UGUGGGCa--GCUGCGG- -5'
miRNA: 3'- uCugCCGUG-----CAUGUGGGC------------AGCUGCGG- -5'
miRNA: 3'- -UCUGCCGUGCAUGUGGGCAGCUGCGG- -5'
miRNA: 3'- -UCUGCCG--UGCA--UGUGg-GCAGcUGCGG- -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 |
| Predicted miRNA align pattern | |||||||
| 11288 | 3' | -57 | NC_003083.1 | + | 51616 | 0.67 | 0.825137 |
|
Target: 5'- -uACGGUGCGUugGCaauuagCGUC-ACGCCa -3' miRNA: 3'- ucUGCCGUGCAugUGg-----GCAGcUGCGG- -5' |
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| 11288 | 3' | -57 | NC_003083.1 | + | 118026 | 0.7 | 0.623116 |
|
Target: 5'- uGGCGGagGCGgagGCACCUGaugCGGCGUCa -3' miRNA: 3'- uCUGCCg-UGCa--UGUGGGCa--GCUGCGG- -5' |
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| 11288 | 3' | -57 | NC_003083.1 | + | 44373 | 0.71 | 0.552526 |
|
Target: 5'- uGugGGCGCcugcaGUGCGCCCGcacgguuauuugUCGGUGCCa -3' miRNA: 3'- uCugCCGUG-----CAUGUGGGC------------AGCUGCGG- -5' |
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| 11288 | 3' | -57 | NC_003083.1 | + | 72972 | 1.12 | 0.001318 |
|
Target: 5'- cAGACGGCACGUACACCCGUCGACGCCg -3' miRNA: 3'- -UCUGCCGUGCAUGUGGGCAGCUGCGG- -5' |
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| 11288 | 3' | -57 | NC_003083.1 | + | 82618 | 0.66 | 0.864965 |
|
Target: 5'- cGGACGGCaaACGUucGCGCagCGUUuGCGUCg -3' miRNA: 3'- -UCUGCCG--UGCA--UGUGg-GCAGcUGCGG- -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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