miRNA: 3'- -GGGgUCCCUCUCu-AAGCUACG----GGAGu -5'
miRNA: 3'- -GGGGUCCCUCuCUaa----GCUa--CGGG---AGU- -5'
miRNA: 3'- ggGGUCCCUCUCuaa-------GCUACGGGagu -5'
miRNA: 3'- ggGGUCCCUCUCuaa------GCUACGGGagu -5'
miRNA: 3'- -GGGGUCCCUCUCUAAGCUACGGGAGU- -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 | |||||||
| 2898 | 5' | -56 | NC_001493.1 | + | 102154 | 0.7 | 0.697716 |
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Target: 5'- aCCCgAGGGGGAGccUUCGGUGCgaccCCUUc -3' miRNA: 3'- -GGGgUCCCUCUCu-AAGCUACG----GGAGu -5' |
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| 2898 | 5' | -56 | NC_001493.1 | + | 54861 | 0.7 | 0.667195 |
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Target: 5'- gCCCCGGGGAGcGAguggugCGAgccGCCCcggUCAg -3' miRNA: 3'- -GGGGUCCCUCuCUaa----GCUa--CGGG---AGU- -5' |
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| 2898 | 5' | -56 | NC_001493.1 | + | 121055 | 0.71 | 0.634359 |
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Target: 5'- -aCCAGGGAGAGuuuccggucaCGGUGCCCa-- -3' miRNA: 3'- ggGGUCCCUCUCuaa-------GCUACGGGagu -5' |
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| 2898 | 5' | -56 | NC_001493.1 | + | 5500 | 0.72 | 0.595361 |
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Target: 5'- -aCCAGGGAGAGuuuccgucaCGGUGCCCa-- -3' miRNA: 3'- ggGGUCCCUCUCuaa------GCUACGGGagu -5' |
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| 2898 | 5' | -56 | NC_001493.1 | + | 23424 | 1.1 | 0.002288 |
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Target: 5'- gCCCCAGGGAGAGAUUCGAUGCCCUCAc -3' miRNA: 3'- -GGGGUCCCUCUCUAAGCUACGGGAGU- -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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