miRNA: 3'- -CAGCG-----AGuCcUG-UGGUGGCCGaCGUG- -5'
miRNA: 3'- caGCGaGUCCUG------UGGUGGCCGa-----CGUg -5'
miRNA: 3'- caGCgAGU---CCUGUgGUGGCCGaCGUG- -5'
miRNA: 3'- cAGCGAGUCCu---GUG-GuGGCCGACGuG- -5'
miRNA: 3'- -CAGCGAGUCCUGUGGUGGCCGACGUG- -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 | |||||||
| 3477 | 3' | -59.2 | NC_001609.1 | + | 5533 | 0.66 | 0.144638 |
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Target: 5'- cGUCGCguuuuUCcGcACgGCCACCGGCgGCACg -3' miRNA: 3'- -CAGCG-----AGuCcUG-UGGUGGCCGaCGUG- -5' |
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| 3477 | 3' | -59.2 | NC_001609.1 | + | 8162 | 0.66 | 0.140273 |
|
Target: 5'- -aCGCaCGGGACaccuccACCACCGGCagacggGCAg -3' miRNA: 3'- caGCGaGUCCUG------UGGUGGCCGa-----CGUg -5' |
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| 3477 | 3' | -59.2 | NC_001609.1 | + | 7548 | 0.67 | 0.109488 |
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Target: 5'- -cCGgUCAgccGGGCAgCACCGGUgGCGCg -3' miRNA: 3'- caGCgAGU---CCUGUgGUGGCCGaCGUG- -5' |
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| 3477 | 3' | -59.2 | NC_001609.1 | + | 8643 | 0.69 | 0.074967 |
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Target: 5'- aUUGCUCGGGuucuCACgC-CCGGCUGC-Cg -3' miRNA: 3'- cAGCGAGUCCu---GUG-GuGGCCGACGuG- -5' |
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| 3477 | 3' | -59.2 | NC_001609.1 | + | 9800 | 1.1 | 0.000029 |
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Target: 5'- cGUCGCUCAGGACACCACCGGCUGCACg -3' miRNA: 3'- -CAGCGAGUCCUGUGGUGGCCGACGUG- -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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