miRNA: 3'- -UGUCCUUUUCGUCCGUUCGGGCGUGU- -5'
miRNA: 3'- -UGuCCUUUUCGUCCgUUCGGG-------------CGUGU- -5'
miRNA: 3'- -UGUCCUUUUCG---UCCGuUCGG--GCGUGU- -5'
miRNA: 3'- -UGUCCU-UUUCG----UCCGUUCGggCgUGu -5'
Results 1 - 4 of 4 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 | |||||||
| 3156 | 5' | -54.7 | NC_001499.1 | + | 2889 | 1.08 | 0.000031 |
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Target: 5'- cACAGGAAAAGCAGGCAAGCCCGCACAg -3' miRNA: 3'- -UGUCCUUUUCGUCCGUUCGGGCGUGU- -5' |
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| 3156 | 5' | -54.7 | NC_001499.1 | + | 2931 | 0.74 | 0.027412 |
|
Target: 5'- gGCcGGGGAGGCAGGgGGGCCCacaaagacaaaauGCACGa -3' miRNA: 3'- -UGuCCUUUUCGUCCgUUCGGG-------------CGUGU- -5' |
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| 3156 | 5' | -54.7 | NC_001499.1 | + | 3775 | 0.74 | 0.031754 |
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Target: 5'- gGCAGGAAAGGUgcaGGGC-AGCUggUGCACAa -3' miRNA: 3'- -UGUCCUUUUCG---UCCGuUCGG--GCGUGU- -5' |
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| 3156 | 5' | -54.7 | NC_001499.1 | + | 2891 | 0.67 | 0.105314 |
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Target: 5'- gGCAGGAgGAGGCggcgGGGCAGGCuuGaGCu -3' miRNA: 3'- -UGUCCU-UUUCG----UCCGUUCGggCgUGu -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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