miRNA: 3'- cGUUAUCUUAAA---AUA---------------ACGUgGUCCGC- -5'
miRNA: 3'- -CGUUAUCUUaaaauaaCGUgGUCCGc -5'
miRNA: 3'- -CGUUauCuuAAaa--UAACGuGGUCCGC- -5'
miRNA: 3'- -CGUUAUCUUAAAAUAACGUGGUCCGC- -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 | |||||||
| 9401 | 3' | -42.4 | NC_002513.1 | + | 7481 | 0.68 | 0.996002 |
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Target: 5'- uCAAUGGAGUUUaacUGUauagauugugguguuUGCAgCAGGUGa -3' miRNA: 3'- cGUUAUCUUAAA---AUA---------------ACGUgGUCCGC- -5' |
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| 9401 | 3' | -42.4 | NC_002513.1 | + | 16433 | 0.68 | 0.994628 |
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Target: 5'- gGCAGUAGAAgcacua-GCGgCGGGCu -3' miRNA: 3'- -CGUUAUCUUaaaauaaCGUgGUCCGc -5' |
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| 9401 | 3' | -42.4 | NC_002513.1 | + | 24320 | 0.69 | 0.989811 |
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Target: 5'- aGCAGgcGggUUcaugAUUGCuCUAGGCGu -3' miRNA: 3'- -CGUUauCuuAAaa--UAACGuGGUCCGC- -5' |
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| 9401 | 3' | -42.4 | NC_002513.1 | + | 24220 | 1.16 | 0.004893 |
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Target: 5'- cGCAAUAGAAUUUUAUUGCACCAGGCGg -3' miRNA: 3'- -CGUUAUCUUAAAAUAACGUGGUCCGC- -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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