miRNA: 3'- -GCCCCACGUACUUCACUUAGGGGAAC- -5'
miRNA: 3'- -GCCCCA--CGUA-CUUC-ACU----UAGGGGaac -5'
miRNA: 3'- gCCCCACG-------------UACUUCACuu-AGGGGaac -5'
miRNA: 3'- -GCCCCaCGuaCUuC-ACUUAGGGGaac -5'
miRNA: 3'- -GC-CCcACGUA-----CUUCACUUAGGGGaac -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 | |||||||
| 12667 | 5' | -52.9 | NC_003345.1 | + | 64314 | 1.1 | 0.002319 |
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Target: 5'- cCGGGGUGCAUGAAGUGAAUCCCCUUGa -3' miRNA: 3'- -GCCCCACGUACUUCACUUAGGGGAAC- -5' |
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| 12667 | 5' | -52.9 | NC_003345.1 | + | 42311 | 0.7 | 0.715785 |
|
Target: 5'- aCGGGGUagGCAUcGAGGcUGAuguuGUCCCCg-- -3' miRNA: 3'- -GCCCCA--CGUA-CUUC-ACU----UAGGGGaac -5' |
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| 12667 | 5' | -52.9 | NC_003345.1 | + | 42841 | 0.66 | 0.883044 |
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Target: 5'- uGGGGUGUcguacagaggucgGUGAGGUGuucUUCCCa-- -3' miRNA: 3'- gCCCCACG-------------UACUUCACuu-AGGGGaac -5' |
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| 12667 | 5' | -52.9 | NC_003345.1 | + | 8812 | 0.66 | 0.883792 |
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Target: 5'- cCGGGG-GUggGAcGaUGAAUCCCCg-- -3' miRNA: 3'- -GCCCCaCGuaCUuC-ACUUAGGGGaac -5' |
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| 12667 | 5' | -52.9 | NC_003345.1 | + | 6934 | 0.66 | 0.891125 |
|
Target: 5'- uCGuGGuUGUAUcccucGAAGUGAAUCCCCg-- -3' miRNA: 3'- -GC-CCcACGUA-----CUUCACUUAGGGGaac -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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