miRNA: 3'- gCGAC---GCCC--UUUUGUCCCGUaaCCUC- -5'
miRNA: 3'- -GCGACGCCCUUUUGUCCCGUAACCUC- -5'
miRNA: 3'- -GCGaCGCCcuUUUGUCCCGua--ACCUc -5'
miRNA: 3'- gCGACGCCCU------------UUUG-UCCCGuaACCUC- -5'
miRNA: 3'- gCGACG-CCCUuuug-UCCCGUAAC-CUC- -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 |
| Predicted miRNA align pattern | |||||||
| 6053 | 5' | -53.8 | NC_001815.1 | + | 1080 | 0.73 | 0.06967 |
|
Target: 5'- aGCUGguuCGGGuaGAGACGGGGCA--GGAGg -3' miRNA: 3'- gCGAC---GCCC--UUUUGUCCCGUaaCCUC- -5' |
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| 6053 | 5' | -53.8 | NC_001815.1 | + | 1843 | 1.08 | 0.000101 |
|
Target: 5'- cCGCUGCGGGAAAACAGGGCAUUGGAGc -3' miRNA: 3'- -GCGACGCCCUUUUGUCCCGUAACCUC- -5' |
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| 6053 | 5' | -53.8 | NC_001815.1 | + | 1859 | 0.67 | 0.224447 |
|
Target: 5'- cCGCaGCGG--AAGCAGGGCugcgUGGGc -3' miRNA: 3'- -GCGaCGCCcuUUUGUCCCGua--ACCUc -5' |
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| 6053 | 5' | -53.8 | NC_001815.1 | + | 4350 | 0.72 | 0.085215 |
|
Target: 5'- uGCUGUGGGGuggccccugaggAAACaAGGGCccUGGAGu -3' miRNA: 3'- gCGACGCCCU------------UUUG-UCCCGuaACCUC- -5' |
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| 6053 | 5' | -53.8 | NC_001815.1 | + | 6854 | 0.67 | 0.231428 |
|
Target: 5'- gGUUGCuGGGGuuugaAGGGUAUUGuGAGa -3' miRNA: 3'- gCGACG-CCCUuuug-UCCCGUAAC-CUC- -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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