miRNA: 3'- -CCC-CCGgCCGUGA------UUCGGUuaaguac -5'
miRNA: 3'- -CCCccGGCCGUGAUU-CGGUUaaguac -5'
miRNA: 3'- -CCCCCGGC-CGUG--AUUCGgUuaaGUac -5'
miRNA: 3'- -CCCCCGGCCGUGAUUCGGUUAAGUAC- -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 | |||||||
| 2513 | 5' | -54 | NC_001454.1 | + | 17131 | 0.66 | 0.649404 |
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Target: 5'- uGGGaGGCgGGCGCUgcugcaGAGCCAc------ -3' miRNA: 3'- -CCC-CCGgCCGUGA------UUCGGUuaaguac -5' |
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| 2513 | 5' | -54 | NC_001454.1 | + | 11243 | 0.66 | 0.637837 |
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Target: 5'- cGGGcaCCGGCACUGAuGCCGAa----- -3' miRNA: 3'- -CCCccGGCCGUGAUU-CGGUUaaguac -5' |
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| 2513 | 5' | -54 | NC_001454.1 | + | 16393 | 0.66 | 0.614696 |
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Target: 5'- uGGGGGCCGuGCGCcuUGAGCgGcggCGg- -3' miRNA: 3'- -CCCCCGGC-CGUG--AUUCGgUuaaGUac -5' |
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| 2513 | 5' | -54 | NC_001454.1 | + | 25539 | 1.1 | 0.000587 |
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Target: 5'- uGGGGGCCGGCACUAAGCCAAUUCAUGc -3' miRNA: 3'- -CCCCCGGCCGUGAUUCGGUUAAGUAC- -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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