miRNA: 3'- ggAUUUGG--AGuCGcCUUUuGGGUGGG- -5'
miRNA: 3'- ggauUUGGAguCGCCUuu--UGGGUGGG- -5'
miRNA: 3'- -GGAU-UUGGAg---UCGCCU---UUUGGG---UGGG- -5'
miRNA: 3'- -GGAUUUGGAGUCGCCUUUUGGGUGGG- -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 | |||||||
| 3493 | 3' | -50.3 | NC_001612.1 | + | 2167 | 0.66 | 0.403294 |
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Target: 5'- -gUGAGCCgaUCuGCuGGGAcCCCACCCc -3' miRNA: 3'- ggAUUUGG--AGuCGcCUUUuGGGUGGG- -5' |
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| 3493 | 3' | -50.3 | NC_001612.1 | + | 7 | 0.66 | 0.392375 |
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Target: 5'- ---cAGCCU--GUGGGuuguACCCACCCa -3' miRNA: 3'- ggauUUGGAguCGCCUuu--UGGGUGGG- -5' |
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| 3493 | 3' | -50.3 | NC_001612.1 | + | 2602 | 0.71 | 0.202995 |
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Target: 5'- cUCUGcAGCCUgcaaGGCGGGgacGAGCCCgguGCCCa -3' miRNA: 3'- -GGAU-UUGGAg---UCGCCU---UUUGGG---UGGG- -5' |
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| 3493 | 3' | -50.3 | NC_001612.1 | + | 5760 | 1.16 | 0.00007 |
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Target: 5'- uCCUAAACCUCAGCGGAAAACCCACCCa -3' miRNA: 3'- -GGAUUUGGAGUCGCCUUUUGGGUGGG- -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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