miRNA: 3'- -UGCC----------UCCCGCUCA--GGACG--GCUUGUUA- -5'
miRNA: 3'- uGCCU-CCCGcu---CAGGACG-GCUUGUUa -5'
miRNA: 3'- ugcCUCCCGCU---------CAGGACGGC-----UUGUUa -5'
miRNA: 3'- uGCcuCCCgCUCA-GGACGGCUUGUUA- -5'
miRNA: 3'- -UGCCUCCCGCUCAGGACGGCUUGUUA- -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 | |||||||
| 12594 | 5' | -57.6 | NC_003345.1 | + | 68488 | 0.66 | 0.667743 |
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Target: 5'- cGCGGggccacccguGGGGCGGGUaaUCUGCauCGGACGGUc -3' miRNA: 3'- -UGCC----------UCCCGCUCA--GGACG--GCUUGUUA- -5' |
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| 12594 | 5' | -57.6 | NC_003345.1 | + | 73780 | 0.67 | 0.582442 |
|
Target: 5'- cCGGAcGGGUuccacGUCCUGCuCGAACAGc -3' miRNA: 3'- uGCCU-CCCGcu---CAGGACG-GCUUGUUa -5' |
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| 12594 | 5' | -57.6 | NC_003345.1 | + | 24690 | 0.69 | 0.49953 |
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Target: 5'- --cGAGGGCGAccucccggcGUCCUGCCGccgagGACGAc -3' miRNA: 3'- ugcCUCCCGCU---------CAGGACGGC-----UUGUUa -5' |
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| 12594 | 5' | -57.6 | NC_003345.1 | + | 23615 | 0.69 | 0.49953 |
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Target: 5'- uCGucGGG-GAGUgCCUGCCGAGCGGUc -3' miRNA: 3'- uGCcuCCCgCUCA-GGACGGCUUGUUA- -5' |
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| 12594 | 5' | -57.6 | NC_003345.1 | + | 10840 | 1.05 | 0.001642 |
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Target: 5'- gACGGAGGGCGAGUCCUGCCGAACAAUc -3' miRNA: 3'- -UGCCUCCCGCUCAGGACGGCUUGUUA- -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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