miRNA: 3'- -UGGuuCGGA--ACCCUCUGGG---AGGgAUC- -5'
miRNA: 3'- ugGUUCGGAa--------CCCU-----CUGGGAGGGauc -5'
miRNA: 3'- -UGGuu-CGGAACCcu-CUgGGAGGGAUC- -5'
miRNA: 3'- -UGGUUCGGAACCCUCUGGGAGGGAUC- -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 | |||||||
| 6191 | 3' | -57.6 | NC_001837.1 | + | 6815 | 0.66 | 0.151922 |
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Target: 5'- uGCCu-GUCUcuUGGGAGGCCCcaaUCUgUAGg -3' miRNA: 3'- -UGGuuCGGA--ACCCUCUGGG---AGGgAUC- -5' |
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| 6191 | 3' | -57.6 | NC_001837.1 | + | 7824 | 0.66 | 0.142703 |
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Target: 5'- -aCAGGUCUggugauuggGGGAgguauGACCCUCCCa-- -3' miRNA: 3'- ugGUUCGGAa--------CCCU-----CUGGGAGGGauc -5' |
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| 6191 | 3' | -57.6 | NC_001837.1 | + | 3971 | 0.71 | 0.063796 |
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Target: 5'- cGCCucuGUCUUGGucuGAgCCUCCCUAGg -3' miRNA: 3'- -UGGuu-CGGAACCcu-CUgGGAGGGAUC- -5' |
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| 6191 | 3' | -57.6 | NC_001837.1 | + | 3912 | 1.09 | 0.00004 |
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Target: 5'- uACCAAGCCUUGGGAGACCCUCCCUAGg -3' miRNA: 3'- -UGGUUCGGAACCCUCUGGGAGGGAUC- -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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