miRNA: 3'- guGCU-CuuCGACCAC-----------CGGGCAC-UCCG- -5'
miRNA: 3'- guGCUcUUCGAccACCGGGCACUCCG- -5'
miRNA: 3'- gUGCuCUuCGACCACCG--GGCACU-CCG- -5'
miRNA: 3'- -GUGCUCUUCGACCACCGGGCACUCCG- -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 | |||||||
| 18010 | 3' | -58 | NC_004665.1 | + | 28426 | 0.66 | 0.434831 |
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Target: 5'- -cCGGuGguGCUGGUGccucguucgcuGCCCGUGuGGGCa -3' miRNA: 3'- guGCU-CuuCGACCAC-----------CGGGCAC-UCCG- -5' |
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| 18010 | 3' | -58 | NC_004665.1 | + | 3990 | 0.69 | 0.281719 |
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Target: 5'- -uCGAcAGGCUc-UGGCCCGUGAGGUu -3' miRNA: 3'- guGCUcUUCGAccACCGGGCACUCCG- -5' |
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| 18010 | 3' | -58 | NC_004665.1 | + | 35961 | 0.7 | 0.274596 |
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Target: 5'- gAUG-GAcGCUGGUGGUuuCCGUGGuGGCu -3' miRNA: 3'- gUGCuCUuCGACCACCG--GGCACU-CCG- -5' |
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| 18010 | 3' | -58 | NC_004665.1 | + | 11611 | 1.1 | 0.000277 |
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Target: 5'- uCACGAGAAGCUGGUGGCCCGUGAGGCc -3' miRNA: 3'- -GUGCUCUUCGACCACCGGGCACUCCG- -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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