miRNA: 3'- -UGUCGGCGCGAaa-----UAgCUUGAa-------AUGU- -5'
miRNA: 3'- -UGUCGGCGCGAaa-UagCUUGaaaUGU- -5'
miRNA: 3'- -UGUCGGCGCGAaa-UAGCU------UG-AAAUGU- -5'
miRNA: 3'- -UGUCGGCGCGAAAUAGCUUGAAAUGU- -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 | |||||||
| 31613 | 5' | -47 | NC_006879.1 | + | 23257 | 0.68 | 0.887988 |
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Target: 5'- gGCGGCCGUGCUggucaccGUgGAGCUggaaugccUGCAa -3' miRNA: 3'- -UGUCGGCGCGAaa-----UAgCUUGAa-------AUGU- -5' |
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| 31613 | 5' | -47 | NC_006879.1 | + | 25782 | 0.68 | 0.879701 |
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Target: 5'- cGCAGCCGCGCUccgGggGAAUcg-GCAc -3' miRNA: 3'- -UGUCGGCGCGAaa-UagCUUGaaaUGU- -5' |
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| 31613 | 5' | -47 | NC_006879.1 | + | 7866 | 0.8 | 0.297856 |
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Target: 5'- gGCGGCCGCGCUgagGUCGGcgggaaGCgUUUGCAa -3' miRNA: 3'- -UGUCGGCGCGAaa-UAGCU------UG-AAAUGU- -5' |
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| 31613 | 5' | -47 | NC_006879.1 | + | 7109 | 1.1 | 0.003408 |
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Target: 5'- gACAGCCGCGCUUUAUCGAACUUUACAu -3' miRNA: 3'- -UGUCGGCGCGAAAUAGCUUGAAAUGU- -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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