miRNA: 3'- cGGGGAGAG---UUGGGAGGACGcGCacg -5'
miRNA: 3'- -CgGGGAgAGUUGG-GAGGaCGCGcACG- -5'
miRNA: 3'- -CGGGGaga-GUuGGGAGG-------ACGCGCACG- -5'
miRNA: 3'- -CGGGGAGAGUUGGGAGGACGCGCACG- -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 | |||||||
| 13019 | 3' | -59 | NC_003390.1 | + | 12121 | 0.66 | 0.459691 |
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Target: 5'- cCUCCUCUUcauAACCCUCCUGUuCGa-- -3' miRNA: 3'- cGGGGAGAG---UUGGGAGGACGcGCacg -5' |
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| 13019 | 3' | -59 | NC_003390.1 | + | 6877 | 0.67 | 0.421433 |
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Target: 5'- gGgCCCUgUUAGCCgCUCUaGCGCcUGCa -3' miRNA: 3'- -CgGGGAgAGUUGG-GAGGaCGCGcACG- -5' |
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| 13019 | 3' | -59 | NC_003390.1 | + | 38817 | 0.67 | 0.420501 |
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Target: 5'- gGCUCCaaggCAcCUCUCCcggcguaUGCGCGUGCg -3' miRNA: 3'- -CGGGGaga-GUuGGGAGG-------ACGCGCACG- -5' |
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| 13019 | 3' | -59 | NC_003390.1 | + | 9189 | 1.13 | 0.000176 |
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Target: 5'- gGCCCCUCUCAACCCUCCUGCGCGUGCa -3' miRNA: 3'- -CGGGGAGAGUUGGGAGGACGCGCACG- -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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