miRNA: 3'- aCGCCC---UCAGCGa---------C-CCGCGCUGCUga -5'
miRNA: 3'- aCGcC-CUCA-GCGaCCCGCGCuGCUGa -5'
miRNA: 3'- aCGCCC-UCAGC--GACCCGCGCUGcUGA- -5'
miRNA: 3'- -ACGCCCuc---AGCGACCCGCGCUG-------CUGA- -5'
miRNA: 3'- -ACGCCCUCAGCGACCCGCGCUGCUGA- -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 | |||||||
| 479 | 5' | -61.5 | AC_000013.1 | + | 29057 | 0.67 | 0.31697 |
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Target: 5'- cGCGGGuacGGUUGCgaaucgagacGcGGCGCGACGGg- -3' miRNA: 3'- aCGCCC---UCAGCGa---------C-CCGCGCUGCUga -5' |
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| 479 | 5' | -61.5 | AC_000013.1 | + | 12286 | 0.67 | 0.280769 |
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Target: 5'- gGCaGaGGGUaCGCgGGGCGCGcCGGCg -3' miRNA: 3'- aCGcC-CUCA-GCGaCCCGCGCuGCUGa -5' |
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| 479 | 5' | -61.5 | AC_000013.1 | + | 5466 | 0.73 | 0.121746 |
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Target: 5'- gGUGGGuAGUUGguCUGGGCGCGGCaGCUu -3' miRNA: 3'- aCGCCC-UCAGC--GACCCGCGCUGcUGA- -5' |
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| 479 | 5' | -61.5 | AC_000013.1 | + | 24701 | 0.74 | 0.102997 |
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Target: 5'- uUGCGGGcuuuuUUGCUGGGCGCGGCaccccgaGACUu -3' miRNA: 3'- -ACGCCCuc---AGCGACCCGCGCUG-------CUGA- -5' |
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| 479 | 5' | -61.5 | AC_000013.1 | + | 9945 | 1.06 | 0.000304 |
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Target: 5'- gUGCGGGAGUCGCUGGGCGCGACGACUc -3' miRNA: 3'- -ACGCCCUCAGCGACCCGCGCUGCUGA- -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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