miRNA: 3'- -GCGGUacaUGUa-CAGCuCCAGCaaGU- -5'
miRNA: 3'- gCGGUacaUGUa-----CAGCUCCAGCaAGU- -5'
miRNA: 3'- -GCGGU------------ACAuGUACAGcUCCAGCA-AGU- -5'
miRNA: 3'- -GCGGUa--CAUGU------ACAGCUCCAGCaagu -5'
miRNA: 3'- -GCGGUACAUGUACAGCUCCAGCAAGU- -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 | |||||||
| 31726 | 3' | -50.6 | NC_006938.1 | + | 2742 | 0.66 | 0.948016 |
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Target: 5'- aCGCCAg--ACAggGUCGuGGUCGacCAg -3' miRNA: 3'- -GCGGUacaUGUa-CAGCuCCAGCaaGU- -5' |
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| 31726 | 3' | -50.6 | NC_006938.1 | + | 15649 | 0.67 | 0.926999 |
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Target: 5'- gGCCAgc-GCGgucggcGUCGAGGUCGgUCGg -3' miRNA: 3'- gCGGUacaUGUa-----CAGCUCCAGCaAGU- -5' |
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| 31726 | 3' | -50.6 | NC_006938.1 | + | 44915 | 0.67 | 0.908231 |
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Target: 5'- cCGCCAucaucuggugguUGUcCGUGUCcGGGUCGUcUCGg -3' miRNA: 3'- -GCGGU------------ACAuGUACAGcUCCAGCA-AGU- -5' |
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| 31726 | 3' | -50.6 | NC_006938.1 | + | 35760 | 0.69 | 0.846099 |
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Target: 5'- cCGCCAcgcGUACGcguucuUGUCGGGGUCGc--- -3' miRNA: 3'- -GCGGUa--CAUGU------ACAGCUCCAGCaagu -5' |
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| 31726 | 3' | -50.6 | NC_006938.1 | + | 52696 | 1.09 | 0.003828 |
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Target: 5'- uCGCCAUGUACAUGUCGAGGUCGUUCAc -3' miRNA: 3'- -GCGGUACAUGUACAGCUCCAGCAAGU- -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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