miRNA: 3'- cUGUCA---------UGUCUGcu------UGGGCUGCCACa -5'
miRNA: 3'- cUGUCAUgUCUGCUUGGGcugCCACa -5'
miRNA: 3'- -CUGuC-AUGUCuGCUUGG-GCUGCCACa -5'
miRNA: 3'- cuGUCAugUCUGCUUGGGCUGC--CACA- -5'
miRNA: 3'- -CUGUCAUGUCUGCUUGGGCUGCCACA- -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 | |||||||
| 2653 | 3' | -53.3 | NC_001491.2 | + | 31983 | 0.66 | 0.976225 |
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Target: 5'- aACGGUcgccgggccACGGGCuccucaucACCCGGCGGUGg -3' miRNA: 3'- cUGUCA---------UGUCUGcu------UGGGCUGCCACa -5' |
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| 2653 | 3' | -53.3 | NC_001491.2 | + | 69298 | 0.67 | 0.957426 |
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Target: 5'- aACGGUAaAGGCGAACCCug-GGUGg -3' miRNA: 3'- cUGUCAUgUCUGCUUGGGcugCCACa -5' |
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| 2653 | 3' | -53.3 | NC_001491.2 | + | 2488 | 0.67 | 0.953516 |
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Target: 5'- gGGCcGcUGCAG-CGGGCCgCGAUGGUGg -3' miRNA: 3'- -CUGuC-AUGUCuGCUUGG-GCUGCCACa -5' |
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| 2653 | 3' | -53.3 | NC_001491.2 | + | 20003 | 0.68 | 0.935493 |
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Target: 5'- -cCAGU--AGACGAAUCCGGCGauGUGUg -3' miRNA: 3'- cuGUCAugUCUGCUUGGGCUGC--CACA- -5' |
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| 2653 | 3' | -53.3 | NC_001491.2 | + | 96923 | 1.08 | 0.005972 |
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Target: 5'- cGACAGUACAGACGAACCCGACGGUGUg -3' miRNA: 3'- -CUGUCAUGUCUGCUUGGGCUGCCACA- -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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