miRNA: 3'- gUUGGG-CGGCaGCAAG---------------UCGU-CCCCCa -5'
miRNA: 3'- guugGGCGGCaGCaaGUCG---UCCCCCa -5'
miRNA: 3'- guuGGGcGgCAGC-AAGUCGUCCCCCA- -5'
miRNA: 3'- -GUUGGGCGGCAGCAAGUCGUCCCCCA- -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 | |||||||
| 485 | 5' | -59.5 | AC_000013.1 | + | 10767 | 0.66 | 0.429636 |
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Target: 5'- aAACCCaGUCGcCGUUCuggucuugggugaccAGCAuGGGGGg -3' miRNA: 3'- gUUGGG-CGGCaGCAAG---------------UCGU-CCCCCa -5' |
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| 485 | 5' | -59.5 | AC_000013.1 | + | 7448 | 0.66 | 0.407278 |
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Target: 5'- ---gCCGCCG-CGagCAGCcugAGGGGGg -3' miRNA: 3'- guugGGCGGCaGCaaGUCG---UCCCCCa -5' |
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| 485 | 5' | -59.5 | AC_000013.1 | + | 20474 | 0.69 | 0.29964 |
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Target: 5'- --uCCCcUgGUCGuUUCGGUAGGGGGUg -3' miRNA: 3'- guuGGGcGgCAGC-AAGUCGUCCCCCA- -5' |
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| 485 | 5' | -59.5 | AC_000013.1 | + | 17750 | 1.07 | 0.000409 |
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Target: 5'- cCAACCCGCCGUCGUUCAGCAGGGGGUg -3' miRNA: 3'- -GUUGGGCGGCAGCAAGUCGUCCCCCA- -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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