miRNA: 3'- cGGUCGCGcACGGGcACGCGugGGCA- -5'
miRNA: 3'- cGGUCGCGCACgGGCA--------------C-GCGUGGGCa -5'
miRNA: 3'- cGGUCGCGCA--------------CGGGCaCG-CGUGGGCa -5'
miRNA: 3'- -CGGUCGCGCACGGGCACGCGUGGGCA- -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 | |||||||
| 333 | 5' | -63.3 | AC_000010.1 | + | 17860 | 0.66 | 0.221433 |
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Target: 5'- cUCAGUGCcUGCCC-UGUGCugCUGUu -3' miRNA: 3'- cGGUCGCGcACGGGcACGCGugGGCA- -5' |
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| 333 | 5' | -63.3 | AC_000010.1 | + | 15501 | 0.69 | 0.139872 |
|
Target: 5'- uCCAGCGCGUGaCCGUuacugacgccagacGcCGCACCUGc -3' miRNA: 3'- cGGUCGCGCACgGGCA--------------C-GCGUGGGCa -5' |
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| 333 | 5' | -63.3 | AC_000010.1 | + | 11049 | 0.7 | 0.122007 |
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Target: 5'- aCUGGCGCGUcugggugcaccaucGCCCGaGCgGCACCCGc -3' miRNA: 3'- cGGUCGCGCA--------------CGGGCaCG-CGUGGGCa -5' |
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| 333 | 5' | -63.3 | AC_000010.1 | + | 16151 | 1.07 | 0.000122 |
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Target: 5'- gGCCAGCGCGUGCCCGUGCGCACCCGUc -3' miRNA: 3'- -CGGUCGCGCACGGGCACGCGUGGGCA- -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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