miRNA: 3'- -UUGGGuCCaAAGCCCGU----CCGGCGGcu -5'
miRNA: 3'- -UUGGGuCCaaaGCC-CGUCCGgCGGcu -5'
miRNA: 3'- uUGGGUCCaaa-GcCCGuCCGGCGGCU- -5'
miRNA: 3'- uUG-GGUCCAaa---GCCCGUCCGGCGGCu -5'
miRNA: 3'- -UUGGGUCCAAAGCCCGUCCGGCGGCU- -5'
Results 21 - 25 of 25 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 | |||||||
| 26565 | 3' | -61.2 | NC_005357.1 | + | 9944 | 0.71 | 0.154712 |
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Target: 5'- cGGCCUuGGaUUCGGGCGcaucGGCCGCCc- -3' miRNA: 3'- -UUGGGuCCaAAGCCCGU----CCGGCGGcu -5' |
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| 26565 | 3' | -61.2 | NC_005357.1 | + | 37064 | 0.71 | 0.150552 |
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Target: 5'- uAACCCuGGgcgCGGuGCAGGCgGCCa- -3' miRNA: 3'- -UUGGGuCCaaaGCC-CGUCCGgCGGcu -5' |
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| 26565 | 3' | -61.2 | NC_005357.1 | + | 11587 | 0.76 | 0.05782 |
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Target: 5'- cGCCCAGGgccgCcGGCuGGCCGCCGGg -3' miRNA: 3'- uUGGGUCCaaa-GcCCGuCCGGCGGCU- -5' |
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| 26565 | 3' | -61.2 | NC_005357.1 | + | 19481 | 0.79 | 0.038567 |
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Target: 5'- uGCgCCAGGUgccggUGGGCAGGCCGCUGc -3' miRNA: 3'- uUG-GGUCCAaa---GCCCGUCCGGCGGCu -5' |
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| 26565 | 3' | -61.2 | NC_005357.1 | + | 19964 | 1.06 | 0.000287 |
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Target: 5'- cAACCCAGGUUUCGGGCAGGCCGCCGAu -3' miRNA: 3'- -UUGGGUCCAAAGCCCGUCCGGCGGCU- -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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