miRNA: 3'- aaCgaCGCG-ACUGGU-UACUGGG--GCCa -5'
miRNA: 3'- aaCgACGCGACUGgUUAC--------UGGGGCCa -5'
miRNA: 3'- aACGACG--CGACugG-UUACuGGGGCCa -5'
miRNA: 3'- -AACGACGCGACUGGUUACUGGGGCCA- -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 | |||||||
| 1081 | 5' | -58.1 | NC_000929.1 | + | 10859 | 0.66 | 0.376996 |
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Target: 5'- -cGgaGCGCgUGACCAgAUGGCCCgcUGGg -3' miRNA: 3'- aaCgaCGCG-ACUGGU-UACUGGG--GCCa -5' |
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| 1081 | 5' | -58.1 | NC_000929.1 | + | 26445 | 0.67 | 0.350381 |
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Target: 5'- -gGgUGCGCUGAUgGAUGcucuugauGCUCCGGg -3' miRNA: 3'- aaCgACGCGACUGgUUAC--------UGGGGCCa -5' |
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| 1081 | 5' | -58.1 | NC_000929.1 | + | 31771 | 0.69 | 0.237808 |
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Target: 5'- gUGCUGUacGCUGugCuGAUG-CCCCGGc -3' miRNA: 3'- aACGACG--CGACugG-UUACuGGGGCCa -5' |
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| 1081 | 5' | -58.1 | NC_000929.1 | + | 18473 | 1.05 | 0.000457 |
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Target: 5'- cUUGCUGCGCUGACCAAUGACCCCGGUg -3' miRNA: 3'- -AACGACGCGACUGGUUACUGGGGCCA- -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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