miRNA: 3'- -ACGG-GCC-GCU---UC-GAGGCCa----CGAUGGG- -5'
miRNA: 3'- aCGGGCCGCU---------UCG-------------AGGCCA-CGAuGGG- -5'
miRNA: 3'- aCGgGCCGCUUCGa-GGCCACGa-UG-GG- -5'
miRNA: 3'- -ACGGGCCGCUUCGAGGCCACGAUGGG- -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 | |||||||
| 11743 | 3' | -60.4 | NC_003215.1 | + | 8707 | 0.67 | 0.105965 |
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Target: 5'- gUGCCaUGGaCGAaacAGuCUCCGGaggugGCUACCUu -3' miRNA: 3'- -ACGG-GCC-GCU---UC-GAGGCCa----CGAUGGG- -5' |
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| 11743 | 3' | -60.4 | NC_003215.1 | + | 7461 | 0.74 | 0.029913 |
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Target: 5'- cGCCCGGCGGcccguccuuGGCcguugcaggccacUCCGGUgGCU-CCCg -3' miRNA: 3'- aCGGGCCGCU---------UCG-------------AGGCCA-CGAuGGG- -5' |
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| 11743 | 3' | -60.4 | NC_003215.1 | + | 5352 | 0.78 | 0.013414 |
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Target: 5'- cGCgCGGCGGAGCgaCCGGUGCcgGCgCCg -3' miRNA: 3'- aCGgGCCGCUUCGa-GGCCACGa-UG-GG- -5' |
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| 11743 | 3' | -60.4 | NC_003215.1 | + | 6022 | 1.11 | 0.000018 |
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Target: 5'- cUGCCCGGCGAAGCUCCGGUGCUACCCg -3' miRNA: 3'- -ACGGGCCGCUUCGAGGCCACGAUGGG- -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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