miRNA: 3'- -AGUGAGC-AACGCGCU-CGUU---UCG-CAGG- -5'
miRNA: 3'- -AGUGAGCa--ACgCGCuCGUuUCGCAGG- -5'
miRNA: 3'- -AGUGAGCAA------CGCGC-----------UCG-UUUCGCAgG- -5'
miRNA: 3'- aGUGAGCAaCGcGCUCGUu----UCGCAGg -5'
miRNA: 3'- -AGUGAGCAACGCGCUCGUUUCGCAGG- -5'
Results 1 - 5 of 5 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 | |||||||
| 12707 | 5' | -52.4 | NC_003349.1 | + | 46147 | 0.66 | 0.974318 |
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Target: 5'- uUCACUCGaUUGUGUGAcGUGAuauGGCuGUUCa -3' miRNA: 3'- -AGUGAGC-AACGCGCU-CGUU---UCG-CAGG- -5' |
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| 12707 | 5' | -52.4 | NC_003349.1 | + | 51738 | 0.66 | 0.968498 |
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Target: 5'- gUCAUUCGcaaUG-GCGuGCAcGGCGUUCa -3' miRNA: 3'- -AGUGAGCa--ACgCGCuCGUuUCGCAGG- -5' |
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| 12707 | 5' | -52.4 | NC_003349.1 | + | 128531 | 0.67 | 0.954167 |
|
Target: 5'- uUCACUUGUUcguugaGCGCGuuguuauuuuuGGCuAAAGCGUgCa -3' miRNA: 3'- -AGUGAGCAA------CGCGC-----------UCG-UUUCGCAgG- -5' |
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| 12707 | 5' | -52.4 | NC_003349.1 | + | 91434 | 0.68 | 0.930797 |
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Target: 5'- gUACUCGUcGC-CGAGCAugaccAGUGUCa -3' miRNA: 3'- aGUGAGCAaCGcGCUCGUu----UCGCAGg -5' |
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| 12707 | 5' | -52.4 | NC_003349.1 | + | 35808 | 1.14 | 0.002723 |
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Target: 5'- uUCACUCGUUGCGCGAGCAAAGCGUCCa -3' miRNA: 3'- -AGUGAGCAACGCGCUCGUUUCGCAGG- -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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