miRNA: 3'- -CCUCcuCGCGGCGG-------CAGU----AGGUG---UUG- -5'
miRNA: 3'- -CCU-------CCUcGCGGCGGCAGuaGGugUUG- -5'
miRNA: 3'- cCUCCUCG--------CGGC-GGCAGUAgGUGU--UG- -5'
miRNA: 3'- -CCUCCUCGCGGCGGCAGUAGGUGUUG- -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 | |||||||
| 28199 | 3' | -57.3 | NC_005891.1 | + | 19583 | 0.66 | 0.519549 |
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Target: 5'- gGGAGccGCGCCGCCauuaaauGUCAauguUCCGCcugGACu -3' miRNA: 3'- -CCUCcuCGCGGCGG-------CAGU----AGGUG---UUG- -5' |
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| 28199 | 3' | -57.3 | NC_005891.1 | + | 12422 | 0.66 | 0.498471 |
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Target: 5'- aGGAauuccuuGGAcUGCCGCCGUCc-CCugAACa -3' miRNA: 3'- -CCU-------CCUcGCGGCGGCAGuaGGugUUG- -5' |
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| 28199 | 3' | -57.3 | NC_005891.1 | + | 33840 | 0.68 | 0.39143 |
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Target: 5'- cGAGGAGUcaaugcucGCCGcCCGUCGUaCGCAccGCa -3' miRNA: 3'- cCUCCUCG--------CGGC-GGCAGUAgGUGU--UG- -5' |
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| 28199 | 3' | -57.3 | NC_005891.1 | + | 10628 | 1.11 | 0.000315 |
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Target: 5'- cGGAGGAGCGCCGCCGUCAUCCACAACc -3' miRNA: 3'- -CCUCCUCGCGGCGGCAGUAGGUGUUG- -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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