miRNA: 3'- -CCUUCaagaCAG----------UCUCCGGUugAGGU- -5'
miRNA: 3'- -CCU---UCAAGA--CA-GUCUCCGGUUGaGgu -5'
miRNA: 3'- -CCuuCaagaCAGUCUCCGGU--UGAGGU- -5'
miRNA: 3'- -CCUUCAAGACAGUCUCCGGUUGAGGU- -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 | |||||||
| 31607 | 5' | -51.4 | NC_006879.1 | + | 7970 | 0.66 | 0.782987 |
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Target: 5'- uGGAAGaggcGUCcaggcguagaGGAGGCCGugUCCGc -3' miRNA: 3'- -CCUUCaagaCAG----------UCUCCGGUugAGGU- -5' |
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| 31607 | 5' | -51.4 | NC_006879.1 | + | 9735 | 0.66 | 0.761492 |
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Target: 5'- gGGAggcGGUUCUcgGUaCAGGGGCCAGC-Cg- -3' miRNA: 3'- -CCU---UCAAGA--CA-GUCUCCGGUUGaGgu -5' |
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| 31607 | 5' | -51.4 | NC_006879.1 | + | 24664 | 0.68 | 0.6589 |
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Target: 5'- cGGggGc---GUCGGGGGCCGggGCUUCGg -3' miRNA: 3'- -CCuuCaagaCAGUCUCCGGU--UGAGGU- -5' |
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| 31607 | 5' | -51.4 | NC_006879.1 | + | 1473 | 1.12 | 0.000874 |
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Target: 5'- uGGAAGUUCUGUCAGAGGCCAACUCCAg -3' miRNA: 3'- -CCUUCAAGACAGUCUCCGGUUGAGGU- -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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