miRNA: 3'- -CGGAcCCUGcGUU---UCGGGuuCGACCG- -5'
miRNA: 3'- cGGaCCCUgCGUuu--CGGGuu---CGACCg -5'
miRNA: 3'- -CGGACccUGCGuuuc-G-GGUUCGACCG- -5'
miRNA: 3'- -CGGA-CCCUG-CG-UUUCG-GGUU-CGACCG- -5'
miRNA: 3'- -CGGaCCCU---GCGUUUCGGG---------UUCG--ACCG- -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 | |||||||
| 20836 | 3' | -56.9 | NC_004689.1 | + | 42178 | 0.66 | 0.698251 |
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Target: 5'- uGUCUuGGAC-CGGaucGGCCUgcGCUGGCg -3' miRNA: 3'- -CGGAcCCUGcGUU---UCGGGuuCGACCG- -5' |
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| 20836 | 3' | -56.9 | NC_004689.1 | + | 54726 | 0.66 | 0.666216 |
|
Target: 5'- aCCgGGGAgGCAuguuGCCCucgacGCUGGg -3' miRNA: 3'- cGGaCCCUgCGUuu--CGGGuu---CGACCg -5' |
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| 20836 | 3' | -56.9 | NC_004689.1 | + | 13370 | 0.66 | 0.655463 |
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Target: 5'- uGCCUGacGCGCcauuuCgCCAAGCUGGCc -3' miRNA: 3'- -CGGACccUGCGuuuc-G-GGUUCGACCG- -5' |
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| 20836 | 3' | -56.9 | NC_004689.1 | + | 32106 | 0.67 | 0.590839 |
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Target: 5'- uGCUUcGGGACgGCgAAGGCuCCGGuGUUGGCc -3' miRNA: 3'- -CGGA-CCCUG-CG-UUUCG-GGUU-CGACCG- -5' |
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| 20836 | 3' | -56.9 | NC_004689.1 | + | 12933 | 0.68 | 0.527384 |
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Target: 5'- uGCCgGGGAugaUGCGAAGCCCugcaucgacGGGUucUGGUg -3' miRNA: 3'- -CGGaCCCU---GCGUUUCGGG---------UUCG--ACCG- -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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