miRNA: 3'- -CGCGGUC-UAaaaCGCAACa---------CCA-------AAGG- -5'
miRNA: 3'- -CGCGGUCuaaaa-----CGCaaca---CCAAAGG- -5'
miRNA: 3'- -CGCGGUcuaaaAC-GCAACACCAAa-----GG- -5'
miRNA: 3'- cgCGGUCUAaaACGCAacaCCaaAGG- -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 | |||||||
| 2734 | 3' | -46.8 | NC_001491.2 | + | 44147 | 0.66 | 0.999952 |
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Target: 5'- gGCGCCGGcAUg--GCGUUGgauaguucucGGUagucaucUUCCg -3' miRNA: 3'- -CGCGGUC-UAaaaCGCAACa---------CCA-------AAGG- -5' |
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| 2734 | 3' | -46.8 | NC_001491.2 | + | 43098 | 0.66 | 0.999944 |
|
Target: 5'- cGCGCCAGcacgguaaagGUGgccagggGGUUUCCg -3' miRNA: 3'- -CGCGGUCuaaaa-----CGCaaca---CCAAAGG- -5' |
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| 2734 | 3' | -46.8 | NC_001491.2 | + | 122900 | 0.67 | 0.999518 |
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Target: 5'- cGCGCCGucca-UGcCGUUGUGGUUcaguggCCg -3' miRNA: 3'- -CGCGGUcuaaaAC-GCAACACCAAa-----GG- -5' |
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| 2734 | 3' | -46.8 | NC_001491.2 | + | 58822 | 0.68 | 0.999398 |
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Target: 5'- -gGCCAGGUgcUGCGUgc-GGgcUCCc -3' miRNA: 3'- cgCGGUCUAaaACGCAacaCCaaAGG- -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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