miRNA: 3'- -CGUCGGCAUgCCUUCAc--GUCaGCUUU- -5'
miRNA: 3'- -CGUCGGCAuGCCuuCA--------------CGUCAGCuuu -5'
miRNA: 3'- -CGUCGGCAUGCCUucaCGUcaGCUUu -5'
miRNA: 3'- -CGUCGGCAUGCCUUCACGUCAGCUUU- -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 | |||||||
| 20769 | 5' | -52.7 | NC_004689.1 | + | 52147 | 0.66 | 0.8785 |
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Target: 5'- uGUAGCCGUA-GGAGGUcauCAG-CGAAAc -3' miRNA: 3'- -CGUCGGCAUgCCUUCAc--GUCaGCUUU- -5' |
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| 20769 | 5' | -52.7 | NC_004689.1 | + | 47251 | 0.66 | 0.876166 |
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Target: 5'- uGUAGUCGU-CGGggGUcugacucggcggggGCAGUCGc-- -3' miRNA: 3'- -CGUCGGCAuGCCuuCA--------------CGUCAGCuuu -5' |
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| 20769 | 5' | -52.7 | NC_004689.1 | + | 57346 | 0.7 | 0.639582 |
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Target: 5'- gGCAGCCGUACGGAuc-GCAc-CGAAu -3' miRNA: 3'- -CGUCGGCAUGCCUucaCGUcaGCUUu -5' |
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| 20769 | 5' | -52.7 | NC_004689.1 | + | 16381 | 1.08 | 0.002645 |
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Target: 5'- uGCAGCCGUACGGAAGUGCAGUCGAAAc -3' miRNA: 3'- -CGUCGGCAUGCCUUCACGUCAGCUUU- -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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