miRNA: 3'- cAGU-UCGGCG-------------UCAGUGUCugUUGuGG- -5'
miRNA: 3'- caGUUCgGCGUCAGUGUCUGU---------UGugG- -5'
miRNA: 3'- caGUUCGGC-GUCaGUGUCUGUUGUGg -5'
miRNA: 3'- -CAGuUCGGCGUCAGUGUcuGUUgUGG- -5'
miRNA: 3'- -CAGUUCGGCGUCAGUGUCUGUUGUGG- -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 | |||||||
| 57 | 5' | -51.6 | AC_000003.1 | + | 29580 | 0.66 | 0.726401 |
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Target: 5'- cUCAgGGCUGUgcgaaggcuuucuAGUCACAGugGGC-CCa -3' miRNA: 3'- cAGU-UCGGCG-------------UCAGUGUCugUUGuGG- -5' |
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| 57 | 5' | -51.6 | AC_000003.1 | + | 16618 | 0.71 | 0.420293 |
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Target: 5'- -aCAGG-CGCGGUCACGGGCAuauuagaugACugCg -3' miRNA: 3'- caGUUCgGCGUCAGUGUCUGU---------UGugG- -5' |
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| 57 | 5' | -51.6 | AC_000003.1 | + | 15762 | 0.72 | 0.410194 |
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Target: 5'- -gCAGGUCGuCGG-CGCGGACGGCGCa -3' miRNA: 3'- caGUUCGGC-GUCaGUGUCUGUUGUGg -5' |
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| 57 | 5' | -51.6 | AC_000003.1 | + | 11857 | 0.75 | 0.249045 |
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Target: 5'- uGUU-AGCCGCAGUCACGucCAAgGCCu -3' miRNA: 3'- -CAGuUCGGCGUCAGUGUcuGUUgUGG- -5' |
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| 57 | 5' | -51.6 | AC_000003.1 | + | 17211 | 1.12 | 0.000632 |
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Target: 5'- gGUCAAGCCGCAGUCACAGACAACACCu -3' miRNA: 3'- -CAGUUCGGCGUCAGUGUCUGUUGUGG- -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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