miRNA: 3'- aCG-UC-GCGACG---CUCaugACGCCGGCA- -5'
miRNA: 3'- aCGU-CGCG-ACGCUCAUGaCgCCGgca -5'
miRNA: 3'- aCGUCg--CGaCGCUCaUGACGCCGGca -5'
miRNA: 3'- -ACGUCGCga-CGC---UCAUGACG---CCGGCa -5'
miRNA: 3'- -ACGUCGCGACGCUCAUGACGCCGGCA- -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 | |||||||
| 311 | 3' | -59.9 | AC_000010.1 | + | 31006 | 0.66 | 0.341804 |
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Target: 5'- gGCgAGuCGCUGUucuGAGg--UGCGGCCGUc -3' miRNA: 3'- aCG-UC-GCGACG---CUCaugACGCCGGCA- -5' |
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| 311 | 3' | -59.9 | AC_000010.1 | + | 3268 | 0.66 | 0.333519 |
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Target: 5'- gGUAcGCGCaUGCGAGUGCgGgGGCa-- -3' miRNA: 3'- aCGU-CGCG-ACGCUCAUGaCgCCGgca -5' |
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| 311 | 3' | -59.9 | AC_000010.1 | + | 30897 | 0.67 | 0.286923 |
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Target: 5'- aGCAGgaaGCaGCGAGgGCUGUGGCUc- -3' miRNA: 3'- aCGUCg--CGaCGCUCaUGACGCCGGca -5' |
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| 311 | 3' | -59.9 | AC_000010.1 | + | 17179 | 0.68 | 0.239222 |
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Target: 5'- uUGCGGCGacgGCGggaAGUACUGCuccGGCUGc -3' miRNA: 3'- -ACGUCGCga-CGC---UCAUGACG---CCGGCa -5' |
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| 311 | 3' | -59.9 | AC_000010.1 | + | 8023 | 1.06 | 0.000253 |
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Target: 5'- gUGCAGCGCUGCGAGUACUGCGGCCGUc -3' miRNA: 3'- -ACGUCGCGACGCUCAUGACGCCGGCA- -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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