miRNA: 3'- uaGAGCU--------UUGCAGCGcaagGUAGCCC- -5'
miRNA: 3'- -UAGAGCuUUGCAGC-GCAagGUaGCCC- -5'
miRNA: 3'- -UAGAGCUUUGCAGCG---CAAGgua--GCCC- -5'
miRNA: 3'- -UAGa---GCUu-UGCAGCGCAa-----GGUAGCCC- -5'
miRNA: 3'- -UAGAGCUUUGCAGCGCAAGGUAGCCC- -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 | |||||||
| 14701 | 3' | -51.6 | NC_003529.1 | + | 20756 | 0.66 | 0.993759 |
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Target: 5'- -gCUCGAucgcguucGGCGUCGCcga-CAUUGGGg -3' miRNA: 3'- uaGAGCU--------UUGCAGCGcaagGUAGCCC- -5' |
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| 14701 | 3' | -51.6 | NC_003529.1 | + | 144988 | 0.66 | 0.991748 |
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Target: 5'- uGUCUCGcAGCGUCGaCGU--CGcCGGGg -3' miRNA: 3'- -UAGAGCuUUGCAGC-GCAagGUaGCCC- -5' |
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| 14701 | 3' | -51.6 | NC_003529.1 | + | 21283 | 0.68 | 0.97023 |
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Target: 5'- aGUUUCGAAGCGUUGCaacGUUCgugcgCGGGc -3' miRNA: 3'- -UAGAGCUUUGCAGCG---CAAGgua--GCCC- -5' |
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| 14701 | 3' | -51.6 | NC_003529.1 | + | 67818 | 0.73 | 0.831712 |
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Target: 5'- gGUCgaacCGAuuGCGUCGCGUcgccggCCGUUGGGa -3' miRNA: 3'- -UAGa---GCUu-UGCAGCGCAa-----GGUAGCCC- -5' |
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| 14701 | 3' | -51.6 | NC_003529.1 | + | 44313 | 1.08 | 0.010002 |
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Target: 5'- cAUCUCGAAACGUCGCGUUCCAUCGGGc -3' miRNA: 3'- -UAGAGCUUUGCAGCGCAAGGUAGCCC- -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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