miRNA: 3'- -GCCGc---AGCAGCU---------UA-GCG-----UCCACGAGC- -5'
miRNA: 3'- gCC-GCAGCaGCUU------AGCG--------------UCCACGAGC- -5'
miRNA: 3'- -GCCGCAGCaGCUUA-----GCGUccACGAGC- -5'
miRNA: 3'- gCCGCAGC-AGCU---UAGCGUcc-----ACGAGC- -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 | |||||||
| 12229 | 3' | -56 | NC_003309.1 | + | 22367 | 0.66 | 0.686244 |
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Target: 5'- gCGGCcugcUCGUCGGcaagccgauGUgCGCcgaucAGGUGCUCGa -3' miRNA: 3'- -GCCGc---AGCAGCU---------UA-GCG-----UCCACGAGC- -5' |
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| 12229 | 3' | -56 | NC_003309.1 | + | 46496 | 0.67 | 0.650614 |
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Target: 5'- uGGcCGUCGgCGGGaacugcUCGCgcauagcgcgguugAGGUGCUCGa -3' miRNA: 3'- gCC-GCAGCaGCUU------AGCG--------------UCCACGAGC- -5' |
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| 12229 | 3' | -56 | NC_003309.1 | + | 6278 | 0.69 | 0.494121 |
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Target: 5'- uCGGCGUCGaCGAGUuugucCGCA--UGCUCGu -3' miRNA: 3'- -GCCGCAGCaGCUUA-----GCGUccACGAGC- -5' |
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| 12229 | 3' | -56 | NC_003309.1 | + | 46565 | 0.7 | 0.473972 |
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Target: 5'- uGGCGUCGaUCGAcggAUCGCAauuccccUGCUCGu -3' miRNA: 3'- gCCGCAGC-AGCU---UAGCGUcc-----ACGAGC- -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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