miRNA: 3'- -CCGG--------GGCCAGG---UCGC--CUCGGUCGAGC- -5'
miRNA: 3'- -CCGGGGcca-GGUC--GCCUCGGU---CGAGC- -5'
miRNA: 3'- cCGGGGCCaGGUCGCc-UCGG-UCgAGC- -5'
miRNA: 3'- -CCG-GGGCCAGGUCGCCuCG-GUCGagc -5'
miRNA: 3'- -CCGGGGCCAGGUCGCCUCGGUCGAGC- -5'
Results 21 - 25 of 25 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 | |||||||
| 7171 | 5' | -63.8 | NC_001900.1 | + | 17475 | 0.71 | 0.136598 |
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Target: 5'- cGGCUcauggaguCCGGUCUgcaGGCGauGGGUCAGCUCGg -3' miRNA: 3'- -CCGG--------GGCCAGG---UCGC--CUCGGUCGAGC- -5' |
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| 7171 | 5' | -63.8 | NC_001900.1 | + | 28830 | 0.72 | 0.116467 |
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Target: 5'- uGGCCCCcgaaCCAGacCGGAGCCAuguGCUCGa -3' miRNA: 3'- -CCGGGGcca-GGUC--GCCUCGGU---CGAGC- -5' |
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| 7171 | 5' | -63.8 | NC_001900.1 | + | 22251 | 0.72 | 0.113394 |
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Target: 5'- cGCCCCGGcCCAGCGauGGCCgAGgUCGu -3' miRNA: 3'- cCGGGGCCaGGUCGCc-UCGG-UCgAGC- -5' |
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| 7171 | 5' | -63.8 | NC_001900.1 | + | 18175 | 0.75 | 0.064076 |
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Target: 5'- cGGCuCCUGGUCCAGCGGuGUgCAGCa-- -3' miRNA: 3'- -CCG-GGGCCAGGUCGCCuCG-GUCGagc -5' |
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| 7171 | 5' | -63.8 | NC_001900.1 | + | 40503 | 1.1 | 0.000123 |
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Target: 5'- uGGCCCCGGUCCAGCGGAGCCAGCUCGa -3' miRNA: 3'- -CCGGGGCCAGGUCGCCUCGGUCGAGC- -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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