miRNA: 3'- cauCUGCCGg--CUCaGGGCGGUa------GCUC- -5'
miRNA: 3'- caUCUGcCGGCUCa------GGGCGGUa--GCUc -5'
miRNA: 3'- caUCUGCCGGCuCAGgg--CGGUAGCuc -5'
miRNA: 3'- caUCU--GCCG-GC---UCAGGGC---GGUAGCUC- -5'
miRNA: 3'- -CAUCUGCcGGCuCAgGGCGG-------UAGCUC- -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 |
| Predicted miRNA align pattern | |||||||
| 11418 | 3' | -58.3 | NC_003085.1 | + | 9228 | 0.68 | 0.425199 |
|
Target: 5'- --cGGCGGCgaaGAG-CCCGCCAccaauggCGAGg -3' miRNA: 3'- cauCUGCCGg--CUCaGGGCGGUa------GCUC- -5' |
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| 11418 | 3' | -58.3 | NC_003085.1 | + | 8483 | 0.67 | 0.444182 |
|
Target: 5'- -aAGGCcGCCGAGgcgcuggCCCGCCAguaCGAc -3' miRNA: 3'- caUCUGcCGGCUCa------GGGCGGUa--GCUc -5' |
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| 11418 | 3' | -58.3 | NC_003085.1 | + | 7758 | 0.73 | 0.204623 |
|
Target: 5'- -aGGACGGCCGuGUCaucaGCCAUCGu- -3' miRNA: 3'- caUCUGCCGGCuCAGgg--CGGUAGCuc -5' |
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| 11418 | 3' | -58.3 | NC_003085.1 | + | 5364 | 0.68 | 0.425199 |
|
Target: 5'- -gGGAcuCGGCgCGuccGGUCCCGucaCCGUCGAGg -3' miRNA: 3'- caUCU--GCCG-GC---UCAGGGC---GGUAGCUC- -5' |
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| 11418 | 3' | -58.3 | NC_003085.1 | + | 810 | 0.67 | 0.482515 |
|
Target: 5'- gGUGGACGuCCGcGUgCCGCCgcaggucGUCGAGc -3' miRNA: 3'- -CAUCUGCcGGCuCAgGGCGG-------UAGCUC- -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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