miRNA: 3'- -CCACUGCCCGaa-----------CAGCCUCGCGucuu -5'
miRNA: 3'- cCACUGCCCGaa------CaGCCUCGCGUcuu -5'
miRNA: 3'- ccaCUGCCCG----AACAgCCUCGC-GUCUu -5'
miRNA: 3'- ccaCUGCCCGaaCaGCCUC-GCGUCuu -5'
miRNA: 3'- -CCaCUGCCCGAACAG-----CCU--CGCGuCUU- -5'
Results 41 - 45 of 45 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 | |||||||
| 13960 | 5' | -57.2 | NC_003521.1 | + | 221965 | 0.71 | 0.689416 |
|
Target: 5'- gGGUGGCGGGCcgccgguguaccaGUCGGAGUGCc--- -3' miRNA: 3'- -CCACUGCCCGaa-----------CAGCCUCGCGucuu -5' |
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| 13960 | 5' | -57.2 | NC_003521.1 | + | 226342 | 0.7 | 0.771061 |
|
Target: 5'- cGUGACGGGCcggccgcgGcCGGGGCGCGc-- -3' miRNA: 3'- cCACUGCCCGaa------CaGCCUCGCGUcuu -5' |
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| 13960 | 5' | -57.2 | NC_003521.1 | + | 227689 | 0.67 | 0.896598 |
|
Target: 5'- --gGGCGGGCgucgUUGUgGGGGUGuCAGAu -3' miRNA: 3'- ccaCUGCCCG----AACAgCCUCGC-GUCUu -5' |
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| 13960 | 5' | -57.2 | NC_003521.1 | + | 238468 | 0.66 | 0.920135 |
|
Target: 5'- --cGGCGGGCggGgCGGAGaCGCGGc- -3' miRNA: 3'- ccaCUGCCCGaaCaGCCUC-GCGUCuu -5' |
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| 13960 | 5' | -57.2 | NC_003521.1 | + | 239185 | 0.71 | 0.69528 |
|
Target: 5'- cGG-GACGGGCUUGUCuucggGGAugGCGCcGAGc -3' miRNA: 3'- -CCaCUGCCCGAACAG-----CCU--CGCGuCUU- -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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