miRNA: 3'- -CCACUGC-CCGaaCAGCcu------------CGCGUCUU- -5'
miRNA: 3'- -CCAC--------UGCCCGaaCaGCCUCGCG--UCUU- -5'
miRNA: 3'- -CCACUGCCCGAACAGCCUCGCGUCUU- -5'
miRNA: 3'- ccaCUGc--CCGaACAGCCUCGCGUCUU- -5'
miRNA: 3'- ccaCUgCCCGaaCAGCCUC-GCGUCUU- -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 | + | 58885 | 0.68 | 0.855653 |
|
Target: 5'- aGGUGGCGcGGCgaGUCGcagcccgucuccauGCGCAGGAu -3' miRNA: 3'- -CCACUGC-CCGaaCAGCcu------------CGCGUCUU- -5' |
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| 13960 | 5' | -57.2 | NC_003521.1 | + | 55351 | 0.66 | 0.914583 |
|
Target: 5'- aGGUGaucgccgaGCGGGUgcGcCGGAGCGCcuAGGGg -3' miRNA: 3'- -CCAC--------UGCCCGaaCaGCCUCGCG--UCUU- -5' |
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| 13960 | 5' | -57.2 | NC_003521.1 | + | 29055 | 1.08 | 0.00371 |
|
Target: 5'- cGGUGACGGGCUUGUCGGAGCGCAGAAa -3' miRNA: 3'- -CCACUGCCCGAACAGCCUCGCGUCUU- -5' |
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| 13960 | 5' | -57.2 | NC_003521.1 | + | 7801 | 0.69 | 0.814921 |
|
Target: 5'- --aGAUuacGGCgUGUCGGGGUGCAGAAc -3' miRNA: 3'- ccaCUGc--CCGaACAGCCUCGCGUCUU- -5' |
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| 13960 | 5' | -57.2 | NC_003521.1 | + | 6366 | 0.72 | 0.665815 |
|
Target: 5'- --aGAgGGGCcgGUCGGGGuCGCGGAGg -3' miRNA: 3'- ccaCUgCCCGaaCAGCCUC-GCGUCUU- -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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