miRNA: 3'- ucACCUGcUUCUGCCaGCGCCuUGGu -5'
miRNA: 3'- ucACCUgCUUcUGCCAGCGCCU---UGGU- -5'
miRNA: 3'- uCACcu--GCuUCUGCCAGCGCC-UUGGU- -5'
miRNA: 3'- -UCACC-------UGCUu----CUgCC-AGCGCCUUGGU- -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 | |||||||
| 20917 | 5' | -55.4 | NC_004689.1 | + | 18608 | 0.66 | 0.800983 |
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Target: 5'- -aUGGAC-AGGAUGGaCGCGGuACCc -3' miRNA: 3'- ucACCUGcUUCUGCCaGCGCCuUGGu -5' |
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| 20917 | 5' | -55.4 | NC_004689.1 | + | 12719 | 0.67 | 0.752221 |
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Target: 5'- -uUGGG-GAGaACGGUCGCGGGcugACCGg -3' miRNA: 3'- ucACCUgCUUcUGCCAGCGCCU---UGGU- -5' |
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| 20917 | 5' | -55.4 | NC_004689.1 | + | 41306 | 0.67 | 0.711055 |
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Target: 5'- cGUGuuguCGcAGACGGUCGCGGuGAUCGu -3' miRNA: 3'- uCACcu--GCuUCUGCCAGCGCC-UUGGU- -5' |
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| 20917 | 5' | -55.4 | NC_004689.1 | + | 59432 | 0.69 | 0.603321 |
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Target: 5'- aGGUGGcccagacGCGAuccuuGAgGGcUUGCGGAACCAu -3' miRNA: 3'- -UCACC-------UGCUu----CUgCC-AGCGCCUUGGU- -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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