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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 | |||||||
| 17440 | 3' | -52.5 | NC_004453.1 | + | 20127 | 0.66 | 0.702592 |
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Target: 5'- uGGCgCCAC-ACCAcgcAGCCGgccgGGUUCc-- -3' miRNA: 3'- -CCG-GGUGuUGGU---UCGGCa---UCAAGacg -5' |
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| 17440 | 3' | -52.5 | NC_004453.1 | + | 20381 | 0.67 | 0.668092 |
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Target: 5'- uGCCCACGGCCAauuggAGCCcaccgAGgaaucUUUGCg -3' miRNA: 3'- cCGGGUGUUGGU-----UCGGca---UCa----AGACG- -5' |
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| 17440 | 3' | -52.5 | NC_004453.1 | + | 19944 | 0.67 | 0.656499 |
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Target: 5'- gGGCCCACAGCgGcuacucgugcGGCUGgcGUUUUa- -3' miRNA: 3'- -CCGGGUGUUGgU----------UCGGCauCAAGAcg -5' |
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| 17440 | 3' | -52.5 | NC_004453.1 | + | 10293 | 0.68 | 0.586827 |
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Target: 5'- uGGCCCGCAccACCGGGuuGUuag-CcGCg -3' miRNA: 3'- -CCGGGUGU--UGGUUCggCAucaaGaCG- -5' |
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| 17440 | 3' | -52.5 | NC_004453.1 | + | 9561 | 0.69 | 0.563828 |
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Target: 5'- cGGCCUugG-CCGcuguucguaAGCCGUcAGUaagUCUGCc -3' miRNA: 3'- -CCGGGugUuGGU---------UCGGCA-UCA---AGACG- -5' |
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| 17440 | 3' | -52.5 | NC_004453.1 | + | 19060 | 0.71 | 0.423071 |
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Target: 5'- aGGCCCACAcagcGCCGcguGCgGUcuaUUCUGCa -3' miRNA: 3'- -CCGGGUGU----UGGUu--CGgCAuc-AAGACG- -5' |
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| 17440 | 3' | -52.5 | NC_004453.1 | + | 20814 | 0.81 | 0.094906 |
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Target: 5'- cGGUCCACAACCcGGCCGUgcuGGUguuucaaugCUGCa -3' miRNA: 3'- -CCGGGUGUUGGuUCGGCA---UCAa--------GACG- -5' |
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| 17440 | 3' | -52.5 | NC_004453.1 | + | 7392 | 1.14 | 0.000447 |
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Target: 5'- cGGCCCACAACCAAGCCGUAGUUCUGCc -3' miRNA: 3'- -CCGGGUGUUGGUUCGGCAUCAAGACG- -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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