Table 1.
Multi alignments of the consensus patterns found by MEME
| Strand | P value | Alignment | |
|---|---|---|---|
| Rarabpm1 | |||
| Case 15 | + | 2.75e-25 | CTTCAAGCGTTAACTCCTTCCTAACTCGGGGGGAGAACGGGGCCAGGCCGC |
| Case 10 | + | 2.75e-25 | CCTCCCTCCTCTTCAAGCGTTAACTCCTTCCTAACTCGGGGGGAGAACGGGGCCA |
| Case 13 | + | 2.75e-25 | CCTCCCTCCTCTTCAAGCGTTAACTCCTTCCTAACTCGGGGGGAGAACGGGGCC |
| Rarabpm2 | TCTTCCCTCCCTACT | ||
| Consensus | G T C TGACTC | ||
| Sequence | A | ||
| Case 5 | − | 1.07e-08 | GCTTATGTCCTCTTCCCTCCCTCCTCTTCAAGCGT |
| Case 10 | − | 1.07e-08 | TCTTCCCTCCCTCCTCTTCAAGCGT |
| Case 13 | + | 1.07e-08 | CTCTTCCCTCCCTCCTCTTCAAGCGT |
| Case 11 | + | 2.38e-07 | CCCTGGGGACTCTTCTCCCTGTATTCAGGGTATCT |
| Case 12 | + | 2.38e-07 | CCCTGGGGACTCTTCTCCCTGTATTCAGGGTATCT |
| Case 3 | + | 2.60e-07 | GCCCCTCCCCTCTTCTCTCTCTAGCCATTG |
| Case 2 | − | 2.66e-06 | GCTCTGTCTGTCTGGCCTCAATACTATGTCCGGGT |
| Case 8 | − | 3.48e-06 | CGCCGTCTGCTCTTCACTCCAACACCAACTGCCCT |
| Case 9 | − | 3.48e-06 | GTTTCCCTGCTCTGCCCTTTGAACCCAGAGCTCGA |
| Rarabpm3 | GCCCAGGGGA | ||
| Consensus sequence | GGGT C | ||
| Case 7 | + | 1.71e-05 | AGAATCTGCTGGGCTGGGGATGGTGTGGGC |
| Case 9 | + | 1.71e-05 | TGGAGGCCTGGGGAGGTGGGGCAT |
| Case 11 | + | 1.71e-05 | GGCTTTTGGGGCCCTGGGGACTCTTCTCCC |
| Case 12 | + | 1.71e-05 | GGCTTTTGGGGCCCTGGGGACTCTTCTCCC |
| Case 6 | − | 3.41e-05 | AGACTGGTGGGGGGAGGGGAGAT |
| Case 8 | + | 3.41e-05 | AGAGCAGACGGCGGTGGGGAG |
| Case 15 | + | 5.74e-05 | GGGCCAGGCCGCCCAGGGGCA |
| Case 16 | + | 5.74e-05 | GGGCCAGGCCGCCCAGGGGCAGGAGCTTTA |
| Case 5 | − | 6.99e-05 | CATAAGCTGGGGGCAGAGGAAACTGG |
| Case 3 | − | 9.31e-05 | AGAGAGAAGAGGGGAGGGGCAGTTAGAGAC |
Cases 1–8 are from the study by Yoshida et al. (33); case 9 is from the study by de The et al. (11); case 10 is from the study by Alcalay et al. (30); cases 11–13 are from the study by Dong et al. (31); and cases 14–16 are from the study by Satoshi et al. (32). The extracted sequences flanking every RARα t(15;17) breakpoint are shown aligned with each other on the match sites of the patterns found by meme, and the 10 sequence positions preceding and following each site are also shown. “+” means the forward extracted sequence, and “−” means the reverse complement of the extracted sequence. The P value gives the probability of a random string (generated from the background letter frequencies) having the same match score or higher. The multilevel consensus sequence corresponding to the pattern is an aid in remembering and understanding the pattern. The cases are sorted in increasing order by P value separately for each column of the pattern.