Table 12 Conservation analysis. The results for conservation analysis of the top 10 word pairs in the bidirectional (a) and unidirectional (b) promoter set. For each word pair, the occurrence location of the pair is given, as well as an identifier for the conservation of the sites, and a PhastCons score for the quality of the conservation across 28 organisms. Conservation can be categorized as: none (no word was conserved), partial (one word was conserved) and complete (all words were conserved).
From: Word-based characterization of promoters involved in human DNA repair pathways
(a) Bidirectional | |||||
|---|---|---|---|---|---|
Word 1 | Word 2 | Location | Conservation | Hit | Score |
TCTGAGGA | TCGCGCCA | chr19:53365272–53366372 | None |  |  |
|  |  | chr19:48776246–48777346 | None |  |  |
|  |  | chr19:7600339–7601439 | Partial | TCGCGCCA | 385 |
ACTCCAGC | TCGCGCCA | chr4:57538069–57539168 | None |  |  |
|  |  | chr19:48776246–48777346 | None |  |  |
|  |  | chr19:7600339–7601439 | Partial | TCGCGCCA | 385 |
GCCCAGCC | TCCGCCGC | chr3:185561446–185562546 | Partial | TCCGCCGC | 310 |
|  |  | chr14:19992129–19993229 | None |  |  |
|  |  | chr11:832429–833529 | None |  |  |
GCCCAGCC | CGGAGCGC | chr3:185561446–185562546 | None |  |  |
|  |  | chr14:19992129–19993229 | None |  |  |
TGCCCGCG | TCCCGGGA | chr19:53365272–53366372 | Partial | TCCCGGGA | 390 |
|  |  | chr13:107668425–107669525 | None |  |  |
|  |  | chr20:5055168–5056268 | None |  |  |
|  |  | chr11:832429–833529 | None |  |  |
GGCAGGGA | GGGCCAGG | chr19:53365272–53366372 | Partial | GGGCCAGG | 390 |
|  |  | chr22:40346240–40347340 | Complete | GGCAGGGA | 325 |
| Â | Â | Â | Â | GGGCCAGG | 522 |
|  |  | chr5:60276548–60277648 | None |  |  |
|  |  | chr12:131773918–131775018 | None |  |  |
TCCCGGGA | TCGCGCCA | chr19:53365272–53366372 | Partial | TCCCGGGA | 390 |
|  |  | chr4:57538069–57539168 | None |  |  |
|  |  | chr19:7600339–7601439 | Partial | TCGCGCCA | 385 |
AGCCTGTC | TCCCGGGA | chr17:38530557–38531657 | None |  |  |
|  |  | chr13:107668425–107669525 | Partial | AGCCTGTC | 244 |
|  |  | chr4:57538069–57539168 | None |  |  |
GGAGGCTG | TCGCGCCA | chr4:57538069–57539168 | None |  |  |
|  |  | chr19:48776246–48777346 | None |  |  |
|  |  | chr19:7600339–7601439 | Partial | TCGCGCCA | 385 |
TCCGCCGC | GCCCCTCC | chr3:185561446–185562546 | Partial | TCCGCCGC | 310 |
|  |  | chr14:19992129–19993229 | None |  |  |
|  |  | chr1:11674165–11675265 | Partial | GCCCCTCC | 360 |
|  |  | chr11:832429–833529 | None |  |  |
(b) Unidirectional | |||||
Word 1 | Word 2 | Location | Conservation | Hit | Score |
GTTCATTC | TCCGCCGG | chr7:73306574–73307674 | None |  |  |
|  |  | chr12:52868924–52870024 | Partial | TCCGCCGG | 325 |
CTGTGTGC | TGCGCCGA | chr10:131154509–131155609 | None |  |  |
|  |  | chr19:1046236–1047336 | None |  |  |
TGACGCGA | CTCCCGCT | chr12:116937892–116938992 | None |  |  |
|  |  | chr17:30330654–30331754 | None |  |  |
AGCCGGCT | GGGGAGTA | chr6:30982955–30984055 | None |  |  |
|  |  | chr16:13920523–13921623 | None |  |  |
ATTGCAGG | ATTCTCTC | chr5:86744492–86745592 | None |  |  |
|  |  | chr17:30330654–30331754 | None |  |  |
GGGGAGTA | AGGAAACA | chr16:13920523–13921623 | None |  |  |
|  |  | chr8:101231014–101232114 | None |  |  |
CTGGGAGC | GTTCATTC | chr7:73306574–73307674 | None |  |  |
|  |  | chr12:52868924–52870024 | None |  |  |
CCTTCCGA | CTGGGAGC | chr5:68890824–68891924 | None |  |  |
|  |  | chr7:73306574–73307674 | None |  |  |
TGGGCGGA | ACCCGCCT | chr6:30982955–30984055 | None |  |  |
|  |  | chr9:99499360–99500460 | None |  |  |
TTTCTCCA | CGGAAACC | chr8:55097461–55098561 | None |  |  |
|  |  | chr11:118471287–118472387 | None |  |  |