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).

(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


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


Lichtenberg et al. BMC Genomics 2009 10(Suppl 1):S18   doi:10.1186/1471-2164-10-S1-S18

Open Data