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Table 3 Motifs derived by Gibbs sampling the indicated modules (see additional File 1).

From: Computational detection of genomic cis- regulatory modules applied to body patterning in the early Drosophila embryo

Module

recovered factors (copies)

novel motifs

eve stripes 2, 3+7

kni(15), bcd(9), hb/cad(9)

 

eve stripes 5, 4+6

hb/cad(6), kni/hb/cad(12)

RTTNSRCGSAAT(9), ATYCYGCARY/bcd (6)

h stripes 5,6,7

Kr(12), hb/cad(14) km (7)

GRCNWG[T/G]TSNSA (9)

hb (both mods)

Kr/tll(6), hb/cad(8)

ATTTTCCNSC (9)

kni (1.1 k)

Kr(7), tll(5), hb/cad(9)

GWGWG[A/C]GWGYG(7)

Kr (700 bp)

bcd(5), hb/cad(7)

TWNTGATCCWS (6)

tll (3 mods)

kni(9), cad(9), Kr(7), hb/cad(8)

TCRAWSAAT/torRE (8)

  1. The criterion for a motif to match a known factor is given in Methods; copies refers to all sequences in the Gibbs derived motif. Only the consensus sequences of the most prominent unclassified motifs are shown with the abbreviations (R = A/G, W = A/T, S = G/C). Matches in italics are marginal and names linked by / co-occur within the same Gibbs motif, possibly on opposite strands.