Table 3 List of the significant blocks detected in the pax6 dataset

pax6 1.1 (UCSC)

CTTAATGATGAGAGATCTTTCCGCTCATTGCCCATTCAAATACAATTGTAGATCGAAGCCGGCCTT GTCAsGTTGAGAAAAAGTGAATTTCTAACATCCAGGACGTGCCTGTCTACT

*Minimal fragment for expression in lens and cornea as described in [46]: 11-117 +

Cap, M00253, NCANHNNN: 25-32 + (0.940); 79-86 - (0.964); 4-11 - (0.946); 1-8 - (0.903)

CCAAT box, M00254, NNNRRCCAATSA: 27-38 + (0.901)

*CdxA, M00100, 'MTTTATR': 1-7 + (0.921)*; 87-93 + (0.913)

*CdxA, M00101, AWTWMTR: 1-7 + (0.934); 4-10 + (0.921); 38-44 + (0.905), 87-93 + (0.988)

c-Ets-1(p54), M00032, NCMGGAWGYN: 98-107 + (0.906)

c-Ets-1(p54), M00074, NNACMGGAWRTNN: 92-104 - (0.901)

En-1, M00396, GTANTNN: 37-43 - (0.967)

GATA-3, M00351, ANAGATMWWA: 11-20 + (0.920)

HSF2, M00147, NGAANNWTCK: 13-22 - (0.933)

p53, M00272, NGRCWTGYCY: 101-110 + (0.949)

pax6 1.2 (UCSC)

CATTATTGTTGCCAGCACGAAGCATCACAATCAATCATAAGGAAGTCCAGTTGGCAGGTGTCAATCTTG

CdxA, M00101, AWTWMTR: 1-7 - (0.995)

Cap, M00253, NCANHNNN: 25-32 + (0.934); 31-38 + (0.903); 35-42 + (0.903); 47-54 + (0.908); 61-68 + (0.937)

CDP CR3+HD, M00106, NATYGATSSS: 27-36 - (0.907)

c-Ets-1(p54), M00074, NNACMGGAWRTNN: 36-48 + (0.902)

*HOXA3, M00395, CNTANNNKN: 1-9 + (0.905)

MyoD, M00184, NNCACCTGNY: 53-62 - (0.956)

*Pbx-1, M00096, ANCAATCAW: 30-38 + (0.986); 2-10 - (0.923)

Sox-5, M00042, NNAACAATNN: 3-12 - (0.932)

SRY, M00148, AAACWAM: 33-39 + (0.910)

USF, M00122, NNRNCACGTGNYNN: 51-64 + (0.913); 51-64 - (0.908)

pax6 1.3 (UCSC)

GAAAAAGTGAATTTCTAACATCCAGGACGTGCCTGTCTACTTTCAGwGAATTGCATCCAATCACCCC

Cap, M00253, NCANHNNN: 3-10 - 0.964

CCAAT box, M00254, NNNRRCCAATSA: 52-63 + (0.949)

CdxA, M00100, 'MTTTATR': 11-17 + (0.913)

CdxA, M00101, AWTWMTR: 11-17 + (0.988)

c-Ets-1(p54), M00032, NCMGGAWGYN: 22-31 + (0.906)

c-Ets-1(p54), M00074, NNACMGGAWRTNN:16-28 - (0.901)

En-1, M00396, GTANTNN: 58-64 - (0.948)

GATA-1, M00075, SNNGATNNNN: 56-65 - (0.930)

GATA-3, M00077, NNGATARNG: 56-64 - (0.917)

NF-Y, M00185, TRRCCAATSRN: 54-64 + (0.910)

p53, M00272, NGRCWTGYCY: 25-34 + (0.949)

SRY, M00148, AAACWAM: 59-65 + (0.917)

pax6 1.4 (UCSC)

GTCTATATTTAATCCAATTATAAGGGTCACGGAGTAAGTGC

*Motif containing homeoboxes described in [46], TTTAATCCAATTATAA: 8-23 +

Cap, M00253, NCANHNNN: 34-41 - (0.904)

CdxA, M00100, 'MTTTATR': 16-22 + (0.907)

CdxA, M00101, AWTWMTR: 16-22 + (0.995); 16-22 - (0.906); 6-12 - (0.931); 4-10 - (0.951)

En-1, M00396, GTANTNN: 15-21 - (0.948)

Nkx2-5, M00240, TYAAGTG: 34-40 + (0.927)

RORalpha1, M00156, NWAWNNAGGTCAN: 18-30 + (0.919)

TCF11, M00285, GTCATNNWNNNNN: 26-38 + (0.906)

pax6 1.5 (UCSC)

GCATCCAATCACCCCCAGGG

Cap, M00253, NCANHNNN: 9-16 + (0.965)

En-1, M00396, GTANTNN: 6-12 - (0.948)

GATA-3, M00077, NNGATARNG: 4-12 - (0.917)

SRY, M00148, AAACWAM: 7-13 + (0.917)

pax6 1.6 (UCSC)

CAsGTTGAGAAAAAGTGAATTTCTAACATCCAGGACGTGCCTGTCTACTTTCAGw GAATTGCATCCAATCACCCCCAGGGAATTCnGCTAATGTCTCC

*Homeobox-binding site described in [46], GCTAATGTCTC: 87-97 +

Cap, M00253, NCANHNNN: 69-76 + (0.965); 87-94 - (0.903); 11-18 - (0.964)

CCAAT box, M00254, NNNRRCCAATSA: 60-71 + (0.949)

CdxA, M00100, 'MTTTATR': 19-25 + (0.913)

CdxA, M00101, AWTWMTR: 19-25 + (0.988)

c-Ets-1(p54), M00032, NCMGGAWGYN: 30-39 + (0.906)

c-Ets-1(p54), M00074, NNACMGGAWRTNN: 24-36 - (0.901)

En-1, M00396, GTANTNN: 66-72 - (0.948)

GATA-1, M00075, SNNGATNNNN: 64-73 - (0.930)

GATA-3, M00077, NNGATARNG: 64-72 - (0.917)

NF-Y, M00185, TRRCCAATSRN: 62-72 + (0.910)

p53, M00272, NGRCWTGYCY: 33-42 + (0.949)

SRY, M00148, AAACWAM: 67-73 + (0.917)

pax6 2.1 (UCSC)

TGGGTCCATTTTCCAGAyGGTTTGTTACTCTTGCTGCmTGATTTrG

Cap, M00253, NCANHNNN: 6-13 + (0.921)

CdxA, M00101, AWTWMTR: 9-15 + (0.918)

SRY, M00148, AAACWAM: 21-27 - (0.942)

pax6 2.2 (-)

ATTTTGGTTGCTTTCAGGTwTAATTAACTTT

Nkx2-5, M00241, CWTAATTG: 21-28 - (0.902)

pax6 2.3 (UCSC)

ATTGTAATCATTTCAATTATCTTCA

Cap, M00253, NCANHNNN: 8-15 + (0.927)

En-1, M00396, GTANTNN: 14-20 - (0.948)

Nkx2-5, M00241, CWTAATTG: 14-21 - (0.930)

pax6 2.4 (-)

GGTTGCTTTCAGGTwTAATTAACTTTGAACAACAAATA

Nkx2-5, M00241, CWTAATTG: 16-23 - (0.902)

pax6 3.1 (UCSC)

TTGTAATTACTGCCCTTCATGTGGTCCGGTGCCTTGAACCATCTTTAATTAAAAGCATAATTAAGG

AML-1a, M00271, TGTGGT: 20-25 + (1.000)

Cap, M00253, NCANHNNN: 39-46 + (0.910); 55-62 + (0.909); 6-13 - (0.916)

CdxA, M00100, MTTTATR: 56-62 - (0.934)

CdxA, M00101, AWTWMTR: 6-12 + (0.988); 44-50 + (0.913); 47-53 + (0.900); 48-54 + (0.905); 59-65 + (0.903); 60-66 + (0.926); 56-62 - (0.998); 47-53 - (0.913); 44-50 - (0.901); 43-49 - (0.907); 2-8 - (0.949);

En-1, M00396, GTANTNN: 3-9 + (0.912); 4-10 - (0.912)

HSF2 , M00147, NGAANNWTCK: 35-44 + (0.908)

Nkx2-5, M00241, CWTAATTG: 56-63 + (0.935), 58-65 - (0.954)

USF, M00217, NCACGTGN: 17-24 - (0.921)

pax6 3.2 (UCSC)

AAGGCTTGCAGCTGCCTCCAAATCAATAGAyGTCAAAGAAATATGAAAACArTC

CdxA, M00101, AWTWMTR: 39-45 + (0.953); 36-42 - (0.925)

SRY, M00148, AAACWAM: 35-41 + (0.961)

Cap, M00253, NCANHNNN: 8-15 + (0.931); 39-46 - (0.940); 8-15 - (0.931)

AP-4, M00175, VDCAGCTGNN: 7-16 - (0.902)

MyoD, M00184, NNCACCTGNY: 7-16 + (0.957)

SRY, M00160, NWWAACAAWANN: 19-30 + (0.928)

pax6 3.3 (UCSC)

GCATAATTAAGGGAAGATCTAAAGAAAGACAATTACCAGATGGTCT

Cap, M00253, NCANHNNN: 1-8 + (0.909)

CdxA, M00100, MTTTATR: 2-8 - (0.934)

CdxA, M00101, AWTWMTR: 5-11 + (0.903); 6-12 + (0.926); 32-38 + (0.939); 2-8 - (0.998)

En-1, M00396, GTANTNN: 30-36 - (1.000)

GATA-1, M00075, SNNGATNNNN: 36-45 + (0.936)

GATA-2, M00076, NNNGATRNNN: 36-45 + (0.922)

GATA-3, M00351, ANAGATMWWA: 13-22 + (0.949)

HOXA3, M00395, CNTANNNKN: 29-37 - (0.939)

Msx-1, M00394, CNGTAWNTG: 30-38 - (0.915)

MyoD, M00184, NNCACCTGNY: 35-44 - (0.919)

Nkx2-5, M00241, CWTAATTG: 2-9 + (0.935); 4-11 - (0.954)

SRY, M00148, AAACWAM: 21-27 + (0.961); 25-31 + (0.927)

USF, M00122, NNRNCACGTGNYNN: 33-46 + (0.907); 33-46 - (0.904)