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Table 1 The optimized 1st order Markov chains for TFBS. The optimized arrangement of dependent positions within TFBS for the 1st order Markov model. N and N D are total number of motif positions and the number of positions significantly dependent, respectively.

From: Optimized mixed Markov models for motif identification

ID# Name N N D Position order
1 V$AP1_Q4_01 8 8 7-3-1-2-0-6-5-4
2 V$AP1_Q6_01 9 8 2-3-1-4-5-7-8-6
3 V$AP1_Q2_01 12 9 4-3-5-6-7-10-11-9-1
4 V$CDPCR1_01 10 9 3-4-2-9-6-5-7-8-1
5 V$ATF_01 14 8 1-0-10-9-11-2-13-12
6 V$CHOP_01 13 10 5-4-6-7-9-10-0-8-11-12
7 V$CDPCR3_01 15 10 3-0-1-8-9-13-4-6-2-5
8 V$CDPCR3HD_01 10 5 1-8-9-2-7
9 V$CREB_Q2_01 14 8 1-11-12-0-2-3-9-8
10 V$CREB_Q4_01 11 6 7-6-1-8-9-10
11 V$CREB_Q3 6 4 4-5-1-0
12 V$CEBP_Q3 12 9 8-9-5-6-4-11-3-2-10
13 V$CEBPB_01 14 4 0-13-11-3
14 V$E2F_Q4_01 11 4 1-8-7-0
15 V$E2F_Q6_01 12 8 8-3-7-0-2-11-9-10
16 V$E2F1DP1_01 8 5 3-4-0-6-7
17 V$E2F1DP2_01 8 5 5-6-7-3-4
18 V$E2F4DP1_01 8 4 3-4-0-1
19 V$E2F4DP2_01 8 5 4-3-7-1-0
20 V$ETS_Q4 12 8 11-2-5-10-4-3-0-1
21 V$ELK1_02 14 4 10-11-2-3
22 V$FAC1_01 14 12 12-6-10-11-13-4-9-8-5-1-0-7
23 V$FOXD3_01 12 11 1-3-8-7-9-10-11-2-0-4-6
24 V$FOXO1_02 14 11 8-9-10-12-7-6-2-0-11-1-3
25 V$HNF4_Q6 9 7 4-3-2-6-8-1-7
26 V$HNF1_Q6 18 15 3-11-12-1-4-8-13-5-9-0-6-16-14-2-10
27 V$HNF3_Q6 13 11 1-10-7-5-3-4-12-9-0-2-8
28 V$E2F1DP1RB_01 8 5 1-7-3-0-4
29 V$IRF7_01 18 13 3-2-0-16-15-17-1-7-6-8-14-9-12
30 V$LUN1_01 17 8 8-9-10-7-12-11-14-13
31 V$MZF1_01 8 4 0-1-4-5
32 V$MYC_Q2 7 4 4-5-3-1
33 V$NFAT_Q4_01 10 4 6-8-9-5
34 V$NFKAPPAB_01 10 4 5-7-9-2
35 V$NKX22_01 10 6 9-8-6-1-0-7
36 V$OCT_Q6 11 10 8-2-0-10-5-3-9-6-4-7
37 V$PAX_Q6 11 10 10-6-7-0-9-3-1-5-4-2
38 V$PAX6_01 21 21 15-17-16-18-6-8-19-13-11-3-2-1-0-20-7-10-4-9-5-14-12
39 V$PBX1_02 15 10 6-12-2-0-3-1-11-13-14-4
40 V$RSRFC4_Q2 17 6 6-7-0-13-2-3
41 V$RSRFC4_01 16 8 6-7-9-1-2-13-12-8
42 V$STAT5A_01 15 7 8-12-1-13-0-4-5
43 V$SOX9_B1 14 9 1-13-0-2-11-5-3-10-4
44 V$SRY_01 7 4 4-6-0-1
45 V$SRY_02 12 4 1-3-11-4
46 V$STAT5A_02 24 16 7-12-20-15-16-17-18-19-22-1-21-13-5-6-9-23
47 V$SP1_Q2_01 10 7 7-3-8-0-4-9-5
48 V$SP1_Q4_01 13 13 0-2-11-12-6-1-3-10-9-8-7-4-5
49 V$SP1_Q6_01 10 10 3-5-8-9-0-7-4-2-6-1
50 V$USF_Q6_01 12 8 3-11-4-5-7-2-1-8
51 V$XBP1_01 17 9 13-5-3-4-15-11-10-12-0
52 V$ZID_01 13 8 6-7-4-8-12-10-9-11
53 I$DRI_01 10 7 6-9-8-7-0-1-2