Table 2. Open in new tab List of...

Alignment-free discovery	Alignment-based discovery
TGATNGATKGAY	59	0.93	75	24	TGATNGAYGGAY	11	0.91	10	3
TGATNGAYKGAT	59	0.93	74	20	TGATNGATKGAY	11	0.82	11	3
TGAYNGATKGAT	54	0.93	68	21	TGAYNGACKGAC	10	0.90	11	3
TGATNGAYWGAT	40	0.88	50	11	TGAYGGAYGGAY	9	1.00	9	3
TGAYNGAYTGAT	36	0.89	48	11	TGATNGAYRGAT	9	0.89	10	3
TGAYTGAYTGAY	33	0.97	42	9	TGAYNGAYTGAC	8	0.88	9	2
TGATNGAYTGAY	32	0.88	40	7	TGACNGAYTGAY	8	0.88	10	3
TGAYNGATWGAT	31	0.84	42	12	TGACNGACWGAY	7	0.86	7	2
TGATNGATWGAY	30	0.83	36	9	TGACAGAYRGAY	3	1.00	4	0
TGATNGATRGAY	29	0.86	39	9
TGAYNGATRGAT	27	0.85	37	9
TGATNGAYRGAT	26	0.85	35	8
TGAYNGATTGAY	25	0.84	34	7
TGAYNGATGGAY	24	0.88	35	9
TGATNGAYGGAY	24	0.88	31	8
TGAYTGAYWGAT	22	0.91	27	6
TGAYNGACTGAY	22	0.91	28	9
TGAYNGAYTGAC	21	0.90	27	8
TGAYNGACKGAC	20	0.90	25	10
Union (all variants)	165	–	213	51	Union (all variants)	37	–	41	10

Alignment-free discovery	Alignment-based discovery
TGATNGATKGAY	59	0.93	75	24	TGATNGAYGGAY	11	0.91	10	3
TGATNGAYKGAT	59	0.93	74	20	TGATNGATKGAY	11	0.82	11	3
TGAYNGATKGAT	54	0.93	68	21	TGAYNGACKGAC	10	0.90	11	3
TGATNGAYWGAT	40	0.88	50	11	TGAYGGAYGGAY	9	1.00	9	3
TGAYNGAYTGAT	36	0.89	48	11	TGATNGAYRGAT	9	0.89	10	3
TGAYTGAYTGAY	33	0.97	42	9	TGAYNGAYTGAC	8	0.88	9	2
TGATNGAYTGAY	32	0.88	40	7	TGACNGAYTGAY	8	0.88	10	3
TGAYNGATWGAT	31	0.84	42	12	TGACNGACWGAY	7	0.86	7	2
TGATNGATWGAY	30	0.83	36	9	TGACAGAYRGAY	3	1.00	4	0
TGATNGATRGAY	29	0.86	39	9
TGAYNGATRGAT	27	0.85	37	9
TGATNGAYRGAT	26	0.85	35	8
TGAYNGATTGAY	25	0.84	34	7
TGAYNGATGGAY	24	0.88	35	9
TGATNGAYGGAY	24	0.88	31	8
TGAYTGAYWGAT	22	0.91	27	6
TGAYNGACTGAY	22	0.91	28	9
TGAYNGAYTGAC	21	0.90	27	8
TGAYNGACKGAC	20	0.90	25	10
Union (all variants)	165	–	213	51	Union (all variants)	37	–	41	10

Table 2.

List of genome-wide conserved ga2ox1-like KN1 motif variants identified by BLSSpeller using both AF and AB discovery

Alignment-free discovery					Alignment-based discovery
KN1 motif variant	$F (15 %)$	$C (15 %)$	$M_{BLS}$	$M_{inters}$	KN1 motif variant	$F (15 %)$	$C (15 %)$	$M_{BLS}$	$M_{inters}$
TGATNGATKGAY	59	0.93	75	24	TGATNGAYGGAY	11	0.91	10	3
TGATNGAYKGAT	59	0.93	74	20	TGATNGATKGAY	11	0.82	11	3
TGAYNGATKGAT	54	0.93	68	21	TGAYNGACKGAC	10	0.90	11	3
TGATNGAYWGAT	40	0.88	50	11	TGAYGGAYGGAY	9	1.00	9	3
TGAYNGAYTGAT	36	0.89	48	11	TGATNGAYRGAT	9	0.89	10	3
TGAYTGAYTGAY	33	0.97	42	9	TGAYNGAYTGAC	8	0.88	9	2
TGATNGAYTGAY	32	0.88	40	7	TGACNGAYTGAY	8	0.88	10	3
TGAYNGATWGAT	31	0.84	42	12	TGACNGACWGAY	7	0.86	7	2
TGATNGATWGAY	30	0.83	36	9	TGACAGAYRGAY	3	1.00	4	0
TGATNGATRGAY	29	0.86	39	9
TGAYNGATRGAT	27	0.85	37	9
TGATNGAYRGAT	26	0.85	35	8
TGAYNGATTGAY	25	0.84	34	7
TGAYNGATGGAY	24	0.88	35	9
TGATNGAYGGAY	24	0.88	31	8
TGAYTGAYWGAT	22	0.91	27	6
TGAYNGACTGAY	22	0.91	28	9
TGAYNGAYTGAC	21	0.90	27	8
TGAYNGACKGAC	20	0.90	25	10
Union (all variants)	165	–	213	51	Union (all variants)	37	–	41	10

Alignment-free discovery					Alignment-based discovery
KN1 motif variant	$F (15 %)$	$C (15 %)$	$M_{BLS}$	$M_{inters}$	KN1 motif variant	$F (15 %)$	$C (15 %)$	$M_{BLS}$	$M_{inters}$
TGATNGATKGAY	59	0.93	75	24	TGATNGAYGGAY	11	0.91	10	3
TGATNGAYKGAT	59	0.93	74	20	TGATNGATKGAY	11	0.82	11	3
TGAYNGATKGAT	54	0.93	68	21	TGAYNGACKGAC	10	0.90	11	3
TGATNGAYWGAT	40	0.88	50	11	TGAYGGAYGGAY	9	1.00	9	3
TGAYNGAYTGAT	36	0.89	48	11	TGATNGAYRGAT	9	0.89	10	3
TGAYTGAYTGAY	33	0.97	42	9	TGAYNGAYTGAC	8	0.88	9	2
TGATNGAYTGAY	32	0.88	40	7	TGACNGAYTGAY	8	0.88	10	3
TGAYNGATWGAT	31	0.84	42	12	TGACNGACWGAY	7	0.86	7	2
TGATNGATWGAY	30	0.83	36	9	TGACAGAYRGAY	3	1.00	4	0
TGATNGATRGAY	29	0.86	39	9
TGAYNGATRGAT	27	0.85	37	9
TGATNGAYRGAT	26	0.85	35	8
TGAYNGATTGAY	25	0.84	34	7
TGAYNGATGGAY	24	0.88	35	9
TGATNGAYGGAY	24	0.88	31	8
TGAYTGAYWGAT	22	0.91	27	6
TGAYNGACTGAY	22	0.91	28	9
TGAYNGAYTGAC	21	0.90	27	8
TGAYNGACKGAC	20	0.90	25	10
Union (all variants)	165	–	213	51	Union (all variants)	37	–	41	10

$F (15 %)$ denotes the number of gene families in which the motif is conserved with $BLS \geq 15 %$ while $C (15 %)$ denotes the corresponding confidence score. $M_{BLS}$ denotes the number of maize genes contained in the gene families while $M_{inters}$ denotes the intersection $M_{BLS} \cap M_{ChIP}$ with experimentally profiled maize genes.

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