; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/dl.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/dl_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/dl.tab
; Output files
;	output	html_ready/dl_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : dl
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	15	33	35	35	15	1	10
c	|	0	0	1	3	1	3	20	22
g	|	37	23	2	0	0	5	0	4
t	|	1	0	2	0	2	15	17	2
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	38	38	38	38	38	38	38	38	304
; c.max	|	37	23	33	35	35	15	20	22	37
; c.min	|	0	0	1	0	0	3	0	2	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	0	0	37	1	|	38	 0.97	 1.25	G	G	GGGGGGGGGGGGGGGGGGGt
2	15	0	23	0	|	38	 0.61	 0.67	g	r	aagggg
3	33	1	2	2	|	38	 0.87	 0.74	A	A	AAAAAAAAAt
4	35	3	0	0	|	38	 0.92	 0.95	A	A	AAAAAAAAAAAAAc
5	35	1	0	2	|	38	 0.92	 0.91	A	A	AAAAAAAAAAAAct
6	15	3	5	15	|	38	 0.39	 0.13	a	w	
7	1	20	0	17	|	38	 0.53	 0.55	c	y	cctt
8	10	22	4	2	|	38	 0.58	 0.35	c	c	ccg
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	| -0.0  0.1  1.0  1.1  1.1  0.1 -0.1 -0.0
c	| -0.0 -0.0 -0.1 -0.1 -0.1 -0.1  0.4  0.5
g	|  1.4  0.6 -0.1 -0.0 -0.0 -0.1 -0.0 -0.1
t	| -0.1 -0.0 -0.1 -0.0 -0.1  0.1  0.2 -0.1
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  1.3  0.7  0.7  1.0  0.9  0.1  0.6  0.3  5.6
; i.max	|  1.4  0.6  1.0  1.1  1.1  0.1  0.4  0.5  1.4
; i.min	| -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	38
>dl_chr2L_15476060_154760
ggaaaacc
>dl_chr3R_2581220_2581229
ggaaatcc
>dl_chr3R_2581102_2581111
ggaaaacc
>dl_chr3L_1445510_1445520
ggaaattc
>dl_chr3L_1445569_1445579
ggaaattc
>dl_chr2L_2456607_2456624
ggaaattc
>dl_chr2L_2456485_2456500
ggaaaatc
>dl_chr2L_15475919_154759
ggaaaatc
>dl_chr2R_18552822_185528
gaaaatcc
>dl_chr2R_18553654_185536
gaaaaatc
>dl_chr2L_15476025_154760
ggaaaaca
>dl_chr2L_2456352_2456369
gaaaattc
>dl_chr2L_2456800_2456816
ggaaaata
>dl_chr2L_15475642_154756
ggaaatta
>dl_chr2L_2456179_2456195
ggaaatta
>dl_chr3L_1445374_1445384
gaaaaaca
>dl_chr3L_1445616_1445626
gaaaagcc
>dl_chr2L_2457291_2457304
ggaaatcg
>dl_chr2R_18552809_185528
gaaaagtc
>dl_chr2L_15475721_154757
gaaaaccc
>dl_chr2R_18553624_185536
gaaaaccc
>dl_chr2R_18553608_185536
ggaaaatg
>dl_chr2R_18552863_185528
gaaaatcg
>dl_chr2L_2456446_2456465
ggaaagta
>dl_chr2R_18553742_185537
gaaaatcg
>dl_chr2L_15475489_154755
ggaattcc
>dl_chr3R_2581170_2581180
gagaaacc
>dl_chr2L_15475577_154755
ggaaatac
>dl_chr2L_2456209_2456223
gataaacc
>dl_chr2L_2456702_2456718
gaaaaatt
>dl_chr2L_2457011_2457028
gggaatca
>dl_chr2L_15475288_154753
ggaaagtt
>dl_chr2L_2456823_2456842
gaacaata
>dl_chr2L_2456426_2456439
ggaatata
>dl_chr2L_15475754_154757
ggtcatcc
>dl_chr2L_2456749_2456764
taaaagcc
>dl_chr2L_15475985_154760
ggccaacc
>dl_chr2L_2456997_2457009
ggaaccca
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.273|c:0.227|g:0.227|t:0.273
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/dl_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	38
;	meme.llr                     	228
;	meme.E-value                 	2.2e-38
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.227
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.55316
;	information.per.column       	0.694145
;	max.possible.info.per.col    	1.48281
;	consensus.strict             	GgAAAacc
;	consensus.strict.rc          	ggtTTTcC
;	consensus.IUPAC              	GrAAAwyc
;	consensus.IUPAC.rc           	grwTTTyC
;	consensus.regexp             	G[ag]AAA[at][ct]c
;	consensus.regexp.rc          	g[ag][at]TTT[ct]C
;	residues.content.crude.freq  	a:0.4737|c:0.1645|g:0.2336|t:0.1283
;	G+C.content.crude.freq       	0.398026
;	residues.content.corrected.freq	a:0.4685|c:0.1661|g:0.2334|t:0.1320
;	G+C.content.corrected.freq   	0.399462
;	min(P(S|M))                  	1.01357e-15
;	max(P(S|M))                  	0.0459248
;	proba_range                  	0.0459248
;	Wmin                         	-23
;	Wmax                         	8.1
;	Wrange                       	31.1
; Job started 2007_12_10.132048
; Job done    2007_12_10.132048