; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/sd.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/sd_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/sd.tab
; Output files
;	output	html_ready/sd_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : sd
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	4	10	4	17	0	1	0	5
c	|	2	4	11	0	0	0	9	9
g	|	9	2	0	1	0	1	0	2
t	|	3	2	3	0	18	16	9	2
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	18	18	18	18	18	18	18	18	144
; c.max	|	9	10	11	17	18	16	9	9	18
; c.min	|	2	2	0	0	0	0	0	2	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	4	2	9	3	|	18	 0.50	 0.26	G	G	G
2	10	4	2	2	|	18	 0.56	 0.16	a	m	g
3	4	11	0	3	|	18	 0.61	 0.51	C	C	CCCt
4	17	0	1	0	|	18	 0.94	 0.79	A	A	AAAAAAAAAg
5	0	0	0	18	|	18	 1.00	 0.93	T	T	TTTTTTTTTTTT
6	1	0	1	16	|	18	 0.89	 0.63	t	t	ttttttt
7	0	9	0	9	|	18	 0.50	 0.62	C	Y	CCtt
8	5	9	2	2	|	18	 0.50	 0.29	C	C	C
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	| -0.1  0.3 -0.1  0.9 -0.1 -0.1 -0.1 -0.0
c	| -0.0  0.1  0.7 -0.0 -0.0 -0.0  0.5  0.5
g	|  0.5 -0.0 -0.0 -0.1 -0.0 -0.1 -0.0 -0.0
t	| -0.1 -0.1 -0.1 -0.1  1.0  0.8  0.2 -0.1
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.3  0.2  0.5  0.8  0.9  0.6  0.6  0.3  4.2
; i.max	|  0.5  0.3  0.7  0.9  1.0  0.8  0.5  0.5  1.0
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	18
>sd_chr2L_11454657_114546
gacattcg
>sd_chr2R_8412777_8412788
aacattcc
>sd_chr2R_19849909_198499
gaaattcc
>sd_chrX_7375895_7375904_
cccattcc
>sd_chr2R_8412503_8412516
gccatgcc
>sd_chr2R_8412416_8412429
ggaattcc
>sd_chr2R_8412379_8412389
gatatttc
>sd_chrX_7376024_7376046_
gacatttt
>sd_chr3L_20641044_206410
gacatttt
>sd_chr3L_20641091_206410
cgcatttc
>sd_chrX_7375625_7375636_
aacattta
>sd_chrX_7375797_7375813_
gtaatttc
>sd_chr3L_20640792_206408
tacatttg
>sd_chrX_7375697_7375723_
aaaattca
>sd_chr3L_20641161_206411
actatttc
>sd_chrX_7375593_7375606_
ttcattca
>sd_chr3L_20640984_206409
tacataca
>sd_chrX_7375676_7375690_
gctgttta
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.329|c:0.171|g:0.171|t:0.329
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/sd_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	18
;	meme.llr                     	88
;	meme.E-value                 	0.0013
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.171
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.18687
;	information.per.column       	0.523359
;	max.possible.info.per.col    	1.76609
;	consensus.strict             	GaCATtCC
;	consensus.strict.rc          	GGaATGtC
;	consensus.IUPAC              	GmCATtYC
;	consensus.IUPAC.rc           	GRaATGkC
;	consensus.regexp             	G[ac]CATt[CT]C
;	consensus.regexp.rc          	G[AG]aATG[gt]C
;	residues.content.crude.freq  	a:0.2847|c:0.2431|g:0.1042|t:0.3681
;	G+C.content.crude.freq       	0.347222
;	residues.content.corrected.freq	a:0.2871|c:0.2393|g:0.1077|t:0.3660
;	G+C.content.corrected.freq   	0.346947
;	min(P(S|M))                  	8.80909e-14
;	max(P(S|M))                  	0.0276479
;	proba_range                  	0.0276479
;	Wmin                         	-17.1
;	Wmax                         	7.9
;	Wrange                       	25
; Job started 2007_12_10.132124
; Job done    2007_12_10.132124