; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Kr.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Kr_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Kr.tab
; Output files
;	output	html_ready/Kr_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Kr
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	30	37	0	3	1	5	4	2
c	|	4	0	35	37	41	9	1	4
g	|	4	2	3	0	0	11	7	0
t	|	6	5	6	4	2	19	32	38
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	44	44	44	44	44	44	44	44	352
; c.max	|	30	37	35	37	41	19	32	38	41
; c.min	|	4	0	0	0	0	5	1	0	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	30	4	4	6	|	44	 0.68	 0.32	a	a	aag
2	37	0	2	5	|	44	 0.84	 0.68	A	A	AAAAAAAAt
3	0	35	3	6	|	44	 0.80	 0.82	C	C	CCCCCCCCgt
4	3	37	0	4	|	44	 0.84	 0.90	C	C	CCCCCCCCCCCt
5	1	41	0	2	|	44	 0.93	 1.16	C	C	CCCCCCCCCCCCCCCCCt
6	5	9	11	19	|	44	 0.43	 0.10	t	k	
7	4	1	7	32	|	44	 0.73	 0.45	t	t	gtttt
8	2	4	0	38	|	44	 0.86	 0.74	T	T	cTTTTTTTTT
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	|  0.6  0.9 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1
c	| -0.1 -0.0  1.0  1.1  1.3 -0.0 -0.1 -0.1
g	| -0.1 -0.1 -0.1 -0.0 -0.0  0.0 -0.0 -0.0
t	| -0.1 -0.1 -0.1 -0.1 -0.1  0.2  0.7  0.9
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.3  0.7  0.8  0.9  1.2  0.1  0.5  0.7  5.2
; i.max	|  0.6  0.9  1.0  1.1  1.3  0.2  0.7  0.9  1.3
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	44
>Kr_chr3L_20630505_206305
aacccttt
>Kr_chr3L_20630537_206305
aacccttt
>Kr_chr3L_8641253_8641262
aacccttt
>Kr_chr3L_20630560_206305
aacccttt
>Kr_chr3L_8639823_8639832
aacccttt
>Kr_chr3L_20630373_206303
aacccttt
>Kr_chr3L_8639587_8639596
aacccttt
>Kr_chr3L_8640829_8640838
aacccgtt
>Kr_chr2R_5490139_5490149
aacccgtt
>Kr_chr2R_5489851_5489860
aacccggt
>Kr_chr2L_11455800_114558
tacccttt
>Kr_chr3L_21022228_210222
tacccttt
>Kr_chr3L_21022078_210220
tacccttt
>Kr_chr3R_12598980_125989
gacccttt
>Kr_chr3R_12636469_126364
cacccttt
>Kr_chr3L_8640882_8640891
gacccgtt
>Kr_chr2R_5489663_5489672
aatccgtt
>Kr_chr3L_8640857_8640866
aagccttt
>Kr_chr3L_8641120_8641129
aagccttt
>Kr_chr2R_5490045_5490055
aatccctt
>Kr_chr2L_11455642_114556
aatccctt
>Kr_chr2R_5490096_5490105
aacccagt
>Kr_chr3L_20630442_206304
aactcttt
>Kr_chr3L_8644087_8644106
aactcttt
>Kr_chr2R_5489926_5489946
aagccctt
>Kr_chr2R_5489577_5489585
tacccggt
>Kr_chr2L_11456018_114560
cacccatt
>Kr_chr2R_5489528_5489537
aacccaat
>Kr_chr3L_8644209_8644261
aacctctt
>Kr_chr2L_11455986_114560
catccttt
>Kr_chr3L_21021993_210220
gtcccctt
>Kr_chr2R_7044648_7044657
aaccagtt
>Kr_chr2R_5489954_5489999
atcccgat
>Kr_chr3L_8639315_8639324
cactcctt
>Kr_chr3R_4520998_4521009
tgcccctt
>Kr_chr3L_8640920_8640929
aacccgaa
>Kr_chr2R_5489612_5489622
gtcccagt
>Kr_chr3L_8641004_8641011
aacatttt
>Kr_chr2R_5489810_5489818
attccgtc
>Kr_chr2R_5489784_5489792
aacacgct
>Kr_chr3L_8639521_8639530
ttccctgc
>Kr_chr3L_8639465_8639474
aactcagc
>Kr_chr3L_8641146_8641155
aacaccaa
>Kr_chr3R_4520681_4520692
agtcccgc
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.287|c:0.213|g:0.213|t:0.287
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Kr_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	44
;	meme.llr                     	241
;	meme.E-value                 	5.5e-40
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.213
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.17117
;	information.per.column       	0.646396
;	max.possible.info.per.col    	1.54646
;	consensus.strict             	aACCCttT
;	consensus.strict.rc          	AaaGGGTt
;	consensus.IUPAC              	aACCCktT
;	consensus.IUPAC.rc           	AamGGGTt
;	consensus.regexp             	aACCC[gt]tT
;	consensus.regexp.rc          	Aa[ac]GGGTt
;	residues.content.crude.freq  	a:0.2330|c:0.3722|g:0.0767|t:0.3182
;	G+C.content.crude.freq       	0.448864
;	residues.content.corrected.freq	a:0.2342|c:0.3686|g:0.0797|t:0.3175
;	G+C.content.corrected.freq   	0.448356
;	min(P(S|M))                  	9.49209e-16
;	max(P(S|M))                  	0.0864747
;	proba_range                  	0.0864747
;	Wmin                         	-22.8
;	Wmax                         	8.7
;	Wrange                       	31.5
; Job started 2007_12_10.132113
; Job done    2007_12_10.132113