<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype   = out/chromosome.txt
chromosomes_display_default = yes

background = white
chromosomes_units           = 1000

<image>
dir = out
svg = yes
file  = map
# radius of inscribed circle in image
radius         = 750p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

units_ok        = bupr
units_nounit    = n

<plots>

<plot>
type             = text
color            = black
file             = out/labels.txt

# on tick scale
r0 = 1r
r1 = 1r+200p

show_links     = yes
link_dims      = 0p,0p,30p,0p,10p
link_thickness = 4p
link_color     = grey

label_size   = 25p
label_font   = condensed

padding  = 0p
rpadding = 0p

</plot>

</plots>

<highlights>

stroke_color = black
stroke_thickness = 2

<highlight>
file       = out/positive_strand.txt
r0         = 0.99r
r1         = 0.90r
fill_color = optred
</highlight>

<highlight>
file       = out/negative_strand.txt
r0         = 0.99r
r1         = 0.90r
fill_color = optorange
</highlight>

<highlight>
file             = out/synteny_1448A_small_plasmid.txt
r0               = 0.7r
r1               = 0.65r
stroke_thickness = 0
fill_color       = optblue
</highlight>

<highlight>
file             = out/synteny_ES4326_plasmid_a.txt
r0               = 0.64r
r1               = 0.59r
stroke_thickness = 0
fill_color       = optgreen
</highlight>

<highlight>
file             = out/synteny_Pf-5_genome.txt
r0               = 0.53r
r1               = 0.48r
stroke_thickness = 0
fill_color       = optyellow
</highlight>

<highlight>
file             = out/synteny_PA7_genome.txt
r0               = 0.47r
r1               = 0.42r
stroke_thickness = 0
fill_color       = optpurple
</highlight>

</highlights>