--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/circos-files/synteny-region-default.conf	Mon Feb 10 09:06:15 2014 -0500
@@ -0,0 +1,110 @@
+# The <ideogram> block defines the position, size, labels and other
+# properties of the segments on which data are drawn. These segments
+# are usually chromosomes, but can be any integer axis.
+
+<ideogram>
+
+<spacing>
+# Spacing between ideograms. Suffix "r" denotes a relative value. It
+# is relative to circle circumference (e.g. space is 0.5% of
+# circumference).
+default = 0.005r
+</spacing>
+
+# Ideogram position, thickness and fill. 
+#
+# Radial position within the image of the ideograms. This value is
+# usually relative ("r" suffix).
+radius           = 0.65r
+
+# Thickness of ideograms, which can be absolute (e.g. pixels, "p"
+# suffix) or relative ("r" suffix). When relative, it is a fraction of
+# image radius.
+thickness        = 30p
+
+# Ideograms can be drawn as filled, outlined, or both. When filled,
+# the color will be taken from the last field in the karyotype file,
+# or set by chromosomes_colors. Color names are discussed in
+#
+# http://www.circos.ca/documentation/tutorials/configuration/configuration_files
+#
+# When stroke_thickness=0p or if the parameter is missing, the ideogram is
+# has no outline and the value of stroke_color is not used.
+
+fill             = yes   # A
+
+stroke_color     = dgrey # B
+stroke_thickness = 1p    # B
+
+# Minimum definition for ideogram labels.
+
+show_label       = yes
+# see etc/fonts.conf for list of font names
+label_font       = bold
+label_radius     = (dims(ideogram,radius_inner)+dims(ideogram,radius_outer)-conf(ideogram,label_size))/2
+label_with_tag   = yes
+
+label_size       = 14 
+label_color = white
+label_parallel   = yes
+
+
+</ideogram>
+
+
+
+show_ticks          = yes
+show_tick_labels    = yes
+
+<ticks>
+
+radius           = 1r
+color            = black
+thickness        = 1p
+
+# the tick label is derived by multiplying the tick position
+# by 'multiplier' and casting it in 'format':
+#
+# sprintf(format,position*multiplier)
+
+multiplier       = 1e-6
+
+# %d   - integer
+# %f   - float
+# %.1f - float with one decimal
+# %.2f - float with two decimals
+#
+# for other formats, see http://perldoc.perl.org/functions/sprintf.html
+
+format           = %d
+
+<tick>
+spacing        = 0.1u
+size           = 5p
+</tick>
+
+<tick>
+spacing        = 1u
+size           = 10p
+show_label     = yes
+label_size     = 12p
+label_offset   = 10p
+format         = %d
+</tick>
+
+</ticks>
+
+#
+# These should be present in every Circos configuration file and
+# overridden as required. To see the content of these files, 
+# look in etc/ in the Circos distribution.
+
+
+
+# RGB/HSV color definitions, color lists, location of fonts, fill patterns.
+# Included from Circos distribution.
+<<include etc/colors_fonts_patterns.conf>> 
+
+# Debugging, I/O an dother system parameters
+# Included from Circos distribution.
+<<include etc/housekeeping.conf>>