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Tutorial
**Eliminate Orphans - Remove comparison maps that don't have correspondences to a reference map.
Map Options
Map Options
Map Set
Add Maps
Left
peanut-AA_A.duranensis_x_A.stenosperma_d
(Reference Set)
pigeonpea-CcCookUCDavis2009
Add Maps
Right
Min.
Correspondences
Align Vertically
Stack
Maps
A02
CcLG01
CcLG08
CcLG10
Start
Stop
Magnification
1/8
1/4
1/2
Original
2
3
4
5
10
20
1/8
1/4
1/2
Original
2
3
4
5
10
20
1/8
1/4
1/2
Original
2
3
4
5
10
20
1/8
1/4
1/2
Original
2
3
4
5
10
20
Flipped
hint: To save time, select the desired options before redrawing the map.
(Hide Map Menu)
Feature Options
Feature Options
Highlight Features:
Feature Types:
Feature
Ignore
Display if
Correspondence
Always Display
QTL_nematode
SNP
SSR
Other
Show Labels:
None
Landmarks
All
Collapse Overlapping
Features:
No
Yes
(Hide Feature Menu)
Correspondence Options
Correspondence Options
Include Correspondence Types:
Evidence
Ignore
Use
Less Than
Score
Greater Than
Score
Score
Automated name-based
automatic
blastn
e-PCR
tblastx
Aggregate Correspondences:
No
1 Line
2 Lines
Correspondence lines drawn to:
Feature
Map
View Intra-Slot Correspondences:
No
yes
Aggregate evidence types separately:
No
yes
(Hide Correspondence Menu)
Display Options
Display Options
Map Size:
tiny
small
medium
large
Custom
Font Size:
Small
Medium
Large
Image Type:
PNG
GIF
SVG *
Clean View (no navigation buttons):
No
Yes
Hide the Legend:
No
Yes
Size of Dot Plot Pixels: 1
1
2
3
4
5
6
7
8
9
10
*
SVG output for high-resolution printing only (no hyperlinks).
(Hide Display Menu)
Advanced Options
Advanced Options
Draw Maps Using
Same Scale:
No
Yes
Clickable Image
Use All
Omit Features
Omit All Buttons
Menu Order of Comparative Maps:
Predefined
Order
Number of
Correspondences
Ignore Image Map
Sanity Check:
No
Yes
(Hide Advanced Menu)