This reports the protocol used to align the Rice_rflp_marker_non_rice features to Maize_BACs.
 Kiran Ratnapu 
Tue Mar 29 19:07:31 2005


Source of Rice_rflp_marker_non_rice : Obtained from Gramene Marker database  

Alignment procedure details 
--------------------------- 

1897 Rice_rflp_marker_non_rice are aligned to Maize_BACs using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Coding' data sets.

Initial summary
# alignments : 240
# unique Features these alignments represent: 212
% of total features these alignments represent : 11.18 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 50
150	 30
200	 30
250	 27
300	 19
350	 25
400	 13
450	 16
500	 3
550	 6
600	 5
650	 2
700	 3
750	 2
800	 1
10000	 8

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 162
# unique Features these remaining alignments represent: 142
% of total features these alignments represent : 7.49 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 130
2	 8
3	 2
4	 1
5	 0
6	 1
8	 0
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 152
# unique Features these remaining alignments represent: 140
% of total features these alignments represent : 7.38 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 2
80	 5
90	 40
95	 80
100	 25

Following is the distribution of Rice gaps
Rice_Gaps	# features
--------	--------
1000	 139
2000	 7
3000	 0
4000	 0
5000	 1
6000	 0
7000	 0
8000	 0
9000	 1
10000	 0

Following is the final summary
# alignments : 152
# unique Features these alignments represent: 140
% of total features these alignments represent : 7.38 %