This reports the protocol used to align the Rice_rflp_marker_rice features to Maize_BACs.
 Kiran Ratnapu 
Tue Mar 29 19:14:57 2005


Source of Rice_rflp_marker_rice : Obtained from Gramene Marker database  

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

4333 Rice_rflp_marker_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 : 380
# unique Features these alignments represent: 305
% of total features these alignments represent : 7.04 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 106
150	 75
200	 57
250	 64
300	 30
350	 27
400	 11
450	 0
500	 0
550	 8
600	 0
650	 0
700	 0
750	 0
800	 0
10000	 2

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 200
# unique Features these remaining alignments represent: 148
% of total features these alignments represent : 3.42 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 119
2	 25
3	 0
4	 0
5	 0
6	 0
8	 4
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 169
# unique Features these remaining alignments represent: 144
% of total features these alignments represent : 3.32 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 2
80	 8
90	 97
95	 49
100	 13

Following is the distribution of Rice gaps
Rice_Gaps	# features
--------	--------
1000	 160
2000	 3
3000	 3
4000	 0
5000	 1
6000	 1
7000	 0
8000	 0
9000	 0
10000	 1

Following is the final summary
# alignments : 169
# unique Features these alignments represent: 144
% of total features these alignments represent : 3.32 %