This reports the protocol used to align the Rice_MarkerRFLP features to Maize_BACs_20060126.
Mon Feb 13 13:58:20 2006


Source of Rice_MarkerRFLP : Obtained from Gramene Marker database 

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

4333 Rice_MarkerRFLP are aligned to Maize_BACs_20060126 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 : 378
# unique Features these alignments represent: 317
% of total features these alignments represent : 7.32 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 109
150	 73
200	 49
250	 68
300	 33
350	 26
400	 10
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 : 196
# unique Features these remaining alignments represent: 152
% of total features these alignments represent : 3.51 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 131
2	 17
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 : 165
# unique Features these remaining alignments represent: 148
% of total features these alignments represent : 3.42 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 1
80	 9
90	 103
95	 44
100	 8

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 156
2000	 2
3000	 3
4000	 1
5000	 1
6000	 1
7000	 0
8000	 0
9000	 0
10000	 1

Following is the final summary
# alignments : 165
# unique Features these alignments represent: 148
% of total features these alignments represent : 3.42 %