This reports the protocol used to align the nonRice_MarkerRFLP features to Maize_BACs_20060126.
Mon Feb 13 12:18:00 2006


Source of nonRice_MarkerRFLP : These are obtained from Cornell 

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

1897 nonRice_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 : 244
# unique Features these alignments represent: 217
% of total features these alignments represent : 11.44 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 54
150	 29
200	 31
250	 27
300	 18
350	 26
400	 12
450	 15
500	 5
550	 5
600	 6
650	 2
700	 4
750	 1
800	 1
10000	 8

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 163
# unique Features these remaining alignments represent: 145
% of total features these alignments represent : 7.64 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 135
2	 6
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 : 153
# unique Features these remaining alignments represent: 143
% of total features these alignments represent : 7.54 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 2
80	 6
90	 42
95	 79
100	 24

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 140
2000	 6
3000	 0
4000	 0
5000	 2
6000	 0
7000	 0
8000	 0
9000	 1
10000	 0

Following is the final summary
# alignments : 153
# unique Features these alignments represent: 143
% of total features these alignments represent : 7.54 %