This reports the protocol used to align the Sorghum_Marker features to Maize_BACs_20060126.
Mon Feb 13 15:25:52 2006


Source of Sorghum_Marker : These are from Paterson 

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

2146 Sorghum_Marker 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 : 287
# unique Features these alignments represent: 253
% of total features these alignments represent : 11.79 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 61
150	 33
200	 40
250	 35
300	 22
350	 36
400	 12
450	 16
500	 5
550	 5
600	 8
650	 2
700	 4
750	 1
800	 1
10000	 6

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 195
# unique Features these remaining alignments represent: 170
% of total features these alignments represent : 7.92 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 157
2	 9
3	 2
4	 0
5	 0
6	 1
8	 1
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 181
# unique Features these remaining alignments represent: 168
% of total features these alignments represent : 7.83 %

% 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	 56
95	 88
100	 29

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 164
2000	 7
3000	 0
4000	 0
5000	 5
6000	 0
7000	 0
8000	 0
9000	 1
10000	 0

Following is the final summary
# alignments : 181
# unique Features these alignments represent: 168
% of total features these alignments represent : 7.83 %