This reports the protocol used to align the Wheat_Marker features to Maize_BACs_20060126.
Mon Feb 13 16:41:22 2006


Source of Wheat_Marker : Downloaded from genbank with query ' txid4564[orgn]  AND  gbdiv_est[PROP]' 

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

3670 Wheat_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 : 503
# unique Features these alignments represent: 464
% of total features these alignments represent : 12.64 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 98
150	 78
200	 86
250	 84
300	 51
350	 36
400	 33
450	 23
500	 9
550	 4
600	 1
650	 0
700	 0
750	 0
800	 0
10000	 0

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 331
# unique Features these remaining alignments represent: 303
% of total features these alignments represent : 8.26 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 279
2	 20
3	 4
4	 0
5	 0
6	 0
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 : 331
# unique Features these remaining alignments represent: 303
% of total features these alignments represent : 8.26 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 0
60	 1
70	 6
80	 49
90	 216
95	 56
100	 2

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 299
2000	 17
3000	 6
4000	 3
5000	 1
6000	 2
7000	 0
8000	 1
9000	 0
10000	 0

Following is the final summary
# alignments : 331
# unique Features these alignments represent: 303
% of total features these alignments represent : 8.26 %