This reports the protocol used to align the Maize_ArrayConsensus_Affy18K features to tigrv4-genome.
Fri Apr 14 17:55:34 2006


Source of Maize_ArrayConsensus_Affy18K : NULL 

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

17555 Maize_ArrayConsensus_Affy18K are aligned to tigrv4-genome 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 : 13156
# unique Features these alignments represent: 12312
% of total features these alignments represent : 70.13 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 1069
150	 1151
200	 1226
250	 1130
300	 1097
350	 1017
400	 949
450	 778
500	 605
550	 496
600	 425
650	 421
700	 353
750	 335
800	 257
10000	 1847

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 10980
# unique Features these remaining alignments represent: 10309
% of total features these alignments represent : 58.72 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 9999
2	 181
3	 46
4	 26
5	 22
6	 8
8	 18
9	 6
10	 2
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 10499
# unique Features these remaining alignments represent: 10226
% of total features these alignments represent : 58.25 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 0
60	 9
70	 52
80	 737
90	 7557
95	 1976
100	 167

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 6307
2000	 2008
3000	 1108
4000	 455
5000	 224
6000	 99
7000	 42
8000	 40
9000	 23
10000	 18

Following is the final summary
# alignments : 10499
# unique Features these alignments represent: 10226
% of total features these alignments represent : 58.25 %