This reports the protocol used to align the MaizeCornchip0_ArrayConsensus_Affy8K features to tigrv4-genome.
Fri Sep 29 14:28:51 2006


Source of MaizeCornchip0_ArrayConsensus_Affy8K : Downloaded from http://www.plexdb.org/modules/PD_general/download_exp.php?exp_no=ZM1 

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

8475 MaizeCornchip0_ArrayConsensus_Affy8K 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 : 4753
# unique Features these alignments represent: 4282
% of total features these alignments represent : 50.53 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 788
150	 874
200	 987
250	 798
300	 680
350	 441
400	 117
450	 40
500	 18
550	 10
600	 0
650	 0
700	 0
750	 0
800	 0
10000	 0

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 3109
# unique Features these remaining alignments represent: 2786
% of total features these alignments represent : 32.87 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2638
2	 92
3	 10
4	 6
5	 19
6	 13
8	 6
9	 2
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 2852
# unique Features these remaining alignments represent: 2740
% of total features these alignments represent : 32.33 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 1
60	 1
70	 9
80	 182
90	 1925
95	 693
100	 41

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 2611
2000	 147
3000	 52
4000	 3
5000	 3
6000	 4
7000	 4
8000	 0
9000	 2
10000	 5

Following is the final summary
# alignments : 2852
# unique Features these alignments represent: 2740
% of total features these alignments represent : 32.33 %