This reports the protocol used to align the Sugarcane_ArrayConsensus_Affy8K features to tigrv4-genome.
Fri Sep 29 14:28:46 2006


Source of Sugarcane_ArrayConsensus_Affy8K : Downloaded from http://www.affymetrix.com/support/technical/byproduct.affx?product=sugarcane 

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

8224 Sugarcane_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 : 6066
# unique Features these alignments represent: 5562
% of total features these alignments represent : 67.63 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 562
150	 586
200	 529
250	 577
300	 500
350	 444
400	 404
450	 365
500	 246
550	 203
600	 186
650	 169
700	 147
750	 126
800	 113
10000	 909

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 4929
# unique Features these remaining alignments represent: 4529
% of total features these alignments represent : 55.07 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 4363
2	 82
3	 27
4	 21
5	 13
6	 10
8	 7
9	 3
10	 2
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 4608
# unique Features these remaining alignments represent: 4472
% of total features these alignments represent : 54.38 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 1
60	 4
70	 12
80	 221
90	 3125
95	 1161
100	 84

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 2844
2000	 908
3000	 455
4000	 189
5000	 71
6000	 33
7000	 21
8000	 11
9000	 4
10000	 3

Following is the final summary
# alignments : 4608
# unique Features these alignments represent: 4472
% of total features these alignments represent : 54.38 %