This reports the protocol used to align the Wheat_Marker features to tigrv4-genome.
Fri Apr 14 11:48:34 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 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 : 3640
# unique Features these alignments represent: 3565
% of total features these alignments represent : 97.14 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 39
150	 90
200	 624
250	 672
300	 603
350	 523
400	 445
450	 314
500	 194
550	 96
600	 33
650	 7
700	 0
750	 0
800	 0
10000	 0

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 3529
# unique Features these remaining alignments represent: 3455
% of total features these alignments represent : 94.14 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 3386
2	 64
3	 5
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 : 3529
# unique Features these remaining alignments represent: 3455
% of total features these alignments represent : 94.14 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 1
70	 26
80	 250
90	 2465
95	 761
100	 26

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 2935
2000	 388
3000	 86
4000	 36
5000	 12
6000	 9
7000	 8
8000	 2
9000	 4
10000	 3

Following is the final summary
# alignments : 3529
# unique Features these alignments represent: 3455
% of total features these alignments represent : 94.14 %