This reports the protocol used to align the Sorghum_Marker features to tigrv4-genome.
Fri Apr 14 11:44:34 2006


Source of Sorghum_Marker : These are from Paterson 

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

2146 Sorghum_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 : 1138
# unique Features these alignments represent: 1086
% of total features these alignments represent : 50.61 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 195
150	 154
200	 183
250	 122
300	 109
350	 117
400	 84
450	 74
500	 37
550	 25
600	 11
650	 4
700	 5
750	 6
800	 2
10000	 10

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 791
# unique Features these remaining alignments represent: 751
% of total features these alignments represent : 35.00 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 727
2	 17
3	 3
4	 1
5	 1
6	 2
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 : 770
# unique Features these remaining alignments represent: 747
% of total features these alignments represent : 34.81 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 1
60	 2
70	 7
80	 48
90	 404
95	 126
100	 182

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 687
2000	 50
3000	 13
4000	 4
5000	 1
6000	 2
7000	 0
8000	 1
9000	 0
10000	 2

Following is the final summary
# alignments : 770
# unique Features these alignments represent: 747
% of total features these alignments represent : 34.81 %