This reports the protocol used to align the Maize_FSTMu features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 17:25:22 2007


Source of Maize_FSTMu : Downloaded from genbank with query ' (txid4577[ORGN] AND Walbot[AUTH] AND RescueMu[TITL])' 

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

178124 Maize_FSTMu are aligned to Oryza_sativa_indica-chromosome-20070724 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-Genomic' data sets.

Initial summary
# alignments : 14972
# unique Features these alignments represent: 12552
% of total features these alignments represent : 7.05 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 10537
150	 2245
200	 796
250	 504
300	 252
350	 144
400	 151
450	 149
500	 102
550	 44
600	 38
650	 9
700	 1
750	 0
800	 0
10000	 0

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 4467
# unique Features these remaining alignments represent: 3510
% of total features these alignments represent : 1.97 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 4389
2000	 17
3000	 4
4000	 2
5000	 2
6000	 0
7000	 0
8000	 3
9000	 1
10000	 0
20000	 2

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 4412
# unique Features these remaining alignments represent: 3462
% of total features these alignments represent : 1.94 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2853
2	 432
3	 113
4	 43
5	 16
6	 0
8	 0
9	 0
10	 0
20	 2
30	 3
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 4056
# unique Features these remaining alignments represent: 3398
% of total features these alignments represent : 1.91 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 0
80	 0
90	 0
100	 4056

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 4056
# unique Features these remaining alignments represent: 3398
% of total features these alignments represent : 1.91 %

Following is the final summary
# alignments : 4056
# unique Features these alignments represent: 3398
% of total features these alignments represent : 1.91 %
  

Last modified: Thu Sep 13 15:01:03 2007