This reports the protocol used to align the Rice_FSTtos17 features to Maize_BACs_20060126.
Mon Feb 13 18:36:13 2006


Source of Rice_FSTtos17 : Downloaded from genbank using the query 'txid4530[orgn] AND tos17[TITL] AND GSS[KYWD]' 

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

18024 Rice_FSTtos17 are aligned to Maize_BACs_20060126 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 : 661
# unique Features these alignments represent: 582
% of total features these alignments represent : 3.23 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 218
150	 144
200	 71
250	 85
300	 56
350	 33
400	 25
450	 15
500	 5
550	 6
600	 2
650	 1
700	 0
750	 0
800	 0
10000	 0

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 443
# unique Features these remaining alignments represent: 381
% of total features these alignments represent : 2.11 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 421
2000	 0
3000	 0
4000	 0
5000	 2
6000	 0
7000	 0
8000	 0
9000	 0
10000	 0
20000	 1

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 421
# unique Features these remaining alignments represent: 367
% of total features these alignments represent : 2.04 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 320
2	 42
3	 3
4	 2
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 : 413
# unique Features these remaining alignments represent: 365
% of total features these alignments represent : 2.03 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 2
40	 2
50	 3
60	 21
70	 57
80	 74
90	 216
100	 38

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 388
# unique Features these remaining alignments represent: 343
% of total features these alignments represent : 1.90 %

Following is the final summary
# alignments : 388
# unique Features these alignments represent: 343
% of total features these alignments represent : 1.90 %