This reports the protocol used to align the Maize_ArrayConsensus_Affy18K features to tigrv4-genome. Fri Apr 14 17:55:34 2006 Source of Maize_ArrayConsensus_Affy18K : NULL Alignment procedure details --------------------------- 17555 Maize_ArrayConsensus_Affy18K 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 : 13156 # unique Features these alignments represent: 12312 % of total features these alignments represent : 70.13 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 1069 150 1151 200 1226 250 1130 300 1097 350 1017 400 949 450 778 500 605 550 496 600 425 650 421 700 353 750 335 800 257 10000 1847 Alignments with matches less than 150 bp are deleted # remaining Alignments : 10980 # unique Features these remaining alignments represent: 10309 % of total features these alignments represent : 58.72 % Frequency distribution of the remaining features # hits # features -------- -------- 1 9999 2 181 3 46 4 26 5 22 6 8 8 18 9 6 10 2 20 1 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 10499 # unique Features these remaining alignments represent: 10226 % of total features these alignments represent : 58.25 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 1 50 0 60 9 70 52 80 737 90 7557 95 1976 100 167 Following is the distribution of gaps Gaps # features -------- -------- 1000 6307 2000 2008 3000 1108 4000 455 5000 224 6000 99 7000 42 8000 40 9000 23 10000 18 Following is the final summary # alignments : 10499 # unique Features these alignments represent: 10226 % of total features these alignments represent : 58.25 %