src/hg/lib/simpleRepeat.as 1.5

Index: src/hg/lib/simpleRepeat.as
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/simpleRepeat.as,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/lib/simpleRepeat.as	3 Feb 2006 19:19:01 -0000	1.4
+++ src/hg/lib/simpleRepeat.as	12 Jan 2010 22:33:35 -0000	1.5
@@ -1,20 +1,20 @@
 table simpleRepeat
 "Describes the Simple Tandem Repeats"
    (
    string chrom;      	"Reference sequence chromosome or scaffold"
    uint   chromStart; 	"Start position in chromosome"
    uint   chromEnd;   	"End position in chromosome"
    string name;       	"Simple Repeats tag name"
    uint   period;     	"Length of repeat unit"
    float  copyNum;    	"Mean number of copies of repeat"
    uint   consensusSize;	"Length of consensus sequence"
    uint   perMatch;  	"Percentage Match"
    uint   perIndel;  	"Percentage Indel"
-   uint   score; 	"Score between  and .  Best is ."
+   uint   score; 	"Alignment Score = 2*match-7*mismatch-7*indel; minscore=50"
    uint   A;  	"Percent of A's in repeat unit"
    uint   C;  	"Percent of C's in repeat unit"
    uint   G;  	"Percent of G's in repeat unit"
    uint   T;  	"Percent of T's in repeat unit"
    float   entropy;  	"Entropy"
    lstring sequence;    	"Sequence of repeat unit element"
    )