a9947a9b812bb9ac68e6758a7976e00dae5f3aec
galt
  Thu May 2 14:46:13 2019 -0700
Further improving hgBlat blat all genomes explanation.

diff --git src/hg/hgBlat/hgBlat.c src/hg/hgBlat/hgBlat.c
index a13fc42..2b520da 100644
--- src/hg/hgBlat/hgBlat.c
+++ src/hg/hgBlat/hgBlat.c
@@ -1924,33 +1924,33 @@
 	    {
 	    slSort(&pfdDone, rcPairsCmp);  
 	    hideWeakerOfQueryRcPairs(pfdDone);
 	    }
 
 	// requires db for chromSize, do database after multi-threading done.
 	changeMaxGenePositionToPositiveStrandCoords(pfdDone);
 
         // sort by maximum hits
 	slSort(&pfdDone, genomeHitsCmp);
 
 	// Print instructions
         printf("The single best alignment found for each assembly is shown below.<br>\n"
 		"The approximate results below are sorted by number of matching 'tiles', "
                 "perfectly matching sub-sequences of length 11 (DNA) "
-                "or 4 (protein). <br>");
+                "or 4 (protein). Using only tile hits, this speedy method can not see mismatches.<br>");
 	printf("Click the 'assembly' link to trigger a full BLAT alignment for that genome. \n");
-	printf("If its alignment score is < 20, including gaps and mismatches, no match will be found.<br>\n");
+	printf("If its alignment score which includes gaps and mismatches is less than 20, no match will be found.<br>\n");
 
 	// Print report  // TODO move to final report at the end of ALL Assemblies
 	int lastSeqNumber = -1;
 	int idCount = 0;
 	char id[256];
 	struct genomeHits *gH = NULL;
 	for (gH = pfdDone; gH; gH = gH->next)
 	    {
 	    if (lastSeqNumber != gH->seqNumber)
 		{
 		if (lastSeqNumber != -1) // end previous table
 		    {
 		    printf("</TABLE><br><br>\n");
 		    }
 		lastSeqNumber = gH->seqNumber;