0690b4ca888dc702e80b96144c6977082b101efe
Merge parents a9947a9 1b5d4cf
galt
  Thu May 2 14:53:53 2019 -0700
finish merge conflict, polished text a little.

diff --cc src/hg/hgBlat/hgBlat.c
index 2b520da,17f6a05..2e83601
--- src/hg/hgBlat/hgBlat.c
+++ src/hg/hgBlat/hgBlat.c
@@@ -1924,33 -1924,34 +1924,34 @@@
  	    {
  	    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 which includes gaps and mismatches is less than 20, no match will be found.<br>\n");
 -	printf("If its alignment score is &lt; 20 bp, including gaps and mismatches, no match will be found.<br>\n");
++	printf("The entire alignment, including mismatches and gaps, must score 20 or higher in order to appear in the Blat output.<br>\n");
+ 	printf("For more details see the <a href='/FAQ/FAQblat.html#blat9'>BLAT FAQ</a>.<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;