e9fe6f3c5455766752d686cc105632684dd326f8
galt
  Fri May 29 18:51:55 2020 -0700
Adding short paragraph explainging the new All Results checkbox. refs #25477.

diff --git src/hg/hgBlat/hgBlat.c src/hg/hgBlat/hgBlat.c
index 151fdbf..659413e 100644
--- src/hg/hgBlat/hgBlat.c
+++ src/hg/hgBlat/hgBlat.c
@@ -1700,31 +1700,31 @@
 cgiMakeDropList("sort", pslSortList, ArraySize(pslSortList), cartOptionalString(cart, "sort"));
 printf("</TD>\n");
 printf("<TD ALIGN=CENTER>\n");
 cgiMakeDropList("output", outputList, ArraySize(outputList), cartOptionalString(cart, "output"));
 printf("</TD>\n");
 printf("</TR>\n<TR>\n");
 userSeq = cartUsualString(cart, "userSeq", "");
 printf("<TD COLSPAN=5 ALIGN=CENTER>\n");
 htmlPrintf("<TEXTAREA NAME=userSeq ROWS=14 COLS=140>%s</TEXTAREA>\n", userSeq);
 printf("</TD>\n");
 printf("</TR>\n");
 
 printf("<TR>\n");
 printf("<TD COLSPAN=1 ALIGN=CENTER style='overflow:hidden;white-space:nowrap;font-size:0.9em'>\n");
 cgiMakeCheckBoxWithId("allResults", allResults, "allResults");
-printf("<span id=allResultsText>All Results (no minimum score of 20bp)<span>");
+printf("<span id=allResultsText>All Results (no minimum matches)");
 // clicking on the All Results text clicks the checkbox.
 jsOnEventById("click", "allResultsText", 
     "document.mainForm.allResults.click();"
     "return false;"   // cancel the default
     );
 printf("</TD>\n");
 
 printf("<TD COLSPAN=4 style='text-align:right'>\n");
 printf("<INPUT style='height:1.5em; width:100px; font-size:1.2em' TYPE=SUBMIT NAME=Submit VALUE=Submit>\n");
 printf("<INPUT style='font-size:1.2em' TYPE=SUBMIT NAME=Lucky VALUE=\"I'm feeling lucky\">\n");
 printf("<INPUT style='font-size:1.2em' TYPE=SUBMIT NAME=Clear VALUE=Clear>\n");
 printf("</TD>\n");
 printf("</TR>\n");
 
 printf("<TR>\n"); 
@@ -1741,30 +1741,35 @@
 puts("Rather than pasting a sequence, you can choose to upload a text file containing "
 	 "the sequence.<BR>");
 puts("Upload sequence: <INPUT TYPE=FILE NAME=\"seqFile\">");
 puts(" <INPUT TYPE=SUBMIT Name=Submit VALUE=\"submit file\"><P>\n");
 printf("%s", 
 "<P>Only DNA sequences of 25,000 or fewer bases and protein or translated \n"
 "sequence of 10000 or fewer letters will be processed.  Up to 25 sequences\n"
 "can be submitted at the same time. The total limit for multiple sequence\n"
 "submissions is 50,000 bases or 25,000 letters.<br> A valid example "
 "is <tt>GTCCTCGGAACCAGGACCTCGGCGTGGCCTAGCG</tt> (human SOD1).\n</P>\n");
 
 printf("%s", 
 "<P>The <b>Search all</b> checkbox allows you to search all\n"
 "genomes at the same time. It will query the default assembly of every organism and BLAT servers of attached hubs.\n");
 
+printf("<P>The <b>All Results</b> checkbox disables minimum matches filtering so all results are seen." 
+" For example, with a human dna search, 20 is minimum matches required, based on the genome size, to filter out lower-quality results.\n"
+"This checkbox can be useful with short queries and with the tiny genomes of microorganisms. \n"
+);
+
 if (hgPcrOk(db))
     printf("<P>For locating PCR primers, use <A HREF=\"../cgi-bin/hgPcr?db=%s\">In-Silico PCR</A>"
            " for best results instead of BLAT.</P>", db);
 puts("</TD></TR></TABLE>\n");
 
 
 
 printf("</FORM>\n");
 
 webNewSection("About BLAT");
 printf( 
 "<P>BLAT on DNA is designed to\n"
 "quickly find sequences of 95%% and greater similarity of length 25 bases or\n"
 "more.  It may miss more divergent or shorter sequence alignments.  It will find\n"
 "perfect sequence matches of 20 bases.\n"