# HG changeset patch
# User iuc
# Date 1669973754 0
# Node ID 2a89f630fa855e42040dd77ff6d6140fa36f98c9
# Parent  c449963debd520c34d80bf306e501621a7a6107f
planemo upload commit 3bb07d25ab817c936018d57b6d81f728915cfadf

diff -r c449963debd5 -r 2a89f630fa85 blat.xml
--- a/blat.xml	Mon Nov 21 11:12:14 2022 +0000
+++ b/blat.xml	Fri Dec 02 09:35:54 2022 +0000
@@ -3,6 +3,23 @@
     <macros>
         <token name="@TOOL_VERSION@">377</token>
         <token name="@VERSION_SUFFIX@">0</token>
+
+        <xml name="mask_cond" tokens="maskarg,label,help">
+            <conditional name="@MASKARG@_type">
+                <param  argument="-@MASKARG@" type="select" label="@LABEL@" help="@HELP@">
+                    <option value="" selected="true">No masking</option>
+                    <option value="lower">lower - mask out lower-cased sequence</option>
+                    <option value="upper">upper - mask out upper-cased sequence</option>
+                    <option value="file.out">out - mask database according to RepeatMasker out</option>
+                </param>
+                <when value="" />
+                <when value="lower" />
+                <when value="upper" />
+                <when value="file.out">
+                    <param name="@MASKARG@_file" type="data" format="txt" label="RepeatMasker file.out" />
+                </when>
+            </conditional>
+        </xml>
     </macros>
     <xrefs>
         <xref type="bio.tools">blat</xref>
@@ -28,31 +45,60 @@
     blat
         -q=$query_type
         -t=$database_type
-        $oneOff
-        #if str($minScore)
-            -minScore=$minScore
+        ## Basic alignment parameters
+        #if str($basic_align.minScore)
+            -minScore=$basic_align.minScore
+        #end if
+        #if str($basic_align.minIdentity)
+            -minIdentity=$basic_align.minIdentity
+        #end if
+        $basic_align.trimT
+        $basic_align.noTrimA
+        $basic_align.trimHardA
+        $basic_align.fastMap
+        $basic_align.fine
+        #if str($basic_align.maxIntron)
+            -maxIntron=$basic_align.maxIntron
+        #end if
+        $basic_align.extendThroughN
+        ## Advanced alignment parameters
+        #if str($adv_align.tileSize)
+            -tileSize=$adv_align.tileSize
+        #end if
+        #if str($adv_align.stepSize)
+            -stepSize=$adv_align.stepSize
         #end if
-        -maxGap=$maxGap
-        #if str($repMatch)
-            -repMatch=$repMatch
+        $adv_align.oneOff
+        #if str($adv_align.minMatch)
+            -minMatch=$adv_align.minMatch
+        #end if
+        -maxGap=$adv_align.maxGap
+        #if str($adv_align.repMatch)
+            -repMatch=$adv_align.repMatch
+        #end if
+        ## Repeat masking parameters
+        #if $repeat.mask_type.mask == "file.out":
+            -mask='$repeat.mask_type.mask_file'
+        #elif $repeat.mask_type.mask:
+            -mask=$repeat.mask_type.mask
         #end if
-        #if $mask_type.mask == "file.out":
-            -mask='$mask_type.mask_file'
-        #else:
-            -mask=$mask_type.mask
+        #if $repeat.qMask_type.qMask == "file.out":
+            -qMask='$repeat.qMask_type.qMask_file'
+        #elif $repeat.qMask_type.qMask:
+            -qmask=$repeat.qMask_type.qMask
         #end if
+        #if $repeat.repeats_type.repeats == "file.out":
+            -repeats='$repeat.repeats_type.repeats_file'
+        #elif $repeat.repeats_type.repeats:
+            -repeats=$repeat.repeats_type.repeats
+        #end if
+        #if str($repeat.minRepDivergence)
+            -minRepDivergence=$repeat.minRepDivergence
+        #end if
+        
         #if str($dots)
             -dots=$dots
         #end if
-        $trimT
-        $noTrimA
-        $trimHardA
-        $fastMap
-        $fine
-        #if str($maxIntron)
-            -maxIntron=$maxIntron
-        #end if
-        $extendThroughN
         '$reference_fasta_filename'
         '$query'
         -out=$out
@@ -67,54 +113,56 @@
             <when value="cached">
                 <param name="database" type="select" label="Select database">
                     <options from_data_table="all_fasta">
+                        <!-- <column name="name" index="0"/>
+                        <column name="value" index="2"/> -->
                         <filter type="sort_by" column="2" />
                     </options>
                     <validator type="no_options" message="A built-in database is not available" />
                 </param>
             </when>
             <when value="history">
-                <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" />
+                <param name="database" type="data" format="fasta,twobit" label="Using database file, either a .fa, .nib or .2bit file" />
             </when>
         </conditional>
         <param name="query" type="data" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/>
         <param argument="-t" name="database_type" type="select" format="txt" multiple="false" label="database type" help="Choose your database type, the default is dnax">
-            <option value="dna">dna - DNA sequence</option>
+            <option value="dna" selected="true">dna - DNA sequence</option>
             <option value="prot">prot - protein sequence</option>
-            <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
+            <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
         </param>
         <param argument="-q" name="query_type" type="select" format="txt" multiple="false" label="query type" help="Choose your query type, the default is rnax">
-            <option value="dna">dna - DNA sequence </option>
+            <option value="dna" selected="true">dna - DNA sequence </option>
             <option value="rna">rna - RNA sequence</option>
             <option value="prot">prot - protein sequence</option>
             <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
-            <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option>
+            <option value="rnax">rnax - DNA sequence translated in three frames to protein</option>
         </param>
-        <param argument="-oneOff" type="boolean" truevalue="-oneOff=1" falsevalue="" label="If set, this allows one mismatch in tile and still triggers an alignments" />
-        <param argument="-minScore" type="integer" value="30" label="Minimum score" help="It is the matches minus the mismatches minus some sort of gap penalty" />
-        <param argument="-maxGap" type="integer" value="2" min="0" max="3" label="Maximum gap between tiles in a clump" help="Usually set from 0 to 3. Only relevant for minMatch > 1" />
-        <param argument="-repMatch" type="integer" value="" optional="true" label="Number of repetitions of a tile allowed before it is marked as overused" help="Typically this is 256 for tileSize 12, 1024 for tileSize 11, 4096 for tileSize 10. Also affected by stepSize. When stepSize is halved repMatch is doubled to compensate" />
-        <conditional name="mask_type">
-            <param  argument="-mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas are ignored entirely in protein or translated searches. Default is lower">
-                <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
-                <option value="upper">upper - mask out upper-cased sequence</option>
-                <option value="out">out - mask according to database.out RepeatMasker .out file</option>
-                <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
-            </param>
-            <when value="lower" />
-            <when value="upper" />
-            <when value="out" />
-            <when value="file.out">
-                <param name="mask_file" type="data" format="txt" label="RepeatMasker file.out" />
-            </when>
-        </conditional>
+        <section name="basic_align" title="Alignment parameters" expanded="true">
+            <param argument="-minScore" type="integer" value="30" label="Minimum score" help="It is the matches minus the mismatches minus some sort of gap penalty" />
+            <param argument="-minIdentity" type="integer" value="" optional="true" min="0" max="100" label="Minimum sequence identity (in percent)" help="Default is 90 for nucleotide searches, 25 for protein or translated protein searches" />
+            <param argument="-trimT" type="boolean" truevalue="-trimT" falsevalue="" label="Trim leading poly-T" />
+            <param argument="-noTrimA" type="boolean" truevalue="-noTrimA" falsevalue="" label="Don't trim trailing poly-A" />
+            <param argument="-trimHardA" type="boolean" truevalue="-trimHardA" falsevalue="" label="Remove poly-A tail from qSize and alignments in .psl output" />
+            <param argument="-fastMap" type="boolean" truevalue="-fastMap" falsevalue="" label="Run for fast DNA/DNA remapping" help="It does not allow introns and require high %ID. Query sizes must not exceed 5000" />
+            <param argument="-fine" type="boolean" truevalue="-fine" falsevalue="" label="Refine search for small initial and terminal exons" help="For high-quality mRNAs. Not recommended for ESTs" />
+            <param argument="-maxIntron" type="integer" value="750000" optional="true" label="Maximum intron size" />
+            <param argument="-extendThroughN" type="boolean" truevalue="-extendThroughN" falsevalue="" label="Allow extension of alignment through large blocks of N's" />
+        </section>
+        <section name="adv_align" title="Advanced alignment parameters" expanded="false">
+            <param argument="-tileSize" type="integer" value="" optional="true" min="1" label="Tile size" help="Sets the size of match that triggers an alignment. Usually between 8 and 12. Default is 11 for DNA and 5 for protein" />
+            <param argument="-stepSize" type="integer" value="" optional="true" min="1" label="Spacing between tiles" help="Default is tileSize" />
+            <param argument="-oneOff" type="boolean" truevalue="-oneOff=1" falsevalue="" label="If set, this allows one mismatch in tile and still triggers an alignments" />
+            <param argument="-minMatch" type="integer" value="" optional="true" min="1" label="Minimum number of tile matches" help="Usually set from 2 to 4. Default is 2 for nucleotide, 1 for protein." />
+            <param argument="-maxGap" type="integer" value="2" min="0" max="3" label="Maximum gap between tiles in a clump" help="Usually set from 0 to 3. Only relevant for minMatch > 1" />
+            <param argument="-repMatch" type="integer" value="" optional="true" label="Number of repetitions of a tile allowed before it is marked as overused" help="Typically this is 256 for tileSize 12, 1024 for tileSize 11, 4096 for tileSize 10. Also affected by stepSize. When stepSize is halved repMatch is doubled to compensate" />
+        </section>
+        <section name="repeat" title="Repeat masking parameters" expanded="true">
+            <expand macro="mask_cond" maskarg="mask" label="Mask out repeats" help="Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas are ignored entirely in protein or translated searches. Default is no masking"/>
+            <expand macro="mask_cond" maskarg="qMask" label="Mask out repeats in query sequence" help="Analoguous to -mask, but for the query sequence"/>
+            <expand macro="mask_cond" maskarg="repeats" label="Report matches in repeats separately" help="Repeat bases will not be masked in any way, but matches in repeat areas will be reported separately from matches in other areas in the output"/>
+            <param argument="-minRepDivergence" type="integer" value=""  min="0" max="100" optional="true" label="Minimum divergence of repeats (percent)" help="to allow them to be unmasked.  Default is 15.  Only relevant for masking using RepeatMasker .out files" />
+        </section>
         <param argument="-dots" type="integer" value="" optional="true" label="Output a dot every N sequences in log" help="Dots show program's progress" />
-        <param argument="-trimT" type="boolean" truevalue="-trimT" falsevalue="" label="Trim leading poly-T" />
-        <param argument="-noTrimA" type="boolean" truevalue="-noTrimA" falsevalue="" label="Don't trim trailing poly-A" />
-        <param argument="-trimHardA" type="boolean" truevalue="-trimHardA" falsevalue="" label="Remove poly-A tail from qSize and alignments in .psl output" />
-        <param argument="-fastMap" type="boolean" truevalue="-fastMap" falsevalue="" label="Run for fast DNA/DNA remapping" help="It does not allow introns and require high %ID. Query sizes must not exceed 5000" />
-        <param argument="-fine" type="boolean" truevalue="-fine" falsevalue="" label="Refine search for small initial and terminal exons" help="For high-quality mRNAs. Not recommended for ESTs" />
-        <param argument="-maxIntron" type="integer" value="750000" optional="true" label="Maximum intron size" />
-        <param argument="-extendThroughN" type="boolean" truevalue="-extendThroughN" falsevalue="" label="Allow extension of alignment through large blocks of N's" />
         <param name="out" type="select" label="Select output file format (-out)">
             <option value="psl">Tab-separated format, no sequence (psl)</option>
             <option value="psl -noHead">Tab-separated format, no sequence, no header (psl -noHead)</option>
@@ -129,44 +177,66 @@
     </inputs>
     <outputs>
         <data name="output" format="tabular" label="${tool.name} on ${on_string}">
-            <change_format>
+            <change_format><!-- add test -->
                 <when input="out" value="axt" format="axt" />
                 <when input="out" value="maf" format="maf" />
                 <when input="out" value="sim4" format="txt" />
-                <when input="out" value="wublast" format="tabular" />
-                <when input="out" value="blast" format="tabular" />
             </change_format>
         </data>
     </outputs>
     <tests>
         <!-- test on query of GenBank RefSeq records for Gallus gallus and database of Amazona vittata -->
         <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
-            <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="database" value="amaVit1_Gallus/amaVit1.fa" ftype="fasta" />
+            </conditional>
+            <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" ftype="fasta" />
             <param name="database_type" value="dnax" />
             <param name="query_type" value="rnax" />
-            <param name="mask" value="lower" />
-            <param name="out" value="psl -noHead" />
-            <output name="output" value="amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl"  sort="true"/>
+            <conditional name="mask_type">
+                <param name="mask" value="lower" />
+            </conditional>
+            <param name="out" value="maf" />
+            <output name="output" value="amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.maf" ftype="maf"/>
+            <assert_command>
+                <has_text text="-tileSize=" negate="true"/>
+                <has_text text="-stepSize=" negate="true"/>
+                <has_text text="-mask=lower"/>
+            </assert_command>
         </test>
-        <!-- test on query of partial mRNA of Drosophila melanogaster and the database of Drosophila biamipes dot chromosome -->
+        <!-- test on query of partial mRNA of Drosophila melanogaster and the 
+            database of Drosophila biamipes dot chromosome 
+            - also test cached reference -->
         <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="database" value="dbia3/dbia3.fa" />
-            <param name="query" value="dbia3/dmel-transcript.fa" />
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="database" value="dbdia display name"/>
+            </conditional>
+            <param name="query" value="dbia3/dmel-transcript.fa" ftype="fasta" />
             <param name="database_type" value="dnax" />
             <param name="query_type" value="rnax" />
-            <param name="mask" value="lower" />
+            <section name="basic_align">
+                <param name="maxIntron" value="" />
+            </section>
+            <section name="adv_align">
+                <param name="tileSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
+                <param name="stepSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
+            </section>
             <param name="out" value="psl -noHead" />
-            <param name="maxIntron" value="" />
-            <output name="output" value="dbia3/dbia3.sorted.psl" sort="true"/>
+            <output name="output" value="dbia3/dbia3.sorted.psl" ftype="tabular" sort="true"/>
+            <assert_command>
+                <has_text text="-tileSize=5"/>
+                <has_text text="-mask" negate="true"/>
+            </assert_command>
         </test>
         <!-- test on the database masked by repeat masker -->
         <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="database" value="dbia3/dbia3_masked.2bit" />
-            <param name="query" value="dbia3/dmel-transcript.fa" />
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="database" value="dbia3/dbia3_masked.2bit" ftype="twobit" />
+            </conditional>
+            <param name="query" value="dbia3/dmel-transcript.fa" ftype="fasta"/>
             <param name="database_type" value="dnax" />
             <param name="query_type" value="rnax" />
             <param name="oneOff" value="false" />
@@ -177,35 +247,87 @@
             <param name="fine" value="false" />
             <param name="maxIntron" value="750000" />
             <param name="extendThroughN" value="false" />
-            <param name="mask" value="file.out" />
-            <param name="mask_file" value="dbia3/dbia3_RM.out" />
-            <param name="out" value="psl -noHead" />
+            <conditional name="mask_type">
+                <param name="mask" value="file.out" />
+                <param name="mask_file" value="dbia3/dbia3_RM.out" />
+            </conditional>
+            <param name="out" value="psl" ftype="tabular" />
             <output name="output" value="dbia3/dbia3_masked.sorted.psl"/>
+            <assert_command>
+                <has_text text="-tileSize=" negate="true"/>
+                <has_text text="-stepSize=" negate="true"/>
+                <has_text text="-mask='/"/>
+            </assert_command>
         </test>
     </tests>
     <help>
         <![CDATA[
 BLAT
 ====
-BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.
+BLAT is a bioinformatics software a tool which performs rapid sequence alignments (mRNA/DNA and cross-species protein).
+It is designed to find sequences of high similarity and have a certain minimum length. With the default setting this is
+
+- >95% similarity and a minimum length of 25 bases for nucleotide sequences
+- >80% similarity and a minimum lenth of 20 amino acids for proteins
 
-blat (version: v36)- Standalone blat sequence search command line tool.
--------------------------------------------------------------------------
+More divergent or shorter sequence alignments may be missed.
+The algorithm works in two phases: 
+
+1. Search phase: find regions of probable homology using an index of the reference sequence
+2. Alignment phase: Detailed Alignment of the sequences in these regions
+
+Search phase
+++++++++++++
 
-usage:
-++++++
+Builds an index of the reference containing the nonoverlapping K-mers and their
+positions (by default, can be changed using `-tileSize` and `-stepSize`).  Hits,
+i.e. exactly matching k-mers in query and reference, are then found by looking
+up each overlapping K-mer of the query sequence.  By enabling `-oneOff` the
+algorithm allows for a single substitition. Note that this increases the run
+time of this phase significantly.
 
-  $ blat database query [-ooc=11.ooc] output.psl
+The hits are then split into buckets of 64k (based on the database position)
+and sorted on the diagonal (database minus query positions). Hits within the
+gap limit form so called proto-clumps. Those are then sorted by database position
+and put into clumps if they are within the window limit (wrt database coordinate).
+
+Clumps with less than the minimum number of hits are discarded (-minMatch) and
+those within 300 bases or 100 amino acids in the database are merged together.
+The resulting clumps define regions of the database which are homologous to the
+query sequence which are then aligned.
 
-where:
-   database and query are each either a .fa, .nib or .2bit file,
-   or a list of these files with one file name per line.
-   -ooc=11.ooc tells the program to load over-occurring 11-mers from
-   an external file.  This will increase the speed
-   by a factor of 40 in many cases, but is not required.
-   output.psl is the name of the output file.
+Alignment phase
++++++++++++++++
+
+The alignment is performed differently for nucleotide and
+aminoacid sequences.
+
+**Alignment for nucleotide sequences**: A hit list (exactly matching k-mers) for
+the query and the homologous region of the database is generated. If necessary
+hits are mode unique by extending them until they are unique or have a maximum
+size. The hits are then extended maximally allowing no mismatches, and overlapping
+hits are merged.
+Subsequent (wrt query and reference) extended hits are then linked in an
+alignment. If there are gaps in query and reference, the algorithm recurses
+using a smaller value for k until no additional hits are found or gaps are
+smaller than 6 bases.
 
-documentation:
+**Protein Alignments**: The hits from the search stage are extended into maximally
+scoring ungapped alignments (HSPs) (match cost 2 and mismatch cost 1). The HSPs
+are organized in a directed graph where an edge connect HSPs A and B if A starts
+before B wrt query and database coordinates. The weight of the edge is then
+defined as the score of B minus a gap penalty based on the distance between A
+and B (overlapping HSPs are treated differently, see Kent 2002).  The maximal
+scoring alignment is then determined as the maximum weight path through the
+graph and the HSPs of this path are removed. This is repeated until no HSPs are
+left.
+
+**Stitching and Filling In**:
+In order to find also alignments of genes scattered across multiple homologous
+regions that have been determined in the search phase a variation of the
+alignment algorithm for proteins is employed. For details see Kent 2002.
+
+Documentation:
 ++++++++++++++
 
 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
diff -r c449963debd5 -r 2a89f630fa85 test-data/all_fasta.loc
--- a/test-data/all_fasta.loc	Mon Nov 21 11:12:14 2022 +0000
+++ b/test-data/all_fasta.loc	Fri Dec 02 09:35:54 2022 +0000
@@ -1,30 +1,2 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a fasta_indexes.loc file
-#similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The fasta_indexes.loc
-#file has this format (white space characters are TAB characters):
-#
-# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
-#
-#So, for example, if you had hg19 Canonical indexed stored in
-#
-# /depot/data2/galaxy/hg19/sam/,
-#
-#then the fasta_indexes.loc entry would look like this:
-#
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
-#
-#and your /depot/data2/galaxy/hg19/sam/ directory
-#would contain hg19canon.fa and hg19canon.fa.fai files.
-#
-#Your fasta_indexes.loc file should include an entry per line for
-#each index set you have stored.  The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file.  For example:
-#
-#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
-#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
-#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
-dbia3   dm3     Dbia3   /home/galaxy/galaxy/tool-data/dm3/seq/dbia3.fa
\ No newline at end of file
+dbia3	dbia3_dbkey	dbdia display name	${__HERE__}/dbia3/dbia3.fa
+
diff -r c449963debd5 -r 2a89f630fa85 test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.maf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.maf	Fri Dec 02 09:35:54 2022 +0000
@@ -0,0 +1,609 @@
+##maf version=1 scoring=blastz
+a score=7638.000000
+s LMAW01000001.1 10027590 110 + 10443977 cgcggtcgggctgggctgggcacggcgcggtacggtgcggccggggcatcatgaaccgcttcaaggcgtccaagttccggcacaccgaggcccggccgcctcgcagggag
+s NM_001006176        296 110 +     3248 cggggcggggctgagggcggcgcggcgcggcgcggcggtcccggcgcaccatgaaccgcttcaaggcgtccaagttccggcacaccgaggcccggctgccccgcagggag
+
+a score=3442.000000
+s LMAW01000001.1 10031154 48 + 10443977 gcctggattgggggtattcgagcaggctccatcacatcctatgggaac
+s NM_001006176        406 48 +     3248 gcctggattgggggtctccgagccagctctgttgcatcctatgggaac
+
+a score=964.000000
+s LMAW01000001.1 10031353 10 + 10443977 catgtggagg
+s NM_001006176        454 10 +     3248 catgtggagg
+
+a score=6198.000000
+s LMAW01000001.1 10031517 76 + 10443977 ggtgtgctgggcattgtgccactggagtgcgaggatggaggcaagaggaccgtgtctcagctgtgctgccactcag
+s NM_001006176        502 76 +     3248 ggagtgctgggcatcgtgccactggagggcagggacggaggcaagaggaccgtgtctcagctctgctgccactcag
+
+a score=4483.000000
+s LMAW01000001.1 10033261 75 + 10443977 atgtggtgacagactttgatttctcaccattcgatcagctcctcctggctactggctctgcagatgagaccgtga
+s NM_001006176        578 75 +     3248 atgcagtgacagactttgacttctcaccctttgacccattcctgctggccacaggctccgctgatgaaatggtga
+
+a score=9006.000000
+s LMAW01000001.1 10033696 152 + 10443977 aggtgtggcgcctgccccagagcagccaggacatacccagcggtgcagggctgaccctgggccccgggggggccccagtggacatgctgcagttccaccccacagcggacggcatcctggcgagtggcacagggaagagagtcaccatctgg
+s NM_001006176        653 152 +     3248 aggtttggcgcctgcctgaggaaggccaggagctgcccagcagtgcagggctgatgttgggtcctggtgggggcacagtggacatgctgcagtttcacccaacggcagatggcatcctgaccagtggtgtgggaaagcgggtcactgtgtgg
+
+a score=3491.000000
+s LMAW01000001.1 10034454 66 + 10443977 cacagggannnnnnnnnnnnnnnnnnntggaagcgagacggcagcctgctcggcacctcctgcaag
+s NM_001006176        844 66 +     3248 catggggaccagctgcagagcctatcctggaagcatgatggccgcctgcttggcacctcctgcaag
+
+a score=4230.000000
+s LMAW01000001.1 10035646 51 + 10443977 gacaagaaactgcggatctttgacccacgagtcagcccagctgcttcccag
+s NM_001006176        910 51 +     3248 gacaagaaactgcggatccttgaccctcgagccagcccagctgcatcccag
+
+a score=7235.000000
+s LMAW01000001.1 10043484 87 + 10443977 agtgtcctgggacacgagaacaacaaggactcccggctgctctggatgggctccagcgattgcctcatctccatcgggttcagccag
+s NM_001006176        961 87 +     3248 agtgtcccaggacatgagaacaacaaggactcccggctgctctggatgggagccagcgattgcctcatctccgtggggttcagccag
+
+a score=5254.000000
+s LMAW01000001.1 10043794 83 + 10443977 atgcgggagcgggaggtgaagctgtgggacatgcggcgattcagcggggcaatgctctccatggcgctggacacctcgcccgg
+s NM_001006176       1048 83 +     3248 atgcgtgagcgggaggtgaagctctgggacacgcggaaattcagtggcgcgactttcaccttggcactggacacctcatctgg
+
+a score=2458.000000
+s LMAW01000001.1 10059668 55 + 10443977 ggcggccatcccactgtacgatgccgacacnnnnnnnnnnnnnnnnnnnnngaag
+s NM_001006176       1131 55 +     3248 ggccgtgatcccactgtatgacgccgacacggggctgctggtgctggcggggaag
+
+a score=4411.000000
+s LMAW01000001.1 10059824 56 + 10443977 ggagaaaacctcctgtactgcttcgaggtggcacccgcacagccggcactcaccca
+s NM_001006176       1186 56 +     3248 ggagaaaacctcctgtactgcttggaggcggcaccggctcagcctgcactcaccca
+
+a score=11117.000000
+s LMAW01000001.1 10059973 148 + 10443977 agtgacccagtgccggacagagggcagcacgcggggcctggccactgtgccacgcctggccctggacgtcatggcctgcgaggtgctccgtgtcctgcagctcaccgacaccgccctngtccctgtcagctacgtggtgccacgcaag
+s NM_001006176       1242 148 +     3248 agtcactcagtgcctgatggagggacccacacggggcctggccaccgtcccccgcctggccctggacgtcatggcctgcgaggtgctccgcgtcctgcagctcaccgacaccttcctcgtccctgtcagctacatcgtgccccgcaag
+
+a score=7272.000000
+s LMAW01000001.1 10060798 96 + 10443977 tctgtccaagacttccatgaggatctgttccccgactgcaccgggacgctgccagccaccggcgcccaggcctggtgggcaggggacagccagcag
+s NM_001006176       1390 96 +     3248 tccaaccaggagttccacgaggatctgttccctgactgcgctgggatgctgccggccacagatgcccaggcctggtgggcaggggacagccagcag
+
+a score=4393.000000
+s LMAW01000001.1 10060979 63 + 10443977 gtggggagggtnagcctgcacccagcaaggagacccacggagaccttcacctcgccagtcatt
+s NM_001006176       1486 63 +     3248 gtggggagggtgagcctgcacccggcacggagacccacagagaccttctgttccccactcatc
+
+a score=1852.000000
+s LMAW01000001.1 10061265 24 + 10443977 ggcagtggctactcctcaccatcc
+s NM_001006176       1609 24 +     3248 ggcagtggctactcttcaccctct
+
+a score=13034.000000
+s LMAW01000001.1 10061487 177 + 10443977 gggcccagctcccgcttccggcacgcacagggcagggtgctgcaccgcgacacgcacttcacaaacctgcgggggctcagcctcaccacgccgggcgagtgtgacggcttctgcgccaaccaccagttcgtcgccttgcccctgctctccgctggtggccagatcgccatcctcgag
+s NM_001006176       1741 177 +     3248 gggcccagctcccgcttccggcacacacagggcacagtgctgcaccgtgacagccacataaccaacctgcgggggctgagcctcaccacgccgggcgagagcgacggcttctgtgccaaccaccagcgtgttgccctcccactgctctctgccggtggccagatcgctgtccttgag
+
+a score=7402.000000
+s LMAW01000001.1 10061740 107 + 10443977 ctctccaagcccggccgtctccctgacgcagccatacccaccatccagaacagcgtggctgtgactgacctgttctgggaccccttcgacccacagcgcctcgctgt
+s NM_001006176       1918 107 +     3248 ctctccaaaccaggccgtctccccgacgtggctgtgcccaccatccagaatggtgcagcggtgtccgacctctcctgggaccccttcgacccacagcgccttgcggt
+
+a score=5654.000000
+s LMAW01000001.1 10061947 83 + 10443977 agctggtgaagatgccaagatccggctgtggcgaatcccggagggagggctgcaggagacactgcaggagcctgaagctgtcc
+s NM_001006176       2025 83 +     3248 tgcgggggaggatgccaagatccggctgtggcgggtgcctgagggggggctgcaggacacgctgcaggagcctgaggccgtgc
+
+a score=10613.000000
+s LMAW01000001.1 10062143 145 + 10443977 taccaggtcacacggagaagatctactccatccgcttccaccccgtggcatccgatctcctggtttcttcctcctatgacatgacagtgcggatctgggagctgagcactgggcgggaagccttgtgcctgcagggacacactga
+s NM_001006176       2108 145 +     3248 tgagagggcacacggagaagatctactccatccgcttccaccccgtggcagccgacctccttgtctcctcttcctatgacatgacagtgcggatttgggatctgggtgctgggcgggaggtgctgtgcctacagggacacacgga
+
+a score=8118.000000
+s LMAW01000001.1 10062365 109 + 10443977 ccagatcttcagcctggcttggagcccggatgggaagaagctggcaacagtgagcaaagatggtcggttacggctctatgagccacggcgcagccctctgcctcaacag
+s NM_001006176       2253 109 +     3248 ccagatcttcagcctggcctggagcccagacgggaggaagctggcgacggtgagcaaggatggccggttgcggctctttgagcctcggtgcagccttcaaccccagcag
+
+a score=5299.000000
+s LMAW01000001.1 10062584 83 + 10443977 gagggtccaggtcccgagggggcccgcggagcacgcctcgtntgggtttgtggtggcgactacctcctggtgtccggctttga
+s NM_001006176       2362 83 +     3248 gagggtccgggccctgagggaggccgtggggcacgcgtggtctgggtgtgcggaggtgacttcctcctcgtgtccggcttcga
+
+a score=11061.000000
+s LMAW01000001.1 10062743 145 + 10443977 cagccgcagcgagaggaggatcctcctgtaccaggctcaggctctgcccaagggacccttgtctgtccttggccttgatgtggccccttccaccctcctgcccttctatgatgaggataccagcgttgtcttcctcactggcaag
+s NM_001006176       2445 145 +     3248 cagccgcagcgagaggaggatccttctgtaccgtgcacaggccctgtccgatgggcccctctacgttctcggcctcgatgtggccccttccacactcctgcccttctatgatgaggacaccagtgttgtcttcctcactggcaag
+
+a score=7338.000000
+s LMAW01000001.1 10063001 90 + 10443977 ggtgacaccagggtcttcctctatgaggtgacgcctgagccaccctatttccttgagtgcaacagcttcacctctggcgaaccccacaag
+s NM_001006176       2590 90 +     3248 ggtgacaccagagtcttcctctacgaggtgacccccgagccaccctatttcctcgaatgcaacagcttcacctccagcgacccccacaag
+
+a score=8651.000000
+s LMAW01000001.1 10063188 117 + 10443977 ggctttatcttcctgcccaaaacggtgtgtgaggtccgggaggtggagttcgcccgggcgctgcgcctcgggcagagcaccctcgagcctgtggctttccatgtgccacgcatcaag
+s NM_001006176       2680 117 +     3248 ggctttgtcttcctgcgcaagacagcgtgcgacgtgcgggaggtggagttcgcccgggcgctgcggctggggcagagcagcctcgagccggtggctttccgtgtgccgcgtgtcaag
+
+a score=7329.000000
+s LMAW01000001.1 10063383 129 + 10443977 aaggagtatttccaggacgacatctacccgccaacccgtgtctggtgggagccggccctcagcggcaccgcctggctgtcgggggaggatgggcagcagcgccnnnnnnnnnnnnnnnnnncagacatg
+s NM_001006176       2797 129 +     3248 aaagagtatttccaagaagacatcttccctcccacccgcgtgtggtgggagccggccctgagcgccagcgcctggctggggggggcggacgggcagcagaaccgcgctgagctccgtcccgccgacatg
+
+a score=5227.000000
+s LMAW01000001.1 10063616 68 + 10443977 ctcccagtgagccaggccccgaaagaggccccagcgcggaagttcgtccctgcggccgtgtacctgga
+s NM_001006176       2926 68 +     3248 gtgccagtgagccaggccccaaaggaggcacctgcgcggaagttcgtccctgcggccgtgtatctggg
+
+a score=5944.000000
+s LMAW01000001.1 10063806 93 + 10443977 gccatggtggcccggctgggcaaccgggaagacccgctgccgcaggactccttcgagggggtggacgaggacgagtgggtaagtgctgggggg
+s NM_001006176       3034 93 +     3248 gccatggtggcccggctggggaaccgccacgacccgctgccgcaggactccttcgaaggcgtggatgaggccgagtgggactaggccgcgggc
+
+a score=2061.000000
+s LMAW01000001.1 10064114 27 + 10443977 ggccccgctattaaagccgctacngca
+s NM_001006176       3203 27 +     3248 ggccccgccattaaagccgctgcagcc
+
+a score=1889.000000
+s LMAW01000002.1 3610886 33 + 5883884 gcggagttggagtttgtacagataatcataatc
+s NM_001031013        69 33 +     971 gctgaactggagtttgttcaaatcatcattatc
+
+a score=3646.000000
+s LMAW01000002.1 3610955 66 + 5883884 tgtctgctgaaccactacaaactctctgcgcgatccttcatcagccggcacagccaggggaggcgg
+s NM_001031013       138 66 +     971 tgcttgttgaaccattacaaactatcgacgcgctcctttatcaaccggcagagccaaagcagaaga
+
+a score=1683.000000
+s LMAW01000002.1 3617941 21 + 5883884 gcctgtggccttcggaaagca
+s NM_001031013       232 21 +     971 gcttgtggccttcggaaagct
+
+a score=24133.000000
+s LMAW01000002.1 3618099 414 + 5883884 tacaccccgagacccagtgaccgcctggcagtgccatccttcctgcagagggaccgctttaaccgattccagccaacctacccctacatgcagcacgagatcgatctgcctcccaccatctcgctgtcggacggcgaagagccccccccgtaccagggaccctgcacgctgcagctgcgggaccccgagcagcaaatggagctcaacagagagtcggtccgggctccccccaacagaaccatctttgacagtgacttgatagataactccgtgtac---ggggggccgtgcccccccagcagtaactctggcatcagcgcgacctgctatgggagcaatggtaggatggagggaccaccaccgacgtacagcgaggtgatagggcactacccagggtcgacgttttaccagcaccag
+s NM_001031013       285 417 +     971 tatgctccaaggtccagggacaggtttaccgccccatcttttatgcagcgggaccgtttcagtcgcttccagcccacttacccatacatgcagcatgagattgaccttcctccaaccatttccctctcagatggggaagagccgccgccataccaaggcccgtgcaccctgcagctccgggacccagagcagcagatggagctcaaccgggaatctgtcagggcaccgcccaaccgaaccatttttgatagcgacttgatagacatttccatgtacaatgggggcccctgcccaccgagcagcaattcgggcataagtgcaaccaactatagcagtaatggaaggatggaaggaccacccccgacgtacagcgaggtcatggggcactacccaggctcctcgtttttccatcaccag
+
+a score=5076.000000
+s LMAW01000001.1 9729332 108 + 10443977 gatgacatccagaagatgaaccctccaaagttctccaaagtggaggacatggcagagctgacttgcctcaatgaagcttcagtgctgcacaatctaagggagagatac
+s NM_204766          262 108 +     5992 gatgacgtgcagtcaatgaaccctcccaaattcgacatgattgaggacatggctatgctgacccatctgaatgaggcatctgtgttgtacaacctgaggaagcgctac
+
+a score=4719.000000
+s LMAW01000001.1 9734141 153 + 10443977 acttattcaggtctcttctgcgtcgtgataaatccatacaaacagctgcccatttactcagagaagatcatcgacatgtacaagggaaagaagaggcacgagatgccnccccacatctatgctatcgcggacacagcctacaggagcatgctg
+s NM_204766          388 153 +     5992 acctactcgggcttgttctgcgtgactataaacccctacaagtggctgcctgtctacaagtcggaggttgttgctgcctacaaaggcaagaggcgctcagaagcccctcctcacatcttctccattgctgataacgcataccacgacatgctg
+
+a score=2557.000000
+s LMAW01000001.1 9751019 66 + 10443977 ggtgaatctggtgctggcaagnnnnnnnnnnnnnnnnnngtgattcagtacctggctgttgttgct
+s NM_204766          574 66 +     5992 ggagaatccggtgctggcaagactgtcaacacaaaaagggtcatccagtactttgccacagtggca
+
+a score=4528.000000
+s LMAW01000001.1 9755220 93 + 10443977 ggagagctggaaaaacagcttctacaggcaaaccctattcttgaagcttttggaaatgccaaaacagtgaagaatgacaactcctccagattt
+s NM_204766          688 93 +     5992 ggaaccttggaagatcaaatcattcaagcaaacccagccctagaagcttttggaaacgccaaaaccctgagaaatgacaactcctcacgtttt
+
+a score=2340.000000
+s LMAW01000001.1 9762042 39 + 10443977 ttcttggggatccttgacattgctggatttgagattttt
+s NM_204766         1414 39 +     5992 ttcattggagtcctggacattgctggctttgaaatcttt
+
+a score=8490.000000
+s LMAW01000001.1 9762555 171 + 10443977 aattcctttgagcagctgtgcatcaattacactaatgagnnnnnnnnnnnnnnnnnnnnncacacaatgtttatactggagcaagaggaataccaacgagagggcattgaatggaatttcattgactttggccttgacctgcaaccttgcattgagctgattgaaagacca
+s NM_204766         1459 171 +     5992 aacagctttgagcaactctgcatcaattacactaatgagaaactgcaacagtttttcaatcatcacatgtttgtcctcgagcaagaagaatataaaaaagaaggcattgaatgggtatttattgattttggcatggacctgcaggcctgtattgatctaattgagaagcca
+
+a score=2620.000000
+s LMAW01000001.1 9764665 99 + 10443977 ttccgtactgttggacaactctacaaagagcagctgactaaactaatgaccaccttgaggaataccaatcccaactttgtccgctgtatcatcccaaat
+s NM_204766         1981 99 +     5992 tttcagacagtgtcctcattacacaaggaaaatttaaataaactaatgactaacctaagatctacagcccctcactttgtacgatgcattattcccaac
+
+a score=4139.000000
+s LMAW01000001.1 9765048 84 + 10443977 gatgcccatttagtactggagcagttgcgntgcaatggtgtcttggaaggtattcgtatctgccgncagggatttcccaacagg
+s NM_204766         2104 84 +     5992 gatgctttccttgtcttgcatcagctccgctgtaatggtgtcctggaaggcatccgcatttgccgtaagggtttcccaaacaga
+
+a score=2891.000000
+s LMAW01000002.1 103604 51 + 5883884 atgctggacatgagccagtttggggaggctgctgagtacctccggaagagc
+s NM_204766          49 51 +    5992 atgatggacatgacggaatttggggaggctgctcccttcctccgaaagagc
+
+a score=4032.000000
+s LMAW01000002.1 104407 78 + 5883884 tggataccggatgagaaagaagcttatatagaagtggaaatcaaagacagcactggtggcaaagtcactgtggaaacc
+s NM_204766         154 78 +    5992 tgggttcctgatgacaagaaagcttacgttgaagctgaaattacagaaagcagtggtggcaaagtgactgttgagaca
+
+a score=8256.000000
+s LMAW01000002.1 107764 132 + 5883884 aaggaggatgagctgcagcccatgaacccacccaagttcgacatgattgaggacatggccatgctgacgcacctcaacgaggcctctgtgctctacaacctgaagcgccgctactcccactggatgatctac
+s NM_204766         256 132 +    5992 aaagaagatgacgtgcagtcaatgaaccctcccaaattcgacatgattgaggacatggctatgctgacccatctgaatgaggcatctgtgttgtacaacctgaggaagcgctacagcaactggatgatttat
+
+a score=291.000000
+s LMAW01000002.1 107909 3 + 5883884 acc
+s NM_204766         388 3 +    5992 acc
+
+a score=8788.000000
+s LMAW01000002.1 108002 152 + 5883884 tactcagggctcttctgtgtcaccatcaacccctacaagtggctgcccgtctacacggcgcctgtggtggcagcctacaagggcaagcggcgcaccgaggctcccccgcacatctactccatcgccgacaatgcctacaatgacatgctgcg
+s NM_204766         391 152 +    5992 tactcgggcttgttctgcgtgactataaacccctacaagtggctgcctgtctacaagtcggaggttgttgctgcctacaaaggcaagaggcgctcagaagcccctcctcacatcttctccattgctgataacgcataccacgacatgctgcg
+
+a score=182.000000
+s LMAW01000002.1 108233 2 + 5883884 ta
+s NM_204766         543 2 +    5992 ta
+
+a score=1787.000000
+s LMAW01000002.1 108257 29 + 5883884 atcgtgaaaaccagtccatgctcatcacg
+s NM_204766         545 29 +    5992 atcgggaaaatcagtcaatgctaatcact
+
+a score=5232.000000
+s LMAW01000002.1 109261 75 + 5883884 ggagaatctggtgctggtaagactgtaaacaccaagcgggtcattcagtactttgccattgtcgcagccttgggc
+s NM_204766         574 75 +    5992 ggagaatccggtgctggcaagactgtcaacacaaaaagggtcatccagtactttgccacagtggcagccctgggt
+
+a score=6158.000000
+s LMAW01000002.1 112047 90 + 5883884 accctcgaagatcaaatcattgaggctaacccagctatggaagcttttggcaatgccaaaaccataaggaatgacaactcctcccgtttt
+s NM_204766         691 90 +    5992 accttggaagatcaaatcattcaagcaaacccagccctagaagcttttggaaacgccaaaaccctgagaaatgacaactcctcacgtttt
+
+a score=3179.000000
+s LMAW01000002.1 112967 70 + 5883884 ggcaagttcatccggatccattttggcccctcagggaagctggcctccgcagacattgacatctgtgagt
+s NM_204766         781 64 +    5992 ggtaaatttatccgaatccattttggaaccacaggcaagctgtcatctgctgacattgagatc------t
+
+a score=5464.000000
+s LMAW01000002.1 113148 95 + 5883884 atcttctggaaaaatcaagagtgattttccagcagcccaaagagcggagctaccacatctactaccagatcctctctgggaagaaaccagagctg
+s NM_204766         845 95 +    5992 atttactggagaaatcccgagtgatttttcagcaaccgggtgagagagactatcacatcttctaccagatcttatcaggaaagaaaccagagttg
+
+a score=5760.000000
+s LMAW01000002.1 114257 81 + 5883884 ccctatgactaccacttctgctctcagggtgtaactactgtggacaacttggatgatggcgaggaactcatggcaacagat
+s NM_204766         967 81 +    5992 ccatatgactaccacttttgctcccaaggagtagttacagtggacaacttggatgacggagaagaactgatggcaacagat
+
+a score=282.000000
+s LMAW01000002.1 114391 3 + 5883884 caa
+s NM_204766        1048 3 +    5992 caa
+
+a score=5303.000000
+s LMAW01000002.1 114866 136 + 5883884 gccatggacatcntgggcttcagcaatgatgagaaatatggctgctataaaatagtgggngctatcatgcacttcggcaacatgaagttcaagcagaagcagcgagnnnnnnnnnnnnnnnnnnacggcactgaaa
+s NM_204766        1051 136 +    5992 gccatggacattttaggatttgtgccagatgagaagtatggtgcctacaagctcacaggtgccattatgcactttgggaacatgaaattcaaacaacgacccagagaagagcaggcagaggctgatggcactgaaa
+
+a score=7426.000000
+s LMAW01000002.1 116183 119 + 5883884 gtgctgacaaagctgcctacctgatgggaatcagctcagctgacctcatcaagggcttgctccatcctcgtgtgaaggtgggcaatgagtacgtgaccaaaggtcagaacgtggagcag
+s NM_204766        1187 119 +    5992 gtgccgacaaagctgcctacctaatgggaatcaactcctctgatttggttaagggcttattacaccctagagtgaaagttggaaatgagtatgtgaccaaaggtcaaagtgttgaacag
+
+a score=8473.000000
+s LMAW01000002.1 116438 157 + 5883884 gttgtctatgcggtgggagcactggctaaagccacctatgaccgcatgttcaagtggctggtgactcggatcaataggaccctggacaccaagctggccaggcagttcttcattggagtactggacattgcaggcttcgagatctttgatgtgagtt
+s NM_204766        1306 152 +    5992 gttttgtatgctgttggggccttatccaaggcagtgtatgatcgaatgttcaagtggctggtggtccgtatcaacaaaacactggacactaagctgccaagacagttcttcattggagtcctggacattgctggctttgaaatctttgat-----tt
+
+a score=9756.000000
+s LMAW01000002.1 116908 169 + 5883884 caacagcnnnnnnnnnnnnnnnnnnnacttcaccaacnnnnnnnnnnnnnnnnnnttcaaccaccacatgtttgtcctggagcaagaagaatataagaaggaaggcatcgaatgggtcttcattgactttggcctggacctgcaggcttgcattgacctgatcgagaag
+s NM_204766        1458 169 +    5992 caacagctttgagcaactctgcatcaattacactaatgagaaactgcaacagtttttcaatcatcacatgtttgtcctcgagcaagaagaatataaaaaagaaggcattgaatgggtatttattgattttggcatggacctgcaggcctgtattgatctaattgagaag
+
+a score=11142.000000
+s LMAW01000002.1 117767 180 + 5883884 ccattgggaatcctgtccatccttgaagaggagtgcatgttcccaaaagcctccgacatgtccttcaaagctaagctctatgacaaccaccttgggaagtcgcccaacttccagaagccccggccagataaaaagaagaagtatgaggcgcactttgagctggtgcactacgctggtgtg
+s NM_204766        1627 180 +    5992 ccactaggaatcctgtctatccttgaagaagaatgtatgttcccaaaagctacagatatgacgttcaaagccaaactttacgacaaccatcttggcaagtcacctaacttgcagaagcccaggcctgataagaaaaggaaatatgaagctcactttgaacttattcattatgctggctca
+
+a score=6654.000000
+s LMAW01000002.1 118030 123 + 5883884 gtgccntacaacatcattgggtggctggacaagaacaaggacccgctgaacgagacagtagtgtctgtcttccaaaagtcccaaaacaagctcctggcttccctctatgagaactacgtgggc
+s NM_204766        1807 123 +    5992 gttccctataacatcattgggtggcttgagaagaacaaagacccacttaatgaaactgtagtaggtattttccaaaagtcgtccaacaagctcctggcaagcctgtttgaaagctacgttggt
+
+a score=2639.000000
+s LMAW01000002.1 118682 48 + 5883884 aaacgtaaaaaggcagcttctttccaaacagtgtctcagctgcacaag
+s NM_204766        1960 48 +    5992 aaacgcaagaaaggtgcttcttttcagacagtgtcctcattacacaag
+
+a score=4326.000000
+s LMAW01000002.1 120119 90 + 5883884 gagaacctcaacaagctgatgaccaacctgcgctccactcagccccactttgtccgctgcatcatccccaacgagacaaagaccccgggt
+s NM_204766        2008 90 +    5992 gaaaatttaaataaactaatgactaacctaagatctacagcccctcactttgtacgatgcattattcccaacgaatcaaaaacaccaggt
+
+a score=6285.000000
+s LMAW01000002.1 120672 117 + 5883884 gccatggatgccttccnnnnnnnnnnnnnnnnnnnctgtaacggtgtccttgaaggcatccgcatctgccgtaaagggttccccaacaggatcctctacgcagacttcaagcagcgg
+s NM_204766        2098 117 +    5992 gaaatggatgctttccttgtcttgcatcagctccgctgtaatggtgtcctggaaggcatccgcatttgccgtaagggtttcccaaacagagtgctttatgctgactttaaacaaagg
+
+a score=4947.000000
+s LMAW01000002.1 121329 123 + 5883884 taccgtatcctgaatccaacagccattccagatgacaagtttgtggacagcagaaagnnnnnnnnnnnnnnnnnnnnnnccctggaactggaccactcncagtacaagttcggtcacaccaag
+s NM_204766        2215 123 +    5992 taccgcattctgaacccaggtgcaatcccagaggacaagtttgtggatagcagaaaagctgccgaaaaactactggcatctttagatattgaccataaccaatatcgtttcgggcatactaag
+
+a score=5873.000000
+s LMAW01000002.1 122185 134 + 5883884 gtgtttttcaaggctggtttgctgggcttgctggaggagatgcgggatgagcgtctggccaagatcctgaccatgctgcaggccagaatccgtgggcacctcatgcgcatcgagtatcagaagatcatcagcag
+s NM_204766        2338 134 +    5992 gtgttcttcaaggctggtctgttgggccacctagaagaaatgagggatgagagacttgcaaagatcctaacaatgatccaggcaagggcacgtggcagactgatgaggatcgagttccagaagatagtggagcg
+
+a score=13053.000000
+s LMAW01000002.1 122724 241 + 5883884 cagggaagccctctataccatccagtggaacatccgggccttcaatgctgtcaagaactggtcctggatgaagctgttcttcaagatcaagcctctgctcaagtctgctcagactgagaaggaaatgtccaacctgaaggaggagctccagaagctgaaggaggctctggaaaagtctgaggctaagaggaagnnnnnnnnnnnnnnnnnnntctccatgatccaggagaagaacgacctg
+s NM_204766        2472 241 +    5992 cagggatgcccttcttgtaattcagtggaatatccgtgcctttatggctgtgaagaattggccctggatgaagcttttctttaagatcaaacctcttctgaagtctgcagaaactgaaaaagagatggccaatatgaaggaagagttcttgaaattgaaggaggccctggaaaaatctgaagcaaggagaaaggaacttgaagagaaacaagtctctttagttcaggaaaaaaatgatttg
+
+a score=13344.000000
+s LMAW01000002.1 123518 261 + 5883884 ctcctgtgcctgtcccaggagcaagacaacctggcagatgcagaggagcgctgtgacctgctgatcaagtccaagatccagctggaggccaaggtgaaggagctgacagagcgcnnnnnnnnnnnnnnnnnnnnnaactcggaactcaccgccaagaagcgcaagctggaggatgagtgcgcagagctgaagaaggacattgatgatctggagatcacgctggccaaggtggagaaggagaagcatgccacagagaacaag
+s NM_204766        2713 261 +    5992 ctattgcagctccaagctgagcaagacactctggcagatgctgaggagcgatgcgacttgttgattaaatccaagattcagctggaggccaaagtcaaagagctgacagagcgagttgaggatgaggaagagatgaattctgagctgacatccaaaaagagaaaattggaagatgaatgctctgagctcaagaaagatattgatgatcttgaaataacacttgcaaaagtagagaaagagaagcatgctactgaaaataag
+
+a score=10407.000000
+s LMAW01000002.1 123945 177 + 5883884 gtgaaaaacctgattgaagagatggctgctctggatgagatcattgccaagctgacnnnnnnnnnnnnnnnnnnncaagaggcccatcagcaggccctggatgacctgcaggctgaggaagacaaagtcaacacactgacaaaagccaaggtcaaactggagcagcaagtggatgat
+s NM_204766        2974 177 +    5992 gtgaaaaatctgacagaagaaatggcgactcttgatgagaacatcagcaaacttactaaggagaagaagtccttgcaggaagctcatcagcaagttctggatgaccttcaagcagaggaagacaaggtcaacacactgagcaaagctaaagtgaaactggaacagcaagtggatgat
+
+a score=6197.000000
+s LMAW01000002.1 124449 146 + 5883884 ctggaaagctctcttgaacaagagaagaaagtccgcatggaccnnnnnnnnnnnnnnnnnnnnnnnnaaggagacctgaagttgacccaagagtctgtaatggatctggagaatgannnnnnnnnnnnnnnnnnnnnnntcaagaa
+s NM_204766        3151 146 +    5992 cttgagggctcgcttgagcaagagaagaaagtgaggatggatctagaaagagcaaaacgcaaactggaaggagatttgaagctgacccaagagagtgtcatggacttggagaatgataagttgcaaatggaagaaaagctgaaaaa
+
+a score=5494.000000
+s LMAW01000002.1 124904 90 + 5883884 aaagactttgaaatgagtcagctgaattcaaggattgaagatgggcaagtgactgaggcccagctgcagaagaagatgaaggaactccag
+s NM_204766        3298 90 +    5992 aaagagtttgaaatgagccaattgaattccaagatagaagatgaacaagctattgtaatgcagctgcagaagaagataaaggaactacag
+
+a score=2368.000000
+s LMAW01000002.1 125793 72 + 5883884 gcccgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngagcgcgctgccagagccaangtggagaagcagcgg
+s NM_204766        3388 72 +    5992 gctcgtatagaagagctggaagaggagctggaagcagaaagagctgctcgagccaaggtggaaaagcagaga
+
+a score=16465.000000
+s LMAW01000002.1 125898 267 + 5883884 gagcggctggaggaggccggcggcgccacggccacgcagctggagatgaacaagaagcgggaagcggagttcctgaagctgcggcgggacctggaggaggcgacgctgcagcacgaatccacggccgctgccctgcgcaagaagcacgcggacagcgtggccgagctgggcgagcagatcgacaacctgcagcgcgtcnnnnnnnnnnnnnnnnnnnnnnnnnnngagttgaagatggaggtggatgacctgtcatccaacatcgag
+s NM_204766        3493 267 +    5992 gagcggcttgaagaggctgggggtgccactgctgcccagctggagatgaacaagaaacgtgaagctgagttcctgaagctggcgcgtgacctcgaggaggccacgctgcactatgaagccacagctgctgctctgaggaagaagcatgcggacagcgtggctgagatgggggagcagctggacaacctgcagcgcgtcaagcagaaactggaaaaggagaaaagcgagctgaaaatggaagtggatgatctgacatccaacatggag
+
+a score=4362.000000
+s LMAW01000002.1 126790 129 + 5883884 gccaacgctgagaagctgtgtcgcacctatgaggaccagctcaacgaggccaagtccaaagtggacgagctgcagcgacagctgaacgacgtgagcacacagcggggcaggctgcagaccgagaacggt
+s NM_204766        3778 129 +    5992 gcaaatgcagaaaaactttgtcgcacttatgaagatcatcttaatgagacaaaaactaaactggatgaaatgactcgcctcatgaatgacctcactactcaaaagacaaaactccagagtgagaatggt
+
+a score=4296.000000
+s LMAW01000002.1 127405 81 + 5883884 atcaaccagctgagccgtggcaagacctcnttcacacagaacattgaggaactcaagaggcagctggatgaagagaccaag
+s NM_204766        3943 81 +    5992 ataagtcagctgtcccgaggaaaaacatcatttacacagcagattgaagaacttaggagacagctagaagaggaaaccaag
+
+a score=191.000000
+s LMAW01000002.1 127543 2 + 5883884 tc
+s NM_204766        4024 2 +    5992 tc
+
+a score=10394.000000
+s LMAW01000002.1 127717 196 + 5883884 caagaacgccctggcccatgccctgcaagcctcccggcacgactgcgacctcctgcgggagcagtacgaggaggaggtggangccaagagcgagctccagaggaacttgtccaaggccaatgcagaagtggcccagtggagaaccaagtacgagacggacgccatccaacggannnnnnnnnnnnnnnnnnnnaag
+s NM_204766        4026 196 +    5992 caaaaatgctctggctcatgccctgcaagcagccaggcatgactgtgatctcttgcgagaacagtacgaggaggagcaagaagccaaggcagagctgcagcgggctctctccaagggaaatgcagaagtggcacaatggagaacaaagtatgaaactgatgccattcagaggactgaggaactggaagatgccaaa
+
+a score=18874.000000
+s LMAW01000002.1 128055 348 + 5883884 aagaagctggccacccggctgcaggaggcggaggaggcggtggaggcngcccatgccaagtgctcctcgctggagaagaccaagcatcggctgcagacagagatcgaggacctctcggtggacctggaacgcgccaacnnnnnnnnnnnnnnnnnngacaagaagcagcgcaactttgacaggatcctggccgagtggaagcagaagtacgaggagacccaggcggagctggaggcgtcgcagaaggagtcgcgcagcctgagcacggagctcttcaagctcaagaacgcctacgaggagtccctggacaacctggagaccctcaagagggagaacaagaacctgcag
+s NM_204766        4222 348 +    5992 aaaaagcttgctgcccgcctgcaagaagctgaggaagcaattgaagctgccaacgccaagtgctcttctctggaaaagacaaagcacaggctgcagaacgagctggaagatatgatgattgatctggaaaaggccaactcagcggctgcctccctggacaagaagcagcgtggctttgacaagatcatcaatgactggaagcagaagtatgaagagtcacaggctgagctggaagcttcccagaaggaggcccgcagcctcagcaccgagctcttcaagctgaagaatgcctatgaagagacactggaccatctggagactctgaaacgggaaaacaagaacctccaa
+
+a score=5811.000000
+s LMAW01000002.1 129238 116 + 5883884 ggggccctggagcacgaggagagcaagactctgcgcatccagctggagctgaaccagatcaaggctgatgtggacaggaagctggcggagaaggacgaggagtttgagaacctgag
+s NM_204766        4696 116 +    5992 ggagctttggagcatgaagaaagcaagacccttcgttttcagcttgagctttctcagcttaaagctgattttgaaaggaagctggcagaaaaggatgaagaaatggaaaatataag
+
+a score=8840.000000
+s LMAW01000002.1 129442 193 + 5883884 gcgcaaccaccagcgcnccatggactccatgcaggccacgctggatgcagaggcgcgggccaagaacgaggcggtgcggctgaggaagaagatggagggagacctgaacgagatggagatccagctgagccacgccaaccgccaggccgccgagttccagaagctggtccggcagctccaggcccagatcaag
+s NM_204766        4812 193 +    5992 gaggaaccaacaacgcaccatagattctctgcagtccacccttgattctgaagcccggagcagaaatgaggccatccggctgaagaagaagatggaaggagacctcaacgagatggaaatccagctcagccatgctaacaggcatgctgcagaagcaaccaagtcagcacgtggcctgcagacacaaatcaag
+
+a score=4511.000000
+s LMAW01000002.1 129761 106 + 5883884 tgaaggagcaggcggccgccctggagcgccgcaacaacctgctgctggccgaggtggaggagctgcgggcggcgctggagcaggcggagcggagcaggaagctggc
+s NM_204766        5051 106 +    5992 tgaaggagcagctggcagtctctgacaggaggaacaaccttctccagtcagagctggatgagctgagggctttgctggaccagactgaacgggcgaggaagctggc
+
+a score=6880.000000
+s LMAW01000002.1 130020 123 + 5883884 acgggcctgatcaaccagaagaagaagctggaagcagacatctcgcagctgagcagcgaggtggaggacgcagtgcaggagtgccgcaacgctgaggacaaggcaaagaaggccatcacagat
+s NM_204766        5212 123 +    5992 acaagcctgatcaatcagaagaagaaactggagggtgacatatcccagatgcagaatgaagtggaggaatcaatccaggagtgccggaacgcagaggaaaaagccaaaaaagcgatcacagat
+
+a score=9597.000000
+s LMAW01000002.1 130254 177 + 5883884 gctgccatgnnnnnnnnnnnnnnnnnnnaggagcaggacacaagcgcacatctggagcggatgaagaagaacatggagcagaccatcaaggacctgcagatgcgcctggatgaagcggagcagattgctctcaaggggggcaagaagcagatccagaagctggaggccagggtgaga
+s NM_204766        5335 177 +    5992 gcagcaatgatggctgaggagcttaaaaaggagcaagatactagtgctcacttggagagaatgaagaagaacatggaacaaaccattaaagatctgcagaaacgactggatgaagcagaacaaatagccctgaaaggtggcaagaaacagatccagaaactggaatccagggttcgt
+
+a score=4656.000000
+s LMAW01000002.1 131103 99 + 5883884 caggctgaggaagaccggaagaacctggcacggatgcaggacctcattgacaagctgcagagcaaggtcaagagctacaagcgccagttcgaggaggcg
+s NM_204766        5608 99 +    5992 cagtcagaagaagataagaaaaatctggcccgaatgcaggatctgatagataagctacaactaaaagtgaagagctacaaacaccaagcagaggaagcc
+
+a score=3832.000000
+s LMAW01000002.1 131337 87 + 5883884 ctggtgaagtaccgcaaggtgcagcacgagctggatgatgccgaggagcgggcggacatngccgagacgcaggtcaacaagctgcgc
+s NM_204766        5728 87 +    5992 ctttcgaagtacagaaaacagcaacatgatctggacgatgctgaagaaagggcagaaatagctgaatctcaagttaacaagctgagg
+
+a score=1481.000000
+s LMAW01000003.1 259524 27 + 4188689 ggggaaagtggtgctggaaagactgta
+s NM_204766         574 27 +    5992 ggagaatccggtgctggcaagactgtc
+
+a score=2239.000000
+s LMAW01000003.1 261255 80 + 4188689 gatattattctacagtccaaccctttactggaggcttttgggaatgcaaaaactgtacggaacaacaactccagcagatt
+s NM_204766         700 80 +    5992 gatcaaatcattcaagcaaacccagccctagaagcttttggaaacgccaaaaccctgagaaatgacaactcctcacgttt
+
+a score=814.000000
+s LMAW01000003.1 261529 11 + 4188689 tggtcaattta
+s NM_204766         780 11 +    5992 tggtaaattta
+
+a score=1806.000000
+s LMAW01000003.1 262379 66 + 4188689 ctactggaaaagtctcgagttgtaatgaggaatcccggagagagnnnnnnnnnnnnnnnnnnncag
+s NM_204766         847 66 +    5992 ttactggagaaatcccgagtgatttttcagcaaccgggtgagagagactatcacatcttctaccag
+
+a score=2219.000000
+s LMAW01000003.1 268797 36 + 4188689 attggtgtccttgacatttatggctttgaaatattc
+s NM_204766        1417 36 +    5992 attggagtcctggacattgctggctttgaaatcttt
+
+a score=3848.000000
+s LMAW01000003.1 2559457 84 + 4188689 aatcagtcaatcattgtcagtggggaatctggggctggaaagactgtctctgctaagtatgccatgaggtactttgccacagtc
+s NM_204766          553 84 +    5992 aatcagtcaatgctaatcactggagaatccggtgctggcaagactgtcaacacaaaaagggtcatccagtactttgccacagtg
+
+a score=2922.000000
+s LMAW01000003.1 2563244 66 + 4188689 ggaaatgccaaaactacgaggaatgacaacagcagtcgttttgggaaatacattgaaattggtttt
+s NM_204766          739 66 +    5992 ggaaacgccaaaaccctgagaaatgacaactcctcacgttttggtaaatttatccgaatccatttt
+
+a score=1645.000000
+s LMAW01000003.1 2563349 33 + 4188689 tacctcttggaaaaatcaagagtggtgtttcag
+s NM_204766          844 33 +    5992 tatttactggagaaatcccgagtgatttttcag
+
+a score=1228.000000
+s LMAW01000003.1 2570767 13 + 4188689 tcaacagctttga
+s NM_204766         1457 13 +    5992 tcaacagctttga
+
+a score=2345.000000
+s LMAW01000003.1 2573327 66 + 4188689 catgtctttaagctagaacaagaagaatatatgaaggaacaaataccatggaccttgattgatttc
+s NM_204766         1522 66 +    5992 cacatgtttgtcctcgagcaagaagaatataaaaaagaaggcattgaatgggtatttattgatttt
+
+a score=9370.000000
+s LMAW01000001.1 9828212 119 - 10443977 cggttcgcccgcaaaggcgccctgcggcagaagaacgtgcacgaggtgaagaaccacaagttcacggcgcggttcttcaagcagcccaccttctgcagccactgcaccgacttcatttg
+s NM_001012804       121 119 +     4592 cgctttgctcgcaaaggggccctgaggcagaagaacgtgcacgaggtgaaggagcacaaattcatcgcgcgcttcttcaagcagcccaccttctgcagccactgcaccgacttcatctg
+
+a score=1915.000000
+s LMAW01000001.1 9828431 32 - 10443977 gggcttcggcaagcagggtttccagtgccaag
+s NM_001012804       240 32 +     4592 gggatttgggaaacaaggatttcagtgccaag
+
+a score=4890.000000
+s LMAW01000001.1 9869264 74 - 10443977 tttgctgcttcgttgtgcacaagcggtgccatgagttcgtcaccttctcctgccccggtgctgataaaggccct
+s NM_001012804       272 74 +     4592 tttgctgttttgtggttcataagagatgccatgagttcgttaccttctcctgtcctggagctgacaagggacct
+
+a score=7050.000000
+s LMAW01000001.1 9881475 112 - 10443977 gatccccggagcaaacacaagtttaaaatccacacgtactccagccccactttctgcgaccactgcgggtcattgctctacgggctcattcaccaggggatgaaatgtgaca
+s NM_001012804       355 112 +     4592 gaccccaggagcaagcacaaatttaagatccacacctatgggagcccaaccttctgtgaccactgtgggtcccttctttatgggctcctacaccaagggatgaaatgtgaca
+
+a score=191.000000
+s LMAW01000001.1 9881600 2 - 10443977 ct
+s NM_001012804       467 2 +     4592 ct
+
+a score=3890.000000
+s LMAW01000001.1 9882641 87 - 10443977 tgtatgatgaacgtgcacaagcgctgcgtgatgaacgtccccagcctgtgcgggacggaccacaccgagcgccgcggccgcatctac
+s NM_001012804       469 87 +     4592 tgtgatatgaatgtgcataagcaatgtgtgataaacgtcccgagcctctgtggcatggatcacactgagaaaaggggaaggatttat
+
+a score=6440.000000
+s LMAW01000001.1 9893172 150 - 10443977 agagatgctaaaaacctagttcctatggaccctaatggcttgtcagacccctacgtgaagcttaaactaatccctgaccccaaaaannnnnnnnnnnnnnnnnnnaaaactatcaagtgctccctgaatcctgagtggaacgagacattt
+s NM_001012804       598 150 +     4592 cgagaagcaaaaaacctaattcccatggatccaaatgggctttcagatccttatgttaaactgaaacttatcccagatcccaagaatgaaagtaaacaaaaaacaaaaaccttccgttctaccctgaatccacactggaatgagtcattc
+
+a score=5859.000000
+s LMAW01000001.1 9893708 114 - 10443977 ctgaaagaggcggacaaagacaggcggttgtctgtggagatttgggactgggatctgaccagcaggaatgatttcatgggctccttgtcctttgggatttcggagctgcagaag
+s NM_001012804       757 114 +     4592 ttaaaacctacagacaaagatcgacggctctctgtagaggtctgggactgggatcgaacaaccaggaatgattttatgggctctctttcatttggggtgtcagagctcatgaag
+
+a score=2349.000000
+s LMAW01000001.1 9899022 39 - 10443977 gatcggatgaaactgtcggatttcaacttcctgatggtg
+s NM_001012804      1066 39 +     4592 gacagggtgaaactgacagatttcaactttcttatggtt
+
+a score=9302.000000
+s LMAW01000001.1 9904744 171 - 10443977 gtgatgctggcggagaggaagggcacggatgagctctatgctgttaagatcttgaagaaggacgttgtaatccaggacgatgatgtagagtgcacgatggtngaaaagcgcgtcctggctctctctgggaagcctccgttcctgacccagctccactcctgctttcagacc
+s NM_001012804      1129 171 +     4592 gtgatgctggcggacaggaagaatacagaggagctctatgcaatcaaaatactgaaaaaagatgtggtgattcaggatgatgatgttgagtgtacaatggttgaaaaacgagtgctagcactgcaggataaaccaccattcctgacacagcttcactcatgtttccaaaca
+
+a score=282.000000
+s LMAW01000001.1 9904997 3 - 10443977 gtt
+s NM_001012804      1300 3 +     4592 gtt
+
+a score=6148.000000
+s LMAW01000001.1 9908755 94 - 10443977 gatcgcttgtattttgtgatggaatatgtgaatggtggggacttgatgtaccagatccagcaggttgggaggtttaaagagccncatgctgtgt
+s NM_001012804      1303 94 +     4592 gaccgcctgtattttgttatggagtatgtgaatggtggggatctcatgtaccacattcagcaagtaggaaaatttaaggagccacaagcagtgt
+
+a score=2175.000000
+s LMAW01000001.1 9909749 58 - 10443977 tctacgcagcagaaatagccatcggcctcttcttcctgcagagcaaaggcatcattta
+s NM_001012804      1397 58 +     4592 tctatgcagctgagatctcagttgggttattctttctccataatagagggattgttta
+
+a score=8515.000000
+s LMAW01000001.1 9911745 142 - 10443977 tagggacctaaagctggataacgtgatgctggatagcgaggggcacataaagatcgcagactttggcatgtgcaaagagaacatctgggatggggtgaccaccaagaccttctgcggcactccagactacattgcacctgag
+s NM_001012804      1455 142 +     4592 tagagatctgaaattggataatgtgatgttggattcagaaggacacattaaaattgctgactttggaatgtgcaaagaacatatgttagatggagtaacaaccaggaccttctgtggcaccccagattacatcgcaccggag
+
+a score=6703.000000
+s LMAW01000001.1 9915154 81 - 10443977 ataattgcttatcagccctacgggaagtctgtggattggtgggcatttggagtcctgctctatgaaatgttagctggccag
+s NM_001012804      1597 81 +     4592 atcattgcttatcagccctatgggaagtctgtggattggtgggcatatggagtgctgctctacgagatgttagctggccag
+
+a score=6328.000000
+s LMAW01000001.1 9915481 107 - 10443977 ctccctttgagggggaagatgaagacgagctcttccagtcnatcatggagcacaacgtcgcctaccccaagtccatgtccaaggaggctgtggcgatctgcaaaggg
+s NM_001012804      1679 107 +     4592 ctccatttgatggagaagatgaagatgaacttttccagtccataatggaacataatgtttcctatccaaaatcgctgtccaaagaagctgtctccatctgcaagggg
+
+a score=7584.000000
+s LMAW01000001.1 9920844 137 - 10443977 ctgatgaccaagcaccctgccaagcgcctgggatgtggcccagaaggggagcgggacatcaaggagcacgcgttcttccgctacattgactgggacaaactggagcggaaggagatccagcctcccttcaagccaaa
+s NM_001012804      1786 137 +     4592 ctaatgactaaacatcccgcaaagcgccttggctgcggcctcgaaggtgaaagagacatcagggaacacgctttcttcaggagaattgactgggagaaactggaaaacagagagatccagccacctttcaagcccaa
+
+a score=3640.000000
+s LMAW01000001.1 9926373 139 - 10443977 ntagtgcggacgcaatgctgagaacttcgaccggtttttcactcgccatccacccgtgctcacacctcccgaccaggaagtcatcaggaacattgaccagtcagaattcgnnnnnnnnnnnnnnnnnnnnnctgagttt
+s NM_001012804      1923 139 +     4592 agtgtgtggcaaaggtgctgaaaacttcgataaattcttcacgcgaggacagccggtgttgaccccgccagaccagctggtcattgctaacatagatcaatccgattttgaagggttctcctatgtcaacccccagttt
+
+a score=3751.000000
+s LMAW01000003.1 1355544 60 - 4188689 gatgaggagaggcagcagaactctgatgatgaggagagacagcagaactctgatgatgag
+s NM_001292086       619 60 +    6644 gatgaggagaagatgcagaactctgatgatgaggagaggccgcaggtgtcggacgaggag
+
+a score=2694.000000
+s LMAW01000003.1 1355538 43 - 4188689 tcagatgatgaggagaggcagcagaactctgatgatgaggaga
+s NM_001292086       562 43 +    6644 tctgatgaagatgagaggccgcagatgtctgacgatgaggaga
+
+a score=3757.000000
+s LMAW01000003.1 1355764 74 - 4188689 gggcccagcactctgatgaggagaaggtacacaactctgatggtgatgaacgggcccagcattctgatgaggag
+s NM_001292086       605 74 +    6644 ggctccagaactcggatgaggagaagatgcagaactctgatgatgaggagaggccgcaggtgtcggacgaggag
+
+a score=5882.000000
+s LMAW01000003.1 1355538 102 - 4188689 tcagatgatgaggagaggcagcagaactctgatgatgaggagagacagcagaactctgatgatgaggagaaagcacagaactctgatgaagatgaaaggccg
+s NM_001292086       508 102 +    6644 tctgatgatgaggagagacagcagaactcggacgatgaggagaaagcacagaactctgatgaagatgagaggccgcagatgtctgacgatgaggagaggctc
+
+a score=7814.000000
+s LMAW01000003.1 1355640 148 - 4188689 caggtatctgatgatgaggaaaggcttcagaactcagatnnnnnnnnnnnnnnnnnnnntgatgatgaggagaggccacaggcctcagatgaggagaagatgcagaactcagatgatgatgaaagggcccagcactctgatgaggaga
+s NM_001292086       634 148 +    6644 cagaactctgatgatgaggagaggccgcaggtgtcggacgaggagaagatgcaaaactcagatgatgatgaaagagcccagcactctgatgaggagaagatgcagaactctgacgatgacgaaagggcccagcgctccgatgaggagg
+
+a score=6015.000000
+s LMAW01000003.1 1355565 110 - 4188689 tctgatgatgaggagagacagcagaactctgatgatgaggagaaagcacagaactctgatgaagatgaaaggccgcaggtatctgatgatgaggaaaggcttcagaactc
+s NM_001292086       481 110 +    6644 tcagatgatgaggagcgacagcagaactctgatgatgaggagagacagcagaactcggacgatgaggagaaagcacagaactctgatgaagatgagaggccgcagatgtc
+
+a score=9080.000000
+s LMAW01000003.1 1355699 140 - 4188689 tgatgatgaggagaggccacaggcctcagatgaggagaagatgcagaactcagatgatgatgaaagggcccagcactctgatgaggagaaggtacacaactctgatggtgatgaacgggcccagcattctgatgaggagg
+s NM_001292086       591 140 +    6644 tgacgatgaggagaggctccagaactcggatgaggagaagatgcagaactctgatgatgaggagaggccgcaggtgtcggacgaggagaagatgcaaaactcagatgatgatgaaagagcccagcactctgatgaggaga
+
+a score=5069.000000
+s LMAW01000003.1 1353551 64 - 4188689 gcggccatggcggatatggaggatctcttcggcagcgacgcggactcggaggccgagcagaaag
+s NM_001292086        10 64 +    6644 gcagccatggccgacatggaggagctgttcggcagcgacgccgactcggaggccgagcagaaag
+
+a score=52268.000000
+s LMAW01000003.1 1355131 727 - 4188689 attccgactctggatctgaatctgattctgatcaggaaaatgctggctctggtagcaatgcttctggaagtgacagtgaccaagacgatgacagagaagcagtaaaacctagtaataaggagttatttggagacgatagtgaagatgaaggggcatcccatcacacagggagtgacaaccattccgaaagatcctacaatcgctctgaagcttcagaacattctgagcatgaagataatgatcagtcggatgtggaccagcacagtgcttcagaagctgctcatgacgatgaggatgatgatcgtgggcatgggtctgatgaaggcagtcatcattcagagggagatggttctgaaaaagcacattcagaggatgagaagtggggcaaggaggacaaaagtgatcagtcagatgatgaggagaggcagcagaactctgatgatgaggagagacagcagaactctgatgatgaggagaaagcacagaactctgatgaagatgaaaggccgcaggtatctgatgatgaggaaaggcttcagaactcagatnnnnnnnnnnnnnnnnnnnntgatgatgaggagaggccacaggcctcagatgaggagaagatgcagaactcagatgatgatgaaagggcccagcactctgatgaggagaaggtacacaactctgatggtgatgaacgggcccagcattctgatgaggaggaccaagagcacaaatctgg
+s NM_001292086        74 727 +    6644 ataccgattccggctcagactccgactctgaccaggagaacgcgggctccggcagcaacgcctcgggcagcgacagcgagcaggacgacgagcgggaggcagcaaagcccagcaacaaggagctgttcggagacgacagcgaggatgaaggagcctcccatcacacgggcagcgacaaccactccgagaggtcgtacaatcgctccgaagcttcggggcactctgagcacgaagacaacgatcagtcggacgtggaccagcacagcgcttcagaagcggctcatgacgatgaggaggacgagcgggggcacggctctgatgagggcagtcaccattctgagggagatggttcagaaaaggcccattcggaggatgagaagtggggcaaggaggacaaaagcgatcagtcagatgatgaggagcgacagcagaactctgatgatgaggagagacagcagaactcggacgatgaggagaaagcacagaactctgatgaagatgagaggccgcagatgtctgacgatgaggagaggctccagaactcggatgaggagaagatgcagaactctgatgatgaggagaggccgcaggtgtcggacgaggagaagatgcaaaactcagatgatgatgaaagagcccagcactctgatgaggagaagatgcagaactctgacgatgacgaaagggcccagcgctccgatgaggaggagcaggagcataaatctgg
+
+a score=8477.000000
+s LMAW01000003.1 1356116 107 - 4188689 agagtctgcgaggggcagtgacagcgaagatgaagtcctgcgaatgaagcgaaagaaaaccattgcttcagattcagaagcagacagtgatacagaaggacagaaag
+s NM_001292086       801 107 +    6644 agagtctgcaagaggcagcgacagtgaagatgaagtcctgcgaatgaagcgaaagaaaccaattgcatcagattcagaggcggacagtgatacagaaggccagaagg
+
+a score=473.000000
+s LMAW01000003.1 1356798 5 - 4188689 aacac
+s NM_001292086       908 5 +    6644 aacac
+
+a score=7274.000000
+s LMAW01000003.1 1356971 90 - 4188689 gcagatgtcatggatctgtttggaggtgcagatgacatttcctcagggagtgatggagaagacaagccaccaactccagggcagcccatt
+s NM_001292086       913 90 +    6644 gcagacgtcatggacctgtttggaggagcagatgacatttcttcgggaagcgatggggaagacaagccgccaactccaggacagcccatt
+
+a score=12261.000000
+s LMAW01000003.1 1357445 146 - 4188689 gatgagaatggactgagtcaggagcaacaggaagaagagcctattccagagactagaatagaagtagaaataccaaaagtgaacacagacttgggtaatgatttgtattttgtgaagctgcccaatttccttagtgtggagcccag
+s NM_001292086      1003 146 +    6644 gatgagaatgggctgagccaagaacagcaggaggaagagcctattccagagacaagaatagaggtagaaataccaaaagtaaacacagacttgggtaacgatttgtattttgtgaagctgcccaacttcctcagtgtggagcccag
+
+a score=6700.000000
+s LMAW01000003.1 1359020 87 - 4188689 accttttgacccccagtattatgaagatgaatttgaagatgaagagatgcttgatgaagagggtagaactaggttaaaactcaaggt
+s NM_001292086      1149 87 +    6644 accatttgatccccagtattatgaggatgaatttgaagatgaggagatgcttgatgaggaagggagaacgagattaaaacttaaggt
+
+a score=7904.000000
+s LMAW01000003.1 1359444 93 - 4188689 agaaaacacaatacgatggcggatgcgacgggatgaggaagggaatgagatcagagaaagtaatgcacggatagtcaagtggtcagatggaag
+s NM_001292086      1236 93 +    6644 agaaaacacaatacggtggcggatgcggcgagatgaggaagggaatgagattagagaaagcaatgcccggatagtcaagtggtcggatggaag
+
+a score=10924.000000
+s LMAW01000003.1 1359816 135 - 4188689 catgtctcttcacttgggcaatgaggtctttgacgtgtacaaggcgccattacagggagatcacaaccatttgttcatcagacaagggacgggtctacaaggacaggctgttttcaagacaaaattaaccttcag
+s NM_001292086      1329 135 +    6644 catgtctctccacttgggaaatgaggtctttgatgtgtacaaggcaccgctgcagggagatcacacccatctgtttatcagacaagggacaggtctgcaaggacaggctgttttcaggacaaagttaaccttcag
+
+a score=11554.000000
+s LMAW01000003.1 1360523 137 - 4188689 gccacactctacagacagtgccactcacaggaagatgactctgtctctggcagatagatgctcaaagacccagaaaatccgtattctgccaatggcaggtcgggatccagagtctcagcggacagaaatgattaagg
+s NM_001292086      1464 137 +    6644 gccacactctacagacagtgccacgcacaggaagatgactctgtctctggcagataggtgttcaaagacccagaaaattcgtattttgccaatggcgggtcgtgatccggagtctcagcgcacagaaatgattaaga
+
+a score=14859.000000
+s LMAW01000003.1 1360971 171 - 4188689 aagagcttccattcgcagagaatctcagcagcgaagaatgcgggagaagcagcatcagcgtggtctgagtgccaattatttggaacctgatcgctatgatgaagaggatgagggagatgatgcaatcagtctagcagctatcaaaaacagatacaaaggtggcatcagagg
+s NM_001292086      1617 171 +    6644 aagagcttccattcgcagagaatctcagcagcgaagaatgagggagaagcagcatcagcgtggtctgagtgctaattacttagaacccgatcgctatgaagaagaggacgagggagacgatgcgatcagtctagcagctatcaaaaacagatacaaaggtggcatcagaga
+
+a score=8115.000000
+s LMAW01000003.1 1361443 93 - 4188689 cgtgctagaatctactcttctgacagtgatgaaggctcggatgaagataaaacacaaagactactcaaggcaaagaaacttaatagtgatgag
+s NM_001292086      1792 93 +    6644 cgtgctagaatctattcttcagacagtgatgaaggctcagatgaagataaaacacaaagactactcaaggcaaagaaacttactagtgatgag
+
+a score=3465.000000
+s LMAW01000003.1 1365082 72 - 4188689 gaaggtgaannnnnnnnnnnnnnnnnnnnnnnnnnnnatgacaaagcaagtaagaagcataagaaatatgtg
+s NM_001292086      1885 72 +    6644 gaaggggagccttctggaaagagaaaagcagaggatgatgacaaagcaagtaagaagcataagaagtatgtc
+
+a score=7181.000000
+s LMAW01000003.1 1365245 90 - 4188689 ttctcttacagcgaagatgtaagtaaccataatggggttattttgataaaggaaaattccattgaagtctgagtttctgttgtgaataaa
+s NM_001292086      2049 90 +    6644 ttctcttacagcaaagatgtaagtagccatattggggttattttgataaaggagaattccattgaaatttgtgtttctggtgtgaataaa
+
+a score=2475.000000
+s LMAW01000003.1 1365351 69 - 4188689 ttannnnnnnnnnnnnnnnnnntactgcagcaactattgcaccagggattgtcacagtgccaattgtta
+s NM_001292086      2163 69 +    6644 ctcatatttttacatcttatcttactgcagcagctgctgcaatggggatcatcatagcatcagttttta
+
+a score=5156.000000
+s LMAW01000003.1 1365525 90 - 4188689 atagaatgcttaaatgataagtttgcctggcaagggtatggtgatctagcttaccatttgtatggaatggttggaaaaacatatgagtgg
+s NM_001292086      2350 90 +    6644 atagaatgcttaaattataagttttctcagccaggttatggagatgaaggttaccatttgtacagaagatttggaatatcatatgagtgg
+
+a score=2007.000000
+s LMAW01000003.1 1366096 23 - 4188689 tatttctaaacaccttatttgat
+s NM_001292086      2918 23 +    6644 tatttttaaacaccttatttgat
+
+a score=2712.000000
+s LMAW01000003.1 1366220 44 - 4188689 ttggtgagagagcattcagatgttatctatgttgctcttttaac
+s NM_001292086      3036 43 +    6644 ttggtgagatagcatttccatgttatctatgttg-ttttttaac
+
+a score=4764.000000
+s LMAW01000003.1 1366474 72 - 4188689 aagtactgtacctcagtttttcctgcctggaaggtacaggaaatgttctagctgcagtggganggagctctg
+s NM_001292086      3366 72 +    6644 aagtactctacctccatttttcttgcctggaaggtgtgggaagcattctagctgcagaggcacagagctctg
+
+a score=7434.000000
+s LMAW01000003.1 1366549 195 - 4188689 taatgnnnnnnnnnnnnnnnnnnnntgcagtgtagacatttgcaagnnnnnnnnnnnnnnnnnnnnnnnnaactcaggagcctgagtgcctgagaannnnnnnnnnnnnnnnnnnnnnaattaaa------ttgttatctaagagttcctgtgcctctttaatgtgcagataaaacctttctccatctgctggaattttga
+s NM_001292086      3445 201 +    6644 taatatattctgctcagcagctgactgcagtgtagacacttgcaaatatgaaaacaaagtgaaaaatgtctactctgaagtctgagtgcctgagaagctgttcttttgttgttgttgttgttgtttttgtacttgtttctaagagttcctgcctctcttccctgtgcagataaaacctttctccatctgctccaattttga
+
+a score=7427.000000
+s LMAW01000003.1 1366749 106 - 4188689 taatcctcttagctgagacctctgctgggagtctggttccttacatgaggttacctgctttccatttgtaaccttctcttgaagaagccagctgcgtagaaaggga
+s NM_001292086      3647 106 +    6644 taatcctcttaggttagacctctgctgggagtctggctcctcacatgtggttacctgcttttctgttgtaacctgctcaggaagaagccagctgtagaaaaaggga
+
+a score=1617.000000
+s LMAW01000003.1 1366889 21 - 4188689 agcctcccagatacttcttaa
+s NM_001292086      3794 21 +    6644 agtctcccagatacctcttga
+
+a score=9044.000000
+s LMAW01000003.1 1367081 185 - 4188689 actttagcttccaaaaattaggctttttgtggattacgaannnnnnnnnnnnnnnnnnnnnnnnctgttgtcctttgtaaattgctcttttacaatcttctttagacatggaannnnnnnnnnnnnnnnnncatcttaaattggtttaacnatcatcctgtaattaaagttgcttgaatgaactt
+s NM_001292086      3985 184 +    6644 actttagcttccaaaaaggaggc-ttttgtggatttaaaagattaaaaggagtgtttttttctactgtcttcttttgtaaattgctcttctaaagtcttattaaaacatagaattttagaaagtgttttctcagcctaaattggtttaacaatcaccttttaattaaagtcacttgaacgaactt
+
+a score=3529.000000
+s LMAW01000003.1 1367332 55 - 4188689 ttctgctgtcctttttcccagcctcc-agtatgagagaagtacttggaattgtttc
+s NM_001292086      4236 56 +    6644 ttttgctctcccttttcccagcctccaagtatgtgacaattacttggaattgtttt
+
+a score=4944.000000
+s LMAW01000003.1 1367558 93 - 4188689 attttatggctattggcaggatgcaggatgaattctcttgaaacnnnnnnnnnnnnnnnnnnnnngctatatagttttgtggtttcaagtata
+s NM_001292086      4476 93 +    6644 attttctggctagtggtagagtgtaggatcagttgtcttgaaaccatcactgaaaggtgttcctagctatatagttttgttgtttcaggtata
+
+a score=1410.000000
+s LMAW01000003.1 1367688 15 - 4188689 gagttttctttctag
+s NM_001292086      4603 15 +    6644 gagttttctttctag
+
+a score=2985.000000
+s LMAW01000003.1 1367786 45 - 4188689 tgggtcagggaatgcccattgaagggagcagctgctcatgcagtc
+s NM_001292086      4688 45 +    6644 tggatcaggggctgccctcagaagggtgcagctgcccatgcagtc
+
+a score=1719.000000
+s LMAW01000003.1 1367837 18 - 4188689 ttctagcagcaggtttgg
+s NM_001292086      4742 18 +    6644 ttctagcagcaggtttgg
+
+a score=1064.000000
+s LMAW01000003.1 1367979 11 - 4188689 agccagctcag
+s NM_001292086      4882 11 +    6644 agccagctcag
+
+a score=1146.000000
+s LMAW01000003.1 1368029 12 - 4188689 tctctttggcag
+s NM_001292086      4941 12 +    6644 tctctttggcag
+
+a score=2914.000000
+s LMAW01000003.1 1368113 54 - 4188689 gtaactgccagagctggcacattgaaaagtcatctgtgcctcgaggtggtgcaa
+s NM_001292086      5031 54 +    6644 gtagctgcctcagctggcacactggtgtgtcggttgtgactggaggtggtgcaa
+
+a score=10302.000000
+s LMAW01000003.1 1368194 162 - 4188689 gcagcaagatttagcacagctctaatacaaagctgcagcctgaggaatatgttaaacatgagatggtggctttcctatgaagtcatgggtacttatttctctgccagcaggcacggaggtccttggtgtcagcccattctagcagagtgcctttgtttaaca
+s NM_001292086      5113 162 +    6644 gcagcaagttttaactcggctcagatgtgaaactgcagccacaggaatgtgttaaacatgagatggtgactttccagtgaagtcataggtatttatttctcagccagtgggcataggagcccatggtgtcggcccattctaatggagtgcttttctctaaca
+
+a score=1839.000000
+s LMAW01000003.1 1368429 27 - 4188689 ctgtttctgataaatgttcttctcatt
+s NM_001292086      5348 27 +    6644 ttgtttctgataaatgttcttttaata
+
diff -r c449963debd5 -r 2a89f630fa85 test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl
--- a/test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl	Mon Nov 21 11:12:14 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-1247	370	0	44	6	280	17	96639	+-	NM_001012804	4592	121	2062	LMAW01000001.1	10443977	517465	615765	18	119,32,74,112,2,87,150,114,39,171,3,94,58,142,81,107,137,139,	121,240,272,355,467,469,598,757,1066,1129,1300,1303,1397,1455,1597,1679,1786,1923,	9828212,9828431,9869264,9881475,9881600,9882641,9893172,9893708,9899022,9904744,9904997,9908755,9909749,9911745,9915154,9915481,9920844,9926373,
-143	58	0	19	3	659	4	9089	++	NM_204766	5992	574	1453	LMAW01000003.1	4188689	259524	268833	5	27,80,11,66,36,	574,700,780,847,1417,	259524,261255,261529,262379,268797,
-182	48	0	20	1	24	0	0	+-	NM_001292086	6644	508	782	LMAW01000003.1	4188689	2832901	2833151	2	102,148,	508,634,	1355538,1355640,
-189	73	0	0	4	773	4	13674	++	NM_204766	5992	553	1588	LMAW01000003.1	4188689	2559457	2573393	5	84,66,33,13,66,	553,739,844,1457,1522,	2559457,2563244,2563349,2570767,2573327,
-200	50	0	0	0	0	1	24	+-	NM_001292086	6644	481	731	LMAW01000003.1	4188689	2832850	2833124	2	110,140,	481,591,	1355565,1355699,
-2134	377	0	62	6	361	28	33978	++	NM_001006176	3248	296	3230	LMAW01000001.1	10443977	10027590	10064141	29	110,48,10,76,75,152,66,51,87,83,55,56,148,96,63,24,177,107,83,145,109,83,145,90,117,129,68,93,27,	296,406,454,502,578,653,844,910,961,1048,1131,1186,1242,1390,1486,1609,1741,1918,2025,2108,2253,2362,2445,2590,2680,2797,2926,3034,3203,	10027590,10031154,10031353,10031517,10033261,10033696,10034454,10035646,10043484,10043794,10059668,10059824,10059973,10060798,10060979,10061265,10061487,10061740,10061947,10062143,10062365,10062584,10062743,10063001,10063188,10063383,10063616,10063806,10064114,
-2710	404	0	198	24	2053	34	11593	+-	NM_001292086	6644	10	5375	LMAW01000003.1	4188689	2820233	2835138	37	64,727,107,5,90,146,87,93,135,137,171,93,72,90,69,90,23,34,9,72,125,70,106,21,23,161,26,29,93,15,45,18,11,12,54,162,27,	10,74,801,908,913,1003,1149,1236,1329,1464,1617,1792,1885,2049,2163,2350,2918,3036,3070,3366,3445,3576,3647,3794,3985,4008,4236,4263,4476,4603,4688,4742,4882,4941,5031,5113,5348,	1353551,1355131,1356116,1356798,1356971,1357445,1359020,1359444,1359816,1360523,1360971,1361443,1365082,1365245,1365351,1365525,1366096,1366220,1366255,1366474,1366549,1366674,1366749,1366889,1367081,1367105,1367332,1367358,1367558,1367688,1367786,1367837,1367979,1368029,1368113,1368194,1368429,
-3724	1107	0	326	14	609	44	22663	++	NM_204766	5992	49	5815	LMAW01000002.1	5883884	103604	131424	45	51,78,132,3,152,2,29,75,90,63,1,95,81,3,136,119,150,2,169,180,123,48,90,117,123,134,241,261,177,146,90,72,267,129,81,2,196,348,116,193,106,123,177,99,87,	49,154,256,388,391,543,545,574,691,781,844,845,967,1048,1051,1187,1306,1456,1458,1627,1807,1960,2008,2098,2215,2338,2472,2713,2974,3151,3298,3388,3493,3778,3943,4024,4026,4222,4696,4812,5051,5212,5335,5608,5728,	103604,104407,107764,107909,108002,108233,108257,109261,112047,112967,113036,113148,114257,114391,114866,116183,116438,116593,116908,117767,118030,118682,120119,120672,121329,122185,122724,123518,123945,124449,124904,125793,125898,126790,127405,127543,127717,128055,129238,129442,129761,130020,130254,131103,131337,
-420	114	0	0	4	99	3	7093	++	NM_001031013	971	69	702	LMAW01000002.1	5883884	3610886	3618513	5	33,66,21,276,138,	69,138,232,285,564,	3610886,3610955,3617941,3618099,3618375,
-49	11	0	0	0	0	0	0	+-	NM_001292086	6644	619	679	LMAW01000003.1	4188689	2833085	2833145	1	60,	619,	1355544,
-537	234	0	42	7	1113	7	34987	++	NM_204766	5992	262	2188	LMAW01000001.1	10443977	9729332	9765132	8	108,153,66,93,39,171,99,84,	262,388,574,688,1414,1459,1981,2104,	9729332,9734141,9751019,9755220,9762042,9762555,9764665,9765048,
-92	25	0	0	0	0	1	183	+-	NM_001292086	6644	562	679	LMAW01000003.1	4188689	2832851	2833151	2	43,74,	562,605,	1355538,1355764,
diff -r c449963debd5 -r 2a89f630fa85 test-data/dbia3/dbia3_masked.sorted.psl
--- a/test-data/dbia3/dbia3_masked.sorted.psl	Mon Nov 21 11:12:14 2022 +0000
+++ b/test-data/dbia3/dbia3_masked.sorted.psl	Fri Dec 02 09:35:54 2022 +0000
@@ -1,3 +1,8 @@
+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
 40	8	0	0	0	0	0	0	++	FBtr0070075	2430	1838	1886	contig14	45010	22563	22611	1	48,	1838,	22563,
 39	9	0	0	0	0	0	0	++	FBtr0070075	2430	1838	1886	contig65	45013	12112	12160	1	48,	1838,	12112,
 39	9	0	0	0	0	0	0	++	FBtr0070075	2430	1838	1886	contig64	40016	32121	32169	1	48,	1838,	32121,
diff -r c449963debd5 -r 2a89f630fa85 tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample	Mon Nov 21 11:12:14 2022 +0000
+++ b/tool-data/all_fasta.loc.sample	Fri Dec 02 09:35:54 2022 +0000
@@ -1,29 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a fasta_indexes.loc file
-#similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The fasta_indexes.loc
-#file has this format (white space characters are TAB characters):
-#
-# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
-#
-#So, for example, if you had hg19 Canonical indexed stored in
-#
-# /depot/data2/galaxy/hg19/sam/,
-#
-#then the fasta_indexes.loc entry would look like this:
-#
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
-#
-#and your /depot/data2/galaxy/hg19/sam/ directory
-#would contain hg19canon.fa and hg19canon.fa.fai files.
-#
-#Your fasta_indexes.loc file should include an entry per line for
-#each index set you have stored.  The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file.  For example:
-#
-#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
-#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
-#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
\ No newline at end of file
diff -r c449963debd5 -r 2a89f630fa85 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Dec 02 09:35:54 2022 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of blat database files -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>
\ No newline at end of file