Mercurial > repos > yating-l > ucsc_blat
changeset 11:2a89f630fa85 draft
planemo upload commit 3bb07d25ab817c936018d57b6d81f728915cfadf
| author | iuc |
|---|---|
| date | Fri, 02 Dec 2022 09:35:54 +0000 |
| parents | c449963debd5 |
| children | e79965d0351c |
| files | blat.xml test-data/all_fasta.loc test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.maf test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl test-data/dbia3/dbia3_masked.sorted.psl tool-data/all_fasta.loc.sample tool_data_table_conf.xml.test |
| diffstat | 7 files changed, 830 insertions(+), 156 deletions(-) [+] |
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--- 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)
--- 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 +
--- /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 +
--- 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,
--- 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,
--- 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
--- /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