--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="2.4.0">progressivemauve</requirement>
+      <requirement type="package" version="2.7">python</requirement>
+      <requirement type="package" version="1.65">biopython</requirement>
+      <requirement type="package" version="0.6.2">bcbiogff</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <token name="@WRAPPER_VERSION@">2.4.0</token>
+  <xml name="stdio">
+    <stdio>
+      <!-- Anything other than zero is an error -->
+      <exit_code range="1:"/>
+      <exit_code range=":-1"/>
+      <!-- In case the return code has not been set propery check stderr too -->
+      <regex match="Error:"/>
+      <regex match="Exception:"/>
+    </stdio>
+  </xml>
+  <xml name="citation">
+      <citations>
+          <citation type="doi">10.1371/journal.pone.0011147</citation>
+      </citations>
+  </xml>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/progressivemauve.xml	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,439 @@
+<?xml version="1.0"?>
+<tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.0">
+  <description>constructs multiple genome alignments</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command>progressiveMauve --version</version_command>
+  <command><![CDATA[
+## Symlink files in with correct extensions
+#for $file in $sequences:
+    ln -s $file `basename $file`;
+#end for
+
+progressiveMauve
+## Input Options
+
+#if $apply_backbone:
+    --apply-backbone=$apply_backbone
+#end if
+--island-gap-size=$island_gap_size
+$mums
+
+#if $seed_weight:
+    --seed-weight=$seed_weight
+#end if
+
+#if $max_gapped_aligner_length:
+    --max-gapped-aligner-length=$max_gapped_aligner_length
+#end if
+
+#if $match_input:
+    --match-input=$match_input
+#end if
+
+$collinear
+--scoring-scheme=$scoring_scheme
+$no_weight_scaling
+
+--max-breakpoint-distance-scale=$max_breakpoint_distance_scale
+--conservation-distance-scale=$conservation_distance_scale
+$skip_refinement
+$skip_gapped_alignment
+
+#if $bp_dist_estimate_min_score:
+    --bp-dist-estimate-min-score=$bp_dist_estimate_min_score
+#end if
+
+#if $gap_open:
+    --gap-open=$gap_open
+#end if
+
+#if $gap_extend:
+    --gap-extend=$gap_extend
+#end if
+
+#if $weight:
+    --weight=$weight
+#end if
+
+#if $min_scaled_penalty:
+    --min-scaled-penalty=$min_scaled_penalty
+#end if
+
+--hmm-p-go-homologous=$hmm_p_go_homologous
+--hmm-p-go-unrelated=$hmm_p_go_unrelated
+--hmm-identity=$hmm_identity
+
+$seed_family
+$solid_seeds
+$coding_seeds
+$no_recursion
+$disable_backbone
+
+## Outputs
+--output=$output
+#if $output_guide_tree:
+    --output-guide-tree=$output_guide_tree_file
+#end if
+
+#if $output_backbone:
+    --backbone-output=$output_backbone_file
+#end if
+
+## Sequences
+#for file in $sequences:
+    `basename "${file}"`
+#end for
+
+]]></command>
+  <inputs>
+      <param type="data" format="fasta" name="sequences" multiple="True"
+          label="Select sequences to align" help="in fasta format" />
+      <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True"
+          help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />
+
+      <param type="integer" label="Island gap size" value="20" name="island_gap_size"
+          help="Alignment gaps above this size in nucleotides are considered to be islands (--island-gap-size)"/>
+
+      <param type="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone"
+          label="Disable backbone" help="Disable backbone detection (--disable-backbone)" />
+
+      <param type="boolean" truevalue="True" falsevalue="" name="output_guide_tree"
+          label="Output Guide Tree" help="Write out the guide tree used for alignment to a file (--output-guide-tree)" />
+
+      <param type="boolean" truevalue="True" falsevalue="" name="output_backbone"
+          label="Output Backbone" help="Write out the backbone to a file (--backbone-output)" />
+
+      <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" name="mums"
+          help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) (--mums)" />
+
+      <param type="integer" label="Seed weight" name="seed_weight" value="0" optional="True"
+          help="Use the specified seed weight for calculating initial anchors (--seed-weight)" />
+
+      <param type="data" format="tabular" label="Match Input" name="match_input" optional="True"
+          help="Use specified match file instead of searching for matches (--match-input)" />
+
+    <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />-->
+    <param type="integer" label="Max gapped aligner length" value="0" optional="True" name="max_gapped_aligner_length"
+        help="Maximum number of base pairs to attempt aligning with the gapped aligner (--max-gapped-aligner-length)" />
+
+    <param type="data" format="nhx" label="input-guide-tree" optional="True" name="input_guide_tree"
+        help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned (--input-guide-tree)" />
+
+    <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" name="collinear"
+        help="Assume that input sequences are collinear--they have no rearrangements (--collinear)" />
+
+    <param type="select" label="Scoring scheme" name="scoring_scheme" help="Selects the anchoring score function. (--scoring-scheme)" >
+        <option value="sp" selected="True">Extant sum-of-pairs (sp)</option>
+        <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option>
+        <option value="ancestral">Ancestral (ancestral)</option>
+    </param>
+
+    <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" name="no_weight_scaling"
+        help="Don't scale LCB weights by conservation distance and breakpoint distance (--no-weight-scaling)" />
+
+    <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" name="max_breakpoint_distance_scale"
+        help="Set the maximum weight scaling by breakpoint distance. (--max-breakpoint-distance-scale)" />
+
+    <param type="float" min="0" max="1"  label="conservation-distance-scale" value="0.5" name="conservation_distance_scale"
+        help="Scale conservation distances by this amount. (--conservation-distance-scale)" />
+
+    <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" name="skip_refinement"
+        help="Do not perform iterative refinement (--skip-refinement)" />
+    <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" name="skip_gapped_alignment"
+        help="Do not perform gapped alignment (--skip-gapped-alignment)" />
+    <param type="integer" label="BP dist estimate min score" name="bp_dist_estimate_min_score" value="0" optional="True"
+        help="Minimum LCB score for estimating pairwise breakpoint distance (--bp-dist-estimate-min-score)" />
+
+    <param type="integer" label="Gap open" name="gap_open" value="0" optional="True"
+        help="Gap open penalty (--gap-open)" />
+
+    <param type="select" label="Repeat penalty" name="repeat_penalty"
+        help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences. (--repeat-penalty)">
+        <option value="negative" selected="True">Negative</option>
+        <option value="zero">Zero</option>
+    </param>
+
+    <param type="integer" label="Gap extend" name="gap_extend" value="0" optional="True"
+        help="Gap extend penalty (--gap-extend)" />
+
+    <!--<param type="data" label="Substitution matrix" -->
+        <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />-->
+
+    <param type="integer" label="Weight" name="weight" value="0" optional="True"
+        help="Minimum pairwise LCB score (--weight)" />
+    <param type="integer" label="Min scaled penalty" name="min_scaled_penalty" value="0" optional="True"
+        help="Minimum breakpoint penalty after scaling the penalty by expected divergence (--min-scaled-penalty)" />
+
+    <param type="float" label="HMM p go homologous" name="hmm_p_go_homologous" min="0" max="1" value="0.00001"
+        help="Probability of transitioning from the unrelated to the homologous state (--hmm-p-go-homologous)" />
+    <param type="float" label="HMM p go unrelated" name="hmm_p_go_unrelated" min="0" max="1" value="0.000000001"
+        help="Probability of transitioning from the homologous to the unrelated state (--hmm-p-go-unrelated)" />
+    <param type="float" label="HMM identity" name="hmm_identity" min="0" max="1" value="0.7"
+        help="Expected level of sequence identity among pairs of sequences(--hmm-identity)" />
+
+    <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" name="seed_family"
+        help="Use a family of spaced seeds to improve sensitivity (--seed-family)" />
+    <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" name="solid_seeds"
+        help="Use solid seeds. Do not permit substitutions in anchor matches. (--solid-seeds)" />
+    <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" name="coding_seeds"
+        help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy. (--coding-seeds)" />
+    <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" name="no_recursion"
+        help="Disable recursive anchor search (--no-recursion)" />
+  </inputs>
+  <outputs>
+    <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}">
+       <change_format>
+           <when input="mums" value="--mums" format="tabular" />
+       </change_format>
+    </data>
+    <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree">
+        <when>output_guide_tree</when>
+    </data>
+    <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone">
+        <when>output_backbone</when>
+    </data>
+  </outputs>
+  <tests>
+      <test>
+          <param name="sequences" value="phagey.fa,karma.fa" />
+          <output name="output" file="1.xmfa" lines_diff="20"/>
+      </test>
+      <test>
+          <param name="sequences" value="merged.fa" />
+          <output name="output" file="1.xmfa" lines_diff="20"/>
+      </test>
+      <test>
+          <param name="sequences" value="merged.fa" />
+          <param name="output_guide_tree" value="True" />
+          <output name="output" file="1.xmfa" lines_diff="20"/>
+          <output name="output_guide_tree_file" file="1.nhx" />
+      </test>
+      <test>
+          <param name="sequences" value="merged.fa" />
+          <param name="mums" value="True" />
+          <output name="output" file="1.mums" compare="sim_size" delta="1000"/>
+      </test>
+      <test>
+          <param name="sequences" value="merged.fa" />
+          <param name="match_input" value="1.mums" />
+          <output name="output" file="1.xmfa" lines_diff="24"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+What it does
+============
+
+Mauve is a system for efficiently constructing multiple genome alignments in
+the presence of large-scale evolutionary events such as rearrangement and
+inversion. Multiple genome alignment provides a basis for research into
+comparative genomics and the study of evolutionary dynamics. Aligning whole
+genomes is a fundamentally different problem than aligning short sequences.
+
+Mauve has been developed with the idea that a multiple genome aligner should
+require only modest computational resources. It employs algorithmic techniques
+that scale well in the amount of sequence being aligned. For example, a pair of
+Y. pestis genomes can be aligned in under a minute, while a group of 9
+divergent Enterobacterial genomes can be aligned in a few hours.
+
+progressiveMauve XMFA alignment visualized with the Mauve tool:
+
+.. image:: $PATH_TO_IMAGES/hemolysin.jpg
+
+Example Usage
+=============
+
++-----------------------------------+-------------+
+| Usage                             | Notes       |
++===================================+=============+
+| Align genomes                     |Simply       |
+|                                   |select as    |
+|                                   |many fasta   |
+|                                   |files with   |
+|                                   |one or more  |
+|                                   |sequences as |
+|                                   |necessary    |
++-----------------------------------+-------------+
+| Align genomes but also save       |Use the      |
+| the guide tree and produce a      |**Output     |
+| backbone file                     |Guide Tree** |
+|                                   |and **Output |
+|                                   |Backbone**   |
+|                                   |options      |
++-----------------------------------+-------------+
+| Align genomes, but do not         |Use the      |
+| detect forced alignment of        |**Disable    |
+| unrelated sequences               |backbone**   |
+|                                   |option       |
++-----------------------------------+-------------+
+| Detect forced alignment of        |Use the      |
+| unrelated sequence in the         |**Apply      |
+| alignment produced                |Backbone**   |
+| in previous example, use          |option and   |
+| custom Homology HMM transition    |specify the  |
+| parameters.                       |XMFA file    |
+|                                   |produced     |
+|                                   |in the       |
+|                                   |previous     |
+|                                   |example      |
++-----------------------------------+-------------+
+| Compute ungapped                  |Use the      |
+| local-multiple alignments among   |**MUMs**     |
+| the input sequences               |option       |
++-----------------------------------+-------------+
+| Compute an alignment of the       |Set the      |
+| same genomes, using previously    |**Match      |
+| computed local-multiple           |Input** to   |
+| alignments                        |the tabular  |
+|                                   |MUMs file    |
+|                                   |produced in  |
+|                                   |the previous |
+|                                   |example      |
++-----------------------------------+-------------+
+| Set a minimum scaled              |Use the      |
+| breakpoint penalty to cope with   |**Min Scaled |
+| the case where most genomes       |Penalty** and|
+| are aligned correctly, but manual |set to a     |
+| inspection reveals that           |value like   |
+| a divergent genome has too        |5000         |
+| many predicted rearrangements.    |             |
++-----------------------------------+-------------+
+| Globally align a set of           |Use the      |
+| collinear virus                   |**Colinear**,|
+| genomes, using seed families      |**Seed       |
+| to improve anchoring sensitivity  |Family**     |
+| in regions below 70% sequence     |options      |
+| identity.                         |             |
++-----------------------------------+-------------+
+
+
+The progressiveMauve algorithm: addressing limitations of the original algorithm
+================================================================================
+
+Comparative genomics has revealed that closely-related bacteria often have
+highly divergent gene content. While the original Mauve algorithm could align
+regions conserved among all organisms, the portion of the genome conserved
+among all taxa (the core genome) shrinks as more taxa are added to the
+analysis. As such, the original Mauve algorithm did not scale well to large
+numbers of taxa because it could not align regions conserved among subsets of
+the genomes under study. progressiveMauve employs a different algorithmic
+approach to scoring alignments that allows alignment of segments conserved
+among subsets of taxa. The progressiveMauve algorithm has been described in
+Aaron Darling's Ph.D. Thesis, and is also the subject of a manuscript published
+in PLoS ONE. A brief overview is given here.
+
+Finding initial local multiple alignments
+-----------------------------------------
+
+progressiveMauve elaborates on the original algorithm for finding local
+multiple alignments. Instead of using a single seed pattern for match
+filtration, progressiveMauve uses a combination of three seed patterns for
+improved sensitivity. The palindromic seed patterns have been described in
+Darling et al. 2006 "Procrastination leads to efficient filtration for local
+multiple alignment"
+
+Seed matches which represent a unique subsequence shared by two or more input
+genomes are subjected to ungapped extension until the seed pattern no longer
+matches. The result is an ungapped local multiple alignment with at most one
+component from each of the input genome sequences.
+
+Computing a pairwise genome content distance matrix and guide tree
+------------------------------------------------------------------
+
+progressiveMauve builds up genome alignments progressively according to a guide
+tree. The guide tree is computed based on an estimate of the shared gene
+content among each pair of input genomes. For a pair of input genomes, g.x and
+g.y, shared gene content is estimated by counting the number of nucleotides in
+gx and gy aligned to each other in the initial set of local multiple
+alignments. The count is normalized to a similarity value between 0 and 1 by
+dividing by the average size of gx and gy. The similarity value is subtracted
+from 1 to arrive at a distance estimate. Neighbor joining is then applied to
+the matrix of distance estimates to yield a guide tree topology. Note that the
+guide tree is not intended to be a phylogeny indicative of the genealogy of
+input genomes. It is merely a computational crutch for progressive genome
+alignment. Also note that alignments are later refined independently of a
+single guide tree toplogy to avoid biasing later phylogenetic inference.
+
+Computing a pairwise breakpoint distance matrix
+-----------------------------------------------
+
+Prior to alignment, progressiveMauve attempts to compute a conservative
+estimate of the number of rearrangement breakpoints among any pair of genomes.
+For each pair of genomes, pairwise alignments are created from the
+local-multiple alignments and the pairwise alignments are subjected to greedy
+breakpoint elimination. The breakpoint penalty used for greedy breakpoint
+elimination is set high for closely related genomes and scaled downward
+according to the estimate of genomic content distance. Because the breakpoint
+penalty is high, the resulting set of locally collinear blocks represent
+robustly supported segmental homology, and a conservative estimate of the
+breakpoint distance can be made on this basis. The conservative estimate of
+breakpoint distance is used later during progressive alignment to scale
+breakpoint penalties.
+
+Progressive genome alignment
+----------------------------
+
+A genome alignment is progressively built up according to the guide tree. At
+each step of the progressive genome alignment, alignment anchors are selected
+from the initial set of local multiple alignments. Anchors are selected so that
+they maximize a Sum-of-pairs scoring scheme which applies a penalty for
+predicting breakpoints among any pair of genomes. Because rates of genomic
+rearrangement are highly variable, especially in some bacterial pathogens, some
+genomes may be expected to exhibit greater rearrangement than others. As such,
+a single choice of scoring penalty is unlikely to yield accurate alignments for
+all genomes. To cope with this phenomenon, progressiveMauve scales the
+breakpoint penalty according to the expected level of sequence divergence and
+the number of well-supported genomic rearrangements among the pair of input
+genomes. These scaling values are taken from the distance matrices computed
+earlier in the algorithm.
+
+Anchored alignment
+------------------
+
+Once anchors have been computed at a node in the guide tree, a global alignment
+is computed on the basis of the anchors. Given a set of anchors among two
+genomes, a genome and an alignment, or a pair of alignments, a modified MUSCLE
+global alignment algorithm is applied to compute an anchored profile-profile
+alignment. MUSCLE is then used to perform tree-independent iterative refinement
+on the global genome alignment.
+
+Rejecting alignment of unrelated sequence
+-----------------------------------------
+
+Although we compute a global alignment among sequences, genomes often contain
+lineage-specific sequence and are thus not globally related. The global
+alignment will often contain forced alignment of unrelated sequence. A simple
+hidden Markov model structure is used to detect forced alignment of unrelated
+sequence, which are then removed from the alignment.
+
+Strengths of the progressiveMauve algorithm
+-------------------------------------------
+
+-  It can be applied to a much larger number of genomes than the original Mauve
+   algorithm
+-  It can align more divergent genomes than the original algorithm. Genomes
+   with as little as 50% nucleotide identity can be alignable
+-  Manual adjustment of the alignment scoring parameters is usually not
+   necessary
+-  It aligns the pan-genome, e.g. regions conserved among subsets of the input
+   genomes
+-  It is more accurate than the previous Mauve algorithm
+
+Notes on Reproducibility
+------------------------
+
+The command line programme progressiveMauve seems to behave differently when::
+
+    --max-breakpoint-distance-scale=0.5 --conservation-distance-scale=0.5
+
+are passed to the tool, compared to when those options are not passed. This
+means that if you wish to precisely replicate the results you see in Galaxy at
+the command line, you'll need to pass these flags with their "default" values.
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation" />
+</tool>

Binary file static/images/hemolysin.jpg has changed

Binary file static/images/xmfa2gff3.png has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.gff3	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,25 @@
+##gff-version 3
+##sequence-region karma 1 1
+karma	progressiveMauve	match	83032	140930	.	-	.	ID=phagey;target=phagey
+karma	progressiveMauve	match_part	83032	83041	50.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83042	83051	60.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83060	83069	60.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83070	83079	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83080	83089	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83108	83117	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83125	83134	70.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83144	83153	60.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83154	83163	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83164	83173	70.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83196	83205	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83206	83215	30.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140791	140800	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140801	140810	20.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140811	140820	60.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140821	140830	50.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140831	140840	50.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140841	140850	60.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140851	140860	20.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140861	140870	50.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140871	140880	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140906	140915	80.0	+	.	Parent=phagey

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.mums	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,409 @@
+FormatVersion	3
+SequenceCount	2
+Sequence0File	test-data/merged.fa
+Sequence0Length	159457
+Sequence1File	test-data/merged.fa
+Sequence1Length	221828
+MatchCount	402
+23	9997	10291	0x9c7f540	0	0
+23	118799	199132	0x9c7f588	0	0
+23	26654	-52948	0x9c7f5c8	0	0
+23	126561	47160	0x9c7f610	0	0
+23	110233	-209064	0x9c7f650	0	0
+23	134387	175263	0x9c7f690	0	0
+23	93373	-185643	0x9c7f700	0	0
+23	6917	167993	0x9c7f740	0	0
+23	47238	48379	0x9c7f780	0	0
+23	8742	-150092	0x9c7f7c0	0	0
+23	144337	65631	0x9c7f800	0	0
+23	138300	-100263	0x9c7f890	0	0
+23	62837	-15551	0x9c7f8d0	0	0
+23	135219	16958	0x9c7f910	0	0
+23	19156	-18956	0x9c7f950	0	0
+23	109152	-48925	0x9c7f990	0	0
+23	76438	-161554	0x9c7f9d0	0	0
+23	71190	-46655	0x9c7fa10	0	0
+23	157575	-160188	0x9c7fa50	0	0
+23	143476	-94179	0x9c7fb20	0	0
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+23	148397	185112	0x9cbaf58	0	0
+23	130431	-112825	0x9cbaf98	0	0
+23	143278	180137	0x9cbafd8	0	0
+23	66424	103325	0x9cbb018	0	0
+23	131360	-111662	0x9cbb058	0	0
+23	156677	153981	0x9cbb098	0	0
+23	143297	20818	0x9cbb0d8	0	0
+23	90241	-111775	0x9cbb118	0	0
+23	20107	18248	0x9cbb158	0	0
+23	83728	82051	0x9cbb198	0	0
+23	65721	104098	0x9cbb1d8	0	0
+23	70625	189133	0x9cbb218	0	0
+23	86074	-115341	0x9cbb258	0	0
+23	37121	-204123	0x9cbb298	0	0
+23	46528	165402	0x9cbb2d8	0	0
+23	106103	104995	0x9cbb318	0	0
+23	86707	-74058	0x9cbb358	0	0
+23	106556	65846	0x9cbb398	0	0
+23	131791	-108777	0x9cbb3d8	0	0
+23	66998	66464	0x9cbb418	0	0
+23	32437	-167760	0x9cbb458	0	0
+23	75950	75816	0x9cbb498	0	0
+23	69770	109722	0x9cbb4d8	0	0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.nhx	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,1 @@
+(seq2:0.476132,seq1:0.476132);

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.xmfa	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,5967 @@
+#FormatVersion Mauve1
+#Sequence1File	test-data/phagey.fa
+#Sequence1Format	FastA
+#Sequence2File	test-data/karma.fa
+#Sequence2Format	FastA
+#BackboneFile	test-data/1.xmfa.bbcols
+> 1:83031-140929 - test-data/phagey.fa
+ttttctcctcttttttcttagt--gaccgagggctttttaccctcggatggtttactttcactgagtct--agatgttaa
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+caggatcgtaactcacttctaagtgcgtataatgccacggttgggaggttatttcgttcttcgactaaacgtaccccctc
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+cactctgttctctaattcctcatatgttttaactatctgccctacagtcattgtacgttgcctcatattaactctcctcc
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+atcaaggccctctacgccgtgggcctggacgtcgacgtgggcatgtcctcggcggcgatcgacgcggccctggccaagtt
+cgggcgcatggccgtccgctatacgacccattcccacctgaaggcggtcaccgacgtcaagaaggacgtcctgatcaagt
+ggtgcgagcaggaagccgacggcgccgactacgaggaggacgaggtcctccagcgctacttcctggccaaggaactgatg
+accccggacgtcgccaagacggtcgagttcaacgggaccgagcacaaggacggcggcatcatggtcaccgtcaagcacgc
+gccgatcgccaagcaccggatcatcgtccccctggcggcggccttcgacatctccaaggtcgcgccgacccagaaggagg
+cgatggacaagtgggccaaggtcccgaccgcgctcgcccgcgaactgggcgtgccgctggacaagtcgtgcctggacccc
+tcgcgcctgttctatctgccgcgtcacgccaagggcaagccgttcgagatcagcctgttcggcggcgacctgttcgactg
+gaagagcctgaccctcgacgatccgttcgaggccgagatcgccaagctgaccaaggggaccagcaagtccaagaccgagg
+ccggtcgcaacctgggccgctggtcgatgaaggccgcccacggcttccaggtcgtccaggtcatggaggagcactgcccc
+gacaagctgcgccaccaagtctcggccggctacgagatcgagtgcccgttcgacgagcttcactccaacgccggcgacac
+cgaggatcgcgcctgtctggcggtcaacgccggcgatggtccgagcgagtggttcaccgtccgctgccagcacgagtcct
+gccgcgagttcaccaatctcgacatgctcggcaagatggtcgaggacggctggttcgaccgcgacgtgctcgacgacgag
+acctacaacatcgtcgaggccgagaacgcccccaacccgcaggcggccaagaagatcgagaaggaggacaaggccaagga
+agcctatatgcaggcgatctttgacctccccgaatccgacttcaccgacgacgacgttgaaaaggtcctgcgcgtctgct
+gcgaggccaatctggggaccctggccgagaacaaggccaaggaagccctcaaggcgcgcctgggcgtcaccggcacggtg
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+ccgcagcatcttcgcctatgcgggcgagttcaacttcgacgaggccttcgcctgctgcttccgcgcgctggtcaacacca
+accgcgagaaggaccagccgatcttctcctgcttgcaggacaagcccgtgcgcatggcgcccgagccggatggtcgtctg
+aagttcaccgagatcggcacggccgcctccatgggggccgaactgaacgagcttgtcaccttcgtgcgcaagaacgagca
+gggccagggcgcgcgcggaagggttcccgacgacgtggcgcgccacgtgttcgagaaggcctacacccgcctgccgcgca
+cgcccgagatcatgt-acaccccgatctatacggccgagggtgacttgat-ccgcaagcccggctggtatcagaacctcg
+acatcctgatggccgacatcggcttcga
+=
+> 1:1-83030 + test-data/phagey.fa
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+cgaaagagatatattccatatggataatgagacagaatttcttttagaagaaacatttaataaggaggacaattaaatgg
+aagtaaatggggatgttatcctaggcggggttgcggcttttgtactttactcgtggttactatacaacagaggatacaga
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+tagaagaaaaatgcagggaggtaaataatatgtatgaaaatgtgttagacgttatcaattgtagaacaaaagaggtagcg
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+acttgaatggtgtactttatctattcgaagaccaaccctgtacatttagtgtaggttgtgacgtagtgatgattatagga
+gaccagacacacttcgatgttgaagactggggagtgtacgaggatgaaaagacgggtaacgtaacgatctataacgcgga
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+caagaatggcaaagttgcccgaccgatggaacgtgtctctacgtgacgatgagagccttaaatcggtaagtaagtctaga
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+acgagtgtgaacgtgggttaatcaacagtgtggtctataacgcagaattagttaacaaatttcttaaacgttataaaact
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+aaaaagaaatgagaaagtcacagcgtactagaaagtttaatgaaagtatttgcttaatggctagtgaagacatggagcta
+atgagaaaaattgttgttggacagtgggccattaatgccgctctttctagtccatttgctagcagatacggattataaaa
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+gttgttggcgaaactggctaattattcctattattatattattttccctataatcgggtagttagtttgttacaggttcc
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+acttggtcggcaataagttcctttgtatccttaattgtgtctgatcccgtccatagtagaccggctacccctaatgaaaa
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+=
+> 1:140930-159457 + test-data/phagey.fa
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+aatgctgtggaaaaacggtcgccggttctttgatttgttagtgctcgggctagtaagtcctctcgcctgcacctgctgga
+tatttgacagctatagaaattattttaacacatggttgggaaatgttaaacacttgtctcttgttcaagtatactattct
+atttttcttctagtgatcggttgggtattgttcggcacaccgacccctgcgagcttcactggatttatcttaaagctact
+ggtcaccattggcgggttctcaaagttaagctctcctccaaaatttgtaagtaaacacttagataatggatcagggtttg
+actcagtatatacaccagctaaagatacagtctctaaaacagttcgtaacttccgagatacagtggacattatccgtaaa
+cctactactgttgtaaagaaggtacacgagcgattacaaactcctgagcgggtaggtaagactcgtatgcaacgtttcca
+cccgccagtaccaaaaccaggtaagtctacgcctaaaccaaaaagaaaataaggagtgaataacatgagtacagtatcag
+tattaattatcattaatcttacctcgcttgttttcagcagcgggatgcagatcgcaaacagtttaatggttatgaagcat
+attaagggggagagaagatgaaaaagctttctgcaaattaccataacctagctaacttgtttatgcctgtagaagatata
+gaaggtcactttgtcgatatccttgaacagattaacgattcggtattcggagtagagacccatttaaccggtgagggggc
+taatacttttgtcattgcaccctctcatatcgaaaccggggcagaacttgttctaagacatcgagaagcgcctacagagg
+gttttaatttcttcgaggggtatttatcggaagcgttctttctccctctcagacaggataagaacggcctcttccttact
+gatttactggacttggctttacatcctgatgaagaggtacatgcgcaatggttattacgcaggcggtatggttggcaaga
+tcgcgcaattgatatgtacgatagctatattcaagggaacgaaaaaccttcttggtctagatggagtcgtaaactgcagg
+ataaagctgttcgagtgttaaacaaaatacagccagaggattacaagccttacgaaccgttagcagaagagaagataaag
+agtgagtgcttccaatttcagctcagaatagcagttaagtccgagagggtaaacgatatcatccagtatattcaatacgc
+tctagggtcttatacggctttaaacgagttgaaactggttaagtcgtcagataaacaatttattactaactatactgact
+gtgtattagcagcttacacaaaagatcaactacttagcttaaacgaagtattctccttattaggtggtacagtagagaaa
+acggaaaaagtattagaagaggtagtggagcgtaaggcgtacccatttgatctgttacctatgtataagcgagagcaagg
+tactctagatgaaggaatagttagtaagctagcggaaggtatgaagcgggtaaaattgattgatacggctaggttataca
+atgaacggattgactgtggggtgcggttaggggttgtccaggtaagtatacctaaagatgtaaccttttctaagattgaa
+aagtccattaatgacttacgagctgcaacaggtattagcgggttaggtgttgagaatggggatattgccgacacggttaa
+gtttacggttcctttagctgcttcaccggttattagtctccgtgaactggttgaaaccgaggagtttatcagtatggtag
+aagaaaaagaattaatgttcgtggctggtgtagatacactaggggagccgatctatctatctttgactgaatgtgtacat
+ttattggtggcagggacaacaggtagcggtaagtcggtcttcgtaaatgtgattattgtaagcatgatgttaatgtatcc
+acctgaaaagctacagtttattatgattgacccggctatggtagagctaagtaagtatgaggatagtccacacgtactag
+acgtagtgacagatgctaaagaagcttgccaagtattagcagggctgacaatggagatggataagcgatatgctcttatg
+aaggaaaaaggtacgaagttgttatctttgtataatgaagtagcggaggagccgttaccctatctagtgtgtattgtaga
+tgaatatgcagatttacgtgctgttgacaaaggggtagaagattatattgctcggttagggcagaaggcaaggaaaacag
+gtatacatttagtggtggctacccagtatcctagtgcagatattgtaagcgggcggattaaggccaacttacctactgcg
+attagttttagactgaacaagaataaggattacacaactatattcggagtcgggttaggtactactgtgttagatggtaa
+gggggatggggttattcggttagcgagtggaggggactttattcgtttccagagtcctatggtcagtgtggatgagaaga
+gagagcagcaggtttgtcgagatatcttcaccttctatcaagggagccgaattgtggactacaagattgctgtcgcagat
+aaaccgttagagcccgtacaagacgttttagaagaagagaaggtaaatacaccagaagagtgtaaagagacccctaagca
+agctctagaggcgttagaggctatgtttagcagtacagaggatgatcccctgtataaattaaagaaaattgttgcaaata
+caggagaaacccgatcaaatccactaagaaaagagctaggtattggtcgtgataagatgaagccccttatgacacagtta
+gttgaagaagggtggctagagaaagataatgaccctacaaaaggctataagctggttgctaccgaagatatgctcgcaga
+atggaaagattgagcctgtataggcttattttttttgtccgttaaaccgttatattactaataagcgtatcaggaaatat
+ttaacaccgtatttaagacccttgatatgactgtgttcttagctgttttatctaaataactgacacattataatcttaac
+gtccctctttatatattatttaattatttataaagatatataagagaataataaatataataatacgaggagcttaaacc
+gtataatatgtcaggaatatttttaaaagtacctctaagccagcaataccaacggattaaaatacgtcaggtacctctaa
+ctctgaaaatttatcaaaatagttgttgacttttagtagtatgtcccgtatacttttgttatgagttacagggatgaata
+catgtcctagtgtaggcgatacagtgtagaacgtttgggaggacttctaccgggtatcatccatactaacagataatcta
+ctgatcttgggagggttcaatggattaactgaactcaggaggtgtaagaatgaactacagagagttatcagatgaggaat
+tacttagccagatgtctaccgtacataatgtactagctaacgaagaatgggtttatcgttatgggatgaatttaccttac
+cgattagacaagtttaatagaattttaaactgtttatcttggcaagtagtagctgactcgacttgcgataaattaatccg
+gagacaggctaacgaggtacgaatggtaaaacagttaagcacctattaaaaaggagctgcttaacaatggcaattagaaa
+atatgaattcaaattaaaaattaaacaactattagcggagagaggaatttctcaagctgacctagctgaaatgactggat
+taaggcgtgccactatttcagagatgtctcgtaattcacggtctgttctgaataaggtacatgtagctaaagtcatggat
+gcgttagacgtaactgagttgaatgatatagtggagcttgaggtcactgaggagttctaaaggagaaaataaaatggata
+gtgtacaaaagtttatttcagaaaatagtcaccaattcggttatatcatgcaagaggctagccgtcaatgggtcgcaaaa
+gaccctatcggagccctaactgtaggtacatgtaagtcttttatagacagctatggagactatcatacgattttagacaa
+gttacaagctattgaagaggctaaagtccctaaaaaagatgtgtataaggcagttatctcgggacatattttcgaagaac
+ctgaatttgggaacagtattgaaatatttactttcgtgaataacgacgttaaaaatacagatatattcacagatgttgaa
+tatgagctgatcgaagagttaaaacataatcttaaatataaggaaagccacttctttacggctattgtgtatgctcgttg
+gtcatcttggcaaagtcaagaaggaactgagtatgatgtagagtacgacatccatgagatcaaacaaattagtgacctag
+ataaaggagcggacttttaatggatacacatttaacgttaactaaactaaaggattctttggatcataattatgtaaaga
+aggtagctagtcatcttatcctggtagttaaacgtggggataagcatgagcagatcgtgttagacaaaccttttgcagag
+aagattgaaaatatttgtaacgaccatgaagaggattgtacattaaagggtgctccccatattaaaatcatcgcagctaa
+gtatacgactacacggttattaacagaaaatctacaaagaattcacgagcatctacaaaagtaaaaacctaaccaaatag
+tgtataatataactataggataaacaattatttacgattatgtttatcctatttgtttttgtccaagatatactaaatta
+tcttaaccagtaaatcctaactaaacagtggatttttcgtgtatatttatacattttcgaaaattaggtgagagatttat
+tatattagagacagaagcttagacagcaaggattatactctgtttaacatatacactattttgagagggttgaaataact
+tatgacaaataaaaaagacctaaaaaagaaaaatattagttccagttcagtacttgtgcagctgtacaataatccaaagt
+tacgatctaaagtagagaatatgcttgacgaggggcaaacatacgactatattcaagagtatcttagttcgaagaacttt
+agtatgtcgaaagcatctcttactaactataagaagaagcgtgaggaatctatcgaaacaggccagccactcattcaatt
+actggacaagcgtgcgaaagataacgtctcttatattgcagataaggaagttaaaccatttagtacagtagaatcaacta
+gtagctcctcagctacagtgcatgatcttagtaagcgagatagtgtttatagtgacctagaactactggacgaaacaatc
+cggaaatcgatgaaaggcttaaagcagtttgatgtggttgaccttcctctaggtatgaaggccattgagctaaaggccaa
+attaactggaaattctcttaacgggctcagcctcgcaggactgagggagcttcacctaagacaggcagcaaaagaggccg
+cgttaattgaagtaatcatgaaatacgtcccagaggatttgcatatagacgtattccaagacctcgaaaattcagaaaaa
+gagttcttcgaaaacctagatttaacagaggaggaaaagagaatatctgcggcaattcgtagaagcggtctaggacttta
+aggaggggaaggtctatgaagtttgagagcaagaaaacagtcccgttggttgacaagatagctatagcagatgagcgagg
+atacacacttaatgaaacggaaaacttcacagtgaactcacaggtacatctgattgaaaattccacaggctttgagtacc
+ttgttcactggggtaactttacgaaaggtataaaacctagtaagacaacattagagagtaaaataaagtatgcagcttca
+cgaggttacactctccataggaaagataattttactacatcatccagtgtagaagttacaaacagattagatggtttaga
+gtacagggtgcaatgggatcactttgtgaaaggggcttcgccagctatcttaaccttagaaggtaagcgacagctggcgc
+gtaatcgaggctatacactcctagaggacacagacttctcaaataggagtaaggttattatccgatgtaacgaaagcgga
+gtagaatatgaagcgaactgggggagctttactaatgggaattctccccgccataccacactaaaccagaaaataaagga
+gacagcggagcgaggttataagctgctagaaacagacaacttctatacaaacagtcaggcaagaataaagtcattagcta
+ctgggagggaatacacggtctggtatgctagttttctacacaaggggtaccaagaaaacaactctaaaggtgaatcaatc
+ctctattactttttcttgtctaaccttgctagtgagtatagctttgagtaccagtatagagtagattactcggagagtaa
+gaaggggttcttcgacttctgtataaaagataaaaatggccgtactttagcttttgtagagtataatggcaaacaacact
+atgaaccttgctttggtcaaaaagctttcgagctgactttactatctgataaactaaagcaggaatacgcagcagttaaa
+aaggtacctttgattgttatcccttatacgtatagtacacaaaaagagatcgtagacttcgcttcacctatccttaaaga
+gtacttactgactgagtacgtggagttcacccctaaatggtcaagtttatcctcaagcaccttagaagacaaacaaagaa
+ttgctgaggaggcaggttacacgttacacccagatactatgtacaattttgttaataaagatagggtgacggtcataaac
+cagcagacaggggaagagtgggaagtccaatggggtcacttcctaaagtgtgtagtaccaaacaagactaaccataaacg
+agtaataaaacttagtctagaagaaaagaagcagatagctagctctatagggtatactttattagaagaagaggacttcc
+cggttattaataaggttcgtttaatgaacgccaacggtgaagagattacaagaggttggcgaactatccacaagcagtat
+aaaaagaggaaagatagaggtgacttatcgtggcgttgaatgaaacagaactactacaatatacgttagttccttttgct
+acatacgaaacgttagaatctaagttacaggccctgttagcaggtgagattttattccttaaaaagtttgaacgtaatga
+aggtgtagacgtacttgttagacttgtacaaaagaaatttacggttacacaagtctcttatgatgttacagtccgggatg
+aagatatcccacgttactggacaacgtataacatcggtctaaatgatatctcactgtttacctgctttaagtttgcagag
+gatgcatttacgaaagaaaataagtatatgattaatgaccgtgtactctatgttagtgttgacgggctaaaggatgcagc
+tattattgaagaggtgtaccaacacaatactgatcctactaagtttgcttatcgtttatctagagacggagcggtttacg
+gtgaagacgagttgtacgataactcttatatgtaagtgaagatacaagacctaaaaagtcttgtattttttttttggaaa
+agctgttgacttctggtaaatagggtgttattatgtaattacagaaggcgatacaagctctcgtttgggaggacgagaga
+ttggtagcttctgaaataagcgtaactaatgggaggagaagtaaatgaaactctacgtgttgagcgaaagagaaattatc
+gattgtgagggtgaatactcttttgtagtaggtgtttttggtagctttaaaaaagcacaagattatgcagcatcccaagg
+ctacaccgagtatatagaagaaggttactacggtgatgactccgaatttatacctacaaaggacaaaagatacacaagag
+attatgatggtaaatcgtatgtgctagatgttgcaaaactagatagacctttgtacgatgatggtataatcgacatgaaa
+gagtatgaacctaaagaagtaacatcctatttaaacggtgagaagattgcaaaagctaaaactataccaggtgacactac
+tagattcaatccagttggtacggtaacaagcggacttgattcgagtaaggaaaacaaatcagcaaaaccaaaaagcaata
+taaacttccctaaagatcaggaggaaaagtaaatggagctgtttgtaactgaaaaggtgttcaatagaaaattaaacggt
+aaagccattcgaattaaaggttatgatacagatggggagaaatgggacggtgtatatctagttaaggaaactagatttga
+ccagattgtagttactagtcgaacaggtaatgaacactttatttatatggaggagttcgaaacaggagaactactaactc
+taatagtattggagggaaattagatgactctaaagtatgattaccgtgtacaagcaaaagccaaccacgtttgtcatatg
+atttgggaagaaacaggaaaagtagatcacccgtcacctaagcttagatcagatgtagaagacaccatgatggctgcagt
+taattattataaggtagcgttagataatgaattacagaagaagaacgagtataagctaaacgaacttagaagaggtatac
+ataggttaaagcctaactcgcatgaagatattatagatttattcgctaaggttatggccggtgaaagtgtacaaacaatg
+aaaccatataaaagggagagagaattagtatgacaaaattgctaaaagaagaatggccgaagaatattgatgaacttatc
+gcttacttccaggagttaaaagagtactctagagattacaacacatctgcggaagcagtagcctatggtacagtagcggc
+atttaactatttagcagcagacgaacacggattgactggattccaggctagttggtctgctatgaaagctttgtctatta
+ttagaaatattgatggtgcgtttactattgttagtacggatgccttaaagtttaataccatcgaagatgaattagctcgt
+gtaaagaagtttttacacgacagcattaaaaagcaggaggagaataacaatgagtaacatatttgttgtccagtattcta
+atgggttagaacatgagcagttagagaccgatgtagtagcggtattcgattctgaaaaggaaatacgagcgtacgcagaa
+cgagaagggtttgttccttataatggtattcttatttgtgggttctatagagagtacaagagcggacaccgggacttact
+atttgtctcaccagtgaaaataaacgagcctattgtggcttgtttggaggagttagagtgagcaagtcagatataactcg
+taggctagaaaaggcaatttacacggcgacgattaaacaaggtgtgtttggttgttttgaggttacaatcggttggttcg
+ggaaagagcgtgtggatttcataacctacgacacaaaaaatatctggcgatgctatgagattaagtcctctgttgcggac
+tttagaagtgaggcttacaagactttctgcggtaattacaactactatgtgatgactaaggaactttatgagaaggttaa
+actagaaattcccacccatattggggtttatattgagggccgttgtgtcaagcgacctaaaaggcaagaagtaactgtgg
+aagaggaaatactaaagaattcactaatacgttcactagctagagaagccgacaaacttgctaagagcaatgatcctgat
+ttgttaaatcggctacgaagaagcttagctagagaacaagaagacaaaagaaggtacagtcgggagtacacagacttgaa
+aaataaattatataggaagtacggccgaaactgggaggaggtactagagttagaatgaattatacagatgctaagatagc
+aattcaagtattacatgcagcgggatataggaaatggataaaaggggagccgtactaccacaaacgatgggaacggggct
+cgaatgactataaccagcttatatcattcaatgaaattaaatattcgctaatggatatcccttggattatacagaagtac
+gaagaaaaagccgaaggagagttagaaaaattaaatgaaggagagtgctgttaaatgggcggttacattgcgttacaacc
+caacgggctatactgcaggtattccacagtggtagaggctttaacacatataaacatgacgagggaagattatgtatcta
+attttacaggtacagtaagaagccgagaggaagcggaagacatcttgggtaactatctacatagcttcagtaccgtagag
+aaaatggtcactcgactgaatgtagaggaagcggaatggaagagaattaagacgcatgttacactacctaaaaacagtat
+atttgtctacccgaaagttttataaaaagtattgacaggtattggttggtgtagtaaactctaactatatcaaccaatac
+aaggaaaggatgagtacaagttggcaaagaagaactttagttgggattcagaggagttactaggtatttaccctgtatca
+gataaaaagcagtttgaatataagttatgtatgctaaaggacaaggagtacgtatcagtagctgagcagcgcatgacaga
+cgaaggctggaagtactacggaaacaaaacgttagagatgagtgtatacagacagttagtagcatttatggacaaccgtt
+aatattttagtaggtggttgacttatagcatatgttagccacctatcatactaaaggaggagttagtaatgcggagaaaa
+attaagtgtgaattgtgtgatggtagcggtgcctcgccttggtctgctctaggagggccttgtatacaatgcgagggtgc
+ggggtttctatttgaacctgaagggaagcctaagtttaaggtagacttcggtgagttagacgggcttactaaaatggaag
+atactacagacttaagtgatccacatattaaaatagatatgaacggcatcagctttaaagacaaggatggtaactggact
+gatccgacaaaaccattcgctaactttgaaaatatcacaattaaccactcaaatggtaaaactataaaaggcgggaaagg
+ggttctgaaaccgatgggattattcgatgattttatggaggctattgaagcagaagagacaggaagaccaatcgtaaagc
+atttgctagtttggagtgttgatgagctactagaccttcacaacgattacaagcagctgtacgatctatttaaggacgag
+gagtacttgctatatatgaaggacgtactaaaagttataaaagcaaaaacaaattagtagtcattctttatagactgcac
+gcatagtataaactataacaagaagggaggaattacagtgaatgcggaagataaacgaattctaatgaaaatagtaggaa
+gtatagccgggatgtttataatgggatacctattcggtttcctaggggttattattagtttagtagctatttactttgtg
+tttaagaatgataatggtaagcaggtaggagaagacccggagagtgaagctaaggccgcctttatctggttctgtgtgat
+gctagtgttagggatcgtgcttgcgtatctattcggtatcattggagtaattatcggtttagggttaatcgcaggagcca
+tctataatataatgttcgggtaaataaagaattttttttaaatagttgttgactttaaagaaacatggtgctagaattag
+cttatcaaccaaaggaggtaacaaagtgagaataacacatgaacagaagatggaaattctcgaagagtggaaccttatag
+gagagaacgattgtagaacggctctacctcacttaacagagctacttactaaaatacttgatagtgtttctgatcctgaa
+aagataaactgtgggtgttatgtgtggagtgaaaaactacaagagcatgttgaacctaatccactctgtaagaaatgcgg
+cgggatgggttggtattacaagagagaaaggaagtaatcgatatgcaacagacagcagctaagaacacacaaccagaagg
+tttacatctttacatggcaattggatcgtatgagtcggccattaacaaatatgcgcacccatataatcctggttactgga
+ataagtataagaaactaaaacagaaaatccttcagtggcagcagcaaa
+=
+> 2:1-81634 + test-data/karma.fa
+gggctctgggcgaagttttgtgggactactatgacttgcattatttcaagcgcaagcggtccgagtggaagtaccaaaga
+tttgctttggtttatcaacaacttgccgacgcggcctcggacacctccatcgcgtccaagtttcagacctacgatcacct
+gccccacctggagccgaaggtgctcaaggcccggcttgacgcgggtcacgccgacgagcgcgggcggccgattccggacc
+gcaaggagcacttccggcgggtggtggtcagcgtcgactcggccaacaagcccggcgcccgcaacgactacagcgtcgcc
+caggtctggggggagacccacgcccgcaagcactacctgatctaccaggagcgcaagaaggtcgacatcaccggcctgac
+cgagatgatcgagcgggtggccaagcgctacgaggtcgacgccatcctggtcgaagacaagggcaacggcaccgcctaca
+tccaggcgcggggccagaccgacagccagcggcggctcgccccggccccgatcgaggcgatccaggtcccgagcacctat
+tccaaggagttccgcttcaacgagatcgtcccgatgatcgaggccggcgaggtcttcctgccgggcaaggccccgtggct
+cgacctgctgatccgcgaaatcggtcagttccccgaaggcgcccatgacgaccaagtcgacgccatgacgcagtacctcc
+gctgggccaagtccaagcgcacgcggttcggcgcgcgcaaggtcggctcgatgggctgacgaggcccgttaaccacgttt
+gttaacctccgccggggccttaaccctaacacggcgagggttaacaggtccagggacccttcgaaattaacctttcgggg
+accctgggaaatcgtaaggcagggaccctggccattttccggctggggaccctggcaaattcaccgccggggaccctccg
+aaattcatcctcggggaccctggcaaatcaaggagccggcgatggccgaatttctcgccctgatccccaacctcgcgccg
+ttcctggtctggggaatcctcctctggatcgccgccgaggtggtctggagcgtctgcctctgggtctatggcctgcggac
+cctgttcaagttgcaccgcgatgatctggccgaggcgatcagcttcgagcgggccttgagccccttcgactaggcgcggc
+ctgccgacctaagtcacggactgtaggtttcgtgacaaggtgagatattccacaacgatttcaaaggcttactgcgatgt
+cgatccgcacgttcttccacgatctggccgtccgtttcgtcgttttggggtggatttttgcccgaaaaccgctgaaatgg
+gctccaaaagggcataattttcagcctaaaccgccggtccaggtcggcgccctggcggccggctcgctcctcgccctcag
+tctggcgctcggcgggctctggttccgcttcacgtttccggacaaaagtcaagtggtctcgcgccggccgcaggctatgt
+catagaccgtgggcttcgtgaccagatcacgcttccgttaccgctccagcccttgtgaggcctcggatgttcgcctttct
+ccgccggctcagcctcgccgccgtccatggcgtgctctgggcgatcctcctggcgatgctcgccctgggcgggccgcgcc
+gcccgctctaaagcgtcatatctgacgcctaaggccccctaaggcctcatctgtgagacattcaacgccctcgtgttcct
+ctgaacgcgggggcgttttgacgtcggcgcatttttgacttgacgcgcgagcgttttgacgcgggcgcatttttgattcg
+acgggcgagcgttttgacgtccgagcatttttcaacttgacgtcgttccatttaccgggagcgccttagggttaacgccg
+gccgccgagccctggggcgatttaccaccgccacgttaacctaacgcctgttaacctatcggttgttaaggttaacgccc
+cgttagggttaacgccccttaaccctgcccgcgttaaggttaacgcgccccggcccaggccctacccgttaaccttaacc
+gcccgacccccgcgcccaggccatacccggtagggcctgacggccctaccgggtatgaccccgcgccccggcggaggcca
+gggaccgccccggcgctttttcgcgccccgtttaccttttgttaacgtctggcctctagggtcgcccttgtccccgccgc
+actcccgcgccgggcaaggagcttcccgccatggtccccgactcgatcatgaacccccgcgaccacttccaccgcctgcg
+cgaggaaaccgcccgcgctctggtcgaggccttcgccgaatccgaccccggcgaggattaccgcgccgaggaaaaggccg
+gcgcgtgggttgtcgcctattacgacgcggcgggcgaattcgtcgcctatctctagccgccttcgccccctggcgccgcg
+ttaacggtttgttaacatgtcggcgccagggtcgccctagcccggcgcgtcgccgcgccttcggagaaaaccgccatgct
+ctacacccccgccgcccgccgccttcgcggctatcgcgaaaccgccgcgaagaacgccgaaattcacgcccgcccgcaca
+tggccggcaacgtcgccggctacaacgagtcggtgtggccgacgacggcgctaggcgtcgccgccaaggccggcgccttc
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+=
+> 2:118886-221828 + test-data/karma.fa
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+ctcttgttaacacctcccggctatggtcgggaggtcgcaaggagacacccgacatgacccgccccggccccgcctcgctc
+ctgaccccgcaagcccgcttctcgtcgccgcgcgtcctgatccttccgggcgcggctcccatgccgattcgccagccgcg
+cggcctttgcgccgtcgagtgcgtcgcccttggcgtgacgctgggcgcggcgctctacctcgccgcccgcgtgttcggtc
+tggtctgaccagacccccgccccgcccccggtcggaccggtcgggggtgtgtcccataatgacacacccccgccacctag
+tatcttttttgattcggagggacccaaaggccccctacgttaaccatttttggcggcgccccc
+=