New upstream version 2.3.5.1

[submodule "third_party/simde"]

	path = third_party/simde

	url = https://github.com/nemequ/simde.git

cmake_policy(SET CMP0048 NEW)

cmake_policy(SET CMP0005 NEW)

project(bowtie2 LANGUAGES CXX VERSION "2.3.4.3")

project(bowtie2 LANGUAGES CXX VERSION "2.3.5.1")

enable_testing()

include(CTest)

include(ExternalProject)

include(ProcessorCount)

include(CheckSymbolExists)

set(CMAKE_CXX_STANDARD 98)

set(NO_TBB ${NO_TBB})

set(NO_SPINLOCK, ${NO_SPINLOCK})

set(NO_SPINLOCK ${NO_SPINLOCK})

set(USE_SRA 0)

set(WITH_THREAD_PROFILING ${WITH_THREAD_PROFILING})

set(POPCNT_CAPABILITY ${POPCNT_CAPABILITY})

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 -g3 -Wall -msse2")

set(CMAKE_EXPORT_COMPILE_COMMANDS on)

if (MINGW)

  option(BOWTIE_MM "Memory mapped files not supported on Windows" OFF)

  option(BOWTIE_SHARED_MEM "Shared memory not supported on Windows" OFF)

if (APPLE)

  set(CMAKE_XCODE_ATTRIBUTE_DEBUG_INFORMATION_FORMAT "dwarf-with-dsym")

  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")

endif(APPLE)

set(BOWTIE2_BIN_LIST

  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -I third_party")

endif()

if (USE_SRA)

  set(NGS_VER 2.9.2)

  set(NCBI_VDB_VER 2.9.2-1)

  find_package(Java COMPONENTS Development REQUIRED)

  find_package(PythonInterp REQUIRED)

  find_package(Perl REQUIRED)

  find_program(MAKE_EXE NAMES gmake nmake make)

  ExternalProject_add(ngs_project

    URL https://github.com/ncbi/ngs/archive/${NGS_VER}.tar.gz

    PREFIX ${CMAKE_CURRENT_BINARY_DIR}/ngs-${NGS_VER}

    BUILD_IN_SOURCE 1

    CONFIGURE_COMMAND ./configure --prefix=install

    BUILD_COMMAND ${MAKE_EXE}

    INSTALL_COMMAND ${MAKE_EXE} install

    )

  ExternalProject_Get_Property(ngs_project SOURCE_DIR)

  set(NGS_INSTALL_DIR ${SOURCE_DIR}/ngs-sdk/install)

  link_directories(${NGS_INSTALL_DIR}/lib64)

  include_directories(${NGS_INSTALL_DIR}/include)

  add_library(ngs-c++-static STATIC IMPORTED)

  add_dependencies(ngs-c++-static ngs_project)

  find_library(LIBNGS_CPP ngs-c++-static PATHS ${NGS_INSTALL_DIR}/lib64 NO_DEFAULT_PATH)

  set_property(TARGET ngs-c++-static PROPERTY IMPORTED_LOCATION ${LIBNGS_CPP})

  link_libraries(ngs-c++-static)

  ExternalProject_add(ncbi_vdb_project

    URL https://github.com/ncbi/ncbi-vdb/archive/${NCBI_VDB_VER}.tar.gz

    PREFIX ${CMAKE_CURRENT_BINARY_DIR}/ncbi-vdb-${NCBI_VDB_VER}

    BUILD_IN_SOURCE 1

    CONFIGURE_COMMAND ./configure --prefix=install --with-ngs-sdk=${NGS_INSTALL_DIR}

    BUILD_COMMAND ${MAKE_EXE}

    INSTALL_COMMAND ${MAKE_EXE} install

    DEPENDS ngs_project

    )

  ExternalProject_Get_Property(ncbi_vdb_project SOURCE_DIR)

  set(NCBI_VDB_INSTALL_DIR ${SOURCE_DIR}/install)

  link_directories(${NCBI_VDB_INSTALL_DIR}/lib64)

  include_directories(${NCBI_VDB_INSTALL_DIR}/include)

  add_library(ncbi-ngs-c++-static STATIC IMPORTED)

  add_dependencies(ncbi-ngs-c++-static ncbi_vdb_project)

  find_library(LIBNCBI_NGS_CPP ncbi-ngs-c++-static PATHS ${NCBI_VDB_INSTALL_DIR}/lib64 NO_DEFAULT_ATH)

  set_property(TARGET ncbi-ngs-c++-static PROPERTY IMPORTED_LOCATION ${LIBNCBI_NGS_CPP})

  add_library(ncbi-vdb-static STATIC IMPORTED)

  add_dependencies(ncbi-vdb-static ncbi_vdb_project)

  find_library(LIBNCBI_VDB ncbi-vdb-static PATHS ${NCBI_VDB_INSTALL_DIR}/lib64 NO_DEFAULT_PATH)

  set_property(TARGET ncbi-vdb-static PROPERTY IMPORTED_LOCATION ${LIBNCBI_VDB})

  link_libraries(ncbi-ngs-c++-static ncbi-vdb-static)

  add_definitions(-DUSE_SRA)

endif()

if (WITH_THREAD_PROFILING)

  add_definitions(-DPER_THREAD_TIMING=1)

endif()

  add_definitions(-DNDEBUG)

endif()

find_package(Threads REQUIRED)

find_package(ZLIB REQUIRED)

find_path(TBB_INCLUDE_PATH tbb)

find_library(TBB_LIBRARY_PATH tbb)

find_library(TBB_MALLOC_LIBRARY_PATH tbbmalloc)

if (ZLIB_FOUND)

    link_libraries(${ZLIB_LIBRARIES})

    include_directories(${ZLIB_INCLUDE_DIRS})

endif()

if (Threads_FOUND)

find_package(Threads REQUIRED)

link_libraries(Threads::Threads)

endif()

if (NOT TBB_LIBRARY_PATH)

if (NO_TBB)

  set(SHARED_CPPS ${SHARED_CPPS} tinythread.cpp)

else()

    if (NOT NO_QUEUELOCK)

        add_definitions(-DWITH_TBB -DWITH_QUEUELOCK=1 -DNO_SPINLOCK)

  find_library(TBB_LIB_PATH tbb)

  if (TBB_LIB_PATH)

    find_path(TBB_INCLUDE_PATH tbb)

    link_libraries(${TBB_LIB_PATH})

    find_library(TBBMALLOC_PROXY_LIB_PATH tbbmalloc_proxy)

    if (NOT TBBMALLOC_PROXY_LIB_PATH)

      find_library(TBBMALLOC_LIB_PATH tbbmalloc)

      link_libraries(${TBBMALLOC_LIB_PATH})

    else()

      link_libraries(${TBBMALLOC_PROXY_LIB_PATH})

    endif()

    include_directories(${TBB_INCLUDE_PATH})

    link_libraries(${TBB_LIBRARY_PATH} ${TBB_MALLOC_LIBRARY_PATH})

  else()

    set(TBB_VER 2019_U4)

    if (CMAKE_SYSTEM_NAME STREQUAL Linux)

      set(tbb_os linux)

    elseif (CMAKE_SYSTEM_NAME STREQUAL Darwin)

      set(tbb_os macos)

    elseif (CMAKE_SYSTEM_NAME STREQUAL Windows)

      set(tbb_os windows)

    else()

      set(tbb_os ${CMAKE_SYSTEM_NAME})

    endif()

    find_program(MAKE_EXE NAMES gmake nmake make)

    ExternalProject_Add(tbb_project

      URL https://github.com/01org/tbb/archive/2019_U4.tar.gz

      PREFIX ${CMAKE_CURRENT_BINARY_DIR}/tbb-${TBB_VER}

      BUILD_IN_SOURCE 1

      CONFIGURE_COMMAND ""

      BUILD_COMMAND ${MAKE_EXE} tbb_build_prefix=${TBB_VER} tbb_os=${tbb_os}

      INSTALL_COMMAND ""

      PREFIX=${CMAKE_CURRENT_BINARY_DIR}/tbb_project

      )

    ExternalProject_Get_Property(tbb_project SOURCE_DIR)

    set(TBB_SOURCE_DIR ${SOURCE_DIR})

    set(TBB_RELEASE_DIR ${TBB_SOURCE_DIR}/build/${TBB_VER}_release)

    include_directories(${TBB_SOURCE_DIR}/include)

    link_directories(${TBB_RELEASE_DIR})

    add_library(tbb SHARED IMPORTED)

    add_dependencies(tbb tbb_project)

    find_library(LIBTBB tbb PATHS ${TBB_RELEASE_DIR} NO_DEFAULT_PATH)

    set_property(TARGET tbb PROPERTY IMPORTED_LOCATION ${LIBTBB})

    add_library(tbbmalloc_proxy SHARED IMPORTED)

    add_dependencies(tbbmalloc_proxy tbb_project)

    find_library(LIBTBBMALLOC_PROXY tbbmalloc_proxy PATHS ${TBB_RELEASE_DIR} NO_DEFAULT_PATH)

    if (NOT LIBTBBMALLOC_PROXY)

      add_library(tbbmalloc SHARED IMPORTED)

      add_dependencies(tbbmalloc tbb_project)

      find_library(LIBTBBMALLOC tbbmalloc PATHS ${TBB_RELEASE_DIR} NO_DEFAULT_PATH)

      set_property(TARGET tbbmalloc PROPERTY IMPORTED_LOCATION ${LIBTBBMALLOC})

      link_libraries(tbb tbbmalloc)

    else()

      set_property(TARGET tbbmalloc_proxy PROPERTY IMPORTED_LOCATION ${LIBTBBMALLOC_PROXY})

      link_libraries(tbb tbbmalloc_proxy)

    endif()

  endif()

  add_definitions(-DWITH_TBB -DWITH_QUEUELOCK=1 -DNO_SPINLOCK)

endif()

if (ZLIB_FOUND)

  link_libraries(${ZLIB_LIBRARIES})

  include_directories(${ZLIB_INCLUDE_DIRS})

endif()

include_directories(${PROJECT_SOURCE_DIR})

set_target_properties(bowtie2-align-l bowtie2-build-l bowtie2-inspect-l PROPERTIES COMPILE_FLAGS "-DBOWTIE2_64BIT_INDEX")

set_target_properties(bowtie2-inspect-s bowtie2-inspect-l PROPERTIES COMPILE_FLAGS "-DBOWTIE_INSPECT_MAIN")

set_target_properties(${BOWTIE2_BIN_LIST} PROPERTIES DEBUG_POSTFIX "-debug")

set_target_properties(${BOWTIE2_BIN_LIST} PROPERTIES DEBUG_POSTFIX -debug)

add_test(NAME simple-align COMMAND ${PROJECT_SOURCE_DIR}/bowtie2 -x example/index/lambda_virus example/reads/longreads.fq)

FROM multiarch/ubuntu-debootstrap:arm64-bionic

WORKDIR /build

COPY . .

RUN uname -a

RUN apt-get update -qq && \

  apt-get install -yq --no-install-suggests --no-install-recommends \

  build-essential \

  ca-certificates \

  gcc \

  git \

  g++ \

  make \

  software-properties-common \

  zlib1g-dev

RUN add-apt-repository -y universe && \

  apt-get install -yq \

  libtbb-dev

CMD bash

simultaneously to achieve greater alignment speed.

Bowtie 2 outputs alignments in SAM format, enabling interoperation with

a large number of other tools (e.g. SAMtools, GATK) that use SAM. Bowtie

a large number of other tools (e.g. SAMtools, GATK) that use SAM. Bowtie

2 is distributed under the GPLv3 license, and it runs on the command

line under Windows, Mac OS X and Linux.

1.  For reads longer than about 50 bp Bowtie 2 is generally faster, more

    sensitive, and uses less memory than Bowtie 1. For relatively short

    reads ( e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or

    reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or

    more sensitive.

2.  Bowtie 2 supports gapped alignment with affine gap penalties. Number

4.  There is no upper limit on read length in Bowtie 2. Bowtie 1 had an

    upper limit of around 1000 bp.

5.  Bowtie 2 allows alignments to overlap ambiguous characters (e.g. Ns)

5.  Bowtie 2 allows alignments to overlap ambiguous characters (e.g. Ns)

    in the reference. Bowtie 1 does not.

6.  Bowtie 2 does away with Bowtie 1’s notion of alignment “stratum”,

Bowtie 2 is geared toward aligning relatively short sequencing reads to

long genomes. That said, it handles arbitrarily small reference

sequences ( e.g. amplicons) and very long reads (i.e. upwards of 10s or

sequences (e.g. amplicons) and very long reads (i.e. upwards of 10s or

100s of kilobases), though it is slower in those settings. It is

optimized for the read lengths and error modes yielded by typical

Illumina sequencers.

conda install bowtie2.

Containerized versions of Bowtie 2 are also available via the

Biocontainers project (e.g. via Docker Hub).

Biocontainers project (e.g. via Docker Hub).

You can also download Bowtie 2 sources and binaries from the Download

section of the Sourceforge site. Binaries are available for the x86_64

Bowtie 2 can be run on many threads. By default, Bowtie 2 uses the

Threading Building Blocks library (TBB) for this. If TBB is not

available on your system (e.g. make prints an error like

available on your system (e.g. make prints an error like

tbb/mutex.h: No such file or directory), you can install it yourself

from source (see Threading Building Blocks library) or install it using

your operating system’s preferred package manager. The table below list

some of the commands for a few of the more popular operating systems.

OS

Sync Package List

Search

Install

Ubuntu, Mint, Debian

    apt-get update

  -----------------------------------------------------------------------

  Operating System Sync Package   Search           Install

                   List                            

  ---------------- -------------- ---------------- ----------------------

  Ubuntu, Mint,    apt-get update apt-cache search apt-get install

  Debian                          tbb              libtbb-dev

    apt-cache search tbb

  Fedora, CentOS   yum            yum search tbb   yum install

                   check-update                    tbb-devel.x86_64

    apt-get install libtbb-dev

  Arch             packman -Sy    pacman -Ss tbb   pacman -S

                                                   extra/intel-tbb

Fedora, CentOS

    yum check-update

  Gentoo           emerge –sync   emerge –search   emerge dev-cpp/tbb

                                  tbb              

yum search tbb

  macOS            brew update    brew search tbb  brew install tbb

    yum install tbb-devel.x86_64

  FreeBSD          pkg update     pkg search tbb   pkg install tbb-2019.1

  -----------------------------------------------------------------------

Arch

    packman -Sy

    pacman -Ss tbb

    pacman -S extra/intel-tbb

Gentoo

    emerge --sync

    emerge --search tbb

    emerge dev-cpp/tbb

MacOS

    brew update

    brew search tbb

    brew install tbb

FreeBSD

    portsnap fetch update

    make search name=tbb

    cd /usr/ports/devel/tbb && make install && make clean

If all fails Bowtie 2 can be built with make NO_TBB=1 to use pthreads or

Windows native multithreading instead.

The Bowtie 2 Makefile also includes recipes for basic automatic

dependency management. Running make static-libs && make STATIC_BUILD=1

compile them as static libraries 3. link the resulting libraries to the

compiled Bowtie 2 binaries

If all fails Bowtie 2 can be built with make NO_TBB=1 to use pthreads or

Windows native multithreading instead.

As of version 2.3.5 bowtie2 now supports aligning SRA reads. Prepackaged

builds will include a package that supports SRA. If you’re building

bowtie2 from source please make sure that the Java runtime is available

on your system. You can then proceed with the build by running

make sra-deps && make USE_SRA=1.

Adding to PATH

Valid alignments meet or exceed the minimum score threshold

For an alignment to be considered “valid” (i.e. “good enough”) by Bowtie

For an alignment to be considered “valid” (i.e. “good enough”) by Bowtie

2, it must have an alignment score no less than the minimum score

threshold. The threshold is configurable and is expressed as a function

of the read length. In end-to-end alignment mode, the default minimum

Usage

    bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i>} -S [<sam>]

    bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | b <bam>} -S [<sam>]

Main arguments

    -1 <m1>

Comma-separated list of files containing mate 1s (filename usually

includes _1), e.g. -1 flyA_1.fq,flyB_1.fq. Sequences specified with this

includes _1), e.g. -1 flyA_1.fq,flyB_1.fq. Sequences specified with this

option must correspond file-for-file and read-for-read with those

specified in <m2>. Reads may be a mix of different lengths. If - is

specified, bowtie2 will read the mate 1s from the “standard in” or

    -2 <m2>

Comma-separated list of files containing mate 2s (filename usually

includes _2), e.g. -2 flyA_2.fq,flyB_2.fq. Sequences specified with this

includes _2), e.g. -2 flyA_2.fq,flyB_2.fq. Sequences specified with this

option must correspond file-for-file and read-for-read with those

specified in <m1>. Reads may be a mix of different lengths. If - is

specified, bowtie2 will read the mate 2s from the “standard in” or

different lengths. If - is specified, bowtie2 gets the reads from the

“standard in” or “stdin” filehandle.

    --interleaved

Reads interleaved FASTQ files where the first two records (8 lines)

represent a mate pair.

    --sra-acc

Reads are SRA accessions. If the accession provided cannot be found in

local storage it will be fetched from the NCBI database. If you find

that SRA alignments are long running please rerun your command with the

-p/--threads parameter set to desired number of threads.

NB: this option is only available if bowtie 2 is compiled with the

necessary SRA libraries. See Obtaining Bowtie 2 for details.

    -b <bam>

Reads are unaligned BAM records sorted by read name. The

--align-paired-reads and --preserve-tags options affect the way Bowtie 2

processes records.

    -S <sam>

File to write SAM alignments to. By default, alignments are written to

usually have extension .fq or .fastq. FASTQ is the default format. See

also: --solexa-quals and --int-quals.

    --interleaved

Reads interleaved FASTQ files where the first two records (8 lines)

represent a mate pair.

    --tab5

Each read or pair is on a single line. An unpaired read line is

    --sensitive

Same as: -D 15 -R 2 -L 22 -i S,1,1.15 (default in --end-to-end mode)

Same as: -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default in --end-to-end

mode)

    --very-sensitive

Sets the length of the seed substrings to align during multiseed

alignment. Smaller values make alignment slower but more sensitive.

Default: the --sensitive preset is used by default, which sets -L to 20

both in --end-to-end mode and in --local mode.

Default: the --sensitive preset is used by default, which sets -L to 22

and 20 in --end-to-end mode and in --local mode.

    -i <func>

clipped”) from the ends in order to achieve the greatest possible

alignment score. The match bonus --ma is used in this mode, and the best

possible alignment score is equal to the match bonus (--ma) times the

length of the read. Specifying --local and one of the presets (e.g.

--local --very-fast) is equivalent to specifying the local version of

the preset (--very-fast-local). This is mutually exclusive with

length of the read. Specifying --local and one of the presets

(e.g. --local --very-fast) is equivalent to specifying the local version

of the preset (--very-fast-local). This is mutually exclusive with

--end-to-end. --end-to-end is the default mode.

Scoring options

non-concordant. See also: Mates can overlap, contain or dovetail each

other. Default: mates can overlap in a concordant alignment.

BAM options

    --align-paired-reads

Bowtie 2 will, by default, attempt to align unpaired BAM reads. Use this

option to align paired-end reads instead.

    --preserve-tags

Preserve tags from the original BAM record by appending them to the end

of the corresponding Bowtie 2 SAM output.

Output options

    -t/--time

    --rg <text>

Add <text> (usually of the form TAG:VAL, e.g. SM:Pool1) as a field on

Add <text> (usually of the form TAG:VAL, e.g. SM:Pool1) as a field on

the @RG header line. Note: in order for the @RG line to appear, --rg-id

must also be specified. This is because the ID tag is required by the

SAM Spec. Specify --rg multiple times to set multiple fields. See the

    @HD VN:1.0  SO:unsorted

    @SQ SN:gi|9626243|ref|NC_001416.1|  LN:48502

    @PG ID:bowtie2  PN:bowtie2  VN:2.0.1

    r1  0   gi|9626243|ref|NC_001416.1| 18401   42  122M    *   0   0   TGAATGCGAACTCCGGGACGCTCAGTAATGTGACGATAGCTGAAAACTGTACGATAAACNGTACGCTGAGGGCAGAAAAAATCGTCGGGGACATTNTAAAGGCGGCGAGCGCGGCTTTTCCG  +"@6<:27(F&5)9)"B:%B+A-%5A?2$HCB0B+0=D<7E/<.03#!.F77@6B==?C"7>;))%;,3-$.A06+<-1/@@?,26">=?*@'0;$:;??G+:#+(A?9+10!8!?()?7C>  AS:i:-5 XN:i:0  XM:i:3  XO:i:0  XG:i:0  NM:i:3  MD:Z:59G13G21G26    YT:Z:UU

    r1  0   gi|9626243|ref|NC_001416.1| 18401   42  122M    *   0   0   TGAATGCGAACTCCGGGACGCTCAGTAATGTGACGATAGCTGAAAACTGTACGATAAACNGTACGCTGAGGGCAGAAAAAATCGTCGGGGACATTNTAAAGGCGGCGAGCGCGGCTTTTCCG  +"@6<:27(F&5)9"B):%B+A-%5A?2$HCB0B+0=D<7E/<.03#!.F77@6B==?C"7>;))%;,3-$.A06+<-1/@@?,26">=?*@'0;$:;??G+:#+(A?9+10!8!?()?7C>  AS:i:-5 XN:i:0  XM:i:3  XO:i:0  XG:i:0  NM:i:3  MD:Z:59G13G21G26    YT:Z:UU

    r2  0   gi|9626243|ref|NC_001416.1| 8886    42  275M    *   0   0   NTTNTGATGCGGGCTTGTGGAGTTCAGCCGATCTGACTTATGTCATTACCTATGAAATGTGAGGACGCTATGCCTGTACCAAATCCTACAATGCCGGTGAAAGGTGCCGGGATCACCCTGTGGGTTTATAAGGGGATCGGTGACCCCTACGCGAATCCGCTTTCAGACGTTGACTGGTCGCGTCTGGCAAAAGTTAAAGACCTGACGCCCGGCGAACTGACCGCTGAGNCCTATGACGACAGCTATCTCGATGATGAAGATGCAGACTGGACTGC (#!!'+!$""%+(+)'%)%!+!(&++)''"#"#&#"!'!("%'""("+&%$%*%%#$%#%#!)*'(#")(($&$'&%+&#%*)*#*%*')(%+!%%*"$%"#+)$&&+)&)*+!"*)!*!("&&"*#+"&"'(%)*("'!$*!!%$&&&$!!&&"(*"$&"#&!$%'%"#)$#+%*+)!&*)+(""#!)!%*#"*)*')&")($+*%%)!*)!('(%""+%"$##"#+(('!*(($*'!"*('"+)&%#&$+('**$$&+*&!#%)')'(+(!%+ AS:i:-14    XN:i:0  XM:i:8  XO:i:0  XG:i:0  NM:i:8  MD:Z:0A0C0G0A108C23G9T81T46 YT:Z:UU

    r3  16  gi|9626243|ref|NC_001416.1| 11599   42  338M    *   0   0   GGGCGCGTTACTGGGATGATCGTGAAAAGGCCCGTCTTGCGCTTGAAGCCGCCCGAAAGAAGGCTGAGCAGCAGACTCAAGAGGAGAAAAATGCGCAGCAGCGGAGCGATACCGAAGCGTCACGGCTGAAATATACCGAAGAGGCGCAGAAGGCTNACGAACGGCTGCAGACGCCGCTGCAGAAATATACCGCCCGTCAGGAAGAACTGANCAAGGCACNGAAAGACGGGAAAATCCTGCAGGCGGATTACAACACGCTGATGGCGGCGGCGAAAAAGGATTATGAAGCGACGCTGTAAAAGCCGAAACAGTCCAGCGTGAAGGTGTCTGCGGGCGAT  7F$%6=$:9B@/F'>=?!D?@0(:A*)7/>9C>6#1<6:C(.CC;#.;>;2'$4D:?&B!>689?(0(G7+0=@37F)GG=>?958.D2E04C<E,*AD%G0.%$+A:'H;?8<72:88?E6((CF)6DF#.)=>B>D-="C'B080E'5BH"77':"@70#4%A5=6.2/1>;9"&-H6)=$/0;5E:<8G!@::1?2DC7C*;@*#.1C0.D>H/20,!"C-#,6@%<+<D(AG-).?&#0.00'@)/F8?B!&"170,)>:?<A7#1(A@0E#&A.*DC.E")AH"+.,5,2>5"2?:G,F"D0B8D-6$65D<D!A/38860.*4;4B<*31?6  AS:i:-22    XN:i:0  XM:i:8  XO:i:0  XG:i:0  NM:i:8  MD:Z:80C4C16A52T23G30A8T76A41   YT:Z:UU

    r4  0   gi|9626243|ref|NC_001416.1| 40075   42  184M    *   0   0   GGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCCATATGACTGCGAGAATTAACNGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGT(=8B)GD04*G%&4F,1'A>.C&7=F$,+#6!))43C,5/5+)?-/0>/D3=-,2/+.1?@->;)00!'3!7BH$G)HG+ADC'#-9F)7<7"$?&.>0)@5;4,!0-#C!15CF8&HB+B==H>7,/)C5)5*+(F5A%D,EA<(>G9E0>7&/E?4%;#'92)<5+@7:A.(BG@BG86@.G AS:i:-1 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:77C106 YT:Z:UU