diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index 959569de56f9..60d26dd34b52 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -1,65 +1,80 @@ PORTNAME= ugene -PORTVERSION= 40.1 -PORTREVISION= 1 +PORTVERSION= 53.1 CATEGORIES= biology science MAINTAINER= makc@FreeBSD.org COMMENT= Integrated bioinformatics toolkit WWW= https://ugene.net/ LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE.txt -BROKEN_aarch64= fails to build: invokes x86 asm -BROKEN_armv7= fails to build: src/SendReportDialog.cpp:435:20: error: invalid output constraint '=a' in asm, see https://github.com/ugeneunipro/ugene/issues/919 -BROKEN_riscv64= fails to build: invokes x86 asm +IGNORE_aarch64= fails to build: https://bugs.freebsd.org/293379 RUN_DEPENDS= bash:shells/bash -USE_GITHUB= yes -GH_ACCOUNT= ugeneunipro - -USES= desktop-file-utils gl qmake qt:5 shared-mime-info sqlite xorg +USES= cmake compiler:c++14-lang desktop-file-utils gl \ + localbase:ldflags qt:5 shared-mime-info shebangfix xorg USE_GL= gl glu -USE_QT= buildtools:build linguisttools:build \ - core gui network opengl printsupport scripttools script \ - sql svg testlib widgets xml \ +USE_QT= buildtools:build linguisttools:build qmake:build \ + core gui network networkauth printsupport \ + svg testlib websockets widgets xml \ imageformats:run USE_XORG= x11 xtst +USE_LDCONFIG= ${UGENE_LIBDIR} -QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \ - INSTALL_MANDIR="${PREFIX}/share/man" \ - UGENE_LRELEASE="${LRELEASE}" UGENE_LUPDATE="${LUPDATE}" \ - UGENE_USE_BUNDLED_SQLITE=0 -ALL_TARGET= release -CXXFLAGS_i386= -msse2 +USE_GITHUB= yes +GH_ACCOUNT= ugeneunipro -OPTIONS_DEFINE= OPENCL +CXXFLAGS_i386= -msse2 +LDFLAGS+= -pthread +SHEBANG_FILES= etc/shared/ugene +PORTDATA= * -OPENCL_QMAKE_ON= UGENE_OPENCL_DETECTED=1 +UGENE_LIBDIR= ${PREFIX}/lib/ugene .include -.if ${ARCH} == i386 -QMAKE_ARGS+= CONFIG+=x86 +.if empty(ARCH:Mamd64) && empty(ARCH:Mi386) +BUILD_DEPENDS+= ${LOCALBASE}/include/sse2neon.h:devel/sse2neon .endif post-patch: -# yes, bash is required, stuff will not execute with sh - @${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \ - ${WRKSRC}/src/gen_bin_script.cmd \ - ${WRKSRC}/etc/shared/ugene ${WRKSRC}/etc/shared/ugened @${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \ ${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp - @${REINPLACE_CMD} 's, -lbreakpad$$$$D,,' \ - ${WRKSRC}/src/corelibs/U2Private/U2Private.pri \ - ${WRKSRC}/src/plugins_checker/plugins_checker.pri \ - ${WRKSRC}/src/ugenecl/ugenecl.pri \ - ${WRKSRC}/src/ugeneui/ugeneui.pri - @${REINPLACE_CMD} -e '/ugene\.desktop/s,share,&d,' \ - ${WRKSRC}/ugene.pri + ${REINPLACE_CMD} 's,stdc++fs,,' \ + ${WRKSRC}/src/libs_3rdparty/QSpec/CMakeLists.txt + ${REINPLACE_CMD} 's,/usr/local/share/ugene,${DATADIR},' \ + ${WRKSRC}/src/ugenecl/src/Main.cpp +# breakpad is not aware of FreeBSD + ${REINPLACE_CMD} '/libs_3rdparty\/breakpad/d' \ + ${WRKSRC}/src/corelibs/U2Private/CMakeLists.txt \ + ${WRKSRC}/CMakeLists.txt + ${REINPLACE_CMD} 's,breakpad,,' \ + ${WRKSRC}/src/ugeneui/CMakeLists.txt \ + ${WRKSRC}/src/ugenecl/CMakeLists.txt \ + ${WRKSRC}/src/corelibs/U2Private/CMakeLists.txt +# Do not alter binary names for debug build + ${REINPLACE_CMD} '/DEBUG_POSTFIX/d' \ + ${WRKSRC}/src/plugins_checker/CMakeLists.txt \ + ${WRKSRC}/src/ugenecl/CMakeLists.txt \ + ${WRKSRC}/src/ugenem/CMakeLists.txt \ + ${WRKSRC}/src/ugeneui/CMakeLists.txt \ + ${WRKSRC}/CMakeLists.txt -post-stage: - @cd ${STAGEDIR}${PREFIX} && ${RM} bin/ecp.* lib/ugene/ecp.* +do-install: + ${MKDIR} ${STAGEDIR}/${UGENE_LIBDIR} + cd ${BUILD_WRKSRC}/dist && ${COPYTREE_SHARE} . ${STAGEDIR}/${UGENE_LIBDIR}/ +.for prog in ugene ugenecl ugenem ugeneui + ${RLN} ${STAGEDIR}${UGENE_LIBDIR}/${prog} ${STAGEDIR}/${PREFIX}/bin/${prog} +.endfor + ${MKDIR} ${STAGEDIR}/${DATADIR} + cd ${WRKSRC} && ${COPYTREE_SHARE} data ${STAGEDIR}/${DATADIR} + ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.desktop ${STAGEDIR}/${DESKTOPDIR} + ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.png ${STAGEDIR}/${PREFIX}/share/pixmaps/ + ${INSTALL_DATA} ${WRKSRC}/etc/shared/application-x-ugene-ext.png ${STAGEDIR}/${PREFIX}/share/pixmaps/ + ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.1.gz ${STAGEDIR}/${PREFIX}/share/man/man1/ + ${MKDIR} ${STAGEDIR}/${PREFIX}/share/mime/packages + ${INSTALL_DATA} ${WRKSRC}/etc/shared/application-x-ugene.xml ${STAGEDIR}/${PREFIX}/share/mime/packages/ .include diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo index 5eff6f289b9d..3d5da3ede80d 100644 --- a/biology/ugene/distinfo +++ b/biology/ugene/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1633934483 -SHA256 (ugeneunipro-ugene-40.1_GH0.tar.gz) = 92b954449f697957c6b6b2da803ba6ae9ad546f44c584bbb2ab8600ac8b45a6e -SIZE (ugeneunipro-ugene-40.1_GH0.tar.gz) = 28791083 +TIMESTAMP = 1775033524 +SHA256 (ugeneunipro-ugene-53.1_GH0.tar.gz) = 3eca3bc97824d855b5dfe4844b7a5d46052f98279fa015c7e152e111f89c4673 +SIZE (ugeneunipro-ugene-53.1_GH0.tar.gz) = 27484438 diff --git a/biology/ugene/files/patch-linux b/biology/ugene/files/patch-linux new file mode 100644 index 000000000000..f334ee07eca0 --- /dev/null +++ b/biology/ugene/files/patch-linux @@ -0,0 +1,42 @@ +--- src/corelibs/U2Private/src/crash_handler/CrashHandler.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/corelibs/U2Private/src/crash_handler/CrashHandler.cpp +@@ -36,7 +36,7 @@ + + #if defined(Q_OS_DARWIN) + # include "CrashHandlerPrivateMac.h" +-#elif defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN) ++#elif defined(Q_OS_LINUX) + # include "CrashHandlerPrivateUnixNotMac.h" + #elif defined(Q_OS_WIN) + # include "CrashHandlerPrivateWin.h" +@@ -124,7 +124,7 @@ void CrashHandler::setupPrivateHandler() { + assert(crashHandlerPrivate == nullptr); + #if defined(Q_OS_DARWIN) + crashHandlerPrivate = new CrashHandlerPrivateMac; +-#elif defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN) ++#elif defined(Q_OS_LINUX) + crashHandlerPrivate = new CrashHandlerPrivateUnixNotMac; + #elif defined(Q_OS_WIN) + crashHandlerPrivate = new CrashHandlerPrivateWin; +--- src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp +@@ -20,7 +20,7 @@ + */ + + #include +-#if defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN) ++#if defined(Q_OS_LINUX) + + # include + +--- src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.h.orig 2026-03-01 18:44:47 UTC ++++ src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.h +@@ -22,7 +22,7 @@ + #pragma once + + #include +-#if defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN) ++#if defined(Q_OS_LINUX) + + # include + diff --git a/biology/ugene/files/patch-qmutex b/biology/ugene/files/patch-qmutex new file mode 100644 index 000000000000..a11b98d3fce2 --- /dev/null +++ b/biology/ugene/files/patch-qmutex @@ -0,0 +1,64 @@ +--- src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.cpp +@@ -30,7 +30,7 @@ SubstMatrixRegistry::SubstMatrixRegistry(QObject* pOwn + namespace U2 { + + SubstMatrixRegistry::SubstMatrixRegistry(QObject* pOwn) +- : QObject(pOwn), mutex(QMutex::Recursive) { ++ : QObject(pOwn), mutex() { + readMatrices(); + } + +--- src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.h.orig 2026-03-01 18:44:47 UTC ++++ src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.h +@@ -53,7 +53,7 @@ class U2ALGORITHM_EXPORT SubstMatrixRegistry : public + void readMatrices(); + static SMatrix parseMatrix(const QString& name, const QByteArray& text, QString& error); + +- mutable QMutex mutex; ++ mutable QRecursiveMutex mutex; + QMap matrixByName; + }; + +--- src/plugins/annotator/src/CollocationsDialogController.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/plugins/annotator/src/CollocationsDialogController.cpp +@@ -313,7 +313,7 @@ CollocationSearchTask::CollocationSearchTask(const QLi + ////////////////////////////////////////////////////////////////////////// + // task + CollocationSearchTask::CollocationSearchTask(const QList& table, const QSet& names, const CollocationsAlgorithmSettings& cfg) +- : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(QMutex::Recursive), keepSourceAnns(false) { ++ : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(), keepSourceAnns(false) { + GCOUNTER(cvar, "CollocationSearchTask"); + assert(cfg.distance >= 0); + assert(!names.isEmpty()); +@@ -342,7 +342,7 @@ CollocationSearchTask::CollocationSearchTask(const QLi + } + + CollocationSearchTask::CollocationSearchTask(const QList& table, const QSet& names, const CollocationsAlgorithmSettings& cfg, bool _keepSourceAnns) +- : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(QMutex::Recursive), keepSourceAnns(_keepSourceAnns) { ++ : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(), keepSourceAnns(_keepSourceAnns) { + assert(cfg.distance >= 0); + assert(!names.isEmpty()); + foreach (const QString& name, names) { +--- src/plugins/annotator/src/CollocationsDialogController.h.orig 2026-03-01 18:44:47 UTC ++++ src/plugins/annotator/src/CollocationsDialogController.h +@@ -105,7 +105,7 @@ class CollocationSearchTask : public Task, public Coll + QMap items; + CollocationsAlgorithmSettings cfg; + QVector results; +- QMutex lock; ++ QRecursiveMutex lock; + + const bool keepSourceAnns; + QList sourceAnns; +--- src/plugins/dna_export/src/ExportSequenceTask.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/plugins/dna_export/src/ExportSequenceTask.cpp +@@ -46,7 +46,7 @@ static const qint64 MAX_CHUNK_LENGTH = 4194305; // (4 + + static const qint64 MAX_CHUNK_LENGTH = 4194305; // (4 MiB + 1) chunk. Remainder of the division by 3 is 2. + +-static QMutex seqRefGuard(QMutex::NonRecursive); ++static QMutex seqRefGuard; + + namespace U2 { + diff --git a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro deleted file mode 100644 index 73f2d4038887..000000000000 --- a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro +++ /dev/null @@ -1,41 +0,0 @@ ---- src/corelibs/U2Private/U2Private.pro.orig 2018-08-16 13:59:12 UTC -+++ src/corelibs/U2Private/U2Private.pro -@@ -12,12 +12,7 @@ HEADERS += src/AppContextImpl.h \ - src/PluginSupportImpl.h \ - src/ServiceRegistryImpl.h \ - src/SettingsImpl.h \ -- src/TaskSchedulerImpl.h \ -- src/crash_handler/CrashHandler.h \ -- src/crash_handler/CrashHandlerArgsHelper.h \ -- src/crash_handler/CrashHandlerPrivate.h \ -- src/crash_handler/CrashLogCache.h \ -- src/crash_handler/StackWalker.h -+ src/TaskSchedulerImpl.h - - SOURCES += src/AppContextImpl.cpp \ - src/AppSettingsImpl.cpp \ -@@ -30,23 +25,13 @@ SOURCES += src/AppContextImpl.cpp \ - src/PluginSupportImpl.cpp \ - src/ServiceRegistryImpl.cpp \ - src/SettingsImpl.cpp \ -- src/TaskSchedulerImpl.cpp \ -- src/crash_handler/CrashHandler.cpp \ -- src/crash_handler/CrashHandlerArgsHelper.cpp \ -- src/crash_handler/CrashHandlerPrivate.cpp \ -- src/crash_handler/CrashLogCache.cpp \ -- src/crash_handler/StackWalker.cpp -+ src/TaskSchedulerImpl.cpp - - TRANSLATIONS += transl/russian.ts - - win32 { - HEADERS += src/crash_handler/CrashHandlerPrivateWin.h - SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp --} -- --unix_not_mac() { -- HEADERS += src/crash_handler/CrashHandlerPrivateUnixNotMac.h -- SOURCES += src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp - } - - mac { diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp deleted file mode 100644 index c6956606c3ed..000000000000 --- a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp +++ /dev/null @@ -1,21 +0,0 @@ -Use the Linux driver for FreeBSD as well. Fixes crash on startup. - ---- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig 2021-09-08 14:18:53 UTC -+++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp -@@ -21,14 +21,14 @@ - - #include "GTKeyboardDriver.h" - --#if defined __linux__ -+#if defined(__linux__) || defined(__FreeBSD__) - # include - # include - #endif - - namespace HI { - --#if defined __linux__ -+#if defined(__linux__) || defined(__FreeBSD__) - - bool GTKeyboardDriver::keyPress(char key, Qt::KeyboardModifiers modifiers) { - DRIVER_CHECK(key != 0, "key = 0"); diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp deleted file mode 100644 index eb0c977bf399..000000000000 --- a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp +++ /dev/null @@ -1,20 +0,0 @@ -Use the Linux driver for FreeBSD as well. Fixes crash on startup. - ---- src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp.orig 2018-09-02 00:23:24 UTC -+++ src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp -@@ -23,13 +23,13 @@ - - #include "GTMouseDriver.h" - --#ifdef __linux__ -+#if defined(__linux__) || defined(__FreeBSD__) - # include - #endif - - namespace HI { - --#ifdef __linux__ -+#if defined(__linux__) || defined(__FreeBSD__) - - # define GT_CLASS_NAME "GTMouseDriver Linux" - QPoint GTMouseDriver::mousePos = QPoint(-1, -1); diff --git a/biology/ugene/files/patch-src_plugins__3rdparty_ball b/biology/ugene/files/patch-src_plugins__3rdparty_ball new file mode 100644 index 000000000000..762c43a53506 --- /dev/null +++ b/biology/ugene/files/patch-src_plugins__3rdparty_ball @@ -0,0 +1,28 @@ +Description: indicating we use signed char, so that we don't depend on the + default choice of the implementation +Author: Pierre Gruet +Forwarded: no +Last-Update: 2024-10-04 + +--- src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h ++++ src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h +@@ -37,7 +37,7 @@ + { + namespace __private + { +- extern const char BALL_EXPORT neighbour_table_[27][3]; ++ extern const signed char BALL_EXPORT neighbour_table_[27][3]; + } + + template class HashGrid3; +--- src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp ++++ src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp +@@ -9,7 +9,7 @@ + { + namespace __private + { +- const char neighbour_table_[27][3] = ++ const signed char neighbour_table_[27][3] = + { + { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 }, + { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 }, diff --git a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp deleted file mode 100644 index e893985f32c3..000000000000 --- a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp +++ /dev/null @@ -1,31 +0,0 @@ ---- src/plugins_checker/src/Main.cpp.orig 2018-08-16 13:59:06 UTC -+++ src/plugins_checker/src/Main.cpp -@@ -39,7 +39,7 @@ - #include - #include - #include --#include -+//#include - - #define TR_SETTINGS_ROOT QString("test_runner/") - -@@ -55,8 +55,10 @@ static void registerCoreServices() { - } - #endif - -+#if 0 - CrashHandler::setupHandler(); - CrashHandler::setSendCrashReports(false); -+#endif - - const char* build = QT_VERSION_STR, *runtime = qVersion(); - if (strcmp(build, runtime) > 0){ -@@ -141,7 +143,7 @@ int main(int argc, char **argv) - delete cmdLineRegistry; - appContext->setCMDLineRegistry(NULL); - -- CrashHandler::shutdown(); -+ //CrashHandler::shutdown(); - - return rc; - } diff --git a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp index 1e91ae0651d0..b14f4f39b5f1 100644 --- a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp +++ b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp @@ -1,36 +1,20 @@ ---- src/ugenecl/src/Main.cpp.orig 2018-08-16 13:59:20 UTC +--- src/ugenecl/src/Main.cpp.orig 2026-03-01 18:44:47 UTC +++ src/ugenecl/src/Main.cpp -@@ -93,7 +93,7 @@ - #include - #include - #include --#include -+//#include - - // local project imports - #include "DumpHelpTask.h" -@@ -191,6 +191,7 @@ static void setSearchPaths() { - } - - int main(int argc, char **argv) { -+#if 0 - if (CrashHandler::isEnabled()) { - CrashHandler::setupHandler(); +@@ -151,7 +151,7 @@ static void setScriptsSearchPath() { + scriptsSearchPath.push_back(appDirPath + RELATIVE_DEV_SCRIPTS_DIR); } -@@ -198,6 +199,7 @@ int main(int argc, char **argv) - if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") { - CrashHandler::setSendCrashReports(false); + if (scriptsSearchPath.empty()) { +- scriptsSearchPath.push_back("/"); ++ scriptsSearchPath.push_back("/usr/local/share/ugene/scripts"); + } + QDir::setSearchPaths(PATH_PREFIX_SCRIPTS, scriptsSearchPath); + } +@@ -178,7 +178,7 @@ static void setDataSearchPaths() { } -+#endif - - if (!Version::checkBuildAndRuntimeVersions()) { - return -1; -@@ -617,7 +619,7 @@ int main(int argc, char **argv) - delete pwr; - appContext->setAlignmentAlgorithmsRegistry(NULL); -- CrashHandler::shutdown(); -+ //CrashHandler::shutdown(); + if (dataSearchPaths.empty()) { +- dataSearchPaths.push_back("/"); ++ dataSearchPaths.push_back("/usr/local/share/ugene/data"); + } - return rc; - } + QDir::setSearchPaths(PATH_PREFIX_DATA, dataSearchPaths); diff --git a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp deleted file mode 100644 index 251f739fbf1e..000000000000 --- a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp +++ /dev/null @@ -1,45 +0,0 @@ ---- src/ugeneui/src/Main.cpp.orig 2020-06-17 15:14:26 UTC -+++ src/ugeneui/src/Main.cpp -@@ -151,7 +151,7 @@ - #include - #include - #include --#include -+//#include - - #include "app_settings/AppSettingsGUIImpl.h" - #include "app_settings/logview_settings/LogSettingsGUIController.h" -@@ -403,6 +403,7 @@ void fixMacFonts() { - } // namespace - - int main(int argc, char **argv) { -+#if 0 - if (CrashHandler::isEnabled()) { - CrashHandler::setupHandler(); - } -@@ -410,6 +411,7 @@ int main(int argc, char **argv) { - if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") { - CrashHandler::setSendCrashReports(false); - } -+#endif - - QT_REQUIRE_VERSION(argc, argv, QT_VERSION_STR); - -@@ -422,7 +424,7 @@ int main(int argc, char **argv) { - //QApplication app(argc, argv); - GApplication app(argc, argv); - --#ifdef Q_OS_LINUX -+#ifdef Q_OS_UNIX - QPixmap pixmap(":/ugene/images/originals/ugene_128.png"); - app.setWindowIcon(pixmap); - #endif -@@ -1088,7 +1090,7 @@ int main(int argc, char **argv) { - } - - UgeneUpdater::onClose(); -- CrashHandler::shutdown(); -+ //CrashHandler::shutdown(); - - return rc; - } diff --git a/biology/ugene/files/patch-sse2neon b/biology/ugene/files/patch-sse2neon new file mode 100644 index 000000000000..145f1a34811e --- /dev/null +++ b/biology/ugene/files/patch-sse2neon @@ -0,0 +1,40 @@ +--- src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp +@@ -1,5 +1,9 @@ + #include ++#if defined(__i386__) || defined(__amd64__) + #include ++#else ++#include ++#endif + #include + + #include +--- src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp +@@ -23,7 +23,11 @@ U2_DISABLE_WARNINGS + * MA 02110-1301, USA. + */ + ++#if defined(__i386__) || defined(__amd64__) + #include ++#else ++#include ++#endif + #include + + #include "SmithWatermanAlgorithmSSE2.h" +--- src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.orig 2026-03-01 18:44:47 UTC ++++ src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h +@@ -21,7 +21,11 @@ + + #pragma once + ++#if defined(__i386__) || defined(__amd64__) + #include ++#else ++#include ++#endif + + #include "SmithWatermanAlgorithm.h" + diff --git a/biology/ugene/files/patch-ugene.pro b/biology/ugene/files/patch-ugene.pro deleted file mode 100644 index 29854f16d39d..000000000000 --- a/biology/ugene/files/patch-ugene.pro +++ /dev/null @@ -1,10 +0,0 @@ ---- ugene.pro.orig 2018-08-16 13:58:51 UTC -+++ ugene.pro -@@ -20,7 +20,6 @@ use_bundled_zlib() { - } - - SUBDIRS += \ -- src/libs_3rdparty/breakpad \ - src/libs_3rdparty/qscore \ - src/libs_3rdparty/sqlite3 \ - src/libs_3rdparty/samtools \ diff --git a/biology/ugene/files/patch-unix b/biology/ugene/files/patch-unix new file mode 100644 index 000000000000..f230ec9ff5d5 --- /dev/null +++ b/biology/ugene/files/patch-unix @@ -0,0 +1,37 @@ +--- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp +@@ -21,14 +21,14 @@ + + #include "GTKeyboardDriver.h" + +-#if defined __linux__ ++#if defined(Q_OS_UNIX) + # include + # include + #endif + + namespace HI { + +-#if defined __linux__ ++#if defined(Q_OS_UNIX) + + void GTKeyboardDriver::releasePressedKeys() { + GTKeyboardDriver::keyRelease(Qt::Key_Control); +--- src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp +@@ -24,13 +24,13 @@ + #include + + #include "GTMouseDriver.h" +-#ifdef __linux__ ++#ifdef Q_OS_UNIX + # include + #endif + + namespace HI { + +-#ifdef __linux__ ++#ifdef Q_OS_UNIX + + # define DELAY_ON_EVERY_N_PX 16 + /** diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist index 10133c926025..028dd4d78d49 100644 --- a/biology/ugene/pkg-plist +++ b/biology/ugene/pkg-plist @@ -1,1318 +1,146 @@ bin/ugene +bin/ugenecl +bin/ugenem +bin/ugeneui lib/ugene/libQSpec.so lib/ugene/libU2Algorithm.so lib/ugene/libU2Core.so lib/ugene/libU2Designer.so lib/ugene/libU2Formats.so lib/ugene/libU2Gui.so lib/ugene/libU2Lang.so lib/ugene/libU2Private.so lib/ugene/libU2Script.so lib/ugene/libU2Test.so lib/ugene/libU2View.so +lib/ugene/libqscore.a +lib/ugene/libqtscript.so +lib/ugene/libsamtools.a +lib/ugene/libugenedb.so +lib/ugene/libzlib.a lib/ugene/plugins/CoreTests.license lib/ugene/plugins/CoreTests.plugin lib/ugene/plugins/GUITestBase.license lib/ugene/plugins/GUITestBase.plugin lib/ugene/plugins/annotator.license lib/ugene/plugins/annotator.plugin lib/ugene/plugins/api_tests.license lib/ugene/plugins/api_tests.plugin lib/ugene/plugins/ball.license lib/ugene/plugins/ball.plugin lib/ugene/plugins/biostruct3d_view.license lib/ugene/plugins/biostruct3d_view.plugin lib/ugene/plugins/chroma_view.license lib/ugene/plugins/chroma_view.plugin lib/ugene/plugins/circular_view.license lib/ugene/plugins/circular_view.plugin -lib/ugene/plugins/clark_support.license -lib/ugene/plugins/clark_support.plugin lib/ugene/plugins/dbi_bam.license lib/ugene/plugins/dbi_bam.plugin -lib/ugene/plugins/diamond_support.license -lib/ugene/plugins/diamond_support.plugin lib/ugene/plugins/dna_export.license lib/ugene/plugins/dna_export.plugin lib/ugene/plugins/dna_flexibility.license lib/ugene/plugins/dna_flexibility.plugin lib/ugene/plugins/dna_graphpack.license lib/ugene/plugins/dna_graphpack.plugin lib/ugene/plugins/dna_stat.license lib/ugene/plugins/dna_stat.plugin lib/ugene/plugins/dotplot.license lib/ugene/plugins/dotplot.plugin lib/ugene/plugins/enzymes.license lib/ugene/plugins/enzymes.plugin lib/ugene/plugins/external_tool_support.license lib/ugene/plugins/external_tool_support.plugin +lib/ugene/plugins/genecut.license +lib/ugene/plugins/genecut.plugin lib/ugene/plugins/genome_aligner.license lib/ugene/plugins/genome_aligner.plugin lib/ugene/plugins/gor4.license lib/ugene/plugins/gor4.plugin lib/ugene/plugins/hmm2.license lib/ugene/plugins/hmm2.plugin -lib/ugene/plugins/kalign.license -lib/ugene/plugins/kalign.plugin -lib/ugene/plugins/kraken_support.license -lib/ugene/plugins/kraken_support.plugin lib/ugene/plugins/libCoreTests.so lib/ugene/plugins/libGUITestBase.so lib/ugene/plugins/libannotator.so lib/ugene/plugins/libapi_tests.so lib/ugene/plugins/libball.so lib/ugene/plugins/libbiostruct3d_view.so lib/ugene/plugins/libchroma_view.so lib/ugene/plugins/libcircular_view.so -lib/ugene/plugins/libclark_support.so lib/ugene/plugins/libdbi_bam.so -lib/ugene/plugins/libdiamond_support.so lib/ugene/plugins/libdna_export.so lib/ugene/plugins/libdna_flexibility.so lib/ugene/plugins/libdna_graphpack.so lib/ugene/plugins/libdna_stat.so lib/ugene/plugins/libdotplot.so lib/ugene/plugins/libenzymes.so lib/ugene/plugins/libexternal_tool_support.so +lib/ugene/plugins/libgenecut.so lib/ugene/plugins/libgenome_aligner.so lib/ugene/plugins/libgor4.so lib/ugene/plugins/libhmm2.so -lib/ugene/plugins/libkalign.so -lib/ugene/plugins/libkraken_support.so lib/ugene/plugins/liblinkdata_support.so -lib/ugene/plugins/libmetaphlan2_support.so -lib/ugene/plugins/libngs_reads_classification.so -lib/ugene/plugins/libopencl_support.so lib/ugene/plugins/liborf_marker.so lib/ugene/plugins/libpcr.so lib/ugene/plugins/libperf_monitor.so lib/ugene/plugins/libphylip.so lib/ugene/plugins/libprimer3.so lib/ugene/plugins/libpsipred.so lib/ugene/plugins/libptools.so lib/ugene/plugins/libquery_designer.so lib/ugene/plugins/libremote_blast.so lib/ugene/plugins/librepeat_finder.so lib/ugene/plugins/libsitecon.so lib/ugene/plugins/libsmith_waterman.so lib/ugene/plugins/libtest_runner.so lib/ugene/plugins/libumuscle.so lib/ugene/plugins/libvariants.so lib/ugene/plugins/libweight_matrix.so -lib/ugene/plugins/libwevote_support.so lib/ugene/plugins/libworkflow_designer.so lib/ugene/plugins/linkdata_support.license lib/ugene/plugins/linkdata_support.plugin -lib/ugene/plugins/metaphlan2_support.license -lib/ugene/plugins/metaphlan2_support.plugin -lib/ugene/plugins/ngs_reads_classification.license -lib/ugene/plugins/ngs_reads_classification.plugin -lib/ugene/plugins/opencl_support.license -lib/ugene/plugins/opencl_support.plugin lib/ugene/plugins/orf_marker.license lib/ugene/plugins/orf_marker.plugin lib/ugene/plugins/pcr.license lib/ugene/plugins/pcr.plugin lib/ugene/plugins/perf_monitor.license lib/ugene/plugins/perf_monitor.plugin lib/ugene/plugins/phylip.license lib/ugene/plugins/phylip.plugin lib/ugene/plugins/primer3.license lib/ugene/plugins/primer3.plugin lib/ugene/plugins/psipred.license lib/ugene/plugins/psipred.plugin lib/ugene/plugins/ptools.license lib/ugene/plugins/ptools.plugin lib/ugene/plugins/query_designer.license lib/ugene/plugins/query_designer.plugin lib/ugene/plugins/remote_blast.license lib/ugene/plugins/remote_blast.plugin lib/ugene/plugins/repeat_finder.license lib/ugene/plugins/repeat_finder.plugin lib/ugene/plugins/sitecon.license lib/ugene/plugins/sitecon.plugin lib/ugene/plugins/smith_waterman.license lib/ugene/plugins/smith_waterman.plugin lib/ugene/plugins/test_runner.license lib/ugene/plugins/test_runner.plugin lib/ugene/plugins/umuscle.license lib/ugene/plugins/umuscle.plugin lib/ugene/plugins/variants.license lib/ugene/plugins/variants.plugin lib/ugene/plugins/weight_matrix.license lib/ugene/plugins/weight_matrix.plugin -lib/ugene/plugins/wevote_support.license -lib/ugene/plugins/wevote_support.plugin lib/ugene/plugins/workflow_designer.license lib/ugene/plugins/workflow_designer.plugin -lib/ugene/plugins_checker +@(root,wheel,755) lib/ugene/plugins_checker lib/ugene/transl_ru.qm lib/ugene/transl_tr.qm -lib/ugene/ugene -lib/ugene/ugenecl -lib/ugene/ugenem -lib/ugene/ugeneui -share/man/man1/ugene.1.gz +@(root,wheel,755) lib/ugene/ugene +@(root,wheel,755) lib/ugene/ugenecl +@(root,wheel,755) lib/ugene/ugenem +@(root,wheel,755) lib/ugene/ugeneui share/applications/ugene.desktop -share/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png +share/man/man1/ugene.1.gz share/mime/packages/application-x-ugene.xml +share/pixmaps/application-x-ugene-ext.png share/pixmaps/ugene.png -share/pixmaps/ugene.xpm -%%DATADIR%%/DBXRefRegistry.txt -%%DATADIR%%/adapters/adapters.fasta -%%DATADIR%%/adapters/illumina/NexteraPE-PE.fa -%%DATADIR%%/adapters/illumina/TruSeq2-PE.fa -%%DATADIR%%/adapters/illumina/TruSeq2-SE.fa -%%DATADIR%%/adapters/illumina/TruSeq3-PE-2.fa -%%DATADIR%%/adapters/illumina/TruSeq3-PE.fa -%%DATADIR%%/adapters/illumina/TruSeq3-SE.fa -%%DATADIR%%/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut -%%DATADIR%%/back_translation/Bacteria/Bacillus_subtilis.cut -%%DATADIR%%/back_translation/Bacteria/Escherichia_coli.cut -%%DATADIR%%/back_translation/Bacteria/Haemophilus_influenzae.cut -%%DATADIR%%/back_translation/Bacteria/Helicobacter_pylori.cut -%%DATADIR%%/back_translation/Bacteria/Listeria_monocytogenes.cut -%%DATADIR%%/back_translation/Bacteria/Neisseria_meningitidis.cut -%%DATADIR%%/back_translation/Bacteria/Salmonella_typhimurium_LT2.cut -%%DATADIR%%/back_translation/Bacteria/Streptomyces_coelicolor_A3(2).cut -%%DATADIR%%/back_translation/Bacteria/Sulfolobus_solfataricus_P2.cut -%%DATADIR%%/back_translation/Invertebrates/Apis_mellifera_(honey_bee).cut -%%DATADIR%%/back_translation/Invertebrates/Caenorhabditis_elegans.cut -%%DATADIR%%/back_translation/Invertebrates/Drosophila_melanogaster_(fruit_fly).cut -%%DATADIR%%/back_translation/Invertebrates/Plasmodium_falciparum_(malaria_parasite_P._falciparum).cut -%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Caenorhabditis_elegans.cut -%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Drosophila_melanogaster_(fruit_fly).cut -%%DATADIR%%/back_translation/Mammalia/Bos_taurus_(cow).cut -%%DATADIR%%/back_translation/Mammalia/Canis_familiaris_(dog).cut -%%DATADIR%%/back_translation/Mammalia/Sus_scrofa_(pig).cut -%%DATADIR%%/back_translation/Mammalia/mitochondrion_Bos_taurus_(cow).cut -%%DATADIR%%/back_translation/Mammalia/mitochondrion_Sus_scrofa_(pig).cut -%%DATADIR%%/back_translation/Plants/Arabidopsis_thaliana_(thale_cress).cut -%%DATADIR%%/back_translation/Plants/Oryza_sativa.cut -%%DATADIR%%/back_translation/Plants/Zea_mays.cut -%%DATADIR%%/back_translation/Primates/Homo_sapiens_(human).cut -%%DATADIR%%/back_translation/Primates/Pan_troglodytes_(chimpanzee).cut -%%DATADIR%%/back_translation/Primates/mitochondrion_Homo_sapiens_(human).cut -%%DATADIR%%/back_translation/Primates/mitochondrion_Pan_troglodytes_(chimpanzee).cut -%%DATADIR%%/back_translation/Rodents/Mus_musculus_(house_mouse).cut -%%DATADIR%%/back_translation/Rodents/Rattus_norvegicus_(Norway_rat).cut -%%DATADIR%%/back_translation/Vertebrates/Gallus_gallus_(chicken).cut -%%DATADIR%%/back_translation/Vertebrates/Takifugu_rubripes_(Fugu_rubripes).cut -%%DATADIR%%/back_translation/Vertebrates/Xenopus_laevis_(African_clawed_frog).cut -%%DATADIR%%/back_translation/Vertebrates/mitochondrion_Gallus_gallus_(chicken).cut -%%DATADIR%%/back_translation/Vertebrates/mitochondrion_Takifugu_rubripes_(Fugu_rubripes).cut -%%DATADIR%%/back_translation/Viruses/Human_immunodeficiency_virus_1_(HIV-1).cut -%%DATADIR%%/back_translation/Viruses/Influenza_A_virus.cut -%%DATADIR%%/back_translation/Yeast/Saccharomyces_cerevisiae_(baker's_yeast).cut -%%DATADIR%%/back_translation/tables.xml -%%DATADIR%%/biostruct3d_plugin/BioStruct3DLinks.txt -%%DATADIR%%/cmdline/align-clustalo.uwl -%%DATADIR%%/cmdline/align-clustalw.uwl -%%DATADIR%%/cmdline/align-kalign.uwl -%%DATADIR%%/cmdline/align-mafft.uwl -%%DATADIR%%/cmdline/align-tcoffee.uwl -%%DATADIR%%/cmdline/align-to-reference.uwl -%%DATADIR%%/cmdline/align.uwl -%%DATADIR%%/cmdline/convert-msa.uwl -%%DATADIR%%/cmdline/convert-seq.uwl -%%DATADIR%%/cmdline/extract-sequence.uwl -%%DATADIR%%/cmdline/extract_consensus_sequence.uwl -%%DATADIR%%/cmdline/extract_consensus_string.uwl -%%DATADIR%%/cmdline/extract_coverage.uwl -%%DATADIR%%/cmdline/fetch-sequence.uwl -%%DATADIR%%/cmdline/find-orfs.uwl -%%DATADIR%%/cmdline/find-repeats.uwl -%%DATADIR%%/cmdline/find-sw.uwl -%%DATADIR%%/cmdline/gene-by-gene.uwl -%%DATADIR%%/cmdline/generate-dna.uwl -%%DATADIR%%/cmdline/hmm2-build.uwl -%%DATADIR%%/cmdline/hmm2-search.uwl -%%DATADIR%%/cmdline/hmm3-build-and-search.uwl -%%DATADIR%%/cmdline/hmm3-search.uwl -%%DATADIR%%/cmdline/join-quality.uwl -%%DATADIR%%/cmdline/local-blast+.uwl -%%DATADIR%%/cmdline/pfm-build.uwl -%%DATADIR%%/cmdline/pfm-search.uwl -%%DATADIR%%/cmdline/pwm-build.uwl -%%DATADIR%%/cmdline/pwm-search.uwl -%%DATADIR%%/cmdline/query.uwl -%%DATADIR%%/cmdline/remote-request.uwl -%%DATADIR%%/cmdline/revcompl.uwl -%%DATADIR%%/cmdline/sitecon-build.uwl -%%DATADIR%%/cmdline/sitecon-search.uwl -%%DATADIR%%/cmdline/snp.uwl -%%DATADIR%%/custom_annotations/plasmid_features.txt -%%DATADIR%%/enzymes/2013_08_01.bairoch.gz -%%DATADIR%%/genome_lengths/danRer7.genome -%%DATADIR%%/genome_lengths/ecoli.genome -%%DATADIR%%/genome_lengths/hg18.genome -%%DATADIR%%/genome_lengths/hg19.genome -%%DATADIR%%/genome_lengths/mm10.genome -%%DATADIR%%/genome_lengths/mm8.genome -%%DATADIR%%/genome_lengths/mm9.genome -%%DATADIR%%/genome_lengths/test.genome -%%DATADIR%%/license -%%DATADIR%%/position_weight_matrix/JASPAR/all_jaspar.csv -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0266.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0267.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0268.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0269.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0270.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0271.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0272.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0273.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0274.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0275.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0276.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0277.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0278.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0279.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0280.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0281.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0282.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0283.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0284.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0285.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0286.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0287.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0288.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0289.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0290.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0291.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0292.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0293.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0294.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0295.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0296.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0297.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0298.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0299.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0300.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0301.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0302.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0303.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0304.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0305.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0306.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0307.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0308.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0309.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0310.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0311.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0312.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0313.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0314.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0315.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0316.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0317.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0318.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0319.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0320.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0321.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0322.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0323.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0324.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0325.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0326.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0327.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0328.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0329.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0330.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0331.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0332.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0333.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0334.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0335.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0336.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0337.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0338.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0339.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0340.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0341.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0342.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0343.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0344.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0345.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0346.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0347.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0348.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0349.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0350.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0351.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0352.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0353.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0354.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0355.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0356.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0357.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0358.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0359.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0360.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0361.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0362.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0363.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0364.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0365.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0366.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0367.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0368.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0369.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0370.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0371.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0372.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0373.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0374.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0375.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0376.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0377.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0378.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0379.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0380.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0381.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0382.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0383.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0384.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0385.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0386.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0387.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0388.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0389.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0390.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0391.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0392.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0393.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0394.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0395.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0396.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0397.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0398.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0399.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0400.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0401.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0402.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0403.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0404.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0405.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0406.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0407.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0408.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0409.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0410.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0411.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0412.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0413.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0414.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0415.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0416.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0417.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0418.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0419.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0420.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0421.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0422.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0423.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0424.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0425.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0426.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0427.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0428.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0429.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0430.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0431.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0432.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0433.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0434.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0435.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0436.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0437.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0438.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0439.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0440.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0441.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/fungi/matrix_list.txt -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0010.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0011.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0012.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0013.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0015.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0016.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0022.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0023.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0026.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA00445.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0049.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0085.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0086.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0094.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0126.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0165.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0166.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0167.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0168.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0169.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0170.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0171.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0172.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0173.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0174.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0175.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0176.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0177.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0178.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0179.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0180.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0181.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0182.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0183.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0184.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0185.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0186.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0187.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0188.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0189.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0190.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0191.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0192.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0193.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0194.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0195.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0196.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0197.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0198.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0199.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0200.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0201.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0202.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0203.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0204.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0205.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0206.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0207.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0208.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0209.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0210.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0211.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0212.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0213.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0214.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0215.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0216.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0217.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0218.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0219.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0220.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0221.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0222.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0223.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0224.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0225.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0226.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0227.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0228.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0229.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0230.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0231.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0232.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0233.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0234.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0235.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0236.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0237.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0238.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0239.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0240.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0241.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0242.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0243.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0244.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0245.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0246.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0247.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0248.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0249.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0250.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0251.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0252.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0253.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0254.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0255.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0256.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0257.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0443.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0444.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0446.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0447.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0448.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0449.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0450.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0451.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0452.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0453.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0454.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0455.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0456.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0457.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0458.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0459.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0460.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/insects/matrix_list.txt -%%DATADIR%%/position_weight_matrix/JASPAR/nematodes/MA0260.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/nematodes/MA0261.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/nematodes/MA0262.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/nematodes/MA0263.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/nematodes/MA0264.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/nematodes/matrix_list.txt -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0001.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0005.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0008.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0020.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0021.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0034.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0044.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0045.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0053.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0054.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0064.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0082.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0096.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0097.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0110.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0120.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0121.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0123.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0127.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0128.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/MA0129.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/plants/matrix_list.txt -%%DATADIR%%/position_weight_matrix/JASPAR/urochordates/MA0118.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/urochordates/matrix_list.txt -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0002.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0003.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0004.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0006.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0007.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0009.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0014.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0017.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0018.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0019.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0024.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0025.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0027.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0028.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0029.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0030.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0031.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0032.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0033.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0035.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0036.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0037.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0038.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0039.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0040.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0041.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0042.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0043.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0046.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0047.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0048.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0050.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0051.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0052.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0055.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0056.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0057.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0058.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0059.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0060.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0061.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0062.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0063.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0065.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0066.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0067.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0068.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0069.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0070.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0071.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0072.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0073.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0074.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0075.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0076.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0077.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0078.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0079.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0080.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0081.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0083.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0084.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0087.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0088.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0089.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0090.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0091.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0092.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0093.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0095.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0098.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0099.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0100.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0101.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0102.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0103.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0104.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0105.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0106.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0107.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0108.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0109.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0111.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0112.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0113.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0114.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0115.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0116.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0117.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0119.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0122.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0124.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0125.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0130.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0131.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0132.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0133.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0135.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0136.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0137.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0138.2.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0139.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0140.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0141.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0142.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0143.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0144.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0145.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0146.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0147.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0148.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0149.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0150.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0151.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0152.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0153.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0154.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0155.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0156.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0157.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0158.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0159.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0160.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0161.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0162.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0163.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0164.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0258.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0259.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/MA0442.1.pfm -%%DATADIR%%/position_weight_matrix/JASPAR/vertebrates/matrix_list.txt -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Alx3_3418.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Alx4_1744.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Arx_1738.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Bapx1_2343.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Barhl1_2590.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Barhl2_3868.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Barx1_2877.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Barx2_3447.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Bsx_3483.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Cart1_0997.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Cart1_1275.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Cdx1_2245.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Cdx2_4272.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Cphx_3484.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Crx_3485.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Cutl1_3494.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Cutl1_3494.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dbx1_3486.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dbx2_3487.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx1_1741.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx2_2273.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx3_1030.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx4_3488.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx5_3419.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dmbx1_2277.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dobox4_3956.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dobox5_3493.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Duxl_1286.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Emx2_3420.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/En1_3123.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/En2_0952.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Esx1_3124.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Evx1_3952.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Evx2_2645.3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gbx1_2883.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gbx2_3110.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gsc_2327.3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gsh2_3990.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hdx_3845.3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hlx1_2350.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hlxb9_3422.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmbox1_2674.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx1_3423.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx2_3424.3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx3_3490.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Homez_1063.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa10_2318.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa11_2218.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa13_3126.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa1_3425.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa2_3079.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa3_2783.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa4_3426.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa5_3415.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa6_1040.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa7_2668.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa7_3750.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa9_2622.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb13_3479.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb3_1720.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb4_2627.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb5_3122.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb6_3428.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb7_3953.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb8_3780.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb9_3413.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc10_2779.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc11_3718.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc12_3480.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc13_3127.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc4_3491.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc5_2630.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc6_3954.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc8_3429.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc9_2367.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd10_2368.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd11_3873.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd12_3481.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd13_2356.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd1_3448.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd3_1742.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd8_2644.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Ipf1_3815.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx2_0900.3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx3_0920.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx3_2226.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx4_2242.3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx5_2385.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx6_2623.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Isl2_3430.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Isx_3445.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lbx2_3869.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx1_2240.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx2_0953.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx3_3431.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx4_1719.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx5_2279.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx6_2272.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx6_3432.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx8_2247.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx9_3492.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lmx1a_2238.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lmx1b_3433.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Meis1_2335.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Meox1_2310.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Mrg1_2246.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Mrg2_2302.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx1_3031.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx2_3449.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx3_3206.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx1-1_3856.3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx1-2_3214.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-2_2823.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-3_3435.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-4_3074.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-5_3436.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-6_3437.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-9_3082.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx3-1_2923.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-3_3446.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox1_3970.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox2_3438.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox3_3439.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox5_2284.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox5_3963.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox6_3440.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Og2x_3719.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otp_3496.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otx1_2325.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otx2_3441.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax4_3989.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax6_3838.3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax7_3783.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pbx1_3203.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Phox2a_3947.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Phox2b_3948.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx1_2312.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx2_2274.3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx3_3497.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pknox1_2364.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pknox2_3077.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou1f1_3818.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f1_3081.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f2_3748.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f3_3986.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f1_3819.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f2_2824.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f3_3235.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f4_3773.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou4f3_2791.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou6f1_1731.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou6f1_3733.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prop1_3949.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prrx1_3442.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prrx2_3072.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rax_3443.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox11_1765.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox11_2205.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox6_4251.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Shox2_2641.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six1_0935.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six2_2307.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six3_1732.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six4_2860.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six6_2267.4.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six6_2267.5.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tcf1_2666.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tcf2_0913.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tgif1_2342.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tgif2_3451.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Titf1_1722.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tlx2_3498.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Uncx4.1_2281.2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vax1_3499.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vax2_3500.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vsx1_1728.1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Aft1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Aro80.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Asg1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Bas1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cbf1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cep3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cha4.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cup9.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ecm22.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fhl1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fkh1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fkh2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gal4.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat4.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gcn4.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gln3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gsm1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gzf3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Hal9.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Leu3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Lys14.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Matalpha2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mbp1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mcm1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Met32.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mga1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ndt80.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nhp6a.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nhp6b.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nrg1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Oaf1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pbf1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pbf2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pdr1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Phd1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pho2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pho4.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Put3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rap1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rdr1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rds1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rds2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rgt1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rph1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rpn4.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc30.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rtg3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfl1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfp1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sip4.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Skn7.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Smp1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Spt15.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Srd1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stb3.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp4.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sum1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sut2.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tbf1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tbs1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tea1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tec1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tye7.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ume6.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Usv1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Xbp1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yap1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yap6.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ybr239c.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ydr520c.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yer130c.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ygr067c.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ykl222c.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yll054c.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yml081w.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ynr063w.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yox1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr013c.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr015c.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr196w.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yrm1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yrr1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Cbf1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Ceh-22.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Oct-1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Rap1.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Zif268.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/Cgd2_3490.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/PF14_0633.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/PFF0200c.pwm -%%DATADIR%%/position_weight_matrix/UniPROBE/all_uniprobe.csv -%%DATADIR%%/primer3/drosophila.w.transposons.txt -%%DATADIR%%/primer3/humrep_and_simple.txt -%%DATADIR%%/primer3/rodent_ref.txt -%%DATADIR%%/primer3/rodrep_and_simple.txt -%%DATADIR%%/query_samples/RepeatsWithORF.uql -%%DATADIR%%/query_samples/SimpleGene.uql -%%DATADIR%%/samples/ABIF/A01.abi -%%DATADIR%%/samples/ACE/BL060C3.ace -%%DATADIR%%/samples/ACE/K26.ace -%%DATADIR%%/samples/APR/DNA.apr -%%DATADIR%%/samples/APR/gyrA.apr -%%DATADIR%%/samples/Assembly/chrM.fa -%%DATADIR%%/samples/Assembly/chrM.sam -%%DATADIR%%/samples/Assembly/chrM.sorted.bam -%%DATADIR%%/samples/CLUSTALW/COI.aln -%%DATADIR%%/samples/CLUSTALW/HIV-1.aln -%%DATADIR%%/samples/CLUSTALW/ty3.aln.gz -%%DATADIR%%/samples/EMBL/AF177870.emb -%%DATADIR%%/samples/EMBL/AL000263.emb -%%DATADIR%%/samples/FASTA/human_T1.fa -%%DATADIR%%/samples/FASTQ/eas.fastq -%%DATADIR%%/samples/GFF/5prime_utr_intron_A20.gff -%%DATADIR%%/samples/GFF/5prime_utr_intron_A21.gff -%%DATADIR%%/samples/Genbank/CVU55762.gb -%%DATADIR%%/samples/Genbank/NC_014267.1.gb -%%DATADIR%%/samples/Genbank/PBR322.gb -%%DATADIR%%/samples/Genbank/murine.gb -%%DATADIR%%/samples/Genbank/sars.gb -%%DATADIR%%/samples/HMM/aligment15900.hmm -%%DATADIR%%/samples/MMDB/1CRN.prt -%%DATADIR%%/samples/MMDB/2JQS.prt -%%DATADIR%%/samples/MSF/HMA.msf -%%DATADIR%%/samples/MSF/lipid8.msf -%%DATADIR%%/samples/MSF/pla2_20.msf -%%DATADIR%%/samples/Newick/COI.nwk -%%DATADIR%%/samples/PDB/1CF7.PDB -%%DATADIR%%/samples/PDB/1CRN.PDB -%%DATADIR%%/samples/PDB/3INS.PDB -%%DATADIR%%/samples/Raw/raw.seq -%%DATADIR%%/samples/SCF/90-JRI-07.scf -%%DATADIR%%/samples/Sanger/alignment.ugenedb -%%DATADIR%%/samples/Stockholm/CBS.sto -%%DATADIR%%/samples/Stockholm/UPSK.sto -%%DATADIR%%/samples/Swiss-Prot/D0VTW9.txt -%%DATADIR%%/samples/Swiss-Prot/P01375.txt -%%DATADIR%%/samples/Swiss-Prot/P16152.txt -%%DATADIR%%/sitecon_models/eukaryotic/CEBP_a.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/CEBPall.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/CLOCK.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/CRE.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/E2F1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/E2F1DP1sel1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/EGR1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/Eklf.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/GATA1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/GATA_ALL.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/Gata2.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/Gata3.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/HMG1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/HNF1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/HNF3_4.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/HNF4.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/MYOGsel3.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/MyoD.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/NF1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/NFATp.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/NFkB_all.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/NFkB_hetero.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/NFkB_homo.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/Nf_e2.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/Nrf2.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/Oct1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/Oct_all.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/PPRE.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/Pu1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/SRE_can.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/STAT.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/STAT1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/TTF1.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/USF.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/cMyc_can.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/er2.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/irf.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/isre.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/nfy.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/p53.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/setCREB.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/setCREBzag.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/srf_all.sitecon.gz -%%DATADIR%%/sitecon_models/eukaryotic/yy1.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/AgaR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/AraC.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/ArcA.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/ArgR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/CpxR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/Crp.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/CysB.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/CytR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/DeoR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/DnaA.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/FUR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/FadR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/FlhDC.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/Fnr.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/Frur.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/GALR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/GALS.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/GLPR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/GNTR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/HNS.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/ICLR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/IHF.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/ISCR1.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/ISCR3.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/LEXA.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/Lrp.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/MALT.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/MARA.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/MELR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/MLC.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/MODE.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/MetJ.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/MetR1.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/NAC.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/NAGC_new2.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/NANR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/NARL2.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/NARP.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/NTRC.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/NarL.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/OmpR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/OxyR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/PHOB.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/PHOP.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/PurR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/ROB.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/RcsB_1core.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/RcsB_2core.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/Rob2.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/TORR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/TRPR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/TyrR.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/fis_new1.sitecon.gz -%%DATADIR%%/sitecon_models/prokaryotic/soxS.sitecon.gz -%%DATADIR%%/snp_scripts/SNPChIPTools.py -%%DATADIR%%/snp_scripts/pdb_uniprot_chain_map.lst.2 -%%DATADIR%%/snp_scripts/protstability1d.py -%%DATADIR%%/snp_scripts/protstability3d.py -%%DATADIR%%/snp_scripts/rsnp.py -%%DATADIR%%/snp_scripts/snp2pdbsite.py -%%DATADIR%%/snp_scripts/update_d_db.py -%%DATADIR%%/translations.txt -%%DATADIR%%/weight_matrix/blosum100.txt -%%DATADIR%%/weight_matrix/blosum30.txt -%%DATADIR%%/weight_matrix/blosum35.txt -%%DATADIR%%/weight_matrix/blosum40.txt -%%DATADIR%%/weight_matrix/blosum45.txt -%%DATADIR%%/weight_matrix/blosum50.txt -%%DATADIR%%/weight_matrix/blosum55.txt -%%DATADIR%%/weight_matrix/blosum60.txt -%%DATADIR%%/weight_matrix/blosum62.txt -%%DATADIR%%/weight_matrix/blosum65.txt -%%DATADIR%%/weight_matrix/blosum70.txt -%%DATADIR%%/weight_matrix/blosum75.txt -%%DATADIR%%/weight_matrix/blosum80.txt -%%DATADIR%%/weight_matrix/blosum85.txt -%%DATADIR%%/weight_matrix/blosum90.txt -%%DATADIR%%/weight_matrix/blosumn.txt -%%DATADIR%%/weight_matrix/dayhoff.txt -%%DATADIR%%/weight_matrix/dna.txt -%%DATADIR%%/weight_matrix/gonnet.txt -%%DATADIR%%/weight_matrix/identity.txt -%%DATADIR%%/weight_matrix/match.txt -%%DATADIR%%/weight_matrix/md_10.txt -%%DATADIR%%/weight_matrix/md_20.txt -%%DATADIR%%/weight_matrix/md_40.txt -%%DATADIR%%/weight_matrix/nuc.4.4.txt -%%DATADIR%%/weight_matrix/pam10.txt -%%DATADIR%%/weight_matrix/pam100.txt -%%DATADIR%%/weight_matrix/pam110.txt -%%DATADIR%%/weight_matrix/pam120.cdi.txt -%%DATADIR%%/weight_matrix/pam120.txt -%%DATADIR%%/weight_matrix/pam130.txt -%%DATADIR%%/weight_matrix/pam140.txt -%%DATADIR%%/weight_matrix/pam150.txt -%%DATADIR%%/weight_matrix/pam160.cdi.txt -%%DATADIR%%/weight_matrix/pam160.txt -%%DATADIR%%/weight_matrix/pam170.txt -%%DATADIR%%/weight_matrix/pam180.txt -%%DATADIR%%/weight_matrix/pam190.txt -%%DATADIR%%/weight_matrix/pam20.txt -%%DATADIR%%/weight_matrix/pam200.cdi.txt -%%DATADIR%%/weight_matrix/pam200.txt -%%DATADIR%%/weight_matrix/pam210.txt -%%DATADIR%%/weight_matrix/pam220.txt -%%DATADIR%%/weight_matrix/pam230.txt -%%DATADIR%%/weight_matrix/pam240.txt -%%DATADIR%%/weight_matrix/pam250.cdi.txt -%%DATADIR%%/weight_matrix/pam250.txt -%%DATADIR%%/weight_matrix/pam260.txt -%%DATADIR%%/weight_matrix/pam270.txt -%%DATADIR%%/weight_matrix/pam280.txt -%%DATADIR%%/weight_matrix/pam290.txt -%%DATADIR%%/weight_matrix/pam30.txt -%%DATADIR%%/weight_matrix/pam300.txt -%%DATADIR%%/weight_matrix/pam310.txt -%%DATADIR%%/weight_matrix/pam320.txt -%%DATADIR%%/weight_matrix/pam330.txt -%%DATADIR%%/weight_matrix/pam340.txt -%%DATADIR%%/weight_matrix/pam350.txt -%%DATADIR%%/weight_matrix/pam360.txt -%%DATADIR%%/weight_matrix/pam370.txt -%%DATADIR%%/weight_matrix/pam380.txt -%%DATADIR%%/weight_matrix/pam390.txt -%%DATADIR%%/weight_matrix/pam40.cdi.txt -%%DATADIR%%/weight_matrix/pam40.txt -%%DATADIR%%/weight_matrix/pam400.txt -%%DATADIR%%/weight_matrix/pam410.txt -%%DATADIR%%/weight_matrix/pam420.txt -%%DATADIR%%/weight_matrix/pam430.txt -%%DATADIR%%/weight_matrix/pam440.txt -%%DATADIR%%/weight_matrix/pam450.txt -%%DATADIR%%/weight_matrix/pam460.txt -%%DATADIR%%/weight_matrix/pam470.txt -%%DATADIR%%/weight_matrix/pam480.txt -%%DATADIR%%/weight_matrix/pam490.txt -%%DATADIR%%/weight_matrix/pam50.txt -%%DATADIR%%/weight_matrix/pam500.txt -%%DATADIR%%/weight_matrix/pam60.txt -%%DATADIR%%/weight_matrix/pam70.txt -%%DATADIR%%/weight_matrix/pam80.cdi.txt -%%DATADIR%%/weight_matrix/pam80.txt -%%DATADIR%%/weight_matrix/pam90.txt -%%DATADIR%%/weight_matrix/rna.txt -%%DATADIR%%/weight_matrix/vtml160.txt -%%DATADIR%%/weight_matrix/vtml200.txt -%%DATADIR%%/workflow_samples/Alignment/basic_align.uwl -%%DATADIR%%/workflow_samples/Alignment/extract_msa_consensus_as_seq.uwl -%%DATADIR%%/workflow_samples/Alignment/extract_msa_consensus_as_text.uwl -%%DATADIR%%/workflow_samples/Conversions/faqual2fastq.uwl -%%DATADIR%%/workflow_samples/Conversions/msa2clustal.uwl -%%DATADIR%%/workflow_samples/Conversions/query2alignment.uwl -%%DATADIR%%/workflow_samples/Conversions/seq2gen.uwl -%%DATADIR%%/workflow_samples/Custom elements/casava-fastq-filter.uwl -%%DATADIR%%/workflow_samples/Custom elements/fastq-trimmer.uwl -%%DATADIR%%/workflow_samples/Custom elements/script-dump-sequence-info.uwl -%%DATADIR%%/workflow_samples/Custom elements/script-linkdata-fetch-seq.uwl -%%DATADIR%%/workflow_samples/Custom elements/script-quality-filter.uwl -%%DATADIR%%/workflow_samples/Data marking/annotation_marker.uwl -%%DATADIR%%/workflow_samples/Data marking/length_marker.uwl -%%DATADIR%%/workflow_samples/Data merging/find-substrings.uwl -%%DATADIR%%/workflow_samples/Data merging/merge-sequence.uwl -%%DATADIR%%/workflow_samples/Data merging/tfbs.uwl -%%DATADIR%%/workflow_samples/HMMER/build-test-HMM.uwl -%%DATADIR%%/workflow_samples/HMMER/searchHMM.uwl -%%DATADIR%%/workflow_samples/NGS/chipseq_coverage.uwl -%%DATADIR%%/workflow_samples/NGS/cistrome.uwl -%%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq.uwl -%%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq_with_control.uwl -%%DATADIR%%/workflow_samples/NGS/consensus.uwl -%%DATADIR%%/workflow_samples/NGS/extract_coverage.uwl -%%DATADIR%%/workflow_samples/NGS/extract_transcript_seq.uwl -%%DATADIR%%/workflow_samples/NGS/fastqc.uwl -%%DATADIR%%/workflow_samples/NGS/from_tools_menu_only/ngs_assembly.uwl -%%DATADIR%%/workflow_samples/NGS/from_tools_menu_only/ngs_classification.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_pe.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_pe_nanopore.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_se.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_paired.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_single.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_paired.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_single.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_paired.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_single.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_classification_de_novo.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_classification_parallel.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_classification_serial.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_transcriptomics_tophat_stringtie.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_transcriptomics_tuxedo.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_variant_annotation.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_variant_calling.uwl -%%DATADIR%%/workflow_samples/NGS/ngs_variant_calling_full.uwl -%%DATADIR%%/workflow_samples/NGS/raw_chip.uwl -%%DATADIR%%/workflow_samples/NGS/raw_dna.uwl -%%DATADIR%%/workflow_samples/NGS/raw_ngs/chipseq/chipseq_paired.uwl -%%DATADIR%%/workflow_samples/NGS/raw_ngs/chipseq/chipseq_single.uwl -%%DATADIR%%/workflow_samples/NGS/raw_ngs/dnaseq/dna_paired.uwl -%%DATADIR%%/workflow_samples/NGS/raw_ngs/dnaseq/dna_single.uwl -%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_paired.uwl -%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_single.uwl -%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_paired.uwl -%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_single.uwl -%%DATADIR%%/workflow_samples/NGS/raw_rna.uwl -%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main.uwl -%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main_paired.uwl -%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr.uwl -%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr_paired.uwl -%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl -%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl -%%DATADIR%%/workflow_samples/NGS/unmapped_reads.uwl -%%DATADIR%%/workflow_samples/Sanger sequencing/trim-and-align.uwl -%%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl -%%DATADIR%%/workflow_samples/Scenarios/find_inverted_repeats.uwl -%%DATADIR%%/workflow_samples/Scenarios/find_sequences.uwl -%%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl -%%DATADIR%%/workflow_samples/Scenarios/group_primers_pairs.uwl -%%DATADIR%%/workflow_samples/Scenarios/intersect_annotations.uwl -%%DATADIR%%/workflow_samples/Scenarios/length_filter.uwl -%%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl -%%DATADIR%%/workflow_samples/Scenarios/pcr.uwl -%%DATADIR%%/workflow_samples/Scenarios/remote_blasting.uwl -%%DATADIR%%/workflow_samples/Scenarios/translate_seq_and_compl.uwl -%%DATADIR%%/workflow_samples/Transcriptomics/SearchTFBS.uwl -%%DATADIR%%/workflow_samples/users/CASAVA FASTQ filter.usa -%%DATADIR%%/workflow_samples/users/Dump sequence info.usa -%%DATADIR%%/workflow_samples/users/FASTQ Trimmer.usa -%%DATADIR%%/workflow_samples/users/Get the first half of sequence.usa -%%DATADIR%%/workflow_samples/users/Get the second half of sequence.usa -%%DATADIR%%/workflow_samples/users/LengthMarker.usa -%%DATADIR%%/workflow_samples/users/LinkData Fetch.usa -%%DATADIR%%/workflow_samples/users/QualityFilter.usa -%%DATADIR%%/workflow_samples/users/Read one sequence.usa