# HG changeset patch
# User dave
# Date 1594411540 14400
# Node ID d38f317fa9d422869f2e70c99888fe0766da2a5a
Uploaded
diff -r 000000000000 -r d38f317fa9d4 interval2maf.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/interval2maf.py Fri Jul 10 16:05:40 2020 -0400
@@ -0,0 +1,145 @@
+#!/usr/bin/env python
+"""
+Reads a list of intervals and a maf. Produces a new maf containing the
+blocks or parts of blocks in the original that overlapped the intervals.
+
+If a MAF file, not UID, is provided the MAF file is indexed before being processed.
+
+NOTE: If two intervals overlap the same block it will be written twice.
+
+usage: %prog maf_file [options]
+ -d, --dbkey=d: Database key, ie hg17
+ -c, --chromCol=c: Column of Chr
+ -s, --startCol=s: Column of Start
+ -e, --endCol=e: Column of End
+ -S, --strandCol=S: Column of Strand
+ -t, --mafType=t: Type of MAF source to use
+ -m, --mafFile=m: Path of source MAF file, if not using cached version
+ -I, --mafIndex=I: Path of precomputed source MAF file index, if not using cached version
+ -i, --interval_file=i: Input interval file
+ -o, --output_file=o: Output MAF file
+ -p, --species=p: Species to include in output
+ -P, --split_blocks_by_species=P: Split blocks by species
+ -r, --remove_all_gap_columns=r: Remove all Gap columns
+ -l, --indexLocation=l: Override default maf_index.loc file
+ -z, --mafIndexFile=z: Directory of local maf index file ( maf_index.loc or maf_pairwise.loc )
+"""
+# Dan Blankenberg
+from __future__ import print_function
+
+import bx.align.maf
+import bx.intervals.io
+from bx.cookbook import doc_optparse
+
+from galaxy.tools.util import maf_utilities
+
+
+def __main__():
+ index = index_filename = None
+
+ # Parse Command Line
+ options, args = doc_optparse.parse(__doc__)
+
+ if options.dbkey:
+ dbkey = options.dbkey
+ else:
+ dbkey = None
+ if dbkey in [None, "?"]:
+ maf_utilities.tool_fail("You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file.")
+
+ species = maf_utilities.parse_species_option(options.species)
+
+ if options.chromCol:
+ chromCol = int(options.chromCol) - 1
+ else:
+ maf_utilities.tool_fail("Chromosome column not set, click the pencil icon in the history item to set the metadata attributes.")
+
+ if options.startCol:
+ startCol = int(options.startCol) - 1
+ else:
+ maf_utilities.tool_fail("Start column not set, click the pencil icon in the history item to set the metadata attributes.")
+
+ if options.endCol:
+ endCol = int(options.endCol) - 1
+ else:
+ maf_utilities.tool_fail("End column not set, click the pencil icon in the history item to set the metadata attributes.")
+
+ if options.strandCol:
+ strandCol = int(options.strandCol) - 1
+ else:
+ strandCol = -1
+
+ if options.interval_file:
+ interval_file = options.interval_file
+ else:
+ maf_utilities.tool_fail("Input interval file has not been specified.")
+
+ if options.output_file:
+ output_file = options.output_file
+ else:
+ maf_utilities.tool_fail("Output file has not been specified.")
+
+ split_blocks_by_species = remove_all_gap_columns = False
+ if options.split_blocks_by_species and options.split_blocks_by_species == 'split_blocks_by_species':
+ split_blocks_by_species = True
+ if options.remove_all_gap_columns and options.remove_all_gap_columns == 'remove_all_gap_columns':
+ remove_all_gap_columns = True
+ else:
+ remove_all_gap_columns = True
+ # Finish parsing command line
+
+ # Open indexed access to MAFs
+ if options.mafType:
+ if options.indexLocation:
+ index = maf_utilities.maf_index_by_uid(options.mafType, options.indexLocation)
+ else:
+ index = maf_utilities.maf_index_by_uid(options.mafType, options.mafIndexFile)
+ if index is None:
+ maf_utilities.tool_fail("The MAF source specified (%s) appears to be invalid." % (options.mafType))
+ elif options.mafFile:
+ index, index_filename = maf_utilities.open_or_build_maf_index(options.mafFile, options.mafIndex, species=[dbkey])
+ if index is None:
+ maf_utilities.tool_fail("Your MAF file appears to be malformed.")
+ else:
+ maf_utilities.tool_fail("Desired source MAF type has not been specified.")
+
+ # Create MAF writter
+ out = bx.align.maf.Writer(open(output_file, "w"))
+
+ # Iterate over input regions
+ num_blocks = 0
+ num_regions = None
+ for num_regions, region in enumerate(bx.intervals.io.NiceReaderWrapper(open(interval_file, 'r'), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False)):
+ src = maf_utilities.src_merge(dbkey, region.chrom)
+ for block in index.get_as_iterator(src, region.start, region.end):
+ if split_blocks_by_species:
+ blocks = [new_block for new_block in maf_utilities.iter_blocks_split_by_species(block) if maf_utilities.component_overlaps_region(new_block.get_component_by_src_start(dbkey), region)]
+ else:
+ blocks = [block]
+ for block in blocks:
+ block = maf_utilities.chop_block_by_region(block, src, region)
+ if block is not None:
+ if species is not None:
+ block = block.limit_to_species(species)
+ block = maf_utilities.orient_block_by_region(block, src, region)
+ if remove_all_gap_columns:
+ block.remove_all_gap_columns()
+ out.write(block)
+ num_blocks += 1
+
+ # Close output MAF
+ out.close()
+
+ # remove index file if created during run
+ maf_utilities.remove_temp_index_file(index_filename)
+
+ if num_blocks:
+ print("%i MAF blocks extracted for %i regions." % (num_blocks, (num_regions + 1)))
+ elif num_regions is not None:
+ print("No MAF blocks could be extracted for %i regions." % (num_regions + 1))
+ else:
+ print("No valid regions have been provided.")
+
+
+if __name__ == "__main__":
+ __main__()
diff -r 000000000000 -r d38f317fa9d4 interval2maf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/interval2maf.xml Fri Jul 10 16:05:40 2020 -0400
@@ -0,0 +1,290 @@
+
+ given a set of genomic intervals
+
+ macros.xml
+
+
+python '$__tool_directory__/interval2maf.py' --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol}
+#if $maf_source_type.maf_source == "user"
+ --mafFile='$maf_source_type.mafFile' --mafIndex='$maf_source_type.mafFile.metadata.maf_index'
+#else
+ --mafType='$maf_source_type.mafType'
+#end if
+--interval_file='$input1' --output_file='$out_file1' --mafIndexFile='${GALAXY_DATA_INDEX_DIR}/maf_indexes.loc' --species=$maf_source_type.species --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species
+#if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species"
+ --remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns
+#end if
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+**What it does**
+
+This tool takes genomic coordinates, superimposes them on multiple alignments (in MAF format) stored on the Galaxy site or from your history, and excises alignment blocks corresponding to each set of coordinates. Alignment blocks that extend past START and/or END positions of an interval are trimmed. Note that a single genomic interval may correspond to two or more alignment blocks.
+
+-----
+
+**Example**
+
+Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval:
+
+.. image:: ${static_path}/images/maf_icons/interval2maf.png
+
+-------
+
+**Split blocks by species**
+
+This option examines each MAF block for multiple occurrences of a species in a single block. When this occurs, a block is split into multiple blocks where every combination of one sequence per species per block is represented.
+
+The interface for this option has two inputs:
+
+ * **MAF file to split**. Choose multiple alignments from history to be split by species.
+ * **Collapse empty alignment columns**. Should alignment columns containing only gaps in the new blocks be removed.
+
+**Example 1**: **Collapse empty alignment columns is Yes**:
+
+For the following alignment::
+
+ ##maf version=1
+ a score=2047408.0
+ s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+the tool will create **a single** history item containing 12 alignment blocks (notice that no columns contain only gaps)::
+
+ ##maf version=1
+ a score=2047408.0
+ s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT-GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC--GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC-GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTAG
+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGCAG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCAG
+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC---AG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC---AG
+
+**Example 2**: **Collapse empty alignment columns is No**:
+
+For the following alignment::
+
+ ##maf version=1
+ a score=2047408.0
+ s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+the tool will create **a single** history item containing 12 alignment blocks (notice that some columns contain only gaps)::
+
+ ##maf version=1
+ a score=2047408.0
+ s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+ a score=2047408.0
+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+
+
diff -r 000000000000 -r d38f317fa9d4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Jul 10 16:05:40 2020 -0400
@@ -0,0 +1,7 @@
+
+
+
+ 10.1093/bioinformatics/btr398
+
+
+
diff -r 000000000000 -r d38f317fa9d4 test-data/1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.bed Fri Jul 10 16:05:40 2020 -0400
@@ -0,0 +1,65 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 -
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 +
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 -
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 -
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 +
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 -
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 -
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 +
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 +
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 -
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 +
+chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 -
+chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 +
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 -
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 +
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 +
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 +
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 -
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
+chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 -
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 +
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 +
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 -
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 +
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 -
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -
diff -r 000000000000 -r d38f317fa9d4 test-data/chrM.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM.maf Fri Jul 10 16:05:40 2020 -0400
@@ -0,0 +1,1323 @@
+##maf version=1 scoring=multiz.v7
+# multiz.v7 R=10 M=0 /cluster/bluearc/hg17/multiz.2004-07-13/danRer1/chrM.maf /cluster/bluearc/hg17/multiz.2004-07-13/panTro1mm5rn3canFam1galGal2fr1/chrM.maf -
+# multiz.v7 R=10 M=0 /cluster/bluearc/hg17/multiz.2004-07-13/fr1/chrM.maf /cluster/bluearc/hg17/multiz.2004-07-13/panTro1mm5rn3canFam1galGal2/chrM.maf -
+# multiz.v7 R=10 M=0 /cluster/bluearc/hg17/multiz.2004-07-13/galGal2/chrM.maf /cluster/bluearc/hg17/multiz.2004-07-13/panTro1mm5rn3canFam1/chrM.maf -
+# multiz.v7 R=10 M=0 /cluster/bluearc/hg17/multiz.2004-07-13/canFam1/chrM.maf /cluster/bluearc/hg17/multiz.2004-07-13/panTro1mm5rn3/chrM.maf -
+# multiz.v7 R=10 M=0 /cluster/bluearc/hg17/multiz.2004-07-13/rn3/chrM.maf /cluster/bluearc/hg17/multiz.2004-07-13/panTro1mm5/chrM.maf -
+# multiz.v7 R=10 M=0 /cluster/bluearc/hg17/multiz.2004-07-13/mm5/chrM.maf /cluster/bluearc/hg17/multiz.2004-07-13/panTro1/chrM.maf -
+a score=373.0
+s hg17.chrM 10 4 + 16571 CTAT
+s mm5.chrUn_random 29351899 4 + 102265694 CTAT
+
+a score=8367.0
+s hg17.chrM 14 46 + 16571 CACCCTATTAACCACTCACGGGAG--CTCTCCATGCATTTGGTATTTT
+s panTro1.chr13 3552480 47 + 134309081 CACCCTATTAACCAGTCACGGGAGGACTGT-CATGCATTTGGTATTTT
+s mm5.chrUn_random 29351903 47 + 102265694 CACTCTATTAACCAGTCATGGGAGCATGAT-CATGAATTTGGTATTTT
+
+a score=11228.0
+s hg17.chrM 60 133 + 16571 ---CGTCTGGGGGGTGTGCACGCGAT-----AGCATTGCGAGACGCTGGAGCC-----GGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATTCTATTATTTA--TCGCACCTACGTTCAATATTACAGGCGAACATA
+s panTro1.chr6 29890008 133 + 161576975 ---CGTCTGGGGGGTGTGCACGCGAT-----AGCATTGCGAAACGCTGGCCCC-----GGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCCCATTCCATTATTTA--TCGCACCTACGTTCAATATTACGAGCGAGCATG
+s mm5.chrUn_random 29351950 137 + 102265694 TAACTTTTAGGA-------ATGCTATCACTCACCATTGCAGAAGGCCTGGTCCCCTCTGAATCAGC---TGTAGACGAACTCGGATTGGATTTCTGCCAAA-TCAATTGTAGAAGCTGAGCTTATATTGAATATTCTAACCTCGCATA
+
+a score=-296.0
+s hg17.chrM 193 11 + 16571 CCTACTAAAGT
+s panTro1.chr6 29890141 11 + 161576975 TTAACCAAGGT
+s mm5.chrUn_random 29352087 11 + 102265694 ACAACCATAAG
+s galGal2.chrM 851 11 + 16775 CCCGGTAAATG
+
+a score=311.0
+s hg17.chrM 204 2 + 16571 GT
+s mm5.chrUn_random 29352098 2 + 102265694 AT
+s galGal2.chrM 862 2 + 16775 GT
+
+a score=9848.0
+s hg17.chrM 206 33 + 16571 GTTAATTAATTAATGCTTGTAGGACATAATAAT
+s panTro1.chr13 3552675 33 + 134309081 GTTAATTAATTCATGCTTGAAAGACATAACAAT
+s mm5.chrUn_random 29352100 29 + 102265694 ----GTTAATTCATGCTTGAAGGACATAATAAT
+s galGal2.chrM 864 33 + 16775 GCTATTTAGTGAATGCTTGTCGGACATATTTTT
+
+a score=5.0
+s hg17.chrM 239 2 + 16571 AA
+s panTro1.chr6 29890187 2 + 161576975 AG
+s galGal2.chrM 897 2 + 16775 AT
+
+a score=-369.0
+s hg17.chrM 239 2 + 16571 AA-
+s galGal2.chrM 897 2 + 16775 -AT
+
+a score=1146.0
+s hg17.chrM 241 2 + 16571 CA
+s panTro1.chr6 29890189 2 + 161576975 CA
+s mm5.chrUn_random 29352129 2 + 102265694 CA
+s galGal2.chrM 899 2 + 16775 CA
+
+a score=-73.0
+s hg17.chrM 243 16 + 16571 ATTGA-ATGTCTGCACA
+s mm5.chrUn_random 29352131 17 + 102265694 ATAGACACATATGCACA
+s galGal2.chrM 901 9 + 16775 --------ATTTTCACT
+
+a score=-48.0
+s hg17.chrM 259 14 + 16571 ---GCCGCTTTCCACAC
+s panTro1.chr6 29890206 14 + 161576975 ---GCCGCTTTTCACAC
+s mm5.chrUn_random 29352148 7 + 102265694 ----------ATCACCT
+s galGal2.chrM 910 17 + 16775 TCCTCTATTTTCTTCAC
+
+a score=-3812.0
+s hg17.chrM 273 28 + 16571 AGACATCATAACAAAAAA----------TTTCCACCAA
+s panTro1.chr6 29890220 27 + 161576975 CAACATCATAACAAAAA-----------TTTCCGCAAA
+s mm5.chrUn_random 29352155 38 + 102265694 ACCCTTATTTTCAAGAACTATTTATGATTTAACTCACA
+s canFam1.chrX 31796412 23 - 126913094 AGACATTATATTAACTAA---------------ACCAA
+s galGal2.chrM 927 22 + 16775 ------AAAACTAGGAAA----------TTCACCACAA
+
+a score=1590.0
+s hg17.chrM 301 35 + 16571 ACCCCCCCCTCCCCCCGCTTCTGGCCACAGCAC--------TT
+s panTro1.chr6 29890247 33 + 161576975 GCCCCCC--TCCCCCCACTTCTGGCCACAGCAC--------TC
+s mm5.chrUn_random 29352193 39 + 102265694 ACCCCCC----CCAACATCTCTGACTTTATCATGGACATAGGT
+s canFam1.chrX 31796435 33 - 126913094 ACCCCCTCTACCCCCCA--TAAACTTATATTAT--------TT
+
+a score=-6005.0
+s hg17.chrM 336 91 + 16571 A-AACACATCT--------------CTGCCAAACCCCAAAAA-CAAAGAAC-----CCTA---ACAC-CAGCCT-----AACCAGATTTC--AAATTTTAT---CTTTAGGC-GGTATGCACTTTTA
+s panTro1.chr6 29890280 92 + 161576975 A-AACACATCT--------------CTGCCAAACCCCAAAAAATAAAGAAC-----CCTA---ACAT-CAGCCC-----AACCAGATCTC--AAATTTCAT---CTTTTGGC-GGTATGCACTTTTA
+s mm5.chrUn_random 29352232 86 + 102265694 A-AATATGCAC--------------TTGTGAAAACCCCAAGA-----GA--------CTA---AAATGCAACCC-----AGTCAGAGCCCAAAAAAGTTAT---ATTTTAAT-CATGAATA-TCCCA
+s canFam1.chrX 31796468 112 - 126913094 ACAATATACCTATTTGTTTTGTGTCCCGCCAAACCCCAAAAA--CAGGA--------CTAAGTAAATGTAGCACTCATAAGCCATGTCT---AAATTTCATACGATTATAAC-TCTAGTTA-ATTTA
+s galGal2.chrM 988 96 + 16775 A-AAAACATTT--------------TTTAAAAAACTAAATTACATACAAACTACCGCATA---AAAT-CCCTCA-----AACTATACA----AACGTTTAT---CGTATAATATATATACATTATTG
+
+a score=583.0
+s hg17.chrM 427 38 + 16571 ACAGTCACCCCCCAACTAACACATTATTTTCCC-----CTCCC
+s panTro1.chr6 29890372 35 + 161576975 ACAGTCACCCCTCAACTAACATATCAT---CCC-----CCTCA
+s mm5.chrUn_random 29352318 43 + 102265694 ACAACTACCCCTTGATTGATATAAAATTTTCCCAAAAATCTCA
+s canFam1.chrX 31796580 15 - 126913094 ACA-----------------AAATAAT-----------TTCCT
+
+a score=-3742.0
+s hg17.chrM 465 34 + 16571 A-----CTCCCATA-----CTACTAATCTC---ATCAATACAACCCC----
+s panTro1.chr6 29890407 34 + 161576975 A-----CTCCTATT-----CTACTAGTCCC---ACCAATGCAACCCC----
+s mm5.chrUn_random 29352361 44 + 102265694 AGATATCTACCAAATAAGCCTCCATATCTA---ATAAATACAGTAAC----
+s canFam1.chrX 31796595 37 - 126913094 A-----CGCCTAAA-----TCTGCAATCTATCTATAGATAGGACTTC----
+s galGal2.chrM 1107 38 + 16775 A-----CTCCACTA-----CCAAAACCATC---ATTAAAACAAAAATTTAC
+
+a score=-3187.0
+s hg17.chrM 499 23 + 16571 C----GCCCATCCTA--CCCAGCACACAC
+s panTro1.chr6 29890441 24 + 161576975 C---TACCCACCCTA--CCCAGCACAGAC
+s mm5.chrUn_random 29352405 23 + 102265694 TAGATTTTCACCCTAATACTAGT------
+s canFam1.chrX 93613525 23 + 126913094 ----CACCCCTTCCA--TTCAACTCACAA
+s galGal2.chrM 1145 23 + 16775 ----ATGCCACTTAA--CTCCCCTCACAA
+
+a score=-6370.0
+s hg17.chrM 522 50 + 16571 ACACCGCTGC-----TAACCCC------------------------ATACCCCGAACCAACCAAACCCCA-------AAGACACCC--
+s panTro1.chr9 125919315 50 - 136640551 ACACCGCTGC-----TAGCCCC------------------------ATACCCCGAGCCAACCAAACCCCA-------AAGACACCC--
+s mm5.chrUn_random 29352428 83 + 102265694 ATAATGCCTTGAATATAACCCTTTGAAAGCACTACCCTAGTGCATGACACTCTAAATCAACTATTCCCTAA---TATAAGAAACCC--
+s canFam1.chrX 93613548 52 + 126913094 ----------AAATCCAATCCC------------------------ACATTCTCATCAACATAATATATAACACCATAAAACACCT--
+s galGal2.chrM 1168 45 + 16775 --ACAATCGT-----TATTT--------------------------ATATTGTTAATTAGCAAACAC----------AAAACCCGCCT
+
+a score=345.0
+s hg17.chrM 572 3 + 16571 CCC
+s panTro1.chr9 125919365 3 - 136640551 CAT
+s mm5.chrUn_random 29352511 3 + 102265694 CCT
+s galGal2.chrM 1213 3 + 16775 TCT
+
+a score=91.0
+s hg17.chrM 575 1 + 16571 A
+s galGal2.chrM 1216 1 + 16775 A
+
+a score=-31.0
+s hg17.chrM 575 1 + 16571 A
+s mm5.chrUn_random 29352629 1 + 102265694 G
+
+a score=91.0
+s hg17.chrM 575 1 + 16571 A
+s panTro1.chr9 125919368 1 - 136640551 A
+
+a score=531.0
+s hg17.chrM 576 2 + 16571 CA
+s panTro1.chr9 31868387 2 - 136640551 CA
+s mm5.chrUn_random 29352630 2 + 102265694 CA
+s galGal2.chrM 1217 2 + 16775 CC
+
+a score=1627.0
+s hg17.chrM 578 4 + 16571 GTTT
+s panTro1.chr9 31868389 4 - 136640551 GTTA
+s mm5.chrUn_random 29352632 4 + 102265694 GTTA
+s galGal2.chrM 1219 4 + 16775 ACTA
+s fr1.chrUn 320907090 4 + 349519338 GCTA
+
+a score=11543.0
+s hg17.chrM 582 12 + 16571 ATGTAGCTTACC
+s panTro1.chr9 31868393 12 - 136640551 ATGTAGCTTAAT
+s mm5.chrM 4 12 + 16299 ATGTAGCTTAAT
+s canFam1.chrM 4 12 + 16727 ATGTAGCTTAAT
+s galGal2.chrM 1231 12 + 16775 CCATAGCTTAAC
+s fr1.chrUn 320907094 12 + 349519338 GCGTAGCTTAAC
+
+a score=-20.0
+s hg17.chrM 594 5 + 16571 TCCTC
+s fr1.chrUn 320907106 1 + 349519338 ----C
+
+a score=-3855.0
+s hg17.chrM 594 4 + 16571 TCCT
+s panTro1.chr9 31868405 4 - 136640551 TATT
+s mm5.chrM 16 2 + 16299 AA--
+s canFam1.chrM 16 4 + 16727 TAAT
+s galGal2.chrM 1243 3 + 16775 CCA-
+
+a score=0.0
+s hg17.chrM 598 1 + 16571 C
+
+a score=38.0
+s hg17.chrM 598 1 + 16571 C
+s panTro1.chr9 31868409 1 - 136640551 T
+s mm5.chrM 18 1 + 16299 C
+
+a score=100.0
+s hg17.chrM 598 1 + 16571 C
+s galGal2.chrM 1246 1 + 16775 C
+
+a score=34712.0
+s hg17.chrM 599 43 + 16571 AAAGCAATACACTGAAAATGTTTAGACGGGCT----CACATCACCCC
+s panTro1.chr9 31868410 43 - 136640551 AAAGCAAGACACTGAAAATGTCTAGATGGGTT--TGCACA--ACCCC
+s mm5.chrM 19 42 + 16299 AAAGCAAAGCACTGAAAATGCTTAGATGGATA--ATTGTA--TCCC-
+s rn3.chr7 48861581 43 - 143082968 AAAGCACAGCACTGAAAATGTTTAGATGAACT-TTTAACA--TCCC-
+s canFam1.chrM 20 42 + 16727 AAAGCAAGGCACTGAAAATGCCAAGATGAGTC---GCACG--ACTCC
+s galGal2.chrM 1247 43 + 16775 AAAGCATGGCACTGAAGATGCCAAGATGGTACCTACTATA--CCT--
+s fr1.chrUn 320907107 44 + 349519338 AAAGCAGAGTACTGAAGATGCTAAGATGGGCCCTGAAAAG--TCCC-
+s danRer1.chrM 968 44 + 16596 AAAGCACGGCACTGAAGCTGCCAAGATGGGCCCTAATAAG--CTCC-
+
+a score=8181.0
+s hg17.chrM 642 9 + 16571 ATAAACAAA
+s panTro1.chr3 35462429 9 - 209662276 ataaacaaa
+s mm5.chrM 61 9 + 16299 ATAAACACA
+s rn3.chr7 48861624 9 - 143082968 ATAAAAAGG
+s canFam1.chrM 62 9 + 16727 ATAAACATA
+s galGal2.chrM 1290 9 + 16775 GTGGGCAAA
+s fr1.chrUn 320907151 9 + 349519338 GCAGGCACA
+s danRer1.chrM 1012 9 + 16596 GCATGCACA
+
+a score=-123.0
+s hg17.chrM 651 1 + 16571 T
+s danRer1.chrM 1021 1 + 16596 A
+
+a score=0.0
+s hg17.chrM 651 1 + 16571 T
+
+a score=-310.0
+s hg17.chrM 651 1 + 16571 T
+s mm5.chrM 70 1 + 16299 A
+s rn3.chr7 48861633 1 - 143082968 T
+s canFam1.chrM 71 1 + 16727 A
+
+a score=-123.0
+s hg17.chrM 651 1 + 16571 T
+s fr1.chrUn 320907160 1 + 349519338 A
+
+a score=58671.0
+s hg17.chrM 652 91 + 16571 AGGTTTGGTCCTAGCCTT-TCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTG------AGTTCACCCTCTAAA--------TCACCACGA-----
+s panTro1.chr3 35462438 80 - 209662276 ----------ctgGCCTT-TTCATTAGCTCTTAGTAGGATTACACATGCAAGCATCCCCACCCCAGTGAAAATGA------CCTCTGGA--------TCACCG-GC-----
+s mm5.chrM 71 88 + 16299 AGGTTTGGTCCTGGCCTT-ATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAA--A------TCCCTTAA--------ACATTT-AC-----
+s rn3.chr18 23098529 91 - 87338544 AGGTTTGGTTCTGACTTTGGTGATTATTTTGAGGTAGATTTACATATGCAAA-ATCACTAAACCATTGTGAA--A------TCCCTTAAAA-----TTCACAT-GG-----
+s canFam1.chrM 72 90 + 16727 AGGTTTGGTCCTAGCCTT-CCTATTAGTTTTTAGTAGACTTACACATGCAAGCCTCCACGCCCCAGTGAGAA--T------GCCCTTAAAA------TCACCA-GT-----
+s galGal2.chrM 1299 94 + 16775 AGACTTAGTCCTAACCTT-TCTATTGGTTTTTGCTAGACATATACATGCAAGTATCCGCATCCCAGTGAAAA--T------GCCCCCAAACCTTTCTTCCCAA--------
+s fr1.chrUn 320907161 88 + 349519338 AAGCTTGGTCCTGACTTT-ACTAACAACTCTGATCAAACTTACACATGCAAGTATCCGCATCCCAGTGAAAA--T------GCCCCCCG--------CCCCCC-GT-----
+s danRer1.chrM 1022 93 + 16596 AGGCATGGTCCCGACCTT-TTGATCAGCTTTTACCTAATTTACACATGCAAGTCTCCGCACCCCTGTGAATA--C------GCCCTCAA--------TCCCCA-AACCTGG
+
+a score=211943.0
+s hg17.chrM 743 295 + 16571 TCAA-----AAGGGACAAG--CATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCT-AGCCACACCCCCACGGG-AAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAAC-CCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAG-AAGC-CGGCGTAAAGAGTGT----TTTAGATC-ACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAAC-TCCAGTT--GACACAAAATAGACT-ACGAAAGTGGCTT--TA
+s panTro1.chr3 35462518 292 - 209662276 TCAA-----AAGGAGCAGG--TATCAAGCATGCACGAATGCAGCTCAAAACACTTTGCTC-AACCATACCCCCAAGGG-AAACAGCAGTGATAAATCCTTAGTAATAAACGAAAGTTTGACCAAGCCATACTAATATTTAGGGTTGGTTAATTTTGTGCCAGCCACTGCGGCCATAAGATTAACTCGAGCTAATAG-AACT-TGGCGTAAAGAGTGT----TTAAGGTCTACCTTC-----AATAAAGCTAAGCTCCATCTAAGCTGTAAAAAAC-TCCAGCT--GACATAAAATATACT-ATGAAAGTGACTT--TA
+s mm5.chrM 159 295 + 16299 TTAAAATTTAAGGAGAGGG--TATCAAGCA--CATTAAAATAGCTTAAGACACCTTGCCT-AGCCACACCCCCACGGG-ACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCT---CTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTA-TCTT-CGGCGTAAAACGTGTCAACTATAAATAAATA--------AATAGAATTAAAATCCAACTTATATGTGAAAATT-CATTGTTAGGACCTAAACTCAATA-ACGAAAGTAATTC--TA
+s rn3.chr7 48861782 267 - 143082968 TTAA-----AAGGGGGGAGATTGTCTAGCATACAGTAA-GTAGCTTCAGAAACCTTGCCT-AGTTTTATCCCTATGGG-ACTCAGC----ATCAGGACTTTG-----------ACTTTGAGTAAGTTATACCT---TTTAGAATTGGTAAACTTCTTGACAGCC-CTGCAGTCATA-GACAAACTCAACTT---------T-TTACATAAAACATGT----TCAAGATATAAACTTT----CATGGAAGTAAAAGCAAATTTATATGTGAAAATT-CATAGTT--GGTTTTAAACCCACTAATGAAAATGATTC--TA
+s canFam1.chrM 164 292 + 16727 TCTA-----AAGGAGCAGG--TATCAAGCACACTCTTAAGTAGCTCATAACACCTTGCTA-AGCCACACCCCCACGGG-ATACAGCAGTGATAAAAATTAAGCCATAAACGAAAGTTTGACTAAGCCATACTA---AATAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATAG-GCCTACGGCGTAAAGCGTGT----TCAAGATACTTTTAC-----ACTAAAGTTAAAACTTAACTAAGCCGTAAAAAGC-TACAGTT--ATCATAAAATAAACC-ACGAAAGTGACTTTATA
+s galGal2.chrM 1393 296 + 16775 GCAA-----AAGGAGCAGG--TATCAGGCACACTCAGCAGTAGCCCAAGACGCCTTGCTTAAGCCACACCCCCACGGGTACTCAGCAGTAATTAACCTTAAGCAATAAGTGTAAACTTGACTTAGCCATAGCAA--CCCAGGGTTGGTAAATCTTGTGCCAGCCACCGCGGTCATACAAGAAACCCAAATCAATAGCTACC-CGGCGTAAAGAGTGG----CCACATGTTATCTGCACCA-GCTAAGATTAAAATGCAACCAAGCTGTCATAAGC-CTAAGATC-CACCTAAACCCAACC---CAAATCCATCT--TA
+s fr1.chrUn 320907252 296 + 349519338 ----GAAATAGGGAGTTGG--TATCAGGCACACAAATTTGTAGCCCATGACACCTAGCTT-TGCCACGCCCCCAAGGGAATTCAGCAGTGATAAACATTAAGCCATAAGTGAAAACTTGACTTAGTCATGATC---TAAAGAGTCGGTAAAACTCGTGCCAGCCACCGCGGTTATACGAGAGACCCAAGTTGTTAG-CCAA-CGGCGTAAAGGGTGG----TTAGAACTAAAAACAACAA-ACTGAGACCGAACACCTTCAAGGCTGTTATACGC-TTCCGAA--GCAACGAAGAACAATAACGAAAGTAGCCT--CA
+s danRer1.chrM 1115 291 + 16596 -----GGACGAGGAGCAGG--TATCAGGCACAAAATTT-TTAGCCCAAGACGCCTAGCCA-AGCCACACCCCCAAGGGGATCCAGCAGTGACAAACATTAAGCTATAAGTGAAAACTTGACTCAGTTAAGGTA---AAGAGAGCCGGTAAAACTCGTGCCAGCAACCGCGGTTAAACGAGAGGCTCTAGTTGATAT-ACTA-CGGCGTAAAGGGTGG----TTAAGGAACAATGTAA----AATAAAGCCAAACGGCCCTTTAACTGTTATACGCTTTTAGAT--GCTAGAGGCCCAAAC-ACGAAAGTAGCTT--TA
+
+a score=156115.0
+s hg17.chrM 1038 167 + 16571 A----------CATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAA-TCAACAAAACTGCTCGCCAGAACACTACGAG--CCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGGAGC
+s panTro1.chr3 35462810 166 - 209662276 A----------TAT-CCTGAAGACACAATAGCTAAAATCCAAACTTGGATTAGATACACCACTATGCTTAGCCCTAAACTCTAATAGTTATA-TTAACAAAACCATTTCCTAGAGTACCACAAG--CAACAGCTTAAAATTCAAAGGACTTGGCGGTGCTTTATATCCCTCTAAAGGAGC
+s mm5.chrM 454 168 + 16299 G---------TCAT-TTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGCCAGAGAACTACTAG--CCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGC
+s rn3.chr7 48862049 149 - 143082968 A----------TTG-ACTCAATACATGGCAGTTAAGATATAAATTAGTACTAAATACCTTACTATGC---------------AGTAATTTAG--CAACAAAA-TAAATGTGGGAGAGTTATTAG--CCACAGCTTAATACTCAAAGGACTTGGAGGGACTTTATATCCACCTAAAGCAGC
+s canFam1.chrM 456 165 + 16727 A----------TAA-TCTGACTACACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACATAGATAATTTTA--CAACAAAATAATTCGCCAGAGGACTACTAG--CAATAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATATCCCTCTAGAGGAGC
+s galGal2.chrM 1689 178 + 16775 GCCTCAACGATTAA-TTTTAACCCACGAAAGCTAGGACCCAAACTGGGATTAGATACCCCACTATGCCTAGCCCTAAATCTAGATACCTCCC-ATCACACATGTATCCGCCTGAGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGCCCCAAACCCACCTAGAGGAGC
+s danRer1.chrM 1406 169 + 16596 -----AATTAATTA-CCTGAACCCACGAAAGCTAAGAAACAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACAAAGACATTTAAT---CACAACAATGTTCGCCCGGACACTACAAG--CATAAGCTTAAAACCCAAAGGACCTGACGGTGCCTTAGATCCCCCTAGAGGAGC
+
+a score=248485.0
+s hg17.chrM 1205 298 + 16571 CTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC----AGCCTATATACCGCCATCTTCAGCAAACC-CTGATGAAGGCTACAAAGTAAGCGCAAGTA-CCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTAC-CCCAGAAAA-C---T--ACGATAGCCC-TTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAGTAGA------GTGCTTAGTTGAACAGGGCCCTG--------------------------------------AAGCGCGTACACACCGCCCGTCACCCTCCTCA
+s panTro1.chr3 35462976 302 - 209662276 CTGTTCTATAATCGATAAACCCTGGTGCTCCTCACCACCTCTTGCCC--CCAGCGTATATACCGCCATCTTCAGCAAACC-CTAA-AAAGGTCACAAAGTAAGTACAAGTA-CACACATAAAAACATTAGGTCAAGGTGTAGCCCATGAGGTGGCACAAAATTGGCTACATTTTCTATGTCCAGAAAATC---T-CACAACAACCT-TTAGGAAATCTAAGGGCTCAAGGAGGATTTAGCAGTAAACCAAGAGCAGA------GTGCTTGGTTGAATAAGGCCATG--------------------------------------AAGCATGCACACACCGCCCGTCACCCTCCTCA
+s mm5.chrM 622 302 + 16299 CTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACC-CTAA-AAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATAAAAGAACA-T---T--ACTATACCCT-TTATGAAACTAAAGGACT-AAGGAGGATTTAGTAGTAAATTAAGAATAGA------GAGCTTAATTGAATTGAGCAATG--------------------------------------AAGTACGCACACACCGCCCGTCACCCTCCTCA
+s rn3.chr7 48862416 326 - 143082968 CTGTT-TATAACCCGTAAACCCCATGTTAACTTACCATC---TGCTAATTTAGCCTATGTACTGATGTCTTCAGTAAACA-CTAA-AACGGAATTGCAGTAAGCAAATGAA-CAATTATAAAAATGTTAGGTTGAGGTGTAGCCTATGGGATGGAAAGTAATAGGCTATATTTTCTCA-ACAAGAACA-CACAT--ATTATTATCT-TTATGAAACTTAAGGAACCAAGGAGGATT------------AAGAATAGA------GAACCTAATTGAATTGAGCAATGACATACACACACACACACACACACACACACACACACACACACACACACACACAGCCTGTCACCTTCCTCA
+s canFam1.chrM 621 303 + 16727 CTGTTCTATAATCGATAAACCCCGATAAACCTCACCACCTTTCGCTAATTCAGTCTATATACCGCCATCTTCAGCAAACC-CTCA-AAAGGTAGAACAGTAAGCACAATCATTTTACATAAAAAAGTTAGGTCAAGGTGTAACTTATGAGGTGGGAAGAAATGGGCTACATTTTCTAC-CCAAGAACA-T---TTCACGAATGTTT-TTATGAAA-TTAAAAACTGAAGGAGGATTTAGTAGTAAATTAAGAATAGA------GAGCTTAATTGAATAGGGCCATG--------------------------------------AAGCACGCACACACCGCCCGTCACCCTCCTCA
+s galGal2.chrM 1867 308 + 16775 CTGTTCTATAATCGATAATCCACGATTCACCCAACCACCCCTTGCCAGCACAGCCTACATACCGCCGTCGCCAGCCCACCTCTAATGAAAGAACAACAGTGAGCTCAATAGCCCCTCGCTAATAAGACAGGTCAAGGTATAGCCTATGGGGTGGGA-GAAATGGGCTACATTTTCTAA-CATAGAACA-A------ACGAAAAAGG-ATGTGAAACCCGCCCTTAGAAGGAGGATTTAGCAGTAAAGTGAGATCATACCCCCTAAGCTCACTTTAAGACGGCTCTG--------------------------------------AGGCACGTACATACCGCCCGTCACCCTCTTCA
+s danRer1.chrM 1575 299 + 16596 CTGTTCTAGAACCGATTATCCCCGTTAAACCTCACCATTTCTAGCAAAATCAGCCTATATACCACCGTCGCCAGCTTACC-CTGT-GAAGGAATAACAGTAAGCAAGATGGGCATAGCCCAGAAAGTCAGGTCGAGGTGTAGCACATGAAATGGGAAGAAATGGGCTACACTTTCTAC-CCCAGAATA-T------ACGAAAATGTAACATGAAAC--AATACTTGAAGGAGGATTTAGCAGTAAAAGAGAAGCAGA------GTGTCTCTTTGAACCCGGCTCTA--------------------------------------AGGCGCGTACACACCGCCCGTCACTCCCTCC-
+
+a score=1049.0
+s hg17.chrM 1503 2 + 16571 AG
+s panTro1.chr3 35463278 2 - 209662276 AA
+s mm5.chrM 924 2 + 16299 AA
+s rn3.chr7 48862742 2 - 143082968 AA
+s canFam1.chrM 924 2 + 16727 AG
+s danRer1.chrM 1874 2 + 16596 GG
+
+a score=69.0
+s hg17.chrM 1503 2 + 16571 AG
+s danRer1.chrM 1874 2 + 16596 GG
+
+a score=273.0
+s hg17.chrM 1505 1 + 16571 T
+s panTro1.chr3 35463280 1 - 209662276 T
+s mm5.chrM 926 1 + 16299 T
+
+a score=-1040.0
+s hg17.chrM 1505 2 + 16571 -TA
+s canFam1.chrM 926 2 + 16727 -TA
+s galGal2.chrM 2175 2 + 16775 -CA
+s danRer1.chrM 1876 2 + 16596 TC-
+
+a score=-196.0
+s hg17.chrM 1506 5 + 16571 ATACT
+s galGal2.chrM 2176 5 + 16775 AAGCC
+s danRer1.chrM 1877 5 + 16596 CAATT
+
+a score=-1173.0
+s hg17.chrM 1506 2 + 16571 -AT
+s panTro1.chr3 35463281 2 - 209662276 -AT
+s galGal2.chrM 2177 1 + 16775 -A-
+s danRer1.chrM 1877 2 + 16596 CA-
+
+a score=-1064.0
+s hg17.chrM 1507 6 + 16571 ---TACTTC
+s galGal2.chrM 2180 3 + 16775 ---CAT---
+s danRer1.chrM 1878 6 + 16596 AATTGC---
+
+a score=-59.0
+s hg17.chrM 1507 4 + 16571 TACT
+s galGal2.chrM 2177 4 + 16775 AGCC
+s danRer1.chrM 1878 4 + 16596 AATT
+
+a score=-3811.0
+s hg17.chrM 1511 2 + 16571 -TC
+s mm5.chrM 927 1 + 16299 --T
+s rn3.chr7 48862744 2 - 143082968 -TT
+s galGal2.chrM 2182 1 + 16775 -T-
+s danRer1.chrM 1882 2 + 16596 GC-
+
+a score=-14425.0
+s hg17.chrM 1513 23 + 16571 AAAGGACAT-------------TTAAC-TAA--AACCCC--
+s mm5.chrM 928 26 + 16299 AAATTAAAC-------------TTAACATAATTAATTTC--
+s rn3.chr7 48862746 23 - 143082968 AAAAAATAT-------------TCT---TTGCCTATATT--
+s canFam1.chrM 928 39 + 16727 ATAAGACACAACCATAACCATATTAACTTAACTAAAACA--
+s galGal2.chrM 2183 21 + 16775 -----------------CAACATCAAT-AAATATATACT--
+s danRer1.chrM 1884 21 + 16596 -------------------ACAAGAAA-TAATTAATACAGA
+
+a score=-271.0
+s hg17.chrM 1536 10 + 16571 TACGCATTTA
+s galGal2.chrM 2208 10 + 16775 CTCCCGGCTA
+s danRer1.chrM 1905 10 + 16596 AGCACAGACA
+
+a score=-3011.0
+s hg17.chrM 1536 9 + 16571 ----TACGCATTT
+s mm5.chrM 954 9 + 16299 ----TAGACATCC
+s rn3.chr7 48862769 9 - 143082968 ----TCAACATTT
+s galGal2.chrM 2206 6 + 16775 -------CCCTCC
+s danRer1.chrM 1905 9 + 16596 AGCACAGAC----
+
+a score=856.0
+s hg17.chrM 1545 4 + 16571 ATAT
+s panTro1.chr3 35463322 4 - 209662276 ATAT
+s mm5.chrM 965 4 + 16299 TTAT
+s rn3.chr7 48862779 2 - 143082968 --AT
+s galGal2.chrM 2215 4 + 16775 CTAA
+
+a score=0.0
+s hg17.chrM 1546 3 + 16571 TAT
+
+a score=-583.0
+s hg17.chrM 1546 3 + 16571 TAT
+s galGal2.chrM 2218 1 + 16775 A--
+
+a score=94180.0
+s hg17.chrM 1549 256 + 16571 AGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACG--AACCAGAGTGTAGCT-TAA---CACAAAGCACCCAACTTA-----CACTTAGGAGAT-----TTCAA-------------CTTAACT--TGACCGCTCTGAGCTAAAC--CTAGCC-------CCAAACCCACTCCACCT---------TACTACCAG--ACAACC---TTAGCCAAACCATTTACCC---AAAT----AA---------AGTATAGGCGATAGAAAT---TGAAACCTGGCGCAATAGA----TATAGTACCGCAAGGGAAAGATGAAA
+s panTro1.chr3 35463326 259 - 209662276 ACAGGAGATAAGTTGCAACATGGTAAGCATACTGGGAAGTGCGCTTGGACA--AACCAAAGTGTAGCT-TAA---ACCAAAGCATCCAGCTTA-----CACCTGGAAGAT-----TTCAT-------------TGTGACC--TGATCACTTTGAGCCAACT--CTAGCC-------CCAAACC---------TCGCTAAAAATACTATTAA--ACTATC---TTAATCAAACGATTTACCTTAGAAA-----AA---------AGTTTAGGCAACAGCAATTTTT--ACCCTGGTGCAATAGA----CATAGTATCATAAGGGAAAGATGAAA
+s mm5.chrM 970 261 + 16299 AGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAAT--AATCATAGTGTAGCT-TAA--TATTAAAGCATCTGGCCTA-----CACCCAGAAGAT-----TTCA----------------TGACCAATGAACACTCTGAACTAATC--CTAGCC-------CTAGCCC---------TACACAAA--TATAATTAT--ACTATTATATAAATCAAAACATTTATCCTACTA------AA---------AGTATTGGAGAAAGAAATTCGTACATCTAGGAGCTATAGA----ACTAGTACCGCAAGGGAAAGATGAAA
+s rn3.chr7 48862782 248 - 143082968 GGAGGCGATGAGCTCTAACATGATAATCGTACTGGAAAGTGTGCTT--------ATCTTAGTATATCA-TAATTTTTAAAAGCATCTGGTCTACCCTCCCCCCAGAAG---------CA-----------------------TGTATGCTCTGAATCAACT--CTAGCA-------TAAAAAC-------CCTAAACTAAAATATATTT----ATTACT---TGAATTAAGTCATTTGGATTAATA------GA---------AATTTTGGTGAGAGAAACTTAT-TTTTTAGGCACTATGGA----AATGGCACCATCA-GGAAAGATGAAA
+s canFam1.chrM 969 258 + 16727 AGAGGAGACAAGTCGTAACAAGGTAAGCATACCGGAAGGTGTGCTTGGATT--AATCAAAGTGTAGCT-TAA----CTAAAGCGTCTGGCCTA-----CACCCAGAAGAT-----TTCA----------------TTACTTATGGCCACTTTGAACAAAAG--CTAGCCCAA----CTAACCC---------CAAACTTAAGTATTACA----GACACA---TAAAATAAAACATTTAGTTAAACAAT---AAA---------AGTATAGGAGATAGAAATTTTA----ATTGGAGCGATAGA----GATAGTACCGTAAGGGAATGATGAAA
+s galGal2.chrM 2219 281 + 16775 AGACGAGGCAAGTCGTAACAAGGTAAGTGTACCGGAAGGTGCACTTAGACT---ACCAAGGCGTAGCTATAA--CTTCAAAGCATTCAGCTTA-----CACCTGAAAGATACC--CTCAACAGACAAGGTCGCCTTGACT--TGCCCCCCCT-----------CTAGCCCGA----CAAACTC---------GTACCCTTAACATA-------AAAAAC---TTACCTCCCCCTCTTAACCAAAACATTATAAA--TTGTCCCAGTATAGGCGATAGAAAAGACT--ACCCCGGCGCAATAGAGGCTAACTGTACCGCAAGGGAAAGATGAAA
+s danRer1.chrM 1915 285 + 16596 AGGGGGGAAAAGTCGTAACAAGGTAAGTGTACCGGAAGGTGCACTTGGACATTATCCAAGACGTGGCT-GAA--CAGTTAAGCATCTCACTTA-----CACCGAGAAAACATCCGTGCA-----------------AATC--GGATCGTCCTGAGCTAAATAGCTAGCTTAACCATCAAGATC---------AACTTAAAAACATCAATAACCTATAAT---CAACCTAAAACCACAAACTAAACCAT----TATATTATCCTAGTATGGGAGACAGAAAAGATA-AAATACTAAGCAATAGA----GAAAGTACCGCAAGGGAACGCTGAAA
+
+a score=152796.0
+s hg17.chrM 1805 245 + 16571 ------------AATTATAACCAAGCA-TAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAA-CCAGACGAGCTACCTAAGAACAG----CTAAAA---GAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCA-AGATA-GAATCTTAGTTCAACTT
+s panTro1.chr3 35463586 243 - 209662276 ------------AACTATA-TCAAGCACTAAAA-AGCAAGGACAAGCCCTTATACTTTCTGCATAATGTATTAACTAGAAATA-CTTTACACAGAAAACTATAGCCAAGTCCCCCAAAA-CCAGATGAGCTACACAAGAATAG----CTGAAA---GAGCACACTCACCTACATGGCAAAATAGTGGGAAGATTCATGAGTAGTGGTGACAAGTCTACCAAGCCTGGTGATAGCTGGTTGTCCA-AGATA-GAATCTTAGTTCAACTT
+s mm5.chrM 1232 245 + 16299 ------------ACTAATT-AAAAGTAAGAACA-AGCAAAGATTAAACCTTGTACCTTTTGCATAATGAACTAACTAGAAAACTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAA-CCAAACGAGCTACCTAAAAACAA----TTTTAT---GAATCAACTCGTCTATGTGGCAAAATAGTGAGAAGATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTTGGTGATAGCTGGTTACCCA-AAAAATGAATTTAAGTTCAATTT
+s canFam1.chrM 1228 246 + 16727 ------------ACATCTT-AACAGTATTAAAC-AGCAAAGATTACCCCTTCTACCTTTTGCATAATGAACTAGCCAGAAACAACTTAACAAAGAGAACTTAAGCTAAGCTCCCCGAAA-CCAGACGAGCTACCCATAAACAAT---CTAAAA---GGATCAACTCATCTATGTAGCAAAATAGTGAGAAGATTTGTGGGTAGAGGTGAAAAGCCTAACGAGCCTGGTGATAGCTGGTTACCCACAGACA-GAATTTTAGTTCAACTT
+s galGal2.chrM 2507 248 + 16775 ------------GAAAACC-ATAAGCAAAAAAC-AGCAAAGACCAACCCTTGTACCTTTTGCATCATGATTTAGCAAGAACAA-CCAAGCAAAGTGAGCTAAAGTTTGCCTTCCCGAAACCCAAGCGAGCTACTTGCGAGCAG----CTAAAATTTGAGCGAACCCGTCTCTGTTGCAAAAGAGCGGGATGACTTGCCAGTAGAGGTGAAAAGCCTACCGAGCTGGGTGATAGCTGGTTACCTG-TCAAACGAATCTAAGTTCCCCCT
+s danRer1.chrM 2200 263 + 16596 GAGAAATGAAATAACCCGT-AAAAGCAATAAAA-AGCAAAGATTAAACCTTGTACCTTTTGCATCATGATTTAGCCAACACCA-CTAGGCAAAGAGACCTTTAGTTTAAAGCCCCGAAT-CCAGGTGAGCTACCCCGAGACAGCCTATTTAACTTAGGGCCAACCCGTCTCTGTGGCAATAGAGTGGGAAGAGCTCCGGGTAGAAGTGACAGACCTATCGAACCCGGCAATAGCTGGTTGTCTG-GGAGATGAATAAAAGTTCAGCTT
+
+a score=2454.0
+s hg17.chrM 2050 19 + 16571 TAAATTTGCCCACAGAA-------CC
+s panTro1.chr3 35463829 17 - 209662276 TAAACTTACCCACAGAA---------
+s mm5.chrM 1477 17 + 16299 TAAACTTGCTAAAAAAA---------
+s canFam1.chrM 1474 17 + 16727 TAAATTTACCtaaaaaa---------
+s galGal2.chrM 2755 26 + 16775 TAACCCACCCCCTAAAGACACCCACC
+
+a score=-424.0
+s hg17.chrM 2069 37 + 16571 CT--CTAAATCCCCTTG---TAAATTTAACTGTTAGTCCAAA
+s panTro1.chr3 35463846 38 - 209662276 -TTACTTAATTTCCCAG---TAAGTTTAACTGTCAGTCTAAA
+s mm5.chrM 1494 38 + 16299 -CAACAAAATCAAAAAG---TAAGTTTAGATTATAGCCAAAA
+s canFam1.chrM 1491 37 + 16727 --aataaaattttaatg---taaatttaaaatataGTCTAAG
+s galGal2.chrM 2781 42 + 16775 TTTGTCAACCTTGAGAACGTTGGGGTTAAGAGCAATTCGATG
+s danRer1.chrM 2499 37 + 16596 --CACAAAATTAAGAGA---AAAATACGAAAGTTAGTTAAAG
+
+a score=163719.0
+s hg17.chrM 2106 463 + 16571 GAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTG-TAGAGAGAGTAA-----AAAAT--------------TTAACACCCATAGTAGGCCTAAAAGCAGCCACCAAT-TAAGAAAGCGTTCAAGCTCA---ACACCCA-CTACCTAAAA----AATCCCAAACATATA----AC-TGAACTCCT-CAC--ACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAA-CATGAA-AAC------ATTCTCCT-CCGCATAAGCCTGCGTCAGATCAAAACACTGA---ACTGACAATTAA-CAG-----------------CCCAATATCTACAATCAAC-----CAACAAGTCATTATTACCCT--------CACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAAC-CTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC--ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACAC---ATGTTTAACG
+s panTro1.chr3 35463884 464 - 209662276 GAGGGACAGCTCTTTAGACCCTAGGAAGCAACCTTCCTACAGAGAGTAA-----AAAATA-------------TTACCACC-ATAGTTGGCCCAAAAGCAACCACCAGT-TAAGAAAGCATTTAAGCTCA---ACATCTAACTATCTTAAATTCTAATC----------ACTCTAC-TGTACTCCT-AAC--ATCACATTGGACTAATCTATTACTTAATAGAAGCAATAATGTTAATATAAGTAA-CATGAA-GAC------ATTCTCCA-TTGCATAAGCTTACATCAGACCAGAATA---ACCCACTGGCAGTTAA-CAG-----------------CCTAATATT---AATAAAC-GATATAATAAGT-------ACCCTATTATTTACACTGTTAACTCAACAAAGGCATGCTC-TAAGGAAAGTTTACAACAAGTAAAAGGAACTCAGCAAAT-CTTACCCTGCCTGTTTACCAAAAACATCACCTCTAGC--ATTACCAGTATTAGAGGCACTGCCTGCCCAGTGACAT---ATGTTCAACT
+s mm5.chrM 1532 472 + 16299 GAGGGACAGCTCTTCTGGAAC--GGAAAAAACCTTT-AATAGTGAATAATTAACAAAACA-----------GCTTTTAACC-ATTGTAGGCCTAAAAGCAGCCACCAAT-AAAGAAAGCGTTCAAGCTCA---ACATAAA---ATTTCAAT---TAATTCCATAATTTAC----AC-CAACTTCCTAAAC--TTAAAATTGGGTTAATCTATAACTTTATAGATGCAACACTGTTAGTATGAGTAA-CAAGAA-TTCC----AATTCTCCA--GGCATACGCGTATAACAACTCGGAT-----AACCATTGTTAGTTAATCAG-----------------ACTATAGGC---AATAATC--ACACTATAAATAATC---CACCTATAACTT-CTCTGTTAACCCAACACCGGAATGCCT-AAAGGAAAGATCCAAAAAGATAAAAGGAACTCGGCAAACAAGAACCCCGCCTGTTTACCAAAAACATCACCTCTAGC--ATTACAAGTATTAGAGGCACTGCCTGCCCAGTGACTA---AAGTTTAACG
+s rn3.chr6 55165806 419 + 147642806 GAAGGGCAGCTCTTTCTAA--TAGGAAATAACTTTA-ATTAGAGAATAA-----AAAAAA----------------------ACAG---------------------------ATATGCATTCAAGGTCA---ACAAACA---ATTTAGAA-----TTCCAGTATTCATG----AG-TAACTTCCTAAAT--TACATATTGGCTTAATCTATAAGGTAGCAGATAAAATTTTATTAAAATTAGTAA-TAAGAA-GAA------ACTCTTCA--TGTGTGAGAACACTTCAAATCAAAT-----ACCCACTGATAATTAAAATG-----------------CCTAGAGAT---AA-------ATTTAATAACACACT---TCTATTTAATT--TATTGTCAACCCTATACAAGAACACAC--AGGGAAAGATTAAAAGAAATGAAAGGAAGTTGGCAATC-AAGAACCCACCTATTCACCAGAAGAGTCTCCTTTGGG--ATTGATAGTATTAGAGGCGCTATATTCCCAGGGTCAG---ACGCTAAATG
+s canFam1.chrM 1528 466 + 16727 AAGGTACAGCTTCTTAGAATC-AGGATACAACCTTT-ATTAGAGAGTAT-----ATACTA-------------ATATCACC-ATAGTTGGCTTAAAAGCAGCCACCAAT-TGAGAAAGCGTTCCAGCTCA---ACAAACA---ATATAACT---TAATCCCAACCATACT----ACATCAACTCCT-AATTATACCCCCTGGGTCATTCTATTTAAGTATAGAAGCAATAATGCTAGTATGAGTAA-CAAGAACCAT------TTTCTCCC--CGCATAAGCTTATATCAGGAACGGATA---GACCACTGATAGTTAA-CAA-----------------TCTGATAAT---ATCAACC-----CAAAAATGAAAT---ACTTATCCACCC-CATTGTTAACCCAACACAGGTATGCATTCAAGGAAAGATTAAAAGGAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTTACCAAAAACATCACCTCCAGC--ATTTCTAGTATTGGAGGCACTGCCTGCCCGGTGACAC---TTGTTTAACG
+s galGal2.chrM 2823 453 + 16775 GGGGTACAGCTCCATCGAAAA-AGAACACAACCTCC-TCCAGCGGATAA-----TAATCAC----------CCCTCCCCGC-ACTGTGGGCCTTCAAGCAGCCACCAACAAAAGAGTGCGTCAAAGCTC---------CC---TCATTAAA----AAATCTAAAACCCTA----TT-TGACTCCCTCAAC----CAAAGCAGGTTAACCTATGAC--AATAGAAGAATCAATGCTAAAATGAGTAATCTGGAA-CCT------ATCCTCCTACGGCGTAAACTTACATTA-------------ATACATT----ATTAA-CAG-----------------AACTCAACT---TATACCCCCACACTAACAAGCAAT---ACGTATTCCTCA-ATCTGTTAAGCCAACCCAGGAGCGCCC--ACAGGATGATTAAAACCTACAGAAGGAACTCGGCAAACCAAAGACCCGACTGTTTCCCAAAAACATAGCCTTCAGCTAACAACAAGTATTGAAGGTGATGCCTGCCCAGTGACCCCCAAAGTTCAACG
+s danRer1.chrM 2536 494 + 16596 AGGGTACAGCCCCTTTAACAA-AGGATACAACCTTT-TCAGGAGAATAA-----AGATCATAATTTACAAAACACGTTGTC-GTAGTGGGCCTGGAAGCAGCCACCTAA-AAAGAAAGCGTTAAAGCTCAGGTAAGAAGA---AATTCATA----ATTCTGACAATAATA----TC-TTACTTCCCTAAA----AATACCAGACTAATCCATACAAATATGGAAGAAATTATGCTAAAATGAGTAA-CAAGAA-GAACCTGTACTTCTCCA--AGCACAAGTGTAAGCCAAGTTGGACA----AACCATTGGCAATTAA-CGAGCCCAAACAAAGAGGGCAATGTGAGT---TAAAAAC--TGAGAAAAATCCACA---ACAGA--------CATCGTTACCCCCACACTGGAGTGCATATAAGGAAAGACTAAAAGAAAGGGAAGGAACTCGGCAAACACAAGCCTCGCCTGTTTACCAAAAACATCGCCTCCTGA--CATCCCAATATAGGAGGTCCAGCCTGCCCAGTGACAA---TAGTTTAACG
+
+a score=23403.0
+s hg17.chrM 2569 19 + 16571 GCCGCGGTACCCTAACCGT
+s panTro1.chr3 35464348 19 - 209662276 GCCACGGTATCCTGACCAT
+s mm5.chrM 2004 19 + 16299 GCCGCGGTATCCTGACCGT
+s canFam1.chrM 1994 19 + 16727 GCCGCGGTATCCTGACCGT
+s galGal2.chrM 3276 19 + 16775 GCCGCGGTATCCTAACCGT
+s danRer1.chrM 3030 19 + 16596 GCCGCGGTATTTTGACCGT
+
+a score=421032.0
+s hg17.chrM 2588 571 + 16571 GCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATGACACAG-CAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAA-CAGTACCT--AACAAACC---CACAGGTCCTAAACT---ACCAAA--CCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTT--CACCAG------------------TCAAAGC-GAACTACTATACTC---------AATTGATCCA---AT-A-A--CTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCAACAA-TAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT-ATCTACT--TCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCC---------------------------------------------TACTTCACA
+s panTro1.chr3 35464367 568 - 209662276 GCAAAGGTAGCATAATCACTTGTTCCCTAAATAGGGACTTGTACGAATTGCTACACGAGGGTTCAGCTGTCTCTTACTTTTAATCAGTGAAATTGACCTATCAGTGAAGAGGTGGATATAAAAAAAATAAGACGAGAAGACCCTATGGAGCTTTAATTCATTAATACAAA-TAAAAACTCAAACAAGCC---AACAGGCCCTAGCCT---ACTATC--CCTGCATTAAAAATGTTGTTTGGGGTGACCCCGGAGCATAATTCAACCTCTGAACGATGTAAACTAAGACCG--CACTAG------------------TCTAAGC-GAGTTAACATAC------------GTTGACTCA---ATTA-A--TTTGATGAGCGGAATAAGTTATCCTAGGGATAACAGCACAATCCTATTCTACAGTCCATGTCAACAA-TAGTGTTTATGACCTCAATGTTGGATCAGGACATCCTAATGGTGCAGCTGCTATTAAGGGTTTGTTTCTTCAGTGATTAA-AGTCCTACCTGATCTGAGGTCAGACTGGAGTAATCCAGGTTGGTTTCT-AACTATT--TAACATTTCTCCTAGTACAAAAGGACAA----AATAGTGCC---------------------------------------------CACTTCATA
+s mm5.chrM 2023 575 + 16299 GCAAAGGTAGCATAATCACTTGTTCCTTAATTAGGGACTAGCATGAACGGCTAAACGAGGGTCCAACTGTCTCTTATCTTTAATCAGTGAAATTGACCTTTCAGTGAAGAGGCTGAAATATAATAA-TAAGACGAGAAGACCCTATGGAGCTTAAATTATATAACTTATC-TATTTAATTTATTAAACC---TAATGGCCCAAAA-----ACTATAG-TATAAGTTTGAAATTTCGGTTGGGGTGACCTCGGAGAATAAAAAATCCTCCGAATGATTATAACCTAGACTT---ACAAG------------------TCAAAGTAAAATCAACATATCT---------TATTGACCCAGATAT-A-T--TTTGATCAACGGACCAAGTTACCCTAGGGATAACAGCGCAATCCTATTTAAGAGTTCATATCGACAATTAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCAATGGTGTAGAAGCTATTAATGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTTTCT-ATCTATT--TACGATTTCTCCCAGTACGAAAGGACAAGAGAAATAGAGCC----------------------------------------------ACCTTACA
+s rn3.chr3 85357956 538 - 170969371 GCATATATAAAATAATGTCTTG-TCTCTAAATAAGGGATTGAATGAATGTCCACACCAGACTTTTATTGCCAATTACTTCTAATCAGTGAAATTGACTTTCCTATGAAAAGAAAGTAATAAATACA-TAAGATGTGAAA------------CTTAATCTATTAGTTCAAT-AAAAAAATT-AATTACCT---TAAGGGACTAAAA-----ATCATGA-TCTAAATTACTAATTTTGTTTAGGGTGAGCTCAGGATATAAATAAATGTCTATATGGC-CAAGCACAGACTC--ACTCTG------------------TCACAAT-AAACACTTTTATTT----------ATTGACCCA---GA-A-A--TTTGATCTACGGGATAAATTATTTTAGGACCAACCCCAC-ATTCTATTGTGTGGTTTATGATCATAG-TCAGGTTTATGATTCCAGTGTTAAATCAAGATGCCCTAACTGTGTAACA--TAATAAAGTTTGATTGCTACA------AA-AGTCCCATGGGGTCTGAGTTCACATTGCA-----CCAGGTT--TCTCTAATCTATA--TTGTTTTTGTCAGAATACAAAGGGGAAA---AAAAGAGGTC---------------------------------------------CAGTTTACA
+s canFam1.chrM 2013 578 + 16727 GCAAAGGTAGCATAATCATTTGTTCTCTAAATAGGGACTTGTATGAATGGCCACACGAGGGTTTAACTGTCTCTTACTCCCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAATACCACAA-TAAGACGAGAAGACCCTATGGAGCTTTAATTAACTAACCCAAACTTATGGATACTAGATACC---TACAAGGCATAACATAACACCATTATTATGAGTTAGCAATTTAGGTTGGGGTGACCTCGGAATATAAAAAAACTCCCGAGTGATTAAAATTTAGACCC---ACAAG------------------TCAAAAT-ACAACATCACTT------------ATTGATCCA---AT-A-ATTTTTGATCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCAAGAGTCCATATCGACAA-TAGGGTTTACGACCTCGATGTTGGATCAGGACATCCTAATGGTGCAGCAGCTATTAAGGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT-ATCTATT-ATACAACCTCCCCCAGTACGAAAGGACAAGGGATGTAAGGCC---------------------------------------------TACCTCACA
+s galGal2.chrM 3295 630 + 16775 GCGAAGGTAGCGCAATCAATTGTCCCGTAAATTGAGACTTGTATGAATGGCTAAACGAGGTCTTAACTGTCTCCTGTAGGTAATCTATGAAATTAGTATTCCCGTGCAAAAACGAGAATGTGAACA-TAAGACGAGAAGACCCTGTGGAACTTTAAAATCACGACCACCT-TACAACCTTACACAGCCC---CACTGGGTCCACCCACACATAAACC-CCTGGTCGACATTTTTCGGTTGGGGCGACCTTGGAGAAAAAAAAATCCTCCAAAC-CCACAGACCACAACTC---TTCAC------------------TAAGACC-AACTCCTCAAAGTACCAACAGTAACCAGACCCA---AT-ATA--ATTGAGCAATGGACCAAGCTACCCCAGGGATAACAGCGCAATCTCCTCCAAGAGCCCATATCGACAA-GGAGGTTTACGACCTCGATGTTGGATCAGGACAACCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTTCAACGATTAACAGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTTTCT-ATCTATG---GACACTCCTCCTAGTACGAAAGGACCGGAGAAGTGGGGTCAATACCACTGAGCACACCCCAACCTTCTAAGCAATGAATACAACTCAACTGCCA
+s danRer1.chrM 3049 597 + 16596 GCAAAGGTAGCGCAATCACTCGTCCTTTAAATAGGGACCTGTATGAATGGCCAAACGAGGGCTTAACTGTCTCCCCCATCAAGTCAGTGAAATTGATCTATCCGTGCAGAAGCGGATATAATAATA-CAAGACGAGAAGACCCTTTGGAGCTTAAGGTACAAGATTTAAT-T--TACATCAAGCAAACCAATAAAAGTGATTAAACT---AGTAAAA-GATAAACCTCTACCTTCGGTTGGGGCGACCACGGAGTAAAAAACAACCTCCAAGCGGAACGGGCACAGCCCTAAAACCAAGAGAAACATCTCTAAGCCTCAGAAC-ACCTGACCAAAGAC---------GATCCGGCCT---AT-A-A--GCCGATCAACGAACCAAGTTACCCTAGGGATAACAGCGCAATCCTCTCTAAGAGTCCATATCGACGA-GGGGGTTTACGACCTCGATGTTGGATCAGGACATCCTAATGGTGCAGCCGCTATTAAGGGTTCGTTTGTTCAACGATTAATAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCAGTTTCT-ATCTGTAAAGCTATTTTTTCCTAGTACGAAAGGATCGGAAAAAGGGGGCC---------------------------------------------CATACTAA-
+
+a score=-368.0
+s hg17.chrM 3159 14 + 16571 AAGCGCCTTC--CCCC
+s panTro1.chr3 35464935 15 - 209662276 AAGCACCCTC-GCCTC
+s mm5.chrM 2601 16 + 16299 AAGCGCTCTCAACTTA
+s canFam1.chrM 2592 16 + 16727 AGGCGCCTTAAAACTA
+s galGal2.chrM 3925 14 + 16775 AGAACCCCTC--CCCC
+s danRer1.chrM 3646 14 + 16596 AAGCACGCCCCACC--
+
+a score=2194.0
+s hg17.chrM 3173 6 + 16571 GTAAAT
+s panTro1.chr3 35464950 6 - 209662276 ATAAAT
+s mm5.chrM 2617 6 + 16299 ATTTAT
+s canFam1.chrM 2608 6 + 16727 ATAGAT
+s danRer1.chrM 3660 6 + 16596 CTAAAT
+
+a score=1283.0
+s hg17.chrM 3179 12 + 16571 G-ATATCATCTCA
+s panTro1.chr3 35464956 12 - 209662276 G-ATGCTATCTCA
+s mm5.chrM 2623 13 + 16299 GAATAAAATCTAA
+s canFam1.chrM 2614 12 + 16727 G-AAGTCAACTCA
+
+a score=-632.0
+s hg17.chrM 3191 15 + 16571 ----ACTTAGTATTATACC
+s mm5.chrM 2636 14 + 16299 ----ATAAAATAT-ATACG
+s canFam1.chrM 2626 18 + 16727 ATCTAACCAGTTT-ATCTC
+
+a score=3123.0
+s hg17.chrM 3206 21 + 16571 CACACCC---ACCCAAGAACAGGG
+s panTro1.chr3 35464984 22 - 209662276 CACACCC--TACCCAGGAACAGGG
+s mm5.chrM 2650 24 + 16299 TACACCCTCTAACCTAGAGAAGGT
+s canFam1.chrM 2644 21 + 16727 CTCATAA---GCCCGAGAAAAGGG
+
+a score=273.0
+s hg17.chrM 3227 1 + 16571 T
+s panTro1.chr3 35465006 1 - 209662276 T
+s mm5.chrM 2674 1 + 16299 T
+
+a score=6671.0
+s hg17.chrM 3228 83 + 16571 TTgttaagatggcagagcccggtaatcgcataaaacttaaaactttacagtcagaggttcaattcctcttcttaacaacaTAC
+s panTro1.chr3 35465007 83 - 209662276 TTgttaagatggcagagcctggtaattgcataaaacttaaaattttataatcagaggttcaactccttttcttaacaATATGC
+
+a score=300.0
+s hg17.chrM 3311 1 + 16571 C
+s panTro1.chr3 35465090 1 - 209662276 C
+s galGal2.chrM 4062 1 + 16775 C
+
+a score=699.0
+s hg17.chrM 3312 5 + 16571 CATGG
+s panTro1.chr3 35465091 5 - 209662276 TATAA
+s galGal2.chrM 4063 5 + 16775 CCTAA
+s danRer1.chrM 3825 5 + 16596 CTTAA
+
+a score=2951.0
+s hg17.chrM 3317 8 + 16571 CCAACCTC
+s panTro1.chr3 35465096 8 - 209662276 TTAACCTT
+s mm5.chrM 2760 8 + 16299 TTAATATC
+s galGal2.chrM 4068 8 + 16775 CAAACCTT
+s danRer1.chrM 3830 8 + 16596 TTAACCCC
+
+a score=2100.0
+s hg17.chrM 3325 5 + 16571 CTACT
+s panTro1.chr3 35465104 5 - 209662276 CTCCT
+s mm5.chrM 2768 5 + 16299 CTAAC
+s rn3.chr3 129984747 5 + 170969371 CTTCT
+s galGal2.chrM 4076 5 + 16775 CTAAT
+s danRer1.chrM 3838 5 + 16596 CTAGC
+
+a score=142225.0
+s hg17.chrM 3330 184 + 16571 CCTCATTGTACCCATTCTAATCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCACATCTACCATCACC
+s panTro1.chr3 35465109 183 - 209662276 ACTTATTATCCCCACTCTTATTGCTATAGCATTCCTTACACTCATCGAATGAAAAATCTTAGGCTATACACAACTATGCAAAGACCCAAA-ATTGTAGGTCCCTATGGGCTGCTTCAGCCATTCGCTGATGGAATAAAACTTTTCACCAAAGAACCCTTACGGCCCTCAACATCCACTATTACC
+s mm5.chrM 2773 184 + 16299 ACTCCTCGTCCCCATTCTAATCGCCATAGCCTTCCTAACATTAGTAGAACGCAAAATCTTAGGGTACATACAACTACGAAAAGGCCCTAACATTGTTGGTCCATACGGCATTTTACAACCATTTGCAGACGCCATAAAATTATTTATAAAAGAACCAATACGCCCTTTAACAACCTCTATATCC
+s rn3.chr3 129984752 171 + 170969371 ATTAATTATCTCCATTTTCATCACTATAGCATTTCTAACTTCTTTTGAATGGAAAAGAATAGGTAATATGTGATTATTAGAAGAACCACGCATTGTAGATCTCCATGGTTTCTTTTAACAACTTCCTGGTGATGTAAAACTTTTCATCAAAGCAACCTTATATCCATTAAC-------------
+s canFam1.chrM 2769 184 + 16727 TCTTATTATCCCAATCCTTCTTGCCGTAGCCTTCCTCACCCTCGTTGAACGAAAAGTCTTAGGCTATATACAACTTCGAAAAGGACCTAATATTGTAGGCCCCTACGGCCTCCTTCAACCAATCGCAGACGCAGTAAAACTCTTCACAAAAGAACCTCTACGACCACTTACATCCTCTATATCA
+s galGal2.chrM 4093 184 + 16775 CTATATTCTCCCCATCCTAATCGCCGTGGCCTTCTTAACACTTGTAGAACGAAAAATCCTAAGCTACATGCAGGCCCGAAAGGGCCCAAACATTGTGGGCCCTTTTGGTCTACTCCAACCCGTTGCAGACGGGGTAAAACTATTCATTAAAGAGCCAATCCGACCATCTACCTCCTCCCCCTTC
+s danRer1.chrM 3843 184 + 16596 CTACGCCGTACCAGTATTAATTGCAGTAGCCTTCCTTACCTTAGTTGAACGAAAAGTGTTAGGCTATATACAACTCCGAAAAGGACCAAATGTAATAGGCCCCCGAGGACTGTTACAATCAGTAGCTGATGGCGTGAAACTTTTTATTAAAGAACCCATTCGACCATCTATGGCTTCTCCAATT
+
+a score=563983.0
+s hg17.chrM 3514 816 + 16571 CTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCC-CCTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAAC-ATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACA---------ACATATGACGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAA----AAACTTCCTACCACTCACCCTAGCATTACTT--ATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTA-----AGAAATATGTCTGA---TAAAAGAGTTACTTTGATAGAGTAAATAATAGGAG-----------------------------------------------------------------------CTTAAACCCCC------TTATTTc
+s panTro1.chr3 35465292 811 - 209662276 CTTTATATTATTGCTTCAACACTAGCCCTTTCCATTGCTCTCCTTTTATGAACTCC-CCTCCCTATACCAGATCGTCTAATTAATTTTAATATAGGCCTCCTATTTATACTAGCAACATCAAGCCAGGCTGTCTACTCTAT-----GATCAGAATGAGCATCAAATTCAAAATATGCACTGATCAGTGCATTACGAGCTGTGGCCCAGACAATTTCATGTAAGGTCACCCTAGCCATTATCCTGCTATCAGTTCTACTGATAAGCGGCTCATTTAACTTATACACACTCATCACAATGCAAGAATTCCTCTGACTGCTCCTACCATCGTGGCCTCTAGCCATAATATGATTCATCTCCACTCTAGCAGAAACTAACCAAGCACCTTTTGATCTAGCAGAAGGAGAGTCAGAGTTAGTCTCAGGCTTCAACATTGAATACGCCACAAGGTCATTTGCCCTCTTCTTTATAGCAGAATATATGAAT-ATTATCATAATAAATGCCCTAACTACTACTATTTTCCTAGGAGCACTACACACTATATAT---------TTACCAGAACTGTACACCACAAATTTCATTACCAAGACCCTTCTTTTAACCACTCTATTTTTATGAATTCGAATGGCATACACTCGATTCCACTATGACCAACTCATACATCTTTTATGAAA----AAACTTCCTACCACTTATGCTAGCATT--TTGCATATGATATATCTCAATGCTTGTCCTAATTTCCAGCATCCCACCCCAAACATA-----GGAAATATGTCAGA---CAAAAGAATTACTTTGATAGAGTAAACAATAGAGG-----------------------------------------------------------------------TTAAAATCCTC------TAATTTc
+s mm5.chrM 2957 815 + 16299 TTATTTATTATTGCACCTACCCTATCACTCACACTAGCATTAAGTCTATGAGTTCC-CCTACCAATACCACACCCATTAATTAATTTAAACCTAGGGATTTTATTTATTTTAGCAACATCTAGCCTATCAGTTTACTCCATTCTATGATCAGGATGAGCCTCAAACTCCAAATACTCACTATTCGGAGCTTTACGAGCCGTAGCCCAAACAATTTCATATGAAGTAACCATAGCTATTATCCTTTTATCAGTTCTATTAATAAATGGATCCTACTCTCTACAAACACTTATTACAACCCAAGAACACATATGATTACTTCTGCCAGCCTGACCCATAGCCATAATATGATTTATCTCAACCCTAGCAGAAACAAACCGGGCCCCCTTCGACCTGACAGAAGGAGAATCAGAATTAGTATCAGGGTTTAACGTAGAATACGCAGCCGGCCCATTCGCGTTATTCTTTATAGCAGAGTACACTAAC-ATTATTCTAATAAACGCCCTAACAACTATTATCTTCCTAGGACCCCTATACTATATCAAT---------TTACCAGAACTCTACTCAACTAACTTCATAATAGAAGCTCTACTACTATCATCAACATTCCTATGGATCCGAGCATCTTATCCACGCTTCCGTTACGATCAACTTATACATCTTCTATGAAA----AAACTTTCTACCCCTAACACTAGCATTATGT--ATGTGACATATTTCTTTACCAATTTTTACAGCGGGAGTACCACCATACATATA------GAAATATGTCTGA---TAAAAGAATTACTTTGATAGAGTAAATTATAGAGG-----------------------------------------------------------------------TTCAAGCCCTC------TTATTTC
+s rn3.chr17 3179538 758 + 97307196 CTTTTTATCATTGCCCCAACCCCACCCCTCACTGTAGCACT----CTATGGATTCCATCTTTTTACCGCTCAATCCCTAACAAACATAGACCATGCGAT----TTTGTTCTAGCTACTTGGAGCCCATCAGTCGACTCGGTTTTATGACTGGAGTGAGTTTCAGCTCCTAAATTCGCAA-GAGTGGAGCCTCCTGAGCTGTAGTTCAGGC----TCAC-TGGAGTAACACTGGTTGCCATTC---TATCAAGTCGACTAATAAACGGACCGCTTACCCCACAGACACTGATTTATACCCAAGCGCATGTATTATTACTTCCACCGAGATGACCCC-AGCCACAATGTGATTCATCTCTCCACTAGCAGAAACCAATAGGACAGTGTTTGACCTAACAAAA------------TTAATACCA---TCCTACATTGGATATACTGCAGGACCATTTACTCTA-TCTTTATGTTGAAGCACACTACCAATTACTGTAATCAATACCCAAATACCCATACCTCCCTTAGAAGTATTGTATGATACCCTC---------CCTCCAGAAATTTTTATAAT---TTTTATAGTTAGAACTTTGCTTCTCACCACTACAGTTTTATAAAATTGAGCGTCTTTCCCTTAATTTTGACATAACCAACTAGTACATTTGTCATGAAGTAATAAACTTTCT--------------------GT--GTGAGACCAATTTCCATCTCTATTTTTATATC---AACCCTCCTCTATGCATA-------GAACACATCTAG---TAAAGG--TTAGTATGGTGTAATAAACAATAGATG-----------------------------------------------------------------------TTTAGTCTGTC------TTATTTC
+s canFam1.chrM 2953 816 + 16727 ATATTCATCCTAGCCCCCATTCTAGCTCTATCACTAGCCCTAACTATGTGAATTCC-CCTCCCAATACCCTACCCACTCATTAATATAAACTTGGGAGTCCTATTCATACTAGCAATATCAAGCCTCGCCGTGTACTCCATCCTCTGATCAGGATGAGCCTCAAACTCCAAATACGCCCTAATCGGAGCCCTTCGAGCAGTAGCTCAAACAATCTCATATGAAGTAACGCTAGCAATTATTCTTCTATCAGTCCTCCTAATAAACGGGTCATTTACACTATCCACGCTAATTATTACCCAAGAACATATATGATTAATCTTTCCGGCCTGACCCCTAGCCATGATATGATTCATCTCTACCCTAGCAGAAACTAATCGAGCCCCCTTCGACTTAACTGAAGGAGAATCCGAACTAGTCTCTGGATTTAACGTAGAGTATGCAGCAGGTCCTTTCGCCCTATTCTTTCTAGCAGAGTACGCAAAT-ATTATTATAATAAACATCCTCACAACAATTCTGTTCTTCGGCGCATTCCACAACCCATTC---------ATACCAGAACTCTACTCTATTAACTTCACTATAAAAACCCTCTTATTAACCATCTGCTTCCTATGAATTCGAGCATCATACCCTCGATTCCGCTACGATCAGTTAATACACTTATTATGAAA----AAATTTTCTACCCTTAACTTTAGCCCTATGC--ATATGACATGTTGCCTTACCCATTATCACCGCAAGTATCCCACCCCAAACATA-----AGAAATATGTCTGA---TAAAAGAGTTACTTTGATAGAGTAAATAATAGAGG-----------------------------------------------------------------------TTTAAATCCTC------TTATTTc
+s galGal2.chrM 4277 892 + 16775 CTCTTCATTATTACTCCAATCCTAGCACTACTCCTAGCCCTGACTATTTGAGTCCC-CCTCCCACTACCATTCCCCCTTGCAGACCTCAACCTAGGACTACTATTTCTCCTAGCCATATCAAGCCTAACTGTCTACTCTCTACTCTGATCCGGATGAGCATCAAACTCCAAGTATGCCCTAATCGGAGCCCTTCGAGCCGTCGCACAAACAATCTCATACGAAGTCACCCTAGCCATCATCCTGTTATCCACAATCATACTGAGCGGCAATTACACCTTAAGCACCCTGGCCATCACCCAAGAGCCCATCTACCTCATTTTTTCCGCATGACCCCTCGCAATAATATGATACATCTCTACCCTTGCTGAAACCAACCGCGCCCCATTTGACCTAACAGAAGGAGAGTCAGAGCTAGTCTCAGGATTTAATGTAGAATATGCCGCCGGACCATTCGCCATATTCTTCTTAGCCGAATACGCCAAC-ATTATACTAATAAACACACTAACCACCGTCCTATTCCTGAACCCAAGCTTCCTAAATCTC---------CCACCAGAATTATTTCCCATTGCACTCGCTACAAAAACCCTCCTCCTTTCATCCTCATTTCTATGAATCCGGGCCTCATATCCACGGTTCCGCTATGACCAACTAATACATCTTCTATGAAA----AAACTTCCTCCCCCTAACCCTAGCCTTATGC--CTCTGACATACCAGCATACCAATCAGCTACGCCGGCCTCC--CCCCAATCTAA-----GGAAGCGTGCCTGAAC-AAAAAGGATCACTATGATAAAGTGAAC-ATAGAGGTATAACAACCCTCTCACTTCCTTAATCCTAGAAAAGTAGGAATCGAACCTACACAGAAGAGATCAAAACTCTTCATACTCCCTCTATATTATTTT
+s danRer1.chrM 4027 824 + 16596 TTATTTTTAACAGCTCCAGTTCTTGCACTAATCCTAGCAATAATGCTATGGGCACC-CATACCCATGCCCTATCCAGTACTCGACCTAAATCTTGGAATTTTATTTATTATAGCCATCTCAAGCCTAGCAGTATACTCAATCCTGGGATCAGGTTGAGCATCAAACTCAAAATACGCATTAATTGGGGCCTTACGAGCTGTAGCGCAAACAATTTCATATGAAGTTAGCCTAGGACTTATTCTATTATCTGCCGTTATTTTTTCTGGGGGATACACCCTACAAACATTTAATACAACTCAGGAAGACACATGACTTCTACTTCCACTATGACCATTAGCCATTATATGATTTATCTCAACGCTGGCAGAAACAAACCGAGCACCGTTCGATCTTACAGAGGGGGAATCAGAACTAGTCTCAGGCTTCAATGTAGAGTATGCAGCAGGACCATTTGCCTTATTCTTTTTGGCTGAGTACTCAAAT-ATTTTACTAATAAACACCCACTCAACAGTACTATTTTTAGGAGCATCGTTTACCCCAGAT---------GCACCTGAGCTAATAACAATCAGTATTGCAACCAAAACTGCAATACTATCTATTTTGTTTCTCTGAATACGAGCATCATACCCACGATTCCGATACGACCAACTTATGCATCTTATCTGGAA----AAACTTTCTTCCAATCACATTAGTTCTAGTA--CTATGACATATCGCCCTACCAATCGCACTAGCTGGTCTACCCCCACAAACATAACTCAAGAACCGTGCCCGAATGCTAAGGGGTCACTTTGATGGAGTGAACCATAGGGG-----------------------------------------------------------------------TTAAAATCCCC------TCGGTTC
+
+a score=0.0
+s hg17.chrM 4330 71 + 16571 taggactatgagaatcgaacccatccctgagaatccaaaattctccgtgccacctatcacaccccatccta
+
+a score=15771.0
+s hg17.chrM 4330 70 + 16571 taggactatgagaatcgaacccatccctgagaatccaaaattctccgtgccaccta--tcacaccccatcct
+s panTro1.chr3 35466103 70 - 209662276 tagtactataggaatttaacctacctctgagaatccaaaattgtctgtgctaccta--tcacaccacgtcct
+s rn3.chr17 3180296 70 + 97307196 TAGACTTACAGGAATCAAACCCAGTCTTTCGAATTCAAAAACTGCCTCACTACCCA--GTATGCCTTATTCT
+s canFam1.chrM 3769 72 + 16727 tagaataataggcttcgaacctaatcttaagaattcaaagatcttcgtgctaccaaacttacactatattct
+
+a score=910.0
+s hg17.chrM 4400 1 + 16571 a
+s panTro1.chr3 35466173 1 - 209662276 a
+s mm5.chrM 3842 1 + 16299 A
+s rn3.chr17 3180366 1 + 97307196 A
+s canFam1.chrM 3841 1 + 16727 a
+
+a score=149630.0
+s hg17.chrM 4401 275 + 16571 AAGTAAGGTCAGCTAAA-TAAGCTATCGGGCCCATACCCCGAAAATGTTGG-TTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTACTCT-ACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTCGTTCCACAGAA---------------------GCTGCCATC-AAGTATTTCCTCACGCAAGCAACCGCATCCATAAT
+s panTro1.chr3 35466174 275 - 209662276 GATTAAGGTCAGCTAAA-TAAGCTATTGGGCCCATATACCAAAAATGTTGG-TTATATCCTTCCCATACTAATTAATCCCTTACCTCAACTTATTAT-TGCCCTCACCGTTTTCACAGGAACTTTTATCACAATGCTAGGCTCACACTGATTTCTCATCTGAACAGGGCTAGAAACAAACATACTAGCCCTTACCCCAATCTTAATTAAAAAAATAAATCCCTGCTCTACAGAA---------------------GCAGCCACC-AAATATTTCCTTACACAAGCAACCACATCTGTAAT
+s mm5.chrM 3843 276 + 16299 TAGTAAGGTCAGCTAAT-TAAGCTATCGGGCCCATACCCCGAAAACGTTGGTTTAAATCCTTCCCGTACTAATAAATCCTATCACCCTTGCCATCATCTACTTC-ACAATCTTCTTAGGTCCTGTAATCACAATATCCAGCACCAACCTAATACTAATATGAGTAGGCCTGGAATTCAGCCTACTAGCAATTATCCCCATACTAATCAACAAAAAAAACCCACGATCAACTGAA---------------------GCAGCAACA-AAATACTTCGTCACACAAGCAACAGCCTCAATAAT
+s rn3.chr17 3180367 265 + 97307196 TAGTAAGGTCA-TGAGA-TGCACCACTGGGCACA-ATCCCCCGAGCATTTG-CTACAGTTTCCCTCTATTAAT-AATCCCATA----------------------GCCATTACATCAAGCTCACTCATCATTATATTTAGTCCACACTTACTATCTACATGACCAGA-CTAGAAATAAGCACACAAGCATGAGTCCTGATTTTTATTAACAAATTG------TGAACTATGGAAGCAGGAGATGGATTTCTTAATGCGACTGCCTAAGTAATTCAT-GTGCAAACCACTACATCCTTACT
+s canFam1.chrM 3842 277 + 16727 CAGTAAGGTCAGCTAAATTAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTTATACCCTTCCCGTACTAATAAAACCCCCTATTCTCATTATCATCATAGCA-ACTATCATGACAGGAACCATAATCGTCATACTAAGCTCGCACTGATTACTGATCTGAATTGGATTCGAAATAAACATGCTAGCCATCATCCCTATTCTCATAAAAAAGTACAATCCACGAGCCATAGAG---------------------GCCTCTACA-AAATATTTTCTTACACAAGCTACAGCCTCAATATT
+s galGal2.chrM 5170 276 + 16775 TAGTAAGGTCAGCTAAC-TAAGCTATCGGGCCCATACCCCGAAAATGATGGTTTAACCCCTTCCCCTACTAATGAACCCCCATGCAAAACTAATCTGCACAGTA-AGCCTCATCATGGGAACCAGCATCACAATCTCCAGCAACCATTGAATCTTAGCCTGAACAGGCTTAGAGATCAACACCTTAGCCATCATCCCCCTCATCTCCAAGTCACACCACCCCCGAGCGATTGAA---------------------GCCACTATC-AAATATTTCCTCACCCAATCAACTGCATCAGCCCT
+s danRer1.chrM 4922 276 + 16596 GGATGAGGTCAGCTAAT-TAAGCTACCGGGCCCATACCCCGAACATGATGGTTAAAGTCCCTCCTTCATCAATGAACCCTTATGTCCTTATAATTTTAATATCC-AGCCTAGGTCTAGGAACCACATTAACTTTTTCTAGCTCACACTGAATTTTAGCCTGAATAGGATTAGAAATTAATACTTTAGCAATTGTCCCTCTAATAGCACAACAACACCACCCACGGGCAGTAGAA---------------------GCCACCACA-AAATACTTCCTTATTCAAGCTGCTGCCGCAGCAAT
+
+a score=31081.0
+s hg17.chrM 4676 152 + 16571 CCTTCT---------AATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAA-----CCATAACCAATACTACCAATCAATACTCATCATTA--ATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCC
+s panTro1.chr3 35466449 150 - 209662276 TCTCAT---------AACAGATATCCTTTCCAATAACCTGTTCTCCGGACAATGAA-----CTATAAT--ACACTATCAATCAATTCTTATCCTTA--ATAATAATAGTGGCCCTAGTAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCTCAGAGGTAATTC
+s mm5.chrM 4119 152 + 16299 TATCCT---------CCTGGCCATCGTACTCAACTATAAACAACTAGGAACATGAATATTTCAACAAC--AAACAAACGGT-----CTTATCCTTAACATAACATTAATAGCCCTATCCATAAAACTAGGCCTCGCCCCATTCCACTTCTGATTACCAGAAGTAACTC
+s rn3.chr3 129986043 145 + 170969371 TTTAATGGACAAATAATTAGTTATTAAATTCAGAAAAATA--------AGAATGTA-----AAATCATTTTGTGGATTAATTAATACT----------GTAACAGTAATTCTTCTGATAAAAAAATCATGCTTTTTTCCATTCTACATTTGAATACCAGAAGCCATTC
+s canFam1.chrM 4119 152 + 16727 ACTAAT---------AATAGGAGTCACTATCAACCTCCTTTACTCCGGCCAATGGG-----TAATCTCAAAAATCTCAAACCCCATCGCATCCATC--ATGATAACCACTGCCCTAACAATAAAACTAGGCCTATCTCCATTCCACTTCTGAGTTCCCGAAGTAACAC
+s galGal2.chrM 5446 152 + 16775 AATCCT---------CTTCTCGAGCATAACCAACGCCTGATCCACCGGACAATGAG-----ACATTACACAACTAAACCACCCGACATCATGCCTA--ATATTAACAATAGCAATCGCAATCAAATTAGGACTAGTCCCATTCCACTTCTGATTCCCAGAAGTACTCC
+s danRer1.chrM 5198 152 + 16596 AATTCT---------ATTCACAAGTACAACAAATGCCTGAATTTCAGGACAATGGG-----ATGTTACAGGTATACCAGGCCCAGCCACCAGTACA--GCAATAATGTTTGCATTGGCTCTCAAAATCGGTCTAGCACCAATACATTTTTGATTACCAGAAGTTCTTC
+
+a score=123662.0
+s hg17.chrM 4828 652 + 16571 AAGGCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCC---CATCTCAATCATATACCAAATCTCTCCCTCACTAAACGTAAGCCTTCTCCT--CACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCTACCGTAC--------------------AACCCTAACATAACCATTC--TTAATTTAACTATTTATATTATCCTAACTACTACCGCATTCCTACT-ACTCAACT------TAAACTCCAGCACCACGACCCT-ACTACTATCTCGCACC--TGAAACAAGCTAACATGACTAA---CACCCTTA---ATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGG----CTTTTTGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCA---TATCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAAC---CCACCCCATTCCTCCCCACACT--------CATCGCCCTTACCACGCTACTCCT
+s panTro1.chr3 35466599 644 - 209662276 AGGGAATCTCTTTGATGTCTGGTATACTTCTCCTCACATGACAAAAACTAGCTCC---TATCTCAATTGTGTTTCAAA-CTTTTCATCAACAAACACGAACATCCTCCTGTCAC------AATCCTATCCATTATAGTGGGTGGTTGAGGGGGACTTAATCAAAC--AACTGTGTAAAATCCTAGCCTACTCCTCAGTCACTCACATAGGTTGAACAACAGCAGTACTAATTTAT--------------------AATCCAAACATTACTACCC--TAAACCTGATTATTTACTTTATCCTAACAACAACCGCATTTCTAGC-ACTCAACCAGAGTATAA------GCACCAGAACCCT-ATCACTATCTCACACC--TGAAACAAATGAGCATGGTTGA---CACCTGTA---ATTCCACTAATTCTACTATCCTTAGGAGGTTTATCCCCATTAACAGGGTTACTTTCT----AAATGAATCATCATTCAAGAATTTACAAAAAACAATAGCCTTACTACCCCAATCATTATAGTTAACATAACC-TACTCAACCTGTACTTTTATATATGCCTAGTCTATTCCTTCTCAGTAACACTATTCCCCA---TATCTAACAATATGAAAATAAAATGACAATTTGAAAACACAGAAC---CCACACTACTCTTCCCCCCACT-----TGTCATCTCTTCTACC---CTCCTCTT
+s mm5.chrM 4271 652 + 16299 AAGGGATCCCACTGCACATAGGACTTATTCTTCTTACATGACAAAAAATTGCTCC---CCTATCAATTTTAATTCAAATTTACCCGCTACTCAACTCTACTATCATTTT--AATACTAGCAATTACTTCTATTTTCATAGGGGCATGAGGAGGACTTAACCAAACACAAATACGAAAAATTATAGCCTATTCATCAATTGCCCACATAGGATGAATATTAGCAATTCTTCCTTAC--------------------AACCCATCCCTCACTCTAC--TCAACCTCATAATCTATATTATTCTTACAGCCCCTATATTCATAGC-ACTTATAC------TAA---ATAACTCTATAACCATCAACTCAATCTCACTTCTATGAAATAAAACTCCAGCAATAC---TAACTATA---ATCTCACTGATATTACTATCCCTAGGAGGCCTTCCACCACTAACAGG----ATTCTTACCAAAATGAATTATCATCACAGAACTTATAAAAAACAACTGTCTAATTATAGCAACACTCATAGCAATAATAGCTCTACTAAACCTATTCTTTTATACTCGCCTAATTTATTCCACTTCACTAACAATATTTCCAA---CCAACAATAACTCAAAAATAATAACTCACCAAACAAAAACTAAAC---CCAACCTAATATTTTCCACCCT-----AGCTATCATAAGCACA---ATAACCCT
+s rn3.chr17 3180986 514 + 97307196 AAGGGGGAGCACTAAAACTTAGCTCGCTTCACTTTGGAATACAAGGAATAACCCAAGGCATTTCCCTAATGTTTGTAATACCTTTCAAACTGA----------CCCCTC--AAATATCCCAATTTTCATTGTTATCTCTGATATATCA--TGTATTAAAGCAAAG-----TATGGGAAAACCTGGTGTAGTAAGCATTTGTCCAGATAGAATGAATAACAGCTGTTATTGTCTACTGTAATATTGCCTGATCCCCAGTTCATATGCCATTAGCCAGTATTCTCAACTCTTTATATTAATTTAAAT-------TATTTATATTAATTTAAAT------TAA----------------CCT-ACCAG-------------CGAAGTAAATTACCTT---TAA---CAGTTTTAACCATCCCAACAATCTTCTT--------------TGACCCTGTTAATGGA----ATTTCTACTTAAGTGAGATGTCAT----------------------------------------------------ATGACT-TCTCTAGTCTATATT----------CCTAATCTTATTTCTATTACAGACATGAC--------------------------ACAAAATAATGACTT-------CAGCAC---CTAAACTACTTAT----GAGCT--------CCTCCTATGTGTT--GTGACTCCT
+s canFam1.chrM 4271 655 + 16727 AGGGAATTACGCTCATATCAGGAATAATCCTACTAACATGACAAAAAATCGCACC---TATATCCATCCTATATCAAATCTCTCCATCAATTAACACTAACCTTCTTAT--ACTAATAGCCCTTACATCCGTTCTAGTAGGAGGCTGAGGCGGACTAAATCAAACTCAACTACGAAAAATCATAGCATACTCCTCCATTGCCCACATAGGCTGAATAGCCGCTATCATTACTTAT--------------------AACCCTACAATAATAGTTC--TAAACTTAACTTTATATATTCTAATAACACTATCTACCTTCATACT-ATTTATAT------TAAACTCATCCACCACGACCCT-ATCTTTATCCCACATA--TGAAACAAATTTCCCCTAATCA---CTTCCATA---ATCTTAATCTTAATACTATCCCTAGGAGGACTACCCCCATTATCTGG----CTTCATCCCCAAATGAATAATTATTCAAGAATTAACGAAAAATAACATAATTATTATTCCAACACTAATGGCTATCACCGCTCTACTTAACTTATATTTCTACCTGCGACTCACATATAGCACCGCACTTACCATATTTCCAT---CCACAAACAACATAAAAATAAAATGACAGTTCGAATACACAAAAAAGGCAACCCTATTACCCCCCTTAAT-----TATTACCTCAACTATA---CTACTCCC
+s galGal2.chrM 5598 649 + 16775 AAGGCTCCTCCCTAATCACTGCCCTACTACTCTCCACCCTAATAAAACTCCCCCC---AATCACACTCCTCCTCCTAACATCACAGTCTCTTAATACCACCTTACTCAC--CCTCCTAGCAATCTCCTCCACCCTAATCGGAGGCTGAATGGGCCTAAACCAAACACAAACACGAAAAATCCTAGCCTTCTCATCCATCTCCCATTTAGGATGAATAATTATAATTATCTCCTAT--------------------AACCCACAACTCACTATTC--TCACCTTCATCCTCTACACAATTATGACCTCAACTGTATTCCTATC--CCTAGCC------CAAATCAAAGTCCTAAAACTGTCAACACTACTCATCTCA--TGAACTAAAACCCCAATACTAAATGCAACTGTA---AT---ACTAACCCTCCTCTCCCTAGCTGGCCTCCCACCATTAACCGG----CTTCATGCCAAAATGACTCATTATCCAAGAACTAACCAAACAAGAAATAACCCCAATAGCCACAATCATCACAATACTATCACTCCTAAGCCTATTCTTCTACCTCCGACTTGCATACCACTCAACAATCACACTCCCCCCCAACTCATCAAACCACATAAAACTCTGA--------CGAACTAACAAAAC---CCTAAACACCCCCACCGCCATTCTAACTGCGCTATCAACCACC---CTATT---
+s danRer1.chrM 5350 652 + 16596 AAGGATTAGATCTGTTGACAGGACTAATTTTGTCAACCTGACAAAAACTTGCCCC---AATAGCATTAATTATCCAAACGACCCAAACCACTGACCCTCTTATTCTTAC--ATCACTAGGAATTGCTTCCTCTCTCATTGGAGGGTGAAGCGGACTTAACCAAACCCAACTCCGAAAAATTCTAGCTTATTCATCAATTGCCCACATAGGGTGAATAATTATTGTTATCCAGTAC--------------------GCTCCGCAACTTACTCTGA--TTGCTTTAGGAACATATATCTTTATAACATCCGCGGCATTCCTTAC-TTTAAAAG------TATTATCAGCCACAAAAATTAA-CACCCTAACAACGACC--TGACCGAAAAGCCCAATCCTGG---CAGCAATT---GCTACTTTAGTTATATTATCACTGGGAGGACTTCCCCCACTGACGGG----ATTCATACCAAAATGATTAATCCTACAAGAGTTAACGAAACAAGACCTACCAGCCACAGCTACTATCATGGCGCTTACCGCCCTCCTAAGCTTATTTTTTTACCTACGTCTATGTCATGCAATAACATTAACGACTTCACCAA---ACACTATCAATTCAGCCCCTCACTGACGGGTACAAACGACCCAAA---ACTCACTACCCCTAACAATCTC-----TGTTACTGTTACTATA---GGACTTTT
+
+a score=211260.0
+s hg17.chrM 5480 399 + 16571 ACCTATCTCCCC------TTTT------ATACTAA---TAATCTTATAGAAATTTAGGTTAAATA-----CAGACCAAGAGCCTTCAAAGCCCTCAGTAAGT--TGCAA--TACT--TAATTTCTGCAACAG-------CTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTT--ACTAGACCAATGGGACTTAAACCCACAAACA---CTTAG-----------TTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACT-TCTCCCGCCGCC----GGGAAAAAAGGCGGGAGAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATG-A-AAA-TCACCTCGGAG---CTGGTAAAAAGAGGCCT--AACCCCTGTCTTTAGATTTACAGTCCAATGCTT---CACT
+s panTro1.chr3 35467243 404 - 209662276 ACCCATCTCTCC------ATTA------ATACTAACTATAA-CTTA--GAAATTTAGGTTAAATA------AGACCAAGAACCTTCAAAGCCCTTAGTAAGT-----AAGTTACTCTTAATTTCTGTAACAGA-----TCTAAACACTGCAAGACTCTATACTGCATCAACTGAACGCAAATCAACCGCTGTAATTAAGCTAAGCCCTT--ATGAGATTGGTGGAATTCAAACC-ACGAATAAAATTTAG-----------TTAACAGCTAAACACCCTAATCAACTGGCTTCAATTTACT----CCCACCGTCATTGGGGGAGAAAGGCAG-AGAAGCCCCAGCAGG-ATTGAAGCTGCTCCTTTGAATTTTCAGTTCAACATG-AGAAA-TCACCTCAGAG---CTGCTAAAAAGAGGCCTT-GACCTCTGTCTTTAGATTTACAGTCTAATGCTT----ACT
+s mm5.chrM 4923 390 + 16299 ACCCCTAGCCCC------CC---------AACTAA---TTA-CCTA--GAAGTTTAGGATATACT------AGTCCGCGAGCCTTCAAAGCCCTAAGAAAACA-CACAAGTT-----TAACTTCTG-------------ATAAGGACTGTAAGACTTCATCCTACATCTATTGAATGCAAATCAATTGCTTTAATTAAGCTAAGACCTC-AACTAGATTGGCAGGAATTAAACCTACGAAAA---TTTAG-----------TTAACAGCTAAATACCCTATT--ACTGGCTTCAATCTACT----TCTACCGCCGAAAAAAAAAAATGGCGGTAGAAGTCTTAGTAGA-GATTTCTCTACACCTTCGAATTTGCAATTCGACATG-A-ATA-TCACCTTAAGACCTCTGGTAAAAAGAGGATTTAAACCTCTGTGTTTAGATTTACAGTCTAATGCTT----ACT
+s rn3.chr14 86906642 384 - 112220682 ACTTACTTTCCC------TTCATCACCCCAACAAA---TCA-ATTA--GAAGTTTAGGATATTCT------AGTCCAAGAGCATTCAAAGCCCTAAGAAAACA-AATAAATT-----TAATTTCTG-------------ATAAGTACTGTAAGACTCTATCCTAAATCTACTGAATGCAAATCCATCTCTTTATTTAAGCTAAGACCTT-AACTATATTGGCAGGAATCAAGCCTGAGAAAA---TTTAAGAGTGAAAATTTTAAGAGTGAAATACCCTACC--TCTGAATTCAATCTAC-----CTCTTCTTCATATCAGAAAGGGGACAGGAGAAGCCTTAGTAAA-----------------------CAAAATTCCATGTC-A-TTA-TCACCTTAAAGA--TTGGTAAAAAGAGGGCTT-ACCCTTTATGTCTAGATTTCCAGTCAAATGCTT----ACT
+s canFam1.chrM 4926 407 + 16727 ACTAACACCTAT------ATTA------TCAGTCT---TGG-ACTA--GGAGTTTAGGTTAGACC------AGACCAAGAGCCTTCAAAGCTCTAAGCAAGTGCTACACACT-----TAACCCCTG-ATCAAATCACCTCTAAGGGCTGCAAGAATCTATCTTACATCAATTGAATGCAAATCAAACACTTTAATTAAGCTAAGCCCTC--CCTAGATTGGTGAGCTTCTACCTCACGAAAT---TTTAG-----------TTAACAGCTAAATACCCTAGT-AACTGGCTTCAATCTACCTTCTCCCGCCGCG--TAGAAAAAAAAGGCGGGAGAAGCCCCGGCGGC-GTCTAGGCTGCTTCTTTGAATTTGCAATTCAATATG-A-AAATTCACCACGGAGC--TTGGCAAAAAGAGGACTTAAACCCCTATCTTTAGATTTACAGTCTAATGCTT----TTA
+s galGal2.chrM 6248 382 + 16775 CCCCTTTCCCCC------CTAA------TTATTAC---CAT-ACTATAGAAACTTAGGATTAACTGTCACCAAACCAAAGGCCTTCAAAGCCTTAAATAAGA--GTTAAACT-CTCTTAGTTTCTG-CCCAA-------CTAAGACCAACAGGACATTAACCTGTATCTCCTGAATGCAAATCAGACGCTTTAATTAAGCTAAGGCCTCTACCTAGACAGATGGGCTTCGATCCCATACAAT---TTTAG-----------TTAACAGCTAAATGCCAACACCAATTGGCTTCTGCCTAC-----------------------------------AGACCCCGGCACA-CTTTAGTGTACATCAACGAGTTTGCAACTCATTATG-A-ACT-TCACTACAGAG---TCGATAAGAAGAGGAATTGAACCTCTGTAAAAAGGACTACAGCCTAACGCTTCAACACT
+s danRer1.chrM 6002 408 + 16596 ACCACTGACCCCAGCCATCTTA------ATATTAA---CAA-CATA--GAGACTTAGGATAACCT------AGACCAAGAGCCTTCAAAGCTCTCAGTAGAA--GTGAAAAT-CTTCTAGTCTCTG-------------ATAGGACTTACA-GACGTTACTCCGCATCTTCTAAATGCAAATCAGATATTTTAATTAAACTAAAGCCCT--ACTAGATGGGAAGGCCTCGATCCTACAAAAT---CTTAG-----------TTAACAGCTAAGCGCCCAAGCCAGCGAGCATCCATCTACT-TTTCCCGCCGTT--GAACCCGGTAAGGCGGGAAAAGCCCCGGCAGGAGGTTTACCTGCGTCTTCAGATTTGCAATCTGATATGTA-TCA-TCACCACGAGGCC-ATGGTAGAAAAAGGACTCAAACCTCTGTCCGCGGAGCTACAATCCGCCGCCTAAACACT
+
+a score=338602.0
+s hg17.chrM 5879 388 + 16571 CAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGAACACTATAC---CTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTC--CTTATTCGAGCCGAGCTGGGCCAGCCAGGCAAC-CTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTT-GTAATAATCTTCTTC-ATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGC-TCGCATCTGCTATAGTGGAGGCCGGA
+s panTro1.chr3 35467647 387 - 209662276 CAGCCACTTTACCTTTCCCCCACCTATGTTCATCAATCGTTGATTGTTTTCAACTAACCACAAAGATATCGGAACACTATACGTGCTAT-----GGCGCCTGAACCGGGGTAGTAGGCACCGCCTTAAGCCTT--CTAATTCGAGCAGAACTCGGCCAACCAGG-AACTCTGTTAGGAGATGATCGGATCTACAATGTTATTGTTACCGCCCACGCATTTCGTTATAATTTTCTTT-ATGGTAACACTGATCATGATAGGGGTTTTTGGCAACTGGCTAGTCCCTCTGACTATTGGTTGACTCGACATGGCATTCCCCTGAATAAATAATATCAGCTTCTGGCTTTTCCCCCTATCTTTTCTACTCCTCC-TTGCGTCTTCAATATTTCAAGCCAGT
+s mm5.chrM 5313 377 + 16299 CAGCCATTTTACCT-----------ATGTTCATTAATCGTTGATTATTCTCAACCAATCACAAAGATATCGGAACCCTCTAT---CTACTATTCGGAGCCTGAGCGGGAATAGTGGGTACTGCACTAAGTATT--TTAATTCGAGCAGAATTAGGTCAACCAGG-TGCACTTTTAGGAGATGACCAAATTTACAATGTTATCGTAACTGCCCATGCTTTT-GTTATAATTTTCTTC-ATAGTAATACCAATAATAATTGGAGGCTTTGGAAACTGACTTGTCCCACTAATAATCGGAGCCCCAGATATAGCATTCCCACGAATAAATAATATAAGTTTTTGACTCCTACCACCATCATTTCTCCTTCTCC-TAGCATCATCAATAGTAGAAGCAGGA
+s rn3.chr2 24388039 379 - 258222147 CAGCTGTTCTATCT----TCTAGCCAGGCTCATTAACCTTTTATGGTTTTCAACAAACCAGACACATATTGACATACTATTT----TATTATTTTGTGCTATAACTAGAGTAGGAGCTACTGCCCTAAGACTTTATTAATCCAAGTAAAATTATGACAAGCGGG-CACATTAGTTAGTGGTAATCAAATTTACATGGGCATTGTT------TATACGTTT-TAAATAACCTCTTTTAATAGTCATGACAGATATAAGTGAAGGACTTTTAA--TTGTTAGTTCTATTAGGGACTGAAGGCCCAGGTAGAACACTCGTTCAACTCCACAAAATAAATTTCTGGCCATTTGCTTCATCAGTTTGACTTCAGCTTTGCCTCCTCAATAGTAGAAACCAGT
+s canFam1.chrM 5334 377 + 16727 CAGCCATTTTACCT-----------ATGTTCATTAACCGATGACTGTTCTCCACTAATCACAAGGATATTGGTACTTTATAC---TTACTATTTGGAGCATGAGCCGGTATAGTAGGCACTGCTTTGAGCCTC--CTCATCCGAGCCGAACTAGGTCAGCCCGG-TACTTTACTAGGTGACGATCAAATTTATAATGTCATCGTAACCGCCCATGCTTTC-GTAATAATCTTCTTC-ATAGTCATGCCCATCATAATTGGGGGCTTTGGAAACTGACTAGTGCCGTTAATAATTGGTGCTCCGGACATGGCATTCCCCCGAATAAATAACATGAGCTTCTGACTCCTTCCTCCATCCTTTCTTCTACTAT-TAGCATCTTCTATGGTAGAAGCAGGT
+s galGal2.chrM 6630 380 + 16775 CAGCCATCTTACCT--------GTGACCTTCATCAACCGATGATTATTCTCAACCAACCACAAAGACATTGGCACTCTTTAC---CTAATTTTCGGCACATGGGCGGGCATAGCCGGCACAGCACTTAGCCTT--CTAATTCGCGCAGAACTAGGACAGCCCGG-AACTCTCTTAGGAGACGATCAAATTTACAATGTAATCGTCACAGCCCATGCTTTC-GTCATAATCTTCTTT-ATAGTTATACCCATCATGATCGGTGGCTTCGGAAACTGACTAGTCCCACTTATAATCGGTGCCCCAGACATAGCATTCCCCCGCATAAATAACATAAGCTTCTGACTCCTCCCTCCCTCCTTCCTTCTCCTAC-TAGCCTCATCTACCGTAGAAGCTGGG
+s danRer1.chrM 6410 377 + 16596 CGGCCACCCTACCT-----------GTGACAATCACACGTTGATTTTTCTCAACTAATCATAAAGACATTGGCACCCTGTAT---CTAGTATTTGGTGCTTGAGCCGGAATAGTAGGGACCGCATTAAGCCTC--TTAATCCGAGCTGAACTTAGCCAACCAGG-AGCACTTCTTGGTGATGATCAAATCTATAATGTTATTGTTACTGCCCATGCTTTT-GTAATAATTTTCTTT-ATAGTAATACCCATTCTTATTGGGGGATTTGGAAACTGACTTGTGCCACTAATGATTGGGGCCCCCGATATGGCATTTCCCCGAATAAATAATATAAGCTTCTGACTTCTTCCACCCTCATTTCTTCTTCTAT-TAGCTTCTTCTGGAGTTGAAGCAGGA
+
+a score=20468.0
+s hg17.chrM 6267 22 + 16571 GCAGGAACAGGTTGAACAGTCT
+s panTro1.chr3 35468034 22 - 209662276 GCTGGAACCAGCTGGACAGTTT
+s mm5.chrM 5690 22 + 16299 GCAGGAACAGGATGAACAGTCT
+s canFam1.chrM 5711 22 + 16727 GCAGGAACGGGATGAACCGTAT
+s galGal2.chrM 7010 22 + 16775 GCCGGCACAGGATGGACAGTTT
+s danRer1.chrM 6787 22 + 16596 GCTGGAACAGGATGAACAGTTT
+
+a score=598760.0
+s hg17.chrM 6289 707 + 16571 ACCCTCCCTTAGCAGGGAACTACTCCCACCCTGG----------AGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTCCT--CTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATA-ACCCA-ATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG----CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACC-ATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGAC
+s panTro1.chr3 35468056 706 - 209662276 GTCCCCCTTTAGCAGGAAAC----------CTAGCACATGCAGAAGCCTCTGTGGCTCTGACCATCTTCTCGTTCCACTTAGCAGGTGTTTTTTTTCTATTTTAGGGGCCattaattttattat--taattattaaCATAAAACCCCCAACCATA-TCCCA-GTATCCAACACCGCTTTTCGTCTGCTCAGTCCGCATTATGGCAGTCCT-CTACTCCTTTCCCTCCCAGTCCTAG----CCGCCGGCATTGCTATGCTATTAACTGACCATAACCTCAACAGTACTTCTTTTGACCCTGCTTGTGG-GGTGACCCCATCTTGTTCCAACATTTATTCTGATTCTTTGGTCGCCCTGAAGTCTACATCCTTATCCTACCGGGCTTCGGGATAATCTCCCACATCGCAACATATTATTCTGGAAAAAAGGAACCCATTTGTGTACATGGGCATAGTATGAGCCATGATATCAGTTGGCATCTTTGGATTTATCGTATGGGCTCACCATATATTTACAGTAGGAATAGACATAGACACACTAGCATACTTCACCTCCACTACCATAATAATTGCCATCCCTACTGGCATCAAGGTCTTTAGCTGATTAGCTACCCTGCACCGCGGTAACATCAGATGATCTCCCGCAATATTCTGAGCCCTAGGATTCATTTTCCTTTACAGAGTAGGAGGTTTAACCGACATCGTACTAGCTAATTCATCACTAGAT
+s mm5.chrM 5712 707 + 16299 ACCCACCTCTAGCCGGAAAT----------CTAGCCCATGCAGGAGCATCAGTAGACCTAACAATTTTCTCCCTTCATTTAGCTGGAGTGTCAT--CTATTTTAGGTGCAATTAATTTTATTACCACTATTATCAACATGAAACCCCCAGCCATA-ACACA-GTATCAAACTCCACTATTTGTCTGATCCGTACTTATTACAGCCGTACTGCTCCTATTATCACTACCAGTGCTAG----CCGCAGGCATTACTATACTACTAACAGACCGCAACCTAAACACAACTTTCTTTGATCCCGCTGGAGGAGGGGACCCAATTCTCTACCAGCATCTGTTCTGATTCTTTGGGCACCCAGAAGTTTATATTCTTATCCTCCCAGGATTTGGAATTATTTCACATGTAGTTACTTACTACTCCGGAAAAAAAGAACC-TTTCGGCTATATAGGAATAGTATGAGCAATAATGTCTATTGGCTTTCTAGGCTTTATTGTATGAGCCCACCACATATTCACAGTAGGATTAGATGTAGACACACGAGCTTACTTTACATCAGCCACTATAATTATCGCAATTCCTACCGGTGTCAAAGTATTTAGCTGACTTGCAACCCTACACGGAGGTAATATTAAATGATCTCCAGCTATACTATGAGCCTTAGGCTTTATTTTCTTATTTACAGTTGGTGGTCTAACCGGAATTGTTTTATCCAACTCATCCCTTGAC
+s rn3.chr2 24388832 523 - 258222147 ATTTACCATTAACCAGAAAT----------CCTGCAGCGACAGGGGCTTCTGTAATTATTGCCATTTTCATGTTACTTTTAGAAAATGTTTCTT--CAGTTTTAAGAATTACTAATTACACCATAACATCCATGAAGATAATAACACCAGCTACAGGCACAGGTACCA---------------CTGAACAGCATTAATTACAGCTGTACTTTTACTCTTAGCTTATCTAATACTAGGACCTAGCTAGCGTCATCATGCTGTACACA-ACAATACTCTTAACATCTCTTTCTTCAATCCAGCGTGAGAAAAT--CCCACTGCTAGATCAATCATGATTCTTATCTTTTGGG-ATCCAGAAACACACGTTATCATCTGATCCTGACTAGGAATGATCTTGCATAGTGTGACA-ACTATTCTTGATCCAAAGAGTC-AAT-GGTTACATGGGG--TATCTGAGCCAGGATAGCGGTTGGTTTGTATGGCTTTCCTGCATGGGTCTACCATATTTTCGCAGTGGCA--------------------------------------------------CATTCC-----------------------------------------------------------------CATTATCCTCATTCATAGGCATGATCTTCTC----------------------------------------------------
+s canFam1.chrM 5733 707 + 16727 ACCCCCCACTGGCTGGCAAT----------CTGGCCCATGCAGGAGCATCCGTTGACCTTACAATTTTCTCCTTACACTTAGCCGGAGTCTCTT--CTATTTTAGGGGCAATTAATTTCATCACTACTATTATCAACATAAAACCCCCTGCAATA-TCCCA-GTATCAAACTCCCCTGTTTGTATGATCAGTACTAATTACAGCAGTTCTACTCTTACTATCCCTGCCTGTACTGG----CTGCTGGAATTACAATACTTTTAACAGACCGGAATCTTAATACAACATTTTTTGATCCCGCTGGAGGAGGAGACCCTATCCTATATCAACACCTATTCTGATTCTTCGGACATCCTGAAGTTTACATTCTTATCCTGCCCGGATTCGGAATAATTTCTCACATTGTCACTTACTACTCAGGGAAAAAAGAGCC-TTTCGGTTATATAGGAATAGTATGAGCAATAATATCTATTGGGTTTTTAGGCTTTATCGTATGAGCTCACCATATGTTTACCGTAGGAATAGATGTAGACACACGAGCGTACTTTACGTCCGCCACTATAATTATCGCTATTCCAACGGGAGTAAAAGTATTTAGTTGACTGGCAACACTTCATGGAGGCAATATTAAATGATCTCCAGCTATGCTATGAGCTTTAGGGTTTATTTTCTTATTTACAGTAGGCGGGTTAACAGGTATTGTCCTAGCTAATTCGTCCTTAGAC
+s galGal2.chrM 7032 704 + 16775 ACCCCCCTTTAGCCGGCAAC----------CTAGCCCACGCTGGCGCATCAGTAGACCTAGCCATCTT-TCATTAC--TTAGCAGGTGTTTCCT--CCATTCTAGGAGCCATCAACTTTATCACTACCATCATCAACATAAAACCCCCCGCACTG-TCACA-ATACCAAACACCCCTATTCGTATGATCCGTCCTCATTACTGCCATCCTACTACTCCTCTCCTTACCCGTCCTAG----CAGCTGGGATTACCATACTACTTACCGACCGCAACCTTAACACCACATTCTTCGACCCAGCTGGAGGAGGAGACCCAATCCTATACCAACACCTATTCTGATTCTTCGGTCACCCCGAAGTTTACATCCTCATCCTCCCAGGTTTCGGAATAATTTCCCACGTAGTAGCATACTATGCAGGAAAAAAAGAACC-ATTCGGATACATAGGAATAGTCTGAGCCATACTGTCAATCGGATTCCTTGGCTTCATTGTATGAGCCCACCATATATTCACAGTCCGAATGGACGTAGACACCCGAGCCTACTTTACATCAGCCACAATAATCATCGCCATCCCAACTGGTATTAAAGTCTTCAGCTGACTAGCAACCCTGCACGGAGGAACAATTAAATGAGACCCCCCTATGCTATGAGCCCTAGGATTCATCTTCCTCTTCACTATCGGAGGCCTAACGGGAATCGTCCTTGCTAACTCATCACTAGAT
+s danRer1.chrM 6809 707 + 16596 ATCCACCTCTTGCAGGCAAC----------CTTGCCCATGCAGGAGCATCTGTTGATCTAACAATTTTTTCACTACACTTAGCAGGTGTTTCAT--CTATTCTTGGAGCAATTAATTTTATTACTACTACAATTAACATGAAGCCACCAACTATC-TCTCA-GTATCAAACTCCATTATTTGTATGAGCTGTCTTAGTTACAGCTGTACTACTTCTTTTATCTTTACCAGTGTTAG----CTGCCGGAATTACAATACTTCTTACAGACCGAAATCTTAACACAACGTTCTTTGACCCGGCAGGAGGGGGAGATCCAATTCTTTATCAACACTTATTTTGATTCTTTGGCCACCCAGAAGTCTACATTCTTATTTTACCAGGATTCGGCATTATCTCCCATGTTGTAGCATACTACGCAGGGAAAAAAGAACC-ATTCGGGTATATAGGAATAGTATGAGCTATAATGGCTATTGGTCTCTTAGGTTTTATTGTATGAGCCCATCACATATTCACTGTAGGAATGGATGTAGACACCCGAGCATACTTCACATCCGCCACAATGATTATTGCTATTCCAACTGGTGTAAAAGTATTTAGCTGATTAGCCACTCTCCACGGAGGAGCTATTAAATGAGAAACCCCTATACTATGGGCACTAGGATTTATTTTCTTATTTACAGTAGGAGGGTTAACCGGAATCGTTTTAGCCAACTCATCATTAGAC
+
+a score=102002.0
+s hg17.chrM 6790 88 + 16571 GAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGC
+s panTro1.chr3 35468556 88 - 209662276 GAATAGACATAGACACACTAGCATACTTCACCTCCACTACCATAATAATTGCCATCCCTACTGGCATCAAGGTCTTTAGCTGATTAGC
+s mm5.chrM 6213 88 + 16299 GATTAGATGTAGACACACGAGCTTACTTTACATCAGCCACTATAATTATCGCAATTCCTACCGGTGTCAAAGTATTTAGCTGACTTGC
+s rn3.chr14 86907881 83 - 112220682 GCCTTGATGGAGAAACATGAGATAACTTTACGTCAGCCATTATTATTATTGTAATTCCTACTGCTGC-----TATTTAGCTGACTTAC
+s canFam1.chrM 6234 88 + 16727 GAATAGATGTAGACACACGAGCGTACTTTACGTCCGCCACTATAATTATCGCTATTCCAACGGGAGTAAAAGTATTTAGTTGACTGGC
+s galGal2.chrM 7530 88 + 16775 GAATGGACGTAGACACCCGAGCCTACTTTACATCAGCCACAATAATCATCGCCATCCCAACTGGTATTAAAGTCTTCAGCTGACTAGC
+s danRer1.chrM 7310 88 + 16596 GAATGGATGTAGACACCCGAGCATACTTCACATCCGCCACAATGATTATTGCTATTCCAACTGGTGTAAAAGTATTTAGCTGATTAGC
+
+a score=448969.0
+s hg17.chrM 6996 444 + 16571 ATCGTACTACACGACACGTACTACGTTGTAGCTCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTATCATATTCATCGGCGTAA---ATCTAACTTTCTTCCC---ACAACACTTTCTCGGCCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAAT----------------AATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAG----AACCCGTATACATAAAA-
+s panTro1.chr3 35468762 441 - 209662276 ATTGTCTTACACGACACATACTATGTTGTAGCCCATTTCCACTACGTTCTATCAATAGGAGCAATATTTGCCATTACAGGAGGCTTTGTCCACTGATTCCCCCTATTTTCAGGTTATACATTTAATCAGACCTATGCTAAAATCCACTTCACCATTATATTCATAGGTGTTA---ACTTAACCTTTTTTCC---ACAGCACTTCCTCAGCCTATCGGGTATGCCTCGACATTACTCCAATTACTCTGATGTGTACACCATATGAAATATTGTCTCATCCATAGGCTCATTTATCTCACTAACAGCTGTTATACTAAT----------------AATCGTTATGATCTGAGAGGCCTTTGCTTCAAAATGAAAAGT----ACAATTGCACAATCATCTACTAATTTAGAGTGACTTTACAGCTGTCCACCACCTTACCACACATTTGAAGAGCCAACCTGTGTG---AAAA-
+s mm5.chrM 6419 444 + 16299 ATCGTGCTTCACGATACATACTATGTAGTAGCCCATTTCCACTATGTTCTATCAATGGGAGCAGTGTTTGCTATCATAGCAGGATTTGTTCACTGATTCCCATTATTTTCAGGCTTCACCCTAGATGACACATGAGCAAAAGCCCACTTCGCCATCATATTCGTAGGAGTAA---ACATAACATTCTTCCC---TCAACATTTCCTGGGCCTTTCAGGAATACCACGACGCTACTCAGACTACCCAGATGCTTACACCACATGAAACACTGTCTCTTCTATAGGATCATTTATTTCACTAACAGCTGTTCTCATCAT----------------GATCTTTATAATTTGAGAGGCCTTTGCTTCAAAACGAGAAGTAATATCAGTATCGTATGCTTCAACAAATTTAGAATGACTTCATGGCTGCCCTCCACCATATCACACATTCGAGGAACCAACCTATGTA---AAA--
+s rn3.chr2 24389355 357 - 258222147 --------------------------------------------------------------------------CATTGTAGATTTCTTTCACTGATTTCCACTCTTTTGAGGTGATGCTCT--ATGAAAACTAAACAAAAAATCATTTTACAATTAAATTTGTAGGTGTTATCCGTTTAAATTTTCTGGCTAATCAATAATTTCACATTCTCT--------------TGCTATTCTTAACAGTC--------ATAGCCCATAAAATCTCAACTCATTGACAAATTCATTTATTAAACTAACAGTAGTAGTGCTAACTCTGTTAGTAGTGCTAATTCTTCATAACTTTCAGTGTTTATGCTTTAAAATAGGAAGTC---TCAGCAGAACATTCAACCACAAATCTTAAATGATTTTATTTCTAGCC--------ACCAGACATTCAAAGAACTTTCTCACGGA---AAA--
+s canFam1.chrM 6440 444 + 16727 ATCGTTCTTCATGATACATATTATGTTGTGGCTCATTTTCACTATGTGCTTTCAATAGGAGCAGTTTTTGCCATTATGGGAGGATTTGCCCACTGATTCCCTTTATTCTCAGGTTATACTCTTAACGATACTTGAGCAAAGATTCACTTTACAATTATGTTTGTGGGAGTAA---ATATAACTTTCTTCCC---TCAACATTTCCTAGGTTTATCTGGAATACCTCGTCGATACTCTGACTACCCAGATGCATATACTACCTGAAATACCGTCTCCTCTATAGGATCGTTTATCTCGCTTACAGCGGTGATGCTTAT----------------AATTTTTATGATCTGGGAAGCCTTTGCATCCAAACGAGAAGTTGCTATAGTAGAACTTACTACAACTAACATTGAGTGACTACATGGATGTCCCCCTCCATACCACACGTTCGAAGAACCTACATATGTG---ATC--
+s galGal2.chrM 7736 444 + 16775 ATTGCCCTTCATGACACCTACTATGTAGTCGCCCACTTCCACTATGTCCTCTCAATGGGGGCAGTTTTTGCCATTCTAGCAGGATTTACCCACTGATTTCCCCTCTTCACAGGCTTTACCCTACACCCATCATGAACCAAGGCACATTTCGGAGTAATATTTACCGGAGTTA---ACCTAACCTTTTTCCC---CCAACATTTCCTGGGCCTAGCTGGAATACCCCGACGATACTCAGATTACCCAGACGCCTACACACTATGAAACACACTATCCTCAATCGGCTCCTTAATTTCAATAACAGCCGTAATCATACT----------------CATATTCATCGTCTGAGAAGCCTTCTCAGCAAAACGAAAAGTACTCCAACCCGAATTAACTGCCACTAATATCGAATGAATTCATGGCTGCCCACCCCCATACCACACCTTCGAAGAACCAGCCTTTGTA---CAA--
+s fr1.chrUn 326222607 444 + 349519338 ATCGTATTACACGACACCTACTACGTAGTTGCCCATTTCCACTACGTCCTCTCCATGGGTGCTGTATTTGCAATTATGGGTGCATTCGTACACTGATTCCCACTATTTTCAGGATACACACTCCACAGCACTTGAACTAAAATCCACTTCGGAGTAATGTTCATTGGTGTCA---ACCTAACCTTCTTCCC---TCAACACTTCCTTGGTCTAGCTGGAATACCTCGACGATACTCCGACTACCCCGACGCCTACGCCCTATGAAACTCCGTCTCCTCAATTGGCTCAATAGTCTCTCTAGTGGCAGTAATTATGTT----------------CCTCTTTATCCTCTGAGAGGCCTTCACCGCTAAGCGAGAAGTCCAATCAGTTGAACTAACAATGACAAATGTAGAATGACTACACGGGTGCCCTCCTCCTTACCACACATTCGAAGAGCCCGCCTTTGTC---CAA--
+s danRer1.chrM 7516 445 + 16596 ATCGTACTACATGACACATACTACGTAGTAGCACACTTTCACTATGTTCTTTCAATAGGAGCTGTATTCGCTATTATAGCAGGCTTTGTTCACTGATTCCCACTATTTACAGGCTACACCCTAAACAGTGTATGAACAAAAATCCATTTCGGGGTTATATTTATCGGAGTAA---ATCTCACATTCTTCCC---ACAACATTTCCTAGGTTTAGCAGGAATACCACGACGGTACTCTGACTACCCAGACGCCTATGCACTCTGAAATACAGTATCTTCTATTGGGTCACTAATTTCTTTAGTAGCAGTAATCATGTT----------------CTTATTTATCTTATGAGAAGCCTTTACCGCCAAACGAGAAGTTCTGTCAGTTGAATTGACCGCAACAAATGTAGAATGATTACACGGCTGCCCTCCCCCCTACCACACATTTGAGGAGCCAGCATTCGTT---CAA-A
+
+a score=81951.0
+s hg17.chrM 7029 51 + 16571 CACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGGC
+s panTro1.chr3 35468795 51 - 209662276 CATTTCCACTACGTTCTATCAATAGGAGCAATATTTGCCATTACAGGAGGC
+s mm5.chrM 6452 51 + 16299 CATTTCCACTATGTTCTATCAATGGGAGCAGTGTTTGCTATCATAGCAGGA
+s rn3.chrUn 51520592 51 + 75822765 CACTTCTACTAGGTACTGTCTATAGGAGCGGCACTCGCTATTACAGCTGGG
+s canFam1.chrM 6473 51 + 16727 CATTTTCACTATGTGCTTTCAATAGGAGCAGTTTTTGCCATTATGGGAGGA
+s galGal2.chrM 7769 51 + 16775 CACTTCCACTATGTCCTCTCAATGGGGGCAGTTTTTGCCATTCTAGCAGGA
+s fr1.chrUn 326222640 51 + 349519338 CATTTCCACTACGTCCTCTCCATGGGTGCTGTATTTGCAATTATGGGTGCA
+s danRer1.chrM 7549 51 + 16596 CACTTTCACTATGTTCTTTCAATAGGAGCTGTATTCGCTATTATAGCAGGC
+
+a score=-1119.0
+s hg17.chrM 7440 9 + 16571 TCTAGACAa
+s panTro1.chr3 35469203 9 - 209662276 CCTAAgtga
+s rn3.chr2 24389713 9 - 258222147 CTTAAATGA
+s canFam1.chrM 6884 9 + 16727 CAAAAAtaa
+s galGal2.chrM 8181 8 + 16775 TGCAAGAA-
+s fr1.chrUn 326223060 9 + 349519338 TCTATCCGA
+s danRer1.chrM 7961 9 + 16596 TTCAATCAA
+
+a score=0.0
+s hg17.chrM 7449 66 + 16571 aaaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggcctccatgactttttc
+
+a score=14522.0
+s hg17.chrM 7449 66 + 16571 aaaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggcctccatgactttttc
+s panTro1.chr3 35469212 65 - 209662276 gaaaggaaggaatcaaaactccagaaactggtttcaagccagtccaataacc-ccatgactctctc
+s rn3.chr2 24389722 59 - 258222147 GAAACAA---GATTAAACCCCTATA----GGCTTCAAGTCAGTCCCATAAGCATCGTTATTTATCC
+s canFam1.chrM 6893 66 + 16727 gaaaggaaggaatcgaaccccctaaaattggtttcaagccaatgtcataaccattatgtctttctc
+
+a score=0.0
+s hg17.chrM 7449 66 + 16571 aaaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggcctccatgactttttc
+
+a score=-609.0
+s hg17.chrM 7515 1 + 16571 ---A
+s panTro1.chr3 35469277 1 - 209662276 ---G
+s mm5.chrM 6938 1 + 16299 ---A
+s canFam1.chrM 6962 1 + 16727 ---C
+s galGal2.chrM 8189 1 + 16775 ---A
+s fr1.chrUn 326223069 4 + 349519338 GAAA
+
+a score=172785.0
+s hg17.chrM 7516 230 + 16571 AAAAG--------------------------------------------------------------------GTATTAGAAAAACC---ATTTCATAACTTTGTCAAAGTTAAATTATAGGC-TAA-A-TCCTATATATCTTA------------ATGG-CACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAA-----TACTA
+s panTro1.chr3 35469278 230 - 209662276 ATAAG--------------------------------------------------------------------ATATTAGTAAAATT---ATTCCATAACTTTGTCAAAGTTAGTTTATAGGT-TAA-A-TCCTATATGTCTTA------------ATGG-CTCATGCAGTTCAATTAGGACTTCAAGATGCTACATCCCTTATTATAGAAGAACTACTCACTTTCCATGACCACACTCTTACAATTATTTTCCTAATTAGTTCCCTAGTCCTATACATTATTTCCCTAATATTCACAACAAAATTAACTCA-----TACTA
+s mm5.chrM 6939 233 + 16299 ATAAG--------------------------------------------------------------------ATATTAGTAAAATC--AATTACATAACTTTGTCAAAGTTAAATTATAGAT-CAATA-ATCTATATATCTTA---T--------ATGG-CCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAAAACTAACACA-----TACAA
+s rn3.chr2 24389781 236 - 258222147 ATAAG-------------------------------------------------------------TTAT---GCATTAGAAATAGT---ATTATGTTACTTGGTCAGCATTAA-TTATAGTTATAA-A-TCATTTTAGTCTTC------------TTGGATATATCCATTCCAATTAGAATTTTAAGATTTCATATCATCTA--GTAAAAAATTTCCCAGGCTTGCATGAGAACATATTAATAAATGTAAT--TTAATAACTCTCTAGTCTGTTATGTTATTCTGTTGGTACCAATAACAAAATCAACTTACAAAGTACTA
+s canFam1.chrM 6963 230 + 16727 AGGAG--------------------------------------------------------------------GTATTAGTAAAAC----ATTACATGACTTTGTCAAAGTTAAATTATAGGT-GAA-ACCCCTATATATCTCT------------ATGG-CGTACCCATTTCAACTCGGATTACAGGACGCAACCTCCCCTATTATAGAGGAGCTACTTCATTTTCATGACCATACACTAATAATTGTATTCTTAATCAGTTCTTTAGTTCTCTATATCATTTCACTAATATTGACTACAAAATTAACCCA-----TACAA
+s galGal2.chrM 8190 297 + 16775 GGAAGGAATCGAACCCTCACATGTTGGTTTCAAGCCAACCGCATCAAACCACTTAATGCTTCTTTCTTATGAGACGTTAGTAAACCA---ATTACATAGACCTGTCAAGACTAAATCACAGGTGCAA-A-CCCTGTACATCTCA---T--------ATGG-CCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTCGTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTACCTTCTAACTCTTATACTTATAGAAAAACTATCATC-----AA---
+s fr1.chrUn 326223073 305 + 349519338 GGGAGGAATCGAACCCCCGTAAACTGGTTTCAAGCCAGCTACAAAACCACTCTGTCACTTTCTTCATAAG---ACTCTAGTAAAATGGCAATTACACTACTTTGTCAAGGTAGAATTGTGGGT-TAA-ACCCCCACGTGTCTTA---T---TATTAATGG-CACATCCTTCACAACTAGGGTTTCAAGATGCAGCTTCACCAGTAATAGAAGAACTCCTTCACTTCCACGACCATGCTCTAATAATCGTATTCCTTATTAGCACATTAGTACTTTACATTATTGTTGCTATAGTCTCCACCAAACTAACTAA-----CAAGT
+s danRer1.chrM 8046 243 + 16596 ATAAG--------------------------------------------------------------------ACATTAGCAAAAAC---ATTACACCACTTTGTCAAGGTGAAATTACAAGT-TAA-AACCTTGTATGTCTTAACCTAAATTCTAATGG-CACACCCTGCACAACTAGGATTCCAAGACGCAGCATCACCTGTAATAGAAGAACTTTTATGTTTTCACGACCATGCTTTAATAATTGTATTTTTAATCAGCACCTTAGTTCTATACATTATCATCGCAATAGTGTCAACCAAACTAACGAA-----TAAAT
+
+a score=69426.0
+s hg17.chrM 7746 69 + 16571 ACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCG
+s panTro1.chr3 35469508 69 - 209662276 GCACCATAGATGCCTAAGAAATCGAGACTGTGTGAACTATTTTGCTTGCCATTATCTTAATTTTAATTG
+s mm5.chrM 7172 69 + 16299 GCACAATAGATGCACAAGAAGTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTG
+s canFam1.chrM 7193 69 + 16727 GCACAATAGACGCACAAGAAGTGGAAACAGTATGAACCATTCTACCCGCCATTATCCTAATCCTAATCG
+s galGal2.chrM 8487 69 + 16775 ACACCGTAGATGCCCAAGAAGTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTG
+s fr1.chrUn 326223378 69 + 349519338 ACATTCTAGACTCTCAAGAGATTGAAATTATCTGAACTATCCTACCAGCTATTATTCTTATCCTCATTG
+s danRer1.chrM 8289 69 + 16596 TTATTCTAGATTCCCAAGAAATCGAAATCGTATGAACAGTCCTTCCGGCCATCATTCTTATTTTGATTG
+
+a score=5283.0
+s hg17.chrM 7815 6 + 16571 CCCTCC
+s panTro1.chr3 35469577 6 - 209662276 CCCTCC
+s mm5.chrM 7241 6 + 16299 CTCTCC
+s canFam1.chrM 7262 6 + 16727 CTCTAC
+s galGal2.chrM 8556 6 + 16775 CCCTCC
+s danRer1.chrM 8358 6 + 16596 CTTTAC
+
+a score=83513.0
+s hg17.chrM 7821 93 + 16571 CATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGA--GT
+s panTro1.chr3 35469583 95 - 209662276 CATCCCTACATATTCTGTAAATAACAGATGAAATTAACAACCCTGCTCTTACAGTCAAAGCAATTGGCCACCAATAATATTGAAACTATGAATGT
+s mm5.chrM 7247 93 + 16299 CCTCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGA--AT
+s rn3.chr2 24391128 92 - 258222147 CTTTTCTGTAAATGCTATACATGATGTATGAAATTAATAATTCTTTAATAAAC-TAAAAACTTCAAGCTATCTATAGTACTAAAGTCATGA--AT
+s canFam1.chrM 7268 93 + 16727 CTTCCCTCCGAATCCTTTATATAATGGACGAAATTAATAACCCCTCTTTAACCGTGAAAACAATAGGCCACCAATGATACTGAAGCTATGA--AT
+s galGal2.chrM 8562 93 + 16775 CCTCCCTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATCGGACACCAATGATACTGAACCTATGA--AT
+s danRer1.chrM 8364 93 + 16596 CATCACTTCGAATTTTATACCTTATAGATGAAATTAATGACCCCCACGTTACTATTAAAGCCGTAGGACATCAATGGTACTGAAGCTACGA--AT
+
+a score=322789.0
+s hg17.chrM 7914 535 + 16571 ACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCC-----------TAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGC---TTAAAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAAC------TTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCC------------------ACCATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAAT-
+s panTro1.chr3 35469678 508 - 209662276 ACA--GACTATGAAGAATTAGGCTTCGATTCTTATATA-----------ATTCCAACAGCAGACTTAAAGCCAGGAGAACTTCAACTCCTCAAAGTTGATAACCAAACAATTCTCCCAATAGATATCCCCATCCGTACATTAATCTCATCTGAAGATGTCCTGCACTCATGAACTATCCCCTCATTGGGC---CTGAAAAGGGATGCAATCCCTGGATG-CTAAATCAAACCACCCTAACTGCTACATGACCAGGCCTTTACTATGGACAGTGCTCAGAAATTTGTGGGTCCAACCACAGTGTTATACCTATTGTCCTAGAATTAACCCCCTTAAAATGCTTCGAAACCTGATCCATGTCCACACTATAATA----------------------TCACTGTAAAGCTATC-------TAGCATTAAACTTTTAAGTTAAAGACTGAGCGGATCTACACCTCTCTGCAGTG-AATGCCTCAACTAGATACTTCCACATAATCCATTGTCATTCTGTCAATAACCATAA--------------CTT----TATTCTCCATTATTCAGTTAAAATT-
+s mm5.chrM 7340 508 + 16299 ATACTGACTATGAAGACCTATGCTTTGATTCATATATAATCCCAACAAACGACC-----------TAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGA---CTTAAAACTGATGCCATCCCAGGCCGACTAAATCAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGTGGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAAAACTGATCTGCTTCAATAATTTAATT----------------------TCACTATGAAGCTAA--------GAGCGTTAACCTTTTAAGTTAAAGTTAGAG---ACCTTAAAATCTCCATAGTGATATGCCACAACTAGATACATCAACATGATTT------------------ATCACAATTATCTCATCAATAATTACCCTATTTATCTTATTTCAACTAAAAGT-
+s rn3.chr2 24391220 461 - 258222147 ATATAGAATAT--TGACCTATCTATTTATTTCTATGTAATTCCTATAATTGAAC-----------TTAACTCAGAAAAGCTAGAGCTGCTAAAAATGAAGAATTACGTAATAAAACCTATATAGATC----TTCATATATTTATCTTAT----AAGTGTCT----CTCCAGAGCTTTCATCT--TTGGGCCTACTAAAAGCAAGTATAATTCCAGGACA-------GATGCAACTCTAATATCCACAAGACTAGATATGTGATGCCAACAATAATCAGAAATTTAAGGATGTAACTACAGCCTTATATAGGTTATACTTAAATTAATTCCAATTAAGTAGCTTGAGATTGAATTAGTATCAATAGTACAATG----------------------TTATTCTAAGTTTAA--------CACCATTGACC-TTTAAGT--AATAATGAG------TAAAATATTTCATAATT-------TCAATCTGATCTATTAGTA----CT------------------ATTGTAA-TATCT--------GTAGCACTATTTCTC-TTATTCAATTAACAAT-
+s canFam1.chrM 7361 524 + 16727 ATACTGACTATGAAGACTTAAACTTTGACTCCTACATAATCCCAACACAAGAAT-----------TAAAGCCAGGAGAACTCCGACTATTAGAAGTAGACAACCGAGTTGTCCTCCCAATAGAAATAACCATCCGAATACTTATCTCTTCAGAAGACGTTTTGCATTCATGAGCCGTTCCATCACTAGGT---CTAAAAACTGACGCTATTCCAGGACGACTAAACCAAACCACCCTTATAGCCATACGACCAGGACTGTACTATGGCCAGTGCTCTGAAATCTGCGGATCTAACCACAGCTTTATACCCATTGTTCTTGAAATAGTCCCCCTATCTTACTTTGAGACCTGATCTGCCTTAATAGTATAACCTAGACTAGATCTAC--------TCATTAAGAAGCTATA-------AAGCATTAACCTTTTAAGTTAAAGACTGGG--AGTTTTAACCTCTCCTTAATGAAATGCCACAGCTAGATACATCCACCTGATTT------------------ATTATAATCTTTTCAATATTTCTCACCCTCTTCATCCTATTTCAACTAAAAAT-
+s galGal2.chrM 8655 498 + 16775 ACACAGACTTCAAGGACCTCTCATTTGACTCCTACATAACCCCAACAACAGACC-----------TCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCATCGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTCCACTCATGAGCCGTACCCGCCCTCGGG---GTAAAAACAGACGCAATCCCTGGACGACTAAATCAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGCGGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAAGCCTGATCCTCACTA-----------------CTGTCATCTTAA----CCATTAAGAAGCTATG----CACCAGCACTAGCCTTTTAAGCTAGAGAGAGGGGACACC----CTCCCCCTTAATGACATGCCCCAATTAAACCCAAACCCATGATTC------------------TCCATCA---------TACTCCTAACTTGATTCACCTTCTCTCTGCTT------
+s fr1.chrUn 326223582 517 + 349519338 ATACAGACTATAGCGA-CTAGCCTTTGACTCATATATAGTCCC-ACACAAGACC-----------TGGCCCCCGGCCAATTCCGCCTTTTAGAAACTGACCATCGAATGGTCGT-TCAGTGGACTCCCCCATTCGAATCCTAGTCTCAGCAGAAGATGTCCTCCACTCCTGAGCCGTCCCCTCTCTAGGT---GTAAAAATGGATGCCGTACCCGGCCGTCTAAACCAAACAGCCTTTATCCTGTCCCGACCTGGTGTTTTCTACGGCCAATGCTCCGAAATCTGCGGAGCTAACCACAGCTTCATACCAATCGTTGTTGAAGCCGTCCCCCTAGAACACTTTGAAAACTGATCCTCACTAATGCTCGAAGATGCCTC------------------ACTAAGAAGCTAAAACGGACACAGCGTTAGCCTTTTAAGCTAAAAATGGTG---CCTACCAAACACCCTTAGTGAAATGCCTCAACTCAACCCCGCACCTTGATTC------------------CTCATTATGGTCTTCTCTTGATGTGTATTCCTAATCTTCCTCCCTCCAAAAAT-
+s danRer1.chrM 8457 520 + 16596 ATACAGACTACGAAAACCTAGAATTTGACTCTTATATAGTACCAACCCAAGACC-----------TCACACCAGGGGGCTTTCGGCTTCTTGAAACAGACCATCGAATAGTAGTTCCCAAAGAATCACCAATTCGAATTTTAGTTTCAGCTGAAGACGTACTGCACTCTTGAGCTGTTCCATCATTAGGC---ATTAAAATAGACGCGGTACCCGGACGATTAAACCAAACCGCTTTTATTGTTTCACGTCCAGGTGTATTCTACGGACAATGCTCTGAAATCTGCGGGGCTAACCACAGCTTTATGCCCATTGTAGTCGAAGCCGTCCCACTTGAATTCTTTGAAAACTGATCTTCAGCTATACTAGAAGACGCC------------------TCACTAAGATGCTAAAATTGGA-TAGCGTTGACCTTTTAAGTCAAAACTTGGT--GCTTACCGACCACCCTTAGTG-AATGCCTCAGCTTAATCCAAAACCCTGATTT------------------ATAATCCTTTTTTTCTCATGAGTCATTTTCCTTACTATTATTCCAACCAAAATC
+
+a score=355.0
+s hg17.chrM 8449 6 + 16571 ATTAAA
+s canFam1.chrM 7885 6 + 16727 TTCAAA
+s galGal2.chrM 9153 6 + 16775 ATCCAA
+s fr1.chrUn 326224100 3 + 349519338 ---ATA
+s danRer1.chrM 8977 6 + 16596 ATTAAT
+
+a score=1195.0
+s hg17.chrM 8449 5 + 16571 ATTAA
+s panTro1.chr3 35470186 5 - 209662276 ATTAA
+s mm5.chrM 7848 5 + 16299 CTCAT
+s canFam1.chrM 7885 5 + 16727 TTCAA
+s galGal2.chrM 9153 5 + 16775 ATCCA
+s fr1.chrUn 326224100 4 + 349519338 -ATAG
+s danRer1.chrM 8977 5 + 16596 ATTAA
+
+a score=91.0
+s hg17.chrM 8454 1 + 16571 A
+s panTro1.chr3 35470191 1 - 209662276 A
+
+a score=0.0
+s hg17.chrM 8454 1 + 16571 A
+
+a score=-28769.0
+s hg17.chrM 8455 36 + 16571 CACAAAC--------TACCACCTAC-----CTCCCTCACCAAAGCC------------CAT
+s mm5.chrM 7853 46 + 16299 CACAAAC-------ATTCCCACTGG-----CACCTTCACCAAAATC---ACTAACAACCAT
+s rn3.chr2 24391681 39 - 258222147 CCCAAAGTATATTTATTCTAATT----------TTTCATCAAAGAA------------TAT
+s canFam1.chrM 7891 36 + 16727 -----------TCACTACTACCCAGA-AAACCCGATAACCAAATCT---GC----------
+s galGal2.chrM 9159 36 + 16775 CCCAAAC--------TTCTTTCATT-----CACTCTAACAAACAAC------------CCT
+s fr1.chrUn 326224106 37 + 349519338 ------------CACTTATTCCCAAATGAACCCTCCTCTCAAAACA------------CTT
+s danRer1.chrM 8983 45 + 16596 -----------CACATTCAACCTAA-----TGACCCAACTCAAGTTGATGCTAAAGAGCAC
+
+a score=321517.0
+s hg17.chrM 8491 590 + 16571 AAAAATAA---------AAAATTATAACAAA-----------CCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT---CTATTGATCCCCACCT---CCAAATATCTC---ATCAACAACCGACTAATCACCACCCAACAATGACTAA-TCAA-----ACTAACCTCAAAACAAATGATA--GCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCTAGCCCACTTCTT--ACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTA-ATT---GGAAGCGCCACCCTAGCAATATCA--------ACCATTAA
+s panTro1.chr3 35470215 591 - 209662276 AAAAATAAT-------CAAAAT----GCAAAAACATAAAGCTCTCTGAGAATTAAAATGAAAGAAAATCTATTTACCCCTTTTACTACCCTGACAATTCTAGGCCTACCCGCAGTAGTATTAATCATTTTATTTCCCACCAAACTAT---TTCCAACCT---CCAGTCATCTA---ATTAGTAACCAACTGATTTCCATTCAACAGTGACTAATTCAACTTGTACT------AAAACAAATAATATTACC---CATAACATTAAAGGACAAACCTGATCCCTTATACTGATCTTCCTAATTCTCTTCATTGCCTCAACCAATCTCCTCGGGCCTCTACCCCATTAATTTACACCAACTACCCAATTATCAATAAATCTAGGTATAGCAATCCCCTTATGAGCAGGTGCAGTAATTATAGGCTTCTGCTTTAAGACGAAA-------------ACCTCTTTAGCCACAAGGCACACCTATACCACTTATCTCTATGCTAGTGATCATTGAAACTATTAGCCTATTCATTCAACCAATGGCATTAGCTGTGCGATTAACAGCCAACCTTACAGCCAGACACCTACTAATGCATTTATATCGGAGGAGGAGCCACACTAGTACTATCA--------ACTATCAG
+s mm5.chrM 7899 581 + 16299 AAAAGTAA---------AAACC--------------------CCTTGAGAATTAAAATGAACGAAAATCTATTTGCCTCATTCATTACCCCAACAATAATAGGATTCCCAATCGTTGTAGCCATCATTATATTTCCTTCAATCCTAT---TCCCATCCT---CAAAACGCCTA---ATCAACAACCGTCTCCATTCTTTCCAACACTGACTAG-TTAA-----ACTTATTATCAAACAAATAATGCTAATCCACACACCA--AAAGGACGAACATGAACCCTAATAATTGTTTCCCTAATCATATTTATTGGATCAACAAATCTCCTAGGCCTTTTACCACATACATTTACACCTACTACCCAACTATCCATAAATCTAAGTATAGCCATTCCACTATGAGCTGGAGCCGTAATTACAGGCTTCCGACACAAACTAAAAAGCTCACTTGCCCACTTCCT--TCCACAAGGAACTCCAATTTCACTAATTCCAATACTTATTATTATTGAAACAATTAGCCTATTTATTCAACCAATGGCATTAGCAGTCCGGCTTACAGCTAACATTACTGCAGGACACTTATTAATACACCTA-ATC---GGAGGAGCTACTCTAGTATTAATA--------AATATTAG
+s rn3.chr2 24391720 540 - 258222147 CAGAGCAT--------CAGAAC----ACAAGTCT--------CAATGAGAAAAAAGATGGCTGAAATTTTCTTTAGCTATAGCACAATCTCAGTGATAAAAGTACTAACTACAGTTGTTTTAATCACCTCATTTTCTAC----CTCT---TTTC--------------ACCTA---AACAAAAATTAATTAACCTTTATTCAA---TGATTAT-GCCATTAATGCT------AAAACAAATAGCA------------ACAATAAAGGCCAGACTTCATTTCTAATATTAACTTCCTTCCTC----TTATTAGGTAAGCAAACTCACTATGATTATTACCATATTCACTTATGTCAACTTTCCAATTATCAATAAA-CTAGGTGTGGCTCCTCCAGT-TGAGCGGAAATAGTCATTATTAGCTTCTGAC-TGAAATGAGAGCCCCATCAGACCATTTTCT--GCTACAAGAAACACTCATTCCATTTCTCCCCATGTCACTAACTATT---------------CCTGTTTAATCCACATCCCTGTCTGTATGATTATCAGGCAATACTGTGGCAGGCCACAAACTGTTCATCCTTCATT---GGCAGAGTCACATTAGTTTTAGCA--------TCCATTAA
+s canFam1.chrM 7928 589 + 16727 AAAATTGCTG-GTCAACATAAT--------------------CCTTGAGAAAACAAATGAACGAAAATCTATTCGCTTCTTTCGCTGCCCCCTCAATAATAGGTCTCCCTATTGTGGTACTGATCGTCATATTCCCTTCCATTTTAT---TCCCAACAC---CCAGTCGCCTA---ATCAATAATCGGTTAATCTCCATTCAGCAATGACTAA-TTCA-----ACTAACATCAAAACAAATACTA--GCAATTCATAACCAAAAGGGACGAACCTGAGCTCTCATACTTATATCACTAATTCTATTTATTGGCTCAACTAATCTACTTGGACTATTACCTCACTCATTTACGCCCACAACACAACTCTCTATAAACCTCGGAATAGCAATTCCCCTATGAGCAGGGACAGTAATTACCGGTTTCCGCTATAAAACCAAAGCATCCTTAGCACACTTTCT--ACCCCAAGGCACCCCTCTCCCCCTAATTCCAATACTAGTAGTCATCGAAACTATTAGTCTATTTATTCAACCCATGGCTCTAGCCGTTCGATTAACCGCCAATATTACTGCAGGACACCTCCTAATCCATTTG-ATT---GGAGGGGCTACCTTAGCTCTTATC--------AATATTAG
+s galGal2.chrM 9195 609 + 16775 -----------GCAAACAAAATTACAACAACTAAACCCACC-CCCTGAACCTGACCATGAACCTAAGCTTCTTCGACCAATTCTCAAGCCCCTGCCTACTAGGAATCCCTCTAATCCTCCCATCACTCCTTCTTCCAGCCCTCCTAC---TTCCATCAC---CAGGAAACCGATGGATCAACAACCGCCTCTCCACCATCCAACTCTGATTCA-CCCA-----CCTAATCACAAAACAACTAATA--ACCCCCCTAAACAAGGCAGGTCACAAATGAGCCCTCCTACTCACCTCACTTATCCTAATACTCCTCTCCATTAACCTCCTAGGCCTCCTCCCCTACACCTTCACCCCAACTACCCAACTATCAATAAACATGGCCTTAGCCCTGCCACTATGACTAGCCACCTTACTAACAGGCCTGCGAAACCAACCCTCCGCCTCCTTAGGACACCTACT--CCCTGAAGGCACCCCCACCCCACTGATTCCAGCCCTAATCATAATCGAAACAACCAGCCTACTTATTCGGCCATTAGCCCTAGGAGTACGCCTAACAGCAAACCTCACAGCTGGTCACCTACTTATCCAACTT-ATC---TCTACAGCCACAATCGCCCTACTACCAATAATGCCATCAA
+s fr1.chrUn 326224143 588 + 349519338 ---------GCCCCAAAGAAAT-----CAAA-----------CCCTGACCCTGATCATGACACTAAGCTTCTTCGACCAATTTCTTAGCCCCACCGCCTTTGGTATTCCCCTGATTGCCCTCGCTCTCCTATTACCTTGGACCCTCT---TCCCCACACCAACCAACCGTTGA---ACCAACAATCGTCTTTTAACACTTCAAAGCCAATTTA-TTAA-----TCGATTTACTCAACAACTGCTC--CTCCCACTAAACATAGGAGGGCACAAATGAGCCCTTATATTCGCCTCATTAATAGTGTTCCTAATTACCATTAATATGCTAGGACTCCTTCCATACACATTCACCCCCACCACACAGCTTTCCGTAAATATAGCCCTAGCTGTACCCCTATGACTCGCAACAGTAATCATCGGAATACGAAACAACCCAACAGCAGCCCTAGGCCACCTTCT--TCCAGAAGGCACCCCCAACGCTCTAATCCCTATCCTAATTATTATCGAAACTGTCAGCCTCTTCATTCGACCTTTAGCACTAGGAGTTCGACTAACCGCTAACCTCACAGCAGGCCACCTGTTGATTCAACTA-ATC---GCTACAGCAGCTTTCGTACTCCTC--------CCCCTTAT
+s danRer1.chrM 9028 580 + 16596 ----------------AAAAATGACACTTGA-----------AACTGA------CCATGATAACAAGCTTCTTCGATCAATTCGCGAGCCCCTACCTTTTAGGTATCCCCCTTATCCTCGTTGCCATACTTCTACCTTGACTTCTTT---TTCCTGCTCCAACATCACGATGA---ATCAACAATCGACTTATCACCGTCCAAACATGATTGA-CTGG-----ACGATTCACAAACCAACTTATG--ACCCCACTAAACTTTAGCGGCCACAAATGAGCACTTTTATTTGCCTCTCTAATAGTATTCTTAATCACAATTAATCTTTTAGGACTTCTTCCTTATACTTTTACACCAACAACCCAACTCTCTCTGAATATAGGATTTGCAGTACCCCTATGACTTGCCACAGTAATTATCGGAATAAAAAATCAACCGACTATTGCCCTAGGACATCTTTT--ACCAGAAGGAACCCCCATCCCATTAATTCCGGCCCTTATTATTATCGAAACAATTAGCTTATTTATTCGACCATTAGCTTTAGGGGTACGACTTACTGCAAACCTCACAGCAGGCCACCTACTAATTCAACTT-ATT---GCCACAGCAGTATTTGTTCTACTA--------CCAATAAT
+
+a score=-3507.0
+s hg17.chrM 9081 17 + 16571 -CCTTCCCTCTACACTTA
+s canFam1.chrM 8517 17 + 16727 -CGCGACCACAGCTTTTA
+s galGal2.chrM 9808 17 + 16775 -CGCCCTAACGGCACTCA
+s fr1.chrUn 326224732 16 + 349519338 -CCAACTGTCGCCATTC-
+s danRer1.chrM 9608 17 + 16596 ACCAGCAGTAGCAATTT-
+
+a score=-5282.0
+s hg17.chrM 9081 7 + 16571 -CCTTCCC
+s panTro1.chr3 35470806 7 - 209662276 -TCTTCCC
+s mm5.chrM 8480 7 + 16299 -CCCACCA
+s canFam1.chrM 8518 6 + 16727 -GCGACC-
+s galGal2.chrM 9806 5 + 16775 -TCCGC--
+s fr1.chrUn 326224732 6 + 349519338 -CCAACT-
+s danRer1.chrM 9608 7 + 16596 ACCAGCA-
+
+a score=-1082.0
+s hg17.chrM 9088 10 + 16571 TCTACACTTA
+s mm5.chrM 8487 10 + 16299 ACAGCTACCA
+s canFam1.chrM 8524 10 + 16727 ACAGCTTTTA
+s galGal2.chrM 9815 10 + 16775 ACGGCACTCA
+s fr1.chrUn 326224739 9 + 349519338 TCGCCATTC-
+s danRer1.chrM 9615 10 + 16596 GTAGCAATTT
+
+a score=894.0
+s hg17.chrM 9098 2 + 16571 TC
+s mm5.chrM 8497 2 + 16299 TT
+s rn3.chr2 24392260 2 - 258222147 TT
+s canFam1.chrM 8534 2 + 16727 TC
+s galGal2.chrM 9825 2 + 16775 TC
+s fr1.chrUn 326224748 2 + 349519338 TG
+s danRer1.chrM 9625 2 + 16596 TA
+
+a score=-1734.0
+s hg17.chrM 9100 12 + 16571 ---ATCTTCACAATT
+s fr1.chrUn 326224752 10 + 349519338 ---ATCAACCCTA--
+s danRer1.chrM 9627 12 + 16596 ACTGCCTCCGTC---
+
+a score=-3437.0
+s hg17.chrM 9100 9 + 16571 ---ATCTTCACA
+s mm5.chrM 8499 9 + 16299 ---ACATTTATT
+s rn3.chr2 24392262 8 - 258222147 ---ATTTGCAG-
+s canFam1.chrM 8536 9 + 16727 ---ACTTTTATT
+s fr1.chrUn 326224750 9 + 349519338 ---ACATCAACC
+s danRer1.chrM 9627 9 + 16596 ACTGCCTCC---
+
+a score=1618.0
+s hg17.chrM 9109 3 + 16571 ATT
+s panTro1.chr3 35470834 3 - 209662276 ATT
+s mm5.chrM 8508 3 + 16299 ATT
+s rn3.chr2 24392270 3 - 258222147 GCC
+s canFam1.chrM 8545 3 + 16727 ATT
+s fr1.chrUn 326224759 2 + 349519338 -CT
+s danRer1.chrM 9636 3 + 16596 GTC
+
+a score=111212.0
+s hg17.chrM 9112 101 + 16571 CTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACC
+s panTro1.chr3 35470837 101 - 209662276 CTAATCTTACTGAGCATCCTTGAATTCACCGTAGCCCTTATTCAGGCCTATGTCTTTGCACTACTTGTAAGCCTTTACCTATATGAAAACACATAATGTCC
+s mm5.chrM 8511 101 + 16299 TTACTTCTACTCACAATTCTAGAATTTGCAGTAGCATTAATTCAAGCCTACGTATTCACCCTCCTAGTAAGCCTATATCTACATGATAATACATAATGACC
+s rn3.chr2 24392273 88 - 258222147 TTCATCAAATGGATTATCTCAATATTACCTTTCTTTTCAATT--------TGCTTTCATGCT-----TAGCCTTTTACCTACAGGATAGTACTTCAAGGCC
+s canFam1.chrM 8548 101 + 16727 CTAATCCTACTTACGATCCTAGAATTTGCTGTTGCCTTAATTCAAGCCTATGTTTTTACCTTACTAGTGAGTCTATACTTACATGACAACACCTAATGACC
+s galGal2.chrM 9827 101 + 16775 CTATTCCTACTAACCATCCTAGAAGTGGCAGTAGCAATAATCCAAGCCTACGTCTTCGTCCTCCTCCTAAGCCTCTACTTACAAGAAAATATTTAATGGCA
+s fr1.chrUn 326224762 101 + 349519338 TTATTCCTCCTGACACTTCTAGAAGTCGCCGTCGCAATAATCCAAGCCTATGTTTTCGTACTTCTTCTAAGCCTCTACCTACAAGAAAACGTTTAATGCCC
+s danRer1.chrM 9639 101 + 16596 CTTTTCTTACTTACCCTGCTAGAAGTTGCAGTAGCAATAATCCAAGCCTACGTCTTTATTCTTCTTTTAAGCCTATATCTGCAAGAAAACATTTAATGGCC
+
+a score=140967.0
+s hg17.chrM 9213 202 + 16571 CACCAATCACATGCCTATCATA---TAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTC----CTAATGACCTCCGG-CCTAGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATA-----------CTAGGCC------------------TACTAACCAACACACTAAC--CATATACCAATGGTGGCGCGATGTAACACGAGAAAGCACATACCAAGGCC
+s panTro1.chr3 35470938 204 - 209662276 CACCAAACACATGCCTACCATA---TAGTCAAACCCAGCCCCTGACCACTAACAGGAGCTCTCTCAGCTCTC----CTAATAACATCTGG-CCTGGCCATGTGATTTCACTTTAACTCTATCAC---CCTTTTA--------ACCCTAGGCT------------------TACTAACCAACACACTAACTATATATACCAGTGATGACGTGACATTATCCAAGAAAGTACATTTCAAGGCC
+s mm5.chrM 8612 202 + 16299 CACCAAACTCATGCATATCACA---TAGTTAATCCAAGTCCATGACCATTAACTGGAGCCTTTTCAGCCCTC----CTTCTAACATCAGG-TCTAGTAATATGATTTCACTATAATTCAATTAC---ACTATTA--------ACCCTTGGCC------------------TACTCACCAATATCCTCAC--AATATATCAATGATGACGAGACGTAATTCGTGAAGGAACCTACCAAGGCC
+s rn3.chr2 24392361 234 - 258222147 TCCCTGAATGACACCTATTATATTGTAGTCAATTCTTGTCCCCAAACACTTACAGAACCATTCCCAGCCAGCAAGGTTCACGACATCCAGTTTTGATAATATGATTCCACTTTTACTCCATTGT-----TTTTAGTAAAACAATACTAAACTAATAATGTTTAGTATTGATGCCTAGCAGAATCTTAAC--AATATATCAGTTAGGTTGGGATGCAACCCAGGAAGCTATATTTCAAGACC
+s canFam1.chrM 8649 202 + 16727 CACCAAACTCACGCTTACCACA---TAGTCAACCCAAGCCCATGACCGCTGACAGGGGCCCTTTCTGCCCTC----CTTATAACATCGGG-TCTTATCATATGATTTCACTATAACTCAATAGC---CCTACTT--------ACATTAGGAT------------------TCACAACCAACCTGTTAAC--CATATGCCAGTGATGACGAGATGTGATCCGAGAAGGCACATTCCAAGGAC
+s galGal2.chrM 9928 202 + 16775 CACCAAGCACACTCCTACCACA---TAGTTGACCCAAGCCCATGACCAATCTTCGGCGCAGCCGCAGCACTA----CTAACCACCTCTGG-CCTAATCATATGGTTCCACTACAGCTCGACCAC---CCTACTG--------ACAATAGGCC------------------TCCTCTCTATACTTCTAGT--CATGCTGCAATGATGACGAGACGTAGTCCGAGAAAGCACCTTCCAGGGCC
+s danRer1.chrM 9740 202 + 16596 CACCAAGCACATGCATATCACA---TAGTTGACCCAAGCCCATGACCACTAACTGGAGCTGTAGCCGCCCTA----TTAATATCATCTGG-CTTAGCAATTTGGTTTCACCTTCACTCAATGAC---ATTAATT--------GTTCTAGGAA------------------TAATTCTTCTTATTTTAAC--TATAATCCAATGATGACGAGACATTATTCGAGAAGGGACCTTTCAAGGCC
+
+a score=6726.0
+s hg17.chrM 9415 8 + 16571 ACCACACA
+s panTro1.chr3 35471142 8 - 209662276 CCCACACA
+s mm5.chrM 8814 8 + 16299 ACCACACT
+s canFam1.chrM 8851 8 + 16727 ATCATACC
+s galGal2.chrM 10130 8 + 16775 ACCACACC
+s danRer1.chrM 9942 8 + 16596 ACCATACC
+
+a score=20191.0
+s hg17.chrM 9423 19 + 16571 CCACCTGTCCAAAAAGGCC
+s panTro1.chr3 35471150 19 - 209662276 TCAATTGTCCAAAAAGGCC
+s mm5.chrM 8822 19 + 16299 CCTATTGTACAAAAAGGAC
+s rn3.chr4 151131657 18 + 187371129 -CCATTTTACAGAAAGGCC
+s canFam1.chrM 8859 19 + 16727 CCTATTGTACAAAAAGGAC
+s galGal2.chrM 10138 19 + 16775 CCAACTGTCCAAAAGGGCC
+s danRer1.chrM 9950 19 + 16596 CCGCCCGTACAAAAAGGGT
+
+a score=138985.0
+s hg17.chrM 9442 130 + 16571 TTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTA--CCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGCACTGGCCCCCAACAGGCATCAC
+s panTro1.chrUn_random 213823712 130 - 240967748 TTCGGTATGGAATAATTTTATTCATCATCTCAGAAGTCTTTTTCTTTGCTGGATTCTTCTGAGCATTCTA--CCACTCCAGCCTAGCCCCTACCCCTCAACTAGGAAGACACTGACCCCCAACAGGCATCAC
+s mm5.chrM 8841 130 + 16299 TACGATATGGTATAATTCTATTCATCGTCTCGGAAGTATTTTTCTTTGCAGGATTCTTCTGAGCGTTCTA--TCATTCTAGCCTCGTACCAACACATGATCTAGGAGGCTGCTGACCTCCAACAGGAATTTC
+s rn3.chr4 151131675 125 + 187371129 TTCGTTATGAAATAGCT------ATTGTATCTGAAGTCTTTTTCTTGACAGGACTTTTCTGAGCTTTCTGCTCCACTCCAGCCTTGTCCC-GCACATGACCTAGAGGGCTGCTGGCCACCTACAGGAATTAC
+s canFam1.chrM 8878 130 + 16727 TACGATACGGAATAGTTCTTTTTATCGTATCAGAAGTATTTTTCTTTGCAGGCTTCTTCTGAGCCTTTTA--CCACTCCAGCCTAGCCCCTACTCCTGAACTTGGGGGTTGCTGACCTCCTACCGGCATTAT
+s galGal2.chrM 10157 130 + 16775 TACGATACGGAATAATCCTTTTCATTACATCAGAGGCCTTCTTCTTCCTAGGATTCTTCTGAGCCTTCTT--CCACTCAAGCCTAGCCCCAACACCAGAACTGGGGGGCCAATGGCCCCCAACAGGAGTCAA
+s danRer1.chrM 9969 130 + 16596 TGCGGTACGGTATAATCCTATTTATTACCTCAGAGGTATTTTTTTTCCTAGGATTTTTCTGAGCTTTTTA--TCATTCAAGTTTAGCCCCCACCCCTGAACTAGGGGGATGTTGACCACCCACAGGGCTAAC
+
+a score=45530.0
+s hg17.chrM 9572 68 + 16571 CCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCA
+s panTro1.chrUn_random 213823842 68 - 240967748 TCCACTCAATCCCCTAGAAGTCCCACTCTTAAACACGTCTGTACTACTCGCATCGGGAGTTTCAATTA
+s mm5.chrM 8971 68 + 16299 ACCACTTAACCCTCTAGAAGTCCCACTACTTAATACTTCAGTACTTCTAGCATCAGGTGTTTCAATTA
+s canFam1.chrM 9008 68 + 16727 TCCTCTTAACCCATTAGAAGTGCCTCTACTCAACACCTCAGTCCTCCTAGCCTCCGGAGTATCTATTA
+s galGal2.chrM 10287 68 + 16775 ACCCCTAAACCCCCTTGAAGTACCCCTACTAAATACAGCAATCCTCCTAGCCTCAGGAGTCACCGTTA
+s danRer1.chrM 10099 68 + 16596 AACTCTTGACCCATTTGAAGTGCCGCTCCTCAATACAGCTGTTTTGCTAGCATCCGGAGTAACAGTAA
+
+a score=151784.0
+s hg17.chrM 9640 173 + 16571 CCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTTGTAGCCACAGGC
+s panTro1.chrUn_random 213823910 173 - 240967748 CTTGAGCTCACCATAGCCTAATAGAGAACAATTGTAATCAAGCAATTCAAGCACTACTTATCACAATCTTACTAGGCATCTACTTCACCCTCCTACAAGTTTCAGAATACTTTGATGCCCCCTTTACTATCGCCAATGGTATCTATGGTTCAACATGTTTTGTAGCTACGGGC
+s mm5.chrM 9039 173 + 16299 CATGAGCTCATCATAGCCTTATAGAAGGTAAACGAAACCACATAAATCAAGCCCTACTAATTACCATTATACTAGGACTTTACTTCACCATCCTCCAAGCTTCAGAATACTTTGAAACATCATTCTCCATTTCAGATGGTATCTATGGTTCTACATTCTTCATGGCTACTGGA
+s rn3.chr10 102082388 167 - 110733352 CCTGAGTCCATCATTGTCTAACAGAAGGAAAACAAAAAGATAGAAACCAAGCCTTATTTATTACAATTTTCCTGG------ACTCTACTGCCCACCAAGCTTCAGAATATTTTGAAACACCAGTCTCCATCTGAGACAGAATTTATGGATCAACATTCTTCATAACAACAGAG
+s canFam1.chrM 9076 173 + 16727 CTTGAGCCCATCATAGTTTAATAGAAGGTAATCGCAAACATATACTTCAAGCCTTATTCATTACAATCTCCTTAGGCGTATATTTTACGCTATTACAGGCCTCCGAATACTATGAGACATCTTTTACAATCTCCGATGGGGTATACGGATCTACCTTTTTTATAGCCACTGGA
+s galGal2.chrM 10355 173 + 16775 CATGGGCTCACCACAGCATCACAGAAGGAAACCGAAAACAAGCCATCCACGCACTAACTCTCACAATCCTCCTAGGATTCTATTTCACAGCCCTACAAGCAATAGAGTACCATGAAGCCTCCTTCTCAATCGCTGACAGCGTCTACGGCTCCACCTTCTTCGTCGCTACAGGG
+s danRer1.chrM 10167 173 + 16596 CATGAGCACATCACAGCCTCATGGAAGGAGAACGAAAACAAGCCATTCAATCTCTTGCTCTTACAATTCTACTAGGATTGTACTTCACAGCACTTCAGGCTATAGAATACTATGAAGCCCCATTTACAATTGCAGACGGAGTATATGGCTCAACATTCTTTGTAGCTACAGGG
+
+a score=106761.0
+s hg17.chrM 9813 128 + 16571 TTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT
+s panTro1.chrUn_random 213824083 128 - 240967748 TTCCACGGGCTCCCCGTCATCATTGGTTCAACATTCCTTACTGTTTGCCTTATCCGCCAACTATTATATCCTTTTACATCCAAGTACCACTTCGGCTTTGAACCCCCCACTTGATACTGACACTTTGT
+s mm5.chrM 9212 128 + 16299 TTCCATGGACTCCATGTAATTATTGGATCAACATTCCTTATTGTTTGCCTACTACGACAACTAAAATTTCACTTCACATCAAAACATCACTTCGGATTTGAAGCCGCAGCATGATACTGACATTTTGT
+s canFam1.chrM 9249 128 + 16727 TTTCACGGATTACACGTAATTATTGGCTCTACATTCCTCATCGTGTGCTTCCTCCGACAGCTATACTACCACTTCACATCAAACCACCACTTCGGATTTGAAGCCGCTGCATGATATTGACACTTTGT
+s galGal2.chrM 10528 128 + 16775 TTCCACGGACTACATGTAATCATTGGATCATCCTTTTTAACAGTTTGCCTCCTACGACTAATCAAATTCCACTTCACACCAAACCACCACTTCGGATTTGAAGCAGCAGCCTGATACTGACACTTCGT
+s danRer1.chrM 10340 128 + 16596 TTTCATGGTCTACACGTTATTATTGGATCAACCTTTTTAGCTGTATGCCTTCTACGCCAAGTTTTATTTCACTTCACATCAGACCACCACTTTGGTTTTGAAGCTGCCGCTTGATATTGACACTTCGT
+
+a score=8380.0
+s hg17.chrM 9941 16 + 16571 AGATGTGGTTTGACTA
+s mm5.chrM 9340 16 + 16299 AGACGTAGTCTGACTT
+s canFam1.chrM 9377 16 + 16727 TGATGTAGTCTGGCTA
+s galGal2.chrM 10656 16 + 16775 AGACATCATCTGACTC
+s danRer1.chrM 10468 16 + 16596 CGACGTAGTCTGACTA
+
+a score=27771.0
+s hg17.chrM 9957 42 + 16571 TTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTT-
+s mm5.chrM 9356 42 + 16299 TTCCTATACGTCTCCATTTATTGATGAGGATCTTACTCCCTT-
+s rn3.chr4 170558950 38 - 187371129 TTTCTATACAT----ACCTATTGATGAGGAGCACACATTCTT-
+s canFam1.chrM 9393 42 + 16727 TTCTTGTATGTATCTATTTATTGATGAGGATCCTATTTCTTT-
+s galGal2.chrM 10672 42 + 16775 TTCCTCTACATATCCATATACTGATGAGGATCTTGCTCTTCT-
+s danRer1.chrM 10484 43 + 16596 TTCCTCTACGTATCAATCTATTGATGAGGCTCATAGCCTTTCT
+
+a score=148393.0
+s hg17.chrM 9999 266 + 16571 AGTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGAC--AACATTCAAAAAAGAGTAATAAACTTCGCCTTA---ATTTTAATAATCAACACCCTCCTAGCC---TTACT---------ACTAATAATTATTA--CATTTTGACTACCACAACTCAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAAT
+s panTro1.chr3 35471726 266 - 209662276 AGTATAAGCAGTACCATTGACTTCTAATCAATTAGTTTCGAT--ATTATCCAAAAGTGAGTAATCAACTTGACATTA---GCTCTAGTAACCAACACCTTACTGGCCCTATTACT---------ACTAATAA-----AAGCATTTTGGCTCCCACAACTTAATATTTATATAGAAAAATCCAACTCCTATGAATGTGGATTTCACCCAATAACCTCTGCCCACCTCCCCTTTTCCATAATATTCTTCCTAGGAGCCGTCACATTCCTCCTCTTTGACTTAGAGAT
+s mm5.chrM 9398 266 + 16299 AGTATAATTAATATAACTGACTTCCAATTAGTAGATTCTGAA--TAAACCCAGAAGAGAGTAATTAACCTGTACACT---GTTATCTTCATTAATATTTTATTATCC---CTAAC---------GCTAATTCTAGTTG--CATTCTGACTCCCCCAAATAAATCTGTACTCAGAAAAAGCAAATCCATATGAATGCGGATTCGACCCTACAAGCTCTGCACGTCTACCATTCTCAATAAAATTTTTCTTGGTAGCAATTACATTTCTATTATTTGACCTAGAAAT
+s rn3.chr4 170558988 240 - 187371129 AGTATAATCAG-----------TCCAGCCAGTTAGATGTAGCG-TAAATCTAGATAGTAATCATAACTTTATACATA-------TAACAACTAACATCAACCTATCC---CTACG---------TTGAATGTCCATTG--CATGTTGATTACCTCAACTTAATATTTATACAGAAAAAGCAAACCCCTATGAATGTGGGTTTGACCTAATAGGCTCATCGAACCTTTCATTTTCCATAAAGTTTTTCCTTGT----------TTTCCACCATTCAG--TACAGCT
+s canFam1.chrM 9435 266 + 16727 AGTATAACTAGTACAATTGACTTCCAATCAGTTAGCTCCAGA--TCAACCTGGAAAGAAGTAATAAACGTTATATTA---ACTTTGATAACTAATGTAACCCTAGCA---TCCTT---------ACTTGTACTAATCG--CATTCTGACTTCCCCAGCTAAATATCTATACAGACAAGACAAGCCCCTACGAATGTGGTTTTGACCCCATGGGATCTGCTCGCCTACCTTTCTCTATAAAATTTTTCCTAGTTGCCATCACATTTCTGCTTTTCGACCTAGAAAT
+s galGal2.chrM 10714 270 + 16775 AGTATACTCATTACAACTGACTTCCAATCTTTAAAATCTGGTA-TCAACCCAGAGAAGAGCAATGAAC------------ACACTTACATTTATACTCTCACTATCCTTTCTACTAAGCGCTGCACTAACTACTATAA--ACTTTTGACTAGCCCAAATAGCCCCAGACACAGAAAAACTGTCACCGTACGAATGCGGATTTGACCCACTAGGATCAGCCCGACTCCCATTCTCAATCCGATTCTTCCTAGTAGCCATCCTATTCCTTTTATTCGACCTAGAAAT
+s danRer1.chrM 10527 271 + 16596 AGTATAACCAGTATAAATGACTTCCAATCATTTGGTCTTGGTGAAAAATCCAGGGAAAGGTAATGAATTTATTTGCAACTATTCTTATTATTATAACGACCTTATCA---TTGGT---------CTTAGCTCTAGTAT--CATTTTGACTACCACAAATGAACTCTGATACAGAAAAGCTATCACCATATGAATGCGGATTTGATCCACTAGGGTCCGCCCGCCTACCATTTTCATTACGATTTTTCTTAGTAGCAGTTTTATTCCCTTTATTTGACTTGGAAAT
+
+a score=73927.0
+s hg17.chrM 10265 153 + 16571 TGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAA---CCTGCCACTAATAGTTATGTCATC--------CCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGA----CTACAAAAAGGATTAGACTGAGCCGAAT---TGGTATATAGTTT
+s panTro1.chr3 35471992 153 - 209662276 TGCTGTACTACTACCTCTGCCATGAGCCCTTCAAACAACCAA---CCTGACACTAATA--------ATCAGCACAGCCCTTGTATTAGTTACCATTTCAATCCTAGGCTTGACTTATGAATGAGCCCC----AAAAGTGTTAGACTGAGTTGAAT---TGGTAAATAGTTT
+s mm5.chrM 9664 156 + 16299 TGCTCTTCTACTTCCACTACCATGAGCAATTCAAACAATTAAAACCTCTACTATAATA--------ATT---ATAGCCTTTATTCTAGTCACAATTCTATCTCTAGGCCTAGCATATGAATGA----ACACAAAAAGGATTAGAATGAACAGAGTAAATGGTAATTAGTTT
+s rn3.chr16 53341827 156 + 90224819 TGCCTTATTACTTCCTCTGCCTTGAGTAATTCAAACAACTAGCATTATTACAATAATA--------TTT---TCAACTTTTATTCTAGTCATTATTTTATCCCTTGGGTTAATCTATCAATGA----TTACAAAAAGGACTAGAATGGACAGAATAATTGGTAATTAGTTT
+s canFam1.chrM 9701 154 + 16727 TGCACTCCTACTCCCACTTCCCTGAGCGTCACAAACCAACAA---GCTAACAACAATA--------CTTATCATAGCACTCCTACTAATCTCCCTCCTAGCTGCGAGCCTAGCGTATGAATGG----ACCGAAAAGGGGCTAGAATGAACCGAATA--TGATAATTAGTTT
+s galGal2.chrM 10984 156 + 16775 CGCCCTGCTTCTTCCCCTTCCATGAGCCATCCAACTTGCACA---CCCTATAATAACC--------CTTACTTGAGCCACCACTATCATCGCCCTCCTCACATTTGGTCTCATCTACGAATGA----ACTCAGGGCGGCTTAGAATGAGCAGAATAACAGAAAGTTAGTCT
+s danRer1.chrM 10798 153 + 16596 TGCTCTCCTATTACCACTCCCATGAGGAGATCAACTTAATAA---CCCAATAGAAACT--------CTCTTTTGAGCTATAACAGTACTGATTTTGCTAACACTAGGACTAGCCTACGAATGA----GCCCAAGGCGGCCTTGAATGAGCAGAGT---AGGGAGCTAGTCC
+
+a score=144767.0
+s hg17.chrM 10418 376 + 16571 -AAA--CAAAACGAATGATTTCGACTCATTAAATTATGATA----ATCATATTTACCAA-ATGCCCCTCATTTACATAAATATTATACTAGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGAAGGAAT-----AATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAA---------CACCCACTCCCTCTTAGC----------CAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTA------------------------------AAACTAATCGTCCCAACAATTATATTAC
+s panTro1.chr3 35472145 374 - 209662276 -AAG-TCAAAATAAATGATTTTGACTCATTAGATTATGATA---GACCATATTTACCAA-ATGACCACtattaatattattattatattaGCATACACCATATCACTGCTAGGAGTATTAGTCTATCAATCCCACCTAATATCATCCCTATTATGCCTAGAAGGCATCAATCAATA-TAT--------ATCATAAATACTCTTATAACTTTAAATATACATTTCACCC---------TAGC--ATCCA---TAATA-----CCCATTATCCTCTTAGTATTTGCTGCCTGAGAAGCCGCAGTGGGCCTTGCCTCACTAGTTTCAATCTCCAGGACATATGGCCTAGATTACATACAAAATCTAAGTTTACTTCAATGCTA------------------------------AAAATTATTACTCCAACAATTATACTGT
+s mm5.chrM 9820 380 + 16299 -AAA--AAAAATTAATGATTTCGACTCATTAGATTATGATGA-TGTTCATAATTACCAATATGCCATCTACCTTCTTCAACCTCACCATAGCCTTCTCACTATCACTTCTAGGGACACTTATATTTCGCTCTCACCTAATATCCACATTACTATGCCTGGAAGGCAT-----AGTATTATCCTTATTTATTATAACTTCAGTAACTTCCCTAAA---------CTCCAACTCCAT--AAGC---TCCATACCAATC-----CCCATCACCATCTTAGTTTTCGCAGCCTGCGAAGCAGCTGTAGGACTAGCCCTACTAGTAAAAGTTTCAAACACGTACGGAACAGATTACGTCCAAAATCTCAACCTACTACAATGCTA------------------------------AAAATTATTCTTCCCTCACTAATGCTAC
+s rn3.chr2 24394176 379 - 258222147 -AGA--TAAAGTGAATGATTCCAACTCATTAGATTTTAATA---TTTAATAACTCCCAATGTGTATTTGGTTTGTTTTAACAATATTCTAGCTTATATAACATGCTTAATAGGACAA------TATCAGTCACACCTATTAAGTTC---ACTACATTTAGAAGGCAT-----AATATTGC------TTATTGGAGGAATGTTTATGCTTTTAAA---------TACCTATTT-----TAACTTATTCACCTCAATA-----CCAGTCCTTTTATTAGT-TTTATAGCCTGCAAGG-----------CTTTCAACTATAATAATGGTATCTAGTACACATGTCCTGGACTATGTGCACCATGTAAACTTTCTCAAATATTATTAAACTAGTATCTGCAAGAAGACACTGTTAAAAT--TCATTCAAACAACTATATGGT
+s canFam1.chrM 9855 379 + 16727 -AAGCCAAAAACAAATGATTTCGACTCATTAGATTATGATTT-ATCTCATAATTATC---ATGTCCATAGTATATATTAATATCTTTCTGGCATTCATTCTTTCTCTAATAGGTATACTTGTTTATCGATCACACCTAATATCATCGCTACTATGCTTAGAGGGCAT-----AATATTATCACTATTTGTAATAATATCTGTAACTATTCTCAA---------CAATCACCTCACATTAGC-----CAGCATGATA-----CCAATCGTACTACTAGTATTTGCTGCCTGCGAAGCAGCATTAGGACTATCTCTACTAGTTATAGTATCTAACACCTACGGGACTGATTACGTACAAAACCTAAACCTTTTACAATGCTA------------------------------AAAATTATCATCCCTACTATCATACTAA
+s galGal2.chrM 11140 379 + 16775 -AAC--TAAGACAGCTGGTTTCGACCCAGCAAATTATAGACC-CACCTATAACTTTCTT-ATGTCTCCCCTACACTTCAGCTTCTATTCTGCATTCACATTCAGCAGCCTAGGACTAGCATTCCACCGAACACACCTCATCTCTGCCCTACTATGCCTAGAGAGCAT-----AATACTATCCATATTCATCCCCCTCTCAATCTGACCAGTAGA---------AAACCAAACCC---CATC--ATTCGCCCTTGTA-----CCTATCCTAATACTAGCCTTCTCAGCATGCGAAGCTGGCACAGGCCTAGCCATACTAGTAGCTTCTGCACGAACACATGGCTCTGACCACCTACACAACCTAAACCTTCTACAATGCTA------------------------------AAGATCATCCTACCAACAATCATACTCT
+s danRer1.chrM 10951 381 + 16596 AAAG--AAAGACCCTTGATTTCGGCTCAAATAATTGCGGTGTAAACCCGTAACTCCCTT-ATGACACCCACGCACTTTAGTCTTAACGCAGCATTTATACTAGGCTTAGCAGGACTTACATTTCACCGTGTTCACCTCCTATCAGCATTATTATGTTTAGAAGGCAT-----AATATTATCTTTATTTATTTCCATAGCCCTTTGAACTTTAAA---------AACAGAGTCAAT--AAGTTTATCCA---CAGCC-----CCTATACTACTACTAGCCTTTTCTGCCTGTGAAGCAAGTGCCGGCCTAGCACTCCTAGTAGCCACAGCTCGAACCCACGGATCTGACCACATAAAAAACCTTAATCTACTACAATGCTA------------------------------AAAGTACTGATCCCCACTATTATGCTAT
+
+a score=36041.0
+s hg17.chrM 10794 154 + 16571 TACCACTGACATGACTTTCCAAAAAGCACATAATTTGAATCAACACAACCACCCACAGCCTAATTATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAACAACCTATTTAG--CTGTTCCCCAACCTTTT------CCTCCGACCCCCTAACAAC
+s panTro1.chr3 35472519 151 - 209662276 TACCAATGATATGATTCTCTAAAAATTATATAATCTGAATCAACGTGGTTATCCACAGCCTGCTCATCAGCTTTATCAGCCTACTATTTTTTAACCAATTGAACGATAACTCATCCAA--CTTCTCATTAATCTTT---------TCTGACCTGCTGACATC
+s mm5.chrM 10200 154 + 16299 TACCACTAACCTGACTATCAAGCCCTAAAAAAACCTGAACAAACGTAACCTCATATAGTTTTCTAATTAGTTTAACCAGCCTAACACTTCTATGACAAACCGACGAAAATTATAAAAA--CTTTTCAAATATATTCT------CCTCAGACCCCCTATCCAC
+s rn3.chr16 53342361 146 + 90224819 TTCCATTAACCTGACTGTTAAAA--------AAACTGAACTAATGTCACCTCTTATAGCTTCTTAGTAAGCTTTATTAGTCTATCACTATTATAGCAAAATGATGAAAATAACTTAAA--TTTCTTAATTATATTTT------CTTTAGCCCCCTTATCTAC
+s canFam1.chrM 10234 154 + 16727 TCCCCCTTACATGAATATCAAAGCCTAACATAATCTGAATTAACACGACAACATATGGTTTGCTAATCAGCTTAATCAGCTTATTCTACCTAAACCAACCAAATGATAATACATTGAA--CTCCTCCTTAATATTTT------TCTCTGATTCCCTATCGGC
+s galGal2.chrM 11519 154 + 16775 TGCCCACAGCCCTCTTATCCCCAGCAAAATCCATATGAACTAACACCACAATATACAGCCTTCTAATCGCCTCGATCAGCCTACACTGACTAACCCCATCATACTACCCCACAAAAA--------CCCTAACCCTCTGAACAGGCATAGACCAAATCTCAAC
+s danRer1.chrM 11332 157 + 16596 TCCCTACAATCTGATTATCTTCATCAAAATGACTGTGAACAACTACAACAATAAACAGCTTTTTAATTGCCTTTATTAGCTTAACATGACTAAAATGAACCTCGGATACAGGGTGAAATGCTTCTAACTCGTACATA-----GCTGCAGACCCACTATCAAC
+
+a score=205901.0
+s hg17.chrM 10948 423 + 16571 CCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGCGAACCACTATCACG--AAAAAAACTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTC-----GAAACCACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTAGCTTACACAATAGCTTTTAT
+s panTro1.chr3 35472670 421 - 209662276 ACCCCTTCTAATCTTAACAGCCTGACTACTGCCTCTTATAATTCTAGCAAGCCAATACCACCTGTCCAATGAATCACCCCCGTG---AAAAAATTCTATATTTTGATATTGATTTCTCTACAGACTTTTTTAATCCTAGCATTCACTGCCACAG-ACTAATCATATTTTATATCCTCTTT-----GAAGCCACACTAGTTCCCACCCTAATTATCATCACCCACTGAGGCAACCAACCAGAACGCCTCAATGCAAGATCACACTTCTTATTTTACACACTAGTAGGATTCCTTCCTTTACTTGTAACATTTGTTTATACTCCAAATACCTCAGGTTCACTAAATATGCTAGTAATAATATTTACTATCCAAGAGCTATTAACCTCCTGATCCAATAATCTTATATCACTAGCATGTATCATGGCCTTCAT
+s mm5.chrM 10354 423 + 16299 ACCATTAATTATTTTAACAGCCTGATTACTGCCACTAATATTAATAGCTAGCCAAAACCACCTAAAAAAAGA--TAATAACGTACTACAAAAACTCTACATCTCAATACTAATCAGCTTACAAATTCTCCTAATCATAACCTTTTCAGCAACTGAACTAATTATATTTTATATTTTATTT-----GAAGCAACCTTAATCCCAACACTTATTATTATTACCCGATGAGGGAACCAAACTGAACGCCTAAACGCAGGGATTTATTTCCTATTTTATACCCTAATCGGTTCTATTCCACTGCTAATTGCCCTCATCTTAATCCAAAACCATGTAGGAACCCTAAACCTCATAATTTTATCATTCACAACACACACCTTAGACGCTTCATGATCTAACAACTTACTATGGTTGGCATGCATAATAGCATTTCT
+s rn3.chr2 24395464 406 - 258222147 CTCTCTTCTAATACTGAAGCCCTGATTACTTTCCTTAATAATCACAACAAGTCAGTGCC-CTTTTCCAAAGATTCAAATACACA--AAAATACTGATACGTGTCAGTATTAACTGTCC-----AGATTCATAATGATTGCATTTTCCTTCATATAGAAAATGCTATTTTATCTTTTTATTCAAAAAAAACCCTACCAATCTCAGCTTTA---ATTATTACCTAATGAGGTATTCAAACAGAATGATTAAAAGCAGG-----ATTTCCTATTCTATGTACTGAGTGG--CCATTATATCTCCTGTAGCAGTTAGTTATATCATGTATACTACTGGCTCACTACAC-TCTTAACGATGTTCAACTAAATTAAAATACTGTCATATTCCCAGTCAAACAG-----GATGAAGAATCCACATTAAGATGTCTCT
+s canFam1.chrM 10388 423 + 16727 ACCACTATTAGCACTCACAACATGACTTCTGCCCCTTATACTTATAGCAAGTCAACACCATTTATCAAAAGAACCCTTAACTCG--AAAAAAACTATATATTTCAATACTAATTCTTCTCCAATTGTTCCTAATTATAACTTTCACAGCCTCTGAACTCATCTTCTTTTACATCCTATTT-----GAAGCAACACTGATTCCGACCCTGATCATTATTACCCGATGAGGAAATCAAACTGAACGACTAAACGCAGGACTCTACTTCTTATTTTATACTTTAATAGGATCCCTCCCACTCCTAGTAGCTCTCCTTTATATCCACAATTTCATGGGCTCCCTAAATTTTCTCATAATTCAATACTGAATCCAGCCTCTGCCAAACTCCTGATCTAATATTTTCCTATGACTGGCATGCATAATAGCATTCAT
+s galGal2.chrM 11673 423 + 16775 TCCCCTCTTAGTACTCTCCTGCTGGTTTCTCCCCCTCATAATTATAGCTAGCCAAGGCCACCTACAACATGAACCCCACAAACG--AAAACGAATATTCATCTCCACCTTAATCATCATCCAACCATTCATCATCCTAGCCTTCTCAGCAACTGAACTCATACTATTCTACATCTCATTC-----GAAGCAACCCTAATCCCAACCCTCATCTTAATCACACGCTGAGGAAACCAACCAGAACGACTTAGCGCAGGCATTTACCTTCTATTCTATACCCTAATTAGCTCTCTTCCCCTACTAGTCTCCATCCTCTACCTTCACACAAATACTGGAACCCTCCACCTACCCATTATCAAACTCACCCACCCCAACCTACCTGCCTCCTGAACAAGCTTATTATCTAGCCTAGCTCTCCTAATAGCCTTTAT
+s danRer1.chrM 11489 423 + 16596 ACCTCTTCTAGTACTAACCTGTTGACTTCTTCCATTAATGATTCTAGCTAGCCAAAATCACATCAACTCGGAGCCTGTAAACCG--ACAACGAATATACATTACACTTCTTGCCTCTTTACAAACTTTCATAATTATGGCGTTTGGCGCTACAAAAATCATTATATTCTACATTATATTC-----GAAGCTACACTTATCCCAACACTAATCATTATTACCCGATGAGGTAATCAAGCTGAGCGCCTTAACGCAGGTACTTACTTTCTTTTCTATACATTAGCAGGCTCTCTACCTCTTTTAGTAGCCCTCCTATTACTGCAACAATCAACAGGAACCCTATCAATACTAGTACTTCAGTACTCAGACCCACTTTTACTTAACTCTTGAGGACATAAAATCTGATGAGCCGGCTGCTTAATTGCATTCCT
+
+a score=87189.0
+s hg17.chrM 11371 111 + 16571 AGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCTA
+s panTro1.chr3 35473091 111 - 209662276 AGTAAAAATACCTCTATATGGACTTCACCTATGACTCCCTAGAGCCCATGTAGAATCCCCTATTGCCAACTCAATAGTACTTGCAGCAGTACTCCTAAAGCTAGGTGGTTA
+s mm5.chrM 10777 111 + 16299 TATTAAAATACCATTATATGGAGTTCACCTATGACTACCAAAAGCCCATGTTGAAGCTCCAATTGCTGGGTCAATAATTCTAGCAGCTATTCTTCTAAAATTAGGTAGTTA
+s rn3.chr2 24395989 80 - 258222147 AAAAAAGATGTCTCT-TACTGCCTCTACC-----------AAACCACAAGTAG--------------GAATGAGTTGTCCTTGCAGTCACAGT-GTAAACCTGGATG----
+s canFam1.chrM 10811 111 + 16727 AGTAAAGATACCTCTATACGGCCTCCACTTGTGACTACCAAAAGCACACGTAGAGGCCCCTATTGCCGGCTCCATAGTACTTGCCGCTGTACTCCTAAAACTAGGGGGCTA
+s galGal2.chrM 12096 111 + 16775 AGTCAAAGCACCCCTATACGGACTACACCTATGACTGCCTAAAGCCCATGTAGAAGCACCAATCGCAGGCTCCATACTACTCGCTGCTCTACTACTAAAACTAGGCGGATA
+s danRer1.chrM 11912 111 + 16596 AGTAAAAATACCGCTATATGGGATACACCTTTGATTACCAAAAGCACATGTAGAAGCCCCTGTAGCAGGATCTATAATTCTAGCGGCAGTGCTACTAAAACTAGGAGGCTA
+
+a score=48447.0
+s hg17.chrM 11482 88 + 16571 TGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATT
+s panTro1.chr11_random 29231538 88 - 53199993 CGGTATAATACGGCTTACCCTTATCCTCAGCCCCCTAACAGAATATATAGCCTACCCCTTCCTCATACTATCCCTATGAGGGATAGTT
+s mm5.chrM 10888 88 + 16299 CGGAATAATTCGCATCTCCATTATTCTAGACCCACTAACAAAATATATAGCATACCCCTTCATCCTTCTCTCCCTATGAGGAATAATT
+s rn3.chr2 24396069 71 - 258222147 TGATGTA---------------ATTTTAAATCTACTCACAGGACATACAATGTACTCAT--CGTCTATTGGCCCCATTAAGAATACTT
+s canFam1.chrM 10922 88 + 16727 TGGCATGATACGAATTACAACCCTACTAAATCCCCTGACCAATTTCATAGCATACCCCTTCATAATATTGTCTCTATGAGGCATAATC
+s galGal2.chrM 12207 88 + 16775 TGGCATCATACGAGTCACCCTCCTAATGGAGCCCGTATCCAACTTCTTACACTACCCCTTCCTCACCCTAGCCCTATGAGGTGCCCTA
+s danRer1.chrM 12023 88 + 16596 CGGTATGATACGAATAATAGTAATATTAGATCCTTTATCTAAGCAACTAGCATACCCGTTTATTATCCTTGCTCTATGAGGAGTAATC
+
+a score=59688.0
+s hg17.chrM 11570 91 + 16571 ATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCA---------------CATAGCCCTCGTAGTAACAGCCA
+s panTro1.chr11_random 29231626 89 - 53199993 ATGACAAGCTCCATTTGTCTACAACAAACCGATCTAAAA----TCATTGCCTACTCCTCTGTAAGCCATATACCACTTGTCATCATAGCTCTC-------------
+s mm5.chrM 10976 91 + 16299 ATAACTAGCTCAATCTGCTTACGCCAAACAGATTTAAAATCACTAATCGCCTACTCCTCAGTTAGCCA---------------CATAGCACTTGTTATTGCATCAA
+s canFam1.chrM 11010 91 + 16727 ATAACAAGCTCTATCTGTCTCCGTCAAACAGATCTAAAATCCCTAATTGCATACTCCTCAGTTAGTCA---------------TATGGCACTGGTTATCGTAGCGG
+s galGal2.chrM 12295 91 + 16775 ATAACTAGCTCTATCTGCTTACGCCAAACAGACCTAAAATCCCTCATTGCCTACTCATCCGTAAGCCA---------------TATGGGCCTAGTCATCGCTGCAA
+s danRer1.chrM 12111 91 + 16596 ATAACAGGATTAGTTTGTCTACGACAAACAGACTTAAAATCGCTAATTGCCTATTCATCAGTAGGCCA---------------TATGGGACTAGTTGCAGGAGGAA
+
+a score=195175.0
+s hg17.chrM 11661 417 + 16571 TTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGACTCACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTC-------GCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCA------CGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTAC----CACAACACAATGGGGCTCACTCACCCACCACAT--TAACAACATAAAACCCTCATTCACAC---GAGAAAACACCCT----------CATGTTCATAC
+s panTro1.chr11_random 29231715 419 - 53199993 --CTAATCCAAACCCCTTGAAGCTTTACAGGTGCCGTCAGCCTTATAATTACCCATGGAGTCACTTCATCCCTGTTATTCTGCCTAGCAAATTCCAACTACGAGTG-------AGTCCAAAACGGAATCATATTACTTACCTGAGGCCTTCAAATACTCCTCCCACTGATAGCCTCATGATGACTTCTAGCAAATCTCACTAATCTTGCCTTA-CCCCTACCATTAATCTAGTAAGGGAACTCTCTGTG------ATCATGGCTTCATTCTCCTGATCAAACATCGCTATTATGCTTACAGGACTTAATATACTAATTACAACCCTCTACTCC--CTACATA--TACCAATCACAACACAATGAGGGACACTTACATATTACAT--TAACA--GTTAAACCTTCCTTTACAC---AAGAAAATACATTAATATTTATACATGT---TAC
+s mm5.chrM 11067 427 + 16299 TCATAATCCAAACTCCATGAAGCTTCATAGGAGCAACAATACTAATAATCGCACATGGCCTCACATCATCACTCCTATTCTGCCTAGCAAACTCCAACTACGAACGGATCCACAGCC-------GTACTATAATCATGGCCCGAGGACTTCAAATGGTCTTCCCACTTATAGCCACATGATGACTGATAGCAAGTCTAGCTAATCTAGCTCTACCCCCTTCAATCAATCTAATAGGAGAATTATTCATT------ACCATATCATTATTTTCTTGATCAAACTTTACCATTATTCTTATAGGAATTAACATTATTATTACAGGTATATACTCAATATACATAATTAT----TACCACCCAACGCGGCAAACTAACCAACCATAT--AATTAACCTCCAACCCTCACACACAC---GAGAACTAACACTAATAGCCCTTCACATAATTCC
+s rn3.chr2 24396826 404 - 258222147 -TTCTACTTGAACACCACGGAGTCCCACAGGCTC-GCAGCCCTGATGAGTGCCCATGGTCTCAAGGTATAAACAGCTGTCTGCCTTACAGTCTCCAACTAAACCTGAATTCATATCC--------AACTACGTTGTTACCTTGCAGGTAACAACCATTACTGTCTTCGATAAC---GTGCTAAGTGTGGGCTAGC------AATCTAGCCTTTACTGTCAGATACCACCTTCTTAGGGAA-TATTTGTG------TTTACAACT-CGTTTTCATGATTTAGTTTTACCCTCATTATGGCAGGATTTACCAGACCAATTAAAACCGTCTACTAGCTCTGCAGAATCAT----CGCAAGGCAATGAGGAAAACTTATATTCCACAT--TAACA--GTACCAACCTCTTCTGCATTTGGAAAAATGACTCTTCTCTTCCCAC----------
+s canFam1.chrM 11101 417 + 16727 TTCTTATTCAAACACCATGAAGTTATATAGGTGCAACAGCTCTAATAATTGCCCATGGTTTAACATCCTCAATACTATTCTGCTTAGCCAACTCCAATTACGAACGAATCCATAGCC-------GTACTATAATTCTCGCACGAGGACTTCAAACTCTCCTTCCCCTAATAGCAGCCTGATGACTATTAGCAAGCCTCACAAATCTGGCTCTCCCTCCAACAATTAATCTTATCGGAGAACTATTTGTA------GTGATATCCTCATTCTCATGATCCAACATTACTATTATCCTAATAGGAATTAACATTATCATCACCGCCCTATACTCACTTTATATATTAAT----CACCACACAACGTGGTAAATATTCCCACCATAT--CAAAAATATCAAACCATCATTCACAC---GAGAAAATGCCCTAATGACCTTGC----------
+s galGal2.chrM 12386 417 + 16775 GTATAATCCAAACCCAATGATCATTCTCAGGTGCAATAATCCTCATAATCTCCCATGGACTAACCTCTTCCCTTTTATTCTGCCTAGCAAACACAAACTACGAACGGACACACAGCC-------GCATTCTTATCCTGACACGAGGCCTCCAACCCCTCCTACCATTGATATCAGTATGATGATTACTAGCCAACTTAACCAACATGGCCCTGCCCCCAACCACCAACCTGATAGCAGAACTAACAATT------ATAGTTGCCCTCTTCAACTGATCCTCCCCCACAATTATCTTAACCGGCACTGCAACACTCCTAACCGCCTCTTACACCCTCTACATACTACT----CTCAACCCAACGAGGCACTCTTCCATCCCACATCACAACAACCCCCAAC--TCAAACACTC---GAGAACATCTTCTCATAACCCTCC----------
+s danRer1.chrM 12202 417 + 16596 TTTTGATTCAAACCCCCTGAGGATTTACAGGAGCAATTATTTTAATAATCGCCCACGGACTAACCTCATCCGCCCTATTTTGCTTAGCTAACACATCGTATGAACGAACTCATAGCC-------GGACCATAATCCTCGCTCGAGGACTCCAGATAGTGCTACCGCTAGCAACAGTATGGTGATTTATTGCTAATCTGGCCAACCTAGCACTTCCACCTCTACCAAACTTGATAGGAGAACTTATGATT------ATCACAGCCCTATTTAACTGATCTCCATGAACAATTATTATTACAGGAATAGGAACCTTAATTACAGCAAATTATTCACTTTATATATTTTT----AACATCTCAACGAGGCTCAATCCCAGAACACAT--CACCAATCTTTCACCATCCCACACCC---GAGAACATCTCTTAATGACTTTAC----------
+
+a score=1681.0
+s hg17.chrM 12078 63 + 16571 ACCTATCCCCCATTCTCCT-CCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTA-------
+s panTro1.chr11_random 29232134 55 - 53199993 ACCT-------ATTCTTCT-ATTAT-CCTAAATCCTAAAATTATTATGGACTTTACATGCTGTA-------
+s mm5.chrM 11494 53 + 16299 ACTT-------ATTCTTCTAACTAC----CAGTCCAAAACTAATTACAGGCCTGACAATATGTG-------
+s canFam1.chrM 11518 63 + 16727 ACCTACTGCCCCTACTCCT-CCTATCCCTTAACCCTAAAATTATTCTCGGTCCCATCTACTGTA-------
+s galGal2.chrM 12803 63 + 16775 ACATCATCCCCATACTAAC-ACTCATCCTCAAACCAGAACTAATCTCAGGAACCCCTCTATGCA-------
+s danRer1.chrM 12619 64 + 16596 ACCTAATTCCTATCATCTT-ACTTATATTAAAACCAGAACTTATGTGAGGT------TGATGTAACTAGTA
+
+a score=871.0
+s hg17.chrM 12141 2 + 16571 AA
+s panTro1.chr11_random 29232189 2 - 53199993 GC
+s mm5.chrM 11547 2 + 16299 AA
+s rn3.chr2 24397331 2 - 258222147 AA
+s canFam1.chrM 11581 2 + 16727 AG
+s galGal2.chrM 12866 2 + 16775 AA
+s danRer1.chrM 12683 2 + 16596 AG
+
+a score=150956.0
+s hg17.chrM 12143 196 + 16571 TATAGTTTAAC-CAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTTATTTACCGAGA--------AAGCT-CACAAGAA---------CTGCTAACTCATG--CC-CCCATGTCTAACAA-CATGGCTTTCTCA--ACTTTTAAAGGATAACAGCT-ATCCATTGGTCTTAGGCCCCAAAAAT-TTTGGTGCAACTCCAAATAAAAGTAAT
+s panTro1.chr3 35473859 196 - 209662276 TATAGTTTAAC-CAAAACATTAGATCGTGGATCTAACAATAGAAGCCTGCAACTTCTTACCTACCAAGA--------AAGTA-TGCAAGAA---------CTGCTAACTCATG--CC-CCCATGTTTAACAA-AATGGCTTTCTCA--ACTTTTAAAGGATTGGAGTT-ATCCATCGGTCTTAGGAACTAAAAAC-ATTGATGTAACTCCAAATAAAAGTAAC
+s mm5.chrM 11549 194 + 16299 TATAGTTTACA-AAAAACATTAGACTGTGAATCTGACAACAGGAAA-TAAACCTCCTTATTCACCAAGA--------AAGAT-TGCAAGAA---------CTGCTAATTCATG--CT-TCCATGTTTAAAAA-CATGGCTTTCTT---ACTTTTATAGGATAATAGTA-ATCCATTGGTCTTAGGAACCAAAAAC-CTTGGTGCAAATCCAAATAAAAGTAAT
+s rn3.chr2 24397333 182 - 258222147 TATATTTTATG-TTAACCATTACATTGTT--TCTAATAACAGAAAATTACAG---CTTGTTCCCTGAGA--------CA-TG-TGAAAGAC---------ATACTGATTCACAGCCC-CCCATGTGTGACAA---------TCTTA--AGTTTGAACAGGTAAAAGTA-ATTTACTACTTTGAAGGGC--AAAAC-TTTGGTCTGACTCCAAATAGAAGTAAT
+s canFam1.chrM 11583 196 + 16727 CATAGTTTAAC-AAAAACATTAGATTGTGAGTCTAACAATAAAAGCTCAAACCTTTTTGCTTACCGAAA--------AAGTACTGCAAGAA---------CTGCTAATTCATG--CT-CCCATGCATAAGAA-CATGGCTTTTTCA--ACTTTTATAGGATAGAAGTA-ATCCGTTGGTCTTAGGAACCAAAAA--ATTGGTGCAACTCCAGATAAAAGTAAT
+s galGal2.chrM 12868 204 + 16775 CATAGTTTAAC-CCAAACATTAGATTGTGATTCTAAAAATAGGAGTTTAACCCTCCTTGTTCGCCGAGGGGAGGCCCAAGCC-AGCAAGAA---------CTGCTAATTCCTG--CA-TCTGAGCTTTAAAC-CTCAGTCCCCTTA--ACTTTTAAAGGATAAGAGCA-ATCCGTTGGTCTTAGGAACCACCTAT-CTTGGTGCAAATCCAAGTAAAAGTAAT
+s danRer1.chrM 12685 210 + 16596 TTTAGTTTAAAGTAAAATTTTAGATCGTGACTCTAAAGATAGGGGTTAAAGCCCCCTCACTCACCGAGG--------AAGAG-TAGGAAAACAGTAAATGCTGCTAATATTTA--CCAACCATGGTTAAACTCCATGGCTTCCTTACCGCTTCTAAAGGATAATAGTACATCCATTGGTCTTAGGAACCAAAAACTCTTGGTGCAACTCCAAGTAGAAGTT--
+
+a score=-27322.0
+s hg17.chrM 12339 84 + 16571 AACCATGCA-------CACTAC------------TATAACCACCCTAACCCTGACTTCCCTAATTCC--------CCCCAT--CCTTAC----------CACCCTCGTTAACCCTAACAAAAA------
+s panTro1.chr3 35474055 84 - 209662276 AAACATG------------TATCTTCCATG--GGTATAACAGCCCTAATCC------CCTTAATTCC-------------------TACTGATTACTATTATCTTAGCCAACTCCTGCAAAAT------
+s mm5.chrM 11743 83 + 16299 CAA----------------TAT------------TTTCACAACCTCAATCTTATTAATCTTCATTCTTCTACTATCCCCAA--TCCTAA----------TTTCAATATCAAACCTAATTAAAC------
+s canFam1.chrM 11779 84 + 16727 AAATATA------------TTTTCTTCATG-CATAATCACAGCCCTAGTTA------TTCTTACTTT--------GCCCAT--CATTAT----------ATCCTCTACTAAACTTTACAAGAA------
+s galGal2.chrM 13072 92 + 16775 --------GGAGACTCCACTGC--TCCTTAACACCCTCACAACATTAACACTACTCACCCTCCTTAC--------CCCTATTATCCTTC----------CCCCCCTCCTAAATCTAAAAA---------
+s danRer1.chrM 12895 86 + 16596 ----------------TATGAC------TGATATGATCATACCTTTAACATTAA---TCCTAATTTT--------CGCAGTTTTATCAT----------ACCCCTTATTAAAACCAAAAAGCTATTCAA
+
+a score=142193.0
+s hg17.chrM 12423 342 + 16571 AAACTCATACCCCCATTATGTAAA---------ATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAAC-----AACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATTTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGG
+s panTro1.chr3 35474139 338 - 209662276 AGGCTCATACCCAAATTATGTAAAA------ACATC---TATCACATATGCCTTCATCATTAGCCTCATCCCAACAACAATGTTTATATGCACAGACCAAGAAGCCATTATCTCAAACTGACATTGAATGATGATCCAGACTCTCAAA-----CTCTCACTAAGCTTCAAACTAGACTACTTCTCCACAAAATTTATCCCAGTAGCGCTATTCATTACCTGAACTATTGTAGAATTATCAATATGATATATAAATTCAGACTCTAACATTAATCAATTTTTCAAG----TACTTATTTTCTTCATCATGATATTAATTCTGGTTACTGCCAACAACCTCTTTCAGCTCTTTATCGG
+s mm5.chrM 11826 343 + 16299 ACA-TCAACTTCCCACTGTACACCACC----ACATC---AATCAAATTCTCCTTCATTATTAGCCTCTTACCCCTATTAATATTTTTCCACAATAATATAGAATATATAATTACAACCTGGCACTGAGTCACCATAAATTC-----AATAGAACTTAAAATAAGCTTCAAAACTGACTTTTTCTCTATCCTGTTTACATCTGTAGCCCTTTTTGTCACATGATCAATTATACAATTCTCTTCATGATATATACACTCAGACCCAAACATCAATCGATTCATTAAATATCTTACACTATTCCTGATTACCATGCTTATCCTCACCTCAGCCAACAACATATTTCAACTTTTCATTGG
+s rn3.chr2 123593513 320 + 258222147 AAA-TCAGTTTCCC-TTCTGTATAAAT----TCATT---TATCAAATATGCTTTCCTTCTTAGCCTATTACCTCTAATATCATTCTACTATTCTGACACA-----CCTGATTACTAACTGATACTGAATTACTATTAATTATTCCAAA---------CTATCAGTTTAACATTTGACTATTTCTGCATATTCTTTTTACTCGTGACTTTATTCATAACCTAATCAGTCATAAAGTTTTCTTCATGATCTATACACCCCAACCTCTCCTAAACTATTTTTATCAAATACCTCCTT-TATTTTTAATTTCATTAATTATCTTTGCTTCAACCAACAAC------------TTTATTGG
+s canFam1.chrM 11864 341 + 16727 AAG-CTATACCCATACTATGTAAAA------ACCGC---TACTTCTTACGCGTTCATAATTAGCATAATTCCCACAATAATATTCATCTACTCAGGACAGGAAACAATCATTTCAAACTGGCATTGAATAACAATCCAAACTATAAAA-----CTATCCATGAGTTTCAAATTAGACTACTTCTCAATAATCTTTGTACCTGTAGCCCTTTTTGTCACGTGGTCTATCATAGAATTCTCTATATGATATATACACTCCGATCCTTACATTAACCGGTTTTTCAAGTACCTTCTCTTATTCCTCATCACTATAATAGTCCTAGTTACCGCAAACAACATATTCCAACTATTCATTGG
+s galGal2.chrM 13164 337 + 16775 -------ACTCCCCCATATCCATCACC----AAAAC---CATTAAAACCGCCTTCCTAATCAGCCTAATCCCAACAACAATCTTCATCCACTCAGGGGCAGAAAGCATTGCCACCCACTGAGAATGACAATTTATCCCCAACTTCAAG-----ATCCCCATCTCCCTAAAAATAGACATATACTCCATAATATTCTTCCCCATTGCACTATTTGTAACCTGATCCATCTTAGAGTTCGCAACATGATACATAGCATCCGAACCATTTATTACAAAATTCTTTACCTACCTACTCACCTTCCTCATCGCCATATTAACACTAACCATCGCAAATAACATATTCCTCCTATTTGTAGG
+s danRer1.chrM 12981 343 + 16596 -----AATCCAACAACTCTTTCCAAGCTTGAAATGC---TGTCCATGTATCTTTCTTAATTAGTCTTATCCCACTTACAATGATGCTGTACAAAGAATCAGACCATGTTGTAATATGCTGAAGCTGAATAAATACACAAGCGTTTAAC-----GTAGACCTAAGTTTTAAATTTGACTACTATTCTGTGACTTTTACCTCAATCGCCTTATTCATCACCTGGTCAATTTTAGAATTTGCATCATGATATATAGCCTCTTATCCACAAAAAGAATTATTTTACAAATATTTACTTCTTTTTCTTATATCAATAATTATCTTAGTTACAGCCAACAATCTATTTCAACTATTTATTGG
+
+a score=543567.0
+s hg17.chrM 12765 648 + 16571 CTGAGAGGGCGTAGGAATTATATC-CTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAGTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCA----CAACAAATAGCCCTTCTAAA------CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTC-CACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACT-AATCCAAACTCTAACACTA-TGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGT-AGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGCACATCTGTACCCAC--GCCTTCTTCAAAGCCATACTATTT-ATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAAT
+s panTro1.chr11_random 29232784 648 - 53199993 ATGAGAAGGTATAGGAATCATGTC-TTTCTTACTAACTGGCTGACAATATGGCCGAGCAGATGCTAATACAGCAGCCCTCCAAGCAGTCCTGCACAATCGCATCGGCGATATTGGTTTTATTTTAGTTATAGCATGGTTCCTCTTTTCCTCCAACACATGAG----AGATTCAACAAGCATTCATTCTAAACCCTACCTCTAATCC---CCT---TCCATTAATTCGCCTTCTCTTAGCAGCAGCAGGAAAGTCAGCTAAATTCGGCCTCCATCCCTGACTTCCATCCGCCATAAAAGGCCCAACCCCAGCCTCAGCCCTGCTC-CACTCCAGCACTGTAGTTGTAGCAGGAGTTTCCCTGCTCATCCGCTTCTACCCTTTAATAGAAAATAACCT-CTGAACCCAAACCTTTACATTA-TCTCCAGGGGCTATTACCATCTTATTTACAGCAATCTGCGCTCTAACACAAAGTGATATTTAAAAAATCAT-AGCATTCTCCACCTCAAGTCAGCTGGGCCTTACGACAGTCACAATTGGCATGAATCAGCCACACCTAGCATTCCTTCACATCTGCAGCCAC--GCCTTTTTTAAAGCTATATTATTT-ATATGCTCAGGCTCCATCATCCACAATCTCAATGATGAACAAGATATTTGAAAAAT
+s mm5.chrM 12169 648 + 16299 CTGAGAAGGGGTGGGAATTATATC-TTTCCTACTAATTGGATGATGGTACGGACGAACAGACGCAAATACTGCAGCCCTACAAGCAATCCTCTATAACCGCATCGGAGACATCGGATTCATTTTAGCTATAGTTTGATTTTCCCTAAACATAAACTCATGAG----AACTTCAACAGATTATATTCTCCAACAACAACGACAATCT---AAT---TCCACTTATAGGCCTATTAATCGCAGCTACAGGAAAATCAGCACAATTTGGCCTCCACCCATGACTACCATCAGCAATAGAAGGCCCTACACCAGTTTCAGCACTACTA-CACTCAAGTACAATAGTAGTTGCAGGAATTTTCCTACTGGTCCGATTCCACCCCCTCACGACTAATAATAA-CTTTATTTTAACAACTATACTT-TGCCTCGGAGCCCTAACCACATTATTTACAGCTATTTGTGCTCTCACCCAAAACGACATCAAAAAAATCAT-TGCCTTCTCTACATCAAGCCAACTAGGCCTGATAATAGTGACGCTAGGAATAAACCAACCACACCTAGCATTCCTACACATCTGTACCCAC--GCATTCTTCAAAGCTATACTCTTT-ATATGCTCTGGCTCAATCATTCATAGCCTGGCAGACGAACAAGACATCCGAAAAAT
+s rn3.chr2 123593833 599 + 258222147 CTGAGAAGACATAGGTATTATATCACTTTCTACCA---------------------------GCAAACAGTGCAGCCCTGCAAGCAGTGTTGTGTAATCACAATGGAGTCATTAGATTAGTTTTAGCTACAGCATGAATCTTTGTAAACATCAACTCCTGAG----AACTTCAACAGATTTTTTTTCTTA-------CATCAACTT---AAC---TCCTCTCCTAGGCCTTCTAATTCCAGCCCCAGGAAAATCAGCACAATTTACTATCCGCTCCTGACTCCCATCAACCACAG-AGGCCCTTCCCCA-TCTCAGCATTCCTCTCATTCAAGTCCTGTAGTTGTTTCAGGAATCTTCTTAGTAATCAGACTTTACTCACTTG----AAATAACTA-CT--------ATTGTGATACTTGTGTCTTGAGTCACTACCCACATTGTTCACAGCCATCTGTGCAATTAC-TAAAATGACATTTAATTTTTTTTAAACATTTCGCACATTTAGCCAGTTAGGCCTTACAATAGTAGCTTTAGGTGTAAGTCAACCCTCTCTAGCTTTCCTTCACATCTGTACACACATACATTCTTCACAGCTATTCAGTTTCATGTGCCCAGG-------GTTCACAGCTTTAATGCTGAACAAGACATCTGGAAAAT
+s canFam1.chrM 12205 648 + 16727 TTGAGAAGGAGTTGGCATTATATC-ATTCCTACTTATTGGATGATGGTACGGCCGAACCGATGCAAATACAGCCGCCCTACAAGCCGTCCTCTACAACCGTATTGGAGATGTAGGCTTCATTATAACCATAGCATGATTTCTACTAAACTTAAACACATGAG----ACCTTCAACAAATCTTCATTACGA---CAAACGATAATTTTAATCT---GCCACTACTTGGCCTACTACTAGCAGCTACCGGTAAATCTGCTCAATTCGGCCTACATCCCTGACTCCCCTCAGCCATAGAAGGCCCCACTCCTGTATCAGCCCTACTT-CACTCAAGCACAATAGTTGTAGCAGGAGTATTTCTTCTTATCCGCTTTCATCCACTAATAGAGCATAACCA-AACTATTCAAACCCTCACTTTA-TGCTTAGGGGCCATTACTACACTATTTACCGCAATCTGCGCTCTTACACAGAATGATATCAAAAAAATTGT-AGCGTTCTCTACCTCAAGCCAACTAGGCCTAATAATAGTAACAATTGGCATTAACCAGCCCTACTTAGCCTTCTTACACATCTGCACTCAC--GCATTTTTTAAAGCTATACTATTC-ATATGCTCAGGGTCAGTTATCCACAGCCTAAACGATGAACAAGACATTCGAAAAAT
+s galGal2.chrM 13501 645 + 16775 ATGAGAAGGAGTAGGAATCATGTC-ATTCCTTCTCATTGGATGATGACAAGGACGAGCTGAAGCCAACACAGCTGCACTACAGGCAATAATCTACAACCGAATCGGAGACATTGGCCTCATCCTAAGCATAGCATGACTAGCCTCTTCCCTAAACACCTGAG----AAATTCAACAAATCACCCACCCAAACCAAA-CACCCACCC-----T---CCCCCTCCTTGGCCTAATCCTAGCCGCCACAGGAAAATCCGCTCAATTTGGCCTTCACCCATGACTTCCAGCAGCAATAGAAGGCCCAACCCCTGTCTCCGCCCTACTC-CATTCCAGCACAATAGTAGTTGCTGGAATTTTTTTACTCATCCGCACCCACCCCTTCCTGTCATCCAATAA-AACAGCCCTGACAACGTGCCTA-TGCTTAGGTGCTCTATCAACACTCTTTGCCGCAACATGCGCTCTCACTCAAAACGACATCAAAAAAATCAT-TGCCTTCTCCACTTCAAGCCAACTAGGCCTCATAATAGTCACAATTGGCCTAGACCTCCCCCAACTAGCCTTCCTCCACATCTCAACCCAT--GCCTTCTTTAAAGCTATATTATTC-CTATGCTCCGGCCTAATTATCCACAGCCTCAATGGAGAACAAGACATCCGCAAAAT
+s danRer1.chrM 13324 651 + 16596 CTGAGAAGGGGTAGGAATCATATC-ATTTTTACTCATTGGCTGATGATTTGGGCGGACAGAGGCTAACACAGCATCTCTACAGGCCGTAATCTACAACCGAATAGGAGACATTGGATTTATCTTAACCTTAGCATGAATAGCAATATACCTCAACTCCTGAG----ACATTCAGCAAATTTTCATTCTTTCAAAAGACTTCGACATGACCAT---TCCCCAAATTGGACTTATTATTGCAGCCACAGGGAAATCAGCCCAATTTACACTTCACCCCTGACTACCATCAGCCATAGAAGGCCCTACACCAGTATCTGCTTTACTT-CACTCTAGCACTATGGTTGTAGCAGGGATTTTCCTTTTAATCCGTCTTCACCCAATTATAGAAACTAACAA-GCTTGCACCAACAATCTGTCTA-TGCCTTGGAGCATTAACAACTCTATTTGCAGCAACCTGTGCTCTAACCCAAAATGATATCAAAAAAATCGT-AGCTTTCTCAACATCAAGCCAACTAGGGCTAATGATAGTAGCAATTGGCCTAAACCAACCACATCTAGCATTTTTCCACATCTGCACTCAC--GCTTTTTTTAAAGCCATATTATTC-TTATGCTCAGGGGCAATTATTCACAGTCTTAACAACGAACAAGACATCCGTAAAAT
+
+a score=1898.0
+s hg17.chrM 13413 2 + 16571 AG
+s mm5.chrM 12817 2 + 16299 AG
+s rn3.chr2 123594432 2 + 258222147 GG
+s canFam1.chrM 12853 2 + 16727 GG
+s galGal2.chrM 14146 2 + 16775 AG
+s danRer1.chrM 13975 2 + 16596 AG
+
+a score=97800.0
+s hg17.chrM 13415 148 + 16571 GAGGACTACTCAAAACCATACCTCTCACTTCAACCTCCCTCACC-------ATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCAAAGACCACATCATCGAAACCGCAAAC--ATATCATACACAAACGCCTGAGCCCT
+s panTro1.chr3 35475123 148 - 209662276 GAGGGCTATTCAAGACTTTGCCCCTCACTTC-------CTCATCCTTTATTACTGGCAGTCTTGCACTTACAGGCATGCCTTTCCTTACAAGCTTTTACTCTAAGG-CCTCATCATTGAAACTGCAAACTCAT-TCATACACCAACGCCTGAGCCCT
+s mm5.chrM 12819 148 + 16299 GAAACATCACAAAAATCATACCATTCACATC-------ATCATGCCTAGTAATCGGAAGCCTCGCCCTCACAGGAATACCATTCCTAACAGGGTTCTACTCAAAAGACCTAATTATTGAAGCAATTAAT--ACCTGCAACACCAACGCCTGAGCCCT
+s rn3.chr2 123594434 146 + 258222147 GTGACTTAATAAAAGCCCTTCCTTTTACATC-------ATCTTGTCTAATTATCAGTGGACTTGCTTTAACTGGCATACC-TTCCTTACAGGATTTTACCCCAAAACCCTAGTCATTGAGGCCAGTAAC--ATCTAATA-ACCAATTCCTGAGCCTT
+s canFam1.chrM 12855 148 + 16727 GTGGCCTATTTAAAGTCCTTCCCTTCACCAC-------AACCTCCCTTATTATCGGAAGCCTCGCATTAACAGGCATGCCTTTCCTTACAGGATTCTACTCCAAAGACCTGATCATCGAGTCCGCTAAC--ACGTCGAATACCAACGCCTGAGCCCT
+s galGal2.chrM 14148 148 + 16775 GATGTCTACAAAAAACCCTCCCAATAACCAC-------CTCCTGCCTAACCATTGGCAACCTCGCTCTAATAGGAACTCCATTCCTAGCAGGCTTCTACTCAAAAGACCTGATCATCGAAAACCTAAAC--ACCTCATACATCAATACCTGAGCCCT
+s danRer1.chrM 13977 148 + 16596 GGGGAACTTACCACACCCTACCAATAACCAC-------AAACTATTTGACCATCGGGAAAATAGCCCTTATGGGTACCCCCTTCCTTGCAGGATTTTTCTCAAAAGACGCTATCCTAGAAGCAATAACC--ACCTCCCATCTTAACGCCTGAGCCCT
+
+a score=20235.0
+s hg17.chrM 13563 55 + 16571 ATCTATTACTCTCATCGCTACCTCCCTGACAAGC----------GCCTATAGCACTCGAATAATT
+s panTro1.chr3 35475271 55 - 209662276 TTCTGTTACTCTTATTGCCACTTCCTTGACA-GCTGTCCATGATACCTATA---------TTATT
+s mm5.chrM 12967 55 + 16299 ACTAATTACACTAATCGCCACTTCTATAACA-GC---------TATGTACAGCATACGAATCATT
+s canFam1.chrM 13003 55 + 16727 CTTAATTACACTCGTTGCCACATCCCTAACC-GC---------TGCCTACAGCACCCGAATTATA
+s galGal2.chrM 14296 55 + 16775 CTCACTTACACTACTTGCCACATCTTTCACT-GC---------AACCTACAGCCTCCGCATAACC
+s danRer1.chrM 14125 55 + 16596 AACACTAACATTAATCGCCACATCATTTACC-GC---------AGTTTATAGCTTCCGAATAATT
+
+a score=63924.0
+s hg17.chrM 13618 214 + 16571 CTTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCT---TACTAACATTAACGAAAATAACCC-CACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGC----ATCCCCCTTCCAAA--CAACAATCCCCCTCTAC-CTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTC
+s panTro1.chr3 35475326 213 - 209662276 TTCTTCGCTCTTATAGGACAACCTTGCTTCACGACTCTGGCTGCTA---TTAATGAAAATAACCC-CTTTCTAATTAACTCAATTAAGCGCCTAACAGTTGGCAGCATATTCACTGGATTCCTCATCACCAACCGTATTATTCCTGCT-TCATCCCC-----AAAAACAACCATACCACTCCAC-CTGAAGCTCACAGCCCTAGGTGTCACCATCTTAGG-CTTC
+s mm5.chrM 13022 214 + 16299 TACTTCGTAACAATAACAAAACCGCGTTTTCCCCCCCTAATCTCCA---TTAACGAAAATGACCC-AGACCTCATAAACCCAATCAAACGCCTAGCATTCGGAAGCATCTTTGCAGGATTTGTCATCTCATATAATATTCCACCAACCAGCATTCCAGTCC------TCACAATACCATGATTT-TTAAAAACCACAGCCCTAATTATTTCAGTATTAGGATTCC
+s canFam1.chrM 13058 213 + 16727 TTCTTTGCTCTACTAGGCCAGCCCCGCTTCTCCCCTATAATCCTTA---TCAACGAGAATAATCC-TCTCCTAATTAACTCTATTAAACGACTCCTTATCGGAAGTGTATTTGCAGGGTATATTATCTCCCACAGCATCACACCCACTACCATCCCA----CAGA--TAACTATGCCTCATTAT-CTAAAAATGACAGCCCTTGCAGTAACCACCTTGGG-TTTC
+s galGal2.chrM 14351 214 + 16775 TTACTAGTCCAAACAGGACACACACGAACCCCCAGCAATCACCCCA---TTAACGAAAACACCCC-CCCAGCCATTCTCCCAATCATACGACTAGCCCTTGGCAGCATTATAGCAGGCCTATTAATCTCATCCCTAATCCTCCCCCCTAAAACCCCT----CCAA--TAACTATACCCACCATC-ACAAAAACTGCTGCCATCATTGTTACAACCCTAGGAATTA
+s fr1.chrUn 320903859 214 + 349519338 --CTTCGTATCCATAGGCCACCCTCGCTTTAATTCCCTTTCACCAA---TCAATGAAAATAACCCATGCTGTAATTAAACCTATCAAACGACTGGCATGAGGCAGCATTATTGCTGGCCTATTAATCACCACACAACTTCTCCCAACAAAAACACCC----GTAA--TATCAATACCTATAGTTGTTAACACTTACTGCTCTTATCGTCACAATCTTAGGACTCC
+s danRer1.chrM 14180 211 + 16596 TACTTAGTCTGTTTAGGAAGCCCCCGACACAAGACCTACGAGACAA---TTGATGAAAA---CCA-CATTCCAACCAATACTATTCAACGGCTTGCCTGAGGAAGCATTATTGCAGGATTAATCATCTCATACACTATAATTCCTCTTAAAACACCC----ATTT--TAACCATGCCTATTTAT-CTAAAATTGGCAGCCATTCTAGTAACTCTACTAGGTATTA
+
+a score=7350.0
+s hg17.chrM 13832 25 + 16571 TAACAGCCCTAGACCTCAAC--TACCT
+s mm5.chrM 13236 25 + 16299 TAATCGCACTAGAACTAAAC--AACCT
+s canFam1.chrM 13272 27 + 16727 TCCTGGCACTAGAACTAAACCTTACCT
+s galGal2.chrM 14565 25 + 16775 TCCTAGCCCTAGAACTCTCA--AGCCT
+s fr1.chrUn 320904073 25 + 349519338 TAATTGCCCTAGAATTAGCT--TCCTT
+s danRer1.chrM 14391 25 + 16596 TCTTAGGACTAGAAATTAGT--ACGCT
+
+a score=-9799.0
+s hg17.chrM 13857 292 + 16571 AACCAACAAACTTAAAATAAAATCCCCACT---ATGCACATTTTATTTCTCCAAC-ATACTCGGATTCTACCCTAGCATC-ACA---CACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAG-CTATTACCTAAAACAATTTCACAGCACCAAATCTC---CACCT---------------CC---ATCATCACCTCAACCCA---AAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCT-----------------AACCCTACTCCTAATC-------------ACATAA
+s panTro1.chr3 35475565 287 - 209662276 AACTAATAACCTTAAACCAAAATACCCATT---ACAGACATTCAACTTCTCCAAC-ATACTAGGATTTTATTC----ATCCACAATTCACCATACAACCCTCCACTCAGGCCTATACACAAGCCAAAATCTGGCTTCACTTCTACTAGACCTAATATGACTAGAAAAGTCTAT-ACCAAAGACCATTACACAAC-CCAAATTTC---AGCCT---------------CC---ATTACCATATCTACTCA---GAACGGCCTAATTAAACTCTACTT----TCTTTTTTTATCCCATCCCTTCT-----------------AACTCTGCTCCTAATT-------------ATCTAA
+s mm5.chrM 13261 286 + 16299 AACCATAAAACTATCAATAAATAAAGCAA----ATCCATATTCATCCTTCTCAACTTTACTGGGGTTTTTCCC----ATCTATTATTCACCGCATTACACCCATAAAATCTCTCAACCTAAGCCTAAAAACATCCCTAACTCTCCTAGACTTGATCTGGTTAGAAAAAACCAT-CCCAAAATCCACCTCAACTCTTCACACAAA---CATAA---------------CC---ACTTTAACAACCAACCA---AAAAGGCTTAATTAAATTGTACTTTATATCATTCCTAATTAACATCATCTT-----------------AATTATTATCTTA-------------------TAC
+s canFam1.chrM 13299 282 + 16727 --CACAAGGACTCAAATTTAACTATCCTTC---TAATTACTTTAAATTCTCCAGC-CTCCTTGGCTACTATCC----AACCATTATGCACCGCCTCACACCTAAAACAAGTTTAACCATTAGCCAGAAATCAGCATCTATACTTCTGGACTCCATCTGACTAGAAAACATCCT-ACCCAAATCAATCTCATATTTCCAAATAAA---ATCTT---------------CT---ACCCTTATTTCAAATCA---AAAAGGTCTCATCAAACTCTATTTCCTATCGTTCATACTAACTATAATCCT-----------------CAGTCTACTAA---------------------TCC
+s galGal2.chrM 14598 290 + 16775 CCCTCACTCCCCCAAAACACAATCCCCTC-----------ATAAACTTCTCCTCC-TCCCTAGGCTACTTTAA----CCCCCTAACTCACCGAATTAGCCCCTCAATCCTCCTACATACCGGACAAAAAATTGCATCCCACTTAATCGACATAGCATGGTACAAAAAAATAGG-CCCCGAAGGCCTTGCCAACCTTCATCTCAC---CATAA---------------CCAAAATCTCAACCACACTCCA---CACAGGCCTAATTAAATCTTACCTGGGTTCCTTCGCCCTCACAATCCTTAC-----------------AACGATCCTACTTATC----------CAAAAATAA
+s fr1.chrUn 320904101 298 + 349519338 CTCCAAACAACTTAAACCTACACCACACCT---GTCCCCCCACCACTTCTCAAAC-ATACTTGGCTTCTTCCC----AACAATTGTACACCGTGCCTCTCCTAAAATTAATCTCATTTTAGGACAAACAATTGCTACCCAAATTATTGACCTAACCTGACTAGAAAAAGTTGG-ACCCAAAACAATTTCATCTATCAATACTCCCCTCATCT---------------CT---ACCATTAGTAACATCCA---ACAAGGATCAATCAAGACATACCTTGTCCTCTTCCTCACGACCCTTGCTCT-----------------ATCAACCCTCGTTCTT----------CTTACCTAA
+s danRer1.chrM 14416 322 + 16596 AGCTAATAAAATTAACAAAAACACTACCCCAGGAATTCCATTCCACTTTTCAATT-TCACTAATCTTCTTTCC----A---ATCCTTCACCGACTAATCCCTATACGAAAATTATTTATAGGGGAGTCAGCAGCC------------------ACTAAAATTGAAAAATCATG-AAGCGAACTATTCGGACCATGCGGAATTGC---ATTTACATTAATAACAGTGGCC---ACCTTTGTTAAGGACCATCGAATAGCGTCAATCAAGTCTTACCTAGCCGTCTTCCTTACCTCTATTATTCTTAAAATAATAATACTGAAACTATACACTTAAATAGCACGAAGCACACCATAA
+
+a score=0.0
+s hg17.chrM 14149 1 + 16571 C
+
+a score=180.0
+s hg17.chrM 14149 1 + 16571 C
+s panTro1.chr3 35475852 1 - 209662276 T
+s mm5.chrM 13547 1 + 16299 T
+s canFam1.chrM 13581 1 + 16727 T
+
+a score=10579.0
+s hg17.chrM 14150 50 + 16571 CTATT--------CCCCCGA-GCAATCTCAATTACAATATATACACCAACAAACAATGT
+s panTro1.chr3 35475853 50 - 209662276 CTATT--------ATCCTGA-GTAATTTCAATCACAACATAAATACCAATAAATAATCA
+s mm5.chrM 13548 51 + 16299 CAATT-------AATCTCGA-GTAATCTCGATAATAATAAAAATACCCGCAAACAAAGA
+s canFam1.chrM 13582 50 + 16727 TAATT--------ACCACGG-GTAACTTCCATGATAACCAACACACCAATTAATAATGA
+s fr1.chrUn 320904399 58 + 349519338 CTGCTCGAAGAGCCCCCCGACCCAACCCCCGCACCAGCTCTAATACT-ACAAGCAACGT
+s danRer1.chrM 14738 50 + 16596 CTAAG--------ACCTCGA-GTAACCTCTAGTACAACAAACAAAGTCAGAAGCAATAC
+
+a score=2145.0
+s hg17.chrM 14200 5 + 16571 TCAAC
+s panTro1.chr3 35475903 5 - 209662276 TCAAC
+s mm5.chrM 13599 5 + 16299 TCACC
+s canFam1.chrM 13632 5 + 16727 TCAGC
+s danRer1.chrM 14788 5 + 16596 CCAAG
+
+a score=126.0
+s hg17.chrM 14200 5 + 16571 TCAAC
+s danRer1.chrM 14788 5 + 16596 CCAAG
+
+a score=2043.0
+s hg17.chrM 14205 148 + 16571 CAGTAACCACTACTAATCAACGCCCATAATCATACAAAGC--CCCCGCACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATACTC
+s panTro1.chr3 35475908 148 - 209662276 CAGCAACTACCACTAATCAGCATCCATAACTGTACAAGGCAGCCACACAC--ACAGAATCTTCACGCAACAACCCTGCCCCCTCACCCTCAAAAATCGTCCAGCTCTTTATGCTATTAAAATTAATCATGATCCTCACTGCATCATGCTC
+s mm5.chrM 13604 145 + 16299 CAGCTACTACCATCATTCAAGTAGCACAACTATATATTGC--CGCTACCCCAATCCCTCCTTCCAACATAACTCCAACATCATCAACCTCATACATCAACCAATCTCCCAAACCATCAAGATTAATT---ACTCCAACTTCATCATAATA
+s rn3.chr8 86333738 140 - 129061546 CAGCCACCATGGTCAACCAAGTCTCACAACTGCATATAGA--TGCTACCCTAGCTGCTTCTCTGTCTAGTCACCCAATCTCATCTCTCTCATAAA--------CACCCCATGTTTTTAAGTTCTACCACCACCCCCACCCCACAGTAACA
+s canFam1.chrM 13637 146 + 16727 CTGTAACAACCACCAACCAAGTCCCATAACTGTACAGAGC--CGCAATACCCATAGCCTCTTCACTAAAAAACCCAGAGTCCCCCGTATCATAGATCACTCAATCCCCTATTCCATTAAACTTTAATACTACCTCCACCTCGTCATCC--
+s fr1.chrUn 320904457 128 + 349519338 CAATAACAA-----GACCCAGGCCCCCAATAGT--AATAC--TCCCCCACCGCTAGAATATATAAGTGAAACCCCGTCCATATCACCTCGAAAAACTGCATCTCAGTCTATCTCTCCAGAA---------ACC----CCTCATCACACCT
+s danRer1.chrM 14793 132 + 16596 CACAAATCACTAATATTTTTCCACCTGACGAATATATTAT--TGCAACCCCGCTTACATCAGCTCGAATAACAGAAAACTCTTTAAAAGCATCAA-----------CCGATATTAATAA-----ACCAGTGTCACCAGTTAATAAAAACC
+
+a score=-17437.0
+s hg17.chrM 14353 57 + 16571 TTTCACCCACAGCACCAATCC--TACCTCCATCG--CTAACCCC---ACTAAAACAC---TCACCAA
+s mm5.chrM 13752 54 + 16299 AAGCACACAAATTAAAAA-----AACCTCTATAA--TCACCCCCAATACTAAAAAAC------CCAA
+s rn3.chr8 86333883 54 - 129061546 TTGTGTATACAGCCCC-------CAACTCCAGAAATATAACCCTAACAACAAACTAC------CTAA
+s canFam1.chrM 13783 59 + 16727 TTCAAAATATAGCAAGCAGTCAACAATTCAGACA--ACAAACC-AGTAATAAAAGCC-----GCTAG
+s fr1.chrUn 320904585 57 + 349519338 ------CTTCATCAAGGACCA--TATTTGTGTAC--AAGATACCAAAAACAAAAAAAAAATATCCAA
+s danRer1.chrM 14925 52 + 16596 ---CAGCCGCCACAATTA-----CAACCAGACCA--TAAACCATAACACGTCAAAAC-----ACCAC
+
+a score=31182.0
+s hg17.chrM 14410 85 + 16571 GACCTCAACC--CCTGACCCCCA--TGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCT
+s panTro1.chr3 35476113 85 - 209662276 GATATCAATA--CTTGACCCTTA--TGTTTCAGGATACTCCTCAGCAGCCATCACCGTGGTATAGCCATAAACAATCATCATACCACAC
+s mm5.chrM 13806 85 + 16299 --AATTAATCAGTTAGATCCCCA--AGTCTCTGGATATTCCTCAGTAGCTATAGCAGTCGTATATCCAAACACAACCAACATCCCCCCT
+s rn3.chr8 86333939 75 - 129061546 TAATTCAATG----AGAACATCA--AGTCTCGGGTTACTTCTCCAAAGCAGT--------TATAATTGAACACAACTAGCATACCACTG
+s canFam1.chrM 13842 85 + 16727 AACAGCCTTA--TTTGAAACTCA--CACCTCAGGGTATTGCTCAGTAGCCATAGCAGTTGTATAACCAAATACTACTAATATACCCCCC
+s fr1.chrUn 320904650 87 + 349519338 AAAACCACCT--GTCAACCTGTAGGCGCCTTAGGATCCTTATCTGCAGACAGCGCTGACGAATAAATAAACACAACCAGTATGCCCCCC
+s danRer1.chrM 14977 76 + 16596 -----------ACGGTCACCCCA--CGCTTCAGGAAAAGGCTCGGCTGCTAGGGCCGCTGAATAAGCAAACACTACAAGCATCCCACCT
+
+a score=35925.0
+s hg17.chrM 14495 109 + 16571 AAATA---AATTAAAAAAACTATTAAACCCATATAA-CCTCCCC----CAAAATTCAGAATAATAACACACCCGACC----ACACCGCTAA------CAATCAGTACTAA-AC------CCCCATAAATAGGAG
+s panTro1.chr3 35476198 107 - 209662276 AAATGGGGAATTAAAAAAAC-ATCAACCCCATGAAA-GCACCAC----CAAAATTCA--------ACAAATTCAACCCACAGCACCACTAA------TAATTAGCCCTAG-AC------CTCCGTAAATAGGAG
+s mm5.chrM 13891 109 + 16299 AAATA---AATTAAAAAAACTATTAAACCTAAAAAC-GATCCAC----CAAACCCTAAAACCATTAAACAACCAACA----AACCCACTAA------CAATTAAACCTAA-AC------CTCCATAAATAGGTG
+s rn3.chr8 86334585 111 - 129061546 AACTA---CATTAGAAATGCAATTAATCCTAAAAGGTAACCCAG----AAAAATTTATGGCAACTAAATAACACATA----CACCCAGTAA------TACTTAAATCTTGTGT------GCCCATAAATAAGAG
+s canFam1.chrM 13927 109 + 16727 AAATA---AATTAAAAATACTATCAACCCTAAAAAA-GAACCCC----CAAAATTCAGAACAATCGCACAACCAATC----CCACCGCTAA------TAATTAGCACAAG-CC------CACCATAAATAGGAG
+s fr1.chrUn 320904737 109 + 349519338 ATATA---AATCATTAACAACACCAAAGACAAGAAA-GTCCCCCCGTGCAAAACTGA----------------AGCC----CCACAGCAAAGAAGTGCAACCAGCACCAA-ATTGAAAACTCCATAAAAAGGAG
+s danRer1.chrM 15053 109 + 16596 AAATA---AATCAAAAAAAGAATTAGAGACAAAAAT-GAACCCC----CATAACTAACTAAAATTCCACATCCAACC----CCTGCCACAA------CTACTAAACCAAA-TG------CAGCAAAATAAGGAG
+
+a score=75856.0
+s hg17.chrM 14604 139 + 16571 AAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTCAACAGAAACAAA------GCATACA---TCATTATTCTCGCACGGACTACAACCACGACCAATGATATGAAAAACCATCGT--TGTATTTCAACTACAAGAAC
+s panTro1.chr3 35476305 139 - 209662276 AAGATTTCAAAGAGAAACCTACAAATCCTATAACCAAAGTGACACTTAATAAAAATATA------GTATATG---CCATTATTCCCACATGGACTATAATCATGACTAATGACATGAAAAATCATTGT--AGTATTTCAACTATAAGAAG
+s mm5.chrM 14000 139 + 16299 AAGGCTTTAATGCTAACCCAAGACAACCAACCAAAAATAATGAACTTAAAACAAAAATA------TAATTAT---TCATTATTTCTACACAGCATTCAACTGCGACCAATGACATGAAAAATCATCGT--TGTAATTCAACTACAGAAAC
+s rn3.chr2 24398790 122 - 258222147 AGGGGTTTGAAGAACATCCTACCAAACCT--------------ACTTAATGTA-----A------GAGTATT---TCATAATTTCCACATAGACTGTAACTGGGAATAATGACACAAAACATCACCACTGTGTACTTTGCCTGTTAGAAT
+s canFam1.chrM 14036 142 + 16727 ATGGTTTAGTGGCAAAACCCACAAAACTCATCACAAAAACGATACTTAAAATAAATACA------ATGTATGTTATCATTATTCCTACATGGAATTTAACCATGACTAATGACATGAAAAATCATCGT--TGTATTTCAACTATAAGAAC
+s fr1.chrUn 320904846 139 + 349519338 CAGGATTTGTAGACAACACAA------TTATCACAACCAACATCCCTAATAAAAGAAAAACAAGCGCATAAA---ACATAGTTTCTGCCAGGATTTTAACCAGGACCTATGGCGTGAAAAACCATCGT--TGTTACTCAACTACAAAAAC
+s danRer1.chrM 15162 139 + 16596 CCGGATTAGAAGCAATAGCAATCATACCCCCAACTAGAGCTGCCATCAAAAAAGACAAA------TAAAATG---CCATAATTCTTACTCAGACTTTAACTGAGACCGGTGACTCGAAAAACCACTGT--TGTAGTTCAACTACAAGAAC
+
+a score=846407.0
+s hg17.chrM 14743 837 + 16571 --ACC-AATGACC-CCAATAC--GCAAAATTAACCCCCTAATAAAA----TTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCT-TGGCGCCTGCCTGATCCTCCAAATCACC-------ACAGGACTATTCCTAGCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTACGGATCATTT------CTCTACTCAGAAACCTG-----AAACATCGGCATTATCCTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAA----TCTGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGA-----ATCA---CCTCCCATTCCGATAAAATCACCTTCCACCCTTACTACACAATCAA----------AGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTA
+s panTro1.chr3 35476444 837 - 209662276 --GCT-AATGGCC---AATATCTGTAAAACACACCCGCTAATAAAAACTATTAATTA--------TTCATTGATCTTCCCATATCATCTAACCTTTCTATATCATGAAACCTTGGCTCACTTTT-TGGTGCCTGCCTAACCCTCCAAATC--CTTACAGGACAGGACTGCTTTTGGCCATGCACTACACATCAAACACCTCAACTGCCTTCTCTTCAGTCGCTCATATCAGCCAACATGTAAACTTCGGCTGAATGGTTCGCTATTTTCATGCTAATGGCAGTTCAATATTTTTTATCTGCCTCTTCTTACACATTGGCTGAGGTTTATACTATGGATCATTTACATTCCT------AGAAACCTG-----AAATATTGGCATCATCCTCCTACTCAAAACAATGGCAACAGCACTCATAGGCTACATGCTCCCATGAGGCCAGATATCATACTGAGGTGCTACAGTAATTACAAATCTACTATCAGCCATCCCATATATTGGAACTGACCTTGTGCAATAAA----TCTGAGGTGGGTTCTCAGTCGACAAAGCCACCCTTACATGATTCTTCACTTTCCATTTCATCTTA-CCTTCATCATTACAGCCCTAGCAGCTGTTCACCTTTTATTCCTACATGAAACAGGATCTAATAACCCTTCAGGGTTTTCATCAGACCCT--------GACAACATTACCTTCCACCCCTACCATACTACCAA----------AGATATTTTAGGTTTAATTTTTCTCCTCCTCCTCCTAATAATTCTAGTACTATTTTCACCTGACTTCCTGGGCGACCCAGATAACTATGCATTAGCCAGCCCCCTCAACACCCCATCCCACATTAAGCCAGAGTGGTACTTTTTGTTTGCCTA
+s mm5.chrM 14139 838 + 16299 --ACCTAATGACA---AACATACGAAAAACACACCCATTATTTAAA----ATTATTAACCACTCATTCATTGACCTACCTGCCCCATCCAACATTTCATCATGATGAAACTTTGGGTCCCTTCT-AGGAGTCTGCCTAATAGTCCAAATCATT-------ACAGGTCTTTTCTTAGCCATACACTACACATCAGATACAATAACAGCCTTTTCATCAGTAACACACATTTGTCGAGACGTAAATTACGGGTGACTAATCCGATATATACACGCAAACGGAGCCTCAATATTTTTTATTTGCTTATTCCTTCATGTCGGACGAGGCTTATATTATGGATCATATACATTTAT------AGAAACCTG-----AAACATTGGAGTACTTCTACTGTTCGCAGTCATAGCCACAGCATTTATAGGCTACGTCCTTCCATGAGGACAAATATCATTCTGAGGTGCCACAGTTATTACAAACCTCCTATCAGCCATCCCATATATTGGAACAACCCTAGTCGAATGAA----TTTGAGGGGGCTTCTCAGTAGACAAAGCCACCTTGACCCGATTCTTCGCTTTCCACTTCATCTTACCATTTATTATCGCGGCCCTAGCAATCGTTCACCTCCTCTTCCTCCACGAAACAGGATCAAACAACCCAACAGGATTAAACTCAGATGCA--------GATAAAATTCCATTTCACCCCTACTATACAATCAA----------AGATATCCTAGGTATCCTAATCATATTCTTAATTCTCATAACCCTAGTATTATTTTTCCCAGACATACTAGGAGACCCAGACAACTACATACCAGCTAATCCACTAAACACCCCACCCCATATTAAACCCGAATGATATTTCCTATTTGCATA
+s rn3.chr2 24398912 776 - 258222147 --ATG-AACAACC---GATACTCCAAAATTCCACTTTTTAACAAAA----ATTAACAATCATTTGTTCATTGATCTACCAGACTGGTAAAACATTTCCGCATGATGAGAGCCTGGATCTGTGGTGGGGAATCTGCCAGGCTCTC----------------A---------TCATAGCCCAGGACTATCCATCACATATAATAATGGCACTCTCTT-----ACCCAAATTTGTCAAGTTGCA----------------TCAGCTGTTTCTATGTGAATAGAACACAAACATTCTTTACCTGCCTGTTAATCCATGAAAGTTGAAGGTCA---TGTGAATTGCATGTTTTTCT------ATAAATCTGGTTAAAAACACTAGGATTTGCTTATTACTCCC--TGATAGCTACAGCATATCTGGCCCATATGTTATTGTAAGGACAAATGGCTTTCTGAGTTCCAACAGTAGTCACAAACTCACTGGCAATGATTCCACATATC---ATTTCACTAATTTTATAGAGTGTTCTGTGGTGGGCA-TGAGATGACAGAAT--GCCTCACTTGTTTTCTCATCATAAAATTTATTTTTTTATTCAT--------CCCTAGTTATTCTG-GTCCCCTGTCTCTCTGTGAGACAAGATACAGGAATCCAC--AGAGTCTCATTTGACTGG--------GGCAAAATCCTGGATCATTTTTGGTGTATAATTAAGCTATCTGGGATGTCTTCTAGGTTTGCTTGTAGTAC-----------------CCAGTGCTATTCTCCTCCAACTTCTTATGATACAGAGACAATCCCATACCAGACAACCCACTTGATATCTTATCTCA-ATCAAGTCAAATAGAAACTT--TGTCTGCCTA
+s canFam1.chrM 14178 837 + 16727 --ATT-AATGACC---AACATTCGAAAAACCCACCCACTAGCCAAA----ATTGTTAATAACTCATTCATTGACCTCCCAGCGCCGTCTAACATCTCTGCTTGATGGAACTTCGGATCCTTACT-AGGAGTATGCTTGATTCTACAGATTCTA-------ACAGGTTTATTCTTAGCTATGCACTATACATCGGACACAGCCACAGCTTTTTCATCAGTCACCCACATCTGCCGAGACGTTAACTACGGCTGAATTATCCGCTATATGCACGCAAATGGCGCTTCCATATTCTTTATCTGCCTATTCCTACATGTAGGACGAGGCCTATATTACGGATCCTATGTATTCAT------AGAAACATG-----AAACATTGGAATTGTACTATTATTCGCAACCATAGCCACAGCATTCATGGGCTATGTACTACCATGAGGACAAATATCATTTTGAGGAGCAACTGTAATCACTAATCTTCTCTCTGCCATCCCTTATATCGGAACTGACTTAGTAGAATGGA----TCTGAGGCGGCTTCTCAGTGGACAAAGCAACCCTAACACGATTCTTTGCATTCCATTTCATCCTCCCTTTCATCATCGCAGCTCTAGCAATAGTACACCTCCTATTTCTACACGAAACCGGATCCAACAACCCTTCAGGAATCACATCAGACTCA--------GACAAAATTCCATTTCACCCTTACTACACAATCAA----------GGATATCCTAGGAGCCTTACTCCTACTCCTAATCCTAATATCACTAGTTTTATTTTCACCTGACCTATTAGGAGACCCAGATAACTACACCCCTGCAAACCCCCTAAACACCCCTCCACATATTAAACCTGAGTGATATTTTCTATTCGCCTA
+s galGal2.chrM 14888 840 + 16775 --ACT-AATGGCACCCAACATTCGAAAATCCCACCCCCTACTAAAA----ATAATTAACAACTCCCTAATCGACCTCCCAGCCCCATCCAACATCTCTGCTTGATGAAATTTCGGCTCCCTATT-AGCAGTCTGCCTCATGACCCAAATCCTC-------ACCGGCCTACTACTAGCCATGCACTACACAGCAGACACATCCCTAGCCTTCTCCTCCGTAGCCCACACTTGCCGGAACGTACAATACGGCTGACTCATCCGGAATCTCCACGCAAACGGCGCCTCATTCTTCTTCATCTGTATCTTCCTTCACATCGGACGAGGCCTATACTACGGCTCCTACCTCTACAA------GGAAACCTG-----AAACACAGGAGTAATCCTCCTCCTCACACTCATAGCCACCGCCTTTGTGGGCTATGTTCTCCCATGGGGCCAAATATCATTCTGAGGGGCCACCGTTATCACAAACCTATTCTCAGCAATTCCCTACATTGGACACACCCTAGTAGAGTGAG----CCTGAGGGGGATTTTCAGTCGACAACCCAACCCTTACCCGATTCTTCGCTTTACACTTCCTCCTCCCCTTTGCAATCGCAGGTATTACTATCATCCACCTCACCTTCCTACACGAATCAGGCTCAAACAACCCCCTAGGCATCTCATCCGACTCT--------GACAAAATTCCATTTCACCCATACTACTCCTTCAA----------AGACATTCTGGGCTTAACTCTCATACTCACCCCATTCCTAACACTAGCCCTATTCTCCCCCAACCTCCTAGGAGACCCAGAAAACTTCACCCCAGCAAACCCACTAGTAACCCCCCCACATATCAAACCAGAATGATATTTTCTATTCGCCTA
+s fr1.chrUn 320904985 837 + 349519338 --ACT-AATGGCC---AGCCTACGCAAAACCCACCCCCTACTAAAA----ATCGTAAACGACATAGTAATTGACCTTCCTACCCCCTCAAACATTTCCGCCTGATGAAACTTTGGCTCTCTACT-CGGATTATGCCTTATTACACAAATCATC-------ACAGGACTGTTCCTTGCAATACACTACACATCCGACATCTCTACCGCCTTTTCATCCGTAGCCCACATTTGCCGAGACGTAAACTACGGCTGACTAATTCGCAATCTACACGCAAACGGTGCCTCATTCTTTTTTATTTGCTTATACTCCCACATCGGCCGAGGTCTTTACTATGGCTCTTACCTAAGTAA------AGAAACCTG-----AAACGTAGGGGTAGTCCTCTTACTTTTAGTAATGGCCACCGCTTTCGTAGGCTACGTTCTCCCATGAGGACAAATATCCTTCTGAGGCGCCACTGTAATTACAAACCTGCTCTCTGCTGTCCCCTACGTAGGAAACACGCTCGTTCAATGAG----TATGAGGAGGCTTTTCAGTAGACAGCGCCACTCTAACACGATTCTTTGCCTTCCACTTCCTCCTCCCATTTATCGTTGCAGCCGCTGCCATCGTACATCTTATTTTTCTTCACGAAACAGGCTCCAACAATCCCCTAGGACTTAATTCAAACGCA--------GACAAAATCCCATTCCACCCATACTTCTCTTACAA----------AGACCTCCTGGGCTTCACAATCATGCTCTCAGCCCTCGCAACACTCGCCCTATTCTCTCCAAACTACCTCGGAGACCCTGACAACTTCACACCAGCCAACCCTCTAGTTACCCCCGCCCACATTAAACCAGAATGGTATTTCCTATTTGCATA
+s danRer1.chrM 15301 839 + 16596 TGCTT-AATGACA---AGCCTGCGAAAAACACACCCAGTTTTAAAA----ATCGCTAATGACGCATTAGTTGATTTGCCAACGCCACTAAATATTTCAGCGTGATGAAATTTTGGATCTCTCCT-TGGATTATGTCTTATTACACAAATTTTA-------ACAGGACTATTTTTAGCAATACACTACACCTCAGACATCTCAACAGCATTTTCATCTGTTGTGCATATTTGCCGAGATGTAAATTTCGGCTGACTTATTCGGAGCATCCATGCCAATGGGGCTTCCTTCTTCTTCATCTGCCTGTATATTCACATCGCCCGAGGACTATATTACGGATCTTATCTTTATAA------TGAAACTTG-----AAACATCGGAGTAGTCCTGTTCTTACTTGTAATAATAACAGCTTTTGTGGGCTACGTCCTTCCATGGGGCCAAATATCATTCTGAGGGGCCACAGTAATTACTAACCTATTATCGGCCGTTCCTTACGTGGGAGATACCCTAGTGCAATGAA----TCTGAGGGGGATTCTCAGTAGACAATGCAACCCTTACACGATTCTTCGCATTCCACTTTTTATTACCATTTATTATCATCGCCATAGTTATTCTACACTTGCTATTTCTCCACGAAACCGGATCAAATAACCCCCTTGGCCTAAACCCCAACATG--------GATAAAATCCCCTTTCATCCTTATTTTTCAAATAA----------AGACCTCCTTGGTTTTGTAATTATATTATTTTCCCTCTCACTATTAGCACTATTCTCACCAAACCTCTTAGGAGATCCAGAAAATTTCACCCCTGCTAACCCTCTAGTAACACCTCCTCACATTAAACCAGAATGATATTTCCTATTCGCATA
+
+a score=109405.0
+s hg17.chrM 15580 134 + 16571 CACAATTCTCCGATCCGTCCCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATC----CTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAAT
+s panTro1.chr18 72834051 133 - 83875239 TGCAATTCTACGATCCATCCCTAACAAACCAGGAGGTGTACTAGCCC--TTA-TATCC-TCCTTTCTCATTCCAGCAATTAT-CCCATACTTCATACGTCTAAACAATAAAGCATAATATTCTGTCCATTAAGTCAAT
+s mm5.chrM 14977 134 + 16299 CGCCATTCTACGCTCAATCCCCAATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATC----CTAATTTTAGCCCTAATACCTTTCCTTCATACCTCAAAGCAACGAAGCCTAATATTCCGCCCAATCACACAAA
+s rn3.chr2 24399688 92 - 258222147 ----------------------TGCAAACT-----------TGGCCCCACAG-------TT----TTAATCTTAACTACAGC-TGAGTAGTTCCTGTAGCTAAA-AATGAAGCACAGTATTCTGACCCTTTGACCCTT
+s canFam1.chrM 15015 134 + 16727 TGCTATCCTACGATCCATTCCTAATAAATTAGGAGGTGTACTCGCCCTAGTATTCTCCATC----CTAATCTTGGCATTCATTCCACTCCTCCACACATCTAAGCAACGCAGCATAATATTCCGGCCCCTTAGCCAAT
+s galGal2.chrM 15728 134 + 16775 TGCCATCCTACGCTCCATCCCCAACAAACTTGGAGGTGTACTAGCCCTAGCAGCCTCAGTC----CTCATCCTCTTCCTAATCCCCTTCCTCCACAAATCTAAACAACGAACAATAACCTTCCGACCACTCTCCCAAA
+s fr1.chrUn 320905822 134 + 349519338 CGCAATTCTACGGTCTATCCCCAATAAACTAGGAGGAGTCCTGGCCCTTCTTGCCTCAATC----TTAATTCTTATAGTAGTTCCTTTCTTACACACCTCTAAACAACGAAGCCTAACATTCCGCCCACTATCACAAT
+s danRer1.chrM 16140 134 + 16596 CGCCATTCTACGATCTATCCCAAACAAACTAGGAGGTGTACTAGCTCTCTTATTTTCCATT----TTAGTATTAATAGTAGTACCAATTTTACACACTTCTAAACAGCGAGGAATAGCATTCCGCCCAGTTACCCAAT
+
+a score=123010.0
+s hg17.chrM 15714 141 + 16571 CACTTTATTGACTCCTAGCCGCAGACC----TCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCT--AATCCTAATACCAACT-----ATCT
+s panTro1.chr11 95342837 135 - 123086034 CACTTTATTGATTCCTAGCCGCAGACC----TCCTCGCCCTAACCTGAATCGGAGGACAACCAGTAAGCTATCCCTTCACCATCATCGGACAAGTAGCCTCCGTACTATACTTCACAAC--------AATTCTAATACCAGCC-----ACCT
+s mm5.chrM 15111 138 + 16299 TTTTGTACTGAATCCTAGTAGCCAACC----TACTTATCTTAACCTGAATTGGGGGCCAACCAGTAGAACACCCATTTATTATCATTGGCCAACTAGCCTCCATCTCATACTTCTCAATCATCTT--AATTCTTATACCA--------ATCT
+s rn3.chr2 24399786 141 - 258222147 ACTTATTTTAAATCCTAGTAGCTGACCCTCATGCTCATATGAATCTGAATTTTAAG---AGTAGTAA------CTTTTATTA--ATTTTATAAATATTATCCATCCTGTATATTCCCATGCTAATGCAATTTTTAAGCTTAATGGGGGAGCT
+s canFam1.chrM 15149 140 + 16727 GCCTATTCTGACTTTTAGTCGCCGATC----TTCTCACTTTAACATGAATTGGAGGACAACCAGTTGAGCACCCTTTCATCATTATCGGACAAGTCGCTTCAATCTTATATTTCACCATCTTATT--GATCCTAATACCAAC------AGTT
+s galGal2.chrM 15862 141 + 16775 CCCTATTCTGACTTCTAGTAGCCAACC----TTCTTATCCTAACCTGAATCGGAAGCCAACCAGTAGAACACCCCTTCATCATCATTGGCCAAATAGCATCCCTCTCTTACTTCACCATCCTACT--TATCCTCTTCCCCACA-----ATCG
+s fr1.chrUn 320905956 140 + 349519338 TCCTATTCTGAACCCTAATTGCCGACG----TCGTCATCCTAACCTGAATTGGAGGCATACCCGTCGAACATCCTTACATTATTATCGGACAAATTGCCTCAGTACTTTACTTCTCTCTCTTCCT--AATCTTGATGCCAAT------AGCC
+s danRer1.chrM 16274 141 + 16596 TTCTGTTCTGAACACTGGTAGCAGACA----TGCTTGTACTAACATGAATTGGAGGGATACCAGTAGAACACCCCTACATCATCATTGGACAAATAGCATCAATCTTATATTTTTCACTATTCTT--AGTCTTATTCCCAATT-----ACAG
+
+a score=59534.0
+s hg17.chrM 15855 162 + 16571 CCCTAATTGAAAACAAAATACTCAA--ATGGGCC---TGTCCTTGTAGTATAAA-CTAATACACCAGTCTTGTAAA-CCGGAGA-CGAAAA--------CCTTTTTCCAAGGACAA----ATCAGAGAAAAAGTCTT--TAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTA
+s panTro1.chr18 72834325 163 - 83875239 CCCTGATGGAAAATAAGCTATTTAA--ATTAAAC---TACCCTTGTAGTATAAT-TCAATACTCTGGTCTTGTAAA-CCAGAAA-TGGAGA----ATTCCC---TTCCCAGGACAA----CTCAGGCAAAAAGCCTTC-CCACTTCACCGTCAACACCCAAAACTGAAATTCTAA-TTAAACTA
+s mm5.chrM 15252 163 + 16299 GAATTATCGAAGACAAAATACTAAA--ATTATATCCATGTCTTGATAGTATAAA--CATTACTCTGGTCTTGTAAA-CCTGAAA-TGAAGAT---CTTCTC---TTCTCAAGACA------TCAAGAAGAAGGAGCT--ACTCCCCACCACCAGCACCCAAAGCTGGTATTCTAA-TTAAACTA
+s rn3.chr2 24399927 140 - 258222147 TCCTAAGTGAAG-------------------------AATTCTTGGAGCATATT-AAACTACTTTGGCTTTGGAAACCCCAAAA-TGGAGA----ACAGTT---CTCTCTAGAGTA----CTCAATCAAGATGCCAT-----TTCTTCCATCACTACCCAACACTGAAATTTTAT-ATGGAATA
+s canFam1.chrM 15290 160 + 16727 GCGTTATCGAAAACAACCTTCTAAA--ATGAAG----AGTCTTTGTAGTATAAT--CATTACCTTGGTCTTGTAAA-CCAAAAA-TGGAGAGTAACCGCCC---TCCCTAAGAC-------TCAAGGAAGAAGCTCT---TGCTCCACCATCAGCACCCAAAGCTGAGATTCTTC-TTAAACTA
+s galGal2.chrM 16003 167 + 16775 GAACACTAGAAAACAAAATACTCAACTACTAAAA---TACTCTAATAGTTTATG--AAAAACATTGGTCTTGTAAA-CCAAAAACTGAAGACT--CCACCC---TTCTTAGAGTA------TCAGAAAAGGAGGGCTCAAACCTCCATCTCCAGCTCCCAAAGCTGGTATTTTCAAATAAACTA
+s fr1.chrUn 320906097 166 + 349519338 GTTGACTAGAAAACAAAATACTAAA--CTAACA----AGCATTAGTAGCTCAGATTCAGAGCGTCGGTCTTGTAAA-CCGAATG-TCGGGGGTTAAAGTCC---CCCCTTATGC-------TCAAAAAGAAGGGACTTCAACCCCCACCACTGGCTCCCAAAGCCAGCATTCTTAATTAAACTA
+s danRer1.chrM 16415 174 + 16596 GGATTTTAGAGAATAAGGCACTCCA--ATGAAGC---TGCCCTAGTAGCTTAGTTTTAAAGCATCGGTCTTGTAAT-CCGAAGA-TCGGAGGTTAGACCCC---TCCCTAGCGCTAAATTACCAGAAAAGAGAGATTTTAACTCACACCCCTGACTCCCAAAGCCAGGATTCTAAATTAAACTA
+
+a score=-1650.0
+s hg17.chrM 16017 3 + 16571 -TTC
+s panTro1.chr18 72834488 3 - 83875239 -TTC
+s rn3.chr2 24400068 2 - 258222147 -TT-
+s canFam1.chrM 15450 3 + 16727 -TTC
+s galGal2.chrM 16170 3 + 16775 -CTC
+s fr1.chrUn 320906264 2 + 349519338 -TT-
+s danRer1.chrM 16589 3 + 16596 TTT-
+
+a score=4076.0
+s hg17.chrM 16017 7 + 16571 TTCTCTG
+s rn3.chr2 24400067 7 - 258222147 ATTTGTA
+s canFam1.chrM 15450 7 + 16727 TTCCCTG
+s galGal2.chrM 16170 7 + 16775 CTCTCTG
+s fr1.chrUn 320906263 7 + 349519338 CTTTTTG
+s danRer1.chrM 16589 7 + 16596 TTTTCTG
+
+a score=4510.0
+s hg17.chrM 16020 4 + 16571 TCTG
+s panTro1.chr11 95343137 4 - 123086034 TCTG
+s rn3.chr2 24400070 4 - 258222147 TGTA
+s canFam1.chrM 15453 4 + 16727 CCTG
+s galGal2.chrM 16173 4 + 16775 TCTG
+s fr1.chrUn 320906266 4 + 349519338 TTTG
+s danRer1.chrM 16592 4 + 16596 TCTG
+
+a score=-745.0
+s hg17.chrM 16024 2 + 16571 TT
+s panTro1.chr11 95343141 2 - 123086034 TT
+s rn3.chr2 24400074 2 - 258222147 TT
+s canFam1.chrM 15457 2 + 16727 AC
+s galGal2.chrM 16177 2 + 16775 AA
+s fr1.chrUn 320906270 2 + 349519338 AT
+
+a score=-677.0
+s hg17.chrM 16024 2 + 16571 TT
+s rn3.chr2 24400074 2 - 258222147 TT
+s canFam1.chrM 15457 2 + 16727 AC
+s galGal2.chrM 16177 2 + 16775 AA
+s fr1.chrUn 320906270 2 + 349519338 AT
+
+a score=0.0
+s hg17.chrM 16026 12 + 16571 CTTTCATGGGGA
+
+a score=-2533.0
+s hg17.chrM 16026 1 + 16571 C---
+s panTro1.chr11 95343143 1 - 123086034 C---
+s rn3.chr2 24400076 1 - 258222147 T---
+s canFam1.chrM 15459 1 + 16727 A---
+s galGal2.chrM 16179 4 + 16775 ACCC
+
+a score=-1884.0
+s hg17.chrM 16026 1 + 16571 C---
+s rn3.chr2 24400076 1 - 258222147 T---
+s canFam1.chrM 15459 1 + 16727 A---
+s galGal2.chrM 16179 4 + 16775 ACCC
+
+a score=-1714.0
+s hg17.chrM 16027 11 + 16571 TTTCATG------GGGA
+s panTro1.chr11 95343144 11 - 123086034 TTTCATG------GGGA
+s mm5.chrM 15415 11 + 16299 CTTCTTG------AGTA
+s rn3.chr2 24400077 17 - 258222147 TTTTCTAACAGACAGAA
+s galGal2.chrM 16183 3 + 16775 --------------TTA
+
+a score=-13109.0
+s hg17.chrM 16038 35 + 16571 AGCAGATTT-----GGGTACCA--CCCAAG--TATTGACTCACC
+s panTro1.chr11 95343155 35 - 123086034 AGCAAATTT-----GGGTACCA--CCCAAG--TATTGGCTCACC
+s mm5.chrM 15426 25 + 16299 CATAAATTT-----ACATAGTA--CAACAG--TA----------
+s rn3.chr2 24400094 42 - 258222147 AACAGACCTTTTAAAAGTACTAGGTCCAAA--TTTCCACTTACC
+s canFam1.chrM 15460 26 + 16727 --------------CCCCTACA--TTCATA--TATTGAATCACC
+s galGal2.chrM 16186 37 + 16775 AACCGCCCG-----AATTGCCC--CCCGAGACAACCCACGCACA
+s fr1.chrUn 320906272 21 + 349519338 AATACATAT-----ATGTATTA--TCCC----------------
+
+a score=-154.0
+s hg17.chrM 16073 3 + 16571 CAT
+s panTro1.chr11 95343190 3 - 123086034 CAT
+s mm5.chrM 15451 3 + 16299 CAT
+s canFam1.chrM 15488 2 + 16727 TA-
+s galGal2.chrM 16231 1 + 16775 --T
+s fr1.chrUn 320906293 3 + 349519338 CAT
+
+a score=0.0
+s hg17.chrM 16076 9 + 16571 CAACAACCG
+
+a score=1632.0
+s hg17.chrM 16076 6 + 16571 -CAACAA
+s panTro1.chr11 95343193 6 - 123086034 -CAACAA
+s galGal2.chrM 16232 7 + 16775 ACAACAA
+
+a score=228.0
+s hg17.chrM 16082 3 + 16571 CCG
+s panTro1.chr11 95343199 3 - 123086034 CCG
+s rn3.chr7 48860662 3 - 143082968 CTG
+s canFam1.chrM 15492 3 + 16727 GTG
+s galGal2.chrM 16239 1 + 16775 --A
+
+a score=-66332.0
+s hg17.chrM 16085 177 + 16571 CTAT----GTATTTC---GTACATTA--CTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATA-AAAACCCAACCCACATCAAACCCCCCCCCCCCAT--------GCTTACAAGCAAGTACAGCAAT-------CAACCTTCAACTATCACACATCAAC--TGCAACTCCAAAGCCA---CC
+s panTro1.chr11 95343202 182 - 123086034 CCAT----GTATATC---GTGCATTA--CTGCCAGCCACCATGAGTATTATATAGTACCATAAATACTTGAACATCCATAGTACATACAAAACCCATCCCACATTAAA-ACCTCCTCCCAAT--------GCTTACAAGCACGAACAGCGATTGGCCCACA-----CAACTACCGAACATTAAC--CCTATCTCCAAAGACAATCCC
+s mm5.chrM 15454 84 + 16299 TTAT----GTATATC---GTACATTA-----------------------------------AACTATTT----------------------------------------------TCCCCAA--------GCATATAAGCTAGTACATTAA---------------------------ATCAATGGTTCAGGTCATAAAATAATCAT
+s rn3.chr7 48860665 152 - 143082968 GCAT----GCA-------GTGCATAA------------TAATGTGTATAGTGCA-------TACTACATTTATGTATATAATATATT--------------AATTTATTTCCCCTCCCATATAATAAAGAGCTAACTACTAAATACAGAAG-----ACTAAACATTCTAATACAAGTAAATATT--TTCATTAACAGGGCCA----T
+s canFam1.chrM 15495 138 + 16727 CTATGTCAGTATCTCCAGGTAAACCCTTCTCCCCTCCCCTATGTACGTCGTGCATT-----AATGGTTT----------------------------------------------GCCCCAT--------GCATATAAGCATGTACATAAT-----ATTATATCCTTACATAGGACATATTAAC--TCAATCTCATAATTCA---CT
+s galGal2.chrM 16240 163 + 16775 CAAA----GCTAACA---ACAAACCT--CACCCAGCCACCAAAAACAACCCAACCCCACATGAATA---AAACACCGCAACTCCACTAAAATCCAACCGAGCAAAAGACACACCCCCGCCAT--------------------CAACAGTAA--------CCACCCCCACCTTTCAAAAATCAAC-GAGCCCTCCCAGAACCA---CC
+s fr1.chrUn 320906296 126 + 349519338 TCAT----ATATATT---AAACATTA-----------ATATAATGCATAACTAAGACATAGTACTATATATTCACCTATAATTCCTATAA---------------------------CCCAT-------------AAAGCAAGTACAGAAA-----ACTAA-------------AAATGCTAAA--AGCATGACTAGAAAAA---TC
+
+a score=-2739.0
+s hg17.chrM 16262 5 + 16571 --CCTCA
+s panTro1.chr11 95343384 5 - 123086034 --CAACA
+s mm5.chrM 15538 5 + 16299 --CAACA
+s rn3.chr7 48860817 5 - 143082968 --TATCA
+s galGal2.chrM 16414 4 + 16775 --CACC-
+s fr1.chrUn 320906422 5 + 349519338 CCTAA--
+
+a score=0.0
+s hg17.chrM 16267 6 + 16571 CCCACT
+
+a score=-2037.0
+s hg17.chrM 16267 6 + 16571 CCCACT
+s panTro1.chr11 95343389 3 - 123086034 C---CT
+s mm5.chrM 15543 1 + 16299 T-----
+s rn3.chr7 48860822 6 - 143082968 TCCAAT
+
+a score=-14864.0
+s hg17.chrM 16273 24 + 16571 AGGATACCAACAA---ACCTACCCACC-
+s panTro1.chr11 95343392 24 - 123086034 AGAATATCAACAG---ACCTGCACATC-
+s mm5.chrM 15544 17 + 16299 ---AAATCAATA-------TATATACC-
+s rn3.chr7 48860828 12 - 143082968 GTCATATCAATG----------------
+s canFam1.chr38 16296834 26 - 26492144 TGAATATCTACAGC-AAAATTAACATG-
+s galGal2.chrM 16418 24 + 16775 ---AAGACAAAACCTAGCCCATACCCC-
+s fr1.chrUn 320906427 24 + 349519338 AAATTGTTGAAG----AACTGAACGAAA
+
+a score=-1707.0
+s hg17.chrM 16297 28 + 16571 CTTAACAG---------TACATAGTAC-------ATAAAGTCAT
+s panTro1.chr11 95343416 29 - 123086034 CTTAACAG--------ATACATAGCAC-------ATACAGTCAT
+s mm5.chrM 15561 44 + 16299 ATGAATATTATCTTAAACACATTAAACTAATGTTATAAGGACAT
+s rn3.chr7 48860840 18 - 143082968 ----------------ATACATAG----------ACATATCTAT
+s canFam1.chr38 16296860 28 - 26492144 ATTAATAT---------TACATAGCAC-------ATAATATTAT
+s fr1.chrUn 320906451 24 + 349519338 ------------TTTAAGACCGAACA--------ATAAACTCAT
+
+a score=831.0
+s hg17.chrM 16325 9 + 16571 -------TTACCGTAC
+s panTro1.chr11 95343445 9 - 123086034 -------TTATCGTAC
+s mm5.chrM 15605 16 + 16299 ATCTGTGTTATCTGAC
+s rn3.chr7 48860858 10 - 143082968 ------GTTATTTTAC
+s canFam1.chr38 16296888 9 - 26492144 -------TGGTTGGAT
+
+a score=7636.0
+s hg17.chrM 16334 51 + 16571 ATAGCACATTACAGTCA-AATCCCTTCTCGTCCCCATG------------GATGACCCCCCTCA
+s panTro1.chrUn_random 225547893 51 - 240967748 ATAGCGCATTACAGTCA-AATCCCTCCTTGCCCCCACG------------GATGCCCCCCCTCA
+s mm5.chrM 15621 51 + 16299 ATA-CACCATACAGTCATAAACTCTTCTCTTCCATATG------------ACTATCCCCTTCCC
+s rn3.chr7 48860868 51 - 143082968 ATAAACCGTTCTAGTCA-AATTACTTTTTTGGCATATA------------GCTATCTCCTTCTC
+s canFam1.chr38 16296897 62 - 26492144 ATACCCCATTA-AGTCA-AATTATTACCAGACAACATGCCTATCATAACTGATAACCACATTTA
+
+a score=1592.0
+s hg17.chrM 16385 18 + 16571 GATAGGGGTCCCTTGACC
+s panTro1.chrUn_random 225547944 18 - 240967748 GATAGGAATCCCTTAATC
+s mm5.chrM 15672 17 + 16299 CATTTG-GTCTATTAATC
+s rn3.chr7 48860919 16 - 143082968 AATTGG--TCTGTTCATC
+s canFam1.chrM 15671 15 + 16727 AATAAGGG---CTTAATC
+
+a score=10758.0
+s hg17.chrM 16403 30 + 16571 ACCATCCTCCGTGAAATCAATATCCC------GCAC
+s panTro1.chr14 78287170 35 + 97804244 ACCAACCTCCAAGAAATCATCATCCCTCTGGGGCA-
+s mm5.chrM 15690 30 + 16299 ACCATCCTCCGTGAAACCAACAACCC------GCCC
+s rn3.chr7 48860936 30 - 143082968 ACCATCCTCTGAGAAACCAACAACCC------AACA
+s canFam1.chrM 15686 30 + 16727 ACCATGCCTCGAGAAACCATCAACCC------TTGC
+
+a score=53286.0
+s hg17.chrM 16433 96 + 16571 AAG-AGTGCTACTCTCCTCGCTCCGGGCCCAT-AACACTTGGGGGTAGCTAAAGTG-AACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAA---GC
+s panTro1.chr14 78287205 92 + 97804244 ------TGTTACTCTCCTCACTCTGGGCCCAT-AACACTTGGGAGTGACTATACTGAAACTATACCTGGCATCTGGTTCTTACCTCAGGGCCAtgaa---ac
+s mm5.chrM 15720 97 + 16299 ACC-AATGCCCCTCTTCTCGCTCCGGGCCCAT-TAAACTTGGGGGTAGCTAAACTGAAACTTTATCAGACATCTGGTTCTTACTTCAGGGCCATCAA---AT
+s rn3.chr7 48860966 98 - 143082968 ATC-TATGCCCATCTTCCTGCTCTAGGCCCATCTTGACTTGGGGGTAGCTAATATGAGACTTTATCAGACATCTGCTTTTTACTCTAGGGCCATTAA---AT
+s canFam1.chrM 15716 102 + 16727 TCGTAATGTCCCTCTTCTCGCTCCGGGCCCATACTAACGTGGGGGTTACTATCATGAAACTATACCTGGCATCTGGTTCTTACTTCAGGGCCATAACCTTAT
+s fr1.chrUn 320906557 96 + 349519338 ATG-CATATTATTATTGAAGGTGAGGGACAAT-AACAGTGGGGGTTTCACTAAATG-AACTATTCCTGGCATTTGGTTCCTACTTCAGGGCCATTAA---TC
+
+a score=8581.0
+s hg17.chrM 16529 36 + 16571 -----------CTAA-ATAGCCCACACGTTCCCCTTAAATAAGACATC
+s panTro1.chr14 78287297 48 + 97804244 taagattgaaactaagattgCCCACACATTTCACTTAAATAAGACGTC
+s mm5.chrM 15817 37 + 16299 -----------GCGTTATCGCCCATACGTTCCCCTTAAATAAGACATC
+s rn3.chr7 48861064 36 - 143082968 -----------GCATTATCAACCATGTGTTCC-CTCAAATAAAACATC
+s canFam1.chrM 15818 37 + 16727 -----------TTACTCCAATCCTACTAATTCTCGCAAATGGGACATC
+
+a score=2403.0
+s hg17.chrM 16565 6 + 16571 ACGATG
+s mm5.chrM 15854 6 + 16299 TCGATG
+s rn3.chr7 48861100 6 - 143082968 TCAATG
+s canFam1.chrM 15855 6 + 16727 TCGATG
+
diff -r 000000000000 -r d38f317fa9d4 test-data/maf_indexes.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maf_indexes.loc Fri Jul 10 16:05:40 2020 -0400
@@ -0,0 +1,17 @@
+#This is a sample file distributed with Galaxy that is used by some
+#alignment tools. The maf_index.loc file has this format (white space
+#characters are TAB characters):
+#
+#
+#
+#ENCODE TBA (hg17) ENCODE_TBA_hg17 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 /depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm001/human.ENm001.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm002/human.ENm002.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm003/human.ENm003.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm004/human.ENm004.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm005/human.ENm005.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm006/human.ENm006.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm007/human.ENm007.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm008/human.ENm008.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm009/human.ENm009.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm010/human.ENm010.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm011/human.ENm011.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm012/human.ENm012.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm013/human.ENm013.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm014/human.ENm014.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr111/human.ENr111.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr112/human.ENr112.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr113/human.ENr113.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr114/human.ENr114.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr121/human.ENr121.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr122/human.ENr122.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr123/human.ENr123.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr131/human.ENr131.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr132/human.ENr132.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr133/human.ENr133.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr211/human.ENr211.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr212/human.ENr212.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr213/human.ENr213.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr221/human.ENr221.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr222/human.ENr222.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr223/human.ENr223.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr231/human.ENr231.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr232/human.ENr232.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr233/human.ENr233.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr311/human.ENr311.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr312/human.ENr312.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr313/human.ENr313.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr321/human.ENr321.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr322/human.ENr322.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr323/human.ENr323.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr324/human.ENr324.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr331/human.ENr331.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr332/human.ENr332.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr333/human.ENr333.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr334/human.ENr334.maf
+#ENCODE MAVID (hg17) ENCODE_MAVID_hg17 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 /depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm001.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm002.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm003.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm004.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm005.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm006.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm007.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm008.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm009.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm010.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm011.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm012.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm013.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm014.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr111.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr112.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr113.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr114.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr121.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr122.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr123.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr131.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr132.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr133.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr211.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr212.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr213.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr221.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr222.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr223.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr231.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr232.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr233.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr311.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr312.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr313.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr321.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr322.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr323.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr324.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr331.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr332.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr333.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr334.maf
+#ENCODE TBA (hg16) ENCODE_TBA_hg16 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant=elephant,fr1,galago,hedgehog,hg16,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant=elephant,fr1,galago,hedgehog,hg16,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 /depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm001.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm002.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm003.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm004.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm005.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm006.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm007.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm008.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm009.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm010.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm011.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm012.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm013.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm014.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr111.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr112.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr113.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr114.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr121.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr122.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr123.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr131.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr132.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr133.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr211.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr212.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr213.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr221.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr222.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr223.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr231.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr232.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr233.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr311.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr312.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr313.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr321.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr322.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr323.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr324.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr331.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr332.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr333.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr334.maf
+#8-way multiZ (hg17) 8_WAY_MULTIZ_hg17 canFam1,danRer1,fr1,galGal2,hg17,mm5,panTro1,rn3 canFam1,danRer1,fr1,galGal2,hg17,mm5,panTro1,rn3 /depot/data2/galaxy/hg17/align/8way-multiZ/chr1.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr10.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr11.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr12.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr12_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr13.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr14.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr15.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr16.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr17.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr18.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr19.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr2.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr20.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr21.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr22.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr3.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr4.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr5.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_hla_hap1.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_hla_hap2.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr7.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr8.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr9.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrM.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrX.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrY.maf
+#17-way multiZ (hg18) 17_WAY_MULTIZ_hg18 hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1 hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1 /depot/data2/galaxy/hg18/align/17way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrY.maf
+#3-way multiZ (hg18,panTro2,rheMac2) 3_WAY_MULTIZ_hg18 hg18,panTro2,rheMac2 hg18,panTro2,rheMac2 /depot/data2/galaxy/hg18/align/3way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrY.maf
+#5-way multiZ (hg18,panTro2,rheMac2,mm8,canFam2) 5_WAY_MULTIZ_hg18 hg18,panTro2,rheMac2,mm8,canFam2 hg18,panTro2,rheMac2,mm8,canFam2 /depot/data2/galaxy/hg18/align/5way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrY.maf
+#28-way multiZ (hg18) 28_WAY_MULTIZ_hg18 hg18 hg18,dasNov1,otoGar1,felCat3,galGal3,panTro2,bosTau3,canFam2,loxAfr1,xenTro2,fr2,cavPor2,eriEur1,equCab1,anoCar1,oryLat1,mm8,monDom4,ornAna1,oryCun1,rn4,rheMac2,sorAra1,gasAcu1,echTel1,tetNig1,tupBel1,danRer4 /depot/data2/galaxy/hg18/align/multiz28way/chr1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr10.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr10_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr11.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr11_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr12.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr13.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr13_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr14.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr15.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr15_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr16.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr16_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr17.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr17_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr18.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr18_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr19.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr19_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr1_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr2.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr20.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr21.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr21_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22_h2_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr2_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr3.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr3_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr4.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr4_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5_h2_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_cox_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_qbl_hap2.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr7.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr7_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr8.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr8_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr9.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr9_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrM.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrX.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrX_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrY.maf.lzo
+#15-way multiZ (dm2) 15_WAY_MULTIZ_dm2 dm2,droSim1,droSec1,droYak2,droEre2,droAna3,dp4,droPer1,droWil1,droVir3,droMoj3,droGri2,anoGam1,apiMel2,triCas2 dm2,droSim1,droSec1,droYak2,droEre2,droAna3,dp4,droPer1,droWil1,droVir3,droMoj3,droGri2,anoGam1,apiMel2,triCas2 /depot/data2/galaxy/dm2/align/multiz15way/chr2L.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr2R.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr2h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3L.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3R.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr4.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr4h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrM.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrU.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrX.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrXh.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrYh.maf
+#17-way multiZ (mm8) 17_WAY_MULTIZ_mm8 mm8 hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1 /depot/data2/galaxy/mm8/align/multiz17way/chr10.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr10_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr11.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr12.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr13.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr13_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr14.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr15.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr15_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr16.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr17.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr17_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr18.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr19.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr1.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr1_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr2.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr3.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr4.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr5.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr5_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr6.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr7.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr7_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr8.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr8_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr9.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr9_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrM.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrUn_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrX.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrX_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY_random.maf.lzo
+#8-way multiZ (ponAbe2) 8_WAY_MULTIZ_ponAbe2 ponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1 ponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1 /depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_h2_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrM.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrUn.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX_random.maf.lzo
diff -r 000000000000 -r d38f317fa9d4 tool-data/maf_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/maf_indexes.loc.sample Fri Jul 10 16:05:40 2020 -0400
@@ -0,0 +1,17 @@
+#This is a sample file distributed with Galaxy that is used by some
+#alignment tools. The maf_index.loc file has this format (white space
+#characters are TAB characters):
+#
+#
+#
+#ENCODE TBA (hg17) ENCODE_TBA_hg17 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 /depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm001/human.ENm001.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm002/human.ENm002.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm003/human.ENm003.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm004/human.ENm004.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm005/human.ENm005.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm006/human.ENm006.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm007/human.ENm007.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm008/human.ENm008.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm009/human.ENm009.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm010/human.ENm010.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm011/human.ENm011.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm012/human.ENm012.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm013/human.ENm013.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm014/human.ENm014.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr111/human.ENr111.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr112/human.ENr112.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr113/human.ENr113.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr114/human.ENr114.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr121/human.ENr121.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr122/human.ENr122.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr123/human.ENr123.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr131/human.ENr131.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr132/human.ENr132.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr133/human.ENr133.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr211/human.ENr211.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr212/human.ENr212.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr213/human.ENr213.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr221/human.ENr221.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr222/human.ENr222.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr223/human.ENr223.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr231/human.ENr231.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr232/human.ENr232.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr233/human.ENr233.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr311/human.ENr311.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr312/human.ENr312.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr313/human.ENr313.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr321/human.ENr321.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr322/human.ENr322.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr323/human.ENr323.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr324/human.ENr324.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr331/human.ENr331.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr332/human.ENr332.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr333/human.ENr333.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr334/human.ENr334.maf
+#ENCODE MAVID (hg17) ENCODE_MAVID_hg17 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 /depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm001.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm002.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm003.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm004.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm005.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm006.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm007.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm008.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm009.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm010.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm011.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm012.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm013.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm014.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr111.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr112.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr113.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr114.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr121.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr122.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr123.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr131.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr132.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr133.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr211.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr212.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr213.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr221.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr222.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr223.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr231.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr232.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr233.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr311.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr312.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr313.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr321.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr322.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr323.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr324.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr331.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr332.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr333.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr334.maf
+#ENCODE TBA (hg16) ENCODE_TBA_hg16 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant=elephant,fr1,galago,hedgehog,hg16,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant=elephant,fr1,galago,hedgehog,hg16,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 /depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm001.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm002.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm003.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm004.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm005.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm006.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm007.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm008.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm009.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm010.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm011.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm012.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm013.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm014.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr111.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr112.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr113.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr114.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr121.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr122.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr123.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr131.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr132.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr133.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr211.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr212.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr213.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr221.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr222.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr223.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr231.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr232.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr233.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr311.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr312.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr313.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr321.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr322.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr323.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr324.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr331.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr332.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr333.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr334.maf
+#8-way multiZ (hg17) 8_WAY_MULTIZ_hg17 canFam1,danRer1,fr1,galGal2,hg17,mm5,panTro1,rn3 canFam1,danRer1,fr1,galGal2,hg17,mm5,panTro1,rn3 /depot/data2/galaxy/hg17/align/8way-multiZ/chr1.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr10.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr11.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr12.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr12_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr13.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr14.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr15.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr16.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr17.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr18.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr19.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr2.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr20.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr21.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr22.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr3.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr4.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr5.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_hla_hap1.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_hla_hap2.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr7.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr8.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr9.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrM.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrX.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrY.maf
+#17-way multiZ (hg18) 17_WAY_MULTIZ_hg18 hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1 hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1 /depot/data2/galaxy/hg18/align/17way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrY.maf
+#3-way multiZ (hg18,panTro2,rheMac2) 3_WAY_MULTIZ_hg18 hg18,panTro2,rheMac2 hg18,panTro2,rheMac2 /depot/data2/galaxy/hg18/align/3way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrY.maf
+#5-way multiZ (hg18,panTro2,rheMac2,mm8,canFam2) 5_WAY_MULTIZ_hg18 hg18,panTro2,rheMac2,mm8,canFam2 hg18,panTro2,rheMac2,mm8,canFam2 /depot/data2/galaxy/hg18/align/5way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrY.maf
+#28-way multiZ (hg18) 28_WAY_MULTIZ_hg18 hg18 hg18,dasNov1,otoGar1,felCat3,galGal3,panTro2,bosTau3,canFam2,loxAfr1,xenTro2,fr2,cavPor2,eriEur1,equCab1,anoCar1,oryLat1,mm8,monDom4,ornAna1,oryCun1,rn4,rheMac2,sorAra1,gasAcu1,echTel1,tetNig1,tupBel1,danRer4 /depot/data2/galaxy/hg18/align/multiz28way/chr1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr10.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr10_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr11.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr11_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr12.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr13.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr13_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr14.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr15.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr15_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr16.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr16_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr17.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr17_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr18.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr18_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr19.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr19_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr1_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr2.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr20.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr21.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr21_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22_h2_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr2_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr3.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr3_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr4.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr4_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5_h2_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_cox_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_qbl_hap2.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr7.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr7_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr8.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr8_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr9.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr9_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrM.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrX.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrX_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrY.maf.lzo
+#15-way multiZ (dm2) 15_WAY_MULTIZ_dm2 dm2,droSim1,droSec1,droYak2,droEre2,droAna3,dp4,droPer1,droWil1,droVir3,droMoj3,droGri2,anoGam1,apiMel2,triCas2 dm2,droSim1,droSec1,droYak2,droEre2,droAna3,dp4,droPer1,droWil1,droVir3,droMoj3,droGri2,anoGam1,apiMel2,triCas2 /depot/data2/galaxy/dm2/align/multiz15way/chr2L.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr2R.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr2h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3L.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3R.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr4.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr4h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrM.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrU.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrX.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrXh.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrYh.maf
+#17-way multiZ (mm8) 17_WAY_MULTIZ_mm8 mm8 hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1 /depot/data2/galaxy/mm8/align/multiz17way/chr10.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr10_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr11.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr12.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr13.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr13_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr14.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr15.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr15_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr16.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr17.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr17_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr18.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr19.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr1.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr1_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr2.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr3.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr4.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr5.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr5_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr6.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr7.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr7_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr8.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr8_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr9.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr9_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrM.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrUn_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrX.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrX_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY_random.maf.lzo
+#8-way multiZ (ponAbe2) 8_WAY_MULTIZ_ponAbe2 ponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1 ponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1 /depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_h2_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrM.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrUn.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX_random.maf.lzo
diff -r 000000000000 -r d38f317fa9d4 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Jul 10 16:05:40 2020 -0400
@@ -0,0 +1,8 @@
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+ name, value, indexed_for, exists_in_maf, path
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diff -r 000000000000 -r d38f317fa9d4 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Fri Jul 10 16:05:40 2020 -0400
@@ -0,0 +1,8 @@
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+ name, value, indexed_for, exists_in_maf, path
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