Mercurial > repos > artbio > small_rna_signatures

--- a/overlapping_reads.py	Fri Sep 08 04:44:22 2017 -0400
+++ b/overlapping_reads.py	Sat Sep 09 11:57:39 2017 -0400
@@ -32,12 +32,20 @@

 class Map:

-    def __init__(self, bam_file):
+    def __init__(self, bam_file, output, minquery=23, maxquery=29,
+                 mintarget=23, maxtarget=29, overlap=10):
         self.bam_object = pysam.AlignmentFile(bam_file, 'rb')
+        self.output = output
+        self.query_range = range(minquery, maxquery + 1)
+        self.target_range = range(mintarget, maxtarget + 1)
+        self.overlap = overlap
         self.chromosomes = dict(zip(self.bam_object.references,
                                 self.bam_object.lengths))
-        self.all_query_positions = self.query_positions(self.bam_object)
+        self.alignement_dic = self.index_alignments(self.bam_object)
+        self.all_query_positions = self.query_positions(self.bam_object,
+                                                        overlap=self.overlap)
         self.readdic = self.make_readdic(self.bam_object)
+        self.pairing()

     def make_readdic(self, bam_object):
         readdic = defaultdict(int)
@@ -45,90 +53,67 @@
             readdic[read.query_sequence] += 1
         return readdic

-    def query_positions(self, bam_object):
-        all_query_positions = defaultdict(list)
+    def index_alignments(self, bam_object):
+        '''
+        dic[(chrom, pos, polarity)]: [readseq1, readseq2, ...]
+        the list value is further converted in set
+        '''
+        dic = defaultdict(list)
         for chrom in self.chromosomes:
             for read in bam_object.fetch(chrom):
-                if not read.is_reverse:
-                    all_query_positions[chrom].append(
-                        read.reference_start)
+                if read.is_reverse:
+                    coord = read.reference_end-1
+                    pol = 'R'
                 else:
-                    all_query_positions[chrom].append(
-                        read.reference_end)
+                    coord = read.reference_start
+                    pol = 'F'
+                dic[(chrom, coord, pol)].append(read.query_sequence)
+        for key in dic:
+            dic[key] = set(dic[key])
+        return dic
+
+    def query_positions(self, bam_object, overlap):
+        all_query_positions = defaultdict(list)
+        for genomicKey in self.alignement_dic.keys():
+            chrom, coord, pol = genomicKey
+            if pol == 'F' and len(self.alignement_dic[(chrom,
+                                                      coord+overlap-1,
+                                                      'R')]) > 0:
+                all_query_positions[chrom].append(coord)
+        for chrom in all_query_positions:
             all_query_positions[chrom] = sorted(
                 list(set(all_query_positions[chrom])))
         return all_query_positions

-    def direct_pairing(self, minquery, maxquery, mintarget, maxtarget,
-                       file, overlap=10):
-        F = open(file, 'w')
-        query_range = range(minquery, maxquery + 1)
-        target_range = range(mintarget, maxtarget + 1)
+    def pairing(self):
+        F = open(self.output, 'w')
+        query_range = self.query_range
+        target_range = self.target_range
+        overlap = self.overlap
         stringresult = []
+        header_template = '>%s|coord=%s|strand %s|size=%s|nreads=%s\n%s\n'
         for chrom in sorted(self.chromosomes):
-            for pos in (self.all_query_positions[chrom]):
-                iterreads_1 = self.bam_object.fetch(chrom,
-                                                    start=pos, end=pos+overlap-1)
-                iterreads_2 = self.bam_object.fetch(chrom,
-                                                    start=pos, end=pos+overlap-1)
-                iterreads_3 = self.bam_object.fetch(chrom,
-                                                    start=pos, end=pos+overlap-1)
-                iterreads_4 = self.bam_object.fetch(chrom,
-                                                    start=pos, end=pos+overlap-1)
-                #  1
-                for queryread in iterreads_1:
-                    if queryread.reference_start == pos and \
-                        queryread.query_alignment_length in query_range \
-                            and not queryread.is_reverse:
-                        for targetread in iterreads_2:
-                            if (targetread.
-                                get_reference_positions()[-1]
-                                == queryread.get_reference_positions(
-                                   )[overlap-1] and
-                                targetread.query_alignment_length in
-                                    target_range and targetread.is_reverse):
-                                targetreadseq = self.revcomp(
-                                    targetread.query_sequence)
-                                stringresult.append(
-                                    '>%s|%s|%s|%s|n=%s\n%s\n' %
-                                    (chrom, queryread.reference_start+1,
-                                     'F', queryread.query_alignment_length,
-                                     self.readdic[queryread.query_sequence],
-                                     queryread.query_sequence))
-                                stringresult.append(
-                                    '>%s|%s|%s|%s|n=%s\n%s\n' %
-                                    (chrom, targetread.reference_start+1,
-                                     'R', targetread.query_alignment_length,
-                                     self.readdic[targetread.query_sequence],
-                                     targetreadseq))
-                #  2
-                for queryread in iterreads_3:
-                    if queryread.reference_end-1 == pos+overlap-1 and \
-                        queryread.query_alignment_length in query_range \
-                            and queryread.is_reverse:
-                        for targetread in iterreads_4:
-                            if (targetread.
-                                reference_start
-                                == pos and targetread.query_alignment_length
-                                    in target_range and not
-                                    targetread.is_reverse):
-                                queryreadseq = self.revcomp(
-                                    queryread.query_sequence)
-                                targetreadseq = targetread.query_sequence
-                                stringresult.append(
-                                    '>%s|%s|%s|%s|n=%s\n%s\n' %
-                                    (chrom, queryread.reference_start+1, 'R',
-                                     queryread.query_alignment_length,
-                                     self.readdic[queryread.query_sequence],
-                                     queryreadseq))
-                                stringresult.append(
-                                    '>%s|%s|%s|%s|n=%s\n%s\n' %
-                                    (chrom, targetread.reference_start+1,
-                                     'F', targetread.query_alignment_length,
-                                     self.readdic[targetread.query_sequence],
-                                     targetreadseq))
-        stringresult = sorted(set(stringresult),
-                              key=lambda x: stringresult.index(x))
+            for pos in self.all_query_positions[chrom]:
+                stringbuffer = []
+                uppers = self.alignement_dic[chrom, pos, 'F']
+                lowers = self.alignement_dic[chrom, pos+overlap-1, 'R']
+                if uppers and lowers:
+                    for upread in uppers:
+                        for downread in lowers:
+                            if (len(upread) in query_range and len(downread) in
+                                target_range) or (len(upread) in target_range
+                                                  and len(downread) in
+                                                  query_range):
+                                stringbuffer.append(
+                                    header_template %
+                                    (chrom, pos+1, '+', len(upread),
+                                     self.readdic[upread], upread))
+                                stringbuffer.append(
+                                    header_template %
+                                    (chrom, pos+overlap-len(downread)+1, '-',
+                                     len(downread), self.readdic[downread],
+                                     self.revcomp(downread)))
+                stringresult.extend(sorted(set(stringbuffer)))
         F.write(''.join(stringresult))

     def revcomp(self, sequence):
@@ -137,13 +122,7 @@
         return "".join([antidict[i] for i in revseq])


-def main(input, minquery, maxquery, mintarget, maxtarget, output, overlap=10):
-    mapobj = Map(input)
-    mapobj.direct_pairing(minquery, maxquery, mintarget, maxtarget,
-                          output, overlap)
-
-
 if __name__ == "__main__":
     args = Parser()
-    main(args.input, args.minquery, args.maxquery, args.mintarget,
-         args.maxtarget, args.output, args.overlap)
+    mapobj = Map(args.input, args.output, args.minquery, args.maxquery,
+                 args.mintarget, args.maxtarget, args.overlap)
--- a/overlapping_reads.xml	Fri Sep 08 04:44:22 2017 -0400
+++ b/overlapping_reads.xml	Sat Sep 09 11:57:39 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="overlapping_reads" name="Get overlapping reads" version="0.9.3">
+<tool id="overlapping_reads" name="Get overlapping reads" version="0.9.4">
     <description />
     <requirements>
         <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
@@ -47,6 +47,24 @@
             <param name="overlap" value="10" />
             <output file="paired_2.fa" ftype="fasta" name="output" />
         </test>
+        <test>
+            <param ftype="bam" name="input" value="sr_bowtie.bam" />
+            <param name="minquery" value="23" />
+            <param name="maxquery" value="29" />
+            <param name="mintarget" value="20" />
+            <param name="maxtarget" value="22" />
+            <param name="overlap" value="10" />
+            <output file="paired_3.fa" ftype="fasta" name="output" />
+        </test>
+        <test>
+            <param ftype="bam" name="input" value="sr_bowtie.bam" />
+            <param name="minquery" value="20" />
+            <param name="maxquery" value="22" />
+            <param name="mintarget" value="20" />
+            <param name="maxtarget" value="22" />
+            <param name="overlap" value="10" />
+            <output file="paired_4.fa" ftype="fasta" name="output" />
+        </test>
     </tests>
     <help>

@@ -70,10 +88,12 @@
 overlap.

 Searching query reads of 20-22 nt that overlap by 10 nt with target
-reads of 23-29 nt is different from searching query reads of 23-29 nt that overlap by 10 nt
-with target reads of 20-22 nt. i.e, searching for siRNAs that pair with piRNAs is distinct
-from searching for siRNAs that pairs with piRNAs, although of course the number of possibly
-formed piRNA/siRNA pairs is the same as the number of possibly formed siRNA/piRNA pairs.
+reads of 23-29 nt is equivalent to searching query reads of 23-29 nt that overlap by 10 nt
+with target reads of 20-22 nt. i.e, searching for siRNAs that pair with piRNAs is equivalent
+to searching for siRNAs that pairs with piRNAs. In contrast, searching query reads of 20-22 nt
+that overlap by 10 nt with target reads of 23-29 nt is different from searching query reads of
+23-29 nt that overlap by 10 nt with target reads of 23-29 nt, since the number of "heterotypic"
+pairs of reads is likely to be different from the number of "homotypic" pairs of reads.

 *Overlap*
 The number of nucleotides by which the pairs of sequences will overlap
@@ -84,17 +104,18 @@

 a fasta file of pairable reads such as :

->FBgn0000004_17.6|5855|F|23|n=1
+>FBgn0000004_17.6|coord=5839|strand -|size=26|nreads=1
+
+TTTTCGTCAATTGTGCCAAATAGGTA
+
+>FBgn0000004_17.6|coord=5855|strand +|size=23|nreads=1

 TTGACGAAAATGATCGAGTGGAT

->FBgn0000004_17.6|5839|R|26|n=1
-
-TTTTCGTCAATTGTGCCAAATAGGTA

 where FBgn0000004_17.6 stands for the chromosome, 5839 stands for the 1-based read position,
-R stand for reverse strand (F forward strand), 26 stands for the size of the sequence and
-n=1 stands for the number of reads of the sequence in the dataset.
+'strand -' stands for lower strand of chromosome, 26 stands for the size of the sequence and
+nreads=1 stands for the number of reads of the sequence in the dataset.

 the second sequence in this example corresponds to 1 read that overlap by 10 nt with
 1 read of the first sequence.
--- a/test-data/paired.fa	Fri Sep 08 04:44:22 2017 -0400
+++ b/test-data/paired.fa	Sat Sep 09 11:57:39 2017 -0400
@@ -1,668 +1,668 @@
->FBgn0000004_17.6|5855|F|23|n=1
-TTGACGAAAATGATCGAGTGGAT
->FBgn0000004_17.6|5839|R|26|n=1
+>FBgn0000004_17.6|coord=5839|strand -|size=26|nreads=1
 TTTTCGTCAATTGTGCCAAATAGGTA
->FBgn0000006_412|759|F|24|n=3
-TTTGGTCGAAAGCTCTAAAGCTAC
->FBgn0000006_412|742|R|27|n=1
+>FBgn0000004_17.6|coord=5855|strand +|size=23|nreads=1
+TTGACGAAAATGATCGAGTGGAT
+>FBgn0000006_412|coord=742|strand -|size=27|nreads=1
 TTCGACCAAACCGGTGGCGTTTGCTGA
->FBgn0000006_412|744|R|25|n=2
+>FBgn0000006_412|coord=744|strand -|size=25|nreads=2
 TTCGACCAAACCGGTGGCGTTTGCT
->FBgn0000006_412|745|R|24|n=2
+>FBgn0000006_412|coord=745|strand -|size=24|nreads=2
 TTCGACCAAACCGGTGGCGTTTGC
->FBgn0000006_412|759|F|25|n=1
+>FBgn0000006_412|coord=759|strand +|size=24|nreads=3
+TTTGGTCGAAAGCTCTAAAGCTAC
+>FBgn0000006_412|coord=759|strand +|size=25|nreads=1
 TTTGGTCGAAAGCTCTAAAGCTACA
->FBgn0000006_412|759|F|27|n=3
+>FBgn0000006_412|coord=759|strand +|size=27|nreads=3
 TTTGGTCGAAAGCTCTAAAGCTACATG
->FBgn0000006_412|760|F|26|n=6
-TTGGTCGAAAGCTCTAAAGCTACATG
->FBgn0000006_412|744|R|26|n=2
+>FBgn0000006_412|coord=744|strand -|size=26|nreads=2
 TTTCGACCAAACCGGTGGCGTTTGCT
->FBgn0000006_412|745|R|25|n=1
+>FBgn0000006_412|coord=745|strand -|size=25|nreads=1
 TTTCGACCAAACCGGTGGCGTTTGC
->FBgn0000007_1731|4555|F|24|n=1
+>FBgn0000006_412|coord=760|strand +|size=26|nreads=6
+TTGGTCGAAAGCTCTAAAGCTACATG
+>FBgn0000007_1731|coord=4539|strand -|size=26|nreads=1
+TTGAGAGCAAAGGCCGAATGAGTAAA
+>FBgn0000007_1731|coord=4555|strand +|size=24|nreads=1
 TTGCTCTCAATGCGCTGAGTTTGG
->FBgn0000007_1731|4539|R|26|n=1
-TTGAGAGCAAAGGCCGAATGAGTAAA
->FBgn0000155_roo|2176|F|24|n=1
-TTTTGACCAAGCGGTATGAGAATA
->FBgn0000155_roo|2159|R|27|n=1
+>FBgn0000155_roo|coord=2159|strand -|size=27|nreads=1
 TTGGTCAAAAACTCCCAAGTGGCTTCA
->FBgn0000155_roo|2161|R|25|n=1
+>FBgn0000155_roo|coord=2161|strand -|size=25|nreads=1
 TTGGTCAAAAACTCCCAAGTGGCTT
->FBgn0000155_roo|2692|F|24|n=1
-TTGGTAAAAAATGTATAAGTGAGC
->FBgn0000155_roo|2675|R|27|n=1
+>FBgn0000155_roo|coord=2176|strand +|size=24|nreads=1
+TTTTGACCAAGCGGTATGAGAATA
+>FBgn0000155_roo|coord=2675|strand -|size=27|nreads=1
 TTTTTACCAAACGGATGCCTCAGACAT
->FBgn0000155_roo|2676|R|26|n=5
+>FBgn0000155_roo|coord=2676|strand -|size=26|nreads=5
 TTTTTACCAAACGGATGCCTCAGACA
->FBgn0000155_roo|2677|R|25|n=14
+>FBgn0000155_roo|coord=2677|strand -|size=25|nreads=14
 TTTTTACCAAACGGATGCCTCAGAC
->FBgn0000155_roo|2678|R|24|n=14
+>FBgn0000155_roo|coord=2678|strand -|size=24|nreads=14
 TTTTTACCAAACGGATGCCTCAGA
->FBgn0000155_roo|2679|R|23|n=2
+>FBgn0000155_roo|coord=2679|strand -|size=23|nreads=2
 TTTTTACCAAACGGATGCCTCAG
->FBgn0000155_roo|2692|F|27|n=1
+>FBgn0000155_roo|coord=2692|strand +|size=24|nreads=1
+TTGGTAAAAAATGTATAAGTGAGC
+>FBgn0000155_roo|coord=2692|strand +|size=27|nreads=1
 TTGGTAAAAAATGTATAAGTGAGCAGC
->FBgn0000155_roo|3149|F|26|n=1
-TTTTAATAAACCGGGTCGCATTGATT
->FBgn0000155_roo|3132|R|27|n=1
+>FBgn0000155_roo|coord=3132|strand -|size=27|nreads=1
 TTTATTAAAATCGGGGTCGGCTAATTT
->FBgn0000155_roo|3241|F|24|n=1
-TTGGGCAAAAAACTGATTTCGGGT
->FBgn0000155_roo|3225|R|26|n=1
+>FBgn0000155_roo|coord=3149|strand +|size=26|nreads=1
+TTTTAATAAACCGGGTCGCATTGATT
+>FBgn0000155_roo|coord=3225|strand -|size=26|nreads=1
 TTTTGCCCAAGGAGACCGTCTATTTT
->FBgn0000155_roo|3226|R|25|n=1
+>FBgn0000155_roo|coord=3226|strand -|size=25|nreads=1
 TTTTGCCCAAGGAGACCGTCTATTT
->FBgn0000155_roo|3227|R|24|n=2
+>FBgn0000155_roo|coord=3227|strand -|size=24|nreads=2
 TTTTGCCCAAGGAGACCGTCTATT
->FBgn0000155_roo|3228|R|23|n=1
+>FBgn0000155_roo|coord=3228|strand -|size=23|nreads=1
 TTTTGCCCAAGGAGACCGTCTAT
->FBgn0000155_roo|3241|F|27|n=1
+>FBgn0000155_roo|coord=3241|strand +|size=24|nreads=1
+TTGGGCAAAAAACTGATTTCGGGT
+>FBgn0000155_roo|coord=3241|strand +|size=27|nreads=1
 TTGGGCAAAAAACTGATTTCGGGTGGA
->FBgn0000155_roo|3241|F|28|n=1
+>FBgn0000155_roo|coord=3241|strand +|size=28|nreads=1
 TTGGGCAAAAAACTGATTTCGGGTGGAT
->FBgn0000155_roo|8655|F|25|n=1
-TTTGGCAGAATGTTCACACATGAAA
->FBgn0000155_roo|8639|R|26|n=1
+>FBgn0000155_roo|coord=8639|strand -|size=26|nreads=1
 TTCTGCCAAAGGGCCAGCAAAGCTGA
->FBgn0000155_roo|8639|R|26|n=1
+>FBgn0000155_roo|coord=8639|strand -|size=26|nreads=1
 TTCTGCCAAAGTGCCAGCAAAGCTGA
->FBgn0000349_copia|670|F|25|n=1
-TTCTTGAGAATTTGGACGCCGTTTA
->FBgn0000349_copia|653|R|27|n=1
+>FBgn0000155_roo|coord=8655|strand +|size=25|nreads=1
+TTTGGCAGAATGTTCACACATGAAA
+>FBgn0000349_copia|coord=653|strand -|size=27|nreads=1
 TTCTCAAGAATCTGACGCGCCGTAATG
->FBgn0000349_copia|657|R|23|n=1
+>FBgn0000349_copia|coord=657|strand -|size=23|nreads=1
 TTCTCAAGAATCTGACGCGCCGT
->FBgn0000349_copia|4628|F|24|n=1
+>FBgn0000349_copia|coord=670|strand +|size=25|nreads=1
+TTCTTGAGAATTTGGACGCCGTTTA
+>FBgn0000349_copia|coord=4614|strand -|size=24|nreads=1
+TTGCAGCAAACCCAATTTGTCTCG
+>FBgn0000349_copia|coord=4628|strand +|size=24|nreads=1
 TTTGCTGCAAGACGACCAATCGAA
->FBgn0000349_copia|4614|R|24|n=1
-TTGCAGCAAACCCAATTTGTCTCG
->FBgn0000349_copia|4628|F|28|n=1
+>FBgn0000349_copia|coord=4628|strand +|size=28|nreads=1
 TTTGCTGCAAGACGACCAATCGAATGCT
->FBgn0000481_Doc|1830|F|25|n=1
-TTCATGCAAAATACTTTGCAAGAGC
->FBgn0000481_Doc|1812|R|28|n=1
+>FBgn0000481_Doc|coord=1812|strand -|size=28|nreads=1
 TTTGCATGAACGTCATGAAGTCTTTCAT
->FBgn0000481_Doc|1815|R|25|n=1
+>FBgn0000481_Doc|coord=1815|strand -|size=25|nreads=1
 TTTGCATGAACGTCATAAAGTCTTT
->FBgn0000481_Doc|1815|R|25|n=1
+>FBgn0000481_Doc|coord=1815|strand -|size=25|nreads=1
 TTTGCATGAACGTCATGAAGTCTTT
->FBgn0000481_Doc|1816|R|24|n=1
+>FBgn0000481_Doc|coord=1816|strand -|size=24|nreads=1
 TTTGCATGAAGGTCATGAAGTCTT
->FBgn0000481_Doc|1830|F|26|n=1
+>FBgn0000481_Doc|coord=1830|strand +|size=25|nreads=1
+TTCATGCAAAATACTTTGCAAGAGC
+>FBgn0000481_Doc|coord=1830|strand +|size=26|nreads=1
 TTCATGCAAAATACTTTGCAAGAGCT
->FBgn0000481_Doc|3548|F|27|n=1
-TTTAGAGAAAAACATGGAACCATCGAA
->FBgn0000481_Doc|3531|R|27|n=1
+>FBgn0000481_Doc|coord=3531|strand -|size=27|nreads=1
 TTTCTCTAAAGCCAAATTGATGTGTTG
->FBgn0000481_Doc|3532|R|26|n=1
+>FBgn0000481_Doc|coord=3532|strand -|size=26|nreads=1
 TTTCTCTAAAGCCAAATTGATGTGTT
->FBgn0000481_Doc|3533|R|25|n=7
+>FBgn0000481_Doc|coord=3533|strand -|size=25|nreads=7
 TTTCTCTAAAGCCAAATTGATGTGT
->FBgn0000481_Doc|3534|R|24|n=1
+>FBgn0000481_Doc|coord=3534|strand -|size=24|nreads=1
 TTTCTCTAAAGCCAAATTGATGTG
->FBgn0000481_Doc|3535|R|23|n=2
+>FBgn0000481_Doc|coord=3535|strand -|size=23|nreads=2
 TTTCTCTAAAGCCAAATTGATGT
->FBgn0000652_F-element|1564|F|23|n=2
-TTTTCTCGAAAGCAGCAAGTTTC
->FBgn0000652_F-element|1546|R|28|n=1
+>FBgn0000481_Doc|coord=3548|strand +|size=27|nreads=1
+TTTAGAGAAAAACATGGAACCATCGAA
+>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1
 TTCGAGAAAATTACTTCAGGATTTGTCT
->FBgn0000652_F-element|1546|R|28|n=1
+>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1
 TTCGGGAAAATTACTTCAGGATTTGTCT
->FBgn0000652_F-element|1547|R|27|n=74
-TTCGAGAAAATTACTTCAGGATTTGTC
->FBgn0000652_F-element|1547|R|27|n=1
+>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1
 TTCGGGAAAATTACTTCAGGATTTGTC
->FBgn0000652_F-element|1547|R|27|n=1
+>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1
 TTTGAGAAAATTACTTCAGGATTTGTC
->FBgn0000652_F-element|1548|R|26|n=3
+>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=74
+TTCGAGAAAATTACTTCAGGATTTGTC
+>FBgn0000652_F-element|coord=1548|strand -|size=26|nreads=3
 TTCGAGAAAATTACTTCAGGATTTGT
->FBgn0000652_F-element|1549|R|25|n=22
-TTCGAGAAAATTACTTCAGGATTTG
->FBgn0000652_F-element|1549|R|25|n=1
+>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=1
 TTCGGGAAAATTACTTCAGGATTTG
->FBgn0000652_F-element|1550|R|24|n=2
+>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=22
+TTCGAGAAAATTACTTCAGGATTTG
+>FBgn0000652_F-element|coord=1550|strand -|size=24|nreads=2
 TTCGAGAAAATTACTTCAGGATTT
->FBgn0000652_F-element|1551|R|23|n=7
+>FBgn0000652_F-element|coord=1551|strand -|size=23|nreads=7
 TTCGAGAAAATTACTTCAGGATT
->FBgn0000652_F-element|1564|F|24|n=2
+>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2
+TTTTCTCGAAAGCAGCAAGTTTC
+>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2
+TTTTCTCGAAAGCAGCTAGTTTC
+>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=2
 TTTTCTCGAAAGCAGCAAGTTTCG
->FBgn0000652_F-element|1564|F|23|n=2
-TTTTCTCGAAAGCAGCTAGTTTC
->FBgn0000652_F-element|1564|F|24|n=5
+>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=5
 TTTTCTCGAAAGCAGCTAGTTTCG
->FBgn0000652_F-element|1564|F|25|n=1
+>FBgn0000652_F-element|coord=1564|strand +|size=25|nreads=1
 TTTTCTCGAAAGCAGCTAGTTTCGC
->FBgn0000652_F-element|3524|F|23|n=1
-TTTCGCGAAAGCCACGGAACCAT
->FBgn0000652_F-element|3507|R|27|n=1
+>FBgn0000652_F-element|coord=3507|strand -|size=27|nreads=1
 TTTCGCGAAATCCAAATTGGTGGGCTG
->FBgn0000652_F-element|3509|R|25|n=6
+>FBgn0000652_F-element|coord=3509|strand -|size=25|nreads=6
 TTTCGCGAAATCCAAATTGGTGGGC
->FBgn0000652_F-element|3510|R|24|n=1
+>FBgn0000652_F-element|coord=3510|strand -|size=24|nreads=1
 TTTCGCGAAATCCAAATTGGTGGG
->FBgn0000652_F-element|3524|F|27|n=1
-TTTCGCGAAAGCCACGGAACCATTGAA
->FBgn0000652_F-element|3524|F|24|n=1
+>FBgn0000652_F-element|coord=3524|strand +|size=23|nreads=1
+TTTCGCGAAAGCCACGGAACCAT
+>FBgn0000652_F-element|coord=3524|strand +|size=24|nreads=1
 TTTCGCGAAAGCCATGGAACCATT
->FBgn0000652_F-element|3524|F|26|n=1
+>FBgn0000652_F-element|coord=3524|strand +|size=26|nreads=1
 TTTCGCGAAAGCCATGGAACCATTGA
->FBgn0002697_mdg1|4313|F|25|n=1
-TTCCAAAGAATGATGACCCTTGCAT
->FBgn0002697_mdg1|4296|R|27|n=1
+>FBgn0000652_F-element|coord=3524|strand +|size=27|nreads=1
+TTTCGCGAAAGCCACGGAACCATTGAA
+>FBgn0002697_mdg1|coord=4296|strand -|size=27|nreads=1
 TTCTTTGGAAAGAATTTGGGGCTATTT
->FBgn0002697_mdg1|4297|R|26|n=2
+>FBgn0002697_mdg1|coord=4297|strand -|size=26|nreads=2
 TTCTTTGGAAAGAATTTGGGGCTATT
->FBgn0002697_mdg1|4298|R|25|n=3
+>FBgn0002697_mdg1|coord=4298|strand -|size=25|nreads=3
 TTCTTTGGAAAGAATTTGGGGCTAT
->FBgn0002697_mdg1|4299|R|24|n=1
+>FBgn0002697_mdg1|coord=4299|strand -|size=24|nreads=1
 TTCTTTGGAAAGAATTTGGGGCTA
->FBgn0002697_mdg1|4686|F|24|n=1
-TTTGTAAAAAGAATGTTCCATTTG
->FBgn0002697_mdg1|4670|R|26|n=2
+>FBgn0002697_mdg1|coord=4313|strand +|size=25|nreads=1
+TTCCAAAGAATGATGACCCTTGCAT
+>FBgn0002697_mdg1|coord=4670|strand -|size=26|nreads=2
 TTTTTACAAAGCCTCGTTAAGTGGCG
->FBgn0002697_mdg1|4671|R|25|n=4
+>FBgn0002697_mdg1|coord=4671|strand -|size=25|nreads=4
 TTTTTACAAAGCCTCGTTAAGTGGC
->FBgn0002697_mdg1|4672|R|24|n=3
+>FBgn0002697_mdg1|coord=4672|strand -|size=24|nreads=3
 TTTTTACAAAGCCTCGTTAAGTGG
->FBgn0002697_mdg1|4673|R|23|n=1
+>FBgn0002697_mdg1|coord=4673|strand -|size=23|nreads=1
 TTTTTACAAAGCCTCGTTAAATG
->FBgn0002697_mdg1|4673|R|23|n=6
+>FBgn0002697_mdg1|coord=4673|strand -|size=23|nreads=6
 TTTTTACAAAGCCTCGTTAAGTG
->FBgn0003122_pogo|1320|F|25|n=1
-TTGTGGTAAATCTACTGTGGAATTT
->FBgn0003122_pogo|1305|R|25|n=1
+>FBgn0002697_mdg1|coord=4686|strand +|size=24|nreads=1
+TTTGTAAAAAGAATGTTCCATTTG
+>FBgn0003122_pogo|coord=1305|strand -|size=25|nreads=1
 TTTACCACAATTAACAGCAATGAGC
->FBgn0003122_pogo|1819|F|26|n=3
-TTCTATGGAAGACAAGCTGTTTAATT
->FBgn0003122_pogo|1804|R|25|n=1
+>FBgn0003122_pogo|coord=1320|strand +|size=25|nreads=1
+TTGTGGTAAATCTACTGTGGAATTT
+>FBgn0003122_pogo|coord=1804|strand -|size=25|nreads=1
 TTCCATAGAATTCAAGTTTTGCAAA
->FBgn0003122_pogo|1806|R|23|n=1
+>FBgn0003122_pogo|coord=1806|strand -|size=23|nreads=1
 TTCCATAGAATTCAAGTTTTGCA
->FBgn0003490_springer|1390|F|24|n=1
-TTGTGGGGAAACATTGGATGCCGT
->FBgn0003490_springer|1376|R|24|n=1
+>FBgn0003122_pogo|coord=1819|strand +|size=26|nreads=3
+TTCTATGGAAGACAAGCTGTTTAATT
+>FBgn0003490_springer|coord=1376|strand -|size=24|nreads=1
 TTCCCCACAAGGGACCAGTCCGGT
->FBgn0003490_springer|4208|F|26|n=1
-TTGTTGAAGAGCAAGAACCGGAGTCG
->FBgn0003490_springer|4195|R|23|n=1
+>FBgn0003490_springer|coord=1390|strand +|size=24|nreads=1
+TTGTGGGGAAACATTGGATGCCGT
+>FBgn0003490_springer|coord=4195|strand -|size=23|nreads=1
 TTTTCAACAACGTTGAGTTGTTG
->FBgn0003490_springer|5284|F|24|n=6
-TTGACAAGAAAACGAGAGAACGCT
->FBgn0003490_springer|5267|R|27|n=7
+>FBgn0003490_springer|coord=4208|strand +|size=26|nreads=1
+TTGTTGAAGAGCAAGAACCGGAGTCG
+>FBgn0003490_springer|coord=5267|strand -|size=27|nreads=7
 TTCTTGTCAAAATCTGGGCGTTTTTGA
->FBgn0003490_springer|5269|R|25|n=1
+>FBgn0003490_springer|coord=5269|strand -|size=25|nreads=1
 TTCTTGTCAAAATCTGGGCGTTTTT
->FBgn0003490_springer|5271|R|23|n=2
+>FBgn0003490_springer|coord=5271|strand -|size=23|nreads=2
 TTCTTGTCAAAATCTGGGCGTTT
->FBgn0003490_springer|5284|F|26|n=1
+>FBgn0003490_springer|coord=5284|strand +|size=24|nreads=6
+TTGACAAGAAAACGAGAGAACGCT
+>FBgn0003490_springer|coord=5284|strand +|size=26|nreads=1
 TTGACAAGAAAACGAGAGAACGCTTC
->FBgn0003490_springer|6929|F|23|n=2
+>FBgn0003490_springer|coord=6910|strand -|size=29|nreads=2
+TTTGCTCCAAGTTCTTTTCACTTAAACGG
+>FBgn0003490_springer|coord=6929|strand +|size=23|nreads=2
 TTGGAGCAAATCAGGAACTTCGA
->FBgn0003490_springer|6910|R|29|n=2
-TTTGCTCCAAGTTCTTTTCACTTAAACGG
->FBgn0003908_R1A1-element|4690|F|23|n=8
-TTGGCGAAAACTGGATCTTCGAG
->FBgn0003908_R1A1-element|4671|R|29|n=1
+>FBgn0003908_R1A1-element|coord=4671|strand -|size=29|nreads=1
 TTTTCGCCAAGGCGCTGCACTCCAAGTCC
->FBgn0003908_R1A1-element|4672|R|28|n=8
+>FBgn0003908_R1A1-element|coord=4672|strand -|size=28|nreads=8
 TTTTCGCCAAGGCGCTGCACTCCAAGTC
->FBgn0003908_R1A1-element|4673|R|27|n=1
+>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=1
 TTTTCGCCAAGGCGCTGCACCCCAAGT
->FBgn0003908_R1A1-element|4673|R|27|n=4
+>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=4
 TTTTCGCCAAGGCGCTGCACTCCAAGT
->FBgn0003908_R1A1-element|4674|R|26|n=1
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1
 TTTTCGCCAAGGCGCTGCACCCCAAG
->FBgn0003908_R1A1-element|4674|R|26|n=29
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1
+TTTTCGTCAAGGCGCTGCACTCCAAG
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=2
+TTTTCGCCAAGGCGCTGCACTTCAAG
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=29
 TTTTCGCCAAGGCGCTGCACTCCAAG
->FBgn0003908_R1A1-element|4674|R|26|n=2
-TTTTCGCCAAGGCGCTGCACTTCAAG
->FBgn0003908_R1A1-element|4674|R|26|n=1
-TTTTCGTCAAGGCGCTGCACTCCAAG
->FBgn0003908_R1A1-element|4675|R|25|n=1
+>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1
 TTTTCGCCAAGGCGCTGCACCCCAA
->FBgn0003908_R1A1-element|4675|R|25|n=10
-TTTTCGCCAAGGCGCTGCACTCCAA
->FBgn0003908_R1A1-element|4675|R|25|n=1
+>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1
 TTTTCGCCAAGGCGCTGCACTTCAA
->FBgn0003908_R1A1-element|4676|R|24|n=21
-TTTTCGCCAAGGCGCTGCACTCCA
->FBgn0003908_R1A1-element|4676|R|24|n=2
+>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=10
+TTTTCGCCAAGGCGCTGCACTCCAA
+>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=2
 TTTTCGCCAAGGCGCTGCACTTCA
->FBgn0003908_R1A1-element|4677|R|23|n=12
+>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=21
+TTTTCGCCAAGGCGCTGCACTCCA
+>FBgn0003908_R1A1-element|coord=4677|strand -|size=23|nreads=12
 TTTTCGCCAAGGCGCTGCACTCC
->FBgn0003908_R1A1-element|4690|F|24|n=9
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=23|nreads=8
+TTGGCGAAAACTGGATCTTCGAG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=7
+TTGGCGAAAACTGGATCTTCGAGG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=9
 TTGGCGAAAACTGGATCTTCGAGA
->FBgn0003908_R1A1-element|4690|F|25|n=11
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=11
 TTGGCGAAAACTGGATCTTCGAGAG
->FBgn0003908_R1A1-element|4690|F|26|n=6
-TTGGCGAAAACTGGATCTTCGAGAGA
->FBgn0003908_R1A1-element|4690|F|27|n=20
-TTGGCGAAAACTGGATCTTCGAGAGAA
->FBgn0003908_R1A1-element|4690|F|28|n=4
-TTGGCGAAAACTGGATCTTCGAGAGAAT
->FBgn0003908_R1A1-element|4690|F|24|n=7
-TTGGCGAAAACTGGATCTTCGAGG
->FBgn0003908_R1A1-element|4690|F|25|n=12
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=12
 TTGGCGAAAACTGGATCTTCGAGGG
->FBgn0003908_R1A1-element|4690|F|26|n=2
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=2
 TTGGCGAAAACTGGATCTTCGAGGGA
->FBgn0003908_R1A1-element|4690|F|27|n=9
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=6
+TTGGCGAAAACTGGATCTTCGAGAGA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=20
+TTGGCGAAAACTGGATCTTCGAGAGAA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=9
 TTGGCGAAAACTGGATCTTCGAGGGAA
->FBgn0003908_R1A1-element|4690|F|28|n=1
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=1
 TTGGCGAAAACTGGATCTTCGAGGGAAT
->FBgn0004082_Tirant|4214|F|25|n=1
-TTCATTAGAATGCCGTTTGGCCTCA
->FBgn0004082_Tirant|4197|R|27|n=1
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=4
+TTGGCGAAAACTGGATCTTCGAGAGAAT
+>FBgn0004082_Tirant|coord=4197|strand -|size=27|nreads=1
 TTCTAATGAACTCGTAGTGGCCCCCCT
->FBgn0005384_3S18|4758|F|23|n=1
-TTTTCTTCAACGAAAGGGCACAA
->FBgn0005384_3S18|4741|R|27|n=2
+>FBgn0004082_Tirant|coord=4214|strand +|size=25|nreads=1
+TTCATTAGAATGCCGTTTGGCCTCA
+>FBgn0005384_3S18|coord=4741|strand -|size=27|nreads=2
 TTGAAGAAAACAGGATTTGCATTGGAA
->FBgn0005384_3S18|4742|R|26|n=2
+>FBgn0005384_3S18|coord=4742|strand -|size=26|nreads=2
 TTGAAGAAAACAGGATTTGCATTGGA
->FBgn0005384_3S18|4743|R|25|n=4
+>FBgn0005384_3S18|coord=4743|strand -|size=25|nreads=4
 TTGAAGAAAACAGGATTTGCATTGG
->FBgn0005384_3S18|4744|R|24|n=1
+>FBgn0005384_3S18|coord=4744|strand -|size=24|nreads=1
 TTGAAGAAAACAGGATTTGCATTG
->FBgn0005384_3S18|4745|R|23|n=2
+>FBgn0005384_3S18|coord=4745|strand -|size=23|nreads=2
 TTGAAGAAAACAGGATTTGCATT
->FBgn0005384_3S18|4758|F|28|n=1
+>FBgn0005384_3S18|coord=4758|strand +|size=23|nreads=1
+TTTTCTTCAACGAAAGGGCACAA
+>FBgn0005384_3S18|coord=4758|strand +|size=28|nreads=1
 TTTTCTTCAACGAAAGGGCACAAGCAAC
->FBgn0005384_3S18|5255|F|25|n=1
-TTGGATCAAAGGCTTTAACGTTTGA
->FBgn0005384_3S18|5237|R|28|n=1
+>FBgn0005384_3S18|coord=5237|strand -|size=28|nreads=1
 TTTGATCCAAGTATTCGTTTCATATGGA
->FBgn0005384_3S18|5241|R|24|n=2
-TTTGATCCAAGTATCCGTTTCATA
->FBgn0005384_3S18|5241|R|24|n=1
+>FBgn0005384_3S18|coord=5241|strand -|size=24|nreads=1
 TTTGATCCAAGTATTCGTTTCATA
->FBgn0005384_3S18|5255|F|28|n=4
+>FBgn0005384_3S18|coord=5241|strand -|size=24|nreads=2
+TTTGATCCAAGTATCCGTTTCATA
+>FBgn0005384_3S18|coord=5255|strand +|size=25|nreads=1
+TTGGATCAAAGGCTTTAACGTTTGA
+>FBgn0005384_3S18|coord=5255|strand +|size=28|nreads=4
 TTGGATCAAAGGCTTTAACGTTTGAGGA
->FBgn0005673_1360|2056|F|24|n=1
-TTTTCACAAAAGTCGAATTGCGAG
->FBgn0005673_1360|2038|R|28|n=1
+>FBgn0005673_1360|coord=2038|strand -|size=28|nreads=1
 TTTGTGAAAATTTAAAAATGTGTAGAGA
->FBgn0005673_1360|2042|R|24|n=3
+>FBgn0005673_1360|coord=2042|strand -|size=24|nreads=3
 TTTGTGAAAATTTAAAAATGTGTA
->FBgn0005673_1360|2178|F|24|n=1
-TTTTCCAAATTCGTGCAAGACAAT
->FBgn0005673_1360|2165|R|23|n=2
+>FBgn0005673_1360|coord=2056|strand +|size=24|nreads=1
+TTTTCACAAAAGTCGAATTGCGAG
+>FBgn0005673_1360|coord=2165|strand -|size=23|nreads=2
 TTTTGGAAAATGATACAGAGTAT
->FBgn0005673_1360|3209|F|23|n=1
-TTCTAGCACAACACGCACACATA
->FBgn0005673_1360|3195|R|24|n=1
+>FBgn0005673_1360|coord=2178|strand +|size=24|nreads=1
+TTTTCCAAATTCGTGCAAGACAAT
+>FBgn0005673_1360|coord=3195|strand -|size=24|nreads=1
 TTTGCTAGAAGACGATTTTCGGGC
->FBgn0005673_1360|3209|F|26|n=1
+>FBgn0005673_1360|coord=3209|strand +|size=23|nreads=1
+TTCTAGCACAACACGCACACATA
+>FBgn0005673_1360|coord=3209|strand +|size=26|nreads=1
 TTCTAGCACAACACGCACACATATAC
->FBgn0005673_1360|3209|F|27|n=1
+>FBgn0005673_1360|coord=3209|strand +|size=27|nreads=1
 TTCTAGCACAACACGCACACATATACG
->FBgn0005773_Bari1|1631|F|24|n=1
+>FBgn0005773_Bari1|coord=1617|strand -|size=24|nreads=1
+TTGCCTGAAATAGTTCTTATCGCT
+>FBgn0005773_Bari1|coord=1631|strand +|size=24|nreads=1
 TTTCAGGCAAATCGGACAACAACA
->FBgn0005773_Bari1|1617|R|24|n=1
-TTGCCTGAAATAGTTCTTATCGCT
->FBgn0010103_aurora-element|1444|F|27|n=1
+>FBgn0010103_aurora-element|coord=1431|strand -|size=23|nreads=1
+TTGCTGGGAACGGCTGGCTGCCG
+>FBgn0010103_aurora-element|coord=1444|strand +|size=27|nreads=1
 TTCCCAGCAACAGTCTGGAGAGAGGAG
->FBgn0010103_aurora-element|1431|R|23|n=1
-TTGCTGGGAACGGCTGGCTGCCG
->FBgn0010302_Burdock|3141|F|23|n=1
-TTTTCTTCAAGGAAAGCGTCGAG
->FBgn0010302_Burdock|3125|R|26|n=1
+>FBgn0010302_Burdock|coord=3125|strand -|size=26|nreads=1
 TTGAAGAAAAACGATTTCTCTTTAGA
->FBgn0010302_Burdock|3127|R|24|n=1
+>FBgn0010302_Burdock|coord=3127|strand -|size=24|nreads=1
 TTGAAGAAAAACGATTTCTCTTTA
->FBgn0010302_Burdock|3141|F|24|n=1
+>FBgn0010302_Burdock|coord=3141|strand +|size=23|nreads=1
+TTTTCTTCAAGGAAAGCGTCGAG
+>FBgn0010302_Burdock|coord=3141|strand +|size=24|nreads=1
 TTTTCTTCAAGGAAAGCGTCGAGT
->FBgn0010302_Burdock|3401|F|25|n=2
+>FBgn0010302_Burdock|coord=3385|strand -|size=26|nreads=1
+TTTCATCGAAAGAAATTGGTATCTTT
+>FBgn0010302_Burdock|coord=3401|strand +|size=25|nreads=2
 TTCGATGAAAGACAATGTTCTGCTT
->FBgn0010302_Burdock|3385|R|26|n=1
-TTTCATCGAAAGAAATTGGTATCTTT
->FBgn0014947_flea|818|F|23|n=1
+>FBgn0014947_flea|coord=801|strand -|size=27|nreads=4
+TTCTCTAGAATTGCTTGTATTTGGTCG
+>FBgn0014947_flea|coord=802|strand -|size=26|nreads=11
+TTCTCTAGAATTGCTTGTATTTGGTC
+>FBgn0014947_flea|coord=803|strand -|size=25|nreads=12
+TTCTCTAGAATTGCTTGTATTTGGT
+>FBgn0014947_flea|coord=804|strand -|size=24|nreads=2
+TTCTCTAGAATTGCTTGTATTTGG
+>FBgn0014947_flea|coord=805|strand -|size=23|nreads=1
+TTCTCTAGAATTGCTTGTATTTG
+>FBgn0014947_flea|coord=818|strand +|size=23|nreads=1
 TTCTAGAGAACGAAAGCGAGGAC
->FBgn0014947_flea|801|R|27|n=4
-TTCTCTAGAATTGCTTGTATTTGGTCG
->FBgn0014947_flea|802|R|26|n=11
-TTCTCTAGAATTGCTTGTATTTGGTC
->FBgn0014947_flea|803|R|25|n=12
-TTCTCTAGAATTGCTTGTATTTGGT
->FBgn0014947_flea|804|R|24|n=2
-TTCTCTAGAATTGCTTGTATTTGG
->FBgn0014947_flea|805|R|23|n=1
-TTCTCTAGAATTGCTTGTATTTG
->FBgn0014947_flea|1182|F|23|n=1
+>FBgn0014947_flea|coord=1164|strand -|size=28|nreads=2
+TTCTAAGAAAAGTTCTGCTGATCCAATC
+>FBgn0014947_flea|coord=1166|strand -|size=26|nreads=2
+TTCTAAGAAAAGTTCTGCTGATCCAA
+>FBgn0014947_flea|coord=1167|strand -|size=25|nreads=1
+TTCTAAGAAAAGTTCTGCTGATCCA
+>FBgn0014947_flea|coord=1168|strand -|size=24|nreads=1
+TTCTAAGAAAAGTTCTGCTGATCC
+>FBgn0014947_flea|coord=1169|strand -|size=23|nreads=1
+TTCTAAGAAAAGTTCTGCTGATC
+>FBgn0014947_flea|coord=1182|strand +|size=23|nreads=1
 TTTCTTAGAATCTGAATGTGTCA
->FBgn0014947_flea|1164|R|28|n=2
-TTCTAAGAAAAGTTCTGCTGATCCAATC
->FBgn0014947_flea|1166|R|26|n=2
-TTCTAAGAAAAGTTCTGCTGATCCAA
->FBgn0014947_flea|1167|R|25|n=1
-TTCTAAGAAAAGTTCTGCTGATCCA
->FBgn0014947_flea|1168|R|24|n=1
-TTCTAAGAAAAGTTCTGCTGATCC
->FBgn0014947_flea|1169|R|23|n=1
-TTCTAAGAAAAGTTCTGCTGATC
->FBgn0014947_flea|1182|F|25|n=2
+>FBgn0014947_flea|coord=1182|strand +|size=25|nreads=2
 TTTCTTAGAATCTGAATGTGTCAGT
->FBgn0014947_flea|2765|F|24|n=4
-TTGGTCTAAAAATAAAATGGAAGA
->FBgn0014947_flea|2749|R|26|n=1
+>FBgn0014947_flea|coord=2749|strand -|size=26|nreads=1
 TTTAGACCAAATTCTGCAGCTCTCTT
->FBgn0014947_flea|2750|R|25|n=9
+>FBgn0014947_flea|coord=2750|strand -|size=25|nreads=9
 TTTAGACCAAATTCTGCAGCTCTCT
->FBgn0014947_flea|2751|R|24|n=1
+>FBgn0014947_flea|coord=2751|strand -|size=24|nreads=1
 TTTAGACCAAATTCTGCAGCTCTC
->FBgn0014947_flea|2752|R|23|n=2
+>FBgn0014947_flea|coord=2752|strand -|size=23|nreads=2
 TTTAGACCAAATTCTGCAGCTCT
->FBgn0014947_flea|2765|F|25|n=1
+>FBgn0014947_flea|coord=2765|strand +|size=24|nreads=4
+TTGGTCTAAAAATAAAATGGAAGA
+>FBgn0014947_flea|coord=2765|strand +|size=25|nreads=1
 TTGGTCTAAAAATAAAATGGAAGAA
->FBgn0014947_flea|2765|F|26|n=1
+>FBgn0014947_flea|coord=2765|strand +|size=26|nreads=1
 TTGGTCTAAAAATAAAATGGAAGAAG
->FBgn0014947_flea|2765|F|28|n=1
+>FBgn0014947_flea|coord=2765|strand +|size=28|nreads=1
 TTGGTCTAAAAATAAAATGGAAGAAGTG
->FBgn0015786_Porto1|1018|F|23|n=1
+>FBgn0015786_Porto1|coord=1003|strand -|size=25|nreads=1
+TTTCTTCCAATGAATTTAAAGCAGT
+>FBgn0015786_Porto1|coord=1018|strand +|size=23|nreads=1
 TTGGAAGAAACACGATATGAACT
->FBgn0015786_Porto1|1003|R|25|n=1
-TTTCTTCCAATGAATTTAAAGCAGT
->FBgn0015786_Porto1|4489|F|25|n=1
+>FBgn0015786_Porto1|coord=4472|strand -|size=27|nreads=1
+TTTGTCTCAAGTTTGAGTTTTGGTGGC
+>FBgn0015786_Porto1|coord=4473|strand -|size=26|nreads=1
+TTTGTCTCAAGTTTGAGTTTTGGTGG
+>FBgn0015786_Porto1|coord=4489|strand +|size=25|nreads=1
 TTGAGACAAATACCGATGACAGAGT
->FBgn0015786_Porto1|4472|R|27|n=1
-TTTGTCTCAAGTTTGAGTTTTGGTGGC
->FBgn0015786_Porto1|4473|R|26|n=1
-TTTGTCTCAAGTTTGAGTTTTGGTGG
->FBgn0015945_GATE|3158|F|23|n=18
+>FBgn0015945_GATE|coord=3140|strand -|size=28|nreads=9
+TTGGAACGAAATTGGCCTGATTAGCGGA
+>FBgn0015945_GATE|coord=3141|strand -|size=27|nreads=4
+TTGGAACGAAATTGGCCTGATTAGCGG
+>FBgn0015945_GATE|coord=3142|strand -|size=26|nreads=17
+TTGGAACGAAATTGGCCTGATTAGCG
+>FBgn0015945_GATE|coord=3143|strand -|size=25|nreads=86
+TTGGAACGAAATTGGCCTGATTAGC
+>FBgn0015945_GATE|coord=3144|strand -|size=24|nreads=17
+TTGGAACGAAATTGGCCTGATTAG
+>FBgn0015945_GATE|coord=3158|strand +|size=23|nreads=18
 TTCGTTCCAAATGAGCAAGCCGG
->FBgn0015945_GATE|3140|R|28|n=9
-TTGGAACGAAATTGGCCTGATTAGCGGA
->FBgn0015945_GATE|3141|R|27|n=4
-TTGGAACGAAATTGGCCTGATTAGCGG
->FBgn0015945_GATE|3142|R|26|n=17
-TTGGAACGAAATTGGCCTGATTAGCG
->FBgn0015945_GATE|3143|R|25|n=86
-TTGGAACGAAATTGGCCTGATTAGC
->FBgn0015945_GATE|3144|R|24|n=17
-TTGGAACGAAATTGGCCTGATTAG
->FBgn0015945_GATE|3158|F|24|n=10
+>FBgn0015945_GATE|coord=3158|strand +|size=24|nreads=10
 TTCGTTCCAAATGAGCAAGCCGGT
->FBgn0015945_GATE|3158|F|25|n=10
+>FBgn0015945_GATE|coord=3158|strand +|size=25|nreads=10
 TTCGTTCCAAATGAGCAAGCCGGTG
->FBgn0015945_GATE|3158|F|26|n=5
+>FBgn0015945_GATE|coord=3158|strand +|size=26|nreads=5
 TTCGTTCCAAATGAGCAAGCCGGTGT
->FBgn0015945_GATE|3158|F|27|n=1
+>FBgn0015945_GATE|coord=3158|strand +|size=27|nreads=1
 TTCGTTCCAAATGAGCAAGCCGGTGTT
->FBgn0015945_GATE|6246|F|25|n=1
+>FBgn0015945_GATE|coord=6230|strand -|size=26|nreads=1
+TTGAAGGAAATCGCGGGAAAGCAGGG
+>FBgn0015945_GATE|coord=6231|strand -|size=25|nreads=1
+TTGAAGGAAATCGAGGGAAAGCAGG
+>FBgn0015945_GATE|coord=6232|strand -|size=24|nreads=2
+TTGAAGGAAATCGCGGGAAAGCAG
+>FBgn0015945_GATE|coord=6246|strand +|size=25|nreads=1
 TTTCCTTCAAGCCGTAAAAGAGTCG
->FBgn0015945_GATE|6230|R|26|n=1
-TTGAAGGAAATCGCGGGAAAGCAGGG
->FBgn0015945_GATE|6231|R|25|n=1
-TTGAAGGAAATCGAGGGAAAGCAGG
->FBgn0015945_GATE|6232|R|24|n=2
-TTGAAGGAAATCGCGGGAAAGCAG
->FBgn0015945_GATE|6246|F|26|n=1
+>FBgn0015945_GATE|coord=6246|strand +|size=26|nreads=1
 TTTCCTTCAAGCCGTAAAAGAGTCGG
->FBgn0022937_Circe|2086|F|25|n=2
+>FBgn0022937_Circe|coord=2068|strand -|size=28|nreads=1
+TTCGAAAGAAATCTTCGTGACGATGACA
+>FBgn0022937_Circe|coord=2069|strand -|size=27|nreads=1
+TTCGAAAGAAATCTTCGTGACGATGAC
+>FBgn0022937_Circe|coord=2070|strand -|size=26|nreads=1
+TTCGAAAGAAATCTTCGTGACGATGA
+>FBgn0022937_Circe|coord=2071|strand -|size=25|nreads=5
+TTCGAAAGAAATCTTCGTGACGATG
+>FBgn0022937_Circe|coord=2086|strand +|size=25|nreads=2
 TTCTTTCGAAGCACCCGGACAAAGC
->FBgn0022937_Circe|2068|R|28|n=1
-TTCGAAAGAAATCTTCGTGACGATGACA
->FBgn0022937_Circe|2069|R|27|n=1
-TTCGAAAGAAATCTTCGTGACGATGAC
->FBgn0022937_Circe|2070|R|26|n=1
-TTCGAAAGAAATCTTCGTGACGATGA
->FBgn0022937_Circe|2071|R|25|n=5
-TTCGAAAGAAATCTTCGTGACGATG
->FBgn0022937_Circe|2086|F|26|n=1
+>FBgn0022937_Circe|coord=2086|strand +|size=26|nreads=1
 TTCTTTCGAAGCACCCGGACAAAGCC
->FBgn0022937_Circe|2086|F|28|n=1
+>FBgn0022937_Circe|coord=2086|strand +|size=28|nreads=1
 TTCTTTCGAAGCACCCGGACAAAGCCAA
->FBgn0022937_Circe|3691|F|26|n=1
-TTTGTCCGAAGTAGCCACCCAATTGC
->FBgn0022937_Circe|3676|R|25|n=1
+>FBgn0022937_Circe|coord=3676|strand -|size=25|nreads=1
 TTCGGACAAATGCAAAAGATGGTCT
->FBgn0022937_Circe|5431|F|24|n=2
-TTTCAAAGAATTCGCTCCAACAGT
->FBgn0022937_Circe|5416|R|25|n=1
+>FBgn0022937_Circe|coord=3691|strand +|size=26|nreads=1
+TTTGTCCGAAGTAGCCACCCAATTGC
+>FBgn0022937_Circe|coord=5416|strand -|size=25|nreads=1
 TTCTTTGAAATTCGTCAGTTCTTGA
->FBgn0022937_Circe|5418|R|23|n=1
+>FBgn0022937_Circe|coord=5418|strand -|size=23|nreads=1
 TTCTTTGAAATTCGTCAGTTCTT
->FBgn0022937_Circe|5431|F|25|n=1
+>FBgn0022937_Circe|coord=5431|strand +|size=24|nreads=2
+TTTCAAAGAATTCGCTCCAACAGT
+>FBgn0022937_Circe|coord=5431|strand +|size=25|nreads=1
 TTTCAAAGAATTCGCTCCAACAGTG
->FBgn0022937_Circe|5431|F|25|n=1
+>FBgn0022937_Circe|coord=5431|strand +|size=25|nreads=1
 TTTCAAAGAATTCGCTCCAACATTG
->FBgn0042231_X-element|285|F|25|n=1
+>FBgn0042231_X-element|coord=269|strand -|size=26|nreads=2
+TTCTAGCCAAAACTTGAACCCTGGGA
+>FBgn0042231_X-element|coord=285|strand +|size=25|nreads=1
 TTGGCTAGAACCCTGGTGATTTGGT
->FBgn0042231_X-element|269|R|26|n=2
-TTCTAGCCAAAACTTGAACCCTGGGA
->FBgn0042231_X-element|3955|F|24|n=2
+>FBgn0042231_X-element|coord=3939|strand -|size=26|nreads=2
+TTGATGCCAATATTCCAACGTCTTGC
+>FBgn0042231_X-element|coord=3955|strand +|size=24|nreads=2
 TTGGCATCAATAGCAGTAAATCCA
->FBgn0042231_X-element|3939|R|26|n=2
-TTGATGCCAATATTCCAACGTCTTGC
->FBgn0042682_Rt1b|1086|F|23|n=1
-TTGCCAAGAATGCTAGCACGGGT
->FBgn0042682_Rt1b|1070|R|26|n=2
+>FBgn0042682_Rt1b|coord=1070|strand -|size=26|nreads=2
 TTCTTGGCGACAGATGCGTAGCTGCC
->FBgn0042682_Rt1b|1071|R|25|n=1
+>FBgn0042682_Rt1b|coord=1071|strand -|size=25|nreads=1
 TTCTTGGAGACAGATGCGTAGCTGC
->FBgn0042682_Rt1b|1071|R|25|n=3
+>FBgn0042682_Rt1b|coord=1071|strand -|size=25|nreads=3
 TTCTTGGCGACAGATGCGTAGCTGC
->FBgn0042682_Rt1b|1072|R|24|n=3
+>FBgn0042682_Rt1b|coord=1072|strand -|size=24|nreads=3
 TTCTTGGCGACAGATGCGTAGCTG
->FBgn0042682_Rt1b|1073|R|23|n=1
+>FBgn0042682_Rt1b|coord=1073|strand -|size=23|nreads=1
 TTCTTGGCGACAGATGCGTAGCT
->FBgn0042682_Rt1b|2920|F|23|n=1
-TTGTTACCAAAAAGCTAAGGAGG
->FBgn0042682_Rt1b|2902|R|28|n=1
+>FBgn0042682_Rt1b|coord=1086|strand +|size=23|nreads=1
+TTGCCAAGAATGCTAGCACGGGT
+>FBgn0042682_Rt1b|coord=2902|strand -|size=28|nreads=1
 TTGGTAACAAGCTTGTAGGCGAGGCCCC
->FBgn0042682_Rt1b|2903|R|27|n=1
+>FBgn0042682_Rt1b|coord=2903|strand -|size=27|nreads=1
 TTGGTAACAAGCTTGTAGGCGAGGCCC
->FBgn0042682_Rt1b|2904|R|26|n=2
+>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=1
+TTGGTAACAAGCTTGTAGGCGAGTCC
+>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=2
 TTGGTAACAAGCTTGTAGGCGAGGCC
->FBgn0042682_Rt1b|2904|R|26|n=1
-TTGGTAACAAGCTTGTAGGCGAGTCC
->FBgn0042682_Rt1b|2905|R|25|n=2
+>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=1
+TTGGTAACAAGCTTGTAGGCGAGGT
+>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=2
 TTGGTAACAAGCTTGTAGGCGAGGC
->FBgn0042682_Rt1b|2905|R|25|n=1
-TTGGTAACAAGCTTGTAGGCGAGGT
->FBgn0042682_Rt1b|2906|R|24|n=25
+>FBgn0042682_Rt1b|coord=2906|strand -|size=24|nreads=25
 TTGGTAACAAGCTTGTAGGCGAGG
->FBgn0042682_Rt1b|2907|R|23|n=1
+>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=1
 TTGGTAACAAGCTTGGAGGCGAG
->FBgn0042682_Rt1b|2907|R|23|n=15
+>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=15
 TTGGTAACAAGCTTGTAGGCGAG
->FBgn0042682_Rt1b|2920|F|25|n=1
-TTGTTACCAAAAAGCTAAGGAGGAG
->FBgn0042682_Rt1b|2920|F|26|n=1
-TTGTTACCAAAAAGCTAAGGAGGAGA
->FBgn0042682_Rt1b|2920|F|27|n=1
-TTGTTACCAAAAAGCTAAGGAGGAGAG
->FBgn0042682_Rt1b|2920|F|23|n=1
+>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1
+TTGTTACCAAAAAGCTAAGGAGG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1
 TTGTTACCAACAAGCTAAGGAGG
->FBgn0042682_Rt1b|2920|F|24|n=2
+>FBgn0042682_Rt1b|coord=2920|strand +|size=24|nreads=2
 TTGTTACCAACAAGCTAAGGAGGA
->FBgn0042682_Rt1b|4376|F|24|n=1
-TTCCAGGCAAGAGGCACACGAGTG
->FBgn0042682_Rt1b|4357|R|29|n=2
+>FBgn0042682_Rt1b|coord=2920|strand +|size=25|nreads=1
+TTGTTACCAAAAAGCTAAGGAGGAG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=26|nreads=1
+TTGTTACCAAAAAGCTAAGGAGGAGA
+>FBgn0042682_Rt1b|coord=2920|strand +|size=27|nreads=1
+TTGTTACCAAAAAGCTAAGGAGGAGAG
+>FBgn0042682_Rt1b|coord=4357|strand -|size=29|nreads=2
 TTGCCTGGAAGCGCCACTCCGCATTAGGC
->FBgn0042682_Rt1b|4359|R|27|n=1
+>FBgn0042682_Rt1b|coord=4359|strand -|size=27|nreads=1
 TTGCCTGGAAGCGCCACTCCGCATTAG
->FBgn0042682_Rt1b|4360|R|26|n=5
+>FBgn0042682_Rt1b|coord=4360|strand -|size=26|nreads=5
 TTGCCTGGAAGCGCCACTCCGCATTA
->FBgn0042682_Rt1b|4361|R|25|n=4
+>FBgn0042682_Rt1b|coord=4361|strand -|size=25|nreads=4
 TTGCCTGGAAGCGCCACTCCGCATA
->FBgn0042682_Rt1b|4361|R|25|n=6
+>FBgn0042682_Rt1b|coord=4361|strand -|size=25|nreads=6
 TTGCCTGGAAGCGCCACTCCGCATT
->FBgn0042682_Rt1b|4362|R|24|n=6
+>FBgn0042682_Rt1b|coord=4362|strand -|size=24|nreads=6
 TTGCCTGGAAGCGCCACTCCGCAT
->FBgn0042682_Rt1b|4363|R|23|n=2
+>FBgn0042682_Rt1b|coord=4363|strand -|size=23|nreads=2
 TTGCCTGGAAGCGCCACTCCGCA
->FBgn0042682_Rt1b|4376|F|26|n=1
+>FBgn0042682_Rt1b|coord=4376|strand +|size=24|nreads=1
+TTCCAGGCAAGAGGCACACGAGTG
+>FBgn0042682_Rt1b|coord=4376|strand +|size=26|nreads=1
 TTCCAGGCAAGAGGCACACGAGTGGC
->FBgn0044355_Quasimodo|1386|F|24|n=1
+>FBgn0044355_Quasimodo|coord=1370|strand -|size=26|nreads=1
+TTCTTAGCAACTCTTCGTATGGGATT
+>FBgn0044355_Quasimodo|coord=1372|strand -|size=24|nreads=1
+TTCTTAGCAACTCTTCGTATGGGA
+>FBgn0044355_Quasimodo|coord=1386|strand +|size=24|nreads=1
 TTGCTAAGAAGACTTTACAACACC
->FBgn0044355_Quasimodo|1370|R|26|n=1
-TTCTTAGCAACTCTTCGTATGGGATT
->FBgn0044355_Quasimodo|1372|R|24|n=1
-TTCTTAGCAACTCTTCGTATGGGA
->FBgn0063427_invader4|707|F|23|n=3
+>FBgn0063427_invader4|coord=691|strand -|size=26|nreads=15
+TTCCTACGAATCGCTGTATGAACAGT
+>FBgn0063427_invader4|coord=707|strand +|size=23|nreads=3
 TTCGTAGGAATTGAGACGTCGGC
->FBgn0063427_invader4|691|R|26|n=15
-TTCCTACGAATCGCTGTATGAACAGT
->FBgn0063428_invader3|440|F|23|n=1
+>FBgn0063428_invader3|coord=425|strand -|size=25|nreads=1
+TTCTGGGGAAATGGCCTGCAGACGC
+>FBgn0063428_invader3|coord=427|strand -|size=23|nreads=1
+TTCTGGGGAAATGGCCTGCAGAC
+>FBgn0063428_invader3|coord=440|strand +|size=23|nreads=1
 TTCCCCAGAAACGCGTGGAGATT
->FBgn0063428_invader3|425|R|25|n=1
-TTCTGGGGAAATGGCCTGCAGACGC
->FBgn0063428_invader3|427|R|23|n=1
-TTCTGGGGAAATGGCCTGCAGAC
->FBgn0063428_invader3|440|F|29|n=1
+>FBgn0063428_invader3|coord=440|strand +|size=27|nreads=1
+TTCCCCAGAAACGCGTGGCGATTCACC
+>FBgn0063428_invader3|coord=440|strand +|size=29|nreads=1
 TTCCCCAGAAACGCGTGGAGATTCACCGC
->FBgn0063428_invader3|440|F|27|n=1
-TTCCCCAGAAACGCGTGGCGATTCACC
->FBgn0063428_invader3|1939|F|25|n=1
+>FBgn0063428_invader3|coord=1923|strand -|size=26|nreads=2
+TTTCGTCCAAGAACTACATTATGACT
+>FBgn0063428_invader3|coord=1939|strand +|size=25|nreads=1
 TTGGACGAAATTTCATGGAAGCGTG
->FBgn0063428_invader3|1923|R|26|n=2
-TTTCGTCCAAGAACTACATTATGACT
->FBgn0063429_invader2|1474|F|25|n=1
+>FBgn0063429_invader2|coord=1460|strand -|size=24|nreads=1
+TTTGCTGCAAAGTGCCCCATCTCA
+>FBgn0063429_invader2|coord=1474|strand +|size=25|nreads=1
 TTGCAGCAAAGTGCCTAAAAAACAA
->FBgn0063429_invader2|1460|R|24|n=1
-TTTGCTGCAAAGTGCCCCATCTCA
->FBgn0063430_invader1|637|F|27|n=4
-TTGTCCGAAAACCAACTGGAAGGCAGC
->FBgn0063430_invader1|621|R|26|n=1
+>FBgn0063430_invader1|coord=621|strand -|size=26|nreads=1
 TTTCGGACAAGATGTAGTCCACCGTT
->FBgn0063430_invader1|1766|F|25|n=1
-TTGTCAAGAATTCCATAGGCGTAGT
->FBgn0063430_invader1|1750|R|26|n=3
+>FBgn0063430_invader1|coord=637|strand +|size=27|nreads=4
+TTGTCCGAAAACCAACTGGAAGGCAGC
+>FBgn0063430_invader1|coord=1750|strand -|size=26|nreads=3
 TTCTTGACAATTTTTGGAACCGGATT
->FBgn0063430_invader1|1751|R|25|n=2
+>FBgn0063430_invader1|coord=1751|strand -|size=25|nreads=2
 TTCTTGACAATTTTTGGAACCGGAT
->FBgn0063430_invader1|1752|R|24|n=3
+>FBgn0063430_invader1|coord=1752|strand -|size=24|nreads=3
 TTCTTGACAATTTTTGGAACCGGA
->FBgn0063430_invader1|1766|F|27|n=1
+>FBgn0063430_invader1|coord=1766|strand +|size=25|nreads=1
+TTGTCAAGAATTCCATAGGCGTAGT
+>FBgn0063430_invader1|coord=1766|strand +|size=27|nreads=1
 TTGTCAAGAATTCCATAGGCGTAGTCG
->FBgn0063430_invader1|2092|F|24|n=1
+>FBgn0063430_invader1|coord=2077|strand -|size=25|nreads=3
+TTTTATCGAACCAATAGAACTCGTA
+>FBgn0063430_invader1|coord=2079|strand -|size=23|nreads=1
+TTTTATCGAACCAATAGAACTCG
+>FBgn0063430_invader1|coord=2092|strand +|size=24|nreads=1
 TTCGATAAAATGTCTAAGTATGTT
->FBgn0063430_invader1|2077|R|25|n=3
-TTTTATCGAACCAATAGAACTCGTA
->FBgn0063430_invader1|2079|R|23|n=1
-TTTTATCGAACCAATAGAACTCG
->FBgn0063430_invader1|2092|F|26|n=1
+>FBgn0063430_invader1|coord=2092|strand +|size=26|nreads=1
 TTCGATAAAATGTCTAAGTATGTTCG
->FBgn0063431_gypsy6|3050|F|25|n=1
-TTCTTAGAAATGCTGAAGACTAGGA
->FBgn0063431_gypsy6|3031|R|29|n=1
+>FBgn0063431_gypsy6|coord=3031|strand -|size=29|nreads=1
 TTTCTAAGAACGCGTTTCTGACTAAGGGT
->FBgn0063433_gypsy4|2753|F|24|n=2
-TTGACCTCAAATCGGGATTTCATC
->FBgn0063433_gypsy4|2735|R|28|n=1
+>FBgn0063431_gypsy6|coord=3050|strand +|size=25|nreads=1
+TTCTTAGAAATGCTGAAGACTAGGA
+>FBgn0063433_gypsy4|coord=2735|strand -|size=28|nreads=1
 TTGAGGTCAAGAGTAGTAAAGTACTGTG
->FBgn0063433_gypsy4|2736|R|27|n=5
+>FBgn0063433_gypsy4|coord=2736|strand -|size=27|nreads=5
 TTGAGGTCAAGAGTAGTAAAGTACTGT
->FBgn0063433_gypsy4|2737|R|26|n=11
+>FBgn0063433_gypsy4|coord=2737|strand -|size=26|nreads=11
 TTGAGGTCAAGAGTAGTAAAGTACTG
->FBgn0063433_gypsy4|2738|R|25|n=5
+>FBgn0063433_gypsy4|coord=2738|strand -|size=25|nreads=1
+TTGAGGTCAAGGGTAGTAAAGTACT
+>FBgn0063433_gypsy4|coord=2738|strand -|size=25|nreads=5
 TTGAGGTCAAGAGTAGTAAAGTACT
->FBgn0063433_gypsy4|2738|R|25|n=1
-TTGAGGTCAAGGGTAGTAAAGTACT
->FBgn0063433_gypsy4|2739|R|24|n=25
+>FBgn0063433_gypsy4|coord=2739|strand -|size=24|nreads=2
+TTGAGGTCAAGGGTAGTAAAGTAC
+>FBgn0063433_gypsy4|coord=2739|strand -|size=24|nreads=25
 TTGAGGTCAAGAGTAGTAAAGTAC
->FBgn0063433_gypsy4|2739|R|24|n=2
-TTGAGGTCAAGGGTAGTAAAGTAC
->FBgn0063433_gypsy4|2740|R|23|n=1
+>FBgn0063433_gypsy4|coord=2740|strand -|size=23|nreads=1
 TTGAGGTCAAGAGTAGTAAAGTA
->FBgn0063433_gypsy4|2770|F|23|n=1
+>FBgn0063433_gypsy4|coord=2753|strand +|size=24|nreads=2
+TTGACCTCAAATCGGGATTTCATC
+>FBgn0063433_gypsy4|coord=2753|strand -|size=27|nreads=1
+TTTGATGAAATCCCGATTTGAGGTCAA
+>FBgn0063433_gypsy4|coord=2754|strand -|size=26|nreads=1
+TTTGATGAAATCCCGATTTGAGGTCA
+>FBgn0063433_gypsy4|coord=2770|strand +|size=23|nreads=1
 TTTCATCAAATCGAATTAGCGGA
->FBgn0063433_gypsy4|2753|R|27|n=1
-TTTGATGAAATCCCGATTTGAGGTCAA
->FBgn0063433_gypsy4|2754|R|26|n=1
-TTTGATGAAATCCCGATTTGAGGTCA
->FBgn0063433_gypsy4|3058|F|24|n=1
+>FBgn0063433_gypsy4|coord=3040|strand -|size=28|nreads=1
+TTTTGAAGAACTTGGATTTTTCTTGAGA
+>FBgn0063433_gypsy4|coord=3044|strand -|size=24|nreads=1
+TTTTGAAGAACTTGGATTTTTCTT
+>FBgn0063433_gypsy4|coord=3058|strand +|size=24|nreads=1
 TTCTTCAAAAAGAGCGTGGAATAT
->FBgn0063433_gypsy4|3040|R|28|n=1
-TTTTGAAGAACTTGGATTTTTCTTGAGA
->FBgn0063433_gypsy4|3044|R|24|n=1
-TTTTGAAGAACTTGGATTTTTCTT
->FBgn0063436_gtwin|5264|F|27|n=1
+>FBgn0063436_gtwin|coord=5250|strand -|size=24|nreads=1
+TTTTAACGAAAACCTCGTCTCCTA
+>FBgn0063436_gtwin|coord=5264|strand +|size=27|nreads=1
 TTCGTTAAAAACAACAGAAGGTTAGGA
->FBgn0063436_gtwin|5250|R|24|n=1
-TTTTAACGAAAACCTCGTCTCCTA
->FBgn0063440_baggins|3312|F|24|n=1
+>FBgn0063440_baggins|coord=3296|strand -|size=26|nreads=3
+TTTTAGCAAAAACGATGTCAAGCTGA
+>FBgn0063440_baggins|coord=3298|strand -|size=24|nreads=1
+TTTTAGCAAAAACGATGTCAAGCT
+>FBgn0063440_baggins|coord=3312|strand +|size=24|nreads=1
 TTTGCTAAAAACGTTCGAAAAGCT
->FBgn0063440_baggins|3296|R|26|n=3
-TTTTAGCAAAAACGATGTCAAGCTGA
->FBgn0063440_baggins|3298|R|24|n=1
-TTTTAGCAAAAACGATGTCAAGCT
->FBgn0063507_G2|1923|F|29|n=1
+>FBgn0063507_G2|coord=1906|strand -|size=27|nreads=1
+TTCCGTGGGATCGCCTGAAGCCAAACT
+>FBgn0063507_G2|coord=1906|strand -|size=27|nreads=1
+TTTCGTGGGATCGCCTGAAGCCAAACT
+>FBgn0063507_G2|coord=1908|strand -|size=25|nreads=3
+TTCCGTGGGATCGCCTGAAGCCAAA
+>FBgn0063507_G2|coord=1923|strand +|size=29|nreads=1
 TTCCACGGAACACCCGAGCAATGCCACCG
->FBgn0063507_G2|1906|R|27|n=1
-TTCCGTGGGATCGCCTGAAGCCAAACT
->FBgn0063507_G2|1906|R|27|n=1
-TTTCGTGGGATCGCCTGAAGCCAAACT
->FBgn0063507_G2|1908|R|25|n=3
-TTCCGTGGGATCGCCTGAAGCCAAA
->FBgn0063534_Doc2-element|342|F|25|n=1
-TTGCAACGAAACAACGCGTACTTCT
->FBgn0063534_Doc2-element|327|R|25|n=1
+>FBgn0063534_Doc2-element|coord=327|strand -|size=25|nreads=1
 TTCGTTGCAATGAGAGCCGGCGATC
->FBgn0063534_Doc2-element|3623|F|23|n=1
-TTCGCAAAAATCACGGAACGATC
->FBgn0063534_Doc2-element|3605|R|28|n=1
+>FBgn0063534_Doc2-element|coord=342|strand +|size=25|nreads=1
+TTGCAACGAAACAACGCGTACTTCT
+>FBgn0063534_Doc2-element|coord=3605|strand -|size=28|nreads=1
 TTTTTGCGAAAGCCAAACTGATGCGATG
->FBgn0063534_Doc2-element|3606|R|27|n=2
+>FBgn0063534_Doc2-element|coord=3606|strand -|size=27|nreads=2
 TTTTTGCGAAAGCCAAACTGATGCGAT
->FBgn0063534_Doc2-element|3607|R|26|n=4
+>FBgn0063534_Doc2-element|coord=3607|strand -|size=26|nreads=4
 TTTTTGCGAAAGCCAAACTGATGCGA
->FBgn0063534_Doc2-element|3608|R|25|n=7
+>FBgn0063534_Doc2-element|coord=3608|strand -|size=25|nreads=7
 TTTTTGCGAAAGCCAAACTGATGCG
->FBgn0063534_Doc2-element|3609|R|24|n=1
+>FBgn0063534_Doc2-element|coord=3609|strand -|size=24|nreads=1
 TTTTTGCGAAAGCCAAACTGATGC
->FBgn0063534_Doc2-element|3610|R|23|n=3
+>FBgn0063534_Doc2-element|coord=3610|strand -|size=23|nreads=3
 TTTTTGCGAAAGCCAAACTGATG
->FBgn0063534_Doc2-element|3623|F|26|n=1
+>FBgn0063534_Doc2-element|coord=3623|strand +|size=23|nreads=1
+TTCGCAAAAATCACGGAACGATC
+>FBgn0063534_Doc2-element|coord=3623|strand +|size=26|nreads=1
 TTCGCAAAAATCACGGAACGATCGAA
->FBgn0063594_Cr1a|2054|F|24|n=2
-TTTGTAACAAGTCCTGAAAGTGTG
->FBgn0063594_Cr1a|2037|R|27|n=1
+>FBgn0063594_Cr1a|coord=2037|strand -|size=27|nreads=1
 TTGTTACAAGACATAGATCCAACAGTC
->FBgn0063594_Cr1a|2039|R|25|n=1
+>FBgn0063594_Cr1a|coord=2039|strand -|size=25|nreads=1
 TTGTTACAAAACATAGATCCAACAG
->FBgn0063919_Max-element|3898|F|23|n=1
-TTCTCAGCAAGTTCTGGGAGGTG
->FBgn0063919_Max-element|3879|R|29|n=1
+>FBgn0063594_Cr1a|coord=2054|strand +|size=24|nreads=2
+TTTGTAACAAGTCCTGAAAGTGTG
+>FBgn0063919_Max-element|coord=3879|strand -|size=29|nreads=1
 TTGCTGAGAAGCGTGTTGAGCGAATCAGG
->FBgn0063919_Max-element|3880|R|28|n=1
+>FBgn0063919_Max-element|coord=3880|strand -|size=28|nreads=1
 TTGCTGAGAAGCGTGTCGAGCGAATCAG
->FBgn0063919_Max-element|3880|R|28|n=1
+>FBgn0063919_Max-element|coord=3880|strand -|size=28|nreads=1
 TTGCTGAGAAGCGTGTTGAGCGAATCAG
->FBgn0063919_Max-element|3882|R|26|n=1
+>FBgn0063919_Max-element|coord=3882|strand -|size=26|nreads=1
 TTGCTGAGAAGCGTGTCGAGCGAATC
->FBgn0063919_Max-element|3883|R|25|n=1
+>FBgn0063919_Max-element|coord=3883|strand -|size=25|nreads=1
 TTGCTGAGAAGCGTGTCGAGCGAAT
->FBgn0063919_Max-element|3884|R|24|n=1
+>FBgn0063919_Max-element|coord=3884|strand -|size=24|nreads=1
 TTGCTGAGAAGCGTGTTGAGCGAA
->FBgn0063919_Max-element|3898|F|24|n=2
-TTCTCAGCAAGTTCTGGGAGGTGG
->FBgn0063919_Max-element|3898|F|25|n=1
-TTCTCAGCAAGTTCTGGGAGGTGGA
->FBgn0063919_Max-element|3898|F|24|n=1
+>FBgn0063919_Max-element|coord=3898|strand +|size=23|nreads=1
+TTCTCAGCAAGTTCTGGGAGGTG
+>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=1
 TTCTCAGCAAGTTCTGGGAGGTGT
->FBgn0067385_invader6|3024|F|26|n=1
-TTGACTAGAATGACTTAGACTTAGAA
->FBgn0067385_invader6|3007|R|27|n=4
+>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=2
+TTCTCAGCAAGTTCTGGGAGGTGG
+>FBgn0063919_Max-element|coord=3898|strand +|size=25|nreads=1
+TTCTCAGCAAGTTCTGGGAGGTGGA
+>FBgn0067385_invader6|coord=3007|strand -|size=27|nreads=4
 TTCTAGTCAAAGTCGAAGGACTGCATA
->FBgn0067385_invader6|3008|R|26|n=3
+>FBgn0067385_invader6|coord=3008|strand -|size=26|nreads=3
 TTCTAGTCAAAGTCGAAGGACTGCAT
->FBgn0067385_invader6|3009|R|25|n=5
+>FBgn0067385_invader6|coord=3009|strand -|size=25|nreads=5
 TTCTAGTCAAAGTCGAAGGACTGCA
->FBgn0067385_invader6|3010|R|24|n=4
+>FBgn0067385_invader6|coord=3010|strand -|size=24|nreads=4
 TTCTAGTCAAAGTCGAAGGACTGC
->FBgn0067385_invader6|3011|R|23|n=1
+>FBgn0067385_invader6|coord=3011|strand -|size=23|nreads=1
 TTCTAGTCAAAGTCGAAGGACTG
->FBgn0067624_BS3|1026|F|26|n=1
-TTGGCATCAATGGTGACAAATCAGCG
->FBgn0067624_BS3|1011|R|25|n=3
+>FBgn0067385_invader6|coord=3024|strand +|size=26|nreads=1
+TTGACTAGAATGACTTAGACTTAGAA
+>FBgn0067624_BS3|coord=1011|strand -|size=25|nreads=3
 TTGATGCCAATGTTCCAGCGTTTTG
->FBgn0067624_BS3|1013|R|23|n=3
+>FBgn0067624_BS3|coord=1013|strand -|size=23|nreads=3
 TTGATGCCAATGTTCCAACGTCT
->FBgn0067624_BS3|1026|F|24|n=1
+>FBgn0067624_BS3|coord=1026|strand +|size=24|nreads=1
 TTGGCATCAATGGTGACAAATCTG
->FBgn0067624_BS3|1026|F|25|n=1
+>FBgn0067624_BS3|coord=1026|strand +|size=25|nreads=1
 TTGGCATCAATGGTGACAAATCTGC
+>FBgn0067624_BS3|coord=1026|strand +|size=26|nreads=1
+TTGGCATCAATGGTGACAAATCAGCG
--- a/test-data/paired_2.fa	Fri Sep 08 04:44:22 2017 -0400
+++ b/test-data/paired_2.fa	Sat Sep 09 11:57:39 2017 -0400
@@ -1,370 +1,416 @@
->FBgn0000004_17.6|5844|R|21|n=1
+>FBgn0000004_17.6|coord=5844|strand -|size=21|nreads=1
 TTTTCGTCAAGTGTGCTAAAT
->FBgn0000004_17.6|5855|F|23|n=1
+>FBgn0000004_17.6|coord=5855|strand +|size=23|nreads=1
 TTGACGAAAATGATCGAGTGGAT
->FBgn0000005_297|1347|F|21|n=1
+>FBgn0000005_297|coord=1334|strand -|size=23|nreads=1
+TTTTGCGCAATGGTAATTAAGGA
+>FBgn0000005_297|coord=1347|strand +|size=21|nreads=1
 TTGCACAAAATGAGGGAATTT
->FBgn0000005_297|1334|R|23|n=1
-TTTTGCGCAATGGTAATTAAGGA
->FBgn0000007_1731|4545|R|20|n=1
+>FBgn0000007_1731|coord=4545|strand -|size=20|nreads=1
 TTGAGAGCAAAGGCCGAATG
->FBgn0000007_1731|4555|F|24|n=1
+>FBgn0000007_1731|coord=4555|strand +|size=24|nreads=1
 TTGCTCTCAATGCGCTGAGTTTGG
->FBgn0000155_roo|2682|R|20|n=2
+>FBgn0000155_roo|coord=2682|strand -|size=20|nreads=2
 TTTTTACCAAACGGATGCCT
->FBgn0000155_roo|2692|F|24|n=1
+>FBgn0000155_roo|coord=2692|strand +|size=24|nreads=1
 TTGGTAAAAAATGTATAAGTGAGC
->FBgn0000155_roo|2692|F|27|n=1
+>FBgn0000155_roo|coord=2692|strand +|size=27|nreads=1
 TTGGTAAAAAATGTATAAGTGAGCAGC
->FBgn0000155_roo|3241|F|20|n=1
-TTGGGCAAAAAACTGATTTC
->FBgn0000155_roo|3225|R|26|n=1
+>FBgn0000155_roo|coord=3225|strand -|size=26|nreads=1
 TTTTGCCCAAGGAGACCGTCTATTTT
->FBgn0000155_roo|3226|R|25|n=1
+>FBgn0000155_roo|coord=3226|strand -|size=25|nreads=1
 TTTTGCCCAAGGAGACCGTCTATTT
->FBgn0000155_roo|3227|R|24|n=2
+>FBgn0000155_roo|coord=3227|strand -|size=24|nreads=2
 TTTTGCCCAAGGAGACCGTCTATT
->FBgn0000155_roo|3228|R|23|n=1
+>FBgn0000155_roo|coord=3228|strand -|size=23|nreads=1
 TTTTGCCCAAGGAGACCGTCTAT
->FBgn0000155_roo|3229|R|22|n=2
+>FBgn0000155_roo|coord=3229|strand -|size=22|nreads=2
 TTTTGCCCAAGGAGACCGTCTA
->FBgn0000155_roo|3241|F|24|n=1
+>FBgn0000155_roo|coord=3230|strand -|size=21|nreads=1
+TTTTGCCCAAGGAGACCGTCT
+>FBgn0000155_roo|coord=3231|strand -|size=20|nreads=2
+TTTTGCCCAAGGAGACCGTC
+>FBgn0000155_roo|coord=3241|strand +|size=20|nreads=1
+TTGGGCAAAAAACTGATTTC
+>FBgn0000155_roo|coord=3241|strand +|size=24|nreads=1
 TTGGGCAAAAAACTGATTTCGGGT
->FBgn0000155_roo|3241|F|27|n=1
+>FBgn0000155_roo|coord=3241|strand +|size=27|nreads=1
 TTGGGCAAAAAACTGATTTCGGGTGGA
->FBgn0000155_roo|3241|F|28|n=1
+>FBgn0000155_roo|coord=3241|strand +|size=28|nreads=1
 TTGGGCAAAAAACTGATTTCGGGTGGAT
->FBgn0000155_roo|8644|R|21|n=1
+>FBgn0000155_roo|coord=8644|strand -|size=21|nreads=1
 TTCTGCCAAAGGGCCAGCAAG
->FBgn0000155_roo|8655|F|25|n=1
+>FBgn0000155_roo|coord=8645|strand -|size=20|nreads=1
+TTCTGCCAAAGGGCCAGCAA
+>FBgn0000155_roo|coord=8655|strand +|size=25|nreads=1
 TTTGGCAGAATGTTCACACATGAAA
->FBgn0000349_copia|658|R|22|n=1
+>FBgn0000349_copia|coord=658|strand -|size=22|nreads=1
 TTCTCAAGAATCTGACGCGCCG
->FBgn0000349_copia|670|F|25|n=1
+>FBgn0000349_copia|coord=670|strand +|size=25|nreads=1
 TTCTTGAGAATTTGGACGCCGTTTA
->FBgn0000349_copia|4628|F|20|n=1
+>FBgn0000349_copia|coord=4614|strand -|size=24|nreads=1
+TTGCAGCAAACCCAATTTGTCTCG
+>FBgn0000349_copia|coord=4628|strand +|size=20|nreads=1
 TTTGCTGCAAGACGACCAAT
->FBgn0000349_copia|4614|R|24|n=1
-TTGCAGCAAACCCAATTTGTCTCG
->FBgn0000652_F-element|1564|F|20|n=2
-TTTTCTCGAAAGCAGCAAGT
->FBgn0000652_F-element|1546|R|28|n=1
+>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1
 TTCGAGAAAATTACTTCAGGATTTGTCT
->FBgn0000652_F-element|1546|R|28|n=1
+>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1
 TTCGGGAAAATTACTTCAGGATTTGTCT
->FBgn0000652_F-element|1547|R|27|n=74
+>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1
+TTCGGGAAAATTACTTCAGGATTTGTC
+>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1
+TTTGAGAAAATTACTTCAGGATTTGTC
+>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=74
 TTCGAGAAAATTACTTCAGGATTTGTC
->FBgn0000652_F-element|1547|R|27|n=1
-TTCGGGAAAATTACTTCAGGATTTGTC
->FBgn0000652_F-element|1547|R|27|n=1
-TTTGAGAAAATTACTTCAGGATTTGTC
->FBgn0000652_F-element|1548|R|26|n=3
+>FBgn0000652_F-element|coord=1548|strand -|size=26|nreads=3
 TTCGAGAAAATTACTTCAGGATTTGT
->FBgn0000652_F-element|1549|R|25|n=22
+>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=1
+TTCGGGAAAATTACTTCAGGATTTG
+>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=22
 TTCGAGAAAATTACTTCAGGATTTG
->FBgn0000652_F-element|1549|R|25|n=1
-TTCGGGAAAATTACTTCAGGATTTG
->FBgn0000652_F-element|1550|R|24|n=2
+>FBgn0000652_F-element|coord=1550|strand -|size=24|nreads=2
 TTCGAGAAAATTACTTCAGGATTT
->FBgn0000652_F-element|1551|R|23|n=7
+>FBgn0000652_F-element|coord=1551|strand -|size=23|nreads=7
 TTCGAGAAAATTACTTCAGGATT
->FBgn0000652_F-element|1554|R|20|n=1
+>FBgn0000652_F-element|coord=1554|strand -|size=20|nreads=1
 TTCGAGAAAATTACTTCAGG
->FBgn0000652_F-element|1564|F|23|n=2
+>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=1
+TTTTCTCGAAAGCAGCTAGT
+>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=2
+TTTTCTCGAAAGCAGCAAGT
+>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2
 TTTTCTCGAAAGCAGCAAGTTTC
->FBgn0000652_F-element|1564|F|24|n=2
+>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2
+TTTTCTCGAAAGCAGCTAGTTTC
+>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=2
 TTTTCTCGAAAGCAGCAAGTTTCG
->FBgn0000652_F-element|1564|F|23|n=2
-TTTTCTCGAAAGCAGCTAGTTTC
->FBgn0000652_F-element|1564|F|24|n=5
+>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=5
 TTTTCTCGAAAGCAGCTAGTTTCG
->FBgn0000652_F-element|1564|F|25|n=1
+>FBgn0000652_F-element|coord=1564|strand +|size=25|nreads=1
 TTTTCTCGAAAGCAGCTAGTTTCGC
->FBgn0000652_F-element|2248|F|20|n=1
-TTTCTTCCAAGCACTAGGGC
->FBgn0000652_F-element|2231|R|27|n=1
+>FBgn0000652_F-element|coord=2231|strand -|size=27|nreads=1
 TTGGAAGAAATCCAGGAATTGAGCTTC
->FBgn0000652_F-element|2233|R|25|n=5
+>FBgn0000652_F-element|coord=2233|strand -|size=25|nreads=5
 TTGGAAGAAATCCAGGAATTGAGCT
->FBgn0000652_F-element|2471|R|21|n=2
+>FBgn0000652_F-element|coord=2248|strand +|size=20|nreads=1
+TTTCTTCCAAGCACTAGGGC
+>FBgn0000652_F-element|coord=2248|strand +|size=21|nreads=1
+TTTCTTCCAAGCACTAGGGCC
+>FBgn0000652_F-element|coord=2471|strand -|size=21|nreads=2
 TTTAACCAAACTGCGGGAAAT
->FBgn0000652_F-element|2482|F|23|n=2
+>FBgn0000652_F-element|coord=2472|strand -|size=20|nreads=1
+TTTAACCAAACTGCGGGAAA
+>FBgn0000652_F-element|coord=2482|strand +|size=23|nreads=2
 TTTGGTTAAAGCTGAATGTCTGC
->FBgn0000652_F-element|2482|F|24|n=2
+>FBgn0000652_F-element|coord=2482|strand +|size=24|nreads=2
 TTTGGTTAAAGCTGAATGTCTGCC
->FBgn0000652_F-element|2482|F|26|n=3
+>FBgn0000652_F-element|coord=2482|strand +|size=26|nreads=3
 TTTGGTTAAAGCTGAATGTCTGCCGG
->FBgn0000652_F-element|2482|F|27|n=1
+>FBgn0000652_F-element|coord=2482|strand +|size=27|nreads=1
 TTTGGTTAAAGCTGAATGTCTGCCGGA
->FBgn0000652_F-element|3524|F|21|n=2
-TTTCGCGAAAGCCACGGAACC
->FBgn0000652_F-element|3507|R|27|n=1
+>FBgn0000652_F-element|coord=3507|strand -|size=27|nreads=1
 TTTCGCGAAATCCAAATTGGTGGGCTG
->FBgn0000652_F-element|3509|R|25|n=6
+>FBgn0000652_F-element|coord=3509|strand -|size=25|nreads=6
 TTTCGCGAAATCCAAATTGGTGGGC
->FBgn0000652_F-element|3510|R|24|n=1
+>FBgn0000652_F-element|coord=3510|strand -|size=24|nreads=1
 TTTCGCGAAATCCAAATTGGTGGG
->FBgn0000652_F-element|3513|R|21|n=3
+>FBgn0000652_F-element|coord=3513|strand -|size=21|nreads=3
 TTTCGCGAAATCCAAATTGGT
->FBgn0000652_F-element|3524|F|23|n=1
+>FBgn0000652_F-element|coord=3524|strand +|size=20|nreads=2
+TTTCGCGAAAGCCATGGAAC
+>FBgn0000652_F-element|coord=3524|strand +|size=21|nreads=2
+TTTCGCGAAAGCCACGGAACC
+>FBgn0000652_F-element|coord=3524|strand +|size=22|nreads=1
+TTTCGCGAAAGCCACGGAACCA
+>FBgn0000652_F-element|coord=3524|strand +|size=23|nreads=1
 TTTCGCGAAAGCCACGGAACCAT
->FBgn0000652_F-element|3524|F|27|n=1
-TTTCGCGAAAGCCACGGAACCATTGAA
->FBgn0000652_F-element|3524|F|24|n=1
+>FBgn0000652_F-element|coord=3524|strand +|size=24|nreads=1
 TTTCGCGAAAGCCATGGAACCATT
->FBgn0000652_F-element|3524|F|26|n=1
+>FBgn0000652_F-element|coord=3524|strand +|size=26|nreads=1
 TTTCGCGAAAGCCATGGAACCATTGA
->FBgn0002697_mdg1|4301|R|22|n=1
+>FBgn0000652_F-element|coord=3524|strand +|size=27|nreads=1
+TTTCGCGAAAGCCACGGAACCATTGAA
+>FBgn0002697_mdg1|coord=4301|strand -|size=22|nreads=1
 TTCTTTGGAAAGAATTTGGGGC
->FBgn0002697_mdg1|4313|F|25|n=1
+>FBgn0002697_mdg1|coord=4302|strand -|size=21|nreads=1
+TTCTTTGGAAAGAATTTGGGG
+>FBgn0002697_mdg1|coord=4303|strand -|size=20|nreads=1
+TTCTTTGGAAAGAATTTGGG
+>FBgn0002697_mdg1|coord=4313|strand +|size=25|nreads=1
 TTCCAAAGAATGATGACCCTTGCAT
->FBgn0003007_opus|5558|F|21|n=1
-TTCCTAGAAATTTATCGTTGC
->FBgn0003007_opus|5540|R|28|n=1
+>FBgn0003007_opus|coord=5540|strand -|size=28|nreads=1
 TTTCTAGGAACGTAGAATGGAATCTCTC
->FBgn0003007_opus|5540|R|28|n=1
+>FBgn0003007_opus|coord=5540|strand -|size=28|nreads=1
 TTTCTAGGAACGTAGAGTGGAATCTCTC
->FBgn0003007_opus|5542|R|26|n=1
+>FBgn0003007_opus|coord=5542|strand -|size=26|nreads=1
 TTTCTAGGAACGTAGAATGGAATCTC
->FBgn0003007_opus|5542|R|26|n=2
+>FBgn0003007_opus|coord=5542|strand -|size=26|nreads=2
 TTTCTAGGAACGTAGAGTGGAATCTC
->FBgn0003007_opus|5543|R|25|n=1
+>FBgn0003007_opus|coord=5543|strand -|size=25|nreads=1
 TTTCTAGGAACGTAGAGTGGAATCT
->FBgn0003007_opus|5544|R|24|n=7
+>FBgn0003007_opus|coord=5544|strand -|size=24|nreads=7
 TTTCTAGGAACGTAGAGTGGAATC
->FBgn0003122_pogo|1819|F|22|n=1
-TTCTATGGAAGACAAGCTGTTT
->FBgn0003122_pogo|1804|R|25|n=1
+>FBgn0003007_opus|coord=5558|strand +|size=21|nreads=1
+TTCCTAGAAATTTATCGTTGC
+>FBgn0003122_pogo|coord=1804|strand -|size=25|nreads=1
 TTCCATAGAATTCAAGTTTTGCAAA
->FBgn0003122_pogo|1806|R|23|n=1
+>FBgn0003122_pogo|coord=1806|strand -|size=23|nreads=1
 TTCCATAGAATTCAAGTTTTGCA
->FBgn0003908_R1A1-element|4690|F|22|n=1
-TTGGCGAAAACTAGATCTTCGA
->FBgn0003908_R1A1-element|4671|R|29|n=1
+>FBgn0003122_pogo|coord=1819|strand +|size=22|nreads=1
+TTCTATGGAAGACAAGCTGTTT
+>FBgn0003908_R1A1-element|coord=4671|strand -|size=29|nreads=1
 TTTTCGCCAAGGCGCTGCACTCCAAGTCC
->FBgn0003908_R1A1-element|4672|R|28|n=8
+>FBgn0003908_R1A1-element|coord=4672|strand -|size=28|nreads=8
 TTTTCGCCAAGGCGCTGCACTCCAAGTC
->FBgn0003908_R1A1-element|4673|R|27|n=1
+>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=1
 TTTTCGCCAAGGCGCTGCACCCCAAGT
->FBgn0003908_R1A1-element|4673|R|27|n=4
+>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=4
 TTTTCGCCAAGGCGCTGCACTCCAAGT
->FBgn0003908_R1A1-element|4674|R|26|n=1
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1
 TTTTCGCCAAGGCGCTGCACCCCAAG
->FBgn0003908_R1A1-element|4674|R|26|n=29
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1
+TTTTCGTCAAGGCGCTGCACTCCAAG
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=2
+TTTTCGCCAAGGCGCTGCACTTCAAG
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=29
 TTTTCGCCAAGGCGCTGCACTCCAAG
->FBgn0003908_R1A1-element|4674|R|26|n=2
-TTTTCGCCAAGGCGCTGCACTTCAAG
->FBgn0003908_R1A1-element|4674|R|26|n=1
-TTTTCGTCAAGGCGCTGCACTCCAAG
->FBgn0003908_R1A1-element|4675|R|25|n=1
+>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1
 TTTTCGCCAAGGCGCTGCACCCCAA
->FBgn0003908_R1A1-element|4675|R|25|n=10
+>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1
+TTTTCGCCAAGGCGCTGCACTTCAA
+>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=10
 TTTTCGCCAAGGCGCTGCACTCCAA
->FBgn0003908_R1A1-element|4675|R|25|n=1
-TTTTCGCCAAGGCGCTGCACTTCAA
->FBgn0003908_R1A1-element|4676|R|24|n=21
+>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=2
+TTTTCGCCAAGGCGCTGCACTTCA
+>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=21
 TTTTCGCCAAGGCGCTGCACTCCA
->FBgn0003908_R1A1-element|4676|R|24|n=2
-TTTTCGCCAAGGCGCTGCACTTCA
->FBgn0003908_R1A1-element|4677|R|23|n=12
+>FBgn0003908_R1A1-element|coord=4677|strand -|size=23|nreads=12
 TTTTCGCCAAGGCGCTGCACTCC
->FBgn0003908_R1A1-element|4678|R|22|n=18
+>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=1
+TTTTCGCCAAGGCGCTGCACTT
+>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=18
 TTTTCGCCAAGGCGCTGCACTC
->FBgn0003908_R1A1-element|4690|F|23|n=8
+>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=1
+TTTTCGCCAAGGCGCTGCACC
+>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=6
+TTTTCGCCAAGGCGCTGCACT
+>FBgn0003908_R1A1-element|coord=4680|strand -|size=20|nreads=4
+TTTTCGCCAAGGCGCTGCAC
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=20|nreads=2
+TTGGCGAAAACTGGATCTTC
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=21|nreads=6
+TTGGCGAAAACTGGATCTTCG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=1
+TTGGCGAAAACTAGATCTTCGA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=8
+TTGGCGAAAACTGGATCTTCGA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=23|nreads=8
 TTGGCGAAAACTGGATCTTCGAG
->FBgn0003908_R1A1-element|4690|F|24|n=9
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=7
+TTGGCGAAAACTGGATCTTCGAGG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=9
 TTGGCGAAAACTGGATCTTCGAGA
->FBgn0003908_R1A1-element|4690|F|25|n=11
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=11
 TTGGCGAAAACTGGATCTTCGAGAG
->FBgn0003908_R1A1-element|4690|F|26|n=6
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=12
+TTGGCGAAAACTGGATCTTCGAGGG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=2
+TTGGCGAAAACTGGATCTTCGAGGGA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=6
 TTGGCGAAAACTGGATCTTCGAGAGA
->FBgn0003908_R1A1-element|4690|F|27|n=20
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=20
 TTGGCGAAAACTGGATCTTCGAGAGAA
->FBgn0003908_R1A1-element|4690|F|28|n=4
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=9
+TTGGCGAAAACTGGATCTTCGAGGGAA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=1
+TTGGCGAAAACTGGATCTTCGAGGGAAT
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=4
 TTGGCGAAAACTGGATCTTCGAGAGAAT
->FBgn0003908_R1A1-element|4690|F|24|n=7
-TTGGCGAAAACTGGATCTTCGAGG
->FBgn0003908_R1A1-element|4690|F|25|n=12
-TTGGCGAAAACTGGATCTTCGAGGG
->FBgn0003908_R1A1-element|4690|F|26|n=2
-TTGGCGAAAACTGGATCTTCGAGGGA
->FBgn0003908_R1A1-element|4690|F|27|n=9
-TTGGCGAAAACTGGATCTTCGAGGGAA
->FBgn0003908_R1A1-element|4690|F|28|n=1
-TTGGCGAAAACTGGATCTTCGAGGGAAT
->FBgn0005673_1360|773|R|22|n=1
+>FBgn0005673_1360|coord=773|strand -|size=22|nreads=1
 TTTTCGCAATCATTCCATCCTG
->FBgn0005673_1360|785|F|26|n=6
+>FBgn0005673_1360|coord=785|strand +|size=26|nreads=6
 TTTGCGAAAAATTGTTTGCTCAGAGC
->FBgn0005673_1360|3197|R|22|n=1
+>FBgn0005673_1360|coord=3197|strand -|size=22|nreads=1
 TTTGCTAGAAGACGATTTTCGG
->FBgn0005673_1360|3209|F|23|n=1
+>FBgn0005673_1360|coord=3209|strand +|size=23|nreads=1
 TTCTAGCACAACACGCACACATA
->FBgn0005673_1360|3209|F|26|n=1
+>FBgn0005673_1360|coord=3209|strand +|size=26|nreads=1
 TTCTAGCACAACACGCACACATATAC
->FBgn0005673_1360|3209|F|27|n=1
+>FBgn0005673_1360|coord=3209|strand +|size=27|nreads=1
 TTCTAGCACAACACGCACACATATACG
->FBgn0010302_Burdock|3390|R|21|n=1
+>FBgn0010302_Burdock|coord=3390|strand -|size=21|nreads=1
 TTTCATCGAAAGAAATTGGTA
->FBgn0010302_Burdock|3401|F|25|n=2
+>FBgn0010302_Burdock|coord=3401|strand +|size=25|nreads=2
 TTCGATGAAAGACAATGTTCTGCTT
->FBgn0014947_flea|818|F|22|n=1
-TTCTAGAGAACGAAAGCGAGGA
->FBgn0014947_flea|801|R|27|n=4
+>FBgn0014947_flea|coord=801|strand -|size=27|nreads=4
 TTCTCTAGAATTGCTTGTATTTGGTCG
->FBgn0014947_flea|802|R|26|n=11
+>FBgn0014947_flea|coord=802|strand -|size=26|nreads=11
 TTCTCTAGAATTGCTTGTATTTGGTC
->FBgn0014947_flea|803|R|25|n=12
+>FBgn0014947_flea|coord=803|strand -|size=25|nreads=12
 TTCTCTAGAATTGCTTGTATTTGGT
->FBgn0014947_flea|804|R|24|n=2
+>FBgn0014947_flea|coord=804|strand -|size=24|nreads=2
 TTCTCTAGAATTGCTTGTATTTGG
->FBgn0014947_flea|805|R|23|n=1
+>FBgn0014947_flea|coord=805|strand -|size=23|nreads=1
 TTCTCTAGAATTGCTTGTATTTG
->FBgn0014947_flea|1182|F|22|n=1
-TTTCTTAGAATCTGAATGTGTC
->FBgn0014947_flea|1164|R|28|n=2
+>FBgn0014947_flea|coord=818|strand +|size=22|nreads=1
+TTCTAGAGAACGAAAGCGAGGA
+>FBgn0014947_flea|coord=1164|strand -|size=28|nreads=2
 TTCTAAGAAAAGTTCTGCTGATCCAATC
->FBgn0014947_flea|1166|R|26|n=2
+>FBgn0014947_flea|coord=1166|strand -|size=26|nreads=2
 TTCTAAGAAAAGTTCTGCTGATCCAA
->FBgn0014947_flea|1167|R|25|n=1
+>FBgn0014947_flea|coord=1167|strand -|size=25|nreads=1
 TTCTAAGAAAAGTTCTGCTGATCCA
->FBgn0014947_flea|1168|R|24|n=1
+>FBgn0014947_flea|coord=1168|strand -|size=24|nreads=1
 TTCTAAGAAAAGTTCTGCTGATCC
->FBgn0014947_flea|1169|R|23|n=1
+>FBgn0014947_flea|coord=1169|strand -|size=23|nreads=1
 TTCTAAGAAAAGTTCTGCTGATC
->FBgn0014947_flea|2754|R|21|n=1
+>FBgn0014947_flea|coord=1182|strand +|size=22|nreads=1
+TTTCTTAGAATCTGAATGTGTC
+>FBgn0014947_flea|coord=2754|strand -|size=21|nreads=1
 TTTAGACCAAATTCTGCAGCT
->FBgn0014947_flea|2765|F|24|n=4
+>FBgn0014947_flea|coord=2765|strand +|size=24|nreads=4
 TTGGTCTAAAAATAAAATGGAAGA
->FBgn0014947_flea|2765|F|25|n=1
+>FBgn0014947_flea|coord=2765|strand +|size=25|nreads=1
 TTGGTCTAAAAATAAAATGGAAGAA
->FBgn0014947_flea|2765|F|26|n=1
+>FBgn0014947_flea|coord=2765|strand +|size=26|nreads=1
 TTGGTCTAAAAATAAAATGGAAGAAG
->FBgn0014947_flea|2765|F|28|n=1
+>FBgn0014947_flea|coord=2765|strand +|size=28|nreads=1
 TTGGTCTAAAAATAAAATGGAAGAAGTG
->FBgn0015945_GATE|3158|F|20|n=3
-TTCGTTCCAAATGAGCAAGC
->FBgn0015945_GATE|3140|R|28|n=9
+>FBgn0015945_GATE|coord=3140|strand -|size=28|nreads=9
 TTGGAACGAAATTGGCCTGATTAGCGGA
->FBgn0015945_GATE|3141|R|27|n=4
+>FBgn0015945_GATE|coord=3141|strand -|size=27|nreads=4
 TTGGAACGAAATTGGCCTGATTAGCGG
->FBgn0015945_GATE|3142|R|26|n=17
+>FBgn0015945_GATE|coord=3142|strand -|size=26|nreads=17
 TTGGAACGAAATTGGCCTGATTAGCG
->FBgn0015945_GATE|3143|R|25|n=86
+>FBgn0015945_GATE|coord=3143|strand -|size=25|nreads=86
 TTGGAACGAAATTGGCCTGATTAGC
->FBgn0015945_GATE|3144|R|24|n=17
+>FBgn0015945_GATE|coord=3144|strand -|size=24|nreads=17
 TTGGAACGAAATTGGCCTGATTAG
->FBgn0015945_GATE|6234|R|22|n=1
+>FBgn0015945_GATE|coord=3158|strand +|size=20|nreads=3
+TTCGTTCCAAATGAGCAAGC
+>FBgn0015945_GATE|coord=3158|strand +|size=21|nreads=1
+TTCGTTCCAAATGAGCAAGCC
+>FBgn0015945_GATE|coord=3158|strand +|size=22|nreads=2
+TTCGTTCCAAATGAGCAAGCCG
+>FBgn0015945_GATE|coord=6234|strand -|size=22|nreads=1
 TTGAAGGAAATCGCGGGAAAGC
->FBgn0015945_GATE|6246|F|25|n=1
+>FBgn0015945_GATE|coord=6246|strand +|size=25|nreads=1
 TTTCCTTCAAGCCGTAAAAGAGTCG
->FBgn0015945_GATE|6246|F|26|n=1
+>FBgn0015945_GATE|coord=6246|strand +|size=26|nreads=1
 TTTCCTTCAAGCCGTAAAAGAGTCGG
->FBgn0042682_Rt1b|1075|R|21|n=1
+>FBgn0042682_Rt1b|coord=1075|strand -|size=21|nreads=1
 TTCTTGGCGACAGATGCGTAG
->FBgn0042682_Rt1b|1086|F|23|n=1
+>FBgn0042682_Rt1b|coord=1076|strand -|size=20|nreads=1
+TTCTTGGCGACAGATGCGTA
+>FBgn0042682_Rt1b|coord=1086|strand +|size=23|nreads=1
 TTGCCAAGAATGCTAGCACGGGT
->FBgn0042682_Rt1b|2920|F|22|n=1
-TTGTTACCAAAAAGCTAAGGAG
->FBgn0042682_Rt1b|2902|R|28|n=1
+>FBgn0042682_Rt1b|coord=2902|strand -|size=28|nreads=1
 TTGGTAACAAGCTTGTAGGCGAGGCCCC
->FBgn0042682_Rt1b|2903|R|27|n=1
+>FBgn0042682_Rt1b|coord=2903|strand -|size=27|nreads=1
 TTGGTAACAAGCTTGTAGGCGAGGCCC
->FBgn0042682_Rt1b|2904|R|26|n=2
-TTGGTAACAAGCTTGTAGGCGAGGCC
->FBgn0042682_Rt1b|2904|R|26|n=1
+>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=1
 TTGGTAACAAGCTTGTAGGCGAGTCC
->FBgn0042682_Rt1b|2905|R|25|n=2
-TTGGTAACAAGCTTGTAGGCGAGGC
->FBgn0042682_Rt1b|2905|R|25|n=1
+>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=2
+TTGGTAACAAGCTTGTAGGCGAGGCC
+>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=1
 TTGGTAACAAGCTTGTAGGCGAGGT
->FBgn0042682_Rt1b|2906|R|24|n=25
+>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=2
+TTGGTAACAAGCTTGTAGGCGAGGC
+>FBgn0042682_Rt1b|coord=2906|strand -|size=24|nreads=25
 TTGGTAACAAGCTTGTAGGCGAGG
->FBgn0042682_Rt1b|2907|R|23|n=1
+>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=1
 TTGGTAACAAGCTTGGAGGCGAG
->FBgn0042682_Rt1b|2907|R|23|n=15
+>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=15
 TTGGTAACAAGCTTGTAGGCGAG
->FBgn0042682_Rt1b|2908|R|22|n=1
+>FBgn0042682_Rt1b|coord=2908|strand -|size=22|nreads=1
 TTGGTAACAAGCTTGTAGGCGA
->FBgn0042682_Rt1b|2920|F|23|n=1
+>FBgn0042682_Rt1b|coord=2909|strand -|size=21|nreads=6
+TTGGTAACAAGCTTGTAGGCG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=22|nreads=1
+TTGTTACCAAAAAGCTAAGGAG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1
 TTGTTACCAAAAAGCTAAGGAGG
->FBgn0042682_Rt1b|2920|F|25|n=1
-TTGTTACCAAAAAGCTAAGGAGGAG
->FBgn0042682_Rt1b|2920|F|26|n=1
-TTGTTACCAAAAAGCTAAGGAGGAGA
->FBgn0042682_Rt1b|2920|F|27|n=1
-TTGTTACCAAAAAGCTAAGGAGGAGAG
->FBgn0042682_Rt1b|2920|F|23|n=1
+>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1
 TTGTTACCAACAAGCTAAGGAGG
->FBgn0042682_Rt1b|2920|F|24|n=2
+>FBgn0042682_Rt1b|coord=2920|strand +|size=24|nreads=2
 TTGTTACCAACAAGCTAAGGAGGA
->FBgn0042682_Rt1b|4364|R|22|n=1
+>FBgn0042682_Rt1b|coord=2920|strand +|size=25|nreads=1
+TTGTTACCAAAAAGCTAAGGAGGAG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=26|nreads=1
+TTGTTACCAAAAAGCTAAGGAGGAGA
+>FBgn0042682_Rt1b|coord=2920|strand +|size=27|nreads=1
+TTGTTACCAAAAAGCTAAGGAGGAGAG
+>FBgn0042682_Rt1b|coord=4364|strand -|size=22|nreads=1
 TTGCCTGGAAGCGCCACTCCGC
->FBgn0042682_Rt1b|4376|F|24|n=1
+>FBgn0042682_Rt1b|coord=4365|strand -|size=21|nreads=1
+TTGCCTGGAAGCGCCACTCCG
+>FBgn0042682_Rt1b|coord=4366|strand -|size=20|nreads=4
+TTGCCTGGAAGCGCCACTCC
+>FBgn0042682_Rt1b|coord=4376|strand +|size=24|nreads=1
 TTCCAGGCAAGAGGCACACGAGTG
->FBgn0042682_Rt1b|4376|F|26|n=1
+>FBgn0042682_Rt1b|coord=4376|strand +|size=26|nreads=1
 TTCCAGGCAAGAGGCACACGAGTGGC
->FBgn0062343_Dm88|4210|R|21|n=1
+>FBgn0062343_Dm88|coord=4210|strand -|size=21|nreads=1
 TTGGTTAGAACATCTGCCATC
->FBgn0062343_Dm88|4221|F|24|n=1
+>FBgn0062343_Dm88|coord=4221|strand +|size=24|nreads=1
 TTCTAACCAAGAATTTGAATAGAT
->FBgn0063427_invader4|707|F|22|n=2
+>FBgn0063427_invader4|coord=691|strand -|size=26|nreads=15
+TTCCTACGAATCGCTGTATGAACAGT
+>FBgn0063427_invader4|coord=707|strand +|size=22|nreads=2
 TTCGTAGGAATGGAGACGTCGG
->FBgn0063427_invader4|691|R|26|n=15
-TTCCTACGAATCGCTGTATGAACAGT
->FBgn0063428_invader3|440|F|22|n=2
+>FBgn0063428_invader3|coord=425|strand -|size=25|nreads=1
+TTCTGGGGAAATGGCCTGCAGACGC
+>FBgn0063428_invader3|coord=427|strand -|size=23|nreads=1
+TTCTGGGGAAATGGCCTGCAGAC
+>FBgn0063428_invader3|coord=440|strand +|size=22|nreads=2
 TTCCCCAGAAACGCGTGGCGAT
->FBgn0063428_invader3|425|R|25|n=1
-TTCTGGGGAAATGGCCTGCAGACGC
->FBgn0063428_invader3|427|R|23|n=1
-TTCTGGGGAAATGGCCTGCAGAC
->FBgn0063430_invader1|2082|R|20|n=1
+>FBgn0063430_invader1|coord=2082|strand -|size=20|nreads=1
 TTTTATCGAACCAATAGAAC
->FBgn0063430_invader1|2092|F|24|n=1
+>FBgn0063430_invader1|coord=2092|strand +|size=24|nreads=1
 TTCGATAAAATGTCTAAGTATGTT
->FBgn0063430_invader1|2092|F|26|n=1
+>FBgn0063430_invader1|coord=2092|strand +|size=26|nreads=1
 TTCGATAAAATGTCTAAGTATGTTCG
->FBgn0063433_gypsy4|3058|F|22|n=1
+>FBgn0063433_gypsy4|coord=3040|strand -|size=28|nreads=1
+TTTTGAAGAACTTGGATTTTTCTTGAGA
+>FBgn0063433_gypsy4|coord=3044|strand -|size=24|nreads=1
+TTTTGAAGAACTTGGATTTTTCTT
+>FBgn0063433_gypsy4|coord=3058|strand +|size=22|nreads=1
 TTCTTCAAAAAGAGCGTGGAAT
->FBgn0063433_gypsy4|3040|R|28|n=1
-TTTTGAAGAACTTGGATTTTTCTTGAGA
->FBgn0063433_gypsy4|3044|R|24|n=1
-TTTTGAAGAACTTGGATTTTTCTT
->FBgn0063440_baggins|5170|F|21|n=1
+>FBgn0063440_baggins|coord=5154|strand -|size=26|nreads=1
+TTTTGTGCAAATGGCTGTGAAGTCGG
+>FBgn0063440_baggins|coord=5170|strand +|size=21|nreads=1
 TTGCACAAAATTGGCATTGCA
->FBgn0063440_baggins|5154|R|26|n=1
-TTTTGTGCAAATGGCTGTGAAGTCGG
->FBgn0063919_Max-element|3887|R|21|n=2
+>FBgn0063919_Max-element|coord=3887|strand -|size=21|nreads=2
 TTGCTGAGAAGCGTGTTGAGC
->FBgn0063919_Max-element|3898|F|23|n=1
+>FBgn0063919_Max-element|coord=3898|strand +|size=23|nreads=1
 TTCTCAGCAAGTTCTGGGAGGTG
->FBgn0063919_Max-element|3898|F|24|n=2
-TTCTCAGCAAGTTCTGGGAGGTGG
->FBgn0063919_Max-element|3898|F|25|n=1
-TTCTCAGCAAGTTCTGGGAGGTGGA
->FBgn0063919_Max-element|3898|F|24|n=1
+>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=1
 TTCTCAGCAAGTTCTGGGAGGTGT
->FBgn0067385_invader6|3024|F|21|n=1
-TTGACTAGAATGACTTAGACT
->FBgn0067385_invader6|3007|R|27|n=4
+>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=2
+TTCTCAGCAAGTTCTGGGAGGTGG
+>FBgn0063919_Max-element|coord=3898|strand +|size=25|nreads=1
+TTCTCAGCAAGTTCTGGGAGGTGGA
+>FBgn0067385_invader6|coord=3007|strand -|size=27|nreads=4
 TTCTAGTCAAAGTCGAAGGACTGCATA
->FBgn0067385_invader6|3008|R|26|n=3
+>FBgn0067385_invader6|coord=3008|strand -|size=26|nreads=3
 TTCTAGTCAAAGTCGAAGGACTGCAT
->FBgn0067385_invader6|3009|R|25|n=5
+>FBgn0067385_invader6|coord=3009|strand -|size=25|nreads=5
 TTCTAGTCAAAGTCGAAGGACTGCA
->FBgn0067385_invader6|3010|R|24|n=4
+>FBgn0067385_invader6|coord=3010|strand -|size=24|nreads=4
 TTCTAGTCAAAGTCGAAGGACTGC
->FBgn0067385_invader6|3011|R|23|n=1
+>FBgn0067385_invader6|coord=3011|strand -|size=23|nreads=1
 TTCTAGTCAAAGTCGAAGGACTG
->FBgn0067385_invader6|3014|R|20|n=1
+>FBgn0067385_invader6|coord=3014|strand -|size=20|nreads=1
 TTCTAGTCAAAGTCGAAGGA
->FBgn0067385_invader6|3024|F|26|n=1
+>FBgn0067385_invader6|coord=3024|strand +|size=21|nreads=1
+TTGACTAGAATGACTTAGACT
+>FBgn0067385_invader6|coord=3024|strand +|size=26|nreads=1
 TTGACTAGAATGACTTAGACTTAGAA
->FBgn0067624_BS3|1016|R|20|n=1
+>FBgn0067624_BS3|coord=1016|strand -|size=20|nreads=1
 TTGATGCCAATGTTCCAACG
->FBgn0067624_BS3|1026|F|26|n=1
+>FBgn0067624_BS3|coord=1026|strand +|size=24|nreads=1
+TTGGCATCAATGGTGACAAATCTG
+>FBgn0067624_BS3|coord=1026|strand +|size=25|nreads=1
+TTGGCATCAATGGTGACAAATCTGC
+>FBgn0067624_BS3|coord=1026|strand +|size=26|nreads=1
 TTGGCATCAATGGTGACAAATCAGCG
->FBgn0067624_BS3|1026|F|24|n=1
-TTGGCATCAATGGTGACAAATCTG
->FBgn0067624_BS3|1026|F|25|n=1
-TTGGCATCAATGGTGACAAATCTGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_3.fa	Sat Sep 09 11:57:39 2017 -0400
@@ -0,0 +1,416 @@
+>FBgn0000004_17.6|coord=5844|strand -|size=21|nreads=1
+TTTTCGTCAAGTGTGCTAAAT
+>FBgn0000004_17.6|coord=5855|strand +|size=23|nreads=1
+TTGACGAAAATGATCGAGTGGAT
+>FBgn0000005_297|coord=1334|strand -|size=23|nreads=1
+TTTTGCGCAATGGTAATTAAGGA
+>FBgn0000005_297|coord=1347|strand +|size=21|nreads=1
+TTGCACAAAATGAGGGAATTT
+>FBgn0000007_1731|coord=4545|strand -|size=20|nreads=1
+TTGAGAGCAAAGGCCGAATG
+>FBgn0000007_1731|coord=4555|strand +|size=24|nreads=1
+TTGCTCTCAATGCGCTGAGTTTGG
+>FBgn0000155_roo|coord=2682|strand -|size=20|nreads=2
+TTTTTACCAAACGGATGCCT
+>FBgn0000155_roo|coord=2692|strand +|size=24|nreads=1
+TTGGTAAAAAATGTATAAGTGAGC
+>FBgn0000155_roo|coord=2692|strand +|size=27|nreads=1
+TTGGTAAAAAATGTATAAGTGAGCAGC
+>FBgn0000155_roo|coord=3225|strand -|size=26|nreads=1
+TTTTGCCCAAGGAGACCGTCTATTTT
+>FBgn0000155_roo|coord=3226|strand -|size=25|nreads=1
+TTTTGCCCAAGGAGACCGTCTATTT
+>FBgn0000155_roo|coord=3227|strand -|size=24|nreads=2
+TTTTGCCCAAGGAGACCGTCTATT
+>FBgn0000155_roo|coord=3228|strand -|size=23|nreads=1
+TTTTGCCCAAGGAGACCGTCTAT
+>FBgn0000155_roo|coord=3229|strand -|size=22|nreads=2
+TTTTGCCCAAGGAGACCGTCTA
+>FBgn0000155_roo|coord=3230|strand -|size=21|nreads=1
+TTTTGCCCAAGGAGACCGTCT
+>FBgn0000155_roo|coord=3231|strand -|size=20|nreads=2
+TTTTGCCCAAGGAGACCGTC
+>FBgn0000155_roo|coord=3241|strand +|size=20|nreads=1
+TTGGGCAAAAAACTGATTTC
+>FBgn0000155_roo|coord=3241|strand +|size=24|nreads=1
+TTGGGCAAAAAACTGATTTCGGGT
+>FBgn0000155_roo|coord=3241|strand +|size=27|nreads=1
+TTGGGCAAAAAACTGATTTCGGGTGGA
+>FBgn0000155_roo|coord=3241|strand +|size=28|nreads=1
+TTGGGCAAAAAACTGATTTCGGGTGGAT
+>FBgn0000155_roo|coord=8644|strand -|size=21|nreads=1
+TTCTGCCAAAGGGCCAGCAAG
+>FBgn0000155_roo|coord=8645|strand -|size=20|nreads=1
+TTCTGCCAAAGGGCCAGCAA
+>FBgn0000155_roo|coord=8655|strand +|size=25|nreads=1
+TTTGGCAGAATGTTCACACATGAAA
+>FBgn0000349_copia|coord=658|strand -|size=22|nreads=1
+TTCTCAAGAATCTGACGCGCCG
+>FBgn0000349_copia|coord=670|strand +|size=25|nreads=1
+TTCTTGAGAATTTGGACGCCGTTTA
+>FBgn0000349_copia|coord=4614|strand -|size=24|nreads=1
+TTGCAGCAAACCCAATTTGTCTCG
+>FBgn0000349_copia|coord=4628|strand +|size=20|nreads=1
+TTTGCTGCAAGACGACCAAT
+>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1
+TTCGAGAAAATTACTTCAGGATTTGTCT
+>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1
+TTCGGGAAAATTACTTCAGGATTTGTCT
+>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1
+TTCGGGAAAATTACTTCAGGATTTGTC
+>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1
+TTTGAGAAAATTACTTCAGGATTTGTC
+>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=74
+TTCGAGAAAATTACTTCAGGATTTGTC
+>FBgn0000652_F-element|coord=1548|strand -|size=26|nreads=3
+TTCGAGAAAATTACTTCAGGATTTGT
+>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=1
+TTCGGGAAAATTACTTCAGGATTTG
+>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=22
+TTCGAGAAAATTACTTCAGGATTTG
+>FBgn0000652_F-element|coord=1550|strand -|size=24|nreads=2
+TTCGAGAAAATTACTTCAGGATTT
+>FBgn0000652_F-element|coord=1551|strand -|size=23|nreads=7
+TTCGAGAAAATTACTTCAGGATT
+>FBgn0000652_F-element|coord=1554|strand -|size=20|nreads=1
+TTCGAGAAAATTACTTCAGG
+>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=1
+TTTTCTCGAAAGCAGCTAGT
+>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=2
+TTTTCTCGAAAGCAGCAAGT
+>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2
+TTTTCTCGAAAGCAGCAAGTTTC
+>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2
+TTTTCTCGAAAGCAGCTAGTTTC
+>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=2
+TTTTCTCGAAAGCAGCAAGTTTCG
+>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=5
+TTTTCTCGAAAGCAGCTAGTTTCG
+>FBgn0000652_F-element|coord=1564|strand +|size=25|nreads=1
+TTTTCTCGAAAGCAGCTAGTTTCGC
+>FBgn0000652_F-element|coord=2231|strand -|size=27|nreads=1
+TTGGAAGAAATCCAGGAATTGAGCTTC
+>FBgn0000652_F-element|coord=2233|strand -|size=25|nreads=5
+TTGGAAGAAATCCAGGAATTGAGCT
+>FBgn0000652_F-element|coord=2248|strand +|size=20|nreads=1
+TTTCTTCCAAGCACTAGGGC
+>FBgn0000652_F-element|coord=2248|strand +|size=21|nreads=1
+TTTCTTCCAAGCACTAGGGCC
+>FBgn0000652_F-element|coord=2471|strand -|size=21|nreads=2
+TTTAACCAAACTGCGGGAAAT
+>FBgn0000652_F-element|coord=2472|strand -|size=20|nreads=1
+TTTAACCAAACTGCGGGAAA
+>FBgn0000652_F-element|coord=2482|strand +|size=23|nreads=2
+TTTGGTTAAAGCTGAATGTCTGC
+>FBgn0000652_F-element|coord=2482|strand +|size=24|nreads=2
+TTTGGTTAAAGCTGAATGTCTGCC
+>FBgn0000652_F-element|coord=2482|strand +|size=26|nreads=3
+TTTGGTTAAAGCTGAATGTCTGCCGG
+>FBgn0000652_F-element|coord=2482|strand +|size=27|nreads=1
+TTTGGTTAAAGCTGAATGTCTGCCGGA
+>FBgn0000652_F-element|coord=3507|strand -|size=27|nreads=1
+TTTCGCGAAATCCAAATTGGTGGGCTG
+>FBgn0000652_F-element|coord=3509|strand -|size=25|nreads=6
+TTTCGCGAAATCCAAATTGGTGGGC
+>FBgn0000652_F-element|coord=3510|strand -|size=24|nreads=1
+TTTCGCGAAATCCAAATTGGTGGG
+>FBgn0000652_F-element|coord=3513|strand -|size=21|nreads=3
+TTTCGCGAAATCCAAATTGGT
+>FBgn0000652_F-element|coord=3524|strand +|size=20|nreads=2
+TTTCGCGAAAGCCATGGAAC
+>FBgn0000652_F-element|coord=3524|strand +|size=21|nreads=2
+TTTCGCGAAAGCCACGGAACC
+>FBgn0000652_F-element|coord=3524|strand +|size=22|nreads=1
+TTTCGCGAAAGCCACGGAACCA
+>FBgn0000652_F-element|coord=3524|strand +|size=23|nreads=1
+TTTCGCGAAAGCCACGGAACCAT
+>FBgn0000652_F-element|coord=3524|strand +|size=24|nreads=1
+TTTCGCGAAAGCCATGGAACCATT
+>FBgn0000652_F-element|coord=3524|strand +|size=26|nreads=1
+TTTCGCGAAAGCCATGGAACCATTGA
+>FBgn0000652_F-element|coord=3524|strand +|size=27|nreads=1
+TTTCGCGAAAGCCACGGAACCATTGAA
+>FBgn0002697_mdg1|coord=4301|strand -|size=22|nreads=1
+TTCTTTGGAAAGAATTTGGGGC
+>FBgn0002697_mdg1|coord=4302|strand -|size=21|nreads=1
+TTCTTTGGAAAGAATTTGGGG
+>FBgn0002697_mdg1|coord=4303|strand -|size=20|nreads=1
+TTCTTTGGAAAGAATTTGGG
+>FBgn0002697_mdg1|coord=4313|strand +|size=25|nreads=1
+TTCCAAAGAATGATGACCCTTGCAT
+>FBgn0003007_opus|coord=5540|strand -|size=28|nreads=1
+TTTCTAGGAACGTAGAATGGAATCTCTC
+>FBgn0003007_opus|coord=5540|strand -|size=28|nreads=1
+TTTCTAGGAACGTAGAGTGGAATCTCTC
+>FBgn0003007_opus|coord=5542|strand -|size=26|nreads=1
+TTTCTAGGAACGTAGAATGGAATCTC
+>FBgn0003007_opus|coord=5542|strand -|size=26|nreads=2
+TTTCTAGGAACGTAGAGTGGAATCTC
+>FBgn0003007_opus|coord=5543|strand -|size=25|nreads=1
+TTTCTAGGAACGTAGAGTGGAATCT
+>FBgn0003007_opus|coord=5544|strand -|size=24|nreads=7
+TTTCTAGGAACGTAGAGTGGAATC
+>FBgn0003007_opus|coord=5558|strand +|size=21|nreads=1
+TTCCTAGAAATTTATCGTTGC
+>FBgn0003122_pogo|coord=1804|strand -|size=25|nreads=1
+TTCCATAGAATTCAAGTTTTGCAAA
+>FBgn0003122_pogo|coord=1806|strand -|size=23|nreads=1
+TTCCATAGAATTCAAGTTTTGCA
+>FBgn0003122_pogo|coord=1819|strand +|size=22|nreads=1
+TTCTATGGAAGACAAGCTGTTT
+>FBgn0003908_R1A1-element|coord=4671|strand -|size=29|nreads=1
+TTTTCGCCAAGGCGCTGCACTCCAAGTCC
+>FBgn0003908_R1A1-element|coord=4672|strand -|size=28|nreads=8
+TTTTCGCCAAGGCGCTGCACTCCAAGTC
+>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=1
+TTTTCGCCAAGGCGCTGCACCCCAAGT
+>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=4
+TTTTCGCCAAGGCGCTGCACTCCAAGT
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1
+TTTTCGCCAAGGCGCTGCACCCCAAG
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1
+TTTTCGTCAAGGCGCTGCACTCCAAG
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=2
+TTTTCGCCAAGGCGCTGCACTTCAAG
+>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=29
+TTTTCGCCAAGGCGCTGCACTCCAAG
+>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1
+TTTTCGCCAAGGCGCTGCACCCCAA
+>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1
+TTTTCGCCAAGGCGCTGCACTTCAA
+>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=10
+TTTTCGCCAAGGCGCTGCACTCCAA
+>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=2
+TTTTCGCCAAGGCGCTGCACTTCA
+>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=21
+TTTTCGCCAAGGCGCTGCACTCCA
+>FBgn0003908_R1A1-element|coord=4677|strand -|size=23|nreads=12
+TTTTCGCCAAGGCGCTGCACTCC
+>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=1
+TTTTCGCCAAGGCGCTGCACTT
+>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=18
+TTTTCGCCAAGGCGCTGCACTC
+>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=1
+TTTTCGCCAAGGCGCTGCACC
+>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=6
+TTTTCGCCAAGGCGCTGCACT
+>FBgn0003908_R1A1-element|coord=4680|strand -|size=20|nreads=4
+TTTTCGCCAAGGCGCTGCAC
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=20|nreads=2
+TTGGCGAAAACTGGATCTTC
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=21|nreads=6
+TTGGCGAAAACTGGATCTTCG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=1
+TTGGCGAAAACTAGATCTTCGA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=8
+TTGGCGAAAACTGGATCTTCGA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=23|nreads=8
+TTGGCGAAAACTGGATCTTCGAG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=7
+TTGGCGAAAACTGGATCTTCGAGG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=9
+TTGGCGAAAACTGGATCTTCGAGA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=11
+TTGGCGAAAACTGGATCTTCGAGAG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=12
+TTGGCGAAAACTGGATCTTCGAGGG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=2
+TTGGCGAAAACTGGATCTTCGAGGGA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=6
+TTGGCGAAAACTGGATCTTCGAGAGA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=20
+TTGGCGAAAACTGGATCTTCGAGAGAA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=9
+TTGGCGAAAACTGGATCTTCGAGGGAA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=1
+TTGGCGAAAACTGGATCTTCGAGGGAAT
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=4
+TTGGCGAAAACTGGATCTTCGAGAGAAT
+>FBgn0005673_1360|coord=773|strand -|size=22|nreads=1
+TTTTCGCAATCATTCCATCCTG
+>FBgn0005673_1360|coord=785|strand +|size=26|nreads=6
+TTTGCGAAAAATTGTTTGCTCAGAGC
+>FBgn0005673_1360|coord=3197|strand -|size=22|nreads=1
+TTTGCTAGAAGACGATTTTCGG
+>FBgn0005673_1360|coord=3209|strand +|size=23|nreads=1
+TTCTAGCACAACACGCACACATA
+>FBgn0005673_1360|coord=3209|strand +|size=26|nreads=1
+TTCTAGCACAACACGCACACATATAC
+>FBgn0005673_1360|coord=3209|strand +|size=27|nreads=1
+TTCTAGCACAACACGCACACATATACG
+>FBgn0010302_Burdock|coord=3390|strand -|size=21|nreads=1
+TTTCATCGAAAGAAATTGGTA
+>FBgn0010302_Burdock|coord=3401|strand +|size=25|nreads=2
+TTCGATGAAAGACAATGTTCTGCTT
+>FBgn0014947_flea|coord=801|strand -|size=27|nreads=4
+TTCTCTAGAATTGCTTGTATTTGGTCG
+>FBgn0014947_flea|coord=802|strand -|size=26|nreads=11
+TTCTCTAGAATTGCTTGTATTTGGTC
+>FBgn0014947_flea|coord=803|strand -|size=25|nreads=12
+TTCTCTAGAATTGCTTGTATTTGGT
+>FBgn0014947_flea|coord=804|strand -|size=24|nreads=2
+TTCTCTAGAATTGCTTGTATTTGG
+>FBgn0014947_flea|coord=805|strand -|size=23|nreads=1
+TTCTCTAGAATTGCTTGTATTTG
+>FBgn0014947_flea|coord=818|strand +|size=22|nreads=1
+TTCTAGAGAACGAAAGCGAGGA
+>FBgn0014947_flea|coord=1164|strand -|size=28|nreads=2
+TTCTAAGAAAAGTTCTGCTGATCCAATC
+>FBgn0014947_flea|coord=1166|strand -|size=26|nreads=2
+TTCTAAGAAAAGTTCTGCTGATCCAA
+>FBgn0014947_flea|coord=1167|strand -|size=25|nreads=1
+TTCTAAGAAAAGTTCTGCTGATCCA
+>FBgn0014947_flea|coord=1168|strand -|size=24|nreads=1
+TTCTAAGAAAAGTTCTGCTGATCC
+>FBgn0014947_flea|coord=1169|strand -|size=23|nreads=1
+TTCTAAGAAAAGTTCTGCTGATC
+>FBgn0014947_flea|coord=1182|strand +|size=22|nreads=1
+TTTCTTAGAATCTGAATGTGTC
+>FBgn0014947_flea|coord=2754|strand -|size=21|nreads=1
+TTTAGACCAAATTCTGCAGCT
+>FBgn0014947_flea|coord=2765|strand +|size=24|nreads=4
+TTGGTCTAAAAATAAAATGGAAGA
+>FBgn0014947_flea|coord=2765|strand +|size=25|nreads=1
+TTGGTCTAAAAATAAAATGGAAGAA
+>FBgn0014947_flea|coord=2765|strand +|size=26|nreads=1
+TTGGTCTAAAAATAAAATGGAAGAAG
+>FBgn0014947_flea|coord=2765|strand +|size=28|nreads=1
+TTGGTCTAAAAATAAAATGGAAGAAGTG
+>FBgn0015945_GATE|coord=3140|strand -|size=28|nreads=9
+TTGGAACGAAATTGGCCTGATTAGCGGA
+>FBgn0015945_GATE|coord=3141|strand -|size=27|nreads=4
+TTGGAACGAAATTGGCCTGATTAGCGG
+>FBgn0015945_GATE|coord=3142|strand -|size=26|nreads=17
+TTGGAACGAAATTGGCCTGATTAGCG
+>FBgn0015945_GATE|coord=3143|strand -|size=25|nreads=86
+TTGGAACGAAATTGGCCTGATTAGC
+>FBgn0015945_GATE|coord=3144|strand -|size=24|nreads=17
+TTGGAACGAAATTGGCCTGATTAG
+>FBgn0015945_GATE|coord=3158|strand +|size=20|nreads=3
+TTCGTTCCAAATGAGCAAGC
+>FBgn0015945_GATE|coord=3158|strand +|size=21|nreads=1
+TTCGTTCCAAATGAGCAAGCC
+>FBgn0015945_GATE|coord=3158|strand +|size=22|nreads=2
+TTCGTTCCAAATGAGCAAGCCG
+>FBgn0015945_GATE|coord=6234|strand -|size=22|nreads=1
+TTGAAGGAAATCGCGGGAAAGC
+>FBgn0015945_GATE|coord=6246|strand +|size=25|nreads=1
+TTTCCTTCAAGCCGTAAAAGAGTCG
+>FBgn0015945_GATE|coord=6246|strand +|size=26|nreads=1
+TTTCCTTCAAGCCGTAAAAGAGTCGG
+>FBgn0042682_Rt1b|coord=1075|strand -|size=21|nreads=1
+TTCTTGGCGACAGATGCGTAG
+>FBgn0042682_Rt1b|coord=1076|strand -|size=20|nreads=1
+TTCTTGGCGACAGATGCGTA
+>FBgn0042682_Rt1b|coord=1086|strand +|size=23|nreads=1
+TTGCCAAGAATGCTAGCACGGGT
+>FBgn0042682_Rt1b|coord=2902|strand -|size=28|nreads=1
+TTGGTAACAAGCTTGTAGGCGAGGCCCC
+>FBgn0042682_Rt1b|coord=2903|strand -|size=27|nreads=1
+TTGGTAACAAGCTTGTAGGCGAGGCCC
+>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=1
+TTGGTAACAAGCTTGTAGGCGAGTCC
+>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=2
+TTGGTAACAAGCTTGTAGGCGAGGCC
+>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=1
+TTGGTAACAAGCTTGTAGGCGAGGT
+>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=2
+TTGGTAACAAGCTTGTAGGCGAGGC
+>FBgn0042682_Rt1b|coord=2906|strand -|size=24|nreads=25
+TTGGTAACAAGCTTGTAGGCGAGG
+>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=1
+TTGGTAACAAGCTTGGAGGCGAG
+>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=15
+TTGGTAACAAGCTTGTAGGCGAG
+>FBgn0042682_Rt1b|coord=2908|strand -|size=22|nreads=1
+TTGGTAACAAGCTTGTAGGCGA
+>FBgn0042682_Rt1b|coord=2909|strand -|size=21|nreads=6
+TTGGTAACAAGCTTGTAGGCG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=22|nreads=1
+TTGTTACCAAAAAGCTAAGGAG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1
+TTGTTACCAAAAAGCTAAGGAGG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1
+TTGTTACCAACAAGCTAAGGAGG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=24|nreads=2
+TTGTTACCAACAAGCTAAGGAGGA
+>FBgn0042682_Rt1b|coord=2920|strand +|size=25|nreads=1
+TTGTTACCAAAAAGCTAAGGAGGAG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=26|nreads=1
+TTGTTACCAAAAAGCTAAGGAGGAGA
+>FBgn0042682_Rt1b|coord=2920|strand +|size=27|nreads=1
+TTGTTACCAAAAAGCTAAGGAGGAGAG
+>FBgn0042682_Rt1b|coord=4364|strand -|size=22|nreads=1
+TTGCCTGGAAGCGCCACTCCGC
+>FBgn0042682_Rt1b|coord=4365|strand -|size=21|nreads=1
+TTGCCTGGAAGCGCCACTCCG
+>FBgn0042682_Rt1b|coord=4366|strand -|size=20|nreads=4
+TTGCCTGGAAGCGCCACTCC
+>FBgn0042682_Rt1b|coord=4376|strand +|size=24|nreads=1
+TTCCAGGCAAGAGGCACACGAGTG
+>FBgn0042682_Rt1b|coord=4376|strand +|size=26|nreads=1
+TTCCAGGCAAGAGGCACACGAGTGGC
+>FBgn0062343_Dm88|coord=4210|strand -|size=21|nreads=1
+TTGGTTAGAACATCTGCCATC
+>FBgn0062343_Dm88|coord=4221|strand +|size=24|nreads=1
+TTCTAACCAAGAATTTGAATAGAT
+>FBgn0063427_invader4|coord=691|strand -|size=26|nreads=15
+TTCCTACGAATCGCTGTATGAACAGT
+>FBgn0063427_invader4|coord=707|strand +|size=22|nreads=2
+TTCGTAGGAATGGAGACGTCGG
+>FBgn0063428_invader3|coord=425|strand -|size=25|nreads=1
+TTCTGGGGAAATGGCCTGCAGACGC
+>FBgn0063428_invader3|coord=427|strand -|size=23|nreads=1
+TTCTGGGGAAATGGCCTGCAGAC
+>FBgn0063428_invader3|coord=440|strand +|size=22|nreads=2
+TTCCCCAGAAACGCGTGGCGAT
+>FBgn0063430_invader1|coord=2082|strand -|size=20|nreads=1
+TTTTATCGAACCAATAGAAC
+>FBgn0063430_invader1|coord=2092|strand +|size=24|nreads=1
+TTCGATAAAATGTCTAAGTATGTT
+>FBgn0063430_invader1|coord=2092|strand +|size=26|nreads=1
+TTCGATAAAATGTCTAAGTATGTTCG
+>FBgn0063433_gypsy4|coord=3040|strand -|size=28|nreads=1
+TTTTGAAGAACTTGGATTTTTCTTGAGA
+>FBgn0063433_gypsy4|coord=3044|strand -|size=24|nreads=1
+TTTTGAAGAACTTGGATTTTTCTT
+>FBgn0063433_gypsy4|coord=3058|strand +|size=22|nreads=1
+TTCTTCAAAAAGAGCGTGGAAT
+>FBgn0063440_baggins|coord=5154|strand -|size=26|nreads=1
+TTTTGTGCAAATGGCTGTGAAGTCGG
+>FBgn0063440_baggins|coord=5170|strand +|size=21|nreads=1
+TTGCACAAAATTGGCATTGCA
+>FBgn0063919_Max-element|coord=3887|strand -|size=21|nreads=2
+TTGCTGAGAAGCGTGTTGAGC
+>FBgn0063919_Max-element|coord=3898|strand +|size=23|nreads=1
+TTCTCAGCAAGTTCTGGGAGGTG
+>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=1
+TTCTCAGCAAGTTCTGGGAGGTGT
+>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=2
+TTCTCAGCAAGTTCTGGGAGGTGG
+>FBgn0063919_Max-element|coord=3898|strand +|size=25|nreads=1
+TTCTCAGCAAGTTCTGGGAGGTGGA
+>FBgn0067385_invader6|coord=3007|strand -|size=27|nreads=4
+TTCTAGTCAAAGTCGAAGGACTGCATA
+>FBgn0067385_invader6|coord=3008|strand -|size=26|nreads=3
+TTCTAGTCAAAGTCGAAGGACTGCAT
+>FBgn0067385_invader6|coord=3009|strand -|size=25|nreads=5
+TTCTAGTCAAAGTCGAAGGACTGCA
+>FBgn0067385_invader6|coord=3010|strand -|size=24|nreads=4
+TTCTAGTCAAAGTCGAAGGACTGC
+>FBgn0067385_invader6|coord=3011|strand -|size=23|nreads=1
+TTCTAGTCAAAGTCGAAGGACTG
+>FBgn0067385_invader6|coord=3014|strand -|size=20|nreads=1
+TTCTAGTCAAAGTCGAAGGA
+>FBgn0067385_invader6|coord=3024|strand +|size=21|nreads=1
+TTGACTAGAATGACTTAGACT
+>FBgn0067385_invader6|coord=3024|strand +|size=26|nreads=1
+TTGACTAGAATGACTTAGACTTAGAA
+>FBgn0067624_BS3|coord=1016|strand -|size=20|nreads=1
+TTGATGCCAATGTTCCAACG
+>FBgn0067624_BS3|coord=1026|strand +|size=24|nreads=1
+TTGGCATCAATGGTGACAAATCTG
+>FBgn0067624_BS3|coord=1026|strand +|size=25|nreads=1
+TTGGCATCAATGGTGACAAATCTGC
+>FBgn0067624_BS3|coord=1026|strand +|size=26|nreads=1
+TTGGCATCAATGGTGACAAATCAGCG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_4.fa	Sat Sep 09 11:57:39 2017 -0400
@@ -0,0 +1,70 @@
+>FBgn0000155_roo|coord=3229|strand -|size=22|nreads=2
+TTTTGCCCAAGGAGACCGTCTA
+>FBgn0000155_roo|coord=3230|strand -|size=21|nreads=1
+TTTTGCCCAAGGAGACCGTCT
+>FBgn0000155_roo|coord=3231|strand -|size=20|nreads=2
+TTTTGCCCAAGGAGACCGTC
+>FBgn0000155_roo|coord=3241|strand +|size=20|nreads=1
+TTGGGCAAAAAACTGATTTC
+>FBgn0000652_F-element|coord=1554|strand -|size=20|nreads=1
+TTCGAGAAAATTACTTCAGG
+>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=1
+TTTTCTCGAAAGCAGCTAGT
+>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=2
+TTTTCTCGAAAGCAGCAAGT
+>FBgn0000652_F-element|coord=2471|strand -|size=21|nreads=2
+TTTAACCAAACTGCGGGAAAT
+>FBgn0000652_F-element|coord=2472|strand -|size=20|nreads=1
+TTTAACCAAACTGCGGGAAA
+>FBgn0000652_F-element|coord=2482|strand +|size=21|nreads=1
+TTTGGTTAAAGCTGAATGTCT
+>FBgn0000652_F-element|coord=2482|strand +|size=22|nreads=2
+TTTGGTTAAAGCTGAATGTCTG
+>FBgn0000652_F-element|coord=3513|strand -|size=21|nreads=3
+TTTCGCGAAATCCAAATTGGT
+>FBgn0000652_F-element|coord=3524|strand +|size=20|nreads=2
+TTTCGCGAAAGCCATGGAAC
+>FBgn0000652_F-element|coord=3524|strand +|size=21|nreads=2
+TTTCGCGAAAGCCACGGAACC
+>FBgn0000652_F-element|coord=3524|strand +|size=22|nreads=1
+TTTCGCGAAAGCCACGGAACCA
+>FBgn0002697_mdg1|coord=4646|strand -|size=21|nreads=1
+TTTCTCAGAAAAGTTCTTAAT
+>FBgn0002697_mdg1|coord=4657|strand +|size=22|nreads=1
+TTCTGAGAAATCACGCCACTTA
+>FBgn0002697_mdg1|coord=5354|strand -|size=21|nreads=2
+TTTCAACAAACACTTATGCTT
+>FBgn0002697_mdg1|coord=5365|strand +|size=21|nreads=2
+TTTGTTGAAAAGAGGAAAACA
+>FBgn0003519_Stalker|coord=6708|strand -|size=21|nreads=1
+TTTGTCTCAAAGCATTTTTGT
+>FBgn0003519_Stalker|coord=6719|strand +|size=21|nreads=1
+TTGAGACAAAACATTGCTAAT
+>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=1
+TTTTCGCCAAGGCGCTGCACTT
+>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=18
+TTTTCGCCAAGGCGCTGCACTC
+>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=1
+TTTTCGCCAAGGCGCTGCACC
+>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=6
+TTTTCGCCAAGGCGCTGCACT
+>FBgn0003908_R1A1-element|coord=4680|strand -|size=20|nreads=4
+TTTTCGCCAAGGCGCTGCAC
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=20|nreads=2
+TTGGCGAAAACTGGATCTTC
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=21|nreads=6
+TTGGCGAAAACTGGATCTTCG
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=1
+TTGGCGAAAACTAGATCTTCGA
+>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=8
+TTGGCGAAAACTGGATCTTCGA
+>FBgn0042682_Rt1b|coord=2908|strand -|size=22|nreads=1
+TTGGTAACAAGCTTGTAGGCGA
+>FBgn0042682_Rt1b|coord=2909|strand -|size=21|nreads=6
+TTGGTAACAAGCTTGTAGGCG
+>FBgn0042682_Rt1b|coord=2920|strand +|size=22|nreads=1
+TTGTTACCAAAAAGCTAAGGAG
+>FBgn0067385_invader6|coord=3014|strand -|size=20|nreads=1
+TTCTAGTCAAAGTCGAAGGA
+>FBgn0067385_invader6|coord=3024|strand +|size=21|nreads=1
+TTGACTAGAATGACTTAGACT