Tandem Repeats Finder Program written by:

                 Gary Benson
      Department of Biomathematical Sciences
          Mount Sinai School of Medicine

Version 4.00

Sequence: contig00000278

Parameters: 2 5 7 80 10 25 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 2395
ACGTcount: A:0.23, C:0.29, G:0.30, T:0.17

Warning! 32 characters in sequence are not A, C, G, or T


Found at i:8 original size:1 final size:1

Alignment explanation

Indices: 3--19 Score: 34 Period size: 1 Copynumber: 17.0 Consensus size: 1 1 AT 3 CCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCC 20 GTTGTTGCTG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 16 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Left flanking sequence: Indices 1 -- 2 AT Right flanking sequence: Indices 20 -- 519 GTTGTTGCTGCAGCTGCTGCTGCGGCTGCGCCGCCAGGGCCACTGTTGAGTCGCCATCTGCGTGG CGGCCANGCAGCAGCAGCAGCAGCTGCTGCTGCTGCGTCTCCTGCTGCTGCTGCTGCTCTGCTGC ACTACACCGTAGATGTGCCTCAAGTGGTGCAGCAGGTAGGGCAGCGGCTGGGCTTCACAGACTGC GGCTGCAACAGCAGCAGCAGCAGCGGCAGCAGCAGCAGCAGCAGCAGCTCAGGGTCCGTGTTGGT TGTTGCAGACGATNGATGCATGCAGCCGCAGCGCAGCAACCTTGGTTCTTGCTGCTGCAATCAGC AGCAGCAGCAGNCAGCAACAACAGCAAGGANCCCNGATGGCAGCTCTTGNCCCAAGTGCTTGGTA GATGGAAAGANTGCGCTGCTGCTGCCGCAGCACATGCAGCAGCTGCGGCGCTGCAGCAGCAGAGC GCCTGCTGTTTGCAGCAACAGTAACAGCAGCAGCAGCAGCAGCAA Found at i:38 original size:3 final size:3 Alignment explanation

Indices: 25--48 Score: 34 Period size: 3 Copynumber: 8.0 Consensus size: 3 15 CCCCCGTTGT * * 25 TGC TGC AGC TGC TGC TGC GGC TGC 1 TGC TGC TGC TGC TGC TGC TGC TGC 49 GCCGCCAGGG Statistics Matches: 17, Mismatches: 4, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 3 17 1.00 ACGTcount: A:0.04, C:0.33, G:0.38, T:0.25 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 1 -- 24 ATCCCCCCCCCCCCCCCCCGTTGT Right flanking sequence: Indices 49 -- 548 GCCGCCAGGGCCACTGTTGAGTCGCCATCTGCGTGGCGGCCANGCAGCAGCAGCAGCAGCTGCTG CTGCTGCGTCTCCTGCTGCTGCTGCTGCTCTGCTGCACTACACCGTAGATGTGCCTCAAGTGGTG CAGCAGGTAGGGCAGCGGCTGGGCTTCACAGACTGCGGCTGCAACAGCAGCAGCAGCAGCGGCAG CAGCAGCAGCAGCAGCAGCTCAGGGTCCGTGTTGGTTGTTGCAGACGATNGATGCATGCAGCCGC AGCGCAGCAACCTTGGTTCTTGCTGCTGCAATCAGCAGCAGCAGCAGNCAGCAACAACAGCAAGG ANCCCNGATGGCAGCTCTTGNCCCAAGTGCTTGGTAGATGGAAAGANTGCGCTGCTGCTGCCGCA GCACATGCAGCAGCTGCGGCGCTGCAGCAGCAGAGCGCCTGCTGTTTGCAGCAACAGTAACAGCA GCAGCAGCAGCAGCAAAGAGGAAGAAGAAGCAGATGTGTTGCTGC Found at i:100 original size:3 final size:3 Alignment explanation

Indices: 92--108 Score: 34 Period size: 3 Copynumber: 5.7 Consensus size: 3 82 TGGCGGCCAN 92 GCA GCA GCA GCA GCA GC 1 GCA GCA GCA GCA GCA GC 109 TGCTGCTGCT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 14 1.00 ACGTcount: A:0.29, C:0.35, G:0.35, T:0.00 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 1 -- 91 ATCCCCCCCCCCCCCCCCCGTTGTTGCTGCAGCTGCTGCTGCGGCTGCGCCGCCAGGGCCACTGT TGAGTCGCCATCTGCGTGGCGGCCAN Right flanking sequence: Indices 109 -- 608 TGCTGCTGCTGCGTCTCCTGCTGCTGCTGCTGCTCTGCTGCACTACACCGTAGATGTGCCTCAAG TGGTGCAGCAGGTAGGGCAGCGGCTGGGCTTCACAGACTGCGGCTGCAACAGCAGCAGCAGCAGC GGCAGCAGCAGCAGCAGCAGCAGCTCAGGGTCCGTGTTGGTTGTTGCAGACGATNGATGCATGCA GCCGCAGCGCAGCAACCTTGGTTCTTGCTGCTGCAATCAGCAGCAGCAGCAGNCAGCAACAACAG CAAGGANCCCNGATGGCAGCTCTTGNCCCAAGTGCTTGGTAGATGGAAAGANTGCGCTGCTGCTG CCGCAGCACATGCAGCAGCTGCGGCGCTGCAGCAGCAGAGCGCCTGCTGTTTGCAGCAACAGTAA CAGCAGCAGCAGCAGCAGCAAAGAGGAAGAAGAAGCAGATGTGTTGCTGCTGCAGCAAGCTGCTG CTGAGACTCTCACTATGTACACGGCGCCGCAGACTCCCCGGCTCT Found at i:113 original size:3 final size:3 Alignment explanation

Indices: 107--149 Score: 58 Period size: 3 Copynumber: 14.7 Consensus size: 3 97 AGCAGCAGCA * * * 107 GCT GCT GCT GCT GCG TCT CCT GCT GCT GCT GCT GCT -CT GCT GC 1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC 150 ACTACACCGT Statistics Matches: 34, Mismatches: 5, Indels: 2 0.83 0.12 0.05 Matches are distributed among these distances: 2 2 0.06 3 32 0.94 ACGTcount: A:0.00, C:0.37, G:0.30, T:0.33 Consensus pattern (3 bp): GCT Left flanking sequence: Indices 1 -- 106 ATCCCCCCCCCCCCCCCCCGTTGTTGCTGCAGCTGCTGCTGCGGCTGCGCCGCCAGGGCCACTGT TGAGTCGCCATCTGCGTGGCGGCCANGCAGCAGCAGCAGCA Right flanking sequence: Indices 150 -- 649 ACTACACCGTAGATGTGCCTCAAGTGGTGCAGCAGGTAGGGCAGCGGCTGGGCTTCACAGACTGC GGCTGCAACAGCAGCAGCAGCAGCGGCAGCAGCAGCAGCAGCAGCAGCTCAGGGTCCGTGTTGGT TGTTGCAGACGATNGATGCATGCAGCCGCAGCGCAGCAACCTTGGTTCTTGCTGCTGCAATCAGC AGCAGCAGCAGNCAGCAACAACAGCAAGGANCCCNGATGGCAGCTCTTGNCCCAAGTGCTTGGTA GATGGAAAGANTGCGCTGCTGCTGCCGCAGCACATGCAGCAGCTGCGGCGCTGCAGCAGCAGAGC GCCTGCTGTTTGCAGCAACAGTAACAGCAGCAGCAGCAGCAGCAAAGAGGAAGAAGAAGCAGATG TGTTGCTGCTGCAGCAAGCTGCTGCTGAGACTCTCACTATGTACACGGCGCCGCAGACTCCCCGG CTCTCTGGAACTGCAGCAGCAGCAGCAGCAGCGCTCGCTGCTGCT Found at i:231 original size:3 final size:3 Alignment explanation

Indices: 219--262 Score: 74 Period size: 3 Copynumber: 14.7 Consensus size: 3 209 GACTGCGGCT * * 219 GCA ACA GCA GCA GCA GCA GCG GCA GCA GCA GCA GCA GCA GCA GC 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC 263 TCAGGGTCCG Statistics Matches: 37, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 3 37 1.00 ACGTcount: A:0.32, C:0.34, G:0.34, T:0.00 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 1 -- 218 ATCCCCCCCCCCCCCCCCCGTTGTTGCTGCAGCTGCTGCTGCGGCTGCGCCGCCAGGGCCACTGT TGAGTCGCCATCTGCGTGGCGGCCANGCAGCAGCAGCAGCAGCTGCTGCTGCTGCGTCTCCTGCT GCTGCTGCTGCTCTGCTGCACTACACCGTAGATGTGCCTCAAGTGGTGCAGCAGGTAGGGCAGCG GCTGGGCTTCACAGACTGCGGCT Right flanking sequence: Indices 263 -- 762 TCAGGGTCCGTGTTGGTTGTTGCAGACGATNGATGCATGCAGCCGCAGCGCAGCAACCTTGGTTC TTGCTGCTGCAATCAGCAGCAGCAGCAGNCAGCAACAACAGCAAGGANCCCNGATGGCAGCTCTT GNCCCAAGTGCTTGGTAGATGGAAAGANTGCGCTGCTGCTGCCGCAGCACATGCAGCAGCTGCGG CGCTGCAGCAGCAGAGCGCCTGCTGTTTGCAGCAACAGTAACAGCAGCAGCAGCAGCAGCAAAGA GGAAGAAGAAGCAGATGTGTTGCTGCTGCAGCAAGCTGCTGCTGAGACTCTCACTATGTACACGG CGCCGCAGACTCCCCGGCTCTCTGGAACTGCAGCAGCAGCAGCAGCAGCGCTCGCTGCTGCTGCT GCTGCTACTGCTGCATTTCGAGCAGCCTTAGTAACCCTGCAGCAGCAAAAAGATNGTGAAGGCCG AGGACGCNNGTCTCAGCAGCAGCAGCAGCAGCAGGAACAGCAGCA Found at i:347 original size:3 final size:3 Alignment explanation

Indices: 341--370 Score: 37 Period size: 3 Copynumber: 9.7 Consensus size: 3 331 CTGCTGCAAT * * 341 CAG CAG CAG CAG CAG NCAG CAA CAA CAG CA 1 CAG CAG CAG CAG CAG -CAG CAG CAG CAG CA 371 AGGANCCCNG Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 3 21 0.88 4 3 0.12 ACGTcount: A:0.40, C:0.33, G:0.23, T:0.00 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 1 -- 340 ATCCCCCCCCCCCCCCCCCGTTGTTGCTGCAGCTGCTGCTGCGGCTGCGCCGCCAGGGCCACTGT TGAGTCGCCATCTGCGTGGCGGCCANGCAGCAGCAGCAGCAGCTGCTGCTGCTGCGTCTCCTGCT GCTGCTGCTGCTCTGCTGCACTACACCGTAGATGTGCCTCAAGTGGTGCAGCAGGTAGGGCAGCG GCTGGGCTTCACAGACTGCGGCTGCAACAGCAGCAGCAGCAGCGGCAGCAGCAGCAGCAGCAGCA GCTCAGGGTCCGTGTTGGTTGTTGCAGACGATNGATGCATGCAGCCGCAGCGCAGCAACCTTGGT TCTTGCTGCTGCAAT Right flanking sequence: Indices 371 -- 870 AGGANCCCNGATGGCAGCTCTTGNCCCAAGTGCTTGGTAGATGGAAAGANTGCGCTGCTGCTGCC GCAGCACATGCAGCAGCTGCGGCGCTGCAGCAGCAGAGCGCCTGCTGTTTGCAGCAACAGTAACA GCAGCAGCAGCAGCAGCAAAGAGGAAGAAGAAGCAGATGTGTTGCTGCTGCAGCAAGCTGCTGCT GAGACTCTCACTATGTACACGGCGCCGCAGACTCCCCGGCTCTCTGGAACTGCAGCAGCAGCAGC AGCAGCGCTCGCTGCTGCTGCTGCTGCTACTGCTGCATTTCGAGCAGCCTTAGTAACCCTGCAGC AGCAAAAAGATNGTGAAGGCCGAGGACGCNNGTCTCAGCAGCAGCAGCAGCAGCAGGAACAGCAG CAGCAGCAGTGCCTTCGACACGCAGCAGACCTGCTAGTGCAGGCTTTGTGGACGGGAAGCACCCA AACAGCAGCAGCAGGAGCAGCAGCAGCAGCAGCAAGCGGCTTTGC Found at i:451 original size:3 final size:3 Alignment explanation

Indices: 436--471 Score: 28 Period size: 3 Copynumber: 12.3 Consensus size: 3 426 TGCTGCTGCC * * * 436 GCA GCA -CA TGCA GCA GCT GCG GC- GCT GCA GCA GCA G 1 GCA GCA GCA -GCA GCA GCA GCA GCA GCA GCA GCA GCA G 472 AGCGCCTGCT Statistics Matches: 27, Mismatches: 3, Indels: 6 0.75 0.08 0.17 Matches are distributed among these distances: 2 4 0.15 3 21 0.78 4 2 0.07 ACGTcount: A:0.22, C:0.33, G:0.36, T:0.08 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 1 -- 435 ATCCCCCCCCCCCCCCCCCGTTGTTGCTGCAGCTGCTGCTGCGGCTGCGCCGCCAGGGCCACTGT TGAGTCGCCATCTGCGTGGCGGCCANGCAGCAGCAGCAGCAGCTGCTGCTGCTGCGTCTCCTGCT GCTGCTGCTGCTCTGCTGCACTACACCGTAGATGTGCCTCAAGTGGTGCAGCAGGTAGGGCAGCG GCTGGGCTTCACAGACTGCGGCTGCAACAGCAGCAGCAGCAGCGGCAGCAGCAGCAGCAGCAGCA GCTCAGGGTCCGTGTTGGTTGTTGCAGACGATNGATGCATGCAGCCGCAGCGCAGCAACCTTGGT TCTTGCTGCTGCAATCAGCAGCAGCAGCAGNCAGCAACAACAGCAAGGANCCCNGATGGCAGCTC TTGNCCCAAGTGCTTGGTAGATGGAAAGANTGCGCTGCTGCTGCC Right flanking sequence: Indices 472 -- 971 AGCGCCTGCTGTTTGCAGCAACAGTAACAGCAGCAGCAGCAGCAGCAAAGAGGAAGAAGAAGCAG ATGTGTTGCTGCTGCAGCAAGCTGCTGCTGAGACTCTCACTATGTACACGGCGCCGCAGACTCCC CGGCTCTCTGGAACTGCAGCAGCAGCAGCAGCAGCGCTCGCTGCTGCTGCTGCTGCTACTGCTGC ATTTCGAGCAGCCTTAGTAACCCTGCAGCAGCAAAAAGATNGTGAAGGCCGAGGACGCNNGTCTC AGCAGCAGCAGCAGCAGCAGGAACAGCAGCAGCAGCAGTGCCTTCGACACGCAGCAGACCTGCTA GTGCAGGCTTTGTGGACGGGAAGCACCCAAACAGCAGCAGCAGGAGCAGCAGCAGCAGCAGCAAG CGGCTTTGCTGCTGCGGGGCTCAAGCCAGCAGCAGCAGCAGCAGCAGATAACGATGGCTGCTGCT GCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCTGCAGC Found at i:507 original size:3 final size:3 Alignment explanation

Indices: 486--518 Score: 45 Period size: 3 Copynumber: 11.0 Consensus size: 3 476 CCTGCTGTTT * * * 486 GCA GCA ACA GTA ACA GCA GCA GCA GCA GCA GCA 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA 519 AAGAGGAAGA Statistics Matches: 24, Mismatches: 6, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 3 24 1.00 ACGTcount: A:0.39, C:0.30, G:0.27, T:0.03 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 1 -- 485 ATCCCCCCCCCCCCCCCCCGTTGTTGCTGCAGCTGCTGCTGCGGCTGCGCCGCCAGGGCCACTGT TGAGTCGCCATCTGCGTGGCGGCCANGCAGCAGCAGCAGCAGCTGCTGCTGCTGCGTCTCCTGCT GCTGCTGCTGCTCTGCTGCACTACACCGTAGATGTGCCTCAAGTGGTGCAGCAGGTAGGGCAGCG GCTGGGCTTCACAGACTGCGGCTGCAACAGCAGCAGCAGCAGCGGCAGCAGCAGCAGCAGCAGCA GCTCAGGGTCCGTGTTGGTTGTTGCAGACGATNGATGCATGCAGCCGCAGCGCAGCAACCTTGGT TCTTGCTGCTGCAATCAGCAGCAGCAGCAGNCAGCAACAACAGCAAGGANCCCNGATGGCAGCTC TTGNCCCAAGTGCTTGGTAGATGGAAAGANTGCGCTGCTGCTGCCGCAGCACATGCAGCAGCTGC GGCGCTGCAGCAGCAGAGCGCCTGCTGTTT Right flanking sequence: Indices 519 -- 1018 AAGAGGAAGAAGAAGCAGATGTGTTGCTGCTGCAGCAAGCTGCTGCTGAGACTCTCACTATGTAC ACGGCGCCGCAGACTCCCCGGCTCTCTGGAACTGCAGCAGCAGCAGCAGCAGCGCTCGCTGCTGC TGCTGCTGCTACTGCTGCATTTCGAGCAGCCTTAGTAACCCTGCAGCAGCAAAAAGATNGTGAAG GCCGAGGACGCNNGTCTCAGCAGCAGCAGCAGCAGCAGGAACAGCAGCAGCAGCAGTGCCTTCGA CACGCAGCAGACCTGCTAGTGCAGGCTTTGTGGACGGGAAGCACCCAAACAGCAGCAGCAGGAGC AGCAGCAGCAGCAGCAAGCGGCTTTGCTGCTGCGGGGCTCAAGCCAGCAGCAGCAGCAGCAGCAG ATAACGATGGCTGCTGCTGCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCTGCAGCAG CAGCAACAACAGGAAAAGCAGCAGCGNGCAGAAACAGGAACAGCA Found at i:549 original size:3 final size:3 Alignment explanation

Indices: 543--566 Score: 25 Period size: 3 Copynumber: 7.7 Consensus size: 3 533 GCAGATGTGT * * 543 TGC TGC TGC AGC AAGC TGC TGC TG 1 TGC TGC TGC TGC -TGC TGC TGC TG 567 AGACTCTCAC Statistics Matches: 18, Mismatches: 2, Indels: 2 0.82 0.09 0.09 Matches are distributed among these distances: 3 15 0.83 4 3 0.17 ACGTcount: A:0.12, C:0.29, G:0.33, T:0.25 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 43 -- 542 GGCTGCGCCGCCAGGGCCACTGTTGAGTCGCCATCTGCGTGGCGGCCANGCAGCAGCAGCAGCAG CTGCTGCTGCTGCGTCTCCTGCTGCTGCTGCTGCTCTGCTGCACTACACCGTAGATGTGCCTCAA GTGGTGCAGCAGGTAGGGCAGCGGCTGGGCTTCACAGACTGCGGCTGCAACAGCAGCAGCAGCAG CGGCAGCAGCAGCAGCAGCAGCAGCTCAGGGTCCGTGTTGGTTGTTGCAGACGATNGATGCATGC AGCCGCAGCGCAGCAACCTTGGTTCTTGCTGCTGCAATCAGCAGCAGCAGCAGNCAGCAACAACA GCAAGGANCCCNGATGGCAGCTCTTGNCCCAAGTGCTTGGTAGATGGAAAGANTGCGCTGCTGCT GCCGCAGCACATGCAGCAGCTGCGGCGCTGCAGCAGCAGAGCGCCTGCTGTTTGCAGCAACAGTA ACAGCAGCAGCAGCAGCAGCAAAGAGGAAGAAGAAGCAGATGTGT Right flanking sequence: Indices 567 -- 1066 AGACTCTCACTATGTACACGGCGCCGCAGACTCCCCGGCTCTCTGGAACTGCAGCAGCAGCAGCA GCAGCGCTCGCTGCTGCTGCTGCTGCTACTGCTGCATTTCGAGCAGCCTTAGTAACCCTGCAGCA GCAAAAAGATNGTGAAGGCCGAGGACGCNNGTCTCAGCAGCAGCAGCAGCAGCAGGAACAGCAGC AGCAGCAGTGCCTTCGACACGCAGCAGACCTGCTAGTGCAGGCTTTGTGGACGGGAAGCACCCAA ACAGCAGCAGCAGGAGCAGCAGCAGCAGCAGCAAGCGGCTTTGCTGCTGCGGGGCTCAAGCCAGC AGCAGCAGCAGCAGCAGATAACGATGGCTGCTGCTGCTGGTGGCTTGTGGCAGATCTCATTGGAC TGCTGTGCCTGCAGCAGCAGCAACAACAGGAAAAGCAGCAGCGNGCAGAAACAGGAACAGCAGCA GCAGACACTGCAGCAGCAGCAGCAAAACCAGGACATACAGATGCT Found at i:625 original size:3 final size:3 Alignment explanation

Indices: 617--636 Score: 40 Period size: 3 Copynumber: 6.7 Consensus size: 3 607 CTCTGGAACT 617 GCA GCA GCA GCA GCA GCA GC 1 GCA GCA GCA GCA GCA GCA GC 637 GCTCGCTGCT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 17 1.00 ACGTcount: A:0.30, C:0.35, G:0.35, T:0.00 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 117 -- 616 CTGCGTCTCCTGCTGCTGCTGCTGCTCTGCTGCACTACACCGTAGATGTGCCTCAAGTGGTGCAG CAGGTAGGGCAGCGGCTGGGCTTCACAGACTGCGGCTGCAACAGCAGCAGCAGCAGCGGCAGCAG CAGCAGCAGCAGCAGCTCAGGGTCCGTGTTGGTTGTTGCAGACGATNGATGCATGCAGCCGCAGC GCAGCAACCTTGGTTCTTGCTGCTGCAATCAGCAGCAGCAGCAGNCAGCAACAACAGCAAGGANC CCNGATGGCAGCTCTTGNCCCAAGTGCTTGGTAGATGGAAAGANTGCGCTGCTGCTGCCGCAGCA CATGCAGCAGCTGCGGCGCTGCAGCAGCAGAGCGCCTGCTGTTTGCAGCAACAGTAACAGCAGCA GCAGCAGCAGCAAAGAGGAAGAAGAAGCAGATGTGTTGCTGCTGCAGCAAGCTGCTGCTGAGACT CTCACTATGTACACGGCGCCGCAGACTCCCCGGCTCTCTGGAACT Right flanking sequence: Indices 637 -- 1136 GCTCGCTGCTGCTGCTGCTGCTACTGCTGCATTTCGAGCAGCCTTAGTAACCCTGCAGCAGCAAA AAGATNGTGAAGGCCGAGGACGCNNGTCTCAGCAGCAGCAGCAGCAGCAGGAACAGCAGCAGCAG CAGTGCCTTCGACACGCAGCAGACCTGCTAGTGCAGGCTTTGTGGACGGGAAGCACCCAAACAGC AGCAGCAGGAGCAGCAGCAGCAGCAGCAAGCGGCTTTGCTGCTGCGGGGCTCAAGCCAGCAGCAG CAGCAGCAGCAGATAACGATGGCTGCTGCTGCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTG TGCCTGCAGCAGCAGCAACAACAGGAAAAGCAGCAGCGNGCAGAAACAGGAACAGCAGCAGCAGA CACTGCAGCAGCAGCAGCAAAACCAGGACATACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGT CGTGGTTTGCTGCTGCTCAGGGAAGAGCAGGCAGCAGCAGCAGCA Found at i:647 original size:3 final size:3 Alignment explanation

Indices: 641--666 Score: 45 Period size: 3 Copynumber: 8.7 Consensus size: 3 631 AGCAGCGCTC * 641 GCT GCT GCT GCT GCT GCT ACT GCT GC 1 GCT GCT GCT GCT GCT GCT GCT GCT GC 667 ATTTCGAGCA Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 3 21 1.00 ACGTcount: A:0.04, C:0.35, G:0.31, T:0.31 Consensus pattern (3 bp): GCT Left flanking sequence: Indices 141 -- 640 CTCTGCTGCACTACACCGTAGATGTGCCTCAAGTGGTGCAGCAGGTAGGGCAGCGGCTGGGCTTC ACAGACTGCGGCTGCAACAGCAGCAGCAGCAGCGGCAGCAGCAGCAGCAGCAGCAGCTCAGGGTC CGTGTTGGTTGTTGCAGACGATNGATGCATGCAGCCGCAGCGCAGCAACCTTGGTTCTTGCTGCT GCAATCAGCAGCAGCAGCAGNCAGCAACAACAGCAAGGANCCCNGATGGCAGCTCTTGNCCCAAG TGCTTGGTAGATGGAAAGANTGCGCTGCTGCTGCCGCAGCACATGCAGCAGCTGCGGCGCTGCAG CAGCAGAGCGCCTGCTGTTTGCAGCAACAGTAACAGCAGCAGCAGCAGCAGCAAAGAGGAAGAAG AAGCAGATGTGTTGCTGCTGCAGCAAGCTGCTGCTGAGACTCTCACTATGTACACGGCGCCGCAG ACTCCCCGGCTCTCTGGAACTGCAGCAGCAGCAGCAGCAGCGCTC Right flanking sequence: Indices 667 -- 1166 ATTTCGAGCAGCCTTAGTAACCCTGCAGCAGCAAAAAGATNGTGAAGGCCGAGGACGCNNGTCTC AGCAGCAGCAGCAGCAGCAGGAACAGCAGCAGCAGCAGTGCCTTCGACACGCAGCAGACCTGCTA GTGCAGGCTTTGTGGACGGGAAGCACCCAAACAGCAGCAGCAGGAGCAGCAGCAGCAGCAGCAAG CGGCTTTGCTGCTGCGGGGCTCAAGCCAGCAGCAGCAGCAGCAGCAGATAACGATGGCTGCTGCT GCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCTGCAGCAGCAGCAACAACAGGAAAAG CAGCAGCGNGCAGAAACAGGAACAGCAGCAGCAGACACTGCAGCAGCAGCAGCAAAACCAGGACA TACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGTGGTTTGCTGCTGCTCAGGGAAGAGCAG GCAGCAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAGTCCTGCG Found at i:788 original size:3 final size:3 Alignment explanation

Indices: 731--769 Score: 64 Period size: 3 Copynumber: 13.0 Consensus size: 3 721 ACGCNNGTCT * * 731 CAG CAG CAG CAG CAG CAG CAG GAA CAG CAG CAG CAG CAG 1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG 770 TGCCTTCGAC Statistics Matches: 32, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 3 32 1.00 ACGTcount: A:0.36, C:0.31, G:0.33, T:0.00 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 231 -- 730 GCAGCAGCGGCAGCAGCAGCAGCAGCAGCAGCTCAGGGTCCGTGTTGGTTGTTGCAGACGATNGA TGCATGCAGCCGCAGCGCAGCAACCTTGGTTCTTGCTGCTGCAATCAGCAGCAGCAGCAGNCAGC AACAACAGCAAGGANCCCNGATGGCAGCTCTTGNCCCAAGTGCTTGGTAGATGGAAAGANTGCGC TGCTGCTGCCGCAGCACATGCAGCAGCTGCGGCGCTGCAGCAGCAGAGCGCCTGCTGTTTGCAGC AACAGTAACAGCAGCAGCAGCAGCAGCAAAGAGGAAGAAGAAGCAGATGTGTTGCTGCTGCAGCA AGCTGCTGCTGAGACTCTCACTATGTACACGGCGCCGCAGACTCCCCGGCTCTCTGGAACTGCAG CAGCAGCAGCAGCAGCGCTCGCTGCTGCTGCTGCTGCTACTGCTGCATTTCGAGCAGCCTTAGTA ACCCTGCAGCAGCAAAAAGATNGTGAAGGCCGAGGACGCNNGTCT Right flanking sequence: Indices 770 -- 1269 TGCCTTCGACACGCAGCAGACCTGCTAGTGCAGGCTTTGTGGACGGGAAGCACCCAAACAGCAGC AGCAGGAGCAGCAGCAGCAGCAGCAAGCGGCTTTGCTGCTGCGGGGCTCAAGCCAGCAGCAGCAG CAGCAGCAGATAACGATGGCTGCTGCTGCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGC CTGCAGCAGCAGCAACAACAGGAAAAGCAGCAGCGNGCAGAAACAGGAACAGCAGCAGCAGACAC TGCAGCAGCAGCAGCAAAACCAGGACATACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGT GGTTTGCTGCTGCTCAGGGAAGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAG TCCTGCGGGTGTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGCAGCAACCAG AGCAGCAAGTGCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAA Found at i:836 original size:3 final size:3 Alignment explanation

Indices: 828--859 Score: 57 Period size: 3 Copynumber: 10.7 Consensus size: 3 818 AGCACCCAAA * 828 CAG CAG CAG CAG GAG CAG CAG CAG CAG CAG CA 1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA 860 AGCGGCTTTG Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 3 27 1.00 ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 328 -- 827 TTGCTGCTGCAATCAGCAGCAGCAGCAGNCAGCAACAACAGCAAGGANCCCNGATGGCAGCTCTT GNCCCAAGTGCTTGGTAGATGGAAAGANTGCGCTGCTGCTGCCGCAGCACATGCAGCAGCTGCGG CGCTGCAGCAGCAGAGCGCCTGCTGTTTGCAGCAACAGTAACAGCAGCAGCAGCAGCAGCAAAGA GGAAGAAGAAGCAGATGTGTTGCTGCTGCAGCAAGCTGCTGCTGAGACTCTCACTATGTACACGG CGCCGCAGACTCCCCGGCTCTCTGGAACTGCAGCAGCAGCAGCAGCAGCGCTCGCTGCTGCTGCT GCTGCTACTGCTGCATTTCGAGCAGCCTTAGTAACCCTGCAGCAGCAAAAAGATNGTGAAGGCCG AGGACGCNNGTCTCAGCAGCAGCAGCAGCAGCAGGAACAGCAGCAGCAGCAGTGCCTTCGACACG CAGCAGACCTGCTAGTGCAGGCTTTGTGGACGGGAAGCACCCAAA Right flanking sequence: Indices 860 -- 1359 AGCGGCTTTGCTGCTGCGGGGCTCAAGCCAGCAGCAGCAGCAGCAGCAGATAACGATGGCTGCTG CTGCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCTGCAGCAGCAGCAACAACAGGAAA AGCAGCAGCGNGCAGAAACAGGAACAGCAGCAGCAGACACTGCAGCAGCAGCAGCAAAACCAGGA CATACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGTGGTTTGCTGCTGCTCAGGGAAGAGC AGGCAGCAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAGTCCTGCGGGTGTCGCACTATTAAAT ACTGCTGTTCTGTGGCAGCAGCTGCAGCAGCAGCAACCAGAGCAGCAAGTGCTGCTGCAGCAGCA GGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTC GAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGC Found at i:894 original size:3 final size:3 Alignment explanation

Indices: 888--908 Score: 42 Period size: 3 Copynumber: 7.0 Consensus size: 3 878 GGGCTCAAGC 888 CAG CAG CAG CAG CAG CAG CAG 1 CAG CAG CAG CAG CAG CAG CAG 909 ATAACGATGG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 18 1.00 ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 388 -- 887 CTCTTGNCCCAAGTGCTTGGTAGATGGAAAGANTGCGCTGCTGCTGCCGCAGCACATGCAGCAGC TGCGGCGCTGCAGCAGCAGAGCGCCTGCTGTTTGCAGCAACAGTAACAGCAGCAGCAGCAGCAGC AAAGAGGAAGAAGAAGCAGATGTGTTGCTGCTGCAGCAAGCTGCTGCTGAGACTCTCACTATGTA CACGGCGCCGCAGACTCCCCGGCTCTCTGGAACTGCAGCAGCAGCAGCAGCAGCGCTCGCTGCTG CTGCTGCTGCTACTGCTGCATTTCGAGCAGCCTTAGTAACCCTGCAGCAGCAAAAAGATNGTGAA GGCCGAGGACGCNNGTCTCAGCAGCAGCAGCAGCAGCAGGAACAGCAGCAGCAGCAGTGCCTTCG ACACGCAGCAGACCTGCTAGTGCAGGCTTTGTGGACGGGAAGCACCCAAACAGCAGCAGCAGGAG CAGCAGCAGCAGCAGCAAGCGGCTTTGCTGCTGCGGGGCTCAAGC Right flanking sequence: Indices 909 -- 1408 ATAACGATGGCTGCTGCTGCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCTGCAGCAG CAGCAACAACAGGAAAAGCAGCAGCGNGCAGAAACAGGAACAGCAGCAGCAGACACTGCAGCAGC AGCAGCAAAACCAGGACATACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGTGGTTTGCTG CTGCTCAGGGAAGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAGTCCTGCGGG TGTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGCAGCAACCAGAGCAGCAAG TGCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCA GGNCAGCACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCA GCAACAGNCAGCAGCAGGGGAGAGACACTCTATGGCGTCCCCNAC Found at i:924 original size:3 final size:3 Alignment explanation

Indices: 918--930 Score: 26 Period size: 3 Copynumber: 4.3 Consensus size: 3 908 GATAACGATG 918 GCT GCT GCT GCT G 1 GCT GCT GCT GCT G 931 GTGGCTTGTG Statistics Matches: 10, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 10 1.00 ACGTcount: A:0.00, C:0.31, G:0.38, T:0.31 Consensus pattern (3 bp): GCT Left flanking sequence: Indices 418 -- 917 GANTGCGCTGCTGCTGCCGCAGCACATGCAGCAGCTGCGGCGCTGCAGCAGCAGAGCGCCTGCTG TTTGCAGCAACAGTAACAGCAGCAGCAGCAGCAGCAAAGAGGAAGAAGAAGCAGATGTGTTGCTG CTGCAGCAAGCTGCTGCTGAGACTCTCACTATGTACACGGCGCCGCAGACTCCCCGGCTCTCTGG AACTGCAGCAGCAGCAGCAGCAGCGCTCGCTGCTGCTGCTGCTGCTACTGCTGCATTTCGAGCAG CCTTAGTAACCCTGCAGCAGCAAAAAGATNGTGAAGGCCGAGGACGCNNGTCTCAGCAGCAGCAG CAGCAGCAGGAACAGCAGCAGCAGCAGTGCCTTCGACACGCAGCAGACCTGCTAGTGCAGGCTTT GTGGACGGGAAGCACCCAAACAGCAGCAGCAGGAGCAGCAGCAGCAGCAGCAAGCGGCTTTGCTG CTGCGGGGCTCAAGCCAGCAGCAGCAGCAGCAGCAGATAACGATG Right flanking sequence: Indices 931 -- 1430 GTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCTGCAGCAGCAGCAACAACAGGAAAAGCAGC AGCGNGCAGAAACAGGAACAGCAGCAGCAGACACTGCAGCAGCAGCAGCAAAACCAGGACATACA GATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGTGGTTTGCTGCTGCTCAGGGAAGAGCAGGCAG CAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAGTCCTGCGGGTGTCGCACTATTAAATACTGCT GTTCTGTGGCAGCAGCTGCAGCAGCAGCAACCAGAGCAGCAAGTGCTGCTGCAGCAGCAGGGCAA NGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCGAAGCA GCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAGGGGAG AGACACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGC Found at i:975 original size:3 final size:3 Alignment explanation

Indices: 967--1045 Score: 56 Period size: 3 Copynumber: 26.0 Consensus size: 3 957 TGCTGTGCCT * * * ** * * * * 967 GCA GCA GCA GCA ACA ACA GGA AAA GCA GCA GCGN GCA GAA ACA GGA 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC-A GCA GCA GCA GCA * * 1013 ACA GCA GCA GCA GACA -CT GCA GCA GCA GCA GCA 1 GCA GCA GCA GCA G-CA GCA GCA GCA GCA GCA GCA 1046 AAACCAGGAC Statistics Matches: 54, Mismatches: 19, Indels: 6 0.68 0.24 0.08 Matches are distributed among these distances: 2 1 0.02 3 49 0.91 4 4 0.07 ACGTcount: A:0.41, C:0.28, G:0.29, T:0.01 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 467 -- 966 AGCAGAGCGCCTGCTGTTTGCAGCAACAGTAACAGCAGCAGCAGCAGCAGCAAAGAGGAAGAAGA AGCAGATGTGTTGCTGCTGCAGCAAGCTGCTGCTGAGACTCTCACTATGTACACGGCGCCGCAGA CTCCCCGGCTCTCTGGAACTGCAGCAGCAGCAGCAGCAGCGCTCGCTGCTGCTGCTGCTGCTACT GCTGCATTTCGAGCAGCCTTAGTAACCCTGCAGCAGCAAAAAGATNGTGAAGGCCGAGGACGCNN GTCTCAGCAGCAGCAGCAGCAGCAGGAACAGCAGCAGCAGCAGTGCCTTCGACACGCAGCAGACC TGCTAGTGCAGGCTTTGTGGACGGGAAGCACCCAAACAGCAGCAGCAGGAGCAGCAGCAGCAGCA GCAAGCGGCTTTGCTGCTGCGGGGCTCAAGCCAGCAGCAGCAGCAGCAGCAGATAACGATGGCTG CTGCTGCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCT Right flanking sequence: Indices 1046 -- 1545 AAACCAGGACATACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGTGGTTTGCTGCTGCTCA GGGAAGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAGTCCTGCGGGTGTCGCA CTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGCAGCAACCAGAGCAGCAAGTGCTGCT GCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGC ACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAG NCAGCAGCAGGGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGCTGCTG CATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAG CAGCAGCAGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCT Found at i:1038 original size:21 final size:21 Alignment explanation

Indices: 968--1049 Score: 80 Period size: 21 Copynumber: 4.0 Consensus size: 21 958 GCTGTGCCTG * * * 968 CAGCAGCAGCAACAACAGGAA 1 CAGCAGCAGCAGCAGCAGAAA * * 989 AAGCAGCAGC-G-NGCAGAAA 1 CAGCAGCAGCAGCAGCAGAAA * * * 1008 CAGGAACAGCAGCAGCAGACA 1 CAGCAGCAGCAGCAGCAGAAA * 1029 CTGCAGCAGCAGCAGCA-AAA 1 CAGCAGCAGCAGCAGCAGAAA 1049 C 1 C 1050 CAGGACATAC Statistics Matches: 45, Mismatches: 14, Indels: 5 0.70 0.22 0.08 Matches are distributed among these distances: 19 12 0.27 20 4 0.09 21 29 0.64 ACGTcount: A:0.43, C:0.28, G:0.27, T:0.01 Consensus pattern (21 bp): CAGCAGCAGCAGCAGCAGAAA Left flanking sequence: Indices 468 -- 967 GCAGAGCGCCTGCTGTTTGCAGCAACAGTAACAGCAGCAGCAGCAGCAGCAAAGAGGAAGAAGAA GCAGATGTGTTGCTGCTGCAGCAAGCTGCTGCTGAGACTCTCACTATGTACACGGCGCCGCAGAC TCCCCGGCTCTCTGGAACTGCAGCAGCAGCAGCAGCAGCGCTCGCTGCTGCTGCTGCTGCTACTG CTGCATTTCGAGCAGCCTTAGTAACCCTGCAGCAGCAAAAAGATNGTGAAGGCCGAGGACGCNNG TCTCAGCAGCAGCAGCAGCAGCAGGAACAGCAGCAGCAGCAGTGCCTTCGACACGCAGCAGACCT GCTAGTGCAGGCTTTGTGGACGGGAAGCACCCAAACAGCAGCAGCAGGAGCAGCAGCAGCAGCAG CAAGCGGCTTTGCTGCTGCGGGGCTCAAGCCAGCAGCAGCAGCAGCAGCAGATAACGATGGCTGC TGCTGCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCTG Right flanking sequence: Indices 1050 -- 1549 CAGGACATACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGTGGTTTGCTGCTGCTCAGGGA AGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAGTCCTGCGGGTGTCGCACTAT TAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGCAGCAACCAGAGCAGCAAGTGCTGCTGCAG CAGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCT TGCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAG CAGCAGGGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATT TTATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGC AGCAGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGA Found at i:1130 original size:3 final size:3 Alignment explanation

Indices: 1117--1149 Score: 57 Period size: 3 Copynumber: 10.7 Consensus size: 3 1107 CTCAGGGAAG 1117 AGC AGGC AGC AGC AGC AGC AGC AGC AGC AGC AG 1 AGC A-GC AGC AGC AGC AGC AGC AGC AGC AGC AG 1150 ACCGCTACAG Statistics Matches: 29, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 3 26 0.90 4 3 0.10 ACGTcount: A:0.33, C:0.30, G:0.36, T:0.00 Consensus pattern (3 bp): AGC Left flanking sequence: Indices 617 -- 1116 GCAGCAGCAGCAGCAGCAGCGCTCGCTGCTGCTGCTGCTGCTACTGCTGCATTTCGAGCAGCCTT AGTAACCCTGCAGCAGCAAAAAGATNGTGAAGGCCGAGGACGCNNGTCTCAGCAGCAGCAGCAGC AGCAGGAACAGCAGCAGCAGCAGTGCCTTCGACACGCAGCAGACCTGCTAGTGCAGGCTTTGTGG ACGGGAAGCACCCAAACAGCAGCAGCAGGAGCAGCAGCAGCAGCAGCAAGCGGCTTTGCTGCTGC GGGGCTCAAGCCAGCAGCAGCAGCAGCAGCAGATAACGATGGCTGCTGCTGCTGGTGGCTTGTGG CAGATCTCATTGGACTGCTGTGCCTGCAGCAGCAGCAACAACAGGAAAAGCAGCAGCGNGCAGAA ACAGGAACAGCAGCAGCAGACACTGCAGCAGCAGCAGCAAAACCAGGACATACAGATGCTTGAAG GACTGCTTTTGCTGCTGCGTCGTGGTTTGCTGCTGCTCAGGGAAG Right flanking sequence: Indices 1150 -- 1649 ACCGCTACAGTCCTGCGGGTGTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAG CAGCAACCAGAGCAGCAAGTGCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCT GCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGC AGCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAGGGGAGAGACACTCTATGGCGTCCCCNACT GAGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTG AGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGAGAAGGCTGCAACGCGGCGTTNGA GAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTCTGCTCTTGCTGCAGCTGCTGCAGCAGCCG CAGCAGCAAAGGGAACTGCAGCAGCGGTGTCACTTNCTTCCCAGC Found at i:1214 original size:3 final size:3 Alignment explanation

Indices: 1199--1250 Score: 39 Period size: 3 Copynumber: 17.3 Consensus size: 3 1189 CTGTTCTGTG * * *** * * 1199 GCA GCA GCT GCA GCA GCA GCAA CCA G-A GCA GCA AGT GCT GCT GCA 1 GCA GCA GCA GCA GCA GCA GC-A GCA GCA GCA GCA GCA GCA GCA GCA 1244 GCA GCA G 1 GCA GCA G 1251 GGCAANGCAG Statistics Matches: 37, Mismatches: 10, Indels: 4 0.73 0.20 0.08 Matches are distributed among these distances: 2 2 0.05 3 33 0.89 4 2 0.05 ACGTcount: A:0.29, C:0.31, G:0.33, T:0.08 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 699 -- 1198 AAAAAGATNGTGAAGGCCGAGGACGCNNGTCTCAGCAGCAGCAGCAGCAGCAGGAACAGCAGCAG CAGCAGTGCCTTCGACACGCAGCAGACCTGCTAGTGCAGGCTTTGTGGACGGGAAGCACCCAAAC AGCAGCAGCAGGAGCAGCAGCAGCAGCAGCAAGCGGCTTTGCTGCTGCGGGGCTCAAGCCAGCAG CAGCAGCAGCAGCAGATAACGATGGCTGCTGCTGCTGGTGGCTTGTGGCAGATCTCATTGGACTG CTGTGCCTGCAGCAGCAGCAACAACAGGAAAAGCAGCAGCGNGCAGAAACAGGAACAGCAGCAGC AGACACTGCAGCAGCAGCAGCAAAACCAGGACATACAGATGCTTGAAGGACTGCTTTTGCTGCTG CGTCGTGGTTTGCTGCTGCTCAGGGAAGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGACCG CTACAGTCCTGCGGGTGTCGCACTATTAAATACTGCTGTTCTGTG Right flanking sequence: Indices 1251 -- 1750 GGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCG AAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAG GGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTG CTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGC AGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTC TGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCACTTN CTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACGCTGCA TGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAA Found at i:1346 original size:3 final size:3 Alignment explanation

Indices: 1338--1380 Score: 70 Period size: 3 Copynumber: 14.0 Consensus size: 3 1328 CAGTAGCCCT * 1338 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG NCAG CAG CAG 1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG -CAG CAG CAG 1381 GGGAGAGACA Statistics Matches: 37, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 3 34 0.92 4 3 0.08 ACGTcount: A:0.35, C:0.33, G:0.30, T:0.00 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 838 -- 1337 AGGAGCAGCAGCAGCAGCAGCAAGCGGCTTTGCTGCTGCGGGGCTCAAGCCAGCAGCAGCAGCAG CAGCAGATAACGATGGCTGCTGCTGCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCTG CAGCAGCAGCAACAACAGGAAAAGCAGCAGCGNGCAGAAACAGGAACAGCAGCAGCAGACACTGC AGCAGCAGCAGCAAAACCAGGACATACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGTGGT TTGCTGCTGCTCAGGGAAGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAGTCC TGCGGGTGTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGCAGCAACCAGAGC AGCAAGTGCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGA GAGGCAGGNCAGCACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCT Right flanking sequence: Indices 1381 -- 1880 GGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTG CTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGC AGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTC TGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCACTTN CTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACGCTGCA TGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAAGCAGTAGCTAGCAGCAGCAG CTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGTAGCTGCTGCTGCTGCAGCAGC ACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTC Found at i:1430 original size:5 final size:5 Alignment explanation

Indices: 1420--1436 Score: 25 Period size: 5 Copynumber: 3.2 Consensus size: 5 1410 GAGGGGGNTC 1420 CGCTG CGCTG CTGCTG C 1 CGCTG CGCTG C-GCTG C 1437 ATTTTATTGC Statistics Matches: 11, Mismatches: 0, Indels: 1 0.92 0.00 0.08 Matches are distributed among these distances: 5 6 0.55 6 5 0.45 ACGTcount: A:0.00, C:0.41, G:0.35, T:0.24 Consensus pattern (5 bp): CGCTG Left flanking sequence: Indices 920 -- 1419 TGCTGCTGCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCTGCAGCAGCAGCAACAACA GGAAAAGCAGCAGCGNGCAGAAACAGGAACAGCAGCAGCAGACACTGCAGCAGCAGCAGCAAAAC CAGGACATACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGTGGTTTGCTGCTGCTCAGGGA AGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAGTCCTGCGGGTGTCGCACTAT TAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGCAGCAACCAGAGCAGCAAGTGCTGCTGCAG CAGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCT TGCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAG CAGCAGGGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTC Right flanking sequence: Indices 1437 -- 1936 ATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGC AGCAGCAGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGA GACTGTGTCTGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGG TGTCACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGA GACGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAAGCAGTAGCTAG CAGCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGTAGCTGCTGCTGC TGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCC TAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAA Found at i:1434 original size:3 final size:3 Alignment explanation

Indices: 1421--1436 Score: 25 Period size: 3 Copynumber: 5.7 Consensus size: 3 1411 AGGGGGNTCC 1421 GCT GC- GCT GCT GCT GC 1 GCT GCT GCT GCT GCT GC 1437 ATTTTATTGC Statistics Matches: 12, Mismatches: 0, Indels: 2 0.86 0.00 0.14 Matches are distributed among these distances: 2 2 0.17 3 10 0.83 ACGTcount: A:0.00, C:0.38, G:0.38, T:0.25 Consensus pattern (3 bp): GCT Left flanking sequence: Indices 921 -- 1420 GCTGCTGCTGGTGGCTTGTGGCAGATCTCATTGGACTGCTGTGCCTGCAGCAGCAGCAACAACAG GAAAAGCAGCAGCGNGCAGAAACAGGAACAGCAGCAGCAGACACTGCAGCAGCAGCAGCAAAACC AGGACATACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGTGGTTTGCTGCTGCTCAGGGAA GAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAGTCCTGCGGGTGTCGCACTATT AAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGCAGCAACCAGAGCAGCAAGTGCTGCTGCAGC AGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTT GCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGC AGCAGGGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTCC Right flanking sequence: Indices 1437 -- 1936 ATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGC AGCAGCAGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGA GACTGTGTCTGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGG TGTCACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGA GACGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAAGCAGTAGCTAG CAGCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGTAGCTGCTGCTGC TGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCC TAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAA Found at i:1483 original size:3 final size:3 Alignment explanation

Indices: 1475--1515 Score: 75 Period size: 3 Copynumber: 13.7 Consensus size: 3 1465 GTGCTTGCTG * 1475 AGC AGC AGC AGC AGC AGC AAC AGC AGC AGC AGC AGC AGC AG 1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG 1516 AGAAGGCTGC Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 3 36 1.00 ACGTcount: A:0.37, C:0.32, G:0.32, T:0.00 Consensus pattern (3 bp): AGC Left flanking sequence: Indices 975 -- 1474 AGCAACAACAGGAAAAGCAGCAGCGNGCAGAAACAGGAACAGCAGCAGCAGACACTGCAGCAGCA GCAGCAAAACCAGGACATACAGATGCTTGAAGGACTGCTTTTGCTGCTGCGTCGTGGTTTGCTGC TGCTCAGGGAAGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGACCGCTACAGTCCTGCGGGT GTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGCAGCAACCAGAGCAGCAAGT GCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAG GNCAGCACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAG CAACAGNCAGCAGCAGGGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTG CTGCTGCATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTG Right flanking sequence: Indices 1516 -- 2015 AGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTCTGCTC TTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCACTTNCTTCC CAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACGCTGCATGCAG TGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAAGCAGTAGCTAGCAGCAGCAGCTAGC CGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGTAGCTGCTGCTGCTGCAGCAGCACCAG TAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTACAATTTGCT GGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTAAACCCTAAACCCTAAANCCCTGCGAC ACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAA Found at i:1594 original size:9 final size:9 Alignment explanation

Indices: 1582--1608 Score: 40 Period size: 9 Copynumber: 3.0 Consensus size: 9 1572 TGTCTGCTCT 1582 TGCTGCAGC 1 TGCTGCAGC 1591 TGCTGCAGC 1 TGCTGCAGC * * 1600 AGCCGCAGC 1 TGCTGCAGC 1609 AGCAAAGGGA Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 9 16 1.00 ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15 Consensus pattern (9 bp): TGCTGCAGC Left flanking sequence: Indices 1082 -- 1581 GCTGCTGCGTCGTGGTTTGCTGCTGCTCAGGGAAGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAG CAGACCGCTACAGTCCTGCGGGTGTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCAG CAGCAGCAACCAGAGCAGCAAGTGCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCTN TCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCTCAGC AGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAGGGGAGAGACACTCTATGGCGTCCCCN ACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTTG CTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGAGAAGGCTGCAACGCGGCGTT NGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTCTGCTCT Right flanking sequence: Indices 1609 -- 2108 AGCAAAGGGAACTGCAGCAGCGGTGTCACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGC AGCAGCAGCAGAGCTGTGCCGGAGACGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGA TGAGAGTTAGAAGCAGTAGCTAGCAGCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCT GCAGCTGCTGTAGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTG TATGTACAGCTCGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAG CAAACCCNNTAAACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCA AGAGAGCCAATTTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGGTGCTGCTGTTG CTGCNTGCTGCTGCTCCTGGAAANGCACCTTGCTGCGGCTGCTGC Found at i:1609 original size:9 final size:9 Alignment explanation

Indices: 1586--1611 Score: 38 Period size: 9 Copynumber: 2.9 Consensus size: 9 1576 TGCTCTTGCT * * 1586 GCAGCTGCT 1 GCAGCAGCC 1595 GCAGCAGCC 1 GCAGCAGCC 1604 GCAGCAGC 1 GCAGCAGC 1612 AAAGGGAACT Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 9 15 1.00 ACGTcount: A:0.19, C:0.38, G:0.35, T:0.08 Consensus pattern (9 bp): GCAGCAGCC Left flanking sequence: Indices 1086 -- 1585 CTGCGTCGTGGTTTGCTGCTGCTCAGGGAAGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGA CCGCTACAGTCCTGCGGGTGTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGC AGCAACCAGAGCAGCAAGTGCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTG CAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCA GCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAGGGGAGAGACACTCTATGGCGTCCCCNACTG AGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGA GCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAG AAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTCTGCTCTTGCT Right flanking sequence: Indices 1612 -- 2111 AAAGGGAACTGCAGCAGCGGTGTCACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGC AGCAGCAGAGCTGTGCCGGAGACGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGA GAGTTAGAAGCAGTAGCTAGCAGCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCA GCTGCTGTAGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTAT GTACAGCTCGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAA ACCCNNTAAACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGA GAGCCAATTTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTG CNTGCTGCTGCTCCTGGAAANGCACCTTGCTGCGGCTGCTGCTGC Found at i:1610 original size:12 final size:12 Alignment explanation

Indices: 1586--1612 Score: 40 Period size: 12 Copynumber: 2.2 Consensus size: 12 1576 TGCTCTTGCT * * 1586 GCAGCTGCTGCA 1 GCAGCCGCAGCA 1598 GCAGCCGCAGCA 1 GCAGCCGCAGCA 1610 GCA 1 GCA 1613 AAGGGAACTG Statistics Matches: 13, Mismatches: 2, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.22, C:0.37, G:0.33, T:0.07 Consensus pattern (12 bp): GCAGCCGCAGCA Left flanking sequence: Indices 1086 -- 1585 CTGCGTCGTGGTTTGCTGCTGCTCAGGGAAGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGA CCGCTACAGTCCTGCGGGTGTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGC AGCAACCAGAGCAGCAAGTGCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTG CAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCA GCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAGGGGAGAGACACTCTATGGCGTCCCCNACTG AGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGA GCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAG AAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTCTGCTCTTGCT Right flanking sequence: Indices 1613 -- 2112 AAGGGAACTGCAGCAGCGGTGTCACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCA GCAGCAGAGCTGTGCCGGAGACGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAG AGTTAGAAGCAGTAGCTAGCAGCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAG CTGCTGTAGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATG TACAGCTCGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAA CCCNNTAAACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAG AGCCAATTTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGC NTGCTGCTGCTCCTGGAAANGCACCTTGCTGCGGCTGCTGCTGCT Found at i:1629 original size:3 final size:3 Alignment explanation

Indices: 1586--1612 Score: 33 Period size: 3 Copynumber: 9.0 Consensus size: 3 1576 TGCTCTTGCT * * * 1586 GCA GCT GCT GCA GCA GCC GCA GCA GCA 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA 1613 AAGGGAACTG Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 3 20 1.00 ACGTcount: A:0.22, C:0.37, G:0.33, T:0.07 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 1086 -- 1585 CTGCGTCGTGGTTTGCTGCTGCTCAGGGAAGAGCAGGCAGCAGCAGCAGCAGCAGCAGCAGCAGA CCGCTACAGTCCTGCGGGTGTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCAGCAGC AGCAACCAGAGCAGCAAGTGCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTG CAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCA GCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAGGGGAGAGACACTCTATGGCGTCCCCNACTG AGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGA GCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAG AAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTCTGCTCTTGCT Right flanking sequence: Indices 1613 -- 2112 AAGGGAACTGCAGCAGCGGTGTCACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCA GCAGCAGAGCTGTGCCGGAGACGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAG AGTTAGAAGCAGTAGCTAGCAGCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAG CTGCTGTAGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATG TACAGCTCGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAA CCCNNTAAACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAG AGCCAATTTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGC NTGCTGCTGCTCCTGGAAANGCACCTTGCTGCGGCTGCTGCTGCT Found at i:1661 original size:3 final size:3 Alignment explanation

Indices: 1646--1684 Score: 71 Period size: 3 Copynumber: 13.0 Consensus size: 3 1636 ACTTNCTTCC * 1646 CAG CAG CAA CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG 1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG 1685 AGCTGTGCCG Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 3 34 1.00 ACGTcount: A:0.36, C:0.33, G:0.31, T:0.00 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 1146 -- 1645 GCAGACCGCTACAGTCCTGCGGGTGTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCA GCAGCAGCAACCAGAGCAGCAAGTGCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCT NTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCTCAG CAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAGGGGAGAGACACTCTATGGCGTCCCC NACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTT GCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGAGAAGGCTGCAACGCGGCGT TNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTCTGCTCTTGCTGCAGCTGCTGCAGCA GCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCACTTNCTTCC Right flanking sequence: Indices 1685 -- 2184 AGCTGTGCCGGAGACGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGA AGCAGTAGCTAGCAGCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGT AGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCT CGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTA AACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAAT TTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGC TGCTCCTGGAAANGCACCTTGCTGCGGCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCA GCAGCAGCAGCAGCAGNCGCGGGGCTTCCGCCNTGTACGGCACAG Found at i:1768 original size:3 final size:3 Alignment explanation

Indices: 1750--1840 Score: 59 Period size: 3 Copynumber: 29.7 Consensus size: 3 1740 GAGAGTTAGA * * * * 1750 AGC AGT AGC TAGC AGC AGC AGC TAGC CGC AGC AGC AGC AGC GGC AGT 1 AGC AGC AGC -AGC AGC AGC AGC -AGC AGC AGC AGC AGC AGC AGC AGC * * * * * * * * * * * 1797 CGC TGC TGC AGC TGC TGT AGC TGC TGC TGC TGC AGC AGC ACC AG 1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG 1841 TAATTCTTAG Statistics Matches: 67, Mismatches: 19, Indels: 4 0.74 0.21 0.04 Matches are distributed among these distances: 3 61 0.91 4 6 0.09 ACGTcount: A:0.21, C:0.32, G:0.33, T:0.14 Consensus pattern (3 bp): AGC Left flanking sequence: Indices 1250 -- 1749 GGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTC GAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCA GGGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATT GCTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAG CAGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGT CTGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCACTT NCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACGCTGC ATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGA Right flanking sequence: Indices 1841 -- 2340 TAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTACAATTTGCT GGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTAAACCCTAAACCCTAAANCCCTGCGAC ACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAAATTNCGAGCAGCAGACGCAC TGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANGCACCTTGCTGCG GCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCGGGGCT TCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTCCTTCT TTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGCTGCTGCTGCT GCTGCTGCACGGCAGTCGTAGCAGCAGCAGCAGCAGCAGCAGCAG Found at i:1772 original size:13 final size:13 Alignment explanation

Indices: 1746--1795 Score: 65 Period size: 13 Copynumber: 3.9 Consensus size: 13 1736 TGATGAGAGT * * 1746 TAGAAGCAGTAGC 1 TAGCAGCAGCAGC 1759 TAGCAGCAGCAGC 1 TAGCAGCAGCAGC * 1772 TAGCCGCAGCAGC 1 TAGCAGCAGCAGC * 1785 -AGCAGCGGCAG 1 TAGCAGCAGCAG 1796 TCGCTGCTGC Statistics Matches: 32, Mismatches: 5, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 12 9 0.28 13 23 0.72 ACGTcount: A:0.30, C:0.28, G:0.34, T:0.08 Consensus pattern (13 bp): TAGCAGCAGCAGC Left flanking sequence: Indices 1246 -- 1745 AGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTT GCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGC AGCAGGGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTT TATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCA GCAGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACT GTGTCTGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTC ACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACG CTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGT Right flanking sequence: Indices 1796 -- 2295 TCGCTGCTGCAGCTGCTGTAGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTA TTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAAT CCTCGCAGCAAACCCNNTAAACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCT GAGAAGCAAGAGAGCCAATTTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGGTGC TGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANGCACCTTGCTGCGGCTGCTGCTGCTGCTGCTAC GAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCGGGGCTTCCGCCNTGTACGGCACAGC AGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTCCTTCTTTGGTCTCCAAACTGCTCCA GCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGCTGCTGCTGCT Found at i:1795 original size:9 final size:9 Alignment explanation

Indices: 1760--1835 Score: 66 Period size: 9 Copynumber: 8.3 Consensus size: 9 1750 AGCAGTAGCT * 1760 AGCAGCAGC 1 AGCTGCAGC * 1769 AGCTAGCCGC 1 AGCT-GCAGC * 1779 AGCAGCAGC 1 AGCTGCAGC * * 1788 AGCGGCAGT 1 AGCTGCAGC * * 1797 CGCTGCTGC 1 AGCTGCAGC * * 1806 AGCTGCTGT 1 AGCTGCAGC * 1815 AGCTGCTGC 1 AGCTGCAGC * 1824 TGCTGCAGC 1 AGCTGCAGC 1833 AGC 1 AGC 1836 ACCAGTAATT Statistics Matches: 50, Mismatches: 16, Indels: 2 0.74 0.24 0.03 Matches are distributed among these distances: 9 43 0.86 10 7 0.14 ACGTcount: A:0.18, C:0.33, G:0.34, T:0.14 Consensus pattern (9 bp): AGCTGCAGC Left flanking sequence: Indices 1260 -- 1759 GCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCGAAGCAGCTG AAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAGGGGAGAGAC ACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTGCTTCTTCTT GCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGAGAA GGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTCTGCTCTTGC TGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCACTTNCTTCCCAGC AGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACGCTGCATGCAGTGCT ACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAAGCAGTAGCT Right flanking sequence: Indices 1836 -- 2335 ACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTACAAT TTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTAAACCCTAAACCCTAAANCCCT GCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAAATTNCGAGCAGCAGA CGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANGCACCTTG CTGCGGCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCG GGGCTTCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTC CTTCTTTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGCTGCTG CTGCTGCTGCTGCACGGCAGTCGTAGCAGCAGCAGCAGCAGCAGC Found at i:1955 original size:7 final size:7 Alignment explanation

Indices: 1943--1965 Score: 37 Period size: 7 Copynumber: 3.1 Consensus size: 7 1933 GCAAACCCNN 1943 TAAACCC 1 TAAACCC 1950 TAAACCC 1 TAAACCC 1957 TAAANCCC 1 TAAA-CCC 1965 T 1 T 1966 GCGACACTNA Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 7 11 0.73 8 4 0.27 ACGTcount: A:0.39, C:0.39, G:0.00, T:0.17 Consensus pattern (7 bp): TAAACCC Left flanking sequence: Indices 1443 -- 1942 TTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGC AGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGT GTCTGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCAC TTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACGCT GCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAAGCAGTAGCTAGCAGCAG CAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGTAGCTGCTGCTGCTGCAGC AGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTAC AATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNN Right flanking sequence: Indices 1966 -- 2395 GCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAAATTNCGAGCAGCAGA CGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANGCACCTTG CTGCGGCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCG GGGCTTCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTC CTTCTTTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGCTGCTG CTGCTGCTGCTGCACGGCAGTCGTAGCAGCAGCAGCAGCAGCAGCAGCAGGGGGGTGGCGAGGAG CAGCAGCAGCAGCAGCAGCAGCAGCATCATGCTGCTGCAG Found at i:2059 original size:3 final size:3 Alignment explanation

Indices: 2053--2118 Score: 44 Period size: 3 Copynumber: 21.3 Consensus size: 3 2043 GCNAAAATGG * * * *** * ** 2053 TGC TGC TGT TGC TGC NTGC TGC TGC TCC TGG AAA NGC ACC TTGC TGC 1 TGC TGC TGC TGC TGC -TGC TGC TGC TGC TGC TGC TGC TGC -TGC TGC * 2100 GGC TGC TGC TGC TGC TGC T 1 TGC TGC TGC TGC TGC TGC T 2119 ACGAGTGCTN Statistics Matches: 44, Mismatches: 17, Indels: 4 0.68 0.26 0.06 Matches are distributed among these distances: 3 40 0.91 4 4 0.09 ACGTcount: A:0.06, C:0.30, G:0.30, T:0.30 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 1553 -- 2052 TCACAGTGGGGCGAGACTGTGTCTGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGG AACTGCAGCAGCGGTGTCACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGC AGAGCTGTGCCGGAGACGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTA GAAGCAGTAGCTAGCAGCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCT GTAGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAG CTCGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNN TAAACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCA ATTTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGG Right flanking sequence: Indices 2119 -- 2395 ACGAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCGGGGCTTCCGCCNTGTACGGCACA GCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTCCTTCTTTGGTCTCCAAACTGCTC CAGCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGCTGCTGCTGCTGCTGCTGCACGGCAGTCG TAGCAGCAGCAGCAGCAGCAGCAGCAGGGGGGTGGCGAGGAGCAGCAGCAGCAGCAGCAGCAGCA GCATCATGCTGCTGCAG Found at i:2142 original size:3 final size:3 Alignment explanation

Indices: 2134--2155 Score: 44 Period size: 3 Copynumber: 7.3 Consensus size: 3 2124 TGCTNGTGCT 2134 GCA GCA GCA GCA GCA GCA GCA G 1 GCA GCA GCA GCA GCA GCA GCA G 2156 NCGCGGGGCT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 19 1.00 ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 1634 -- 2133 TCACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGA CGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAAGCAGTAGCTAGCA GCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGTAGCTGCTGCTGCTG CAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTA GTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTAAACCCTAAACCCTA AANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAAATTNCGAG CAGCAGACGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANG CACCTTGCTGCGGCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCT Right flanking sequence: Indices 2156 -- 2395 NCGCGGGGCTTCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCAT ATTTCCTTCTTTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGC TGCTGCTGCTGCTGCTGCACGGCAGTCGTAGCAGCAGCAGCAGCAGCAGCAGCAGGGGGGTGGCG AGGAGCAGCAGCAGCAGCAGCAGCAGCAGCATCATGCTGCTGCAG Found at i:2284 original size:3 final size:3 Alignment explanation

Indices: 2276--2303 Score: 56 Period size: 3 Copynumber: 9.3 Consensus size: 3 2266 AACAAGTGAT 2276 CTG CTG CTG CTG CTG CTG CTG CTG CTG C 1 CTG CTG CTG CTG CTG CTG CTG CTG CTG C 2304 ACGGCAGTCG Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 25 1.00 ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32 Consensus pattern (3 bp): CTG Left flanking sequence: Indices 1776 -- 2275 CGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGTAGCTGCTGCTGCTGCAGCAGCACCAG TAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTACAATTTGCT GGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTAAACCCTAAACCCTAAANCCCTGCGAC ACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAAATTNCGAGCAGCAGACGCAC TGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANGCACCTTGCTGCG GCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCGGGGCT TCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTCCTTCT TTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACAAGTGAT Right flanking sequence: Indices 2304 -- 2395 ACGGCAGTCGTAGCAGCAGCAGCAGCAGCAGCAGCAGGGGGGTGGCGAGGAGCAGCAGCAGCAGC AGCAGCAGCAGCATCATGCTGCTGCAG Found at i:2321 original size:3 final size:3 Alignment explanation

Indices: 2315--2381 Score: 76 Period size: 3 Copynumber: 22.3 Consensus size: 3 2305 CGGCAGTCGT * * * * * * 2315 AGC AGC AGC AGC AGC AGC AGC AGC AG- GGG GGT GGC GAGG AGC AGC 1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC -AGC AGC AGC 2360 AGC AGC AGC AGC AGC AGC AGC A 1 AGC AGC AGC AGC AGC AGC AGC A 2382 TCATGCTGCT Statistics Matches: 56, Mismatches: 6, Indels: 4 0.85 0.09 0.06 Matches are distributed among these distances: 2 1 0.02 3 54 0.96 4 1 0.02 ACGTcount: A:0.30, C:0.27, G:0.42, T:0.01 Consensus pattern (3 bp): AGC Left flanking sequence: Indices 1815 -- 2314 AGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCT CGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTA AACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAAT TTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGC TGCTCCTGGAAANGCACCTTGCTGCGGCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCA GCAGCAGCAGCAGCAGNCGCGGGGCTTCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCG CATTTGAAAACAGCATATTTCCTTCTTTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACA AGTGATCTGCTGCTGCTGCTGCTGCTGCTGCTGCACGGCAGTCGT Right flanking sequence: Indices 2382 -- 2395 TCATGCTGCTGCAG Done.