TRAP (Tandem Repeats Analysis Program)

TRF Version 4.00

Sequence: contig00000278

tutorial_data.fasta.s3.2.5.7.80.10.25.1000.txt.html

Found at i: 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: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: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: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: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