Tandem Repeats Finder Program written by:

                 Gary Benson
      Department of Biomathematical Sciences
          Mount Sinai School of Medicine

Version 4.00

Sequence: contig00000153

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: 2483
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24

Warning! 34 characters in sequence are not A, C, G, or T


Found at i:53 original size:6 final size:6

Alignment explanation

Indices: 42--56 Score: 30 Period size: 6 Copynumber: 2.5 Consensus size: 6 32 GAGCNTGAAA 42 CCTCCC CCTCCC CCT 1 CCTCCC CCTCCC CCT 57 ANCCTGCGTA Statistics Matches: 9, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 9 1.00 ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20 Consensus pattern (6 bp): CCTCCC Left flanking sequence: Indices 1 -- 41 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAA Right flanking sequence: Indices 57 -- 556 ANCCTGCGTAGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTGCNTGCTGCTGCTGTTGCTGCTGCT GCTCTTGCTGCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGCTGCTGCGCCTTT GCAATTGGGATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTTGCTGCAGCTG CAGCAGCAGCGGCAGCAGCTGCTGCTCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAATGTCTT TTCTTTCTTTCACAAAGCAAAGCAACGCCGACCTGCATGCGCCCAGAAGTCTAGGGTTTAGGGTT TAGGGTTTGGGGCTTGGTAGCTGCGGAGCCAGAGGGGCGCAACAGAGCAAGGGTTTAGGGTCTAG GGTTTGGGGTTTTGCAGCTCACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTTCCTCTA CCAACTCCGAGCCTGCCACCTGCAGCAGCAGCAGCAGCAGCAACA Found at i:80 original size:3 final size:3 Alignment explanation

Indices: 72--180 Score: 132 Period size: 3 Copynumber: 36.0 Consensus size: 3 62 GCGTAGNCCT * * * * 72 TGC TGC TGC TGT TGC TGC TTC TGT TGC NTGC TGC TGC TGT TGC TGC 1 TGC TGC TGC TGC TGC TGC TGC TGC TGC -TGC TGC TGC TGC TGC TGC ** ** ** 118 TGC TGC TCT TGC TGC TGC TGC TCT TGC TGC TGC TGC TCT TGC TGC TGC 1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC * 166 CGC TGC TGC TGC TGC 1 TGC TGC TGC TGC TGC 181 GCCTTTGCAA Statistics Matches: 83, Mismatches: 22, Indels: 2 0.78 0.21 0.02 Matches are distributed among these distances: 3 80 0.96 4 3 0.04 ACGTcount: A:0.00, C:0.31, G:0.29, T:0.39 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 1 -- 71 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCT Right flanking sequence: Indices 181 -- 680 GCCTTTGCAATTGGGATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTTGCTG CAGCTGCAGCAGCAGCGGCAGCAGCTGCTGCTCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAA TGTCTTTTCTTTCTTTCACAAAGCAAAGCAACGCCGACCTGCATGCGCCCAGAAGTCTAGGGTTT AGGGTTTAGGGTTTGGGGCTTGGTAGCTGCGGAGCCAGAGGGGCGCAACAGAGCAAGGGTTTAGG GTCTAGGGTTTGGGGTTTTGCAGCTCACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTT CCTCTACCAACTCCGAGCCTGCCACCTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCAACATA AGAGAACGACAGCTCTTCCAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNT TCTTAAGAAGGCTCTGGACATCGTAGCTGCTCTGCTGCTCCAGGA Found at i:120 original size:15 final size:15 Alignment explanation

Indices: 72--180 Score: 153 Period size: 15 Copynumber: 7.2 Consensus size: 15 62 GCGTAGNCCT * * 72 TGCTGCTGCTGTTGC 1 TGCTGCTGTTGCTGC * 87 TGCTTCTGTTGCNTGC 1 TGCTGCTGTTGC-TGC 103 TGCTGCTGTTGCTGC 1 TGCTGCTGTTGCTGC * 118 TGCTGCTCTTGCTGC 1 TGCTGCTGTTGCTGC * 133 TGCTGCTCTTGCTGC 1 TGCTGCTGTTGCTGC * 148 TGCTGCTCTTGCTGC 1 TGCTGCTGTTGCTGC * * 163 TGCCGCTGCTGCTGC 1 TGCTGCTGTTGCTGC 178 TGC 1 TGC 181 GCCTTTGCAA Statistics Matches: 85, Mismatches: 8, Indels: 2 0.89 0.08 0.02 Matches are distributed among these distances: 15 71 0.84 16 14 0.16 ACGTcount: A:0.00, C:0.31, G:0.29, T:0.39 Consensus pattern (15 bp): TGCTGCTGTTGCTGC Left flanking sequence: Indices 1 -- 71 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCT Right flanking sequence: Indices 181 -- 680 GCCTTTGCAATTGGGATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTTGCTG CAGCTGCAGCAGCAGCGGCAGCAGCTGCTGCTCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAA TGTCTTTTCTTTCTTTCACAAAGCAAAGCAACGCCGACCTGCATGCGCCCAGAAGTCTAGGGTTT AGGGTTTAGGGTTTGGGGCTTGGTAGCTGCGGAGCCAGAGGGGCGCAACAGAGCAAGGGTTTAGG GTCTAGGGTTTGGGGTTTTGCAGCTCACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTT CCTCTACCAACTCCGAGCCTGCCACCTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCAACATA AGAGAACGACAGCTCTTCCAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNT TCTTAAGAAGGCTCTGGACATCGTAGCTGCTCTGCTGCTCCAGGA Found at i:253 original size:6 final size:6 Alignment explanation

Indices: 242--276 Score: 42 Period size: 6 Copynumber: 5.8 Consensus size: 6 232 TACTCGGTTT * * * * 242 GCTGCA GCTGCA GCAGCA GCGGCA GCAGCT GCTGC 1 GCTGCA GCTGCA GCTGCA GCTGCA GCTGCA GCTGC 277 TCTGCTGCAG Statistics Matches: 24, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 6 24 1.00 ACGTcount: A:0.17, C:0.34, G:0.37, T:0.11 Consensus pattern (6 bp): GCTGCA Left flanking sequence: Indices 1 -- 241 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTGCNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCT GCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGG ATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTT Right flanking sequence: Indices 277 -- 776 TCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTTTCACAAAGCAAAGCAA CGCCGACCTGCATGCGCCCAGAAGTCTAGGGTTTAGGGTTTAGGGTTTGGGGCTTGGTAGCTGCG GAGCCAGAGGGGCGCAACAGAGCAAGGGTTTAGGGTCTAGGGTTTGGGGTTTTGCAGCTCACTCG TGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGCCTGCCACCTGCAG CAGCAGCAGCAGCAGCAACAACAACAGCAACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTT TGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCT CTGCTGCTCCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCG CTGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTG Found at i:259 original size:3 final size:3 Alignment explanation

Indices: 245--270 Score: 38 Period size: 3 Copynumber: 8.7 Consensus size: 3 235 TCGGTTTGCT * * 245 GCA GCT GCA GCA GCA GCG GCA GCA GC 1 GCA GCA GCA GCA GCA GCA GCA GCA GC 271 TGCTGCTCTG Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 3 19 1.00 ACGTcount: A:0.23, C:0.35, G:0.38, T:0.04 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 1 -- 244 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTGCNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCT GCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGG ATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTTGCT Right flanking sequence: Indices 271 -- 770 TGCTGCTCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTTTCACAAAGCA AAGCAACGCCGACCTGCATGCGCCCAGAAGTCTAGGGTTTAGGGTTTAGGGTTTGGGGCTTGGTA GCTGCGGAGCCAGAGGGGCGCAACAGAGCAAGGGTTTAGGGTCTAGGGTTTGGGGTTTTGCAGCT CACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGCCTGCCAC CTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCAACATAAGAGAACGACAGCTCTTCCAGCACC AGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAAGGCTCTGGACATCGTA GCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTG CTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTG Found at i:275 original size:3 final size:3 Alignment explanation

Indices: 241--284 Score: 32 Period size: 3 Copynumber: 15.0 Consensus size: 3 231 ATACTCGGTT * * * * * * * 241 TGC TGC AGC TGC AGC AGC AGC GGC AGC AGC TGC TGC T-C TGC TGC 1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC 285 AGCACAGTAG Statistics Matches: 34, Mismatches: 6, Indels: 2 0.81 0.14 0.05 Matches are distributed among these distances: 2 2 0.06 3 32 0.94 ACGTcount: A:0.14, C:0.34, G:0.34, T:0.18 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 1 -- 240 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTGCNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCT GCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGG ATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTT Right flanking sequence: Indices 285 -- 784 AGCACAGTAGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTTTCACAAAGCAAAGCAACGCCGACC TGCATGCGCCCAGAAGTCTAGGGTTTAGGGTTTAGGGTTTGGGGCTTGGTAGCTGCGGAGCCAGA GGGGCGCAACAGAGCAAGGGTTTAGGGTCTAGGGTTTGGGGTTTTGCAGCTCACTCGTGTTCTCC CGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGCCTGCCACCTGCAGCAGCAGCA GCAGCAGCAACAACAACAGCAACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTTTGGGATCG AGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCTCTGCTGCT CCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCG GGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTGTTGCTGGC Found at i:337 original size:5 final size:5 Alignment explanation

Indices: 329--341 Score: 26 Period size: 5 Copynumber: 2.6 Consensus size: 5 319 CTTTCTTTCA 329 CAAAG CAAAG CAA 1 CAAAG CAAAG CAA 342 CGCCGACCTG Statistics Matches: 8, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 8 1.00 ACGTcount: A:0.62, C:0.23, G:0.15, T:0.00 Consensus pattern (5 bp): CAAAG Left flanking sequence: Indices 1 -- 328 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTGCNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCT GCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGG ATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTTGCTGCAGCTGCAGCAGCAG CGGCAGCAGCTGCTGCTCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTT TCA Right flanking sequence: Indices 342 -- 841 CGCCGACCTGCATGCGCCCAGAAGTCTAGGGTTTAGGGTTTAGGGTTTGGGGCTTGGTAGCTGCG GAGCCAGAGGGGCGCAACAGAGCAAGGGTTTAGGGTCTAGGGTTTGGGGTTTTGCAGCTCACTCG TGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGCCTGCCACCTGCAG CAGCAGCAGCAGCAGCAACAACAACAGCAACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTT TGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCT CTGCTGCTCCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCG CTGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGC GCTGCTGCGNGCTGCTGCTGCTGCTGCCAGNCGCTGAGCACACAG Found at i:380 original size:7 final size:7 Alignment explanation

Indices: 368--393 Score: 45 Period size: 7 Copynumber: 3.7 Consensus size: 7 358 CCCAGAAGTC 368 TAGGGTT 1 TAGGGTT 375 TAGGGTT 1 TAGGGTT 382 TAGGGTT 1 TAGGGTT * 389 TGGGG 1 TAGGG 394 CTTGGTAGCT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.12, C:0.00, G:0.50, T:0.38 Consensus pattern (7 bp): TAGGGTT Left flanking sequence: Indices 1 -- 367 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTGCNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCT GCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGG ATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTTGCTGCAGCTGCAGCAGCAG CGGCAGCAGCTGCTGCTCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTT TCACAAAGCAAAGCAACGCCGACCTGCATGCGCCCAGAAGTC Right flanking sequence: Indices 394 -- 893 CTTGGTAGCTGCGGAGCCAGAGGGGCGCAACAGAGCAAGGGTTTAGGGTCTAGGGTTTGGGGTTT TGCAGCTCACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGC CTGCCACCTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCAACATAAGAGAACGACAGCTCTTC CAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAAGGCTCTGGA CATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCTGCTGCTGCT GCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTGTTGCTGG CACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGCCAGNCGCTGAGCACACAGGCACANC NTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGTTTAGGGT Found at i:456 original size:7 final size:7 Alignment explanation

Indices: 431--458 Score: 42 Period size: 7 Copynumber: 4.0 Consensus size: 7 421 CAACAGAGCA 431 AGGGTTT 1 AGGGTTT * 438 AGGGTCT 1 AGGGTTT 445 AGGGTTT 1 AGGGTTT * 452 GGGGTTT 1 AGGGTTT 459 TGCAGCTCAC Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.11, C:0.04, G:0.46, T:0.39 Consensus pattern (7 bp): AGGGTTT Left flanking sequence: Indices 1 -- 430 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTGCNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCT GCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGG ATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTTGCTGCAGCTGCAGCAGCAG CGGCAGCAGCTGCTGCTCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTT TCACAAAGCAAAGCAACGCCGACCTGCATGCGCCCAGAAGTCTAGGGTTTAGGGTTTAGGGTTTG GGGCTTGGTAGCTGCGGAGCCAGAGGGGCGCAACAGAGCA Right flanking sequence: Indices 459 -- 958 TGCAGCTCACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGC CTGCCACCTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCAACATAAGAGAACGACAGCTCTTC CAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAAGGCTCTGGA CATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCTGCTGCTGCT GCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTGTTGCTGG CACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGCCAGNCGCTGAGCACACAGGCACANC NTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGTTTAGGGTTTAGGGTTTAGGGTTCAGGG TTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCTTGAGG Found at i:541 original size:3 final size:3 Alignment explanation

Indices: 533--565 Score: 45 Period size: 3 Copynumber: 11.0 Consensus size: 3 523 CCTGCCACCT * * * 533 GCA GCA GCA GCA GCA GCA GCA ACA ACA ACA GCA 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA 566 ACATAAGAGA Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 3 28 1.00 ACGTcount: A:0.42, C:0.33, G:0.24, T:0.00 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 33 -- 532 AGCNTGAAACCTCCCCCTCCCCCTANCCTGCGTAGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTG CNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGC TGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGGATTCGCCACAGCTCTTCGTTTTTTTTCATCTC TTCATACTCGGTTTGCTGCAGCTGCAGCAGCAGCGGCAGCAGCTGCTGCTCTGCTGCAGCACAGT AGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTTTCACAAAGCAAAGCAACGCCGACCTGCATGCG CCCAGAAGTCTAGGGTTTAGGGTTTAGGGTTTGGGGCTTGGTAGCTGCGGAGCCAGAGGGGCGCA ACAGAGCAAGGGTTTAGGGTCTAGGGTTTGGGGTTTTGCAGCTCACTCGTGTTCTCCCGCTTTCC CGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGCCTGCCACCT Right flanking sequence: Indices 566 -- 1065 ACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTT ACTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGAC TGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCT GCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGCCA GNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGTTTAG GGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCTTG AGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGAAATAG CAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAAC Found at i:622 original size:7 final size:7 Alignment explanation

Indices: 610--631 Score: 44 Period size: 7 Copynumber: 3.1 Consensus size: 7 600 TTTGGGATCG 610 AGGGTTT 1 AGGGTTT 617 AGGGTTT 1 AGGGTTT 624 AGGGTTT 1 AGGGTTT 631 A 1 A 632 CTNTTCTTAA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 15 1.00 ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41 Consensus pattern (7 bp): AGGGTTT Left flanking sequence: Indices 110 -- 609 GTTGCTGCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGC TGCTGCGCCTTTGCAATTGGGATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGT TTGCTGCAGCTGCAGCAGCAGCGGCAGCAGCTGCTGCTCTGCTGCAGCACAGTAGCGTTCTGCTG CTGCAATGTCTTTTCTTTCTTTCACAAAGCAAAGCAACGCCGACCTGCATGCGCCCAGAAGTCTA GGGTTTAGGGTTTAGGGTTTGGGGCTTGGTAGCTGCGGAGCCAGAGGGGCGCAACAGAGCAAGGG TTTAGGGTCTAGGGTTTGGGGTTTTGCAGCTCACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGG CCTTTTCCTCTACCAACTCCGAGCCTGCCACCTGCAGCAGCAGCAGCAGCAGCAACAACAACAGC AACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTTTGGGATCG Right flanking sequence: Indices 632 -- 1131 CTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGACT GCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCTG CTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGCCAG NCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGTTTAGG GTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCTTGA GGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGAAATAGC AAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACCCTAAACCCTAAAC CCTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGT Found at i:716 original size:3 final size:3 Alignment explanation

Indices: 690--823 Score: 117 Period size: 3 Copynumber: 44.7 Consensus size: 3 680 AATCGCCGTA * ** 690 GCT GACT GC- GCT GCT -CT TCT GCT GCT GCT GCT GCT GCT GTC GCT 1 GCT G-CT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT * * * ** * * 734 GCT GCG GGT GTT GCT GCT GCT GCT GCT GCT GCT GCT GTC CCT GTT GCT 1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT ** * * ** * 782 GGC ACG GCT GCT GGC GCT GCT GCGN GCT GCT GCT GCT GCT GC 1 GCT GCT GCT GCT GCT GCT GCT GC-T GCT GCT GCT GCT GCT GC 824 CAGNCGCTGA Statistics Matches: 96, Mismatches: 31, Indels: 8 0.71 0.23 0.06 Matches are distributed among these distances: 2 4 0.04 3 87 0.91 4 5 0.05 ACGTcount: A:0.01, C:0.32, G:0.35, T:0.31 Consensus pattern (3 bp): GCT Left flanking sequence: Indices 190 -- 689 ATTGGGATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTTGCTGCAGCTGCAG CAGCAGCGGCAGCAGCTGCTGCTCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAATGTCTTTTC TTTCTTTCACAAAGCAAAGCAACGCCGACCTGCATGCGCCCAGAAGTCTAGGGTTTAGGGTTTAG GGTTTGGGGCTTGGTAGCTGCGGAGCCAGAGGGGCGCAACAGAGCAAGGGTTTAGGGTCTAGGGT TTGGGGTTTTGCAGCTCACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCA ACTCCGAGCCTGCCACCTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCAACATAAGAGAACGA CAGCTCTTCCAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAA GGCTCTGGACATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTA Right flanking sequence: Indices 824 -- 1323 CAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGTTT AGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCT TGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGAAAT AGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACCCTAAACCCTA AACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATTTGAGGGTCGT GCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCAGCTGCTGCTGCAGCTGCTTC TGCTGCGGCGGGAGCTGCTGCAGCAGCTGCAGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTT CTGCATGAANAAGCTCTATCGCTGCACACCAAAACAAACCCTAAA Found at i:896 original size:7 final size:7 Alignment explanation

Indices: 871--918 Score: 64 Period size: 7 Copynumber: 6.6 Consensus size: 7 861 CTGTAAGTTG 871 TTAGNGGT 1 TTAG-GGT * 879 TTANAGGT 1 TTA-GGGT 887 TTAGGGT 1 TTAGGGT 894 TTAGGGT 1 TTAGGGT 901 TTAGGGT 1 TTAGGGT * 908 TCAGGGT 1 TTAGGGT 915 TTAG 1 TTAG 919 AGCTCAGACT Statistics Matches: 35, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 7 26 0.74 8 9 0.26 ACGTcount: A:0.17, C:0.02, G:0.38, T:0.40 Consensus pattern (7 bp): TTAGGGT Left flanking sequence: Indices 371 -- 870 GGTTTAGGGTTTAGGGTTTGGGGCTTGGTAGCTGCGGAGCCAGAGGGGCGCAACAGAGCAAGGGT TTAGGGTCTAGGGTTTGGGGTTTTGCAGCTCACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGC CTTTTCCTCTACCAACTCCGAGCCTGCCACCTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCA ACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTT ACTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGAC TGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCT GCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGCCA GNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTG Right flanking sequence: Indices 919 -- 1418 AGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCTTGAGGGTTTACGATTTATGTTTTAGGGTTT AGGGCATAGAGTTCAAAATGGCATTGAAGGGAAATAGCAAAGAAAAAAAATACCGAACAAAAAAC GGGCGCTCCCACCAAACCCTAAACCCTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGTA GATGGAGGCTAACTCCGTTTCTATTTGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCA GGTAGAGCTCCCGCAGCTGCTGCTGCAGCTGCTTCTGCTGCGGCGGGAGCTGCTGCAGCAGCTGC AGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACC AAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGGC GAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTC Found at i:984 original size:7 final size:7 Alignment explanation

Indices: 956--987 Score: 36 Period size: 7 Copynumber: 4.6 Consensus size: 7 946 TGGCAGCTTG 956 AGGGTTT 1 AGGGTTT * * 963 ACGATTT 1 AGGGTTT * * 970 ATGTTTT 1 AGGGTTT 977 AGGGTTT 1 AGGGTTT 984 AGGG 1 AGGG 988 CATAGAGTTC Statistics Matches: 19, Mismatches: 6, Indels: 0 0.76 0.24 0.00 Matches are distributed among these distances: 7 19 1.00 ACGTcount: A:0.19, C:0.03, G:0.34, T:0.44 Consensus pattern (7 bp): AGGGTTT Left flanking sequence: Indices 456 -- 955 TTTTGCAGCTCACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCAACTCCG AGCCTGCCACCTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCAACATAAGAGAACGACAGCTC TTCCAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAAGGCTCT GGACATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCTGCTGCT GCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTGTTGC TGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGCCAGNCGCTGAGCACACAGGCAC ANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGTTTAGGGTTTAGGGTTTAGGGTTCA GGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCTTG Right flanking sequence: Indices 988 -- 1487 CATAGAGTTCAAAATGGCATTGAAGGGAAATAGCAAAGAAAAAAAATACCGAACAAAAAACGGGC GCTCCCACCAAACCCTAAACCCTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGTAGATG GAGGCTAACTCCGTTTCTATTTGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTA GAGCTCCCGCAGCTGCTGCTGCAGCTGCTTCTGCTGCGGCGGGAGCTGCTGCAGCAGCTGCAGCA CCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACCAAAA CAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGGCGAGC CTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCTTGGATTCTCAAGC AGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGT Found at i:1034 original size:16 final size:16 Alignment explanation

Indices: 1015--1047 Score: 45 Period size: 16 Copynumber: 2.1 Consensus size: 16 1005 CATTGAAGGG * * 1015 AAATAGCAAAGAAAAA 1 AAATACCAAACAAAAA * 1031 AAATACCGAACAAAAA 1 AAATACCAAACAAAAA 1047 A 1 A 1048 CGGGCGCTCC Statistics Matches: 14, Mismatches: 3, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.73, C:0.12, G:0.09, T:0.06 Consensus pattern (16 bp): AAATACCAAACAAAAA Left flanking sequence: Indices 515 -- 1014 ACTCCGAGCCTGCCACCTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCAACATAAGAGAACGA CAGCTCTTCCAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAA GGCTCTGGACATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCT GCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCC TGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGCCAGNCGCTGAGCACAC AGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGTTTAGGGTTTAGGGTTTAG GGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCTTGAGGGTTTACGATTT ATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGG Right flanking sequence: Indices 1048 -- 1547 CGGGCGCTCCCACCAAACCCTAAACCCTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGT AGATGGAGGCTAACTCCGTTTCTATTTGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCC AGGTAGAGCTCCCGCAGCTGCTGCTGCAGCTGCTTCTGCTGCGGCGGGAGCTGCTGCAGCAGCTG CAGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACAC CAAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGG CGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCTTGGATTCT CAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGC TGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGC Found at i:1074 original size:7 final size:7 Alignment explanation

Indices: 1062--1089 Score: 56 Period size: 7 Copynumber: 4.0 Consensus size: 7 1052 CGCTCCCACC 1062 AAACCCT 1 AAACCCT 1069 AAACCCT 1 AAACCCT 1076 AAACCCT 1 AAACCCT 1083 AAACCCT 1 AAACCCT 1090 GATTTGTGCA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 21 1.00 ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14 Consensus pattern (7 bp): AAACCCT Left flanking sequence: Indices 562 -- 1061 AGCAACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGG GTTTACTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTAGC TGACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGC TGCTGCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCT GCCAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGT TTAGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAG CTTGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGAA ATAGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACC Right flanking sequence: Indices 1090 -- 1589 GATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATTTGAGGGTCGTGCAGCA AACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCAGCTGCTGCTGCAGCTGCTTCTGCTGC GGCGGGAGCTGCTGCAGCAGCTGCAGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGCAT GAANAAGCTCTATCGCTGCACACCAAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA AACCCTAAGCGCTAACCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTT TGTCTCACTCTTCCTTGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCT GCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGC TGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGA Found at i:1202 original size:3 final size:3 Alignment explanation

Indices: 1194--1243 Score: 44 Period size: 3 Copynumber: 16.7 Consensus size: 3 1184 AGCTCCCGCA * * * * ** * * 1194 GCT GCT GCT GCA GCT GCT TCT GCT GCG GCG GGA GCT GCT GCA GCA GCT 1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT 1242 GC 1 GC 1244 AGCACCTCAG Statistics Matches: 36, Mismatches: 11, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 3 36 1.00 ACGTcount: A:0.08, C:0.32, G:0.38, T:0.22 Consensus pattern (3 bp): GCT Left flanking sequence: Indices 694 -- 1193 ACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTG CTGCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGC CAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGTTT AGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCT TGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGAAAT AGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACCCTAAACCCTA AACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATTTGAGGGTCGT GCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCA Right flanking sequence: Indices 1244 -- 1743 AGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACC AAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGGC GAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCTTGGATTCTC AAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGCT GCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGC TGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGC AGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAACCCTCGCGNAAATAAC GCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAA Found at i:1206 original size:12 final size:12 Alignment explanation

Indices: 1191--1243 Score: 50 Period size: 12 Copynumber: 4.7 Consensus size: 12 1181 TAGAGCTCCC 1191 GCAGCTGCTGCT 1 GCAGCTGCTGCT 1203 GCAGCTGCT--T 1 GCAGCTGCTGCT * * * 1213 -CTGCTGCGGCG 1 GCAGCTGCTGCT * * 1224 GGAGCTGCTGCA 1 GCAGCTGCTGCT 1236 GCAGCTGC 1 GCAGCTGC 1244 AGCACCTCAG Statistics Matches: 30, Mismatches: 8, Indels: 6 0.68 0.18 0.14 Matches are distributed among these distances: 9 6 0.20 10 1 0.03 12 23 0.77 ACGTcount: A:0.09, C:0.32, G:0.38, T:0.21 Consensus pattern (12 bp): GCAGCTGCTGCT Left flanking sequence: Indices 691 -- 1190 CTGACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTG CTGCTGCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGC TGCCAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGG TTTAGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCA GCTTGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGA AATAGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACCCTAAACC CTAAACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATTTGAGGGT CGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCC Right flanking sequence: Indices 1244 -- 1743 AGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACC AAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGGC GAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCTTGGATTCTC AAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGCT GCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGC TGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGC AGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAACCCTCGCGNAAATAAC GCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAA Found at i:1218 original size:15 final size:15 Alignment explanation

Indices: 1191--1243 Score: 64 Period size: 15 Copynumber: 3.5 Consensus size: 15 1181 TAGAGCTCCC 1191 GCAGCTGCTGCTGCA 1 GCAGCTGCTGCTGCA * * * 1206 GCTGCTTCTGCTGCG 1 GCAGCTGCTGCTGCA * ** 1221 GCGGGAGCTGCTGCA 1 GCAGCTGCTGCTGCA 1236 GCAGCTGC 1 GCAGCTGC 1244 AGCACCTCAG Statistics Matches: 27, Mismatches: 11, Indels: 0 0.71 0.29 0.00 Matches are distributed among these distances: 15 27 1.00 ACGTcount: A:0.09, C:0.32, G:0.38, T:0.21 Consensus pattern (15 bp): GCAGCTGCTGCTGCA Left flanking sequence: Indices 691 -- 1190 CTGACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTG CTGCTGCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGC TGCCAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGG TTTAGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCA GCTTGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGA AATAGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACCCTAAACC CTAAACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATTTGAGGGT CGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCC Right flanking sequence: Indices 1244 -- 1743 AGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACC AAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGGC GAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCTTGGATTCTC AAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGCT GCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGC TGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGC AGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAACCCTCGCGNAAATAAC GCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAA Found at i:1247 original size:9 final size:9 Alignment explanation

Indices: 1226--1274 Score: 45 Period size: 9 Copynumber: 5.3 Consensus size: 9 1216 CTGCGGCGGG * 1226 AGCTGCTGC 1 AGCAGCTGC 1235 AGCAGCTGC 1 AGCAGCTGC * 1244 AGCACCT-C 1 AGCAGCTGC * 1252 AGCAGCAGGC 1 AGCAGC-TGC * 1262 AGCGGGCTGC 1 AGC-AGCTGC 1272 AGC 1 AGC 1275 TCTTCTGCAT Statistics Matches: 31, Mismatches: 6, Indels: 5 0.74 0.14 0.12 Matches are distributed among these distances: 8 6 0.19 9 14 0.45 10 9 0.29 11 2 0.06 ACGTcount: A:0.20, C:0.35, G:0.35, T:0.10 Consensus pattern (9 bp): AGCAGCTGC Left flanking sequence: Indices 726 -- 1225 CTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTGTTGCTGGCACGGCT GCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGCCAGNCGCTGAGCACACAGGCACANCNTTTGGG GACTACTGTAAGTTGTTAGNGGTTTANAGGTTTAGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAG CTCAGACTGAGGAGGAGCGGTTTACTGGCAGCTTGAGGGTTTACGATTTATGTTTTAGGGTTTAG GGCATAGAGTTCAAAATGGCATTGAAGGGAAATAGCAAAGAAAAAAAATACCGAACAAAAAACGG GCGCTCCCACCAAACCCTAAACCCTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGTAGA TGGAGGCTAACTCCGTTTCTATTTGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGG TAGAGCTCCCGCAGCTGCTGCTGCAGCTGCTTCTGCTGCGGCGGG Right flanking sequence: Indices 1275 -- 1774 TCTTCTGCATGAANAAGCTCTATCGCTGCACACCAAAACAAACCCTAAACCCTAAACCCTAAACC CTAAACCCTAAACCCTAAGCGCTAACCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGG GTTTAGGGTTTGTCTCACTCTTCCTTGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGC AACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTG TTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGG ACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCC TAAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAAN GAAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACAT Found at i:1257 original size:3 final size:3 Alignment explanation

Indices: 1233--1264 Score: 27 Period size: 3 Copynumber: 10.7 Consensus size: 3 1223 GGGAGCTGCT * * * 1233 GCA GCA GCT GCA GCA -CC TCA GCA GCA GGCA GC 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA -GCA GC 1265 GGGCTGCAGC Statistics Matches: 22, Mismatches: 5, Indels: 4 0.71 0.16 0.13 Matches are distributed among these distances: 2 1 0.05 3 18 0.82 4 3 0.14 ACGTcount: A:0.25, C:0.38, G:0.31, T:0.06 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 733 -- 1232 TGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCG CTGCTGCGNGCTGCTGCTGCTGCTGCCAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACT GTAAGTTGTTAGNGGTTTANAGGTTTAGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGAC TGAGGAGGAGCGGTTTACTGGCAGCTTGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAG AGTTCAAAATGGCATTGAAGGGAAATAGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCC CACCAAACCCTAAACCCTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGC TAACTCCGTTTCTATTTGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCT CCCGCAGCTGCTGCTGCAGCTGCTTCTGCTGCGGCGGGAGCTGCT Right flanking sequence: Indices 1265 -- 1764 GGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACCAAAACAAACCCTAAACCCTAA ACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGGCGAGCCTGGCCACCTGCGAGTT AGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCTTGGATTCTCAAGCAGCACGAGAGGAGCAAA GCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTT GCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGA TCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAA CCCTAAACCCTAAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAG GGNCCAAAANGAAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAA Found at i:1326 original size:7 final size:7 Alignment explanation

Indices: 1314--1357 Score: 88 Period size: 7 Copynumber: 6.3 Consensus size: 7 1304 ACACCAAAAC 1314 AAACCCT 1 AAACCCT 1321 AAACCCT 1 AAACCCT 1328 AAACCCT 1 AAACCCT 1335 AAACCCT 1 AAACCCT 1342 AAACCCT 1 AAACCCT 1349 AAACCCT 1 AAACCCT 1356 AA 1 AA 1358 GCGCTAACCA Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 37 1.00 ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14 Consensus pattern (7 bp): AAACCCT Left flanking sequence: Indices 814 -- 1313 CTGCTGCTGCCAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGT TTANAGGTTTAGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTT ACTGGCAGCTTGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATT GAAGGGAAATAGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACC CTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATT TGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCAGCTGCTGCTG CAGCTGCTTCTGCTGCGGCGGGAGCTGCTGCAGCAGCTGCAGCACCTCAGCAGCAGGCAGCGGGC TGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACCAAAAC Right flanking sequence: Indices 1358 -- 1857 GCGCTAACCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCAC TCTTCCTTGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGT TGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTG CTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCT TTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAA CCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAACAGC AGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGGGCCTCTT CAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCC Found at i:1338 original size:21 final size:21 Alignment explanation

Indices: 1314--1364 Score: 88 Period size: 21 Copynumber: 2.4 Consensus size: 21 1304 ACACCAAAAC 1314 AAACCCTAAACCCTAAACCCT 1 AAACCCTAAACCCTAAACCCT 1335 AAACCCTAAACCCTAAACCCT 1 AAACCCTAAACCCTAAACCCT * * 1356 AAGCGCTAA 1 AAACCCTAA 1365 CCAGCTGGCG Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 21 28 1.00 ACGTcount: A:0.43, C:0.39, G:0.04, T:0.14 Consensus pattern (21 bp): AAACCCTAAACCCTAAACCCT Left flanking sequence: Indices 814 -- 1313 CTGCTGCTGCCAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGT TTANAGGTTTAGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTT ACTGGCAGCTTGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATT GAAGGGAAATAGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACC CTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATT TGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCAGCTGCTGCTG CAGCTGCTTCTGCTGCGGCGGGAGCTGCTGCAGCAGCTGCAGCACCTCAGCAGCAGGCAGCGGGC TGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACCAAAAC Right flanking sequence: Indices 1365 -- 1864 CCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCT TGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGCT GCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTGC ACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCGG AGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAACCCTCGC GNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAACAGCAGNCNAA AAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGGGCCTCTTCAGTTTG CCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAAATAA Found at i:1405 original size:7 final size:7 Alignment explanation

Indices: 1393--1415 Score: 46 Period size: 7 Copynumber: 3.3 Consensus size: 7 1383 CACCTGCGAG 1393 TTAGGGT 1 TTAGGGT 1400 TTAGGGT 1 TTAGGGT 1407 TTAGGGT 1 TTAGGGT 1414 TT 1 TT 1416 GTCTCACTCT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 16 1.00 ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48 Consensus pattern (7 bp): TTAGGGT Left flanking sequence: Indices 893 -- 1392 TTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCTTGAG GGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGAAATAGCA AAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACCCTAAACCCTAAACC CTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATTTGAGGGTCGTGCAG CAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCAGCTGCTGCTGCAGCTGCTTCTGCT GCGGCGGGAGCTGCTGCAGCAGCTGCAGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGC ATGAANAAGCTCTATCGCTGCACACCAAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACCC TAAACCCTAAGCGCTAACCAGCTGGCGAGCCTGGCCACCTGCGAG Right flanking sequence: Indices 1416 -- 1915 GTCTCACTCTTCCTTGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTG CTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCT GCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTT TCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAA CCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAA CAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGG GCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAAATAAGGGTTT AGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCAT Found at i:1571 original size:3 final size:3 Alignment explanation

Indices: 1473--1559 Score: 123 Period size: 3 Copynumber: 28.7 Consensus size: 3 1463 CCGCAGCAAC * * * 1473 GCT GCCT GCT GCT GTT GCT GCT GCT GCT GCT GCT CCT GCT GTT GCT 1 GCT G-CT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT * * * 1519 GCT GTT GCT CCT GCT GTT GCT GCT GCT GCT GCT GCT GCT GC 1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC 1560 ACCACCTGCT Statistics Matches: 71, Mismatches: 12, Indels: 2 0.84 0.14 0.02 Matches are distributed among these distances: 3 68 0.96 4 3 0.04 ACGTcount: A:0.00, C:0.32, G:0.31, T:0.37 Consensus pattern (3 bp): GCT Left flanking sequence: Indices 973 -- 1472 TTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGAAATAGCAAAGAAAAAAAATACC GAACAAAAAACGGGCGCTCCCACCAAACCCTAAACCCTAAACCCTAAACCCTGATTTGTGCACCT CGATCAATGTAGATGGAGGCTAACTCCGTTTCTATTTGAGGGTCGTGCAGCAAACCCTGCAGCAG CAAATGCTCCAGGTAGAGCTCCCGCAGCTGCTGCTGCAGCTGCTTCTGCTGCGGCGGGAGCTGCT GCAGCAGCTGCAGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGCATGAANAAGCTCTAT CGCTGCACACCAAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCGCT AACCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTC CTTGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAAC Right flanking sequence: Indices 1560 -- 2059 ACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCGG AGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAACCCTCGC GNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAACAGCAGNCNAA AAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGGGCCTCTTCAGTTTG CCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAAATAAGGGTTTAGGGTTTAGGGTTT GGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGGACTGGCTTGGATACGCTGCAGCAG TTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGGTTTAAGGTTTGCAGCAGACCTTAA ACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGAAGCA Found at i:1642 original size:9 final size:9 Alignment explanation

Indices: 1625--1643 Score: 31 Period size: 9 Copynumber: 2.1 Consensus size: 9 1615 CCTTTGCCGG 1625 AGAGCCTGC 1 AGAGCCTGC * 1634 AGAGTCTGC 1 AGAGCCTGC 1643 A 1 A 1644 TGCAAAACAA Statistics Matches: 9, Mismatches: 1, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 9 9 1.00 ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16 Consensus pattern (9 bp): AGAGCCTGC Left flanking sequence: Indices 1125 -- 1624 ACTCCGTTTCTATTTGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCC CGCAGCTGCTGCTGCAGCTGCTTCTGCTGCGGCGGGAGCTGCTGCAGCAGCTGCAGCACCTCAGC AGCAGGCAGCGGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACCAAAACAAACCC TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGGCGAGCCTGGCCA CCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCTTGGATTCTCAAGCAGCACGA GAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGT TGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAG CAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCGG Right flanking sequence: Indices 1644 -- 2143 TGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGA GGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACA TGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGAC ACAGCAGCACAACCACTCCGAAATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCT AGCGCTGGGCATTCGGGCGCGGACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCT GCTGAGGGTTTAGGGCTTAGGGTTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGA GGGTTTAGGGTTTAGGGTTTGAAGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAA ATACAGCAAAAATAAACNGGCAGTCTTCCACACTGCNAAGTGCAC Found at i:1664 original size:7 final size:7 Alignment explanation

Indices: 1652--1686 Score: 63 Period size: 7 Copynumber: 5.0 Consensus size: 7 1642 CATGCAAAAC 1652 AAACCCT 1 AAACCCT 1659 AAACCCT 1 AAACCCT * 1666 AAACTCT 1 AAACCCT 1673 AAACCCT 1 AAACCCT 1680 AAACCCT 1 AAACCCT 1687 CGCGNAAATA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 7 26 1.00 ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17 Consensus pattern (7 bp): AAACCCT Left flanking sequence: Indices 1152 -- 1651 GCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCAGCTGCTGCTGCAGCTGCTTCTGC TGCGGCGGGAGCTGCTGCAGCAGCTGCAGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTG CATGAANAAGCTCTATCGCTGCACACCAAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACC CTAAACCCTAAGCGCTAACCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGG GTTTGTCTCACTCTTCCTTGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTG CCTGCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGC TGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGC GGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAAC Right flanking sequence: Indices 1687 -- 2186 CGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAACAGCAGNC NAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGGGCCTCTTCAGT TTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAAATAAGGGTTTAGGGTTTAGGG TTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGGACTGGCTTGGATACGCTGCAG CAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGGTTTAAGGTTTGCAGCAGACCT TAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGAAGCAAACCTGCAACAACGCAG CTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCAGTCTTCCACACTGCNAAGTGC ACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGCN Found at i:1876 original size:7 final size:7 Alignment explanation

Indices: 1864--1888 Score: 43 Period size: 7 Copynumber: 3.6 Consensus size: 7 1854 CTCCGAAATA 1864 AGGGTTT 1 AGGGTTT 1871 AGGGTTT 1 AGGGTTT 1878 AGGGTTT 1 AGGGTTT * 1885 GGGG 1 AGGG 1889 CTCAGTCTTG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 7 17 1.00 ACGTcount: A:0.12, C:0.00, G:0.52, T:0.36 Consensus pattern (7 bp): AGGGTTT Left flanking sequence: Indices 1364 -- 1863 ACCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCC TTGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGC TGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTG CACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCG GAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAACCCTCG CGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAACAGCAGNCNA AAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGGGCCTCTTCAGTTT GCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAAATA Right flanking sequence: Indices 1889 -- 2388 CTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGGACTGGCTTGGATACGCTGCAGCAGTTTT TGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGGTTTAAGGTTTGCAGCAGACCTTAAACCC AAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGAAGCAAACCTGCAACAACGCAGCTAGGGC ATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCAGTCTTCCACACTGCNAAGTGCACCCCAG GNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGCNTGCTGCTGCTGCTGCTGCAGAGCTTCC GGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTACACCAAACACACCTTCAA CACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGACTCAAACCCTAACCCTAAACCTTAG GGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAA Found at i:1988 original size:7 final size:7 Alignment explanation

Indices: 1969--1994 Score: 31 Period size: 7 Copynumber: 3.7 Consensus size: 7 1959 CTGAGACTCT * 1969 GCTGAGG 1 GCTTAGG * 1976 GTTTAGG 1 GCTTAGG 1983 GCTTAGG 1 GCTTAGG * 1990 GTTTA 1 GCTTA 1995 AGGTTTGCAG Statistics Matches: 15, Mismatches: 4, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 7 15 1.00 ACGTcount: A:0.15, C:0.08, G:0.42, T:0.35 Consensus pattern (7 bp): GCTTAGG Left flanking sequence: Indices 1469 -- 1968 CAACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCT GTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGG GACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACC CTAAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAA NGAAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTC AGGAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCG AAATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGC GGACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCT Right flanking sequence: Indices 1995 -- 2483 AGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGAAGCA AACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCAGTCT TCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGCNTGC TGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTC TACCTACACCAAACACACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGAC TCAAACCCTAACCCTAAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCC CAAATTGNNAGGGTNNTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTT ACGAGGAGCTTGAGAAGAATCGTGTCAATGGCCT Found at i:1999 original size:7 final size:7 Alignment explanation

Indices: 1973--2000 Score: 42 Period size: 7 Copynumber: 4.0 Consensus size: 7 1963 GACTCTGCTG 1973 AGGGTTT 1 AGGGTTT * 1980 AGGGCTT 1 AGGGTTT 1987 AGGGTTT 1 AGGGTTT * 1994 AAGGTTT 1 AGGGTTT 2001 GCAGCAGACC Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.18, C:0.04, G:0.39, T:0.39 Consensus pattern (7 bp): AGGGTTT Left flanking sequence: Indices 1473 -- 1972 GCTGCCTGCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTG CTGCTGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACA ATGCGGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCCTAA ACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAA GCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGA GCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAAAT AAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGGAC TGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTG Right flanking sequence: Indices 2001 -- 2483 GCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGAAGCAAACCTG CAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCAGTCTTCCACA CTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGCNTGCTGCTGC TGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTA CACCAAACACACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGACTCAAAC CCTAACCCTAAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATT GNNAGGGTNNTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGG AGCTTGAGAAGAATCGTGTCAATGGCCT Found at i:2043 original size:7 final size:7 Alignment explanation

Indices: 2033--2053 Score: 42 Period size: 7 Copynumber: 3.0 Consensus size: 7 2023 CCCTAAGCTG 2033 AGGGTTT 1 AGGGTTT 2040 AGGGTTT 1 AGGGTTT 2047 AGGGTTT 1 AGGGTTT 2054 GAAGCAAACC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 14 1.00 ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43 Consensus pattern (7 bp): AGGGTTT Left flanking sequence: Indices 1533 -- 2032 TGTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGG GGACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAAC CCTAAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAA ANGAAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGT CAGGAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCC GAAATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCG CGGACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTA GGGTTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTG Right flanking sequence: Indices 2054 -- 2483 GAAGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGG CAGTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCT GCNTGCTGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATC TGCTTCTACCTACACCAAACACACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACC CTAGACTCAAACCCTAACCCTAAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCA AGCGCCCAAATTGNNAGGGTNNTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGA GGACTTACGAGGAGCTTGAGAAGAATCGTGTCAATGGCCT Found at i:2174 original size:3 final size:3 Alignment explanation

Indices: 2166--2204 Score: 60 Period size: 3 Copynumber: 12.3 Consensus size: 3 2156 CTCCTCTCGN 2166 CTG CTG CTG NCTG CTG CTG CNTG CTG CTG CTG CTG CTG C 1 CTG CTG CTG -CTG CTG CTG C-TG CTG CTG CTG CTG CTG C 2205 AGAGCTTCCG Statistics Matches: 34, Mismatches: 0, Indels: 4 0.89 0.00 0.11 Matches are distributed among these distances: 3 28 0.82 4 6 0.18 ACGTcount: A:0.00, C:0.33, G:0.31, T:0.31 Consensus pattern (3 bp): CTG Left flanking sequence: Indices 1666 -- 2165 AAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANG AAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAG GAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAA ATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGG ACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGG TTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGA AGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCA GTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGN Right flanking sequence: Indices 2205 -- 2483 AGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTACACCAAACA CACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGACTCAAACCCTAACCCT AAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTN NTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGA AGAATCGTGTCAATGGCCT Found at i:2181 original size:10 final size:9 Alignment explanation

Indices: 2166--2204 Score: 60 Period size: 10 Copynumber: 4.1 Consensus size: 9 2156 CTCCTCTCGN 2166 CTGCTGCTG 1 CTGCTGCTG 2175 NCTGCTGCTG 1 -CTGCTGCTG 2185 CNTGCTGCTG 1 C-TGCTGCTG 2195 CTGCTGCTG 1 CTGCTGCTG 2204 C 1 C 2205 AGAGCTTCCG Statistics Matches: 28, Mismatches: 0, Indels: 3 0.90 0.00 0.10 Matches are distributed among these distances: 9 10 0.36 10 18 0.64 ACGTcount: A:0.00, C:0.33, G:0.31, T:0.31 Consensus pattern (9 bp): CTGCTGCTG Left flanking sequence: Indices 1666 -- 2165 AAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANG AAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAG GAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAA ATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGG ACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGG TTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGA AGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCA GTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGN Right flanking sequence: Indices 2205 -- 2483 AGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTACACCAAACA CACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGACTCAAACCCTAACCCT AAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTN NTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGA AGAATCGTGTCAATGGCCT Found at i:2182 original size:13 final size:12 Alignment explanation

Indices: 2166--2204 Score: 60 Period size: 13 Copynumber: 3.1 Consensus size: 12 2156 CTCCTCTCGN 2166 CTGCTGCTGNCTG 1 CTGCTGCTG-CTG 2179 CTGCTGCNTGCTG 1 CTGCTGC-TGCTG 2192 CTGCTGCTGCTG 1 CTGCTGCTGCTG 2204 C 1 C 2205 AGAGCTTCCG Statistics Matches: 25, Mismatches: 0, Indels: 3 0.89 0.00 0.11 Matches are distributed among these distances: 12 6 0.24 13 17 0.68 14 2 0.08 ACGTcount: A:0.00, C:0.33, G:0.31, T:0.31 Consensus pattern (12 bp): CTGCTGCTGCTG Left flanking sequence: Indices 1666 -- 2165 AAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANG AAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAG GAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAA ATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGG ACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGG TTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGA AGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCA GTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGN Right flanking sequence: Indices 2205 -- 2483 AGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTACACCAAACA CACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGACTCAAACCCTAACCCT AAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTN NTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGA AGAATCGTGTCAATGGCCT Found at i:2313 original size:7 final size:6 Alignment explanation

Indices: 2296--2339 Score: 40 Period size: 6 Copynumber: 6.8 Consensus size: 6 2286 CCCTAGAAAA * * * 2296 AAACCC AAACCAC AAACCC TAGACTC AAACCC TAACCC TAAACC 1 AAACCC AAACC-C AAACCC -AAACCC AAACCC AAACCC -AAACC 2340 TTAGGGCCAG Statistics Matches: 29, Mismatches: 6, Indels: 5 0.72 0.15 0.12 Matches are distributed among these distances: 6 15 0.52 7 14 0.48 ACGTcount: A:0.45, C:0.43, G:0.02, T:0.09 Consensus pattern (6 bp): AAACCC Left flanking sequence: Indices 1796 -- 2295 GAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAA ATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGG ACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGG TTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGA AGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCA GTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGC NTGCTGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTG CTTCTACCTACACCAAACACACCTTCAACACTAAACCCTAGAAAA Right flanking sequence: Indices 2340 -- 2483 TTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTNNTTAG GGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGAAGAAT CGTGTCAATGGCCT Found at i:2325 original size:26 final size:26 Alignment explanation

Indices: 2283--2343 Score: 73 Period size: 26 Copynumber: 2.3 Consensus size: 26 2273 CTTCAACACT 2283 AAACCCTAGAAAAAAACCCAAACCAC 1 AAACCCTAGAAAAAAACCCAAACCAC *** * ** 2309 AAACCCTAGACTCAAACCCTAACCCT 1 AAACCCTAGAAAAAAACCCAAACCAC * 2335 AAACCTTAG 1 AAACCCTAG 2344 GGCCAGCCCT Statistics Matches: 28, Mismatches: 7, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 26 28 1.00 ACGTcount: A:0.48, C:0.36, G:0.05, T:0.11 Consensus pattern (26 bp): AAACCCTAGAAAAAAACCCAAACCAC Left flanking sequence: Indices 1783 -- 2282 GCTGCTGCGTCAGGAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCA CAACCACTCCGAAATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGG CATTCGGGCGCGGACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGT TTAGGGCTTAGGGTTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGG GTTTAGGGTTTGAAGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAA AAATAAACNGGCAGTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGC TGNCTGCTGCTGCNTGCTGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCAC CGAGGGTCATCTGCTTCTACCTACACCAAACACACCTTCAACACT Right flanking sequence: Indices 2344 -- 2483 GGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTNNTTAGGGTT TGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGAAGAATCGTG TCAATGGCCT Found at i:2338 original size:13 final size:12 Alignment explanation

Indices: 2296--2339 Score: 47 Period size: 13 Copynumber: 3.4 Consensus size: 12 2286 CCCTAGAAAA * 2296 AAACCCAAACCAC 1 AAACCCTAACC-C * 2309 AAACCCTAGACTC 1 AAACCCTA-ACCC 2322 AAACCCTAACCC 1 AAACCCTAACCC 2334 TAAACC 1 -AAACC 2340 TTAGGGCCAG Statistics Matches: 26, Mismatches: 3, Indels: 4 0.79 0.09 0.12 Matches are distributed among these distances: 12 3 0.12 13 21 0.81 14 2 0.08 ACGTcount: A:0.45, C:0.43, G:0.02, T:0.09 Consensus pattern (12 bp): AAACCCTAACCC Left flanking sequence: Indices 1796 -- 2295 GAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAA ATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGG ACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGG TTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGA AGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCA GTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGC NTGCTGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTG CTTCTACCTACACCAAACACACCTTCAACACTAAACCCTAGAAAA Right flanking sequence: Indices 2340 -- 2483 TTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTNNTTAG GGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGAAGAAT CGTGTCAATGGCCT Found at i:2422 original size:8 final size:7 Alignment explanation

Indices: 2401--2436 Score: 33 Period size: 7 Copynumber: 4.9 Consensus size: 7 2391 GNNAGGGTNN 2401 TTAGGGT 1 TTAGGGT 2408 TTGAGGGT 1 TT-AGGGT 2416 NTTAGGGT 1 -TTAGGGT * * 2424 NTTGGGT 1 TTAGGGT * 2431 TGAGGG 1 TTAGGG 2437 CNTTAGAGGA Statistics Matches: 22, Mismatches: 5, Indels: 4 0.71 0.16 0.13 Matches are distributed among these distances: 7 10 0.45 8 10 0.45 9 2 0.09 ACGTcount: A:0.11, C:0.00, G:0.47, T:0.36 Consensus pattern (7 bp): TTAGGGT Left flanking sequence: Indices 1901 -- 2400 GCTAGCGCTGGGCATTCGGGCGCGGACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGAC TCTGCTGAGGGTTTAGGGCTTAGGGTTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGC TGAGGGTTTAGGGTTTAGGGTTTGAAGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCC CAAATACAGCAAAAATAAACNGGCAGTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCT CTCGNCTGCTGCTGNCTGCTGCTGCNTGCTGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGC AGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTACACCAAACACACCTTCAACACTAAACCCTA GAAAAAAACCCAAACCACAAACCCTAGACTCAAACCCTAACCCTAAACCTTAGGGCCAGCCCTAA GGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTNN Right flanking sequence: Indices 2437 -- 2483 CNTTAGAGGACTTACGAGGAGCTTGAGAAGAATCGTGTCAATGGCCT Done.