Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr13

Parameters: 2 7 7 80 10 50 1000

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

Length: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32

Warning! 2011935 characters in sequence are not A, C, G, or T


File 62 of 141

Found at i:20195568 original size:23 final size:23

Alignment explanation

Indices: 20195536--20195587 Score: 61 Period size: 23 Copynumber: 2.2 Consensus size: 23 20195526 ATTAAATATG * 20195536 AAAAAGAAA-TAATAAAGAAATAA 1 AAAAACAAATTAATAAA-AAATAA * 20195559 AAAAACAAATTAATTAAAAATAA 1 AAAAACAAATTAATAAAAAATAA 20195582 AGAAAA 1 A-AAAA 20195588 TAAAAAAAAG Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 23 15 0.60 24 10 0.40 ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15 Consensus pattern (23 bp): AAAAACAAATTAATAAAAAATAA Found at i:20196152 original size:21 final size:21 Alignment explanation

Indices: 20196110--20196169 Score: 88 Period size: 21 Copynumber: 2.9 Consensus size: 21 20196100 TACAAAATCA * 20196110 CATATTCTAAGATT--ACATAT 1 CATA-TCTAAGATTGCATATAT 20196130 CATATCTAAGATTGCATATAT 1 CATATCTAAGATTGCATATAT 20196151 CATATCTAAGATTGCATAT 1 CATATCTAAGATTGCATAT 20196170 CCTCGAAGAT Statistics Matches: 37, Mismatches: 1, Indels: 3 0.90 0.02 0.07 Matches are distributed among these distances: 19 9 0.24 20 4 0.11 21 24 0.65 ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38 Consensus pattern (21 bp): CATATCTAAGATTGCATATAT Found at i:20197654 original size:9 final size:9 Alignment explanation

Indices: 20197640--20197706 Score: 73 Period size: 9 Copynumber: 7.4 Consensus size: 9 20197630 TTTGGTTAAA 20197640 AATTAACCG 1 AATTAACCG * 20197649 AATTAAACG 1 AATTAACCG * 20197658 AATTAACCT 1 AATTAACCG * 20197667 AATT-ACTTG 1 AATTAAC-CG 20197676 AATTAACCG 1 AATTAACCG * 20197685 AATTACCCG 1 AATTAACCG * 20197694 AATTAATCG 1 AATTAACCG 20197703 AATT 1 AATT 20197707 GAATCACTAC Statistics Matches: 47, Mismatches: 9, Indels: 4 0.78 0.15 0.07 Matches are distributed among these distances: 8 2 0.04 9 43 0.91 10 2 0.04 ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30 Consensus pattern (9 bp): AATTAACCG Found at i:20198341 original size:2 final size:2 Alignment explanation

Indices: 20198334--20198362 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 20198324 CTTTATATTT 20198334 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 20198363 GTCTTTGCAT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:20208516 original size:25 final size:25 Alignment explanation

Indices: 20208488--20208536 Score: 80 Period size: 25 Copynumber: 2.0 Consensus size: 25 20208478 TTCAAGTGAG 20208488 CTATATCAGGAAGCTCACAAAGAGC 1 CTATATCAGGAAGCTCACAAAGAGC * * 20208513 CTATATCAGGACGCTCATAAAGAG 1 CTATATCAGGAAGCTCACAAAGAG 20208537 TTGTGGTATG Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 25 22 1.00 ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18 Consensus pattern (25 bp): CTATATCAGGAAGCTCACAAAGAGC Found at i:20208623 original size:64 final size:64 Alignment explanation

Indices: 20208514--20208640 Score: 148 Period size: 64 Copynumber: 2.0 Consensus size: 64 20208504 ACAAAGAGCC * * * * * ** * 20208514 TATATCAGGACGCTCATAAAGAGTTGTGGTATGTCCGCATTATATGC-AGGATCCATACCGATCA 1 TATAACAGGACGCTCACAAAGAGCTGCGGTATGACCGCAACATATGCAAGG-TCAATACCGATCA * * 20208578 TATAACAGGATGCTCACAAAGAGCTGCGGTATGACTGCAACATATGCAAGGTCAATACCGATC 1 TATAACAGGACGCTCACAAAGAGCTGCGGTATGACCGCAACATATGCAAGGTCAATACCGATC 20208641 GGGATGCTTG Statistics Matches: 52, Mismatches: 10, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 64 49 0.94 65 3 0.06 ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24 Consensus pattern (64 bp): TATAACAGGACGCTCACAAAGAGCTGCGGTATGACCGCAACATATGCAAGGTCAATACCGATCA Found at i:20212984 original size:22 final size:22 Alignment explanation

Indices: 20212933--20212984 Score: 63 Period size: 21 Copynumber: 2.4 Consensus size: 22 20212923 TAACAACCTT * 20212933 TAAACATGTTCAAAACATCCCA 1 TAAACATGTTCAAAACATACCA 20212955 -AAACCATG-TCAAAACATACCA 1 TAAA-CATGTTCAAAACATACCA 20212976 TAAATCATG 1 TAAA-CATG 20212985 ATCCCAAACA Statistics Matches: 26, Mismatches: 2, Indels: 4 0.81 0.06 0.12 Matches are distributed among these distances: 21 15 0.58 22 11 0.42 ACGTcount: A:0.48, C:0.25, G:0.06, T:0.21 Consensus pattern (22 bp): TAAACATGTTCAAAACATACCA Found at i:20214070 original size:23 final size:23 Alignment explanation

Indices: 20214044--20214088 Score: 90 Period size: 23 Copynumber: 2.0 Consensus size: 23 20214034 CTATATAGTA 20214044 ATTCATTTCGATTTATCAATTCT 1 ATTCATTTCGATTTATCAATTCT 20214067 ATTCATTTCGATTTATCAATTC 1 ATTCATTTCGATTTATCAATTC 20214089 AAACTACCTT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 22 1.00 ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51 Consensus pattern (23 bp): ATTCATTTCGATTTATCAATTCT Found at i:20217876 original size:21 final size:22 Alignment explanation

Indices: 20217852--20217903 Score: 63 Period size: 21 Copynumber: 2.4 Consensus size: 22 20217842 TGGCCAGTAC * 20217852 AAATAACAA-AAACAATAGC-AA 1 AAATAACAACAAA-AACAGCAAA 20217873 AAATAACAACAAAAACAGCAGAA 1 AAATAACAACAAAAACAGCA-AA 20217896 AAATAACA 1 AAATAACA 20217904 CCACCAAAAC Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 21 14 0.52 22 3 0.11 23 10 0.37 ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08 Consensus pattern (22 bp): AAATAACAACAAAAACAGCAAA Found at i:20217897 original size:23 final size:24 Alignment explanation

Indices: 20217856--20217903 Score: 71 Period size: 24 Copynumber: 2.0 Consensus size: 24 20217846 CAGTACAAAT * 20217856 AACAAAAACAATAGCAAAAATAAC 1 AACAAAAACAACAGCAAAAATAAC * 20217880 AACAAAAACAGCAG-AAAAATAAC 1 AACAAAAACAACAGCAAAAATAAC 20217903 A 1 A 20217904 CCACCAAAAC Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 23 10 0.45 24 12 0.55 ACGTcount: A:0.71, C:0.17, G:0.06, T:0.06 Consensus pattern (24 bp): AACAAAAACAACAGCAAAAATAAC Found at i:20218439 original size:25 final size:26 Alignment explanation

Indices: 20218405--20218455 Score: 77 Period size: 25 Copynumber: 2.0 Consensus size: 26 20218395 TTTGACTCTA * 20218405 ATTTTTTTTAAATTTCTC-TCAATTT 1 ATTTTTTTTAAATTTATCGTCAATTT * 20218430 ATTTTTTTTAACTTTATCGTCAATTT 1 ATTTTTTTTAAATTTATCGTCAATTT 20218456 GCTTTAGTCT Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 25 16 0.70 26 7 0.30 ACGTcount: A:0.24, C:0.12, G:0.02, T:0.63 Consensus pattern (26 bp): ATTTTTTTTAAATTTATCGTCAATTT Found at i:20218548 original size:11 final size:11 Alignment explanation

Indices: 20218528--20218571 Score: 61 Period size: 11 Copynumber: 3.9 Consensus size: 11 20218518 CTCAACACCA 20218528 AAATTGAGAGG 1 AAATTGAGAGG * 20218539 AAATTTAGAGG 1 AAATTGAGAGG * 20218550 AAACTGAGAGG 1 AAATTGAGAGG 20218561 AAATTTGAGAG 1 AAA-TTGAGAG 20218572 ATGATTAATT Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 11 22 0.79 12 6 0.21 ACGTcount: A:0.45, C:0.02, G:0.32, T:0.20 Consensus pattern (11 bp): AAATTGAGAGG Found at i:20219680 original size:3 final size:3 Alignment explanation

Indices: 20219672--20219703 Score: 64 Period size: 3 Copynumber: 10.7 Consensus size: 3 20219662 TCTATCTACC 20219672 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA 20219704 CCATCACATG Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 29 1.00 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (3 bp): TAT Found at i:20224733 original size:31 final size:32 Alignment explanation

Indices: 20224683--20224742 Score: 77 Period size: 31 Copynumber: 1.9 Consensus size: 32 20224673 TTGCTTGGCA * * 20224683 AAGTGGAATGAAAATTAGAAAGATGGAAATTG 1 AAGTGGAATGAAAAATAGAAAGATAGAAATTG * * 20224715 AAGTGGTA-GAAAAATAGAAGGATAGAAA 1 AAGTGGAATGAAAAATAGAAAGATAGAAA 20224743 ATATAATTTC Statistics Matches: 24, Mismatches: 4, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 31 17 0.71 32 7 0.29 ACGTcount: A:0.53, C:0.00, G:0.28, T:0.18 Consensus pattern (32 bp): AAGTGGAATGAAAAATAGAAAGATAGAAATTG Found at i:20232663 original size:24 final size:24 Alignment explanation

Indices: 20232635--20232680 Score: 65 Period size: 24 Copynumber: 1.9 Consensus size: 24 20232625 AGAACAGTCC * * 20232635 CAAAAGTAAATGCAGGAGCAGCTT 1 CAAAAGAAAATGAAGGAGCAGCTT * 20232659 CAAAAGAAAATGAATGAGCAGC 1 CAAAAGAAAATGAAGGAGCAGC 20232681 AAAAAATGAT Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 24 19 1.00 ACGTcount: A:0.48, C:0.15, G:0.24, T:0.13 Consensus pattern (24 bp): CAAAAGAAAATGAAGGAGCAGCTT Found at i:20240764 original size:44 final size:45 Alignment explanation

Indices: 20240705--20241036 Score: 167 Period size: 44 Copynumber: 7.6 Consensus size: 45 20240695 CACATCTAGT ** 20240705 CTTATCTCTTTGAAGTTGCAGTGGAGTAGACT-AAG-TAAGCAAATC 1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAT-AGCAAA-C * * 20240750 C-TATCTTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCAAAC 1 CTTATCTCCCTGAAGTTGCAGTGGA-GTAGACTGAAGATAGCAAAC * ** * * 20240794 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCT-G-ATAATC 1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCA-AA-C * * ** * * **** * 20240839 C-TATCTCCCTAAAGTTGTAGTGGAGCGGA-TTAAAATATTGGAT 1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCAAAC * * * * * * * 20240882 CTTATCTCTCTGAAGTTGTAG-AGAGCAGA-TCG--CAT--CTAAT 1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-GAAGATAGCAAAC * * ** 20240922 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGTAAGT 1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAT-AGCAAAC * * * 20240966 CTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAAC 1 CTTATCTC-CCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCAAAC 20241011 CTTATCTCCCTGAAGTTGCAGTGGAG 1 CTTATCTCCCTGAAGTTGCAGTGGAG 20241037 CAGGTTAAAG Statistics Matches: 222, Mismatches: 43, Indels: 44 0.72 0.14 0.14 Matches are distributed among these distances: 40 21 0.09 41 8 0.04 42 3 0.01 43 16 0.07 44 102 0.46 45 67 0.30 46 5 0.02 ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29 Consensus pattern (45 bp): CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCAAAC Found at i:20240999 original size:217 final size:217 Alignment explanation

Indices: 20240619--20241368 Score: 891 Period size: 217 Copynumber: 3.5 Consensus size: 217 20240609 AAAGCCAATG * 20240619 ATCCTATCTCCCTGAAGTTGCACTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC 1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC * * ** * * * 20240684 AGAGAGCAGATCACATCTAGTCTTATCTCTTTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAAT 66 AGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGT * * * * 20240749 CCTATCTTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA 131 CTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA 20240814 GTGGAGCAGGTTAAAGCTGATA 196 GTGGAGCAGGTTAAAGCTGATA * * ** 20240836 ATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAAT-ATTGGATCTTATCTCTCTGAAGTTG 1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCA-CAGATCTTATCTCTCTGAAGTTG * 20240900 TAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAG 65 CAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAG 20240965 TCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGC 130 TCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGC 20241030 AGTGGAGCAGGTTAAA---G--- 195 AGTGGAGCAGGTTAAAGCTGATA ** * * * 20241047 -----------CTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA-A-ATCCTATCT-TCCTGAAGT 1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA--AATCACAGATCTTATCTCT-CTGAAGT * * * * * 20241098 TGCAGTGAGGTAGA-CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG 63 TGCAGAGA-GCAGATC-G--CAT--CTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG * ** 20241162 TAAGTAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGAAAATATTATCTCCCT 122 TAAGTAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCT * * ** 20241227 GAAGTTGCAGTGGAGCAGATTAAGGCCAATA 187 GAAGTTGCAGTGGAGCAGGTTAAAGCTGATA ** * 20241258 ATATTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTAC 1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC * 20241323 AGAG-GCAGATCGCATCTAGTCTTATCTCCCTGACA-TTGCAGTGGAG 66 AGAGAGCAGATCGCATCTAATCTTATCTCCCTGA-AGTTGCAGTGGAG 20241369 TACACAGCAG Statistics Matches: 451, Mismatches: 49, Indels: 67 0.80 0.09 0.12 Matches are distributed among these distances: 199 1 0.00 200 42 0.09 201 5 0.01 202 2 0.00 203 3 0.01 205 122 0.27 214 1 0.00 216 27 0.06 217 192 0.43 218 2 0.00 220 9 0.02 221 2 0.00 222 42 0.09 223 1 0.00 ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28 Consensus pattern (217 bp): ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC AGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGT CTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA GTGGAGCAGGTTAAAGCTGATA Found at i:20241135 original size:116 final size:116 Alignment explanation

Indices: 20240931--20241155 Score: 387 Period size: 116 Copynumber: 1.9 Consensus size: 116 20240921 TCTTATCTCC * * * * 20240931 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGA 1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCCTCCTGAAGTTGCAGTGAGGCAGA 20240996 CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAG 66 CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAG * * * 20241047 CTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAATCCTATCTTCCTGAAGTTGCAGTGAGGTAGA 1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCCTCCTGAAGTTGCAGTGAGGCAGA 20241112 CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAG 66 CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAG 20241156 ACTAAGTAAG Statistics Matches: 102, Mismatches: 7, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 116 102 1.00 ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24 Consensus pattern (116 bp): CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCCTCCTGAAGTTGCAGTGAGGCAGA CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAG Found at i:20241140 original size:45 final size:44 Alignment explanation

Indices: 20241047--20241286 Score: 199 Period size: 44 Copynumber: 5.4 Consensus size: 44 20241037 CAGGTTAAAG * * 20241047 CTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAATCC-TATCTTC 1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA-CCTTATCTCC * * 20241091 CTGAAGTTGCAGT-GAGGTAGACTGAAG-ATGGCAAACCTTATCTCC 1 CTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCAAACCTTATCTCC * ** 20241136 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCTTATC-CTC 1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAACCTTATCTC-C * * * ** 20241180 CTGAAGTTGCAGTGGGGCAGACTGAAG-ATGGAAAATATTATCTCC 1 CTGAAGTTGCAGTGGAGCAGACT-AAGTA-AGCAAACCTTATCTCC * ** 20241225 CTGAAGTTGCAGTGGAGCAGATTAAG---GCCAATAATATTATCTCC 1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAG-C-A-AACCTTATCTCC 20241269 CTGAAGTTGCAGTGGAGC 1 CTGAAGTTGCAGTGGAGC 20241287 GGATTAAAAT Statistics Matches: 168, Mismatches: 15, Indels: 26 0.80 0.07 0.12 Matches are distributed among these distances: 41 1 0.01 43 4 0.02 44 92 0.55 45 68 0.40 46 3 0.02 ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26 Consensus pattern (44 bp): CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAACCTTATCTCC Found at i:20241202 original size:89 final size:88 Alignment explanation

Indices: 20241047--20241283 Score: 307 Period size: 89 Copynumber: 2.7 Consensus size: 88 20241037 CAGGTTAAAG * * * * * * 20241047 CTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAATCCTATCTTCCTGAAGTTGCAGTGAGGTAGA 1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAG-TAATCTTATCCTCCTGAAGTTGCAGTGGGGCAGA * * 20241112 CTGAAGATGGCAAACCTTATCTCC 65 CTGAAGATGGAAAACATTATCTCC 20241136 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGA 1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAA-TCTTATCCTCCTGAAGTTGCAGTGGGGCAGA * 20241201 CTGAAGATGGAAAATATTATCTCC 65 CTGAAGATGGAAAACATTATCTCC * * * 20241225 CTGAAGTTGCAGTGGAGCAGATTAAGGCCAA-TAATATTAT-CTCCCTGAAGTTGCAGTGG 1 CTGAAGTTGCAGTGGAGCAGACTAA-G-TAAGTAATCTTATCCT-CCTGAAGTTGCAGTGG 20241284 AGCGGATTAA Statistics Matches: 132, Mismatches: 12, Indels: 8 0.87 0.08 0.05 Matches are distributed among these distances: 88 4 0.03 89 122 0.92 90 4 0.03 91 2 0.02 ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26 Consensus pattern (88 bp): CTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAATCTTATCCTCCTGAAGTTGCAGTGGGGCAGAC TGAAGATGGAAAACATTATCTCC Found at i:20241309 original size:44 final size:43 Alignment explanation

Indices: 20241047--20241320 Score: 173 Period size: 44 Copynumber: 6.2 Consensus size: 43 20241037 CAGGTTAAAG * * * * * 20241047 CTGAAGTTGCAGTGGAGTAGACTAAGTAAGC-AAATCCTATCTTC 1 CTGAAGTTGCAGTGGAGCAGATTAA--AATCAAAATCTTATCTCC * * * * 20241091 CTGAAGTTGCAGT-GAGGTAGACTGAAGATGGC-AAACCTTATCTCC 1 CTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CAAAATCTTATCTCC * * 20241136 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGT--AAGTCTTATC-CTC 1 CTGAAGTTGCAGTGGAGCAGATTAA--AA-TCAAAATCTTATCTC-C * * * * * 20241180 CTGAAGTTGCAGTGGGGCAGACTGAAGATGGAAAATATTATCTCC 1 CTGAAGTTGCAGTGGAGCAGA-TTAAAAT-CAAAATCTTATCTCC *** * 20241225 CTGAAGTTGCAGTGGAGCAGATTAAGGCCAATAATATTATCTCC 1 CTGAAGTTGCAGTGGAGCAGATTAAAATCAA-AATCTTATCTCC * * * 20241269 CTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCT 1 CTGAAGTTGCAGTGGAGCAGATTAAAATCA-AAATCTTATCTCC 20241313 CTGAAGTT 1 CTGAAGTT 20241321 ACAGAGGCAG Statistics Matches: 183, Mismatches: 31, Indels: 32 0.74 0.13 0.13 Matches are distributed among these distances: 42 1 0.01 43 7 0.04 44 108 0.59 45 62 0.34 46 4 0.02 47 1 0.01 ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27 Consensus pattern (43 bp): CTGAAGTTGCAGTGGAGCAGATTAAAATCAAAATCTTATCTCC Found at i:20243107 original size:16 final size:17 Alignment explanation

Indices: 20243062--20243108 Score: 53 Period size: 17 Copynumber: 2.8 Consensus size: 17 20243052 TCATGTACTT 20243062 TTTATATTTTTTTGCTA 1 TTTATATTTTTTTGCTA * 20243079 TTTAT-TTGTTTTTTC-A 1 TTTATATT-TTTTTGCTA * 20243095 TTTATATTATTTTG 1 TTTATATTTTTTTG 20243109 TTCGTTTATG Statistics Matches: 25, Mismatches: 3, Indels: 5 0.76 0.09 0.15 Matches are distributed among these distances: 16 12 0.48 17 13 0.52 ACGTcount: A:0.17, C:0.04, G:0.06, T:0.72 Consensus pattern (17 bp): TTTATATTTTTTTGCTA Found at i:20248265 original size:31 final size:32 Alignment explanation

Indices: 20248230--20248290 Score: 106 Period size: 32 Copynumber: 1.9 Consensus size: 32 20248220 ATAAATTGCT * 20248230 CTCCCTTA-ATAAAATTCATTTTCAATTTAAG 1 CTCCCCTATATAAAATTCATTTTCAATTTAAG 20248261 CTCCCCTATATAAAATTCATTTTCAATTTA 1 CTCCCCTATATAAAATTCATTTTCAATTTA 20248291 GGGCTTAAAA Statistics Matches: 28, Mismatches: 1, Indels: 1 0.93 0.03 0.03 Matches are distributed among these distances: 31 7 0.25 32 21 0.75 ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43 Consensus pattern (32 bp): CTCCCCTATATAAAATTCATTTTCAATTTAAG Found at i:20250731 original size:41 final size:41 Alignment explanation

Indices: 20250685--20250809 Score: 162 Period size: 41 Copynumber: 3.0 Consensus size: 41 20250675 AGAATAATGA * * 20250685 TGAATTGCACATACGTGTCCCTGTTTGTACTTCGGTACCCT 1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCT * 20250726 TGAATTGCACATACGTGCCCCTATTTGTACTTCAGTAACCC- 1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGT-ACCCT * * * * * 20250767 TGTATTGCATAGACGTGCCCCTCTTTGTACTTTGGTACCCT 1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCT 20250808 TG 1 TG 20250810 GATGTACTTT Statistics Matches: 73, Mismatches: 9, Indels: 4 0.85 0.10 0.05 Matches are distributed among these distances: 40 4 0.05 41 65 0.89 42 4 0.05 ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36 Consensus pattern (41 bp): TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCT Found at i:20252615 original size:51 final size:50 Alignment explanation

Indices: 20252455--20252641 Score: 166 Period size: 51 Copynumber: 3.7 Consensus size: 50 20252445 AGTGAAAGTG * * * * * 20252455 ATGGTCACATGTTTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT 1 ATGGTCACATGTGTAGTACTATGTGCAGACTACTACGTATATCGG-ATGGT ** * * * 20252506 A-GGTTGCATGTGTAGTACTATGTACAGGCTACTATGCGTAT-T-GGATAGT 1 ATGGTCACATGTGTAGTACTATGTGCAGACTACTA--CGTATATCGGATGGT * ** * 20252555 TTCAATCACATGTGTAGTACTATGTGCAGACTACTACGTATATCTGATGGT 1 AT-GGTCACATGTGTAGTACTATGTGCAGACTACTACGTATATCGGATGGT 20252606 AATGGTCACATGTGTAGTACTATGTGCA-AGCTACTA 1 -ATGGTCACATGTGTAGTACTATGTGCAGA-CTACTA 20252642 TTTGAACTAA Statistics Matches: 108, Mismatches: 20, Indels: 16 0.75 0.14 0.11 Matches are distributed among these distances: 49 8 0.07 50 33 0.31 51 62 0.57 52 5 0.05 ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33 Consensus pattern (50 bp): ATGGTCACATGTGTAGTACTATGTGCAGACTACTACGTATATCGGATGGT Found at i:20257979 original size:51 final size:51 Alignment explanation

Indices: 20257916--20258047 Score: 158 Period size: 51 Copynumber: 2.6 Consensus size: 51 20257906 TGATAGGTCG * * 20257916 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGT-TTCGATCA 1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGAATAGTAAT-GATCA * * * * * * * 20257967 CGTGTGTAGTACTATGTACAGGCTTCTACGTGTATCGAATGGTAATGGTCA 1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGAATAGTAATGATCA * 20258018 CATGTGTAGTACTATGTGTAGGCTACTATG 1 CATGTGTAGTACTATGTGCAGGCTACTATG 20258048 TGAACCAAAC Statistics Matches: 66, Mismatches: 14, Indels: 2 0.80 0.17 0.02 Matches are distributed among these distances: 51 65 0.98 52 1 0.02 ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34 Consensus pattern (51 bp): CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGAATAGTAATGATCA Found at i:20258007 original size:100 final size:102 Alignment explanation

Indices: 20257864--20258047 Score: 293 Period size: 102 Copynumber: 1.8 Consensus size: 102 20257854 AAAGTGATGG * * 20257864 TCACGTGTGTAGTACATGTGCAGGCTTCTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGTA 1 TCACGTGTGTAGTACATGTACAGGCTTCTACGTGTACCGGAATGATAATGGTCACATGTGTAGTA 20257927 CTATGTGCAGGCTACTATGCGTATCGGATAGTTTCGA 66 CTATGTGCAGGCTACTATGCGTATCGGATAGTTTCGA * * 20257964 TCACGTGTGTAGTACTATGTACAGGCTTCTACGTGTATC-GAATGGTAATGGTCACATGTGTAGT 1 TCACGTGTGTAGTAC-ATGTACAGGCTTCTACGTGTACCGGAATGATAATGGTCACATGTGTAGT * 20258028 ACTATGTGTAGGCTACTATG 65 ACTATGTGCAGGCTACTATG 20258048 TGAACCAAAC Statistics Matches: 76, Mismatches: 5, Indels: 4 0.89 0.06 0.05 Matches are distributed among these distances: 100 21 0.28 101 22 0.29 102 33 0.43 ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33 Consensus pattern (102 bp): TCACGTGTGTAGTACATGTACAGGCTTCTACGTGTACCGGAATGATAATGGTCACATGTGTAGTA CTATGTGCAGGCTACTATGCGTATCGGATAGTTTCGA Found at i:20258107 original size:45 final size:45 Alignment explanation

Indices: 20258056--20258144 Score: 151 Period size: 45 Copynumber: 2.0 Consensus size: 45 20258046 TGTGAACCAA * * * 20258056 ACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCCACCGG 1 ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCGG 20258101 ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCG 1 ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCG 20258145 AGTATCTGTT Statistics Matches: 41, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 45 41 1.00 ACGTcount: A:0.26, C:0.16, G:0.25, T:0.34 Consensus pattern (45 bp): ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCGG Found at i:20276705 original size:39 final size:39 Alignment explanation

Indices: 20276649--20276903 Score: 308 Period size: 39 Copynumber: 6.5 Consensus size: 39 20276639 AGATGTTTTG * * 20276649 AGTATTGTGATATATGCTTAAGTATTATGAGATTATATGT 1 AGTATTGTGATATATGCTTAA-TGTTATGTGATTATATGT * * 20276689 A-TATTGTGATATATGCTTGAATATTATGTGATTATACG- 1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT * 20276727 AGTATTGTGATATATGCTTACATGTTATGAGATTATATGT 1 AGTATTGTGATATATGCTTA-ATGTTATGTGATTATATGT * * 20276767 A-TATTATGATATATGCTTGAATGTTATGTGATTATA-CT 1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT 20276805 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG- 1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT * * 20276844 AGTATTGTGATATATGCTTGGATGTTAGGTGATTATATGT 1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT * 20276884 -GTAATAG-GATATATGCTTAA 1 AGT-ATTGTGATATATGCTTAA 20276904 AAGTGAATAT Statistics Matches: 190, Mismatches: 16, Indels: 20 0.84 0.07 0.09 Matches are distributed among these distances: 38 5 0.03 39 177 0.93 40 8 0.04 ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45 Consensus pattern (39 bp): AGTATTGTGATATATGCTTAATGTTATGTGATTATATGT Found at i:20276862 original size:117 final size:117 Alignment explanation

Indices: 20276651--20276903 Score: 348 Period size: 117 Copynumber: 2.2 Consensus size: 117 20276641 ATGTTTTGAG * * * 20276651 TATTGTGATATATGCTTAAGTATTATGAGATTATATGTATATTGTGATATATGCTTGAATATTAT 1 TATTATGATATATGCTTAAGTATTATGAGATTATATCTATATTGTGATATATGCTTAAATATTAT * 20276716 GTGATTATACGAGTATTGTGATATATGCTTACATGTTATGAGATTATATGTA 66 GTGATTATACGAGTATTGTGATATATGCTTACATGTTAGGAGATTATATGTA * * * 20276768 TATTATGATATATGCTTGAA-TGTTATGTGATTATA-CTAGTATTGTGATATATGCTTAAATGTT 1 TATTATGATATATGCTT-AAGTATTATGAGATTATATCTA-TATTGTGATATATGCTTAAATATT * ** * * 20276831 ATGTGATTATATGAGTATTGTGATATATGCTTGGATGTTAGGTGATTATATGTG 64 ATGTGATTATACGAGTATTGTGATATATGCTTACATGTTAGGAGATTATATGTA * * 20276885 TAATAGGATATATGCTTAA 1 TATTATGATATATGCTTAA 20276904 AAGTGAATAT Statistics Matches: 120, Mismatches: 14, Indels: 5 0.86 0.10 0.04 Matches are distributed among these distances: 116 4 0.03 117 114 0.95 118 2 0.02 ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45 Consensus pattern (117 bp): TATTATGATATATGCTTAAGTATTATGAGATTATATCTATATTGTGATATATGCTTAAATATTAT GTGATTATACGAGTATTGTGATATATGCTTACATGTTAGGAGATTATATGTA Found at i:20276904 original size:78 final size:78 Alignment explanation

Indices: 20276647--20276904 Score: 369 Period size: 78 Copynumber: 3.3 Consensus size: 78 20276637 AAAGATGTTT * * * 20276647 TGAGTATTGTGATATATGCTTAAGTATTATGAGATTATATGTATATTGTGATATATGCTTGAATA 1 TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTATATTGTGATATATGCTTGAATG 20276712 TTATGTGATTATA 66 TTATGTGATTATA * * * 20276725 CGAGTATTGTGATATATGCTTACATGTTATGAGATTATATGTATATTATGATATATGCTTGAATG 1 TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTATATTGTGATATATGCTTGAATG 20276790 TTATGTGATTATA 66 TTATGTGATTATA * * 20276803 CT-AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG-AGTATTGTGATATATGCTTGGA 1 -TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTA-TATTGTGATATATGCTTGAA * 20276866 TGTTAGGTGATTATA 64 TGTTATGTGATTATA * * 20276881 TGTGTAATAG-GATATATGCTTAAA 1 TGAGT-ATTGTGATATATGCTTAAA 20276905 AGTGAATATA Statistics Matches: 162, Mismatches: 14, Indels: 8 0.88 0.08 0.04 Matches are distributed among these distances: 77 2 0.01 78 157 0.97 79 3 0.02 ACGTcount: A:0.31, C:0.04, G:0.21, T:0.45 Consensus pattern (78 bp): TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTATATTGTGATATATGCTTGAATG TTATGTGATTATA Found at i:20283650 original size:19 final size:20 Alignment explanation

Indices: 20283626--20283665 Score: 64 Period size: 19 Copynumber: 2.0 Consensus size: 20 20283616 AAATACATGA * 20283626 TTTTTTATTTTATC-TGAGT 1 TTTTTTATGTTATCTTGAGT 20283645 TTTTTTATGTTATCTTGAGT 1 TTTTTTATGTTATCTTGAGT 20283665 T 1 T 20283666 ATGGAATGCT Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 19 13 0.68 20 6 0.32 ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68 Consensus pattern (20 bp): TTTTTTATGTTATCTTGAGT Found at i:20295709 original size:116 final size:116 Alignment explanation

Indices: 20295505--20295778 Score: 406 Period size: 116 Copynumber: 2.4 Consensus size: 116 20295495 TCATCGATCA * *** 20295505 ATGAAAAATGATGGTTTTGACCATCGATTATGAAAAGGGATAGTTTCGACTATCGACTATGAAAA 1 ATGAAAAAGGATGGTGACGACCATCGATTATGAAAAGGGATAGTTTCGACTATCGACTATGAAAA * * 20295570 GGGATGGTCACGACCATCAACTATGAAAAGGGATGGTGACGACTATAAACT 66 GGGATGGTCACGACCATCAACTATGAAAAGGGATGGTAACGACCATAAACT * * 20295621 ATGAAAAGGGATGGTGACGACCATCG-TATATGAAAAGGGATAGTTTTGACTATCGACTATGAAA 1 ATGAAAAAGGATGGTGACGACCATCGAT-TATGAAAAGGGATAGTTTCGACTATCGACTATGAAA * ** 20295685 AGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTAACGACCATCTACT 65 AGGGATGGTCACGACCATCAACTATGAAAAGGGATGGTAACGACCATAAACT * * 20295737 ATGAAAAAGGATGGTGACAACCATCGATTAATGAAAAAGGAT 1 ATGAAAAAGGATGGTGACGACCATCGATT-ATGAAAAGGGAT 20295779 GGTGACGACC Statistics Matches: 141, Mismatches: 14, Indels: 5 0.88 0.09 0.03 Matches are distributed among these distances: 115 1 0.01 116 128 0.91 117 12 0.09 ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23 Consensus pattern (116 bp): ATGAAAAAGGATGGTGACGACCATCGATTATGAAAAGGGATAGTTTCGACTATCGACTATGAAAA GGGATGGTCACGACCATCAACTATGAAAAGGGATGGTAACGACCATAAACT Found at i:20295799 original size:29 final size:29 Alignment explanation

Indices: 20295523--20295807 Score: 302 Period size: 29 Copynumber: 9.8 Consensus size: 29 20295513 TGATGGTTTT * * * ** 20295523 GACCATCGATTATGAAAAGGGATAGTTTC 1 GACCATCAACTATGAAAAGGGATGGTGAC * * * 20295552 GACTATCGACTATGAAAAGGGATGGTCAC 1 GACCATCAACTATGAAAAGGGATGGTGAC 20295581 GACCATCAACTATGAAAAGGGATGGTGAC 1 GACCATCAACTATGAAAAGGGATGGTGAC * * 20295610 GACTATAAACTATGAAAAGGGATGGTGAC 1 GACCATCAACTATGAAAAGGGATGGTGAC * * *** 20295639 GACCATCGTA-TATGAAAAGGGATAGTTTT 1 GACCATC-AACTATGAAAAGGGATGGTGAC * * 20295668 GACTATCGACTATGAAAAGGGATGGTGAC 1 GACCATCAACTATGAAAAGGGATGGTGAC * 20295697 GACCATCAACTATGAAAAGGGATGGTAAC 1 GACCATCAACTATGAAAAGGGATGGTGAC * * 20295726 GACCATCTACTATGAAAAAGGATGGTGAC 1 GACCATCAACTATGAAAAGGGATGGTGAC * * * * 20295755 AACCATCGATTAATGAAAAAGGATGGTGAC 1 GACCATCAACT-ATGAAAAGGGATGGTGAC ** * 20295785 GACCATCAAAAATGAAAGGGGAT 1 GACCATCAACTATGAAAAGGGAT 20295808 AGTTATGATC Statistics Matches: 215, Mismatches: 38, Indels: 6 0.83 0.15 0.02 Matches are distributed among these distances: 28 1 0.00 29 188 0.87 30 26 0.12 ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21 Consensus pattern (29 bp): GACCATCAACTATGAAAAGGGATGGTGAC Found at i:20305381 original size:16 final size:15 Alignment explanation

Indices: 20305356--20305389 Score: 50 Period size: 16 Copynumber: 2.2 Consensus size: 15 20305346 AAGTTTGATA * 20305356 ATAATTAATATATATT 1 ATAATCAATATA-ATT 20305372 ATAATCAATATAATT 1 ATAATCAATATAATT 20305387 ATA 1 ATA 20305390 CACTAGTTAT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 15 6 0.35 16 11 0.65 ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44 Consensus pattern (15 bp): ATAATCAATATAATT Found at i:20305638 original size:16 final size:15 Alignment explanation

Indices: 20305613--20305646 Score: 50 Period size: 16 Copynumber: 2.2 Consensus size: 15 20305603 AAGTTTGATA * 20305613 ATAATTAATATATATT 1 ATAATCAATATA-ATT 20305629 ATAATCAATATAATT 1 ATAATCAATATAATT 20305644 ATA 1 ATA 20305647 CACTAGTTAT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 15 6 0.35 16 11 0.65 ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44 Consensus pattern (15 bp): ATAATCAATATAATT Found at i:20305657 original size:125 final size:125 Alignment explanation

Indices: 20305271--20305659 Score: 332 Period size: 125 Copynumber: 3.1 Consensus size: 125 20305261 ACATATTACT 20305271 TTATTATTTGCTACTAATTTATTGAAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTA 1 TTATTATTTGCTACTAATTTATTGAAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTA 20305336 ATTCTATGCAAAGTTTGATAATAATTAATATATATTATAATCAATATAATTATACACTAG 66 ATTCTATGCAAAGTTTGATAATAATTAATATATATTATAATCAATATAATTATACACTAG * * ** * * * * * * 20305396 TTATTATCAT-CTTATTTGTTAAATT-AAATTAAAAAC-ATTTATTCCTAGATGC-CTTTGAAAA 1 TTATTAT-TTGC-TACTAATT-TATTGAAA-TAAAAACTA-TGAAT-AT-GAT-CAATTT-TAAA * ** **** * * * * 20305457 T-ATTTACAAAAAGAGACGTCTAA-TTT-TTAATAAAGTTAATACA-ATTAATAAAT-AATATAA 57 TGA-AT-CCTAATTCTATG-CAAAGTTTGATAAT-AA-TTAATATATATT-AT-AATCAATATAA * * 20305517 TACATATTACT-- 115 T-TATA-CACTAG 20305528 TTATTATTTGCTACTAATTTATTGAAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTA 1 TTATTATTTGCTACTAATTTATTGAAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTA 20305593 ATTCTATGCAAAGTTTGATAATAATTAATATATATTATAATCAATATAATTATACACTAG 66 ATTCTATGCAAAGTTTGATAATAATTAATATATATTATAATCAATATAATTATACACTAG 20305653 TTATTAT 1 TTATTAT 20305660 CATCTTATTT Statistics Matches: 189, Mismatches: 46, Indels: 58 0.65 0.16 0.20 Matches are distributed among these distances: 123 3 0.02 124 6 0.03 125 35 0.19 126 23 0.12 127 23 0.12 128 8 0.04 129 8 0.04 130 23 0.12 131 23 0.12 132 28 0.15 133 6 0.03 134 3 0.02 ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41 Consensus pattern (125 bp): TTATTATTTGCTACTAATTTATTGAAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTA ATTCTATGCAAAGTTTGATAATAATTAATATATATTATAATCAATATAATTATACACTAG Found at i:20305696 original size:257 final size:258 Alignment explanation

Indices: 20305230--20305745 Score: 1025 Period size: 257 Copynumber: 2.0 Consensus size: 258 20305220 AATTCTACAC 20305230 AAAGTTAATAACAATTAATAAATAATATAATACATATTACTTTATTATTTGCTACTAATTTATTG 1 AAAGTTAATAACAATTAATAAATAATATAATACATATTACTTTATTATTTGCTACTAATTTATTG 20305295 AAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTAATTCTATGCAAAGTTTGATAATAA 66 AAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTAATTCTATGCAAAGTTTGATAATAA 20305360 TTAATATATATTATAATCAATATAATTATACACTAGTTATTATCATCTTATTTGTTAAATTAAAT 131 TTAATATATATTATAATCAATATAATTATACACTAGTTATTATCATCTTATTTGTTAAATTAAAT 20305425 TAAAAACATTTATTCCTAGATGCCTTTGAAAATATTTACAAAAAGAGACGTCTAATTTTTAAT 196 TAAAAACATTTATTCCTAGATGCCTTTGAAAATATTTACAAAAAGAGACGTCTAATTTTTAAT 20305488 AAAGTTAAT-ACAATTAATAAATAATATAATACATATTACTTTATTATTTGCTACTAATTTATTG 1 AAAGTTAATAACAATTAATAAATAATATAATACATATTACTTTATTATTTGCTACTAATTTATTG 20305552 AAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTAATTCTATGCAAAGTTTGATAATAA 66 AAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTAATTCTATGCAAAGTTTGATAATAA 20305617 TTAATATATATTATAATCAATATAATTATACACTAGTTATTATCATCTTATTTGTTAAATTAAAT 131 TTAATATATATTATAATCAATATAATTATACACTAGTTATTATCATCTTATTTGTTAAATTAAAT 20305682 TAAAAACATTTATTCCTAGATGCCTTTGAAAATATTTACAAAAAGAGACGTCTAATTTTTAAT 196 TAAAAACATTTATTCCTAGATGCCTTTGAAAATATTTACAAAAAGAGACGTCTAATTTTTAAT 20305745 A 1 A 20305746 TTTACAAAAA Statistics Matches: 258, Mismatches: 0, Indels: 1 1.00 0.00 0.00 Matches are distributed among these distances: 257 249 0.97 258 9 0.03 ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40 Consensus pattern (258 bp): AAAGTTAATAACAATTAATAAATAATATAATACATATTACTTTATTATTTGCTACTAATTTATTG AAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTAATTCTATGCAAAGTTTGATAATAA TTAATATATATTATAATCAATATAATTATACACTAGTTATTATCATCTTATTTGTTAAATTAAAT TAAAAACATTTATTCCTAGATGCCTTTGAAAATATTTACAAAAAGAGACGTCTAATTTTTAAT Found at i:20321815 original size:43 final size:43 Alignment explanation

Indices: 20321779--20321878 Score: 146 Period size: 43 Copynumber: 2.3 Consensus size: 43 20321769 TCCCGGGCAG * 20321779 GGTCTTACACGAAAACACAAGTCAATTCCAACGTCCCAAACGT 1 GGTCTTACACGAAAACACAAGTCAATGCCAACGTCCCAAACGT * * * * * 20321822 GGTCTTACATGAAAACATAAGTCAATGCCAACATTCCAGACGT 1 GGTCTTACACGAAAACACAAGTCAATGCCAACGTCCCAAACGT 20321865 GGTCTTACACGAAA 1 GGTCTTACACGAAA 20321879 TCACTTATCA Statistics Matches: 50, Mismatches: 7, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 43 50 1.00 ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21 Consensus pattern (43 bp): GGTCTTACACGAAAACACAAGTCAATGCCAACGTCCCAAACGT Found at i:20330113 original size:43 final size:43 Alignment explanation

Indices: 20330066--20330165 Score: 155 Period size: 43 Copynumber: 2.3 Consensus size: 43 20330056 TCCTGGACAG * 20330066 GGTCTTACACGAAAACACAAGTCAATGCCAACGACTCAGACGT 1 GGTCTTACACGAAAACACAAGTCAATGCCAACGACCCAGACGT * *** 20330109 GGTCTTACACGAAAACACAAGTCGATGCCAATTTCCCAGACGT 1 GGTCTTACACGAAAACACAAGTCAATGCCAACGACCCAGACGT 20330152 GGTCTTACACGAAA 1 GGTCTTACACGAAA 20330166 TCACTTATCA Statistics Matches: 52, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 43 52 1.00 ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19 Consensus pattern (43 bp): GGTCTTACACGAAAACACAAGTCAATGCCAACGACCCAGACGT Found at i:20335064 original size:30 final size:30 Alignment explanation

Indices: 20335008--20335064 Score: 71 Period size: 30 Copynumber: 1.9 Consensus size: 30 20334998 CATAGTCTGG * * 20335008 CACATGGCCATGTGTCCACCAGGTGTGGCT 1 CACACGGCCATGTGTCCACCACGTGTGGCT * 20335038 CACACGGCCGTGTGTCCAGCC-CGTGTG 1 CACACGGCCATGTGTCCA-CCACGTGTG 20335065 ACTCTTAAAA Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 30 21 0.91 31 2 0.09 ACGTcount: A:0.14, C:0.33, G:0.32, T:0.21 Consensus pattern (30 bp): CACACGGCCATGTGTCCACCACGTGTGGCT Found at i:20342322 original size:12 final size:13 Alignment explanation

Indices: 20342289--20342319 Score: 53 Period size: 13 Copynumber: 2.4 Consensus size: 13 20342279 ATATGGTTCA 20342289 TAAAAACATAGCT 1 TAAAAACATAGCT * 20342302 TAAAAACATATCT 1 TAAAAACATAGCT 20342315 TAAAA 1 TAAAA 20342320 CATTTAAAAT Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26 Consensus pattern (13 bp): TAAAAACATAGCT Found at i:20345318 original size:4 final size:4 Alignment explanation

Indices: 20345306--20345372 Score: 125 Period size: 4 Copynumber: 16.8 Consensus size: 4 20345296 TTTATGCATG * 20345306 CATA TATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA 1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA 20345354 CATA CATA CATA CATA CAT 1 CATA CATA CATA CATA CAT 20345373 GGCTTTTCAT Statistics Matches: 61, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 4 61 1.00 ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27 Consensus pattern (4 bp): CATA Found at i:20353473 original size:24 final size:24 Alignment explanation

Indices: 20353445--20353490 Score: 92 Period size: 24 Copynumber: 1.9 Consensus size: 24 20353435 AGTTGTAAAT 20353445 CATCCATTGTTCCATTGTATTTTG 1 CATCCATTGTTCCATTGTATTTTG 20353469 CATCCATTGTTCCATTGTATTT 1 CATCCATTGTTCCATTGTATTT 20353491 AAAAGAGTTC Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 22 1.00 ACGTcount: A:0.17, C:0.22, G:0.11, T:0.50 Consensus pattern (24 bp): CATCCATTGTTCCATTGTATTTTG Found at i:20353604 original size:50 final size:50 Alignment explanation

Indices: 20353545--20353640 Score: 147 Period size: 50 Copynumber: 1.9 Consensus size: 50 20353535 CGATTTGCAC * 20353545 GAGGCACTGCTAAGAAGTGTGTTAGAGAGTTTAAAGAACTTATGCTTCAA 1 GAGGCACTGCTAAGAAGTATGTTAGAGAGTTTAAAGAACTTATGCTTCAA ** * * 20353595 GAGGCACTGCTGGGGAGTATGTTCGAGAGTTTAAAGAACTTATGCT 1 GAGGCACTGCTAAGAAGTATGTTAGAGAGTTTAAAGAACTTATGCT 20353641 CCAAATTTTA Statistics Matches: 41, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 50 41 1.00 ACGTcount: A:0.30, C:0.12, G:0.29, T:0.28 Consensus pattern (50 bp): GAGGCACTGCTAAGAAGTATGTTAGAGAGTTTAAAGAACTTATGCTTCAA Found at i:20361570 original size:22 final size:22 Alignment explanation

Indices: 20361545--20361594 Score: 64 Period size: 22 Copynumber: 2.3 Consensus size: 22 20361535 TTTTTTTCCT * 20361545 TATTTTCATTGATTTTCTAATC 1 TATTTTCATTGATTTACTAATC ** 20361567 TATTTTTGTTGATTTACTAATC 1 TATTTTCATTGATTTACTAATC * 20361589 TGTTTT 1 TATTTT 20361595 GGTCTCTTTA Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 22 24 1.00 ACGTcount: A:0.20, C:0.10, G:0.08, T:0.62 Consensus pattern (22 bp): TATTTTCATTGATTTACTAATC Found at i:20365463 original size:8 final size:8 Alignment explanation

Indices: 20365450--20365477 Score: 56 Period size: 8 Copynumber: 3.5 Consensus size: 8 20365440 ATAATTTAAA 20365450 AAAATTCT 1 AAAATTCT 20365458 AAAATTCT 1 AAAATTCT 20365466 AAAATTCT 1 AAAATTCT 20365474 AAAA 1 AAAA 20365478 AATATAAATA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 20 1.00 ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32 Consensus pattern (8 bp): AAAATTCT Found at i:20365520 original size:21 final size:20 Alignment explanation

Indices: 20365496--20365538 Score: 50 Period size: 21 Copynumber: 2.1 Consensus size: 20 20365486 TATAAACTTT * 20365496 AAAAATTCAAAATAATATATA 1 AAAAATTAAAAAT-ATATATA * * 20365517 AAAATTTAAAAATATATTTA 1 AAAAATTAAAAATATATATA 20365537 AA 1 AA 20365539 TTTAAAAAAT Statistics Matches: 19, Mismatches: 3, Indels: 1 0.83 0.13 0.04 Matches are distributed among these distances: 20 8 0.42 21 11 0.58 ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33 Consensus pattern (20 bp): AAAAATTAAAAATATATATA Found at i:20365532 original size:18 final size:18 Alignment explanation

Indices: 20365495--20365546 Score: 59 Period size: 18 Copynumber: 2.8 Consensus size: 18 20365485 ATATAAACTT * 20365495 TAAAAATTCAAAATAATATA 1 TAAAAATT-TAAA-AATATA 20365515 TAAAAATTTAAAAATATA 1 TAAAAATTTAAAAATATA ** 20365533 TTTAAATTTAAAAA 1 TAAAAATTTAAAAA 20365547 ATNNNNNNNN Statistics Matches: 29, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 18 18 0.62 19 3 0.10 20 8 0.28 ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35 Consensus pattern (18 bp): TAAAAATTTAAAAATATA Found at i:20366368 original size:14 final size:14 Alignment explanation

Indices: 20366349--20366377 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 20366339 GATATGTTCT 20366349 CACACTTATCTTAA 1 CACACTTATCTTAA 20366363 CACACTTATCTTAA 1 CACACTTATCTTAA 20366377 C 1 C 20366378 TTTTCTGTTG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34 Consensus pattern (14 bp): CACACTTATCTTAA Found at i:20367016 original size:42 final size:42 Alignment explanation

Indices: 20366910--20367072 Score: 272 Period size: 42 Copynumber: 3.9 Consensus size: 42 20366900 TTATAAGAAA * * 20366910 AAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTGCCCAA 1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTG-CCAC * * * 20366953 AAACGCCGCTAAAAAATATGACCTTTAGTGGCGCTTTGCCAC 1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCAC 20366995 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCAC 1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCAC 20367037 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTT 1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTT 20367073 ATGAAAAAAC Statistics Matches: 112, Mismatches: 8, Indels: 1 0.93 0.07 0.01 Matches are distributed among these distances: 42 78 0.70 43 34 0.30 ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20 Consensus pattern (42 bp): AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCAC Found at i:20367083 original size:42 final size:42 Alignment explanation

Indices: 20366908--20367090 Score: 269 Period size: 42 Copynumber: 4.3 Consensus size: 42 20366898 ATTTATAAGA * 20366908 AAAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTGCCC 1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTG-CC * * * 20366951 AAAAACGCCGCTAAAAAATATGACCTTTAGTGGCGCTTTGCC 1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCC * 20366993 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCC 1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCC * * 20367035 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTATG-A 1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTT-TGCC * 20367077 AAAAACGCGGCTAA 1 AAAAACGCCGCTAA 20367091 TTTTGACAAA Statistics Matches: 128, Mismatches: 11, Indels: 3 0.90 0.08 0.02 Matches are distributed among these distances: 42 90 0.70 43 38 0.30 ACGTcount: A:0.33, C:0.27, G:0.20, T:0.19 Consensus pattern (42 bp): AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCC Found at i:20368289 original size:86 final size:85 Alignment explanation

Indices: 20368140--20368468 Score: 394 Period size: 86 Copynumber: 3.8 Consensus size: 85 20368130 GTTTATGTGA * ** *** * * 20368140 AACAAATTAGCAAAAATCAACTATTCATAGTTCATATATTTACCGGTAA-TAGGGCTAAATTTTC 1 AACAAATTAGCAAAAATCAACTGTTCA-AGTTCATGCATTTACCAACAACCA-GACTAAATTTTC * * 20368204 AATTTCTATAACGATTTATATGC 64 AATTT-TATAACAACTTATATGC * * * * 20368227 AACAAATTAGCAAAAATCAA-TGGTTCAAGTTCATGTATTTACCAAAAATCAGACTAATTTTTCA 1 AACAAATTAGCAAAAATCAACT-GTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCA 20368291 ATATTTATAACAACTTATATGC 65 AT-TTTATAACAACTTATATGC * 20368313 AACAAATTAGCAAAAAT-AAATGGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCA 1 AACAAATTAGCAAAAATCAACT-GTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCA * 20368377 ATTTTTATAACAACTTATGTGC 65 A-TTTTATAACAACTTATATGC * * * 20368399 AACAAATTAGAAAAAATCAACTGTTCAAGTTCATGCATTCACCAACAACCAGACCAAATTTTCAA 1 AACAAATTAGCAAAAATCAACTGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCAA 20368464 CTTTT 66 -TTTT 20368469 TTAAAGTAGA Statistics Matches: 216, Mismatches: 20, Indels: 13 0.87 0.08 0.05 Matches are distributed among these distances: 85 2 0.01 86 183 0.85 87 31 0.14 ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32 Consensus pattern (85 bp): AACAAATTAGCAAAAATCAACTGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCAA TTTTATAACAACTTATATGC Found at i:20373983 original size:11 final size:11 Alignment explanation

Indices: 20373967--20374026 Score: 65 Period size: 10 Copynumber: 5.7 Consensus size: 11 20373957 AAAATGAAAG 20373967 TTTAAAATCTT 1 TTTAAAATCTT 20373978 TTTAAAA--TT 1 TTTAAAATCTT * 20373987 TTTAAAA-ATT 1 TTTAAAATCTT 20373997 TTTAAAATC-T 1 TTTAAAATCTT * 20374007 TTTAAAATTCAT 1 TTTAAAA-TCTT 20374019 TTTAAAAT 1 TTTAAAAT 20374027 TTTAAATCAT Statistics Matches: 44, Mismatches: 1, Indels: 8 0.83 0.02 0.15 Matches are distributed among these distances: 9 9 0.20 10 17 0.39 11 10 0.23 12 8 0.18 ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52 Consensus pattern (11 bp): TTTAAAATCTT Found at i:20374032 original size:20 final size:19 Alignment explanation

Indices: 20373967--20374029 Score: 74 Period size: 19 Copynumber: 3.1 Consensus size: 19 20373957 AAAATGAAAG 20373967 TTTAAAATCTTTTTAAAATT 1 TTTAAAATC-TTTTAAAATT 20373987 TTTAAAAAT-TTTTAAAATCT 1 TTT-AAAATCTTTTAAAAT-T 20374007 TTTAAAATTCATTTTAAAATT 1 TTTAAAA-TC-TTTTAAAATT 20374028 TT 1 TT 20374030 AAATCATGAA Statistics Matches: 38, Mismatches: 0, Indels: 9 0.81 0.00 0.19 Matches are distributed among these distances: 19 13 0.34 20 8 0.21 21 8 0.21 22 9 0.24 ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54 Consensus pattern (19 bp): TTTAAAATCTTTTAAAATT Found at i:20374225 original size:40 final size:40 Alignment explanation

Indices: 20374179--20374258 Score: 142 Period size: 40 Copynumber: 2.0 Consensus size: 40 20374169 TGTTTTTAAA 20374179 CAATGAAATGGGTGATTCGGGTAAAACGAGCTTAAAGTTG 1 CAATGAAATGGGTGATTCGGGTAAAACGAGCTTAAAGTTG * * 20374219 CAATGAAATGGGTGATTTGGGTAAAACGAGCTTGAAGTTG 1 CAATGAAATGGGTGATTCGGGTAAAACGAGCTTAAAGTTG 20374259 GAAAAGTTTT Statistics Matches: 38, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 40 38 1.00 ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26 Consensus pattern (40 bp): CAATGAAATGGGTGATTCGGGTAAAACGAGCTTAAAGTTG Found at i:20374632 original size:15 final size:15 Alignment explanation

Indices: 20374585--20374635 Score: 54 Period size: 15 Copynumber: 3.5 Consensus size: 15 20374575 CTAGTTAATC 20374585 TAAACCCT-AAACCA 1 TAAACCCTAAAACCA ** 20374599 TAAA-CCTAAGCCCCA 1 TAAACCCTAA-AACCA 20374614 -AAACCCTAAAACCA 1 TAAACCCTAAAACCA 20374628 TAAACCCT 1 TAAACCCT 20374636 TAACACATAA Statistics Matches: 29, Mismatches: 4, Indels: 7 0.73 0.10 0.17 Matches are distributed among these distances: 13 3 0.10 14 11 0.38 15 15 0.52 ACGTcount: A:0.47, C:0.37, G:0.02, T:0.14 Consensus pattern (15 bp): TAAACCCTAAAACCA Found at i:20374844 original size:41 final size:41 Alignment explanation

Indices: 20374736--20374896 Score: 227 Period size: 41 Copynumber: 3.9 Consensus size: 41 20374726 TTTTAAATCC * * * 20374736 CTGAGCATTAGTGGCGCTTTTTAGAAAACGCCGCT-AAA-A 1 CTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACA * 20374775 GTAGAGCATTAGCGGCGCTTTCTCAAAAAACGCCGCTAAAACA 1 CT-GAGCATTAGCGGCGCTTTCT-AAAAAACGCCGCTAAAACA * 20374818 CTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACC 1 CTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACA * * 20374859 CTGAGCATTAGCGGCGCTTTCTTAAAAATGCCGCTAAA 1 CTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAA 20374897 GCCCCAAAAG Statistics Matches: 110, Mismatches: 8, Indels: 6 0.89 0.06 0.05 Matches are distributed among these distances: 39 1 0.01 40 18 0.16 41 66 0.60 42 23 0.21 43 2 0.02 ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22 Consensus pattern (41 bp): CTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACA Found at i:20375003 original size:39 final size:40 Alignment explanation

Indices: 20374976--20375070 Score: 127 Period size: 40 Copynumber: 2.4 Consensus size: 40 20374966 AATGCTTATT * * * 20374976 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATTCTCGATC 1 TTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATTCTCGATA * * * 20375016 TTTAGTGGCATTTTCCAAAAAGCGCCGCTAATTCTCGATA 1 TTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATTCTCGATA * 20375056 TTTAGCGACGTTTTT 1 TTTAGCGGCGTTTTT 20375071 TATCCAAACG Statistics Matches: 45, Mismatches: 10, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 40 45 1.00 ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36 Consensus pattern (40 bp): TTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATTCTCGATA Found at i:20384353 original size:22 final size:21 Alignment explanation

Indices: 20384321--20384362 Score: 57 Period size: 22 Copynumber: 2.0 Consensus size: 21 20384311 AATTAATTTC 20384321 ATAAAGAAGAAATTAAAGAAA 1 ATAAAGAAGAAATTAAAGAAA * * 20384342 ATAAATGAAGAACTTTAAGAA 1 ATAAA-GAAGAAATTAAAGAA 20384363 GCTTTTGCCG Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 21 5 0.28 22 13 0.72 ACGTcount: A:0.64, C:0.02, G:0.14, T:0.19 Consensus pattern (21 bp): ATAAAGAAGAAATTAAAGAAA Found at i:20385416 original size:22 final size:22 Alignment explanation

Indices: 20385391--20385434 Score: 52 Period size: 22 Copynumber: 2.0 Consensus size: 22 20385381 AGTTTGAAGG * * 20385391 TTAAGAGGGTTTTAGGTTTTAA 1 TTAAAAGGGTTTTAGGATTTAA * * 20385413 TTAAAAGTGTTTTGGGATTTAA 1 TTAAAAGGGTTTTAGGATTTAA 20385435 ATAGGGTAAG Statistics Matches: 18, Mismatches: 4, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45 Consensus pattern (22 bp): TTAAAAGGGTTTTAGGATTTAA Found at i:20385464 original size:23 final size:23 Alignment explanation

Indices: 20385433--20385479 Score: 60 Period size: 23 Copynumber: 2.0 Consensus size: 23 20385423 TTTGGGATTT 20385433 AAATAGGGT-AAGTTAAGGGTTTA 1 AAATAGGGTGAAGTTAA-GGTTTA * * 20385456 AAATTGGGTGAATTTAAGGTTTA 1 AAATAGGGTGAAGTTAAGGTTTA 20385479 A 1 A 20385480 TTAACTGGGT Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 23 15 0.71 24 6 0.29 ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34 Consensus pattern (23 bp): AAATAGGGTGAAGTTAAGGTTTA Found at i:20387137 original size:9 final size:9 Alignment explanation

Indices: 20387123--20387159 Score: 56 Period size: 9 Copynumber: 4.1 Consensus size: 9 20387113 TATAGTTTGA 20387123 TATTCGAAT 1 TATTCGAAT 20387132 TATTCGAAT 1 TATTCGAAT * 20387141 TATTCGAGT 1 TATTCGAAT * 20387150 TATTCAAAT 1 TATTCGAAT 20387159 T 1 T 20387160 TGAAAACTCA Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 9 25 1.00 ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46 Consensus pattern (9 bp): TATTCGAAT Found at i:20388765 original size:18 final size:18 Alignment explanation

Indices: 20388722--20388757 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 20388712 TGAATTTAAT 20388722 AAATAAAACACGAAAGAA 1 AAATAAAACACGAAAGAA * 20388740 AAATAAAACATGAAAGAA 1 AAATAAAACACGAAAGAA 20388758 TTATAAAAAA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.72, C:0.08, G:0.11, T:0.08 Consensus pattern (18 bp): AAATAAAACACGAAAGAA Found at i:20394118 original size:21 final size:22 Alignment explanation

Indices: 20394079--20394119 Score: 57 Period size: 21 Copynumber: 1.9 Consensus size: 22 20394069 CTTTATTTAA * * 20394079 TTATTAAATTACCTTAATAACC 1 TTATTAAATTAACTAAATAACC 20394101 TTATT-AATTAACTAAATAA 1 TTATTAAATTAACTAAATAA 20394120 AACATCTAAT Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 21 12 0.71 22 5 0.29 ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41 Consensus pattern (22 bp): TTATTAAATTAACTAAATAACC Found at i:20397149 original size:21 final size:21 Alignment explanation

Indices: 20397102--20397149 Score: 53 Period size: 20 Copynumber: 2.3 Consensus size: 21 20397092 CATGTGACCC * * 20397102 TTGTTTCCCAATTTTTGTAAT 1 TTGTTTCCCAAATTTTCTAAT * * 20397123 TT-TTTCCTAAATTTTCTGAT 1 TTGTTTCCCAAATTTTCTAAT 20397143 TTGTTTC 1 TTGTTTC 20397150 AAATTGGTCC Statistics Matches: 22, Mismatches: 4, Indels: 2 0.79 0.14 0.07 Matches are distributed among these distances: 20 16 0.73 21 6 0.27 ACGTcount: A:0.17, C:0.15, G:0.08, T:0.60 Consensus pattern (21 bp): TTGTTTCCCAAATTTTCTAAT Found at i:20399127 original size:13 final size:13 Alignment explanation

Indices: 20399109--20399134 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 20399099 TAATGAGAAG 20399109 ATATCATTTACCC 1 ATATCATTTACCC 20399122 ATATCATTTACCC 1 ATATCATTTACCC 20399135 TTTTCTTAGG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38 Consensus pattern (13 bp): ATATCATTTACCC Found at i:20414248 original size:22 final size:22 Alignment explanation

Indices: 20414222--20414267 Score: 76 Period size: 22 Copynumber: 2.1 Consensus size: 22 20414212 ATTTTTTTAA 20414222 TTTC-AAATTTTTTTCGAATTTT 1 TTTCAAAATTTTTTT-GAATTTT 20414244 TTTCAAAATTTTTTTGAATTTT 1 TTTCAAAATTTTTTTGAATTTT 20414266 TT 1 TT 20414268 GAATTTTTTT Statistics Matches: 23, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 22 13 0.57 23 10 0.43 ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65 Consensus pattern (22 bp): TTTCAAAATTTTTTTGAATTTT Found at i:20414277 original size:10 final size:11 Alignment explanation

Indices: 20414222--20414278 Score: 66 Period size: 11 Copynumber: 5.4 Consensus size: 11 20414212 ATTTTTTTAA * 20414222 TTTCAAATTTT 1 TTTCGAATTTT 20414233 TTTCGAATTTT 1 TTTCGAATTTT * 20414244 TTTCAAAATTTT 1 TTTC-GAATTTT 20414256 TTT-GAA-TTT 1 TTTCGAATTTT 20414265 TTT-GAATTTT 1 TTTCGAATTTT 20414275 TTTC 1 TTTC 20414279 ACGTACCTAT Statistics Matches: 40, Mismatches: 3, Indels: 6 0.82 0.06 0.12 Matches are distributed among these distances: 9 9 0.22 10 8 0.20 11 14 0.35 12 9 0.22 ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65 Consensus pattern (11 bp): TTTCGAATTTT Found at i:20414505 original size:22 final size:22 Alignment explanation

Indices: 20414480--20414597 Score: 94 Period size: 23 Copynumber: 5.2 Consensus size: 22 20414470 TTAGCTAGGG 20414480 AATGGTATTGGTTTTGGTACGA 1 AATGGTATTGGTTTTGGTACGA * * 20414502 AATGGGGT-TTGGTATAGGTACGA 1 AAT--GGTATTGGTTTTGGTACGA * * 20414525 AATGGTATAGGTTTTGGTATGA 1 AATGGTATTGGTTTTGGTACGA * * * ** 20414547 AATGAATTTTGGTGTAAGTACGA 1 AATG-GTATTGGTTTTGGTACGA * * 20414570 AAGGGTATAGGTTTTGGTACGGA 1 AATGGTATTGGTTTTGGTAC-GA 20414593 AATGG 1 AATGG 20414598 ATCAAAAAGG Statistics Matches: 70, Mismatches: 21, Indels: 9 0.70 0.21 0.09 Matches are distributed among these distances: 21 3 0.04 22 28 0.40 23 36 0.51 24 3 0.04 ACGTcount: A:0.28, C:0.03, G:0.34, T:0.35 Consensus pattern (22 bp): AATGGTATTGGTTTTGGTACGA Found at i:20414530 original size:45 final size:45 Alignment explanation

Indices: 20414480--20414598 Score: 157 Period size: 45 Copynumber: 2.6 Consensus size: 45 20414470 TTAGCTAGGG * * * 20414480 AATGGTATTGGTTTTGGTACGAAATGGGGTTTGGTATAGGTACGA 1 AATGGTATAGGTTTTGGTACGAAATGGAGTTTGGTATAAGTACGA * * * * 20414525 AATGGTATAGGTTTTGGTATGAAATGAATTTTGGTGTAAGTACGA 1 AATGGTATAGGTTTTGGTACGAAATGGAGTTTGGTATAAGTACGA * 20414570 AAGGGTATAGGTTTTGGTACGGAAATGGA 1 AATGGTATAGGTTTTGGTAC-GAAATGGA 20414599 TCAAAAAGGT Statistics Matches: 63, Mismatches: 10, Indels: 1 0.85 0.14 0.01 Matches are distributed among these distances: 45 56 0.89 46 7 0.11 ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34 Consensus pattern (45 bp): AATGGTATAGGTTTTGGTACGAAATGGAGTTTGGTATAAGTACGA Found at i:20415495 original size:20 final size:20 Alignment explanation

Indices: 20415470--20415514 Score: 56 Period size: 20 Copynumber: 2.2 Consensus size: 20 20415460 TAAATTCACA 20415470 TAATTAAAACT-AGACACAAT 1 TAATT-AAACTAAGACACAAT ** 20415490 TAATTAAGTTAAGACACAAT 1 TAATTAAACTAAGACACAAT 20415510 TAATT 1 TAATT 20415515 CGGTTAGGAA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 19 3 0.14 20 19 0.86 ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31 Consensus pattern (20 bp): TAATTAAACTAAGACACAAT Found at i:20418861 original size:38 final size:40 Alignment explanation

Indices: 20418778--20418862 Score: 104 Period size: 38 Copynumber: 2.1 Consensus size: 40 20418768 CTCATTGATT ** * 20418778 TCTTTTTTTACTCTCTTTTCATTTTCTTTTGCAATTTTCCC 1 TCTTTTTTTACTCAATTTTCATTTTCTTTTG-AATTTTCAC 20418819 TCTTTTTTT-CTCAATTTT-ATTTTCCTTTTG-ATTTTCAC 1 TCTTTTTTTACTCAATTTTCATTTT-CTTTTGAATTTTCAC 20418857 TCTTTT 1 TCTTTT 20418863 CTTTTGTTTT Statistics Matches: 40, Mismatches: 3, Indels: 5 0.83 0.06 0.10 Matches are distributed among these distances: 38 13 0.32 39 5 0.12 40 13 0.32 41 9 0.22 ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66 Consensus pattern (40 bp): TCTTTTTTTACTCAATTTTCATTTTCTTTTGAATTTTCAC Found at i:20421407 original size:44 final size:45 Alignment explanation

Indices: 20421253--20421416 Score: 213 Period size: 45 Copynumber: 3.6 Consensus size: 45 20421243 TTAATTATGG * * * * * 20421253 AATGATATCGGTTTTGGTAGGAAATGGGTTTTGGTATAGGTACGA 1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA * * * 20421298 AATGATATAGGTTTTGGTACAAAATAGATTTTGGTGTAGGTACGA 1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA * 20421343 AATGGTATAGGTTTTGGTACGACATGGATTTTGGTGTAGGTAC-A 1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA * * 20421387 AAAGGTATAAGTTTTGGTACGAAAATGGAT 1 AATGGTATAGGTTTTGGTACG-AAATGGAT 20421417 CAAAAAGGTC Statistics Matches: 105, Mismatches: 13, Indels: 2 0.88 0.11 0.02 Matches are distributed among these distances: 44 20 0.19 45 85 0.81 ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35 Consensus pattern (45 bp): AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA Found at i:20422327 original size:20 final size:20 Alignment explanation

Indices: 20422302--20422346 Score: 63 Period size: 20 Copynumber: 2.2 Consensus size: 20 20422292 TAAATTCACA 20422302 TAATTAAAACAAGACACAAT 1 TAATTAAAACAAGACACAAT *** 20422322 TAATTAAGTTAAGACACAAT 1 TAATTAAAACAAGACACAAT 20422342 TAATT 1 TAATT 20422347 CGGTTAGGAC Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29 Consensus pattern (20 bp): TAATTAAAACAAGACACAAT Found at i:20425697 original size:38 final size:40 Alignment explanation

Indices: 20425614--20425698 Score: 104 Period size: 38 Copynumber: 2.1 Consensus size: 40 20425604 CTCATTGATT ** * 20425614 TCTTTTTTTACTCTCTTTTCATTTTCTTTTGCAATTTTCCC 1 TCTTTTTTTACTCAATTTTCATTTTCTTTTG-AATTTTCAC 20425655 TCTTTTTTT-CTCAATTTT-ATTTTCCTTTTG-ATTTTCAC 1 TCTTTTTTTACTCAATTTTCATTTT-CTTTTGAATTTTCAC 20425693 TCTTTT 1 TCTTTT 20425699 CTTTTGTTTT Statistics Matches: 40, Mismatches: 3, Indels: 5 0.83 0.06 0.10 Matches are distributed among these distances: 38 13 0.32 39 5 0.12 40 13 0.32 41 9 0.22 ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66 Consensus pattern (40 bp): TCTTTTTTTACTCAATTTTCATTTTCTTTTGAATTTTCAC Found at i:20428240 original size:44 final size:45 Alignment explanation

Indices: 20428086--20428249 Score: 213 Period size: 45 Copynumber: 3.6 Consensus size: 45 20428076 TTAATTATGG * * * * * 20428086 AATGATATCGGTTTTGGTAGGAAATGGGTTTTGGTATAGGTACGA 1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA * * * 20428131 AATGATATAGGTTTTGGTACAAAATAGATTTTGGTGTAGGTACGA 1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA * 20428176 AATGGTATAGGTTTTGGTACGACATGGATTTTGGTGTAGGTAC-A 1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA * * 20428220 AAAGGTATAAGTTTTGGTACGAAAATGGAT 1 AATGGTATAGGTTTTGGTACG-AAATGGAT 20428250 CAAAAAGGTC Statistics Matches: 105, Mismatches: 13, Indels: 2 0.88 0.11 0.02 Matches are distributed among these distances: 44 20 0.19 45 85 0.81 ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35 Consensus pattern (45 bp): AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA Found at i:20429160 original size:20 final size:20 Alignment explanation

Indices: 20429135--20429179 Score: 63 Period size: 20 Copynumber: 2.2 Consensus size: 20 20429125 TAAATTCACA 20429135 TAATTAAAACAAGACACAAT 1 TAATTAAAACAAGACACAAT *** 20429155 TAATTAAGTTAAGACACAAT 1 TAATTAAAACAAGACACAAT 20429175 TAATT 1 TAATT 20429180 CGGTTAGGAC Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29 Consensus pattern (20 bp): TAATTAAAACAAGACACAAT Found at i:20432530 original size:38 final size:40 Alignment explanation

Indices: 20432447--20432531 Score: 104 Period size: 38 Copynumber: 2.1 Consensus size: 40 20432437 CTCATTGATT ** * 20432447 TCTTTTTTTACTCTCTTTTCATTTTCTTTTGCAATTTTCCC 1 TCTTTTTTTACTCAATTTTCATTTTCTTTTG-AATTTTCAC 20432488 TCTTTTTTT-CTCAATTTT-ATTTTCCTTTTG-ATTTTCAC 1 TCTTTTTTTACTCAATTTTCATTTT-CTTTTGAATTTTCAC 20432526 TCTTTT 1 TCTTTT 20432532 CTTTTGTTTT Statistics Matches: 40, Mismatches: 3, Indels: 5 0.83 0.06 0.10 Matches are distributed among these distances: 38 13 0.32 39 5 0.12 40 13 0.32 41 9 0.22 ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66 Consensus pattern (40 bp): TCTTTTTTTACTCAATTTTCATTTTCTTTTGAATTTTCAC Found at i:20434968 original size:45 final size:45 Alignment explanation

Indices: 20434919--20435028 Score: 157 Period size: 45 Copynumber: 2.4 Consensus size: 45 20434909 TTAATTATGG * ** * * 20434919 AATGATATCGGTTTTGGTAGGAAATGGGTTTTGGTATAGGTACGA 1 AATGATATAGGTTTTGGTACAAAATAGATTTTGGTATAGGTACGA * 20434964 AATGATATAGGTTTTGGTACAAAATAGATTTTGGTGTAGGTACGA 1 AATGATATAGGTTTTGGTACAAAATAGATTTTGGTATAGGTACGA * 20435009 AATGGTATAGGTTTTGGTAC 1 AATGATATAGGTTTTGGTAC 20435029 GACATGTGAA Statistics Matches: 58, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 45 58 1.00 ACGTcount: A:0.29, C:0.05, G:0.30, T:0.36 Consensus pattern (45 bp): AATGATATAGGTTTTGGTACAAAATAGATTTTGGTATAGGTACGA Found at i:20435005 original size:23 final size:22 Alignment explanation

Indices: 20434947--20435012 Score: 69 Period size: 23 Copynumber: 3.0 Consensus size: 22 20434937 AGGAAATGGG 20434947 TTTTGGTATAGGTACGAAATGA 1 TTTTGGTATAGGTACGAAATGA * * * * * 20434969 TATAGGTTTTGGTACAAAATAGA 1 TTTTGGTATAGGTACGAAAT-GA * 20434992 TTTTGGTGTAGGTACGAAATG 1 TTTTGGTATAGGTACGAAATG 20435013 GTATAGGTTT Statistics Matches: 33, Mismatches: 10, Indels: 2 0.73 0.22 0.04 Matches are distributed among these distances: 22 16 0.48 23 17 0.52 ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36 Consensus pattern (22 bp): TTTTGGTATAGGTACGAAATGA Found at i:20435029 original size:22 final size:22 Alignment explanation

Indices: 20434919--20435030 Score: 89 Period size: 22 Copynumber: 5.0 Consensus size: 22 20434909 TTAATTATGG * * 20434919 AATGATATCGGTTTTGGTAGGA 1 AATGATATAGGTTTTGGTACGA * * * * * 20434941 AATGGGTTTTGGTATAGGTACGA 1 AAT-GATATAGGTTTTGGTACGA * 20434964 AATGATATAGGTTTTGGTACAA 1 AATGATATAGGTTTTGGTACGA * * * * 20434986 AATAGATTTTGGTGTAGGTACGA 1 AAT-GATATAGGTTTTGGTACGA * 20435009 AATGGTATAGGTTTTGGTACGA 1 AATGATATAGGTTTTGGTACGA 20435031 CATGTGAACA Statistics Matches: 66, Mismatches: 22, Indels: 4 0.72 0.24 0.04 Matches are distributed among these distances: 22 33 0.50 23 33 0.50 ACGTcount: A:0.29, C:0.04, G:0.30, T:0.36 Consensus pattern (22 bp): AATGATATAGGTTTTGGTACGA Found at i:20435101 original size:20 final size:20 Alignment explanation

Indices: 20435076--20435120 Score: 56 Period size: 20 Copynumber: 2.2 Consensus size: 20 20435066 TAAATTCACA 20435076 TAATTAAAACT-AGACACAAT 1 TAATT-AAACTAAGACACAAT ** 20435096 TAATTAAGTTAAGACACAAT 1 TAATTAAACTAAGACACAAT 20435116 TAATT 1 TAATT 20435121 CGGTTAGGAA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 19 3 0.14 20 19 0.86 ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31 Consensus pattern (20 bp): TAATTAAACTAAGACACAAT Found at i:20438754 original size:191 final size:192 Alignment explanation

Indices: 20438429--20438811 Score: 750 Period size: 191 Copynumber: 2.0 Consensus size: 192 20438419 ATTTTTCTTA 20438429 AATCCTACAGCTCATTAATAAGCTTATTGCATGTTTTTAATATGTTTTTTGTTCTAACCGAATTA 1 AATCCTACAGCTCATTAATAAGCTTATTGCATGTTTTTAATATGTTTTTTGTTCTAACCGAATTA 20438494 CTGGTGTCTTAGCTTAATTAAACTTGTCTAGTTTTTTTTTAATTATGTGTATTTAAATTGTCCAA 66 CTGGTGTCTTAGCTTAATTAAACTTGTCTAGTTTTTTTTTAATTATGTGTATTTAAATTGTCCAA 20438559 GTTATGTTTTCAATTATGTTCAACTGAATGTGAATTAATTTAAGTTGGTTCATCTATGTTTG 131 GTTATGTTTTCAATTATGTTCAACTGAATGTGAATTAATTTAAGTTGGTTCATCTATGTTTG 20438621 AATCCTACAG-TCATTAATAAGCTTATTGCATGTTTTTAATATGTTTTTTGTTCTAACCGAATTA 1 AATCCTACAGCTCATTAATAAGCTTATTGCATGTTTTTAATATGTTTTTTGTTCTAACCGAATTA 20438685 CTGGTGTCTTAGCTTAATTAAACTTGTCTAGTTTTTTTTTAATTATGTGTATTTAAATTGTCCAA 66 CTGGTGTCTTAGCTTAATTAAACTTGTCTAGTTTTTTTTTAATTATGTGTATTTAAATTGTCCAA * 20438750 GTTATGTTTTCAATTATGTTCAGCTGAATGTGAATTAATTTAAGTTGGTTCATCTATGTTTG 131 GTTATGTTTTCAATTATGTTCAACTGAATGTGAATTAATTTAAGTTGGTTCATCTATGTTTG 20438812 TAGGTTGGCC Statistics Matches: 190, Mismatches: 1, Indels: 1 0.99 0.01 0.01 Matches are distributed among these distances: 191 180 0.95 192 10 0.05 ACGTcount: A:0.26, C:0.11, G:0.14, T:0.48 Consensus pattern (192 bp): AATCCTACAGCTCATTAATAAGCTTATTGCATGTTTTTAATATGTTTTTTGTTCTAACCGAATTA CTGGTGTCTTAGCTTAATTAAACTTGTCTAGTTTTTTTTTAATTATGTGTATTTAAATTGTCCAA GTTATGTTTTCAATTATGTTCAACTGAATGTGAATTAATTTAAGTTGGTTCATCTATGTTTG Found at i:20451194 original size:6 final size:6 Alignment explanation

Indices: 20451183--20451215 Score: 50 Period size: 6 Copynumber: 5.7 Consensus size: 6 20451173 ACAAAAATGT * 20451183 AATGAC AATGAC AATGAA AATG-C AATGAC AATG 1 AATGAC AATGAC AATGAC AATGAC AATGAC AATG 20451216 TATACTTATC Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 5 4 0.17 6 20 0.83 ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18 Consensus pattern (6 bp): AATGAC Found at i:20463180 original size:39 final size:39 Alignment explanation

Indices: 20463137--20463263 Score: 143 Period size: 40 Copynumber: 3.3 Consensus size: 39 20463127 AACCTATGTT * * * 20463137 TTATATTACCTGAGAATCC-ACGACAAGGGTTGGATCTCA 1 TTATATTACCTGAGAATCCTACAACAA-GGCTAGATCTCA * * 20463176 TTATATTGCCTGAGAA-CCTGCAACAAGGCTAGATCTCA 1 TTATATTACCTGAGAATCCTACAACAAGGCTAGATCTCA * 20463214 TTATATTACCCTTGAGAAT-CTGCAACAAGGCTAGATCTCA 1 TTATATTA-CC-TGAGAATCCTACAACAAGGCTAGATCTCA * 20463254 TTGTATTACC 1 TTATATTACC 20463264 CCAAGAATCT Statistics Matches: 77, Mismatches: 7, Indels: 8 0.84 0.08 0.09 Matches are distributed among these distances: 38 19 0.25 39 24 0.31 40 34 0.44 ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30 Consensus pattern (39 bp): TTATATTACCTGAGAATCCTACAACAAGGCTAGATCTCA Found at i:20463220 original size:38 final size:40 Alignment explanation

Indices: 20463169--20463264 Score: 151 Period size: 40 Copynumber: 2.5 Consensus size: 40 20463159 ACAAGGGTTG * 20463169 GATCTCATTATATT-GCC-TGAGAACCTGCAACAAGGCTA 1 GATCTCATTATATTACCCTTGAGAACCTGCAACAAGGCTA * 20463207 GATCTCATTATATTACCCTTGAGAATCTGCAACAAGGCTA 1 GATCTCATTATATTACCCTTGAGAACCTGCAACAAGGCTA * 20463247 GATCTCATTGTATTACCC 1 GATCTCATTATATTACCC 20463265 CAAGAATCTG Statistics Matches: 53, Mismatches: 3, Indels: 2 0.91 0.05 0.03 Matches are distributed among these distances: 38 14 0.26 39 2 0.04 40 37 0.70 ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30 Consensus pattern (40 bp): GATCTCATTATATTACCCTTGAGAACCTGCAACAAGGCTA Found at i:20463240 original size:40 final size:39 Alignment explanation

Indices: 20463137--20463280 Score: 166 Period size: 39 Copynumber: 3.7 Consensus size: 39 20463127 AACCTATGTT ** * * * 20463137 TTATATTA-CCTGAGAATCCACGACAAGGGTTGGATCTCA 1 TTATATTACCCTGAGAATCTGCAACAA-GGCTAGATCTCA * * 20463176 TTATATT-GCCTGAGAACCTGCAACAAGGCTAGATCTCA 1 TTATATTACCCTGAGAATCTGCAACAAGGCTAGATCTCA 20463214 TTATATTACCCTTGAGAATCTGCAACAAGGCTAGATCTCA 1 TTATATTACCC-TGAGAATCTGCAACAAGGCTAGATCTCA * ** 20463254 TTGTATTACCCCAAGAATCTGCAACAA 1 TTATATTACCCTGAGAATCTGCAACAA 20463281 AAACTAGATA Statistics Matches: 91, Mismatches: 11, Indels: 6 0.84 0.10 0.06 Matches are distributed among these distances: 38 17 0.19 39 37 0.41 40 37 0.41 ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28 Consensus pattern (39 bp): TTATATTACCCTGAGAATCTGCAACAAGGCTAGATCTCA Found at i:20463288 original size:40 final size:40 Alignment explanation

Indices: 20463169--20463298 Score: 122 Period size: 40 Copynumber: 3.3 Consensus size: 40 20463159 ACAAGGGTTG * * * ** 20463169 GATCTCATTATATT-GCCT-GAGAACCTGCAACAAGGCTA 1 GATCTCATTATATTACCCTCAAGAATCTGCAACAAAACTA ** ** 20463207 GATCTCATTATATTACCCTTGAGAATCTGCAACAAGGCTA 1 GATCTCATTATATTACCCTCAAGAATCTGCAACAAAACTA * 20463247 GATCTCATTGTATTACCC-CAAGAATCTGCAACAAAAACTA 1 GATCTCATTATATTACCCTCAAGAATCTGCAAC-AAAACTA * * 20463287 GATATTATTATA 1 GATCTCATTATA 20463299 ATCTATAATA Statistics Matches: 79, Mismatches: 10, Indels: 4 0.85 0.11 0.04 Matches are distributed among these distances: 38 14 0.18 39 15 0.19 40 50 0.63 ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29 Consensus pattern (40 bp): GATCTCATTATATTACCCTCAAGAATCTGCAACAAAACTA Found at i:20464401 original size:21 final size:22 Alignment explanation

Indices: 20464364--20464404 Score: 66 Period size: 21 Copynumber: 1.9 Consensus size: 22 20464354 TGTTTAATCA * 20464364 AATTTTAATATATATTTTTAAT 1 AATTTTAATAAATATTTTTAAT 20464386 AATTTT-ATAAATATTTTTA 1 AATTTTAATAAATATTTTTA 20464405 TTTTATATTT Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 21 12 0.67 22 6 0.33 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (22 bp): AATTTTAATAAATATTTTTAAT Found at i:20464955 original size:21 final size:22 Alignment explanation

Indices: 20464916--20464956 Score: 57 Period size: 22 Copynumber: 1.9 Consensus size: 22 20464906 ACATTTTAAA * 20464916 TAAAAAATAATCTAGTTAATTT 1 TAAAAAAAAATCTAGTTAATTT * 20464938 TAAAAAAAAATTTA-TTAAT 1 TAAAAAAAAATCTAGTTAAT 20464957 GTGAAGTTTT Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 21 5 0.29 22 12 0.71 ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39 Consensus pattern (22 bp): TAAAAAAAAATCTAGTTAATTT Found at i:20466812 original size:43 final size:43 Alignment explanation

Indices: 20466758--20466888 Score: 208 Period size: 43 Copynumber: 3.0 Consensus size: 43 20466748 TTTTCTTTGC * * * 20466758 AACGCCGCTATAAACCATGGTCTTTAGCGGCGCTTAGCCTAAA 1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAA * 20466801 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCGAAA 1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAA * * 20466844 AACGCCACTATAGACGATGGTCTTTAGCGGCGCTTATCCAAAA 1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAA 20466887 AA 1 AA 20466889 TGCCGCTAAT Statistics Matches: 82, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 43 82 1.00 ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22 Consensus pattern (43 bp): AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAA Found at i:20467244 original size:21 final size:21 Alignment explanation

Indices: 20467196--20467253 Score: 71 Period size: 21 Copynumber: 2.8 Consensus size: 21 20467186 TTATGCTATT * * * 20467196 CTACTTCCCTCGCTGTAGCCT 1 CTACTTCCCTCGCTGCAACCG 20467217 CTACTTCCCTCGCTGCAACCG 1 CTACTTCCCTCGCTGCAACCG * * 20467238 CTGCTTCTCTCGCTGC 1 CTACTTCCCTCGCTGC 20467254 CGCATCTTCT Statistics Matches: 32, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 21 32 1.00 ACGTcount: A:0.09, C:0.45, G:0.16, T:0.31 Consensus pattern (21 bp): CTACTTCCCTCGCTGCAACCG Found at i:20467355 original size:66 final size:64 Alignment explanation

Indices: 20467240--20467404 Score: 190 Period size: 65 Copynumber: 2.5 Consensus size: 64 20467230 TGCAACCGCT * ** 20467240 GCTTCTCTCGCTGCCGCATCTTCTTTAAGCTACTGCTGCAGTTGCTCATA-CTTTCGTTGAACCT 1 GCTTCTCTCGCTGCCGCATCTGCTTTAAG-TTGTGCTGCAGTTGCTCATATCTTT--TTGAACCT 20467304 CA 63 CA * 20467306 GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTT-CTTCATATCTTTTTGAACCTC 1 GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGT-GCTGCAGTTGC-TCATATCTTTTTGAACCTC 20467370 A 64 A * ** * * 20467371 GCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGTG 1 GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTG 20467405 TAATTTGCTC Statistics Matches: 87, Mismatches: 9, Indels: 8 0.84 0.09 0.08 Matches are distributed among these distances: 64 1 0.01 65 41 0.47 66 41 0.47 67 4 0.05 ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39 Consensus pattern (64 bp): GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTGCTGCAGTTGCTCATATCTTTTTGAACCTCA Found at i:20478499 original size:113 final size:113 Alignment explanation

Indices: 20478314--20478659 Score: 631 Period size: 113 Copynumber: 3.1 Consensus size: 113 20478304 GCTTAACGCT * * * 20478314 AAACGCCGCTAAAGAACGGA-TTATTAGCGGCGTTTGGGCAAAAACCGCCACTAGTGTTCCCAAA 1 AAACGCCGCTGAAGAACGGAGTT-TTAGCGGCGCTTGGG-AAAAACCGCCACTAATGTTCCCAAA 20478378 TATATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA 64 TATATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA 20478428 AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA 1 AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA 20478493 TATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA 66 TATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA 20478541 AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA 1 AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA * 20478606 TATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTGTA 66 TATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA 20478654 AAACGC 1 AAACGC 20478660 TGCTAATGCT Statistics Matches: 227, Mismatches: 4, Indels: 3 0.97 0.02 0.01 Matches are distributed among these distances: 113 192 0.85 114 33 0.15 115 2 0.01 ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26 Consensus pattern (113 bp): AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA TATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA Found at i:20478783 original size:41 final size:40 Alignment explanation

Indices: 20478697--20478786 Score: 101 Period size: 40 Copynumber: 2.2 Consensus size: 40 20478687 TTTTATGTAG * * 20478697 CGCCGCTAATGCTCGATATTTTGAGGCGTTTTTCGTAAAA 1 CGCCGCTAATGCTCGATATTTAGAGGCATTTTTCGTAAAA * * * * 20478737 TGCCGCTAATGCTCGAT-TATTAGTGGCATTTTTTGTCCAAA 1 CGCCGCTAATGCTCGATAT-TTAGAGGCATTTTTCGT-AAAA 20478778 CGCCGCTAA 1 CGCCGCTAA 20478787 AAGTGCCGCT Statistics Matches: 41, Mismatches: 7, Indels: 3 0.80 0.14 0.06 Matches are distributed among these distances: 39 1 0.02 40 29 0.71 41 11 0.27 ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34 Consensus pattern (40 bp): CGCCGCTAATGCTCGATATTTAGAGGCATTTTTCGTAAAA Found at i:20483497 original size:27 final size:27 Alignment explanation

Indices: 20483439--20483526 Score: 108 Period size: 27 Copynumber: 3.3 Consensus size: 27 20483429 ATGGTATCAA * * * 20483439 AGATAGTTCGACGAGATGTTAAACA-A 1 AGATAGTTCGATGGGATGTTAAACACG 20483465 ATGATAGTTCGATGGGATGTTAAACACG 1 A-GATAGTTCGATGGGATGTTAAACACG * 20483493 GGATAG-TCTGATGGGATGTTAAACACG 1 AGATAGTTC-GATGGGATGTTAAACACG 20483520 AGATAGT 1 AGATAGT 20483527 CCACTAGGAC Statistics Matches: 53, Mismatches: 5, Indels: 6 0.83 0.08 0.09 Matches are distributed among these distances: 26 3 0.06 27 50 0.94 ACGTcount: A:0.35, C:0.10, G:0.28, T:0.26 Consensus pattern (27 bp): AGATAGTTCGATGGGATGTTAAACACG Found at i:20486629 original size:201 final size:201 Alignment explanation

Indices: 20486284--20486652 Score: 711 Period size: 201 Copynumber: 1.8 Consensus size: 201 20486274 TACTCGAATG * 20486284 TTGTTGATTAATGATATATATTACATTGTGTTGTATTGAATGGTATCAAAATTAATGATTGTTAC 1 TTGTTGATTAATGATACATATTACATTGTGTTGTATTGAATGGTATCAAAATTAATGATTGTTAC 20486349 TCGAGTGAATGATGACCTATGCTCATACACCATTTGACATCAATTTGATAGTGGCTATGTAATGA 66 TCGAGTGAATGATGACCTATGCTCATACACCATTTGACATCAATTTGATAGTGGCTATGTAATGA 20486414 TATGAAATTCTAATGATGGTTTTGTGTTCTTCTGATAATGCTAACATGTTTCAATATATTTGATA 131 TATGAAATTCTAATGATGGTTTTGTGTTCTTCTGATAATGCTAACATGTTTCAATATATTTGATA 20486479 TTTATC 196 TTTATC * 20486485 TTGTTGATTAATGATACATATTGCATTGTGTTGTATTGAATGGTATCAAAATTAATGATTGTTAC 1 TTGTTGATTAATGATACATATTACATTGTGTTGTATTGAATGGTATCAAAATTAATGATTGTTAC * 20486550 TCGAGTGAATGATGACCTATGCTCATACACCATTTGGCATCAATTTGATAGTGGCTATGTAATGA 66 TCGAGTGAATGATGACCTATGCTCATACACCATTTGACATCAATTTGATAGTGGCTATGTAATGA 20486615 TATGAAATTCTAATGATGGTTTTGTGTTCTTCTGATAA 131 TATGAAATTCTAATGATGGTTTTGTGTTCTTCTGATAA 20486653 CTCACACTGA Statistics Matches: 165, Mismatches: 3, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 201 165 1.00 ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41 Consensus pattern (201 bp): TTGTTGATTAATGATACATATTACATTGTGTTGTATTGAATGGTATCAAAATTAATGATTGTTAC TCGAGTGAATGATGACCTATGCTCATACACCATTTGACATCAATTTGATAGTGGCTATGTAATGA TATGAAATTCTAATGATGGTTTTGTGTTCTTCTGATAATGCTAACATGTTTCAATATATTTGATA TTTATC Found at i:20487788 original size:15 final size:15 Alignment explanation

Indices: 20487768--20487799 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 20487758 ACATTTCATG * 20487768 TTATGTCTTTTATAT 1 TTATGTCTTTCATAT 20487783 TTATGTCTTTCATAT 1 TTATGTCTTTCATAT 20487798 TT 1 TT 20487800 TGCATTCATA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.19, C:0.09, G:0.06, T:0.66 Consensus pattern (15 bp): TTATGTCTTTCATAT Found at i:20495827 original size:69 final size:69 Alignment explanation

Indices: 20495716--20495868 Score: 288 Period size: 69 Copynumber: 2.2 Consensus size: 69 20495706 CAGGACTAAA 20495716 ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAAAAAATAAACACGGTGAAACATAAGGTG 1 ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAAAAAATAAACACGGTGAAACATAAGGTG 20495781 TAAG 66 TAAG * 20495785 ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAGAAAATAAACACGGTGAAACATAAGGTG 1 ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAAAAAATAAACACGGTGAAACATAAGGTG 20495850 TAAG 66 TAAG * 20495854 ACCATAGCTGGACTA 1 ACCATAGTTGGACTA 20495869 AAGCCACTGC Statistics Matches: 82, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 69 82 1.00 ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22 Consensus pattern (69 bp): ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAAAAAATAAACACGGTGAAACATAAGGTG TAAG Found at i:20496039 original size:27 final size:27 Alignment explanation

Indices: 20496008--20496060 Score: 88 Period size: 27 Copynumber: 2.0 Consensus size: 27 20495998 ACGACAACAA * 20496008 AGATAGTCTGACGGGACATTAAACATG 1 AGATAGTCTGACGGGACATCAAACATG * 20496035 AGATAGTTTGACGGGACATCAAACAT 1 AGATAGTCTGACGGGACATCAAACAT 20496061 AGGGTTGTTC Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 27 24 1.00 ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23 Consensus pattern (27 bp): AGATAGTCTGACGGGACATCAAACATG Found at i:20498532 original size:42 final size:43 Alignment explanation

Indices: 20498446--20498567 Score: 169 Period size: 42 Copynumber: 2.9 Consensus size: 43 20498436 GGCTCGTACA * * * 20498446 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACAGATCG 1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACAAATCG * 20498489 ATGCC-ACTGTCCCAGACAG-GGT-TTACAAGAAAACACAAATCG 1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAAACACAAATCG 20498531 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACAC 1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACAC 20498568 TTTTCGAAAA Statistics Matches: 69, Mismatches: 5, Indels: 10 0.82 0.06 0.12 Matches are distributed among these distances: 41 1 0.01 42 35 0.51 43 32 0.46 44 1 0.01 ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20 Consensus pattern (43 bp): ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACAAATCG Found at i:20502509 original size:27 final size:27 Alignment explanation

Indices: 20502412--20502509 Score: 90 Period size: 27 Copynumber: 3.6 Consensus size: 27 20502402 TTGCAACTCA * 20502412 ACTGGCAAACCCC-GGTTCGCCAAATAG 1 ACTGGCAAACCCCAGCTT-GCCAAATAG * ** * * 20502439 AATGGTGAACCCCAACTAGCCAAATAG 1 ACTGGCAAACCCCAGCTTGCCAAATAG * * * 20502466 ACTAGCAAACCCTAGCTTGCCAAACAG 1 ACTGGCAAACCCCAGCTTGCCAAATAG * 20502493 ACTGGCGAACCCCAGCT 1 ACTGGCAAACCCCAGCT 20502510 CATCAGCACG Statistics Matches: 53, Mismatches: 17, Indels: 2 0.74 0.24 0.03 Matches are distributed among these distances: 27 52 0.98 28 1 0.02 ACGTcount: A:0.34, C:0.33, G:0.19, T:0.14 Consensus pattern (27 bp): ACTGGCAAACCCCAGCTTGCCAAATAG Found at i:20502941 original size:9 final size:9 Alignment explanation

Indices: 20502927--20502957 Score: 53 Period size: 9 Copynumber: 3.4 Consensus size: 9 20502917 GTTAAACGAA 20502927 TCGAGTTAT 1 TCGAGTTAT * 20502936 TCGAGTTAA 1 TCGAGTTAT 20502945 TCGAGTTAT 1 TCGAGTTAT 20502954 TCGA 1 TCGA 20502958 ATCAACTCGA Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 9 20 1.00 ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39 Consensus pattern (9 bp): TCGAGTTAT Found at i:20503027 original size:9 final size:9 Alignment explanation

Indices: 20503010--20503046 Score: 65 Period size: 9 Copynumber: 4.1 Consensus size: 9 20503000 TGAGTTTTCA 20503010 AATTCGAAT 1 AATTCGAAT * 20503019 AACTCGAAT 1 AATTCGAAT 20503028 AATTCGAAT 1 AATTCGAAT 20503037 AATTCGAAT 1 AATTCGAAT 20503046 A 1 A 20503047 TCAAACTATA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 9 26 1.00 ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30 Consensus pattern (9 bp): AATTCGAAT Found at i:20504361 original size:7 final size:7 Alignment explanation

Indices: 20504349--20504394 Score: 65 Period size: 7 Copynumber: 6.6 Consensus size: 7 20504339 TAAATTTGAA * 20504349 TAAACCT 1 TAAACCC 20504356 TAAACCC 1 TAAACCC * 20504363 TAAATCC 1 TAAACCC 20504370 TAAACCC 1 TAAACCC * 20504377 TAAATCC 1 TAAACCC 20504384 TAAACCC 1 TAAACCC 20504391 TAAA 1 TAAA 20504395 AAATTAAGAT Statistics Matches: 34, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 7 34 1.00 ACGTcount: A:0.46, C:0.33, G:0.00, T:0.22 Consensus pattern (7 bp): TAAACCC Found at i:20504373 original size:14 final size:14 Alignment explanation

Indices: 20504356--20504394 Score: 78 Period size: 14 Copynumber: 2.8 Consensus size: 14 20504346 GAATAAACCT 20504356 TAAACCCTAAATCC 1 TAAACCCTAAATCC 20504370 TAAACCCTAAATCC 1 TAAACCCTAAATCC 20504384 TAAACCCTAAA 1 TAAACCCTAAA 20504395 AAATTAAGAT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 25 1.00 ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21 Consensus pattern (14 bp): TAAACCCTAAATCC Found at i:20513111 original size:30 final size:30 Alignment explanation

Indices: 20513070--20513130 Score: 97 Period size: 30 Copynumber: 2.0 Consensus size: 30 20513060 AAACCTCTTT 20513070 ACTTTCCCCCAAAACTTTTACT-CCCTTCC 1 ACTTTCCCCCAAAACTTTTACTCCCCTTCC * 20513099 ACTTTCCCCCCAAAACTTTTTCTCCCCTTCC 1 ACTTT-CCCCCAAAACTTTTACTCCCCTTCC 20513130 A 1 A 20513131 TCCCACCCCC Statistics Matches: 29, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 29 5 0.17 30 16 0.55 31 8 0.28 ACGTcount: A:0.20, C:0.46, G:0.00, T:0.34 Consensus pattern (30 bp): ACTTTCCCCCAAAACTTTTACTCCCCTTCC Found at i:20513140 original size:31 final size:30 Alignment explanation

Indices: 20513075--20513140 Score: 80 Period size: 30 Copynumber: 2.2 Consensus size: 30 20513065 TCTTTACTTT ** 20513075 CCCCCAAAACTTTTACTCCCTTCCACTTTC 1 CCCCCAAAACTTTTACTCCCTTCCACTCCC * 20513105 CCCCCAAAACTTTTTCTCCCCTTCCA-TCCC 1 CCCCCAAAACTTTTACT-CCCTTCCACTCCC 20513135 ACCCCC 1 -CCCCC 20513141 TTCTACCCCA Statistics Matches: 31, Mismatches: 3, Indels: 3 0.84 0.08 0.08 Matches are distributed among these distances: 30 18 0.58 31 13 0.42 ACGTcount: A:0.18, C:0.53, G:0.00, T:0.29 Consensus pattern (30 bp): CCCCCAAAACTTTTACTCCCTTCCACTCCC Found at i:20513260 original size:18 final size:19 Alignment explanation

Indices: 20513228--20513265 Score: 69 Period size: 19 Copynumber: 2.1 Consensus size: 19 20513218 AATCCCTCAA 20513228 CCCCCAAAACTTTTTATTT 1 CCCCCAAAACTTTTTATTT 20513247 CCCCCAAAAC-TTTTATTT 1 CCCCCAAAACTTTTTATTT 20513265 C 1 C 20513266 TCACCTTTTA Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 18 9 0.47 19 10 0.53 ACGTcount: A:0.26, C:0.34, G:0.00, T:0.39 Consensus pattern (19 bp): CCCCCAAAACTTTTTATTT Found at i:20514601 original size:2 final size:2 Alignment explanation

Indices: 20514596--20514633 Score: 67 Period size: 2 Copynumber: 19.0 Consensus size: 2 20514586 AAAAAAAAAA * 20514596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 20514634 TAATAAAGTG Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50 Consensus pattern (2 bp): AT Found at i:20515395 original size:30 final size:31 Alignment explanation

Indices: 20515331--20515400 Score: 83 Period size: 31 Copynumber: 2.4 Consensus size: 31 20515321 ATTCAAAAAA * 20515331 TTTTATTTAAGCCACTGAACTATTTAAAAGT 1 TTTTATTTAAGCCACTGAACTAGTTAAAAGT * * 20515362 TTTTATTTAAGTCATTGAACT-GTT-AAA-T 1 TTTTATTTAAGCCACTGAACTAGTTAAAAGT * 20515390 TTTTTTTTAAG 1 TTTTATTTAAG 20515401 TTTCACCACT Statistics Matches: 35, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 28 11 0.31 29 3 0.09 30 2 0.06 31 19 0.54 ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50 Consensus pattern (31 bp): TTTTATTTAAGCCACTGAACTAGTTAAAAGT Found at i:20523122 original size:48 final size:47 Alignment explanation

Indices: 20522997--20523131 Score: 144 Period size: 48 Copynumber: 2.8 Consensus size: 47 20522987 CTATTTACCT * * * * ** 20522997 TGTAGATTTAACCCTAACGGGTAACTAGACACTATTACTCATTATTTG 1 TGTAGGTTTAACCCTAAC-GGTAACCAGGCACTATTATTCATTATTCA * * * 20523045 TGTAGGTTTAACCTTGACGAGTAATCAGGCACTATTATTCATTATTCA 1 TGTAGGTTTAACCCTAACG-GTAACCAGGCACTATTATTCATTATTCA ** 20523093 TGTAGGTTTAACCGAAACAGGTAACCAGGCACTATTATT 1 TGTAGGTTTAACCCTAAC-GGTAACCAGGCACTATTATT 20523132 TTCACCTGTG Statistics Matches: 72, Mismatches: 13, Indels: 4 0.81 0.15 0.04 Matches are distributed among these distances: 47 1 0.01 48 70 0.97 49 1 0.01 ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34 Consensus pattern (47 bp): TGTAGGTTTAACCCTAACGGTAACCAGGCACTATTATTCATTATTCA Found at i:20526806 original size:28 final size:28 Alignment explanation

Indices: 20526766--20526822 Score: 96 Period size: 28 Copynumber: 2.0 Consensus size: 28 20526756 AGTAAGTCTA * 20526766 TTGGGACAGTAAACACGAGCTAGGTTTG 1 TTGGGACAGTAAACACGAGCTAAGTTTG * 20526794 TTGGGACAGTAAACACGAGGTAAGTTTG 1 TTGGGACAGTAAACACGAGCTAAGTTTG 20526822 T 1 T 20526823 CGGGGTACTA Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 28 27 1.00 ACGTcount: A:0.30, C:0.12, G:0.32, T:0.26 Consensus pattern (28 bp): TTGGGACAGTAAACACGAGCTAAGTTTG Found at i:20530739 original size:43 final size:42 Alignment explanation

Indices: 20530692--20530793 Score: 116 Period size: 43 Copynumber: 2.4 Consensus size: 42 20530682 TCTAGAACAT * * * * 20530692 TGGCATTGATATGAGATTACGTGTAAGACCCTGTTTGGGACA 1 TGGCATTGATATGAGATAACATGTAAGACCATATTTGGGACA * * * 20530734 GTGGCATCGATATGTGATAACATGTAAGACCATATTTGGGATA 1 -TGGCATTGATATGAGATAACATGTAAGACCATATTTGGGACA * 20530777 TGGCATTG-TATGTGATA 1 TGGCATTGATATGAGATA 20530794 TATGTGTTTT Statistics Matches: 51, Mismatches: 8, Indels: 2 0.84 0.13 0.03 Matches are distributed among these distances: 41 9 0.18 42 7 0.14 43 35 0.69 ACGTcount: A:0.28, C:0.12, G:0.27, T:0.32 Consensus pattern (42 bp): TGGCATTGATATGAGATAACATGTAAGACCATATTTGGGACA Found at i:20531577 original size:35 final size:34 Alignment explanation

Indices: 20531510--20531577 Score: 82 Period size: 35 Copynumber: 2.0 Consensus size: 34 20531500 TATTAAAGTG * 20531510 TGGTTGTTTTACATATTACAATGATATCCAAATA 1 TGGTTGTTTTACATATTACAATGATATACAAATA * * * * 20531544 TGGTTGTTTTTACATGTTATAATGTTGTACAAAT 1 TGGTTG-TTTTACATATTACAATGATATACAAAT 20531578 TAGTGCTTAA Statistics Matches: 28, Mismatches: 5, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 34 6 0.21 35 22 0.79 ACGTcount: A:0.31, C:0.09, G:0.15, T:0.46 Consensus pattern (34 bp): TGGTTGTTTTACATATTACAATGATATACAAATA Found at i:20535677 original size:54 final size:52 Alignment explanation

Indices: 20535611--20535765 Score: 161 Period size: 54 Copynumber: 2.9 Consensus size: 52 20535601 TGGCCATGGG * 20535611 AAGAAGACCATATAGTGTAAGACCTAATCTGGGACTATGGCATCATAT-AGGA 1 AAGAAGA-CATATAGTGTAAGACCTAGTCTGGGACTATGGCATCATATAAGGA * * 20535663 AACTGAAGATCATATAGTGTAAGACCTAGTCATTATGG-CCATGGCATCATATAAGGA 1 AA--GAAGA-CATATAGTGTAAGACCTAGTC--T-GGGACTATGGCATCATATAAGGA * * * * 20535720 AAGAAGACTACATAGTGTAAGACCTAGTTTGAGACTATGGTATCAT 1 AAGAAGAC-ATATAGTGTAAGACCTAGTCTGGGACTATGGCATCAT 20535766 GTGGGAAAAA Statistics Matches: 85, Mismatches: 10, Indels: 15 0.77 0.09 0.14 Matches are distributed among these distances: 52 3 0.04 53 11 0.13 54 26 0.31 55 23 0.27 56 14 0.16 57 8 0.09 ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26 Consensus pattern (52 bp): AAGAAGACATATAGTGTAAGACCTAGTCTGGGACTATGGCATCATATAAGGA Found at i:20537840 original size:43 final size:43 Alignment explanation

Indices: 20537793--20537903 Score: 134 Period size: 43 Copynumber: 2.6 Consensus size: 43 20537783 AAATAGAAGA * 20537793 AAATATACTGGCACACACAGTGCATCATTGGACAAACCAAAGC 1 AAATATACTGGAACACACAGTGCATCATTGGACAAACCAAAGC * * * * * * * 20537836 AAATATACTAGTATAGACATTGTATCATTGGACGAACCAAAGC 1 AAATATACTGGAACACACAGTGCATCATTGGACAAACCAAAGC 20537879 AAATATACTGGAACACGA-AGTGCAT 1 AAATATACTGGAACAC-ACAGTGCAT 20537904 AAACCCGTAC Statistics Matches: 54, Mismatches: 13, Indels: 2 0.78 0.19 0.03 Matches are distributed among these distances: 43 53 0.98 44 1 0.02 ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21 Consensus pattern (43 bp): AAATATACTGGAACACACAGTGCATCATTGGACAAACCAAAGC Found at i:20542099 original size:555 final size:555 Alignment explanation

Indices: 20541049--20542159 Score: 2222 Period size: 555 Copynumber: 2.0 Consensus size: 555 20541039 ACATAAGCAA 20541049 CTAGTGCTTAGTAAGCTCATATAAATCATAAACGTAAACTTACCAAATAGGCTCAATTTATACAA 1 CTAGTGCTTAGTAAGCTCATATAAATCATAAACGTAAACTTACCAAATAGGCTCAATTTATACAA 20541114 TTCATTCATAATTTCATTAACAAGTTCACAAGTTTATTCAATTCCTGTACACATCACAAATCTCA 66 TTCATTCATAATTTCATTAACAAGTTCACAAGTTTATTCAATTCCTGTACACATCACAAATCTCA 20541179 CAAGTTAGTGAGTTCACATTTATATAAGAACATAAAACCATATCATATCATATAATGTTCATAAA 131 CAAGTTAGTGAGTTCACATTTATATAAGAACATAAAACCATATCATATCATATAATGTTCATAAA 20541244 TAACAATTGTAATTTAATCATCCATCTTATGCCGATCATATGTGACACATTCCATTCAATGTTTG 196 TAACAATTGTAATTTAATCATCCATCTTATGCCGATCATATGTGACACATTCCATTCAATGTTTG 20541309 ATACCATATAACCATTTCAGAAATGTCCTTTTCATAAATCAAATTACATATAGCCATTTCATATA 261 ATACCATATAACCATTTCAGAAATGTCCTTTTCATAAATCAAATTACATATAGCCATTTCATATA 20541374 ACTCATTTGTATATCACTTAATACCCGATGAACCATAGTGATATAACATTGGATACATGGGAAAA 326 ACTCATTTGTATATCACTTAATACCCGATGAACCATAGTGATATAACATTGGATACATGGGAAAA 20541439 TGCTCACACGAGCTGTAACTGTAAATGCTCATATGATTTGTAACTGTAAATGCTTACACAAGCTG 391 TGCTCACACGAGCTGTAACTGTAAATGCTCATATGATTTGTAACTGTAAATGCTTACACAAGCTG 20541504 TGAAATGGGCCTACTCGCACGAGCTATGGGTCAGGATGCTAGGCTACACGATGCTGCTCACATGA 456 TGAAATGGGCCTACTCGCACGAGCTATGGGTCAGGATGCTAGGCTACACGATGCTGCTCACATGA 20541569 GTTGTGAAGAGTCCACAACAAATGCAAGACCTTAG 521 GTTGTGAAGAGTCCACAACAAATGCAAGACCTTAG 20541604 CTAGTGCTTAGTAAGCTCATATAAATCATAAACGTAAACTTACCAAATAGGCTCAATTTATACAA 1 CTAGTGCTTAGTAAGCTCATATAAATCATAAACGTAAACTTACCAAATAGGCTCAATTTATACAA 20541669 TTCATTCATAATTTCATTAACAAGTTCACAAGTTTATTCAATTCCTGTACACATCACAAATCTCA 66 TTCATTCATAATTTCATTAACAAGTTCACAAGTTTATTCAATTCCTGTACACATCACAAATCTCA 20541734 CAAGTTAGTGAGTTCACATTTATATAAGAACATAAAACCATATCATATCATATAATGTTCATAAA 131 CAAGTTAGTGAGTTCACATTTATATAAGAACATAAAACCATATCATATCATATAATGTTCATAAA 20541799 TAACAATTGTAATTTAATCATCCATCTTATGCCGATCATATGTGACACATTCCATTCAATGTTTG 196 TAACAATTGTAATTTAATCATCCATCTTATGCCGATCATATGTGACACATTCCATTCAATGTTTG 20541864 ATACCATATAACCATTTCAGAAATGTCCTTTTCATAAATCAAATTACATATAGCCATTTCATATA 261 ATACCATATAACCATTTCAGAAATGTCCTTTTCATAAATCAAATTACATATAGCCATTTCATATA 20541929 ACTCATTTGTATATCACTTAATACCCGATGAACCATAGTGATATAACATTGGATACATGGGAAAA 326 ACTCATTTGTATATCACTTAATACCCGATGAACCATAGTGATATAACATTGGATACATGGGAAAA 20541994 TGCTCACACGAGCTGTAACTGTAAATGCTCATATGATTTGTAACTGTAAATGCTTACACAAGCTG 391 TGCTCACACGAGCTGTAACTGTAAATGCTCATATGATTTGTAACTGTAAATGCTTACACAAGCTG 20542059 TGAAATGGGCCTACTCGCACGAGCTATGGGTCAGGATGCTAGGCTACACGATGCTGCTCACATGA 456 TGAAATGGGCCTACTCGCACGAGCTATGGGTCAGGATGCTAGGCTACACGATGCTGCTCACATGA 20542124 GTTGTGAAGAGTCCACAACAAATGCAAGACCTTAG 521 GTTGTGAAGAGTCCACAACAAATGCAAGACCTTAG 20542159 C 1 C 20542160 CACCGGTAGG Statistics Matches: 556, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 555 556 1.00 ACGTcount: A:0.36, C:0.20, G:0.14, T:0.31 Consensus pattern (555 bp): CTAGTGCTTAGTAAGCTCATATAAATCATAAACGTAAACTTACCAAATAGGCTCAATTTATACAA TTCATTCATAATTTCATTAACAAGTTCACAAGTTTATTCAATTCCTGTACACATCACAAATCTCA CAAGTTAGTGAGTTCACATTTATATAAGAACATAAAACCATATCATATCATATAATGTTCATAAA TAACAATTGTAATTTAATCATCCATCTTATGCCGATCATATGTGACACATTCCATTCAATGTTTG ATACCATATAACCATTTCAGAAATGTCCTTTTCATAAATCAAATTACATATAGCCATTTCATATA ACTCATTTGTATATCACTTAATACCCGATGAACCATAGTGATATAACATTGGATACATGGGAAAA TGCTCACACGAGCTGTAACTGTAAATGCTCATATGATTTGTAACTGTAAATGCTTACACAAGCTG TGAAATGGGCCTACTCGCACGAGCTATGGGTCAGGATGCTAGGCTACACGATGCTGCTCACATGA GTTGTGAAGAGTCCACAACAAATGCAAGACCTTAG Found at i:20546881 original size:5 final size:5 Alignment explanation

Indices: 20546871--20546895 Score: 50 Period size: 5 Copynumber: 5.0 Consensus size: 5 20546861 AGCTTGCACC 20546871 AATAT AATAT AATAT AATAT AATAT 1 AATAT AATAT AATAT AATAT AATAT 20546896 TTATTTAACT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 20 1.00 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (5 bp): AATAT Done.