Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold196

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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33

Warning! 125249 characters in sequence are not A, C, G, or T


File 25 of 47

Found at i:3877124 original size:24 final size:24

Alignment explanation

Indices: 3877091--3877137 Score: 69 Period size: 24 Copynumber: 2.0 Consensus size: 24 3877081 AAAGAGACAA 3877091 AAAAACAAAAAAAACGAA-AAAAAT 1 AAAAACAAAAAAAAC-AATAAAAAT * 3877115 AAAAAGAAAAAAAACAATAAAAA 1 AAAAACAAAAAAAACAATAAAAA 3877138 GGGTCCAGAT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 23 2 0.10 24 19 0.90 ACGTcount: A:0.85, C:0.06, G:0.04, T:0.04 Consensus pattern (24 bp): AAAAACAAAAAAAACAATAAAAAT Found at i:3877128 original size:18 final size:18 Alignment explanation

Indices: 3877079--3877138 Score: 59 Period size: 18 Copynumber: 3.3 Consensus size: 18 3877069 GCATCCTCCC * * * 3877079 AAAAAGAGACAAAAAAAC 1 AAAAAGAAAAAAAAAAAT * 3877097 AAAAA-AAACGAAAAAAAT 1 AAAAAGAAA-AAAAAAAAT * 3877115 AAAAAGAAAAAAAACAAT 1 AAAAAGAAAAAAAAAAAT 3877133 AAAAAG 1 AAAAAG 3877139 GGTCCAGATG Statistics Matches: 35, Mismatches: 5, Indels: 4 0.80 0.11 0.09 Matches are distributed among these distances: 17 2 0.06 18 30 0.86 19 3 0.09 ACGTcount: A:0.82, C:0.07, G:0.08, T:0.03 Consensus pattern (18 bp): AAAAAGAAAAAAAAAAAT Found at i:3877136 original size:9 final size:8 Alignment explanation

Indices: 3877087--3877137 Score: 50 Period size: 9 Copynumber: 6.1 Consensus size: 8 3877077 CCAAAAAGAG 3877087 ACAAAAAA 1 ACAAAAAA 3877095 ACAAAAAAA 1 AC-AAAAAA 3877104 ACGAAAAAA 1 AC-AAAAAA * * 3877113 ATAAAAAG 1 ACAAAAAA 3877121 A-AAAAAA 1 ACAAAAAA 3877128 ACAATAAAA 1 ACAA-AAAA 3877137 A 1 A 3877138 GGGTCCAGAT Statistics Matches: 36, Mismatches: 4, Indels: 5 0.80 0.09 0.11 Matches are distributed among these distances: 7 6 0.17 8 10 0.28 9 20 0.56 ACGTcount: A:0.84, C:0.08, G:0.04, T:0.04 Consensus pattern (8 bp): ACAAAAAA Found at i:3878661 original size:57 final size:55 Alignment explanation

Indices: 3878572--3878750 Score: 211 Period size: 57 Copynumber: 3.2 Consensus size: 55 3878562 CCTCACCTTC * 3878572 AAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCA 1 AAAGCCCACAAGTCAGTGGC-ACCTTTC-AAAGCCCACAAGTCAGTGGCAAC-TTTCA * * * 3878629 AAAGCCCACAGGTTAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGGCAACCTTT-A 1 AAAGCCCACAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTCAGTGGCAA-CTTTCA * * * 3878685 GAAGCCCACAAGTCGGTGGCATCCCTTTCAAAGCCCACAAGT-AGTGGCAACCTTCA 1 AAAGCCCACAAGTCAGTGGCA--CCTTTCAAAGCCCACAAGTCAGTGGCAACTTTCA 3878741 AAAGCCCACA 1 AAAGCCCACA 3878751 CAAGTTGGTG Statistics Matches: 105, Mismatches: 11, Indels: 13 0.81 0.09 0.10 Matches are distributed among these distances: 55 3 0.03 56 39 0.37 57 57 0.54 58 6 0.06 ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19 Consensus pattern (55 bp): AAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCAACTTTCA Found at i:3878673 original size:85 final size:85 Alignment explanation

Indices: 3878569--3878750 Score: 255 Period size: 85 Copynumber: 2.2 Consensus size: 85 3878559 ATTCCTCACC * 3878569 TTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAAG 1 TTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCATCCCTTTC-AAAG * 3878633 CCCACAGGTTAGTGGC-ACCTT 65 CCCACAAG-TAGTGGCAACCTT * * * * 3878654 TTCAAAGCCCATAAGTCAGTGGCAACCTTTAGAAGCCCACAAGTCGGTGGCATCCCTTTCAAAGC 1 TTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCATCCCTTTCAAAGC 3878719 CCACAAGTAGTGGCAACC-- 66 CCACAAGTAGTGGCAACCTT 3878737 TTCAAAAGCCCACA 1 TTC-AAAGCCCACA 3878751 CAAGTTGGTG Statistics Matches: 87, Mismatches: 7, Indels: 7 0.86 0.07 0.07 Matches are distributed among these distances: 83 3 0.03 84 16 0.18 85 63 0.72 86 5 0.06 ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20 Consensus pattern (85 bp): TTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCATCCCTTTCAAAGC CCACAAGTAGTGGCAACCTT Found at i:3878754 original size:29 final size:28 Alignment explanation

Indices: 3878566--3878750 Score: 209 Period size: 28 Copynumber: 6.6 Consensus size: 28 3878556 GATATTCCTC 3878566 ACCTTC-AAAGCCCACAAGTCAGTGGCA 1 ACCTTCAAAAGCCCACAAGTCAGTGGCA 3878593 ACCTTCAAAAGCCCACAAGTCAGTGGCA 1 ACCTTCAAAAGCCCACAAGTCAGTGGCA * * * * 3878621 TCTTTTCAAAAGCCCACAGGTTAGTGGC- 1 AC-CTTCAAAAGCCCACAAGTCAGTGGCA * 3878649 ACCTTTTC-AAAGCCCATAAGTCAGTGGCA 1 ACC--TTCAAAAGCCCACAAGTCAGTGGCA * * * 3878678 ACCTTTAGAAGCCCACAAGTCGGTGGCA 1 ACCTTCAAAAGCCCACAAGTCAGTGGCA * 3878706 TCCCTTTC-AAAGCCCACAAGT-AGTGGCA 1 -ACC-TTCAAAAGCCCACAAGTCAGTGGCA 3878734 ACCTTCAAAAGCCCACA 1 ACCTTCAAAAGCCCACA 3878751 CAAGTTGGTG Statistics Matches: 131, Mismatches: 18, Indels: 18 0.78 0.11 0.11 Matches are distributed among these distances: 26 3 0.02 27 20 0.15 28 64 0.49 29 42 0.32 30 2 0.02 ACGTcount: A:0.31, C:0.31, G:0.18, T:0.19 Consensus pattern (28 bp): ACCTTCAAAAGCCCACAAGTCAGTGGCA Found at i:3878891 original size:49 final size:49 Alignment explanation

Indices: 3878767--3879100 Score: 340 Period size: 49 Copynumber: 6.8 Consensus size: 49 3878757 GGTGGCATAT * * * 3878767 TCTTCTAAGTCCAATATCGTTGGCCTTGAATCAGCATATT-G-A-C-ACA 1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA * * * * * 3878813 --TTTAAGTCCAATGTTGCTGGCCTTAAATCAACAAATTGGCACCTTCA 1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA * * * ** 3878860 CCGTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCATTTGTCA 1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-GCACCT-TCA * * * 3878912 TCTTTAAGTCCAATGTTGCTAGCCTTGAATCAGCACATTGGCACCTTCA 1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA * * 3878961 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA 1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCA * * 3879013 CCTTTAAGTCCAA-AGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCA 1 TCTTTAAGTCCAATA-TCGCTGGCCTTGAATCAGCACATTGGCACCTTCA * * * 3879062 TCTTTAAGTCCAATGTCGCTGACCTTGAATCAACACATT 1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT 3879101 AGCATTTTTC Statistics Matches: 237, Mismatches: 37, Indels: 25 0.79 0.12 0.08 Matches are distributed among these distances: 43 29 0.12 44 3 0.01 45 1 0.00 46 1 0.00 47 2 0.01 49 110 0.46 50 6 0.03 51 7 0.03 52 78 0.33 ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32 Consensus pattern (49 bp): TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA Found at i:3878988 original size:101 final size:101 Alignment explanation

Indices: 3878813--3879153 Score: 463 Period size: 101 Copynumber: 3.4 Consensus size: 101 3878803 TATTGACACA * * * * * 3878813 TTTAAGTCCAATGTTGCTGGCCTTAAATCAACAAATTGGCACCTTCACCGTTAAGTCCAATATCG 1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG * 3878878 CTGGCCTTGAATCAGCATATTGGTGCATTTGTCATC 66 CTGGCCTTGAATCAGCATATTGGAGCATTTGTCATC * 3878914 TTTAAGTCCAATGTTGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG 1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG * * * 3878979 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACC 66 CTGGCCTTGAATCAGCATATTGGAGCATTTGTCATC * * 3879015 TTTAAGTCCAAAGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCG 1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG * * * * 3879080 CTGACCTTGAATCAACACATT--AGCATTTTTCTCATC 66 CTGGCCTTGAATCAGCATATTGGAGCA--TTTGTCATC * * * 3879116 TTCAAGTCTAATGTTGCT-GACTGTGAATCAGCACATTG 1 TTTAAGTCCAATGTTGCTGGCCT-TGAATCAGCACATTG 3879154 ACATTCTTTA Statistics Matches: 214, Mismatches: 23, Indels: 6 0.88 0.09 0.02 Matches are distributed among these distances: 99 2 0.01 100 3 0.01 101 209 0.98 ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33 Consensus pattern (101 bp): TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG CTGGCCTTGAATCAGCATATTGGAGCATTTGTCATC Found at i:3879168 original size:52 final size:51 Alignment explanation

Indices: 3878865--3879179 Score: 216 Period size: 52 Copynumber: 6.2 Consensus size: 51 3878855 CTTCACCGTT * * * * * * 3878865 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCATT-TGTCATCTTT 1 AAGTCCAATGTCGCTGACCTTGAATCAGCACATT-G-ACATTCTTTCATCTTC * * * * 3878917 AAGTCCAATGTTGCT-AGCCTTGAATCAGCACATTGGCA--CCTTCATCTTT 1 AAGTCCAATGTCGCTGA-CCTTGAATCAGCACATTGACATTCTTTCATCTTC * * * * * * * * 3878966 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTT-TGTCACCTTT 1 AAGTCCAATGTCGCTGACCTTGAATCAGCACATT-G-ACATTCTTTCATCTTC * * * * * * 3879018 AAGTCCAAAGTTGCTGGCCTTGAATCAGCACATTGGCA--CCTTCATCTTT 1 AAGTCCAATGTCGCTGACCTTGAATCAGCACATTGACATTCTTTCATCTTC * * 3879067 AAGTCCAATGTCGCTGACCTTGAATCAACACATT-AGCATTTTTCTCATCTTC 1 AAGTCCAATGTCGCTGACCTTGAATCAGCACATTGA-CATTCTT-TCATCTTC * * * 3879119 AAGTCTAATGTTGCTGA-CTGTGAATCAGCACATTGACATTCTTTACATCTTG 1 AAGTCCAATGTCGCTGACCT-TGAATCAGCACATTGACATTCTTT-CATCTTC * 3879171 AAGCCCAAT 1 AAGTCCAAT 3879180 ATCACTAGTC Statistics Matches: 211, Mismatches: 37, Indels: 30 0.76 0.13 0.11 Matches are distributed among these distances: 49 76 0.36 50 6 0.03 51 8 0.04 52 120 0.57 53 1 0.00 ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33 Consensus pattern (51 bp): AAGTCCAATGTCGCTGACCTTGAATCAGCACATTGACATTCTTTCATCTTC Found at i:3879885 original size:13 final size:13 Alignment explanation

Indices: 3879867--3879891 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3879857 CATTATTCAA 3879867 TGTATCGATACAT 1 TGTATCGATACAT 3879880 TGTATCGATACA 1 TGTATCGATACA 3879892 AAGCTACCAT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:3879889 original size:33 final size:33 Alignment explanation

Indices: 3879847--3879984 Score: 93 Period size: 33 Copynumber: 4.0 Consensus size: 33 3879837 GCTAAGGAAA 3879847 TGTATCGATACATTATTCAATGTATCGATACAT 1 TGTATCGATACATTATTCAATGTATCGATACAT * * * * * * 3879880 TGTATCGATACA-AAGCTACCATGCATACTGCCA-AGGAAA 1 TGTATCGATACATTA--TTCAATG--TA-T-CGATA--CAT * 3879919 TGTATCGATACATTATTCAATGTATCAATACAT 1 TGTATCGATACATTATTCAATGTATCGATACAT ** 3879952 TGTATCGATACATTGA-TCTTTGTATCGATACAT 1 TGTATCGATACATT-ATTCAATGTATCGATACAT 3879985 CTAGGAATTT Statistics Matches: 79, Mismatches: 15, Indels: 22 0.68 0.13 0.19 Matches are distributed among these distances: 32 1 0.01 33 41 0.52 34 8 0.10 35 2 0.03 36 4 0.05 37 2 0.03 38 7 0.09 39 13 0.16 40 1 0.01 ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35 Consensus pattern (33 bp): TGTATCGATACATTATTCAATGTATCGATACAT Found at i:3879925 original size:72 final size:72 Alignment explanation

Indices: 3879808--3879963 Score: 285 Period size: 72 Copynumber: 2.2 Consensus size: 72 3879798 AAACAGTAAA * * 3879808 TGTATCGATACAAAGCTACCCTGCATACTGCTAAGGAAATGTATCGATACATTATTCAATGTATC 1 TGTATCGATACAAAGCTACCATGCATACTGCCAAGGAAATGTATCGATACATTATTCAATGTATC * 3879873 GATACAT 66 AATACAT 3879880 TGTATCGATACAAAGCTACCATGCATACTGCCAAGGAAATGTATCGATACATTATTCAATGTATC 1 TGTATCGATACAAAGCTACCATGCATACTGCCAAGGAAATGTATCGATACATTATTCAATGTATC 3879945 AATACAT 66 AATACAT 3879952 TGTATCGATACA 1 TGTATCGATACA 3879964 TTGATCTTTG Statistics Matches: 81, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 72 81 1.00 ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30 Consensus pattern (72 bp): TGTATCGATACAAAGCTACCATGCATACTGCCAAGGAAATGTATCGATACATTATTCAATGTATC AATACAT Found at i:3880926 original size:20 final size:19 Alignment explanation

Indices: 3880897--3880971 Score: 87 Period size: 20 Copynumber: 3.8 Consensus size: 19 3880887 AAAAAGACAT 3880897 AATGTATCGATACATTGAA 1 AATGTATCGATACATTGAA * * 3880916 GAATATATCGATACATTCATA 1 -AATGTATCGATACATTGA-A * * 3880937 CATGTATCGATATATTGAAA 1 AATGTATCGATACATTG-AA 3880957 AATGTATCGATACAT 1 AATGTATCGATACAT 3880972 CTGGGTAAAA Statistics Matches: 45, Mismatches: 8, Indels: 4 0.79 0.14 0.07 Matches are distributed among these distances: 20 43 0.96 21 2 0.04 ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33 Consensus pattern (19 bp): AATGTATCGATACATTGAA Found at i:3880954 original size:40 final size:39 Alignment explanation

Indices: 3880894--3880971 Score: 120 Period size: 40 Copynumber: 2.0 Consensus size: 39 3880884 GGTAAAAAGA * 3880894 CATAATGTATCGATACATTGAAGAATATATCGATACATT 1 CATAATGTATCGATACATTGAAAAATATATCGATACATT * * 3880933 CATACATGTATCGATATATTGAAAAATGTATCGATACAT 1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT 3880972 CTGGGTAAAA Statistics Matches: 35, Mismatches: 3, Indels: 1 0.90 0.08 0.03 Matches are distributed among these distances: 39 4 0.11 40 31 0.89 ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33 Consensus pattern (39 bp): CATAATGTATCGATACATTGAAAAATATATCGATACATT Found at i:3881656 original size:28 final size:28 Alignment explanation

Indices: 3881583--3881849 Score: 300 Period size: 28 Copynumber: 9.3 Consensus size: 28 3881573 CACTGACACG * ** 3881583 TGTGGGCTTTGAAAAGAGTGTTACTAACT 1 TGTGGGCTTTG-AAAGGGTGCCACTAACT * * 3881612 TGCGTGGGCTTTAAAAGGGTGCCACTGACT 1 T--GTGGGCTTTGAAAGGGTGCCACTAACT * 3881642 TGTGGGCTTTGAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTAACT * * * 3881670 TGTGGGCTTTAAAAGAGTGCCACTAAAT 1 TGTGGGCTTTGAAAGGGTGCCACTAACT * * 3881698 TGTGGGCTTCGCAAGGGTGCCACTAACT 1 TGTGGGCTTTGAAAGGGTGCCACTAACT * * 3881726 TGTGGGCTTCGAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTAACT * * * 3881754 TGTGGGCTGTAAAAGGAGTGCCACTGACTT 1 TGTGGGCTTTGAAAGG-GTGCCACTAAC-T 3881784 GTGTGGGCTTTGAAAGGGTGCCACTAACT 1 -TGTGGGCTTTGAAAGGGTGCCACTAACT * ** * 3881813 TGTGGGCTTCGAAATAGTGCCACTAAAT 1 TGTGGGCTTTGAAAGGGTGCCACTAACT 3881841 TGTGGGCTT 1 TGTGGGCTT 3881850 CACAAGGGTT Statistics Matches: 206, Mismatches: 27, Indels: 11 0.84 0.11 0.05 Matches are distributed among these distances: 28 145 0.70 29 13 0.06 30 25 0.12 31 23 0.11 ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28 Consensus pattern (28 bp): TGTGGGCTTTGAAAGGGTGCCACTAACT Found at i:3881850 original size:28 final size:28 Alignment explanation

Indices: 3881542--3881858 Score: 278 Period size: 28 Copynumber: 10.9 Consensus size: 28 3881532 AAAATTTGCT * * 3881542 ACTAACTTGTGTAGGCTTCGAAAAAAGTTGCC 1 ACTAACTTGTG--GGCTTCG--AAAGGGTGCC * * * ** 3881574 ACTGACACGTGTGGGCTTTGAAAAGAGTGTT 1 ACT-A-ACTTGTGGGCTTCG-AAAGGGTGCC ** 3881605 ACTAACTTGCGTGGGCTTTAAAAGGGTGCC 1 ACTAACTT--GTGGGCTTCGAAAGGGTGCC * * 3881635 ACTGACTTGTGGGCTTTGAAAGGGTGCC 1 ACTAACTTGTGGGCTTCGAAAGGGTGCC * ** * 3881663 ACTGACTTGTGGGCTTTAAAAGAGTGCC 1 ACTAACTTGTGGGCTTCGAAAGGGTGCC * * 3881691 ACTAAATTGTGGGCTTCGCAAGGGTGCC 1 ACTAACTTGTGGGCTTCGAAAGGGTGCC 3881719 ACTAACTTGTGGGCTTCGAAAGGGTGCC 1 ACTAACTTGTGGGCTTCGAAAGGGTGCC * * 3881747 ACTGACTTGTGGGCTGT-AAAAGGAGTGCC 1 ACTAACTTGTGGGCT-TCGAAAGG-GTGCC * * 3881776 ACTGACTTGTGTGGGCTTTGAAAGGGTGCC 1 ACTAAC-T-TGTGGGCTTCGAAAGGGTGCC ** 3881806 ACTAACTTGTGGGCTTCGAAATAGTGCC 1 ACTAACTTGTGGGCTTCGAAAGGGTGCC * 3881834 ACTAAATTGTGGGCTTC-ACAAGGGT 1 ACTAACTTGTGGGCTTCGA-AAGGGT 3881859 TGGGCTTTGA Statistics Matches: 241, Mismatches: 34, Indels: 24 0.81 0.11 0.08 Matches are distributed among these distances: 27 1 0.00 28 150 0.62 29 16 0.07 30 27 0.11 31 31 0.13 32 9 0.04 33 1 0.00 34 6 0.02 ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27 Consensus pattern (28 bp): ACTAACTTGTGGGCTTCGAAAGGGTGCC Found at i:3881899 original size:28 final size:28 Alignment explanation

Indices: 3881859--3885448 Score: 2652 Period size: 28 Copynumber: 128.5 Consensus size: 28 3881849 TCACAAGGGT 3881859 TGGGCTTTGAAAGGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * * 3881887 TGGGCTTTAAAAGAGTGCCACTAAATTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * * 3881915 TAGGCTTCGCAAGGGTGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3881943 TGGGCTTCGAAAGGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3881971 TGGGCTCTAAAAGGAGTGCCACTGACTTGTG 1 TGGGCTTTGAAAGG-GTGCCACTGAC-T-TG 3882002 TGGGCTTTGAAAGGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * ** * * 3882030 TGGGCTTCGAAATAGTGCCACTAAATTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3882058 TGGGC-TTCACAAGGGTGCCACTGACTTG 1 TGGGCTTTGA-AAGGGTGCCACTGACTTG ** * 3882086 TGGGCTTCAAAAGGGTGCCACTGACTCG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG ** 3882114 TGGGCTTTGAAAATGTGCCACTGACTTGCG 1 TGGGCTTTGAAAGGGTGCCACTGACTT--G * * 3882144 TGAGCTTTAAAAGGAGTGCCACTGACTTGTG 1 TGGGCTTTGAAAGG-GTGCCACTGAC-T-TG * * 3882175 TGGGCTTTGAAAGGGTCCCATTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3882203 TGGGCTTTGAAAGAGTGCCACTAAATTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * * 3882231 TGGGCTTCGTATGGGTGCCACCGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG 3882259 TGGGCTTTGAAAGGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3882287 TGGGCTCTAAAAGGAGTGCCATTGACTTG 1 TGGGCTTTGAAAGG-GTGCCACTGACTTG * 3882316 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3882344 TGGGC-TTGAAAAGAGTGCCACTGACTTG 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG * * 3882372 TGGGC-TTGAAAAGGTGCCATTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3882399 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3882427 TGGGCTTTGAAAGGATGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3882455 TGGGCTTTGAAAGAGTGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3882483 TGGGC-TTGAAAAGGTACCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3882510 TGGGC-TTAAAAAGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG ** 3882537 TGGGCTTTGAAATAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3882565 TGGGCTTTGAAAGGATGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3882593 TGGGCTTTGAAAGAGTGCCACTGACTTA 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3882621 TGGGCTTTGAAAGGATGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3882649 TGGGCTTTGAAAGAGTGCCACTGACTAG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3882677 TGGGCTTTGAAAGGATGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3882705 TGGGCTTTGAAAAGAGTGCCACTGACTTG 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG * ** * 3882734 TGGGC-TTAAAAACGTACCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3882761 TGGAC-TTAAAAAGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3882788 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3882816 TGGGCTTTGAAAGGATGCCACTGTCTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3882844 TGGGCTTGGAAAGAGTGCCATTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3882872 TGGGC-TTGAAAAGGTACCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3882899 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * ** 3882927 TGGGCTTTGAAAATGGTGCCACTGACTCA 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG * * * 3882956 TGGGCTTTGAAAGGGATGAACATTCTAAAC-AG 1 TGGGCTTTGAAAGGG-TG-CCA--CT-GACTTG ** * * *** ** * *** 3882988 -AAGTTCTTGACGATAATTTC-TTGACAAA 1 TGGGCT-TTGA-AAGGGTGCCACTGACTTG * * * * * 3883016 T-GGC---AAAAGGGT--C-TTGGCCTA 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * ** *** *** * ** 3883037 AGATG-ATAAAAAGAAAAGAGTCTTACCCG 1 TG-GGCTTTGAAAG-GGTGCCACTGACTTG *** * * ** 3883066 AATG--ATG-TAGGGT--TTCTAGAGCTTG 1 TGGGCTTTGAAAGGGTGCCACT-GA-CTTG ** ** * * * * ** 3883091 AAGTTTTTGCCAAGGCTTCCGCAGTGGTTTAG 1 TGGGCTTTG-AAAGG-GTGC-CACTGACTT-G * * * 3883123 CAGGCCTGGTCTG-AA--GTG--A-T-A-TTA 1 -TGGGCT--T-TGAAAGGGTGCCACTGACTTG ****** * ** * 3883147 TAAAAAATG-ATGTATG--A-TGGTA-TTA 1 TGGGCTTTGAAAGGGTGCCACT-G-ACTTG * * * * 3883172 TGAATG-TATG-ATGGTTTAG-CACTGACTTG 1 TG--GGCTTTGAAAGG-GT-GCCACTGACTTG * * 3883201 TGGGCTTTGAAAGAGTGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883229 TGGGCTTTAAAAGGAGTGCCACTGACTTGTG 1 TGGGCTTTGAAAGG-GTGCCACTGAC-T-TG * * 3883260 TGGGCTTTGAAAGGGTCCCATTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3883288 TGGGCTTTGAAAGTGTGCCACTAAATTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3883316 TGGGCTTCGCAAA-GGTGCCACCGACTTG 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG 3883344 TGGGCTTTGAAAGGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3883372 TGGGCTCTAAAAGGAGTGCCACTAACTTG 1 TGGGCTTTGAAAGG-GTGCCACTGACTTG * * 3883401 TGGGCTTTGAAAGAGTGCCACTGACTTA 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883429 TGGGC-TTGAAAAGAGTGCCACTGACTTG 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG * * 3883457 TGGGC-TTGAAAAGGTGCCATTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883484 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3883512 TGGGCTTTGAAAGGATGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883540 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3883568 TGTAGGC-TTGAAAAGGTACCACTGACTTG 1 TG--GGCTTTGAAAGGGTGCCACTGACTTG * * * 3883597 TGGAC-TTAAAAAGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883624 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3883652 TGGGCTTTGAAAGGATGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883680 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3883708 TGGGC-TTGAAAAGGTACCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3883735 TGGGC-TTAAAAAGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883762 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883790 TGGGCTTTGAAAGGATGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883818 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883846 TGGGCTTTGAAAGGATGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3883874 TAGGCTTTGAAAGAGTGCCACTGACTAG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3883902 TGGGCTTTGAAAGGATGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3883930 TGGGCTTTGAAAAGAGTGCCACTGACTTG 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG ** * 3883959 TGGGC-TTGAAAACGTACCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3883986 TGGAC-TTAAAAAGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3884013 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3884041 TGGGCTTTGAAAGGATGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3884069 TGGGCTTGGAAAGAGTGCCATTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3884097 TGGGC-TTGAGAA-GGTACCACTGACTTG 1 TGGGCTTTGA-AAGGGTGCCACTGACTTG * 3884124 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * ** 3884152 TGGGCTTTGAAAATGGTGCCACTGACTCA 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG * * * 3884181 TGGGCTTTGAAAGGGATGAACATTCTAAAC-AG 1 TGGGCTTTGAAAGGG-TG-CCA--CT-GACTTG ** * * *** ** * * *** 3884213 -AAGTTCTTGACGATAATTTC-TTCACAAA 1 TGGGCT-TTGA-AAGGGTGCCACTGACTTG * * * * * 3884241 T-GGC---AAAAGGGT--C-TTGGCCTA 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * ** *** *** * ** 3884262 AGATG-ATAAAAAGAAAAGAGTCTTACCCG 1 TG-GGCTTTGAAAG-GGTGCCACTGACTTG *** * * ** 3884291 AATG--ATG-TAGGGT--TTCTAGAGCTTG 1 TGGGCTTTGAAAGGGTGCCACT-GA-CTTG ** ** * * * * ** 3884316 AAGTTTTTGCCAAGGCTTCCGCAGTGGTTTAG 1 TGGGCTTTG-AAAGG-GTGC-CACTGACTT-G * * * 3884348 CCGGCCTGGTCTG-AA--GTG--A-T-A-TTA 1 -TGGGCT--T-TGAAAGGGTGCCACTGACTTG ****** * ** * 3884372 TAAAAAATG-ATGTATG--A-TGGTA-TTA 1 TGGGCTTTGAAAGGGTGCCACT-G-ACTTG * * * * 3884397 TGAATG-TATG-ATGGTTTAG-CACTGACTTG 1 TG--GGCTTTGAAAGG-GT-GCCACTGACTTG * * 3884426 TGTGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3884454 TGGG-TTTAAAAGGAGTGCCACTGACTTGTG 1 TGGGCTTTGAAAGG-GTGCCACTGAC-T-TG * * 3884484 TGGGCTTTGAAAGGGTCCCATTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3884512 TGGGCTTTGAAAGTGTGCCACTAAATTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3884540 TGGGCTTCGCAAA-GGTGCCACCGACTTG 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG 3884568 TGGGCTTTGAAAGGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3884596 TGGGCTCTAAAAGGAGTGCCACTAACTTG 1 TGGGCTTTGAAAGG-GTGCCACTGACTTG * 3884625 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3884653 TGGGC-TTGAAAAGAGTGCCACTGACTTG 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG * * 3884681 TGGGC-TTGAAAAGGTGCCATTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3884708 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3884736 TGGGCTTTGAAAGGATGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3884764 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3884792 TGGGC-TTGAAAAGGTACCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3884819 TGGAC-TTAAAAAGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG ** 3884846 TGGGCTTTGAAAGAATGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3884874 TGGGCTTTAAAAGGATGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3884902 TGGGCTTGGAAAGAGTGCCATTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3884930 TGGGC-TTGAAAAGGTACCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3884957 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3884985 TGGGCTTTGAAAGGATGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3885013 TGAGCTTTGAAAGAGTGCCACTGACTAG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3885041 TGGGCTTTGAAAGGATGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3885069 T-GGCTTTGAAAAGAGTGCCACTGACTTG 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG * 3885097 TGGGC-TTGAAAAGGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3885124 TGGGCTTTGAAAGAGTGCCATTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3885152 TGGGCTTTGAAAGGATGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3885180 TGGGCTTTGAAAGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * * 3885208 TGAGC-TTAAAAAGGTACCACTGACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * 3885235 TGGGCTTTGAAAGAGTGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * * * 3885263 TGGGCTTTGAAAGGATGCCTCTGACTTT 1 TGGGCTTTGAAAGGGTGCCACTGACTTG 3885291 TGGGCTTTG-AAGGAGTGCCACTGACTTG 1 TGGGCTTTGAAAGG-GTGCCACTGACTTG * * 3885319 TGGGCTTTGAAAGGATGCCACTAACTTG 1 TGGGCTTTGAAAGGGTGCCACTGACTTG * 3885347 TGGGCTTTGAAAAGAGTGCCACTGACTTG 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG * * 3885376 TGGGTTTTGAAATGGGTGCCACTGACATG 1 TGGGCTTTGAAA-GGGTGCCACTGACTTG * * ** 3885405 TGGGCTTTGAAAATGGTACCACTGACTCA 1 TGGGCTTTG-AAAGGGTGCCACTGACTTG 3885434 TGGGCTTTGAAAGGG 1 TGGGCTTTGAAAGGG 3885449 ATGAACATTC Statistics Matches: 2865, Mismatches: 545, Indels: 304 0.77 0.15 0.08 Matches are distributed among these distances: 20 6 0.00 21 11 0.00 22 8 0.00 23 12 0.00 24 4 0.00 25 32 0.01 26 16 0.01 27 482 0.17 28 1783 0.62 29 324 0.11 30 71 0.02 31 73 0.03 32 19 0.01 33 14 0.00 34 4 0.00 35 2 0.00 36 4 0.00 ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28 Consensus pattern (28 bp): TGGGCTTTGAAAGGGTGCCACTGACTTG Found at i:3881904 original size:72 final size:72 Alignment explanation

Indices: 3881787--3881930 Score: 234 Period size: 72 Copynumber: 2.0 Consensus size: 72 3881777 CTGACTTGTG * * * 3881787 TGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTCGAAATAGTGCCACTAAATTGTGGGCTTCA 1 TGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTCAAAAGAGTGCCACTAAATTGTAGGCTTCA 3881852 CAAGGGT 66 CAAGGGT * * * 3881859 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGAGTGCCACTAAATTGTAGGCTTCG 1 TGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTCAAAAGAGTGCCACTAAATTGTAGGCTTCA 3881924 CAAGGGT 66 CAAGGGT 3881931 GCCACTAACT Statistics Matches: 66, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 72 66 1.00 ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28 Consensus pattern (72 bp): TGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTCAAAAGAGTGCCACTAAATTGTAGGCTTCA CAAGGGT Found at i:3882454 original size:111 final size:114 Alignment explanation

Indices: 3881859--3885445 Score: 2776 Period size: 111 Copynumber: 31.6 Consensus size: 114 3881849 TCACAAGGGT * * * 3881859 TGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTT-AAAAGAGTGCCACTAAATTGTAGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * * * * * 3881922 CGCAAGGGTGCCACTAACTTGTGGGCTTCGAAAGGGTGCCACTGACTTG 66 TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * * * 3881971 TGGGCTCTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC 1 TGGGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC * * * * * 3882035 TTCGAAATA-GTGCCACTAAATTGTGGGC-TTCACAAGGGTGCCACTGACTTG 64 TTTGAAA-AGGTGCCACTGACTTGTGGGCTTTGA-AAGAGTGCCACTGACTTG ** * * * 3882086 TGGGCTTCAAAAGG-GTGCCACTGACTCGTGGGCTTTGAAAA-TGTGCCACTGACTTGCGTGAGC 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGC * * * 3882149 TTT-AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTCCCATTGACTTG 64 TTTGAAAA-G-GTGCCACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACTTG * * * * * * * 3882203 TGGGCTTTGAAA-GAGTGCCACTAAATTGTGGGCTTCG-TATGGGTGCCACCGACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * * * 3882266 TGAAAGGGTGCCACTGACTTGTGGGCTCTAAAAGGAGTGCCATTGACTTG 66 TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTG 3882316 TGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGC-TTGAAAAGAGTGCCACTGACTTGTGGGC-T 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * 3882378 TGAAAAGGTGCCATTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG 66 TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * * 3882427 TGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTAACTTGTGGGC-T 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * ** 3882489 TGAAAAGGTACCACTGACTTGTGGGCTTAAAAAG-GTGCCACTGACTTG 66 TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * * 3882537 TGGGCTTTGAAA-TAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * 3882600 TG-AAAGAGTGCCACTGACTTATGGGCTTTGAAAG-GATGCCACTGACTTG 66 TGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCACTGACTTG * * * 3882649 TGGGCTTTGAAA-GAGTGCCACTGACTAGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * 3882712 TGAAAAGAGTGCCACTGACTTGTGGGC-TT-AAAAACGTACCACTGACTTG 66 TGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACTTG * * * 3882761 TGGAC-TTAAAAAG-GTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * * 3882823 TG-AAAGGATGCCACTGTCTTGTGGGCTTGGAAAGAGTGCCATTGACTTG 66 TGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * * 3882872 TGGGC-TTGAAAAG-GTACCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT ** * 3882934 TGAAAATGGTGCCACTGACTCATGGGCTTTGAAAG-G-G--A-TGAACAT- 66 TGAAAA-GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG-ACTTG * * * * * * * * * * * * * * 3882979 T---C--TAAACAGAAGTTCTTGACGATAATTTCTTGACAAATGGCAAAAG-G-GTC-TTGGCCT 1 TGGGCTTTGAA-AGGAGTGC--CAC--TGACTTGTGGGC--TTTG-AAAAGAGTGCCACT-GACT * ****** * * * ** * * * 3883036 AAGATGATAAAAAGAAAAGAGT-CTTACCCGAATGATGTAGGG-TTT-CTAGAGCTTG-AAGT-T 57 -TG-TG-GGCTTTGAAAAG-GTGC-CA-CTGACT--TGT-GGGCTTTGAAAGAG--TGCCACTGA * 3883096 TTTG 111 CTTG ** * ** ** * * * * * * 3883100 CCAAGGCTTCCGCAGTGGTTTAG-CAGGCCTG-GTCTGAAGTGATATT-ATAAAAAATG--A-TG 1 --TGGGCTT-TG-AAAGGAGT-GCCA---CTGACT-TG-TGGGCT-TTGA-AAAGAGTGCCACTG ** 3883159 --TATGATGGTATTATGAATGTATGATGGTTTAG-CACTGACTTGTGGGCTTTGAAAGAGTGCCA 54 ACT-TG-TGGGCTT-TGAA---A--A-GG--T-GCCACTGACTTGTGGGCTTTGAAAGAGTGCCA * 3883221 CTAACTTG 107 CTGACTTG * * * * 3883229 TGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTG-AAAGGGTCCCATTGACTTGTGGGC 1 TGGGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC * * * * 3883293 TTTG-AAAGTGTGCCACTAAATTGTGGGCTTCGCAAAG-GTGCCACCGACTTG 64 TTTGAAAAG-GTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTG * * 3883344 TGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTCT-AAAAGGAGTGCCACTAACTTGTGGGCT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAA-GAGTGCCACTGACTTGTGGGCT * 3883407 TTG-AAAGAGTGCCACTGACTTATGGGC-TTGAAAAGAGTGCCACTGACTTG 65 TTGAAAAG-GTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTG * * 3883457 TGGGC-TTGAAAAG-GTGCCATTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * 3883519 TG-AAAGGATGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG 66 TGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * * * * 3883568 TGTAGGC-TTGAAAAG-GTACCACTGACTTGTGGAC-TTAAAAAG-GTGCCACTGACTTGTGGGC 1 TG--GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC * 3883629 TTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTAACTTG 64 TTTGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCACTGACTTG * 3883680 TGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGC-TTGAAAAG-GTACCACTGACTTGTGGGC-T 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * 3883741 TAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG 66 TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG 3883790 TGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * 3883853 TG-AAAGGATGCCACTGACTTGTAGGCTTTGAAAGAGTGCCACTGACTAG 66 TGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * 3883902 TGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC-T 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * * ** 3883965 TGAAAACGTACCACTGACTTGTGGACTTAAAAAG-GTGCCACTGACTTG 66 TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * 3884013 TGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGC-T 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * * 3884075 TGGAAAGAGTGCCATTGACTTGTGGGC-TTGAGAAG-GTACCACTGACTTG 66 TGAAAAG-GTGCCACTGACTTGTGGGCTTTGA-AAGAGTGCCACTGACTTG ** 3884124 TGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAATG-GTGCCACTGACTCATGGGCT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAA-GAGTGCCACTGACTTGTGGGCT * * * * ** * * * * ** * * *** 3884187 TTGAAAGGGATGAACATTCTAAAC-AG-AAGTTCTTGACGATAATTTC-TTCACAAA 65 TTGAAAAGG-TG-CCA--CT-GACTTGTGGGCT-TTGA-AAGAGTGCCACTGACTTG * * * * ****** * * * 3884241 T-GGC---AAAAGG-GT--C-TTGGCCTAAGATGATAAAAAGAAAAGAGT-CTTACCCGAATGAT 1 TGGGCTTTGAAAGGAGTGCCACT-GACT-TG-TG-GGCTTTGAAAAGAGTGC-CA-CTGACT--T ** * * * * ** ** * * * * * 3884297 GTAGGG-TTTCTAGAGCTTG-AAGT-TTTTGCCAAGGCTTCCG-CAGTGGTTTAGCCGGCCTG-G 58 GT-GGGCTTTGAAAAG-GTGCCACTGACTTG--TGGGCTT-TGAAAG-AG--T-GCC--ACTGAC 3884357 TCTG 112 T-TG * * * ** * ** * 3884361 AAGTGATATT-ATAAAAAATG--A-TG--TATGATGGTATTATGAATGTATGATGGTTTAG-CAC 1 -TGGGCT-TTGA-AAGGAGTGCCACTGACT-TG-TGGGCTT-TGAA---AAGA--G--T-GCCAC * * 3884419 TGACTTGTGTGCTTTG-AAAGAGTGCCACTGACTTGTGGG-TTTAAAAGGAGTGCCACTGACTTG 52 TGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAC-T- 3884482 TG 113 TG * * * * * 3884484 TGGGCTTTGAAAGG-GTCCCATTGACTTGTGGGCTTTG-AAAGTGTGCCACTAAATTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * * * 3884547 CGCAAAGGTGCCACCGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG 66 TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * * * 3884596 TGGGCTCTAAAAGGAGTGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGC-T 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * 3884659 TGAAAAGAGTGCCACTGACTTGTGGGC-TTGAAA-AGGTGCCATTGACTTG 66 TGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACTTG * * 3884708 TGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * 3884771 TG-AAAGAGTGCCACTGACTTGTGGGC-TTGAAA-AGGTACCACTGACTTG 66 TGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACTTG * * * * 3884819 TGGAC-TTAAAAAG-GTGCCACTGACTTGTGGGCTTTG-AAAGAATGCCACTGACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * 3884881 T-AAAAGGATGCCACTGACTTGTGGGCTTGGAAAGAGTGCCATTGACTTG 66 TGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * * 3884930 TGGGC-TTGAAAAG-GTACCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * 3884992 TG-AAAGGATGCCACTGACTTGTGAGCTTTGAAAGAGTGCCACTGACTAG 66 TGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * 3885041 TGGGCTTTGAAAGGA-TGCCACTAACTTGT-GGCTTTGAAAAGAGTGCCACTGACTTGTGGGC-T 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * 3885103 TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCATTGACTTG 66 TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * 3885152 TGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGAGC-T 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * * * 3885214 TAAAAAGGTACCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAACTTG 66 TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG * * * 3885263 TGGGCTTTGAAAGGA-TGCCTCTGACTTTTGGGCTTTG-AAGGAGTGCCACTGACTTGTGGGCTT 1 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT * 3885326 TG-AAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG 66 TGAAAAGG-TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTG * * * ** 3885376 TGGGTTTTGAAATGG-GTGCCACTGACATGTGGGCTTTGAAAATG-GTACCACTGACTCATGGGC 1 TGGGCTTTGAAA-GGAGTGCCACTGACTTGTGGGCTTTGAAAA-GAGTGCCACTGACTTGTGGGC 3885439 TTTGAAA 64 TTTGAAA 3885446 GGGATGAACA Statistics Matches: 2829, Mismatches: 412, Indels: 464 0.76 0.11 0.13 Matches are distributed among these distances: 103 3 0.00 104 2 0.00 105 3 0.00 107 5 0.00 108 4 0.00 109 14 0.00 110 274 0.10 111 957 0.34 112 584 0.21 113 347 0.12 114 130 0.05 115 190 0.07 116 23 0.01 117 91 0.03 118 13 0.00 119 1 0.00 120 4 0.00 121 13 0.00 122 15 0.01 123 21 0.01 124 32 0.01 125 10 0.00 126 11 0.00 127 32 0.01 128 19 0.01 129 16 0.01 130 11 0.00 131 4 0.00 ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28 Consensus pattern (114 bp): TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT TGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG Found at i:3886701 original size:21 final size:22 Alignment explanation

Indices: 3886677--3886719 Score: 70 Period size: 22 Copynumber: 2.0 Consensus size: 22 3886667 TTTTTGCTAG 3886677 TTTTTCTTT-TTTTTGTTTTGT 1 TTTTTCTTTGTTTTTGTTTTGT * 3886698 TTTTTCTTTGTTTTTTTTTTGT 1 TTTTTCTTTGTTTTTGTTTTGT 3886720 GGGTGTAAAG Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 21 9 0.45 22 11 0.55 ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86 Consensus pattern (22 bp): TTTTTCTTTGTTTTTGTTTTGT Found at i:3886702 original size:16 final size:15 Alignment explanation

Indices: 3886676--3886717 Score: 59 Period size: 15 Copynumber: 2.7 Consensus size: 15 3886666 TTTTTTGCTA 3886676 GTTTTTCTTTTT-TTT 1 GTTTTT-TTTTTCTTT 3886691 GTTTTGTTTTTTCTTT 1 GTTTT-TTTTTTCTTT 3886707 GTTTTTTTTTT 1 GTTTTTTTTTT 3886718 GTGGGTGTAA Statistics Matches: 25, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 15 16 0.64 16 9 0.36 ACGTcount: A:0.00, C:0.05, G:0.10, T:0.86 Consensus pattern (15 bp): GTTTTTTTTTTCTTT Found at i:3886718 original size:11 final size:11 Alignment explanation

Indices: 3886677--3886719 Score: 54 Period size: 11 Copynumber: 4.0 Consensus size: 11 3886667 TTTTTGCTAG 3886677 TTTTTCTTT-T 1 TTTTTCTTTGT 3886687 TTTTGT-TTTGT 1 TTTT-TCTTTGT 3886698 TTTTTCTTTGT 1 TTTTTCTTTGT * 3886709 TTTTTTTTTGT 1 TTTTTCTTTGT 3886720 GGGTGTAAAG Statistics Matches: 29, Mismatches: 1, Indels: 5 0.83 0.03 0.14 Matches are distributed among these distances: 10 8 0.28 11 21 0.72 ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86 Consensus pattern (11 bp): TTTTTCTTTGT Found at i:3888979 original size:15 final size:16 Alignment explanation

Indices: 3888953--3888982 Score: 53 Period size: 15 Copynumber: 1.9 Consensus size: 16 3888943 TTAAAGGACG 3888953 ACCAAGCACTGGCGGT 1 ACCAAGCACTGGCGGT 3888969 ACCAA-CACTGGCGG 1 ACCAAGCACTGGCGG 3888983 GTTTGACAAA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 9 0.64 16 5 0.36 ACGTcount: A:0.27, C:0.33, G:0.30, T:0.10 Consensus pattern (16 bp): ACCAAGCACTGGCGGT Found at i:3899815 original size:22 final size:22 Alignment explanation

Indices: 3899787--3899837 Score: 102 Period size: 22 Copynumber: 2.3 Consensus size: 22 3899777 CATGTTAAAG 3899787 ATGCATGAAACATAATAAAAAA 1 ATGCATGAAACATAATAAAAAA 3899809 ATGCATGAAACATAATAAAAAA 1 ATGCATGAAACATAATAAAAAA 3899831 ATGCATG 1 ATGCATG 3899838 GTCAAAGGCT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 29 1.00 ACGTcount: A:0.59, C:0.10, G:0.12, T:0.20 Consensus pattern (22 bp): ATGCATGAAACATAATAAAAAA Found at i:3900776 original size:20 final size:19 Alignment explanation

Indices: 3900747--3900821 Score: 87 Period size: 20 Copynumber: 3.8 Consensus size: 19 3900737 AAAAAGACAT 3900747 AATGTATCGATACATTGAA 1 AATGTATCGATACATTGAA * * 3900766 GAATATATCGATACATTCATA 1 -AATGTATCGATACATTGA-A * * 3900787 CATGTATCGATATATTGAAA 1 AATGTATCGATACATTG-AA 3900807 AATGTATCGATACAT 1 AATGTATCGATACAT 3900822 CTGGGTAAAA Statistics Matches: 45, Mismatches: 8, Indels: 4 0.79 0.14 0.07 Matches are distributed among these distances: 20 43 0.96 21 2 0.04 ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33 Consensus pattern (19 bp): AATGTATCGATACATTGAA Found at i:3900804 original size:40 final size:39 Alignment explanation

Indices: 3900744--3900821 Score: 120 Period size: 40 Copynumber: 2.0 Consensus size: 39 3900734 GGTAAAAAGA * 3900744 CATAATGTATCGATACATTGAAGAATATATCGATACATT 1 CATAATGTATCGATACATTGAAAAATATATCGATACATT * * 3900783 CATACATGTATCGATATATTGAAAAATGTATCGATACAT 1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT 3900822 CTGGGTAAAA Statistics Matches: 35, Mismatches: 3, Indels: 1 0.90 0.08 0.03 Matches are distributed among these distances: 39 4 0.11 40 31 0.89 ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33 Consensus pattern (39 bp): CATAATGTATCGATACATTGAAAAATATATCGATACATT Found at i:3901505 original size:28 final size:28 Alignment explanation

Indices: 3901432--3902578 Score: 1347 Period size: 28 Copynumber: 40.6 Consensus size: 28 3901422 CACTGACACG * ** * 3901432 TGTGGGCTTTGAAAAGAGTGTTACTAACT 1 TGTGGGCTTTG-AAAGGGTGCCACTGACT * 3901461 TGCGTGGGCTTTAAAAGGGTGCCACTGACT 1 T--GTGGGCTTTGAAAGGGTGCCACTGACT 3901491 TGTGGGCTTTGAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * * 3901519 TGTGGGCTTTAAAAGAGTGCCACTAAAT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3901547 TGTGGGCTTCGCAAGGGTGCCACTAACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3901575 TGTGGGCTTCGAAAGGGTGCCATTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3901603 TGTGGGCTCTAAAAGGAGTGCCACTGACTT 1 TGTGGGCTTTGAAAGG-GTGCCACTGAC-T 3901633 GTGTGGGCTTTGAAAGGGTGCCACTGACT 1 -TGTGGGCTTTGAAAGGGTGCCACTGACT * ** * * 3901662 TGTGGGCTTCGAAATAGTGCCACTAAAT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3901690 TGTGGGC-TTCACAAGGGTGCCACTGACT 1 TGTGGGCTTTGA-AAGGGTGCCACTGACT ** 3901718 TGTGGGCTTCAAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * ** * 3901746 CGTGGGCTTTGAAAATGTGCCACTAACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3901774 TGCGTGAGCTTTAAAAGGAGTGCCACTGACTT 1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T * * 3901806 GTGTGGGCTTTGAAAGGGTCCCATTGACT 1 -TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3901835 TGTGGGCTTTGAAAGAGTGCCACTAAAT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3901863 TGTGGGCTTCGTAAGGGTGCCACCGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT 3901891 TGT-GGCTTTGAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3901918 TGTGGGCTCTAAAAGGAGTGCCATTGACT 1 TGTGGGCTTTGAAAGG-GTGCCACTGACT * 3901947 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT ** 3901975 TGTGGGC-TTGAAAACAGTGCCACTGACT 1 TGTGGGCTTTG-AAAGGGTGCCACTGACT * * 3902003 TGTGGGC-TTGAAAAGGTGCCATTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3902030 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3902058 TGTGGGCTTTGAAAGGATGCCACTAACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3902086 TGTGGGCTTTGAAAGAGTGCCACTAACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3902114 TGTGGGC-TTGAAAAGGTACCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3902141 GGTGGGC-TTAAAAAGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3902168 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3902196 TGTGGGCTTTGAAAGGATGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3902224 TGTGGGCTTTGAAAGAGTGCCACTAACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3902252 TGTGGGCTTTGAAAGGATGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3902280 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3902308 AGTGGGCTTTGAAAGGATGCCACTAACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3902336 TGTGGGCTTTGAAAAGAGTGCCACTGACT 1 TGTGGGCTTTG-AAAGGGTGCCACTGACT ** * 3902365 TGTGGGC-TTGAAAACGTACCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3902392 TGTGGGC-TTAAAAAGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3902419 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3902447 TGTGGGCTTTGAAAGGATGCCACTAACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3902475 TGTGGGCTTTGAAAAGAGTGCCACTGACT 1 TGTGGGCTTTG-AAAGGGTGCCACTGACT * * * 3902504 TGTGGGTTTTAAAATGGGTGCCACTGACA 1 TGTGGGCTTTGAAA-GGGTGCCACTGACT * 3902533 TGTGGGCTTTGAAAATGGTGCCACTGACT 1 TGTGGGCTTTG-AAAGGGTGCCACTGACT ** 3902562 CATGGGCTTTGAAAGGG 1 TGTGGGCTTTGAAAGGG 3902579 ATGAACATTC Statistics Matches: 955, Mismatches: 141, Indels: 45 0.84 0.12 0.04 Matches are distributed among these distances: 27 141 0.15 28 592 0.62 29 125 0.13 30 49 0.05 31 46 0.05 32 1 0.00 33 1 0.00 ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28 Consensus pattern (28 bp): TGTGGGCTTTGAAAGGGTGCCACTGACT Found at i:3908441 original size:28 final size:28 Alignment explanation

Indices: 3908368--3910159 Score: 2216 Period size: 28 Copynumber: 63.5 Consensus size: 28 3908358 CACTGACACG * ** 3908368 TGTGGGCTTTGAAAAGAGTGTTACTGACT 1 TGTGGGCTTTG-AAAGGGTGCCACTGACT * 3908397 TGCGTGGGCTTTAAAAGGGTGCCACTGACT 1 T--GTGGGCTTTGAAAGGGTGCCACTGACT * 3908427 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * * 3908455 TGTGGGCTTTAAAAGAGTGCCACTAAAT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3908483 TGTGGGCTTCGCAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3908511 TGTGGGCTTCGAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3908539 TGTGGGCTCTAAAAGGAGTGCCACTGACTT 1 TGTGGGCTTTGAAAGG-GTGCCACTGAC-T 3908569 GTGTGGGCTTTGAAAGGGTGCCACTGACT 1 -TGTGGGCTTTGAAAGGGTGCCACTGACT ** * * 3908598 TGTGGGCTTTGAAATAGTGCCACTCAAT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3908626 TGTGGGCTTCGCAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT ** 3908654 TGTGGGCTTCAAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3908682 CGTGGGCTTTGAAAAGGAGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3908710 TGCGTGGGCTTTAAAAGGAGTGCCACTGACTT 1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T * * * 3908742 GTGTGGGCTTTGGAAGGGTCCCATTGACT 1 -TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3908771 TGTGGGCTTTGAAAGAGTGCCACTAAAT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3908799 TGTGGGCTTCGCAAGGGTGCCACCGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3908827 TGTGGGCTTTGAAAGGGTGCCACTGAAT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3908855 TGTGGGCTCTAAAAGGAGTGCCACTAACT 1 TGTGGGCTTTGAAAGG-GTGCCACTGACT * 3908884 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3908912 TGTAGGC-TTGAAAAGGTGCCATTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3908939 TGTGAGCTTTGAAAGAGTGCCATTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3908967 TGTGGGCTTTGAATGGATGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3908995 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3909023 TGTGGGCTTCGAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909051 TGTGGGCTCTAAAAGGAGTGCCACTGACTT 1 TGTGGGCTTTGAAAGG-GTGCCACTGAC-T 3909081 GTGTGGGCTTTGAAAGGGTGCCACTGACT 1 -TGTGGGCTTTGAAAGGGTGCCACTGACT ** * * 3909110 TGTGGGCTTTGAAATAGTGCCACTCAAT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909138 TGTGGGCTTCGCAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT ** 3909166 TGTGGGCTTCAAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909194 CGTGGGCTTTGAAAAGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3909222 TGCGTGGGCTTTAAAAGGAGTGCCACTGACTT 1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T * * 3909254 ATGTGGGCTTTGAAAGGGTCCCATTGACT 1 -TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3909283 TGTGGGCTTTGAAAGAGTGCCACTAAAT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3909311 TGTGGGCTTCGCAAGGGTGCCACCGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3909339 TGTGGGCTTTGAAAGGGTGCCACTGAAT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909367 TGTGGGCTCTAAAAGGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGG-GTGCCACTGACT * 3909396 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3909424 TGTAGGC-TTGAAAAGGTGCCATTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3909451 TGTGAGCTTTGAAAGAGTGCCATTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3909479 TGTGGGCTTTGAAAGGATGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3909507 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909535 TGTGGGC-TTGAAAAGGTACCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909562 TGTGGGC-TTAAAAAGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909589 TGTGGGCTTTGAAAGAGTGCCATTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909617 TGTAGGCTTTGAAAGGATGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3909645 TGTAGGC-TTGAAAAGGTGCCATTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3909672 TGTGAGCTTTGAAAGAGTGCCATTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3909700 TGTGGGCTTTGAAAGGATGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3909728 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909756 TGTGGGC-TTGAAAAGGTACCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909783 TGTGGGC-TTAAAAAGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3909810 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909838 TGTAGGCTTTGAAAGGATGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909866 TGTGAGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3909894 TGTGGGCTTTGAAAGGATGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909922 TGTGGGCTTTGAAAGAGTGCCACTCACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3909950 AGTGGGCTTTGAAAGGATGCCACTAACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * 3909978 TGTGGGCTTTGAAAAGAGTGGCACTGACT 1 TGTGGGCTTTG-AAAGGGTGCCACTGACT * 3910007 TGTGGGC-TTGAAAAGGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3910034 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3910062 TGTGGGCTTTGAAAGGATGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * 3910090 TGTGGGCTTTGAAAGAGTGCCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT * * * 3910118 TGTGAGC-TTGAAAAGGTACCACTGACT 1 TGTGGGCTTTGAAAGGGTGCCACTGACT 3910145 TGTGGGCTTTGAAAG 1 TGTGGGCTTTGAAAG 3910160 AGTGTTACTG Statistics Matches: 1514, Mismatches: 221, Indels: 57 0.84 0.12 0.03 Matches are distributed among these distances: 27 208 0.14 28 1040 0.69 29 94 0.06 30 83 0.05 31 85 0.06 32 2 0.00 33 2 0.00 ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28 Consensus pattern (28 bp): TGTGGGCTTTGAAAGGGTGCCACTGACT Found at i:3909378 original size:512 final size:509 Alignment explanation

Indices: 3908368--3910153 Score: 2590 Period size: 512 Copynumber: 3.5 Consensus size: 509 3908358 CACTGACACG ** * * * 3908368 TGTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGG 1 TGTGGGCTTTG-AAAGAGTGCCACTGACTT--GTAGGCTTGAAAA-GGTGCCACTGACTTGTGAG * * * * 3908433 CTTTGAAAGAGTGCCACTGACTTGTGGGCTTT-AAAAGAGTGCCACTAAATTGTGGGCTTCGCAA 62 CTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA * 3908497 GGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTAAAAGGAGTGCCA 127 GAGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTAAAAGGAGTGCCA * 3908562 CTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAATAGTGCCACTCAATT 192 CTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-AGTGCCACTCAATT 3908627 GTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCAAAAGGGTGCCACTGACTCGTGGGCTTT 254 GTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCAAAAGGGTGCCACTGACTCGTGGGCTTT * * 3908692 GAAAAGGAGCCACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGGAA 319 GAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGACTT-TGTGGGCTTTGAAA 3908757 GGGTCCCATTGACTTGTGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTCGCAAGGGTGCCAC 383 GGGTCCCATTGACTTGTGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTCGCAAGGGTGCCAC * 3908822 CGACTTGTGGGCTTTGAAAGGGTGCCACTGAATTGTGGGCTCTAAAAGGAGTGCCACTAACT 448 CGACTTGTGGGCTTTGAAAGGGTGCCACTGAATTGTGGGCTCTAAAAGGAGTGCCACTGACT * 3908884 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGGCTTGAAAAGGTGCCATTGACTTGTGAGCTTT 1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGGCTTGAAAAGGTGCCACTGACTTGTGAGCTTT * ** 3908949 GAAAGAGTGCCATTGACTTGTGGGCTTTGAATGGA-TGCCACTGACTTGTGGGCTTTGAAAGAGT 66 GAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGT 3909013 GCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTAAAAGGAGTGCCACTGA 131 GCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTAAAAGGAGTGCCACTGA * 3909078 CTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAATAGTGCCACTCAATTGTGG 196 C-T-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-AGTGCCACTCAATTGTGG 3909143 GCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCAAAAGGGTGCCACTGACTCGTGGGCTTTGAAA 258 GCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCAAAAGGGTGCCACTGACTCGTGGGCTTTGAAA 3909208 AGGTGCCACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGACTTATGTGGGCTTTGAAAGGGT 323 AGGTGCCACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGACTT-TGTGGGCTTTGAAAGGGT 3909273 CCCATTGACTTGTGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTCGCAAGGGTGCCACCGAC 387 CCCATTGACTTGTGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTCGCAAGGGTGCCACCGAC 3909338 TTGTGGGCTTTGAAAGGGTGCCACTGAATTGTGGGCTCTAAAAGGAGTGCCACTGACT 452 TTGTGGGCTTTGAAAGGGTGCCACTGAATTGTGGGCTCTAAAAGGAGTGCCACTGACT * 3909396 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGGCTTGAAAAGGTGCCATTGACTTGTGAGCTTT 1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGGCTTGAAAAGGTGCCACTGACTTGTGAGCTTT * * 3909461 GAAAGAGTGCCATTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGAGT 66 GAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGT * * * 3909525 GCCACTGACTTGTGGGCTT-GAAAAGGTACCACTGACTTGTGGGCT-TAAAAAG-GTGCCACTGA 131 GCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTAAAAGGAGTGCCACTGA * * * * * * 3909587 CTTGTGGGCTTTGAAAGAGTGCCATTGACTTGTAGGCTTTGAAAGGATGCCACTGACTTGTAGGC 196 CTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-TGCCACTCAATTGTGGGC * * * * ** * * * 3909652 TT-GAAAAGGTGCCATTGACTTGTGAGCTTTGAAAGAGTGCCATTGACTTGTGGGCTTTG-AAAG 260 TTCGCAAGGGTGCCACTGACTTGTGGGCTTCAAAAGGGTGCCACTGACTCGTGGGCTTTGAAAAG * * * 3909715 GATGCCACTGACTT--GTGGGCTTTGAAA-GAGTGCCACTGAC-TTGTGGGC-TTGAAAAGGTAC 325 G-TGCCACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGACTTTGTGGGCTTTGAAAGGGTCC * ** * * * * * * 3909775 CACTGACTTGTGGGCTTAAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTT 389 CATTGACTTGTGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTCGCAAGGGTGCCACCGACTT * * * * * * 3909839 GTAGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTGAAA-GAGTGCCACTGACT 454 GTGGGCTTTGAAAGGGTGCCACTGAATTGTGGGCTCTAAAAGGAGTGCCACTGACT * * * * 3909894 TGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTCACTAGTGGGC 1 TGTGGGCTTTGAAAGAG-TGCCACTGACTTGTAGGC-TTGAAAAG-GTGCCACTGACTTGTGAGC * * 3909957 TTTGAAAG-GATGCCACTAACTTGTGGGCTTTGAAAAGAGTGGCACTGACTTGTGGGC-TTGAAA 63 TTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA * * * * 3910020 -AGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCC 127 GA-GTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTAAAAGGAGTGCC * * * * 3910083 ACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGAGC-TTGAAAAGGTACCACTGACTTG 191 ACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA-GTGCCACTCAATTG 3910147 TGGGCTT 255 TGGGCTT 3910154 TGAAAGAGTG Statistics Matches: 1181, Mismatches: 76, Indels: 42 0.91 0.06 0.03 Matches are distributed among these distances: 497 1 0.00 498 52 0.04 499 148 0.13 500 94 0.08 501 56 0.05 502 1 0.00 503 13 0.01 504 12 0.01 505 5 0.00 506 61 0.05 507 56 0.05 508 1 0.00 509 11 0.01 510 6 0.01 511 24 0.02 512 598 0.51 513 15 0.01 515 16 0.01 516 11 0.01 ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28 Consensus pattern (509 bp): TGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGGCTTGAAAAGGTGCCACTGACTTGTGAGCTTT GAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGT GCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTAAAAGGAGTGCCACTGA CTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGTGCCACTCAATTGTGGGCT TCGCAAGGGTGCCACTGACTTGTGGGCTTCAAAAGGGTGCCACTGACTCGTGGGCTTTGAAAAGG TGCCACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGACTTTGTGGGCTTTGAAAGGGTCCCA TTGACTTGTGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTCGCAAGGGTGCCACCGACTTGT GGGCTTTGAAAGGGTGCCACTGAATTGTGGGCTCTAAAAGGAGTGCCACTGACT Found at i:3913478 original size:25 final size:25 Alignment explanation

Indices: 3913444--3913513 Score: 72 Period size: 25 Copynumber: 2.8 Consensus size: 25 3913434 GTTATCAGCC * 3913444 GTTGTCGTTGCTTGGTGTTGTTGTT 1 GTTGTTGTTGCTTGGTGTTGTTGTT 3913469 GTTGTTGTTGC-T-GTCGTTGGTTGTT 1 GTTGTTGTTGCTTGGT-GTT-GTTGTT * * * 3913494 GCTATTGATGCTTGGTGTTG 1 GTTGTTGTTGCTTGGTGTTG 3913514 CTGCTGCTAG Statistics Matches: 37, Mismatches: 4, Indels: 8 0.76 0.08 0.16 Matches are distributed among these distances: 23 2 0.05 24 4 0.11 25 25 0.68 26 4 0.11 27 2 0.05 ACGTcount: A:0.03, C:0.09, G:0.36, T:0.53 Consensus pattern (25 bp): GTTGTTGTTGCTTGGTGTTGTTGTT Found at i:3914080 original size:36 final size:36 Alignment explanation

Indices: 3914010--3914142 Score: 189 Period size: 36 Copynumber: 3.8 Consensus size: 36 3914000 ATTTCATGCA * * * * 3914010 TTGCCATTTC-TCCATCTTG-TTGCAGCAACTGACT 1 TTGCCATTTCTTTCTTCTTGTTTTCAACAACTGACT * 3914044 TTGCCGTTTCTTTCTTCTTGTTTTCAACAACTGACT 1 TTGCCATTTCTTTCTTCTTGTTTTCAACAACTGACT * * 3914080 TTGTCATTTCTTTCTTCTTGTTTTCTACAACTGACT 1 TTGCCATTTCTTTCTTCTTGTTTTCAACAACTGACT 3914116 TTGCCATTTCTTTCTTCTTGTTTTCAA 1 TTGCCATTTCTTTCTTCTTGTTTTCAA 3914143 TAGCTGATCA Statistics Matches: 87, Mismatches: 10, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 34 9 0.10 35 7 0.08 36 71 0.82 ACGTcount: A:0.14, C:0.25, G:0.11, T:0.50 Consensus pattern (36 bp): TTGCCATTTCTTTCTTCTTGTTTTCAACAACTGACT Found at i:3914301 original size:16 final size:15 Alignment explanation

Indices: 3914280--3914319 Score: 53 Period size: 16 Copynumber: 2.6 Consensus size: 15 3914270 GACTTCGGCC 3914280 TTTTTTTATTATTATT 1 TTTTTTTATTATT-TT * 3914296 TTTTTTTATTCTTTT 1 TTTTTTTATTATTTT * 3914311 TTTGTTTAT 1 TTTTTTTAT 3914320 CTTAGAGATT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 15 10 0.45 16 12 0.55 ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82 Consensus pattern (15 bp): TTTTTTTATTATTTT Found at i:3914313 original size:13 final size:14 Alignment explanation

Indices: 3914279--3914313 Score: 54 Period size: 13 Copynumber: 2.6 Consensus size: 14 3914269 TGACTTCGGC 3914279 CTTTTTTTATTATT 1 CTTTTTTTATTATT * 3914293 ATTTTTTT-TTATT 1 CTTTTTTTATTATT 3914306 CTTTTTTT 1 CTTTTTTT 3914314 GTTTATCTTA Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 13 12 0.63 14 7 0.37 ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83 Consensus pattern (14 bp): CTTTTTTTATTATT Found at i:3918246 original size:3 final size:3 Alignment explanation

Indices: 3918238--3918262 Score: 50 Period size: 3 Copynumber: 8.3 Consensus size: 3 3918228 ATAAAACAAG 3918238 ATT ATT ATT ATT ATT ATT ATT ATT A 1 ATT ATT ATT ATT ATT ATT ATT ATT A 3918263 ATAAAAATTA Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 22 1.00 ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64 Consensus pattern (3 bp): ATT Found at i:3918274 original size:16 final size:17 Alignment explanation

Indices: 3918253--3918287 Score: 54 Period size: 16 Copynumber: 2.1 Consensus size: 17 3918243 TATTATTATT 3918253 ATTATTATTAA-TAAAA 1 ATTATTATTAATTAAAA * 3918269 ATTATTTTTAATTAAAA 1 ATTATTATTAATTAAAA 3918286 AT 1 AT 3918288 GAATTTTATC Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 10 0.59 17 7 0.41 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (17 bp): ATTATTATTAATTAAAA Found at i:3924784 original size:30 final size:27 Alignment explanation

Indices: 3924748--3924803 Score: 76 Period size: 27 Copynumber: 2.0 Consensus size: 27 3924738 TTAATATTTT 3924748 GAAAATAAAAACGGGGTTGGAGTATCCCTC 1 GAAAATAAAAA---GGTTGGAGTATCCCTC * 3924778 GAAAATAACAAGGTTGGAGTATCCCT 1 GAAAATAAAAAGGTTGGAGTATCCCT 3924804 AAGATGAAAG Statistics Matches: 25, Mismatches: 1, Indels: 3 0.86 0.03 0.10 Matches are distributed among these distances: 27 15 0.60 30 10 0.40 ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21 Consensus pattern (27 bp): GAAAATAAAAAGGTTGGAGTATCCCTC Found at i:3924797 original size:78 final size:78 Alignment explanation

Indices: 3924572--3924800 Score: 300 Period size: 79 Copynumber: 2.9 Consensus size: 78 3924562 TAACCCCAAT * * 3924572 GATGAAAATTTTAATATTTTG-AAAT-AAAACGAGGTTGGAGTATCCTCTCGAAAATAATGGGGT 1 GATGAAAATTTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCC-CTCGAAAATAATGAGGT * 3924635 TAGAGTATCTCCGA 65 TGGAGTATCTCCGA * * ** * * * 3924649 GGTGAAAAATTTAATATTTCAAAAATAAAAATGGGGTTGGAGTATCCCCTCAAAAATAATGTGGT 1 GATGAAAATTTTAATATTTTGAAAATAAAAACGGGGTTGGAGTAT-CCCTCGAAAATAATGAGGT * * 3924714 TGGAGTGTCTTCGA 65 TGGAGTATCTCCGA ** 3924728 GATGAAAATTTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCTCGAAAATAACAAGGTT 1 GATGAAAATTTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCTCGAAAATAATGAGGTT 3924793 GGAGTATC 66 GGAGTATC 3924801 CCTAAGATGA Statistics Matches: 128, Mismatches: 21, Indels: 5 0.83 0.14 0.03 Matches are distributed among these distances: 77 17 0.13 78 27 0.21 79 82 0.64 80 2 0.02 ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30 Consensus pattern (78 bp): GATGAAAATTTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCTCGAAAATAATGAGGTT GGAGTATCTCCGA Found at i:3924809 original size:78 final size:78 Alignment explanation

Indices: 3924554--3924812 Score: 274 Period size: 79 Copynumber: 3.3 Consensus size: 78 3924544 TTGAATACAG * * * 3924554 GGTTAGAGTAACCCCAATGATGAAAATTTTAATATTTTG-AAAT-AAAACGAGGTTGGAGTATCC 1 GGTTAGAGTATCCCTAA-GATGAAAATTTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCC * 3924617 TCTCGAAAATAATGG 65 -CTCGAAAATAATGA * * * ** * 3924632 GGTTAGAGTATCTCC-GAGGTGAAAAATTTAATATTTCAAAAATAAAAATGGGGTTGGAGTATCC 1 GGTTAGAGTATC-CCTAAGATGAAAATTTTAATATTTTGAAAATAAAAACGGGGTTGGAGTAT-C * * 3924696 CCTCAAAAATAATGT 64 CCTCGAAAATAATGA * * * * 3924711 GGTTGGAGTGT-CTTCGAGATGAAAATTTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCC 1 GGTTAGAGTATCCCT-AAGATGAAAATTTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCC ** 3924775 CTCGAAAATAACAA 65 CTCGAAAATAATGA * 3924789 GGTTGGAGTATCCCTAAGATGAAA 1 GGTTAGAGTATCCCTAAGATGAAA 3924813 GATGACAAAT Statistics Matches: 149, Mismatches: 25, Indels: 14 0.79 0.13 0.07 Matches are distributed among these distances: 77 18 0.12 78 46 0.31 79 83 0.56 80 2 0.01 ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29 Consensus pattern (78 bp): GGTTAGAGTATCCCTAAGATGAAAATTTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCCC TCGAAAATAATGA Found at i:3924877 original size:51 final size:51 Alignment explanation

Indices: 3924812--3924908 Score: 133 Period size: 51 Copynumber: 1.9 Consensus size: 51 3924802 CTAAGATGAA * * 3924812 AGATGACAAATTTAATATTTTGGAAATAAAAATAAGGTTAGAGTATCCTTG 1 AGATGACAAATTTAATATTTTGAAAATAAAAACAAGGTTAGAGTATCCTTG * ** 3924863 AGATGA-AAACTTTAATATTTTGAAAATTAAAACGGGGTTAGAGTAT 1 AGATGACAAA-TTTAATATTTTGAAAATAAAAACAAGGTTAGAGTAT 3924909 TCCCTTGAAA Statistics Matches: 40, Mismatches: 5, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 50 3 0.08 51 37 0.93 ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33 Consensus pattern (51 bp): AGATGACAAATTTAATATTTTGAAAATAAAAACAAGGTTAGAGTATCCTTG Found at i:3926493 original size:13 final size:13 Alignment explanation

Indices: 3926475--3926499 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3926465 CATTATGCTT 3926475 TGTATCGATACAA 1 TGTATCGATACAA 3926488 TGTATCGATACA 1 TGTATCGATACA 3926500 TGCATAATTG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:3926575 original size:20 final size:20 Alignment explanation

Indices: 3926550--3926613 Score: 79 Period size: 20 Copynumber: 3.5 Consensus size: 20 3926540 CTACCACTGT 3926550 TTGTATCGATACATGGCACA 1 TTGTATCGATACATGGCACA 3926570 TTGTATCGAT--A---CA-A 1 TTGTATCGATACATGGCACA 3926584 -TGTATCGATACATGGCACA 1 TTGTATCGATACATGGCACA 3926603 TTGTATCGATA 1 TTGTATCGATA 3926614 TAATGTATTG Statistics Matches: 37, Mismatches: 0, Indels: 14 0.73 0.00 0.27 Matches are distributed among these distances: 13 9 0.24 14 1 0.03 15 3 0.08 18 3 0.08 19 1 0.03 20 20 0.54 ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33 Consensus pattern (20 bp): TTGTATCGATACATGGCACA Found at i:3926588 original size:33 final size:33 Alignment explanation

Indices: 3926551--3926648 Score: 151 Period size: 33 Copynumber: 3.0 Consensus size: 33 3926541 TACCACTGTT 3926551 TGTATCGATACATGGCACATTGTATCGATACAA 1 TGTATCGATACATGGCACATTGTATCGATACAA * 3926584 TGTATCGATACATGGCACATTGTATCGATATAA 1 TGTATCGATACATGGCACATTGTATCGATACAA * ** * 3926617 TGTATTGATACATGATAAATTGTATCGATACA 1 TGTATCGATACATGGCACATTGTATCGATACA 3926649 TTGCTTCAAA Statistics Matches: 59, Mismatches: 6, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 33 59 1.00 ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34 Consensus pattern (33 bp): TGTATCGATACATGGCACATTGTATCGATACAA Found at i:3926589 original size:13 final size:13 Alignment explanation

Indices: 3926571--3926595 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3926561 CATGGCACAT 3926571 TGTATCGATACAA 1 TGTATCGATACAA 3926584 TGTATCGATACA 1 TGTATCGATACA 3926596 TGGCACATTG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:3928878 original size:13 final size:13 Alignment explanation

Indices: 3928860--3928885 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 3928850 CATTATTCAA 3928860 TGTATCGATACAT 1 TGTATCGATACAT 3928873 TGTATCGATACAT 1 TGTATCGATACAT 3928886 CGATCTTTGT 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:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:3928949 original size:20 final size:20 Alignment explanation

Indices: 3928924--3929011 Score: 93 Period size: 20 Copynumber: 4.8 Consensus size: 20 3928914 TTTACCCAGA * 3928924 TGTATCGATACATT-TTGCAT 1 TGTATCGATACATTGCT-CAT 3928944 TGTATCGATACATTGCTCAT 1 TGTATCGATACATTGCTCAT 3928964 TGTATCGATA-A------AT 1 TGTATCGATACATTGCTCAT 3928977 TGTATCGATACATTGCTCAT 1 TGTATCGATACATTGCTCAT * 3928997 TGTATTGATACATTG 1 TGTATCGATACATTG 3929012 TATCGATACA Statistics Matches: 58, Mismatches: 2, Indels: 16 0.76 0.03 0.21 Matches are distributed among these distances: 13 12 0.21 14 1 0.02 19 1 0.02 20 43 0.74 21 1 0.02 ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42 Consensus pattern (20 bp): TGTATCGATACATTGCTCAT Found at i:3928984 original size:33 final size:33 Alignment explanation

Indices: 3928942--3929023 Score: 146 Period size: 33 Copynumber: 2.5 Consensus size: 33 3928932 TACATTTTGC 3928942 ATTGTATCGATACATTGCTCATTGTATCGATAA 1 ATTGTATCGATACATTGCTCATTGTATCGATAA * * 3928975 ATTGTATCGATACATTGCTCATTGTATTGATAC 1 ATTGTATCGATACATTGCTCATTGTATCGATAA 3929008 ATTGTATCGATACATT 1 ATTGTATCGATACATT 3929024 CAGGCATTTT Statistics Matches: 47, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 33 47 1.00 ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41 Consensus pattern (33 bp): ATTGTATCGATACATTGCTCATTGTATCGATAA Found at i:3929010 original size:13 final size:13 Alignment explanation

Indices: 3928961--3929023 Score: 66 Period size: 13 Copynumber: 5.3 Consensus size: 13 3928951 ATACATTGCT 3928961 CATTGTATCGATA 1 CATTGTATCGATA * 3928974 AATTGTATCGATA 1 CATTGTATCGATA 3928987 CATTG---C--T- 1 CATTGTATCGATA * 3928994 CATTGTATTGATA 1 CATTGTATCGATA 3929007 CATTGTATCGATA 1 CATTGTATCGATA 3929020 CATT 1 CATT 3929024 CAGGCATTTT Statistics Matches: 40, Mismatches: 4, Indels: 12 0.71 0.07 0.21 Matches are distributed among these distances: 7 5 0.12 8 1 0.03 10 1 0.03 12 1 0.03 13 32 0.80 ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41 Consensus pattern (13 bp): CATTGTATCGATA Found at i:3931408 original size:51 final size:50 Alignment explanation

Indices: 3931232--3931408 Score: 189 Period size: 51 Copynumber: 3.5 Consensus size: 50 3931222 ATTTCTAGAT * * * 3931232 TTTTCAT-CTCGGGGATACTCCAA-TCCCAGTTTCATTTCCAAAACA-TCAA 1 TTTTCATAATCGGGGATACTCCAACTCCGA-TTTTATTTCCAAAACACT-AA * * * ** 3931281 TTTTTCTTAATCGGGGATACTCCAACTCTGATTTTATTTCTAAAACACCCA 1 -TTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAA * * 3931332 TTTTCCATAATCAGGGATACTCCAACTCCGATTTTATTTCCAAAACACTGAC 1 TTTT-CATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACT-AA * 3931384 TTTTCACAATCGGGGATACTCCAAC 1 TTTTCATAATCGGGGATACTCCAAC 3931409 CCTGTTATTT Statistics Matches: 105, Mismatches: 17, Indels: 9 0.80 0.13 0.07 Matches are distributed among these distances: 50 10 0.10 51 88 0.84 52 7 0.07 ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34 Consensus pattern (50 bp): TTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAA Found at i:3931586 original size:79 final size:79 Alignment explanation

Indices: 3931345--3931642 Score: 408 Period size: 79 Copynumber: 3.8 Consensus size: 79 3931335 TCCATAATCA * * * * 3931345 GGGATACTCCAACTCCGATTTTATTTCCAAAACA-CTGACTTTTCACAATCGGGGATACTCCAAC 1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATC-AATTTTTCACAATCGGGGATACTCCAAC * 3931409 CCTGTTATTTTAGAG 65 CCCGTTATTTTAGAG * * 3931424 GGGACACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTT--C-ATCGGGGATACTCCAACC 1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC * 3931486 CCGTTATTTTCGAG 66 CCGTTATTTTAGAG * * 3931500 GGGATACTCCAACCCTGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACC 1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC 3931565 CCGTTATTTCT-GAG 66 CCGTTATTT-TAGAG * * * * * 3931579 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATATTCCAAC 1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC 3931643 TCCGATTTTA Statistics Matches: 195, Mismatches: 19, Indels: 10 0.87 0.08 0.04 Matches are distributed among these distances: 76 70 0.36 77 1 0.01 79 122 0.63 80 2 0.01 ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31 Consensus pattern (79 bp): GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC CCGTTATTTTAGAG Found at i:3931750 original size:53 final size:51 Alignment explanation

Indices: 3931578--3931742 Score: 222 Period size: 51 Copynumber: 3.2 Consensus size: 51 3931568 TTATTTCTGA * * 3931578 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATC 1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATC * * * * * 3931629 GGGGATATTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATC 1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATC * * * 3931680 GGGGATACTCCAACCCCGATTTTTTATTTCTAGAACACCGATTTTCCATAATC 1 GGGGATACTCCAACCCCGA--TTTTATTTCTAAAACACCAATTTTCCACAATC 3931733 GGGGATACTC 1 GGGGATACTC 3931743 TAGCCCCGTT Statistics Matches: 97, Mismatches: 15, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 51 61 0.63 53 36 0.37 ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32 Consensus pattern (51 bp): GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATC Found at i:3931763 original size:104 final size:102 Alignment explanation

Indices: 3931578--3931765 Score: 252 Period size: 104 Copynumber: 1.8 Consensus size: 102 3931568 TTATTTCTGA * 3931578 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATATTCCAAC 1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC * * 3931643 TCCGATTTTATTTCCAAAACACTAATTTTTCACAATC 66 CCCGATTTTATCTCCAAAACACTAATTTTTCACAATC * * * * * * 3931680 GGGGATACTCCAACCCCGATTTTTTATTTCTAGAACACCGATTTTCCATAATCGGGGATACTCTA 1 GGGGATACTCCAACCCCG--GTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCA * 3931745 GCCCCG-TTGTTATCTCCAAAA 64 ACCCCGATT-TTATCTCCAAAA 3931766 TATTAAATTT Statistics Matches: 73, Mismatches: 10, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 102 18 0.25 103 2 0.03 104 53 0.73 ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31 Consensus pattern (102 bp): GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC CCCGATTTTATCTCCAAAACACTAATTTTTCACAATC Found at i:3939103 original size:20 final size:19 Alignment explanation

Indices: 3939057--3939113 Score: 69 Period size: 19 Copynumber: 2.9 Consensus size: 19 3939047 TTGTATCGAT * * 3939057 ACATTGTATCGATTCATGT 1 ACATTGTATCGATACATGC * 3939076 TCATTGTATCGATACATGC 1 ACATTGTATCGATACATGC * 3939095 ACAATTGTATTGATACATG 1 AC-ATTGTATCGATACATG 3939114 AAACTGGCAG Statistics Matches: 32, Mismatches: 5, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 19 17 0.53 20 15 0.47 ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39 Consensus pattern (19 bp): ACATTGTATCGATACATGC Found at i:3939204 original size:33 final size:33 Alignment explanation

Indices: 3939143--3939207 Score: 85 Period size: 33 Copynumber: 2.0 Consensus size: 33 3939133 TATTACTATT * * 3939143 TGTATCGATACATGGCACATTATATCGATACAA 1 TGTATCGATACATGACAAATTATATCGATACAA * * * 3939176 TGTATCGATACATGATAAATTGTGTCGATACA 1 TGTATCGATACATGACAAATTATATCGATACA 3939208 TTGCCTCAAA Statistics Matches: 27, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 33 27 1.00 ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32 Consensus pattern (33 bp): TGTATCGATACATGACAAATTATATCGATACAA Found at i:3941039 original size:22 final size:21 Alignment explanation

Indices: 3941011--3941065 Score: 67 Period size: 20 Copynumber: 2.6 Consensus size: 21 3941001 ATGAGAAATA 3941011 TATCGATACAATTGTAAGCATG 1 TATCGATACAATT-TAAGCATG *** 3941033 TATCGATAC-ATTTACTTATG 1 TATCGATACAATTTAAGCATG 3941053 TATCGATACAATT 1 TATCGATACAATT 3941066 CCTTGGCAGT Statistics Matches: 29, Mismatches: 3, Indels: 3 0.83 0.09 0.09 Matches are distributed among these distances: 20 14 0.48 21 6 0.21 22 9 0.31 ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38 Consensus pattern (21 bp): TATCGATACAATTTAAGCATG Found at i:3944956 original size:54 final size:54 Alignment explanation

Indices: 3944889--3945071 Score: 147 Period size: 54 Copynumber: 3.3 Consensus size: 54 3944879 ACATTGAAGA 3944889 ATGTATCGATACATTTTGGTCAAAAACCCAGAATATATTGATACAATTGTAGGC 1 ATGTATCGATACATTTTGGTCAAAAACCCAGAATATATTGATACAATTGTAGGC ** * * * * * * ** * 3944943 ATGTATCGATACA-TTTGGT-AATGTATCGATACATTTTCTTGGCAGTATACAGGGT-GGTT 1 ATGTATCGATACATTTTGGTCAA-AAACCCAGA-A-TATATT-G-A-TACA-ATTGTAGG-C * * * 3945002 TTGTATCGATACATTTTGGTCAAAAACTCAGAATATATCGATACAATTGTAGGC 1 ATGTATCGATACATTTTGGTCAAAAACCCAGAATATATTGATACAATTGTAGGC 3945056 ATGTATCGATACATTT 1 ATGTATCGATACATTT 3945072 GGTAATGTAT Statistics Matches: 92, Mismatches: 26, Indels: 22 0.66 0.19 0.16 Matches are distributed among these distances: 52 2 0.02 53 10 0.11 54 32 0.35 55 9 0.10 56 2 0.02 57 2 0.02 58 8 0.09 59 16 0.17 60 9 0.10 61 2 0.02 ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36 Consensus pattern (54 bp): ATGTATCGATACATTTTGGTCAAAAACCCAGAATATATTGATACAATTGTAGGC Found at i:3945065 original size:22 final size:21 Alignment explanation

Indices: 3945037--3945088 Score: 63 Period size: 20 Copynumber: 2.5 Consensus size: 21 3945027 ACTCAGAATA * 3945037 TATCGATACAATTGTAGG-CATG 1 TATCGATACAATT-T-GGTAATG 3945059 TATCGATAC-ATTTGGTAATG 1 TATCGATACAATTTGGTAATG 3945079 TATCGATACA 1 TATCGATACA 3945089 TTTTCTTGGC Statistics Matches: 27, Mismatches: 1, Indels: 5 0.82 0.03 0.15 Matches are distributed among these distances: 19 2 0.07 20 13 0.48 21 3 0.11 22 9 0.33 ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35 Consensus pattern (21 bp): TATCGATACAATTTGGTAATG Found at i:3945088 original size:113 final size:113 Alignment explanation

Indices: 3944890--3945130 Score: 464 Period size: 113 Copynumber: 2.1 Consensus size: 113 3944880 CATTGAAGAA * 3944890 TGTATCGATACATTTTGGTCAAAAACCCAGAATATATTGATACAATTGTAGGCATGTATCGATAC 1 TGTATCGATACATTTTGGTCAAAAACCCAGAATATATCGATACAATTGTAGGCATGTATCGATAC 3944955 ATTTGGTAATGTATCGATACATTTTCTTGGCAGTATACAGGGTGGTTT 66 ATTTGGTAATGTATCGATACATTTTCTTGGCAGTATACAGGGTGGTTT * 3945003 TGTATCGATACATTTTGGTCAAAAACTCAGAATATATCGATACAATTGTAGGCATGTATCGATAC 1 TGTATCGATACATTTTGGTCAAAAACCCAGAATATATCGATACAATTGTAGGCATGTATCGATAC 3945068 ATTTGGTAATGTATCGATACATTTTCTTGGCAGTATACAGGGTGGTTT 66 ATTTGGTAATGTATCGATACATTTTCTTGGCAGTATACAGGGTGGTTT 3945116 TGTATCGATACATTT 1 TGTATCGATACATTT 3945131 ACTGTTTGCA Statistics Matches: 126, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 113 126 1.00 ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37 Consensus pattern (113 bp): TGTATCGATACATTTTGGTCAAAAACCCAGAATATATCGATACAATTGTAGGCATGTATCGATAC ATTTGGTAATGTATCGATACATTTTCTTGGCAGTATACAGGGTGGTTT Found at i:3949867 original size:158 final size:157 Alignment explanation

Indices: 3949676--3949975 Score: 372 Period size: 158 Copynumber: 1.9 Consensus size: 157 3949666 AAGGGTATTT * * * * * 3949676 TAGTAATTTTCTTCAAAATTGAGTCCTAGGTAGTCACCTGGTCACTTTTATGCGAAAAGTTTACA 1 TAGTAATTTTCCTCAAAACTGAGTCCTAGGTAGTCACCGGGTCACTTTTATGCCAAAAGTATACA * ** 3949741 TTTAGGATAGGTTTATCCTTTTAGGATTTTTTTTTTGT-TTCTTCTAGCGTTAC-GAAGATACTT 66 TTTAGGATAGGTTCATCCTTTTAGGATTTTTTTTTCATATTCTT-TAGCGTTACTG-AGATAC-T 3949804 TCACATTGAAAGTATACCCTAGAAGCATTC 128 TCACATTGAAAGTATACCCTAGAAGCATTC * * * ** * 3949834 TAGTAATTTTCC-CTAAAACTGAGTCCTAGGTAGTTATCGGGTCGCTTTTATGCCAAGGGTATAT 1 TAGTAATTTTCCTC-AAAACTGAGTCCTAGGTAGTCACCGGGTCACTTTTATGCCAAAAGTATAC * * * 3949898 GTTTAGGATAGGTTCATCCTTTTATGATTTTTTTTTCATATTCTTTAGGGTTACTGAGATACTTC 65 ATTTAGGATAGGTTCATCCTTTTAGGATTTTTTTTTCATATTCTTTAGCGTTACTGAGATACTTC * * 3949963 ACGTTGAAGGTAT 130 ACATTGAAAGTAT 3949976 CCTTCGGGGC Statistics Matches: 120, Mismatches: 19, Indels: 7 0.82 0.13 0.05 Matches are distributed among these distances: 157 15 0.12 158 99 0.82 159 6 0.05 ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42 Consensus pattern (157 bp): TAGTAATTTTCCTCAAAACTGAGTCCTAGGTAGTCACCGGGTCACTTTTATGCCAAAAGTATACA TTTAGGATAGGTTCATCCTTTTAGGATTTTTTTTTCATATTCTTTAGCGTTACTGAGATACTTCA CATTGAAAGTATACCCTAGAAGCATTC Found at i:3950909 original size:19 final size:19 Alignment explanation

Indices: 3950885--3950955 Score: 106 Period size: 19 Copynumber: 3.7 Consensus size: 19 3950875 CACACCCAGA 3950885 TGTATCGATACATATTCAT 1 TGTATCGATACATATTCAT 3950904 TGTATCGATACATATTCAT 1 TGTATCGATACATATTCAT *** 3950923 TGTATCGATACATGCACAAT 1 TGTATCGATACATATTC-AT 3950943 TGTATCGATACAT 1 TGTATCGATACAT 3950956 GAAACTGGCA Statistics Matches: 48, Mismatches: 3, Indels: 1 0.92 0.06 0.02 Matches are distributed among these distances: 19 33 0.69 20 15 0.31 ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38 Consensus pattern (19 bp): TGTATCGATACATATTCAT Found at i:3957260 original size:20 final size:20 Alignment explanation

Indices: 3957222--3957261 Score: 55 Period size: 20 Copynumber: 1.9 Consensus size: 20 3957212 TTTCAAATTT 3957222 CTTCATTTTCACTTCAAAATA 1 CTTCATTTTCAC-TCAAAATA 3957243 CTTCATTTTTCA-TCAAAAT 1 CTTCA-TTTTCACTCAAAAT 3957262 TATCAACAAA Statistics Matches: 18, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 20 7 0.39 21 5 0.28 22 6 0.33 ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45 Consensus pattern (20 bp): CTTCATTTTCACTCAAAATA Found at i:3958986 original size:31 final size:28 Alignment explanation

Indices: 3958944--3959030 Score: 95 Period size: 31 Copynumber: 2.9 Consensus size: 28 3958934 AGTAAATTTT 3958944 TTATCAAGGGGAAGAAAATCTTTTAAACAA 1 TTATCAAGGGG-AGAAAAT-TTTTAAACAA * * 3958974 TTATCAAAGGGGAGAAATTTTTTTTAAACGA 1 TTATC-AAGGGGAGAAA--ATTTTTAAACAA 3959005 TTATCAA-GGGAGAGAAATTTTTAAAC 1 TTATCAAGGGGAGA-AAATTTTTAAAC 3959031 GAGAACCTTA Statistics Matches: 50, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 28 9 0.18 29 6 0.12 30 14 0.28 31 20 0.40 32 1 0.02 ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31 Consensus pattern (28 bp): TTATCAAGGGGAGAAAATTTTTAAACAA Found at i:3959613 original size:20 final size:19 Alignment explanation

Indices: 3959567--3959623 Score: 78 Period size: 19 Copynumber: 2.9 Consensus size: 19 3959557 TTATATCGAT * 3959567 ACATTGTATCGATACATGT 1 ACATTGTATCGATACATGC * * 3959586 TCATTGTATCAATACATGC 1 ACATTGTATCGATACATGC 3959605 ACAATTGTATCGATACATG 1 AC-ATTGTATCGATACATG 3959624 AAACTGGCAG Statistics Matches: 32, Mismatches: 5, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 19 17 0.53 20 15 0.47 ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35 Consensus pattern (19 bp): ACATTGTATCGATACATGC Found at i:3962069 original size:51 final size:51 Alignment explanation

Indices: 3962003--3962429 Score: 320 Period size: 51 Copynumber: 8.4 Consensus size: 51 3961993 TGAAAATAAT * * * ** 3962003 GGGGTTGGAGCATCCCCAATTATGAGAAATTAATATTTTAGAAATAAGGCC 1 GGGGTTGGAGTATCCCCGATTGTGAGAAATTAATATTTTAGAAATAAAACC * * * * ** 3962054 GGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAAAGTC 1 GGGGTTGGAGTATCCCCGATTGTGAGAAATTAATATTTTAGAAATAAAACC * ** * * 3962105 GGGGTTGGAGTATCCCCGATTATG-GAGAATTGGTGTTTTAAAAATAAAACC 1 GGGGTTGGAGTATCCCCGATTGTGAGA-AATTAATATTTTAGAAATAAAACC * ** * * * 3962156 GGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGGAAATAAAATC 1 GGGGTTGGAGTATCCCCGATTGTGAGAAATTAATATTTTAGAAATAAAACC * * * * * * * 3962207 GGAGTTGGAGTATCCCCAATTGTGAAAAATTAGTGTTTT-GAAAAAACAATC 1 GGGGTTGGAGTATCCCCGATTGTGAGAAATTAATATTTTAGAAATAA-AACC * * * * * * * * 3962258 AGAGTTAGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATC 1 GGGGTTGGAGTATCCCCGATTGTGAGAAATTAATATTTTAGAAATAAAACC * * * *** * * 3962309 GGAGTTGGAATATCCCCGATTATG-GAAAATGGGTGTTTTAGAAATAAAATC 1 GGGGTTGGAGTATCCCCGATTGTGAG-AAATTAATATTTTAGAAATAAAACC * ** * * * * 3962360 GGAGTTGGAGTATCCCCGATTAAGAGAAATTGATGTTTTGGAAATGAAACC 1 GGGGTTGGAGTATCCCCGATTGTGAGAAATTAATATTTTAGAAATAAAACC * * 3962411 GGGATTAGAGTATCCCCGA 1 GGGGTTGGAGTATCCCCGA 3962430 GATGAAAAAT Statistics Matches: 315, Mismatches: 55, Indels: 12 0.82 0.14 0.03 Matches are distributed among these distances: 50 8 0.03 51 299 0.95 52 8 0.03 ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29 Consensus pattern (51 bp): GGGGTTGGAGTATCCCCGATTGTGAGAAATTAATATTTTAGAAATAAAACC Found at i:3962099 original size:130 final size:129 Alignment explanation

Indices: 3961824--3962122 Score: 309 Period size: 130 Copynumber: 2.3 Consensus size: 129 3961814 ACAAGAAATT * * * * 3961824 TAATATTTTGGAGATAATAACGGGGTTGGAGTATCCCC-TCGAAAAAAACGGGGTTGGGGTATCC 1 TAATATTTTGGAAATAA-ATCGGGGTTGGAGTATCCCCGTCGAAAAAAACGGGGTTGGAGCATCC * * * * 3961888 CCGATTGTGAAAAATCGATGATTTAGAAATAAGGCAAGGGTTAAAGTGTCCCCGATTATAGAAAA 65 CCAATTATGAAAAATCAATGATTTAGAAATAAGGCAAGGGTTAAAGTATCCCCGATTATAGAAAA * *** * * * 3961953 TAGATGTTTCAAAAATAACATCGGGATTGGAGTATCCCCGT-GAAAATAATGGGGTTGGAGCATC 1 TA-ATATTTTGGAAATAA-ATCGGGGTTGGAGTATCCCCGTCGAAAAAAACGGGGTTGGAGCATC * * ** * * * 3962017 CCCAATTATGAGAAATTAAT-ATTTTAGAAATAAGGCCGGGGTTGAAGTATCCCTGATTGT-GAG 64 CCCAATTATGAAAAATCAATGA-TTTAGAAATAAGGCAAGGGTTAAAGTATCCCCGATTATAGA- 3962080 AAA 127 AAA 3962083 TCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCG 1 T-AATATTTTGGAAATAAA-TCGGGGTTGGAGTATCCCCG 3962123 ATTATGGAGA Statistics Matches: 136, Mismatches: 28, Indels: 11 0.78 0.16 0.06 Matches are distributed among these distances: 129 6 0.04 130 128 0.94 131 2 0.01 ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27 Consensus pattern (129 bp): TAATATTTTGGAAATAAATCGGGGTTGGAGTATCCCCGTCGAAAAAAACGGGGTTGGAGCATCCC CAATTATGAAAAATCAATGATTTAGAAATAAGGCAAGGGTTAAAGTATCCCCGATTATAGAAAA Found at i:3962179 original size:102 final size:102 Alignment explanation

Indices: 3962003--3962429 Score: 444 Period size: 102 Copynumber: 4.2 Consensus size: 102 3961993 TGAAAATAAT * * * * * ** * * 3962003 GGGGTTGGAGCATCCCCAATTAT-GAGAAATTAATATTTTAGAAATAAGGCCGGGGTTGAAGTAT 1 GGGGTTGGAGTATCCCCGATTATGGA-AAATTAGTGTTTTAAAAATAAAACCGGAGTTGGAGTAT * * * * 3962067 CCCTGATTGTGAGAAATCAATATTTTGGAAATAAAGTC 65 CCCCGATTGTGAAAAATCAATGTTTTGGAAATAAAATC * * * 3962105 GGGGTTGGAGTATCCCCGATTATGGAGAATTGGTGTTTTAAAAATAAAACCGGGGTTGGAGTATC 1 GGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAAAAATAAAACCGGAGTTGGAGTATC * 3962170 CCCGATTGTGAAAAATCGATGTTTTGGAAATAAAATC 66 CCCGATTGTGAAAAATCAATGTTTTGGAAATAAAATC * * * * * * * * 3962207 GGAGTTGGAGTATCCCCAATTGTGAAAAATTAGTGTTTTGAAAAA-ACAATCAGAGTTAGAGTAT 1 GGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTT-AAAAATAAAACCGGAGTTGGAGTAT * * 3962271 CCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATC 65 CCCCGATTGTGAAAAATCAATGTTTTGGAAATAAAATC * * ** * * 3962309 GGAGTTGGAATATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGAGTTGGAGTATC 1 GGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAAAAATAAAACCGGAGTTGGAGTATC ** * ** * * 3962374 CCCGATTAAGAGAAATTGATGTTTTGGAAATGAAACC 66 CCCGATTGTGAAAAATCAATGTTTTGGAAATAAAATC * * 3962411 GGGATTAGAGTATCCCCGA 1 GGGGTTGGAGTATCCCCGA 3962430 GATGAAAAAT Statistics Matches: 272, Mismatches: 50, Indels: 6 0.83 0.15 0.02 Matches are distributed among these distances: 101 4 0.01 102 261 0.96 103 7 0.03 ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29 Consensus pattern (102 bp): GGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAAAAATAAAACCGGAGTTGGAGTATC CCCGATTGTGAAAAATCAATGTTTTGGAAATAAAATC Found at i:3962419 original size:153 final size:151 Alignment explanation

Indices: 3962014--3962439 Score: 433 Period size: 153 Copynumber: 2.8 Consensus size: 151 3962004 GGGTTGGAGC * * ** * *** * * * 3962014 ATCCCCAATTATGAGAAATTAATATTTTAGAAATAAGGCCGGGGTTGAAGTATCCCTGATTGTGA 1 ATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTGTGA * * * * * * * 3962079 GAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCGATTATGGAGAATTGGTGTTTT 66 GAAAT-TATGTTTTGGAAATAAA-TCGGGATTAGAGTATCCCCGATTATGAAAAATTAGTGTTTT * * 3962144 AAAAATAAAACCGGGGTTGGAGT 129 AAAAATAAAACCGGAGTTGGAAT * * * 3962167 ATCCCCGATTGTGAAAAATCGATGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCAATTGTGA 1 ATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTGTGA * * * * * 3962232 AAAATTAGTGTTTTGAAAAAACAATC-AGAGTTAGAGTATCCCCGATTGTGAAAAATTAGTGTTT 66 GAAATTA-TGTTTTGGAAATA-AATCGGGA-TTAGAGTATCCCCGATTATGAAAAATTAGTGTTT ** * 3962296 TGGAAATAAAATCGGAGTTGGAAT 128 TAAAAATAAAACCGGAGTTGGAAT * * * ** 3962320 ATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGA 1 ATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTGTGA * * 3962385 GAAATTGATGTTTTGGAAATGAAACCGGGATTAGAGTATCCCCGA-GATGAAAAAT 66 GAAATT-ATGTTTTGGAAAT-AAATCGGGATTAGAGTATCCCCGATTATGAAAAAT 3962440 CTAGAAATTT Statistics Matches: 221, Mismatches: 46, Indels: 13 0.79 0.16 0.05 Matches are distributed among these distances: 152 10 0.05 153 205 0.93 154 6 0.03 ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29 Consensus pattern (151 bp): ATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTGTGA GAAATTATGTTTTGGAAATAAATCGGGATTAGAGTATCCCCGATTATGAAAAATTAGTGTTTTAA AAATAAAACCGGAGTTGGAAT Found at i:3964870 original size:13 final size:13 Alignment explanation

Indices: 3964848--3964905 Score: 53 Period size: 13 Copynumber: 4.0 Consensus size: 13 3964838 GGCAGTAGCT * 3964848 TTGTAGCGATACA 1 TTGTATCGATACA 3964861 TTGTATCGATACAAAA 1 TTGTATCGATAC---A 3964877 CTTATGTATCGATACA 1 --T-TGTATCGATACA 3964893 TTGTATCGATACA 1 TTGTATCGATACA 3964906 GTTACTATCT Statistics Matches: 38, Mismatches: 1, Indels: 12 0.75 0.02 0.24 Matches are distributed among these distances: 13 23 0.61 14 1 0.03 16 2 0.05 18 1 0.03 19 11 0.29 ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34 Consensus pattern (13 bp): TTGTATCGATACA Found at i:3968509 original size:111 final size:109 Alignment explanation

Indices: 3968294--3968620 Score: 325 Period size: 111 Copynumber: 2.9 Consensus size: 109 3968284 GACTTGAAAG * * * * * * * 3968294 AACATCAAATTTGTCTGATTTTCAAAGAAATTTATGTTTTATACAACTTGATTCATTCAAGCCTA 1 AACAACAAATTTGTCTGA-TTTCAAAGAAA-TCATGTTTTATAAAACATGATCCATTCATGCTTA * * * 3968359 GGAAAATGGGGCATATATCTTATCAGTTTTGAAATTTTTAAGCCAAC 64 GGAAAAT-GGGCATGTATCTTATCAATTTTAAAATTTTTAAGCCAAC * 3968406 AACACCAAATTTGTCTGATTTCAAAGAAATCCATGTTTTATAAAACATGATCCATTCATGCTTAG 1 AACAACAAATTTGTCTGATTTCAAAGAAAT-CATGTTTTATAAAACATGATCCATTCATGCTTAG * * 3968471 GAAAATAGGGCATGTATCCTA-CTAATTTTAAAAATTTTAAGCCAAC 65 GAAAAT-GGGCATGTATCTTATC-AATTTTAAAATTTTTAAGCCAAC * * * * * * * ** * * 3968517 AGCAATAAATTTGTCTAATTTAAAAAAAAAATCATGTTTTATATGACCA-GATCTTTTCGTCCTT 1 AACAACAAATTTGTCTGATTT--CAAAGAAATCATGTTTTATA-AAACATGATCCATTCATGCTT * 3968581 AGGAAAATGGGTCATGTATCTTATGAATTTTAAAATTTTT 63 AGGAAAATGGG-CATGTATCTTATCAATTTTAAAATTTTT 3968621 TAGCAAATCA Statistics Matches: 180, Mismatches: 28, Indels: 14 0.81 0.13 0.06 Matches are distributed among these distances: 110 2 0.01 111 97 0.54 112 71 0.39 113 10 0.06 ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37 Consensus pattern (109 bp): AACAACAAATTTGTCTGATTTCAAAGAAATCATGTTTTATAAAACATGATCCATTCATGCTTAGG AAAATGGGCATGTATCTTATCAATTTTAAAATTTTTAAGCCAAC Found at i:3969723 original size:119 final size:120 Alignment explanation

Indices: 3969525--3969824 Score: 338 Period size: 119 Copynumber: 2.5 Consensus size: 120 3969515 AGTCTTGGGT * * * 3969525 TCACCCAAGTCATTGTTTAGGTTTCTCATTTTATCTAGACCATTTAGTTGAGTCTTGGTTTCACC 1 TCACCCAAGTCATTGTTTAGGTTTCTCAGTTTATCCAAACCATTTAGTTGAGTCTTGGTTTCACC * * * 3969590 CAAGTCATTGTTTAGGATTT-T-AGTTTTATTTAGGCCACTTAGTTGAGTCATGATC 66 CAAGTCAGTATTTAGG-TTTCTGA-TTTTATCTAGGCCACTTAGTTGAGTCATGATC ** 3969645 TCACCCAAGTCATTGTTTAGGTTT-TTGGTTTATCCAAACCATTTAGTTGAGTCTTGGTTTCACC 1 TCACCCAAGTCATTGTTTAGGTTTCTCAGTTTATCCAAACCATTTAGTTGAGTCTTGGTTTCACC * * * * * 3969709 CAAGTTAGTATTTAGGTTTCTGATTTTATCTAGGCCATTTAGTTGAGTCTTGGTT 66 CAAGTCAGTATTTAGGTTTCTGATTTTATCTAGGCCACTTAGTTGAGTCATGATC * * * * * ** * * * 3969764 TCACTCTAGTAATTATTTAGATTTCT-AGTTTAATCCAGGCTATTTTGTTGAGTTTTGGTTT 1 TCACCCAAGTCATTGTTTAGGTTTCTCAGTTT-ATCCAAACCATTTAGTTGAGTCTTGGTTT 3969825 TGCCTTAATC Statistics Matches: 152, Mismatches: 24, Indels: 8 0.83 0.13 0.04 Matches are distributed among these distances: 118 3 0.02 119 99 0.65 120 50 0.33 ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45 Consensus pattern (120 bp): TCACCCAAGTCATTGTTTAGGTTTCTCAGTTTATCCAAACCATTTAGTTGAGTCTTGGTTTCACC CAAGTCAGTATTTAGGTTTCTGATTTTATCTAGGCCACTTAGTTGAGTCATGATC Found at i:3969781 original size:60 final size:59 Alignment explanation

Indices: 3969506--3969824 Score: 343 Period size: 60 Copynumber: 5.3 Consensus size: 59 3969496 TATCCAAGCT * * * 3969506 ATTTAGTTTAGTCTTGGGTTCACCCAAGTCATTGTTTAGGTTTCTCATTTTATCTAGACC 1 ATTTAGTTGAGTCTTGGTTTCACCCAAGTCATTGTTTAGGTTTCT-ATTTTATCTAGGCC * 3969566 ATTTAGTTGAGTCTTGGTTTCACCCAAGTCATTGTTTAGGATTT-TAGTTTTATTTAGGCC 1 ATTTAGTTGAGTCTTGGTTTCACCCAAGTCATTGTTTAGG-TTTCTA-TTTTATCTAGGCC * * * * * ** * ** 3969626 ACTTAGTTGAGTCATGATCTCACCCAAGTCATTGTTTAGGTTTTTGGTTTATCCAAACC 1 ATTTAGTTGAGTCTTGGTTTCACCCAAGTCATTGTTTAGGTTTCTATTTTATCTAGGCC * * * 3969685 ATTTAGTTGAGTCTTGGTTTCACCCAAGTTAGTATTTAGGTTTCTGATTTTATCTAGGCC 1 ATTTAGTTGAGTCTTGGTTTCACCCAAGTCATTGTTTAGGTTTCT-ATTTTATCTAGGCC * * * * * * * * 3969745 ATTTAGTTGAGTCTTGGTTTCACTCTAGTAATTATTTAGATTTCTAGTTTAATCCAGGCT 1 ATTTAGTTGAGTCTTGGTTTCACCCAAGTCATTGTTTAGGTTTCTA-TTTTATCTAGGCC * * 3969805 ATTTTGTTGAGTTTTGGTTT 1 ATTTAGTTGAGTCTTGGTTT 3969825 TGCCTTAATC Statistics Matches: 217, Mismatches: 37, Indels: 10 0.82 0.14 0.04 Matches are distributed among these distances: 59 50 0.23 60 164 0.76 61 3 0.01 ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46 Consensus pattern (59 bp): ATTTAGTTGAGTCTTGGTTTCACCCAAGTCATTGTTTAGGTTTCTATTTTATCTAGGCC Found at i:3970135 original size:40 final size:40 Alignment explanation

Indices: 3970068--3970199 Score: 131 Period size: 40 Copynumber: 3.3 Consensus size: 40 3970058 TGTCCCTATT * * 3970068 AACTTTTCTCATCTTTTAACTTGTCGATTTCATCTCGGTC 1 AACTTTTCTCATCTATTAACTTATCGATTTCATCTCGGTC * * * * * 3970108 AACTTTTTTTATCTATTGACTTATCGATTTCATTTCAGTC 1 AACTTTTCTCATCTATTAACTTATCGATTTCATCTCGGTC * * * * * * 3970148 ATCTCTTCCCATCCATTAACTAATCGATTTCATCTTGGTC 1 AACTTTTCTCATCTATTAACTTATCGATTTCATCTCGGTC 3970188 AACTATTT-TCAT 1 AACT-TTTCTCAT 3970200 TGTTGACTTA Statistics Matches: 70, Mismatches: 21, Indels: 2 0.75 0.23 0.02 Matches are distributed among these distances: 40 68 0.97 41 2 0.03 ACGTcount: A:0.22, C:0.23, G:0.08, T:0.47 Consensus pattern (40 bp): AACTTTTCTCATCTATTAACTTATCGATTTCATCTCGGTC Found at i:3971530 original size:6 final size:6 Alignment explanation

Indices: 3971521--3971556 Score: 56 Period size: 6 Copynumber: 6.2 Consensus size: 6 3971511 TTTATGATTA * 3971521 TTAATT TTAATT TTAATT TTAATT TT-CTT TTAATT T 1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT T 3971557 GGGATTTTTT Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 5 4 0.15 6 23 0.85 ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69 Consensus pattern (6 bp): TTAATT Found at i:3972500 original size:16 final size:16 Alignment explanation

Indices: 3972475--3972527 Score: 63 Period size: 16 Copynumber: 3.3 Consensus size: 16 3972465 AATGTATGCA * * 3972475 GTTCAAATTATTCTAG 1 GTTCAGATTATTTTAG * 3972491 GTTCAGATTATTTTAT 1 GTTCAGATTATTTTAG 3972507 GTAT-AGATTATTTTAG 1 GT-TCAGATTATTTTAG 3972523 GTTCA 1 GTTCA 3972528 AGCTAAAGAT Statistics Matches: 31, Mismatches: 4, Indels: 4 0.79 0.10 0.10 Matches are distributed among these distances: 15 1 0.03 16 29 0.94 17 1 0.03 ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49 Consensus pattern (16 bp): GTTCAGATTATTTTAG Found at i:3985991 original size:51 final size:51 Alignment explanation

Indices: 3985936--3986047 Score: 215 Period size: 51 Copynumber: 2.2 Consensus size: 51 3985926 TGCTTTGATA 3985936 AAGGGGGAGAATTATATTATATCTAGGGGGAGAAAATCTCTTTAAACGATT 1 AAGGGGGAGAATTATATTATATCTAGGGGGAGAAAATCTCTTTAAACGATT * 3985987 AAGGGAGAGAATTATATTATATCTAGGGGGAGAAAATCTCTTTAAACGATT 1 AAGGGGGAGAATTATATTATATCTAGGGGGAGAAAATCTCTTTAAACGATT 3986038 AAGGGGGAGA 1 AAGGGGGAGA 3986048 TTTTTTTTCT Statistics Matches: 59, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 51 59 1.00 ACGTcount: A:0.38, C:0.07, G:0.28, T:0.27 Consensus pattern (51 bp): AAGGGGGAGAATTATATTATATCTAGGGGGAGAAAATCTCTTTAAACGATT Found at i:3986598 original size:13 final size:15 Alignment explanation

Indices: 3986566--3986603 Score: 53 Period size: 13 Copynumber: 2.7 Consensus size: 15 3986556 AACCCTTGAA * 3986566 TGTATCGATATGCCT 1 TGTATCGATATGCAT 3986581 TGTATCGAT-T-CAT 1 TGTATCGATATGCAT 3986594 TGTATCGATA 1 TGTATCGATA 3986604 CATATTCATT Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 13 11 0.52 14 1 0.05 15 9 0.43 ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42 Consensus pattern (15 bp): TGTATCGATATGCAT Found at i:3986612 original size:19 final size:19 Alignment explanation

Indices: 3986588--3986625 Score: 76 Period size: 19 Copynumber: 2.0 Consensus size: 19 3986578 CCTTGTATCG 3986588 ATTCATTGTATCGATACAT 1 ATTCATTGTATCGATACAT 3986607 ATTCATTGTATCGATACAT 1 ATTCATTGTATCGATACAT 3986626 GGACAATTGT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42 Consensus pattern (19 bp): ATTCATTGTATCGATACAT Found at i:3986636 original size:20 final size:19 Alignment explanation

Indices: 3986591--3986728 Score: 89 Period size: 20 Copynumber: 6.8 Consensus size: 19 3986581 TGTATCGATT ** 3986591 CATTGTATCGATACATATT 1 CATTGTATCGATACATAGA * 3986610 CATTGTATCGATACATGGA 1 CATTGTATCGATACATAGA * 3986629 CAATTGTATCGATATAT-GA 1 C-ATTGTATCGATACATAGA * * * * * * * 3986648 AACTAGCAGTAGCTACCCTACCA 1 CA-TTGTA-TCGATA-CATA-GA 3986671 CTATTTGTATCGATACATAGGA 1 C-AT-TGTATCGATACATA-GA 3986693 CATTGTATCGATACATAGGA 1 CATTGTATCGATACATA-GA 3986713 CATTGTATCGATACAT 1 CATTGTATCGATACAT 3986729 TGAATCAATA Statistics Matches: 91, Mismatches: 20, Indels: 15 0.72 0.16 0.12 Matches are distributed among these distances: 18 1 0.01 19 22 0.24 20 51 0.56 21 3 0.03 22 5 0.05 23 6 0.07 24 3 0.03 ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33 Consensus pattern (19 bp): CATTGTATCGATACATAGA Found at i:3986740 original size:33 final size:33 Alignment explanation

Indices: 3986692--3986763 Score: 101 Period size: 33 Copynumber: 2.2 Consensus size: 33 3986682 GATACATAGG * * 3986692 ACATTGTATCGATACAT-AGGACATTGTATCGAT 1 ACATTGAATCAATACATGAGGA-ATTGTATCGAT * 3986725 ACATTGAATCAATACATGATGAATTGTATCGAT 1 ACATTGAATCAATACATGAGGAATTGTATCGAT 3986758 ACATTG 1 ACATTG 3986764 CTTATAACGG Statistics Matches: 35, Mismatches: 3, Indels: 2 0.88 0.08 0.05 Matches are distributed among these distances: 33 32 0.91 34 3 0.09 ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33 Consensus pattern (33 bp): ACATTGAATCAATACATGAGGAATTGTATCGAT Found at i:3988389 original size:49 final size:48 Alignment explanation

Indices: 3988207--3988404 Score: 146 Period size: 49 Copynumber: 4.2 Consensus size: 48 3988197 TTGACAGAAG * * * * 3988207 GTACAAAACTAACCCTAAAAGACTTAAATTTGGTTAGTTTCT-ATAAAAA 1 GTACAAAACTAACTCTAAAAGACTCAATTTTGG-TAGTTT-TGATAATAA * * 3988256 GTACAAAACTAACTCT-AAAG-----ATTTTGGTGTGTTTTGATGATAA 1 GTACAAAACTAACTCTAAAAGACTCAATTTTGGT-AGTTTTGATAATAA * * * 3988299 GTACAAAACTAACTCTAAAAGACTCGATTTTAGTAGATTTTGATAATAG 1 GTACAAAACTAACTCTAAAAGACTCAATTTTGGTAG-TTTTGATAATAA * * 3988348 GTACAAAAGTAAC-CTTTAAAGAGC-CAATTTTGGTCAGTTTTGACTAA-AA 1 GTACAAAACTAACTC-TAAAAGA-CTCAATTTTGGT-AGTTTTGA-TAATAA * 3988397 GTATAAAA 1 GTACAAAA 3988405 TTAAAAGACT Statistics Matches: 121, Mismatches: 15, Indels: 26 0.75 0.09 0.16 Matches are distributed among these distances: 42 2 0.02 43 31 0.26 44 4 0.03 48 6 0.05 49 72 0.60 50 6 0.05 ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32 Consensus pattern (48 bp): GTACAAAACTAACTCTAAAAGACTCAATTTTGGTAGTTTTGATAATAA Found at i:3988551 original size:59 final size:58 Alignment explanation

Indices: 3988443--3988682 Score: 268 Period size: 59 Copynumber: 4.1 Consensus size: 58 3988433 AATAAATAGA * * * * 3988443 CCTTAGATTATGAAAAATAACCTAAAATAACCTTAAAATGCGTAAAAATTGCTAAATGAT 1 CCTTAGATTATGGAAAATAACCT-AAATAACCCTAAAATGCATGAAAATTGCTAAAT-AT * * * * * 3988503 CTTTAGATCATGGAAAACAATCTAAATAACCCTAAAATTCATGAAAATTGCTAAATAAT 1 CCTTAGATTATGGAAAATAACCTAAATAACCCTAAAATGCATGAAAATTGCTAAAT-AT * * * 3988562 CCCTAGATTATGGAAAATAACCTAAA-AATCCTAAAATGCATGGAAATTGCTAAATAT 1 CCTTAGATTATGGAAAATAACCTAAATAACCCTAAAATGCATGAAAATTGCTAAATAT * ** ** 3988619 CCTTAGATTATGGAAAATAACCAAAATGAA-CCTAAAATAAATGAAAATAACTAAATAGT 1 CCTTAGATTATGGAAAATAACCTAAAT-AACCCTAAAATGCATGAAAATTGCTAAATA-T 3988678 CCTTA 1 CCTTA 3988683 ATATACAAGA Statistics Matches: 152, Mismatches: 25, Indels: 7 0.83 0.14 0.04 Matches are distributed among these distances: 57 26 0.17 58 48 0.32 59 60 0.39 60 18 0.12 ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27 Consensus pattern (58 bp): CCTTAGATTATGGAAAATAACCTAAATAACCCTAAAATGCATGAAAATTGCTAAATAT Found at i:3988559 original size:29 final size:29 Alignment explanation

Indices: 3988524--3988617 Score: 86 Period size: 29 Copynumber: 3.2 Consensus size: 29 3988514 GGAAAACAAT 3988524 CTAAATAACCCTAAAATTCATGAAAATTG 1 CTAAATAACCCTAAAATTCATGAAAATTG * ** 3988553 CTAAATAATCCCT-AGATT-ATGGAAAATAAC 1 CTAAATAA-CCCTAAAATTCAT-GAAAAT-TG * * * 3988583 CTAAA-AATCCTAAAATGCATGGAAATTG 1 CTAAATAACCCTAAAATTCATGAAAATTG 3988611 CTAAATA 1 CTAAATA 3988618 TCCTTAGATT Statistics Matches: 50, Mismatches: 9, Indels: 12 0.70 0.13 0.17 Matches are distributed among these distances: 28 10 0.20 29 29 0.58 30 11 0.22 ACGTcount: A:0.48, C:0.16, G:0.10, T:0.27 Consensus pattern (29 bp): CTAAATAACCCTAAAATTCATGAAAATTG Found at i:3989330 original size:8 final size:8 Alignment explanation

Indices: 3989309--3989343 Score: 52 Period size: 8 Copynumber: 4.2 Consensus size: 8 3989299 TTTAGTTGAG 3989309 CTTTTTCTT 1 CTTTTT-TT * 3989318 TTTTTTTT 1 CTTTTTTT 3989326 CTTTTTTT 1 CTTTTTTT 3989334 CTTTTTTT 1 CTTTTTTT 3989342 CT 1 CT 3989344 CTCTTTATAG Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 8 19 0.79 9 5 0.21 ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86 Consensus pattern (8 bp): CTTTTTTT Found at i:3995073 original size:20 final size:20 Alignment explanation

Indices: 3995036--3995089 Score: 72 Period size: 20 Copynumber: 2.6 Consensus size: 20 3995026 TTCTATAATT * 3995036 TGTATCTATACAATAAGTGAA 1 TGTATCAATAC-ATAAGTGAA * * 3995057 TGTGTCGATACATAAGTGAA 1 TGTATCAATACATAAGTGAA 3995077 TGTATCAATACAT 1 TGTATCAATACAT 3995090 GCTTAAAATG Statistics Matches: 29, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 20 20 0.69 21 9 0.31 ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33 Consensus pattern (20 bp): TGTATCAATACATAAGTGAA Found at i:3995173 original size:19 final size:20 Alignment explanation

Indices: 3995147--3995193 Score: 78 Period size: 19 Copynumber: 2.4 Consensus size: 20 3995137 CTAGAAAGAA 3995147 AATGTATCGATACATT-TTC 1 AATGTATCGATACATTCTTC * 3995166 ATTGTATCGATACATTCTTC 1 AATGTATCGATACATTCTTC 3995186 AATGTATC 1 AATGTATC 3995194 AATATATGCA Statistics Matches: 25, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 19 15 0.60 20 10 0.40 ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43 Consensus pattern (20 bp): AATGTATCGATACATTCTTC Found at i:3998977 original size:20 final size:20 Alignment explanation

Indices: 3998927--3998977 Score: 75 Period size: 20 Copynumber: 2.5 Consensus size: 20 3998917 TTGCCTGCAT * 3998927 TATCGATACAATAAATAATG 1 TATCGATACATTAAATAATG * * 3998947 TATCGATACATTGAATCATG 1 TATCGATACATTAAATAATG 3998967 TATCGATACAT 1 TATCGATACAT 3998978 CTGGGTAAAA Statistics Matches: 28, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 28 1.00 ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33 Consensus pattern (20 bp): TATCGATACATTAAATAATG Found at i:3999066 original size:15 final size:13 Alignment explanation

Indices: 3999035--3999059 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3999025 ACAAAACTTA 3999035 TGTATCGATACAT 1 TGTATCGATACAT 3999048 TGTATCGATACA 1 TGTATCGATACA 3999060 AATTGTAAAA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:3999880 original size:52 final size:52 Alignment explanation

Indices: 3999785--4000456 Score: 201 Period size: 52 Copynumber: 12.8 Consensus size: 52 3999775 GTGGGAAAGG * * * 3999785 TGCCAATATGCTGATTCAAGGCCAACGATATTGAGCTTAAAGATACA-AGGAA 1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGAGCTTAAAGATA-AGAAGAA * * * * 3999837 TGTCAATGTGCTGATTCACGGCCAATGACATT-AGACTTGAAGATAAGAAGAA 1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGAG-CTTAAAGATAAGAAGAA * * * * 3999889 TGCCAATGTACTGATTCAAAGCCAGCGACATTTG-GCTTAGGAATG-TTA-AA-AA 1 TGCCAATGTGCTGATTCAAGGCCAACGACA-TTGAGCTTA--AA-GATAAGAAGAA * * * * * * 3999941 TGCTAATATACTGATTCAAGGCCAGCGATATT-AGACTCAAAGAT--GATAG-- 1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGAG-CTTAAAGATAAGA-AGAA * * * * * 3999990 TGCTAATGTGCTGATTCAAGGCCAGCAACATTG-GACTTAAAGAT--GGAG-G 1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGAG-CTTAAAGATAAGAAGAA * * * 4000039 TGCCAATGTGCTAATTCAAGGCCAGCGACATTGAGCTTACGAATG-TTA-AAG-A 1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGAGCTTA--AA-GATAAGAAGAA * * * * * * * 4000091 TGTCAATATGCTGATTCGAGACCAACAATATCG-GACTTAAAGAT--GATAG-- 1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGAG-CTTAAAGATAAGA-AGAA * ** * * * * * 4000140 TACCAATGTATTGATTCAAGGCCAGCAACATTG-GATTTAAGGATGAGAAGGATGATAAA 1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGAG-CTTAA--A-GATAA-GA--A-GAA * * * ** * 4000199 GGTGCCAATATGCTGATCCAAGGCCAGCGACATTGAGCTTAGGAATCTTA-AAG-A 1 --TGCCAATGTGCTGATTCAAGGCCAACGACATTGAGCTTA--AAGATAAGAAGAA * * * ** * * 4000253 TGCCAATATGATAATTCAAGGCCAACGATGTTGGGCTTAAAGATGAGAAAAATGATAAAA 1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGAGCTTAAAGAT------AA-GA-AGAA * * * * * ** 4000313 GTGCCAATATGCTGATTCAAGACCAATGATATTGGGCTTAAAGATGTGAAGAA 1 -TGCCAATGTGCTGATTCAAGGCCAACGACATTGAGCTTAAAGATAAGAAGAA * * * * * * 4000366 TGTCAATGTACTGATTTAAGGCCAGCAACATTG-GACTTAAAGATGAGAAGAA 1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGAG-CTTAAAGATAAGAAGAA * * * * 4000418 TGCCAATGTGCTAATTCAAGGCCAGCAACATTAAGCTTA 1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGAGCTTA 4000457 GGAGGAGATG Statistics Matches: 467, Mismatches: 100, Indels: 106 0.69 0.15 0.16 Matches are distributed among these distances: 48 2 0.00 49 106 0.23 50 13 0.03 51 12 0.03 52 235 0.50 53 9 0.02 54 7 0.01 55 3 0.01 56 3 0.01 58 2 0.00 59 1 0.00 60 2 0.00 61 70 0.15 62 1 0.00 63 1 0.00 ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25 Consensus pattern (52 bp): TGCCAATGTGCTGATTCAAGGCCAACGACATTGAGCTTAAAGATAAGAAGAA Found at i:4000011 original size:49 final size:49 Alignment explanation

Indices: 3999841--4000070 Score: 165 Period size: 49 Copynumber: 4.6 Consensus size: 49 3999831 AAGGAATGTC * ** ** * * 3999841 AATGTGCTGATTCACGGCCAATGACATTAGACTTGAAGATAAGAAGAATGCC 1 AATGTGCTGATTCAAGGCCAGCGACATTAGACTCAAAGAT-GGAAG--TGCT * * * * * * ** * 3999893 AATGTACTGATTCAAAGCCAGCGACATTTGGCTTAGGAATGTTAAAAATGCT 1 AATGTGCTGATTCAAGGCCAGCGACATTAGACTCA--AA-GATGGAAGTGCT * * * 3999945 AATATACTGATTCAAGGCCAGCGATATTAGACTCAAAGAT-GATAGTGCT 1 AATGTGCTGATTCAAGGCCAGCGACATTAGACTCAAAGATGGA-AGTGCT * * * * * 3999994 AATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGGAGGTGCC 1 AATGTGCTGATTCAAGGCCAGCGACATTAGACTCAAAGATGGAAGTGCT * 4000043 AATGTGCTAATTCAAGGCCAGCGACATT 1 AATGTGCTGATTCAAGGCCAGCGACATT 4000071 GAGCTTACGA Statistics Matches: 142, Mismatches: 31, Indels: 13 0.76 0.17 0.07 Matches are distributed among these distances: 48 1 0.01 49 71 0.50 50 4 0.03 52 59 0.42 54 5 0.04 55 2 0.01 ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25 Consensus pattern (49 bp): AATGTGCTGATTCAAGGCCAGCGACATTAGACTCAAAGATGGAAGTGCT Found at i:4000083 original size:150 final size:150 Alignment explanation

Indices: 3999889--4000184 Score: 389 Period size: 150 Copynumber: 2.0 Consensus size: 150 3999879 ATAAGAAGAA * * 3999889 TGCCAATGTACTGATTCAAAGCCAGCGACATTTGGCTTAGGAATGTTAAAAATG-CTAATATACT 1 TGCCAATGTACTAATTCAAAGCCAGCGACATTTGGCTTACGAATGTTAAAAATGTC-AATATACT * * * * * * * 3999953 GATTCAAGGCCAGCGATATTAGACTCAAAGATGATAGTGCTAATGTGCTGATTCAAGGCCAGCAA 65 GATTCAAGACCAACAATATCAGACTCAAAGATGATAGTACCAATGTACTGATTCAAGGCCAGCAA 4000018 CATTGGACTTAAAGATGGAGG 130 CATTGGACTTAAAGATGGAGG * * * * 4000039 TGCCAATGTGCTAATTCAAGGCCAGCGACA-TTGAGCTTACGAATGTTAAAGATGTCAATATGCT 1 TGCCAATGTACTAATTCAAAGCCAGCGACATTTG-GCTTACGAATGTTAAAAATGTCAATATACT * * * * 4000103 GATTCGAGACCAACAATATCGGACTTAAAGATGATAGTACCAATGTATTGATTCAAGGCCAGCAA 65 GATTCAAGACCAACAATATCAGACTCAAAGATGATAGTACCAATGTACTGATTCAAGGCCAGCAA * * 4000168 CATTGGATTTAAGGATG 130 CATTGGACTTAAAGATG 4000185 AGAAGGATGA Statistics Matches: 125, Mismatches: 19, Indels: 4 0.84 0.13 0.03 Matches are distributed among these distances: 149 3 0.02 150 121 0.97 151 1 0.01 ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26 Consensus pattern (150 bp): TGCCAATGTACTAATTCAAAGCCAGCGACATTTGGCTTACGAATGTTAAAAATGTCAATATACTG ATTCAAGACCAACAATATCAGACTCAAAGATGATAGTACCAATGTACTGATTCAAGGCCAGCAAC ATTGGACTTAAAGATGGAGG Found at i:4000348 original size:61 final size:62 Alignment explanation

Indices: 4000248--4000367 Score: 170 Period size: 61 Copynumber: 2.0 Consensus size: 62 4000238 TAGGAATCTT * * 4000248 AAAGATGCCAATATGATAATTCAAGGCCAACGATGTTGGGCTTAAAGATGAGAAAAATGATA 1 AAAGATGCCAATATGATAATTCAAGACCAACGATATTGGGCTTAAAGATGAGAAAAATGATA * * * * * 4000310 AAAG-TGCCAATATGCTGATTCAAGACCAATGATATTGGGCTTAAAGATGTGAAGAATG 1 AAAGATGCCAATATGATAATTCAAGACCAACGATATTGGGCTTAAAGATGAGAAAAATG 4000368 TCAATGTACT Statistics Matches: 51, Mismatches: 7, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 61 47 0.92 62 4 0.08 ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24 Consensus pattern (62 bp): AAAGATGCCAATATGATAATTCAAGACCAACGATATTGGGCTTAAAGATGAGAAAAATGATA Found at i:4000541 original size:32 final size:32 Alignment explanation

Indices: 4000505--4000589 Score: 143 Period size: 32 Copynumber: 2.7 Consensus size: 32 4000495 GTTGAAACCG * * 4000505 ACTTGTGTGGGTTTTAAAGAAAGTTGCCACTA 1 ACTTGTGTGGGCTTTAAAGAAAGTTGCCACCA 4000537 ACTTGTGTGGGCTTTAAAGAAAGTTGCCACCA 1 ACTTGTGTGGGCTTTAAAGAAAGTTGCCACCA * 4000569 ACTTGTGTGGGCTTTAGAGAA 1 ACTTGTGTGGGCTTTAAAGAA 4000590 GGTTCCTCCA Statistics Matches: 50, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 32 50 1.00 ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32 Consensus pattern (32 bp): ACTTGTGTGGGCTTTAAAGAAAGTTGCCACCA Found at i:4000819 original size:28 final size:28 Alignment explanation

Indices: 4000767--4000837 Score: 92 Period size: 28 Copynumber: 2.6 Consensus size: 28 4000757 ATACAGCAAC * 4000767 TGCCACTGA-TTGTGGATTCCGAAAAGA 1 TGCCACTGACTTGTGGATTCCAAAAAGA * 4000794 TGCCACTGACTTGTGGACTT-CAAAAAGG 1 TGCCACTGACTTGTGGA-TTCCAAAAAGA * 4000822 TGCCACTGACTAGTGG 1 TGCCACTGACTTGTGG 4000838 GCTTTGAGGA Statistics Matches: 39, Mismatches: 3, Indels: 3 0.87 0.07 0.07 Matches are distributed among these distances: 27 9 0.23 28 28 0.72 29 2 0.05 ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25 Consensus pattern (28 bp): TGCCACTGACTTGTGGATTCCAAAAAGA Found at i:4002204 original size:12 final size:12 Alignment explanation

Indices: 4002187--4002233 Score: 58 Period size: 12 Copynumber: 3.7 Consensus size: 12 4002177 TTTCTTCCCC 4002187 TTTTTTGTTTTT 1 TTTTTTGTTTTT 4002199 TTTTTTGTTTTGT 1 TTTTTTGTTTT-T * 4002212 TTTGTTTTTTGTTT 1 TTT-TTTGTT-TTT 4002226 TTTTTTGT 1 TTTTTTGT 4002234 AGAGGATGCC Statistics Matches: 30, Mismatches: 2, Indels: 5 0.81 0.05 0.14 Matches are distributed among these distances: 12 11 0.37 13 8 0.27 14 9 0.30 15 2 0.07 ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87 Consensus pattern (12 bp): TTTTTTGTTTTT Found at i:4002211 original size:17 final size:17 Alignment explanation

Indices: 4002189--4002231 Score: 70 Period size: 17 Copynumber: 2.6 Consensus size: 17 4002179 TCTTCCCCTT 4002189 TTTTGTTTTTTTTTTTG 1 TTTTGTTTTTTTTTTTG * 4002206 TTTTGTTTTGTTTTTTG 1 TTTTGTTTTTTTTTTTG 4002223 TTTT-TTTTT 1 TTTTGTTTTT 4002232 GTAGAGGATG Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 16 4 0.17 17 20 0.83 ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88 Consensus pattern (17 bp): TTTTGTTTTTTTTTTTG Found at i:4002214 original size:22 final size:22 Alignment explanation

Indices: 4002189--4002233 Score: 74 Period size: 22 Copynumber: 2.0 Consensus size: 22 4002179 TCTTCCCCTT 4002189 TTTTGTTTTTT-TTTTTGTTTTG 1 TTTTGTTTTTTGTTTTT-TTTTG 4002211 TTTTGTTTTTTGTTTTTTTTTG 1 TTTTGTTTTTTGTTTTTTTTTG 4002233 T 1 T 4002234 AGAGGATGCC Statistics Matches: 22, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 22 17 0.77 23 5 0.23 ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87 Consensus pattern (22 bp): TTTTGTTTTTTGTTTTTTTTTG Found at i:4007177 original size:27 final size:27 Alignment explanation

Indices: 4007121--4007178 Score: 64 Period size: 27 Copynumber: 2.1 Consensus size: 27 4007111 TTAAAAACGG * * * * 4007121 GGTTGGAGTATTCCTTCTGAAGAATGA 1 GGTTAGAGTATTCCCTCTGAAAAATAA 4007148 GGTTAGAGTATTCCCTC-GAAAAAATAA 1 GGTTAGAGTATTCCCTCTG-AAAAATAA 4007175 GGTT 1 GGTT 4007179 GAAGTATCCT Statistics Matches: 26, Mismatches: 4, Indels: 2 0.81 0.12 0.06 Matches are distributed among these distances: 26 1 0.04 27 25 0.96 ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31 Consensus pattern (27 bp): GGTTAGAGTATTCCCTCTGAAAAATAA Found at i:4012009 original size:148 final size:148 Alignment explanation

Indices: 4011715--4011983 Score: 342 Period size: 148 Copynumber: 1.8 Consensus size: 148 4011705 CATAGAAAAC * * * ** ** 4011715 AAAAGCGAACCTACGCTTAATACATACCCTCGACATAGAAGCGAGTCGGTGACAAATTAAGACTC 1 AAAAGCAAACCTACGCCTAATACATACCCTCGACATAGAAACGACCCAATGACAAATTAAGACTC * * * * 4011780 AATTCTAGAAAATTATGAAAATGCCCTTATGGGTATACCTTCAACATGAAAGTATCCCAGTAACC 66 AATTCTAGAAAATTATAAAAATGCCCCTATAGGTATACCTTCAACATGAAAATATCCCAGTAACC * 4011845 CTAAAGGACTTAAAAAGA 131 CTAAAAGACTTAAAAAGA * * * * 4011863 AAAAGCAAACCTATGCCTAATACATACCCTCGACATAGAAATGACCCAATGACAAGTTAGGACTC 1 AAAAGCAAACCTACGCCTAATACATACCCTCGACATAGAAACGACCCAATGACAAATTAAGACTC ** ** 4011928 GGTTCTAGAAAAATTATAAAAATGCCCCTA-AGGTATACCTTTGACATGAAAATATC 66 AATTCTAG-AAAATTATAAAAATGCCCCTATAGGTATACCTTCAACATGAAAATATC 4011984 TCGATACATT Statistics Matches: 101, Mismatches: 19, Indels: 2 0.83 0.16 0.02 Matches are distributed among these distances: 148 82 0.81 149 19 0.19 ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23 Consensus pattern (148 bp): AAAAGCAAACCTACGCCTAATACATACCCTCGACATAGAAACGACCCAATGACAAATTAAGACTC AATTCTAGAAAATTATAAAAATGCCCCTATAGGTATACCTTCAACATGAAAATATCCCAGTAACC CTAAAAGACTTAAAAAGA Found at i:4013827 original size:166 final size:166 Alignment explanation

Indices: 4013619--4014165 Score: 549 Period size: 167 Copynumber: 3.3 Consensus size: 166 4013609 TATCTTATGA * * * * * * 4013619 AAAAAATGAAAAACTCAT-AGAATAATTTGTATTTTGCAAAACTAATTTAATGTGAATTTAATGA 1 AAAAAATAAAAAACTCATGAAAATAA-ATGAATTTTGCAAAACTAATTTAATATGAATTAAATGA * 4013683 CAATATTAT-ATGAATTTTAAAAATTTTAAATCAAGAAAAATCCTCTCAAAAATATTTATGGAGT 65 CAATATT-TGATGAATTTTAAAAATTTTAAATCAAGAAAAATCCTCTCAAAAACATTTATGGAGT * * 4013747 AGAAAATTCGATTTTTTTAGAACAAGAGA-ATTTTAAGG 129 AGAAAACTCG-TTTTTTTAGAAAAAGAGAGATTTTAAGG * * * * 4013785 AAAAAATGAAAAATTCATGAAAATAAATGAATTTTTCAAAACTAATTTACTATGAATTAAATGAT 1 AAAAAATAAAAAACTCATGAAAATAAATGAATTTTGCAAAACTAATTTAATATGAATTAAATGA- * * * * 4013850 GAA-ATTTGCTGAATTTTAAAAATTTTAAATCAAGAAAAATTCC-CTTAAAAACATTTATGGAAT 65 CAATATTTGATGAATTTTAAAAATTTTAAATCAAGAAAAA-TCCTCTCAAAAACATTTATGGAGT * * * 4013913 AGAAAACTC-TGTTTTTCGTAAATAG-GAAGATTTTCAAGG 129 AGAAAACTCGTTTTTTTAG-AAAAAGAG-AGATTTT-AAGG * * * * ** * * * 4013952 AAAAACTAAAAAACTCAAGAAAATAAATAAATTTTTCAAAACTTCTTTACTATAAATTAAATGAT 1 AAAAAATAAAAAACTCATGAAAATAAATGAATTTTGCAAAACTAATTTAATATGAATTAAATGAC * * * 4014017 GATATTTGATAAATTTTAAAAAATTTTAAA-CTAAAAAAAAT-CTCTCCAAAAACATTTATGGAG 66 AATATTTGATGAATTTT-AAAAATTTTAAATC-AAGAAAAATCCTCT-CAAAAACATTTATGGAG * * * * * 4014080 TAGAAAACTCCTTATTTT-GAAAATAGGGAGATTTCAAAG 128 TAGAAAACTCGTTTTTTTAGAAAA-AGAGAGATTTTAAGG * * 4014119 AAAAAATAAAAAACTCATG-AAATAAAAAGAATTTTGAAAAACTAATT 1 AAAAAATAAAAAACTCATGAAAAT-AAATGAATTTTGCAAAACTAATT 4014166 CAATGGTAAT Statistics Matches: 318, Mismatches: 46, Indels: 33 0.80 0.12 0.08 Matches are distributed among these distances: 164 8 0.03 165 6 0.02 166 118 0.37 167 127 0.40 168 53 0.17 169 6 0.02 ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33 Consensus pattern (166 bp): AAAAAATAAAAAACTCATGAAAATAAATGAATTTTGCAAAACTAATTTAATATGAATTAAATGAC AATATTTGATGAATTTTAAAAATTTTAAATCAAGAAAAATCCTCTCAAAAACATTTATGGAGTAG AAAACTCGTTTTTTTAGAAAAAGAGAGATTTTAAGG Found at i:4019299 original size:166 final size:165 Alignment explanation

Indices: 4019123--4019809 Score: 718 Period size: 167 Copynumber: 4.1 Consensus size: 165 4019113 TTTTTTTCTT * * * * 4019123 CGTAAATTTTTTCAGGAGAATTTTCATGGGTTTAACATTTTGAAAATTCATCAAATA-TATTTAT 1 CGTAAATTTTTTCAGG-GATTTTTCATGGTTTTTA-ATTTTTAAAATTCATCAAATATTA-TTAT * * * * * 4019187 TTAATTCATATTATATTAGTTTTTACAAATTTATTCATTTTCATTAGTTTTTGAA-TGTTTCCTT 63 TTAATTTATATTAAATTAGTTTTTAAAAATTCATTCATTTTCATTAGTTTTTGAATTTTTTCCTT ** ** 4019251 AAAATTTTTCTATTTTTAAAATATGGAGTTTTCTACTC 128 AAAATTTCCCTATTTTTAAAATACAGAGTTTTCTACTC * * * * 4019289 CGTAAATTTTTTTCGAGGGATTTTTAATGGTTTTTAGTTTTTAATATTTCATAAAATATTATTAT 1 CGTAAA-TTTTTTC-AGGGATTTTTCATGGTTTTTAATTTTTAA-AATTCATCAAATATTATTAT * * * * 4019354 TTATTTTATAGTAAATCAGTTTTAAAAAATTCATTCATTTTCATTAGTTTTTGAATTTTTTCCTT 63 TTAATTTATATTAAATTAGTTTTTAAAAATTCATTCATTTTCATTAGTTTTTGAATTTTTTCCTT * * 4019419 ATAATTTCCCTA-TTTTAGAAATACAGATTTTTCTACTC 128 AAAATTTCCCTATTTTTA-AAATACAGAGTTTTCTACTC * ** * 4019457 CGTAAATGTTTTT-GGGAGATTTTTGTTGGTTTTTAATTTTTAAAATTTAT-AAATTATTATTAT 1 CGTAAAT-TTTTTCAGG-GATTTTTCATGGTTTTTAATTTTTAAAATTCATCAAA-TATTATTAT * 4019520 TTATTTTATATTAAATTAGTTTTTAAAAATTCATTCATTTTCATTAGTTTTTGAATTTTTTTCCT 63 TTAATTTATATTAAATTAGTTTTTAAAAATTCATTCATTTTCATTAGTTTTTGAA-TTTTTTCCT * * * 4019585 TGAAA-TTCTCT-TGTTTTCGAAATACAGAGTTTT-TCACTC 127 TAAAATTTCCCTAT-TTTT-AAAATACAGAGTTTTCT-ACTC * * 4019624 CGTAAATTTTTTTGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTT 1 CGTAAA-TTTTTTCAGGGATTTTTCATGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTT * * * * * 4019689 AATTTATATTAAATAATTTTTTAAAAATTCATTCATTTTCATGA-ATTTT---TTATTT--TTAA 65 AATTTATATTAAATTAGTTTTTAAAAATTCATTCATTTTCATTAGTTTTTGAATTTTTTCCTTAA * ** * * 4019748 AATTTTCCTATTTCCAAAATATAGAGTTTTCTATTC 130 AATTTCCCTATTTTTAAAATACAGAGTTTTCTACTC * * 4019784 TGTAAATGTTTTCAAGGTGATTTTTC 1 CGTAAATTTTTTC-AGG-GATTTTTC 4019810 TCACTTGAAA Statistics Matches: 442, Mismatches: 57, Indels: 49 0.81 0.10 0.09 Matches are distributed among these distances: 159 5 0.01 160 29 0.07 161 15 0.03 162 6 0.01 165 3 0.01 166 90 0.20 167 238 0.54 168 56 0.13 ACGTcount: A:0.30, C:0.09, G:0.09, T:0.53 Consensus pattern (165 bp): CGTAAATTTTTTCAGGGATTTTTCATGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTA ATTTATATTAAATTAGTTTTTAAAAATTCATTCATTTTCATTAGTTTTTGAATTTTTTCCTTAAA ATTTCCCTATTTTTAAAATACAGAGTTTTCTACTC Found at i:4020394 original size:13 final size:13 Alignment explanation

Indices: 4020369--4020410 Score: 59 Period size: 13 Copynumber: 3.3 Consensus size: 13 4020359 AGGTTCAGCT * 4020369 GAAA-AAAAAAGA 1 GAAAGAAAAGAGA 4020381 GAAAGAAAAGAGA 1 GAAAGAAAAGAGA * 4020394 GAAAGAAAAGAGG 1 GAAAGAAAAGAGA 4020407 GAAA 1 GAAA 4020411 AATAGAAAAT Statistics Matches: 27, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 12 4 0.15 13 23 0.85 ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00 Consensus pattern (13 bp): GAAAGAAAAGAGA Found at i:4022991 original size:2 final size:2 Alignment explanation

Indices: 4022984--4023023 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 4022974 TTCACAATTC 4022984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 4023024 CACAATTAGG Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:4023600 original size:7 final size:7 Alignment explanation

Indices: 4023584--4023622 Score: 51 Period size: 7 Copynumber: 5.6 Consensus size: 7 4023574 ACAACAACTC * 4023584 ATTTTTA 1 ATTTTCA 4023591 ATTTTCA 1 ATTTTCA 4023598 ATTTTCA 1 ATTTTCA * 4023605 ATGTTCA 1 ATTTTCA * 4023612 ATATTCA 1 ATTTTCA 4023619 ATTT 1 ATTT 4023623 CAAAATCATT Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 7 28 1.00 ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56 Consensus pattern (7 bp): ATTTTCA Found at i:4027287 original size:23 final size:23 Alignment explanation

Indices: 4027255--4027315 Score: 90 Period size: 23 Copynumber: 2.7 Consensus size: 23 4027245 TAATTACAAA * 4027255 TAAA-ATATTAATATTTATTTAT 1 TAAACATATTAATATTCATTTAT 4027277 TAAACATATTAATATTCATTTAT 1 TAAACATATTAATATTCATTTAT * 4027300 TAAACAAATTAA-ATTC 1 TAAACATATTAATATTC 4027316 GAATAATTTT Statistics Matches: 36, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 22 8 0.22 23 28 0.78 ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46 Consensus pattern (23 bp): TAAACATATTAATATTCATTTAT Found at i:4027756 original size:127 final size:130 Alignment explanation

Indices: 4027497--4027758 Score: 449 Period size: 127 Copynumber: 2.0 Consensus size: 130 4027487 TTCTATTCAG * 4027497 AATTATTTAATCACGTTTTAATGTTCTTAAACAGCAATTTCATTTAATTTAAATAAATTAACTAA 1 AATTATTTAATCACGTTTTAATGTTCTTAAACAGCAATTTCATTTAATTTAAACAAATT-A-TAA 4027562 ACTAAACTAAACTCAAATAATCACATAATAATTCACTTAAATTCAAACACAATTTTAAAAAAACA 64 ACTAAACTAAACTCAAATAATCACATAATAATTCACTTAAATTCAAACACAATTTTAAAAAAACA 4027627 AA 129 AA * 4027629 AATTATTTAATCACGTTTTAATGTTCTTAATCAGCAATTTCATTTAATTTAAACAAA-T-T-AAC 1 AATTATTTAATCACGTTTTAATGTTCTTAAACAGCAATTTCATTTAATTTAAACAAATTATAAAC ** 4027691 TAAACTAAACTCAAATAATCACATAATAATTCACTTAAATTCAAACACAATTTTAAAAATTCAAA 66 TAAACTAAACTCAAATAATCACATAATAATTCACTTAAATTCAAACACAATTTTAAAAAAACAAA 4027756 AAT 1 AAT 4027759 AAATTATAAA Statistics Matches: 126, Mismatches: 4, Indels: 5 0.93 0.03 0.04 Matches are distributed among these distances: 127 69 0.55 128 1 0.01 131 1 0.01 132 55 0.44 ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35 Consensus pattern (130 bp): AATTATTTAATCACGTTTTAATGTTCTTAAACAGCAATTTCATTTAATTTAAACAAATTATAAAC TAAACTAAACTCAAATAATCACATAATAATTCACTTAAATTCAAACACAATTTTAAAAAAACAAA Found at i:4028260 original size:150 final size:153 Alignment explanation

Indices: 4028004--4028289 Score: 454 Period size: 153 Copynumber: 1.9 Consensus size: 153 4027994 TAAAAACTAC * * * 4028004 ATTCATGTAAACCACAATTGAAATATCTTCTGTTTACAAAATGGAATAAAAAAAAAAACCTTACA 1 ATTCATGTAAACCACAATTGAAATATCGTCCGTTCACAAAATGGAAT-AAAAAAAAAACCTTACA * * 4028069 GAAATGAATAAAAAAACCCACAGCTCTACCATATAAAG-AAAAAAAAAAAGAAGCCGAAAACGAT 65 GAAATGAATAAAAAAACCCACAGCTCTACCATATAAAGAAAAAAAAAAAAAAAGCCGAAAACGAG 4028133 CCGCCTATAAAAACTACCATTTCT 130 CCGCCTATAAAAACTACCATTTCT * 4028157 ATTCATGTAAACCACAATTGAAATATCGTCCGTTCACATAATGGAAT-AAAAAAAAA-CTTACAG 1 ATTCATGTAAACCACAATTGAAATATCGTCCGTTCACAAAATGGAATAAAAAAAAAACCTTACAG * 4028220 AAATGAAATAAAAAAACCC-CAGCTCTACTATATAAAGAAAAAAAAAAAAAAAAGCCGAAAACGA 66 AAATG-AATAAAAAAACCCACAGCTCTACCATATAAAG-AAAAAAAAAAAAAAAGCCGAAAACGA 4028284 GCCGCC 129 GCCGCC 4028290 AAAACTGGGA Statistics Matches: 123, Mismatches: 7, Indels: 7 0.90 0.05 0.05 Matches are distributed among these distances: 150 29 0.24 151 22 0.18 152 29 0.24 153 43 0.35 ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19 Consensus pattern (153 bp): ATTCATGTAAACCACAATTGAAATATCGTCCGTTCACAAAATGGAATAAAAAAAAAACCTTACAG AAATGAATAAAAAAACCCACAGCTCTACCATATAAAGAAAAAAAAAAAAAAAGCCGAAAACGAGC CGCCTATAAAAACTACCATTTCT Found at i:4030836 original size:23 final size:23 Alignment explanation

Indices: 4030809--4030854 Score: 83 Period size: 23 Copynumber: 2.0 Consensus size: 23 4030799 AAATATGATA 4030809 TGTTCTTATATTAATATTGAATC 1 TGTTCTTATATTAATATTGAATC * 4030832 TGTTCTTATATTAATTTTGAATC 1 TGTTCTTATATTAATATTGAATC 4030855 GATTGATTCA Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 23 22 1.00 ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54 Consensus pattern (23 bp): TGTTCTTATATTAATATTGAATC Found at i:4031173 original size:235 final size:239 Alignment explanation

Indices: 4030881--4031363 Score: 841 Period size: 236 Copynumber: 2.0 Consensus size: 239 4030871 TCTAATATTC * 4030881 AATATATAAATATATCATAGTTTATATTATGTATATATATAAATATAATTGTAAATATTAATAAC 1 AATATATAAATATATCATAGTTTATATTATGTATATATATAAATATAATTATAAATATTAATAAC 4030946 TAAATTAAAATAGGTAAATAATAATATTTAAAAGAGAAATAAGATTAATTTAATAATTGATAAGA 66 TAAATTAAAATAGGTAAATAATAATATTTAAAAGAGAAATAAGATTAATTTAATAATTGATAAGA * 4031011 TAATG-AAAAAATTAAATTAGTTATTACTCAATTAATTAGCTAAATGTTTAAATTTTATTTAAGA 131 TAATGAAAAAAATTAAATTAATTATTACTCAATTAATTAGCTAAATGTTTAAATTTTATTTAAGA 4031075 TCTGAAATTTTTAAGAAATAATGA-TTAAAAATTAC-TT-TATAT 196 TCTGAAATTTTTAAGAAATAAT-ATTTAAAAATTACTTTATATAT * * * 4031117 AATATATAAATATATCATAGTTTAT-TTATGTATATGTATAAATATATTTATAAATATTAATAAT 1 AATATATAAATATATCATAGTTTATATTATGTATATATATAAATATAATTATAAATATTAATAAC * * * 4031181 TAAATTAAAATAGGTAAATAATAATATTTGAAGGAGAAATAAGATTAATTTAATAATTGATAATA 66 TAAATTAAAATAGGTAAATAATAATATTTAAAAGAGAAATAAGATTAATTTAATAATTGATAAGA * 4031246 TAATGAAAAAAATTAAATTAATTATTACTCAATTAATTAGCTTAATGTTTAAATTTTATTTAAGA 131 TAATGAAAAAAATTAAATTAATTATTACTCAATTAATTAGCTAAATGTTTAAATTTTATTTAAGA 4031311 TCTGAAATTTTTAAGAAATAATATTTAAAAATTACTTTATATAT 196 TCTGAAATTTTTAAGAAATAATATTTAAAAATTACTTTATATAT 4031355 AATATATAA 1 AATATATAA 4031364 TTAAATATTT Statistics Matches: 234, Mismatches: 9, Indels: 6 0.94 0.04 0.02 Matches are distributed among these distances: 235 103 0.44 236 115 0.49 237 2 0.01 238 14 0.06 ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41 Consensus pattern (239 bp): AATATATAAATATATCATAGTTTATATTATGTATATATATAAATATAATTATAAATATTAATAAC TAAATTAAAATAGGTAAATAATAATATTTAAAAGAGAAATAAGATTAATTTAATAATTGATAAGA TAATGAAAAAAATTAAATTAATTATTACTCAATTAATTAGCTAAATGTTTAAATTTTATTTAAGA TCTGAAATTTTTAAGAAATAATATTTAAAAATTACTTTATATAT Found at i:4031416 original size:235 final size:235 Alignment explanation

Indices: 4030881--4031418 Score: 782 Period size: 235 Copynumber: 2.3 Consensus size: 235 4030871 TCTAATATTC * * * * ** * 4030881 AATATATAAATATATCATAGTTTATATTATGTATATATATAAATATAATTGTAAATATTAATAAC 1 AATATATAAATAAATCATAGTTTAT-TTATGTATATGTACAAATATAATTATAAATAAGAATAAT 4030946 TAAATTAAAATAGGTAAATAATAATATTTAAAAGAGAAATAAGATTAATTTAATAATTGATAAGA 65 TAAATTAAAATAGGTAAATAATAATATTTAAAAGAGAAATAAGATTAATTTAATAATTGATAAGA * 4031011 TAATGAAAAAATTAAATTAGTTATTACTCAATTAATTAGCTAAATGTTTAAATTTTATTTAAGAT 130 TAATGAAAAAATTAAATTAATTATTACTCAATTAATTAGCTAAATGTTTAAATTTTATTTAAGAT 4031076 CTGAAATTTTTAAGAAATAATGATTAAAAATTACTTTATAT 195 CTGAAATTTTTAAGAAATAATGATTAAAAATTACTTTATAT * * * ** 4031117 AATATATAAATATATCATAGTTTATTTATGTATATGTATAAATATATTTATAAATATTAATAATT 1 AATATATAAATAAATCATAGTTTATTTATGTATATGTACAAATATAATTATAAATAAGAATAATT * * * 4031182 AAATTAAAATAGGTAAATAATAATATTTGAAGGAGAAATAAGATTAATTTAATAATTGATAATAT 66 AAATTAAAATAGGTAAATAATAATATTTAAAAGAGAAATAAGATTAATTTAATAATTGATAAGAT * 4031247 AATGAAAAAAATTAAATTAATTATTACTCAATTAATTAGCTTAATGTTTAAATTTTATTTAAGAT 131 AATG-AAAAAATTAAATTAATTATTACTCAATTAATTAGCTAAATGTTTAAATTTTATTTAAGAT 4031312 CTGAAATTTTTAAGAAATAAT-ATTTAAAAATTACTTTATATAT 195 CTGAAATTTTTAAGAAATAATGA-TTAAAAATTAC-TT-TATAT * * * * 4031355 AATATATAATTAAAT-AT-TTTTA-TTATTTTTAT-T-CAAATAGTAATTATTAAATAAGAATAA 1 AATATATAAATAAATCATAGTTTATTTATGTATATGTACAAATA-TAATTA-TAAATAAGAATAA 4031415 TTAA 64 TTAA 4031419 TGAAGATGTG Statistics Matches: 278, Mismatches: 18, Indels: 13 0.90 0.06 0.04 Matches are distributed among these distances: 233 5 0.02 234 6 0.02 235 126 0.45 236 119 0.43 237 4 0.01 238 18 0.06 ACGTcount: A:0.49, C:0.03, G:0.07, T:0.42 Consensus pattern (235 bp): AATATATAAATAAATCATAGTTTATTTATGTATATGTACAAATATAATTATAAATAAGAATAATT AAATTAAAATAGGTAAATAATAATATTTAAAAGAGAAATAAGATTAATTTAATAATTGATAAGAT AATGAAAAAATTAAATTAATTATTACTCAATTAATTAGCTAAATGTTTAAATTTTATTTAAGATC TGAAATTTTTAAGAAATAATGATTAAAAATTACTTTATAT Found at i:4032254 original size:16 final size:16 Alignment explanation

Indices: 4032235--4032268 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 4032225 TAGATTTTGA 4032235 TTATTTCAAAGTTAAG 1 TTATTTCAAAGTTAAG * * 4032251 TTATTTTAAATTTAAG 1 TTATTTCAAAGTTAAG 4032267 TT 1 TT 4032269 TTTATCTAGT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53 Consensus pattern (16 bp): TTATTTCAAAGTTAAG Found at i:4035180 original size:13 final size:13 Alignment explanation

Indices: 4035140--4035191 Score: 62 Period size: 13 Copynumber: 4.5 Consensus size: 13 4035130 CCGTTATAAG 4035140 CAATGTATCGATA 1 CAATGTATCGATA 4035153 CAA--T-TC-AT- 1 CAATGTATCGATA 4035161 C-ATGTATCGATA 1 CAATGTATCGATA 4035173 CAATGTATCGATA 1 CAATGTATCGATA 4035186 CAATGT 1 CAATGT 4035192 CTTATATATC Statistics Matches: 33, Mismatches: 0, Indels: 12 0.73 0.00 0.27 Matches are distributed among these distances: 7 1 0.03 8 1 0.03 9 3 0.09 10 4 0.12 11 3 0.09 12 1 0.03 13 20 0.61 ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33 Consensus pattern (13 bp): CAATGTATCGATA Found at i:4035182 original size:33 final size:33 Alignment explanation

Indices: 4035140--4035208 Score: 104 Period size: 33 Copynumber: 2.1 Consensus size: 33 4035130 CCGTTATAAG * 4035140 CAATGTATCGATACAAT-TCATCATGTATCGATA 1 CAATGTATCGATACAATGTC-TCATATATCGATA * 4035173 CAATGTATCGATACAATGTCTTATATATCGATA 1 CAATGTATCGATACAATGTCTCATATATCGATA 4035206 CAA 1 CAA 4035209 ACAGTGGTAG Statistics Matches: 33, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 33 31 0.94 34 2 0.06 ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33 Consensus pattern (33 bp): CAATGTATCGATACAATGTCTCATATATCGATA Found at i:4035275 original size:13 final size:13 Alignment explanation

Indices: 4035257--4035283 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 4035247 TACAATGAAT 4035257 ATGTATCGATACA 1 ATGTATCGATACA 4035270 ATGTATCGATACA 1 ATGTATCGATACA 4035283 A 1 A 4035284 GGCATAATGT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30 Consensus pattern (13 bp): ATGTATCGATACA Found at i:4035279 original size:32 final size:33 Alignment explanation

Indices: 4035238--4035302 Score: 105 Period size: 32 Copynumber: 2.0 Consensus size: 33 4035228 TGCCACTTTC * 4035238 ATGTATCGATACAATGAAT-ATGTATCGATACA 1 ATGTATCGATACAAGGAATAATGTATCGATACA * 4035270 ATGTATCGATACAAGGCATAATGTATCGATACA 1 ATGTATCGATACAAGGAATAATGTATCGATACA 4035303 TCTGGGTGTG Statistics Matches: 30, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 32 17 0.57 33 13 0.43 ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29 Consensus pattern (33 bp): ATGTATCGATACAAGGAATAATGTATCGATACA Found at i:4037829 original size:13 final size:13 Alignment explanation

Indices: 4037811--4037837 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 4037801 ATAGAAACCC 4037811 ATGTATCGATACA 1 ATGTATCGATACA 4037824 ATGTATCGATACA 1 ATGTATCGATACA 4037837 A 1 A 4037838 GGAATATTGT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30 Consensus pattern (13 bp): ATGTATCGATACA Found at i:4038241 original size:32 final size:32 Alignment explanation

Indices: 4038165--4038526 Score: 220 Period size: 27 Copynumber: 11.9 Consensus size: 32 4038155 ATTTCTTGTC * 4038165 CCTTTTAAGTCCACAACTCCGTGGCACCTTGTC 1 CCTTTTAAGTCCACAACTCCGTGGCACCTT-TT * 4038198 CCTTTTAAGTCCATAACTCCGTGGCACCTTTT 1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTT * * * 4038230 CTTTTTAAGTCCACGATTCCGTGGCA-C---- 1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTT * ** * 4038257 CCTTTTAAGCCCACAACTCCAAGGTACTCCTTGTT 1 CCTTTTAAGTCCACAACTCCGTGG--CACCTT-TT 4038292 CCTTTTAAGTCCACAACTCCGTGGCACCTTTT 1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTT * * 4038324 CTTTTTAAGTCCACGACTCCGTGGCA-C---- 1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTT * 4038351 CCTTTTAAG-CTTACAACTCCGTGGCA-C---- 1 CCTTTTAAGTC-CACAACTCCGTGGCACCTTTT * * 4038378 CCTTTTAAG-CTTAAAACTCCGTGGCACTCTTTTT 1 CCTTTTAAGTC-CACAACTCCGTGGCAC-C-TTTT * * * 4038412 CCCTTGAAGTCCACAACTCAGTGGCA-C---- 1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTT * * * 4038439 CCTTTTAAATCCATAACTCAGTGGCA-C---- 1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTT ** 4038466 CCTTTTAAGTCCACAACTCCGTGGCATTTTTTT 1 CCTTTTAAGTCCACAACTCCGTGGCA-CCTTTT ** * * 4038499 CCTTTTAACCCCACAAGTCAGTGGCACC 1 CCTTTTAAGTCCACAACTCCGTGGCACC 4038527 CCTTTCAAAG Statistics Matches: 264, Mismatches: 42, Indels: 47 0.75 0.12 0.13 Matches are distributed among these distances: 26 1 0.00 27 111 0.42 29 2 0.01 30 1 0.00 31 2 0.01 32 50 0.19 33 56 0.21 34 19 0.07 35 22 0.08 ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32 Consensus pattern (32 bp): CCTTTTAAGTCCACAACTCCGTGGCACCTTTT Found at i:4038323 original size:94 final size:92 Alignment explanation

Indices: 4038164--4038370 Score: 315 Period size: 94 Copynumber: 2.2 Consensus size: 92 4038154 CATTTCTTGT * ** * 4038164 CCCTTTTAAGTCCACAACTCCGTGGCACCTTGTCCCTTTTAAGTCCATAACTCCGTGGCACCTTT 1 CCCTTTTAAGCCCACAACTCCAAGGCACCTTGTCCCTTTTAAGTCCACAACTCCGTGGCACCTTT * 4038229 TCTTTTTAAGTCCACGATTCCGTGGCA 66 TCTTTTTAAGTCCACGACTCCGTGGCA * * 4038256 CCCTTTTAAGCCCACAACTCCAAGGTACTCCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCT 1 CCCTTTTAAGCCCACAACTCCAAGG--CACCTTGTCCCTTTTAAGTCCACAACTCCGTGGCACCT 4038321 TTTCTTTTTAAGTCCACGACTCCGTGGCA 64 TTTCTTTTTAAGTCCACGACTCCGTGGCA ** 4038350 CCCTTTTAAGCTTACAACTCC 1 CCCTTTTAAGCCCACAACTCC 4038371 GTGGCACCCT Statistics Matches: 104, Mismatches: 9, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 92 22 0.21 94 82 0.79 ACGTcount: A:0.20, C:0.34, G:0.14, T:0.33 Consensus pattern (92 bp): CCCTTTTAAGCCCACAACTCCAAGGCACCTTGTCCCTTTTAAGTCCACAACTCCGTGGCACCTTT TCTTTTTAAGTCCACGACTCCGTGGCA Found at i:4038446 original size:88 final size:88 Alignment explanation

Indices: 4038292--4038558 Score: 283 Period size: 88 Copynumber: 3.0 Consensus size: 88 4038282 ACTCCTTGTT * * * * 4038292 CCTTTTAAGTCCACAACTCCGTGGCAC-C-TTTTCTTTTTAAGTCCACGACTCCGTGGCACCCTT 1 CCTTTTAAGTCCAAAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCAGTGGCACCCTT * * * 4038355 TT-AAGCTTACAACTCCGTGGCAC 66 TTAAATC-CACAACTCAGTGGCAC * * * 4038378 CCTTTTAAG-CTTAAAACTCCGTGGCACTCTTTTTCCCTTGAAGTCCACAACTCAGTGGCACCCT 1 CCTTTTAAGTC-CAAAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCAGTGGCACCCT * 4038442 TTTAAATCCATAACTCAGTGGCAC 65 TTTAAATCCACAACTCAGTGGCAC * * ** * 4038466 CCTTTTAAGTCCACAACTCCGTGGCA-TTTTTTTCCTTTTAACCCCACAAGTCAGTGGCACCCCT 1 CCTTTTAAGTCCAAAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCAGTGGCA-CCCT * * * * 4038530 TTCAAAGCCCACAAGTCAGTGGCAA 65 TTTAAA-TCCACAACTCAGTGGCAC 4038555 CCTT 1 CCTT 4038559 CAAAAGCACA Statistics Matches: 150, Mismatches: 24, Indels: 11 0.81 0.13 0.06 Matches are distributed among these distances: 85 1 0.01 86 23 0.15 87 28 0.19 88 76 0.51 89 22 0.15 ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30 Consensus pattern (88 bp): CCTTTTAAGTCCAAAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCAGTGGCACCCTT TTAAATCCACAACTCAGTGGCAC Found at i:4038558 original size:28 final size:29 Alignment explanation

Indices: 4038508--4038599 Score: 109 Period size: 29 Copynumber: 3.2 Consensus size: 29 4038498 TCCTTTTAAC * 4038508 CCCACAAGTCAGTGGCACCCCTTTC-AAAG 1 CCCACAAGTCAGTGGCA-ACCTTTCAAAAG 4038537 CCCACAAGTCAGTGGCAACC-TTCAAAAG 1 CCCACAAGTCAGTGGCAACCTTTCAAAAG * ** 4038565 CACACAAGTTGGT-GCAACCCTTTCAAAAG 1 CCCACAAGTCAGTGGCAA-CCTTTCAAAAG 4038594 CCCACA 1 CCCACA 4038600 CAAGTTGGTG Statistics Matches: 55, Mismatches: 5, Indels: 6 0.83 0.08 0.09 Matches are distributed among these distances: 27 7 0.13 28 18 0.33 29 30 0.55 ACGTcount: A:0.33, C:0.35, G:0.16, T:0.16 Consensus pattern (29 bp): CCCACAAGTCAGTGGCAACCTTTCAAAAG Found at i:4038603 original size:31 final size:30 Alignment explanation

Indices: 4038526--4038609 Score: 97 Period size: 28 Copynumber: 2.9 Consensus size: 30 4038516 TCAGTGGCAC ** 4038526 CCCTTTC-AAAGCC-CACAAGTCAGTGGCAA 1 CCCTTTCAAAAGCCACACAAGTTGGT-GCAA 4038555 -CC-TTCAAAAG-CACACAAGTTGGTGCAA 1 CCCTTTCAAAAGCCACACAAGTTGGTGCAA 4038582 CCCTTTCAAAAGCCCACACAAGTTGGTG 1 CCCTTTCAAAAG-CCACACAAGTTGGTG 4038610 GCATCTTCTT Statistics Matches: 47, Mismatches: 2, Indels: 10 0.80 0.03 0.17 Matches are distributed among these distances: 27 8 0.17 28 17 0.36 29 8 0.17 31 14 0.30 ACGTcount: A:0.32, C:0.31, G:0.18, T:0.19 Consensus pattern (30 bp): CCCTTTCAAAAGCCACACAAGTTGGTGCAA Found at i:4038786 original size:87 final size:87 Alignment explanation

Indices: 4038628--4038918 Score: 442 Period size: 87 Copynumber: 3.3 Consensus size: 87 4038618 TTCTAAGTCT * * 4038628 AATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG-ACTAATGTTGCTGGCCTT 1 AATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGAAC-AATGTTGCTGGCCTT * 4038692 GAATCAGCACATTAGCATAAGCCC 64 GAATCAGCACATTGGCATAAGCCC * * 4038716 AATATCGGT-GCTCTTGAATCAGCATATTGGCACCTTGTCTTTAAGAACAATGTCGCTGGCCTTG 1 AATATCGCTGGC-CTTGAATCAGCATATTGGCACCTTGTCTTTAAGAACAATGTTGCTGGCCTTG * 4038780 AATCAGCACATTGGCATAAGCCT 65 AATCAGCACATTGGCATAAGCCC * * 4038803 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCGTTAAGACCAATGTTGCTGGCCTTGA 1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGAACAATGTTGCTGGCCTTGA * 4038868 ATCAGCATATTGGCATAAGCCC 66 ATCAGCACATTGGCATAAGCCC * * 4038890 ACTATCGCTGGCCTTGAATCAGCACATTG 1 AATATCGCTGGCCTTGAATCAGCATATTG 4038919 ACACAAGCCA Statistics Matches: 187, Mismatches: 13, Indels: 7 0.90 0.06 0.03 Matches are distributed among these distances: 87 153 0.82 88 34 0.18 ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30 Consensus pattern (87 bp): AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGAACAATGTTGCTGGCCTTGA ATCAGCACATTGGCATAAGCCC Done.