Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A10

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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 1825971 characters in sequence are not A, C, G, or T


File 7 of 343

Found at i:2417624 original size:25 final size:26

Alignment explanation

Indices: 2417584--2417632 Score: 66 Period size: 25 Copynumber: 1.9 Consensus size: 26 2417574 TGCATTGCAA * 2417584 CAAAGAACCAGTAGCAGA-AAATTGAT 1 CAAAGAACCAGCAGCA-ACAAATTGAT 2417610 CAAAG-ACCAGCAGCAACAAATTG 1 CAAAGAACCAGCAGCAACAAATTG 2417633 TATAATTTGA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 24 1 0.05 25 15 0.71 26 5 0.24 ACGTcount: A:0.49, C:0.20, G:0.18, T:0.12 Consensus pattern (26 bp): CAAAGAACCAGCAGCAACAAATTGAT Found at i:2437301 original size:30 final size:30 Alignment explanation

Indices: 2437266--2437329 Score: 83 Period size: 30 Copynumber: 2.1 Consensus size: 30 2437256 CATATTGAAT * * 2437266 TTTGGTGATAAAAAAAATAAAATTGAACAA 1 TTTGGTAATAAAAAAAATAAAATTAAACAA ** * 2437296 TTTGGTAATAAAAATGATAAAATTAAATAA 1 TTTGGTAATAAAAAAAATAAAATTAAACAA 2437326 TTTG 1 TTTG 2437330 ACGATAAATA Statistics Matches: 29, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 30 29 1.00 ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33 Consensus pattern (30 bp): TTTGGTAATAAAAAAAATAAAATTAAACAA Found at i:2438818 original size:16 final size:14 Alignment explanation

Indices: 2438797--2438834 Score: 58 Period size: 14 Copynumber: 2.6 Consensus size: 14 2438787 TAAAATAATT 2438797 TTTTTAAATTTAAATA 1 TTTTTAAATTT--ATA 2438813 TTTTTAAATTTATA 1 TTTTTAAATTTATA 2438827 TTTTTAAA 1 TTTTTAAA 2438835 AAATTTATAA Statistics Matches: 22, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 14 11 0.50 16 11 0.50 ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (14 bp): TTTTTAAATTTATA Found at i:2438860 original size:33 final size:31 Alignment explanation

Indices: 2438780--2438860 Score: 76 Period size: 33 Copynumber: 2.5 Consensus size: 31 2438770 TCTCTCAATA ** 2438780 AAAATTTTAAAATA-ATTTTTTTAAATTTA- 1 AAAATTTTAAAATATATTTTTAAAAATTTAT * * 2438809 AATATTTTTAAATTTATATTTTTAAAAAATTTAT 1 AA-AATTTTAAA-ATATATTTTT-AAAAATTTAT 2438843 AAACATTTTAAAATATAT 1 AAA-ATTTTAAAATATAT 2438861 AAAGAAAAAA Statistics Matches: 40, Mismatches: 6, Indels: 8 0.74 0.11 0.15 Matches are distributed among these distances: 29 2 0.05 30 8 0.20 31 2 0.05 32 6 0.15 33 13 0.32 34 9 0.22 ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51 Consensus pattern (31 bp): AAAATTTTAAAATATATTTTTAAAAATTTAT Found at i:2440407 original size:11 final size:11 Alignment explanation

Indices: 2440391--2440423 Score: 66 Period size: 11 Copynumber: 3.0 Consensus size: 11 2440381 TATTGTTGTG 2440391 TCTGGTTTTAA 1 TCTGGTTTTAA 2440402 TCTGGTTTTAA 1 TCTGGTTTTAA 2440413 TCTGGTTTTAA 1 TCTGGTTTTAA 2440424 CTTAGGTAAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 22 1.00 ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55 Consensus pattern (11 bp): TCTGGTTTTAA Found at i:2442043 original size:4 final size:4 Alignment explanation

Indices: 2442034--2442059 Score: 52 Period size: 4 Copynumber: 6.5 Consensus size: 4 2442024 TATTGCAGAA 2442034 ATGT ATGT ATGT ATGT ATGT ATGT AT 1 ATGT ATGT ATGT ATGT ATGT ATGT AT 2442060 CAACATAATG Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 22 1.00 ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50 Consensus pattern (4 bp): ATGT Found at i:2444744 original size:19 final size:19 Alignment explanation

Indices: 2444720--2444756 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 2444710 AATATGTATG * 2444720 AAATTAAAATGAACAAAAT 1 AAATTAAAATAAACAAAAT * 2444739 AAATTAAATTAAACAAAA 1 AAATTAAAATAAACAAAA 2444757 CAAAATTTAA Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 16 1.00 ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22 Consensus pattern (19 bp): AAATTAAAATAAACAAAAT Found at i:2445423 original size:11 final size:11 Alignment explanation

Indices: 2445409--2445451 Score: 59 Period size: 11 Copynumber: 3.9 Consensus size: 11 2445399 CGCAAATGCC * 2445409 AACAAAATAGT 1 AACAAAATAAT * 2445420 AACAATATAAT 1 AACAAAATAAT * 2445431 AGCAAAATAAT 1 AACAAAATAAT 2445442 AACAAAATAA 1 AACAAAATAA 2445452 CAGGAAAATG Statistics Matches: 27, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 11 27 1.00 ACGTcount: A:0.67, C:0.09, G:0.05, T:0.19 Consensus pattern (11 bp): AACAAAATAAT Found at i:2445439 original size:22 final size:22 Alignment explanation

Indices: 2445411--2445460 Score: 64 Period size: 22 Copynumber: 2.3 Consensus size: 22 2445401 CAAATGCCAA * * * 2445411 CAAAATAGTAACAATATAATAG 1 CAAAATAATAACAAAATAACAG 2445433 CAAAATAATAACAAAATAACAG 1 CAAAATAATAACAAAATAACAG * 2445455 GAAAAT 1 CAAAAT 2445461 GGCAGCAAAA Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 22 24 1.00 ACGTcount: A:0.64, C:0.10, G:0.08, T:0.18 Consensus pattern (22 bp): CAAAATAATAACAAAATAACAG Found at i:2446104 original size:22 final size:22 Alignment explanation

Indices: 2446064--2446119 Score: 71 Period size: 22 Copynumber: 2.6 Consensus size: 22 2446054 TTAAAAAATA * 2446064 TAAATTTAAA-AGTTTTAT-AT 1 TAAATTTAAATAATTTTATAAT * 2446084 TCAAATTTATATAATTTTATAAT 1 T-AAATTTAAATAATTTTATAAT 2446107 TAAATTTAAATAA 1 TAAATTTAAATAA 2446120 AATAATATGT Statistics Matches: 30, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 20 1 0.03 21 8 0.27 22 18 0.60 23 3 0.10 ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48 Consensus pattern (22 bp): TAAATTTAAATAATTTTATAAT Found at i:2453292 original size:21 final size:22 Alignment explanation

Indices: 2453268--2453310 Score: 63 Period size: 22 Copynumber: 2.0 Consensus size: 22 2453258 CGGGAAACCA 2453268 AATT-AAAATTTT-AATTTAATT 1 AATTAAAAATTTTCAA-TTAATT 2453289 AATTAAAAATTTTCAATTAATT 1 AATTAAAAATTTTCAATTAATT 2453311 TACTTGTTTA Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 21 4 0.20 22 14 0.70 23 2 0.10 ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49 Consensus pattern (22 bp): AATTAAAAATTTTCAATTAATT Found at i:2454941 original size:17 final size:19 Alignment explanation

Indices: 2454921--2454964 Score: 58 Period size: 17 Copynumber: 2.4 Consensus size: 19 2454911 ACAGATGTAA 2454921 AAAAAATTATAGAAA-A-T 1 AAAAAATTATAGAAATATT 2454938 -AAAAATATATAGAAATATT 1 AAAAAAT-TATAGAAATATT 2454957 AAAAAATT 1 AAAAAATT 2454965 TAAATTCATA Statistics Matches: 23, Mismatches: 0, Indels: 6 0.79 0.00 0.21 Matches are distributed among these distances: 16 6 0.26 17 8 0.35 18 1 0.04 19 2 0.09 20 6 0.26 ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27 Consensus pattern (19 bp): AAAAAATTATAGAAATATT Found at i:2455830 original size:26 final size:27 Alignment explanation

Indices: 2455779--2455831 Score: 72 Period size: 26 Copynumber: 2.0 Consensus size: 27 2455769 AAAAAAGTCA * 2455779 TAAATATTTATCACCTTTTTGAATTTT 1 TAAATATTTATCACCTTTTTAAATTTT ** 2455806 TAAATATTT-TCATTTTTTTAAATTTT 1 TAAATATTTATCACCTTTTTAAATTTT 2455832 AATAATTTTT Statistics Matches: 23, Mismatches: 3, Indels: 1 0.85 0.11 0.04 Matches are distributed among these distances: 26 14 0.61 27 9 0.39 ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60 Consensus pattern (27 bp): TAAATATTTATCACCTTTTTAAATTTT Found at i:2457073 original size:15 final size:17 Alignment explanation

Indices: 2457044--2457086 Score: 54 Period size: 15 Copynumber: 2.6 Consensus size: 17 2457034 TTTAACCTTT 2457044 TAAAAGTTATAAAAAT-A 1 TAAAA-TTATAAAAATAA * 2457061 T-AAATTATTAAAATAA 1 TAAAATTATAAAAATAA 2457077 TAAAATTATA 1 TAAAATTATA 2457087 TTTTTACTAT Statistics Matches: 22, Mismatches: 2, Indels: 4 0.79 0.07 0.14 Matches are distributed among these distances: 15 9 0.41 16 5 0.23 17 8 0.36 ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35 Consensus pattern (17 bp): TAAAATTATAAAAATAA Found at i:2458190 original size:31 final size:30 Alignment explanation

Indices: 2458114--2458190 Score: 75 Period size: 31 Copynumber: 2.5 Consensus size: 30 2458104 TTCAAAAATA 2458114 TTGAAGGATCTAATTAAAAATTTTAAAACTT 1 TTGAAGGA-CTAATTAAAAATTTTAAAACTT * * ** 2458145 TTGAATGG-CTTAATTAGACATTTTAAATTTT 1 TTGAA-GGAC-TAATTAAAAATTTTAAAACTT 2458176 TTGAAGGGACTAATT 1 TTGAA-GGACTAATT 2458191 CAGATTTTCA Statistics Matches: 38, Mismatches: 5, Indels: 6 0.78 0.10 0.12 Matches are distributed among these distances: 30 1 0.03 31 34 0.89 32 3 0.08 ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42 Consensus pattern (30 bp): TTGAAGGACTAATTAAAAATTTTAAAACTT Found at i:2460372 original size:35 final size:37 Alignment explanation

Indices: 2460303--2460378 Score: 102 Period size: 35 Copynumber: 2.1 Consensus size: 37 2460293 AAACAATAAA * 2460303 AATACAATATTAAAATATATATATATAATGTATACAT 1 AATACAATATTAAAATATATATATATAATATATACAT * ** 2460340 AATATAATATTAAAATAT-T-TATATGGTATATACAT 1 AATACAATATTAAAATATATATATATAATATATACAT 2460375 AATA 1 AATA 2460379 ATGTAAAAAA Statistics Matches: 35, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 35 17 0.49 36 1 0.03 37 17 0.49 ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39 Consensus pattern (37 bp): AATACAATATTAAAATATATATATATAATATATACAT Found at i:2460981 original size:40 final size:39 Alignment explanation

Indices: 2460870--2461024 Score: 238 Period size: 40 Copynumber: 3.9 Consensus size: 39 2460860 TTGATTCCAC * * * 2460870 TCCCCCATGCTACTTTGTTTTATTATTAATTAAAACTAC 1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACTAT * 2460909 TCCTCCATACTATTTTGTTTTATTATTAATTAAAACTAT 1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACTAT * 2460948 TCCCCCGTACTATTTTGTTTTTATTATTAATTAAAACTAT 1 TCCCCCATACTATTTTG-TTTTATTATTAATTAAAACTAT * 2460988 TCCCTCATACTATTTTGTTTTTATTATTAATTAAAAC 1 TCCCCCATACTATTTTG-TTTTATTATTAATTAAAAC 2461025 CATACTTTAT Statistics Matches: 107, Mismatches: 8, Indels: 1 0.92 0.07 0.01 Matches are distributed among these distances: 39 50 0.47 40 57 0.53 ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49 Consensus pattern (39 bp): TCCCCCATACTATTTTGTTTTATTATTAATTAAAACTAT Found at i:2461514 original size:22 final size:23 Alignment explanation

Indices: 2461466--2461522 Score: 71 Period size: 22 Copynumber: 2.5 Consensus size: 23 2461456 AACCCCCTCT ** 2461466 AATACAATCTCTTCTGTCCCCAA 1 AATACAATCGATTCTGTCCCCAA * 2461489 AATACAATCGATTCT-TCCTCAA 1 AATACAATCGATTCTGTCCCCAA * 2461511 AATACCATCGAT 1 AATACAATCGAT 2461523 CCCCCCCTTA Statistics Matches: 30, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 22 17 0.57 23 13 0.43 ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30 Consensus pattern (23 bp): AATACAATCGATTCTGTCCCCAA Found at i:2476412 original size:41 final size:41 Alignment explanation

Indices: 2476366--2476454 Score: 160 Period size: 41 Copynumber: 2.2 Consensus size: 41 2476356 TATTGATGAA 2476366 AAAATATGGGTCAATAATTAATAACGATTCACCTAAAAACT 1 AAAATATGGGTCAATAATTAATAACGATTCACCTAAAAACT * * 2476407 AAAATATGGGTCAATAATTAATAACGATTCACCTGAAGACT 1 AAAATATGGGTCAATAATTAATAACGATTCACCTAAAAACT 2476448 AAAATAT 1 AAAATAT 2476455 AGAAATGATC Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 41 46 1.00 ACGTcount: A:0.48, C:0.13, G:0.11, T:0.27 Consensus pattern (41 bp): AAAATATGGGTCAATAATTAATAACGATTCACCTAAAAACT Found at i:2477108 original size:18 final size:20 Alignment explanation

Indices: 2477073--2477110 Score: 53 Period size: 18 Copynumber: 2.0 Consensus size: 20 2477063 AGTCCACTAT * 2477073 TTTTATTTTAGAATATTTAA 1 TTTTATTTTAGAAAATTTAA 2477093 TTTT-TTTTA-AAAATTTAA 1 TTTTATTTTAGAAAATTTAA 2477111 GTCCAATTAT Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 18 8 0.47 19 5 0.29 20 4 0.24 ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61 Consensus pattern (20 bp): TTTTATTTTAGAAAATTTAA Found at i:2479994 original size:22 final size:23 Alignment explanation

Indices: 2479969--2480028 Score: 65 Period size: 22 Copynumber: 2.7 Consensus size: 23 2479959 TATAAGAATC 2479969 AAATTA-AACATTGAAAAAAA-TT 1 AAATTACAA-ATTGAAAAAAACTT 2479991 AAA-TACTAAATTGAAAAAAACTT 1 AAATTAC-AAATTGAAAAAAACTT * 2480014 AAA-TACAAAATGAAA 1 AAATTACAAATTGAAA 2480029 CATTGAAATT Statistics Matches: 34, Mismatches: 1, Indels: 6 0.83 0.02 0.15 Matches are distributed among these distances: 21 2 0.06 22 22 0.65 23 10 0.29 ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23 Consensus pattern (23 bp): AAATTACAAATTGAAAAAAACTT Found at i:2480015 original size:23 final size:21 Alignment explanation

Indices: 2479978--2480028 Score: 75 Period size: 22 Copynumber: 2.3 Consensus size: 21 2479968 CAAATTAAAC 2479978 ATTGAAAAAAATTAAATACTAA 1 ATTGAAAAAAATTAAATAC-AA 2480000 ATTGAAAAAAACTTAAATACAA 1 ATTGAAAAAAA-TTAAATACAA * 2480022 AATGAAA 1 ATTGAAA 2480029 CATTGAAATT Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 22 19 0.70 23 8 0.30 ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24 Consensus pattern (21 bp): ATTGAAAAAAATTAAATACAA Found at i:2481177 original size:154 final size:154 Alignment explanation

Indices: 2480975--2481594 Score: 889 Period size: 154 Copynumber: 4.0 Consensus size: 154 2480965 ATATGTTTGA * * * * * 2480975 TGTGTGAATTACATTTGTTTTTATTAAGCTTCTTGTAAACGAGTCTTGTTTTGTTATAATTCAGT 1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT * 2481040 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAGT 66 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT 2481105 GTTTTGTGTTGATTTTCAGTGAGT 131 GTTTTGTGTTGATTTTCAGTGAGT * 2481129 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGGCTTGTTTTTTTATAATTCAGT 1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT * * 2481194 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTCGGAA--TG--TTTAGT 66 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT 2481255 GTTTTGTGTTGATTTTCAGTGAGT 131 GTTTTGTGTTGATTTTCAGTGAGT * 2481279 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAATGAGTCTTG-TTTTTTATAATTCAGT 1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT * 2481343 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTCGATTGGCTGGTTTTTGAAATGTGAATTTAGT 66 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT * * * * 2481408 GTTTTGTATTGATGTT-AGTGGGC 131 GTTTTGTGTTGATTTTCAGTGAGT ** 2481431 TGTGAGAATTACATTTCATTTTGATTAAGCTTCTTATAAACGTTTCTTGTTTTTTTATAATTCAG 1 TGTGAGAATTACATTT-ATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAG * * * * * * 2481496 TTTAGGATTCAATTTTTT-GCTTTGGTTTG-TTTGGTCGATTGGCTGTTTTTTTTAAACGTGAAT 65 TTTACGATTC-GTTTTTTCGCTTTGG--TGATTTGGTAGATTGGCTG-GTTTTTGAAATGTGAAT * * * 2481559 TGAGTGTTTCGTGTTG-TTGTTTAGTGAGT 126 TTAGTGTTTTGTGTTGATT-TTCAGTGAGT 2481588 TGTGAGA 1 TGTGAGA 2481595 TTGAGTCAAA Statistics Matches: 424, Mismatches: 30, Indels: 21 0.89 0.06 0.04 Matches are distributed among these distances: 149 66 0.16 150 76 0.18 151 2 0.00 152 23 0.05 153 49 0.12 154 142 0.33 155 23 0.05 156 31 0.07 157 12 0.03 ACGTcount: A:0.19, C:0.08, G:0.22, T:0.50 Consensus pattern (154 bp): TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT GTTTTGTGTTGATTTTCAGTGAGT Found at i:2486259 original size:18 final size:18 Alignment explanation

Indices: 2486213--2486263 Score: 54 Period size: 18 Copynumber: 2.9 Consensus size: 18 2486203 TCATCTTAAC * 2486213 TTATTTTTAT-TGTT-TG 1 TTATTTTTATATATTATG * 2486229 TAATATTTT-TATATTATG 1 TTAT-TTTTATATATTATG 2486247 TTATTTTTATATATTAT 1 TTATTTTTATATATTAT 2486264 ATAATTTATA Statistics Matches: 28, Mismatches: 3, Indels: 6 0.76 0.08 0.16 Matches are distributed among these distances: 16 4 0.14 17 11 0.39 18 13 0.46 ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69 Consensus pattern (18 bp): TTATTTTTATATATTATG Found at i:2511678 original size:20 final size:20 Alignment explanation

Indices: 2511642--2511688 Score: 71 Period size: 19 Copynumber: 2.5 Consensus size: 20 2511632 GAATCGAATT * 2511642 TATAAAT-AATTTTTTATAC 1 TATAAATAAATCTTTTATAC 2511661 TATAAATAAATCTTTTATAC 1 TATAAATAAATCTTTTATAC 2511681 -ATAAATAA 1 TATAAATAA 2511689 TGAAAATAAT Statistics Matches: 26, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 19 15 0.58 20 11 0.42 ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45 Consensus pattern (20 bp): TATAAATAAATCTTTTATAC Found at i:2517383 original size:32 final size:32 Alignment explanation

Indices: 2517306--2517383 Score: 79 Period size: 32 Copynumber: 2.5 Consensus size: 32 2517296 AAATATGTTG * * 2517306 TTAGT-CTCTGTA-TTTTGATAGAATTTGAGAT 1 TTAGTCCT-TGTACTTTTGATAGAATATGAAAT * * * * 2517337 TTAATCTTTATACTTTTTATAGAATATGAAAT 1 TTAGTCCTTGTACTTTTGATAGAATATGAAAT 2517369 TTAGTCCTTGTACTT 1 TTAGTCCTTGTACTT 2517384 AAAACGTTGA Statistics Matches: 36, Mismatches: 9, Indels: 3 0.75 0.19 0.06 Matches are distributed among these distances: 31 7 0.19 32 29 0.81 ACGTcount: A:0.28, C:0.09, G:0.13, T:0.50 Consensus pattern (32 bp): TTAGTCCTTGTACTTTTGATAGAATATGAAAT Found at i:2519496 original size:17 final size:17 Alignment explanation

Indices: 2519446--2519497 Score: 50 Period size: 20 Copynumber: 2.9 Consensus size: 17 2519436 ATATATAAAA * * 2519446 TATAAATTTTAAATATT 1 TATAAAATTTAATTATT * 2519463 TTTAAGTAATATTAATTATT 1 TATAA--AAT-TTAATTATT 2519483 TATAAAATTTAATTA 1 TATAAAATTTAATTA 2519498 AAATATATAA Statistics Matches: 28, Mismatches: 4, Indels: 6 0.74 0.11 0.16 Matches are distributed among these distances: 17 11 0.39 18 3 0.11 19 2 0.07 20 12 0.43 ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52 Consensus pattern (17 bp): TATAAAATTTAATTATT Found at i:2523860 original size:11 final size:11 Alignment explanation

Indices: 2523844--2523868 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 2523834 ACATTTATGA 2523844 TTTTCTCTTTT 1 TTTTCTCTTTT 2523855 TTTTCTCTTTT 1 TTTTCTCTTTT 2523866 TTT 1 TTT 2523869 GTAATAGATT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84 Consensus pattern (11 bp): TTTTCTCTTTT Found at i:2529113 original size:75 final size:75 Alignment explanation

Indices: 2529003--2529252 Score: 430 Period size: 75 Copynumber: 3.3 Consensus size: 75 2528993 CATTGTTGTA * * 2529003 CTCATTGTTACCATTGTAATAGTTGTTGTTG-TTCTGGTTTTCCTTAGTACTCCATCCTTTCTCA 1 CTCATTGTTACCATTGTAATAGTTGTTG-CGATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCA * 2529067 GTGAACATGGC 65 GTGAACAAGGC * 2529078 CTCATTGTTACCGTTGTAATAGTTGTTGCGATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCAG 1 CTCATTGTTACCATTGTAATAGTTGTTGCGATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCAG 2529143 TGAACAAGGC 66 TGAACAAGGC * * 2529153 CTCATTGTTACCATTGTAATAGTTGTTGCTATTCTGGTTTTCCTTGGTACTCCACCCTTTCTCAG 1 CTCATTGTTACCATTGTAATAGTTGTTGCGATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCAG 2529218 TGAACAAGGC 66 TGAACAAGGC 2529228 CTCATTGTTACCATTGTAATAGTTG 1 CTCATTGTTACCATTGTAATAGTTG 2529253 ACATTGTAGT Statistics Matches: 167, Mismatches: 7, Indels: 2 0.95 0.04 0.01 Matches are distributed among these distances: 74 1 0.01 75 166 0.99 ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41 Consensus pattern (75 bp): CTCATTGTTACCATTGTAATAGTTGTTGCGATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCAG TGAACAAGGC Found at i:2534951 original size:26 final size:24 Alignment explanation

Indices: 2534921--2534970 Score: 73 Period size: 26 Copynumber: 2.0 Consensus size: 24 2534911 AAATAAAAAA * 2534921 ATTTAAAAATATAATAAATCAAATAT 1 ATTTAAAAACATAA-AAA-CAAATAT 2534947 ATTTAAAAACATAAAAACAAATAT 1 ATTTAAAAACATAAAAACAAATAT 2534971 TAAAACAAAT Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 24 7 0.30 25 3 0.13 26 13 0.57 ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30 Consensus pattern (24 bp): ATTTAAAAACATAAAAACAAATAT Found at i:2537772 original size:3 final size:3 Alignment explanation

Indices: 2537764--2537790 Score: 54 Period size: 3 Copynumber: 9.0 Consensus size: 3 2537754 GAGAGAGATG 2537764 TAA TAA TAA TAA TAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA 2537791 AAGGTCTGAA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 24 1.00 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (3 bp): TAA Found at i:2551921 original size:23 final size:23 Alignment explanation

Indices: 2551895--2551947 Score: 97 Period size: 23 Copynumber: 2.3 Consensus size: 23 2551885 ATAAGTGCCA 2551895 CACTGATATGTAGCCGAAGCTAC 1 CACTGATATGTAGCCGAAGCTAC * 2551918 CACTGAAATGTAGCCGAAGCTAC 1 CACTGATATGTAGCCGAAGCTAC 2551941 CACTGAT 1 CACTGAT 2551948 CAATAACACT Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 23 28 1.00 ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21 Consensus pattern (23 bp): CACTGATATGTAGCCGAAGCTAC Found at i:2552047 original size:8 final size:8 Alignment explanation

Indices: 2552034--2552062 Score: 58 Period size: 8 Copynumber: 3.6 Consensus size: 8 2552024 ACCCGGGACT 2552034 CACTGTAA 1 CACTGTAA 2552042 CACTGTAA 1 CACTGTAA 2552050 CACTGTAA 1 CACTGTAA 2552058 CACTG 1 CACTG 2552063 GTCTCTAGTG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 21 1.00 ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24 Consensus pattern (8 bp): CACTGTAA Found at i:2552193 original size:18 final size:17 Alignment explanation

Indices: 2552167--2552205 Score: 53 Period size: 18 Copynumber: 2.2 Consensus size: 17 2552157 ATTTTCCTTC 2552167 CACATTC-AATATTAATT 1 CACATTCAAATA-TAATT 2552184 CACATATCAAATATAATT 1 CACAT-TCAAATATAATT 2552202 CACA 1 CACA 2552206 ATTTATACAA Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 17 5 0.25 18 11 0.55 19 4 0.20 ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33 Consensus pattern (17 bp): CACATTCAAATATAATT Found at i:2562787 original size:21 final size:21 Alignment explanation

Indices: 2562763--2562815 Score: 63 Period size: 21 Copynumber: 2.5 Consensus size: 21 2562753 TATGGACTCT 2562763 TTTTATTATATTATTT-ATAAA 1 TTTTATTA-ATTATTTAATAAA * * 2562784 TTTTTTTAATTATTTAATATA 1 TTTTATTAATTATTTAATAAA * 2562805 TTTTAGTAATT 1 TTTTATTAATT 2562816 TTTCTATGTC Statistics Matches: 27, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 20 7 0.26 21 20 0.74 ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64 Consensus pattern (21 bp): TTTTATTAATTATTTAATAAA Found at i:2565341 original size:16 final size:16 Alignment explanation

Indices: 2565316--2565347 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 2565306 TTTTTATTGC 2565316 TAAAAACTTAAAATTT 1 TAAAAACTTAAAATTT * 2565332 TAAAACCTTAAAATTT 1 TAAAAACTTAAAATTT 2565348 CGACAAATCA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38 Consensus pattern (16 bp): TAAAAACTTAAAATTT Found at i:2576250 original size:29 final size:30 Alignment explanation

Indices: 2576190--2576250 Score: 72 Period size: 30 Copynumber: 2.1 Consensus size: 30 2576180 TCAACTCTTT * * 2576190 TTTTTTAAAAGGCTGATAGTCAAATTTGAA 1 TTTTTTAAAAGACTGATAGTCAAAATTGAA * 2576220 TTTTTTAAAAGATTGA-AGATCAAAATT-AA 1 TTTTTTAAAAGACTGATAG-TCAAAATTGAA 2576249 TT 1 TT 2576251 AAAAAAAGAA Statistics Matches: 27, Mismatches: 3, Indels: 3 0.82 0.09 0.09 Matches are distributed among these distances: 29 6 0.22 30 21 0.78 ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41 Consensus pattern (30 bp): TTTTTTAAAAGACTGATAGTCAAAATTGAA Found at i:2586361 original size:28 final size:28 Alignment explanation

Indices: 2586321--2586380 Score: 84 Period size: 28 Copynumber: 2.1 Consensus size: 28 2586311 GTCATTATCA 2586321 ACCCCATAAGTTATAAAACCCTTCCTAT 1 ACCCCATAAGTTATAAAACCCTTCCTAT * * ** 2586349 ACCCCATAAGTTATTAGACTTTTCCTAT 1 ACCCCATAAGTTATAAAACCCTTCCTAT 2586377 ACCC 1 ACCC 2586381 ATTAATATGG Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32 Consensus pattern (28 bp): ACCCCATAAGTTATAAAACCCTTCCTAT Found at i:2600150 original size:17 final size:17 Alignment explanation

Indices: 2600128--2600161 Score: 68 Period size: 17 Copynumber: 2.0 Consensus size: 17 2600118 AACCGCTTCA 2600128 TTTGAACAAATCACATT 1 TTTGAACAAATCACATT 2600145 TTTGAACAAATCACATT 1 TTTGAACAAATCACATT 2600162 AATAAAAGAG Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35 Consensus pattern (17 bp): TTTGAACAAATCACATT Found at i:2602259 original size:13 final size:13 Alignment explanation

Indices: 2602241--2602268 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 2602231 ATTTAAATCT 2602241 TAATGCAAAACAA 1 TAATGCAAAACAA 2602254 TAATGCAAAACAA 1 TAATGCAAAACAA 2602267 TA 1 TA 2602269 TTCGTTAAAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 15 1.00 ACGTcount: A:0.61, C:0.14, G:0.07, T:0.18 Consensus pattern (13 bp): TAATGCAAAACAA Found at i:2604719 original size:11 final size:10 Alignment explanation

Indices: 2604703--2604744 Score: 57 Period size: 11 Copynumber: 4.0 Consensus size: 10 2604693 TTTTTCTCAC 2604703 AAAATTAAATA 1 AAAATTAAA-A 2604714 AAAATTATAAA 1 AAAATTA-AAA * 2604725 AAAATTGAAA 1 AAAATTAAAA 2604735 AAAATTAAAA 1 AAAATTAAAA 2604745 TTAGTATAAA Statistics Matches: 28, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 10 12 0.43 11 14 0.50 12 2 0.07 ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24 Consensus pattern (10 bp): AAAATTAAAA Found at i:2604725 original size:9 final size:9 Alignment explanation

Indices: 2604711--2604835 Score: 55 Period size: 9 Copynumber: 13.7 Consensus size: 9 2604701 ACAAAATTAA 2604711 ATAAAAATT 1 ATAAAAATT 2604720 ATAAAAAAATT 1 AT--AAAAATT 2604731 GA-AAAAA-- 1 -ATAAAAATT * 2604738 ATTAAAATT 1 ATAAAAATT * 2604747 AGTATAAACTT 1 A-TA-AAAATT * 2604758 ATTAAAATT 1 ATAAAAATT * 2604767 ATAAAAAAT 1 ATAAAAATT * 2604776 ATAAATATT 1 ATAAAAATT 2604785 AT-AAAATCT 1 ATAAAAAT-T * 2604794 A-ATAAATCT 1 ATAAAAAT-T * 2604803 A-ATAAATT 1 ATAAAAATT * 2604811 GTAAAAATAT 1 ATAAAAAT-T * 2604821 ATAAAAATA 1 ATAAAAATT 2604830 ATAAAA 1 ATAAAA 2604836 CTTGTTTAAA Statistics Matches: 89, Mismatches: 15, Indels: 24 0.70 0.12 0.19 Matches are distributed among these distances: 6 1 0.01 7 4 0.04 8 5 0.06 9 55 0.62 10 10 0.11 11 13 0.15 12 1 0.01 ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31 Consensus pattern (9 bp): ATAAAAATT Found at i:2604800 original size:19 final size:19 Alignment explanation

Indices: 2604776--2604826 Score: 52 Period size: 19 Copynumber: 2.8 Consensus size: 19 2604766 TATAAAAAAT 2604776 ATAAATATTATAAAATCTA 1 ATAAATATTATAAAATCTA * * * * 2604795 ATAAATCTAATAAATTGTA 1 ATAAATATTATAAAATCTA 2604814 A-AAATA-TATAAAA 1 ATAAATATTATAAAA 2604827 ATAATAAAAC Statistics Matches: 25, Mismatches: 7, Indels: 2 0.74 0.21 0.06 Matches are distributed among these distances: 17 5 0.20 18 4 0.16 19 16 0.64 ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33 Consensus pattern (19 bp): ATAAATATTATAAAATCTA Found at i:2605106 original size:32 final size:32 Alignment explanation

Indices: 2605039--2605110 Score: 83 Period size: 32 Copynumber: 2.2 Consensus size: 32 2605029 AATTTTTTAT * 2605039 TTTTTTAATATTTTTATCAAATCAAAATTAAA 1 TTTTTAAATATTTTTATCAAATCAAAATTAAA * ** * 2605071 TTTTGTAAATATTTTTAT-ATATCTTAATTAGA 1 TTTT-TAAATATTTTTATCAAATCAAAATTAAA 2605103 TTTTTAAA 1 TTTTTAAA 2605111 CTTCTATAAG Statistics Matches: 34, Mismatches: 5, Indels: 3 0.81 0.12 0.07 Matches are distributed among these distances: 31 4 0.12 32 18 0.53 33 12 0.35 ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54 Consensus pattern (32 bp): TTTTTAAATATTTTTATCAAATCAAAATTAAA Found at i:2606964 original size:30 final size:28 Alignment explanation

Indices: 2606929--2607010 Score: 85 Period size: 29 Copynumber: 2.8 Consensus size: 28 2606919 ATAATTTATG 2606929 AAATTTTAAATTAATAATAAAATTAT-ATTTT 1 AAATTTTAAA--AATAATAAAATT-TGA-TTT * 2606960 AATTTTTTAAAAATAATAAAATTTGATTT 1 AA-ATTTTAAAAATAATAAAATTTGATTT * 2606989 AAATTTTAAAAAAATATAAAAT 1 AAATTTTAAAAATA-ATAAAAT 2607011 ATAAAATATT Statistics Matches: 45, Mismatches: 3, Indels: 8 0.80 0.05 0.14 Matches are distributed among these distances: 28 10 0.22 29 13 0.29 30 13 0.29 31 2 0.04 32 7 0.16 ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44 Consensus pattern (28 bp): AAATTTTAAAAATAATAAAATTTGATTT Found at i:2607023 original size:8 final size:7 Alignment explanation

Indices: 2606999--2607033 Score: 52 Period size: 7 Copynumber: 4.7 Consensus size: 7 2606989 AAATTTTAAA 2606999 AAAATAT 1 AAAATAT 2607006 AAAATAT 1 AAAATAT 2607013 AAAATATT 1 AAAATA-T 2607021 AAAATAAT 1 AAAAT-AT 2607029 AAAAT 1 AAAAT 2607034 TATATATATA Statistics Matches: 26, Mismatches: 0, Indels: 3 0.90 0.00 0.10 Matches are distributed among these distances: 7 13 0.50 8 12 0.46 9 1 0.04 ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29 Consensus pattern (7 bp): AAAATAT Found at i:2607023 original size:25 final size:24 Alignment explanation

Indices: 2606989--2607037 Score: 62 Period size: 25 Copynumber: 2.0 Consensus size: 24 2606979 AATTTGATTT * 2606989 AAATTTTAAAAAAATATAAAATATA 1 AAATATTAAAAAAATA-AAAATATA * * 2607014 AAATATTAAAATAATAAAATTATA 1 AAATATTAAAAAAATAAAAATATA 2607038 TATATAATTT Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 24 7 0.33 25 14 0.67 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (24 bp): AAATATTAAAAAAATAAAAATATA Found at i:2607030 original size:16 final size:14 Alignment explanation

Indices: 2606999--2607033 Score: 52 Period size: 16 Copynumber: 2.4 Consensus size: 14 2606989 AAATTTTAAA 2606999 AAAATATAAAATAT 1 AAAATATAAAATAT 2607013 AAAATATTAAAATAAT 1 AAAATA-TAAAAT-AT 2607029 AAAAT 1 AAAAT 2607034 TATATATATA Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 14 6 0.32 15 6 0.32 16 7 0.37 ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29 Consensus pattern (14 bp): AAAATATAAAATAT Found at i:2610134 original size:19 final size:18 Alignment explanation

Indices: 2610106--2610141 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 2610096 ATGCTTCACA 2610106 TTAAATCTAAACTAACAT 1 TTAAATCTAAACTAACAT * 2610124 TTAACATCTAACCTAACA 1 TTAA-ATCTAAACTAACA 2610142 ATCAAATATA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 4 0.25 19 12 0.75 ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31 Consensus pattern (18 bp): TTAAATCTAAACTAACAT Found at i:2613956 original size:3 final size:3 Alignment explanation

Indices: 2613948--2613976 Score: 58 Period size: 3 Copynumber: 9.7 Consensus size: 3 2613938 ATCACATGTT 2613948 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 2613977 TGGATGTAAT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 26 1.00 ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69 Consensus pattern (3 bp): TTA Found at i:2614096 original size:73 final size:73 Alignment explanation

Indices: 2613977--2614162 Score: 363 Period size: 73 Copynumber: 2.5 Consensus size: 73 2613967 TATTATTATT * 2613977 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT 1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT 2614042 ATTTTAAG 66 ATTTTAAG 2614050 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT 1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT 2614115 ATTTTAAG 66 ATTTTAAG 2614123 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT 1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT 2614163 GTCAAGTTGT Statistics Matches: 112, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 73 112 1.00 ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41 Consensus pattern (73 bp): TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT ATTTTAAG Found at i:2637898 original size:5 final size:5 Alignment explanation

Indices: 2637888--2637913 Score: 52 Period size: 5 Copynumber: 5.2 Consensus size: 5 2637878 AAAATTTTTA 2637888 AAAAT AAAAT AAAAT AAAAT AAAAT A 1 AAAAT AAAAT AAAAT AAAAT AAAAT A 2637914 TCATATTTTA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 21 1.00 ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19 Consensus pattern (5 bp): AAAAT Found at i:2642089 original size:25 final size:29 Alignment explanation

Indices: 2642040--2642111 Score: 86 Period size: 25 Copynumber: 2.7 Consensus size: 29 2642030 TGTTGAGTTG 2642040 TATTTATTTTAATATTATTTAAATAAAAA 1 TATTTATTTTAATATTATTTAAATAAAAA 2642069 TATTT-TTTTAAT-TT-TTT-AAT--AAA 1 TATTTATTTTAATATTATTTAAATAAAAA * 2642092 TATCTATTTTAATATT-TTTA 1 TATTTATTTTAATATTATTTA 2642112 GTAATTTTAA Statistics Matches: 39, Mismatches: 1, Indels: 9 0.80 0.02 0.18 Matches are distributed among these distances: 23 7 0.18 24 7 0.18 25 8 0.21 26 3 0.08 27 2 0.05 28 7 0.18 29 5 0.13 ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60 Consensus pattern (29 bp): TATTTATTTTAATATTATTTAAATAAAAA Found at i:2642101 original size:26 final size:28 Alignment explanation

Indices: 2642040--2642111 Score: 75 Period size: 24 Copynumber: 2.7 Consensus size: 28 2642030 TGTTGAGTTG 2642040 TATTTATTTTAATATTATTTAAATAAAAA 1 TATTT-TTTTAATATTATTTAAATAAAAA 2642069 TATTTTTTTAAT-TT-TTT-AAT--AAA 1 TATTTTTTTAATATTATTTAAATAAAAA * 2642092 TATCTATTTTAATATT-TTTA 1 TAT-TTTTTTAATATTATTTA 2642112 GTAATTTTAA Statistics Matches: 39, Mismatches: 1, Indels: 9 0.80 0.02 0.18 Matches are distributed among these distances: 23 6 0.15 24 8 0.21 25 8 0.21 26 3 0.08 27 2 0.05 28 7 0.18 29 5 0.13 ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60 Consensus pattern (28 bp): TATTTTTTTAATATTATTTAAATAAAAA Found at i:2649369 original size:14 final size:14 Alignment explanation

Indices: 2649330--2649371 Score: 59 Period size: 14 Copynumber: 3.0 Consensus size: 14 2649320 CAATTTTTTA 2649330 GTTTAGGGTTTGA- 1 GTTTAGGGTTTGAG * 2649343 GTTTAAGGTTTTGAG 1 GTTT-AGGGTTTGAG 2649358 GTTTAGGGTTTGAG 1 GTTTAGGGTTTGAG 2649372 ATTCTGGGTA Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 13 4 0.16 14 17 0.68 15 4 0.16 ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45 Consensus pattern (14 bp): GTTTAGGGTTTGAG Found at i:2649694 original size:20 final size:20 Alignment explanation

Indices: 2649649--2649696 Score: 62 Period size: 20 Copynumber: 2.4 Consensus size: 20 2649639 AAATTCTATT * 2649649 TGTATTTTATAATAATTAAT 1 TGTATTTTATAATAATTAAA * 2649669 TCTATTTT-TAATAATTTAAA 1 TGTATTTTATAATAA-TTAAA 2649689 TGTATTTT 1 TGTATTTT 2649697 CTTTAAAATT Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 19 6 0.25 20 18 0.75 ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58 Consensus pattern (20 bp): TGTATTTTATAATAATTAAA Found at i:2650721 original size:31 final size:33 Alignment explanation

Indices: 2650659--2650721 Score: 76 Period size: 34 Copynumber: 1.9 Consensus size: 33 2650649 TACTATAAAA * * 2650659 ATTTATTATTAAACATTTATAAATTTTAATATAT 1 ATTTATTATTAAACA-TTATAAATATAAATATAT * 2650693 ATTTATTATTAAA-A-TATGAATATAAATAT 1 ATTTATTATTAAACATTATAAATATAAATAT 2650722 TTTCAAAAAT Statistics Matches: 26, Mismatches: 3, Indels: 3 0.81 0.09 0.09 Matches are distributed among these distances: 31 12 0.46 33 1 0.04 34 13 0.50 ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49 Consensus pattern (33 bp): ATTTATTATTAAACATTATAAATATAAATATAT Found at i:2650755 original size:12 final size:11 Alignment explanation

Indices: 2650696--2650820 Score: 55 Period size: 11 Copynumber: 11.2 Consensus size: 11 2650686 AATATATATT 2650696 TATTATTAAAA 1 TATTATTAAAA * * 2650707 TATGAATATAAA 1 TATTATTA-AAA 2650719 TATT-TTCAAAA 1 TATTATT-AAAA 2650730 -ATATATTAAGAA 1 TAT-TATTAA-AA 2650742 TATTATTTAAAA 1 TATTA-TTAAAA * * 2650754 TA-TAATAATAT 1 TATTATTAA-AA * * 2650765 TATTTTTAAATTT 1 TATTATTAAA--A 2650778 TATTATTAAAA 1 TATTATTAAAA ** * 2650789 TAAAATTATAA 1 TATTATTAAAA 2650800 TATTA--AAAA 1 TATTATTAAAA 2650809 -ATTATTAAAA 1 TATTATTAAAA 2650819 TA 1 TA 2650821 ATAGATTATA Statistics Matches: 84, Mismatches: 16, Indels: 28 0.66 0.12 0.22 Matches are distributed among these distances: 8 4 0.05 9 3 0.04 10 9 0.11 11 31 0.37 12 21 0.25 13 16 0.19 ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44 Consensus pattern (11 bp): TATTATTAAAA Found at i:2650768 original size:23 final size:22 Alignment explanation

Indices: 2650696--2650774 Score: 70 Period size: 23 Copynumber: 3.5 Consensus size: 22 2650686 AATATATATT * 2650696 TATTATTAAAATATGAAT-ATAAA 1 TATTTTTAAAATAT-AATAAT-AA * * * 2650719 TATTTTCAAAAATATATTAAGAA 1 TATTTT-TAAAATATAATAATAA * 2650742 TATTATTTAAAATATAATAATAT 1 TATT-TTTAAAATATAATAATAA 2650765 TATTTTTAAA 1 TATTTTTAAA 2650775 TTTTATTATT Statistics Matches: 45, Mismatches: 8, Indels: 7 0.75 0.13 0.12 Matches are distributed among these distances: 22 6 0.13 23 29 0.64 24 10 0.22 ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44 Consensus pattern (22 bp): TATTTTTAAAATATAATAATAA Found at i:2650813 original size:30 final size:32 Alignment explanation

Indices: 2650779--2650838 Score: 97 Period size: 30 Copynumber: 1.9 Consensus size: 32 2650769 TTTAAATTTT 2650779 ATTATTAAAATAA-A-ATTATAATATTAAAAA 1 ATTATTAAAATAATAGATTATAATATTAAAAA * 2650809 ATTATTAAAATAATAGATTATATTATTAAA 1 ATTATTAAAATAATAGATTATAATATTAAA 2650839 TATAAATAAT Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 30 13 0.48 31 1 0.04 32 13 0.48 ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40 Consensus pattern (32 bp): ATTATTAAAATAATAGATTATAATATTAAAAA Found at i:2652733 original size:17 final size:18 Alignment explanation

Indices: 2652703--2652736 Score: 61 Period size: 17 Copynumber: 1.9 Consensus size: 18 2652693 ATTTAAATTG 2652703 CGGTCGCGGTCGCGTTTT 1 CGGTCGCGGTCGCGTTTT 2652721 CGGTCGC-GTCGCGTTT 1 CGGTCGCGGTCGCGTTT 2652737 GTCGCGGACA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 17 9 0.56 18 7 0.44 ACGTcount: A:0.00, C:0.29, G:0.38, T:0.32 Consensus pattern (18 bp): CGGTCGCGGTCGCGTTTT Found at i:2653892 original size:16 final size:16 Alignment explanation

Indices: 2653871--2653905 Score: 70 Period size: 16 Copynumber: 2.2 Consensus size: 16 2653861 ATTTCAAGTC 2653871 TTACAGCCTATTAATT 1 TTACAGCCTATTAATT 2653887 TTACAGCCTATTAATT 1 TTACAGCCTATTAATT 2653903 TTA 1 TTA 2653906 GTCAAAGTGC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 19 1.00 ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46 Consensus pattern (16 bp): TTACAGCCTATTAATT Found at i:2655621 original size:12 final size:12 Alignment explanation

Indices: 2655604--2655628 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 2655594 TCTTTCACGT 2655604 TCTGTATATCTA 1 TCTGTATATCTA 2655616 TCTGTATATCTA 1 TCTGTATATCTA 2655628 T 1 T 2655629 TAAGGAGATA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52 Consensus pattern (12 bp): TCTGTATATCTA Found at i:2662859 original size:12 final size:12 Alignment explanation

Indices: 2662844--2662869 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 2662834 GCAAACATTA 2662844 ATGACCAAATTT 1 ATGACCAAATTT 2662856 ATGACCAAATTT 1 ATGACCAAATTT 2662868 AT 1 AT 2662870 AATTAATCCT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35 Consensus pattern (12 bp): ATGACCAAATTT Found at i:2663085 original size:17 final size:17 Alignment explanation

Indices: 2663065--2663104 Score: 53 Period size: 17 Copynumber: 2.3 Consensus size: 17 2663055 AAAAAATCCT 2663065 AAAATTAAAATAATTTA 1 AAAATTAAAATAATTTA * * 2663082 AAAATTAAATTTATTTA 1 AAAATTAAAATAATTTA 2663099 ATAAAT 1 A-AAAT 2663105 ATACTTATTA Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 17 16 0.80 18 4 0.20 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (17 bp): AAAATTAAAATAATTTA Found at i:2664637 original size:13 final size:13 Alignment explanation

Indices: 2664621--2664651 Score: 53 Period size: 13 Copynumber: 2.4 Consensus size: 13 2664611 CCTTCTCCTT 2664621 CCCTTTCCCCTAC 1 CCCTTTCCCCTAC * 2664634 CCCTTTCCCTTAC 1 CCCTTTCCCCTAC 2664647 CCCTT 1 CCCTT 2664652 CCCTTTCCCG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.06, C:0.58, G:0.00, T:0.35 Consensus pattern (13 bp): CCCTTTCCCCTAC Found at i:2664637 original size:31 final size:31 Alignment explanation

Indices: 2664602--2664660 Score: 93 Period size: 31 Copynumber: 1.9 Consensus size: 31 2664592 CCATTCTTCT * 2664602 CCCCTTTCCCCTT-CTCCTTCCCTTTCCCCTA 1 CCCCTTT-CCCTTACCCCTTCCCTTTCCCCTA 2664633 CCCCTTTCCCTTACCCCTTCCCTTTCCC 1 CCCCTTTCCCTTACCCCTTCCCTTTCCC 2664661 GTTTTGAAGC Statistics Matches: 26, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 30 5 0.19 31 21 0.81 ACGTcount: A:0.03, C:0.59, G:0.00, T:0.37 Consensus pattern (31 bp): CCCCTTTCCCTTACCCCTTCCCTTTCCCCTA Found at i:2664653 original size:12 final size:12 Alignment explanation

Indices: 2664603--2664656 Score: 56 Period size: 12 Copynumber: 4.4 Consensus size: 12 2664593 CATTCTTCTC * 2664603 CCCTTTCCCCTT 1 CCCTTACCCCTT * 2664615 CTCCTT-CCCTTT 1 C-CCTTACCCCTT * 2664627 CCCCTACCCCTTT 1 CCCTTACCCC-TT 2664640 CCCTTACCCCTT 1 CCCTTACCCCTT 2664652 CCCTT 1 CCCTT 2664657 TCCCGTTTTG Statistics Matches: 35, Mismatches: 4, Indels: 6 0.78 0.09 0.13 Matches are distributed among these distances: 11 3 0.09 12 17 0.49 13 15 0.43 ACGTcount: A:0.04, C:0.57, G:0.00, T:0.39 Consensus pattern (12 bp): CCCTTACCCCTT Found at i:2664657 original size:18 final size:18 Alignment explanation

Indices: 2664603--2664660 Score: 73 Period size: 18 Copynumber: 3.2 Consensus size: 18 2664593 CATTCTTCTC 2664603 CCCTTTCCCCTTCTCC-TT 1 CCCTTTCCCCTTC-CCTTT * 2664621 CCCTTTCCCCTACCCCTTT 1 CCCTTTCCCCT-TCCCTTT * 2664640 CCCTTACCCCTTCCCTTT 1 CCCTTTCCCCTTCCCTTT 2664658 CCC 1 CCC 2664661 GTTTTGAAGC Statistics Matches: 35, Mismatches: 3, Indels: 4 0.83 0.07 0.10 Matches are distributed among these distances: 18 22 0.63 19 13 0.37 ACGTcount: A:0.03, C:0.59, G:0.00, T:0.38 Consensus pattern (18 bp): CCCTTTCCCCTTCCCTTT Found at i:2670301 original size:12 final size:13 Alignment explanation

Indices: 2670284--2670320 Score: 51 Period size: 12 Copynumber: 3.0 Consensus size: 13 2670274 GAACCGGACA 2670284 CGAACCGAA-CTC 1 CGAACCGAAGCTC 2670296 CGAACC-AAGCTC 1 CGAACCGAAGCTC * 2670308 CGAACCGTAGCTC 1 CGAACCGAAGCTC 2670321 TGATGCCACT Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 11 2 0.09 12 15 0.68 13 5 0.23 ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11 Consensus pattern (13 bp): CGAACCGAAGCTC Found at i:2673283 original size:3 final size:3 Alignment explanation

Indices: 2673275--2673308 Score: 52 Period size: 3 Copynumber: 11.7 Consensus size: 3 2673265 TGTTTTTCTT * 2673275 TTA TTA TTA TTA TTA TTA TTA TT- TTG TTA TTA TT 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 2673309 TAATGTATGT Statistics Matches: 29, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 2 2 0.07 3 27 0.93 ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71 Consensus pattern (3 bp): TTA Found at i:2674614 original size:16 final size:15 Alignment explanation

Indices: 2674595--2674634 Score: 53 Period size: 16 Copynumber: 2.5 Consensus size: 15 2674585 AATTTTCAAT 2674595 AAATAAAAAATATATA 1 AAATAAAAAATAT-TA * 2674611 AAATAATTAAATATTA 1 AAATAA-AAAATATTA 2674627 AAATAAAA 1 AAATAAAA 2674635 TGATATAAAT Statistics Matches: 21, Mismatches: 2, Indels: 3 0.81 0.08 0.12 Matches are distributed among these distances: 15 1 0.05 16 14 0.67 17 6 0.29 ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28 Consensus pattern (15 bp): AAATAAAAAATATTA Found at i:2674824 original size:28 final size:28 Alignment explanation

Indices: 2674793--2674849 Score: 105 Period size: 28 Copynumber: 2.0 Consensus size: 28 2674783 AACCCGGCCC * 2674793 ATTATTACCTCTGCATCAAATTAAGATT 1 ATTATCACCTCTGCATCAAATTAAGATT 2674821 ATTATCACCTCTGCATCAAATTAAGATT 1 ATTATCACCTCTGCATCAAATTAAGATT 2674849 A 1 A 2674850 GGACTATGAA Statistics Matches: 28, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37 Consensus pattern (28 bp): ATTATCACCTCTGCATCAAATTAAGATT Found at i:2678655 original size:23 final size:23 Alignment explanation

Indices: 2678621--2678666 Score: 83 Period size: 23 Copynumber: 2.0 Consensus size: 23 2678611 ACTAGGAGTC * 2678621 AGTTTTATTATTAAAAATTGGTT 1 AGTTTTACTATTAAAAATTGGTT 2678644 AGTTTTACTATTAAAAATTGGTT 1 AGTTTTACTATTAAAAATTGGTT 2678667 CTCATACACC 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:0.35, C:0.02, G:0.13, T:0.50 Consensus pattern (23 bp): AGTTTTACTATTAAAAATTGGTT Found at i:2680695 original size:18 final size:20 Alignment explanation

Indices: 2680658--2680700 Score: 56 Period size: 21 Copynumber: 2.2 Consensus size: 20 2680648 GATTGGAAAA 2680658 TGAAATATACTTGTTTTGGTT 1 TGAAATATACTTGTTTTGG-T 2680679 TGAAATA-A-TTG-TTTGGT 1 TGAAATATACTTGTTTTGGT 2680696 TGAAA 1 TGAAA 2680701 ATTTTTAGGT Statistics Matches: 22, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 17 6 0.27 18 5 0.23 19 3 0.14 20 1 0.05 21 7 0.32 ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47 Consensus pattern (20 bp): TGAAATATACTTGTTTTGGT Found at i:2680702 original size:18 final size:20 Alignment explanation

Indices: 2680658--2680702 Score: 51 Period size: 18 Copynumber: 2.4 Consensus size: 20 2680648 GATTGGAAAA * 2680658 TGAAATATACTTGTTTTGGTT 1 TGAAA-ATAATTGTTTTGGTT 2680679 TG-AAATAATTG-TTTGG-T 1 TGAAAATAATTGTTTTGGTT 2680696 TGAAAAT 1 TGAAAAT 2680703 TTTTAGGTAT Statistics Matches: 22, Mismatches: 1, Indels: 5 0.79 0.04 0.18 Matches are distributed among these distances: 17 3 0.14 18 9 0.41 19 6 0.27 20 2 0.09 21 2 0.09 ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47 Consensus pattern (20 bp): TGAAAATAATTGTTTTGGTT Found at i:2680960 original size:20 final size:20 Alignment explanation

Indices: 2680935--2680986 Score: 68 Period size: 20 Copynumber: 2.6 Consensus size: 20 2680925 CAGCTGCAGG * * * 2680935 ACACGGGCATGTTCTAGGCC 1 ACACGGGCATGTCCCAAGCC * 2680955 ACACGGGCGTGTCCCAAGCC 1 ACACGGGCATGTCCCAAGCC 2680975 ACACGGGCATGT 1 ACACGGGCATGT 2680987 GCCCCTATCT Statistics Matches: 27, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 20 27 1.00 ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15 Consensus pattern (20 bp): ACACGGGCATGTCCCAAGCC Found at i:2681820 original size:28 final size:29 Alignment explanation

Indices: 2681767--2681834 Score: 79 Period size: 29 Copynumber: 2.3 Consensus size: 29 2681757 TTTTATTTTA 2681767 TTATTAAAATTTAAATATTAAATAAT-TGT 1 TTATTAAAA-TTAAATATTAAATAATATGT * 2681796 TTATTAAAATTAAA-ATTAATTTAATGATGT 1 TTATTAAAATTAAATATTAA-ATAAT-ATGT 2681826 TT-TTAAAAT 1 TTATTAAAAT 2681835 CATTCAGTTA Statistics Matches: 35, Mismatches: 1, Indels: 6 0.83 0.02 0.14 Matches are distributed among these distances: 27 5 0.14 28 9 0.26 29 16 0.46 30 5 0.14 ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49 Consensus pattern (29 bp): TTATTAAAATTAAATATTAAATAATATGT Found at i:2684162 original size:26 final size:26 Alignment explanation

Indices: 2684124--2684185 Score: 115 Period size: 26 Copynumber: 2.3 Consensus size: 26 2684114 GTAACTTATA 2684124 ATTATTATAAATATGATTATAATTAAT 1 ATTA-TATAAATATGATTATAATTAAT 2684151 ATTATATAAATATGATTATAATTAAT 1 ATTATATAAATATGATTATAATTAAT 2684177 ATTATATAA 1 ATTATATAA 2684186 TTTTAAAATC Statistics Matches: 35, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 26 31 0.89 27 4 0.11 ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47 Consensus pattern (26 bp): ATTATATAAATATGATTATAATTAAT Found at i:2684184 original size:14 final size:14 Alignment explanation

Indices: 2684141--2684187 Score: 55 Period size: 14 Copynumber: 3.5 Consensus size: 14 2684131 TAAATATGAT 2684141 TATAATTAATATTA 1 TATAATTAATATTA * 2684155 TAT-A--AATATGA 1 TATAATTAATATTA 2684166 TTATAATTAATATTA 1 -TATAATTAATATTA 2684181 TATAATT 1 TATAATT 2684188 TTAAAATCTA Statistics Matches: 27, Mismatches: 2, Indels: 8 0.73 0.05 0.22 Matches are distributed among these distances: 11 6 0.22 12 3 0.11 13 2 0.07 14 10 0.37 15 6 0.22 ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49 Consensus pattern (14 bp): TATAATTAATATTA Found at i:2688347 original size:23 final size:23 Alignment explanation

Indices: 2688321--2688364 Score: 54 Period size: 23 Copynumber: 1.9 Consensus size: 23 2688311 AATATTAGTA 2688321 AGTAAAG-AAAAAGGAATAATAAT 1 AGTAAAGTAAAAA-GAATAATAAT * * 2688344 AGTATAGTAAAAATAATAATA 1 AGTAAAGTAAAAAGAATAATA 2688365 TGTTAATGAA Statistics Matches: 18, Mismatches: 2, Indels: 2 0.82 0.09 0.09 Matches are distributed among these distances: 23 13 0.72 24 5 0.28 ACGTcount: A:0.64, C:0.00, G:0.14, T:0.23 Consensus pattern (23 bp): AGTAAAGTAAAAAGAATAATAAT Found at i:2690590 original size:122 final size:122 Alignment explanation

Indices: 2690366--2690593 Score: 269 Period size: 122 Copynumber: 1.9 Consensus size: 122 2690356 AGGTTAAAAC * * * * * 2690366 GTTTTGTTAGTCCCTGTACTTAGACAAACTTTAAAATTTAGTTCCTGTAACATCATTAGTATTTT 1 GTTTTGTTAGTCCCTGTACTTAGACAAAATTGAAAATGTAGATCCTGTAACATCAGTAGTATTTT * * * * * 2690431 CTGCCAAATTTTGCCATGAGATGTTAATTACACTGCCTCATTTCATATTGCATAAAT 66 CTACCAAAATTTACCATGACATCTTAATTACACTGCCTCATTTCATATTGCATAAAT * * * * 2690488 GTTTTTTTAGTCCTTGTACTTGGACAAAATTGAAAATGTA-ATCCATGTAACATTAGTAGTATTT 1 GTTTTGTTAGTCCCTGTACTTAGACAAAATTGAAAATGTAGATCC-TGTAACATCAGTAGTATTT * * * * * 2690552 TCTACCAAAATTTATCGTGACATCTTGATTAGATTGCCTCAT 65 TCTACCAAAATTTACCATGACATCTTAATTACACTGCCTCAT 2690594 ATAACATTAG Statistics Matches: 86, Mismatches: 19, Indels: 2 0.80 0.18 0.02 Matches are distributed among these distances: 121 3 0.03 122 83 0.97 ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41 Consensus pattern (122 bp): GTTTTGTTAGTCCCTGTACTTAGACAAAATTGAAAATGTAGATCCTGTAACATCAGTAGTATTTT CTACCAAAATTTACCATGACATCTTAATTACACTGCCTCATTTCATATTGCATAAAT Found at i:2692471 original size:59 final size:59 Alignment explanation

Indices: 2692379--2692496 Score: 236 Period size: 59 Copynumber: 2.0 Consensus size: 59 2692369 ATTTCAACTG 2692379 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT 1 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT 2692438 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT 1 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT 2692497 TTTGGTTACC Statistics Matches: 59, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 59 59 1.00 ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34 Consensus pattern (59 bp): CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT Found at i:2703431 original size:28 final size:28 Alignment explanation

Indices: 2703399--2703455 Score: 114 Period size: 28 Copynumber: 2.0 Consensus size: 28 2703389 ATATATGTTG 2703399 AATCAGTGAATTAATTGAGGTATTTACC 1 AATCAGTGAATTAATTGAGGTATTTACC 2703427 AATCAGTGAATTAATTGAGGTATTTACC 1 AATCAGTGAATTAATTGAGGTATTTACC 2703455 A 1 A 2703456 TTAACTTCTT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 29 1.00 ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35 Consensus pattern (28 bp): AATCAGTGAATTAATTGAGGTATTTACC Found at i:2710033 original size:19 final size:19 Alignment explanation

Indices: 2710009--2710050 Score: 84 Period size: 19 Copynumber: 2.2 Consensus size: 19 2709999 AAAAATAAAA 2710009 TAAAGGTAAGGTTAAGTAC 1 TAAAGGTAAGGTTAAGTAC 2710028 TAAAGGTAAGGTTAAGTAC 1 TAAAGGTAAGGTTAAGTAC 2710047 TAAA 1 TAAA 2710051 TATATATCAT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 23 1.00 ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26 Consensus pattern (19 bp): TAAAGGTAAGGTTAAGTAC Found at i:2725973 original size:18 final size:18 Alignment explanation

Indices: 2725946--2726038 Score: 123 Period size: 18 Copynumber: 5.2 Consensus size: 18 2725936 TACGACCGTT 2725946 TACGGTACTATTCACGTA 1 TACGGTACTATTCACGTA * * * 2725964 TACGGCACTATTTATGTA 1 TACGGTACTATTCACGTA * 2725982 TACGGTACTATTTACGTA 1 TACGGTACTATTCACGTA * * 2726000 TACGGCACTATTAACGTA 1 TACGGTACTATTCACGTA * 2726018 TACGGTACTGTTCACGTA 1 TACGGTACTATTCACGTA 2726036 TAC 1 TAC 2726039 AGTAGTTGGG Statistics Matches: 65, Mismatches: 10, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 18 65 1.00 ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34 Consensus pattern (18 bp): TACGGTACTATTCACGTA Found at i:2725993 original size:36 final size:36 Alignment explanation

Indices: 2725946--2726038 Score: 150 Period size: 36 Copynumber: 2.6 Consensus size: 36 2725936 TACGACCGTT * * 2725946 TACGGTACTATTCACGTATACGGCACTATTTATGTA 1 TACGGTACTATTCACGTATACGGCACTATTAACGTA * 2725982 TACGGTACTATTTACGTATACGGCACTATTAACGTA 1 TACGGTACTATTCACGTATACGGCACTATTAACGTA * 2726018 TACGGTACTGTTCACGTATAC 1 TACGGTACTATTCACGTATAC 2726039 AGTAGTTGGG Statistics Matches: 52, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 36 52 1.00 ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34 Consensus pattern (36 bp): TACGGTACTATTCACGTATACGGCACTATTAACGTA Found at i:2734235 original size:27 final size:27 Alignment explanation

Indices: 2734205--2734256 Score: 104 Period size: 27 Copynumber: 1.9 Consensus size: 27 2734195 ATGACTTGTT 2734205 TTCAAAAGAAATTGATGAAAATACTTA 1 TTCAAAAGAAATTGATGAAAATACTTA 2734232 TTCAAAAGAAATTGATGAAAATACT 1 TTCAAAAGAAATTGATGAAAATACT 2734257 CATCTTTTAA Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 25 1.00 ACGTcount: A:0.52, C:0.08, G:0.12, T:0.29 Consensus pattern (27 bp): TTCAAAAGAAATTGATGAAAATACTTA Found at i:2734392 original size:23 final size:24 Alignment explanation

Indices: 2734362--2734407 Score: 85 Period size: 23 Copynumber: 2.0 Consensus size: 24 2734352 TTTAAATTTG 2734362 TAAAAATTAATATAATAT-TATTA 1 TAAAAATTAATATAATATGTATTA 2734385 TAAAAATTAATATAATATGTATT 1 TAAAAATTAATATAATATGTATT 2734408 TCATTGGGCA Statistics Matches: 22, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 23 18 0.82 24 4 0.18 ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43 Consensus pattern (24 bp): TAAAAATTAATATAATATGTATTA Found at i:2734398 original size:12 final size:12 Alignment explanation

Indices: 2734362--2734399 Score: 51 Period size: 12 Copynumber: 3.2 Consensus size: 12 2734352 TTTAAATTTG 2734362 TAAAAATTAATA 1 TAAAAATTAATA * * 2734374 T-AATATTATTA 1 TAAAAATTAATA 2734385 TAAAAATTAATA 1 TAAAAATTAATA 2734397 TAA 1 TAA 2734400 TATGTATTTC Statistics Matches: 21, Mismatches: 4, Indels: 2 0.78 0.15 0.07 Matches are distributed among these distances: 11 9 0.43 12 12 0.57 ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39 Consensus pattern (12 bp): TAAAAATTAATA Found at i:2742753 original size:32 final size:33 Alignment explanation

Indices: 2742686--2742757 Score: 94 Period size: 33 Copynumber: 2.2 Consensus size: 33 2742676 ATTGTAGAAA * * * 2742686 AAACTTTAAATCAAACATTTGAATAAAAATTTT 1 AAACTTTAAATCAAACAATAGAATAAAAATATT 2742719 AAACTTTAAATCAAACAAATAGAA-AAAAA-ATT 1 AAACTTTAAATCAAAC-AATAGAATAAAAATATT 2742751 AAACTTT 1 AAACTTT 2742758 TTAGAGAATT Statistics Matches: 35, Mismatches: 3, Indels: 3 0.85 0.07 0.07 Matches are distributed among these distances: 32 9 0.26 33 21 0.60 34 5 0.14 ACGTcount: A:0.57, C:0.10, G:0.03, T:0.31 Consensus pattern (33 bp): AAACTTTAAATCAAACAATAGAATAAAAATATT Found at i:2753229 original size:20 final size:20 Alignment explanation

Indices: 2753204--2753243 Score: 80 Period size: 20 Copynumber: 2.0 Consensus size: 20 2753194 TCTGATCTGA 2753204 TCCTTTATTATCCCATAAAC 1 TCCTTTATTATCCCATAAAC 2753224 TCCTTTATTATCCCATAAAC 1 TCCTTTATTATCCCATAAAC 2753244 AAGTGGTCAA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40 Consensus pattern (20 bp): TCCTTTATTATCCCATAAAC Found at i:2766448 original size:212 final size:199 Alignment explanation

Indices: 2766118--2766734 Score: 781 Period size: 212 Copynumber: 3.0 Consensus size: 199 2766108 TTAATTTTAA * * * * * 2766118 TGAGTGAGTGGATAATTC-TTCAATTTTCAATCATCTCATGTTTTAAAATTGTTTATTGGATGCA 1 TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTACTGGATGCA * * * 2766182 TGAGTCCACTTCACAGTCATTTTTTTATTTGTTAGCCTGTACATTGGATCTGTTGCAGGTTGGAT 66 --AGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTACATTGTATCTGTTGCAGGTTGGAT * * 2766247 GATTTTGATTTTGATTCAGCCCTGAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAGTAA 129 GATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAGCAA 2766312 AGACGC 194 AGACGC * ** * 2766318 TGAGTGAGTGGATTATTCTTTTATTTTTCAGTTATCTCATGTACAATCTTTTGCTTTGAAATTGT 1 TGAGTGAGTGGATAATTCTTTTATTTTT-A---A----A--T-C-ATCTCATGCTTTAAAATTGT * 2766383 TTACTGGACATGCAAGTCAACTTCACATTCA-TTTTTTATTTGTTAGCCTGTATATTGTATCTGT 54 TTACTGG--ATGCAAGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTACATTGTATCTGT * 2766447 TGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAA 117 TGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAA ** * * 2766512 TAAGGAATGCAAAGCCGC 182 CCAGGAAAGCAAAGACGC * 2766530 TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTGCTGGATGCA 1 TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTACTGGATGC- * * 2766595 TAAGTCAACTTAACATTCATTTTTTTTAATTTATTAGCCTGTACATTGTATCTGTTGCAGGTTGG 65 -AAGTCAACTTCACATTCA-TTTTTTT-ATTTGTTAGCCTGTACATTGTATCTGTTGCAGGTTGG ** * 2766660 ATGATTTTGATTTTGATTC-GACCCTAAATATTGGAGAGAAGACTAGTAAGAAAAACCAGGAAGG 127 ATGATTTTGATTTTGATTCAG-CCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAG * 2766724 CAAAGCCGC 191 CAAAGACGC 2766733 TG 1 TG 2766735 CTTCTGAGAG Statistics Matches: 362, Mismatches: 34, Indels: 39 0.83 0.08 0.09 Matches are distributed among these distances: 198 4 0.01 200 57 0.16 201 8 0.02 202 7 0.02 203 103 0.28 204 1 0.00 205 1 0.00 208 1 0.00 209 1 0.00 211 2 0.01 212 135 0.37 213 37 0.10 215 5 0.01 ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37 Consensus pattern (199 bp): TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTACTGGATGCA AGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTACATTGTATCTGTTGCAGGTTGGATGA TTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAGCAAAG ACGC Found at i:2766698 original size:203 final size:199 Alignment explanation

Indices: 2766369--2766734 Score: 572 Period size: 203 Copynumber: 1.8 Consensus size: 199 2766359 TACAATCTTT * * * 2766369 TGCTTTGAAATTGTTTACTGGACATGCAAGTCAACTTCACATTCATTTTTTATTTGTTAGCCTGT 1 TGCTTTAAAATTGTTTACTGGACAT-CAAGTCAACTTAACATTCATTTTTTATTTATTAGCCTGT * 2766434 ATATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGA 65 ACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGA * * 2766499 CTAGTAAGAAAAATAAGGAATGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTAAATCA 130 CTAGTAAGAAAAACAAGGAAGGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTAAATCA 2766564 TCTCA 195 TCTCA * 2766569 TGCTTTAAAATTGTTTGCTGGATGCAT-AAGTCAACTTAACATTCATTTTTTTTAATTTATTAGC 1 TGCTTTAAAATTGTTTACTGGA--CATCAAGTCAACTTAACATTCA--TTTTTT-ATTTATTAGC * ** 2766633 CTGTACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCGACCCTAAATATTGGAGAG 61 CTGTACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAG * 2766698 AAGACTAGTAAGAAAAACCAGGAAGGCAAAGCCGCTG 126 AAGACTAGTAAGAAAAACAAGGAAGGCAAAGCCGCTG 2766735 CTTCTGAGAG Statistics Matches: 150, Mismatches: 11, Indels: 7 0.89 0.07 0.04 Matches are distributed among these distances: 200 37 0.25 202 9 0.06 203 104 0.69 ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36 Consensus pattern (199 bp): TGCTTTAAAATTGTTTACTGGACATCAAGTCAACTTAACATTCATTTTTTATTTATTAGCCTGTA CATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGAC TAGTAAGAAAAACAAGGAAGGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTAAATCAT CTCA Found at i:2771420 original size:15 final size:15 Alignment explanation

Indices: 2771402--2771431 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 2771392 CTCTCTGCCC 2771402 TTCTCCTCCACCTCT 1 TTCTCCTCCACCTCT * 2771417 TTCTCCTCCCCCTCT 1 TTCTCCTCCACCTCT 2771432 CTCAGTCAAA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.03, C:0.57, G:0.00, T:0.40 Consensus pattern (15 bp): TTCTCCTCCACCTCT Found at i:2772564 original size:23 final size:24 Alignment explanation

Indices: 2772519--2772566 Score: 62 Period size: 24 Copynumber: 2.0 Consensus size: 24 2772509 AAATAATTTA * 2772519 TTTTTAGAAATTTAAAATTTATAT 1 TTTTTAGAAATTTAAAATATATAT 2772543 TTTTTA-AAATTTAAAGAATATATA 1 TTTTTAGAAATTT-AA-AATATATA 2772567 AAGAAAGTTA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 23 6 0.29 24 8 0.38 25 7 0.33 ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50 Consensus pattern (24 bp): TTTTTAGAAATTTAAAATATATAT Found at i:2776196 original size:4 final size:4 Alignment explanation

Indices: 2776179--2776209 Score: 53 Period size: 4 Copynumber: 7.8 Consensus size: 4 2776169 CAATGACAAG * 2776179 ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATA 1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA 2776210 AAACCCTTTT Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 4 25 1.00 ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29 Consensus pattern (4 bp): ATAC Found at i:2785067 original size:5 final size:5 Alignment explanation

Indices: 2785057--2785082 Score: 52 Period size: 5 Copynumber: 5.2 Consensus size: 5 2785047 TTGCTATGAT 2785057 TTTTA TTTTA TTTTA TTTTA TTTTA T 1 TTTTA TTTTA TTTTA TTTTA TTTTA T 2785083 ATATGTTGTT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 21 1.00 ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81 Consensus pattern (5 bp): TTTTA Found at i:2786353 original size:44 final size:44 Alignment explanation

Indices: 2786290--2786375 Score: 154 Period size: 44 Copynumber: 2.0 Consensus size: 44 2786280 TGATTGAATT * * 2786290 GAATTGACTCGAATAAAAAATATTTGAGTTAGTCAAGTTGACAA 1 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGACAA 2786334 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGAC 1 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGAC 2786376 GAGTTTTATT Statistics Matches: 40, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 44 40 1.00 ACGTcount: A:0.44, C:0.09, G:0.17, T:0.29 Consensus pattern (44 bp): GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGACAA Found at i:2786755 original size:20 final size:20 Alignment explanation

Indices: 2786723--2786775 Score: 65 Period size: 20 Copynumber: 2.7 Consensus size: 20 2786713 AACCTTTATT 2786723 TTTTA-AAATTTTTATAAAAA 1 TTTTAGAAA-TTTTATAAAAA * 2786743 TTTTAGAAATTTTATAAATA 1 TTTTAGAAATTTTATAAAAA * 2786763 TTTT-GAAAATTTA 1 TTTTAGAAATTTTA 2786776 AGGTTATATT Statistics Matches: 30, Mismatches: 2, Indels: 3 0.86 0.06 0.09 Matches are distributed among these distances: 19 8 0.27 20 19 0.63 21 3 0.10 ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51 Consensus pattern (20 bp): TTTTAGAAATTTTATAAAAA Found at i:2786759 original size:45 final size:45 Alignment explanation

Indices: 2786672--2786759 Score: 117 Period size: 46 Copynumber: 2.0 Consensus size: 45 2786662 TTTATCATTT * * * 2786672 TTTATTTTTTTAATTTTTTAAAGATTTTTAGAATTTTATATAACC 1 TTTATTTTTTAAATTTTTTAAAGAATTTTAGAAATTTATATAACC 2786717 TTTATTTTTTAAAATTTTTATAAA-AATTTTAGAAATTT-TATAA 1 TTTATTTTTT-AAATTTTT-TAAAGAATTTTAGAAATTTATATAA 2786760 ATATTTTGAA Statistics Matches: 38, Mismatches: 3, Indels: 4 0.84 0.07 0.09 Matches are distributed among these distances: 45 15 0.39 46 19 0.50 47 4 0.11 ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58 Consensus pattern (45 bp): TTTATTTTTTAAATTTTTTAAAGAATTTTAGAAATTTATATAACC Found at i:2793859 original size:12 final size:12 Alignment explanation

Indices: 2793842--2793866 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 2793832 AATTTCTATA 2793842 TATATATATATT 1 TATATATATATT 2793854 TATATATATATT 1 TATATATATATT 2793866 T 1 T 2793867 TAAATGTCAT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (12 bp): TATATATATATT Found at i:2799989 original size:16 final size:16 Alignment explanation

Indices: 2799968--2800002 Score: 52 Period size: 16 Copynumber: 2.2 Consensus size: 16 2799958 AAAATTCAAA * 2799968 ATATTTATAAAAATTT 1 ATATTTATAAAAAATT * 2799984 ATATTTTTAAAAAATT 1 ATATTTATAAAAAATT 2800000 ATA 1 ATA 2800003 ATATTTTTTA Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (16 bp): ATATTTATAAAAAATT Found at i:2800008 original size:19 final size:19 Alignment explanation

Indices: 2799957--2800017 Score: 65 Period size: 20 Copynumber: 3.3 Consensus size: 19 2799947 AATAAGGTTC * * 2799957 AAAAATTCAAAATATTTAT- 1 AAAAATT-ATAATATTTTTA 2799976 AAAAATT-T-ATATTTTTA 1 AAAAATTATAATATTTTTA 2799993 AAAAATTATAATATTTTTTA 1 AAAAATTATAATA-TTTTTA 2800013 AAAAA 1 AAAAA 2800018 ATTAAAGAAT Statistics Matches: 36, Mismatches: 2, Indels: 7 0.80 0.04 0.16 Matches are distributed among these distances: 16 7 0.19 17 7 0.19 18 1 0.03 19 10 0.28 20 11 0.31 ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43 Consensus pattern (19 bp): AAAAATTATAATATTTTTA Found at i:2805818 original size:55 final size:55 Alignment explanation

Indices: 2805757--2805866 Score: 168 Period size: 55 Copynumber: 2.0 Consensus size: 55 2805747 TGATATGTCT * * * 2805757 GGTAATGCCTCGTAACCCTATTTCGGA-GACGGTTTGGGGTTAAAAGGGTGTTACA 1 GGTAATGCCTCGTAACCCTATTTC-AACGACGATTTGCGGTTAAAAGGGTGTTACA * 2805812 GGTAATGCCTCGTAACCCTATTTCAACGACGATTTGCGGTTAAAGGGGTGTTACA 1 GGTAATGCCTCGTAACCCTATTTCAACGACGATTTGCGGTTAAAAGGGTGTTACA 2805867 ATATTCTGGA Statistics Matches: 50, Mismatches: 4, Indels: 2 0.89 0.07 0.04 Matches are distributed among these distances: 54 1 0.02 55 49 0.98 ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29 Consensus pattern (55 bp): GGTAATGCCTCGTAACCCTATTTCAACGACGATTTGCGGTTAAAAGGGTGTTACA Found at i:2807438 original size:6 final size:6 Alignment explanation

Indices: 2807427--2807453 Score: 54 Period size: 6 Copynumber: 4.5 Consensus size: 6 2807417 AGCAATAGTT 2807427 TGAATG TGAATG TGAATG TGAATG TGA 1 TGAATG TGAATG TGAATG TGAATG TGA 2807454 GGTGAAGTGG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 21 1.00 ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33 Consensus pattern (6 bp): TGAATG Found at i:2808949 original size:63 final size:63 Alignment explanation

Indices: 2808809--2809257 Score: 376 Period size: 63 Copynumber: 7.1 Consensus size: 63 2808799 AAACCGGGCT * * * * * 2808809 ACACCGAAAAGCA-ATACAAAC-AAAGACCACTGTTGTCTTC-AATGAGAAAGCAATGAAACCCT 1 ACACCCAAAAGCATA-ACAAACGAAA-ACCACTGTTGTCTGCAAATAAAAAAG-AGT-AAACCCT 2808871 AA 62 AA * * * 2808873 ACACCCAAAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAA 1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA * * * * * * * * 2808936 ACACTCAAAAGCATTACAAAC-AAATACCAGTATTGTCTTC-AATGAGAAAGAAATGAAACCCTA 1 ACACCCAAAAGCATAACAAACGAAA-ACCACTGTTGTCTGCAAATAAAAAAG-AGT-AAACCCTA 2808999 A 63 A * * * * 2809000 ACACCCAAAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAGCCCCAA 1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA * * * * * * * * 2809063 ACACTCAAAAGCATTACAAAC-AAAGACCAGTATTGTCTTC-AATTAGAAAGCAATGAAACCCTA 1 ACACCCAAAAGCATAACAAACGAAA-ACCACTGTTGTCTGCAAATAAAAAAG-AGT-AAACCCTA 2809126 A 63 A * * * * * 2809127 ACACCCAAAGGAATAACAAACGAAAACCACTGTTGTCTGCAAACAAAAAGGAGTAAAGCCTAA 1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA * * * * * * 2809190 ACACCCAAAAGCATTACAAACAAAAACCAC-GTTGATCAGC-AATGAAAAAGCAATCAACCCTAA 1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTG-TCTGCAAATAAAAAAG-AGTAAACCCTAA 2809253 ACACC 1 ACACC 2809258 AATTGAGTTA Statistics Matches: 303, Mismatches: 67, Indels: 31 0.76 0.17 0.08 Matches are distributed among these distances: 62 33 0.11 63 129 0.43 64 109 0.36 65 32 0.11 ACGTcount: A:0.49, C:0.24, G:0.12, T:0.15 Consensus pattern (63 bp): ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA Found at i:2809041 original size:127 final size:127 Alignment explanation

Indices: 2808815--2809257 Score: 658 Period size: 127 Copynumber: 3.5 Consensus size: 127 2808805 GGCTACACCG * * * 2808815 AAAAGCAATACAAACAAAGACCACTGTTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA 1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA * * * * 2808880 AAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAAACACTC 66 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC * * 2808942 AAAAGCATTACAAACAAATACCAGTATTGTCTTCAATGAGAAAGAAATGAAACCCTAAACACCCA 1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA * 2809007 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAGCCCCAAACACTC 66 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC * 2809069 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATTAGAAAGCAATGAAACCCTAAACACCCA 1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA * * * * * 2809134 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAACAAAAAGGAGTAAAGCCTAAACACCC 66 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC * ** * * 2809196 AAAAGCATTACAAACAAAAACCACG--TTGATCAGCAATGAAAAAGCAAT-CAACCCTAAACACC 1 AAAAGCATTACAAACAAAGACCA-GTATTG-TCTTCAATGAGAAAGCAATGAAACCCTAAACACC 2809258 AATTGAGTTA Statistics Matches: 289, Mismatches: 25, Indels: 5 0.91 0.08 0.02 Matches are distributed among these distances: 126 16 0.06 127 272 0.94 128 1 0.00 ACGTcount: A:0.49, C:0.23, G:0.12, T:0.15 Consensus pattern (127 bp): AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC Found at i:2809614 original size:10 final size:10 Alignment explanation

Indices: 2809601--2809679 Score: 53 Period size: 10 Copynumber: 8.2 Consensus size: 10 2809591 TTTTTAAGAC 2809601 TTATTAAAAA 1 TTATTAAAAA 2809611 TTA-TAAAAA 1 TTATTAAAAA * * 2809620 -TATTTGAACA 1 TTA-TTAAAAA 2809630 -TATTAAAAA 1 TTATTAAAAA 2809639 TT-TGT-AAAA 1 TTAT-TAAAAA 2809648 TTATTAAAAA 1 TTATTAAAAA * * 2809658 ATAATAAAAA 1 TTATTAAAAA 2809668 TT-TTAAACAA 1 TTATTAAA-AA 2809678 TT 1 TT 2809680 GTGAAAATCA Statistics Matches: 54, Mismatches: 8, Indels: 14 0.71 0.11 0.18 Matches are distributed among these distances: 8 2 0.04 9 23 0.43 10 29 0.54 ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38 Consensus pattern (10 bp): TTATTAAAAA Found at i:2809652 original size:19 final size:19 Alignment explanation

Indices: 2809607--2809760 Score: 67 Period size: 19 Copynumber: 8.2 Consensus size: 19 2809597 AGACTTATTA * 2809607 AAAATTATAAAAATATTTG- 1 AAAATTATTAAAA-ATTTGT * 2809626 AACA-TATTAAAAATTTGT 1 AAAATTATTAAAAATTTGT * ** 2809644 AAAATTATTAAAAAATAAT 1 AAAATTATTAAAAATTTGT 2809663 AAAAATT-TTAAACAA-TTGT 1 -AAAATTATTAAA-AATTTGT * * 2809682 GAAAATCATTTAAAAAATT-T 1 -AAAATTA-TTAAAAATTTGT * 2809702 -AAATTGATTAAAAA-ATGT 1 AAAATT-ATTAAAAATTTGT ** * 2809720 AAGAATTATTTGAAATTTAT 1 AA-AATTATTAAAAATTTGT 2809740 AAGAATT-TT-AAAATTT-T 1 AA-AATTATTAAAAATTTGT 2809757 AAAA 1 AAAA 2809761 AATTATAATA Statistics Matches: 106, Mismatches: 17, Indels: 27 0.71 0.11 0.18 Matches are distributed among these distances: 16 2 0.02 17 9 0.08 18 28 0.26 19 36 0.34 20 24 0.23 21 7 0.07 ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37 Consensus pattern (19 bp): AAAATTATTAAAAATTTGT Found at i:2809652 original size:29 final size:28 Alignment explanation

Indices: 2809602--2809674 Score: 83 Period size: 29 Copynumber: 2.6 Consensus size: 28 2809592 TTTTAAGACT * ** * 2809602 TATTAAAAATTATAAAAATATTTGAACA 1 TATTAAAAATTTTAAAAATATTAAAAAA * 2809630 TATTAAAAATTTGTAAAATTATTAAAAAA 1 TATTAAAAATTT-TAAAAATATTAAAAAA * 2809659 TAATAAAAATTTTAAA 1 TATTAAAAATTTTAAA 2809675 CAATTGTGAA Statistics Matches: 38, Mismatches: 6, Indels: 2 0.83 0.13 0.04 Matches are distributed among these distances: 28 15 0.39 29 23 0.61 ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37 Consensus pattern (28 bp): TATTAAAAATTTTAAAAATATTAAAAAA Found at i:2809674 original size:9 final size:9 Alignment explanation

Indices: 2809604--2809761 Score: 54 Period size: 9 Copynumber: 16.8 Consensus size: 9 2809594 TTAAGACTTA 2809604 TTAAAAATT 1 TTAAAAATT * 2809613 ATAAAAATAT 1 TTAAAAAT-T * * * 2809623 TTGAACATA 1 TTAAAAATT 2809632 TTAAAAATT 1 TTAAAAATT 2809641 TGT-AAAATT 1 T-TAAAAATT * 2809650 ATTAAAAAATA 1 -TT-AAAAATT * 2809661 ATAAAAATT 1 TTAAAAATT 2809670 TTAAACAATT 1 TTAAA-AATT * * 2809680 GTGAAAATCAT 1 TTAAAAAT--T * 2809691 TTAAAAAAT 1 TTAAAAATT 2809700 TT--AAATT 1 TTAAAAATT * 2809707 GATTAAAAAAT 1 --TTAAAAATT * * 2809718 GTAAGAATT 1 TTAAAAATT ** 2809727 ATTTGAAATT 1 -TTAAAAATT * 2809737 TATAAGAATT 1 T-TAAAAATT 2809747 TT-AAAATT 1 TTAAAAATT 2809755 TTAAAAA 1 TTAAAAA 2809762 ATTATAATAT Statistics Matches: 104, Mismatches: 30, Indels: 30 0.63 0.18 0.18 Matches are distributed among these distances: 7 4 0.04 8 7 0.07 9 51 0.49 10 27 0.26 11 15 0.14 ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37 Consensus pattern (9 bp): TTAAAAATT Found at i:2811029 original size:9 final size:9 Alignment explanation

Indices: 2811017--2811069 Score: 52 Period size: 9 Copynumber: 5.6 Consensus size: 9 2811007 TTTTAATACC 2811017 TTTTATTAT 1 TTTTATTAT 2811026 TTTTATTAT 1 TTTTATTAT * 2811035 TTTATATGAT 1 TTT-TATTAT * 2811045 TTTATGATTTT 1 TTT-T-ATTAT * 2811056 TTTTTTTAT 1 TTTTATTAT 2811065 TTTTA 1 TTTTA 2811070 CCCATGTGGT Statistics Matches: 36, Mismatches: 6, Indels: 4 0.78 0.13 0.09 Matches are distributed among these distances: 9 19 0.53 10 11 0.31 11 6 0.17 ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75 Consensus pattern (9 bp): TTTTATTAT Found at i:2813379 original size:7 final size:7 Alignment explanation

Indices: 2813369--2813464 Score: 51 Period size: 7 Copynumber: 13.9 Consensus size: 7 2813359 AGGTTTATAG 2813369 TTTAAGA 1 TTTAAGA 2813376 TTTAAGA 1 TTTAAGA 2813383 TTTAA-A 1 TTTAAGA * 2813389 TTTTAGA 1 TTTAAGA 2813396 GTTTAAG- 1 -TTTAAGA * * 2813403 TTTAGGTT 1 TTTAAG-A * 2813411 TTTAACA 1 TTTAAGA 2813418 -TT-AGA 1 TTTAAGA * 2813423 GTTTAGGA 1 -TTTAAGA 2813431 TTTATAG- 1 TTTA-AGA 2813438 TTTAAGA 1 TTTAAGA 2813445 TTTAAG- 1 TTTAAGA * 2813451 TTTTAGA 1 TTTAAGA 2813458 GTTTAAG 1 -TTTAAG 2813465 TTGAGATTTT Statistics Matches: 67, Mismatches: 11, Indels: 21 0.68 0.11 0.21 Matches are distributed among these distances: 5 2 0.03 6 19 0.28 7 29 0.43 8 17 0.25 ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48 Consensus pattern (7 bp): TTTAAGA Found at i:2813379 original size:14 final size:13 Alignment explanation

Indices: 2813357--2813466 Score: 73 Period size: 14 Copynumber: 8.0 Consensus size: 13 2813347 TTATTTCGTG * 2813357 TAAGGTTTATAGTT 1 TAAGATTTA-AGTT 2813371 TAAGATTTAAGATT 1 TAAGATTTAAG-TT 2813385 TAA-ATTTTAGAGTT 1 TAAGA-TTTA-AGTT * 2813399 TAAG-TTTAGGTTTT 1 TAAGATTTAAG--TT * 2813413 TAACA-TTAGAGTT 1 TAAGATTTA-AGTT * 2813426 TAGGATTTATAGTT 1 TAAGATTTA-AGTT 2813440 TAAGATTTAAGTT 1 TAAGATTTAAGTT * 2813453 TTAGAGTTTAAGTT 1 TAAGA-TTTAAGTT 2813467 GAGATTTTTA Statistics Matches: 77, Mismatches: 9, Indels: 20 0.73 0.08 0.19 Matches are distributed among these distances: 12 1 0.01 13 20 0.26 14 53 0.69 15 3 0.04 ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48 Consensus pattern (13 bp): TAAGATTTAAGTT Found at i:2813413 original size:21 final size:20 Alignment explanation

Indices: 2813389--2813466 Score: 77 Period size: 21 Copynumber: 3.8 Consensus size: 20 2813379 AAGATTTAAA 2813389 TTTTAGAGTTTAAGTTTAGG 1 TTTTAGAGTTTAAGTTTAGG ** 2813409 TTTTTA-ACATTAGAGTTTAGG 1 -TTTTAGAGTTTA-AGTTTAGG * * * 2813430 ATTTATAGTTTAAGATTTAAG 1 TTTTAGAGTTTAAG-TTTAGG 2813451 TTTTAGAGTTTAAGTT 1 TTTTAGAGTTTAAGTT 2813467 GAGATTTTTA Statistics Matches: 46, Mismatches: 8, Indels: 7 0.75 0.13 0.11 Matches are distributed among these distances: 20 12 0.26 21 34 0.74 ACGTcount: A:0.29, C:0.01, G:0.19, T:0.50 Consensus pattern (20 bp): TTTTAGAGTTTAAGTTTAGG Found at i:2819655 original size:31 final size:31 Alignment explanation

Indices: 2819620--2819682 Score: 81 Period size: 31 Copynumber: 2.0 Consensus size: 31 2819610 ACAACTCGAC * * 2819620 TTTTTAAAAAAAATTAATAGTTAAATTTAAT 1 TTTTTAAAAAAAATTAAGAGTAAAATTTAAT *** 2819651 TTTTTTTTAAAAATTAAGAGTAAAATTTAAT 1 TTTTTAAAAAAAATTAAGAGTAAAATTTAAT 2819682 T 1 T 2819683 AAAAAATAAA Statistics Matches: 27, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 31 27 1.00 ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48 Consensus pattern (31 bp): TTTTTAAAAAAAATTAAGAGTAAAATTTAAT Found at i:2823169 original size:17 final size:17 Alignment explanation

Indices: 2823149--2823215 Score: 52 Period size: 17 Copynumber: 4.1 Consensus size: 17 2823139 CAATAAATAA 2823149 AAATATATAAAAATATT 1 AAATATATAAAAATATT * 2823166 AAATAT-T-AAAATAAT 1 AAATATATAAAAATATT * * 2823181 ATAATATA-AATAATTTT 1 A-AATATATAAAAATATT * 2823198 AAA-AAATCAAAAATATT 1 AAATATAT-AAAAATATT 2823215 A 1 A 2823216 TAGGAGGGTT Statistics Matches: 38, Mismatches: 7, Indels: 10 0.69 0.13 0.18 Matches are distributed among these distances: 15 10 0.26 16 8 0.21 17 20 0.53 ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34 Consensus pattern (17 bp): AAATATATAAAAATATT Found at i:2823186 original size:16 final size:15 Alignment explanation

Indices: 2823143--2823190 Score: 51 Period size: 16 Copynumber: 3.1 Consensus size: 15 2823133 AAATTTCAAT * 2823143 AAATAAAAATATATAA 1 AAATAATAA-ATATAA * * 2823159 AAATATTAAATATTA 1 AAATAATAAATATAA 2823174 AAATAATATAATATAA 1 AAATAATA-AATATAA 2823190 A 1 A 2823191 TAATTTTAAA Statistics Matches: 26, Mismatches: 5, Indels: 2 0.79 0.15 0.06 Matches are distributed among these distances: 15 12 0.46 16 14 0.54 ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31 Consensus pattern (15 bp): AAATAATAAATATAA Found at i:2827723 original size:12 final size:12 Alignment explanation

Indices: 2827706--2827734 Score: 58 Period size: 12 Copynumber: 2.4 Consensus size: 12 2827696 CAGTGCTTGT 2827706 TTGTTTGTTTGC 1 TTGTTTGTTTGC 2827718 TTGTTTGTTTGC 1 TTGTTTGTTTGC 2827730 TTGTT 1 TTGTT 2827735 CTCATTCAAT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 17 1.00 ACGTcount: A:0.00, C:0.07, G:0.24, T:0.69 Consensus pattern (12 bp): TTGTTTGTTTGC Done.