Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr13

Parameters: 2 7 7 80 10 50 1000

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

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

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


File 56 of 141

Found at i:18406895 original size:17 final size:18

Alignment explanation

Indices: 18406873--18406907 Score: 54 Period size: 18 Copynumber: 2.0 Consensus size: 18 18406863 ATGTTTTTAT 18406873 AATTGG-TCCAGTAGTTG 1 AATTGGTTCCAGTAGTTG * 18406890 AATTGGTTCGAGTAGTTG 1 AATTGGTTCCAGTAGTTG 18406908 GTCCAGTTTG Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 6 0.38 18 10 0.62 ACGTcount: A:0.23, C:0.09, G:0.31, T:0.37 Consensus pattern (18 bp): AATTGGTTCCAGTAGTTG Found at i:18406935 original size:12 final size:12 Alignment explanation

Indices: 18406918--18406951 Score: 52 Period size: 12 Copynumber: 2.8 Consensus size: 12 18406908 GTCCAGTTTG 18406918 ATTAAATAAATT 1 ATTAAATAAATT 18406930 ATTAAA-AAATT 1 ATTAAATAAATT 18406941 ATTAAAATAAA 1 ATT-AAATAAA 18406952 AATATTAGAA Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 11 8 0.40 12 9 0.45 13 3 0.15 ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35 Consensus pattern (12 bp): ATTAAATAAATT Found at i:18406941 original size:11 final size:11 Alignment explanation

Indices: 18406918--18406947 Score: 51 Period size: 11 Copynumber: 2.6 Consensus size: 11 18406908 GTCCAGTTTG 18406918 ATTAAATAAATT 1 ATTAAA-AAATT 18406930 ATTAAAAAATT 1 ATTAAAAAATT 18406941 ATTAAAA 1 ATTAAAA 18406948 TAAAAATATT Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 11 12 0.67 12 6 0.33 ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37 Consensus pattern (11 bp): ATTAAAAAATT Found at i:18406953 original size:16 final size:17 Alignment explanation

Indices: 18406932--18406971 Score: 50 Period size: 15 Copynumber: 2.5 Consensus size: 17 18406922 AATAAATTAT 18406932 TAAAAAATTATTA-AAA 1 TAAAAAATTATTAGAAA 18406948 T-AAAAA-TATTAGAAA 1 TAAAAAATTATTAGAAA 18406963 TAGAAAAAT 1 TA-AAAAAT 18406972 ATAGTACAAT Statistics Matches: 20, Mismatches: 0, Indels: 6 0.77 0.00 0.23 Matches are distributed among these distances: 14 5 0.25 15 9 0.45 16 1 0.05 17 5 0.25 ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28 Consensus pattern (17 bp): TAAAAAATTATTAGAAA Found at i:18409773 original size:105 final size:105 Alignment explanation

Indices: 18409595--18410539 Score: 1096 Period size: 105 Copynumber: 9.1 Consensus size: 105 18409585 ACCAGGCTAC * * * * * 18409595 CACTTTTCGGTAGTCTGGACAATCTACGTAAGCT--TGTG--GTTCAATAGTTTGTCCGCTAATA 1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA * 18409656 TTTCTTACAGCATCTGGGGTACTTTCTTTCATTGAAGGGA 66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA *** * * * 18409696 CACTTTTCGATAGTCTGGATGGTCTAGGTAAGCTAGAGTCCCGTTTAGTAGTTTGTCTGGTAATA 1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA * * 18409761 TTCCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGG 66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA * * * * * * * 18409801 CCCTTCTCAATAGTTTGGACGATCTAGGTAAGCTAGAGTGCCTTTCAGTAGTTTGTCTGCTTATA 1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA * 18409866 TTTCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGA 66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA * * * * * * 18409906 CACTTTTCAATAGTTTGGACAACCTAGGTAAGCTAAAGTGCCTTTCAGTAGTTTGTCTGCTCATA 1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA * * 18409971 TTTCTTACAGCATTTTGGGTACTTTCTTTAATTGAAGGGA 66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA * * * * * 18410011 CACTTATCAATAGTTTGGACGATCTAGGTAAGCTAAAGTGCCGTTCAGTAGTTTGTCTGCTAATA 1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA ** 18410076 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAATAGA 66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA * ** * * * * 18410116 CAGTTTTCGATAGTCCAGACAATCTAGGTAAGCTAGAGCGCGGTTCGGTAGTTTGTCTGCAAATA 1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA * ** * ** * 18410181 TCTCGAACAGCATTTTGGGTACTTTCTTTTGTTGAAGAGA 66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA * ** * * * * * 18410221 CGCTTTTCGATAGTCCAGATAGTCTAGGTAAGCTATGA--G--GTTTAATAGTTTGTCCGCTAAT 1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTA-GAGTGCCGTTCAGTAGTTTGTCTGCTAAT * * * * * * 18410282 ATTTCTTTCAGTATTTTGAGTACTTTCTTTCATTGAGGGGG 65 ATTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA * * * ** 18410323 CACTTTTTGATAGTCTGGACAATCTAGGCAACCTAGAGTGTGGTTCAGTAGTTTGTCTGCTAATA 1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA * 18410388 TTTCTTACAGCATTTGGGGTACTTTGTTTCATTGAAGGGA 66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA * * ** ** 18410428 CAATTATCGATAGTCCAGACAATCTAGGTAAGCTAGAGTGTGGTTCAGTAGTTTGTCTGCTAATA 1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA * * * * 18410493 TTTCTTACTGCATTAGGGGTACTTTCTATCGTTGAAGGGA 66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA 18410533 CACTTTT 1 CACTTTT 18410540 ATTGACCTTG Statistics Matches: 720, Mismatches: 115, Indels: 14 0.85 0.14 0.02 Matches are distributed among these distances: 101 31 0.04 102 74 0.10 103 3 0.00 104 1 0.00 105 609 0.85 106 2 0.00 ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38 Consensus pattern (105 bp): CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA Found at i:18414025 original size:25 final size:23 Alignment explanation

Indices: 18413993--18414041 Score: 62 Period size: 25 Copynumber: 2.0 Consensus size: 23 18413983 GTTTTTTCAT 18413993 TATTTTACTATCATTTCTCTATTA 1 TATTTTACTATCATTTCT-TATTA ** 18414017 TATTATTACTATTTTTTCTTATTA 1 TATT-TTACTATCATTTCTTATTA 18414041 T 1 T 18414042 TAAATACTAA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 24 10 0.45 25 12 0.55 ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63 Consensus pattern (23 bp): TATTTTACTATCATTTCTTATTA Found at i:18414042 original size:22 final size:22 Alignment explanation

Indices: 18413984--18414043 Score: 54 Period size: 25 Copynumber: 2.7 Consensus size: 22 18413974 TTTATCATTG 18413984 TTTTTTC--ATTATT-TTACTA 1 TTTTTTCTTATTATTATTACTA ** 18414003 TCATTTCTCTATTATATTATTACTA 1 TTTTTTCT-TA-T-TATTATTACTA 18414028 TTTTTTCTTATTATTA 1 TTTTTTCTTATTATTA 18414044 AATACTAATA Statistics Matches: 31, Mismatches: 4, Indels: 9 0.70 0.09 0.20 Matches are distributed among these distances: 19 5 0.16 22 6 0.19 23 2 0.06 24 6 0.19 25 12 0.39 ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65 Consensus pattern (22 bp): TTTTTTCTTATTATTATTACTA Found at i:18423096 original size:23 final size:23 Alignment explanation

Indices: 18423069--18423134 Score: 96 Period size: 23 Copynumber: 2.9 Consensus size: 23 18423059 TGTTATGATC * * * 18423069 AGTGGTAGCTACGACTACATTAT 1 AGTGGTAGCTTCGGCTACATTAG * 18423092 CGTGGTAGCTTCGGCTACATTAG 1 AGTGGTAGCTTCGGCTACATTAG 18423115 AGTGGTAGCTTCGGCTACAT 1 AGTGGTAGCTTCGGCTACAT 18423135 ATCAGTGTGG Statistics Matches: 38, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 23 38 1.00 ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30 Consensus pattern (23 bp): AGTGGTAGCTTCGGCTACATTAG Found at i:18423141 original size:23 final size:23 Alignment explanation

Indices: 18423066--18423141 Score: 93 Period size: 23 Copynumber: 3.3 Consensus size: 23 18423056 CAGTGTTATG * * 18423066 ATCAGTGGTAGCTACGACTACATT 1 ATCAGTGGTAGCTTCGGCTACA-T 18423090 ATC-GTGGTAGCTTCGGCTACAT 1 ATCAGTGGTAGCTTCGGCTACAT * 18423112 -TAGAGTGGTAGCTTCGGCTACAT 1 AT-CAGTGGTAGCTTCGGCTACAT 18423135 ATCAGTG 1 ATCAGTG 18423142 TGGCACTTAT Statistics Matches: 45, Mismatches: 4, Indels: 7 0.80 0.07 0.12 Matches are distributed among these distances: 21 1 0.02 22 1 0.02 23 39 0.87 24 4 0.09 ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30 Consensus pattern (23 bp): ATCAGTGGTAGCTTCGGCTACAT Found at i:18423252 original size:23 final size:25 Alignment explanation

Indices: 18423206--18423253 Score: 64 Period size: 23 Copynumber: 2.0 Consensus size: 25 18423196 GGATTTGCTA * * 18423206 AGAAATGTTTGATTAGTTATATGAG 1 AGAAATGTTTAATTAGTTAAATGAG 18423231 AGAAATG-TTAATT-GTTAAATGAG 1 AGAAATGTTTAATTAGTTAAATGAG 18423254 TATTTATAGT Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 23 9 0.43 24 5 0.24 25 7 0.33 ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38 Consensus pattern (25 bp): AGAAATGTTTAATTAGTTAAATGAG Found at i:18429690 original size:42 final size:41 Alignment explanation

Indices: 18429621--18429743 Score: 122 Period size: 42 Copynumber: 3.0 Consensus size: 41 18429611 GAGTTTCAAA * * * * 18429621 TTAACCC-TATTGGGTTTCTGTTTAGCTCTTTTGAGCTTCAG 1 TTAACCCTTA-TGGGTTTCCGTTCAGCTCTTATGAGCTTCAC * 18429662 TATAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTCCC 1 T-TAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTCAC * * * * * 18429704 TTCAATCCTTATGGGTTTCCATTTAGCACTTATGTGCTTC 1 TT-AACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTC 18429744 TGTGTAGCCT Statistics Matches: 69, Mismatches: 10, Indels: 5 0.82 0.12 0.06 Matches are distributed among these distances: 41 2 0.03 42 65 0.94 43 2 0.03 ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43 Consensus pattern (41 bp): TTAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTCAC Found at i:18429695 original size:21 final size:21 Alignment explanation

Indices: 18429669--18429737 Score: 59 Period size: 21 Copynumber: 3.3 Consensus size: 21 18429659 CAGTATAACC * 18429669 CTTATGGGTTTCCGTTCAGCT 1 CTTATGGGTTTCCATTCAGCT * * * * 18429690 CTTATGAGCTTCCCTTCA-AT 1 CTTATGGGTTTCCATTCAGCT * * 18429710 CCTTATGGGTTTCCATTTAGCA 1 -CTTATGGGTTTCCATTCAGCT 18429732 CTTATG 1 CTTATG 18429738 TGCTTCTGTG Statistics Matches: 36, Mismatches: 10, Indels: 4 0.72 0.20 0.08 Matches are distributed among these distances: 20 1 0.03 21 35 0.97 ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42 Consensus pattern (21 bp): CTTATGGGTTTCCATTCAGCT Found at i:18435921 original size:27 final size:27 Alignment explanation

Indices: 18435878--18435964 Score: 102 Period size: 27 Copynumber: 3.2 Consensus size: 27 18435868 TGGCAACTAA * * 18435878 GATAGTCAACCGAGACAGTAAACATGG 1 GATAGTCCACTGAGACAGTAAACATGG * * * 18435905 GATAGTCCATTGGGACAGTAAACACGG 1 GATAGTCCACTGAGACAGTAAACATGG * * * 18435932 AATATTCCACTGAGATAGTAAACATGG 1 GATAGTCCACTGAGACAGTAAACATGG 18435959 GATAGT 1 GATAGT 18435965 TTGCCGGGAC Statistics Matches: 47, Mismatches: 13, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 27 47 1.00 ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21 Consensus pattern (27 bp): GATAGTCCACTGAGACAGTAAACATGG Found at i:18438316 original size:31 final size:31 Alignment explanation

Indices: 18438278--18438336 Score: 91 Period size: 31 Copynumber: 1.9 Consensus size: 31 18438268 ACAGGGCCGT * * 18438278 GTATCTAAACTGTGTCACAGACTGAAGCAAC 1 GTATCTAAACCGTGTCACAGACTAAAGCAAC * 18438309 GTATCTAAACCGTGTCACCGACTAAAGC 1 GTATCTAAACCGTGTCACAGACTAAAGC 18438337 TGTGCAAAAC Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 31 25 1.00 ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22 Consensus pattern (31 bp): GTATCTAAACCGTGTCACAGACTAAAGCAAC Found at i:18441365 original size:34 final size:34 Alignment explanation

Indices: 18441322--18441386 Score: 130 Period size: 34 Copynumber: 1.9 Consensus size: 34 18441312 TTAAAGTTGA 18441322 TCGAATAACGTAGCTTCCATAGTTTTCTTTTTGG 1 TCGAATAACGTAGCTTCCATAGTTTTCTTTTTGG 18441356 TCGAATAACGTAGCTTCCATAGTTTTCTTTT 1 TCGAATAACGTAGCTTCCATAGTTTTCTTTT 18441387 CTCCCATTTT Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 34 31 1.00 ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45 Consensus pattern (34 bp): TCGAATAACGTAGCTTCCATAGTTTTCTTTTTGG Found at i:18457942 original size:16 final size:17 Alignment explanation

Indices: 18457912--18457945 Score: 61 Period size: 16 Copynumber: 2.1 Consensus size: 17 18457902 ATATTTTAAA 18457912 ATCTTTTCAAATTTTCG 1 ATCTTTTCAAATTTTCG 18457929 ATCTTTTC-AATTTTCG 1 ATCTTTTCAAATTTTCG 18457945 A 1 A 18457946 CACTAAGACA Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 9 0.53 17 8 0.47 ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53 Consensus pattern (17 bp): ATCTTTTCAAATTTTCG Found at i:18469628 original size:4 final size:4 Alignment explanation

Indices: 18469614--18469652 Score: 69 Period size: 4 Copynumber: 9.8 Consensus size: 4 18469604 ATCTTTTCAT * 18469614 GTTA ATTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTT 1 GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTT 18469653 GATAAGTTCC Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 4 33 1.00 ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51 Consensus pattern (4 bp): GTTA Found at i:18469804 original size:27 final size:26 Alignment explanation

Indices: 18469774--18469830 Score: 62 Period size: 26 Copynumber: 2.2 Consensus size: 26 18469764 CATTATTTAC 18469774 TTTTGAGTTAATAAAATTCTC-TTTGAG 1 TTTT-AGTTAA-AAAATTCTCTTTTGAG * * * 18469801 TTTTCGTTTAAAAATTTTCTTTTGAG 1 TTTTAGTTAAAAAATTCTCTTTTGAG 18469827 TTTT 1 TTTT 18469831 TTTTGAAGAG Statistics Matches: 26, Mismatches: 3, Indels: 3 0.81 0.09 0.09 Matches are distributed among these distances: 25 8 0.31 26 14 0.54 27 4 0.15 ACGTcount: A:0.25, C:0.07, G:0.12, T:0.56 Consensus pattern (26 bp): TTTTAGTTAAAAAATTCTCTTTTGAG Found at i:18471396 original size:20 final size:20 Alignment explanation

Indices: 18471367--18471406 Score: 71 Period size: 20 Copynumber: 2.0 Consensus size: 20 18471357 AGACTTTGAA 18471367 CCATTCCATTTACTTAATTT 1 CCATTCCATTTACTTAATTT * 18471387 CCATTGCATTTACTTAATTT 1 CCATTCCATTTACTTAATTT 18471407 AGCTTAAATA Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.25, C:0.23, G:0.03, T:0.50 Consensus pattern (20 bp): CCATTCCATTTACTTAATTT Found at i:18472383 original size:137 final size:138 Alignment explanation

Indices: 18472124--18472392 Score: 308 Period size: 137 Copynumber: 2.0 Consensus size: 138 18472114 AAAATGGGCT * * * * * 18472124 TGCTTACACAAGCTGAAGGTCAGAATGTAAGCTCCACGATGCTGCTCACTCAAGCAGATGAGTAT 1 TGCTCACACAAGCTGAAGGTCAAAATGTAAGCTACACGATGCTGCTCACACAAGCAGACGAGTAT ** * * * * * ** * * 18472189 CCGTAACTAATGTCAGACCTCAACCATCGGTAGGACATTTAGGACTAGCACCCGAAACATGGTAA 66 CCACAACTAATGCCAGAACTCAACCATCAGTAGAAAATACAAGACCAGCACCCGAAACATGGTAA 18472254 CCTGGGTC 131 CCTGGGTC *** * * 18472262 TGCTCACACAAGCTGGCTGTCAAAATGT-AGCTACACGATGCTGCTTACACAAGCTGACGAGTAT 1 TGCTCACACAAGCTGAAGGTCAAAATGTAAGCTACACGATGCTGCTCACACAAGCAGACGAGTAT ** 18472326 CCACAAC-ATATGCCAGAACTCAACCATCAGTAGAAAATACAAGACCAGCACTTGAAACATGGTA 66 CCACAACTA-ATGCCAGAACTCAACCATCAGTAGAAAATACAAGACCAGCACCCGAAACATGGTA 18472390 ACC 130 ACC 18472393 CTAATGACAT Statistics Matches: 107, Mismatches: 23, Indels: 3 0.80 0.17 0.02 Matches are distributed among these distances: 136 1 0.01 137 83 0.78 138 23 0.21 ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20 Consensus pattern (138 bp): TGCTCACACAAGCTGAAGGTCAAAATGTAAGCTACACGATGCTGCTCACACAAGCAGACGAGTAT CCACAACTAATGCCAGAACTCAACCATCAGTAGAAAATACAAGACCAGCACCCGAAACATGGTAA CCTGGGTC Found at i:18479230 original size:20 final size:18 Alignment explanation

Indices: 18479205--18479272 Score: 64 Period size: 20 Copynumber: 3.5 Consensus size: 18 18479195 NNNNNTAAAT 18479205 ATTATAAAATATCATAGAAA 1 ATTATAAAATAT-AT-GAAA ** 18479225 ATTATAAAAGCTATGAAA 1 ATTATAAAATATATGAAA * 18479243 AATATTAAAATATTATTGAAA 1 ATTA-TAAAATA-TA-TGAAA 18479264 ATTATAAAA 1 ATTATAAAA 18479273 ATTTAAAAAG Statistics Matches: 39, Mismatches: 6, Indels: 6 0.76 0.12 0.12 Matches are distributed among these distances: 18 7 0.18 19 7 0.18 20 17 0.44 21 8 0.21 ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32 Consensus pattern (18 bp): ATTATAAAATATATGAAA Found at i:18479279 original size:8 final size:9 Alignment explanation

Indices: 18479200--18479281 Score: 51 Period size: 9 Copynumber: 8.7 Consensus size: 9 18479190 NNNNNNNNNN * 18479200 TAAATATTA 1 TAAAAATTA * 18479209 TAAAATATCA 1 TAAAA-ATTA 18479219 TAGAAAATTA 1 TA-AAAATTA ** 18479229 TAAAAGCTA 1 TAAAAATTA 18479238 TGAAAAA-TA 1 T-AAAAATTA 18479247 TTAAAATATTA 1 -TAAAA-ATTA * 18479258 TTGAAAATTA 1 -TAAAAATTA 18479268 TAAAAATT- 1 TAAAAATTA 18479276 TAAAAA 1 TAAAAA 18479282 GTACCACTCT Statistics Matches: 59, Mismatches: 8, Indels: 13 0.74 0.10 0.16 Matches are distributed among these distances: 8 6 0.10 9 23 0.39 10 20 0.34 11 10 0.17 ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33 Consensus pattern (9 bp): TAAAAATTA Found at i:18479550 original size:9 final size:8 Alignment explanation

Indices: 18479533--18479634 Score: 59 Period size: 9 Copynumber: 12.1 Consensus size: 8 18479523 TGACTTTTTT 18479533 TTTTATAA 1 TTTTATAA 18479541 TTTCTATAA 1 TTT-TATAA 18479550 TTTTATCAA 1 TTTTAT-AA 18479559 TTTTCATAA 1 TTTT-ATAA * 18479568 TTTTAATTAT 1 TTTT-A-TAA * 18479578 TTTTATCA 1 TTTTATAA 18479586 TTTTAATAAA 1 TTTT-AT-AA * 18479596 TTTTTTAAA 1 TTTTAT-AA 18479605 TTTT-T-- 1 TTTTATAA 18479610 TTTTATAA 1 TTTTATAA * 18479618 TTTTTATGA 1 -TTTTATAA 18479627 TTTT-TAA 1 TTTTATAA 18479634 T 1 T 18479635 AATTCTTAAT Statistics Matches: 76, Mismatches: 8, Indels: 21 0.72 0.08 0.20 Matches are distributed among these distances: 5 4 0.05 6 1 0.01 7 3 0.04 8 16 0.21 9 39 0.51 10 13 0.17 ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64 Consensus pattern (8 bp): TTTTATAA Found at i:18479553 original size:18 final size:17 Alignment explanation

Indices: 18479532--18479649 Score: 59 Period size: 18 Copynumber: 6.8 Consensus size: 17 18479522 ATGACTTTTT * 18479532 TTTTTATAATTTCTATAA 1 TTTTAATAATTT-TATAA 18479550 TTTT-ATCAATTTTCATAA 1 TTTTAAT-AATTTT-ATAA * * 18479568 TTTTAATTATTTTTATCA 1 TTTTAA-TAATTTTATAA * 18479586 TTTTAATAAATTTTTTAAA 1 TTTTAAT-AATTTTAT-AA 18479605 TTTT--T--TTTTATAA 1 TTTTAATAATTTTATAA * * 18479618 TTTTTATGATTTTTAATAA 1 TTTTAAT-AATTTT-ATAA 18479637 TTCTTAAT-ATTTT 1 TT-TTAATAATTTT 18479650 TTGCTACACT Statistics Matches: 79, Mismatches: 8, Indels: 26 0.70 0.07 0.23 Matches are distributed among these distances: 13 6 0.08 14 5 0.06 15 1 0.01 17 5 0.06 18 40 0.51 19 17 0.22 20 5 0.06 ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64 Consensus pattern (17 bp): TTTTAATAATTTTATAA Found at i:18479579 original size:27 final size:26 Alignment explanation

Indices: 18479532--18479650 Score: 68 Period size: 27 Copynumber: 4.5 Consensus size: 26 18479522 ATGACTTTTT * 18479532 TTTTTATAATTTCTATAA-TTTTATCAA 1 TTTTAATAATTT-TATAATTTTTATC-A * * 18479559 TTTTCATAATTTTAATTATTTTTATCA 1 TTTTAATAATTTT-ATAATTTTTATCA * * 18479586 TTTTAATAAATTTTTTAAATTTT-T-- 1 TTTTAAT-AATTTTATAATTTTTATCA * * 18479610 TTTT-ATAATTTTTATGATTTTTAATAA 1 TTTTAATAA-TTTTATAATTTTT-ATCA * 18479637 TTCTTAATATTTTT 1 TT-TTAATAATTTT 18479651 TGCTACACTA Statistics Matches: 72, Mismatches: 10, Indels: 19 0.71 0.10 0.19 Matches are distributed among these distances: 22 2 0.03 23 12 0.17 24 4 0.06 25 1 0.01 26 2 0.03 27 29 0.40 28 19 0.26 29 3 0.04 ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64 Consensus pattern (26 bp): TTTTAATAATTTTATAATTTTTATCA Found at i:18479648 original size:19 final size:19 Alignment explanation

Indices: 18479608--18479650 Score: 52 Period size: 19 Copynumber: 2.3 Consensus size: 19 18479598 TTTTAAATTT * * 18479608 TTTTTTATAATTTTTATGA 1 TTTTTAATAATTTTAATGA 18479627 TTTTTAATAATTCTTAAT-A 1 TTTTTAATAATT-TTAATGA 18479646 TTTTT 1 TTTTT 18479651 TGCTACACTA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 19 17 0.81 20 4 0.19 ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67 Consensus pattern (19 bp): TTTTTAATAATTTTAATGA Found at i:18480906 original size:6 final size:6 Alignment explanation

Indices: 18480895--18480935 Score: 55 Period size: 6 Copynumber: 6.8 Consensus size: 6 18480885 ATTCTAAACG * * * 18480895 TTAAAA TTAAAA TTAAAA TTAAAA TTAGAA TAAAAA GTAAA 1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAA 18480936 GAAAAATTTC Statistics Matches: 30, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 6 30 1.00 ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29 Consensus pattern (6 bp): TTAAAA Found at i:18492138 original size:18 final size:18 Alignment explanation

Indices: 18492115--18492149 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 18492105 TAGTCTTTTA * 18492115 GATGCACTTGTTGAGTGT 1 GATGCACTGGTTGAGTGT 18492133 GATGCACTGGTTGAGTG 1 GATGCACTGGTTGAGTG 18492150 CTAATCACAT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.17, C:0.11, G:0.37, T:0.34 Consensus pattern (18 bp): GATGCACTGGTTGAGTGT Found at i:18494920 original size:112 final size:113 Alignment explanation

Indices: 18494766--18494991 Score: 436 Period size: 112 Copynumber: 2.0 Consensus size: 113 18494756 ACTTAAAATT 18494766 AAACTATTATTAAATTAAGTTATTGAACCTAATTAATAATTTTAAAACTTATATTTTCAAATTAT 1 AAACTATTATTAAATTAAGTTATTGAACCTAATTAATAATTTTAAAACTTATATTTTCAAATTAT 18494831 AAATATATTTATATGGATGTAATTGAAATATATTTGCATGTATATATA 66 AAATATATTTATATGGATGTAATTGAAATATATTTGCATGTATATATA * 18494879 AAACTATTATT-AATTAAGTTATTGAACCTAATTAATAATTTTAAAACTTATATTTTCATATTAT 1 AAACTATTATTAAATTAAGTTATTGAACCTAATTAATAATTTTAAAACTTATATTTTCAAATTAT 18494943 AAATATATTTATATGGATGTAATTGAAATATATTTGCATGTATATATA 66 AAATATATTTATATGGATGTAATTGAAATATATTTGCATGTATATATA 18494991 A 1 A 18494992 TATATAATTT Statistics Matches: 112, Mismatches: 1, Indels: 1 0.98 0.01 0.01 Matches are distributed among these distances: 112 101 0.90 113 11 0.10 ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45 Consensus pattern (113 bp): AAACTATTATTAAATTAAGTTATTGAACCTAATTAATAATTTTAAAACTTATATTTTCAAATTAT AAATATATTTATATGGATGTAATTGAAATATATTTGCATGTATATATA Found at i:18500526 original size:14 final size:15 Alignment explanation

Indices: 18500507--18500536 Score: 53 Period size: 14 Copynumber: 2.1 Consensus size: 15 18500497 CAACTTCACC 18500507 TCCCAGCTCG-CTAT 1 TCCCAGCTCGCCTAT 18500521 TCCCAGCTCGCCTAT 1 TCCCAGCTCGCCTAT 18500536 T 1 T 18500537 TGCGAGGAGG Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 10 0.67 15 5 0.33 ACGTcount: A:0.13, C:0.43, G:0.13, T:0.30 Consensus pattern (15 bp): TCCCAGCTCGCCTAT Found at i:18504484 original size:20 final size:20 Alignment explanation

Indices: 18504459--18504496 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 18504449 ATGAATATTA 18504459 TGTGGTGTCAATAGTGGTTT 1 TGTGGTGTCAATAGTGGTTT * * 18504479 TGTGGTGTGATTAGTGGT 1 TGTGGTGTCAATAGTGGT 18504497 CGGTAAGGAG Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.13, C:0.03, G:0.39, T:0.45 Consensus pattern (20 bp): TGTGGTGTCAATAGTGGTTT Found at i:18504827 original size:31 final size:31 Alignment explanation

Indices: 18504792--18504863 Score: 108 Period size: 31 Copynumber: 2.3 Consensus size: 31 18504782 ATGCCTTTTA * * * 18504792 TATTTCAAATCTATAATTTCCCTAGCTCACT 1 TATTTGAAATCAATAATTTCCCTACCTCACT * 18504823 TATTTGAAAACAATAATTTCCCTACCTCACT 1 TATTTGAAATCAATAATTTCCCTACCTCACT 18504854 TATTTGAAAT 1 TATTTGAAAT 18504864 ATGAAAGGAA Statistics Matches: 36, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 31 36 1.00 ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40 Consensus pattern (31 bp): TATTTGAAATCAATAATTTCCCTACCTCACT Found at i:18514016 original size:8 final size:8 Alignment explanation

Indices: 18514005--18514029 Score: 50 Period size: 8 Copynumber: 3.1 Consensus size: 8 18513995 ATTTTATTAT 18514005 ATATAATA 1 ATATAATA 18514013 ATATAATA 1 ATATAATA 18514021 ATATAATA 1 ATATAATA 18514029 A 1 A 18514030 CATACATTCA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 17 1.00 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (8 bp): ATATAATA Found at i:18514277 original size:8 final size:8 Alignment explanation

Indices: 18514264--18514288 Score: 50 Period size: 8 Copynumber: 3.1 Consensus size: 8 18514254 TATTTTATTT 18514264 ATATAATA 1 ATATAATA 18514272 ATATAATA 1 ATATAATA 18514280 ATATAATA 1 ATATAATA 18514288 A 1 A 18514289 CATACATTCA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 17 1.00 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (8 bp): ATATAATA Found at i:18514463 original size:259 final size:260 Alignment explanation

Indices: 18513993--18514511 Score: 1031 Period size: 259 Copynumber: 2.0 Consensus size: 260 18513983 TTTGAAAAAA 18513993 TTATTTTATTATATATAATAATATAATAATATAATAACATACATTCATTCACATACATTCCCTTA 1 TTATTTTATTATATATAATAATATAATAATATAATAACATACATTCATTCACATACATTCCCTTA 18514058 AATATGCTTATAATTACAAGAATGTTACATCTTACAAAAAATTAATCACACATGAAGATAGAAAA 66 AATATGCTTATAATTACAAGAATGTTACATCTTACAAAAAATTAATCACACATGAAGATAGAAAA 18514123 TTTTGGTATTAGTTTATACTATAATATAGCACAACCTAGCTCTGATACCAATTGTTGGAAAATAT 131 TTTTGGTATTAGTTTATACTATAATATAGCACAACCTAGCTCTGATACCAATTGTTGGAAAATAT 18514188 TCTTTTCAAAAATGATTCTTGCATAGAAGAAAATTAAAATTTTGGAAACCGAGTCAATTTGTAAT 196 TCTTTTCAAAAATGATTCTTGCATAGAAGAAAATTAAAATTTTGGAAACCGAGTCAATTTGTAAT 18514253 TTATTTTATT-TATATAATAATATAATAATATAATAACATACATTCATTCACATACATTCCCTTA 1 TTATTTTATTATATATAATAATATAATAATATAATAACATACATTCATTCACATACATTCCCTTA 18514317 AATATGCTTATAATTACAAGAATGTTACATCTTACAAAAAATTAATCACACATGAAGATAGAAAA 66 AATATGCTTATAATTACAAGAATGTTACATCTTACAAAAAATTAATCACACATGAAGATAGAAAA 18514382 TTTTGGTATTAGTTTATACTATAATATAGCACAACCTAGCTCTGATACCAATTGTTGGAAAATAT 131 TTTTGGTATTAGTTTATACTATAATATAGCACAACCTAGCTCTGATACCAATTGTTGGAAAATAT 18514447 TCTTTTCAAAAATGATTCTTGCATAGAAGAAAATTAAAATTTTGGAAACCGAGTCAATTTGTAAT 196 TCTTTTCAAAAATGATTCTTGCATAGAAGAAAATTAAAATTTTGGAAACCGAGTCAATTTGTAAT 18514512 ATTTATAGTA Statistics Matches: 259, Mismatches: 0, Indels: 1 1.00 0.00 0.00 Matches are distributed among these distances: 259 249 0.96 260 10 0.04 ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36 Consensus pattern (260 bp): TTATTTTATTATATATAATAATATAATAATATAATAACATACATTCATTCACATACATTCCCTTA AATATGCTTATAATTACAAGAATGTTACATCTTACAAAAAATTAATCACACATGAAGATAGAAAA TTTTGGTATTAGTTTATACTATAATATAGCACAACCTAGCTCTGATACCAATTGTTGGAAAATAT TCTTTTCAAAAATGATTCTTGCATAGAAGAAAATTAAAATTTTGGAAACCGAGTCAATTTGTAAT Found at i:18520638 original size:22 final size:22 Alignment explanation

Indices: 18520608--18520650 Score: 68 Period size: 22 Copynumber: 2.0 Consensus size: 22 18520598 ACACCAAAAC * 18520608 AGGCTTTTAGCGGCGCTTTTTT 1 AGGCCTTTAGCGGCGCTTTTTT * 18520630 AGGCCTTTAGCTGCGCTTTTT 1 AGGCCTTTAGCGGCGCTTTTT 18520651 AGTGTCGCAA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 19 1.00 ACGTcount: A:0.09, C:0.21, G:0.26, T:0.44 Consensus pattern (22 bp): AGGCCTTTAGCGGCGCTTTTTT Found at i:18521006 original size:43 final size:43 Alignment explanation

Indices: 18520745--18521031 Score: 174 Period size: 43 Copynumber: 6.7 Consensus size: 43 18520735 TTTTAGAAAT ** * * 18520745 AAACGCCGCTAAAGACCAAGACCTTTAGTGGCG-C-TTTCACCAC 1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTTTTCA--AC * ** * * ** 18520788 AACCGCCGCTAAAGGTCATGGTCTTTAGCGGCG-CTTACCAAAC 1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTTTTC-AAC *** * * * * 18520831 AAACGCCGCTAAAGAAAATGACCTTTAGCGACG-CTACTCCAAC 1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCT-TTTCAAC * * * * * 18520874 AATCACCGCTAAATACCCTGATCTTTAACGGCG-CTTCTCCAGA- 1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTT-TTCA-AC * * 18520917 AAATGCCGCTACAGACCCTGATCTTTAGCGGCGCCTTTTCAAC 1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTTTTCAAC * * * ** 18520960 AAACGCTGCTAAAGTCCCTGATCTTTAGCGGCG-TTTTTCTCTC 1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTTTTC-AAC * * 18521003 AAACGCCGCTGAAGACCATGATCTTTAGC 1 AAACGCCGCTAAAGACCCTGATCTTTAGC 18521032 AGCACTTTTC Statistics Matches: 190, Mismatches: 46, Indels: 16 0.75 0.18 0.06 Matches are distributed among these distances: 42 6 0.03 43 175 0.92 44 8 0.04 45 1 0.01 ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23 Consensus pattern (43 bp): AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTTTTCAAC Found at i:18521408 original size:21 final size:21 Alignment explanation

Indices: 18521375--18521419 Score: 63 Period size: 21 Copynumber: 2.1 Consensus size: 21 18521365 TTTTACGCTG * * 18521375 CTCTGCTTCCCTCGCTGTAGC 1 CTCTACTTCCCTCGCTGCAGC * 18521396 CTCTACTTTCCTCGCTGCAGC 1 CTCTACTTCCCTCGCTGCAGC 18521417 CTC 1 CTC 18521420 AGCTTCTCTC Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 21 1.00 ACGTcount: A:0.07, C:0.44, G:0.16, T:0.33 Consensus pattern (21 bp): CTCTACTTCCCTCGCTGCAGC Found at i:18521430 original size:21 final size:22 Alignment explanation

Indices: 18521375--18521430 Score: 57 Period size: 21 Copynumber: 2.7 Consensus size: 22 18521365 TTTTACGCTG * * 18521375 CTCT-GCTTCCCTCGCTGTAGC 1 CTCTAGCTTCTCTCGCTGCAGC 18521396 CTCTA-CTT-TCCTCGCTGCAGC 1 CTCTAGCTTCT-CTCGCTGCAGC 18521417 CTC-AGCTTCTCTCG 1 CTCTAGCTTCTCTCG 18521431 ATGCCCCATC Statistics Matches: 29, Mismatches: 2, Indels: 8 0.74 0.05 0.21 Matches are distributed among these distances: 20 1 0.03 21 27 0.93 22 1 0.03 ACGTcount: A:0.07, C:0.43, G:0.16, T:0.34 Consensus pattern (22 bp): CTCTAGCTTCTCTCGCTGCAGC Found at i:18521513 original size:65 final size:66 Alignment explanation

Indices: 18521416--18521568 Score: 186 Period size: 66 Copynumber: 2.3 Consensus size: 66 18521406 CTCGCTGCAG *** ** 18521416 CCTCAGCTTCTCTCGATGCCCCATCTGTTTTAAGCTGCT-GCT-GAGTTCTTCATA-CTTTCGTT 1 CCTCAGCTTCTCTCGATGTTGCATCTACTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT 18521478 GAA 64 GAA * * * * 18521481 TCTCAGCTTCTCTCGCTGTTGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA 1 CCTCAGCTTCTCTCGATGTTGCATCTACTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA 18521546 A 66 A 18521547 CCTCAGCTTCTCTCGATGTTGC 1 CCTCAGCTTCTCTCGATGTTGC 18521569 CTCCGCTTTA Statistics Matches: 74, Mismatches: 11, Indels: 5 0.82 0.12 0.06 Matches are distributed among these distances: 64 1 0.01 65 32 0.43 66 37 0.50 67 4 0.05 ACGTcount: A:0.15, C:0.27, G:0.17, T:0.41 Consensus pattern (66 bp): CCTCAGCTTCTCTCGATGTTGCATCTACTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA A Found at i:18521555 original size:66 final size:66 Alignment explanation

Indices: 18521458--18521582 Score: 180 Period size: 66 Copynumber: 1.9 Consensus size: 66 18521448 AGCTGCTGCT * * * 18521458 GAGTTCTTCATACTTTCGTTGAATCTCAGCTTCTCTCGCTGTTGCATCTACTTTAAGTTGTAGCT 1 GAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGTTGCATCCACTTTAAGTTGTAGCT 18521523 G 66 G * * * 18521524 GAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTT 1 GAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGATGTTGCATCCACTTTAAGTT 18521583 TTGTAATTTG Statistics Matches: 52, Mismatches: 6, Indels: 2 0.87 0.10 0.03 Matches are distributed among these distances: 66 48 0.92 67 4 0.08 ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43 Consensus pattern (66 bp): GAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGTTGCATCCACTTTAAGTTGTAGCT G Found at i:18521813 original size:30 final size:30 Alignment explanation

Indices: 18521777--18521836 Score: 120 Period size: 30 Copynumber: 2.0 Consensus size: 30 18521767 TGATAATCCG 18521777 GTTATCAATGTCGTCAATATGAACAGAACT 1 GTTATCAATGTCGTCAATATGAACAGAACT 18521807 GTTATCAATGTCGTCAATATGAACAGAACT 1 GTTATCAATGTCGTCAATATGAACAGAACT 18521837 ATCACTGGAA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 30 30 1.00 ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30 Consensus pattern (30 bp): GTTATCAATGTCGTCAATATGAACAGAACT Found at i:18523242 original size:12 final size:11 Alignment explanation

Indices: 18523184--18523252 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18523174 ATAATTTATT 18523184 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18523197 TAAGTTATATA 1 TAAGTTATGTG * * 18523208 TAAGTTTATATA 1 TAAG-TTATGTG 18523220 TAAGTTA--TG 1 TAAGTTATGTG 18523229 TAAGTTATTGTG 1 TAAGTTA-TGTG 18523241 TAAGTTATGTG 1 TAAGTTATGTG 18523252 T 1 T 18523253 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18523338 original size:12 final size:11 Alignment explanation

Indices: 18523280--18523348 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18523270 AAACTTTATT 18523280 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18523293 TAAGTTATATA 1 TAAGTTATGTG * * 18523304 TAAGTTTATATA 1 TAAG-TTATGTG 18523316 TAAGTTA--TG 1 TAAGTTATGTG 18523325 TAAGTTATTGTG 1 TAAGTTA-TGTG 18523337 TAAGTTATGTG 1 TAAGTTATGTG 18523348 T 1 T 18523349 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18523342 original size:96 final size:96 Alignment explanation

Indices: 18523178--18525128 Score: 3823 Period size: 96 Copynumber: 20.3 Consensus size: 96 18523168 ACAACAATAA 18523178 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18523243 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18523274 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18523339 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18523370 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18523435 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18523466 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18523531 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18523562 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18523627 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18523658 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18523723 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18523754 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18523819 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18523850 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18523915 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18523946 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18524011 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18524042 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18524107 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18524138 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18524203 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18524234 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18524299 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18524330 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18524395 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18524426 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18524491 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18524522 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18524587 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18524618 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18524683 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18524714 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18524779 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC 18524810 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18524875 AGTTATGTGTTGTGTAAGTTTATATATAAAC 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC * 18524906 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTATGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA * * 18524971 AGTTATCTGTTGTGTAAGTTTATATATAAAT 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC * 18525002 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTATGTA 1 TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA 18525067 AGTTATGTGTTGTGTAAGTTTATATATAAA- 66 AGTTATGTGTTGTGTAAGTTTATATATAAAC * * * 18525097 TTTATATATGTTATGTATGTAAATTATGATAT 1 TTTATTTAAGTTATGTATGTAAGTTAT-ATAT 18525129 GATGGATAAA Statistics Matches: 1847, Mismatches: 7, Indels: 2 1.00 0.00 0.00 Matches are distributed among these distances: 95 24 0.01 96 1823 0.99 ACGTcount: A:0.33, C:0.01, G:0.16, T:0.49 Consensus pattern (96 bp): TTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTA AGTTATGTGTTGTGTAAGTTTATATATAAAC Found at i:18523434 original size:12 final size:11 Alignment explanation

Indices: 18523376--18523444 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18523366 AAACTTTATT 18523376 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18523389 TAAGTTATATA 1 TAAGTTATGTG * * 18523400 TAAGTTTATATA 1 TAAG-TTATGTG 18523412 TAAGTTA--TG 1 TAAGTTATGTG 18523421 TAAGTTATTGTG 1 TAAGTTA-TGTG 18523433 TAAGTTATGTG 1 TAAGTTATGTG 18523444 T 1 T 18523445 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18523530 original size:12 final size:11 Alignment explanation

Indices: 18523472--18523540 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18523462 AAACTTTATT 18523472 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18523485 TAAGTTATATA 1 TAAGTTATGTG * * 18523496 TAAGTTTATATA 1 TAAG-TTATGTG 18523508 TAAGTTA--TG 1 TAAGTTATGTG 18523517 TAAGTTATTGTG 1 TAAGTTA-TGTG 18523529 TAAGTTATGTG 1 TAAGTTATGTG 18523540 T 1 T 18523541 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18523626 original size:12 final size:11 Alignment explanation

Indices: 18523568--18523636 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18523558 AAACTTTATT 18523568 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18523581 TAAGTTATATA 1 TAAGTTATGTG * * 18523592 TAAGTTTATATA 1 TAAG-TTATGTG 18523604 TAAGTTA--TG 1 TAAGTTATGTG 18523613 TAAGTTATTGTG 1 TAAGTTA-TGTG 18523625 TAAGTTATGTG 1 TAAGTTATGTG 18523636 T 1 T 18523637 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18523722 original size:12 final size:11 Alignment explanation

Indices: 18523664--18523732 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18523654 AAACTTTATT 18523664 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18523677 TAAGTTATATA 1 TAAGTTATGTG * * 18523688 TAAGTTTATATA 1 TAAG-TTATGTG 18523700 TAAGTTA--TG 1 TAAGTTATGTG 18523709 TAAGTTATTGTG 1 TAAGTTA-TGTG 18523721 TAAGTTATGTG 1 TAAGTTATGTG 18523732 T 1 T 18523733 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18523818 original size:12 final size:11 Alignment explanation

Indices: 18523760--18523828 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18523750 AAACTTTATT 18523760 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18523773 TAAGTTATATA 1 TAAGTTATGTG * * 18523784 TAAGTTTATATA 1 TAAG-TTATGTG 18523796 TAAGTTA--TG 1 TAAGTTATGTG 18523805 TAAGTTATTGTG 1 TAAGTTA-TGTG 18523817 TAAGTTATGTG 1 TAAGTTATGTG 18523828 T 1 T 18523829 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18523914 original size:12 final size:11 Alignment explanation

Indices: 18523856--18523924 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18523846 AAACTTTATT 18523856 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18523869 TAAGTTATATA 1 TAAGTTATGTG * * 18523880 TAAGTTTATATA 1 TAAG-TTATGTG 18523892 TAAGTTA--TG 1 TAAGTTATGTG 18523901 TAAGTTATTGTG 1 TAAGTTA-TGTG 18523913 TAAGTTATGTG 1 TAAGTTATGTG 18523924 T 1 T 18523925 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18524010 original size:12 final size:11 Alignment explanation

Indices: 18523952--18524020 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18523942 AAACTTTATT 18523952 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18523965 TAAGTTATATA 1 TAAGTTATGTG * * 18523976 TAAGTTTATATA 1 TAAG-TTATGTG 18523988 TAAGTTA--TG 1 TAAGTTATGTG 18523997 TAAGTTATTGTG 1 TAAGTTA-TGTG 18524009 TAAGTTATGTG 1 TAAGTTATGTG 18524020 T 1 T 18524021 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18524106 original size:12 final size:11 Alignment explanation

Indices: 18524048--18524116 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18524038 AAACTTTATT 18524048 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18524061 TAAGTTATATA 1 TAAGTTATGTG * * 18524072 TAAGTTTATATA 1 TAAG-TTATGTG 18524084 TAAGTTA--TG 1 TAAGTTATGTG 18524093 TAAGTTATTGTG 1 TAAGTTA-TGTG 18524105 TAAGTTATGTG 1 TAAGTTATGTG 18524116 T 1 T 18524117 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18524202 original size:12 final size:11 Alignment explanation

Indices: 18524144--18524212 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18524134 AAACTTTATT 18524144 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18524157 TAAGTTATATA 1 TAAGTTATGTG * * 18524168 TAAGTTTATATA 1 TAAG-TTATGTG 18524180 TAAGTTA--TG 1 TAAGTTATGTG 18524189 TAAGTTATTGTG 1 TAAGTTA-TGTG 18524201 TAAGTTATGTG 1 TAAGTTATGTG 18524212 T 1 T 18524213 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18524298 original size:12 final size:11 Alignment explanation

Indices: 18524240--18524308 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18524230 AAACTTTATT 18524240 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18524253 TAAGTTATATA 1 TAAGTTATGTG * * 18524264 TAAGTTTATATA 1 TAAG-TTATGTG 18524276 TAAGTTA--TG 1 TAAGTTATGTG 18524285 TAAGTTATTGTG 1 TAAGTTA-TGTG 18524297 TAAGTTATGTG 1 TAAGTTATGTG 18524308 T 1 T 18524309 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18524394 original size:12 final size:11 Alignment explanation

Indices: 18524336--18524404 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18524326 AAACTTTATT 18524336 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18524349 TAAGTTATATA 1 TAAGTTATGTG * * 18524360 TAAGTTTATATA 1 TAAG-TTATGTG 18524372 TAAGTTA--TG 1 TAAGTTATGTG 18524381 TAAGTTATTGTG 1 TAAGTTA-TGTG 18524393 TAAGTTATGTG 1 TAAGTTATGTG 18524404 T 1 T 18524405 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18524490 original size:12 final size:11 Alignment explanation

Indices: 18524432--18524500 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18524422 AAACTTTATT 18524432 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18524445 TAAGTTATATA 1 TAAGTTATGTG * * 18524456 TAAGTTTATATA 1 TAAG-TTATGTG 18524468 TAAGTTA--TG 1 TAAGTTATGTG 18524477 TAAGTTATTGTG 1 TAAGTTA-TGTG 18524489 TAAGTTATGTG 1 TAAGTTATGTG 18524500 T 1 T 18524501 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18524586 original size:12 final size:11 Alignment explanation

Indices: 18524528--18524596 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18524518 AAACTTTATT 18524528 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18524541 TAAGTTATATA 1 TAAGTTATGTG * * 18524552 TAAGTTTATATA 1 TAAG-TTATGTG 18524564 TAAGTTA--TG 1 TAAGTTATGTG 18524573 TAAGTTATTGTG 1 TAAGTTA-TGTG 18524585 TAAGTTATGTG 1 TAAGTTATGTG 18524596 T 1 T 18524597 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18524682 original size:12 final size:11 Alignment explanation

Indices: 18524624--18524692 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18524614 AAACTTTATT 18524624 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18524637 TAAGTTATATA 1 TAAGTTATGTG * * 18524648 TAAGTTTATATA 1 TAAG-TTATGTG 18524660 TAAGTTA--TG 1 TAAGTTATGTG 18524669 TAAGTTATTGTG 1 TAAGTTA-TGTG 18524681 TAAGTTATGTG 1 TAAGTTATGTG 18524692 T 1 T 18524693 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18524778 original size:12 final size:11 Alignment explanation

Indices: 18524720--18524788 Score: 52 Period size: 12 Copynumber: 6.1 Consensus size: 11 18524710 AAACTTTATT 18524720 TAAGTTATGTATG 1 TAAGTTATG--TG * * 18524733 TAAGTTATATA 1 TAAGTTATGTG * * 18524744 TAAGTTTATATA 1 TAAG-TTATGTG 18524756 TAAGTTA--TG 1 TAAGTTATGTG 18524765 TAAGTTATTGTG 1 TAAGTTA-TGTG 18524777 TAAGTTATGTG 1 TAAGTTATGTG 18524788 T 1 T 18524789 TGTGTAAGTT Statistics Matches: 49, Mismatches: 3, Indels: 10 0.79 0.05 0.16 Matches are distributed among these distances: 9 8 0.16 11 13 0.27 12 20 0.41 13 8 0.16 ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48 Consensus pattern (11 bp): TAAGTTATGTG Found at i:18524850 original size:12 final size:12 Alignment explanation

Indices: 18524793--18525049 Score: 78 Period size: 12 Copynumber: 21.5 Consensus size: 12 18524783 ATGTGTTGTG 18524793 TAAGTTTATATA 1 TAAGTTTATATA * 18524805 TAAACTTTAT-T- 1 T-AAGTTTATATA * * 18524816 TAAGTTATGTATG 1 TAAGTT-TATATA 18524829 TAAG-TTATATA 1 TAAGTTTATATA 18524840 TAAGTTTATATA 1 TAAGTTTATATA * 18524852 TAAG--T-TATG 1 TAAGTTTATATA * * 18524861 TAAG-TTATTGTG 1 TAAGTTTA-TATA * * * 18524873 TAAGTTATGTGTTG 1 TAAGTT-TAT-ATA 18524887 TGTAAGTTTATATA 1 T--AAGTTTATATA * 18524901 TAAACTTTAT-T- 1 T-AAGTTTATATA * * 18524912 TAAGTTATGTATG 1 TAAGTT-TATATA 18524925 TAAG-TTATATA 1 TAAGTTTATATA 18524936 TAAGTTTATATA 1 TAAGTTTATATA * 18524948 TAAG--T-TATG 1 TAAGTTTATATA * 18524957 TAAG-TTATTATG 1 TAAGTTTA-TATA * * * 18524969 TAAGTTATCTGTTGTG 1 TAAG-T-T-T-ATATA 18524985 TAAGTTTATATA 1 TAAGTTTATATA * * 18524997 TAAATTT-TATT 1 TAAGTTTATATA * * 18525008 TAAGTTATGTATG 1 TAAGTT-TATATA 18525021 TAAG-TTATATA 1 TAAGTTTATATA 18525032 TAAGTTTATATA 1 TAAGTTTATATA 18525044 TAAGTT 1 TAAGTT 18525050 ATGTAAGTTA Statistics Matches: 187, Mismatches: 30, Indels: 56 0.68 0.11 0.21 Matches are distributed among these distances: 9 14 0.07 10 12 0.06 11 38 0.20 12 67 0.36 13 32 0.17 14 7 0.04 15 4 0.02 16 13 0.07 ACGTcount: A:0.35, C:0.01, G:0.14, T:0.49 Consensus pattern (12 bp): TAAGTTTATATA Found at i:18525156 original size:19 final size:19 Alignment explanation

Indices: 18525134--18525174 Score: 57 Period size: 19 Copynumber: 2.2 Consensus size: 19 18525124 GATATGATGG * 18525134 ATAAATTTTTCAA-ATATAT 1 ATAAAATTTT-AATATATAT 18525153 ATAAAATTTTAATATATAT 1 ATAAAATTTTAATATATAT 18525172 ATA 1 ATA 18525175 TATATATATT Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 18 2 0.10 19 18 0.90 ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46 Consensus pattern (19 bp): ATAAAATTTTAATATATAT Found at i:18525196 original size:29 final size:29 Alignment explanation

Indices: 18525147--18525208 Score: 81 Period size: 29 Copynumber: 2.1 Consensus size: 29 18525137 AATTTTTCAA * * * 18525147 ATATATATAAAATTTTAATATATATATAT 1 ATATATATAAAACTGTAATATAAATATAT 18525176 ATATATATTAAAACTGT-ATATAAATATAT 1 ATATATA-TAAAACTGTAATATAAATATAT 18525205 ATAT 1 ATAT 18525209 CAAAGATGTT Statistics Matches: 29, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 29 22 0.76 30 7 0.24 ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45 Consensus pattern (29 bp): ATATATATAAAACTGTAATATAAATATAT Found at i:18528059 original size:4 final size:4 Alignment explanation

Indices: 18528050--18528079 Score: 51 Period size: 4 Copynumber: 7.5 Consensus size: 4 18528040 AATTTCACGT * 18528050 TTTA TTTA TTTA TTTA TATA TTTA TTTA TT 1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT 18528080 GTATGTTTCA Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 4 24 1.00 ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73 Consensus pattern (4 bp): TTTA Found at i:18528133 original size:113 final size:114 Alignment explanation

Indices: 18527994--18528222 Score: 424 Period size: 113 Copynumber: 2.0 Consensus size: 114 18527984 CCGTTTTGGG 18527994 AAATTTGTATATATAGTAACGACATTTTTTTCTAAAAACGCCGCTAAATTTCACGTTTTATTTAT 1 AAATTTG-ATATATAGTAACGACATTTTTTTCTAAAAACGCCGCTAAATTTCACGTTTTATTTAT 18528059 TTATTTATATATTTATTTATTGTATGTTTCATTAAAATTTTAAGTAAATA 65 TTATTTATATATTTATTTATTGTATGTTTCATTAAAATTTTAAGTAAATA 18528109 AAATTTG-TATATAGTAACGACATTTTTTTCTAAAAACGCCGCTAAATTTCACGTTTTATTTATT 1 AAATTTGATATATAGTAACGACATTTTTTTCTAAAAACGCCGCTAAATTTCACGTTTTATTTATT ** 18528173 TATTTATATATTTATTTATTGTATGTTTTTTTAAAATTTTAAGTAAATA 66 TATTTATATATTTATTTATTGTATGTTTCATTAAAATTTTAAGTAAATA 18528222 A 1 A 18528223 TTATTAAAGT Statistics Matches: 112, Mismatches: 2, Indels: 2 0.97 0.02 0.02 Matches are distributed among these distances: 113 105 0.94 115 7 0.06 ACGTcount: A:0.34, C:0.08, G:0.08, T:0.49 Consensus pattern (114 bp): AAATTTGATATATAGTAACGACATTTTTTTCTAAAAACGCCGCTAAATTTCACGTTTTATTTATT TATTTATATATTTATTTATTGTATGTTTCATTAAAATTTTAAGTAAATA Found at i:18528172 original size:4 final size:4 Alignment explanation

Indices: 18528163--18528192 Score: 51 Period size: 4 Copynumber: 7.5 Consensus size: 4 18528153 AATTTCACGT * 18528163 TTTA TTTA TTTA TTTA TATA TTTA TTTA TT 1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT 18528193 GTATGTTTTT Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 4 24 1.00 ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73 Consensus pattern (4 bp): TTTA Found at i:18528270 original size:21 final size:21 Alignment explanation

Indices: 18528204--18528270 Score: 59 Period size: 20 Copynumber: 3.2 Consensus size: 21 18528194 TATGTTTTTT 18528204 TAAAA-TTTTAAGTAAATAATTA 1 TAAAAGTTTTAAGT-AA-AATTA * * 18528226 TTAAAGTTTTAAGTAATATT- 1 TAAAAGTTTTAAGTAAAATTA * 18528246 TAAAAGTTTT-TGATAAAATTA 1 TAAAAGTTTTAAG-TAAAATTA 18528267 TAAA 1 TAAA 18528271 TTTTAGTTTT Statistics Matches: 37, Mismatches: 5, Indels: 7 0.76 0.10 0.14 Matches are distributed among these distances: 19 1 0.03 20 15 0.41 21 7 0.19 22 6 0.16 23 8 0.22 ACGTcount: A:0.49, C:0.00, G:0.07, T:0.43 Consensus pattern (21 bp): TAAAAGTTTTAAGTAAAATTA Found at i:18528302 original size:10 final size:10 Alignment explanation

Indices: 18528289--18528320 Score: 55 Period size: 10 Copynumber: 3.2 Consensus size: 10 18528279 TTTTATTTCC 18528289 TTTTTATATT 1 TTTTTATATT 18528299 TTTTTATATT 1 TTTTTATATT * 18528309 TTCTTATATT 1 TTTTTATATT 18528319 TT 1 TT 18528321 GGTCCTGTCC Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 10 21 1.00 ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78 Consensus pattern (10 bp): TTTTTATATT Found at i:18529435 original size:7 final size:7 Alignment explanation

Indices: 18529425--18529457 Score: 52 Period size: 7 Copynumber: 5.0 Consensus size: 7 18529415 CTCTTAACAT 18529425 CTAACCC 1 CTAACCC 18529432 CTAA--C 1 CTAACCC 18529437 CTAACCC 1 CTAACCC 18529444 CTAACCC 1 CTAACCC 18529451 CTAACCC 1 CTAACCC 18529458 ATAAACCTTA Statistics Matches: 24, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 5 5 0.21 7 19 0.79 ACGTcount: A:0.30, C:0.55, G:0.00, T:0.15 Consensus pattern (7 bp): CTAACCC Found at i:18529442 original size:12 final size:12 Alignment explanation

Indices: 18529425--18529449 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 18529415 CTCTTAACAT 18529425 CTAACCCCTAAC 1 CTAACCCCTAAC 18529437 CTAACCCCTAAC 1 CTAACCCCTAAC 18529449 C 1 C 18529450 CCTAACCCAT 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:0.32, C:0.52, G:0.00, T:0.16 Consensus pattern (12 bp): CTAACCCCTAAC Found at i:18529513 original size:14 final size:15 Alignment explanation

Indices: 18529491--18529524 Score: 52 Period size: 15 Copynumber: 2.3 Consensus size: 15 18529481 CTTAAACAAA * 18529491 AATCCCTAA-TCCAT 1 AATCTCTAATTCCAT 18529505 AATCTCTAATTCCAT 1 AATCTCTAATTCCAT 18529520 AATCT 1 AATCT 18529525 ATAAAACTTA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 14 8 0.44 15 10 0.56 ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35 Consensus pattern (15 bp): AATCTCTAATTCCAT Found at i:18529977 original size:41 final size:41 Alignment explanation

Indices: 18529951--18530245 Score: 324 Period size: 41 Copynumber: 7.2 Consensus size: 41 18529941 CTTTTACAAA * * * * 18529951 GCCGCTAAAGATCTGAGTACTAGCGGCGCTTTTCTATAAAC 1 GCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAAC * * * * ** 18529992 GCCGCTAAAGATTTGAGTA-T-GCGGTGATTTTGGAAAAAC 1 GCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAAC * * * * * 18530031 GCCGATAAAGATCTGAGCATTAGCAGCGCTTCTACAGAAAC 1 GCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAAC * * 18530072 GCCGCTAAATATCTGAGCATTACCGGCGCTTTTCCAAAAAC 1 GCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAAC * * * 18530113 GCCGCTAAAGACCTGAGCATTAGCGGCGCTTATCAAAAAAC 1 GCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAAC * * 18530154 GCCGCCAAAGATCTGAGCATTAGCGGCGCTTTTACAAAAAC 1 GCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAAC * * *** 18530195 GCCGCTAAAGATCTGGGAATTAGCGGCGCTTTTTTTTAAAAC 1 GCCGCTAAAGATCTGAGCATTAGCGGCGC-TTTTCCAAAAAC 18530237 GCCGCTAAA 1 GCCGCTAAA 18530246 TCCCCGAAAG Statistics Matches: 212, Mismatches: 39, Indels: 5 0.83 0.15 0.02 Matches are distributed among these distances: 39 30 0.14 40 2 0.01 41 162 0.76 42 18 0.08 ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23 Consensus pattern (41 bp): GCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAAC Found at i:18530333 original size:39 final size:39 Alignment explanation

Indices: 18530289--18530416 Score: 134 Period size: 40 Copynumber: 3.2 Consensus size: 39 18530279 TAGGTTTTTT * 18530289 GCCGCTAATGCAC-ATTTTTAGCGGCAATTTT-TTTGAAGC 1 GCCGCTAATGCTCGATTTTTAGCGGC-ATTTTATTT-AAGC * * ** 18530328 GCCGCTAATGCTCGATCTTTAGCGGCGTTTTACATAATGC 1 GCCGCTAATGCTCGATTTTTAGCGGCATTTTATTTAA-GC * * 18530368 GCCGCTAATGCTCGATTTTTAGCGGCATTTTCTGTTCAAAC 1 GCCGCTAATGCTCGATTTTTAGCGGCATTTTAT-TT-AAGC 18530409 GCCGCTAA 1 GCCGCTAA 18530417 AAATACCGCT Statistics Matches: 73, Mismatches: 11, Indels: 8 0.79 0.12 0.09 Matches are distributed among these distances: 39 18 0.25 40 43 0.59 41 10 0.14 42 2 0.03 ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34 Consensus pattern (39 bp): GCCGCTAATGCTCGATTTTTAGCGGCATTTTATTTAAGC Found at i:18534737 original size:2 final size:2 Alignment explanation

Indices: 18534730--18534763 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 18534720 TTTGTACTAT 18534730 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 18534764 CCATCTATTA Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:18548201 original size:28 final size:28 Alignment explanation

Indices: 18548124--18548201 Score: 104 Period size: 28 Copynumber: 2.8 Consensus size: 28 18548114 TATAATATGT * 18548124 ATAAATTAAAAGGTTAAAATAAGTTTGA 1 ATAAATTAAAATGTTAAAATAAGTTTGA * * 18548152 ATAAATTAACAATATTGAAATAAG-TTGA 1 ATAAATTAA-AATGTTAAAATAAGTTTGA 18548180 GATAAATTAAAATGTTAAAATA 1 -ATAAATTAAAATGTTAAAATA 18548202 TTGGAAAGAG Statistics Matches: 43, Mismatches: 5, Indels: 4 0.83 0.10 0.08 Matches are distributed among these distances: 28 23 0.53 29 20 0.47 ACGTcount: A:0.55, C:0.01, G:0.12, T:0.32 Consensus pattern (28 bp): ATAAATTAAAATGTTAAAATAAGTTTGA Found at i:18548499 original size:23 final size:24 Alignment explanation

Indices: 18548464--18548508 Score: 56 Period size: 23 Copynumber: 1.9 Consensus size: 24 18548454 TGGAAATTTA * 18548464 AATAATGATACATAATAAATTTTG 1 AATAATGAAACATAATAAATTTTG ** 18548488 AATAAT-AAACATGGTAAATTT 1 AATAATGAAACATAATAAATTT 18548509 ATATAATATT Statistics Matches: 18, Mismatches: 3, Indels: 1 0.82 0.14 0.05 Matches are distributed among these distances: 23 12 0.67 24 6 0.33 ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36 Consensus pattern (24 bp): AATAATGAAACATAATAAATTTTG Found at i:18549226 original size:20 final size:19 Alignment explanation

Indices: 18549192--18549247 Score: 58 Period size: 20 Copynumber: 2.8 Consensus size: 19 18549182 TTTTTCATAT * 18549192 AGAAAATAGAAAGAAACAA 1 AGAAAACAGAAAGAAACAA ** 18549211 AGAAAACAGTAAAGAAACGC 1 AGAAAACAG-AAAGAAACAA * 18549231 AGAGAAAGAGAAAGAAA 1 AGA-AAACAGAAAGAAA 18549248 AAGAGAAAGA Statistics Matches: 31, Mismatches: 4, Indels: 3 0.82 0.11 0.08 Matches are distributed among these distances: 19 8 0.26 20 18 0.58 21 5 0.16 ACGTcount: A:0.68, C:0.07, G:0.21, T:0.04 Consensus pattern (19 bp): AGAAAACAGAAAGAAACAA Found at i:18549379 original size:28 final size:28 Alignment explanation

Indices: 18549347--18549401 Score: 76 Period size: 28 Copynumber: 2.0 Consensus size: 28 18549337 AAAAAAACTG * 18549347 ATCTTTTCCT-TTTCCTTTTTTCTTTGCC 1 ATCTTTTCCTATTTCCTGTTTT-TTTGCC * 18549375 ATCTTTTCCTATTTTCTGTTTTTTTGC 1 ATCTTTTCCTATTTCCTGTTTTTTTGC 18549402 TCCCTTTTGT Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 28 15 0.62 29 9 0.38 ACGTcount: A:0.05, C:0.24, G:0.05, T:0.65 Consensus pattern (28 bp): ATCTTTTCCTATTTCCTGTTTTTTTGCC Found at i:18550359 original size:175 final size:175 Alignment explanation

Indices: 18550068--18550819 Score: 1315 Period size: 175 Copynumber: 4.3 Consensus size: 175 18550058 CTATTCCACC * 18550068 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGAGAGATAAGACCTGATGCGATCT 1 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT * * 18550133 ACTCTACTGTAACTTCAGAGAGATAAGATTCTTTATTTTAATCCGTTCCACTATAATCTTAAGGA 66 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGA * * * 18550198 AATAGGATTACTGGCTTCAATTTGCTCTGTTGTAATCTCAGGGAG 131 AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG * * 18550243 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGAGAGATAAGACCTGATACGATCT 1 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT * * * 18550308 ACTCTACTGTAACTTCAGAGACATAAGATCCTTTATTTTAATCTGTTCCACTATAATCTCAGGGA 66 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGA * 18550373 AATATGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG 131 AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG * 18550418 ATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT 1 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT * * * 18550483 ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCGTTCCACTGTAATCTCAAGGA 66 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGA * 18550548 AATAGGATTACTGTCTTCAATCTGCTCCGCTGTAATCTCAGGGAG 131 AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG * 18550593 ATAAGATCTGTGATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT 1 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT * * 18550658 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGGA 66 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGA 18550723 AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG 131 AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG * 18550768 ATAAGATCTGTAATTCTTCGGTCTATTCCACTATAATCTCAGGGAGATAAGA 1 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGA 18550820 TCTGTAATTC Statistics Matches: 548, Mismatches: 29, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 175 548 1.00 ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33 Consensus pattern (175 bp): ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGA AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG Found at i:18550454 original size:46 final size:46 Alignment explanation

Indices: 18550228--18550957 Score: 533 Period size: 46 Copynumber: 16.5 Consensus size: 46 18550218 TTTGCTCTGT * 18550228 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC 1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC * * * * * * 18550274 TGTAATCTCAGAGAGATAAGACCTG--ATAC--GA-TCTACTCTAC 1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC * * * * * 18550315 TGTAA-CTTCAGAGACATAAGATCCT-TTATT-TT-AATCTGTTCCAC 1 TGTAATC-TCAGGGAGATAAGAT-CTGTAATTCTTCAGTCTATTCCAC * * * * * * ** * 18550359 TATAATCTCAGGGAAATATGA--T-TACTGGCTTCAATCTGCTCCGC 1 TGTAATCTCAGGGAGATAAGATCTGTAAT-TCTTCAGTCTATTCCAC 18550403 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC 1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC * * * * * 18550449 TGTAATCTCAGGGAGATAAGACCTG--ATGC--GA-TCTACTCTAC 1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC * * * * * 18550490 TGTAA-CTTCAGAGAGATAAGATCAT-TTATT-TTAATTC-GTTCCAC 1 TGTAATC-TCAGGGAGATAAGATC-TGTAATTCTTCAGTCTATTCCAC * * * * * ** * 18550534 TGTAATCTCAAGGAAATAGGA--T-TACTGTCTTCAATCTGCTCCGC 1 TGTAATCTCAGGGAGATAAGATCTGTAAT-TCTTCAGTCTATTCCAC * * 18550578 TGTAATCTCAGGGAGATAAGATCTGTGATTCTTCGGTCTATTCCAC 1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC * * * * * 18550624 TGTAATCTCAGGGAGATAAGACCTG--ATGC--GA-TCTACTCTAC 1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC * * * ** 18550665 TGTAA-CTTCAGAGAGATAAGATCCT-TTATT-TT-AATCCGTTCCAC 1 TGTAATC-TCAGGGAGATAAGAT-CTGTAATTCTTCAGTCTATTCCAC * * * * * ** * 18550709 TGTAATCTCAGGGAAATAGGA--T-TACTGGCTTCAATCTGCTCCGC 1 TGTAATCTCAGGGAGATAAGATCTGTAAT-TCTTCAGTCTATTCCAC * 18550753 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC 1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC * * 18550799 TATAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC 1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC * * 18550845 TGTAATCTCAGGGAGATAAGATCTATAATTCTTCGGTCTATTCCAC 1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC * * 18550891 TGTAATCTCAGGGAGATAAGATCTATAATTCTTCGGTCTATTCCAC 1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC 18550937 TGTAATCTCAGGGAGATAAGA 1 TGTAATCTCAGGGAGATAAGA 18550958 CCTGATGCGA Statistics Matches: 545, Mismatches: 97, Indels: 84 0.75 0.13 0.12 Matches are distributed among these distances: 40 3 0.01 41 88 0.16 42 7 0.01 43 17 0.03 44 152 0.28 45 5 0.01 46 265 0.49 47 8 0.01 ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33 Consensus pattern (46 bp): TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC Found at i:18550629 original size:221 final size:225 Alignment explanation

Indices: 18550402--18550913 Score: 546 Period size: 221 Copynumber: 2.3 Consensus size: 225 18550392 ATCTGCTCCG 18550402 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATA 1 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATA * * * * * * * * 18550467 AGA-CC-TGA-TGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCATTTATTTTAAT-TC 66 AGATCCTTGATTGCAATCCACTCCACTGTAATC-TCAGAGAAATAAGATCACTGACTTCAATCT- * * * * * * 18550527 GTTCCACTGTAATCTCAAGGAAATAGGA-T-TACTGTCTTCAATCTGCTCCGCTGTAATCTCAGG 129 GCTCCACTGTAATCTCAAGGAAATAAGACTGTAAT-TCTTCAATCTACTCCACTATAATCTCAGG * 18550590 GAGATAAGATCTGTGATTCTTCGGTCTATTCCA 193 GAGATAAGATCTGTAATTCTTCGGTCTATTCCA * * * * * * 18550623 CTGTAATCTCAGGGAGATAAGACCTG--ATGC--GA-TCTACTCTACTGTAA-CTTCAGAGAGAT 1 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATC-TCAGGGAGAT * ** ** * * * * 18550682 AAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTG 65 AAGATCCTTGATTGCAATCCACTCCACTGTAATCTCAGAGAAATAAGATCACTGACTTCAATCTG * * * ** * 18550747 CTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCACTATAATCTCAGGG 130 CTCCACTGTAATCTCAAGGAAATAAGA-CTGTAATTCTTCAATCTACTCCACTATAATCTCAGGG 18550812 AGATAAGATCTGTAATTCTTCGGTCTATTCCA 194 AGATAAGATCTGTAATTCTTCGGTCTATTCCA * * 18550844 CTGTAATCTCAGGGAGATAAGATCTATAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATA 1 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATA 18550909 AGATC 66 AGATC 18550914 TATAATTCTT Statistics Matches: 232, Mismatches: 44, Indels: 25 0.77 0.15 0.08 Matches are distributed among these distances: 215 1 0.00 216 26 0.11 217 3 0.01 218 2 0.01 219 58 0.25 220 2 0.01 221 105 0.45 222 3 0.01 223 3 0.01 226 28 0.12 227 1 0.00 ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33 Consensus pattern (225 bp): CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATA AGATCCTTGATTGCAATCCACTCCACTGTAATCTCAGAGAAATAAGATCACTGACTTCAATCTGC TCCACTGTAATCTCAAGGAAATAAGACTGTAATTCTTCAATCTACTCCACTATAATCTCAGGGAG ATAAGATCTGTAATTCTTCGGTCTATTCCA Found at i:18561515 original size:25 final size:25 Alignment explanation

Indices: 18561468--18561515 Score: 60 Period size: 25 Copynumber: 1.9 Consensus size: 25 18561458 TTTGTATTAA * ** 18561468 AAAAACAAAAATTTTAGTTGTCGAC 1 AAAAACAAAAAATTTAGGAGTCGAC * 18561493 AAAAACAAAAAATTTGGGAGTCG 1 AAAAACAAAAAATTTAGGAGTCG 18561516 CCACTGATCT Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 25 19 1.00 ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23 Consensus pattern (25 bp): AAAAACAAAAAATTTAGGAGTCGAC Found at i:18562572 original size:28 final size:28 Alignment explanation

Indices: 18562496--18562573 Score: 104 Period size: 28 Copynumber: 2.8 Consensus size: 28 18562486 TATAATATGT * 18562496 ATAAATTAAAAGGTTAAAATAAGTTTGA 1 ATAAATTAAAATGTTAAAATAAGTTTGA * * 18562524 ATAAATTAACAATATTGAAATAAG-TTGAA 1 ATAAATTAA-AATGTTAAAATAAGTTTG-A 18562553 ATAAATTAAAATGTTAAAATA 1 ATAAATTAAAATGTTAAAATA 18562574 TTGGAAAGAG Statistics Matches: 43, Mismatches: 5, Indels: 4 0.83 0.10 0.08 Matches are distributed among these distances: 28 22 0.51 29 21 0.49 ACGTcount: A:0.56, C:0.01, G:0.10, T:0.32 Consensus pattern (28 bp): ATAAATTAAAATGTTAAAATAAGTTTGA Found at i:18562871 original size:23 final size:24 Alignment explanation

Indices: 18562836--18562880 Score: 56 Period size: 23 Copynumber: 1.9 Consensus size: 24 18562826 TGGAAATTTA * 18562836 AATAATGATACATAATAAATTTTG 1 AATAATGAAACATAATAAATTTTG ** 18562860 AATAAT-AAACATGGTAAATTT 1 AATAATGAAACATAATAAATTT 18562881 ATATAATATT Statistics Matches: 18, Mismatches: 3, Indels: 1 0.82 0.14 0.05 Matches are distributed among these distances: 23 12 0.67 24 6 0.33 ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36 Consensus pattern (24 bp): AATAATGAAACATAATAAATTTTG Found at i:18563593 original size:20 final size:19 Alignment explanation

Indices: 18563559--18563626 Score: 59 Period size: 20 Copynumber: 3.6 Consensus size: 19 18563549 TTTTTCGTAT * 18563559 AGAAAATAGAAAGAAACAA 1 AGAAAACAGAAAGAAACAA ** 18563578 AGAAAACAGTAAAGAAACGC 1 AGAAAACAG-AAAGAAACAA * 18563598 AGAGAAAGAGAAAG-AA-AA 1 AGA-AAACAGAAAGAAACAA * 18563616 AGAAAAGAGAA 1 AGAAAACAGAA 18563627 CCACCTTAAA Statistics Matches: 41, Mismatches: 6, Indels: 6 0.77 0.11 0.11 Matches are distributed among these distances: 17 8 0.20 18 3 0.07 19 10 0.24 20 15 0.37 21 5 0.12 ACGTcount: A:0.69, C:0.06, G:0.22, T:0.03 Consensus pattern (19 bp): AGAAAACAGAAAGAAACAA Found at i:18564167 original size:16 final size:17 Alignment explanation

Indices: 18564148--18564188 Score: 50 Period size: 16 Copynumber: 2.5 Consensus size: 17 18564138 ATTTTGTTTT 18564148 TTTTATTT-TTTATATA 1 TTTTATTTGTTTATATA * 18564164 TTTT-TTTGTTTATTTA 1 TTTTATTTGTTTATATA * 18564180 TTTGATTTG 1 TTTTATTTG 18564189 GGCTGAGCAA Statistics Matches: 21, Mismatches: 2, Indels: 3 0.81 0.08 0.12 Matches are distributed among these distances: 15 3 0.14 16 14 0.67 17 4 0.19 ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76 Consensus pattern (17 bp): TTTTATTTGTTTATATA Found at i:18573657 original size:20 final size:21 Alignment explanation

Indices: 18573632--18573671 Score: 55 Period size: 20 Copynumber: 2.0 Consensus size: 21 18573622 TCTAACTAGT 18573632 TTTGAACATTTTTA-TATATA 1 TTTGAACATTTTTACTATATA ** 18573652 TTTGAATTTTTTTACTATAT 1 TTTGAACATTTTTACTATAT 18573672 TTTTATTTGG Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 20 12 0.71 21 5 0.29 ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60 Consensus pattern (21 bp): TTTGAACATTTTTACTATATA Found at i:18579407 original size:17 final size:17 Alignment explanation

Indices: 18579387--18579424 Score: 67 Period size: 17 Copynumber: 2.2 Consensus size: 17 18579377 GGTTGTCTAT * 18579387 TTTTCTTTATTTATTTA 1 TTTTCATTATTTATTTA 18579404 TTTTCATTATTTATTTA 1 TTTTCATTATTTATTTA 18579421 TTTT 1 TTTT 18579425 TATTTCCTTA Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 17 20 1.00 ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76 Consensus pattern (17 bp): TTTTCATTATTTATTTA Found at i:18580511 original size:18 final size:18 Alignment explanation

Indices: 18580483--18580524 Score: 57 Period size: 18 Copynumber: 2.3 Consensus size: 18 18580473 CAAATATACA * 18580483 AATACTAAATAAAATTAAT 1 AATA-TAAATAAAAATAAT * 18580502 TATATAAATAAAAATAAT 1 AATATAAATAAAAATAAT 18580520 AATAT 1 AATAT 18580525 GTGGGAGATT Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 18 17 0.85 19 3 0.15 ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33 Consensus pattern (18 bp): AATATAAATAAAAATAAT Found at i:18586556 original size:23 final size:24 Alignment explanation

Indices: 18586529--18586576 Score: 62 Period size: 23 Copynumber: 2.0 Consensus size: 24 18586519 CATTATCAAG * * 18586529 TCATTCCAAACTTGC-CATAAGAT 1 TCATTCAAAACATGCACATAAGAT 18586552 TCATTCAAAACATGCATCATAAGAT 1 TCATTCAAAACATGCA-CATAAGAT 18586577 AACCAAAATG Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 23 13 0.62 25 8 0.38 ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29 Consensus pattern (24 bp): TCATTCAAAACATGCACATAAGAT Found at i:18587244 original size:42 final size:42 Alignment explanation

Indices: 18587185--18587282 Score: 169 Period size: 42 Copynumber: 2.3 Consensus size: 42 18587175 TTTACCTCAT * 18587185 TGCTCACACGAGCTATGGGTCAAAATGTAAGCTATACGATAC 1 TGCTCACACGAGCTATGGGTCAAAATGTAAGCTACACGATAC * * 18587227 TGCTCTCACGAGCTATGGGTCAAAATGTAAGCTACATGATAC 1 TGCTCACACGAGCTATGGGTCAAAATGTAAGCTACACGATAC 18587269 TGCTCACACGAGCT 1 TGCTCACACGAGCT 18587283 GTGGAGTATC Statistics Matches: 52, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 42 52 1.00 ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24 Consensus pattern (42 bp): TGCTCACACGAGCTATGGGTCAAAATGTAAGCTACACGATAC Found at i:18595023 original size:22 final size:22 Alignment explanation

Indices: 18594974--18595026 Score: 63 Period size: 22 Copynumber: 2.5 Consensus size: 22 18594964 TATAAGTCCA ** 18594974 AAAAAT-AAAATAAAAACAGCT 1 AAAAATAAAAATAAAAACAAAT * * 18594995 AACAATAAAAATAAAAATAAAT 1 AAAAATAAAAATAAAAACAAAT 18595017 AAAAATAAAA 1 AAAAATAAAA 18595027 CTAATACTGT Statistics Matches: 26, Mismatches: 5, Indels: 1 0.81 0.16 0.03 Matches are distributed among these distances: 21 5 0.19 22 21 0.81 ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15 Consensus pattern (22 bp): AAAAATAAAAATAAAAACAAAT Found at i:18595597 original size:14 final size:14 Alignment explanation

Indices: 18595578--18595604 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 18595568 GACTGTTATT 18595578 TTTTAATTTTTTAA 1 TTTTAATTTTTTAA 18595592 TTTTAATTTTTTA 1 TTTTAATTTTTTA 18595605 TTAATACAAA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74 Consensus pattern (14 bp): TTTTAATTTTTTAA Found at i:18598738 original size:19 final size:19 Alignment explanation

Indices: 18598714--18598805 Score: 148 Period size: 19 Copynumber: 4.8 Consensus size: 19 18598704 AGTCTTCAAG 18598714 GATATGCAATCTTAGATAT 1 GATATGCAATCTTAGATAT * 18598733 GATATGTAATCTTAGATAT 1 GATATGCAATCTTAGATAT * * 18598752 GATATGCGACCTTAGATAT 1 GATATGCAATCTTAGATAT * 18598771 GATATGTAATCTTAGATAT 1 GATATGCAATCTTAGATAT 18598790 GATATGCAATCTTAGA 1 GATATGCAATCTTAGA 18598806 AGATATGATT Statistics Matches: 65, Mismatches: 8, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 65 1.00 ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37 Consensus pattern (19 bp): GATATGCAATCTTAGATAT Found at i:18598757 original size:38 final size:38 Alignment explanation

Indices: 18598714--18598828 Score: 167 Period size: 38 Copynumber: 2.9 Consensus size: 38 18598704 AGTCTTCAAG 18598714 GATATGCAATCTTAGATATGATATGTAATCTTAGATAT 1 GATATGCAATCTTAGATATGATATGTAATCTTAGATAT * * 18598752 GATATGCGACCTTAGATATGATATGTAATCTTAGATAT 1 GATATGCAATCTTAGATATGATATGTAATCTTAGATAT * 18598790 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA 1 GATATGCAATCTT---AGATATGA-TATGTAATCTTAGA 18598829 GATTTAATTT Statistics Matches: 68, Mismatches: 5, Indels: 4 0.88 0.06 0.05 Matches are distributed among these distances: 38 47 0.69 41 8 0.12 42 13 0.19 ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38 Consensus pattern (38 bp): GATATGCAATCTTAGATATGATATGTAATCTTAGATAT Found at i:18599062 original size:23 final size:23 Alignment explanation

Indices: 18599018--18599062 Score: 54 Period size: 23 Copynumber: 2.0 Consensus size: 23 18599008 TCTTATTTTG * * 18599018 TTGATTTGTGTATCATTTATTTA 1 TTGATTTGTATATCATTGATTTA ** 18599041 TTGATTTGTATATTGTTGATTT 1 TTGATTTGTATATCATTGATTT 18599063 CAAATCTCTT Statistics Matches: 18, Mismatches: 4, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 23 18 1.00 ACGTcount: A:0.20, C:0.02, G:0.16, T:0.62 Consensus pattern (23 bp): TTGATTTGTATATCATTGATTTA Found at i:18605718 original size:175 final size:176 Alignment explanation

Indices: 18605417--18605810 Score: 594 Period size: 175 Copynumber: 2.2 Consensus size: 176 18605407 ATCAGTGAAG * * * * * 18605417 ATAGTAGATCTTGCCTTCCTGCGCCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG 1 ATAGCAGATATTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG * 18605482 GGTTGCAGCGGAGCAGGTTAAAAATTACAGATCTTGCCTTTCTGCACCGACAGCAAAGCAGATCG 66 GGTTGCAGCGGAGCAGGTTAAAAATTACAGATCTTGCCTTCCTGCACCGACAGCAAAGCAGATCG ** * * 18605547 AAGACACCAGCCTTACCTCCCT-GGTTGTAGCGGAGCAGGTTAAAA 131 AAGACACCAGCCTTACCTCCCTGGGTTACAGCGAAGCAGATTAAAA * * 18605592 ATAGCATATATTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAACCTTGCCTCCCTG 1 ATAGCAGATATTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG * * * 18605657 GGTTGTAGCGGAGCAGGTTAAAAA-TAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATC 66 GGTTGCAGCGGAGCAGGTTAAAAATTA-CAGATCTTGCCTTCCTGCACCGACAGCAAAGCAGATC * * 18605721 GAAGACACTAGCCTTGCCTCCCTGGGTTACAGCGAAGCAGATTAAAA 130 GAAGACACCAGCCTTACCTCCCTGGGTTACAGCGAAGCAGATTAAAA * * 18605768 ATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGA 1 ATAGCAGATATTGCCTTCCTGCACCGACAGCGAAGCAGATCGA 18605811 TGACCCCAGC Statistics Matches: 196, Mismatches: 21, Indels: 3 0.89 0.10 0.01 Matches are distributed among these distances: 174 2 0.01 175 136 0.69 176 58 0.30 ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21 Consensus pattern (176 bp): ATAGCAGATATTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG GGTTGCAGCGGAGCAGGTTAAAAATTACAGATCTTGCCTTCCTGCACCGACAGCAAAGCAGATCG AAGACACCAGCCTTACCTCCCTGGGTTACAGCGAAGCAGATTAAAA Found at i:18605737 original size:44 final size:44 Alignment explanation

Indices: 18605677--18605810 Score: 110 Period size: 44 Copynumber: 3.0 Consensus size: 44 18605667 GAGCAGGTTA * * * 18605677 AAAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCG 1 AAAACAGCAGACCTTGCCTTCCTG-ACCAACAGCGAAGCAGATCG * * **** ** 18605722 AAGACA-CTAG-CCTTGCCTCCCTGGGTTACAGCGAAGCAGATTA 1 AAAACAGC-AGACCTTGCCTTCCTGACCAACAGCGAAGCAGATCG * * 18605765 AAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCG 1 AAAACAGCAGACCTTGCCTTCCTG-ACCAACAGCGAAGCAGATCG 18605810 A 1 A 18605811 TGACCCCAGC Statistics Matches: 65, Mismatches: 20, Indels: 8 0.70 0.22 0.09 Matches are distributed among these distances: 43 20 0.31 44 24 0.37 45 21 0.32 ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19 Consensus pattern (44 bp): AAAACAGCAGACCTTGCCTTCCTGACCAACAGCGAAGCAGATCG Found at i:18605805 original size:45 final size:44 Alignment explanation

Indices: 18605663--18605807 Score: 132 Period size: 45 Copynumber: 3.3 Consensus size: 44 18605653 CCTGGGTTGT * * * 18605663 AGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACCGAC 1 AGCGAAGCAGATTAAAAATAGCAGATCTTGCCTTCCTG-ACCAAC ** * * * * **** 18605708 AGCGAAGCAGATCGAAGACA-CTAG-CCTTGCCTCCCTGGGTTAC 1 AGCGAAGCAGATTAAAAATAGC-AGATCTTGCCTTCCTGACCAAC 18605751 AGCGAAGCAGATTAAAAATAGCAGATCTTGCCTTCCTGCACCAAC 1 AGCGAAGCAGATTAAAAATAGCAGATCTTGCCTTCCTG-ACCAAC 18605796 AGCGAAGCAGAT 1 AGCGAAGCAGAT 18605808 CGATGACCCC Statistics Matches: 74, Mismatches: 22, Indels: 8 0.71 0.21 0.08 Matches are distributed among these distances: 43 20 0.27 44 24 0.32 45 30 0.41 ACGTcount: A:0.31, C:0.26, G:0.23, T:0.19 Consensus pattern (44 bp): AGCGAAGCAGATTAAAAATAGCAGATCTTGCCTTCCTGACCAAC Found at i:18605833 original size:88 final size:88 Alignment explanation

Indices: 18605417--18605821 Score: 607 Period size: 88 Copynumber: 4.6 Consensus size: 88 18605407 ATCAGTGAAG * * * 18605417 ATAGTAGATCTTGCCTTCCTGCGCCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG 1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG 18605482 GGTTGCAGCGGAGCAGGTTAAAA 66 GGTTGCAGCGGAGCAGGTTAAAA * * * 18605505 ATTA-CAGATCTTGCCTTTCTGCACCGACAGCAAAGCAGATCGAAGACACCAGCCTTACCTCCCT 1 A-TAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT * 18605569 -GGTTGTAGCGGAGCAGGTTAAAA 65 GGGTTGCAGCGGAGCAGGTTAAAA * * * * 18605592 ATAGCATATATTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAACCTTGCCTCCCTG 1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG * 18605657 GGTTGTAGCGGAGCAGGTTAAAA 66 GGTTGCAGCGGAGCAGGTTAAAA * * 18605680 ATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTG 1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG * * * 18605745 GGTTACAGCGAAGCAGATTAAAA 66 GGTTGCAGCGGAGCAGGTTAAAA * * * 18605768 ATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGATGACCCCAGCC 1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC 18605822 CTATCTCCCT Statistics Matches: 285, Mismatches: 29, Indels: 6 0.89 0.09 0.02 Matches are distributed among these distances: 86 2 0.01 87 76 0.27 88 205 0.72 89 2 0.01 ACGTcount: A:0.28, C:0.28, G:0.23, T:0.20 Consensus pattern (88 bp): ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG GGTTGCAGCGGAGCAGGTTAAAA Found at i:18605873 original size:44 final size:44 Alignment explanation

Indices: 18605821--18605939 Score: 152 Period size: 44 Copynumber: 2.7 Consensus size: 44 18605811 TGACCCCAGC * 18605821 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGT-AAGT 1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAAATTGTGAA-T * * * 18605865 CTTATCTCCCTGGTCAGCAGTGGAATAAGTTGAAAATTGTGAAT 1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAAATTGTGAAT * * 18605909 CCTATCTCCCT-GAGCAACAGTGGAGTAGGTT 1 CCTATCTCCCTGGA-CAGCAGTGGAATAGGTT 18605940 ATAAATAGCA Statistics Matches: 64, Mismatches: 9, Indels: 4 0.83 0.12 0.05 Matches are distributed among these distances: 43 1 0.02 44 61 0.95 45 2 0.03 ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29 Consensus pattern (44 bp): CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAAATTGTGAAT Found at i:18606485 original size:44 final size:43 Alignment explanation

Indices: 18606434--18606777 Score: 204 Period size: 45 Copynumber: 7.9 Consensus size: 43 18606424 GATCGCATCT 18606434 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA 1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA * * * * 18606478 AGTCTTATC-CTCCTGAAGTTGTAGT-AAGGCAGAGTGAAGATGGCGA 1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGC-A * 18606524 A-TCTTATCTCCCT-ACAGTTGCAGTGGAGCAGA-TTA-AAGCCAA 1 AGTCTTATCTCCCTGA-AGTTGCAGTGGAGCAGACTAAGAAG-C-A * * ** * * 18606566 TAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAA-AATCA 1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA * * * * * * * * 18606609 CAGATCTTATTTCTCTGAAGTTGCAG-AGAACAGA-T-CGCATCG 1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA * * * * * * * 18606651 GGTCTTATCTCCCTAAAGATACAGTGGAGTAGACCCAAGAAAGCG 1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAG-AAGCA * 18606696 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCA 1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-AAGCA * * * 18606741 AGTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTAA 1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA 18606778 NNNNNNNNNN Statistics Matches: 229, Mismatches: 50, Indels: 42 0.71 0.16 0.13 Matches are distributed among these distances: 40 17 0.07 41 7 0.03 42 7 0.03 43 10 0.04 44 81 0.35 45 103 0.45 46 4 0.02 ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26 Consensus pattern (43 bp): AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA Found at i:18606678 original size:217 final size:218 Alignment explanation

Indices: 18606295--18606716 Score: 625 Period size: 217 Copynumber: 1.9 Consensus size: 218 18606285 TTTAAAAGAC * ** 18606295 TGAAGATGGCGAATCTTATCTCCCTGAAGTTGTAGTGAATTAGATTAAAGCCAATAATCCTATCT 1 TGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCAATAATCCTATCT ** 18606360 CCCTAAAGTCGCAATGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGTAG 66 CCCTAAAGTCGCAATGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAACAG * * * * * * 18606425 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGTAAGCAAGTCTTATC-C 131 ATCGCATCGAGTCTTATCTCCCTAAAGATACAGTGGAGCAGACCCAAGAAAGCAAGTCTTATCTC 18606488 TCCTGAAGTTGTAGTAAGGCAGAG 196 -CCTGAAGTTGTAGTAAGGCAGAG * 18606512 TGAAGATGGCGAATCTTATCTCCCT-ACAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATC 1 TGAAGATGGCGAATCTTATCTCCCTGA-AGTTGCAGTGAAGCAGATTAAAGCCAATAATCCTATC * * * * * 18606576 TCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATTTCTCTGAAGTTGCAGAGAACA 65 TCCCTAAAGTCGCAATGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAACA * * * 18606641 GATCGCATCGGGTCTTATCTCCCTAAAGATACAGTGGAGTAGACCCAAGAAAGCGAGTCTTATCT 130 GATCGCATCGAGTCTTATCTCCCTAAAGATACAGTGGAGCAGACCCAAGAAAGCAAGTCTTATCT 18606706 CCCTGAAGTTG 195 CCCTGAAGTTG 18606717 CAGTGGAGCA Statistics Matches: 182, Mismatches: 20, Indels: 5 0.88 0.10 0.02 Matches are distributed among these distances: 216 1 0.01 217 153 0.84 218 27 0.15 219 1 0.01 ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28 Consensus pattern (218 bp): TGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCAATAATCCTATCT CCCTAAAGTCGCAATGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAACAG ATCGCATCGAGTCTTATCTCCCTAAAGATACAGTGGAGCAGACCCAAGAAAGCAAGTCTTATCTC CCTGAAGTTGTAGTAAGGCAGAG Found at i:18607354 original size:22 final size:23 Alignment explanation

Indices: 18607326--18607370 Score: 74 Period size: 23 Copynumber: 2.0 Consensus size: 23 18607316 ATGCAATCTT 18607326 AGATATGA-TATGTAATCTTAGA 1 AGATATGATTATGTAATCTTAGA * 18607348 AGATATGATTTTGTAATCTTAGA 1 AGATATGATTATGTAATCTTAGA 18607371 GATTTAATTT Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 22 8 0.38 23 13 0.62 ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40 Consensus pattern (23 bp): AGATATGATTATGTAATCTTAGA Found at i:18607380 original size:22 final size:23 Alignment explanation

Indices: 18607336--18607380 Score: 65 Period size: 23 Copynumber: 2.0 Consensus size: 23 18607326 AGATATGATA * 18607336 TGTAATCTTAGAAGATATGATTT 1 TGTAATCTTAGAAGATATAATTT * 18607359 TGTAATCTTAG-AGATTTAATTT 1 TGTAATCTTAGAAGATATAATTT 18607381 GTAGATACCT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 22 9 0.45 23 11 0.55 ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47 Consensus pattern (23 bp): TGTAATCTTAGAAGATATAATTT Found at i:18612657 original size:22 final size:22 Alignment explanation

Indices: 18612627--18612669 Score: 59 Period size: 22 Copynumber: 2.0 Consensus size: 22 18612617 ACACCAAAAC * 18612627 AGGCTTTTAAAGGCGCTTTTTT 1 AGGCCTTTAAAGGCGCTTTTTT ** 18612649 AGGCCTTTAGCGGCGCTTTTT 1 AGGCCTTTAAAGGCGCTTTTT 18612670 AGCACCGCAA Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42 Consensus pattern (22 bp): AGGCCTTTAAAGGCGCTTTTTT Found at i:18612887 original size:43 final size:43 Alignment explanation

Indices: 18612835--18612938 Score: 140 Period size: 43 Copynumber: 2.4 Consensus size: 43 18612825 TGAGATAGNT 18612835 GTCTTTAGCGGCGTTTTTGT-TGA-AAGCGCCGCTATAGATCAGG 1 GTCTTTAGCGGCGTTTTT-TAT-ATAAGCGCCGCTATAGATCAGG * * 18612878 GTCTGTAGCGGTGTTTTTTATATAAGCGCCGCTATAGATCAGG 1 GTCTTTAGCGGCGTTTTTTATATAAGCGCCGCTATAGATCAGG * * 18612921 GCCTTTAGCGGCGCTTTT 1 GTCTTTAGCGGCGTTTTT 18612939 CCCAAAAACG Statistics Matches: 53, Mismatches: 6, Indels: 4 0.84 0.10 0.06 Matches are distributed among these distances: 42 2 0.04 43 51 0.96 ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35 Consensus pattern (43 bp): GTCTTTAGCGGCGTTTTTTATATAAGCGCCGCTATAGATCAGG Found at i:18612951 original size:43 final size:43 Alignment explanation

Indices: 18612861--18612958 Score: 106 Period size: 43 Copynumber: 2.3 Consensus size: 43 18612851 TTGTTGAAAG * * * * * * * 18612861 CGCCGCTATAGATCAGGGTCTGTAGCGGTGTTTTTTATATAAG 1 CGCCGCTATAGATCAGGGCCTGTAGCGGCGCTTTTCACAAAAA * * 18612904 CGCCGCTATAGATCAGGGCCTTTAGCGGCGCTTTTCCCAAAAA 1 CGCCGCTATAGATCAGGGCCTGTAGCGGCGCTTTTCACAAAAA * 18612947 CGCCGCAATAGA 1 CGCCGCTATAGA 18612959 CCCTAATCTA Statistics Matches: 45, Mismatches: 10, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 43 45 1.00 ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27 Consensus pattern (43 bp): CGCCGCTATAGATCAGGGCCTGTAGCGGCGCTTTTCACAAAAA Found at i:18612973 original size:43 final size:42 Alignment explanation

Indices: 18612926--18613169 Score: 193 Period size: 43 Copynumber: 5.6 Consensus size: 42 18612916 TCAGGGCCTT 18612926 TAGCGGCGCTTTTCCCAAAAACGCCGCAATAGACCCTAATCTA 1 TAGCGGCGCTTTTCCCAAAAACGCCGCAA-AGACCCTAATCTA ** * * * * 18612969 TAGCGGCATTTTTCCCACAAACGCTGCAATAGACCCTGATCTC 1 TAGCGGCGCTTTTCCCAAAAACGCCGCAA-AGACCCTAATCTA * * ** * * ** 18613012 TAGCGGCGCTTCTGCCGCAAGCGCCACTAAAGACCCGGATCTA 1 TAGCGGCGCTTTTCCCAAAAACGCCGC-AAAGACCCTAATCTA * * ** 18613055 TAGCGGCGCTTAT-CCAGAAAACGCCGCTAAATACCCTTGTCTATA 1 TAGCGGCGCTTTTCCCA-AAAACGCCGC-AAAGACCCTAATC--TA * ** * * 18613100 TAGTGGCGCTTCGCGCAAAAACGCCGTTAAAGACCCTAATCTA 1 TAGCGGCGCTTTTCCCAAAAACGCCG-CAAAGACCCTAATCTA * 18613143 TAGCGGCGCTTTTACCAAAAACGCCGC 1 TAGCGGCGCTTTTCCCAAAAACGCCGC 18613170 TAAATTTGGT Statistics Matches: 156, Mismatches: 39, Indels: 13 0.75 0.19 0.06 Matches are distributed among these distances: 42 2 0.01 43 119 0.76 44 2 0.01 45 31 0.20 46 2 0.01 ACGTcount: A:0.27, C:0.32, G:0.20, T:0.21 Consensus pattern (42 bp): TAGCGGCGCTTTTCCCAAAAACGCCGCAAAGACCCTAATCTA Found at i:18613538 original size:22 final size:21 Alignment explanation

Indices: 18613480--18613597 Score: 166 Period size: 21 Copynumber: 5.6 Consensus size: 21 18613470 TTTGACGCTG * 18613480 CTCTGCTTCCCTCGCTGCT-GC 1 CTCTGCTTCCCTCGCT-TTAGC * 18613501 CTCTACTTCCCTCGCTTTAGC 1 CTCTGCTTCCCTCGCTTTAGC * * 18613522 CTCTGGTTTCCTCCGCTTTAGC 1 CTCTGCTTCCCT-CGCTTTAGC 18613544 CTCTGCTTCCCTCGCTTTAGC 1 CTCTGCTTCCCTCGCTTTAGC * 18613565 CTTTGCTTCCCTCGCTTTAGC 1 CTCTGCTTCCCTCGCTTTAGC 18613586 CTCTGCTTCCCT 1 CTCTGCTTCCCT 18613598 TGCTGCAGCT Statistics Matches: 86, Mismatches: 9, Indels: 4 0.87 0.09 0.04 Matches are distributed among these distances: 20 1 0.01 21 66 0.77 22 19 0.22 ACGTcount: A:0.04, C:0.42, G:0.14, T:0.39 Consensus pattern (21 bp): CTCTGCTTCCCTCGCTTTAGC Found at i:18613547 original size:43 final size:42 Alignment explanation

Indices: 18613480--18613597 Score: 166 Period size: 43 Copynumber: 2.8 Consensus size: 42 18613470 TTTGACGCTG * * 18613480 CTCTGCTTCCCTCGCTGCT-GCCTCTACTTCCCTCGCTTTAGC 1 CTCTGCTTCCCTCGCT-TTAGCCTCTGCTTCCCTCGCTTTAGC * * 18613522 CTCTGGTTTCCTCCGCTTTAGCCTCTGCTTCCCTCGCTTTAGC 1 CTCTGCTTCCCT-CGCTTTAGCCTCTGCTTCCCTCGCTTTAGC * 18613565 CTTTGCTTCCCTCGCTTTAGCCTCTGCTTCCCT 1 CTCTGCTTCCCTCGCTTTAGCCTCTGCTTCCCT 18613598 TGCTGCAGCT Statistics Matches: 67, Mismatches: 7, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 42 32 0.48 43 35 0.52 ACGTcount: A:0.04, C:0.42, G:0.14, T:0.39 Consensus pattern (42 bp): CTCTGCTTCCCTCGCTTTAGCCTCTGCTTCCCTCGCTTTAGC Found at i:18613639 original size:21 final size:21 Alignment explanation

Indices: 18613480--18613636 Score: 154 Period size: 21 Copynumber: 7.4 Consensus size: 21 18613470 TTTGACGCTG 18613480 CTCTGCTTCCCTCGCTGCT-GC 1 CTCTGCTTCCCTCGCTG-TAGC * * 18613501 CTCTACTTCCCTCGCTTTAGC 1 CTCTGCTTCCCTCGCTGTAGC * * * 18613522 CTCTGGTTTCCTCCGCTTTAGC 1 CTCTGCTTCCCT-CGCTGTAGC * 18613544 CTCTGCTTCCCTCGCTTTAGC 1 CTCTGCTTCCCTCGCTGTAGC * * 18613565 CTTTGCTTCCCTCGCTTTAGC 1 CTCTGCTTCCCTCGCTGTAGC * * 18613586 CTCTGCTTCCCTTGCTGCAGC 1 CTCTGCTTCCCTCGCTGTAGC * * * * * 18613607 TTGTTCTTCTCTCGCTGTCGC 1 CTCTGCTTCCCTCGCTGTAGC 18613628 CTCTGCTTC 1 CTCTGCTTC 18613637 TCTTGCTGCC Statistics Matches: 112, Mismatches: 22, Indels: 4 0.81 0.16 0.03 Matches are distributed among these distances: 20 1 0.01 21 92 0.82 22 19 0.17 ACGTcount: A:0.04, C:0.41, G:0.16, T:0.39 Consensus pattern (21 bp): CTCTGCTTCCCTCGCTGTAGC Found at i:18613644 original size:21 final size:21 Alignment explanation

Indices: 18613480--18613655 Score: 122 Period size: 21 Copynumber: 8.3 Consensus size: 21 18613470 TTTGACGCTG 18613480 CTCTGCTTCCCTCGCTG-CTGC 1 CTCTGCTTCCCTCGCTGTC-GC * * * 18613501 CTCTACTTCCCTCGCTTTAGC 1 CTCTGCTTCCCTCGCTGTCGC * * * * 18613522 CTCTGGTTTCCTCCGCTTTAGC 1 CTCTGCTTCCCT-CGCTGTCGC * * 18613544 CTCTGCTTCCCTCGCTTTAGC 1 CTCTGCTTCCCTCGCTGTCGC * * * 18613565 CTTTGCTTCCCTCGCTTTAGC 1 CTCTGCTTCCCTCGCTGTCGC * 18613586 CTCTGCTTCCCTTGCTG-CAGC 1 CTCTGCTTCCCTCGCTGTC-GC * * * * 18613607 TTGTTCTTCTCTCGCTGTCGC 1 CTCTGCTTCCCTCGCTGTCGC * * * 18613628 CTCTGCTTCTCTTGCTGCCGC 1 CTCTGCTTCCCTCGCTGTCGC * 18613649 ATCTGCT 1 CTCTGCT 18613656 CTAAGCTGCT Statistics Matches: 127, Mismatches: 24, Indels: 8 0.80 0.15 0.05 Matches are distributed among these distances: 21 107 0.84 22 20 0.16 ACGTcount: A:0.04, C:0.40, G:0.16, T:0.39 Consensus pattern (21 bp): CTCTGCTTCCCTCGCTGTCGC Found at i:18613711 original size:66 final size:66 Alignment explanation

Indices: 18613627--18613772 Score: 197 Period size: 66 Copynumber: 2.2 Consensus size: 66 18613617 CTCGCTGTCG * * 18613627 CCTCTGCTTCTCTTGCTGCCGCATCTGCTCTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT 1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT 18613690 GAA 64 GAA * * * * 18613693 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA 1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA 18613758 A 66 A * 18613759 CATCAGCTTCTCTC 1 CCTCAGCTTCTCTC 18613773 AATGTTGCCT Statistics Matches: 71, Mismatches: 7, Indels: 4 0.87 0.09 0.05 Matches are distributed among these distances: 65 1 0.01 66 66 0.93 67 4 0.06 ACGTcount: A:0.14, C:0.29, G:0.18, T:0.40 Consensus pattern (66 bp): CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA A Found at i:18613789 original size:66 final size:66 Alignment explanation

Indices: 18613666--18613796 Score: 183 Period size: 66 Copynumber: 2.0 Consensus size: 66 18613656 CTAAGCTGCT * ** * 18613666 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGT 1 GCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCAATGCTGCATCCGCTTTAAGTTGT 18613731 A 66 A * * * 18613732 GCTGGAGTTCTTCATATCTTT-TTTGAACATCAGCTTCTCTCAATGTTGCCTCCGCTTTAAGTTG 1 GCTGGAGTTCTTCATA-CTTTCGTTGAACATCAGCTTCTCTCAATGCTGCATCCGCTTTAAGTTG 18613796 T 65 T 18613797 GTAATTTTCT Statistics Matches: 57, Mismatches: 7, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 66 53 0.93 67 4 0.07 ACGTcount: A:0.16, C:0.24, G:0.18, T:0.41 Consensus pattern (66 bp): GCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCAATGCTGCATCCGCTTTAAGTTGT A Found at i:18621098 original size:16 final size:16 Alignment explanation

Indices: 18621073--18621103 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 18621063 AACCCCCTAG * 18621073 CCCCTTACCCCTAAAT 1 CCCCTAACCCCTAAAT 18621089 CCCCTAACCCCTAAA 1 CCCCTAACCCCTAAA 18621104 GCATAACCCT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.29, C:0.52, G:0.00, T:0.19 Consensus pattern (16 bp): CCCCTAACCCCTAAAT Found at i:18622045 original size:42 final size:41 Alignment explanation

Indices: 18621972--18622313 Score: 497 Period size: 41 Copynumber: 8.3 Consensus size: 41 18621962 ACTTAGATAC ** * * * 18621972 AAACGCCGCTGA-AGACAGGAGAATTAGCGGCGCATAGGCGA 1 AAACGCCGCT-ATAGACCCGAGCATTAGCGGCGCTTAGACGA * 18622013 AAACGCCGCTATAGACCCATAGCATTAGCGGCGCTTAGACGA 1 AAACGCCGCTATAGACCC-GAGCATTAGCGGCGCTTAGACGA * * 18622055 AAACGCCGCTAAAGACTCGGAGCATTAGCGGCGCTTAGACGA 1 AAACGCCGCTATAGAC-CCGAGCATTAGCGGCGCTTAGACGA * * * * 18622097 AAGCGCTGCTAAAGACTCGAAGCATTAGCGGCGCTTAGACGA 1 AAACGCCGCTATAGACCCG-AGCATTAGCGGCGCTTAGACGA * 18622139 AAACGCCGCTATAGACCCGAGCGTTAGCGGCGCTTAGACGA 1 AAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACGA * 18622180 AAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACAA 1 AAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACGA * 18622221 AAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACAA 1 AAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACGA * 18622262 AAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACAA 1 AAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACGA 18622303 AAACGCCGCTA 1 AAACGCCGCTA 18622314 AATGTTTAAA Statistics Matches: 277, Mismatches: 20, Indels: 8 0.91 0.07 0.03 Matches are distributed among these distances: 40 1 0.00 41 168 0.61 42 107 0.39 43 1 0.00 ACGTcount: A:0.31, C:0.27, G:0.27, T:0.14 Consensus pattern (41 bp): AAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACGA Found at i:18622408 original size:39 final size:40 Alignment explanation

Indices: 18622365--18622479 Score: 126 Period size: 40 Copynumber: 2.9 Consensus size: 40 18622355 GTTTTTTGTT * * 18622365 GCGCTTTATATAAAACGCCGCTAATTC-CTATTTTTAGCG 1 GCGCTTTGTATAAAACGCCGCTAATGCTCTATTTTTAGCG * * ** 18622404 GCGCTTCCGTAT-AAACGCCGCTGATGCTCTACCTTTAGCG 1 GCGCTT-TGTATAAAACGCCGCTAATGCTCTATTTTTAGCG ** * 18622444 GCGCTTTGGCTAAATCGCCGCTAATGCTCTATTTTT 1 GCGCTTTGTATAAAACGCCGCTAATGCTCTATTTTT 18622480 TGTGGGGCTT Statistics Matches: 60, Mismatches: 13, Indels: 5 0.77 0.17 0.06 Matches are distributed among these distances: 39 21 0.35 40 39 0.65 ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34 Consensus pattern (40 bp): GCGCTTTGTATAAAACGCCGCTAATGCTCTATTTTTAGCG Found at i:18624312 original size:26 final size:28 Alignment explanation

Indices: 18624283--18624334 Score: 72 Period size: 27 Copynumber: 1.9 Consensus size: 28 18624273 TTGTTCAAAC * 18624283 TCTTCTAAA-AAAAACTCA-AGAGAAAT 1 TCTTCAAAAGAAAAACTCAGAGAGAAAT * 18624309 TCTTGAAAAGAAAAACTCAGAGAGAA 1 TCTTCAAAAGAAAAACTCAGAGAGAA 18624335 TTTATTAACT Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 26 7 0.32 27 9 0.41 28 6 0.27 ACGTcount: A:0.54, C:0.13, G:0.13, T:0.19 Consensus pattern (28 bp): TCTTCAAAAGAAAAACTCAGAGAGAAAT Found at i:18632284 original size:26 final size:26 Alignment explanation

Indices: 18632254--18632313 Score: 93 Period size: 26 Copynumber: 2.3 Consensus size: 26 18632244 GTAGCTCCGG 18632254 AGAGCCATTAATCGGGAAGCTCACAA 1 AGAGCCATTAATCGGGAAGCTCACAA * * * 18632280 AGAGCCTTTAATCGGGAAGCTTACGA 1 AGAGCCATTAATCGGGAAGCTCACAA 18632306 AGAGCCAT 1 AGAGCCAT 18632314 ATAACAGGAC Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 26 30 1.00 ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18 Consensus pattern (26 bp): AGAGCCATTAATCGGGAAGCTCACAA Done.