Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: At_chr10

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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31

Warning! 2980117 characters in sequence are not A, C, G, or T


File 177 of 284

Found at i:59622932 original size:43 final size:41

Alignment explanation

Indices: 59622850--59622930 Score: 135 Period size: 41 Copynumber: 2.0 Consensus size: 41 59622840 CTAATTATGG * 59622850 GCACTTAGTGTGCGAGATTGAGATAGCTTTGGTTATATATT 1 GCACTTAGTGTGCGAGATTGAGATAGCTTCGGTTATATATT * * 59622891 GCACTTAGTGTGTGAGATTGAGATAGCTTCGGCTATATAT 1 GCACTTAGTGTGCGAGATTGAGATAGCTTCGGTTATATAT 59622931 ATACATTGGC Statistics Matches: 37, Mismatches: 3, Indels: 0 0.93 0.08 0.00 Matches are distributed among these distances: 41 37 1.00 ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37 Consensus pattern (41 bp): GCACTTAGTGTGCGAGATTGAGATAGCTTCGGTTATATATT Found at i:59625531 original size:43 final size:43 Alignment explanation

Indices: 59625426--59625532 Score: 153 Period size: 43 Copynumber: 2.5 Consensus size: 43 59625416 TAGCCTAGCT * * 59625426 ATGGTCTT-TCACAAAATCAAATAATGATGCCAATGTCCCAAAC 1 ATGGTCTTAT-ACATAATCACATAATGATGCCAATGTCCCAAAC * * 59625469 ATGGTCTTACACGTAATCACATAATGATGCCAATGTCCCAAAC 1 ATGGTCTTATACATAATCACATAATGATGCCAATGTCCCAAAC * 59625512 GTGGTCTTATACATAATCACA 1 ATGGTCTTATACATAATCACA 59625533 ACTCATCAAT Statistics Matches: 56, Mismatches: 7, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 43 56 1.00 ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27 Consensus pattern (43 bp): ATGGTCTTATACATAATCACATAATGATGCCAATGTCCCAAAC Found at i:59631068 original size:15 final size:17 Alignment explanation

Indices: 59631035--59631068 Score: 59 Period size: 17 Copynumber: 2.0 Consensus size: 17 59631025 TTATTTAAGT * 59631035 TATATATAAGTATTATA 1 TATATATAAATATTATA 59631052 TATATATAAATATTATA 1 TATATATAAATATTATA 59631069 ATTATTAACC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47 Consensus pattern (17 bp): TATATATAAATATTATA Found at i:59631100 original size:3 final size:3 Alignment explanation

Indices: 59631094--59631129 Score: 63 Period size: 3 Copynumber: 12.0 Consensus size: 3 59631084 TATGGTTTTA * 59631094 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT 59631130 AAAATAAAGT Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 3 31 1.00 ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67 Consensus pattern (3 bp): TAT Found at i:59632573 original size:23 final size:23 Alignment explanation

Indices: 59632546--59632627 Score: 98 Period size: 23 Copynumber: 3.7 Consensus size: 23 59632536 AGCTTTGCCG 59632546 ATCAGGCACTTTATGTGTCGTAT 1 ATCAGGCACTTTATGTGTCGTAT 59632569 ATCAGGCACTTTATGTGTCGTAT 1 ATCAGGCACTTTATGTGTCGTAT * * * * * 59632592 TTTAGGCACTTCATGCGTGGT-T 1 ATCAGGCACTTTATGTGTCGTAT 59632614 -TCAGGCAC-TTATGT 1 ATCAGGCACTTTATGT 59632628 AACACCCCAA Statistics Matches: 51, Mismatches: 8, Indels: 3 0.82 0.13 0.05 Matches are distributed among these distances: 20 4 0.08 21 7 0.14 22 1 0.02 23 39 0.76 ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39 Consensus pattern (23 bp): ATCAGGCACTTTATGTGTCGTAT Found at i:59634201 original size:28 final size:28 Alignment explanation

Indices: 59634169--59634238 Score: 99 Period size: 28 Copynumber: 2.5 Consensus size: 28 59634159 ATAGTAAGTC 59634169 CGCACACTTAGTGCT-TA-ATAGTCAAACT 1 CGCACACTTAGTGCTATACA-A-TCAAACT * 59634197 CGCACACTTAGTGCTATACAATTAAACT 1 CGCACACTTAGTGCTATACAATCAAACT 59634225 CGCACACTTAGTGC 1 CGCACACTTAGTGC 59634239 CAATCTCATT Statistics Matches: 39, Mismatches: 1, Indels: 4 0.89 0.02 0.09 Matches are distributed among these distances: 28 35 0.90 29 3 0.08 30 1 0.03 ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27 Consensus pattern (28 bp): CGCACACTTAGTGCTATACAATCAAACT Found at i:59649879 original size:7 final size:7 Alignment explanation

Indices: 59649864--59649908 Score: 54 Period size: 7 Copynumber: 6.3 Consensus size: 7 59649854 TCAAATATAC 59649864 ATTATAAA 1 ATTA-AAA 59649872 ATTAAAA 1 ATTAAAA 59649879 ATTAAAA 1 ATTAAAA * 59649886 ATAAAAA 1 ATTAAAA * 59649893 ATTTAAA 1 ATTAAAA * 59649900 ATTTAAA 1 ATTAAAA 59649907 AT 1 AT 59649909 AGAAATCTTA Statistics Matches: 34, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 7 30 0.88 8 4 0.12 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (7 bp): ATTAAAA Found at i:59649893 original size:21 final size:21 Alignment explanation

Indices: 59649869--59649909 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 59649859 TATACATTAT 59649869 AAAATTAAAAATTAAAAATAA 1 AAAATTAAAAATTAAAAATAA * * 59649890 AAAATTTAAAATTTAAAATA 1 AAAATTAAAAATTAAAAATA 59649910 GAAATCTTAT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29 Consensus pattern (21 bp): AAAATTAAAAATTAAAAATAA Found at i:59658205 original size:49 final size:49 Alignment explanation

Indices: 59658082--59658288 Score: 296 Period size: 49 Copynumber: 4.3 Consensus size: 49 59658072 CTTCGGGACT * * * * * * 59658082 TATCACAT-T-TATACACTTTCACATCCACCACGTTGGCCACTCGGCCC 1 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC * 59658129 TGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC 1 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC 59658176 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC 1 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC * * * 59658225 TATCACATATATACACACTTTCACATTCATCACATCGGCCATTAAGCCT 1 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC 59658274 TATCACATATATATA 1 TATCACATATATATA 59658289 NNNNNNNNNN Statistics Matches: 144, Mismatches: 12, Indels: 6 0.89 0.07 0.04 Matches are distributed among these distances: 46 1 0.01 47 42 0.29 49 101 0.70 ACGTcount: A:0.30, C:0.31, G:0.08, T:0.30 Consensus pattern (49 bp): TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC Found at i:59661982 original size:50 final size:50 Alignment explanation

Indices: 59661928--59662077 Score: 225 Period size: 50 Copynumber: 3.0 Consensus size: 50 59661918 CATCGCCTAC 59661928 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATAT 1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATAT * * * * 59661978 ATATTTGACA-TTGACCATTCAGCTTTACCACATATACATATCTC--ATAC 1 ATATTTCACACTAG-CCATTCGGCTTTACCACATATACATATCTCATATAT * 59662026 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACAT 1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATAT 59662076 AT 1 AT 59662078 TTCCAATTTA Statistics Matches: 87, Mismatches: 9, Indels: 8 0.84 0.09 0.08 Matches are distributed among these distances: 48 41 0.47 49 4 0.05 50 42 0.48 ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35 Consensus pattern (50 bp): ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATAT Found at i:59662051 original size:48 final size:48 Alignment explanation

Indices: 59661925--59662080 Score: 242 Period size: 48 Copynumber: 3.2 Consensus size: 48 59661915 GCACATCGCC 59661925 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA 1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTC--A * * * * 59661975 TATATATTTGACA-TTGACCATTCAGCTTTACCACATATACATATCTCA 1 TACATATTTCACACTAG-CCATTCGGCTTTACCACATATACATATCTCA 59662023 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA 1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA 59662071 TACATATTTC 1 TACATATTTC 59662081 CAATTTAATA Statistics Matches: 96, Mismatches: 8, Indels: 6 0.87 0.07 0.05 Matches are distributed among these distances: 48 52 0.54 49 4 0.04 50 40 0.42 ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36 Consensus pattern (48 bp): TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA Found at i:59666884 original size:37 final size:36 Alignment explanation

Indices: 59666814--59666885 Score: 90 Period size: 37 Copynumber: 2.0 Consensus size: 36 59666804 AAAAATGTAC * * * 59666814 TCCAACCGAAACATGGCAAACGTTCATAAGAGCTAA 1 TCCAACCGAAACACGCCAAACGCTCATAAGAGCTAA * * 59666850 TCCAACCGATAACACGCCAAATGCTCATATGAGCTA 1 TCCAACCGA-AACACGCCAAACGCTCATAAGAGCTA 59666886 TATATCCGCC Statistics Matches: 30, Mismatches: 5, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 36 9 0.30 37 21 0.70 ACGTcount: A:0.39, C:0.28, G:0.15, T:0.18 Consensus pattern (36 bp): TCCAACCGAAACACGCCAAACGCTCATAAGAGCTAA Found at i:59668323 original size:15 final size:15 Alignment explanation

Indices: 59668303--59668342 Score: 71 Period size: 15 Copynumber: 2.7 Consensus size: 15 59668293 TAATTTCATG * 59668303 AAATTTACTTGTTTA 1 AAATTTAATTGTTTA 59668318 AAATTTAATTGTTTA 1 AAATTTAATTGTTTA 59668333 AAATTTAATT 1 AAATTTAATT 59668343 TGTCTCTAAT Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 15 24 1.00 ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53 Consensus pattern (15 bp): AAATTTAATTGTTTA Found at i:59670937 original size:33 final size:33 Alignment explanation

Indices: 59670900--59670988 Score: 178 Period size: 33 Copynumber: 2.7 Consensus size: 33 59670890 GTTTCAATTG 59670900 GGATTTAGCCTGGACTGGTAATCCTAATTGACT 1 GGATTTAGCCTGGACTGGTAATCCTAATTGACT 59670933 GGATTTAGCCTGGACTGGTAATCCTAATTGACT 1 GGATTTAGCCTGGACTGGTAATCCTAATTGACT 59670966 GGATTTAGCCTGGACTGGTAATC 1 GGATTTAGCCTGGACTGGTAATC 59670989 TAGATTCGAC Statistics Matches: 56, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 33 56 1.00 ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33 Consensus pattern (33 bp): GGATTTAGCCTGGACTGGTAATCCTAATTGACT Found at i:59676854 original size:21 final size:21 Alignment explanation

Indices: 59676830--59676889 Score: 111 Period size: 21 Copynumber: 2.9 Consensus size: 21 59676820 GGATCACATG 59676830 CCCGTGTGGCCATGGGACGCA 1 CCCGTGTGGCCATGGGACGCA * 59676851 CCCGTGTGGCCATGAGACGCA 1 CCCGTGTGGCCATGGGACGCA 59676872 CCCGTGTGGCCATGGGAC 1 CCCGTGTGGCCATGGGAC 59676890 ACGCCCTCGA Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 37 1.00 ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15 Consensus pattern (21 bp): CCCGTGTGGCCATGGGACGCA Found at i:59678171 original size:33 final size:32 Alignment explanation

Indices: 59678134--59678210 Score: 82 Period size: 33 Copynumber: 2.3 Consensus size: 32 59678124 TGGCCTTGCC * * 59678134 ATGGTCTTACACTCGTAGTGCCATAACCCAATT 1 ATGGTCTTACACTCG-AATGCCATAACCCAACT * * * * 59678167 ATGGTCTTATCATTTGAATGCCATATCCCAGCT 1 ATGGTCTTA-CACTCGAATGCCATAACCCAACT 59678200 ATGGTCTTACA 1 ATGGTCTTACA 59678211 TACAAATATT Statistics Matches: 37, Mismatches: 6, Indels: 3 0.80 0.13 0.07 Matches are distributed among these distances: 32 2 0.05 33 31 0.84 34 4 0.11 ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34 Consensus pattern (32 bp): ATGGTCTTACACTCGAATGCCATAACCCAACT Found at i:59678204 original size:66 final size:66 Alignment explanation

Indices: 59678085--59678210 Score: 155 Period size: 66 Copynumber: 1.9 Consensus size: 66 59678075 ATCATTTTTT ** * ** 59678085 GTGCCATAGTCCAACTATGGTCTTACATGTGAATTGCCATGGCCTTGCCATGGTCTTACACTCGT 1 GTGCCATAACCCAACTATGGTCTTACATGTGAATTGCCATAGCCCAGCCATGGTCTTACACTCGT 59678150 A 66 A * * * * 59678151 GTGCCATAACCCAATTATGGTCTTATCATTTGAA-TGCCATATCCCAGCTATGGTCTTACA 1 GTGCCATAACCCAACTATGGTCTTA-CATGTGAATTGCCATAGCCCAGCCATGGTCTTACA 59678211 TACAAATATT Statistics Matches: 50, Mismatches: 9, Indels: 2 0.82 0.15 0.03 Matches are distributed among these distances: 66 43 0.86 67 7 0.14 ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33 Consensus pattern (66 bp): GTGCCATAACCCAACTATGGTCTTACATGTGAATTGCCATAGCCCAGCCATGGTCTTACACTCGT A Found at i:59685138 original size:21 final size:21 Alignment explanation

Indices: 59685114--59685166 Score: 52 Period size: 21 Copynumber: 2.5 Consensus size: 21 59685104 GTTCGGATTA * 59685114 TATCGGTAGAACCAAAAGTTG 1 TATCGGTAGAACCAAAAGTTC * * *** 59685135 TATCTGTATAACTTCAAGTTC 1 TATCGGTAGAACCAAAAGTTC 59685156 TATCGGTAGAA 1 TATCGGTAGAA 59685167 TTCTGTAGCC Statistics Matches: 24, Mismatches: 8, Indels: 0 0.75 0.25 0.00 Matches are distributed among these distances: 21 24 1.00 ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32 Consensus pattern (21 bp): TATCGGTAGAACCAAAAGTTC Found at i:59685589 original size:17 final size:16 Alignment explanation

Indices: 59685564--59685603 Score: 53 Period size: 17 Copynumber: 2.4 Consensus size: 16 59685554 TAGAATTTAG * 59685564 TTGAGAAAATTATTTAA 1 TTGA-AAAATTAATTAA 59685581 TTAGAAAAATTAATTAA 1 TT-GAAAAATTAATTAA 59685598 TTGAAA 1 TTGAAA 59685604 TTAATTTAAT Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 16 4 0.19 17 15 0.71 18 2 0.10 ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38 Consensus pattern (16 bp): TTGAAAAATTAATTAA Found at i:59686144 original size:27 final size:28 Alignment explanation

Indices: 59686114--59686184 Score: 90 Period size: 27 Copynumber: 2.6 Consensus size: 28 59686104 TATTTTAATG 59686114 CATGTTTTTAATATGTCATAGT-TAGTA 1 CATGTTTTTAATATGTCATAGTCTAGTA * * * * 59686141 CATGTTATTAATTTGTCTTAGTCTATTA 1 CATGTTTTTAATATGTCATAGTCTAGTA * 59686169 CATATTTTTAATATGT 1 CATGTTTTTAATATGT 59686185 TCTAGCTTTA Statistics Matches: 36, Mismatches: 7, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 27 19 0.53 28 17 0.47 ACGTcount: A:0.28, C:0.08, G:0.11, T:0.52 Consensus pattern (28 bp): CATGTTTTTAATATGTCATAGTCTAGTA Found at i:59686179 original size:28 final size:27 Alignment explanation

Indices: 59686118--59686184 Score: 80 Period size: 28 Copynumber: 2.4 Consensus size: 27 59686108 TTAATGCATG * 59686118 TTTTTAATATGTCATAGTTAGTACATG 1 TTTTTAATATGTCATAGTTAGTACATA * * * * 59686145 TTATTAATTTGTCTTAGTCTATTACATA 1 TTTTTAATATGTCATAGT-TAGTACATA 59686173 TTTTTAATATGT 1 TTTTTAATATGT 59686185 TCTAGCTTTA Statistics Matches: 32, Mismatches: 7, Indels: 1 0.80 0.17 0.03 Matches are distributed among these distances: 27 15 0.47 28 17 0.53 ACGTcount: A:0.28, C:0.07, G:0.10, T:0.54 Consensus pattern (27 bp): TTTTTAATATGTCATAGTTAGTACATA Found at i:59691954 original size:10 final size:10 Alignment explanation

Indices: 59691939--59691988 Score: 54 Period size: 9 Copynumber: 5.4 Consensus size: 10 59691929 TTAATAAATG 59691939 TTTTATATAT 1 TTTTATATAT 59691949 TTTTATAT-T 1 TTTTATATAT * 59691958 TTTTGTAT-T 1 TTTTATATAT * 59691967 TTTT-TATAA 1 TTTTATATAT 59691976 TTTTATA-AT 1 TTTTATATAT 59691985 TTTT 1 TTTT 59691989 GCAAGTATTT Statistics Matches: 35, Mismatches: 3, Indels: 5 0.81 0.07 0.12 Matches are distributed among these distances: 8 3 0.09 9 22 0.63 10 10 0.29 ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74 Consensus pattern (10 bp): TTTTATATAT Found at i:59691978 original size:11 final size:10 Alignment explanation

Indices: 59691939--59691988 Score: 50 Period size: 10 Copynumber: 5.2 Consensus size: 10 59691929 TTAATAAATG * 59691939 TTTTATATAT 1 TTTTATATTT 59691949 TTTTATA-TT 1 TTTTATATTT * 59691958 TTTTGTATTT 1 TTTTATATTT * 59691968 TTTTATAATT 1 TTTTATATTT * 59691978 TTATA-ATTT 1 TTTTATATTT 59691987 TT 1 TT 59691989 GCAAGTATTT Statistics Matches: 33, Mismatches: 6, Indels: 3 0.79 0.14 0.07 Matches are distributed among these distances: 9 12 0.36 10 21 0.64 ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74 Consensus pattern (10 bp): TTTTATATTT Found at i:59691979 original size:27 final size:27 Alignment explanation

Indices: 59691939--59692016 Score: 75 Period size: 27 Copynumber: 2.9 Consensus size: 27 59691929 TTAATAAATG * * * * * 59691939 TTTTATATATTTTTATATTTTTTGTAT 1 TTTTTTATAATTTTATAATTTTTGCAA 59691966 TTTTTTATAATTTTATAATTTTTGCAA 1 TTTTTTATAATTTTATAATTTTTGCAA * * * 59691993 GTATTTATAATTTTAATACTTTTT 1 TTTTTTATAATTTT-ATAATTTTT 59692017 AAATAAATTT Statistics Matches: 42, Mismatches: 8, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 27 34 0.81 28 8 0.19 ACGTcount: A:0.27, C:0.03, G:0.04, T:0.67 Consensus pattern (27 bp): TTTTTTATAATTTTATAATTTTTGCAA Found at i:59701455 original size:31 final size:31 Alignment explanation

Indices: 59701403--59701477 Score: 96 Period size: 31 Copynumber: 2.4 Consensus size: 31 59701393 TAAAAACTTA * * * * 59701403 AATATAATAAATAAATTATATTTATATTATTT 1 AATATAAT-GATAAATGATATTTAAATAATTT 59701435 AATATAATGATAAATGATATTTAAATAATTT 1 AATATAATGATAAATGATATTTAAATAATTT * 59701466 GATATAATGATA 1 AATATAATGATA 59701478 CATAAATTAT Statistics Matches: 38, Mismatches: 5, Indels: 1 0.86 0.11 0.02 Matches are distributed among these distances: 31 30 0.79 32 8 0.21 ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44 Consensus pattern (31 bp): AATATAATGATAAATGATATTTAAATAATTT Found at i:59701468 original size:23 final size:23 Alignment explanation

Indices: 59701430--59701477 Score: 64 Period size: 22 Copynumber: 2.1 Consensus size: 23 59701420 ATATTTATAT 59701430 TATTTAATATAATGATA-AATGA 1 TATTTAATATAATGATATAATGA 59701452 TATTTAA-ATAATTTGATATAATGA 1 TATTTAATATAA--TGATATAATGA 59701476 TA 1 TA 59701478 CATAAATTAT Statistics Matches: 23, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 21 4 0.17 22 7 0.30 23 5 0.22 24 7 0.30 ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44 Consensus pattern (23 bp): TATTTAATATAATGATATAATGA Found at i:59701491 original size:31 final size:31 Alignment explanation

Indices: 59701403--59701502 Score: 85 Period size: 31 Copynumber: 3.2 Consensus size: 31 59701393 TAAAAACTTA * * * * * 59701403 AATATAATAAATAAATTATATTTATATTATTT 1 AATATAAT-GATAAATGAAATTTAAATAATTT * 59701435 AATATAATGATAAATGATATTTAAATAATTT 1 AATATAATGATAAATGAAATTTAAATAATTT * * * 59701466 GATATAATGATACAT-AAATTATAAATTAATCT 1 AATATAATGATAAATGAAATT-TAAA-TAATTT 59701498 AATAT 1 AATAT 59701503 TTTTTTAGAT Statistics Matches: 57, Mismatches: 9, Indels: 4 0.81 0.13 0.06 Matches are distributed among these distances: 30 4 0.07 31 36 0.63 32 17 0.30 ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43 Consensus pattern (31 bp): AATATAATGATAAATGAAATTTAAATAATTT Found at i:59701816 original size:118 final size:118 Alignment explanation

Indices: 59701608--59701845 Score: 350 Period size: 118 Copynumber: 2.0 Consensus size: 118 59701598 ACACTTGAAT * * * 59701608 GAAAAAAAAACTTTTTCATCACAATTTTGACCCCAAAAGCCAGATGTCCTTCATTGCCCTTGCAG 1 GAAAAAAAAACTTTTTCACCACAATTTTGACCCCAAAAACCAGATGTCCTTCATTGCCCATGCAG 59701673 TGAAAATCCACTTTTGGCTTCTCAAATGCAATGAAGAATGAGACTTTAATAAA 66 TGAAAATCCACTTTTGGCTTCTCAAATGCAATGAAGAATGAGACTTTAATAAA * * * * * * ** 59701726 GAAAAAGACACTTTTTCACCCCAATTTTGACCCCAAAAACTAGATGTCTTTCATTGCTCATGTGG 1 GAAAAAAAAACTTTTTCACCACAATTTTGACCCCAAAAACCAGATGTCCTTCATTGCCCATGCAG * * * 59701791 TGAAAATCTACTTTTGGCTTCTCAAATGCAATGAAGAATGTGACTTTAGTAAA 66 TGAAAATCCACTTTTGGCTTCTCAAATGCAATGAAGAATGAGACTTTAATAAA 59701844 GA 1 GA 59701846 CAACGACGAC Statistics Matches: 106, Mismatches: 14, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 118 106 1.00 ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30 Consensus pattern (118 bp): GAAAAAAAAACTTTTTCACCACAATTTTGACCCCAAAAACCAGATGTCCTTCATTGCCCATGCAG TGAAAATCCACTTTTGGCTTCTCAAATGCAATGAAGAATGAGACTTTAATAAA Found at i:59712818 original size:24 final size:24 Alignment explanation

Indices: 59712761--59712833 Score: 71 Period size: 26 Copynumber: 3.0 Consensus size: 24 59712751 TCTCGATTAC 59712761 GGCTCT-TCGTGAGCTTCCT-ATTAATT 1 GGCTCTAT-GTGAGCTTCCTGA-T-A-T 59712787 GGCTCTATGTGAGCTTCCTGATAT 1 GGCTCTATGTGAGCTTCCTGATAT * * 59712811 GGCTCTAT-TGAACTTTCTGATAT 1 GGCTCTATGTGAGCTTCCTGATAT 59712834 ATGGATATCC Statistics Matches: 43, Mismatches: 2, Indels: 7 0.83 0.04 0.13 Matches are distributed among these distances: 23 13 0.30 24 9 0.21 25 1 0.02 26 18 0.42 27 2 0.05 ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41 Consensus pattern (24 bp): GGCTCTATGTGAGCTTCCTGATAT Found at i:59715235 original size:48 final size:48 Alignment explanation

Indices: 59715158--59715535 Score: 307 Period size: 48 Copynumber: 7.9 Consensus size: 48 59715148 GGGTAAATTA * * 59715158 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACAT-GTCGAGA 1 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACATAAT-GAGG * * * * * 59715206 CCGATGCCATGTCCCAGACGTAGTTTTACACTGACTCTCATAATGTGG 1 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACATAATGAGG * * * * 59715254 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACAT-GTCGAGG 1 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACATAAT-GAGG * * * * 59715302 CCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAATGTGG 1 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACATAATGAGG * * ** * * * 59715350 CCGATGCCATGTCCCAAACATGGTCTTACACTAACACACAT-ATCAATG 1 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACATAAT-GAGG * * * * * * * ** 59715398 TCGACGCCATGTCCCAAATATGGTCTTACACTAG-TACACAT-ATCAACA 1 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCT-CACATAAT-GAGG * * * ** * 59715446 CCGATGCCATGTCCCAAACATGGTCTTACACTGCCTCTTATAATGTGG 1 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACATAATGAGG * * * * 59715494 CCGATTCCATGTCCCAGACATGGTCTTACACTAGCACACATA 1 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACATA 59715536 TCACCCAATT Statistics Matches: 267, Mismatches: 56, Indels: 14 0.79 0.17 0.04 Matches are distributed among these distances: 47 3 0.01 48 259 0.97 49 5 0.02 ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26 Consensus pattern (48 bp): CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACATAATGAGG Found at i:59715331 original size:96 final size:96 Alignment explanation

Indices: 59715158--59715525 Score: 411 Period size: 96 Copynumber: 3.8 Consensus size: 96 59715148 GGGTAAATTA * * * * * 59715158 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACATGTCGAGACCGATGCCATGTCCCAG 1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGCCGATGCCATGTCCCAG * * * 59715223 ACGTAGTTTTACACTGACTCTCATAATGTGG 66 ACATGGTCTTACACTGACTCTCATAATGTGG * 59715254 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCCGATGCCATGTCCCAG 1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGCCGATGCCATGTCCCAG * * 59715319 ACATGGTCTTACATTGGCTCTCATAATGTGG 66 ACATGGTCTTACACTGACTCTCATAATGTGG * * * * * * * 59715350 CCGATGCCATGTCCCAAACATGGTCTTACACTAACACACATATCAATGTCGACGCCATGTCCCAA 1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGCCGATGCCATGTCCCAG * * * **** 59715415 ATATGGTCTTACACT-AGTACACAT-ATCAACA 66 ACATGGTCTTACACTGACT-CTCATAAT-GTGG ** * * 59715446 CCGATGCCATGTCCCAAACATGGTCTTACACT-GCCTCTTATAAT-GTGGCCGATTCCATGTCCC 1 CCGATGCCATGTCCCAAACATGGTCTTACACTAG-CTCACAT-ATCGAGGCCGATGCCATGTCCC 59715509 AGACATGGTCTTACACT 64 AGACATGGTCTTACACT 59715526 AGCACACATA Statistics Matches: 230, Mismatches: 38, Indels: 8 0.83 0.14 0.03 Matches are distributed among these distances: 95 3 0.01 96 225 0.98 97 2 0.01 ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26 Consensus pattern (96 bp): CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGCCGATGCCATGTCCCAG ACATGGTCTTACACTGACTCTCATAATGTGG Found at i:59715421 original size:144 final size:145 Alignment explanation

Indices: 59715157--59715538 Score: 470 Period size: 144 Copynumber: 2.6 Consensus size: 145 59715147 AGGGTAAATT * * * * * 59715157 ACCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACAT-GTCGAGACCGATGCCATGTCCC 1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCCATGTCCC * * * * * * * 59715221 AGACGTAGTTTTACACTGACTCTC--AT-AATGTGGCCGATGCCATGTCCCAAACATGGTCTTAC 65 AGACATGGTCTTACACTAACACACATATCAATGT-G-CGACGCCATGTCCCAAACATGGTCTTAC * * * 59715283 ACTAGCT-CACATGTCGAG 128 ACTAG-TACACATATCAAC * * 59715301 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAATGTGGCCGATGCCATGTCCCA 1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATGTCCCA * * 59715366 AACATGGTCTTACACTAACACACATATCAATGT-CGACGCCATGTCCCAAATATGGTCTTACACT 66 GACATGGTCTTACACTAACACACATATCAATGTGCGACGCCATGTCCCAAACATGGTCTTACACT 59715430 AGTACACATATCAAC 131 AGTACACATATCAAC * * * * 59715445 ACCGATGCCATGTCCCAAACATGGTCTTACACTGCCTCTTATAATGTGGCCGATTCCATGTCCCA 1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATGTCCCA * 59715510 GACATGGTCTTACACTAGCACACATATCA 66 GACATGGTCTTACACTAACACACATATCA 59715539 CCCAATTGTC Statistics Matches: 206, Mismatches: 27, Indels: 10 0.85 0.11 0.04 Matches are distributed among these distances: 143 1 0.00 144 197 0.96 145 1 0.00 146 2 0.01 147 5 0.02 ACGTcount: A:0.27, C:0.30, G:0.18, T:0.26 Consensus pattern (145 bp): ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATGTCCCA GACATGGTCTTACACTAACACACATATCAATGTGCGACGCCATGTCCCAAACATGGTCTTACACT AGTACACATATCAAC Found at i:59717773 original size:47 final size:47 Alignment explanation

Indices: 59717721--59717910 Score: 163 Period size: 47 Copynumber: 4.1 Consensus size: 47 59717711 TGGTTGGACG * * * * * 59717721 ATGGCAAC-ATGTGATATGTGATTTCCGTATAAGACCATAGCTGGGCT 1 ATGGCATCGATGTGATATGTG-CTTCCATATAAGACCATAGCTGAGAT * * * * 59717768 ATGGCATCGGTGTGATATGAGCTTCCGTATAAGACCATATCTGAGAT 1 ATGGCATCGATGTGATATGTGCTTCCATATAAGACCATAGCTGAGAT * * * * * 59717815 ATGGCATCGGTATGATATGTGCTTCTATGTAAGACCATATCT-AGGAT 1 ATGGCATCGATGTGATATGTGCTTCCATATAAGACCATAGCTGA-GAT * * * * 59717862 ATGGCATC-AGTGTGATATGTG-ATCCATGTAAGACCATGGCTGAGCT 1 ATGGCATCGA-TGTGATATGTGCTTCCATATAAGACCATAGCTGAGAT 59717908 ATG 1 ATG 59717911 ACTTCAGTGT Statistics Matches: 120, Mismatches: 19, Indels: 9 0.81 0.13 0.06 Matches are distributed among these distances: 46 22 0.18 47 88 0.73 48 10 0.08 ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31 Consensus pattern (47 bp): ATGGCATCGATGTGATATGTGCTTCCATATAAGACCATAGCTGAGAT Found at i:59724044 original size:49 final size:49 Alignment explanation

Indices: 59723988--59724083 Score: 192 Period size: 49 Copynumber: 2.0 Consensus size: 49 59723978 TATTCATGAG 59723988 CCAGATGTAGGCATAGATGTAACTTACTCATTACCAACCATACAAGTAC 1 CCAGATGTAGGCATAGATGTAACTTACTCATTACCAACCATACAAGTAC 59724037 CCAGATGTAGGCATAGATGTAACTTACTCATTACCAACCATACAAGT 1 CCAGATGTAGGCATAGATGTAACTTACTCATTACCAACCATACAAGT 59724084 CACATAATAT Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 49 47 1.00 ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25 Consensus pattern (49 bp): CCAGATGTAGGCATAGATGTAACTTACTCATTACCAACCATACAAGTAC Found at i:59724324 original size:47 final size:49 Alignment explanation

Indices: 59724255--59724471 Score: 240 Period size: 47 Copynumber: 4.6 Consensus size: 49 59724245 GTAAGGTTCT 59724255 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTC-AAGTC 1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGTC * * * * 59724302 GATGCCATGTACTAGACATGGTCTTACACTGACT-ATCATCTCGTAGTC 1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGTC * * * * 59724350 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTTA-CATTTCGAGGCC 1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGTC * * * 59724396 GATG-CATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTC--AGTGCC 1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGT--C 59724442 GATGCCATGTCCCAGACATGGTCTTACACT 1 GATGCCATGTCCCAGACATGGTCTTACACT 59724472 AGCTTCCATA Statistics Matches: 144, Mismatches: 18, Indels: 15 0.81 0.10 0.08 Matches are distributed among these distances: 44 1 0.01 46 62 0.43 47 63 0.44 48 18 0.12 ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28 Consensus pattern (49 bp): GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGTC Found at i:59724497 original size:94 final size:93 Alignment explanation

Indices: 59724255--59724523 Score: 300 Period size: 94 Copynumber: 2.9 Consensus size: 93 59724245 GTAAGGTTCT * * * * * 59724255 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TCATATCTCAAGTCGATGCCATGTACTAGAC 1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATATGT--GGCCGATG-CATGTCCCAGAC * 59724319 ATGGTCTTACACT-G-ACTATCATCTCGTAGTC 63 AT-GTCTTACACTAGCAC-ATCATCTCGTAGCC * * 59724350 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATTTCGAGGCCGATGCATGTCCCAGACA 1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATAT-GTGGCCGATGCATGTCCCAGACA * 59724413 TGTCTTACACTAGCAC-TCGTCTCAGT-GCC 64 TGTCTTACACTAGCACATCATCTC-GTAGCC * * 59724442 GATGCCATGTCCCAGACATGGTCTTACACTAGCTTCCATAATGTGGCCGATGCATGTCCCAGAAA 1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CAT-ATGTGGCCGATGCATGTCCCAGACA 59724507 TGTCTTACACTAGCACA 64 TGTCTTACACTAGCACA 59724524 CACAAGTGAC Statistics Matches: 150, Mismatches: 14, Indels: 20 0.82 0.08 0.11 Matches are distributed among these distances: 92 22 0.15 93 42 0.28 94 77 0.51 95 9 0.06 ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28 Consensus pattern (93 bp): GATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATATGTGGCCGATGCATGTCCCAGACATG TCTTACACTAGCACATCATCTCGTAGCC Found at i:59724498 original size:47 final size:45 Alignment explanation

Indices: 59724255--59724520 Score: 213 Period size: 46 Copynumber: 5.7 Consensus size: 45 59724245 GTAAGGTTCT * * * 59724255 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TCATATCTCAAGTC 1 GATGCCATGTCCCAGACAT-GTCTTACACTAGCTTCATATGT--AGCC * * * * 59724302 GATGCCATGTACTAGACATGGTCTTACACT-GACTATCATCTCGTAGTC 1 GATGCCATGTCCCAGACAT-GTCTTACACTAG-CT-TCATAT-GTAGCC * * 59724350 GATG-CATGTCCCAGACATGTCTTACACTGGCTTACATTTCG-AGGCC 1 GATGCCATGTCCCAGACATGTCTTACACTAGCTT-CATAT-GTA-GCC * * * 59724396 GATG-CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAGT-GCC 1 GATGCCATGTCCCAGACATGTCTTACACTAGC-TTCATAT--GTAGCC * 59724442 GATGCCATGTCCCAGACATGGTCTTACACTAGCTTCCATAATGTGGCC 1 GATGCCATGTCCCAGACAT-GTCTTACACTAGCTT-CAT-ATGTAGCC * 59724490 GATG-CATGTCCCAGAAATGTCTTACACTAGC 1 GATGCCATGTCCCAGACATGTCTTACACTAGC 59724521 ACACACAAGT Statistics Matches: 187, Mismatches: 17, Indels: 31 0.80 0.07 0.13 Matches are distributed among these distances: 45 2 0.01 46 74 0.40 47 74 0.40 48 30 0.16 49 6 0.03 50 1 0.01 ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28 Consensus pattern (45 bp): GATGCCATGTCCCAGACATGTCTTACACTAGCTTCATATGTAGCC Found at i:59724512 original size:140 final size:141 Alignment explanation

Indices: 59724255--59724517 Score: 342 Period size: 140 Copynumber: 1.9 Consensus size: 141 59724245 GTAAGGTTCT * * * 59724255 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTACTAGACA 1 GATGCCATGTCCCAGACATGGTCTTACACTAGCACATATCTCAAGTCGATGCCATGTACCAGACA * * * 59724320 TGGTCTTACACTGACTATCATCTCGTAGTCGATGCATGTCCCAGACATGTCTTACACTGGCTTAC 66 TGGTCTTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGAAATGTCTTACACTGGCTTAC 59724385 ATTTCGAGGCC 131 ATTTCGAGGCC * * 59724396 GATG-CATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTC-AGTGCCGATGCCATGTCCCAG 1 GATGCCATGTCCCAGACATGGTCTTACACTAGCACAT-ATCTCAAGT--CGATGCCATGTACCAG * 59724457 ACATGGTCTTACACT-AGCT-TCCATAAT-GTGGCCGATGCATGTCCCAGAAATGTCTTACACT 63 ACATGGTCTTACACTGA-CTAT-CAT-ATCGTAGCCGATGCATGTCCCAGAAATGTCTTACACT 59724518 AGCACACACA Statistics Matches: 107, Mismatches: 9, Indels: 13 0.83 0.07 0.10 Matches are distributed among these distances: 138 4 0.04 139 19 0.18 140 79 0.74 141 5 0.05 ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28 Consensus pattern (141 bp): GATGCCATGTCCCAGACATGGTCTTACACTAGCACATATCTCAAGTCGATGCCATGTACCAGACA TGGTCTTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGAAATGTCTTACACTGGCTTAC ATTTCGAGGCC Found at i:59727353 original size:28 final size:29 Alignment explanation

Indices: 59727303--59727357 Score: 78 Period size: 28 Copynumber: 1.9 Consensus size: 29 59727293 CTAAGGTACA * 59727303 GGGGACACACGGCCAGACAACATGCCCAT 1 GGGGACACACAGCCAGACAACATGCCCAT 59727332 GGGG-CACACAGCCTAGAC-ACATGCCC 1 GGGGACACACAGCC-AGACAACATGCCC 59727358 GTGTGTCTAC Statistics Matches: 24, Mismatches: 1, Indels: 3 0.86 0.04 0.11 Matches are distributed among these distances: 28 16 0.67 29 8 0.33 ACGTcount: A:0.29, C:0.36, G:0.27, T:0.07 Consensus pattern (29 bp): GGGGACACACAGCCAGACAACATGCCCAT Found at i:59731642 original size:30 final size:30 Alignment explanation

Indices: 59731608--59731665 Score: 73 Period size: 30 Copynumber: 1.9 Consensus size: 30 59731598 TAGGCACTTC * 59731608 CACACAGGT-GATCCACACGTCCGGGTGTGA 1 CACACAGGTAGA-CCACACGCCCGGGTGTGA * * 59731638 CACACGGGTAGACCACACGCCCGTGTGT 1 CACACAGGTAGACCACACGCCCGGGTGT 59731666 CATGGTCGTG Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 30 22 0.92 31 2 0.08 ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16 Consensus pattern (30 bp): CACACAGGTAGACCACACGCCCGGGTGTGA Found at i:59736313 original size:15 final size:15 Alignment explanation

Indices: 59736273--59736322 Score: 57 Period size: 15 Copynumber: 3.3 Consensus size: 15 59736263 CTTGCTCTCT * 59736273 TTCTCTTCTTCGTTCCC 1 TTCTCTT-TTC-TTTCC 59736290 TTCTC-TTTCTTTCC 1 TTCTCTTTTCTTTCC * 59736304 TTCTCTTTTCTTTCT 1 TTCTCTTTTCTTTCC 59736319 TTCT 1 TTCT 59736323 TTCCTCTTTC Statistics Matches: 30, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 14 9 0.30 15 15 0.50 16 1 0.03 17 5 0.17 ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64 Consensus pattern (15 bp): TTCTCTTTTCTTTCC Found at i:59736349 original size:21 final size:19 Alignment explanation

Indices: 59736269--59736360 Score: 73 Period size: 19 Copynumber: 4.7 Consensus size: 19 59736259 TCTTCTTGCT 59736269 CTCTTTCTCTTC-TTCGTTCC 1 CTCTTTCT-TTCTTTC-TTCC * * 59736289 CT-TCTCTTTCTTTCCTTCT 1 CTCTTTCTTTCTTT-CTTCC * 59736308 CT-TTTCTTTCTTTCTTTC 1 CTCTTTCTTTCTTTCTTCC 59736326 CTCTTTCTTTCACTTTCTTCC 1 CTCTTTCTTT--CTTTCTTCC * 59736347 CTCTCCTCTTTCTT 1 CTCT-TTCTTTCTT 59736361 CCCCATTTCC Statistics Matches: 59, Mismatches: 7, Indels: 12 0.76 0.09 0.15 Matches are distributed among these distances: 18 8 0.14 19 28 0.47 20 6 0.10 21 12 0.20 22 5 0.08 ACGTcount: A:0.01, C:0.37, G:0.01, T:0.61 Consensus pattern (19 bp): CTCTTTCTTTCTTTCTTCC Found at i:59738963 original size:30 final size:30 Alignment explanation

Indices: 59738928--59738985 Score: 82 Period size: 30 Copynumber: 1.9 Consensus size: 30 59738918 TAGGCACTTC 59738928 CACACGGGT-GATCCACATGCCCGTGTGTGA 1 CACACGGGTAGA-CCACATGCCCGTGTGTGA * * 59738958 CACACGGGTAGACCACATGTCGGTGTGT 1 CACACGGGTAGACCACATGCCCGTGTGT 59738986 CATAGCCGTG Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 30 23 0.92 31 2 0.08 ACGTcount: A:0.21, C:0.28, G:0.31, T:0.21 Consensus pattern (30 bp): CACACGGGTAGACCACATGCCCGTGTGTGA Found at i:59744947 original size:325 final size:325 Alignment explanation

Indices: 59744357--59745007 Score: 1284 Period size: 325 Copynumber: 2.0 Consensus size: 325 59744347 AAATTTTAAG 59744357 TAGGAGGTCCTTAAATATTAATTAAACCATTGTATAACTTTTTGGACAAAAATGGCCTTGTTTGG 1 TAGGAGGTCCTTAAATATTAATTAAACCATTGTATAACTTTTTGGACAAAAATGGCCTTGTTTGG 59744422 GTAAAATTTGAAAGAATAGTAAAAAGGACATTTTGGTCATTTAGGGGTAAAATGAATTAAAAGAC 66 GTAAAATTTGAAAGAATAGTAAAAAGGACATTTTGGTCATTTAGGGGTAAAATGAATTAAAAGAC 59744487 AAATTTTAAACCCCAAATGTGTCCCTCTCTTCTTGATACAATAGAATGTACCAAAAGCAGCCATG 131 AAATTTTAAACCCCAAATGTGTCCCTCTCTTCTTGATACAATAGAATGTACCAAAAGCAGCCATG 59744552 GTTAGGGTTTGGCCAAGCTTCCAAGCTTAATAGTAAGTGATTCCGAGCTCCGTTTTTAATGTTCT 196 GTTAGGGTTTGGCCAAGCTTCCAAGCTTAATAGTAAGTGATTCCGAGCTCCGTTTTTAATGTTCT * * 59744617 ATGTATTTTTGAAATCCCGGTAACATGATTTGCTCATTTCTACCATTATTTTGAGTTAGGATTTA 261 ATGTATTTTTGAAATCCCGGTAACATGATCTGCTCATTTCTACCATTATTTTGAGCTAGGATTTA 59744682 TAGGAGGTCCTTAAATATTAATTAAACCATTGTATAACTTTTTGGACAAAAATGGCCTTGTTTGG 1 TAGGAGGTCCTTAAATATTAATTAAACCATTGTATAACTTTTTGGACAAAAATGGCCTTGTTTGG 59744747 GTAAAATTTGAAAGAATAGTAAAAAGGACATTTTGGTCATTTAGGGGTAAAATGAATTAAAAGAC 66 GTAAAATTTGAAAGAATAGTAAAAAGGACATTTTGGTCATTTAGGGGTAAAATGAATTAAAAGAC 59744812 AAATTTTAAACCCCAAATGTGTCCCTCTCTTCTTGATACAATAGAATGTACCAAAAGCAGCCATG 131 AAATTTTAAACCCCAAATGTGTCCCTCTCTTCTTGATACAATAGAATGTACCAAAAGCAGCCATG 59744877 GTTAGGGTTTGGCCAAGCTTCCAAGCTTAATAGTAAGTGATTCCGAGCTCCGTTTTTAATGTTCT 196 GTTAGGGTTTGGCCAAGCTTCCAAGCTTAATAGTAAGTGATTCCGAGCTCCGTTTTTAATGTTCT 59744942 ATGTATTTTTGAAATCCCGGTAACATGATCTGCTCATTTCTACCATTATTTTGAGCTAGGATTTA 261 ATGTATTTTTGAAATCCCGGTAACATGATCTGCTCATTTCTACCATTATTTTGAGCTAGGATTTA 59745007 T 1 T 59745008 GTTTAAAAAT Statistics Matches: 324, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 325 324 1.00 ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35 Consensus pattern (325 bp): TAGGAGGTCCTTAAATATTAATTAAACCATTGTATAACTTTTTGGACAAAAATGGCCTTGTTTGG GTAAAATTTGAAAGAATAGTAAAAAGGACATTTTGGTCATTTAGGGGTAAAATGAATTAAAAGAC AAATTTTAAACCCCAAATGTGTCCCTCTCTTCTTGATACAATAGAATGTACCAAAAGCAGCCATG GTTAGGGTTTGGCCAAGCTTCCAAGCTTAATAGTAAGTGATTCCGAGCTCCGTTTTTAATGTTCT ATGTATTTTTGAAATCCCGGTAACATGATCTGCTCATTTCTACCATTATTTTGAGCTAGGATTTA Found at i:59745730 original size:49 final size:49 Alignment explanation

Indices: 59745641--59745877 Score: 202 Period size: 49 Copynumber: 4.9 Consensus size: 49 59745631 TCTATTGTGA * * * * * 59745641 GGTCACGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT 1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATT * * * 59745690 GGTCGCATGTGTAGTACTAAGTGCAGGCTATTATGCGTACCTGATAACTTT 1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA--TT * * * *** * ** 59745741 GATCACGTGTGTAGTACTAAGTGCAGGCTACGACATGTATCAGATGGTT 1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATT * * 59745790 AGGTCACGTGTGTAGTACTAAGTGCAGG------T--GTACCGGATAATT 1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATT * * 59745832 GGTCGCATGTGTAGTACTAAGTGAAGGCTACTATGCGTACCAGATA 1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA 59745878 GCTTTGGCTA Statistics Matches: 148, Mismatches: 29, Indels: 22 0.74 0.15 0.11 Matches are distributed among these distances: 41 24 0.16 42 9 0.06 47 1 0.01 49 51 0.34 50 26 0.18 51 37 0.25 ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29 Consensus pattern (49 bp): GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATT Found at i:59748533 original size:2 final size:2 Alignment explanation

Indices: 59748526--59748550 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 59748516 AACTGATTAT 59748526 AC AC AC AC AC AC AC AC AC AC AC AC A 1 AC AC AC AC AC AC AC AC AC AC AC AC A 59748551 TATATATGAA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:59751292 original size:51 final size:49 Alignment explanation

Indices: 59751171--59751414 Score: 274 Period size: 51 Copynumber: 4.9 Consensus size: 49 59751161 TATTGTGAGG * * * * 59751171 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGAATTATTGG 1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCG-ATAATTGA * ** * 59751220 TCGCAAGTGTAGTACTAAGTGCAGTCTACTATGCGTACCCGATAACTTCGA 1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAA-TT-GA * * * * * 59751271 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTATTGG 1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAATTGA * ** * 59751320 TCGCAAGTGTAGTACTAAGTGCAGTCTACTATGCGTACCCGATAACTTCGA 1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAA-TT-GA * 59751371 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA 1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATA 59751415 GCTTTGGCTG Statistics Matches: 159, Mismatches: 31, Indels: 8 0.80 0.16 0.04 Matches are distributed among these distances: 49 72 0.45 50 9 0.06 51 78 0.49 ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29 Consensus pattern (49 bp): TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAATTGA Found at i:59751409 original size:100 final size:100 Alignment explanation

Indices: 59751171--59751401 Score: 453 Period size: 100 Copynumber: 2.3 Consensus size: 100 59751161 TATTGTGAGG 59751171 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATTATTGGTCGCAAGTGTAGTACT 1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATTATTGGTCGCAAGTGTAGTACT 59751236 AAGTGCAGTCTACTATGCGTACCCGATAACTTCGA 66 AAGTGCAGTCTACTATGCGTACCCGATAACTTCGA * 59751271 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTATTGGTCGCAAGTGTAGTACT 1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATTATTGGTCGCAAGTGTAGTACT 59751336 AAGTGCAGTCTACTATGCGTACCCGATAACTTCGA 66 AAGTGCAGTCTACTATGCGTACCCGATAACTTCGA 59751371 TCACGTGTGTAGTACTAAGTGCAGGCTACTA 1 TCACGTGTGTAGTACTAAGTGCAGGCTACTA 59751402 TGCGTACCAG Statistics Matches: 130, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 100 130 1.00 ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29 Consensus pattern (100 bp): TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATTATTGGTCGCAAGTGTAGTACT AAGTGCAGTCTACTATGCGTACCCGATAACTTCGA Found at i:59752924 original size:48 final size:48 Alignment explanation

Indices: 59752848--59753035 Score: 268 Period size: 48 Copynumber: 3.9 Consensus size: 48 59752838 GGTAAATTAT * * * * * 59752848 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGC 1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGC * * * 59752896 CGATGCCATGTCCTAGACATGGTATTACACTAGCATACATATCAATGC 1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGC * * * * 59752944 CAATTCCATGTCTCAGACATGGTTTTACACTAGCACACATATCAATGC 1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGC 59752992 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCA 1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCA 59753036 CCCAATTGTC Statistics Matches: 122, Mismatches: 18, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 48 122 1.00 ACGTcount: A:0.28, C:0.29, G:0.18, T:0.26 Consensus pattern (48 bp): CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGC Found at i:59754342 original size:31 final size:31 Alignment explanation

Indices: 59754304--59754382 Score: 158 Period size: 31 Copynumber: 2.5 Consensus size: 31 59754294 TTTAACGGTT 59754304 ACTGGGCCGAAGCCTTTTCATAAATCATATC 1 ACTGGGCCGAAGCCTTTTCATAAATCATATC 59754335 ACTGGGCCGAAGCCTTTTCATAAATCATATC 1 ACTGGGCCGAAGCCTTTTCATAAATCATATC 59754366 ACTGGGCCGAAGCCTTT 1 ACTGGGCCGAAGCCTTT 59754383 ACTGTAAACG Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 31 48 1.00 ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28 Consensus pattern (31 bp): ACTGGGCCGAAGCCTTTTCATAAATCATATC Found at i:59754453 original size:42 final size:42 Alignment explanation

Indices: 59754406--59754497 Score: 148 Period size: 42 Copynumber: 2.2 Consensus size: 42 59754396 TGGCCCTTAG * ** * 59754406 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA 1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA 59754448 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA 1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA 59754490 GCCCATTT 1 GCCCATTT 59754498 GGGGAGACTA Statistics Matches: 46, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 42 46 1.00 ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29 Consensus pattern (42 bp): GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA Found at i:59754673 original size:25 final size:25 Alignment explanation

Indices: 59754645--59754714 Score: 113 Period size: 25 Copynumber: 2.8 Consensus size: 25 59754635 CTCTTTTAAT * 59754645 AACTGGGGCAAAGCCCTTTTTGATA 1 AACTGGGGCAAAGCCCTTTTCGATA * 59754670 AACTGGGGCAAAGCCCTTTTCGGTA 1 AACTGGGGCAAAGCCCTTTTCGATA * 59754695 AACTGGGGCATAGCCCTTTT 1 AACTGGGGCAAAGCCCTTTT 59754715 AGCACTTCCT Statistics Matches: 42, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 25 42 1.00 ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27 Consensus pattern (25 bp): AACTGGGGCAAAGCCCTTTTCGATA Found at i:59758072 original size:19 final size:19 Alignment explanation

Indices: 59758048--59758088 Score: 55 Period size: 19 Copynumber: 2.2 Consensus size: 19 59758038 AACCTTGTTT * 59758048 CGGTGATAGATACGGATTA 1 CGGTGACAGATACGGATTA * * 59758067 CGGTGACAGATATGGGTTA 1 CGGTGACAGATACGGATTA 59758086 CGG 1 CGG 59758089 ATGTTACATT Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.27, C:0.12, G:0.37, T:0.24 Consensus pattern (19 bp): CGGTGACAGATACGGATTA Found at i:59763308 original size:13 final size:13 Alignment explanation

Indices: 59763290--59763316 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 59763280 GAAGAAATTG 59763290 CACACGGGCGTGT 1 CACACGGGCGTGT 59763303 CACACGGGCGTGT 1 CACACGGGCGTGT 59763316 C 1 C 59763317 CCTGTTGAGC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15 Consensus pattern (13 bp): CACACGGGCGTGT Found at i:59767226 original size:56 final size:56 Alignment explanation

Indices: 59767166--59767301 Score: 247 Period size: 56 Copynumber: 2.4 Consensus size: 56 59767156 TCCCAGACAG * 59767166 GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGT 1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT 59767222 GGTCTTACTCGCACACATATA-CTGGAATCACATATCGATGCCAACGTATTAAACGT 1 GGTCTTACTCGCACACATATATC-GGAATCACATATCGATGCCAACGTATTAAACGT 59767278 GGTCTTACTCGCACACATATATCG 1 GGTCTTACTCGCACACATATATCG 59767302 ATGCCATGGT Statistics Matches: 77, Mismatches: 1, Indels: 4 0.94 0.01 0.05 Matches are distributed among these distances: 55 1 0.01 56 75 0.97 57 1 0.01 ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27 Consensus pattern (56 bp): GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT Found at i:59773395 original size:53 final size:53 Alignment explanation

Indices: 59773313--59773517 Score: 203 Period size: 53 Copynumber: 3.8 Consensus size: 53 59773303 CTTTCCTTTT * * * 59773313 TAAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTA 1 TAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA * * * * * * * 59773366 TGAACTCACCATTGCTATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTA 1 TAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA ** * * * * * 59773419 TCATAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTG 1 T-A-AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA ** * 59773474 TAAAACTTACCAATGCCATGCCTTGGTATGGTCTTACTTGGTAT 1 T-AAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTAT 59773518 TCTTAAAATA Statistics Matches: 118, Mismatches: 32, Indels: 3 0.77 0.21 0.02 Matches are distributed among these distances: 53 46 0.39 54 32 0.27 55 40 0.34 ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38 Consensus pattern (53 bp): TAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA Found at i:59776997 original size:44 final size:44 Alignment explanation

Indices: 59776947--59777030 Score: 123 Period size: 44 Copynumber: 1.9 Consensus size: 44 59776937 TCCCAGACAG 59776947 GGTCTTACTCACACACATATATCAGAAACACATATCGATGTCAA 1 GGTCTTACTCACACACATATATCAGAAACACATATCGATGTCAA * ** * * 59776991 GGTCTTACTCGCACACATATATTGGAATCATATATCGATG 1 GGTCTTACTCACACACATATATCAGAAACACATATCGATG 59777031 CCAACATATT Statistics Matches: 35, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 44 35 1.00 ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29 Consensus pattern (44 bp): GGTCTTACTCACACACATATATCAGAAACACATATCGATGTCAA Found at i:59786072 original size:49 final size:48 Alignment explanation

Indices: 59785920--59786240 Score: 226 Period size: 49 Copynumber: 6.7 Consensus size: 48 59785910 TAGGGACAAT * * * * 59785920 GCCGACGCCATGTTCCAAACATGGTCTTACACCGGCTCTCAC-ATCTAA 1 GCCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCACTATCTAA * * * * * * * * * 59785968 GTCGATGCCATGTCCTAGACATGCCTTACACTGACTTATGTA-TATCGAG 1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGC-TCT-CACTATCTAA * ** 59786017 GCCGATGCCATGTCCCAGACAAGTCTTACACTGGCTCTCACTTATCTGT 1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCAC-TATCTAA * * ** * * 59786066 GTCGATGCCATGTCCCAGATAGGTCTTACACT--AACACAC-CTC-AA 1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTATCTAA * * * * 59786110 GCCGATGCCATGTCCCAAACAGGTCTTACGCTAGCT-TGCA-TATCTTGAG 1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCT-CACTATC-T-AA * * * 59786159 GCCGGTGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTTATTTAT 1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCAC-TATCTAA ** * 59786208 GTTGATGCCATGTCCTAGACAGGTCTTACACTG 1 GCCGATGCCATGTCCCAGACAGGTCTTACACTG 59786241 ACACACACAT Statistics Matches: 207, Mismatches: 51, Indels: 29 0.72 0.18 0.10 Matches are distributed among these distances: 44 28 0.14 45 2 0.01 46 4 0.02 47 15 0.07 48 20 0.10 49 133 0.64 50 2 0.01 51 3 0.01 ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27 Consensus pattern (48 bp): GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTATCTAA Found at i:59786137 original size:93 final size:95 Alignment explanation

Indices: 59785920--59786190 Score: 257 Period size: 93 Copynumber: 2.8 Consensus size: 95 59785910 TAGGGACAAT * * * * * 59785920 GCCGACGCCATGTTCCAAACATGGTCTTACACCGGCTCTCAC-ATCTAAGTCGATGCCATGTCCT 1 GCCGATGCCATGTCCCAAACA-GGTCTTACACTGGCTCTCACTATCTGAGTCGATGCCATGTCCC * * * * * * 59785984 AGACATGCCTTACACTGACTTATGTATATCGAG 65 AGACAGGTCTTACACTAAC-TA-GCACATCGAA * * * 59786017 GCCGATGCCATGTCCCAGACAAGTCTTACACTGGCTCTCACTTATCTGTGTCGATGCCATGTCCC 1 GCCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCAC-TATCTGAGTCGATGCCATGTCCC * * 59786082 AGATAGGTCTTACACTAAC-A-CACCTC-AA 65 AGACAGGTCTTACACTAACTAGCACATCGAA * * * * 59786110 GCCGATGCCATGTCCCAAACAGGTCTTACGCTAGCT-TGCA-TATCTTGAGGCCGGTGCCATGTC 1 GCCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCT-CACTATC-TGA-GTCGATGCCATGTC 59786173 CCAGACAGGTCTTACACT 63 CCAGACAGGTCTTACACT 59786191 GGCTCTCACT Statistics Matches: 145, Mismatches: 24, Indels: 14 0.79 0.13 0.08 Matches are distributed among these distances: 91 4 0.03 92 3 0.02 93 64 0.44 94 3 0.02 96 19 0.13 97 18 0.12 98 34 0.23 ACGTcount: A:0.24, C:0.31, G:0.20, T:0.26 Consensus pattern (95 bp): GCCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCACTATCTGAGTCGATGCCATGTCCCA GACAGGTCTTACACTAACTAGCACATCGAA Found at i:59792703 original size:10 final size:12 Alignment explanation

Indices: 59792677--59792707 Score: 62 Period size: 12 Copynumber: 2.6 Consensus size: 12 59792667 CAGTATGCTC 59792677 CACACGGCCCAA 1 CACACGGCCCAA 59792689 CACACGGCCCAA 1 CACACGGCCCAA 59792701 CACACGG 1 CACACGG 59792708 ACATGTGACT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 19 1.00 ACGTcount: A:0.32, C:0.48, G:0.19, T:0.00 Consensus pattern (12 bp): CACACGGCCCAA Found at i:59792921 original size:8 final size:9 Alignment explanation

Indices: 59792890--59792930 Score: 55 Period size: 9 Copynumber: 4.2 Consensus size: 9 59792880 AGAATTGATT 59792890 AAAAAATAGA 1 AAAAAATA-A 59792900 AAACAAAGTAA 1 AAA-AAA-TAA 59792911 AAAAAATAA 1 AAAAAATAA 59792920 AAAAAATAA 1 AAAAAATAA 59792929 AA 1 AA 59792931 TTATAATGCA Statistics Matches: 29, Mismatches: 0, Indels: 5 0.85 0.00 0.15 Matches are distributed among these distances: 9 14 0.48 10 6 0.21 11 7 0.24 12 2 0.07 ACGTcount: A:0.83, C:0.02, G:0.05, T:0.10 Consensus pattern (9 bp): AAAAAATAA Found at i:59794421 original size:22 final size:22 Alignment explanation

Indices: 59794394--59794437 Score: 61 Period size: 22 Copynumber: 2.0 Consensus size: 22 59794384 GAAAATGATA * 59794394 AAAATTAATAAAAATTTATTAT 1 AAAATTAATAAAAATTCATTAT * * 59794416 AAAATTATTTAAAATTCATTAT 1 AAAATTAATAAAAATTCATTAT 59794438 GTTAATAATT Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 22 19 1.00 ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43 Consensus pattern (22 bp): AAAATTAATAAAAATTCATTAT Found at i:59794984 original size:56 final size:56 Alignment explanation

Indices: 59794922--59795036 Score: 196 Period size: 56 Copynumber: 2.1 Consensus size: 56 59794912 GTTGGTAACA * * 59794922 TAGAAACTTGAATCAATAGGTCTTTTAAATAGGTTGTT-ATGTGGCTAGGCTAGTGG 1 TAGAAACTTGAATCAATAGGTCTTTTAAATAGGTT-TTAACGTGGCTAGGCTAGGGG 59794978 TAGAAACTTGAATCAATAGGTCTTTTAAATAGGTTTTAACGTGGCTAGGCTAGGGG 1 TAGAAACTTGAATCAATAGGTCTTTTAAATAGGTTTTAACGTGGCTAGGCTAGGGG 59795034 TAG 1 TAG 59795037 GTAAAAGATA Statistics Matches: 56, Mismatches: 2, Indels: 2 0.93 0.03 0.03 Matches are distributed among these distances: 55 2 0.04 56 54 0.96 ACGTcount: A:0.30, C:0.10, G:0.27, T:0.34 Consensus pattern (56 bp): TAGAAACTTGAATCAATAGGTCTTTTAAATAGGTTTTAACGTGGCTAGGCTAGGGG Found at i:59802188 original size:52 final size:49 Alignment explanation

Indices: 59802056--59802284 Score: 170 Period size: 50 Copynumber: 4.8 Consensus size: 49 59802046 TGGTAGTACG * * * * * 59802056 TGTGATCCTATGTAAGACTATATCTGGGATATGGCATTGGCATCAACATG 1 TGTGATCCTATGTAAGACCATATCTGGGACATGGCATTGGCAT-GATATA * * * * * * 59802106 TGTGGTCCCATGTAAGACGATGTTTAGGACATGGCATTGGCACTGATATTTA 1 TGTGATCCTATGTAAGACCATATCTGGGACATGGCATTGGCA-TGATA--TA * * 59802158 TGTGATCCTATGTAAGACCATGTCTGGGACATGGAATTGGCATCGATATA 1 TGTGATCCTATGTAAGACCATATCTGGGACATGGCATTGGCAT-GATATA * * * * 59802208 TCTTAT-C-ATGTAAGACCATATCTGGGATATGGC----G-TTG--ATA 1 TGTGATCCTATGTAAGACCATATCTGGGACATGGCATTGGCATGATATA * * * 59802248 TGAGATCCTATATAAGACCATGTCTGGGACATGGCAT 1 TGTGATCCTATGTAAGACCATATCTGGGACATGGCAT 59802285 CAGTATAATT Statistics Matches: 143, Mismatches: 28, Indels: 22 0.74 0.15 0.11 Matches are distributed among these distances: 40 6 0.04 41 1 0.01 42 24 0.17 43 1 0.01 44 1 0.01 48 23 0.16 49 1 0.01 50 43 0.30 51 2 0.01 52 41 0.29 ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31 Consensus pattern (49 bp): TGTGATCCTATGTAAGACCATATCTGGGACATGGCATTGGCATGATATA Found at i:59802443 original size:48 final size:48 Alignment explanation

Indices: 59802059--59802443 Score: 182 Period size: 48 Copynumber: 8.0 Consensus size: 48 59802049 TAGTACGTGT * * * * * * * 59802059 GATCCTATGTAAGACTATATCTGGGATATGGCATTGGCATCAACATGTGT 1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC--GATATGA * * * * * 59802109 GGTCCCATGTAAGACGATGTTTAGGACATGGCATTGGCA-CTGATATTTATGT 1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC-G--A--TATGA * * 59802161 GATCCTATGTAAGACCATGTCTGGGACATGGAATTGGCATCGATAT-A 1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGA ** ** * * * 59802208 TCTTATCATGTAAGACCATATCTGGG--AT---A-TGGCGTTGATATGA 1 -GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGA * * ** * * 59802251 GATCCTATATAAGACCATGTCTGGGACATGGCATCAGTAT-AATTATGA 1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA-TATGA * * * * * * ** * 59802299 GACCCCGTATAAGACCACGTCTAGGACCTGGCACCGGCGTCG-TATGA 1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGA * * * * * * * * 59802346 GGTCCCGTATAAGACCATATATGGGATATGGCATCGACA-CTGAGT-TGA 1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC-GA-TATGA * 59802394 GATCCCATGTAAGACCATGTCTGGTACATGGCATTGGCATCGATATGA 1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGA 59802442 GA 1 GA 59802444 CATCATTTAA Statistics Matches: 247, Mismatches: 68, Indels: 42 0.69 0.19 0.12 Matches are distributed among these distances: 42 28 0.11 43 2 0.01 44 2 0.01 46 3 0.01 47 37 0.15 48 99 0.40 49 3 0.01 50 34 0.14 52 38 0.15 53 1 0.00 ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28 Consensus pattern (48 bp): GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGA Found at i:59805154 original size:40 final size:40 Alignment explanation

Indices: 59805071--59805333 Score: 325 Period size: 40 Copynumber: 6.6 Consensus size: 40 59805061 TTGAATGCTG * * * * * * 59805071 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA * * * * * 59805111 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA 1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA 59805151 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA 59805191 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA * 59805231 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA * * * 59805271 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA * * * 59805310 ACCGGGCTATGTCCCGAAGGCATT 1 TCCGGGTTAAGTCCCGAAGGCATT 59805334 TGAACGAGGA Statistics Matches: 201, Mismatches: 19, Indels: 7 0.89 0.08 0.03 Matches are distributed among these distances: 39 35 0.17 40 158 0.79 41 8 0.04 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27 Consensus pattern (40 bp): TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA Found at i:59805353 original size:79 final size:80 Alignment explanation

Indices: 59805110--59805368 Score: 256 Period size: 80 Copynumber: 3.3 Consensus size: 80 59805100 AAGTGAATAT * * * * * * 59805110 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT 1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT ** * * 59805174 TCGTGCGAGTTA-TTAA 65 TCGAACGAG-GAGCTAA * * * 59805190 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT 1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT ** ** * 59805255 CGTGCGAGTTGTTAA 66 CGAACGAGGAGCTAA * * * 59805270 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT 1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT * * 59805334 TGAACGAGGAGCTAT 66 CGAACGAGGAGCTAA * 59805349 ATCC-GGTTAAATCCCGAAGG 1 ATCCGGGTTAAGTCCCGAAGG 59805369 TACGTGATTT Statistics Matches: 156, Mismatches: 21, Indels: 6 0.85 0.11 0.03 Matches are distributed among these distances: 78 14 0.09 79 48 0.31 80 94 0.60 ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26 Consensus pattern (80 bp): ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT CGAACGAGGAGCTAA Found at i:59813107 original size:40 final size:40 Alignment explanation

Indices: 59813024--59813286 Score: 325 Period size: 40 Copynumber: 6.6 Consensus size: 40 59813014 TTGAATGCTG * * * * * * 59813024 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA * * * * * 59813064 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA 1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA 59813104 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA 59813144 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA * 59813184 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA * * * 59813224 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA * * * 59813263 ACCGGGCTATGTCCCGAAGGCATT 1 TCCGGGTTAAGTCCCGAAGGCATT 59813287 TGAACGAGGA Statistics Matches: 201, Mismatches: 19, Indels: 7 0.89 0.08 0.03 Matches are distributed among these distances: 39 35 0.17 40 158 0.79 41 8 0.04 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27 Consensus pattern (40 bp): TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA Found at i:59813306 original size:79 final size:80 Alignment explanation

Indices: 59813063--59813321 Score: 256 Period size: 80 Copynumber: 3.3 Consensus size: 80 59813053 AAGTGAATAT * * * * * * 59813063 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT 1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT ** * * 59813127 TCGTGCGAGTTA-TTAA 65 TCGAACGAG-GAGCTAA * * * 59813143 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT 1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT ** ** * 59813208 CGTGCGAGTTGTTAA 66 CGAACGAGGAGCTAA * * * 59813223 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT 1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT * * 59813287 TGAACGAGGAGCTAT 66 CGAACGAGGAGCTAA * 59813302 ATCC-GGTTAAATCCCGAAGG 1 ATCCGGGTTAAGTCCCGAAGG 59813322 TACGTGATTT Statistics Matches: 156, Mismatches: 21, Indels: 6 0.85 0.11 0.03 Matches are distributed among these distances: 78 14 0.09 79 48 0.31 80 94 0.60 ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26 Consensus pattern (80 bp): ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT CGAACGAGGAGCTAA Found at i:59817366 original size:45 final size:49 Alignment explanation

Indices: 59817201--59817375 Score: 141 Period size: 49 Copynumber: 3.7 Consensus size: 49 59817191 TAGGGTATAA * * * * * 59817201 TGCCGATACCATGTCCCAAACATGGTCTTACACTGACTATCA-A-AATCG 1 TGCCGATGCCATGTCCCAGACATGGTCTTACAGT-AGTATCACATACTCG * ** * * * 59817249 AGGCCGACACCATGTCCCAGACATGGTCTTACATTAGGTCTCACATATTCG 1 -TGCCGATGCCATGTCCCAGACATGGTCTTACAGTA-GTATCACATACTCG * 59817300 TGCCGATGCCATGTCCTAGACATGGTCTTACAGT-G-AT-ACAT-CTCG 1 TGCCGATGCCATGTCCCAGACATGGTCTTACAGTAGTATCACATACTCG * 59817345 TAGCCGATG-TATGTCCCAGACAT-GTCTTACA 1 T-GCCGATGCCATGTCCCAGACATGGTCTTACA 59817376 CTAGGTCTTG Statistics Matches: 106, Mismatches: 16, Indels: 13 0.79 0.12 0.10 Matches are distributed among these distances: 44 8 0.08 45 16 0.15 46 11 0.10 47 1 0.01 48 2 0.02 49 34 0.32 50 30 0.28 51 4 0.04 ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27 Consensus pattern (49 bp): TGCCGATGCCATGTCCCAGACATGGTCTTACAGTAGTATCACATACTCG Found at i:59820785 original size:39 final size:40 Alignment explanation

Indices: 59820714--59820858 Score: 172 Period size: 40 Copynumber: 3.6 Consensus size: 40 59820704 GCTCCTCGTT * * 59820714 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * 59820754 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA * * * * 59820793 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA 59820834 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 59820859 CATCATTCAA Statistics Matches: 90, Mismatches: 9, Indels: 12 0.81 0.08 0.11 Matches are distributed among these distances: 38 3 0.03 39 31 0.34 40 44 0.49 41 12 0.13 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA Found at i:59825757 original size:50 final size:50 Alignment explanation

Indices: 59825682--59825904 Score: 204 Period size: 50 Copynumber: 4.7 Consensus size: 50 59825672 TGAGGCTAAC * * 59825682 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCCGTGCCGAT 1 GCCATGTCCCAAACATAGTCTTACACTAGCTCTCGCATATCCGTGCCGAT * * * * * 59825732 GCCATGTCCTAAACATAGTCTTACACT-G---ACACATCT-CGTAGCCAAT 1 GCCATGTCCCAAACATAGTCTTACACTAGCTCTCGCATATCCGT-GCCGAT * 59825778 G-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGCATATCCGTGCCGAT 1 GCCATGTCCCAAACATAGTCTTACACTAGCTCTCGCATATCCGTGCCGAT * * * * * 59825826 GCCATGTCCTAAACATAGTCTTACACT-G---ACACATCT-CGTAGCCAAT 1 GCCATGTCCCAAACATAGTCTTACACTAGCTCTCGCATATCCGT-GCCGAT * 59825872 G-CATGTCCCAGACAT-GTCTTACACTAGCTCTCG 1 GCCATGTCCCAAACATAGTCTTACACTAGCTCTCG 59825905 TCTCAATGCC Statistics Matches: 137, Mismatches: 23, Indels: 28 0.73 0.12 0.15 Matches are distributed among these distances: 44 20 0.15 45 32 0.23 46 22 0.16 48 12 0.09 49 17 0.12 50 34 0.25 ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26 Consensus pattern (50 bp): GCCATGTCCCAAACATAGTCTTACACTAGCTCTCGCATATCCGTGCCGAT Found at i:59825799 original size:44 final size:45 Alignment explanation

Indices: 59825734--59825896 Score: 179 Period size: 45 Copynumber: 3.6 Consensus size: 45 59825724 GTGCCGATGC * 59825734 CATGTCCTAAACATAGTCTTACACTGACACATCTCGTAGCCAATG 1 CATGTCCCAAACATAGTCTTACACTGACACATCTCGTAGCCAATG * * * * * 59825779 CATGTCCCAGACAT-GTCTTACACTAGCTCTCGCATATCCGT-GCCGATG 1 CATGTCCCAAACATAGTCTTACACT-G---ACACATCT-CGTAGCCAATG * 59825827 CCATGTCCTAAACATAGTCTTACACTGACACATCTCGTAGCCAATG 1 -CATGTCCCAAACATAGTCTTACACTGACACATCTCGTAGCCAATG * 59825873 CATGTCCCAGACAT-GTCTTACACT 1 CATGTCCCAAACATAGTCTTACACT 59825897 AGCTCTCGTC Statistics Matches: 96, Mismatches: 14, Indels: 17 0.76 0.11 0.13 Matches are distributed among these distances: 44 20 0.21 45 28 0.29 46 11 0.11 48 11 0.11 49 16 0.17 50 10 0.10 ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27 Consensus pattern (45 bp): CATGTCCCAAACATAGTCTTACACTGACACATCTCGTAGCCAATG Found at i:59825813 original size:94 final size:94 Alignment explanation

Indices: 59825684--59825904 Score: 433 Period size: 94 Copynumber: 2.3 Consensus size: 94 59825674 AGGCTAACGC 59825684 CATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCCGTGCCGATGCCATGTCCTAAACATA 1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCGCATATCCGTGCCGATGCCATGTCCTAAACATA 59825749 GTCTTACACTGACACATCTCGTAGCCAATG 65 GTCTTACACTGACACATCTCGTAGCCAATG 59825779 CATGTCCCAGACATGTCTTACACTAGCTCTCGCATATCCGTGCCGATGCCATGTCCTAAACATAG 1 CATGTCCCAGACATGTCTTACACTAGCTCTCGCATATCCGTGCCGATGCCATGTCCTAAACATAG 59825844 TCTTACACTGACACATCTCGTAGCCAATG 66 TCTTACACTGACACATCTCGTAGCCAATG 59825873 CATGTCCCAGACATGTCTTACACTAGCTCTCG 1 CATGTCCCAGACATGTCTTACACTAGCTCTCG 59825905 TCTCAATGCC Statistics Matches: 126, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 94 112 0.89 95 14 0.11 ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27 Consensus pattern (94 bp): CATGTCCCAGACATGTCTTACACTAGCTCTCGCATATCCGTGCCGATGCCATGTCCTAAACATAG TCTTACACTGACACATCTCGTAGCCAATG Found at i:59826134 original size:29 final size:29 Alignment explanation

Indices: 59826092--59826151 Score: 111 Period size: 29 Copynumber: 2.1 Consensus size: 29 59826082 ATCATACATA 59826092 ATCATTTCCACAAACAAGCAATTTATGCT 1 ATCATTTCCACAAACAAGCAATTTATGCT * 59826121 ATCATTTTCACAAACAAGCAATTTATGCT 1 ATCATTTCCACAAACAAGCAATTTATGCT 59826150 AT 1 AT 59826152 ATCAATTCAA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 29 30 1.00 ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33 Consensus pattern (29 bp): ATCATTTCCACAAACAAGCAATTTATGCT Found at i:59831065 original size:46 final size:46 Alignment explanation

Indices: 59831015--59831187 Score: 219 Period size: 46 Copynumber: 3.7 Consensus size: 46 59831005 TGGTTGAGCA 59831015 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 59831061 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G * 59831106 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * 59831154 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA 59831188 GGGGCGGGTT Statistics Matches: 109, Mismatches: 9, Indels: 18 0.80 0.07 0.13 Matches are distributed among these distances: 42 2 0.02 43 5 0.05 45 3 0.03 46 61 0.56 47 29 0.27 48 3 0.03 50 4 0.04 51 2 0.02 ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29 Consensus pattern (46 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG Found at i:59831171 original size:93 final size:93 Alignment explanation

Indices: 59831012--59831182 Score: 315 Period size: 93 Copynumber: 1.8 Consensus size: 93 59831002 GGATGGTTGA * * 59831012 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 59831077 TGAGTCCGAGTTCGTGAGATGTAACTAG 66 TGAGTCCGAGTTCGTGAGATGTAACTAG * 59831105 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 59831170 TGAGTCCGAGTTC 66 TGAGTCCGAGTTC 59831183 ACTTAGGGGC Statistics Matches: 75, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 75 1.00 ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT TGAGTCCGAGTTCGTGAGATGTAACTAG Found at i:59834342 original size:42 final size:44 Alignment explanation

Indices: 59834291--59834407 Score: 134 Period size: 43 Copynumber: 2.7 Consensus size: 44 59834281 ATGCAATTCA ** 59834291 ATATCGATGCCTCTGTCCCAGACAGGGTCTTATACG-AAATCAG 1 ATATCGATGCCGATGTCCCAGACAGGGTCTTATACGTAAATCAG * * ** 59834334 ATAT-GATGCCGATGTCCTAGACATGGTCTTATACGTAAATCTC 1 ATATCGATGCCGATGTCCCAGACAGGGTCTTATACGTAAATCAG * 59834377 A-ATCGA-GCCCGATGTCCCAGACACGGTCTTA 1 ATATCGATG-CCGATGTCCCAGACAGGGTCTTA 59834408 CACGATATCT Statistics Matches: 63, Mismatches: 8, Indels: 6 0.82 0.10 0.08 Matches are distributed among these distances: 42 30 0.48 43 33 0.52 ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26 Consensus pattern (44 bp): ATATCGATGCCGATGTCCCAGACAGGGTCTTATACGTAAATCAG Found at i:59840320 original size:27 final size:27 Alignment explanation

Indices: 59840289--59840466 Score: 205 Period size: 27 Copynumber: 6.6 Consensus size: 27 59840279 TAAATTGTAC 59840289 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * ** * 59840316 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 59840342 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGATTTGACTATGT * 59840370 GGCACTAAGTGTGCGAGTTTGACTATGT 1 AGCACTAAGTGTGCGA-TTTGACTATGT * * 59840398 AGCACTAAGTGTGCGATTTGATTACGT 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 59840425 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGACTATGT * 59840452 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 59840467 GACTCAATAT Statistics Matches: 129, Mismatches: 19, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 27 106 0.82 28 23 0.18 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGACTATGT Found at i:59840403 original size:82 final size:81 Alignment explanation

Indices: 59840290--59840445 Score: 233 Period size: 82 Copynumber: 1.9 Consensus size: 81 59840280 AAATTGTACA * * 59840290 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG 1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG 59840354 TGCGAATTGACCATGCG 65 TGCGAATTGACCATGCG ** * 59840371 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG 1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG * 59840436 TGCGAGTTGA 65 TGCGAATTGA 59840446 TTATATAGCA Statistics Matches: 67, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 81 15 0.22 82 51 0.76 83 1 0.01 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29 Consensus pattern (81 bp): GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT GCGAATTGACCATGCG Found at i:59840457 original size:82 final size:81 Alignment explanation

Indices: 59840286--59840466 Score: 229 Period size: 82 Copynumber: 2.2 Consensus size: 81 59840276 GATTAAATTG * * 59840286 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA 1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA 59840351 GTGTGCGAATTGACCA 66 GTGTGCGAATTGACCA * * ** * 59840367 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT 1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT * ** 59840431 AAGTGTGCGAGTTGATTA 64 AAGTGTGCGAATTGACCA * * 59840449 TATAGCACTGAGTGTGCG 1 TACAGCACTAAGTGTGCG 59840467 GACTCAATAT Statistics Matches: 84, Mismatches: 14, Indels: 3 0.83 0.14 0.03 Matches are distributed among these distances: 81 18 0.21 82 66 0.79 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (81 bp): TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA GTGTGCGAATTGACCA Found at i:59848383 original size:27 final size:27 Alignment explanation

Indices: 59848352--59848529 Score: 205 Period size: 27 Copynumber: 6.6 Consensus size: 27 59848342 TAAATTGTAC 59848352 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * ** * 59848379 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 59848405 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGATTTGACTATGT * 59848433 GGCACTAAGTGTGCGAGTTTGACTATGT 1 AGCACTAAGTGTGCGA-TTTGACTATGT * * 59848461 AGCACTAAGTGTGCGATTTGATTACGT 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 59848488 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGACTATGT * 59848515 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 59848530 GACTCAATAT Statistics Matches: 129, Mismatches: 19, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 27 106 0.82 28 23 0.18 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGACTATGT Found at i:59848466 original size:82 final size:81 Alignment explanation

Indices: 59848353--59848508 Score: 233 Period size: 82 Copynumber: 1.9 Consensus size: 81 59848343 AAATTGTACA * * 59848353 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG 1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG 59848417 TGCGAATTGACCATGCG 65 TGCGAATTGACCATGCG ** * 59848434 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG 1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG * 59848499 TGCGAGTTGA 65 TGCGAATTGA 59848509 TTATATAGCA Statistics Matches: 67, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 81 15 0.22 82 51 0.76 83 1 0.01 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29 Consensus pattern (81 bp): GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT GCGAATTGACCATGCG Found at i:59848520 original size:82 final size:81 Alignment explanation

Indices: 59848349--59848529 Score: 229 Period size: 82 Copynumber: 2.2 Consensus size: 81 59848339 GATTAAATTG * * 59848349 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA 1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA 59848414 GTGTGCGAATTGACCA 66 GTGTGCGAATTGACCA * * ** * 59848430 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT 1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT * ** 59848494 AAGTGTGCGAGTTGATTA 64 AAGTGTGCGAATTGACCA * * 59848512 TATAGCACTGAGTGTGCG 1 TACAGCACTAAGTGTGCG 59848530 GACTCAATAT Statistics Matches: 84, Mismatches: 14, Indels: 3 0.83 0.14 0.03 Matches are distributed among these distances: 81 18 0.21 82 66 0.79 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (81 bp): TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA GTGTGCGAATTGACCA Found at i:59853837 original size:48 final size:47 Alignment explanation

Indices: 59853755--59853938 Score: 233 Period size: 48 Copynumber: 3.9 Consensus size: 47 59853745 CAATTGGGTA * * * 59853755 ATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCAC 1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC * * * * 59853802 ATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTG 1 A-TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTC * 59853851 ATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC 1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC * * ** 59853898 GACATGTGAACTAGTGTAAGACCATGTCTGAAACATGGCAT 1 -ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCAT 59853939 TAGCAATTTA Statistics Matches: 117, Mismatches: 17, Indels: 5 0.84 0.12 0.04 Matches are distributed among these distances: 47 2 0.02 48 114 0.97 49 1 0.01 ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25 Consensus pattern (47 bp): ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC Found at i:59853919 original size:96 final size:96 Alignment explanation

Indices: 59853755--59853938 Score: 271 Period size: 96 Copynumber: 1.9 Consensus size: 96 59853745 CAATTGGGTA * * 59853755 ATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACATTATGAGAGCCAGTGTA 1 ATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACATCATGAGAACCAGTGTA ** 59853820 AGACCATGTCTGGGACATGGCATCGGCGTTG 66 AGACCATGTCTGAAACATGGCATCGGCGTTG * * * * * 59853851 ATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-CATGTGAACTAGTGT 1 ATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCAC-ATCATGAGAACCAGTGT 59853915 AAGACCATGTCTGAAACATGGCAT 65 AAGACCATGTCTGAAACATGGCAT 59853939 TAGCAATTTA Statistics Matches: 78, Mismatches: 9, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 96 77 0.99 97 1 0.01 ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25 Consensus pattern (96 bp): ATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACATCATGAGAACCAGTGTA AGACCATGTCTGAAACATGGCATCGGCGTTG Found at i:59862049 original size:12 final size:12 Alignment explanation

Indices: 59862032--59862056 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 59862022 TGGACAAAAA 59862032 TTGGCTTTTAAT 1 TTGGCTTTTAAT 59862044 TTGGCTTTTAAT 1 TTGGCTTTTAAT 59862056 T 1 T 59862057 CATTTAATAA 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:0.16, C:0.08, G:0.16, T:0.60 Consensus pattern (12 bp): TTGGCTTTTAAT Found at i:59863991 original size:89 final size:89 Alignment explanation

Indices: 59863831--59864151 Score: 480 Period size: 89 Copynumber: 3.6 Consensus size: 89 59863821 TAAAATTACA * * * * 59863831 ATGGTTGTCACCATCCCTTTTCATAGTTTGATAGCTGAAGCTATCCCTTTTCATATTTCGATAGT 1 ATGGTTGTCACCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTCGATGGT * * * 59863896 CATCACCATCCCTTTTCATTGTTG 66 CGTCACCATCCTTTTTCATGGTTG * 59863920 ATGGTTGTCACCATCCCTTTTCATAATTCGATAGCCGAAGTTATCCCTTTTCATATTTCGATGGT 1 ATGGTTGTCACCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTCGATGGT 59863985 CGTCACCATCCTTTTTCATGGTTG 66 CGTCACCATCCTTTTTCATGGTTG * * * * 59864009 ATGGTTGTCACCATCCCATTTCATAATTCGATAGCCAAAGCTATCCCTTTCCATAGTTCGATGGT 1 ATGGTTGTCACCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTCGATGGT * 59864074 CGTCACTATCCTTTTTCATGGTTG 66 CGTCACCATCCTTTTTCATGGTTG * * * * * 59864098 ATGGTCGCCACCATCCCTTTTCATATTTTGATAGCCGAAGTTATCCCTTTTCAT 1 ATGGTTGTCACCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCAT 59864152 TGGTTGATGA Statistics Matches: 210, Mismatches: 22, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 89 210 1.00 ACGTcount: A:0.20, C:0.26, G:0.15, T:0.40 Consensus pattern (89 bp): ATGGTTGTCACCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTCGATGGT CGTCACCATCCTTTTTCATGGTTG Found at i:59864129 original size:30 final size:30 Alignment explanation

Indices: 59863831--59864122 Score: 211 Period size: 30 Copynumber: 9.8 Consensus size: 30 59863821 TAAAATTACA * * 59863831 ATGGTTGTCACCATCCCTTTTCATAGTTTG 1 ATGGTCGTCACCATCCCTTTTCATAGTTCG * * * * 59863861 ATAG-C-TGAAGCTATCCCTTTTCATATTTCG 1 ATGGTCGT-CA-CCATCCCTTTTCATAGTTCG * * * 59863891 ATAGTCATCACCATCCCTTTTCATTGTT-G 1 ATGGTCGTCACCATCCCTTTTCATAGTTCG * * 59863920 ATGGTTGTCACCATCCCTTTTCATAATTCG 1 ATGGTCGTCACCATCCCTTTTCATAGTTCG * * * ** * 59863950 ATAGCCG-AAGTTATCCCTTTTCATATTTCG 1 ATGGTCGTCA-CCATCCCTTTTCATAGTTCG * * 59863980 ATGGTCGTCACCATCCTTTTTCATGGTT-G 1 ATGGTCGTCACCATCCCTTTTCATAGTTCG * * * 59864009 ATGGTTGTCACCATCCCATTTCATAATTCG 1 ATGGTCGTCACCATCCCTTTTCATAGTTCG * *** * * 59864039 ATAG-CCAAAGCTATCCCTTTCCATAGTTCG 1 ATGGTCGTCA-CCATCCCTTTTCATAGTTCG * * * 59864069 ATGGTCGTCACTATCCTTTTTCATGGTT-G 1 ATGGTCGTCACCATCCCTTTTCATAGTTCG * 59864098 ATGGTCGCCACCATCCCTTTTCATA 1 ATGGTCGTCACCATCCCTTTTCATA 59864123 TTTTGATAGC Statistics Matches: 197, Mismatches: 55, Indels: 21 0.72 0.20 0.08 Matches are distributed among these distances: 28 1 0.01 29 73 0.37 30 117 0.59 31 5 0.03 32 1 0.01 ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39 Consensus pattern (30 bp): ATGGTCGTCACCATCCCTTTTCATAGTTCG Found at i:59864383 original size:21 final size:22 Alignment explanation

Indices: 59864359--59864402 Score: 63 Period size: 21 Copynumber: 2.0 Consensus size: 22 59864349 ATAAATACAA * * 59864359 TCAATTTAATCAATATTC-TAT 1 TCAATTCAATCAAAATTCATAT 59864380 TCAATTCAATCAAAATTCATAT 1 TCAATTCAATCAAAATTCATAT 59864402 T 1 T 59864403 TTTGTAAAAT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 21 16 0.80 22 4 0.20 ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43 Consensus pattern (22 bp): TCAATTCAATCAAAATTCATAT Found at i:59868216 original size:30 final size:30 Alignment explanation

Indices: 59868180--59868257 Score: 147 Period size: 30 Copynumber: 2.6 Consensus size: 30 59868170 TACAATGGTT 59868180 GTCACCATCCCTTTTCATATTTCAATAGCC 1 GTCACCATCCCTTTTCATATTTCAATAGCC * 59868210 GTCACCATCCCTTTTCATATTTCAATGGCC 1 GTCACCATCCCTTTTCATATTTCAATAGCC 59868240 GTCACCATCCCTTTTCAT 1 GTCACCATCCCTTTTCAT 59868258 TGTTGATGGT Statistics Matches: 47, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 30 47 1.00 ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37 Consensus pattern (30 bp): GTCACCATCCCTTTTCATATTTCAATAGCC Found at i:59868315 original size:30 final size:29 Alignment explanation

Indices: 59868276--59868436 Score: 128 Period size: 30 Copynumber: 5.4 Consensus size: 29 59868266 GTCATTGCCG 59868276 TCCCTTTTCATAATTCGATAGCAGAAGCTA 1 TCCCTTTTCATAATTCGATAGC-GAAGCTA * * * * * 59868306 TCCTTTTTCATATTTCGATGGTCGTCA-CCA 1 TCCCTTTTCATAATTCGATAG-CG-AAGCTA 59868336 TCCCTTTTCATAATTCGATAGCTGAAGCTA 1 TCCCTTTTCATAATTCGATAGC-GAAGCTA * * * * * 59868366 TCCCTTTTCATAGTTCGGTTGTTGTCA-CTA 1 TCCCTTTTCATAATTCGATAG-CG-AAGCTA * * * 59868396 TACCTTTTCACAATTAGATAGCCGAAGCTA 1 TCCCTTTTCATAATTCGATAG-CGAAGCTA 59868426 TCCCTTTTCAT 1 TCCCTTTTCAT 59868437 TGGTTGATGA Statistics Matches: 98, Mismatches: 26, Indels: 14 0.71 0.19 0.10 Matches are distributed among these distances: 29 3 0.03 30 92 0.94 31 3 0.03 ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39 Consensus pattern (29 bp): TCCCTTTTCATAATTCGATAGCGAAGCTA Found at i:59868346 original size:60 final size:60 Alignment explanation

Indices: 59868186--59868436 Score: 256 Period size: 60 Copynumber: 4.2 Consensus size: 60 59868176 GGTTGTCACC * * * * * * * * 59868186 ATCCCTTTTCATATTTCAATAGCCGTCACCATCCCTTTTCATATTTCAATGGCCGTCA-CC 1 ATCCCTTTTCATATTTCGATGGTCGTCACCATCCCTTTTCATAATTCGATAGCCG-AAGCT * ** * * 59868246 ATCCCTTTTCAT-TGTT-GATGGTCATTGCCGTCCCTTTTCATAATTCGATAGCAGAAGCT 1 ATCCCTTTTCATAT-TTCGATGGTCGTCACCATCCCTTTTCATAATTCGATAGCCGAAGCT * * 59868305 ATCCTTTTTCATATTTCGATGGTCGTCACCATCCCTTTTCATAATTCGATAGCTGAAGCT 1 ATCCCTTTTCATATTTCGATGGTCGTCACCATCCCTTTTCATAATTCGATAGCCGAAGCT * * * * * * * * 59868365 ATCCCTTTTCATAGTTCGGTTGTTGTCACTATACCTTTTCACAATTAGATAGCCGAAGCT 1 ATCCCTTTTCATATTTCGATGGTCGTCACCATCCCTTTTCATAATTCGATAGCCGAAGCT 59868425 ATCCCTTTTCAT 1 ATCCCTTTTCAT 59868437 TGGTTGATGA Statistics Matches: 158, Mismatches: 29, Indels: 8 0.81 0.15 0.04 Matches are distributed among these distances: 58 1 0.01 59 42 0.27 60 115 0.73 ACGTcount: A:0.22, C:0.27, G:0.13, T:0.39 Consensus pattern (60 bp): ATCCCTTTTCATATTTCGATGGTCGTCACCATCCCTTTTCATAATTCGATAGCCGAAGCT Found at i:59868694 original size:21 final size:19 Alignment explanation

Indices: 59868648--59868695 Score: 51 Period size: 21 Copynumber: 2.4 Consensus size: 19 59868638 CTAAATGAAT * 59868648 AAATTCAATCAATTTAATC 1 AAATTCAATCAATTCAATC * 59868667 AATATTCTATTCAATTCAATCC 1 AA-ATTC-AATCAATTCAAT-C 59868689 AAATTCA 1 AAATTCA 59868696 CATTTTTGTA Statistics Matches: 24, Mismatches: 2, Indels: 5 0.77 0.06 0.16 Matches are distributed among these distances: 19 2 0.08 20 5 0.21 21 14 0.58 22 3 0.12 ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38 Consensus pattern (19 bp): AAATTCAATCAATTCAATC Found at i:59872640 original size:17 final size:17 Alignment explanation

Indices: 59872614--59872651 Score: 69 Period size: 17 Copynumber: 2.3 Consensus size: 17 59872604 AAGTGAGGTT 59872614 AATT-TAGTAATTAATA 1 AATTATAGTAATTAATA 59872630 AATTATAGTAATTAATA 1 AATTATAGTAATTAATA 59872647 AATTA 1 AATTA 59872652 ACTTTAAAAT Statistics Matches: 21, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 16 4 0.19 17 17 0.81 ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42 Consensus pattern (17 bp): AATTATAGTAATTAATA Found at i:59876750 original size:44 final size:41 Alignment explanation

Indices: 59876682--59876838 Score: 176 Period size: 44 Copynumber: 3.7 Consensus size: 41 59876672 ATGTGTTATT * 59876682 GTGTTAGACCACGTCTGGGACGTTGGCATCGACTTATGATTTAC 1 GTGTAAGACCACGTCTGGGACGTTGGCATCGA-TT-TGA-TTAC * 59876726 GTGTAAGACCATGTCTGGGACGTTGGCATCGTATTTGATT-C 1 GTGTAAGACCACGTCTGGGACGTTGGCATCG-ATTTGATTAC * 59876767 GTGTAAGACC-CTGTCTGGAACAG-TGGCATCGATATTTGATTAC 1 GTGTAAGACCAC-GTCTGGGAC-GTTGGCATCG--ATTTGATTAC * * 59876810 ATGTAAGACCACGTCTGGGATGTTGGCAT 1 GTGTAAGACCACGTCTGGGACGTTGGCAT 59876839 TGTACGAGCT Statistics Matches: 99, Mismatches: 7, Indels: 15 0.82 0.06 0.12 Matches are distributed among these distances: 41 27 0.27 42 13 0.13 43 26 0.26 44 32 0.32 45 1 0.01 ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31 Consensus pattern (41 bp): GTGTAAGACCACGTCTGGGACGTTGGCATCGATTTGATTAC Found at i:59876782 original size:41 final size:42 Alignment explanation

Indices: 59876694--59876838 Score: 172 Period size: 41 Copynumber: 3.4 Consensus size: 42 59876684 GTTAGACCAC * 59876694 GTCTGGGACGTTGGCATCG-ACTTATGATTTACGTGTAAGACCAT 1 GTCTGGGACGTTGGCATCGTA-TT-TGA-TTACGTGTAAGACCCT 59876738 GTCTGGGACGTTGGCATCGTATTTGATT-CGTGTAAGACCCT 1 GTCTGGGACGTTGGCATCGTATTTGATTACGTGTAAGACCCT * * 59876779 GTCTGGAACAG-TGGCATCGATATTTGATTACATGTAAGACCAC- 1 GTCTGGGAC-GTTGGCATCG-TATTTGATTACGTGTAAGACC-CT * 59876822 GTCTGGGATGTTGGCAT 1 GTCTGGGACGTTGGCAT 59876839 TGTACGAGCT Statistics Matches: 90, Mismatches: 5, Indels: 13 0.83 0.05 0.12 Matches are distributed among these distances: 41 28 0.31 42 13 0.14 43 26 0.29 44 22 0.24 45 1 0.01 ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32 Consensus pattern (42 bp): GTCTGGGACGTTGGCATCGTATTTGATTACGTGTAAGACCCT Found at i:59878907 original size:79 final size:82 Alignment explanation

Indices: 59878796--59878980 Score: 238 Period size: 79 Copynumber: 2.3 Consensus size: 82 59878786 GCTACTCGTT * * 59878796 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC * * 59878859 GGATTTAGTAAC-TCGCA 65 GGATATAGTAACTTAGCA * ** 59878876 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG * * 59878939 GATATGGTCACTTAGCA 66 GATATAGTAACTTAGCA 59878956 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 59878981 CATCATTCAA Statistics Matches: 92, Mismatches: 9, Indels: 8 0.84 0.08 0.07 Matches are distributed among these distances: 78 3 0.03 79 55 0.60 80 34 0.37 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24 Consensus pattern (82 bp): CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG GATATAGTAACTTAGCA Found at i:59878980 original size:40 final size:40 Alignment explanation

Indices: 59878777--59878980 Score: 238 Period size: 40 Copynumber: 5.1 Consensus size: 40 59878767 CGGAATTTAA ** * 59878777 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC 1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC * * 59878817 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * 59878857 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * * 59878896 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT 1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC * * * 59878936 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC 1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC 59878976 CCGGA 1 CCGGA 59878981 CATCATTCAA Statistics Matches: 141, Mismatches: 16, Indels: 14 0.82 0.09 0.08 Matches are distributed among these distances: 38 2 0.01 39 33 0.23 40 94 0.67 41 12 0.09 ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25 Consensus pattern (40 bp): CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC Found at i:59886848 original size:79 final size:78 Alignment explanation

Indices: 59886746--59886968 Score: 272 Period size: 79 Copynumber: 2.8 Consensus size: 78 59886736 GCTCCTCGTT * * 59886746 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG 1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG * 59886811 ATTTAGTAACTCGCA 64 AATTAGTAACTCGCA * * 59886826 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA 1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA * 59886890 ATTAGTATCTCGCA 65 ATTAGTAACTCGCA * * * * * 59886904 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG 1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG 59886967 GA 63 GA 59886969 CATCATTCAA Statistics Matches: 125, Mismatches: 13, Indels: 11 0.84 0.09 0.07 Matches are distributed among these distances: 78 45 0.36 79 60 0.48 80 20 0.16 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25 Consensus pattern (78 bp): CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA TTAGTAACTCGCA Found at i:59886863 original size:39 final size:40 Alignment explanation

Indices: 59886746--59886968 Score: 280 Period size: 39 Copynumber: 5.7 Consensus size: 40 59886736 GCTCCTCGTT * * 59886746 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA * * 59886786 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA * 59886826 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA * 59886865 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA * * * 59886904 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA 59886945 C-AA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 59886969 CATCATTCAA Statistics Matches: 167, Mismatches: 10, Indels: 13 0.88 0.05 0.07 Matches are distributed among these distances: 38 2 0.01 39 88 0.53 40 67 0.40 41 10 0.06 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA Found at i:59899857 original size:11 final size:11 Alignment explanation

Indices: 59899821--59899876 Score: 57 Period size: 11 Copynumber: 5.5 Consensus size: 11 59899811 CATGGTATGT 59899821 ATGATATGCAC 1 ATGATATGCAC * * 59899832 ATGACATG--T 1 ATGATATGCAC 59899841 ATGATATGCAC 1 ATGATATGCAC * 59899852 ATGATATG--T 1 ATGATATGCAC 59899861 ATGATATGCAC 1 ATGATATGCAC 59899872 ATGAT 1 ATGAT 59899877 GTATTCATAA Statistics Matches: 35, Mismatches: 6, Indels: 8 0.71 0.12 0.16 Matches are distributed among these distances: 9 15 0.43 11 20 0.57 ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32 Consensus pattern (11 bp): ATGATATGCAC Found at i:59899876 original size:20 final size:20 Alignment explanation

Indices: 59899810--59899876 Score: 116 Period size: 20 Copynumber: 3.4 Consensus size: 20 59899800 ATTTTGATAA * 59899810 ACATGGTATGTATGATATGC 1 ACATGATATGTATGATATGC * 59899830 ACATGACATGTATGATATGC 1 ACATGATATGTATGATATGC 59899850 ACATGATATGTATGATATGC 1 ACATGATATGTATGATATGC 59899870 ACATGAT 1 ACATGAT 59899877 GTATTCATAA Statistics Matches: 44, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 44 1.00 ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33 Consensus pattern (20 bp): ACATGATATGTATGATATGC Found at i:59899952 original size:24 final size:24 Alignment explanation

Indices: 59899925--59900020 Score: 142 Period size: 24 Copynumber: 4.0 Consensus size: 24 59899915 GGAGGAAGAG 59899925 TAAAAGGGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTAT 59899949 T-AAAGGGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTAT * 59899972 TAAAAGGGCTTTTGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTAT * 59899996 TAAAAGAGGC-TAGGCCTCCAGTTAT 1 TAAAAG-GGCTTATGCC-CCAGTTAT 59900021 ATGATAAAGC Statistics Matches: 66, Mismatches: 3, Indels: 5 0.89 0.04 0.07 Matches are distributed among these distances: 23 23 0.35 24 32 0.48 25 11 0.17 ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29 Consensus pattern (24 bp): TAAAAGGGCTTATGCCCCAGTTAT Found at i:59899956 original size:23 final size:23 Alignment explanation

Indices: 59899927--59899999 Score: 128 Period size: 23 Copynumber: 3.1 Consensus size: 23 59899917 AGGAAGAGTA 59899927 AAAGGGCTTATGCCCCAGTTATT 1 AAAGGGCTTATGCCCCAGTTATT 59899950 AAAGGGCTTATGCCCCAGTTATT 1 AAAGGGCTTATGCCCCAGTTATT * 59899973 AAAAGGGCTTTTGCCCCAGTTATT 1 -AAAGGGCTTATGCCCCAGTTATT 59899997 AAA 1 AAA 59900000 AGAGGCTAGG Statistics Matches: 48, Mismatches: 1, Indels: 2 0.94 0.02 0.04 Matches are distributed among these distances: 23 26 0.54 24 22 0.46 ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30 Consensus pattern (23 bp): AAAGGGCTTATGCCCCAGTTATT Found at i:59900247 original size:31 final size:31 Alignment explanation

Indices: 59900212--59900275 Score: 110 Period size: 31 Copynumber: 2.1 Consensus size: 31 59900202 CGTTTACAGT 59900212 AAAGGCTTCGGCCCAGTAATATGAAATATGA 1 AAAGGCTTCGGCCCAGTAATATGAAATATGA ** 59900243 AAAGGCTTCGGCCCAGTGTTATGAAATATGA 1 AAAGGCTTCGGCCCAGTAATATGAAATATGA 59900274 AA 1 AA 59900276 TATGAAAAGG Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 31 31 1.00 ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23 Consensus pattern (31 bp): AAAGGCTTCGGCCCAGTAATATGAAATATGA Found at i:59903080 original size:40 final size:40 Alignment explanation

Indices: 59903003--59903220 Score: 334 Period size: 40 Copynumber: 5.5 Consensus size: 40 59902993 AAACCAAGTA * * 59903003 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG 1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG * 59903042 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 59903082 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 59903122 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * * * 59903162 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATT 1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG 59903202 CCTTCGGGACTTAGCCCGG 1 CCTTCGGGACTTAGCCCGG 59903221 TTATCATCTG Statistics Matches: 167, Mismatches: 9, Indels: 5 0.92 0.05 0.03 Matches are distributed among these distances: 39 15 0.09 40 152 0.91 ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24 Consensus pattern (40 bp): CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG Found at i:59909801 original size:25 final size:24 Alignment explanation

Indices: 59909768--59909815 Score: 60 Period size: 25 Copynumber: 2.0 Consensus size: 24 59909758 TTATAACATG * * * 59909768 AAAAAGACCGTTTTGCCCCTAGGT 1 AAAAAGACCATTATACCCCTAGGT 59909792 AAAAATGACCATTATACCCCTAGG 1 AAAAA-GACCATTATACCCCTAGG 59909816 GTTTATATAT Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 24 5 0.25 25 15 0.75 ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23 Consensus pattern (24 bp): AAAAAGACCATTATACCCCTAGGT Found at i:59909881 original size:20 final size:20 Alignment explanation

Indices: 59909852--59909898 Score: 76 Period size: 20 Copynumber: 2.4 Consensus size: 20 59909842 ATTTTGATAA * * 59909852 ACATGGTATGTATGATATGC 1 ACATGATATGTATGATAGGC 59909872 ACATGATATGTATGATAGGC 1 ACATGATATGTATGATAGGC 59909892 ACATGAT 1 ACATGAT 59909899 GTATTCATAA Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 20 25 1.00 ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32 Consensus pattern (20 bp): ACATGATATGTATGATAGGC Found at i:59909976 original size:24 final size:24 Alignment explanation

Indices: 59909949--59910025 Score: 154 Period size: 24 Copynumber: 3.2 Consensus size: 24 59909939 GAGGAAGTGC 59909949 AAAAGGGCTTATGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT 59909973 AAAAGGGCTTATGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT 59909997 AAAAGGGCTTATGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT 59910021 AAAAG 1 AAAAG 59910026 NNNNNNNNNN Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 53 1.00 ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27 Consensus pattern (24 bp): AAAAGGGCTTATGCCCCAGTTATT Found at i:59917655 original size:33 final size:34 Alignment explanation

Indices: 59917608--59917674 Score: 93 Period size: 33 Copynumber: 2.0 Consensus size: 34 59917598 GTTTCAATTA * 59917608 GGATTTAGCATGGACT-AGTAATCCTAATT-GACT 1 GGATTTAGCATGGACTGA-TAATCCAAATTAGACT * 59917641 GGATTTAGCCTGGACTGATAATCCAAATTAGACT 1 GGATTTAGCATGGACTGATAATCCAAATTAGACT 59917675 CTATAGGGAA Statistics Matches: 30, Mismatches: 2, Indels: 3 0.86 0.06 0.09 Matches are distributed among these distances: 33 25 0.83 34 5 0.17 ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31 Consensus pattern (34 bp): GGATTTAGCATGGACTGATAATCCAAATTAGACT Found at i:59920144 original size:11 final size:11 Alignment explanation

Indices: 59920128--59920158 Score: 62 Period size: 11 Copynumber: 2.8 Consensus size: 11 59920118 GCCAGTTTTC 59920128 AATAACACAAA 1 AATAACACAAA 59920139 AATAACACAAA 1 AATAACACAAA 59920150 AATAACACA 1 AATAACACA 59920159 TTTGATTGTG Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.71, C:0.19, G:0.00, T:0.10 Consensus pattern (11 bp): AATAACACAAA Found at i:59920677 original size:46 final size:45 Alignment explanation

Indices: 59920588--59920798 Score: 214 Period size: 46 Copynumber: 4.6 Consensus size: 45 59920578 GTGTCAATGC * * * 59920588 CATGTCCCAGACATGGTCTTTCACTA-C-ACATCTCGTA-GCCGATG 1 CATGTCCCAGACAT-GTCTTACACTAGCTTCGTCTCG-AGGCCGATG * * 59920632 CTTGTCCCAGACATTTCTTACACTAGCTTACGTCTCGAGGCCGATG 1 CATGTCCCAGACATGTCTTACACTAGCTT-CGTCTCGAGGCCGATG * * * 59920678 CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATGCCGATG 1 CATGTCCCAGACATGTCTTACACTAGC-TTCGTCTCGAGGCCGATG * * * * * 59920724 CCATGTCCCAGACATGGTCTTACACTGGCTTCATAAT-GTGGCTGATG 1 -CATGTCCCAGACAT-GTCTTACACTAGCTTCGT-CTCGAGGCCGATG 59920771 CATGTCCCAGACATGTCTTACACTAGCT 1 CATGTCCCAGACATGTCTTACACTAGCT 59920799 CACATGAGTG Statistics Matches: 140, Mismatches: 19, Indels: 15 0.80 0.11 0.09 Matches are distributed among these distances: 43 9 0.06 44 14 0.10 45 14 0.10 46 66 0.47 47 24 0.17 48 13 0.09 ACGTcount: A:0.22, C:0.30, G:0.19, T:0.28 Consensus pattern (45 bp): CATGTCCCAGACATGTCTTACACTAGCTTCGTCTCGAGGCCGATG Found at i:59920733 original size:93 final size:90 Alignment explanation

Indices: 59920538--59920797 Score: 242 Period size: 93 Copynumber: 2.8 Consensus size: 90 59920528 ACATCGACGC * * * ** * * 59920538 CATGTCCCAGACATGGTCTTACACAAGTTTTAATATATCTGTGTCAATGCCATGTCCCAGACATG 1 CATGTCCCAGACATGGTCTTACACTAG-CTTCATA-ATGAG-GCCGATG-CATGTCCCAGACAT- * 59920603 GTCTTTCACTA-CACATCTCGTAGCCGATG 61 GTCTTACACTAGCACATCTCGTAGCCGATG * * * * 59920632 CTTGTCCCAGACAT-TTCTTACACTAGCTTACGT-CTCGAGGCCGATGCATGTCCCAGACATGTC 1 CATGTCCCAGACATGGTCTTACACTAGCTT-CATAAT-GAGGCCGATGCATGTCCCAGACATGTC 59920695 TTACACTAGCAC-TCGTC-TCAATGCCGATG 64 TTACACTAGCACATC-TCGT--A-GCCGATG * * * 59920724 CCATGTCCCAGACATGGTCTTACACTGGCTTCATAATGTGGCTGATGCATGTCCCAGACATGTCT 1 -CATGTCCCAGACATGGTCTTACACTAGCTTCATAATGAGGCCGATGCATGTCCCAGACATGTCT 59920789 TACACTAGC 65 TACACTAGC 59920798 TCACATGAGT Statistics Matches: 137, Mismatches: 19, Indels: 21 0.77 0.11 0.12 Matches are distributed among these distances: 89 13 0.09 90 19 0.14 91 7 0.05 92 10 0.07 93 61 0.45 94 27 0.20 ACGTcount: A:0.23, C:0.29, G:0.18, T:0.29 Consensus pattern (90 bp): CATGTCCCAGACATGGTCTTACACTAGCTTCATAATGAGGCCGATGCATGTCCCAGACATGTCTT ACACTAGCACATCTCGTAGCCGATG Found at i:59927481 original size:39 final size:39 Alignment explanation

Indices: 59927423--59927561 Score: 226 Period size: 39 Copynumber: 3.6 Consensus size: 39 59927413 TTGTGATCTG * * 59927423 AAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACGA 1 AAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGA 59927462 AAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAAC-A 1 AAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGA * * 59927500 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG 1 -AAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGA 59927540 AAGCCCGAAGGCTAACTGAAGC 1 AAGCCCGAAGGCTAACTGAAGC 59927562 TTATCAGAGC Statistics Matches: 94, Mismatches: 4, Indels: 4 0.92 0.04 0.04 Matches are distributed among these distances: 38 1 0.01 39 93 0.99 ACGTcount: A:0.39, C:0.24, G:0.24, T:0.12 Consensus pattern (39 bp): AAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGA Found at i:59934072 original size:46 final size:46 Alignment explanation

Indices: 59934015--59934106 Score: 157 Period size: 46 Copynumber: 2.0 Consensus size: 46 59934005 AGCTTCACTA * 59934015 GCACTCATCTCAATACCGATGCCATGTCCCAGACATGGTCTTACGC 1 GCACTCATCTCAATACCGATACCATGTCCCAGACATGGTCTTACGC * * 59934061 GCACTCGTCTCAATGCCGATACCATGTCCCAGACATGGTCTTACGC 1 GCACTCATCTCAATACCGATACCATGTCCCAGACATGGTCTTACGC 59934107 TGGCTCTCAT Statistics Matches: 43, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 46 43 1.00 ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24 Consensus pattern (46 bp): GCACTCATCTCAATACCGATACCATGTCCCAGACATGGTCTTACGC Found at i:59935990 original size:38 final size:38 Alignment explanation

Indices: 59935948--59936023 Score: 152 Period size: 38 Copynumber: 2.0 Consensus size: 38 59935938 GCATAGTCCA 59935948 AATATTTTTTTTCAATAAATTGTCAATCCTCCAAAAAT 1 AATATTTTTTTTCAATAAATTGTCAATCCTCCAAAAAT 59935986 AATATTTTTTTTCAATAAATTGTCAATCCTCCAAAAAT 1 AATATTTTTTTTCAATAAATTGTCAATCCTCCAAAAAT 59936024 GGCAAGTTGC Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 38 38 1.00 ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42 Consensus pattern (38 bp): AATATTTTTTTTCAATAAATTGTCAATCCTCCAAAAAT Found at i:59936627 original size:22 final size:21 Alignment explanation

Indices: 59936577--59936630 Score: 74 Period size: 22 Copynumber: 2.6 Consensus size: 21 59936567 TTTCAAAATA 59936577 TCAAGT-TTGACGTCGTGACG 1 TCAAGTCTTGACGTCGTGACG ** 59936597 TCACCTCTTGCACGTCGTGACG 1 TCAAGTCTTG-ACGTCGTGACG 59936619 TCAAGTCTTGAC 1 TCAAGTCTTGAC 59936631 CTCAAGCCAT Statistics Matches: 28, Mismatches: 4, Indels: 3 0.80 0.11 0.09 Matches are distributed among these distances: 20 4 0.14 21 5 0.18 22 19 0.68 ACGTcount: A:0.19, C:0.28, G:0.24, T:0.30 Consensus pattern (21 bp): TCAAGTCTTGACGTCGTGACG Found at i:59937801 original size:410 final size:410 Alignment explanation

Indices: 59936917--59938140 Score: 1258 Period size: 410 Copynumber: 3.0 Consensus size: 410 59936907 GGGTATGTTC * * * * 59936917 AGTGTACTAACAATATAGGTAGTCATGGTTGATGGTAGAGATAGTTGTGGAGAACATGTACTCAA 1 AGTGTACTAGCAATATAGGTAGTCATGGTTGATGGTAGAGATGGTTGTTGAGAACTTGTACTC-A * * * * * * * * 59936982 AATATTTCGGGAGTGATCATATGAAAACTAGTTGTTGCTAGAAGTATCTCAGAAAAAAAAAACAT 65 AATATTT-GGTAATGATCATATGGAAACCAGTTGTTGTTGGAAGTATCTCAG-AAAAACATACA- * * ** * * * * 59937047 ATCGACTAGTTGGAGTTGAGATTCTTTATAGGTTCGTCTTTTCAAAACTTGTCCCCATGCAGGAT 127 A---ATTAGTTGGAGCTGAGATTCTTGGTAGGTTGGTCTTTT-GAAACTTGTCACCATGTAGGAT * * * * * * * * 59937112 AATGTTAGGGCTAAAACTCTTTCTCAAAAGGTTGGGAGGAGTCATCATAAGTGGTTGGGTTGACT 188 AATGTTTGGGCT-AAACTCTCTATCAAAAGGTTAGGAGGAGCCATCGTAAGTGGTTGGGCTAACT * * ** 59937177 CAAGAATAGAGGTGTTAGCAATTGTAAAGTTAGGTTGAATTGAGGGAGAATCC-ATGGCTTTTAG 252 CAAGAACAGGGGTGTTAGCAATTGTAAAGTTAGGTTGAATCAAGGGAGAA-CCTATGGCTTTTAG * * * * ** *** * * * 59937241 TTCAGTATTCTCCCAGATTGTGCCAATTGTTGATGTCTCTTTCACTGGGCTCGGAGATTGGTTGA 316 TTTAATATTCTCACAAACAGTGCCAATTGTTGATGTCTCTTTTGTTGGGCTTGGAGACTAGTTGA 59937306 GCTAAACTTTATAGCCAGAAAATCTACCAA 381 GCTAAACTTTATAGCCAGAAAATCTACCAA * * * * 59937336 AGTGTACTAGTAATATGGGTAGTCATGGTTGATGGTAGATATGATTG-TGAGAACTTGTACTC-A 1 AGTGTACTAGCAATATAGGTAGTCATGGTTGATGGTAGAGATGGTTGTTGAGAACTTGTACTCAA * * * 59937399 ATATTTGGTAATGATCATATGGCAACCAATTGTTGTTGGAAGTATGTCAGAAAAACATACAAATT 66 ATATTTGGTAATGATCATATGGAAACCAGTTGTTGTTGGAAGTATCTCAGAAAAACATACAAATT * * * * * * 59937464 AGTTGGAGCTGATATTCTTGGTGGGTTGGTCTTTCTGGACCTTGTCACCACGTAGGAAAATGTTT 131 AGTTGGAGCTGAGATTCTTGGTAGGTTGGTCTTT-TGAAACTTGTCACCATGTAGGATAATGTTT * * 59937529 GGGCTCAAACTCTCAATCAAAAGGTTAAGAGGAGCCATCGTAAGTGGTTGGGCTAACTCAAGAAC 195 GGGCT-AAACTCTCTATCAAAAGGTTAGGAGGAGCCATCGTAAGTGGTTGGGCTAACTCAAGAAC * * ** 59937594 AGGGGCGTTAGCAATTGTAAAGTTAGCTTGAATCAAGGGAGAACCTATAACTTTTAGTTTAATAT 259 AGGGGTGTTAGCAATTGTAAAGTTAGGTTGAATCAAGGGAGAACCTATGGCTTTTAGTTTAATAT * * * * 59937659 TCTCATAAACAGTGCCACTTGTTGATGTCTCTTTTGTTGGGCTTGAAGACTAGTTGAGCTACACT 324 TCTCACAAACAGTGCCAATTGTTGATGTCTCTTTTGTTGGGCTTGGAGACTAGTTGAGCTAAACT * 59937724 TTATAGCC-GAACAATCT-GCAA 389 TTATAGCCAGAA-AATCTACCAA * * * * 59937745 AGTGTTCTAGCAATATAGATAGTCATGGTTGATGGTAGAGATGGTTGTTAAGAACTTGTATTCAA 1 AGTGTACTAGCAATATAGGTAGTCATGGTTGATGGTAGAGATGGTTGTTGAGAACTTGTACTC-A * * ** * * * *** 59937810 AATATTTTGGTAATGATCGTATGGAAACCGGTTACTATTGAAAGTATCT-AAAAAAACATATTGA 65 AATA-TTTGGTAATGATCATATGGAAACCAGTTGTTGTTGGAAGTATCTCAGAAAAACATACAAA * * * 59937874 TTGGTTGGAGCTGAGATTCTTGGTAAGTTGGTCTTTTTGAAACTTGT-ATCCATGTGGGATAATG 129 TTAGTTGGAGCTGAGATTCTTGGTAGGTTGGTC-TTTTGAAACTTGTCA-CCATGTAGGATAATG * * * * * * * 59937938 TTTGGGCTAGTACTCTCTATCAAAACG-TAGGGAGGAGCTATCGTAAGTAGATGGGCTAATTAAA 192 TTTGGGCTA-AACTCTCTATCAAAAGGTTA-GGAGGAGCCATCGTAAGTGGTTGGGCTAACTCAA * * *** * * * * ** 59938002 GAACAAGGGTGTCAATTACTATAAAGTTAGGTTAAATCGAGAGAGAGAATATATGGCTTTTAGTT 255 GAACAGGGGTGTTAGCAATTGTAAAGTTAGGTTGAATC-A-AGGGAGAACCTATGGCTTTTAGTT * * 59938067 TAATATTCTCACAAACAGTGCCAATTGTTGATATCTCTTTTGTTGGGCTTGGATACTAGTTGAGC 318 TAATATTCTCACAAACAGTGCCAATTGTTGATGTCTCTTTTGTTGGGCTTGGAGACTAGTTGAGC 59938132 TAAACTTTA 383 TAAACTTTA 59938141 AGATACTATT Statistics Matches: 663, Mismatches: 129, Indels: 31 0.81 0.16 0.04 Matches are distributed among these distances: 409 49 0.07 410 235 0.35 411 5 0.01 412 142 0.21 413 40 0.06 414 96 0.14 415 35 0.05 416 7 0.01 418 13 0.02 419 41 0.06 ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33 Consensus pattern (410 bp): AGTGTACTAGCAATATAGGTAGTCATGGTTGATGGTAGAGATGGTTGTTGAGAACTTGTACTCAA ATATTTGGTAATGATCATATGGAAACCAGTTGTTGTTGGAAGTATCTCAGAAAAACATACAAATT AGTTGGAGCTGAGATTCTTGGTAGGTTGGTCTTTTGAAACTTGTCACCATGTAGGATAATGTTTG GGCTAAACTCTCTATCAAAAGGTTAGGAGGAGCCATCGTAAGTGGTTGGGCTAACTCAAGAACAG GGGTGTTAGCAATTGTAAAGTTAGGTTGAATCAAGGGAGAACCTATGGCTTTTAGTTTAATATTC TCACAAACAGTGCCAATTGTTGATGTCTCTTTTGTTGGGCTTGGAGACTAGTTGAGCTAAACTTT ATAGCCAGAAAATCTACCAA Found at i:59939041 original size:44 final size:44 Alignment explanation

Indices: 59938987--59939076 Score: 135 Period size: 44 Copynumber: 2.0 Consensus size: 44 59938977 ATTTAAGTAA * * * * * 59938987 AATAGAAGTTGTGATAATTATACATTTACAAATAATTATAATTT 1 AATAAAAGTTGTGATAATTAAACATTAAAAAATAATTAGAATTT 59939031 AATAAAAGTTGTGATAATTAAACATTAAAAAATAATTAGAATTT 1 AATAAAAGTTGTGATAATTAAACATTAAAAAATAATTAGAATTT 59939075 AA 1 AA 59939077 ATTCAAATTA Statistics Matches: 41, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 44 41 1.00 ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37 Consensus pattern (44 bp): AATAAAAGTTGTGATAATTAAACATTAAAAAATAATTAGAATTT Done.