Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: At_chr3

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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31

Warning! 3062571 characters in sequence are not A, C, G, or T


File 188 of 290

Found at i:64541513 original size:38 final size:38

Alignment explanation

Indices: 64541470--64541542 Score: 137 Period size: 38 Copynumber: 1.9 Consensus size: 38 64541460 AATATTAGAG 64541470 TCAGATTAACAGAACATATATACCGAATCCTACCCCTA 1 TCAGATTAACAGAACATATATACCGAATCCTACCCCTA * 64541508 TCAGATTAACAGAACATATATACTGAATCCTACCC 1 TCAGATTAACAGAACATATATACCGAATCCTACCC 64541543 TCATCCTCTA Statistics Matches: 34, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 38 34 1.00 ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25 Consensus pattern (38 bp): TCAGATTAACAGAACATATATACCGAATCCTACCCCTA Found at i:64544439 original size:14 final size:11 Alignment explanation

Indices: 64544403--64544442 Score: 62 Period size: 11 Copynumber: 3.6 Consensus size: 11 64544393 ATTCTTGTCT * 64544403 ATAAATATATA 1 ATAATTATATA 64544414 ATAATTATATA 1 ATAATTATATA * 64544425 ATAATTATAAA 1 ATAATTATATA 64544436 ATAATTA 1 ATAATTA 64544443 AAATGTACTT Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 11 27 1.00 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (11 bp): ATAATTATATA Found at i:64545373 original size:20 final size:18 Alignment explanation

Indices: 64545337--64545376 Score: 62 Period size: 20 Copynumber: 2.1 Consensus size: 18 64545327 ACTTGTGATG 64545337 TTAATATGCTTAATTTAA 1 TTAATATGCTTAATTTAA 64545355 TTAATATGGCTTAAATTTAA 1 TTAATAT-GCTT-AATTTAA 64545375 TT 1 TT 64545377 CGTGTTAGGT Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 18 7 0.35 19 4 0.20 20 9 0.45 ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50 Consensus pattern (18 bp): TTAATATGCTTAATTTAA Found at i:64547140 original size:10 final size:10 Alignment explanation

Indices: 64547127--64547208 Score: 61 Period size: 9 Copynumber: 8.6 Consensus size: 10 64547117 TCGTAAAAAA 64547127 TATAAAATTT 1 TATAAAATTT 64547137 TAT-AAATTT 1 TATAAAATTT * 64547146 TATAAAAATTG 1 TAT-AAAATTT 64547157 TA-AAAA-TT 1 TATAAAATTT * 64547165 TATAAAA-TA 1 TATAAAATTT 64547174 TATAGAAA--- 1 TATA-AAATTT * 64547182 TATAAAATAAT 1 TATAAAAT-TT 64547193 TATAAAATTT 1 TATAAAATTT 64547203 TATAAA 1 TATAAA 64547209 TTCGTAAGAA Statistics Matches: 60, Mismatches: 4, Indels: 16 0.75 0.05 0.20 Matches are distributed among these distances: 7 3 0.05 8 7 0.12 9 22 0.37 10 13 0.22 11 15 0.25 ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40 Consensus pattern (10 bp): TATAAAATTT Found at i:64547142 original size:19 final size:19 Alignment explanation

Indices: 64547140--64547208 Score: 54 Period size: 19 Copynumber: 3.6 Consensus size: 19 64547130 AAAATTTTAT * * 64547140 AAATTTTATAAAAATTGTA 1 AAATTTTATAAAAAATATA * * 64547159 AAAATTTATAAAATATATA 1 AAATTTTATAAAAAATATA 64547178 GAAA---TATAAAATAATTATA 1 -AAATTTTATAAAA-AA-TATA 64547197 AAATTTTATAAA 1 AAATTTTATAAA 64547209 TTCGTAAGAA Statistics Matches: 39, Mismatches: 5, Indels: 10 0.72 0.09 0.19 Matches are distributed among these distances: 17 7 0.18 18 4 0.10 19 19 0.49 20 3 0.08 21 6 0.15 ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38 Consensus pattern (19 bp): AAATTTTATAAAAAATATA Found at i:64547151 original size:28 final size:28 Alignment explanation

Indices: 64547120--64547208 Score: 90 Period size: 28 Copynumber: 3.1 Consensus size: 28 64547110 ATAAAAATCG 64547120 TAAAAAATATAAAATTTTATAAATTTTA 1 TAAAAAATATAAAATTTTATAAATTTTA * * * * * 64547148 TAAAAATTGTAAAAATTTATAAAATATA 1 TAAAAAATATAAAATTTTATAAATTTTA * * 64547176 T-AGAAATATAAAATAATTATAAAATTTTA 1 TAAAAAATATAAAAT-TTTAT-AAATTTTA 64547205 TAAA 1 TAAA 64547209 TTCGTAAGAA Statistics Matches: 45, Mismatches: 13, Indels: 4 0.73 0.21 0.06 Matches are distributed among these distances: 27 9 0.20 28 28 0.62 29 7 0.16 30 1 0.02 ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38 Consensus pattern (28 bp): TAAAAAATATAAAATTTTATAAATTTTA Found at i:64547171 original size:9 final size:9 Alignment explanation

Indices: 64547127--64547208 Score: 62 Period size: 10 Copynumber: 8.7 Consensus size: 9 64547117 TCGTAAAAAA 64547127 TATAAAATTT 1 TATAAAA-TT * 64547137 TATAAATTT 1 TATAAAATT 64547146 TATAAAAATT 1 TAT-AAAATT 64547156 GTA-AAAATT 1 -TATAAAATT * 64547165 TATAAAATA 1 TATAAAATT 64547174 TATAGAAA-- 1 TATA-AAATT 64547182 TATAAAATAAT 1 TATAAAAT--T 64547193 TATAAAATTT 1 TATAAAA-TT 64547203 TATAAA 1 TATAAA 64547209 TTCGTAAGAA Statistics Matches: 60, Mismatches: 3, Indels: 18 0.74 0.04 0.22 Matches are distributed among these distances: 7 3 0.05 8 6 0.10 9 20 0.33 10 21 0.35 11 9 0.15 12 1 0.02 ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40 Consensus pattern (9 bp): TATAAAATT Found at i:64547229 original size:9 final size:9 Alignment explanation

Indices: 64547103--64547272 Score: 60 Period size: 9 Copynumber: 18.0 Consensus size: 9 64547093 AAATTAGAAA * 64547103 AAAAAATAT 1 AAAAATTAT ** 64547112 AAAAATCGT 1 AAAAATTAT * 64547121 AAAAAATAT 1 AAAAATTAT * 64547130 AAAATTTTAT 1 AAAA-ATTAT ** 64547140 AAATTTTAT 1 AAAAATTAT * 64547149 AAAAATTGT 1 AAAAATTAT 64547158 AAAAATT-T 1 AAAAATTAT 64547166 ATAAAATATAT 1 A-AAAAT-TAT * 64547177 AGAAA-TAT 1 AAAAATTAT 64547185 AAAATAATTAT 1 -AAA-AATTAT * 64547196 -AAAATTTT 1 AAAAATTAT * * 64547204 ATAAATTCGT 1 AAAAATT-AT 64547214 AAGAAAATTAT 1 -A-AAAATTAT 64547225 AAAAAATT-T 1 -AAAAATTAT * 64547234 AAAGAAATAT 1 AAA-AATTAT ** * 64547244 AAATTTCTTAA 1 AAA--AATTAT 64547255 AAAAATTAT 1 AAAAATTAT 64547264 AAAAATTAT 1 AAAAATTAT 64547273 TGTACCAAAA Statistics Matches: 119, Mismatches: 28, Indels: 28 0.68 0.16 0.16 Matches are distributed among these distances: 8 13 0.11 9 64 0.54 10 23 0.19 11 14 0.12 12 5 0.04 ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35 Consensus pattern (9 bp): AAAAATTAT Found at i:64547266 original size:20 final size:19 Alignment explanation

Indices: 64547202--64547266 Score: 53 Period size: 19 Copynumber: 3.4 Consensus size: 19 64547192 TTATAAAATT * * 64547202 TTATAAATTCGTAAGAAAA 1 TTATAAATTCTTAAAAAAA * * 64547221 TTATAAAAAAT-TTAAAGAAA 1 TTAT--AAATTCTTAAAAAAA 64547241 -TATAAATTTCTTAAAAAAA 1 TTATAAA-TTCTTAAAAAAA 64547260 TTATAAA 1 TTATAAA 64547267 AATTATTGTA Statistics Matches: 35, Mismatches: 6, Indels: 9 0.70 0.12 0.18 Matches are distributed among these distances: 17 3 0.09 18 1 0.03 19 15 0.43 20 12 0.34 21 4 0.11 ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34 Consensus pattern (19 bp): TTATAAATTCTTAAAAAAA Found at i:64552320 original size:34 final size:34 Alignment explanation

Indices: 64552282--64552358 Score: 86 Period size: 34 Copynumber: 2.3 Consensus size: 34 64552272 TGAACACTTA * * 64552282 ATAAGCATGACT-TTTGCTACTGA-GTTGATCTATT 1 ATAAGCAT-ACTATTTACTACT-ATGTTGAACTATT * * 64552316 ATAAGCATATTATTTACTACTATGTTGAACTGTT 1 ATAAGCATACTATTTACTACTATGTTGAACTATT 64552350 ATAAGCATA 1 ATAAGCATA 64552359 TTGATTGCTA Statistics Matches: 37, Mismatches: 4, Indels: 4 0.82 0.09 0.09 Matches are distributed among these distances: 33 3 0.08 34 34 0.92 ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40 Consensus pattern (34 bp): ATAAGCATACTATTTACTACTATGTTGAACTATT Found at i:64552370 original size:34 final size:34 Alignment explanation

Indices: 64552294--64552371 Score: 97 Period size: 34 Copynumber: 2.3 Consensus size: 34 64552284 AAGCATGACT * 64552294 TTTGCTACTGAGTTGATCTATTATAAGCATATTA 1 TTTGCTACTGAGTTGAACTATTATAAGCATATTA * * 64552328 TTTACTACT-ATGTTGAACTGTTATAAGCATATTGA 1 TTTGCTACTGA-GTTGAACTATTATAAGCATATT-A 64552363 -TTGCTACTG 1 TTTGCTACTG 64552372 TATTGTTTTT Statistics Matches: 37, Mismatches: 4, Indels: 5 0.80 0.09 0.11 Matches are distributed among these distances: 33 1 0.03 34 35 0.95 35 1 0.03 ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44 Consensus pattern (34 bp): TTTGCTACTGAGTTGAACTATTATAAGCATATTA Found at i:64553190 original size:5 final size:5 Alignment explanation

Indices: 64553180--64553208 Score: 58 Period size: 5 Copynumber: 5.8 Consensus size: 5 64553170 CATGCATGAC 64553180 ATTTA ATTTA ATTTA ATTTA ATTTA ATTT 1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTT 64553209 TAGGATACTG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 24 1.00 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (5 bp): ATTTA Found at i:64553441 original size:23 final size:20 Alignment explanation

Indices: 64553403--64553452 Score: 55 Period size: 23 Copynumber: 2.3 Consensus size: 20 64553393 TCCACTCAGG 64553403 ATTTTTTTAAAAATAAATTAA 1 ATTTTTTTAAAAATAAA-TAA * 64553424 ATTTTCTTCTAAATATAAATAA 1 ATTTT-TT-TAAAAATAAATAA 64553446 ATATTTT 1 AT-TTTT 64553453 AAATTAATTA Statistics Matches: 25, Mismatches: 1, Indels: 5 0.81 0.03 0.16 Matches are distributed among these distances: 21 5 0.20 22 8 0.32 23 12 0.48 ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50 Consensus pattern (20 bp): ATTTTTTTAAAAATAAATAA Found at i:64555689 original size:28 final size:27 Alignment explanation

Indices: 64555646--64555771 Score: 100 Period size: 28 Copynumber: 4.6 Consensus size: 27 64555636 TCGTGTGTAT * 64555646 CCTATTTTTCAAATTTTATAGTCTTGC 1 CCTATTTTTCAAATTTTATAGTTTTGC * 64555673 CACTATTTTTCAGATTTTATTA-TTTTGTC 1 C-CTATTTTTCAAATTTTA-TAGTTTTG-C 64555702 CCTAATTTTT-AAATTTTATAGTTTTG- 1 CCT-ATTTTTCAAATTTTATAGTTTTGC * * * * 64555728 CCTTTATTTTCAGA-TTTACAGTTTTTCC 1 CCTAT-TTTTCAAATTTTATAG-TTTTGC * 64555756 CCTATTTTAC-AATTTT 1 CCTATTTTTCAAATTTT 64555772 CATATTAGAC Statistics Matches: 79, Mismatches: 10, Indels: 20 0.72 0.09 0.18 Matches are distributed among these distances: 25 1 0.01 26 14 0.18 27 16 0.20 28 38 0.48 29 10 0.13 ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56 Consensus pattern (27 bp): CCTATTTTTCAAATTTTATAGTTTTGC Found at i:64559286 original size:11 final size:11 Alignment explanation

Indices: 64559270--64559294 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 64559260 TGACTATGCC 64559270 ATTACAAGCCT 1 ATTACAAGCCT 64559281 ATTACAAGCCT 1 ATTACAAGCCT 64559292 ATT 1 ATT 64559295 CTACAGGTCC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32 Consensus pattern (11 bp): ATTACAAGCCT Found at i:64559863 original size:223 final size:223 Alignment explanation

Indices: 64559475--64559921 Score: 894 Period size: 223 Copynumber: 2.0 Consensus size: 223 64559465 CAAAAACACT 64559475 CAAATGACAGCCATTTCTTGCTTCCTTCAACTCCGGTACTCCTCTTCTTCATCCAACGTTAGGTA 1 CAAATGACAGCCATTTCTTGCTTCCTTCAACTCCGGTACTCCTCTTCTTCATCCAACGTTAGGTA 64559540 AACATTTTTCCTTCCGCTGTTCCTTTCATTTTCCTGTCTGTCATTTTTTCTTACCCACAAATTTT 66 AACATTTTTCCTTCCGCTGTTCCTTTCATTTTCCTGTCTGTCATTTTTTCTTACCCACAAATTTT 64559605 TTCTACCTCTTTGTGTTACTGCTTCATTCACCATCATCTCTAATATTCTTTTAATAAATAAAGTC 131 TTCTACCTCTTTGTGTTACTGCTTCATTCACCATCATCTCTAATATTCTTTTAATAAATAAAGTC 64559670 TCTGAAATCTTGGATCTGAATTTTTGTC 196 TCTGAAATCTTGGATCTGAATTTTTGTC 64559698 CAAATGACAGCCATTTCTTGCTTCCTTCAACTCCGGTACTCCTCTTCTTCATCCAACGTTAGGTA 1 CAAATGACAGCCATTTCTTGCTTCCTTCAACTCCGGTACTCCTCTTCTTCATCCAACGTTAGGTA 64559763 AACATTTTTCCTTCCGCTGTTCCTTTCATTTTCCTGTCTGTCATTTTTTCTTACCCACAAATTTT 66 AACATTTTTCCTTCCGCTGTTCCTTTCATTTTCCTGTCTGTCATTTTTTCTTACCCACAAATTTT 64559828 TTCTACCTCTTTGTGTTACTGCTTCATTCACCATCATCTCTAATATTCTTTTAATAAATAAAGTC 131 TTCTACCTCTTTGTGTTACTGCTTCATTCACCATCATCTCTAATATTCTTTTAATAAATAAAGTC 64559893 TCTGAAATCTTGGATCTGAATTTTTGTC 196 TCTGAAATCTTGGATCTGAATTTTTGTC 64559921 C 1 C 64559922 TACCAGGCTT Statistics Matches: 224, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 223 224 1.00 ACGTcount: A:0.21, C:0.26, G:0.09, T:0.43 Consensus pattern (223 bp): CAAATGACAGCCATTTCTTGCTTCCTTCAACTCCGGTACTCCTCTTCTTCATCCAACGTTAGGTA AACATTTTTCCTTCCGCTGTTCCTTTCATTTTCCTGTCTGTCATTTTTTCTTACCCACAAATTTT TTCTACCTCTTTGTGTTACTGCTTCATTCACCATCATCTCTAATATTCTTTTAATAAATAAAGTC TCTGAAATCTTGGATCTGAATTTTTGTC Found at i:64562210 original size:15 final size:15 Alignment explanation

Indices: 64562190--64562223 Score: 59 Period size: 15 Copynumber: 2.3 Consensus size: 15 64562180 GGTATTATAA 64562190 AATTAAGAAAAAATC 1 AATTAAGAAAAAATC * 64562205 AATTAATAAAAAATC 1 AATTAAGAAAAAATC 64562220 AATT 1 AATT 64562224 GAACTGGGTT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26 Consensus pattern (15 bp): AATTAAGAAAAAATC Found at i:64562633 original size:25 final size:24 Alignment explanation

Indices: 64562583--64562629 Score: 67 Period size: 24 Copynumber: 2.0 Consensus size: 24 64562573 AAACACTAAA * * 64562583 AAAAAAGATAGAAATTATAGAAAT 1 AAAAAACATAGAAATTATAAAAAT * 64562607 AAAAAACATATAAATTATAAAAA 1 AAAAAACATAGAAATTATAAAAA 64562630 ATAATAATAT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 24 20 1.00 ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21 Consensus pattern (24 bp): AAAAAACATAGAAATTATAAAAAT Found at i:64562967 original size:17 final size:17 Alignment explanation

Indices: 64562938--64562970 Score: 50 Period size: 17 Copynumber: 1.9 Consensus size: 17 64562928 AAAAACAATA 64562938 ATTATATTTTTATAAAT 1 ATTATATTTTTATAAAT 64562955 ATTAT-TTTATTATAAA 1 ATTATATTT-TTATAAA 64562971 ATTTAGACAA Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 3 0.20 17 12 0.80 ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58 Consensus pattern (17 bp): ATTATATTTTTATAAAT Found at i:64567277 original size:44 final size:46 Alignment explanation

Indices: 64567208--64567300 Score: 111 Period size: 44 Copynumber: 2.1 Consensus size: 46 64567198 TATAACATCT * * * 64567208 ATTCCATTCGACCAAACACAAGAATT-CT-ATTATAGTTCTATTCC 1 ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTCC * * 64567252 ATTCCATTCAACCAAACA-ATTGAATTATTGATTACAGCTCTATTCC 1 ATTCCATTCAACCAAACACA-AGAATTACTGATTACAGCTCTATTCC 64567298 ATT 1 ATT 64567301 ATAGTGAACC Statistics Matches: 41, Mismatches: 5, Indels: 4 0.82 0.10 0.08 Matches are distributed among these distances: 43 1 0.02 44 22 0.54 45 1 0.02 46 17 0.41 ACGTcount: A:0.34, C:0.24, G:0.06, T:0.35 Consensus pattern (46 bp): ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTCC Found at i:64570807 original size:39 final size:40 Alignment explanation

Indices: 64570762--64570929 Score: 106 Period size: 40 Copynumber: 4.2 Consensus size: 40 64570752 CGGGGTTTAG * * * 64570762 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC *** * * 64570801 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC 1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC ** * * * ** 64570841 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT 1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC * ** * * * * 64570881 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC 1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC 64570922 CCGGATAT 1 CCGGATAT 64570930 CATTCGAGTA Statistics Matches: 109, Mismatches: 16, Indels: 6 0.83 0.12 0.05 Matches are distributed among these distances: 39 18 0.17 40 61 0.56 41 27 0.25 42 3 0.03 ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24 Consensus pattern (40 bp): CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC Found at i:64570912 original size:41 final size:40 Alignment explanation

Indices: 64570785--64570929 Score: 193 Period size: 40 Copynumber: 3.6 Consensus size: 40 64570775 CTCGCACAAG * * * * * 64570785 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT 1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT 64570825 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT 1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT * * * 64570865 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA 1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT 64570906 GCCTTCGGGACTTAGCCCGGATAT 1 GCCTTCGGGACTTAGCCCGGATAT 64570930 CATTCGAGTA Statistics Matches: 92, Mismatches: 10, Indels: 5 0.86 0.09 0.05 Matches are distributed among these distances: 39 3 0.03 40 59 0.64 41 27 0.29 42 3 0.03 ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26 Consensus pattern (40 bp): GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT Found at i:64576305 original size:49 final size:49 Alignment explanation

Indices: 64576230--64576328 Score: 180 Period size: 49 Copynumber: 2.0 Consensus size: 49 64576220 CAGTTACCGG * * 64576230 AGGTATTGTAGGTGTGGGGGTTGTATTAGTCGGGAATGGAGGTTGTGGA 1 AGGTATTGTAGGTGCGGGGGTGGTATTAGTCGGGAATGGAGGTTGTGGA 64576279 AGGTATTGTAGGTGCGGGGGTGGTATTAGTCGGGAATGGAGGTTGTGGA 1 AGGTATTGTAGGTGCGGGGGTGGTATTAGTCGGGAATGGAGGTTGTGGA 64576328 A 1 A 64576329 CAGCCGTATT Statistics Matches: 48, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 49 48 1.00 ACGTcount: A:0.19, C:0.03, G:0.47, T:0.30 Consensus pattern (49 bp): AGGTATTGTAGGTGCGGGGGTGGTATTAGTCGGGAATGGAGGTTGTGGA Found at i:64580738 original size:51 final size:51 Alignment explanation

Indices: 64580662--64580763 Score: 195 Period size: 51 Copynumber: 2.0 Consensus size: 51 64580652 TAGAAAAGGG * 64580662 AAAGATCAAATTGAATAGGTAGAATCGGTGTTGGGAACCTTAGTGAGCTTT 1 AAAGAGCAAATTGAATAGGTAGAATCGGTGTTGGGAACCTTAGTGAGCTTT 64580713 AAAGAGCAAATTGAATAGGTAGAATCGGTGTTGGGAACCTTAGTGAGCTTT 1 AAAGAGCAAATTGAATAGGTAGAATCGGTGTTGGGAACCTTAGTGAGCTTT 64580764 CCTTGAACTT Statistics Matches: 50, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 51 50 1.00 ACGTcount: A:0.33, C:0.10, G:0.28, T:0.28 Consensus pattern (51 bp): AAAGAGCAAATTGAATAGGTAGAATCGGTGTTGGGAACCTTAGTGAGCTTT Found at i:64585155 original size:39 final size:39 Alignment explanation

Indices: 64585101--64585186 Score: 127 Period size: 39 Copynumber: 2.2 Consensus size: 39 64585091 TTTAGTTATT * * * 64585101 TTAGTTTGTGTCTTTAATTATGTCATAATTTGAGCATCA 1 TTAGTATGAGTCTTTAATTATGTCATAATTTGAACATCA * 64585140 TTAGTATGAGTCTTTAATTATGTCATAGTTTGAACATCA 1 TTAGTATGAGTCTTTAATTATGTCATAATTTGAACATCA * 64585179 TTAATATG 1 TTAGTATG 64585187 TGTTCTGCAT Statistics Matches: 42, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 39 42 1.00 ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47 Consensus pattern (39 bp): TTAGTATGAGTCTTTAATTATGTCATAATTTGAACATCA Found at i:64585312 original size:26 final size:26 Alignment explanation

Indices: 64585276--64585329 Score: 108 Period size: 26 Copynumber: 2.1 Consensus size: 26 64585266 TGTAACTCCT 64585276 ATGTTAGTTAAAGTTTGCATCATTAA 1 ATGTTAGTTAAAGTTTGCATCATTAA 64585302 ATGTTAGTTAAAGTTTGCATCATTAA 1 ATGTTAGTTAAAGTTTGCATCATTAA 64585328 AT 1 AT 64585330 TAAGTCATGC Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 28 1.00 ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43 Consensus pattern (26 bp): ATGTTAGTTAAAGTTTGCATCATTAA Found at i:64591389 original size:25 final size:25 Alignment explanation

Indices: 64591353--64591402 Score: 75 Period size: 25 Copynumber: 2.0 Consensus size: 25 64591343 TTGTAAATCA 64591353 GGAAAATATCTTTAGA-AATTTTCT 1 GGAAAATATCTTTAGAGAATTTTCT * 64591377 GGAATAATCTCTTTAGAGAATTTTCT 1 GGAA-AATATCTTTAGAGAATTTTCT 64591403 CTCTACAACT Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 24 4 0.17 25 11 0.48 26 8 0.35 ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42 Consensus pattern (25 bp): GGAAAATATCTTTAGAGAATTTTCT Found at i:64595517 original size:27 final size:27 Alignment explanation

Indices: 64595486--64595539 Score: 99 Period size: 27 Copynumber: 2.0 Consensus size: 27 64595476 AAGAGTCGAA 64595486 GAGAAATAGATTTTGATCCTGATTGAT 1 GAGAAATAGATTTTGATCCTGATTGAT * 64595513 GAGAAATGGATTTTGATCCTGATTGAT 1 GAGAAATAGATTTTGATCCTGATTGAT 64595540 CGCAAAATCT Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 27 26 1.00 ACGTcount: A:0.31, C:0.07, G:0.24, T:0.37 Consensus pattern (27 bp): GAGAAATAGATTTTGATCCTGATTGAT Found at i:64603245 original size:8 final size:8 Alignment explanation

Indices: 64603207--64603234 Score: 56 Period size: 8 Copynumber: 3.5 Consensus size: 8 64603197 AAAGTTATAA 64603207 AAAATTTT 1 AAAATTTT 64603215 AAAATTTT 1 AAAATTTT 64603223 AAAATTTT 1 AAAATTTT 64603231 AAAA 1 AAAA 64603235 AAATTCTAAA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 20 1.00 ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43 Consensus pattern (8 bp): AAAATTTT Found at i:64609858 original size:39 final size:40 Alignment explanation

Indices: 64609763--64610024 Score: 337 Period size: 39 Copynumber: 6.7 Consensus size: 40 64609753 TTGAATGATG * 64609763 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT * 64609801 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT 1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT 64609842 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT 64609881 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT * * 64609920 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT * 64609959 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT * * 64609998 AACCGGGCTATGTCCCGAAGGCATTTG 1 -TCCGGGCTAAGTCCCGAAGGCATTTG 64610025 AACGAGGAGC Statistics Matches: 203, Mismatches: 11, Indels: 17 0.88 0.05 0.07 Matches are distributed among these distances: 39 132 0.65 40 59 0.29 41 11 0.05 42 1 0.00 ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT Found at i:64617872 original size:39 final size:40 Alignment explanation

Indices: 64617777--64618038 Score: 337 Period size: 39 Copynumber: 6.7 Consensus size: 40 64617767 TTGAATGATG * 64617777 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT * 64617815 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT 1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT 64617856 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT 64617895 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT * * 64617934 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT * 64617973 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT * * 64618012 AACCGGGCTATGTCCCGAAGGCATTTG 1 -TCCGGGCTAAGTCCCGAAGGCATTTG 64618039 AACGAGGAGC Statistics Matches: 203, Mismatches: 11, Indels: 17 0.88 0.05 0.07 Matches are distributed among these distances: 39 132 0.65 40 59 0.29 41 11 0.05 42 1 0.00 ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT Found at i:64620546 original size:48 final size:48 Alignment explanation

Indices: 64620484--64621101 Score: 576 Period size: 48 Copynumber: 12.9 Consensus size: 48 64620474 GATATTTGGG * * * * * 64620484 TGATATGTGTGCCAGTGTAAGACCTTGTCTAGGACATGACATCGGCCA 1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA * * ** 64620532 TGATATGAGAGCCAGT-TAAGACCATGTTTGGAACATGGCATCGGTGA 1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA * * * 64620579 TGTTGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GACA 1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA * * * 64620626 TTGATAT-ATGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCA 1 -TGATATGA-GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA * * * * * * 64620675 -CATTATGAGAGCCAATGTAAGGCCATGTCTAGGACATGACATC-GACA 1 TGA-TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA * * * * * * 64620722 TTGAGACGAGAGCTAGTGTAAGACCATGTCTAGGACATGGTATCAGCCA 1 -TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA * * * * * 64620771 TGATATGAGAGCCATTGTAAGACCATGTTTGGAACATGGTATCGGCGA 1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA * * * * 64620819 TGTTGTGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCAG-CA 1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA * * * * 64620866 TTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGACACA 1 -TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GGC-CA * 64620917 T--TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGACACA 1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GGC-CA * *** 64620965 T--TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATC-AATA 1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA * * * * 64621010 TTGAGACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGTC- 1 -TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA * * * * 64621058 TCGACATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATC 1 T-GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC 64621102 AACAATTTAC Statistics Matches: 470, Mismatches: 82, Indels: 36 0.80 0.14 0.06 Matches are distributed among these distances: 45 1 0.00 46 2 0.00 47 47 0.10 48 409 0.87 49 8 0.02 50 1 0.00 51 2 0.00 ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24 Consensus pattern (48 bp): TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA Found at i:64626368 original size:26 final size:26 Alignment explanation

Indices: 64626339--64626446 Score: 189 Period size: 26 Copynumber: 4.2 Consensus size: 26 64626329 TGGTACAAAT 64626339 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * * 64626365 TGATAATGGATTAGGTAAATATTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 64626391 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * 64626417 TGATAATGGTTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 64626443 TGAT 1 TGAT 64626447 GGGCATTTCA Statistics Matches: 77, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 26 77 1.00 ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36 Consensus pattern (26 bp): TGATAATGGGTTAGGTAAATGTTCCA Found at i:64633466 original size:26 final size:26 Alignment explanation

Indices: 64633437--64633544 Score: 189 Period size: 26 Copynumber: 4.2 Consensus size: 26 64633427 TGGTACAAAT 64633437 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * * 64633463 TGATAATGGATTAGGTAAATATTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 64633489 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * 64633515 TGATAATGGTTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 64633541 TGAT 1 TGAT 64633545 GGGCATTTCA Statistics Matches: 77, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 26 77 1.00 ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36 Consensus pattern (26 bp): TGATAATGGGTTAGGTAAATGTTCCA Found at i:64637880 original size:15 final size:15 Alignment explanation

Indices: 64637848--64637876 Score: 51 Period size: 14 Copynumber: 2.0 Consensus size: 15 64637838 TTTTTCTGTG 64637848 TTTATTATGTGTGAA 1 TTTATTATGTGTGAA 64637863 TTTATT-TGTGTGAA 1 TTTATTATGTGTGAA 64637877 ATTTTCGTGC Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 14 8 0.57 15 6 0.43 ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55 Consensus pattern (15 bp): TTTATTATGTGTGAA Found at i:64640147 original size:37 final size:37 Alignment explanation

Indices: 64640097--64640175 Score: 115 Period size: 37 Copynumber: 2.1 Consensus size: 37 64640087 TTATTACGAA * * 64640097 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG 1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG * 64640134 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG 1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG 64640171 GTCTT 1 GTCTT 64640176 TAGAGCTCGG Statistics Matches: 38, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 37 36 0.95 38 2 0.05 ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25 Consensus pattern (37 bp): GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG Found at i:64640372 original size:47 final size:47 Alignment explanation

Indices: 64640294--64640857 Score: 410 Period size: 47 Copynumber: 11.5 Consensus size: 47 64640284 CCCTTCGGGA * * * * * * * 64640294 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 64640341 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 64640388 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 64640435 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * **** *** 64640482 GTTATCACATATATACACTTTC-CGTT-ATCACATATATACACTTTCAC 1 CTTATCACATATATACACTTTCACATTCATCACAT-CGGCCA-TTAGGC * * ** * 64640529 ATTCATCACATCGGCTATTAGGC-CTTATCACACATATACACTTTCACATTCATCACA-TCGG- 1 CTT-ATCACAT---ATA-TA--CACTT-T--CACAT-T-CA---TCACA-TCGGC-CATTAGGC * * * * * ** 64640590 C-TATTAGGCCT-TATCACACATATACACTTTCA-CATTCATC--ACATCGGCCATTAGGC 1 CTTATCA--CATATAT-ACAC-T-TTCACATTCATCA--CATCGGCCAT---TA----GGC 64640646 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 64640695 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 64640742 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 64640789 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTGGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 64640836 CTTATCACATATATACACTTTC 1 CTTATCACATATATACACTTTC 64640858 TTGGCTGAAT Statistics Matches: 421, Mismatches: 51, Indels: 90 0.75 0.09 0.16 Matches are distributed among these distances: 45 7 0.02 46 4 0.01 47 305 0.72 48 7 0.02 49 13 0.03 50 2 0.00 51 5 0.01 52 2 0.00 53 5 0.01 54 7 0.02 55 16 0.04 56 10 0.02 57 15 0.04 58 5 0.01 59 3 0.01 60 2 0.00 61 2 0.00 62 1 0.00 63 7 0.02 64 3 0.01 ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:64640510 original size:23 final size:23 Alignment explanation

Indices: 64640481--64640526 Score: 92 Period size: 23 Copynumber: 2.0 Consensus size: 23 64640471 GGCTATTAGG 64640481 CGTTATCACATATATACACTTTC 1 CGTTATCACATATATACACTTTC 64640504 CGTTATCACATATATACACTTTC 1 CGTTATCACATATATACACTTTC 64640527 ACATTCATCA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 23 1.00 ACGTcount: A:0.30, C:0.26, G:0.04, T:0.39 Consensus pattern (23 bp): CGTTATCACATATATACACTTTC Found at i:64640517 original size:70 final size:70 Alignment explanation

Indices: 64640436--64640573 Score: 249 Period size: 70 Copynumber: 2.0 Consensus size: 70 64640426 CCATTAGGCC * * * 64640436 TTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCGTTATCACATATATACACT 1 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT 64640501 TTCCG 66 TTCCG 64640506 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT 1 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT 64640571 TTC 66 TTC 64640574 ACATTCATCA Statistics Matches: 65, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 70 65 1.00 ACGTcount: A:0.30, C:0.26, G:0.07, T:0.36 Consensus pattern (70 bp): TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT TTCCG Found at i:64640523 original size:117 final size:117 Alignment explanation

Indices: 64640389--64640620 Score: 419 Period size: 117 Copynumber: 2.0 Consensus size: 117 64640379 CCATTAGGCC * * 64640389 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACT 1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACT * * 64640454 TTCACATTCATCACATCGGCTATTAGGCGTTATCACATATATACACTTTCCG 66 TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCCG * 64640506 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT 1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACT 64640571 TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTC 66 TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTC 64640621 ACATTCATCA Statistics Matches: 110, Mismatches: 5, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 117 110 1.00 ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34 Consensus pattern (117 bp): TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACT TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCCG Found at i:64640536 original size:25 final size:23 Alignment explanation

Indices: 64640483--64640539 Score: 87 Period size: 23 Copynumber: 2.4 Consensus size: 23 64640473 CTATTAGGCG * 64640483 TTATCACATATATACACTTTCCG 1 TTATCACATATATACACTTTCCA 64640506 TTATCACATATATACACTTTCACA 1 TTATCACATATATACACTTTC-CA 64640530 TTCATCACAT 1 TT-ATCACAT 64640540 CGGCTATTAG Statistics Matches: 31, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 23 21 0.68 24 3 0.10 25 7 0.23 ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39 Consensus pattern (23 bp): TTATCACATATATACACTTTCCA Found at i:64640829 original size:190 final size:188 Alignment explanation

Indices: 64640506--64640857 Score: 677 Period size: 190 Copynumber: 1.9 Consensus size: 188 64640496 ACACTTTCCG 64640506 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT 1 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT 64640571 TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG 66 TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG 64640636 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCC 131 GCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCC 64640696 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT 1 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT 64640761 TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG 66 TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG * 64640826 GCCATTGGGCCTTATCACATATATACACTTTC 131 GCCATTAGGCCTTATCACATATATACACTTTC 64640858 TTGGCTGAAT Statistics Matches: 161, Mismatches: 1, Indels: 2 0.98 0.01 0.01 Matches are distributed among these distances: 188 14 0.09 190 147 0.91 ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33 Consensus pattern (188 bp): TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC Found at i:64646116 original size:33 final size:33 Alignment explanation

Indices: 64646059--64646198 Score: 138 Period size: 33 Copynumber: 4.2 Consensus size: 33 64646049 ACATCATCAG * * 64646059 TCCAACCAAACACACTAGATGCTCACTCA-AGCCAA 1 TCCAACC-ATCACACTA-ATGCTCA-TAAGAGCCAA * * * 64646094 TCTATCCATCACACTAATGCTCATAAGAGCTAA 1 TCCAACCATCACACTAATGCTCATAAGAGCCAA * * 64646127 TCCAACCATCACACCAATGCTCATAAGAGCTAA 1 TCCAACCATCACACTAATGCTCATAAGAGCCAA * * * * * 64646160 ACCAACCATCATACCAATGCTCATACGAGCTAA 1 TCCAACCATCACACTAATGCTCATAAGAGCCAA 64646193 TCCAAC 1 TCCAAC 64646199 TAGCACACCA Statistics Matches: 92, Mismatches: 12, Indels: 4 0.85 0.11 0.04 Matches are distributed among these distances: 32 2 0.02 33 77 0.84 34 8 0.09 35 5 0.05 ACGTcount: A:0.39, C:0.34, G:0.09, T:0.19 Consensus pattern (33 bp): TCCAACCATCACACTAATGCTCATAAGAGCCAA Found at i:64646209 original size:33 final size:33 Alignment explanation

Indices: 64646099--64646209 Score: 168 Period size: 33 Copynumber: 3.4 Consensus size: 33 64646089 GCCAATCTAT * 64646099 CCATCACACTAATGCTCATAAGAGCTAATCCAA 1 CCATCACACCAATGCTCATAAGAGCTAATCCAA * 64646132 CCATCACACCAATGCTCATAAGAGCTAAACCAA 1 CCATCACACCAATGCTCATAAGAGCTAATCCAA * * 64646165 CCATCATACCAATGCTCATACGAGCTAATCCAA 1 CCATCACACCAATGCTCATAAGAGCTAATCCAA * * 64646198 CTAGCACACCAA 1 CCATCACACCAA 64646210 ATAGAGAGTA Statistics Matches: 70, Mismatches: 8, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 33 70 1.00 ACGTcount: A:0.40, C:0.33, G:0.09, T:0.18 Consensus pattern (33 bp): CCATCACACCAATGCTCATAAGAGCTAATCCAA Found at i:64647304 original size:37 final size:37 Alignment explanation

Indices: 64647249--64647319 Score: 115 Period size: 37 Copynumber: 1.9 Consensus size: 37 64647239 TCATAGGGTA * * * 64647249 ATAATAGTCATTTTATCACATAGGGGCATAATAGCGC 1 ATAACAGTCATTTTATCACACAAGGGCATAATAGCGC 64647286 ATAACAGTCATTTTATCACACAAGGGCATAATAG 1 ATAACAGTCATTTTATCACACAAGGGCATAATAG 64647320 TTGTAGAAAG Statistics Matches: 31, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 37 31 1.00 ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28 Consensus pattern (37 bp): ATAACAGTCATTTTATCACACAAGGGCATAATAGCGC Found at i:64648621 original size:21 final size:20 Alignment explanation

Indices: 64648588--64648628 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 20 64648578 ATTTTATGTG * 64648588 ATTTTATCATTTTATCATTC 1 ATTTTATCATTTTATAATTC * 64648608 ATTTATATCCTTTTATAATTC 1 ATTT-TATCATTTTATAATTC 64648629 TGAAATTTCA Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 20 4 0.22 21 14 0.78 ACGTcount: A:0.27, C:0.15, G:0.00, T:0.59 Consensus pattern (20 bp): ATTTTATCATTTTATAATTC Found at i:64648848 original size:3 final size:3 Alignment explanation

Indices: 64648840--64648864 Score: 50 Period size: 3 Copynumber: 8.3 Consensus size: 3 64648830 TGTTTTGTCA 64648840 TAT TAT TAT TAT TAT TAT TAT TAT T 1 TAT TAT TAT TAT TAT TAT TAT TAT T 64648865 TTAACCATTT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 22 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TAT Found at i:64649180 original size:24 final size:25 Alignment explanation

Indices: 64649152--64649200 Score: 66 Period size: 24 Copynumber: 2.0 Consensus size: 25 64649142 TAATTTCAAA 64649152 TTTTTAGTTTCCA-CTTG-TTATTTT 1 TTTTTA-TTTCCAGCTTGTTTATTTT * 64649176 TTTTTATTTCTAGCTTGTTTATTTT 1 TTTTTATTTCCAGCTTGTTTATTTT 64649201 CGGACTTATA Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 23 5 0.23 24 10 0.45 25 7 0.32 ACGTcount: A:0.12, C:0.10, G:0.08, T:0.69 Consensus pattern (25 bp): TTTTTATTTCCAGCTTGTTTATTTT Found at i:64652835 original size:27 final size:27 Alignment explanation

Indices: 64652774--64652826 Score: 79 Period size: 27 Copynumber: 2.0 Consensus size: 27 64652764 TCATACATCT ** * 64652774 CATAGGGTAATAATAGTCATTTTATCA 1 CATAGGGGCATAATAGCCATTTTATCA 64652801 CATAGGGGCATAATAGCCATTTTATC 1 CATAGGGGCATAATAGCCATTTTATC 64652827 GATTAGGGGT Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 27 23 1.00 ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34 Consensus pattern (27 bp): CATAGGGGCATAATAGCCATTTTATCA Found at i:64655786 original size:40 final size:40 Alignment explanation

Indices: 64655548--64655772 Score: 296 Period size: 40 Copynumber: 5.7 Consensus size: 40 64655538 TTGAATGATG * * * * 64655548 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA * * * 64655588 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * 64655628 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA * 64655667 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA * 64655707 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA * 64655748 -CCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 64655773 AACGAGTAGC Statistics Matches: 165, Mismatches: 15, Indels: 10 0.87 0.08 0.05 Matches are distributed among these distances: 39 34 0.21 40 121 0.73 41 10 0.06 ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA Found at i:64655794 original size:119 final size:119 Alignment explanation

Indices: 64655548--64655805 Score: 292 Period size: 119 Copynumber: 2.2 Consensus size: 119 64655538 TTGAATGATG * * 64655548 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT 1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT * ** 64655613 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA 66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA * * * ** 64655667 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT 1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT * * * * 64655730 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA 64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA * * 64655787 TCC-GGTTAAATTCCGAAGG 1 TCCGGGTTAAGTCCCGAAGG 64655806 TACGTGATTT Statistics Matches: 118, Mismatches: 16, Indels: 10 0.82 0.11 0.07 Matches are distributed among these distances: 118 3 0.03 119 84 0.71 120 31 0.26 ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25 Consensus pattern (119 bp): TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA Found at i:64658099 original size:27 final size:27 Alignment explanation

Indices: 64658058--64658120 Score: 117 Period size: 27 Copynumber: 2.3 Consensus size: 27 64658048 ATGGTTACAT 64658058 TTCAAACATGCATTATTTTACCTATAA 1 TTCAAACATGCATTATTTTACCTATAA * 64658085 TTCAAACATGTATTATTTTACCTATAA 1 TTCAAACATGCATTATTTTACCTATAA 64658112 TTCAAACAT 1 TTCAAACAT 64658121 ACCAAATCTC Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 27 35 1.00 ACGTcount: A:0.38, C:0.17, G:0.03, T:0.41 Consensus pattern (27 bp): TTCAAACATGCATTATTTTACCTATAA Found at i:64660766 original size:27 final size:26 Alignment explanation

Indices: 64660728--64660778 Score: 75 Period size: 27 Copynumber: 1.9 Consensus size: 26 64660718 CGAGGCTGCC * 64660728 AGATATTGTGACGAAGTCACCAGAAT 1 AGATATTGTGACGAAGCCACCAGAAT * 64660754 AGATATATGTGACGAGGCCACCAGA 1 AGATAT-TGTGACGAAGCCACCAGA 64660779 TTATAGTGAG Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 26 6 0.27 27 16 0.73 ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20 Consensus pattern (26 bp): AGATATTGTGACGAAGCCACCAGAAT Found at i:64667912 original size:71 final size:67 Alignment explanation

Indices: 64667835--64667975 Score: 183 Period size: 67 Copynumber: 2.0 Consensus size: 67 64667825 CACCAGATAT * * 64667835 AGATATTGTGGCTAGGCCACCAGAACAGATATATACATATGGCAAAGCCACCAGATTGCAGCGAG 1 AGATATTGTGACGAGGCCACCAGAACAG--ATAT--ATATGGCAAAGCCACCAGATTGCAGCGAG 64667900 GCTGCC 62 GCTGCC * * * * * 64667906 AGATATTGTGACGATGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTG 1 AGATATTGTGACGAGGCCACCAGAACAGATATATATGGCAAAGCCACCAGATTGCAGCGAGGCTG 64667971 CC 66 CC 64667973 AGA 1 AGA 64667976 ACGCTTCCTC Statistics Matches: 63, Mismatches: 7, Indels: 4 0.85 0.09 0.05 Matches are distributed among these distances: 67 35 0.56 69 4 0.06 71 24 0.38 ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18 Consensus pattern (67 bp): AGATATTGTGACGAGGCCACCAGAACAGATATATATGGCAAAGCCACCAGATTGCAGCGAGGCTG CC Found at i:64667953 original size:27 final size:26 Alignment explanation

Indices: 64667905--64667956 Score: 68 Period size: 27 Copynumber: 2.0 Consensus size: 26 64667895 GCGAGGCTGC * * 64667905 CAGATATTGTGACGATGTCACCAGAA 1 CAGATATTGTGACGAGGCCACCAGAA * 64667931 CAGATATATGTGGCGAGGCCACCAGA 1 CAGATAT-TGTGACGAGGCCACCAGA 64667957 TTGCAGCGAG Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 26 7 0.32 27 15 0.68 ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19 Consensus pattern (26 bp): CAGATATTGTGACGAGGCCACCAGAA Found at i:64670544 original size:43 final size:43 Alignment explanation

Indices: 64670437--64670550 Score: 140 Period size: 43 Copynumber: 2.7 Consensus size: 43 64670427 TCGATACCAC * * * * * * 64670437 TGTCCTAGACAGGGTCTTACACGAAATCGATTAACGATGCCAA 1 TGTCCTAGACATGGTCTTACATGTAATCCAATAACAATGCCAA * * 64670480 TGTCCCAAACATGGTCTTACATGTAATCTCAAT-ACAATGCCAA 1 TGTCCTAGACATGGTCTTACATGTAATC-CAATAACAATGCCAA 64670523 TGTCCTAGACATGGTCTTACATGTAATC 1 TGTCCTAGACATGGTCTTACATGTAATC 64670551 ACATCTCGAT Statistics Matches: 60, Mismatches: 10, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 43 58 0.97 44 2 0.03 ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28 Consensus pattern (43 bp): TGTCCTAGACATGGTCTTACATGTAATCCAATAACAATGCCAA Found at i:64674131 original size:15 final size:16 Alignment explanation

Indices: 64674111--64674150 Score: 55 Period size: 16 Copynumber: 2.6 Consensus size: 16 64674101 TAAATTGGAA 64674111 AAATGAAAAGTT-ATT 1 AAATGAAAAGTTAATT * * 64674126 AAATGACAATTTAATT 1 AAATGAAAAGTTAATT 64674142 AAATGAAAA 1 AAATGAAAA 64674151 AGAAAACAAT Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 15 10 0.48 16 11 0.52 ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30 Consensus pattern (16 bp): AAATGAAAAGTTAATT Found at i:64674392 original size:19 final size:20 Alignment explanation

Indices: 64674356--64674393 Score: 60 Period size: 20 Copynumber: 1.9 Consensus size: 20 64674346 CATGGATGAA * 64674356 TATGTTAGAAATATGAAATT 1 TATGGTAGAAATATGAAATT 64674376 TATGGTAGAAA-ATGAAAT 1 TATGGTAGAAATATGAAAT 64674394 ATTGTTGATA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 19 7 0.41 20 10 0.59 ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34 Consensus pattern (20 bp): TATGGTAGAAATATGAAATT Found at i:64674599 original size:232 final size:232 Alignment explanation

Indices: 64674193--64674658 Score: 932 Period size: 232 Copynumber: 2.0 Consensus size: 232 64674183 TTTCTATGGA 64674193 AACCCTAGGAGAGAGGAAGAAGACTTATCAAGCTTATTTGGGTAAGTAATCAAGTACCGTTTTTA 1 AACCCTAGGAGAGAGGAAGAAGACTTATCAAGCTTATTTGGGTAAGTAATCAAGTACCGTTTTTA 64674258 GTAATTTTTATATTTTTGAAACCCGGATAGTCTAATCTATTTATTTGGGGGATTGATTTGAAAAG 66 GTAATTTTTATATTTTTGAAACCCGGATAGTCTAATCTATTTATTTGGGGGATTGATTTGAAAAG 64674323 CTATCAAAGTATGAAATTTGGGTCATGGATGAATATGTTAGAAATATGAAATTTATGGTAGAAAA 131 CTATCAAAGTATGAAATTTGGGTCATGGATGAATATGTTAGAAATATGAAATTTATGGTAGAAAA 64674388 TGAAATATTGTTGATAGATAAACAACTTTTACAAAGC 196 TGAAATATTGTTGATAGATAAACAACTTTTACAAAGC 64674425 AACCCTAGGAGAGAGGAAGAAGACTTATCAAGCTTATTTGGGTAAGTAATCAAGTACCGTTTTTA 1 AACCCTAGGAGAGAGGAAGAAGACTTATCAAGCTTATTTGGGTAAGTAATCAAGTACCGTTTTTA 64674490 GTAATTTTTATATTTTTGAAACCCGGATAGTCTAATCTATTTATTTGGGGGATTGATTTGAAAAG 66 GTAATTTTTATATTTTTGAAACCCGGATAGTCTAATCTATTTATTTGGGGGATTGATTTGAAAAG 64674555 CTATCAAAGTATGAAATTTGGGTCATGGATGAATATGTTAGAAATATGAAATTTATGGTAGAAAA 131 CTATCAAAGTATGAAATTTGGGTCATGGATGAATATGTTAGAAATATGAAATTTATGGTAGAAAA 64674620 TGAAATATTGTTGATAGATAAACAACTTTTACAAAGC 196 TGAAATATTGTTGATAGATAAACAACTTTTACAAAGC 64674657 AA 1 AA 64674659 TTTTTGATGG Statistics Matches: 234, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 232 234 1.00 ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34 Consensus pattern (232 bp): AACCCTAGGAGAGAGGAAGAAGACTTATCAAGCTTATTTGGGTAAGTAATCAAGTACCGTTTTTA GTAATTTTTATATTTTTGAAACCCGGATAGTCTAATCTATTTATTTGGGGGATTGATTTGAAAAG CTATCAAAGTATGAAATTTGGGTCATGGATGAATATGTTAGAAATATGAAATTTATGGTAGAAAA TGAAATATTGTTGATAGATAAACAACTTTTACAAAGC Found at i:64674624 original size:19 final size:20 Alignment explanation

Indices: 64674588--64674625 Score: 60 Period size: 20 Copynumber: 1.9 Consensus size: 20 64674578 CATGGATGAA * 64674588 TATGTTAGAAATATGAAATT 1 TATGGTAGAAATATGAAATT 64674608 TATGGTAGAAA-ATGAAAT 1 TATGGTAGAAATATGAAAT 64674626 ATTGTTGATA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 19 7 0.41 20 10 0.59 ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34 Consensus pattern (20 bp): TATGGTAGAAATATGAAATT Found at i:64680147 original size:71 final size:71 Alignment explanation

Indices: 64680050--64680184 Score: 243 Period size: 71 Copynumber: 1.9 Consensus size: 71 64680040 CTTGGCATGC * 64680050 AAAGGTTGATTATTTTGCTATATTGGGACGACAAGAGTTGGTGTTGGTTTTAAACTCTGGTGATT 1 AAAGGTTGATTATTTTACTATATTGGGACGACAAGAGTTGGTGTTGGTTTTAAACTCTGGTGATT 64680115 GCACGG 66 GCACGG * * 64680121 AAAGGTTGATTATTTTACTATGTTGGGACGGCAAGAGTTGGTGTTGGTTTTAAACTCTGGTGAT 1 AAAGGTTGATTATTTTACTATATTGGGACGACAAGAGTTGGTGTTGGTTTTAAACTCTGGTGAT 64680185 GGAGGGATCC Statistics Matches: 61, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 71 61 1.00 ACGTcount: A:0.24, C:0.09, G:0.30, T:0.38 Consensus pattern (71 bp): AAAGGTTGATTATTTTACTATATTGGGACGACAAGAGTTGGTGTTGGTTTTAAACTCTGGTGATT GCACGG Found at i:64681691 original size:324 final size:324 Alignment explanation

Indices: 64681102--64681719 Score: 1218 Period size: 324 Copynumber: 1.9 Consensus size: 324 64681092 NNNNNNNNNN * 64681102 ATAACAAATAAACGGTGATATAATGATTCTATTTGAATTATATGTCGAGATAATTAGTTTATACT 1 ATAACAAATAAACGGTGATATAACGATTCTATTTGAATTATATGTCGAGATAATTAGTTTATACT 64681167 TATGACGGGTAGCCGAATGTGCATAGAGATCATGTCATAAAGCAAATCAAATCATGCTCTTTGTA 66 TATGACGGGTAGCCGAATGTGCATAGAGATCATGTCATAAAGCAAATCAAATCATGCTCTTTGTA 64681232 TGTGGCTATTGAGCCGAAAATGGGAATGGTTGACAAGTGTCTTGTGTTTGAGTTCTAGTGATGAA 131 TGTGGCTATTGAGCCGAAAATGGGAATGGTTGACAAGTGTCTTGTGTTTGAGTTCTAGTGATGAA 64681297 AATGAAATATAGATGTGATATGATTTATTGATATATGTGCATGAATATTCGGATGGTAACCGGGC 196 AATGAAATATAGATGTGATATGATTTATTGATATATGTGCATGAATATTCGGATGGTAACCGGGC 64681362 TAAGTCCCGAAGGTATTTGTGCTAGTGACTAATTTATGATTTGATTAAGTTATGACATATAAGC 261 TAAGTCCCGAAGGTATTTGTGCTAGTGACTAATTTATGATTTGATTAAGTTATGACATATAAGC * 64681426 ATAACAAATAAACGGTGATATAACGATTCTATTTGAATTATATGTCGAGATAGTTAGTTTATACT 1 ATAACAAATAAACGGTGATATAACGATTCTATTTGAATTATATGTCGAGATAATTAGTTTATACT 64681491 TATGACGGGTAGCCGAATGTGCATAGAGATCATGTCATAAAGCAAATCAAATCATGCTCTTTGTA 66 TATGACGGGTAGCCGAATGTGCATAGAGATCATGTCATAAAGCAAATCAAATCATGCTCTTTGTA 64681556 TGTGGCTATTGAGCCGAAAATGGGAATGGTTGACAAGTGTCTTGTGTTTGAGTTCTAGTGATGAA 131 TGTGGCTATTGAGCCGAAAATGGGAATGGTTGACAAGTGTCTTGTGTTTGAGTTCTAGTGATGAA 64681621 AATGAAATATAGATGTGATATGATTTATTGATATATGTGCATGAATATTCGGATGGTAACCGGGC 196 AATGAAATATAGATGTGATATGATTTATTGATATATGTGCATGAATATTCGGATGGTAACCGGGC 64681686 TAAGTCCCGAAGGTATTTGTGCTAGTGACTAATT 261 TAAGTCCCGAAGGTATTTGTGCTAGTGACTAATT 64681720 CCGGGCTAAG Statistics Matches: 292, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 324 292 1.00 ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34 Consensus pattern (324 bp): ATAACAAATAAACGGTGATATAACGATTCTATTTGAATTATATGTCGAGATAATTAGTTTATACT TATGACGGGTAGCCGAATGTGCATAGAGATCATGTCATAAAGCAAATCAAATCATGCTCTTTGTA TGTGGCTATTGAGCCGAAAATGGGAATGGTTGACAAGTGTCTTGTGTTTGAGTTCTAGTGATGAA AATGAAATATAGATGTGATATGATTTATTGATATATGTGCATGAATATTCGGATGGTAACCGGGC TAAGTCCCGAAGGTATTTGTGCTAGTGACTAATTTATGATTTGATTAAGTTATGACATATAAGC Found at i:64681797 original size:40 final size:41 Alignment explanation

Indices: 64681680--64681797 Score: 195 Period size: 40 Copynumber: 2.9 Consensus size: 41 64681670 CGGATGGTAA * * * 64681680 CCGGGCTAAGTCCCGAAGGTATTTGTGCTAGTGACTA-ATT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATT 64681720 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATT 64681760 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT 64681798 CACATATAAG Statistics Matches: 74, Mismatches: 3, Indels: 2 0.94 0.04 0.03 Matches are distributed among these distances: 40 73 0.99 41 1 0.01 ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28 Consensus pattern (41 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATT Found at i:64682118 original size:40 final size:40 Alignment explanation

Indices: 64682063--64682167 Score: 167 Period size: 40 Copynumber: 2.6 Consensus size: 40 64682053 CGGATGGTAA * * 64682063 CCGGGCTAAGTCCCGAAGGTATTTGTGCTAGTGACTA-ATT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-T * 64682103 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT 64682143 CCGGGCTAAGTCCCGAAGGCATTTG 1 CCGGGCTAAGTCCCGAAGGCATTTG 64682168 AGTGAGTAGC Statistics Matches: 61, Mismatches: 3, Indels: 2 0.92 0.05 0.03 Matches are distributed among these distances: 40 60 0.98 41 1 0.02 ACGTcount: A:0.22, C:0.23, G:0.29, T:0.27 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT Found at i:64682123 original size:383 final size:383 Alignment explanation

Indices: 64681416--64682167 Score: 1504 Period size: 383 Copynumber: 2.0 Consensus size: 383 64681406 TTAAGTTATG 64681416 ACATATAAGCATAACAAATAAACGGTGATATAACGATTCTATTTGAATTATATGTCGAGATAGTT 1 ACATATAAGCATAACAAATAAACGGTGATATAACGATTCTATTTGAATTATATGTCGAGATAGTT 64681481 AGTTTATACTTATGACGGGTAGCCGAATGTGCATAGAGATCATGTCATAAAGCAAATCAAATCAT 66 AGTTTATACTTATGACGGGTAGCCGAATGTGCATAGAGATCATGTCATAAAGCAAATCAAATCAT 64681546 GCTCTTTGTATGTGGCTATTGAGCCGAAAATGGGAATGGTTGACAAGTGTCTTGTGTTTGAGTTC 131 GCTCTTTGTATGTGGCTATTGAGCCGAAAATGGGAATGGTTGACAAGTGTCTTGTGTTTGAGTTC 64681611 TAGTGATGAAAATGAAATATAGATGTGATATGATTTATTGATATATGTGCATGAATATTCGGATG 196 TAGTGATGAAAATGAAATATAGATGTGATATGATTTATTGATATATGTGCATGAATATTCGGATG 64681676 GTAACCGGGCTAAGTCCCGAAGGTATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA 261 GTAACCGGGCTAAGTCCCGAAGGTATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA 64681741 TTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATC 326 TTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATC 64681799 ACATATAAGCATAACAAATAAACGGTGATATAACGATTCTATTTGAATTATATGTCGAGATAGTT 1 ACATATAAGCATAACAAATAAACGGTGATATAACGATTCTATTTGAATTATATGTCGAGATAGTT 64681864 AGTTTATACTTATGACGGGTAGCCGAATGTGCATAGAGATCATGTCATAAAGCAAATCAAATCAT 66 AGTTTATACTTATGACGGGTAGCCGAATGTGCATAGAGATCATGTCATAAAGCAAATCAAATCAT 64681929 GCTCTTTGTATGTGGCTATTGAGCCGAAAATGGGAATGGTTGACAAGTGTCTTGTGTTTGAGTTC 131 GCTCTTTGTATGTGGCTATTGAGCCGAAAATGGGAATGGTTGACAAGTGTCTTGTGTTTGAGTTC 64681994 TAGTGATGAAAATGAAATATAGATGTGATATGATTTATTGATATATGTGCATGAATATTCGGATG 196 TAGTGATGAAAATGAAATATAGATGTGATATGATTTATTGATATATGTGCATGAATATTCGGATG 64682059 GTAACCGGGCTAAGTCCCGAAGGTATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA 261 GTAACCGGGCTAAGTCCCGAAGGTATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA 64682124 TTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG 326 TTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG 64682168 AGTGAGTAGC Statistics Matches: 369, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 383 369 1.00 ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32 Consensus pattern (383 bp): ACATATAAGCATAACAAATAAACGGTGATATAACGATTCTATTTGAATTATATGTCGAGATAGTT AGTTTATACTTATGACGGGTAGCCGAATGTGCATAGAGATCATGTCATAAAGCAAATCAAATCAT GCTCTTTGTATGTGGCTATTGAGCCGAAAATGGGAATGGTTGACAAGTGTCTTGTGTTTGAGTTC TAGTGATGAAAATGAAATATAGATGTGATATGATTTATTGATATATGTGCATGAATATTCGGATG GTAACCGGGCTAAGTCCCGAAGGTATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA TTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATC Found at i:64682200 original size:39 final size:40 Alignment explanation

Indices: 64682063--64682200 Score: 156 Period size: 40 Copynumber: 3.5 Consensus size: 40 64682053 CGGATGGTAA * * * * 64682063 CCGGGCTAAGTCCCGAAGGTATTTGTGCTAGTGACTA-ATT 1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATA-T * 64682103 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATAT * * 64682143 CCGGGCTAAGTCCCGAAGGCATTTGAGTGAG-TAGCTATGT 1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTA-CTATAT * * 64682183 CC-GGCTAAATTCCGAAGG 1 CCGGGCTAAGTCCCGAAGG 64682201 TACTTGGTTT Statistics Matches: 88, Mismatches: 8, Indels: 5 0.87 0.08 0.05 Matches are distributed among these distances: 39 16 0.18 40 71 0.81 41 1 0.01 ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATAT Found at i:64690078 original size:40 final size:40 Alignment explanation

Indices: 64690021--64690268 Score: 335 Period size: 40 Copynumber: 6.2 Consensus size: 40 64690011 CGGATGGTAA * 64690021 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGT-CTA-ATT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-TACTATA-T * * * 64690061 CTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T * 64690101 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * 64690141 CCGGGCTAAGTCCCGAAGGCATTTATGCGAGTTACTATCT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 64690181 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * * 64690221 CCGAGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATGT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT 64690261 CC-GGCTAA 1 CCGGGCTAA 64690269 ATTCCAAAGG Statistics Matches: 190, Mismatches: 15, Indels: 7 0.90 0.07 0.03 Matches are distributed among these distances: 39 7 0.04 40 182 0.96 41 1 0.01 ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT Found at i:64692471 original size:27 final size:26 Alignment explanation

Indices: 64692419--64692478 Score: 75 Period size: 27 Copynumber: 2.3 Consensus size: 26 64692409 CCACATATAT * 64692419 ATATCTGTTCTGGTGGCCTAGCCACA 1 ATATCTGTTCTGGTGACCTAGCCACA * * * 64692445 ATATCTGTATCTGGTGACTTCGTCACA 1 ATATCTGT-TCTGGTGACCTAGCCACA 64692472 ATATCTG 1 ATATCTG 64692479 GCAGCTTCGC Statistics Matches: 29, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 26 8 0.28 27 21 0.72 ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35 Consensus pattern (26 bp): ATATCTGTTCTGGTGACCTAGCCACA Found at i:64692767 original size:20 final size:22 Alignment explanation

Indices: 64692720--64692767 Score: 55 Period size: 20 Copynumber: 2.3 Consensus size: 22 64692710 CTATTGTGAA * 64692720 AGTTGGATGGTCTAATTTAGTT 1 AGTTGGATGGTCTAAATTAGTT * * 64692742 AATTGGAT-G-CTAAATTATTT 1 AGTTGGATGGTCTAAATTAGTT 64692762 AGTTGG 1 AGTTGG 64692768 GATTTGATTG Statistics Matches: 22, Mismatches: 4, Indels: 2 0.79 0.14 0.07 Matches are distributed among these distances: 20 14 0.64 21 1 0.05 22 7 0.32 ACGTcount: A:0.27, C:0.04, G:0.25, T:0.44 Consensus pattern (22 bp): AGTTGGATGGTCTAAATTAGTT Found at i:64703704 original size:40 final size:40 Alignment explanation

Indices: 64703614--64703707 Score: 118 Period size: 40 Copynumber: 2.4 Consensus size: 40 64703604 CGGATGATAA * * 64703614 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTT 1 CCGGGCTAAGTCCCAAAGGCATTTGCGCGAGTGACTAGTT * * * 64703654 CCGAGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTA-TAT 1 CCGGGCTAAGTCCCAAAGGCATTTGCGCGAGTGACTAGT-T * 64703694 CCGGGTTAAGTCCC 1 CCGGGCTAAGTCCC 64703708 GGACTTGTGT Statistics Matches: 46, Mismatches: 7, Indels: 2 0.84 0.13 0.04 Matches are distributed among these distances: 39 1 0.02 40 45 0.98 ACGTcount: A:0.22, C:0.26, G:0.27, T:0.26 Consensus pattern (40 bp): CCGGGCTAAGTCCCAAAGGCATTTGCGCGAGTGACTAGTT Found at i:64703854 original size:179 final size:178 Alignment explanation

Indices: 64703530--64703880 Score: 587 Period size: 179 Copynumber: 2.0 Consensus size: 178 64703520 CTTAATACGT 64703530 GACTTGTGTTTGAACTCTAATTATGAAAATGAGATATAGATGTGTCATGATTTATTGATATGTGC 1 GACTTGTGTTTGAACTCTAATTATGAAAATGAGATATAGATGTGTCATGATTTATTGATATGTGC * ** 64703595 ATGAATATTCGGATGATAACCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGAGC 66 ATGAATATTCGGATGATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTACATCCGAGC * * 64703660 TAAGTCCCAAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAAGTCCCG 131 TAAGTCCCAAAGGCATTCGAGCGAG-TAGCTATATCC-GGTTAAGTCCCG 64703709 GACTTGTGTTTGAACTCTAATTATGAAAATGAGATATAGATGTGTCATGATTTATTGATATGTGC 1 GACTTGTGTTTGAACTCTAATTATGAAAATGAGATATAGATGTGTCATGATTTATTGATATGTGC * * * 64703774 ATGAATATTCGGATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGC 66 ATGAATATTCGGATGATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTACATCCGAGC * * 64703839 TATGTCCCGAAGGCATTCGAGCGAGTAGCTATATCCGGTTAA 131 TAAGTCCCAAAGGCATTCGAGCGAGTAGCTATATCCGGTTAA 64703881 ATCCGGTTAT Statistics Matches: 161, Mismatches: 10, Indels: 3 0.93 0.06 0.02 Matches are distributed among these distances: 178 8 0.05 179 153 0.95 ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31 Consensus pattern (178 bp): GACTTGTGTTTGAACTCTAATTATGAAAATGAGATATAGATGTGTCATGATTTATTGATATGTGC ATGAATATTCGGATGATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTACATCCGAGC TAAGTCCCAAAGGCATTCGAGCGAGTAGCTATATCCGGTTAAGTCCCG Found at i:64711611 original size:40 final size:40 Alignment explanation

Indices: 64711556--64711813 Score: 351 Period size: 40 Copynumber: 6.5 Consensus size: 40 64711546 TCGATGATAA * * * 64711556 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT 64711596 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * * 64711636 CCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTCACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * 64711676 CCGGGCTAAGCCCCGAAGGCAATTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * 64711716 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * * 64711756 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT * * 64711796 CC-GGTTAAATCCCGAAGG 1 CCGGGCTAAGTCCCGAAGG 64711814 TACCTGGATT Statistics Matches: 195, Mismatches: 21, Indels: 5 0.88 0.10 0.02 Matches are distributed among these distances: 39 16 0.08 40 179 0.92 ACGTcount: A:0.23, C:0.24, G:0.28, T:0.24 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT Found at i:64714193 original size:27 final size:26 Alignment explanation

Indices: 64714154--64714213 Score: 84 Period size: 27 Copynumber: 2.3 Consensus size: 26 64714144 CCACAAATAT * * 64714154 ATATCTGTTCTGGTGACTTTGTCACA 1 ATATCTGTTCTGGTAACTTCGTCACA * 64714180 ATATTTGTATCTGGTAACTTCGTCACA 1 ATATCTGT-TCTGGTAACTTCGTCACA 64714207 ATATCTG 1 ATATCTG 64714214 GCAGCTTCGC Statistics Matches: 29, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 26 7 0.24 27 22 0.76 ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42 Consensus pattern (26 bp): ATATCTGTTCTGGTAACTTCGTCACA Found at i:64718195 original size:27 final size:27 Alignment explanation

Indices: 64718165--64718342 Score: 180 Period size: 27 Copynumber: 6.6 Consensus size: 27 64718155 ATATCGAGTC * * 64718165 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTACATAATCAACT * 64718192 CGCACACTTAGTGCTACATAATCAAAT 1 CGCACACTTAGTGCTACATAATCAACT * * 64718219 CGCACACTTAGTGCTACATAGTTAGACT 1 CGCACACTTAGTGCTACATAATCA-ACT ** ** * 64718247 CGCACACTTAGTGCCGCATGGTCAATT 1 CGCACACTTAGTGCTACATAATCAACT * ** 64718274 CGCACACTTAGTGC-ATCATATTCATTT 1 CGCACACTTAGTGCTA-CATAATCAACT * * 64718301 CGCACACTTAGTGCAACATAGTCGAA-T 1 CGCACACTTAGTGCTACATAATC-AACT 64718328 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 64718343 GTACAATTTA Statistics Matches: 129, Mismatches: 18, Indels: 8 0.83 0.12 0.05 Matches are distributed among these distances: 27 105 0.81 28 24 0.19 ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28 Consensus pattern (27 bp): CGCACACTTAGTGCTACATAATCAACT Found at i:64718304 original size:82 final size:81 Alignment explanation

Indices: 64718186--64718341 Score: 224 Period size: 82 Copynumber: 1.9 Consensus size: 81 64718176 TGCTATATAA * * 64718186 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA 1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA 64718251 CACTTAGTGCCGCATGG 65 CACTTAGTGCCGCATGG * * ** * 64718268 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA 1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA 64718332 CACTTAGTGC 65 CACTTAGTGC 64718342 TGTACAATTT Statistics Matches: 66, Mismatches: 7, Indels: 3 0.87 0.09 0.04 Matches are distributed among these distances: 81 19 0.29 82 47 0.71 ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28 Consensus pattern (81 bp): TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC ACTTAGTGCCGCATGG Found at i:64718852 original size:136 final size:136 Alignment explanation

Indices: 64718608--64718879 Score: 535 Period size: 136 Copynumber: 2.0 Consensus size: 136 64718598 ATTCCGAGTC 64718608 GGCTACTCGATGACCTTCGATTTCCCCTTGTTGGACGCCTCTCCTTTAGGTTCTTGAGCTTAAAT 1 GGCTACTCGATGACCTTCGATTTCCCCTTGTTGGACGCCTCTCCTTTAGGTTCTTGAGCTTAAAT 64718673 AATACAAATAAGAGTATTCAATATTTAACCCAATAACATGAATTTATTTATCACATTCGGCAATC 66 AATACAAATAAGAGTATTCAATATTTAACCCAATAACATGAATTTATTTATCACATTCGGCAATC 64718738 ACACAT 131 ACACAT 64718744 GGCTACTCGATGACCTTCGATTTCCCCTTGTTGGACGCCTCTCCTTTAGGTTCTTGAGCTTAAAT 1 GGCTACTCGATGACCTTCGATTTCCCCTTGTTGGACGCCTCTCCTTTAGGTTCTTGAGCTTAAAT * 64718809 AATACAGATAAGAGTATTCAATATTTAACCCAATAACATGAATTTATTTATCACATTCGGCAATC 66 AATACAAATAAGAGTATTCAATATTTAACCCAATAACATGAATTTATTTATCACATTCGGCAATC 64718874 ACACAT 131 ACACAT 64718880 CATTAAATTT Statistics Matches: 135, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 136 135 1.00 ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34 Consensus pattern (136 bp): GGCTACTCGATGACCTTCGATTTCCCCTTGTTGGACGCCTCTCCTTTAGGTTCTTGAGCTTAAAT AATACAAATAAGAGTATTCAATATTTAACCCAATAACATGAATTTATTTATCACATTCGGCAATC ACACAT Found at i:64727175 original size:31 final size:31 Alignment explanation

Indices: 64727128--64727207 Score: 106 Period size: 31 Copynumber: 2.5 Consensus size: 31 64727118 TATCAGAACT * * * 64727128 AGAATCAGAATTAGAATCAGTATCAGGTAAC 1 AGAATCAAAATCAGAATCAATATCAGGTAAC * 64727159 ATAATCAAAATCAGAATCAATATCAGGTAAC 1 AGAATCAAAATCAGAATCAATATCAGGTAAC * 64727190 AGAATAAAAAATCAGAAT 1 AGAAT-CAAAATCAGAAT 64727208 GTGAATGCAA Statistics Matches: 42, Mismatches: 6, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 31 31 0.74 32 11 0.26 ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21 Consensus pattern (31 bp): AGAATCAAAATCAGAATCAATATCAGGTAAC Found at i:64727386 original size:27 final size:26 Alignment explanation

Indices: 64727344--64727445 Score: 114 Period size: 27 Copynumber: 3.8 Consensus size: 26 64727334 GCTCAGTTAT * * 64727344 CAGATATTGTGACAGAGTCACCAGATA 1 CAGATATTGTGGCAGAGCCACCAGA-A * 64727371 GAGATATTGTGGCAGAGCCACCAGAA 1 CAGATATTGTGGCAGAGCCACCAGAA * 64727397 CAGATATTTGTGGCATAGCCACCAGAAA 1 CAGATA-TTGTGGCAGAGCCACCAG-AA * * * 64727425 CAGATAATATGGCAAAGCCAC 1 CAGATATTGTGGCAGAGCCAC 64727446 TTAACAGAAT Statistics Matches: 65, Mismatches: 8, Indels: 4 0.84 0.10 0.05 Matches are distributed among these distances: 26 6 0.09 27 51 0.78 28 8 0.12 ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19 Consensus pattern (26 bp): CAGATATTGTGGCAGAGCCACCAGAA Found at i:64727632 original size:22 final size:22 Alignment explanation

Indices: 64727604--64727668 Score: 69 Period size: 22 Copynumber: 3.0 Consensus size: 22 64727594 GCAAATACGT * 64727604 TTGGCACACAGCCATAATCAGG 1 TTGGCACAAAGCCATAATCAGG * * 64727626 TTGGCACAGAGCCAT-ATGTAGG 1 TTGGCACAAAGCCATAAT-CAGG * * 64727648 TTGACACAAAGCCTTAATCAG 1 TTGGCACAAAGCCATAATCAG 64727669 AAGGCTTTAA Statistics Matches: 35, Mismatches: 6, Indels: 4 0.78 0.13 0.09 Matches are distributed among these distances: 21 2 0.06 22 31 0.89 23 2 0.06 ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22 Consensus pattern (22 bp): TTGGCACAAAGCCATAATCAGG Found at i:64728152 original size:27 final size:27 Alignment explanation

Indices: 64728095--64728289 Score: 250 Period size: 27 Copynumber: 7.3 Consensus size: 27 64728085 GGGGAAAAAT * * * 64728095 GGTAATTTTACCCCACAA-GGTATCTC 1 GGTAATTCTACCCTACAAGGGTATTTC * * * * 64728121 GGTAATTCCACCCTATAGGGGTATTTT 1 GGTAATTCTACCCTACAAGGGTATTTC * * 64728148 AGTAATACTACCCTACAAGGGTATTTC 1 GGTAATTCTACCCTACAAGGGTATTTC * 64728175 GGTAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAAGGGTATTTC * 64728202 GATAATTCTACCCTACAAGGGTATTTC 1 GGTAATTCTACCCTACAAGGGTATTTC * 64728229 GGTAATT-TCACCCTACAGGGGTATTTC 1 GGTAATTCT-ACCCTACAAGGGTATTTC * 64728256 GGTATTTCTACCCTACAAGGGTATTTC 1 GGTAATTCTACCCTACAAGGGTATTTC 64728283 GGTAATT 1 GGTAATT 64728290 TTGTAAATTG Statistics Matches: 143, Mismatches: 23, Indels: 5 0.84 0.13 0.03 Matches are distributed among these distances: 26 14 0.10 27 128 0.90 28 1 0.01 ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34 Consensus pattern (27 bp): GGTAATTCTACCCTACAAGGGTATTTC Found at i:64728290 original size:54 final size:54 Alignment explanation

Indices: 64728095--64728290 Score: 279 Period size: 54 Copynumber: 3.6 Consensus size: 54 64728085 GGGGAAAAAT * * * * * * 64728095 GGTAATTTTACCCCACAA-GGTATCTCGGTAATTCCACCCTATAGGGGTATTTT 1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTTCACCCTACAGGGGTATTTC * * 64728148 AGTAATACTACCCTACAAGGGTATTTCGGTAA-TTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTTC-ACCCTACAGGGGTATTTC * 64728202 GATAATTCTACCCTACAAGGGTATTTCGGTAATTTCACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTTCACCCTACAGGGGTATTTC * 64728256 GGTATTTCTACCCTACAAGGGTATTTCGGTAATTT 1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTT 64728291 TGTAAATTGA Statistics Matches: 127, Mismatches: 13, Indels: 5 0.88 0.09 0.03 Matches are distributed among these distances: 53 16 0.13 54 108 0.85 55 3 0.02 ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34 Consensus pattern (54 bp): GGTAATTCTACCCTACAAGGGTATTTCGGTAATTTCACCCTACAGGGGTATTTC Found at i:64728303 original size:27 final size:26 Alignment explanation

Indices: 64728271--64728485 Score: 99 Period size: 27 Copynumber: 8.0 Consensus size: 26 64728261 TTCTACCCTA 64728271 CAAGGGTATTTCGGTAATTTTGTAAAT 1 CAAGGGTATTT-GGTAATTTTGTAAAT ** ** 64728298 TGAGGGTAAAATGGTAATTTTGTAAAT 1 CAAGGGT-ATTTGGTAATTTTGTAAAT ** * 64728325 CAAGGGTATTTTGGTAATTTTACAAGT 1 CAAGGGTA-TTTGGTAATTTTGTAAAT ** ** ** 64728352 CAAGGGTATTTCAATAATTTTACAGGT 1 CAAGGGTATTT-GGTAATTTTGTAAAT * * *** 64728379 CGAGGGTATTTCAGTAATTTCACAAAT 1 CAAGGGTATTT-GGTAATTTTGTAAAT * ** 64728406 CAGGGGTATTTTGGTAATTTTACAAA- 1 CAAGGGTA-TTTGGTAATTTTGTAAAT * * * * 64728432 CTAGGGGTATTTTAGTAATTTTATAAAC 1 C-AAGGGTA-TTTGGTAATTTTGTAAAT * * 64728460 CAAGGGTATTTTAGTAATTTGGTAAA 1 CAAGGGTA-TTTGGTAATTTTGTAAA 64728486 CTAAAGCATT Statistics Matches: 154, Mismatches: 28, Indels: 12 0.79 0.14 0.06 Matches are distributed among these distances: 26 5 0.03 27 143 0.93 28 6 0.04 ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39 Consensus pattern (26 bp): CAAGGGTATTTGGTAATTTTGTAAAT Found at i:64728370 original size:54 final size:54 Alignment explanation

Indices: 64728311--64728479 Score: 178 Period size: 54 Copynumber: 3.1 Consensus size: 54 64728301 GGGTAAAATG ** * * * 64728311 GTAATTTTGTAAATCAAGGGTATTTTGGTAATTTTACAAGTCAAGGGTATTTCA 1 GTAATTTTACAAATCAAGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTTA * ** * * * * * 64728365 ATAATTTTACAGGTCGAGGGTATTTCAGTAATTTCACAAATCAGGGGTATTTTG 1 GTAATTTTACAAATCAAGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTTA * * * 64728419 GTAATTTTACAAA-CTAGGGGTATTTTAGTAATTTTATAAACCAAGGGTATTTTA 1 GTAATTTTACAAATC-AAGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTTA 64728473 GTAATTT 1 GTAATTT 64728480 GGTAAACTAA Statistics Matches: 90, Mismatches: 24, Indels: 2 0.78 0.21 0.02 Matches are distributed among these distances: 53 1 0.01 54 89 0.99 ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40 Consensus pattern (54 bp): GTAATTTTACAAATCAAGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTTA Found at i:64728466 original size:81 final size:81 Alignment explanation

Indices: 64728321--64728479 Score: 203 Period size: 81 Copynumber: 2.0 Consensus size: 81 64728311 GTAATTTTGT * *** * 64728321 AAATCAAGGGTATTTTGGTAATTTTACAAGTCAAGGGTATTTCAATAATTTTACAGGTCGAGGGT 1 AAATCAAGGGTATTTTGGTAATTTTACAACTCAAGGGTATTTCAATAATTTTACAAACCAAGGGT 64728386 ATTTCAGTAATTTCAC 66 ATTTCAGTAATTTCAC * * * * * 64728402 AAATCAGGGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTAGTAATTTTATAAACCAAGGG 1 AAATCAAGGGTATTTTGGTAATTTTAC-AACTCAAGGGTATTTCAATAATTTTACAAACCAAGGG * 64728466 TATTTTAGTAATTT 65 TATTTCAGTAATTT 64728480 GGTAAACTAA Statistics Matches: 66, Mismatches: 11, Indels: 2 0.84 0.14 0.03 Matches are distributed among these distances: 81 63 0.95 82 3 0.05 ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39 Consensus pattern (81 bp): AAATCAAGGGTATTTTGGTAATTTTACAACTCAAGGGTATTTCAATAATTTTACAAACCAAGGGT ATTTCAGTAATTTCAC Found at i:64728486 original size:27 final size:27 Alignment explanation

Indices: 64728311--64728479 Score: 158 Period size: 27 Copynumber: 6.3 Consensus size: 27 64728301 GGGTAAAATG ** * * 64728311 GTAATTTTGTAAATCAAGGGTATTTTG 1 GTAATTTTACAAACCAAGGGTATTTTA ** * 64728338 GTAATTTTACAAGTCAAGGGTATTTCA 1 GTAATTTTACAAACCAAGGGTATTTTA * *** * * 64728365 ATAATTTTACAGGTCGAGGGTATTTCA 1 GTAATTTTACAAACCAAGGGTATTTTA * * * * 64728392 GTAATTTCACAAATCAGGGGTATTTTG 1 GTAATTTTACAAACCAAGGGTATTTTA * * 64728419 GTAATTTTACAAACTAGGGGTATTTTA 1 GTAATTTTACAAACCAAGGGTATTTTA * 64728446 GTAATTTTATAAACCAAGGGTATTTTA 1 GTAATTTTACAAACCAAGGGTATTTTA 64728473 GTAATTT 1 GTAATTT 64728480 GGTAAACTAA Statistics Matches: 119, Mismatches: 23, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 27 119 1.00 ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40 Consensus pattern (27 bp): GTAATTTTACAAACCAAGGGTATTTTA Found at i:64736216 original size:47 final size:47 Alignment explanation

Indices: 64736138--64736642 Score: 886 Period size: 47 Copynumber: 10.7 Consensus size: 47 64736128 CCCTTCGGGA * * * * * * 64736138 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * * 64736185 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 64736232 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 64736279 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 64736326 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 64736373 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 64736420 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 64736467 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 64736514 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 64736561 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * * 64736608 CTTATCTCATATATGCA-TGTTCACATCCATCACAT 1 CTTATCACATATATACACT-TTCACATTCATCACAT 64736643 AGAATCCTAA Statistics Matches: 442, Mismatches: 15, Indels: 2 0.96 0.03 0.00 Matches are distributed among these distances: 46 1 0.00 47 441 1.00 ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:64741987 original size:40 final size:40 Alignment explanation

Indices: 64741939--64742122 Score: 171 Period size: 40 Copynumber: 4.6 Consensus size: 40 64741929 GCTACTCGTT * 64741939 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACA 1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA * * * * * 64741979 CAATTGCCTTCAGGACTTAACCCGGATT-TAGTAACTCGCG 1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCACA * * * 64742019 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCACA * * * * * 64742058 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTACCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAACTCA-CA 64742099 CAAA-GCCTTCGGGACTTAGCCCGG 1 CAAATGCCTTCGGGACTTAGCCCGG 64742123 ACATCATTCA Statistics Matches: 116, Mismatches: 20, Indels: 16 0.76 0.13 0.11 Matches are distributed among these distances: 38 2 0.02 39 30 0.26 40 72 0.62 41 12 0.10 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA Found at i:64742083 original size:79 final size:82 Alignment explanation

Indices: 64741939--64742123 Score: 204 Period size: 79 Copynumber: 2.3 Consensus size: 82 64741929 GCTACTCGTT * * * 64741939 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCACACAATTGCCTTCAGGACTTAACCCG 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCAGGACTTAACCCG * * 64742003 GATTTAGTAAC-T-CGCG 66 GATATAGTAACTTAC-CA * * ** 64742019 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCAGGA-CTTAACCC * * 64742081 GGATATGGTCACTTACCA 65 GGATATAGTAACTTACCA 64742099 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 64742124 CATCATTCAA Statistics Matches: 89, Mismatches: 11, Indels: 10 0.81 0.10 0.09 Matches are distributed among these distances: 78 3 0.03 79 53 0.60 80 32 0.36 81 1 0.01 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25 Consensus pattern (82 bp): CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCAGGACTTAACCCG GATATAGTAACTTACCA Found at i:64748475 original size:40 final size:39 Alignment explanation

Indices: 64748391--64748575 Score: 185 Period size: 40 Copynumber: 4.6 Consensus size: 39 64748381 TTGAATGATG * * * * 64748391 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA 1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA * * * 64748431 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT 1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA * * 64748471 TCCGGGCTAAGCCCGAAGGCATTTGCGCGAGTTACTAAA 1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA * * * 64748510 TCCGGGTTAAGTCCTGAAGGCAATTGTGTGAGTTACTATAA 1 TCCGGGCTAAGTCC-GAAGGCATTTGTGCGAGTTACTA-AA * 64748551 -CCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGT-CCGAAGGCATTTG 64748576 AACGAGTAGC Statistics Matches: 120, Mismatches: 20, Indels: 10 0.80 0.13 0.07 Matches are distributed among these distances: 39 36 0.30 40 72 0.60 41 12 0.10 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (39 bp): TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA Found at i:64748529 original size:79 final size:81 Alignment explanation

Indices: 64748391--64748575 Score: 209 Period size: 79 Copynumber: 2.3 Consensus size: 81 64748381 TTGAATGATG * * * 64748391 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTTGCGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT 64748455 TGTGCGAGATACTA-A 66 TGTGCGAGATACTATA * * * ** 64748470 TTCCGGGCTAAG-CCCGAAGGCATTTGCGC-GAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCA 1 -TCCGGGCTAAGTCCCGAAGGCATTTGCGCTAAGTGACCAAATCCGGACTAAGATCC-GAAGGCA * * 64748532 ATTGTGTGAGTTACTATA 64 ATTGTGCGAGATACTATA * * 64748550 ACCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 64748576 AACGAGTAGC Statistics Matches: 89, Mismatches: 12, Indels: 8 0.82 0.11 0.07 Matches are distributed among these distances: 78 3 0.03 79 54 0.61 80 32 0.36 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (81 bp): TCCGGGCTAAGTCCCGAAGGCATTTGCGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT TGTGCGAGATACTATA Found at i:64748597 original size:79 final size:78 Alignment explanation

Indices: 64748392--64748608 Score: 192 Period size: 79 Copynumber: 2.7 Consensus size: 78 64748382 TGAATGATGT ** * * * * * 64748392 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT 1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTTACTATATCCGG-TTAAGATCCGAAGGCAATT * 64748456 GTGCGAGATACTAATT 63 GTGCGAGATACTAATA ** * 64748472 CCGGGCTAAGCCCGAAGGCATTTGCGCGAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCAATTG 1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTATATCC-GGTTAAGATCC-GAAGGCAATTG * * 64748536 TGTGAGTTACT-ATAA 64 TGCGAGATACTAAT-A * 64748551 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAA-ATTCCGAAGG 1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTATATCCGGTTAAGA-TCCGAAGG 64748609 TACGTGATTT Statistics Matches: 115, Mismatches: 14, Indels: 17 0.79 0.10 0.12 Matches are distributed among these distances: 78 5 0.04 79 64 0.56 80 46 0.40 ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25 Consensus pattern (78 bp): CCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTATATCCGGTTAAGATCCGAAGGCAATTGTG CGAGATACTAATA Found at i:64749071 original size:118 final size:119 Alignment explanation

Indices: 64748863--64749101 Score: 435 Period size: 118 Copynumber: 2.0 Consensus size: 119 64748853 AGCTATTTGA * 64748863 ATGCTATACTTTTGTTGTGCTGGAATTCCTTGCTCAAAACTTACTAAGCATAAATTGCTTACTCC 1 ATGCTATACTTTTGCTGTGCTGGAATTCCTTGCTCAAAACTTACTAAGCATAAATTGCTTACTCC ** 64748928 GTTTCATTGCTCCTCTGTTTTATAGA-TTTGGTTCTCCAGCTATCGGACTCGGG 66 GTTTCATTGAACCTCTGTTTTATAGATTTTGGTTCTCCAGCTATCGGACTCGGG 64748981 ATGCTATACTTTTGCTGTGCTGGAATTCCTTGCTCAAAACTTACTAAGCATAAATTGCTTACTCC 1 ATGCTATACTTTTGCTGTGCTGGAATTCCTTGCTCAAAACTTACTAAGCATAAATTGCTTACTCC * 64749046 GTTTCTTTGAACCTCTGTTTTATAGATTTTGGTTCTCCAGCTATCGGACTCGGG 66 GTTTCATTGAACCTCTGTTTTATAGATTTTGGTTCTCCAGCTATCGGACTCGGG 64749100 AT 1 AT 64749102 TTTGAAGTCG Statistics Matches: 116, Mismatches: 4, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 118 87 0.75 119 29 0.25 ACGTcount: A:0.21, C:0.22, G:0.18, T:0.40 Consensus pattern (119 bp): ATGCTATACTTTTGCTGTGCTGGAATTCCTTGCTCAAAACTTACTAAGCATAAATTGCTTACTCC GTTTCATTGAACCTCTGTTTTATAGATTTTGGTTCTCCAGCTATCGGACTCGGG Found at i:64750536 original size:131 final size:132 Alignment explanation

Indices: 64750187--64750789 Score: 985 Period size: 131 Copynumber: 4.6 Consensus size: 132 64750177 TTGACAGCGA * * 64750187 AGCAGATCGAAGATGGCGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT 1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT * * * * * 64750252 TCTACTTCCCTGGACAATAGTGCAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGCAGTAGT 66 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAGT 64750317 GG 131 GG 64750319 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT 1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT * * 64750384 TCTACTTCCCTGGGCAACAGTGGAATAGATAGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT 66 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAGT 64750449 GG 131 GG * * 64750451 AGCAGATCGAAGATGGAGGA-TTCACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT 1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT * 64750515 TCTACTTCCCTGGGCAACAGTGGAATGGATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAGT 66 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAGT 64750580 GG 131 GG * * * 64750582 AGGAGATCGAAGATGGAGGA-TTCACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT 1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT * 64750646 TCTACTTCCCTGGGCAACAGTGGAATGGATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAGT 66 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAGT 64750711 GG 131 GG * * * * * * * 64750713 AGTAGATCGAAGATGGCGGATTTTACCTCTCTGTAGTTACAATAGAGTACATTGAAGCCAATAAT 1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT 64750778 TCTACTTCCCTG 66 TCTACTTCCCTG 64750790 AACAATAGTT Statistics Matches: 448, Mismatches: 22, Indels: 2 0.95 0.05 0.00 Matches are distributed among these distances: 131 255 0.57 132 193 0.43 ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28 Consensus pattern (132 bp): AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAGT GG Found at i:64752748 original size:21 final size:21 Alignment explanation

Indices: 64752724--64752763 Score: 53 Period size: 21 Copynumber: 1.9 Consensus size: 21 64752714 CGACCGTACC * * 64752724 TTAACATATTGAATCAAAAAG 1 TTAACAGATAGAATCAAAAAG * 64752745 TTAATAGATAGAATCAAAA 1 TTAACAGATAGAATCAAAA 64752764 TCGAACCACA Statistics Matches: 16, Mismatches: 3, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 21 16 1.00 ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28 Consensus pattern (21 bp): TTAACAGATAGAATCAAAAAG Found at i:64753817 original size:51 final size:51 Alignment explanation

Indices: 64753702--64753844 Score: 136 Period size: 51 Copynumber: 2.9 Consensus size: 51 64753692 CTCACTCTCT * ** * * 64753702 TTTTCAGTTTTCTTTTCTTTTTCACACTCAT-TT-TTATTC--TCAATCTCA 1 TTTTCAATTTTCTTTTCTTGCTCACACTCATCTTCTTTTTCTTTC-ATTTCA 64753750 TTTTCAATTTTCTTTTCTAT-CTCACACTCATCTTCTTTTTCTTTCATTTCA 1 TTTTCAATTTTCTTTTCT-TGCTCACACTCATCTTCTTTTTCTTTCATTTCA * * * * 64753801 TTTTC-TTTTTCATTTTCTTGCTCGCACTCTTTTTCTTTTTCTTT 1 TTTTCAATTTTC-TTTTCTTGCTCACACTCATCTTCTTTTTCTTT 64753845 TTCACATGCT Statistics Matches: 80, Mismatches: 8, Indels: 11 0.81 0.08 0.11 Matches are distributed among these distances: 48 27 0.34 49 3 0.04 50 11 0.14 51 37 0.46 52 2 0.03 ACGTcount: A:0.13, C:0.24, G:0.02, T:0.62 Consensus pattern (51 bp): TTTTCAATTTTCTTTTCTTGCTCACACTCATCTTCTTTTTCTTTCATTTCA Found at i:64754825 original size:10 final size:11 Alignment explanation

Indices: 64754810--64754850 Score: 66 Period size: 11 Copynumber: 3.8 Consensus size: 11 64754800 AATAATAATT 64754810 AATTTTTTTC- 1 AATTTTTTTCG 64754820 AATTTTTTTCG 1 AATTTTTTTCG * 64754831 ATTTTTTTTCG 1 AATTTTTTTCG 64754842 AATTTTTTT 1 AATTTTTTT 64754851 TACAATCTCA Statistics Matches: 28, Mismatches: 2, Indels: 1 0.90 0.06 0.03 Matches are distributed among these distances: 10 10 0.36 11 18 0.64 ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71 Consensus pattern (11 bp): AATTTTTTTCG Found at i:64754828 original size:11 final size:11 Alignment explanation

Indices: 64754812--64754856 Score: 56 Period size: 12 Copynumber: 4.0 Consensus size: 11 64754802 TAATAATTAA 64754812 TTTTTTTCAA- 1 TTTTTTTCAAT * 64754822 TTTTTTTCGAT 1 TTTTTTTCAAT 64754833 TTTTTTTCGAAT 1 TTTTTTTC-AAT 64754845 TTTTTTTACAAT 1 TTTTTTT-CAAT 64754857 CTCATAATAC Statistics Matches: 30, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 10 9 0.30 11 8 0.27 12 12 0.40 13 1 0.03 ACGTcount: A:0.18, C:0.09, G:0.04, T:0.69 Consensus pattern (11 bp): TTTTTTTCAAT Found at i:64754837 original size:12 final size:12 Alignment explanation

Indices: 64754812--64754851 Score: 59 Period size: 10 Copynumber: 3.6 Consensus size: 12 64754802 TAATAATTAA 64754812 TTTTTTTC-AA- 1 TTTTTTTCGAAT 64754822 TTTTTTTCG-AT 1 TTTTTTTCGAAT 64754833 TTTTTTTCGAAT 1 TTTTTTTCGAAT 64754845 TTTTTTT 1 TTTTTTT 64754852 ACAATCTCAT Statistics Matches: 27, Mismatches: 0, Indels: 4 0.87 0.00 0.13 Matches are distributed among these distances: 10 9 0.33 11 9 0.33 12 9 0.33 ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75 Consensus pattern (12 bp): TTTTTTTCGAAT Found at i:64756759 original size:132 final size:132 Alignment explanation

Indices: 64756522--64757327 Score: 1177 Period size: 132 Copynumber: 6.2 Consensus size: 132 64756512 GGGATCACAT * * 64756522 CAACAGTGGAATAGATTGAAGATTTCAGATCATATCTCCCTAAGCAGTAATGGAGCAGATCGAAG 1 CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG * * 64756587 ATGGCAGATTTTACCTCTCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTG 66 ATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTG * 64756652 AA 131 GA * * * * 64756654 CAACAGTGGAATAGATTAAATATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAG 1 CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG * * * 64756719 ATGACAGATTTTAACTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAG----------TCCCTG 66 ATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTG 64756774 GA 131 GA * 64756776 CAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG 1 CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG * * * 64756841 ATGGCGGATTTTACCTCCCTCTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCTG 66 ATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTG 64756906 GA 131 GA * * 64756908 CAACAATGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG 1 CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG * * * * 64756973 ATGGTAGATTTTACCTCCCTCTGGTTACAGCGGAGTACATTGAAGCCAGTAATTCTACTTCTCTG 66 ATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTG 64757038 GA 131 GA * * * 64757040 CAATAGTGGAATAGATGGAAGACTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG 1 CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG * * 64757105 ATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTG 66 ATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTG * 64757170 GG 131 GA * * 64757172 CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCTCTAAGCAGTAGTGGAGTAGATCGAAG 1 CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG * * * 64757237 ATGGCGGATTTTACCTCACTGTGGTTACAGTGGAGTACATTGAAGCTAGTAA-TCATA-TCTCCC 66 ATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC-TACT-TCCC * 64757300 TGGT 129 TGGA ** * 64757304 CAGTAGTGGAATAGGTTGAAGATT 1 CAACAGTGGAATAGATTGAAGATT 64757328 GTAGGTCCTA Statistics Matches: 609, Mismatches: 53, Indels: 24 0.89 0.08 0.03 Matches are distributed among these distances: 122 110 0.18 131 3 0.00 132 496 0.81 ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29 Consensus pattern (132 bp): CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG ATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTG GA Found at i:64757677 original size:19 final size:19 Alignment explanation

Indices: 64757653--64757763 Score: 177 Period size: 19 Copynumber: 5.8 Consensus size: 19 64757643 AATCTTTAGG 64757653 GATATGCAATCTTAGATAT 1 GATATGCAATCTTAGATAT 64757672 GATATGCAATCTTAGATAT 1 GATATGCAATCTTAGATAT * ** 64757691 AATATATAATCTTAGATAT 1 GATATGCAATCTTAGATAT 64757710 GATATGCAATCTTAGATAT 1 GATATGCAATCTTAGATAT ** 64757729 GATATATAATCTTAGATAT 1 GATATGCAATCTTAGATAT 64757748 GATATGCAATCTTAGA 1 GATATGCAATCTTAGA 64757764 AGATATGATT Statistics Matches: 82, Mismatches: 10, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 82 1.00 ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38 Consensus pattern (19 bp): GATATGCAATCTTAGATAT Found at i:64757703 original size:38 final size:38 Alignment explanation

Indices: 64757660--64757763 Score: 199 Period size: 38 Copynumber: 2.7 Consensus size: 38 64757650 AGGGATATGC 64757660 AATCTTAGATATGATATGCAATCTTAGATATAATATAT 1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT * 64757698 AATCTTAGATATGATATGCAATCTTAGATATGATATAT 1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT 64757736 AATCTTAGATATGATATGCAATCTTAGA 1 AATCTTAGATATGATATGCAATCTTAGA 64757764 AGATATGATT Statistics Matches: 65, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 38 65 1.00 ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38 Consensus pattern (38 bp): AATCTTAGATATGATATGCAATCTTAGATATAATATAT Found at i:64757789 original size:22 final size:21 Alignment explanation

Indices: 64757653--64757789 Score: 114 Period size: 19 Copynumber: 6.9 Consensus size: 21 64757643 AATCTTTAGG * 64757653 GATATGCAATCTT--AGATAT 1 GATATGTAATCTTAGAGATAT * 64757672 GATATGCAATCTT--AGATAT 1 GATATGTAATCTTAGAGATAT * * 64757691 AATATATAATCTT--AGATAT 1 GATATGTAATCTTAGAGATAT * 64757710 GATATGCAATCTT--AGATAT 1 GATATGTAATCTTAGAGATAT * 64757729 GATATATAATCTT--AGATAT 1 GATATGTAATCTTAGAGATAT * 64757748 GATATGCAATCTTAGAAGATAT 1 GATATGTAATCTTAG-AGATAT * 64757770 GATTTTGTAATCTTAGAGAT 1 GA-TATGTAATCTTAGAGAT 64757790 TTAATTTGTA Statistics Matches: 102, Mismatches: 12, Indels: 5 0.86 0.10 0.04 Matches are distributed among these distances: 19 79 0.77 22 12 0.12 23 11 0.11 ACGTcount: A:0.39, C:0.08, G:0.15, T:0.39 Consensus pattern (21 bp): GATATGTAATCTTAGAGATAT Found at i:64762520 original size:245 final size:245 Alignment explanation

Indices: 64761292--64762488 Score: 2286 Period size: 245 Copynumber: 4.9 Consensus size: 245 64761282 TATTAGCAAG * * 64761292 GCCTTAGATGCGTACACGAAGGAAAAAGAAAATCAATATTCACTTTCTTGTTTTCAAGAAAATCA 1 GCCTTAGATGCGTATACGAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCA 64761357 AGAAACCGAATCTTGGTCCAATTTTGCTGTTTGGGGCGATTTCAAGAATCAAGAGAATCAAGATT 66 AGAAACCGAATCTTGGTCCAATTTTGCTGTTTGGGGCGATTTCAAGAATCAAGAGAATCAAGATT 64761422 TCAAATCTTTGAAATCTTGGTCCAAGAAACTGAATCTTGCAGCTAAGGCACATTGGATCTCTGTT 131 TCAAATCTTTGAAATCTTGGTCCAAGAAACTGAATCTTGCAGCTAAGGCACATTGGATCTCTGTT 64761487 ACGAGCATCAATTAACCAATTTTGGAAGGAAACTGATACGAGTCACAAAT 196 ACGAGCATCAATTAACCAATTTTGGAAGGAAACTGATACGAGTCACAAAT 64761537 GCCTTAGATGCGTATACGAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCA 1 GCCTTAGATGCGTATACGAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCA 64761602 AGAAACCGAATCTTGGTCCAATTTTGCTGTTTGGGGCGATTTCAAGAATCAAGAGAATCAAGATT 66 AGAAACCGAATCTTGGTCCAATTTTGCTGTTTGGGGCGATTTCAAGAATCAAGAGAATCAAGATT 64761667 TCAAATCTTTGAAATCTTGGTCCAAGAAACTGAATCTTGCAGCTAAGGCACATTGGATCTCTGTT 131 TCAAATCTTTGAAATCTTGGTCCAAGAAACTGAATCTTGCAGCTAAGGCACATTGGATCTCTGTT 64761732 ACGAGCATCAATTAACCAATTTTGGAAGGAAACTGATACGAGTCACAAAT 196 ACGAGCATCAATTAACCAATTTTGGAAGGAAACTGATACGAGTCACAAAT 64761782 GCCTTAGATGCGTATACGAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCA 1 GCCTTAGATGCGTATACGAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCA 64761847 AGAAACCGAATCTTGGTCCAATTTTGCTGTTTGGGGCGATTTCAAGAATCAAGAGAATCAAGATT 66 AGAAACCGAATCTTGGTCCAATTTTGCTGTTTGGGGCGATTTCAAGAATCAAGAGAATCAAGATT 64761912 TCAAATCTTTGAAATCTTGGTCCAAGAAACTGAATCTTGCAGCTAAGGCACATTGGATCTCTGTT 131 TCAAATCTTTGAAATCTTGGTCCAAGAAACTGAATCTTGCAGCTAAGGCACATTGGATCTCTGTT 64761977 ACGAGCATCAATTAACCAATTTTGGAAGGAAACTGATACGAGTCACAAAT 196 ACGAGCATCAATTAACCAATTTTGGAAGGAAACTGATACGAGTCACAAAT 64762027 GCCTTAGATGCGTATACGAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCA 1 GCCTTAGATGCGTATACGAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCA 64762092 AGAAACCGAATCTTGGTCCAATTTTGCTGTTTGGGGCGATTTCAAGAATCAAGAGAATCAAGATT 66 AGAAACCGAATCTTGGTCCAATTTTGCTGTTTGGGGCGATTTCAAGAATCAAGAGAATCAAGATT 64762157 TCAAATCTTTGAAATCTTGGTCCAAGAAACTGAATCTTGCAGCTAAGGCACATTGGATCTCTGTT 131 TCAAATCTTTGAAATCTTGGTCCAAGAAACTGAATCTTGCAGCTAAGGCACATTGGATCTCTGTT 64762222 ACGAGCATCAATTAACCAATTTTGGAAGGAAACTGATACGAGTCACAAAT 196 ACGAGCATCAATTAACCAATTTTGGAAGGAAACTGATACGAGTCACAAAT 64762272 GCCTTAGATGCGTATACGAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCA 1 GCCTTAGATGCGTATACGAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCA * * * * 64762337 AGAAACCGAATCTTGGTCCAATTTTGCTATTTTGAGCGATTTCAAGAATCAAGAAAATCAAGATT 66 AGAAACCGAATCTTGGTCCAATTTTGCTGTTTGGGGCGATTTCAAGAATCAAGAGAATCAAGATT * * * * 64762402 TCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCTTGCAGCTAAGGCGCATTGGATCTCAGTT 131 TCAAATCTTTGAAATCTTGGTCCAAGAAACTGAATCTTGCAGCTAAGGCACATTGGATCTCTGTT ** 64762467 ACGAGCATCAACGAACCAATTT 196 ACGAGCATCAATTAACCAATTT 64762489 CGGGAGAGAA Statistics Matches: 940, Mismatches: 12, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 245 940 1.00 ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28 Consensus pattern (245 bp): GCCTTAGATGCGTATACGAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCA AGAAACCGAATCTTGGTCCAATTTTGCTGTTTGGGGCGATTTCAAGAATCAAGAGAATCAAGATT TCAAATCTTTGAAATCTTGGTCCAAGAAACTGAATCTTGCAGCTAAGGCACATTGGATCTCTGTT ACGAGCATCAATTAACCAATTTTGGAAGGAAACTGATACGAGTCACAAAT Found at i:64770793 original size:23 final size:22 Alignment explanation

Indices: 64770741--64770793 Score: 56 Period size: 23 Copynumber: 2.4 Consensus size: 22 64770731 TCCACGTCTT * 64770741 TTTCTTTTGTTTCTTTTTCTAA 1 TTTCTTTTCTTTCTTTTTCTAA 64770763 -TTCATTTTCTCTTCTTTCTTC-AA 1 TTTC-TTTTCT-TTCTTT-TTCTAA 64770786 TTTCTTTT 1 TTTCTTTT 64770794 TCACTCTCAA Statistics Matches: 26, Mismatches: 1, Indels: 7 0.76 0.03 0.21 Matches are distributed among these distances: 21 3 0.12 22 5 0.19 23 12 0.46 24 6 0.23 ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70 Consensus pattern (22 bp): TTTCTTTTCTTTCTTTTTCTAA Found at i:64779863 original size:55 final size:54 Alignment explanation

Indices: 64779768--64779917 Score: 149 Period size: 55 Copynumber: 2.8 Consensus size: 54 64779758 CTACTTTGTT * ** * * 64779768 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG 1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG * * * * ** * 64779822 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG 1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG * * 64779877 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG 1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG 64779918 GGCTCAATAT Statistics Matches: 79, Mismatches: 15, Indels: 4 0.81 0.15 0.04 Matches are distributed among these distances: 54 37 0.47 55 42 0.53 ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29 Consensus pattern (54 bp): GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG Found at i:64779880 original size:27 final size:27 Alignment explanation

Indices: 64779740--64779917 Score: 146 Period size: 27 Copynumber: 6.6 Consensus size: 27 64779730 NNNNTTGTAC 64779740 AGCACTAAGTGTGCGATTCT-ACTT-TGT 1 AGCACTAAGTGTGCGATT-TGA-TTATGT * ** * 64779767 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGATTTGATTATGT * ** * 64779793 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGATTTGATTATGT * * * 64779821 GGCACTAAGTGTGCGGGTTTGACTATGT 1 AGCACTAAGTGTGC-GATTTGATTATGT * 64779849 AGCACTAAGTGTGCGATTTGATTACGT 1 AGCACTAAGTGTGCGATTTGATTATGT * * * * 64779876 GGCACTAAATGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGATTATGT * 64779903 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 64779918 GGCTCAATAT Statistics Matches: 121, Mismatches: 25, Indels: 10 0.78 0.16 0.06 Matches are distributed among these distances: 26 2 0.02 27 97 0.80 28 22 0.18 ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGATTATGT Found at i:64779881 original size:82 final size:81 Alignment explanation

Indices: 64779741--64779896 Score: 190 Period size: 82 Copynumber: 1.9 Consensus size: 81 64779731 NNNTTGTACA * * * * 64779741 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT 1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT 64779806 GCGAATTGACCATGCG 66 GCGAATTGACCATGCG * ** * 64779822 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA 1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA * 64779885 TGTGCGAGTTGA 63 TGTGCGAATTGA 64779897 TTATATAGCA Statistics Matches: 63, Mismatches: 9, Indels: 5 0.82 0.12 0.06 Matches are distributed among these distances: 81 15 0.24 82 48 0.76 ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30 Consensus pattern (81 bp): GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT GCGAATTGACCATGCG Found at i:64784441 original size:56 final size:56 Alignment explanation

Indices: 64784355--64784460 Score: 194 Period size: 56 Copynumber: 1.9 Consensus size: 56 64784345 GTTGCCTTAA * 64784355 AGATGATGCATGAATGATTCAATACAATGAATGGAAGAGTGCATGAATATCCACCT 1 AGATGATGCATGAATGATTCAATACAATGAATGGAAGAATGCATGAATATCCACCT * 64784411 AGATGATGCATGAATGATTTAATACAATGAATGGAAGAATGCATGAATAT 1 AGATGATGCATGAATGATTCAATACAATGAATGGAAGAATGCATGAATAT 64784461 TCACTTACAT Statistics Matches: 48, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 56 48 1.00 ACGTcount: A:0.42, C:0.10, G:0.22, T:0.26 Consensus pattern (56 bp): AGATGATGCATGAATGATTCAATACAATGAATGGAAGAATGCATGAATATCCACCT Found at i:64790846 original size:14 final size:14 Alignment explanation

Indices: 64790816--64790859 Score: 61 Period size: 14 Copynumber: 3.1 Consensus size: 14 64790806 TCTTTTCTTC * 64790816 CTTTTTCTTTTCACT 1 CTTTTTCTTTT-TCT * 64790831 CTTTTTGTTTTTCT 1 CTTTTTCTTTTTCT 64790845 CTTTTTCTTTTTCT 1 CTTTTTCTTTTTCT 64790859 C 1 C 64790860 GCTCAATAGA Statistics Matches: 26, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 14 16 0.62 15 10 0.38 ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73 Consensus pattern (14 bp): CTTTTTCTTTTTCT Found at i:64790856 original size:15 final size:15 Alignment explanation

Indices: 64790805--64790856 Score: 54 Period size: 15 Copynumber: 3.5 Consensus size: 15 64790795 ACTCTCCTCA 64790805 TTCTTTTCTTC-CTTT 1 TTCTTTT-TTCTCTTT ** 64790820 TTCTTTTCACTCTTT 1 TTCTTTTTTCTCTTT * 64790835 TT-GTTTTTCTCTTT 1 TTCTTTTTTCTCTTT 64790849 TTCTTTTT 1 TTCTTTTT 64790857 CTCGCTCAAT Statistics Matches: 29, Mismatches: 6, Indels: 4 0.74 0.15 0.10 Matches are distributed among these distances: 14 12 0.41 15 17 0.59 ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75 Consensus pattern (15 bp): TTCTTTTTTCTCTTT Found at i:64792364 original size:11 final size:10 Alignment explanation

Indices: 64792339--64792399 Score: 54 Period size: 10 Copynumber: 6.1 Consensus size: 10 64792329 ACCAATAAAA 64792339 TAAA-TGAGC 1 TAAATTGAGC * 64792348 TGAATTGTAGC 1 TAAATTG-AGC 64792359 TAAATTGAGC 1 TAAATTGAGC ** 64792369 TCGATTGAGC 1 TAAATTGAGC 64792379 TGAAA-TGAGC 1 T-AAATTGAGC * 64792389 TCAATTGAGC 1 TAAATTGAGC 64792399 T 1 T 64792400 GGTCGGAGTT Statistics Matches: 41, Mismatches: 7, Indels: 7 0.75 0.13 0.13 Matches are distributed among these distances: 9 5 0.12 10 26 0.63 11 10 0.24 ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30 Consensus pattern (10 bp): TAAATTGAGC Found at i:64792400 original size:20 final size:20 Alignment explanation

Indices: 64792340--64792400 Score: 79 Period size: 20 Copynumber: 3.0 Consensus size: 20 64792330 CCAATAAAAT * 64792340 AAATGAGCTGAATTGTAGCT- 1 AAATGAGCTCAATTG-AGCTG * 64792360 AAATTGAGCTCGATTGAGCTG 1 AAA-TGAGCTCAATTGAGCTG 64792381 AAATGAGCTCAATTGAGCTG 1 AAATGAGCTCAATTGAGCTG 64792401 GTCGGAGTTG Statistics Matches: 36, Mismatches: 3, Indels: 4 0.84 0.07 0.09 Matches are distributed among these distances: 20 23 0.64 21 13 0.36 ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28 Consensus pattern (20 bp): AAATGAGCTCAATTGAGCTG Found at i:64796966 original size:25 final size:25 Alignment explanation

Indices: 64796928--64796991 Score: 65 Period size: 25 Copynumber: 2.6 Consensus size: 25 64796918 TCGATTTCAG * * * 64796928 CTCGTATGAACTTACTGATACTCAA 1 CTCGAATGAGCTTACCGATACTCAA * * 64796953 CTCGAATGAGCTTACCGTTATTCAA 1 CTCGAATGAGCTTACCGATACTCAA * * 64796978 CTCGGAGGAGCTTA 1 CTCGAATGAGCTTA 64796992 TCGTTTACAA Statistics Matches: 32, Mismatches: 7, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 25 32 1.00 ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30 Consensus pattern (25 bp): CTCGAATGAGCTTACCGATACTCAA Found at i:64796996 original size:25 final size:24 Alignment explanation

Indices: 64796949--64797005 Score: 69 Period size: 25 Copynumber: 2.3 Consensus size: 24 64796939 TTACTGATAC * 64796949 TCAACTCGAATGAGCTTACCGTTAT 1 TCAACTCGAAGGAGCTTACCGTT-T * * 64796974 TCAACTCGGAGGAGCTTATCGTTT 1 TCAACTCGAAGGAGCTTACCGTTT * 64796998 ACAACTCG 1 TCAACTCG 64797006 TAAGAGCATA Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 24 8 0.29 25 20 0.71 ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30 Consensus pattern (24 bp): TCAACTCGAAGGAGCTTACCGTTT Found at i:64797012 original size:24 final size:24 Alignment explanation

Indices: 64796950--64797017 Score: 66 Period size: 25 Copynumber: 2.8 Consensus size: 24 64796940 TACTGATACT * 64796950 CAACTCGAATGAGCTTACCGTTATT 1 CAACTCGAA-GAGCTTACCGTTATA * * 64796975 CAACTCGGAGGAGCTTATCGTT-TA 1 CAACTC-GAAGAGCTTACCGTTATA * 64796999 CAACTCGTAAGAGCATACC 1 CAACTCG-AAGAGCTTACC 64797018 AATTTAGAGC Statistics Matches: 35, Mismatches: 6, Indels: 5 0.76 0.13 0.11 Matches are distributed among these distances: 23 1 0.03 24 15 0.43 25 17 0.49 26 2 0.06 ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26 Consensus pattern (24 bp): CAACTCGAAGAGCTTACCGTTATA Found at i:64814343 original size:35 final size:35 Alignment explanation

Indices: 64814297--64814365 Score: 129 Period size: 35 Copynumber: 2.0 Consensus size: 35 64814287 ATGGCTGTAC 64814297 ACTTATACATTTCAGAAAGTACTCGAAAGACAACG 1 ACTTATACATTTCAGAAAGTACTCGAAAGACAACG * 64814332 ACTTATACATTTCATAAAGTACTCGAAAGACAAC 1 ACTTATACATTTCAGAAAGTACTCGAAAGACAAC 64814366 AATGGGTAGT Statistics Matches: 33, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 35 33 1.00 ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25 Consensus pattern (35 bp): ACTTATACATTTCAGAAAGTACTCGAAAGACAACG Found at i:64814965 original size:40 final size:40 Alignment explanation

Indices: 64814865--64815089 Score: 285 Period size: 40 Copynumber: 5.7 Consensus size: 40 64814855 GCTCCTCGTT * * ** * 64814865 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA * 64814905 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA 64814944 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA * 64814984 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA * * * * * * 64815024 CGAATGCCTTCGGAACTTAATCCGGATATATTC-ACTTAGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCA * 64815065 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAACCCGGA 64815090 CAGCATTCAA Statistics Matches: 167, Mismatches: 15, Indels: 6 0.89 0.08 0.03 Matches are distributed among these distances: 39 35 0.21 40 124 0.74 41 8 0.05 ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA Found at i:64816704 original size:200 final size:200 Alignment explanation

Indices: 64816361--64816760 Score: 791 Period size: 200 Copynumber: 2.0 Consensus size: 200 64816351 GCACTAATAG 64816361 GTCCTCACACATTGACCTATCACATTTTAGAATTTTCTCACATAAGTCCTATTGACTAAATTCAC 1 GTCCTCACACATTGACCTATCACATTTTAGAATTTTCTCACATAAGTCCTATTGACTAAATTCAC 64816426 ATGAAATCAACCAAATTGAAGCTTGAAATTTTCACACATTCATAATTACATATTCTAGACAATAA 66 ATGAAATCAACCAAATTGAAGCTTGAAATTTTCACACATTCATAATTACATATTCTAGACAATAA 64816491 GTATCACATTCAAACATTTCGGTGACTCGGTTTAGCGGTCCCGAAACCACTTCCCGACTAGGGTC 131 GTATCACATTCAAACATTTCGGTGACTCGGTTTAGCGGTCCCGAAACCACTTCCCGACTAGGGTC 64816556 AACTT 196 AACTT 64816561 GTCCTCACACATTGACCTATCACATTTTAGAATTTTCTCACATAAGTCCTATTGACTAAATTCAC 1 GTCCTCACACATTGACCTATCACATTTTAGAATTTTCTCACATAAGTCCTATTGACTAAATTCAC 64816626 ATGAAATCAACCAAATTGAAGCTTGAAATTTTCACACATTCATAATTACATATTCTAGACAATAA 66 ATGAAATCAACCAAATTGAAGCTTGAAATTTTCACACATTCATAATTACATATTCTAGACAATAA * 64816691 GTATCACATTCAAACATTTCGGTGACTCGGTTTAGCGGTCCCGAAGCCACTTCCCGACTAGGGTC 131 GTATCACATTCAAACATTTCGGTGACTCGGTTTAGCGGTCCCGAAACCACTTCCCGACTAGGGTC 64816756 AACTT 196 AACTT 64816761 TGGGCTGTCA Statistics Matches: 199, Mismatches: 1, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 200 199 1.00 ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31 Consensus pattern (200 bp): GTCCTCACACATTGACCTATCACATTTTAGAATTTTCTCACATAAGTCCTATTGACTAAATTCAC ATGAAATCAACCAAATTGAAGCTTGAAATTTTCACACATTCATAATTACATATTCTAGACAATAA GTATCACATTCAAACATTTCGGTGACTCGGTTTAGCGGTCCCGAAACCACTTCCCGACTAGGGTC AACTT Found at i:64823061 original size:40 final size:40 Alignment explanation

Indices: 64822963--64823945 Score: 1792 Period size: 40 Copynumber: 24.6 Consensus size: 40 64822953 TCCTCGTTCA * * ** * 64822963 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACAC- 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG * * * 64823002 AATGCCTTCGGGACATAACCCGGATTTAACAACTCTCACA 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823042 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823082 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823122 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823162 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823202 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823242 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823282 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823322 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823362 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823402 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823442 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823482 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823522 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823562 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823602 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823642 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823682 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823722 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823762 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823802 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 64823842 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG * * * * * 64823882 AATGCCTTCGGAACTTAATCCGGATATATTC-ACTTAGCAC- 1 AATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCACG * * 64823922 AAAGCCTTCGGGACTTAGCCCGGA 1 AATGCCTTCGGGACTTAACCCGGA 64823946 CAGCATTCAA Statistics Matches: 925, Mismatches: 16, Indels: 5 0.98 0.02 0.01 Matches are distributed among these distances: 39 35 0.04 40 884 0.96 41 6 0.01 ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23 Consensus pattern (40 bp): AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG Found at i:64826305 original size:12 final size:12 Alignment explanation

Indices: 64826288--64826316 Score: 58 Period size: 12 Copynumber: 2.4 Consensus size: 12 64826278 GATTGGCCCC 64826288 ATTGGCAGTTCA 1 ATTGGCAGTTCA 64826300 ATTGGCAGTTCA 1 ATTGGCAGTTCA 64826312 ATTGG 1 ATTGG 64826317 ATCATCCCCT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 17 1.00 ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34 Consensus pattern (12 bp): ATTGGCAGTTCA Done.