Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr14

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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31

Warning! 4503000 characters in sequence are not A, C, G, or T


File 315 of 770

Found at i:96340571 original size:29 final size:29

Alignment explanation

Indices: 96340538--96340669 Score: 165 Period size: 29 Copynumber: 4.6 Consensus size: 29 96340528 GTGACGAGAT * * 96340538 TGGCACTAAGTGTGCGTGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAAAATA * * 96340567 TGGCACTAAGTGTGCGTGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAAAATA * 96340596 AGGCACTAAGTGTGCATGCTGGAAAAATA 1 TGGCACTAAGTGTGCATGCTGGAAAAATA * * * 96340625 TGACACTATGTGTGCAAGCTGGAAAAATA 1 TGGCACTAAGTGTGCATGCTGGAAAAATA * ** 96340654 CGGCACTGGGTGTGCA 1 TGGCACTAAGTGTGCA 96340670 AGCTCGGAGG Statistics Matches: 92, Mismatches: 11, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 29 92 1.00 ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24 Consensus pattern (29 bp): TGGCACTAAGTGTGCATGCTGGAAAAATA Found at i:96346065 original size:40 final size:40 Alignment explanation

Indices: 96346020--96346181 Score: 256 Period size: 40 Copynumber: 4.1 Consensus size: 40 96346010 CTAAGATCCA * * 96346020 AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCG 1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG 96346060 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG 1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG 96346100 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG 1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG * ** * 96346140 AAGGCATTTGTGTGAGTTGTTATATCC-GGCTAAAT-CCG 1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG 96346178 AAGG 1 AAGG 96346182 TACTTGGGTT Statistics Matches: 116, Mismatches: 6, Indels: 2 0.94 0.05 0.02 Matches are distributed among these distances: 38 7 0.06 39 7 0.06 40 102 0.88 ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28 Consensus pattern (40 bp): AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG Found at i:96356266 original size:26 final size:26 Alignment explanation

Indices: 96356237--96356287 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96356227 AAATTAATGC 96356237 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96356263 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96356288 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96357813 original size:47 final size:47 Alignment explanation

Indices: 96357761--96358003 Score: 364 Period size: 47 Copynumber: 5.2 Consensus size: 47 96357751 TTCCACGTTT * * 96357761 ATCACATTGGCCATTCTACCTTATCACACATATGCATGTTCACATTT 1 ATCACATTGGCCATTCTGCCTTATCACACATATGCATGTTCACATTC * * 96357808 GTCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC 1 ATCACATTGGCCATTCTGCCTTATCACACATATGCATGTTCACATTC * * 96357855 ATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTC 1 ATCACATTGGCCATTCTGCCTTATCACACATATGCATGTTCACATTC * * 96357902 ATCACATTGGCCATT-TGGCCTTATCACCCATATGCATGTTCACACTC 1 ATCACATTGGCCATTCT-GCCTTATCACACATATGCATGTTCACATTC * * 96357949 ATCACATTGGCCATT-TGGCCTTATCACATATATGCATGTCCACATTC 1 ATCACATTGGCCATTCT-GCCTTATCACACATATGCATGTTCACATTC 96357996 ATCACATT 1 ATCACATT 96358004 AAGTCCTAAA Statistics Matches: 181, Mismatches: 14, Indels: 2 0.92 0.07 0.01 Matches are distributed among these distances: 47 181 1.00 ACGTcount: A:0.26, C:0.29, G:0.12, T:0.34 Consensus pattern (47 bp): ATCACATTGGCCATTCTGCCTTATCACACATATGCATGTTCACATTC Found at i:96357887 original size:141 final size:141 Alignment explanation

Indices: 96357715--96358004 Score: 397 Period size: 141 Copynumber: 2.1 Consensus size: 141 96357705 CATACATATC * * * 96357715 TCACATTAGCCATTCGGCTTCGCCACATATATACACT-TCCACGTTTATCACATTGGCCATTCT- 1 TCACATTAGCCATTCGGCTTCACCACATATATACA-TGTCCACATTCATCACATTGGCCATT-TG * ** 96357778 ACCTTATCACACATATGCATGTTCACATTTGTCACATTGGCCATTCGGCCTTATCACACATATGC 64 ACCTTATCACACATATGCATGTTCACACTCATCACATTGGCCATTCGGCCTTATCACACATATGC * 96357843 ATGTTCACATTCA 129 ATGTCCACATTCA * * * * * 96357856 TCACATTGGCCATTCGGCCTT-ATCACATATATGCATGTTCACATTCATCACATTGGCCATTTGG 1 TCACATTAGCCATTCGG-CTTCACCACATATATACATGTCCACATTCATCACATTGGCCATTTGA * * * 96357920 CCTTATCACCCATATGCATGTTCACACTCATCACATTGGCCATTTGGCCTTATCACATATATGCA 65 CCTTATCACACATATGCATGTTCACACTCATCACATTGGCCATTCGGCCTTATCACACATATGCA 96357985 TGTCCACATTCA 130 TGTCCACATTCA 96357997 TCACATTA 1 TCACATTA 96358005 AGTCCTAAAT Statistics Matches: 130, Mismatches: 16, Indels: 6 0.86 0.11 0.04 Matches are distributed among these distances: 140 2 0.02 141 125 0.96 142 3 0.02 ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33 Consensus pattern (141 bp): TCACATTAGCCATTCGGCTTCACCACATATATACATGTCCACATTCATCACATTGGCCATTTGAC CTTATCACACATATGCATGTTCACACTCATCACATTGGCCATTCGGCCTTATCACACATATGCAT GTCCACATTCA Found at i:96357975 original size:22 final size:22 Alignment explanation

Indices: 96357855--96357977 Score: 72 Period size: 22 Copynumber: 5.3 Consensus size: 22 96357845 GTTCACATTC * 96357855 ATCACATTGGCCATTCGGCCTT 1 ATCACATTGGCCATTTGGCCTT * ** * 96357877 ATCACATATATG-CATGTTCACATT 1 ATCACAT-T-GGCCAT-TTGGCCTT 96357901 CATCACATTGGCCATTTGGCCTT 1 -ATCACATTGGCCATTTGGCCTT ** * 96357924 ATCACCCATAT-G-CATGTTCACACTC 1 ATCA--CAT-TGGCCAT-TTGGC-CTT 96357949 ATCACATTGGCCATTTGGCCTT 1 ATCACATTGGCCATTTGGCCTT 96357971 ATCACAT 1 ATCACAT 96357978 ATATGCATGT Statistics Matches: 74, Mismatches: 15, Indels: 24 0.65 0.13 0.21 Matches are distributed among these distances: 22 21 0.28 23 20 0.27 24 19 0.26 25 14 0.19 ACGTcount: A:0.24, C:0.29, G:0.13, T:0.33 Consensus pattern (22 bp): ATCACATTGGCCATTTGGCCTT Found at i:96362176 original size:14 final size:15 Alignment explanation

Indices: 96362155--96362191 Score: 51 Period size: 14 Copynumber: 2.6 Consensus size: 15 96362145 GTGTACTATA 96362155 TCCCATATTGCTTTT 1 TCCCATATTGCTTTT * 96362170 T-CCATA-TGTTTTT 1 TCCCATATTGCTTTT 96362183 TCCCATATT 1 TCCCATATT 96362192 ACCTCTAGAT Statistics Matches: 19, Mismatches: 1, Indels: 4 0.79 0.04 0.17 Matches are distributed among these distances: 13 7 0.37 14 10 0.53 15 2 0.11 ACGTcount: A:0.16, C:0.24, G:0.05, T:0.54 Consensus pattern (15 bp): TCCCATATTGCTTTT Found at i:96362416 original size:26 final size:26 Alignment explanation

Indices: 96362387--96362437 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96362377 AAATTAATGC 96362387 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96362413 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96362438 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96364527 original size:26 final size:26 Alignment explanation

Indices: 96364498--96364548 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96364488 AAATTAATGC 96364498 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96364524 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96364549 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96366586 original size:26 final size:26 Alignment explanation

Indices: 96366557--96366607 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96366547 AAATTAATGC 96366557 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96366583 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96366608 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96368827 original size:25 final size:26 Alignment explanation

Indices: 96368790--96368841 Score: 72 Period size: 25 Copynumber: 2.0 Consensus size: 26 96368780 TCAAACATGC 96368790 ATTTAGGTCAATTTAAC-CCTAGGGGT 1 ATTTAGGTCAATTT-ACTCCTAGGGGT * 96368816 ATTTCGGT-AATTTACTCCTAGGGGT 1 ATTTAGGTCAATTTACTCCTAGGGGT 96368841 A 1 A 96368842 AAATTAAATT Statistics Matches: 24, Mismatches: 1, Indels: 3 0.86 0.04 0.11 Matches are distributed among these distances: 24 2 0.08 25 15 0.62 26 7 0.29 ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37 Consensus pattern (26 bp): ATTTAGGTCAATTTACTCCTAGGGGT Found at i:96370356 original size:26 final size:26 Alignment explanation

Indices: 96370320--96370403 Score: 150 Period size: 26 Copynumber: 3.2 Consensus size: 26 96370310 CATGAAATTC 96370320 TTATCATGAAACATTTACCTAACCCA 1 TTATCATGAAACATTTACCTAACCCA 96370346 TTATCATGAAACATTTACCTAACCCA 1 TTATCATGAAACATTTACCTAACCCA * * 96370372 TTATCATGGAACATTTACCTAACCTA 1 TTATCATGAAACATTTACCTAACCCA 96370398 TTATCA 1 TTATCA 96370404 ATTTGTATCA Statistics Matches: 56, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 26 56 1.00 ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33 Consensus pattern (26 bp): TTATCATGAAACATTTACCTAACCCA Found at i:96375206 original size:12 final size:12 Alignment explanation

Indices: 96375189--96375231 Score: 77 Period size: 12 Copynumber: 3.6 Consensus size: 12 96375179 AGTACTACGT 96375189 CGGCCTCGACCA 1 CGGCCTCGACCA 96375201 CGGCCTCGACCA 1 CGGCCTCGACCA * 96375213 CGGCCTTGACCA 1 CGGCCTCGACCA 96375225 CGGCCTC 1 CGGCCTC 96375232 TTCCCCGAGT Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 12 29 1.00 ACGTcount: A:0.14, C:0.49, G:0.26, T:0.12 Consensus pattern (12 bp): CGGCCTCGACCA Found at i:96376906 original size:25 final size:27 Alignment explanation

Indices: 96376869--96376921 Score: 74 Period size: 26 Copynumber: 2.0 Consensus size: 27 96376859 TCAAACATGC 96376869 ATTTAGGTCAATTTAAC-CCTAGGGGT 1 ATTTAGGTCAATTTAACTCCTAGGGGT * * 96376895 ATTTCGGT-AATTTATCTCCTAGGGGT 1 ATTTAGGTCAATTTAACTCCTAGGGGT 96376921 A 1 A 96376922 AAACTGTAAA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 25 7 0.29 26 17 0.71 ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38 Consensus pattern (27 bp): ATTTAGGTCAATTTAACTCCTAGGGGT Found at i:96378439 original size:26 final size:26 Alignment explanation

Indices: 96378403--96378486 Score: 150 Period size: 26 Copynumber: 3.2 Consensus size: 26 96378393 CATGAAATTC 96378403 TTATCATGAAACATTTACCTAACCCA 1 TTATCATGAAACATTTACCTAACCCA 96378429 TTATCATGAAACATTTACCTAACCCA 1 TTATCATGAAACATTTACCTAACCCA * * 96378455 TTATCATGGAACATTTACCTAACCTA 1 TTATCATGAAACATTTACCTAACCCA 96378481 TTATCA 1 TTATCA 96378487 ATTTGTATCA Statistics Matches: 56, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 26 56 1.00 ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33 Consensus pattern (26 bp): TTATCATGAAACATTTACCTAACCCA Found at i:96378497 original size:10 final size:10 Alignment explanation

Indices: 96378482--96378506 Score: 50 Period size: 10 Copynumber: 2.5 Consensus size: 10 96378472 CCTAACCTAT 96378482 TATCAATTTG 1 TATCAATTTG 96378492 TATCAATTTG 1 TATCAATTTG 96378502 TATCA 1 TATCA 96378507 TAAATTATGG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 15 1.00 ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48 Consensus pattern (10 bp): TATCAATTTG Found at i:96379742 original size:26 final size:26 Alignment explanation

Indices: 96379713--96379763 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96379703 AAATTAATGC 96379713 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96379739 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96379764 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96381819 original size:26 final size:26 Alignment explanation

Indices: 96381790--96381840 Score: 84 Period size: 26 Copynumber: 2.0 Consensus size: 26 96381780 AAATTAATGC * 96381790 TAATTAAACTGAAATATTGATTGTTA 1 TAATTAAACTGAAATATTGAATGTTA * 96381816 TAATTAAATTGAAATATTGAATGTT 1 TAATTAAACTGAAATATTGAATGTT 96381841 TTCTTTTATT Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 26 23 1.00 ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43 Consensus pattern (26 bp): TAATTAAACTGAAATATTGAATGTTA Found at i:96383488 original size:27 final size:28 Alignment explanation

Indices: 96383448--96383515 Score: 113 Period size: 28 Copynumber: 2.5 Consensus size: 28 96383438 TTTAAAACCC * 96383448 TAGGGGT-ATATCGGTAA-TTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 96383474 TAGGGGTAATTTCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 96383502 TAGGGGTAATTTCG 1 TAGGGGTAATTTCG 96383516 TGATCTACGC Statistics Matches: 39, Mismatches: 1, Indels: 2 0.93 0.02 0.05 Matches are distributed among these distances: 26 7 0.18 27 9 0.23 28 23 0.59 ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43 Consensus pattern (28 bp): TAGGGGTAATTTCGGTAATTTTGCTCTT Found at i:96385338 original size:19 final size:18 Alignment explanation

Indices: 96385301--96385344 Score: 54 Period size: 19 Copynumber: 2.4 Consensus size: 18 96385291 ATACATACAG 96385301 TAAT-ATTTTTCTAATAA 1 TAATAATTTTTCTAATAA * 96385318 TAATAATTTTATCTCATAA 1 TAATAATTTT-TCTAATAA * 96385337 TACTAATT 1 TAATAATT 96385345 AAAATTTCAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 17 4 0.17 18 5 0.22 19 14 0.61 ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50 Consensus pattern (18 bp): TAATAATTTTTCTAATAA Found at i:96387741 original size:27 final size:28 Alignment explanation

Indices: 96387701--96387768 Score: 113 Period size: 28 Copynumber: 2.5 Consensus size: 28 96387691 TTTAAAACCC * 96387701 TAGGGGT-ATATCGGTAA-TTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 96387727 TAGGGGTAATTTCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 96387755 TAGGGGTAATTTCG 1 TAGGGGTAATTTCG 96387769 TGATCTACGC Statistics Matches: 39, Mismatches: 1, Indels: 2 0.93 0.02 0.05 Matches are distributed among these distances: 26 7 0.18 27 9 0.23 28 23 0.59 ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43 Consensus pattern (28 bp): TAGGGGTAATTTCGGTAATTTTGCTCTT Found at i:96391379 original size:26 final size:26 Alignment explanation

Indices: 96391350--96391400 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96391340 AAATTAATGC 96391350 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96391376 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96391401 TTTTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96398272 original size:26 final size:26 Alignment explanation

Indices: 96398243--96398293 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96398233 AAATTAATGC 96398243 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96398269 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96398294 TTTTTTATTG Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96400349 original size:26 final size:26 Alignment explanation

Indices: 96400320--96400370 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96400310 AAATTAATGC 96400320 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96400346 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96400371 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96402433 original size:26 final size:26 Alignment explanation

Indices: 96402404--96402454 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96402394 AAATTAATGC 96402404 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96402430 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96402455 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96404509 original size:26 final size:26 Alignment explanation

Indices: 96404480--96404530 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96404470 AAATTAATGC 96404480 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96404506 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96404531 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96406588 original size:26 final size:26 Alignment explanation

Indices: 96406559--96406609 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96406549 AAATTAATGC 96406559 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96406585 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96406610 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96408664 original size:26 final size:26 Alignment explanation

Indices: 96408635--96408685 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96408625 AAATTAATGC 96408635 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96408661 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96408686 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96410744 original size:26 final size:26 Alignment explanation

Indices: 96410715--96410765 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96410705 AAATTAATGC 96410715 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96410741 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96410766 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96412161 original size:130 final size:129 Alignment explanation

Indices: 96411989--96412244 Score: 485 Period size: 130 Copynumber: 2.0 Consensus size: 129 96411979 GTAACAGTGG * 96411989 TACTAGGCCAGAGCCCTTTTCAGATTATAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGT 1 TACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGT 96412054 ATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAACATATGCAAGCCCATTTGGGTAA 66 ATGG-CCATAGGCCCATTTCAAAATACATGCAACATCAATAACATATGCAAGCCCATTTGGGTAA * 96412119 TACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGT 1 TACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGT 96412184 ATGGCCATAGGCCCATTTCAAAATACATGCAACATCAATAACATATGCAAGCCCATTTGGG 66 ATGGCCATAGGCCCATTTCAAAATACATGCAACATCAATAACATATGCAAGCCCATTTGGG 96412245 GAGACTACTC Statistics Matches: 124, Mismatches: 2, Indels: 1 0.98 0.02 0.01 Matches are distributed among these distances: 129 57 0.46 130 67 0.54 ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26 Consensus pattern (129 bp): TACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGT ATGGCCATAGGCCCATTTCAAAATACATGCAACATCAATAACATATGCAAGCCCATTTGGGTAA Found at i:96412280 original size:21 final size:21 Alignment explanation

Indices: 96412251--96412298 Score: 62 Period size: 21 Copynumber: 2.3 Consensus size: 21 96412241 TGGGGAGACT * 96412251 ACTCAACCC-ACCAACCACTAC 1 ACTCCACCCTACCAACCA-TAC * 96412272 ACTCCACCCTACCAGCCATAC 1 ACTCCACCCTACCAACCATAC 96412293 ACTCCA 1 ACTCCA 96412299 TGTGGGGAAT Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 21 17 0.71 22 7 0.29 ACGTcount: A:0.33, C:0.52, G:0.02, T:0.12 Consensus pattern (21 bp): ACTCCACCCTACCAACCATAC Found at i:96414045 original size:26 final size:26 Alignment explanation

Indices: 96414009--96414118 Score: 175 Period size: 26 Copynumber: 4.2 Consensus size: 26 96413999 ACATGAATTC * 96414009 TTATCATGAAACATTTACCTAAACCA 1 TTATCATGAAACATTTACCTAACCCA 96414035 TTATCATGAAACATTTACCTAACCCA 1 TTATCATGAAACATTTACCTAACCCA * * * 96414061 TTATCATGGAATATTTACCTAATCCA 1 TTATCATGAAACATTTACCTAACCCA * 96414087 TTATCATGGAACATTTACCTAACCCA 1 TTATCATGAAACATTTACCTAACCCA 96414113 TTATCA 1 TTATCA 96414119 ATTTGTATCA Statistics Matches: 78, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 26 78 1.00 ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34 Consensus pattern (26 bp): TTATCATGAAACATTTACCTAACCCA Found at i:96416060 original size:26 final size:26 Alignment explanation

Indices: 96416031--96416081 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96416021 AAATTAATGC 96416031 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96416057 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96416082 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96420946 original size:27 final size:27 Alignment explanation

Indices: 96420909--96421021 Score: 124 Period size: 27 Copynumber: 4.2 Consensus size: 27 96420899 AGCATGGCTG * * 96420909 CCAGA-ACAGATAATGTGACAGAGTCA 1 CCAGATACAGATAATGTGGCAGAGCCA 96420935 CCAGATACAGATAATCGTGGCAGAGCCA 1 CCAGATACAGATAAT-GTGGCAGAGCCA * * 96420963 CCA-AAACAAATATATGTGGCAGAGCCA 1 CCAGATACAGATA-ATGTGGCAGAGCCA * * 96420990 CCAGAT-CAGATATTTGTGGCATAGCCA 1 CCAGATACAGATA-ATGTGGCAGAGCCA 96421017 CCAGA 1 CCAGA 96421022 ACGCTTCCTC Statistics Matches: 75, Mismatches: 8, Indels: 7 0.83 0.09 0.08 Matches are distributed among these distances: 26 5 0.07 27 54 0.72 28 16 0.21 ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17 Consensus pattern (27 bp): CCAGATACAGATAATGTGGCAGAGCCA Found at i:96421017 original size:54 final size:54 Alignment explanation

Indices: 96420913--96421019 Score: 144 Period size: 54 Copynumber: 2.0 Consensus size: 54 96420903 TGGCTGCCAG * * 96420913 AACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCACCAA 1 AACAAATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCAA * * * * 96420967 AACAAATATATGTGGCAGAGCCACCAGAT-CAGATATTTGTGGCATAGCCACCA 1 AACAAATA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCA 96421020 GAACGCTTCC Statistics Matches: 46, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 54 28 0.61 55 18 0.39 ACGTcount: A:0.38, C:0.22, G:0.21, T:0.18 Consensus pattern (54 bp): AACAAATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCAA Found at i:96422670 original size:26 final size:26 Alignment explanation

Indices: 96422632--96422715 Score: 141 Period size: 26 Copynumber: 3.2 Consensus size: 26 96422622 CATGAAATTC * * 96422632 TTATCATGAAACATTTACCTAACCCA 1 TTATCATGGAACATTTACCTAACCTA 96422658 TTATCATGGAACATTTACCTAACCTA 1 TTATCATGGAACATTTACCTAACCTA * 96422684 TTATCATTGAACATTTACCTAACCTA 1 TTATCATGGAACATTTACCTAACCTA 96422710 TTATCA 1 TTATCA 96422716 ATTTGTATCA Statistics Matches: 55, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 26 55 1.00 ACGTcount: A:0.36, C:0.24, G:0.05, T:0.36 Consensus pattern (26 bp): TTATCATGGAACATTTACCTAACCTA Found at i:96428965 original size:27 final size:26 Alignment explanation

Indices: 96428928--96429042 Score: 149 Period size: 27 Copynumber: 4.3 Consensus size: 26 96428918 AGCATGGCTG * * 96428928 CCAGAACAGATAATGTGACAGAGTCA 1 CCAGAACAGATAATGTGGCAGAGCCA 96428954 CCAGATACAGATAATCGTGGCAGAGCCA 1 CCAGA-ACAGATAAT-GTGGCAGAGCCA 96428982 CCAGAACAGATATATGTGGCAGAGCCA 1 CCAGAACAGATA-ATGTGGCAGAGCCA * * * 96429009 CCAGATCAGATATTTGTGGCATAGCCA 1 CCAGAACAGATA-ATGTGGCAGAGCCA 96429036 CCAGAAC 1 CCAGAAC 96429043 GCTTCCTCCA Statistics Matches: 80, Mismatches: 6, Indels: 5 0.88 0.07 0.05 Matches are distributed among these distances: 26 5 0.06 27 58 0.73 28 17 0.21 ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17 Consensus pattern (26 bp): CCAGAACAGATAATGTGGCAGAGCCA Found at i:96428992 original size:54 final size:54 Alignment explanation

Indices: 96428928--96429042 Score: 169 Period size: 54 Copynumber: 2.1 Consensus size: 54 96428918 AGCATGGCTG * 96428928 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA 1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA * * * * 96428982 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA 1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA 96429036 CCAGAAC 1 CCAGAAC 96429043 GCTTCCTCCA Statistics Matches: 55, Mismatches: 5, Indels: 2 0.89 0.08 0.03 Matches are distributed among these distances: 54 37 0.67 55 18 0.33 ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17 Consensus pattern (54 bp): CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA Found at i:96430701 original size:26 final size:26 Alignment explanation

Indices: 96430663--96430746 Score: 123 Period size: 26 Copynumber: 3.2 Consensus size: 26 96430653 CATGAAATTC * * * 96430663 TTATCATGAAACATTTACCGAACCCA 1 TTATCATGGAACATTTACCTAACCTA 96430689 TTATCATGGAACATTTACCTAACCTA 1 TTATCATGGAACATTTACCTAACCTA * * 96430715 TTATCATTGAACATTTGCCTAACCTA 1 TTATCATGGAACATTTACCTAACCTA 96430741 TTATCA 1 TTATCA 96430747 ATTTGTATCA Statistics Matches: 53, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 26 53 1.00 ACGTcount: A:0.35, C:0.24, G:0.07, T:0.35 Consensus pattern (26 bp): TTATCATGGAACATTTACCTAACCTA Found at i:96431231 original size:26 final size:26 Alignment explanation

Indices: 96431202--96431252 Score: 77 Period size: 26 Copynumber: 2.0 Consensus size: 26 96431192 AAATTAATGC * 96431202 TAATTAAACT-GAAATTTTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96431228 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96431253 TTCTTTTGTT Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 25 1 0.04 26 22 0.96 ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96434007 original size:40 final size:40 Alignment explanation

Indices: 96433948--96434116 Score: 173 Period size: 40 Copynumber: 4.2 Consensus size: 40 96433938 CGGGACTTTA * * * 96433948 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG 1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG * * 96433988 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG 1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG * * * * * 96434028 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA 1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG * * * 96434068 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG 1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG 96434108 CCCGGATAT 1 CCCGGATAT 96434117 CATTCAATTT Statistics Matches: 106, Mismatches: 20, Indels: 6 0.80 0.15 0.05 Matches are distributed among these distances: 37 3 0.03 38 3 0.03 39 1 0.01 40 99 0.93 ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28 Consensus pattern (40 bp): CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG Found at i:96441788 original size:40 final size:40 Alignment explanation

Indices: 96441729--96441897 Score: 173 Period size: 40 Copynumber: 4.2 Consensus size: 40 96441719 CGGGACTTTA * * * 96441729 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG 1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG * * 96441769 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG 1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG * * * * * 96441809 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA 1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG * * * 96441849 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG 1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG 96441889 CCCGGATAT 1 CCCGGATAT 96441898 CATTCAATTT Statistics Matches: 106, Mismatches: 20, Indels: 6 0.80 0.15 0.05 Matches are distributed among these distances: 37 3 0.03 38 3 0.03 39 1 0.01 40 99 0.93 ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28 Consensus pattern (40 bp): CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG Found at i:96444397 original size:26 final size:26 Alignment explanation

Indices: 96444368--96444418 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96444358 AAATTAATGC 96444368 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96444394 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96444419 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96446479 original size:26 final size:26 Alignment explanation

Indices: 96446450--96446500 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96446440 AAATTAATGC 96446450 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96446476 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96446501 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96448346 original size:14 final size:15 Alignment explanation

Indices: 96448325--96448361 Score: 51 Period size: 14 Copynumber: 2.6 Consensus size: 15 96448315 GTGTACTATA 96448325 TCCCATATTGCTTTT 1 TCCCATATTGCTTTT * 96448340 T-CCATA-TGTTTTT 1 TCCCATATTGCTTTT 96448353 TCCCATATT 1 TCCCATATT 96448362 ACCTTCTAGA Statistics Matches: 19, Mismatches: 1, Indels: 4 0.79 0.04 0.17 Matches are distributed among these distances: 13 7 0.37 14 10 0.53 15 2 0.11 ACGTcount: A:0.16, C:0.24, G:0.05, T:0.54 Consensus pattern (15 bp): TCCCATATTGCTTTT Found at i:96448587 original size:26 final size:26 Alignment explanation

Indices: 96448558--96448608 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96448548 AAATTAATGC 96448558 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96448584 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96448609 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96450454 original size:14 final size:15 Alignment explanation

Indices: 96450433--96450469 Score: 51 Period size: 14 Copynumber: 2.6 Consensus size: 15 96450423 GTGTACTATA 96450433 TCCCATATTGCTTTT 1 TCCCATATTGCTTTT * 96450448 T-CCATA-TGTTTTT 1 TCCCATATTGCTTTT 96450461 TCCCATATT 1 TCCCATATT 96450470 ACCTTCTAGA Statistics Matches: 19, Mismatches: 1, Indels: 4 0.79 0.04 0.17 Matches are distributed among these distances: 13 7 0.37 14 10 0.53 15 2 0.11 ACGTcount: A:0.16, C:0.24, G:0.05, T:0.54 Consensus pattern (15 bp): TCCCATATTGCTTTT Found at i:96450695 original size:26 final size:26 Alignment explanation

Indices: 96450666--96450716 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96450656 AAATTAATGC 96450666 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96450692 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96450717 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96452666 original size:26 final size:26 Alignment explanation

Indices: 96452637--96452687 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96452627 AAATTAATGC 96452637 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96452663 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96452688 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96454959 original size:19 final size:19 Alignment explanation

Indices: 96454935--96455040 Score: 189 Period size: 19 Copynumber: 5.7 Consensus size: 19 96454925 TAATATCTTC * 96454935 AAGATTGCATATCATATCA 1 AAGATTGCATATCATATCT 96454954 AAGATTGCATATCATATCT 1 AAGATTGCATATCATATCT 96454973 AAGATTG--TATCATATCT 1 AAGATTGCATATCATATCT 96454990 AAGATTGCATATCATATCT 1 AAGATTGCATATCATATCT 96455009 AAGATTGCATATCATATCT 1 AAGATTGCATATCATATCT 96455028 AAGATTGCATATC 1 AAGATTGCATATC 96455041 CTTAAAGATT Statistics Matches: 84, Mismatches: 1, Indels: 4 0.94 0.01 0.04 Matches are distributed among these distances: 17 17 0.20 19 67 0.80 ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36 Consensus pattern (19 bp): AAGATTGCATATCATATCT Found at i:96455049 original size:55 final size:54 Alignment explanation

Indices: 96454927--96455050 Score: 180 Period size: 55 Copynumber: 2.2 Consensus size: 54 96454917 TTACAAGATA 96454927 ATATCTTCAAGATTGCATATCATATCAAAGATTGCATATCATATCTAAGATTGTATC 1 ATATCTT-AAGATTGCATATCATATCAAAGATTGCATATCATATCTAAGATTG--TC * 96454984 ATATC-TAAGATTGCATATCATATCTAAGATTGCATATCATATCTAAGATTG-C 1 ATATCTTAAGATTGCATATCATATCAAAGATTGCATATCATATCTAAGATTGTC 96455036 ATATCCTTAAAGATT 1 ATAT-CTT-AAGATT 96455051 ATATTTCCAT Statistics Matches: 63, Mismatches: 1, Indels: 8 0.88 0.01 0.11 Matches are distributed among these distances: 52 5 0.08 53 1 0.02 54 1 0.02 55 50 0.79 56 1 0.02 57 5 0.08 ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37 Consensus pattern (54 bp): ATATCTTAAGATTGCATATCATATCAAAGATTGCATATCATATCTAAGATTGTC Found at i:96455050 original size:36 final size:38 Alignment explanation

Indices: 96454935--96455040 Score: 189 Period size: 36 Copynumber: 2.8 Consensus size: 38 96454925 TAATATCTTC * 96454935 AAGATTGCATATCATATCAAAGATTGCATATCATATCT 1 AAGATTGCATATCATATCTAAGATTGCATATCATATCT 96454973 AAGATTG--TATCATATCTAAGATTGCATATCATATCT 1 AAGATTGCATATCATATCTAAGATTGCATATCATATCT 96455009 AAGATTGCATATCATATCTAAGATTGCATATC 1 AAGATTGCATATCATATCTAAGATTGCATATC 96455041 CTTAAAGATT Statistics Matches: 65, Mismatches: 1, Indels: 4 0.93 0.01 0.06 Matches are distributed among these distances: 36 35 0.54 38 30 0.46 ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36 Consensus pattern (38 bp): AAGATTGCATATCATATCTAAGATTGCATATCATATCT Found at i:96456507 original size:26 final size:26 Alignment explanation

Indices: 96456478--96456528 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96456468 AAATTAATGC 96456478 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96456504 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96456529 TTCTTTTATT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96458593 original size:26 final size:26 Alignment explanation

Indices: 96458564--96458614 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 96458554 AAATTAATGC 96458564 TAATTAAACT-GAAATATTGAATGTTA 1 TAATTAAA-TAGAAATATTGAATGTTA 96458590 TAATTAAATAGAAATATTGAATGTT 1 TAATTAAATAGAAATATTGAATGTT 96458615 TTCTTTATTG Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 25 1 0.04 26 23 0.96 ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39 Consensus pattern (26 bp): TAATTAAATAGAAATATTGAATGTTA Found at i:96460688 original size:17 final size:18 Alignment explanation

Indices: 96460646--96460694 Score: 50 Period size: 17 Copynumber: 2.8 Consensus size: 18 96460636 AGTTGAAAAG 96460646 GAGCATGATTGTCATACTT 1 GAGCATGA-TGTCATACTT * 96460665 G-GCCATGATG-CATTCTT 1 GAG-CATGATGTCATACTT 96460682 GAGCATGAT-TCAT 1 GAGCATGATGTCAT 96460695 GCTTCTTGCA Statistics Matches: 26, Mismatches: 1, Indels: 8 0.74 0.03 0.23 Matches are distributed among these distances: 17 16 0.62 18 4 0.15 19 6 0.23 ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35 Consensus pattern (18 bp): GAGCATGATGTCATACTT Found at i:96461594 original size:39 final size:40 Alignment explanation

Indices: 96461512--96461676 Score: 160 Period size: 40 Copynumber: 4.2 Consensus size: 40 96461502 AATTGAATGA * * ** * 96461512 TATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATTA 1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTGATTC * * * 96461551 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT- 1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTC * * 96461590 TATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTATTC 1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGATTC * * 96461630 TATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATTA 1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGATTC 96461670 TATCCGG 1 TATCCGG 96461677 TTATATTCCG Statistics Matches: 104, Mismatches: 16, Indels: 11 0.79 0.12 0.08 Matches are distributed among these distances: 38 3 0.03 39 43 0.41 40 56 0.54 41 2 0.02 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (40 bp): TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTC Found at i:96468667 original size:17 final size:18 Alignment explanation

Indices: 96468625--96468673 Score: 50 Period size: 17 Copynumber: 2.8 Consensus size: 18 96468615 AGTTGAAAAG 96468625 GAGCATGATTGTCATACTT 1 GAGCATGA-TGTCATACTT * 96468644 G-GCCATGATG-CATTCTT 1 GAG-CATGATGTCATACTT 96468661 GAGCATGAT-TCAT 1 GAGCATGATGTCAT 96468674 GCTTCTTGCA Statistics Matches: 26, Mismatches: 1, Indels: 8 0.74 0.03 0.23 Matches are distributed among these distances: 17 16 0.62 18 4 0.15 19 6 0.23 ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35 Consensus pattern (18 bp): GAGCATGATGTCATACTT Found at i:96469561 original size:40 final size:40 Alignment explanation

Indices: 96469495--96469661 Score: 169 Period size: 40 Copynumber: 4.2 Consensus size: 40 96469485 AAATTGAATG * * * 96469495 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * ** 96469534 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * 96469574 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT * * ** * 96469614 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT 96469654 ATATCCGG 1 ATATCCGG 96469662 TTATATTCCG Statistics Matches: 105, Mismatches: 18, Indels: 9 0.80 0.14 0.07 Matches are distributed among these distances: 39 16 0.15 40 87 0.83 41 2 0.02 ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT Found at i:96486905 original size:13 final size:13 Alignment explanation

Indices: 96486887--96486911 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 96486877 ACAAACGATA 96486887 AAATTTTCACACT 1 AAATTTTCACACT 96486900 AAATTTTCACAC 1 AAATTTTCACAC 96486912 ATATAAATTA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36 Consensus pattern (13 bp): AAATTTTCACACT Found at i:96488505 original size:27 final size:26 Alignment explanation

Indices: 96488460--96488518 Score: 68 Period size: 27 Copynumber: 2.2 Consensus size: 26 96488450 AATACATAGT 96488460 TTTAATATGTCTAGTTTA-GGACATTAA 1 TTTAATATGTCTAGTTTAGGGACA--AA * 96488487 TTTAATGTGTCTA-TCTTAGGGACAAA 1 TTTAATATGTCTAGT-TTAGGGACAAA 96488513 TTTAAT 1 TTTAAT 96488519 TAGCTGTTGA Statistics Matches: 29, Mismatches: 1, Indels: 5 0.83 0.03 0.14 Matches are distributed among these distances: 26 9 0.31 27 15 0.52 28 5 0.17 ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44 Consensus pattern (26 bp): TTTAATATGTCTAGTTTAGGGACAAA Found at i:96492923 original size:43 final size:43 Alignment explanation

Indices: 96492876--96493027 Score: 162 Period size: 43 Copynumber: 3.5 Consensus size: 43 96492866 AGATATGATT * 96492876 TCGTGTAAGACCACGTCTGGGACATTGGCATCAATTTGAGATA 1 TCGTGTAAGACCACGTCTGGGACACTGGCATCAATTTGAGATA ** * * * 96492919 TCGTGTAAGACCGTGTCTGGGACACTGGCATCGATTAGAGATT 1 TCGTGTAAGACCACGTCTGGGACACTGGCATCAATTTGAGATA ** * * * * * 96492962 TCGTGTAAGACCTTGTCTGGGATAGTAGCATCAATATGTGATTA 1 TCGTGTAAGACCACGTCTGGGACACTGGCATCAATTTGAGA-TA * 96493006 T-ATGTAAGACCACGTCTGGGAC 1 TCGTGTAAGACCACGTCTGGGAC 96493028 GTTGTCATTG Statistics Matches: 89, Mismatches: 19, Indels: 2 0.81 0.17 0.02 Matches are distributed among these distances: 43 87 0.98 44 2 0.02 ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29 Consensus pattern (43 bp): TCGTGTAAGACCACGTCTGGGACACTGGCATCAATTTGAGATA Found at i:96497699 original size:22 final size:21 Alignment explanation

Indices: 96497666--96497706 Score: 55 Period size: 22 Copynumber: 1.9 Consensus size: 21 96497656 TTATTGTTAT * 96497666 TTTAAAAAATTATATATAATA 1 TTTAAAAAATTAAATATAATA * 96497687 TTTATAAATATTAAATATAA 1 TTTA-AAAAATTAAATATAA 96497707 AATATTAATC Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 21 4 0.24 22 13 0.76 ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44 Consensus pattern (21 bp): TTTAAAAAATTAAATATAATA Found at i:96501438 original size:7 final size:7 Alignment explanation

Indices: 96501426--96501545 Score: 66 Period size: 7 Copynumber: 17.0 Consensus size: 7 96501416 ATTAATTAAT 96501426 CTAAACC 1 CTAAACC * 96501433 CTAAACTT 1 CTAAAC-C * 96501441 CTAATCC 1 CTAAACC * 96501448 CTAATCC 1 CTAAACC * 96501455 CTAATCC 1 CTAAACC 96501462 CTAAACC 1 CTAAACC * 96501469 ATAAACC 1 CTAAACC * * 96501476 TTAAATC 1 CTAAACC * 96501483 CTAAAAC 1 CTAAACC * 96501490 ATAAACC 1 CTAAACC * * 96501497 CT-TACA 1 CTAAACC * 96501503 CTGAACCC 1 CT-AAACC * 96501511 CTAACCC 1 CTAAACC 96501518 CT-AACC 1 CTAAACC 96501524 CTTAAACC 1 C-TAAACC 96501532 CT-AACC 1 CTAAACC 96501538 CTTAAACC 1 C-TAAACC 96501546 ATAATCATAA Statistics Matches: 88, Mismatches: 18, Indels: 13 0.74 0.15 0.11 Matches are distributed among these distances: 6 13 0.15 7 58 0.66 8 17 0.19 ACGTcount: A:0.38, C:0.38, G:0.01, T:0.23 Consensus pattern (7 bp): CTAAACC Found at i:96501558 original size:21 final size:23 Alignment explanation

Indices: 96501534--96501587 Score: 62 Period size: 21 Copynumber: 2.5 Consensus size: 23 96501524 CTTAAACCCT 96501534 AACCCTTAAACCA-TAA-TCATA 1 AACCCTTAAACCAGTAACTCATA * * 96501555 AACCTTTAAA-TAGTAACTCATA 1 AACCCTTAAACCAGTAACTCATA 96501577 AA-CCTTAAACC 1 AACCCTTAAACC 96501588 CTTAACCATA Statistics Matches: 26, Mismatches: 4, Indels: 5 0.74 0.11 0.14 Matches are distributed among these distances: 20 1 0.04 21 18 0.69 22 7 0.27 ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26 Consensus pattern (23 bp): AACCCTTAAACCAGTAACTCATA Found at i:96501597 original size:21 final size:21 Alignment explanation

Indices: 96501460--96501597 Score: 52 Period size: 21 Copynumber: 6.6 Consensus size: 21 96501450 AATCCCTAAT * 96501460 CCCTAAACCATAAACCTTAAA 1 CCCTTAACCATAAACCTTAAA * * * 96501481 TCCTAAAACATAAACCCTT--A 1 CCCTTAACCATAAA-CCTTAAA * * * * * 96501501 CACTGAACCCCTAACCCCT-AA 1 CCCTTAA-CCATAAACCTTAAA * * 96501522 CCCTTAAACCCTAACCCTTAAA 1 CCCTT-AACCATAAACCTTAAA * * 96501544 -CCATAATCATAAACCTTTAAA 1 CCCTTAACCATAAACC-TTAAA *** 96501565 -TAGTAACTCATAAACCTTAAA 1 CCCTTAAC-CATAAACCTTAAA 96501586 CCCTTAACCATA 1 CCCTTAACCATA 96501598 TGCCCTAAAT Statistics Matches: 86, Mismatches: 23, Indels: 16 0.69 0.18 0.13 Matches are distributed among these distances: 20 16 0.19 21 50 0.58 22 20 0.23 ACGTcount: A:0.42, C:0.33, G:0.01, T:0.23 Consensus pattern (21 bp): CCCTTAACCATAAACCTTAAA Found at i:96503349 original size:36 final size:36 Alignment explanation

Indices: 96503302--96503374 Score: 137 Period size: 36 Copynumber: 2.0 Consensus size: 36 96503292 CTCTTAACAT 96503302 ACTGTTCATATGATCGTTTCGTTACTCTCCTACGAA 1 ACTGTTCATATGATCGTTTCGTTACTCTCCTACGAA * 96503338 ACTGTTCATATGATCGTTTCGTTACTCTCCTATGAA 1 ACTGTTCATATGATCGTTTCGTTACTCTCCTACGAA 96503374 A 1 A 96503375 ATAGACTCTT Statistics Matches: 36, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 36 36 1.00 ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40 Consensus pattern (36 bp): ACTGTTCATATGATCGTTTCGTTACTCTCCTACGAA Found at i:96504262 original size:40 final size:40 Alignment explanation

Indices: 96504192--96504398 Score: 231 Period size: 40 Copynumber: 5.2 Consensus size: 40 96504182 CGGGATTTAA ** * * 96504192 CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAGC 1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC * * 96504231 CCGGATAT-GATCACTAGCATAAATGCCTTCGGGACTTAGC 1 CCGGATATAG-TCACTAGCACAAATGCCTTCGGGTCTTAGC * * 96504271 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTTTTGGC 1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC * * * * 96504311 CCGGATATAGTAACTCGCATAAATGCCTTCGGATCTTAG- 1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC * * * * 96504350 TCGGATATAGTCACTTAACACAAAAGCCTTCGGGACTTAGC 1 CCGGATATAGTCAC-TAGCACAAATGCCTTCGGGTCTTAGC 96504391 CCGGATAT 1 CCGGATAT 96504399 CATTCGAATA Statistics Matches: 138, Mismatches: 25, Indels: 8 0.81 0.15 0.05 Matches are distributed among these distances: 39 27 0.20 40 103 0.75 41 8 0.06 ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25 Consensus pattern (40 bp): CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:96504313 original size:80 final size:79 Alignment explanation

Indices: 96504178--96504398 Score: 259 Period size: 80 Copynumber: 2.8 Consensus size: 79 96504168 GAATCACGTA * * ** * * 96504178 CCTTCGGGATTTAACCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAGCCCGGATAT-GA 1 CCTTCGGGACTTAGCCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAG- * 96504241 TCACTAGCATAAATG 65 TAACTAGCATAAATG * * * 96504256 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTTTTGGCCCGGATATAG 1 CCTTCGGGACTTAG-CCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAG * 96504321 TAACTCGCATAAATG 65 TAACTAGCATAAATG * * * 96504336 CCTTC-GGATCTTAGTCGGATATAGTCACTTAACACAAAAGCCTTCGGGACTTAGCCCGGATAT 1 CCTTCGGGA-CTTAGCCGGATATAGTCAC-TAGCACAAAAGCCTTCGGGTCTTAGCCCGGATAT 96504399 CATTCGAATA Statistics Matches: 122, Mismatches: 16, Indels: 8 0.84 0.11 0.05 Matches are distributed among these distances: 78 12 0.10 79 33 0.27 80 76 0.62 81 1 0.01 ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26 Consensus pattern (79 bp): CCTTCGGGACTTAGCCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGT AACTAGCATAAATG Found at i:96512383 original size:40 final size:40 Alignment explanation

Indices: 96512313--96512520 Score: 222 Period size: 40 Copynumber: 5.2 Consensus size: 40 96512303 CGGGATTTAA ** * * 96512313 CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAGC 1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC * * * 96512352 CCGGATAT-GATCACTAGCATAAATGCCTTCGGGACTTATC 1 CCGGATATAG-TCACTAGCACAAATGCCTTCGGGTCTTAGC * * * 96512392 CCGGATATAGTCGCTAGCACAAATGCCTTCGGGTTTTGGC 1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC * * * * * 96512432 CCGGATATAGTAACTCGCATAAATGCCTTCGGATCTTAGT 1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC * * * 96512472 CCGGATATAGTCACTTAACACAAAAGCCTTCGGGACTTAGC 1 CCGGATATAGTCAC-TAGCACAAATGCCTTCGGGTCTTAGC 96512513 CCGGATAT 1 CCGGATAT 96512521 CATTCGAATA Statistics Matches: 136, Mismatches: 29, Indels: 6 0.80 0.17 0.04 Matches are distributed among these distances: 39 15 0.11 40 93 0.68 41 28 0.21 ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25 Consensus pattern (40 bp): CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:96518702 original size:27 final size:27 Alignment explanation

Indices: 96518661--96518832 Score: 193 Period size: 27 Copynumber: 6.4 Consensus size: 27 96518651 TGGATAAGTT * 96518661 GTAGAATTACCGAAATTCCCCTGTAGG 1 GTAGAATTACCGAAATACCCCTGTAGG ** 96518688 GTAGAATTATTGAAATACCCCTGTAGG 1 GTAGAATTACCGAAATACCCCTGTAGG * 96518715 GTAGAATTACCGAAATACCCTTGTAGG 1 GTAGAATTACCGAAATACCCCTGTAGG * ** * 96518742 ATAGAATTATTGAAATA-CCCTATAGG 1 GTAGAATTACCGAAATACCCCTGTAGG * * * * 96518768 GTAGAAATACCAAAATAACCCTATAGG 1 GTAGAATTACCGAAATACCCCTGTAGG * * * 96518795 GTAGAATTACCGAGATACCCTTGTGGG 1 GTAGAATTACCGAAATACCCCTGTAGG * 96518822 GTAAAATTACC 1 GTAGAATTACC 96518833 ATTTTGCCCC Statistics Matches: 120, Mismatches: 24, Indels: 2 0.82 0.16 0.01 Matches are distributed among these distances: 26 19 0.16 27 101 0.84 ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26 Consensus pattern (27 bp): GTAGAATTACCGAAATACCCCTGTAGG Found at i:96524037 original size:40 final size:40 Alignment explanation

Indices: 96523972--96524179 Score: 294 Period size: 40 Copynumber: 5.2 Consensus size: 40 96523962 TCTTCGGAAT * ** * 96523972 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC * * * 96524011 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC * 96524051 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC 96524091 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC * * * 96524131 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC 1 TTAGCCCGGATATAA-CAACTCGCACAAATGCCTTCGGGTC 96524171 TTAGCCCGG 1 TTAGCCCGG 96524180 GTATCATTCA Statistics Matches: 152, Mismatches: 15, Indels: 3 0.89 0.09 0.02 Matches are distributed among these distances: 39 3 0.02 40 148 0.97 41 1 0.01 ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23 Consensus pattern (40 bp): TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC Found at i:96527469 original size:29 final size:31 Alignment explanation

Indices: 96527423--96527535 Score: 146 Period size: 31 Copynumber: 3.7 Consensus size: 31 96527413 TCAGTCTCAA * * 96527423 CATAT-ACTAGGCCGAAGCC-TTTCATTAAA 1 CATATCACTGGGCCGAAGCCTTTTCATTAAT 96527452 CGAT-T-ACTGGGCCGAAGCCTTTTCA-TAATT 1 C-ATATCACTGGGCCGAAGCCTTTTCATTAA-T * 96527482 CATATCACTGGGCCGAAGCCTTTTCATTATT 1 CATATCACTGGGCCGAAGCCTTTTCATTAAT 96527513 CATATCACTGGGCCGAAGCCTTT 1 CATATCACTGGGCCGAAGCCTTT 96527536 ACTGTAAACG Statistics Matches: 75, Mismatches: 3, Indels: 10 0.85 0.03 0.11 Matches are distributed among these distances: 29 20 0.27 30 9 0.12 31 44 0.59 32 2 0.03 ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31 Consensus pattern (31 bp): CATATCACTGGGCCGAAGCCTTTTCATTAAT Found at i:96527495 original size:31 final size:31 Alignment explanation

Indices: 96527457--96527535 Score: 149 Period size: 31 Copynumber: 2.5 Consensus size: 31 96527447 TTAAACGATT 96527457 ACTGGGCCGAAGCCTTTTCATAATTCATATC 1 ACTGGGCCGAAGCCTTTTCATAATTCATATC * 96527488 ACTGGGCCGAAGCCTTTTCATTATTCATATC 1 ACTGGGCCGAAGCCTTTTCATAATTCATATC 96527519 ACTGGGCCGAAGCCTTT 1 ACTGGGCCGAAGCCTTT 96527536 ACTGTAAACG Statistics Matches: 47, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 31 47 1.00 ACGTcount: A:0.23, C:0.27, G:0.19, T:0.32 Consensus pattern (31 bp): ACTGGGCCGAAGCCTTTTCATAATTCATATC Found at i:96527880 original size:11 final size:11 Alignment explanation

Indices: 96527850--96527894 Score: 51 Period size: 11 Copynumber: 4.4 Consensus size: 11 96527840 TGAATACATT 96527850 ATGTGCATATC 1 ATGTGCATATC * 96527861 A--TACATATC 1 ATGTGCATATC 96527870 ATGTGCATATC 1 ATGTGCATATC * 96527881 ATGT-CAAATC 1 ATGTGCATATC 96527891 ATGT 1 ATGT 96527895 ACATCAAAAT Statistics Matches: 29, Mismatches: 3, Indels: 5 0.78 0.08 0.14 Matches are distributed among these distances: 9 8 0.28 10 9 0.31 11 12 0.41 ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36 Consensus pattern (11 bp): ATGTGCATATC Found at i:96527958 original size:25 final size:25 Alignment explanation

Indices: 96527930--96527977 Score: 78 Period size: 25 Copynumber: 1.9 Consensus size: 25 96527920 CATAATTAAC * * 96527930 CCTAGGGGTATAATGGTCATTTTTA 1 CCTAGGGGTAAAATAGTCATTTTTA 96527955 CCTAGGGGTAAAATAGTCATTTT 1 CCTAGGGGTAAAATAGTCATTTT 96527978 CCATATTATA Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 25 21 1.00 ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38 Consensus pattern (25 bp): CCTAGGGGTAAAATAGTCATTTTTA Found at i:96531364 original size:47 final size:49 Alignment explanation

Indices: 96531147--96531402 Score: 439 Period size: 49 Copynumber: 5.3 Consensus size: 49 96531137 GTATGAGGTA 96531147 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG 1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG 96531196 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG 1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG * 96531245 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA 1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG 96531294 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAG-GTG 1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG * * * 96531341 TATATATGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAAA--GTG 1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG * 96531388 TATAAATGTGATAAG 1 TATATATGTGATAAG 96531403 TCCCGAAGGG Statistics Matches: 199, Mismatches: 7, Indels: 4 0.95 0.03 0.02 Matches are distributed among these distances: 47 56 0.28 48 5 0.03 49 138 0.69 ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30 Consensus pattern (49 bp): TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG Found at i:96533763 original size:40 final size:40 Alignment explanation

Indices: 96533699--96533819 Score: 199 Period size: 40 Copynumber: 3.0 Consensus size: 40 96533689 AAGTCTCGAC * 96533699 GATG-ATCCGGGCTAAGTCCTGAAGAGCATTCATGCTAGT 1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT 96533738 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT 1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT * * * 96533778 GATGTATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT 1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT 96533818 GA 1 GA 96533820 CGTGTATTCG Statistics Matches: 77, Mismatches: 4, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 39 4 0.05 40 73 0.95 ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24 Consensus pattern (40 bp): GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT Found at i:96537572 original size:47 final size:49 Alignment explanation

Indices: 96537355--96537610 Score: 439 Period size: 49 Copynumber: 5.3 Consensus size: 49 96537345 GTATGAGGTA 96537355 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG 1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG 96537404 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG 1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG * 96537453 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA 1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG 96537502 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAG-GTG 1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG * * * 96537549 TATATATGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAAA--GTG 1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG * 96537596 TATAAATGTGATAAG 1 TATATATGTGATAAG 96537611 TCCCGAAGGG Statistics Matches: 199, Mismatches: 7, Indels: 4 0.95 0.03 0.02 Matches are distributed among these distances: 47 56 0.28 48 5 0.03 49 138 0.69 ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30 Consensus pattern (49 bp): TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG Found at i:96540787 original size:2 final size:2 Alignment explanation

Indices: 96540780--96540815 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 96540770 TTGGCTGTCT 96540780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 96540816 CCTTCGAATA Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:96541597 original size:49 final size:49 Alignment explanation

Indices: 96541470--96541735 Score: 450 Period size: 49 Copynumber: 5.5 Consensus size: 49 96541460 CCCTTCGGGA * * 96541470 CTTATCACAT-T-TATACACTTTCACATTCATCACATTGGCCATTAAGC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 96541517 CTTATCAC--ATATATACACCTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 96541564 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTTGGC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 96541613 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 96541662 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC 96541711 CTTATCACATATATATACACTTTCA 1 CTTATCACATATATATACACTTTCA 96541736 TGTACAGACT Statistics Matches: 207, Mismatches: 8, Indels: 6 0.94 0.04 0.03 Matches are distributed among these distances: 46 1 0.00 47 49 0.24 49 157 0.76 ACGTcount: A:0.30, C:0.29, G:0.07, T:0.33 Consensus pattern (49 bp): CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:96543388 original size:2 final size:2 Alignment explanation

Indices: 96543381--96543410 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 96543371 TGCCGAATAC 96543381 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 96543411 CATCATCAAA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:96543596 original size:2 final size:2 Alignment explanation

Indices: 96543591--96543620 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 96543581 ATATTCGGCA 96543591 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 96543621 GACTAAAACA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:96545128 original size:29 final size:29 Alignment explanation

Indices: 96545090--96545192 Score: 93 Period size: 29 Copynumber: 3.6 Consensus size: 29 96545080 GGTTGGAGAA 96545090 CTCGCACACACAGTGCCTCATTTACCGAT 1 CTCGCACACACAGTGCCTCATTTACCGAT * * * * ** 96545119 CTCGCTCACATAGTG-CTCGGTTAAGGGAAT 1 CTCGCACACACAGTGCCTC-ATTTACCG-AT * * 96545149 -TCGCACACACAGTGCCTCAATTACTGAT 1 CTCGCACACACAGTGCCTCATTTACCGAT * 96545177 CTCGCACACATAGTGC 1 CTCGCACACACAGTGC 96545193 TCGGTTAAAG Statistics Matches: 56, Mismatches: 14, Indels: 8 0.72 0.18 0.10 Matches are distributed among these distances: 28 5 0.09 29 46 0.82 30 5 0.09 ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24 Consensus pattern (29 bp): CTCGCACACACAGTGCCTCATTTACCGAT Found at i:96545180 original size:58 final size:58 Alignment explanation

Indices: 96545056--96545208 Score: 238 Period size: 58 Copynumber: 2.7 Consensus size: 58 96545046 GTGCCCACTG * * 96545056 ACCGATCTCGCACACATAGTGCTCGGTT--GGAGAACTCGCACACACAGTGCCTCATTT 1 ACCGATCTCGCACACATAGTGCTCGGTTAAGG-GAATTCGCACACACAGTGCCTCAATT * 96545113 ACCGATCTCGCTCACATAGTGCTCGGTTAAGGGAATTCGCACACACAGTGCCTCAATT 1 ACCGATCTCGCACACATAGTGCTCGGTTAAGGGAATTCGCACACACAGTGCCTCAATT * * 96545171 ACTGATCTCGCACACATAGTGCTCGGTTAAAGGAATTC 1 ACCGATCTCGCACACATAGTGCTCGGTTAAGGGAATTC 96545209 ATACGGTAAT Statistics Matches: 88, Mismatches: 6, Indels: 3 0.91 0.06 0.03 Matches are distributed among these distances: 57 27 0.31 58 59 0.67 59 2 0.02 ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24 Consensus pattern (58 bp): ACCGATCTCGCACACATAGTGCTCGGTTAAGGGAATTCGCACACACAGTGCCTCAATT Found at i:96545306 original size:43 final size:43 Alignment explanation

Indices: 96545252--96545507 Score: 485 Period size: 43 Copynumber: 6.0 Consensus size: 43 96545242 CATCGGCATT * 96545252 AAGCCTGCTAGGCACGAAGACCCGAATACATATCACCGGCACA 1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA * 96545295 AAGCCTGCTAGGCTCGAAGGCCCGAATACATATCACCGGCACA 1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA * 96545338 AAGCCTGCTAGGCTCGAAGGCCCGAATACATATCACCGGCACA 1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA 96545381 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA 1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA 96545424 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA 1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA 96545467 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCA 1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCA 96545508 TAACTGCTCT Statistics Matches: 210, Mismatches: 3, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 43 210 1.00 ACGTcount: A:0.32, C:0.32, G:0.23, T:0.12 Consensus pattern (43 bp): AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA Found at i:96545593 original size:40 final size:42 Alignment explanation

Indices: 96545486--96545659 Score: 133 Period size: 40 Copynumber: 4.2 Consensus size: 42 96545476 AGGCACGAAG * * * * * * 96545486 GCCCGAATACATATCACCGGCA-TAACTGCTCTTCGGGACCTG 1 GCCCGGATATATATCACCAGCACGAA-TGCTCTTCGGGACTTA * * * * * * 96545528 GTCCGG--ATACATCACTAGCATGAATGCTCTTCGAGATTTA 1 GCCCGGATATATATCACCAGCACGAATGCTCTTCGGGACTTA * * 96545568 GCCCGGATGTA-A-CACCAGCACGAATGCTCTACGGGACTTA 1 GCCCGGATATATATCACCAGCACGAATGCTCTTCGGGACTTA * * * 96545608 ACCTGGATATATATATCGCCAGCACGAATGCTCTTCGGGACTTA 1 GCCCGG--ATATATATCACCAGCACGAATGCTCTTCGGGACTTA 96545652 GCCCGGAT 1 GCCCGGAT 96545660 CATCGTCGAG Statistics Matches: 100, Mismatches: 25, Indels: 14 0.72 0.18 0.10 Matches are distributed among these distances: 40 54 0.54 41 3 0.03 42 12 0.12 43 1 0.01 44 30 0.30 ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24 Consensus pattern (42 bp): GCCCGGATATATATCACCAGCACGAATGCTCTTCGGGACTTA Found at i:96546842 original size:2 final size:2 Alignment explanation

Indices: 96546835--96546864 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 96546825 TTGGCTGTCT 96546835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 96546865 CCTTCGAATA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:96547646 original size:49 final size:49 Alignment explanation

Indices: 96547519--96547784 Score: 450 Period size: 49 Copynumber: 5.5 Consensus size: 49 96547509 CCCTTCGGGA * * 96547519 CTTATCACAT-T-TATACACTTTCACATTCATCACATTGGCCATTAAGC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 96547566 CTTATCAC--ATATATACACCTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 96547613 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTTGGC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 96547662 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 96547711 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC 96547760 CTTATCACATATATATACACTTTCA 1 CTTATCACATATATATACACTTTCA 96547785 TGTACAGACT Statistics Matches: 207, Mismatches: 8, Indels: 6 0.94 0.04 0.03 Matches are distributed among these distances: 46 1 0.00 47 49 0.24 49 157 0.76 ACGTcount: A:0.30, C:0.29, G:0.07, T:0.33 Consensus pattern (49 bp): CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:96555902 original size:42 final size:43 Alignment explanation

Indices: 96555794--96555913 Score: 120 Period size: 42 Copynumber: 2.8 Consensus size: 43 96555784 AACAAGTACA * * * 96555794 ATGCCGATG-CCCTTAACGTGGTCTTACATGTAATTCAATATCG 1 ATGCCGATGTCCC-AAACATGGTCTTACATGTAAATCAATATCG ** * * 96555837 ATGCCTCTGTCCCAAATAGGGTCTTACATG-AAATCAGATAT-G 1 ATGCCGATGTCCCAAACATGGTCTTACATGTAAATCA-ATATCG * * 96555879 ATGCCGATGTCCCAGACATGGTCTTATATGTAAAT 1 ATGCCGATGTCCCAAACATGGTCTTACATGTAAAT 96555914 ATCAATCGAG Statistics Matches: 61, Mismatches: 13, Indels: 6 0.76 0.16 0.08 Matches are distributed among these distances: 42 30 0.49 43 28 0.46 44 3 0.05 ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31 Consensus pattern (43 bp): ATGCCGATGTCCCAAACATGGTCTTACATGTAAATCAATATCG Found at i:96558101 original size:39 final size:40 Alignment explanation

Indices: 96558011--96558229 Score: 274 Period size: 39 Copynumber: 5.5 Consensus size: 40 96558001 ACCCAAGTAT * * 96558011 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC 1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC * ** 96558050 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC 1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC 96558090 CTTC-GGACTTAGCCCGGATATAGTCACTAGCACAAATGC 1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC 96558129 CTTCGGGACTTAGCCCGG-TATAG-CAACTACTTGCACAAATGC 1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC * * 96558171 CTTC-GGACTTAGCCC-GATATAGTAACTTGCACAAATGC 1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC 96558209 CTTCGGGACTTAG-CCGGATAT 1 CTTCGGGACTTAGCCCGGATAT 96558230 CATCCGAATA Statistics Matches: 159, Mismatches: 10, Indels: 22 0.83 0.05 0.12 Matches are distributed among these distances: 38 17 0.11 39 69 0.43 40 39 0.25 41 20 0.13 42 14 0.09 ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25 Consensus pattern (40 bp): CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC Found at i:96558142 original size:79 final size:80 Alignment explanation

Indices: 96558011--96558229 Score: 281 Period size: 79 Copynumber: 2.8 Consensus size: 80 96558001 ACCCAAGTAT * * * 96558011 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG 1 CTTC-GGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG ** 96558074 TC-ACTA-GCATGAATGC 64 -CAACTATGCACAAATGC 96558090 CTTCGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG-TATAGCA 1 CTTCGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGCA 96558154 ACTACTTGCACAAATGC 66 ACTA--TGCACAAATGC * * 96558171 CTTCGGACTTAGCCC-GATATAGTAACTTGCACAAATGCCTTCGGGACTTAG-CCGGATAT 1 CTTCGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT 96558230 CATCCGAATA Statistics Matches: 126, Mismatches: 7, Indels: 13 0.86 0.05 0.09 Matches are distributed among these distances: 77 1 0.01 78 16 0.13 79 48 0.38 80 38 0.30 81 23 0.18 ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25 Consensus pattern (80 bp): CTTCGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGCA ACTATGCACAAATGC Found at i:96572167 original size:48 final size:48 Alignment explanation

Indices: 96572102--96572573 Score: 822 Period size: 48 Copynumber: 9.9 Consensus size: 48 96572092 TATATATGTG * 96572102 TGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96572150 TGTGGTAAAGCCGAATGGCTACTGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96572198 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96572246 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * * 96572294 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGAATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 96572342 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTA-A 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96572389 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 96572437 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96572485 TGTGGTAAAGCCGAATGGC-AAGTGTGAAATTTGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAA-TGTGAAATATGTATGAGATATGTATA * * * 96572533 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATTTAGGAGAT 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT 96572574 GTGTGTATAT Statistics Matches: 404, Mismatches: 17, Indels: 6 0.95 0.04 0.01 Matches are distributed among these distances: 47 48 0.12 48 355 0.88 49 1 0.00 ACGTcount: A:0.35, C:0.07, G:0.28, T:0.31 Consensus pattern (48 bp): TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA Found at i:96572816 original size:37 final size:37 Alignment explanation

Indices: 96572714--96572804 Score: 173 Period size: 37 Copynumber: 2.5 Consensus size: 37 96572704 GGAAATATAT 96572714 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * 96572751 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 96572788 TCCGGGTAAGACCCGAT 1 TCCGGGTAAGACCCGAT 96572805 AGCTACTTGT Statistics Matches: 53, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 37 53 1.00 ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24 Consensus pattern (37 bp): TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG Found at i:96574145 original size:40 final size:40 Alignment explanation

Indices: 96574099--96574384 Score: 414 Period size: 40 Copynumber: 7.2 Consensus size: 40 96574089 TATATAGCCA * * * 96574099 GGCTAAGTCCCGAAGAGCATTCGTGCT-GATGTTATATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAG-TGATGTATCCG * * * 96574139 GGCTAAGTCCCGAAGAGCATTCGTGCT-GATGTTATATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAG-TGATGTATCCG * * 96574179 GGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATTCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG 96574219 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG * 96574259 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCTG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG * * 96574299 AGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG * * * 96574339 GGTTAAGTTTCGAAGAGCATTCGTGCTAGTGATATATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG 96574379 GGCTAA 1 GGCTAA 96574385 ACCTTGAAGG Statistics Matches: 230, Mismatches: 15, Indels: 2 0.93 0.06 0.01 Matches are distributed among these distances: 40 229 1.00 41 1 0.00 ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28 Consensus pattern (40 bp): GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG Found at i:96574483 original size:29 final size:29 Alignment explanation

Indices: 96574444--96574545 Score: 118 Period size: 29 Copynumber: 3.6 Consensus size: 29 96574434 CTTCAACTGA * * * 96574444 GCACTATGTGTGCCAGATCAGTAGTTGAG 1 GCACTATGTGTGCGAGATTAGTAATTGAG ** * 96574473 GCACTATGTGTGCGAG-TTTTTCAATCGA- 1 GCACTATGTGTGCGAGATTAGT-AATTGAG * 96574501 GCACTATGTGTGCGAGATTGGTAATTGAG 1 GCACTATGTGTGCGAGATTAGTAATTGAG 96574530 GCACTATGTGTGCGAG 1 GCACTATGTGTGCGAG 96574546 TTCTTTAATC Statistics Matches: 61, Mismatches: 9, Indels: 6 0.80 0.12 0.08 Matches are distributed among these distances: 28 23 0.38 29 38 0.62 ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30 Consensus pattern (29 bp): GCACTATGTGTGCGAGATTAGTAATTGAG Found at i:96574503 original size:57 final size:57 Alignment explanation

Indices: 96574412--96574600 Score: 215 Period size: 57 Copynumber: 3.3 Consensus size: 57 96574402 GCTGGAGTTA * * * 96574412 TGAGGCACTGTGTGTGCAAGTTCTTCAA-CTGAGCACTATGTGTGCCAGATCAGTAGT 1 TGAGGCACTATGTGTGCGAGTTTTTCAATC-GAGCACTATGTGTGCCAGATCAGTAGT * ** * 96574469 TGAGGCACTATGTGTGCGAGTTTTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT 1 TGAGGCACTATGTGTGCGAGTTTTTCAATCGAGCACTATGTGTGCCAGATCAGTAGT * * * 96574526 TGAGGCACTATGTGTGCGAGTTCTTT-AATCGAGCGCTATGTGTGCTAAATCAGTTAG- 1 TGAGGCACTATGTGTGCGAGTT-TTTCAATCGAGCACTATGTGTGCCAGATCAG-TAGT * * 96574583 TG-GGCACTGTGTATGCGA 1 TGAGGCACTATGTGTGCGA 96574601 AGTGTGTTTC Statistics Matches: 114, Mismatches: 15, Indels: 7 0.84 0.11 0.05 Matches are distributed among these distances: 56 14 0.12 57 94 0.82 58 6 0.05 ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32 Consensus pattern (57 bp): TGAGGCACTATGTGTGCGAGTTTTTCAATCGAGCACTATGTGTGCCAGATCAGTAGT Found at i:96574554 original size:29 final size:28 Alignment explanation

Indices: 96574416--96574570 Score: 134 Period size: 28 Copynumber: 5.5 Consensus size: 28 96574406 GAGTTATGAG * * * * 96574416 GCACTGTGTGTGCAAGTTCTTCAACTGA 1 GCACTATGTGTGCGAGTTCTTTAATTGA * * ** * 96574444 GCACTATGTGTGCCAGATCAGTAGTTGA 1 GCACTATGTGTGCGAGTTCTTTAATTGA * 96574472 GGCACTATGTGTGCGAGTT-TTTCAATCGA 1 -GCACTATGTGTGCGAGTTCTTT-AATTGA ** 96574501 GCACTATGTGTGCGAGATT-GGTAATTGA 1 GCACTATGTGTGCGAG-TTCTTTAATTGA * 96574529 GGCACTATGTGTGCGAGTTCTTTAATCGA 1 -GCACTATGTGTGCGAGTTCTTTAATTGA * 96574558 GCGCTATGTGTGC 1 GCACTATGTGTGC 96574571 TAAATCAGTT Statistics Matches: 101, Mismatches: 21, Indels: 10 0.77 0.16 0.08 Matches are distributed among these distances: 28 56 0.55 29 45 0.45 ACGTcount: A:0.21, C:0.17, G:0.29, T:0.32 Consensus pattern (28 bp): GCACTATGTGTGCGAGTTCTTTAATTGA Found at i:96576610 original size:2 final size:2 Alignment explanation

Indices: 96576603--96576628 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 96576593 AAATGGCATA 96576603 AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT 96576629 GTGTGTGTGT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:96577799 original size:48 final size:48 Alignment explanation

Indices: 96577734--96578205 Score: 822 Period size: 48 Copynumber: 9.9 Consensus size: 48 96577724 TATATATGTG * 96577734 TGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96577782 TGTGGTAAAGCCGAATGGCTACTGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96577830 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96577878 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * * 96577926 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGAATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 96577974 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTA-A 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96578021 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 96578069 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96578117 TGTGGTAAAGCCGAATGGC-AAGTGTGAAATTTGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAA-TGTGAAATATGTATGAGATATGTATA * * * 96578165 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATTTAGGAGAT 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT 96578206 GTGTGTATAT Statistics Matches: 404, Mismatches: 17, Indels: 6 0.95 0.04 0.01 Matches are distributed among these distances: 47 48 0.12 48 355 0.88 49 1 0.00 ACGTcount: A:0.35, C:0.07, G:0.28, T:0.31 Consensus pattern (48 bp): TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA Found at i:96578448 original size:37 final size:37 Alignment explanation

Indices: 96578346--96578436 Score: 173 Period size: 37 Copynumber: 2.5 Consensus size: 37 96578336 GGAAATATAT 96578346 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * 96578383 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 96578420 TCCGGGTAAGACCCGAT 1 TCCGGGTAAGACCCGAT 96578437 AGCTACTTGT Statistics Matches: 53, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 37 53 1.00 ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24 Consensus pattern (37 bp): TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG Found at i:96579824 original size:40 final size:40 Alignment explanation

Indices: 96579730--96580014 Score: 405 Period size: 40 Copynumber: 7.2 Consensus size: 40 96579720 TATATAGCCA * * * 96579730 GGCTAAGTCCCGAAGAGCATTCGTGCT-GATGTTATATCC- 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAG-TGATGTATCCG * * * 96579769 GGCTAAGTCCCGAAGAGCATTCGTGCT-GATGTTATATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAG-TGATGTATCCG * * 96579809 GGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATTCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG 96579849 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG * 96579889 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCTG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG * * 96579929 AGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG * * * 96579969 GGTTAAGTTTCGAAGAGCATTCGTGCTAGTGATATATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG 96580009 GGCTAA 1 GGCTAA 96580015 ACCTTGAAGG Statistics Matches: 229, Mismatches: 15, Indels: 3 0.93 0.06 0.01 Matches are distributed among these distances: 39 39 0.17 40 189 0.83 41 1 0.00 ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28 Consensus pattern (40 bp): GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG Found at i:96580113 original size:29 final size:29 Alignment explanation

Indices: 96580074--96580175 Score: 118 Period size: 29 Copynumber: 3.6 Consensus size: 29 96580064 CTTCAACTGA * * * 96580074 GCACTATGTGTGCCAGATCAGTAGTTGAG 1 GCACTATGTGTGCGAGATTAGTAATTGAG ** * 96580103 GCACTATGTGTGCGAG-TTTTTCAATCGA- 1 GCACTATGTGTGCGAGATTAGT-AATTGAG * 96580131 GCACTATGTGTGCGAGATTGGTAATTGAG 1 GCACTATGTGTGCGAGATTAGTAATTGAG 96580160 GCACTATGTGTGCGAG 1 GCACTATGTGTGCGAG 96580176 TTCTTTAATC Statistics Matches: 61, Mismatches: 9, Indels: 6 0.80 0.12 0.08 Matches are distributed among these distances: 28 23 0.38 29 38 0.62 ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30 Consensus pattern (29 bp): GCACTATGTGTGCGAGATTAGTAATTGAG Found at i:96580133 original size:57 final size:57 Alignment explanation

Indices: 96580042--96580230 Score: 215 Period size: 57 Copynumber: 3.3 Consensus size: 57 96580032 GCTGGAGTTA * * * 96580042 TGAGGCACTGTGTGTGCAAGTTCTTCAA-CTGAGCACTATGTGTGCCAGATCAGTAGT 1 TGAGGCACTATGTGTGCGAGTTTTTCAATC-GAGCACTATGTGTGCCAGATCAGTAGT * ** * 96580099 TGAGGCACTATGTGTGCGAGTTTTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT 1 TGAGGCACTATGTGTGCGAGTTTTTCAATCGAGCACTATGTGTGCCAGATCAGTAGT * * * 96580156 TGAGGCACTATGTGTGCGAGTTCTTT-AATCGAGCGCTATGTGTGCTAAATCAGTTAG- 1 TGAGGCACTATGTGTGCGAGTT-TTTCAATCGAGCACTATGTGTGCCAGATCAG-TAGT * * 96580213 TG-GGCACTGTGTATGCGA 1 TGAGGCACTATGTGTGCGA 96580231 AGTGTGTTTC Statistics Matches: 114, Mismatches: 15, Indels: 7 0.84 0.11 0.05 Matches are distributed among these distances: 56 14 0.12 57 94 0.82 58 6 0.05 ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32 Consensus pattern (57 bp): TGAGGCACTATGTGTGCGAGTTTTTCAATCGAGCACTATGTGTGCCAGATCAGTAGT Found at i:96580184 original size:29 final size:28 Alignment explanation

Indices: 96580046--96580200 Score: 134 Period size: 28 Copynumber: 5.5 Consensus size: 28 96580036 GAGTTATGAG * * * * 96580046 GCACTGTGTGTGCAAGTTCTTCAACTGA 1 GCACTATGTGTGCGAGTTCTTTAATTGA * * ** * 96580074 GCACTATGTGTGCCAGATCAGTAGTTGA 1 GCACTATGTGTGCGAGTTCTTTAATTGA * 96580102 GGCACTATGTGTGCGAGTT-TTTCAATCGA 1 -GCACTATGTGTGCGAGTTCTTT-AATTGA ** 96580131 GCACTATGTGTGCGAGATT-GGTAATTGA 1 GCACTATGTGTGCGAG-TTCTTTAATTGA * 96580159 GGCACTATGTGTGCGAGTTCTTTAATCGA 1 -GCACTATGTGTGCGAGTTCTTTAATTGA * 96580188 GCGCTATGTGTGC 1 GCACTATGTGTGC 96580201 TAAATCAGTT Statistics Matches: 101, Mismatches: 21, Indels: 10 0.77 0.16 0.08 Matches are distributed among these distances: 28 56 0.55 29 45 0.45 ACGTcount: A:0.21, C:0.17, G:0.29, T:0.32 Consensus pattern (28 bp): GCACTATGTGTGCGAGTTCTTTAATTGA Found at i:96582240 original size:2 final size:2 Alignment explanation

Indices: 96582233--96582272 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 96582223 AAATGGCATA 96582233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 96582273 GTGTGTGTGT Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:96584084 original size:29 final size:29 Alignment explanation

Indices: 96584051--96584115 Score: 121 Period size: 29 Copynumber: 2.2 Consensus size: 29 96584041 GTGACGAGAT 96584051 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA 96584080 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA * 96584109 CGGCACT 1 TGGCACT 96584116 GGGTGTGCGA Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 29 35 1.00 ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26 Consensus pattern (29 bp): TGGCACTAAGTGTGCATGCTGGAAATATA Found at i:96592017 original size:29 final size:29 Alignment explanation

Indices: 96591984--96592048 Score: 121 Period size: 29 Copynumber: 2.2 Consensus size: 29 96591974 GTGACGAGAT 96591984 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA 96592013 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA * 96592042 CGGCACT 1 TGGCACT 96592049 GGGTGTGCGA Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 29 35 1.00 ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26 Consensus pattern (29 bp): TGGCACTAAGTGTGCATGCTGGAAATATA Found at i:96594542 original size:48 final size:48 Alignment explanation

Indices: 96594477--96594948 Score: 829 Period size: 48 Copynumber: 9.9 Consensus size: 48 96594467 TATATATGTG * 96594477 TGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96594525 TGTGGTAAAGCCGAATGGCTACTGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96594573 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96594621 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * * 96594669 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGAATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 96594717 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTA-A 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96594764 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 96594812 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * * 96594860 TGTGGTAAAGCCGAATGGCTAGTGTGAAATTTGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * * * 96594908 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATTTAGGAGAT 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT 96594949 GTGTGTATAT Statistics Matches: 406, Mismatches: 17, Indels: 2 0.96 0.04 0.00 Matches are distributed among these distances: 47 46 0.11 48 360 0.89 ACGTcount: A:0.35, C:0.07, G:0.28, T:0.31 Consensus pattern (48 bp): TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA Found at i:96595143 original size:37 final size:37 Alignment explanation

Indices: 96595089--96595191 Score: 170 Period size: 37 Copynumber: 2.8 Consensus size: 37 96595079 GGAAATATAT * 96595089 TCCGGGTAAGACTCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * 96595126 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * * 96595163 TCCAGGTAAGACCCGATAACTACGTGTGG 1 TCCGGGTAAGACCCGATGACTACGTGTGG 96595192 GGACTATTCG Statistics Matches: 62, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 37 62 1.00 ACGTcount: A:0.24, C:0.19, G:0.31, T:0.25 Consensus pattern (37 bp): TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG Found at i:96596520 original size:40 final size:40 Alignment explanation

Indices: 96596474--96596759 Score: 423 Period size: 40 Copynumber: 7.2 Consensus size: 40 96596464 TATATAGCCA * * * 96596474 GGCTAAGTCCCGAAGAGCATTCGTGCT-GATGTTATATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAG-TGATGTATCCG * * * 96596514 GGCTAAGTCCCGAAGAGCATTCGTGCT-GATGTTATATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAG-TGATGTATCCG * * 96596554 GGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATTCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG * 96596594 GGCTAAGTTCTGAAGAGCATTCGTGCTAGTGATGTATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG 96596634 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG * * 96596674 AGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG * * 96596714 GGTTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCG 1 GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG 96596754 GGCTAA 1 GGCTAA 96596760 ACCTTGAAGG Statistics Matches: 231, Mismatches: 14, Indels: 2 0.94 0.06 0.01 Matches are distributed among these distances: 40 230 1.00 41 1 0.00 ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28 Consensus pattern (40 bp): GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG Found at i:96596858 original size:29 final size:29 Alignment explanation

Indices: 96596819--96596920 Score: 118 Period size: 29 Copynumber: 3.6 Consensus size: 29 96596809 CTTCAACTGA * * * 96596819 GCACTATGTGTGCCAGATCAGTAGTTGAG 1 GCACTATGTGTGCGAGATTAGTAATTGAG ** * 96596848 GCACTATGTGTGCGAG-TTTTTCAATCGA- 1 GCACTATGTGTGCGAGATTAGT-AATTGAG * 96596876 GCACTATGTGTGCGAGATTGGTAATTGAG 1 GCACTATGTGTGCGAGATTAGTAATTGAG 96596905 GCACTATGTGTGCGAG 1 GCACTATGTGTGCGAG 96596921 TTCTTTAATC Statistics Matches: 61, Mismatches: 9, Indels: 6 0.80 0.12 0.08 Matches are distributed among these distances: 28 23 0.38 29 38 0.62 ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30 Consensus pattern (29 bp): GCACTATGTGTGCGAGATTAGTAATTGAG Found at i:96596878 original size:57 final size:57 Alignment explanation

Indices: 96596787--96596975 Score: 215 Period size: 57 Copynumber: 3.3 Consensus size: 57 96596777 GCTGGAGTTA * * * 96596787 TGAGGCACTGTGTGTGCAAGTTCTTCAA-CTGAGCACTATGTGTGCCAGATCAGTAGT 1 TGAGGCACTATGTGTGCGAGTTTTTCAATC-GAGCACTATGTGTGCCAGATCAGTAGT * ** * 96596844 TGAGGCACTATGTGTGCGAGTTTTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT 1 TGAGGCACTATGTGTGCGAGTTTTTCAATCGAGCACTATGTGTGCCAGATCAGTAGT * * * 96596901 TGAGGCACTATGTGTGCGAGTTCTTT-AATCGAGCGCTATGTGTGCTAAATCAGTTAG- 1 TGAGGCACTATGTGTGCGAGTT-TTTCAATCGAGCACTATGTGTGCCAGATCAG-TAGT * * 96596958 TG-GGCACTGTGTATGCGA 1 TGAGGCACTATGTGTGCGA 96596976 AGTGTGTTTC Statistics Matches: 114, Mismatches: 15, Indels: 7 0.84 0.11 0.05 Matches are distributed among these distances: 56 14 0.12 57 94 0.82 58 6 0.05 ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32 Consensus pattern (57 bp): TGAGGCACTATGTGTGCGAGTTTTTCAATCGAGCACTATGTGTGCCAGATCAGTAGT Found at i:96596929 original size:29 final size:28 Alignment explanation

Indices: 96596791--96596945 Score: 134 Period size: 28 Copynumber: 5.5 Consensus size: 28 96596781 GAGTTATGAG * * * * 96596791 GCACTGTGTGTGCAAGTTCTTCAACTGA 1 GCACTATGTGTGCGAGTTCTTTAATTGA * * ** * 96596819 GCACTATGTGTGCCAGATCAGTAGTTGA 1 GCACTATGTGTGCGAGTTCTTTAATTGA * 96596847 GGCACTATGTGTGCGAGTT-TTTCAATCGA 1 -GCACTATGTGTGCGAGTTCTTT-AATTGA ** 96596876 GCACTATGTGTGCGAGATT-GGTAATTGA 1 GCACTATGTGTGCGAG-TTCTTTAATTGA * 96596904 GGCACTATGTGTGCGAGTTCTTTAATCGA 1 -GCACTATGTGTGCGAGTTCTTTAATTGA * 96596933 GCGCTATGTGTGC 1 GCACTATGTGTGC 96596946 TAAATCAGTT Statistics Matches: 101, Mismatches: 21, Indels: 10 0.77 0.16 0.08 Matches are distributed among these distances: 28 56 0.55 29 45 0.45 ACGTcount: A:0.21, C:0.17, G:0.29, T:0.32 Consensus pattern (28 bp): GCACTATGTGTGCGAGTTCTTTAATTGA Found at i:96598987 original size:2 final size:2 Alignment explanation

Indices: 96598980--96599005 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 96598970 AAATGGCATA 96598980 AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT 96599006 GTGTGTGTGT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:96600178 original size:48 final size:48 Alignment explanation

Indices: 96600113--96600729 Score: 1072 Period size: 48 Copynumber: 12.9 Consensus size: 48 96600103 TATATATGTG 96600113 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * * 96600161 TGTGGTAAAGCCAAATGGCTACTGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96600209 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 96600257 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96600305 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * * 96600353 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGAATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * * * 96600401 TGTGGTAAAGCCAAATGGCTAGTATGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 96600449 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * ** 96600497 TGTGGTAAAGACTTATGGCTAATGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96600545 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGAATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * * 96600593 TGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * 96600641 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA * * 96600689 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT 1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT 96600730 GTGTGTATAT Statistics Matches: 542, Mismatches: 27, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 48 542 1.00 ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31 Consensus pattern (48 bp): TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA Found at i:96600920 original size:37 final size:37 Alignment explanation

Indices: 96600870--96600972 Score: 152 Period size: 37 Copynumber: 2.8 Consensus size: 37 96600860 GGAAATATAT * * 96600870 TCCGGGTAAGACCCAATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGACATTATG * * 96600907 TCCGGGTAAGACCCGATGACTACTTGTGGACATTTTG 1 TCCGGGTAAGACCCGATGACTACGTGTGGACATTATG * * 96600944 TCCAGGTAAGACCCGATAACTACGTGTGG 1 TCCGGGTAAGACCCGATGACTACGTGTGG 96600973 GGACTATTCG Statistics Matches: 59, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 37 59 1.00 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25 Consensus pattern (37 bp): TCCGGGTAAGACCCGATGACTACGTGTGGACATTATG Found at i:96607906 original size:6 final size:6 Alignment explanation

Indices: 96607896--96607925 Score: 51 Period size: 6 Copynumber: 5.0 Consensus size: 6 96607886 CACCGTAAGG * 96607896 GTAACA CTAACA GTAACA GTAACA GTAACA 1 GTAACA GTAACA GTAACA GTAACA GTAACA 96607926 ATACTGGTAC Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 6 22 1.00 ACGTcount: A:0.50, C:0.20, G:0.13, T:0.17 Consensus pattern (6 bp): GTAACA Found at i:96608741 original size:15 final size:15 Alignment explanation

Indices: 96608717--96608754 Score: 51 Period size: 15 Copynumber: 2.6 Consensus size: 15 96608707 CTAATTTTCC * 96608717 CTTTTCTTTTTCTTT 1 CTTTTCTTTTTCCTT * 96608732 CTTTTTTTTTTCCTT 1 CTTTTCTTTTTCCTT 96608747 C-TTTCTTT 1 CTTTTCTTT 96608755 CCCTGCTCAT Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 14 6 0.30 15 14 0.70 ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79 Consensus pattern (15 bp): CTTTTCTTTTTCCTT Found at i:96608885 original size:16 final size:17 Alignment explanation

Indices: 96608832--96608885 Score: 51 Period size: 16 Copynumber: 3.4 Consensus size: 17 96608822 ATTAATATAT * * 96608832 TATAATTATATAATTTA 1 TATAATTATTTACTTTA * * 96608849 -AT-ATAATTTACTTTT 1 TATAATTATTTACTTTA 96608864 TATAATTATTTAC-TTA 1 TATAATTATTTACTTTA 96608880 TATAAT 1 TATAAT 96608886 AAGTAAATAC Statistics Matches: 29, Mismatches: 6, Indels: 5 0.73 0.15 0.12 Matches are distributed among these distances: 15 9 0.31 16 12 0.41 17 8 0.28 ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56 Consensus pattern (17 bp): TATAATTATTTACTTTA Found at i:96613943 original size:40 final size:41 Alignment explanation

Indices: 96613899--96614000 Score: 156 Period size: 40 Copynumber: 2.6 Consensus size: 41 96613889 GCTCAACTGC 96613899 CTTCGGGACTTAGCCCGGA-TATAGTAACTCGCACAAATGA 1 CTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGA * * 96613939 CTTCGGGACTTAGCCC-GATTATAGTAGCTCGCACAAATGC 1 CTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGA * 96613979 CTTTGGGACTTAGCCCGG-TTAT 1 CTTCGGGACTTAGCCCGGATTAT 96614001 CATCCGAATA Statistics Matches: 57, Mismatches: 3, Indels: 4 0.89 0.05 0.06 Matches are distributed among these distances: 39 2 0.04 40 54 0.95 41 1 0.02 ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26 Consensus pattern (41 bp): CTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGA Done.