Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: chr2

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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31

Warning! 2030548 characters in sequence are not A, C, G, or T


File 36 of 106

Found at i:13777005 original size:25 final size:25

Alignment explanation

Indices: 13776977--13777028 Score: 86 Period size: 25 Copynumber: 2.1 Consensus size: 25 13776967 ATATATGATT * 13776977 AACTAACAATTGAAAACTATTCCAC 1 AACTAACAATTAAAAACTATTCCAC * 13777002 AACTAACAATTAAAAACTATTCTAC 1 AACTAACAATTAAAAACTATTCCAC 13777027 AA 1 AA 13777029 TTAAAATCAA Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 25 25 1.00 ACGTcount: A:0.52, C:0.21, G:0.02, T:0.25 Consensus pattern (25 bp): AACTAACAATTAAAAACTATTCCAC Found at i:13777508 original size:86 final size:86 Alignment explanation

Indices: 13777394--13777662 Score: 394 Period size: 86 Copynumber: 3.1 Consensus size: 86 13777384 AAACATTGTT * * * * * * 13777394 GTTTGCATCCTAGTTAAAGAAATATAAATTAATTTTACATTTTTTAATTTACAAGTTTAACTAAA 1 GTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAGTTTAACTAAT 13777459 ATTAAAATTTTATATATTTAA 66 ATTAAAATTTTATATATTTAA * * 13777480 GTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAATTCAACTAAT 1 GTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAGTTTAACTAAT * 13777545 ATTAAAATTTTATATTTTTAA 66 ATTAAAATTTTATATATTTAA * * * * 13777566 GATTACATCATAGTTCAAGTAATATAAATTACTTTTACATTTGTTAGTTTACAAGTTTAACTAAT 1 GTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAGTTTAACTAAT * * * 13777631 ATAAAAATTTTATATATGTAC 66 ATTAAAATTTTATATATTTAA 13777652 GTTTGCATCAT 1 GTTTGCATCAT 13777663 TGTGTTGGGT Statistics Matches: 162, Mismatches: 21, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 86 162 1.00 ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45 Consensus pattern (86 bp): GTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAGTTTAACTAAT ATTAAAATTTTATATATTTAA Found at i:13777509 original size:48 final size:46 Alignment explanation

Indices: 13777457--13777596 Score: 127 Period size: 46 Copynumber: 3.1 Consensus size: 46 13777447 AGTTTAACTA 13777457 AAATTAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATAT 1 AAATTAAAATTTTATAT-TTTAAGTTT-CATCATAGTTCAAGTAATAT * * * * 13777505 AAATT--AATTTTACATTTATTAGTTT-A-CA-AATTCAACT-A-AT 1 AAATTAAAATTTTATATTT-TAAGTTTCATCATAGTTCAAGTAATAT * 13777545 --ATTAAAATTTTATATTTTTAAGATTACATCATAGTTCAAGTAATAT 1 AAATTAAAATTTTATA-TTTTAAG-TTTCATCATAGTTCAAGTAATAT 13777591 AAATTA 1 AAATTA 13777597 CTTTTACATT Statistics Matches: 71, Mismatches: 9, Indels: 24 0.68 0.09 0.23 Matches are distributed among these distances: 38 3 0.04 40 13 0.18 41 6 0.08 42 8 0.11 43 4 0.06 44 8 0.11 45 3 0.04 46 17 0.24 48 9 0.13 ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44 Consensus pattern (46 bp): AAATTAAAATTTTATATTTTAAGTTTCATCATAGTTCAAGTAATAT Found at i:13777545 original size:42 final size:39 Alignment explanation

Indices: 13777414--13777642 Score: 161 Period size: 42 Copynumber: 5.4 Consensus size: 39 13777404 TAGTTAAAGA * * 13777414 AATATAAATTAATTTTACATTTTTTAATTTACAAGTTTAACT 1 AATATAAA--AATTTTACA-TTTTTAGTTTACAAGTTCAACT * * * * * 13777456 AAAATTAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGT 1 AATATAAAAATTTTACAT-TTTTAGTTT--A-CA-AGTTCAACT * 13777500 AATATAAATTAATTTTACATTTATTAGTTTACAAATTCAACT 1 AATATAAA--AATTTTACATTT-TTAGTTTACAAGTTCAACT * * * * 13777542 AATATTAAAATTTTATATTTTTAAGATTACATCATAGTTCAAGT 1 AATATAAAAATTTTACATTTTT-AG-TT-TA-CA-AGTTCAACT * * 13777586 AATATAAATTACTTTTACATTTGTTAGTTTACAAGTTTAACT 1 AATATAAA--AATTTTACATTT-TTAGTTTACAAGTTCAACT 13777628 AATATAAAAATTTTA 1 AATATAAAAATTTTA 13777643 TATATGTACG Statistics Matches: 146, Mismatches: 25, Indels: 34 0.71 0.12 0.17 Matches are distributed among these distances: 39 3 0.02 40 34 0.23 41 2 0.01 42 37 0.25 43 8 0.05 44 29 0.20 45 4 0.03 46 27 0.18 47 2 0.01 ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46 Consensus pattern (39 bp): AATATAAAAATTTTACATTTTTAGTTTACAAGTTCAACT Found at i:13778415 original size:36 final size:35 Alignment explanation

Indices: 13778308--13778622 Score: 312 Period size: 35 Copynumber: 8.9 Consensus size: 35 13778298 AGTTCTTAAG **** * 13778308 AAGCCCAATTAACTTAATTGTTTAATTTAATCGATT 1 AAGCCCAA-TAACTTAATTAAACAATTTAATCAATT * * * 13778344 AGGCCCAATAACTTAATTAAATAATTTAATTAATT 1 AAGCCCAATAACTTAATTAAACAATTTAATCAATT * * 13778379 AAGCCCAACAATTTAATTAAACAATTTTAATCAATT 1 AAGCCCAATAACTTAATTAAACAA-TTTAATCAATT * 13778415 AAGCCCAATGACTTAATTAAACGAATTTAATCAATT 1 AAGCCCAATAACTTAATTAAAC-AATTTAATCAATT * * 13778451 AAGTCCAATGACTTAATTAAACGAATTTAATCAATT 1 AAGCCCAATAACTTAATTAAAC-AATTTAATCAATT **** * 13778487 AAGCCCAATAACTTAATTGTTTAATTTAATTAATT 1 AAGCCCAATAACTTAATTAAACAATTTAATCAATT * * * * 13778522 AGGCTCAATGACTTAATTAAACAATTTAATTAATT 1 AAGCCCAATAACTTAATTAAACAATTTAATCAATT * * * * * 13778557 AGGCCCAATGATTTAATTAAATAATTTAATTAATT 1 AAGCCCAATAACTTAATTAAACAATTTAATCAATT * 13778592 -AG-GC-ATAACTTAATTAAACAATTTTAATCAA 1 AAGCCCAATAACTTAATTAAACAA-TTTAATCAA 13778623 GTGCTTGAGA Statistics Matches: 238, Mismatches: 38, Indels: 9 0.84 0.13 0.03 Matches are distributed among these distances: 32 14 0.06 33 9 0.04 34 1 0.00 35 114 0.48 36 98 0.41 37 2 0.01 ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37 Consensus pattern (35 bp): AAGCCCAATAACTTAATTAAACAATTTAATCAATT Found at i:13778432 original size:18 final size:18 Alignment explanation

Indices: 13778411--13778470 Score: 50 Period size: 18 Copynumber: 3.3 Consensus size: 18 13778401 AATTTTAATC * 13778411 AATTAAGCCCAATGACTT 1 AATTAAGACCAATGACTT * * * * 13778429 AATTAA-ACGAATTTAATC 1 AATTAAGACCAA-TGACTT * 13778447 AATTAAGTCCAATGACTT 1 AATTAAGACCAATGACTT 13778465 AATTAA 1 AATTAA 13778471 ACGAATTTAA Statistics Matches: 30, Mismatches: 10, Indels: 4 0.68 0.23 0.09 Matches are distributed among these distances: 17 3 0.10 18 24 0.80 19 3 0.10 ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32 Consensus pattern (18 bp): AATTAAGACCAATGACTT Found at i:13778486 original size:18 final size:18 Alignment explanation

Indices: 13778429--13778488 Score: 59 Period size: 18 Copynumber: 3.3 Consensus size: 18 13778419 CCAATGACTT 13778429 AATTAAACGAATTTAATC 1 AATTAAACGAATTTAATC * * * * * 13778447 AATTAAGTCCAA-TGACTT 1 AATTAA-ACGAATTTAATC 13778465 AATTAAACGAATTTAATC 1 AATTAAACGAATTTAATC 13778483 AATTAA 1 AATTAA 13778489 GCCCAATAAC Statistics Matches: 30, Mismatches: 10, Indels: 4 0.68 0.23 0.09 Matches are distributed among these distances: 17 3 0.10 18 24 0.80 19 3 0.10 ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33 Consensus pattern (18 bp): AATTAAACGAATTTAATC Found at i:13780720 original size:38 final size:40 Alignment explanation

Indices: 13780632--13780734 Score: 120 Period size: 38 Copynumber: 2.6 Consensus size: 40 13780622 ACCCAGCTCA * * * 13780632 TGTGCATCCCCACACATCGTGCACATAGCCAGAGTCATCG 1 TGTGCATCCCCCCACATCGTGCACATAGACAGAGCCATCG * * * 13780672 TGTGCGTCCCCCCACATCGTGCACA-A-ATAGTGCCATCG 1 TGTGCATCCCCCCACATCGTGCACATAGACAGAGCCATCG * * 13780710 TGTGCATCCCCCTACATCATGCACA 1 TGTGCATCCCCCCACATCGTGCACA 13780735 CGGGCACTTT Statistics Matches: 54, Mismatches: 9, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 38 30 0.56 39 1 0.02 40 23 0.43 ACGTcount: A:0.23, C:0.37, G:0.18, T:0.21 Consensus pattern (40 bp): TGTGCATCCCCCCACATCGTGCACATAGACAGAGCCATCG Found at i:13780858 original size:2 final size:2 Alignment explanation

Indices: 13780851--13780905 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 13780841 AATGCACAAC 13780851 AT 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 AT 13780893 AT AT AT AT AT AT A 1 AT AT AT AT AT AT A 13780906 NNNNNNNNNN Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:13781724 original size:23 final size:23 Alignment explanation

Indices: 13781698--13781742 Score: 81 Period size: 23 Copynumber: 2.0 Consensus size: 23 13781688 AGGAAGAAGA 13781698 AGAAGAAGCTACTGGAAAATGAG 1 AGAAGAAGCTACTGGAAAATGAG * 13781721 AGAAGAAGCTACTGGAAGATGA 1 AGAAGAAGCTACTGGAAAATGA 13781743 TATTTATAAC Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 23 21 1.00 ACGTcount: A:0.47, C:0.09, G:0.31, T:0.13 Consensus pattern (23 bp): AGAAGAAGCTACTGGAAAATGAG Found at i:13786228 original size:180 final size:180 Alignment explanation

Indices: 13786014--13786342 Score: 518 Period size: 180 Copynumber: 1.8 Consensus size: 180 13786004 TTAATAGCCT * * * * 13786014 AAATCAGCTTGTTTGGCCATGAAAATTTCCAGAAATAATCCTCATTGAACATTTTAATAAAGATA 1 AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA * * 13786079 ATTTT-TCTGGAATTTTTCAGAATTAATTTTCC-AGAGTTTCTTGTCAATTAAAACTGAAATTCA 66 GTTTTCT-TGGAATTTTTCAGAATTAA-TTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCA 13786142 TGCCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAATTTTCTTGCTCG 129 TGCCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAATTTTCTTGCTCG * * * 13786194 AAATCAGCATATTTGACCATGATATTTTCCAGAAATAATCCTTATTAAACATTTTAATAAAGATA 1 AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA * 13786259 GTTTTCTTGGAATTTTTCAGAATTAATTTCCAAGACTTTCTTGTTAATTAAAACTGAAATTCATG 66 GTTTTCTTGGAATTTTTCAGAATTAATTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCATG * * 13786324 TCATAACAGTGAGCTGGAC 131 CCAAAACAGTGAGCTGGAC 13786343 TGCTTTCACT Statistics Matches: 135, Mismatches: 12, Indels: 4 0.89 0.08 0.03 Matches are distributed among these distances: 179 5 0.04 180 129 0.96 181 1 0.01 ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37 Consensus pattern (180 bp): AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA GTTTTCTTGGAATTTTTCAGAATTAATTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCATG CCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAATTTTCTTGCTCG Found at i:13786369 original size:180 final size:180 Alignment explanation

Indices: 13786014--13786386 Score: 511 Period size: 180 Copynumber: 2.1 Consensus size: 180 13786004 TTAATAGCCT * * * * 13786014 AAATCAGCTTGTTTGGCCATGAAAATTTCCAGAAATAATCCTCATTGAACATTTTAATAAAGATA 1 AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA * 13786079 ATTTTTCTGGAATTTTTCAGAATTAATTTTCCAGAGTTTCTTGTCAATTAAAACTGAAATTCATG 66 ATTTTTCTGGAATTTTTCAGAATTAATTTTCCAGACTTTCTTGTCAATTAAAACTGAAATTCATG * * 13786144 CCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAATTTTCTTGCTCG 131 CCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAAATTTCTTGCTCA * * * 13786194 AAATCAGCATATTTGACCATGATATTTTCCAGAAATAATCCTTATTAAACATTTTAATAAAGAT- 1 AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA * * 13786258 AGTTTTCTTGGAATTTTTCAGAATTAA-TTTCCAAGACTTTCTTGTTAATTAAAACTGAAATTCA 66 ATTTTTC-TGGAATTTTTCAGAATTAATTTTCC-AGACTTTCTTGTCAATTAAAACTGAAATTCA * * * * * * 13786322 TGTCATAACAGTGAGCTGGACTGCTTTCACT-TTTGC-TCAAATTTCTTGCTTA 129 TGCCAAAACAGTGAGCTGGACAGATTT-A-TATTTGCACCAAATTTCTTGCTCA * 13786374 AAATCAGCCTATT 1 AAATCAGCATATT 13786387 CAATCATGAA Statistics Matches: 170, Mismatches: 19, Indels: 8 0.86 0.10 0.04 Matches are distributed among these distances: 179 11 0.06 180 152 0.89 181 6 0.04 182 1 0.01 ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38 Consensus pattern (180 bp): AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA ATTTTTCTGGAATTTTTCAGAATTAATTTTCCAGACTTTCTTGTCAATTAAAACTGAAATTCATG CCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAAATTTCTTGCTCA Found at i:13787113 original size:35 final size:35 Alignment explanation

Indices: 13787088--13787300 Score: 243 Period size: 35 Copynumber: 6.1 Consensus size: 35 13787078 TTAATTGTTT * 13787088 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC 1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC * * * 13787123 AATTTAATTAATTAAGCCCAACAATTTAATTAAAC 1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC * **** 13787158 AAATTTAATCAATTAGGCCCAATAACTTAATTGTTT 1 -AATTTAATTAATTAGGCCCAATAACTTAATTAAAC * * 13787194 AATTTAATTAATTATGCCCAATGACTTAATTAAAC 1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC * * * * * 13787229 AATTTAATTAATTAGGCCCATTGATTTAATGAAAT 1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC * 13787264 AATTTAATTAATTAGG--C-ACAACTTAATTAAAC 1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC 13787296 AATTT 1 AATTT 13787301 TAACCAAGTG Statistics Matches: 147, Mismatches: 30, Indels: 5 0.81 0.16 0.03 Matches are distributed among these distances: 32 14 0.10 33 1 0.01 35 105 0.71 36 27 0.18 ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37 Consensus pattern (35 bp): AATTTAATTAATTAGGCCCAATAACTTAATTAAAC Found at i:13787182 original size:71 final size:71 Alignment explanation

Indices: 13787088--13787303 Score: 269 Period size: 71 Copynumber: 3.1 Consensus size: 71 13787078 TTAATTGTTT * * 13787088 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTAAT 1 AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT 13787153 TAAACA 66 TAAACA *** * ** 13787159 AATTTAATCAATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTATGCCCAATGACTTAAT 1 AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT 13787224 TAAAC- 66 TAAACA * * * * * * 13787229 AATTTAATTAATTAGGCCCATTGATTTAATGAAATAATTTAATTAATT-AG-GC-ACAACTTAAT 1 AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT 13787291 TAAACA 66 TAAACA * 13787297 ATTTTAA 1 AATTTAA 13787304 CCAAGTGCTT Statistics Matches: 123, Mismatches: 21, Indels: 5 0.83 0.14 0.03 Matches are distributed among these distances: 67 13 0.11 68 7 0.06 69 1 0.01 70 40 0.33 71 62 0.50 ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37 Consensus pattern (71 bp): AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT TAAACA Found at i:13787184 original size:106 final size:105 Alignment explanation

Indices: 13787068--13787280 Score: 318 Period size: 106 Copynumber: 2.0 Consensus size: 105 13787058 TCCTTAAGAA * 13787068 GCCCATTAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA 1 GCCCAATAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA * 13787133 ATTAAGCCCAACAATTTAATTAAACAAATTTAATCAATTAG 66 ATTAAGCCCAACAATTTAATGAAA-AAATTTAATCAATTAG * * * 13787174 GCCCAATAACTTAATTGTTTAATTTAATTAATTATGCCCAATGACTTAATTAAACAATTTAATTA 1 GCCCAATAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA * *** * * 13787239 ATTAGGCCCATTGATTTAATGAAATAATTTAATTAATTAG 66 ATTAAGCCCAACAATTTAATGAAAAAATTTAATCAATTAG 13787279 GC 1 GC 13787281 ACAACTTAAT Statistics Matches: 96, Mismatches: 11, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 105 16 0.17 106 80 0.83 ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38 Consensus pattern (105 bp): GCCCAATAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA ATTAAGCCCAACAATTTAATGAAAAAATTTAATCAATTAG Found at i:13799420 original size:2 final size:2 Alignment explanation

Indices: 13799413--13799437 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 13799403 AAGAAAACAA 13799413 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 13799438 AAAGTTAAGA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:13801287 original size:20 final size:22 Alignment explanation

Indices: 13801262--13801307 Score: 67 Period size: 22 Copynumber: 2.1 Consensus size: 22 13801252 CTTTAAGATC 13801262 AAAA-AATGAGTTAAGGAAAAAA 1 AAAAGAATGAGTTAAGG-AAAAA * 13801284 AAAAGAATGAGTTATGGAAAAA 1 AAAAGAATGAGTTAAGGAAAAA 13801306 AA 1 AA 13801308 GGGAAAAAAA Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 22 11 0.50 23 11 0.50 ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15 Consensus pattern (22 bp): AAAAGAATGAGTTAAGGAAAAA Found at i:13801294 original size:23 final size:22 Alignment explanation

Indices: 13801262--13801307 Score: 74 Period size: 23 Copynumber: 2.0 Consensus size: 22 13801252 CTTTAAGATC 13801262 AAAAAATGAGTTAAGGAAAAAA 1 AAAAAATGAGTTAAGGAAAAAA * 13801284 AAAAGAATGAGTTATGGAAAAAA 1 AAAA-AATGAGTTAAGGAAAAAA 13801307 A 1 A 13801308 GGGAAAAAAA Statistics Matches: 22, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 22 4 0.18 23 18 0.82 ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15 Consensus pattern (22 bp): AAAAAATGAGTTAAGGAAAAAA Found at i:13801358 original size:51 final size:51 Alignment explanation

Indices: 13801302--13801448 Score: 192 Period size: 51 Copynumber: 2.9 Consensus size: 51 13801292 GAGTTATGGA * * 13801302 AAAAAAGGGAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGTCTAAATG 1 AAAAAAGAGAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGTCT-AAGG * * 13801354 AAAAAGAAAGAAAAAAAG-AAA-AAAAATAATTCCAAAATTTGAG-CTAAGG 1 AAAAA-AGAGAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGTCTAAGG * * 13801403 AAAAAATGAGAAAAAAGGAAAAGAAAAATAATTACAAAATTTGGGT 1 AAAAAA-GAGAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGT 13801449 TTAGATAGCA Statistics Matches: 82, Mismatches: 8, Indels: 10 0.82 0.08 0.10 Matches are distributed among these distances: 48 1 0.01 49 17 0.21 50 5 0.06 51 41 0.50 52 8 0.10 53 10 0.12 ACGTcount: A:0.63, C:0.05, G:0.16, T:0.16 Consensus pattern (51 bp): AAAAAAGAGAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGTCTAAGG Found at i:13804510 original size:12 final size:12 Alignment explanation

Indices: 13804495--13804529 Score: 61 Period size: 12 Copynumber: 2.9 Consensus size: 12 13804485 AAAAATGAGG * 13804495 AAAAAAAGACAA 1 AAAAAAAGAAAA 13804507 AAAAAAAGAAAA 1 AAAAAAAGAAAA 13804519 AAAAAAAGAAA 1 AAAAAAAGAAA 13804530 GTCTTTTTTT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 12 22 1.00 ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00 Consensus pattern (12 bp): AAAAAAAGAAAA Found at i:13809337 original size:80 final size:80 Alignment explanation

Indices: 13809252--13809404 Score: 254 Period size: 80 Copynumber: 1.9 Consensus size: 80 13809242 TCATACTCAA * * 13809252 CCCATAGTGTATATGACTGT-CTCAACTCATACATCACATGGCATACATTTCATAACCTCATAAA 1 CCCATAGTGTATATGA-TATACTCAACACATACATCACATGGCATACATTTCATAACCTCATAAA 13809316 TCACTTACATGCCCAG 65 TCACTTACATGCCCAG * * 13809332 CCCATAGTGTATATGATATACTTAACACATACATCTCATGGCATACATTTCATAACCTCATAAAT 1 CCCATAGTGTATATGATATACTCAACACATACATCACATGGCATACATTTCATAACCTCATAAAT 13809397 CACTTACA 66 CACTTACA 13809405 AGCATCCAAC Statistics Matches: 68, Mismatches: 4, Indels: 2 0.92 0.05 0.03 Matches are distributed among these distances: 79 2 0.03 80 66 0.97 ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30 Consensus pattern (80 bp): CCCATAGTGTATATGATATACTCAACACATACATCACATGGCATACATTTCATAACCTCATAAAT CACTTACATGCCCAG Found at i:13814628 original size:21 final size:22 Alignment explanation

Indices: 13814603--13814643 Score: 66 Period size: 21 Copynumber: 1.9 Consensus size: 22 13814593 CCTAGGTGGA * 13814603 AAAATTCAAGGGAA-AAGTGTG 1 AAAATTCAAGGAAACAAGTGTG 13814624 AAAATTCAAGGAAACAAGTG 1 AAAATTCAAGGAAACAAGTG 13814644 AAAAAAAAGT Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 21 13 0.72 22 5 0.28 ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17 Consensus pattern (22 bp): AAAATTCAAGGAAACAAGTGTG Found at i:13814644 original size:20 final size:21 Alignment explanation

Indices: 13814603--13814647 Score: 58 Period size: 20 Copynumber: 2.2 Consensus size: 21 13814593 CCTAGGTGGA * 13814603 AAAATTCAAGGGAAAAGTGTG 1 AAAATTCAAGGGAAAAGAGTG 13814624 AAAATTCAA-GGAAACA-AGTG 1 AAAATTCAAGGGAAA-AGAGTG 13814644 AAAA 1 AAAA 13814648 AAAAGTAAGA Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 20 12 0.55 21 10 0.45 ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16 Consensus pattern (21 bp): AAAATTCAAGGGAAAAGAGTG Found at i:13814648 original size:21 final size:20 Alignment explanation

Indices: 13814601--13814648 Score: 60 Period size: 21 Copynumber: 2.3 Consensus size: 20 13814591 ACCCTAGGTG * 13814601 GAAAAATTCAAGGGAAAAGT 1 GAAAAATTCAAGGAAAAAGT * 13814621 GTGAAAATTCAAGGAAACAAGT 1 G-AAAAATTCAAGGAAA-AAGT 13814643 GAAAAA 1 GAAAAA 13814649 AAAGTAAGAT Statistics Matches: 23, Mismatches: 3, Indels: 3 0.79 0.10 0.10 Matches are distributed among these distances: 20 1 0.04 21 17 0.74 22 5 0.22 ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15 Consensus pattern (20 bp): GAAAAATTCAAGGAAAAAGT Found at i:13826590 original size:20 final size:20 Alignment explanation

Indices: 13826565--13826602 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 13826555 AAATGATGCT 13826565 AACAAAACGAAAAACAAAAC 1 AACAAAACGAAAAACAAAAC ** 13826585 AACAAAGGGAAAAACAAA 1 AACAAAACGAAAAACAAA 13826603 GAAAAATCAA Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.74, C:0.16, G:0.11, T:0.00 Consensus pattern (20 bp): AACAAAACGAAAAACAAAAC Found at i:13826974 original size:8 final size:7 Alignment explanation

Indices: 13826928--13826997 Score: 52 Period size: 8 Copynumber: 9.1 Consensus size: 7 13826918 TGGAAGTTGC 13826928 AAAAAGA 1 AAAAAGA 13826935 AAAAGAGA 1 AAAA-AGA 13826943 TGAAAAA-A 1 --AAAAAGA 13826951 AAAGAAGA 1 AAA-AAGA * 13826959 AGAAAGA 1 AAAAAGA 13826966 AACAAAGA 1 AA-AAAGA 13826974 AAATAAGA 1 AAA-AAGA * 13826982 AATAAATA 1 AA-AAAGA 13826990 AAAAAGA 1 AAAAAGA 13826997 A 1 A 13826998 CNNNNNNNNN Statistics Matches: 51, Mismatches: 4, Indels: 16 0.72 0.06 0.23 Matches are distributed among these distances: 6 3 0.06 7 17 0.33 8 25 0.49 9 2 0.04 10 4 0.08 ACGTcount: A:0.77, C:0.01, G:0.16, T:0.06 Consensus pattern (7 bp): AAAAAGA Found at i:13827185 original size:17 final size:19 Alignment explanation

Indices: 13827137--13827175 Score: 71 Period size: 19 Copynumber: 2.1 Consensus size: 19 13827127 TGGAAGTTGC 13827137 AAAAAGAAAAAGAGATGAA 1 AAAAAGAAAAAGAGATGAA 13827156 AAAAAGAAAAAGAGA-GAA 1 AAAAAGAAAAAGAGATGAA 13827174 AA 1 AA 13827176 GAAACAAAGA Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 18 5 0.25 19 15 0.75 ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03 Consensus pattern (19 bp): AAAAAGAAAAAGAGATGAA Found at i:13831189 original size:20 final size:20 Alignment explanation

Indices: 13831166--13831209 Score: 61 Period size: 20 Copynumber: 2.2 Consensus size: 20 13831156 AAGCATAAAT * * 13831166 TTCTAATTTCCAGCAGCTTC 1 TTCTAACTTCCAGCAACTTC * 13831186 TTCTAGCTTCCAGCAACTTC 1 TTCTAACTTCCAGCAACTTC 13831206 TTCT 1 TTCT 13831210 TCTTCCTCAC Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41 Consensus pattern (20 bp): TTCTAACTTCCAGCAACTTC Found at i:13832210 original size:35 final size:35 Alignment explanation

Indices: 13832171--13832272 Score: 119 Period size: 35 Copynumber: 3.1 Consensus size: 35 13832161 AAGAATGCTT * * 13832171 ATGATGATACTAAAATGTGCGAGTAGGGAGTGCAC 1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCAC 13832206 ATGATGATATTGAAATGT---A--A--GAGTGCAC 1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCAC * * 13832234 ATGATGATATTGAAATGTGCGTGTAGGGAGTGTAC 1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCAC 13832269 ATGA 1 ATGA 13832273 GCTGAATGAA Statistics Matches: 56, Mismatches: 4, Indels: 14 0.76 0.05 0.19 Matches are distributed among these distances: 28 26 0.46 30 1 0.02 32 1 0.02 33 1 0.02 35 27 0.48 ACGTcount: A:0.34, C:0.08, G:0.30, T:0.27 Consensus pattern (35 bp): ATGATGATATTGAAATGTGCGAGTAGGGAGTGCAC Found at i:13832238 original size:28 final size:28 Alignment explanation

Indices: 13832198--13832251 Score: 108 Period size: 28 Copynumber: 1.9 Consensus size: 28 13832188 TGCGAGTAGG 13832198 GAGTGCACATGATGATATTGAAATGTAA 1 GAGTGCACATGATGATATTGAAATGTAA 13832226 GAGTGCACATGATGATATTGAAATGT 1 GAGTGCACATGATGATATTGAAATGT 13832252 GCGTGTAGGG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 26 1.00 ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30 Consensus pattern (28 bp): GAGTGCACATGATGATATTGAAATGTAA Found at i:13833590 original size:21 final size:18 Alignment explanation

Indices: 13833548--13833580 Score: 52 Period size: 17 Copynumber: 1.9 Consensus size: 18 13833538 TCATTTTTCC 13833548 ACCAT-TCAATCATGCAT 1 ACCATGTCAATCATGCAT 13833565 A-CATGTCAATCATGCA 1 ACCATGTCAATCATGCA 13833581 CATGACCATG 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:0.36, C:0.27, G:0.09, T:0.27 Consensus pattern (18 bp): ACCATGTCAATCATGCAT Found at i:13833804 original size:21 final size:21 Alignment explanation

Indices: 13833778--13833875 Score: 81 Period size: 22 Copynumber: 4.6 Consensus size: 21 13833768 AAGCCTCCTG * 13833778 GTACATTTTCAAAACCTTAAA 1 GTACATTTTCAAAACCTTCAA * * * 13833799 GTACATCTTCAACACC-TCCA 1 GTACATTTTCAAAACCTTCAA ** * 13833819 GTACACCTTCAAATCCTTCAA 1 GTACATTTTCAAAACCTTCAA * * 13833840 GTATAATTTTGAAAACCTTCAA 1 GTA-CATTTTCAAAACCTTCAA * 13833862 GTAACAATTTCAAA 1 GT-ACATTTTCAAA 13833876 TCTTCTAAGT Statistics Matches: 58, Mismatches: 16, Indels: 5 0.73 0.20 0.06 Matches are distributed among these distances: 20 15 0.26 21 20 0.34 22 22 0.38 23 1 0.02 ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31 Consensus pattern (21 bp): GTACATTTTCAAAACCTTCAA Found at i:13834153 original size:22 final size:22 Alignment explanation

Indices: 13834113--13834179 Score: 71 Period size: 22 Copynumber: 3.0 Consensus size: 22 13834103 ATCTTGAAAT * * 13834113 CCTCTAAATACATTTTCCAAAA 1 CCTCTAAGTACATTCTCCAAAA * 13834135 CCTTTAAGTACATTCTCCAAAA 1 CCTCTAAGTACATTCTCCAAAA * * * * 13834157 TCTCTAGGTACAATCTACAAAA 1 CCTCTAAGTACATTCTCCAAAA 13834179 C 1 C 13834180 TTCCGGGTAC Statistics Matches: 36, Mismatches: 9, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 22 36 1.00 ACGTcount: A:0.39, C:0.27, G:0.04, T:0.30 Consensus pattern (22 bp): CCTCTAAGTACATTCTCCAAAA Found at i:13834190 original size:44 final size:43 Alignment explanation

Indices: 13834142--13834256 Score: 108 Period size: 44 Copynumber: 2.6 Consensus size: 43 13834132 AAACCTTTAA * * * 13834142 GTACATTCTCCAAAATCTCTAGGTACAATCTACAAAACTTCCGG 1 GTACATT-TCCAAAATCTCTAGGTACAATATACAAAACCTCCAG * * * 13834186 GTACATTTTCTAAAA-CATCTAGGTATAATATTCAAAACCTCCAG 1 GTACA-TTTCCAAAATC-TCTAGGTACAATATACAAAACCTCCAG * 13834230 GTACAATTTTCAAAATCT-TCAGGTACA 1 GTAC-ATTTCCAAAATCTCT-AGGTACA 13834257 TTTTTTGAAA Statistics Matches: 57, Mismatches: 9, Indels: 10 0.75 0.12 0.13 Matches are distributed among these distances: 43 2 0.04 44 51 0.89 45 4 0.07 ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30 Consensus pattern (43 bp): GTACATTTCCAAAATCTCTAGGTACAATATACAAAACCTCCAG Found at i:13834399 original size:67 final size:67 Alignment explanation

Indices: 13834322--13834470 Score: 181 Period size: 67 Copynumber: 2.2 Consensus size: 67 13834312 ATTTGGTTAC * ** * 13834322 AATCTCCAAAACCTCCAAGTATATTCTTTAAAACCTCAAGGCAGTTATTTTCAAAACCTCTAAGT 1 AATCTCCAAAACCTCCAAGTACATTCTCCAAAACCTCAAGGCAATTATTTTCAAAACCTCTAAGT 13834387 AT 66 AT * ** * ** * * 13834389 AATCTTCAAAACCTTTAAGTACATTCTCCAAAATCTGGAGGTAATTATTTTCAAAACCTCTAGGT 1 AATCTCCAAAACCTCCAAGTACATTCTCCAAAACCTCAAGGCAATTATTTTCAAAACCTCTAAGT 13834454 AT 66 AT * 13834456 ATTCTCCAAAACCTC 1 AATCTCCAAAACCTC 13834471 TAGATACATC Statistics Matches: 67, Mismatches: 15, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 67 67 1.00 ACGTcount: A:0.36, C:0.23, G:0.08, T:0.32 Consensus pattern (67 bp): AATCTCCAAAACCTCCAAGTACATTCTCCAAAACCTCAAGGCAATTATTTTCAAAACCTCTAAGT AT Found at i:13834471 original size:22 final size:22 Alignment explanation

Indices: 13834328--13834473 Score: 107 Period size: 22 Copynumber: 6.5 Consensus size: 22 13834318 TTACAATCTC * * 13834328 CAAAACCTCCAAGTATATTCTT 1 CAAAACCTCTAGGTATATTCTT * * * 13834350 TAAAACCTCAAGGCAGTTATT-TT 1 CAAAACCTCTAGGTA--TATTCTT * * 13834373 CAAAACCTCTAAGTATAATCTT 1 CAAAACCTCTAGGTATATTCTT * * * * 13834395 CAAAACCTTTAAGTACATTCTC 1 CAAAACCTCTAGGTATATTCTT * ** 13834417 CAAAATCTGGAGGTAATTATT-TT 1 CAAAACCTCTAGGT-A-TATTCTT * 13834440 CAAAACCTCTAGGTATATTCTC 1 CAAAACCTCTAGGTATATTCTT 13834462 CAAAACCTCTAG 1 CAAAACCTCTAG 13834474 ATACATCTGT Statistics Matches: 95, Mismatches: 23, Indels: 12 0.73 0.18 0.09 Matches are distributed among these distances: 21 7 0.07 22 55 0.58 23 26 0.27 24 7 0.07 ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32 Consensus pattern (22 bp): CAAAACCTCTAGGTATATTCTT Found at i:13834507 original size:43 final size:43 Alignment explanation

Indices: 13834460--13834564 Score: 120 Period size: 43 Copynumber: 2.4 Consensus size: 43 13834450 AGGTATATTC * 13834460 TCCAAAACCTCTAGATACATCTGTAAAACCTTCAAGTAACAAT 1 TCCAAAACCTCTAGATACATCTCTAAAACCTTCAAGTAACAAT * * * * * * 13834503 TCCAAAACCTCTAGGTAAATCTCTAAAGCCTTCGAGTAATAGT 1 TCCAAAACCTCTAGATACATCTCTAAAACCTTCAAGTAACAAT ** * 13834546 TTTAAAACCTCAAGATACA 1 TCCAAAACCTCTAGATACA 13834565 ATCTTCAAAG Statistics Matches: 50, Mismatches: 12, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 43 50 1.00 ACGTcount: A:0.40, C:0.24, G:0.10, T:0.27 Consensus pattern (43 bp): TCCAAAACCTCTAGATACATCTCTAAAACCTTCAAGTAACAAT Found at i:13834520 original size:22 final size:22 Alignment explanation

Indices: 13834128--13834525 Score: 92 Period size: 22 Copynumber: 18.1 Consensus size: 22 13834118 AAATACATTT * * * 13834128 TCCAAAACCTTTAAGTACATTC 1 TCCAAAACCTCTAGGTACAATC * 13834150 TCCAAAATCTCTAGGTACAATC 1 TCCAAAACCTCTAGGTACAATC * * ** * * 13834172 TACAAAACTTCCGGGTACATTT 1 TCCAAAACCTCTAGGTACAATC * * * * 13834194 TCTAAAACATCTAGGTATAATA 1 TCCAAAACCTCTAGGTACAATC * * * 13834216 TTCAAAACCTCCAGGTACAATT 1 TCCAAAACCTCTAGGTACAATC * * * * 13834238 TTCAAAATCT-TCAGGTACATTT 1 TCCAAAACCTCT-AGGTACAATC *** * * 13834260 TTTGAAA-CTTTAAGGAACAATC 1 TCCAAAACCTCT-AGGTACAATC * * * * * 13834282 TTCAAAACGTCTAGATACATTT 1 TCCAAAACCTCTAGGTACAATC * * * * 13834304 TTCGAAACAT-TTGGTTACAATC 1 TCCAAAACCTCTAGG-TACAATC * * * * 13834326 TCCAAAACCTCCAAGTATATTC 1 TCCAAAACCTCTAGGTACAATC ** * * ** * 13834348 TTTAAAACCTCAAGGCAGTTATT 1 TCCAAAACCTCTAGGTA-CAATC * * * 13834371 TTCAAAACCTCTAAGTATAATC 1 TCCAAAACCTCTAGGTACAATC * * * * 13834393 TTCAAAACCTTTAAGTACATTC 1 TCCAAAACCTCTAGGTACAATC * ** * 13834415 TCCAAAATCTGGAGGTA-ATTATT 1 TCCAAAACCTCTAGGTACA--ATC * * * 13834438 TTCAAAACCTCTAGGTATATTC 1 TCCAAAACCTCTAGGTACAATC * 13834460 TCCAAAACCTCTAGATAC-ATC 1 TCCAAAACCTCTAGGTACAATC ** * 13834481 TGTAAAACCT-TCAAGTAACAAT- 1 TCCAAAACCTCT-AGGT-ACAATC 13834503 TCCAAAACCTCTAGGTA-AATC 1 TCCAAAACCTCTAGGTACAATC 13834524 TC 1 TC 13834526 TAAAGCCTTC Statistics Matches: 265, Mismatches: 97, Indels: 29 0.68 0.25 0.07 Matches are distributed among these distances: 20 4 0.02 21 20 0.08 22 205 0.77 23 35 0.13 24 1 0.00 ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32 Consensus pattern (22 bp): TCCAAAACCTCTAGGTACAATC Found at i:13834601 original size:22 final size:23 Alignment explanation

Indices: 13834441--13834630 Score: 98 Period size: 22 Copynumber: 8.7 Consensus size: 23 13834431 AATTATTTTC * * ** 13834441 AAAACCTCTAGGT-ATATTCTCC 1 AAAACCTCTAGGTAACAATCTTT * * 13834463 AAAACCTCTAGAT-AC-ATCTGT 1 AAAACCTCTAGGTAACAATCTTT * ** 13834484 AAAACCT-TCAAGTAACAAT-TCC 1 AAAACCTCT-AGGTAACAATCTTT * 13834506 AAAACCTCTAGGT-A-AATCTCT 1 AAAACCTCTAGGTAACAATCTTT * * * * 13834527 AAAGCCT-TCGAGTAATAGT-TTT 1 AAAACCTCTAG-GTAACAATCTTT * * * 13834549 AAAACCTCAAGAT-ACAATCTTC 1 AAAACCTCTAGGTAACAATCTTT * 13834571 AAAGCCTCTAGGTAACAAT-TTT 1 AAAACCTCTAGGTAACAATCTTT * 13834593 AAAACCTCTGGGTAA-AATCTTT 1 AAAACCTCTAGGTAACAATCTTT * 13834615 AAAACCTTTAGGTAAC 1 AAAACCTCTAGGTAAC 13834631 CTTTTCAAAA Statistics Matches: 125, Mismatches: 30, Indels: 25 0.69 0.17 0.14 Matches are distributed among these distances: 20 6 0.05 21 29 0.23 22 79 0.63 23 11 0.09 ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29 Consensus pattern (23 bp): AAAACCTCTAGGTAACAATCTTT Found at i:13834612 original size:44 final size:43 Alignment explanation

Indices: 13834495--13834630 Score: 123 Period size: 44 Copynumber: 3.1 Consensus size: 43 13834485 AAACCTTCAA ** * 13834495 GTAACAATTCCAAAACCTCTAGGT-AAATC-TCTAAAGCCTTCG 1 GTAACAATTTTAAAACCTCTAGGTAAAATCTTC-AAAGCCTTAG * * * * * 13834537 AGTAATAGTTTTAAAACCTCAAGATACAATCTTCAAAGCCTCTAG 1 -GTAACAATTTTAAAACCTCTAGGTAAAATCTTCAAAGCCT-TAG * * * 13834582 GTAACAATTTTAAAACCTCTGGGTAAAATCTTTAAAACCTTTAG 1 GTAACAATTTTAAAACCTCTAGGTAAAATCTTCAAAGCC-TTAG 13834626 GTAAC 1 GTAAC 13834631 CTTTTCAAAA Statistics Matches: 73, Mismatches: 16, Indels: 7 0.76 0.17 0.07 Matches are distributed among these distances: 43 18 0.25 44 50 0.68 45 5 0.07 ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29 Consensus pattern (43 bp): GTAACAATTTTAAAACCTCTAGGTAAAATCTTCAAAGCCTTAG Found at i:13834831 original size:5 final size:5 Alignment explanation

Indices: 13834822--13834851 Score: 51 Period size: 5 Copynumber: 6.0 Consensus size: 5 13834812 ATTTAAGGCA * 13834822 ATTTT TTTTT ATTTT ATTTT ATTTT ATTTT 1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT 13834852 GTTTCATATA Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 5 23 1.00 ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83 Consensus pattern (5 bp): ATTTT Found at i:13842915 original size:42 final size:42 Alignment explanation

Indices: 13842860--13842993 Score: 178 Period size: 42 Copynumber: 3.2 Consensus size: 42 13842850 ACCATCCAAC * * * 13842860 CATCATCAGCTCATGTGCACTCCCACTCGCACATAGCTGGGT 1 CATCATCAGCTCATGTGCACTCCTACACGCACATGGCTGGGT * * * * 13842902 CAGCATCAACTCATATGCACTCCTACACGTACATGGCTGGGT 1 CATCATCAGCTCATGTGCACTCCTACACGCACATGGCTGGGT * * * 13842944 CATCATCAGCTCATGTGTACTTCTACACGCACATGGTTGGGT 1 CATCATCAGCTCATGTGCACTCCTACACGCACATGGCTGGGT 13842986 CATCATCA 1 CATCATCA 13842994 TCACAAAAAA Statistics Matches: 78, Mismatches: 14, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 42 78 1.00 ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26 Consensus pattern (42 bp): CATCATCAGCTCATGTGCACTCCTACACGCACATGGCTGGGT Found at i:13844884 original size:23 final size:22 Alignment explanation

Indices: 13844857--13844907 Score: 75 Period size: 23 Copynumber: 2.3 Consensus size: 22 13844847 TCAAGAGCAA * * 13844857 TTTTTAGATTCTTTTCTTTTTTT 1 TTTTTAGATTCTTTT-TTATTCT 13844880 TTTTTAGATTCTTTTTTATTCT 1 TTTTTAGATTCTTTTTTATTCT 13844902 TTTTTA 1 TTTTTA 13844908 AAGAGATTGA Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 22 11 0.42 23 15 0.58 ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76 Consensus pattern (22 bp): TTTTTAGATTCTTTTTTATTCT Found at i:13848570 original size:17 final size:17 Alignment explanation

Indices: 13848526--13848579 Score: 58 Period size: 17 Copynumber: 3.2 Consensus size: 17 13848516 AATTACTATA 13848526 TTAAATATATACTAATACT 1 TTAAATATATA-T-ATACT * * 13848545 TTTAGTATATATATACT 1 TTAAATATATATATACT 13848562 TTAAATATA-ATATA-T 1 TTAAATATATATATACT 13848577 TTA 1 TTA 13848580 TTTTTTATTT Statistics Matches: 31, Mismatches: 4, Indels: 4 0.79 0.10 0.10 Matches are distributed among these distances: 15 4 0.13 16 5 0.16 17 12 0.39 18 1 0.03 19 9 0.29 ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48 Consensus pattern (17 bp): TTAAATATATATATACT Found at i:13848625 original size:15 final size:17 Alignment explanation

Indices: 13848595--13848627 Score: 52 Period size: 15 Copynumber: 2.1 Consensus size: 17 13848585 TATTTTATCT 13848595 TAACATTATAAAAATTA 1 TAACATTATAAAAATTA 13848612 TAAC-TTAT-AAAATTA 1 TAACATTATAAAAATTA 13848627 T 1 T 13848628 TAATTGTAAT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 8 0.50 16 4 0.25 17 4 0.25 ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39 Consensus pattern (17 bp): TAACATTATAAAAATTA Found at i:13848690 original size:2 final size:2 Alignment explanation

Indices: 13848636--13848674 Score: 60 Period size: 2 Copynumber: 19.5 Consensus size: 2 13848626 ATTAATTGTA * * 13848636 AT AT AT AT GT TT AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 13848675 CACTTTATAG Statistics Matches: 34, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51 Consensus pattern (2 bp): AT Found at i:13849204 original size:40 final size:40 Alignment explanation

Indices: 13849118--13849256 Score: 161 Period size: 40 Copynumber: 3.5 Consensus size: 40 13849108 TATAATTTTT * * * 13849118 GTTATTTAAGTTTATGTTATTTGTTTGGATCTTTGTGTTTA 1 GTTATTTAAGTTTATGTT-GTTGTTTGGATATTTATGTTTA * * * 13849159 GTTATTTAAGTTTATGTTGTTATTTGGGTATTTATGTATA 1 GTTATTTAAGTTTATGTTGTTGTTTGGATATTTATGTTTA * * * * * * 13849199 ATTATTTAAGTTTATATAGTTGTATGGATATTTATTTTTT 1 GTTATTTAAGTTTATGTTGTTGTTTGGATATTTATGTTTA 13849239 GTTATTTAAGTTTATGTT 1 GTTATTTAAGTTTATGTT 13849257 TGAGATCTTT Statistics Matches: 80, Mismatches: 18, Indels: 1 0.81 0.18 0.01 Matches are distributed among these distances: 40 62 0.77 41 18 0.22 ACGTcount: A:0.22, C:0.01, G:0.17, T:0.60 Consensus pattern (40 bp): GTTATTTAAGTTTATGTTGTTGTTTGGATATTTATGTTTA Found at i:13850490 original size:27 final size:27 Alignment explanation

Indices: 13850452--13850505 Score: 108 Period size: 27 Copynumber: 2.0 Consensus size: 27 13850442 TCGATACTTG 13850452 GTACCTAGAAATCATTCTATTTAAAAT 1 GTACCTAGAAATCATTCTATTTAAAAT 13850479 GTACCTAGAAATCATTCTATTTAAAAT 1 GTACCTAGAAATCATTCTATTTAAAAT 13850506 ATATTTATAC Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 27 1.00 ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37 Consensus pattern (27 bp): GTACCTAGAAATCATTCTATTTAAAAT Found at i:13851190 original size:15 final size:16 Alignment explanation

Indices: 13851170--13851207 Score: 53 Period size: 15 Copynumber: 2.5 Consensus size: 16 13851160 TAGAGATTTT 13851170 GATTTTAAAGCTTT-G 1 GATTTTAAAGCTTTCG * 13851185 GATTTTAAAGTTTTCG 1 GATTTTAAAGCTTTCG 13851201 G-TTTTAA 1 GATTTTAA 13851208 CGTTGTTTTA Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 15 19 0.90 16 2 0.10 ACGTcount: A:0.26, C:0.05, G:0.18, T:0.50 Consensus pattern (16 bp): GATTTTAAAGCTTTCG Found at i:13855629 original size:43 final size:43 Alignment explanation

Indices: 13855566--13855791 Score: 194 Period size: 43 Copynumber: 5.3 Consensus size: 43 13855556 TCGTGACAAG * * * 13855566 GTAAATCTTTCCCTTAATGATAATGTGTATGGGTATTGATTAT 1 GTAAATCTTACCCTTGATGATAATGTGAATGGGTATTGATTAT * * * * 13855609 CTAAATCTTACCCATGATGATAATGTGAATGGATGTTGATTAT 1 GTAAATCTTACCCTTGATGATAATGTGAATGGGTATTGATTAT * * * * 13855652 GGAAAT-TCTACCCTTGATGATAATGTGCATAGGTAATGATTAT 1 GTAAATCT-TACCCTTGATGATAATGTGAATGGGTATTGATTAT * * * * ** 13855695 GAAAATCTTA-CCTTGA-GCGTAAGGCGAATGGGTATTGATGGT 1 GTAAATCTTACCCTTGATG-ATAATGTGAATGGGTATTGATTAT * * * 13855737 GAAAATC-TA-CCTTAAATGATAATGTGAATGGGTATTGATTAC 1 GTAAATCTTACCCTT-GATGATAATGTGAATGGGTATTGATTAT * 13855779 ATAAATC-TACCCT 1 GTAAATCTTACCCT 13855792 ACTATGATTA Statistics Matches: 144, Mismatches: 33, Indels: 12 0.76 0.17 0.06 Matches are distributed among these distances: 41 7 0.05 42 56 0.39 43 80 0.56 44 1 0.01 ACGTcount: A:0.32, C:0.12, G:0.20, T:0.35 Consensus pattern (43 bp): GTAAATCTTACCCTTGATGATAATGTGAATGGGTATTGATTAT Found at i:13855785 original size:42 final size:40 Alignment explanation

Indices: 13855577--13855789 Score: 133 Period size: 42 Copynumber: 5.0 Consensus size: 40 13855567 TAAATCTTTC * * 13855577 CCTTAATGATAATGTGTATGGGTATTGATTATCTAAATCTTA 1 CCTTAATGATAATGTGAATGGGTATTGATTA-CAAAATC-TA * * * * * * 13855619 CCCATGATGATAATGTGAATGGATGTTGATTATGGAAATTCTA 1 -CCTTAATGATAATGTGAATGGGTATTGATTA--CAAAATCTA * * * * * 13855662 CCCTTGATGATAATGTGCATAGGTAATGATTATGAAAATCTTA 1 -CCTTAATGATAATGTGAATGGGTATTGATTA-CAAAATC-TA * * * * * 13855705 CCTTGA-GCGTAAGGCGAATGGGTATTGATGGT-GAAAATCTA 1 CCTTAATG-ATAATGTGAATGGGTATTGAT--TACAAAATCTA 13855746 CCTTAAATGATAATGTGAATGGGTATTGATTACATAAATCTA 1 CCTT-AATGATAATGTGAATGGGTATTGATTACA-AAATCTA 13855788 CC 1 CC 13855790 CTACTATGAT Statistics Matches: 133, Mismatches: 28, Indels: 19 0.74 0.16 0.11 Matches are distributed among these distances: 40 1 0.01 41 8 0.06 42 62 0.47 43 57 0.43 44 5 0.04 ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35 Consensus pattern (40 bp): CCTTAATGATAATGTGAATGGGTATTGATTACAAAATCTA Found at i:13865557 original size:2 final size:2 Alignment explanation

Indices: 13865550--13865592 Score: 86 Period size: 2 Copynumber: 21.5 Consensus size: 2 13865540 TTTGATGATT 13865550 TA TA TA 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 TA TA TA 13865592 T 1 T 13865593 GTTGTGCATG Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 41 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:13876398 original size:29 final size:29 Alignment explanation

Indices: 13876334--13876398 Score: 121 Period size: 29 Copynumber: 2.2 Consensus size: 29 13876324 ATAAATGACC * 13876334 ATGTTTACCACAATTATAACATCTAGGTA 1 ATGTTTTCCACAATTATAACATCTAGGTA 13876363 ATGTTTTCCACAATTATAACATCTAGGTA 1 ATGTTTTCCACAATTATAACATCTAGGTA 13876392 ATGTTTT 1 ATGTTTT 13876399 AGCTAAATTT 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:0.34, C:0.15, G:0.11, T:0.40 Consensus pattern (29 bp): ATGTTTTCCACAATTATAACATCTAGGTA Found at i:13884217 original size:43 final size:43 Alignment explanation

Indices: 13884120--13884287 Score: 196 Period size: 43 Copynumber: 3.9 Consensus size: 43 13884110 TCATTCATTG * * * 13884120 TCATGTGCACTCCCTAC-TCGCACATGGTCGGGTCATCATCGGC 1 TCATGTGCACTCCC-ACATCGCACATAGCCGGGTCATCATCAGC * ** * 13884163 TTATGCACACTCTCTAC-TCGCACATAGCCGGGTCATCATCAGC 1 TCATGTGCACTC-CCACATCGCACATAGCCGGGTCATCATCAGC * * * 13884206 TCATGTGCACTCCCACATCGTACATAACTGGGTCATCATCAGC 1 TCATGTGCACTCCCACATCGCACATAGCCGGGTCATCATCAGC ** 13884249 TCATGTGCACTCCCACATCGCACATAGTTGGGTCATCAT 1 TCATGTGCACTCCCACATCGCACATAGCCGGGTCATCAT 13884288 TATCACACAA Statistics Matches: 106, Mismatches: 17, Indels: 4 0.83 0.13 0.03 Matches are distributed among these distances: 42 3 0.03 43 102 0.96 44 1 0.01 ACGTcount: A:0.22, C:0.33, G:0.18, T:0.26 Consensus pattern (43 bp): TCATGTGCACTCCCACATCGCACATAGCCGGGTCATCATCAGC Found at i:13887787 original size:27 final size:27 Alignment explanation

Indices: 13887751--13887815 Score: 94 Period size: 27 Copynumber: 2.4 Consensus size: 27 13887741 AATTGGAAAG * * 13887751 AAAAAAAATATCGGAGGACTAAATTGA 1 AAAAAAAATATCAGAGGACTAAATGGA * 13887778 AAAAAAAATATTAGAGGACTAAATGGA 1 AAAAAAAATATCAGAGGACTAAATGGA 13887805 AAAGAAAAATA 1 AAA-AAAAATA 13887816 AATTATTTAG Statistics Matches: 34, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 27 27 0.79 28 7 0.21 ACGTcount: A:0.62, C:0.05, G:0.17, T:0.17 Consensus pattern (27 bp): AAAAAAAATATCAGAGGACTAAATGGA Found at i:13887845 original size:31 final size:30 Alignment explanation

Indices: 13887739--13887847 Score: 111 Period size: 31 Copynumber: 3.7 Consensus size: 30 13887729 GGAAAAGGTT * * 13887739 TAAATTGGAAAGAAAAA-AAATATCGGAGGAC 1 TAAATTGAAAAGAAAAATAAAT-T-AGAGGAC 13887770 TAAATTGAAAA-AAAAAT--ATTAGAGGAC 1 TAAATTGAAAAGAAAAATAAATTAGAGGAC * * 13887797 TAAATGGAAAAGAAAAATAAATTATTTA-GAC 1 TAAATTGAAAAGAAAAATAAATTA--GAGGAC 13887828 TAAATTGAAAAGAAAAATAA 1 TAAATTGAAAAGAAAAATAA 13887848 GGAATGAGGT Statistics Matches: 67, Mismatches: 5, Indels: 12 0.80 0.06 0.14 Matches are distributed among these distances: 27 16 0.24 28 7 0.10 29 2 0.03 30 9 0.13 31 32 0.48 32 1 0.01 ACGTcount: A:0.60, C:0.04, G:0.16, T:0.21 Consensus pattern (30 bp): TAAATTGAAAAGAAAAATAAATTAGAGGAC Found at i:13895908 original size:20 final size:21 Alignment explanation

Indices: 13895874--13895916 Score: 61 Period size: 20 Copynumber: 2.1 Consensus size: 21 13895864 GGCATAAATA * * 13895874 TCAAAGTTTCTAGCAAGTTCT 1 TCAAAGTTTCCAGCAACTTCT 13895895 TCAAA-TTTCCAGCAACTTCT 1 TCAAAGTTTCCAGCAACTTCT 13895915 TC 1 TC 13895917 TTCTTCTTCT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 20 15 0.75 21 5 0.25 ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37 Consensus pattern (21 bp): TCAAAGTTTCCAGCAACTTCT Found at i:13896095 original size:21 final size:21 Alignment explanation

Indices: 13896069--13896109 Score: 82 Period size: 21 Copynumber: 2.0 Consensus size: 21 13896059 ACCTTAAAAC 13896069 CCTCAAAAGTCTTTGTTCAGT 1 CCTCAAAAGTCTTTGTTCAGT 13896090 CCTCAAAAGTCTTTGTTCAG 1 CCTCAAAAGTCTTTGTTCAG 13896110 CACTTTCTCT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 20 1.00 ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37 Consensus pattern (21 bp): CCTCAAAAGTCTTTGTTCAGT Found at i:13898372 original size:90 final size:90 Alignment explanation

Indices: 13898214--13898393 Score: 252 Period size: 90 Copynumber: 2.0 Consensus size: 90 13898204 CTTTTTATGC * * * * 13898214 CAACTATGAGTATCAGTTTTATCACCATGGTCAGTGTATTGTAAAACGTGTGTCTTTATCTTTTA 1 CAACTAAGAGTATCAATTTTATCACCATGGTCAGTATATTGTAAAACGTGTGTCTTTATCTTTGA * 13898279 ACTGTAGAAGGTTTGTTATTTCTTA 66 ACTGTAAAAGGTTTGTTATTTCTTA * * * *** 13898304 CAACTAAGAGTGTCAATTTTATCACTATGGTTAGTATATTGTTTTACGTGTGTCTTTATCTTTGA 1 CAACTAAGAGTATCAATTTTATCACCATGGTCAGTATATTGTAAAACGTGTGTCTTTATCTTTGA * 13898369 ACTGTAAAAGGTTTGTTGTTTCTTA 66 ACTGTAAAAGGTTTGTTATTTCTTA 13898394 TTCTTTTGCC Statistics Matches: 78, Mismatches: 12, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 90 78 1.00 ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45 Consensus pattern (90 bp): CAACTAAGAGTATCAATTTTATCACCATGGTCAGTATATTGTAAAACGTGTGTCTTTATCTTTGA ACTGTAAAAGGTTTGTTATTTCTTA Found at i:13902489 original size:2 final size:2 Alignment explanation

Indices: 13902484--13902532 Score: 82 Period size: 2 Copynumber: 25.0 Consensus size: 2 13902474 ATATATATAT * 13902484 AG AG AG AG AG AG AG AG AG A- AG AG AG CG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 13902525 AG AG AG AG 1 AG AG AG AG 13902533 GAATTGGCTG Statistics Matches: 44, Mismatches: 2, Indels: 2 0.92 0.04 0.04 Matches are distributed among these distances: 1 1 0.02 2 43 0.98 ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:13904707 original size:134 final size:134 Alignment explanation

Indices: 13904512--13904781 Score: 540 Period size: 134 Copynumber: 2.0 Consensus size: 134 13904502 TTCCATCAAA 13904512 TATACTTACCTAGTATTGACCATGTTGATTGATGTTGACGTCATGTTGATTGTGTTGATTGATAT 1 TATACTTACCTAGTATTGACCATGTTGATTGATGTTGACGTCATGTTGATTGTGTTGATTGATAT 13904577 TAGCACGGCATGGCATTGACTAAAAATATTTTTTATTTTAGAAATTAAAATAAACCAAAAATAAA 66 TAGCACGGCATGGCATTGACTAAAAATATTTTTTATTTTAGAAATTAAAATAAACCAAAAATAAA 13904642 TTTT 131 TTTT 13904646 TATACTTACCTAGTATTGACCATGTTGATTGATGTTGACGTCATGTTGATTGTGTTGATTGATAT 1 TATACTTACCTAGTATTGACCATGTTGATTGATGTTGACGTCATGTTGATTGTGTTGATTGATAT 13904711 TAGCACGGCATGGCATTGACTAAAAATATTTTTTATTTTAGAAATTAAAATAAACCAAAAATAAA 66 TAGCACGGCATGGCATTGACTAAAAATATTTTTTATTTTAGAAATTAAAATAAACCAAAAATAAA 13904776 TTTT 131 TTTT 13904780 TA 1 TA 13904782 AAAAAATTCC Statistics Matches: 136, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 134 136 1.00 ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40 Consensus pattern (134 bp): TATACTTACCTAGTATTGACCATGTTGATTGATGTTGACGTCATGTTGATTGTGTTGATTGATAT TAGCACGGCATGGCATTGACTAAAAATATTTTTTATTTTAGAAATTAAAATAAACCAAAAATAAA TTTT Found at i:13906616 original size:35 final size:35 Alignment explanation

Indices: 13906571--13906638 Score: 91 Period size: 35 Copynumber: 1.9 Consensus size: 35 13906561 GACAAAGTTT * ** * 13906571 AACCCATCTACATTTTCTATGGTTAAGGTATAATC 1 AACCAATCTACATTTTAAATGGCTAAGGTATAATC * 13906606 AACCAATCTACCTTTTAAATGGCTAAGGTATAA 1 AACCAATCTACATTTTAAATGGCTAAGGTATAA 13906639 CTAATATCAA Statistics Matches: 28, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 35 28 1.00 ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34 Consensus pattern (35 bp): AACCAATCTACATTTTAAATGGCTAAGGTATAATC Found at i:13907045 original size:60 final size:60 Alignment explanation

Indices: 13906975--13907109 Score: 148 Period size: 60 Copynumber: 2.2 Consensus size: 60 13906965 AAAACCCATG * * * ** * 13906975 AAAATATATCGATACAGTTTGAAATTTATCTATACATTTTTTATCAAAACCA-T-ACTGCTT 1 AAAATTTATCGATACAGTTTGAAATGTATCAATACATTTTCGATCAAAAACATTCACT--TT * * * * 13907035 AAAATTTATCGATACATTTTGGAATGTATCAATATATTTTCGGTCAAAAACATTCACTTT 1 AAAATTTATCGATACAGTTTGAAATGTATCAATACATTTTCGATCAAAAACATTCACTTT 13907095 AAAATTTATCGATAC 1 AAAATTTATCGATAC 13907110 TTTTCATAAT Statistics Matches: 63, Mismatches: 10, Indels: 4 0.82 0.13 0.05 Matches are distributed among these distances: 60 59 0.94 61 1 0.02 62 3 0.05 ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39 Consensus pattern (60 bp): AAAATTTATCGATACAGTTTGAAATGTATCAATACATTTTCGATCAAAAACATTCACTTT Found at i:13907121 original size:60 final size:59 Alignment explanation

Indices: 13907018--13907173 Score: 172 Period size: 60 Copynumber: 2.6 Consensus size: 59 13907008 ACATTTTTTA * * * * 13907018 TCAAAACCATACTGCTTAAAATTTATCGATACATTTTGGAATGTATCAATATATTTTCGG 1 TCAAAACTATTCTACTTAAAATTTATCGATAC-TTTTAGAATGTATCAATATATTTTCGG * ** 13907078 TCAAAAAC-ATTC-ACTTTAAAATTTATCGATACTTTTCATAATGTATGGATATATTTTCGG 1 TC-AAAACTATTCTAC-TTAAAATTTATCGATACTTTT-AGAATGTATCAATATATTTTCGG * * * 13907138 TCAGAACTATTCTACTTAAAATCTATCAATACTTTT 1 TCAAAACTATTCTACTTAAAATTTATCGATACTTTT 13907174 GGGCCAAATA Statistics Matches: 82, Mismatches: 9, Indels: 10 0.81 0.09 0.10 Matches are distributed among these distances: 59 9 0.11 60 66 0.80 61 7 0.09 ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40 Consensus pattern (59 bp): TCAAAACTATTCTACTTAAAATTTATCGATACTTTTAGAATGTATCAATATATTTTCGG Found at i:13910134 original size:19 final size:19 Alignment explanation

Indices: 13910110--13910151 Score: 66 Period size: 19 Copynumber: 2.2 Consensus size: 19 13910100 CTTCTTCACC 13910110 TTCATGCTCCCACGCCATT 1 TTCATGCTCCCACGCCATT * * 13910129 TTCATGCTTCCATGCCATT 1 TTCATGCTCCCACGCCATT 13910148 TTCA 1 TTCA 13910152 CCTTGCCACC Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 19 21 1.00 ACGTcount: A:0.17, C:0.36, G:0.10, T:0.38 Consensus pattern (19 bp): TTCATGCTCCCACGCCATT Found at i:13910264 original size:16 final size:14 Alignment explanation

Indices: 13910241--13910286 Score: 58 Period size: 16 Copynumber: 3.1 Consensus size: 14 13910231 ATCAGTTGGA 13910241 AAAAAGGAGAAAGG 1 AAAAAGGAGAAAGG 13910255 AAAGAAAGGAGAAA-G 1 -AA-AAAGGAGAAAGG 13910270 AAAAAGAGAGAAAGG 1 AAAAAG-GAGAAAGG 13910285 AA 1 AA 13910287 GAAAAAGCTT Statistics Matches: 28, Mismatches: 0, Indels: 6 0.82 0.00 0.18 Matches are distributed among these distances: 13 4 0.14 14 8 0.29 15 6 0.21 16 10 0.36 ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00 Consensus pattern (14 bp): AAAAAGGAGAAAGG Found at i:13913438 original size:35 final size:35 Alignment explanation

Indices: 13913365--13913467 Score: 116 Period size: 35 Copynumber: 2.9 Consensus size: 35 13913355 TCTGAATATT * * * * * 13913365 TGTGTGATACAACGCCCCACATCTGGCCCTTGTTA 1 TGTGTGATATAACGCCCTACATCTAGCCCTTATCA * * 13913400 TGTGTGATATAACGCCCTATATCTAGCCTTTATCA 1 TGTGTGATATAACGCCCTACATCTAGCCCTTATCA * * * 13913435 TGTGTGGTATAACACCTTACATCTAGCCCTTAT 1 TGTGTGATATAACGCCCTACATCTAGCCCTTAT 13913468 TCTCATATAA Statistics Matches: 56, Mismatches: 12, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 35 56 1.00 ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34 Consensus pattern (35 bp): TGTGTGATATAACGCCCTACATCTAGCCCTTATCA Found at i:13918413 original size:17 final size:17 Alignment explanation

Indices: 13918362--13918403 Score: 61 Period size: 16 Copynumber: 2.5 Consensus size: 17 13918352 TTTTTTTATA 13918362 ATTTTACTTAAT-AAATT 1 ATTTTA-TTAATAAAATT 13918379 -TTTTATTAATAAAATT 1 ATTTTATTAATAAAATT 13918395 ATTTTATTA 1 ATTTTATTA 13918404 TTTAATTTAT Statistics Matches: 23, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 15 5 0.22 16 10 0.43 17 8 0.35 ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57 Consensus pattern (17 bp): ATTTTATTAATAAAATT Found at i:13918429 original size:21 final size:23 Alignment explanation

Indices: 13918400--13918447 Score: 64 Period size: 22 Copynumber: 2.2 Consensus size: 23 13918390 AAATTATTTT * 13918400 ATTATTTAATTT-ATAAATTAAA 1 ATTATTTAATTTGATAAATAAAA * 13918422 ATTA-TTAATTTGATAAGTAAAA 1 ATTATTTAATTTGATAAATAAAA 13918444 ATTA 1 ATTA 13918448 AACACATTGA Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 21 7 0.30 22 16 0.70 ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46 Consensus pattern (23 bp): ATTATTTAATTTGATAAATAAAA Found at i:13919458 original size:19 final size:20 Alignment explanation

Indices: 13919423--13919475 Score: 63 Period size: 21 Copynumber: 2.5 Consensus size: 20 13919413 AACTTTACCC 13919423 ATATTAATATTTGTAAATAA-A 1 ATATTAATA--TGTAAATAACA 13919444 ATATTAATATGTAAATAATCA 1 ATATTAATATGTAAATAA-CA 13919465 ATTATTAATAT 1 A-TATTAATAT 13919476 TTTAAACAAA Statistics Matches: 29, Mismatches: 0, Indels: 5 0.85 0.00 0.15 Matches are distributed among these distances: 19 9 0.31 21 11 0.38 22 9 0.31 ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43 Consensus pattern (20 bp): ATATTAATATGTAAATAACA Found at i:13919581 original size:122 final size:127 Alignment explanation

Indices: 13919443--13919756 Score: 409 Period size: 122 Copynumber: 2.5 Consensus size: 127 13919433 TTGTAAATAA * * 13919443 AATATTAATATGTAAATAATCAATTATTAATATTTTAAACAAATTATAAATTATTAATA-TTAAA 1 AATATTAATATTTAAATTATCAATTATTAATATTTTAAACAAATTATAAATTATTAATATTTAAA * * * 13919507 TAATAAAATAATAATAAATAAT-A-A-CAT-TT-AAATTATAAATAAAATAATAATATTTTAT 66 T-ATAAAATAAAAATAAATAATCATATAATATTGAAATTAAAAATAAAATAATAATATTTTAT * * 13919565 AATATTAATATTTAAATTATCAATTAATAATATTTTAAATAAATTATAAATTATTAATATTTAAA 1 AATATTAATATTTAAATTATCAATTATTAATATTTTAAACAAATTATAAATTATTAATATTTAAA 13919630 TATAAAATAAAAATAAATAATCATATTAATATTGAAATTAAAAATAAAATAATAATATTTTAT 66 TATAAAATAAAAATAAATAATCATA-TAATATTGAAATTAAAAATAAAATAATAATATTTTAT * * * 13919693 AATATTAATGA-TTAAATTATAAAAATATTAATA-TTT----AAATTATCAATTATTAATATTTT 1 AATATTAAT-ATTTAAATTAT-CAATTATTAATATTTTAAACAAATTATAAATTATTAATA-TTT 13919752 AAATA 63 AAATA 13919757 AATTATAATT Statistics Matches: 171, Mismatches: 11, Indels: 17 0.86 0.06 0.09 Matches are distributed among these distances: 122 74 0.43 123 7 0.04 124 19 0.11 125 8 0.05 126 2 0.01 127 2 0.01 128 49 0.29 129 10 0.06 ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42 Consensus pattern (127 bp): AATATTAATATTTAAATTATCAATTATTAATATTTTAAACAAATTATAAATTATTAATATTTAAA TATAAAATAAAAATAAATAATCATATAATATTGAAATTAAAAATAAAATAATAATATTTTAT Found at i:13919639 original size:26 final size:27 Alignment explanation

Indices: 13919586--13919785 Score: 73 Period size: 27 Copynumber: 6.8 Consensus size: 27 13919576 TTAAATTATC * 13919586 AATTAATAATATTTTAAATAAATTATA 1 AATTAATAATATTTTAAATAAATAATA * * 13919613 AATTATTAATATTTAAATATAAAATAA-A 1 AATTAATAATATTTTAA-AT-AAATAATA * * 13919641 AATAAATAATCATATTAATATTGAAATTAAAAATA 1 AATTAATAAT-ATTTTAA-A-T-AAA-T---AATA * * 13919676 AAATAATAATATTTTATAATATTAATGATTA 1 AATTAATAATATTTTA-AATA--AAT-AATA * * * * 13919707 AATT-ATAAAAATATTAATATTTAAATTATC 1 AATTAAT-AATATTTTAA-A--TAAATAATA * * 13919737 AATTATTAATATTTTAAATAAATTAT- 1 AATTAATAATATTTTAAATAAATAATA * * 13919763 AATTATTAATATTTAAAAATAAA 1 AATTAATAATATTT-TAAATAAA 13919786 ATAAAATAAA Statistics Matches: 132, Mismatches: 23, Indels: 36 0.69 0.12 0.19 Matches are distributed among these distances: 26 14 0.11 27 30 0.23 28 11 0.08 29 13 0.10 30 20 0.15 31 19 0.14 32 1 0.01 33 4 0.03 34 10 0.08 35 10 0.08 ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42 Consensus pattern (27 bp): AATTAATAATATTTTAAATAAATAATA Found at i:13919660 original size:37 final size:35 Alignment explanation

Indices: 13919616--13919685 Score: 97 Period size: 37 Copynumber: 1.9 Consensus size: 35 13919606 AATTATAAAT * 13919616 TATTAATATTTAAA-TATAAAATAAAAATAAATAATCA 1 TATTAATATTGAAATTA-AAAAT-AAAAT-AATAATCA 13919653 TATTAATATTGAAATTAAAAATAAAATAATAAT 1 TATTAATATTGAAATTAAAAATAAAATAATAAT 13919686 ATTTTATAAT Statistics Matches: 31, Mismatches: 1, Indels: 4 0.86 0.03 0.11 Matches are distributed among these distances: 35 6 0.19 36 5 0.16 37 18 0.58 38 2 0.06 ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36 Consensus pattern (35 bp): TATTAATATTGAAATTAAAAATAAAATAATAATCA Found at i:13919698 original size:42 final size:42 Alignment explanation

Indices: 13919625--13919716 Score: 105 Period size: 42 Copynumber: 2.2 Consensus size: 42 13919615 TTATTAATAT * * 13919625 TTAAATATAAAATAAAAATAAATAATCATATTAAT-ATTGAAA 1 TTAAAAATAAAATAAAAATAAATAATAATATTAATGATT-AAA * ** * 13919667 TTAAAAATAAAATAATAATATTTTATAATATTAATGATTAAA 1 TTAAAAATAAAATAAAAATAAATAATAATATTAATGATTAAA 13919709 TTATAAAA 1 TTA-AAAA 13919717 ATATTAATAT Statistics Matches: 42, Mismatches: 6, Indels: 3 0.82 0.12 0.06 Matches are distributed among these distances: 42 35 0.83 43 7 0.17 ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37 Consensus pattern (42 bp): TTAAAAATAAAATAAAAATAAATAATAATATTAATGATTAAA Found at i:13919752 original size:23 final size:23 Alignment explanation

Indices: 13919693--13919779 Score: 79 Period size: 23 Copynumber: 3.7 Consensus size: 23 13919683 AATATTTTAT 13919693 AATATTAATGA-TTAAATTATAAA 1 AATATTAAT-ATTTAAATTATAAA * 13919716 AATATTAATATTTAAATTAT-CA 1 AATATTAATATTTAAATTATAAA * * * 13919738 ATTATTAATATTTTAAATAAATTATA 1 AATATTAATA-TTTAAAT-TA-TAAA * 13919764 ATTATTAATATTTAAA 1 AATATTAATATTTAAA 13919780 AATAAAATAA Statistics Matches: 55, Mismatches: 4, Indels: 8 0.82 0.06 0.12 Matches are distributed among these distances: 22 11 0.20 23 25 0.45 24 1 0.02 25 7 0.13 26 11 0.20 ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46 Consensus pattern (23 bp): AATATTAATATTTAAATTATAAA Found at i:13922538 original size:8 final size:8 Alignment explanation

Indices: 13922525--13922555 Score: 53 Period size: 8 Copynumber: 3.9 Consensus size: 8 13922515 GTGTACATGA 13922525 ATATATAC 1 ATATATAC 13922533 ATATATAC 1 ATATATAC * 13922541 ATATATCC 1 ATATATAC 13922549 ATATATA 1 ATATATA 13922556 TGTATGTATA Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 8 21 1.00 ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39 Consensus pattern (8 bp): ATATATAC Found at i:13943087 original size:15 final size:15 Alignment explanation

Indices: 13943067--13943101 Score: 70 Period size: 15 Copynumber: 2.3 Consensus size: 15 13943057 TCACACCTTT 13943067 GAACCCTTTTGACTA 1 GAACCCTTTTGACTA 13943082 GAACCCTTTTGACTA 1 GAACCCTTTTGACTA 13943097 GAACC 1 GAACC 13943102 TTTGAATTCT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 20 1.00 ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29 Consensus pattern (15 bp): GAACCCTTTTGACTA Found at i:13943831 original size:43 final size:43 Alignment explanation

Indices: 13943768--13943879 Score: 163 Period size: 43 Copynumber: 2.6 Consensus size: 43 13943758 TATTGACTTG * * 13943768 GCTATGTGCGGGTAGGGAGTGCGCATAAGCCGAGGATGACCC- 1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCA * * 13943810 GATTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCCA 1 G-CTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCA * 13943854 GCCATGTGCGAGTAGGGAGTGCGCAT 1 GCTATGTGCGAGTAGGGAGTGCGCAT 13943880 GAGCTGGTGA Statistics Matches: 62, Mismatches: 6, Indels: 3 0.87 0.08 0.04 Matches are distributed among these distances: 42 1 0.02 43 60 0.97 44 1 0.02 ACGTcount: A:0.23, C:0.21, G:0.38, T:0.19 Consensus pattern (43 bp): GCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCA Found at i:13943891 original size:43 final size:43 Alignment explanation

Indices: 13943771--13943892 Score: 149 Period size: 43 Copynumber: 2.8 Consensus size: 43 13943761 TGACTTGGCT * ** 13943771 ATGTGCGGGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGATT 1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCGACC * * 13943814 ATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCC-AGCC 1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCGA-CC * * 13943857 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA 1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA 13943893 TGATGATGGG Statistics Matches: 68, Mismatches: 9, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 42 1 0.01 43 67 0.99 ACGTcount: A:0.24, C:0.19, G:0.39, T:0.19 Consensus pattern (43 bp): ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCGACC Found at i:13943940 original size:2 final size:2 Alignment explanation

Indices: 13943933--13943965 Score: 57 Period size: 2 Copynumber: 16.5 Consensus size: 2 13943923 GGTATATGCG * 13943933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 13943966 GTAAATATGT Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48 Consensus pattern (2 bp): TA Found at i:13944304 original size:39 final size:39 Alignment explanation

Indices: 13944250--13944336 Score: 113 Period size: 39 Copynumber: 2.2 Consensus size: 39 13944240 TTCTCGCTGT * * * 13944250 AGCGAGAAACTTTCTGTTT-TTGGGTAGCAATTTCACTGC 1 AGCGAGAAACCTTCTGTTTCTAGGGTA-CAATTTCACCGC * 13944289 AGCGAGAAACCTTCTGTTTCTAGGTTACAATTTCACCGC 1 AGCGAGAAACCTTCTGTTTCTAGGGTACAATTTCACCGC * 13944328 AGTGAGAAA 1 AGCGAGAAA 13944337 GAATCTCGCT Statistics Matches: 42, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 39 37 0.88 40 5 0.12 ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31 Consensus pattern (39 bp): AGCGAGAAACCTTCTGTTTCTAGGGTACAATTTCACCGC Found at i:13945347 original size:15 final size:15 Alignment explanation

Indices: 13945327--13945389 Score: 54 Period size: 15 Copynumber: 4.2 Consensus size: 15 13945317 ATCTTTCTAG 13945327 TAATCACATTCTCAA 1 TAATCACATTCTCAA * * * 13945342 TAATCATATACCCAA 1 TAATCACATTCTCAA * * * 13945357 CAATCACATTCACGA 1 TAATCACATTCTCAA * * 13945372 TAATAACATTTTCAA 1 TAATCACATTCTCAA 13945387 TAA 1 TAA 13945390 AATACCAAAC Statistics Matches: 35, Mismatches: 13, Indels: 0 0.73 0.27 0.00 Matches are distributed among these distances: 15 35 1.00 ACGTcount: A:0.44, C:0.24, G:0.02, T:0.30 Consensus pattern (15 bp): TAATCACATTCTCAA Found at i:13949362 original size:20 final size:20 Alignment explanation

Indices: 13949337--13949377 Score: 73 Period size: 20 Copynumber: 2.0 Consensus size: 20 13949327 ATAGGCCTTG * 13949337 TTGATTTTTATGAAATGAAA 1 TTGATTTATATGAAATGAAA 13949357 TTGATTTATATGAAATGAAA 1 TTGATTTATATGAAATGAAA 13949377 T 1 T 13949378 GAGATTGGAT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44 Consensus pattern (20 bp): TTGATTTATATGAAATGAAA Found at i:13949393 original size:25 final size:25 Alignment explanation

Indices: 13949346--13949395 Score: 66 Period size: 25 Copynumber: 2.0 Consensus size: 25 13949336 GTTGATTTTT * 13949346 ATGAAATGAAATTGATTTATATGAA 1 ATGAAATGAAATTGATGTATATGAA * 13949371 ATGAAATGAGATTGGATGT-TATGAA 1 ATGAAATGAAATT-GATGTATATGAA 13949396 TCATATTATG Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 25 18 0.82 26 4 0.18 ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34 Consensus pattern (25 bp): ATGAAATGAAATTGATGTATATGAA Found at i:13965502 original size:22 final size:20 Alignment explanation

Indices: 13965471--13965515 Score: 54 Period size: 22 Copynumber: 2.1 Consensus size: 20 13965461 ATAAATAAAA 13965471 TATTAATATTTAAATGATTAAT 1 TATTAATATTTAAA--ATTAAT * * 13965493 TATTAGTATTTTAAATTAAT 1 TATTAATATTTAAAATTAAT 13965513 TAT 1 TAT 13965516 AAATGATTGA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 20 9 0.43 22 12 0.57 ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53 Consensus pattern (20 bp): TATTAATATTTAAAATTAAT Found at i:13965620 original size:42 final size:41 Alignment explanation

Indices: 13965573--13965654 Score: 112 Period size: 41 Copynumber: 2.0 Consensus size: 41 13965563 TAATAACATT * * 13965573 TAAATTATAAATT-AATTATTAATATTTTAAAATATTAATTAC 1 TAAATTAT-AATTAAAATATTAATA-TTTAAAATATAAATTAC * 13965615 TAAATTATAATTAAAATATTAATATTTAAATTATAAATTA 1 TAAATTATAATTAAAATATTAATATTTAAAATATAAATTA 13965655 TGAATTTTTT Statistics Matches: 36, Mismatches: 3, Indels: 3 0.86 0.07 0.07 Matches are distributed among these distances: 41 18 0.50 42 18 0.50 ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46 Consensus pattern (41 bp): TAAATTATAATTAAAATATTAATATTTAAAATATAAATTAC Found at i:13965632 original size:26 final size:26 Alignment explanation

Indices: 13965599--13965650 Score: 79 Period size: 26 Copynumber: 2.0 Consensus size: 26 13965589 TATTAATATT 13965599 TTAAAATATTAAT-TACTAAATTATAA 1 TTAAAATATTAATAT-CTAAATTATAA * 13965625 TTAAAATATTAATATTTAAATTATAA 1 TTAAAATATTAATATCTAAATTATAA 13965651 ATTATGAATT Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 26 23 0.96 27 1 0.04 ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44 Consensus pattern (26 bp): TTAAAATATTAATATCTAAATTATAA Found at i:13972302 original size:89 final size:89 Alignment explanation

Indices: 13972143--13972311 Score: 241 Period size: 89 Copynumber: 1.9 Consensus size: 89 13972133 GGTGTTTGTA * * * ** 13972143 GGTTATCACTTGATCTCGTTAAAAAGCAAGAATCCCTTTGTGGATTGTGTAAGGGTTATTGCTTG 1 GGTTATCACTTGATCCCATTAAAAAGCAAGAATCACTTTGTGGATTGTGTAAGGGTTATCACTTG 13972208 ATCCCGTGAAAAAGTTATTGTGAG 66 ATCCCGTGAAAAAGTTATTGTGAG * * * 13972232 GGTTATCGCTTGATCCCATTAAAAAGCAAGAATCACTTTGTGGATTGTGTGAGTGTTATCACTTT 1 GGTTATCACTTGATCCCATTAAAAAGCAAGAATCACTTTGTGGATTGTGTAAGGGTTATCAC-TT * 13972297 G-TCCCGTTAAAAAGT 65 GATCCCGTGAAAAAGT 13972312 AAGAGTCCTT Statistics Matches: 70, Mismatches: 9, Indels: 2 0.86 0.11 0.02 Matches are distributed among these distances: 89 67 0.96 90 3 0.04 ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35 Consensus pattern (89 bp): GGTTATCACTTGATCCCATTAAAAAGCAAGAATCACTTTGTGGATTGTGTAAGGGTTATCACTTG ATCCCGTGAAAAAGTTATTGTGAG Found at i:13972745 original size:139 final size:139 Alignment explanation

Indices: 13972524--13972805 Score: 501 Period size: 139 Copynumber: 2.0 Consensus size: 139 13972514 TAGCTAGCAA 13972524 TTAAACTTAAGAAAAATATTTTACTTTGATAGATTATTTTTATGCTTAATGATTTATTGTTGGAA 1 TTAAACTTAAGAAAAATATTTTACTTTGATAGATTATTTTTATGCTTAATGATTTATTGTTGGAA * * 13972589 ACTTGATTTTGATGCTAGAAAATATATTTGGGTGAAGAAGTTTTGATTTTTTTAATTAGATTTTC 66 ACTTGATTTTGATGCTAGAAAATATATTTGGGTGAAAAAGTTTTGATTTTTATAATTAGATTTTC * 13972654 AAGAAATTT 131 AAGAAAATT * * 13972663 TTAAACTTAGGAAAAATATTTTACTTTGATTGATTATTTTTATGCTTAATGATTTATTGTTGGAA 1 TTAAACTTAAGAAAAATATTTTACTTTGATAGATTATTTTTATGCTTAATGATTTATTGTTGGAA ** 13972728 TTTTGATTTTGATGCTAGAAAATATATTTGGGTGAAAAAGTTTTGATTTTTATAATTAGATTTTC 66 ACTTGATTTTGATGCTAGAAAATATATTTGGGTGAAAAAGTTTTGATTTTTATAATTAGATTTTC 13972793 AAGAAAATT 131 AAGAAAATT 13972802 TTAA 1 TTAA 13972806 TATATCAATT Statistics Matches: 136, Mismatches: 7, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 139 136 1.00 ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47 Consensus pattern (139 bp): TTAAACTTAAGAAAAATATTTTACTTTGATAGATTATTTTTATGCTTAATGATTTATTGTTGGAA ACTTGATTTTGATGCTAGAAAATATATTTGGGTGAAAAAGTTTTGATTTTTATAATTAGATTTTC AAGAAAATT Found at i:13976761 original size:57 final size:54 Alignment explanation

Indices: 13976671--13976783 Score: 199 Period size: 57 Copynumber: 2.0 Consensus size: 54 13976661 TTTCAAATAC 13976671 TTTTAACATTCACAAATTTCTAAGGTATCTACCAATTTATGCTTTTCCACAAAATT 1 TTTTAACATTCACAAATTTCTAAGGTATCTACCAATTTATGC-TTTCCAC-AAATT 13976727 TTNTTAACATTCACAAATTTCTAAGGTATCTACCAATTTATGCTTTCCACAAATT 1 TT-TTAACATTCACAAATTTCTAAGGTATCTACCAATTTATGCTTTCCACAAATT 13976782 TT 1 TT 13976784 CATTTAAAAT Statistics Matches: 56, Mismatches: 0, Indels: 3 0.95 0.00 0.05 Matches are distributed among these distances: 55 7 0.12 56 9 0.16 57 40 0.71 ACGTcount: A:0.33, C:0.19, G:0.05, T:0.42 Consensus pattern (54 bp): TTTTAACATTCACAAATTTCTAAGGTATCTACCAATTTATGCTTTCCACAAATT Found at i:13976812 original size:2 final size:2 Alignment explanation

Indices: 13976805--13976879 Score: 132 Period size: 2 Copynumber: 37.5 Consensus size: 2 13976795 AATCAACACG 13976805 TA TA TA 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 TA TA TA * * 13976847 TA TA TG TA TA TA TA TA TA TA TA TA CA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 13976880 GGAAATAGCG Statistics Matches: 69, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 69 1.00 ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49 Consensus pattern (2 bp): TA Found at i:13977327 original size:4 final size:4 Alignment explanation

Indices: 13977316--13977389 Score: 64 Period size: 4 Copynumber: 19.2 Consensus size: 4 13977306 TCCTTACCTT * * * * 13977316 TTTC -TTC TTTC -TCC TTTC TTTC TTTC TTCC TTTC TTCC TTTC -TCC 1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC * * * 13977361 TTTC TTTC TTTC TTCC CTTC TTCC TTTC T 1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T 13977390 CCTTTCCTTC Statistics Matches: 53, Mismatches: 14, Indels: 6 0.73 0.19 0.08 Matches are distributed among these distances: 3 7 0.13 4 46 0.87 ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65 Consensus pattern (4 bp): TTTC Found at i:13977338 original size:15 final size:15 Alignment explanation

Indices: 13977316--13977395 Score: 108 Period size: 15 Copynumber: 5.3 Consensus size: 15 13977306 TCCTTACCTT 13977316 TTTC-TTCTTTCTCC 1 TTTCTTTCTTTCTCC 13977330 TTTCTTTCTTTCTTCC 1 TTTCTTTCTTTC-TCC * 13977346 TTTCTTCCTTTCTCC 1 TTTCTTTCTTTCTCC 13977361 TTTCTTTCTTTCTTCC 1 TTTCTTTCTTTC-TCC * * 13977377 CTTCTTCCTTTCTCC 1 TTTCTTTCTTTCTCC 13977392 TTTC 1 TTTC 13977396 CTTCCAAGCC Statistics Matches: 58, Mismatches: 5, Indels: 5 0.85 0.07 0.07 Matches are distributed among these distances: 14 4 0.07 15 27 0.47 16 27 0.47 ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64 Consensus pattern (15 bp): TTTCTTTCTTTCTCC Found at i:13977342 original size:8 final size:8 Alignment explanation

Indices: 13977316--13977400 Score: 106 Period size: 8 Copynumber: 11.0 Consensus size: 8 13977306 TCCTTACCTT 13977316 TTTCTT-C 1 TTTCTTCC 13977323 TTTC-TCC 1 TTTCTTCC * 13977330 TTTCTTTC 1 TTTCTTCC 13977338 TTTCTTCC 1 TTTCTTCC 13977346 TTTCTTCC 1 TTTCTTCC 13977354 TTTC-TCC 1 TTTCTTCC * 13977361 TTTCTTTC 1 TTTCTTCC 13977369 TTTCTTCC 1 TTTCTTCC * 13977377 CTTCTTCC 1 TTTCTTCC 13977385 TTTC-TCC 1 TTTCTTCC 13977392 TTTCCTTCC 1 TTT-CTTCC 13977401 AAGCCGATCT Statistics Matches: 67, Mismatches: 6, Indels: 8 0.83 0.07 0.10 Matches are distributed among these distances: 6 1 0.01 7 22 0.33 8 41 0.61 9 3 0.04 ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62 Consensus pattern (8 bp): TTTCTTCC Found at i:13977359 original size:31 final size:31 Alignment explanation

Indices: 13977316--13977395 Score: 144 Period size: 31 Copynumber: 2.6 Consensus size: 31 13977306 TCCTTACCTT 13977316 TTTCTT-CTTTCTCCTTTCTTTCTTTCTTCC 1 TTTCTTCCTTTCTCCTTTCTTTCTTTCTTCC 13977346 TTTCTTCCTTTCTCCTTTCTTTCTTTCTTCC 1 TTTCTTCCTTTCTCCTTTCTTTCTTTCTTCC * 13977377 CTTCTTCCTTTCTCCTTTC 1 TTTCTTCCTTTCTCCTTTC 13977396 CTTCCAAGCC Statistics Matches: 48, Mismatches: 1, Indels: 1 0.96 0.02 0.02 Matches are distributed among these distances: 30 6 0.12 31 42 0.88 ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64 Consensus pattern (31 bp): TTTCTTCCTTTCTCCTTTCTTTCTTTCTTCC Found at i:13979298 original size:23 final size:22 Alignment explanation

Indices: 13979266--13979308 Score: 59 Period size: 23 Copynumber: 1.9 Consensus size: 22 13979256 AACCTATCTT * * 13979266 AATAATATTAACACCAAATTAAG 1 AATAAAATTAAC-CAAAATTAAG 13979289 AATAAAATTAACCAAAATTA 1 AATAAAATTAACCAAAATTA 13979309 GATTGACTCA Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 22 7 0.39 23 11 0.61 ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26 Consensus pattern (22 bp): AATAAAATTAACCAAAATTAAG Found at i:13980290 original size:18 final size:19 Alignment explanation

Indices: 13980263--13980312 Score: 52 Period size: 18 Copynumber: 2.8 Consensus size: 19 13980253 ACACGTTTAC * * 13980263 TTAATCGTGTTAT-CGTGT 1 TTAAACGTGTTATACGTAT * 13980281 TTAAATGTG-TATACGTAT 1 TTAAACGTGTTATACGTAT 13980299 TTAAACGTG-TATAC 1 TTAAACGTGTTATAC 13980313 ATGACATGTT Statistics Matches: 27, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 17 3 0.11 18 24 0.89 ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44 Consensus pattern (19 bp): TTAAACGTGTTATACGTAT Found at i:13980566 original size:9 final size:9 Alignment explanation

Indices: 13980549--13980632 Score: 114 Period size: 9 Copynumber: 9.3 Consensus size: 9 13980539 ATATTTTTAT 13980549 TTAATCGTG 1 TTAATCGTG * 13980558 TTAAACGTG 1 TTAATCGTG 13980567 TTAATCGTG 1 TTAATCGTG * 13980576 TTAAACGTG 1 TTAATCGTG * 13980585 CTAATCGTG 1 TTAATCGTG * 13980594 TTAATCATG 1 TTAATCGTG * 13980603 TTAAACGTG 1 TTAATCGTG 13980612 TTAATCGTG 1 TTAATCGTG * 13980621 TTAAACGTG 1 TTAATCGTG 13980630 TTA 1 TTA 13980633 TTAATCGTAT Statistics Matches: 64, Mismatches: 11, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 9 64 1.00 ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39 Consensus pattern (9 bp): TTAATCGTG Found at i:13981839 original size:8 final size:8 Alignment explanation

Indices: 13981821--13981880 Score: 61 Period size: 8 Copynumber: 7.8 Consensus size: 8 13981811 TTTTTTTTGT 13981821 TGGGT-AA 1 TGGGTAAA 13981828 TGGGTAAA 1 TGGGTAAA * * 13981836 TGGGTTAG 1 TGGGTAAA * 13981844 TGGGTAAG 1 TGGGTAAA * 13981852 TGGGTAAG 1 TGGGTAAA * 13981860 GGGGTAAA 1 TGGGTAAA 13981868 TGGGT-AA 1 TGGGTAAA 13981875 TGGGTA 1 TGGGTA 13981881 GTCCACATGA Statistics Matches: 45, Mismatches: 6, Indels: 3 0.83 0.11 0.06 Matches are distributed among these distances: 7 12 0.27 8 33 0.73 ACGTcount: A:0.27, C:0.00, G:0.47, T:0.27 Consensus pattern (8 bp): TGGGTAAA Found at i:13981849 original size:16 final size:16 Alignment explanation

Indices: 13981821--13981880 Score: 79 Period size: 16 Copynumber: 3.9 Consensus size: 16 13981811 TTTTTTTTGT 13981821 TGGGTAA-TGGGTAAA 1 TGGGTAAGTGGGTAAA * * 13981836 TGGGTTAGTGGGTAAG 1 TGGGTAAGTGGGTAAA * 13981852 TGGGTAAGGGGGTAAA 1 TGGGTAAGTGGGTAAA 13981868 TGGGTAA-TGGGTA 1 TGGGTAAGTGGGTA 13981881 GTCCACATGA Statistics Matches: 38, Mismatches: 6, Indels: 2 0.83 0.13 0.04 Matches are distributed among these distances: 15 11 0.29 16 27 0.71 ACGTcount: A:0.27, C:0.00, G:0.47, T:0.27 Consensus pattern (16 bp): TGGGTAAGTGGGTAAA Found at i:13982337 original size:17 final size:17 Alignment explanation

Indices: 13982302--13982336 Score: 54 Period size: 16 Copynumber: 2.1 Consensus size: 17 13982292 TTAATAATTT * 13982302 AATAATTAAATAAATAA 1 AATAATTAAAAAAATAA 13982319 AATAA-TAAAAAAATAA 1 AATAATTAAAAAAATAA 13982335 AA 1 AA 13982337 AGAAAGTAAG Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 12 0.71 17 5 0.29 ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23 Consensus pattern (17 bp): AATAATTAAAAAAATAA Found at i:13983755 original size:21 final size:21 Alignment explanation

Indices: 13983704--13983767 Score: 92 Period size: 21 Copynumber: 3.0 Consensus size: 21 13983694 TTGAATGGAG * * * 13983704 GCATCAGTCCTTATCATAAAT 1 GCATCAGTCTTTGTCATGAAT * 13983725 GCATCAGTCTTTGTTATGAAT 1 GCATCAGTCTTTGTCATGAAT 13983746 GCATCAGTCTTTGTCATGAAT 1 GCATCAGTCTTTGTCATGAAT 13983767 G 1 G 13983768 TGAGACCTCG Statistics Matches: 38, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 38 1.00 ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38 Consensus pattern (21 bp): GCATCAGTCTTTGTCATGAAT Found at i:13985070 original size:42 final size:42 Alignment explanation

Indices: 13985011--13985101 Score: 164 Period size: 42 Copynumber: 2.2 Consensus size: 42 13985001 TTATGTGATA * 13985011 ATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCTG 1 ATGATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTG * 13985053 ATGATGACCCAATTATGTGCGTGTGGGAGTGCACATGAGCTG 1 ATGATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTG 13985095 ATGATGA 1 ATGATGA 13985102 TGGGATGGTA Statistics Matches: 47, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 42 47 1.00 ACGTcount: A:0.24, C:0.16, G:0.34, T:0.25 Consensus pattern (42 bp): ATGATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTG Found at i:13985462 original size:39 final size:39 Alignment explanation

Indices: 13985402--13985499 Score: 153 Period size: 39 Copynumber: 2.5 Consensus size: 39 13985392 TCATTCTTGT * * 13985402 TGCAGTGAGAAACTTTCTGTTTTG-CTGCTTGAATTTCGC 1 TGCAGCGAGAAACTTTCTGTTTTGCCT-CTTGAATCTCGC * 13985441 TGTAGCGAGAAACTTTCTGTTTTGCCTCTTGAATCTCGC 1 TGCAGCGAGAAACTTTCTGTTTTGCCTCTTGAATCTCGC 13985480 TGCAGCGAGAAACTTTCTGT 1 TGCAGCGAGAAACTTTCTGT 13985500 CCAGCATGCT Statistics Matches: 54, Mismatches: 4, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 39 52 0.96 40 2 0.04 ACGTcount: A:0.19, C:0.20, G:0.22, T:0.38 Consensus pattern (39 bp): TGCAGCGAGAAACTTTCTGTTTTGCCTCTTGAATCTCGC Found at i:13989337 original size:19 final size:19 Alignment explanation

Indices: 13989313--13989378 Score: 107 Period size: 19 Copynumber: 3.5 Consensus size: 19 13989303 TAATATTTTC * 13989313 ATATTATTTTACTCATAAA 1 ATATTATTTTATTCATAAA 13989332 ATATTATTTTATTCATAAA 1 ATATTATTTTATTCATAAA 13989351 ATATTATTTTATTC-TAAA 1 ATATTATTTTATTCATAAA * 13989369 ATATTCTTTT 1 ATATTATTTT 13989379 CACCGGTCAC Statistics Matches: 45, Mismatches: 2, Indels: 1 0.94 0.04 0.02 Matches are distributed among these distances: 18 13 0.29 19 32 0.71 ACGTcount: A:0.38, C:0.08, G:0.00, T:0.55 Consensus pattern (19 bp): ATATTATTTTATTCATAAA Found at i:13989793 original size:24 final size:24 Alignment explanation

Indices: 13989765--13989811 Score: 85 Period size: 24 Copynumber: 2.0 Consensus size: 24 13989755 TTTGATTAAA * 13989765 CATTTATGTGAATATATTTGTATG 1 CATTTATGTGAATATATGTGTATG 13989789 CATTTATGTGAATATATGTGTAT 1 CATTTATGTGAATATATGTGTAT 13989812 TTGTTGATTT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 22 1.00 ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49 Consensus pattern (24 bp): CATTTATGTGAATATATGTGTATG Found at i:13990873 original size:26 final size:27 Alignment explanation

Indices: 13990839--13990891 Score: 72 Period size: 26 Copynumber: 2.0 Consensus size: 27 13990829 CGAGTATAAG * * 13990839 GGGCAAAATAGTCATTTGC-CACCCAA 1 GGGCAAAATAGTAATTTACACACCCAA * 13990865 GGGCAAAATTGTAATTTACACACCCAA 1 GGGCAAAATAGTAATTTACACACCCAA 13990892 CACTTGTCAT Statistics Matches: 23, Mismatches: 3, Indels: 1 0.85 0.11 0.04 Matches are distributed among these distances: 26 16 0.70 27 7 0.30 ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21 Consensus pattern (27 bp): GGGCAAAATAGTAATTTACACACCCAA Found at i:13991169 original size:21 final size:22 Alignment explanation

Indices: 13991144--13991184 Score: 66 Period size: 21 Copynumber: 1.9 Consensus size: 22 13991134 CCTAGGTGGA * 13991144 AAAATTCAAGGGAA-AAGTGTG 1 AAAATTCAAGGAAACAAGTGTG 13991165 AAAATTCAAGGAAACAAGTG 1 AAAATTCAAGGAAACAAGTG 13991185 AAAAAANNNN Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 21 13 0.72 22 5 0.28 ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17 Consensus pattern (22 bp): AAAATTCAAGGAAACAAGTGTG Found at i:13991185 original size:20 final size:21 Alignment explanation

Indices: 13991144--13991188 Score: 58 Period size: 20 Copynumber: 2.2 Consensus size: 21 13991134 CCTAGGTGGA * 13991144 AAAATTCAAGGGAAAAGTGTG 1 AAAATTCAAGGGAAAAGAGTG 13991165 AAAATTCAA-GGAAACA-AGTG 1 AAAATTCAAGGGAAA-AGAGTG 13991185 AAAA 1 AAAA 13991189 AANNNNNNNN Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 20 12 0.55 21 10 0.45 ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16 Consensus pattern (21 bp): AAAATTCAAGGGAAAAGAGTG Found at i:13991189 original size:21 final size:20 Alignment explanation

Indices: 13991142--13991189 Score: 60 Period size: 21 Copynumber: 2.3 Consensus size: 20 13991132 ACCCTAGGTG * 13991142 GAAAAATTCAAGGGAAAAGT 1 GAAAAATTCAAGGAAAAAGT * 13991162 GTGAAAATTCAAGGAAACAAGT 1 G-AAAAATTCAAGGAAA-AAGT 13991184 GAAAAA 1 GAAAAA 13991190 ANNNNNNNNN Statistics Matches: 23, Mismatches: 3, Indels: 3 0.79 0.10 0.10 Matches are distributed among these distances: 20 1 0.04 21 17 0.74 22 5 0.22 ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15 Consensus pattern (20 bp): GAAAAATTCAAGGAAAAAGT Found at i:14011749 original size:2 final size:2 Alignment explanation

Indices: 14011742--14011772 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 14011732 ACTTTCTATA 14011742 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 14011773 TATATATATA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:14011777 original size:2 final size:2 Alignment explanation

Indices: 14011772--14011796 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 14011762 ACACACACAC 14011772 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 14011797 CATACATCAT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:14011893 original size:37 final size:37 Alignment explanation

Indices: 14011846--14011927 Score: 155 Period size: 37 Copynumber: 2.2 Consensus size: 37 14011836 AATGCAATAT 14011846 CATCATCATGTGTGCACTCCCTACTCACACACTCCAA 1 CATCATCATGTGTGCACTCCCTACTCACACACTCCAA * 14011883 CATCATCATGTGTGCACTCCCTACTCACACACTTCAA 1 CATCATCATGTGTGCACTCCCTACTCACACACTCCAA 14011920 CATCATCA 1 CATCATCA 14011928 CATAACATTA Statistics Matches: 44, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 37 44 1.00 ACGTcount: A:0.28, C:0.39, G:0.07, T:0.26 Consensus pattern (37 bp): CATCATCATGTGTGCACTCCCTACTCACACACTCCAA Found at i:14021427 original size:26 final size:26 Alignment explanation

Indices: 14021398--14021535 Score: 75 Period size: 27 Copynumber: 5.1 Consensus size: 26 14021388 CATCGGTCAT 14021398 CAGCTCATGTGCACTCCCACACCGCA 1 CAGCTCATGTGCACTCCCACACCGCA * * * * 14021424 CAGC-AATGATGTA-TACAACCACCGGTCA 1 CAGCTCATG-TGCACTCCCA-CACC-G-CA 14021452 TCAGCTCATGTGCACTCCCACACCGCA 1 -CAGCTCATGTGCACTCCCACACCGCA * * ** ** * 14021479 CAGTAATCATATATACAACCAC-CGGTCA 1 CAG--CTCATGTGCACTCCCACACCG-CA 14021507 TCAGCTCATGTGCACTCCCACACCGCA 1 -CAGCTCATGTGCACTCCCACACCGCA 14021534 CA 1 CA 14021536 TAGCTGGAAT Statistics Matches: 78, Mismatches: 22, Indels: 24 0.63 0.18 0.19 Matches are distributed among these distances: 25 6 0.08 26 16 0.21 27 18 0.23 28 18 0.23 29 14 0.18 30 6 0.08 ACGTcount: A:0.29, C:0.38, G:0.14, T:0.18 Consensus pattern (26 bp): CAGCTCATGTGCACTCCCACACCGCA Found at i:14021464 original size:55 final size:55 Alignment explanation

Indices: 14021376--14021535 Score: 275 Period size: 55 Copynumber: 2.9 Consensus size: 55 14021366 ATCTCTATAG * * 14021376 CATATATACACCCATCGGTCATCAGCTCATGTGCACTCCCACACCGCACAGCAAT 1 CATATATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACAGCAAT * * * 14021431 GATGTATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACAGTAAT 1 CATATATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACAGCAAT 14021486 CATATATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACA 1 CATATATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACA 14021536 TAGCTGGAAT Statistics Matches: 98, Mismatches: 7, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 55 98 1.00 ACGTcount: A:0.29, C:0.38, G:0.14, T:0.19 Consensus pattern (55 bp): CATATATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACAGCAAT Found at i:14021475 original size:29 final size:29 Alignment explanation

Indices: 14021391--14021531 Score: 88 Period size: 29 Copynumber: 5.1 Consensus size: 29 14021381 ATACACCCAT 14021391 CGGTCATCAGCTCATGTGCACTCCCACAC 1 CGGTCATCAGCTCATGTGCACTCCCACAC * * * * 14021420 C-G-CA-CAGC-AATGATGTA-TACAACCAC 1 CGGTCATCAGCTCATG-TGCACTCCCA-CAC 14021446 CGGTCATCAGCTCATGTGCACTCCCACAC 1 CGGTCATCAGCTCATGTGCACTCCCACAC * * * * 14021475 C-G-CA-CAGTAATCATAT--A-TACAACCAC 1 CGGTCATCAG--CTCATGTGCACTCCCA-CAC 14021501 CGGTCATCAGCTCATGTGCACTCCCACAC 1 CGGTCATCAGCTCATGTGCACTCCCACAC 14021530 CG 1 CG 14021532 CACATAGCTG Statistics Matches: 80, Mismatches: 16, Indels: 32 0.62 0.12 0.25 Matches are distributed among these distances: 25 9 0.11 26 19 0.24 27 11 0.14 28 11 0.14 29 21 0.26 30 9 0.11 ACGTcount: A:0.28, C:0.38, G:0.16, T:0.19 Consensus pattern (29 bp): CGGTCATCAGCTCATGTGCACTCCCACAC Found at i:14021645 original size:2 final size:2 Alignment explanation

Indices: 14021628--14021678 Score: 84 Period size: 2 Copynumber: 25.0 Consensus size: 2 14021618 TTATCAATAC * 14021628 AT AT CAT AT AT CT 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 AT 14021671 AT AT AT AT 1 AT AT AT AT 14021679 CAACATAACA Statistics Matches: 46, Mismatches: 2, Indels: 2 0.92 0.04 0.04 Matches are distributed among these distances: 2 44 0.96 3 2 0.04 ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:14026285 original size:38 final size:38 Alignment explanation

Indices: 14026198--14026339 Score: 187 Period size: 38 Copynumber: 3.7 Consensus size: 38 14026188 CACCCGGCTA * * * * 14026198 ATGTACATCCCCCCACATTGTGTACATAGCCG-GCACCATC 1 ATGTACATCCCCCCACATCGTGCACA-ATCAGTG--CCATC * 14026238 ATGTGCATCCCCCCACATCGTGCACAATCAGTGCCATC 1 ATGTACATCCCCCCACATCGTGCACAATCAGTGCCATC * 14026276 ATGTACATCCCCCCACATTGTGCACAATCAGTGCCATC 1 ATGTACATCCCCCCACATCGTGCACAATCAGTGCCATC * 14026314 GTGTACATCCCCCCACATCGTGCACA 1 ATGTACATCCCCCCACATCGTGCACA 14026340 TGGGCACTAT Statistics Matches: 92, Mismatches: 9, Indels: 4 0.88 0.09 0.04 Matches are distributed among these distances: 38 65 0.71 39 3 0.03 40 24 0.26 ACGTcount: A:0.25, C:0.39, G:0.15, T:0.22 Consensus pattern (38 bp): ATGTACATCCCCCCACATCGTGCACAATCAGTGCCATC Found at i:14026334 original size:19 final size:19 Alignment explanation

Indices: 14026199--14026340 Score: 63 Period size: 19 Copynumber: 7.4 Consensus size: 19 14026189 ACCCGGCTAA * 14026199 TGTACATCCCCCCACATTG 1 TGTACATCCCCCCACATCG * ** * 14026218 TGTACATAGCCGGCACCATCA 1 TGTACAT-CCCCCCA-CATCG * 14026239 TGTGCATCCCCCCACATCG 1 TGTACATCCCCCCACATCG * **** * 14026258 TGCACAATCAGTGC-CATCA 1 TGTAC-ATCCCCCCACATCG * 14026277 TGTACATCCCCCCACATTG 1 TGTACATCCCCCCACATCG * **** 14026296 TGCACAATCAGTGC-CATCG 1 TGTAC-ATCCCCCCACATCG 14026315 TGTACATCCCCCCACATCG 1 TGTACATCCCCCCACATCG * 14026334 TGCACAT 1 TGTACAT 14026341 GGGCACTATC Statistics Matches: 81, Mismatches: 36, Indels: 12 0.63 0.28 0.09 Matches are distributed among these distances: 18 8 0.10 19 48 0.59 20 16 0.20 21 9 0.11 ACGTcount: A:0.24, C:0.39, G:0.15, T:0.23 Consensus pattern (19 bp): TGTACATCCCCCCACATCG Found at i:14034174 original size:38 final size:40 Alignment explanation

Indices: 14034090--14034191 Score: 118 Period size: 38 Copynumber: 2.6 Consensus size: 40 14034080 CCGGCTCAGG * * 14034090 TACATCCCCTCACATCGTGCACATAGCCAGGGCCATCATG 1 TACATCCCCCCACATCGTGCACATAGCCAGGGCCATCATA * ** * * 14034130 TGCATCCCCCCACATCGTGCACA-A-TTAGTGCCATCCTA 1 TACATCCCCCCACATCGTGCACATAGCCAGGGCCATCATA * 14034168 TACATCCCCCTACATCGTGCACAT 1 TACATCCCCCCACATCGTGCACAT 14034192 GGGCACTATC Statistics Matches: 52, Mismatches: 9, Indels: 3 0.81 0.14 0.05 Matches are distributed among these distances: 38 30 0.58 39 1 0.02 40 21 0.40 ACGTcount: A:0.25, C:0.39, G:0.14, T:0.23 Consensus pattern (40 bp): TACATCCCCCCACATCGTGCACATAGCCAGGGCCATCATA Done.