Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4

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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 6100 characters in sequence are not A, C, G, or T


File 14 of 132

Found at i:3992405 original size:106 final size:106

Alignment explanation

Indices: 3992216--3992648 Score: 661 Period size: 106 Copynumber: 4.0 Consensus size: 106 3992206 CTGCAGGTCT * * * 3992216 CAACGTCATCCCCTCGAAATTGAAGTGGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA 1 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA * 3992281 GAGTGGATAACACATCTTCATCTCCGAAATTGAAGTAAGAG 66 GAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAG 3992322 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA 1 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA 3992387 GAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAG 66 GAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAG * 3992428 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA 1 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA * * 3992493 GAGTGGATAACAGAGTGGATAATACGTCTTGATCTCTGAAATTGAAGTAAGAG 66 GAGTGGATAAC------------ACGTCTTCATCTCCGAAATTGAAGTAAGAG 3992546 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA 1 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA * 3992611 GAGTGGATAACGCGTCTTCATC-CCTTGAAATTGAAGTA 66 GAGTGGATAACACGTCTTCATCTCC--GAAATTGAAGTA 3992649 GAGTGGATAA Statistics Matches: 302, Mismatches: 11, Indels: 27 0.89 0.03 0.08 Matches are distributed among these distances: 105 1 0.00 106 186 0.62 107 12 0.04 118 103 0.34 ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27 Consensus pattern (106 bp): CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA GAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAG Found at i:3992449 original size:68 final size:67 Alignment explanation

Indices: 3992366--3992492 Score: 220 Period size: 68 Copynumber: 1.9 Consensus size: 67 3992356 TAACACGTCT 3992366 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCC-GAAATTGAAGTAAGAGCA 1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATC-CCTGAAATTGAAGTAAGAGCA 3992430 ACG 65 ACG 3992433 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA 1 TCAT-CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCC-TGAAATTGAAGTA 3992493 GAGTGGATAA Statistics Matches: 57, Mismatches: 0, Indels: 4 0.93 0.00 0.07 Matches are distributed among these distances: 67 6 0.11 68 39 0.68 69 12 0.21 ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28 Consensus pattern (67 bp): TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTGAAATTGAAGTAAGAGCAA CG Found at i:3992594 original size:118 final size:118 Alignment explanation

Indices: 3992386--3992621 Score: 436 Period size: 118 Copynumber: 2.0 Consensus size: 118 3992376 AAATTGAAGT * 3992386 AGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGA 1 AGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA 3992451 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAAC 66 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAAC * * * 3992504 AGAGTGGATAATACGTCTTGATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA 1 AGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA 3992569 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAAC 66 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAAC 3992622 GCGTCTTCAT Statistics Matches: 114, Mismatches: 4, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 118 114 1.00 ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26 Consensus pattern (118 bp): AGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAAC Found at i:3992708 original size:224 final size:221 Alignment explanation

Indices: 3992280--3992726 Score: 618 Period size: 224 Copynumber: 2.0 Consensus size: 221 3992270 AAATTGAAGT 3992280 AGAGTGGATAACACATCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA 1 AGAGTGGATAACACATCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA 3992345 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT 66 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT * * * 3992410 CCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCA 131 CCGAAATTGAAGTAAGAGAAACGTCATCACCTTGAAATTGAAGTAGA--GGAGAACACG--TTCA * 3992475 TCCCTTGAAATTGAAGTAGAG-TGGATAAC 192 TCCCTTGAAATTGAAGTAAAGTTGGATAAC * * * * 3992504 AGAGTGGATAATACGTCTTGATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA 1 AGAGTGGATAACACATCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA * 3992569 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACGCGTCTTCATC- 66 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT * * * * 3992633 CCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA-A-GAGCA-ACG 131 CC--GAAATTGAAGTA-A---GAGAA-ACGTCATCACCT-TGAAATTGAAGTAGAGGAGAACACG 3992695 -TCATCCTCTTGAAATTGAAGTAAAGTTGGATA 188 TTCATCC-CTTGAAATTGAAGTAAAGTTGGATA 3992727 GCAAAGTCTT Statistics Matches: 200, Mismatches: 13, Indels: 19 0.86 0.06 0.08 Matches are distributed among these distances: 223 8 0.04 224 141 0.70 225 18 0.09 226 4 0.02 227 3 0.01 229 3 0.01 230 10 0.05 231 13 0.06 ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27 Consensus pattern (221 bp): AGAGTGGATAACACATCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT CCGAAATTGAAGTAAGAGAAACGTCATCACCTTGAAATTGAAGTAGAGGAGAACACGTTCATCCC TTGAAATTGAAGTAAAGTTGGATAAC Found at i:3993049 original size:6 final size:6 Alignment explanation

Indices: 3993024--3993106 Score: 71 Period size: 6 Copynumber: 13.7 Consensus size: 6 3993014 TTAAATTTAG * * * 3993024 TTAAAT TTAGAT TT-ATT TTAAAT TTAAAT ATCTAAAT TT-AAT TTGAAT 1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -T-TAAAT TTAAAT TTAAAT ** * 3993072 TTAAAT TTAAAT AAAAAT TAAAAT ATTAAAT TTAA 1 TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAA 3993107 CATTAAAAGT Statistics Matches: 63, Mismatches: 9, Indels: 10 0.77 0.11 0.12 Matches are distributed among these distances: 5 8 0.13 6 43 0.68 7 7 0.11 8 5 0.08 ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47 Consensus pattern (6 bp): TTAAAT Found at i:3993063 original size:31 final size:31 Alignment explanation

Indices: 3993025--3993084 Score: 95 Period size: 31 Copynumber: 1.9 Consensus size: 31 3993015 TAAATTTAGT * 3993025 TAAATTTAGATTT-ATTTTAAATTTAAATATC 1 TAAATTTA-ATTTGAATTTAAATTTAAATATC 3993056 TAAATTTAATTTGAATTTAAATTTAAATA 1 TAAATTTAATTTGAATTTAAATTTAAATA 3993085 AAAATTAAAA Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 30 4 0.15 31 23 0.85 ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50 Consensus pattern (31 bp): TAAATTTAATTTGAATTTAAATTTAAATATC Found at i:3993207 original size:13 final size:15 Alignment explanation

Indices: 3993190--3993226 Score: 53 Period size: 13 Copynumber: 2.7 Consensus size: 15 3993180 ACCCATTTTT 3993190 TGGCCCAAATTA-AA 1 TGGCCCAAATTACAA 3993204 -GGCCC-AATTACAA 1 TGGCCCAAATTACAA 3993217 TGGCCCAAAT 1 TGGCCCAAAT 3993227 AGGCCCAATG Statistics Matches: 20, Mismatches: 0, Indels: 5 0.80 0.00 0.20 Matches are distributed among these distances: 12 5 0.25 13 7 0.35 14 5 0.25 15 3 0.15 ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19 Consensus pattern (15 bp): TGGCCCAAATTACAA Found at i:3993304 original size:15 final size:15 Alignment explanation

Indices: 3993284--3993314 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 3993274 GCCTATGCTG 3993284 CTGCCACCACCAGCT 1 CTGCCACCACCAGCT 3993299 CTGCCACCACCAGCT 1 CTGCCACCACCAGCT 3993314 C 1 C 3993315 CATCCACCAT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13 Consensus pattern (15 bp): CTGCCACCACCAGCT Found at i:3995002 original size:30 final size:30 Alignment explanation

Indices: 3994962--3995148 Score: 269 Period size: 30 Copynumber: 6.4 Consensus size: 30 3994952 AAACAATTCG * * 3994962 AAAATTACATTTTGACCCTAAAACTTTTCC 1 AAAATTACATTTTAACCCCAAAACTTTTCC * 3994992 AAAATCACATTTTAACCCCAAAACTTTTCC 1 AAAATTACATTTTAACCCCAAAACTTTTCC * * 3995022 AAAATCATATTTTAACCCCAAAACTTTTCC 1 AAAATTACATTTTAACCCCAAAACTTTTCC * 3995052 --AA--A-A-TTTGACCCCAAAACTTTTCC 1 AAAATTACATTTTAACCCCAAAACTTTTCC * 3995076 AAAATTATATTTTAACCCCAAAACTTTTCC 1 AAAATTACATTTTAACCCCAAAACTTTTCC 3995106 AAAATTACATTTTAACCCCAAAACTTTTCC 1 AAAATTACATTTTAACCCCAAAACTTTTCC 3995136 AAAATTACATTTT 1 AAAATTACATTTT 3995149 GATCCTAAAA Statistics Matches: 144, Mismatches: 7, Indels: 12 0.88 0.04 0.07 Matches are distributed among these distances: 24 19 0.13 25 1 0.01 26 3 0.02 28 3 0.02 29 1 0.01 30 117 0.81 ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34 Consensus pattern (30 bp): AAAATTACATTTTAACCCCAAAACTTTTCC Found at i:3995063 original size:24 final size:24 Alignment explanation

Indices: 3995036--3995081 Score: 92 Period size: 24 Copynumber: 1.9 Consensus size: 24 3995026 TCATATTTTA 3995036 ACCCCAAAACTTTTCCAAAATTTG 1 ACCCCAAAACTTTTCCAAAATTTG 3995060 ACCCCAAAACTTTTCCAAAATT 1 ACCCCAAAACTTTTCCAAAATT 3995082 ATATTTTAAC Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 22 1.00 ACGTcount: A:0.39, C:0.30, G:0.02, T:0.28 Consensus pattern (24 bp): ACCCCAAAACTTTTCCAAAATTTG Found at i:3995068 original size:54 final size:54 Alignment explanation

Indices: 3995006--3995111 Score: 203 Period size: 54 Copynumber: 2.0 Consensus size: 54 3994996 TCACATTTTA 3995006 ACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTTTCCAAAATTTG 1 ACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTTTCCAAAATTTG * 3995060 ACCCCAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTTCCAAAATT 1 ACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTTTCCAAAATT 3995112 ACATTTTAAC Statistics Matches: 51, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 54 51 1.00 ACGTcount: A:0.40, C:0.27, G:0.01, T:0.32 Consensus pattern (54 bp): ACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTTTCCAAAATTTG Found at i:3995118 original size:84 final size:84 Alignment explanation

Indices: 3994972--3995141 Score: 295 Period size: 84 Copynumber: 2.0 Consensus size: 84 3994962 AAAATTACAT * * 3994972 TTTGACCCTAAAACTTTTCCAAAATCACATTTTAACCCCAAAACTTTTCCAAAATCATATTTTAA 1 TTTGACCCCAAAACTTTTCCAAAATCACATTTTAACCCCAAAACTTTTCCAAAATCACATTTTAA 3995037 CCCCAAAACTTTTCCAAAA 66 CCCCAAAACTTTTCCAAAA * * * 3995056 TTTGACCCCAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAA 1 TTTGACCCCAAAACTTTTCCAAAATCACATTTTAACCCCAAAACTTTTCCAAAATCACATTTTAA 3995121 CCCCAAAACTTTTCCAAAA 66 CCCCAAAACTTTTCCAAAA 3995140 TT 1 TT 3995142 ACATTTTGAT Statistics Matches: 81, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 84 81 1.00 ACGTcount: A:0.39, C:0.26, G:0.01, T:0.34 Consensus pattern (84 bp): TTTGACCCCAAAACTTTTCCAAAATCACATTTTAACCCCAAAACTTTTCCAAAATCACATTTTAA CCCCAAAACTTTTCCAAAA Found at i:3996626 original size:3 final size:3 Alignment explanation

Indices: 3996618--3996651 Score: 68 Period size: 3 Copynumber: 11.3 Consensus size: 3 3996608 GTATATTCAA 3996618 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A 3996652 TGTTTTTTTG Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 31 1.00 ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32 Consensus pattern (3 bp): AAT Found at i:3998359 original size:21 final size:21 Alignment explanation

Indices: 3998335--3998381 Score: 67 Period size: 21 Copynumber: 2.2 Consensus size: 21 3998325 GATTCCTTCC * 3998335 GATACAAGTGACAGTTCTACA 1 GATACAAGTGACACTTCTACA * * 3998356 GATACAAGTGACTCTTCTACC 1 GATACAAGTGACACTTCTACA 3998377 GATAC 1 GATAC 3998382 TAGTCTTACT Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 23 1.00 ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26 Consensus pattern (21 bp): GATACAAGTGACACTTCTACA Found at i:3998645 original size:114 final size:117 Alignment explanation

Indices: 3998432--3998661 Score: 297 Period size: 114 Copynumber: 2.0 Consensus size: 117 3998422 GAAATCTTAC * ** * * * 3998432 CCTGTTACTTCTACCGATATATGTATGCGAACTACCTATATTTCTAAATACATGACTACCAATAA 1 CCTGTTACTTCTACCGATACAAATATGCGAAATACCGATACTTCTAAATACATGACTACCAATAA * * * 3998497 TTGTTATTCATCTACTGATACAACCCAAGTCAGTGTACAA-CTTCTCTCCTAT 66 TAGTTATTCATCTACCGATACAACCCAAGTCAGTGAACAATC-TCTCTCCTAT * ** * 3998549 CCTG-TACTTCTACCGATACAAATATGC-AAATATCGATACTTCTAAATACATGACTACTGATAC 1 CCTGTTACTTCTACCGATACAAATATGCGAAATACCGATACTTCTAAATACATGACTACCAATAA * 3998612 TAGTTATT-ATCTACCGATACAACTCAAGTCAGTGAACAATCTCTCTCCTA 66 TAGTTATTCATCTACCGATACAACCCAAGTCAGTGAACAATCTCTCTCCTA 3998662 CTTTCTACTT Statistics Matches: 98, Mismatches: 14, Indels: 5 0.84 0.12 0.04 Matches are distributed among these distances: 114 37 0.38 115 37 0.38 116 20 0.20 117 4 0.04 ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33 Consensus pattern (117 bp): CCTGTTACTTCTACCGATACAAATATGCGAAATACCGATACTTCTAAATACATGACTACCAATAA TAGTTATTCATCTACCGATACAACCCAAGTCAGTGAACAATCTCTCTCCTAT Found at i:4001888 original size:28 final size:28 Alignment explanation

Indices: 4001783--4001889 Score: 101 Period size: 28 Copynumber: 3.8 Consensus size: 28 4001773 TTTTTGATGT * ** 4001783 TTGAGGATAAAATGGTAATTTTGGACTT 1 TTGAGGGTAAAATGGTAATTTTGGACAA * 4001811 TTGAGGGTAAAATGGTAATTTTGGAAAAA 1 TTGAGGGTAAAATGGTAATTTTGG-ACAA * * 4001840 TTTAGGGTTAAAAT-G-ACATTTTAGACAA 1 TTGAGGG-TAAAATGGTA-ATTTTGGACAA * * 4001868 TCGAGGGTAAAATGGTGATTTT 1 TTGAGGGTAAAATGGTAATTTT 4001890 TAGAAAAAAT Statistics Matches: 64, Mismatches: 10, Indels: 10 0.76 0.12 0.12 Matches are distributed among these distances: 27 6 0.09 28 38 0.59 29 14 0.22 30 6 0.09 ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36 Consensus pattern (28 bp): TTGAGGGTAAAATGGTAATTTTGGACAA Found at i:4001901 original size:146 final size:145 Alignment explanation

Indices: 4001645--4001921 Score: 403 Period size: 146 Copynumber: 1.9 Consensus size: 145 4001635 ACCCGAGGGC 4001645 AAAATAGTAATTTTAGACTCTCGAGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG 1 AAAATAGTAATTTTAGACTCTCGAGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG *** * * 4001710 ACATTTTAGATGTTCGAGGGTAAAATGGTAATTTTTGGAAGAATCGGGATAAAAAACGAGACTTT 66 ACATTTTAGACAATCGAGGGTAAAATGGTAATTTTTGAAAAAATCGGGATAAAAAACGAGA-TTT 4001775 TTTGATGTTTGAGGAT 130 TTTGATGTTTGAGGAT * * * * * * 4001791 AAAATGGTAATTTTGGACTTTTGAGGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTA-AAATG 1 AAAATAGTAATTTTAGACTCTCGAGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG * * * 4001855 ACATTTTAGACAATCGAGGGTAAAATGGTGATTTTTAGAAAAAATCGGGATCAAAAATGAGATTT 66 ACATTTTAGACAATCGAGGGTAAAATGGTAATTTTT-GAAAAAATCGGGATAAAAAACGAGATTT 4001920 TT 130 TT 4001922 GGAAGTTAAG Statistics Matches: 116, Mismatches: 14, Indels: 3 0.87 0.11 0.02 Matches are distributed among these distances: 145 41 0.35 146 75 0.65 ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33 Consensus pattern (145 bp): AAAATAGTAATTTTAGACTCTCGAGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG ACATTTTAGACAATCGAGGGTAAAATGGTAATTTTTGAAAAAATCGGGATAAAAAACGAGATTTT TTGATGTTTGAGGAT Found at i:4001941 original size:146 final size:145 Alignment explanation

Indices: 4001645--4001978 Score: 399 Period size: 146 Copynumber: 2.3 Consensus size: 145 4001635 ACCCGAGGGC * * * * 4001645 AAAATAGTAATTTTAGACTCTCGAGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG 1 AAAAT-GTAATTTTGGACTTTTGAGGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG *** * * 4001710 ACATTTTAGATGTTCGAGGGTAAAATGGTAATTTTTGGAAGAATCGGGATAAAAAACGAGACTTT 65 ACATTTTAGACAATCGAGGGTAAAATGGTAATTTTTGAAAAAATCGGGATAAAAAACGAGACTTT * * * 4001775 TTTGATGTTTGAGGAT 130 TTGGAAGTTAGAGGAT * 4001791 AAAATGGTAATTTTGGACTTTTGAGGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTA-AAATG 1 AAAAT-GTAATTTTGGACTTTTGAGGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG * * * 4001855 ACATTTTAGACAATCGAGGGTAAAATGGTGATTTTTAGAAAAAATCGGGATCAAAAATGAGA-TT 65 ACATTTTAGACAATCGAGGGTAAAATGGTAATTTTT-GAAAAAATCGGGATAAAAAACGAGACTT * 4001919 TTTGGAAGTTA-AGGGGT 129 TTTGGAAGTTAGA-GGAT * 4001936 AAAAATGTAATTTTGGGAAGTTTT-AGGGTCAAAATGG-AATTTT 1 -AAAATGTAATTTT-GG-ACTTTTGAGGGT-AAAATGGTAATTTT 4001979 AAGAAGTTTA Statistics Matches: 163, Mismatches: 19, Indels: 12 0.84 0.10 0.06 Matches are distributed among these distances: 144 1 0.01 145 57 0.35 146 93 0.57 147 12 0.07 ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33 Consensus pattern (145 bp): AAAATGTAATTTTGGACTTTTGAGGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAGA CATTTTAGACAATCGAGGGTAAAATGGTAATTTTTGAAAAAATCGGGATAAAAAACGAGACTTTT TGGAAGTTAGAGGAT Found at i:4001985 original size:58 final size:57 Alignment explanation

Indices: 4001923--4002213 Score: 185 Period size: 59 Copynumber: 5.0 Consensus size: 57 4001913 GAGATTTTTG 4001923 GAAGTTAAGGGGTAAAAATGTAATTTTGGGAAGTTTTAGGGTCAAAATGGAATTTTAA 1 GAAGTT-AGGGGTAAAAATGTAATTTTGGGAAGTTTTAGGGTCAAAATGGAATTTTAA * * * * * * ** 4001981 GAAGTTTAGGGGCAAAAATGTAATTTTTGGAAGTTTCAAGGTAAAAAATGGGATTTTTG 1 GAAG-TTAGGGGTAAAAATGTAATTTTGGGAAGTTTTAGGGT-CAAAATGGAATTTTAA * ** * ** 4002040 GATA-TTCGAGGGTAAAAACATAATTTTGGGAAGTTTTGGGGTCAAAAATGGAATTTTTG 1 GA-AGTTAG-GGGTAAAAATGTAATTTTGGGAAGTTTTAGGGTC-AAAATGGAATTTTAA ** * * * ** * 4002099 GAAGCTCGGGGGCAAGAATGTAAGTTTT-GGAAGTCTCGGGGTCAAAAATGTAATTTTTAA 1 GAAG-TTAGGGGTAAAAATGTAA-TTTTGGGAAGTTTTAGGGTC-AAAATGGAA-TTTTAA ** * * * * * 4002159 -AAGTTTTGTGTCAAAATGCAATTTTGGAGAAATTTT-GGGATCAAAATGTAATTTT 1 GAAGTTAGGGGTAAAAATGTAATTTTGG-GAAGTTTTAGGG-TCAAAATGGAATTTT 4002214 TAGATAATTT Statistics Matches: 181, Mismatches: 40, Indels: 25 0.74 0.16 0.10 Matches are distributed among these distances: 57 8 0.04 58 62 0.34 59 100 0.55 60 11 0.06 ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34 Consensus pattern (57 bp): GAAGTTAGGGGTAAAAATGTAATTTTGGGAAGTTTTAGGGTCAAAATGGAATTTTAA Found at i:4002109 original size:29 final size:30 Alignment explanation

Indices: 4001899--4002156 Score: 192 Period size: 29 Copynumber: 8.8 Consensus size: 30 4001889 TTAGAAAAAA * 4001899 TCGGGATCAAAAAT-GAGATTTTTGGAAGTT 1 TCGGGGTCAAAAATGGA-ATTTTTGGAAGTT ** * * 4001929 AAGGGGT-AAAAATGTAATTTTGGGAAGTT 1 TCGGGGTCAAAAATGGAATTTTTGGAAGTT ** ** 4001958 TTAGGGTC-AAAATGGAATTTTAAGAAGTT 1 TCGGGGTCAAAAATGGAATTTTTGGAAGTT * * 4001987 TAGGGG-CAAAAATGTAATTTTTGGAAGTT 1 TCGGGGTCAAAAATGGAATTTTTGGAAGTT ** * * 4002016 TCAAGGTAAAAAATGGGATTTTTGG-A-TAT 1 TCGGGGTCAAAAATGGAATTTTTGGAAGT-T * * 4002045 TCGAGGGTAAAAACAT--AATTTTGGGAAGTT 1 TCG-GGGTCAAAA-ATGGAATTTTTGGAAGTT * * 4002075 TTGGGGTCAAAAATGGAATTTTTGGAAG-C 1 TCGGGGTCAAAAATGGAATTTTTGGAAGTT * * * * * 4002104 TCGGGGGCAAGAATGTAAGTTTTGGAAGTC 1 TCGGGGTCAAAAATGGAATTTTTGGAAGTT * 4002134 TCGGGGTCAAAAATGTAATTTTT 1 TCGGGGTCAAAAATGGAATTTTT 4002157 AAAAGTTTTG Statistics Matches: 178, Mismatches: 38, Indels: 24 0.74 0.16 0.10 Matches are distributed among these distances: 28 4 0.02 29 107 0.60 30 64 0.36 31 3 0.02 ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33 Consensus pattern (30 bp): TCGGGGTCAAAAATGGAATTTTTGGAAGTT Found at i:4002154 original size:59 final size:59 Alignment explanation

Indices: 4001899--4002156 Score: 247 Period size: 59 Copynumber: 4.4 Consensus size: 59 4001889 TTAGAAAAAA * * * 4001899 TCGGGATCAAAAAT-GAGATTTTTGGAAGTTAAGGGGTAAAAATGTAATTTTGGGAAGTT 1 TCGGGGTCAAAAATGGA-ATTTTTGGAAGTTCAGGGGCAAAAATGTAATTTTGGGAAGTT ** ** * * 4001958 TTAGGGTC-AAAATGGAATTTTAAGAAGTTTAGGGGCAAAAATGTAATTTTTGGAAGTT 1 TCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGCAAAAATGTAATTTTGGGAAGTT ** * * * ** 4002016 TCAAGGTAAAAAATGGGATTTTTGGATA-TTC-GAGGGTAAAAACATAATTTTGGGAAGTT 1 TCGGGGTCAAAAATGGAATTTTTGGA-AGTTCAG-GGGCAAAAATGTAATTTTGGGAAGTT * * * * * 4002075 TTGGGGTCAAAAATGGAATTTTTGGAAGCTCGGGGGCAAGAATGTAAGTTTT-GGAAGTC 1 TCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGCAAAAATGTAA-TTTTGGGAAGTT * 4002134 TCGGGGTCAAAAATGTAATTTTT 1 TCGGGGTCAAAAATGGAATTTTT 4002157 AAAAGTTTTG Statistics Matches: 160, Mismatches: 32, Indels: 14 0.78 0.16 0.07 Matches are distributed among these distances: 58 49 0.31 59 105 0.66 60 6 0.04 ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33 Consensus pattern (59 bp): TCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGCAAAAATGTAATTTTGGGAAGTT Found at i:4002223 original size:30 final size:29 Alignment explanation

Indices: 4002143--4002228 Score: 95 Period size: 30 Copynumber: 2.9 Consensus size: 29 4002133 CTCGGGGTCA * 4002143 AAAATGTAATTTTTA-AAAGTTTTGTG-TC 1 AAAATGTAATTTTTAGAAA-TTTTGGGATC * * 4002171 AAAATGCAATTTTGGAGAAATTTTGGGATC 1 AAAATGTAATTTT-TAGAAATTTTGGGATC * 4002201 AAAATGTAATTTTTAGATAATTTAGGGA 1 AAAATGTAATTTTTAGA-AATTTTGGGA 4002229 CCTCTAGGGT Statistics Matches: 48, Mismatches: 6, Indels: 6 0.80 0.10 0.10 Matches are distributed among these distances: 28 12 0.25 29 10 0.21 30 26 0.54 ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40 Consensus pattern (29 bp): AAAATGTAATTTTTAGAAATTTTGGGATC Found at i:4003900 original size:22 final size:22 Alignment explanation

Indices: 4003867--4003911 Score: 56 Period size: 22 Copynumber: 2.0 Consensus size: 22 4003857 TTTGCAGGTC 4003867 GGCTTGGAGGCTGATA-CAGTG 1 GGCTTGGAGGCTGATAGCAGTG * * 4003888 GGCTATGGTGGCTTATAGCAGTG 1 GGCT-TGGAGGCTGATAGCAGTG 4003911 G 1 G 4003912 CGGTGCAACT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 21 4 0.20 22 10 0.50 23 6 0.30 ACGTcount: A:0.18, C:0.13, G:0.42, T:0.27 Consensus pattern (22 bp): GGCTTGGAGGCTGATAGCAGTG Found at i:4004220 original size:17 final size:17 Alignment explanation

Indices: 4004198--4004247 Score: 64 Period size: 17 Copynumber: 2.9 Consensus size: 17 4004188 TAAAATTAAT * 4004198 TAAATTTAAATTTAAGA 1 TAAATTTAAATTTAAAA * 4004215 TAAATTTAAAATTAAAA 1 TAAATTTAAATTTAAAA * 4004232 TTAATTTAAACTTTAA 1 TAAATTTAAA-TTTAA 4004248 TTAAAAATCA Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 17 24 0.86 18 4 0.14 ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42 Consensus pattern (17 bp): TAAATTTAAATTTAAAA Found at i:4004241 original size:23 final size:24 Alignment explanation

Indices: 4004197--4004247 Score: 59 Period size: 23 Copynumber: 2.2 Consensus size: 24 4004187 TTAAAATTAA * * 4004197 TTAAATTTAAATTTAAGATAAA-T 1 TTAAAATTAAAATTAAGATAAACT ** 4004220 TTAAAATTAAAATTAATTTAAACT 1 TTAAAATTAAAATTAAGATAAACT 4004244 TTAA 1 TTAA 4004248 TTAAAAATCA Statistics Matches: 23, Mismatches: 4, Indels: 1 0.82 0.14 0.04 Matches are distributed among these distances: 23 18 0.78 24 5 0.22 ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43 Consensus pattern (24 bp): TTAAAATTAAAATTAAGATAAACT Found at i:4004947 original size:19 final size:19 Alignment explanation

Indices: 4004916--4004953 Score: 51 Period size: 19 Copynumber: 2.0 Consensus size: 19 4004906 AAAAATCACA * 4004916 TTTTTTACATTTAACATAT 1 TTTTTTACATTTAAAATAT 4004935 TTTTTTA-ATTTTAAAATAT 1 TTTTTTACA-TTTAAAATAT 4004954 ATGGTGACGA Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 18 1 0.06 19 16 0.94 ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61 Consensus pattern (19 bp): TTTTTTACATTTAAAATAT Found at i:4006057 original size:20 final size:21 Alignment explanation

Indices: 4006032--4006080 Score: 59 Period size: 20 Copynumber: 2.4 Consensus size: 21 4006022 TTTAAGCGAA 4006032 ATAAAAATCATAAATTTTA-G 1 ATAAAAATCATAAATTTTATG * 4006052 ATAAAATAT-TTAAATTTTATG 1 ATAAAA-ATCATAAATTTTATG 4006073 -TAAAAATC 1 ATAAAAATC 4006081 TATTGAATAA Statistics Matches: 25, Mismatches: 1, Indels: 6 0.78 0.03 0.19 Matches are distributed among these distances: 19 2 0.08 20 20 0.80 21 3 0.12 ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39 Consensus pattern (21 bp): ATAAAAATCATAAATTTTATG Found at i:4008853 original size:20 final size:20 Alignment explanation

Indices: 4008828--4008893 Score: 75 Period size: 20 Copynumber: 3.4 Consensus size: 20 4008818 AAAATCAATC 4008828 ATTATTTATATTTATTTATA 1 ATTATTTATATTTATTTATA * * 4008848 ATTATTGATATTT-TTAAATA 1 ATTATTTATATTTATT-TATA * 4008868 ATT-TTT-TATATATTTATA 1 ATTATTTATATTTATTTATA 4008886 ATTATTTA 1 ATTATTTA 4008894 AGAAACTATT Statistics Matches: 37, Mismatches: 5, Indels: 8 0.74 0.10 0.16 Matches are distributed among these distances: 18 10 0.27 19 9 0.24 20 18 0.49 ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62 Consensus pattern (20 bp): ATTATTTATATTTATTTATA Found at i:4012855 original size:41 final size:41 Alignment explanation

Indices: 4012798--4012893 Score: 174 Period size: 41 Copynumber: 2.3 Consensus size: 41 4012788 CCACTAATGG 4012798 TTTGCAGGTAAACTGGCAATAGCTATGGATACACAACAAAT 1 TTTGCAGGTAAACTGGCAATAGCTATGGATACACAACAAAT * 4012839 TTTGCAGGTAAACTGGCAATAGCTATGGATACTCAACAAAT 1 TTTGCAGGTAAACTGGCAATAGCTATGGATACACAACAAAT * 4012880 TTTGCAGATAAACT 1 TTTGCAGGTAAACT 4012894 ACCGATACTT Statistics Matches: 53, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 41 53 1.00 ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27 Consensus pattern (41 bp): TTTGCAGGTAAACTGGCAATAGCTATGGATACACAACAAAT Found at i:4013883 original size:28 final size:26 Alignment explanation

Indices: 4013844--4013901 Score: 64 Period size: 28 Copynumber: 2.2 Consensus size: 26 4013834 TTAAGATGAC * 4013844 TATATAAAAATTTAATAAATAAAA-AA 1 TATATAAAAATTAAAT-AATAAAATAA * 4013870 TATATAAATTAATTAAATATTAAAATAA 1 TATATAAA--AATTAAATAATAAAATAA 4013898 TATA 1 TATA 4013902 ATATAAATAT Statistics Matches: 27, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 26 8 0.30 27 6 0.22 28 13 0.48 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (26 bp): TATATAAAAATTAAATAATAAAATAA Found at i:4016972 original size:30 final size:30 Alignment explanation

Indices: 4016938--4016998 Score: 79 Period size: 30 Copynumber: 2.0 Consensus size: 30 4016928 AATATGAAGC * 4016938 AATATAATAAGCAGAT-AAATAATATGCGAA 1 AATATAAGAAGCAGATCAAATAA-ATGCGAA * 4016968 AATATAAGATGCAGATGCAAATAAATGCGAA 1 AATATAAGAAGCAGAT-CAAATAAATGCGAA 4016999 TATTGGTGAG Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 30 14 0.52 31 7 0.26 32 6 0.22 ACGTcount: A:0.54, C:0.08, G:0.16, T:0.21 Consensus pattern (30 bp): AATATAAGAAGCAGATCAAATAAATGCGAA Found at i:4019147 original size:11 final size:11 Alignment explanation

Indices: 4019133--4019226 Score: 64 Period size: 11 Copynumber: 8.2 Consensus size: 11 4019123 ATATTTTCAT * 4019133 AATTTGATTTA 1 AATTTAATTTA 4019144 AATTTAAATTTA 1 AATTT-AATTTA * * 4019156 AAATAAATTTA 1 AATTTAATTTA 4019167 AATAGTTGAATTTA 1 AAT--TT-AATTTA ** 4019181 AATTTAAAATA 1 AATTTAATTTA 4019192 AATTTAAATTTA 1 AATTT-AATTTA * * 4019204 AA-TAAATTAA 1 AATTTAATTTA * 4019214 AAATTAATTTA 1 AATTTAATTTA 4019225 AA 1 AA 4019227 AACATAAAGT Statistics Matches: 64, Mismatches: 13, Indels: 12 0.72 0.15 0.13 Matches are distributed among these distances: 10 7 0.11 11 31 0.48 12 16 0.25 13 1 0.02 14 9 0.14 ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43 Consensus pattern (11 bp): AATTTAATTTA Found at i:4019150 original size:6 final size:6 Alignment explanation

Indices: 4019139--4019226 Score: 78 Period size: 6 Copynumber: 15.2 Consensus size: 6 4019129 TCATAATTTG * * 4019139 ATTTAA ATTTAA ATTTAA A-ATAA ATTTAA ATAGTTGA ATTTAA ATTTAA 1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA * * * 4019188 A-ATAA ATTTAA ATTTAA A--TAA ATTAAA AATT-A ATTTAA A 1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A 4019227 AACATAAAGT Statistics Matches: 65, Mismatches: 10, Indels: 14 0.73 0.11 0.16 Matches are distributed among these distances: 4 4 0.06 5 12 0.18 6 44 0.68 8 5 0.08 ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42 Consensus pattern (6 bp): ATTTAA Found at i:4019217 original size:17 final size:17 Alignment explanation

Indices: 4019175--4019220 Score: 58 Period size: 16 Copynumber: 2.8 Consensus size: 17 4019165 TAAATAGTTG * 4019175 AATTTAAATTTAAAATA 1 AATTAAAATTTAAAATA * 4019192 AATTTAAATTT-AAATA 1 AATTAAAATTTAAAATA * 4019208 AATTAAAAATTAA 1 AATTAAAATTTAA 4019221 TTTAAAAACA Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 16 14 0.54 17 12 0.46 ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39 Consensus pattern (17 bp): AATTAAAATTTAAAATA Found at i:4020465 original size:6 final size:6 Alignment explanation

Indices: 4020454--4020487 Score: 68 Period size: 6 Copynumber: 5.7 Consensus size: 6 4020444 TTCCAGTGTG 4020454 GAGTCT GAGTCT GAGTCT GAGTCT GAGTCT GAGT 1 GAGTCT GAGTCT GAGTCT GAGTCT GAGTCT GAGT 4020488 TGACTCAAGA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 28 1.00 ACGTcount: A:0.18, C:0.15, G:0.35, T:0.32 Consensus pattern (6 bp): GAGTCT Found at i:4021969 original size:14 final size:14 Alignment explanation

Indices: 4021952--4021979 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 4021942 ATTTTAAATT 4021952 TTTAATTAATTAAA 1 TTTAATTAATTAAA 4021966 TTTAATTAATTAAA 1 TTTAATTAATTAAA 4021980 AATGTATTCT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (14 bp): TTTAATTAATTAAA Found at i:4021974 original size:18 final size:18 Alignment explanation

Indices: 4021936--4021978 Score: 58 Period size: 16 Copynumber: 2.6 Consensus size: 18 4021926 TTTTCAGTTA 4021936 TAATTAATT--TTAAATT 1 TAATTAATTAATTAAATT 4021952 T--TTAATTAATTAAATT 1 TAATTAATTAATTAAATT 4021968 TAATTAATTAA 1 TAATTAATTAA 4021979 AAATGTATTC Statistics Matches: 23, Mismatches: 0, Indels: 6 0.79 0.00 0.21 Matches are distributed among these distances: 14 6 0.26 16 9 0.39 18 8 0.35 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (18 bp): TAATTAATTAATTAAATT Found at i:4023624 original size:32 final size:32 Alignment explanation

Indices: 4023556--4023625 Score: 92 Period size: 33 Copynumber: 2.2 Consensus size: 32 4023546 ACTTTTTCAT 4023556 ATTTTTT--TATTATTTAATAATATTTTAATA 1 ATTTTTTCATATTATTTAATAATATTTTAATA * 4023586 ATTTTTTCATATTA-TTAATACATAATTTTGATA 1 ATTTTTTCATATTATTTAATA-AT-ATTTTAATA 4023619 ATTTTTT 1 ATTTTTT 4023626 ACTCCGAATT Statistics Matches: 35, Mismatches: 1, Indels: 5 0.85 0.02 0.12 Matches are distributed among these distances: 30 7 0.20 31 6 0.17 32 7 0.20 33 15 0.43 ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61 Consensus pattern (32 bp): ATTTTTTCATATTATTTAATAATATTTTAATA Found at i:4023693 original size:33 final size:33 Alignment explanation

Indices: 4023648--4023726 Score: 95 Period size: 33 Copynumber: 2.3 Consensus size: 33 4023638 AAACATTGAT * * ** 4023648 CTCGAATCTCAAATTTTGAATATGAATCCTGAAC 1 CTCGAA-CTCAAACTCTGAATAAAAATCCTGAAC * 4023682 CTCGAACTCAAACTCTGAATAAAAATCTTGAAC 1 CTCGAACTCAAACTCTGAATAAAAATCCTGAAC 4023715 CTCGAAACTCAA 1 CTCG-AACTCAA 4023727 TCTTAAACCC Statistics Matches: 39, Mismatches: 5, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 33 26 0.67 34 13 0.33 ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27 Consensus pattern (33 bp): CTCGAACTCAAACTCTGAATAAAAATCCTGAAC Found at i:4023761 original size:28 final size:29 Alignment explanation

Indices: 4023729--4023797 Score: 81 Period size: 28 Copynumber: 2.4 Consensus size: 29 4023719 AAACTCAATC * 4023729 TTAAACCCTAAACTTT-AAATATT-GAACT 1 TTAAACCCTAAACTTTAAAAT-TTAAAACT * 4023757 TTAAACCTTAAA-TTTAAAATTTAAAACT 1 TTAAACCCTAAACTTTAAAATTTAAAACT * 4023785 CTAAACCCTAAAC 1 TTAAACCCTAAAC 4023798 ATAAAACTTC Statistics Matches: 34, Mismatches: 4, Indels: 5 0.79 0.09 0.12 Matches are distributed among these distances: 27 5 0.15 28 29 0.85 ACGTcount: A:0.46, C:0.19, G:0.01, T:0.33 Consensus pattern (29 bp): TTAAACCCTAAACTTTAAAATTTAAAACT Found at i:4032203 original size:17 final size:17 Alignment explanation

Indices: 4032181--4032213 Score: 50 Period size: 17 Copynumber: 1.9 Consensus size: 17 4032171 CTTTCAACAA 4032181 AAAATACAA-AATAATTC 1 AAAATA-AATAATAATTC 4032198 AAAATAAATAATAATT 1 AAAATAAATAATAATT 4032214 TTGGGATTTA Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 2 0.13 17 13 0.87 ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27 Consensus pattern (17 bp): AAAATAAATAATAATTC Found at i:4044163 original size:22 final size:22 Alignment explanation

Indices: 4044107--4044163 Score: 62 Period size: 22 Copynumber: 2.6 Consensus size: 22 4044097 ATATCCAAAC * 4044107 AATAATAATAAAATAGTAGCAA 1 AATAATAATAAAATAGCAGCAA * * 4044129 TATAATAGTAAAATTA-CAGCAA 1 AATAATAATAAAA-TAGCAGCAA * 4044151 AATAATAACAAAA 1 AATAATAATAAAA 4044164 AAAATTAGGT Statistics Matches: 28, Mismatches: 6, Indels: 2 0.78 0.17 0.06 Matches are distributed among these distances: 22 26 0.93 23 2 0.07 ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23 Consensus pattern (22 bp): AATAATAATAAAATAGCAGCAA Found at i:4050013 original size:2 final size:2 Alignment explanation

Indices: 4050001--4050035 Score: 61 Period size: 2 Copynumber: 17.5 Consensus size: 2 4049991 AAGTACTTTT * 4050001 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 4050036 TTCAAGAACA Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): TA Found at i:4052952 original size:42 final size:43 Alignment explanation

Indices: 4052900--4053112 Score: 288 Period size: 43 Copynumber: 5.0 Consensus size: 43 4052890 TTTGTTAATA * * * * 4052900 TTAGTGGCGTTTGTGGGAAAA-TGCCACTAAAGACCATGTTCT 1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT * * * 4052942 TTAGCGGCGTTTGCGGGAAAAGTGCCGCTAAAGATCATGGTCT 1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT * 4052985 TTAGCGGCGTTTGT-GGAATAAGCGCCGCTAAAGATCGTGTTCT 1 TTAGCGGCGTTTGTGGGAA-AAGCGCCGCTAAAGATCATGTTCT * * * 4053028 TTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAGATCGTGTTCT 1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT * 4053071 TTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGACCATGTTCT 1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT 4053113 ATAACGGCAT Statistics Matches: 153, Mismatches: 15, Indels: 6 0.88 0.09 0.03 Matches are distributed among these distances: 42 47 0.31 43 103 0.67 44 3 0.02 ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28 Consensus pattern (43 bp): TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT Found at i:4059154 original size:29 final size:29 Alignment explanation

Indices: 4059064--4059208 Score: 104 Period size: 30 Copynumber: 4.9 Consensus size: 29 4059054 GACACTTTAA * 4059064 GGGTAAAATGGTAATTTTTAGAAA-ATTTG 1 GGGTAAAATGGTAATTTTT-GAAAGTTTTG * * ** 4059093 AGGTCAAAAATGGT-ATTTTTGGACA--TCCG 1 GGGT--AAAATGGTAATTTTT-GAAAGTTTTG 4059122 GGGTAAAATGGTAATTTTTGAAAGTTTTG 1 GGGTAAAATGGTAATTTTTGAAAGTTTTG * 4059151 GGGTCAAAAAT-GTAATTTTTGAAAGTTTAG 1 GGGT--AAAATGGTAATTTTTGAAAGTTTTG * * 4059181 GGGCAAAAAT-GTGATTTTTGAAAAGTTT 1 GGG-TAAAATGGTAATTTTTG-AAAGTTT 4059209 AGGTTTTCAA Statistics Matches: 95, Mismatches: 12, Indels: 17 0.77 0.10 0.14 Matches are distributed among these distances: 27 11 0.12 28 6 0.06 29 28 0.29 30 37 0.39 31 13 0.14 ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37 Consensus pattern (29 bp): GGGTAAAATGGTAATTTTTGAAAGTTTTG Found at i:4059168 original size:30 final size:29 Alignment explanation

Indices: 4059126--4059211 Score: 127 Period size: 30 Copynumber: 2.9 Consensus size: 29 4059116 CATCCGGGGT * 4059126 AAAATGGTAATTTTTGAAAGTTTTGGGGTCA 1 AAAAT-GTAATTTTTGAAAGTTTAGGGG-CA 4059157 AAAATGTAATTTTTGAAAGTTTAGGGGCA 1 AAAATGTAATTTTTGAAAGTTTAGGGGCA * 4059186 AAAATGTGATTTTTGAAAAGTTTAGG 1 AAAATGTAATTTTTG-AAAGTTTAGG 4059212 TTTTCAATGC Statistics Matches: 52, Mismatches: 2, Indels: 3 0.91 0.04 0.05 Matches are distributed among these distances: 29 16 0.31 30 31 0.60 31 5 0.10 ACGTcount: A:0.36, C:0.02, G:0.24, T:0.37 Consensus pattern (29 bp): AAAATGTAATTTTTGAAAGTTTAGGGGCA Found at i:4059259 original size:30 final size:30 Alignment explanation

Indices: 4059135--4059259 Score: 91 Period size: 30 Copynumber: 4.2 Consensus size: 30 4059125 TAAAATGGTA * 4059135 ATTTTTGAAA-GTTTTGGGGTCAAAA-ATG 1 ATTTTTGAAATGTTTAGGGGTCAAAATATG * 4059163 TAATTTTTGAAA-GTTTAGGGG-CAAAAATGTG 1 --ATTTTTGAAATGTTTAGGGGTC-AAAATATG * ** *** 4059194 ATTTTTGAAAAGTTTAGGTTTTC--AATGCA 1 ATTTTTGAAATGTTTAGG-GGTCAAAATATG * 4059223 ATTTTTGAAATCTTTAGGGGTCAAAATATG 1 ATTTTTGAAATGTTTAGGGGTCAAAATATG 4059253 ATTTTTG 1 ATTTTTG 4059260 GATAGTCTAA Statistics Matches: 75, Mismatches: 13, Indels: 14 0.74 0.13 0.14 Matches are distributed among these distances: 28 2 0.03 29 31 0.41 30 39 0.52 31 2 0.03 32 1 0.01 ACGTcount: A:0.32, C:0.05, G:0.22, T:0.42 Consensus pattern (30 bp): ATTTTTGAAATGTTTAGGGGTCAAAATATG Found at i:4061231 original size:433 final size:433 Alignment explanation

Indices: 4060425--4061279 Score: 1674 Period size: 433 Copynumber: 2.0 Consensus size: 433 4060415 TTACATAGTT 4060425 ATCATAAAATATTTAGAAATTAATAATAAATAATAATAACCGGTGACTGTATTAATATGCTAGTT 1 ATCATAAAATATTTAGAAATTAATAATAAATAATAATAACCGGTGACTGTATTAATATGCTAGTT 4060490 AATGCATATGAAACGTTGTAAACCTTAAACAAGAACTTAAACAAACAATGAATATACCTCTAGAA 66 AATGCATATGAAACGTTGTAAACCTTAAACAAGAACTTAAACAAACAATGAATATACCTCTAGAA 4060555 CCAGTGTTGTTTGGTTGCTTGGATCTGTTGGGCTTTAATTCTTGACTTTGGATGCTCTTCCTTCT 131 CCAGTGTTGTTTGGTTGCTTGGATCTGTTGGGCTTTAATTCTTGACTTTGGATGCTCTTCCTTCT 4060620 GTATTTGAATTGAAACTATCCGATTAATTGCCAATAGTCTCTGTATCTAAAGAAAACTAGTAACT 196 GTATTTGAATTGAAACTATCCGATTAATTGCCAATAGTCTCTGTATCTAAAGAAAACTAGTAACT 4060685 GTGTATTGATTTTTGAATGTTCCAAAGGTCAGTAACCTCCTACAATTTATTTCAATTCTGGCTTT 261 GTGTATTGATTTTTGAATGTTCCAAAGGTCAGTAACCTCCTACAATTTATTTCAATTCTGGCTTT * 4060750 ATAGCCATGTTTACAATCATCTTATTTTGTTTTCTTCTAACTAAATGCTTGTCTTCTTTTCTTTT 326 ATAGCCATGTTTACAATCATCTTATTTTGTTTTCTTCTAACTAAATGCTTGTCTTCTCTTCTTTT 4060815 TGCAGGTCGACTTACAGTGGTCGCTGTGGCAGGTCGGTTTACA 391 TGCAGGTCGACTTACAGTGGTCGCTGTGGCAGGTCGGTTTACA 4060858 ATCATAAAATATTTAGAAATTAATAATAAATAATAATAACCGGTGACTGTATTAATATGCTAGTT 1 ATCATAAAATATTTAGAAATTAATAATAAATAATAATAACCGGTGACTGTATTAATATGCTAGTT * 4060923 AATGCATATGAAACGTTGTAAACCTTAAACAAGAACTTAAACAAACAATGAATATACCTTTAGAA 66 AATGCATATGAAACGTTGTAAACCTTAAACAAGAACTTAAACAAACAATGAATATACCTCTAGAA 4060988 CCAGTGTTGTTTGGTTGCTTGGATCTGTTGGGCTTTAATTCTTGACTTTGGATGCTCTTCCTTCT 131 CCAGTGTTGTTTGGTTGCTTGGATCTGTTGGGCTTTAATTCTTGACTTTGGATGCTCTTCCTTCT 4061053 GTATTTGAATTGAAACTATCCGATTAATTGCCAATAGTCTCTGTATCTAAAGAAAACTAGTAACT 196 GTATTTGAATTGAAACTATCCGATTAATTGCCAATAGTCTCTGTATCTAAAGAAAACTAGTAACT 4061118 GTGTATTGATTTTTGAATGTTCCAAAGGTCAGTAACCTCCTACAATTTATTTCAATTCTGGCTTT 261 GTGTATTGATTTTTGAATGTTCCAAAGGTCAGTAACCTCCTACAATTTATTTCAATTCTGGCTTT 4061183 ATAGCCATGTTTACAATCATCTTATTTTGTTTTCTTCTAACTAAATGCTTGTCTTCTCTTCTTTT 326 ATAGCCATGTTTACAATCATCTTATTTTGTTTTCTTCTAACTAAATGCTTGTCTTCTCTTCTTTT * * 4061248 TGCAGGTCGGCTTACAGTGGTGGCTGTGGCAG 391 TGCAGGTCGACTTACAGTGGTCGCTGTGGCAG 4061280 TGACGGTGCA Statistics Matches: 418, Mismatches: 4, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 433 418 1.00 ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38 Consensus pattern (433 bp): ATCATAAAATATTTAGAAATTAATAATAAATAATAATAACCGGTGACTGTATTAATATGCTAGTT AATGCATATGAAACGTTGTAAACCTTAAACAAGAACTTAAACAAACAATGAATATACCTCTAGAA CCAGTGTTGTTTGGTTGCTTGGATCTGTTGGGCTTTAATTCTTGACTTTGGATGCTCTTCCTTCT GTATTTGAATTGAAACTATCCGATTAATTGCCAATAGTCTCTGTATCTAAAGAAAACTAGTAACT GTGTATTGATTTTTGAATGTTCCAAAGGTCAGTAACCTCCTACAATTTATTTCAATTCTGGCTTT ATAGCCATGTTTACAATCATCTTATTTTGTTTTCTTCTAACTAAATGCTTGTCTTCTCTTCTTTT TGCAGGTCGACTTACAGTGGTCGCTGTGGCAGGTCGGTTTACA Found at i:4061538 original size:23 final size:22 Alignment explanation

Indices: 4061498--4061540 Score: 68 Period size: 23 Copynumber: 1.9 Consensus size: 22 4061488 TTGGACATTA * 4061498 TAAATTTAAATAATTTTAAACT 1 TAAATTTAAATAAATTTAAACT 4061520 TAAATTTATAATAAATTTAAA 1 TAAATTTA-AATAAATTTAAA 4061541 TTCTGTTGAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 22 8 0.42 23 11 0.58 ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44 Consensus pattern (22 bp): TAAATTTAAATAAATTTAAACT Found at i:4069013 original size:13 final size:13 Alignment explanation

Indices: 4068997--4069021 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 4068987 ATTAAAGACA 4068997 ATAATTTTTATTG 1 ATAATTTTTATTG 4069010 ATAATTTTTATT 1 ATAATTTTTATT 4069022 TAAAACATCA 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:0.32, C:0.00, G:0.04, T:0.64 Consensus pattern (13 bp): ATAATTTTTATTG Found at i:4077810 original size:24 final size:24 Alignment explanation

Indices: 4077783--4077846 Score: 67 Period size: 24 Copynumber: 2.7 Consensus size: 24 4077773 TAATCTAGAG * 4077783 TAATAAGAGTTTGACTCAAACAAA 1 TAATAAGAGTTTAACTCAAACAAA * * * 4077807 TAATTAGAGTTTAATTGAAACAAA 1 TAATAAGAGTTTAACTCAAACAAA * 4077831 TAA-ACAAAGTTTAACT 1 TAATA-AGAGTTTAACT 4077847 GAAAGACTAT Statistics Matches: 32, Mismatches: 7, Indels: 2 0.78 0.17 0.05 Matches are distributed among these distances: 24 32 1.00 ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30 Consensus pattern (24 bp): TAATAAGAGTTTAACTCAAACAAA Found at i:4077849 original size:24 final size:24 Alignment explanation

Indices: 4077790--4077850 Score: 68 Period size: 24 Copynumber: 2.5 Consensus size: 24 4077780 GAGTAATAAG * * ** * 4077790 AGTTTGACTCAAACAAATAATTAG 1 AGTTTAACTGAAACAAATAAACAA * 4077814 AGTTTAATTGAAACAAATAAACAA 1 AGTTTAACTGAAACAAATAAACAA 4077838 AGTTTAACTGAAA 1 AGTTTAACTGAAA 4077851 GACTATTTCT Statistics Matches: 30, Mismatches: 7, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 24 30 1.00 ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28 Consensus pattern (24 bp): AGTTTAACTGAAACAAATAAACAA Found at i:4089234 original size:185 final size:186 Alignment explanation

Indices: 4088921--4089356 Score: 732 Period size: 185 Copynumber: 2.3 Consensus size: 186 4088911 AAAGTTTCGA * * * * 4088921 AGTATAGTGGTAAGAATTCCCACCTGTCACGCGGGTGACCCGGATTCGATCCCCGGCAACAGCGA 1 AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA * 4088986 CCGTGTATATTTGTTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATATCAGAT 66 CCGTGTATATTTATTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATATCAGAT ** * ** 4089051 TTATTTTGAATCAATCA-AGTTTTGTCAAATCCTCGTACTAACAACAAAGTCGTTGT 131 TTAGATTGAATCAATCATA-TCTTGTCAAATCCTCACACTAACAACAAAGTCGTTGT 4089107 AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCG- 1 AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA * 4089171 CCGTGTTTATTTATTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATATCAGAT 66 CCGTGTATATTTATTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATATCAGAT * * 4089236 TTAGATTGAATCAATCATATCTTGTCAAATCCTTACACTAACATCAAAGTCGTTGT 131 TTAGATTGAATCAATCATATCTTGTCAAATCCTCACACTAACAACAAAGTCGTTGT 4089292 AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA 1 AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA 4089357 TCTGTTTTTG Statistics Matches: 235, Mismatches: 13, Indels: 4 0.93 0.05 0.02 Matches are distributed among these distances: 185 174 0.74 186 61 0.26 ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33 Consensus pattern (186 bp): AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA CCGTGTATATTTATTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATATCAGAT TTAGATTGAATCAATCATATCTTGTCAAATCCTCACACTAACAACAAAGTCGTTGT Found at i:4098159 original size:19 final size:20 Alignment explanation

Indices: 4098127--4098167 Score: 66 Period size: 19 Copynumber: 2.1 Consensus size: 20 4098117 GGTTAATATG * 4098127 ATTTTAATATATTATTTTTA 1 ATTTTAATATATTATTTATA 4098147 ATTTTAA-ATATTATTTATA 1 ATTTTAATATATTATTTATA 4098166 AT 1 AT 4098168 ATATATAGTT Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 19 13 0.65 20 7 0.35 ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (20 bp): ATTTTAATATATTATTTATA Found at i:4099749 original size:9 final size:9 Alignment explanation

Indices: 4099735--4099762 Score: 56 Period size: 9 Copynumber: 3.1 Consensus size: 9 4099725 AAGACAACGG 4099735 TTCTTCCAA 1 TTCTTCCAA 4099744 TTCTTCCAA 1 TTCTTCCAA 4099753 TTCTTCCAA 1 TTCTTCCAA 4099762 T 1 T 4099763 CACATCCAAA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 19 1.00 ACGTcount: A:0.21, C:0.32, G:0.00, T:0.46 Consensus pattern (9 bp): TTCTTCCAA Found at i:4105985 original size:21 final size:22 Alignment explanation

Indices: 4105959--4106006 Score: 62 Period size: 21 Copynumber: 2.2 Consensus size: 22 4105949 TTATAAAATG * * 4105959 ATTTTATTTTATGA-ATTTTAA 1 ATTTTATTTGATAATATTTTAA 4105980 ATTTTATTTGATAATATTTTAA 1 ATTTTATTTGATAATATTTTAA * 4106002 GTTTT 1 ATTTT 4106007 TTAAAAATAT Statistics Matches: 23, Mismatches: 3, Indels: 1 0.85 0.11 0.04 Matches are distributed among these distances: 21 12 0.52 22 11 0.48 ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62 Consensus pattern (22 bp): ATTTTATTTGATAATATTTTAA Found at i:4106600 original size:42 final size:42 Alignment explanation

Indices: 4106553--4106634 Score: 164 Period size: 42 Copynumber: 2.0 Consensus size: 42 4106543 TTTACAAACA 4106553 TTCTGTAAATAGTTCTGGAAGTACATAAGTATTGGGATAACT 1 TTCTGTAAATAGTTCTGGAAGTACATAAGTATTGGGATAACT 4106595 TTCTGTAAATAGTTCTGGAAGTACATAAGTATTGGGATAA 1 TTCTGTAAATAGTTCTGGAAGTACATAAGTATTGGGATAA 4106635 TTTAATATTT Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 42 40 1.00 ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35 Consensus pattern (42 bp): TTCTGTAAATAGTTCTGGAAGTACATAAGTATTGGGATAACT Found at i:4110285 original size:32 final size:32 Alignment explanation

Indices: 4110249--4110325 Score: 145 Period size: 32 Copynumber: 2.4 Consensus size: 32 4110239 TAATAATTAA * 4110249 AGAAACACAAGCAATATCATATAAGCCCTTGC 1 AGAAACACAAGCAAGATCATATAAGCCCTTGC 4110281 AGAAACACAAGCAAGATCATATAAGCCCTTGC 1 AGAAACACAAGCAAGATCATATAAGCCCTTGC 4110313 AGAAACACAAGCA 1 AGAAACACAAGCA 4110326 CAACACATAA Statistics Matches: 44, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 32 44 1.00 ACGTcount: A:0.47, C:0.25, G:0.14, T:0.14 Consensus pattern (32 bp): AGAAACACAAGCAAGATCATATAAGCCCTTGC Found at i:4115707 original size:30 final size:29 Alignment explanation

Indices: 4115673--4115796 Score: 167 Period size: 30 Copynumber: 4.1 Consensus size: 29 4115663 CATTCAAACA 4115673 GGGTTAAATTTGAATTTTTAAAAATTTTAG 1 GGGTTAAATTTGAATTTTTAAAAA-TTTAG 4115703 GGGTTAAATTTGAATTTTTGAAAAATTTAG 1 GGGTTAAATTTGAATTTTT-AAAAATTTAG * * 4115733 GGGTGAAATTTGAATTTTTAGAAAATTTGG 1 GGGTTAAATTTGAATTTTTA-AAAATTTAG * * * 4115763 GGGTCAAATTTGAATTTTTGAAAACTTTGG 1 GGGTTAAATTTGAATTTTT-AAAAATTTAG 4115793 GGGT 1 GGGT 4115797 CAAAAAATGA Statistics Matches: 87, Mismatches: 4, Indels: 6 0.90 0.04 0.06 Matches are distributed among these distances: 29 1 0.01 30 80 0.92 31 6 0.07 ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42 Consensus pattern (29 bp): GGGTTAAATTTGAATTTTTAAAAATTTAG Found at i:4115772 original size:60 final size:60 Alignment explanation

Indices: 4115673--4115796 Score: 187 Period size: 60 Copynumber: 2.1 Consensus size: 60 4115663 CATTCAAACA * * 4115673 GGGTTAAATTTGAATTTTTAAAAATTTTAGGGGTTAAATTTGAATTTTTGAAAAATTTAG 1 GGGTGAAATTTGAATTTTTAAAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAG * * * 4115733 GGGTGAAATTTGAATTTTTAGAAAA-TTTGGGGGTCAAATTTGAATTTTTGAAAACTTTGG 1 GGGTGAAATTTGAATTTTTA-AAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAG 4115793 GGGT 1 GGGT 4115797 CAAAAAATGA Statistics Matches: 58, Mismatches: 5, Indels: 2 0.89 0.08 0.03 Matches are distributed among these distances: 60 54 0.93 61 4 0.07 ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42 Consensus pattern (60 bp): GGGTGAAATTTGAATTTTTAAAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAG Found at i:4115810 original size:29 final size:29 Alignment explanation

Indices: 4115683--4115810 Score: 105 Period size: 30 Copynumber: 4.3 Consensus size: 29 4115673 GGGTTAAATT * * * ** 4115683 TGAATTTTTAAAAATTTTAGGGGTTAAATT 1 TGAATTTTTGAAAA-TTTGGGGGTCAAAAA * * ** 4115713 TGAATTTTTGAAAAATTTAGGGGTGAAATT 1 TGAATTTTTG-AAAATTTGGGGGTCAAAAA ** 4115743 TGAATTTTTAGAAAATTTGGGGGTCAAATT 1 TGAATTTTT-GAAAATTTGGGGGTCAAAAA 4115773 TGAATTTTTGAAAACTTTGGGGGTCAAAAAA 1 TGAATTTTTGAAAA-TTTGGGGGTC-AAAAA 4115804 TG-ATTTT 1 TGAATTTT 4115811 AAAATAAATC Statistics Matches: 88, Mismatches: 6, Indels: 8 0.86 0.06 0.08 Matches are distributed among these distances: 29 5 0.06 30 73 0.83 31 10 0.11 ACGTcount: A:0.35, C:0.02, G:0.21, T:0.41 Consensus pattern (29 bp): TGAATTTTTGAAAATTTGGGGGTCAAAAA Found at i:4115810 original size:60 final size:60 Alignment explanation

Indices: 4115683--4115814 Score: 162 Period size: 60 Copynumber: 2.2 Consensus size: 60 4115673 GGGTTAAATT * * ** 4115683 TGAATTTTTAAAAATTTTAGGGGTTAAATTTGAATTTTTGAAAAATTTAGGGGTGAAATT 1 TGAATTTTTAAAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAGGGGTAAAAAA * * * 4115743 TGAATTTTTAGAAAA-TTTGGGGGTCAAATTTGAATTTTTGAAAACTTTGGGGGTCAAAAAA 1 TGAATTTTTA-AAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAGGGGT-AAAAAA 4115804 TG-A-TTTTAAAA 1 TGAATTTTTAAAA 4115815 TAAATCAAGG Statistics Matches: 63, Mismatches: 7, Indels: 6 0.83 0.09 0.08 Matches are distributed among these distances: 58 3 0.05 59 5 0.08 60 46 0.73 61 9 0.14 ACGTcount: A:0.37, C:0.02, G:0.20, T:0.40 Consensus pattern (60 bp): TGAATTTTTAAAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAGGGGTAAAAAA Found at i:4116580 original size:11 final size:11 Alignment explanation

Indices: 4116564--4116588 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 4116554 TTTATTTATT 4116564 TAATAAATAAA 1 TAATAAATAAA 4116575 TAATAAATAAA 1 TAATAAATAAA 4116586 TAA 1 TAA 4116589 AATAATAAAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28 Consensus pattern (11 bp): TAATAAATAAA Found at i:4116732 original size:33 final size:33 Alignment explanation

Indices: 4116690--4116757 Score: 111 Period size: 33 Copynumber: 2.1 Consensus size: 33 4116680 TCTCTTGTCG 4116690 TATTTGTGGTTATGAATAGAAAA-ATATATTGCA 1 TATTTGTGGTTATGAATA-AAAAGATATATTGCA * 4116723 TATTTGTGGTTATGAATAAAAAGATATTTTGCA 1 TATTTGTGGTTATGAATAAAAAGATATATTGCA 4116756 TA 1 TA 4116758 GTTTAATAGC Statistics Matches: 33, Mismatches: 1, Indels: 2 0.92 0.03 0.06 Matches are distributed among these distances: 32 4 0.12 33 29 0.88 ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41 Consensus pattern (33 bp): TATTTGTGGTTATGAATAAAAAGATATATTGCA Found at i:4133141 original size:3 final size:3 Alignment explanation

Indices: 4133133--4133170 Score: 76 Period size: 3 Copynumber: 12.7 Consensus size: 3 4133123 ATTTATTGAT 4133133 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 4133171 TTAAAGTGTG Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TTA Found at i:4135954 original size:18 final size:18 Alignment explanation

Indices: 4135917--4135951 Score: 54 Period size: 17 Copynumber: 2.0 Consensus size: 18 4135907 ATGTTATGTG 4135917 AAAAATATAAAAAAAATT 1 AAAAATATAAAAAAAATT * 4135935 AAAAATA-AAAATAAATT 1 AAAAATATAAAAAAAATT 4135952 TAACATATTA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 9 0.56 18 7 0.44 ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23 Consensus pattern (18 bp): AAAAATATAAAAAAAATT Found at i:4145879 original size:25 final size:24 Alignment explanation

Indices: 4145836--4145900 Score: 71 Period size: 25 Copynumber: 2.8 Consensus size: 24 4145826 ATCACTAATT * * 4145836 ACCAAAAAAAAATACAAAAACAAAA 1 ACCAAAAAAAAAGAGAAAAA-AAAA ** 4145861 ACCAAAAAAAAAGAGAAAAAACCA 1 ACCAAAAAAAAAGAGAAAAAAAAA 4145885 A--AAAAAAAAAGAGAAA 1 ACCAAAAAAAAAGAGAAA 4145901 CCTAAGTATG Statistics Matches: 36, Mismatches: 4, Indels: 3 0.84 0.09 0.07 Matches are distributed among these distances: 22 15 0.42 24 3 0.08 25 18 0.50 ACGTcount: A:0.80, C:0.12, G:0.06, T:0.02 Consensus pattern (24 bp): ACCAAAAAAAAAGAGAAAAAAAAA Found at i:4145880 original size:26 final size:26 Alignment explanation

Indices: 4145836--4145888 Score: 72 Period size: 25 Copynumber: 2.0 Consensus size: 26 4145826 ATCACTAATT * * 4145836 ACCAAAAAAAAATACAAAAA-CAAAA 1 ACCAAAAAAAAAGAAAAAAACCAAAA 4145861 ACCAAAAAAAAAGAGAAAAAACCAAAA 1 ACCAAAAAAAAAGA-AAAAAACCAAAA 4145888 A 1 A 4145889 AAAAAAGAGA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 25 13 0.54 26 5 0.21 27 6 0.25 ACGTcount: A:0.79, C:0.15, G:0.04, T:0.02 Consensus pattern (26 bp): ACCAAAAAAAAAGAAAAAAACCAAAA Found at i:4148857 original size:21 final size:21 Alignment explanation

Indices: 4148811--4148858 Score: 53 Period size: 21 Copynumber: 2.3 Consensus size: 21 4148801 TCAATCCTAA * * 4148811 AATATATTATTATTTTATTTT 1 AATATATTATTACTTTATTAT * 4148832 GATATATTATGTACTTTA-TAT 1 AATATATTAT-TACTTTATTAT 4148853 AATATA 1 AATATA 4148859 AAATTTAAAT Statistics Matches: 22, Mismatches: 4, Indels: 2 0.79 0.14 0.07 Matches are distributed among these distances: 21 16 0.73 22 6 0.27 ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56 Consensus pattern (21 bp): AATATATTATTACTTTATTAT Found at i:4150079 original size:20 final size:20 Alignment explanation

Indices: 4150054--4150093 Score: 80 Period size: 20 Copynumber: 2.0 Consensus size: 20 4150044 TAATTCAACG 4150054 CAGGGGTGTAATTAGGGGGC 1 CAGGGGTGTAATTAGGGGGC 4150074 CAGGGGTGTAATTAGGGGGC 1 CAGGGGTGTAATTAGGGGGC 4150094 TATCAGGGCC Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.20, C:0.10, G:0.50, T:0.20 Consensus pattern (20 bp): CAGGGGTGTAATTAGGGGGC Found at i:4150217 original size:31 final size:32 Alignment explanation

Indices: 4150141--4150217 Score: 81 Period size: 31 Copynumber: 2.5 Consensus size: 32 4150131 CATTTAGGTT * * 4150141 TTTTAAAATTT-TTAAAAATTGCATTTTGATC 1 TTTTAAAATTTATAAAAAATTGCATTTTAATC * * 4150172 CTTTAAAA-TGATAAAAAATTTG-A-TTTAATC 1 TTTTAAAATTTATAAAAAA-TTGCATTTTAATC 4150202 TTTTAAAATTTATAAA 1 TTTTAAAATTTATAAA 4150218 GATATAAACT Statistics Matches: 37, Mismatches: 6, Indels: 6 0.76 0.12 0.12 Matches are distributed among these distances: 30 14 0.38 31 20 0.54 32 3 0.08 ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47 Consensus pattern (32 bp): TTTTAAAATTTATAAAAAATTGCATTTTAATC Found at i:4152905 original size:29 final size:30 Alignment explanation

Indices: 4152831--4152995 Score: 212 Period size: 30 Copynumber: 5.6 Consensus size: 30 4152821 CAAAAAATGA * * 4152831 GGTCAAAAATGAAATTTTGG-AAAG-TTCGG 1 GGTC-AAAATGTAATTTTGGAAAAGTTTTGG * 4152860 AGGT-AAAATATAATTTT-GAAAAGTTTTGG 1 -GGTCAAAATGTAATTTTGGAAAAGTTTTGG 4152889 GGTCAAAATGTAATTTTGGAAAAGTTTTGG 1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG * 4152919 GGTCAAAATGTAATTTTGGAAAAGTTTTAG 1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG * * * 4152949 GGTTAAAATATAATTTTGGAAAAGTTTTAG 1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG * 4152979 GATCAAAATGTAATTTT 1 GGTCAAAATGTAATTTT 4152996 TGGACAATTT Statistics Matches: 121, Mismatches: 10, Indels: 8 0.87 0.07 0.06 Matches are distributed among these distances: 27 1 0.01 28 18 0.15 29 16 0.13 30 86 0.71 ACGTcount: A:0.38, C:0.03, G:0.22, T:0.36 Consensus pattern (30 bp): GGTCAAAATGTAATTTTGGAAAAGTTTTGG Found at i:4152907 original size:19 final size:19 Alignment explanation

Indices: 4152883--4152937 Score: 54 Period size: 19 Copynumber: 3.3 Consensus size: 19 4152873 TTTTGAAAAG 4152883 TTTTGGGGTCAAAATGTAA 1 TTTTGGGGTCAAAATGTAA 4152902 TTTT--GG--AAAA-G--- 1 TTTTGGGGTCAAAATGTAA 4152913 TTTTGGGGTCAAAATGTAA 1 TTTTGGGGTCAAAATGTAA 4152932 TTTTGG 1 TTTTGG 4152938 AAAAGTTTTA Statistics Matches: 28, Mismatches: 0, Indels: 16 0.64 0.00 0.36 Matches are distributed among these distances: 11 4 0.14 13 2 0.07 14 1 0.04 15 8 0.29 16 1 0.04 17 2 0.07 19 10 0.36 ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40 Consensus pattern (19 bp): TTTTGGGGTCAAAATGTAA Found at i:4155049 original size:6 final size:6 Alignment explanation

Indices: 4155040--4155150 Score: 106 Period size: 6 Copynumber: 18.8 Consensus size: 6 4155030 TTTTTTAATG * ** * 4155040 TTAAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- TTAAAT 1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT * 4155088 TTAAAT AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAA- -TAAAT 1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT * 4155135 TTAAA- ATAAAT TTAAA 1 TTAAAT TTAAAT TTAAA 4155151 ATCAATTTAA Statistics Matches: 87, Mismatches: 10, Indels: 16 0.77 0.09 0.14 Matches are distributed among these distances: 4 4 0.05 5 12 0.14 6 60 0.69 7 5 0.06 8 6 0.07 ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47 Consensus pattern (6 bp): TTAAAT Found at i:4155075 original size:31 final size:30 Alignment explanation

Indices: 4155065--4155172 Score: 109 Period size: 31 Copynumber: 3.7 Consensus size: 30 4155055 TAATTTTTAT * 4155065 TTAAATTTAAATTCAAATTAAATTTAAATAA 1 TTAAATTTAAATTTAAATTAAATTT-AATAA * * 4155096 TTAAATTTAAATTTAAAATAAATTTAA-AT 1 TTAAATTTAAATTTAAATTAAATTTAATAA * 4155125 TTAAA--TAAATTTAAAATAAATTTAA-AA 1 TTAAATTTAAATTTAAATTAAATTTAATAA * * * 4155152 -TCAATTTAACTCTAAATTAAA 1 TTAAATTTAAATTTAAATTAAA 4155173 CGAAAAGTCC Statistics Matches: 67, Mismatches: 8, Indels: 7 0.82 0.10 0.09 Matches are distributed among these distances: 26 3 0.04 27 21 0.31 28 12 0.18 29 6 0.09 30 2 0.03 31 23 0.34 ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41 Consensus pattern (30 bp): TTAAATTTAAATTTAAATTAAATTTAATAA Found at i:4155083 original size:37 final size:36 Alignment explanation

Indices: 4155041--4155160 Score: 111 Period size: 37 Copynumber: 3.2 Consensus size: 36 4155031 TTTTTAATGT * ** * 4155041 TAAATTTAATATTTTAAT-TTTTATTTAAATTTAAAT 1 TAAATTTAA-ATTTAAATATTAAATTTAAATTTAAAA 4155077 TCAAA-TTAAATTTAAATAATTAAATTTAAATTTAAAA 1 T-AAATTTAAATTTAAAT-ATTAAATTTAAATTTAAAA * 4155114 TAAATTTAAATTTAAATAAATTTAAA-ATAAATTTAAAA 1 TAAATTTAAATTTAAAT--A-TTAAATTTAAATTTAAAA * 4155152 TCAATTTAA 1 TAAATTTAA 4155161 CTCTAAATTA Statistics Matches: 72, Mismatches: 6, Indels: 10 0.82 0.07 0.11 Matches are distributed among these distances: 35 7 0.10 36 8 0.11 37 31 0.43 38 21 0.29 39 5 0.07 ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46 Consensus pattern (36 bp): TAAATTTAAATTTAAATATTAAATTTAAATTTAAAA Found at i:4155085 original size:11 final size:11 Alignment explanation

Indices: 4155063--4155160 Score: 83 Period size: 11 Copynumber: 8.5 Consensus size: 11 4155053 TTTAATTTTT 4155063 ATTTAAATTTAA 1 ATTTAAA-TTAA * 4155075 ATTCAAATTAA 1 ATTTAAATTAA 4155086 ATTTAAATAATTAA 1 ATTT--A-AATTAA 4155100 ATTTAAATTTAA 1 ATTTAAA-TTAA * 4155112 A-ATAAATTTAA 1 ATTTAAA-TTAA 4155123 ATTTAAA-TAA 1 ATTTAAATTAA * 4155133 ATTTAAAATAA 1 ATTTAAATTAA * * 4155144 ATTTAAAATCA 1 ATTTAAATTAA 4155155 ATTTAA 1 ATTTAA 4155161 CTCTAAATTA Statistics Matches: 75, Mismatches: 5, Indels: 13 0.81 0.05 0.14 Matches are distributed among these distances: 10 10 0.13 11 38 0.51 12 16 0.21 13 1 0.01 14 10 0.13 ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42 Consensus pattern (11 bp): ATTTAAATTAA Found at i:4155085 original size:17 final size:17 Alignment explanation

Indices: 4155065--4155139 Score: 104 Period size: 17 Copynumber: 4.6 Consensus size: 17 4155055 TAATTTTTAT * 4155065 TTAAATTTAAATTCAAA 1 TTAAATTTAAATTTAAA 4155082 TTAAATTTAAA--T-AA 1 TTAAATTTAAATTTAAA 4155096 TTAAATTTAAATTTAAA 1 TTAAATTTAAATTTAAA * 4155113 ATAAATTTAAATTTAAA 1 TTAAATTTAAATTTAAA 4155130 -TAAATTTAAA 1 TTAAATTTAAA 4155140 ATAAATTTAA Statistics Matches: 53, Mismatches: 2, Indels: 7 0.85 0.03 0.11 Matches are distributed among these distances: 14 13 0.25 16 11 0.21 17 29 0.55 ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43 Consensus pattern (17 bp): TTAAATTTAAATTTAAA Found at i:4155553 original size:38 final size:36 Alignment explanation

Indices: 4155511--4156107 Score: 311 Period size: 31 Copynumber: 17.4 Consensus size: 36 4155501 ATCTTTCTCT * * 4155511 TACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTC 1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCC-ACTC * * * * * 4155549 TACTTAAATTTCA-AGAGGATGAC-G-T-TGCTCT- 1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC 4155580 TACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTC 1 TACTTCAATTTCAGAGATGAAGA-CTGTTATCC-ACTC * * * * 4155618 TACTTCAATTTCA-AGAGGATGAC-G-T-TGCTCT- 1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC * 4155649 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC 1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC ** * * * * 4155686 TACTTCAATTTCA-AGGGGATGAC--AT-TGCTCT- 1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC * 4155717 TACTTCAATTTCAGAGATGAAGACTTGTTATCCAAGTC 1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCC-ACTC * * * * * * 4155755 TACTTCGATTTCA-ATAGGATGAC-G-T-TGCTCT- 1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC * 4155786 TACTTCAATTTCAGAGATGAAAACGTGTTATCCACTC 1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC * * * * * 4155823 TACTTCAATTTCA-AGAGGATGAC--AT-TGCTCT- 1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC * 4155854 TACTTCAATTTCAGAGATAAAGACTTGTTATCCACTC 1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC * * ** * * * 4155891 AACTTTAATTTCA-AGCGGATGAC-G-T-TGCTCT- 1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC * 4155922 TACTTCAATTTCAGAGATGAAAACGTGTTATCCACTC 1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC * * * * * 4155959 AACTTCAATTTCA-AGAGGATGAC-ATT-T-CTCT- 1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC * * 4155990 TACTTCAATTTCAAAGATGAAGACTTGTTATTCACTC 1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC * * ** * * * 4156027 AACTTTAATTTC-GAGCGGATGAC-G-T-TGCTCT- 1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC * 4156058 TACTTCAATTTTAGAGATGAAGACGTGTTATCCACTC 1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC 4156095 TACTTCAATTTCA 1 TACTTCAATTTCA 4156108 AGCGGGTTGG Statistics Matches: 404, Mismatches: 105, Indels: 101 0.66 0.17 0.17 Matches are distributed among these distances: 31 95 0.24 32 80 0.20 33 12 0.03 34 14 0.03 35 11 0.03 36 61 0.15 37 94 0.23 38 37 0.09 ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35 Consensus pattern (36 bp): TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC Found at i:4156112 original size:68 final size:68 Alignment explanation

Indices: 4155507--4156109 Score: 909 Period size: 68 Copynumber: 8.8 Consensus size: 68 4155497 AATGATCTTT * * * 4155507 CTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTAAATTTCAAGAGGATGAC 1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAC 4155572 GTTG 65 GTTG * 4155576 CTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC 1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAC 4155641 GTTG 65 GTTG * * * 4155645 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACA 1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG 4155710 TTG 66 TTG * * * * 4155713 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAAGTCTACTTCGATTTCAATAGGATGAC 1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAC 4155778 GTTG 65 GTTG * * 4155782 CTCTTACTTCAATTTCAGAGATGAAAACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACA 1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG 4155847 TTG 66 TTG * * * * * 4155850 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCAACTTTAATTTCAAGCGGATGACG 1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG 4155915 TTG 66 TTG * * * 4155918 CTCTTACTTCAATTTCAGAGATGAAAACGTGTTATCCACTCAACTTCAATTTCAAGAGGATGACA 1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG * 4155983 TTT 66 TTG * * * * * * * 4155986 CTCTTACTTCAATTTCAAAGATGAAGACTTGTTATTCACTCAACTTTAATTTCGAGCGGATGACG 1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG 4156051 TTG 66 TTG * 4156054 CTCTTACTTCAATTTTAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAG 1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAG 4156110 CGGGTTGGAA Statistics Matches: 482, Mismatches: 51, Indels: 3 0.90 0.10 0.01 Matches are distributed among these distances: 68 321 0.67 69 161 0.33 ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35 Consensus pattern (68 bp): CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG TTG Found at i:4167984 original size:28 final size:29 Alignment explanation

Indices: 4167953--4168105 Score: 148 Period size: 30 Copynumber: 5.2 Consensus size: 29 4167943 TCAAAAATGA 4167953 AATTTTGGAAAG-TTCGGAGG-CAAAATAT 1 AATTTTGGAAAGTTTCGG-GGTCAAAATAT * * * 4167981 AATTTTGAAAAGTTTTGGGGTCAAAATGT 1 AATTTTGGAAAGTTTCGGGGTCAAAATAT * ** * 4168010 AATTTTGGCAAAATTTTAGGGTCAAAATGT 1 AATTTTGG-AAAGTTTCGGGGTCAAAATAT * ** 4168040 AATTTTGGTAAATTTTTAGGGTCAAAATAT 1 AATTTTGG-AAAGTTTCGGGGTCAAAATAT * * 4168070 AATTTTGGAAAAGTTTTGGGGTTAAAATAT 1 AATTTTGG-AAAGTTTCGGGGTCAAAATAT 4168100 AATTTT 1 AATTTT 4168106 TGGACAATTT Statistics Matches: 109, Mismatches: 13, Indels: 4 0.87 0.10 0.03 Matches are distributed among these distances: 28 13 0.12 29 18 0.17 30 78 0.72 ACGTcount: A:0.37, C:0.04, G:0.21, T:0.39 Consensus pattern (29 bp): AATTTTGGAAAGTTTCGGGGTCAAAATAT Found at i:4168034 original size:30 final size:30 Alignment explanation

Indices: 4167973--4168105 Score: 180 Period size: 30 Copynumber: 4.5 Consensus size: 30 4167963 AGTTCGGAGG * 4167973 CAAAATATAATTTT-GAAAAGTTTTGGGGT 1 CAAAATATAATTTTGGAAAAGTTTTAGGGT * 4168002 CAAAATGTAATTTTGGCAAAA-TTTTAGGGT 1 CAAAATATAATTTTGG-AAAAGTTTTAGGGT * * * 4168032 CAAAATGTAATTTTGGTAAATTTTTAGGGT 1 CAAAATATAATTTTGGAAAAGTTTTAGGGT * 4168062 CAAAATATAATTTTGGAAAAGTTTTGGGGT 1 CAAAATATAATTTTGGAAAAGTTTTAGGGT * 4168092 TAAAATATAATTTT 1 CAAAATATAATTTT 4168106 TGGACAATTT Statistics Matches: 93, Mismatches: 8, Indels: 5 0.88 0.08 0.05 Matches are distributed among these distances: 29 16 0.17 30 73 0.78 31 4 0.04 ACGTcount: A:0.38, C:0.04, G:0.19, T:0.40 Consensus pattern (30 bp): CAAAATATAATTTTGGAAAAGTTTTAGGGT Found at i:4170159 original size:6 final size:6 Alignment explanation

Indices: 4170150--4170249 Score: 91 Period size: 6 Copynumber: 16.8 Consensus size: 6 4170140 TTTTTTAATG * ** * 4170150 TTAAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- TTAAAT 1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT * * 4170198 TTAAAT AATTACAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAA- -TAAAT 1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT 4170245 TTAAA 1 TTAAA 4170250 ATCAATTTAA Statistics Matches: 77, Mismatches: 10, Indels: 14 0.76 0.10 0.14 Matches are distributed among these distances: 4 4 0.05 5 8 0.10 6 55 0.71 7 5 0.06 8 5 0.06 ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48 Consensus pattern (6 bp): TTAAAT Found at i:4170193 original size:37 final size:36 Alignment explanation

Indices: 4170151--4170241 Score: 105 Period size: 37 Copynumber: 2.5 Consensus size: 36 4170141 TTTTTAATGT * ** * 4170151 TAAATTTAATATTTTAAT-TTTTATTTAAATTTAAAT 1 TAAATTTAA-ATTTAAATATTACATTTAAATTTAAAA 4170187 TCAAA-TTAAATTTAAATAATTACATTTAAATTTAAAA 1 T-AAATTTAAATTTAAAT-ATTACATTTAAATTTAAAA 4170224 TAAATTTAAATTTAAATA 1 TAAATTTAAATTTAAATA 4170242 AATTTAAAAT Statistics Matches: 47, Mismatches: 4, Indels: 8 0.80 0.07 0.14 Matches are distributed among these distances: 35 7 0.15 36 9 0.19 37 31 0.66 ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48 Consensus pattern (36 bp): TAAATTTAAATTTAAATATTACATTTAAATTTAAAA Found at i:4170195 original size:17 final size:17 Alignment explanation

Indices: 4170175--4170259 Score: 88 Period size: 17 Copynumber: 5.2 Consensus size: 17 4170165 TAATTTTTAT 4170175 TTAAATTTAAATTCAAA 1 TTAAATTTAAATTCAAA 4170192 TTAAATTTAAA-T--AA 1 TTAAATTTAAATTCAAA * * 4170206 TTACATTTAAATTTAAA 1 TTAAATTTAAATTCAAA * * 4170223 ATAAATTTAAATTTAAA 1 TTAAATTTAAATTCAAA * * 4170240 -TAAATTTAAAATCAAT 1 TTAAATTTAAATTCAAA 4170256 TTAA 1 TTAA 4170260 CTCTAAATTA Statistics Matches: 58, Mismatches: 6, Indels: 8 0.81 0.08 0.11 Matches are distributed among these distances: 14 12 0.21 15 1 0.02 16 14 0.24 17 31 0.53 ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42 Consensus pattern (17 bp): TTAAATTTAAATTCAAA Found at i:4170213 original size:14 final size:14 Alignment explanation

Indices: 4170175--4170242 Score: 56 Period size: 14 Copynumber: 5.0 Consensus size: 14 4170165 TAATTTTTAT 4170175 TTAAATTTAAATTCAAA 1 TTAAATTTAAA-T--AA 4170192 TTAAATTTAAATAA 1 TTAAATTTAAATAA * 4170206 TTACATTTAAAT-- 1 TTAAATTTAAATAA * 4170218 TTAAA-ATAAAT-- 1 TTAAATTTAAATAA 4170229 TTAAATTTAAATAA 1 TTAAATTTAAATAA 4170243 ATTTAAAATC Statistics Matches: 44, Mismatches: 4, Indels: 9 0.77 0.07 0.16 Matches are distributed among these distances: 11 10 0.23 12 9 0.20 14 13 0.30 16 1 0.02 17 11 0.25 ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43 Consensus pattern (14 bp): TTAAATTTAAATAA Found at i:4170266 original size:27 final size:27 Alignment explanation

Indices: 4170213--4170267 Score: 83 Period size: 27 Copynumber: 2.0 Consensus size: 27 4170203 TAATTACATT * 4170213 TAAATTTAAAATAAATTTAAATTTAAA 1 TAAATTTAAAATAAATTTAAATCTAAA * * 4170240 TAAATTTAAAATCAATTTAACTCTAAA 1 TAAATTTAAAATAAATTTAAATCTAAA 4170267 T 1 T 4170268 TAAACGAAAA Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 27 25 1.00 ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40 Consensus pattern (27 bp): TAAATTTAAAATAAATTTAAATCTAAA Found at i:4171532 original size:3 final size:3 Alignment explanation

Indices: 4171524--4171557 Score: 68 Period size: 3 Copynumber: 11.3 Consensus size: 3 4171514 TCAGCCCCAT 4171524 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C 1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C 4171558 TTCTTCGATA Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 31 1.00 ACGTcount: A:0.32, C:0.35, G:0.32, T:0.00 Consensus pattern (3 bp): CAG Found at i:4173526 original size:23 final size:25 Alignment explanation

Indices: 4173480--4173528 Score: 75 Period size: 23 Copynumber: 2.0 Consensus size: 25 4173470 TTTTAATCAT * 4173480 ACTAAAATATAGTAATCAAAATTTA 1 ACTAAAATATAATAATCAAAATTTA 4173505 ACTAAAA-ATAATAAT-AAAATTTA 1 ACTAAAATATAATAATCAAAATTTA 4173528 A 1 A 4173529 TTAGGAGAAG Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 23 9 0.39 24 7 0.30 25 7 0.30 ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31 Consensus pattern (25 bp): ACTAAAATATAATAATCAAAATTTA Found at i:4174179 original size:29 final size:30 Alignment explanation

Indices: 4174141--4174204 Score: 87 Period size: 29 Copynumber: 2.2 Consensus size: 30 4174131 AGTTTATATC * 4174141 TTTATAATTTTTAAAGA-TT-AAATCATAAT 1 TTTATAATTTTTAAAAAGTTAAAAT-ATAAT * 4174170 TTTATTATTTTTAAAAAGTTAAAATATAAT 1 TTTATAATTTTTAAAAAGTTAAAATATAAT 4174200 TTTAT 1 TTTAT 4174205 CTTTATTAAT Statistics Matches: 31, Mismatches: 2, Indels: 3 0.86 0.06 0.08 Matches are distributed among these distances: 29 15 0.48 30 12 0.39 31 4 0.13 ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52 Consensus pattern (30 bp): TTTATAATTTTTAAAAAGTTAAAATATAAT Found at i:4174806 original size:17 final size:18 Alignment explanation

Indices: 4174781--4174819 Score: 53 Period size: 17 Copynumber: 2.2 Consensus size: 18 4174771 TTTATTGATT * 4174781 TATAAAAAAAAA-CTTAA 1 TATAAAAAAAAATCTAAA * 4174798 TATAGAAAAAAATCTAAA 1 TATAAAAAAAAATCTAAA 4174816 TATA 1 TATA 4174820 TAGATTGATT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 17 11 0.58 18 8 0.42 ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26 Consensus pattern (18 bp): TATAAAAAAAAATCTAAA Found at i:4174808 original size:18 final size:17 Alignment explanation

Indices: 4174781--4174819 Score: 51 Period size: 18 Copynumber: 2.2 Consensus size: 17 4174771 TTTATTGATT * 4174781 TATAAAAAAAAACTTAA 1 TATAAAAAAAAACTAAA * 4174798 TATAGAAAAAAATCTAAA 1 TATA-AAAAAAAACTAAA 4174816 TATA 1 TATA 4174820 TAGATTGATT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 17 4 0.21 18 15 0.79 ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26 Consensus pattern (17 bp): TATAAAAAAAAACTAAA Found at i:4177952 original size:25 final size:27 Alignment explanation

Indices: 4177934--4178007 Score: 87 Period size: 27 Copynumber: 2.7 Consensus size: 27 4177924 GGTATTATGA 4177934 TATTTTT-TTTAATTTGGTATTTAAAT 1 TATTTTTGTTTAATTTGGTATTTAAAT * * 4177960 TTTTTTTGTTTAATTTGGTATTTATACT 1 TATTTTTGTTTAATTTGGTATTTA-AAT * 4177988 TGATTCTTGTTTTAATTTGG 1 T-ATTTTTG-TTTAATTTGG 4178008 CATCTAATCT Statistics Matches: 40, Mismatches: 4, Indels: 4 0.83 0.08 0.08 Matches are distributed among these distances: 26 6 0.15 27 16 0.40 28 3 0.08 29 5 0.12 30 10 0.25 ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65 Consensus pattern (27 bp): TATTTTTGTTTAATTTGGTATTTAAAT Found at i:4178215 original size:14 final size:13 Alignment explanation

Indices: 4178186--4178219 Score: 50 Period size: 14 Copynumber: 2.5 Consensus size: 13 4178176 TCAATTACTT * 4178186 TTAATTTTATTTA 1 TTAATTTCATTTA 4178199 TTAATTTCATGTTA 1 TTAATTTCAT-TTA 4178213 TTAATTT 1 TTAATTT 4178220 AAAATAATGA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 13 9 0.47 14 10 0.53 ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65 Consensus pattern (13 bp): TTAATTTCATTTA Found at i:4188199 original size:23 final size:23 Alignment explanation

Indices: 4188181--4188224 Score: 79 Period size: 23 Copynumber: 1.9 Consensus size: 23 4188171 AAGGTTTAAG * 4188181 GTTTGGGTTTGGGATGGTTCAAA 1 GTTTGGGTTTGAGATGGTTCAAA 4188204 GTTTGGGTTTGAGATGGTTCA 1 GTTTGGGTTTGAGATGGTTCA 4188225 TGGTTCATGG Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 23 20 1.00 ACGTcount: A:0.16, C:0.05, G:0.39, T:0.41 Consensus pattern (23 bp): GTTTGGGTTTGAGATGGTTCAAA Found at i:4188764 original size:16 final size:16 Alignment explanation

Indices: 4188739--4188785 Score: 58 Period size: 16 Copynumber: 2.9 Consensus size: 16 4188729 ACCCGAGTCC * ** 4188739 AAAAAAATTCAAATTT 1 AAAAATATTCAAACCT 4188755 AAAAATATTCAAACCT 1 AAAAATATTCAAACCT * 4188771 AAAAATATCCAAACC 1 AAAAATATTCAAACC 4188786 CGGATTGAAT Statistics Matches: 27, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 16 27 1.00 ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23 Consensus pattern (16 bp): AAAAATATTCAAACCT Found at i:4192617 original size:41 final size:41 Alignment explanation

Indices: 4192552--4192637 Score: 100 Period size: 41 Copynumber: 2.1 Consensus size: 41 4192542 GATATTGCGT * * * ** * * 4192552 TGTATATTATCATGCTTTGTGCCTAGTAGGCTTTGTGTCGG 1 TGTATATTATCAGGCCTTGGGCCTAACAAGCTTCGTGTCGG * 4192593 TGTATATTATTAGGCCTTGGGCCTAACAAGCTTCGTGTCGG 1 TGTATATTATCAGGCCTTGGGCCTAACAAGCTTCGTGTCGG 4192634 TGTA 1 TGTA 4192638 ATAAATCAAA Statistics Matches: 37, Mismatches: 8, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 41 37 1.00 ACGTcount: A:0.17, C:0.16, G:0.27, T:0.40 Consensus pattern (41 bp): TGTATATTATCAGGCCTTGGGCCTAACAAGCTTCGTGTCGG Found at i:4193815 original size:31 final size:32 Alignment explanation

Indices: 4193777--4193854 Score: 122 Period size: 31 Copynumber: 2.5 Consensus size: 32 4193767 TTCATTTCAA 4193777 ATATATGAAAAATGTGAAAAATA-TTTATTAG 1 ATATATGAAAAATGTGAAAAATATTTTATTAG * * 4193808 ATGTATGAAAAATGTGAATAATATTTTATTAG 1 ATATATGAAAAATGTGAAAAATATTTTATTAG * 4193840 ATAAATGAAAAATGT 1 ATATATGAAAAATGT 4193855 AAAGAGGAAA Statistics Matches: 42, Mismatches: 4, Indels: 1 0.89 0.09 0.02 Matches are distributed among these distances: 31 21 0.50 32 21 0.50 ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36 Consensus pattern (32 bp): ATATATGAAAAATGTGAAAAATATTTTATTAG Found at i:4194811 original size:114 final size:115 Alignment explanation

Indices: 4194645--4194872 Score: 356 Period size: 114 Copynumber: 2.0 Consensus size: 115 4194635 ATGAAACAAG * 4194645 TTATTAATGGTAGAAAAACTTCTACATAGGTCCTAGTAGTAGTTGTACTTTTTTTTGATGGAATA 1 TTATTAATGGTAGAAAAACTTCTACATAGGTCCTAGTAGTAGCTGTA-TTTTTTTT-ATGGAATA * 4194710 GTATTTG-AAAAAAAA-AA-ATGAAATTGTGATTTCACGTCATTCATATCAA 64 GTATTTGAAAAAAAAACAATATGAAATTATGATTTCACGTCATTCATATCAA * 4194759 TTATTAATGGTAGAAAAAC-TCTTATATAGGTCCTAGTAGTAGCTGTATTTTTTTTATGGAATAG 1 TTATTAATGGTAGAAAAACTTC-TACATAGGTCCTAGTAGTAGCTGTATTTTTTTTATGGAATAG * 4194823 TATTTGAAAAAAAAAACAATATGAAATTATGATTTTACGTCATTCATATC 65 TATTTG-AAAAAAAAACAATATGAAATTATGATTTCACGTCATTCATATC 4194873 CATTTTCAAT Statistics Matches: 105, Mismatches: 4, Indels: 8 0.90 0.03 0.07 Matches are distributed among these distances: 112 15 0.14 113 10 0.10 114 50 0.48 115 2 0.02 116 28 0.27 ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39 Consensus pattern (115 bp): TTATTAATGGTAGAAAAACTTCTACATAGGTCCTAGTAGTAGCTGTATTTTTTTTATGGAATAGT ATTTGAAAAAAAAACAATATGAAATTATGATTTCACGTCATTCATATCAA Found at i:4200536 original size:37 final size:36 Alignment explanation

Indices: 4200487--4200607 Score: 111 Period size: 37 Copynumber: 3.3 Consensus size: 36 4200477 ATGTAATTCT * * * 4200487 TTTTA-ATTTTAAATATAGTTTTAATTTTACCTTTAC 1 TTTTATATATTAAATGTAGTTTTAATTTTA-CTTTAA * * 4200523 TTTTATATATTAAATGTAGTTTATACTTTTATTTTAA 1 TTTTATATATTAAATGTAGTTT-TAATTTTACTTTAA * * * * 4200560 TTATATATCTTATATGTAGTTTTAATTTTAATGCTTAA 1 TTTTATATATTAAATGTAGTTTTAATTTTACT--TTAA 4200598 TTTT-TATATT 1 TTTTATATATT 4200608 TAATTATGTA Statistics Matches: 69, Mismatches: 12, Indels: 7 0.78 0.14 0.08 Matches are distributed among these distances: 36 13 0.19 37 42 0.61 38 14 0.20 ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60 Consensus pattern (36 bp): TTTTATATATTAAATGTAGTTTTAATTTTACTTTAA Found at i:4200572 original size:26 final size:25 Alignment explanation

Indices: 4200543--4200622 Score: 67 Period size: 26 Copynumber: 3.1 Consensus size: 25 4200533 TAAATGTAGT 4200543 TTATACTTTTATTTTAATTATATATC 1 TTATA-TTTTATTTTAATTATATATC * * 4200569 TTATA-TGTAGTTTTAATTTTA-ATGC 1 TTATATTTTA-TTTTAATTATATAT-C * 4200594 TTA-ATTTTTATATTTAATTATGTATC 1 TTATA-TTTTAT-TTTAATTATATATC 4200620 TTA 1 TTA 4200623 AATTGCTTTG Statistics Matches: 43, Mismatches: 5, Indels: 12 0.72 0.08 0.20 Matches are distributed among these distances: 24 6 0.14 25 15 0.35 26 20 0.47 27 2 0.05 ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60 Consensus pattern (25 bp): TTATATTTTATTTTAATTATATATC Found at i:4200785 original size:7 final size:7 Alignment explanation

Indices: 4200775--4200799 Score: 50 Period size: 7 Copynumber: 3.6 Consensus size: 7 4200765 CATTAAAGTA 4200775 TAAATTT 1 TAAATTT 4200782 TAAATTT 1 TAAATTT 4200789 TAAATTT 1 TAAATTT 4200796 TAAA 1 TAAA 4200800 AAAATACATA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (7 bp): TAAATTT Found at i:4201721 original size:22 final size:22 Alignment explanation

Indices: 4201673--4201724 Score: 77 Period size: 22 Copynumber: 2.4 Consensus size: 22 4201663 ATTAACAAAT * * 4201673 TTAACATTAAAATAAATTATTA 1 TTAATATTAAAATAAATTAATA * 4201695 TTAATATTATAATAAATTAATA 1 TTAATATTAAAATAAATTAATA 4201717 TTAATATT 1 TTAATATT 4201725 CATACATGAA Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 27 1.00 ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46 Consensus pattern (22 bp): TTAATATTAAAATAAATTAATA Found at i:4201770 original size:16 final size:16 Alignment explanation

Indices: 4201749--4201780 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 4201739 TTTTGTGTTA * 4201749 TTTTAATATTAAATAT 1 TTTTAAAATTAAATAT 4201765 TTTTAAAATTAAATAT 1 TTTTAAAATTAAATAT 4201781 ATTAATATAA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (16 bp): TTTTAAAATTAAATAT Found at i:4202295 original size:24 final size:25 Alignment explanation

Indices: 4202247--4202296 Score: 66 Period size: 25 Copynumber: 2.0 Consensus size: 25 4202237 AATTAATTTT * 4202247 TAAAAATTTTAAAAACATTTTATAA 1 TAAAAATTTTAAAAACATTTAATAA * * 4202272 TAAAAATTTTAATAA-GTTTAATAA 1 TAAAAATTTTAAAAACATTTAATAA 4202296 T 1 T 4202297 TTTTAATTTT Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 24 8 0.36 25 14 0.64 ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42 Consensus pattern (25 bp): TAAAAATTTTAAAAACATTTAATAA Found at i:4204009 original size:29 final size:29 Alignment explanation

Indices: 4203951--4204011 Score: 79 Period size: 29 Copynumber: 2.1 Consensus size: 29 4203941 TTAATTTAAT * 4203951 AAATGGTAAAATTATACATTTAACTCTTA 1 AAATGATAAAATTATACATTTAACTCTTA * * 4203980 AAATGATAAAATT-TTCATTTAATCTTTTA 1 AAATGATAAAATTATACATTTAA-CTCTTA 4204009 AAA 1 AAA 4204012 ATTATAAATA Statistics Matches: 28, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 28 8 0.29 29 20 0.71 ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41 Consensus pattern (29 bp): AAATGATAAAATTATACATTTAACTCTTA Found at i:4204290 original size:7 final size:8 Alignment explanation

Indices: 4204261--4204295 Score: 52 Period size: 8 Copynumber: 4.2 Consensus size: 8 4204251 ATTAATCTTT 4204261 TAAAAATTA 1 TAAAAA-TA 4204270 TAAAAATA 1 TAAAAATA 4204278 TAAAAATA 1 TAAAAATA * 4204286 TAAAATTA 1 TAAAAATA 4204294 TA 1 TA 4204296 TTTTTATTAT Statistics Matches: 25, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 8 19 0.76 9 6 0.24 ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31 Consensus pattern (8 bp): TAAAAATA Found at i:4216586 original size:22 final size:21 Alignment explanation

Indices: 4216547--4216592 Score: 65 Period size: 22 Copynumber: 2.1 Consensus size: 21 4216537 TAATAAATTG * * 4216547 AATTCAAGATAATTAAATTCA 1 AATTCAAGAAAATCAAATTCA 4216568 AATTACAAGAAAATCAAATTCA 1 AATT-CAAGAAAATCAAATTCA 4216590 AAT 1 AAT 4216593 CGAAAATGAT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 21 4 0.18 22 18 0.82 ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28 Consensus pattern (21 bp): AATTCAAGAAAATCAAATTCA Found at i:4222597 original size:29 final size:28 Alignment explanation

Indices: 4222532--4222597 Score: 69 Period size: 29 Copynumber: 2.3 Consensus size: 28 4222522 CTTCACAAAG 4222532 TTAAAATTTAATCCCTATACTTTTAACT 1 TTAAAATTTAATCCCTATACTTTTAACT * * * * * 4222560 TTAGGAATTTAATTCCTTTATTTTTAGATT 1 TTA-AAATTTAATCCCTATACTTTTA-ACT 4222590 TTAAAATT 1 TTAAAATT 4222598 CAGGTTCGAT Statistics Matches: 30, Mismatches: 6, Indels: 3 0.77 0.15 0.08 Matches are distributed among these distances: 28 3 0.10 29 22 0.73 30 5 0.17 ACGTcount: A:0.33, C:0.11, G:0.05, T:0.52 Consensus pattern (28 bp): TTAAAATTTAATCCCTATACTTTTAACT Found at i:4222870 original size:6 final size:6 Alignment explanation

Indices: 4222854--4222890 Score: 67 Period size: 6 Copynumber: 6.3 Consensus size: 6 4222844 ATATATTTTA 4222854 ATATA- ATATAG ATATAG ATATAG ATATAG ATATAG AT 1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT 4222891 TTTATATAGA Statistics Matches: 31, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 5 5 0.16 6 26 0.84 ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35 Consensus pattern (6 bp): ATATAG Found at i:4222882 original size:18 final size:17 Alignment explanation

Indices: 4222854--4222900 Score: 67 Period size: 18 Copynumber: 2.7 Consensus size: 17 4222844 ATATATTTTA 4222854 ATATAATATAGATATAG 1 ATATAATATAGATATAG 4222871 ATATAGATATAGATATAG 1 ATATA-ATATAGATATAG * * 4222889 ATTTTATATAGA 1 ATATAATATAGA 4222901 ATTGTAGGAA Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 17 12 0.44 18 15 0.56 ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38 Consensus pattern (17 bp): ATATAATATAGATATAG Found at i:4225483 original size:21 final size:22 Alignment explanation

Indices: 4225457--4225507 Score: 61 Period size: 21 Copynumber: 2.3 Consensus size: 22 4225447 TTTAATTCGA * 4225457 TTAATTT-ATCGGTAGTT-AATT 1 TTAATTTGATCAG-AGTTAAATT 4225478 TTAATTTGATCAGAGTTAAATT 1 TTAATTTGATCAGAGTTAAATT 4225500 TATAATTT 1 T-TAATTT 4225508 TTTTAAATTT Statistics Matches: 26, Mismatches: 1, Indels: 4 0.84 0.03 0.13 Matches are distributed among these distances: 21 11 0.42 22 9 0.35 23 6 0.23 ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51 Consensus pattern (22 bp): TTAATTTGATCAGAGTTAAATT Found at i:4228560 original size:21 final size:20 Alignment explanation

Indices: 4228518--4228560 Score: 50 Period size: 21 Copynumber: 2.1 Consensus size: 20 4228508 ATAATATATC * * * 4228518 AAATACACTTAAAAATATTA 1 AAATAAACTTAAAAAAAATA 4228538 AAATAAACATTAAAAAAAATA 1 AAATAAAC-TTAAAAAAAATA 4228559 AA 1 AA 4228561 TTTAAAATAT Statistics Matches: 19, Mismatches: 3, Indels: 1 0.83 0.13 0.04 Matches are distributed among these distances: 20 7 0.37 21 12 0.63 ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23 Consensus pattern (20 bp): AAATAAACTTAAAAAAAATA Found at i:4228765 original size:12 final size:12 Alignment explanation

Indices: 4228727--4228778 Score: 50 Period size: 12 Copynumber: 4.3 Consensus size: 12 4228717 AAACAGCAAA * * 4228727 AAAAATAATAGT 1 AAAAATAACAGC * * 4228739 AAAAATAATAAC 1 AAAAATAACAGC 4228751 AAAAATAACAGC 1 AAAAATAACAGC * * 4228763 AAAAGTAACACC 1 AAAAATAACAGC 4228775 AAAA 1 AAAA 4228779 TAGTAAAAAA Statistics Matches: 34, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 12 34 1.00 ACGTcount: A:0.69, C:0.12, G:0.06, T:0.13 Consensus pattern (12 bp): AAAAATAACAGC Found at i:4228777 original size:24 final size:24 Alignment explanation

Indices: 4228727--4228778 Score: 59 Period size: 24 Copynumber: 2.2 Consensus size: 24 4228717 AAACAGCAAA * * * 4228727 AAAAATAATAGTAAAAATAATAAC 1 AAAAATAACAGCAAAAATAACAAC * * 4228751 AAAAATAACAGCAAAAGTAACACC 1 AAAAATAACAGCAAAAATAACAAC 4228775 AAAA 1 AAAA 4228779 TAGTAAAAAA Statistics Matches: 23, Mismatches: 5, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 24 23 1.00 ACGTcount: A:0.69, C:0.12, G:0.06, T:0.13 Consensus pattern (24 bp): AAAAATAACAGCAAAAATAACAAC Found at i:4229281 original size:21 final size:18 Alignment explanation

Indices: 4229238--4229273 Score: 63 Period size: 19 Copynumber: 1.9 Consensus size: 18 4229228 TATATTATTT 4229238 TATAAACATTAAAAAATA 1 TATAAACATTAAAAAATA 4229256 TATAATACATTAAAAAAT 1 TATAA-ACATTAAAAAAT 4229274 TAATATAAAT Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 18 5 0.29 19 12 0.71 ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31 Consensus pattern (18 bp): TATAAACATTAAAAAATA Found at i:4229445 original size:8 final size:9 Alignment explanation

Indices: 4229416--4229448 Score: 52 Period size: 8 Copynumber: 3.9 Consensus size: 9 4229406 ACAATATCCA 4229416 AATAATAAC 1 AATAATAAC 4229425 AATAA-AAC 1 AATAATAAC 4229433 AATAATAAC 1 AATAATAAC 4229442 -ATAATAA 1 AATAATAA 4229449 TGAAATGATA Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 8 15 0.65 9 8 0.35 ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21 Consensus pattern (9 bp): AATAATAAC Found at i:4229478 original size:19 final size:20 Alignment explanation

Indices: 4229456--4229499 Score: 63 Period size: 22 Copynumber: 2.1 Consensus size: 20 4229446 TAATGAAATG 4229456 ATAGT-AAAACAATGAGAAA 1 ATAGTAAAAACAATGAGAAA 4229475 ATAGTAACAAAACAATGAGAAA 1 ATAGT-A-AAAACAATGAGAAA 4229497 ATA 1 ATA 4229500 ATAACAAATC Statistics Matches: 22, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 19 5 0.23 22 17 0.77 ACGTcount: A:0.64, C:0.07, G:0.14, T:0.16 Consensus pattern (20 bp): ATAGTAAAAACAATGAGAAA Found at i:4229486 original size:22 final size:22 Alignment explanation

Indices: 4229461--4229512 Score: 86 Period size: 22 Copynumber: 2.4 Consensus size: 22 4229451 AAATGATAGT * 4229461 AAAACAATGAGAAAATAGTAAC 1 AAAACAATGAGAAAATAATAAC 4229483 AAAACAATGAGAAAATAATAAC 1 AAAACAATGAGAAAATAATAAC * 4229505 AAATCAAT 1 AAAACAAT 4229513 TTTTTTTGCA Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 22 28 1.00 ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15 Consensus pattern (22 bp): AAAACAATGAGAAAATAATAAC Found at i:4232439 original size:18 final size:20 Alignment explanation

Indices: 4232398--4232439 Score: 54 Period size: 18 Copynumber: 2.2 Consensus size: 20 4232388 ACAAAACCAT * 4232398 CAAAATTTAAAAGACACAAA 1 CAAAATTTAAAAGACAAAAA 4232418 -AAAATTT-AAAGA-AAAAA 1 CAAAATTTAAAAGACAAAAA 4232435 CAAAA 1 CAAAA 4232440 CTAAACCCAA Statistics Matches: 20, Mismatches: 1, Indels: 4 0.80 0.04 0.16 Matches are distributed among these distances: 17 4 0.20 18 9 0.45 19 7 0.35 ACGTcount: A:0.71, C:0.10, G:0.05, T:0.14 Consensus pattern (20 bp): CAAAATTTAAAAGACAAAAA Done.