Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold160

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: 5021213
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 92036 characters in sequence are not A, C, G, or T


File 27 of 30

Found at i:4452447 original size:20 final size:20

Alignment explanation

Indices: 4452422--4452495 Score: 121 Period size: 20 Copynumber: 3.7 Consensus size: 20 4452412 GTTAGGCTCA * 4452422 ATGTATCGATACAATTTACC 1 ATGTATCGATACAATTCACC 4452442 ATGTATCGATACAATTCACC 1 ATGTATCGATACAATTCACC * * 4452462 ATGTATTGATACAATTCATC 1 ATGTATCGATACAATTCACC 4452482 ATGTATCGATACAA 1 ATGTATCGATACAA 4452496 AGTGAGTTTT Statistics Matches: 50, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 20 50 1.00 ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34 Consensus pattern (20 bp): ATGTATCGATACAATTCACC Found at i:4452621 original size:19 final size:18 Alignment explanation

Indices: 4452585--4452621 Score: 56 Period size: 18 Copynumber: 2.0 Consensus size: 18 4452575 TTAAGCAATA * 4452585 TGTATCGATACTTCTAGG 1 TGTATCGATACATCTAGG 4452603 TGTATCGATACAATCTAGG 1 TGTATCGATAC-ATCTAGG 4452622 GTTTTGACCT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 18 11 0.65 19 6 0.35 ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35 Consensus pattern (18 bp): TGTATCGATACATCTAGG Found at i:4452716 original size:20 final size:21 Alignment explanation

Indices: 4452691--4452731 Score: 66 Period size: 22 Copynumber: 2.0 Consensus size: 21 4452681 ATATTTTGAA 4452691 TTATTTTTA-CTTGAAAAACG 1 TTATTTTTAGCTTGAAAAACG 4452711 TTATTTTTATGCTTGAAAAAC 1 TTATTTTTA-GCTTGAAAAAC 4452732 ATTTATACTT Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 20 9 0.47 22 10 0.53 ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46 Consensus pattern (21 bp): TTATTTTTAGCTTGAAAAACG Found at i:4453378 original size:22 final size:22 Alignment explanation

Indices: 4453333--4453374 Score: 61 Period size: 22 Copynumber: 2.0 Consensus size: 22 4453323 AGCATCTCCA 4453333 TGAATGTTACTCATGATTTTCT 1 TGAATGTTACTCATGATTTTCT 4453355 TGAATGTT-CATCATG-TTTTC 1 TGAATGTTAC-TCATGATTTTC 4453375 CTTGTCAAAA Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 21 6 0.32 22 13 0.68 ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50 Consensus pattern (22 bp): TGAATGTTACTCATGATTTTCT Found at i:4463821 original size:19 final size:18 Alignment explanation

Indices: 4463797--4463864 Score: 83 Period size: 19 Copynumber: 3.9 Consensus size: 18 4463787 CAGTAGCTAA 4463797 TTATGTATCGATACAATAC 1 TTATGTATCGATACAA-AC 4463816 TTATGTATCGATAC--A- 1 TTATGTATCGATACAAAC 4463831 -T-TGTATCGATACAACAC 1 TTATGTATCGATACAA-AC 4463848 TTATGTATCGATACAAA 1 TTATGTATCGATACAAA 4463865 TCTTTGAATT Statistics Matches: 43, Mismatches: 0, Indels: 13 0.77 0.00 0.23 Matches are distributed among these distances: 13 11 0.26 14 1 0.02 16 2 0.05 18 2 0.05 19 27 0.63 ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35 Consensus pattern (18 bp): TTATGTATCGATACAAAC Found at i:4463837 original size:13 final size:13 Alignment explanation

Indices: 4463819--4463843 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 4463809 ACAATACTTA 4463819 TGTATCGATACAT 1 TGTATCGATACAT 4463832 TGTATCGATACA 1 TGTATCGATACA 4463844 ACACTTATGT 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:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:4463841 original size:32 final size:32 Alignment explanation

Indices: 4463800--4463862 Score: 117 Period size: 32 Copynumber: 2.0 Consensus size: 32 4463790 TAGCTAATTA * 4463800 TGTATCGATACAATACTTATGTATCGATACAT 1 TGTATCGATACAACACTTATGTATCGATACAT 4463832 TGTATCGATACAACACTTATGTATCGATACA 1 TGTATCGATACAACACTTATGTATCGATACA 4463863 AATCTTTGAA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 30 1.00 ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35 Consensus pattern (32 bp): TGTATCGATACAACACTTATGTATCGATACAT Found at i:4464619 original size:92 final size:92 Alignment explanation

Indices: 4464439--4465040 Score: 1062 Period size: 92 Copynumber: 6.6 Consensus size: 92 4464429 GTTTTGCAAT * * * * * * * 4464439 GTGCCACTGTGCAGATTCAAGGCCTGCCACACTGGACTTAAAGAT-GAGGTGCCAATATGCTGAT 1 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAT * 4464503 TCAAAGCCAGCTATATTGGACTTAAAG 66 TCAAGGCCAGCTATATTGGACTTAAAG * * 4464530 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGAT 1 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAT * 4464595 TCAAGGCCAACTATATTGGACTTAAAG 66 TCAAGGCCAGCTATATTGGACTTAAAG * 4464622 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAT 1 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAT 4464687 TCAAGGCCAGCTATATTGGACTTAAAG 66 TCAAGGCCAGCTATATTGGACTTAAAG * 4464714 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAATGTGCCAATATGCTGAT 1 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAT 4464779 TCAAGGCCAGCTATATTGGACTTAAAG 66 TCAAGGCCAGCTATATTGGACTTAAAG * 4464806 GTGCTAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAT 1 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAT 4464871 TCAAGGCCAGCTATATTGGACTTAAAG 66 TCAAGGCCAGCTATATTGGACTTAAAG * 4464898 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAATGTGCCAATATGCTGAT 1 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAT 4464963 TCAAGGCCAGCTATATTGGACTTAAAG 66 TCAAGGCCAGCTATATTGGACTTAAAG 4464990 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGT 1 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGT 4465041 CCCCACATGT Statistics Matches: 493, Mismatches: 17, Indels: 1 0.96 0.03 0.00 Matches are distributed among these distances: 91 40 0.08 92 453 0.92 ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26 Consensus pattern (92 bp): GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAT TCAAGGCCAGCTATATTGGACTTAAAG Found at i:4465151 original size:20 final size:21 Alignment explanation

Indices: 4465126--4465178 Score: 90 Period size: 20 Copynumber: 2.6 Consensus size: 21 4465116 TCTACAGACA * 4465126 TGTATCGATACATTCACTT-T 1 TGTATCGATACATCCACTTAT 4465146 TGTATCGATACATCCACTTAT 1 TGTATCGATACATCCACTTAT 4465167 TGTATCGATACA 1 TGTATCGATACA 4465179 AATGGTTGAA Statistics Matches: 31, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 20 18 0.58 21 13 0.42 ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40 Consensus pattern (21 bp): TGTATCGATACATCCACTTAT Found at i:4466059 original size:20 final size:20 Alignment explanation

Indices: 4466034--4466077 Score: 63 Period size: 20 Copynumber: 2.2 Consensus size: 20 4466024 TTTTTTTTAG 4466034 TTTCTTT-TTTTTCTCTATTT 1 TTTCTTTCTTTTTCT-TATTT * 4466054 TTTCTTTCTTTTTCTTTTTT 1 TTTCTTTCTTTTTCTTATTT 4466074 TTTC 1 TTTC 4466078 GTAAATTTTC Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 20 15 0.68 21 7 0.32 ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82 Consensus pattern (20 bp): TTTCTTTCTTTTTCTTATTT Found at i:4466065 original size:11 final size:10 Alignment explanation

Indices: 4466034--4466077 Score: 54 Period size: 10 Copynumber: 4.4 Consensus size: 10 4466024 TTTTTTTTAG 4466034 TTTC-TTTTT 1 TTTCTTTTTT * 4466043 TTTCTCTATTT 1 TTTCT-TTTTT * 4466054 TTTCTTTCTT 1 TTTCTTTTTT 4466064 TTTCTTTTTT 1 TTTCTTTTTT 4466074 TTTC 1 TTTC 4466078 GTAAATTTTC Statistics Matches: 29, Mismatches: 4, Indels: 3 0.81 0.11 0.08 Matches are distributed among these distances: 9 4 0.14 10 16 0.55 11 9 0.31 ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82 Consensus pattern (10 bp): TTTCTTTTTT Found at i:4466575 original size:27 final size:26 Alignment explanation

Indices: 4466545--4466611 Score: 107 Period size: 27 Copynumber: 2.5 Consensus size: 26 4466535 GTATAAAACC 4466545 TTAATTGAAAGTTTATATGTGAAAGGT 1 TTAATTGAAAGTTTATATGTGAAA-GT 4466572 TTAATTGAAAGTTTTATATGTGAAAGT 1 TTAATTGAAAG-TTTATATGTGAAAGT * 4466599 TTAATTAAAAGTT 1 TTAATTGAAAGTT 4466612 CCATATGTAA Statistics Matches: 38, Mismatches: 1, Indels: 3 0.90 0.02 0.07 Matches are distributed among these distances: 26 2 0.05 27 23 0.61 28 13 0.34 ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43 Consensus pattern (26 bp): TTAATTGAAAGTTTATATGTGAAAGT Found at i:4466597 original size:15 final size:15 Alignment explanation

Indices: 4466550--4466600 Score: 72 Period size: 15 Copynumber: 3.6 Consensus size: 15 4466540 AAACCTTAAT 4466550 TGAAAG-TTTATATG 1 TGAAAGTTTTATATG * 4466564 TGAAAGGTTTA-AT- 1 TGAAAGTTTTATATG 4466577 TGAAAGTTTTATATG 1 TGAAAGTTTTATATG 4466592 TGAAAGTTT 1 TGAAAGTTT 4466601 AATTAAAAGT Statistics Matches: 33, Mismatches: 1, Indels: 5 0.85 0.03 0.13 Matches are distributed among these distances: 13 10 0.30 14 10 0.30 15 13 0.39 ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43 Consensus pattern (15 bp): TGAAAGTTTTATATG Found at i:4466617 original size:27 final size:26 Alignment explanation

Indices: 4466545--4466679 Score: 94 Period size: 27 Copynumber: 5.0 Consensus size: 26 4466535 GTATAAAACC * * 4466545 TTAATTGAAAGTTTATATGTGAAAGGT 1 TTAATTAAAAGTTCATATGTGAAA-GT * * 4466572 TTAATTGAAAGTTTTATATGTGAAAGT 1 TTAATTAAAAG-TTCATATGTGAAAGT * 4466599 TTAATTAAAAGTTCCATATGT-AAGGGT 1 TTAATTAAAAGTT-CATATGTGAA-AGT * * * 4466626 TCAATTAAAAATTTTACATATG-AAAAGT 1 TTAATT-AAAA-GTT-CATATGTGAAAGT * * 4466654 TTAATTAAAAATATCATATGTAAAAG 1 TTAATTAAAAGT-TCATATGTGAAAG 4466680 GATAACCCAA Statistics Matches: 91, Mismatches: 9, Indels: 16 0.78 0.08 0.14 Matches are distributed among these distances: 26 11 0.12 27 46 0.51 28 24 0.26 29 10 0.11 ACGTcount: A:0.43, C:0.04, G:0.15, T:0.39 Consensus pattern (26 bp): TTAATTAAAAGTTCATATGTGAAAGT Found at i:4466658 original size:55 final size:53 Alignment explanation

Indices: 4466545--4466677 Score: 149 Period size: 54 Copynumber: 2.4 Consensus size: 53 4466535 GTATAAAACC * * * * * * * 4466545 TTAATTGAAAGTTTATATGTGAAAGGTTTAATTGAAAGTTTTATATGTGAAAGT 1 TTAATTAAAAGTTCATATGT-AAAGGTTCAATTAAAAATTTTACATATGAAAGT * 4466599 TTAATTAAAAGTTCCATATGTAAGGGTTCAATTAAAAATTTTACATATGAAAAGT 1 TTAATTAAAAGTT-CATATGTAAAGGTTCAATTAAAAATTTTACATATG-AAAGT * 4466654 TTAATTAAAAATATCATATGTAAA 1 TTAATTAAAAGT-TCATATGTAAA 4466678 AGGATAACCC Statistics Matches: 66, Mismatches: 10, Indels: 5 0.81 0.12 0.06 Matches are distributed among these distances: 54 34 0.52 55 31 0.47 56 1 0.02 ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39 Consensus pattern (53 bp): TTAATTAAAAGTTCATATGTAAAGGTTCAATTAAAAATTTTACATATGAAAGT Found at i:4467274 original size:18 final size:20 Alignment explanation

Indices: 4467243--4467284 Score: 52 Period size: 18 Copynumber: 2.2 Consensus size: 20 4467233 GAACTAGAAC * 4467243 GAAAAAAGAGAAGACTAAGA 1 GAAAAAAGAGAAGACAAAGA * 4467263 GAAAAAA-A-AAGAGAAAGA 1 GAAAAAAGAGAAGACAAAGA 4467281 GAAA 1 GAAA 4467285 TAAATTACAA Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 18 12 0.60 19 1 0.05 20 7 0.35 ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02 Consensus pattern (20 bp): GAAAAAAGAGAAGACAAAGA Found at i:4468270 original size:2 final size:2 Alignment explanation

Indices: 4468263--4468300 Score: 58 Period size: 2 Copynumber: 19.0 Consensus size: 2 4468253 TGAGAGTTTA * * 4468263 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AC AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 4468301 TTAGGAACTC Statistics Matches: 32, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47 Consensus pattern (2 bp): AT Found at i:4468625 original size:20 final size:21 Alignment explanation

Indices: 4468593--4468631 Score: 55 Period size: 20 Copynumber: 1.9 Consensus size: 21 4468583 TTTTTATAAA 4468593 ATTTGACCAAAG-TTGATCAT 1 ATTTGACCAAAGTTTGATCAT 4468613 ATTTGA-CATAAGTTTGATC 1 ATTTGACCA-AAGTTTGATC 4468632 GAGTTTAACT Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 19 2 0.12 20 9 0.53 21 6 0.35 ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38 Consensus pattern (21 bp): ATTTGACCAAAGTTTGATCAT Found at i:4470410 original size:14 final size:16 Alignment explanation

Indices: 4470391--4470427 Score: 51 Period size: 14 Copynumber: 2.4 Consensus size: 16 4470381 AGAATTTAAT 4470391 AATTTTAA-ATTT-TA 1 AATTTTAATATTTATA 4470405 AATTTTAATATTTATA 1 AATTTTAATATTTATA * 4470421 ATTTTTA 1 AATTTTA 4470428 TTTATTTTCA Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 14 8 0.40 15 4 0.20 16 8 0.40 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (16 bp): AATTTTAATATTTATA Found at i:4477273 original size:79 final size:79 Alignment explanation

Indices: 4477175--4477480 Score: 594 Period size: 79 Copynumber: 3.9 Consensus size: 79 4477165 GTAAACACAC 4477175 CAAAGTCTAAATTTAGTTAGCTTCTTCTTAGGTGCTTTACTTATGAAACAATTTGGGGATGACAT 1 CAAAGTCTAAATTTAGTTAGCTTCTTCTTAGGTGCTTTACTTATGAAACAATTTGGGGATGACAT 4477240 GTTTACTTATGAAA 66 GTTTACTTATGAAA 4477254 CAAAGTCTAAATTTAGTTAGCTTCTTCTTAGGTGCTTTACTTATGAAACAATTTGGGGATGACAT 1 CAAAGTCTAAATTTAGTTAGCTTCTTCTTAGGTGCTTTACTTATGAAACAATTTGGGGATGACAT 4477319 GTTTACTTATGAAA 66 GTTTACTTATGAAA 4477333 CAAAGTCTAAATTTAGTTAGCTTCTTCTTAGGTGCTTTACTTATGAAACAATTTGGGGATGACAT 1 CAAAGTCTAAATTTAGTTAGCTTCTTCTTAGGTGCTTTACTTATGAAACAATTTGGGGATGACAT 4477398 GTTTACTTATGAAA 66 GTTTACTTATGAAA * * 4477412 CAAAGTCTAAATTTAGTTAGCTTCTTCTTCGGTGCTTTACTTATGAAACAATTTGGGGATGACAG 1 CAAAGTCTAAATTTAGTTAGCTTCTTCTTAGGTGCTTTACTTATGAAACAATTTGGGGATGACAT 4477477 GTTT 66 GTTT 4477481 CTATATCTTA Statistics Matches: 225, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 79 225 1.00 ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39 Consensus pattern (79 bp): CAAAGTCTAAATTTAGTTAGCTTCTTCTTAGGTGCTTTACTTATGAAACAATTTGGGGATGACAT GTTTACTTATGAAA Found at i:4479693 original size:20 final size:20 Alignment explanation

Indices: 4479670--4479714 Score: 81 Period size: 20 Copynumber: 2.2 Consensus size: 20 4479660 TAAGTAAAAC 4479670 AAATTTATTTCATATAAATA 1 AAATTTATTTCATATAAATA 4479690 AAATTTATTTCATATAAATA 1 AAATTTATTTCATATAAATA * 4479710 TAATT 1 AAATT 4479715 AAATAATTAT Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 20 24 1.00 ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47 Consensus pattern (20 bp): AAATTTATTTCATATAAATA Found at i:4488012 original size:13 final size:13 Alignment explanation

Indices: 4487994--4488019 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 4487984 TACACAAAGT 4487994 ATGTATCGATACA 1 ATGTATCGATACA 4488007 ATGTATCGATACA 1 ATGTATCGATACA 4488020 CAAAAAATTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:4488017 original size:32 final size:33 Alignment explanation

Indices: 4487976--4488039 Score: 103 Period size: 32 Copynumber: 2.0 Consensus size: 33 4487966 TAGCCAAACT ** 4487976 TGTATCGATACACAAAGTA-TGTATCGATACAA 1 TGTATCGATACACAAAAAATTGTATCGATACAA 4488008 TGTATCGATACACAAAAAATTGTATCGATACA 1 TGTATCGATACACAAAAAATTGTATCGATACA 4488040 TTGGCTTGTA Statistics Matches: 29, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 32 17 0.59 33 12 0.41 ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28 Consensus pattern (33 bp): TGTATCGATACACAAAAAATTGTATCGATACAA Found at i:4492100 original size:15 final size:15 Alignment explanation

Indices: 4492080--4492110 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 4492070 TAAAAATGTC * 4492080 CAAAATGAGGAAGCT 1 CAAAATGAAGAAGCT 4492095 CAAAATGAAGAAGCT 1 CAAAATGAAGAAGCT 4492110 C 1 C 4492111 CAAACGAAAT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13 Consensus pattern (15 bp): CAAAATGAAGAAGCT Found at i:4494202 original size:13 final size:13 Alignment explanation

Indices: 4494180--4494217 Score: 58 Period size: 13 Copynumber: 2.9 Consensus size: 13 4494170 CATTTTTCTT * 4494180 TGTATTGATACAA 1 TGTATCGATACAA * 4494193 TGTATCGATACAC 1 TGTATCGATACAA 4494206 TGTATCGATACA 1 TGTATCGATACA 4494218 GGGGGATTAT Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 13 23 1.00 ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34 Consensus pattern (13 bp): TGTATCGATACAA Found at i:4496775 original size:13 final size:13 Alignment explanation

Indices: 4496757--4496782 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 4496747 TACACAAAGT 4496757 ATGTATCGATACA 1 ATGTATCGATACA 4496770 ATGTATCGATACA 1 ATGTATCGATACA 4496783 CAAAAAATTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:4496782 original size:32 final size:33 Alignment explanation

Indices: 4496741--4496802 Score: 99 Period size: 32 Copynumber: 1.9 Consensus size: 33 4496731 GCCAAACTTA ** 4496741 TATCGATACACAAAGTA-TGTATCGATACAATG 1 TATCGATACACAAAAAATTGTATCGATACAATG 4496773 TATCGATACACAAAAAATTGTATCGATACA 1 TATCGATACACAAAAAATTGTATCGATACA 4496803 TTGGCTTGTA Statistics Matches: 27, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 32 15 0.56 33 12 0.44 ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27 Consensus pattern (33 bp): TATCGATACACAAAAAATTGTATCGATACAATG Found at i:4498698 original size:20 final size:20 Alignment explanation

Indices: 4498673--4498713 Score: 55 Period size: 20 Copynumber: 2.0 Consensus size: 20 4498663 ATATTTTATA * 4498673 ATCATATTATATTTAAAATT 1 ATCATATAATATTTAAAATT * * 4498693 ATCATATAATTTTTTAAATT 1 ATCATATAATATTTAAAATT 4498713 A 1 A 4498714 ATATTACATC Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51 Consensus pattern (20 bp): ATCATATAATATTTAAAATT Found at i:4504640 original size:52 final size:52 Alignment explanation

Indices: 4504562--4504690 Score: 231 Period size: 52 Copynumber: 2.5 Consensus size: 52 4504552 CGAAATATGA * 4504562 AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC 1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC * * 4504614 AAATTTGCCTGTATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC 1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC 4504666 AAATTTGCCTGCATGTATCGATACA 1 AAATTTGCCTGCATGTATCGATACA 4504691 AAGATTAGCG Statistics Matches: 73, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 52 73 1.00 ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36 Consensus pattern (52 bp): AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC Found at i:4504704 original size:52 final size:52 Alignment explanation

Indices: 4504562--4504709 Score: 192 Period size: 52 Copynumber: 2.8 Consensus size: 52 4504552 CGAAATATGA * * 4504562 AAATTTACCTGCATGTATCGATACATTTCA-TAGTGTATCGATACATCTGGGC 1 AAATTTGCCTGCATGTATCGATACA-ATCATTAGTGTATCGATACATCTGGGC * ** 4504614 AAATTTGCCTGTATGTATCGATAC-ATTTTATAGTGTATCGATACATCTGGGC 1 AAATTTGCCTGCATGTATCGATACAATCAT-TAGTGTATCGATACATCTGGGC ** * 4504666 AAATTTGCCTGCATGTATCGATACAAAGATTAGCGTATCGATAC 1 AAATTTGCCTGCATGTATCGATACAATCATTAGTGTATCGATAC 4504710 GATGTATCGA Statistics Matches: 83, Mismatches: 10, Indels: 6 0.84 0.10 0.06 Matches are distributed among these distances: 50 1 0.01 52 80 0.96 53 2 0.02 ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34 Consensus pattern (52 bp): AAATTTGCCTGCATGTATCGATACAATCATTAGTGTATCGATACATCTGGGC Found at i:4504737 original size:21 final size:21 Alignment explanation

Indices: 4504711--4504768 Score: 116 Period size: 21 Copynumber: 2.8 Consensus size: 21 4504701 TATCGATACG 4504711 ATGTATCGATACATTTGAGTA 1 ATGTATCGATACATTTGAGTA 4504732 ATGTATCGATACATTTGAGTA 1 ATGTATCGATACATTTGAGTA 4504753 ATGTATCGATACATTT 1 ATGTATCGATACATTT 4504769 TCTTGGCAGT Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 37 1.00 ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40 Consensus pattern (21 bp): ATGTATCGATACATTTGAGTA Found at i:4504831 original size:32 final size:32 Alignment explanation

Indices: 4504790--4504891 Score: 168 Period size: 32 Copynumber: 3.2 Consensus size: 32 4504780 GCTTCGTAGT * * * 4504790 GATACATTGTATCGATATAAAACTTATGTAAC 1 GATACATTGTATCGATACAACACTTATGTATC * 4504822 GATACATTGTATGGATACAACACTTATGTATC 1 GATACATTGTATCGATACAACACTTATGTATC 4504854 GATACATTGTATCGATACAACACTTATGTATC 1 GATACATTGTATCGATACAACACTTATGTATC 4504886 GATACA 1 GATACA 4504892 AATCGTTGAA Statistics Matches: 65, Mismatches: 5, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 32 65 1.00 ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33 Consensus pattern (32 bp): GATACATTGTATCGATACAACACTTATGTATC Found at i:4504857 original size:19 final size:19 Alignment explanation

Indices: 4504829--4504892 Score: 77 Period size: 19 Copynumber: 3.7 Consensus size: 19 4504819 AACGATACAT * 4504829 TGTATGGATACAACACTTA 1 TGTATCGATACAACACTTA 4504848 TGTATCGAT---ACA--T- 1 TGTATCGATACAACACTTA 4504861 TGTATCGATACAACACTTA 1 TGTATCGATACAACACTTA 4504880 TGTATCGATACAA 1 TGTATCGATACAA 4504893 ATCGTTGAAA Statistics Matches: 38, Mismatches: 1, Indels: 12 0.75 0.02 0.24 Matches are distributed among these distances: 13 9 0.24 14 1 0.03 16 6 0.16 18 1 0.03 19 21 0.55 ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33 Consensus pattern (19 bp): TGTATCGATACAACACTTA Found at i:4504866 original size:13 final size:13 Alignment explanation

Indices: 4504848--4504872 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 4504838 ACAACACTTA 4504848 TGTATCGATACAT 1 TGTATCGATACAT 4504861 TGTATCGATACA 1 TGTATCGATACA 4504873 ACACTTATGT 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:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:4506436 original size:19 final size:18 Alignment explanation

Indices: 4506400--4506445 Score: 58 Period size: 19 Copynumber: 2.5 Consensus size: 18 4506390 AATTAATTAA 4506400 AAAATTTATTTTATTATT 1 AAAATTTATTTTATTATT 4506418 AAAATATTATTTT-TATATT 1 AAAAT-TTATTTTAT-TATT * 4506437 AATATTTAT 1 AAAATTTAT 4506446 ATAATATTAT Statistics Matches: 25, Mismatches: 1, Indels: 4 0.83 0.03 0.13 Matches are distributed among these distances: 18 10 0.40 19 15 0.60 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (18 bp): AAAATTTATTTTATTATT Found at i:4507354 original size:21 final size:22 Alignment explanation

Indices: 4507313--4507354 Score: 59 Period size: 21 Copynumber: 2.0 Consensus size: 22 4507303 GAAAGTATGA * 4507313 GAAAATATTGCTAAATTTCAAC 1 GAAAATATTGCTAAATCTCAAC * 4507335 GAAAATA-TGTTAAATCTCAA 1 GAAAATATTGCTAAATCTCAA 4507355 TACGAATTCA Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 21 11 0.61 22 7 0.39 ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31 Consensus pattern (22 bp): GAAAATATTGCTAAATCTCAAC Found at i:4509556 original size:46 final size:46 Alignment explanation

Indices: 4509497--4509587 Score: 164 Period size: 46 Copynumber: 2.0 Consensus size: 46 4509487 ATATAAGGTC * 4509497 CCAACGATTAAAAATTCAAAATTTTCACAATTTGTATCGATACATA 1 CCAACGATCAAAAATTCAAAATTTTCACAATTTGTATCGATACATA * 4509543 CCAACGGTCAAAAATTCAAAATTTTCACAATTTGTATCGATACAT 1 CCAACGATCAAAAATTCAAAATTTTCACAATTTGTATCGATACAT 4509588 TCTTCACTGT Statistics Matches: 43, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 46 43 1.00 ACGTcount: A:0.42, C:0.19, G:0.08, T:0.32 Consensus pattern (46 bp): CCAACGATCAAAAATTCAAAATTTTCACAATTTGTATCGATACATA Found at i:4509664 original size:50 final size:50 Alignment explanation

Indices: 4509575--4509709 Score: 182 Period size: 50 Copynumber: 2.7 Consensus size: 50 4509565 TTTCACAATT * * * * 4509575 TGTATCGATACATTCTTCACTGTATTGATATATTCTGGGTTTTACCTAGA 1 TGTATCGATACATTCTTTAATGTATCGATACATTCTGGGTTTTACCTAGA * * * 4509625 TGTGTCGATACATTCTTTATTGTATCGATACATTTTGGGTTTTACCTAGA 1 TGTATCGATACATTCTTTAATGTATCGATACATTCTGGGTTTTACCTAGA * 4509675 TGTATCGATACATT-TCTTAATGGATCGATACATTC 1 TGTATCGATACATTCT-TTAATGTATCGATACATTC 4509710 AGGCATTTTT Statistics Matches: 74, Mismatches: 10, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 49 1 0.01 50 73 0.99 ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44 Consensus pattern (50 bp): TGTATCGATACATTCTTTAATGTATCGATACATTCTGGGTTTTACCTAGA Found at i:4514808 original size:87 final size:87 Alignment explanation

Indices: 4514662--4514836 Score: 341 Period size: 87 Copynumber: 2.0 Consensus size: 87 4514652 CCAATTTACA 4514662 AGACAAAGTGCTGACATTATGATGTTGTTCAGCTGATAATGGGATAGGTTGGTGGCCAATTCAAT 1 AGACAAAGTGCTGACATTATGATGTTGTTCAGCTGATAATGGGATAGGTTGGTGGCCAATTCAAT 4514727 GGTCTTCCAACTCTAAAGTGTG 66 GGTCTTCCAACTCTAAAGTGTG 4514749 AGACAAAGTGCTGACATTATGATGTTGTTCAGCTGATAATGGGATAGGTTGGTGGCCAATTCAAT 1 AGACAAAGTGCTGACATTATGATGTTGTTCAGCTGATAATGGGATAGGTTGGTGGCCAATTCAAT * 4514814 GGTCTTCCAATTCTAAAGTGTG 66 GGTCTTCCAACTCTAAAGTGTG 4514836 A 1 A 4514837 TGGTGAGGAG Statistics Matches: 87, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 87 87 1.00 ACGTcount: A:0.28, C:0.14, G:0.26, T:0.31 Consensus pattern (87 bp): AGACAAAGTGCTGACATTATGATGTTGTTCAGCTGATAATGGGATAGGTTGGTGGCCAATTCAAT GGTCTTCCAACTCTAAAGTGTG Found at i:4515120 original size:20 final size:20 Alignment explanation

Indices: 4515095--4515187 Score: 159 Period size: 20 Copynumber: 4.7 Consensus size: 20 4515085 AACAGAATGT 4515095 AAATGTATCGATACATTGAA 1 AAATGTATCGATACATTGAA 4515115 AAATGTATCGATACATTGAA 1 AAATGTATCGATACATTGAA * * 4515135 AAATGTATCGATACATTCAT 1 AAATGTATCGATACATTGAA * 4515155 ACATGTATCGATACATTGAA 1 AAATGTATCGATACATTGAA 4515175 AAATGTATCGATA 1 AAATGTATCGATA 4515188 TATTTGGGTA Statistics Matches: 67, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 67 1.00 ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31 Consensus pattern (20 bp): AAATGTATCGATACATTGAA Found at i:4516362 original size:78 final size:78 Alignment explanation

Indices: 4516127--4516523 Score: 455 Period size: 78 Copynumber: 5.1 Consensus size: 78 4516117 TCATTGATGT * * * * * 4516127 TTTTATTTCTAAAATACCGATTTTTCACCATTGGGGATACTTCAATCC-CGTTATTTTCGAAGGA 1 TTTTATTTCTAAAACACCGATTTTTCA-CAATCGGGATACTCCAA-CCTCGTTATTTTCGAAGGG * 4516191 ATACTCCAACCCTGA 64 ATACTCCAACCCCGA * * * * 4516206 TTTTATTTCTAAAACATCGATTTTTCACTATCGGGGACTACTCCAACC-CAGTTATTTTCAAAAG 1 TTTTATTTCTAAAACACCGATTTTTCACAATC-GGGA-TACTCCAACCTC-GTTATTTTCGAAGG 4516270 GATACTCCAACCCCGA 63 GATACTCCAACCCCGA * * 4516286 TTTTATTTCTAAAACACCGATTTTCCACAATCGGGATACTCCAACCTCATTA-TTTCTGAAGGGA 1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGATACTCCAACCTCGTTATTTTC-GAAGGGA * * 4516350 TACTCTAACCCCGG 65 TACTCCAACCCCGA * * * 4516364 TTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTTCAACCTCGTTATTTTCGATA-GG 1 TTTTATTTCTAAAACACCGATTTTTCACAATC-GGGATACTCCAACCTCGTTATTTTCGA-AGGG * 4516428 ATACTCCAACCCTGA 64 ATACTCCAACCCCGA * * * * 4516443 TTTTATTTCTAAAATACCGA-TTTTCACCATCGGAGATACTCCAACCTCGTTATTTTTGAGGGGA 1 TTTTATTTCTAAAACACCGATTTTTCACAATCGG-GATACTCCAACCTCGTTATTTTCGAAGGGA * * 4516507 TACGCTAACCCC-A 65 TACTCCAACCCCGA 4516520 TTTT 1 TTTT 4516524 TATCTCCAAA Statistics Matches: 272, Mismatches: 36, Indels: 22 0.82 0.11 0.07 Matches are distributed among these distances: 77 11 0.04 78 105 0.39 79 89 0.33 80 67 0.25 ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35 Consensus pattern (78 bp): TTTTATTTCTAAAACACCGATTTTTCACAATCGGGATACTCCAACCTCGTTATTTTCGAAGGGAT ACTCCAACCCCGA Found at i:4516439 original size:79 final size:78 Alignment explanation

Indices: 4516127--4516498 Score: 466 Period size: 79 Copynumber: 4.7 Consensus size: 78 4516117 TCATTGATGT * * * * 4516127 TTTTATTTCTAAAATACCGATTTTTCACCATTGGGGATACTTCAATCC-CGTTATTTTCGAAGGA 1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAA-CCTCGTTATTTTCGAAGG- * 4516191 ATACTCCAACCCTGA 64 ATACTCCAACCCCGA * * * 4516206 TTTTATTTCTAAAACATCGATTTTTCACTATCGGGGACTACTCCAACC-CAGTTATTTTCAAAAG 1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGA-TACTCCAACCTC-GTTATTTTC-GAAG 4516270 GATACTCCAACCCCGA 63 GATACTCCAACCCCGA * * 4516286 TTTTATTTCTAAAACACCGATTTTCCACAATC-GGGATACTCCAACCTCATTA-TTTCTGAAGGG 1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTTC-GAA-GG * * 4516349 ATACTCTAACCCCGG 64 ATACTCCAACCCCGA * * * 4516364 TTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTTCAACCTCGTTATTTTCGATAGGA 1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTTCGA-AGGA * 4516429 TACTCCAACCCTGA 65 TACTCCAACCCCGA * * * 4516443 TTTTATTTCTAAAATACCGA-TTTTCACCATCGGAGATACTCCAACCTCGTTATTTT 1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTT 4516499 TGAGGGGATA Statistics Matches: 256, Mismatches: 29, Indels: 17 0.85 0.10 0.06 Matches are distributed among these distances: 77 6 0.02 78 89 0.35 79 93 0.36 80 64 0.25 81 4 0.02 ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36 Consensus pattern (78 bp): TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTTCGAAGGAT ACTCCAACCCCGA Found at i:4516483 original size:157 final size:156 Alignment explanation

Indices: 4516127--4516523 Score: 534 Period size: 157 Copynumber: 2.5 Consensus size: 156 4516117 TCATTGATGT * * * 4516127 TTTTATTTCTAAAATACCGATTTTTCACCATTGGGGATACTTCAATCC-CGTTATTTTCGAAGGA 1 TTTTATTTCTAAAATACCGA-TTTTCACCA-TCGGGATACTCCAA-CCTCGTTATTTT-GAAGGG * * 4516191 ATACTCCAACCCTGATTTTATTTCTAAAACATCGATTTTTCACTATCGGGGACTACTCCAACCCA 62 ATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTTCACTATCGGGGACTACTCCAACCCA 4516256 GTTATTTTCAAAAGGATACTCCAACCCCGA 127 GTTATTTTCAAAAGGATACTCCAACCCCGA * * * 4516286 TTTTATTTCTAAAACACCGATTTTCCACAATCGGGATACTCCAACCTCATTATTTCTGAAGGGAT 1 TTTTATTTCTAAAATACCGATTTT-CACCATCGGGATACTCCAACCTCGTTATTT-TGAAGGGAT * * 4516351 ACTCTAACCCCGGTTTTATTTCTAAAACATCGATTTTTCA-TAATCGGGGA-TACTTCAACCTC- 64 ACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTTCACT-ATCGGGGACTACTCCAACC-CA * * * 4516413 GTTATTTTCGATAGGATACTCCAACCCTGA 127 GTTATTTTCAAAAGGATACTCCAACCCCGA * 4516443 TTTTATTTCTAAAATACCGATTTTCACCATCGGAGATACTCCAACCTCGTTATTTTTGAGGGGAT 1 TTTTATTTCTAAAATACCGATTTTCACCATCGG-GATACTCCAACCTCGTTA-TTTTGAAGGGAT * 4516508 ACGCTAACCCC-ATTTT 64 ACTCTAACCCCGATTTT 4516524 TATCTCCAAA Statistics Matches: 212, Mismatches: 19, Indels: 17 0.85 0.08 0.07 Matches are distributed among these distances: 156 12 0.06 157 97 0.46 158 79 0.37 159 24 0.11 ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35 Consensus pattern (156 bp): TTTTATTTCTAAAATACCGATTTTCACCATCGGGATACTCCAACCTCGTTATTTTGAAGGGATAC TCTAACCCCGATTTTATTTCTAAAACATCGATTTTTCACTATCGGGGACTACTCCAACCCAGTTA TTTTCAAAAGGATACTCCAACCCCGA Found at i:4518583 original size:78 final size:79 Alignment explanation

Indices: 4518410--4518603 Score: 225 Period size: 78 Copynumber: 2.5 Consensus size: 79 4518400 TGGAGATGAA * * * ** 4518410 AAAAATTCGGTATTTTGGAAGTAAAAATGAGGTTGGAGTATCCCTTTGGAGATGGTGGGGTTGTA 1 AAAAATTCAGTATTTTGGAAGTAAAAAAG-GGTTGGAATATCCCTTTAAAGATGGTGGGGTTGTA ** 4518475 GTATCTCCAGCGATG 65 GTATCTCCAAAGATG * * * 4518490 AAAAATTGA-TATTTTGAAAGTAAAAACAGGGTTGGAATAT-CTTTTAAAGATGGTGGGGTTAG- 1 AAAAATTCAGTATTTTGGAAGTAAAAA-AGGGTTGGAATATCCCTTTAAAGATGGTGGGGTT-GT 4518552 AGTATC-CCAAAGATG 64 AGTATCTCCAAAGATG * 4518567 AAAAATTCAGTGTTTTGGAAGTAAAAATAGGGTTGGA 1 AAAAATTCAGTATTTTGGAAGTAAAAA-AGGGTTGGA 4518604 GTGCCCCTTT Statistics Matches: 97, Mismatches: 14, Indels: 8 0.82 0.12 0.07 Matches are distributed among these distances: 77 15 0.15 78 47 0.48 79 27 0.28 80 8 0.08 ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30 Consensus pattern (79 bp): AAAAATTCAGTATTTTGGAAGTAAAAAAGGGTTGGAATATCCCTTTAAAGATGGTGGGGTTGTAG TATCTCCAAAGATG Found at i:4521422 original size:155 final size:155 Alignment explanation

Indices: 4521142--4522113 Score: 1059 Period size: 155 Copynumber: 6.3 Consensus size: 155 4521132 TATAGGTACT * * * * * 4521142 TTCGACGTAAAAGTATCTGATACCCTTAAAAGACTTAAAAAGG-T-TTGAAATGGGATGAACCTA 1 TTCGACGTAAAAGTATCCGATACCCTTAAAGGACTTAAAAAGGATAAT-AGATGAGATGAACCTA * ** * * * 4521205 TCCTAACTGCCTACCTTTAGCATAAAAGCGGA-TCTGGTGACAACCTAAGACTCGGTTCTAAAAA 65 TCCTAAATATCTACCTTCAGCATAAAAGCAGACTC-GGTGACAACCTAAGACTCGATTCTAAAAA * * * 4521269 AATACGAAAATACCCCTAAAGAATACT 129 ATTACGAAAATACCCCTAAAGGATACC * * * * * 4521296 TTCGATGTAAAAGTATCCGATACTCATAAAGGACTTAAAGAGGATAATAGATGAGATAAACCTAT 1 TTCGACGTAAAAGTATCCGATACCCTTAAAGGACTTAAAAAGGATAATAGATGAGATGAACCTAT * * 4521361 CCTAAATATCTACCTTCATCATAAAAGCAGACTCGGTGACAACCTAAGACTC-AGTTTTAAAAAA 66 CCTAAATATCTACCTTCAGCATAAAAGCAGACTCGGTGACAACCTAAGACTCGA-TTCTAAAAAA * 4521425 TTACGAAAATA-CCCTTAAGGATACC 130 TTACGAAAATACCCCTAAAGGATACC * * * 4521450 TTCGACGTAAAAGTATCCGACACCCCTAAAAGACTTAAAAAGGATAATAGATGAGATGAACCTAT 1 TTCGACGTAAAAGTATCCGATACCCTTAAAGGACTTAAAAAGGATAATAGATGAGATGAACCTAT * * * * 4521515 CCTAAATATCTACCTTCAGGCATAAAAGCGGATTCGGTGACAACTTAGGACTCGATTCTAAAAAA 66 CCTAAATATCTACCTTCA-GCATAAAAGCAGACTCGGTGACAACCTAAGACTCGATTCTAAAAAA ** 4521580 TTACGAAAATACCCC-AGGGGATACC 130 TTACGAAAATACCCCTAAAGGATACC * * * 4521605 TTCGACGTGAAAGTACCCTGATACCCTTAAATGACTTAAAAAGGATAATAGATGAGATGAACCTA 1 TTCGACGTAAAAGTATCC-GATACCCTTAAAGGACTTAAAAAGGATAATAGATGAGATGAACCTA * * * * * 4521670 TCCTAAATATCTAACTTCAGCATAAAAACGGACCCGGTGACAACCTAAGACTCGGTTCT-AAAAA 65 TCCTAAATATCTACCTTCAGCATAAAAGCAGACTCGGTGACAACCTAAGACTCGATTCTAAAAAA ** * * 4521734 TTACGAAAATA-CTTTTAGGGATACC 130 TTACGAAAATACCCCTAAAGGATACC * * 4521759 TTCGACGTAAAAGTA-CTCGATACCTTTAAAGAACTTAAAAAGGATAATAGATGAGATGAACCTT 1 TTCGACGTAAAAGTATC-CGATACCCTTAAAGGACTTAAAAAGGATAATAGATGAGATGAACC-T * * * * * * * * 4521823 ATCCTAAATATTTACCTTCGGCATAAAAGCATACCCGGTGATAACCTAGGACTCGATTTTGAAAA 64 ATCCTAAATATCTACCTTCAGCATAAAAGCAGACTCGGTGACAACCTAAGACTCGATTCTAAAAA ** * * 4521888 ATTATAAAAAT-GCCCTATGAAGGATACT 129 ATTACGAAAATACCCCTA--AAGGATACC * * * 4521916 TTCGATGTAAAAGTACCCGATACTCC-TAAAGAACTTAAAAAGGATAATAGATGAGATGAACCTA 1 TTCGACGTAAAAGTATCCGATAC-CCTTAAAGGACTTAAAAAGGATAATAGATGAGATGAACCTA * * * * * * * * 4521980 TCCTAAATATTTACCTTCGGAATAAAAGTAGAC-CTGGTGCCAATCTAAGACTTGATTTTAAAAA 65 TCCTAAATATCTACCTTCAGCATAAAAGCAGACTC-GGTGACAACCTAAGACTCGATTCTAAAAA * * * * 4522044 ATTACGAAAATGCCTCTAGAGGAGACC 129 ATTACGAAAATACCCCTAAAGGATACC * * ** * * 4522071 TTCAATGTAAAAGTATTAGATGCCCTTAGAGGACTTAAAAAGG 1 TTCGACGTAAAAGTATCCGATACCCTTAAAGGACTTAAAAAGG 4522114 TTTGAAATGA Statistics Matches: 698, Mismatches: 100, Indels: 39 0.83 0.12 0.05 Matches are distributed among these distances: 153 43 0.06 154 216 0.31 155 238 0.34 156 132 0.19 157 67 0.10 158 2 0.00 ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25 Consensus pattern (155 bp): TTCGACGTAAAAGTATCCGATACCCTTAAAGGACTTAAAAAGGATAATAGATGAGATGAACCTAT CCTAAATATCTACCTTCAGCATAAAAGCAGACTCGGTGACAACCTAAGACTCGATTCTAAAAAAT TACGAAAATACCCCTAAAGGATACC Found at i:4523436 original size:11 final size:11 Alignment explanation

Indices: 4523420--4523454 Score: 52 Period size: 11 Copynumber: 3.1 Consensus size: 11 4523410 TCCAAAAATC 4523420 TTTTCTTTTCT 1 TTTTCTTTTCT * 4523431 TTTTCTTCTCT 1 TTTTCTTTTCT 4523442 TTTTCATTTTCT 1 TTTTC-TTTTCT 4523454 T 1 T 4523455 CTCGTCAATT Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 11 15 0.71 12 6 0.29 ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77 Consensus pattern (11 bp): TTTTCTTTTCT Found at i:4523451 original size:17 final size:17 Alignment explanation

Indices: 4523425--4523457 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 4523415 AAATCTTTTC * 4523425 TTTTCTTTTTCTTCTCT 1 TTTTCATTTTCTTCTCT 4523442 TTTTCATTTTCTTCTC 1 TTTTCATTTTCTTCTC 4523458 GTCAATTTTG Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73 Consensus pattern (17 bp): TTTTCATTTTCTTCTCT Found at i:4523769 original size:14 final size:13 Alignment explanation

Indices: 4523750--4523783 Score: 50 Period size: 14 Copynumber: 2.5 Consensus size: 13 4523740 CAATAAAAAT 4523750 AATTAAATTATAAA 1 AATTAAATT-TAAA 4523764 AATTAAAATTTAAA 1 AATT-AAATTTAAA 4523778 AATTAA 1 AATTAA 4523784 GATAAAATTT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 13 2 0.11 14 12 0.63 15 5 0.26 ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35 Consensus pattern (13 bp): AATTAAATTTAAA Found at i:4524278 original size:163 final size:165 Alignment explanation

Indices: 4523996--4524397 Score: 451 Period size: 163 Copynumber: 2.4 Consensus size: 165 4523986 TATTAAATGA * ** * 4523996 ATTTTAAAAATTTTA-A-ATAAAAAAAATCACCCT-AAAAATATTTACGGAATAGAAAACTCAGT 1 ATTTTAAAAATTTTAGACCT-AAAAAAATC-CCCTCGGAAATATTTATGGAATAGAAAACTCA-T ** ** * 4524058 TTTTTGTGAAAGTAGGCATTTCAAGGAAAAAAATAAAAAATTCATGAAAATGAATTAAATTTTC- 63 TTTTTGAAAAAAAAGGCATTTCAA-GAAAAAAATAAAAAACTCATGAAAATGAATTAAATTTTCA * * * * 4524122 AAAACGAATTTAATGGAAATTCTATGACATTGTTAGATAC 127 AAAACG-ATTTAATGGAAATTCCATGAAATTATTACATAC * * 4524162 ATTTTAAAAATTTTAGACC-AAGGAAAATCCCCTCGGAAATATTTATGGAATAGGAAACTCGATT 1 ATTTTAAAAATTTTAGACCTAA-AAAAATCCCCTCGGAAATATTTATGGAATAGAAAACTC-ATT ** * 4524226 TTTTGAAAAAAAAGG-ATTTC-A-AAAAAAATCCAAAACTCATGAATATGAATTAAATTTTCAAA 64 TTTTGAAAAAAAAGGCATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATTAAATTTTCAAA * * 4524288 AATGATTTAATGGGAATTCCATGAAATTATTACATAC 129 AACGATTTAATGGAAATTCCATGAAATTATTACATAC * * * * 4524325 ATTTTAAAAATTTTAGACCTAAAAAAATCCCTTTGGACATATTTATGGAATAGAAAAATCAATTT 1 ATTTTAAAAATTTTAGACCTAAAAAAATCCCCTCGGAAATATTTATGGAATAGAAAACTC-ATTT * 4524390 TTCGAAAA 65 TTTGAAAA 4524398 TAGAAAAATT Statistics Matches: 201, Mismatches: 28, Indels: 17 0.82 0.11 0.07 Matches are distributed among these distances: 163 124 0.62 164 7 0.03 165 1 0.00 166 26 0.13 167 42 0.21 168 1 0.00 ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32 Consensus pattern (165 bp): ATTTTAAAAATTTTAGACCTAAAAAAATCCCCTCGGAAATATTTATGGAATAGAAAACTCATTTT TTGAAAAAAAAGGCATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATTAAATTTTCAAAAA CGATTTAATGGAAATTCCATGAAATTATTACATAC Found at i:4526991 original size:78 final size:77 Alignment explanation

Indices: 4526759--4527014 Score: 247 Period size: 78 Copynumber: 3.3 Consensus size: 77 4526749 GAGATAAGAG * * * * * 4526759 CGGGGTTGGAGTAT-CTCCAATGGTGGAAAATCGATGTTTTGGAAACAAACCGGGGTTGGAGTAT 1 CGGGGTTGGAGTATCCT-CGATTGT-GAAAATCGATGTTTTGAAAAAAAACTGGGGTTGGAGTAT 4526823 -CCTCTCAGAAATAA 64 CCCT-TCAGAAATAA * * * ** * * 4526837 CGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATATTTT-AGAAATAAGGTCGGGATTAGAGTA 1 CGGGGTTGGAGTATCCTCGATTGTG-AAAATCGATGTTTTGA-AAAAAAACT-GGGGTTGGAGTA * * 4526901 -CTCGTC-GAAAATAA 63 TCCCTTCAG-AAATAA 4526915 CGGGGTTGGAGTATTCC-CGATTGTGAAAAGTC-AGTGTTTTGAAAAAAAACTGGGGTTGGAGTA 1 CGGGGTTGGAGTA-TCCTCGATTGTGAAAA-TCGA-TGTTTTGAAAAAAAACTGGGGTTGGAGTA 4526978 TCCCTTCAGAAATAA 63 TCCCTTCAGAAATAA 4526993 CGGGGTTGGAGTATCCTCGATT 1 CGGGGTTGGAGTATCCTCGATT 4527015 ATAAAATTTT Statistics Matches: 143, Mismatches: 22, Indels: 26 0.75 0.12 0.14 Matches are distributed among these distances: 77 20 0.14 78 105 0.73 79 18 0.13 ACGTcount: A:0.30, C:0.13, G:0.29, T:0.28 Consensus pattern (77 bp): CGGGGTTGGAGTATCCTCGATTGTGAAAATCGATGTTTTGAAAAAAAACTGGGGTTGGAGTATCC CTTCAGAAATAA Found at i:4528504 original size:16 final size:16 Alignment explanation

Indices: 4528477--4528525 Score: 71 Period size: 16 Copynumber: 3.0 Consensus size: 16 4528467 TTTTTTAATT 4528477 ATTTTTTGATTTTTTTG 1 ATTTTTT-ATTTTTTTG * 4528494 ATTTTTTATTTCTTTG 1 ATTTTTTATTTTTTTG * 4528510 ATTTTTAATTTTTTTG 1 ATTTTTTATTTTTTTG 4528526 TGTCGAAAAC Statistics Matches: 29, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 16 22 0.76 17 7 0.24 ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76 Consensus pattern (16 bp): ATTTTTTATTTTTTTG Found at i:4528524 original size:9 final size:9 Alignment explanation

Indices: 4528478--4528515 Score: 53 Period size: 9 Copynumber: 4.4 Consensus size: 9 4528468 TTTTTAATTA 4528478 TTTTTTGAT 1 TTTTTTGAT 4528487 TTTTTTGA- 1 TTTTTTGAT 4528495 TTTTTT-AT 1 TTTTTTGAT * 4528503 TTCTTTGAT 1 TTTTTTGAT 4528512 TTTT 1 TTTT 4528516 AATTTTTTTG Statistics Matches: 25, Mismatches: 2, Indels: 4 0.81 0.06 0.13 Matches are distributed among these distances: 7 1 0.04 8 11 0.44 9 13 0.52 ACGTcount: A:0.11, C:0.03, G:0.08, T:0.79 Consensus pattern (9 bp): TTTTTTGAT Found at i:4529217 original size:43 final size:43 Alignment explanation

Indices: 4529153--4529246 Score: 116 Period size: 43 Copynumber: 2.2 Consensus size: 43 4529143 AGAAGAGTGA * * * 4529153 TAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTT 1 TAAAGATGCCAATATGATGATTCAAAGCCAGCGACATTGGGTT * * * ** 4529196 TAAAGGTGCCAATGTGATGATTCAAAGCCAGTGACATTGGACT 1 TAAAGATGCCAATATGATGATTCAAAGCCAGCGACATTGGGTT 4529239 TAAAGATG 1 TAAAGATG 4529247 ACAGAGGTGT Statistics Matches: 42, Mismatches: 9, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 43 42 1.00 ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27 Consensus pattern (43 bp): TAAAGATGCCAATATGATGATTCAAAGCCAGCGACATTGGGTT Found at i:4529351 original size:61 final size:63 Alignment explanation

Indices: 4529258--4529593 Score: 333 Period size: 61 Copynumber: 5.5 Consensus size: 63 4529248 CAGAGGTGTT * * * 4529258 AATATGCTAATTCAAGGCCAACGATATCGGGCTTG-AAGTTGAGAA-AATTGATAAAGGTGCC 1 AATATACTGATTCAAGGCCAACGATATCGGGCTTGAAAGATGAGAAGAATTGATAAAGGTGCC * * * * 4529319 AATATGCTGATTCAAAGCCAGCGATATTGGGCTTGAAAGATGAGAAGAA-TGATAAAGGTGCC 1 AATATACTGATTCAAGGCCAACGATATCGGGCTTGAAAGATGAGAAGAATTGATAAAGGTGCC * * * * 4529381 AATATACTGATTCAAGGCCAGCGATATTGGGCTTGAAAGA-AAGAAGATTTGA-AAA-GTGCC 1 AATATACTGATTCAAGGCCAACGATATCGGGCTTGAAAGATGAGAAGAATTGATAAAGGTGCC * * * * * * 4529441 AATGTATTGATTCAAGGCCAACGACATCGAGATTGAAA-ATGAGAA-AACTGATAAAGGTGCC 1 AATATACTGATTCAAGGCCAACGATATCGGGCTTGAAAGATGAGAAGAATTGATAAAGGTGCC * * 4529502 AATATACTGATTCAAGGCCAACGATA-CTGGACTT-AAAGAT--GAAG-ATT--TAACGAGTGCC 1 AATATACTGATTCAAGGCCAACGATATC-GGGCTTGAAAGATGAGAAGAATTGATAAAG-GTGCC * ** * * 4529560 AATGTGTTGATTCAAGGCCAACGACATTGGGCTT 1 AATATACTGATTCAAGGCCAACGATATCGGGCTT 4529594 AGAAGGGTTA Statistics Matches: 231, Mismatches: 33, Indels: 25 0.80 0.11 0.09 Matches are distributed among these distances: 57 4 0.02 58 32 0.14 59 10 0.04 60 47 0.20 61 73 0.32 62 63 0.27 63 2 0.01 ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24 Consensus pattern (63 bp): AATATACTGATTCAAGGCCAACGATATCGGGCTTGAAAGATGAGAAGAATTGATAAAGGTGCC Found at i:4529477 original size:60 final size:59 Alignment explanation

Indices: 4529305--4529586 Score: 182 Period size: 62 Copynumber: 4.7 Consensus size: 59 4529295 GTTGAGAAAA * * * * * * * 4529305 TTGATAAAGGTGCCAATATGCTGATTCAAAGCCAGCGATATTGGGCTTGAAAGATGAGAAGA- 1 TTGA-AAA-GTGCCAATATACTGATTCAAGGCCAACGACA-TCGGATTGAAAGA-AAGAAGAT * * * * * 4529367 ATGATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGGCTTGAAAGAAAGAAGAT 1 TTGA-AAA-GTGCCAATATACTGATTCAAGGCCAACGACA-TCGGATTGAAAGAAAGAAGAT * * * * 4529429 TTGAAAAGTGCCAATGTATTGATTCAAGGCCAACGACATCGAGATTGAAA-ATGAGAA-AA 1 TTGAAAAGTGCCAATATACTGATTCAAGGCCAACGACATCG-GATTGAAAGA-AAGAAGAT * * * 4529488 CTGATAAAGGTGCCAATATACTGATTCAAGGCCAACGATA-CTGGACTT-AAAG-ATGAAGAT 1 TTGA-AAA-GTGCCAATATACTGATTCAAGGCCAACGACATC-GGA-TTGAAAGAAAGAAGAT * * ** 4529548 TT-AACGAGTGCCAATGTGTTGATTCAAGGCCAACGACAT 1 TTGAA-AAGTGCCAATATACTGATTCAAGGCCAACGACAT 4529587 TGGGCTTAGA Statistics Matches: 183, Mismatches: 26, Indels: 25 0.78 0.11 0.11 Matches are distributed among these distances: 58 28 0.15 59 12 0.07 60 49 0.27 61 40 0.22 62 54 0.30 ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23 Consensus pattern (59 bp): TTGAAAAGTGCCAATATACTGATTCAAGGCCAACGACATCGGATTGAAAGAAAGAAGAT Found at i:4529496 original size:183 final size:179 Alignment explanation

Indices: 4529267--4529593 Score: 440 Period size: 183 Copynumber: 1.8 Consensus size: 179 4529257 TAATATGCTA * * * ** * * 4529267 ATTCAAGGCCAACGATATCGGGCTTGAAGTTGAGAAAATTGATAAAGGTGCCAATATGCTGATTC 1 ATTCAAGGCCAACGACATCGAGATTGAAAATGAGAAAACTGATAAAGGTGCCAATATACTGATTC * * * 4529332 AAAGCCAGCGATATTGGGCTTGAAAGATGAGAAGAATGATAAAG-GTGCCAATATACTGATTCAA 66 AAAGCCAACGATACTGGACTT-AAAGAT--GAAG-AT-ATAAAGAGTGCCAATATACTGATTCAA * * 4529396 GGCCAGCGATATTGGGCTTGAAAGAAAGAAGATTTGAAAAGTGCCAATGTATTG 126 GGCCAACGACATTGGGCTTGAAAGAAAGAAGATTTGAAAAGTGCCAATGTATTG 4529450 ATTCAAGGCCAACGACATCGAGATTGAAAATGAGAAAACTGATAAAGGTGCCAATATACTGATTC 1 ATTCAAGGCCAACGACATCGAGATTGAAAATGAGAAAACTGATAAAGGTGCCAATATACTGATTC * * * * ** 4529515 AAGGCCAACGATACTGGACTTAAAGATGAAGATTTAACGAGTGCCAATGTGTTGATTCAAGGCCA 66 AAAGCCAACGATACTGGACTTAAAGATGAAGATATAAAGAGTGCCAATATACTGATTCAAGGCCA 4529580 ACGACATTGGGCTT 131 ACGACATTGGGCTT 4529594 AGAAGGGTTA Statistics Matches: 125, Mismatches: 18, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 178 4 0.03 179 36 0.29 180 4 0.03 182 6 0.05 183 75 0.60 ACGTcount: A:0.37, C:0.15, G:0.25, T:0.24 Consensus pattern (179 bp): ATTCAAGGCCAACGACATCGAGATTGAAAATGAGAAAACTGATAAAGGTGCCAATATACTGATTC AAAGCCAACGATACTGGACTTAAAGATGAAGATATAAAGAGTGCCAATATACTGATTCAAGGCCA ACGACATTGGGCTTGAAAGAAAGAAGATTTGAAAAGTGCCAATGTATTG Found at i:4529667 original size:32 final size:31 Alignment explanation

Indices: 4529608--4529680 Score: 103 Period size: 32 Copynumber: 2.3 Consensus size: 31 4529598 GGGTTATGTA * 4529608 GGCTTTAGAAGGGTTGCCACCGACTTGTGTG 1 GGCTTTAGAAAGGTTGCCACCGACTTGTGTG * 4529639 GGCTTTGAGAAAGGTTGTCACC-AGCTTGTGTG 1 GGCTTT-AGAAAGGTTGCCACCGA-CTTGTGTG 4529671 GGCTTTAGAA 1 GGCTTTAGAA 4529681 GGGTCCCACT Statistics Matches: 38, Mismatches: 2, Indels: 4 0.86 0.05 0.09 Matches are distributed among these distances: 31 11 0.29 32 27 0.71 ACGTcount: A:0.19, C:0.16, G:0.34, T:0.30 Consensus pattern (31 bp): GGCTTTAGAAAGGTTGCCACCGACTTGTGTG Found at i:4529744 original size:28 final size:28 Alignment explanation

Indices: 4529667--4530265 Score: 455 Period size: 28 Copynumber: 21.1 Consensus size: 28 4529657 CACCAGCTTG * * * 4529667 TGTGGGCTTT-AGAAGGGTCCCACTAACT 1 TGTGGGCTTTGA-AAAGGTGCCACTGACT * * * 4529695 TGTAGGCTTTTGAAATGATGCCACTGACT 1 TGTGGGC-TTTGAAAAGGTGCCACTGACT * * * 4529724 CGTGGGCTTTGAAAAGGTGCCATTAACT 1 TGTGGGCTTTGAAAAGGTGCCACTGACT * * 4529752 CGTGGGATTT-AAAAGGATGCCACTGACT 1 TGTGGGCTTTGAAAAGG-TGCCACTGACT ** 4529780 TGTGGGCTTT-AAGCGGATGCCACTGACT 1 TGTGGGCTTTGAAAAGG-TGCCACTGACT * * 4529808 TGTGGGCTTTG-AACGAGTGTCACTGACT 1 TGTGGGCTTTGAAAAG-GTGCCACTGACT ** * 4529836 TGTGGGCTTT-AAGCGGATGCCACTAACT 1 TGTGGGCTTTGAAAAGG-TGCCACTGACT * ** 4529864 TGTGGTCTTTGAATGGGTGCCACTGACT 1 TGTGGGCTTTGAAAAGGTGCCACTGACT * * 4529892 TATGGGCTTTGAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAAGGTGCCACTGACT * * 4529920 CGTGGGCTTT-AAAAGGGTGCCACTAACT 1 TGTGGGCTTTGAAAA-GGTGCCACTGACT * * * * 4529948 CGTGGGCTTTAAAAAGATGCTACTGACT 1 TGTGGGCTTTGAAAAGGTGCCACTGACT * * 4529976 TGTGGGCTTT-AAAAGGGTACCACTAACT 1 TGTGGGCTTTGAAAA-GGTGCCACTGACT * * * 4530004 TATGGGCTTTGAAAAGGAGCCACTAACT 1 TGTGGGCTTTGAAAAGGTGCCACTGACT ** * * * 4530032 CATGGGCATTG-GAAGGATGCCACTAACT 1 TGTGGGCTTTGAAAAGG-TGCCACTGACT * * 4530060 TGTGGGCTTAGAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAAGGTGCCACTGACT * * 4530088 GGTGGGTTTTGAAAAGGTGCCACTGACT 1 TGTGGGCTTTGAAAAGGTGCCACTGACT *** 4530116 CAAGGGCTTT-AAAAGGGTGCCACTGACT 1 TGTGGGCTTTGAAAA-GGTGCCACTGACT * 4530144 TGTGGGCTTT-AAAAGGTTGCCACTAACT 1 TGTGGGCTTTGAAAAGG-TGCCACTGACT * 4530172 TGTGGGCTTTGAAAAGGTCCCA-TCGACT 1 TGTGGGCTTTGAAAAGGTGCCACT-GACT ** * ** 4530200 CATGGGCTTTGGAGAAGGTTGCCACCAACT 1 TGTGGGCTTT-GAAAAGG-TGCCACTGACT * ** 4530230 TGTATGGGCTTTAGAGAAGGTTGCCACCAACT 1 TG--TGGGCTTT-GAAAAGG-TGCCACTGACT 4530262 TGTG 1 TGTG 4530266 TGGGCTTTAA Statistics Matches: 469, Mismatches: 79, Indels: 44 0.79 0.13 0.07 Matches are distributed among these distances: 27 25 0.05 28 357 0.76 29 48 0.10 30 10 0.02 32 29 0.06 ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28 Consensus pattern (28 bp): TGTGGGCTTTGAAAAGGTGCCACTGACT Found at i:4529817 original size:84 final size:84 Alignment explanation

Indices: 4529608--4530188 Score: 496 Period size: 84 Copynumber: 6.8 Consensus size: 84 4529598 GGGTTATGTA * * * * * 4529608 GGCTTTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAAGGTTGTCACCAGCTTGTGTGGG 1 GGCTTTA-AA-GGATGCCACTGAC-T-TGTGGGCTTTGA-AAAGG-TGCCACTAAC-T-TGTGGG * * * * * 4529673 CTTT-AGAAGGGTCCCACTAACTTGTA 58 CTTTGAAAAGGATGCCACTAACTCGTG * * * * * 4529699 GGCTTTTGAAATGATGCCACTGACTCGTGGGCTTTGAAAAGGTGCCATTAACTCGTGGGATTT-A 1 GGC-TTT-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGA * * 4529763 AAAGGATGCCACTGACTTGTG 64 AAAGGATGCCACTAACTCGTG * * * * 4529784 GGCTTTAAGCGGATGCCACTGACTTGTGGGCTTTG-AACGAGTGTCACTGACTTGTGGGCTTT-A 1 GGCTTTAA-AGGATGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTAACTTGTGGGCTTTGA ** * 4529847 AGCGGATGCCACTAACTTGTG 64 AAAGGATGCCACTAACTCGTG * * * * * * * 4529868 GTCTTTGAATGGGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACTCGTGGGCTTT-AA 1 GGCTTT-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGAA * 4529932 AAGGGTGCCACTAACTCGTG 65 AAGGATGCCACTAACTCGTG * * * * 4529952 GGCTTTAAAAAGATGCTACTGACTTGTGGGCTTT-AAAAGGGTACCACTAACTTATGGGCTTTGA 1 GGCTTT-AAAGGATGCCACTGACTTGTGGGCTTTGAAAA-GGTGCCACTAACTTGTGGGCTTTGA * 4530016 AAAGGA-GCCACTAACTCATG 64 AAAGGATGCCACTAACTCGTG ** * * * * * * 4530036 GGCATTGGAAGGATGCCACTAACTTGTGGGCTTAGAAAGGGTGCCACTGACTGGTGGGTTTTGAA 1 GGC-TTTAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGAA * ** 4530101 AAGG-TGCCACTGACTCAAG 65 AAGGATGCCACTAACTCGTG * 4530120 GGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTT-AAAAGGTTGCCACTAACTTGTGGGCTTTGA 1 GGCTTT-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTAACTTGTGGGCTTTGA 4530184 AAAGG 64 AAAGG 4530189 TCCCATCGAC Statistics Matches: 402, Mismatches: 75, Indels: 33 0.79 0.15 0.06 Matches are distributed among these distances: 83 15 0.04 84 300 0.75 85 44 0.11 86 1 0.00 87 6 0.01 88 5 0.01 89 11 0.03 90 1 0.00 91 13 0.03 92 5 0.01 93 1 0.00 ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28 Consensus pattern (84 bp): GGCTTTAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGAAA AGGATGCCACTAACTCGTG Found at i:4530189 original size:84 final size:83 Alignment explanation

Indices: 4529667--4530276 Score: 506 Period size: 84 Copynumber: 7.2 Consensus size: 83 4529657 CACCAGCTTG * * ** * * * * 4529667 TGTGGGCTTTAGAAGGGTCCCACTAACTTGTAGGCTTTTGAAATGATGCCACTGACTCGTGGGCT 1 TGTGGGCTTTA-AAAGGTGCCACTAACTCATGGGC-TTTAAAAGGATGCCACTGACTTGTGGGCT * 4529732 TTGAAAA-GGTGCCATTAACT 64 TT-AAAAGGGTGCCACTAACT * * * ** ** 4529752 CGTGGGATTTAAAAGGATGCCACTGACTTGTGGGCTTTAAGCGGATGCCACTGACTTGTGGGCTT 1 TGTGGGCTTTAAAAGG-TGCCACTAACTCATGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTT * * * * * 4529817 TGAACGAGTGTCACTGACT 65 TAAAAGGGTGCCACTAACT ** ** * * * * * 4529836 TGTGGGCTTTAAGCGGATGCCACTAACTTGTGGTCTTTGAATGGGTGCCACTGACTTATGGGCTT 1 TGTGGGCTTTAAAAGG-TGCCACTAACTCATGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTT * * 4529901 TGAAAGGGTGCCACTGACT 65 TAAAAGGGTGCCACTAACT * * * * 4529920 CGTGGGCTTTAAAAGGGTGCCACTAACTCGTGGGCTTTAAAAAGATGCTACTGACTTGTGGGCTT 1 TGTGGGCTTTAAAA-GGTGCCACTAACTCATGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTT * 4529985 TAAAAGGGTACCACTAACT 65 TAAAAGGGTGCCACTAACT * * * ** * 4530004 TATGGGCTTTGAAAAGGAGCCACTAACTCATGGGCATTGGAAGGATGCCACTAACTTGTGGGC-T 1 TGTGGGCTTT-AAAAGGTGCCACTAACTCATGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTT * 4530068 TAGAAAGGGTGCCACTGACT 65 TA-AAAGGGTGCCACTAACT * * * * * 4530088 GGTGGGTTTTGAAAAGGTGCCACTGACTCAAGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTT 1 TGTGGGCTTT-AAAAGGTGCCACTAACTCATGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTT * 4530153 TAAAAGGTTGCCACTAACT 65 TAAAAGGGTGCCACTAACT * * * * ** 4530172 TGTGGGCTTTGAAAAGGTCCCA-TCGACTCATGGGCTTTGGAGAAGGTTGCCACCAACTTGTATG 1 TGTGGGCTTT-AAAAGGTGCCACT-AACTCATGGGCTTT--AAAAGGATGCCACTGACTTG--TG * * 4530236 GGCTTTAGAGAAGGTTGCCACCAACTT 60 GGCTTTA-A-AAGGGTGCCACTAAC-T 4530263 GTGTGGGCTTTAAA 1 -TGTGGGCTTTAAA 4530277 GAAGGTTTCT Statistics Matches: 431, Mismatches: 79, Indels: 24 0.81 0.15 0.04 Matches are distributed among these distances: 83 6 0.01 84 338 0.78 85 33 0.08 86 16 0.04 88 9 0.02 89 1 0.00 90 14 0.03 91 4 0.01 92 10 0.02 ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28 Consensus pattern (83 bp): TGTGGGCTTTAAAAGGTGCCACTAACTCATGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTT AAAAGGGTGCCACTAACT Found at i:4530238 original size:32 final size:32 Alignment explanation

Indices: 4530146--4530283 Score: 139 Period size: 32 Copynumber: 4.6 Consensus size: 32 4530136 CACTGACTTG * 4530146 TGGGCTTTA-A-AAGGTTGCCACTAACTTG-- 1 TGGGCTTTAGAGAAGGTTGCCACCAACTTGTA * * * * * 4530174 TGGGCTTT-GAAAAGG-TCCCATCGAC-T-CA 1 TGGGCTTTAGAGAAGGTTGCCACCAACTTGTA * 4530202 TGGGCTTTGGAGAAGGTTGCCACCAACTTGTA 1 TGGGCTTTAGAGAAGGTTGCCACCAACTTGTA * 4530234 TGGGCTTTAGAGAAGGTTGCCACCAACTTGTG 1 TGGGCTTTAGAGAAGGTTGCCACCAACTTGTA * 4530266 TGGGCTTTAAAGAAGGTT 1 TGGGCTTTAGAGAAGGTT 4530284 TCTCCACTGG Statistics Matches: 90, Mismatches: 12, Indels: 12 0.79 0.11 0.11 Matches are distributed among these distances: 27 1 0.01 28 23 0.26 29 10 0.11 30 7 0.08 31 1 0.01 32 48 0.53 ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29 Consensus pattern (32 bp): TGGGCTTTAGAGAAGGTTGCCACCAACTTGTA Found at i:4530531 original size:28 final size:28 Alignment explanation

Indices: 4530455--4530538 Score: 107 Period size: 28 Copynumber: 3.0 Consensus size: 28 4530445 TATATAGCAA * 4530455 GTGCCACTGA-TTGTGGACTTCGAAAAG 1 GTGCCACTGACTTGTGGACTTTGAAAAG * * * 4530482 ATGCCACTGACTTGTAGACTTTGAAGAG 1 GTGCCACTGACTTGTGGACTTTGAAAAG * * 4530510 GTGCCACTGACTAGTGGGCTTTGAAAAG 1 GTGCCACTGACTTGTGGACTTTGAAAAG 4530538 G 1 G 4530539 GATTCGTGTT Statistics Matches: 47, Mismatches: 9, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 27 9 0.19 28 38 0.81 ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26 Consensus pattern (28 bp): GTGCCACTGACTTGTGGACTTTGAAAAG Found at i:4545589 original size:21 final size:20 Alignment explanation

Indices: 4545538--4545596 Score: 66 Period size: 20 Copynumber: 2.9 Consensus size: 20 4545528 ATAATCACAC 4545538 TAGGTATCGATACCACACCT 1 TAGGTATCGATACCACACCT * 4545558 TAGGCATCGATACCA-AGCCT 1 TAGGTATCGATACCACA-CCT * * 4545578 TCATGTATCGATACTACAC 1 T-AGGTATCGATACCACAC 4545597 ATGGATATTC Statistics Matches: 32, Mismatches: 4, Indels: 5 0.78 0.10 0.12 Matches are distributed among these distances: 19 1 0.03 20 18 0.56 21 12 0.38 22 1 0.03 ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25 Consensus pattern (20 bp): TAGGTATCGATACCACACCT Found at i:4546667 original size:9 final size:9 Alignment explanation

Indices: 4546647--4546703 Score: 57 Period size: 9 Copynumber: 6.4 Consensus size: 9 4546637 TCTTATTCTC 4546647 TTTT-CTTT 1 TTTTGCTTT * 4546655 TTTTGTGTTT 1 TTTTG-CTTT 4546665 TTTTGCTTT 1 TTTTGCTTT 4546674 TTTT--TTCT 1 TTTTGCTT-T * 4546682 TTTTCCTTT 1 TTTTGCTTT 4546691 TTTTGCTTT 1 TTTTGCTTT 4546700 TTTT 1 TTTT 4546704 TTCTATTAGT Statistics Matches: 41, Mismatches: 3, Indels: 9 0.77 0.06 0.17 Matches are distributed among these distances: 7 2 0.05 8 9 0.22 9 20 0.49 10 10 0.24 ACGTcount: A:0.00, C:0.11, G:0.07, T:0.82 Consensus pattern (9 bp): TTTTGCTTT Found at i:4560201 original size:19 final size:18 Alignment explanation

Indices: 4560155--4560272 Score: 94 Period size: 19 Copynumber: 6.8 Consensus size: 18 4560145 ATTTCAACAA * 4560155 TTTGTATCGATACAAACAG 1 TTTGTATCGATACATA-AG 4560174 TAATTGTATCGATACATAAG 1 T--TTGTATCGATACATAAG 4560194 TGTTGTATCGATAC--AA- 1 T-TTGTATCGATACATAAG 4560210 --TGTATCGATACATAAG 1 TTTGTATCGATACATAAG * 4560226 TGGTGTATCGATAC--AA- 1 T-TTGTATCGATACATAAG 4560242 --TGTATCGATACATAAG 1 TTTGTATCGATACATAAG 4560258 TATTGTATCGATACA 1 T-TTGTATCGATACA 4560273 ATGTATCGTT Statistics Matches: 83, Mismatches: 2, Indels: 28 0.73 0.02 0.25 Matches are distributed among these distances: 13 22 0.27 15 4 0.05 17 4 0.05 19 36 0.43 20 3 0.04 21 14 0.17 ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34 Consensus pattern (18 bp): TTTGTATCGATACATAAG Found at i:4560215 original size:13 final size:13 Alignment explanation

Indices: 4560197--4560253 Score: 60 Period size: 13 Copynumber: 3.9 Consensus size: 13 4560187 ACATAAGTGT 4560197 TGTATCGATACAA 1 TGTATCGATACAA 4560210 TGTATCGATACATAA 1 TGTATCGATAC--AA 4560225 GTGGTGTATCGATACAA 1 ----TGTATCGATACAA 4560242 TGTATCGATACA 1 TGTATCGATACA 4560254 TAAGTATTGT Statistics Matches: 38, Mismatches: 0, Indels: 12 0.76 0.00 0.24 Matches are distributed among these distances: 13 23 0.61 15 2 0.05 17 2 0.05 19 11 0.29 ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:4560219 original size:32 final size:32 Alignment explanation

Indices: 4560178--4560280 Score: 188 Period size: 32 Copynumber: 3.2 Consensus size: 32 4560168 AAACAGTAAT 4560178 TGTATCGATACATAAGTGTTGTATCGATACAA 1 TGTATCGATACATAAGTGTTGTATCGATACAA * 4560210 TGTATCGATACATAAGTGGTGTATCGATACAA 1 TGTATCGATACATAAGTGTTGTATCGATACAA * 4560242 TGTATCGATACATAAGTATTGTATCGATACAA 1 TGTATCGATACATAAGTGTTGTATCGATACAA 4560274 TGTATCG 1 TGTATCG 4560281 TTACGAAGCT Statistics Matches: 68, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 32 68 1.00 ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34 Consensus pattern (32 bp): TGTATCGATACATAAGTGTTGTATCGATACAA Found at i:4560342 original size:13 final size:13 Alignment explanation

Indices: 4560324--4560351 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 4560314 CATTACTCAA 4560324 TGTATCGATACAT 1 TGTATCGATACAT 4560337 TGTATCGATACAT 1 TGTATCGATACAT 4560350 TG 1 TG 4560352 AGTAATGTAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 15 1.00 ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39 Consensus pattern (13 bp): TGTATCGATACAT Found at i:4561853 original size:13 final size:13 Alignment explanation

Indices: 4561835--4561860 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 4561825 TACACAAAGT 4561835 ATGTATCGATACA 1 ATGTATCGATACA 4561848 ATGTATCGATACA 1 ATGTATCGATACA 4561861 CAAAAAATTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:4561858 original size:32 final size:33 Alignment explanation

Indices: 4561817--4561880 Score: 103 Period size: 32 Copynumber: 2.0 Consensus size: 33 4561807 TAGCCAAACT ** 4561817 TGTATCGATACACAAAGTA-TGTATCGATACAA 1 TGTATCGATACACAAAAAATTGTATCGATACAA 4561849 TGTATCGATACACAAAAAATTGTATCGATACA 1 TGTATCGATACACAAAAAATTGTATCGATACA 4561881 TTGGCTTGTA Statistics Matches: 29, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 32 17 0.59 33 12 0.41 ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28 Consensus pattern (33 bp): TGTATCGATACACAAAAAATTGTATCGATACAA Found at i:4568044 original size:13 final size:13 Alignment explanation

Indices: 4568026--4568062 Score: 56 Period size: 13 Copynumber: 2.8 Consensus size: 13 4568016 ACATTTTTCT 4568026 TTGTATCGATACA 1 TTGTATCGATACA * 4568039 TTGTATAGATACA 1 TTGTATCGATACA * 4568052 CTGTATCGATA 1 TTGTATCGATA 4568063 TAGGGGGATT Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 13 21 1.00 ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38 Consensus pattern (13 bp): TTGTATCGATACA Found at i:4569726 original size:23 final size:21 Alignment explanation

Indices: 4569684--4569726 Score: 50 Period size: 23 Copynumber: 2.0 Consensus size: 21 4569674 GTTTAATGTT ** 4569684 TTTGCTTGACTTTGTGTTTTA 1 TTTGCTTGACTTTGAATTTTA 4569705 TTTGCATTGTACTTTGAATTTT 1 TTTGC-TTG-ACTTTGAATTTT 4569727 TAATCTATAA Statistics Matches: 18, Mismatches: 2, Indels: 2 0.82 0.09 0.09 Matches are distributed among these distances: 21 5 0.28 22 3 0.17 23 10 0.56 ACGTcount: A:0.14, C:0.09, G:0.16, T:0.60 Consensus pattern (21 bp): TTTGCTTGACTTTGAATTTTA Found at i:4575771 original size:80 final size:80 Alignment explanation

Indices: 4575660--4575836 Score: 212 Period size: 80 Copynumber: 2.2 Consensus size: 80 4575650 GGTGTTTTGG * ** * 4575660 AAGTAAAAACGGGGTTGGAGCTTCCCCTCAGAGATTTTGGGGTTGGAATATCCTCAGAGATGTAA 1 AAGTAAAAACGGGGTTGAAGCTTCCCCTCAGAGATGATGGGGTTGGAATATCCTCAGAGATGAAA * 4575725 AATTCAATATTATGA 66 AAATCAATATTATGA * * * * * 4575740 AAGTAAAAACGGGGTTGAAG-TATCTCTTCAGAGATGATGGGGTTGGAGTATCTTCGGAGATGAA 1 AAGTAAAAACGGGGTTGAAGCT-TCCCCTCAGAGATGATGGGGTTGGAATATCCTCAGAGATGAA * * * 4575804 AAAATCGATGTTTTGA 65 AAAATCAATATTATGA * 4575820 AAGTAAAAATGGGGTTG 1 AAGTAAAAACGGGGTTG 4575837 GAGTGCCCCT Statistics Matches: 82, Mismatches: 14, Indels: 2 0.84 0.14 0.02 Matches are distributed among these distances: 79 1 0.01 80 81 0.99 ACGTcount: A:0.33, C:0.10, G:0.28, T:0.28 Consensus pattern (80 bp): AAGTAAAAACGGGGTTGAAGCTTCCCCTCAGAGATGATGGGGTTGGAATATCCTCAGAGATGAAA AAATCAATATTATGA Found at i:4575800 original size:26 final size:27 Alignment explanation

Indices: 4575750--4575802 Score: 72 Period size: 26 Copynumber: 2.0 Consensus size: 27 4575740 AAGTAAAAAC 4575750 GGGGTTGAAGTATCTCTTCAGAGATGAT 1 GGGGTTGAAGTA-CTCTTCAGAGATGAT * * 4575778 GGGGTTGGAGTA-TCTTCGGAGATGA 1 GGGGTTGAAGTACTCTTCAGAGATGA 4575803 AAAAATCGAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 26 12 0.52 28 11 0.48 ACGTcount: A:0.23, C:0.09, G:0.38, T:0.30 Consensus pattern (27 bp): GGGGTTGAAGTACTCTTCAGAGATGAT Found at i:4578259 original size:19 final size:19 Alignment explanation

Indices: 4578216--4578288 Score: 76 Period size: 20 Copynumber: 3.7 Consensus size: 19 4578206 CATATCCAGA * 4578216 TGTATCGATACAT-TATGCTT 1 TGTATCGATACATGT-T-CAT 4578236 TGTATCGATACATGTTCAT 1 TGTATCGATACATGTTCAT ** 4578255 TGTATCGATACATGCACAAT 1 TGTATCGATACATGTTC-AT * 4578275 TTTATCGATACATG 1 TGTATCGATACATG 4578289 AAACTGACAA Statistics Matches: 47, Mismatches: 4, Indels: 4 0.85 0.07 0.07 Matches are distributed among these distances: 19 17 0.36 20 29 0.62 21 1 0.02 ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40 Consensus pattern (19 bp): TGTATCGATACATGTTCAT Found at i:4578342 original size:20 final size:20 Alignment explanation

Indices: 4578317--4578410 Score: 145 Period size: 20 Copynumber: 4.7 Consensus size: 20 4578307 CTACCACTGT * 4578317 TTGTATCGATACATGGAA-TA 1 TTGTATCGATACAT-GAAGAA * 4578337 TTGTATCAATACATGAAGAA 1 TTGTATCGATACATGAAGAA 4578357 TTGTATCGATACATGAAGAA 1 TTGTATCGATACATGAAGAA * 4578377 TTGTATTGATACATGAAGAA 1 TTGTATCGATACATGAAGAA 4578397 TTGTATCGATACAT 1 TTGTATCGATACAT 4578411 TATCTCAAAC Statistics Matches: 68, Mismatches: 5, Indels: 2 0.91 0.07 0.03 Matches are distributed among these distances: 19 3 0.04 20 65 0.96 ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34 Consensus pattern (20 bp): TTGTATCGATACATGAAGAA Found at i:4580875 original size:13 final size:13 Alignment explanation

Indices: 4580857--4580881 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 4580847 CATAAAGTGT 4580857 TGTATCGATACAA 1 TGTATCGATACAA 4580870 TGTATCGATACA 1 TGTATCGATACA 4580882 TAAGTTTTGT 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:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:4580897 original size:32 final size:33 Alignment explanation

Indices: 4580837--4580902 Score: 116 Period size: 32 Copynumber: 2.0 Consensus size: 33 4580827 TTCAACGATT 4580837 TGTATCGATACATAAAGTGTTGTATCGATACAA 1 TGTATCGATACATAAAGTGTTGTATCGATACAA * 4580870 TGTATCGATACAT-AAGTTTTGTATCGATACAA 1 TGTATCGATACATAAAGTGTTGTATCGATACAA 4580902 T 1 T 4580903 TTAAGCTACT Statistics Matches: 32, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 32 19 0.59 33 13 0.41 ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36 Consensus pattern (33 bp): TGTATCGATACATAAAGTGTTGTATCGATACAA Found at i:4580961 original size:13 final size:13 Alignment explanation

Indices: 4580943--4580967 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 4580933 ATTACTCAAA 4580943 TGTATCGATACAT 1 TGTATCGATACAT 4580956 TGTATCGATACA 1 TGTATCGATACA 4580968 CTAATCTTTG 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:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:4588055 original size:20 final size:20 Alignment explanation

Indices: 4588030--4588127 Score: 80 Period size: 20 Copynumber: 5.6 Consensus size: 20 4588020 AAAACCAAGA 4588030 TGTATCGATACAATGTTCCT 1 TGTATCGATACAATGTTCCT 4588050 TGTATCGATAC-A------T 1 TGTATCGATACAATGTTCCT * 4588063 TATATCGATACAATGTTCCT 1 TGTATCGATACAATGTTCCT 4588083 TGTATCGATAC-A------T 1 TGTATCGATACAATGTTCCT * 4588096 TATATCGATACAATGTTCCT 1 TGTATCGATACAATGTTCCT 4588116 TGTATCGATACA 1 TGTATCGATACA 4588128 TTATATCGAT Statistics Matches: 60, Mismatches: 4, Indels: 28 0.65 0.04 0.30 Matches are distributed among these distances: 13 22 0.37 14 2 0.03 19 2 0.03 20 34 0.57 ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39 Consensus pattern (20 bp): TGTATCGATACAATGTTCCT Found at i:4588074 original size:33 final size:33 Alignment explanation

Indices: 4588032--4588144 Score: 226 Period size: 33 Copynumber: 3.4 Consensus size: 33 4588022 AACCAAGATG 4588032 TATCGATACAATGTTCCTTGTATCGATACATTA 1 TATCGATACAATGTTCCTTGTATCGATACATTA 4588065 TATCGATACAATGTTCCTTGTATCGATACATTA 1 TATCGATACAATGTTCCTTGTATCGATACATTA 4588098 TATCGATACAATGTTCCTTGTATCGATACATTA 1 TATCGATACAATGTTCCTTGTATCGATACATTA 4588131 TATCGATACAATGT 1 TATCGATACAATGT 4588145 ATCAATACAT Statistics Matches: 80, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 33 80 1.00 ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39 Consensus pattern (33 bp): TATCGATACAATGTTCCTTGTATCGATACATTA Found at i:4590659 original size:13 final size:13 Alignment explanation

Indices: 4590641--4590667 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 4590631 ATATTATGCT 4590641 TTGTATCGATACA 1 TTGTATCGATACA 4590654 TTGTATCGATACA 1 TTGTATCGATACA 4590667 T 1 T 4590668 GTTCATTGTA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41 Consensus pattern (13 bp): TTGTATCGATACA Found at i:4590701 original size:20 final size:19 Alignment explanation

Indices: 4590651--4590707 Score: 78 Period size: 19 Copynumber: 2.9 Consensus size: 19 4590641 TTGTATCGAT * 4590651 ACATTGTATCGATACATGT 1 ACATTGTATCGATACATGC * 4590670 TCATTGTATCGATACATGC 1 ACATTGTATCGATACATGC * 4590689 ACAATTTTATCGATACATG 1 AC-ATTGTATCGATACATG 4590708 AAACTAGCAG Statistics Matches: 33, Mismatches: 4, Indels: 1 0.87 0.11 0.03 Matches are distributed among these distances: 19 18 0.55 20 15 0.45 ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37 Consensus pattern (19 bp): ACATTGTATCGATACATGC Found at i:4591152 original size:13 final size:13 Alignment explanation

Indices: 4591134--4591158 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 4591124 ATAATGCACA 4591134 GTATCGATACATT 1 GTATCGATACATT 4591147 GTATCGATACAT 1 GTATCGATACAT 4591159 GACCAAATGT 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:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): GTATCGATACATT Found at i:4591171 original size:20 final size:22 Alignment explanation

Indices: 4591146--4591198 Score: 67 Period size: 21 Copynumber: 2.5 Consensus size: 22 4591136 ATCGATACAT * 4591146 TGTATCGATACATGAC-CA-AA 1 TGTATCGATACATGACAAAGAA * 4591166 TGTATCGATAC-TTACAAAGAA 1 TGTATCGATACATGACAAAGAA 4591187 TGTATCGATACA 1 TGTATCGATACA 4591199 GGTGATTGGC Statistics Matches: 28, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 19 3 0.11 20 12 0.43 21 13 0.46 ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28 Consensus pattern (22 bp): TGTATCGATACATGACAAAGAA Found at i:4591276 original size:13 final size:13 Alignment explanation

Indices: 4591258--4591283 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 4591248 TACACACAAG 4591258 ATGTATCGATACA 1 ATGTATCGATACA 4591271 ATGTATCGATACA 1 ATGTATCGATACA 4591284 TCTCAAATTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:4591301 original size:33 final size:32 Alignment explanation

Indices: 4591240--4591303 Score: 94 Period size: 33 Copynumber: 2.0 Consensus size: 32 4591230 CTTAACCGTT 4591240 TGTATCGATACACACAAGATGTATCGATACAA 1 TGTATCGATACACACAAGATGTATCGATACAA * 4591272 TGTATCGATACATCTCAA-ATTGTATCGATACA 1 TGTATCGATACA-CACAAGA-TGTATCGATACA 4591304 TTGGCTTGTA Statistics Matches: 29, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 32 13 0.45 33 16 0.55 ACGTcount: A:0.38, C:0.19, G:0.14, T:0.30 Consensus pattern (32 bp): TGTATCGATACACACAAGATGTATCGATACAA Found at i:4597224 original size:8 final size:8 Alignment explanation

Indices: 4597211--4597236 Score: 52 Period size: 8 Copynumber: 3.2 Consensus size: 8 4597201 ATTTGATTAA 4597211 ATTTTGTG 1 ATTTTGTG 4597219 ATTTTGTG 1 ATTTTGTG 4597227 ATTTTGTG 1 ATTTTGTG 4597235 AT 1 AT 4597237 GCTTGTTGTT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 18 1.00 ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62 Consensus pattern (8 bp): ATTTTGTG Found at i:4597461 original size:13 final size:13 Alignment explanation

Indices: 4597439--4597476 Score: 58 Period size: 13 Copynumber: 2.9 Consensus size: 13 4597429 CAGCATTCTC * * 4597439 TGTATTGATACAT 1 TGTATCGATACAG 4597452 TGTATCGATACAG 1 TGTATCGATACAG 4597465 TGTATCGATACA 1 TGTATCGATACA 4597477 AAGGGTTTAT Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 13 23 1.00 ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37 Consensus pattern (13 bp): TGTATCGATACAG Found at i:4599336 original size:16 final size:16 Alignment explanation

Indices: 4599317--4599348 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 4599307 GTGATTAAAA * 4599317 GAAATTGTTAATTTGC 1 GAAATTGTTAAATTGC 4599333 GAAATTGTTAAATTGC 1 GAAATTGTTAAATTGC 4599349 TTTATTATGG 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:0.34, C:0.06, G:0.19, T:0.41 Consensus pattern (16 bp): GAAATTGTTAAATTGC Found at i:4599927 original size:20 final size:19 Alignment explanation

Indices: 4599898--4599936 Score: 69 Period size: 20 Copynumber: 2.0 Consensus size: 19 4599888 AGGTCAAAAC 4599898 CCTTAAATGTATCGATACA 1 CCTTAAATGTATCGATACA 4599917 CCTTCAAATGTATCGATACA 1 CCTT-AAATGTATCGATACA 4599937 TAATGCACAG Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 19 4 0.21 20 15 0.79 ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31 Consensus pattern (19 bp): CCTTAAATGTATCGATACA Found at i:4599964 original size:13 final size:13 Alignment explanation

Indices: 4599946--4599970 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 4599936 ATAATGCACA 4599946 GTATCGATACATT 1 GTATCGATACATT 4599959 GTATCGATACAT 1 GTATCGATACAT 4599971 GACCAATGTA 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:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): GTATCGATACATT Found at i:4601786 original size:21 final size:19 Alignment explanation

Indices: 4601760--4601810 Score: 66 Period size: 20 Copynumber: 2.5 Consensus size: 19 4601750 GCCAAGGCCT 4601760 GTATCGATACAATCACACTAG 1 GTATCGATAC-A-CACACTAG * 4601781 GTATCGATATCACACCCTAG 1 GTATCGATA-CACACACTAG 4601801 GTATCGATAC 1 GTATCGATAC 4601811 CAAGCCTTCA Statistics Matches: 28, Mismatches: 1, Indels: 4 0.85 0.03 0.12 Matches are distributed among these distances: 19 1 0.04 20 16 0.57 21 10 0.36 22 1 0.04 ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25 Consensus pattern (19 bp): GTATCGATACACACACTAG Found at i:4605422 original size:26 final size:26 Alignment explanation

Indices: 4605386--4605438 Score: 97 Period size: 26 Copynumber: 2.0 Consensus size: 26 4605376 AAGGTATCGA 4605386 TAACTTGTCATAGGGTGTTAATACTT 1 TAACTTGTCATAGGGTGTTAATACTT * 4605412 TAACTTGTCATGGGGTGTTAATACTT 1 TAACTTGTCATAGGGTGTTAATACTT 4605438 T 1 T 4605439 GACTCTTACA Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 26 1.00 ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43 Consensus pattern (26 bp): TAACTTGTCATAGGGTGTTAATACTT Found at i:4606208 original size:26 final size:26 Alignment explanation

Indices: 4606159--4606210 Score: 95 Period size: 26 Copynumber: 2.0 Consensus size: 26 4606149 AAAAGAAAAA * 4606159 ATATAGAGCTAAGGGAAAATAAACTT 1 ATATAAAGCTAAGGGAAAATAAACTT 4606185 ATATAAAGCTAAGGGAAAATAAACTT 1 ATATAAAGCTAAGGGAAAATAAACTT 4606211 GGCTAAGGCA Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 25 1.00 ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23 Consensus pattern (26 bp): ATATAAAGCTAAGGGAAAATAAACTT Found at i:4606224 original size:26 final size:26 Alignment explanation

Indices: 4606169--4606224 Score: 67 Period size: 26 Copynumber: 2.2 Consensus size: 26 4606159 ATATAGAGCT * * 4606169 AAGGGAAAATAAACTTATATAAAGCT 1 AAGGGAAAATAAACTTAGATAAAGCA * * * 4606195 AAGGGAAAATAAACTTGGCTAAGGCA 1 AAGGGAAAATAAACTTAGATAAAGCA 4606221 AAGG 1 AAGG 4606225 ACAAAGGAAA Statistics Matches: 25, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 26 25 1.00 ACGTcount: A:0.50, C:0.09, G:0.23, T:0.18 Consensus pattern (26 bp): AAGGGAAAATAAACTTAGATAAAGCA Found at i:4608922 original size:20 final size:21 Alignment explanation

Indices: 4608897--4608954 Score: 100 Period size: 21 Copynumber: 2.8 Consensus size: 21 4608887 TTTTGCCTAC 4608897 ATGTATCGATACATTTCA-TA 1 ATGTATCGATACATTTCAGTA * 4608917 ATGTATCGATACATTTGAGTA 1 ATGTATCGATACATTTCAGTA 4608938 ATGTATCGATACATTTC 1 ATGTATCGATACATTTC 4608955 CTTGGCAGTA Statistics Matches: 35, Mismatches: 2, Indels: 1 0.92 0.05 0.03 Matches are distributed among these distances: 20 17 0.49 21 18 0.51 ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40 Consensus pattern (21 bp): ATGTATCGATACATTTCAGTA Found at i:4608992 original size:13 final size:13 Alignment explanation

Indices: 4608974--4609025 Score: 50 Period size: 13 Copynumber: 3.5 Consensus size: 13 4608964 AGCTTCGTAG 4608974 CGATACATTGTAT 1 CGATACATTGTAT 4608987 CGATACAAAACTTATGTAT 1 CGATAC---A-TT--GTAT 4609006 CGATACATTGTAT 1 CGATACATTGTAT 4609019 CGATACA 1 CGATACA 4609026 ACACTTATGT Statistics Matches: 33, Mismatches: 0, Indels: 12 0.73 0.00 0.27 Matches are distributed among these distances: 13 17 0.52 15 2 0.06 16 2 0.06 17 2 0.06 19 10 0.30 ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33 Consensus pattern (13 bp): CGATACATTGTAT Found at i:4609006 original size:19 final size:18 Alignment explanation

Indices: 4608982--4609044 Score: 73 Period size: 19 Copynumber: 3.7 Consensus size: 18 4608972 AGCGATACAT 4608982 TGTATCGATACAAAACTTA 1 TGTATCGATAC-AAACTTA 4609001 TGTATCGATAC--A--T- 1 TGTATCGATACAAACTTA 4609014 TGTATCGATACAACACTTA 1 TGTATCGATACAA-ACTTA 4609033 TGTATCGATACA 1 TGTATCGATACA 4609045 GTTACGATTT Statistics Matches: 38, Mismatches: 0, Indels: 12 0.76 0.00 0.24 Matches are distributed among these distances: 13 11 0.29 14 1 0.03 16 2 0.05 18 1 0.03 19 23 0.61 ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33 Consensus pattern (18 bp): TGTATCGATACAAACTTA Found at i:4609015 original size:32 final size:32 Alignment explanation

Indices: 4608974--4609044 Score: 133 Period size: 32 Copynumber: 2.2 Consensus size: 32 4608964 AGCTTCGTAG 4608974 CGATACATTGTATCGATACAAAACTTATGTAT 1 CGATACATTGTATCGATACAAAACTTATGTAT * 4609006 CGATACATTGTATCGATACAACACTTATGTAT 1 CGATACATTGTATCGATACAAAACTTATGTAT 4609038 CGATACA 1 CGATACA 4609045 GTTACGATTT Statistics Matches: 38, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 38 1.00 ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32 Consensus pattern (32 bp): CGATACATTGTATCGATACAAAACTTATGTAT Found at i:4614541 original size:12 final size:12 Alignment explanation

Indices: 4614524--4614548 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 4614514 TTCATCCTGA 4614524 AATTTCATAAAT 1 AATTTCATAAAT 4614536 AATTTCATAAAT 1 AATTTCATAAAT 4614548 A 1 A 4614549 CATGAACAAG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40 Consensus pattern (12 bp): AATTTCATAAAT Found at i:4616700 original size:106 final size:107 Alignment explanation

Indices: 4616512--4616801 Score: 277 Period size: 106 Copynumber: 2.7 Consensus size: 107 4616502 AATTGATCGG * * * * * * 4616512 AACGAAACCATATA-AATA-ACAAGTTAAAAGGGTTGACCATGA-CAAAACCATATTAATCT-AC 1 AACGAAACCATA-AGAACAGACAAGTTAGAAGGGTTGACTA-GACCAAAACCATATGAGT-TAAT * * * 4616573 GAAAAGTGACTAGGG-CAAAACCTAAGTCGAAAAAAAGTTGGCCAG 63 GAAAGGTGACCAGGGTC-AAACCTAAGTCGAAAAAAAGTTGGCCAA * * ** * ** * 4616618 GACGAAATCATAAGAACCTATAAGTTAGAAGGGTTGACTAGA-TGAAACCATATGAGTTAATGAT 1 AACGAAACCATAAGAACAGACAAGTTAGAAGGGTTGACTAGACCAAAACCATATGAGTTAATGAA * * ** 4616682 AGGTGATCAGGGTCAAACCTTAGTCGAAAAGGAGTTGGCCAA 66 AGGTGACCAGGGTCAAACCTAAGTCGAAAAAAAGTTGGCCAA * * * * 4616724 AATGAAACCATATGAATAGACAAGTTAGATGGGTTGACTAGACCAAAACCATATGAGTTAATGAA 1 AACGAAACCATAAGAACAGACAAGTTAGAAGGGTTGACTAGACCAAAACCATATGAGTTAATGAA 4616789 AGGTGACCAGGGT 66 AGGTGACCAGGGT 4616802 GGAACCTTCA Statistics Matches: 146, Mismatches: 33, Indels: 9 0.78 0.18 0.05 Matches are distributed among these distances: 105 2 0.01 106 94 0.64 107 50 0.34 ACGTcount: A:0.42, C:0.14, G:0.22, T:0.21 Consensus pattern (107 bp): AACGAAACCATAAGAACAGACAAGTTAGAAGGGTTGACTAGACCAAAACCATATGAGTTAATGAA AGGTGACCAGGGTCAAACCTAAGTCGAAAAAAAGTTGGCCAA Found at i:4617030 original size:41 final size:41 Alignment explanation

Indices: 4616980--4617066 Score: 104 Period size: 41 Copynumber: 2.1 Consensus size: 41 4616970 ACATATGAAC * ** * 4616980 CAACGAGTTAGA-AAGGTTAACCAAGATGAAATCAAACGAGT 1 CAACAAGTTAGAGAA-GTTAACCAAGACAAAACCAAACGAGT * * 4617021 CAACAAGTTAGAGAAGTTGACCAAGACAAAACCATACGAGT 1 CAACAAGTTAGAGAAGTTAACCAAGACAAAACCAAACGAGT 4617062 CAACA 1 CAACA 4617067 TGGTGACTAA Statistics Matches: 39, Mismatches: 6, Indels: 2 0.83 0.13 0.04 Matches are distributed among these distances: 41 37 0.95 42 2 0.05 ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15 Consensus pattern (41 bp): CAACAAGTTAGAGAAGTTAACCAAGACAAAACCAAACGAGT Found at i:4617145 original size:147 final size:145 Alignment explanation

Indices: 4616874--4617208 Score: 397 Period size: 147 Copynumber: 2.3 Consensus size: 145 4616864 AGTTTATAAT * * 4616874 TCAAAAAGTTAGACAAGTTGACCAAGACAAAACCATACAAGTTAACAGATGACCAAGGTAAAACA 1 TCAAAAAGTTAGACAAGTTGACCAAGACAAAACCATACGAGTCAACAGATGACCAAGGTAAAACA * * * * 4616939 TTTAGTCGCAAAAGGGTTGGTTGGGACAATAACATATGAACCAACGAGTTAGAAAGGTTAACCAA 66 CTTAATCGCAAAAGGGTTGGATGGGACAAT-ACATATAAACCAACGAGTTAGAAAGGTTAACCAA * * * 4617004 GATGAAATCAAACGAG 130 GACGAAACCAAACAAG * * * * 4617020 TCAACAAGTTAGAGAAGTTGACCAAGACAAAACCATACGAGTCAACATGGTGACTAAGGTAAAAC 1 TCAAAAAGTTAGACAAGTTGACCAAGACAAAACCATACGAGTCAACA-GATGACCAAGGTAAAAC * * * 4617085 CCTTAATCG-AAAAGAGGTTGGCCATGATGA-AAT-CATATAAACCAACGAGTTAGAAGGGTTAA 65 ACTTAATCGCAAAAG-GGTTGG--ATG-GGACAATACATATAAACCAACGAGTTAGAAAGGTTAA * 4617147 CCAAGACGAAACCATACAAG 126 CCAAGACGAAACCAAACAAG * * * * * 4617167 TCAAAAAGTTAGATAGGTTGACCAAAACGAAACCATATGAGT 1 TCAAAAAGTTAGACAAGTTGACCAAGACAAAACCATACGAGT 4617209 TAATAAGGTG Statistics Matches: 161, Mismatches: 23, Indels: 9 0.83 0.12 0.05 Matches are distributed among these distances: 146 48 0.30 147 106 0.66 149 5 0.03 150 2 0.01 ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19 Consensus pattern (145 bp): TCAAAAAGTTAGACAAGTTGACCAAGACAAAACCATACGAGTCAACAGATGACCAAGGTAAAACA CTTAATCGCAAAAGGGTTGGATGGGACAATACATATAAACCAACGAGTTAGAAAGGTTAACCAAG ACGAAACCAAACAAG Found at i:4617530 original size:107 final size:105 Alignment explanation

Indices: 4617370--4617714 Score: 343 Period size: 106 Copynumber: 3.3 Consensus size: 105 4617360 GAGTTAGAAG * * * * * * ** * 4617370 GGTTGATCAGGATAAAACCATACGAGTAAACG-AGTTATGACCAAAGCAGAACCTAAGTCAAAAA 1 GGTTGACCAAGATAAAACCATATGAGTCAACGAAG-GATAACCAGGGCAAAACCTAAGTCAAAAA *** 4617434 GGAGTTGGTTGGGATAAAACCATACGAAACCAACAAGTTTAAA 65 -GAGTTGGCCAGGATAAAACCATACG-AACCAACAAGTTTAAA * * * * * 4617477 GGTTGACCAAGATGAAACCATATGAGTCAACGAAGGATGACCGGGGTAAAACCTAAGTCGAAATA 1 GGTTGACCAAGATAAAACCATATGAGTCAACGAAGGATAACCAGGGCAAAACCTAAGTC-AAAAA * * 4617542 GAGTTGGCCAGGATAAAACCATACGAACTAGCAAGTTTAAA 65 GAGTTGGCCAGGATAAAACCATACGAACCAACAAGTTTAAA * * * * * * * * 4617583 GGTTAACTATGACAAAACCATACGAGTCAATGAAGGGTAACCAGGGCAAAACCTAAGTAAAAAAA 1 GGTTGACCAAGATAAAACCATATGAGTCAACGAAGGATAACCAGGGCAAAACCTAAGT-CAAAAA * * 4617648 GAATTGGCCAGGACAAAACCATAC-AACCAACAAGTTTAAA 65 GAGTTGGCCAGGATAAAACCATACGAACCAACAAGTTTAAA ** * 4617688 ATTTGACCAGGATAAAACCATATGAGT 1 GGTTGACCAAGATAAAACCATATGAGT 4617715 TAACAAGTCA Statistics Matches: 194, Mismatches: 41, Indels: 8 0.80 0.17 0.03 Matches are distributed among these distances: 105 34 0.18 106 87 0.45 107 67 0.35 108 6 0.03 ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18 Consensus pattern (105 bp): GGTTGACCAAGATAAAACCATATGAGTCAACGAAGGATAACCAGGGCAAAACCTAAGTCAAAAAG AGTTGGCCAGGATAAAACCATACGAACCAACAAGTTTAAA Found at i:4617971 original size:65 final size:65 Alignment explanation

Indices: 4617869--4618334 Score: 409 Period size: 65 Copynumber: 7.2 Consensus size: 65 4617859 GGTAAAACCT * ** * * * 4617869 TACAAGTCAACAAAAGGTGACTAGGACAAAACCTAAGTCAAAAAAGTTTGACCAGGGTTAAACCA 1 TACAA-TCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCA 4617934 A 65 A * * * * * 4617935 TACAATCAATTAAAGATGACTAGGATGAAACTTAAGTCAAAAAAGGTTGA-CAAGGGTAAACCAG 1 TACAATCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCAA ** * * * * * * 4617999 TACGGTCAACTAAAGGTGACTAGGACGAAATCTAAGTCAAAAAGGGTTTACCAAGGCTAAACTAG 1 TACAATCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCAA * * * * * 4618064 TATAATAAACTAAAGGTTACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAAGGCTAAA-CAA 1 TACAATCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCAA * * * * 4618128 GTA-AAGTCAACTAAAGGTAACTAAGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAATCT 1 -TACAA-TCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACC * 4618192 AG 64 AA * * * ** * * ** * * 4618194 TA-AAGTCAACTAAAGGTGGCTAAGATGAAAACTAAGTTGAAAAGGGTTTATTATGGCTAAACTA 1 TACAA-TCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCA * 4618258 G 65 A * * * * * * * * * 4618259 TATAGTCAATTAAAAGTGACTAGGATGAAACCTAAGTCGAAAAAGGTTAACTAGGGCTAAACCAG 1 TACAATCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCAA * 4618324 TACAGTCAACT 1 TACAATCAACT 4618335 GAATTATCAA Statistics Matches: 329, Mismatches: 66, Indels: 11 0.81 0.16 0.03 Matches are distributed among these distances: 64 55 0.17 65 267 0.81 66 7 0.02 ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21 Consensus pattern (65 bp): TACAATCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCAA Found at i:4618149 original size:34 final size:33 Alignment explanation

Indices: 4618097--4618202 Score: 94 Period size: 34 Copynumber: 3.2 Consensus size: 33 4618087 GATGAAACCT 4618097 AAGTCAAAAAAGGTTAACTAAGGCTAAACAAGTA 1 AAGTCAAAAAAGGTTAACTAAGGCTAAAC-AGTA * * * 4618131 AAGTCAACTAAAGG-TAACTAA-GATGAAAC-CT- 1 AAGTCAA-AAAAGGTTAACTAAGGCT-AAACAGTA * * * 4618162 AAGTCAAAAAAGGTTGACCAAGGCTAATCTAGTA 1 AAGTCAAAAAAGGTTAACTAAGGCTAAAC-AGTA 4618196 AAGTCAA 1 AAGTCAA 4618203 CTAAAGGTGG Statistics Matches: 56, Mismatches: 9, Indels: 14 0.71 0.11 0.18 Matches are distributed among these distances: 30 5 0.09 31 15 0.27 32 3 0.05 33 3 0.05 34 25 0.45 35 5 0.09 ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19 Consensus pattern (33 bp): AAGTCAAAAAAGGTTAACTAAGGCTAAACAGTA Found at i:4618182 original size:130 final size:129 Alignment explanation

Indices: 4617872--4618334 Score: 487 Period size: 130 Copynumber: 3.6 Consensus size: 129 4617862 AAAACCTTAC * * * * * * 4617872 AAGTCAACAAAAGGTGACTAGGACAAAACCTAAGTCAAAAAAGTTTGACCAGGGTTAAACCAATA 1 AAGTCAACTAAAGGTGACTAGGACGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCAGTA * * * * * * 4617937 CAATCAATTAAAGATGACTAGGATGAAACTTAAGTCAAAAAAGGTTGAC-AAGGGTAAACCAGTA 66 -AATCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAAGGCTAAACAAGTA ** * * * * 4618001 CGGTCAACTAAAGGTGACTAGGACGAAATCTAAGTCAAAAAGGGTTTACCAAGGCTAAACTAGTA 1 AAGTCAACTAAAGGTGACTAGGACGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCAGTA * * 4618066 TAATAAACTAAAGGTTACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAAGGCTAAACAAGTA 66 -AATCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAAGGCTAAACAAGTA * * * * * 4618131 AAGTCAACTAAAGGTAACTAAGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAATCTAGTA 1 AAGTCAACTAAAGGTGACTAGGACGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCAGTA * * * ** * * * * * 4618196 AAGTCAACTAAAGGTGGCTAAGATGAAAACTAAGTTGAAAAGGGTTTATTATGGCTAAACTAGTA 66 AA-TCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAAGGCTAAACAAGTA * * * * * * * * 4618261 TAGTCAATTAAAAGTGACTAGGATGAAACCTAAGTCGAAAAAGGTTAACTAGGGCTAAACCAGTA 1 AAGTCAACTAAAGGTGACTAGGACGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCAGTA * 4618326 CAGTCAACT 66 -AATCAACT 4618335 GAATTATCAA Statistics Matches: 277, Mismatches: 54, Indels: 5 0.82 0.16 0.01 Matches are distributed among these distances: 129 97 0.35 130 179 0.65 131 1 0.00 ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21 Consensus pattern (129 bp): AAGTCAACTAAAGGTGACTAGGACGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAAACCAGTA AATCAACTAAAGGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAAGGCTAAACAAGTA Found at i:4618283 original size:195 final size:194 Alignment explanation

Indices: 4617880--4618334 Score: 554 Period size: 195 Copynumber: 2.3 Consensus size: 194 4617870 ACAAGTCAAC ** * * * * 4617880 AAAAGGTGACTAGGACAAAACCTAAGTCAAAAAAGTTTGACCAGGGTTAAACCAA-TACAA-TCA 1 AAAA-GTGACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAGGGCTAAA-CAAGTA-AAGTCA * * * * * ** 4617943 ATTAAAGATGACTAGGATGAAACTTAAGTCAAAAAAGGTTGACAAGGGTAAACCAGTACGGTCAA 63 ACTAAAGATAACTAAGATGAAACCTAAGTCAAAAAAGGTTGACAAGGCTAAACCAGTAAAGTCAA * * 4618008 CTAAAGGTGACTAGGACGAAATCTAAGTCAAAAAGGGTTTACCAAGGCTAAACTAGTATAATAAA 128 CTAAAGGTGACTAAGACGAAAACTAAGTCAAAAAGGGTTTACCAAGGCTAAACTAGTATAATAAA 4618073 CT 193 CT * * * 4618075 AAAGGTTACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAAGGCTAAACAAGTAAAGTCAACT 1 AAAAGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAGGGCTAAACAAGTAAAGTCAACT * * * 4618140 AAAGGTAACTAAGATGAAACCTAAGTCAAAAAAGGTTGACCAAGGCTAATCTAGTAAAGTCAACT 66 AAAGATAACTAAGATGAAACCTAAGTCAAAAAAGGTTGA-CAAGGCTAAACCAGTAAAGTCAACT * * ** ** * * * * 4618205 AAAGGTGGCTAAGATGAAAACTAAGTTGAAAAGGGTTTATTATGGCTAAACTAGTATAGTCAATT 130 AAAGGTGACTAAGACGAAAACTAAGTCAAAAAGGGTTTACCAAGGCTAAACTAGTATAATAAACT * * * 4618270 AAAAGTGACTAGGATGAAACCTAAGTCGAAAAAGGTTAACTAGGGCTAAACCAGTACAGTCAACT 1 AAAAGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAGGGCTAAACAAGTAAAGTCAACT 4618335 GAATTATCAA Statistics Matches: 220, Mismatches: 37, Indels: 6 0.84 0.14 0.02 Matches are distributed among these distances: 193 5 0.02 194 80 0.36 195 135 0.61 ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21 Consensus pattern (194 bp): AAAAGTGACTAGGATGAAACCTAAGTCAAAAAAGGTTAACTAGGGCTAAACAAGTAAAGTCAACT AAAGATAACTAAGATGAAACCTAAGTCAAAAAAGGTTGACAAGGCTAAACCAGTAAAGTCAACTA AAGGTGACTAAGACGAAAACTAAGTCAAAAAGGGTTTACCAAGGCTAAACTAGTATAATAAACT Found at i:4619685 original size:165 final size:165 Alignment explanation

Indices: 4619485--4619798 Score: 425 Period size: 165 Copynumber: 1.9 Consensus size: 165 4619475 TATGTGAAAC * * * 4619485 AATGTAAATGCAAGAATCAATAAAGTGGCAAATACACT-CGAAACAAGGCAAATACCAATGTCAT 1 AATGCAAATGCAAGAATCAATAAAGTGGCAAATACA-TACGAAACAAGGCAAATACCAATATAAT * * * 4619549 -TGAAAGTGCAAATGTACGTAAAATGATGCAAATGCAAGCATCGATAAAGTGGCAAATGCATATG 65 CT-AAAGTGCAAATGTACGTAAAATGATACAAATACAAGCATCAATAAAGTGGCAAATGCATATG * 4619613 AAATGATACAAATACCAATGTCATCAGATGTACGTGA 129 AAACGATACAAATACCAATGTCATCAGATGTACGTGA * * * * ** * 4619650 AATGCAAATGCAAGCATCGATAAAGTGGTAAATACATATGAAATGATGCAAATACCAATATAATC 1 AATGCAAATGCAAGAATCAATAAAGTGGCAAATACATACGAAACAAGGCAAATACCAATATAATC * * * 4619715 TAAAGTGTAAATGTACGTGAAATGATACAAATACAAGCATCAATAAAGTGGCAAATGTATATGAA 66 TAAAGTGCAAATGTACGTAAAATGATACAAATACAAGCATCAATAAAGTGGCAAATGCATATGAA * * 4619780 ACGATGCAAATGCCAATGT 131 ACGATACAAATACCAATGT 4619799 GGTCTAATTC Statistics Matches: 128, Mismatches: 19, Indels: 4 0.85 0.13 0.03 Matches are distributed among these distances: 164 1 0.01 165 126 0.98 166 1 0.01 ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22 Consensus pattern (165 bp): AATGCAAATGCAAGAATCAATAAAGTGGCAAATACATACGAAACAAGGCAAATACCAATATAATC TAAAGTGCAAATGTACGTAAAATGATACAAATACAAGCATCAATAAAGTGGCAAATGCATATGAA ACGATACAAATACCAATGTCATCAGATGTACGTGA Found at i:4619701 original size:44 final size:44 Alignment explanation

Indices: 4619651--4619792 Score: 137 Period size: 44 Copynumber: 3.2 Consensus size: 44 4619641 TGTACGTGAA * ** 4619651 ATGCAAATGCAAGCATCGATAAAGTGGTAAATACATATGAAATG 1 ATGCAAATGCAAGCATCAATAAAGTGGTAAATGTATATGAAATG * * ** 4619695 ATGCAAATACCAA-TAT-AATCTAAAGT-GTAAATGTACGTGAAATG 1 ATGCAAAT-GCAAGCATCAA--TAAAGTGGTAAATGTATATGAAATG * * * * 4619739 ATACAAATACAAGCATCAATAAAGTGGCAAATGTATATGAAACG 1 ATGCAAATGCAAGCATCAATAAAGTGGTAAATGTATATGAAATG 4619783 ATGCAAATGC 1 ATGCAAATGC 4619793 CAATGTGGTC Statistics Matches: 76, Mismatches: 16, Indels: 12 0.73 0.15 0.12 Matches are distributed among these distances: 43 10 0.13 44 55 0.72 45 11 0.14 ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23 Consensus pattern (44 bp): ATGCAAATGCAAGCATCAATAAAGTGGTAAATGTATATGAAATG Found at i:4620434 original size:11 final size:10 Alignment explanation

Indices: 4620410--4620451 Score: 57 Period size: 11 Copynumber: 4.0 Consensus size: 10 4620400 CATTCTTGCA 4620410 TTTTTTCTTT 1 TTTTTTCTTT 4620420 TTTTTTCTTT 1 TTTTTTCTTT * 4620430 CTTTTCTCTTT 1 -TTTTTTCTTT 4620441 TTCTTTTCTTT 1 TT-TTTTCTTT 4620452 GATTGTTTTA Statistics Matches: 28, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 10 12 0.43 11 16 0.57 ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83 Consensus pattern (10 bp): TTTTTTCTTT Found at i:4620443 original size:13 final size:13 Alignment explanation

Indices: 4620411--4620449 Score: 51 Period size: 13 Copynumber: 2.9 Consensus size: 13 4620401 ATTCTTGCAT * * 4620411 TTTTTCTTTTTTT 1 TTTTTCTTTTCTC 4620424 TTCTTTCTTTTCTC 1 TT-TTTCTTTTCTC 4620438 TTTTTCTTTTCT 1 TTTTTCTTTTCT 4620450 TTGATTGTTT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 13 12 0.52 14 11 0.48 ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82 Consensus pattern (13 bp): TTTTTCTTTTCTC Found at i:4620715 original size:15 final size:17 Alignment explanation

Indices: 4620695--4620730 Score: 51 Period size: 14 Copynumber: 2.3 Consensus size: 17 4620685 GAATACTACA 4620695 TTTTTTT-A-TTTCT-T 1 TTTTTTTCATTTTCTCT 4620709 TTTTTTTCATTTTCTCT 1 TTTTTTTCATTTTCTCT 4620726 TTTTT 1 TTTTT 4620731 CTTGCTATTT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 14 7 0.37 15 1 0.05 16 5 0.26 17 6 0.32 ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83 Consensus pattern (17 bp): TTTTTTTCATTTTCTCT Found at i:4620728 original size:18 final size:18 Alignment explanation

Indices: 4620705--4620759 Score: 56 Period size: 20 Copynumber: 2.9 Consensus size: 18 4620695 TTTTTTTATT * 4620705 TCTTTTTTTTTCATTTTC 1 TCTTTTTTTTTCATTTGC * 4620723 TCTTTTTTCTTGCTATTTGC 1 TCTTTTTT-TTTC-ATTTGC * 4620743 ACTTTTCTTTTTCATTT 1 TCTTTT-TTTTTCATTT 4620760 CACGCTTTTT Statistics Matches: 30, Mismatches: 4, Indels: 5 0.77 0.10 0.13 Matches are distributed among these distances: 18 8 0.27 19 7 0.23 20 13 0.43 21 2 0.07 ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71 Consensus pattern (18 bp): TCTTTTTTTTTCATTTGC Found at i:4623343 original size:25 final size:25 Alignment explanation

Indices: 4623293--4623372 Score: 76 Period size: 25 Copynumber: 3.2 Consensus size: 25 4623283 ATAATTATAT ** 4623293 AAATATAATATAAATA-AAAGAATTA 1 AAATATAATATAAATATAAA-TTTTA * 4623318 AAATATAATATAAATATATATTTTA 1 AAATATAATATAAATATAAATTTTA * 4623343 AAAT-TTATAT-AATATAAATTATTA 1 AAATATAATATAAATATAAATT-TTA * 4623367 ATATAT 1 AAATAT 4623373 TAAATTTTAT Statistics Matches: 46, Mismatches: 6, Indels: 6 0.79 0.10 0.10 Matches are distributed among these distances: 23 9 0.20 24 11 0.24 25 24 0.52 26 2 0.04 ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40 Consensus pattern (25 bp): AAATATAATATAAATATAAATTTTA Found at i:4623353 original size:16 final size:16 Alignment explanation

Indices: 4623332--4623385 Score: 56 Period size: 16 Copynumber: 3.4 Consensus size: 16 4623322 ATAATATAAA * 4623332 TATATATTTTAAAATT 1 TATATATTTTAAATTT * * 4623348 TATATAATATAAATTAT 1 TATATATTTTAAATT-T * 4623365 TA-ATATATTAAATTT 1 TATATATTTTAAATTT 4623380 TATATA 1 TATATA 4623386 ATTATATAAT Statistics Matches: 30, Mismatches: 6, Indels: 4 0.75 0.15 0.10 Matches are distributed among these distances: 15 3 0.10 16 24 0.80 17 3 0.10 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (16 bp): TATATATTTTAAATTT Found at i:4623382 original size:32 final size:29 Alignment explanation

Indices: 4623320--4623397 Score: 93 Period size: 32 Copynumber: 2.5 Consensus size: 29 4623310 AAGAATTAAA * 4623320 ATATAATATAAATATATATTTTAAAATTT 1 ATATAATATAAATATATATATTAAAATTT * 4623349 ATATAATATAAATTATTAATATATTAAATTTT 1 ATATAATATAAA-TA-T-ATATATTAAAATTT 4623381 ATATAATTATATAATAT 1 ATATAA-TATA-AATAT 4623398 TTTAAATATA Statistics Matches: 42, Mismatches: 2, Indels: 7 0.82 0.04 0.14 Matches are distributed among these distances: 29 12 0.29 30 2 0.05 31 1 0.02 32 19 0.45 33 6 0.14 34 2 0.05 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (29 bp): ATATAATATAAATATATATATTAAAATTT Found at i:4623391 original size:20 final size:21 Alignment explanation

Indices: 4623368--4623412 Score: 58 Period size: 22 Copynumber: 2.1 Consensus size: 21 4623358 AAATTATTAA 4623368 TATATTAA-ATTTT-ATATAAT 1 TATA-TAATATTTTAATATAAT 4623388 TATATAATATTTTAAATATAAT 1 TATATAATATTTT-AATATAAT 4623410 TAT 1 TAT 4623413 GATATAATAA Statistics Matches: 22, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 19 3 0.14 20 9 0.41 22 10 0.45 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (21 bp): TATATAATATTTTAATATAAT Found at i:4623600 original size:23 final size:23 Alignment explanation

Indices: 4623567--4623616 Score: 73 Period size: 23 Copynumber: 2.2 Consensus size: 23 4623557 AGAGTACTGA * * 4623567 ATATTCCTAAGAATATAATCTGT 1 ATATTCCTAAGAATATAAACTAT * 4623590 ATATTCTTAAGAATATAAACTAT 1 ATATTCCTAAGAATATAAACTAT 4623613 ATAT 1 ATAT 4623617 GTACAGATGA Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 23 24 1.00 ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40 Consensus pattern (23 bp): ATATTCCTAAGAATATAAACTAT Done.