Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr14

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

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

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


File 291 of 770

Found at i:88732391 original size:15 final size:15

Alignment explanation

Indices: 88732371--88732400 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 88732361 GTGAAAATAT 88732371 ATTTGAATAAGTTTA 1 ATTTGAATAAGTTTA * 88732386 ATTTGAATATGTTTA 1 ATTTGAATAAGTTTA 88732401 GATTAAGAAC Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50 Consensus pattern (15 bp): ATTTGAATAAGTTTA Found at i:88732814 original size:41 final size:43 Alignment explanation

Indices: 88732709--88732816 Score: 130 Period size: 45 Copynumber: 2.5 Consensus size: 43 88732699 ATATGTGTTC * * * 88732709 TCGTGTAAGACCATGTCTGGGACGTTGGCATTGATATATGAGGT 1 TCGTGTAAGACCATGTCTGGGACATCGGCATCGATATATGA-GT * * 88732753 TACATGTAAGACCATGTCTGGGACATCGGCATCG-TATTTGA-T 1 T-CGTGTAAGACCATGTCTGGGACATCGGCATCGATATATGAGT * 88732795 TCGTGTAAGACCCTGTCTGGGA 1 TCGTGTAAGACCATGTCTGGGA 88732817 TAGTGGCATT Statistics Matches: 56, Mismatches: 7, Indels: 5 0.82 0.10 0.07 Matches are distributed among these distances: 41 19 0.34 42 2 0.04 44 7 0.12 45 28 0.50 ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31 Consensus pattern (43 bp): TCGTGTAAGACCATGTCTGGGACATCGGCATCGATATATGAGT Found at i:88742347 original size:42 final size:41 Alignment explanation

Indices: 88742295--88742449 Score: 193 Period size: 42 Copynumber: 3.7 Consensus size: 41 88742285 CTAAGACTAT 88742295 GTGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTC 1 GTGTAAGACCATATCTGGGATATGGCATCAATATGAGA-TTC * * 88742337 GTGTAAGACCATATCTGAGATATGGCATCAATGTGAGATTTC 1 GTGTAAGACCATATCTGGGATATGGCATCAATATGAGA-TTC * * * * * * 88742379 TTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATCCC 1 GTGTAAGACCATATCTGGGATA-TGGCATCAATATGAGAT-TC * 88742422 ATGTAAGACCATATCTGGGATATGGCAT 1 GTGTAAGACCATATCTGGGATATGGCAT 88742450 TGGTATGGTA Statistics Matches: 97, Mismatches: 14, Indels: 4 0.84 0.12 0.03 Matches are distributed among these distances: 42 64 0.66 43 33 0.34 ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28 Consensus pattern (41 bp): GTGTAAGACCATATCTGGGATATGGCATCAATATGAGATTC Found at i:88746979 original size:24 final size:24 Alignment explanation

Indices: 88746947--88746997 Score: 102 Period size: 24 Copynumber: 2.1 Consensus size: 24 88746937 TATAATTGTT 88746947 ACATAATACATTGTGATAGGTCGA 1 ACATAATACATTGTGATAGGTCGA 88746971 ACATAATACATTGTGATAGGTCGA 1 ACATAATACATTGTGATAGGTCGA 88746995 ACA 1 ACA 88746998 GATGTATCAC Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 27 1.00 ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27 Consensus pattern (24 bp): ACATAATACATTGTGATAGGTCGA Found at i:88754339 original size:21 final size:20 Alignment explanation

Indices: 88754270--88754340 Score: 61 Period size: 21 Copynumber: 3.3 Consensus size: 20 88754260 AATATATGAT * 88754270 TTTTTTAAAATGAAATTTTAGAA 1 TTTTTTAAAA--ATATTTT-GAA * 88754293 TTTTTTTATAAATATTTTGAA 1 -TTTTTTAAAAATATTTTGAA * * 88754314 ATTTTTAAAAATTATTTTGTA 1 TTTTTTAAAAA-TATTTTGAA 88754335 TTTTTT 1 TTTTTT 88754341 TTTGTTGAAA Statistics Matches: 40, Mismatches: 6, Indels: 5 0.78 0.12 0.10 Matches are distributed among these distances: 20 9 0.22 21 16 0.40 22 6 0.15 24 9 0.22 ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59 Consensus pattern (20 bp): TTTTTTAAAAATATTTTGAA Found at i:88757185 original size:40 final size:40 Alignment explanation

Indices: 88757126--88757333 Score: 222 Period size: 40 Copynumber: 5.2 Consensus size: 40 88757116 CAGAATACGA * * 88757126 CCGGATATAACCAC-ATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACGACTA-GCACAAATGCCTTCGGGTCTTAGC * * * 88757166 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACGACTAGCACAAATGCCTTCGGGTCTTAGC * * * * 88757206 CCGGATTTAACAACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACGACTAGCACAAATGCCTTCGGGTCTTAGC * * * * 88757246 CCGGATGTAGTC-ACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATA-ACGACTAGCACAAATGCCTTCGGGTCTTAGC ** * * * 88757286 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAACGACTAGCACAAATGCCTTCGGGTCTTAGC 88757326 CCGGATAT 1 CCGGATAT 88757334 CATTCAATTG Statistics Matches: 140, Mismatches: 25, Indels: 6 0.82 0.15 0.04 Matches are distributed among these distances: 40 139 0.99 41 1 0.01 ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25 Consensus pattern (40 bp): CCGGATATAACGACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:88762947 original size:19 final size:19 Alignment explanation

Indices: 88762923--88762962 Score: 80 Period size: 19 Copynumber: 2.1 Consensus size: 19 88762913 ATCCTTGAAG 88762923 CGTTTACACATAATAGCTT 1 CGTTTACACATAATAGCTT 88762942 CGTTTACACATAATAGCTT 1 CGTTTACACATAATAGCTT 88762961 CG 1 CG 88762963 GACGAAATGC Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 21 1.00 ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35 Consensus pattern (19 bp): CGTTTACACATAATAGCTT Found at i:88769151 original size:41 final size:41 Alignment explanation

Indices: 88769106--88769223 Score: 98 Period size: 41 Copynumber: 3.1 Consensus size: 41 88769096 TGAAAGATAA 88769106 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC * * * * * 88769147 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A 1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 88769177 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 88769218 ATGTAG 1 ATGTAG 88769224 ACAAGAGAGC Statistics Matches: 54, Mismatches: 10, Indels: 26 0.60 0.11 0.29 Matches are distributed among these distances: 29 1 0.02 30 8 0.15 31 9 0.17 32 1 0.02 33 3 0.06 34 1 0.02 35 1 0.02 36 1 0.02 37 1 0.02 38 3 0.06 39 1 0.02 40 9 0.17 41 14 0.26 42 1 0.02 ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21 Consensus pattern (41 bp): ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC Found at i:88769162 original size:71 final size:71 Alignment explanation

Indices: 88769074--88769237 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 88769064 GAGATGTATC 88769074 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 88769139 AGGACA 66 AGGACA 88769145 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 88769210 AGGACA 66 AGGACA 88769216 CCATGTAGACAAGAGAGCTACG 1 CCATGTAGACAAGAGAGCTACG 88769238 AGACAAATCG Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19 Consensus pattern (71 bp): CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA AGGACA Found at i:88779838 original size:47 final size:47 Alignment explanation

Indices: 88779775--88779903 Score: 168 Period size: 47 Copynumber: 2.7 Consensus size: 47 88779765 TGCGAATAAC * * *** * 88779775 ACCTTGATTTGGCTACGGGCCATGATATATGTATTTTGAGAGGAGTT 1 ACCTTGATTTGGCTACGGGCCATGATATAGGTACTCCAAGAGAAGTT * * 88779822 ACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAAGATAAGTT 1 ACCTTGATTTGGCTACGGGCCATGATATAGGTACTCCAAGAGAAGTT * * 88779869 ACCTTGATTTGGCTACGGGTCATGATGTAGGTACT 1 ACCTTGATTTGGCTACGGGCCATGATATAGGTACT 88779904 TATCGATTAT Statistics Matches: 71, Mismatches: 11, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 47 71 1.00 ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33 Consensus pattern (47 bp): ACCTTGATTTGGCTACGGGCCATGATATAGGTACTCCAAGAGAAGTT Found at i:88786236 original size:56 final size:58 Alignment explanation

Indices: 88786167--88786277 Score: 145 Period size: 56 Copynumber: 1.9 Consensus size: 58 88786157 AAGTTCACAT * * 88786167 ACCTATATCTGGCCCATTAAGCCC-AATCATATTCATAT-GCCCATTAGGCCCAAATC 1 ACCTATATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAAATC * * * * * 88786223 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCTCGTTAGGCCCAA 1 ACCTATATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAA 88786278 TCATATTCAT Statistics Matches: 46, Mismatches: 7, Indels: 2 0.84 0.13 0.04 Matches are distributed among these distances: 56 21 0.46 57 12 0.26 58 13 0.28 ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27 Consensus pattern (58 bp): ACCTATATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAAATC Found at i:88786289 original size:28 final size:29 Alignment explanation

Indices: 88786176--88786289 Score: 128 Period size: 29 Copynumber: 4.0 Consensus size: 29 88786166 TACCTATATC * * 88786176 TGGCCCATTAAGCCC-AATCATATTCATA 1 TGGCCCATTAGGCCCAAATCACATTCATA * 88786204 T-GCCCATTAGGCCCAAATCACCTGT-ATA 1 TGGCCCATTAGGCCCAAATCACAT-TCATA * 88786232 TGGCCCATTAGGCCCAAATCACATTTATA 1 TGGCCCATTAGGCCCAAATCACATTCATA * * * 88786261 TGGCTCGTTAGGCCC-AATCATATTCATA 1 TGGCCCATTAGGCCCAAATCACATTCATA 88786289 T 1 T 88786290 TCATGCTTAC Statistics Matches: 74, Mismatches: 8, Indels: 8 0.82 0.09 0.09 Matches are distributed among these distances: 27 12 0.16 28 24 0.32 29 38 0.51 ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29 Consensus pattern (29 bp): TGGCCCATTAGGCCCAAATCACATTCATA Found at i:88787806 original size:16 final size:16 Alignment explanation

Indices: 88787774--88787825 Score: 68 Period size: 16 Copynumber: 3.2 Consensus size: 16 88787764 ACAAAGAAAG * 88787774 TTTGGGATTTCGAGATT 1 TTTGGG-TTTCGGGATT 88787791 TTTGGGTTTCGGGATT 1 TTTGGGTTTCGGGATT ** 88787807 TTTGGGTTTATGGATT 1 TTTGGGTTTCGGGATT 88787823 TTT 1 TTT 88787826 AGGGCGTTAC Statistics Matches: 32, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 16 26 0.81 17 6 0.19 ACGTcount: A:0.12, C:0.04, G:0.31, T:0.54 Consensus pattern (16 bp): TTTGGGTTTCGGGATT Found at i:88789808 original size:2 final size:2 Alignment explanation

Indices: 88789803--88789828 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 88789793 AAAAACGCGT 88789803 TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA 88789829 ACAAAAAAAC Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:88793433 original size:135 final size:135 Alignment explanation

Indices: 88793191--88793464 Score: 539 Period size: 135 Copynumber: 2.0 Consensus size: 135 88793181 CTACAATTAT 88793191 GTACTTGTGACCAAGGAAATGTTACATTCAGTCCCTTAATCACTTAACACAATTTAATGTGTGAG 1 GTACTTGTGACCAAGGAAATGTTACATTCAGTCCCTTAATCACTTAACACAATTTAATGTGTGAG * 88793256 ATCATTCTACATACATACATACATATATACATATATATATGCTGAACCTCAGAAAAACTAGAGAA 66 ATCATTCTACACACATACATACATATATACATATATATATGCTGAACCTCAGAAAAACTAGAGAA 88793321 AGGCA 131 AGGCA 88793326 GTACTTGTGACCAAGGAAATGTTACATTCAGTCCCTTAATCACTTAACACAATTTAATGTGTGAG 1 GTACTTGTGACCAAGGAAATGTTACATTCAGTCCCTTAATCACTTAACACAATTTAATGTGTGAG 88793391 ATCATTCTACACACATACATACATATATACATATATATATGCTGAACCTCAGAAAAACTAGAGAA 66 ATCATTCTACACACATACATACATATATACATATATATATGCTGAACCTCAGAAAAACTAGAGAA 88793456 AGGCA 131 AGGCA 88793461 GTAC 1 GTAC 88793465 AAAGATACAA Statistics Matches: 138, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 135 138 1.00 ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28 Consensus pattern (135 bp): GTACTTGTGACCAAGGAAATGTTACATTCAGTCCCTTAATCACTTAACACAATTTAATGTGTGAG ATCATTCTACACACATACATACATATATACATATATATATGCTGAACCTCAGAAAAACTAGAGAA AGGCA Found at i:88794260 original size:17 final size:19 Alignment explanation

Indices: 88794238--88794275 Score: 62 Period size: 17 Copynumber: 2.1 Consensus size: 19 88794228 GGTCAGCTTA 88794238 CATGTTTAAC-T-CATATG 1 CATGTTTAACTTACATATG 88794255 CATGTTTAACTTACATATG 1 CATGTTTAACTTACATATG 88794274 CA 1 CA 88794276 ATGATAATTT Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 17 10 0.53 18 1 0.05 19 8 0.42 ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39 Consensus pattern (19 bp): CATGTTTAACTTACATATG Found at i:88796206 original size:3 final size:3 Alignment explanation

Indices: 88796200--88796246 Score: 53 Period size: 3 Copynumber: 16.3 Consensus size: 3 88796190 TTTTAGTTAG * * * 88796200 ATT ATT ATT ATT ATT ATT ATT ATT A-A ATT -TT AAT ATG ATT ATT ATT 1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 88796246 A 1 A 88796247 AAAATAATTT Statistics Matches: 36, Mismatches: 6, Indels: 4 0.78 0.13 0.09 Matches are distributed among these distances: 2 3 0.08 3 33 0.92 ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60 Consensus pattern (3 bp): ATT Found at i:88796264 original size:15 final size:15 Alignment explanation

Indices: 88796246--88796274 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 88796236 GATTATTATT 88796246 AAAAATAATTTAATA 1 AAAAATAATTTAATA 88796261 AAAAATAATTTAAT 1 AAAAATAATTTAAT 88796275 CATATTTTAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34 Consensus pattern (15 bp): AAAAATAATTTAATA Found at i:88796273 original size:26 final size:26 Alignment explanation

Indices: 88796242--88796321 Score: 74 Period size: 26 Copynumber: 3.1 Consensus size: 26 88796232 ATATGATTAT 88796242 TATTAAAAATAATTTAATAAAAAATAA 1 TATTAAAAATAATTTAAT-AAAAATAA ** * * * * 88796269 T-TTAATCATATTTTAATATAATTAT 1 TATTAAAAATAATTTAATAAAAATAA 88796294 TATTAAATAA-AATTTAATAAAAATAA 1 TATTAAA-AATAATTTAATAAAAATAA 88796320 TA 1 TA 88796322 ATATACAATT Statistics Matches: 39, Mismatches: 12, Indels: 5 0.70 0.21 0.09 Matches are distributed among these distances: 25 6 0.15 26 31 0.79 27 2 0.05 ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41 Consensus pattern (26 bp): TATTAAAAATAATTTAATAAAAATAA Found at i:88798457 original size:24 final size:23 Alignment explanation

Indices: 88798395--88798463 Score: 79 Period size: 24 Copynumber: 3.0 Consensus size: 23 88798385 TCCCTATTAA * 88798395 AAACTCTTATGAGTTACTTG-TT 1 AAACTCTTATGAGTTTCTTGTTT * * * 88798417 AAGCTC-AATGAGCTTCTTGTTCT 1 AAACTCTTATGAGTTTCTTGTT-T 88798440 AAACTCTTATGAGTTTCTTGTTT 1 AAACTCTTATGAGTTTCTTGTTT 88798463 A 1 A 88798464 GCTCGGATAA Statistics Matches: 37, Mismatches: 7, Indels: 5 0.76 0.14 0.10 Matches are distributed among these distances: 21 10 0.27 22 6 0.16 23 8 0.22 24 13 0.35 ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45 Consensus pattern (23 bp): AAACTCTTATGAGTTTCTTGTTT Found at i:88808051 original size:40 final size:40 Alignment explanation

Indices: 88808007--88808142 Score: 105 Period size: 40 Copynumber: 3.4 Consensus size: 40 88807997 ACACTAGCCT * 88808007 GAAGCCTGCTAGGCACTAAGC-CTGATA-ATTACACCGACAC 1 GAAGCCTGCTAGGCACTAAGCAC-GATAGA-TACACCAACAC * * ** 88808047 GAAGCTTGCTAGGCATTAAGCACGATAGATACATTAACAC 1 GAAGCCTGCTAGGCACTAAGCACGATAGATACACCAACAC * * ** * * * * * * 88808087 GAACCCTGCTAGGCATTGGGCCCAATAGAAACACTAGCAT 1 GAAGCCTGCTAGGCACTAAGCACGATAGATACACCAACAC 88808127 GAAGCCTGCTAGGCAC 1 GAAGCCTGCTAGGCAC 88808143 AAGGCCCGAT Statistics Matches: 77, Mismatches: 17, Indels: 4 0.79 0.17 0.04 Matches are distributed among these distances: 40 75 0.97 41 2 0.03 ACGTcount: A:0.33, C:0.26, G:0.22, T:0.18 Consensus pattern (40 bp): GAAGCCTGCTAGGCACTAAGCACGATAGATACACCAACAC Found at i:88815404 original size:46 final size:46 Alignment explanation

Indices: 88815259--88815428 Score: 150 Period size: 47 Copynumber: 3.7 Consensus size: 46 88815249 GGTAAGGTGC * * * * ** 88815259 CGATGCCATGTCCTAAACACGGTCTTACACTGGCTCATATCTCAAGT 1 CGATGCCATGTCCCAAACA-TGTCTTACACTGGCTTACATCTTGAGT * * * 88815306 CGATGCCATGTCCCAGACATGGTCTTACACTGAC-TATCAT-TTCGTAGC 1 CGATGCCATGTCCCAAACAT-GTCTTACACTGGCTTA-CATCTT-G-AGT * 88815354 CGATG-CATGTCCCAAACATGTCTTACATTGGCTTACATCTTGAGGT 1 CGATGCCATGTCCCAAACATGTCTTACACTGGCTTACATCTTGA-GT * * 88815400 CGATG-CATGTCCCAGACATGCCTTACACT 1 CGATGCCATGTCCCAAACATGTCTTACACT 88815429 AGCTCATGAA Statistics Matches: 100, Mismatches: 16, Indels: 15 0.76 0.12 0.11 Matches are distributed among these distances: 45 1 0.01 46 44 0.44 47 48 0.48 48 7 0.07 ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29 Consensus pattern (46 bp): CGATGCCATGTCCCAAACATGTCTTACACTGGCTTACATCTTGAGT Found at i:88819076 original size:21 final size:21 Alignment explanation

Indices: 88819047--88819095 Score: 71 Period size: 21 Copynumber: 2.3 Consensus size: 21 88819037 TATTTCTTGC * * 88819047 ATTTATTACGTGTGTTCAATT 1 ATTTCTTACGCGTGTTCAATT * 88819068 ATTTCTTACGCGTGTTCCATT 1 ATTTCTTACGCGTGTTCAATT 88819089 ATTTCTT 1 ATTTCTT 88819096 GCATATGTTC Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 25 1.00 ACGTcount: A:0.18, C:0.16, G:0.12, T:0.53 Consensus pattern (21 bp): ATTTCTTACGCGTGTTCAATT Found at i:88826553 original size:18 final size:17 Alignment explanation

Indices: 88826532--88826565 Score: 50 Period size: 18 Copynumber: 1.9 Consensus size: 17 88826522 ACATGTGTTA 88826532 AAATAAAATTCATATATC 1 AAATAAAATT-ATATATC * 88826550 AAATTAAATTATATAT 1 AAATAAAATTATATAT 88826566 ATTTACTTAT Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 6 0.40 18 9 0.60 ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38 Consensus pattern (17 bp): AAATAAAATTATATATC Found at i:88827432 original size:12 final size:11 Alignment explanation

Indices: 88827413--88827443 Score: 53 Period size: 12 Copynumber: 2.7 Consensus size: 11 88827403 TGTATAAAAC 88827413 TTATTTTATTA 1 TTATTTTATTA 88827424 TTAATTTTATTA 1 TT-ATTTTATTA 88827436 TTATTTTA 1 TTATTTTA 88827444 AAGGCATTTG Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 11 8 0.42 12 11 0.58 ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71 Consensus pattern (11 bp): TTATTTTATTA Found at i:88827468 original size:31 final size:30 Alignment explanation

Indices: 88827424--88827484 Score: 104 Period size: 31 Copynumber: 2.0 Consensus size: 30 88827414 TATTTTATTA 88827424 TTAATTTTATTATTATTTTAAAGGCATTTG 1 TTAATTTTATTATTATTTTAAAGGCATTTG * 88827454 TTAATTATTATTATTATTTTAAAGGTATTTG 1 TTAATT-TTATTATTATTTTAAAGGCATTTG 88827485 CTTATTAAGT Statistics Matches: 29, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 30 6 0.21 31 23 0.79 ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57 Consensus pattern (30 bp): TTAATTTTATTATTATTTTAAAGGCATTTG Found at i:88829619 original size:19 final size:20 Alignment explanation

Indices: 88829582--88829619 Score: 51 Period size: 19 Copynumber: 1.9 Consensus size: 20 88829572 ATAGGGACAA * 88829582 TATGATTAAATTATGATGTG 1 TATGATTAAATGATGATGTG * 88829602 TATG-TTAAATGATTATGT 1 TATGATTAAATGATGATGT 88829620 AAATGTTCGT Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 19 12 0.75 20 4 0.25 ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47 Consensus pattern (20 bp): TATGATTAAATGATGATGTG Found at i:88835528 original size:19 final size:20 Alignment explanation

Indices: 88835504--88835541 Score: 60 Period size: 19 Copynumber: 1.9 Consensus size: 20 88835494 TAGTCTTAAA * 88835504 ATAAAATAA-AAGTAAAAAC 1 ATAAAATAATAAATAAAAAC 88835523 ATAAAATAATAAATAAAAA 1 ATAAAATAATAAATAAAAA 88835542 TTTTTAAACA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 19 9 0.53 20 8 0.47 ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18 Consensus pattern (20 bp): ATAAAATAATAAATAAAAAC Found at i:88844943 original size:46 final size:48 Alignment explanation

Indices: 88844835--88845001 Score: 166 Period size: 46 Copynumber: 3.6 Consensus size: 48 88844825 AAGCTGACAC * * * 88844835 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCGAGGCCGATG 1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAAGGCAGATG * * ** 88844883 CATGTCCCAAACATGTCTTACACTAGCTT-T-TGTCTCAATTCAGATG 1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAAGGCAGATG * * * * 88844929 CATGTCCCAGACATGTCTTACACTGGCTCT-CATAATGT---GGCCGATG 1 CATGTCCCAGACATGTCTTACACTAGCT-TGTAT-ATCTCAAGGCAGATG * 88844975 CATGTCCCAGACATATCTTACACTAGC 1 CATGTCCCAGACATGTCTTACACTAGC 88845002 ACACATATCA Statistics Matches: 99, Mismatches: 17, Indels: 8 0.80 0.14 0.06 Matches are distributed among these distances: 46 67 0.68 47 2 0.02 48 28 0.28 49 2 0.02 ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29 Consensus pattern (48 bp): CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAAGGCAGATG Found at i:88847262 original size:21 final size:21 Alignment explanation

Indices: 88847237--88847279 Score: 86 Period size: 21 Copynumber: 2.0 Consensus size: 21 88847227 AAAATGAGTT 88847237 AGTTAAAAGATGAACTAAGTA 1 AGTTAAAAGATGAACTAAGTA 88847258 AGTTAAAAGATGAACTAAGTA 1 AGTTAAAAGATGAACTAAGTA 88847279 A 1 A 88847280 ATTAGGAGGT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 22 1.00 ACGTcount: A:0.53, C:0.05, G:0.19, T:0.23 Consensus pattern (21 bp): AGTTAAAAGATGAACTAAGTA Found at i:88848006 original size:41 final size:40 Alignment explanation

Indices: 88847950--88848054 Score: 156 Period size: 44 Copynumber: 2.5 Consensus size: 40 88847940 TTTTATCTTA * 88847950 GAAAAAATAATTTAAAAAGAGAAGATAATCTTGGGTTGTT 1 GAAAAAACAATTTAAAAAGAGAAGATAATCTTGGGTTGTT 88847990 GAAAAAAACAATTTAAAAAGAGGAGAAGATAATCTTGGGTTGTT 1 G-AAAAAACAATTT-AAAA-A-GAGAAGATAATCTTGGGTTGTT * 88848034 GAAAAAAGAATTTAAAAAGAG 1 GAAAAAACAATTTAAAAAGAG 88848055 CAGAAGATAA Statistics Matches: 59, Mismatches: 2, Indels: 8 0.86 0.03 0.12 Matches are distributed among these distances: 40 4 0.07 41 12 0.20 42 8 0.14 43 12 0.20 44 23 0.39 ACGTcount: A:0.51, C:0.03, G:0.21, T:0.25 Consensus pattern (40 bp): GAAAAAACAATTTAAAAAGAGAAGATAATCTTGGGTTGTT Found at i:88848053 original size:43 final size:43 Alignment explanation

Indices: 88847950--88848076 Score: 179 Period size: 43 Copynumber: 3.0 Consensus size: 43 88847940 TTTTATCTTA * 88847950 GAAAAAATAATTT-AAAA-A-GAGAAGATAATCTTGGGTTGTT 1 GAAAAAACAATTTAAAAAGAGGAGAAGATAATCTTGGGTTGTT 88847990 GAAAAAAACAATTTAAAAAGAGGAGAAGATAATCTTGGGTTGTT 1 G-AAAAAACAATTTAAAAAGAGGAGAAGATAATCTTGGGTTGTT * * * * 88848034 GAAAAAAGAATTTAAAAAGAGCAGAAGATAAACATGGGTTGTT 1 GAAAAAACAATTTAAAAAGAGGAGAAGATAATCTTGGGTTGTT 88848077 TGTTTTACCT Statistics Matches: 78, Mismatches: 5, Indels: 5 0.89 0.06 0.06 Matches are distributed among these distances: 40 1 0.01 41 11 0.14 42 4 0.05 43 39 0.50 44 23 0.29 ACGTcount: A:0.49, C:0.04, G:0.22, T:0.25 Consensus pattern (43 bp): GAAAAAACAATTTAAAAAGAGGAGAAGATAATCTTGGGTTGTT Found at i:88851898 original size:30 final size:30 Alignment explanation

Indices: 88851864--88851923 Score: 93 Period size: 30 Copynumber: 2.0 Consensus size: 30 88851854 ATTTAATACG 88851864 AACTTTGGAAAAATTACACTTTTGCCCCTA 1 AACTTTGGAAAAATTACACTTTTGCCCCTA * * * 88851894 AACTTTTGCATAATTACACTTTTGCCCCTA 1 AACTTTGGAAAAATTACACTTTTGCCCCTA 88851924 GGCTCGGGAA Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 30 27 1.00 ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37 Consensus pattern (30 bp): AACTTTGGAAAAATTACACTTTTGCCCCTA Found at i:88858927 original size:46 final size:45 Alignment explanation

Indices: 88858829--88858914 Score: 129 Period size: 46 Copynumber: 1.9 Consensus size: 45 88858819 AACCCGCCCC * * 88858829 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-ATGCCCATCCA * 88858875 TAAGTGAACTCGGACTTAACTCAACGAGTTCGG-ATGCCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATGCCCA 88858915 AATATCCTAG Statistics Matches: 37, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 44 5 0.14 46 32 0.86 ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22 Consensus pattern (45 bp): TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATGCCCATCCA Found at i:88859361 original size:30 final size:29 Alignment explanation

Indices: 88859327--88859385 Score: 82 Period size: 30 Copynumber: 2.0 Consensus size: 29 88859317 ATTTAATACG 88859327 AACTTTAGAAAAATTACACTTTTGCCCCTA 1 AACTTTAGAAAAATTACACTTTT-CCCCTA * * * 88859357 AACTTTTGCATAATTACACTTTTCCCCTA 1 AACTTTAGAAAAATTACACTTTTCCCCTA 88859386 GGCTCGGGAA Statistics Matches: 26, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 29 6 0.23 30 20 0.77 ACGTcount: A:0.32, C:0.25, G:0.05, T:0.37 Consensus pattern (29 bp): AACTTTAGAAAAATTACACTTTTCCCCTA Found at i:88882805 original size:25 final size:28 Alignment explanation

Indices: 88882770--88882837 Score: 115 Period size: 25 Copynumber: 2.5 Consensus size: 28 88882760 TTAGTGAGTC 88882770 CGCACACTTAGTGCTATAT-ATC-AACT 1 CGCACACTTAGTGCTATATGATCAAACT 88882796 CGCA-ACTTAGTGCTATATGATCAAACT 1 CGCACACTTAGTGCTATATGATCAAACT 88882823 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 88882838 GTACAATTTT Statistics Matches: 39, Mismatches: 0, Indels: 4 0.91 0.00 0.09 Matches are distributed among these distances: 25 14 0.36 26 7 0.18 27 8 0.21 28 10 0.26 ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29 Consensus pattern (28 bp): CGCACACTTAGTGCTATATGATCAAACT Found at i:88888255 original size:39 final size:40 Alignment explanation

Indices: 88888145--88888276 Score: 205 Period size: 40 Copynumber: 3.3 Consensus size: 40 88888135 GCTACTCGTT * * 88888145 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA 88888185 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA * * 88888225 CCAATGCCTTCGGG-CTTAACCCGGAATTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 88888264 CAAATGCCTTCGG 1 CAAATGCCTTCGG 88888277 ATCTTAGTCT Statistics Matches: 86, Mismatches: 5, Indels: 3 0.91 0.05 0.03 Matches are distributed among these distances: 39 36 0.42 40 48 0.56 41 2 0.02 ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA Found at i:88888313 original size:79 final size:80 Alignment explanation

Indices: 88888145--88888329 Score: 189 Period size: 79 Copynumber: 2.3 Consensus size: 80 88888135 GCTACTCGTT * * * * 88888145 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG 1 CAAA-GCCTTCGGGACTTAACCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA * * 88888209 GATTTAGTAACTCGCAC 64 GATATAGTAACTAGCAC * ** * 88888226 CAATGCCTTCGGG-CTTAACCCGGAATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCTAG 1 CAAAGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCAG * * 88888289 ATATGGTCACTTAGCA- 65 ATATAGTAAC-TAGCAC * 88888305 CAAAGCCTTCGGGACTTAGCCCGGA 1 CAAAGCCTTCGGGACTTAACCCGGA 88888330 CATCATTCGA Statistics Matches: 86, Mismatches: 14, Indels: 9 0.79 0.13 0.08 Matches are distributed among these distances: 78 3 0.03 79 56 0.65 80 24 0.28 81 3 0.03 ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24 Consensus pattern (80 bp): CAAAGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGA TATAGTAACTAGCAC Found at i:88890893 original size:16 final size:15 Alignment explanation

Indices: 88890853--88890894 Score: 50 Period size: 14 Copynumber: 2.8 Consensus size: 15 88890843 GGATCATCTC * 88890853 ATATAAATATCACAA 1 ATATAAATATTACAA * 88890868 TTAT-AATATTACATA 1 ATATAAATATTACA-A 88890883 ATATAAATATTA 1 ATATAAATATTA 88890895 TAAACAATTA Statistics Matches: 22, Mismatches: 3, Indels: 3 0.79 0.11 0.11 Matches are distributed among these distances: 14 8 0.36 15 7 0.32 16 7 0.32 ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38 Consensus pattern (15 bp): ATATAAATATTACAA Found at i:88894390 original size:16 final size:15 Alignment explanation

Indices: 88894367--88894399 Score: 57 Period size: 16 Copynumber: 2.1 Consensus size: 15 88894357 AAATAAAAGG 88894367 AATAATGAATAAATA 1 AATAATGAATAAATA 88894382 AATAGATGAATAAATA 1 AATA-ATGAATAAATA 88894398 AA 1 AA 88894400 GAATTAAAAT Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 4 0.24 16 13 0.76 ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24 Consensus pattern (15 bp): AATAATGAATAAATA Found at i:88895124 original size:50 final size:50 Alignment explanation

Indices: 88895065--88895161 Score: 194 Period size: 50 Copynumber: 1.9 Consensus size: 50 88895055 TACGGCGACA 88895065 GAACGCGAAGAGTCAGGTAACTTCGACCATTTTTTTTTATTTTTCTTACG 1 GAACGCGAAGAGTCAGGTAACTTCGACCATTTTTTTTTATTTTTCTTACG 88895115 GAACGCGAAGAGTCAGGTAACTTCGACCATTTTTTTTTATTTTTCTT 1 GAACGCGAAGAGTCAGGTAACTTCGACCATTTTTTTTTATTTTTCTT 88895162 TCTTAAAAAA Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 50 47 1.00 ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41 Consensus pattern (50 bp): GAACGCGAAGAGTCAGGTAACTTCGACCATTTTTTTTTATTTTTCTTACG Found at i:88902915 original size:40 final size:40 Alignment explanation

Indices: 88902860--88903077 Score: 289 Period size: 40 Copynumber: 5.5 Consensus size: 40 88902850 CGGATGATAA ** * * 88902860 CCGGGCTAAGTCCCGAAGGCATTTACGCTAGTGACTAGT-T 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT 88902900 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * 88902940 TCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * 88902980 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * * 88903020 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT * * 88903060 CC-GGTTAAATCCCGAAGG 1 CCGGGCTAAGTCCCGAAGG 88903078 TACCTGGCTT Statistics Matches: 160, Mismatches: 16, Indels: 5 0.88 0.09 0.03 Matches are distributed among these distances: 39 16 0.10 40 144 0.90 ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT Found at i:88908679 original size:39 final size:40 Alignment explanation

Indices: 88908548--88908684 Score: 129 Period size: 40 Copynumber: 3.5 Consensus size: 40 88908538 GGATATAACG * * * ** 88908548 ACTCGCTCAAATGCCTTCGGGAC-GAAGCCCGG-TTATAGCG 1 ACTCGCACGAATGCCTTCGGGACTTAA-CCCGGATT-TAGTA * 88908588 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA 1 ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA * * * * * 88908628 ACTTGCAC-AATGCCTTTGGG-CTTAGCTCGGATTTATTA 1 ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA 88908666 ACTCGCACGAATGCCTTCG 1 ACTCGCACGAATGCCTTCG 88908685 ATCCTAGTCC Statistics Matches: 81, Mismatches: 13, Indels: 7 0.80 0.13 0.07 Matches are distributed among these distances: 38 21 0.26 39 20 0.25 40 36 0.44 41 4 0.05 ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26 Consensus pattern (40 bp): ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA Found at i:88908714 original size:78 final size:78 Alignment explanation

Indices: 88908588--88908737 Score: 178 Period size: 78 Copynumber: 1.9 Consensus size: 78 88908578 GGTTATAGCG * * * * * 88908588 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCACAATGCCTTTGGG-CTTA 1 ACTCGCACGAATGCCTTC-GGACCTAACCCGGATATAGTAACTTGCACAAAGCCTTCGGGACTTA * 88908652 GCTCGGATTTATTA 65 GCCCGGATTTATTA ** * 88908666 ACTCGCACGAATGCCTTC-GATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT 1 ACTCGCACGAATGCCTTCGGA-CCTAACCCGGATATAGTAACTT-GCACAAAGCCTTCGGGACTT 88908730 AGCCCGGA 64 AGCCCGGA 88908738 CATCATTCGA Statistics Matches: 60, Mismatches: 9, Indels: 5 0.81 0.12 0.07 Matches are distributed among these distances: 76 2 0.03 77 16 0.27 78 32 0.53 79 10 0.17 ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27 Consensus pattern (78 bp): ACTCGCACGAATGCCTTCGGACCTAACCCGGATATAGTAACTTGCACAAAGCCTTCGGGACTTAG CCCGGATTTATTA Found at i:88912687 original size:40 final size:40 Alignment explanation

Indices: 88912632--88912849 Score: 273 Period size: 40 Copynumber: 5.5 Consensus size: 40 88912622 CGGATGATAA * * 88912632 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T 1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACTA-TAT 88912672 CCGGGCTAAGTCCCGAAGGCATTT-CTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGC-GCGAGTTACTATAT * * * 88912712 TCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACTATAT * * 88912752 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT 1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACTATAT * * * 88912792 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTA-CTATAT * * 88912832 CC-GGTTAAATCCCGAAGG 1 CCGGGCTAAGTCCCGAAGG 88912850 TACCTAGCTT Statistics Matches: 159, Mismatches: 15, Indels: 9 0.87 0.08 0.05 Matches are distributed among these distances: 39 17 0.11 40 142 0.89 ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACTATAT Found at i:88918283 original size:18 final size:18 Alignment explanation

Indices: 88918260--88918296 Score: 58 Period size: 18 Copynumber: 2.1 Consensus size: 18 88918250 TTCATGTTAT 88918260 TATTTAT-TTATTTTTAAA 1 TATTTATATTA-TTTTAAA 88918278 TATTTATATTATTTTAAA 1 TATTTATATTATTTTAAA 88918296 T 1 T 88918297 TGAATATTTA Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 18 15 0.83 19 3 0.17 ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65 Consensus pattern (18 bp): TATTTATATTATTTTAAA Found at i:88918985 original size:21 final size:22 Alignment explanation

Indices: 88918924--88918988 Score: 73 Period size: 21 Copynumber: 3.0 Consensus size: 22 88918914 TAACTTCTTT 88918924 TATAA-TTTTATAATTTTCTTTA 1 TATAATTTTTATAATTTT-TTTA * * 88918946 TATATTTTTTAGAATTTTTTT- 1 TATAATTTTTATAATTTTTTTA 88918967 TGA-AATTTTTATAATTTTTTTA 1 T-ATAATTTTTATAATTTTTTTA 88918989 AAAAATAAAT Statistics Matches: 36, Mismatches: 4, Indels: 6 0.78 0.09 0.13 Matches are distributed among these distances: 21 17 0.47 22 8 0.22 23 11 0.31 ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66 Consensus pattern (22 bp): TATAATTTTTATAATTTTTTTA Found at i:88921146 original size:99 final size:99 Alignment explanation

Indices: 88920962--88921170 Score: 321 Period size: 99 Copynumber: 2.1 Consensus size: 99 88920952 AAATTGAAGG * 88920962 ACCAAAAGTGAAAATAACGCAATTTCTTGTAACATGGGATTGGTATGTAAGGACCAAATTGAATA 1 ACCAAAAGTGAAAATAACCCAATTTCTTGTAACATGGGATTGGTATGTAAGGACCAAATTGAATA * 88921027 AATGGAGAAATATAAGGGACTTAATCATAATATT 66 AATGGAGAAATATAAGGGACTTAATCACAATATT * * * * * 88921061 ACTAAGAGTGAAAATAACCCAATTTCTTGTAACATGGGATTGGTGTGTAGGGACCAAATTGAATG 1 ACCAAAAGTGAAAATAACCCAATTTCTTGTAACATGGGATTGGTATGTAAGGACCAAATTGAATA * * 88921126 AGTGGAGAAATATGAA-GGACTTAATCACAATTTT 66 AATGGAGAAATAT-AAGGGACTTAATCACAATATT 88921160 ACCAAAAGTGA 1 ACCAAAAGTGA 88921171 GAAGTGATTC Statistics Matches: 98, Mismatches: 11, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 99 96 0.98 100 2 0.02 ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27 Consensus pattern (99 bp): ACCAAAAGTGAAAATAACCCAATTTCTTGTAACATGGGATTGGTATGTAAGGACCAAATTGAATA AATGGAGAAATATAAGGGACTTAATCACAATATT Found at i:88923200 original size:27 final size:27 Alignment explanation

Indices: 88923162--88923263 Score: 91 Period size: 27 Copynumber: 3.8 Consensus size: 27 88923152 AACATGTAAA * 88923162 AAAAGAAAGCCTTTATGGCAAACCATG 1 AAAAGAAAGCCTTTATGGCAAACAATG * * * 88923189 AAAAGAAAGCCTTTGTGACGAACAATG 1 AAAAGAAAGCCTTTATGGCAAACAATG ** * 88923216 AATTGAAAGCCTTTTTGGCAAA-AAT- 1 AAAAGAAAGCCTTTATGGCAAACAATG * * 88923241 AGAAAGATTAGCCTTTGTGGCAA 1 A-AAAGA-AAGCCTTTATGGCAA 88923264 TCTCTATAAG Statistics Matches: 60, Mismatches: 13, Indels: 4 0.78 0.17 0.05 Matches are distributed among these distances: 25 1 0.02 26 6 0.10 27 53 0.88 ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24 Consensus pattern (27 bp): AAAAGAAAGCCTTTATGGCAAACAATG Found at i:88926110 original size:21 final size:20 Alignment explanation

Indices: 88926085--88926125 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 20 88926075 AAGAAACAAT * 88926085 GTAATTACTTTCAATAGAAAA 1 GTAATTACTCTCAATA-AAAA * 88926106 GTAATTTCTCTCAATAAAAA 1 GTAATTACTCTCAATAAAAA 88926126 CCGAAAATAC Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 20 4 0.22 21 14 0.78 ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34 Consensus pattern (20 bp): GTAATTACTCTCAATAAAAA Found at i:88927809 original size:93 final size:93 Alignment explanation

Indices: 88927697--88927868 Score: 317 Period size: 93 Copynumber: 1.8 Consensus size: 93 88927687 GCCCATAAGT * * 88927697 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 88927762 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 88927790 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 88927855 CGAGTTCGGATGCC 66 CGAGTTCGGATGCC 88927869 CAAATATCCC Statistics Matches: 76, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 76 1.00 ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:88927864 original size:46 final size:46 Alignment explanation

Indices: 88927689--88927864 Score: 232 Period size: 46 Copynumber: 3.8 Consensus size: 46 88927679 TGTAACCCGC * * * 88927689 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT * * 88927735 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT * * 88927785 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 88927828 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 88927865 TGCCCAAATA Statistics Matches: 112, Mismatches: 11, Indels: 14 0.82 0.08 0.10 Matches are distributed among these distances: 43 3 0.03 44 1 0.01 45 2 0.02 46 68 0.61 47 32 0.29 48 2 0.02 49 1 0.01 50 3 0.03 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT Found at i:88930289 original size:28 final size:28 Alignment explanation

Indices: 88930247--88930309 Score: 83 Period size: 28 Copynumber: 2.2 Consensus size: 28 88930237 CAAAGATAAC 88930247 AAGAAAACCGAATAAAGAAATCCA-ATA 1 AAGAAAACCGAATAAAGAAATCCAGATA * * 88930274 AAGAAATCCAGAATAAAGAGATCCAGGATA 1 AAGAAAACC-GAATAAAGAAATCCA-GATA 88930304 AAGAAA 1 AAGAAA 88930310 CCCAAGATAC Statistics Matches: 31, Mismatches: 2, Indels: 3 0.86 0.06 0.08 Matches are distributed among these distances: 27 8 0.26 28 14 0.45 30 9 0.29 ACGTcount: A:0.60, C:0.13, G:0.16, T:0.11 Consensus pattern (28 bp): AAGAAAACCGAATAAAGAAATCCAGATA Found at i:88930290 original size:15 final size:14 Alignment explanation

Indices: 88930247--88930309 Score: 74 Period size: 15 Copynumber: 4.4 Consensus size: 14 88930237 CAAAGATAAC * 88930247 AAGAAAACCGAATA 1 AAGAAATCCGAATA 88930261 AAGAAATCC-AATA 1 AAGAAATCCGAATA 88930274 AAGAAATCCAGAATA 1 AAGAAATCC-GAATA * * 88930289 AAGAGATCCAGGATA 1 AAGAAATCC-GAATA 88930304 AAGAAA 1 AAGAAA 88930310 CCCAAGATAC Statistics Matches: 43, Mismatches: 4, Indels: 3 0.86 0.08 0.06 Matches are distributed among these distances: 13 13 0.30 14 8 0.19 15 22 0.51 ACGTcount: A:0.60, C:0.13, G:0.16, T:0.11 Consensus pattern (14 bp): AAGAAATCCGAATA Found at i:88933340 original size:93 final size:93 Alignment explanation

Indices: 88933228--88933399 Score: 317 Period size: 93 Copynumber: 1.8 Consensus size: 93 88933218 GCCCATAAGT * * 88933228 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 88933293 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 88933321 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 88933386 CGAGTTCGGATGCC 66 CGAGTTCGGATGCC 88933400 CAAATATCCA Statistics Matches: 76, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 76 1.00 ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:88933395 original size:46 final size:46 Alignment explanation

Indices: 88933220--88933395 Score: 232 Period size: 46 Copynumber: 3.8 Consensus size: 46 88933210 TGTAACCCGC * * * 88933220 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT * * 88933266 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT * * 88933316 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 88933359 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 88933396 TGCCCAAATA Statistics Matches: 112, Mismatches: 11, Indels: 14 0.82 0.08 0.10 Matches are distributed among these distances: 43 3 0.03 44 1 0.01 45 2 0.02 46 68 0.61 47 32 0.29 48 2 0.02 49 1 0.01 50 3 0.03 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT Found at i:88936474 original size:3 final size:3 Alignment explanation

Indices: 88936468--88936508 Score: 73 Period size: 3 Copynumber: 13.7 Consensus size: 3 88936458 TTTTCTTTCT * 88936468 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TT 1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT 88936509 GTGTTTGATG Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 3 36 1.00 ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71 Consensus pattern (3 bp): TTC Found at i:88936485 original size:9 final size:9 Alignment explanation

Indices: 88936458--88936505 Score: 60 Period size: 9 Copynumber: 5.1 Consensus size: 9 88936448 TAAAAAAACA 88936458 TTTTCTTTCT 1 TTTTC-TTCT 88936468 TTCTTCTTCT 1 TT-TTCTTCT 88936478 TTTTCTTCT 1 TTTTCTTCT * 88936487 TCTTCTTCT 1 TTTTCTTCT * 88936496 TCTTCTTCT 1 TTTTCTTCT 88936505 T 1 T 88936506 CTTGTGTTTG Statistics Matches: 36, Mismatches: 1, Indels: 3 0.90 0.03 0.08 Matches are distributed among these distances: 9 25 0.69 10 8 0.22 11 3 0.08 ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73 Consensus pattern (9 bp): TTTTCTTCT Found at i:88937495 original size:15 final size:16 Alignment explanation

Indices: 88937475--88937514 Score: 55 Period size: 15 Copynumber: 2.5 Consensus size: 16 88937465 TAATTGCTAC 88937475 AAAACAATCT-AAAAT 1 AAAACAATCTAAAAAT * 88937490 AAAACATTCTAAAAAT 1 AAAACAATCTAAAAAT 88937506 AAAATCAAT 1 AAAA-CAAT 88937515 AATAACTATA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 15 9 0.43 16 9 0.43 17 3 0.14 ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23 Consensus pattern (16 bp): AAAACAATCTAAAAAT Found at i:88943630 original size:93 final size:93 Alignment explanation

Indices: 88943502--88943672 Score: 263 Period size: 93 Copynumber: 1.8 Consensus size: 93 88943492 GCCCCTAAGT * * * 88943502 GAACTCAGACTCAACTCAATGAGCTTGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA 1 GAACTCAGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA 88943567 CGAGTTCAGATGCCTAGTTACATTTCAC 66 CGAGTTCAGATGCCTAGTTACATTTCAC * * 88943595 GAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 GAACTCAGACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA * * 88943659 ATGAGTTCGGATGC 65 ACGAGTTCAGATGC 88943673 TCAACCATCC Statistics Matches: 70, Mismatches: 7, Indels: 2 0.89 0.09 0.03 Matches are distributed among these distances: 92 2 0.03 93 68 0.97 ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23 Consensus pattern (93 bp): GAACTCAGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA CGAGTTCAGATGCCTAGTTACATTTCAC Found at i:88943659 original size:46 final size:46 Alignment explanation

Indices: 88943497--88943669 Score: 158 Period size: 46 Copynumber: 3.7 Consensus size: 46 88943487 AACCCGCCCC * * * 88943497 TAAGTGAACTCAGACTCAACTCAATGAGCTT-GGGCGTTCGCATCCA 1 TAAGTGAACTCAGACTCAACTCAACGAG-TTCGGACATTCGCATCCA * * * 88943543 TAAGTGAACTCAGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT--T 1 TAAGTGAACTCAGACTCAACTCAACGAGTTC-G--GAC-A-TTCGCATCCA * * * 88943591 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA 1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA * * 88943636 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGA 1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA 88943670 TGCTCAACCA Statistics Matches: 103, Mismatches: 14, Indels: 20 0.75 0.10 0.15 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 44 2 0.02 45 4 0.04 46 56 0.54 47 26 0.25 48 2 0.02 49 2 0.02 50 3 0.03 51 2 0.02 ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24 Consensus pattern (46 bp): TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA Found at i:88944129 original size:30 final size:30 Alignment explanation

Indices: 88944106--88944184 Score: 158 Period size: 30 Copynumber: 2.6 Consensus size: 30 88944096 ACTTTGGAAA 88944106 AATTACACTTTTGCCCCTAAACTTTTGCAT 1 AATTACACTTTTGCCCCTAAACTTTTGCAT 88944136 AATTACACTTTTGCCCCTAAACTTTTGCAT 1 AATTACACTTTTGCCCCTAAACTTTTGCAT 88944166 AATTACACTTTTGCCCCTA 1 AATTACACTTTTGCCCCTA 88944185 GGCTCGGGAA Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 30 49 1.00 ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39 Consensus pattern (30 bp): AATTACACTTTTGCCCCTAAACTTTTGCAT Found at i:88944131 original size:14 final size:14 Alignment explanation

Indices: 88944112--88944163 Score: 50 Period size: 14 Copynumber: 3.6 Consensus size: 14 88944102 GAAAAATTAC 88944112 ACTTTTGCCCCTAA 1 ACTTTTGCCCCTAA *** * 88944126 ACTTTTGCATAATTAC 1 ACTTTTGC--CCCTAA 88944142 ACTTTTGCCCCTAA 1 ACTTTTGCCCCTAA 88944156 ACTTTTGC 1 ACTTTTGC 88944164 ATAATTACAC Statistics Matches: 28, Mismatches: 8, Indels: 4 0.70 0.20 0.10 Matches are distributed among these distances: 14 18 0.64 16 10 0.36 ACGTcount: A:0.23, C:0.29, G:0.08, T:0.40 Consensus pattern (14 bp): ACTTTTGCCCCTAA Found at i:88944147 original size:16 final size:16 Alignment explanation

Indices: 88944126--88944179 Score: 58 Period size: 16 Copynumber: 3.5 Consensus size: 16 88944116 TTGCCCCTAA 88944126 ACTTTTGCATAATTAC 1 ACTTTTGCATAATTAC *** * 88944142 ACTTTTGC--CCCTAA 1 ACTTTTGCATAATTAC 88944156 ACTTTTGCATAATTAC 1 ACTTTTGCATAATTAC 88944172 ACTTTTGC 1 ACTTTTGC 88944180 CCCTAGGCTC Statistics Matches: 28, Mismatches: 8, Indels: 4 0.70 0.20 0.10 Matches are distributed among these distances: 14 10 0.36 16 18 0.64 ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43 Consensus pattern (16 bp): ACTTTTGCATAATTAC Found at i:88947489 original size:18 final size:19 Alignment explanation

Indices: 88947452--88947491 Score: 55 Period size: 20 Copynumber: 2.1 Consensus size: 19 88947442 GCTCTTACTA * 88947452 TTTCTGAAAAATAATTTATT 1 TTTCTAAAAAATAA-TTATT 88947472 TTTCTAAAAAATAA-TATT 1 TTTCTAAAAAATAATTATT 88947490 TT 1 TT 88947492 ATTATATTTA Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 18 6 0.32 20 13 0.68 ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50 Consensus pattern (19 bp): TTTCTAAAAAATAATTATT Found at i:88948008 original size:16 final size:16 Alignment explanation

Indices: 88947977--88948013 Score: 58 Period size: 16 Copynumber: 2.3 Consensus size: 16 88947967 ATGTGAATAA 88947977 TATTATTTAAAATTAT 1 TATTATTTAAAATTAT 88947993 TATT-TTTAAAATTTAT 1 TATTATTTAAAA-TTAT 88948009 TATTA 1 TATTA 88948014 AAATAAAATT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 15 7 0.37 16 12 0.63 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (16 bp): TATTATTTAAAATTAT Found at i:88949792 original size:28 final size:28 Alignment explanation

Indices: 88949723--88949823 Score: 114 Period size: 28 Copynumber: 3.5 Consensus size: 28 88949713 GACAAGATTG * * * * 88949723 GCACTAAGTGTGCGGGTTTAAAATTGTACA 1 GCACTAAGTGTGCGAGTTT--GATTATATA 88949753 GCACTAAGTGTGCGAGTTTGATTATATA 1 GCACTAAGTGTGCGAGTTTGATTATATA * 88949781 GCACTAAGTGTGCGAG-TTGAATACATATA 1 GCACTAAGTGTGCGAGTTTG-AT-TATATA 88949810 GCACTAAGTGTGCG 1 GCACTAAGTGTGCG 88949824 GATTCACTAT Statistics Matches: 64, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 27 3 0.05 28 24 0.38 29 19 0.30 30 18 0.28 ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30 Consensus pattern (28 bp): GCACTAAGTGTGCGAGTTTGATTATATA Found at i:88951963 original size:14 final size:15 Alignment explanation

Indices: 88951930--88951973 Score: 63 Period size: 14 Copynumber: 3.0 Consensus size: 15 88951920 TTGATAAATT * * 88951930 AAAAATTAAATGTTG 1 AAAAAATAAGTGTTG 88951945 AAAAAATAAGTGTTG 1 AAAAAATAAGTGTTG 88951960 -AAAAATAAGTGTTG 1 AAAAAATAAGTGTTG 88951974 TTATATAATA Statistics Matches: 27, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 14 14 0.52 15 13 0.48 ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30 Consensus pattern (15 bp): AAAAAATAAGTGTTG Found at i:88951984 original size:3 final size:3 Alignment explanation

Indices: 88951978--88952013 Score: 72 Period size: 3 Copynumber: 12.0 Consensus size: 3 88951968 GTGTTGTTAT 88951978 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 88952014 CAAAGAGCAC Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 33 1.00 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (3 bp): ATA Found at i:88959373 original size:6 final size:5 Alignment explanation

Indices: 88959350--88959514 Score: 171 Period size: 5 Copynumber: 31.8 Consensus size: 5 88959340 TATGTCTTTC 88959350 AAAAT AAAAT --AAT AAAATT AAAAT GAAAAT AAAAAT AAAAAT AAAAAT 1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT -AAAAT 88959398 AAAAAT AAAAT AAAAT AAAAT AAAAT AAAAAT AAAAAT AAAAAT AAAAAT 1 -AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT -AAAAT -AAAAT * 88959448 AAAAT AAAAT AAAAT AAAAT AAAAC AAAAT AAAAT AAAACT -AAAT -AAAT 1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT 88959497 AAAACT -AAAT -AAAT AAAA 1 AAAA-T AAAAT AAAAT AAAA 88959515 AAATAGGAGG Statistics Matches: 148, Mismatches: 3, Indels: 18 0.88 0.02 0.11 Matches are distributed among these distances: 3 3 0.02 4 10 0.07 5 77 0.52 6 58 0.39 ACGTcount: A:0.79, C:0.02, G:0.01, T:0.19 Consensus pattern (5 bp): AAAAT Found at i:88959423 original size:44 final size:43 Alignment explanation

Indices: 88959360--88959519 Score: 213 Period size: 44 Copynumber: 3.7 Consensus size: 43 88959350 AAAATAAAAT 88959360 AATAAAATTAAAATGAAAATAAAAATAAAAATAAAAATAAAAATAA 1 AATAAAA-TAAAAT-AAAATAAAAA-AAAAATAAAAATAAAAATAA 88959406 AATAAAATAAAATAAAATAAAAATAAAAATAAAAATAAAAATAA 1 AATAAAATAAAATAAAATAAAAA-AAAAATAAAAATAAAAATAA * * 88959450 AATAAAATAAAATAAAAT-AAAACAAAAT-AAAATAAAACT-A 1 AATAAAATAAAATAAAATAAAAAAAAAATAAAAATAAAAATAA 88959490 AAT-AAATAAAACT-AAATAAATAAAAAAATA 1 AATAAAATAAAA-TAAAATAAA-AAAAAAATA 88959520 GGAGGATTTA Statistics Matches: 107, Mismatches: 3, Indels: 12 0.88 0.02 0.10 Matches are distributed among these distances: 39 12 0.11 40 7 0.07 41 17 0.16 42 5 0.05 43 4 0.04 44 49 0.46 45 6 0.06 46 7 0.07 ACGTcount: A:0.79, C:0.02, G:0.01, T:0.19 Consensus pattern (43 bp): AATAAAATAAAATAAAATAAAAAAAAAATAAAAATAAAAATAA Found at i:88964836 original size:13 final size:13 Alignment explanation

Indices: 88964818--88964842 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 88964808 GGTTTGTTTA 88964818 TTAAACTAATTAT 1 TTAAACTAATTAT 88964831 TTAAACTAATTA 1 TTAAACTAATTA 88964843 ACTCATTTAA 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:0.48, C:0.08, G:0.00, T:0.44 Consensus pattern (13 bp): TTAAACTAATTAT Found at i:88986556 original size:34 final size:34 Alignment explanation

Indices: 88986505--88986657 Score: 184 Period size: 34 Copynumber: 4.5 Consensus size: 34 88986495 GAATATACAT * * * 88986505 AGTCTGCTGGGACAGTAAATGCAGAACAGAGATA 1 AGTCTGCTAGGACAATAAATACAGAACAGAGATA * * * * 88986539 AGTCAGCTAAGG-TAGTAAATACAGAATAGAGAT- 1 AGTCTGCT-AGGACAATAAATACAGAACAGAGATA * * 88986572 AGTCTGCTAGGACAATAAATACAGATCAAAGATA 1 AGTCTGCTAGGACAATAAATACAGAACAGAGATA * 88986606 AGTCTGCTAGGACAATAAATACAGATCAGAGATA 1 AGTCTGCTAGGACAATAAATACAGAACAGAGATA * 88986640 AGTCTACTAGGACAATAA 1 AGTCTGCTAGGACAATAA 88986658 GCATAAAAAA Statistics Matches: 103, Mismatches: 13, Indels: 6 0.84 0.11 0.05 Matches are distributed among these distances: 32 3 0.03 33 23 0.22 34 75 0.73 35 2 0.02 ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20 Consensus pattern (34 bp): AGTCTGCTAGGACAATAAATACAGAACAGAGATA Found at i:88986577 original size:67 final size:67 Alignment explanation

Indices: 88986481--88986657 Score: 205 Period size: 67 Copynumber: 2.6 Consensus size: 67 88986471 AAGTCTGTTG * * * * * * * 88986481 GGATAGTAAACACAGAATATACATAGTCTGCTGGGACAGTAAATGCAGAACAGAGATAAGTCAGC 1 GGATAGTAAATACAGAATAGAGATAGTCTGCTAGGACAATAAATACAGAACAAAGATAAGTCAGC 88986546 TAA 66 T-A * * 88986549 GG-TAGTAAATACAGAATAGAGATAGTCTGCTAGGACAATAAATACAGATCAAAGATAAGTCTGC 1 GGATAGTAAATACAGAATAGAGATAGTCTGCTAGGACAATAAATACAGAACAAAGATAAGTCAGC 88986613 TA 66 TA * * * 88986615 GGACAATAAATACAG-ATCAGAGATAAGTCTACTAGGACAATAA 1 GGATAGTAAATACAGAAT-AGAGAT-AGTCTGCTAGGACAATAA 88986658 GCATAAAAAA Statistics Matches: 94, Mismatches: 12, Indels: 6 0.84 0.11 0.05 Matches are distributed among these distances: 66 5 0.05 67 70 0.74 68 19 0.20 ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20 Consensus pattern (67 bp): GGATAGTAAATACAGAATAGAGATAGTCTGCTAGGACAATAAATACAGAACAAAGATAAGTCAGC TA Found at i:88987121 original size:32 final size:32 Alignment explanation

Indices: 88987079--88987143 Score: 121 Period size: 32 Copynumber: 2.0 Consensus size: 32 88987069 GTTCGAAGTA * 88987079 AAACATGTGTTATTTGGTTTGTCTAAAATCAT 1 AAACACGTGTTATTTGGTTTGTCTAAAATCAT 88987111 AAACACGTGTTATTTGGTTTGTCTAAAATCAT 1 AAACACGTGTTATTTGGTTTGTCTAAAATCAT 88987143 A 1 A 88987144 TCTTTTTAGT Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 32 1.00 ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42 Consensus pattern (32 bp): AAACACGTGTTATTTGGTTTGTCTAAAATCAT Found at i:88992967 original size:28 final size:29 Alignment explanation

Indices: 88992934--88993006 Score: 94 Period size: 28 Copynumber: 2.5 Consensus size: 29 88992924 TATAGTGAAT * * 88992934 CCGCACACTTAGTGCTATAGAA-TCAAAC 1 CCGCACACTTAGTGCTATACAATTAAAAC * * 88992962 TCGCACACTTAGTGCTGTACAATTTAAAAC 1 CCGCACACTTAGTGCTATACAA-TTAAAAC 88992992 CCGCACACTTAGTGC 1 CCGCACACTTAGTGC 88993007 CAATCTTGTC Statistics Matches: 38, Mismatches: 5, Indels: 2 0.84 0.11 0.04 Matches are distributed among these distances: 28 19 0.50 30 19 0.50 ACGTcount: A:0.32, C:0.29, G:0.15, T:0.25 Consensus pattern (29 bp): CCGCACACTTAGTGCTATACAATTAAAAC Found at i:89000880 original size:30 final size:29 Alignment explanation

Indices: 89000786--89000887 Score: 109 Period size: 28 Copynumber: 3.5 Consensus size: 29 89000776 TATAGTGAAT * * * 89000786 CCGCACACTTAGTGCTATATATTTTCAGC 1 CCGCACACTTAGTGCTATAAATTTTAAAC * * 89000815 TCGCACACTTAGTGCTATAGAA--TCAAAC 1 CCGCACACTTAGTGCTATA-AATTTTAAAC * * 89000843 TCGCACACTTAGTGCTGTACAATTTTAAAC 1 CCGCACACTTAGTGCTATA-AATTTTAAAC 89000873 CCGCACACTTAGTGC 1 CCGCACACTTAGTGC 89000888 CAATCTTGTC Statistics Matches: 61, Mismatches: 9, Indels: 5 0.81 0.12 0.07 Matches are distributed among these distances: 28 23 0.38 29 18 0.30 30 20 0.33 ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29 Consensus pattern (29 bp): CCGCACACTTAGTGCTATAAATTTTAAAC Found at i:89006242 original size:29 final size:29 Alignment explanation

Indices: 89006139--89006269 Score: 140 Period size: 29 Copynumber: 4.6 Consensus size: 29 89006129 TACTCGATTT ** * * 89006139 CGCACACTTAGTGCCATGCGATTT-AAGCC 1 CGCACACTTAGTGCCAT-ATATTTCCAGCA * *** * * 89006168 CGCACACATAGTGCCATACCCTTCGAGCT 1 CGCACACTTAGTGCCATATATTTCCAGCA 89006197 CGCACACTT-GTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA * 89006225 TGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 89006254 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 89006270 ATCTCGTCAC Statistics Matches: 85, Mismatches: 15, Indels: 4 0.82 0.14 0.04 Matches are distributed among these distances: 28 24 0.28 29 61 0.72 ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:89013696 original size:29 final size:29 Alignment explanation

Indices: 89013601--89013732 Score: 140 Period size: 29 Copynumber: 4.6 Consensus size: 29 89013591 TACTCGATTT ** * * 89013601 CGCACACTTAGTGCCATGCGATTT-AAGCC 1 CGCACACTTAGTGCCAT-ATATTTCCAGCA * *** * * 89013630 CGCACACATAGTGCCATACCCTTCGAGCT 1 CGCACACTTAGTGCCATATATTTCCAGCA * 89013659 CGCATACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA * 89013688 TGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 89013717 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 89013733 ATCTCGTCAC Statistics Matches: 85, Mismatches: 17, Indels: 2 0.82 0.16 0.02 Matches are distributed among these distances: 28 2 0.02 29 83 0.98 ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:89017138 original size:15 final size:15 Alignment explanation

Indices: 89017114--89017148 Score: 61 Period size: 15 Copynumber: 2.3 Consensus size: 15 89017104 ACCGAAGGCG * 89017114 AATGGCATCGTCAGA 1 AATGGAATCGTCAGA 89017129 AATGGAATCGTCAGA 1 AATGGAATCGTCAGA 89017144 AATGG 1 AATGG 89017149 CATTGATATT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 15 19 1.00 ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20 Consensus pattern (15 bp): AATGGAATCGTCAGA Found at i:89025109 original size:140 final size:137 Alignment explanation

Indices: 89024826--89025129 Score: 321 Period size: 140 Copynumber: 2.2 Consensus size: 137 89024816 CTGCCGATGC * * * 89024826 CATGTCCCAGACATAGTCTTACACTGGCTCTCATATATGCATGCTGATGCATGTCCCAGACATGT 1 CATGTCCCAGACAT-GTCTTACACTAGCACTCATATATG-A-GCTGAAGCATGTCCCAGACATGT * * * * * 89024891 CTTACACTAGCACAACTCTTAGCCGATGCGTGTCCCAGACACATCTTACATTGGCTATCTCTGTC 63 CTTACACTAGCACAACTCTGAGCCGATGCATGTCCCAGACACATCTTACACTGGCTATCTATATC 89024956 GAGGCCAATG 128 GAGGCCAATG * 89024966 CATGTCCCAGACATGTCTTACTCTAGCACTCATAATATG-GCTGAAGCATGTCCCAGACATGTCT 1 CATGTCCCAGACATGTCTTACACTAGCACTCAT-ATATGAGCTGAAGCATGTCCCAGACATGTCT ** ** * 89025030 TACACTAGC-CCTCGTCTGGATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-TAT 65 TACACTAGCACAAC-TCT-GA-GCCGATG-CATGTCCCAGACA-CATCTTACACTGGCTATCTAT * 89025093 AAT-GTGGCCGAA-G 125 -ATCGAGGCC-AATG * * 89025106 CATGTCCTAGACATCTCTTACACT 1 CATGTCCCAGACATGTCTTACACT 89025130 GGCGCACAAA Statistics Matches: 138, Mismatches: 18, Indels: 16 0.80 0.10 0.09 Matches are distributed among these distances: 136 2 0.01 137 36 0.26 138 1 0.01 139 23 0.17 140 60 0.43 141 16 0.12 ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28 Consensus pattern (137 bp): CATGTCCCAGACATGTCTTACACTAGCACTCATATATGAGCTGAAGCATGTCCCAGACATGTCTT ACACTAGCACAACTCTGAGCCGATGCATGTCCCAGACACATCTTACACTGGCTATCTATATCGAG GCCAATG Found at i:89025110 original size:47 final size:46 Alignment explanation

Indices: 89024826--89025129 Score: 185 Period size: 47 Copynumber: 6.5 Consensus size: 46 89024816 CTGCCGATGC * * * * 89024826 CATGTCCCAGACATAGTCTTACACTGGCTCTCATATATGCAT-GCTGATG 1 CATGTCCCAGACAT-GTCTTACACTAGCACTCATA-ATG--TGGCCGAAG * * * * 89024875 CATGTCCCAGACATGTCTTACACTAGCA--CA-ACTCTTAGCCGATG 1 CATGTCCCAGACATGTCTTACACTAGCACTCATAAT-GTGGCCGAAG * ** * * * * 89024919 CGTGTCCCAGACACATCTTACATTGGCTATCTC-T-GTCGAGGCC-AATG 1 CATGTCCCAGACATGTCTTACACTAGC-A-CTCATAAT-GTGGCCGAA-G * * * 89024966 CATGTCCCAGACATGTCTTACTCTAGCACTCATAATATGGCTGAAG 1 CATGTCCCAGACATGTCTTACACTAGCACTCATAATGTGGCCGAAG * * * * 89025012 CATGTCCCAGACATGTCTTACACTAGCCCTCGT-CTG-GATGCCGATG 1 CATGTCCCAGACATGTCTTACACTAGCACTCATAATGTG--GCCGAAG * * * 89025058 CCATGTCCCAGACATGGTCTTACACTGGCTCTTATAATGTGGCCGAAG 1 -CATGTCCCAGACAT-GTCTTACACTAGCACTCATAATGTGGCCGAAG * * 89025106 CATGTCCTAGACATCTCTTACACT 1 CATGTCCCAGACATGTCTTACACT 89025130 GGCGCACAAA Statistics Matches: 198, Mismatches: 40, Indels: 37 0.72 0.15 0.13 Matches are distributed among these distances: 43 1 0.01 44 30 0.15 45 6 0.03 46 53 0.27 47 57 0.29 48 34 0.17 49 16 0.08 50 1 0.01 ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28 Consensus pattern (46 bp): CATGTCCCAGACATGTCTTACACTAGCACTCATAATGTGGCCGAAG Found at i:89025262 original size:15 final size:17 Alignment explanation

Indices: 89025242--89025273 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 89025232 TATAACTTAG 89025242 CAATTC-AT-ACAATAT 1 CAATTCAATGACAATAT 89025257 CAATTCAATGACAATAT 1 CAATTCAATGACAATAT 89025274 GAATACAAGT Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 15 6 0.40 16 2 0.13 17 7 0.47 ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31 Consensus pattern (17 bp): CAATTCAATGACAATAT Found at i:89026564 original size:40 final size:40 Alignment explanation

Indices: 89026520--89026602 Score: 157 Period size: 40 Copynumber: 2.1 Consensus size: 40 89026510 ATTAATAAAC * 89026520 ACTTAGTAGTTTGCCTATTATCATTCAAATCTAATCCATG 1 ACTTAGTAGTTCGCCTATTATCATTCAAATCTAATCCATG 89026560 ACTTAGTAGTTCGCCTATTATCATTCAAATCTAATCCATG 1 ACTTAGTAGTTCGCCTATTATCATTCAAATCTAATCCATG 89026600 ACT 1 ACT 89026603 CTTTATCATA Statistics Matches: 42, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 40 42 1.00 ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39 Consensus pattern (40 bp): ACTTAGTAGTTCGCCTATTATCATTCAAATCTAATCCATG Found at i:89027314 original size:20 final size:20 Alignment explanation

Indices: 89027276--89027322 Score: 55 Period size: 19 Copynumber: 2.5 Consensus size: 20 89027266 ATCAGCCCAT * 89027276 ATTTATCA-ATATTTCACAC 1 ATTTATCACACATTTCACAC * 89027295 ATTTATCACACATTTTACAC 1 ATTTATCACACATTTCACAC 89027315 -TTT-TCACA 1 ATTTATCACA 89027323 AATTAGTCCT Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 18 5 0.20 19 11 0.44 20 9 0.36 ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43 Consensus pattern (20 bp): ATTTATCACACATTTCACAC Found at i:89028915 original size:31 final size:31 Alignment explanation

Indices: 89028877--89028938 Score: 115 Period size: 31 Copynumber: 2.0 Consensus size: 31 89028867 AATCCATAAA 89028877 GTATGTGAAATTGAACAATATTTATTGATAC 1 GTATGTGAAATTGAACAATATTTATTGATAC * 89028908 GTATGTGAAATTGAACACTATTTATTGATAC 1 GTATGTGAAATTGAACAATATTTATTGATAC 89028939 CAACACAATG Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 30 1.00 ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39 Consensus pattern (31 bp): GTATGTGAAATTGAACAATATTTATTGATAC Found at i:89032297 original size:40 final size:42 Alignment explanation

Indices: 89032203--89032300 Score: 119 Period size: 40 Copynumber: 2.3 Consensus size: 42 89032193 GAATGATTCT * * * 89032203 GCACACTTAGTGCCATTTCAATTAACTGAAGCTATCTCGGCATC 1 GCACACTTAGTGCC--TTCAAATAACCGAAGCTATCTCGGAATC ** 89032247 GCACACTTAGTGCC-TCAAATAACCGAAGCTAT-TTTGAATC 1 GCACACTTAGTGCCTTCAAATAACCGAAGCTATCTCGGAATC 89032287 GCACACTTAGTGCC 1 GCACACTTAGTGCC 89032301 AAATACCATT Statistics Matches: 49, Mismatches: 5, Indels: 4 0.84 0.09 0.07 Matches are distributed among these distances: 40 19 0.39 41 16 0.33 44 14 0.29 ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28 Consensus pattern (42 bp): GCACACTTAGTGCCTTCAAATAACCGAAGCTATCTCGGAATC Found at i:89034004 original size:36 final size:35 Alignment explanation

Indices: 89033888--89034018 Score: 126 Period size: 35 Copynumber: 3.7 Consensus size: 35 89033878 AATTTCAATA * 89033888 GGCATGCTTAACATGC-AATTCAGAAATAGT-ATAGT 1 GGCATGCTTAACATGCGAA-TCAGAAA-AGTAATAAT * * * 89033923 GGCATGCTTAGCATGCAAATCA-AAAA-CAATTTAAT 1 GGCATGCTTAACATGCGAATCAGAAAAGTAA--TAAT * * 89033958 GACATACTTAACATGCGAATCAGAATAAGTAATAAT 1 GGCATGCTTAACATGCGAATCAGAA-AAGTAATAAT * 89033994 GGCATGCTTAACATGCGAATAAGAA 1 GGCATGCTTAACATGCGAATCAGAA 89034019 TATCAATAGA Statistics Matches: 78, Mismatches: 11, Indels: 13 0.76 0.11 0.13 Matches are distributed among these distances: 33 2 0.03 34 3 0.04 35 39 0.50 36 30 0.38 37 2 0.03 38 2 0.03 ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25 Consensus pattern (35 bp): GGCATGCTTAACATGCGAATCAGAAAAGTAATAAT Found at i:89035449 original size:35 final size:35 Alignment explanation

Indices: 89035409--89035478 Score: 131 Period size: 35 Copynumber: 2.0 Consensus size: 35 89035399 TGTATGTCAA * 89035409 AAACTCTAACTAGCAAGCTGCATATGAAGTAGCAT 1 AAACTCTAACTAGCAAGCTGCATATAAAGTAGCAT 89035444 AAACTCTAACTAGCAAGCTGCATATAAAGTAGCAT 1 AAACTCTAACTAGCAAGCTGCATATAAAGTAGCAT 89035479 CCTTATGCTC Statistics Matches: 34, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 35 34 1.00 ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23 Consensus pattern (35 bp): AAACTCTAACTAGCAAGCTGCATATAAAGTAGCAT Found at i:89041155 original size:47 final size:47 Alignment explanation

Indices: 89041101--89041426 Score: 423 Period size: 47 Copynumber: 7.1 Consensus size: 47 89041091 TTAGGATTTT * ** * * *** 89041101 ATGTGATGAATATGAATGTGTATATATGAGATAAGGCCGAATGAAAA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * 89041148 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * 89041195 ATGTGATGAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * 89041242 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * 89041289 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * 89041336 A--TG-TG-A--TGAACATGCATATATGTGATAAGGCAGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * * * * * 89041377 ATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAATGGCTA 1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCCA 89041424 ATG 1 ATG 89041427 CGAAATGTGT Statistics Matches: 253, Mismatches: 19, Indels: 14 0.88 0.07 0.05 Matches are distributed among these distances: 41 34 0.13 43 3 0.01 44 4 0.02 45 3 0.01 47 206 0.81 48 3 0.01 ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26 Consensus pattern (47 bp): ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA Found at i:89041295 original size:22 final size:22 Alignment explanation

Indices: 89041268--89041342 Score: 57 Period size: 22 Copynumber: 3.3 Consensus size: 22 89041258 CATGCATATG 89041268 TGTGATAAGGCCGAATGGCCAA 1 TGTGATAAGGCCGAATGGCCAA * * 89041290 TGTGATGAATG-TGAACAT-G-CATA 1 TGTGAT-AAGGCCG-A-ATGGCCA-A 89041313 TGTGTGATAAGGCCGAATGGCCAA 1 --TGTGATAAGGCCGAATGGCCAA 89041337 TGTGAT 1 TGTGAT 89041343 GAACATGCAT Statistics Matches: 40, Mismatches: 4, Indels: 18 0.65 0.06 0.29 Matches are distributed among these distances: 22 15 0.38 23 8 0.20 24 8 0.20 25 9 0.22 ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25 Consensus pattern (22 bp): TGTGATAAGGCCGAATGGCCAA Found at i:89041456 original size:46 final size:46 Alignment explanation

Indices: 89041400--89041582 Score: 294 Period size: 46 Copynumber: 4.0 Consensus size: 46 89041390 GGAAGTGTAT * 89041400 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG 1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG * 89041446 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG 1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG * 89041492 ATATGAGGTAAAGCCGAATGGCTAATGCGAAAAGTGTATGAGATGG 1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG * * * * * 89041538 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG 1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG 89041583 TGTATACATA Statistics Matches: 128, Mismatches: 9, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 46 128 1.00 ACGTcount: A:0.35, C:0.09, G:0.32, T:0.25 Consensus pattern (46 bp): ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG Found at i:89043909 original size:48 final size:48 Alignment explanation

Indices: 89043789--89044119 Score: 403 Period size: 48 Copynumber: 6.9 Consensus size: 48 89043779 AGGGTAAGAT * * * * 89043789 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTTTCATATATC-AG 1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGC--TCACATATCAAG * * 89043838 TGCCGATGCCATGTTCCAAACATGATCTTACACTAGCTCACATATCAAG 1 -GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAG * * * * 89043887 GCCGATCCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAT 1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAG * * * 89043935 ACCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCGAG 1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAG * * * * 89043983 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATATCGAG 1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAG * * * * * 89044031 GTCGATGCTATGTCCCATACATGGTCTTACACTAGCTCTCATATCAAT 1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAG * * * 89044079 GTCGATGCCATGTTCCAAACATGGCCTTACACTAGCTCACA 1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACA 89044120 AAACCCTAGT Statistics Matches: 245, Mismatches: 35, Indels: 4 0.86 0.12 0.01 Matches are distributed among these distances: 48 212 0.87 49 2 0.01 50 31 0.13 ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27 Consensus pattern (48 bp): GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAG Found at i:89043966 original size:96 final size:96 Alignment explanation

Indices: 89043789--89044116 Score: 449 Period size: 96 Copynumber: 3.4 Consensus size: 96 89043779 AGGGTAAGAT * * * * 89043789 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTTTCATATATCAGTGCCGATGCCATGTTC 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC--ATATCAATGCCGATGCCATGTTC * 89043854 CAAACATGATCTTACACTAGCTCACATATCAAG 64 CAAACATGGTCTTACACTAGCTCACATATCAAG * * 89043887 GCCGATCCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATACCGATGCCATGTTCCA 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCA * 89043952 AACATGGTCTTACACTAGCTCACATATCGAG 66 AACATGGTCTTACACTAGCTCACATATCAAG * * * * * * 89043983 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATATCGAGGTCGATGCTATGTCCCA 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCA * * * 89044048 TACATGGTCTTACACTAGCTCTCATATCAAT 66 AACATGGTCTTACACTAGCTCACATATCAAG * * * * 89044079 GTCGATGCCATGTTCCAAACATGGCCTTACACTAGCTC 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC 89044117 ACAAAACCCT Statistics Matches: 205, Mismatches: 25, Indels: 2 0.88 0.11 0.01 Matches are distributed among these distances: 96 169 0.82 98 36 0.18 ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27 Consensus pattern (96 bp): GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCA AACATGGTCTTACACTAGCTCACATATCAAG Found at i:89044053 original size:144 final size:144 Alignment explanation

Indices: 89043790--89044119 Score: 464 Period size: 144 Copynumber: 2.3 Consensus size: 144 89043780 GGGTAAGATG * * * * * * 89043790 CCGATGCCATGTCCCAGACATGGTCTTACATTGGCTTTCATATATCAGTGCCGATGCCATGTTCC 1 CCGATGCCATGTTCCAAACATGGTCTTACACTAGC--TCACATATCAGTGCCGATGCCATGTCCC * 89043855 AAACATGATCTTACACTAGCTCACATATCAAGGCCGATCCCATGTCCCAGACATGGTCTTACACT 64 AAACATGATCTTACACTAGCACACATATCAAGGCCGATCCCATGTCCCAGACATGGTCTTACACT 89043920 AGCTCTCATATCAATA 129 AGCTCTCATATCAATA 89043936 CCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCGAG-GCCGATGCCATGTCCCA 1 CCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATC-AGTGCCGATGCCATGTCCCA * * * * * * * * 89044000 GACATGGTCTTACACTAGCACTCATATCGAGGTCGATGCTATGTCCCATACATGGTCTTACACTA 65 AACATGATCTTACACTAGCACACATATCAAGGCCGATCCCATGTCCCAGACATGGTCTTACACTA * 89044065 GCTCTCATATCAATG 130 GCTCTCATATCAATA * * 89044080 TCGATGCCATGTTCCAAACATGGCCTTACACTAGCTCACA 1 CCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACA 89044120 AAACCCTAGT Statistics Matches: 165, Mismatches: 18, Indels: 4 0.88 0.10 0.02 Matches are distributed among these distances: 144 132 0.80 145 2 0.01 146 31 0.19 ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27 Consensus pattern (144 bp): CCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCAGTGCCGATGCCATGTCCCAA ACATGATCTTACACTAGCACACATATCAAGGCCGATCCCATGTCCCAGACATGGTCTTACACTAG CTCTCATATCAATA Found at i:89046402 original size:31 final size:31 Alignment explanation

Indices: 89046359--89046504 Score: 249 Period size: 31 Copynumber: 4.7 Consensus size: 31 89046349 TTAGTCTTGA * 89046359 CATAT-ACTGGGCCGAAGCCTTTTTATAAAT 1 CATATCACTGGGCCGAAGCCTTTTCATAAAT * 89046389 CATATCACTGGGCCGAAGCCATTTCATAAAT 1 CATATCACTGGGCCGAAGCCTTTTCATAAAT 89046420 CATATCACTGGGCCGAAGCCTTTTCATAAAT 1 CATATCACTGGGCCGAAGCCTTTTCATAAAT * 89046451 CATATCACTAGGCCGAAGCCTTTTCATAAAT 1 CATATCACTGGGCCGAAGCCTTTTCATAAAT * 89046482 CATATCACTAGGCCGAAGCCTTT 1 CATATCACTGGGCCGAAGCCTTT 89046505 ACTGTAAATG Statistics Matches: 111, Mismatches: 4, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 30 5 0.05 31 106 0.95 ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29 Consensus pattern (31 bp): CATATCACTGGGCCGAAGCCTTTTCATAAAT Found at i:89046587 original size:42 final size:42 Alignment explanation

Indices: 89046528--89046619 Score: 175 Period size: 42 Copynumber: 2.2 Consensus size: 42 89046518 TGGCCCTTAG 89046528 GCCCATTTCAATATCACATGCAATGTCAATGAATGTATGCAA 1 GCCCATTTCAATATCACATGCAATGTCAATGAATGTATGCAA * 89046570 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA 1 GCCCATTTCAATATCACATGCAATGTCAATGAATGTATGCAA 89046612 GCCCATTT 1 GCCCATTT 89046620 GGGGAGACTA Statistics Matches: 49, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 42 49 1.00 ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30 Consensus pattern (42 bp): GCCCATTTCAATATCACATGCAATGTCAATGAATGTATGCAA Found at i:89046836 original size:25 final size:26 Alignment explanation

Indices: 89046767--89046836 Score: 99 Period size: 25 Copynumber: 2.8 Consensus size: 26 89046757 CTCTTTTAAT * 89046767 AACTGGGGCAAAGCCC-TTTCTGATA 1 AACTGGGGCAGAGCCCTTTTCTGATA * * 89046792 AACTGGGGCAGAGCCTTTTTC-GGTA 1 AACTGGGGCAGAGCCCTTTTCTGATA 89046817 AACTGGGGCAGAGCCCTTTT 1 AACTGGGGCAGAGCCCTTTT 89046837 AGCACTTCCT Statistics Matches: 40, Mismatches: 4, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 25 36 0.90 26 4 0.10 ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26 Consensus pattern (26 bp): AACTGGGGCAGAGCCCTTTTCTGATA Found at i:89047665 original size:27 final size:28 Alignment explanation

Indices: 89047634--89047699 Score: 77 Period size: 27 Copynumber: 2.5 Consensus size: 28 89047624 TACGGAACAT * 89047634 AAGGGCATATT-CG-TCATTTTACCATAC 1 AAGGGC-TATTACGATCACTTTACCATAC * 89047661 AAGGG-TATTACGATCACTTTACCCTAC 1 AAGGGCTATTACGATCACTTTACCATAC 89047688 AAGGGCT-TTACG 1 AAGGGCTATTACG 89047700 GTCTTTTTAC Statistics Matches: 34, Mismatches: 2, Indels: 6 0.81 0.05 0.14 Matches are distributed among these distances: 25 4 0.12 26 2 0.06 27 27 0.79 28 1 0.03 ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30 Consensus pattern (28 bp): AAGGGCTATTACGATCACTTTACCATAC Found at i:89047708 original size:27 final size:27 Alignment explanation

Indices: 89047647--89047710 Score: 76 Period size: 27 Copynumber: 2.4 Consensus size: 27 89047637 GGCATATTCG 89047647 TCATTTTACCATACAAGGGTATTACGA 1 TCATTTTACCATACAAGGGTATTACGA * * * 89047674 TCACTTTACCCTACAAGGGCT-TTACGG 1 TCATTTTACCATACAAGGG-TATTACGA * 89047701 TCTTTTTACC 1 TCATTTTACC 89047711 TATTAGGGGT Statistics Matches: 31, Mismatches: 5, Indels: 2 0.82 0.13 0.05 Matches are distributed among these distances: 27 30 0.97 28 1 0.03 ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36 Consensus pattern (27 bp): TCATTTTACCATACAAGGGTATTACGA Found at i:89047794 original size:27 final size:28 Alignment explanation

Indices: 89047764--89047870 Score: 114 Period size: 27 Copynumber: 3.9 Consensus size: 28 89047754 GTAAATCTAC 89047764 AAACCAAGGGTATTTTAGTAA-TTTTGT 1 AAACCAAGGGTATTTTAGTAATTTTTGT * * 89047791 AAACCAATGGTATTTTA-TAATTTTTGA 1 AAACCAAGGGTATTTTAGTAATTTTTGT * 89047818 AAAGTCAA-GGTATTTCT-GTAATTTTTGT 1 AAA-CCAAGGGTATTT-TAGTAATTTTTGT * * * 89047846 AAATCAGGGGTATTTTGGTAATTTT 1 AAACCAAGGGTATTTTAGTAATTTT 89047871 ACAAATTGAG Statistics Matches: 69, Mismatches: 5, Indels: 11 0.81 0.06 0.13 Matches are distributed among these distances: 26 3 0.04 27 35 0.51 28 31 0.45 ACGTcount: A:0.32, C:0.07, G:0.18, T:0.44 Consensus pattern (28 bp): AAACCAAGGGTATTTTAGTAATTTTTGT Found at i:89047883 original size:27 final size:25 Alignment explanation

Indices: 89047826--89047949 Score: 104 Period size: 27 Copynumber: 4.6 Consensus size: 25 89047816 GAAAAGTCAA * ** 89047826 GGTATTTCTGTAATTTTTGTAAATCAGG 1 GGTATTTCGGTAA-TTTTACAAAT-A-G * 89047854 GGTATTTTGGTAATTTTACAAATTGAG 1 GGTATTTCGGTAATTTTACAAA-T-AG * * 89047881 GGTATTTCGGTAATTTCACAAACCAG 1 GGTATTTCGGTAATTTTACAAA-TAG 89047907 TGGTATTTCGGTAATTTTACAAACTAGG 1 -GGTATTTCGGTAATTTTACAAA-TA-G * 89047935 GGTATTTTGGTAATT 1 GGTATTTCGGTAATT 89047950 CTATCCTACA Statistics Matches: 81, Mismatches: 12, Indels: 7 0.81 0.12 0.07 Matches are distributed among these distances: 26 2 0.02 27 65 0.80 28 14 0.17 ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42 Consensus pattern (25 bp): GGTATTTCGGTAATTTTACAAATAG Found at i:89047966 original size:54 final size:54 Alignment explanation

Indices: 89047850--89047991 Score: 148 Period size: 54 Copynumber: 2.6 Consensus size: 54 89047840 TTTTGTAAAT * * 89047850 CAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAAC 1 CAGGGGTATTTCGGTAATTTTACAAATAGAGGGTATTTCGGTAATTTCACAAAC * * ** 89047904 CAGTGGTATTTCGGTAATTTTACAAACTAG-GGGTATTTTGGTAA-TTCTATCCTA- 1 CAGGGGTATTTCGGTAATTTTACAAA-TAGAGGGTATTTCGGTAATTTC-A-CAAAC * * * 89047958 CAGGGGTATTTCAGTAATTTCAC-AATCGAGGGTA 1 CAGGGGTATTTCGGTAATTTTACAAATAGAGGGTA 89047992 AAACGGTAAT Statistics Matches: 74, Mismatches: 10, Indels: 9 0.80 0.11 0.10 Matches are distributed among these distances: 52 2 0.03 53 10 0.14 54 58 0.78 55 4 0.05 ACGTcount: A:0.28, C:0.13, G:0.23, T:0.37 Consensus pattern (54 bp): CAGGGGTATTTCGGTAATTTTACAAATAGAGGGTATTTCGGTAATTTCACAAAC Found at i:89047989 original size:27 final size:26 Alignment explanation

Indices: 89047847--89047989 Score: 103 Period size: 27 Copynumber: 5.3 Consensus size: 26 89047837 AATTTTTGTA * * 89047847 AATCAGGGGTATTTTGGTAATTTTAC 1 AATCAGGGGTATTTCGGTAATTTCAC * 89047873 AAAT-TGAGGGTATTTCGGTAATTTCAC 1 -AATCAG-GGGTATTTCGGTAATTTCAC * * * 89047900 AAACCAGTGGTATTTCGGTAATTTTAC 1 -AATCAGGGGTATTTCGGTAATTTCAC * * 89047927 AAACTAGGGGTATTTTGGTAA-TTCTATC 1 AATC-AGGGGTATTTCGGTAATTTC-A-C * * 89047955 -CTACAGGGGTATTTCAGTAATTTCAC 1 AAT-CAGGGGTATTTCGGTAATTTCAC 89047981 AATCGAGGG 1 AATC-AGGG 89047990 TAAAACGGTA Statistics Matches: 91, Mismatches: 16, Indels: 18 0.73 0.13 0.14 Matches are distributed among these distances: 26 8 0.09 27 77 0.85 28 6 0.07 ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36 Consensus pattern (26 bp): AATCAGGGGTATTTCGGTAATTTCAC Found at i:89048015 original size:27 final size:27 Alignment explanation

Indices: 89047981--89048072 Score: 132 Period size: 27 Copynumber: 3.4 Consensus size: 27 89047971 GTAATTTCAC 89047981 AATCGAGGGTAAAACGGTAATTTTGTA 1 AATCGAGGGTAAAACGGTAATTTTGTA * 89048008 AA-CTGAGGGTAAAATGGTAATTTTGTA 1 AATC-GAGGGTAAAACGGTAATTTTGTA * * * 89048035 AATCGAGGGTAAAACGATAATTCTATA 1 AATCGAGGGTAAAACGGTAATTTTGTA 89048062 AATCGAGGGTA 1 AATCGAGGGTA 89048073 CTTTGGTAAT Statistics Matches: 58, Mismatches: 5, Indels: 4 0.87 0.07 0.06 Matches are distributed among these distances: 26 1 0.02 27 56 0.97 28 1 0.02 ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28 Consensus pattern (27 bp): AATCGAGGGTAAAACGGTAATTTTGTA Found at i:89048095 original size:54 final size:53 Alignment explanation

Indices: 89047971--89048097 Score: 141 Period size: 54 Copynumber: 2.4 Consensus size: 53 89047961 GGGTATTTCA * * * * 89047971 GTAATTTCACAATCGAGGGTAAAACGGTAATTTTGTAAACTGAGGGTAAAATG 1 GTAATTTTACAATCGAGGGTAAAACGATAATTCTATAAACTGAGGGTAAAATG *** 89048024 GTAATTTTGTA-AATCGAGGGTAAAACGATAATTCTATAAA-TCGAGGGTACTTTG 1 GTAA-TTT-TACAATCGAGGGTAAAACGATAATTCTATAAACT-GAGGGTAAAATG 89048078 GTAATTTTACAAGTCGAGGG 1 GTAATTTTACAA-TCGAGGG 89048098 CATTTCAATA Statistics Matches: 62, Mismatches: 7, Indels: 9 0.79 0.09 0.12 Matches are distributed among these distances: 52 2 0.03 53 10 0.16 54 49 0.79 55 1 0.02 ACGTcount: A:0.35, C:0.09, G:0.24, T:0.31 Consensus pattern (53 bp): GTAATTTTACAATCGAGGGTAAAACGATAATTCTATAAACTGAGGGTAAAATG Found at i:89051196 original size:14 final size:14 Alignment explanation

Indices: 89051177--89051204 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 89051167 CCATTATAAT 89051177 TTCATTATTTTGTC 1 TTCATTATTTTGTC 89051191 TTCATTATTTTGTC 1 TTCATTATTTTGTC 89051205 CTTACCTATC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64 Consensus pattern (14 bp): TTCATTATTTTGTC Found at i:89052372 original size:16 final size:16 Alignment explanation

Indices: 89052332--89052374 Score: 50 Period size: 16 Copynumber: 2.7 Consensus size: 16 89052322 TAATTCCACT * 89052332 ATAATAAAATATAATT 1 ATAATAAAATATAATA * * * 89052348 GTAACAAAATCTAATA 1 ATAATAAAATATAATA 89052364 ATAATAAAATA 1 ATAATAAAATA 89052375 CAAAAATAGA Statistics Matches: 20, Mismatches: 7, Indels: 0 0.74 0.26 0.00 Matches are distributed among these distances: 16 20 1.00 ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30 Consensus pattern (16 bp): ATAATAAAATATAATA Found at i:89052876 original size:23 final size:22 Alignment explanation

Indices: 89052849--89052898 Score: 64 Period size: 23 Copynumber: 2.2 Consensus size: 22 89052839 TCTTAAATTA 89052849 TTAAATATTAAATTAAAAATAAT 1 TTAAATATTAAATTAAAAA-AAT *** 89052872 TTAAATATTTTTTTAAAAAAAT 1 TTAAATATTAAATTAAAAAAAT 89052894 TTAAA 1 TTAAA 89052899 ATAATTTGGG Statistics Matches: 24, Mismatches: 3, Indels: 1 0.86 0.11 0.04 Matches are distributed among these distances: 22 8 0.33 23 16 0.67 ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44 Consensus pattern (22 bp): TTAAATATTAAATTAAAAAAAT Found at i:89055207 original size:17 final size:18 Alignment explanation

Indices: 89055185--89055218 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 89055175 GGTAAAATGC * 89055185 ATTGA-TAAGTATATTGA 1 ATTGATTAAGTAAATTGA 89055202 ATTGATTAAGTAAATTG 1 ATTGATTAAGTAAATTG 89055219 TTATGTTTTG Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 5 0.33 18 10 0.67 ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41 Consensus pattern (18 bp): ATTGATTAAGTAAATTGA Found at i:89058636 original size:27 final size:28 Alignment explanation

Indices: 89058580--89058649 Score: 115 Period size: 27 Copynumber: 2.5 Consensus size: 28 89058570 AAATTTGTAC 89058580 AGCACTAAGTGTGCGAGTTTGATCATAT 1 AGCACTAAGTGTGCGAGTTTGATCATAT * * 89058608 AGCACTAAGTGTGCTAG-TTGATTATAT 1 AGCACTAAGTGTGCGAGTTTGATCATAT 89058635 AGCACTAAGTGTGCG 1 AGCACTAAGTGTGCG 89058650 GACTCACTAT Statistics Matches: 39, Mismatches: 3, Indels: 1 0.91 0.07 0.02 Matches are distributed among these distances: 27 23 0.59 28 16 0.41 ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31 Consensus pattern (28 bp): AGCACTAAGTGTGCGAGTTTGATCATAT Found at i:89058660 original size:27 final size:27 Alignment explanation

Indices: 89058580--89058661 Score: 69 Period size: 27 Copynumber: 3.0 Consensus size: 27 89058570 AAATTTGTAC * * 89058580 AGCACTAAGTGTGCGAGTTTGA-TCATAT 1 AGCACTAAGTGTGCGAG-CTCACT-ATAT * * * * 89058608 AGCACTAAGTGTGCTAGTTGATTATAT 1 AGCACTAAGTGTGCGAGCTCACTATAT 89058635 AGCACTAAGTGTGCG-GACTCACTATAT 1 AGCACTAAGTGTGCGAG-CTCACTATAT 89058662 GCTTTTGAAT Statistics Matches: 47, Mismatches: 5, Indels: 5 0.82 0.09 0.09 Matches are distributed among these distances: 26 1 0.02 27 29 0.62 28 17 0.36 ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32 Consensus pattern (27 bp): AGCACTAAGTGTGCGAGCTCACTATAT Found at i:89064291 original size:41 final size:41 Alignment explanation

Indices: 89064209--89064508 Score: 392 Period size: 41 Copynumber: 7.4 Consensus size: 41 89064199 CGTTTTAAGA ** * ** 89064209 AAAACGCCGCTAAAAA-CAGAGCAACAGTGGCG-TTTTAGT 1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT * * * 89064248 AAAAAACGCCAC-AAAAA-TAGAGCATTAGCGGTGCTTTCGGT 1 --AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT * * * 89064289 AAAACGCCACTAAAAACCAGAGAATTAGCGGCGTTTTCGGT 1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT * 89064330 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT 1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT * * * 89064371 AAAACGCCGCTAAAAACCAGAGAATTAGCAGCGCTTTCAGT 1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT * * 89064412 AAAACGCCGCTAAAAACCAGAGCATTAGCGTCGCTTTCAGT 1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT * 89064453 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT 1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT 89064494 AAAACGCCGCTAAAA 1 AAAACGCCGCTAAAA 89064509 GTCATATAAC Statistics Matches: 230, Mismatches: 26, Indels: 6 0.88 0.10 0.02 Matches are distributed among these distances: 39 10 0.04 40 21 0.09 41 199 0.87 ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18 Consensus pattern (41 bp): AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT Found at i:89064951 original size:25 final size:25 Alignment explanation

Indices: 89064922--89064975 Score: 108 Period size: 25 Copynumber: 2.2 Consensus size: 25 89064912 GTGGTTTTGA 89064922 ATGTGGAATTAGCATTTGTTGAACT 1 ATGTGGAATTAGCATTTGTTGAACT 89064947 ATGTGGAATTAGCATTTGTTGAACT 1 ATGTGGAATTAGCATTTGTTGAACT 89064972 ATGT 1 ATGT 89064976 ATAATTTCCA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 29 1.00 ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41 Consensus pattern (25 bp): ATGTGGAATTAGCATTTGTTGAACT Found at i:89065613 original size:15 final size:15 Alignment explanation

Indices: 89065593--89065624 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 89065583 TTTAATTTAG * 89065593 AAGATAAATGTATAT 1 AAGATAAATATATAT 89065608 AAGATAAATATATAT 1 AAGATAAATATATAT 89065623 AA 1 AA 89065625 ATTATTATTT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31 Consensus pattern (15 bp): AAGATAAATATATAT Found at i:89065663 original size:24 final size:23 Alignment explanation

Indices: 89065596--89065663 Score: 73 Period size: 24 Copynumber: 2.8 Consensus size: 23 89065586 AATTTAGAAG * 89065596 ATAAATGTATATAAGATAAATATAT 1 ATAAAT-TATATATGA-AAATATAT * * 89065621 ATAAATTATTATTTTAAAATATAT 1 ATAAATTA-TATATGAAAATATAT 89065645 ATAAATATATATATGAAAA 1 ATAAAT-TATATATGAAAA 89065664 GTGGTTTAGT Statistics Matches: 36, Mismatches: 5, Indels: 5 0.78 0.11 0.11 Matches are distributed among these distances: 24 24 0.67 25 12 0.33 ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40 Consensus pattern (23 bp): ATAAATTATATATGAAAATATAT Found at i:89069310 original size:7 final size:7 Alignment explanation

Indices: 89069298--89069328 Score: 62 Period size: 7 Copynumber: 4.4 Consensus size: 7 89069288 AGCAATTGAT 89069298 TTTAATA 1 TTTAATA 89069305 TTTAATA 1 TTTAATA 89069312 TTTAATA 1 TTTAATA 89069319 TTTAATA 1 TTTAATA 89069326 TTT 1 TTT 89069329 TTAAATGTCT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 24 1.00 ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (7 bp): TTTAATA Found at i:89070968 original size:476 final size:476 Alignment explanation

Indices: 89070063--89071316 Score: 2483 Period size: 476 Copynumber: 2.6 Consensus size: 476 89070053 TTCTCTCCAA 89070063 CTTATTTTAAATA-TTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATC 1 CTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATC 89070127 GAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAA 66 GAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAA 89070192 TTCAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCAAT 131 TTCAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCAAT 89070257 TTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGTTA 196 TTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGTTA 89070322 TATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGTTATAACTAATTTT 261 TATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGTTATAACTAATTTT 89070387 TATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTGGT 326 TATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTGGT 89070452 TCAACTTAATTATTATTTGATTCAACTTAAGTATGAATAAGTATGAATTAATTTTATTACCATAT 391 TCAACTTAATTATTATTTGATTCAACTTAAGTATGAATAAGTATGAATTAATTTTATTACCATAT 89070517 ATGTAGCTTGCTTGTCCATTC 456 ATGTAGCTTGCTTGTCCATTC 89070538 CTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATC 1 CTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATC 89070603 GAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAA 66 GAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAA 89070668 TTCAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCAAT 131 TTCAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCAAT 89070733 TTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGTTA 196 TTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGTTA 89070798 TATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGTTATAACTAATTTT 261 TATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGTTATAACTAATTTT 89070863 TATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTGGT 326 TATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTGGT 89070928 TCAACTTAATTATTATTTGATTCAACTTAAGTATGAATAAGTATGAATTAATTTTATTACCATAT 391 TCAACTTAATTATTATTTGATTCAACTTAAGTATGAATAAGTATGAATTAATTTTATTACCATAT 89070993 ATGTAGCTTGCTTGTCCATTC 456 ATGTAGCTTGCTTGTCCATTC * 89071014 CTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACGGGTTGCCTTATATC 1 CTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATC 89071079 GAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAA 66 GAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAA 89071144 TTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCAA 131 TTC-AAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCAA 89071209 TTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGTT 195 TTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGTT 89071274 ATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGT 260 ATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGT 89071317 ATTTGTATAA Statistics Matches: 776, Mismatches: 1, Indels: 2 1.00 0.00 0.00 Matches are distributed among these distances: 475 13 0.02 476 594 0.77 477 169 0.22 ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41 Consensus pattern (476 bp): CTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATC GAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAA TTCAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCAAT TTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGTTA TATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGTTATAACTAATTTT TATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTGGT TCAACTTAATTATTATTTGATTCAACTTAAGTATGAATAAGTATGAATTAATTTTATTACCATAT ATGTAGCTTGCTTGTCCATTC Found at i:89077141 original size:21 final size:21 Alignment explanation

Indices: 89077115--89077162 Score: 87 Period size: 21 Copynumber: 2.3 Consensus size: 21 89077105 TCAACTTAGA 89077115 GCGGAGGCAGCAGCGAGGGAG 1 GCGGAGGCAGCAGCGAGGGAG * 89077136 GCGGAGGCAGTAGCGAGGGAG 1 GCGGAGGCAGCAGCGAGGGAG 89077157 GCGGAG 1 GCGGAG 89077163 CAGAACAGGA Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 21 26 1.00 ACGTcount: A:0.23, C:0.17, G:0.58, T:0.02 Consensus pattern (21 bp): GCGGAGGCAGCAGCGAGGGAG Found at i:89077512 original size:43 final size:43 Alignment explanation

Indices: 89077455--89077699 Score: 284 Period size: 43 Copynumber: 5.7 Consensus size: 43 89077445 ACTGGGAAAA * 89077455 TTAGCGGCG-TTTTTAAAAAAGCGCCGCTAAAAGTACAT-GTCT 1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGT-CCTGGTCT * * * 89077497 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCT 1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT * * * * 89077540 CTAGCGGCGTTTTTTATAAAAGCGTCGCTAAAGGTCCTGGT-T 1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT * * 89077582 TCTAGCGGC-TTTTTTTAAAAAGCGCCGCTAAAGGTCCTGGTCT 1 T-TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT * * ** 89077625 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAATGTCCTAATCT 1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT * 89077668 TTACCGGCGTTTTTTCTAAAAAA-CGCCGCTAA 1 TTAGCGGCG-TTTTT-TAAAAAAGCGCCGCTAA 89077700 TTTTTGTGGC Statistics Matches: 176, Mismatches: 20, Indels: 12 0.85 0.10 0.06 Matches are distributed among these distances: 42 46 0.26 43 110 0.62 44 14 0.08 45 6 0.03 ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32 Consensus pattern (43 bp): TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT Done.