Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: At_chr12

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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31

Warning! 4026412 characters in sequence are not A, C, G, or T


File 195 of 297

Found at i:66158967 original size:21 final size:21

Alignment explanation

Indices: 66158941--66159010 Score: 61 Period size: 21 Copynumber: 3.3 Consensus size: 21 66158931 AAGACACGTG 66158941 ACTTCAATCAATTCCACTGAA 1 ACTTCAATCAATTCCACTGAA ** ** * 66158962 ACTTCAAGGAGA-TCTGCTGTA 1 ACTTCAATCA-ATTCCACTGAA * * 66158983 GCTTCGATCAATTCCACTGAA 1 ACTTCAATCAATTCCACTGAA 66159004 ACTTCAA 1 ACTTCAA 66159011 GGAGATCTGC Statistics Matches: 33, Mismatches: 14, Indels: 4 0.65 0.27 0.08 Matches are distributed among these distances: 20 1 0.03 21 31 0.94 22 1 0.03 ACGTcount: A:0.33, C:0.26, G:0.13, T:0.29 Consensus pattern (21 bp): ACTTCAATCAATTCCACTGAA Found at i:66159000 original size:42 final size:42 Alignment explanation

Indices: 66158942--66159028 Score: 156 Period size: 42 Copynumber: 2.1 Consensus size: 42 66158932 AGACACGTGA 66158942 CTTCAATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAG 1 CTTCAATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAG * * 66158984 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTGG 1 CTTCAATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAG 66159026 CTT 1 CTT 66159029 TTAGCTGCTC Statistics Matches: 43, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 42 43 1.00 ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30 Consensus pattern (42 bp): CTTCAATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAG Found at i:66159743 original size:43 final size:44 Alignment explanation

Indices: 66159674--66159760 Score: 113 Period size: 43 Copynumber: 2.0 Consensus size: 44 66159664 GGGAGACAAA * * 66159674 ATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAG 1 ATCTGTAAATTTCAACCTATTACCCTACTACTTAGGGGGTTAAG * * * * 66159718 ATCTGTAAATTT-AACCTGTTACCCTACTGCTTATGGGTTTAAG 1 ATCTGTAAATTTCAACCTATTACCCTACTACTTAGGGGGTTAAG 66159761 GCTTGGTGAA Statistics Matches: 37, Mismatches: 6, Indels: 1 0.84 0.14 0.02 Matches are distributed among these distances: 43 26 0.70 44 11 0.30 ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38 Consensus pattern (44 bp): ATCTGTAAATTTCAACCTATTACCCTACTACTTAGGGGGTTAAG Found at i:66172162 original size:289 final size:289 Alignment explanation

Indices: 66171643--66172220 Score: 1102 Period size: 289 Copynumber: 2.0 Consensus size: 289 66171633 AATGATAACT 66171643 AACGATAATAATAATAACATGAATAATAATAGTATAATGTAAATATGAAGAAATGGGGAACATAT 1 AACGATAATAATAATAACATGAATAATAATAGTATAATGTAAATATGAAGAAATGGGGAACATAT 66171708 ATATGTAAAAAGCGTAGTACTAGACTAAAAAATAATATTTATTGAAAACAGTTATATAAATACAA 66 ATATGTAAAAAGCGTAGTACTAGACTAAAAAATAATATTTATTGAAAACAGTTATATAAATACAA * 66171773 TAGTAACTAAATAATAACAATACATAAATACATACATGCAAGTATTGAAATATATACGTAATAAT 131 TAGTAACTAAATAATAACAATACATAAATACATACATGCAAGTATCGAAATATATACGTAATAAT 66171838 AGAAATAATAATAAAAATATACGTGGTATTAAAATATATGTACATGATATAGTTTTAAGAATATG 196 AGAAATAATAATAAAAATATACGTGGTATTAAAATATATGTACATGATATAGTTTTAAGAATATG 66171903 CACAACATGCATGGTATTAAAAATGGTAC 261 CACAACATGCATGGTATTAAAAATGGTAC * 66171932 AACGATAATAATAATAACATGAATAATAATAGTATAATGTAAATATGAAGTAATGGGGAACATAT 1 AACGATAATAATAATAACATGAATAATAATAGTATAATGTAAATATGAAGAAATGGGGAACATAT * 66171997 ATATGTAAAAAGCGTAGTACTAGACTAAAAAATAATATTTATTGAAAACAGTTATATATATACAA 66 ATATGTAAAAAGCGTAGTACTAGACTAAAAAATAATATTTATTGAAAACAGTTATATAAATACAA * 66172062 TAGTAATTAAATAATAACAATACATAAATACATACATGCAAGTATCGAAATATATACGTAATAAT 131 TAGTAACTAAATAATAACAATACATAAATACATACATGCAAGTATCGAAATATATACGTAATAAT * 66172127 AGAAATAATAATAAAAATATACGTGGTATTAAAATATATGTGCATGATATAGTTTTAAGAATATG 196 AGAAATAATAATAAAAATATACGTGGTATTAAAATATATGTACATGATATAGTTTTAAGAATATG * 66172192 TACAACATGCATGGTATTAAAAATGGTAC 261 CACAACATGCATGGTATTAAAAATGGTAC 66172221 TAAAAAAACA Statistics Matches: 283, Mismatches: 6, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 289 283 1.00 ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30 Consensus pattern (289 bp): AACGATAATAATAATAACATGAATAATAATAGTATAATGTAAATATGAAGAAATGGGGAACATAT ATATGTAAAAAGCGTAGTACTAGACTAAAAAATAATATTTATTGAAAACAGTTATATAAATACAA TAGTAACTAAATAATAACAATACATAAATACATACATGCAAGTATCGAAATATATACGTAATAAT AGAAATAATAATAAAAATATACGTGGTATTAAAATATATGTACATGATATAGTTTTAAGAATATG CACAACATGCATGGTATTAAAAATGGTAC Found at i:66172396 original size:3 final size:3 Alignment explanation

Indices: 66172390--66172431 Score: 66 Period size: 3 Copynumber: 14.0 Consensus size: 3 66172380 ACACTACTAT * * 66172390 ATA ATA ATA ATA ATA ATA GTG ATA ATA ATA ATA ATA ATA ATA 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 66172432 TAGAAATACA Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33 Consensus pattern (3 bp): ATA Found at i:66172551 original size:3 final size:3 Alignment explanation

Indices: 66172537--66172662 Score: 57 Period size: 3 Copynumber: 42.0 Consensus size: 3 66172527 AAATATACAC * * * 66172537 TAA TATA TAA TAA TAA TAG TAA TAA TAA TAA TAT TAA -AA GCTAT TAA 1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA * ** * 66172584 TAA TAC TATA TAA T-A TAA TATA TATA TAA GCA TCA -AA TAA -AA TAA 1 TAA TAA TA-A TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA * * * * 66172629 TAA TAA T-A GAA CAC TAA TAA AAA T-A TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 66172663 CAGTAATAAA Statistics Matches: 93, Mismatches: 19, Indels: 22 0.69 0.14 0.16 Matches are distributed among these distances: 2 10 0.11 3 70 0.75 4 12 0.13 5 1 0.01 ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33 Consensus pattern (3 bp): TAA Found at i:66172605 original size:12 final size:13 Alignment explanation

Indices: 66172537--66172612 Score: 63 Period size: 12 Copynumber: 6.0 Consensus size: 13 66172527 AAATATACAC 66172537 TAATATATAATAA 1 TAATATATAATAA 66172550 TAATAGTAATAATAA 1 TAATA-T-ATAATAA 66172565 TAATAT-TAA-AA 1 TAATATATAATAA ** 66172576 -GCTAT-TAATAA 1 TAATATATAATAA * 66172587 TACTATATAAT-A 1 TAATATATAATAA 66172599 TAATATATATATAA 1 TAATATATA-ATAA 66172613 GCATCAAATA Statistics Matches: 52, Mismatches: 4, Indels: 13 0.75 0.06 0.19 Matches are distributed among these distances: 10 6 0.12 11 4 0.08 12 16 0.31 13 11 0.21 14 3 0.06 15 12 0.23 ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38 Consensus pattern (13 bp): TAATATATAATAA Found at i:66172664 original size:23 final size:25 Alignment explanation

Indices: 66172622--66172672 Score: 70 Period size: 23 Copynumber: 2.1 Consensus size: 25 66172612 AGCATCAAAT 66172622 AAAATAATAATAATAGAACACTAATA 1 AAAATAATAATAATA-AACACTAATA * 66172648 AAAAT-ATAATAAT-AACAGTAATA 1 AAAATAATAATAATAAACACTAATA 66172671 AA 1 AA 66172673 TGTAATAGCA Statistics Matches: 24, Mismatches: 1, Indels: 3 0.86 0.04 0.11 Matches are distributed among these distances: 23 11 0.46 25 8 0.33 26 5 0.21 ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24 Consensus pattern (25 bp): AAAATAATAATAATAAACACTAATA Found at i:66173290 original size:15 final size:16 Alignment explanation

Indices: 66173272--66173301 Score: 53 Period size: 15 Copynumber: 1.9 Consensus size: 16 66173262 ATTTTTCTCC 66173272 TTTTTTAT-TTTTTAT 1 TTTTTTATGTTTTTAT 66173287 TTTTTTATGTTTTTA 1 TTTTTTATGTTTTTA 66173302 ATATATGTAT Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 8 0.57 16 6 0.43 ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83 Consensus pattern (16 bp): TTTTTTATGTTTTTAT Found at i:66174069 original size:22 final size:22 Alignment explanation

Indices: 66174041--66174085 Score: 81 Period size: 22 Copynumber: 2.0 Consensus size: 22 66174031 CAAAAGCATA 66174041 TATAGGGGACTTAGTCATTTTG 1 TATAGGGGACTTAGTCATTTTG * 66174063 TATAGGGGACTTGGTCATTTTG 1 TATAGGGGACTTAGTCATTTTG 66174085 T 1 T 66174086 TATGTGTCAT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.20, C:0.09, G:0.29, T:0.42 Consensus pattern (22 bp): TATAGGGGACTTAGTCATTTTG Found at i:66180973 original size:15 final size:14 Alignment explanation

Indices: 66180947--66180977 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 14 66180937 TATGGTTTTA 66180947 TATTAGATTATTAT 1 TATTAGATTATTAT 66180961 TATTAGCATTATTAT 1 TATTAG-ATTATTAT 66180976 TA 1 TA 66180978 AATAAATTAA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 6 0.38 15 10 0.62 ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55 Consensus pattern (14 bp): TATTAGATTATTAT Found at i:66188168 original size:16 final size:16 Alignment explanation

Indices: 66188147--66188177 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 66188137 GATATTTTAA 66188147 TATATTATATTAATAT 1 TATATTATATTAATAT * 66188163 TATATTATGTTAATA 1 TATATTATATTAATA 66188178 AAATAATAAA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55 Consensus pattern (16 bp): TATATTATATTAATAT Found at i:66188274 original size:12 final size:12 Alignment explanation

Indices: 66188257--66188287 Score: 53 Period size: 12 Copynumber: 2.6 Consensus size: 12 66188247 GAAGCAGGGG 66188257 AGAAAAAGAGAA 1 AGAAAAAGAGAA * 66188269 AGAAAAAGGGAA 1 AGAAAAAGAGAA 66188281 AGAAAAA 1 AGAAAAA 66188288 TAAAAGAGAA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 18 1.00 ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00 Consensus pattern (12 bp): AGAAAAAGAGAA Found at i:66193247 original size:21 final size:21 Alignment explanation

Indices: 66193222--66193262 Score: 73 Period size: 21 Copynumber: 2.0 Consensus size: 21 66193212 GAAACGTATG 66193222 GAAGAACACAAAGAAACAAAA 1 GAAGAACACAAAGAAACAAAA * 66193243 GAAGAACATAAAGAAACAAA 1 GAAGAACACAAAGAAACAAA 66193263 TGTGAAACAT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.71, C:0.12, G:0.15, T:0.02 Consensus pattern (21 bp): GAAGAACACAAAGAAACAAAA Found at i:66195612 original size:43 final size:44 Alignment explanation

Indices: 66195551--66195638 Score: 151 Period size: 43 Copynumber: 2.0 Consensus size: 44 66195541 CTAGTAAAAC * 66195551 TAGAGTTTCCAGGGTAAATAGTATAAAT-CTTAAAAGATAAAGA 1 TAGAGTTTCCAGGGTAAATAGTATAAATCCTAAAAAGATAAAGA * 66195594 TAGAGTTTTCAGGGTAAATAGTATAAATCCTAAAAAGATAAAGA 1 TAGAGTTTCCAGGGTAAATAGTATAAATCCTAAAAAGATAAAGA 66195638 T 1 T 66195639 TGTATAGAAT Statistics Matches: 42, Mismatches: 2, Indels: 1 0.93 0.04 0.02 Matches are distributed among these distances: 43 27 0.64 44 15 0.36 ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28 Consensus pattern (44 bp): TAGAGTTTCCAGGGTAAATAGTATAAATCCTAAAAAGATAAAGA Found at i:66196867 original size:197 final size:197 Alignment explanation

Indices: 66196532--66196916 Score: 621 Period size: 197 Copynumber: 2.0 Consensus size: 197 66196522 CTGTTTTCCA * * * 66196532 TACTTGATGCCTTTTAATGCTCAAAAATTGTTTTTCATACTTGAAGCCTTTTATGGCCTAAACTC 1 TACTTGAGGCCTTTAAATGCTCAAAAATTGTTTTCCATACTTGAAGCCTTTTATGGCCTAAACTC * * * * 66196597 ACTGCTATTGATTGGCAACCATTTTTAGATTGCATCTGTATGGAAAAGTTGTTGGTACCCTACGA 66 ACTGCTATTGATTGGCAACCATTTTCAGATTGCATCTATATGGAAAAGTTCTTGGTACCCTACAA 66196662 TATGTTTGTCTTACCAGACTAGATATTTCTTACAGTGAACAAAATAAGTCAATACATGCTATTGA 131 TATGTTTGTCTTACCAGACTAGATATTTCTTACAGTGAACAAAATAAGTCAATACATGCTATTGA 66196727 CT 196 CT * 66196729 TACTTGAGGCCTTTAAATGCTCAAAAATTGTTTTCCATACTTGAGGCCTTTTATGGCCTAAACTC 1 TACTTGAGGCCTTTAAATGCTCAAAAATTGTTTTCCATACTTGAAGCCTTTTATGGCCTAAACTC * * * * 66196794 TA-TGTTTTTGA-TGGTCAACTATTTTCAGATTGCATCTATATGGAAAAGTTCTTGGTACCTTAC 66 -ACTGCTATTGATTGG-CAACCATTTTCAGATTGCATCTATATGGAAAAGTTCTTGGTACCCTAC * 66196857 AATATGTTTGTCTTACCAGACTAGATATTTCTTACAGTGAACAAAGTAAGTCAATACATG 129 AATATGTTTGTCTTACCAGACTAGATATTTCTTACAGTGAACAAAATAAGTCAATACATG 66196917 AATATTCCTT Statistics Matches: 173, Mismatches: 13, Indels: 4 0.91 0.07 0.02 Matches are distributed among these distances: 196 3 0.02 197 169 0.98 198 1 0.01 ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38 Consensus pattern (197 bp): TACTTGAGGCCTTTAAATGCTCAAAAATTGTTTTCCATACTTGAAGCCTTTTATGGCCTAAACTC ACTGCTATTGATTGGCAACCATTTTCAGATTGCATCTATATGGAAAAGTTCTTGGTACCCTACAA TATGTTTGTCTTACCAGACTAGATATTTCTTACAGTGAACAAAATAAGTCAATACATGCTATTGA CT Found at i:66206692 original size:47 final size:44 Alignment explanation

Indices: 66206572--66206744 Score: 118 Period size: 46 Copynumber: 3.8 Consensus size: 44 66206562 TCACTTGTGT * * 66206572 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA 1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAG-C-CATTAAGA * * * 66206618 GAGCCAGTGTAGGACTATGTTTGGGACATGGCATCAG-CATTAAGA 1 GAGCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCAGCCATTAAGA * * ** 66206663 CGAGTGCTAGTGTAAGACATGTCTAGGACACGC-TCCAGCC-TCGAGA 1 -GA--GCTAGTGTAAGACATGTCTGGGACATGCAT-CAGCCATTAAGA * * * 66206709 CGTAAGCCAATATAAGACATGTCTGGGACATGCATC 1 -G--AGCTAGTGTAAGACATGTCTGGGACATGCATC 66206745 GGCTACAAGA Statistics Matches: 100, Mismatches: 17, Indels: 20 0.73 0.12 0.15 Matches are distributed among these distances: 45 8 0.08 46 50 0.50 47 24 0.24 48 18 0.18 ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23 Consensus pattern (44 bp): GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATTAAGA Found at i:66221131 original size:21 final size:22 Alignment explanation

Indices: 66221105--66221145 Score: 66 Period size: 22 Copynumber: 1.9 Consensus size: 22 66221095 CTCTTAACAC 66221105 AGGGGC-ACACGCCCGTGTGGG 1 AGGGGCAACACGCCCGTGTGGG * 66221126 AGGGGCAACATGCCCGTGTG 1 AGGGGCAACACGCCCGTGTG 66221146 ACATTTTAAC Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 21 6 0.33 22 12 0.67 ACGTcount: A:0.17, C:0.27, G:0.44, T:0.12 Consensus pattern (22 bp): AGGGGCAACACGCCCGTGTGGG Found at i:66231667 original size:58 final size:57 Alignment explanation

Indices: 66231529--66231672 Score: 166 Period size: 57 Copynumber: 2.5 Consensus size: 57 66231519 TATCATATTA * * 66231529 CAGGATTACCAGTCCAGGCTAAATCCTTTATGTAACATATTCTCAGAAGAGCTTAAT 1 CAGGATTACCAGTCCAGGCTAAATCCTTTATGTAACATATGCCCAGAAGAGCTTAAT * * * * 66231586 TAGGATTACCAGTCCAGGTTAAATCC-TTATTGTATCATATGCCCGAGAGGAG-TTATAT 1 CAGGATTACCAGTCCAGGCTAAATCCTTTA-TGTAACATATGCCC-AGAAGAGCTTA-AT * ** 66231644 CAGGATTACCTGTCTGGGCTAAATCCTTT 1 CAGGATTACCAGTCCAGGCTAAATCCTTT 66231673 CTATAATGAG Statistics Matches: 72, Mismatches: 11, Indels: 6 0.81 0.12 0.07 Matches are distributed among these distances: 56 3 0.04 57 38 0.53 58 29 0.40 59 2 0.03 ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32 Consensus pattern (57 bp): CAGGATTACCAGTCCAGGCTAAATCCTTTATGTAACATATGCCCAGAAGAGCTTAAT Found at i:66253851 original size:16 final size:18 Alignment explanation

Indices: 66253825--66253862 Score: 76 Period size: 18 Copynumber: 2.1 Consensus size: 18 66253815 TTTAATTTGA 66253825 TTTTCTCTCTCCTCCAGC 1 TTTTCTCTCTCCTCCAGC 66253843 TTTTCTCTCTCCTCCAGC 1 TTTTCTCTCTCCTCCAGC 66253861 TT 1 TT 66253863 CTATTCCTTG Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.05, C:0.42, G:0.05, T:0.47 Consensus pattern (18 bp): TTTTCTCTCTCCTCCAGC Found at i:66254107 original size:11 final size:11 Alignment explanation

Indices: 66254091--66254115 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 66254081 TTATATATAC 66254091 TAATAAAATAA 1 TAATAAAATAA 66254102 TAATAAAATAA 1 TAATAAAATAA 66254113 TAA 1 TAA 66254116 AATATCATAT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28 Consensus pattern (11 bp): TAATAAAATAA Found at i:66254420 original size:31 final size:30 Alignment explanation

Indices: 66254385--66254443 Score: 75 Period size: 31 Copynumber: 1.9 Consensus size: 30 66254375 CACCCTTAAA * 66254385 ATATTTGCACTGTT-AGCCCTTCAAATTTTTC 1 ATATTTACACT-TTAAGCCC-TCAAATTTTTC * 66254416 ATATTTACACTTTAATCCCTCAAATTTT 1 ATATTTACACTTTAAGCCCTCAAATTTT 66254444 GAGTATTTAC Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 30 11 0.44 31 14 0.56 ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46 Consensus pattern (30 bp): ATATTTACACTTTAAGCCCTCAAATTTTTC Found at i:66258468 original size:18 final size:18 Alignment explanation

Indices: 66258431--66258469 Score: 53 Period size: 18 Copynumber: 2.2 Consensus size: 18 66258421 TTGGAAATCA * 66258431 AAATTATTAAAAGATGAT 1 AAATTATTAAAAGATAAT 66258449 AAATTATTAAATAGA-AAT 1 AAATTATTAAA-AGATAAT 66258467 AAA 1 AAA 66258470 AATCATTTTT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 18 16 0.84 19 3 0.16 ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31 Consensus pattern (18 bp): AAATTATTAAAAGATAAT Found at i:66267908 original size:6 final size:6 Alignment explanation

Indices: 66267897--66268083 Score: 163 Period size: 6 Copynumber: 30.8 Consensus size: 6 66267887 AACCAAAATG * 66267897 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT 1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC * * 66267945 AGTAA-C AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC 1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC * * * * * 66267994 AGAATC A-ATAAC AGAATC AAAATC AGAATC AGTATT AGTAA-C AAAATC 1 AGAATC AGA-ATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC * 66268042 AGAATC AGAATC AGAATT ACGTAA-C AGAATC AGAATC AGAAT 1 AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAAT 66268084 GTGAATGCAA Statistics Matches: 147, Mismatches: 18, Indels: 32 0.75 0.09 0.16 Matches are distributed among these distances: 5 11 0.07 6 123 0.84 7 9 0.06 8 4 0.03 ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20 Consensus pattern (6 bp): AGAATC Found at i:66267912 original size:30 final size:30 Alignment explanation

Indices: 66267897--66268083 Score: 253 Period size: 30 Copynumber: 6.4 Consensus size: 30 66267887 AACCAAAATG * 66267897 AGAATCAGAATCAGAATCAGTAACAGAATC 1 AGAATCAGAATCAGAATTAGTAACAGAATC 66267927 AGAATCAGAATCA-ATATTAGTAACAGAATC 1 AGAATCAGAATCAGA-ATTAGTAACAGAATC * 66267957 AGAATCAGAATCAGAATTAGGTGACAGAATC 1 AGAATCAGAATCAGAATTA-GTAACAGAATC 66267988 AGAATCAGAATC---A--A-TAACAGAATC 1 AGAATCAGAATCAGAATTAGTAACAGAATC * * * 66268012 AAAATCAGAATCAGTATTAGTAACAAAATC 1 AGAATCAGAATCAGAATTAGTAACAGAATC 66268042 AGAATCAGAATCAGAATTACGTAACAGAATC 1 AGAATCAGAATCAGAATTA-GTAACAGAATC 66268073 AGAATCAGAAT 1 AGAATCAGAAT 66268084 GTGAATGCAA Statistics Matches: 139, Mismatches: 8, Indels: 19 0.84 0.05 0.11 Matches are distributed among these distances: 24 20 0.14 26 1 0.01 27 1 0.01 28 1 0.01 29 2 0.01 30 70 0.50 31 44 0.32 ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20 Consensus pattern (30 bp): AGAATCAGAATCAGAATTAGTAACAGAATC Found at i:66267997 original size:85 final size:85 Alignment explanation

Indices: 66267897--66268083 Score: 320 Period size: 85 Copynumber: 2.2 Consensus size: 85 66267887 AACCAAAATG * * * 66267897 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT 1 AGAATCAGAATCAGAATCAATAACAGAATCAAAATCAGAATCAATATTAGTAACAAAATCAGAAT * * 66267962 CAGAATCAGAATTAGGTGAC 66 CAGAATCAGAATTACGTAAC * 66267982 AGAATCAGAATCAGAATCAATAACAGAATCAAAATCAGAATCAGTATTAGTAACAAAATCAGAAT 1 AGAATCAGAATCAGAATCAATAACAGAATCAAAATCAGAATCAATATTAGTAACAAAATCAGAAT 66268047 CAGAATCAGAATTACGTAAC 66 CAGAATCAGAATTACGTAAC 66268067 AGAATCAGAATCAGAAT 1 AGAATCAGAATCAGAAT 66268084 GTGAATGCAA Statistics Matches: 96, Mismatches: 6, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 85 96 1.00 ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20 Consensus pattern (85 bp): AGAATCAGAATCAGAATCAATAACAGAATCAAAATCAGAATCAATATTAGTAACAAAATCAGAAT CAGAATCAGAATTACGTAAC Found at i:66268238 original size:27 final size:26 Alignment explanation

Indices: 66268201--66268266 Score: 78 Period size: 27 Copynumber: 2.5 Consensus size: 26 66268191 AGCATGGCTG * 66268201 CCAGAACAGATATCGTGACAGAGTCA 1 CCAGAACAGATATCGTGACAGAGCCA * * 66268227 CCAGATACAGATATTGTGGCAGAGCCA 1 CCAGA-ACAGATATCGTGACAGAGCCA * 66268254 CCACAATCAGATA 1 CCAGAA-CAGATA 66268267 ATGTTGCAAA Statistics Matches: 34, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 26 6 0.18 27 28 0.82 ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17 Consensus pattern (26 bp): CCAGAACAGATATCGTGACAGAGCCA Found at i:66268487 original size:22 final size:22 Alignment explanation

Indices: 66268439--66268497 Score: 64 Period size: 22 Copynumber: 2.7 Consensus size: 22 66268429 GTAAATACGT * 66268439 TTGGCACGAAGCCATAGTTAAG 1 TTGGCACAAAGCCATAGTTAAG * * * 66268461 ATGGCACAAAGCCATATTTAGG 1 TTGGCACAAAGCCATAGTTAAG * * 66268483 TTGGCATAGAGCCAT 1 TTGGCACAAAGCCAT 66268498 TAATAATGGG Statistics Matches: 30, Mismatches: 7, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 22 30 1.00 ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24 Consensus pattern (22 bp): TTGGCACAAAGCCATAGTTAAG Found at i:66268664 original size:27 final size:26 Alignment explanation

Indices: 66268585--66268667 Score: 112 Period size: 27 Copynumber: 3.1 Consensus size: 26 66268575 TCGATCGGTC * * * 66268585 AACAGATATTGTGACAGAGTCACCAA 1 AACAGATATTGTGGCAGAGCCACCAG 66268611 ATACAGATATTGTGGCAGAGCCACCAG 1 A-ACAGATATTGTGGCAGAGCCACCAG * 66268638 AACAGATATTTGTGGCATAGCCACCAG 1 AACAGATA-TTGTGGCAGAGCCACCAG 66268665 AAC 1 AAC 66268668 GCTTCCTCCG Statistics Matches: 51, Mismatches: 4, Indels: 3 0.88 0.07 0.05 Matches are distributed among these distances: 26 8 0.16 27 43 0.84 ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19 Consensus pattern (26 bp): AACAGATATTGTGGCAGAGCCACCAG Found at i:66268896 original size:27 final size:27 Alignment explanation

Indices: 66268866--66269061 Score: 230 Period size: 27 Copynumber: 7.3 Consensus size: 27 66268856 GGGGCAAAAT * * * * 66268866 GGTAATTTTACCCCACACGGGTATCTC 1 GGTAATTCTACCCTACAGGGGTATTTC 66268893 GGTAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * * 66268920 GGTATTTTTACCCTACAAGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 66268947 GATAATTCTACCCTACAGGGGTATTTT 1 GGTAATTCTACCCTACAGGGGTATTTC * * * 66268974 GGTAATTCTATCCTATAAGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * * 66269001 AGTAATTCTACCCTATAGGTGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC ** 66269028 GAAAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 66269055 AGTAATT 1 GGTAATT 66269062 TCACAATCAA Statistics Matches: 140, Mismatches: 29, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 27 140 1.00 ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36 Consensus pattern (27 bp): GGTAATTCTACCCTACAGGGGTATTTC Found at i:66269105 original size:27 final size:27 Alignment explanation

Indices: 66269066--66269610 Score: 711 Period size: 27 Copynumber: 20.2 Consensus size: 27 66269056 GTAATTTCAC * * 66269066 AATCAAGGCTAAAACGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA * 66269093 AATCGAGGGTAAAACGATAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA * 66269120 AA-CTGAGGGT-AAACTAGTAATTCTGTA 1 AATC-GAGGGTAAAAC-GGTAATTCTGTA * * * ** 66269147 AATCAAGGGTAAAACAGTAATTTTACA 1 AATCGAGGGTAAAACGGTAATTCTGTA * 66269174 AATCGAGGGTAAAACGGTAATTCTATA 1 AATCGAGGGTAAAACGGTAATTCTGTA ** 66269201 AATCGAGGGTAAAATAGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA 66269228 AA-CTGAGGGTAAAACGGTAATTCTGTA 1 AATC-GAGGGTAAAACGGTAATTCTGTA * 66269255 AATTGAGGGTAAAACGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA ** * ** 66269282 AATCGAGGGTAAAATAGTAATTTTACA 1 AATCGAGGGTAAAACGGTAATTCTGTA * * 66269309 AATCGAAGGTAAAACGGTAATTCTATA 1 AATCGAGGGTAAAACGGTAATTCTGTA * 66269336 AATCGAGGGTAAAACAGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA 66269363 AA-CTGAGGGTAAAACGGTAATTCTGTA 1 AATC-GAGGGTAAAACGGTAATTCTGTA * * ** 66269390 AATCGAGGGTAAAACGATAATTTTACA 1 AATCGAGGGTAAAACGGTAATTCTGTA 66269417 AATCGAGGGTAAAACGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA * * ** 66269444 AATCGAGGGTAAAACAGTAATTTTAAA 1 AATCGAGGGTAAAACGGTAATTCTGTA * 66269471 AATCGAGGGTAAAATGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA 66269498 AATCGAGGGTAAAACGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA * * ** 66269525 AATCGAGGGTAAAACAGTAATTTTAAA 1 AATCGAGGGTAAAACGGTAATTCTGTA * 66269552 AATCGAGGGTAAAATGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA 66269579 AATCGAGGGTAAAACGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTGTA 66269606 AATCG 1 AATCG 66269611 GGAGTACTTT Statistics Matches: 448, Mismatches: 62, Indels: 16 0.85 0.12 0.03 Matches are distributed among these distances: 26 7 0.02 27 435 0.97 28 6 0.01 ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27 Consensus pattern (27 bp): AATCGAGGGTAAAACGGTAATTCTGTA Found at i:66271711 original size:6 final size:6 Alignment explanation

Indices: 66271700--66271861 Score: 147 Period size: 6 Copynumber: 26.8 Consensus size: 6 66271690 AACCAAAATG * 66271700 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT 1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC * * * 66271748 AGTAA-C AGAATC AGAATC AAAATC AGAATT AG-GTGAC AGAATC AGAATC 1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC * * * * 66271797 AGAATC A-ATAAC AGAATC AGAATC AGAATC AGTATT AGTAA-C AAAATC 1 AGAATC AGA-ATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC 66271845 AGAATC AGAATC AGAAT 1 AGAATC AGAATC AGAAT 66271862 TAAGTGACAG Statistics Matches: 127, Mismatches: 16, Indels: 26 0.75 0.09 0.15 Matches are distributed among these distances: 5 9 0.07 6 109 0.86 7 7 0.06 8 2 0.02 ACGTcount: A:0.51, C:0.14, G:0.15, T:0.20 Consensus pattern (6 bp): AGAATC Found at i:66271715 original size:30 final size:30 Alignment explanation

Indices: 66271700--66271886 Score: 235 Period size: 30 Copynumber: 6.4 Consensus size: 30 66271690 AACCAAAATG * 66271700 AGAATCAGAATCAGAATCAGTAACAGAATC 1 AGAATCAGAATCAGAATTAGTAACAGAATC 66271730 AGAATCAGAATCA-ATATTAGTAACAGAATC 1 AGAATCAGAATCAGA-ATTAGTAACAGAATC * * 66271760 AGAATCAAAATCAGAATTAGGTGACAGAATC 1 AGAATCAGAATCAGAATTA-GTAACAGAATC 66271791 AGAATCAGAATC---A--A-TAACAGAATC 1 AGAATCAGAATCAGAATTAGTAACAGAATC * * 66271815 AGAATCAGAATCAGTATTAGTAACAAAATC 1 AGAATCAGAATCAGAATTAGTAACAGAATC * 66271845 AGAATCAGAATCAGAATTAAGTGACAGAATC 1 AGAATCAGAATCAGAATT-AGTAACAGAATC * 66271876 AAAATCAGAAT 1 AGAATCAGAAT 66271887 GTGAATGCAA Statistics Matches: 137, Mismatches: 10, Indels: 19 0.83 0.06 0.11 Matches are distributed among these distances: 24 21 0.15 26 1 0.01 27 1 0.01 28 1 0.01 29 2 0.01 30 69 0.50 31 42 0.31 ACGTcount: A:0.51, C:0.14, G:0.16, T:0.20 Consensus pattern (30 bp): AGAATCAGAATCAGAATTAGTAACAGAATC Found at i:66271800 original size:85 final size:85 Alignment explanation

Indices: 66271700--66271886 Score: 320 Period size: 85 Copynumber: 2.2 Consensus size: 85 66271690 AACCAAAATG * * 66271700 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT 1 AGAATCAGAATCAGAATCAATAACAGAATCAGAATCAGAATCAATATTAGTAACAAAATCAGAAT * 66271765 CAAAATCAGAATTAGGTGAC 66 CAAAATCAGAATTAAGTGAC * 66271785 AGAATCAGAATCAGAATCAATAACAGAATCAGAATCAGAATCAGTATTAGTAACAAAATCAGAAT 1 AGAATCAGAATCAGAATCAATAACAGAATCAGAATCAGAATCAATATTAGTAACAAAATCAGAAT * 66271850 CAGAATCAGAATTAAGTGAC 66 CAAAATCAGAATTAAGTGAC * 66271870 AGAATCAAAATCAGAAT 1 AGAATCAGAATCAGAAT 66271887 GTGAATGCAA Statistics Matches: 96, Mismatches: 6, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 85 96 1.00 ACGTcount: A:0.51, C:0.14, G:0.16, T:0.20 Consensus pattern (85 bp): AGAATCAGAATCAGAATCAATAACAGAATCAGAATCAGAATCAATATTAGTAACAAAATCAGAAT CAAAATCAGAATTAAGTGAC Found at i:66272041 original size:27 final size:26 Alignment explanation

Indices: 66272004--66272069 Score: 78 Period size: 27 Copynumber: 2.5 Consensus size: 26 66271994 AGCATGGCTG * 66272004 CCAGAACAGATATCGTAACAGAGTCA 1 CCAGAACAGATATCGTAACAGAGCCA * ** 66272030 CCAGATACAGATATTGTGGCAGAGCCA 1 CCAGA-ACAGATATCGTAACAGAGCCA 66272057 CCAGAATCAGATA 1 CCAGAA-CAGATA 66272070 ATGTGGCAAA Statistics Matches: 34, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 26 6 0.18 27 28 0.82 ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17 Consensus pattern (26 bp): CCAGAACAGATATCGTAACAGAGCCA Found at i:66272074 original size:27 final size:27 Alignment explanation

Indices: 66272022--66272077 Score: 78 Period size: 27 Copynumber: 2.1 Consensus size: 27 66272012 GATATCGTAA * * 66272022 CAGAGTCACCAGATACAGATATTGTGG 1 CAGAGCCACCAGATACAGATAATGTGG 66272049 CAGAGCCACCAGA-ATCAGATAATGTGG 1 CAGAGCCACCAGATA-CAGATAATGTGG 66272076 CA 1 CA 66272078 AACCCACCTA Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 26 1 0.04 27 25 0.96 ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18 Consensus pattern (27 bp): CAGAGCCACCAGATACAGATAATGTGG Found at i:66272084 original size:27 final size:27 Alignment explanation

Indices: 66272028--66272085 Score: 73 Period size: 27 Copynumber: 2.1 Consensus size: 27 66272018 GTAACAGAGT * * * 66272028 CACCAGATACAGATATTGTGGCAGAGC 1 CACCAGATACAGATAATGTGGCAAACC 66272055 CACCAGA-ATCAGATAATGTGGCAAACC 1 CACCAGATA-CAGATAATGTGGCAAACC 66272082 CACC 1 CACC 66272086 TAACAGAATA Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 26 1 0.04 27 26 0.96 ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16 Consensus pattern (27 bp): CACCAGATACAGATAATGTGGCAAACC Found at i:66272290 original size:22 final size:22 Alignment explanation

Indices: 66272242--66272300 Score: 64 Period size: 22 Copynumber: 2.7 Consensus size: 22 66272232 GTAAATACGT * 66272242 TTGGCACGAAGCCATAATCAAG 1 TTGGCACAAAGCCATAATCAAG * * * * 66272264 ATGGCACAAAGCCATATTTAGG 1 TTGGCACAAAGCCATAATCAAG * 66272286 TTGGCACAGAGCCAT 1 TTGGCACAAAGCCAT 66272301 TAATAACGGG Statistics Matches: 30, Mismatches: 7, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 22 30 1.00 ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20 Consensus pattern (22 bp): TTGGCACAAAGCCATAATCAAG Found at i:66272427 original size:27 final size:26 Alignment explanation

Indices: 66272388--66272471 Score: 96 Period size: 27 Copynumber: 3.2 Consensus size: 26 66272378 TCGATCGGTC * 66272388 AACAGATATTGTGACAGAGTCACCAA 1 AACAGATATTGTGACAGAGCCACCAA * * 66272414 ATACAGATATTGTGGCAGAGCCACCAG 1 A-ACAGATATTGTGACAGAGCCACCAA * * * 66272441 AACAGATATTTGTGGCATAGCCACCAG 1 AACAGATA-TTGTGACAGAGCCACCAA 66272468 AACA 1 AACA 66272472 CTCCCTCCGT Statistics Matches: 52, Mismatches: 4, Indels: 3 0.88 0.07 0.05 Matches are distributed among these distances: 26 8 0.15 27 44 0.85 ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19 Consensus pattern (26 bp): AACAGATATTGTGACAGAGCCACCAA Found at i:66272699 original size:27 final size:27 Alignment explanation

Indices: 66272669--66272864 Score: 207 Period size: 27 Copynumber: 7.3 Consensus size: 27 66272659 GGGGCAAAAT * * 66272669 GGTAATTTTACTCC-ACAAGGGTATCTC 1 GGTAATTCTAC-CCTACAAGGGTATTTC * 66272696 GGTAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAAGGGTATTTC * * 66272723 GATATTTCTACCCTACAAGGGTATTTC 1 GGTAATTCTACCCTACAAGGGTATTTC * * * 66272750 GATAATTCTACCCTACAGGGGTATTTT 1 GGTAATTCTACCCTACAAGGGTATTTC * * * 66272777 GGTAATTCTATCCTATAAGGGTATTTT 1 GGTAATTCTACCCTACAAGGGTATTTC * * * 66272804 AGTAATTCTACCCTATAGGGGTATTTC 1 GGTAATTCTACCCTACAAGGGTATTTC * * 66272831 AGAAATTCTACCCTAC-AGAGGTATTTC 1 GGTAATTCTACCCTACAAG-GGTATTTC * 66272858 AGTAATT 1 GGTAATT 66272865 TCACAATCAA Statistics Matches: 146, Mismatches: 21, Indels: 4 0.85 0.12 0.02 Matches are distributed among these distances: 26 3 0.02 27 143 0.98 ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36 Consensus pattern (27 bp): GGTAATTCTACCCTACAAGGGTATTTC Found at i:66272905 original size:27 final size:27 Alignment explanation

Indices: 66272869--66273413 Score: 614 Period size: 27 Copynumber: 20.2 Consensus size: 27 66272859 GTAATTTCAC * * 66272869 AATCAAGGGTAAAACGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTATA * 66272896 AATCGAGGGTAAAACGATAATTCTATA 1 AATCGAGGGTAAAACGGTAATTCTATA * * 66272923 AA-CTGAGGGT-AAACTAGTAATTCTGTA 1 AATC-GAGGGTAAAAC-GGTAATTCTATA * * * * 66272950 AATCAAGGGTAAAACAGTAATTTTACA 1 AATCGAGGGTAAAACGGTAATTCTATA 66272977 AATCGAGGGTAAAACGGTAATTCTATA 1 AATCGAGGGTAAAACGGTAATTCTATA ** * 66273004 AATCGAGGGTAAAATAGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTATA * * 66273031 AA-CTGAGGGTAAAACGATAATTCTGTA 1 AATC-GAGGGTAAAACGGTAATTCTATA ** * * 66273058 AATCGAGGGTAAAATAGTAATTTTACA 1 AATCGAGGGTAAAACGGTAATTCTATA 66273085 AATCGAGGGTAAAACGGTAATTCTATA 1 AATCGAGGGTAAAACGGTAATTCTATA * * 66273112 AATCGAGGGTAAAACAGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTATA * * 66273139 AA-CTGTGGGTAAAACGGTAATTCTGTA 1 AATC-GAGGGTAAAACGGTAATTCTATA * ** * * 66273166 AATCGAAGGTAAAATAGTAATTTTACA 1 AATCGAGGGTAAAACGGTAATTCTATA 66273193 AATCGAGGGTAAAACGGTAATTCTATA 1 AATCGAGGGTAAAACGGTAATTCTATA * ** * 66273220 AATTGAGGGTAAAATAGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTATA * 66273247 AA-CTGAGGGTAAAACGGTAATTCTGTA 1 AATC-GAGGGTAAAACGGTAATTCTATA * * 66273274 AATCGAGGGTAAAACGGTAATTTTACA 1 AATCGAGGGTAAAACGGTAATTCTATA * * * 66273301 AATCGAGGGTAAAACAGTAATTTTGTA 1 AATCGAGGGTAAAACGGTAATTCTATA * * * * 66273328 AATTGAGGGTAAAACAGTAATTTTAAA 1 AATCGAGGGTAAAACGGTAATTCTATA * * 66273355 AATCAAGGGTAAAACGGTAATTCTGTA 1 AATCGAGGGTAAAACGGTAATTCTATA * 66273382 AATCAAGGGTAAAACGGTAATTCTATA 1 AATCGAGGGTAAAACGGTAATTCTATA 66273409 AATCG 1 AATCG 66273414 GGAGTACTTT Statistics Matches: 438, Mismatches: 70, Indels: 20 0.83 0.13 0.04 Matches are distributed among these distances: 26 7 0.02 27 423 0.97 28 8 0.02 ACGTcount: A:0.42, C:0.10, G:0.21, T:0.28 Consensus pattern (27 bp): AATCGAGGGTAAAACGGTAATTCTATA Found at i:66273430 original size:54 final size:55 Alignment explanation

Indices: 66272874--66273412 Score: 686 Period size: 54 Copynumber: 10.0 Consensus size: 55 66272864 TTCACAATCA 66272874 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC-GATAATTCTATAAA-CTG 1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAG-TAATTCTATAAATCTG * * * * 66272928 AGGGT-AAACTAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTTTACAAATC-G 1 AGGGTAAAAC-GGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCTG * * * 66272982 AGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAA-CTG 1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCTG * * * * 66273036 AGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATAGTAATTTTACAAATC-G 1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCTG * * 66273090 AGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTGTAAA-CTG 1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCTG * * * * * 66273144 TGGGTAAAACGGTAATTCTGTAAATCGAAGGTAAAATAGTAATTTTACAAATC-G 1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCTG * * * * 66273198 AGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATAGTAATTCTGTAAA-CTG 1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCTG * * * 66273252 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATC-G 1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCTG * * * * * * 66273306 AGGGTAAAACAGTAATTTTGTAAATTGAGGGTAAAACAGTAATTTTAAAAATC-A 1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCTG * * 66273360 AGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATC 1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATC 66273413 GGGAGTACTT Statistics Matches: 419, Mismatches: 56, Indels: 20 0.85 0.11 0.04 Matches are distributed among these distances: 53 7 0.02 54 403 0.96 55 9 0.02 ACGTcount: A:0.42, C:0.10, G:0.21, T:0.28 Consensus pattern (55 bp): AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCTG Found at i:66273444 original size:108 final size:108 Alignment explanation

Indices: 66272857--66273413 Score: 811 Period size: 108 Copynumber: 5.2 Consensus size: 108 66272847 AGAGGTATTT * * * 66272857 CAGTAATTTCAC-AATCAAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC-GATAATTCT 1 CAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAG-TAATTCT * * 66272920 ATAAACTGAGGGT-AAACTAGTAATTCTGTAAATCAAGGGTAAAA 65 GTAAACTGAGGGTAAAAC-GGTAATTCTGTAAATCAAGGGTAAAA * 66272964 CAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTG 1 CAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTG * * 66273029 TAAACTGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAA 66 TAAACTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAA * 66273072 TAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTG 1 CAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTG * 66273137 TAAACTGTGGGTAAAACGGTAATTCTGTAAATCGAA-GGTAAAA 66 TAAACTGAGGGTAAAACGGTAATTCTGTAAATC-AAGGGTAAAA * * * 66273180 TAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATAGTAATTCTG 1 CAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTG * 66273245 TAAACTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA 66 TAAACTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAA * * * * * 66273288 CGGTAATTTTACAAATCGAGGGTAAAACAGTAATTTTGTAAATTGAGGGTAAAACAGTAATT-T- 1 CAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTG * * 66273351 TAAAAATCAAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAA 66 T-AAACT-GAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAA * * * 66273396 CGGTAATTCTATAAATCG 1 CAGTAATTTTACAAATCG 66273414 GGAGTACTTT Statistics Matches: 415, Mismatches: 28, Indels: 13 0.91 0.06 0.03 Matches are distributed among these distances: 106 1 0.00 107 17 0.04 108 391 0.94 109 6 0.01 ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28 Consensus pattern (108 bp): CAGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTG TAAACTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAA Found at i:66276284 original size:40 final size:40 Alignment explanation

Indices: 66276247--66276431 Score: 193 Period size: 40 Copynumber: 4.7 Consensus size: 40 66276237 GCTACTCGTT * 66276247 CAAATGCCTTCGGGACATAGCCCGG-TTAAAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATT-AAGTAACTCGCA * * 66276287 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATTAAGTAACTCGCA * * * 66276327 CCAATGCCTTCAGG-CTTAGCCCGGAATT-AGTAACTCACA 1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAAGTAACTCGCA * * * * 66276366 CAAATGCCTTC-GGATCTTAGTCCGGA-TATGGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGATTA-AGTAAC-TCGCA 66276407 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 66276432 CATCATTCGA Statistics Matches: 123, Mismatches: 14, Indels: 16 0.80 0.09 0.10 Matches are distributed among these distances: 38 3 0.02 39 30 0.24 40 78 0.63 41 12 0.10 ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGATTAAGTAACTCGCA Found at i:66276361 original size:39 final size:40 Alignment explanation

Indices: 66276276--66276384 Score: 150 Period size: 39 Copynumber: 2.8 Consensus size: 40 66276266 GCCCGGTTAA * * 66276276 AGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTT 1 AGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAATT * * 66276316 AGTAACTCGCACCAATGCCTTCAGG-CTTAGCCCGGAATT 1 AGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAATT * 66276355 AGTAACTCACACAAATGCCTTC-GGATCTTA 1 AGTAACTCGCACAAATGCCTTCAGGA-CTTA 66276385 GTCCGGATAT Statistics Matches: 61, Mismatches: 6, Indels: 4 0.86 0.08 0.06 Matches are distributed among these distances: 38 2 0.03 39 32 0.52 40 27 0.44 ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25 Consensus pattern (40 bp): AGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAATT Found at i:66276415 original size:79 final size:80 Alignment explanation

Indices: 66276276--66276431 Score: 192 Period size: 79 Copynumber: 2.0 Consensus size: 80 66276266 GCCCGGTTAA * * * * 66276276 AGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCAGG 1 AGTAACTCACACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCAGG 66276341 -CTTAGCCCGGAATT 66 ACTTAGCCCGGAATT ** * * * 66276355 AGTAACTCACACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTCG 1 AGTAACTCACACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACCAAAGCCTTCA 66276418 GGACTTAGCCCGGA 64 GGACTTAGCCCGGA 66276432 CATCATTCGA Statistics Matches: 65, Mismatches: 9, Indels: 5 0.82 0.11 0.06 Matches are distributed among these distances: 78 3 0.05 79 47 0.72 80 15 0.23 ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24 Consensus pattern (80 bp): AGTAACTCACACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCAGG ACTTAGCCCGGAATT Found at i:66285232 original size:15 final size:13 Alignment explanation

Indices: 66285212--66285245 Score: 54 Period size: 12 Copynumber: 2.8 Consensus size: 13 66285202 TTCATTAAGT 66285212 AATTATTATTTAA 1 AATTATTATTTAA 66285225 AATT-TTATTTAA 1 AATTATTATTTAA 66285237 AA-TATTATT 1 AATTATTATT 66285246 ATTTTATTAA Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 11 1 0.05 12 15 0.75 13 4 0.20 ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56 Consensus pattern (13 bp): AATTATTATTTAA Found at i:66286030 original size:5 final size:5 Alignment explanation

Indices: 66286014--66286045 Score: 55 Period size: 5 Copynumber: 6.4 Consensus size: 5 66286004 CTAAGACTAG * 66286014 TTATT TTCTT TTATT TTATT TTATT TTATT TT 1 TTATT TTATT TTATT TTATT TTATT TTATT TT 66286046 TATAAGTTTT Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 5 25 1.00 ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81 Consensus pattern (5 bp): TTATT Found at i:66287232 original size:33 final size:33 Alignment explanation

Indices: 66287190--66287263 Score: 112 Period size: 33 Copynumber: 2.2 Consensus size: 33 66287180 AATGCACACG 66287190 CCCGTGTGCTTTGGGACACACCAGTGTCCCCTA 1 CCCGTGTGCTTTGGGACACACCAGTGTCCCCTA * ** * 66287223 CCCGTGTGCTTTGGGACACGCTTGTGTGCCCTA 1 CCCGTGTGCTTTGGGACACACCAGTGTCCCCTA 66287256 CCCGTGTG 1 CCCGTGTG 66287264 GAATTAATAG Statistics Matches: 37, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 33 37 1.00 ACGTcount: A:0.11, C:0.34, G:0.28, T:0.27 Consensus pattern (33 bp): CCCGTGTGCTTTGGGACACACCAGTGTCCCCTA Found at i:66288888 original size:27 final size:27 Alignment explanation

Indices: 66288870--66288938 Score: 120 Period size: 27 Copynumber: 2.6 Consensus size: 27 66288860 ATAGACTAGT 66288870 ATTACTGAAATACCCCTATAGGGTAGA 1 ATTACTGAAATACCCCTATAGGGTAGA * * 66288897 ATTACTGAAATGCCCCTGTAGGGTAGA 1 ATTACTGAAATACCCCTATAGGGTAGA 66288924 ATTACTGAAATACCC 1 ATTACTGAAATACCC 66288939 TTGGTTTACA Statistics Matches: 39, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 27 39 1.00 ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26 Consensus pattern (27 bp): ATTACTGAAATACCCCTATAGGGTAGA Found at i:66288977 original size:27 final size:27 Alignment explanation

Indices: 66288948--66289264 Score: 214 Period size: 27 Copynumber: 11.7 Consensus size: 27 66288938 CTTGGTTTAC * * 66288948 AAAATTACCAAAATACCCTCGACTAGC 1 AAAATTACCAAAATACCCTCGACTTGT * * * 66288975 AAAATTACCAAAATACCC-CTAGTTTGA 1 AAAATTACCAAAATACCCTCGA-CTTGT * * 66289002 AAAATTATCAAAATACCC-CTGATTTGT 1 AAAATTACCAAAATACCCTC-GACTTGT * * * 66289029 AAAATTATCGAAATACCCTCGACCTGT 1 AAAATTACCAAAATACCCTCGACTTGT * * 66289056 AAAATTATCGAAATACCCTCGACTTGT 1 AAAATTACCAAAATACCCTCGACTTGT * 66289083 AAAATTACCAAAATACCCTCGATTTGT 1 AAAATTACCAAAATACCCTCGACTTGT *** * 66289110 AAAATTACCAAAATACCC-CTTTTTTGG 1 AAAATTACCAAAATACCCTC-GACTTGT * * ** 66289137 AAAATTACAAAAATACCC-CTGATTTAC 1 AAAATTACCAAAATACCCTC-GACTTGT * * * 66289164 AAAATTACAAAAATACCCTTGACTTTT 1 AAAATTACCAAAATACCCTCGACTTGT * * * * * 66289191 AAAAATTA-TAGAAATACCAT-TAGTTTGC 1 -AAAATTACCA-AAATACCCTCGA-CTTGT * * ** 66289219 AAAATTACCAAAATACGCTTGGTTTGT 1 AAAATTACCAAAATACCCTCGACTTGT * * 66289246 AAATTTACCAAAACACCCT 1 AAAATTACCAAAATACCCT 66289265 TTTAGGGTAA Statistics Matches: 239, Mismatches: 41, Indels: 20 0.80 0.14 0.07 Matches are distributed among these distances: 26 3 0.01 27 216 0.90 28 20 0.08 ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29 Consensus pattern (27 bp): AAAATTACCAAAATACCCTCGACTTGT Found at i:66289008 original size:81 final size:81 Alignment explanation

Indices: 66288923--66289127 Score: 227 Period size: 81 Copynumber: 2.5 Consensus size: 81 66288913 TGTAGGGTAG * * ** 66288923 AATTACTGAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGA-CTAGCAAAATTACCAAA 1 AATTACTAAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCGACCT-GCAAAATTACCAAA * 66288987 ATACCCCTAG-TTTGAAA 65 ATA-CCCTAGACTTGAAA * * * * * * 66289004 AATTA-TCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCGACCTGTAAAATTATCGAA 1 AATTACT-AAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCGACCTGCAAAATTACCAAA * * 66289068 ATACCCTCGACTTGTAA 65 ATACCCTAGACTTGAAA * * 66289085 AATTACCAAAATACCCTCGATTTGTAAAATTACCAAAATACCC 1 AATTACTAAAATACCCTTGATTTGTAAAATTACCAAAATACCC 66289128 CTTTTTTGGA Statistics Matches: 102, Mismatches: 18, Indels: 8 0.80 0.14 0.06 Matches are distributed among these distances: 80 6 0.06 81 94 0.92 82 2 0.02 ACGTcount: A:0.41, C:0.23, G:0.08, T:0.27 Consensus pattern (81 bp): AATTACTAAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCGACCTGCAAAATTACCAAAA TACCCTAGACTTGAAA Found at i:66289562 original size:41 final size:41 Alignment explanation

Indices: 66289504--66289626 Score: 192 Period size: 41 Copynumber: 3.0 Consensus size: 41 66289494 GAAGGAAGAA * * * * 66289504 ATTAAGGATTGCTTGGTTGCTTAACGACCATGGATCCACCG 1 ATTAAGGATTGCATGGTTGCTTGATGACCGTGGATCCACCG * * 66289545 ATTAAGGATCGCATGGTTGCTTGATGACCGTGGATCCACTG 1 ATTAAGGATTGCATGGTTGCTTGATGACCGTGGATCCACCG 66289586 ATTAAGGATTGCATGGTTGCTTGATGACCGTGGATCCACCG 1 ATTAAGGATTGCATGGTTGCTTGATGACCGTGGATCCACCG 66289627 GTGGCTTTTA Statistics Matches: 74, Mismatches: 8, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 41 74 1.00 ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29 Consensus pattern (41 bp): ATTAAGGATTGCATGGTTGCTTGATGACCGTGGATCCACCG Found at i:66289820 original size:22 final size:22 Alignment explanation

Indices: 66289768--66289832 Score: 60 Period size: 22 Copynumber: 3.0 Consensus size: 22 66289758 GCCAATTATT * ** 66289768 CTGATTATGGCTTTGCACCAAC 1 CTGATTATGGCTCTGTGCCAAC * 66289790 CT-ACATATGGCTCTGTGCCAAC 1 CTGA-TTATGGCTCTGTGCCAAC * * 66289812 CTGATTATGGTTGTGTGCCAA 1 CTGATTATGGCTCTGTGCCAA 66289833 ACGTATTTGC Statistics Matches: 34, Mismatches: 7, Indels: 4 0.76 0.16 0.09 Matches are distributed among these distances: 21 1 0.03 22 32 0.94 23 1 0.03 ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32 Consensus pattern (22 bp): CTGATTATGGCTCTGTGCCAAC Found at i:66292075 original size:43 final size:43 Alignment explanation

Indices: 66292024--66292219 Score: 315 Period size: 43 Copynumber: 4.6 Consensus size: 43 66292014 CGGCATTACG 66292024 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA 1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA * * * 66292067 CCTACTAGGCACGAAGGCCAGAATACACATCACCGGC-CGAAG 1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA 66292109 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA 1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA * * 66292152 CCTGCCAGGCACGAACGCCCGAATACACATCACCGGCAC-AAA 1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA * 66292194 GCCTGCTAGGAACGAAGGCCCGAATA 1 -CCTGCTAGGCACGAAGGCCCGAATA 66292220 TAATACCAGC Statistics Matches: 140, Mismatches: 11, Indels: 4 0.90 0.07 0.03 Matches are distributed among these distances: 42 42 0.30 43 98 0.70 ACGTcount: A:0.33, C:0.35, G:0.23, T:0.09 Consensus pattern (43 bp): CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA Found at i:66292166 original size:85 final size:86 Alignment explanation

Indices: 66292023--66292219 Score: 333 Period size: 85 Copynumber: 2.3 Consensus size: 86 66292013 CCGGCATTAC * * 66292023 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAACCTACTAGGCACGAAGGCCAG 1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAACCTACCAGGCACGAACGCCAG * 66292088 AATACACATCACCGGC-CGAA 66 AATACACATCACCGGCACAAA * * 66292108 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAACCTGCCAGGCACGAACGCCCG 1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAACCTACCAGGCACGAACGCCAG 66292173 AATACACATCACCGGCACAAA 66 AATACACATCACCGGCACAAA * 66292194 GCCTGCTAGGAACGAAGGCCCGAATA 1 GCCTGCTAGGCACGAAGGCCCGAATA 66292220 TAATACCAGC Statistics Matches: 105, Mismatches: 6, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 85 77 0.73 86 28 0.27 ACGTcount: A:0.32, C:0.35, G:0.24, T:0.09 Consensus pattern (86 bp): GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAACCTACCAGGCACGAACGCCAG AATACACATCACCGGCACAAA Found at i:66292260 original size:38 final size:38 Alignment explanation

Indices: 66292212--66292413 Score: 271 Period size: 38 Copynumber: 5.3 Consensus size: 38 66292202 GGAACGAAGG * * * * 66292212 CCCGAATATAATACCAGCACTAGGCCTGCAGGATTTAT 1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA * 66292250 CCCGGATATAATACCAGCACGAATCCTGC-GAGATTTAA 1 CCCGGATATAATACCAGCACGAAGCCTGCAG-GATTTAA ** * * 66292288 CCCGGATATTTTACCAGCACGAAGCCTGTAGGTCTTTAA 1 CCCGGATATAATACCAGCACGAAGCCTGCAGG-ATTTAA * * 66292327 GCCCGGATATAATACTAGCACGAAGCCTGCGGGATTTAA 1 -CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA 66292366 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA 1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA 66292404 CCCGGATATA 1 CCCGGATATA 66292414 CATCGAATAT Statistics Matches: 142, Mismatches: 18, Indels: 8 0.85 0.11 0.05 Matches are distributed among these distances: 37 1 0.01 38 103 0.73 39 11 0.08 40 27 0.19 ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22 Consensus pattern (38 bp): CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA Found at i:66292341 original size:78 final size:76 Alignment explanation

Indices: 66292212--66292413 Score: 287 Period size: 78 Copynumber: 2.6 Consensus size: 76 66292202 GGAACGAAGG * * * * * 66292212 CCCGAATATAATACCAGCACTAGGCCTGCAGGATTTATCCCGGATATAATACCAGCACGAATCCT 1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGGATATAATACCAGCACGAAGCCT 66292277 GCGAGATTTAA 66 GCGAGATTTAA ** * * * 66292288 CCCGGATATTTTACCAGCACGAAGCCTGTAGGTCTTTAAGCCCGGATATAATACTAGCACGAAGC 1 CCCGGATATAATACCAGCACGAAGCCTGCAGG-ATTTAA-CCCGGATATAATACCAGCACGAAGC * 66292353 CTGCGGGATTTAA 64 CTGCGAGATTTAA 66292366 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGGATATA 1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGGATATA 66292414 CATCGAATAT Statistics Matches: 109, Mismatches: 15, Indels: 4 0.85 0.12 0.03 Matches are distributed among these distances: 76 36 0.33 77 9 0.08 78 64 0.59 ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22 Consensus pattern (76 bp): CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGGATATAATACCAGCACGAAGCCT GCGAGATTTAA Found at i:66294930 original size:47 final size:47 Alignment explanation

Indices: 66294872--66295074 Score: 293 Period size: 47 Copynumber: 4.3 Consensus size: 47 66294862 TGTACAAGTA * * 66294872 TATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAACATG 1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG * * 66294919 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG 1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG * * 66294966 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG 1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG * * 66295013 TATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAA-GTG 1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GAACATG * 66295060 TATAAATGTGATAAG 1 TATATATGTGATAAG 66295075 TCCCGAAGGG Statistics Matches: 141, Mismatches: 13, Indels: 4 0.89 0.08 0.03 Matches are distributed among these distances: 46 1 0.01 47 137 0.97 48 3 0.02 ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27 Consensus pattern (47 bp): TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG Found at i:66294952 original size:22 final size:22 Alignment explanation

Indices: 66294925--66295046 Score: 61 Period size: 22 Copynumber: 5.3 Consensus size: 22 66294915 CATGTGTATG 66294925 TGTGATAAGGCCGAATGGCCAA 1 TGTGATAAGGCCGAATGGCCAA * * * 66294947 TGTGATGAATG-TGAACAT-GCATATA 1 TGTGAT-AAGGCCG-A-ATGGC-CA-A * 66294972 TGAGATAAGGCCGAATGGCCAA 1 TGTGATAAGGCCGAATGGCCAA * * *** 66294994 TGTGATGAATG-TGAAAGTGTATATA 1 TGTGAT-AAGGCCG-AA-TGGCCA-A 66295019 TGTGATAAGGCCGAATGGCCAA 1 TGTGATAAGGCCGAATGGCCAA 66295041 TGTGAT 1 TGTGAT 66295047 GGATGTGGAA Statistics Matches: 70, Mismatches: 18, Indels: 24 0.62 0.16 0.21 Matches are distributed among these distances: 22 21 0.30 23 17 0.24 24 17 0.24 25 15 0.21 ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25 Consensus pattern (22 bp): TGTGATAAGGCCGAATGGCCAA Found at i:66301433 original size:38 final size:38 Alignment explanation

Indices: 66301385--66301586 Score: 269 Period size: 38 Copynumber: 5.3 Consensus size: 38 66301375 GGCACGAAGG * * * * 66301385 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT 1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA * 66301423 CCCGGATATAATACCAGCACGAAGCCTGCGAGATTTAA 1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA ** * ** 66301461 CCCGGATATTTTACCAGCACGAAGCCTGTAGGTCTTTAA 1 CCCGGATATAATACCAGCACGAAGCCTG-CGGGATTTAA * 66301500 GCCAGGATATAATACCAGCACGAAGCCTGCGGGATTTAA 1 -CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA * * 66301539 CCCGGATATAATACCAACACGAAGCCTGCAGGATTTAA 1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA 66301577 CCCGGATATA 1 CCCGGATATA 66301587 CATCGAATAT Statistics Matches: 142, Mismatches: 20, Indels: 4 0.86 0.12 0.02 Matches are distributed among these distances: 38 104 0.73 39 13 0.09 40 25 0.18 ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21 Consensus pattern (38 bp): CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA Found at i:66311228 original size:7 final size:7 Alignment explanation

Indices: 66311218--66311322 Score: 58 Period size: 7 Copynumber: 15.0 Consensus size: 7 66311208 ATGTATTTTC 66311218 ATTATAT 1 ATTATAT * 66311225 ATTATTT 1 ATTATAT 66311232 ATT-T-T 1 ATTATAT * 66311237 ACTATAT 1 ATTATAT * * 66311244 TTTATCT 1 ATTATAT 66311251 ATTATATT 1 ATTATA-T * 66311259 ATTATAC 1 ATTATAT * 66311266 ATT-TTT 1 ATTATAT * 66311272 AATTTTTAT 1 -A-TTATAT * 66311281 CATATATTT 1 -AT-TATAT 66311290 ATTATAT 1 ATTATAT 66311297 ATTATAT 1 ATTATAT 66311304 ATT-TAT 1 ATTATAT 66311310 ATT-TAT 1 ATTATAT 66311316 ATTATAT 1 ATTATAT 66311323 GTTTTTAGTA Statistics Matches: 75, Mismatches: 15, Indels: 16 0.71 0.14 0.15 Matches are distributed among these distances: 5 3 0.04 6 15 0.20 7 39 0.52 8 12 0.16 9 6 0.08 ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62 Consensus pattern (7 bp): ATTATAT Found at i:66311248 original size:19 final size:19 Alignment explanation

Indices: 66311194--66311253 Score: 57 Period size: 19 Copynumber: 3.0 Consensus size: 19 66311184 TATTTGCATC * 66311194 TTACTATATGTTATATGTATT 1 TTACTATAT-TT-TATCTATT * * * 66311215 TTCATTATATATTATTTATT 1 TT-ACTATATTTTATCTATT 66311235 TTACTATATTTTATCTATT 1 TTACTATATTTTATCTATT 66311254 ATATTATTAT Statistics Matches: 32, Mismatches: 6, Indels: 4 0.76 0.14 0.10 Matches are distributed among these distances: 19 14 0.44 20 9 0.28 21 3 0.09 22 6 0.19 ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62 Consensus pattern (19 bp): TTACTATATTTTATCTATT Found at i:66311261 original size:17 final size:16 Alignment explanation

Indices: 66311204--66311378 Score: 61 Period size: 17 Copynumber: 10.9 Consensus size: 16 66311194 TTACTATATG 66311204 TTATATGTATTTTCATTA 1 TTATAT-TATTTT-ATTA 66311222 -TATATTA-TTTATT- 1 TTATATTATTTTATTA 66311235 TTACTA-TATTTTATCTA 1 TTA-TATTATTTTAT-TA * * 66311252 TTATATTATTATACATTT 1 TTATATTATT-T-TATTA 66311270 TTA-ATT-TTTATCATATA 1 TTATATTATTT-T-AT-TA * 66311287 TT-TATTA-TATATTA 1 TTATATTATTTTATTA 66311301 -TATATTTATATTTA-TA 1 TTATA-TTAT-TTTATTA * 66311317 TTATATGT-TTTTAGTA 1 TTATAT-TATTTTATTA * * * 66311333 -CATATTATTCTATAA 1 TTATATTATTTTATTA * 66311348 TTATATTATTCATATTA 1 TTATATTATT-TTATTA * 66311365 TTATA-CATTTTATT 1 TTATATTATTTTATT 66311379 TATAAATTTA Statistics Matches: 120, Mismatches: 15, Indels: 47 0.66 0.08 0.26 Matches are distributed among these distances: 13 1 0.01 14 12 0.10 15 34 0.28 16 27 0.22 17 39 0.32 18 5 0.04 19 2 0.02 ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61 Consensus pattern (16 bp): TTATATTATTTTATTA Found at i:66311329 original size:21 final size:20 Alignment explanation

Indices: 66311218--66311322 Score: 75 Period size: 19 Copynumber: 5.7 Consensus size: 20 66311208 ATGTATTTTC * 66311218 ATTATATATTATTTATTT-T 1 ATTATATATTATATATTTAT * * * 66311237 ACTATATTTTATCTA-TTAT 1 ATTATATATTATATATTTAT * * 66311256 ATTAT-TA-TACATTTTTA- 1 ATTATATATTATATATTTAT * * 66311273 ATT-TTTATCATATA-TT-T 1 ATTATATATTATATATTTAT 66311290 ATTATATATTATATATTTAT 1 ATTATATATTATATATTTAT 66311310 ATT-TATATTATAT 1 ATTATATATTATAT 66311323 GTTTTTAGTA Statistics Matches: 65, Mismatches: 13, Indels: 16 0.69 0.14 0.17 Matches are distributed among these distances: 16 1 0.02 17 13 0.20 18 18 0.28 19 29 0.45 20 4 0.06 ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62 Consensus pattern (20 bp): ATTATATATTATATATTTAT Found at i:66311383 original size:36 final size:34 Alignment explanation

Indices: 66311253--66311383 Score: 101 Period size: 36 Copynumber: 3.8 Consensus size: 34 66311243 TTTTATCTAT * 66311253 TATATTATTATACATTTTTAATT-T--TTATCA-TA 1 TATATTATTATACA-TTTTATTTATAATTAT-ATTA * * 66311285 TAT-TTATTATATATTATATATTTATATTTATATTA 1 TATATTATTATACATT-T-TATTTATAATTATATTA * * * 66311320 TATGTTTTTAGTACATATTATTCTATAATTATATTA 1 TATATTATTA-TACATTTTATT-TATAATTATATTA 66311356 TTCATATTATTATACATTTTATTTATAA 1 -T-ATATTATTATACATTTTATTTATAA 66311384 ATTTAGTATA Statistics Matches: 79, Mismatches: 9, Indels: 18 0.75 0.08 0.17 Matches are distributed among these distances: 30 2 0.03 31 10 0.13 32 7 0.09 33 1 0.01 34 1 0.01 35 13 0.16 36 23 0.29 37 15 0.19 38 7 0.09 ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59 Consensus pattern (34 bp): TATATTATTATACATTTTATTTATAATTATATTA Found at i:66311518 original size:14 final size:14 Alignment explanation

Indices: 66311482--66311519 Score: 58 Period size: 14 Copynumber: 2.7 Consensus size: 14 66311472 ATACGTTCTT * 66311482 CATATATTGTATTA 1 CATATATTTTATTA * 66311496 TATATATTTTATTA 1 CATATATTTTATTA 66311510 CATATATTTT 1 CATATATTTT 66311520 TATTGCTATA Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 14 21 1.00 ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58 Consensus pattern (14 bp): CATATATTTTATTA Found at i:66311529 original size:14 final size:16 Alignment explanation

Indices: 66311483--66311555 Score: 57 Period size: 14 Copynumber: 4.8 Consensus size: 16 66311473 TACGTTCTTC * 66311483 ATATATTGTATT--AT 1 ATATATTTTATTACAT 66311497 ATATATTTTATTACAT 1 ATATATTTTATTACAT * 66311513 ATAT-TTTTATTGC-T 1 ATATATTTTATTACAT * 66311527 ATATGATTTATATTA-TT 1 ATAT-ATTT-TATTACAT * 66311544 ACATATTTTATT 1 ATATATTTTATT 66311556 TATAAATAAT Statistics Matches: 49, Mismatches: 4, Indels: 11 0.77 0.06 0.17 Matches are distributed among these distances: 14 16 0.33 15 12 0.24 16 13 0.27 17 8 0.16 ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59 Consensus pattern (16 bp): ATATATTTTATTACAT Found at i:66327646 original size:23 final size:22 Alignment explanation

Indices: 66327586--66327647 Score: 54 Period size: 23 Copynumber: 2.7 Consensus size: 22 66327576 TCAAAATGCG * * 66327586 TAATATAAG-TAAAGTAATTAT 1 TAATATAAGTTAAAATAAGTAT * * 66327607 TAACATATAAATAAAAATAAGTAT 1 T-A-ATATAAGTTAAAATAAGTAT 66327631 ATAATATAAGTTAAAAT 1 -TAATATAAGTTAAAAT 66327648 CTTTAATAAT Statistics Matches: 31, Mismatches: 6, Indels: 6 0.72 0.14 0.14 Matches are distributed among these distances: 21 1 0.03 22 1 0.03 23 18 0.58 24 10 0.32 25 1 0.03 ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34 Consensus pattern (22 bp): TAATATAAGTTAAAATAAGTAT Found at i:66327678 original size:14 final size:16 Alignment explanation

Indices: 66327656--66327692 Score: 51 Period size: 14 Copynumber: 2.4 Consensus size: 16 66327646 ATCTTTAATA * 66327656 ATAATAATAT-ATAG- 1 ATAAAAATATAATAGT 66327670 ATAAAAATATAATAGT 1 ATAAAAATATAATAGT 66327686 ATAAAAA 1 ATAAAAA 66327693 ATGACATAAT Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 14 9 0.45 15 4 0.20 16 7 0.35 ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30 Consensus pattern (16 bp): ATAAAAATATAATAGT Found at i:66327792 original size:37 final size:33 Alignment explanation

Indices: 66327746--66327840 Score: 93 Period size: 37 Copynumber: 2.7 Consensus size: 33 66327736 TATATAATAT 66327746 ATATAAATAATTAATAAATATATAATACAAGTAAAA 1 ATATAAATAA-TAATAAATA-ATAATA-AAGTAAAA ** 66327782 AGTATAAATAATAATGTAAATAATAATAATTTAAAA 1 A-TATAAATAATAA--TAAATAATAATAAAGTAAAA 66327818 ATATATAATAAATAAT-AATAATA 1 ATATA-AAT-AATAATAAATAATA 66327841 TGAAATAATA Statistics Matches: 52, Mismatches: 2, Indels: 12 0.79 0.03 0.18 Matches are distributed among these distances: 34 7 0.13 35 5 0.10 36 14 0.27 37 20 0.38 38 6 0.12 ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33 Consensus pattern (33 bp): ATATAAATAATAATAAATAATAATAAAGTAAAA Found at i:66327808 original size:15 final size:14 Alignment explanation

Indices: 66327788--66327850 Score: 67 Period size: 15 Copynumber: 4.3 Consensus size: 14 66327778 AAAAAGTATA 66327788 AATAATAATGTAAAT 1 AATAATAAT-TAAAT 66327803 AATAATAATTTAAA- 1 AATAATAA-TTAAAT 66327817 AATATATAA-TAAAT 1 AATA-ATAATTAAAT 66327831 AATAATAATATGAAAT 1 AATAATAAT-T-AAAT 66327847 AATA 1 AATA 66327851 TAAGGTTAAT Statistics Matches: 42, Mismatches: 0, Indels: 11 0.79 0.00 0.21 Matches are distributed among these distances: 13 8 0.19 14 8 0.19 15 17 0.40 16 9 0.21 ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33 Consensus pattern (14 bp): AATAATAATTAAAT Found at i:66327830 original size:28 final size:28 Alignment explanation

Indices: 66327736--66327839 Score: 85 Period size: 28 Copynumber: 3.8 Consensus size: 28 66327726 GTTATATATG * 66327736 TATATAATATAT-ATAAATAA-TTAATAAA 1 TATATAATAAATAAT-AATAATTTAA-AAA * * 66327764 TATATAATACAAGTAA-AA-AGTATAAATAA 1 TATATAATA-AA-TAATAATAATTTAAA-AA * 66327793 TA-AT-GTAAATAATAATAATTTAAAAA 1 TATATAATAAATAATAATAATTTAAAAA 66327819 TATATAATAAATAATAATAAT 1 TATATAATAAATAATAATAAT 66327840 ATGAAATAAT Statistics Matches: 60, Mismatches: 7, Indels: 18 0.71 0.08 0.21 Matches are distributed among these distances: 25 3 0.05 26 8 0.13 27 10 0.17 28 27 0.45 29 10 0.17 30 1 0.02 31 1 0.02 ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35 Consensus pattern (28 bp): TATATAATAAATAATAATAATTTAAAAA Found at i:66327998 original size:20 final size:19 Alignment explanation

Indices: 66327970--66328011 Score: 59 Period size: 20 Copynumber: 2.2 Consensus size: 19 66327960 AAGAAGGTAT 66327970 TAAGTAAT-ATAATAAAATA 1 TAAGTAATAAT-ATAAAATA 66327989 TAAGTAAATAATATAAAATA 1 TAAGT-AATAATATAAAATA 66328009 TAA 1 TAA 66328012 TACATATATT Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 19 5 0.24 20 14 0.67 21 2 0.10 ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31 Consensus pattern (19 bp): TAAGTAATAATATAAAATA Found at i:66330183 original size:204 final size:204 Alignment explanation

Indices: 66329694--66330240 Score: 801 Period size: 205 Copynumber: 2.7 Consensus size: 204 66329684 TCTGAAGGTG * * * 66329694 AGATCTGCTACGTATCTGCTCCCCATTGAAGTGGAGATGCCAGACTTCGATTTGCTCTCTGACAA 1 AGATCTGCTATGTGTCTGCTCCCCATTGAAGTGGAGATGCCAGACTTCGATTTGATCTCTGACAA 66329759 TACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATG 66 TACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATG * 66329824 TCTTCGATTTAATCCTTGTAAACACAAGGATGCCAAATCATCTTGGATCTACTCCAGATAAACAT 131 TCTTCGATTTAATCCTTGTAAACACAAGGATGCCAAACCATCTTGGATCTACTCCAGATAAACAT 66329889 ATGAAGGCC 196 ATGAAGGCC * * ** * * * * 66329898 AGATCTGCTATGTGTCTGCTCTCTACCGAATATGGAGACGCCAAACTTCGATTTGACCTCTGACA 1 AGATCTGCTATGTGTCTGCTCCCCATTGAA-GTGGAGATGCCAGACTTCGATTTGATCTCTGACA * * * 66329963 ACACAGAGATGCCAAATCATCTTAG-TTTGCCTCATCGTAAGCACGTGAAAGCCAAAATCAGCTA 65 ATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCC-AAATCAGCTA ** * * * 66330027 TGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTACTTCAGTATAGA 129 TGTCTTCGATTTAATCCTTGTAAACACAAGGATGCCAAACCATCTTGGATCTACTCCAG-ATAAA * *** 66330092 CATCTGAAGTTT 193 CATATGAAGGCC * * 66330104 GGATCTGCTATGTGTCTGC-CCCCATTGAAGTGGAGATGCCAGACTTCGATTTGTTCTCTGACAA 1 AGATCTGCTATGTGTCTGCTCCCCATTGAAGTGGAGATGCCAGACTTCGATTTGATCTCTGACAA * * 66330168 TACAGAGATGCCAAATCATCTTAGATTTTCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATG 66 TACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATG 66330233 TCTTCGAT 131 TCTTCGAT 66330241 CTACTCTCCG Statistics Matches: 300, Mismatches: 39, Indels: 8 0.86 0.11 0.02 Matches are distributed among these distances: 204 123 0.41 205 147 0.49 206 30 0.10 ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29 Consensus pattern (204 bp): AGATCTGCTATGTGTCTGCTCCCCATTGAAGTGGAGATGCCAGACTTCGATTTGATCTCTGACAA TACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATG TCTTCGATTTAATCCTTGTAAACACAAGGATGCCAAACCATCTTGGATCTACTCCAGATAAACAT ATGAAGGCC Found at i:66330554 original size:132 final size:132 Alignment explanation

Indices: 66330300--66330580 Score: 431 Period size: 132 Copynumber: 2.1 Consensus size: 132 66330290 CTTTGACAAT * * 66330300 ACAGAGATGCCAAATCTGCTATCTTTAACTTGTTCCCTATAAACACAGGGATACCATGCTGAAAT 1 ACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATACCATGCTGAAAT * * * * * 66330365 CCTCGATCTGCTTCGCTGTAAGCACAAGAGTGTCAGATCTATTATTTTCGATTTGTTCCCTATAA 66 CCTCCATCTGCTTCGCTGTAAGCACAAGAATGTAAGATCTACTATTTTCGATCTGTTCCCTATAA 66330430 AC 131 AC * 66330432 ACAGGGATGCCAAATCTGCTATCTTCAACTTGCTT-CCTATAAACACAGGGATGCCATGCTGAAA 1 ACAGGGATGCCAAATCTGCTATCTTCAACTTG-TTCCCTATAAACACAGGGATACCATGCTGAAA * * * 66330496 TCTTCCATCTGCTTCGCTGTAAGCACAGGAATGTAAGATCTGCTATCTTT-GATCTGTTCCCTAT 65 TCCTCCATCTGCTTCGCTGTAAGCACAAGAATGTAAGATCTACTAT-TTTCGATCTGTTCCCTAT 66330560 AAAC 129 AAAC 66330564 ACAGGGATGCCAAATCT 1 ACAGGGATGCCAAATCT 66330581 TGTTTCTTTG Statistics Matches: 136, Mismatches: 11, Indels: 4 0.90 0.07 0.03 Matches are distributed among these distances: 132 131 0.96 133 5 0.04 ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30 Consensus pattern (132 bp): ACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATACCATGCTGAAAT CCTCCATCTGCTTCGCTGTAAGCACAAGAATGTAAGATCTACTATTTTCGATCTGTTCCCTATAA AC Found at i:66330594 original size:44 final size:45 Alignment explanation

Indices: 66330256--66330580 Score: 171 Period size: 44 Copynumber: 7.4 Consensus size: 45 66330246 CTCCGCCAAT * * * * * 66330256 ACAGAGATGCCAAATCTGGTATCTTTGATCTGC-T--CTTTGACAAT 1 ACAGGGATGCCAAATCTGCTATCTTTCATCTGCTTCCCTAT-A-AAC * * 66330300 ACAGAGATGCCAAATCTGCTATCTTT-AACTTG-TTCCCTATAAAC 1 ACAGGGATGCCAAATCTGCTATCTTTCATC-TGCTTCCCTATAAAC * ** * * * * 66330344 ACAGGGATACC--ATGCTGAAATC-CTCGATCTGCTTCGCTGTAAGC 1 ACAGGGATGCCAAAT-CTGCTATCTTTC-ATCTGCTTCCCTATAAAC * * * ** * 66330388 ACA-AGAGTGTCAGATCTATTAT-TTTCGATTTG-TTCCCTATAAAC 1 ACAGGGA-TGCCAAATCTGCTATCTTTC-ATCTGCTTCCCTATAAAC * 66330432 ACAGGGATGCCAAATCTGCTATC-TTCAACTTGCTT-CCTATAAAC 1 ACAGGGATGCCAAATCTGCTATCTTTCATC-TGCTTCCCTATAAAC ** * * * * 66330476 ACAGGGATGCC--ATGCTGAAATCTTCCATCTGCTTCGCTGTAAGC 1 ACAGGGATGCCAAAT-CTGCTATCTTTCATCTGCTTCCCTATAAAC * * * 66330520 ACAGGAATG-TAAGATCTGCTATCTTTGATCTG-TTCCCTATAAAC 1 ACAGGGATGCCAA-ATCTGCTATCTTTCATCTGCTTCCCTATAAAC 66330564 ACAGGGATGCCAAATCT 1 ACAGGGATGCCAAATCT 66330581 TGTTTCTTTG Statistics Matches: 209, Mismatches: 49, Indels: 46 0.69 0.16 0.15 Matches are distributed among these distances: 42 5 0.02 43 24 0.11 44 142 0.68 45 31 0.15 46 7 0.03 ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31 Consensus pattern (45 bp): ACAGGGATGCCAAATCTGCTATCTTTCATCTGCTTCCCTATAAAC Found at i:66331442 original size:46 final size:46 Alignment explanation

Indices: 66331382--66331501 Score: 179 Period size: 46 Copynumber: 2.6 Consensus size: 46 66331372 TTTGACGTGA * * * * 66331382 TGCCATAGTGTCTTTCAACTATGGTCTTACTCCTTTTC-TGTCATGT 1 TGCCATGGTATCTTTCAACCATGGTCTTA-TCCTTTTCATGTCACGT * 66331428 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT 1 TGCCATGGTATCTTTCAACCATGGTCTTATCCTTTTCATGTCACGT 66331474 TGCCATGGTATCTTTCAACCATGGTCTT 1 TGCCATGGTATCTTTCAACCATGGTCTT 66331502 TGTAACACCC Statistics Matches: 68, Mismatches: 5, Indels: 2 0.91 0.07 0.03 Matches are distributed among these distances: 45 7 0.10 46 61 0.90 ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43 Consensus pattern (46 bp): TGCCATGGTATCTTTCAACCATGGTCTTATCCTTTTCATGTCACGT Found at i:66332339 original size:37 final size:37 Alignment explanation

Indices: 66332262--66332340 Score: 104 Period size: 37 Copynumber: 2.1 Consensus size: 37 66332252 TTATTACGAA * * * * 66332262 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG 1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATAGG * * 66332299 GTCTTACCCGGACAAAATCCCCACACGTAGTCATATG 1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATAGG 66332336 GTCTT 1 GTCTT 66332341 TAGAGCTCGG Statistics Matches: 36, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 37 36 1.00 ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25 Consensus pattern (37 bp): GTCTTACCCGGACAAAATCCCCACACGAAGTCATAGG Found at i:66332537 original size:47 final size:47 Alignment explanation

Indices: 66332459--66332648 Score: 308 Period size: 47 Copynumber: 4.0 Consensus size: 47 66332449 CCCTTCGGGA * * * * * * 66332459 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 66332506 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 66332553 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 66332600 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 66332647 CT 1 CT 66332649 CACTTTCACA Statistics Matches: 133, Mismatches: 10, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 47 133 1.00 ACGTcount: A:0.27, C:0.32, G:0.09, T:0.32 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:66332796 original size:47 final size:47 Alignment explanation

Indices: 66332720--66332838 Score: 148 Period size: 47 Copynumber: 2.5 Consensus size: 47 66332710 CTTCGGGACT * * * * 66332720 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC 1 TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC * * * * 66332767 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT 1 TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC * * 66332814 TATCACATATATATACATTCACATC 1 TATCACATATATACACTTTCACATC 66332839 ACAATTATCC Statistics Matches: 60, Mismatches: 12, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 47 60 1.00 ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32 Consensus pattern (47 bp): TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC Found at i:66334043 original size:7 final size:7 Alignment explanation

Indices: 66334023--66334114 Score: 130 Period size: 7 Copynumber: 12.6 Consensus size: 7 66334013 TTTAAAATAG 66334023 AAACCCT 1 AAACCCT 66334030 AAAACCCT 1 -AAACCCT 66334038 AAACCCT 1 AAACCCT 66334045 AAACCCT 1 AAACCCT 66334052 AAAACCCT 1 -AAACCCT 66334060 AAACCCCT 1 AAA-CCCT 66334068 AAACCCT 1 AAACCCT * 66334075 AAACCAT 1 AAACCCT * 66334082 AACCCCT 1 AAACCCT 66334089 AAACCCT 1 AAACCCT 66334096 AAACCCT 1 AAACCCT 66334103 AAAACCCT 1 -AAACCCT 66334111 AAAC 1 AAAC 66334115 TCGAAAAAGG Statistics Matches: 77, Mismatches: 4, Indels: 7 0.88 0.05 0.08 Matches are distributed among these distances: 7 49 0.64 8 28 0.36 ACGTcount: A:0.46, C:0.41, G:0.00, T:0.13 Consensus pattern (7 bp): AAACCCT Found at i:66334043 original size:15 final size:14 Alignment explanation

Indices: 66334023--66334114 Score: 130 Period size: 15 Copynumber: 6.3 Consensus size: 14 66334013 TTTAAAATAG 66334023 AAACCCTAAAACCCT 1 AAACCCT-AAACCCT 66334038 AAACCCTAAACCCT 1 AAACCCTAAACCCT 66334052 AAAACCCTAAACCCCT 1 -AAACCCTAAA-CCCT * 66334068 AAACCCTAAACCAT 1 AAACCCTAAACCCT * 66334082 AACCCCTAAACCCT 1 AAACCCTAAACCCT 66334096 AAACCCTAAAACCCT 1 AAACCCT-AAACCCT 66334111 AAAC 1 AAAC 66334115 TCGAAAAAGG Statistics Matches: 70, Mismatches: 4, Indels: 6 0.88 0.05 0.08 Matches are distributed among these distances: 14 28 0.40 15 38 0.54 16 4 0.06 ACGTcount: A:0.46, C:0.41, G:0.00, T:0.13 Consensus pattern (14 bp): AAACCCTAAACCCT Found at i:66343458 original size:15 final size:15 Alignment explanation

Indices: 66343428--66343458 Score: 55 Period size: 14 Copynumber: 2.1 Consensus size: 15 66343418 ATTCTGGTTC 66343428 AATTTCATTTAGAAA 1 AATTTCATTTAGAAA 66343443 AATTT-ATTTAGAAA 1 AATTTCATTTAGAAA 66343457 AA 1 AA 66343459 GAATATCTTT Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 11 0.69 15 5 0.31 ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39 Consensus pattern (15 bp): AATTTCATTTAGAAA Found at i:66346572 original size:84 final size:84 Alignment explanation

Indices: 66346431--66346603 Score: 346 Period size: 84 Copynumber: 2.1 Consensus size: 84 66346421 ATTTTGAAAA 66346431 TTAGGGTTCACTCAAAGTATGGACACTAAGTTAGCCTTTTTGAAAATCCCTATCTCGAAACAACA 1 TTAGGGTTCACTCAAAGTATGGACACTAAGTTAGCCTTTTTGAAAATCCCTATCTCGAAACAACA 66346496 AAACGCCATATCCAATAAG 66 AAACGCCATATCCAATAAG 66346515 TTAGGGTTCACTCAAAGTATGGACACTAAGTTAGCCTTTTTGAAAATCCCTATCTCGAAACAACA 1 TTAGGGTTCACTCAAAGTATGGACACTAAGTTAGCCTTTTTGAAAATCCCTATCTCGAAACAACA 66346580 AAACGCCATATCCAATAAG 66 AAACGCCATATCCAATAAG 66346599 TTAGG 1 TTAGG 66346604 ACATATTGCT Statistics Matches: 89, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 84 89 1.00 ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27 Consensus pattern (84 bp): TTAGGGTTCACTCAAAGTATGGACACTAAGTTAGCCTTTTTGAAAATCCCTATCTCGAAACAACA AAACGCCATATCCAATAAG Found at i:66347511 original size:23 final size:21 Alignment explanation

Indices: 66347460--66347521 Score: 61 Period size: 23 Copynumber: 2.7 Consensus size: 21 66347450 TCAAAATGTG * * 66347460 TAATATAAGTAAAGTAATTAT 1 TAATATAAGTAAAATAAGTAT 66347481 TGACATATAAGTAAAAATAAGTAT 1 T-A-ATATAAGT-AAAATAAGTAT 66347505 ATAATATAAGTTAAAAT 1 -TAATATAAG-TAAAAT 66347522 CTTTAATAAC Statistics Matches: 34, Mismatches: 2, Indels: 8 0.77 0.05 0.18 Matches are distributed among these distances: 21 1 0.03 22 1 0.03 23 20 0.59 24 11 0.32 25 1 0.03 ACGTcount: A:0.55, C:0.02, G:0.10, T:0.34 Consensus pattern (21 bp): TAATATAAGTAAAATAAGTAT Found at i:66347554 original size:14 final size:16 Alignment explanation

Indices: 66347535--66347566 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 66347525 TAATAACAAT 66347535 AATAT-ATAG-ATAAA 1 AATATAATAGTATAAA 66347549 AATATAATAGTATAAA 1 AATATAATAGTATAAA 66347565 AA 1 AA 66347567 ATGACATAAT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 14 5 0.31 15 4 0.25 16 7 0.44 ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28 Consensus pattern (16 bp): AATATAATAGTATAAA Found at i:66347662 original size:37 final size:33 Alignment explanation

Indices: 66347620--66347714 Score: 93 Period size: 37 Copynumber: 2.7 Consensus size: 33 66347610 TATATAATAT 66347620 ATATAAATAATTAATAAATATATAATACAAGTAAAA 1 ATATAAATAA-TAATAAATA-ATAATA-AAGTAAAA ** 66347656 AGTATAAATAATAATGTAAATAATAATAATTTAAAA 1 A-TATAAATAATAA--TAAATAATAATAAAGTAAAA 66347692 ATATATAATAAATAAT-AATAATA 1 ATATA-AAT-AATAATAAATAATA 66347715 TGAAATAATA Statistics Matches: 52, Mismatches: 2, Indels: 12 0.79 0.03 0.18 Matches are distributed among these distances: 34 7 0.13 35 5 0.10 36 14 0.27 37 20 0.38 38 6 0.12 ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33 Consensus pattern (33 bp): ATATAAATAATAATAAATAATAATAAAGTAAAA Found at i:66347682 original size:15 final size:14 Alignment explanation

Indices: 66347662--66347724 Score: 67 Period size: 15 Copynumber: 4.3 Consensus size: 14 66347652 AAAAAGTATA 66347662 AATAATAATGTAAAT 1 AATAATAAT-TAAAT 66347677 AATAATAATTTAAA- 1 AATAATAA-TTAAAT 66347691 AATATATAA-TAAAT 1 AATA-ATAATTAAAT 66347705 AATAATAATATGAAAT 1 AATAATAAT-T-AAAT 66347721 AATA 1 AATA 66347725 TAAGGTTAAT Statistics Matches: 42, Mismatches: 0, Indels: 11 0.79 0.00 0.21 Matches are distributed among these distances: 13 8 0.19 14 8 0.19 15 17 0.40 16 9 0.21 ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33 Consensus pattern (14 bp): AATAATAATTAAAT Found at i:66347704 original size:28 final size:28 Alignment explanation

Indices: 66347610--66347713 Score: 85 Period size: 28 Copynumber: 3.8 Consensus size: 28 66347600 GGTACATATG * 66347610 TATATAATATAT-ATAAATAA-TTAATAAA 1 TATATAATAAATAAT-AATAATTTAA-AAA * * 66347638 TATATAATACAAGTAA-AA-AGTATAAATAA 1 TATATAATA-AA-TAATAATAATTTAAA-AA * 66347667 TA-AT-GTAAATAATAATAATTTAAAAA 1 TATATAATAAATAATAATAATTTAAAAA 66347693 TATATAATAAATAATAATAAT 1 TATATAATAAATAATAATAAT 66347714 ATGAAATAAT Statistics Matches: 60, Mismatches: 7, Indels: 18 0.71 0.08 0.21 Matches are distributed among these distances: 25 3 0.05 26 8 0.13 27 10 0.17 28 27 0.45 29 10 0.17 30 1 0.02 31 1 0.02 ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35 Consensus pattern (28 bp): TATATAATAAATAATAATAATTTAAAAA Found at i:66349875 original size:131 final size:134 Alignment explanation

Indices: 66349634--66349907 Score: 509 Period size: 131 Copynumber: 2.1 Consensus size: 134 66349624 ATATATCATT * 66349634 TATGTATTAAATGTTATTTTATAATTATTATTTGATGTTATATTTTATGAACATGTACATTGATA 1 TATGT-TTTAATGTTATTTTATAATTATTATTTGATGTTATATTTTATGAACATGTACATTGATA 66349699 TTATATTATTTTTTATATATATTAAATTGTATATCATGCATCATTTTTTAATTATTACTTTATAT 65 TTATATTATTTTTTATATATATTAAATTGTATATCATGCATCATTTTTTAATTATTACTTTATAT 66349764 GTTTG 130 GTTTG 66349769 TATGTTTTAATGTTATTTTATAATTATTATTTGATGTTATATTTTATGAACATGTACATTGATA- 1 TATGTTTTAATGTTATTTTATAATTATTATTTGATGTTATATTTTATGAACATGTACATTGATAT 66349833 T-TATT-TTTTTTATATATATTAAATTGTATATCATGCATCATTTTTTAATTATTACTTTATATG 66 TATATTATTTTTTATATATATTAAATTGTATATCATGCATCATTTTTTAATTATTACTTTATATG 66349896 TTTG 131 TTTG 66349900 TATGTTTT 1 TATGTTTT 66349908 GTTTATTCGT Statistics Matches: 138, Mismatches: 1, Indels: 4 0.97 0.01 0.03 Matches are distributed among these distances: 131 70 0.51 132 4 0.03 133 1 0.01 134 58 0.42 135 5 0.04 ACGTcount: A:0.30, C:0.04, G:0.08, T:0.57 Consensus pattern (134 bp): TATGTTTTAATGTTATTTTATAATTATTATTTGATGTTATATTTTATGAACATGTACATTGATAT TATATTATTTTTTATATATATTAAATTGTATATCATGCATCATTTTTTAATTATTACTTTATATG TTTG Found at i:66350491 original size:210 final size:210 Alignment explanation

Indices: 66350126--66350544 Score: 793 Period size: 210 Copynumber: 2.0 Consensus size: 210 66350116 AACAAGATTC 66350126 CAAAGTTTTCAAAAATAAAAAGGCAATGCTTGGTGTTTGGAAGCTTCGAGAAAAGTAGTGCCCTA 1 CAAAGTTTTCAAAAATAAAAAGGCAATGCTTGGTGTTTGGAAGCTTCGAGAAAAGTAGTGCCCTA * 66350191 ACTTATTGGGTTGCAATTTTTCTCGTTGAGTTCGAATAGTCAAGTACCCTTCTAAGTTTTTTAAA 66 ACTTATTGGGTTGCAATTTTTCTCGTTGAGTTCAAATAGTCAAGTACCCTTCTAAGTTTTTTAAA * * 66350256 ATTTTCAAAATATGAGCATCTGTCTTGGAATTTCAAAGCGTTGTGTCCTAACTTACTGGATGTGG 131 ATTTTCAAAATATGAGCAACTGTCTTGAAATTTCAAAGCGTTGTGTCCTAACTTACTGGATGTGG 66350321 CGTTTTGTCGTTTCA 196 CGTTTTGTCGTTTCA * 66350336 CAAAGTTTTCAAAAATAAAAAGGCAATGCTTGGTGTTTGGAAGCTTCGAGAAAAGTAGTGTCCTA 1 CAAAGTTTTCAAAAATAAAAAGGCAATGCTTGGTGTTTGGAAGCTTCGAGAAAAGTAGTGCCCTA 66350401 ACTTATTGGGTTGCAATTTTTCTCGTTGAGTTCAAATAGTCAAGTACCCTTCTAAGTTTTTTAAA 66 ACTTATTGGGTTGCAATTTTTCTCGTTGAGTTCAAATAGTCAAGTACCCTTCTAAGTTTTTTAAA * 66350466 ATTTTCAAAATATGAGCAACTGTCTTGAAATTTCAAAGCGTTGTGTCCTAACTTACTGGGTGTGG 131 ATTTTCAAAATATGAGCAACTGTCTTGAAATTTCAAAGCGTTGTGTCCTAACTTACTGGATGTGG 66350531 CGTTTTGTCGTTTC 196 CGTTTTGTCGTTTC 66350545 GAAATAGGGA Statistics Matches: 204, Mismatches: 5, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 210 204 1.00 ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37 Consensus pattern (210 bp): CAAAGTTTTCAAAAATAAAAAGGCAATGCTTGGTGTTTGGAAGCTTCGAGAAAAGTAGTGCCCTA ACTTATTGGGTTGCAATTTTTCTCGTTGAGTTCAAATAGTCAAGTACCCTTCTAAGTTTTTTAAA ATTTTCAAAATATGAGCAACTGTCTTGAAATTTCAAAGCGTTGTGTCCTAACTTACTGGATGTGG CGTTTTGTCGTTTCA Found at i:66362557 original size:206 final size:206 Alignment explanation

Indices: 66362192--66363120 Score: 1441 Period size: 206 Copynumber: 4.5 Consensus size: 206 66362182 GCAGATCTGG * ** * 66362192 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGAGTACAAGGAGCAAATCGAAGACATAGCT 1 CTGAAGC-AGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAATCGAAGACATAGCT * * * 66362257 GATTTGG-TTTC-CGCATGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTTTGTATTGTT 65 GATTTGGCTTTCACG--TGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTC * 66362320 AGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAAACACATAGCAGATCCAACC 128 AGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCCAACC 66362385 TTCAGATGTTTATA 193 TTCAGATGTTTATA * 66362399 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG 1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAATCGAAGACATAGCTG * 66362464 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAAA 66 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA * * * 66362529 GAACAAATCAAAGTTTGGCGTTTCCATATTCGACGGAGGGCAGGCACATAGTAGATCCAACCTTC 131 GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCCAACCTTC * 66362594 AGATATTTATA 196 AGATGTTTATA * * 66362605 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGAGCTTACAAGGAGAAAAAAT-AAAGACATAGC 1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAG--AAAATCGAAGACATAGC 66362669 TGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA 64 TGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA * * * 66362734 GAGAACAAATCAAAGTTTGGCGTCTCCAAATTCGATGGAGGGCAGACACATAGTAGATCCAACCT 129 GAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCCAACCT 66362799 TCAGATGTTTATA 194 TCAGATGTTTATA 66362812 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAATCGAAGACATAGCTG 1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAATCGAAGACATAGCTG * 66362877 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATAATTTGGCATCTCTGTATTGTCAGA 66 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA * * * * * * * 66362942 GAACAAATCGAAGTTTGGCGTTTCCATATTCGACAGAGAGCAGACACATAACAGATCTAACTTTC 131 GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCCAACCTTC * * * 66363007 AGACGATTAGA 196 AGATGTTTATA * * * * * * * 66363018 CTGAAGCAAATCCAAGATGATTTGGCATCCTTGTGGTCACAATGAGAAAATCGAAGACATAGCAG 1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAATCGAAGACATAGCTG * * 66363083 ATTTGGCTTTCACGTGTTTACATTGAAGCAAATCTAAG 66 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAG 66363121 CATCTCTATA Statistics Matches: 671, Mismatches: 46, Indels: 11 0.92 0.06 0.02 Matches are distributed among these distances: 205 5 0.01 206 457 0.68 207 203 0.30 208 6 0.01 ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28 Consensus pattern (206 bp): CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAATCGAAGACATAGCTG ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCCAACCTTC AGATGTTTATA Found at i:66362959 original size:413 final size:412 Alignment explanation

Indices: 66362192--66363120 Score: 1470 Period size: 413 Copynumber: 2.2 Consensus size: 412 66362182 GCAGATCTGG * * 66362192 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGAGTACAAGGAGCAAATCGAAGACATAGCT 1 CTGAAGC-AGATCCAAGATGGTTTGGCATCCTTGTGATTACAAGGAGAAAATCGAAGACATAGCT * * * 66362257 GATTTGG-TTTC-CGCATGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTTTGTATTGTT 65 GATTTGGCTTTCACG--TGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTC * 66362320 AGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAAACACATAGCAGATCCAACC 128 AGAGAACAAATCAAAGTTTGGCGTCTCCAAATTCGACGGAGGGCAAACACATAGCAGATCCAACC * 66362385 TTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAAT 193 TTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAAT * 66362450 CGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATC 258 CGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATAATTTGGCATC * * * * 66362515 TCTGTATTGTCAAAGAACAAATCAAAGTTTGGCGTTTCCATATTCGACGGAGGGCAGGCACATAG 323 TCTGTATTGTCAAAGAACAAATCAAAGTTTGGCGTTTCCATATTCGACAGAGAGCAGACACATAA * * * 66362580 TAGATCCAACCTTCAGA-TATTTATA 388 CAGATCCAACCTTCAGACGA-TTAGA * * * * 66362605 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGAGCTTACAAGGAGAAAAAAT-AAAGACATAGC 1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGATTACAAGGAG--AAAATCGAAGACATAGC 66362669 TGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA 64 TGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA * * * 66362734 GAGAACAAATCAAAGTTTGGCGTCTCCAAATTCGATGGAGGGCAGACACATAGTAGATCCAACCT 129 GAGAACAAATCAAAGTTTGGCGTCTCCAAATTCGACGGAGGGCAAACACATAGCAGATCCAACCT 66362799 TCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAATC 194 TCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAATC 66362864 GAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATAATTTGGCATCT 259 GAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATAATTTGGCATCT * * 66362929 CTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTTTCCATATTCGACAGAGAGCAGACACATAAC 324 CTGTATTGTCAAAGAACAAATCAAAGTTTGGCGTTTCCATATTCGACAGAGAGCAGACACATAAC * * 66362994 AGATCTAACTTTCAGACGATTAGA 389 AGATCCAACCTTCAGACGATTAGA * * * * * * 66363018 CTGAAGCAAATCCAAGATGATTTGGCATCCTTGTGGTCACAATGAGAAAATCGAAGACATAGCAG 1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGATTACAAGGAGAAAATCGAAGACATAGCTG * * 66363083 ATTTGGCTTTCACGTGTTTACATTGAAGCAAATCTAAG 66 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAG 66363121 CATCTCTATA Statistics Matches: 473, Mismatches: 37, Indels: 13 0.90 0.07 0.02 Matches are distributed among these distances: 411 5 0.01 412 82 0.17 413 375 0.79 414 9 0.02 415 2 0.00 ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28 Consensus pattern (412 bp): CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGATTACAAGGAGAAAATCGAAGACATAGCTG ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA GAACAAATCAAAGTTTGGCGTCTCCAAATTCGACGGAGGGCAAACACATAGCAGATCCAACCTTC AGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAATCGA AGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATAATTTGGCATCTCT GTATTGTCAAAGAACAAATCAAAGTTTGGCGTTTCCATATTCGACAGAGAGCAGACACATAACAG ATCCAACCTTCAGACGATTAGA Found at i:66364757 original size:38 final size:38 Alignment explanation

Indices: 66364687--66364770 Score: 109 Period size: 38 Copynumber: 2.2 Consensus size: 38 66364677 TGACTATATG * * 66364687 TAGAGATTATGTCCGGCTAAAGACCCGATGGCTAT-GTA 1 TAGAGATTATGTCCGGATAAAGACCCGATGGCT-TCATA * 66364725 TAGAGATTATGTCCGGATTAAGACCC-ACTGGCTTCATA 1 TAGAGATTATGTCCGGATAAAGACCCGA-TGGCTTCATA 66364763 TAGAGATT 1 TAGAGATT 66364771 TCATCCGAGC Statistics Matches: 41, Mismatches: 3, Indels: 4 0.85 0.06 0.08 Matches are distributed among these distances: 37 2 0.05 38 39 0.95 ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29 Consensus pattern (38 bp): TAGAGATTATGTCCGGATAAAGACCCGATGGCTTCATA Found at i:66364859 original size:40 final size:40 Alignment explanation

Indices: 66364802--66365033 Score: 365 Period size: 40 Copynumber: 5.8 Consensus size: 40 66364792 ACGATGATCT * * 66364802 GGGCTAAGTCCCGAAGGGCATTCGTGCTGGTGTTATATCC 1 GGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCC * * 66364842 TGGCTAAATCCCAAAGGGCATTCGTGCCGGTGTTATATCC 1 GGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCC * 66364882 GGGCTAAATCTCGAAGGGCATTCGTGCCGGTGTTATATCC 1 GGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCC * 66364922 GGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATTC 1 GGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCC * * * 66364962 GGGCTAAATCCTGAAGGGTATTCGTGCCGATGTTATATCC 1 GGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCC * * 66365002 GGGCTAAGTCCCGAAGGGCATTCGTGCAGGTG 1 GGGCTAAATCCCGAAGGGCATTCGTGCCGGTG 66365034 ATATGTATTC Statistics Matches: 174, Mismatches: 18, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 40 174 1.00 ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27 Consensus pattern (40 bp): GGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCC Found at i:66369493 original size:47 final size:47 Alignment explanation

Indices: 66369442--66369546 Score: 192 Period size: 47 Copynumber: 2.2 Consensus size: 47 66369432 TAGTATTAAT * 66369442 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA 1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA 66369489 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA 1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA * 66369536 AATGTGATAAG 1 TATGTGATAAG 66369547 TCCCGAAGGG Statistics Matches: 56, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 47 56 1.00 ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28 Consensus pattern (47 bp): TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA Found at i:66383824 original size:27 final size:27 Alignment explanation

Indices: 66383786--66383898 Score: 133 Period size: 27 Copynumber: 4.2 Consensus size: 27 66383776 AGCATGGCTG * * 66383786 CCAGA-ACAGATAATGTGACAGAGTCA 1 CCAGATACAGATAATGTGGCAGAGCCA * 66383812 CCAGATATAGATAATCGTGGCAGAGCCA 1 CCAGATACAGATAAT-GTGGCAGAGCCA 66383840 CCAGA-ACAGATATATGTGGCAGAGCCA 1 CCAGATACAGATA-ATGTGGCAGAGCCA * * 66383867 CCAGAT-CAGATATTTGTGGCATAGCCA 1 CCAGATACAGATA-ATGTGGCAGAGCCA 66383894 CCAGA 1 CCAGA 66383899 ACGCTTCCTC Statistics Matches: 77, Mismatches: 6, Indels: 7 0.86 0.07 0.08 Matches are distributed among these distances: 26 5 0.06 27 55 0.71 28 17 0.22 ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18 Consensus pattern (27 bp): CCAGATACAGATAATGTGGCAGAGCCA Found at i:66383850 original size:54 final size:54 Alignment explanation

Indices: 66383786--66383900 Score: 160 Period size: 54 Copynumber: 2.1 Consensus size: 54 66383776 AGCATGGCTG * * 66383786 CCAGAACAGATA-ATGTGACAGAGTCACCAGATATAGATAATCGTGGCAGAGCCA 1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA * * * * 66383840 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA 1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA 66383894 CCAGAAC 1 CCAGAAC 66383901 GCTTCCTCCA Statistics Matches: 54, Mismatches: 6, Indels: 2 0.87 0.10 0.03 Matches are distributed among these distances: 54 36 0.67 55 18 0.33 ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17 Consensus pattern (54 bp): CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA Found at i:66385556 original size:26 final size:26 Alignment explanation

Indices: 66385518--66385601 Score: 141 Period size: 26 Copynumber: 3.2 Consensus size: 26 66385508 CATGAAATTC * * 66385518 TTATCATGAAACATTTACCTAACCCA 1 TTATCATGGAACATTTACCTAACCTA * 66385544 TTATTATGGAACATTTACCTAACCTA 1 TTATCATGGAACATTTACCTAACCTA 66385570 TTATCATGGAACATTTACCTAACCTA 1 TTATCATGGAACATTTACCTAACCTA 66385596 TTATCA 1 TTATCA 66385602 ATTTGTATCA Statistics Matches: 54, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 26 54 1.00 ACGTcount: A:0.36, C:0.23, G:0.06, T:0.36 Consensus pattern (26 bp): TTATCATGGAACATTTACCTAACCTA Found at i:66403751 original size:36 final size:36 Alignment explanation

Indices: 66403704--66403776 Score: 128 Period size: 36 Copynumber: 2.0 Consensus size: 36 66403694 CGGGCCGGGC 66403704 AACAAGTGTTACATAGCTTACAGTACTTGTTCAATA 1 AACAAGTGTTACATAGCTTACAGTACTTGTTCAATA * * 66403740 AACAAGTGTTACATAGCTTTCAGTAGTTGTTCAATA 1 AACAAGTGTTACATAGCTTACAGTACTTGTTCAATA 66403776 A 1 A 66403777 GTTAGGTTAG Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 36 35 1.00 ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34 Consensus pattern (36 bp): AACAAGTGTTACATAGCTTACAGTACTTGTTCAATA Found at i:66408745 original size:29 final size:29 Alignment explanation

Indices: 66408678--66408829 Score: 136 Period size: 29 Copynumber: 5.3 Consensus size: 29 66408668 ACCCCTACAT * * 66408678 ACATGCATATGGCCCA-CTATGCCC-ATTC 1 ACATTCATATGGCCCATCT-GGCCCAATTC * * 66408706 TCATTTATATGGCCCATCTGGCCCAATTC 1 ACATTCATATGGCCCATCTGGCCCAATTC * * * 66408735 ACGTTCATATGACCCATCAGGCCCAATTC 1 ACATTCATATGGCCCATCTGGCCCAATTC * 66408764 ACATTCATATAGCCCAT-TAGGCCCAATCTC 1 ACATTCATATGGCCCATCT-GGCCCAAT-TC * * * 66408794 A-TTTC-TATGGCCCATCCGGCCCAAATC 1 ACATTCATATGGCCCATCTGGCCCAATTC 66408821 ACATT-ATAT 1 ACATTCATAT 66408830 TCATGCTCAC Statistics Matches: 99, Mismatches: 18, Indels: 14 0.76 0.14 0.11 Matches are distributed among these distances: 27 3 0.03 28 38 0.38 29 55 0.56 30 3 0.03 ACGTcount: A:0.26, C:0.33, G:0.12, T:0.28 Consensus pattern (29 bp): ACATTCATATGGCCCATCTGGCCCAATTC Found at i:66408787 original size:58 final size:56 Alignment explanation

Indices: 66408710--66408829 Score: 145 Period size: 57 Copynumber: 2.1 Consensus size: 56 66408700 CCATTCTCAT * 66408710 TTATATGGCCCATCTGGCCCAAT-TCACGTTCATATGACCCATCAGGCCCAATTCACA 1 TTATATAGCCCATCTGGCCCAATCTCA-GTTC-TATGACCCATCAGGCCCAATTCACA * * * * 66408767 TTCATATAGCCCAT-TAGGCCCAATCTCATTTCTATGGCCCATCCGGCCCAAATCACA 1 TT-ATATAGCCCATCT-GGCCCAATCTCAGTTCTATGACCCATCAGGCCCAATTCACA 66408824 TTATAT 1 TTATAT 66408830 TCATGCTCAC Statistics Matches: 55, Mismatches: 5, Indels: 7 0.82 0.07 0.10 Matches are distributed among these distances: 56 4 0.07 57 27 0.49 58 21 0.38 59 3 0.05 ACGTcount: A:0.27, C:0.33, G:0.12, T:0.28 Consensus pattern (56 bp): TTATATAGCCCATCTGGCCCAATCTCAGTTCTATGACCCATCAGGCCCAATTCACA Found at i:66412732 original size:29 final size:29 Alignment explanation

Indices: 66412661--66412812 Score: 143 Period size: 29 Copynumber: 5.3 Consensus size: 29 66412651 ACCCCTACAT * * 66412661 ACATGCATATGGCCCA-CTAGGTCCAA-TC 1 ACATTCATATGGCCCATC-AGGCCCAATTC * * * * * 66412689 TCATTTATATAGCCCATCCGACCCAATTC 1 ACATTCATATGGCCCATCAGGCCCAATTC * 66412718 ACGTTCATATGGCCCATCAGGCCCAATTC 1 ACATTCATATGGCCCATCAGGCCCAATTC * 66412747 ACATTCATATGGCCCATTAGGCCCAATCTC 1 ACATTCATATGGCCCATCAGGCCCAAT-TC * * * 66412777 A-TTTC-TATGGCCCATCCGGCCCAAATC 1 ACATTCATATGGCCCATCAGGCCCAATTC 66412804 ACATT-ATAT 1 ACATTCATAT 66412813 TCATGCTCAC Statistics Matches: 99, Mismatches: 20, Indels: 10 0.77 0.16 0.08 Matches are distributed among these distances: 27 3 0.03 28 39 0.39 29 54 0.55 30 3 0.03 ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27 Consensus pattern (29 bp): ACATTCATATGGCCCATCAGGCCCAATTC Found at i:66412744 original size:57 final size:58 Alignment explanation

Indices: 66412666--66412812 Score: 151 Period size: 57 Copynumber: 2.6 Consensus size: 58 66412656 TACATACATG * * * * 66412666 CATATGGCCCA-CTAGGTCCAA-TCTCATTTATATAGCCCATCCGACCCAAT-TCACGTT 1 CATATGGCCCATC-AGGCCCAATTCACATTCATATAGCCCATCAGACCCAATCTCA-GTT * * * * 66412723 CATATGGCCCATCAGGCCCAATTCACATTCATATGGCCCATTAGGCCCAATCTCATTT 1 CATATGGCCCATCAGGCCCAATTCACATTCATATAGCCCATCAGACCCAATCTCAGTT * * 66412781 C-TATGGCCCATCCGGCCCAAATCACATT-ATAT 1 CATATGGCCCATCAGGCCCAATTCACATTCATAT 66412813 TCATGCTCAC Statistics Matches: 77, Mismatches: 10, Indels: 7 0.82 0.11 0.07 Matches are distributed among these distances: 56 4 0.05 57 43 0.56 58 27 0.35 59 3 0.04 ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27 Consensus pattern (58 bp): CATATGGCCCATCAGGCCCAATTCACATTCATATAGCCCATCAGACCCAATCTCAGTT Found at i:66412894 original size:17 final size:17 Alignment explanation

Indices: 66412872--66412912 Score: 73 Period size: 17 Copynumber: 2.4 Consensus size: 17 66412862 TGCCTAATAT 66412872 GGGCCCAATAGCCCCTC 1 GGGCCCAATAGCCCCTC 66412889 GGGCCCAATAGCCCCTC 1 GGGCCCAATAGCCCCTC * 66412906 GAGCCCA 1 GGGCCCA 66412913 TTTAGCCCAT Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 17 23 1.00 ACGTcount: A:0.20, C:0.46, G:0.24, T:0.10 Consensus pattern (17 bp): GGGCCCAATAGCCCCTC Found at i:66423265 original size:36 final size:36 Alignment explanation

Indices: 66423224--66423298 Score: 141 Period size: 36 Copynumber: 2.1 Consensus size: 36 66423214 CTTCCTTGTC 66423224 CTAATTTTTTCCAAGAACTTAAAATTGGTCAAATTT 1 CTAATTTTTTCCAAGAACTTAAAATTGGTCAAATTT * 66423260 CTAATTTTTTCCATGAACTTAAAATTGGTCAAATTT 1 CTAATTTTTTCCAAGAACTTAAAATTGGTCAAATTT 66423296 CTA 1 CTA 66423299 TTTAAGATCT Statistics Matches: 38, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 36 38 1.00 ACGTcount: A:0.35, C:0.15, G:0.08, T:0.43 Consensus pattern (36 bp): CTAATTTTTTCCAAGAACTTAAAATTGGTCAAATTT Found at i:66423974 original size:85 final size:85 Alignment explanation

Indices: 66423848--66424016 Score: 320 Period size: 85 Copynumber: 2.0 Consensus size: 85 66423838 AAACACATCA * 66423848 TGAATCTTCTCTAATTCAGGTGGTAGCGCTAGCCGATATGCCACTAGTCCAACTTTTTCAATTAT 1 TGAATCTTCTCTAATTCAGGTGGTAGCGCTAGCCGATATGCCACCAGTCCAACTTTTTCAATTAT 66423913 TTCATACGATCCAATAAAAG 66 TTCATACGATCCAATAAAAG 66423933 TGAATCTTCTCTAATTCAGGTGGTAGCGCTAGCCGATATGCCACCAGTCCAACTTTTTCAATTAT 1 TGAATCTTCTCTAATTCAGGTGGTAGCGCTAGCCGATATGCCACCAGTCCAACTTTTTCAATTAT * 66423998 TTCATACGGTCCAATAAAA 66 TTCATACGATCCAATAAAA 66424017 CACGGACTTA Statistics Matches: 82, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 85 82 1.00 ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33 Consensus pattern (85 bp): TGAATCTTCTCTAATTCAGGTGGTAGCGCTAGCCGATATGCCACCAGTCCAACTTTTTCAATTAT TTCATACGATCCAATAAAAG Found at i:66426193 original size:113 final size:113 Alignment explanation

Indices: 66425995--66426219 Score: 441 Period size: 113 Copynumber: 2.0 Consensus size: 113 66425985 TGTCCAGGTA 66425995 TGGCCGAAATATGCGATTCATTAAGTCCATAAACACAGCAGGAGCATTTGTCAACCCGAATGGCA 1 TGGCCGAAATATGCGATTCATTAAGTCCATAAACACAGCAGGAGCATTTGTCAACCCGAATGGCA 66426060 TAACTAAAAATTCATAATGACCGTACCTTGTTCTAAAAGCAGTTTTAT 66 TAACTAAAAATTCATAATGACCGTACCTTGTTCTAAAAGCAGTTTTAT * 66426108 TGGCCGAAATATGCGATTCATTAAGTCCATAAACACAGCAGGAGTATTTGTCAACCCGAATGGCA 1 TGGCCGAAATATGCGATTCATTAAGTCCATAAACACAGCAGGAGCATTTGTCAACCCGAATGGCA 66426173 TAACTAAAAATTCATAATGACCGTACCTTGTTCTAAAAGCAGTTTTA 66 TAACTAAAAATTCATAATGACCGTACCTTGTTCTAAAAGCAGTTTTA 66426220 GGCACATCTG Statistics Matches: 111, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 113 111 1.00 ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28 Consensus pattern (113 bp): TGGCCGAAATATGCGATTCATTAAGTCCATAAACACAGCAGGAGCATTTGTCAACCCGAATGGCA TAACTAAAAATTCATAATGACCGTACCTTGTTCTAAAAGCAGTTTTAT Found at i:66437082 original size:17 final size:18 Alignment explanation

Indices: 66437060--66437099 Score: 55 Period size: 17 Copynumber: 2.3 Consensus size: 18 66437050 GTATGAAAGG * * 66437060 AATTAATTTATTGTAT-A 1 AATTAATATATTGCATGA 66437077 AATTAATATATTGCATGA 1 AATTAATATATTGCATGA 66437095 AATTA 1 AATTA 66437100 TTACTTTAGA Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 17 14 0.70 18 6 0.30 ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45 Consensus pattern (18 bp): AATTAATATATTGCATGA Found at i:66449668 original size:36 final size:36 Alignment explanation

Indices: 66449621--66449693 Score: 137 Period size: 36 Copynumber: 2.0 Consensus size: 36 66449611 CGGGCCGGGC 66449621 AACAAGTGTTACATAGCTTACAGTACTTGTTCAATA 1 AACAAGTGTTACATAGCTTACAGTACTTGTTCAATA * 66449657 AACAAGTGTTACATAGCTTACAGTAGTTGTTCAATA 1 AACAAGTGTTACATAGCTTACAGTACTTGTTCAATA 66449693 A 1 A 66449694 GTTAGGTTAG Statistics Matches: 36, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 36 36 1.00 ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33 Consensus pattern (36 bp): AACAAGTGTTACATAGCTTACAGTACTTGTTCAATA Found at i:66453715 original size:17 final size:18 Alignment explanation

Indices: 66453693--66453726 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 66453683 CACATTGAAG 66453693 TGTTTT-AGTGAAAACCT 1 TGTTTTCAGTGAAAACCT * 66453710 TGTTTTCATTGAAAACC 1 TGTTTTCAGTGAAAACC 66453727 CTTCCTTAAG 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:0.29, C:0.15, G:0.15, T:0.41 Consensus pattern (18 bp): TGTTTTCAGTGAAAACCT Found at i:66454833 original size:29 final size:29 Alignment explanation

Indices: 66454766--66454911 Score: 131 Period size: 29 Copynumber: 5.1 Consensus size: 29 66454756 ACCCCTACAT * * 66454766 ACATGCATATGGCCCA-CTATGCCC-ATTC 1 ACATTCATATGGCCCATCT-GGCCCAATTC * * 66454794 TCATTTATATGGCCCATCTGGCCCAATTC 1 ACATTCATATGGCCCATCTGGCCCAATTC * * * 66454823 ACGTTCATATGACCCATCAGGCCCAATTC 1 ACATTCATATGGCCCATCTGGCCCAATTC * 66454852 ACATTCATATAGCCCAT-TAGGCCCAATCTC 1 ACATTCATATGGCCCATCT-GGCCCAAT-TC * * * 66454882 A-TTTC-TATGGCCCATCCGGCCCAAATC 1 ACATTCATATGGCCCATCTGGCCCAATTC 66454909 ACA 1 ACA 66454912 GTATATTCAT Statistics Matches: 94, Mismatches: 18, Indels: 12 0.76 0.15 0.10 Matches are distributed among these distances: 27 3 0.03 28 33 0.35 29 55 0.59 30 3 0.03 ACGTcount: A:0.26, C:0.34, G:0.13, T:0.27 Consensus pattern (29 bp): ACATTCATATGGCCCATCTGGCCCAATTC Found at i:66455136 original size:16 final size:16 Alignment explanation

Indices: 66455117--66455152 Score: 54 Period size: 16 Copynumber: 2.2 Consensus size: 16 66455107 AACTTTCGGC 66455117 TTTTCGGCATTTCAGA 1 TTTTCGGCATTTCAGA * * 66455133 TTTTCGGTATTTCAGC 1 TTTTCGGCATTTCAGA 66455149 TTTT 1 TTTT 66455153 ACCGATCTAC Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.14, C:0.17, G:0.17, T:0.53 Consensus pattern (16 bp): TTTTCGGCATTTCAGA Found at i:66459406 original size:57 final size:58 Alignment explanation

Indices: 66459343--66459489 Score: 160 Period size: 57 Copynumber: 2.6 Consensus size: 58 66459333 TACATACATG * * * * 66459343 CATATGGCCCA-CTAGGTCCAA-TCTCATTTATATAGCCCATTCGACCCAAT-TCACGTT 1 CATATGGCCCATC-AGGCCCAATTCACATTCATATAGCCCATTAGACCCAATCTCA-GTT * * * 66459400 CATATGGCCCATCAGGCCCAATTCACATTCATATGGCCCATTAGGCCCAATCTCATTT 1 CATATGGCCCATCAGGCCCAATTCACATTCATATAGCCCATTAGACCCAATCTCAGTT * * 66459458 C-TATGGCCCATCCGGCCCAAATCACATT-ATAT 1 CATATGGCCCATCAGGCCCAATTCACATTCATAT 66459490 TCATGCTCAC Statistics Matches: 78, Mismatches: 9, Indels: 7 0.83 0.10 0.07 Matches are distributed among these distances: 56 4 0.05 57 43 0.55 58 28 0.36 59 3 0.04 ACGTcount: A:0.27, C:0.33, G:0.13, T:0.28 Consensus pattern (58 bp): CATATGGCCCATCAGGCCCAATTCACATTCATATAGCCCATTAGACCCAATCTCAGTT Found at i:66459409 original size:29 final size:29 Alignment explanation

Indices: 66459338--66459489 Score: 134 Period size: 29 Copynumber: 5.3 Consensus size: 29 66459328 ACCCCTACAT * * * * 66459338 ACATGCATATGGCCCACTAGGTCCAA-TC 1 ACATTCATATGGCCCATTCGGCCCAATTC * * * * 66459366 TCATTTATATAGCCCATTCGACCCAATTC 1 ACATTCATATGGCCCATTCGGCCCAATTC * 66459395 ACGTTCATATGGCCCA-TCAGGCCCAATTC 1 ACATTCATATGGCCCATTC-GGCCCAATTC * 66459424 ACATTCATATGGCCCATTAGGCCCAATCTC 1 ACATTCATATGGCCCATTCGGCCCAAT-TC * * * 66459454 A-TTTC-TATGGCCCATCCGGCCCAAATC 1 ACATTCATATGGCCCATTCGGCCCAATTC 66459481 ACATT-ATAT 1 ACATTCATAT 66459490 TCATGCTCAC Statistics Matches: 98, Mismatches: 20, Indels: 12 0.75 0.15 0.09 Matches are distributed among these distances: 27 3 0.03 28 42 0.43 29 49 0.50 30 4 0.04 ACGTcount: A:0.27, C:0.32, G:0.13, T:0.28 Consensus pattern (29 bp): ACATTCATATGGCCCATTCGGCCCAATTC Found at i:66459571 original size:17 final size:17 Alignment explanation

Indices: 66459549--66459589 Score: 73 Period size: 17 Copynumber: 2.4 Consensus size: 17 66459539 TGCCTAATAT 66459549 GGGCCCAATAGCCCCTC 1 GGGCCCAATAGCCCCTC 66459566 GGGCCCAATAGCCCCTC 1 GGGCCCAATAGCCCCTC * 66459583 GAGCCCA 1 GGGCCCA 66459590 TTTAGCCCAT Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 17 23 1.00 ACGTcount: A:0.20, C:0.46, G:0.24, T:0.10 Consensus pattern (17 bp): GGGCCCAATAGCCCCTC Found at i:66469579 original size:225 final size:225 Alignment explanation

Indices: 66469257--66469703 Score: 867 Period size: 225 Copynumber: 2.0 Consensus size: 225 66469247 TTATCAACCC 66469257 GAGGGTTAAGAACATACCTGTCCAAAGTGTCCATTTCACAACACTTACCAATACGTCGCTTGCAT 1 GAGGGTTAAGAACATACCTGTCCAAAGTGTCCATTTCACAACACTTACCAATACGTCGCTTGCAT 66469322 CTTAAGTGTTCTTTCATTTCACTAGAAATTTCACCCGTTGAACACATCGGAATACAACTCGGATA 66 CTTAAGTGTTCTTTCATTTCACTAGAAATTTCACCCGTTGAACACATCGGAATACAACTCGGATA 66469387 CACGGATAATTTGCACATAAGTGCCTCATATGTAATCAAGAAATCATGTAACCCGCCCCTAAGTG 131 CACGGATAATTTGCACATAAGTGCCTCATATGTAATCAAGAAATCATGTAACCCGCCCCTAAGTG 66469452 AACTCAGACTCAACTCAACGAGCTCGGCCG 196 AACTCAGACTCAACTCAACGAGCTCGGCCG 66469482 GAGGGTTAAGAACATACCTGTCCAAAGTGTCCATTTCACAACACTTACCAATACGTCGCTTGCAT 1 GAGGGTTAAGAACATACCTGTCCAAAGTGTCCATTTCACAACACTTACCAATACGTCGCTTGCAT 66469547 CTTAAGTGTTCTTTCATTTCACTAGAAATTTCACCCGTTGAACACATCGGAATACAACTCGGATA 66 CTTAAGTGTTCTTTCATTTCACTAGAAATTTCACCCGTTGAACACATCGGAATACAACTCGGATA * 66469612 CACGGATAATTTGTACATAAGTGCCTCATATGTAATCAAGAAATCATGTAACCCGCCCCTAAGTG 131 CACGGATAATTTGCACATAAGTGCCTCATATGTAATCAAGAAATCATGTAACCCGCCCCTAAGTG * * 66469677 AACTCGGACTCAACTCAACGAGTTCGG 196 AACTCAGACTCAACTCAACGAGCTCGG 66469704 ATGCTCAACC Statistics Matches: 219, Mismatches: 3, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 225 219 1.00 ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26 Consensus pattern (225 bp): GAGGGTTAAGAACATACCTGTCCAAAGTGTCCATTTCACAACACTTACCAATACGTCGCTTGCAT CTTAAGTGTTCTTTCATTTCACTAGAAATTTCACCCGTTGAACACATCGGAATACAACTCGGATA CACGGATAATTTGCACATAAGTGCCTCATATGTAATCAAGAAATCATGTAACCCGCCCCTAAGTG AACTCAGACTCAACTCAACGAGCTCGGCCG Found at i:66477207 original size:93 final size:93 Alignment explanation

Indices: 66477098--66477268 Score: 297 Period size: 93 Copynumber: 1.8 Consensus size: 93 66477088 GCCCCTAAGT * * * 66477098 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA * 66477163 TGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 66477191 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 66477256 CGAGTTCGGATGC 66 CGAGTTCGGATGC 66477269 TCAACCATCC Statistics Matches: 73, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 93 73 1.00 ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22 Consensus pattern (93 bp): GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:66477265 original size:46 final size:46 Alignment explanation

Indices: 66477093--66477265 Score: 201 Period size: 46 Copynumber: 3.7 Consensus size: 46 66477083 AACCCGCCCC * * * 66477093 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA * * 66477139 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT-C- 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA * * * 66477187 TCA-CGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA 66477232 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 66477266 TGCTCAACCA Statistics Matches: 105, Mismatches: 13, Indels: 18 0.77 0.10 0.13 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 44 2 0.02 45 2 0.02 46 59 0.56 47 27 0.26 48 2 0.02 49 2 0.02 50 3 0.03 51 2 0.02 ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22 Consensus pattern (46 bp): TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA Done.