Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A01

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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31

Warning! 5450143 characters in sequence are not A, C, G, or T


File 113 of 349

Found at i:35547127 original size:29 final size:29

Alignment explanation

Indices: 35547088--35547166 Score: 106 Period size: 29 Copynumber: 2.7 Consensus size: 29 35547078 CTTAATAATC * 35547088 AACCACGCACACTTAGTGCCATGTACTTT-A 1 AACC-CGCACACTTAGTGCCATGCA-TTTCA * 35547118 AACTCGCACACTTAGTGCCATGCATTTCA 1 AACCCGCACACTTAGTGCCATGCATTTCA * 35547147 AGCCCGCACACTTAGTGCCA 1 AACCCGCACACTTAGTGCCA 35547167 ATCTCACAAC Statistics Matches: 44, Mismatches: 4, Indels: 3 0.86 0.08 0.06 Matches are distributed among these distances: 28 3 0.07 29 38 0.86 30 3 0.07 ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24 Consensus pattern (29 bp): AACCCGCACACTTAGTGCCATGCATTTCA Found at i:35547209 original size:43 final size:43 Alignment explanation

Indices: 35547148--35547336 Score: 342 Period size: 43 Copynumber: 4.4 Consensus size: 43 35547138 TGCATTTCAA * 35547148 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACCTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT 35547191 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT * * 35547234 GCCCGCACACTTACTGCCAATCTCACAACCGTGAATACTTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT * 35547277 GCCCGCACACTTACTGCCAATCTCACAACCGTGAACACTTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT 35547320 GCCCGCACACTTAGTGC 1 GCCCGCACACTTAGTGC 35547337 TGAAAACCAA Statistics Matches: 141, Mismatches: 5, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 43 141 1.00 ACGTcount: A:0.27, C:0.37, G:0.14, T:0.23 Consensus pattern (43 bp): GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT Found at i:35548837 original size:47 final size:47 Alignment explanation

Indices: 35548759--35549112 Score: 567 Period size: 47 Copynumber: 7.6 Consensus size: 47 35548749 CCCTTCGGGA * * * * * * 35548759 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 35548806 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 35548853 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 35548900 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC 35548949 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 35548996 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 35549043 CTTATCACATATATACACTTTCACA-T--T---ATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 35549084 CTTATCACATATATATACACTTTCACATT 1 CTTATCAC--ATATATACACTTTCACATT 35549113 TATTCAAATA Statistics Matches: 294, Mismatches: 8, Indels: 13 0.93 0.03 0.04 Matches are distributed among these distances: 41 22 0.07 43 17 0.06 44 2 0.01 46 1 0.00 47 205 0.70 49 47 0.16 ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:35549028 original size:143 final size:143 Alignment explanation

Indices: 35548759--35549112 Score: 566 Period size: 143 Copynumber: 2.5 Consensus size: 143 35548749 CCCTTCGGGA * * * * * * 35548759 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCTTGTCACATATATAC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC 35548822 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA 66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA 35548887 TCGGCCATTAGGC 131 TCGGCCATTAGGC 35548900 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC 35548965 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA 66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA 35549030 TCGGCCATTAGGC 131 TCGGCCATTAGGC 35549043 CTTATCAC--ATATATACACTTTCACA-T--T---ATCGGCCATTAGGCCTTATCACATATATAT 1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT 35549100 ACACTTTCACATT 64 ACACTTTCACATT 35549113 TATTCAAATA Statistics Matches: 203, Mismatches: 6, Indels: 12 0.92 0.03 0.05 Matches are distributed among these distances: 135 22 0.11 137 19 0.09 138 1 0.00 140 1 0.00 141 27 0.13 142 1 0.00 143 132 0.65 ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33 Consensus pattern (143 bp): CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA TCGGCCATTAGGC Found at i:35552734 original size:26 final size:27 Alignment explanation

Indices: 35552705--35552766 Score: 99 Period size: 28 Copynumber: 2.3 Consensus size: 27 35552695 TTTACTAAAC * 35552705 TACCCCTAAGTATG-AAATTACCATTA 1 TACCCCTAAGTATGAAAATGACCATTA 35552731 TACCCCTAAGTATGCAAAATGACCATTA 1 TACCCCTAAGTATG-AAAATGACCATTA 35552759 TACCCCTA 1 TACCCCTA 35552767 GGGTTAATTT Statistics Matches: 33, Mismatches: 1, Indels: 2 0.92 0.03 0.06 Matches are distributed among these distances: 26 14 0.42 28 19 0.58 ACGTcount: A:0.37, C:0.27, G:0.08, T:0.27 Consensus pattern (27 bp): TACCCCTAAGTATGAAAATGACCATTA Found at i:35552941 original size:27 final size:26 Alignment explanation

Indices: 35552870--35552982 Score: 136 Period size: 27 Copynumber: 4.2 Consensus size: 26 35552860 TGGAGGAAGC 35552870 GTTCTGGTGGCTATGCCACAATTATCT 1 GTTCTGGTGGCTATGCCACAA-TATCT 35552897 GTTTCTGGTGGCTATGCCACAGATATCT 1 G-TTCTGGTGGCTATGCCACA-ATATCT * * * 35552925 GTTCTGGTGGCTCTGCCACAGTATTT 1 GTTCTGGTGGCTATGCCACAATATCT * * * 35552951 GTATCTGGTGACTCTGTCACAATATCT 1 GT-TCTGGTGGCTATGCCACAATATCT 35552978 GTTCT 1 GTTCT 35552983 AGCAGCCATG Statistics Matches: 76, Mismatches: 7, Indels: 7 0.84 0.08 0.08 Matches are distributed among these distances: 26 9 0.12 27 41 0.54 28 25 0.33 29 1 0.01 ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38 Consensus pattern (26 bp): GTTCTGGTGGCTATGCCACAATATCT Found at i:35553855 original size:31 final size:31 Alignment explanation

Indices: 35553817--35553880 Score: 101 Period size: 31 Copynumber: 2.1 Consensus size: 31 35553807 CCTTTTCATA * 35553817 TTTCATATTTCATAACACTGGGCTGAAGCCT 1 TTTCATATTTCATAACACTGGGCCGAAGCCT ** 35553848 TTTCATATTTCATATTACTGGGCCGAAGCCT 1 TTTCATATTTCATAACACTGGGCCGAAGCCT 35553879 TT 1 TT 35553881 ACTGTAAACG Statistics Matches: 30, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 31 30 1.00 ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39 Consensus pattern (31 bp): TTTCATATTTCATAACACTGGGCCGAAGCCT Found at i:35554138 original size:24 final size:24 Alignment explanation

Indices: 35554074--35554190 Score: 161 Period size: 23 Copynumber: 5.0 Consensus size: 24 35554064 GCTTAATCAT * 35554074 ATAACTGGAGGCCT-AGCCTCTTTTA 1 ATAACTGG-GGCATAAGCC-CTTTTA 35554099 ATAACTGGGGCA-AAGCCCTTTTA 1 ATAACTGGGGCATAAGCCCTTTTA 35554122 ATAACTGGGGCATAAGCCC-TTTA 1 ATAACTGGGGCATAAGCCCTTTTA * 35554145 ATAACTGGGGCATAAGGCC-TTTA 1 ATAACTGGGGCATAAGCCCTTTTA * 35554168 ATAACTGGGACATAAGCCCTTTT 1 ATAACTGGGGCATAAGCCCTTTT 35554191 TCACTTCCTC Statistics Matches: 85, Mismatches: 4, Indels: 7 0.89 0.04 0.07 Matches are distributed among these distances: 23 61 0.72 24 16 0.19 25 8 0.09 ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28 Consensus pattern (24 bp): ATAACTGGGGCATAAGCCCTTTTA Found at i:35554269 original size:20 final size:20 Alignment explanation

Indices: 35554240--35554280 Score: 73 Period size: 20 Copynumber: 2.0 Consensus size: 20 35554230 TTACGAATAC * 35554240 ATCATGTGCATATCATACAT 1 ATCATATGCATATCATACAT 35554260 ATCATATGCATATCATACAT 1 ATCATATGCATATCATACAT 35554280 A 1 A 35554281 CCATGTTTAT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34 Consensus pattern (20 bp): ATCATATGCATATCATACAT Found at i:35554271 original size:11 final size:11 Alignment explanation

Indices: 35554240--35554276 Score: 51 Period size: 11 Copynumber: 3.5 Consensus size: 11 35554230 TTACGAATAC * 35554240 ATCATGTGCAT 1 ATCATATGCAT 35554251 ATCATA--CAT 1 ATCATATGCAT 35554260 ATCATATGCAT 1 ATCATATGCAT 35554271 ATCATA 1 ATCATA 35554277 CATACCATGT Statistics Matches: 23, Mismatches: 1, Indels: 4 0.82 0.04 0.14 Matches are distributed among these distances: 9 9 0.39 11 14 0.61 ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35 Consensus pattern (11 bp): ATCATATGCAT Found at i:35554355 original size:25 final size:25 Alignment explanation

Indices: 35554323--35554370 Score: 78 Period size: 25 Copynumber: 1.9 Consensus size: 25 35554313 ATATATAAAC * * 35554323 CCTAGGGGTATAATGGTCATTTTTA 1 CCTAGGGGTAAAATGATCATTTTTA 35554348 CCTAGGGGTAAAATGATCATTTT 1 CCTAGGGGTAAAATGATCATTTT 35554371 CATATTATAA Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 25 21 1.00 ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38 Consensus pattern (25 bp): CCTAGGGGTAAAATGATCATTTTTA Found at i:35561379 original size:78 final size:79 Alignment explanation

Indices: 35561196--35561415 Score: 259 Period size: 78 Copynumber: 2.8 Consensus size: 79 35561186 GCTCCTCATT * * * 35561196 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG 1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACCAATGCCTTCGGGACTT-AGCCG * 35561260 GATTTAGTAACTCGCA 64 GAATTAGTAACTCGCA * * 35561276 CAAATGCCATCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAATGCCTTCGGGACTTAGCCGGA * 35561340 ATTAGTATCTCGCA 66 ATTAGTAACTCGCA * * * * * * 35561354 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCC 1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACCAATGCCTTCGGGACTTAGCC 35561416 CGGACATCAT Statistics Matches: 121, Mismatches: 15, Indels: 9 0.83 0.10 0.06 Matches are distributed among these distances: 77 3 0.02 78 55 0.45 79 14 0.12 80 47 0.39 81 2 0.02 ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25 Consensus pattern (79 bp): CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAATGCCTTCGGGACTTAGCCGGA ATTAGTAACTCGCA Found at i:35561407 original size:118 final size:120 Alignment explanation

Indices: 35561198--35561419 Score: 283 Period size: 118 Copynumber: 1.9 Consensus size: 120 35561188 TCCTCATTCA * 35561198 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT 1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT * * 35561263 TTAGTAACTCGCACAAATGCCATCGGGACTTAACCCGGATTTAGTAACTCGCACC 66 ATAGTAACTAGCACAAATGCCATCGGGACTTAACCCGGATTTAGTAACTCGCACC * * ** 35561318 AATGCCTTCGGG-CTTAG-CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG 1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG * * * * 35561379 ATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA 64 ATATAGTAAC-TAGCACAAATGCCATCGGGACTTAACCCGGA 35561420 CATCATTCAA Statistics Matches: 88, Mismatches: 11, Indels: 8 0.82 0.10 0.07 Matches are distributed among these distances: 117 4 0.05 118 60 0.68 119 12 0.14 120 12 0.14 ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24 Consensus pattern (120 bp): AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT ATAGTAACTAGCACAAATGCCATCGGGACTTAACCCGGATTTAGTAACTCGCACC Found at i:35561419 original size:40 final size:40 Alignment explanation

Indices: 35561196--35561419 Score: 269 Period size: 40 Copynumber: 5.7 Consensus size: 40 35561186 GCTCCTCATT * * 35561196 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * * 35561236 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * * * 35561276 CAAATGCCATCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * * 35561316 CCAATGCCTTCGGG-CTTAG-CCGGA-ATTAGTATCTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA * * * * 35561354 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA 35561395 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 35561420 CATCATTCAA Statistics Matches: 161, Mismatches: 16, Indels: 14 0.84 0.08 0.07 Matches are distributed among these distances: 37 2 0.01 38 26 0.16 39 9 0.06 40 112 0.70 41 12 0.07 ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA Found at i:35573347 original size:54 final size:54 Alignment explanation

Indices: 35573256--35573453 Score: 317 Period size: 54 Copynumber: 3.7 Consensus size: 54 35573246 TGGAGGAAGC * 35573256 GTCCTGGTGGCCATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT * * * 35573310 GTCCTGGTGGCTATGCCACAATTATCTAATCTAGTGGCTCAGCCACATATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT * 35573364 GTCCTGGTGGCTACGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT * * 35573418 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG 1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG 35573454 ACTTCGTCAC Statistics Matches: 132, Mismatches: 11, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 53 6 0.05 54 126 0.95 ACGTcount: A:0.19, C:0.26, G:0.22, T:0.32 Consensus pattern (54 bp): GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT Found at i:35573449 original size:32 final size:27 Alignment explanation

Indices: 35573259--35573453 Score: 217 Period size: 27 Copynumber: 7.2 Consensus size: 27 35573249 AGGAAGCGTC 35573259 CTGGTGGC-CATGCCACA-ATTATCTGAT 1 CTGGTGGCTC-TGCCACATA-TATCTGAT 35573286 CTGGTGGCTCTGCCACATATATCTG-T 1 CTGGTGGCTCTGCCACATATATCTGAT * * 35573312 CCTGGTGGCTATGCCACA-ATTATCTAAT 1 -CTGGTGGCTCTGCCACATA-TATCTGAT * * 35573340 CTAGTGGCTCAGCCACATATATCTG-T 1 CTGGTGGCTCTGCCACATATATCTGAT 35573366 CCTGGTGGCTAC-GCCACA-ATTATCTGAT 1 -CTGGTGGCT-CTGCCACATA-TATCTGAT * 35573394 CTGGTGGCTCTGCCACATATATCTGTT 1 CTGGTGGCTCTGCCACATATATCTGAT 35573421 CTGGTGGCTCTGCCACA-ATATCTGTAT 1 CTGGTGGCTCTGCCACATATATCTG-AT 35573448 CTGGTG 1 CTGGTG 35573454 ACTTCGTCAC Statistics Matches: 146, Mismatches: 9, Indels: 26 0.81 0.05 0.14 Matches are distributed among these distances: 26 12 0.08 27 127 0.87 28 7 0.05 ACGTcount: A:0.19, C:0.26, G:0.22, T:0.32 Consensus pattern (27 bp): CTGGTGGCTCTGCCACATATATCTGAT Found at i:35576674 original size:13 final size:13 Alignment explanation

Indices: 35576656--35576680 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 35576646 TAATGGTATA 35576656 TTGAATCCATGAT 1 TTGAATCCATGAT 35576669 TTGAATCCATGA 1 TTGAATCCATGA 35576681 AAATTTAGTA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TTGAATCCATGAT Found at i:35578650 original size:47 final size:47 Alignment explanation

Indices: 35578596--35579331 Score: 1242 Period size: 47 Copynumber: 15.6 Consensus size: 47 35578586 TATTTGAATA 35578596 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 35578643 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * 35578690 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 35578737 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * 35578784 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * * 35578831 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGTCGATGTGATG 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG 35578880 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * 35578927 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 35578974 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG * 35579023 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * 35579070 AATGTGAAAGTGTATATATGTGATTAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * * 35579117 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 35579164 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG 35579213 AATGTGAAA--GTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * * * * * * * 35579258 AATGTGAAAGTGTATATTTGTGACAGGGCCGAGTGGCCAACGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * * 35579305 GATGTGAAAGTGTATAAATGTGATAAG 1 AATGTGAAAGTGTATATATGTGATAAG 35579332 TCCCGAAGGG Statistics Matches: 653, Mismatches: 28, Indels: 16 0.94 0.04 0.02 Matches are distributed among these distances: 45 44 0.07 47 475 0.73 49 134 0.21 ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30 Consensus pattern (47 bp): AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG Found at i:35578895 original size:143 final size:143 Alignment explanation

Indices: 35578596--35579331 Score: 1254 Period size: 143 Copynumber: 5.2 Consensus size: 143 35578586 TATTTGAATA 35578596 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 35578661 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAAT 66 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT 35578724 AGCCGATGTGATG 131 AGCCGATGTGATG 35578737 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA * 35578802 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT 66 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT * 35578867 AGTCGATGTGATG 131 AGCCGATGTGATG 35578880 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA * 35578945 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT 66 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT * 35579010 GGCCGATGTGATG 131 AGCCGATGTGATG * 35579023 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA * * 35579088 TGTGATTAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGTCTAAT 66 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT 35579151 AGCCGATGTGATG 131 AGCCGATGTGATG 35579164 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTATA 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA * * * 35579227 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT-T-TGTGACAGGGCCGA 64 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA * * * * 35579290 GTGGCCAACGTGATG 129 ATAGCCGATGTGATG * * 35579305 GATGTGAAAGTGTATAAATGTGATAAG 1 AATGTGAAAGTGTATATATGTGATAAG 35579332 TCCCGAAGGG Statistics Matches: 568, Mismatches: 21, Indels: 14 0.94 0.03 0.02 Matches are distributed among these distances: 139 14 0.02 141 229 0.40 142 1 0.00 143 324 0.57 ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30 Consensus pattern (143 bp): AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT AGCCGATGTGATG Found at i:35579551 original size:37 final size:37 Alignment explanation

Indices: 35579450--35579551 Score: 177 Period size: 37 Copynumber: 2.8 Consensus size: 37 35579440 CCGAGCTCTA * 35579450 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT 1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT 35579487 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT 1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT * * 35579524 AAGACCCGATAACTTCGTGTGGAGATTT 1 AAGACCCGATGACTACGTGTGGAGATTT 35579552 CGTCTGAGCC Statistics Matches: 62, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 37 62 1.00 ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26 Consensus pattern (37 bp): AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT Found at i:35580861 original size:40 final size:40 Alignment explanation

Indices: 35580817--35581128 Score: 425 Period size: 40 Copynumber: 7.8 Consensus size: 40 35580807 GAGAATTGAG 35580817 AGTGATGTATCCGGGCTAAGTCCTGAAGAGCATTCGTGCT 1 AGTGATGTATCCGGGCTAAGTCCTGAAGAGCATTCGTGCT * 35580857 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT 1 AGTGATGTATCCGGGCTAAGTCCTGAAGAGCATTCGTGCT 35580897 AGTGATGTATCCGGGCTAAGT-CTCGAAGAGCATTCGTGCT 1 AGTGATGTATCCGGGCTAAGTCCT-GAAGAGCATTCGTGCT 35580937 AGTGATGTATCCGGGCTAAGT-CTCGAAGAGCATTCGTGCT 1 AGTGATGTATCCGGGCTAAGTCCT-GAAGAGCATTCGTGCT 35580977 AGTGATGTATCCGGGCTAAGT-CTCGAAGAGCATTCGTGCT 1 AGTGATGTATCCGGGCTAAGTCCT-GAAGAGCATTCGTGCT * 35581017 AGTGATGTATCCGGACTAAGTTCC-GAAGAGCATTCGTGCT 1 AGTGATGTATCCGGGCTAAG-TCCTGAAGAGCATTCGTGCT * * * ** * * 35581057 AGTGATATATCTGTGCTAAACCCCGAAGAGCATTCCTGCT 1 AGTGATGTATCCGGGCTAAGTCCTGAAGAGCATTCGTGCT * * * * * * 35581097 AGTGTTATATCAGAGTTAAGTCCCGAAGAGCA 1 AGTGATGTATCCGGGCTAAGTCCTGAAGAGCA 35581129 ATCATGCTGG Statistics Matches: 252, Mismatches: 16, Indels: 8 0.91 0.06 0.03 Matches are distributed among these distances: 39 3 0.01 40 247 0.98 41 1 0.00 42 1 0.00 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27 Consensus pattern (40 bp): AGTGATGTATCCGGGCTAAGTCCTGAAGAGCATTCGTGCT Found at i:35580950 original size:80 final size:80 Alignment explanation

Indices: 35580817--35581128 Score: 473 Period size: 80 Copynumber: 3.9 Consensus size: 80 35580807 GAGAATTGAG 35580817 AGTGATGTATCCGGGCTAAGTC-CTGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCC 1 AGTGATGTATCCGGGCTAAGTCTC-GAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCC 35580881 GAAGAGCATTCGTGCT 65 GAAGAGCATTCGTGCT * 35580897 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCG 1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCG 35580962 AAGAGCATTCGTGCT 66 AAGAGCATTCGTGCT * * 35580977 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCG 1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCG 35581042 AAGAGCATTCGTGCT 66 AAGAGCATTCGTGCT * * * ** * * * * * * * 35581057 AGTGATATATCTGTGCTAAACCCCGAAGAGCATTCCTGCTAGTGTTATATCAGAGTTAAGTCCCG 1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCG 35581122 AAGAGCA 66 AAGAGCA 35581129 ATCATGCTGG Statistics Matches: 213, Mismatches: 18, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 80 212 1.00 81 1 0.00 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27 Consensus pattern (80 bp): AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCG AAGAGCATTCGTGCT Found at i:35582954 original size:13 final size:13 Alignment explanation

Indices: 35582936--35582960 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 35582926 TAATGGTATA 35582936 TTGAATCCATGAT 1 TTGAATCCATGAT 35582949 TTGAATCCATGA 1 TTGAATCCATGA 35582961 AAATTTAGTA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TTGAATCCATGAT Found at i:35584297 original size:23 final size:23 Alignment explanation

Indices: 35584267--35584313 Score: 94 Period size: 23 Copynumber: 2.0 Consensus size: 23 35584257 CAGTGCAGAA 35584267 TGACACTGTAATCCTCTGTTCTG 1 TGACACTGTAATCCTCTGTTCTG 35584290 TGACACTGTAATCCTCTGTTCTG 1 TGACACTGTAATCCTCTGTTCTG 35584313 T 1 T 35584314 TTTTAGAAAA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 24 1.00 ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40 Consensus pattern (23 bp): TGACACTGTAATCCTCTGTTCTG Found at i:35584951 original size:47 final size:47 Alignment explanation

Indices: 35584897--35585348 Score: 746 Period size: 47 Copynumber: 9.6 Consensus size: 47 35584887 TATTTGAATA 35584897 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * 35584944 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGACCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * 35584991 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATG 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG 35585040 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * 35585087 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * 35585134 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG 35585181 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG 35585230 AATGTGAAA--GTATATATGTGATAAGGCCTAATGGCCGATGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * * * * * * 35585275 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG * * 35585322 GATGTGAAAGTGTATAAATGTGATAAG 1 AATGTGAAAGTGTATATATGTGATAAG 35585349 TCCCGAAGGG Statistics Matches: 383, Mismatches: 16, Indels: 12 0.93 0.04 0.03 Matches are distributed among these distances: 45 44 0.11 47 251 0.66 49 88 0.23 ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29 Consensus pattern (47 bp): AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG Found at i:35585060 original size:143 final size:141 Alignment explanation

Indices: 35584897--35585348 Score: 748 Period size: 143 Copynumber: 3.2 Consensus size: 141 35584887 TATTTGAATA 35584897 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 35584962 TGTGATAAGGCCTAATGACCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT 66 TGTGATAAGGCCTAATGACCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAAT 35585027 AGCCGATGTGATG 129 AGCCGATGTGATG 35585040 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 35585105 TGTGATAAGGCCTAAT-AGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATA 66 TGTGATAAGGCCTAATGA-CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATA 35585169 GCCGATGTGATG 130 GCCGATGTGATG 35585181 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTATA 1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA * * * * * 35585244 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGT 64 TATGTGATAAGGCCTAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT * * * 35585309 GGCCAACGTGATG 129 AGCCGATGTGATG * * 35585322 GATGTGAAAGTGTATAAATGTGATAAG 1 AATGTGAAAGTGTATATATGTGATAAG 35585349 TCCCGAAGGG Statistics Matches: 295, Mismatches: 10, Indels: 12 0.93 0.03 0.04 Matches are distributed among these distances: 139 14 0.05 141 132 0.45 142 1 0.00 143 148 0.50 ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29 Consensus pattern (141 bp): AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA TGTGATAAGGCCTAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAG CCGATGTGATG Found at i:35585568 original size:37 final size:37 Alignment explanation

Indices: 35585467--35585568 Score: 150 Period size: 37 Copynumber: 2.8 Consensus size: 37 35585457 CCGAGCTCTA * * 35585467 AAGACCCGATGACTACGTATGGAGATTATGTCCGGGT 1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT * 35585504 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT 1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT * * * 35585541 AAGACTCGATAACTTCGTGTGGAGATTT 1 AAGACCCGATGACTACGTGTGGAGATTT 35585569 CGTCTGAGCT Statistics Matches: 58, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 37 58 1.00 ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27 Consensus pattern (37 bp): AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT Found at i:35590075 original size:26 final size:26 Alignment explanation

Indices: 35590046--35590101 Score: 112 Period size: 26 Copynumber: 2.2 Consensus size: 26 35590036 TGATAAAAAT 35590046 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 35590072 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 35590098 TGAT 1 TGAT 35590102 GGGCATTTCA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 30 1.00 ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36 Consensus pattern (26 bp): TGATAATGGGTTAGGTAAATGTTCCA Found at i:35590825 original size:27 final size:27 Alignment explanation

Indices: 35590783--35590922 Score: 173 Period size: 27 Copynumber: 5.2 Consensus size: 27 35590773 AGGAAGCGTC * 35590783 CTGGTGGCTATGCCACAATTATCTGAT 1 CTGGTGGCTCTGCCACAATTATCTGAT * 35590810 CTGGTGGCTCTACCAC-ATATATCTG-T 1 CTGGTGGCTCTGCCACAAT-TATCTGAT * 35590836 CCTGGTGGCTATGCCACAATTAT-TGAT 1 -CTGGTGGCTCTGCCACAATTATCTGAT * 35590863 CTGGTGGCTCTGCCAC-ATATATCTGTT 1 CTGGTGGCTCTGCCACAAT-TATCTGAT 35590890 CTGGTGGCTCTGCCACAA-TATCTGTAT 1 CTGGTGGCTCTGCCACAATTATCTG-AT 35590917 CTGGTG 1 CTGGTG 35590923 ACTTCGTCAC Statistics Matches: 98, Mismatches: 7, Indels: 16 0.81 0.06 0.13 Matches are distributed among these distances: 25 2 0.02 26 29 0.30 27 64 0.65 28 3 0.03 ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34 Consensus pattern (27 bp): CTGGTGGCTCTGCCACAATTATCTGAT Found at i:35590884 original size:53 final size:54 Alignment explanation

Indices: 35590780--35590922 Score: 236 Period size: 53 Copynumber: 2.7 Consensus size: 54 35590770 TGGAGGAAGC 35590780 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT * 35590834 GTCCTGGTGGCTATGCCACAATTAT-TGATCTGGTGGCTCTGCCACATATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT * * 35590887 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG 1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG 35590923 ACTTCGTCAC Statistics Matches: 84, Mismatches: 3, Indels: 4 0.92 0.03 0.04 Matches are distributed among these distances: 52 3 0.04 53 48 0.57 54 33 0.39 ACGTcount: A:0.18, C:0.24, G:0.23, T:0.34 Consensus pattern (54 bp): GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT Found at i:35590933 original size:27 final size:26 Alignment explanation

Indices: 35590783--35590940 Score: 140 Period size: 27 Copynumber: 5.9 Consensus size: 26 35590773 AGGAAGCGTC * * * 35590783 CTGGTGGCTATGCCACAATTATCTGAT 1 CTGGTGACTCTGCCACAA-TATCTGTT * * * 35590810 CTGGTGGCTCTACCACATATATCTGTC 1 CTGGTGACTCTGCCACA-ATATCTGTT * * * 35590837 CTGGTGGCTATGCCACAATTAT-TGAT 1 CTGGTGACTCTGCCACAA-TATCTGTT * 35590863 CTGGTGGCTCTGCCACATATATCTGTT 1 CTGGTGACTCTGCCACA-ATATCTGTT * 35590890 CTGGTGGCTCTGCCACAATATCTGTAT 1 CTGGTGACTCTGCCACAATATCTGT-T * 35590917 CTGGTGACT-TCGTCACAATATCTG 1 CTGGTGACTCT-GCCACAATATCTG 35590941 GCAGCCTCGC Statistics Matches: 113, Mismatches: 12, Indels: 12 0.82 0.09 0.09 Matches are distributed among these distances: 26 31 0.27 27 81 0.72 28 1 0.01 ACGTcount: A:0.20, C:0.25, G:0.22, T:0.34 Consensus pattern (26 bp): CTGGTGACTCTGCCACAATATCTGTT Found at i:35590938 original size:53 final size:53 Alignment explanation

Indices: 35590780--35590940 Score: 213 Period size: 53 Copynumber: 3.0 Consensus size: 53 35590770 TGGAGGAAGC 35590780 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTC-TACCACATATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCGT--CACATATATCT * 35590834 GTCCTGGTGGCTATGCCACAATTAT-TGATCTGGTGGCTCTGCCACATATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTC-GTCACATATATCT * * * 35590887 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTGACTTCGTCACA-ATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTGGC-TCGTCACATATATCT 35590940 G 1 G 35590941 GCAGCCTCGC Statistics Matches: 97, Mismatches: 5, Indels: 11 0.86 0.04 0.10 Matches are distributed among these distances: 52 3 0.03 53 53 0.55 54 39 0.40 55 2 0.02 ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34 Consensus pattern (53 bp): GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCGTCACATATATCT Found at i:35605632 original size:46 final size:46 Alignment explanation

Indices: 35605501--35605666 Score: 162 Period size: 46 Copynumber: 3.5 Consensus size: 46 35605491 GTGCTAATGC * * * * 35605501 CATGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTG-TGCCGATG 1 CATGTCCCAGACATGGTCTTACACTAG-AC-A-CATCTC-GAGGCCGATG * 35605550 CTGTGTCCCAGACATGGTCTTACAC-AGACACATCTCGCA-GCCGATG 1 C-ATGTCCCAGACATGGTCTTACACTAGACACATCTCG-AGGCCGATG * 35605596 CATGTCCCAGACAT-GTCTTACACTA-ACTTACGTCTCGAGGCCGATG 1 CATGTCCCAGACATGGTCTTACACTAGAC--ACATCTCGAGGCCGATG * 35605642 AATGTCCCAGACATGGTCTTACACT 1 CATGTCCCAGACATGGTCTTACACT 35605667 GGCTCTCATA Statistics Matches: 103, Mismatches: 6, Indels: 18 0.81 0.05 0.14 Matches are distributed among these distances: 44 11 0.11 45 15 0.15 46 40 0.39 47 11 0.11 48 1 0.01 49 3 0.03 50 22 0.21 ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25 Consensus pattern (46 bp): CATGTCCCAGACATGGTCTTACACTAGACACATCTCGAGGCCGATG Found at i:35626565 original size:30 final size:29 Alignment explanation

Indices: 35626529--35626589 Score: 95 Period size: 30 Copynumber: 2.1 Consensus size: 29 35626519 GGTGTCAAGT ** 35626529 TTTGGCACTAAGTGTGTGATTTAAACTAGC 1 TTTGGCACTAAGTGTGCCATTT-AACTAGC 35626559 TTTGGCACTAAGTGTGCCATTTAACTAGC 1 TTTGGCACTAAGTGTGCCATTTAACTAGC 35626588 TT 1 TT 35626590 CGGTTACTTG Statistics Matches: 29, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 29 9 0.31 30 20 0.69 ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38 Consensus pattern (29 bp): TTTGGCACTAAGTGTGCCATTTAACTAGC Found at i:35631159 original size:39 final size:40 Alignment explanation

Indices: 35631051--35631235 Score: 191 Period size: 40 Copynumber: 4.7 Consensus size: 40 35631041 TTGAATGATG * * * * 35631051 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA 1 TCCGGGCTAAGTCCAGAAGGCATTTGTGC-GAGTTACTAAA * * 35631091 TCCGGACTAAGATCC-GAAGGCATTTGTGCGAGTTACTAAT 1 TCCGGGCTAAG-TCCAGAAGGCATTTGTGCGAGTTACTAAA * 35631131 TCCGGGCTAAG-CCAGAAGGCATTGGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCAGAAGGCATTTGTGCGAGTTACTAAA * * * * 35631170 TCCGGGTTAAGTCCCGAAGGCATTTATGCGAGTTGCTATAA 1 TCCGGGCTAAGTCCAGAAGGCATTTGTGCGAGTTACTA-AA * 35631211 -CCGGGCTATGTCTC-GAAGGCATTTG 1 TCCGGGCTAAGTC-CAGAAGGCATTTG 35631236 AACGAGTAGC Statistics Matches: 123, Mismatches: 16, Indels: 12 0.81 0.11 0.08 Matches are distributed among these distances: 38 2 0.02 39 33 0.27 40 75 0.61 41 13 0.11 ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26 Consensus pattern (40 bp): TCCGGGCTAAGTCCAGAAGGCATTTGTGCGAGTTACTAAA Found at i:35631187 original size:79 final size:80 Alignment explanation

Indices: 35631051--35631203 Score: 195 Period size: 79 Copynumber: 1.9 Consensus size: 80 35631041 TTGAATGATG * * * 35631051 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT 1 TCCGGGCTAAGTCCAGAAGGCTTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT * 35631116 GTGCGAGTTACTAAT 66 ATGCGAGTTACTAAT * * ** 35631131 TCCGGGCTAAG-CCAGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT 1 TCCGGGCTAAGTCCAGAAGGC-TTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCAT 35631193 TTATGCGAGTT 64 TTATGCGAGTT 35631204 GCTATAACCG Statistics Matches: 63, Mismatches: 8, Indels: 5 0.83 0.11 0.07 Matches are distributed among these distances: 78 1 0.02 79 45 0.71 80 17 0.27 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26 Consensus pattern (80 bp): TCCGGGCTAAGTCCAGAAGGCTTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT ATGCGAGTTACTAAT Found at i:35631257 original size:79 final size:78 Alignment explanation

Indices: 35631085--35631258 Score: 176 Period size: 79 Copynumber: 2.2 Consensus size: 78 35631075 GTGCTAAGTG * * * 35631085 ACTATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCAGAAGG 1 ACTATATCCGG-TTAAGATCCGAAGGCATTTATGCGAGTTACTAATACCGGGCTAAGCCAGAAGG ** 35631150 CATTGGTGCGAGTT 65 CATTGGAACGAGTT * * * 35631164 ACTAAATCCGGGTTAAG-TCCCGAAGGCATTTATGCGAGTTGCT-ATAACCGGGCTATGTCTC-G 1 ACTATATCC-GGTTAAGAT-CCGAAGGCATTTATGCGAGTTACTAAT-ACCGGGCTAAG-C-CAG * 35631226 AAGGCATTTGAACGAG-T 61 AAGGCATTGGAACGAGTT 35631243 AGCTATATCCGGTTAA 1 A-CTATATCCGGTTAA 35631259 ATTCTAAAGG Statistics Matches: 79, Mismatches: 10, Indels: 12 0.78 0.10 0.12 Matches are distributed among these distances: 78 3 0.04 79 51 0.65 80 24 0.30 81 1 0.01 ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26 Consensus pattern (78 bp): ACTATATCCGGTTAAGATCCGAAGGCATTTATGCGAGTTACTAATACCGGGCTAAGCCAGAAGGC ATTGGAACGAGTT Found at i:35639380 original size:3 final size:3 Alignment explanation

Indices: 35639367--35639404 Score: 67 Period size: 3 Copynumber: 12.7 Consensus size: 3 35639357 AATTTGGATG * 35639367 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 35639405 TTGTATGTTT Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 3 33 1.00 ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66 Consensus pattern (3 bp): TTA Found at i:35641097 original size:27 final size:27 Alignment explanation

Indices: 35641067--35641128 Score: 92 Period size: 26 Copynumber: 2.3 Consensus size: 27 35641057 ATTTACTAAA 35641067 ATACCCCTAAGTATG-AAAATTACCATT 1 ATACCCCTAAG-ATGCAAAATTACCATT * 35641094 ATACCCCT-AGGTGCAAAATTACCATT 1 ATACCCCTAAGATGCAAAATTACCATT 35641120 ATACCCCTA 1 ATACCCCTA 35641129 GGGTTAATTT Statistics Matches: 32, Mismatches: 1, Indels: 4 0.86 0.03 0.11 Matches are distributed among these distances: 25 2 0.06 26 22 0.69 27 8 0.25 ACGTcount: A:0.37, C:0.27, G:0.08, T:0.27 Consensus pattern (27 bp): ATACCCCTAAGATGCAAAATTACCATT Found at i:35641273 original size:27 final size:27 Alignment explanation

Indices: 35641235--35641340 Score: 142 Period size: 27 Copynumber: 3.9 Consensus size: 27 35641225 GAGGAAGCTT 35641235 TCTGGTGGCTCTGCCACAAATATCTG-A 1 TCTGGTGGCTCTGCCAC-AATATCTGTA * * 35641262 TCTGGTGGCTCTACCACAAATATCTGTT 1 TCTGGTGGCTCTGCCAC-AATATCTGTA * 35641290 TTTGGTGGCTCTGCCACAATATCTGTA 1 TCTGGTGGCTCTGCCACAATATCTGTA * * 35641317 TCTGGTGACTCTGTCACAATATCT 1 TCTGGTGGCTCTGCCACAATATCT 35641341 ATTTTGGCAG Statistics Matches: 70, Mismatches: 8, Indels: 2 0.88 0.10 0.03 Matches are distributed among these distances: 27 55 0.79 28 15 0.21 ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35 Consensus pattern (27 bp): TCTGGTGGCTCTGCCACAATATCTGTA Found at i:35641321 original size:55 final size:54 Alignment explanation

Indices: 35641237--35641345 Score: 157 Period size: 55 Copynumber: 2.0 Consensus size: 54 35641227 GGAAGCTTTC * * 35641237 TGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTCTACCACAAATATCTGTTTT 1 TGGTGGCTCTGCCACAAATATCTGATCTGGTGACTCTACCAC-AATATCTATTTT ** 35641292 TGGTGGCTCTGCCAC-AATATCTGTATCTGGTGACTCTGTCACAATATCTATTTT 1 TGGTGGCTCTGCCACAAATATCTG-ATCTGGTGACTCTACCACAATATCTATTTT 35641346 GGCAGCCATG Statistics Matches: 49, Mismatches: 4, Indels: 3 0.88 0.07 0.05 Matches are distributed among these distances: 54 19 0.39 55 30 0.61 ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37 Consensus pattern (54 bp): TGGTGGCTCTGCCACAAATATCTGATCTGGTGACTCTACCACAATATCTATTTT Found at i:35656997 original size:40 final size:40 Alignment explanation

Indices: 35656918--35657094 Score: 225 Period size: 40 Copynumber: 4.5 Consensus size: 40 35656908 CGGATGATAA * * * * 35656918 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT * * * * 35656958 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT * * 35656998 CCGGGCTAAGACCCGAAGGTATTTGTGCGAGTTGCTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT 35657038 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT 35657078 CC-GGCTAA-ATCCCGAAG 1 CCGGGCTAAGA-CCCGAAG 35657095 ATACTTGGGT Statistics Matches: 118, Mismatches: 16, Indels: 7 0.84 0.11 0.05 Matches are distributed among these distances: 38 1 0.01 39 15 0.13 40 100 0.85 41 2 0.02 ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT Found at i:35657362 original size:22 final size:22 Alignment explanation

Indices: 35657322--35657363 Score: 59 Period size: 22 Copynumber: 1.9 Consensus size: 22 35657312 GAATGTGCAT * 35657322 ATATGAAGTTATTCATTTAGCC 1 ATATGAAGTTATACATTTAGCC 35657344 ATATGAATGTTATAC-TTTAG 1 ATATGAA-GTTATACATTTAG 35657364 TCAAAACTAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 22 12 0.67 23 6 0.33 ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43 Consensus pattern (22 bp): ATATGAAGTTATACATTTAGCC Found at i:35662183 original size:29 final size:27 Alignment explanation

Indices: 35662165--35662234 Score: 113 Period size: 27 Copynumber: 2.6 Consensus size: 27 35662155 ATATTAAGTC 35662165 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTCAGTGCTATATAATCAACT * 35662192 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTCAGTGCTATATAATC-AACT * 35662220 CGCACACTTAGTGCT 1 CGCACACTCAGTGCT 35662235 GTACAATTTA Statistics Matches: 41, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 27 22 0.54 28 19 0.46 ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27 Consensus pattern (27 bp): CGCACACTCAGTGCTATATAATCAACT Found at i:35662228 original size:28 final size:28 Alignment explanation

Indices: 35662165--35662262 Score: 135 Period size: 28 Copynumber: 3.5 Consensus size: 28 35662155 ATATTAAGTC * 35662165 CGCACACTCAGTGCTATATAATC-AACT 1 CGCACACTTAGTGCTATATAATCAAACT 35662192 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 35662220 CGCACACTTAGTGCTGTACAATTTAAACC 1 CGCACACTTAGTGCTATATAA-TCAAACT 35662249 CGCACACTTAGTGC 1 CGCACACTTAGTGC 35662263 CAATCTCATG Statistics Matches: 64, Mismatches: 5, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 27 22 0.34 28 23 0.36 29 19 0.30 ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27 Consensus pattern (28 bp): CGCACACTTAGTGCTATATAATCAAACT Found at i:35668099 original size:40 final size:40 Alignment explanation

Indices: 35668016--35668192 Score: 198 Period size: 40 Copynumber: 4.5 Consensus size: 40 35668006 CGGATGATAA * * * * * * * 35668016 CCGGACTAAGATCCGAAGGCATTCGTACGAGTTGCTATGT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT * * * * 35668056 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-TTATAT * 35668096 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGCTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT * 35668136 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT 35668176 CC-GGCTAA-ATCCCGAAG 1 CCGGGCTAAGA-CCCGAAG 35668193 ATACTTGGGT Statistics Matches: 117, Mismatches: 17, Indels: 7 0.83 0.12 0.05 Matches are distributed among these distances: 38 1 0.01 39 15 0.13 40 99 0.85 41 2 0.02 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT Found at i:35668154 original size:80 final size:80 Alignment explanation

Indices: 35668016--35668192 Score: 225 Period size: 80 Copynumber: 2.2 Consensus size: 80 35668006 CGGATGATAA * * * * * * 35668016 CCGGACTAAGATCCGAAGGCATTCGTACGAGTTGCTATGTCCGGGCTATGTCCCGAAGGCATTTA 1 CCGGGCTAAGACCCGAAGGCATTCGTACAAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA * 35668081 TGCTAG-TGATTATAT 66 TGCGAGTTG-TTATAT * * * 35668096 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTG 1 CCGGGCTAAGACCCGAAGGCATTCGTACAAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA 35668161 TGCGAGTTGTTATAT 66 TGCGAGTTGTTATAT 35668176 CC-GGCTAA-ATCCCGAAG 1 CCGGGCTAAGA-CCCGAAG 35668193 ATACTTGGGT Statistics Matches: 85, Mismatches: 10, Indels: 5 0.85 0.10 0.05 Matches are distributed among these distances: 78 1 0.01 79 13 0.15 80 69 0.81 81 2 0.02 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (80 bp): CCGGGCTAAGACCCGAAGGCATTCGTACAAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA TGCGAGTTGTTATAT Found at i:35668460 original size:22 final size:22 Alignment explanation

Indices: 35668420--35668461 Score: 59 Period size: 22 Copynumber: 1.9 Consensus size: 22 35668410 GAATGTGCAT * 35668420 ATATGAAGTTATTCATTTAGCC 1 ATATGAAGTTATACATTTAGCC 35668442 ATATGAATGTTATAC-TTTAG 1 ATATGAA-GTTATACATTTAG 35668462 TCAAAACTAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 22 12 0.67 23 6 0.33 ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43 Consensus pattern (22 bp): ATATGAAGTTATACATTTAGCC Found at i:35670058 original size:34 final size:34 Alignment explanation

Indices: 35670015--35670085 Score: 108 Period size: 34 Copynumber: 2.1 Consensus size: 34 35670005 GTATAGATCT 35670015 CTGATACTG-TACTGAAATGGGGCTAAGGCCCACA 1 CTGATACTGTTACTGAAAT-GGGCTAAGGCCCACA * * 35670049 CTGATACTGTTACTGTAATGGGCTAAGGCCCAGA 1 CTGATACTGTTACTGAAATGGGCTAAGGCCCACA 35670083 CTG 1 CTG 35670086 TTTTGCACTA Statistics Matches: 34, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 34 26 0.76 35 8 0.24 ACGTcount: A:0.27, C:0.23, G:0.27, T:0.24 Consensus pattern (34 bp): CTGATACTGTTACTGAAATGGGCTAAGGCCCACA Found at i:35680355 original size:55 final size:55 Alignment explanation

Indices: 35680238--35680362 Score: 133 Period size: 55 Copynumber: 2.3 Consensus size: 55 35680228 TACGATATGG * ** * * * 35680238 CCATGGTCGAGCCTGCCAAAATAACACAGGTGTGCGACACAACCGTGTGGAAGAA 1 CCATGGTCGAGCCTGCCAAAACAACACAGGCATGCGACACAACCATGTGAAACAA ** ** * 35680293 CCATGGTCGAGCCTGCCAAAACAACACAGGCATTTGACACGCCCATGTGAAACAC 1 CCATGGTCGAGCCTGCCAAAACAACACAGGCATGCGACACAACCATGTGAAACAA * * 35680348 CCGTGGTCGACCCTG 1 CCATGGTCGAGCCTG 35680363 TTAAATTAAC Statistics Matches: 57, Mismatches: 13, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 55 57 1.00 ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15 Consensus pattern (55 bp): CCATGGTCGAGCCTGCCAAAACAACACAGGCATGCGACACAACCATGTGAAACAA Found at i:35686897 original size:40 final size:39 Alignment explanation

Indices: 35686812--35686917 Score: 106 Period size: 40 Copynumber: 2.6 Consensus size: 39 35686802 TTCGGCACTG * * 35686812 AGTGTGCGATTCAAAATAGCTTCGGCTATAAATAGCACTA 1 AGTGTGCAATTCAAAATAGCTTCGGCTAT-AATAGCAATA * * 35686852 TGTGTGCAATTCAAAATAGCTTTGGCTAT-ATGAGGCAATA 1 AGTGTGCAATTCAAAATAGCTTCGGCTATAAT-A-GCAATA * * * 35686892 AGTGTGCGATATCGAGATAGCTTCGG 1 AGTGTGCAAT-TCAAAATAGCTTCGG 35686918 TTAGCTTCGA Statistics Matches: 54, Mismatches: 9, Indels: 5 0.79 0.13 0.07 Matches are distributed among these distances: 38 2 0.04 39 1 0.02 40 39 0.72 41 12 0.22 ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29 Consensus pattern (39 bp): AGTGTGCAATTCAAAATAGCTTCGGCTATAATAGCAATA Found at i:35696438 original size:33 final size:34 Alignment explanation

Indices: 35696392--35696459 Score: 102 Period size: 33 Copynumber: 2.0 Consensus size: 34 35696382 CTAAGCCCAG * 35696392 ATCAGTAACAGTCTGGGCCTGAGCCCTATTCAGT 1 ATCAGTAACAGTCTGGGCCTGAGCCCTATACAGT ** 35696426 ATCAGT-ACAGTCTGGGCCTTCGCCCTATACAGT 1 ATCAGTAACAGTCTGGGCCTGAGCCCTATACAGT 35696459 A 1 A 35696460 ATAGTGTGGC Statistics Matches: 31, Mismatches: 3, Indels: 1 0.89 0.09 0.03 Matches are distributed among these distances: 33 25 0.81 34 6 0.19 ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26 Consensus pattern (34 bp): ATCAGTAACAGTCTGGGCCTGAGCCCTATACAGT Found at i:35696490 original size:60 final size:61 Alignment explanation

Indices: 35696371--35696496 Score: 157 Period size: 60 Copynumber: 2.1 Consensus size: 61 35696361 AGTGAATAAC * * * 35696371 ACAGTCTGGGCCTAAGCCCAGATCAGTAACAGTCTGGGCCTGAGCCCTATTCAGTATCAGT 1 ACAGTCTGGGCCTAAGCCCAGATCAGTAACAGTCTGGGCCTAAGCCCAATACAGTATCAGT ** * * * 35696432 ACAGTCTGGGCCTTCGCCC-TATACAGTAATAGTGT-GGCCTAAGCCCAATACAGTATCAGT 1 ACAGTCTGGGCCTAAGCCCAGAT-CAGTAACAGTCTGGGCCTAAGCCCAATACAGTATCAGT 35696492 ACAGT 1 ACAGT 35696497 GTAATGCAAT Statistics Matches: 56, Mismatches: 8, Indels: 3 0.84 0.12 0.04 Matches are distributed among these distances: 60 29 0.52 61 27 0.48 ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24 Consensus pattern (61 bp): ACAGTCTGGGCCTAAGCCCAGATCAGTAACAGTCTGGGCCTAAGCCCAATACAGTATCAGT Found at i:35696873 original size:27 final size:26 Alignment explanation

Indices: 35696843--35697068 Score: 195 Period size: 27 Copynumber: 8.4 Consensus size: 26 35696833 GCATAATTCC * * 35696843 CATTTTACCATACAAGAATATTACGGT 1 CATTTTACC-TACAGGGATATTACGGT * 35696870 CATTTTATCCTACAGGGACATTACGGT 1 CATTTTA-CCTACAGGGATATTACGGT 35696897 CATTTTACCCTACAGGGATATTACGGT 1 CATTTTA-CCTACAGGGATATTACGGT * 35696924 CATTTTACACTACATGGG-CATTACGGT 1 CATTTTAC-CTACA-GGGATATTACGGT * * * 35696951 TATTTTACTTATAGAGG-TATTACGGT 1 CATTTTACCTACAG-GGATATTACGGT * *** 35696977 CATTTTACCTTATAGGGGCGTTACGGT 1 CATTTTACC-TACAGGGATATTACGGT * * * 35697004 CATTTTACCCTATAGGGGTATTACAGT 1 CATTTTA-CCTACAGGGATATTACGGT * ** * 35697031 CATTTTACCCTATAGGGGCATTACGAT 1 CATTTTA-CCTACAGGGATATTACGGT 35697058 CATTTTACCTA 1 CATTTTACCTA 35697069 TTTTGGGGTT Statistics Matches: 172, Mismatches: 20, Indels: 15 0.83 0.10 0.07 Matches are distributed among these distances: 25 1 0.01 26 27 0.16 27 137 0.80 28 7 0.04 ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36 Consensus pattern (26 bp): CATTTTACCTACAGGGATATTACGGT Found at i:35696918 original size:54 final size:53 Alignment explanation

Indices: 35696843--35697066 Score: 254 Period size: 54 Copynumber: 4.2 Consensus size: 53 35696833 GCATAATTCC * * * * 35696843 CATTTTACCATACAAGAATATTACGGTCATTTTATCCTACAGGGACATTACGGT 1 CATTTTACCCTACAGGGATATTACGGTCATTTTA-CCTACAGGGGCATTACGGT * 35696897 CATTTTACCCTACAGGGATATTACGGTCATTTTACACTACATGGGCATTACGGT 1 CATTTTACCCTACAGGGATATTACGGTCATTTTAC-CTACAGGGGCATTACGGT * * * * * 35696951 TATTTTA-CTTATAGAGG-TATTACGGTCATTTTACCTTATAGGGGCGTTACGGT 1 CATTTTACCCTACAG-GGATATTACGGTCATTTTACC-TACAGGGGCATTACGGT * * * * * 35697004 CATTTTACCCTATAGGGGTATTACAGTCATTTTACCCTATAGGGGCATTACGAT 1 CATTTTACCCTACAGGGATATTACGGTCATTTTA-CCTACAGGGGCATTACGGT 35697058 CATTTTACC 1 CATTTTACC 35697067 TATTTTGGGG Statistics Matches: 148, Mismatches: 16, Indels: 12 0.84 0.09 0.07 Matches are distributed among these distances: 52 1 0.01 53 45 0.30 54 100 0.68 55 2 0.01 ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36 Consensus pattern (53 bp): CATTTTACCCTACAGGGATATTACGGTCATTTTACCTACAGGGGCATTACGGT Found at i:35697009 original size:107 final size:107 Alignment explanation

Indices: 35696861--35697065 Score: 295 Period size: 107 Copynumber: 1.9 Consensus size: 107 35696851 CATACAAGAA * 35696861 TATTACGGTCATTTTATCCTACAGGGACATTACGGTCATTTTACCCTACAGGGATATTACGGTCA 1 TATTACGGTCATTTTATCCTACAGGGACATTACGGTCATTTTACCCTACAGGGATATTACAGTCA * * * 35696926 TTTTACACTACATGGGCATTACGGTTATTTTACTTATAGAGG 66 TTTTACACTACAGGGGCATTACGATCATTTTACTTATAGAGG * * * * * 35696968 TATTACGGTCATTTTA-CCTTATAGGGGCGTTACGGTCATTTTACCCTATAGGGGTATTACAGTC 1 TATTACGGTCATTTTATCC-TACAGGGACATTACGGTCATTTTACCCTACAGGGATATTACAGTC * * 35697032 ATTTTACCCTATAGGGGCATTACGATCATTTTAC 65 ATTTTACACTACAGGGGCATTACGATCATTTTAC 35697066 CTATTTTGGG Statistics Matches: 86, Mismatches: 11, Indels: 2 0.87 0.11 0.02 Matches are distributed among these distances: 106 2 0.02 107 84 0.98 ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37 Consensus pattern (107 bp): TATTACGGTCATTTTATCCTACAGGGACATTACGGTCATTTTACCCTACAGGGATATTACAGTCA TTTTACACTACAGGGGCATTACGATCATTTTACTTATAGAGG Found at i:35697342 original size:132 final size:132 Alignment explanation

Indices: 35697103--35697365 Score: 481 Period size: 132 Copynumber: 2.0 Consensus size: 132 35697093 GACCCCTCCA * 35697103 AAGGTCTACAATCGCCTCGAATGACACAAATAACCAAAATGATCATAACGGTGTAAATGGGCCCA 1 AAGGTCTACAATCGCCTCGAACGACACAAATAACCAAAATGATCATAACGGTGTAAATGGGCCCA 35697168 AGGCACATTACTCGGCCCAAGTGGGCCCACACGCTCGCGTGGCCCATTTAGCCCAAACTTAGTTA 66 AGGCACATTACTCGGCCCAAGTGGGCCCACACGCTCGCGTGGCCCATTTAGCCCAAACTTAGTTA 35697233 CC 131 CC * 35697235 AAGGTCTACAATCGCCTCGAACGACACAAATAACCTAAATGATCATAACGGTGTAAATGGGCCCA 1 AAGGTCTACAATCGCCTCGAACGACACAAATAACCAAAATGATCATAACGGTGTAAATGGGCCCA * * * 35697300 AGGCGCATTACTCGGCCCAAGTGGGCCCACACGCTCGTGTGGCCCATTTAGCCCAAATTTAGTTA 66 AGGCACATTACTCGGCCCAAGTGGGCCCACACGCTCGCGTGGCCCATTTAGCCCAAACTTAGTTA 35697365 C 131 C 35697366 GGCTATGTGA Statistics Matches: 126, Mismatches: 5, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 132 126 1.00 ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20 Consensus pattern (132 bp): AAGGTCTACAATCGCCTCGAACGACACAAATAACCAAAATGATCATAACGGTGTAAATGGGCCCA AGGCACATTACTCGGCCCAAGTGGGCCCACACGCTCGCGTGGCCCATTTAGCCCAAACTTAGTTA CC Found at i:35699151 original size:40 final size:40 Alignment explanation

Indices: 35699027--35699251 Score: 210 Period size: 40 Copynumber: 5.7 Consensus size: 40 35699017 TTGAATGCTG * * * * 35699027 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ATTAAA ** * * 35699067 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAGT 1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATATTAA-A * * 35699107 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATATTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA * 35699147 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TCATTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGAT-ATTAAA * * * 35699187 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA * * * 35699226 ACCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGTTAAGTCCCGAAGGCATTTG 35699252 AACGAGGAGC Statistics Matches: 156, Mismatches: 20, Indels: 18 0.80 0.10 0.09 Matches are distributed among these distances: 39 33 0.21 40 110 0.71 41 12 0.08 42 1 0.01 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25 Consensus pattern (40 bp): TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA Found at i:35699164 original size:80 final size:78 Alignment explanation

Indices: 35699080--35699251 Score: 204 Period size: 79 Copynumber: 2.2 Consensus size: 78 35699070 GGACTAAGAT * * 35699080 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAT 1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC * * 35699143 TAAATCCGGGTTAAGTC 62 TAAAACCGGGCTAAGTC * * * * 35699160 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA 1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA * 35699225 AACCGGGCTATGTC 65 AACCGGGCTAAGTC 35699239 CCGAAGGCATTTG 1 CCGAAGGCATTTG 35699252 AACGAGGAGC Statistics Matches: 79, Mismatches: 10, Indels: 7 0.82 0.10 0.07 Matches are distributed among these distances: 79 37 0.47 80 37 0.47 82 3 0.04 83 2 0.03 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (78 bp): CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA ACCGGGCTAAGTC Found at i:35699269 original size:79 final size:80 Alignment explanation

Indices: 35699107--35699284 Score: 191 Period size: 79 Copynumber: 2.2 Consensus size: 80 35699097 AGATACAAGT * * * * * 35699107 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTCCCGAAGGCATTC 1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC ** * 35699172 GTGCGAGTCATTAAA 66 GAACGAGTCACTAAA * * * * 35699187 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT 1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC * * 35699251 GAACGAG-GAGCTATA 66 GAACGAGTCA-CTAAA * 35699266 TCC-GGTTAAATCCCGAAGG 1 TCCGGGTTAAGTCCCGAAGG 35699285 TACGTGATTT Statistics Matches: 82, Mismatches: 15, Indels: 4 0.81 0.15 0.04 Matches are distributed among these distances: 78 16 0.20 79 47 0.57 80 19 0.23 ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24 Consensus pattern (80 bp): TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC GAACGAGTCACTAAA Found at i:35707075 original size:27 final size:27 Alignment explanation

Indices: 35707044--35707221 Score: 205 Period size: 27 Copynumber: 6.6 Consensus size: 27 35707034 TAAATTGTAC 35707044 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * ** * 35707071 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 35707097 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGATTTGACTATGT * 35707125 GGCACTAAGTGTGCGAGTTTGACTATGT 1 AGCACTAAGTGTGCGA-TTTGACTATGT * * 35707153 AGCACTAAGTGTGCGATTTGATTACGT 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 35707180 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGACTATGT * 35707207 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 35707222 GACTCAATAT Statistics Matches: 129, Mismatches: 19, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 27 106 0.82 28 23 0.18 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGACTATGT Found at i:35707158 original size:82 final size:81 Alignment explanation

Indices: 35707045--35707200 Score: 233 Period size: 82 Copynumber: 1.9 Consensus size: 81 35707035 AAATTGTACA * * 35707045 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG 1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG 35707109 TGCGAATTGACCATGCG 65 TGCGAATTGACCATGCG ** * 35707126 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG 1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG * 35707191 TGCGAGTTGA 65 TGCGAATTGA 35707201 TTATATAGCA Statistics Matches: 67, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 81 15 0.22 82 51 0.76 83 1 0.01 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29 Consensus pattern (81 bp): GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT GCGAATTGACCATGCG Found at i:35707212 original size:82 final size:81 Alignment explanation

Indices: 35707041--35707221 Score: 229 Period size: 82 Copynumber: 2.2 Consensus size: 81 35707031 GATTAAATTG * * 35707041 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA 1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA 35707106 GTGTGCGAATTGACCA 66 GTGTGCGAATTGACCA * * ** * 35707122 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT 1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT * ** 35707186 AAGTGTGCGAGTTGATTA 64 AAGTGTGCGAATTGACCA * * 35707204 TATAGCACTGAGTGTGCG 1 TACAGCACTAAGTGTGCG 35707222 GACTCAATAT Statistics Matches: 84, Mismatches: 14, Indels: 3 0.83 0.14 0.03 Matches are distributed among these distances: 81 18 0.21 82 66 0.79 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (81 bp): TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA GTGTGCGAATTGACCA Found at i:35715258 original size:27 final size:27 Alignment explanation

Indices: 35715227--35715404 Score: 205 Period size: 27 Copynumber: 6.6 Consensus size: 27 35715217 TAAATTGTAC 35715227 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * ** * 35715254 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 35715280 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGATTTGACTATGT * 35715308 GGCACTAAGTGTGCGAGTTTGACTATGT 1 AGCACTAAGTGTGCGA-TTTGACTATGT * * 35715336 AGCACTAAGTGTGCGATTTGATTACGT 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 35715363 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGACTATGT * 35715390 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 35715405 GACTCAATAT Statistics Matches: 129, Mismatches: 19, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 27 106 0.82 28 23 0.18 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGACTATGT Found at i:35715341 original size:82 final size:81 Alignment explanation

Indices: 35715228--35715383 Score: 233 Period size: 82 Copynumber: 1.9 Consensus size: 81 35715218 AAATTGTACA * * 35715228 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG 1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG 35715292 TGCGAATTGACCATGCG 65 TGCGAATTGACCATGCG ** * 35715309 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG 1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG * 35715374 TGCGAGTTGA 65 TGCGAATTGA 35715384 TTATATAGCA Statistics Matches: 67, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 81 15 0.22 82 51 0.76 83 1 0.01 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29 Consensus pattern (81 bp): GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT GCGAATTGACCATGCG Found at i:35715395 original size:82 final size:81 Alignment explanation

Indices: 35715224--35715404 Score: 229 Period size: 82 Copynumber: 2.2 Consensus size: 81 35715214 GATTAAATTG * * 35715224 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA 1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA 35715289 GTGTGCGAATTGACCA 66 GTGTGCGAATTGACCA * * ** * 35715305 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT 1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT * ** 35715369 AAGTGTGCGAGTTGATTA 64 AAGTGTGCGAATTGACCA * * 35715387 TATAGCACTGAGTGTGCG 1 TACAGCACTAAGTGTGCG 35715405 GACTCAATAT Statistics Matches: 84, Mismatches: 14, Indels: 3 0.83 0.14 0.03 Matches are distributed among these distances: 81 18 0.21 82 66 0.79 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (81 bp): TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA GTGTGCGAATTGACCA Found at i:35720180 original size:46 final size:46 Alignment explanation

Indices: 35720130--35720302 Score: 190 Period size: 46 Copynumber: 3.7 Consensus size: 46 35720120 TGGTTGAGCA * 35720130 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACG * * * * * * 35720176 TCCGAACTCGTTGAGTTGACTCCGAGTTC-GTGA--AATGTAACTAGGCA 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AA--A-ACG * * 35720223 TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACG * * 35720269 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA 35720303 GGGGCGGGTT Statistics Matches: 102, Mismatches: 18, Indels: 14 0.76 0.13 0.10 Matches are distributed among these distances: 43 3 0.03 44 2 0.02 45 2 0.02 46 61 0.60 47 28 0.27 48 2 0.02 49 1 0.01 50 3 0.03 ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29 Consensus pattern (46 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACG Found at i:35720286 original size:93 final size:93 Alignment explanation

Indices: 35720127--35720297 Score: 288 Period size: 93 Copynumber: 1.8 Consensus size: 93 35720117 GGATGGTTGA * * * 35720127 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAATGTCCGAACTCGTTGAGT 1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACGCCCGAACTCGTTGAGT 35720192 TGACTCCGAGTTCGTGAAATGTAACTAG 66 TGACTCCGAGTTCGTGAAATGTAACTAG * * 35720220 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGT 1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACGCCCGAACTCGTTGAGT * 35720285 TGAGTCCGAGTTC 66 TGACTCCGAGTTC 35720298 ACTTAGGGGC Statistics Matches: 72, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 93 72 1.00 ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28 Consensus pattern (93 bp): GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACGCCCGAACTCGTTGAGT TGACTCCGAGTTCGTGAAATGTAACTAG Found at i:35722995 original size:16 final size:16 Alignment explanation

Indices: 35722974--35723006 Score: 57 Period size: 16 Copynumber: 2.1 Consensus size: 16 35722964 TAAAACTGTC * 35722974 TCAAACAATTCATATA 1 TCAAACAATTCAGATA 35722990 TCAAACAATTCAGATA 1 TCAAACAATTCAGATA 35723006 T 1 T 35723007 TCCACATAAT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.48, C:0.18, G:0.03, T:0.30 Consensus pattern (16 bp): TCAAACAATTCAGATA Found at i:35734400 original size:37 final size:37 Alignment explanation

Indices: 35734294--35734402 Score: 182 Period size: 37 Copynumber: 2.9 Consensus size: 37 35734284 AGCTCAGACG * * * 35734294 AAATCTCCACACGAAGTTATCGGGTCTTACCCAGACA 1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA 35734331 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA 1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA * 35734368 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA 1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA 35734403 ATATATTTCC Statistics Matches: 68, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 37 68 1.00 ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23 Consensus pattern (37 bp): AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA Found at i:35734672 original size:48 final size:49 Alignment explanation

Indices: 35734548--35734684 Score: 215 Period size: 50 Copynumber: 2.8 Consensus size: 49 35734538 GCACATCGCC * 35734548 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA 1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA-A * * 35734598 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTC-A 1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCAA 35734646 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA 1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA 35734685 TGCATGTTCA Statistics Matches: 80, Mismatches: 5, Indels: 6 0.88 0.05 0.07 Matches are distributed among these distances: 48 36 0.45 49 2 0.03 50 42 0.52 ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36 Consensus pattern (49 bp): TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAA Found at i:35734686 original size:50 final size:50 Alignment explanation

Indices: 35734548--35734783 Score: 210 Period size: 47 Copynumber: 4.9 Consensus size: 50 35734538 GCACATCGCC * 35734548 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA--CATATCTCATA 1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTC--A * 35734598 TATATATTTCACATT-GACCATTCGGCTTTACCAC--ATATGCATATCTCA 1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATATGCATATCTCA * 35734646 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGT-TCA 1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTCA ** * * * * * 35734695 T--AT-TCACCACATTGGCCATTCGGCCTTATCACACATATGCAT-GCTC- 1 TACATAT-TTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTCA * * * * 35734741 -ACAT-TCATCACATTGGCCATTCGGCCTTATCACATATATGCAT 1 TACATAT-TTCACATTAGCCATTCGGCTTTACCACATATATGCAT 35734784 GTTCACATTC Statistics Matches: 163, Mismatches: 13, Indels: 23 0.82 0.07 0.12 Matches are distributed among these distances: 46 1 0.01 47 74 0.45 48 35 0.21 49 6 0.04 50 47 0.29 ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34 Consensus pattern (50 bp): TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTCA Found at i:35734733 original size:47 final size:47 Alignment explanation

Indices: 35734654--35734847 Score: 289 Period size: 47 Copynumber: 4.1 Consensus size: 47 35734644 CATACATATT * * * * 35734654 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA 1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA * * * 35734701 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA 1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA 35734748 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA 1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA * * ** 35734795 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA 1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA 35734842 TCACAT 1 TCACAT 35734848 AAAATCCTAA Statistics Matches: 133, Mismatches: 14, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 47 133 1.00 ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33 Consensus pattern (47 bp): TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA Found at i:35734774 original size:22 final size:22 Alignment explanation

Indices: 35734747--35734818 Score: 58 Period size: 22 Copynumber: 3.1 Consensus size: 22 35734737 GCTCACATTC 35734747 ATCACATTGGCCATTCGGCCTT 1 ATCACATTGGCCATTCGGCCTT * * * 35734769 ATCACATATATG-CATGTTC-ACATT 1 ATCACAT-T-GGCCA--TTCGGCCTT 35734793 CATCACATTGGCCATTCGGCCTT 1 -ATCACATTGGCCATTCGGCCTT 35734816 ATC 1 ATC 35734819 TCATATATAC Statistics Matches: 37, Mismatches: 6, Indels: 14 0.65 0.11 0.25 Matches are distributed among these distances: 22 13 0.35 23 7 0.19 24 7 0.19 25 10 0.27 ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33 Consensus pattern (22 bp): ATCACATTGGCCATTCGGCCTT Found at i:35734778 original size:94 final size:93 Alignment explanation

Indices: 35734607--35734847 Score: 297 Period size: 94 Copynumber: 2.5 Consensus size: 93 35734597 ATATATATTT * * * 35734607 CACATTGACCATTCGGCTTTA-CCACATATGCATATCTCATACATAT-TTCACATTAGCCATTCG 1 CACATTGGCCATTCGGCCTTATCCACATATGCATA-CTC--ACAT-TCATCACATTAGCCATTCG * * 35734670 GCTTTACCACATATATGCATGTTCATATTCAC 62 GCCTTACCACATATATGCATGTTCACATTCAC * * 35734702 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCC 1 CACATTGGCCATTCGGCCTTATC-CACATATGCATACTCACATTCATCACATTAGCCATTCGGCC * * 35734767 TTATCACATATATGCATGTTCACATTCAT 65 TTACCACATATATGCATGTTCACATTCAC * * * * 35734796 CACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT 1 CACATTGGCCATTCGGCCTTATC-CACATATGCATACTCACATTCATCACAT 35734848 AAAATCCTAA Statistics Matches: 128, Mismatches: 15, Indels: 7 0.85 0.10 0.05 Matches are distributed among these distances: 93 1 0.01 94 93 0.73 95 19 0.15 96 4 0.03 97 11 0.09 ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33 Consensus pattern (93 bp): CACATTGGCCATTCGGCCTTATCCACATATGCATACTCACATTCATCACATTAGCCATTCGGCCT TACCACATATATGCATGTTCACATTCAC Found at i:35738740 original size:47 final size:47 Alignment explanation

Indices: 35738686--35738922 Score: 321 Period size: 47 Copynumber: 5.0 Consensus size: 47 35738676 TTAGGATTTT ** * * 35738686 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA 1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA * 35738733 ATGTGATGAATGTGAACCAGTATATATATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAA-CA-TGTATATA--TGTGATAAGGCCGAATGGCCA * ** * 35738784 ATGTGATGAATGTGAACAAGCGTATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA * * 35738831 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA * * 35738878 ATGTGAGGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGC 1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGC 35738923 TAATAAGAAA Statistics Matches: 168, Mismatches: 18, Indels: 8 0.87 0.09 0.04 Matches are distributed among these distances: 47 121 0.72 49 10 0.06 50 2 0.01 51 35 0.21 ACGTcount: A:0.34, C:0.11, G:0.30, T:0.26 Consensus pattern (47 bp): ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA Found at i:35739037 original size:46 final size:46 Alignment explanation

Indices: 35738901--35739037 Score: 193 Period size: 46 Copynumber: 3.0 Consensus size: 46 35738891 GAACATGTAT * * * 35738901 ATATGTGGTAAGGCCGAATGGCTAATAAGAAATGTGTATGAGATAG 1 ATATGTGGTAAAGCCGAATGGCTAATGAGAAATGTGTATGAGATGG * * * 35738947 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG 1 ATATGTGGTAAAGCCGAATGGCTAATGAGAAATGTGTATGAGATGG * * * 35738993 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATGTGTATGAGATG 1 ATATGTGGTAAAGCCGAATGGCTAATGAGAAATGTGTATGAGATG 35739038 TGTATATACA Statistics Matches: 80, Mismatches: 11, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 46 80 1.00 ACGTcount: A:0.35, C:0.08, G:0.31, T:0.26 Consensus pattern (46 bp): ATATGTGGTAAAGCCGAATGGCTAATGAGAAATGTGTATGAGATGG Found at i:35740591 original size:40 final size:40 Alignment explanation

Indices: 35740533--35740886 Score: 600 Period size: 40 Copynumber: 8.8 Consensus size: 40 35740523 TTGAGAGTTA 35740533 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT 1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT * 35740573 TACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT 1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT * * 35740613 TATATCCGAGCTAAGTCCCGAAGAGCATTCATGCTAGTGT 1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT * * * 35740653 TATATCCGGGCTAAGTCTCGAACAGCATTTGTGCTAGTGT 1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT 35740693 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT 1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT * 35740733 TATATTCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT 1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT 35740773 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT 1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT * * 35740813 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGT 1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT * * * 35740853 TACATCCGGGCTAAGTCCTGAAGGGCATTCGTGC 1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGC 35740887 CGGTGATGTG Statistics Matches: 294, Mismatches: 20, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 40 294 1.00 ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28 Consensus pattern (40 bp): TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT Found at i:35741093 original size:25 final size:25 Alignment explanation

Indices: 35741053--35741108 Score: 78 Period size: 25 Copynumber: 2.2 Consensus size: 25 35741043 ATGTGTAATA 35741053 ACGAATGAATATAGGCACTATGTGT 1 ACGAATGAATATAGGCACTATGTGT * * 35741078 GCGAATGAAT-TGAGGCACTGTGTGT 1 ACGAATGAATAT-AGGCACTATGTGT 35741103 ACGAAT 1 ACGAAT 35741109 TCTTTAACTG Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 24 1 0.04 25 26 0.96 ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27 Consensus pattern (25 bp): ACGAATGAATATAGGCACTATGTGT Found at i:35745087 original size:47 final size:47 Alignment explanation

Indices: 35745031--35745319 Score: 371 Period size: 47 Copynumber: 6.1 Consensus size: 47 35745021 TTAGGATTTT ** * * * 35745031 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * * * 35745078 AAGTGATGAATGTGAACCTGTATATATATGTGTGATAAGGTCGAATGGCCA 1 ATGTGATGAATGTGAACATG--CATATA--TGTGATAAGGCCGAATGGCCA * * * 35745129 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * 35745176 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * 35745223 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * * * 35745270 ATGTGAGGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA 35745317 ATG 1 ATG 35745320 AGAAATGTGT Statistics Matches: 216, Mismatches: 22, Indels: 8 0.88 0.09 0.03 Matches are distributed among these distances: 47 171 0.79 49 9 0.04 51 36 0.17 ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27 Consensus pattern (47 bp): ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA Found at i:35745169 original size:25 final size:25 Alignment explanation

Indices: 35745141--35745212 Score: 64 Period size: 22 Copynumber: 3.0 Consensus size: 25 35745131 GTGATGAATG 35745141 TGAACATGCGTATGTGTGATAAGGC 1 TGAACATGCGTATGTGTGATAAGGC * * * 35745166 TG-A-ATG-GCCA-ATGTGATGAATG- 1 TGAACATGCG-TATGTGTGAT-AAGGC 35745188 TGAACATGCGTATGTGTGATAAGGC 1 TGAACATGCGTATGTGTGATAAGGC 35745213 CGAATGGCCA Statistics Matches: 34, Mismatches: 6, Indels: 14 0.63 0.11 0.26 Matches are distributed among these distances: 22 9 0.26 23 8 0.24 24 8 0.24 25 9 0.26 ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28 Consensus pattern (25 bp): TGAACATGCGTATGTGTGATAAGGC Found at i:35745429 original size:46 final size:46 Alignment explanation

Indices: 35745293--35745429 Score: 202 Period size: 46 Copynumber: 3.0 Consensus size: 46 35745283 GAACATGTAT * * * 35745293 ATATGTGGTAAGGCCGAATGGCTAATGAGAAATGTGTATGAGATAG 1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATGTGTATGAGATGG * * 35745339 ATATGAGGTAAAGCCGAATGGCTAATGTGAAACGTGTATGAGATGG 1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATGTGTATGAGATGG * * * 35745385 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG 1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATGTGTATGAGATG 35745430 TGTATATATA Statistics Matches: 81, Mismatches: 10, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 46 81 1.00 ACGTcount: A:0.35, C:0.07, G:0.31, T:0.26 Consensus pattern (46 bp): ATATGTGGTAAAGCCGAATGGCTAATGTGAAATGTGTATGAGATGG Found at i:35748536 original size:20 final size:20 Alignment explanation

Indices: 35748511--35748555 Score: 63 Period size: 20 Copynumber: 2.2 Consensus size: 20 35748501 AGGGACTAAA * 35748511 ATGAAAAGTTGTAAAATTTG 1 ATGAAAAATTGTAAAATTTG * * 35748531 ATGAAAAATTTTAAAATTTT 1 ATGAAAAATTGTAAAATTTG 35748551 ATGAA 1 ATGAA 35748556 TACATGTGCT Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38 Consensus pattern (20 bp): ATGAAAAATTGTAAAATTTG Found at i:35756970 original size:23 final size:23 Alignment explanation

Indices: 35756927--35756970 Score: 61 Period size: 23 Copynumber: 1.9 Consensus size: 23 35756917 ATTTACTGCG ** 35756927 TTACTATTAGCAGCTTTGCTGGA 1 TTACTATTAGCAGCTACGCTGGA * 35756950 TTACTATTAGTAGCTACGCTG 1 TTACTATTAGCAGCTACGCTG 35756971 CGATATTGGT Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 23 18 1.00 ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39 Consensus pattern (23 bp): TTACTATTAGCAGCTACGCTGGA Found at i:35763911 original size:28 final size:28 Alignment explanation

Indices: 35763851--35763911 Score: 68 Period size: 28 Copynumber: 2.2 Consensus size: 28 35763841 AATAACCAAA * * 35763851 ATACCCCTAAGGGGTAAAAATTACTGTT 1 ATACCCCTAAGGGGTAAAAATGACTGCT * * * * 35763879 CTACCCCTAATGGGTGAAAATGATTGCT 1 ATACCCCTAAGGGGTAAAAATGACTGCT 35763907 ATACC 1 ATACC 35763912 TTAGAGGTAG Statistics Matches: 26, Mismatches: 7, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 28 26 1.00 ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28 Consensus pattern (28 bp): ATACCCCTAAGGGGTAAAAATGACTGCT Found at i:35768511 original size:40 final size:40 Alignment explanation

Indices: 35768451--35768674 Score: 270 Period size: 40 Copynumber: 5.5 Consensus size: 40 35768441 TATTCGGATG * 35768451 ATATACGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * * 35768491 ATATCCGGGCTAAGTCCCGAAGGCATTTTTGCGAGTAGTTGCT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT * * * 35768534 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * ** * * 35768574 ATATCCAGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * * * 35768614 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * * 35768654 ATATCC-GACTAAATCCCGAAG 1 ATATCCGGGCTAAGTCCCGAAG 35768675 ATACTTGGGT Statistics Matches: 159, Mismatches: 22, Indels: 7 0.85 0.12 0.04 Matches are distributed among these distances: 39 12 0.08 40 110 0.69 41 1 0.01 43 36 0.23 ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26 Consensus pattern (40 bp): ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT Found at i:35768595 original size:83 final size:79 Alignment explanation

Indices: 35768456--35768674 Score: 280 Period size: 83 Copynumber: 2.7 Consensus size: 79 35768446 GGATGATATA * ** 35768456 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTTT 1 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCC-GGCTAAGTCCCGAAGGCATTCAT 35768521 GCGAGTAGTTG-CTATACC 65 GC---TAG-TGACTATACC * 35768539 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTCCCGAAGGCATTCAT 1 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCC-GGCTAAGTCCCGAAGGCATTCAT * 35768604 GCTAGTGACTATATC 65 GCTAGTGACTATACC * * * * 35768619 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCCGACTAAATCCCGAAG 1 CGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGCTAAGTCCCGAAG 35768675 ATACTTGGGT Statistics Matches: 124, Mismatches: 10, Indels: 8 0.87 0.07 0.06 Matches are distributed among these distances: 79 15 0.12 80 45 0.36 81 2 0.02 83 62 0.50 ACGTcount: A:0.25, C:0.24, G:0.26, T:0.26 Consensus pattern (79 bp): CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGCTAAGTCCCGAAGGCATTCATG CTAGTGACTATACC Found at i:35779493 original size:26 final size:27 Alignment explanation

Indices: 35779444--35779507 Score: 103 Period size: 26 Copynumber: 2.4 Consensus size: 27 35779434 ATTTACTAAA * 35779444 ATACCCCTAAGTATGAAAATTACCATT 1 ATACCCCTAGGTATGAAAATTACCATT * 35779471 ATACCCCTAGGTGT-AAAATTACCATT 1 ATACCCCTAGGTATGAAAATTACCATT 35779497 ATACCCCTAGG 1 ATACCCCTAGG 35779508 GTTAATTTTG Statistics Matches: 35, Mismatches: 2, Indels: 1 0.92 0.05 0.03 Matches are distributed among these distances: 26 23 0.66 27 12 0.34 ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28 Consensus pattern (27 bp): ATACCCCTAGGTATGAAAATTACCATT Found at i:35779649 original size:27 final size:27 Alignment explanation

Indices: 35779611--35779722 Score: 138 Period size: 27 Copynumber: 4.2 Consensus size: 27 35779601 GAGGAAGCGT 35779611 TCTGGTGGCTCTACCATAAATATCT-TA 1 TCTGGTGGCTCTACCAT-AATATCTATA * 35779638 TCTGGTGGCTCTACCATAATATCTATT 1 TCTGGTGGCTCTACCATAATATCTATA * * * 35779665 TCTGGTGGCTCTGCCACAATATCTGTA 1 TCTGGTGGCTCTACCATAATATCTATA * * * 35779692 TCTGGTGACTCTATCACAATATCTAT- 1 TCTGGTGGCTCTACCATAATATCTATA 35779718 TCTGG 1 TCTGG 35779723 CAGCTATGCT Statistics Matches: 75, Mismatches: 9, Indels: 3 0.86 0.10 0.03 Matches are distributed among these distances: 26 12 0.16 27 63 0.84 ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38 Consensus pattern (27 bp): TCTGGTGGCTCTACCATAATATCTATA Found at i:35779694 original size:54 final size:53 Alignment explanation

Indices: 35779610--35779722 Score: 156 Period size: 54 Copynumber: 2.1 Consensus size: 53 35779600 GGAGGAAGCG * * 35779610 TTCTGGTGGCTCTACCATAAATATCTTATCTGGTGGCTCTACCATAATATCTA 1 TTCTGGTGGCTCTACCATAAATATCTTATCTGGTGACTCTACCACAATATCTA * * * 35779663 TTTCTGGTGGCTCTGCCA-CAATATCTGTATCTGGTGACTCTATCACAATATCTA 1 -TTCTGGTGGCTCTACCATAAATATCT-TATCTGGTGACTCTACCACAATATCTA 35779717 TTCTGG 1 TTCTGG 35779723 CAGCTATGCT Statistics Matches: 53, Mismatches: 5, Indels: 3 0.87 0.08 0.05 Matches are distributed among these distances: 53 13 0.25 54 40 0.75 ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38 Consensus pattern (53 bp): TTCTGGTGGCTCTACCATAAATATCTTATCTGGTGACTCTACCACAATATCTA Found at i:35783017 original size:34 final size:34 Alignment explanation

Indices: 35782974--35783047 Score: 123 Period size: 34 Copynumber: 2.2 Consensus size: 34 35782964 ATATGGATCT 35782974 CTGATACTG-TACTGAAATGGGGCTAAGGCCCACA 1 CTGATACTGTTACTGAAAT-GGGCTAAGGCCCACA * 35783008 CTGATACTGTTACTGTAATGGGCTAAGGCCCACA 1 CTGATACTGTTACTGAAATGGGCTAAGGCCCACA 35783042 CTGATA 1 CTGATA 35783048 TTGCCATTAA Statistics Matches: 38, Mismatches: 1, Indels: 2 0.93 0.02 0.05 Matches are distributed among these distances: 34 30 0.79 35 8 0.21 ACGTcount: A:0.28, C:0.23, G:0.24, T:0.24 Consensus pattern (34 bp): CTGATACTGTTACTGAAATGGGCTAAGGCCCACA Found at i:35783065 original size:34 final size:34 Alignment explanation

Indices: 35782993--35783073 Score: 99 Period size: 34 Copynumber: 2.4 Consensus size: 34 35782983 TACTGAAATG ** ** * 35782993 GGGCTAAGGCCCACACTGATACTGTTACTGTAAT 1 GGGCTAAGGCCCACACTGATACTGCCACTAAAAA * * 35783027 GGGCTAAGGCCCACACTGATATTGCCATTAAAAA 1 GGGCTAAGGCCCACACTGATACTGCCACTAAAAA 35783061 GGGCTAAGGCCCA 1 GGGCTAAGGCCCA 35783074 GACTATTTTG Statistics Matches: 40, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 34 40 1.00 ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21 Consensus pattern (34 bp): GGGCTAAGGCCCACACTGATACTGCCACTAAAAA Found at i:35791432 original size:32 final size:32 Alignment explanation

Indices: 35791396--35791466 Score: 115 Period size: 32 Copynumber: 2.2 Consensus size: 32 35791386 ATCATTGCTG 35791396 CTGTTTCCTAACTATTCCATGGCCAACTCTAA 1 CTGTTTCCTAACTATTCCATGGCCAACTCTAA * * 35791428 CTGTTTCCTAACTGTTCCATGGCCAACTCTTA 1 CTGTTTCCTAACTATTCCATGGCCAACTCTAA * 35791460 CTCTTTC 1 CTGTTTC 35791467 ATACTTTATT Statistics Matches: 36, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 32 36 1.00 ACGTcount: A:0.20, C:0.32, G:0.10, T:0.38 Consensus pattern (32 bp): CTGTTTCCTAACTATTCCATGGCCAACTCTAA Found at i:35792000 original size:53 final size:53 Alignment explanation

Indices: 35791932--35792138 Score: 216 Period size: 53 Copynumber: 3.8 Consensus size: 53 35791922 TTCCTTTTTA * * * 35791932 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG 1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG * * * * * * 35791985 AACTCACCATTGCCATGCCTTGGCATGGTTTTACATGGGATCTTTGCCTTATTG 1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA-TG ** * * * * * * 35792039 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA 1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G * * 35792094 AACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT 1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT 35792139 AAACCCTAAT Statistics Matches: 122, Mismatches: 29, Indels: 5 0.78 0.19 0.03 Matches are distributed among these distances: 53 44 0.36 54 40 0.33 55 38 0.31 ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38 Consensus pattern (53 bp): AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG Found at i:35792506 original size:30 final size:30 Alignment explanation

Indices: 35792472--35792528 Score: 78 Period size: 30 Copynumber: 1.9 Consensus size: 30 35792462 CCTTAACTCT 35792472 AACTTTGGAAAAATTACAATTTTGCCCTTA 1 AACTTTGGAAAAATTACAATTTTGCCCTTA * * * * 35792502 AACTTTTGCAAATTTACACTTTTGCCC 1 AACTTTGGAAAAATTACAATTTTGCCC 35792529 CAAGGCTCGA Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 30 23 1.00 ACGTcount: A:0.32, C:0.21, G:0.09, T:0.39 Consensus pattern (30 bp): AACTTTGGAAAAATTACAATTTTGCCCTTA Found at i:35793115 original size:37 final size:37 Alignment explanation

Indices: 35793073--35793148 Score: 152 Period size: 37 Copynumber: 2.1 Consensus size: 37 35793063 TGAAAACCTA 35793073 ATGATCTAATTACCATTTAAGGACCTCTACTTTAATT 1 ATGATCTAATTACCATTTAAGGACCTCTACTTTAATT 35793110 ATGATCTAATTACCATTTAAGGACCTCTACTTTAATT 1 ATGATCTAATTACCATTTAAGGACCTCTACTTTAATT 35793147 AT 1 AT 35793149 ACTCATTAAT Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 37 39 1.00 ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41 Consensus pattern (37 bp): ATGATCTAATTACCATTTAAGGACCTCTACTTTAATT Found at i:35794156 original size:123 final size:122 Alignment explanation

Indices: 35793937--35794184 Score: 433 Period size: 123 Copynumber: 2.0 Consensus size: 122 35793927 CTCAATTTTC * * * 35793937 AAAAGACAAATGATTTTCAACTACCACGTTTCGCAACTTGTTTTAAAAGCTTTTGCAATGAACAA 1 AAAAGACAAATGATTTTCAACTACCACGTTCCGCAACTCGTTTTAAAAGCTTTTGCAATGAAAAA * * 35794002 TGTTTTTAAAATGTAATAACAACTTATTATGACACTTGTTTTGCTAAAAAAAACCTTT 66 TGTTTTTAAAATGTAATAACAACTTAGTATGACACTTGTTTTGC-AAAAAAAACCTGT 35794060 AAAAGACAAATGATTTTCAACTACCACGTTCCGCAACTCGTTTTAAAAGCTTTTGCAATGAAAAA 1 AAAAGACAAATGATTTTCAACTACCACGTTCCGCAACTCGTTTTAAAAGCTTTTGCAATGAAAAA * 35794125 TGTTTTTAAAATGTAATAACAACTTAGTATGACACTTGTTTTGCAAAACAAACCTGT 66 TGTTTTTAAAATGTAATAACAACTTAGTATGACACTTGTTTTGCAAAAAAAACCTGT 35794182 AAA 1 AAA 35794185 TTAACAAGGA Statistics Matches: 119, Mismatches: 6, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 122 14 0.12 123 105 0.88 ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33 Consensus pattern (122 bp): AAAAGACAAATGATTTTCAACTACCACGTTCCGCAACTCGTTTTAAAAGCTTTTGCAATGAAAAA TGTTTTTAAAATGTAATAACAACTTAGTATGACACTTGTTTTGCAAAAAAAACCTGT Found at i:35816524 original size:40 final size:40 Alignment explanation

Indices: 35816465--35816577 Score: 122 Period size: 40 Copynumber: 2.8 Consensus size: 40 35816455 GACTATGTTC * * 35816465 GGCACTGAGTGTGTGATTCAAAATAGCTTCGGCTATAAAT-A 1 GGCACTAAGTGTGCGATTCAAAATAGCTTCGGCTAT--ATGA * * * 35816506 -GCACTAAGTGTGCAATTCAAAATAGTTTTGGCTATATGA 1 GGCACTAAGTGTGCGATTCAAAATAGCTTCGGCTATATGA * * 35816545 GGCACTAAGTGTGCGATATCGAGATAGCTTCGG 1 GGCACTAAGTGTGCGAT-TCAAAATAGCTTCGG 35816578 TTAGCTTCGA Statistics Matches: 59, Mismatches: 10, Indels: 6 0.79 0.13 0.08 Matches are distributed among these distances: 38 2 0.03 39 1 0.02 40 45 0.76 41 11 0.19 ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29 Consensus pattern (40 bp): GGCACTAAGTGTGCGATTCAAAATAGCTTCGGCTATATGA Found at i:35825432 original size:20 final size:22 Alignment explanation

Indices: 35825403--35825446 Score: 58 Period size: 21 Copynumber: 2.1 Consensus size: 22 35825393 TTGCCTGTAC 35825403 TTAGGTACATT-TAGTT-GTATT 1 TTAGGTACATTCTA-TTAGTATT 35825424 TTAGG-ACATTCTATTAGTATT 1 TTAGGTACATTCTATTAGTATT 35825445 TT 1 TT 35825447 TCTTGTTTTA Statistics Matches: 21, Mismatches: 0, Indels: 4 0.84 0.00 0.16 Matches are distributed among these distances: 20 7 0.33 21 14 0.67 ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52 Consensus pattern (22 bp): TTAGGTACATTCTATTAGTATT Found at i:35826625 original size:54 final size:52 Alignment explanation

Indices: 35826548--35826775 Score: 260 Period size: 54 Copynumber: 4.2 Consensus size: 52 35826538 GAGCATAATT * * * * 35826548 GTCATTTTACCATACAAGAATATTACGATCATTTTATCCTACAGGGACATTACA 1 GTCATTTTACC-TACAGGGATATTACGATCATTTTA-CCTACAGGGGCATTACG * 35826602 GTCATTTTATCCTACAGGGATATTACGGTCATTTTACACTACAGGGGCATTACG 1 GTCATTTTA-CCTACAGGGATATTACGATCATTTTAC-CTACAGGGGCATTACG * * * 35826656 GTCATTTTACTTATAGAGG-TATTACGGTCATTTTACCCTACAGGGGCATTACG 1 GTCATTTTACCTACAG-GGATATTACGATCATTTTA-CCTACAGGGGCATTACG * * * * * 35826709 GTCATTTTACCCCACAGGGGTATTACAATCATTTTACCTTATAAGGGCATTACG 1 GTCATTTTA-CCTACAGGGATATTACGATCATTTTACC-TACAGGGGCATTACG 35826763 GTCATTTTACCTA 1 GTCATTTTACCTA 35826776 TTTTAGGGTT Statistics Matches: 152, Mismatches: 15, Indels: 15 0.84 0.08 0.08 Matches are distributed among these distances: 53 54 0.36 54 96 0.63 55 2 0.01 ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35 Consensus pattern (52 bp): GTCATTTTACCTACAGGGATATTACGATCATTTTACCTACAGGGGCATTACG Found at i:35826707 original size:80 final size:81 Alignment explanation

Indices: 35826569--35826773 Score: 247 Period size: 80 Copynumber: 2.5 Consensus size: 81 35826559 ATACAAGAAT * * * * * 35826569 ATTACGATCATTTTATCC-TA-CAGGGACATTACAGTCATTTTATCCTACAGGGATATTACGGTC 1 ATTACAATCATTTTA-CCTTATAAGGG-CATTACGGTCATTTTACCCTACAGGGACATTACGGTC * 35826632 ATTTTACACTACAGGGGC 64 ATTTTACACCACAGGGGC ** * * 35826650 ATTACGGTCATTTTA-CTTAT-AGAGGTATTACGGTCATTTTACCCTACAGGGGCATTACGGTCA 1 ATTACAATCATTTTACCTTATAAG-GGCATTACGGTCATTTTACCCTACAGGGACATTACGGTCA * * 35826713 TTTTACCCCACAGGGGT 65 TTTTACACCACAGGGGC 35826730 ATTACAATCATTTTACCTTATAAGGGCATTACGGTCATTTTACC 1 ATTACAATCATTTTACCTTATAAGGGCATTACGGTCATTTTACC 35826774 TATTTTAGGG Statistics Matches: 107, Mismatches: 12, Indels: 10 0.83 0.09 0.08 Matches are distributed among these distances: 79 1 0.01 80 64 0.60 81 40 0.37 82 2 0.02 ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35 Consensus pattern (81 bp): ATTACAATCATTTTACCTTATAAGGGCATTACGGTCATTTTACCCTACAGGGACATTACGGTCAT TTTACACCACAGGGGC Found at i:35826713 original size:107 final size:107 Alignment explanation

Indices: 35826568--35826772 Score: 295 Period size: 107 Copynumber: 1.9 Consensus size: 107 35826558 CATACAAGAA * * * ** 35826568 TATTACGATCATTTTATCCTACAGGGACATTACAGTCATTTTATCCTACAGGGATATTACGGTCA 1 TATTACGATCATTTTACCCTACAGGGACATTACAGTCATTTTACCCCACAGGGATATTACAATCA * 35826633 TTTTACAC-TACAGGGGCATTACGGTCATTTTACTTATAGAGG 66 TTTTAC-CTTACAAGGGCATTACGGTCATTTTACTTATAGAGG * * * * 35826675 TATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCCACAGGGGTATTACAATCA 1 TATTACGATCATTTTACCCTACAGGGACATTACAGTCATTTTACCCCACAGGGATATTACAATCA * 35826740 TTTTACCTTATAAGGGCATTACGGTCATTTTAC 66 TTTTACCTTACAAGGGCATTACGGTCATTTTAC 35826773 CTATTTTAGG Statistics Matches: 86, Mismatches: 11, Indels: 2 0.87 0.11 0.02 Matches are distributed among these distances: 106 1 0.01 107 85 0.99 ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35 Consensus pattern (107 bp): TATTACGATCATTTTACCCTACAGGGACATTACAGTCATTTTACCCCACAGGGATATTACAATCA TTTTACCTTACAAGGGCATTACGGTCATTTTACTTATAGAGG Found at i:35826745 original size:27 final size:27 Alignment explanation

Indices: 35826548--35826773 Score: 229 Period size: 27 Copynumber: 8.4 Consensus size: 27 35826538 GAGCATAATT * * ** 35826548 GTCATTTTACCATACAAGAATATTACG 1 GTCATTTTACCCTACAGGGGTATTACG * * ** * 35826575 ATCATTTTATCCTACAGGGACATTACA 1 GTCATTTTACCCTACAGGGGTATTACG * * 35826602 GTCATTTTATCCTACAGGGATATTACG 1 GTCATTTTACCCTACAGGGGTATTACG * * 35826629 GTCATTTTACACTACAGGGGCATTACG 1 GTCATTTTACCCTACAGGGGTATTACG * * * 35826656 GTCATTTTA-CTTATAGAGGTATTACG 1 GTCATTTTACCCTACAGGGGTATTACG * 35826682 GTCATTTTACCCTACAGGGGCATTACG 1 GTCATTTTACCCTACAGGGGTATTACG * * 35826709 GTCATTTTACCCCACAGGGGTATTACA 1 GTCATTTTACCCTACAGGGGTATTACG * * * * * 35826736 ATCATTTTACCTTATAAGGGCATTACG 1 GTCATTTTACCCTACAGGGGTATTACG 35826763 GTCATTTTACC 1 GTCATTTTACC 35826774 TATTTTAGGG Statistics Matches: 164, Mismatches: 34, Indels: 2 0.82 0.17 0.01 Matches are distributed among these distances: 26 21 0.13 27 143 0.87 ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35 Consensus pattern (27 bp): GTCATTTTACCCTACAGGGGTATTACG Found at i:35827051 original size:132 final size:132 Alignment explanation

Indices: 35826814--35827072 Score: 437 Period size: 132 Copynumber: 2.0 Consensus size: 132 35826804 CCTCCGAAGG 35826814 TCTACAATCGCCTCGAACGACACAGATAACCAAAATGATCATAACGATGTAAATAGGCCCAAGGC 1 TCTACAATCGCCTCGAACGACACAGATAACCAAAATGATCATAACGATGTAAATAGGCCCAAGGC * 35826879 CCATTACTCGGCCCAAGTGGGCCCACACGCTCGCGTGGCCCATTTAGCCCAAATTTAGTTACAAA 66 CCATTACTCGGCCCAAGTGGGCCCACACGCTCGCGTGGCCCATTTAGCCCAAATTTACTTACAAA 35826944 GT 131 GT * * ** * * * 35826946 TCTACAATCGCCTCGAATGATACAGATAACTTAAATGATCATAACGGTGTAAATGGGCCCGAGGC 1 TCTACAATCGCCTCGAACGACACAGATAACCAAAATGATCATAACGATGTAAATAGGCCCAAGGC * 35827011 CCATTACTCGGCCCAAGTGGGCCCACACGCTCGTGTGGCCCATTTAGCCCAAATTTACTTAC 66 CCATTACTCGGCCCAAGTGGGCCCACACGCTCGCGTGGCCCATTTAGCCCAAATTTACTTAC 35827073 GGCTATGTGA Statistics Matches: 118, Mismatches: 9, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 132 118 1.00 ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22 Consensus pattern (132 bp): TCTACAATCGCCTCGAACGACACAGATAACCAAAATGATCATAACGATGTAAATAGGCCCAAGGC CCATTACTCGGCCCAAGTGGGCCCACACGCTCGCGTGGCCCATTTAGCCCAAATTTACTTACAAA GT Found at i:35832802 original size:39 final size:39 Alignment explanation

Indices: 35832776--35832887 Score: 206 Period size: 39 Copynumber: 2.9 Consensus size: 39 35832766 TTCCAGTACG * 35832776 TAGCCTGCGGACCTCAAGTCCGGATATATTTCCAGCATA 1 TAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATA 35832815 TAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATA 1 TAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATA * 35832854 TAGCCTGCAGACCTCATGTCCGGATATATTTCCA 1 TAGCCTGCGGACCTCATGTCCGGATATATTTCCA 35832888 ATCTCATATA Statistics Matches: 71, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 39 71 1.00 ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28 Consensus pattern (39 bp): TAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATA Found at i:35854374 original size:40 final size:39 Alignment explanation

Indices: 35854337--35854511 Score: 178 Period size: 40 Copynumber: 4.5 Consensus size: 39 35854327 ATATCCGGAC * 35854337 TAAGATCCGAAGGCATTTGTGCGAGATAC-AAGTTCCGGGT 1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAA-ATCCGGGT * * * 35854377 TAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGT 1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT * * * 35854417 TAAGTCCCGAAGGCATTCGTGCGAGTTA-TTAATCCGGGT 1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT * * * 35854456 TAAGTCCGAAGGCA-TTGTGTGAGTTACTAAA-CCGGGC 1 TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT * 35854493 TATGTCCCGAAGGCATTTG 1 TAAGT-CCGAAGGCATTTG 35854512 AACGAGGAGC Statistics Matches: 115, Mismatches: 15, Indels: 11 0.82 0.11 0.08 Matches are distributed among these distances: 37 19 0.17 38 21 0.18 39 18 0.16 40 55 0.48 41 2 0.02 ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26 Consensus pattern (39 bp): TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT Found at i:35854427 original size:80 final size:77 Alignment explanation

Indices: 35854290--35854511 Score: 225 Period size: 80 Copynumber: 2.8 Consensus size: 77 35854280 TTGAATGCTG * * * * * * 35854290 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT 1 TCCGGGTTAAG-CCCGAAGGCTTTGTGCGAGGT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT 35854354 TGTGCGAGATA-CAA 63 TGTGCGAGATATCAA * 35854368 GTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCAT 1 --TCCGGGTTAAG-CCCGAAGG-CTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCAT * * * 35854433 TCGTGCGAGTTATTAA 62 TTGTGCGAGATATCAA * * * * * 35854449 TCCGGGTTAAGTCCGAAGGCATTGTGTGAGTTACTAAA-CCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGTTAAGCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG 35854512 AACGAGGAGC Statistics Matches: 121, Mismatches: 18, Indels: 10 0.81 0.12 0.07 Matches are distributed among these distances: 76 22 0.18 77 16 0.13 78 7 0.06 79 12 0.10 80 51 0.42 81 13 0.11 ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26 Consensus pattern (77 bp): TCCGGGTTAAGCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGT GCGAGATATCAA Found at i:35854544 original size:77 final size:79 Alignment explanation

Indices: 35854370--35854544 Score: 180 Period size: 76 Copynumber: 2.3 Consensus size: 79 35854360 AGATACAAGT ** * * 35854370 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTC 1 TCCGGGTTAAATCCCGAAGGCCATTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTC ** * * 35854435 GTGCGAGTTATTAA 66 GAACGAGTGACTAA * * * * * 35854449 TCCGGGTTAAGT-CCGAAGG-CATTGTGTGAGTTACTAAA-CCGGGCTATGTCCCGAAGGCATTT 1 TCCGGGTTAAATCCCGAAGGCCATTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTC 35854511 GAACGAG-GAGCTATA 66 GAACGAGTGA-CTA-A 35854526 TCC-GGTTAAATCCCGAAGG 1 TCCGGGTTAAATCCCGAAGG 35854545 TACGTGATTT Statistics Matches: 81, Mismatches: 12, Indels: 8 0.80 0.12 0.08 Matches are distributed among these distances: 75 1 0.01 76 35 0.43 77 27 0.33 78 7 0.09 79 11 0.14 ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25 Consensus pattern (79 bp): TCCGGGTTAAATCCCGAAGGCCATTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTC GAACGAGTGACTAA Found at i:35858013 original size:46 final size:48 Alignment explanation

Indices: 35857958--35858078 Score: 156 Period size: 46 Copynumber: 2.6 Consensus size: 48 35857948 TGATATGTGT * * * 35857958 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA-CGA-GA 1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATAGACAA * * * 35858004 GCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGATATACAA 1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATAGACAA * * 35858052 GCTAGTGTAAGACCTATCTGGGACATG 1 GCTAGTGTAAGACATGTCTGGGACATG 35858079 GCGTCAACTT Statistics Matches: 65, Mismatches: 8, Indels: 2 0.87 0.11 0.03 Matches are distributed among these distances: 46 38 0.58 47 1 0.02 48 26 0.40 ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24 Consensus pattern (48 bp): GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATAGACAA Found at i:35858159 original size:49 final size:49 Alignment explanation

Indices: 35857961--35858270 Score: 212 Period size: 49 Copynumber: 6.5 Consensus size: 49 35857951 TATGTGTGCT * * * * 35857961 AGTGTAAGACATGTCTGGGACAT-GCATCGGCATTG--AGACGAGAGCT 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGAGAGCC * * * * * * * * * 35858007 AGTGTAAGACATGTCTGGGACAT-GCATTGGCCTCGAGATAT-ACAAGCT 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGA-GAGCC * * * * * * 35858055 AGTGTAAGACCTATCTGGGACATGGCGTCAAC-TTG-T---TGTGTGTC 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGAGAGCC 35858099 AGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGAGAGCC 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGAGAGCC * ** * * * * ** 35858148 AGTGTAAGACCTGTTTGGGACACAGCATCGGCCTTGATATATGAAAGTT 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGAGAGCC * * ** 35858197 AGTGTAAGACCTATCTGGGACATGGCATCGACTTTGAT-G-TGCTAGCC 1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGAGAGCC * * 35858244 AGTGTAAGATCATGTCTAGGACATGGC 1 AGTGTAAGA-CCTGTCTGGGACATGGC 35858271 GTCAGTATCT Statistics Matches: 205, Mismatches: 48, Indels: 20 0.75 0.18 0.07 Matches are distributed among these distances: 44 31 0.15 45 3 0.01 46 33 0.16 47 14 0.07 48 43 0.21 49 81 0.40 ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26 Consensus pattern (49 bp): AGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGAGAGCC Found at i:35858219 original size:142 final size:139 Alignment explanation

Indices: 35857952--35858270 Score: 392 Period size: 142 Copynumber: 2.2 Consensus size: 139 35857942 ATTGGGTGAT * * 35857952 ATGTGTGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCATTGAGACGAGAGCTAGTGTAAGA 1 ATGTGTGC-AGTGTAAGACATGTCTGGGACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGA * * 35858016 CATGTCTGGGACATGCATTGGCCTCGAGATATACAAGCTAGTGTAAGACCTATCTGGGACATGGC 65 CATGTCTGGGACAAGCATCGGCCTCGAGATATACAAGCTAGTGTAAGACCTATCTGGGACATGGC * 35858081 GTCAAC-TTG 130 ATCAACTTTG * * * 35858090 TTGTGTGTCAGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGAGAGCCAGTGTAA 1 ATGTGTG-CAGTGTAAGACATGTCTGGGACATGGCATCGACATTG--AGACGAGAGCCAGTGTAA * * * * * 35858155 GACCTGTTTGGGACACAGCATCGGCCTTGATATATGA-AAGTTAGTGTAAGACCTATCTGGGACA 63 GACATGTCTGGGACA-AGCATCGGCCTCGAGATAT-ACAAGCTAGTGTAAGACCTATCTGGGACA * 35858219 TGGCATCGACTTTG 126 TGGCATCAACTTTG * 35858233 ATGTGCTAGCCAGTGTAAGATCATGTCTAGGACATGGC 1 ATGTG-T-G-CAGTGTAAGA-CATGTCTGGGACATGGC 35858271 GTCAGTATCT Statistics Matches: 153, Mismatches: 18, Indels: 12 0.84 0.10 0.07 Matches are distributed among these distances: 138 28 0.18 139 12 0.08 141 29 0.19 142 49 0.32 143 8 0.05 144 1 0.01 145 11 0.07 146 15 0.10 ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27 Consensus pattern (139 bp): ATGTGTGCAGTGTAAGACATGTCTGGGACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGAC ATGTCTGGGACAAGCATCGGCCTCGAGATATACAAGCTAGTGTAAGACCTATCTGGGACATGGCA TCAACTTTG Found at i:35861786 original size:43 final size:43 Alignment explanation

Indices: 35861719--35861836 Score: 150 Period size: 43 Copynumber: 2.7 Consensus size: 43 35861709 TAAGCTTGTA * * 35861719 CAATGCCAACGTCCCAGACGTGGTCTTACATGT-AATCAAATAT 1 CAATGCCAACGTCCCAGATGTGGTCTTACATGTAAATCAAA-AC * * * 35861762 CGATGCC-ACTGTCCCAGATATGGTCTTACACGTAAATCAAAAC 1 CAATGCCAAC-GTCCCAGATGTGGTCTTACATGTAAATCAAAAC * 35861805 CAATGCCAACGTCCCAGTTGTGGTCTTACATG 1 CAATGCCAACGTCCCAGATGTGGTCTTACATG 35861837 AAAACACATA Statistics Matches: 63, Mismatches: 9, Indels: 6 0.81 0.12 0.08 Matches are distributed among these distances: 42 2 0.03 43 52 0.83 44 9 0.14 ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25 Consensus pattern (43 bp): CAATGCCAACGTCCCAGATGTGGTCTTACATGTAAATCAAAAC Found at i:35868409 original size:7 final size:7 Alignment explanation

Indices: 35868397--35868422 Score: 52 Period size: 7 Copynumber: 3.7 Consensus size: 7 35868387 CCATATCTTA 35868397 TTCATGT 1 TTCATGT 35868404 TTCATGT 1 TTCATGT 35868411 TTCATGT 1 TTCATGT 35868418 TTCAT 1 TTCAT 35868423 TTACACATAT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 19 1.00 ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58 Consensus pattern (7 bp): TTCATGT Found at i:35868453 original size:21 final size:22 Alignment explanation

Indices: 35868417--35868460 Score: 63 Period size: 21 Copynumber: 2.0 Consensus size: 22 35868407 ATGTTTCATG 35868417 TTTCATTTACACATAT-TCACA 1 TTTCATTTACACATATATCACA * * 35868438 TTTCATTTCCATATATATCACA 1 TTTCATTTACACATATATCACA 35868460 T 1 T 35868461 AACATTCTTT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 21 14 0.70 22 6 0.30 ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45 Consensus pattern (22 bp): TTTCATTTACACATATATCACA Found at i:35868715 original size:44 final size:44 Alignment explanation

Indices: 35868624--35868753 Score: 133 Period size: 43 Copynumber: 3.0 Consensus size: 44 35868614 AGCTCGTACA ** * * 35868624 ATGCCAACATCCCAGATGTGGTCTTACATGT-AATCA-AATATTG 1 ATGCCAACATCCCAGACATGGTCTTACACGTAAATCACAA-ATCG * 35868667 ATGCC-ACTATCCTAGACATGGTCTTACACGTAAATCACAAATCG 1 ATGCCAAC-ATCCCAGACATGGTCTTACACGTAAATCACAAATCG * * * * 35868711 ATGCCAACGTCCCAGACGTGGTCTTACACG-AAAACACATATCG 1 ATGCCAACATCCCAGACATGGTCTTACACGTAAATCACAAATCG 35868754 TGTAACGCCC Statistics Matches: 73, Mismatches: 10, Indels: 8 0.80 0.11 0.09 Matches are distributed among these distances: 42 2 0.03 43 35 0.48 44 32 0.44 45 4 0.05 ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25 Consensus pattern (44 bp): ATGCCAACATCCCAGACATGGTCTTACACGTAAATCACAAATCG Found at i:35870785 original size:27 final size:27 Alignment explanation

Indices: 35870714--35870787 Score: 94 Period size: 27 Copynumber: 2.7 Consensus size: 27 35870704 CGTACCTGAA * * * * 35870714 CCCTTATGAGACAAAATAACTATTTTT 1 CCCTTATGAGATAAAATGACAATTTTG * * 35870741 CCTTTATGTGATAAAATGACAATTTTG 1 CCCTTATGAGATAAAATGACAATTTTG 35870768 CCCTTATGAGATAAAATGAC 1 CCCTTATGAGATAAAATGAC 35870788 TGTAATACCC Statistics Matches: 39, Mismatches: 8, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 27 39 1.00 ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35 Consensus pattern (27 bp): CCCTTATGAGATAAAATGACAATTTTG Found at i:35870798 original size:27 final size:26 Alignment explanation

Indices: 35870768--35870870 Score: 93 Period size: 27 Copynumber: 3.8 Consensus size: 26 35870758 GACAATTTTG * 35870768 CCCTTATGAGATAAAATGACTGTAATA 1 CCCTTAT-AGGTAAAATGACTGTAATA * * 35870795 CCCTCATAGGGTAAAATGA-TCGAAATA 1 CCCTTATA-GGTAAAATGACT-GTAATA * 35870822 CCCCTATAAGGTAAAATGACTGTAATA 1 CCCTTAT-AGGTAAAATGACTGTAATA * 35870849 CCTCTGTA-AGGTAAAATAACTG 1 CC-CT-TATAGGTAAAATGACTG 35870871 ATTTTCCCTA Statistics Matches: 62, Mismatches: 8, Indels: 12 0.76 0.10 0.15 Matches are distributed among these distances: 26 2 0.03 27 55 0.89 28 3 0.05 29 2 0.03 ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26 Consensus pattern (26 bp): CCCTTATAGGTAAAATGACTGTAATA Found at i:35875333 original size:47 final size:47 Alignment explanation

Indices: 35875276--35875577 Score: 416 Period size: 47 Copynumber: 6.4 Consensus size: 47 35875266 ATTGATGTAC * * * 35875276 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA 1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA * 35875323 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA 1 AAGTGTATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA * * 35875372 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA 1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA * * 35875419 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA 1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA * 35875466 ACA-TG--TGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA 1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA * * 35875511 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGG 1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA * 35875558 AAGTGTATAAATGTGATAAG 1 AAGTGTATATATGTGATAAG 35875578 TCCCGAAGGG Statistics Matches: 238, Mismatches: 11, Indels: 12 0.91 0.04 0.05 Matches are distributed among these distances: 44 1 0.00 45 41 0.17 47 155 0.65 49 40 0.17 50 1 0.00 ACGTcount: A:0.32, C:0.09, G:0.31, T:0.27 Consensus pattern (47 bp): AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA Found at i:35875526 original size:139 final size:142 Alignment explanation

Indices: 35875287--35875556 Score: 422 Period size: 139 Copynumber: 1.9 Consensus size: 142 35875277 AGTATATATA * * * 35875287 TGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAAAGTATATATATGCGTGATAAGGCCGAAT 1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGCATATATAT-CGTGATAAGGCCGAAT * * 35875352 GGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGT 65 GGCCAATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT 35875417 GAACATGTGTATG 130 GAACATGTGTATG * * 35875430 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTG-AA-CATGTGTAT-GTGATAAGGCCGAATG 1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGCATATATATCGTGATAAGGCCGAATG * 35875492 GCCAATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGT 66 GCCAATGTGATGAATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT 35875556 G 130 G 35875557 GAAGTGTATA Statistics Matches: 118, Mismatches: 8, Indels: 6 0.89 0.06 0.05 Matches are distributed among these distances: 138 1 0.01 139 76 0.64 141 6 0.05 142 2 0.02 143 33 0.28 ACGTcount: A:0.30, C:0.10, G:0.32, T:0.27 Consensus pattern (142 bp): TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGCATATATATCGTGATAAGGCCGAATG GCCAATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG AACATGTGTATG Found at i:35875538 original size:92 final size:92 Alignment explanation

Indices: 35875285--35875556 Score: 438 Period size: 92 Copynumber: 2.9 Consensus size: 92 35875275 CAAGTATATA * * * 35875285 TATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAAAGTATATATATGCGTGATAAGGCCGA 1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT--GTGATAAGGCCGA 35875350 ATGGCCAATGTGATGAATGTGAACATGTG 64 ATGGCCAATGTGATGAATGTGAACATGTG * * 35875379 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGTGTATGTGTGATAAGGCCG 1 TA--TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCG 35875443 AATGGCCAATGTGATGAATGTGAACATGTG 63 AATGGCCAATGTGATGAATGTGAACATGTG 35875473 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAT 1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAT * 35875538 GGCCAATGTGATGGATGTG 66 GGCCAATGTGATGAATGTG 35875557 GAAGTGTATA Statistics Matches: 166, Mismatches: 8, Indels: 10 0.90 0.04 0.05 Matches are distributed among these distances: 91 1 0.01 92 77 0.46 94 46 0.28 96 41 0.25 97 1 0.01 ACGTcount: A:0.31, C:0.10, G:0.32, T:0.27 Consensus pattern (92 bp): TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAT GGCCAATGTGATGAATGTGAACATGTG Done.