Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold1009

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1861391
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29

Warning! 223269 characters in sequence are not A, C, G, or T


File 6 of 5

Found at i:1522799 original size:21 final size:21

Alignment explanation

Indices: 1522773--1522814 Score: 59 Period size: 21 Copynumber: 2.0 Consensus size: 21 1522763 ATAATTTGAA * 1522773 AGCATT-AGCACAACAATAATG 1 AGCATTCAGAACAACAA-AATG 1522794 AGCATTCAGAACAACAAAATG 1 AGCATTCAGAACAACAAAATG 1522815 GTAAATACAG Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 21 10 0.53 22 9 0.47 ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17 Consensus pattern (21 bp): AGCATTCAGAACAACAAAATG Found at i:1524370 original size:2 final size:2 Alignment explanation

Indices: 1524365--1524423 Score: 118 Period size: 2 Copynumber: 29.5 Consensus size: 2 1524355 TGTTAAAAAT 1524365 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1524407 GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA G 1524424 TGTGAGTAGC Statistics Matches: 57, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 57 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:1527235 original size:15 final size:15 Alignment explanation

Indices: 1527215--1527249 Score: 54 Period size: 15 Copynumber: 2.3 Consensus size: 15 1527205 ATGACTTGCA 1527215 TTATATTTT-TGATTT 1 TTATATTTTAT-ATTT 1527230 TTATATTTTATATTT 1 TTATATTTTATATTT 1527245 TTATA 1 TTATA 1527250 AACTGAACTG Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 15 18 0.95 16 1 0.05 ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71 Consensus pattern (15 bp): TTATATTTTATATTT Found at i:1531347 original size:13 final size:13 Alignment explanation

Indices: 1531329--1531358 Score: 51 Period size: 13 Copynumber: 2.3 Consensus size: 13 1531319 CACAACAAGA 1531329 TTCATATGGGATT 1 TTCATATGGGATT * 1531342 TTCATATGGGGTT 1 TTCATATGGGATT 1531355 TTCA 1 TTCA 1531359 CGAAATTCCT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.20, C:0.10, G:0.23, T:0.47 Consensus pattern (13 bp): TTCATATGGGATT Found at i:1534532 original size:2 final size:2 Alignment explanation

Indices: 1534525--1534573 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 1534515 TATTTAAATA 1534525 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1534567 TC TC TC T 1 TC TC TC T 1534574 GTTAATCATC Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1538606 original size:56 final size:54 Alignment explanation

Indices: 1538540--1538662 Score: 138 Period size: 55 Copynumber: 2.2 Consensus size: 54 1538530 TATAAAGTGG * * 1538540 ATGAAAAAATATCAAAGAGACCATTAAAATGTAAAATGAAGTGCTACTTATCATTT 1 ATGAATAAATATCAAA-AGA-CATGAAAATGTAAAATGAAGTGCTACTTATCATTT *** * * * 1538596 ATGAATAAATATTTTTAAGATATGCAAATGTAAAATTAAGTGCTACTTATCATTT 1 ATGAATAAATA-TCAAAAGACATGAAAATGTAAAATGAAGTGCTACTTATCATTT * 1538651 GTGAATAAATAT 1 ATGAATAAATAT 1538663 TGTAGTTGTT Statistics Matches: 57, Mismatches: 9, Indels: 4 0.81 0.13 0.06 Matches are distributed among these distances: 54 1 0.02 55 41 0.72 56 13 0.23 57 2 0.04 ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34 Consensus pattern (54 bp): ATGAATAAATATCAAAAGACATGAAAATGTAAAATGAAGTGCTACTTATCATTT Found at i:1540223 original size:2 final size:2 Alignment explanation

Indices: 1540216--1540255 Score: 62 Period size: 2 Copynumber: 20.0 Consensus size: 2 1540206 AATTTTTCAC * * 1540216 CT CT CT CT CT CT CT CT CT CT CT CT TT TT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1540256 TTCAAATTCA Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55 Consensus pattern (2 bp): CT Found at i:1549656 original size:2 final size:2 Alignment explanation

Indices: 1549651--1549692 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 1549641 TATATATATA 1549651 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 1549693 ACAAGACATA Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50 Consensus pattern (2 bp): TG Found at i:1553158 original size:21 final size:21 Alignment explanation

Indices: 1553133--1553266 Score: 171 Period size: 21 Copynumber: 6.4 Consensus size: 21 1553123 ATATGCCACC 1553133 ACTTGTCAGATAATTATGTCG 1 ACTTGTCAGATAATTATGTCG ** 1553154 ACTTGTCAGATCTTTATGTCG 1 ACTTGTCAGATAATTATGTCG 1553175 ACTTGTCAGATAATTATGTCG 1 ACTTGTCAGATAATTATGTCG * 1553196 ACTTGTCAGAT-CTTGATGTCG 1 ACTTGTCAGATAATT-ATGTCG * * 1553217 ACTTGTCAGATAATCATGTTG 1 ACTTGTCAGATAATTATGTCG * ** * 1553238 ACTTGTCAGTTCTTTAAGTCG 1 ACTTGTCAGATAATTATGTCG 1553259 ACTTGTCA 1 ACTTGTCA 1553267 CTTATTCACG Statistics Matches: 97, Mismatches: 14, Indels: 4 0.84 0.12 0.03 Matches are distributed among these distances: 20 2 0.02 21 94 0.97 22 1 0.01 ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40 Consensus pattern (21 bp): ACTTGTCAGATAATTATGTCG Found at i:1553192 original size:42 final size:42 Alignment explanation

Indices: 1553133--1553266 Score: 223 Period size: 42 Copynumber: 3.2 Consensus size: 42 1553123 ATATGCCACC 1553133 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTTATGTCG 1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTTATGTCG * 1553175 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGATGTCG 1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTTATGTCG * * * * 1553217 ACTTGTCAGATAATCATGTTGACTTGTCAGTTCTTTAAGTCG 1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTTATGTCG 1553259 ACTTGTCA 1 ACTTGTCA 1553267 CTTATTCACG Statistics Matches: 86, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 42 86 1.00 ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40 Consensus pattern (42 bp): ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTTATGTCG Found at i:1553367 original size:21 final size:21 Alignment explanation

Indices: 1553343--1553502 Score: 182 Period size: 21 Copynumber: 7.7 Consensus size: 21 1553333 AATAATATTT ** 1553343 TCTGACAAGTCGACATAAGGA 1 TCTGACAAGTCGACATAATTA * 1553364 TCTGACAAGTTGACATAATCATA 1 TCTGACAAGTCGACATAAT--TA * 1553387 TTTG--AAGTCGACATAATTA 1 TCTGACAAGTCGACATAATTA * * 1553406 TTTGACAAGGCGACATAATTA 1 TCTGACAAGTCGACATAATTA 1553427 TCTGACAAGTCGACATAATTA 1 TCTGACAAGTCGACATAATTA * * * 1553448 TTTGACAAGACGACATAA-CA 1 TCTGACAAGTCGACATAATTA * * 1553468 TCTGACAAGTCAACATCATTA 1 TCTGACAAGTCGACATAATTA 1553489 TCTGACAAGTCGAC 1 TCTGACAAGTCGAC 1553503 TTATAATATG Statistics Matches: 117, Mismatches: 17, Indels: 10 0.81 0.12 0.07 Matches are distributed among these distances: 19 6 0.05 20 15 0.13 21 92 0.79 23 4 0.03 ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27 Consensus pattern (21 bp): TCTGACAAGTCGACATAATTA Found at i:1553734 original size:21 final size:21 Alignment explanation

Indices: 1553709--1553789 Score: 99 Period size: 21 Copynumber: 3.9 Consensus size: 21 1553699 ATAGTTATTT * * 1553709 TCTGACATGTCAACATAAAGA 1 TCTGACAAGTCAACATAAACA ** * 1553730 TCTGACAAGTTGACATAAATA 1 TCTGACAAGTCAACATAAACA * 1553751 TCTGACAAGTCAACATAATCA 1 TCTGACAAGTCAACATAAACA * 1553772 TCTGACAAGTCGACATAA 1 TCTGACAAGTCAACATAA 1553790 TTTTCTGACA Statistics Matches: 51, Mismatches: 9, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 51 1.00 ACGTcount: A:0.42, C:0.20, G:0.14, T:0.25 Consensus pattern (21 bp): TCTGACAAGTCAACATAAACA Found at i:1553768 original size:42 final size:42 Alignment explanation

Indices: 1553709--1553802 Score: 134 Period size: 42 Copynumber: 2.2 Consensus size: 42 1553699 ATAGTTATTT * * * 1553709 TCTGACATGTCAACATAAAGATCTGACAAGTTGACATAAATA 1 TCTGACAAGTCAACATAAACATCTGACAAGTCGACATAAATA * * * 1553751 TCTGACAAGTCAACATAATCATCTGACAAGTCGACATAATTT 1 TCTGACAAGTCAACATAAACATCTGACAAGTCGACATAAATA 1553793 TCTGACAAGT 1 TCTGACAAGT 1553803 GGTGGCAGAT Statistics Matches: 46, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 42 46 1.00 ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28 Consensus pattern (42 bp): TCTGACAAGTCAACATAAACATCTGACAAGTCGACATAAATA Found at i:1553790 original size:21 final size:20 Alignment explanation

Indices: 1553709--1553802 Score: 98 Period size: 21 Copynumber: 4.5 Consensus size: 20 1553699 ATAGTTATTT * * 1553709 TCTGACATGTCAACATAAAGA 1 TCTGACAAGTCAACAT-AATA ** 1553730 TCTGACAAGTTGACATAAATA 1 TCTGACAAGTCAACAT-AATA 1553751 TCTGACAAGTCAACATAATCA 1 TCTGACAAGTCAACATAAT-A * * 1553772 TCTGACAAGTCGACATAATTT 1 TCTGACAAGTCAACATAA-TA 1553793 TCTGACAAGT 1 TCTGACAAGT 1553803 GGTGGCAGAT Statistics Matches: 63, Mismatches: 8, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 20 3 0.05 21 59 0.94 22 1 0.02 ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28 Consensus pattern (20 bp): TCTGACAAGTCAACATAATA Found at i:1560316 original size:18 final size:18 Alignment explanation

Indices: 1560289--1560323 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 1560279 GAGGACGGAC * 1560289 AGTGATAAAAGTAATAAA 1 AGTGACAAAAGTAATAAA 1560307 AGTGACAAAAGTAATAA 1 AGTGACAAAAGTAATAA 1560324 TTCCTTTCTA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20 Consensus pattern (18 bp): AGTGACAAAAGTAATAAA Found at i:1575918 original size:2 final size:2 Alignment explanation

Indices: 1575911--1575959 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 1575901 CCTCGTTTTA 1575911 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1575953 AG AG AG A 1 AG AG AG A 1575960 ATTATTTATT Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1589139 original size:2 final size:2 Alignment explanation

Indices: 1589132--1589162 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 1589122 CCTGTCTGAN 1589132 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1589163 AACCTAGCAG Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:1596027 original size:18 final size:17 Alignment explanation

Indices: 1596000--1596036 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 17 1595990 CCCATGTCCC 1596000 CAAACACTGTACATATA 1 CAAACACTGTACATATA * 1596017 CAAACCACTGTATATATA 1 CAAA-CACTGTACATATA 1596035 CA 1 CA 1596037 TGTGTAATTT Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 17 4 0.22 18 14 0.78 ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24 Consensus pattern (17 bp): CAAACACTGTACATATA Found at i:1596295 original size:2 final size:2 Alignment explanation

Indices: 1596288--1596321 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 1596278 GACGAATGAT 1596288 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1596322 CCGTATAGAA Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1609762 original size:22 final size:23 Alignment explanation

Indices: 1609733--1609999 Score: 154 Period size: 22 Copynumber: 11.8 Consensus size: 23 1609723 NNNNNNNNAA 1609733 TTTCTGATATCAGAAAATATAAT 1 TTTCTGATATCAGAAAATATAAT * * 1609756 TCT-TGATATCAAAAAATCAGTTTCAA- 1 TTTCTGATATCAGAAAAT-A---T-AAT * 1609782 TTTCTGATATCA-AAAA-ATCAT 1 TTTCTGATATCAGAAAATATAAT * ** 1609803 TTTCTGATATCAAAAAATCGAA- 1 TTTCTGATATCAGAAAATATAAT 1609825 TTTCTGATATCAGAAAATGAT--T 1 TTTCTGATATCAGAAAAT-ATAAT ** 1609847 TTT-TGATATCAGAAAAT-CGAT 1 TTTCTGATATCAGAAAATATAAT * * 1609868 TTTTTGATATCAGAAAATGGATCGTAT 1 TTTCTGATATCAGAAAAT--AT--AAT * 1609895 TTTCTGATATCA-AGAAT-TCGAA- 1 TTTCTGATATCAGAAAATAT--AAT * 1609917 TTTCTGATATCA-AAAA-ATCAT 1 TTTCTGATATCAGAAAATATAAT * ** 1609938 TTTCTGATATCAGAAATTCGAAT 1 TTTCTGATATCAGAAAATATAAT * * 1609961 TCT-TGATATCA-AAAA-ATCAT 1 TTTCTGATATCAGAAAATATAAT 1609981 TTTCTGATATCAGAAAATA 1 TTTCTGATATCAGAAAATA 1610000 CCTCAAAAAT Statistics Matches: 190, Mismatches: 28, Indels: 52 0.70 0.10 0.19 Matches are distributed among these distances: 20 6 0.03 21 54 0.28 22 82 0.43 23 13 0.07 24 1 0.01 26 11 0.06 27 23 0.12 ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37 Consensus pattern (23 bp): TTTCTGATATCAGAAAATATAAT Found at i:1609832 original size:43 final size:43 Alignment explanation

Indices: 1609731--1609998 Score: 279 Period size: 43 Copynumber: 6.0 Consensus size: 43 1609721 NNNNNNNNNN * * 1609731 AATTTCTGATATCAGAAAAT-ATAATTCTTGATATCAAAAAATCAG 1 AATTTCTGATATCAAAAAATCAT-TTTC-TGATATCAAAAAATC-G 1609776 TTTCAATTTCTGATATCAAAAAATCATTTTCTGATATCAAAAAATCG 1 ----AATTTCTGATATCAAAAAATCATTTTCTGATATCAAAAAATCG * * * * 1609823 AATTTCTGATATCAGAAAATGATTTTTTGATATCAGAAAATCG 1 AATTTCTGATATCAAAAAATCATTTTCTGATATCAAAAAATCG * * * * 1609866 ATTTTTTGATATCAGAAAATGGATCGTATTTTCTGATATCAAGAATTCG 1 AATTTCTGATATCA-AAAA---ATC--ATTTTCTGATATCAAAAAATCG * * 1609915 AATTTCTGATATCAAAAAATCATTTTCTGATATCAGAAATTCG 1 AATTTCTGATATCAAAAAATCATTTTCTGATATCAAAAAATCG * 1609958 AA-TTCTTGATATCAAAAAATCATTTTCTGATATCAGAAAAT 1 AATTTC-TGATATCAAAAAATCATTTTCTGATATCAAAAAAT 1609999 ACCTCAAAAA Statistics Matches: 192, Mismatches: 19, Indels: 22 0.82 0.08 0.09 Matches are distributed among these distances: 42 3 0.02 43 107 0.56 44 3 0.02 45 3 0.02 47 3 0.02 48 19 0.10 49 52 0.27 50 2 0.01 ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37 Consensus pattern (43 bp): AATTTCTGATATCAAAAAATCATTTTCTGATATCAAAAAATCG Found at i:1609897 original size:92 final size:85 Alignment explanation

Indices: 1609731--1609998 Score: 302 Period size: 92 Copynumber: 3.0 Consensus size: 85 1609721 NNNNNNNNNN * * * 1609731 AATTTCTGATATCAGAAAATATAATTCTTGATATCAAAAAATCAGTTTCAATTTCTGATATCAAA 1 AATTTCTGATATCAGAAAATAT--TTTTTGATATCAGAAAATC-GATT---TTT-TGATATCAAA 1609796 AAATCATTTTCTGATATCAAAAAATCG 59 AAATCATTTTCTGATATCAAAAAATCG 1609823 AATTTCTGATATCAGAAAATGATTTTTTGATATCAGAAAATCGATTTTTTGATATCAGAAAATGG 1 AATTTCTGATATCAGAAAAT-ATTTTTTGATATCAGAAAATCGATTTTTTGATATCA-AAAA--- * * 1609888 ATCGTATTTTCTGATATCAAGAATTCG 61 ATC--ATTTTCTGATATCAAAAAATCG * * * * * 1609915 AATTTCTGATATCAAAAAATCATTTTCTGATATCAGAAATTCGAATTCTTGATATCAAAAAATCA 1 AATTTCTGATATCAGAAAAT-ATTTTTTGATATCAGAAAATCGATTTTTTGATATCAAAAAATCA * 1609980 TTTTCTGATATCAGAAAAT 65 TTTTCTGATATCAAAAAAT 1609999 ACCTCAAAAA Statistics Matches: 155, Mismatches: 14, Indels: 20 0.82 0.07 0.11 Matches are distributed among these distances: 86 25 0.16 87 7 0.05 88 3 0.02 90 6 0.04 91 21 0.14 92 91 0.59 93 2 0.01 ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37 Consensus pattern (85 bp): AATTTCTGATATCAGAAAATATTTTTTGATATCAGAAAATCGATTTTTTGATATCAAAAAATCAT TTTCTGATATCAAAAAATCG Found at i:1613888 original size:63 final size:63 Alignment explanation

Indices: 1613683--1613897 Score: 198 Period size: 63 Copynumber: 3.4 Consensus size: 63 1613673 CTTCTGGTGC * ** * * * * * * 1613683 TGCAGTTATTTCAGGTGATTTTTCTTGGCTTGGTGTAGTTAGCTCAGAAGATTCTTCCAGAGC 1 TGCAGTTATTTTAGACGATTTTTCTTGGCTTGATGTAGTTAACTTAGAGGATTCTTCCAGTGA * * * * * * * 1613746 TGCAATTTTTTTGGACGATTTTTCCTGGCTTGATATAGTT-ACTTCAGAGGATTCTTCCATTGT 1 TGCAGTTATTTTAGACGATTTTTCTTGGCTTGATGTAGTTAACTT-AGAGGATTCTTCCAGTGA ** * * * 1613809 TATAGTTATTTCAGACGATTTTTCTTGGTTTGATGTAGTTAAATTAGAGGATTCTTCCAGTGA 1 TGCAGTTATTTTAGACGATTTTTCTTGGCTTGATGTAGTTAACTTAGAGGATTCTTCCAGTGA ** * 1613872 TGCAGTCGTTTTAGACGATTCTTCTT 1 TGCAGTTATTTTAGACGATTTTTCTT 1613898 CATCTAATGA Statistics Matches: 117, Mismatches: 33, Indels: 4 0.76 0.21 0.03 Matches are distributed among these distances: 62 2 0.02 63 112 0.96 64 3 0.03 ACGTcount: A:0.20, C:0.14, G:0.21, T:0.44 Consensus pattern (63 bp): TGCAGTTATTTTAGACGATTTTTCTTGGCTTGATGTAGTTAACTTAGAGGATTCTTCCAGTGA Found at i:1614275 original size:15 final size:15 Alignment explanation

Indices: 1614255--1614288 Score: 68 Period size: 15 Copynumber: 2.3 Consensus size: 15 1614245 TCTGTTATAA 1614255 CTGTTTCAGATGAAT 1 CTGTTTCAGATGAAT 1614270 CTGTTTCAGATGAAT 1 CTGTTTCAGATGAAT 1614285 CTGT 1 CTGT 1614289 GAAAGCTGTT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 19 1.00 ACGTcount: A:0.24, C:0.15, G:0.21, T:0.41 Consensus pattern (15 bp): CTGTTTCAGATGAAT Found at i:1616934 original size:2 final size:2 Alignment explanation

Indices: 1616929--1616974 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 1616919 GAAAGGTGTG 1616929 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1616971 CT CT 1 CT CT 1616975 ATTTATACGT Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1621732 original size:9 final size:9 Alignment explanation

Indices: 1621718--1621794 Score: 100 Period size: 9 Copynumber: 8.2 Consensus size: 9 1621708 CATGTACTTA 1621718 TTGTTCTTC 1 TTGTTCTTC 1621727 TTGTTCTTC 1 TTGTTCTTC * 1621736 TTCTTCTTGTTC 1 TTGTTC---TTC 1621748 TTGTTCTTC 1 TTGTTCTTC 1621757 TTGTTCTTC 1 TTGTTCTTC 1621766 TTGTTCTTC 1 TTGTTCTTC * 1621775 TTCTTCTTC 1 TTGTTCTTC * 1621784 TTCTTCTTC 1 TTGTTCTTC 1621793 TT 1 TT 1621795 TTCAAAGAGT Statistics Matches: 62, Mismatches: 3, Indels: 6 0.87 0.04 0.08 Matches are distributed among these distances: 9 54 0.87 12 8 0.13 ACGTcount: A:0.00, C:0.25, G:0.08, T:0.68 Consensus pattern (9 bp): TTGTTCTTC Found at i:1621739 original size:6 final size:6 Alignment explanation

Indices: 1621721--1621794 Score: 103 Period size: 6 Copynumber: 12.3 Consensus size: 6 1621711 GTACTTATTG * * * * * 1621721 TTCTTC TTGTTC TTCTTC TTCTTG TTCTTG TTCTTC TTGTTC TTCTTG 1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC 1621769 TTCTTC TTCTTC TTCTTC TTCTTC TT 1 TTCTTC TTCTTC TTCTTC TTCTTC TT 1621795 TTCAAAGAGT Statistics Matches: 60, Mismatches: 8, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 6 60 1.00 ACGTcount: A:0.00, C:0.26, G:0.07, T:0.68 Consensus pattern (6 bp): TTCTTC Found at i:1621741 original size:15 final size:15 Alignment explanation

Indices: 1621721--1621794 Score: 112 Period size: 15 Copynumber: 4.9 Consensus size: 15 1621711 GTACTTATTG 1621721 TTCTTCTTGTTCTTC 1 TTCTTCTTGTTCTTC * 1621736 TTCTTCTTGTTCTTG 1 TTCTTCTTGTTCTTC 1621751 TTCTTCTTGTTCTTC 1 TTCTTCTTGTTCTTC * * 1621766 TTGTTCTTCTTCTTC 1 TTCTTCTTGTTCTTC * 1621781 TTCTTCTTCTTCTT 1 TTCTTCTTGTTCTT 1621795 TTCAAAGAGT Statistics Matches: 54, Mismatches: 5, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 15 54 1.00 ACGTcount: A:0.00, C:0.26, G:0.07, T:0.68 Consensus pattern (15 bp): TTCTTCTTGTTCTTC Found at i:1627890 original size:20 final size:20 Alignment explanation

Indices: 1627865--1627921 Score: 62 Period size: 20 Copynumber: 2.8 Consensus size: 20 1627855 TTTTAAATTA 1627865 TATATAATTTATAATTATAT 1 TATATAATTTATAATTATAT ** 1627885 TATAT-ATGAATAAATTATAT 1 TATATAATTTAT-AATTATAT 1627905 TATCATAATTTTATAAT 1 TAT-ATAA-TTTATAAT 1627922 ACATGTACAT Statistics Matches: 29, Mismatches: 4, Indels: 6 0.74 0.10 0.15 Matches are distributed among these distances: 19 4 0.14 20 16 0.55 21 2 0.07 22 4 0.14 23 3 0.10 ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51 Consensus pattern (20 bp): TATATAATTTATAATTATAT Found at i:1628841 original size:12 final size:12 Alignment explanation

Indices: 1628818--1628847 Score: 53 Period size: 12 Copynumber: 2.6 Consensus size: 12 1628808 ATCACATTTT 1628818 GTCTGT-CGTCC 1 GTCTGTCCGTCC 1628829 GTCTGTCCGTCC 1 GTCTGTCCGTCC 1628841 GTCTGTC 1 GTCTGTC 1628848 TGTCTGTCCA Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 11 6 0.33 12 12 0.67 ACGTcount: A:0.00, C:0.37, G:0.27, T:0.37 Consensus pattern (12 bp): GTCTGTCCGTCC Found at i:1633352 original size:2 final size:2 Alignment explanation

Indices: 1633345--1633389 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 1633335 NNNNNNNNNN 1633345 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1633387 TC T 1 TC T 1633390 TTTACAAAGT Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1638446 original size:169 final size:169 Alignment explanation

Indices: 1638060--1638557 Score: 741 Period size: 169 Copynumber: 2.9 Consensus size: 169 1638050 AGAACCATTA * * * 1638060 AGCCAGGAAAGCTGAAACTTTTGTGGAAGCATCTTCAGGTAGTGTAGATTCAAAATTGTGAAAAT 1 AGCCAGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT * * * 1638125 CATGACTTCTAGGGGTAGGGTGGGGCCACAAT--GGGGGGGGGGTCAAAGTTTAACATAGGAATA 66 CATGACTTCTGGGGGTAGGGTGGGACCACAATGGGGGGGGGGGGTCAAAGTTTAACATTGGAATA * * * 1638188 TATAGAGTAAATCTCTATAAATCTTCTTTACAAAAACTAATC 131 TATTGAGTAAATCT-TAAAAAT-TT-TCTACAAAAACTAATC * * 1638230 AGCCAGGAAAGCTTAAACTTATGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAGTTGTGAAAAT 1 AGCCAGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT * * * 1638295 CATGACTTCTGGGGGAAGGATGGGACCACAATGGGGGGAGGGGGGTCAAAATTTAACATTGGAAT 66 CATGACTTCTGGGGGTAGGGTGGGACCACAATGGGGGG-GGGGGGTCAAAGTTTAACATTGGAAT ** 1638360 ATATTGAGTAAATCTTAAAAATTTTCT-CAGTAACTAATC 130 ATATTGAGTAAATCTTAAAAATTTTCTACAAAAACTAATC * * 1638399 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTAAAAAT 1 AGCCAGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT 1638464 CATGACTTCTGGGGGTAGGGTGGGACCACAATTGGGGGGGGGGGGTGTCAAAGTTTAACATTGGA 66 CATGACTTCTGGGGGTAGGGTGGGACCACAA-T-GGGGGGGGGGG-GTCAAAGTTTAACATTGGA * 1638529 ATATATTGAGTAAATCTTAAAAATCTTCT 128 ATATATTGAGTAAATCTTAAAAATTTTCT 1638558 TCTCTTTATG Statistics Matches: 298, Mismatches: 24, Indels: 11 0.89 0.07 0.03 Matches are distributed among these distances: 169 100 0.34 170 96 0.32 171 54 0.18 172 10 0.03 173 38 0.13 ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27 Consensus pattern (169 bp): AGCCAGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT CATGACTTCTGGGGGTAGGGTGGGACCACAATGGGGGGGGGGGGTCAAAGTTTAACATTGGAATA TATTGAGTAAATCTTAAAAATTTTCTACAAAAACTAATC Found at i:1639381 original size:172 final size:170 Alignment explanation

Indices: 1638836--1639513 Score: 895 Period size: 168 Copynumber: 4.0 Consensus size: 170 1638826 AGAACCATTA * * * * 1638836 AGCCAGGAAAGCTGATACTTGTTTGGAAGCATCTTCAGGTAGTGTAGATTCAAAATTGTGAAAAT 1 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT * * * * 1638901 CATGA--CTTTGGGGGTAGGGTGGGGCCACAATGGGGGGGGGGGTCGCAGTTTAACATAGGAATA 66 CATGACCCCTT-GGCGTAGGGT-GGGCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATA * * * * 1638964 TATAGAGTAAATCTTTATAAATCTTCTTTACAAAAACTAATC 129 TATTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATC * * * 1639006 GGCCAGGAAAGCTTAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAAT 1 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT * * * * 1639071 CATGACCCCCTTGGCGTAGGGTTGTCCACAAT---GGGGGGGATCCAAGTTTTACATAGGAATAT 66 CATGA-CCCCTTGGCGTAGGGTGGGCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATAT * * 1639133 ATAT-AGTAAATCTTTAAAAAAACTTCTTTTCAGAAACAAATC 130 AT-TGAGTAAATCTTT-AAAAATCTTCTTTTCAGAAACTAATC * * 1639175 AGCCAGGAAAGCTTAAACTTGTGTGGAAGCATCCTCAGG-AGTGTAGATTTAAAGTTGTGAAAAT 1 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT * * * 1639239 CATGACCCCCTTGGCGTAGAGCT-GTCCACAACTGGGGGAGGGGGATCGAAGTTTTACATAGGAA 66 CATGA-CCCCTTGGCGTAG-GGTGGGCCACAA-TGGGGG-GGGGGATCGAAGTTTAACATAGGAA 1639303 TATATTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATC 127 TATATTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATC 1639347 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT 1 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT ** * * * * * * 1639412 CATGACTTCTGGGGGTAGGGTGGGGCCACAATGGGGGGGGGGGTCAAAATTTAACATTGGAATAT 66 CATGACCCCTTGGCGTAGGGT-GGGCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATAT * 1639477 ATTGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT 130 ATTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACT 1639514 CGGCTTTAGG Statistics Matches: 453, Mismatches: 40, Indels: 29 0.87 0.08 0.06 Matches are distributed among these distances: 168 91 0.20 169 62 0.14 170 63 0.14 171 69 0.15 172 89 0.20 173 79 0.17 ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28 Consensus pattern (170 bp): AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT CATGACCCCTTGGCGTAGGGTGGGCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATATA TTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATC Found at i:1639513 original size:171 final size:171 Alignment explanation

Indices: 1638796--1639513 Score: 886 Period size: 172 Copynumber: 4.2 Consensus size: 171 1638786 ATGAAAATTT * * * * 1638796 TTGAG-AAAT-TTTCAAAAATCTTCCTTCTCA-AGAACCATTAAGCCAGGAAAGCTGATACTTGT 1 TTGAGTAAATCTTT-AAAAATCTT-CTTCTCAGA-AACTAATCAGCCAGGAAAGCTGAAACTTGT * * * ** * 1638858 TTGGAAGCATCTTCAGGTAGTGTAGATTCAAAATTGTGAAAATCATGA--CTTTGGGGGTAGGGT 63 GTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCTGGGCGTAGGGT * * 1638921 GGGGCCACAATGGGGGGGGGGGTCGCAGTTTAACATAGGAATATA 128 -GGGCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATATA * * * * * 1638966 TAGAGTAAATCTTTATAAATCTTCTT-TACAAAAACTAATCGGCCAGGAAAGCTTAAACTTGTGT 1 TTGAGTAAATCTTTAAAAATCTTCTTCT-CAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGT * * * 1639030 GGAAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAATCATGACCCCCTTGGCGTAGGGTTG 65 GGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCTGGGCGTAGGGTGG * * * 1639095 TCCACAAT---GGGGGGGATCCAAGTTTTACATAGGAATATA 130 GCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATATA * * * * 1639134 TAT-AGTAAATCTTTAAAAAAACTTCTTTTCAGAAACAAATCAGCCAGGAAAGCTTAAACTTGTG 1 T-TGAGTAAATCTTT-AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG * * * 1639198 TGGAAGCATCCTCAGG-AGTGTAGATTTAAAGTTGTGAAAATCATGACCCCCTTGGCGTAGAGCT 64 TGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCTGGGCGTAG-GGT * * 1639262 -GTCCACAACTGGGGGAGGGGGATCGAAGTTTTACATAGGAATATA 128 GGGCCACAA-TGGGGG-GGGGGATCGAAGTTTAACATAGGAATATA * 1639307 TTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTG 1 TTGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTG ** * 1639372 GAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGA-CTTCTGGGGGTAGGGTGGG 66 GAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCTGGGCGTAGGGT-GG * * * * 1639436 GCCACAATGGGGGGGGGGGTCAAAATTTAACATTGGAATATA 130 GCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATATA 1639478 TTGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT 1 TTGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT 1639514 CGGCTTTAGG Statistics Matches: 483, Mismatches: 46, Indels: 37 0.85 0.08 0.07 Matches are distributed among these distances: 168 91 0.19 169 62 0.13 170 78 0.16 171 82 0.17 172 94 0.19 173 76 0.16 ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28 Consensus pattern (171 bp): TTGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTG GAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCTGGGCGTAGGGTGGG CCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATATA Found at i:1643462 original size:30 final size:30 Alignment explanation

Indices: 1643426--1643488 Score: 126 Period size: 30 Copynumber: 2.1 Consensus size: 30 1643416 GGTTCCGACG 1643426 CCTATGAGCTATTCACTGCGTATGAATTTA 1 CCTATGAGCTATTCACTGCGTATGAATTTA 1643456 CCTATGAGCTATTCACTGCGTATGAATTTA 1 CCTATGAGCTATTCACTGCGTATGAATTTA 1643486 CCT 1 CCT 1643489 GTAATTTACA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 30 33 1.00 ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37 Consensus pattern (30 bp): CCTATGAGCTATTCACTGCGTATGAATTTA Found at i:1647037 original size:27 final size:27 Alignment explanation

Indices: 1646984--1647040 Score: 80 Period size: 27 Copynumber: 2.1 Consensus size: 27 1646974 GATCTTTAAC ** 1646984 TGCAGCCCTTCTAAATAGAGTTGTGCA 1 TGCAGCCCTTCTAAATAGAGTCCTGCA 1647011 TGCAGCCCTTCTAAAT-GAAGTCCTGCA 1 TGCAGCCCTTCTAAATAG-AGTCCTGCA 1647038 TGC 1 TGC 1647041 CTATAAGCAT Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 26 1 0.04 27 26 0.96 ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28 Consensus pattern (27 bp): TGCAGCCCTTCTAAATAGAGTCCTGCA Found at i:1648310 original size:16 final size:16 Alignment explanation

Indices: 1648289--1648333 Score: 81 Period size: 16 Copynumber: 2.8 Consensus size: 16 1648279 CATACGGTAT 1648289 CAGGAGAAAACGTACC 1 CAGGAGAAAACGTACC 1648305 CAGGAGAAAACGTACC 1 CAGGAGAAAACGTACC * 1648321 CAAGAGAAAACGT 1 CAGGAGAAAACGT 1648334 TCCTAATTTC Statistics Matches: 28, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 16 28 1.00 ACGTcount: A:0.47, C:0.22, G:0.24, T:0.07 Consensus pattern (16 bp): CAGGAGAAAACGTACC Found at i:1649457 original size:16 final size:16 Alignment explanation

Indices: 1649439--1649502 Score: 101 Period size: 16 Copynumber: 4.0 Consensus size: 16 1649429 CCCTAGAAAT * 1649439 TGGGTACGTTTTCTCT 1 TGGGTACGTTTTCTCC 1649455 TGGGTACGTTTTCTCC 1 TGGGTACGTTTTCTCC 1649471 TGGGTACGTTTTCTCC 1 TGGGTACGTTTTCTCC * * 1649487 TAGGTATGTTTTCTCC 1 TGGGTACGTTTTCTCC 1649503 AGCATTCTTT Statistics Matches: 45, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 45 1.00 ACGTcount: A:0.08, C:0.22, G:0.23, T:0.47 Consensus pattern (16 bp): TGGGTACGTTTTCTCC Found at i:1651033 original size:2 final size:2 Alignment explanation

Indices: 1651026--1651051 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 1651016 TTGTATACAT 1651026 GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA 1651052 ATGAGAATGT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1661202 original size:24 final size:24 Alignment explanation

Indices: 1661175--1661247 Score: 146 Period size: 24 Copynumber: 3.0 Consensus size: 24 1661165 GCGGTCGTTG 1661175 TACATGTATATGGATCAATTGTTA 1 TACATGTATATGGATCAATTGTTA 1661199 TACATGTATATGGATCAATTGTTA 1 TACATGTATATGGATCAATTGTTA 1661223 TACATGTATATGGATCAATTGTTA 1 TACATGTATATGGATCAATTGTTA 1661247 T 1 T 1661248 GTTAAGAATC Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 49 1.00 ACGTcount: A:0.33, C:0.08, G:0.16, T:0.42 Consensus pattern (24 bp): TACATGTATATGGATCAATTGTTA Found at i:1666901 original size:27 final size:27 Alignment explanation

Indices: 1666878--1667305 Score: 608 Period size: 27 Copynumber: 15.9 Consensus size: 27 1666868 TACTGTAATT * 1666878 TAACGATACTATATGGTATATGTACTG 1 TAACGATACTATATGGTACATGTACTG * * 1666905 TAATGATACTATATGGTGCATGTACTG 1 TAACGATACTATATGGTACATGTACTG * * * * 1666932 TTATGATACTATATGGTAGAGGTACTG 1 TAACGATACTATATGGTACATGTACTG * 1666959 TAACAATACTATATGGTACATGTACTG 1 TAACGATACTATATGGTACATGTACTG * * * 1666986 TAACAAGACTATATGGTTCATGTACTG 1 TAACGATACTATATGGTACATGTACTG 1667013 TAACGATACTATATGGTACATGTACTG 1 TAACGATACTATATGGTACATGTACTG 1667040 TAACGATACTATATGGTACATGTACTG 1 TAACGATACTATATGGTACATGTACTG * 1667067 TAACGGTACTATATGGTACATGTACT- 1 TAACGATACTATATGGTACATGTACTG * ** 1667093 CAAGCGATTTTATATGGTACATGTACTG 1 TAA-CGATACTATATGGTACATGTACTG 1667121 TAACGATACTATATGGTACATGTACTG 1 TAACGATACTATATGGTACATGTACTG * 1667148 TAACGATACTATATTGTACATGTACTG 1 TAACGATACTATATGGTACATGTACTG * * 1667175 TAATGTTACTATATGGTACATGTACTG 1 TAACGATACTATATGGTACATGTACTG * * 1667202 TAACAATACTCTATGGTACATGTACTG 1 TAACGATACTATATGGTACATGTACTG * * 1667229 TAAGGATAGTA-ATTGGTACATGTACTG 1 TAACGATACTATA-TGGTACATGTACTG * 1667256 TAACAATACTATATGGTACATGTACTG 1 TAACGATACTATATGGTACATGTACTG * 1667283 TAACGATATTATATGGTACATGT 1 TAACGATACTATATGGTACATGT 1667306 NCTCGAAAAC Statistics Matches: 355, Mismatches: 42, Indels: 8 0.88 0.10 0.02 Matches are distributed among these distances: 26 3 0.01 27 349 0.98 28 3 0.01 ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35 Consensus pattern (27 bp): TAACGATACTATATGGTACATGTACTG Found at i:1667496 original size:27 final size:27 Alignment explanation

Indices: 1667408--1667487 Score: 133 Period size: 27 Copynumber: 3.0 Consensus size: 27 1667398 TATTTATATA * 1667408 ATGGTGCATGTACTGTAACGATACTAT 1 ATGGTACATGTACTGTAACGATACTAT * 1667435 ATGGTATATGTACTGTAACGATACTAT 1 ATGGTACATGTACTGTAACGATACTAT * 1667462 ATGGTACATGTACTGTAATGATACTA 1 ATGGTACATGTACTGTAACGATACTA 1667488 AACTTTACAA Statistics Matches: 49, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 27 49 1.00 ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35 Consensus pattern (27 bp): ATGGTACATGTACTGTAACGATACTAT Found at i:1667552 original size:20 final size:20 Alignment explanation

Indices: 1667523--1667613 Score: 128 Period size: 20 Copynumber: 4.5 Consensus size: 20 1667513 TTCACTATGT * * 1667523 AAGTTCTGTAAGGATACTAC 1 AAGTACTGTAACGATACTAC * 1667543 AAGTATTGTAACGATACTAC 1 AAGTACTGTAACGATACTAC * 1667563 AAGTATTGTAACGATACTAC 1 AAGTACTGTAACGATACTAC * 1667583 AAGTACTGTAACGATATTAC 1 AAGTACTGTAACGATACTAC * 1667603 ATGTACTGTAA 1 AAGTACTGTAA 1667614 AGACCCTAGG Statistics Matches: 65, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 65 1.00 ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31 Consensus pattern (20 bp): AAGTACTGTAACGATACTAC Found at i:1674902 original size:16 final size:18 Alignment explanation

Indices: 1674881--1674918 Score: 53 Period size: 19 Copynumber: 2.2 Consensus size: 18 1674871 TCAATGCGTT 1674881 ACATAG-TAC-TAGTGTA 1 ACATAGATACATAGTGTA 1674897 ACATAGTATACATAGTGTA 1 ACATAG-ATACATAGTGTA 1674916 ACA 1 ACA 1674919 CTAAATCAAT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 16 6 0.32 18 3 0.16 19 10 0.53 ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29 Consensus pattern (18 bp): ACATAGATACATAGTGTA Found at i:1676372 original size:23 final size:23 Alignment explanation

Indices: 1676342--1676391 Score: 100 Period size: 23 Copynumber: 2.2 Consensus size: 23 1676332 ATATCGAAAC 1676342 CAGGGCGTGGTCGCTGTATATAT 1 CAGGGCGTGGTCGCTGTATATAT 1676365 CAGGGCGTGGTCGCTGTATATAT 1 CAGGGCGTGGTCGCTGTATATAT 1676388 CAGG 1 CAGG 1676392 ATTCCGGTCC Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 27 1.00 ACGTcount: A:0.18, C:0.18, G:0.36, T:0.28 Consensus pattern (23 bp): CAGGGCGTGGTCGCTGTATATAT Found at i:1679225 original size:10 final size:11 Alignment explanation

Indices: 1679194--1679224 Score: 62 Period size: 11 Copynumber: 2.8 Consensus size: 11 1679184 CCCCCCCCAA 1679194 AAAAAAAAAAC 1 AAAAAAAAAAC 1679205 AAAAAAAAAAC 1 AAAAAAAAAAC 1679216 AAAAAAAAA 1 AAAAAAAAA 1679225 CCCCCAACAA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00 Consensus pattern (11 bp): AAAAAAAAAAC Found at i:1679445 original size:30 final size:30 Alignment explanation

Indices: 1679411--1679531 Score: 206 Period size: 30 Copynumber: 4.0 Consensus size: 30 1679401 TTTTCTCGAC * * * 1679411 TTGACGAAAAAGGCCGAGCAATGTTTCGAT 1 TTGACGGAAAAGGCCGAGCGATGTTCCGAT 1679441 TTGACGGAAAAGGCCGAGCGATGTTCCGAT 1 TTGACGGAAAAGGCCGAGCGATGTTCCGAT 1679471 TTGACGGAAAAGGCCGAGCGATGTTCCGAT 1 TTGACGGAAAAGGCCGAGCGATGTTCCGAT * 1679501 TTTACGGAAAAGGCCGAGCGATGTTCCGAT 1 TTGACGGAAAAGGCCGAGCGATGTTCCGAT 1679531 T 1 T 1679532 AATAATACTC Statistics Matches: 87, Mismatches: 4, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 30 87 1.00 ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22 Consensus pattern (30 bp): TTGACGGAAAAGGCCGAGCGATGTTCCGAT Found at i:1687687 original size:2 final size:2 Alignment explanation

Indices: 1687680--1687723 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 1687670 TTGTTTAATA 1687680 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1687722 CT 1 CT 1687724 GTTATATACA Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1688057 original size:17 final size:17 Alignment explanation

Indices: 1688037--1688071 Score: 54 Period size: 17 Copynumber: 2.1 Consensus size: 17 1688027 CCCAAAAAAT 1688037 ACAAAAGAAA-AAAACAA 1 ACAAAA-AAACAAAACAA 1688054 ACAAAAAAACAAAACAA 1 ACAAAAAAACAAAACAA 1688071 A 1 A 1688072 ATTTAAAAAA Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 16 3 0.18 17 14 0.82 ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00 Consensus pattern (17 bp): ACAAAAAAACAAAACAA Found at i:1688059 original size:12 final size:13 Alignment explanation

Indices: 1688029--1688072 Score: 63 Period size: 12 Copynumber: 3.4 Consensus size: 13 1688019 CCCCCGCCCC 1688029 CAAAAAATACAAAA 1 CAAAAAA-ACAAAA * 1688043 GAAAAAAAC-AAA 1 CAAAAAAACAAAA 1688055 CAAAAAAACAAAA 1 CAAAAAAACAAAA 1688068 CAAAA 1 CAAAA 1688073 TTTAAAAAAC Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 12 11 0.41 13 10 0.37 14 6 0.22 ACGTcount: A:0.82, C:0.14, G:0.02, T:0.02 Consensus pattern (13 bp): CAAAAAAACAAAA Found at i:1690194 original size:2 final size:2 Alignment explanation

Indices: 1690187--1690254 Score: 118 Period size: 2 Copynumber: 34.0 Consensus size: 2 1690177 AATCTAGCAT 1690187 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * * 1690229 TC TC TC TC CC TC TC TC TC TC CC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC 1690255 CATTTATCTC Statistics Matches: 62, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 62 1.00 ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47 Consensus pattern (2 bp): TC Found at i:1692923 original size:200 final size:200 Alignment explanation

Indices: 1692580--1692980 Score: 802 Period size: 200 Copynumber: 2.0 Consensus size: 200 1692570 CGGAGGGGTC 1692580 ATTTTGGTCAGCTCCTGCAACAGCAGATTCTGTGAATGTGGTGAGTCGTTAGGAGATGAATAAGT 1 ATTTTGGTCAGCTCCTGCAACAGCAGATTCTGTGAATGTGGTGAGTCGTTAGGAGATGAATAAGT 1692645 CCGCTGCCAGCCTTGTGCTCCAGAATTCCGTGGTCAATACTTGTAGCTGGTTTCACCAGTGGAAA 66 CCGCTGCCAGCCTTGTGCTCCAGAATTCCGTGGTCAATACTTGTAGCTGGTTTCACCAGTGGAAA 1692710 TTAAGCAATTATATTACTGGAATTGTCTTGACTTGCAGGTCAGTTTTCCAATCAATTGATTTGAA 131 TTAAGCAATTATATTACTGGAATTGTCTTGACTTGCAGGTCAGTTTTCCAATCAATTGATTTGAA 1692775 GCTAA 196 GCTAA 1692780 ATTTTGGTCAGCTCCTGCAACAGCAGATTCTGTGAATGTGGTGAGTCGTTAGGAGATGAATAAGT 1 ATTTTGGTCAGCTCCTGCAACAGCAGATTCTGTGAATGTGGTGAGTCGTTAGGAGATGAATAAGT 1692845 CCGCTGCCAGCCTTGTGCTCCAGAATTCCGTGGTCAATACTTGTAGCTGGTTTCACCAGTGGAAA 66 CCGCTGCCAGCCTTGTGCTCCAGAATTCCGTGGTCAATACTTGTAGCTGGTTTCACCAGTGGAAA 1692910 TTAAGCAATTATATTACTGGAATTGTCTTGACTTGCAGGTCAGTTTTCCAATCAATTGATTTGAA 131 TTAAGCAATTATATTACTGGAATTGTCTTGACTTGCAGGTCAGTTTTCCAATCAATTGATTTGAA 1692975 GCTAA 196 GCTAA 1692980 A 1 A 1692981 GATAAGGACT Statistics Matches: 201, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 200 201 1.00 ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32 Consensus pattern (200 bp): ATTTTGGTCAGCTCCTGCAACAGCAGATTCTGTGAATGTGGTGAGTCGTTAGGAGATGAATAAGT CCGCTGCCAGCCTTGTGCTCCAGAATTCCGTGGTCAATACTTGTAGCTGGTTTCACCAGTGGAAA TTAAGCAATTATATTACTGGAATTGTCTTGACTTGCAGGTCAGTTTTCCAATCAATTGATTTGAA GCTAA Found at i:1720573 original size:21 final size:21 Alignment explanation

Indices: 1720549--1720888 Score: 366 Period size: 21 Copynumber: 16.2 Consensus size: 21 1720539 ATTGAATCCG 1720549 AAGATTAAAGTTGGAAATTCC 1 AAGATTAAAGTTGGAAATTCC 1720570 AAGATTAAAGTTGGAAATTCC 1 AAGATTAAAGTTGGAAATTCC ** * 1720591 AACTTTAAAGTTGGAAAAAT-C 1 AAGATTAAAGTTGG-AAATTCC ** * 1720612 AACTTTAAAGTTGGAAAAAT-C 1 AAGATTAAAGTTGG-AAATTCC ** 1720633 AACTTTAAAGTTGGAAATTCC 1 AAGATTAAAGTTGGAAATTCC 1720654 AAGATTAAAGTTGGAAATTCC 1 AAGATTAAAGTTGGAAATTCC * 1720675 AAGATTAAAGTTGGAATTTCC 1 AAGATTAAAGTTGGAAATTCC ** * 1720696 AACTTTAAAGTTGGAAAAAT-C 1 AAGATTAAAGTTGG-AAATTCC ** * 1720717 AACTTTAAAATTGGAAATTCC 1 AAGATTAAAGTTGGAAATTCC ** * 1720738 AACTTTAAAGTTTGAAATTCC 1 AAGATTAAAGTTGGAAATTCC 1720759 AAGATTAAAGTTGGAAATTCC 1 AAGATTAAAGTTGGAAATTCC * 1720780 AAGATTAAAGTTGGAATTTCC 1 AAGATTAAAGTTGGAAATTCC * 1720801 AACG-TTAAAGTTGGAAAAAT-C 1 AA-GATTAAAGTTGG-AAATTCC ** * 1720822 AACTTTAAAGTTTGAAATTCC 1 AAGATTAAAGTTGGAAATTCC 1720843 AAGATTAAAGTTGGAAATTCC 1 AAGATTAAAGTTGGAAATTCC ** * 1720864 AACTTTAAAGTTCGAAATTCC 1 AAGATTAAAGTTGGAAATTCC 1720885 AAGA 1 AAGA 1720889 AAAAAAAAAT Statistics Matches: 279, Mismatches: 32, Indels: 16 0.85 0.10 0.05 Matches are distributed among these distances: 20 12 0.04 21 256 0.92 22 11 0.04 ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31 Consensus pattern (21 bp): AAGATTAAAGTTGGAAATTCC Found at i:1720731 original size:105 final size:105 Alignment explanation

Indices: 1720549--1720888 Score: 565 Period size: 105 Copynumber: 3.2 Consensus size: 105 1720539 ATTGAATCCG * 1720549 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAAAATCAA 1 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTTAAAGTTGGAAAAATCAA * 1720614 CTTTAAAGTTGGAAAAAT-CAACTTTAAAGTTGGAAATTCC 66 CTTTAAAGTTGG-AAATTCCAACTTTAAAGTTGGAAATTCC 1720654 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTTAAAGTTGGAAAAATCAA 1 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTTAAAGTTGGAAAAATCAA * * 1720719 CTTTAAAATTGGAAATTCCAACTTTAAAGTTTGAAATTCC 66 CTTTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCC * 1720759 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACGTTAAAGTTGGAAAAATCAA 1 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTTAAAGTTGGAAAAATCAA * ** 1720824 CTTTAAAGTTTGAAATTCCAAGATTAAAGTTGGAAATTCC 66 CTTTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCC ** * 1720864 AACTTTAAAGTTCGAAATTCCAAGA 1 AAGATTAAAGTTGGAAATTCCAAGA 1720889 AAAAAAAAAT Statistics Matches: 221, Mismatches: 13, Indels: 2 0.94 0.06 0.01 Matches are distributed among these distances: 104 4 0.02 105 217 0.98 ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31 Consensus pattern (105 bp): AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTTAAAGTTGGAAAAATCAA CTTTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCC Found at i:1720886 original size:84 final size:84 Alignment explanation

Indices: 1720553--1720880 Score: 446 Period size: 84 Copynumber: 3.9 Consensus size: 84 1720543 AATCCGAAGA ** ** * 1720553 TTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAAAAT-CAACTT 1 TTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCCAAGATTAAAGTTGG-AAATTCCAACTT 1720617 TAAAGTTGGAAAAATCAACT 65 TAAAGTTGGAAAAATCAACT ** * 1720637 TTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTT 1 TTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTTT 1720702 AAAGTTGGAAAAATCAACT 66 AAAGTTGGAAAAATCAACT * * ** 1720721 TTAAAATTGGAAATTCCAACTTTAAAGTTTGAAATTCCAAGATTAAAGTTGGAAATTCCAAGATT 1 TTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTTT ** * 1720786 AAAGTTGG-AATTTCCAACG 66 AAAGTTGGAAAAAT-CAACT * * 1720805 TTAAAGTTGGAAAAAT-CAACTTTAAAGTTTGAAATTCCAAGATTAAAGTTGGAAATTCCAACTT 1 TTAAAGTTGG-AAATTCCAACTTTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTT * 1720869 TAAAGTTCGAAA 65 TAAAGTTGGAAA 1720881 TTCCAAGAAA Statistics Matches: 221, Mismatches: 19, Indels: 7 0.89 0.08 0.03 Matches are distributed among these distances: 83 6 0.03 84 209 0.95 85 6 0.03 ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31 Consensus pattern (84 bp): TTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTTT AAAGTTGGAAAAATCAACT Found at i:1729039 original size:145 final size:145 Alignment explanation

Indices: 1728765--1729060 Score: 436 Period size: 145 Copynumber: 2.0 Consensus size: 145 1728755 ACATGACACA 1728765 GACA-GAATTTAGCATTTTTGAAACAATGACCTTGAACTTCCTCAATTGACCTTGGGTCAAGGTC 1 GACACGAATTTAGCATTTTTGAAACAATGACCTTGAACTTCCTCAATTGACCTTGGGTCAAGGTC * * * * 1728829 ATGACATACCCTTTGGTTATAAGCAATATTTGTGTGAAGTAAGAACATTCAATGCTTCTCAATAA 66 AAGACACACCCTTAGGTTATAAGCAATATTTGTGTGAAGTAAGAACATTCAATGCTTATCAATAA 1728894 GAAAGATATGGACCG 131 GAAAGATATGGACCG * * * 1728909 GACACGAATTTAGCATTTTTGAAACAATGACCTTGACCTTGCC-CGATTGACCTTGGGTCATGGT 1 GACACGAATTTAGCATTTTTGAAACAATGACCTTGAACTT-CCTCAATTGACCTTGGGTCAAGGT * * * * * 1728973 CAAGACACACCCTTAGGTTATAAGCAATCTTTGTGTGAAGTAAGAA-TTTCCCATGTTTATCCAT 65 CAAGACACACCCTTAGGTTATAAGCAATATTTGTGTGAAGTAAGAACATT-CAATGCTTATCAAT * 1729037 AAGAAAGATATGGACTG 129 AAGAAAGATATGGACCG 1729054 GACACGA 1 GACACGA 1729061 TTGCACAGAC Statistics Matches: 136, Mismatches: 13, Indels: 5 0.88 0.08 0.03 Matches are distributed among these distances: 144 6 0.04 145 128 0.94 146 2 0.01 ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30 Consensus pattern (145 bp): GACACGAATTTAGCATTTTTGAAACAATGACCTTGAACTTCCTCAATTGACCTTGGGTCAAGGTC AAGACACACCCTTAGGTTATAAGCAATATTTGTGTGAAGTAAGAACATTCAATGCTTATCAATAA GAAAGATATGGACCG Found at i:1745966 original size:1 final size:1 Alignment explanation

Indices: 1745960--1745998 Score: 78 Period size: 1 Copynumber: 39.0 Consensus size: 1 1745950 TCTCTCCTCA 1745960 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 1745999 TTTCTTCAAC Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 38 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:1761039 original size:2 final size:2 Alignment explanation

Indices: 1761032--1761088 Score: 114 Period size: 2 Copynumber: 28.5 Consensus size: 2 1761022 ATCCTGTCAT 1761032 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1761074 TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC T 1761089 GTTTTAAAAA Statistics Matches: 55, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 55 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1764075 original size:199 final size:199 Alignment explanation

Indices: 1763735--1764137 Score: 806 Period size: 199 Copynumber: 2.0 Consensus size: 199 1763725 CATGAATATC 1763735 ATTTTATTTAAAATAAAAACATCTTGAATATTCATAACATGTACTTCATGCAAAAAATATAAATA 1 ATTTTATTTAAAATAAAAACATCTTGAATATTCATAACATGTACTTCATGCAAAAAATATAAATA 1763800 ACATTTAAAAATCATATGAAATCTGAACAACATATTTTAATTAAATTACATTTCACATTACAAAA 66 ACATTTAAAAATCATATGAAATCTGAACAACATATTTTAATTAAATTACATTTCACATTACAAAA 1763865 ATAAACTCGTAATTATACATGTCCAATGTTCAAAGTTCAATGATTGTACTGTAAAATAAATATTC 131 ATAAACTCGTAATTATACATGTCCAATGTTCAAAGTTCAATGATTGTACTGTAAAATAAATATTC 1763930 ATGT 196 ATGT 1763934 ATTTTATTTAAAATAAAAACATCTTGAATATTCATAACATGTACTTCATGCAAAAAATATAAATA 1 ATTTTATTTAAAATAAAAACATCTTGAATATTCATAACATGTACTTCATGCAAAAAATATAAATA 1763999 ACATTTAAAAATCATATGAAATCTGAACAACATATTTTAATTAAATTACATTTCACATTACAAAA 66 ACATTTAAAAATCATATGAAATCTGAACAACATATTTTAATTAAATTACATTTCACATTACAAAA 1764064 ATAAACTCGTAATTATACATGTCCAATGTTCAAAGTTCAATGATTGTACTGTAAAATAAATATTC 131 ATAAACTCGTAATTATACATGTCCAATGTTCAAAGTTCAATGATTGTACTGTAAAATAAATATTC 1764129 ATGT 196 ATGT 1764133 ATTTT 1 ATTTT 1764138 TGAACAGTAT Statistics Matches: 204, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 199 204 1.00 ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36 Consensus pattern (199 bp): ATTTTATTTAAAATAAAAACATCTTGAATATTCATAACATGTACTTCATGCAAAAAATATAAATA ACATTTAAAAATCATATGAAATCTGAACAACATATTTTAATTAAATTACATTTCACATTACAAAA ATAAACTCGTAATTATACATGTCCAATGTTCAAAGTTCAATGATTGTACTGTAAAATAAATATTC ATGT Found at i:1774904 original size:4 final size:4 Alignment explanation

Indices: 1774895--1775026 Score: 264 Period size: 4 Copynumber: 33.0 Consensus size: 4 1774885 NNNNNNNNNN 1774895 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 1774943 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 1774991 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 1775027 GTTTCTGAAA Statistics Matches: 128, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 128 1.00 ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25 Consensus pattern (4 bp): AGAT Found at i:1783275 original size:22 final size:22 Alignment explanation

Indices: 1783222--1783275 Score: 65 Period size: 22 Copynumber: 2.5 Consensus size: 22 1783212 AAACGGTGAG * 1783222 TGAACCCAAAGTAAACCCGGAG 1 TGAACCCAAAGTAAACCCGGAC * 1783244 TGGACCCAAAGTAAACACC-GAC 1 TGAACCCAAAGTAAAC-CCGGAC * 1783266 TGAACACAAA 1 TGAACCCAAA 1783276 TTTTCAAACA Statistics Matches: 27, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 22 25 0.93 23 2 0.07 ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09 Consensus pattern (22 bp): TGAACCCAAAGTAAACCCGGAC Found at i:1794827 original size:12 final size:12 Alignment explanation

Indices: 1794810--1794835 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 1794800 TTTATATTGC 1794810 GTTTATCAGGTT 1 GTTTATCAGGTT 1794822 GTTTATCAGGTT 1 GTTTATCAGGTT 1794834 GT 1 GT 1794836 CAGAACTTTG Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.15, C:0.08, G:0.27, T:0.50 Consensus pattern (12 bp): GTTTATCAGGTT Found at i:1804793 original size:17 final size:18 Alignment explanation

Indices: 1804763--1804803 Score: 50 Period size: 17 Copynumber: 2.3 Consensus size: 18 1804753 CATTTAAATA * 1804763 GAAAATAACATTTTGCAT 1 GAAAATAACATTTTACAT 1804781 -AAAATAA-ATTTTTACAT 1 GAAAATAACA-TTTTACAT 1804798 GAAAAT 1 GAAAAT 1804804 TGCACTGCTC Statistics Matches: 20, Mismatches: 1, Indels: 4 0.80 0.04 0.16 Matches are distributed among these distances: 16 1 0.05 17 14 0.70 18 5 0.25 ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34 Consensus pattern (18 bp): GAAAATAACATTTTACAT Found at i:1814121 original size:2 final size:2 Alignment explanation

Indices: 1814114--1814147 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 1814104 TCTATTTTGC 1814114 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1814148 GTGGCACATT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1825948 original size:11 final size:11 Alignment explanation

Indices: 1825932--1825971 Score: 55 Period size: 11 Copynumber: 3.7 Consensus size: 11 1825922 TAAGCAAGTC 1825932 CTTAAAGGTGG 1 CTTAAAGGTGG * 1825943 CTTAAAGGTGA 1 CTTAAAGGTGG * 1825954 CTTAAAGG-AG 1 CTTAAAGGTGG 1825964 CTTAAAGG 1 CTTAAAGG 1825972 CTATACAACC Statistics Matches: 26, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 10 8 0.31 11 18 0.69 ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25 Consensus pattern (11 bp): CTTAAAGGTGG Found at i:1826090 original size:10 final size:11 Alignment explanation

Indices: 1826042--1826091 Score: 84 Period size: 11 Copynumber: 4.6 Consensus size: 11 1826032 GTCCAAACTT 1826042 CTTTAAGCCAC 1 CTTTAAGCCAC 1826053 CTTTAAGCCAC 1 CTTTAAGCCAC 1826064 CTTTAAGCCAC 1 CTTTAAGCCAC * 1826075 CTTTAAG-CAT 1 CTTTAAGCCAC 1826085 CTTTAAG 1 CTTTAAG 1826092 TGGCATTTAC Statistics Matches: 38, Mismatches: 1, Indels: 1 0.95 0.03 0.03 Matches are distributed among these distances: 10 9 0.24 11 29 0.76 ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:1826141 original size:22 final size:22 Alignment explanation

Indices: 1826084--1826144 Score: 70 Period size: 22 Copynumber: 2.8 Consensus size: 22 1826074 CCTTTAAGCA * * 1826084 TCTTTAAGTGGCATTTACGCTC 1 TCTTTAAGTGGCCTTTACACTC * * 1826106 TCTTTACACT-GCCTTTACACTG 1 TCTTTA-AGTGGCCTTTACACTC 1826128 TCTTTAAGTGGCCTTTA 1 TCTTTAAGTGGCCTTTA 1826145 AGTCAATATT Statistics Matches: 32, Mismatches: 5, Indels: 4 0.78 0.12 0.10 Matches are distributed among these distances: 21 2 0.06 22 28 0.88 23 2 0.06 ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43 Consensus pattern (22 bp): TCTTTAAGTGGCCTTTACACTC Found at i:1826478 original size:2 final size:2 Alignment explanation

Indices: 1826473--1826516 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 1826463 GTGAAAAAAA 1826473 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1826515 TC 1 TC 1826517 AGTTCATCCG Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1826928 original size:112 final size:112 Alignment explanation

Indices: 1826731--1826953 Score: 428 Period size: 112 Copynumber: 2.0 Consensus size: 112 1826721 AGTTTTGTTC * 1826731 GTTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA 1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA * 1826796 GAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCAT 66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT 1826843 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA 1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA 1826908 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA 66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA 1826954 CGTCAGGGTT Statistics Matches: 109, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 112 109 1.00 ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30 Consensus pattern (112 bp): GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT Found at i:1827978 original size:11 final size:11 Alignment explanation

Indices: 1827964--1828017 Score: 99 Period size: 11 Copynumber: 4.9 Consensus size: 11 1827954 TTTTTTTTAA 1827964 TGGCTTAAAGG 1 TGGCTTAAAGG 1827975 TGGCTTAAAGG 1 TGGCTTAAAGG * 1827986 TAGCTTAAAGG 1 TGGCTTAAAGG 1827997 TGGCTTAAAGG 1 TGGCTTAAAGG 1828008 TGGCTTAAAG 1 TGGCTTAAAG 1828018 AAGTTTGGAC Statistics Matches: 41, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 41 1.00 ACGTcount: A:0.30, C:0.09, G:0.33, T:0.28 Consensus pattern (11 bp): TGGCTTAAAGG Found at i:1828196 original size:11 final size:11 Alignment explanation

Indices: 1828180--1828218 Score: 53 Period size: 11 Copynumber: 3.6 Consensus size: 11 1828170 TAAAGATCGT 1828180 CTTTAAGCTAC 1 CTTTAAGCTAC * 1828191 CTTTAAAC-AC 1 CTTTAAGCTAC * 1828201 CTTTAAGCTAT 1 CTTTAAGCTAC 1828212 CTTTAAG 1 CTTTAAG 1828219 GAGGACTCAA Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 10 9 0.38 11 15 0.62 ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38 Consensus pattern (11 bp): CTTTAAGCTAC Found at i:1853277 original size:2 final size:2 Alignment explanation

Indices: 1853270--1853294 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 1853260 NNNNNNNNNN 1853270 TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA T 1853295 CTTAGCCATA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:1854772 original size:12 final size:12 Alignment explanation

Indices: 1854755--1854780 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 1854745 AGCAATTTCA 1854755 AACAGACTTTTT 1 AACAGACTTTTT 1854767 AACAGACTTTTT 1 AACAGACTTTTT 1854779 AA 1 AA 1854781 TATTATACCT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38 Consensus pattern (12 bp): AACAGACTTTTT Done.