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 5 of 5

Found at i:1041392 original size:21 final size:21

Alignment explanation

Indices: 1041209--1041407 Score: 86 Period size: 21 Copynumber: 9.5 Consensus size: 21 1041199 AATGATAGTT * 1041209 TCGCGAAAGTTAT-GCTTTATA 1 TCGCGAAAGTT-TCGCGTTATA * * 1041230 TCGCGAAAGTTACGCGTTTTA 1 TCGCGAAAGTTTCGCGTTATA * * *** * 1041251 TAGCAAAAGTAAAGTGTTCAT- 1 TCGCGAAAGTTTCGCGTT-ATA * * ** 1041272 TCGCAAAACTAACGCGTTATA 1 TCGCGAAAGTTTCGCGTTATA * * * 1041293 GCGCGAAAATTTTGCGTT-TA 1 TCGCGAAAGTTTCGCGTTATA * 1041313 TTCGCGAAAGTTACGCGTTATA 1 -TCGCGAAAGTTTCGCGTTATA 1041335 TCGC-AAACGTTTCGCGTT-TA 1 TCGCGAAA-GTTTCGCGTTATA * **** 1041355 TTCGCAAAACAAACGCGTTATA 1 -TCGCGAAAGTTTCGCGTTATA * * 1041377 TCGCGAAATTTTCGCGTTTATT 1 TCGCGAAAGTTTCGCG-TTATA 1041399 TC-CGAAAGT 1 TCGCGAAAGT 1041408 AACGCGTTTA Statistics Matches: 133, Mismatches: 35, Indels: 20 0.71 0.19 0.11 Matches are distributed among these distances: 20 9 0.07 21 110 0.83 22 14 0.11 ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32 Consensus pattern (21 bp): TCGCGAAAGTTTCGCGTTATA Found at i:1056946 original size:2 final size:2 Alignment explanation

Indices: 1056941--1056976 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 1056931 CCCCCCCCCC 1056941 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 1056977 GTTCATAAGT Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1063519 original size:21 final size:21 Alignment explanation

Indices: 1063493--1063564 Score: 144 Period size: 21 Copynumber: 3.4 Consensus size: 21 1063483 TTAGTTGATA 1063493 TATAACGGTCTGGGTGAGGGG 1 TATAACGGTCTGGGTGAGGGG 1063514 TATAACGGTCTGGGTGAGGGG 1 TATAACGGTCTGGGTGAGGGG 1063535 TATAACGGTCTGGGTGAGGGG 1 TATAACGGTCTGGGTGAGGGG 1063556 TATAACGGT 1 TATAACGGT 1063565 GAAATAGCAA Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 51 1.00 ACGTcount: A:0.21, C:0.10, G:0.44, T:0.25 Consensus pattern (21 bp): TATAACGGTCTGGGTGAGGGG Found at i:1070239 original size:168 final size:168 Alignment explanation

Indices: 1069959--1070391 Score: 735 Period size: 168 Copynumber: 2.6 Consensus size: 168 1069949 NNNNNNNNNN * * * 1069959 ATATGGCCATATTGGCCCCACCCTAGAGCCTGAACACCTA--ACAAAGGGGTCAAGAATTTTACA 1 ATATGGCCATATTGGCCCCACCCTAGAGCCTG-A-ACCTATGACCAAGGGGTCATGAATTTCACA * * * 1070022 ATTTTGGTAGAGGGCTTCATGGACATTATAACCAGGCATTTATTTTTAAACAAATATATATGGGA 64 ATTTTGGTAGAGGGCCTCATGGACATCATAACCAGGCATTTAGTTTTAAACAAATATATATGGGA * 1070087 GTAAAGAACAAGATTTTCTAAGATTTAATACATTTTTACT 129 GTAAAGAACAAGATTTTCTAAGATTTAATACATTTTAACT * 1070127 ATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCTATGACCCAGGGGTCATGAATTTCACAAT 1 ATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCTATGACCAAGGGGTCATGAATTTCACAAT 1070192 TTTGGTAGAGGGCCTCATGGACATCATAACCAGGCATTTAGTTTTAAACAAATATATATGGGAGT 66 TTTGGTAGAGGGCCTCATGGACATCATAACCAGGCATTTAGTTTTAAACAAATATATATGGGAGT * 1070257 AGAGAACAAGATTTTCTAAGATTTAATACATTTTAACT 131 AAAGAACAAGATTTTCTAAGATTTAATACATTTTAACT * * 1070295 ATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCATGACCAAGGGGTCATGAATTTCGCAAT 1 ATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCTATGACCAAGGGGTCATGAATTTCACAAT 1070360 TTTGGTAGAGGGCCTCATGGACATCATAACCA 66 TTTGGTAGAGGGCCTCATGGACATCATAACCA 1070392 TACATTCAGT Statistics Matches: 251, Mismatches: 12, Indels: 4 0.94 0.04 0.01 Matches are distributed among these distances: 166 5 0.02 167 1 0.00 168 245 0.98 ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28 Consensus pattern (168 bp): ATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCTATGACCAAGGGGTCATGAATTTCACAAT TTTGGTAGAGGGCCTCATGGACATCATAACCAGGCATTTAGTTTTAAACAAATATATATGGGAGT AAAGAACAAGATTTTCTAAGATTTAATACATTTTAACT Found at i:1071824 original size:36 final size:36 Alignment explanation

Indices: 1071748--1071824 Score: 93 Period size: 36 Copynumber: 2.1 Consensus size: 36 1071738 TACATACATG * * * * * 1071748 TATCTTGGACGTGTACCCATTGTCTACATATATACT 1 TATCTTGAACCTGTACCCATGGTCAACATATATACA 1071784 TATCTTGAACCTGTACCCATGGTCAACATAGTA-ACA 1 TATCTTGAACCTGTACCCATGGTCAACATA-TATACA 1071820 TATCT 1 TATCT 1071825 CTCTGACTTG Statistics Matches: 35, Mismatches: 5, Indels: 2 0.83 0.12 0.05 Matches are distributed among these distances: 36 33 0.94 37 2 0.06 ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35 Consensus pattern (36 bp): TATCTTGAACCTGTACCCATGGTCAACATATATACA Found at i:1072022 original size:36 final size:36 Alignment explanation

Indices: 1071829--1072313 Score: 424 Period size: 36 Copynumber: 13.4 Consensus size: 36 1071819 ATATCTCTCT * * * ** 1071829 GACTTGAATCCATCGTCTACATATGAACATCTCTTG 1 GACTTGAACCCATGGCCTACATATTTACATCTCTTG * * * * * 1071865 GATTTGAGCCCACT-GCCTACATATTAACACCTCTTCA 1 GACTTGAACCCA-TGGCCTACATATTTACATCTCTT-G * * * 1071902 GACTTGAACCCATGGTCTATATATTCACA-CATCTTG 1 GACTTGAACCCATGGCCTACATATTTACATC-TCTTG * * * * * 1071938 AATTTGAACCCATGGACTTCAT-TCTTACAACTCTCTTT 1 GACTTGAACCCATGGCCTACATAT-TTAC-A-TCTCTTG * * * ** * 1071976 TACTTAAACCCATGGTCTACATATGAATATCTCTTG 1 GACTTGAACCCATGGCCTACATATTTACATCTCTTG * 1072012 GACTTGAACCCATGGTCTACATATTTACATCTCTTG 1 GACTTGAACCCATGGCCTACATATTTACATCTCTTG * ** * ** * 1072048 GACTTGCACCTTTGGTCTATGTA-TTACATCTCTGG 1 GACTTGAACCCATGGCCTACATATTTACATCTCTTG * * * * 1072083 GA-TATGAAGACAATGACCTACAT-TTTAACATCTCTAG 1 GACT-TGAA-CCCATGGCCTACATATTT-ACATCTCTTG * * 1072120 GACTTGAACCCATGGCCTCCATATTTACATCTCTAG 1 GACTTGAACCCATGGCCTACATATTTACATCTCTTG * * 1072156 GACTTGAACCCATGGCCTCCATATTTACATCTCTAG 1 GACTTGAACCCATGGCCTACATATTTACATCTCTTG * * 1072192 GACTTGAACCCATGGCCTCCATATTTACATCTCTAG 1 GACTTGAACCCATGGCCTACATATTTACATCTCTTG * * 1072228 GACTTGAACCCATGGCCTCCATATTTACATCTCTAG 1 GACTTGAACCCATGGCCTACATATTTACATCTCTTG * * * 1072264 GACTTGAACCCATGACCTCCATATTTACATCTCTAG 1 GACTTGAACCCATGGCCTACATATTTACATCTCTTG 1072300 GACTTGAACCCATG 1 GACTTGAACCCATG 1072314 TTCTGTCCGT Statistics Matches: 380, Mismatches: 54, Indels: 30 0.82 0.12 0.06 Matches are distributed among these distances: 34 1 0.00 35 17 0.04 36 290 0.76 37 47 0.12 38 23 0.06 39 2 0.01 ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33 Consensus pattern (36 bp): GACTTGAACCCATGGCCTACATATTTACATCTCTTG Found at i:1074267 original size:2 final size:2 Alignment explanation

Indices: 1074260--1074309 Score: 100 Period size: 2 Copynumber: 25.0 Consensus size: 2 1074250 TTAGATTCAT 1074260 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 1074302 TC TC TC TC 1 TC TC TC TC 1074310 CAACAGGATG Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1076983 original size:41 final size:41 Alignment explanation

Indices: 1076896--1077938 Score: 982 Period size: 41 Copynumber: 25.0 Consensus size: 41 1076886 TTACAGGCCC * * 1076896 AGTAGGAATACCTTGTTACAAGAAGACTGTTATATTAGCAGGCT 1 AGTAGGAATACCTTGTTAC---AAGACTGTTATATTACCAGCCT * * ** 1076940 TGTAGGAATAACTTGTTACAAGACTGTTATATTAGAAGCCT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * 1076981 TGTAGGAATACTTTGTTACAAGAAGACTGTTATATTAGCAGCCT 1 AGTAGGAATACCTTGTTAC---AAGACTGTTATATTACCAGCCT * * * ** * * * * 1077025 TGTAGGAATAACTTGTTACAAGAATAATATATAATCA-ACA 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * 1077065 AGTAGGAATATCTTGTTACAAGACTGTTATTTTACCAG-CT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * 1077105 AGTAGGAATA-TTTGTTACAAGAAGACTGTTATATTACAAGCCT 1 AGTAGGAATACCTTGTTAC---AAGACTGTTATATTACCAGCCT * * * * 1077148 AGAAGAAATAACTTATTACAAGACTGTTATATTACCAGCCT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * 1077189 AGTAGGAAAACCTTGTTACAGGACCACTGTTATATTACGAGCCT 1 AGTAGGAATACCTTGTTACA--A-GACTGTTATATTACCAGCCT * * 1077233 AGAAGGAATACCTTGTTACAAGACTGTTATATTACTAGCCT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * * 1077274 CGAAGGAATACCTTGTTACAAGAAGACTGTTATTTTACAAGCCT 1 AGTAGGAATACCTTGTTAC---AAGACTGTTATATTACCAGCCT * * * * 1077318 AGAAGAAATAACTTATTACAAGACTGTTATATTACCAGCCT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT ** * * 1077359 AGTAGGAATACCTTAATA-AGAAACTGTTATGTTACCAG-CT 1 AGTAGGAATACCTTGTTACA-AGACTGTTATATTACCAGCCT * * * * 1077399 AGTAGTAATACTTTGTTACAAGAATGTTATTTTACCAGCCT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * * 1077440 AGTAAGAATACTTTGTTCCAAGACTGTTATATAACCAG-CT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * * ** * 1077480 AGAAGGAATACTTTGTTAAAAGACTTTTGCATTACCAGCCA 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * * * 1077521 AGAAGAAATACCTTATTACAAGACTGTTATATTACCATCTT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * * 1077562 GGTAGGAATCCCGTGTTACAAGAAGACTGTTATATTACAAGCCT 1 AGTAGGAATACCTTGTTAC---AAGACTGTTATATTACCAGCCT ** * 1077606 AGTAGGAATACCTTGTTACAGGAAGACTGTTATATTATAAGCGT 1 AGTAGGAATACCTTGTTAC---AAGACTGTTATATTACCAGCCT * * * * 1077650 AGAAGAAATACCTTGCTACAAGACTGTTATATTACAAGCCT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT ** * 1077691 AGTAGGAATACCTTGTTACAGGAAGACTGTTATATTATAAGCGT 1 AGTAGGAATACCTTGTTAC---AAGACTGTTATATTACCAGCCT * * 1077735 AGAAGGAATACCTTGTTACAAGACTGTTATATTACCGGCCT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * 1077776 AGAAGAAATACCTTGTTACAAGACTGTAATATTACCAGCCT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * 1077817 AGTAAGAATACCTTGTTACAAGACTGTTATATTACCGGCCA 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * * * 1077858 AGAAAGAATGCCTTGTTACAAGAATGTTATTTTACCAGCCT 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT * * * 1077899 AGTAAGAATACTTTGTTCCAAGACTGTTATATTACCAGCC 1 AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCC 1077939 AAAAAAGAAT Statistics Matches: 832, Mismatches: 142, Indels: 53 0.81 0.14 0.05 Matches are distributed among these distances: 39 7 0.01 40 105 0.13 41 448 0.54 42 18 0.02 43 11 0.01 44 243 0.29 ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31 Consensus pattern (41 bp): AGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCT Found at i:1077040 original size:85 final size:82 Alignment explanation

Indices: 1076885--1077938 Score: 988 Period size: 85 Copynumber: 12.6 Consensus size: 82 1076875 TTCTTTTTAC * * * * * 1076885 ATTACAGGCCCAGTAGGAATACCTTGTTACAAGAAGACTGTTATATTAGCAGGCTTGTAGGAATA 1 ATTACAAGCCTAGTAGGAATACCTTGTTAC---AAGACTGTTATATTACCAGCCTAGTAGGAATA * 1076950 ACTTGTTACAAGACTGTTAT 63 CCTTGTTACAAGACTGTTAT * * * * * 1076970 ATTAGAAGCCTTGTAGGAATACTTTGTTACAAGAAGACTGTTATATTAGCAGCCTTGTAGGAATA 1 ATTACAAGCCTAGTAGGAATACCTTGTTAC---AAGACTGTTATATTACCAGCCTAGTAGGAATA * * ** 1077035 ACTTGTTACAAGAATAATAT 63 CCTTGTTACAAGACTGTTAT * * * * * 1077055 ATAATCAA--CAAGTAGGAATATCTTGTTACAAGACTGTTATTTTACCAG-CTAGTAGGAATA-T 1 ATTA-CAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCTAGTAGGAATACC 1077116 TTGTTACAAGAAGACTGTTAT 65 TTGTTAC---AAGACTGTTAT * * * * * 1077137 ATTACAAGCCTAGAAGAAATAACTTATTACAAGACTGTTATATTACCAGCCTAGTAGGAAAACCT 1 ATTACAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCTAGTAGGAATACCT * 1077202 TGTTACAGGACCACTGTTAT 66 TGTTACA--A-GACTGTTAT * * * * * 1077222 ATTACGAGCCTAGAAGGAATACCTTGTTACAAGACTGTTATATTACTAGCCTCGAAGGAATACCT 1 ATTACAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCTAGTAGGAATACCT 1077287 TGTTACAAGAAGACTGTTAT 66 TGTTAC---AAGACTGTTAT * * * * * 1077307 TTTACAAGCCTAGAAGAAATAACTTATTACAAGACTGTTATATTACCAGCCTAGTAGGAATACCT 1 ATTACAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCTAGTAGGAATACCT ** * 1077372 TAATA-AGAAACTGTTAT 66 TGTTACA-AGACTGTTAT * * * * * * * * 1077389 GTTACCAG-CTAGTAGTAATACTTTGTTACAAGAATGTTATTTTACCAGCCTAGTAAGAATACTT 1 ATTACAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCTAGTAGGAATACCT * 1077453 TGTTCCAAGACTGTTAT 66 TGTTACAAGACTGTTAT * * * * * * ** * * * 1077470 ATAACCAG-CTAGAAGGAATACTTTGTTAAAAGACTTTTGCATTACCAGCCAAGAAGAAATACCT 1 ATTACAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCTAGTAGGAATACCT * 1077534 TATTACAAGACTGTTAT 66 TGTTACAAGACTGTTAT * * * * * * * 1077551 ATTACCATCTTGGTAGGAATCCCGTGTTACAAGAAGACTGTTATATTACAAGCCTAGTAGGAATA 1 ATTACAAGCCTAGTAGGAATACCTTGTTAC---AAGACTGTTATATTACCAGCCTAGTAGGAATA 1077616 CCTTGTTACAGGAAGACTGTTAT 63 CCTTGTTAC---AAGACTGTTAT * * * * * * 1077639 ATTATAAGCGTAGAAGAAATACCTTGCTACAAGACTGTTATATTACAAGCCTAGTAGGAATACCT 1 ATTACAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCTAGTAGGAATACCT 1077704 TGTTACAGGAAGACTGTTAT 66 TGTTAC---AAGACTGTTAT * * * * * * 1077724 ATTATAAGCGTAGAAGGAATACCTTGTTACAAGACTGTTATATTACCGGCCTAGAAGAAATACCT 1 ATTACAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCTAGTAGGAATACCT * 1077789 TGTTACAAGACTGTAAT 66 TGTTACAAGACTGTTAT * * * * * * * 1077806 ATTACCAGCCTAGTAAGAATACCTTGTTACAAGACTGTTATATTACCGGCCAAGAAAGAATGCCT 1 ATTACAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCTAGTAGGAATACCT * 1077871 TGTTACAAGAATGTTAT 66 TGTTACAAGACTGTTAT * * * * * 1077888 TTTACCAGCCTAGTAAGAATACTTTGTTCCAAGACTGTTATATTACCAGCC 1 ATTACAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCC 1077939 AAAAAAGAAT Statistics Matches: 813, Mismatches: 133, Indels: 49 0.82 0.13 0.05 Matches are distributed among these distances: 79 7 0.01 80 11 0.01 81 149 0.18 82 170 0.21 83 34 0.04 84 29 0.04 85 378 0.46 86 3 0.00 88 32 0.04 ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31 Consensus pattern (82 bp): ATTACAAGCCTAGTAGGAATACCTTGTTACAAGACTGTTATATTACCAGCCTAGTAGGAATACCT TGTTACAAGACTGTTAT Found at i:1077080 original size:40 final size:40 Alignment explanation

Indices: 1077026--1077127 Score: 116 Period size: 40 Copynumber: 2.6 Consensus size: 40 1077016 TAGCAGCCTT * * 1077026 GTAGGAATAACTTGTTACAAGAATAATATATAATCAACAA 1 GTAGGAATATCTTGTTACAAGAATAATATATAACCAACAA * ** * * * * 1077066 GTAGGAATATCTTGTTACAAGACTGTTATTTTACCAGCTA 1 GTAGGAATATCTTGTTACAAGAATAATATATAACCAACAA 1077106 GTAGGAATAT-TTGTTACAAGAA 1 GTAGGAATATCTTGTTACAAGAA 1077128 GACTGTTATA Statistics Matches: 52, Mismatches: 10, Indels: 1 0.83 0.16 0.02 Matches are distributed among these distances: 39 11 0.21 40 41 0.79 ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32 Consensus pattern (40 bp): GTAGGAATATCTTGTTACAAGAATAATATATAACCAACAA Found at i:1078246 original size:44 final size:44 Alignment explanation

Indices: 1078187--1078295 Score: 137 Period size: 44 Copynumber: 2.5 Consensus size: 44 1078177 TCTTCAAGAA ** * * * 1078187 TGTTATATTCCCAGCCAAGTAGGAATGCTTTGTTACAAGAAAAC 1 TGTTATATAACCAGCCTAGTAGGAATACTTTGTAACAAGAAAAC * * * 1078231 TGTTGTATAACCAGCCTAGAAGGAATACTTTGTAACAAGAAGAC 1 TGTTATATAACCAGCCTAGTAGGAATACTTTGTAACAAGAAAAC * 1078275 TGTTATATTACCAGCCTAGTA 1 TGTTATATAACCAGCCTAGTA 1078296 AGAAAACCTT Statistics Matches: 54, Mismatches: 11, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 44 54 1.00 ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29 Consensus pattern (44 bp): TGTTATATAACCAGCCTAGTAGGAATACTTTGTAACAAGAAAAC Found at i:1084744 original size:57 final size:57 Alignment explanation

Indices: 1084656--1084826 Score: 317 Period size: 57 Copynumber: 3.0 Consensus size: 57 1084646 TAGAGTTTAA * 1084656 ACAGAATTACA-AGATTGGACTTACACTTCAACGCTAGCGATCAGCTTATGGGGATCT 1 ACAGAA-TACAGAGGTTGGACTTACACTTCAACGCTAGCGATCAGCTTATGGGGATCT 1084713 ACAGAATACAGAGGTTGGACTTACACTTCAACGCTAGCGATCAGCTTATGGGGATCT 1 ACAGAATACAGAGGTTGGACTTACACTTCAACGCTAGCGATCAGCTTATGGGGATCT 1084770 ACAGAATACAGAGGTTGGACTTACACTTCAACGCTAGCGATCAGCTTATGGGGATCT 1 ACAGAATACAGAGGTTGGACTTACACTTCAACGCTAGCGATCAGCTTATGGGGATCT 1084827 CCACTGCGTG Statistics Matches: 112, Mismatches: 1, Indels: 2 0.97 0.01 0.02 Matches are distributed among these distances: 56 4 0.04 57 108 0.96 ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25 Consensus pattern (57 bp): ACAGAATACAGAGGTTGGACTTACACTTCAACGCTAGCGATCAGCTTATGGGGATCT Found at i:1086028 original size:41 final size:41 Alignment explanation

Indices: 1085983--1086871 Score: 1141 Period size: 41 Copynumber: 21.8 Consensus size: 41 1085973 ATGTCACCTG * * 1085983 ATGTCATAAATGATATCTCTTGAGATACAGTAAG-TAATACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAA-ACA * * * 1086024 ATGTCATATATGATATTTTC-TGAGACACAGTACGTTAAACA 1 ATGTCATATATGATA-TCTCATGAGATACAGTAAGTTAAACA * * * * * * 1086065 AAGTCATATTTGATATCTCATAAGACAGAGTAAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA 1086106 ATGTCATATATGATATCTCATGAGATACAGTAAG-TAACACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAA-ACA * 1086147 ATGTCATATATGATTTCTCATGAGATACAGTAAG-TAACACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAA-ACA * * 1086188 ATGTCATATATGATATCTCAGGAGATACAGTAAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * 1086229 ATGTCATATATGATATCTCATGAGATACATTAAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * * * 1086270 ATGTCATATTTGATATCTCATGTGATACATTAAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * * * 1086311 ATGTCTTATTTGATATCTCATGAGATACATTAAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * 1086352 ATGTCTTATATGATATCTCATGAGATACAGTAAG-TAACACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAA-ACA * * * * 1086393 ATGCCATATATGATATCTCATGAGTTAAAGTAAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA 1086434 ATGTC--ATATGATATCTCATGAGATACAGT-AG-TAACACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAA-ACA * * * 1086472 ATGTCATATATGATATCTCATGCGATAAAGTAAGTAAAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * * * 1086513 ATGCCATATAAGTTATCTAATGAGATACAGTAAG-TAACACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAA-ACA * * ** 1086554 ATGCCATATATGATATCTCATGAGATAAAGTAAGCAAAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * * 1086595 ATGCCATATATGATATCTCATGAGATACATTAAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * 1086636 ATGTCATATATGATATCTCATGAGATACATTAAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * 1086677 ATGTCATATATGATATCTCATGAGATACATTAAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * 1086718 ATGTCATATATGATATCTCATGAGATACAGTTAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * 1086759 ATGTCTTATATGATATCTCATGAGATACATTAAGTTAAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * * 1086800 ATGTCATATATGATATCTCATTAGATACAGTTAGTTGAACA 1 ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA * * 1086841 ATGTCTTATATGATATCTCGTGAGATACAGT 1 ATGTCATATATGATATCTCATGAGATACAGT 1086872 CAGTAACACA Statistics Matches: 760, Mismatches: 74, Indels: 28 0.88 0.09 0.03 Matches are distributed among these distances: 37 2 0.00 38 10 0.01 39 22 0.03 40 31 0.04 41 681 0.90 42 14 0.02 ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33 Consensus pattern (41 bp): ATGTCATATATGATATCTCATGAGATACAGTAAGTTAAACA Found at i:1092625 original size:14 final size:14 Alignment explanation

Indices: 1092606--1092632 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 1092596 TTTATCTTGA 1092606 AAAAAGAGAGAGAG 1 AAAAAGAGAGAGAG 1092620 AAAAAGAGAGAGA 1 AAAAAGAGAGAGA 1092633 TTCTTACCTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00 Consensus pattern (14 bp): AAAAAGAGAGAGAG Found at i:1101725 original size:15 final size:17 Alignment explanation

Indices: 1101705--1101745 Score: 50 Period size: 17 Copynumber: 2.5 Consensus size: 17 1101695 GACGTCATTT 1101705 TATAAC-AAATT-CAGA 1 TATAACGAAATTACAGA * 1101720 TATAACGAATTTACAGA 1 TATAACGAAATTACAGA * 1101737 TATAGCGAA 1 TATAACGAA 1101746 CTGATTTTGA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 15 6 0.27 16 4 0.18 17 12 0.55 ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27 Consensus pattern (17 bp): TATAACGAAATTACAGA Found at i:1109298 original size:12 final size:12 Alignment explanation

Indices: 1109276--1109331 Score: 76 Period size: 12 Copynumber: 4.6 Consensus size: 12 1109266 GGAATCACCT * 1109276 TGTCCGTCCGTC 1 TGTCTGTCCGTC * 1109288 CGTCTGTCCGTC 1 TGTCTGTCCGTC * 1109300 TGTCTGTCTGTC 1 TGTCTGTCCGTC 1109312 TTGTCTGTCCGTC 1 -TGTCTGTCCGTC 1109325 TGTCTGT 1 TGTCTGT 1109332 GCAATCGTGT Statistics Matches: 38, Mismatches: 5, Indels: 2 0.84 0.11 0.04 Matches are distributed among these distances: 12 27 0.71 13 11 0.29 ACGTcount: A:0.00, C:0.32, G:0.25, T:0.43 Consensus pattern (12 bp): TGTCTGTCCGTC Found at i:1109300 original size:8 final size:8 Alignment explanation

Indices: 1109276--1109328 Score: 70 Period size: 8 Copynumber: 6.5 Consensus size: 8 1109266 GGAATCACCT 1109276 TGTCCGTC 1 TGTCCGTC * 1109284 CGTCCGTC 1 TGTCCGTC 1109292 TGTCCGTC 1 TGTCCGTC * 1109300 TGTCTGTC 1 TGTCCGTC * 1109308 TGTCTTGTC 1 TGTC-CGTC 1109317 TGTCCGTC 1 TGTCCGTC 1109325 TGTC 1 TGTC 1109329 TGTGCAATCG Statistics Matches: 40, Mismatches: 4, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 8 32 0.80 9 8 0.20 ACGTcount: A:0.00, C:0.34, G:0.25, T:0.42 Consensus pattern (8 bp): TGTCCGTC Found at i:1109304 original size:4 final size:4 Alignment explanation

Indices: 1109289--1109331 Score: 59 Period size: 4 Copynumber: 10.5 Consensus size: 4 1109279 CCGTCCGTCC * * 1109289 GTCT GTCC GTCT GTCT GTCT GTCTT GTCT GTCC GTCT GTCT GT 1 GTCT GTCT GTCT GTCT GTCT GTC-T GTCT GTCT GTCT GTCT GT 1109332 GCAATCGTGT Statistics Matches: 34, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 4 30 0.88 5 4 0.12 ACGTcount: A:0.00, C:0.28, G:0.26, T:0.47 Consensus pattern (4 bp): GTCT Found at i:1109319 original size:17 final size:17 Alignment explanation

Indices: 1109285--1109329 Score: 65 Period size: 17 Copynumber: 2.7 Consensus size: 17 1109275 TTGTCCGTCC * 1109285 GTCCGTCTGTC-CGTCT 1 GTCCGTCTGTCTTGTCT * 1109301 GTCTGTCTGTCTTGTCT 1 GTCCGTCTGTCTTGTCT 1109318 GTCCGTCTGTCT 1 GTCCGTCTGTCT 1109330 GTGCAATCGT Statistics Matches: 25, Mismatches: 3, Indels: 1 0.86 0.10 0.03 Matches are distributed among these distances: 16 10 0.40 17 15 0.60 ACGTcount: A:0.00, C:0.31, G:0.24, T:0.44 Consensus pattern (17 bp): GTCCGTCTGTCTTGTCT Found at i:1109533 original size:146 final size:146 Alignment explanation

Indices: 1109336--1109878 Score: 928 Period size: 146 Copynumber: 3.7 Consensus size: 146 1109326 GTCTGTGCAA * 1109336 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC 1 TCGTGTCAGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * 1109401 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATCTGGGCAAAGTCAAGGTCACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATCTGGGCAAGGTCAAGGTCACTGGC * * 1109466 AGAAAAAATACAAAAT 131 AGAAAAAGTGCAAAAT * 1109482 TCGTGTGAGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC 1 TCGTGTCAGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC 1109547 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATCTGGGCAAGGTCAAGGTCACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATCTGGGCAAGGTCAAGGTCACTGGC 1109612 AGAAAAAGTGCAAAAT 131 AGAAAAAGTGCAAAAT * * * * 1109628 TTGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTAGAAGTTCTTACTTCACACAAAGATTGC 1 TCGTGTCAGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * 1109693 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATCTGGGCAAGGTCAAGGTCACTGGC 1109758 AGAAAAAGTGCAAAAT 131 AGAAAAAGTGCAAAAT * * * 1109774 TCGTGTCCA-GTCCATATCTTTCTTATGGGGAAACATTGGAAGTTCTTACTTTAAACAAAGATTG 1 TCGTGT-CAGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTG * 1109838 CTTATGA-TTAAAGGGTGTGTCATGACCTTGACCCAAGGTCA 65 CTTATGACCT-AAGGGTGTGTCATGACCTTGACCCAAGGTCA 1109879 ATTGAGAAAG Statistics Matches: 378, Mismatches: 17, Indels: 4 0.95 0.04 0.01 Matches are distributed among these distances: 145 1 0.00 146 376 0.99 147 1 0.00 ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29 Consensus pattern (146 bp): TCGTGTCAGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATCTGGGCAAGGTCAAGGTCACTGGC AGAAAAAGTGCAAAAT Found at i:1110498 original size:23 final size:23 Alignment explanation

Indices: 1110472--1110518 Score: 85 Period size: 23 Copynumber: 2.0 Consensus size: 23 1110462 AATGGTCACA 1110472 AATAACATTCCACTATTCACTCC 1 AATAACATTCCACTATTCACTCC * 1110495 AATAACATTCCACTATTCATTCC 1 AATAACATTCCACTATTCACTCC 1110518 A 1 A 1110519 GCAAGTTGAT Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 23 23 1.00 ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32 Consensus pattern (23 bp): AATAACATTCCACTATTCACTCC Found at i:1110517 original size:12 final size:12 Alignment explanation

Indices: 1110477--1110518 Score: 50 Period size: 12 Copynumber: 3.6 Consensus size: 12 1110467 TCACAAATAA 1110477 CATTCCACTATT 1 CATTCCACTATT * * * 1110489 CACTCCAATA-A 1 CATTCCACTATT 1110500 CATTCCACTATT 1 CATTCCACTATT 1110512 CATTCCA 1 CATTCCA 1110519 GCAAGTTGAT Statistics Matches: 23, Mismatches: 6, Indels: 2 0.74 0.19 0.06 Matches are distributed among these distances: 11 8 0.35 12 15 0.65 ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33 Consensus pattern (12 bp): CATTCCACTATT Found at i:1123082 original size:23 final size:23 Alignment explanation

Indices: 1123021--1123093 Score: 84 Period size: 23 Copynumber: 3.3 Consensus size: 23 1123011 TGATATTACA 1123021 GTTT-CGGGAGGGCAATATAACT 1 GTTTCCGGGAGGGCAATATAACT * * 1123043 ATTTCCTGTGA----AATATAACT 1 GTTTCC-GGGAGGGCAATATAACT 1123063 GTTTCCGGGAGGGCAATATAACT 1 GTTTCCGGGAGGGCAATATAACT 1123086 GTTTCCGG 1 GTTTCCGG 1123094 TGTGATTCAG Statistics Matches: 41, Mismatches: 4, Indels: 11 0.73 0.07 0.20 Matches are distributed among these distances: 19 3 0.07 20 14 0.34 22 3 0.07 23 18 0.44 24 3 0.07 ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32 Consensus pattern (23 bp): GTTTCCGGGAGGGCAATATAACT Found at i:1127694 original size:27 final size:27 Alignment explanation

Indices: 1127656--1127752 Score: 97 Period size: 27 Copynumber: 3.6 Consensus size: 27 1127646 GAACGAGACT * * * 1127656 ACGGGCGGACAGAAAGAGCAAAGTCTG 1 ACGGACGGACAGAAACAGCAAAGTTTG * * * * 1127683 ACGGACGAACAGGAGACAACGAAA-TTTA 1 ACGGACGGACA-GAAACAGC-AAAGTTTG 1127711 ACGGACGGACAGAAACAGCAAAGTTTG 1 ACGGACGGACAGAAACAGCAAAGTTTG * 1127738 ACGGACGGTCAGAAA 1 ACGGACGGACAGAAA 1127753 GTTCAAAGAG Statistics Matches: 55, Mismatches: 12, Indels: 6 0.75 0.16 0.08 Matches are distributed among these distances: 26 3 0.05 27 32 0.58 28 17 0.31 29 3 0.05 ACGTcount: A:0.41, C:0.19, G:0.31, T:0.09 Consensus pattern (27 bp): ACGGACGGACAGAAACAGCAAAGTTTG Found at i:1130211 original size:2 final size:2 Alignment explanation

Indices: 1130204--1130242 Score: 69 Period size: 2 Copynumber: 19.5 Consensus size: 2 1130194 GTACATTCAC * 1130204 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1130243 TTTCTTTCCT Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): GA Found at i:1135085 original size:11 final size:10 Alignment explanation

Indices: 1135056--1135086 Score: 53 Period size: 10 Copynumber: 3.0 Consensus size: 10 1135046 GCGGCTGGGC 1135056 GGGGTGTGTG 1 GGGGTGTGTG 1135066 GGGGTGTGTG 1 GGGGTGTGTG 1135076 GGGGTCGTGTG 1 GGGGT-GTGTG 1135087 TCGATTTCCG Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 10 15 0.75 11 5 0.25 ACGTcount: A:0.00, C:0.03, G:0.68, T:0.29 Consensus pattern (10 bp): GGGGTGTGTG Found at i:1140434 original size:55 final size:55 Alignment explanation

Indices: 1140350--1140461 Score: 215 Period size: 55 Copynumber: 2.0 Consensus size: 55 1140340 GTGTCTCACA 1140350 TCTACCTGACACCCCCAAACCCATCACTTAAGTCCTCCCACTGGCAGTTTCATGT 1 TCTACCTGACACCCCCAAACCCATCACTTAAGTCCTCCCACTGGCAGTTTCATGT * 1140405 TCTACCTGACACCCCCAAACCCATCACTTAAGTCCTCCCATTGGCAGTTTCATGT 1 TCTACCTGACACCCCCAAACCCATCACTTAAGTCCTCCCACTGGCAGTTTCATGT 1140460 TC 1 TC 1140462 ATATTGTTAA Statistics Matches: 56, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 55 56 1.00 ACGTcount: A:0.23, C:0.39, G:0.11, T:0.27 Consensus pattern (55 bp): TCTACCTGACACCCCCAAACCCATCACTTAAGTCCTCCCACTGGCAGTTTCATGT Found at i:1147461 original size:16 final size:17 Alignment explanation

Indices: 1147428--1147470 Score: 52 Period size: 17 Copynumber: 2.6 Consensus size: 17 1147418 TGAAAAAACA 1147428 AAAAAAACAAAACGAAC 1 AAAAAAACAAAACGAAC ** 1147445 AAAAAAACCCAAC-AAC 1 AAAAAAACAAAACGAAC * 1147461 AAACAAACAA 1 AAAAAAACAA 1147471 TAATCAAACA Statistics Matches: 21, Mismatches: 5, Indels: 1 0.78 0.19 0.04 Matches are distributed among these distances: 16 10 0.48 17 11 0.52 ACGTcount: A:0.74, C:0.23, G:0.02, T:0.00 Consensus pattern (17 bp): AAAAAAACAAAACGAAC Found at i:1148395 original size:40 final size:40 Alignment explanation

Indices: 1148292--1148816 Score: 658 Period size: 40 Copynumber: 13.3 Consensus size: 40 1148282 CTTTGTTTTG 1148292 GAGTTGTTGACCAG---TATTGTCACTTACCCATTGTGTT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT * * 1148329 GAGTTGTTGA--TGTCTTATTGTCACTTACCCATTGCGTT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT * * 1148367 GAGTTGTTGACCAGTCTTACTGTCACTTACCCACTGTGTT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT * * 1148407 GAGTTGTTGACCAGTCTTATTATCACTTACCCACTGTGTT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT ** * * 1148447 GAGTTGTTGATAAGTCTCATTGTCACTTACCCATTATGTT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT ** * 1148487 GAGTTGTTGATAAGTCTTATTGTCACTTACCCATTGCGTT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT * 1148527 GAGTTGTTGACCAGTCTTATTGTCATTTACCCATTGTGTT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT * * * * 1148567 CAGTTGTTGACCAGTCTTATTGTCATTTACCCACTGTATT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT * * * * 1148607 GA-TCTGTTGACCAGTCTTACTGTAATTTACCCACTGTGTT 1 GAGT-TGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT * * * * * 1148647 GAGTTGTTGACCAGTCTAACTGTCATTTACCCACTGTATT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT * * * 1148687 GA-TCTGTTGACCAGTCTTACTATCACTTACCCATTGCGTT 1 GAGT-TGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT ** 1148727 GAAATGTTGACCAGTC----TGTCACTTACCCATTGTGTT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT * 1148763 GAGTTGTTGACCAGTCTTACTGTCACTTACCCATTGTGTT 1 GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT 1148803 GAGTTGTTGACCAG 1 GAGTTGTTGACCAG 1148817 GCCCCACCAG Statistics Matches: 433, Mismatches: 42, Indels: 23 0.87 0.08 0.05 Matches are distributed among these distances: 35 1 0.00 36 32 0.07 37 10 0.02 38 32 0.07 39 2 0.00 40 355 0.82 41 1 0.00 ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40 Consensus pattern (40 bp): GAGTTGTTGACCAGTCTTATTGTCACTTACCCATTGTGTT Found at i:1151536 original size:44 final size:44 Alignment explanation

Indices: 1151439--1151536 Score: 124 Period size: 44 Copynumber: 2.2 Consensus size: 44 1151429 TTAGATATCT * * 1151439 GACTGGTTTGGTACCAACCCATTTTTTAATTCTCCGATAACATA 1 GACTGGTTTGGTACCAACCCATTTTCTAATTCTCCGATAACACA * * * * * * 1151483 AACTTGTTTGGTACCTACCCATTTTCTGATTCTCTGATATCACA 1 GACTGGTTTGGTACCAACCCATTTTCTAATTCTCCGATAACACA 1151527 GACTGGTTTG 1 GACTGGTTTG 1151537 TTTGAGGGAG Statistics Matches: 44, Mismatches: 10, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 44 44 1.00 ACGTcount: A:0.23, C:0.22, G:0.15, T:0.39 Consensus pattern (44 bp): GACTGGTTTGGTACCAACCCATTTTCTAATTCTCCGATAACACA Found at i:1151897 original size:41 final size:41 Alignment explanation

Indices: 1151848--1152008 Score: 216 Period size: 41 Copynumber: 4.0 Consensus size: 41 1151838 CACATGTATG * ** 1151848 GATGTCTATCATATAAAGTACAGCTAAAACTTTACACAATT 1 GATGTCTATCATAGAAAACACAGCTAAAACTTTACACAATT * * * 1151889 GATGTCTATCATAAAAAACACAGTTTAAACTTTACACAATT 1 GATGTCTATCATAGAAAACACAGCTAAAACTTTACACAATT * * * 1151930 GATGTCTATCATAGAAAACACAGTTTAAACTTTACACAA-G 1 GATGTCTATCATAGAAAACACAGCTAAAACTTTACACAATT ** 1151970 GATGTCTATCATAGAAAGTACAGCTAAAACTTTACACAA 1 GATGTCTATCATAGAAAACACAGCTAAAACTTTACACAA 1152009 AAAATTACCC Statistics Matches: 109, Mismatches: 11, Indels: 1 0.90 0.09 0.01 Matches are distributed among these distances: 40 35 0.32 41 74 0.68 ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29 Consensus pattern (41 bp): GATGTCTATCATAGAAAACACAGCTAAAACTTTACACAATT Found at i:1153054 original size:13 final size:13 Alignment explanation

Indices: 1153036--1153063 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 1153026 AGCATTCAGA 1153036 CTGTCGTGAATAG 1 CTGTCGTGAATAG 1153049 CTGTCGTGAATAG 1 CTGTCGTGAATAG 1153062 CT 1 CT 1153064 CAACACCTTC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 15 1.00 ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32 Consensus pattern (13 bp): CTGTCGTGAATAG Found at i:1160768 original size:2 final size:2 Alignment explanation

Indices: 1160761--1160792 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 1160751 ATTATTAGTG 1160761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1160793 GAGAGAGAGA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:1160797 original size:2 final size:2 Alignment explanation

Indices: 1160792--1160840 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 1160782 ATATATATAT 1160792 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 1160834 AG AG AG A 1 AG AG AG A 1160841 TAACTGCAGT 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:1161610 original size:9 final size:9 Alignment explanation

Indices: 1161598--1161637 Score: 55 Period size: 9 Copynumber: 4.4 Consensus size: 9 1161588 TAATTAAGAT 1161598 ATTAATTAG 1 ATTAATTAG * 1161607 ATTAGATAAG 1 ATTA-ATTAG 1161617 ATTAATTAG 1 ATTAATTAG 1161626 ATTAATTA- 1 ATTAATTAG 1161634 ATTA 1 ATTA 1161638 TAATATTTGA Statistics Matches: 28, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 8 4 0.14 9 16 0.57 10 8 0.29 ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42 Consensus pattern (9 bp): ATTAATTAG Found at i:1164573 original size:21 final size:21 Alignment explanation

Indices: 1164543--1164626 Score: 98 Period size: 21 Copynumber: 4.0 Consensus size: 21 1164533 TTCTATTAAT * 1164543 TATGTGGACATGCAAGATAAA 1 TATGTTGACATGCAAGATAAA ** 1164564 TATGTTGACATGCAAGATAGT 1 TATGTTGACATGCAAGATAAA ** * * 1164585 TATGTCAACATGCAACATAAC 1 TATGTTGACATGCAAGATAAA 1164606 TATGTTGACATGCAAGA-AAA 1 TATGTTGACATGCAAGATAAA 1164626 T 1 T 1164627 TGCAATCAAA Statistics Matches: 51, Mismatches: 12, Indels: 1 0.80 0.19 0.02 Matches are distributed among these distances: 20 3 0.06 21 48 0.94 ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27 Consensus pattern (21 bp): TATGTTGACATGCAAGATAAA Found at i:1164725 original size:21 final size:21 Alignment explanation

Indices: 1164701--1164955 Score: 321 Period size: 21 Copynumber: 12.1 Consensus size: 21 1164691 ATACGCTACC * 1164701 TATTGATGTCAACATGCAACT 1 TATTTATGTCAACATGCAACT * 1164722 TATTTATGTTAACATGCAACT 1 TATTTATGTCAACATGCAACT * * 1164743 TCTTTATGTCGACATGCAACT 1 TATTTATGTCAACATGCAACT * 1164764 TATTTATGTCGACATGCAACT 1 TATTTATGTCAACATGCAACT * * 1164785 TAGTTATGTTAACATGCAACT 1 TATTTATGTCAACATGCAACT * 1164806 TCTTTATGTCAACATGCAACT 1 TATTTATGTCAACATGCAACT * 1164827 TATTTATGTCGACATGCAACT 1 TATTTATGTCAACATGCAACT * * 1164848 TAGTTATGTTAACATGCAACT 1 TATTTATGTCAACATGCAACT * 1164869 TCTTTATGTCAACATGCAACT 1 TATTTATGTCAACATGCAACT * 1164890 TATTTATGTCGACATGCAACT 1 TATTTATGTCAACATGCAACT * * * 1164911 TAGTTATGTTAACATGCGACT 1 TATTTATGTCAACATGCAACT * * ** * 1164932 AAGTTATGTTGACATACAACT 1 TATTTATGTCAACATGCAACT 1164953 TAT 1 TAT 1164956 AAGTTGCATG Statistics Matches: 202, Mismatches: 32, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 21 202 1.00 ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38 Consensus pattern (21 bp): TATTTATGTCAACATGCAACT Found at i:1164955 original size:63 final size:63 Alignment explanation

Indices: 1164701--1164927 Score: 418 Period size: 63 Copynumber: 3.6 Consensus size: 63 1164691 ATACGCTACC * * * * 1164701 TATTGATGTCAACATGCAACTTATTTATGTTAACATGCAACTTCTTTATGTCGACATGCAACT 1 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAACTTCTTTATGTCAACATGCAACT 1164764 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAACTTCTTTATGTCAACATGCAACT 1 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAACTTCTTTATGTCAACATGCAACT 1164827 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAACTTCTTTATGTCAACATGCAACT 1 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAACTTCTTTATGTCAACATGCAACT 1164890 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGC 1 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGC 1164928 GACTAAGTTA Statistics Matches: 160, Mismatches: 4, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 63 160 1.00 ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38 Consensus pattern (63 bp): TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAACTTCTTTATGTCAACATGCAACT Found at i:1165014 original size:42 final size:42 Alignment explanation

Indices: 1164954--1165141 Score: 232 Period size: 42 Copynumber: 4.5 Consensus size: 42 1164944 CATACAACTT 1164954 ATAAGTTGCATGTCAACATATTTATCTCGCATGTTAACATAA 1 ATAAGTTGCATGTCAACATATTTATCTCGCATGTTAACATAA * * * * 1164996 CTAAGTTGCATGTCAACATATTCATCTCACATGTCAACATAA 1 ATAAGTTGCATGTCAACATATTTATCTCGCATGTTAACATAA * ** ** ** * * 1165038 GTAAGTTGCATGTTGACATAAATAAGTTGCATGTTGACATAA 1 ATAAGTTGCATGTCAACATATTTATCTCGCATGTTAACATAA * * 1165080 ATAAGTTGCATGTCAGCATATTTATCTTGCATGTTAACATAA 1 ATAAGTTGCATGTCAACATATTTATCTCGCATGTTAACATAA * 1165122 ATAAGTTGCATGTCGACATA 1 ATAAGTTGCATGTCAACATA 1165142 AAAAGGTAGC Statistics Matches: 119, Mismatches: 27, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 42 119 1.00 ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34 Consensus pattern (42 bp): ATAAGTTGCATGTCAACATATTTATCTCGCATGTTAACATAA Found at i:1165049 original size:21 final size:21 Alignment explanation

Indices: 1164954--1165143 Score: 150 Period size: 21 Copynumber: 9.0 Consensus size: 21 1164944 CATACAACTT * 1164954 ATAAGTTGCATGTCAACATAT 1 ATAAGTTGCATGTCAACATAA * ** * * 1164975 TTATCTCGCATGTTAACATAA 1 ATAAGTTGCATGTCAACATAA * 1164996 CTAAGTTGCATGTCAACAT-A 1 ATAAGTTGCATGTCAACATAA * * * 1165016 TTCA-TCTCACATGTCAACATAA 1 ATAAGT-T-GCATGTCAACATAA * ** 1165038 GTAAGTTGCATGTTGACATAA 1 ATAAGTTGCATGTCAACATAA ** 1165059 ATAAGTTGCATGTTGACATAA 1 ATAAGTTGCATGTCAACATAA * * 1165080 ATAAGTTGCATGTCAGCATAT 1 ATAAGTTGCATGTCAACATAA * ** * 1165101 TTATCTTGCATGTTAACATAA 1 ATAAGTTGCATGTCAACATAA * 1165122 ATAAGTTGCATGTCGACATAA 1 ATAAGTTGCATGTCAACATAA 1165143 A 1 A 1165144 AAGGTAGCAT Statistics Matches: 130, Mismatches: 35, Indels: 8 0.75 0.20 0.05 Matches are distributed among these distances: 19 1 0.01 20 4 0.03 21 120 0.92 22 4 0.03 23 1 0.01 ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34 Consensus pattern (21 bp): ATAAGTTGCATGTCAACATAA Found at i:1165143 original size:63 final size:63 Alignment explanation

Indices: 1164954--1165143 Score: 231 Period size: 63 Copynumber: 3.0 Consensus size: 63 1164944 CATACAACTT * * * 1164954 ATAAGTTGCATGTCAACATATTTATCTCGCATGTTAACATAACTAAGTTGCATGTCAACAT-A 1 ATAAGTTGCATGTCAACATATTTATCTTGCATGTTAACATAAATAAGTTGCATGTCGACATAA * * * ** ** * * 1165016 TTCA-TCTCACATGTCAACATAAGTAAGTTGCATGTTGACATAAATAAGTTGCATGTTGACATAA 1 ATAAGT-T-GCATGTCAACATATTTATCTTGCATGTTAACATAAATAAGTTGCATGTCGACATAA * 1165080 ATAAGTTGCATGTCAGCATATTTATCTTGCATGTTAACATAAATAAGTTGCATGTCGACATAA 1 ATAAGTTGCATGTCAACATATTTATCTTGCATGTTAACATAAATAAGTTGCATGTCGACATAA 1165143 A 1 A 1165144 AAGGTAGCAT Statistics Matches: 102, Mismatches: 22, Indels: 7 0.78 0.17 0.05 Matches are distributed among these distances: 61 1 0.01 62 3 0.03 63 93 0.91 64 4 0.04 65 1 0.01 ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34 Consensus pattern (63 bp): ATAAGTTGCATGTCAACATATTTATCTTGCATGTTAACATAAATAAGTTGCATGTCGACATAA Found at i:1165301 original size:42 final size:42 Alignment explanation

Indices: 1165227--1165311 Score: 134 Period size: 42 Copynumber: 2.0 Consensus size: 42 1165217 ATCTAATTGC * * * 1165227 AATTTTCTTGCATGTCAACATAGTTATGTTGCATGTTGACAT 1 AATTATCTTGCATGTCAACATAGTTATCTTGCATGTCGACAT * 1165269 AATTATCTTGCATGTCAACATATTTATCTTGCATGTCGACAT 1 AATTATCTTGCATGTCAACATAGTTATCTTGCATGTCGACAT 1165311 A 1 A 1165312 TTTGATGGAA Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 42 39 1.00 ACGTcount: A:0.28, C:0.16, G:0.14, T:0.41 Consensus pattern (42 bp): AATTATCTTGCATGTCAACATAGTTATCTTGCATGTCGACAT Found at i:1165312 original size:21 final size:21 Alignment explanation

Indices: 1165228--1165314 Score: 113 Period size: 21 Copynumber: 4.2 Consensus size: 21 1165218 TCTAATTGCA 1165228 ATTT-TCTTGCATGTCAACAT 1 ATTTATCTTGCATGTCAACAT * * ** 1165248 AGTTATGTTGCATGTTGACAT 1 ATTTATCTTGCATGTCAACAT * 1165269 AATTATCTTGCATGTCAACAT 1 ATTTATCTTGCATGTCAACAT * 1165290 ATTTATCTTGCATGTCGACAT 1 ATTTATCTTGCATGTCAACAT 1165311 ATTT 1 ATTT 1165315 GATGGAAAAA Statistics Matches: 56, Mismatches: 10, Indels: 1 0.84 0.15 0.01 Matches are distributed among these distances: 20 3 0.05 21 53 0.95 ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44 Consensus pattern (21 bp): ATTTATCTTGCATGTCAACAT Found at i:1179798 original size:46 final size:47 Alignment explanation

Indices: 1179731--1179824 Score: 163 Period size: 46 Copynumber: 2.0 Consensus size: 47 1179721 TTAAAAAGTT 1179731 AACATAATTTTCTTGCATGTTGATAAAATTT-GAGAGAGAAAGAGAG 1 AACATAATTTTCTTGCATGTTGATAAAATTTAGAGAGAGAAAGAGAG * * 1179777 AACATAATTTTCTTGCATGTTGATATAATTTAGAGAGAGAGAGAGAG 1 AACATAATTTTCTTGCATGTTGATAAAATTTAGAGAGAGAAAGAGAG 1179824 A 1 A 1179825 GAGAGAAAGA Statistics Matches: 45, Mismatches: 2, Indels: 1 0.94 0.04 0.02 Matches are distributed among these distances: 46 30 0.67 47 15 0.33 ACGTcount: A:0.40, C:0.06, G:0.22, T:0.31 Consensus pattern (47 bp): AACATAATTTTCTTGCATGTTGATAAAATTTAGAGAGAGAAAGAGAG Found at i:1179815 original size:2 final size:2 Alignment explanation

Indices: 1179808--1179872 Score: 121 Period size: 2 Copynumber: 32.5 Consensus size: 2 1179798 GATATAATTT * 1179808 AG AG AG AG AG AG AG AG AG AG AG AA 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 1179850 AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG A 1179873 AAACCATATA Statistics Matches: 61, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 2 61 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:1180265 original size:13 final size:14 Alignment explanation

Indices: 1180237--1180279 Score: 52 Period size: 14 Copynumber: 3.1 Consensus size: 14 1180227 TAATGTTAAA * 1180237 TTGTACAATTTGTT 1 TTGTACAATTTTTT 1180251 TTGTA-AATTTTTT 1 TTGTACAATTTTTT * * 1180264 TTATATAATTTTTT 1 TTGTACAATTTTTT 1180278 TT 1 TT 1180280 TCAAGGAACA Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 13 11 0.42 14 15 0.58 ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67 Consensus pattern (14 bp): TTGTACAATTTTTT Found at i:1180320 original size:2 final size:2 Alignment explanation

Indices: 1180313--1180371 Score: 118 Period size: 2 Copynumber: 29.5 Consensus size: 2 1180303 GACATTCAGC 1180313 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA 1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA 1180355 CA CA CA CA CA CA CA CA C 1 CA CA CA CA CA CA CA CA C 1180372 TTATGAAAAA 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:0.51, G:0.00, T:0.00 Consensus pattern (2 bp): CA Found at i:1183905 original size:2 final size:2 Alignment explanation

Indices: 1183898--1183955 Score: 116 Period size: 2 Copynumber: 29.0 Consensus size: 2 1183888 ATACTTTGCG 1183898 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 1183940 TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC 1183956 GCGCGCGCGC Statistics Matches: 56, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 56 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1191378 original size:144 final size:144 Alignment explanation

Indices: 1191114--1191500 Score: 383 Period size: 144 Copynumber: 2.8 Consensus size: 144 1191104 CTGTCTGTGC * 1191114 AAAATTCGTGTCCGCTCCATATCTTTCTTATGGAAAAACATTAGAAGTTTTTACTTCACAAAAAG 1 AAAATTCGTGTCCGCTCCATATCTTTCTTATGGAAAAACATTAGAAGTTCTTACTTCACAAAAAG * 1191179 ATTGCATATGACCTAAAGGTGTGTCATGACCTTGACCCAAGGTCATTCGGACAAGGTCAGGGTCA 66 ATTGCATAAGACCTAAAGGTGTGTCATGACCTTGACCCAAGGTCATTCGGACAAGGTCAGGGTCA 1191244 CTGGTAGGAAGTGA 131 CTGGTAGGAAGTGA * * * * * * * 1191258 AAAATTTGTGTCTGGTCCATAT-TATTCTTATGGAGAAACATTGGAAGTTCTTACTTCATACAAA 1 AAAATTCGTGTCCGCTCCATATCT-TTCTTATGGAAAAACATTAGAAGTTCTTACTTCACAAAAA * ** * * * 1191322 GATTGCTTAAGACC-AGGGTGTGTGTCATGACC-TGACCCAATGTCATTTTTGG-CAAGGTCATT 65 GATTGCATAAGACCTAAAG-GTGTGTCATGACCTTGACCCAAGGTCA--TTCGGACAAGGTCA-G * 1191384 GG-CA--GG-A-AAAGTGAA 126 GGTCACTGGTAGGAAGTG-A * * * * 1191399 AAAATTCGTGTCCG-TTCATATCTTTCTTATGTAGAAACATTAGAA---CTT-CTT-A-AACAGA 1 AAAATTCGTGTCCGCTCCATATCTTTCTTATGGAAAAACATTAGAAGTTCTTACTTCACAA-AAA * * * * 1191457 GATTGCTTATGACCTGAAGGTGTGACATGACCTTGACCCAAGGT 65 GATTGCATAAGACCTAAAGGTGTGTCATGACCTTGACCCAAGGT 1191501 AATTTGGGCA Statistics Matches: 204, Mismatches: 29, Indels: 28 0.78 0.11 0.11 Matches are distributed among these distances: 134 1 0.00 135 28 0.14 136 14 0.07 137 3 0.01 140 31 0.15 141 15 0.07 142 2 0.01 143 15 0.07 144 89 0.44 145 6 0.03 ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31 Consensus pattern (144 bp): AAAATTCGTGTCCGCTCCATATCTTTCTTATGGAAAAACATTAGAAGTTCTTACTTCACAAAAAG ATTGCATAAGACCTAAAGGTGTGTCATGACCTTGACCCAAGGTCATTCGGACAAGGTCAGGGTCA CTGGTAGGAAGTGA Found at i:1193948 original size:2 final size:2 Alignment explanation

Indices: 1193941--1193981 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 1193931 TATAATCTAC 1193941 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1193982 TTATTCTGAA Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:1207398 original size:102 final size:102 Alignment explanation

Indices: 1207261--1207444 Score: 269 Period size: 102 Copynumber: 1.8 Consensus size: 102 1207251 TAGCTCTCAA * ** 1207261 TCCTGTAAAATGACATAAGGGGACCCCTGGTCACCCTACAATGGATGACCAATGACTCTCCATAG 1 TCCTGTAAAATGACATAAGGGGACACCTGGTCACCCTACAATAAATGACCAATGACTCTCCATAG 1207326 TGTAAAATGACATAAGGTCATGACTGGTGATTCTCTG 66 TGTAAAATGACATAAGGTCATGACTGGTGATTCTCTG * * * ** ** * 1207363 TCCTGTAAAATGACATAAGGTGACATCTGGTCACCCTACAGTAAATGACCGGTGACTCTCTGTAT 1 TCCTGTAAAATGACATAAGGGGACACCTGGTCACCCTACAATAAATGACCAATGACTCTCCATAG 1207428 TGTAAAATGACATAAGG 66 TGTAAAATGACATAAGG 1207445 GGACCCCTAG Statistics Matches: 71, Mismatches: 11, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 102 71 1.00 ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26 Consensus pattern (102 bp): TCCTGTAAAATGACATAAGGGGACACCTGGTCACCCTACAATAAATGACCAATGACTCTCCATAG TGTAAAATGACATAAGGTCATGACTGGTGATTCTCTG Found at i:1207423 original size:62 final size:61 Alignment explanation

Indices: 1207345--1207580 Score: 247 Period size: 62 Copynumber: 3.8 Consensus size: 61 1207335 ACATAAGGTC * * * * * ** 1207345 ATGACTGGTGATTCTCTGTCCTGTAAAATGACATAAGGTGACATCTGGTCACCCTACAGTAA 1 ATGACCGGTGACTCTCTATACTGTAAAATGACATAAGGTGAC-CCTGGTCACCCTACAGTGG * * * * * * 1207407 ATGACCGGTGACTCTCTGTATTGTAAAATGACATAAGGGGACCCCTAGTCACCTTACAATGG 1 ATGACCGGTGACTCTCTATACTGTAAAATGACATAAGGTGA-CCCTGGTCACCCTACAGTGG * * * * * 1207469 ATGACCGGTCACTCTCCATAGTGTAAAATGACATAAGGTGACCCTTGGGCACCCTTCAGTGG 1 ATGACCGGTGACTCTCTATACTGTAAAATGACATAAGGTGACCC-TGGTCACCCTACAGTGG * * * 1207531 ATGACTGGTGACTCTCTATCCTGTAAAATGACATAAGGTGATCCATGGTC 1 ATGACCGGTGACTCTCTATACTGTAAAATGACATAAGGTGA-CCCTGGTC 1207581 TCCGTATTGA Statistics Matches: 143, Mismatches: 28, Indels: 6 0.81 0.16 0.03 Matches are distributed among these distances: 61 3 0.02 62 137 0.96 63 3 0.02 ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27 Consensus pattern (61 bp): ATGACCGGTGACTCTCTATACTGTAAAATGACATAAGGTGACCCTGGTCACCCTACAGTGG Found at i:1208493 original size:23 final size:23 Alignment explanation

Indices: 1208467--1208512 Score: 92 Period size: 23 Copynumber: 2.0 Consensus size: 23 1208457 AATCATCAGT 1208467 CATCCACTGTAGGATGACCAGGG 1 CATCCACTGTAGGATGACCAGGG 1208490 CATCCACTGTAGGATGACCAGGG 1 CATCCACTGTAGGATGACCAGGG 1208513 GTCACCTTAT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 23 1.00 ACGTcount: A:0.26, C:0.26, G:0.30, T:0.17 Consensus pattern (23 bp): CATCCACTGTAGGATGACCAGGG Found at i:1208576 original size:62 final size:62 Alignment explanation

Indices: 1208490--1209292 Score: 635 Period size: 62 Copynumber: 13.1 Consensus size: 62 1208480 ATGACCAGGG * * * * * * 1208490 CATCCACTGTAGGATGACCAGGGGTCACCTTATGTCATTTTACACTTTGGAGAGTGATCGAT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT * * * 1208552 CATCCTCTTTAGGGTGACCTGGGGTC-CAGTTATGTCATTTTTA-ACTATGGAGAGTCACCGGT 1 CATCCTCTGTAGGGTGACCAGGGGTCAC-CTTATGTCA-TTTTACACTATGGAGAGTCACCGGT * * * * * * 1208614 CATCCTCGGTAAGGTGACCAGGGGTCACCTTATATCCTTTAACACGATGGAGAGTCACCGGT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT * * * * * * * ** * * 1208676 CATCCACTGCAGAGTTACCAGGGGTCCCCGTATGTCATTTAACACGGTTGAGAGTCATCGGT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT * * * 1208738 CATCCACTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACAATGAAGAGTCACCGGT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT * * * * * * * 1208800 CATCCTCTTTAGGGTGACCAGGGGTAACCTTATATCATTTTACACGATAGAGAGTCATCGTT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT * * * * * 1208862 CATCCTTTGTTA-GGTGACTAGGGGTCCCCATATGTCATTTTATA-TGATGGAGAGTCACCGGT 1 CATCCTCTG-TAGGGTGACCAGGGGTCACCTTATGTCATTTTACACT-ATGGAGAGTCACCGGT * * * ** * * * * * * 1208924 CATTCACCGTAGTATCACCAGGGGTGACCTTATATTATTTTACACAATGGAGAGTCATCGGT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT * * * * * * * * * 1208986 TATCATCTGCAGGGTGGCCAGGAGTCACTTTATGTCATTTTACACTTTGGAGAGTCAGCAGT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT * ** * * * * * * * 1209048 CGTCAACTGCAGGGTGACCAGGGGTCTCCGTATGTCATTTAACACGATGAATAGTCACCGGT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT * * * * * * * 1209110 CATCCACTGCAGGGT-A--A------A-CTTATGTCATTTTACACGATAGATAGACACTGGT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT * * * * * * * 1209162 CATCCACTGTAGGTTGAACAGGGGTCACCTTATGTCATTTTACACGATAGAGAGACACTGGT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT ** * * * * * 1209224 CATCCTCTGTAGGGTGACCAGTTGTCACTTTATGTCATTTGACGCCATGGAGAGTCATCGGT 1 CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT * 1209286 TATCCTC 1 CATCCTC 1209293 GGGAGGATGA Statistics Matches: 584, Mismatches: 139, Indels: 36 0.77 0.18 0.05 Matches are distributed among these distances: 52 41 0.07 53 1 0.00 55 1 0.00 59 1 0.00 61 9 0.02 62 523 0.90 63 8 0.01 ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30 Consensus pattern (62 bp): CATCCTCTGTAGGGTGACCAGGGGTCACCTTATGTCATTTTACACTATGGAGAGTCACCGGT Found at i:1213912 original size:13 final size:13 Alignment explanation

Indices: 1213894--1213919 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 1213884 ACCTGTTCTG 1213894 ATAAATTTGGAAA 1 ATAAATTTGGAAA 1213907 ATAAATTTGGAAA 1 ATAAATTTGGAAA 1213920 CCATAAAATC Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31 Consensus pattern (13 bp): ATAAATTTGGAAA Found at i:1219329 original size:2 final size:2 Alignment explanation

Indices: 1219322--1219367 Score: 76 Period size: 2 Copynumber: 23.5 Consensus size: 2 1219312 GTGCTAACAT * 1219322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG T- TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1219363 TA TA T 1 TA TA T 1219368 TTGAGTGAAT Statistics Matches: 42, Mismatches: 1, Indels: 2 0.93 0.02 0.04 Matches are distributed among these distances: 1 1 0.02 2 41 0.98 ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52 Consensus pattern (2 bp): TA Found at i:1233487 original size:29 final size:30 Alignment explanation

Indices: 1233413--1233522 Score: 204 Period size: 30 Copynumber: 3.7 Consensus size: 30 1233403 TTTTAGCAAA * 1233413 ATTTGATTATGAAAATGGGTACTGTATATT 1 ATTTGATTATGAAAATGGGTACCGTATATT 1233443 ATTTGATTATGAAAATGGGTACCGTATATT 1 ATTTGATTATGAAAATGGGTACCGTATATT 1233473 A-TTGATTATGAAAATGGGTACCGTATATT 1 ATTTGATTATGAAAATGGGTACCGTATATT 1233502 ATTTGATTATGAAAATGGGTA 1 ATTTGATTATGAAAATGGGTA 1233523 TATTAGTTTT Statistics Matches: 78, Mismatches: 1, Indels: 2 0.96 0.01 0.02 Matches are distributed among these distances: 29 29 0.37 30 49 0.63 ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40 Consensus pattern (30 bp): ATTTGATTATGAAAATGGGTACCGTATATT Found at i:1243372 original size:12 final size:12 Alignment explanation

Indices: 1243349--1243381 Score: 59 Period size: 12 Copynumber: 2.8 Consensus size: 12 1243339 ATCACATTTT 1243349 GTCTGT-CGTCC 1 GTCTGTCCGTCC 1243360 GTCTGTCCGTCC 1 GTCTGTCCGTCC 1243372 GTCTGTCCGT 1 GTCTGTCCGT 1243382 AAACTTTTCA Statistics Matches: 21, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 11 6 0.29 12 15 0.71 ACGTcount: A:0.00, C:0.36, G:0.27, T:0.36 Consensus pattern (12 bp): GTCTGTCCGTCC Found at i:1247735 original size:22 final size:23 Alignment explanation

Indices: 1247687--1247735 Score: 64 Period size: 23 Copynumber: 2.2 Consensus size: 23 1247677 GGTGAAAGAA * * * 1247687 AATTCGTTATAGTTATTATTACG 1 AATTCGTTATACTGATTATAACG 1247710 AATTCGTTATACTGA-TATAACG 1 AATTCGTTATACTGATTATAACG 1247732 AATT 1 AATT 1247736 ACGGATATAA Statistics Matches: 23, Mismatches: 3, Indels: 1 0.85 0.11 0.04 Matches are distributed among these distances: 22 10 0.43 23 13 0.57 ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43 Consensus pattern (23 bp): AATTCGTTATACTGATTATAACG Found at i:1248382 original size:8 final size:8 Alignment explanation

Indices: 1248369--1248432 Score: 82 Period size: 8 Copynumber: 8.5 Consensus size: 8 1248359 GGTTTCACCT 1248369 TGTCCGTC 1 TGTCCGTC 1248377 TGTCCGTC 1 TGTCCGTC 1248385 --T--GTC 1 TGTCCGTC 1248389 TGTCCGTC 1 TGTCCGTC * * 1248397 CGTCTGTC 1 TGTCCGTC 1248405 TGTCCGTC 1 TGTCCGTC 1248413 TGTCCGTC 1 TGTCCGTC 1248421 TGTCCGTC 1 TGTCCGTC 1248429 TGTC 1 TGTC 1248433 TGTAGACGCA Statistics Matches: 48, Mismatches: 4, Indels: 8 0.80 0.07 0.13 Matches are distributed among these distances: 4 3 0.06 6 2 0.04 8 43 0.90 ACGTcount: A:0.00, C:0.36, G:0.25, T:0.39 Consensus pattern (8 bp): TGTCCGTC Found at i:1248391 original size:12 final size:12 Alignment explanation

Indices: 1248374--1248435 Score: 79 Period size: 12 Copynumber: 5.2 Consensus size: 12 1248364 CACCTTGTCC 1248374 GTCTGTCCGTCT 1 GTCTGTCCGTCT * 1248386 GTCTGTCCGTCC 1 GTCTGTCCGTCT * * 1248398 GTCTGTCTGTCC 1 GTCTGTCCGTCT 1248410 GTCTGTCCGTCT 1 GTCTGTCCGTCT * * 1248422 GTCCGTCTGTCT 1 GTCTGTCCGTCT 1248434 GT 1 GT 1248436 AGACGCAACT Statistics Matches: 44, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 12 44 1.00 ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40 Consensus pattern (12 bp): GTCTGTCCGTCT Found at i:1263850 original size:20 final size:19 Alignment explanation

Indices: 1263821--1263878 Score: 73 Period size: 20 Copynumber: 3.0 Consensus size: 19 1263811 TTTCAAATTA 1263821 CCTATAGGAATATTGATTTT 1 CCTATAGGAATATT-ATTTT * * 1263841 CCTATGGGAAAAATTATTTT 1 CCTATAGG-AATATTATTTT 1263861 CCTATAGGAAT-TTATTTT 1 CCTATAGGAATATTATTTT 1263879 TGAAAGGTAA Statistics Matches: 33, Mismatches: 4, Indels: 4 0.80 0.10 0.10 Matches are distributed among these distances: 18 7 0.21 19 2 0.06 20 19 0.58 21 5 0.15 ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45 Consensus pattern (19 bp): CCTATAGGAATATTATTTT Found at i:1270443 original size:166 final size:165 Alignment explanation

Indices: 1270030--1271055 Score: 1321 Period size: 166 Copynumber: 6.3 Consensus size: 165 1270020 TATTTTTCAA * * * * * 1270030 AAATCTTCTTCTCAAAAACTATTCGGCCTGAAAAGCTTAAACTT---GTGTGGAGGCATCCTCAG 1 AAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAAATG-GGA-GAATCCTCAG ** * * * * * * ** 1270092 GCAGTGTAAATTCAAGTTTGTTCAAATCATGGTCCACGGGGGAAGGGAGGGGCCACAAGAGGGGG 63 ATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGTAA-GGTGGTGCCACAATTGGGGG 1270157 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTTT 127 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTTT * * 1270196 AAA---TCTTCTAAAAAACTATTAGGCCAAAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATA 1 AAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATA * * 1270258 GTGTAGATTCAAGTTTGTTCAAAT-ATTGGTCCCCAGGGGTAAGGTGGTGCCACAGTTGGGGGAT 66 GTGTAGATTCAAGTTTGTTCAAATCA-TAGTCCCC-GGGGTAAGGTGGTGCCACAATTGGGGGAT 1270322 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTTT 129 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTTT * 1270359 AAATCTTCTTCTCAAAAACTATTAGGCCAAAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATA 1 AAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATA * * * 1270424 GTGTAGATTCAGGTTTGTTCAAATCATGGTCCCCAGGGGTAGGGTGGTGCCACAATTGGGGGATC 66 GTGTAGATTCAAGTTTGTTCAAATCATAGTCCCC-GGGGTAAGGTGGTGCCACAATTGGGGGATC * ** 1270489 AAGTTTTACATAGGAATATAAAGAGAAAATCTTTAA 130 AAGTTTTACATAGGAATATATAGAGAAAATCTTTTT * * * * * * ** 1270525 AAATCTTCTTTTCAAAAACAATTTGGCCAGAAAAGCTCAAATTATAATGGAAGCATTTTCAGATA 1 AAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATA ** * 1270590 GTGTAGATTCAAGTTTGTTCATGTCATAGTCCCCGGGAGTAGGGTGGTGCCACAATTGGGGGATC 66 GTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGG-GTAAGGTGGTGCCACAATTGGGGGATC * * 1270655 ATGTTTTACAAAGGAATATATAGAGAAAATCTTTTT 130 AAGTTTTACATAGGAATATATAGAGAAAATCTTTTT * 1270691 AAATCTTCTTCTCAAAAACTATCAGGCCAGAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATA 1 AAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATA * * 1270756 GTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGTGGTTAAGGTGGTGCCACAATTGGGGGATC 66 GTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCG-GGGTAAGGTGGTGCCACAATTGGGGGATC 1270821 AAGTTTTACATAGGAATATATAGAG---A------- 130 AAGTTTTACATAGGAATATATAGAGAAAATCTTTTT * * ** * * * 1270847 AAATCTTCTTCTCAAAAACTATTTGGCCAGAAATGCTCAAATTTGAGTGGAAGCATCCTCAGATA 1 AAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATA * * ** 1270912 GTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGTGGGTAAGGTGGGGCCACAACGGGGGGATC 66 GTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCG-GGGTAAGGTGGTGCCACAATTGGGGGATC * ** 1270977 AAGTGTTACATAGGAATATATAGAGAAAATCTTTAA 130 AAGTTTTACATAGGAATATATAGAGAAAATCTTTTT * * 1271013 AAATCTTCTTCTCAAAAACTATTTGGCCAGAAATGCTCAAATT 1 AAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATT 1271056 TGAGTGGAAG Statistics Matches: 768, Mismatches: 71, Indels: 42 0.87 0.08 0.05 Matches are distributed among these distances: 156 142 0.18 159 1 0.00 162 3 0.00 163 128 0.17 164 9 0.01 165 5 0.01 166 477 0.62 167 3 0.00 ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29 Consensus pattern (165 bp): AAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATA GTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGTAAGGTGGTGCCACAATTGGGGGATCA AGTTTTACATAGGAATATATAGAGAAAATCTTTTT Found at i:1271030 original size:488 final size:486 Alignment explanation

Indices: 1270028--1271055 Score: 1427 Period size: 488 Copynumber: 2.1 Consensus size: 486 1270018 GGTATTTTTC * * * * * * * 1270028 AAAAATCTTCTTCTCAAAAACTATTCGGCCTGAAAAGCTTAAACTTGTGTGGAGGCATCCTCAGG 1 AAAAATCTTCTTCTCAAAAACTATTTGGCCAGAAAAGCTCAAA-TTATATGGAAGCATCCTCAGA * * 1270093 CAGTGTAAATTCAAGTTTGTTCAAATCATGGTCCACGGGGGAAGGGAGGGGCCACAAGAGGGGGA 65 CAGTGTAAATTCAAGTTTGTTCAAATCATAGTCCACGGGAGAAGGGAGGGGCCACAAGAGGGGGA * * 1270158 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTTTTAAATCTTCTAAAAAACTATTAGGCCAA 130 TCAAGTTTTACAAAGGAATATATAGAGAAAATCTTTTTAAATCTTCTAAAAAACTATCAGGCCAA * 1270223 AAAAGCTCAAATTAAAATGGGAGAATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATATTGGT 195 AAAAGCTCAAATTAAAATGGGAGAATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATATTAGT * 1270288 CCCCAGGGGTAAGGTGGTGCCACAGTTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAAT 260 CCCCAGGGGTAAGGTGGTGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAG--AA- * 1270353 CTTTTTAAATCTTCTTCTCAAAAACTATTAGGCCAAAAAAGCTCAAATTAAAATGGGAGAATCCT 322 -----TAAATCTTCTTCTCAAAAACTATTAGGCCAAAAAAGCTCAAATTAAAATGGAAGAATCCT * * * * ** 1270418 CAGATAGTGTAGATTCAGGTTTGTTCAAATCATGGTCCCCAGGGGTAGGGTGGTGCCACAATTGG 382 CAGATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCAGGGGTAAGGTGGGGCCACAACGGG * 1270483 GGGATCAAGTTTTACATAGGAATATAAAGAGAAAATCTTT 447 GGGATCAAGTGTTACATAGGAATATAAAGAGAAAATCTTT * * ** 1270523 AAAAATCTTCTTTTCAAAAACAATTTGGCCAGAAAAGCTCAAATTATAATGGAAGCATTTTCAGA 1 AAAAATCTTCTTCTCAAAAACTATTTGGCCAGAAAAGCTCAAATTAT-ATGGAAGCATCCTCAGA * * ** * * * * ** 1270588 TAGTGTAGATTCAAGTTTGTTCATGTCATAGTCCCCGGGAGTAGGGTGGTGCCACAATTGGGGGA 65 CAGTGTAAATTCAAGTTTGTTCAAATCATAGTCCACGGGAGAAGGGAGGGGCCACAAGAGGGGGA * * 1270653 TCATGTTTTACAAAGGAATATATAGAGAAAATCTTTTTAAATCTTCTTCTCAAAAACTATCAGGC 130 TCAAGTTTTACAAAGGAATATATAGAGAAAATCTTTTTAAA---TCTTCTAAAAAACTATCAGGC * 1270718 CAGAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCA- 192 CAAAAAAGCTCAAATTAAAATGGGAGAATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAAT-AT * * 1270782 TAGT-CCCTGTGGTTAAGGTGGTGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAG 256 TAGTCCCCAG-GGGTAAGGTGGTGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAG * * * ** * * 1270846 -A-AAATCTTCTTCTCAAAAACTATTTGGCCAGAAATGCTCAAATTTGAGTGGAAGCATCCTCAG 320 AATAAATCTTCTTCTCAAAAACTATTAGGCCAAAAAAGCTCAAATTAAAATGGAAGAATCCTCAG * 1270909 ATAGTGTAGATTCAAGTTTGTTCAAATCATAGT-CCCTGTGGGTAAGGTGGGGCCACAACGGGGG 385 ATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCAG-GGGTAAGGTGGGGCCACAACGGGGG * 1270973 GATCAAGTGTTACATAGGAATATATAGAGAAAATCTTT 449 GATCAAGTGTTACATAGGAATATAAAGAGAAAATCTTT * 1271011 AAAAATCTTCTTCTCAAAAACTATTTGGCCAGAAATGCTCAAATT 1 AAAAATCTTCTTCTCAAAAACTATTTGGCCAGAAAAGCTCAAATT 1271056 TGAGTGGAAG Statistics Matches: 474, Mismatches: 52, Indels: 21 0.87 0.10 0.04 Matches are distributed among these distances: 487 4 0.01 488 184 0.39 494 3 0.01 495 143 0.30 497 4 0.01 498 135 0.28 499 1 0.00 ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29 Consensus pattern (486 bp): AAAAATCTTCTTCTCAAAAACTATTTGGCCAGAAAAGCTCAAATTATATGGAAGCATCCTCAGAC AGTGTAAATTCAAGTTTGTTCAAATCATAGTCCACGGGAGAAGGGAGGGGCCACAAGAGGGGGAT CAAGTTTTACAAAGGAATATATAGAGAAAATCTTTTTAAATCTTCTAAAAAACTATCAGGCCAAA AAAGCTCAAATTAAAATGGGAGAATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATATTAGTC CCCAGGGGTAAGGTGGTGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAATAAA TCTTCTTCTCAAAAACTATTAGGCCAAAAAAGCTCAAATTAAAATGGAAGAATCCTCAGATAGTG TAGATTCAAGTTTGTTCAAATCATAGTCCCCAGGGGTAAGGTGGGGCCACAACGGGGGGATCAAG TGTTACATAGGAATATAAAGAGAAAATCTTT Found at i:1272263 original size:9 final size:9 Alignment explanation

Indices: 1272241--1272274 Score: 50 Period size: 9 Copynumber: 3.7 Consensus size: 9 1272231 ACAATTAGTC 1272241 CGTTGTCTGT 1 CGTTGTC-GT 1272251 CGTTGTCGT 1 CGTTGTCGT 1272260 CGTTGTCGT 1 CGTTGTCGT * 1272269 TGTTGT 1 CGTTGT 1272275 AAACTTTTCA Statistics Matches: 23, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 9 16 0.70 10 7 0.30 ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50 Consensus pattern (9 bp): CGTTGTCGT Found at i:1272718 original size:166 final size:165 Alignment explanation

Indices: 1272444--1273277 Score: 915 Period size: 166 Copynumber: 5.0 Consensus size: 165 1272434 GGTATTTTTC * * * *** ** 1272444 AAAAATCTTCTTCTCAAAAACTATTTGGCCTGAAAAGCTTAAACTT-GTGTGGAGGCATCCTCAG 1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAAATGGAAACATCCTCAG * * * 1272508 GTAGTGTAGATTTAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAAGAGTGGG 65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-AGGGGG * 1272573 ATCAAGTTTTACATAGGAATATGTAGAGAAAATCTTT 129 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT * * 1272610 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAACATTCTCATG 1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAACATCCTCAGG * 1272675 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA 66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-AGGGGGA ** 1272740 TCAAGTTTTACATAGGAATATATAGAGAAAATCTAAA 130 TCAAGTTTTACATAGGAATATATAGAGAAAATCT-TT ** * ** * * * * 1272777 AAAAAAATTCTTCTCAAAAACTATCAGGCCAGAAAAGCTCAAATTTGAGTGGAAGCATTCTCAGA 1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAACATCCTCAGG * * * * * * * 1272842 TAATGTAGATTCAATTTTGTTCAAAACATAGTCCCTGGTGGTATGGTGGGGCCACAAAGGGGGAA 66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAAGGGGG-A ** * 1272907 TGGA-TGTTTACATAGGAATATATAGAGAAAATCTGT 130 TCAAGT-TTTACATAGGAATATATAGAGAAAATCTTT * * 1272943 AAAAATCTTCTTCTCAAAAACTTTTAGGCCAGAAAAGCTCAAACTAAAAT-GAAAGCATCCTCAG 1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAA-CATCCTCAG * ** 1273007 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCTCGGGGGTAGGGTGGGGCCACAATTTGGGG 65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-AGGGGG 1273072 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT 129 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT * * * * * *** * ** * 1273109 AAAAATCTTCTTTTTAAAGACTATTTGGCCAGAAAAGCTTAAACTT-GTGTAGAGGCATCCTCGG 1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAAATGGAAACATCCTCAG * ** ** * * *** * 1273173 GTAGTGTAAATTCAAGTTTG--CAAAATCACAGTCCCTAGTGGTAGGGCGGGGCCGTGATGGCGG 65 GTAGTGTAGATTCAAGTTTGTTC-AAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAAGG-GG ** * * 1273236 TTTGAATTTTTACATAGGAATATATAGAGAAAATCTTT 128 GATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT 1273274 AAAA 1 AAAA 1273278 TTATCCTGGG Statistics Matches: 565, Mismatches: 92, Indels: 23 0.83 0.14 0.03 Matches are distributed among these distances: 164 3 0.01 165 70 0.12 166 347 0.61 167 145 0.26 ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28 Consensus pattern (165 bp): AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAACATCCTCAGG TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAAGGGGGAT CAAGTTTTACATAGGAATATATAGAGAAAATCTTT Found at i:1272939 original size:333 final size:331 Alignment explanation

Indices: 1272451--1273277 Score: 1122 Period size: 333 Copynumber: 2.5 Consensus size: 331 1272441 TTCAAAAATC * 1272451 TTCTTCTCAAAAACTATTTGGCCTGAAAAGCTTAAACTTGTGTGGAGGCATCCTCAGGTAGTGTA 1 TTCTTCTCAAAAACTATTTGGCCAGAAAAGCTTAAACTTGTGTGGAGGCATCCTCAGGTAGTGTA * * * * * * * 1272516 GATTTAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAAGAGTGGGATCAA-GT 66 GATTCAAGTTTGTTCAAAACATAGTCCCTGGTGGTAGGGAGGGGCCACAA-AGGGGGATGAATG- * 1272580 TTTACATAGGAATATGTAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAA 129 TTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAA * * * 1272645 AGCTCAAATTAAAATGGAAA-CATTCTCATGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCC 194 AGCTCAAACTAAAAT-GAAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCC 1272709 CCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCT 258 CCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCT 1272774 AAAAAAAAAA 323 -AAAAAAAAA ** * * * * * * * 1272784 TTCTTCTCAAAAACTATCAGGCCAGAAAAGCTCAAATTTGAGTGGAAGCATTCTCAGATAATGTA 1 TTCTTCTCAAAAACTATTTGGCCAGAAAAGCTTAAACTTGTGTGGAGGCATCCTCAGGTAGTGTA * * * * 1272849 GATTCAATTTTGTTCAAAACATAGTCCCTGGTGGTATGGTGGGGCCACAAAGGGGGAATGGATGT 66 GATTCAAGTTTGTTCAAAACATAGTCCCTGGTGGTAGGGAGGGGCCACAAAGGGGG-ATGAATGT * * 1272914 TTACATAGGAATATATAGAGAAAATCTGTAAAAATCTTCTTCTCAAAAACTTTTAGGCCAGAAAA 130 TTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAA * 1272979 GCTCAAACTAAAATGAAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCTC 195 GCTCAAACTAAAATGAAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCC * ** 1273044 GGGGGTAGGGTGGGGCCACAATTTGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT 260 GGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTAA ** 1273109 AAAAATC 325 AAAAAAA * * * * * 1273116 TTCTTTTTAAAGACTATTTGGCCAGAAAAGCTTAAACTTGTGTAGAGGCATCCTCGGGTAGTGTA 1 TTCTTCTCAAAAACTATTTGGCCAGAAAAGCTTAAACTTGTGTGGAGGCATCCTCAGGTAGTGTA * * * * *** * ** * 1273181 AATTCAAGTTTG--CAAAATCACAGTCCCTAGTGGTAGGGCGGGGCCGTGATGGCGGTTTGAATT 66 GATTCAAGTTTGTTCAAAA-CATAGTCCCTGGTGGTAGGGAGGGGCCACAAAGG-GGGATGAATG 1273244 TTTACATAGGAATATATAGAGAAAATCTTTAAAA 129 TTTACATAGGAATATATAGAGAAAATCTTTAAAA 1273278 TTATCCTGGG Statistics Matches: 427, Mismatches: 62, Indels: 12 0.85 0.12 0.02 Matches are distributed among these distances: 330 5 0.01 331 63 0.15 332 77 0.18 333 281 0.66 334 1 0.00 ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28 Consensus pattern (331 bp): TTCTTCTCAAAAACTATTTGGCCAGAAAAGCTTAAACTTGTGTGGAGGCATCCTCAGGTAGTGTA GATTCAAGTTTGTTCAAAACATAGTCCCTGGTGGTAGGGAGGGGCCACAAAGGGGGATGAATGTT TACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAG CTCAAACTAAAATGAAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCG GGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTAAA AAAAAA Found at i:1274101 original size:26 final size:26 Alignment explanation

Indices: 1274052--1274103 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 1274042 CTTTCTTTAA ** 1274052 ATTTTGCTTTTATTTGGCTTCCTGGT 1 ATTTTGCTTTTATTTGGCCGCCTGGT 1274078 ATTTTGCTTTTATTTGGCCGCCTGGT 1 ATTTTGCTTTTATTTGGCCGCCTGGT 1274104 TTTCTGGGGG Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 26 24 1.00 ACGTcount: A:0.08, C:0.17, G:0.21, T:0.54 Consensus pattern (26 bp): ATTTTGCTTTTATTTGGCCGCCTGGT Found at i:1274140 original size:22 final size:21 Alignment explanation

Indices: 1274110--1274162 Score: 61 Period size: 22 Copynumber: 2.4 Consensus size: 21 1274100 TGGTTTTCTG * 1274110 GGGGGGGGGGGTGGCATTTTTT 1 GGGGAGGGGGGTGG-ATTTTTT * * 1274132 GGGGAGGGGGTTGGTTTTTTT 1 GGGGAGGGGGGTGGATTTTTT 1274153 GGAGGAGGGG 1 GG-GGAGGGG 1274163 TCCTCCCAAT Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 21 8 0.30 22 19 0.70 ACGTcount: A:0.08, C:0.02, G:0.60, T:0.30 Consensus pattern (21 bp): GGGGAGGGGGGTGGATTTTTT Found at i:1276799 original size:2 final size:2 Alignment explanation

Indices: 1276792--1276823 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 1276782 GTACGCCGAT 1276792 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 1276824 NTTTGTTCGT Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1294397 original size:17 final size:16 Alignment explanation

Indices: 1294372--1294406 Score: 52 Period size: 17 Copynumber: 2.1 Consensus size: 16 1294362 CTGGCGTGCG 1294372 ACCAGTTCTCGCCGAGT 1 ACCAGTTCTCGCC-AGT * 1294389 ACCATTTCTCGCCAGT 1 ACCAGTTCTCGCCAGT 1294405 AC 1 AC 1294407 ATTGTGACGT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 5 0.29 17 12 0.71 ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26 Consensus pattern (16 bp): ACCAGTTCTCGCCAGT Found at i:1294490 original size:17 final size:16 Alignment explanation

Indices: 1294463--1294497 Score: 52 Period size: 17 Copynumber: 2.1 Consensus size: 16 1294453 ACGTCACAAT 1294463 GTACTGGCGAGAAATG 1 GTACTGGCGAGAAATG * 1294479 GTACTCGGCGAGAACTG 1 GTACT-GGCGAGAAATG 1294496 GT 1 GT 1294498 CGCGCGCCAG Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 5 0.29 17 12 0.71 ACGTcount: A:0.26, C:0.17, G:0.37, T:0.20 Consensus pattern (16 bp): GTACTGGCGAGAAATG Found at i:1298807 original size:5 final size:5 Alignment explanation

Indices: 1298797--1298821 Score: 50 Period size: 5 Copynumber: 5.0 Consensus size: 5 1298787 AAAGTTGACA 1298797 AGGAT AGGAT AGGAT AGGAT AGGAT 1 AGGAT AGGAT AGGAT AGGAT AGGAT 1298822 GCACGATGCA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 20 1.00 ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20 Consensus pattern (5 bp): AGGAT Found at i:1298866 original size:5 final size:5 Alignment explanation

Indices: 1298856--1298891 Score: 56 Period size: 5 Copynumber: 7.4 Consensus size: 5 1298846 AAATTAAGTT * 1298856 CTATC CTATC CTATC CAATC CTAT- CTATC CTATC CT 1 CTATC CTATC CTATC CTATC CTATC CTATC CTATC CT 1298892 GCATCCTGTA Statistics Matches: 28, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 4 4 0.14 5 24 0.86 ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39 Consensus pattern (5 bp): CTATC Found at i:1308480 original size:16 final size:16 Alignment explanation

Indices: 1308461--1308505 Score: 72 Period size: 16 Copynumber: 2.8 Consensus size: 16 1308451 CCCGTGCTGT * 1308461 AAGAGCCGGAGCTACG 1 AAGAGCCGGAGCCACG * 1308477 AAGAGCAGGAGCCACG 1 AAGAGCCGGAGCCACG 1308493 AAGAGCCGGAGCC 1 AAGAGCCGGAGCC 1308506 GCGCTGAAAG Statistics Matches: 26, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 26 1.00 ACGTcount: A:0.33, C:0.27, G:0.38, T:0.02 Consensus pattern (16 bp): AAGAGCCGGAGCCACG Found at i:1308567 original size:14 final size:15 Alignment explanation

Indices: 1308513--1308568 Score: 62 Period size: 15 Copynumber: 3.9 Consensus size: 15 1308503 GCCGCGCTGA 1308513 AAGAGCCGGAGCCAT 1 AAGAGCCGGAGCCAT * * * * 1308528 TATAGCC-GTGCTAT 1 AAGAGCCGGAGCCAT 1308542 AAGAGCCGGAGCCAT 1 AAGAGCCGGAGCCAT 1308557 AAGAGCC-GAGCC 1 AAGAGCCGGAGCC 1308569 TGCATATAAG Statistics Matches: 32, Mismatches: 8, Indels: 3 0.74 0.19 0.07 Matches are distributed among these distances: 14 15 0.47 15 17 0.53 ACGTcount: A:0.30, C:0.27, G:0.30, T:0.12 Consensus pattern (15 bp): AAGAGCCGGAGCCAT Found at i:1310238 original size:147 final size:147 Alignment explanation

Indices: 1309988--1310255 Score: 371 Period size: 147 Copynumber: 1.8 Consensus size: 147 1309978 GAGTACTTTT * * 1309988 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAATTTAAGCTGTTTTTTTTCCATAAATAAATC 1 TATGCAATATTTTGCCAAAAAATGACCAAGTTCAA--TAAGCTGTTTGTTTTCCATAAAT-AATC * * 1310053 AGAAATCAAACTCCTAGCAATATACACACCTCTAATATAAGAACAATTGATTTGCAGGAGTTATC 63 AGAAATCAAAATCCTAGCAATATACACACCTCTAATATAAGAACAATTGATCTGCAGGAGTTATC 1310118 CGTACAATCGGGGTACCCTA 128 CGTACAATCGGGGTACCCTA * 1310138 TATGCAATATTTTGCCAAAATATGACCAAGTTCAA-AAGCTGGTATTGTTTT-CATAAACT-ATC 1 TATGCAATATTTTGCCAAAAAATGACCAAGTTCAATAAGCT-GT-TTGTTTTCCATAAA-TAATC * * * * * 1310200 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGAACATTTGATCTGCA 63 AGAAATCAAAATCCTAGCAATATACACACCTCTAATATAAGAACAATTGATCTGCA 1310256 AAAGGCCAAC Statistics Matches: 105, Mismatches: 10, Indels: 9 0.85 0.08 0.07 Matches are distributed among these distances: 147 57 0.54 148 8 0.08 149 7 0.07 150 33 0.31 ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31 Consensus pattern (147 bp): TATGCAATATTTTGCCAAAAAATGACCAAGTTCAATAAGCTGTTTGTTTTCCATAAATAATCAGA AATCAAAATCCTAGCAATATACACACCTCTAATATAAGAACAATTGATCTGCAGGAGTTATCCGT ACAATCGGGGTACCCTA Found at i:1310413 original size:180 final size:178 Alignment explanation

Indices: 1310110--1310675 Score: 746 Period size: 180 Copynumber: 3.2 Consensus size: 178 1310100 TGATTTGCAG * * 1310110 GAGTTATCCGTACAATCG-GGGTACCCTATATGCAATATTTTGCCAAAATATGACCAAGTTCAAA 1 GAGTTATCCGTACAAT-GAGGGTACCCTATATGCAATATTTTGCCAAAAAATGA-TAAGTTCAAA * * 1310174 AGCTGGTATTGTTTTCATAAACTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATA 64 AGCTGGTATTATTTTCATAAATTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATA * ** * * 1310239 TGAACATTTGATCTGCAAAAGGCCAACTTTCTATTTTGAGAACTGTAGGA 129 TGTACATTTGATCTGCAAAAGAACAACTTTCTATCTTGAAAACTGTAGGA 1310289 GAAGTTATCCGTACAATGAGGGTACCCTATATGCAATATTTTGCCAAAAAATGATAAAGTTCAAA 1 G-AGTTATCCGTACAATGAGGGTACCCTATATGCAATATTTTGCCAAAAAATGAT-AAGTTCAAA * 1310354 AGCTGGTATTATTTTCATAAATTATTGGAAATCAAAATCCTAGCAATAAT-CACACCTCTGATAT 64 AGCTGGTATTATTTTCATAAATTATCGGAAATCAAAATCCTAGCAAT-ATGCACACCTCTGATAT * * 1310418 AAGTACAATAT-ATCTGCAAAAGAACAAC-TTCGTATCTTGAAAACTGTAGGA 128 ATGTAC-ATTTGATCTGCAAAAGAACAACTTTC-TATCTTGAAAACTGTAGGA * * * * * * * 1310469 TGAGTTATCCGTACAACGAGGGTATCTTATATGCAATATATTACCAACAAATGACTATGTTCAAA 1 -GAGTTATCCGTACAATGAGGGTACCCTATATGCAATATTTTGCCAAAAAATGA-TAAGTTCAAA * * * * 1310534 AGCTGGTATTTTTTTCATTAATTATCGGAAATCAAAATCCTAGCAATATGCACACTTCCG-TATA 64 AGCTGGTATTATTTTCATAAATTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATA * * ** 1310598 TGTACAATTGATCTGCAAAAGAACAAGTGCCTATCTTGAAAACTGTAGGA 129 TGTACATTTGATCTGCAAAAGAACAACTTTCTATCTTGAAAACTGTAGGA * * 1310648 GGAGTTATCCGTACAATAAGGGTTCCCT 1 -GAGTTATCCGTACAATGAGGGTACCCT 1310676 TTTGGCAGCT Statistics Matches: 340, Mismatches: 36, Indels: 22 0.85 0.09 0.06 Matches are distributed among these distances: 178 2 0.01 179 72 0.21 180 259 0.76 181 7 0.02 ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30 Consensus pattern (178 bp): GAGTTATCCGTACAATGAGGGTACCCTATATGCAATATTTTGCCAAAAAATGATAAGTTCAAAAG CTGGTATTATTTTCATAAATTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATG TACATTTGATCTGCAAAAGAACAACTTTCTATCTTGAAAACTGTAGGA Found at i:1317505 original size:11 final size:11 Alignment explanation

Indices: 1317489--1317533 Score: 53 Period size: 11 Copynumber: 4.5 Consensus size: 11 1317479 AGAAAATTTG 1317489 TCAAAATTTCA 1 TCAAAATTTCA * 1317500 TCAAAACTTCA 1 TCAAAATTTCA 1317511 TCAAAA---CA 1 TCAAAATTTCA 1317519 TC-AAATTTCA 1 TCAAAATTTCA 1317529 TCAAA 1 TCAAA 1317534 CAAAATAAAC Statistics Matches: 29, Mismatches: 1, Indels: 8 0.76 0.03 0.21 Matches are distributed among these distances: 7 3 0.10 8 4 0.14 10 4 0.14 11 18 0.62 ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29 Consensus pattern (11 bp): TCAAAATTTCA Found at i:1318336 original size:21 final size:21 Alignment explanation

Indices: 1318307--1318405 Score: 99 Period size: 21 Copynumber: 4.7 Consensus size: 21 1318297 TACAAGATAA * 1318307 ACGAGAGGATAGGATTCACGC 1 ACGATAGGATAGGATTCACGC * 1318328 ACGATAGGATAGGATTAACGC 1 ACGATAGGATAGGATTCACGC * * * * 1318349 ACGATAGAACAGTATACACGC 1 ACGATAGGATAGGATTCACGC * * ** 1318370 ACGATATGATAGGATTGATAC 1 ACGATAGGATAGGATTCACGC * 1318391 ACGATAGGAAAGGAT 1 ACGATAGGATAGGAT 1318406 AAACGATGTT Statistics Matches: 61, Mismatches: 17, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 21 61 1.00 ACGTcount: A:0.39, C:0.15, G:0.27, T:0.18 Consensus pattern (21 bp): ACGATAGGATAGGATTCACGC Found at i:1321565 original size:21 final size:21 Alignment explanation

Indices: 1321531--1321664 Score: 110 Period size: 21 Copynumber: 6.4 Consensus size: 21 1321521 CGATAAACCT * 1321531 GATAGGATTCACGCACGATAG 1 GATAGGATTAACGCACGATAG * 1321552 GATAGCATTAACGCACGATAG 1 GATAGGATTAACGCACGATAG * * * * 1321573 AACAGTA-TACACGCACGAAAG 1 GATAGGATTA-ACGCACGATAG 1321594 GATAGGATTAACGCACGATAG 1 GATAGGATTAACGCACGATAG * * * * 1321615 AACAGTA-TACACGCACGATAC 1 GATAGGATTA-ACGCACGATAG * ** * 1321636 GATAGGATTGATACACGATAC 1 GATAGGATTAACGCACGATAG 1321657 GATAGGAT 1 GATAGGAT 1321665 AGGATGGTAA Statistics Matches: 89, Mismatches: 20, Indels: 8 0.76 0.17 0.07 Matches are distributed among these distances: 20 4 0.04 21 82 0.92 22 3 0.03 ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18 Consensus pattern (21 bp): GATAGGATTAACGCACGATAG Found at i:1321655 original size:42 final size:42 Alignment explanation

Indices: 1321540--1321644 Score: 183 Period size: 42 Copynumber: 2.5 Consensus size: 42 1321530 TGATAGGATT * 1321540 CACGCACGATAGGATAGCATTAACGCACGATAGAACAGTATA 1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA * 1321582 CACGCACGAAAGGATAGGATTAACGCACGATAGAACAGTATA 1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA * 1321624 CACGCACGATACGATAGGATT 1 CACGCACGATAGGATAGGATT 1321645 GATACACGAT Statistics Matches: 59, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 42 59 1.00 ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16 Consensus pattern (42 bp): CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA Found at i:1336181 original size:202 final size:201 Alignment explanation

Indices: 1335835--1336227 Score: 777 Period size: 202 Copynumber: 2.0 Consensus size: 201 1335825 NNNNNNNNNN 1335835 TGAGAAATTGTATTCACATCTGCGGCACTGTCAAGTTGAAATCTAATGTCACACTCATTGATACG 1 TGAGAAATTGTATTCACATCTGCGGCACTGTCAAGTTGAAATCTAATGTCACACTCATTGATACG 1335900 CATTATTGCAGTCACTTCTTTGCCACCAGAACTAACAGCTTTCAACCATTGGTCCTCGTTGAATT 66 CATTATTGCAGTCACTTCTTTGCCACCAGAACTAACAGCTTTCAACCATTGGTCCTCGTTGAATT 1335965 CTTCTTCCTGACTGACTGAATGTATCTTCTTGCACTTTGCTTTGAAGTGATTCCTTCCACCNGAC 131 CTTCTTCCTGACTGACTGAATGTATCTTCTTGCACTTTGCTTTGAAGTGATTCCTTCCACC-GAC 1336030 ATAACGC 195 ATAACGC 1336037 TGAGAAATTGTATTCACATCTGCGGCACTGTCAAGTTGAAATCTAATGTCACACTCATTGATACG 1 TGAGAAATTGTATTCACATCTGCGGCACTGTCAAGTTGAAATCTAATGTCACACTCATTGATACG 1336102 CATTATTGCAGTCACTTCTTTGCCACCAGAACTAACAGCTTTCAACCATTGGTCCTCGTTGAATT 66 CATTATTGCAGTCACTTCTTTGCCACCAGAACTAACAGCTTTCAACCATTGGTCCTCGTTGAATT 1336167 CTTCTTCCTGACTGACTGAATGTATCTTCTTGCACTTTGCTTTGAAGTGATTCCTTCCACC 131 CTTCTTCCTGACTGACTGAATGTATCTTCTTGCACTTTGCTTTGAAGTGATTCCTTCCACC 1336228 ACACTGTTCA Statistics Matches: 191, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 202 191 1.00 ACGTcount: A:0.24, C:0.25, G:0.16, T:0.34 Consensus pattern (201 bp): TGAGAAATTGTATTCACATCTGCGGCACTGTCAAGTTGAAATCTAATGTCACACTCATTGATACG CATTATTGCAGTCACTTCTTTGCCACCAGAACTAACAGCTTTCAACCATTGGTCCTCGTTGAATT CTTCTTCCTGACTGACTGAATGTATCTTCTTGCACTTTGCTTTGAAGTGATTCCTTCCACCGACA TAACGC Found at i:1338805 original size:21 final size:20 Alignment explanation

Indices: 1338764--1338805 Score: 57 Period size: 20 Copynumber: 2.0 Consensus size: 20 1338754 GTGTATATCG * * 1338764 TTCTATCGTGCTTAGTCCTA 1 TTCTATCGTGCATAATCCTA 1338784 TTCTATCGTGCGATAATCCTA 1 TTCTATCGTGC-ATAATCCTA 1338805 T 1 T 1338806 CAGGTTAATT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 20 11 0.58 21 8 0.42 ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43 Consensus pattern (20 bp): TTCTATCGTGCATAATCCTA Found at i:1341590 original size:2 final size:2 Alignment explanation

Indices: 1341583--1341616 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 1341573 AACGGGGATT 1341583 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 1341617 TCTTCATTCT 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:1342326 original size:13 final size:13 Alignment explanation

Indices: 1342310--1342334 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 1342300 GAAAATGTCC 1342310 AAAAAAAATATAA 1 AAAAAAAATATAA 1342323 AAAAAAAATATA 1 AAAAAAAATATA 1342335 TTCAATCCAA 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:0.84, C:0.00, G:0.00, T:0.16 Consensus pattern (13 bp): AAAAAAAATATAA Found at i:1343766 original size:13 final size:13 Alignment explanation

Indices: 1343748--1343776 Score: 58 Period size: 13 Copynumber: 2.2 Consensus size: 13 1343738 GGGGTTTTAC 1343748 CAAAAAACAACAA 1 CAAAAAACAACAA 1343761 CAAAAAACAACAA 1 CAAAAAACAACAA 1343774 CAA 1 CAA 1343777 CAAGGGGGTT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00 Consensus pattern (13 bp): CAAAAAACAACAA Found at i:1343774 original size:16 final size:15 Alignment explanation

Indices: 1343749--1343779 Score: 53 Period size: 16 Copynumber: 2.0 Consensus size: 15 1343739 GGGTTTTACC 1343749 AAAAAACAACAACAA 1 AAAAAACAACAACAA 1343764 AAAACAACAACAACAA 1 AAAA-AACAACAACAA 1343780 GGGGGTTGGC Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 4 0.27 16 11 0.73 ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00 Consensus pattern (15 bp): AAAAAACAACAACAA Found at i:1347136 original size:15 final size:16 Alignment explanation

Indices: 1347106--1347154 Score: 55 Period size: 17 Copynumber: 3.1 Consensus size: 16 1347096 AATACAGCTT * * 1347106 ACTCCACTTATATTGA 1 ACTCCGCTTATTTTGA 1347122 ACT-CGCTTATTTTGAA 1 ACTCCGCTTATTTTG-A * 1347138 ATTCCGCTTATTTTGA 1 ACTCCGCTTATTTTGA 1347154 A 1 A 1347155 ATAGAAATAA Statistics Matches: 28, Mismatches: 3, Indels: 4 0.80 0.09 0.11 Matches are distributed among these distances: 15 9 0.32 16 8 0.29 17 11 0.39 ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43 Consensus pattern (16 bp): ACTCCGCTTATTTTGA Found at i:1352724 original size:14 final size:14 Alignment explanation

Indices: 1352707--1352736 Score: 51 Period size: 14 Copynumber: 2.1 Consensus size: 14 1352697 CCATGTTTCT * 1352707 GAGTGCATGCAAAG 1 GAGTGAATGCAAAG 1352721 GAGTGAATGCAAAG 1 GAGTGAATGCAAAG 1352735 GA 1 GA 1352737 AATCAAGACG Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.40, C:0.10, G:0.37, T:0.13 Consensus pattern (14 bp): GAGTGAATGCAAAG Found at i:1360952 original size:14 final size:13 Alignment explanation

Indices: 1360931--1360971 Score: 64 Period size: 13 Copynumber: 3.1 Consensus size: 13 1360921 CCCCCCCAAA 1360931 AAAAAAAAACAAC 1 AAAAAAAAACAAC * 1360944 AACAAAAAACAAC 1 AAAAAAAAACAAC 1360957 AAAAACAAAACAAC 1 AAAAA-AAAACAAC 1360971 A 1 A 1360972 GGCACTATTT Statistics Matches: 25, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 13 16 0.64 14 9 0.36 ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00 Consensus pattern (13 bp): AAAAAAAAACAAC Found at i:1360952 original size:16 final size:16 Alignment explanation

Indices: 1360931--1360966 Score: 54 Period size: 16 Copynumber: 2.2 Consensus size: 16 1360921 CCCCCCCAAA * 1360931 AAAAAAAAACAACAAC 1 AAAAAAAAACAAAAAC * 1360947 AAAAAACAACAAAAAC 1 AAAAAAAAACAAAAAC 1360963 AAAA 1 AAAA 1360967 CAACAGGCAC Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00 Consensus pattern (16 bp): AAAAAAAAACAAAAAC Found at i:1364467 original size:13 final size:14 Alignment explanation

Indices: 1364449--1364477 Score: 51 Period size: 13 Copynumber: 2.1 Consensus size: 14 1364439 ATTTGGGATG 1364449 GAAAGATGCT-GGT 1 GAAAGATGCTCGGT 1364462 GAAAGATGCTCGGT 1 GAAAGATGCTCGGT 1364476 GA 1 GA 1364478 CAGGAAAGCC Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 13 10 0.67 14 5 0.33 ACGTcount: A:0.31, C:0.10, G:0.38, T:0.21 Consensus pattern (14 bp): GAAAGATGCTCGGT Found at i:1380239 original size:168 final size:171 Alignment explanation

Indices: 1379960--1380387 Score: 535 Period size: 173 Copynumber: 2.5 Consensus size: 171 1379950 ATCTTTTGAT * * * * * * 1379960 ACTATATGGCCATATTGGCCACACCTTACAGCCGGAATCCCTGACCCAGGTGTCATGAGTTTCAC 1 ACTATATGGCCATATTGGCCACACCCTAGAGCCTGAACCCCTGACCCAGGGGCCATGA-TTTCAC * * * 1380025 AATTTTGGTAGAGGGCTTCCTGGACATCATACCCATGCAATTAG-TTTTTAACCAATATATATGA 65 AATTTTGGTAGAGGGCTTCATGGACATCATAACCATGCAATTAGTTTTTTAACAAATATATATG- * * ** 1380089 GG-GT-AGA-GAA-GAAGATTTTCTATGATTTTGTACATTTTC 129 GGAGTAAGATGAATGAAGATTTTCAAAGATTTAATACATTTTC * * * 1380128 ACTATATAGCCATATTGGCCA-ATCCCTAGAGCCTGAACCCCTGACCAAGGGGCCATGGATTACA 1 ACTATATGGCCATATTGGCCACA-CCCTAGAGCCTGAACCCCTGACCCAGGGGCCAT-GATTTCA * * * * 1380192 TAATTTTGGTAGAGGGCTTCATGGACATCATAACCATGTATTTAGTTTTTTTACAAATATATATG 64 CAATTTTGGTAGAGGGCTTCATGGACATCATAACCATGCAATTAGTTTTTTAACAAATATATATG * * 1380257 GGAGTAGAGATGAATTAAGATTTTCAAAGATTTAATACATTTTT 129 GGAGTA-AGATGAATGAAGATTTTCAAAGATTTAATACATTTTC * * 1380301 ACTTTATGGCCATATTGGCCACACCCTAGAGCCTGAACCCCTGACCCAGGGGCCATTCATTTCAC 1 ACTATATGGCCATATTGGCCACACCCTAGAGCCTGAACCCCTGACCCAGGGGCCA-TGATTTCAC * 1380366 AATTTTGGCAGAGGGCTTCATG 65 AATTTTGGTAGAGGGCTTCATG 1380388 AACAGTCTTT Statistics Matches: 221, Mismatches: 29, Indels: 15 0.83 0.11 0.06 Matches are distributed among these distances: 167 1 0.00 168 92 0.42 169 21 0.10 171 3 0.01 172 3 0.01 173 99 0.45 174 2 0.01 ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31 Consensus pattern (171 bp): ACTATATGGCCATATTGGCCACACCCTAGAGCCTGAACCCCTGACCCAGGGGCCATGATTTCACA ATTTTGGTAGAGGGCTTCATGGACATCATAACCATGCAATTAGTTTTTTAACAAATATATATGGG AGTAAGATGAATGAAGATTTTCAAAGATTTAATACATTTTC Found at i:1382747 original size:21 final size:21 Alignment explanation

Indices: 1382721--1382785 Score: 76 Period size: 21 Copynumber: 3.1 Consensus size: 21 1382711 CTAAAACGCA * 1382721 TGCAACGAATGCGAGAGCTCG 1 TGCAACGTATGCGAGAGCTCG * * * 1382742 TGCAACGTACGCGAGAGTTAG 1 TGCAACGTATGCGAGAGCTCG * * 1382763 TGCAACGTGTGAGAGAGCTCG 1 TGCAACGTATGCGAGAGCTCG 1382784 TG 1 TG 1382786 AGAATCTAAA Statistics Matches: 35, Mismatches: 9, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 21 35 1.00 ACGTcount: A:0.26, C:0.20, G:0.35, T:0.18 Consensus pattern (21 bp): TGCAACGTATGCGAGAGCTCG Found at i:1382878 original size:32 final size:32 Alignment explanation

Indices: 1382837--1382908 Score: 126 Period size: 32 Copynumber: 2.2 Consensus size: 32 1382827 CTAGCCATCT 1382837 TTCCCCCCGGAAAAATAGCTATATAGCAGTTC 1 TTCCCCCCGGAAAAATAGCTATATAGCAGTTC * * 1382869 TTCCCCCCGGAAAAATGGCTATATAGCAGTTT 1 TTCCCCCCGGAAAAATAGCTATATAGCAGTTC 1382901 TTCCCCCC 1 TTCCCCCC 1382909 ACGGAAAGCT Statistics Matches: 38, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 32 38 1.00 ACGTcount: A:0.26, C:0.32, G:0.15, T:0.26 Consensus pattern (32 bp): TTCCCCCCGGAAAAATAGCTATATAGCAGTTC Found at i:1382925 original size:34 final size:32 Alignment explanation

Indices: 1382837--1382928 Score: 114 Period size: 32 Copynumber: 2.8 Consensus size: 32 1382827 CTAGCCATCT 1382837 TTCCCCCCGGAAAAAT-AGCTATATAGCAGTTC 1 TTCCCCCCGGAAAAATGA-CTATATAGCAGTTC * * 1382869 TTCCCCCCGGAAAAATGGCTATATAGCAGTTT 1 TTCCCCCCGGAAAAATGACTATATAGCAGTTC ** 1382901 TTCCCCCCACGGAAAGCTGACTATATAG 1 TT-CCCCC-CGGAAAAATGACTATATAG 1382929 TGGGCTTTCC Statistics Matches: 52, Mismatches: 5, Indels: 4 0.85 0.08 0.07 Matches are distributed among these distances: 32 31 0.60 33 5 0.10 34 16 0.31 ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25 Consensus pattern (32 bp): TTCCCCCCGGAAAAATGACTATATAGCAGTTC Found at i:1391737 original size:45 final size:42 Alignment explanation

Indices: 1391611--1391742 Score: 149 Period size: 43 Copynumber: 3.0 Consensus size: 42 1391601 GGCAATTTTT * ** 1391611 AATTTTATTTTTGCCGATTTAGTTGGTCTCCGAATTTGGAGAC 1 AATTTTATTTTTGCCGATTTGGCAGGTCTCCG-ATTTGGAGAC ** * 1391654 AATTTTATTTTTGCTAATTTGGCAAGG-CTCCGATTTGGAGGC 1 AATTTTATTTTTGCCGATTTGGC-AGGTCTCCGATTTGGAGAC * 1391696 AATTTTTAATTTTTGTCCGATTTGGCAGGTCTCCGAGTTGGAGAC 1 AA-TTTT-ATTTTTG-CCGATTTGGCAGGTCTCCGATTTGGAGAC 1391741 AA 1 AA 1391743 GTTTGAATGG Statistics Matches: 74, Mismatches: 10, Indels: 8 0.80 0.11 0.09 Matches are distributed among these distances: 42 11 0.15 43 28 0.38 44 12 0.16 45 23 0.31 ACGTcount: A:0.22, C:0.14, G:0.23, T:0.41 Consensus pattern (42 bp): AATTTTATTTTTGCCGATTTGGCAGGTCTCCGATTTGGAGAC Found at i:1391756 original size:28 final size:28 Alignment explanation

Indices: 1391723--1391777 Score: 74 Period size: 28 Copynumber: 2.0 Consensus size: 28 1391713 CGATTTGGCA * 1391723 GGTCTCCGAGTTGGAGACAAGTTTGAAT 1 GGTCTCCAAGTTGGAGACAAGTTTGAAT * * * 1391751 GGTCTCCAATTTGGGGGCAAGTTTGAA 1 GGTCTCCAAGTTGGAGACAAGTTTGAA 1391778 AATTTTTGCA Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 28 23 1.00 ACGTcount: A:0.24, C:0.15, G:0.33, T:0.29 Consensus pattern (28 bp): GGTCTCCAAGTTGGAGACAAGTTTGAAT Found at i:1396295 original size:17 final size:17 Alignment explanation

Indices: 1396273--1396313 Score: 82 Period size: 17 Copynumber: 2.4 Consensus size: 17 1396263 ATTGTAAAAA 1396273 CTTTTCTAAACCAATTG 1 CTTTTCTAAACCAATTG 1396290 CTTTTCTAAACCAATTG 1 CTTTTCTAAACCAATTG 1396307 CTTTTCT 1 CTTTTCT 1396314 TTCATGTGTT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 24 1.00 ACGTcount: A:0.24, C:0.24, G:0.05, T:0.46 Consensus pattern (17 bp): CTTTTCTAAACCAATTG Found at i:1402452 original size:43 final size:43 Alignment explanation

Indices: 1402391--1402510 Score: 195 Period size: 43 Copynumber: 2.8 Consensus size: 43 1402381 ATAGAGTAAA * * * * 1402391 ATTATTATAGGAAGAGTGAATGTACTTCGACATATTATGACCC 1 ATTATTTTAGGAAAAGTGAATGTACTTTGACATATTATGACAC * 1402434 ATTATTTTAGGAAAAGTGAATGTACTTTGACATATTTTGACAC 1 ATTATTTTAGGAAAAGTGAATGTACTTTGACATATTATGACAC 1402477 ATTATTTTAGGAAAAGTGAATGTACTTTGACATA 1 ATTATTTTAGGAAAAGTGAATGTACTTTGACATA 1402511 CTGTGATATC Statistics Matches: 72, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 43 72 1.00 ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37 Consensus pattern (43 bp): ATTATTTTAGGAAAAGTGAATGTACTTTGACATATTATGACAC Found at i:1407602 original size:11 final size:11 Alignment explanation

Indices: 1407586--1407618 Score: 52 Period size: 11 Copynumber: 3.2 Consensus size: 11 1407576 GGAGATTTGA 1407586 ATTATCCAAAT 1 ATTATCCAAAT 1407597 ATTATCC-AA- 1 ATTATCCAAAT 1407606 ATTATCCAAAT 1 ATTATCCAAAT 1407617 AT 1 AT 1407619 GATATCGCCT Statistics Matches: 20, Mismatches: 0, Indels: 4 0.83 0.00 0.17 Matches are distributed among these distances: 9 7 0.35 10 4 0.20 11 9 0.45 ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36 Consensus pattern (11 bp): ATTATCCAAAT Found at i:1416401 original size:21 final size:21 Alignment explanation

Indices: 1416377--1416426 Score: 73 Period size: 21 Copynumber: 2.4 Consensus size: 21 1416367 GCCAAGACAA * 1416377 TAGCATCTTACCAATAACTTC 1 TAGCATCTTACCAATAACCTC * 1416398 TAGCATCTTGCCAATAACCTC 1 TAGCATCTTACCAATAACCTC * 1416419 TATCATCT 1 TAGCATCT 1416427 GAGGTCATCT Statistics Matches: 26, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 26 1.00 ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34 Consensus pattern (21 bp): TAGCATCTTACCAATAACCTC Found at i:1417719 original size:34 final size:34 Alignment explanation

Indices: 1417681--1417749 Score: 104 Period size: 34 Copynumber: 2.0 Consensus size: 34 1417671 CTATCAATGA * 1417681 AACATCTCT-CTCTTTCTTTTACTGTTAATTTATT 1 AACATCTCTAC-CTTTCTTTAACTGTTAATTTATT * 1417715 AACATTTCTACCTTTCTTTAACTGTTAATTTATT 1 AACATCTCTACCTTTCTTTAACTGTTAATTTATT 1417749 A 1 A 1417750 TGTCAAATAT Statistics Matches: 32, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 34 31 0.97 35 1 0.03 ACGTcount: A:0.25, C:0.19, G:0.03, T:0.54 Consensus pattern (34 bp): AACATCTCTACCTTTCTTTAACTGTTAATTTATT Found at i:1418062 original size:2 final size:2 Alignment explanation

Indices: 1418055--1418081 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 1418045 TCACATGTTT 1418055 TA 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 TA T 1418082 GACTAATATT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:1421687 original size:28 final size:28 Alignment explanation

Indices: 1421654--1421710 Score: 105 Period size: 28 Copynumber: 2.0 Consensus size: 28 1421644 TTTTCGAGAT * 1421654 AATCATTTCAGAGATTATAAATCAATAC 1 AATCATTTCAGAGATAATAAATCAATAC 1421682 AATCATTTCAGAGATAATAAATCAATAC 1 AATCATTTCAGAGATAATAAATCAATAC 1421710 A 1 A 1421711 CCGCCAGACA Statistics Matches: 28, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30 Consensus pattern (28 bp): AATCATTTCAGAGATAATAAATCAATAC Found at i:1422828 original size:131 final size:131 Alignment explanation

Indices: 1422594--1422850 Score: 471 Period size: 131 Copynumber: 2.0 Consensus size: 131 1422584 CATCGCAGTT * 1422594 TATGGTATTGTTAAAATGTTTCTAGTTGGAGAAACTTGCATTTTAGGAGAAGGTTGATAGGCAAA 1 TATGGTATTGTTAAAATGTTTCTAGTTGGAGAAACTTGCATTTTAAGAGAAGGTTGATAGGCAAA * * 1422659 ACAAAGTCTACGGTAGCCAAATCAAGAATTATACATAACAGCACATTCTGTGATGTTTGAAAAGT 66 ACAAAGTATACAGTAGCCAAATCAAGAATTATACATAACAGCACATTCTGTGATGTTTGAAAAGT 1422724 C 131 C 1422725 TATGGTATTGTTAAAATGTTTCTAGTTGGAGAAACTTGCATTTTAAGAGAAGGTTGATAGGCAAA 1 TATGGTATTGTTAAAATGTTTCTAGTTGGAGAAACTTGCATTTTAAGAGAAGGTTGATAGGCAAA 1422790 ACAAAGTATACAGTAGCCAAATCAATG-ATTATACATAACAGCACATTCTGTGATGTTTGAA 66 ACAAAGTATACAGTAGCCAAATCAA-GAATTATACATAACAGCACATTCTGTGATGTTTGAA 1422851 TGGTGCTCCT Statistics Matches: 122, Mismatches: 3, Indels: 2 0.96 0.02 0.02 Matches are distributed among these distances: 131 121 0.99 132 1 0.01 ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31 Consensus pattern (131 bp): TATGGTATTGTTAAAATGTTTCTAGTTGGAGAAACTTGCATTTTAAGAGAAGGTTGATAGGCAAA ACAAAGTATACAGTAGCCAAATCAAGAATTATACATAACAGCACATTCTGTGATGTTTGAAAAGT C Found at i:1432323 original size:11 final size:12 Alignment explanation

Indices: 1432295--1432320 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 1432285 GTCTCGATTG 1432295 TTTCAATATTCT 1 TTTCAATATTCT 1432307 TTTCAATATTCT 1 TTTCAATATTCT 1432319 TT 1 TT 1432321 CAAACATCGG 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:0.23, C:0.15, G:0.00, T:0.62 Consensus pattern (12 bp): TTTCAATATTCT Found at i:1450297 original size:20 final size:20 Alignment explanation

Indices: 1450268--1450315 Score: 69 Period size: 20 Copynumber: 2.4 Consensus size: 20 1450258 CCAGGACGGT 1450268 GGGAAATACTGGTAATTCCC 1 GGGAAATACTGGTAATTCCC * * * 1450288 GGGAATTACTGGTATTTCCT 1 GGGAAATACTGGTAATTCCC 1450308 GGGAAATA 1 GGGAAATA 1450316 TTGGGAAATA Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 20 24 1.00 ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29 Consensus pattern (20 bp): GGGAAATACTGGTAATTCCC Found at i:1455823 original size:1 final size:1 Alignment explanation

Indices: 1455819--1455844 Score: 52 Period size: 1 Copynumber: 26.0 Consensus size: 1 1455809 ACCCCCACAT 1455819 CCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 1455845 ACACACAATC Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 25 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:1462886 original size:14 final size:14 Alignment explanation

Indices: 1462869--1462910 Score: 66 Period size: 14 Copynumber: 3.0 Consensus size: 14 1462859 CACATTTCTA * 1462869 AATATGCAATCATG 1 AATATACAATCATG * 1462883 AATATACAATTATG 1 AATATACAATCATG 1462897 AATATACAATCATG 1 AATATACAATCATG 1462911 TGAATTTGCA Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 14 25 1.00 ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31 Consensus pattern (14 bp): AATATACAATCATG Found at i:1462900 original size:28 final size:28 Alignment explanation

Indices: 1462850--1462910 Score: 77 Period size: 28 Copynumber: 2.2 Consensus size: 28 1462840 TGATTCCCAG * * * 1462850 TCATGAATACACATTTCTAAATATGCAA 1 TCATGAATACACAATTATAAATATACAA * * 1462878 TCATGAATATACAATTATGAATATACAA 1 TCATGAATACACAATTATAAATATACAA 1462906 TCATG 1 TCATG 1462911 TGAATTTGCA Statistics Matches: 28, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33 Consensus pattern (28 bp): TCATGAATACACAATTATAAATATACAA Found at i:1463386 original size:17 final size:16 Alignment explanation

Indices: 1463355--1463400 Score: 65 Period size: 17 Copynumber: 2.8 Consensus size: 16 1463345 ATAACAGAGG * 1463355 AAGAAAGAGAAAAGAA 1 AAGAAAGAAAAAAGAA 1463371 AAGAATAGAAAAAAGAA 1 AAGAA-AGAAAAAAGAA 1463388 AAGCAAAGAAAAA 1 AAG-AAAGAAAAA 1463401 GGTACCTAGT Statistics Matches: 27, Mismatches: 1, Indels: 3 0.87 0.03 0.10 Matches are distributed among these distances: 16 5 0.19 17 20 0.74 18 2 0.07 ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02 Consensus pattern (16 bp): AAGAAAGAAAAAAGAA Found at i:1479762 original size:27 final size:27 Alignment explanation

Indices: 1479724--1479905 Score: 301 Period size: 27 Copynumber: 6.7 Consensus size: 27 1479714 ATAAACAACT * 1479724 CATGGATACGACAACACATCGATAGTC 1 CATGGATATGACAACACATCGATAGTC * 1479751 CATGGATACGACAACACATCGATAGTC 1 CATGGATATGACAACACATCGATAGTC * 1479778 CATGGATATGACAACACATCGATATTC 1 CATGGATATGACAACACATCGATAGTC 1479805 CATGGATATGACAACACATCGATAGTC 1 CATGGATATGACAACACATCGATAGTC * 1479832 CATGGATATGCCAACACATCGATAGTC 1 CATGGATATGACAACACATCGATAGTC * * 1479859 CGTGGATATGACAACACATCGATATTC 1 CATGGATATGACAACACATCGATAGTC * 1479886 CATGGATACGACAACACATC 1 CATGGATATGACAACACATC 1479906 ACACTGATAC Statistics Matches: 146, Mismatches: 9, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 27 146 1.00 ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21 Consensus pattern (27 bp): CATGGATATGACAACACATCGATAGTC Found at i:1489286 original size:421 final size:420 Alignment explanation

Indices: 1488502--1489342 Score: 1610 Period size: 421 Copynumber: 2.0 Consensus size: 420 1488492 TCGAACATCG 1488502 TCTGAACTTGTAGATAAATCATTAACGTTTGTTAAATAATCGGCATTGTTCTTGATTTCAGGACT 1 TCTGAACTTGTAGATAAATCATTAACGTTTGTTAAATAATCGGCATTGTTCTTGATTTCAGGACT * 1488567 CGAGGTGTTGTTTCTAAGAGCAGCCAACATAATGTTGTTATGGCGTCGTTTGAAGGCCTGCTTCA 66 CGAGGTGTTGTTTCTAAGAGCAGCCAACATAATGTTGTTATGGCGTCGTTTGAAAGCCTGCTTCA * 1488632 TTTCGGGGTCAGAACTTCTCCGCTGGTACTGAGTTCGCGGACCCAGTCTATGGACCTCGGCCGTC 131 TTTCGGGGTCAGAACTTCTCCGCTGATACTGAGTTCGCGGACCCAGTCTATGGACCTCGGCCGTC * 1488697 ACGTGCATTGTGCTCTCACTAGGAGCCGGCGATCGACTACGCGATGGGTCTCTCTCACACAGGCT 196 ACGTGCATCGTGCTCTCACTAGGAGCCGGCGATCGACTACGCGATGGGTCTCTCTCACACAGGCT * * 1488762 TCCCACAGAATGACGTATCGGATCGTGGAATGTCACACACCGCGGTCCACTCCGTCTATGTCGAT 261 CCCCACAGAATGACGTATCGGATCGTGAAATGTCACACACCGCGGTCCACTCCGTCTATGTCGAT 1488827 TTCTGCGCACGATGACGTCACTGGGGAAGCCATTTTCAATGCTGTCTTCATGGACCGGGGCTAGC 326 TTCTGCGCACGATGACGTCACTGGGGAAGCCATTTTCAATGCTGTCTTCATGGACCGGGGCTAGC 1488892 ACTGTCCCATAGCGGTCATCCTCGGACGAC 391 ACTGTCCCATAGCGGTCATCCTCGGACGAC 1488922 NTCTGAACTTGTAGATAAATCATTAACGTTTGTTAAATAATCGGCATTGTTCTTGATTTCAGGAC 1 -TCTGAACTTGTAGATAAATCATTAACGTTTGTTAAATAATCGGCATTGTTCTTGATTTCAGGAC 1488987 TCGAGGTGTTGTTTCTAAGAGCAGCCAACATAATGTTGTTATGGCGTCGTTTGAAAGCCTGCTTC 65 TCGAGGTGTTGTTTCTAAGAGCAGCCAACATAATGTTGTTATGGCGTCGTTTGAAAGCCTGCTTC 1489052 ATTTCGGGGTCAGAACTTCTCCGCTGATACTGAGTTCGCGGACCCAGTCTATGGACCTCGGCCGT 130 ATTTCGGGGTCAGAACTTCTCCGCTGATACTGAGTTCGCGGACCCAGTCTATGGACCTCGGCCGT * 1489117 CACGTGCATCGTGCTCTCACTAGGAGCCGGCGATCGACTACGTGATGGGTCTCTCTCACACAGGC 195 CACGTGCATCGTGCTCTCACTAGGAGCCGGCGATCGACTACGCGATGGGTCTCTCTCACACAGGC 1489182 TCCCCACAGAATGACGTATCGGATCGTGAAATGTCACACACCGCGGTCCACTCCGTCTATGTCGA 260 TCCCCACAGAATGACGTATCGGATCGTGAAATGTCACACACCGCGGTCCACTCCGTCTATGTCGA * 1489247 TTTCTGCGCACGATGACGTCACTGGGGAAGCCGTTTTCAATGCTGTCTTCATGGACCGGGGCTAG 325 TTTCTGCGCACGATGACGTCACTGGGGAAGCCATTTTCAATGCTGTCTTCATGGACCGGGGCTAG 1489312 CACTGTCCCATAGCGGTCATCCTCGGACGAC 390 CACTGTCCCATAGCGGTCATCCTCGGACGAC 1489343 AACCCTACTT Statistics Matches: 413, Mismatches: 7, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 421 413 1.00 ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28 Consensus pattern (420 bp): TCTGAACTTGTAGATAAATCATTAACGTTTGTTAAATAATCGGCATTGTTCTTGATTTCAGGACT CGAGGTGTTGTTTCTAAGAGCAGCCAACATAATGTTGTTATGGCGTCGTTTGAAAGCCTGCTTCA TTTCGGGGTCAGAACTTCTCCGCTGATACTGAGTTCGCGGACCCAGTCTATGGACCTCGGCCGTC ACGTGCATCGTGCTCTCACTAGGAGCCGGCGATCGACTACGCGATGGGTCTCTCTCACACAGGCT CCCCACAGAATGACGTATCGGATCGTGAAATGTCACACACCGCGGTCCACTCCGTCTATGTCGAT TTCTGCGCACGATGACGTCACTGGGGAAGCCATTTTCAATGCTGTCTTCATGGACCGGGGCTAGC ACTGTCCCATAGCGGTCATCCTCGGACGAC Found at i:1499118 original size:15 final size:15 Alignment explanation

Indices: 1499098--1499127 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 1499088 GGTAAGTGAA 1499098 GCGTCCGGATATCTG 1 GCGTCCGGATATCTG 1499113 GCGTCCGGATATCTG 1 GCGTCCGGATATCTG 1499128 AGGCTCCACT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27 Consensus pattern (15 bp): GCGTCCGGATATCTG Found at i:1504592 original size:35 final size:36 Alignment explanation

Indices: 1504501--1504594 Score: 111 Period size: 35 Copynumber: 2.7 Consensus size: 36 1504491 CAGCATAATT * * * * * 1504501 AAAATGATGATGTTTATAGAACGAGCAACAGCTTTG 1 AAAATCATGATCTTTATAGAATGAACAACAGCATTG * 1504537 -AAATCATGATCTTTATAGAATGAACAATAGCATTG 1 AAAATCATGATCTTTATAGAATGAACAACAGCATTG * 1504572 AAAAT-ATGATTTTTATAGAATGA 1 AAAATCATGATCTTTATAGAATGA 1504595 TTTATTTTAA Statistics Matches: 50, Mismatches: 7, Indels: 3 0.83 0.12 0.05 Matches are distributed among these distances: 35 46 0.92 36 4 0.08 ACGTcount: A:0.43, C:0.09, G:0.17, T:0.32 Consensus pattern (36 bp): AAAATCATGATCTTTATAGAATGAACAACAGCATTG Found at i:1506415 original size:42 final size:42 Alignment explanation

Indices: 1506356--1506442 Score: 147 Period size: 42 Copynumber: 2.1 Consensus size: 42 1506346 TAAAAAGCAA * * * 1506356 TTTCTACGCAATCTGTGCATATTTCACTTGATATCAACATTC 1 TTTCTACACAATCTGTGCATATTTCACTCGATATCAACATCC 1506398 TTTCTACACAATCTGTGCATATTTCACTCGATATCAACATCC 1 TTTCTACACAATCTGTGCATATTTCACTCGATATCAACATCC 1506440 TTT 1 TTT 1506443 TAATTTGATA Statistics Matches: 42, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 42 42 1.00 ACGTcount: A:0.26, C:0.25, G:0.08, T:0.40 Consensus pattern (42 bp): TTTCTACACAATCTGTGCATATTTCACTCGATATCAACATCC Found at i:1509221 original size:14 final size:14 Alignment explanation

Indices: 1509204--1509232 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 1509194 ATGATACTAA 1509204 ACATGTACAGATAT 1 ACATGTACAGATAT 1509218 ACATGTACAGATAT 1 ACATGTACAGATAT 1509232 A 1 A 1509233 TATAATTTGG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28 Consensus pattern (14 bp): ACATGTACAGATAT Found at i:1517680 original size:11 final size:11 Alignment explanation

Indices: 1517664--1517689 Score: 52 Period size: 11 Copynumber: 2.4 Consensus size: 11 1517654 TACCTTTTGA 1517664 AAAACATATAC 1 AAAACATATAC 1517675 AAAACATATAC 1 AAAACATATAC 1517686 AAAA 1 AAAA 1517690 TTCATTAAGC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 15 1.00 ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15 Consensus pattern (11 bp): AAAACATATAC Done.