Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold601

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: 1259944
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29

Warning! 136746 characters in sequence are not A, C, G, or T


File 3 of 5

Found at i:254321 original size:13 final size:13

Alignment explanation

Indices: 254303--254355 Score: 54 Period size: 13 Copynumber: 3.9 Consensus size: 13 254293 CTTGTTTATG 254303 TTTTGTTTTTTGT 1 TTTTGTTTTTTGT 254316 TTTTGTTTTTTTGT 1 TTTTG-TTTTTTGT * 254330 GTTTT-TTTTTTAT 1 -TTTTGTTTTTTGT * 254343 TTATTTTTTTTTG 1 TT-TTGTTTTTTG 254356 GGGGGGGGGG Statistics Matches: 34, Mismatches: 2, Indels: 7 0.79 0.05 0.16 Matches are distributed among these distances: 12 2 0.06 13 14 0.41 14 14 0.41 15 4 0.12 ACGTcount: A:0.04, C:0.00, G:0.11, T:0.85 Consensus pattern (13 bp): TTTTGTTTTTTGT Found at i:254327 original size:14 final size:13 Alignment explanation

Indices: 254303--254355 Score: 61 Period size: 14 Copynumber: 3.9 Consensus size: 13 254293 CTTGTTTATG * 254303 TTTTGTTTTTTGT 1 TTTTTTTTTTTGT 254316 TTTTGTTTTTTTGT 1 TTTT-TTTTTTTGT * * 254330 GTTTTTTTTTTAT 1 TTTTTTTTTTTGT 254343 TTATTTTTTTTTG 1 TT-TTTTTTTTTG 254356 GGGGGGGGGG Statistics Matches: 33, Mismatches: 5, Indels: 3 0.80 0.12 0.07 Matches are distributed among these distances: 13 13 0.39 14 20 0.61 ACGTcount: A:0.04, C:0.00, G:0.11, T:0.85 Consensus pattern (13 bp): TTTTTTTTTTTGT Found at i:254332 original size:16 final size:14 Alignment explanation

Indices: 254303--254354 Score: 59 Period size: 15 Copynumber: 3.5 Consensus size: 14 254293 CTTGTTTATG * 254303 TTTTGTTTTTTGTT 1 TTTTTTTTTTTGTT 254317 TTTGTTTTTTTGTGTT 1 TTT-TTTTTTT-TGTT * 254333 TTTTTTTTATTTATT 1 TTTTTTTT-TTTGTT 254348 TTTTTTT 1 TTTTTTT 254355 GGGGGGGGGG Statistics Matches: 33, Mismatches: 2, Indels: 5 0.82 0.05 0.12 Matches are distributed among these distances: 14 3 0.09 15 21 0.64 16 9 0.27 ACGTcount: A:0.04, C:0.00, G:0.10, T:0.87 Consensus pattern (14 bp): TTTTTTTTTTTGTT Found at i:257773 original size:2 final size:2 Alignment explanation

Indices: 257766--257815 Score: 100 Period size: 2 Copynumber: 25.0 Consensus size: 2 257756 CAAAATAATT 257766 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 257808 GA GA GA GA 1 GA GA GA GA 257816 TATTTTTACC 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:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:260313 original size:2 final size:2 Alignment explanation

Indices: 260306--260336 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 260296 ACAAGACAGA 260306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 260337 NNNNNNNNNN Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:265634 original size:17 final size:17 Alignment explanation

Indices: 265612--265716 Score: 76 Period size: 17 Copynumber: 6.4 Consensus size: 17 265602 CCCCTTGGCC * 265612 TGGCCTGGCCTCAAAGT 1 TGGCCTGGCCTCAAAAT 265629 TGGCCTGGCCTC---AT 1 TGGCCTGGCCTCAAAAT ** 265643 T--TTTGGCCTCAAAAT 1 TGGCCTGGCCTCAAAAT * * * 265658 TGGTCTGGCCCCAAATTT 1 TGGCCTGGCCTCAAA-AT 265676 TGGCCTGGCCTCAAAAAT 1 TGGCCTGGCCTC-AAAAT * * * 265694 TGGCCTGGTCTCTAATT 1 TGGCCTGGCCTCAAAAT 265711 TGGCCT 1 TGGCCT 265717 CTTTAAAAAT Statistics Matches: 69, Mismatches: 12, Indels: 14 0.73 0.13 0.15 Matches are distributed among these distances: 12 7 0.10 14 2 0.03 15 3 0.04 17 31 0.45 18 23 0.33 19 3 0.04 ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31 Consensus pattern (17 bp): TGGCCTGGCCTCAAAAT Found at i:265683 original size:18 final size:18 Alignment explanation

Indices: 265653--265701 Score: 62 Period size: 18 Copynumber: 2.7 Consensus size: 18 265643 TTTTGGCCTC * 265653 AAAATTGGTCTGGCCCCA 1 AAAATTGGCCTGGCCCCA ** * 265671 AATTTTGGCCTGGCCTCA 1 AAAATTGGCCTGGCCCCA 265689 AAAATTGGCCTGG 1 AAAATTGGCCTGG 265702 TCTCTAATTT Statistics Matches: 25, Mismatches: 6, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 18 25 1.00 ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27 Consensus pattern (18 bp): AAAATTGGCCTGGCCCCA Found at i:265716 original size:35 final size:35 Alignment explanation

Indices: 265612--265701 Score: 102 Period size: 29 Copynumber: 2.7 Consensus size: 35 265602 CCCCTTGGCC * * 265612 TGGCCTGGCCTCAAAGTTGGCCTGGCCTC--ATTT 1 TGGCCTGGCCTCAAAATTGGCCTGGCCCCAAATTT * 265645 T----TGGCCTCAAAATTGGTCTGGCCCCAAATTT 1 TGGCCTGGCCTCAAAATTGGCCTGGCCCCAAATTT 265676 TGGCCTGGCCTCAAAAATTGGCCTGG 1 TGGCCTGGCCTC-AAAATTGGCCTGG 265702 TCTCTAATTT Statistics Matches: 46, Mismatches: 4, Indels: 11 0.75 0.07 0.18 Matches are distributed among these distances: 29 21 0.46 31 5 0.11 33 1 0.02 35 7 0.15 36 12 0.26 ACGTcount: A:0.18, C:0.28, G:0.26, T:0.29 Consensus pattern (35 bp): TGGCCTGGCCTCAAAATTGGCCTGGCCCCAAATTT Found at i:266808 original size:17 final size:17 Alignment explanation

Indices: 266788--266892 Score: 112 Period size: 17 Copynumber: 6.4 Consensus size: 17 266778 ATTTTGGAAG 266788 AGGCCAAATTTGAGGCC 1 AGGCCAAATTTGAGGCC * 266805 AGGCCAATTTTTGAGGCC 1 AGGCCAA-ATTTGAGGCC * 266823 AGGCCAAAATTTGGGGCC 1 AGGCC-AAATTTGAGGCC * 266841 AGGCCAATTTTGAGGCC 1 AGGCCAAATTTGAGGCC * 266858 A----AAA-GTGAGGCC 1 AGGCCAAATTTGAGGCC * 266870 AGGCCAACTTTGAGGCC 1 AGGCCAAATTTGAGGCC 266887 AGGCCA 1 AGGCCA 266893 GGCCAATGGG Statistics Matches: 72, Mismatches: 9, Indels: 14 0.76 0.09 0.15 Matches are distributed among these distances: 12 8 0.11 13 2 0.03 16 2 0.03 17 31 0.43 18 27 0.38 19 2 0.03 ACGTcount: A:0.28, C:0.24, G:0.30, T:0.18 Consensus pattern (17 bp): AGGCCAAATTTGAGGCC Found at i:266874 original size:29 final size:30 Alignment explanation

Indices: 266823--266887 Score: 96 Period size: 29 Copynumber: 2.2 Consensus size: 30 266813 TTTTGAGGCC * * * 266823 AGGCCAAAATTTGGGGCCAGGCCAATTTTG 1 AGGCCAAAATGTGAGGCCAGGCCAACTTTG 266853 AGGCCAAAA-GTGAGGCCAGGCCAACTTTG 1 AGGCCAAAATGTGAGGCCAGGCCAACTTTG 266882 AGGCCA 1 AGGCCA 266888 GGCCAGGCCA Statistics Matches: 32, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 29 23 0.72 30 9 0.28 ACGTcount: A:0.29, C:0.23, G:0.31, T:0.17 Consensus pattern (30 bp): AGGCCAAAATGTGAGGCCAGGCCAACTTTG Found at i:270493 original size:11 final size:11 Alignment explanation

Indices: 270477--270514 Score: 58 Period size: 11 Copynumber: 3.5 Consensus size: 11 270467 ATATTGTGTA 270477 TTTTCAATTAC 1 TTTTCAATTAC 270488 TTTTCAATTAC 1 TTTTCAATTAC * * 270499 ATCTCAATTAC 1 TTTTCAATTAC 270510 TTTTC 1 TTTTC 270515 TCCAAGTTTA Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 11 23 1.00 ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53 Consensus pattern (11 bp): TTTTCAATTAC Found at i:281217 original size:25 final size:25 Alignment explanation

Indices: 281188--281307 Score: 231 Period size: 25 Copynumber: 4.8 Consensus size: 25 281178 AGACTACAGA 281188 GTATGGCTAATAACCATTTACAGGT 1 GTATGGCTAATAACCATTTACAGGT 281213 GTATGGCTAATAACCATTTACAGGT 1 GTATGGCTAATAACCATTTACAGGT 281238 GTATGGCTAATAACCATTTACAGGT 1 GTATGGCTAATAACCATTTACAGGT 281263 GTATGGCTAATAACCATTTACAGGT 1 GTATGGCTAATAACCATTTACAGGT * 281288 GTATGGCTAATAATCATTTA 1 GTATGGCTAATAACCATTTA 281308 AACTAGTTAA Statistics Matches: 94, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 25 94 1.00 ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33 Consensus pattern (25 bp): GTATGGCTAATAACCATTTACAGGT Found at i:289717 original size:43 final size:43 Alignment explanation

Indices: 289669--289764 Score: 174 Period size: 43 Copynumber: 2.2 Consensus size: 43 289659 TTGGGCCATT * 289669 TTGTGTTTGGTTATTTTGTTGGGGTACAGTTGGTACCGCTTTG 1 TTGTGTTTGGTTATTTTGTTGGGGTACAGTTGGTACCACTTTG 289712 TTGTGTTTGGTTATTTTGTTGGGGTACAGTTGGTACCACTTTG 1 TTGTGTTTGGTTATTTTGTTGGGGTACAGTTGGTACCACTTTG * 289755 TGGTGTTTGG 1 TTGTGTTTGG 289765 GCCGTTTTAT Statistics Matches: 51, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 43 51 1.00 ACGTcount: A:0.09, C:0.08, G:0.33, T:0.49 Consensus pattern (43 bp): TTGTGTTTGGTTATTTTGTTGGGGTACAGTTGGTACCACTTTG Found at i:299929 original size:22 final size:20 Alignment explanation

Indices: 299904--299947 Score: 52 Period size: 20 Copynumber: 2.1 Consensus size: 20 299894 CTGCTGTGAA 299904 ATTTAATATGAAGATAAATGGT 1 ATTTAATA--AAGATAAATGGT * * 299926 ATTTCATAAAGATATATGGT 1 ATTTAATAAAGATAAATGGT 299946 AT 1 AT 299948 CTCATAAATA Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 20 13 0.65 22 7 0.35 ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39 Consensus pattern (20 bp): ATTTAATAAAGATAAATGGT Found at i:299939 original size:20 final size:20 Alignment explanation

Indices: 299914--299955 Score: 66 Period size: 20 Copynumber: 2.1 Consensus size: 20 299904 ATTTAATATG * 299914 AAGATAAATGGTATTTCATA 1 AAGATAAATGGTATCTCATA * 299934 AAGATATATGGTATCTCATA 1 AAGATAAATGGTATCTCATA 299954 AA 1 AA 299956 TAAAAAATCA Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33 Consensus pattern (20 bp): AAGATAAATGGTATCTCATA Found at i:301756 original size:2 final size:2 Alignment explanation

Indices: 301749--301809 Score: 122 Period size: 2 Copynumber: 30.5 Consensus size: 2 301739 TAATATGCCC 301749 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 301791 AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG A 301810 TTTTCAAGTA Statistics Matches: 59, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 59 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:305842 original size:37 final size:35 Alignment explanation

Indices: 305763--305845 Score: 103 Period size: 35 Copynumber: 2.3 Consensus size: 35 305753 TTATCTATGC * 305763 AACATTTTGTCTATAGTGAGTTTAGAAACTATTAT 1 AACATTTTGTCTATAGTAAGTTTAGAAACTATTAT * * * 305798 AATATTTTGTCTATAGTAAGTTTATATATATTATTAT 1 AACATTTTGTCTATAGTAAGTTTAGA-A-ACTATTAT * 305835 GACATTTTGTC 1 AACATTTTGTC 305846 AACTGCAGAG Statistics Matches: 40, Mismatches: 6, Indels: 2 0.83 0.12 0.04 Matches are distributed among these distances: 35 23 0.57 36 1 0.03 37 16 0.40 ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48 Consensus pattern (35 bp): AACATTTTGTCTATAGTAAGTTTAGAAACTATTAT Found at i:309486 original size:30 final size:30 Alignment explanation

Indices: 309452--309511 Score: 84 Period size: 30 Copynumber: 2.0 Consensus size: 30 309442 TTTTGATGAC 309452 AGTTTAATTAAGATGTACATATTTGTGATA 1 AGTTTAATTAAGATGTACATATTTGTGATA * * * * 309482 AGTTTAATTGATATGTTCATCTTTGTGATA 1 AGTTTAATTAAGATGTACATATTTGTGATA 309512 TCAGCGGGAG Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 30 26 1.00 ACGTcount: A:0.32, C:0.05, G:0.17, T:0.47 Consensus pattern (30 bp): AGTTTAATTAAGATGTACATATTTGTGATA Found at i:312787 original size:17 final size:17 Alignment explanation

Indices: 312765--312800 Score: 63 Period size: 17 Copynumber: 2.1 Consensus size: 17 312755 GTGGAGTGTG * 312765 ATAAATATCAGAATGAT 1 ATAAATAACAGAATGAT 312782 ATAAATAACAGAATGAT 1 ATAAATAACAGAATGAT 312799 AT 1 AT 312801 GATCACATTG Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28 Consensus pattern (17 bp): ATAAATAACAGAATGAT Found at i:313326 original size:38 final size:38 Alignment explanation

Indices: 312977--313327 Score: 431 Period size: 38 Copynumber: 9.2 Consensus size: 38 312967 TACTACAGAC * 312977 TGTT-TGTTTTACA-AACTGTAAATGTAATGCTGAGGG 1 TGTTCTGTTTTACAGGACTGTAAATGTAATGCTGAGGG ** 313013 TGTTCCT-TTTTACAGGACTGTAAATGTAATATTGAGGG 1 TGTT-CTGTTTTACAGGACTGTAAATGTAATGCTGAGGG * * 313051 TGTTCTTTTCCTTTTACAGGACTGTAAATGTAATGCCGAGGG 1 TGTTC---T-GTTTTACAGGACTGTAAATGTAATGCTGAGGG * 313093 TGTTCAGTTTTACAGGACTGTAAATGTAATGCTGAGGG 1 TGTTCTGTTTTACAGGACTGTAAATGTAATGCTGAGGG * * * 313131 TGTTCTTTTTTACAGGACTGTAAATGAAATGCGGAGGG 1 TGTTCTGTTTTACAGGACTGTAAATGTAATGCTGAGGG * * * * ** 313169 TGTTCTGATTTACAGGATTGTTAATGTTATTATGAGGG 1 TGTTCTGTTTTACAGGACTGTAAATGTAATGCTGAGGG * 313207 TGTTCTGTTCTACAGGACTGTAAATGTAATGCTGAGGG 1 TGTTCTGTTTTACAGGACTGTAAATGTAATGCTGAGGG * * * ** 313245 TGTTCTGTTTTACAGGATTGTTTAA-GTTATTATGAGGG 1 TGTTCTGTTTTACAGGACTG-TAAATGTAATGCTGAGGG 313283 TGTTCTGTTTTACAGGACTGTAAATGTAATGCTGAGGG 1 TGTTCTGTTTTACAGGACTGTAAATGTAATGCTGAGGG 313321 TGTTCTG 1 TGTTCTG 313328 AACCGGGACA Statistics Matches: 265, Mismatches: 40, Indels: 18 0.82 0.12 0.06 Matches are distributed among these distances: 36 4 0.02 37 11 0.04 38 213 0.80 39 3 0.01 40 1 0.00 42 33 0.12 ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39 Consensus pattern (38 bp): TGTTCTGTTTTACAGGACTGTAAATGTAATGCTGAGGG Found at i:316642 original size:27 final size:27 Alignment explanation

Indices: 316605--316775 Score: 288 Period size: 27 Copynumber: 6.3 Consensus size: 27 316595 CGACTCAGTA 316605 ACAAGTCATTATCTCTATAAACTCAAC 1 ACAAGTCATTATCTCTATAAACTCAAC 316632 ACAAGTCATTATCTCTATAAACTCAAC 1 ACAAGTCATTATCTCTATAAACTCAAC * * * 316659 ACAAGTCATTATCTTTGTAAACTCAAG 1 ACAAGTCATTATCTCTATAAACTCAAC 316686 ACAAGTCATTATCTCTATAAACTCAAC 1 ACAAGTCATTATCTCTATAAACTCAAC * 316713 ACAAGTCATTATCTTTATAAACTCAAC 1 ACAAGTCATTATCTCTATAAACTCAAC * 316740 ACAAGTCATTATCTTTATAAACTCAAC 1 ACAAGTCATTATCTCTATAAACTCAAC * 316767 AAAAGTCAT 1 ACAAGTCAT 316776 CTATACTACG Statistics Matches: 136, Mismatches: 8, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 27 136 1.00 ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31 Consensus pattern (27 bp): ACAAGTCATTATCTCTATAAACTCAAC Found at i:319497 original size:94 final size:95 Alignment explanation

Indices: 319250--319684 Score: 490 Period size: 94 Copynumber: 4.4 Consensus size: 95 319240 TTCTTGATTT * * * 319250 CAGCCTGTGACAGCTGTGTAAAAATCACATCCTGCTGGATGATGTGTTGTGTATCTGTCATTGGT 1 CAGCCTGTGACAGCTGTGT-----TCACATCCTGCTGGATGATGTGTTATGTTTCTGACATTGGT * * 319315 TCCTGGTTGTAATGTATATATATCTCTGTTATTTGTTC 61 CCCTGGTTG--ATGTATATATATCTCTGTT-TTTTTTC 319353 CAGCCTGTGACAGCTGTGTAAAAATCACATCCTGCTGGATGATGTGTTATGTTTCTGACATTGGG 1 CAGCCTGTGACAGCTGTGT-----TCACATCCTGCTGGATGATGTGTTATGTTTCTGACATT-GG * 319418 TCCCT-GTTG-TGT-TATATAT-TTTGTATTTATTTTC 60 TCCCTGGTTGATGTATATATATCTCTGT-TTT-TTTTC * * * * * 319452 TAGCCTGTGACAGCTGTGTTCACACCCTGCTGGATGATGTGTTATGTTTTTGTCATTGGTTCCTG 1 CAGCCTGTGACAGCTGTGTTCACATCCTGCTGGATGATGTGTTATGTTTCTGACATTGGTCCCTG 319517 GTTGTAATGTATATATATCTCTGTTTTTTGTTC 66 GTTG--ATGTATATATATCTCTGTTTTTT-TTC * 319550 CAGCCTGTGACAGCTGTGTTTACATCCTGCTGGATGATGTGTTATGTTTCTGACATTGGGTCCCT 1 CAGCCTGTGACAGCTGTGTTCACATCCTGCTGGATGATGTGTTATGTTTCTGACATT-GGTCCCT * 319615 -GTTG-TGT-TATATAT-TTTGTATTTATTTTC 65 GGTTGATGTATATATATCTCTGT-TTT-TTTTC * 319644 TAGCCTGTGACAGCTGTGTTCACATCCTGCTGGATGATGTG 1 CAGCCTGTGACAGCTGTGTTCACATCCTGCTGGATGATGTG 319685 GAGGCCTTAC Statistics Matches: 298, Mismatches: 21, Indels: 35 0.84 0.06 0.10 Matches are distributed among these distances: 93 10 0.03 94 91 0.31 95 5 0.02 97 5 0.02 98 75 0.25 99 40 0.13 100 3 0.01 103 63 0.21 104 6 0.02 ACGTcount: A:0.18, C:0.17, G:0.23, T:0.43 Consensus pattern (95 bp): CAGCCTGTGACAGCTGTGTTCACATCCTGCTGGATGATGTGTTATGTTTCTGACATTGGTCCCTG GTTGATGTATATATATCTCTGTTTTTTTTC Found at i:319654 original size:192 final size:193 Alignment explanation

Indices: 319247--319684 Score: 727 Period size: 192 Copynumber: 2.2 Consensus size: 193 319237 CTGTTCTTGA * 319247 TTTC-AGCCTGTGACAGCTGTGTAAAAATCACATCCTGCTGGATGATGTGTTGTGTATCTGTCAT 1 TTTCTAGCCTGTGACAGCTGTGT-----TCACATCCTGCTGGATGATGTGTTATGTATCTGTCAT 319311 TGGTTCCTGGTTGTAATGTATATATATCTCTGTTATTTGTTCCAGCCTGTGACAGCTGTGTAAAA 61 TGGTTCCTGGTTGTAATGTATATATATCTCTGTTATTTGTTCCAGCCTGTGACAGCTGTGT---- 319376 ATCACATCCTGCTGGATGATGTGTTATGTTTCTGACATTGGGTCCCTGTTGTGTTATATATTTTG 122 ATCACATCCTGCTGGATGATGTGTTATGTTTCTGACATTGGGTCCCTGTTGTGTTATATATTTTG 319441 TATTTAT 187 TATTTAT * * * 319448 TTTCTAGCCTGTGACAGCTGTGTTCACACCCTGCTGGATGATGTGTTATGTTTTTGTCATTGGTT 1 TTTCTAGCCTGTGACAGCTGTGTTCACATCCTGCTGGATGATGTGTTATGTATCTGTCATTGGTT * * 319513 CCTGGTTGTAATGTATATATATCTCTGTTTTTTGTTCCAGCCTGTGACAGCTGTGT-TTACATCC 66 CCTGGTTGTAATGTATATATATCTCTGTTATTTGTTCCAGCCTGTGACAGCTGTGTATCACATCC 319577 TGCTGGATGATGTGTTATGTTTCTGACATTGGGTCCCTGTTGTGTTATATATTTTGTATTTAT 131 TGCTGGATGATGTGTTATGTTTCTGACATTGGGTCCCTGTTGTGTTATATATTTTGTATTTAT 319640 TTTCTAGCCTGTGACAGCTGTGTTCACATCCTGCTGGATGATGTG 1 TTTCTAGCCTGTGACAGCTGTGTTCACATCCTGCTGGATGATGTG 319685 GAGGCCTTAC Statistics Matches: 229, Mismatches: 7, Indels: 11 0.93 0.03 0.04 Matches are distributed among these distances: 192 114 0.50 197 93 0.41 201 4 0.02 202 18 0.08 ACGTcount: A:0.18, C:0.17, G:0.23, T:0.43 Consensus pattern (193 bp): TTTCTAGCCTGTGACAGCTGTGTTCACATCCTGCTGGATGATGTGTTATGTATCTGTCATTGGTT CCTGGTTGTAATGTATATATATCTCTGTTATTTGTTCCAGCCTGTGACAGCTGTGTATCACATCC TGCTGGATGATGTGTTATGTTTCTGACATTGGGTCCCTGTTGTGTTATATATTTTGTATTTAT Found at i:322530 original size:22 final size:22 Alignment explanation

Indices: 322502--322648 Score: 204 Period size: 22 Copynumber: 6.7 Consensus size: 22 322492 TGGACAGGAC * 322502 AGAAGTGGGTCAGTATCTATAA 1 AGAAGTGGGTCAGTATCTATAT * * 322524 AGAAGTGTGTCAGTATCTCTAT 1 AGAAGTGGGTCAGTATCTATAT 322546 AGAAGTGGGTCAGTATCTATAT 1 AGAAGTGGGTCAGTATCTATAT * * 322568 AGAAGTGTGTCAGTATCTATAA 1 AGAAGTGGGTCAGTATCTATAT * * 322590 AGAAGTGGGTCAGTGTCTCTAT 1 AGAAGTGGGTCAGTATCTATAT * * 322612 AGATGTGGGTCAGTATCTCTAT 1 AGAAGTGGGTCAGTATCTATAT * 322634 AGAAGTGGGCCAGTA 1 AGAAGTGGGTCAGTA 322649 CACTCAGTAT Statistics Matches: 110, Mismatches: 15, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 22 110 1.00 ACGTcount: A:0.30, C:0.12, G:0.28, T:0.31 Consensus pattern (22 bp): AGAAGTGGGTCAGTATCTATAT Found at i:322585 original size:66 final size:66 Alignment explanation

Indices: 322502--322648 Score: 240 Period size: 66 Copynumber: 2.2 Consensus size: 66 322492 TGGACAGGAC * 322502 AGAAGTGGGTCAGTATCTATAAAGAAGTGTGTCAGTATCTCTATAGAAGTGGGTCAGTATCTATA 1 AGAAGTGGGTCAGTATCTATAAAGAAGTGGGTCAGTATCTCTATAGAAGTGGGTCAGTATCTATA 322567 T 66 T * * * * 322568 AGAAGTGTGTCAGTATCTATAAAGAAGTGGGTCAGTGTCTCTATAGATGTGGGTCAGTATCTCTA 1 AGAAGTGGGTCAGTATCTATAAAGAAGTGGGTCAGTATCTCTATAGAAGTGGGTCAGTATCTATA 322633 T 66 T * 322634 AGAAGTGGGCCAGTA 1 AGAAGTGGGTCAGTA 322649 CACTCAGTAT Statistics Matches: 74, Mismatches: 7, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 66 74 1.00 ACGTcount: A:0.30, C:0.12, G:0.28, T:0.31 Consensus pattern (66 bp): AGAAGTGGGTCAGTATCTATAAAGAAGTGGGTCAGTATCTCTATAGAAGTGGGTCAGTATCTATA T Found at i:322753 original size:53 final size:53 Alignment explanation

Indices: 322670--323360 Score: 1301 Period size: 53 Copynumber: 13.0 Consensus size: 53 322660 TATACTTTTG * * 322670 AGTGATCATAGAGCAGTTAGTGTTTATCTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC * 322723 AGTGATCATAGAGCAGTTAGTGTTTGTCTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC * 322776 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGCC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC * 322829 AGTGATCATAGAGCAGTTAGTGTTTGTCTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC * 322882 AGTGATCATAGAGCAGTTAGTGTTTGTCTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 322935 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 322988 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 323041 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 323094 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC * 323147 AGTGATCATAGAGCAGTTAGTGTTTGTCTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC * 323200 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGCC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 323253 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC * 323306 AGTGATCATAGAGCAGTTAGTGTTTGTCTGATGAGATACTGCATGATACAGAC 1 AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC 323359 AG 1 AG 323361 CATATCAACT Statistics Matches: 627, Mismatches: 11, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 53 627 1.00 ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30 Consensus pattern (53 bp): AGTGATCATAGAGCAGTTAGTGTTTGTGTGATGAGATACTGCATGATACAGAC Found at i:324289 original size:44 final size:44 Alignment explanation

Indices: 324239--324340 Score: 116 Period size: 44 Copynumber: 2.3 Consensus size: 44 324229 TTGCTGGCAT * * 324239 TATTGTA-ATCATTTAAAGTTTATATTGCTGCCATTTTACATTTA 1 TATTGTAGA-CATTTAAAGTTTATAGTGCTGCCATTTCACATTTA * * * * ** 324283 TATTGTAGACGTTTTAGGTTTATAGTGCTGGCATTTCAGGTTTA 1 TATTGTAGACATTTAAAGTTTATAGTGCTGCCATTTCACATTTA 324327 TATTGTAGACATTT 1 TATTGTAGACATTT 324341 TAGGTTTTTG Statistics Matches: 48, Mismatches: 9, Indels: 2 0.81 0.15 0.03 Matches are distributed among these distances: 44 47 0.98 45 1 0.02 ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48 Consensus pattern (44 bp): TATTGTAGACATTTAAAGTTTATAGTGCTGCCATTTCACATTTA Found at i:324345 original size:22 final size:22 Alignment explanation

Indices: 324256--324347 Score: 89 Period size: 22 Copynumber: 4.2 Consensus size: 22 324246 ATCATTTAAA * * 324256 GTTTATATTGCTGCCATTTTAC 1 GTTTATATTGCTGACATTTTAG * * 324278 ATTTATATTG-TAGACGTTTTAG 1 GTTTATATTGCT-GACATTTTAG * * * 324300 GTTTATAGTGCTGGCATTTCAG 1 GTTTATATTGCTGACATTTTAG 324322 GTTTATATTG-TAGACATTTTAG 1 GTTTATATTGCT-GACATTTTAG 324344 GTTT 1 GTTT 324348 TTGTTTAAGG Statistics Matches: 55, Mismatches: 12, Indels: 6 0.75 0.16 0.08 Matches are distributed among these distances: 21 2 0.04 22 52 0.95 23 1 0.02 ACGTcount: A:0.22, C:0.10, G:0.20, T:0.49 Consensus pattern (22 bp): GTTTATATTGCTGACATTTTAG Found at i:324362 original size:44 final size:44 Alignment explanation

Indices: 324256--324347 Score: 130 Period size: 44 Copynumber: 2.1 Consensus size: 44 324246 ATCATTTAAA * * * ** * 324256 GTTTATATTGCTGCCATTTTACATTTATATTGTAGACGTTTTAG 1 GTTTATAGTGCTGGCATTTCAGGTTTATATTGTAGACATTTTAG 324300 GTTTATAGTGCTGGCATTTCAGGTTTATATTGTAGACATTTTAG 1 GTTTATAGTGCTGGCATTTCAGGTTTATATTGTAGACATTTTAG 324344 GTTT 1 GTTT 324348 TTGTTTAAGG Statistics Matches: 42, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 44 42 1.00 ACGTcount: A:0.22, C:0.10, G:0.20, T:0.49 Consensus pattern (44 bp): GTTTATAGTGCTGGCATTTCAGGTTTATATTGTAGACATTTTAG Found at i:325445 original size:38 final size:38 Alignment explanation

Indices: 325391--325539 Score: 174 Period size: 38 Copynumber: 3.9 Consensus size: 38 325381 GTACCTGATC * * 325391 AAGGCCAAGAGGTGAGTCTGAATAAGTCTGTGGTAATA 1 AAGGCCAAAAGATGAGTCTGAATAAGTCTGTGGTAATA * 325429 AAGGCTAAAAGATGAGTCTGAATAAGTCTGTGGTAATA 1 AAGGCCAAAAGATGAGTCTGAATAAGTCTGTGGTAATA * * * * * 325467 AAGGCCAAAAGGTGAGTCGGAATAAGTCTGTGTTGATC 1 AAGGCCAAAAGATGAGTCTGAATAAGTCTGTGGTAATA ** * ** 325505 AAGGCCAGGAGGTGAGTCTGGGTAAGTCTG-GGTAA 1 AAGGCCAAAAGATGAGTCTGAATAAGTCTGTGGTAA 325540 GTCTGGGGTG Statistics Matches: 95, Mismatches: 16, Indels: 1 0.85 0.14 0.01 Matches are distributed among these distances: 37 3 0.03 38 92 0.97 ACGTcount: A:0.33, C:0.11, G:0.33, T:0.23 Consensus pattern (38 bp): AAGGCCAAAAGATGAGTCTGAATAAGTCTGTGGTAATA Found at i:325534 original size:10 final size:10 Alignment explanation

Indices: 325519--325546 Score: 56 Period size: 10 Copynumber: 2.8 Consensus size: 10 325509 CCAGGAGGTG 325519 AGTCTGGGTA 1 AGTCTGGGTA 325529 AGTCTGGGTA 1 AGTCTGGGTA 325539 AGTCTGGG 1 AGTCTGGG 325547 GTGATCAAGG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 18 1.00 ACGTcount: A:0.18, C:0.11, G:0.43, T:0.29 Consensus pattern (10 bp): AGTCTGGGTA Found at i:325560 original size:48 final size:48 Alignment explanation

Indices: 325489--325584 Score: 165 Period size: 48 Copynumber: 2.0 Consensus size: 48 325479 TGAGTCGGAA * * 325489 TAAGTCTGTGTTGATCAAGGCCAGGAGGTGAGTCTGGGTAAGTCTGGG 1 TAAGTCTGGGGTGATCAAGGCCAGGAGGTGAGTCTGGGTAAGTCTGGG * 325537 TAAGTCTGGGGTGATCAAGGCCAGGAGGTGAGTCTGGGTAATTCTGGG 1 TAAGTCTGGGGTGATCAAGGCCAGGAGGTGAGTCTGGGTAAGTCTGGG 325585 GTGATCAAGG Statistics Matches: 45, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 48 45 1.00 ACGTcount: A:0.21, C:0.12, G:0.41, T:0.26 Consensus pattern (48 bp): TAAGTCTGGGGTGATCAAGGCCAGGAGGTGAGTCTGGGTAAGTCTGGG Found at i:326035 original size:10 final size:10 Alignment explanation

Indices: 326020--326047 Score: 56 Period size: 10 Copynumber: 2.8 Consensus size: 10 326010 CCAGGAGGTG 326020 AGTCTGGGTA 1 AGTCTGGGTA 326030 AGTCTGGGTA 1 AGTCTGGGTA 326040 AGTCTGGG 1 AGTCTGGG 326048 GTGATCAAGG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 18 1.00 ACGTcount: A:0.18, C:0.11, G:0.43, T:0.29 Consensus pattern (10 bp): AGTCTGGGTA Found at i:327014 original size:2 final size:2 Alignment explanation

Indices: 327007--327043 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 326997 TGAAAATAAT 327007 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 327044 GTTGTACATG Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:332520 original size:65 final size:65 Alignment explanation

Indices: 332422--332913 Score: 867 Period size: 65 Copynumber: 7.4 Consensus size: 65 332412 GTACACAGAT 332422 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA * * 332487 GATAAGTACTATGTCGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTGTTTTATTACACA 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC- 332552 GA 65 -A 332554 TGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC 1 -GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC 332619 A 65 A 332620 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA * * 332685 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCAATGTTTTATTACACA 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC- 332750 GA 65 -A 332752 TGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC 1 -GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC 332817 A 65 A 332818 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC- 332883 GA 65 -A 332885 TGATAAGTACTATGTGGGTCTGGACTTTG 1 -GATAAGTACTATGTGGGTCTGGACTTTG 332914 CCTTTAACCT Statistics Matches: 410, Mismatches: 8, Indels: 15 0.95 0.02 0.03 Matches are distributed among these distances: 65 253 0.62 66 2 0.00 67 3 0.01 68 152 0.37 ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37 Consensus pattern (65 bp): GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA Found at i:332622 original size:133 final size:132 Alignment explanation

Indices: 332422--332913 Score: 875 Period size: 133 Copynumber: 3.7 Consensus size: 132 332412 GTACACAGAT 332422 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC- 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA * * 332486 A-GATAAGTACTATGTCGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTGTTTTATTACA 66 ATGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACA 332550 CAGA 131 C--A 332554 TGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC 1 -GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC 332619 -A-GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTAC 65 AATGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTAC 332682 ACA 130 ACA * * 332685 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCAATGTTTTATTACACA 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA 332750 GATGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTAC 66 -ATGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTAC 332815 ACA 130 ACA 332818 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA 332883 GATGATAAGTACTATGTGGGTCTGGACTTTG 66 -ATGATAAGTACTATGTGGGTCTGGACTTTG 332914 CCTTTAACCT Statistics Matches: 350, Mismatches: 6, Indels: 6 0.97 0.02 0.02 Matches are distributed among these distances: 130 62 0.18 131 1 0.00 132 1 0.00 133 286 0.82 ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37 Consensus pattern (132 bp): GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA ATGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACA CA Found at i:332742 original size:198 final size:198 Alignment explanation

Indices: 332422--332913 Score: 939 Period size: 198 Copynumber: 2.5 Consensus size: 198 332412 GTACACAGAT 332422 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA * * 332487 GATAAGTACTATGTCGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTGTTTTATTACACA 66 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCAATGTTTTATTACACA 332552 GATGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTAC 131 GATGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTAC 332617 ACA 196 ACA 332620 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA 332685 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCAATGTTTTATTACACA 66 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCAATGTTTTATTACACA 332750 GATGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTAC 131 GATGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTAC 332815 ACA 196 ACA 332818 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA 1 GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACAC- 332883 GATGATAAGTACTATGTGGGTCTGGACTTTG 65 -A-GATAAGTACTATGTGGGTCTGGACTTTG 332914 CCTTTAACCT Statistics Matches: 289, Mismatches: 2, Indels: 3 0.98 0.01 0.01 Matches are distributed among these distances: 198 260 0.90 200 1 0.00 201 28 0.10 ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37 Consensus pattern (198 bp): GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTACACA GATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCAATGTTTTATTACACA GATGATAAGTACTATGTGGGTCTGGACTTTGATTACATAGAGCTAACTGTCCATTATTTTATTAC ACA Found at i:335737 original size:10 final size:10 Alignment explanation

Indices: 335707--335731 Score: 50 Period size: 10 Copynumber: 2.5 Consensus size: 10 335697 TGAGCTTTTC 335707 TGTTCACCGT 1 TGTTCACCGT 335717 TGTTCACCGT 1 TGTTCACCGT 335727 TGTTC 1 TGTTC 335732 GTCGTTCGTC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 15 1.00 ACGTcount: A:0.08, C:0.28, G:0.20, T:0.44 Consensus pattern (10 bp): TGTTCACCGT Found at i:340293 original size:15 final size:15 Alignment explanation

Indices: 340273--340329 Score: 80 Period size: 15 Copynumber: 3.8 Consensus size: 15 340263 GCACCTATTC * 340273 TGTTTCGC-CCTGAGA 1 TGTTTCGCACCT-CGA * 340288 TGTTTCCCACCTCGA 1 TGTTTCGCACCTCGA 340303 TGTTTCGCACCTCGA 1 TGTTTCGCACCTCGA 340318 TGTTTCGCACCT 1 TGTTTCGCACCT 340330 GCATCGGAGC Statistics Matches: 38, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 15 35 0.92 16 3 0.08 ACGTcount: A:0.12, C:0.33, G:0.19, T:0.35 Consensus pattern (15 bp): TGTTTCGCACCTCGA Found at i:343142 original size:24 final size:23 Alignment explanation

Indices: 343110--343154 Score: 63 Period size: 23 Copynumber: 1.9 Consensus size: 23 343100 TTCACAAAGC 343110 TGTCATAAGATTTATCATAAGACA 1 TGTCATAAGA-TTATCATAAGACA * * 343134 TGTCTTAAGATTGTCATAAGA 1 TGTCATAAGATTATCATAAGA 343155 TTTGACTTAT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 23 10 0.53 24 9 0.47 ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36 Consensus pattern (23 bp): TGTCATAAGATTATCATAAGACA Found at i:343163 original size:23 final size:23 Alignment explanation

Indices: 343115--343183 Score: 75 Period size: 23 Copynumber: 3.0 Consensus size: 23 343105 AAAGCTGTCA * * 343115 TAAGATTTATCATAAGACATGTCT 1 TAAGA-TTATCATAAGATATGACT * * 343139 TAAGATTGTCATAAGATTTGACT 1 TAAGATTATCATAAGATATGACT * * 343162 TATGATTATCATTAGATATGAC 1 TAAGATTATCATAAGATATGAC 343184 ATAGCTGTTT Statistics Matches: 37, Mismatches: 8, Indels: 1 0.80 0.17 0.02 Matches are distributed among these distances: 23 32 0.86 24 5 0.14 ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39 Consensus pattern (23 bp): TAAGATTATCATAAGATATGACT Found at i:351709 original size:177 final size:175 Alignment explanation

Indices: 351424--352036 Score: 725 Period size: 177 Copynumber: 3.4 Consensus size: 175 351414 GCTATTATTT * * * * * * 351424 GTCCTATCTTCACCAAACTTGCATGGATGATGCATC-T-GGACCTACTTATGGACTTGA-AAGAC 1 GTCCTAACTTCACCAAACTTGCATGGATGATGCGTCTTATGA--TACTGATGCACCTGACAAG-C * * * ** * * * * 351486 TTGGATGCTGAATCTGGGTC-CTAAATTTCAGATGCTGGAGGAGGTTAAGGTTGTTGGACCAGGT 63 TTGAATGCTGAATCTGAG-CAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTT-TTAGAGCTGGT * 351550 TAAAGTTTTTGTTGCAGGTGCCCAT-TGATAGCA-ATATCTAAGTTACTACTG 126 TAAAGTTTTTGTTGCAGGTGCCC-TCTGAT-G-ATATATCTTAGTTACTACTG * 351601 GTCCTAACTTCACCAAACTTGTATGGATGATGCGTCTTATGATACTGATGCACCTGACAAGCTTG 1 GTCCTAACTTCACCAAACTTGCATGGATGATGCGTCTTATGATACTGATGCACCTGACAAGCTTG * 351666 AATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCTGGTTAAA 66 AATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGG-TTTTAGAGCTGGTTAAA 351731 GTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTG 130 GTTTTTGTTGCAGGTGCCCTCTGATGA-TATATCTTAGTTACTACTG * * * 351778 GTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAAGCTTG 1 GTCCTAACTTCACCAAACTTGCATGGATGATGCGTCTTATGATACTGATGCACCTGACAAGCTTG 351843 AATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAAA 66 AATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTT-AGAGCTGG-T--- *** * * * * 351908 TAAAGTTTTTGAAACAGGTGCCCTCTGATGATGGTATCTTGGTTATTACTT 126 TAAAGTTTTTGTTGCAGGTGCCCTCTGATGAT-ATATCTTAGTTACTACTG * * * * * * 351959 GTCCTTACTTCACCAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCTGACAGGCTTG 1 GTCCTAACTTCACCAAACTTGCATGGATGATGCGTCTTATGATACTGATGCACCTGACAAGCTTG * 352024 AATGCTGAGTCTG 66 AATGCTGAATCTG 352037 GTTTCGGATG Statistics Matches: 388, Mismatches: 34, Indels: 24 0.87 0.08 0.05 Matches are distributed among these distances: 175 1 0.00 176 7 0.02 177 256 0.66 178 7 0.02 179 2 0.01 180 1 0.00 181 114 0.29 ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33 Consensus pattern (175 bp): GTCCTAACTTCACCAAACTTGCATGGATGATGCGTCTTATGATACTGATGCACCTGACAAGCTTG AATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAGAGCTGGTTAAAG TTTTTGTTGCAGGTGCCCTCTGATGATATATCTTAGTTACTACTG Found at i:352674 original size:20 final size:20 Alignment explanation

Indices: 352651--352693 Score: 68 Period size: 20 Copynumber: 2.1 Consensus size: 20 352641 TATGATATAG 352651 TATTGTATGATATGAAACAA 1 TATTGTATGATATGAAACAA * * 352671 TATTGTTTGATATGATACAA 1 TATTGTATGATATGAAACAA 352691 TAT 1 TAT 352694 GATATCTTAT Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42 Consensus pattern (20 bp): TATTGTATGATATGAAACAA Found at i:354159 original size:20 final size:20 Alignment explanation

Indices: 354136--354178 Score: 68 Period size: 20 Copynumber: 2.1 Consensus size: 20 354126 TATGATATAG 354136 TATTGTATGATATGAAACAA 1 TATTGTATGATATGAAACAA * * 354156 TATTGTTTGATATGATACAA 1 TATTGTATGATATGAAACAA 354176 TAT 1 TAT 354179 GATATCTTAT Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42 Consensus pattern (20 bp): TATTGTATGATATGAAACAA Found at i:354451 original size:15 final size:15 Alignment explanation

Indices: 354418--354564 Score: 64 Period size: 15 Copynumber: 9.3 Consensus size: 15 354408 ATATTCTATA * ** 354418 ATATTGTATCATACA 1 ATATTGTATAATATG 354433 ATATTGTATAATATG 1 ATATTGTATAATATG 354448 ATATTGGTTTCAGTAATATAG 1 ATATT-G--T-A-TAATAT-G * * * 354469 A-ATTATATCACATG 1 ATATTGTATAATATG * 354483 AAATTGTATAATATG 1 ATATTGTATAATATG * * 354498 ATATTGTAGTATTTTATA 1 ATATTGTA-TA--ATATG * * 354516 ATATTGTATCATACG 1 ATATTGTATAATATG * * 354531 ATAGTGTATGATATG 1 ATATTGTATAATATG * 354546 ATATTGGT-TTATATG 1 ATATT-GTATAATATG 354561 ATAT 1 ATAT 354565 ATTATCATAT Statistics Matches: 100, Mismatches: 21, Indels: 22 0.70 0.15 0.15 Matches are distributed among these distances: 14 2 0.02 15 66 0.66 16 6 0.06 17 2 0.02 18 12 0.12 19 1 0.01 20 9 0.09 21 2 0.02 ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44 Consensus pattern (15 bp): ATATTGTATAATATG Found at i:354493 original size:50 final size:49 Alignment explanation

Indices: 354435--354600 Score: 153 Period size: 50 Copynumber: 3.4 Consensus size: 49 354425 ATCATACAAT 354435 ATTGTATAATATGATATTGGTTTCAGTA-ATATAGAATTATATCACATGAA 1 ATTGTATAATATGATATTGGTTT-AGTATATATA-AATTATATCACATGAA * * * * * 354485 ATTGTATAATATGATATT-G--TAGTATTTTATAATATTGTATCATACGAT 1 ATTGTATAATATGATATTGGTTTAGTA-TATATAA-ATTATATCACATGAA * * * * 354533 AGTGTATGATATGATATTGGTTTA-TATGATATATTATCATATCACATGAA 1 ATTGTATAATATGATATTGGTTTAGTAT-ATATA-AATTATATCACATGAA * 354583 ATTGTATTATATGATATT 1 ATTGTATAATATGATATT 354601 ATAATATATA Statistics Matches: 92, Mismatches: 16, Indels: 16 0.74 0.13 0.13 Matches are distributed among these distances: 46 4 0.04 47 2 0.02 48 31 0.34 49 3 0.03 50 50 0.54 51 2 0.02 ACGTcount: A:0.37, C:0.05, G:0.14, T:0.45 Consensus pattern (49 bp): ATTGTATAATATGATATTGGTTTAGTATATATAAATTATATCACATGAA Found at i:354525 original size:98 final size:96 Alignment explanation

Indices: 354401--354600 Score: 285 Period size: 98 Copynumber: 2.1 Consensus size: 96 354391 CTATGATACA * 354401 ATATTGTATATTCTATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTCAGTA-AT 1 ATATTGTATATTCTATAATATTGTATCATACAATAGTGTATAATATGATATTGGTTT-A-TAGAT * 354465 ATAGAATTATATCACATGAAATTGTATAATATG 64 ATAGAATCATATCACATGAAATTGTATAATATG * * * 354498 ATATTGTAGTATTTTATAATATTGTATCATACGATAGTGTATGATATGATATTGGTTTATATGAT 1 ATATTGTA-TATTCTATAATATTGTATCATACAATAGTGTATAATATGATATTGGTTTATA-GAT ** * 354563 ATATTATCATATCACATGAAATTGTATTATATG 64 ATAGAATCATATCACATGAAATTGTATAATATG 354596 ATATT 1 ATATT 354601 ATAATATATA Statistics Matches: 92, Mismatches: 8, Indels: 5 0.88 0.08 0.05 Matches are distributed among these distances: 96 2 0.02 97 9 0.10 98 81 0.88 ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45 Consensus pattern (96 bp): ATATTGTATATTCTATAATATTGTATCATACAATAGTGTATAATATGATATTGGTTTATAGATAT AGAATCATATCACATGAAATTGTATAATATG Found at i:355204 original size:16 final size:16 Alignment explanation

Indices: 355171--355212 Score: 52 Period size: 16 Copynumber: 2.8 Consensus size: 16 355161 ATATAAAATG * 355171 ATAAAGGTG--GTCTT 1 ATAAAGGTGATGTCTC 355185 ATAAAGGTGATGTCTC 1 ATAAAGGTGATGTCTC * 355201 ATAAGGGTGATG 1 ATAAAGGTGATG 355213 CTCCGTCTCG Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 14 9 0.38 16 15 0.62 ACGTcount: A:0.31, C:0.07, G:0.31, T:0.31 Consensus pattern (16 bp): ATAAAGGTGATGTCTC Found at i:356932 original size:20 final size:20 Alignment explanation

Indices: 356907--356962 Score: 94 Period size: 20 Copynumber: 2.8 Consensus size: 20 356897 CAAACAACTT * 356907 ATTTGTTCGGACGAATTGGG 1 ATTTGTTCGGACGAATTAGG * 356927 ATTTGTTCGGAAGAATTAGG 1 ATTTGTTCGGACGAATTAGG 356947 ATTTGTTCGGACGAAT 1 ATTTGTTCGGACGAAT 356963 AAGTTATTAA Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 33 1.00 ACGTcount: A:0.25, C:0.09, G:0.30, T:0.36 Consensus pattern (20 bp): ATTTGTTCGGACGAATTAGG Found at i:356995 original size:2 final size:2 Alignment explanation

Indices: 356988--357024 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 356978 GTACATGTAT 356988 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 G 357025 TCATAATCAT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:357125 original size:9 final size:9 Alignment explanation

Indices: 357111--357136 Score: 52 Period size: 9 Copynumber: 2.9 Consensus size: 9 357101 GGGTAGTGGG 357111 TATCCTAAA 1 TATCCTAAA 357120 TATCCTAAA 1 TATCCTAAA 357129 TATCCTAA 1 TATCCTAA 357137 TTCGTCCGAA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 17 1.00 ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35 Consensus pattern (9 bp): TATCCTAAA Found at i:357155 original size:20 final size:21 Alignment explanation

Indices: 357126--357214 Score: 126 Period size: 21 Copynumber: 4.2 Consensus size: 21 357116 TAAATATCCT 357126 AAATATCCTAATTCGTCCGAAC 1 AAATA-CCTAATTCGTCCGAAC 357148 AAAT-CCTAATTCGTCCGAAC 1 AAATACCTAATTCGTCCGAAC * * 357168 AAATAACTTATTCGTCCGAAC 1 AAATACCTAATTCGTCCGAAC * 357189 AAATAGCTAATTCGTCCGAAC 1 AAATACCTAATTCGTCCGAAC * 357210 GAATA 1 AAATA 357215 AGATTAATTT Statistics Matches: 61, Mismatches: 5, Indels: 3 0.88 0.07 0.04 Matches are distributed among these distances: 20 20 0.33 21 37 0.61 22 4 0.07 ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26 Consensus pattern (21 bp): AAATACCTAATTCGTCCGAAC Found at i:358960 original size:22 final size:22 Alignment explanation

Indices: 358932--358976 Score: 65 Period size: 22 Copynumber: 2.0 Consensus size: 22 358922 TCATCATAAG * 358932 TCATTCAGGTGAC-CTATTGCTA 1 TCATTCAGATGACTC-ATTGCTA 358954 TCATTCAGATGACTCATTGCTA 1 TCATTCAGATGACTCATTGCTA 358976 T 1 T 358977 TGGTCTTCGT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 22 20 0.95 23 1 0.05 ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38 Consensus pattern (22 bp): TCATTCAGATGACTCATTGCTA Found at i:366194 original size:168 final size:169 Alignment explanation

Indices: 365797--366221 Score: 493 Period size: 171 Copynumber: 2.5 Consensus size: 169 365787 CCGTTAGGCC * * * 365797 AGGAAAACTAAAACTTTTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATG 1 AGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATG ** * * * 365862 ACCCTCAAGAGTAGGGTGGGGCCACATTGGGGGGTCGCCTTTTATCCAAGGAATATATACATGTA 66 ACCCTCGGGAGTAGGGTGGGGCCAAAATGGGGGGTCGCCTTTTATACAAGGAATATATACA-GTA * * ** * 365927 GAGTAAATCTTTAAAAATCCTTTCTCAGAAAGTATTCAGCC 130 -AGTAAATCTTTAAAAATCATTTCGCAGAAACCATTCAGCA * * 365968 AGGAAAGCTGAAACTTGTGTGGAAGCATTCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATG 1 AGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATG * * * ** * * 366033 ATCCTCGGGGGTAGGATGGGGCCAAAATGGGGGGTCGATTTTTTTTACATATGAATATA-A-A-T 66 ACCCTCGGGAGTAGGGTGGGGCCAAAATGGGGGGTCG-CCTTTTATACA-AGGAATATATACAGT ** 366095 -AGTAAATCTTTAAAAAT-ATTACTCGCA-AGAACCATTTGGCA 129 AAGTAAATCTTTAAAAATCATT--TCGCAGA-AACCATTCAGCA * * 366136 AGGAAAGTTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAATTTGTGAAAATCATG 1 AGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATG * * 366201 ACCCTTGGGTGTAGGGTGGGG 66 ACCCTCGGGAGTAGGGTGGGG 366222 TAATTGGTCA Statistics Matches: 218, Mismatches: 31, Indels: 13 0.83 0.12 0.05 Matches are distributed among these distances: 166 2 0.01 167 18 0.08 168 89 0.41 169 1 0.00 171 92 0.42 172 8 0.04 173 8 0.04 ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28 Consensus pattern (169 bp): AGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATG ACCCTCGGGAGTAGGGTGGGGCCAAAATGGGGGGTCGCCTTTTATACAAGGAATATATACAGTAA GTAAATCTTTAAAAATCATTTCGCAGAAACCATTCAGCA Found at i:367143 original size:141 final size:139 Alignment explanation

Indices: 366888--367155 Score: 331 Period size: 141 Copynumber: 1.9 Consensus size: 139 366878 ACAGAAAAAA ** * * * 366888 TCTTTAAAAATCTTCTTCTCAGGAACCATTTTGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCC 1 TCTTTAAAAATCTTCTTCTCAAAAACAATTTGGCCAGGAAAGCTGAAACTTGTATGAAAGCATCC * * * * * 366953 TCGGGTAGTGTAAATTAATGGTTGTAAAAATCATGACCCTCGGGAGTAGGGTGGGGCGACTTTTC 66 TCAGGTAGTATAAATCAATAGTTGTAAAAATCATGACACTCGGGAGTAGGGTGGGGC-ACTTTTC 367018 ACATATGAAT 130 ACATATGAAT * * * * 367028 TCTTTAAAAATCTTTTTCTCAAAAATAATTTGGCCAGGAAAAGCTGAAACTTTTATGGAAGCATC 1 TCTTTAAAAATCTTCTTCTCAAAAACAATTTGGCCAGG-AAAGCTGAAACTTGTATGAAAGCATC * * * * * 367093 CTCAGGTAGTATAGAATCAA-AGTTGTGAAAATCATGATATTGGGGGGTAGGGTGGGGCACTTT 65 CTCAGGTAGTATA-AATCAATAGTTGTAAAAATCATGACACTCGGGAGTAGGGTGGGGCACTTT 367156 GGGGGTCGAC Statistics Matches: 107, Mismatches: 19, Indels: 4 0.82 0.15 0.03 Matches are distributed among these distances: 140 37 0.35 141 65 0.61 142 5 0.05 ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31 Consensus pattern (139 bp): TCTTTAAAAATCTTCTTCTCAAAAACAATTTGGCCAGGAAAGCTGAAACTTGTATGAAAGCATCC TCAGGTAGTATAAATCAATAGTTGTAAAAATCATGACACTCGGGAGTAGGGTGGGGCACTTTTCA CATATGAAT Found at i:367304 original size:163 final size:164 Alignment explanation

Indices: 367028--367432 Score: 469 Period size: 163 Copynumber: 2.4 Consensus size: 164 367018 ACATATGAAT ** * ** * 367028 TCTTTAAAAATCTTTTTCTCAAAAATAATTTGGCCAGGAAAAGCTGAAACTTTTATGGAAGCATC 1 TCTTTAAAAATCTTCCTCTC-AAAATAATTAGGCCAGG-AAAGCTGAAACTGGTATAGAAGCATC * 367093 CTCAGGTAGTATAGAATCAAAGTTGTGAAAATCATGATATTGGGGGGTAGGGTGGGGCACTT-TG 64 CTCAGGTAATATAGAATCAAAGTTGTGAAAATCATGATATTGGGGGGTAGGGTGGGGC-CTTATG * * * * 367157 GGGGT-CGACTTTTTACTTATGAATAT-GTAGAGTATA 128 GGGGTACGAATTTTTACATAGGAATATAGTA-AGTAAA * * * 367193 TCTTTAAAAATCTTCCTCTCAAAATCATTAGGCCAGGAAAGCTGAAACTGGTGTAGAAGCATTCT 1 TCTTTAAAAATCTTCCTCTCAAAATAATTAGGCCAGGAAAGCTGAAACTGGTATAGAAGCATCCT * * * 367258 CAGGTAATGTAGATTCAAAGTTGTGAAAATCATG-TCCGTT-GGGGGTAGGGTGGGGCCTTAATG 66 CAGGTAATATAGAATCAAAGTTGTGAAAATCATGAT--ATTGGGGGGTAGGGTGGGGCCTT-ATG * 367321 GGGGTGACGAATTTTTACATAGGAATATATTAAGTAAA 128 GGGGT-ACGAATTTTTACATAGGAATATAGTAAGTAAA * * * * 367359 TCTTTAAAAATCTTCTTCTCTCAGAAATTATTATGCCAGGAAAGCTGAAACTTGTATGGAAGCAT 1 TCTTTAAAAATCTTC--CTCTCA-AAATAATTAGGCCAGGAAAGCTGAAACTGGTATAGAAGCAT * 367424 CCCCAGGTA 63 CCTCAGGTA 367433 GGGAAAAATC Statistics Matches: 205, Mismatches: 25, Indels: 16 0.83 0.10 0.07 Matches are distributed among these distances: 162 4 0.02 163 70 0.34 164 24 0.12 165 18 0.09 166 38 0.19 167 2 0.01 168 6 0.03 169 43 0.21 ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31 Consensus pattern (164 bp): TCTTTAAAAATCTTCCTCTCAAAATAATTAGGCCAGGAAAGCTGAAACTGGTATAGAAGCATCCT CAGGTAATATAGAATCAAAGTTGTGAAAATCATGATATTGGGGGGTAGGGTGGGGCCTTATGGGG GTACGAATTTTTACATAGGAATATAGTAAGTAAA Found at i:371194 original size:19 final size:19 Alignment explanation

Indices: 371172--371209 Score: 58 Period size: 19 Copynumber: 2.0 Consensus size: 19 371162 ATGCTGGATG * 371172 TGGTTAAGGTTTTTAGAGC 1 TGGTTAAAGTTTTTAGAGC * 371191 TGGTTAAAGTTTTTGGAGC 1 TGGTTAAAGTTTTTAGAGC 371210 AGATGCCCTC Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 17 1.00 ACGTcount: A:0.21, C:0.05, G:0.32, T:0.42 Consensus pattern (19 bp): TGGTTAAAGTTTTTAGAGC Found at i:372019 original size:13 final size:13 Alignment explanation

Indices: 372003--372029 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 371993 ATTTGTTGTA 372003 TATTATGATATTG 1 TATTATGATATTG 372016 TATTATGATATTG 1 TATTATGATATTG 372029 T 1 T 372030 TGTGTATAGT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56 Consensus pattern (13 bp): TATTATGATATTG Found at i:372170 original size:10 final size:10 Alignment explanation

Indices: 372152--372191 Score: 55 Period size: 10 Copynumber: 4.1 Consensus size: 10 372142 TATGTATCAT * 372152 ATATGATACA 1 ATATCATACA * 372162 ATATCATACT 1 ATATCATACA 372172 ATAT-ATACA 1 ATATCATACA 372181 ATATCATACA 1 ATATCATACA 372191 A 1 A 372192 CATAATTTCA Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 9 8 0.31 10 18 0.69 ACGTcount: A:0.50, C:0.15, G:0.03, T:0.33 Consensus pattern (10 bp): ATATCATACA Found at i:372181 original size:19 final size:20 Alignment explanation

Indices: 372151--372189 Score: 71 Period size: 19 Copynumber: 2.0 Consensus size: 20 372141 TTATGTATCA 372151 TATATGATACAATATCATAC 1 TATATGATACAATATCATAC 372171 TATAT-ATACAATATCATAC 1 TATATGATACAATATCATAC 372190 AACATAATTT Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 19 14 0.74 20 5 0.26 ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36 Consensus pattern (20 bp): TATATGATACAATATCATAC Found at i:383956 original size:1 final size:1 Alignment explanation

Indices: 383952--384002 Score: 57 Period size: 1 Copynumber: 51.0 Consensus size: 1 383942 CAAAAAGGAT * ** * * 383952 AAAAAACAAAAAAAAAAACCAAAAAACAAAAAACAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 384003 TACTATGGTT Statistics Matches: 42, Mismatches: 8, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 1 42 1.00 ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:383964 original size:7 final size:7 Alignment explanation

Indices: 383952--384002 Score: 72 Period size: 7 Copynumber: 7.7 Consensus size: 7 383942 CAAAAAGGAT 383952 AAAAAAC 1 AAAAAAC 383959 AAAAAA- 1 AAAAAAC * 383965 AAAAACC 1 AAAAAAC 383972 AAAAAAC 1 AAAAAAC 383979 AAAAAAC 1 AAAAAAC 383986 AAAAAA- 1 AAAAAAC 383992 AAAAAA- 1 AAAAAAC 383998 AAAAA 1 AAAAA 384003 TACTATGGTT Statistics Matches: 41, Mismatches: 2, Indels: 3 0.89 0.04 0.07 Matches are distributed among these distances: 6 16 0.39 7 25 0.61 ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00 Consensus pattern (7 bp): AAAAAAC Found at i:383999 original size:15 final size:15 Alignment explanation

Indices: 383959--383999 Score: 64 Period size: 15 Copynumber: 2.7 Consensus size: 15 383949 GATAAAAAAC * 383959 AAAAAAAAAAACCAA 1 AAAAAAAAAAACAAA * 383974 AAAACAAAAAACAAA 1 AAAAAAAAAAACAAA 383989 AAAAAAAAAAA 1 AAAAAAAAAAA 384000 AAATACTATG Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 15 23 1.00 ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00 Consensus pattern (15 bp): AAAAAAAAAAACAAA Found at i:392329 original size:16 final size:16 Alignment explanation

Indices: 392304--392335 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 392294 TTTTGGGCGG * 392304 CGTCCGTCTGTCTGTC 1 CGTCCATCTGTCTGTC 392320 CGTCCATCTGTCTGTC 1 CGTCCATCTGTCTGTC 392336 TGTAAACTTT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.03, C:0.38, G:0.22, T:0.38 Consensus pattern (16 bp): CGTCCATCTGTCTGTC Found at i:393140 original size:320 final size:316 Alignment explanation

Indices: 392518--393142 Score: 725 Period size: 320 Copynumber: 2.0 Consensus size: 316 392508 AAAAATATTC * * * * 392518 TTCTCAGAAACCATTTGCCCAGAATAGCTGAGACTTTGCAAAAGCATCCTCAGATAGTGTAGATT 1 TTCTCAAAAACCATTTGCCCAGAAAAGCTGAGACTTTGCAAAAGCATCCTCAAAGAGTGTAGATT * * * 392583 CAAATTTGGTCAAATCATTGTCCCCGGGGGGAAGGTGGGGTCACAATTGGGGTCAAAGTTTTACA 66 CAAATTTGGTCAAATCATTGTCCCCGGGGAGAAGGTGGGGCCACAATGGGGGTCAAAGTTTTACA * * 392648 TAGAATATATAGAGTAAATTTTTTAAAATCTTTTCCTCAGAAACCAATTAGCAAGGAAAGATAAA 131 TAGAATATATAGAGTAAATCTTTTAAAATCTTTTCCTCAGAAACCAATCAGCAAGGAAAGATAAA * * * * ** * * * 392713 ACTTGTGTTGAAGCTTCCTCATGTAGTGTAGATTTAAAGTCGTGAAAATTATGACCCCAAGGTGT 196 ACTTGGGTGGAAGCATCCTCATGTAATGTAGATAGAAAGTCATGAAAATCATGACCCCAAGGAGT ** * * * * 392778 AGGGTGGGGCCACAATGGGGGGTCGTATTTTTACATAGGAATATATACATAGATTT 261 AGGGTGAAGCCACAATGGGGGGTCGAACTTTAACAAAGGAATATATACATAGATTT * *** * 392834 TTCTCAAAAACCATTTGGCCAGAAAAGCTCTGAGACTTGTGTGGAAGCATCCTCAAAGGGTGTAG 1 TTCTCAAAAACCATTTGCCCAGAAAAG--CTGAGACTT-TGCAAAAGCATCCTCAAAGAGTGTAG * * 392899 ATTCAAATTT-GTACATATCATTGTCCCCGGGGATAAGGTGGGGCCACAATGGGGGTCAAAGTTT 63 ATTCAAATTTGGT-CAAATCATTGTCCCCGGGGAGAAGGTGGGGCCACAATGGGGGTCAAAGTTT ** * * * * ** * 392963 TATTTTGGAATATATATAGTAAATCTTTTAAAATCTTTTTCTCAGAAACTAATCAGCCCGGGAAG 127 TA-CATAGAATATATAGAGTAAATCTTTTAAAATCTTTTCCTCAGAAACCAATCAGCAAGGAAAG * * * * * * * ** 393028 CTGAAATTTGGGTGGAAGCATCCTTATGTAATGTAGATAGAAATTTATGAAAATCATGA-CTCTG 191 ATAAAACTTGGGTGGAAGCATCCTCATGTAATGTAGATAGAAAGTCATGAAAATCATGACCCCAA 393092 GGAG-AGGGTGAAGCCACAATGAGGGGGGTCGAACTTTAACAAAGGAATATA 256 GGAGTAGGGTGAAGCCACAAT--GGGGGGTCGAACTTTAACAAAGGAATATA 393143 GTGTAAATCT Statistics Matches: 253, Mismatches: 49, Indels: 10 0.81 0.16 0.03 Matches are distributed among these distances: 316 24 0.09 318 25 0.10 319 83 0.33 320 121 0.48 ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29 Consensus pattern (316 bp): TTCTCAAAAACCATTTGCCCAGAAAAGCTGAGACTTTGCAAAAGCATCCTCAAAGAGTGTAGATT CAAATTTGGTCAAATCATTGTCCCCGGGGAGAAGGTGGGGCCACAATGGGGGTCAAAGTTTTACA TAGAATATATAGAGTAAATCTTTTAAAATCTTTTCCTCAGAAACCAATCAGCAAGGAAAGATAAA ACTTGGGTGGAAGCATCCTCATGTAATGTAGATAGAAAGTCATGAAAATCATGACCCCAAGGAGT AGGGTGAAGCCACAATGGGGGGTCGAACTTTAACAAAGGAATATATACATAGATTT Found at i:398353 original size:15 final size:15 Alignment explanation

Indices: 398333--398372 Score: 64 Period size: 15 Copynumber: 2.7 Consensus size: 15 398323 TCTCCATATT 398333 TTTATTATATTTATA 1 TTTATTATATTTATA * 398348 TTTATTATATTTTTA 1 TTTATTATATTTATA 398363 TTTATT-TATT 1 TTTATTATATT 398373 ATAAATATAA Statistics Matches: 24, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 14 4 0.17 15 20 0.83 ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72 Consensus pattern (15 bp): TTTATTATATTTATA Found at i:402626 original size:21 final size:22 Alignment explanation

Indices: 402590--402630 Score: 66 Period size: 21 Copynumber: 1.9 Consensus size: 22 402580 TAAGCAAGTC * 402590 CTTAAAGGTGGCTTAAAGGCGA 1 CTTAAAGGTAGCTTAAAGGCGA 402612 CTTAAAGG-AGCTTAAAGGC 1 CTTAAAGGTAGCTTAAAGGC 402631 TATACGACCT Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 21 10 0.56 22 8 0.44 ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22 Consensus pattern (22 bp): CTTAAAGGTAGCTTAAAGGCGA Found at i:402737 original size:10 final size:11 Alignment explanation

Indices: 402700--402738 Score: 62 Period size: 11 Copynumber: 3.6 Consensus size: 11 402690 GTCCAAACTT 402700 CTTTAAGCCAC 1 CTTTAAGCCAC 402711 CTTTAAGCCAC 1 CTTTAAGCCAC * 402722 CTTTAAG-CAT 1 CTTTAAGCCAC 402732 CTTTAAG 1 CTTTAAG 402739 TGGCATTTAC Statistics Matches: 27, Mismatches: 1, Indels: 1 0.93 0.03 0.03 Matches are distributed among these distances: 10 9 0.33 11 18 0.67 ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:402788 original size:22 final size:22 Alignment explanation

Indices: 402731--402791 Score: 70 Period size: 22 Copynumber: 2.8 Consensus size: 22 402721 CCTTTAAGCA * * 402731 TCTTTAAGTGGCATTTACGCTC 1 TCTTTAAGTGGCCTTTACACTC * * 402753 TCTTTACACT-GCCTTTACACTG 1 TCTTTA-AGTGGCCTTTACACTC 402775 TCTTTAAGTGGCCTTTA 1 TCTTTAAGTGGCCTTTA 402792 AGTCAATATT Statistics Matches: 32, Mismatches: 5, Indels: 4 0.78 0.12 0.10 Matches are distributed among these distances: 21 2 0.06 22 28 0.88 23 2 0.06 ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43 Consensus pattern (22 bp): TCTTTAAGTGGCCTTTACACTC Found at i:402902 original size:51 final size:51 Alignment explanation

Indices: 402826--402930 Score: 210 Period size: 51 Copynumber: 2.1 Consensus size: 51 402816 ATAAACACAT 402826 ATATTAAATGCAAAAGCTCTTTTATAGAGATGGACGGGGGTCATCCGAGTG 1 ATATTAAATGCAAAAGCTCTTTTATAGAGATGGACGGGGGTCATCCGAGTG 402877 ATATTAAATGCAAAAGCTCTTTTATAGAGATGGACGGGGGTCATCCGAGTG 1 ATATTAAATGCAAAAGCTCTTTTATAGAGATGGACGGGGGTCATCCGAGTG 402928 ATA 1 ATA 402931 ATATAATTTC Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 51 54 1.00 ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28 Consensus pattern (51 bp): ATATTAAATGCAAAAGCTCTTTTATAGAGATGGACGGGGGTCATCCGAGTG Found at i:403173 original size:2 final size:2 Alignment explanation

Indices: 403168--403221 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 403158 GTGAAAAAAA 403168 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 403210 TC TC TC TC TC TC 1 TC TC TC TC TC TC 403222 AGTTCATCCG Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:413422 original size:20 final size:20 Alignment explanation

Indices: 413394--413460 Score: 89 Period size: 20 Copynumber: 3.4 Consensus size: 20 413384 AGGCGAATGT * 413394 AATCTTAATTCGTCCGAACC 1 AATCATAATTCGTCCGAACC * * * 413414 AATCATAATTTGTTCGAACA 1 AATCATAATTCGTCCGAACC * 413434 AATCCTAATTCGTCCGAACC 1 AATCATAATTCGTCCGAACC 413454 AATCATA 1 AATCATA 413461 GTTTGTTCAA Statistics Matches: 38, Mismatches: 9, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 20 38 1.00 ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30 Consensus pattern (20 bp): AATCATAATTCGTCCGAACC Found at i:413454 original size:40 final size:40 Alignment explanation

Indices: 413394--413574 Score: 152 Period size: 40 Copynumber: 4.5 Consensus size: 40 413384 AGGCGAATGT * * 413394 AATCTTAATTCGTCCGAACCAATCATAATTTGTTCGAACA 1 AATCCTAATTCGTCCGAACCAATCATAATTTGTTCAAACA * 413434 AATCCTAATTCGTCCGAACCAATCATAGTTTGTTCAAACA 1 AATCCTAATTCGTCCGAACCAATCATAATTTGTTCAAACA * * * * * 413474 AATAGCTAAATCGTCCGAACAAATTGCA-AA-TTGTACAAAAA 1 AAT-CCTAATTCGTCCGAACCAA-T-CATAATTTGTTCAAACA * * * * * * * * 413515 AATTCAAATTCGTCTGAACAAAAGC-TAAATCGTCCAAAACA 1 AATCCTAATTCGTCCGAAC-CAATCATAATTTGTTC-AAACA 413556 AATCCTAATTCGTCCGAAC 1 AATCCTAATTCGTCCGAAC 413575 AGATAATTTA Statistics Matches: 114, Mismatches: 20, Indels: 13 0.78 0.14 0.09 Matches are distributed among these distances: 39 3 0.03 40 56 0.49 41 51 0.45 42 2 0.02 43 2 0.02 ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27 Consensus pattern (40 bp): AATCCTAATTCGTCCGAACCAATCATAATTTGTTCAAACA Found at i:413496 original size:21 final size:21 Alignment explanation

Indices: 413470--413619 Score: 103 Period size: 21 Copynumber: 7.3 Consensus size: 21 413460 AGTTTGTTCA 413470 AACAAATAGCTAAATCGTCCG 1 AACAAATAGCTAAATCGTCCG * * * * 413491 AACAAATTGC-AAATTGTACA 1 AACAAATAGCTAAATCGTCCG * * * 413511 AAAAAAT-TC-AAATTCGTCTG 1 AACAAATAGCTAAA-TCGTCCG * 413531 AACAAA-AGCTAAATCGTCCAA 1 AACAAATAGCTAAATCGTCC-G * * 413552 AACAAAT-CCTAATTCGTCCG 1 AACAAATAGCTAAATCGTCCG * ** * 413572 AACAGATAATTTAATCGTCCG 1 AACAAATAGCTAAATCGTCCG * * 413593 AACAAATAGCGAATTCGTCCG 1 AACAAATAGCTAAATCGTCCG 413614 AACAAA 1 AACAAA 413620 GAATATTTTA Statistics Matches: 95, Mismatches: 28, Indels: 12 0.70 0.21 0.09 Matches are distributed among these distances: 19 4 0.04 20 33 0.35 21 58 0.61 ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22 Consensus pattern (21 bp): AACAAATAGCTAAATCGTCCG Found at i:413575 original size:41 final size:40 Alignment explanation

Indices: 413430--413619 Score: 116 Period size: 41 Copynumber: 4.7 Consensus size: 40 413420 AATTTGTTCG * * ** * * 413430 AACAAATCCTAATTCGTCCGAAC-CAATCATAGTTTGTTCA 1 AACAAATCCTAATTCGTCCGAACAAAAGC-TAAATCGTCCA * * * * * 413470 AACAAATAGCTAAATCGTCCGAACAAATTGC-AAATTGTACA 1 AACAAAT-CCTAATTCGTCCGAACAAA-AGCTAAATCGTCCA * * * * 413511 AAAAAATTCAAATTCGTCTGAACAAAAGCTAAATCGTCCAA 1 AACAAATCCTAATTCGTCCGAACAAAAGCTAAATCGTCC-A * * * 413552 AACAAATCCTAATTCGTCCGAACAGATAA-TTTAATCGTCCG 1 AACAAATCCTAATTCGTCCGAACA-A-AAGCTAAATCGTCCA * * 413593 AACAAATAGCGAATTCGTCCGAACAAA 1 AACAAAT-CCTAATTCGTCCGAACAAA 413620 GAATATTTTA Statistics Matches: 117, Mismatches: 25, Indels: 16 0.74 0.16 0.10 Matches are distributed among these distances: 39 2 0.02 40 30 0.26 41 56 0.48 42 26 0.22 43 3 0.03 ACGTcount: A:0.43, C:0.22, G:0.12, T:0.24 Consensus pattern (40 bp): AACAAATCCTAATTCGTCCGAACAAAAGCTAAATCGTCCA Found at i:422148 original size:21 final size:21 Alignment explanation

Indices: 422121--422642 Score: 407 Period size: 21 Copynumber: 25.0 Consensus size: 21 422111 TTATGTCAAA * 422121 TAACTTTCGCGAATGAACGCG 1 TAACTTTCGCGAATAAACGCG * 422142 AAACTTTCGCGAAT-AACGCG 1 TAACTTTCGCGAATAAACGCG * * 422162 TTACTTTCGCGAATATACGCG 1 TAACTTTCGCGAATAAACGCG * * 422183 TTACTTTCGCGAATATACGCG 1 TAACTTTCGCGAATAAACGCG * * 422204 TTACTTTCGCGAATGAACGCG 1 TAACTTTCGCGAATAAACGCG * * ** 422225 TGACTTTGGCGAATAAAATCG 1 TAACTTTCGCGAATAAACGCG 422246 TAACTTTCGCGAATAAACGCG 1 TAACTTTCGCGAATAAACGCG * 422267 TAACTTTCGCGGATAAACGCG 1 TAACTTTCGCGAATAAACGCG * * * * 422288 AAACATTTTGCAAATGAACGCG 1 TAAC-TTTCGCGAATAAACGCG * * * 422310 TAACTTTGGCGATTAAAGGCG 1 TAACTTTCGCGAATAAACGCG * * 422331 TAACTTTGGCGAATAAGCGCG 1 TAACTTTCGCGAATAAACGCG * 422352 TAACTTTCGCGGATAAACGCG 1 TAACTTTCGCGAATAAACGCG * * * 422373 AAATCTTT-GCAAATTAACGCG 1 TAA-CTTTCGCGAATAAACGCG * 422394 TTACTTTCGCGAATAAACGC- 1 TAACTTTCGCGAATAAACGCG ** 422414 TAAACTTTCGCGAATAAATTTTCG 1 T-AACTTTCGCGAATAAA--CGCG * * * **** 422438 TAGC--T---AAAAAAAATAT 1 TAACTTTCGCGAATAAACGCG *** 422454 TTTTTTTCGCGAATAAACGCG 1 TAACTTTCGCGAATAAACGCG * * 422475 TAACCTTCGCAAATAAACGCG 1 TAACTTTCGCGAATAAACGCG * * * 422496 TAACTTTCGCAAATGAACGTG 1 TAACTTTCGCGAATAAACGCG * * 422517 TAATTTTGGCGAATAAACGCG 1 TAACTTTCGCGAATAAACGCG 422538 TAACTTTCGCTG-ATAAACGCG 1 TAACTTTCGC-GAATAAACGCG * * 422559 CAAAACTTTCGTGAATAAACGCG 1 --TAACTTTCGCGAATAAACGCG * *** 422582 AAACTTTCAATAATAAACGCG 1 TAACTTTCGCGAATAAACGCG * 422603 TAAATTT-GCGAATAAACGCG 1 TAACTTTCGCGAATAAACGCG * * 422623 TAACTTTTGCGAATTAACGC 1 TAACTTTCGCGAATAAACGC 422643 AAAACCATTT Statistics Matches: 397, Mismatches: 86, Indels: 36 0.76 0.17 0.07 Matches are distributed among these distances: 16 2 0.01 18 6 0.02 20 39 0.10 21 307 0.77 22 22 0.06 23 20 0.05 24 1 0.00 ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27 Consensus pattern (21 bp): TAACTTTCGCGAATAAACGCG Found at i:422598 original size:44 final size:41 Alignment explanation

Indices: 422486--422629 Score: 137 Period size: 44 Copynumber: 3.4 Consensus size: 41 422476 AACCTTCGCA * * * * * 422486 AATAAACGCGTAACTTTCGCA-AATGAACGTGTAATTTTGGCG 1 AATAAACGCGTAACTTTC-AATAATAAACGCGAAAATTT-GCG ** * * 422528 AATAAACGCGTAACTTTCGCTGATAAACGCGCAAAACTTTCGTG 1 AATAAACGCGTAACTTTCAATAATAAACGCG-AAAA-TTT-GCG * * 422572 AATAAACGCGAAACTTTCAATAATAAACGCGTAAATTTGCG 1 AATAAACGCGTAACTTTCAATAATAAACGCGAAAATTTGCG 422613 AATAAACGCGTAACTTT 1 AATAAACGCGTAACTTT 422630 TGCGAATTAA Statistics Matches: 83, Mismatches: 16, Indels: 7 0.78 0.15 0.07 Matches are distributed among these distances: 41 18 0.22 42 28 0.34 43 5 0.06 44 32 0.39 ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26 Consensus pattern (41 bp): AATAAACGCGTAACTTTCAATAATAAACGCGAAAATTTGCG Found at i:423353 original size:4 final size:4 Alignment explanation

Indices: 423344--423385 Score: 75 Period size: 4 Copynumber: 10.5 Consensus size: 4 423334 GTTACCCTGT * 423344 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCTG TCCG TCCG TC 1 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TC 423386 TGTCACGTTT Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 4 36 1.00 ACGTcount: A:0.00, C:0.48, G:0.24, T:0.29 Consensus pattern (4 bp): TCCG Found at i:424111 original size:163 final size:163 Alignment explanation

Indices: 423908--424302 Score: 555 Period size: 163 Copynumber: 2.4 Consensus size: 163 423898 TGGAGTAGCT * * * * * 423908 ACATCATCTCTTGGGATATAATTGGGGCTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAA 1 ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAA * * 423973 ATTTCATCCTGGGAGTC-AAATAGTAGCAGAAAATTGACGTTTATCAC-TAAAAAATCAAACATT 66 ATTTCATCCAGGGAGTCAAAAT-GTAGCAGAAAATTGACGTTTATCACTTAAAAAA--AAACATA * 424036 GATCCAAGAGCTCCTCTTATGATTTAATGGATAGAC 128 GATCCAAGAACTCCTCTTATGATTTAATGGATAGAC * * 424072 A-ATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTCAAAATTTAA 1 ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAA * 424136 ATTTCATCCAGGGAGTCAAAATGTAGCAGAAAATTGACGTTTATCACTTTAAAAAAAACATAGAT 66 ATTTCATCCAGGGAGTCAAAATGTAGCAGAAAATTGACGTTTATCACTTAAAAAAAAACATAGAT * * 424201 CCTAGAACTCCTTTTATGATTTAATGGATAGAC 131 CCAAGAACTCCTCTTATGATTTAATGGATAGAC * * * * ** 424234 ACATCATATCTTGGGATATGAAAGGAACTGTTCCATAGATGTGCATTACCGTTTTGAAAAA-TTA 1 ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTT-AAAAATTTA 424298 AATTT 65 AATTT 424303 AACCCTGAGG Statistics Matches: 207, Mismatches: 20, Indels: 9 0.88 0.08 0.04 Matches are distributed among these distances: 162 40 0.19 163 152 0.73 164 15 0.07 ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33 Consensus pattern (163 bp): ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAA ATTTCATCCAGGGAGTCAAAATGTAGCAGAAAATTGACGTTTATCACTTAAAAAAAAACATAGAT CCAAGAACTCCTCTTATGATTTAATGGATAGAC Found at i:424642 original size:134 final size:135 Alignment explanation

Indices: 424356--424648 Score: 353 Period size: 134 Copynumber: 2.2 Consensus size: 135 424346 CTTTAAGGAT * 424356 CAAGAATATATATGG-TTAAGGGGTGGGGATCTCAACCGTTTTCGAGATATTCGTGCACTTCCTG 1 CAAGAATATATATGGTTTAA-GGGTGGGGATCTCAACCGTTTTCGAGATATTAGTGCACTTCCTG * * * * * * 424420 TTCAAGGGGGGTCATGACAACCCCCGGGGCCCATGACCTACATACCGTTTAATGCCCCTTGACAC 65 TTCAAGGGGCGTCAGGACAACCCACAGGGCCCATGACCTACATAACATTTAATGCCCCTTGACAC ** 424485 AAGGTA 130 AAGAAA * * * 424491 CAAGAATATATATGGTTTAAGGGTGGGGATCTCAACTGTTTT-GAAGATATTAAG-GGACTTGCT 1 CAAGAATATATATGGTTTAAGGGTGGGGATCTCAACCGTTTTCG-AGATATT-AGTGCACTTCCT ** * * 424554 GTTTGA-GGGCGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTTGACA 64 GTTCAAGGGGCGTCAGGACAACCCACAGGGCCCATGACCTACATAACATTTAATGCCCCTTGACA 424618 TC-AGAAA 129 -CAAGAAA * * 424625 CATGAATATATATGGTTTAGGGGT 1 CAAGAATATATATGGTTTAAGGGT 424649 CATGATTATT Statistics Matches: 136, Mismatches: 18, Indels: 9 0.83 0.11 0.06 Matches are distributed among these distances: 134 76 0.56 135 55 0.40 136 5 0.04 ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27 Consensus pattern (135 bp): CAAGAATATATATGGTTTAAGGGTGGGGATCTCAACCGTTTTCGAGATATTAGTGCACTTCCTGT TCAAGGGGCGTCAGGACAACCCACAGGGCCCATGACCTACATAACATTTAATGCCCCTTGACACA AGAAA Found at i:427523 original size:16 final size:17 Alignment explanation

Indices: 427502--427534 Score: 59 Period size: 16 Copynumber: 2.0 Consensus size: 17 427492 AGATAAGATT 427502 TTCCGTTTTCC-TTCCG 1 TTCCGTTTTCCGTTCCG 427518 TTCCGTTTTCCGTTCCG 1 TTCCGTTTTCCGTTCCG 427535 CGTTTTAGCA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 11 0.69 17 5 0.31 ACGTcount: A:0.00, C:0.36, G:0.15, T:0.48 Consensus pattern (17 bp): TTCCGTTTTCCGTTCCG Found at i:430644 original size:22 final size:22 Alignment explanation

Indices: 430616--430658 Score: 68 Period size: 22 Copynumber: 2.0 Consensus size: 22 430606 AAAAATATTT * 430616 TTGAATTTGATATAACGAATTC 1 TTGAATTTGATAAAACGAATTC * 430638 TTGAATTTGTTAAAACGAATT 1 TTGAATTTGATAAAACGAATT 430659 TAAATCGTTA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 19 1.00 ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42 Consensus pattern (22 bp): TTGAATTTGATAAAACGAATTC Found at i:430673 original size:19 final size:20 Alignment explanation

Indices: 430626--430744 Score: 89 Period size: 19 Copynumber: 5.7 Consensus size: 20 430616 TTGAATTTGA * * 430626 TATAACGAATTCTTGAATTTGT 1 TATAACGAA-T-TTAAATTCGT * 430648 TAAAACGAATTTAAA-TCGT 1 TATAACGAATTTAAATTCGT * * 430667 TATAACGAATTGTTGAATCCGT 1 TATAACGAA-T-TTAAATTCGT * 430689 TATAACGAA-TTAAATTTGT 1 TATAACGAATTTAAATTCGT * 430708 TATAACAAATTTTAGGAATTCGT 1 TATAACGAA-TTTA--AATTCGT * 430731 TACAACGAATTTAA 1 TATAACGAATTTAA 430745 TCTGTTATTA Statistics Matches: 77, Mismatches: 13, Indels: 16 0.73 0.12 0.15 Matches are distributed among these distances: 19 26 0.34 20 6 0.08 21 8 0.10 22 24 0.31 23 13 0.17 ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38 Consensus pattern (20 bp): TATAACGAATTTAAATTCGT Found at i:430683 original size:41 final size:40 Alignment explanation

Indices: 430626--430752 Score: 132 Period size: 41 Copynumber: 3.1 Consensus size: 40 430616 TTGAATTTGA * 430626 TATAACGAATTCTTGAATTTGTTAAAACGAATTTAAATCGT 1 TATAACGAATT-TTGAATTCGTTAAAACGAATTTAAATCGT * * * 430667 TATAACGAATTGTTGAATCCGTTATAACGAA-TTAAATTTGT 1 TATAACGAATT-TTGAATTCGTTAAAACGAATTTAAA-TCGT * * 430708 TATAACAAATTTTAGGAATTCGTTACAACGAATTT-AATCTGT 1 TATAACGAATTTT--GAATTCGTTAAAACGAATTTAAATC-GT 430750 TAT 1 TAT 430753 TACAAATTCA Statistics Matches: 72, Mismatches: 9, Indels: 9 0.80 0.10 0.10 Matches are distributed among these distances: 40 7 0.10 41 41 0.57 42 22 0.31 43 2 0.03 ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39 Consensus pattern (40 bp): TATAACGAATTTTGAATTCGTTAAAACGAATTTAAATCGT Found at i:430692 original size:22 final size:20 Alignment explanation

Indices: 430626--430699 Score: 78 Period size: 22 Copynumber: 3.5 Consensus size: 20 430616 TTGAATTTGA * 430626 TATAACGAATTCTTGAATTTGT 1 TATAACGAATT-TTGAA-TCGT * * 430648 TAAAACGAA-TTTAAATCGT 1 TATAACGAATTTTGAATCGT 430667 TATAACGAATTGTTGAATCCGT 1 TATAACGAATT-TTGAAT-CGT 430689 TATAACGAATT 1 TATAACGAATT 430700 AAATTTGTTA Statistics Matches: 44, Mismatches: 5, Indels: 6 0.80 0.09 0.11 Matches are distributed among these distances: 19 11 0.25 20 5 0.11 21 6 0.14 22 22 0.50 ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38 Consensus pattern (20 bp): TATAACGAATTTTGAATCGT Found at i:430769 original size:42 final size:40 Alignment explanation

Indices: 430639--430774 Score: 121 Period size: 42 Copynumber: 3.3 Consensus size: 40 430629 AACGAATTCT * * * 430639 TGAATTTGTTAAAACGAATTTAAATC-GTTATAACGAATTGT 1 TGAATTCGTTAAAACGAATTT-AATCTGTTATAACAAATT-A * * * * 430680 TGAATCCGTTATAACGAATTAAATTTGTTATAACAAATTTTA 1 TGAATTCGTTAAAACGAATTTAATCTGTTATAACAAA--TTA * * * 430722 GGAATTCGTTACAACGAATTTAATCTGTTATTACAAATTCA 1 TGAATTCGTTAAAACGAATTTAATCTGTTATAACAAATT-A 430763 CTGAATTCGTTA 1 -TGAATTCGTTA 430775 TTTCAAATTT Statistics Matches: 76, Mismatches: 14, Indels: 9 0.77 0.14 0.09 Matches are distributed among these distances: 40 5 0.07 41 28 0.37 42 41 0.54 43 2 0.03 ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39 Consensus pattern (40 bp): TGAATTCGTTAAAACGAATTTAATCTGTTATAACAAATTA Found at i:430987 original size:22 final size:20 Alignment explanation

Indices: 430959--431021 Score: 56 Period size: 22 Copynumber: 3.0 Consensus size: 20 430949 GCGTAAGACG 430959 TATAACGGATTCAACAATTCGT 1 TATAAC-GATTCAA-AATTCGT * 430981 TATAACGATT-TAAATTCGT 1 TATAACGATTCAAAATTCGT * * 431000 TTTAACAAATTCAAGAATTCGT 1 TATAAC-GATTCAA-AATTCGT 431022 AATATCAAAT Statistics Matches: 34, Mismatches: 4, Indels: 6 0.77 0.09 0.14 Matches are distributed among these distances: 19 12 0.35 20 4 0.12 21 5 0.15 22 13 0.38 ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37 Consensus pattern (20 bp): TATAACGATTCAAAATTCGT Found at i:449772 original size:4 final size:4 Alignment explanation

Indices: 449763--449858 Score: 165 Period size: 4 Copynumber: 24.0 Consensus size: 4 449753 TTGTAAGTAC * * * 449763 ATCT ATCT ATCG CTCG ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT 1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT 449811 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT 1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT 449859 GTCTGTCTGT Statistics Matches: 88, Mismatches: 4, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 4 88 1.00 ACGTcount: A:0.24, C:0.26, G:0.02, T:0.48 Consensus pattern (4 bp): ATCT Found at i:463166 original size:16 final size:15 Alignment explanation

Indices: 463134--463177 Score: 56 Period size: 15 Copynumber: 2.9 Consensus size: 15 463124 AAACTGAGAA 463134 TTTTCAAATTTTAAT 1 TTTTCAAATTTTAAT 463149 TTTTCACAA-TTTAGAT 1 TTTTCA-AATTTTA-AT 463165 TTTT-AAATTTTAA 1 TTTTCAAATTTTAA 463178 AAATTTAATT Statistics Matches: 26, Mismatches: 0, Indels: 7 0.79 0.00 0.21 Matches are distributed among these distances: 14 3 0.12 15 15 0.58 16 8 0.31 ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57 Consensus pattern (15 bp): TTTTCAAATTTTAAT Found at i:464002 original size:165 final size:164 Alignment explanation

Indices: 463601--465832 Score: 3126 Period size: 165 Copynumber: 13.4 Consensus size: 164 463591 CAGGAAAGTC * * 463601 TACATAGGAATATATAGAGTAATTCTTTGAAAA---TCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * * * 463663 CTGAAACTCGTGTGGAAGTATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGA-TCCTG * 463728 GGGGTAGGGTGGGGCCACAATGGGGGGTCGATGTTT 130 GGGGTAGGGTGGGG-CACAATGGGGGGTCGAAGTTT 463764 TACATAGGAATATATCA-AGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAA 1 TACATAGGAATATAT-AGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAA * * 463828 GCTGAAACTTGTGTGGAAGTATCCTCAGGTGGTGTAGATTCAAAGTTGTGAAAATCATGA-CCTG 65 GCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCTG * 463892 CAGGGGTAGGGCGGGGCACAATGGGGGGTCGAAGTTT 130 --GGGGTAGGGTGGGGCACAATGGGGGGTCGAAGTTT * 463929 TACATAGGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * 463994 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGA-TCCTG ** 464059 GATGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTT 130 GGGGTAGGGTGGGG-CACAATGGGGGGTCGAAGTTT * * 464095 TACATAGGAATATAATATAGACTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCTAGGA 1 TACATAGG-A-AT-ATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGA * * * * * 464160 AAGCTGAGACTTGCGTGGAAGCATTCTCAGGTAGTGTAGATTCAAAGTTGTAAAAATCATGACCC 63 AAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGA-TC * * * 464225 CCGGGGGTAGGGTGCGGCCACAAT-GGGGGTCGATGTTT 127 CTGGGGGTAGGGTG-GGGCACAATGGGGGGTCGAAGTTT * * 464263 TACATAGGAATATATAGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACAAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * 464328 CTGAAACTTGTATGGAAGTATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGAT-CCTG * * 464393 GGGGTAGGGTGGGGCACAATGGAGGGTCGAAATTT 130 GGGGTAGGGTGGGGCACAATGGGGGGTCGAAGTTT * * * 464428 TACA-ATGGAATATATTGAGTAAATCTTTAAAATTCTACTTCTCAGAAACTAATCAGCCAGGAAA 1 TACATA-GGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAA * 464492 GCTGAAACTTGTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAGTTGTGAAAATCATGATCCAT 65 GCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCC-T 464557 GGGGGTA-GGTCGGGGCACAATGGGGGGTCGAAGTTT 129 GGGGGTAGGGT-GGGGCACAATGGGGGGTCGAAGTTT * * 464593 TACATAGGAATATATAGAGTAAATCTTTGAAAATCATCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * 464658 CTGAAACTTGTGTGGAAGCATCCTCAGGCAGTGTAGATTCATAGTTGTGAAAATCATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGAT-CCTG * 464723 GGGGTAGGGTGGGGCACAATGGGGGGGGGGTCGAAG-TC 130 GGGGTAGGGTGGGGCACAAT----GGGGGGTCGAAGTTT * * 464761 TACATAGGAATATATAGAGTAATTCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * 464826 CTGAAACTCGTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAGTTGTGAAATTCATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGAT-CCTG 464891 GGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTT 130 GGGGTAGGGTGGGG-CACAATGGGGGGTCGAAGTTT * 464927 TACATAGGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * * * * * 464992 CTCAAACATGTGTGTAAGCATTCTCAGGTAGTGTAGATTCATAGTTGTGAAAATCATGACCCCCG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGA-TCCTG * 465057 GGGGTAGGGTGGGGCCACAATGGGGTGGTCCAAGTTT 130 GGGGTAGGGTGGGG-CACAATGGGG-GGTCGAAGTTT 465094 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * ** 465159 CAGAAACTTATGTGGAAGCATCATCAGGTAGTACAGATTCAAAGTTGTGAAAATCATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGAT-CCTG * * * 465224 GGGGTAGGGTGAGGCCACATTGGGGGGGGGGGTTGTTAAAGTTT 130 GGGGTAGGGTG-GGGCACAAT-----GGGGGGTCG---AAGTTT * * * 465268 TACATA-GAA-ATATAGAGTTAATCTTTGAAAATCTTC--ATCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * ** 465329 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCA 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGA-TCCTG 465394 GGGGTAGGGTGGGGCCACAATGGGGGGTGGTCGAAGTTT 130 GGGGTAGGGTGGGG-CACAAT--GGGG-GGTCGAAGTTT * * 465433 TACATAGGAATATATGGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * 465498 CTGAAA-TTCGTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAATTTGTGAAATTCATGATCCCT 66 CTGAAACTT-GTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGAT-CCT 465562 GGGGGTAGGGTGGGGCACAATGGGGGGTCGAAGTTT 129 GGGGGTAGGGTGGGGCACAATGGGGGGTCGAAGTTT * 465598 TACATAGGAATATATAGAGTAAATATTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * 465663 CTGAAACTTGTGTTGAAGTATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAA-CATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGAT-CCTG * * * * 465727 GGGGTACGGTGAGGCCACATTGGGGGGTGTTGGGTGTTAAAGTTT 130 GGGGTAGGGTG-GGGCACAAT-GGGGG-G-T---CG---AAGTTT * * 465772 TACAAAGGAATATATAGAGTAAATCTTTTAAAATCTTCTTCTCAGAAACTAATCAGCCAGG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGG 465833 TGATTCTTTA Statistics Matches: 1873, Mismatches: 136, Indels: 109 0.88 0.06 0.05 Matches are distributed among these distances: 163 29 0.02 164 39 0.02 165 708 0.38 166 291 0.16 167 180 0.10 168 178 0.10 169 238 0.13 170 98 0.05 171 4 0.00 172 29 0.02 173 3 0.00 174 76 0.04 ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27 Consensus pattern (164 bp): TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCTGG GGGTAGGGTGGGGCACAATGGGGGGTCGAAGTTT Found at i:464285 original size:334 final size:331 Alignment explanation

Indices: 463601--465832 Score: 3258 Period size: 334 Copynumber: 6.7 Consensus size: 331 463591 CAGGAAAGTC * 463601 TACATAGGAATATATAGAGTAATTCTTTGAAAA---TCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * * 463663 CTGAAACTCGTGTGGAAGTATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTG * 463728 GGGGTAGGGTGGGGCCACAATGGGGGGTCGATGTTTTACATAGGAATATATCA-AGTAAATCTTT 131 GGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATAT-AGAGTAAATCTTT * 463792 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGTATCCTCAGG 195 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG ** * * 463857 TGGTGTAGATTCAAAGTTGTGAAAATCATGA--CCTGCAGGGGTAGGGCGGGGCACAATGGGGGG 260 CAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTG--GGGGTAGGGTGGGCCACAATGGGGGG 463920 TCGAAGTTT 323 TCGAAGTTT * * 463929 TACATAGGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * 463994 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTG ** * 464059 GATGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATAATATAGACTAAATCT 131 GGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGG-A-AT-ATATAGAGTAAATCT * * * * 464124 TTAAAAATCTTCTTCTCAGAAACTAATCAGCTAGGAAAGCTGAGACTTGCGTGGAAGCATTCTCA 193 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA * * * * 464189 GGTAGTGTAGATTCAAAGTTGTAAAAATCATGACCCCCGGGGGTAGGGTGCGGCCACAAT-GGGG 258 GGCAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTG-GGCCACAATGGGGG * 464253 GTCGATGTTT 322 GTCGAAGTTT * 464263 TACATAGGAATATATAGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACAAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * 464328 CTGAAACTTGTATGGAAGTATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTG * * * 464393 GGGGTAGGGTGGGG-CACAATGGAGGGTCGAAATTTTACA-ATGGAATATATTGAGTAAATCTTT 131 GGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATA-GGAATATATAGAGTAAATCTTT * * 464456 AAAATTCTACTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG 195 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * * 464521 CAGTGTAGATTCAAAGTTGTGAAAATCATGATCCATGGGGGTA-GGTCGGGGCACAATGGGGGGT 260 CAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGT-GGGCCACAATGGGGGGT 464585 CGAAGTTT 324 CGAAGTTT * 464593 TACATAGGAATATATAGAGTAAATCTTTGAAAATCATCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * 464658 CTGAAACTTGTGTGGAAGCATCCTCAGGCAGTGTAGATTCATAGTTGTGAAAATCATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTG * * 464723 GGGGTAGGGTGGGG-CACAATGGGGGGGGGGTCGAAG-TCTACATAGGAATATATAGAGTAATTC 131 GGGGTAGGGTGGGGCCACAAT----GGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATC * * 464786 TTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTCGTGTGGAAGCATCCTC 192 TTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTC * 464851 AGGCAGTGTAGATTCAAAGTTGTGAAATTCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGG 257 AGGCAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGT-GGGCCACAATGGGG 464916 GGTCGAAGTTT 321 GGTCGAAGTTT * * 464927 TACATAGGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * * * * 464992 CTCAAACATGTGTGTAAGCATTCTCAGGTAGTGTAGATTCATAGTTGTGAAAATCATGACCCCCG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTG * 465057 GGGGTAGGGTGGGGCCACAATGGGGTGGTCCAAGTTTTACATAGGAATATATAGAGTAAATCTTT 131 GGGGTAGGGTGGGGCCACAATGGGG-GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT * * * 465122 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCAGAAACTTATGTGGAAGCATCATCAGG 195 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * ** * 465187 TAGTACAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGAGGCCACATTGGGGGGG 260 CAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTG-GGCCACAAT-----GG * 465252 GGGGTTGTTAAAGTTT 319 GGGGTCG---AAGTTT * * 465268 TACATA-GAA-ATATAGAGTTAATCTTTGAAAATCTTC--ATCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG ** 465329 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCA 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTG * 465394 GGGGTAGGGTGGGGCCACAATGGGGGGTGGTCGAAGTTTTACATAGGAATATATGGAGTAAATCT 131 GGGGTAGGGTGGGGCCACAAT--GGGG-GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCT * 465459 TTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAA-TTCGTGTGGAAGCATCCTC 193 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTT-GTGTGGAAGCATCCTC * * * 465523 AGGCAGTGTAGATTCAAATTTGTGAAATTCATGATCCCTGGGGGTAGGGTGGGGCACAATGGGGG 257 AGGCAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGCCACAATGGGGG 465588 GTCGAAGTTT 322 GTCGAAGTTT * * 465598 TACATAGGAATATATAGAGTAAATATTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * 465663 CTGAAACTTGTGTTGAAGTATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAA-CATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTG * * * * * 465727 GGGGTACGGTGAGGCCACATTGGGGGGTGTTGGGTGTTAAAGTTTTACAAAGGAATATATAGAGT 131 GGGGTAGGGTGGGGCCACAAT-GGGGG-G-T---CG---AAGTTTTACATAGGAATATATAGAGT * 465792 AAATCTTTTAAAATCTTCTTCTCAGAAACTAATCAGCCAGG 187 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGG 465833 TGATTCTTTA Statistics Matches: 1728, Mismatches: 130, Indels: 81 0.89 0.07 0.04 Matches are distributed among these distances: 328 30 0.02 329 11 0.01 330 282 0.16 331 142 0.08 332 41 0.02 333 329 0.19 334 508 0.29 335 14 0.01 336 4 0.00 337 104 0.06 338 17 0.01 339 231 0.13 340 3 0.00 341 12 0.01 ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27 Consensus pattern (331 bp): TACATAGGAATATATAGAGTAAATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTG GGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA AAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGC AGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGCCACAATGGGGGGTCG AAGTTT Found at i:464754 original size:499 final size:502 Alignment explanation

Indices: 463601--465832 Score: 3345 Period size: 499 Copynumber: 4.5 Consensus size: 502 463591 CAGGAAAGTC * * 463601 TACATAGGAATATATAGAGTAATTCTTTGAAAA---TCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * * * 463663 CTGAAACTCGTGTGGAAGTATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTG * * 463728 GGGGTAGGGTGGGGCCACAAT----GGGGGGTCGATGTTTTACATAGGAATATATCA-AGTAAAT 131 GGGGTAGGGTGAGGCCACAATGGGGGGGGGGTCGAAGTTTTACATAGGAATATAT-AGAGTAAAT * * 463788 CTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGTATCCT 195 CTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCT * * 463853 CAGGTGGTGTAGATTCAAAGTTGTGAAAATCATGA--CCTGCAGGGGTAGGGCGGGG-CACAATG 260 CAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTG--GGGGTAGGGTGGGGCCACAATG 463915 GGGGGTCGAAGTTTTACATAGGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTA 323 GGGGGTCGAAGTTTTACATAGGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTA * 463980 ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAA 388 ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAGTTGTGAA * ** 464045 ATTCATGACCCCTGGATGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTT 453 AATCATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTT * * 464095 TACATAGGAATATAATATAGACTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCTAGGA 1 TACATAGG-A-AT-ATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGA * * * * * 464160 AAGCTGAGACTTGCGTGGAAGCATTCTCAGGTAGTGTAGATTCAAAGTTGTAAAAATCATGACCC 63 AAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCC * * * 464225 CCGGGGGTAGGGTGCGGCCACAAT-----GGGGGTCGATGTTTTACATAGGAATATATAGAGTAA 128 CTGGGGGTAGGGTGAGGCCACAATGGGGGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAA * * * 464285 ATCTTTGAAAATCTTCTTCTCAGAAACAAATCAGCCAGGAAAGCTGAAACTTGTATGGAAGTATC 193 ATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATC 464350 CTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGG-CACAATG 258 CTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATG * * * * * 464414 GAGGGTCGAAATTTTACA-ATGGAATATATTGAGTAAATCTTTAAAATTCTACTTCTCAGAAACT 323 GGGGGTCGAAGTTTTACATA-GGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT 464478 AATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAGTTGTGA 387 AATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAGTTGTGA * * 464543 AAATCATGATCCATGGGGGTA-GGTCGGGG-CACAATGGGGGGTCGAAGTTT 452 AAATCATGACCCCTGGGGGTAGGGT-GGGGCCACAATGGGGGGTCGAAGTTT * * 464593 TACATAGGAATATATAGAGTAAATCTTTGAAAATCATCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * 464658 CTGAAACTTGTGTGGAAGCATCCTCAGGCAGTGTAGATTCATAGTTGTGAAAATCATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTG * * * 464723 GGGGTAGGGTG-GGGCACAATGGGGGGGGGGTCGAAG-TCTACATAGGAATATATAGAGTAATTC 131 GGGGTAGGGTGAGGCCACAATGGGGGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATC * 464786 TTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTCGTGTGGAAGCATCCTC 196 TTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTC * * 464851 AGGCAGTGTAGATTCAAAGTTGTGAAATTCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGG 261 AGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGG 464916 GGTCGAAGTTTTACATAGGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC 326 GGTCGAAGTTTTACATAGGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC * * * * * * 464981 AGCCAGGAAAGCTCAAACATGTGTGTAAGCATTCTCAGGTAGTGTAGATTCATAGTTGTGAAAAT 391 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAGTTGTGAAAAT * * 465046 CATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGTGGTCCAAGTTT 456 CATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGG-GGTCGAAGTTT 465094 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * * ** 465159 CAGAAACTTATGTGGAAGCATCATCAGGTAGTACAGATTCAAAGTTGTGAAAATCATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTG * * * 465224 GGGGTAGGGTGAGGCCACATTGGGGGGGGGGGTTGTTAAAGTTTTACATA-GAA-ATATAGAGTT 131 GGGGTAGGGTGAGGCCACAAT-GGGGGGGGGGTCG---AAGTTTTACATAGGAATATATAGAGTA * 465287 AATCTTTGAAAATCTTC--ATCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCAT 192 AATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCAT * ** 465350 CCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGGGCCACAAT 257 CCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAAT * 465415 GGGGGGTGGTCGAAGTTTTACATAGGAATATATGGAGTAAATCTTTGAAAATCTTCTTCTCAGAA 322 --GGGG-GGTCGAAGTTTTACATAGGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAA * 465480 ACTAATCAGCCAGGAAAGCTGAAA-TTCGTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAATTT 384 ACTAATCAGCCAGGAAAGCTGAAACTT-GTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAGTT * * 465544 GTGAAATTCATGATCCCTGGGGGTAGGGTGGGG-CACAATGGGGGGTCGAAGTTT 448 GTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTT * 465598 TACATAGGAATATATAGAGTAAATATTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG 1 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG * * 465663 CTGAAACTTGTGTTGAAGTATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAA-CATGATCCCTG 66 CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTG * * * 465727 GGGGTACGGTGAGGCCACATTGGGGGGTGTTGGGT-GTTAAAGTTTTACAAAGGAATATATAGAG 131 GGGGTAGGGTGAGGCCACAATGGGGGG-G--GGGTCG---AAGTTTTACATAGGAATATATAGAG * 465791 TAAATCTTTTAAAATCTTCTTCTCAGAAACTAATCAGCCAGG 190 TAAATCTTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGG 465833 TGATTCTTTA Statistics Matches: 1588, Mismatches: 112, Indels: 62 0.90 0.06 0.04 Matches are distributed among these distances: 494 16 0.01 495 119 0.07 496 4 0.00 497 20 0.01 498 172 0.11 499 448 0.28 500 120 0.08 501 146 0.09 502 13 0.01 503 148 0.09 504 135 0.09 505 47 0.03 506 173 0.11 507 7 0.00 508 20 0.01 ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27 Consensus pattern (502 bp): TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG CTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTG GGGGTAGGGTGAGGCCACAATGGGGGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATC TTTGAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTC AGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGG GGTCGAAGTTTTACATAGGAATATATGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAGTTGTGAAAAT CATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTT Found at i:470436 original size:165 final size:164 Alignment explanation

Indices: 469578--470433 Score: 920 Period size: 165 Copynumber: 5.3 Consensus size: 164 469568 AAACTTTCCC * * * * * *** 469578 AGAATATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAGTTCAAACCGCCATCACGGCCCC 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATT-TATCCCCCATTGTGGCCCC * * ** * * * * * 469643 GCCCTACCACTAGGGACTGTGATTTTG--CAAACTTGAATTTACACTACCCGAGGATGCCTCTAC 65 -CCCTACCCCCAGGGACCATGA-TTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCAC * * * * * * * 469706 ACAAGTTTAAGCTTTTCTGGCCAAATAGTCTTTGAAA 128 TCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGA * * * * 469743 AGAAGATTTTTAAAAATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCCATTGTAGCCTCA 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTTATCCCCCATTGTGGCC-CC * ** * * * * * 469808 CCCTA-CCCC-TGGATTATTATTTAAACAAACTTGAATCTATACGATCTTAGGATGCTTCCACTC 65 CCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTC 469871 AAATTTGAGCTTTCCTGGCCTAATAG-TTTTGAGA 130 AAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGA * * 469905 AGAAGATTTATAAAGATTTTCTC--TATA----TA--TAAAAATTTATCCCCCATTGTGGCCCGC 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTTATCCCCCATTGTGGCCCCC * * *** * 469962 CCTACCCCCCAGGGACCATGATTTGAACAAACTTGAATCTACATTATCTGAGGATGGTGATACGC 66 CCTA-CCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTC * * * * 470027 CAATTTGAGCTTT-CTAGGCCAAAAAGTTTTT-AAA 130 AAATTTGAGCTTTCCT-GGCCTAATAGTTTTTGAGA * * 470061 AGAA-ATTTTTTAAAAGATTTTCT-TCATATATTCCTGTATAAAAATTTATCCCCCAATTGTGGC 1 AGAAGA-TTTTT-AAAGATTTTCTCT-ATATATTCCTATGTAAAAATTTATCCCCC-ATTGTGGC * * 470124 CCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTATCT-TGGATGCTTCC 62 CCC-CCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCC * * * 470188 ACTCAAATTTGAGCTTTCCTGGTCTAAAAGCTTTTGAGA 126 ACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGA * * 470227 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCC 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTTATCCCCC-ATTGTGGCCCC * * 470292 CCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATATACACTATCTGAGGATGCTTCCACTC 65 CCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTC * * 470357 AATTTTGAGCTTTCCTGGCCTGATAGTTTTTGAGA 130 AAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGA * 470392 AGAAGAGTTTTAAAGATTTTCTCTATATATTCCTATGTAAAA 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAA 470434 CTTTGGCTCA Statistics Matches: 581, Mismatches: 84, Indels: 52 0.81 0.12 0.07 Matches are distributed among these distances: 153 6 0.01 154 23 0.04 155 7 0.01 156 72 0.12 157 15 0.03 159 4 0.01 160 4 0.01 161 3 0.01 162 33 0.06 163 54 0.09 164 63 0.11 165 225 0.39 166 66 0.11 167 6 0.01 ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34 Consensus pattern (164 bp): AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTTATCCCCCATTGTGGCCCCC CCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTCA AATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGA Found at i:474473 original size:1 final size:1 Alignment explanation

Indices: 474469--474496 Score: 56 Period size: 1 Copynumber: 28.0 Consensus size: 1 474459 TAGTGGAAGT 474469 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 474497 CACAAGCAAA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 27 1.00 ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00 Consensus pattern (1 bp): G Found at i:486569 original size:2 final size:2 Alignment explanation

Indices: 486564--486603 Score: 73 Period size: 2 Copynumber: 20.5 Consensus size: 2 486554 CTTCGAGAGA 486564 CT CT CT CT CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 486604 ACATTAATCT Statistics Matches: 37, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 1 1 0.03 2 36 0.97 ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47 Consensus pattern (2 bp): CT Found at i:490205 original size:21 final size:21 Alignment explanation

Indices: 490181--490234 Score: 81 Period size: 21 Copynumber: 2.6 Consensus size: 21 490171 CAACGAATGC * 490181 GAGAACTCGTGCACCGTATGA 1 GAGAGCTCGTGCACCGTATGA * 490202 GAGAGCTCATGCACCGTATGA 1 GAGAGCTCGTGCACCGTATGA * 490223 GAGGGCTCGTGC 1 GAGAGCTCGTGC 490235 GAATCTAAAA Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 29 1.00 ACGTcount: A:0.24, C:0.24, G:0.33, T:0.19 Consensus pattern (21 bp): GAGAGCTCGTGCACCGTATGA Found at i:491306 original size:38 final size:38 Alignment explanation

Indices: 491263--491341 Score: 124 Period size: 37 Copynumber: 2.1 Consensus size: 38 491253 AACTCCGAGA 491263 TTTGTTACCTATATCCTTCATATTTCAC-AAAAAAAAAT 1 TTTGTT-CCTATATCCTTCATATTTCACAAAAAAAAAAT ** 491301 TTTGTTTNTATATCCTTCATATTTCACAAAAAAAAAAT 1 TTTGTTCCTATATCCTTCATATTTCACAAAAAAAAAAT 491339 TTT 1 TTT 491342 TTTAAAACAT Statistics Matches: 38, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 37 19 0.50 38 19 0.50 ACGTcount: A:0.38, C:0.15, G:0.03, T:0.43 Consensus pattern (38 bp): TTTGTTCCTATATCCTTCATATTTCACAAAAAAAAAAT Found at i:494058 original size:2 final size:2 Alignment explanation

Indices: 494051--494140 Score: 162 Period size: 2 Copynumber: 45.0 Consensus size: 2 494041 TTTGGCTCAC * * 494051 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CC CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 494093 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 494135 CT CT CT 1 CT CT CT 494141 GAGACTAATC Statistics Matches: 84, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 84 1.00 ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48 Consensus pattern (2 bp): CT Found at i:499176 original size:17 final size:16 Alignment explanation

Indices: 499149--499192 Score: 52 Period size: 17 Copynumber: 2.6 Consensus size: 16 499139 TTTCGATAGA 499149 TGTTTGGTTTTTAGTT 1 TGTTTGGTTTTTAGTT * 499165 TGTTTGGGTTTTTGGTTTT 1 TGTTT-GGTTTTTAG--TT 499184 TGTTTGGTT 1 TGTTTGGTT 499193 GGTTTGCTTT Statistics Matches: 24, Mismatches: 1, Indels: 4 0.83 0.03 0.14 Matches are distributed among these distances: 16 5 0.21 17 8 0.33 18 4 0.17 19 7 0.29 ACGTcount: A:0.02, C:0.00, G:0.30, T:0.68 Consensus pattern (16 bp): TGTTTGGTTTTTAGTT Found at i:501582 original size:21 final size:21 Alignment explanation

Indices: 501556--501638 Score: 112 Period size: 21 Copynumber: 4.0 Consensus size: 21 501546 TTTTTCTATC 501556 AAATATGTCGACATGCAAGAT 1 AAATATGTCGACATGCAAGAT * 501577 AAATATGTTGACATGCAAGAT 1 AAATATGTCGACATGCAAGAT * * * 501598 AATTATGTCAACATGCAACAT 1 AAATATGTCGACATGCAAGAT * * 501619 AACTATGTAGACATGCAAGA 1 AAATATGTCGACATGCAAGA 501639 AAAGTGCAAT Statistics Matches: 53, Mismatches: 9, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 53 1.00 ACGTcount: A:0.43, C:0.14, G:0.17, T:0.25 Consensus pattern (21 bp): AAATATGTCGACATGCAAGAT Found at i:501626 original size:42 final size:42 Alignment explanation

Indices: 501559--501638 Score: 124 Period size: 42 Copynumber: 1.9 Consensus size: 42 501549 TTCTATCAAA * * * 501559 TATGTCGACATGCAAGATAAATATGTTGACATGCAAGATAAT 1 TATGTCAACATGCAACATAAATATGTAGACATGCAAGATAAT * 501601 TATGTCAACATGCAACATAACTATGTAGACATGCAAGA 1 TATGTCAACATGCAACATAAATATGTAGACATGCAAGA 501639 AAAGTGCAAT Statistics Matches: 34, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 42 34 1.00 ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26 Consensus pattern (42 bp): TATGTCAACATGCAACATAAATATGTAGACATGCAAGATAAT Found at i:501746 original size:21 final size:21 Alignment explanation

Indices: 501717--501937 Score: 164 Period size: 21 Copynumber: 10.5 Consensus size: 21 501707 AAGATGCTAG * * 501717 ATGCTACTTTTTTATGTCTAC 1 ATGCAACTTATTTATGTCTAC 501738 ATGCAACTTATTTATGT-TAAC 1 ATGCAACTTATTTATGTCT-AC ** ** * 501759 ATGCAAGATAAATATG-CTGAT 1 ATGCAACTTATTTATGTCT-AC * 501780 ATGCAACTTATTTATGTCAAC 1 ATGCAACTTATTTATGTCTAC * 501801 ATGCAACTTATTTATGTCAAC 1 ATGCAACTTATTTATGTCTAC * 501822 ATGCAACTTATTTATGTCGAC 1 ATGCAACTTATTTATGTCTAC * 501843 ATGCAACTTACTTATGT-TGAC 1 ATGCAACTTATTTATGTCT-AC * ** ** 501864 ATGCGAGATAAATATGT-TGAC 1 ATGCAACTTATTTATGTCT-AC * * 501885 ATGCAACTTAGTTATGTTTAC 1 ATGCAACTTATTTATGTCTAC ** ** 501906 ATGCAAGATAAATATGT-TAAC 1 ATGCAACTTATTTATGTCT-AC 501927 ATGCAACTTAT 1 ATGCAACTTAT 501938 AAGTTGTATG Statistics Matches: 160, Mismatches: 34, Indels: 12 0.78 0.17 0.06 Matches are distributed among these distances: 20 2 0.01 21 156 0.98 22 2 0.01 ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38 Consensus pattern (21 bp): ATGCAACTTATTTATGTCTAC Found at i:501847 original size:63 final size:63 Alignment explanation

Indices: 501717--501937 Score: 192 Period size: 63 Copynumber: 3.5 Consensus size: 63 501707 AAGATGCTAG * * * ** * * 501717 ATGCTACTTTTTTATGTCTACATGCAACTTATTTATGTTAACATGCAAGATAAATATG-CTGAT 1 ATGCAACTTATTTATGTCAACATGCAACTTATTTATGTTAACATGCAACTTAATTATGTC-GAC * * 501780 ATGCAACTTATTTATGTCAACATGCAACTTATTTATGTCAACATGCAACTTATTTATGTCGAC 1 ATGCAACTTATTTATGTCAACATGCAACTTATTTATGTTAACATGCAACTTAATTATGTCGAC * ** * ** ** * * ** 501843 ATGCAACTTACTTATGTTGACATGCGAGATAAATATGTTGACATGCAACTTAGTTATGTTTAC 1 ATGCAACTTATTTATGTCAACATGCAACTTATTTATGTTAACATGCAACTTAATTATGTCGAC ** ** * 501906 ATGCAAGATAAATATGTTAACATGCAACTTAT 1 ATGCAACTTATTTATGTCAACATGCAACTTAT 501938 AAGTTGTATG Statistics Matches: 126, Mismatches: 31, Indels: 2 0.79 0.19 0.01 Matches are distributed among these distances: 63 125 0.99 64 1 0.01 ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38 Consensus pattern (63 bp): ATGCAACTTATTTATGTCAACATGCAACTTATTTATGTTAACATGCAACTTAATTATGTCGAC Found at i:502060 original size:63 final size:63 Alignment explanation

Indices: 501945--502122 Score: 212 Period size: 63 Copynumber: 2.8 Consensus size: 63 501935 TATAAGTTGT * * * ** ** *** * 501945 ATGTCAACATAACTTAGTTGCTTGTCGACATAAATGTGTTGCATGTCAACATATTTATCTTGC 1 ATGTTAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTTGACATAAAGAACTTGC * 502008 ATGTTAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTTGACATAAAGAAGTTGC 1 ATGTTAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTTGACATAAAGAACTTGC * ** * 502071 ATGTTAACATAAATAAGTTGCATGTTAACATAATTAAGTTGCATGTTGACAT 1 ATGTTAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTTGACAT 502123 CAATAGGTAG Statistics Matches: 99, Mismatches: 16, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 63 99 1.00 ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35 Consensus pattern (63 bp): ATGTTAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTTGACATAAAGAACTTGC Found at i:502117 original size:21 final size:21 Alignment explanation

Indices: 501936--502127 Score: 186 Period size: 21 Copynumber: 9.1 Consensus size: 21 501926 CATGCAACTT * * 501936 ATAAGTTGTATGTCAACATAA 1 ATAAGTTGCATGTTAACATAA * * * ** 501957 CTTAGTTGCTTGTCGACATAA 1 ATAAGTTGCATGTTAACATAA ** * * 501978 ATGTGTTGCATGTCAACATAT 1 ATAAGTTGCATGTTAACATAA * ** 501999 TTATCTTGCATGTTAACATAA 1 ATAAGTTGCATGTTAACATAA * ** 502020 CTAAGTTGCATGTCGACATAA 1 ATAAGTTGCATGTTAACATAA * 502041 ATAAGTTGCATGTTGACATAA 1 ATAAGTTGCATGTTAACATAA * 502062 AGAAGTTGCATGTTAACATAA 1 ATAAGTTGCATGTTAACATAA 502083 ATAAGTTGCATGTTAACATAA 1 ATAAGTTGCATGTTAACATAA * * * 502104 TTAAGTTGCATGTTGACATCA 1 ATAAGTTGCATGTTAACATAA 502125 ATA 1 ATA 502128 GGTAGCGTAT Statistics Matches: 141, Mismatches: 30, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 21 141 1.00 ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35 Consensus pattern (21 bp): ATAAGTTGCATGTTAACATAA Found at i:502225 original size:21 final size:21 Alignment explanation

Indices: 502201--502263 Score: 56 Period size: 21 Copynumber: 3.0 Consensus size: 21 502191 ATTTGATTGC 502201 AGTTTTCTTGCATGTCAACAT 1 AGTTTTCTTGCATGTCAACAT * ** 502222 AGTTATGC-TGCATGTTGACAT 1 AGTT-TTCTTGCATGTCAACAT ** * 502243 AACTATCTTGCATGTCAACAT 1 AGTTTTCTTGCATGTCAACAT 502264 NNNNNNNNNN Statistics Matches: 31, Mismatches: 9, Indels: 4 0.70 0.20 0.09 Matches are distributed among these distances: 20 1 0.03 21 28 0.90 22 2 0.06 ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38 Consensus pattern (21 bp): AGTTTTCTTGCATGTCAACAT Found at i:505459 original size:44 final size:44 Alignment explanation

Indices: 505318--505818 Score: 407 Period size: 44 Copynumber: 11.6 Consensus size: 44 505308 TATGGGTGTC * * * 505318 ATAACACTGCTGGGTGAGGAACCAGTGGGTGTGGTTATCTGGGTT 1 ATAACACTGCTGGGTGAGGGACCAG-GGGTGTGGTTGTCTGGGTA * * 505363 ATAACACTGATGGGTGAGGGACCA-GGGTGTGTTTG-CAT-GG-- 1 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTC-TGGGTA * * * 505403 ATAACACTGCTGGGTGAAGGACCGGGGGAGTGGTTGTCTGGGTA 1 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTCTGGGTA * * 505447 ATAGCACTGCTGGGCT-AGGGACAAGGGGTGTGGTTGTCTGGGTA 1 ATAACACTGCTGGG-TGAGGGACCAGGGGTGTGGTTGTCTGGGTA * * * * * * * * 505491 AAAACAGTGATGAGTGAGGAACCAGGGGTGTGGTTGTATGGATG 1 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTCTGGGTA * * * 505535 ATAACACTGC----TGAGGGACCGGGGGTGTGGATGTCCT-GGTG 1 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGT-CTGGGTA * * * 505575 ATAGA-ACTGCTGGGTAAGGGACCTGGGAGTATGGTTGTCT-GG-- 1 ATA-ACACTGCTGGGTGAGGGACCAGGG-GTGTGGTTGTCTGGGTA * * * 505617 ACAACACTGCTAGGTGAAGGACCAGGGGTGTGGTTGTCT-GG-- 1 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTCTGGGTA * * 505658 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTATGGGTG 1 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTCTGGGTA * * * 505702 ATAACACAGCTGGGTGAGGGACCAGGGAATGTGTTTGTCT-GG-- 1 ATAACACTGCTGGGTGAGGGACCAGGG-GTGTGGTTGTCTGGGTA * * * * * 505744 ATAGCACTGATAGGTGAGGGACCGGGGGTGTGGTTGTATGGGTGATA 1 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTCT-GG-G-TA * 505791 GATAACACTGCTGGGGGAGGGACC-GGGG 1 -ATAACACTGCTGGGTGAGGGACCAGGGG 505819 ATGAATTCAA Statistics Matches: 367, Mismatches: 62, Indels: 52 0.76 0.13 0.11 Matches are distributed among these distances: 40 52 0.14 41 70 0.19 42 50 0.14 43 12 0.03 44 120 0.33 45 40 0.11 47 4 0.01 48 19 0.05 ACGTcount: A:0.21, C:0.13, G:0.42, T:0.24 Consensus pattern (44 bp): ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTCTGGGTA Found at i:505702 original size:127 final size:126 Alignment explanation

Indices: 505301--505780 Score: 419 Period size: 127 Copynumber: 3.7 Consensus size: 126 505291 TTGCTAGAGA * * * 505301 GTGGTTGTATGGGTGTCATA-ACACTGCTGGGTGAGGAACCAGTGG-GTGTGGTTATCTGGGTTA 1 GTGGTTGTCTGGGTG--ATAGA-ACTGCTGGGT-AGGGACCAG-GGAGTGTGGTTGTCT-GG--A * * * * * 505364 TAACACTGATGGGTGAGGGACCA-GGGTGTGTTTG-CATGGATAACACTGCTGGGTGAAGGACCG 58 AAACACTGATAGGTGAAGGACCAGGGGTGTGGTTGTC-TGGATAACACTGCTGGGTGAGGGACCG * 505427 GGGGA 122 GGGGT * * * 505432 GTGGTTGTCTGGGTAATAGCACTGCTGGGCTAGGGACAAGGG-GTGTGGTTGTCTGGGTAAAAAC 1 GTGGTTGTCTGGGTGATAGAACTGCTGGG-TAGGGACCAGGGAGTGTGGTTGTCT-GG--AAAAC * * 505496 AGTGAT-GAGTG-AGGAACCAGGGGTGTGGTTGTATGGATGATAACACTGC----TGAGGGACCG 62 ACTGATAG-GTGAAGG-ACCAGGGGTGTGGTTGTCT-G--GATAACACTGCTGGGTGAGGGACCG 505555 GGGGT 122 GGGGT * * * * 505560 GTGGATGTCCT-GGTGATAGAACTGCTGGGTAAGGGACCTGGGAGTATGGTTGTCTGGACAACAC 1 GTGGTTGT-CTGGGTGATAGAACTGCTGGGT-AGGGACCAGGGAGTGTGGTTGTCTGGAAAACAC * * 505624 TGCTAGGTGAAGGACCAGGGGTGTGGTTGTCTGGATAACACTGCTGGGTGAGGGACCAGGGGT 64 TGATAGGTGAAGGACCAGGGGTGTGGTTGTCTGGATAACACTGCTGGGTGAGGGACCGGGGGT * * * * * * 505687 GTGGTTGTATGGGTGATA-ACACAGCTGGGTGAGGGACCAGGGAATGTGTTTGTCTGGATAGCAC 1 GTGGTTGTCTGGGTGATAGA-ACTGCTGGGT-AGGGACCAGGGAGTGTGGTTGTCTGGAAAACAC * * 505751 TGATAGGTGAGGGACCGGGGGTGTGGTTGT 64 TGATAGGTGAAGGACCAGGGGTGTGGTTGT 505781 ATGGGTGATA Statistics Matches: 291, Mismatches: 38, Indels: 44 0.78 0.10 0.12 Matches are distributed among these distances: 123 11 0.04 125 1 0.00 126 31 0.11 127 99 0.34 128 80 0.27 129 43 0.15 130 2 0.01 131 13 0.04 132 11 0.04 ACGTcount: A:0.21, C:0.13, G:0.42, T:0.25 Consensus pattern (126 bp): GTGGTTGTCTGGGTGATAGAACTGCTGGGTAGGGACCAGGGAGTGTGGTTGTCTGGAAAACACTG ATAGGTGAAGGACCAGGGGTGTGGTTGTCTGGATAACACTGCTGGGTGAGGGACCGGGGGT Found at i:505760 original size:86 final size:85 Alignment explanation

Indices: 505318--505818 Score: 450 Period size: 85 Copynumber: 5.8 Consensus size: 85 505308 TATGGGTGTC * * * * * 505318 ATAACACTGCTGGGTGAGGAACCAGTGGGTGTGGTTATCTGGGTTATAACACTGATGGGTGAGGG 1 ATAACACTGCTGGGTGAGGGACCAG-GGGTGTGGTTGTATGGGTGATAACACTGCTGGGTGAGGG * 505383 ACCA-GGGTGTGTTTG-CATGG 65 ACCAGGGGTGTGGTTGTC-TGG * * * * * * 505403 ATAACACTGCTGGGTGAAGGACCGGGGGAGTGGTTGTCTGGGTAATAGCACTGCTGGGCT-AGGG 1 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTATGGGTGATAACACTGCTGGG-TGAGGG * 505467 ACAAGGGGTGTGGTTGTCTGGG 65 ACCAGGGGTGTGGTTGTCT-GG * * * * * * 505489 TAAAAACAGTGATGAGTGAGGAACCAGGGGTGTGGTTGTATGGATGATAACACTGC----TGAGG 1 --ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTATGGGTGATAACACTGCTGGGTGAGG * * 505550 GACCGGGGGTGTGGATGTCCTGGTG 64 GACCAGGGGTGTGGTTGT-CT-G-G * * * * * * * 505575 ATAGA-ACTGCTGGGTAAGGGACCTGGGAGTATGGTTGTCT--G-GACAACACTGCTAGGTGAAG 1 ATA-ACACTGCTGGGTGAGGGACCAGGG-GTGTGGTTGTATGGGTGATAACACTGCTGGGTGAGG 505636 GACCAGGGGTGTGGTTGTCTGG 64 GACCAGGGGTGTGGTTGTCTGG * 505658 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTATGGGTGATAACACAGCTGGGTGAGGGA 1 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTATGGGTGATAACACTGCTGGGTGAGGGA * * 505723 CCAGGGAATGTGTTTGTCTGG 66 CCAGGG-GTGTGGTTGTCTGG * * * * * 505744 ATAGCACTGATAGGTGAGGGACCGGGGGTGTGGTTGTATGGGTGATAGATAACACTGCTGGGGGA 1 ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTAT-GG-G-T-GATAACACTGCTGGGTGA 505809 GGGACC-GGGG 62 GGGACCAGGGG 505819 ATGAATTCAA Statistics Matches: 336, Mismatches: 56, Indels: 45 0.77 0.13 0.10 Matches are distributed among these distances: 82 21 0.06 83 25 0.07 84 73 0.22 85 75 0.22 86 71 0.21 87 2 0.01 88 43 0.13 89 4 0.01 90 22 0.07 ACGTcount: A:0.21, C:0.13, G:0.42, T:0.24 Consensus pattern (85 bp): ATAACACTGCTGGGTGAGGGACCAGGGGTGTGGTTGTATGGGTGATAACACTGCTGGGTGAGGGA CCAGGGGTGTGGTTGTCTGG Found at i:513620 original size:20 final size:20 Alignment explanation

Indices: 513597--513637 Score: 82 Period size: 20 Copynumber: 2.0 Consensus size: 20 513587 CAGCCACCTC 513597 CTGTCTTGATTTGTCATCTT 1 CTGTCTTGATTTGTCATCTT 513617 CTGTCTTGATTTGTCATCTT 1 CTGTCTTGATTTGTCATCTT 513637 C 1 C 513638 ATTCATTCAG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.10, C:0.22, G:0.15, T:0.54 Consensus pattern (20 bp): CTGTCTTGATTTGTCATCTT Found at i:519012 original size:22 final size:21 Alignment explanation

Indices: 518946--519025 Score: 115 Period size: 21 Copynumber: 3.8 Consensus size: 21 518936 AATAGACTGA * 518946 AAATTACATGCAGATACTTTT 1 AAATTACATGCAGATAATTTT * 518967 AAATTATATGCAGATAATTTT 1 AAATTACATGCAGATAATTTT * * 518988 AAATCACATGCGGATAATTTTT 1 AAATTACATGCAGATAA-TTTT 519010 AAATTACATGCAGATA 1 AAATTACATGCAGATA 519026 CTTTCCGCAG Statistics Matches: 51, Mismatches: 7, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 21 33 0.65 22 18 0.35 ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36 Consensus pattern (21 bp): AAATTACATGCAGATAATTTT Found at i:523240 original size:7 final size:7 Alignment explanation

Indices: 523228--523257 Score: 53 Period size: 7 Copynumber: 4.4 Consensus size: 7 523218 AAGCAACAAC 523228 CAAAAAA 1 CAAAAAA 523235 CAAAAAA 1 CAAAAAA 523242 C-AAAAA 1 CAAAAAA 523248 CAAAAAA 1 CAAAAAA 523255 CAA 1 CAA 523258 GACAAATAAT Statistics Matches: 22, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 6 6 0.27 7 16 0.73 ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00 Consensus pattern (7 bp): CAAAAAA Found at i:523248 original size:13 final size:13 Alignment explanation

Indices: 523230--523257 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 523220 GCAACAACCA 523230 AAAAACAAAAAAC 1 AAAAACAAAAAAC 523243 AAAAACAAAAAAC 1 AAAAACAAAAAAC 523256 AA 1 AA 523258 GACAAATAAT 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:0.86, C:0.14, G:0.00, T:0.00 Consensus pattern (13 bp): AAAAACAAAAAAC Found at i:534522 original size:19 final size:19 Alignment explanation

Indices: 534500--534536 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 534490 ATAGTTTAAA * 534500 TATAATGTATCAATTATAG 1 TATAATGTATAAATTATAG * 534519 TATAATTTATAAATTATA 1 TATAATGTATAAATTATA 534537 TACCATTCGC Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 16 1.00 ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46 Consensus pattern (19 bp): TATAATGTATAAATTATAG Found at i:537560 original size:2 final size:2 Alignment explanation

Indices: 537553--537597 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 537543 CAAACCGTGG 537553 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 537595 CT C 1 CT C 537598 AAAGTTTTCG Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:542177 original size:18 final size:19 Alignment explanation

Indices: 542125--542183 Score: 102 Period size: 19 Copynumber: 3.2 Consensus size: 19 542115 TATCATCATG 542125 TTACGAGAGCCCCTTTGGT 1 TTACGAGAGCCCCTTTGGT 542144 TTACGAGAGCCCCTTTGGT 1 TTACGAGAGCCCCTTTGGT * 542163 TTACAAGAG-CCCTTTGGT 1 TTACGAGAGCCCCTTTGGT 542181 TTA 1 TTA 542184 TAATAGTCCC Statistics Matches: 39, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 18 12 0.31 19 27 0.69 ACGTcount: A:0.19, C:0.24, G:0.24, T:0.34 Consensus pattern (19 bp): TTACGAGAGCCCCTTTGGT Found at i:558869 original size:15 final size:15 Alignment explanation

Indices: 558849--558877 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 558839 CACAATGATA 558849 ATGTTATGTAATGAG 1 ATGTTATGTAATGAG 558864 ATGTTATGTAATGA 1 ATGTTATGTAATGA 558878 TAATGTATTA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41 Consensus pattern (15 bp): ATGTTATGTAATGAG Found at i:560049 original size:19 final size:18 Alignment explanation

Indices: 560016--560061 Score: 58 Period size: 19 Copynumber: 2.5 Consensus size: 18 560006 AACCTACTTG * 560016 TAAACAAAAAGGTATATA 1 TAAACAAAAACGTATATA 560034 TAAACACAAAACGTATATGA 1 TAAACA-AAAACGTATAT-A 560054 -AAACAAAA 1 TAAACAAAA 560062 CAATAAGGAA Statistics Matches: 25, Mismatches: 1, Indels: 4 0.83 0.03 0.13 Matches are distributed among these distances: 18 9 0.36 19 15 0.60 20 1 0.04 ACGTcount: A:0.63, C:0.11, G:0.09, T:0.17 Consensus pattern (18 bp): TAAACAAAAACGTATATA Found at i:560059 original size:17 final size:17 Alignment explanation

Indices: 560030--560062 Score: 50 Period size: 17 Copynumber: 1.9 Consensus size: 17 560020 CAAAAAGGTA 560030 TATATAAACACAAAACG 1 TATATAAACACAAAACG 560047 TATATGAAA-ACAAAAC 1 TATAT-AAACACAAAAC 560063 AATAAGGAAA Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 17 12 0.80 18 3 0.20 ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18 Consensus pattern (17 bp): TATATAAACACAAAACG Found at i:560362 original size:46 final size:46 Alignment explanation

Indices: 560295--560387 Score: 177 Period size: 46 Copynumber: 2.0 Consensus size: 46 560285 AAACATGTGA * 560295 TATTTCCTACGTAAATATTCCGCCAAAAATATAGTCCTTGTTAGAT 1 TATTTCCTACGCAAATATTCCGCCAAAAATATAGTCCTTGTTAGAT 560341 TATTTCCTACGCAAATATTCCGCCAAAAATATAGTCCTTGTTAGAT 1 TATTTCCTACGCAAATATTCCGCCAAAAATATAGTCCTTGTTAGAT 560387 T 1 T 560388 TTAAACATTG Statistics Matches: 46, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 46 46 1.00 ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37 Consensus pattern (46 bp): TATTTCCTACGCAAATATTCCGCCAAAAATATAGTCCTTGTTAGAT Done.