Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold204

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: 1152859
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31

Warning! 64757 characters in sequence are not A, C, G, or T


File 2 of 3

Found at i:3087 original size:4 final size:4

Alignment explanation

Indices: 3078--3108 Score: 55 Period size: 4 Copynumber: 8.0 Consensus size: 4 3068 GAAAAGCAAA 3078 AAAT AAAT AAAT AAAT AAAT AAAT AAA- AAAT 1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT 3109 TAAAAATTAA Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 3 3 0.12 4 23 0.88 ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23 Consensus pattern (4 bp): AAAT Found at i:3145 original size:7 final size:7 Alignment explanation

Indices: 3082--3145 Score: 58 Period size: 7 Copynumber: 8.7 Consensus size: 7 3072 AGCAAAAAAT 3082 AAATAAA 1 AAATAAA 3089 TAAATAAA 1 -AAATAAA 3097 TAAATAAA 1 -AAATAAA 3105 AAATTAAA 1 AAA-TAAA * 3113 AATTAAA 1 AAATAAA 3120 AAA-AGAA 1 AAATA-AA * 3127 AAAGAAA 1 AAATAAA * 3134 GAATAAA 1 AAATAAA 3141 AAATA 1 AAATA 3146 TTAAAGAAAT Statistics Matches: 48, Mismatches: 5, Indels: 7 0.80 0.08 0.12 Matches are distributed among these distances: 6 1 0.02 7 25 0.52 8 22 0.46 ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17 Consensus pattern (7 bp): AAATAAA Found at i:17368 original size:12 final size:12 Alignment explanation

Indices: 17351--17381 Score: 55 Period size: 12 Copynumber: 2.7 Consensus size: 12 17341 CAAATAATTT 17351 TGATGAAACAAG 1 TGATGAAACAAG 17363 TGATGAAACAAG 1 TGATGAAACAAG 17375 TG-TGAAA 1 TGATGAAA 17382 AAATTAGAAA Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 11 5 0.26 12 14 0.74 ACGTcount: A:0.48, C:0.06, G:0.26, T:0.19 Consensus pattern (12 bp): TGATGAAACAAG Found at i:18962 original size:19 final size:19 Alignment explanation

Indices: 18938--18974 Score: 58 Period size: 19 Copynumber: 1.9 Consensus size: 19 18928 AGAAAGGATT 18938 TTGAATTGC-ATAGTGCATA 1 TTGAATT-CAATAGTGCATA 18957 TTGAATTCAATAGTGCAT 1 TTGAATTCAATAGTGCAT 18975 TAAGGATTTT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 1 0.06 19 16 0.94 ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38 Consensus pattern (19 bp): TTGAATTCAATAGTGCATA Found at i:23444 original size:21 final size:21 Alignment explanation

Indices: 23420--23491 Score: 81 Period size: 21 Copynumber: 3.4 Consensus size: 21 23410 ATTATGCCGG * 23420 CATGCAAGATAAATATGTTGA 1 CATGCAAGATAAATATGTTAA ** * 23441 CATGCAAGATAGTTATGTCAA 1 CATGCAAGATAAATATGTTAA * * * 23462 CATGCAACATAACTAAGTTAA 1 CATGCAAGATAAATATGTTAA 23483 CATGCAAGA 1 CATGCAAGA 23492 AAACTGCAAT Statistics Matches: 41, Mismatches: 10, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 21 41 1.00 ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25 Consensus pattern (21 bp): CATGCAAGATAAATATGTTAA Found at i:23585 original size:21 final size:21 Alignment explanation

Indices: 23561--23731 Score: 164 Period size: 21 Copynumber: 8.1 Consensus size: 21 23551 AGATGCTACC * * 23561 TATTGATGTCAACATGCAACT 1 TATTTATGTTAACATGCAACT 23582 TATTTATGTTAACATGCAACT 1 TATTTATGTTAACATGCAACT * ** 23603 TCTTTATGTCGACATGCAACT 1 TATTTATGTTAACATGCAACT * 23624 TATTTATGTTGACATGCAACT 1 TATTTATGTTAACATGCAACT * ** 23645 TAGTTATGTTAACATGCAAGA 1 TATTTATGTTAACATGCAACT ** * 23666 TAAATATGTTGACATGCAA-T 1 TATTTATGTTAACATGCAACT ** 23686 ATATTTATGTCGACATGCAACT 1 -TATTTATGTTAACATGCAACT * * * * 23708 TAGTTATGTTGACATACAAAT 1 TATTTATGTTAACATGCAACT 23729 TAT 1 TAT 23732 AAGCTGCATT Statistics Matches: 125, Mismatches: 23, Indels: 4 0.82 0.15 0.03 Matches are distributed among these distances: 21 124 0.99 22 1 0.01 ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38 Consensus pattern (21 bp): TATTTATGTTAACATGCAACT Found at i:23625 original size:42 final size:42 Alignment explanation

Indices: 23561--23731 Score: 200 Period size: 42 Copynumber: 4.1 Consensus size: 42 23551 AGATGCTACC * * 23561 TATTGATGTCAACATGCAACTTATTTATGTTAACATGCAACT 1 TATTTATGTCAACATGCAACTTATTTATGTTGACATGCAACT * * 23603 TCTTTATGTCGACATGCAACTTATTTATGTTGACATGCAACT 1 TATTTATGTCAACATGCAACTTATTTATGTTGACATGCAACT * * ** ** 23645 TAGTTATGTTAACATGCAAGATAAATATGTTGACATGCAA-T 1 TATTTATGTCAACATGCAACTTATTTATGTTGACATGCAACT * * * * 23686 ATATTTATGTCGACATGCAACTTAGTTATGTTGACATACAAAT 1 -TATTTATGTCAACATGCAACTTATTTATGTTGACATGCAACT 23729 TAT 1 TAT 23732 AAGCTGCATT Statistics Matches: 107, Mismatches: 20, Indels: 4 0.82 0.15 0.03 Matches are distributed among these distances: 41 1 0.01 42 105 0.98 43 1 0.01 ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38 Consensus pattern (42 bp): TATTTATGTCAACATGCAACTTATTTATGTTGACATGCAACT Found at i:23674 original size:63 final size:63 Alignment explanation

Indices: 23561--23722 Score: 209 Period size: 63 Copynumber: 2.6 Consensus size: 63 23551 AGATGCTACC * * * * *** 23561 TATTGATGTCAACATGCAACTTATTTATGTTAACATGCAACTTCTTTATGTCGACATGCAACT- 1 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAACATAAATATGTCGACATGCAA-TA * * * 23624 TATTTATGTTGACATGCAACTTAGTTATGTTAACATGCAAGATAAATATGTTGACATGCAATA 1 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAACATAAATATGTCGACATGCAATA * 23687 TATTTATGTCGACATGCAACTTAGTTATGTTGACAT 1 TATTTATGTCGACATGCAACTTAGTTATGTTAACAT 23723 ACAAATTATA Statistics Matches: 86, Mismatches: 12, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 62 1 0.01 63 85 0.99 ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38 Consensus pattern (63 bp): TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAACATAAATATGTCGACATGCAATA Found at i:23790 original size:21 final size:21 Alignment explanation

Indices: 23764--23946 Score: 174 Period size: 21 Copynumber: 8.7 Consensus size: 21 23754 TATCTATCTC * 23764 GCATGTCAACAAAAATAAGTT 1 GCATGTCAACATAAATAAGTT * * 23785 GCATGTCAACAT-ATTCA-TCT 1 GCATGTCAACATAAATAAGT-T * * 23805 CGCTTGTCAACATAAGTAAGTT 1 -GCATGTCAACATAAATAAGTT ** * 23827 GCATGTTGACATAAAAAAGTT 1 GCATGTCAACATAAATAAGTT * 23848 GCATGTCGACATAAATAAGTT 1 GCATGTCAACATAAATAAGTT ** 23869 GCATGTTGACATAAATAAGTT 1 GCATGTCAACATAAATAAGTT * ** 23890 GCATGTCAGCATATTTATA-TT 1 GCATGTCAACATAAATA-AGTT * 23911 GCATGTTAACATAAATAAGTT 1 GCATGTCAACATAAATAAGTT * 23932 GCATGTCGACATAAA 1 GCATGTCAACATAAA 23947 AAGGTAGCAT Statistics Matches: 131, Mismatches: 25, Indels: 12 0.78 0.15 0.07 Matches are distributed among these distances: 19 1 0.01 20 5 0.04 21 119 0.91 22 5 0.04 23 1 0.01 ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31 Consensus pattern (21 bp): GCATGTCAACATAAATAAGTT Found at i:23795 original size:48 final size:45 Alignment explanation

Indices: 23730--23883 Score: 115 Period size: 42 Copynumber: 3.5 Consensus size: 45 23720 CATACAAATT * * 23730 ATAAGCTGCATTTCAACATAAAATTATCTATCTCGCATGTCAACAAAA 1 ATAAGTTGCATGTCAACATAAAA-T-TC-ATCTCGCATGTCAACAAAA * * 23778 ATAAGTTGCATGTCAACAT---ATTCATCTCGCTTGTCAACATAA 1 ATAAGTTGCATGTCAACATAAAATTCATCTCGCATGTCAACAAAA * ** * * * 23820 GTAAGTTGCATGTTGACATAAAA--AAGT-T-GCATGTCGACATAA 1 ATAAGTTGCATGTCAACATAAAATTCA-TCTCGCATGTCAACAAAA ** 23862 ATAAGTTGCATGTTGACATAAA 1 ATAAGTTGCATGTCAACATAAA 23884 TAAGTTGCAT Statistics Matches: 91, Mismatches: 11, Indels: 14 0.78 0.09 0.12 Matches are distributed among these distances: 42 66 0.73 43 4 0.04 44 2 0.02 45 2 0.02 48 17 0.19 ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31 Consensus pattern (45 bp): ATAAGTTGCATGTCAACATAAAATTCATCTCGCATGTCAACAAAA Found at i:24106 original size:21 final size:21 Alignment explanation

Indices: 24031--24117 Score: 95 Period size: 21 Copynumber: 4.2 Consensus size: 21 24021 TCTGATTGCA * 24031 ATTT-TCTTGCATTTCAACAT 1 ATTTATCTTGCATGTCAACAT * * ** 24051 AATTATGTTGCATGTTGACAT 1 ATTTATCTTGCATGTCAACAT * 24072 AATTATCTTGCATGTCAACAT 1 ATTTATCTTGCATGTCAACAT * * 24093 ATTTATCTTGCATGTCGATAT 1 ATTTATCTTGCATGTCAACAT 24114 ATTT 1 ATTT 24118 GATAGAATAT Statistics Matches: 55, Mismatches: 11, Indels: 1 0.82 0.16 0.01 Matches are distributed among these distances: 20 3 0.05 21 52 0.95 ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46 Consensus pattern (21 bp): ATTTATCTTGCATGTCAACAT Found at i:35231 original size:166 final size:166 Alignment explanation

Indices: 34944--36331 Score: 2077 Period size: 166 Copynumber: 8.4 Consensus size: 166 34934 NNNNNNNGAT * * * * ** * 34944 GATGCTTCCATTTTAATTTGAGCTTTTCTGGCCTTATAGTTTTTCAGGGGAAGATTTTTAAATAT 1 GATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGAT * 35009 TTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCATCCTACCCCCGGGGAC 66 TTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGAC * * 35074 CATGATTTGAACAAACTTGAATCTACATTACCTGAG 131 CATGATTTGAACAAACTTGAATCTACACTATCTGAG * * * 35110 GATGCTGT-CATTTTAATTTGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGA 1 GATGCT-TCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGA * 35174 TTTTCTCTATATATTCTTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGA 65 TTTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGA 35239 CCATGATTTGAACAAACTTGAATCTACACTATCTGAG 130 CCATGATTTGAACAAACTTGAATCTACACTATCTGAG * ** * * * 35276 AATGCTTCCACCCAAAGTTGAGCTTTTCTGGCCTAATGGTTTTTGAGAAGAAGATTTTTAAATAT 1 GATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGAT * * 35341 TTTCTATATATATTCCTATGTAAAACAAGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGAC 66 TTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGAC * 35406 CATGATTTGAACAAACTTGAATCTACACTACCTGAG 131 CATGATTTGAACAAACTTGAATCTACACTATCTGAG * * * 35442 AATGCTTCCACTCAAAGGTGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGAT 1 GATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGAT * * * 35507 TTTCTCTATATAATCTTATGTAAAACATGATCCCCCAATTGTGGCCCCTCCCTACCCCCCGGGGA 66 TTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTA-CCCCCGGGGA * 35572 CCATGATTTGAACAAACTTGAATCTGCACTATCTGAG 130 CCATGATTTGAACAAACTTGAATCTACACTATCTGAG * ** * 35609 GATGCTTCCACTTGAAGTTGAGCTTCCCTGG-CTTAATAGTTTTTGAGAAGAAGATTTTTATAGA 1 GATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTT-ATAGTTTTTGAGAAGAAGATTTTTAAAGA * * * 35673 TTTTCTCTACATATTCCTATGTAAAACATGATCCCCAAATTGTGGCCCTACCCTACCCCCGGGGA 65 TTTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGA ** * 35738 CCATGATTTGAACAAACTTGAATCTGTACTATCTGTG 130 CCATGATTTGAACAAACTTGAATCTACACTATCTGAG ** 35775 GATGCTTCCACTTAAAGTTGAGCTTCCCTGG-CTTAATAGTTTTTGAGAAGAAGATTTTTAAAGA 1 GATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTT-ATAGTTTTTGAGAAGAAGATTTTTAAAGA * * 35839 TTTTCTCTACATATTCCTATGTAAAATATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGA 65 TTTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGA ** * 35904 CCATGATTTGAACAAACTTGAATCTGTACTATCTGTG 130 CCATGATTTGAACAAACTTGAATCTACACTATCTGAG ** 35941 GATGCTTCCACTTAAAGTTGAGCTTCCCTGG-CTTAATAGTTTTTGAGAAGAAGATTTTTAAAGA 1 GATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTT-ATAGTTTTTGAGAAGAAGATTTTTAAAGA * * 36005 TTTTCTCTACATATTCCTATGTAAAATATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGA 65 TTTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGA * 36070 CCATGATTTGAACAAACTTGAATCTGCACTATCTGAG 130 CCATGATTTGAACAAACTTGAATCTACACTATCTGAG 36107 GATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGAT 1 GATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGAT * * ** * * 36172 GTTCTCTATATATTCCTATGTAAAACGTGATCCCCCTCTAGTGGCCCCTCCCTACCCCCGGGGAC 66 TTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGAC * * 36237 CATGATTTGAACAAACTTGAATCTACACTACCTGAT 131 CATGATTTGAACAAACTTGAATCTACACTATCTGAG * * * ** * 36273 GATGCCTCCAC--ACAAGTTTAAGCTTTTCAGGCCGAATAGCTTTTGAGAAGAAGATTTTT 1 GATGCTTCCACTTA-AAG-TTGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTT 36332 GAAAAATACC Statistics Matches: 1141, Mismatches: 74, Indels: 14 0.93 0.06 0.01 Matches are distributed among these distances: 164 1 0.00 165 4 0.00 166 985 0.86 167 151 0.13 ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33 Consensus pattern (166 bp): GATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGAT TTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGAC CATGATTTGAACAAACTTGAATCTACACTATCTGAG Found at i:35882 original size:499 final size:498 Alignment explanation

Indices: 34962--36331 Score: 2070 Period size: 499 Copynumber: 2.7 Consensus size: 498 34952 CATTTTAATT * ** * 34962 TGAGCTTTTCTGGCCTTATAGTTTTTCAGGGGAAGATTTTTAAATATTTTCTCTATATATTCCTA 1 TGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTA 35027 TGTAAAACATGATCCCCCAATTGTGGCCCCAT-CCTACCCCCGGGGACCATGATTTGAACAAACT 66 TGTAAAACATGATCCCCCAATTGTGGCCCC-TCCCTACCCCCGGGGACCATGATTTGAACAAACT * * * * * * 35091 TGAATCTACATTACCTGAGGATGCTGT-CATTTTAATTTGAGCTTTTCTGGCCTTATAGTTTTTG 130 TGAATCTGCACTATCTGAGGATGCT-TCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTG * 35155 AGAAGAAGATTTTTAAAGATTTTCTCTATATATTCTTATGTAAAACATGATCCCCCAATTGTGGC 194 AGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGC * 35220 CCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGAATGCTTCC 259 CCTACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGAATGCTTCC ** * * * 35285 ACCCAAAGTTGAGCTTTTCTGGCCTAATGGTTTTTGAGAAGAAGATTTTTAAATATTTTCTATAT 324 ACCCAAAGTTGAGCTTCCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTATAC 35350 ATATTCCTATGTAAAACAAGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTG 389 ATATTCCTATGTAAAACAAGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTG 35415 AACAAACTTGAATCTACACTACCTGAGAATGCTTCCACTCAAAGG 454 AACAAACTTGAATCTACACTACCTGAGAATGCTTCCACTCAAAGG * * 35460 TGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATAATCTTA 1 TGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTA 35525 TGTAAAACATGATCCCCCAATTGTGGCCCCTCCCTACCCCCCGGGGACCATGATTTGAACAAACT 66 TGTAAAACATGATCCCCCAATTGTGGCCCCTCCCTA-CCCCCGGGGACCATGATTTGAACAAACT * ** 35590 TGAATCTGCACTATCTGAGGATGCTTCCACTTGAAGTTGAGCTTCCCTGG-CTTAATAGTTTTTG 130 TGAATCTGCACTATCTGAGGATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTT-ATAGTTTTTG * * * 35654 AGAAGAAGATTTTTATAGATTTTCTCTACATATTCCTATGTAAAACATGATCCCCAAATTGTGGC 194 AGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGC ** * * 35719 CCTACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTGTACTATCTGTGGATGCTTCC 259 CCTACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGAATGCTTCC ** * * 35784 ACTTAAAGTTGAGCTTCCCTGGCTTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTAC 324 ACCCAAAGTTGAGCTTCCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTATAC * * 35849 ATATTCCTATGTAAAATATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTG 389 ATATTCCTATGTAAAACAAGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTG ** * * * * * 35914 AACAAACTTGAATCTGTACTATCTGTGGATGCTTCCACTTAAAGT 454 AACAAACTTGAATCTACACTACCTGAGAATGCTTCCACTCAAAGG ** * 35959 TGAGCTTCCCTGG-CTTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTACATATTCCT 1 TGAGCTTTTCTGGCCTT-ATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCT * * 36023 ATGTAAAATATGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACT 65 ATGTAAAACATGATCCCCCAATTGTGGCCCCTCCCTACCCCCGGGGACCATGATTTGAACAAACT 36088 TGAATCTGCACTATCTGAGGATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTGA 130 TGAATCTGCACTATCTGAGGATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTGA * * ** * 36153 GAAGAAGATTTTTAAAGATGTTCTCTATATATTCCTATGTAAAACGTGATCCCCCTCTAGTGGCC 195 GAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGG-C * * 36218 CCT-CCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGATG-ATGCCTC 259 CCTACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGA-GAATGCTTC * * ** * * * 36281 CACAC-AAGTTTAAGCTTTTCAGGCCGAATAGCTTTTGAGAAGAAGATTTTT 323 CACCCAAAG-TTGAGCTTCCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTT 36332 GAAAAATACC Statistics Matches: 790, Mismatches: 73, Indels: 18 0.90 0.08 0.02 Matches are distributed among these distances: 497 4 0.01 498 332 0.42 499 454 0.57 ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33 Consensus pattern (498 bp): TGAGCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTA TGTAAAACATGATCCCCCAATTGTGGCCCCTCCCTACCCCCGGGGACCATGATTTGAACAAACTT GAATCTGCACTATCTGAGGATGCTTCCACTTAAAGTTGAGCTTTTCTGGCCTTATAGTTTTTGAG AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCC TACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGAATGCTTCCAC CCAAAGTTGAGCTTCCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTATACAT ATTCCTATGTAAAACAAGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAA CAAACTTGAATCTACACTACCTGAGAATGCTTCCACTCAAAGG Found at i:38040 original size:2 final size:2 Alignment explanation

Indices: 38035--38078 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 38025 TGCACACATA 38035 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 38077 CT 1 CT 38079 TTTAAATTAC Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:55085 original size:20 final size:20 Alignment explanation

Indices: 55060--55114 Score: 92 Period size: 20 Copynumber: 2.7 Consensus size: 20 55050 TAAATAAAAT 55060 ATATATACCTCACAATATAA 1 ATATATACCTCACAATATAA * 55080 ATATATACCTCATAATATAA 1 ATATATACCTCACAATATAA 55100 ACTATATACCTCACA 1 A-TATATACCTCACA 55115 TCGATATGCA Statistics Matches: 32, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 20 20 0.62 21 12 0.38 ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31 Consensus pattern (20 bp): ATATATACCTCACAATATAA Found at i:69016 original size:161 final size:161 Alignment explanation

Indices: 68726--69151 Score: 615 Period size: 161 Copynumber: 2.7 Consensus size: 161 68716 TCGCTCGCCT * * * 68726 ATCATACCCAA-AACAAACTTGACCAAGATATTAT-ATAGATAAACCTGCATACCAAATTTCATA 1 ATCATACCCAATATCAAACTTGACCTAGATATTATCAT-GATAAACCTGTATACCAAATTTCAT- ** * * * * 68789 TT-AATATGTGCACCCTCTGCGAAGAAAATGAGTGGAAACTGCAAATAACTCGAATTTTTCTAAG 64 TTCAATATGTTAATCCTATGCGAAGAAAATGAGCGGAAACTGCAAATAACTCAAATTTTTCTAAG 68853 TCCAAGGGCCATAACTCTGTCGAAAATTACTCG 129 TCCAAGGGCCATAACTCTGTCGAAAATTACTCG * * * 68886 ATCATACCCAATATCGAACTTAACCTAGATATTATCATGATAAACCTGTATACCGAATTTCATTT 1 ATCATACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTT * * * 68951 CAATATCTTAATCCTATGCGAAGTAAATGAGCAGAAACTGCAAATAACTCAAATTTTTCTAAGTC 66 CAATATGTTAATCCTATGCGAAGAAAATGAGCGGAAACTGCAAATAACTCAAATTTTTCTAAGTC * 69016 CAAGGGCCATAACTCTGTCGAAAATTGCTCG 131 CAAGGGCCATAACTCTGTCGAAAATTACTCG * * 69047 ATCGTACCCCATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTT 1 ATCATACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTT * * * * 69112 CAATATGTTTATCCTTTGCAAAGAAAATGAACGGAAACTG 66 CAATATGTTAATCCTATGCGAAGAAAATGAGCGGAAACTG 69152 TTGGTGGACC Statistics Matches: 235, Mismatches: 28, Indels: 5 0.88 0.10 0.02 Matches are distributed among these distances: 160 13 0.06 161 220 0.94 162 2 0.01 ACGTcount: A:0.38, C:0.21, G:0.13, T:0.29 Consensus pattern (161 bp): ATCATACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTT CAATATGTTAATCCTATGCGAAGAAAATGAGCGGAAACTGCAAATAACTCAAATTTTTCTAAGTC CAAGGGCCATAACTCTGTCGAAAATTACTCG Found at i:72078 original size:38 final size:38 Alignment explanation

Indices: 72021--72274 Score: 276 Period size: 38 Copynumber: 6.7 Consensus size: 38 72011 AAGTTATTAC * * * * * 72021 CTTTATCCTGCTGGCAGTAATTTCATGTAGAGACTTGG 1 CTTTATCTTACTGACAGTAATTACCTGTAGAGACTTGG * * * * 72059 CTTTATCTTACTGATAGTAATAACCTATAGAGACTTAG 1 CTTTATCTTACTGACAGTAATTACCTGTAGAGACTTGG * * * * * 72097 CTTTATCTTACGGATAGAAATTACCTGGT-GTGACTTGA 1 CTTTATCTTACTGACAGTAATTACCT-GTAGAGACTTGG * * * 72135 CTTTATTTTACTGACAGTAATTACCTGCAGCGACTTGG 1 CTTTATCTTACTGACAGTAATTACCTGTAGAGACTTGG * * * 72173 CTTTATCTTATTGACAGTAATTACCTGTAGAGACTAGT 1 CTTTATCTTACTGACAGTAATTACCTGTAGAGACTTGG * * 72211 CTTTATCTTACTGACAGTAATTACCTGTAGAGATTTGT 1 CTTTATCTTACTGACAGTAATTACCTGTAGAGACTTGG * * 72249 CTTTATTTTACTAACAGTAATTACCT 1 CTTTATCTTACTGACAGTAATTACCT 72275 TAATCTTACA Statistics Matches: 180, Mismatches: 34, Indels: 4 0.83 0.16 0.02 Matches are distributed among these distances: 37 1 0.01 38 178 0.99 39 1 0.01 ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39 Consensus pattern (38 bp): CTTTATCTTACTGACAGTAATTACCTGTAGAGACTTGG Found at i:72181 original size:114 final size:114 Alignment explanation

Indices: 72052--72274 Score: 315 Period size: 114 Copynumber: 2.0 Consensus size: 114 72042 TTCATGTAGA * * 72052 GACTTGGCTTTATCTTACTGATAGTAATAACCTATAGAGACTTAG-CTTTATCTTACGGATAGAA 1 GACTTGGCTTTATCTTACTGACAGTAATAACCTATAGAGAC-TAGTCTTTATCTTACGGACAGAA * * 72116 ATTACCTGGT-GTGACTTGACTTTATTTTACTGACAGTAATTACCTGCAGC 65 ATTACCT-GTAGAGACTTGACTTTATTTTACTAACAGTAATTACCTGCAGC * * * * * 72166 GACTTGGCTTTATCTTATTGACAGTAATTACCTGTAGAGACTAGTCTTTATCTTACTGACAGTAA 1 GACTTGGCTTTATCTTACTGACAGTAATAACCTATAGAGACTAGTCTTTATCTTACGGACAGAAA * * 72231 TTACCTGTAGAGATTTGTCTTTATTTTACTAACAGTAATTACCT 66 TTACCTGTAGAGACTTGACTTTATTTTACTAACAGTAATTACCT 72275 TAATCTTACA Statistics Matches: 96, Mismatches: 11, Indels: 4 0.86 0.10 0.04 Matches are distributed among these distances: 113 5 0.05 114 91 0.95 ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39 Consensus pattern (114 bp): GACTTGGCTTTATCTTACTGACAGTAATAACCTATAGAGACTAGTCTTTATCTTACGGACAGAAA TTACCTGTAGAGACTTGACTTTATTTTACTAACAGTAATTACCTGCAGC Found at i:72352 original size:99 final size:100 Alignment explanation

Indices: 72188--72373 Score: 259 Period size: 99 Copynumber: 1.9 Consensus size: 100 72178 TCTTATTGAC * * * * * * 72188 AGTAATTACCTGTAGAGACTAGTCTTTATCTTACTGACAGTAATTACCTGTAGAGATTTGTCTTT 1 AGTAATTACCTGCAGAGACTAGACTTTATCTTACTGACAGCAAGTACCTGTAGAGACTTGGCTTT * 72253 ATTTTACTAACAGTAATTACCTTAATCTTACAAAT 66 ATCTTACTAACAGTAATTACCTTAATCTTACAAAT * 72288 AGTAATTACCTGCCA-AGACT-GACTTTATCTTACTGACAGCAAGTACCTGTAGATACTTGGCTT 1 AGTAATTACCTG-CAGAGACTAGACTTTATCTTACTGACAGCAAGTACCTGTAGAGACTTGGCTT * * 72351 TATCTTATTGACAGTAATTACCT 65 TATCTTACTAACAGTAATTACCT 72374 GTACAAACTC Statistics Matches: 75, Mismatches: 10, Indels: 3 0.85 0.11 0.03 Matches are distributed among these distances: 99 57 0.76 100 17 0.23 101 1 0.01 ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38 Consensus pattern (100 bp): AGTAATTACCTGCAGAGACTAGACTTTATCTTACTGACAGCAAGTACCTGTAGAGACTTGGCTTT ATCTTACTAACAGTAATTACCTTAATCTTACAAAT Found at i:72407 original size:38 final size:38 Alignment explanation

Indices: 72288--72411 Score: 126 Period size: 38 Copynumber: 3.3 Consensus size: 38 72278 TCTTACAAAT * * 72288 AGTAATTACCTG-CCAAGACT-GACTTTATCTTACTGAC 1 AGTAATTACCTGTACAA-ACTCAACTTTATCTTACTGAC * * * * *** * 72325 AGCAAGTACCTGTAGATACTTGGCTTTATCTTATTGAC 1 AGTAATTACCTGTACAAACTCAACTTTATCTTACTGAC 72363 AGTAATTACCTGTACAAACTCAACTTTATCTTACTGAC 1 AGTAATTACCTGTACAAACTCAACTTTATCTTACTGAC * 72401 ATTAATTACCT 1 AGTAATTACCT 72412 TAATCTTACT Statistics Matches: 69, Mismatches: 16, Indels: 3 0.78 0.18 0.03 Matches are distributed among these distances: 37 13 0.19 38 56 0.81 ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35 Consensus pattern (38 bp): AGTAATTACCTGTACAAACTCAACTTTATCTTACTGAC Found at i:72419 original size:137 final size:138 Alignment explanation

Indices: 72150--72464 Score: 364 Period size: 137 Copynumber: 2.3 Consensus size: 138 72140 TTTTACTGAC * * * * * * 72150 AGTAATTACCTGCAGCGACTTGGCTTTATCTTATTGACAGTAATTACCTGTAGAGACTAGTCTTT 1 AGTAATTACCTGCAGAGACTTGACTTTATCTTACTGACAGCAAGTACCTGTAGAGACTAGGCTTT * * * *** * 72215 ATCTTACTGACAGTAATTACCTGTAGAGATTTGTCTTTATTTTACTAACAGTAATTACCTTAATC 66 ATCTTACTGACAGTAATTACCTGTACAAACTCAACTTTATCTTACTAACAGTAATTACCTTAATC 72280 TTACAAAT 131 TTACAAAT * * 72288 AGTAATTACCTGCCA-AGAC-TGACTTTATCTTACTGACAGCAAGTACCTGTAGATACTTGGCTT 1 AGTAATTACCTG-CAGAGACTTGACTTTATCTTACTGACAGCAAGTACCTGTAGAGACTAGGCTT * * * 72351 TATCTTATTGACAGTAATTACCTGTACAAACTCAACTTTATCTTACTGACATTAATTACCTTAAT 65 TATCTTACTGACAGTAATTACCTGTACAAACTCAACTTTATCTTACTAACAGTAATTACCTTAAT ** * 72416 CTTACTGAC 130 CTTACAAAT * * * * ** 72425 AGTTATTTCCTGGAGGGACTCCACTTTATCTTACTGACAG 1 AGTAATTACCTGCAGAGACTTGACTTTATCTTACTGACAG 72465 TATTAATAAG Statistics Matches: 147, Mismatches: 27, Indels: 6 0.82 0.15 0.03 Matches are distributed among these distances: 136 1 0.01 137 111 0.76 138 33 0.22 139 2 0.01 ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37 Consensus pattern (138 bp): AGTAATTACCTGCAGAGACTTGACTTTATCTTACTGACAGCAAGTACCTGTAGAGACTAGGCTTT ATCTTACTGACAGTAATTACCTGTACAAACTCAACTTTATCTTACTAACAGTAATTACCTTAATC TTACAAAT Found at i:72703 original size:19 final size:19 Alignment explanation

Indices: 72676--72719 Score: 79 Period size: 19 Copynumber: 2.3 Consensus size: 19 72666 ATGACAGATA * 72676 TTTAAACCAAATATATATT 1 TTTACACCAAATATATATT 72695 TTTACACCAAATATATATT 1 TTTACACCAAATATATATT 72714 TTTACA 1 TTTACA 72720 TTTGGTTCAA Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 19 24 1.00 ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43 Consensus pattern (19 bp): TTTACACCAAATATATATT Found at i:74226 original size:97 final size:95 Alignment explanation

Indices: 74039--74232 Score: 336 Period size: 97 Copynumber: 2.0 Consensus size: 95 74029 GGAAATCCCA 74039 ATGAATTAACAGTAACACAATTGGCCACTGAATCTTTGTTTATTCCTTGTCATGAATTAAAATTA 1 ATGAATTAACAGTAACACAATTGGCCACTGAATCTTTGTTTATTCCTTGTCATGAATTAAAATTA 74104 TCTGTTTATTTAATATCTTCTCCTATAAAC 66 TCTGTTTATTTAATATCTTCTCCTATAAAC * * 74134 ATGAATTAACAGTAACA-ATATTGGCTACTGAATCTTTGTTTTTTCCTTATGTCATGAATTAAAA 1 ATGAATTAACAGTAACACA-ATTGGCCACTGAATCTTTGTTTATTCC-T-TGTCATGAATTAAAA 74198 TTATCTGTTTATTTAATATCTTCTCCTATAAAC 63 TTATCTGTTTATTTAATATCTTCTCCTATAAAC 74231 AT 1 AT 74233 TAATCTATAA Statistics Matches: 94, Mismatches: 2, Indels: 4 0.94 0.02 0.04 Matches are distributed among these distances: 94 1 0.01 95 42 0.45 96 1 0.01 97 50 0.53 ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43 Consensus pattern (95 bp): ATGAATTAACAGTAACACAATTGGCCACTGAATCTTTGTTTATTCCTTGTCATGAATTAAAATTA TCTGTTTATTTAATATCTTCTCCTATAAAC Found at i:76032 original size:39 final size:39 Alignment explanation

Indices: 75989--76932 Score: 1656 Period size: 39 Copynumber: 24.0 Consensus size: 39 75979 CTTTGATGTT * * * 75989 TGTGATGGTATCTAGCAAAATAATGTCTTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76028 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACT-GCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA * * 76066 TGTGATGACATCTAGCTAAATAATGTCCACTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76105 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76144 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76183 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76222 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76261 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76300 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76339 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76378 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76417 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76456 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76495 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76534 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA * 76573 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAACA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76612 TGTGATGGCATCTAGCTATTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGC---TAAATAATGTCCTCTGACTAGCA 76654 TGTGATGGCATCTAGCTATTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGC---TAAATAATGTCCTCTGACTAGCA * * 76696 TGTGATGGCATCTACCTATTAAATTATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGC---TAAATAATGTCCTCTGACTAGCA * 76738 TGTGATGGCATCTAGCTAAATAATGTTCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA * * * * 76777 TGTGATGTCATCAAGCTAAAGAATGTTCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA * 76816 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAACA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA * * 76855 TGTGATGGCATCTAGCTCAATAATGTCCTCTGACTAACA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76894 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 1 TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA 76933 AAGGAGATTA Statistics Matches: 876, Mismatches: 25, Indels: 8 0.96 0.03 0.01 Matches are distributed among these distances: 38 36 0.04 39 721 0.82 42 119 0.14 ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31 Consensus pattern (39 bp): TGTGATGGCATCTAGCTAAATAATGTCCTCTGACTAGCA Found at i:77847 original size:55 final size:55 Alignment explanation

Indices: 77763--77987 Score: 369 Period size: 55 Copynumber: 4.1 Consensus size: 55 77753 TTCATCACTA 77763 GTGTACAGCTAAGGTACTGACCTGAGTAGCACTTCGTGCATGGTCTGTGCTATGT 1 GTGTACAGCTAAGGTACTGACCTGAGTAGCACTTCGTGCATGGTCTGTGCTATGT * * * 77818 GTGTACATCTATGGTACTGACCTGAGTAGCACTTTGTGCATGGTCTGTGCTATGT 1 GTGTACAGCTAAGGTACTGACCTGAGTAGCACTTCGTGCATGGTCTGTGCTATGT * * * * 77873 ATATAGAGCTAAGGTACTGACCTGAGTAGCACTTTGTGCATGGTCTGTGCTATGT 1 GTGTACAGCTAAGGTACTGACCTGAGTAGCACTTCGTGCATGGTCTGTGCTATGT * * 77928 GTGTACAGCTAAGGTACTGACCTAAGTAGCACTTCGTGCATAGTCTGTGCTATGT 1 GTGTACAGCTAAGGTACTGACCTGAGTAGCACTTCGTGCATGGTCTGTGCTATGT 77983 GTGTA 1 GTGTA 77988 TCATCCACTT Statistics Matches: 156, Mismatches: 14, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 55 156 1.00 ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33 Consensus pattern (55 bp): GTGTACAGCTAAGGTACTGACCTGAGTAGCACTTCGTGCATGGTCTGTGCTATGT Found at i:83811 original size:26 final size:26 Alignment explanation

Indices: 83782--83833 Score: 95 Period size: 26 Copynumber: 2.0 Consensus size: 26 83772 AAAAATCAAC * 83782 GATCTACTAAGTAATTTAATATAAAT 1 GATCTACTAAGTAATTTAATAAAAAT 83808 GATCTACTAAGTAATTTAATAAAAAT 1 GATCTACTAAGTAATTTAATAAAAAT 83834 TGGATTTTAA Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 25 1.00 ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37 Consensus pattern (26 bp): GATCTACTAAGTAATTTAATAAAAAT Found at i:83877 original size:13 final size:16 Alignment explanation

Indices: 83845--83883 Score: 57 Period size: 16 Copynumber: 2.6 Consensus size: 16 83835 GGATTTTAAA 83845 ATATCATCATACTACT 1 ATATCATCATACTACT 83861 ATATCATCATA-T-C- 1 ATATCATCATACTACT 83874 ATATCATCAT 1 ATATCATCAT 83884 CATATATAAT Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 13 10 0.43 14 1 0.04 15 1 0.04 16 11 0.48 ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38 Consensus pattern (16 bp): ATATCATCATACTACT Found at i:87698 original size:56 final size:56 Alignment explanation

Indices: 87612--88197 Score: 947 Period size: 56 Copynumber: 10.3 Consensus size: 56 87602 AAGAGAGGAG * * 87612 AAAGAAAGTCCATTACAAGAGGCCTGGGGTAAGTCCAGACAGTGAAGGTTGCAAGT 1 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT * * * 87668 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCAAGACTGGGAAGGTTACAAGT 1 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT * 87724 AAAGAGAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT 1 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT * * 87780 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCAAGACAGTGAAGGTTGCAAGT 1 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT * * * 87836 AAAGATCAGGACTGTTCCATTACAAGAGAACTGGGGTAAGTCCAGACAGGGAAGGCTACAAGT 1 AAAGA--A--A--G-TCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT * * 87899 AAAGAGAGTCCATTACAAGAGGACTGGGGTTAGTCCAGACAGTGAAGGTTACAAGT 1 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT 87955 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT 1 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT * 88011 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTGCAAGT 1 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT 88067 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT 1 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT * * * 88123 AAAGAAAGTCTATTACAAGAGGACTGGGGTAAGTCCAGACAGGGAAGGCTACAAGT 1 AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT * 88179 AAAGAAAGTCCATTGCAAG 1 AAAGAAAGTCCATTACAAG 88198 GGGAATGGAC Statistics Matches: 492, Mismatches: 31, Indels: 14 0.92 0.06 0.03 Matches are distributed among these distances: 56 439 0.89 57 1 0.00 58 1 0.00 59 1 0.00 60 1 0.00 62 1 0.00 63 48 0.10 ACGTcount: A:0.38, C:0.15, G:0.30, T:0.18 Consensus pattern (56 bp): AAAGAAAGTCCATTACAAGAGGACTGGGGTAAGTCCAGACAGTGAAGGTTACAAGT Found at i:92240 original size:34 final size:32 Alignment explanation

Indices: 92202--92281 Score: 88 Period size: 33 Copynumber: 2.4 Consensus size: 32 92192 ATTGTCCCTG * * 92202 GGTAAGTCCTCCGCACGCCCTCACATTGTTTTTA 1 GGTAAGTCCTCC-CACG-CCACACATTGTCTTTA * * * 92236 GGTAAGTCTTTCCCTCGCCACACATTGTCTTTG 1 GGTAAGTC-CTCCCACGCCACACATTGTCTTTA 92269 GGTAAGTCCTCCC 1 GGTAAGTCCTCCC 92282 CAGAGGAGTT Statistics Matches: 39, Mismatches: 6, Indels: 4 0.80 0.12 0.08 Matches are distributed among these distances: 32 4 0.10 33 21 0.54 34 11 0.28 35 3 0.08 ACGTcount: A:0.16, C:0.33, G:0.19, T:0.33 Consensus pattern (32 bp): GGTAAGTCCTCCCACGCCACACATTGTCTTTA Found at i:112241 original size:2 final size:2 Alignment explanation

Indices: 112169--112223 Score: 103 Period size: 2 Copynumber: 28.0 Consensus size: 2 112159 TCATTCATAT 112169 TC TC TC TC -C 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 112210 TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC 112224 ACTCATTCCC Statistics Matches: 52, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 1 1 0.02 2 51 0.98 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): TC Found at i:116761 original size:167 final size:167 Alignment explanation

Indices: 116485--116821 Score: 674 Period size: 167 Copynumber: 2.0 Consensus size: 167 116475 TTTGTCTTCC 116485 TGAACAAAGCCCGCCTCTCGATCCACGGAAAGGTTATCAAAACTGTCCTGGCTCCTGGATCCGGA 1 TGAACAAAGCCCGCCTCTCGATCCACGGAAAGGTTATCAAAACTGTCCTGGCTCCTGGATCCGGA 116550 GCTGGATCTCCGTTTGGAGCGACCCATCAGTTTCAGGAAGGAGCTTCGGACTTTACTCCTGGAAA 66 GCTGGATCTCCGTTTGGAGCGACCCATCAGTTTCAGGAAGGAGCTTCGGACTTTACTCCTGGAAA 116615 AGCTTTCACTTTGCTGTGAGCCAGCTGTGTCCATACT 131 AGCTTTCACTTTGCTGTGAGCCAGCTGTGTCCATACT 116652 TGAACAAAGCCCGCCTCTCGATCCACGGAAAGGTTATCAAAACTGTCCTGGCTCCTGGATCCGGA 1 TGAACAAAGCCCGCCTCTCGATCCACGGAAAGGTTATCAAAACTGTCCTGGCTCCTGGATCCGGA 116717 GCTGGATCTCCGTTTGGAGCGACCCATCAGTTTCAGGAAGGAGCTTCGGACTTTACTCCTGGAAA 66 GCTGGATCTCCGTTTGGAGCGACCCATCAGTTTCAGGAAGGAGCTTCGGACTTTACTCCTGGAAA 116782 AGCTTTCACTTTGCTGTGAGCCAGCTGTGTCCATACT 131 AGCTTTCACTTTGCTGTGAGCCAGCTGTGTCCATACT 116819 TGA 1 TGA 116822 GGTAGAGCCT Statistics Matches: 170, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 167 170 1.00 ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26 Consensus pattern (167 bp): TGAACAAAGCCCGCCTCTCGATCCACGGAAAGGTTATCAAAACTGTCCTGGCTCCTGGATCCGGA GCTGGATCTCCGTTTGGAGCGACCCATCAGTTTCAGGAAGGAGCTTCGGACTTTACTCCTGGAAA AGCTTTCACTTTGCTGTGAGCCAGCTGTGTCCATACT Found at i:121303 original size:2 final size:2 Alignment explanation

Indices: 121296--121334 Score: 71 Period size: 2 Copynumber: 20.0 Consensus size: 2 121286 TTCTCTGTCC 121296 CT CT CT CT CT CT C- 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 121335 GACTTACCTA Statistics Matches: 36, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 1 1 0.03 2 35 0.97 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:138979 original size:2 final size:2 Alignment explanation

Indices: 138972--139017 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 138962 TATTTTTCTG 138972 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 139014 GA GA 1 GA GA 139018 TTGGGAAAAC Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:142505 original size:21 final size:21 Alignment explanation

Indices: 142487--142612 Score: 146 Period size: 21 Copynumber: 6.0 Consensus size: 21 142477 GCAACATACG 142487 TAAGTTGCATGTTGACATAAA 1 TAAGTTGCATGTTGACATAAA * 142508 TAAGTTGCATGTCGACATAAA 1 TAAGTTGCATGTTGACATAAA 142529 TAAGTTGCATGTTGACATAAA 1 TAAGTTGCATGTTGACATAAA * *** 142550 TAAGTTGCATG-TCAGCATTTT 1 TAAGTTGCATGTTGA-CATAAA ** * 142571 TATCTTGCATGTTAACATAAA 1 TAAGTTGCATGTTGACATAAA ** 142592 TAAGTTGCATGTCAACATAAA 1 TAAGTTGCATGTTGACATAAA 142613 AAAGGTAACA Statistics Matches: 88, Mismatches: 15, Indels: 4 0.82 0.14 0.04 Matches are distributed among these distances: 20 2 0.02 21 84 0.95 22 2 0.02 ACGTcount: A:0.37, C:0.13, G:0.17, T:0.34 Consensus pattern (21 bp): TAAGTTGCATGTTGACATAAA Found at i:142539 original size:42 final size:41 Alignment explanation

Indices: 142487--142612 Score: 171 Period size: 42 Copynumber: 3.0 Consensus size: 41 142477 GCAACATACG 142487 TAAGTTGCATGTTGACATAAATAAGTTGCATGTCGACATAAA 1 TAAGTTGCATGTTGACATAAATAAGTTGCATGTC-ACATAAA *** 142529 TAAGTTGCATGTTGACATAAATAAGTTGCATGTCAGCATTTT 1 TAAGTTGCATGTTGACATAAATAAGTTGCATGTCA-CATAAA ** * 142571 TATCTTGCATGTTAACATAAATAAGTTGCATGTCAACATAAA 1 TAAGTTGCATGTTGACATAAATAAGTTGCATGTC-ACATAAA 142613 AAAGGTAACA Statistics Matches: 73, Mismatches: 9, Indels: 4 0.85 0.10 0.05 Matches are distributed among these distances: 41 1 0.01 42 71 0.97 43 1 0.01 ACGTcount: A:0.37, C:0.13, G:0.17, T:0.34 Consensus pattern (41 bp): TAAGTTGCATGTTGACATAAATAAGTTGCATGTCACATAAA Found at i:142630 original size:63 final size:63 Alignment explanation

Indices: 142512--142630 Score: 150 Period size: 63 Copynumber: 1.9 Consensus size: 63 142502 CATAAATAAG * ** * ** * 142512 TTGCATGTCGACATAAATAAGTTGCATGTTGACATAAATAAGTTGCATGTCAGCATTTTTATC 1 TTGCATGTCAACATAAATAAGTTGCATGTCAACATAAAAAAGTAACATCTCAGCATTTTTATC * 142575 TTGCATGTTAACATAAATAAGTTGCATGTCAACATAAAAAAGGTAACATCT-AGCAT 1 TTGCATGTCAACATAAATAAGTTGCATGTCAACATAAAAAA-GTAACATCTCAGCAT 142631 CTTGGATGTC Statistics Matches: 47, Mismatches: 8, Indels: 2 0.82 0.14 0.04 Matches are distributed among these distances: 63 41 0.87 64 6 0.13 ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33 Consensus pattern (63 bp): TTGCATGTCAACATAAATAAGTTGCATGTCAACATAAAAAAGTAACATCTCAGCATTTTTATC Found at i:142725 original size:21 final size:20 Alignment explanation

Indices: 142697--142778 Score: 92 Period size: 21 Copynumber: 4.0 Consensus size: 20 142687 ATTGCAATTT 142697 TCTTGCATGTCAACATAGTTA 1 TCTTGCATGTCAACATA-TTA * * ** 142718 TGTTGCATTTTGACATAATTA 1 TCTTGCATGTCAACAT-ATTA 142739 TCTTGCATGTCAACATATTAA 1 TCTTGCATGTCAACATATT-A * 142760 TCTTGCATGTCGACATATT 1 TCTTGCATGTCAACATATT 142779 TGATAGAAAA Statistics Matches: 50, Mismatches: 9, Indels: 4 0.79 0.14 0.06 Matches are distributed among these distances: 20 3 0.06 21 46 0.92 22 1 0.02 ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41 Consensus pattern (20 bp): TCTTGCATGTCAACATATTA Found at i:142766 original size:42 final size:42 Alignment explanation

Indices: 142692--142776 Score: 118 Period size: 42 Copynumber: 2.0 Consensus size: 42 142682 ATCTGATTGC * * * * 142692 AATTTTCTTGCATGTCAACATAGTTATGTTGCATTTTGACAT 1 AATTATCTTGCATGTCAACATAGTTATCTTGCATGTCGACAT 142734 AATTATCTTGCATGTCAACATA-TTAATCTTGCATGTCGACAT 1 AATTATCTTGCATGTCAACATAGTT-ATCTTGCATGTCGACAT 142776 A 1 A 142777 TTTGATAGAA Statistics Matches: 38, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 41 2 0.05 42 36 0.95 ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41 Consensus pattern (42 bp): AATTATCTTGCATGTCAACATAGTTATCTTGCATGTCGACAT Found at i:143706 original size:57 final size:57 Alignment explanation

Indices: 143637--143773 Score: 222 Period size: 57 Copynumber: 2.4 Consensus size: 57 143627 TCTAATAAAG * 143637 ATCTTTCATGAATTTTCTCGAAACCCCTTTTGGCAAATAAATCGGCACTAAG-GTAGA 1 ATCTTTCATGAATTCTCTCGAAACCCCTTTTGGCAAATAAATCGGCACT-AGTGTAGA * * * 143694 ATCTTTCATGAATTCTCTCGAAACCCTTTTTGGCAAATAAATCGGCACTGGTGTGGA 1 ATCTTTCATGAATTCTCTCGAAACCCCTTTTGGCAAATAAATCGGCACTAGTGTAGA 143751 ATCTTTCATGAATTCTCTCGAAA 1 ATCTTTCATGAATTCTCTCGAAA 143774 TCTACTTAGC Statistics Matches: 75, Mismatches: 4, Indels: 2 0.93 0.05 0.02 Matches are distributed among these distances: 56 1 0.01 57 74 0.99 ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34 Consensus pattern (57 bp): ATCTTTCATGAATTCTCTCGAAACCCCTTTTGGCAAATAAATCGGCACTAGTGTAGA Found at i:150119 original size:21 final size:21 Alignment explanation

Indices: 150095--150166 Score: 85 Period size: 21 Copynumber: 3.4 Consensus size: 21 150085 ATCTGCCACC 150095 ACTTGTCAGATAATTATGTCG 1 ACTTGTCAGATAATTATGTCG * 150116 ACTTGTCAGAT-CTTGATGTCG 1 ACTTGTCAGATAATT-ATGTCG ** 150137 ACTTGTTTGATAATTATGTTC- 1 ACTTGTCAGATAATTATG-TCG 150158 ACTTGTCAG 1 ACTTGTCAG 150167 TTCTTTAAGT Statistics Matches: 42, Mismatches: 6, Indels: 6 0.78 0.11 0.11 Matches are distributed among these distances: 20 2 0.05 21 36 0.86 22 4 0.10 ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42 Consensus pattern (21 bp): ACTTGTCAGATAATTATGTCG Found at i:150311 original size:42 final size:42 Alignment explanation

Indices: 150264--150403 Score: 140 Period size: 42 Copynumber: 3.4 Consensus size: 42 150254 TAATATTTTC *** 150264 TGACAAGTCGACATAATCATCTTTTAAGTCGAT-ATAATTATT 1 TGACAAGTCGACATAATCATCTGACAAGTCG-TCATAATTATT * * 150306 TGACAAGTCGACATTATTATCTGACAAGTCGTCATAATTATT 1 TGACAAGTCGACATAATCATCTGACAAGTCGTCATAATTATT * * * * ** * * 150348 TGACAAGACGACA-AAACATCAGACAAGACAACATCATTATC 1 TGACAAGTCGACATAATCATCTGACAAGTCGTCATAATTATT 150389 TGACAAGTCGACATA 1 TGACAAGTCGACATA 150404 CAATATGAAT Statistics Matches: 80, Mismatches: 16, Indels: 4 0.80 0.16 0.04 Matches are distributed among these distances: 41 32 0.40 42 48 0.60 ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29 Consensus pattern (42 bp): TGACAAGTCGACATAATCATCTGACAAGTCGTCATAATTATT Found at i:150395 original size:21 final size:21 Alignment explanation

Indices: 150262--150403 Score: 106 Period size: 21 Copynumber: 6.8 Consensus size: 21 150252 AATAATATTT * * 150262 TCTGACAAGTCGACATAATCA 1 TCTGACAAGACGACATAATTA *** * * 150283 TCTTTTAAGTCGATATAATTA 1 TCTGACAAGACGACATAATTA * * * 150304 TTTGACAAGTCGACATTATTA 1 TCTGACAAGACGACATAATTA * * 150325 TCTGACAAGTCGTCATAATTA 1 TCTGACAAGACGACATAATTA * ** 150346 TTTGACAAGACGACA-AAACA 1 TCTGACAAGACGACATAATTA * * * 150366 TCAGACAAGACAACATCATTA 1 TCTGACAAGACGACATAATTA * 150387 TCTGACAAGTCGACATA 1 TCTGACAAGACGACATA 150404 CAATATGAAT Statistics Matches: 91, Mismatches: 29, Indels: 2 0.75 0.24 0.02 Matches are distributed among these distances: 20 15 0.16 21 76 0.84 ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29 Consensus pattern (21 bp): TCTGACAAGACGACATAATTA Found at i:150478 original size:21 final size:21 Alignment explanation

Indices: 150452--150612 Score: 135 Period size: 21 Copynumber: 7.7 Consensus size: 21 150442 TTATTTTTTC * * 150452 TGTCAGATAATAATGTTAACT 1 TGTCAGATAATTATGTCAACT ** * 150473 TGTCAGATCTTTATGTCGACT 1 TGTCAGATAATTATGTCAACT ** 150494 TGAT-AGATAATTATGTTTACT 1 TG-TCAGATAATTATGTCAACT ** * 150515 TGTCAGATCTTTATGTCGACT 1 TGTCAGATAATTATGTCAACT * * 150536 TGACAGATAATTATGTTAACT 1 TGTCAGATAATTATGTCAACT ** * 150557 TGTCAGATCTTTATGTCGACT 1 TGTCAGATAATTATGTCAACT * * 150578 TGTCAGATGATTATGTAAACT 1 TGTCAGATAATTATGTCAACT * * 150599 TTTCAGATATTTAT 1 TGTCAGATAATTAT 150613 TTCGACTTAT Statistics Matches: 108, Mismatches: 30, Indels: 4 0.76 0.21 0.03 Matches are distributed among these distances: 20 1 0.01 21 106 0.98 22 1 0.01 ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43 Consensus pattern (21 bp): TGTCAGATAATTATGTCAACT Found at i:150504 original size:42 final size:42 Alignment explanation

Indices: 150456--150620 Score: 242 Period size: 42 Copynumber: 3.9 Consensus size: 42 150446 TTTTTCTGTC * 150456 AGATAATAATGTTAACTTGTCAGATCTTTATGTCGACTTGAT 1 AGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTTGAT * * 150498 AGATAATTATGTTTACTTGTCAGATCTTTATGTCGACTTGAC 1 AGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTTGAT 150540 AGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTTG-T 1 AGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTTGAT * * * * * 150581 CAGATGATTATGTAAACTTTTCAGATATTTATTTCGACTT 1 -AGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTT 150621 ATATGAAATA Statistics Matches: 112, Mismatches: 10, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 42 112 1.00 ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43 Consensus pattern (42 bp): AGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTTGAT Found at i:150620 original size:21 final size:21 Alignment explanation

Indices: 150470--150620 Score: 144 Period size: 21 Copynumber: 7.2 Consensus size: 21 150460 AATAATGTTA * 150470 ACTTGTCAGATCTTTATGTCG 1 ACTTGTCAGATATTTATGTCG * ** 150491 ACTTGAT-AGATAATTATGTTT 1 ACTTG-TCAGATATTTATGTCG * 150512 ACTTGTCAGATCTTTATGTCG 1 ACTTGTCAGATATTTATGTCG * * ** 150533 ACTTGACAGATAATTATGTTA 1 ACTTGTCAGATATTTATGTCG * 150554 ACTTGTCAGATCTTTATGTCG 1 ACTTGTCAGATATTTATGTCG ** 150575 ACTTGTCAGATGA-TTATGTAA 1 ACTTGTCAGAT-ATTTATGTCG * * 150596 ACTTTTCAGATATTTATTTCG 1 ACTTGTCAGATATTTATGTCG 150617 ACTT 1 ACTT 150621 ATATGAAATA Statistics Matches: 101, Mismatches: 25, Indels: 8 0.75 0.19 0.06 Matches are distributed among these distances: 20 2 0.02 21 98 0.97 22 1 0.01 ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44 Consensus pattern (21 bp): ACTTGTCAGATATTTATGTCG Found at i:150738 original size:21 final size:21 Alignment explanation

Indices: 150712--150805 Score: 91 Period size: 21 Copynumber: 4.5 Consensus size: 21 150702 ATGGTTATTT * 150712 TCTGACAAGTCAACATAAAGA 1 TCTGACAAGTCAACATAAATA ** 150733 TCTGACAAGTTGACATAAATA 1 TCTGACAAGTCAACATAAATA * * 150754 TCTGACAAGTCGACAT-TATCA 1 TCTGACAAGTCAACATAAAT-A * * * * 150775 TATGATAAGTTAACATAATTA 1 TCTGACAAGTCAACATAAATA 150796 TCTGACAAGT 1 TCTGACAAGT 150806 GGTGGCAGAT Statistics Matches: 58, Mismatches: 13, Indels: 4 0.77 0.17 0.05 Matches are distributed among these distances: 20 2 0.03 21 55 0.95 22 1 0.02 ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29 Consensus pattern (21 bp): TCTGACAAGTCAACATAAATA Found at i:152368 original size:2 final size:2 Alignment explanation

Indices: 152361--152411 Score: 102 Period size: 2 Copynumber: 25.5 Consensus size: 2 152351 TACGTGTCTG 152361 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 152403 CT CT CT CT C 1 CT CT CT CT C 152412 AGCGGGATGT Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 49 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:155388 original size:13 final size:13 Alignment explanation

Indices: 155370--155394 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 155360 TTCTACGGGC 155370 TTAGTGGCTGCTG 1 TTAGTGGCTGCTG 155383 TTAGTGGCTGCT 1 TTAGTGGCTGCT 155395 AGCTTCAGTC Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.08, C:0.16, G:0.36, T:0.40 Consensus pattern (13 bp): TTAGTGGCTGCTG Found at i:156738 original size:23 final size:23 Alignment explanation

Indices: 156712--156757 Score: 65 Period size: 23 Copynumber: 2.0 Consensus size: 23 156702 TGTATGTAAG 156712 CCCCCTACATTAAATGCACAATA 1 CCCCCTACATTAAATGCACAATA * * * 156735 CCCCGTACATTAGATTCACAATA 1 CCCCCTACATTAAATGCACAATA 156758 GCCCATGCAG Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 23 20 1.00 ACGTcount: A:0.37, C:0.33, G:0.07, T:0.24 Consensus pattern (23 bp): CCCCCTACATTAAATGCACAATA Found at i:162677 original size:5 final size:5 Alignment explanation

Indices: 162658--162753 Score: 126 Period size: 5 Copynumber: 19.4 Consensus size: 5 162648 CTGTAAAGTG * * 162658 CGAAA CGAAA TCGAAA CGAAA CGAAA CGAAA CGAAA CCAAT CGAAA CGAAA 1 CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA * 162709 CGAAA CCAAA CGAAA CGAAA C-AAA --AAA TCGAAA CGAAA CGAAA CG 1 CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA -CGAAA CGAAA CGAAA CG 162754 GAATTTAAAC Statistics Matches: 81, Mismatches: 6, Indels: 8 0.85 0.06 0.08 Matches are distributed among these distances: 3 3 0.04 4 3 0.04 5 67 0.83 6 8 0.10 ACGTcount: A:0.58, C:0.22, G:0.17, T:0.03 Consensus pattern (5 bp): CGAAA Found at i:162945 original size:5 final size:5 Alignment explanation

Indices: 162935--163036 Score: 125 Period size: 5 Copynumber: 20.2 Consensus size: 5 162925 TCGATTTTTG * * * * 162935 GTTTC GTTTC GTTTG GTTTC GTTTG GTTTC GATTG GTTTC GTTTC GTTTC 1 GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC * * 162985 GATTG GTTTC GTTTC GTTTC G-TTC GATTTC GTTTC GTTTC GATTTC GTTTC 1 GTTTC GTTTC GTTTC GTTTC GTTTC G-TTTC GTTTC GTTTC G-TTTC GTTTC 163036 G 1 G 163037 CACTTTACAG Statistics Matches: 82, Mismatches: 12, Indels: 6 0.82 0.12 0.06 Matches are distributed among these distances: 4 4 0.05 5 69 0.84 6 9 0.11 ACGTcount: A:0.04, C:0.16, G:0.25, T:0.56 Consensus pattern (5 bp): GTTTC Found at i:162963 original size:20 final size:20 Alignment explanation

Indices: 162935--163036 Score: 141 Period size: 20 Copynumber: 5.0 Consensus size: 20 162925 TCGATTTTTG 162935 GTTTCGTTTCGTTTGGTTTC 1 GTTTCGTTTCGTTTGGTTTC * * 162955 GTTTGGTTTCGATTGGTTTC 1 GTTTCGTTTCGTTTGGTTTC * 162975 GTTTCGTTTCGATTGGTTTC 1 GTTTCGTTTCGTTTGGTTTC * * 162995 GTTTCGTTTCGTTCGATTTC 1 GTTTCGTTTCGTTTGGTTTC * 163015 GTTTCGTTTCGATTTCGTTTC 1 GTTTCGTTTCG-TTTGGTTTC 163036 G 1 G 163037 CACTTTACAG Statistics Matches: 72, Mismatches: 9, Indels: 1 0.88 0.11 0.01 Matches are distributed among these distances: 20 65 0.90 21 7 0.10 ACGTcount: A:0.04, C:0.16, G:0.25, T:0.56 Consensus pattern (20 bp): GTTTCGTTTCGTTTGGTTTC Found at i:167680 original size:2 final size:2 Alignment explanation

Indices: 167675--167715 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 167665 TGCTCTTCAG 167675 CT CT CT CT CT CT CT CT CT CT CT 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 167716 CACACACACA Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:170954 original size:1 final size:1 Alignment explanation

Indices: 170948--170974 Score: 54 Period size: 1 Copynumber: 27.0 Consensus size: 1 170938 ATGGAAAATT 170948 AAAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 170975 GCTCTGAATA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 26 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:171040 original size:2 final size:2 Alignment explanation

Indices: 171033--171057 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 171023 TGTTCAACAA 171033 CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT C 171058 CTAATGAATG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48 Consensus pattern (2 bp): CT Found at i:174362 original size:161 final size:161 Alignment explanation

Indices: 174091--175041 Score: 1350 Period size: 161 Copynumber: 6.0 Consensus size: 161 174081 AATATAATAT * * * * ** * 174091 AACTGGAATTTTTCTAAGTTCAAGGGCCATAACTCTGTCTAAAATTGCTCTATCACACCCAAAAT 1 AACTAGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAATAT * ** * * * * * ** * 174156 CAAACTTGACCTAGATATTATTTTGATAAATCTGTATATCAAATTTCATATCCATATGTGCACCC 66 CGAACTTGACCTAGATATTATCATGATAAACCTATATACCAAATTTCATTTCAATATGTTTATCC ** * 174221 TCTGCGAAGAAAATGAGCAAAAACTGCAAAT 131 TCTGCGAAGAAAATGAGCGGAAACTGCAAAA * * * 174252 ATCTCGAATTTTTCTATGTCCAAGAGG-CATAACTCTGTCGAAAATTGCTCGATCGTACCCAATA 1 AACTAGAATTTTTCTAAGTCCAAG-GGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAATA * 174316 TCGAACTTGACCTAGATATTATCATGATAAACCTATATACCAAATTTCATTTCAATTTGTTTATC 65 TCGAACTTGACCTAGATATTATCATGATAAACCTATATACCAAATTTCATTTCAATATGTTTATC * * 174381 CTCTGCAAAGAAAATGAGCGGAAACTGCAAAT 130 CTCTGCGAAGAAAATGAGCGGAAACTGCAAAA * * * * * 174413 AACTGGAATTTTTTTTACGTCCAAGGGCTATAACTCTGTCGAAAATTGCTCGATTGTACCCAATA 1 AACTAGAA-TTTTTCTAAGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAATA * * * 174478 TCGAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAATATGTTCATT 65 TCGAACTTGACCTAGATATTATCATGATAAACCTATATACCAAATTTCATTTCAATATGTTTATC * 174543 CTCTGCGAAGAAAATGAGCAGAAACTGCAAAA 130 CTCTGCGAAGAAAATGAGCGGAAACTGCAAAA * * 174575 AACTAGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATTGTATCCAATAT 1 AACTAGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAATAT ** 174640 TAAACTTGACCTAGATA--ATC---AT--A--TAT-T-CCAAATTTCATTTCAATATGTTTATCC 66 CGAACTTGACCTAGATATTATCATGATAAACCTATATACCAAATTTCATTTCAATATGTTTATCC * 174694 TCTGCGAAGAAAATGAGCGGAAACTGCAGAA 131 TCTGCGAAGAAAATGAGCGGAAACTGCAAAA * * 174725 AACTAGAATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATTGTACCCAATAT 1 AACTAGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAATAT * * * * 174790 CGAACTTGACTTAGATATTATCATGATGAACCTGTATACTAAATTTCATTTCAATATGTTTATCC 66 CGAACTTGACCTAGATATTATCATGATAAACCTATATACCAAATTTCATTTCAATATGTTTATCC 174855 TCTGCGAAGAAAATGAGCGGAAACTGCAAAA 131 TCTGCGAAGAAAATGAGCGGAAACTGCAAAA 174886 AACTAGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAATAT 1 AACTAGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAATAT * 174951 CGAACTTGACCTAGATATTATCATGATAATCCTATATACCAAATTTCATTTCAATATGTTTATCC 66 CGAACTTGACCTAGATATTATCATGATAAACCTATATACCAAATTTCATTTCAATATGTTTATCC * * 175016 CCTGCGAAGAAAATGAACGGAAACTG 131 TCTGCGAAGAAAATGAGCGGAAACTG 175042 TTGGTGGACC Statistics Matches: 710, Mismatches: 66, Indels: 28 0.88 0.08 0.03 Matches are distributed among these distances: 150 131 0.18 151 1 0.00 152 5 0.01 154 1 0.00 155 2 0.00 156 2 0.00 157 1 0.00 159 5 0.01 160 1 0.00 161 413 0.58 162 148 0.21 ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31 Consensus pattern (161 bp): AACTAGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAATAT CGAACTTGACCTAGATATTATCATGATAAACCTATATACCAAATTTCATTTCAATATGTTTATCC TCTGCGAAGAAAATGAGCGGAAACTGCAAAA Found at i:174848 original size:311 final size:317 Alignment explanation

Indices: 174089--175041 Score: 1375 Period size: 311 Copynumber: 3.0 Consensus size: 317 174079 AAAATATAAT * * * * *** * 174089 ATAACTGGAATTTTTCTAAGTTCAAGGGCCATAACTCTGTCTAAAATTGCTCTATCACACCCAAA 1 ATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATTGTACCCAAT * ** * * * * 174154 ATCAAACTTGACCTAGATATTATTTTGATAAATCTGTATA-TCAAATTTCATATCCATATGTGCA 66 ATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACT-AAATTTCATTTCAATATGTTCA * * * * * * 174218 CCCTCTGCGAAGAAAATGAGCAAAAACTGCAAATATCTCGAATTTTTCTATGTCCAAGAGG-CAT 130 TCCTCTGCGAAGAAAATGAGCAGAAACTGCAAAAAACTAGAATTTTTCTAAGTCCAAG-GGCCAT 174282 AACTCTGTCGAAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATATTATCATGATAAA 194 AACTCTGTCGAAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATA-TATCA--AT-AA * * 174347 CCTATATACCAAATTTCATTTCAATTTGTTTATCCTCTGCAAAGAAAATGAGCGGAAACTGCAA 255 -CTATATACCAAATTTCATTTCAATATGTTTATCCTCTGCGAAGAAAATGAGCGGAAACTGCAA * * 174411 ATAACTGGAATTTTTTTTACGTCCAAGGGCTATAACTCTGTCGAAAATTGCTCGATTGTACCCAA 1 ATAACTGGAA-TTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATTGTACCCAA * 174476 TATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAATATGTTCA 65 TATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACTAAATTTCATTTCAATATGTTCA * 174541 TTCTCTGCGAAGAAAATGAGCAGAAACTGCAAAAAACTAGAATTTTTCTAAGTCCAAGGGCCATA 130 TCCTCTGCGAAGAAAATGAGCAGAAACTGCAAAAAACTAGAATTTTTCTAAGTCCAAGGGCCATA * * ** 174606 ACTCTGTCGAAAATTGCTCGATTGTATCCAATATTAAACTTGACCTAGATA-ATC-AT-A-TAT- 195 ACTCTGTCGAAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATATATCAATAACTATA 174666 T-CCAAATTTCATTTCAATATGTTTATCCTCTGCGAAGAAAATGAGCGGAAACTGCAGA 260 TACCAAATTTCATTTCAATATGTTTATCCTCTGCGAAGAAAATGAGCGGAAACTGCA-A * 174724 A-AACTAGAATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATTGTACCCAAT 1 ATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATTGTACCCAAT * * * 174788 ATCGAACTTGACTTAGATATTATCATGATGAACCTGTATACTAAATTTCATTTCAATATGTTTAT 66 ATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACTAAATTTCATTTCAATATGTTCAT * 174853 CCTCTGCGAAGAAAATGAGCGGAAACTGCAAAAAACTAGAATTTTTCTAAGTCCAAGGGCCATAA 131 CCTCTGCGAAGAAAATGAGCAGAAACTGCAAAAAACTAGAATTTTTCTAAGTCCAAGGGCCATAA 174918 CTCTGTCGAAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATATTATCATGATAATCC 196 CTCTGTCGAAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATA-TATCA--ATAA--C * * 174983 TATATACCAAATTTCATTTCAATATGTTTATCCCCTGCGAAGAAAATGAACGGAAACTG 256 TATATACCAAATTTCATTTCAATATGTTTATCCTCTGCGAAGAAAATGAGCGGAAACTG 175042 TTGGTGGACC Statistics Matches: 570, Mismatches: 46, Indels: 30 0.88 0.07 0.05 Matches are distributed among these distances: 311 223 0.39 312 60 0.11 313 6 0.01 314 3 0.01 316 3 0.01 317 1 0.00 318 2 0.00 320 3 0.01 321 4 0.01 322 63 0.11 323 202 0.35 ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31 Consensus pattern (317 bp): ATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATTGTACCCAAT ATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACTAAATTTCATTTCAATATGTTCAT CCTCTGCGAAGAAAATGAGCAGAAACTGCAAAAAACTAGAATTTTTCTAAGTCCAAGGGCCATAA CTCTGTCGAAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATATATCAATAACTATAT ACCAAATTTCATTTCAATATGTTTATCCTCTGCGAAGAAAATGAGCGGAAACTGCAA Found at i:175061 original size:8 final size:8 Alignment explanation

Indices: 175056--175085 Score: 51 Period size: 8 Copynumber: 3.8 Consensus size: 8 175046 TGGACCGAGC 175056 GACCGACA 1 GACCGACA 175064 GACCGACA 1 GACCGACA * 175072 GACCGACC 1 GACCGACA 175080 GACCGA 1 GACCGA 175086 AGCAAAGCAA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 8 21 1.00 ACGTcount: A:0.33, C:0.40, G:0.27, T:0.00 Consensus pattern (8 bp): GACCGACA Found at i:179154 original size:11 final size:10 Alignment explanation

Indices: 179137--179165 Score: 58 Period size: 10 Copynumber: 2.9 Consensus size: 10 179127 TAAATAATAA 179137 TAAAAAAAAT 1 TAAAAAAAAT 179147 TAAAAAAAAT 1 TAAAAAAAAT 179157 TAAAAAAAA 1 TAAAAAAAA 179166 CCAATTCAGA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 19 1.00 ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17 Consensus pattern (10 bp): TAAAAAAAAT Found at i:184527 original size:37 final size:37 Alignment explanation

Indices: 184477--185082 Score: 408 Period size: 37 Copynumber: 17.2 Consensus size: 37 184467 TGTAGAAGAC * * 184477 CCCCTTCCTGTTTTGTATTTGTAAGAGCCTTCCTGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT * * 184514 CCCCTTCCTGTTTTAAATTTTTAGGAGCCTTCCTGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT * ** * * 184551 CCCGTTTTTGTTTTATATTTTTAGAAGCCTTCCTGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT * * * 184588 CCCCTTCCGGTTTTGTATTTGTAGGAACCTTCCTGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT * * * 184625 CCTCTTCCTG--------TT-T-GCAGCCCT-CTGGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCT-GAT * * * 184652 CCCCTTCCTGTTTTATATTTATATGATG-CTTTCTGAT 1 CCCCTTCCTGTTTTATATTTGTAGGA-GCCTTCCTGAT * * 184689 --CC--CCTGTTTTATATTTGTATGAGCCTCCCTGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT * * * * * 184722 CCCCTTTCTGTTATATATTTTTAGGAGTCTTCCCGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT 184759 CCCCTTCCTGTTTTATATTT-TAAGGAGCCTTCCTGAT 1 CCCCTTCCTGTTTTATATTTGT-AGGAGCCTTCCTGAT * * ** * * 184796 TCCGTTTTTGTTTTATATTTTTA-GAGGCCTTCCTTAT 1 CCCCTTCCTGTTTTATATTTGTAGGA-GCCTTCCTGAT * * * * 184833 CCCCTTCCGGTTGTGTATTTGTAGGAACCTTCCTGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT * * * * 184870 --CC-T-C--TTCT-TGTTT-T-GCAGCCCT-CTGGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCT-GAT * * 184898 CCCCTTCCTGTTTTATATTTATATGATG-CTTCCTGAT 1 CCCCTTCCTGTTTTATATTTGTAGGA-GCCTTCCTGAT ** * 184935 CCCCTTTTTGTTTTATAATTGTAGGAGCCTTCCTGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT * * * 184972 CCTCTTCCTG--------TT-TAGCAGCCCT-CTGGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCT-GAT * * 185000 CCCCTTCCTGTTTCATATTTATAGGAGCCTTCCTGAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT ** * 185037 CCCCTTTTTGTTTTATATTTGTAGGAGCCTTCCTCAT 1 CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT 185074 CCCCTTCCT 1 CCCCTTCCT 185083 CTTCTTCCTG Statistics Matches: 438, Mismatches: 85, Indels: 92 0.71 0.14 0.15 Matches are distributed among these distances: 26 2 0.00 27 21 0.05 28 29 0.07 29 5 0.01 30 6 0.01 31 4 0.01 32 2 0.00 33 27 0.06 34 4 0.01 35 12 0.03 36 8 0.02 37 307 0.70 38 11 0.03 ACGTcount: A:0.14, C:0.27, G:0.15, T:0.45 Consensus pattern (37 bp): CCCCTTCCTGTTTTATATTTGTAGGAGCCTTCCTGAT Found at i:184721 original size:33 final size:33 Alignment explanation

Indices: 184658--184726 Score: 95 Period size: 33 Copynumber: 2.1 Consensus size: 33 184648 GGATCCCCTT ** 184658 CCTGTTTTATATTTATATGATGCTTTCTGATCC 1 CCTGTTTTATATTTATATGATGCTCCCTGATCC * 184691 CCTGTTTTATATTTGTATGA-GCCTCCCTGATCC 1 CCTGTTTTATATTTATATGATG-CTCCCTGATCC 184724 CCT 1 CCT 184727 TTCTGTTATA Statistics Matches: 32, Mismatches: 3, Indels: 2 0.86 0.08 0.05 Matches are distributed among these distances: 32 1 0.03 33 31 0.97 ACGTcount: A:0.16, C:0.25, G:0.13, T:0.46 Consensus pattern (33 bp): CCTGTTTTATATTTATATGATGCTCCCTGATCC Found at i:184984 original size:102 final size:102 Alignment explanation

Indices: 184851--185082 Score: 376 Period size: 102 Copynumber: 2.3 Consensus size: 102 184841 GGTTGTGTAT * * * * 184851 TTGTAGGAACCTTCCTGATCCTCTTCTTGTTTTGCAGCCCTCTGGATCCCCTTCCTGTTTTATAT 1 TTGTAGGAGCCTTCCTGATCCTCTTCCTGTTTAGCAGCCCTCTGGATCCCCTTCCTGTTTCATAT * 184916 TTATATGATG-CTTCCTGATCCCCTTTTTGTTTTATAA 66 TTATAGGA-GCCTTCCTGATCCCCTTTTTGTTTTATAA 184953 TTGTAGGAGCCTTCCTGATCCTCTTCCTGTTTAGCAGCCCTCTGGATCCCCTTCCTGTTTCATAT 1 TTGTAGGAGCCTTCCTGATCCTCTTCCTGTTTAGCAGCCCTCTGGATCCCCTTCCTGTTTCATAT * 185018 TTATAGGAGCCTTCCTGATCCCCTTTTTGTTTTATAT 66 TTATAGGAGCCTTCCTGATCCCCTTTTTGTTTTATAA * * 185055 TTGTAGGAGCCTTCCTCATCCCCTTCCT 1 TTGTAGGAGCCTTCCTGATCCTCTTCCT 185083 CTTCTTCCTG Statistics Matches: 121, Mismatches: 8, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 101 1 0.01 102 120 0.99 ACGTcount: A:0.14, C:0.28, G:0.15, T:0.43 Consensus pattern (102 bp): TTGTAGGAGCCTTCCTGATCCTCTTCCTGTTTAGCAGCCCTCTGGATCCCCTTCCTGTTTCATAT TTATAGGAGCCTTCCTGATCCCCTTTTTGTTTTATAA Found at i:189780 original size:2 final size:2 Alignment explanation

Indices: 189773--189835 Score: 126 Period size: 2 Copynumber: 31.5 Consensus size: 2 189763 ACCCACTTCC 189773 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 189815 GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA G 189836 CCCGGTACCT Statistics Matches: 61, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 61 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:221428 original size:15 final size:16 Alignment explanation

Indices: 221391--221431 Score: 57 Period size: 17 Copynumber: 2.6 Consensus size: 16 221381 TTAAAATTAC 221391 TTCGTTATAGCCGTAAA 1 TTCGTTATAGCCGT-AA * 221408 TTCGTTATAGCCGT-G 1 TTCGTTATAGCCGTAA 221423 TTCGTTATA 1 TTCGTTATA 221432 CATGTATACA Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 15 9 0.39 17 14 0.61 ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41 Consensus pattern (16 bp): TTCGTTATAGCCGTAA Found at i:224488 original size:21 final size:21 Alignment explanation

Indices: 224464--224507 Score: 88 Period size: 21 Copynumber: 2.1 Consensus size: 21 224454 AATACATTAC 224464 ACAGTTTATGATCATTTTTTA 1 ACAGTTTATGATCATTTTTTA 224485 ACAGTTTATGATCATTTTTTA 1 ACAGTTTATGATCATTTTTTA 224506 AC 1 AC 224508 CGAAGAACAA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 23 1.00 ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50 Consensus pattern (21 bp): ACAGTTTATGATCATTTTTTA Found at i:231328 original size:12 final size:12 Alignment explanation

Indices: 231311--231340 Score: 60 Period size: 12 Copynumber: 2.5 Consensus size: 12 231301 TAAAGGGTTA 231311 AAAATTGTTTAT 1 AAAATTGTTTAT 231323 AAAATTGTTTAT 1 AAAATTGTTTAT 231335 AAAATT 1 AAAATT 231341 AAACAATATG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 18 1.00 ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47 Consensus pattern (12 bp): AAAATTGTTTAT Found at i:236814 original size:8 final size:8 Alignment explanation

Indices: 236801--236859 Score: 64 Period size: 8 Copynumber: 7.4 Consensus size: 8 236791 TTTCCTCTGC * 236801 GTCCGTCA 1 GTCCGTCT 236809 GTCCGTCT 1 GTCCGTCT * 236817 GTCTGTCT 1 GTCCGTCT * * 236825 GTCTGTCC 1 GTCCGTCT 236833 GTCCGTCT 1 GTCCGTCT * * 236841 GTCTGTCC 1 GTCCGTCT 236849 GTCCGTCT 1 GTCCGTCT 236857 GTC 1 GTC 236860 TGTCCCACAG Statistics Matches: 42, Mismatches: 9, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 8 42 1.00 ACGTcount: A:0.02, C:0.36, G:0.25, T:0.37 Consensus pattern (8 bp): GTCCGTCT Found at i:236820 original size:4 final size:4 Alignment explanation

Indices: 236813--236863 Score: 66 Period size: 4 Copynumber: 12.8 Consensus size: 4 236803 CCGTCAGTCC * * * * 236813 GTCT GTCT GTCT GTCT GTCC GTCC GTCT GTCT GTCC GTCC GTCT GTCT 1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT 236861 GTC 1 GTC 236864 CCACAGTTTT Statistics Matches: 43, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 4 43 1.00 ACGTcount: A:0.00, C:0.33, G:0.25, T:0.41 Consensus pattern (4 bp): GTCT Found at i:236842 original size:16 final size:16 Alignment explanation

Indices: 236800--236864 Score: 94 Period size: 16 Copynumber: 4.1 Consensus size: 16 236790 CTTTCCTCTG * * 236800 CGTCCGTCAGTCCGTC 1 CGTCCGTCTGTCTGTC * * 236816 TGTCTGTCTGTCTGTC 1 CGTCCGTCTGTCTGTC 236832 CGTCCGTCTGTCTGTC 1 CGTCCGTCTGTCTGTC 236848 CGTCCGTCTGTCTGTC 1 CGTCCGTCTGTCTGTC 236864 C 1 C 236865 CACAGTTTTC Statistics Matches: 43, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 16 43 1.00 ACGTcount: A:0.02, C:0.37, G:0.25, T:0.37 Consensus pattern (16 bp): CGTCCGTCTGTCTGTC Found at i:236864 original size:12 final size:12 Alignment explanation

Indices: 236809--236859 Score: 75 Period size: 12 Copynumber: 4.2 Consensus size: 12 236799 GCGTCCGTCA 236809 GTCCGTCTGTCT 1 GTCCGTCTGTCT * * 236821 GTCTGTCTGTCC 1 GTCCGTCTGTCT 236833 GTCCGTCTGTCT 1 GTCCGTCTGTCT * 236845 GTCCGTCCGTCT 1 GTCCGTCTGTCT 236857 GTC 1 GTC 236860 TGTCCCACAG Statistics Matches: 34, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 12 34 1.00 ACGTcount: A:0.00, C:0.35, G:0.25, T:0.39 Consensus pattern (12 bp): GTCCGTCTGTCT Found at i:239318 original size:12 final size:12 Alignment explanation

Indices: 239301--239339 Score: 78 Period size: 12 Copynumber: 3.2 Consensus size: 12 239291 ATTTGCAAGA 239301 CATTTGATATAT 1 CATTTGATATAT 239313 CATTTGATATAT 1 CATTTGATATAT 239325 CATTTGATATAT 1 CATTTGATATAT 239337 CAT 1 CAT 239340 ATACCATATC Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 27 1.00 ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49 Consensus pattern (12 bp): CATTTGATATAT Found at i:239329 original size:24 final size:24 Alignment explanation

Indices: 239301--239356 Score: 78 Period size: 24 Copynumber: 2.3 Consensus size: 24 239291 ATTTGCAAGA * * 239301 CATTTGATATATCATTTGA-TATAT 1 CATTTGATATATCATAT-ACCATAT 239325 CATTTGATATATCATATACCATAT 1 CATTTGATATATCATATACCATAT 239349 CATTTGAT 1 CATTTGAT 239357 TTGATATGAA Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 23 1 0.03 24 28 0.97 ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46 Consensus pattern (24 bp): CATTTGATATATCATATACCATAT Found at i:244084 original size:2 final size:2 Alignment explanation

Indices: 244077--244114 Score: 76 Period size: 2 Copynumber: 19.0 Consensus size: 2 244067 TTTTCATTAT 244077 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 244115 GTTAGTTATT Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:249953 original size:15 final size:15 Alignment explanation

Indices: 249933--249963 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 249923 TTTTGTAATC 249933 TTGCATAAATGTTCA 1 TTGCATAAATGTTCA * 249948 TTGCATACATGTTCA 1 TTGCATAAATGTTCA 249963 T 1 T 249964 CTTTTAGTGT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42 Consensus pattern (15 bp): TTGCATAAATGTTCA Found at i:251918 original size:186 final size:181 Alignment explanation

Indices: 251598--251999 Score: 608 Period size: 186 Copynumber: 2.2 Consensus size: 181 251588 GGCTGCCAAA * 251598 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA * * * * * * 251663 GATAAATTTTCCGTACATTAGAGGTGTGCATATTGCTAGTATTTAGATTTCTGATTATTTAT-GA 66 GATAAATTGTACATACATCAGAGGTGTGCATATTGCTAGGATTTAGATTTCTGATTATTTATAAA * * 251727 AAAAAATACCAGCTTTTGAACATAGTCATTTTTTGGCAAAAACCTGCATATATATAT 131 AAAAAATACCAGCTTTTGAACATAATCATTTTTTGGC-AAAA--T--AT-TACATAT * 251784 AGGGTACCCTCATTGTATGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA * * 251849 GATAAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTAGATTTCTGATTTTTTATAAA 66 GATAAATTGTACATACATCAGAGGTGTGCATATTGCTAGGATTTAGATTTCTGATTATTTATAAA * * 251914 AAAAAATACCAGCTTTTGAACTTAATCATTTTTTGGCAAAATATTGCATAT 131 AAAAAATACCAGCTTTTGAACATAATCATTTTTTGGCAAAATATTACATAT * 251965 AGGCTACCCTCATTGTACGGATAACTCCTCCTACA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACA 252000 NNNNNNNNNN Statistics Matches: 199, Mismatches: 16, Indels: 7 0.90 0.07 0.03 Matches are distributed among these distances: 181 38 0.19 182 2 0.01 184 1 0.01 186 122 0.61 187 36 0.18 ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37 Consensus pattern (181 bp): AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA GATAAATTGTACATACATCAGAGGTGTGCATATTGCTAGGATTTAGATTTCTGATTATTTATAAA AAAAAATACCAGCTTTTGAACATAATCATTTTTTGGCAAAATATTACATAT Found at i:253282 original size:21 final size:21 Alignment explanation

Indices: 253252--253301 Score: 57 Period size: 21 Copynumber: 2.4 Consensus size: 21 253242 TTTTCCTGAT * * 253252 ACACGCACGATC-CCGCATGTC 1 ACACGAACGATCACC-CACGTC * 253273 ACACGAACGATCACCCACGTT 1 ACACGAACGATCACCCACGTC 253294 ACACGAAC 1 ACACGAAC 253302 TAATTAACAC Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 21 23 0.92 22 2 0.08 ACGTcount: A:0.32, C:0.40, G:0.16, T:0.12 Consensus pattern (21 bp): ACACGAACGATCACCCACGTC Found at i:258804 original size:11 final size:11 Alignment explanation

Indices: 258788--258812 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 258778 CTCAATGGCC 258788 GAATCCATAGT 1 GAATCCATAGT 258799 GAATCCATAGT 1 GAATCCATAGT 258810 GAA 1 GAA 258813 ATTAACTATC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24 Consensus pattern (11 bp): GAATCCATAGT Found at i:261514 original size:12 final size:12 Alignment explanation

Indices: 261499--261523 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 261489 AAGCACATGC 261499 AAAAAAAAAACA 1 AAAAAAAAAACA 261511 AAAAAAAAAACA 1 AAAAAAAAAACA 261523 A 1 A 261524 CGAGCAGAGA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00 Consensus pattern (12 bp): AAAAAAAAAACA Found at i:264231 original size:16 final size:15 Alignment explanation

Indices: 264199--264238 Score: 53 Period size: 16 Copynumber: 2.5 Consensus size: 15 264189 TTAATATATG 264199 TGATTATTATTTGTTT 1 TGATT-TTATTTGTTT 264215 TGATTTTATTTGATTT 1 TGATTTTATTTG-TTT 264231 TAGATTTT 1 T-GATTTT 264239 TCTTTTGACA Statistics Matches: 22, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 15 7 0.32 16 9 0.41 17 6 0.27 ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68 Consensus pattern (15 bp): TGATTTTATTTGTTT Found at i:265557 original size:2 final size:2 Alignment explanation

Indices: 265550--265580 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 265540 CGGTTCGTAG 265550 CT CT CT CT CT CT 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 C 265581 AACTATGACG Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48 Consensus pattern (2 bp): CT Found at i:265868 original size:16 final size:16 Alignment explanation

Indices: 265847--265895 Score: 50 Period size: 16 Copynumber: 3.2 Consensus size: 16 265837 TATACCATAG 265847 CATAGCATTAAAATCT 1 CATAGCATTAAAATCT ** * 265863 CATAGCA-TAGCA--G 1 CATAGCATTAAAATCT 265876 CATAGCATTAAAATCT 1 CATAGCATTAAAATCT 265892 CATA 1 CATA 265896 CATGTAGCCT Statistics Matches: 24, Mismatches: 6, Indels: 6 0.67 0.17 0.17 Matches are distributed among these distances: 13 7 0.29 14 3 0.12 15 3 0.12 16 11 0.46 ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27 Consensus pattern (16 bp): CATAGCATTAAAATCT Found at i:266152 original size:10 final size:10 Alignment explanation

Indices: 266137--266170 Score: 50 Period size: 10 Copynumber: 3.4 Consensus size: 10 266127 GTTCAAATCT 266137 CATAGCATAC 1 CATAGCATAC * 266147 CATAGCATAG 1 CATAGCATAC * 266157 CATACCATAC 1 CATAGCATAC 266167 CATA 1 CATA 266171 CCATTAAGCC Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 10 21 1.00 ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21 Consensus pattern (10 bp): CATAGCATAC Found at i:266157 original size:15 final size:15 Alignment explanation

Indices: 266137--266170 Score: 59 Period size: 15 Copynumber: 2.3 Consensus size: 15 266127 GTTCAAATCT * 266137 CATAGCATACCATAG 1 CATAGCATACCATAC 266152 CATAGCATACCATAC 1 CATAGCATACCATAC 266167 CATA 1 CATA 266171 CCATTAAGCC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21 Consensus pattern (15 bp): CATAGCATACCATAC Found at i:269531 original size:4 final size:4 Alignment explanation

Indices: 269522--269600 Score: 158 Period size: 4 Copynumber: 19.8 Consensus size: 4 269512 AATATCTAAA 269522 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC 1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC 269570 TATC TATC TATC TATC TATC TATC TATC TAT 1 TATC TATC TATC TATC TATC TATC TATC TAT 269601 ATATTCGTCT Statistics Matches: 75, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 75 1.00 ACGTcount: A:0.25, C:0.24, G:0.00, T:0.51 Consensus pattern (4 bp): TATC Found at i:272314 original size:14 final size:14 Alignment explanation

Indices: 272282--272313 Score: 57 Period size: 14 Copynumber: 2.4 Consensus size: 14 272272 AAAATGTGTG 272282 TTTTTGCTTTTTGT 1 TTTTTGCTTTTTGT 272296 TTTTTGCTTTTT-T 1 TTTTTGCTTTTTGT 272309 TTTTT 1 TTTTT 272314 TTACCAAAAA Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 13 6 0.33 14 12 0.67 ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84 Consensus pattern (14 bp): TTTTTGCTTTTTGT Found at i:277092 original size:22 final size:19 Alignment explanation

Indices: 277046--277082 Score: 58 Period size: 19 Copynumber: 2.0 Consensus size: 19 277036 GTAACTATGA * 277046 ACATATATTAATATATATT 1 ACATATATTAATATATAAT 277065 ACATATATT-ATATATAAT 1 ACATATATTAATATATAAT 277083 TAATACATAT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 18 8 0.47 19 9 0.53 ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46 Consensus pattern (19 bp): ACATATATTAATATATAAT Found at i:280835 original size:41 final size:41 Alignment explanation

Indices: 280790--280869 Score: 124 Period size: 41 Copynumber: 2.0 Consensus size: 41 280780 CCCCCTCCTT ** * 280790 TTGAAACATCTGTGAAGAAAATGAATGGAAACTGCAAATTA 1 TTGAAACATCTGCAAAGAAAATGAAAGGAAACTGCAAATTA * 280831 TTGAAACATCTGCAAAGCAAATGAAAGGAAACTGCAAAT 1 TTGAAACATCTGCAAAGAAAATGAAAGGAAACTGCAAAT 280870 ATCGGAATTT Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 41 35 1.00 ACGTcount: A:0.47, C:0.12, G:0.19, T:0.21 Consensus pattern (41 bp): TTGAAACATCTGCAAAGAAAATGAAAGGAAACTGCAAATTA Found at i:284028 original size:166 final size:166 Alignment explanation

Indices: 283700--284043 Score: 519 Period size: 166 Copynumber: 2.1 Consensus size: 166 283690 AAAACTTTCC * 283700 AAGAATATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCC 1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCC * * * * * 283765 GACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACTCTATCTGAGGATGCTTCCAA 66 CACCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCAA * * * * 283830 TCAATTTTGAGCTTTCCTGGCCTAAAAGTTTTTGAG 131 TCAAGTTTAAGCTTTCCAGGCCGAAAAGTTTTTGAG ** * 283866 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCTCTTGTTGCCC 1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCC * * 283931 CTCCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGATGATGCCTCCAC 66 CACCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCA- * * 283996 A-CAAGTTTAAGCTTTTCAGGCCGAATAGTTTTTGAG 130 ATCAAGTTTAAGCTTTCCAGGCCGAAAAGTTTTTGAG 284032 AAGAAGATTTTT 1 AAGAAGATTTTT 284044 GAAAAATACC Statistics Matches: 160, Mismatches: 17, Indels: 2 0.89 0.09 0.01 Matches are distributed among these distances: 166 159 0.99 167 1 0.01 ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33 Consensus pattern (166 bp): AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCC CACCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCAA TCAAGTTTAAGCTTTCCAGGCCGAAAAGTTTTTGAG Found at i:284228 original size:6 final size:6 Alignment explanation

Indices: 284217--284257 Score: 50 Period size: 6 Copynumber: 7.0 Consensus size: 6 284207 AAGTTAACAC * 284217 CGACAA CGACAA CGACGA CGACAA CGAC-A -GACAA CGGACAA 1 CGACAA CGACAA CGACAA CGACAA CGACAA CGACAA C-GACAA 284258 ATTGTGATTA Statistics Matches: 30, Mismatches: 2, Indels: 5 0.81 0.05 0.14 Matches are distributed among these distances: 4 3 0.10 5 2 0.07 6 20 0.67 7 5 0.17 ACGTcount: A:0.46, C:0.32, G:0.22, T:0.00 Consensus pattern (6 bp): CGACAA Found at i:288560 original size:2 final size:2 Alignment explanation

Indices: 288547--288598 Score: 95 Period size: 2 Copynumber: 26.0 Consensus size: 2 288537 CTGTACGTCA * 288547 TC TC TC TT 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 288589 TC TC TC TC TC 1 TC TC TC TC TC 288599 ATCCACACAT Statistics Matches: 48, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:289537 original size:19 final size:19 Alignment explanation

Indices: 289513--289551 Score: 78 Period size: 19 Copynumber: 2.1 Consensus size: 19 289503 AGTACAATCC 289513 ATTTTTAAACGTTTCTTTA 1 ATTTTTAAACGTTTCTTTA 289532 ATTTTTAAACGTTTCTTTA 1 ATTTTTAAACGTTTCTTTA 289551 A 1 A 289552 CTTTAATAGT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.28, C:0.10, G:0.05, T:0.56 Consensus pattern (19 bp): ATTTTTAAACGTTTCTTTA Found at i:289696 original size:60 final size:60 Alignment explanation

Indices: 289624--289743 Score: 231 Period size: 60 Copynumber: 2.0 Consensus size: 60 289614 TCATACGGTT * 289624 AAATGGTTATGAAAAGATGAGTCGAAAATATTGTTTTCTTTTAAATTTCTTTCAAACAAA 1 AAATGGTTATGAAAAGATGAGTCGAAAATATTGTTTTCTTATAAATTTCTTTCAAACAAA 289684 AAATGGTTATGAAAAGATGAGTCGAAAATATTGTTTTCTTATAAATTTCTTTCAAACAAA 1 AAATGGTTATGAAAAGATGAGTCGAAAATATTGTTTTCTTATAAATTTCTTTCAAACAAA 289744 TATAATTGGT Statistics Matches: 59, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 60 59 1.00 ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38 Consensus pattern (60 bp): AAATGGTTATGAAAAGATGAGTCGAAAATATTGTTTTCTTATAAATTTCTTTCAAACAAA Found at i:292150 original size:2 final size:2 Alignment explanation

Indices: 292143--292196 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 292133 ATATTATACG 292143 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 292185 CT CT CT CT CT CT 1 CT CT CT CT CT CT 292197 TAACTAAGGT 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): CT Found at i:294213 original size:32 final size:33 Alignment explanation

Indices: 294173--294235 Score: 101 Period size: 32 Copynumber: 1.9 Consensus size: 33 294163 AAAAAAAATA * 294173 AAAAATTATCTATCTATATTTC-ATCTATCTTT 1 AAAAATTATCTATCTATATATCTATCTATCTTT * 294205 AAAAATTATCTATCTATCTATCTATCTATCT 1 AAAAATTATCTATCTATATATCTATCTATCT 294236 GTCTATCTAT Statistics Matches: 28, Mismatches: 2, Indels: 1 0.90 0.06 0.03 Matches are distributed among these distances: 32 20 0.71 33 8 0.29 ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48 Consensus pattern (33 bp): AAAAATTATCTATCTATATATCTATCTATCTTT Found at i:294218 original size:4 final size:4 Alignment explanation

Indices: 294211--294263 Score: 97 Period size: 4 Copynumber: 13.2 Consensus size: 4 294201 CTTTAAAAAT * 294211 TATC TATC TATC TATC TATC TATC TGTC TATC TATC TATC TATC TATC 1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC 294259 TATC T 1 TATC T 294264 GTATATCTGT Statistics Matches: 47, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 4 47 1.00 ACGTcount: A:0.23, C:0.25, G:0.02, T:0.51 Consensus pattern (4 bp): TATC Found at i:294270 original size:16 final size:16 Alignment explanation

Indices: 294211--294285 Score: 87 Period size: 16 Copynumber: 4.7 Consensus size: 16 294201 CTTTAAAAAT * 294211 TATCTATCTATCTATC 1 TATCTATATATCTATC * * 294227 TATCTATCTGTCTATC 1 TATCTATATATCTATC * 294243 TATCTATCTATCTATC 1 TATCTATATATCTATC * * * 294259 TATCTGTATATCTGTA 1 TATCTATATATCTATC 294275 TATCTATATAT 1 TATCTATATAT 294286 ATCTGTATAT Statistics Matches: 52, Mismatches: 7, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 16 52 1.00 ACGTcount: A:0.25, C:0.20, G:0.04, T:0.51 Consensus pattern (16 bp): TATCTATATATCTATC Found at i:298015 original size:32 final size:32 Alignment explanation

Indices: 297976--298039 Score: 128 Period size: 32 Copynumber: 2.0 Consensus size: 32 297966 TTCCGTAGTG 297976 AGTCAGTAACTAACCTAATAAGTGTTTTAATC 1 AGTCAGTAACTAACCTAATAAGTGTTTTAATC 298008 AGTCAGTAACTAACCTAATAAGTGTTTTAATC 1 AGTCAGTAACTAACCTAATAAGTGTTTTAATC 298040 TTAATAATGT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 32 32 1.00 ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34 Consensus pattern (32 bp): AGTCAGTAACTAACCTAATAAGTGTTTTAATC Found at i:306730 original size:180 final size:180 Alignment explanation

Indices: 306427--306972 Score: 936 Period size: 180 Copynumber: 3.0 Consensus size: 180 306417 GGCTGCCAAA 306427 AGGGTACCCTCATTGTATGGATAACTCCTCCTACAGATTTCAAGATAGGAAGTTATTGTTTTGCA 1 AGGGTACCCTCATTGTATGGATAACTCCTCCTACAGATTTCAAGATAGGAAGTTATTGTTTTGCA * 306492 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA * * * * 306557 AAAAATACCAGCTTTTGAACTAAGTCATTTTTTGGCAAAATATTGCATAT 131 AAAAATACCACCTTTTGAACTTATTCACTTTTTGGCAAAATATTGCATAT * 306607 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGATTTCAAGATAGGAAGTTATTGTTTTGCA 1 AGGGTACCCTCATTGTATGGATAACTCCTCCTACAGATTTCAAGATAGGAAGTTATTGTTTTGCA 306672 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA 306737 AAAAATACCACCTTTTGAACTTATTCACTTTTTGGCAAAATATTGCATAT 131 AAAAATACCACCTTTTGAACTTATTCACTTTTTGGCAAAATATTGCATAT * * * 306787 AGGGTACCCTCATTGTATGTATAA---CTCCTACAGATTTCAAGATAGGAAGTTGTTCTTTTGCA 1 AGGGTACCCTCATTGTATGGATAACTCCTCCTACAGATTTCAAGATAGGAAGTTATTGTTTTGCA * 306849 GATCAATTGTACATACGGTATATCAGAGGTATGCATATTGCTAGGATTTTGATTTCTGATAATTT 66 GATCAATTGTAC--A---TATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTT 306914 ATGAAAAAAATACCACCTTTTGAACTTATTCACTTTTTGGCAAAATATTGCATAT 126 ATGAAAAAAATACCACCTTTTGAACTTATTCACTTTTTGGCAAAATATTGCATAT 306969 AGGG 1 AGGG 306973 GTACACCATT Statistics Matches: 350, Mismatches: 11, Indels: 8 0.95 0.03 0.02 Matches are distributed among these distances: 177 48 0.14 179 1 0.00 180 196 0.56 182 105 0.30 ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36 Consensus pattern (180 bp): AGGGTACCCTCATTGTATGGATAACTCCTCCTACAGATTTCAAGATAGGAAGTTATTGTTTTGCA GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA AAAAATACCACCTTTTGAACTTATTCACTTTTTGGCAAAATATTGCATAT Found at i:313478 original size:13 final size:13 Alignment explanation

Indices: 313460--313484 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 313450 AATGTGTTAC 313460 AAAATATACTAGA 1 AAAATATACTAGA 313473 AAAATATACTAG 1 AAAATATACTAG 313485 CAAAGGTAAA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24 Consensus pattern (13 bp): AAAATATACTAGA Found at i:317445 original size:2 final size:2 Alignment explanation

Indices: 317440--317486 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 317430 TACACACACA 317440 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 317482 CT CT C 1 CT CT C 317487 ATACTGTCAA Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:319216 original size:14 final size:14 Alignment explanation

Indices: 319197--319224 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 319187 ACTCTAAGAA 319197 AAAGTTATACTTAG 1 AAAGTTATACTTAG 319211 AAAGTTATACTTAG 1 AAAGTTATACTTAG 319225 GATATGGATG Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36 Consensus pattern (14 bp): AAAGTTATACTTAG Found at i:330195 original size:30 final size:30 Alignment explanation

Indices: 330159--330215 Score: 87 Period size: 30 Copynumber: 1.9 Consensus size: 30 330149 AGTATTTGCA * 330159 TTGTCAATGTTGAACATATCTGAACTCATG 1 TTGTCAATGATGAACATATCTGAACTCATG * * 330189 TTGTCAATGATGCACATATTTGAACTC 1 TTGTCAATGATGAACATATCTGAACTC 330216 GACGTAAACT Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 30 24 1.00 ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37 Consensus pattern (30 bp): TTGTCAATGATGAACATATCTGAACTCATG Found at i:333229 original size:4 final size:4 Alignment explanation

Indices: 333216--333273 Score: 73 Period size: 4 Copynumber: 14.8 Consensus size: 4 333206 AAAGTTTACA * * * * 333216 GACG GACA GACA GACG GACG GACA GACG GACG GACG GACG GACA GACG 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG 333264 GAC- GACG GAC 1 GACG GACG GAC 333274 AAAAAGTGAT Statistics Matches: 47, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 3 3 0.06 4 44 0.94 ACGTcount: A:0.33, C:0.26, G:0.41, T:0.00 Consensus pattern (4 bp): GACG Found at i:333237 original size:16 final size:16 Alignment explanation

Indices: 333216--333267 Score: 86 Period size: 16 Copynumber: 3.2 Consensus size: 16 333206 AAAGTTTACA 333216 GACGGACAGACAGACG 1 GACGGACAGACAGACG * 333232 GACGGACAGACGGACG 1 GACGGACAGACAGACG * 333248 GACGGACGGACAGACG 1 GACGGACAGACAGACG 333264 GACG 1 GACG 333268 ACGGACAAAA Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 16 33 1.00 ACGTcount: A:0.33, C:0.25, G:0.42, T:0.00 Consensus pattern (16 bp): GACGGACAGACAGACG Found at i:333596 original size:11 final size:11 Alignment explanation

Indices: 333580--333608 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 333570 TAAAGACTAT 333580 CTTTAAGCCAC 1 CTTTAAGCCAC 333591 CTTTAAGCCAC 1 CTTTAAGCCAC 333602 CTTTAAG 1 CTTTAAG 333609 GACAACTTAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:333656 original size:11 final size:11 Alignment explanation

Indices: 333640--333693 Score: 90 Period size: 11 Copynumber: 4.9 Consensus size: 11 333630 GTCCAAACTT 333640 CTTTAAGCCAC 1 CTTTAAGCCAC 333651 CTTTAAGCCAC 1 CTTTAAGCCAC * * 333662 TTTTAAGCTAC 1 CTTTAAGCCAC 333673 CTTTAAGCCAC 1 CTTTAAGCCAC 333684 CTTTAAGCCA 1 CTTTAAGCCA 333694 TTAAACAAAT Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 11 39 1.00 ACGTcount: A:0.28, C:0.31, G:0.09, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:334948 original size:10 final size:11 Alignment explanation

Indices: 334933--334972 Score: 55 Period size: 11 Copynumber: 3.7 Consensus size: 11 334923 GGTTGTATAG * 334933 CCTTTAAG-CT 1 CCTTTAAGCCA * 334943 CCTTTAAGTCA 1 CCTTTAAGCCA 334954 CCTTTAAGCCA 1 CCTTTAAGCCA 334965 CCTTTAAG 1 CCTTTAAG 334973 GACAACTTAT Statistics Matches: 27, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 10 8 0.30 11 19 0.70 ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35 Consensus pattern (11 bp): CCTTTAAGCCA Found at i:335436 original size:22 final size:22 Alignment explanation

Indices: 335408--335468 Score: 70 Period size: 22 Copynumber: 2.8 Consensus size: 22 335398 AATATTGACT * 335408 TAAAGGCCACTTAAAGACAGTG 1 TAAAGGCCACTTAAAGACAGCG * * 335430 TAAAGG-CAGTGTAAAGAGAGCG 1 TAAAGGCCACT-TAAAGACAGCG * 335452 TAAATGCCACTTAAAGA 1 TAAAGGCCACTTAAAGA 335469 TGCTTAAAGG Statistics Matches: 32, Mismatches: 5, Indels: 4 0.78 0.12 0.10 Matches are distributed among these distances: 21 3 0.09 22 26 0.81 23 3 0.09 ACGTcount: A:0.43, C:0.15, G:0.25, T:0.18 Consensus pattern (22 bp): TAAAGGCCACTTAAAGACAGCG Found at i:335484 original size:11 final size:11 Alignment explanation

Indices: 335461--335499 Score: 53 Period size: 11 Copynumber: 3.6 Consensus size: 11 335451 GTAAATGCCA * 335461 CTTAAAGAT-G 1 CTTAAAGGTGG 335471 CTTAAAGGTGG 1 CTTAAAGGTGG * 335482 CTTAAATGTGG 1 CTTAAAGGTGG 335493 CTTAAAG 1 CTTAAAG 335500 AAGTTTGGAC Statistics Matches: 25, Mismatches: 3, Indels: 1 0.86 0.10 0.03 Matches are distributed among these distances: 10 8 0.32 11 17 0.68 ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31 Consensus pattern (11 bp): CTTAAAGGTGG Found at i:335595 original size:11 final size:10 Alignment explanation

Indices: 335569--335608 Score: 53 Period size: 11 Copynumber: 3.8 Consensus size: 10 335559 GGTTGTATAG * 335569 CCTTTAAGCT 1 CCTTTAAGCA 335579 CCTTTAAGTCA 1 CCTTTAAG-CA 335590 CCTTTAAGCAA 1 CCTTTAAGC-A 335601 CCTTTAAG 1 CCTTTAAG 335609 GACTTGCTTA Statistics Matches: 27, Mismatches: 1, Indels: 3 0.87 0.03 0.10 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:0.35 Consensus pattern (10 bp): CCTTTAAGCA Found at i:337667 original size:21 final size:21 Alignment explanation

Indices: 337392--337680 Score: 227 Period size: 21 Copynumber: 13.8 Consensus size: 21 337382 AAAAAAAAAA * * 337392 TTCGCGAATATACGCGAAACT 1 TTCGCGAATAAACGCGTAACT * * 337413 TTTGCG-ATATAACGCGTAAGT 1 TTCGCGAATA-AACGCGTAACT * * 337434 TTCGCAAATAAACGCGAAACT 1 TTCGCGAATAAACGCGTAACT 337455 TTCGCG-ATATAACGCGT-ACAT 1 TTCGCGAATA-AACGCGTAAC-T * 337476 TTTGCGAATAAACGCG-AACAT 1 TTCGCGAATAAACGCGTAAC-T ** * 337497 TTCTTG-ATATAACGCGTAAGT 1 TTCGCGAATA-AACGCGTAACT * * * * * 337518 TTTGCTAGTAAAGGCGTAAGT 1 TTCGCGAATAAACGCGTAACT * 337539 TTCGCGAATAAACGCGTAATT 1 TTCGCGAATAAACGCGTAACT 337560 TTCGCG-ATATAACGCGTTAA-T 1 TTCGCGAATA-AACGCG-TAACT * 337581 TTTGCGAATAAACGCG-AATCT 1 TTCGCGAATAAACGCGTAA-CT * * 337602 TTTGCG-ATATAAGGCGTAACT 1 TTCGCGAATA-AACGCGTAACT * * 337623 TTTGGGAATAAACGCGTAACT 1 TTCGCGAATAAACGCGTAACT 337644 TTCGCGAATAAACGCGTAACT 1 TTCGCGAATAAACGCGTAACT * * 337665 TTCGCAAATTAACGCG 1 TTCGCGAATAAACGCG 337681 AAATCATTAT Statistics Matches: 217, Mismatches: 34, Indels: 34 0.76 0.12 0.12 Matches are distributed among these distances: 19 2 0.01 20 17 0.08 21 177 0.82 22 21 0.10 ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29 Consensus pattern (21 bp): TTCGCGAATAAACGCGTAACT Found at i:337680 original size:105 final size:105 Alignment explanation

Indices: 337399--337669 Score: 363 Period size: 105 Copynumber: 2.6 Consensus size: 105 337389 AAATTCGCGA * * * 337399 ATAT-ACGCGAAACTTTTGCG-ATATAACGCGTAAGTTTCGCAAATAAACGCGAAACTTTCGCGA 1 ATATAACGCGTAACTTTTGCGAATA-AACGCGTAAGTTTCGCGAATAAACGCGTAACTTTCGCGA * 337462 TATAACGCGTACATTTTGCGAATAAACGCGAACATTTCTTG 65 TATAACGCGTACATTTTGCGAATAAACGCGAACATTTCTCG * * * * * 337503 ATATAACGCGTAAGTTTTGCTAGTAAAGGCGTAAGTTTCGCGAATAAACGCGTAATTTTCGCGAT 1 ATATAACGCGTAACTTTTGCGAATAAACGCGTAAGTTTCGCGAATAAACGCGTAACTTTCGCGAT 337568 ATAACGCGTTA-ATTTTGCGAATAAACGCGAATC-TTT-TGCG 66 ATAACGCG-TACATTTTGCGAATAAACGCGAA-CATTTCT-CG * * * 337608 ATATAAGGCGTAACTTTTGGGAATAAACGCGTAACTTTCGCGAATAAACGCGTAACTTTCGC 1 ATATAACGCGTAACTTTTGCGAATAAACGCGTAAGTTTCGCGAATAAACGCGTAACTTTCGC 337670 AAATTAACGC Statistics Matches: 145, Mismatches: 17, Indels: 9 0.85 0.10 0.05 Matches are distributed among these distances: 104 5 0.03 105 135 0.93 106 5 0.03 ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29 Consensus pattern (105 bp): ATATAACGCGTAACTTTTGCGAATAAACGCGTAAGTTTCGCGAATAAACGCGTAACTTTCGCGAT ATAACGCGTACATTTTGCGAATAAACGCGAACATTTCTCG Found at i:338582 original size:42 final size:42 Alignment explanation

Indices: 338535--338625 Score: 146 Period size: 42 Copynumber: 2.2 Consensus size: 42 338525 TTTGCGTTTA 338535 ATCGCGAAAGTTTCGTATTTAATCGCGAAAATAACGCGTGAT 1 ATCGCGAAAGTTTCGTATTTAATCGCGAAAATAACGCGTGAT * * * * 338577 ATCGCGAAAGTTTCGTGTTTATTCGCGAAAGTAACGCGTTAT 1 ATCGCGAAAGTTTCGTATTTAATCGCGAAAATAACGCGTGAT 338619 ATCGCGA 1 ATCGCGA 338626 TTGTTACGCA Statistics Matches: 45, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 42 45 1.00 ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30 Consensus pattern (42 bp): ATCGCGAAAGTTTCGTATTTAATCGCGAAAATAACGCGTGAT Found at i:338623 original size:63 final size:62 Alignment explanation

Indices: 338556--338691 Score: 148 Period size: 63 Copynumber: 2.2 Consensus size: 62 338546 TTCGTATTTA * * * * 338556 ATCGCGAAAATAACGCGTG-ATATCGCGAAAGTTTCGTGTTTATTCGCGAAAGTAACGCGTTAT 1 ATCGCGAAAATAACGCATGTAT-TCGCGAAAGTTTCGCGTTTATTCGCAAAACTAACGCGTT-T *** * * * 338619 ATCGCGATTGTTACGCATGTATTCGCTAAAGTTTCGCGTTTATTTGCAAAACTAACGCGTTT 1 ATCGCGAAAATAACGCATGTATTCGCGAAAGTTTCGCGTTTATTCGCAAAACTAACGCGTTT 338681 ATTCGCGAAAA 1 A-TCGCGAAAA 338692 AAATATTTTG Statistics Matches: 58, Mismatches: 13, Indels: 4 0.77 0.17 0.05 Matches are distributed among these distances: 62 2 0.03 63 54 0.93 64 2 0.03 ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32 Consensus pattern (62 bp): ATCGCGAAAATAACGCATGTATTCGCGAAAGTTTCGCGTTTATTCGCAAAACTAACGCGTTT Found at i:338662 original size:21 final size:21 Alignment explanation

Indices: 338528--338690 Score: 105 Period size: 21 Copynumber: 7.8 Consensus size: 21 338518 TTTAAGTTTT * * 338528 GCGTTTAATCGCGAAAGTTTC 1 GCGTTTATTCGCGAAAGTTAC ** * * * 338549 GTATTTAATCGCGAAAATAAC 1 GCGTTTATTCGCGAAAGTTAC * * 338570 GCG-TGATATCGCGAAAGTTTC 1 GCGTTTAT-TCGCGAAAGTTAC * * 338591 GTGTTTATTCGCGAAAGTAAC 1 GCGTTTATTCGCGAAAGTTAC ** 338612 GCG-TTATATCGCGATTGTTAC 1 GCGTTTAT-TCGCGAAAGTTAC * * * * 338633 GCATGTATTCGCTAAAGTTTC 1 GCGTTTATTCGCGAAAGTTAC * * * * 338654 GCGTTTATTTGCAAAACTAAC 1 GCGTTTATTCGCGAAAGTTAC 338675 GCGTTTATTCGCGAAA 1 GCGTTTATTCGCGAAA 338691 AAAATATTTT Statistics Matches: 103, Mismatches: 35, Indels: 8 0.71 0.24 0.05 Matches are distributed among these distances: 20 6 0.06 21 91 0.88 22 6 0.06 ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33 Consensus pattern (21 bp): GCGTTTATTCGCGAAAGTTAC Found at i:344160 original size:2 final size:2 Alignment explanation

Indices: 344153--344183 Score: 55 Period size: 2 Copynumber: 16.0 Consensus size: 2 344143 CTAAAAGCAT 344153 GA GA GA GA GA G- 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 344184 TTTAGTCTTT Statistics Matches: 28, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 1 1 0.04 2 27 0.96 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:348957 original size:36 final size:36 Alignment explanation

Indices: 348917--348990 Score: 130 Period size: 36 Copynumber: 2.1 Consensus size: 36 348907 GATTTCTTTA 348917 TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTG 1 TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTG * * 348953 TTAGGTCTTTGCACCTTTCAGTTGAAAGACCTTTTG 1 TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTG 348989 TT 1 TT 348991 TCCTTTATGT Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 36 36 1.00 ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42 Consensus pattern (36 bp): TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTG Found at i:349016 original size:54 final size:54 Alignment explanation

Indices: 348948--349062 Score: 194 Period size: 54 Copynumber: 2.1 Consensus size: 54 348938 GTGAAAGACC * * * 348948 TTTTGTTAGGTCTTTGCACCTTTCAGTTGAAAGACCTTTTGTTTCCTTTATGTT 1 TTTTATTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTGTTTCCTTTATGTT * 349002 TTTTATTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTGTTTTCTTTATGTT 1 TTTTATTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTGTTTCCTTTATGTT 349056 TTTTATT 1 TTTTATT 349063 CTTATTAGTT Statistics Matches: 57, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 54 57 1.00 ACGTcount: A:0.16, C:0.16, G:0.15, T:0.54 Consensus pattern (54 bp): TTTTATTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTGTTTCCTTTATGTT Found at i:351540 original size:426 final size:430 Alignment explanation

Indices: 350634--351575 Score: 1120 Period size: 426 Copynumber: 2.2 Consensus size: 430 350624 CTTGTTTACG * ** 350634 AAAA-GCTTGTTATCGCTACTTCTCTGAAACCATAAGAGA-ATGAGACCGGAAACTTTTACCAAT 1 AAAATGCTTGTTATCGCTACTCCTCT-AAACCATAAGAGATA-GAGACTTGAAACTTTTACCAAT * * * 350697 GTCTTCAGTTCACTTAGAGGGTTCTTCAATCTACTAATACCGAAAAGATCCGAGACCCCGTTCTA 64 GTCTTCAGTACACTTAGACGGTTCTTCAATCTACTAATACCGAAAAGATCCGAGACCCCGATCTA ** * * 350762 TCAGTTGTTGCCCCTGAAAGTATTTGAATTTCCATAAAATCACTTTCAACTGTTTTATTATTAAT 129 GAAGTTATTGCCCCTGAAAGTATTTGAATTTCCATAAAATCACTTTCAACTGTTTTATAATTAAT * * * * 350827 CATAGAGACCTTGGACCTCTTTGAATGGAAGCATCTACCTTGGCCAAACAAAATGACATAAAGGT 194 CATAGAGACCTTGGACCACTTGGAATGGAAGCATCTACCGTGGCCAAAC-AAA-GACATAAAGCT * * 350892 CAAAGGTCAAGGTCATTTGGAAATCTGTTAATTAATGAGTTTTTAGATCTCTTTTATTAAGGGTG 257 CAAAGGTCAAGGTCATTTGGAAATCTCTAAATTAATGAGTTTTTAGATCTCTTTTATTAAGGGTG * * ** * * * * 350957 GTAGAGTAAAACTTTTTCATGGATGTATTAGGACATCTTAAGACATTTTAAAATATAGCCCCTCG 322 GCAGAGAAAAACTTTTTCATGGATGTAAAAGGACATCATAAGACATTTCAAAATATAACCCATCG * * * * * * 351022 GCTCATACCTTTGAATAAATACAAAAATATTGCCCCTTTTGTAC 387 ACCCATACCTATGAACAAATACAAAAATATTACCCCTATTGTAC * * * * 351066 GAAATGTTTGTTATCGCTACTCCTCTGACACCATAAGAGATCGAGACTTGAAACTTTTACCAATG 1 AAAATGCTTGTTATCGCTACTCCTCT-AAACCATAAGAGATAGAGACTTGAAACTTTTACCAATG * * * * ** 351131 TCTTCAGTACACATAGACGGTTCTTCAATCTATTCATACC-AAAAGGATCTGAGGTTCCC-ATCT 65 TCTTCAGTACACTTAGACGGTTCTTCAATCTACTAATACCGAAAA-GATCCGA-GACCCCGATCT * 351194 AGAAGTTATTGCCCCTGAAAGTATTT-ACATTTCCATAAAATCAC-TTCAAACTTTTTTATAACT 128 AGAAGTTATTGCCCCTGAAAGTATTTGA-ATTTCCATAAAATCACTTTC-AACTGTTTTATAA-T * * 351257 T-ATCATAGAGA-CTTCGGACCACTTGGGATGGAAGCATCTACCGTGGCCGAAC-AA-A-AT-AA 190 TAATCATAGAGACCTT-GGACCACTTGGAATGGAAGCATCTACCGTGGCCAAACAAAGACATAAA * * 351316 -CTCAAAGGTCAAGGTCATTTGGAAATCTCTAAATTAATGAGTTTTTAGATCTCTTTTGTTTAGG 254 GCTCAAAGGTCAAGGTCATTTGGAAATCTCTAAATTAATGAGTTTTTAGATCTCTTTTATTAAGG * * * 351380 GTGGCAGAGAAAAACTTTTTCATGTATTTAAAAGGACATCATAAGACATTTCAAAATGTAACCCA 319 GTGGCAGAGAAAAACTTTTTCATGGATGTAAAAGGACATCATAAGACATTTCAAAATATAACCCA * * * * * ** 351445 TTGACCCTTTCCATAT-AACAATTATAAAGTTATTACCCCTATTGTAC 384 TCGACCCATACC-TATGAACAAATACAAAAATATTACCCCTATTGTAC * * * * * 351492 AAAATGCTTGTTATCGCTACTCCTCATTAACCGTTAGAGATAGAGACTTGAAACGTTTACTAATG 1 AAAATGCTTGTTATCGCTACTCCTC-TAAACCATAAGAGATAGAGACTTGAAACTTTTACCAATG * 351557 TATTCAGTACACTTAGACG 65 TCTTCAGTACACTTAGACG 351576 CTCCTATCAT Statistics Matches: 434, Mismatches: 66, Indels: 26 0.83 0.13 0.05 Matches are distributed among these distances: 426 215 0.50 427 5 0.01 428 2 0.00 429 1 0.00 431 2 0.00 432 14 0.03 433 189 0.44 434 6 0.01 ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33 Consensus pattern (430 bp): AAAATGCTTGTTATCGCTACTCCTCTAAACCATAAGAGATAGAGACTTGAAACTTTTACCAATGT CTTCAGTACACTTAGACGGTTCTTCAATCTACTAATACCGAAAAGATCCGAGACCCCGATCTAGA AGTTATTGCCCCTGAAAGTATTTGAATTTCCATAAAATCACTTTCAACTGTTTTATAATTAATCA TAGAGACCTTGGACCACTTGGAATGGAAGCATCTACCGTGGCCAAACAAAGACATAAAGCTCAAA GGTCAAGGTCATTTGGAAATCTCTAAATTAATGAGTTTTTAGATCTCTTTTATTAAGGGTGGCAG AGAAAAACTTTTTCATGGATGTAAAAGGACATCATAAGACATTTCAAAATATAACCCATCGACCC ATACCTATGAACAAATACAAAAATATTACCCCTATTGTAC Found at i:351691 original size:426 final size:427 Alignment explanation

Indices: 350634--351759 Score: 966 Period size: 426 Copynumber: 2.6 Consensus size: 427 350624 CTTGTTTACG * * ** * 350634 AAAA-GCTTGTTATCGCTACTTCTCTGAAACCATAAGAGA-ATGAGACCGGAAACTTTTACCAAT 1 AAAATGCTTGTTATCGCTACTCCTCTGACACCATAAGAGATA-GAGACTTGAAACGTTTACCAAT * * * * * * * * * * ** * 350697 GTCTTCAGTTCACTTAGAGGGTTCTTCAATCTACTAATACCGAAAA-GATCC-GAGACCCCGTTC 65 GTATTCAGTACACATAGACGCTCCTTCAATCTATTCATAAC-AAAAGGATCCAAAGTTCCC-ATC ** * * * ** * 350760 TATCAGTTGTTGCCCCTGAAAGTATTTGA-ATTTCCATAAAATCACTTTC-AACTGTTTT-ATTA 128 TAGAAGTTATTGCCCCTGAAAGTA-TTAACATTTCAATAAAATCAC-AACAAACT-TTTTAATAA * ** * * * * 350822 -TTAATCATAGAGACCTTGGACCTCTTTGAATGGAAGCATCTACCTTGGCCA-AACAAAATGACA 190 CTT-ATCATAGAGACATCAGACCACTTGGGATGGAAGCATCTACCGTGG-CAGAACAAAAT---A * * * 350885 TAAAGGTCAAAGGTCAAGGTCATTTGGAAATCTGTTAATTAATGAGTTTTTAGATCTCTTTTATT 250 -ACA--TCAAAGGTCAAGGTCATTTGGAAATCTCTAAATTAATGAGTTTTTAGATCTCTTTTATT * * ** * * * 350950 AAGGGTGGTAGAGTAAAACTTTTTCATGGATGTATTAGGACATCTTAAGACATTTTAAAATATAG 312 AAGGGTGGCAGAGAAAAACTTTTTCATGGATGTAAAAGGACATCATAAGACATTTCAAAATATAA * * * * * * * 351015 CCCCTCGGCTCATACCTTTGAATAAATACAAAAATATTGCCCCTTTTGTAC 377 CCCATCGACCCATACCTATGAACAAATACAAAAATATTACCCCTATTGTAC * * * * 351066 GAAATGTTTGTTATCGCTACTCCTCTGACACCATAAGAGATCGAGACTTGAAACTTTTACCAATG 1 AAAATGCTTGTTATCGCTACTCCTCTGACACCATAAGAGATAGAGACTTGAAACGTTTACCAATG * * * * ** * 351131 TCTTCAGTACACATAGACGGTTCTTCAATCTATTCATACCAAAAGGATCTGAGGTTCCCATCTAG 66 TATTCAGTACACATAGACGCTCCTTCAATCTATTCATAACAAAAGGATCCAAAGTTCCCATCTAG * * ** * 351196 AAGTTATTGCCCCTGAAAGTATTTACATTTCCATAAAATCACTTCAAACTTTTTTATAACTTATC 131 AAGTTATTGCCCCTGAAAGTATTAACATTTCAATAAAATCACAACAAACTTTTTAATAACTTATC * * * 351261 ATAGAGACTTCGGACCACTTGGGATGGAAGCATCTACCGTGGCCGAACAAAATAAC-TCAAAGGT 196 ATAGAGACATCAGACCACTTGGGATGGAAGCATCTACCGTGGCAGAACAAAATAACATCAAAGGT * * 351325 CAAGGTCATTTGGAAATCTCTAAATTAATGAGTTTTTAGATCTCTTTTGTTTAGGGTGGCAGAGA 261 CAAGGTCATTTGGAAATCTCTAAATTAATGAGTTTTTAGATCTCTTTTATTAAGGGTGGCAGAGA * * * * * * 351390 AAAACTTTTTCATGTATTTAAAAGGACATCATAAGACATTTCAAAATGTAACCCATTGACCCTTT 326 AAAACTTTTTCATGGATGTAAAAGGACATCATAAGACATTTCAAAATATAACCCATCGACCCATA * * ** 351455 CCATAT-AACAATTATAAAGTTATTACCCCTATTGTAC 391 CC-TATGAACAAATACAAAAATATTACCCCTATTGTAC * * * * 351492 AAAATGCTTGTTATCGCTACTCCTCATTA-ACCGTTAGAGATAGAGACTTGAAACGTTTACTAAT 1 AAAATGCTTGTTATCGCTACTCCTC-TGACACCATAAGAGATAGAGACTTGAAACGTTTACCAAT * * * * * 351556 GTATTCAGTACACTTAGACGCTCCTATC-ATTTATTCATAACGAAAGGGTCCAAAG-TCCC-TTT 65 GTATTCAGTACACATAGACGCTCCT-TCAATCTATTCATAACAAAAGGATCCAAAGTTCCCATCT 351618 CATGCAA-TTATTGCCCCTGAAAGT-TTCAAACATTT-AATTAAAA-CACAAACAAA-TTTTTAA 129 -A-G-AAGTTATTGCCCCTGAAAGTATT--AACATTTCAA-TAAAATCAC-AACAAACTTTTTAA * * * * * * * * 351678 TCAA--TATTCATAGATACATCAGACCACTTGGTATTGAAGCGTCTACCTTGTCAGATCAAAATG 187 T-AACTTA-TCATAGAGACATCAGACCACTTGGGATGGAAGCATCTACCGTGGCAGAACAAAATA 351741 ACAT-AAAGGTCAAAGGTCA 250 ACATCAAAGGTC-AAGGTCA 351760 AGGTCAAGTA Statistics Matches: 576, Mismatches: 95, Indels: 51 0.80 0.13 0.07 Matches are distributed among these distances: 424 2 0.00 425 9 0.02 426 321 0.56 427 33 0.06 429 1 0.00 430 1 0.00 432 18 0.03 433 185 0.32 434 6 0.01 ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32 Consensus pattern (427 bp): AAAATGCTTGTTATCGCTACTCCTCTGACACCATAAGAGATAGAGACTTGAAACGTTTACCAATG TATTCAGTACACATAGACGCTCCTTCAATCTATTCATAACAAAAGGATCCAAAGTTCCCATCTAG AAGTTATTGCCCCTGAAAGTATTAACATTTCAATAAAATCACAACAAACTTTTTAATAACTTATC ATAGAGACATCAGACCACTTGGGATGGAAGCATCTACCGTGGCAGAACAAAATAACATCAAAGGT CAAGGTCATTTGGAAATCTCTAAATTAATGAGTTTTTAGATCTCTTTTATTAAGGGTGGCAGAGA AAAACTTTTTCATGGATGTAAAAGGACATCATAAGACATTTCAAAATATAACCCATCGACCCATA CCTATGAACAAATACAAAAATATTACCCCTATTGTAC Done.