Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A10

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 1825971 characters in sequence are not A, C, G, or T


File 295 of 343

Found at i:96949306 original size:44 final size:43

Alignment explanation

Indices: 96949256--96949746 Score: 360 Period size: 44 Copynumber: 11.0 Consensus size: 43 96949246 GGGTATAGGA * * 96949256 TTGTAGCTTTATCTTGCTCCATTGCAACTTCAAGAAGATAAGAT 1 TTGTAGCTTAATC-TGCTCCACTGCAACTTCAAGAAGATAAGAT * * 96949300 TTGTAGCTTTATCTTGCTCCACTGCAACTTCGAGAAGATAAGAT 1 TTGTAGCTTAATC-TGCTCCACTGCAACTTCAAGAAGATAAGAT * * ** 96949344 TGGTAGCTTCAATCTGCTTCACTGCAACTTCAAGGTGATAAGAT 1 TTGTAGCTT-AATCTGCTCCACTGCAACTTCAAGAAGATAAGAT * * * * * 96949388 TCGTAGCTTCAATCTGCTTCACTACAACTTTAGGAAGATAAGAT 1 TTGTAGCTT-AATCTGCTCCACTGCAACTTCAAGAAGATAAGAT * * * * * 96949432 TTGTAGTTTCAATCTGCTCTACTGCAACTTCAGGGAGATGAGAT 1 TTGTAGCTT-AATCTGCTCCACTGCAACTTCAAGAAGATAAGAT * * ** 96949476 TTGTAACTTCAATCTGCTCCACTACAA-TTTTAGAGAGATAAGAT 1 TTGTAGCTT-AATCTGCTCCACTGCAACTTCAAGA-AGATAAGAT * * * * * 96949520 TTGTAGCTTCATCTTGCTCCACTACAACTTTAGGGAGATAAGATTCGT 1 TTGTAGCTTAATC-TGCTCCACTGCAACTTCAAGAAGATAAGA----T * * * * * ** 96949568 TATGGTAGATTCAATCCGAC-CCACTACATCTT-TAGGGGTATAAGAT 1 T-T-GTAGCTT-AATCTG-CTCCACTGCAACTTCAAGAAG-ATAAGAT * * ** * 96949614 TTTTAGCATCAATCTATTTCACTGCAACTTC-AGAGAGATAAGAT 1 TTGTAGC-TTAATCTGCTCCACTGCAACTTCAAGA-AGATAAGAT * * * * 96949658 TTGTAGCTTTAATTTGCTCCACTGCAATTTTAAGGAGATAAGAT 1 TTGTAGC-TTAATCTGCTCCACTGCAACTTCAAGAAGATAAGAT * * 96949702 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT 1 TTGTAGCTT-AATCTGCTCCACTGCAACTTCAAGAAGATAAGAT 96949746 T 1 T 96949747 CTTTATGGTA Statistics Matches: 360, Mismatches: 68, Indels: 38 0.77 0.15 0.08 Matches are distributed among these distances: 43 8 0.02 44 304 0.84 45 12 0.03 46 2 0.01 48 2 0.01 49 4 0.01 50 24 0.07 51 4 0.01 ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34 Consensus pattern (43 bp): TTGTAGCTTAATCTGCTCCACTGCAACTTCAAGAAGATAAGAT Found at i:96949370 original size:88 final size:87 Alignment explanation

Indices: 96949256--96949746 Score: 463 Period size: 88 Copynumber: 5.5 Consensus size: 87 96949246 GGGTATAGGA * * * * * 96949256 TTGTAGCTT-TATCTTGCTCCATTGCAACTTCAAGAAGATAAGATTTGTAGCTT-TATCTTGCTC 1 TTGTAGCTTCAATC-TGCTTCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATC-TGCTC * * 96949319 CACTGCAACTTCGAGAAGATAAGAT 64 CACTACAACTT-TAGAAGATAAGAT * * * * 96949344 TGGTAGCTTCAATCTGCTTCACTGCAACTTCAAGGTGATAAGATTCGTAGCTTCAATCTGCTTCA 1 TTGTAGCTTCAATCTGCTTCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCCA 96949409 CTACAACTTTAGGAAGATAAGAT 66 CTACAACTTTA-GAAGATAAGAT * * * * 96949432 TTGTAGTTTCAATCTGC-TCTACTGCAACTTCAGGGAGATGAGATTTGTAACTTCAATCTGCTCC 1 TTGTAGCTTCAATCTGCTTC-ACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCC * 96949496 ACTACAATTTTAGAGAGATAAGAT 65 ACTACAACTTTAGA-AGATAAGAT * * * * * 96949520 TTGTAGCTTC-ATCTTGCTCCACTACAACTTTAGGGAGATAAGATTCGTTATGGTAGATTCAATC 1 TTGTAGCTTCAATC-TGCTTCACTGCAACTTCAAGGAGATAAGA----TT-T-GTAGCTTCAATC * * ** 96949584 CGAC-CCACTACATCTTTAGGGGTATAAGAT 59 TG-CTCCACTACAACTTTAGAAG-ATAAGAT * * ** * * 96949614 TTTTAGCATCAATCTATTTCACTGCAACTTC-AGAGAGATAAGATTTGTAGCTTTAATTTGCTCC 1 TTGTAGCTTCAATCTGCTTCACTGCAACTTCAAG-GAGATAAGATTTGTAGCTTCAATCTGCTCC * * * 96949678 ACTGCAATTTTAAGGAGATAAGAT 65 ACTACAACTTT-AGAAGATAAGAT * * 96949702 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT 1 TTGTAGCTTCAATCTGCTTCACTGCAACTTCAAGGAGATAAGATT 96949747 CTTTATGGTA Statistics Matches: 329, Mismatches: 54, Indels: 40 0.78 0.13 0.09 Matches are distributed among these distances: 87 9 0.03 88 236 0.72 89 13 0.04 90 2 0.01 92 2 0.01 93 3 0.01 94 60 0.18 95 4 0.01 ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34 Consensus pattern (87 bp): TTGTAGCTTCAATCTGCTTCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCCA CTACAACTTTAGAAGATAAGAT Found at i:96949436 original size:132 final size:131 Alignment explanation

Indices: 96949161--96949746 Score: 467 Period size: 132 Copynumber: 4.4 Consensus size: 131 96949151 AAGGGTATAG * 96949161 GATTTGTAGCTTTATCTTGCTCCACTGCAACTTCAGAAGATAAGATTTGCTATAGTAAG-TTCAA 1 GATTTGTAGCTTTATC-TGCTCCACTGCAACTTCAGGAGATAAGA-TTG-----GT-AGCTTCAA * * * * * * * 96949225 TCCAAC-CCACTGTAACTTCAG-GGGTATAGGA-TTGTAGCTT-TATCTTGCTCCATTGCAACTT 58 T-CTACTCCACTGCAACTTCAGAGAG-ATAAGATTTGTAGCTTCAATCTTGCTCCACTACAACTT * * 96949286 CAAGAAGATAA 121 TAGGAAGATAA * * 96949297 GATTTGTAGCTTTATCTTGCTCCACTGCAACTTCGAGAAGATAAGATTGGTAGCTTCAATCTGCT 1 GATTTGTAGCTTTATC-TGCTCCACTGCAACTTC-AGGAGATAAGATTGGTAGCTTCAATCTACT * * * * 96949362 TCACTGCAACTTCA-AGGTGATAAGATTCGTAGCTTCAATC-TGCTTCACTACAACTTTAGGAAG 64 CCACTGCAACTTCAGA-GAGATAAGATTTGTAGCTTCAATCTTGCTCCACTACAACTTTAGGAAG 96949425 ATAA 128 ATAA * * * * * 96949429 GATTTGTAG-TTTCAATCTGCTCTACTGCAACTTCAGGGAGATGAGATTTGTAACTTCAATCTGC 1 GATTTGTAGCTTT--ATCTGCTCCACTGCAACTTCA-GGAGATAAGATTGGTAGCTTCAATCTAC * * * * 96949493 TCCACTACAATTTTAGAGAGATAAGATTTGTAGCTTC-ATCTTGCTCCACTACAACTTTAGGGAG 63 TCCACTGCAACTTCAGAGAGATAAGATTTGTAGCTTCAATCTTGCTCCACTACAACTTTAGGAAG 96949557 ATAA 128 ATAA * * * * * * * ** * 96949561 GATTCGTTATGGTAGATTCAATCCGAC-CCACTACATCTTTAGGGGTATAAGATTTTTAGCATCA 1 GA----TT-T-GTAGCTT-TATCTG-CTCCACTGCAACTTCAGGAG-ATAAGATTGGTAGCTTCA * * * * * 96949625 ATCTATTTCACTGCAACTTCAGAGAGATAAGATTTGTAGCTTTAAT-TTGCTCCACTGCAATTTT 57 ATCTACTCCACTGCAACTTCAGAGAGATAAGATTTGTAGCTTCAATCTTGCTCCACTACAACTTT 96949689 AAGG-AGATAA 122 -AGGAAGATAA * 96949699 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT 1 GATTTGTAGCTT-TATCTGCTCCACTGCAACTTCA-GGAGATAAGATT 96949747 CTTTATGGTA Statistics Matches: 372, Mismatches: 52, Indels: 56 0.77 0.11 0.12 Matches are distributed among these distances: 130 4 0.01 131 33 0.09 132 168 0.45 133 11 0.03 134 2 0.01 136 39 0.10 137 15 0.04 138 92 0.25 139 8 0.02 ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33 Consensus pattern (131 bp): GATTTGTAGCTTTATCTGCTCCACTGCAACTTCAGGAGATAAGATTGGTAGCTTCAATCTACTCC ACTGCAACTTCAGAGAGATAAGATTTGTAGCTTCAATCTTGCTCCACTACAACTTTAGGAAGATA A Found at i:96949789 original size:182 final size:182 Alignment explanation

Indices: 96949161--96949791 Score: 519 Period size: 182 Copynumber: 3.5 Consensus size: 182 96949151 AAGGGTATAG * * * * * * 96949161 GATTTGTAGCTTTATCTTGCTCCACTGCAACTTCA-GAAGATAAGATTTGCTATAGTA-AGTTCA 1 GATTTGTAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAGATTCGTTATGGTAGA-TTCA * ** * * ** * * 96949224 ATCCAACCCACTGTAACTTCAGGGGTATAGGA-TTGTAGC-TTTATCT-TGCTCCATTGCAACTT 65 ACCCAACCCACTACAACTTCAGGGGTATAAGATTTTTAGCATCAATCTAT--TTCACTGCAACTT * * * * * 96949286 CA-AGAAGATAAGATTTGTAGCTT-TATCTTGCTCCACTGCAA-CTTCGAGAAGATAA 128 CAGAG-AGATAAGATTTGTAACTTCAATC-TGCTCCACTACAATTTTAGAG-AGATAA * * * * * * 96949341 GATTGGTAGCTTCAATC-TGCTTCACTGCAACTTCAAGGTGATAAGATTC------GTAGCTTCA 1 GATTTGTAGCTTC-ATCTTGCTCCACTACAACTTCAGGGAGATAAGATTCGTTATGGTAGATTCA * ** * * * * ** ** 96949399 A-TCTGCTTCACTACAACTTTAGGAAG-ATAAGATTTGTAGTTTCAATCT-GCTCTACTGCAACT 65 ACCCAAC-CCACTACAACTTCAGG-GGTATAAGATTTTTAGCATCAATCTATTTC-ACTGCAACT * * 96949461 TCAGGGAGATGAGATTTGTAACTTCAATCTGCTCCACTACAATTTTAGAGAGATAA 127 TCAGAGAGATAAGATTTGTAACTTCAATCTGCTCCACTACAATTTTAGAGAGATAA * 96949517 GATTTGTAGCTTCATCTTGCTCCACTACAACTTTAGGGAGATAAGATTCGTTATGGTAGATTCAA 1 GATTTGTAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAGATTCGTTATGGTAGATTCAA * * * * 96949582 TCCGACCCACTACATCTTTAGGGGTATAAGATTTTTAGCATCAATCTATTTCACTGCAACTTCAG 66 CCCAACCCACTACAACTTCAGGGGTATAAGATTTTTAGCATCAATCTATTTCACTGCAACTTCAG * * * * 96949647 AGAGATAAGATTTGTAGCTTTAATTTGCTCCACTGCAATTTTA-AGGAGATAA 131 AGAGATAAGATTTGTAACTTCAATCTGCTCCACTACAATTTTAGA-GAGATAA * * * 96949699 GATTTGTAGCTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTCTTTATGGTATATTCA 1 GATTTGTAGCTTC-ATCTTGCTCCACTACAACTTCAGGGAGATAAGATTCGTTATGGTAGATTCA * * ** 96949763 ACCCAATCTACTGTAACTTCAGGGGTATA 65 ACCCAACCCACTACAACTTCAGGGGTATA 96949792 GGGTTTGTGG Statistics Matches: 362, Mismatches: 66, Indels: 44 0.77 0.14 0.09 Matches are distributed among these distances: 174 2 0.01 175 29 0.08 176 91 0.25 177 14 0.04 180 28 0.08 181 15 0.04 182 176 0.49 183 7 0.02 ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34 Consensus pattern (182 bp): GATTTGTAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAGATTCGTTATGGTAGATTCAA CCCAACCCACTACAACTTCAGGGGTATAAGATTTTTAGCATCAATCTATTTCACTGCAACTTCAG AGAGATAAGATTTGTAACTTCAATCTGCTCCACTACAATTTTAGAGAGATAA Found at i:96950217 original size:22 final size:22 Alignment explanation

Indices: 96950189--96950233 Score: 90 Period size: 22 Copynumber: 2.0 Consensus size: 22 96950179 AACCTTTTAG 96950189 AGTAATATGCAAAAATCCTTTT 1 AGTAATATGCAAAAATCCTTTT 96950211 AGTAATATGCAAAAATCCTTTT 1 AGTAATATGCAAAAATCCTTTT 96950233 A 1 A 96950234 CTTGAATATT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 23 1.00 ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36 Consensus pattern (22 bp): AGTAATATGCAAAAATCCTTTT Found at i:96954950 original size:18 final size:19 Alignment explanation

Indices: 96954929--96954964 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 96954919 TATTAGTTTT 96954929 ATTTTTA-TTATTTTGGGG 1 ATTTTTACTTATTTTGGGG * 96954947 ATTTTTACTTTTTTTGGG 1 ATTTTTACTTATTTTGGG 96954965 AAGTTCACGT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 7 0.44 19 9 0.56 ACGTcount: A:0.14, C:0.03, G:0.19, T:0.64 Consensus pattern (19 bp): ATTTTTACTTATTTTGGGG Found at i:96976887 original size:28 final size:28 Alignment explanation

Indices: 96976847--96976903 Score: 114 Period size: 28 Copynumber: 2.0 Consensus size: 28 96976837 ACATACGGAA 96976847 GATATTATTAGAGTGTCAAACCTACTAG 1 GATATTATTAGAGTGTCAAACCTACTAG 96976875 GATATTATTAGAGTGTCAAACCTACTAG 1 GATATTATTAGAGTGTCAAACCTACTAG 96976903 G 1 G 96976904 CAGATCAGTT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 29 1.00 ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32 Consensus pattern (28 bp): GATATTATTAGAGTGTCAAACCTACTAG Found at i:96984189 original size:46 final size:46 Alignment explanation

Indices: 96984137--96984456 Score: 435 Period size: 46 Copynumber: 7.0 Consensus size: 46 96984127 AGTGTGCTCT 96984137 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC * 96984183 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC * 96984229 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC * 96984275 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC * *** *** * 96984321 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC * * ** 96984367 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC * * * * * * 96984413 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA 1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA 96984457 TCATGTCAAA Statistics Matches: 251, Mismatches: 22, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 45 1 0.00 46 250 1.00 ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21 Consensus pattern (46 bp): CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC Found at i:96985528 original size:11 final size:11 Alignment explanation

Indices: 96985512--96985540 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 96985502 GACTCGAAAG 96985512 GATTGGAAGAT 1 GATTGGAAGAT 96985523 GATTGGAAGAT 1 GATTGGAAGAT 96985534 GATTGGA 1 GATTGGA 96985541 GAGTCAAAAC 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:0.34, C:0.00, G:0.38, T:0.28 Consensus pattern (11 bp): GATTGGAAGAT Found at i:96987612 original size:19 final size:18 Alignment explanation

Indices: 96987590--96987625 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 96987580 ATAAAAAGGA 96987590 TAAAGAAATAATAAATAAG 1 TAAAGAAATAA-AAATAAG * 96987609 TAAATAAATAAAAATAA 1 TAAAGAAATAAAAATAA 96987626 TAATTCATAA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 6 0.38 19 10 0.62 ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22 Consensus pattern (18 bp): TAAAGAAATAAAAATAAG Found at i:96988937 original size:14 final size:14 Alignment explanation

Indices: 96988918--96988963 Score: 58 Period size: 14 Copynumber: 3.3 Consensus size: 14 96988908 GACTTGAATT 96988918 TTTTTATTTTTTGG 1 TTTTTATTTTTTGG * 96988932 TTTTTATATTTT-G 1 TTTTTATTTTTTGG * 96988945 TTTATTTTTTTTTGG 1 TTT-TTATTTTTTGG 96988960 TTTT 1 TTTT 96988964 GGGCTAGATG Statistics Matches: 27, Mismatches: 3, Indels: 4 0.79 0.09 0.12 Matches are distributed among these distances: 13 4 0.15 14 19 0.70 15 4 0.15 ACGTcount: A:0.09, C:0.00, G:0.11, T:0.80 Consensus pattern (14 bp): TTTTTATTTTTTGG Found at i:96990135 original size:30 final size:27 Alignment explanation

Indices: 96990074--96990137 Score: 76 Period size: 27 Copynumber: 2.3 Consensus size: 27 96990064 CTAAATTTAT * 96990074 ATACCAAATTAGACAAAAAAAACTTAA 1 ATACCAAATTAGACAAAAAAAAATTAA 96990101 ATACCAAATTAAGA-AAAAAATCAAATTCAA 1 ATACCAAATT-AGACAAAAAA--AAATT-AA 96990131 ATACCAA 1 ATACCAA 96990138 CTATTATATT Statistics Matches: 32, Mismatches: 1, Indels: 5 0.84 0.03 0.13 Matches are distributed among these distances: 27 16 0.50 28 3 0.09 29 4 0.12 30 9 0.28 ACGTcount: A:0.62, C:0.16, G:0.03, T:0.19 Consensus pattern (27 bp): ATACCAAATTAGACAAAAAAAAATTAA Found at i:96991862 original size:19 final size:19 Alignment explanation

Indices: 96991836--96991882 Score: 76 Period size: 19 Copynumber: 2.5 Consensus size: 19 96991826 TAATATATTG * 96991836 AATTTTGTTGTAAAGTTCG 1 AATTTTGTTGTAAAGTTCA * 96991855 ATTTTTGTTGTAAAGTTCA 1 AATTTTGTTGTAAAGTTCA 96991874 AATTTTGTT 1 AATTTTGTT 96991883 TATATTAGTT Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 25 1.00 ACGTcount: A:0.26, C:0.04, G:0.17, T:0.53 Consensus pattern (19 bp): AATTTTGTTGTAAAGTTCA Found at i:96998058 original size:5 final size:5 Alignment explanation

Indices: 96998045--96998092 Score: 87 Period size: 5 Copynumber: 9.6 Consensus size: 5 96998035 ATCTTTTCAC * 96998045 AATAA AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT 1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT 96998093 TTTTTTGGTA Statistics Matches: 42, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 5 42 1.00 ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38 Consensus pattern (5 bp): AATAT Found at i:97002764 original size:172 final size:172 Alignment explanation

Indices: 97002478--97002820 Score: 632 Period size: 172 Copynumber: 2.0 Consensus size: 172 97002468 GACATAATCG * * 97002478 GTAAAAATCCCTAATATTCATAAGTACATGTTAGAGTGTGAATTTGATGTTGCTATAGAAGGGAA 1 GTAAAAATACCTAATATTCATAAGCACATGTTAGAGTGTGAATTTGATGTTGCTATAGAAGGGAA * * 97002543 AAATGATTAGCATGTCATAAAACATAAGAAAATAGGATGAGGTTTAATTTACGAGCCTTGGGGCA 66 AAATGATCAGCATGTCATAAAACATAAGAAAATAGGATGAGGCTTAATTTACGAGCCTTGGGGCA * 97002608 AAAGTGTAAATATGTGAAAGTTTAGGGGTAAAATGGTAATTA 131 AAAGTGTAAATATGTGAAAGTTTAGGGGCAAAATGGTAATTA 97002650 GTAAAAATACCTAATATTCATAAGCACATGTTAGAGTGTGAATTTGATGTTGCTATAGAAGGGAA 1 GTAAAAATACCTAATATTCATAAGCACATGTTAGAGTGTGAATTTGATGTTGCTATAGAAGGGAA * 97002715 AAATGATCAGCATGTCATAAAACATAAGAAAGTAGGATGAGGCTTAATTTACGAGCCTTGGGGCA 66 AAATGATCAGCATGTCATAAAACATAAGAAAATAGGATGAGGCTTAATTTACGAGCCTTGGGGCA 97002780 AAAGTGTAAATATGTGAAAGTTTAGGGGCAAAATGGTAATT 131 AAAGTGTAAATATGTGAAAGTTTAGGGGCAAAATGGTAATT 97002821 TTGCCAAATC Statistics Matches: 165, Mismatches: 6, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 172 165 1.00 ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29 Consensus pattern (172 bp): GTAAAAATACCTAATATTCATAAGCACATGTTAGAGTGTGAATTTGATGTTGCTATAGAAGGGAA AAATGATCAGCATGTCATAAAACATAAGAAAATAGGATGAGGCTTAATTTACGAGCCTTGGGGCA AAAGTGTAAATATGTGAAAGTTTAGGGGCAAAATGGTAATTA Found at i:97003284 original size:46 final size:46 Alignment explanation

Indices: 97003232--97003407 Score: 162 Period size: 46 Copynumber: 3.8 Consensus size: 46 97003222 TATTTGGGCA ** 97003232 TCCGAGCTCGTTGAGTCAAGTCCGAGTTCACTTATGGATGTGAATG 1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG * * * 97003278 TCCGAGCTCATTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGG 1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T--G * * * * * 97003323 CATCCAAGCTCGTTGAGTTGAGCCCGATTTCACTTATGGATGCGAACG 1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG * * * 97003371 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG 1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG 97003408 GTGGGTTACA Statistics Matches: 102, Mismatches: 19, Indels: 18 0.73 0.14 0.13 Matches are distributed among these distances: 42 2 0.02 43 6 0.06 45 3 0.03 46 57 0.56 47 25 0.25 48 3 0.03 50 4 0.04 51 2 0.02 ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30 Consensus pattern (46 bp): TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG Found at i:97003387 original size:93 final size:93 Alignment explanation

Indices: 97003228--97003400 Score: 256 Period size: 93 Copynumber: 1.9 Consensus size: 93 97003218 AGGATATTTG * * * * * 97003228 GGCATCCGAGCTCGTTGAGTCAAGTCCGAGTTCACTTATGGATGTGAATGTCCGAGCTCATTGAG 1 GGCATCCAAGCTCGTTGAGTCAAGCCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG 97003293 TTGAGTCCGAGTTCGTGAGATGTAACTA 66 TTGAGTCCGAGTTCGTGAGATGTAACTA ** * * 97003321 GGCATCCAAGCTCGTTGAGTTGAGCCCGATTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG 1 GGCATCCAAGCTCGTTGAGTCAAGCCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG * 97003386 TTGAGTCTGAGTTCG 66 TTGAGTCCGAGTTCG 97003401 CTTATGGGTG Statistics Matches: 70, Mismatches: 10, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 93 70 1.00 ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28 Consensus pattern (93 bp): GGCATCCAAGCTCGTTGAGTCAAGCCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG TTGAGTCCGAGTTCGTGAGATGTAACTA Found at i:97004799 original size:16 final size:17 Alignment explanation

Indices: 97004778--97004811 Score: 61 Period size: 16 Copynumber: 2.1 Consensus size: 17 97004768 ACACGAAACA 97004778 AAAATAAAA-AATATTT 1 AAAATAAAATAATATTT 97004794 AAAATAAAATAATATTT 1 AAAATAAAATAATATTT 97004811 A 1 A 97004812 TTTATACATT Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 9 0.53 17 8 0.47 ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32 Consensus pattern (17 bp): AAAATAAAATAATATTT Found at i:97015873 original size:27 final size:27 Alignment explanation

Indices: 97015843--97015898 Score: 85 Period size: 27 Copynumber: 2.1 Consensus size: 27 97015833 AAGATACATC * * 97015843 TTTTGCTTAATAAATTTCATGTCTAAT 1 TTTTGCTTAAAAAAATTCATGTCTAAT * 97015870 TTTTTCTTAAAAAAATTCATGTCTAAT 1 TTTTGCTTAAAAAAATTCATGTCTAAT 97015897 TT 1 TT 97015899 AAAATTTAAA Statistics Matches: 26, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 27 26 1.00 ACGTcount: A:0.32, C:0.11, G:0.05, T:0.52 Consensus pattern (27 bp): TTTTGCTTAAAAAAATTCATGTCTAAT Found at i:97023936 original size:10 final size:9 Alignment explanation

Indices: 97023918--97024061 Score: 55 Period size: 10 Copynumber: 15.4 Consensus size: 9 97023908 TACAAATTCT * 97023918 TTTTCATAA 1 TTTTAATAA 97023927 TTTTATATAA 1 TTTTA-ATAA 97023937 TTTTAATAA 1 TTTTAATAA * * 97023946 CTTTACATTAT 1 TTTTA-A-TAA 97023957 TTTTAATAA 1 TTTTAATAA ** 97023966 TTCTTTGTAAA 1 TT-TTAAT-AA * * 97023977 TTTTTATAT 1 TTTTAATAA 97023986 TTTTCAA-AA 1 TTTT-AATAA * * 97023995 TTCT-AT-T 1 TTTTAATAA 97024002 TTTTAAT-- 1 TTTTAATAA 97024009 TTTTAATAA 1 TTTTAATAA * 97024018 TTTTATATTA 1 TTTTA-ATAA * 97024028 TGTTTAACAAA 1 T-TTTAA-TAA 97024039 TTTTAATAA 1 TTTTAATAA * 97024048 TGTTTTATAA 1 T-TTTAATAA 97024058 TTTT 1 TTTT 97024062 TGCAATTTTT Statistics Matches: 102, Mismatches: 19, Indels: 28 0.68 0.13 0.19 Matches are distributed among these distances: 7 11 0.11 8 2 0.02 9 36 0.35 10 37 0.36 11 16 0.16 ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59 Consensus pattern (9 bp): TTTTAATAA Found at i:97023945 original size:19 final size:20 Alignment explanation

Indices: 97023918--97023967 Score: 57 Period size: 19 Copynumber: 2.5 Consensus size: 20 97023908 TACAAATTCT * * 97023918 TTTTCATAATTTTATA-TAA 1 TTTTAATAATTTTACATTAA * * 97023937 TTTTAATAACTTTACATTAT 1 TTTTAATAATTTTACATTAA 97023957 TTTTAATAATT 1 TTTTAATAATT 97023968 CTTTGTAAAT Statistics Matches: 25, Mismatches: 5, Indels: 1 0.81 0.16 0.03 Matches are distributed among these distances: 19 13 0.52 20 12 0.48 ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58 Consensus pattern (20 bp): TTTTAATAATTTTACATTAA Found at i:97024134 original size:28 final size:27 Alignment explanation

Indices: 97024076--97024133 Score: 75 Period size: 27 Copynumber: 2.1 Consensus size: 27 97024066 ATTTTTATGG * 97024076 TTTTATAATTTTCTAAACTTCTAAACT 1 TTTTATAATTTTCTAAAATTCTAAACT 97024103 TTTTATAATTTT-TGAAAAATTCT-AACT 1 TTTTATAATTTTCT--AAAATTCTAAACT 97024130 TTTT 1 TTTT 97024134 TTTTAAAAAA Statistics Matches: 28, Mismatches: 1, Indels: 4 0.85 0.03 0.12 Matches are distributed among these distances: 26 1 0.04 27 20 0.71 28 7 0.25 ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55 Consensus pattern (27 bp): TTTTATAATTTTCTAAAATTCTAAACT Found at i:97034402 original size:22 final size:22 Alignment explanation

Indices: 97034374--97034419 Score: 92 Period size: 22 Copynumber: 2.1 Consensus size: 22 97034364 GCAATTAAAG 97034374 AAAGATGAACAGTAAATATTTT 1 AAAGATGAACAGTAAATATTTT 97034396 AAAGATGAACAGTAAATATTTT 1 AAAGATGAACAGTAAATATTTT 97034418 AA 1 AA 97034420 CTCATAACAG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 24 1.00 ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30 Consensus pattern (22 bp): AAAGATGAACAGTAAATATTTT Found at i:97039604 original size:27 final size:27 Alignment explanation

Indices: 97039554--97039605 Score: 70 Period size: 27 Copynumber: 1.9 Consensus size: 27 97039544 GTTGGATTTA * * 97039554 TAAAAAAATAATTTAATTATAATATGT 1 TAAAAAAATAATTTAATGAAAATATGT 97039581 TAAAAAAATAATTTTAA-GAAAATAT 1 TAAAAAAATAA-TTTAATGAAAATAT 97039606 TGTATTGAAA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 27 17 0.77 28 5 0.23 ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37 Consensus pattern (27 bp): TAAAAAAATAATTTAATGAAAATATGT Found at i:97041002 original size:14 final size:13 Alignment explanation

Indices: 97040961--97041002 Score: 50 Period size: 14 Copynumber: 3.2 Consensus size: 13 97040951 AGTAATGTAG 97040961 AAATAAAT-TTTA 1 AAATAAATATTTA 97040973 AAATAAATATTATA 1 AAATAAATATT-TA * 97040987 AAGTAAATAGTTTA 1 AAATAAATA-TTTA 97041001 AA 1 AA 97041003 TGAAAGTTTG Statistics Matches: 26, Mismatches: 1, Indels: 4 0.84 0.03 0.13 Matches are distributed among these distances: 12 8 0.31 13 2 0.08 14 14 0.54 15 2 0.08 ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36 Consensus pattern (13 bp): AAATAAATATTTA Found at i:97042866 original size:24 final size:24 Alignment explanation

Indices: 97042815--97042867 Score: 63 Period size: 24 Copynumber: 2.2 Consensus size: 24 97042805 AATTCATTGG * * * 97042815 ATAATATTTTTTAAGTGATGTAAA 1 ATAATATTATTTAAATGATGCAAA 97042839 ATAATATTATTTAAATGAT-CAAA 1 ATAATATTATTTAAATGATGCAAA 97042862 TATAAT 1 -ATAAT 97042868 TAAAACGTAT Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 23 3 0.12 24 22 0.88 ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43 Consensus pattern (24 bp): ATAATATTATTTAAATGATGCAAA Found at i:97043586 original size:9 final size:9 Alignment explanation

Indices: 97043574--97043602 Score: 58 Period size: 9 Copynumber: 3.2 Consensus size: 9 97043564 AAGATAAAAA 97043574 ATAAAAGTT 1 ATAAAAGTT 97043583 ATAAAAGTT 1 ATAAAAGTT 97043592 ATAAAAGTT 1 ATAAAAGTT 97043601 AT 1 AT 97043603 TAAATATTAA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 20 1.00 ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34 Consensus pattern (9 bp): ATAAAAGTT Found at i:97043978 original size:15 final size:15 Alignment explanation

Indices: 97043953--97043989 Score: 56 Period size: 15 Copynumber: 2.5 Consensus size: 15 97043943 ATCTGTTTTT * 97043953 CAGTAGTGTTGGAAA 1 CAGTGGTGTTGGAAA * 97043968 TAGTGGTGTTGGAAA 1 CAGTGGTGTTGGAAA 97043983 CAGTGGT 1 CAGTGGT 97043990 TTCGAGGCCA Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 15 19 1.00 ACGTcount: A:0.27, C:0.05, G:0.38, T:0.30 Consensus pattern (15 bp): CAGTGGTGTTGGAAA Found at i:97044587 original size:5 final size:5 Alignment explanation

Indices: 97044571--97044608 Score: 69 Period size: 5 Copynumber: 7.8 Consensus size: 5 97044561 AAGTATTAAG 97044571 TATAT T-TAT TATAT TATAT TATAT TATAT TATAT TATA 1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA 97044609 ATAAAACAAA Statistics Matches: 32, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 4 4 0.12 5 28 0.88 ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (5 bp): TATAT Found at i:97045840 original size:40 final size:39 Alignment explanation

Indices: 97045717--97045841 Score: 103 Period size: 40 Copynumber: 3.2 Consensus size: 39 97045707 GACTTCGAGT * * 97045717 CGATGAGACACTAAGTGTCAATTTACTACTTCGAATTAATT 1 CGATGAGACACTGAGTGTCAATTTA-TACTTCGAATT-ATC * * * ** * 97045758 CAATGATG-CACTGGGTGCCAA-TT-TACTTCGGTTTAGC 1 CGATGA-GACACTGAGTGTCAATTTATACTTCGAATTATC * * 97045795 TGATGAGACATTGAGTGTCAATTTAGTACTTCGAATTATC 1 CGATGAGACACTGAGTGTCAATTTA-TACTTCGAATTATC 97045835 CGATGAG 1 CGATGAG 97045842 GCATTGGGTG Statistics Matches: 62, Mismatches: 17, Indels: 11 0.69 0.19 0.12 Matches are distributed among these distances: 36 1 0.02 37 15 0.24 38 11 0.18 40 19 0.31 41 15 0.24 42 1 0.02 ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34 Consensus pattern (39 bp): CGATGAGACACTGAGTGTCAATTTATACTTCGAATTATC Found at i:97052066 original size:21 final size:21 Alignment explanation

Indices: 97052025--97052067 Score: 61 Period size: 20 Copynumber: 2.0 Consensus size: 21 97052015 ATTTGAATTT * 97052025 TTTAATTTAAAAATATGAATA 1 TTTAATTTAAAAATATAAATA 97052046 TTTAA-TTAAAAATATCAAATA 1 TTTAATTTAAAAATAT-AAATA 97052067 T 1 T 97052068 ATATTTTAGT Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 20 10 0.50 21 10 0.50 ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42 Consensus pattern (21 bp): TTTAATTTAAAAATATAAATA Found at i:97054787 original size:26 final size:27 Alignment explanation

Indices: 97054751--97054890 Score: 88 Period size: 30 Copynumber: 4.9 Consensus size: 27 97054741 ATTTTTCTCA 97054751 TAAAATTTATAACAAATTA-AAAATAT 1 TAAAATTTATAACAAATTATAAAATAT * * 97054777 TAAAATTTATAATAAATTATAAAATTT 1 TAAAATTTATAACAAATTATAAAATAT * * * 97054804 TATAAAATTAGTAA-AACATATTTAAAATTT 1 TA-AAATTTA-TAACAA-AT-TATAAAATAT * 97054834 TATAATGACTTATAA-AAACTTATAAATAATAT 1 TA-AA--ATTTATAACAAA-TTAT-AA-AATAT * * * 97054866 AAAAATATCTAACAAATTATAAAAT 1 TAAAATTTATAACAAATTATAAAAT 97054891 TTATAAAAAA Statistics Matches: 92, Mismatches: 11, Indels: 21 0.74 0.09 0.17 Matches are distributed among these distances: 26 18 0.20 27 11 0.12 28 10 0.11 29 14 0.15 30 20 0.22 31 10 0.11 32 9 0.10 ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37 Consensus pattern (27 bp): TAAAATTTATAACAAATTATAAAATAT Found at i:97054810 original size:29 final size:28 Alignment explanation

Indices: 97054750--97054898 Score: 103 Period size: 29 Copynumber: 5.2 Consensus size: 28 97054740 TATTTTTCTC * 97054750 ATAAAATTTATAACAAATTA-AAAA-TAT 1 ATAAAATTTATAA-AAATTATAAAATTTT 97054777 -TAAAATTTATAATAAATTATAAAATTTT 1 ATAAAATTTATAA-AAATTATAAAATTTT * 97054805 ATAAAA-TTAGTAAAACATATTTAAAATTTT 1 ATAAAATTTA-TAAAA-AT-TATAAAATTTT * * ** 97054835 ATAATGACTTATAAAAACTTAT-AAATAAT 1 ATAA-AATTTATAAAAA-TTATAAAATTTT * * 97054864 ATAAAAATATCTAACAAATTATAAAA-TTT 1 AT-AAAATTTATAA-AAATTATAAAATTTT 97054893 ATAAAA 1 ATAAAA 97054899 AAAAAAAGTC Statistics Matches: 97, Mismatches: 13, Indels: 23 0.73 0.10 0.17 Matches are distributed among these distances: 26 18 0.19 27 4 0.04 28 11 0.11 29 29 0.30 30 25 0.26 31 7 0.07 32 3 0.03 ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37 Consensus pattern (28 bp): ATAAAATTTATAAAAATTATAAAATTTT Found at i:97054813 original size:18 final size:20 Alignment explanation

Indices: 97054777--97054819 Score: 56 Period size: 19 Copynumber: 2.2 Consensus size: 20 97054767 TTAAAAATAT 97054777 TAAAATTTATAATAAATTA- 1 TAAAATTTATAATAAATTAG 97054796 TAAAATTT-T-ATAAAATTAG 1 TAAAATTTATAAT-AAATTAG 97054815 TAAAA 1 TAAAA 97054820 CATATTTAAA Statistics Matches: 22, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 17 2 0.09 18 7 0.32 19 13 0.59 ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40 Consensus pattern (20 bp): TAAAATTTATAATAAATTAG Found at i:97054847 original size:50 final size:47 Alignment explanation

Indices: 97054768--97054899 Score: 133 Period size: 50 Copynumber: 2.7 Consensus size: 47 97054758 TATAACAAAT ** 97054768 TAAAAATATTAAAATTTATAATAAATTATAAAATTTTATAAAATTAG 1 TAAAAATATTAAAATTTATAATAAATTATAAAAACTTATAAAATTAG * * * 97054815 TAAAACATATTTAAAATTTTATAATGACTTATAAAAACTTATAAATAATA- 1 TAAAA-ATA-TTAAAA-TTTATAATAAATTATAAAAACTTATAAA-ATTAG * * 97054865 TAAAAATATCTAACAAATTATAA-AATTTATAAAAA 1 TAAAAATAT-TAA-AATTTATAATAAATTATAAAAA 97054900 AAAAAAGTCA Statistics Matches: 71, Mismatches: 8, Indels: 11 0.79 0.09 0.12 Matches are distributed among these distances: 47 5 0.07 48 14 0.20 49 18 0.25 50 31 0.44 51 3 0.04 ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37 Consensus pattern (47 bp): TAAAAATATTAAAATTTATAATAAATTATAAAAACTTATAAAATTAG Found at i:97055678 original size:19 final size:20 Alignment explanation

Indices: 97055654--97055709 Score: 62 Period size: 19 Copynumber: 2.9 Consensus size: 20 97055644 ATTAGAATTT 97055654 TTTATAAGTTTTTATAA-AA 1 TTTATAAGTTTTTATAATAA * ** 97055673 TTTATAAGCTTTTATGAATTT 1 TTTATAAGTTTTTAT-AATAA 97055694 TTTATAA-TTTTTATAA 1 TTTATAAGTTTTTATAA 97055710 GTTTATAGAA Statistics Matches: 31, Mismatches: 4, Indels: 4 0.79 0.10 0.10 Matches are distributed among these distances: 19 16 0.52 20 8 0.26 21 7 0.23 ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57 Consensus pattern (20 bp): TTTATAAGTTTTTATAATAA Found at i:97055813 original size:10 final size:10 Alignment explanation

Indices: 97055634--97055814 Score: 86 Period size: 10 Copynumber: 18.0 Consensus size: 10 97055624 ATTGGGATTA 97055634 TTTATAATTT 1 TTTATAATTT * * 97055644 ATTAGAATTT 1 TTTATAATTT * 97055654 TTTATAAGTT 1 TTTATAATTT ** 97055664 TTTATAA-AA 1 TTTATAATTT ** 97055673 TTTATAAGCT 1 TTTATAATTT 97055683 TTTATGAATTT 1 TTTAT-AATTT 97055694 TTTATAA-TT 1 TTTATAATTT * 97055703 TTTATAAGTT 1 TTTATAATTT * * ** 97055713 TATAGAAAGT 1 TTTATAATTT * 97055723 TTTA-AATAT 1 TTTATAATTT 97055732 TTTA-AATATGT 1 TTTATAAT-T-T 97055743 TTTAT-ATTAT 1 TTTATAATT-T * 97055753 TTTATAATAT 1 TTTATAATTT * * 97055763 ATTAGAATTT 1 TTTATAATTT * 97055773 TTTATAA-TA 1 TTTATAATTT * 97055782 TATATAAGTTTT 1 TTTATAA--TTT * 97055794 TTTTTGAATTT 1 TTTAT-AATTT 97055805 TTTATAATTT 1 TTTATAATTT 97055815 ACAAGTTTAT Statistics Matches: 128, Mismatches: 32, Indels: 22 0.70 0.18 0.12 Matches are distributed among these distances: 9 33 0.26 10 65 0.51 11 24 0.19 12 4 0.03 13 2 0.02 ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58 Consensus pattern (10 bp): TTTATAATTT Found at i:97056088 original size:2 final size:2 Alignment explanation

Indices: 97056081--97056106 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 97056071 ACTCTTACTA 97056081 AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT 97056107 TTCAATTATA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:97062237 original size:24 final size:23 Alignment explanation

Indices: 97062193--97062238 Score: 58 Period size: 23 Copynumber: 2.0 Consensus size: 23 97062183 ATGCATAATC * 97062193 TTATTAAACACTAATTTATGCAG 1 TTATTAAACACTAATTCATGCAG 97062216 TTATTAAA-ACTTAATGTCATGCA 1 TTATTAAACAC-TAAT-TCATGCA 97062239 ATCAAATCAT Statistics Matches: 20, Mismatches: 1, Indels: 3 0.83 0.04 0.12 Matches are distributed among these distances: 22 2 0.10 23 12 0.60 24 6 0.30 ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39 Consensus pattern (23 bp): TTATTAAACACTAATTCATGCAG Found at i:97063843 original size:40 final size:40 Alignment explanation

Indices: 97063780--97063875 Score: 131 Period size: 40 Copynumber: 2.4 Consensus size: 40 97063770 ATACCGACCA * * 97063780 GAAGCCTACTAGGGCATTAAGCCCGACA-ATTACACCGGCAC 1 GAAGCCTGCTA-GGCATTAAGCCCGACAGA-TACACCAGCAC * * 97063821 GAAGCCTGCTAGGCATTAAGCCCGATAGATACACCAGTAC 1 GAAGCCTGCTAGGCATTAAGCCCGACAGATACACCAGCAC 97063861 GAAGCCTGCTAGGCA 1 GAAGCCTGCTAGGCA 97063876 CAAGGCTCGA Statistics Matches: 50, Mismatches: 4, Indels: 3 0.88 0.07 0.05 Matches are distributed among these distances: 40 39 0.78 41 11 0.22 ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16 Consensus pattern (40 bp): GAAGCCTGCTAGGCATTAAGCCCGACAGATACACCAGCAC Found at i:97063917 original size:46 final size:46 Alignment explanation

Indices: 97063865--97063970 Score: 149 Period size: 46 Copynumber: 2.3 Consensus size: 46 97063855 CAGTACGAAG * * 97063865 CCTGCTAGGCACAAGGCTCGATACATTACAGTACACCGGCATAAAA 1 CCTGCTAGGCACAAGGCCCAATACATTACAGTACACCGGCATAAAA * * * * 97063911 CCTGCTAGGCATAAGGCCCAATACATTACAGTACACTGGTATAAAG 1 CCTGCTAGGCACAAGGCCCAATACATTACAGTACACCGGCATAAAA * 97063957 CCTGGTAGGCACAA 1 CCTGCTAGGCACAA 97063971 AGAGCTAATT Statistics Matches: 52, Mismatches: 8, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 46 52 1.00 ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19 Consensus pattern (46 bp): CCTGCTAGGCACAAGGCCCAATACATTACAGTACACCGGCATAAAA Found at i:97066258 original size:24 final size:24 Alignment explanation

Indices: 97066222--97066316 Score: 145 Period size: 24 Copynumber: 4.0 Consensus size: 24 97066212 GAAGCTTCAT 97066222 TGTTGTGGTCAAGCCACTCAATAA 1 TGTTGTGGTCAAGCCACTCAATAA * * 97066246 TGTTGTGGACAAGCCACTCAATAG 1 TGTTGTGGTCAAGCCACTCAATAA * 97066270 TGTTGTGGCCAAGCCACTCAATAA 1 TGTTGTGGTCAAGCCACTCAATAA * * 97066294 CGTTGTGGTCAAGCCGCTCAATA 1 TGTTGTGGTCAAGCCACTCAATA 97066317 TTGCAGTAAA Statistics Matches: 64, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 24 64 1.00 ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26 Consensus pattern (24 bp): TGTTGTGGTCAAGCCACTCAATAA Found at i:97068390 original size:25 final size:27 Alignment explanation

Indices: 97068353--97068405 Score: 74 Period size: 26 Copynumber: 2.0 Consensus size: 27 97068343 TCAAACATGC 97068353 ATTTAGGTCAATTTAAC-CCTAGGGGT 1 ATTTAGGTCAATTTAACTCCTAGGGGT * * 97068379 ATTTCGGT-AATTTATCTCCTAGGGGT 1 ATTTAGGTCAATTTAACTCCTAGGGGT 97068405 A 1 A 97068406 AAACTGTAAA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 25 7 0.29 26 17 0.71 ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38 Consensus pattern (27 bp): ATTTAGGTCAATTTAACTCCTAGGGGT Found at i:97069923 original size:26 final size:26 Alignment explanation

Indices: 97069892--97069999 Score: 180 Period size: 26 Copynumber: 4.2 Consensus size: 26 97069882 TGAAATGCCC * * 97069892 ATCATGAAACATTTACCTAAACCATT 1 ATCATGGAACATTTACCTAACCCATT 97069918 ATCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT * * 97069944 ATCATGGAATATTTACCTAATCCATT 1 ATCATGGAACATTTACCTAACCCATT 97069970 ATCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT 97069996 ATCA 1 ATCA 97070000 ATTTGTACCA Statistics Matches: 76, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 26 76 1.00 ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32 Consensus pattern (26 bp): ATCATGGAACATTTACCTAACCCATT Found at i:97077173 original size:20 final size:20 Alignment explanation

Indices: 97077148--97077185 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 97077138 CTAAAAACGC * 97077148 CAGTATAGCTTAACTTTTCA 1 CAGTATAGCTTAAATTTTCA * 97077168 CAGTATAGTTTAAATTTT 1 CAGTATAGCTTAAATTTT 97077186 TGTGGCGTTT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45 Consensus pattern (20 bp): CAGTATAGCTTAAATTTTCA Found at i:97077988 original size:15 final size:15 Alignment explanation

Indices: 97077965--97078015 Score: 50 Period size: 15 Copynumber: 3.5 Consensus size: 15 97077955 ATACCCATGG * 97077965 CCATTAAACCTTAAA 1 CCATAAAACCTTAAA * 97077980 CCATAAAACCCTAAA 1 CCATAAAACCTTAAA * * 97077995 TCAT-AGACCTTAAA 1 CCATAAAACCTTAAA * 97078009 CCTTAAA 1 CCATAAA 97078016 TATTAAACCG Statistics Matches: 27, Mismatches: 8, Indels: 2 0.73 0.22 0.05 Matches are distributed among these distances: 14 10 0.37 15 17 0.63 ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24 Consensus pattern (15 bp): CCATAAAACCTTAAA Found at i:97078432 original size:41 final size:40 Alignment explanation

Indices: 97078264--97078432 Score: 214 Period size: 41 Copynumber: 4.1 Consensus size: 40 97078254 GTTATATGAC * * * 97078264 TTTTAGCGGCGTTTTTATCAAAAGCGCCGCTAATGCT-TCGAC 1 TTTTAGCGGCG-TTTTAACAAAAGCGCCGCTATTGCTCT-G-T * 97078306 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT 1 TTTTAGCGGCGTTTTAACAAAAGCGCCGCTATTGCTCTGT ** * 97078346 TTTTAGCGGCGTTTTAACAAAAAATGCCGCTATTGCACTGT 1 TTTTAGCGGCGTTTTAAC-AAAAGCGCCGCTATTGCTCTGT * 97078387 TTTTAGCGGCGTTTTAACAAAAGCGCCGCTATTACTCTGT 1 TTTTAGCGGCGTTTTAACAAAAGCGCCGCTATTGCTCTGT 97078427 GTTTTA 1 -TTTTA 97078433 CAATTTTTGC Statistics Matches: 113, Mismatches: 11, Indels: 7 0.86 0.08 0.05 Matches are distributed among these distances: 40 35 0.31 41 66 0.58 42 12 0.11 ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36 Consensus pattern (40 bp): TTTTAGCGGCGTTTTAACAAAAGCGCCGCTATTGCTCTGT Found at i:97083384 original size:24 final size:23 Alignment explanation

Indices: 97083347--97083397 Score: 75 Period size: 24 Copynumber: 2.2 Consensus size: 23 97083337 TTTCTAGAAG * * 97083347 ATTTAGTATTATTAGTATAATAT 1 ATTTAGGATTATTAGCATAATAT 97083370 ATTTAGGATTTATTAGCATAATAT 1 ATTTAGGA-TTATTAGCATAATAT 97083394 ATTT 1 ATTT 97083398 GACATTGATT Statistics Matches: 25, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 23 7 0.28 24 18 0.72 ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51 Consensus pattern (23 bp): ATTTAGGATTATTAGCATAATAT Found at i:97083408 original size:24 final size:24 Alignment explanation

Indices: 97083347--97083408 Score: 65 Period size: 24 Copynumber: 2.6 Consensus size: 24 97083337 TTTCTAGAAG * * 97083347 ATTTAGTATT-ATTAGTATAATAT 1 ATTTAGCATTGATTAGCATAATAT * * 97083370 ATTTAGGATTTATTAGCATAATAT 1 ATTTAGCATTGATTAGCATAATAT 97083394 ATTT-GACATTGATTA 1 ATTTAG-CATTGATTA 97083409 TAATTAAGTT Statistics Matches: 33, Mismatches: 4, Indels: 3 0.82 0.10 0.08 Matches are distributed among these distances: 23 10 0.30 24 23 0.70 ACGTcount: A:0.37, C:0.03, G:0.11, T:0.48 Consensus pattern (24 bp): ATTTAGCATTGATTAGCATAATAT Found at i:97086963 original size:28 final size:28 Alignment explanation

Indices: 97086931--97086993 Score: 69 Period size: 28 Copynumber: 2.3 Consensus size: 28 97086921 ATTTTCCCTC 97086931 ATTTTCT-CTCACTTTATATATTTTTGA-A 1 ATTTTCTACTCACTTT-TAT-TTTTTGATA * * 97086959 ATTTT-TATTTACTTTTATTTTTTGATA 1 ATTTTCTACTCACTTTTATTTTTTGATA 97086986 ATTTTCTA 1 ATTTTCTA 97086994 AAATTGTTGA Statistics Matches: 30, Mismatches: 2, Indels: 6 0.79 0.05 0.16 Matches are distributed among these distances: 26 7 0.23 27 10 0.33 28 13 0.43 ACGTcount: A:0.24, C:0.10, G:0.03, T:0.63 Consensus pattern (28 bp): ATTTTCTACTCACTTTTATTTTTTGATA Found at i:97091681 original size:46 final size:48 Alignment explanation

Indices: 97091537--97091802 Score: 282 Period size: 47 Copynumber: 5.7 Consensus size: 48 97091527 GTTGTTGGCT * ** * 97091537 AGTGTAAGA-CATGTCTGGGACAT-GCATTGGCC-ACATTATGAGAGCC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGA-GATGAGAGCC * * * 97091583 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGAGCT 1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATGAGAGCC * * * * 97091631 AGTGTAAGA-CATGTCAGGGACAT-GCATCGGCCTCGATACGTA-AGCC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATG-AGAGCC * * * * 97091677 AGTGTAAGA-CATGTCTTGTACAT-GCATCGG-CTATGAGATGATAGTC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-TGAGATGAGAGCC * * 97091723 AGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGAGATGTGAGCC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATGAGAGCC 97091770 AGTGTAAGACCATGTCTGGGACATGGCATCGGC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC 97091803 ACCTTACCCA Statistics Matches: 185, Mismatches: 25, Indels: 18 0.81 0.11 0.08 Matches are distributed among these distances: 45 3 0.02 46 69 0.37 47 81 0.44 48 31 0.17 49 1 0.01 ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23 Consensus pattern (48 bp): AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATGAGAGCC Found at i:97091791 original size:140 final size:141 Alignment explanation

Indices: 97091537--97091802 Score: 376 Period size: 140 Copynumber: 1.9 Consensus size: 141 97091527 GTTGTTGGCT * * 97091537 AGTGTAAGACATGTCTGGGACATGCATTGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG 1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG * * 97091602 GACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCAGGGACAT-GCATCGGCCTCG 66 GACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCAGGGACATGGCATCGGCCTCG 97091666 ATACGTAAGCC 131 ATACGTAAGCC * * * * * * 97091677 AGTGTAAGACATGTCTTGTACATGCATCGGCTATGA-GATGATAGTCAGTGTAAGACCATGTCTG 1 AGTGTAAGACATGTCTGGGACATGCATCGGCCA-CATGATGAGAGCCAGTGTAAGACCATGTCTG * * * 97091741 GGACATGGCATCGAC-TTGAGATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC 65 GGACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGA-CATGTCAGGGACATGGCATCGGC 97091803 ACCTTACCCA Statistics Matches: 110, Mismatches: 13, Indels: 5 0.86 0.10 0.04 Matches are distributed among these distances: 139 20 0.18 140 81 0.74 141 9 0.08 ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23 Consensus pattern (141 bp): AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG GACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCAGGGACATGGCATCGGCCTCG ATACGTAAGCC Found at i:97096120 original size:15 final size:15 Alignment explanation

Indices: 97096100--97096134 Score: 61 Period size: 15 Copynumber: 2.3 Consensus size: 15 97096090 TAGGAAGATA * 97096100 TTATTTTATTTTTAT 1 TTATTTTATTTTAAT 97096115 TTATTTTATTTTAAT 1 TTATTTTATTTTAAT 97096130 TTATT 1 TTATT 97096135 AAATTACTTA Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 15 19 1.00 ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77 Consensus pattern (15 bp): TTATTTTATTTTAAT Found at i:97096276 original size:41 final size:40 Alignment explanation

Indices: 97096219--97096302 Score: 114 Period size: 41 Copynumber: 2.1 Consensus size: 40 97096209 TACTTTTGTA * * 97096219 TTCCTACTTCAATTTGGAATTGGATTATTCTCTCTTCTCTT 1 TTCCTACTTCAATTTGGAATTGAATTATTATCTCTTCT-TT * * * 97096260 TTCCTATTTCTATTTGGAATTGAATTATTATCTTTTCTTT 1 TTCCTACTTCAATTTGGAATTGAATTATTATCTCTTCTTT 97096300 TTC 1 TTC 97096303 AATTTGACGT Statistics Matches: 38, Mismatches: 5, Indels: 1 0.86 0.11 0.02 Matches are distributed among these distances: 40 5 0.13 41 33 0.87 ACGTcount: A:0.18, C:0.18, G:0.08, T:0.56 Consensus pattern (40 bp): TTCCTACTTCAATTTGGAATTGAATTATTATCTCTTCTTT Found at i:97102745 original size:41 final size:40 Alignment explanation

Indices: 97102688--97102771 Score: 114 Period size: 41 Copynumber: 2.1 Consensus size: 40 97102678 TACTTTTGTA * * 97102688 TTCCTACTTCAATTTGGAATTGGATTATTTTCTCTTCTCTT 1 TTCCTACTTCAATTTGGAATTGAAATATTTTCTCTTCT-TT * * * 97102729 TTCCTATTTCCATTTGGAATTGAAATATTTTCTTTTCTTT 1 TTCCTACTTCAATTTGGAATTGAAATATTTTCTCTTCTTT 97102769 TTC 1 TTC 97102772 AATTTGATGT Statistics Matches: 38, Mismatches: 5, Indels: 1 0.86 0.11 0.02 Matches are distributed among these distances: 40 5 0.13 41 33 0.87 ACGTcount: A:0.18, C:0.18, G:0.08, T:0.56 Consensus pattern (40 bp): TTCCTACTTCAATTTGGAATTGAAATATTTTCTCTTCTTT Found at i:97113099 original size:28 final size:28 Alignment explanation

Indices: 97113068--97113121 Score: 108 Period size: 28 Copynumber: 1.9 Consensus size: 28 97113058 TATGACCCGA 97113068 GTTAGTATACTGAAAGTGTAAAGTTTCG 1 GTTAGTATACTGAAAGTGTAAAGTTTCG 97113096 GTTAGTATACTGAAAGTGTAAAGTTT 1 GTTAGTATACTGAAAGTGTAAAGTTT 97113122 TGGTAGTGTC Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 26 1.00 ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37 Consensus pattern (28 bp): GTTAGTATACTGAAAGTGTAAAGTTTCG Found at i:97117305 original size:27 final size:27 Alignment explanation

Indices: 97117266--97117325 Score: 93 Period size: 27 Copynumber: 2.2 Consensus size: 27 97117256 TGGAAAAAGG * * * 97117266 TTCTTTCTTCAAGATATTATTCTCTAT 1 TTCTCTCTGCAAGATATTACTCTCTAT 97117293 TTCTCTCTGCAAGATATTACTCTCTAT 1 TTCTCTCTGCAAGATATTACTCTCTAT 97117320 TTCTCT 1 TTCTCT 97117326 TTCTTAAATC Statistics Matches: 30, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 27 30 1.00 ACGTcount: A:0.20, C:0.23, G:0.05, T:0.52 Consensus pattern (27 bp): TTCTCTCTGCAAGATATTACTCTCTAT Found at i:97119877 original size:12 final size:13 Alignment explanation

Indices: 97119860--97119892 Score: 50 Period size: 12 Copynumber: 2.5 Consensus size: 13 97119850 GCAATTTAAA 97119860 TTTTATT-CTAAT 1 TTTTATTACTAAT 97119872 TTTTATTACTAAT 1 TTTTATTACTAAT 97119885 TCTTTATT 1 T-TTTATT 97119893 TTCCCTTTTT Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 12 7 0.37 13 6 0.32 14 6 0.32 ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67 Consensus pattern (13 bp): TTTTATTACTAAT Found at i:97120723 original size:43 final size:43 Alignment explanation

Indices: 97120661--97120747 Score: 156 Period size: 43 Copynumber: 2.0 Consensus size: 43 97120651 ACTCGGGAGA * * 97120661 TGATTGATGCAGCCGCTGGAGGAATTATCAATAATAAGACACC 1 TGATTGATGCAGCCACTGGAGGAACTATCAATAATAAGACACC 97120704 TGATTGATGCAGCCACTGGAGGAACTATCAATAATAAGACACC 1 TGATTGATGCAGCCACTGGAGGAACTATCAATAATAAGACACC 97120747 T 1 T 97120748 AAGATGGCTT Statistics Matches: 42, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 43 42 1.00 ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23 Consensus pattern (43 bp): TGATTGATGCAGCCACTGGAGGAACTATCAATAATAAGACACC Found at i:97126613 original size:110 final size:110 Alignment explanation

Indices: 97126488--97126687 Score: 269 Period size: 110 Copynumber: 1.8 Consensus size: 110 97126478 AAGATTGGAA * * * * * * * 97126488 TGGCATATTACGATACATGAAAGTGTGTGA-GTCCATGTGGCTAAGACCCACT-GTAAGATATGA 1 TGGCAGATCACGATACATGAAAATGTGT-ACGTCCATATGGCTAAGA-CCAATGGCAAGATACGA 97126551 CTGCATGAATGTTCATGATGTAGCCTTTAATAGTGTGAACATTGAAC 64 CTGCATGAATGTTCATGATGTAGCCTTTAATAGTGTGAACATTGAAC * * 97126598 TGGCAGATCACGATACATGAAAATGTGTACGTCCATATGGCTGAGACCAATGGCAAGATACGATT 1 TGGCAGATCACGATACATGAAAATGTGTACGTCCATATGGCTAAGACCAATGGCAAGATACGACT * * 97126663 GTATGAATGTTCATGGTGTAGCCTT 66 GCATGAATGTTCATGATGTAGCCTT 97126688 CGATAATATG Statistics Matches: 77, Mismatches: 11, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 109 5 0.06 110 72 0.94 ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29 Consensus pattern (110 bp): TGGCAGATCACGATACATGAAAATGTGTACGTCCATATGGCTAAGACCAATGGCAAGATACGACT GCATGAATGTTCATGATGTAGCCTTTAATAGTGTGAACATTGAAC Found at i:97126716 original size:110 final size:110 Alignment explanation

Indices: 97126497--97126728 Score: 252 Period size: 110 Copynumber: 2.1 Consensus size: 110 97126487 ATGGCATATT * * * * * 97126497 ACGATACATGAAAGTGTGTGAGTCCATGTGGCTAAGACCCACTGTAAGATATGACTGCATGAATG 1 ACGATACATGAAAATGTGTGAGTCCATATGGCTAAGACCCAATGCAAGATACGACTGCATGAATG * * * * *** 97126562 TTCATGATGTAGCCTTTAATAGTGTGAACATTGAACTGGCAGATC 66 TTCATGATGTAGCCTTCAATAATATGAACATAGAACAAACAGATC * * * 97126607 ACGATACATGAAAATGTGT-ACGTCCATATGGCTGAGA-CCAATGGCAAGATACGATTGTATGAA 1 ACGATACATGAAAATGTGTGA-GTCCATATGGCTAAGACCCAAT-GCAAGATACGACTGCATGAA * * * 97126670 TGTTCATGGTGTAGCCTTCGATAATATGAACATAGAACAAATAGATC 64 TGTTCATGATGTAGCCTTCAATAATATGAACATAGAACAAACAGATC ** 97126717 ATAATACATGAA 1 ACGATACATGAA 97126729 TTTATGTATA Statistics Matches: 100, Mismatches: 20, Indels: 4 0.81 0.16 0.03 Matches are distributed among these distances: 109 5 0.05 110 95 0.95 ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27 Consensus pattern (110 bp): ACGATACATGAAAATGTGTGAGTCCATATGGCTAAGACCCAATGCAAGATACGACTGCATGAATG TTCATGATGTAGCCTTCAATAATATGAACATAGAACAAACAGATC Found at i:97126848 original size:23 final size:24 Alignment explanation

Indices: 97126801--97126849 Score: 64 Period size: 23 Copynumber: 2.0 Consensus size: 24 97126791 TAAACACGTA * 97126801 ATTTTGTATGTCGCCTTTGTAGCAT 1 ATTTTGTATG-CGCCCTTGTAGCAT * 97126826 ATTTTGTATG-GCCCTTGTGGCAT 1 ATTTTGTATGCGCCCTTGTAGCAT 97126849 A 1 A 97126850 CTTTAATAAG Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 23 12 0.55 25 10 0.45 ACGTcount: A:0.16, C:0.16, G:0.22, T:0.45 Consensus pattern (24 bp): ATTTTGTATGCGCCCTTGTAGCAT Found at i:97149905 original size:23 final size:23 Alignment explanation

Indices: 97149854--97149908 Score: 101 Period size: 23 Copynumber: 2.4 Consensus size: 23 97149844 ACAAGTGAAT * 97149854 TAATTAAAAATTGAATTTAAAGC 1 TAATTCAAAATTGAATTTAAAGC 97149877 TAATTCAAAATTGAATTTAAAGC 1 TAATTCAAAATTGAATTTAAAGC 97149900 TAATTCAAA 1 TAATTCAAA 97149909 TTGGGTCCAG Statistics Matches: 31, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 23 31 1.00 ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35 Consensus pattern (23 bp): TAATTCAAAATTGAATTTAAAGC Found at i:97157127 original size:34 final size:34 Alignment explanation

Indices: 97157084--97157151 Score: 136 Period size: 34 Copynumber: 2.0 Consensus size: 34 97157074 AAAGAGTGAA 97157084 GGAAGAAGAAAGGAGTTTGTCCAAGCATTGGTTG 1 GGAAGAAGAAAGGAGTTTGTCCAAGCATTGGTTG 97157118 GGAAGAAGAAAGGAGTTTGTCCAAGCATTGGTTG 1 GGAAGAAGAAAGGAGTTTGTCCAAGCATTGGTTG 97157152 AAAGTACTTC Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 34 34 1.00 ACGTcount: A:0.32, C:0.09, G:0.35, T:0.24 Consensus pattern (34 bp): GGAAGAAGAAAGGAGTTTGTCCAAGCATTGGTTG Found at i:97159578 original size:23 final size:23 Alignment explanation

Indices: 97159547--97159624 Score: 95 Period size: 23 Copynumber: 3.4 Consensus size: 23 97159537 TCGTAAGAGT * * 97159547 TTACTGTTTCAGCTCACTGGAGC 1 TTACCGTTTCAGCTCAATGGAGC * 97159570 TTACCGTTTCAGCTCATTGGAGC 1 TTACCGTTTCAGCTCAATGGAGC * * 97159593 TTACTGTTT-AGCTCAATAGAGC 1 TTACCGTTTCAGCTCAATGGAGC * 97159615 TTACCATTTC 1 TTACCGTTTC 97159625 TGTAATGCGG Statistics Matches: 47, Mismatches: 7, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 22 18 0.38 23 29 0.62 ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37 Consensus pattern (23 bp): TTACCGTTTCAGCTCAATGGAGC Found at i:97160209 original size:7 final size:7 Alignment explanation

Indices: 97160197--97160221 Score: 50 Period size: 7 Copynumber: 3.6 Consensus size: 7 97160187 GTTATTATAT 97160197 TATATTA 1 TATATTA 97160204 TATATTA 1 TATATTA 97160211 TATATTA 1 TATATTA 97160218 TATA 1 TATA 97160222 AATAAGTAAA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56 Consensus pattern (7 bp): TATATTA Found at i:97160685 original size:24 final size:20 Alignment explanation

Indices: 97160659--97160699 Score: 82 Period size: 20 Copynumber: 2.0 Consensus size: 20 97160649 AATATATAAA 97160659 AGTAAGTGAATTTAGTTAGG 1 AGTAAGTGAATTTAGTTAGG 97160679 AGTAAGTGAATTTAGTTAGG 1 AGTAAGTGAATTTAGTTAGG 97160699 A 1 A 97160700 TTAAATTGAA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34 Consensus pattern (20 bp): AGTAAGTGAATTTAGTTAGG Found at i:97161983 original size:12 final size:12 Alignment explanation

Indices: 97161966--97161990 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 97161956 GCCGACTACT 97161966 GTTACTGTTACC 1 GTTACTGTTACC 97161978 GTTACTGTTACC 1 GTTACTGTTACC 97161990 G 1 G 97161991 ATTTGGCACT 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:0.16, C:0.24, G:0.20, T:0.40 Consensus pattern (12 bp): GTTACTGTTACC Found at i:97162020 original size:51 final size:50 Alignment explanation

Indices: 97161962--97162091 Score: 157 Period size: 45 Copynumber: 2.7 Consensus size: 50 97161952 ATGTGCCGAC 97161962 TACTGTTACTGTTACCGTTACTGTTACCGATTTGGCACTTTGTGTGTCT-AA 1 TACTGTTACTGTTACCGTTACTGTT-CCGATTTGGCACTTTGTGTGT-TGAA * 97162013 TACTGTTACTGTTACCGTTATCTATT-C-A----GCACTTTGTGTGTTGAA 1 TACTGTTACTGTTACCGTTA-CTGTTCCGATTTGGCACTTTGTGTGTTGAA * 97162058 TACTGTTACTGTTACTGTTACTGTTCCGAATTTG 1 TACTGTTACTGTTACCGTTACTGTTCCG-ATTTG 97162092 TTCCGCTGAG Statistics Matches: 67, Mismatches: 3, Indels: 18 0.76 0.03 0.20 Matches are distributed among these distances: 44 5 0.07 45 35 0.52 47 1 0.01 49 1 0.01 50 1 0.01 51 20 0.30 52 4 0.06 ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45 Consensus pattern (50 bp): TACTGTTACTGTTACCGTTACTGTTCCGATTTGGCACTTTGTGTGTTGAA Found at i:97162069 original size:6 final size:6 Alignment explanation

Indices: 97162058--97162082 Score: 50 Period size: 6 Copynumber: 4.2 Consensus size: 6 97162048 GTGTGTTGAA 97162058 TACTGT TACTGT TACTGT TACTGT T 1 TACTGT TACTGT TACTGT TACTGT T 97162083 CCGAATTTGT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 19 1.00 ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52 Consensus pattern (6 bp): TACTGT Found at i:97162269 original size:18 final size:18 Alignment explanation

Indices: 97162246--97162448 Score: 142 Period size: 18 Copynumber: 11.3 Consensus size: 18 97162236 AAAGGTATAA * * 97162246 AATAATTGATTATTACTG 1 AATAATTGACTGTTACTG * 97162264 AATAATTGACTGTTACCG 1 AATAATTGACTGTTACTG 97162282 AATAATTGACTGTTACTG 1 AATAATTGACTGTTACTG * * * 97162300 GATAATAGACTGTTACCG 1 AATAATTGACTGTTACTG * * * 97162318 AATAACTGAATATTACTG 1 AATAATTGACTGTTACTG * 97162336 AATAATTGA-TCATTACTG 1 AATAATTGACT-GTTACTG * * * * * 97162354 AATAACTAATTGTCATTG 1 AATAATTGACTGTTACTG * * 97162372 AATAAATGACTATTACTG 1 AATAATTGACTGTTACTG * * * * 97162390 AATAACTTAATTGCTATTG 1 AATAA-TTGACTGTTACTG * * 97162409 AAT-ATCTGA-TTTTACTA 1 AATAAT-TGACTGTTACTG 97162426 AATAATTGACTGTTACTG 1 AATAATTGACTGTTACTG * 97162444 GATAA 1 AATAA 97162449 CCGATCAATT Statistics Matches: 140, Mismatches: 39, Indels: 12 0.73 0.20 0.06 Matches are distributed among these distances: 17 12 0.09 18 117 0.84 19 11 0.08 ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37 Consensus pattern (18 bp): AATAATTGACTGTTACTG Found at i:97162503 original size:18 final size:18 Alignment explanation

Indices: 97162468--97162527 Score: 57 Period size: 18 Copynumber: 3.3 Consensus size: 18 97162458 TGATCGATAC * * 97162468 TGAATAACTGGTTATTAT 1 TGAATAACTGATTGTTAT * 97162486 TGAATAATTGATTGTTAT 1 TGAATAACTGATTGTTAT * * * * 97162504 CGAATAAGTGACTGTTAC 1 TGAATAACTGATTGTTAT 97162522 TGAATA 1 TGAATA 97162528 TATAATTGTT Statistics Matches: 34, Mismatches: 8, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 18 34 1.00 ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40 Consensus pattern (18 bp): TGAATAACTGATTGTTAT Found at i:97165508 original size:22 final size:21 Alignment explanation

Indices: 97165478--97165524 Score: 58 Period size: 22 Copynumber: 2.2 Consensus size: 21 97165468 TACAAATTAA 97165478 ATCTCCAAGATTACAAGATCAT 1 ATCTCCAAGATTAC-AGATCAT * * * 97165500 ATCTTCAAGATTGCATATCAT 1 ATCTCCAAGATTACAGATCAT 97165521 ATCT 1 ATCT 97165525 AAGATTGTAT Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 21 10 0.45 22 12 0.55 ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34 Consensus pattern (21 bp): ATCTCCAAGATTACAGATCAT Found at i:97165530 original size:19 final size:19 Alignment explanation

Indices: 97165495--97165573 Score: 117 Period size: 19 Copynumber: 4.2 Consensus size: 19 97165485 AGATTACAAG 97165495 ATCATATCTTCAAGATTGCAT 1 ATCATATC-T-AAGATTGCAT 97165516 ATCATATCTAAGATTG--T 1 ATCATATCTAAGATTGCAT * 97165533 ATCATACCTAAGATTGCAT 1 ATCATATCTAAGATTGCAT 97165552 ATCATATCTAAGATTGCAT 1 ATCATATCTAAGATTGCAT 97165571 ATC 1 ATC 97165574 CTTAAAGATT Statistics Matches: 54, Mismatches: 2, Indels: 6 0.87 0.03 0.10 Matches are distributed among these distances: 17 16 0.30 19 29 0.54 20 1 0.02 21 8 0.15 ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37 Consensus pattern (19 bp): ATCATATCTAAGATTGCAT Found at i:97165582 original size:36 final size:35 Alignment explanation

Indices: 97165497--97165583 Score: 115 Period size: 36 Copynumber: 2.4 Consensus size: 35 97165487 ATTACAAGAT 97165497 CATAT-CTTCAAGATTGCATATCATATCTAAGATTG 1 CATATCCTT-AAGATTGCATATCATATCTAAGATTG * 97165532 TATCATACC-TAAGATTGCATATCATATCTAAGATTG 1 CAT-AT-CCTTAAGATTGCATATCATATCTAAGATTG 97165568 CATATCCTTAAAGATT 1 CATATCCTT-AAGATT 97165584 ATATTTCCAT Statistics Matches: 45, Mismatches: 2, Indels: 9 0.80 0.04 0.16 Matches are distributed among these distances: 34 2 0.04 35 5 0.11 36 36 0.80 37 1 0.02 38 1 0.02 ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37 Consensus pattern (35 bp): CATATCCTTAAGATTGCATATCATATCTAAGATTG Found at i:97168823 original size:7 final size:7 Alignment explanation

Indices: 97168796--97168840 Score: 51 Period size: 7 Copynumber: 6.6 Consensus size: 7 97168786 AAATTGTTAT 97168796 TATATTA 1 TATATTA 97168803 TAT-TATA 1 TATAT-TA 97168810 TTATATTA 1 -TATATTA 97168818 TATA-T- 1 TATATTA 97168823 TATATTA 1 TATATTA 97168830 TATATTA 1 TATATTA 97168837 TATA 1 TATA 97168841 AATAAGTAAA Statistics Matches: 33, Mismatches: 0, Indels: 10 0.77 0.00 0.23 Matches are distributed among these distances: 5 4 0.12 6 3 0.09 7 20 0.61 8 5 0.15 9 1 0.03 ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58 Consensus pattern (7 bp): TATATTA Found at i:97168823 original size:12 final size:12 Alignment explanation

Indices: 97168796--97168839 Score: 74 Period size: 12 Copynumber: 3.8 Consensus size: 12 97168786 AAATTGTTAT 97168796 TATATTATA-T- 1 TATATTATATTA 97168806 TATATTATATTA 1 TATATTATATTA 97168818 TATATTATATTA 1 TATATTATATTA 97168830 TATATTATAT 1 TATATTATAT 97168840 AAATAAGTAA Statistics Matches: 32, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 10 9 0.28 11 1 0.03 12 22 0.69 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (12 bp): TATATTATATTA Found at i:97168839 original size:5 final size:5 Alignment explanation

Indices: 97168793--97168832 Score: 62 Period size: 5 Copynumber: 7.6 Consensus size: 5 97168783 AAGAAATTGT 97168793 TATTA TATTA TATTA TATTA TATTATA TATTA TATTA TAT 1 TATTA TATTA TATTA TATTA TA-T-TA TATTA TATTA TAT 97168833 ATTATATAAA Statistics Matches: 33, Mismatches: 0, Indels: 4 0.89 0.00 0.11 Matches are distributed among these distances: 5 27 0.82 6 2 0.06 7 4 0.12 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (5 bp): TATTA Found at i:97170607 original size:45 final size:45 Alignment explanation

Indices: 97170555--97170665 Score: 143 Period size: 45 Copynumber: 2.5 Consensus size: 45 97170545 CGACTACTAT * * * 97170555 TACTGTTACCGTTACTGTTACCGATT-TGACACTTTGTGTGTCGAA 1 TACTGTTACTGTTACTGTTACCAATTCAG-CACTTTGTGTGTCGAA * * * * 97170600 TGCTGTTACTGTTACAGTTATCAATTCAGCACTTTGTGTGTTGAA 1 TACTGTTACTGTTACTGTTACCAATTCAGCACTTTGTGTGTCGAA 97170645 TACTGTTACTGTTACTGTTAC 1 TACTGTTACTGTTACTGTTAC 97170666 TGTTCCAAAT Statistics Matches: 55, Mismatches: 10, Indels: 2 0.82 0.15 0.03 Matches are distributed among these distances: 45 54 0.98 46 1 0.02 ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42 Consensus pattern (45 bp): TACTGTTACTGTTACTGTTACCAATTCAGCACTTTGTGTGTCGAA Found at i:97170656 original size:6 final size:6 Alignment explanation

Indices: 97170645--97170669 Score: 50 Period size: 6 Copynumber: 4.2 Consensus size: 6 97170635 GTGTGTTGAA 97170645 TACTGT TACTGT TACTGT TACTGT T 1 TACTGT TACTGT TACTGT TACTGT T 97170670 CCAAATTTGT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 19 1.00 ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52 Consensus pattern (6 bp): TACTGT Found at i:97170872 original size:18 final size:18 Alignment explanation

Indices: 97170851--97171041 Score: 127 Period size: 18 Copynumber: 10.6 Consensus size: 18 97170841 TAACTGATTA 97170851 TTACTGAATAATTGACTG 1 TTACTGAATAATTGACTG ** 97170869 TTACCAAATAATTGACTG 1 TTACTGAATAATTGACTG * * 97170887 TTACTGGATAATAGACTG 1 TTACTGAATAATTGACTG * * * 97170905 TTACTGAATAACTGAATA 1 TTACTGAATAATTGACTG * 97170923 TTACTGAATAATTGA-TCA 1 TTACTGAATAATTGACT-G * * 97170941 TTACTGAATAACTGATTG 1 TTACTGAATAATTGACTG * * * * * 97170959 TCACTAAATAAATAATTG 1 TTACTGAATAATTGACTG * * * 97170977 TTACTAAATAACTTAATTG 1 TTACTGAATAA-TTGACTG * * * 97170996 CTATTGAAT-ATCTGA-TT 1 TTACTGAATAAT-TGACTG * 97171013 TTACTAAATAATTGACTG 1 TTACTGAATAATTGACTG * 97171031 TTACTGGATAA 1 TTACTGAATAA 97171042 CCGATCAATT Statistics Matches: 136, Mismatches: 31, Indels: 12 0.76 0.17 0.07 Matches are distributed among these distances: 17 12 0.09 18 111 0.82 19 13 0.10 ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38 Consensus pattern (18 bp): TTACTGAATAATTGACTG Found at i:97170945 original size:36 final size:36 Alignment explanation

Indices: 97170839--97170955 Score: 137 Period size: 36 Copynumber: 3.2 Consensus size: 36 97170829 AAAGGTATAA * ** 97170839 AATAACTGATTATTACTGAATAATTGACTGTTACCA 1 AATAACTGAATATTACTGAATAATTGACTGTTACTG * * * * * 97170875 AATAATTGACTGTTACTGGATAATAGACTGTTACTG 1 AATAACTGAATATTACTGAATAATTGACTGTTACTG * 97170911 AATAACTGAATATTACTGAATAATTGA-TCATTACTG 1 AATAACTGAATATTACTGAATAATTGACT-GTTACTG 97170947 AATAACTGA 1 AATAACTGA 97170956 TTGTCACTAA Statistics Matches: 67, Mismatches: 13, Indels: 2 0.82 0.16 0.02 Matches are distributed among these distances: 35 1 0.01 36 66 0.99 ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35 Consensus pattern (36 bp): AATAACTGAATATTACTGAATAATTGACTGTTACTG Found at i:97170979 original size:72 final size:72 Alignment explanation

Indices: 97170838--97170989 Score: 173 Period size: 72 Copynumber: 2.1 Consensus size: 72 97170828 TAAAGGTATA * * * * ** 97170838 AAATAACTGATTATTACTGAATAATTGACTGTTACCAAATAATTGACTGTTACTGGATAATAGAC 1 AAATAACTGAATATTACTGAATAATTGACTATTACCAAATAACTGACTGTCACTAAATAATAGAC 97170903 TGTTACT 66 TGTTACT * ** * 97170910 GAATAACTGAATATTACTGAATAATTGA-TCATTACTGAATAACTGATTGTCACTAAATAAATA- 1 AAATAACTGAATATTACTGAATAATTGACT-ATTACCAAATAACTGACTGTCACTAAAT-AATAG * 97170973 ATTGTTACT 64 ACTGTTACT 97170982 AAATAACT 1 AAATAACT 97170990 TAATTGCTAT Statistics Matches: 66, Mismatches: 12, Indels: 4 0.80 0.15 0.05 Matches are distributed among these distances: 71 1 0.02 72 61 0.92 73 4 0.06 ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36 Consensus pattern (72 bp): AAATAACTGAATATTACTGAATAATTGACTATTACCAAATAACTGACTGTCACTAAATAATAGAC TGTTACT Found at i:97171130 original size:18 final size:18 Alignment explanation

Indices: 97171079--97171134 Score: 60 Period size: 18 Copynumber: 3.2 Consensus size: 18 97171069 TGGTTATTAT * 97171079 TGAATAATTGATTGTTAC 1 TGAATAAATGATTGTTAC * * * 97171097 CGAATAAGTGACTGTTAC 1 TGAATAAATGATTGTTAC * 97171115 TGAATAAATAATTGTT-C 1 TGAATAAATGATTGTTAC 97171132 TGA 1 TGA 97171135 TTGTTAATAA Statistics Matches: 31, Mismatches: 7, Indels: 1 0.79 0.18 0.03 Matches are distributed among these distances: 17 4 0.13 18 27 0.87 ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38 Consensus pattern (18 bp): TGAATAAATGATTGTTAC Found at i:97174021 original size:20 final size:19 Alignment explanation

Indices: 97173989--97174026 Score: 76 Period size: 19 Copynumber: 2.0 Consensus size: 19 97173979 CGTATACGTG 97173989 GTATTTTTGAAAAACATTT 1 GTATTTTTGAAAAACATTT 97174008 GTATTTTTGAAAAACATTT 1 GTATTTTTGAAAAACATTT 97174027 ATCTTTCGAA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47 Consensus pattern (19 bp): GTATTTTTGAAAAACATTT Found at i:97174037 original size:18 final size:19 Alignment explanation

Indices: 97173989--97174038 Score: 59 Period size: 19 Copynumber: 2.7 Consensus size: 19 97173979 CGTATACGTG * 97173989 GTATTTTTGAAAAACATTT 1 GTATTTTCGAAAAACATTT * 97174008 GTATTTTTGAAAAACA-TT 1 GTATTTTCGAAAAACATTT 97174026 -TATCTTTCGAAAA 1 GTAT-TTTCGAAAA 97174039 CCCGTGCCCT Statistics Matches: 29, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 17 3 0.10 18 10 0.34 19 16 0.55 ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44 Consensus pattern (19 bp): GTATTTTCGAAAAACATTT Found at i:97175669 original size:27 final size:27 Alignment explanation

Indices: 97175639--97175703 Score: 85 Period size: 27 Copynumber: 2.4 Consensus size: 27 97175629 ATTACCAAAG * * * 97175639 TACCCTCGATTTATAGAATTATCATTT 1 TACCCTCGATTTACAAAATTACCATTT * * 97175666 TACCCTTGATTTACAAAATTACCGTTT 1 TACCCTCGATTTACAAAATTACCATTT 97175693 TACCCTCGATT 1 TACCCTCGATT 97175704 ATGAAATTAC Statistics Matches: 32, Mismatches: 6, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 27 32 1.00 ACGTcount: A:0.28, C:0.23, G:0.08, T:0.42 Consensus pattern (27 bp): TACCCTCGATTTACAAAATTACCATTT Found at i:97175765 original size:27 final size:27 Alignment explanation

Indices: 97175735--97175912 Score: 180 Period size: 27 Copynumber: 6.6 Consensus size: 27 97175725 TGTAGGATAG * * * 97175735 AATTACCAAAACACCCCTATTTTGCAA 1 AATTACCAAAATACCCCTAGTTTGTAA 97175762 AATTACCAAAATACCCCTAGTTTGTAA 1 AATTACCAAAATACCCCTAGTTTGTAA * 97175789 AATTACCAAAATATCCCTAGTTTGTAA 1 AATTACCAAAATACCCCTAGTTTGTAA ** * * * 97175816 AATTACTGAAATACCACTGGTTTGTGA 1 AATTACCAAAATACCCCTAGTTTGTAA * * * * 97175843 AATTATCGAAATA-CCTTCAATTTGTAA 1 AATTACCAAAATACCCCT-AGTTTGTAA * ** 97175870 AATTACCAAAATACCCCTAATTTACAA 1 AATTACCAAAATACCCCTAGTTTGTAA 97175897 AATTA-CAGAAATACCC 1 AATTACCA-AAATACCC 97175913 TCGACTTTCT Statistics Matches: 126, Mismatches: 22, Indels: 6 0.82 0.14 0.04 Matches are distributed among these distances: 26 4 0.03 27 119 0.94 28 3 0.02 ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30 Consensus pattern (27 bp): AATTACCAAAATACCCCTAGTTTGTAA Found at i:97175839 original size:54 final size:54 Alignment explanation

Indices: 97175707--97175967 Score: 172 Period size: 54 Copynumber: 4.8 Consensus size: 54 97175697 CTCGATTATG ** * * * * 97175707 AAATTACTGAAATACCCCT-GTAGGATAGAATTACCAAAACACCC-CTATTTTGCA 1 AAATTACTGAAATACCCCTAGTTTG-TAAAATTACCAAAATACCCTC-AATTTGTA ** * 97175761 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATATCCCT-AGTTTGTA 1 AAATTACTGAAATACCCCTAGTTTGTAAAATTACCAAAATA-CCCTCAATTTGTA * * * * * * 97175815 AAATTACTGAAATACCACTGGTTTGTGAAATTATCGAAATACCTTCAATTTGTA 1 AAATTACTGAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTA ** * ** * * 97175869 AAATTACCAAAATACCCCTAATTTACAAAATTA-CAGAAATACCCTCGACTTTCTAA 1 AAATTACTGAAATACCCCTAGTTTGTAAAATTACCA-AAATACCCTC-AATTTGT-A * * ** ** 97175925 AAATTA-TAGAAATACCACTGGTTTACAAAATTACTGAAATACC 1 AAATTACT-GAAATACCCCTAGTTTGTAAAATTACCAAAATACC 97175968 ATTGGTTTGT Statistics Matches: 162, Mismatches: 36, Indels: 16 0.76 0.17 0.07 Matches are distributed among these distances: 53 4 0.02 54 112 0.69 55 11 0.07 56 35 0.22 ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30 Consensus pattern (54 bp): AAATTACTGAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTA Found at i:97175963 original size:27 final size:27 Alignment explanation

Indices: 97175814--97175975 Score: 82 Period size: 27 Copynumber: 5.9 Consensus size: 27 97175804 CCTAGTTTGT ** 97175814 AAAATTACTGAAATACCACTGGTTTGT 1 AAAATTACTGAAATACCACTGGTTTAC * * ** ** 97175841 GAAATTA-TCGAAATACC-TTCAATTTGT 1 AAAATTACT-GAAATACCACT-GGTTTAC ** * ** 97175868 AAAATTACCAAAATACCCCTAATTTAC 1 AAAATTACTGAAATACCACTGGTTTAC * * 97175895 AAAATTACAGAAATACC-CTCGACTTT-C 1 AAAATTACTGAAATACCACT-G-GTTTAC 97175922 TAAAAATTA-TAGAAATACCACTGGTTTAC 1 --AAAATTACT-GAAATACCACTGGTTTAC * 97175951 AAAATTACTGAAATACCATTGGTTT 1 AAAATTACTGAAATACCACTGGTTT 97175976 GTAGATTTAC Statistics Matches: 106, Mismatches: 17, Indels: 24 0.72 0.12 0.16 Matches are distributed among these distances: 26 4 0.04 27 75 0.71 28 8 0.08 29 17 0.16 30 2 0.02 ACGTcount: A:0.41, C:0.18, G:0.09, T:0.31 Consensus pattern (27 bp): AAAATTACTGAAATACCACTGGTTTAC Found at i:97176983 original size:24 final size:24 Alignment explanation

Indices: 97176900--97176983 Score: 98 Period size: 25 Copynumber: 3.4 Consensus size: 24 97176890 GAGGGAGTGC * * * 97176900 TAAAAGGGCTCTACCCCAGTTTACC 1 TAAAAGGGCTTTGCCCCAGTTTA-T * 97176925 AAAAAGGGCTTTGCCCCAGTTTAT 1 TAAAAGGGCTTTGCCCCAGTTTAT 97176949 TAGAAAGGGCTTTGCCCCAG-TTAT 1 TA-AAAGGGCTTTGCCCCAGTTTAT 97176973 TAAAAGAGGCT 1 TAAAAG-GGCT 97176984 AGGCCTCTAG Statistics Matches: 52, Mismatches: 5, Indels: 5 0.84 0.08 0.08 Matches are distributed among these distances: 23 4 0.08 24 11 0.21 25 37 0.71 ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26 Consensus pattern (24 bp): TAAAAGGGCTTTGCCCCAGTTTAT Found at i:97177177 original size:42 final size:42 Alignment explanation

Indices: 97177118--97177209 Score: 166 Period size: 42 Copynumber: 2.2 Consensus size: 42 97177108 TAGTCTCCCC ** 97177118 AAATGGGCTTACATACATTTATTGACATTACATGTGATATTG 1 AAATGGGCTTACATACATCCATTGACATTACATGTGATATTG 97177160 AAATGGGCTTACATACATCCATTGACATTACATGTGATATTG 1 AAATGGGCTTACATACATCCATTGACATTACATGTGATATTG 97177202 AAATGGGC 1 AAATGGGC 97177210 CTAAGGGCCA Statistics Matches: 48, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 42 48 1.00 ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34 Consensus pattern (42 bp): AAATGGGCTTACATACATCCATTGACATTACATGTGATATTG Found at i:97177268 original size:31 final size:30 Alignment explanation

Indices: 97177233--97177348 Score: 189 Period size: 31 Copynumber: 3.8 Consensus size: 30 97177223 CGTTTACAGT 97177233 AAAGGCTTCGGCCCAGTGATATAGTTTATGA 1 AAAGGCTTCGGCCCAGTGATAT-GTTTATGA 97177264 AAAGGCTTCGGCCCAGTGATATGGTTTATGA 1 AAAGGCTTCGGCCCAGTGATAT-GTTTATGA * 97177295 AAAGGCTTCGGCCCAGTGATATGATTTATGG 1 AAAGGCTTCGGCCCAGTGATATG-TTTATGA 97177326 AAAGGCTTCGGCCCAGT-ATATGT 1 AAAGGCTTCGGCCCAGTGATATGT 97177349 CAAGACTAAA Statistics Matches: 82, Mismatches: 2, Indels: 4 0.93 0.02 0.05 Matches are distributed among these distances: 29 1 0.01 30 6 0.07 31 75 0.91 ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28 Consensus pattern (30 bp): AAAGGCTTCGGCCCAGTGATATGTTTATGA Found at i:97179659 original size:27 final size:27 Alignment explanation

Indices: 97179629--97179720 Score: 123 Period size: 27 Copynumber: 3.4 Consensus size: 27 97179619 ATTACCAAAG * * 97179629 TACCCTCGATTTATAGAATTATCGTTT 1 TACCCTCGATTTATAAAATTACCGTTT * * 97179656 TACCCTTGATTTATAAAATTACCATTT 1 TACCCTCGATTTATAAAATTACCGTTT * 97179683 TACCCTC-AGTTTACAAAATTACCGTTT 1 TACCCTCGA-TTTATAAAATTACCGTTT 97179710 TACCCTCGATT 1 TACCCTCGATT 97179721 GTGAAATTAC Statistics Matches: 56, Mismatches: 7, Indels: 4 0.84 0.10 0.06 Matches are distributed among these distances: 26 1 0.02 27 54 0.96 28 1 0.02 ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41 Consensus pattern (27 bp): TACCCTCGATTTATAAAATTACCGTTT Found at i:97179675 original size:54 final size:54 Alignment explanation

Indices: 97179617--97179720 Score: 129 Period size: 54 Copynumber: 1.9 Consensus size: 54 97179607 TCGACTTGTT * * * * 97179617 AAATTACCAAAGTACCCTC-GATTTATAGAATTATCGTTTTACCCTTGATTTATA 1 AAATTACCAAAGTACCCTCAG-TTTACAAAATTACCGTTTTACCCTCGATTTATA *** 97179671 AAATTACCATTTTACCCTCAGTTTACAAAATTACCGTTTTACCCTCGATT 1 AAATTACCAAAGTACCCTCAGTTTACAAAATTACCGTTTTACCCTCGATT 97179721 GTGAAATTAC Statistics Matches: 42, Mismatches: 7, Indels: 2 0.82 0.14 0.04 Matches are distributed among these distances: 54 41 0.98 55 1 0.02 ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38 Consensus pattern (54 bp): AAATTACCAAAGTACCCTCAGTTTACAAAATTACCGTTTTACCCTCGATTTATA Found at i:97179782 original size:27 final size:27 Alignment explanation

Indices: 97179752--97179929 Score: 225 Period size: 27 Copynumber: 6.6 Consensus size: 27 97179742 TGTAGGATAG * 97179752 AATTACCAAAATACCCCTAGTTTGTAA 1 AATTACCAAAATACCCCTAATTTGTAA 97179779 AATTACCAAAATACCCCTAATTTGTAA 1 AATTACCAAAATACCCCTAATTTGTAA * * 97179806 AATTACCAAAATATCCCTAGTTTGTAA 1 AATTACCAAAATACCCCTAATTTGTAA * * ** * 97179833 AATTACCGAAATACCACTGGTTTGTGA 1 AATTACCAAAATACCCCTAATTTGTAA * 97179860 AATTACTAAAATA-CCCTCAATTTGTAA 1 AATTACCAAAATACCCCT-AATTTGTAA ** 97179887 AATTACCAAAATACCCCTAATTTACAA 1 AATTACCAAAATACCCCTAATTTGTAA 97179914 AATTA-CAGAAATACCC 1 AATTACCA-AAATACCC 97179930 TTGACTTTCT Statistics Matches: 131, Mismatches: 17, Indels: 6 0.85 0.11 0.04 Matches are distributed among these distances: 26 5 0.04 27 122 0.93 28 4 0.03 ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29 Consensus pattern (27 bp): AATTACCAAAATACCCCTAATTTGTAA Found at i:97179845 original size:81 final size:81 Alignment explanation

Indices: 97179752--97179929 Score: 250 Period size: 81 Copynumber: 2.2 Consensus size: 81 97179742 TGTAGGATAG * 97179752 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC-CTAATTTGTAAAATTACCAAA 1 AATTACCGAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTC-AATTTGTAAAATTACCAAA * * ** 97179816 ATATCCCTAGTTTGTAA 65 ATACCCCTAATTTACAA * * * * 97179833 AATTACCGAAATACCACTGGTTTGTGAAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAA 1 AATTACCGAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAA 97179898 TACCCCTAATTTACAA 66 TACCCCTAATTTACAA * 97179914 AATTACAGAAATACCC 1 AATTACCGAAATACCC 97179930 TTGACTTTCT Statistics Matches: 85, Mismatches: 11, Indels: 2 0.87 0.11 0.02 Matches are distributed among these distances: 81 84 0.99 82 1 0.01 ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29 Consensus pattern (81 bp): AATTACCGAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAA TACCCCTAATTTACAA Found at i:97179980 original size:27 final size:27 Alignment explanation

Indices: 97179907--97179992 Score: 77 Period size: 27 Copynumber: 3.1 Consensus size: 27 97179897 ATACCCCTAA * * * 97179907 TTTACAAAATTACAGAAATACCCTTGAC 1 TTTACAAAATTATAGAAATACCATTG-G * 97179935 TTT-CTAAAAATTATAGAAATACTATTGG 1 TTTAC--AAAATTATAGAAATACCATTGG * 97179963 TTTACAAAATTACT-GAAATACCCTTGG 1 TTTACAAAATTA-TAGAAATACCATTGG 97179990 TTT 1 TTT 97179993 GTAGATTTAC Statistics Matches: 48, Mismatches: 6, Indels: 9 0.76 0.10 0.14 Matches are distributed among these distances: 27 22 0.46 28 7 0.15 29 19 0.40 ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36 Consensus pattern (27 bp): TTTACAAAATTATAGAAATACCATTGG Found at i:97180953 original size:25 final size:25 Alignment explanation

Indices: 97180920--97180989 Score: 95 Period size: 25 Copynumber: 2.8 Consensus size: 25 97180910 AAGGAGTGCT * * 97180920 AAAAGGGCTCTACCCCAGTTTACCA 1 AAAAGGGCTTTGCCCCAGTTTACCA ** 97180945 AAAAGGGCTTTGCCCCAGTTTATTA 1 AAAAGGGCTTTGCCCCAGTTTACCA * 97180970 GAAAGGGCTTTGCCCCAGTT 1 AAAAGGGCTTTGCCCCAGTT 97180990 ATTAAAAGAG Statistics Matches: 40, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 25 40 1.00 ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26 Consensus pattern (25 bp): AAAAGGGCTTTGCCCCAGTTTACCA Found at i:97181002 original size:24 final size:23 Alignment explanation

Indices: 97180945--97181016 Score: 90 Period size: 25 Copynumber: 3.0 Consensus size: 23 97180935 CAGTTTACCA 97180945 AAAAGGGCTTTGCCCCAGTTTATT 1 AAAAGGGCTTTGCCCCAG-TTATT 97180969 AGAAAGGGCTTTGCCCCAGTTATT 1 A-AAAGGGCTTTGCCCCAGTTATT ** 97180993 AAAAGAGGCTAGGCCTCCAGTTAT 1 AAAAG-GGCTTTGCC-CCAGTTAT 97181017 ATGATAAAGC Statistics Matches: 43, Mismatches: 2, Indels: 5 0.86 0.04 0.10 Matches are distributed among these distances: 23 4 0.09 24 14 0.33 25 25 0.58 ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28 Consensus pattern (23 bp): AAAAGGGCTTTGCCCCAGTTATT Found at i:97181196 original size:42 final size:42 Alignment explanation

Indices: 97181137--97181270 Score: 250 Period size: 42 Copynumber: 3.2 Consensus size: 42 97181127 TAGTCTCCCC 97181137 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG 1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG * 97181179 AAATGGGCTTGCATACATTCATTGACATTACATATGATATTG 1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG * 97181221 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG 1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG 97181263 AAATGGGC 1 AAATGGGC 97181271 CTAAGGGCCA Statistics Matches: 89, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 42 89 1.00 ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34 Consensus pattern (42 bp): AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG Found at i:97181329 original size:31 final size:31 Alignment explanation

Indices: 97181294--97181439 Score: 240 Period size: 31 Copynumber: 4.7 Consensus size: 31 97181284 CGTTTACAGT * * 97181294 AAAGGCTTCGGCCAAGTGATATGGTTTATGA 1 AAAGGCTTCGGCCCAGTGATATGATTTATGA ** 97181325 AAAGGCTTTAGCCCAGTGATATGATTTATGA 1 AAAGGCTTCGGCCCAGTGATATGATTTATGA 97181356 AAAGGCTTCGGCCCAGTGATATGATTTATGA 1 AAAGGCTTCGGCCCAGTGATATGATTTATGA * 97181387 AAAGGCTTCGGCCCAGTGATATGATTTATGG 1 AAAGGCTTCGGCCCAGTGATATGATTTATGA 97181418 AAAGGCTTCGGCCCAGT-ATATG 1 AAAGGCTTCGGCCCAGTGATATG 97181440 TCAAGACTAA Statistics Matches: 108, Mismatches: 7, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 30 5 0.05 31 103 0.95 ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29 Consensus pattern (31 bp): AAAGGCTTCGGCCCAGTGATATGATTTATGA Found at i:97182368 original size:27 final size:27 Alignment explanation

Indices: 97182338--97182493 Score: 91 Period size: 27 Copynumber: 5.8 Consensus size: 27 97182328 GGCAAAACAG * 97182338 TCATCTTACCATATAAGGGAAAAATAA 1 TCATTTTACCATATAAGGGAAAAATAA * * * 97182365 TCATTTTACC-TCACAAGGGCAAAACAA 1 TCATTTTACCAT-ATAAGGGAAAAATAA ** * 97182392 TCATTTTACCACGTAAGGGAAAAATAG 1 TCATTTTACCATATAAGGGAAAAATAA * * * * * * * * * 97182419 TTATTTAATCACACAGGGGTAATACAA 1 TCATTTTACCATATAAGGGAAAAATAA * * * * 97182446 TCATTTTACCACA-AAGAGACAAAACAG 1 TCATTTTACCATATAAGGGA-AAAATAA * 97182473 TCATTTTACCACATAAGGGAA 1 TCATTTTACCATATAAGGGAA 97182494 GTCATTCCAT Statistics Matches: 96, Mismatches: 29, Indels: 8 0.72 0.22 0.06 Matches are distributed among these distances: 26 4 0.04 27 87 0.91 28 5 0.05 ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25 Consensus pattern (27 bp): TCATTTTACCATATAAGGGAAAAATAA Found at i:97182446 original size:54 final size:54 Alignment explanation

Indices: 97182327--97182457 Score: 154 Period size: 54 Copynumber: 2.4 Consensus size: 54 97182317 CATTACATAG * * ** * * 97182327 GGGCAAAACAGTCATCTTACCATATAAGGGAAAAATAATCATTTTACCTCACAA 1 GGGCAAAACAATCATTTTACCACGTAAGGGAAAAATAATCATTTAACCACACAA * * * * 97182381 GGGCAAAACAATCATTTTACCACGTAAGGGAAAAATAGTTATTTAATCACACAG 1 GGGCAAAACAATCATTTTACCACGTAAGGGAAAAATAATCATTTAACCACACAA * * 97182435 GGGTAATACAATCATTTTACCAC 1 GGGCAAAACAATCATTTTACCAC 97182458 AAAGAGACAA Statistics Matches: 65, Mismatches: 12, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 54 65 1.00 ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25 Consensus pattern (54 bp): GGGCAAAACAATCATTTTACCACGTAAGGGAAAAATAATCATTTAACCACACAA Found at i:97190679 original size:20 final size:20 Alignment explanation

Indices: 97190643--97190681 Score: 53 Period size: 20 Copynumber: 1.9 Consensus size: 20 97190633 CTAAGTTCTT 97190643 AATTCTATTTGAATTAGTCA 1 AATTCTATTTGAATTAGTCA * 97190663 AATT-TATTATGATTTAGTC 1 AATTCTATT-TGAATTAGTC 97190682 CTTTGTCCAA Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 19 4 0.24 20 13 0.76 ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49 Consensus pattern (20 bp): AATTCTATTTGAATTAGTCA Found at i:97198019 original size:17 final size:18 Alignment explanation

Indices: 97198006--97198163 Score: 91 Period size: 18 Copynumber: 8.8 Consensus size: 18 97197996 TAATCTTCAA 97198006 TGATATGCAATCTTAGATG 1 TGATATGCAATCTTAGA-G 97198025 TGATATGCAATCTTAGA- 1 TGATATGCAATCTTAGAG * * 97198042 T-ATGATACAATCTTAGATA 1 TGAT-ATGCAATCTTAGA-G * * 97198061 TGAT-TGTAATCTTAGATA 1 TGATATGCAATCTTAGA-G * 97198079 TGAT-TGCAATATTAGA- 1 TGATATGCAATCTTAGAG * * 97198095 T-ATGATACAATCTTAGATA 1 TGAT-ATGCAATCTTAGA-G 97198114 TGAT-TGCAATCTTAGA- 1 TGATATGCAATCTTAGAG * * 97198130 T-ATGATACAATCTTAGATA 1 TGAT-ATGCAATCTTAGA-G * 97198149 TGATATACAATCTTA 1 TGATATGCAATCTTA 97198164 AAAGATATGA Statistics Matches: 116, Mismatches: 9, Indels: 28 0.76 0.06 0.18 Matches are distributed among these distances: 15 4 0.03 16 4 0.03 17 34 0.29 18 37 0.32 19 31 0.27 20 6 0.05 ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38 Consensus pattern (18 bp): TGATATGCAATCTTAGAG Found at i:97198045 original size:14 final size:15 Alignment explanation

Indices: 97198026--97198151 Score: 92 Period size: 18 Copynumber: 7.5 Consensus size: 15 97198016 TCTTAGATGT 97198026 GATATG-CAATCTTA 1 GATATGACAATCTTA 97198040 GATATGATACAATCTTA 1 GATATG--ACAATCTTA * 97198057 GATATGATTGTAATCTTA 1 GATATGA---CAATCTTA * 97198075 GATATGATTGCAATATTA 1 GATATGA---CAATCTTA 97198093 GATATGATACAATCTTA 1 GATATG--ACAATCTTA 97198110 GATATGATTGCAATCTTA 1 GATATGA---CAATCTTA 97198128 GATATGATACAATCTTA 1 GATATG--ACAATCTTA 97198145 GATATGA 1 GATATGA 97198152 TATACAATCT Statistics Matches: 95, Mismatches: 4, Indels: 25 0.77 0.03 0.20 Matches are distributed among these distances: 14 6 0.06 15 3 0.03 17 41 0.43 18 43 0.45 20 2 0.02 ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37 Consensus pattern (15 bp): GATATGACAATCTTA Found at i:97198078 original size:35 final size:35 Alignment explanation

Indices: 97198013--97198163 Score: 205 Period size: 35 Copynumber: 4.2 Consensus size: 35 97198003 CAATGATATG * 97198013 CAATCTTAGATGTGATATGCAATCTTAGATATGA-TA 1 CAATCTTAGATATGATA--CAATCTTAGATATGATTA ** * 97198049 CAATCTTAGATATGATTGTAATCTTAGATATGATTG 1 CAATCTTAGATATGA-TACAATCTTAGATATGATTA * * 97198085 CAATATTAGATATGATACAATCTTAGATATGATTG 1 CAATCTTAGATATGATACAATCTTAGATATGATTA 97198120 CAATCTTAGATATGATACAATCTTAGATATGATATA 1 CAATCTTAGATATGATACAATCTTAGATATGAT-TA 97198156 CAATCTTA 1 CAATCTTA 97198164 AAAGATATGA Statistics Matches: 103, Mismatches: 9, Indels: 6 0.87 0.08 0.05 Matches are distributed among these distances: 35 64 0.62 36 38 0.37 37 1 0.01 ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38 Consensus pattern (35 bp): CAATCTTAGATATGATACAATCTTAGATATGATTA Found at i:97198087 original size:53 final size:53 Alignment explanation

Indices: 97198005--97198163 Score: 239 Period size: 53 Copynumber: 2.9 Consensus size: 53 97197995 ATAATCTTCA * 97198005 ATGATATGCAATCTTAGATGTGATATGCAATCTTAGATATGATACAATCTTAGAT 1 ATGAT-TGCAATCTTAGATATGAT-TGCAATCTTAGATATGATACAATCTTAGAT * * 97198060 ATGATTGTAATCTTAGATATGATTGCAATATTAGATATGATACAATCTTAGAT 1 ATGATTGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT * 97198113 ATGATTGCAATCTTAGATATGA-TACAATCTTAGATATGATATACAATCTTA 1 ATGATTGCAATCTTAGATATGATTGCAATCTTAGATATG--ATACAATCTTA 97198164 AAAGATATGA Statistics Matches: 96, Mismatches: 6, Indels: 5 0.90 0.06 0.05 Matches are distributed among these distances: 52 14 0.15 53 50 0.52 54 27 0.28 55 5 0.05 ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38 Consensus pattern (53 bp): ATGATTGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT Found at i:97198170 original size:17 final size:19 Alignment explanation

Indices: 97198007--97198171 Score: 109 Period size: 17 Copynumber: 9.3 Consensus size: 19 97197997 AATCTTCAAT * ** 97198007 GATATGCAATCTTAGATGT 1 GATATACAATCTTAGATAA * * 97198026 GATATGCAATCTTAGATAT 1 GATATACAATCTTAGATAA * 97198045 G--ATACAATCTTAGATAT 1 GATATACAATCTTAGATAA ** * 97198062 GAT-TGTAATCTTAGATAT 1 GATATACAATCTTAGATAA * * * 97198080 GAT-TGCAATATTAGATAT 1 GATATACAATCTTAGATAA * 97198098 G--ATACAATCTTAGATAT 1 GATATACAATCTTAGATAA * * 97198115 GAT-TGCAATCTTAGATAT 1 GATATACAATCTTAGATAA * 97198133 G--ATACAATCTTAGATAT 1 GATATACAATCTTAGATAA 97198150 GATATACAATCTTA-A-AA 1 GATATACAATCTTAGATAA 97198167 GATAT 1 GATAT 97198172 GATTTTGTAA Statistics Matches: 127, Mismatches: 11, Indels: 18 0.81 0.07 0.12 Matches are distributed among these distances: 17 51 0.40 18 46 0.36 19 30 0.24 ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37 Consensus pattern (19 bp): GATATACAATCTTAGATAA Found at i:97203926 original size:16 final size:17 Alignment explanation

Indices: 97203903--97203947 Score: 65 Period size: 16 Copynumber: 2.7 Consensus size: 17 97203893 CTTCTATTTC * 97203903 AAAAGAAAAAAAAA-AG 1 AAAAGAAAAAAAAAGAA * 97203919 AGAAGAAAAAAAAAGAA 1 AAAAGAAAAAAAAAGAA 97203936 AAAAGAAAAAAA 1 AAAAGAAAAAAA 97203948 TAAAAATGGA Statistics Matches: 25, Mismatches: 3, Indels: 1 0.86 0.10 0.03 Matches are distributed among these distances: 16 13 0.52 17 12 0.48 ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00 Consensus pattern (17 bp): AAAAGAAAAAAAAAGAA Found at i:97203929 original size:15 final size:13 Alignment explanation

Indices: 97203903--97203946 Score: 61 Period size: 13 Copynumber: 3.3 Consensus size: 13 97203893 CTTCTATTTC 97203903 AAAAGAAAAAAAA 1 AAAAGAAAAAAAA * * 97203916 AAGAGAAGAAAAA 1 AAAAGAAAAAAAA 97203929 AAAAGAAAAAAGAA 1 AAAAGAAAAAA-AA 97203943 AAAA 1 AAAA 97203947 ATAAAAATGG Statistics Matches: 26, Mismatches: 4, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 13 20 0.77 14 6 0.23 ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00 Consensus pattern (13 bp): AAAAGAAAAAAAA Found at i:97203937 original size:20 final size:18 Alignment explanation

Indices: 97203903--97203953 Score: 57 Period size: 19 Copynumber: 2.7 Consensus size: 18 97203893 CTTCTATTTC * * 97203903 AAAAGAAAAAAAAAAGAG 1 AAAAAAAAAAAAAAAAAG 97203921 AAGAAAAAAAAAGAAAAAAG 1 AA-AAAAAAAAA-AAAAAAG 97203941 AAAAAAATAAAAA 1 AAAAAAA-AAAAA 97203954 TGGAGAGGCC Statistics Matches: 28, Mismatches: 2, Indels: 5 0.80 0.06 0.14 Matches are distributed among these distances: 18 2 0.07 19 14 0.50 20 12 0.43 ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02 Consensus pattern (18 bp): AAAAAAAAAAAAAAAAAG Found at i:97203937 original size:22 final size:19 Alignment explanation

Indices: 97203903--97203953 Score: 57 Period size: 20 Copynumber: 2.6 Consensus size: 19 97203893 CTTCTATTTC * * 97203903 AAAAGAAAAAAAAAAGAGA 1 AAAAAAAAAAAAAAAAAGA * 97203922 AGAAAAAAAAAGAAAAAAGA 1 A-AAAAAAAAAAAAAAAAGA 97203942 AAAAAATAAAAA 1 AAAAAA-AAAAA 97203954 TGGAGAGGCC Statistics Matches: 26, Mismatches: 4, Indels: 3 0.79 0.12 0.09 Matches are distributed among these distances: 19 6 0.23 20 20 0.77 ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02 Consensus pattern (19 bp): AAAAAAAAAAAAAAAAAGA Found at i:97203947 original size:15 final size:14 Alignment explanation

Indices: 97203908--97203953 Score: 56 Period size: 15 Copynumber: 3.1 Consensus size: 14 97203898 ATTTCAAAAG 97203908 AAAAAAAAAAGAGAA 1 AAAAAAAAAAGA-AA * 97203923 GAAAAAAAAAGAAA 1 AAAAAAAAAAGAAA * 97203937 AAAGAAAAAAATAAA 1 AAA-AAAAAAAGAAA 97203952 AA 1 AA 97203954 TGGAGAGGCC Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 14 4 0.15 15 23 0.85 ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02 Consensus pattern (14 bp): AAAAAAAAAAGAAA Found at i:97203953 original size:16 final size:15 Alignment explanation

Indices: 97203903--97203953 Score: 57 Period size: 17 Copynumber: 3.2 Consensus size: 15 97203893 CTTCTATTTC 97203903 AAAAGAAAAAAAAAA 1 AAAAGAAAAAAAAAA * 97203918 GAGAAGAAAAAAAAAGAA 1 -AAAAG-AAAAAAAA-AA * 97203936 AAAAGAAAAAAATAA 1 AAAAGAAAAAAAAAA 97203951 AAA 1 AAA 97203954 TGGAGAGGCC Statistics Matches: 30, Mismatches: 3, Indels: 5 0.79 0.08 0.13 Matches are distributed among these distances: 15 5 0.17 16 11 0.37 17 12 0.40 18 2 0.07 ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02 Consensus pattern (15 bp): AAAAGAAAAAAAAAA Found at i:97204960 original size:44 final size:44 Alignment explanation

Indices: 97204910--97205045 Score: 118 Period size: 44 Copynumber: 3.2 Consensus size: 44 97204900 CACTTTAATC 97204910 CCCTAAGCAGTGGGGTAACAGGTTAAATTTGCAGATCTTATTCT 1 CCCTAAGCAGTGGGGTAACAGGTTAAATTTGCAGATCTTATTCT * * * * ** *** * * * 97204954 CCCTAAGCAATAGTGG-AGCAGATCGAA-GACCCG-CCTTAATC- 1 CCCTAAGCAGT-GGGGTAACAGGTTAAATTTGCAGATCTTATTCT * 97204995 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATTCT 1 CCCTAAGCAGTGGGGTAACAGGTTAAATTTGCAGATCTTATTCT 97205039 CCCTAAG 1 CCCTAAG 97205046 AAGTAGTGGA Statistics Matches: 62, Mismatches: 25, Indels: 10 0.64 0.26 0.10 Matches are distributed among these distances: 40 2 0.03 41 17 0.27 42 8 0.13 43 8 0.13 44 24 0.39 45 3 0.05 ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26 Consensus pattern (44 bp): CCCTAAGCAGTGGGGTAACAGGTTAAATTTGCAGATCTTATTCT Found at i:97205011 original size:85 final size:84 Alignment explanation

Indices: 97204904--97205272 Score: 484 Period size: 85 Copynumber: 4.4 Consensus size: 84 97204894 ATTCAGCACT * 97204904 TTAATCCCCTAAGCAGTGGGGTAACAGGTTAAATTTGCAGATCTTATTCTCCCTAAGCAATAGTG 1 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTA-TCTCCCTAAGCAATAGTG * 97204969 GAGCAGATCGAAGACCCGCC 65 GAGCAGATCGAAGACTCGCC 97204989 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATTCTCCCTAAG-AAGTAGT 1 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTA-TCTCCCTAAGCAA-TAGT 97205053 GGAGCAGATCGAAGACTCGCC 64 GGAGCAGATCGAAGACTCGCC * * * * * * 97205074 TTAATCTCCTAAGCAGTAGGGTAAC-----AAGTTCGCAGATATTATCTCCCTAAGCAGTAGCGG 1 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATAGTGG 97205134 AGCAGATCGATGACGACTCGCC 66 AGCAGATCGA--A-GACTCGCC * * * * 97205156 TTAATCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCGGATCTTATCTCCCTAAGCAGTAGTGG 1 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATAGTGG * * 97205221 AGTAGATCGAAGA-TGTGCC 66 AGCAGATCGAAGACT-CGCC 97205240 TTAA-CCCCTTAAGCAGTAGGGTAACAGGTTAAA 1 TTAATCCCC-TAAGCAGTAGGGTAACAGGTTAAA 97205273 GTATAGCATA Statistics Matches: 254, Mismatches: 18, Indels: 25 0.86 0.06 0.08 Matches are distributed among these distances: 79 25 0.10 80 14 0.06 81 1 0.00 82 32 0.13 83 5 0.02 84 34 0.13 85 105 0.41 87 38 0.15 ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25 Consensus pattern (84 bp): TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAATAGTGG AGCAGATCGAAGACTCGCC Found at i:97205255 original size:166 final size:165 Alignment explanation

Indices: 97204904--97205265 Score: 480 Period size: 166 Copynumber: 2.2 Consensus size: 165 97204894 ATTCAGCACT * * * * * 97204904 TTAATCCCCTAAGCAGTGGGGTAACAGGTTAAATTTGCAGATCTTATTCTCCCTAAGCAATAGTG 1 TTAATCCCCTAAGCAGTAGGGTAAC-----AAGTTCGCAGATATTATTCTCCCTAAGCAATAGCG * * 97204969 GAGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTT 61 GAGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCAGATCTT 97205034 ATTCTCCCTAAGAAGTAGTGGAGCAGATCGAAGACTCGCC 126 ATTCTCCCTAAGAAGTAGTGGAGCAGATCGAAGACTCGCC * * 97205074 TTAATCTCCTAAGCAGTAGGGTAACAAGTTCGCAGATATTA-TCTCCCTAAGCAGTAGCGGAGCA 1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTCGCAGATATTATTCTCCCTAAGCAATAGCGGAGCA * * 97205138 GATCGATGACGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCGGATCTTA- 66 GATCGA--A-GACCCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCAGATCTTAT * * * 97205202 TCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA-TGTGCC 128 TCTCCCTAAGAAGTAGTGGAGCAGATCGAAGACT-CGCC 97205240 TTAA-CCCCTTAAGCAGTAGGGTAACA 1 TTAATCCCC-TAAGCAGTAGGGTAACA 97205266 GGTTAAAGTA Statistics Matches: 172, Mismatches: 15, Indels: 14 0.86 0.07 0.07 Matches are distributed among these distances: 164 27 0.16 165 17 0.10 166 55 0.32 167 50 0.29 170 23 0.13 ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25 Consensus pattern (165 bp): TTAATCCCCTAAGCAGTAGGGTAACAAGTTCGCAGATATTATTCTCCCTAAGCAATAGCGGAGCA GATCGAAGACCCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCAGATCTTATTCT CCCTAAGAAGTAGTGGAGCAGATCGAAGACTCGCC Found at i:97205752 original size:207 final size:206 Alignment explanation

Indices: 97205397--97206110 Score: 1122 Period size: 207 Copynumber: 3.5 Consensus size: 206 97205387 TAGAAAGCAG * * * * 97205397 ATCGAAGACATAGCTAATTTAGCTTTCACGTGCTTATGATGAAGCAAATCTAAGATGATTTGGCA 1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCA * 97205462 TCTTTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT 66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT * 97205527 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGTAAAATCCAAGATGGTTTGGTATCCTTGTGCT 131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAG-AAGATCCAAGATGGTTTGGTATCCTTGTGCT 97205592 TACAAGGAACAA 195 TACAAGGAACAA * * * 97205604 ATCGAAGACATAGTTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA 1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCA * * * * * 97205669 TCTCTGTATTGTCAGAGAACAAATCCAAGTTTGGCGTCTCCATATTCAATGGAGGGTAGGCACAT 66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT * 97205734 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT 131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAG-AAGATCCAAGATGGTTTGGTATCCTTGTGCT 97205799 TACAAGGAACAA 195 TACAAGGAACAA * * * 97205811 ATCGAAGACATAGCTGATTTGGATTTCACGTGCTTACGTTGAAGCAAGTATAAGATGATTTGGCA 1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCA * * * ** 97205876 TCTCTGTATTTTCAGAGAGCAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGACAGACTTAT 66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT ** * * 97205941 AGCAGATCTAACCTTCAGATGTTTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTT 131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGAAGATCCAAGATGGTTTGGTATCCTTGTGCTT * 97206006 ACAAGGAGCAA 196 ACAAGGAACAA * * 97206017 ATCGAAGACATAGCTGATTTGGCTTTCGCGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCA 1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCA * * 97206082 TCTCTGTATTGTCAGGGAACAAATTGAAG 66 TCTCTGTATTGTCAGAGAACAAATCGAAG 97206111 AAGCAGATTT Statistics Matches: 462, Mismatches: 45, Indels: 1 0.91 0.09 0.00 Matches are distributed among these distances: 206 125 0.27 207 337 0.73 ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30 Consensus pattern (206 bp): ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCA TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT AGCAGATCTGGCCTTCAGATGTTTATACTGAAGAAGATCCAAGATGGTTTGGTATCCTTGTGCTT ACAAGGAACAA Done.