Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold334

Parameters: 2 7 7 80 10 50 500

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

Length: 1116604
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.28

Warning! 144470 characters in sequence are not A, C, G, or T


File 2 of 6

Found at i:6729 original size:69 final size:69

Alignment explanation

Indices: 6648--6913 Score: 312 Period size: 66 Copynumber: 3.9 Consensus size: 69 6638 TATTTTAATT 6648 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTTCGGTTTCTTTTTCAATTCT 1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTTCGGTTTCTTTTTCAATTCT 6713 ATTA 66 ATTA * 6717 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAT-TGTTTCTTTTTC-A--C 1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCT-TCGGTTTCTTTTTCAATTC * * 6778 TTTTC 65 TATTA * *** * 6783 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTAATGTTTCTTTTTCACTTTT 1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTTCGGTTTCTTTTTCA--ATT 6848 CTTATTA 64 C-TATTA * * * * 6855 TTATTAAGGTCTTCCGT-TTCCAACGGAAGA-CCTTAT-TGTTTTCGTTCGGTTTCTTTTTC 1 TTATTAGGGTCTTCCGTCTT-CAGCGGAAGACCCTTCTAT-TATTC-TTCGGTTTCTTTTTC 6914 CCTATTATTA Statistics Matches: 170, Mismatches: 16, Indels: 19 0.83 0.08 0.09 Matches are distributed among these distances: 66 60 0.35 68 1 0.01 69 56 0.33 70 2 0.01 71 11 0.06 72 40 0.24 ACGTcount: A:0.17, C:0.21, G:0.15, T:0.48 Consensus pattern (69 bp): TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTTCGGTTTCTTTTTCAATTCT ATTA Found at i:6823 original size:66 final size:66 Alignment explanation

Indices: 6648--6854 Score: 326 Period size: 66 Copynumber: 3.1 Consensus size: 66 6638 TATTTTAATT * 6648 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCT-TCGGTTTCTTTTTCAATTC 1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAT-TGTTTCTTTTTC-A--C * * 6712 TATTA 62 TTTTC 6717 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTTT 1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTTT 6782 C 66 C * * 6783 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTAATGTTTCTTTTTCACTTTT 1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTTT 6848 C 66 C 6849 TTATTA 1 TTATTA 6855 TTATTAAGGT Statistics Matches: 132, Mismatches: 5, Indels: 5 0.93 0.04 0.04 Matches are distributed among these distances: 66 74 0.56 68 1 0.01 69 56 0.42 70 1 0.01 ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48 Consensus pattern (66 bp): TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTTT C Found at i:6922 original size:135 final size:134 Alignment explanation

Indices: 6648--6923 Score: 330 Period size: 135 Copynumber: 2.0 Consensus size: 134 6638 TATTTTAATT ** 6648 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTTCGGTTTCTTTTTCAATTCT 1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAAGGTTTCTTTTTCAATTCT * * * * 6713 ATTATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCAC 66 ATTATTATTAAGGTCTTCCGTCTTCAACGGAAGACCCTTATATTATTCTATGGTTTCTTTTTCAC * * 6778 TTTTC 131 -TCTA * * * 6783 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTAATGTTTCTTTTTCACTTTT 1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAAGGTTTCTTTTTCA--ATT * 6848 CTTATTATTATTAAGGTCTTCCGT-TTCCAACGGAAGA-CCTTAT-TGTTTTCGT-TCGGTTTCT 64 C-TATTATTATTAAGGTCTTCCGTCTT-CAACGGAAGACCCTTATAT-TATTC-TAT-GGTTTCT 6909 TTTTC-C-CTA 124 TTTTCACTCTA 6918 TTATTA 1 TTATTA 6924 TTATTTTTTT Statistics Matches: 122, Mismatches: 12, Indels: 14 0.82 0.08 0.09 Matches are distributed among these distances: 135 63 0.52 136 1 0.01 137 16 0.13 138 42 0.34 ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48 Consensus pattern (134 bp): TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAAGGTTTCTTTTTCAATTCT ATTATTATTAAGGTCTTCCGTCTTCAACGGAAGACCCTTATATTATTCTATGGTTTCTTTTTCAC TCTA Found at i:10386 original size:436 final size:435 Alignment explanation

Indices: 9652--10636 Score: 1475 Period size: 436 Copynumber: 2.3 Consensus size: 435 9642 TTGATGTGAC * * * 9652 ATCAAGAAAAAGGGGCTGACCCTTCAAATAAGGGGCTGAGGGGGCTCTAAAGTCTTTAAATGATA 1 ATCATGAAAAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGG-TCTAAAGTCTTTTAATGATA * * * ** 9717 ACTTGTTACCGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTACCGTTATTT 65 ACTTTTTACTGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGTTATCC * * * * 9782 ACCTATACATGGCAATTATTTACTCCTATGTTACGTAATTAGGGATTTTAAGGGGCCAAAAGACC 130 ACATATACATGGCAATCATTCACTCCTATGTTACGTAATTAGGGATTCTAAGGGGCCAAAAGACC * 9847 AAAACTTTCATGCTAAATATCTCAAAATGGAGGAACATTTTGAAAAGCAATATTGAACAAAAGAT 195 AAAACTTTCATGCTAAATATCTCAAAATGGAGGAAAATTTTGAAAAGCAATATTGAACAAAAGAT * 9912 GCTCAAAATATTAAGCTTAACAATAATTAACCATTATTTCTTTGTTATGCGGTCCCTAAAAGGAG 260 GCTCAAAATACTAAGCTTAACAATAATTAACCATTATTTCTTTGTTATGCGGTCCCTAAAAGGAG * * 9977 TTACAGGGTCGGCCCCTAAAACGACCCTCTCAAAATATCTCGAGAACGGTACAAAATTTGTAAAC 325 TTA-AGGATCGGCCCCTAAAACGACCCTCTCAAAATATCTCAAGAACGGTACAAAATTTGTAAAC * * 10042 ACATGTTGAACAAAATATGTTTGAATTGATTAAAGCTTTCATTTAAA 389 ACATATTGAACAAAAAATGTTTGAATTGATTAAAGCTTTCATTTAAA * 10089 ATCATGAAAAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGTTTAAAGTCTTTTAATGATAA 1 ATCATGAAAAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGTCTAAAGTCTTTTAATGATAA 10154 CTTTTTACTGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGTTATCCA 66 CTTTTTACTGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGTTATCCA * * * * 10219 CATATACATGGTAATCATTCCCTCCTATGTTACGTAATTAGGGATTCTAAGGGGCCAGAAGTCCA 131 CATATACATGGCAATCATTCACTCCTATGTTACGTAATTAGGGATTCTAAGGGGCCAAAAGACCA * * 10284 AAACTTTGATGCTCAATATCTCAAAATGGAGGAAAATTTTGAAAAGCAATATTGAACAAAAGATG 196 AAACTTTCATGCTAAATATCTCAAAATGGAGGAAAATTTTGAAAAGCAATATTGAACAAAAGATG * * * * * 10349 CTCAAAATACTGAGCTTAACAATAATTAACCATTATTTCTTTGTTATGTGGTCCTTTAAGGGAGT 261 CTCAAAATACTAAGCTTAACAATAATTAACCATTATTTCTTTGTTATGCGGTCCCTAAAAGGAGT ** * * ** 10414 TAAGGATCGGCTTCTAAAACGACCCTCTCAAGATATCTCAAGAATGGTACAAAATTTGTAATTAC 326 TAAGGATCGGCCCCTAAAACGACCCTCTCAAAATATCTCAAGAACGGTACAAAATTTGTAAACAC * * * * * * 10479 TTATTGAACAAAAAATGTTTTAATTGATTAGAGTTTTTATTTGAA 391 ATATTGAACAAAAAATGTTTGAATTGATTAAAGCTTTCATTTAAA * * * * * 10524 ATCTTGAAACAGAGGCTGGCCCTTTAAATAAGGGGCTGAGGGGGCCTAAAGTCTTTTAATGATAA 1 ATCATGAAAAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGTCTAAAGTCTTTTAATGATAA * * * * * * 10589 CTTTTTACTGAGAGATTTTTTGTGAAAGGTTATAGAAGCAAATATGTT 66 CTTTTTACTGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTT 10637 TATCCCACAG Statistics Matches: 494, Mismatches: 54, Indels: 2 0.90 0.10 0.00 Matches are distributed among these distances: 435 193 0.39 436 259 0.52 437 42 0.09 ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32 Consensus pattern (435 bp): ATCATGAAAAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGTCTAAAGTCTTTTAATGATAA CTTTTTACTGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGTTATCCA CATATACATGGCAATCATTCACTCCTATGTTACGTAATTAGGGATTCTAAGGGGCCAAAAGACCA AAACTTTCATGCTAAATATCTCAAAATGGAGGAAAATTTTGAAAAGCAATATTGAACAAAAGATG CTCAAAATACTAAGCTTAACAATAATTAACCATTATTTCTTTGTTATGCGGTCCCTAAAAGGAGT TAAGGATCGGCCCCTAAAACGACCCTCTCAAAATATCTCAAGAACGGTACAAAATTTGTAAACAC ATATTGAACAAAAAATGTTTGAATTGATTAAAGCTTTCATTTAAA Found at i:12561 original size:435 final size:436 Alignment explanation

Indices: 11827--13331 Score: 2220 Period size: 435 Copynumber: 3.5 Consensus size: 436 11817 ACACCAAGAG * * 11827 AAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGAGGGCTCTAAAGTCTTTTAATGATAACTTTTCA 1 AAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGCTCTAAAGTCTTTTAATGATAACTTTTTA * * * * * 11892 CTGTGAAAAAATTAGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGCTATAT-ACCTAGA 66 CTGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGTTAT-TCACCTATA * * * 11956 CTTGG-ATATTATTTACTCCTATGTTACGTAATTAGGGGTTTTAAGGGGCCAGAAGTCCAAAACT 130 CATGGCA-ATCATTTACT-CTATGTTACGTAATTAGGAGTTTTAAGGGGCCAGAAGTCCAAAACT * 12020 TTGATGCTTAATATCTCAAAATGGAGGAAAATTTTGAAAAGCAATATTGAACAAAAGATGCTCAA 193 TTGATGCTCAATATCTCAAAATGGAGGAAAATTTTGAAAAGCAATATTGAACAAAAGATGCTCAA * 12085 AAT-TCTGAGCTTAACAATCTGCAACCATAATTTCTTTGTTATGCGGTCCCTAAAAGGAGTTGCA 258 AATAT-TGAGCTTAACAATCTGCAACCATAATTTCTTTGTTATGCGGTCCCTAAAAGGAGTTACA * 12149 GGGTCGGCCCCTAAAACGACCCTCTCAGGATATCTCGAGAACGGTACAAAATTTGTAAACACTTG 322 GGGTCGGCCCCTAAAACGACCCTCTCAAGATATCTCGAGAACGGTACAAAATTTGTAAACACTTG 12214 TTGAACAAAAAGTGTTTGAATTGATTAGAGCTTTCATTTAAAATCATGAA 387 TTGAACAAAAAGTGTTTGAATTGATTAGAGCTTTCATTTAAAATCATGAA 12264 AAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGCTCTAAAGTCTTTTAATGATAACTTTTTA 1 AAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGCTCTAAAGTCTTTTAATGATAACTTTTTA * 12329 CCGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGTTATTCACCTATAC 66 CTGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGTTATTCACCTATAC * * 12394 ATGGCAGTCATTTACT-TCTGTTACGTAATTAGGAGTTTTAAGGGGCCAGAAGTCCAAAACTTTG 131 ATGGCAATCATTTACTCTATGTTACGTAATTAGGAGTTTTAAGGGGCCAGAAGTCCAAAACTTTG * * * 12458 ATGCTCAATATCTCAAAATGGA-GAACAATTTTGATATGCAATATTGAACAAAAGATGCTCAGAA 196 ATGCTCAATATCTCAAAATGGAGGAA-AATTTTGAAAAGCAATATTGAACAAAAGATGCTCAAAA * ** * 12522 TATTGAGCTTAACAACCTGTTACCATAATTTCTTTGTTATGCAGTCCCTAAAAGGAGTTACAGGG 260 TATTGAGCTTAACAATCTGCAACCATAATTTCTTTGTTATGCGGTCCCTAAAAGGAGTTACAGGG * * 12587 TCGGCCCCTAAAATGACCCTCTGAAGATATCTCGAGAACGGTACAAAATTTGTAAACACTTGTTG 325 TCGGCCCCTAAAACGACCCTCTCAAGATATCTCGAGAACGGTACAAAATTTGTAAACACTTGTTG 12652 AACAAAAAGTGTTTGAATTGATTAGAGCTTTCATTTAAAATCATGAA 390 AACAAAAAGTGTTTGAATTGATTAGAGCTTTCATTTAAAATCATGAA * * ** * 12699 AAAGGGGCTCGCCCTTCAAAAAAGGGGCAAAGGGGGCTCTAAAGTCTTTTAATGATAACTTATTA 1 AAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGCTCTAAAGTCTTTTAATGATAACTTTTTA * * * * 12764 CTGTGAAATATTTTGTGATGCGTTATAGAGGCAATTATGTTCATTCTAATGTTATTTACCTATAC 66 CTGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGTTATTCACCTATAC * * * 12829 ATGGCAGTCATTTACTCCTATGTTACGTAATTAGGAATATTAAGGGGCCAGAAGTCCAAAACTTT 131 ATGGCAATCATTTACT-CTATGTTACGTAATTAGGAGTTTTAAGGGGCCAGAAGTCCAAAACTTT * * * 12894 TATGCTCAATATTTCAAAATAGAGGAAAATTTTGAAAAGCAATATTGAACAAAAGATGCTCAAAA 195 GATGCTCAATATCTCAAAATGGAGGAAAATTTTGAAAAGCAATATTGAACAAAAGATGCTCAAAA * * 12959 TATTGAGCTTAACAATTTGCAACCATAATTTCTTTGTTATGCGGTCCTTAAAAGGAGTTACAGGG 260 TATTGAGCTTAACAATCTGCAACCATAATTTCTTTGTTATGCGGTCCCTAAAAGGAGTTACAGGG * * * * * * 13024 TCGGCCCCTAAAACGACTCTGTCAAGATATCTCGAGAATGGTACAGAATTTATAAACACTTCTTG 325 TCGGCCCCTAAAACGACCCTCTCAAGATATCTCGAGAACGGTACAAAATTTGTAAACACTTGTTG * ** ** * * * * 13089 AACAAAATGTGTTTGAGCTGACAAGA-ATACTC-TTATGACATCA--AA 390 AACAAAAAGTGTTTGAATTGATTAGAGCT-TTCATT-TAAAATCATGAA * * * 13134 AAAGGGGCTGGCCCTTCAATTAAGGGGCTGAGGGGGCTCTAAAGTATTTTAATGATAAATTTTTA 1 AAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGCTCTAAAGTCTTTTAATGATAACTTTTTA * * * * * * 13199 CTGTAAAATATTTTGTGATACGTTCTAGAGGCAATTAAGTTCATTCTAAGGTTATTCATCTATAC 66 CTGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGTTATTCACCTATAC * * * * 13264 ATGGTAATCATTCACTCCTATGTTATGTAATTAGG-GATTTTAAGGGGCCAGAAGTCCAACACTT 131 ATGGCAATCATTTACT-CTATGTTACGTAATTAGGAG-TTTTAAGGGGCCAGAAGTCCAAAACTT 13328 TGAT 194 TGAT 13332 CTTCAATCTG Statistics Matches: 968, Mismatches: 90, Indels: 22 0.90 0.08 0.02 Matches are distributed among these distances: 434 3 0.00 435 581 0.60 436 5 0.01 437 375 0.39 438 4 0.00 ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31 Consensus pattern (436 bp): AAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGCTCTAAAGTCTTTTAATGATAACTTTTTA CTGTGAAATATTTTGTGATACGTTATAGAAGCAATTATGTTCATTCTAACGTTATTCACCTATAC ATGGCAATCATTTACTCTATGTTACGTAATTAGGAGTTTTAAGGGGCCAGAAGTCCAAAACTTTG ATGCTCAATATCTCAAAATGGAGGAAAATTTTGAAAAGCAATATTGAACAAAAGATGCTCAAAAT ATTGAGCTTAACAATCTGCAACCATAATTTCTTTGTTATGCGGTCCCTAAAAGGAGTTACAGGGT CGGCCCCTAAAACGACCCTCTCAAGATATCTCGAGAACGGTACAAAATTTGTAAACACTTGTTGA ACAAAAAGTGTTTGAATTGATTAGAGCTTTCATTTAAAATCATGAA Found at i:17226 original size:143 final size:144 Alignment explanation

Indices: 16987--17248 Score: 391 Period size: 143 Copynumber: 1.8 Consensus size: 144 16977 AAACGAGAGG * * * * * * * 16987 TCTATAGATGAGATGATCGAGTTAGAGATTCAGGAGAGTGCACTCAAGGAGGCCGAGCGCGAGAT 1 TCTATAGAAGAAATGATCGAGTTAAAGATCCAGGAGAGGGCACTCAAGGAGACCGAGCGCAAGAT * * 17052 CGAGGAGATCAGGTGAGATATAGCAAAATCAGTAATGACATATTGAGTCTTGGTAATGGGAAAAC 66 CGAGGAGATCAGATGAGATATAGCAAAATCAGTAATGACATATTGACTCTTGGTAATGGGAAAAC 17117 ACAAAATTGACAAA 131 ACAAAATTGACAAA * * 17131 TCTATAGAAGAAATGATC-AGTTAAAGATCCAGGAGAGGGTACTCAATGAGACCGAGCGCAAGAT 1 TCTATAGAAGAAATGATCGAGTTAAAGATCCAGGAGAGGGCACTCAAGGAGACCGAGCGCAAGAT ** * 17195 CGAGGAGATCAGATGAGATATAGTGAGATCAGTAATGACATATTGACTCTTGGT 66 CGAGGAGATCAGATGAGATATAGCAAAATCAGTAATGACATATTGACTCTTGGT 17249 GATAAAGGTA Statistics Matches: 104, Mismatches: 14, Indels: 1 0.87 0.12 0.01 Matches are distributed among these distances: 143 88 0.85 144 16 0.15 ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22 Consensus pattern (144 bp): TCTATAGAAGAAATGATCGAGTTAAAGATCCAGGAGAGGGCACTCAAGGAGACCGAGCGCAAGAT CGAGGAGATCAGATGAGATATAGCAAAATCAGTAATGACATATTGACTCTTGGTAATGGGAAAAC ACAAAATTGACAAA Found at i:18148 original size:22 final size:22 Alignment explanation

Indices: 18120--18959 Score: 896 Period size: 22 Copynumber: 38.5 Consensus size: 22 18110 GAGCTCAGGT * * 18120 TGTCTATCAAATATACATCTGA 1 TGTCAATCAAATATACATCTCA * * 18142 TGTCTATCAAATATACATCTGA 1 TGTCAATCAAATATACATCTCA * * 18164 TGTCTATCAAATATACATCTGA 1 TGTCAATCAAATATACATCTCA * 18186 TGTCAATCAAATATACATCTGA 1 TGTCAATCAAATATACATCTCA * 18208 TGTCAATCAAATATACATCTGA 1 TGTCAATCAAATATACATCTCA * 18230 TGTCAATCAATTATACATCTCA 1 TGTCAATCAAATATACATCTCA * * * * 18252 TGTCTATCAAATATTCATGTTA 1 TGTCAATCAAATATACATCTCA * * * 18274 TATCAATAAAATATACATCTGA 1 TGTCAATCAAATATACATCTCA * 18296 TGTCAATCAAATATACATCTGA 1 TGTCAATCAAATATACATCTCA * * 18318 TGTCAATCAAATATACTTCTGA 1 TGTCAATCAAATATACATCTCA * 18340 TGTCAATCGAATATACATCTCA 1 TGTCAATCAAATATACATCTCA * 18362 TGTCAATCAGATATACATCTCA 1 TGTCAATCAAATATACATCTCA * 18384 TGTAAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCA * * 18406 TGTCTATCAAATGTAC-TACTCA 1 TGTCAATCAAATATACAT-CTCA * * 18428 TATCAATCAAATATATATCTCA 1 TGTCAATCAAATATACATCTCA 18450 TGTCAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCA * * * 18472 TTTCAATCAAATAATTCATCACA 1 TGTCAATCAAAT-ATACATCTCA * 18495 TGTCAATCAAAATATAAATCTCA 1 TGTCAATC-AAATATACATCTCA * 18518 TGTCAATCAAATATACATCACA 1 TGTCAATCAAATATACATCTCA 18540 TGTCAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCA * 18562 TGTCAATCAAATA-ACTCATCACA 1 TGTCAATCAAATATA--CATCTCA * * * 18585 TGTAAATCAAATATTCAACTCA 1 TGTCAATCAAATATACATCTCA * * 18607 TGTCAATCAAATAATTCATCACA 1 TGTCAATCAAAT-ATACATCTCA * 18630 TGTCAATCAATTATACATCT-A 1 TGTCAATCAAATATACATCTCA * * 18651 AGTCAATCAAATATACATATCA 1 TGTCAATCAAATATACATCTCA * * ** * * * ** 18673 TAT-TATTGATTGTATATCAAA 1 TGTCAATCAAATATACATCTCA * * 18694 TATACAATCAAATATACATCTGA 1 TGT-CAATCAAATATACATCTCA * * 18717 TTTCAATCATATATACATCTCA 1 TGTCAATCAAATATACATCTCA * * 18739 TGACAATCATATATACA--TC- 1 TGTCAATCAAATATACATCTCA * 18758 --TCAATCAAATATACATCTGA 1 TGTCAATCAAATATACATCTCA * 18778 TGTCAATCAAATATACATATCA 1 TGTCAATCAAATATACATCTCA * 18800 TGTCAATCAAATATACATCTCT 1 TGTCAATCAAATATACATCTCA 18822 TGTCAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCA * * 18844 CGTCAATCAAATATACATGTCA 1 TGTCAATCAAATATACATCTCA * * 18866 TGACAATCAATTATACATCTCA 1 TGTCAATCAAATATACATCTCA * 18888 TGTCAATCAAAAATACATCTCA 1 TGTCAATCAAATATACATCTCA * * 18910 T-T---TTAATTATACATCTCA 1 TGTCAATCAAATATACATCTCA * ** * * 18928 TTTTGATCAATTATATATCTCA 1 TGTCAATCAAATATACATCTCA 18950 TGTCAATCAA 1 TGTCAATCAA 18960 CTAATTTTTT Statistics Matches: 692, Mismatches: 106, Indels: 40 0.83 0.13 0.05 Matches are distributed among these distances: 17 13 0.02 18 14 0.02 19 2 0.00 20 2 0.00 21 33 0.05 22 544 0.79 23 80 0.12 24 4 0.01 ACGTcount: A:0.41, C:0.20, G:0.06, T:0.34 Consensus pattern (22 bp): TGTCAATCAAATATACATCTCA Found at i:18764 original size:17 final size:17 Alignment explanation

Indices: 18719--18775 Score: 60 Period size: 17 Copynumber: 3.1 Consensus size: 17 18709 ACATCTGATT 18719 TCAATCATATATACATCTC 1 TCAATCATATATACA--TC 18738 ATGACAATCATATATACATC 1 -T--CAATCATATATACATC * 18758 TCAATCAAATATACATC 1 TCAATCATATATACATC 18775 T 1 T 18776 GATGTCAATC Statistics Matches: 34, Mismatches: 1, Indels: 7 0.81 0.02 0.17 Matches are distributed among these distances: 17 16 0.47 19 1 0.03 20 3 0.09 22 14 0.41 ACGTcount: A:0.42, C:0.23, G:0.02, T:0.33 Consensus pattern (17 bp): TCAATCATATATACATC Found at i:19520 original size:35 final size:35 Alignment explanation

Indices: 19474--19993 Score: 562 Period size: 35 Copynumber: 14.9 Consensus size: 35 19464 ACTAGATATA * 19474 TATCACTGGGCTCAGGGTAAATACAGGACACACTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * * ** 19509 TATCACTGGGCTCAGGGTAAATATAGGTCATACAC 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * * * 19544 TATCACTGGGATCAGGGTAAATACAGGACACATTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * * * * * 19579 TATCACTGAGATC-GAGTAAATACAGGACACATTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * * * 19613 TATCACTGAGAC-CAGGGT-AATACAGGACACCCTG 1 TATCACTG-GGCTCAGGGTAAATATAGGACACACTG * 19647 TATCACTGGGCTCAGGGTAAATATAGGTCACACTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * * 19682 CATCACTGGGCTCAGGGTAAATATAGGTCACACTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * * * 19717 CATCACTGGGCTTAGGGTAAATATAGGGCACACTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * * * * 19752 TATCTCTGGGCTAATGTTAAATATAGGACACACTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * * 19787 TATCACTGGGCTCAGGGTTAATATAGGTCACACTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * 19822 TATCACTGGGCTCAGGGTAAATATAGGTCACACTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * 19857 TATCACTGGGCTCAGGGTAAATATAGGGCACACTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG ** ** * ** 19892 TATCACTAAGCTTGGGGTAGATATAGGATTCACTG 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG * * ** * * * * 19927 TATAATTCAGCT-TGGGTAAATAAAGGATACACTT 1 TATCACTGGGCTCAGGGTAAATATAGGACACACTG ** * * 19961 TATCACTGAACTCGGGGTAAATATAGGATACAC 1 TATCACTGGGCTCAGGGTAAATATAGGACACAC 19994 ATTCACTGAG Statistics Matches: 417, Mismatches: 63, Indels: 10 0.85 0.13 0.02 Matches are distributed among these distances: 33 2 0.00 34 82 0.20 35 333 0.80 ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25 Consensus pattern (35 bp): TATCACTGGGCTCAGGGTAAATATAGGACACACTG Found at i:20195 original size:39 final size:39 Alignment explanation

Indices: 20129--20231 Score: 154 Period size: 39 Copynumber: 2.6 Consensus size: 39 20119 TTATCAGCCA * 20129 TCTATGCTGTGGGCAGTATGCTTTCTGACACTGTCAGTT-T 1 TCTATGCTGT-GGCAGTATGCTGTCTGACACTGTCA-TTCT * * 20169 TCTATGGTGTGGCAGTATGCTGTCTGATACTGTCATTCT 1 TCTATGCTGTGGCAGTATGCTGTCTGACACTGTCATTCT 20208 TCTATGCTGTGGCAGTATGCTGTC 1 TCTATGCTGTGGCAGTATGCTGTC 20232 CAAAACTGAC Statistics Matches: 58, Mismatches: 4, Indels: 3 0.89 0.06 0.05 Matches are distributed among these distances: 38 2 0.03 39 47 0.81 40 9 0.16 ACGTcount: A:0.15, C:0.19, G:0.26, T:0.40 Consensus pattern (39 bp): TCTATGCTGTGGCAGTATGCTGTCTGACACTGTCATTCT Found at i:20272 original size:99 final size:99 Alignment explanation

Indices: 20149--20330 Score: 258 Period size: 99 Copynumber: 1.8 Consensus size: 99 20139 GGGCAGTATG * * * ** * * 20149 CTTTCTGACACTGTCAGTTTTCTATGGTGTGGCAGTATGCTGTCTGATACTGTCATTCT-TCTAT 1 CTTTCTGACACTGTCAGTTTTCTATGCTGTGGCAGTATGCTGCCTGACACTACCA-GCTAACTAT 20213 GCTGTGGCAGTATGCTGTCCAAAACTGACAGTTGT 65 GCTGTGGCAGTATGCTGTCCAAAACTGACAGTTGT * * * 20248 CTTTCTGATACTGTCAGTTTTCTATGCTGTGGCAGTGTGCTGCCTGACATTACCAGCTAACTATG 1 CTTTCTGACACTGTCAGTTTTCTATGCTGTGGCAGTATGCTGCCTGACACTACCAGCTAACTATG 20313 CTGTGGCAGTATGCTGTC 66 CTGTGGCAGTATGCTGTC 20331 TGACATTGTC Statistics Matches: 72, Mismatches: 10, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 98 2 0.03 99 70 0.97 ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37 Consensus pattern (99 bp): CTTTCTGACACTGTCAGTTTTCTATGCTGTGGCAGTATGCTGCCTGACACTACCAGCTAACTATG CTGTGGCAGTATGCTGTCCAAAACTGACAGTTGT Found at i:20351 original size:39 final size:39 Alignment explanation

Indices: 20259--20378 Score: 134 Period size: 39 Copynumber: 3.1 Consensus size: 39 20249 TTTCTGATAC * * * 20259 TGTCAGTTTTCTATGCTGTGGCAGTGTGCTGCCTGACAT 1 TGTCAGTCTTCTATGCTGTGGCAGTATGCTGTCTGACAT ** * 20298 TACCAG-CTAACTATGCTGTGGCAGTATGCTGTCTGACAT 1 TGTCAGTCT-TCTATGCTGTGGCAGTATGCTGTCTGACAT * * * * 20337 TGTCAGTCTTCTATGCTGTAGTAGCAGGCTGTCTGACAT 1 TGTCAGTCTTCTATGCTGTGGCAGTATGCTGTCTGACAT 20376 TGT 1 TGT 20379 TTTAATGTAA Statistics Matches: 66, Mismatches: 13, Indels: 4 0.80 0.16 0.05 Matches are distributed among these distances: 38 1 0.02 39 63 0.95 40 2 0.03 ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36 Consensus pattern (39 bp): TGTCAGTCTTCTATGCTGTGGCAGTATGCTGTCTGACAT Found at i:49900 original size:6 final size:7 Alignment explanation

Indices: 49883--49909 Score: 54 Period size: 7 Copynumber: 3.9 Consensus size: 7 49873 AAACGGTGTT 49883 TTTTTTG 1 TTTTTTG 49890 TTTTTTG 1 TTTTTTG 49897 TTTTTTG 1 TTTTTTG 49904 TTTTTT 1 TTTTTT 49910 TTGGGGTTTT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 20 1.00 ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89 Consensus pattern (7 bp): TTTTTTG Found at i:49900 original size:16 final size:16 Alignment explanation

Indices: 49879--49912 Score: 52 Period size: 16 Copynumber: 2.1 Consensus size: 16 49869 GAGGAAACGG 49879 TGTTTTTTTTGTTTTT 1 TGTTTTTTTTGTTTTT 49895 TGTTTTTTGTT-TTTTT 1 TGTTTTTT-TTGTTTTT 49911 TG 1 TG 49913 GGGTTTTTTT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 16 15 0.88 17 2 0.12 ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85 Consensus pattern (16 bp): TGTTTTTTTTGTTTTT Found at i:49923 original size:23 final size:23 Alignment explanation

Indices: 49879--49927 Score: 64 Period size: 23 Copynumber: 2.1 Consensus size: 23 49869 GAGGAAACGG ** 49879 TGTTTTTTTTGTTTTTTGTTTTT 1 TGTTTTTTTTGGGTTTTGTTTTT 49902 TGTTTTTTTTGGGGTTTT-TTTTT 1 TGTTTTTTTT-GGGTTTTGTTTTT 49925 TGT 1 TGT 49928 CTTGTAAAGA Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 23 18 0.78 24 5 0.22 ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82 Consensus pattern (23 bp): TGTTTTTTTTGGGTTTTGTTTTT Found at i:54299 original size:21 final size:21 Alignment explanation

Indices: 54270--54317 Score: 71 Period size: 21 Copynumber: 2.3 Consensus size: 21 54260 ACTTCTTCAG * 54270 TTCAGCAATGGT-CTGTGTGAT 1 TTCATCAATGGTGC-GTGTGAT 54291 TTCATCAATGGTGCGTGTGAT 1 TTCATCAATGGTGCGTGTGAT 54312 TTCATC 1 TTCATC 54318 TTGCTGTTTG Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 21 24 0.96 22 1 0.04 ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40 Consensus pattern (21 bp): TTCATCAATGGTGCGTGTGAT Found at i:56067 original size:2 final size:2 Alignment explanation

Indices: 56062--56117 Score: 112 Period size: 2 Copynumber: 28.0 Consensus size: 2 56052 TACCCCCCAC 56062 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 56104 CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT 56118 GTTATCCATT Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 54 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:57875 original size:2 final size:2 Alignment explanation

Indices: 57868--57913 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 57858 TGTGAAAATA 57868 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 57910 TC TC 1 TC TC 57914 AACTAATGCT Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:61446 original size:42 final size:42 Alignment explanation

Indices: 61387--61725 Score: 468 Period size: 42 Copynumber: 7.8 Consensus size: 42 61377 NNNNNNNNNN * 61387 AATTGAAATCAATATACCCATAAATGTA-AACATTTTATGTTC 1 AATTGAAATCAATATA-CCATAAATGTATTACATTTTATGTTC * 61429 AATTGAAATCAATATACCATAAATGTATTACATTTTTTGTTC 1 AATTGAAATCAATATACCATAAATGTATTACATTTTATGTTC 61471 AATTGAAATCAATATACCATAACCATAAACGTATTACATTTTATGTTC 1 AATTGAAATCAATATACCATAA--AT----GTATTACATTTTATGTTC * 61519 AATTGAAATCAATATACCATAAATGTA-AACATTTTATGTTC 1 AATTGAAATCAATATACCATAAATGTATTACATTTTATGTTC * 61560 AATTGAAATCAATATACCATAAACGTATTACATTTTATGTTC 1 AATTGAAATCAATATACCATAAATGTATTACATTTTATGTTC * 61602 AATTGAAATCAATATACATGTACCATAAATGTA-AACATTTTATGTTC 1 AATTGAAATC-A-AT--A--TACCATAAATGTATTACATTTTATGTTC 61649 AATTGAAATCAATATACCATAAATGTATTACATTTTATGTTC 1 AATTGAAATCAATATACCATAAATGTATTACATTTTATGTTC * ** 61691 GATTGAAATCAATATACTGTAAATGTATTACATTT 1 AATTGAAATCAATATACCATAAATGTATTACATTT 61726 GGCTCTGTAT Statistics Matches: 270, Mismatches: 12, Indels: 30 0.87 0.04 0.10 Matches are distributed among these distances: 41 63 0.23 42 121 0.45 43 2 0.01 44 4 0.01 45 2 0.01 46 4 0.01 47 23 0.09 48 51 0.19 ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38 Consensus pattern (42 bp): AATTGAAATCAATATACCATAAATGTATTACATTTTATGTTC Found at i:61573 original size:89 final size:89 Alignment explanation

Indices: 61416--61717 Score: 412 Period size: 89 Copynumber: 3.4 Consensus size: 89 61406 ATAAATGTAA * * 61416 ACATTTTATGTTCAATTGAAATCAATATACCATAAATGTATTACATTTTTTGTTCAATTGAAATC 1 ACATTTTATGTTCAATTGAAATCAATATACCATAAATGTA-AACATTTTATGTTCAATTGAAATC 61481 AATATACCATAACCATAAACGTATT 65 AATATACCATAACCATAAACGTATT 61506 ACATTTTATGTTCAATTGAAATCAATATACCATAAATGTAAACATTTTATGTTCAATTGAAATC- 1 ACATTTTATGTTCAATTGAAATCAATATACCATAAATGTAAACATTTTATGTTCAATTGAAATCA 61570 A-AT---AT-ACCATAAACGTATT 66 ATATACCATAACCATAAACGTATT 61589 ACATTTTATGTTCAATTGAAATCAATATACATGTACCATAAATGTAAACATTTTATGTTCAATTG 1 ACATTTTATGTTCAATTGAAATC-A-AT--A--TACCATAAATGTAAACATTTTATGTTCAATTG 61654 AAATCAATATACCATAA--AT----GTATT 60 AAATCAATATACCATAACCATAAACGTATT * ** 61678 ACATTTTATGTTCGATTGAAATCAATATACTGTAAATGTA 1 ACATTTTATGTTCAATTGAAATCAATATACCATAAATGTA 61718 TTACATTTGG Statistics Matches: 195, Mismatches: 5, Indels: 31 0.84 0.02 0.13 Matches are distributed among these distances: 83 48 0.25 84 3 0.02 85 3 0.02 87 5 0.03 88 2 0.01 89 86 0.44 90 41 0.21 91 2 0.01 93 2 0.01 94 2 0.01 95 1 0.01 ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38 Consensus pattern (89 bp): ACATTTTATGTTCAATTGAAATCAATATACCATAAATGTAAACATTTTATGTTCAATTGAAATCA ATATACCATAACCATAAACGTATT Found at i:61627 original size:131 final size:130 Alignment explanation

Indices: 61387--61725 Score: 554 Period size: 131 Copynumber: 2.6 Consensus size: 130 61377 NNNNNNNNNN 61387 AATTGAAATCAATATACCCATAAATGTAAACATTTTATGTTCAATTGAAATCAATATACCATAAA 1 AATTGAAATCAATATA-CCATAAATGTAAACATTTTATGTTCAATTGAAATCAATATACCATAAA * * 61452 TGTATTACATTTTTTGTTCAATTGAAATCAATATACCATAACCATAAACGTATTACATTTTATGT 65 TGTATTACATTTTATGTTCAATTGAAATCAATATACCATAACCATAAACGTA-AACATTTTATGT 61517 TC 129 TC * 61519 AATTGAAATCAATATACCATAAATGTAAACATTTTATGTTCAATTGAAATCAATATACCATAAAC 1 AATTGAAATCAATATACCATAAATGTAAACATTTTATGTTCAATTGAAATCAATATACCATAAAT * * 61584 GTATTACATTTTATGTTCAATTGAAATCAATATA-CATGTACCATAAATGTAAACATTTTATGTT 66 GTATTACATTTTATGTTCAATTGAAATCAATATACCAT-AACCATAAACGTAAACATTTTATGTT 61648 C 130 C * * ** 61649 AATTGAAATCAATATACCATAAATGTATTACATTTTATGTTCGATTGAAATCAATATACTGTAAA 1 AATTGAAATCAATATACCATAAATGTA-AACATTTTATGTTCAATTGAAATCAATATACCATAAA 61714 TGTATTACATTT 65 TGTATTACATTT 61726 GGCTCTGTAT Statistics Matches: 195, Mismatches: 10, Indels: 5 0.93 0.05 0.02 Matches are distributed among these distances: 130 43 0.22 131 136 0.70 132 16 0.08 ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38 Consensus pattern (130 bp): AATTGAAATCAATATACCATAAATGTAAACATTTTATGTTCAATTGAAATCAATATACCATAAAT GTATTACATTTTATGTTCAATTGAAATCAATATACCATAACCATAAACGTAAACATTTTATGTTC Found at i:64326 original size:28 final size:28 Alignment explanation

Indices: 64286--64370 Score: 161 Period size: 28 Copynumber: 3.0 Consensus size: 28 64276 TAGCTCAAGT 64286 GAGCTATTCTGATCACATTTTGTCTGTC 1 GAGCTATTCTGATCACATTTTGTCTGTC * 64314 GAGCTATTCTGATCAAATTTTGTCTGTC 1 GAGCTATTCTGATCACATTTTGTCTGTC 64342 GAGCTATTCTGATCACATTTTGTCTGTC 1 GAGCTATTCTGATCACATTTTGTCTGTC 64370 G 1 G 64371 TCCGTCTGTC Statistics Matches: 55, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 28 55 1.00 ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42 Consensus pattern (28 bp): GAGCTATTCTGATCACATTTTGTCTGTC Found at i:65253 original size:166 final size:167 Alignment explanation

Indices: 64558--65256 Score: 1071 Period size: 167 Copynumber: 4.2 Consensus size: 167 64548 AGAAATTTTC * * * * * * 64558 AAAAATCTTCTTCTCACAAAC-CATAAGACCAGGAAAGCTGAAATTTGTGTGAAAGCATCGTCTG 1 AAAAATCTTCTTCTCAAAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAG * * * 64622 GTAGTATAGATTCAAAGTTGTGAAAATCATGACCCCC-GGGGGTAGGGTGGGGGCCACAATAGGG 65 GTAGTGTAGATACAAAGTTATGAAAATCATGACCCCCGGGGGGTAGGGT-GGGGCCACAATAGGG * 64686 GGTTGAAGTTTTACATAGGAATATACAGAGTAAATCTTT 129 GGTCGAAGTTTTACATAGGAATATACAGAGTAAATCTTT * * * 64725 AATAATCATCTTCTCAAAAATTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGG 1 AAAAATCTTCTTCTCAAAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGG 64790 TAGTGTAGATACAAAGTTATGAAAATCATGACCCCCGGGGGGTAGGGTGGGGCCACAATAGGGGG 66 TAGTGTAGATACAAAGTTATGAAAATCATGACCCCCGGGGGGTAGGGTGGGGCCACAATAGGGGG 64855 TCGAAGTTTTACATAGGAATATACAGAGTAAATCTTT 131 TCGAAGTTTTACATAGGAATATACAGAGTAAATCTTT * * 64892 AAAAACCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGG 1 AAAAATCTTCTTCTCAAAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGG * 64957 TAGTGTGGATACAAAGTTATGAAAATCATGACCCCCGGGGGGTAGGGTGGGGCCACAATAGGGGG 66 TAGTGTAGATACAAAGTTATGAAAATCATGACCCCCGGGGGGTAGGGTGGGGCCACAATAGGGGG 65022 TCGAAGTTTTACATAGGAATATACAGAGTAAATCTTT 131 TCGAAGTTTTACATAGGAATATACAGAGTAAATCTTT * * 65059 AAAAATCTTCTTCTCAAAAACTAATCAGCCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCAGG 1 AAAAATCTTCTTCTCAAAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGG * * ** * * * 65124 TAGTGTAGATTCAAAGTTGTGAAAATCATGATACCC-AGGGGTAGGGTGAGGCCACAATGGGGGG 66 TAGTGTAGATACAAAGTTATGAAAATCATGACCCCCGGGGGGTAGGGTGGGGCCACAATAGGGGG * * * ** 65188 TCAAAGTTTAACAAAGGAATATATGGAGTAAATCTTT 131 TCGAAGTTTTACATAGGAATATACAGAGTAAATCTTT * * 65225 AAAAATCTTCTCCTCAGAAACTAATCAGCCAG 1 AAAAATCTTCTTCTCAAAAACTAATCAGCCAG 65257 ATGATTCTTT Statistics Matches: 492, Mismatches: 38, Indels: 5 0.92 0.07 0.01 Matches are distributed among these distances: 166 87 0.18 167 390 0.79 168 15 0.03 ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24 Consensus pattern (167 bp): AAAAATCTTCTTCTCAAAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGG TAGTGTAGATACAAAGTTATGAAAATCATGACCCCCGGGGGGTAGGGTGGGGCCACAATAGGGGG TCGAAGTTTTACATAGGAATATACAGAGTAAATCTTT Found at i:66422 original size:144 final size:144 Alignment explanation

Indices: 66182--66444 Score: 447 Period size: 144 Copynumber: 1.8 Consensus size: 144 66172 AAAGGACAGG * * * * 66182 TCTATAGAGGAGATGATCGAGTTAGAGATCCAGGAGAGGGCACTCAAGGAGGCCGAGCGCGAGAT 1 TCTATAGAAGAAATGATCAAGTTAGAGATCCAGGAGAGGGCACTCAAGGAGACCGAGCGCGAGAT * * 66247 CGAGGAGATCAGGTGAGATATAGGAAAATCAGTAATGACATATTGAGTCTTGGTAATGGGAAAAC 66 CGAGGAGATCAGATGAGATATAGGAAAATCAGTAATGACATATTGACTCTTGGTAATGGGAAAAC 66312 CCAAAATTGACAAA 131 CCAAAATTGACAAA 66326 TCTATAGAAGAAATGATCAAGTTAGAGATCCAGGAGAGGGCACTCAAGGAGACCGAGCGCGAGAT 1 TCTATAGAAGAAATGATCAAGTTAGAGATCCAGGAGAGGGCACTCAAGGAGACCGAGCGCGAGAT * 66391 CGAGGAGATCAGATGAGATATAGTG-AGATCAGTAATGACATATTGACTCTTGGT 66 CGAGGAGATCAGATGAGATATAG-GAAAATCAGTAATGACATATTGACTCTTGGT 66445 GATAAAGGAA Statistics Matches: 111, Mismatches: 7, Indels: 2 0.93 0.06 0.02 Matches are distributed among these distances: 144 110 0.99 145 1 0.01 ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20 Consensus pattern (144 bp): TCTATAGAAGAAATGATCAAGTTAGAGATCCAGGAGAGGGCACTCAAGGAGACCGAGCGCGAGAT CGAGGAGATCAGATGAGATATAGGAAAATCAGTAATGACATATTGACTCTTGGTAATGGGAAAAC CCAAAATTGACAAA Found at i:67338 original size:22 final size:22 Alignment explanation

Indices: 67308--67566 Score: 419 Period size: 22 Copynumber: 11.8 Consensus size: 22 67298 GAGCTCAGGT * * * 67308 TGTCTATCAAATATACACCTGA 1 TGTCAATCAAATATACATCTCA * 67330 TGTCAATCAATTATACATCTCA 1 TGTCAATCAAATATACATCTCA * 67352 TATCAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCA * 67374 TGTCAATCAAATATTCATCTCA 1 TGTCAATCAAATATACATCTCA * 67396 TGTCAATCAAATATGCATCTCA 1 TGTCAATCAAATATACATCTCA 67418 TGTCAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCA 67440 TGTCAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCA * 67462 TGTAAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCA * 67484 TGTCAATCAAATATACATCACA 1 TGTCAATCAAATATACATCTCA * * 67506 TGTCAATCAATTATACATCTAA 1 TGTCAATCAAATATACATCTCA 67528 TGTCAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCA 67550 TGTCAATCAAATATACA 1 TGTCAATCAAATATACA 67567 ATCAAATATA Statistics Matches: 219, Mismatches: 18, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 22 219 1.00 ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32 Consensus pattern (22 bp): TGTCAATCAAATATACATCTCA Found at i:67377 original size:44 final size:44 Alignment explanation

Indices: 67308--67665 Score: 452 Period size: 44 Copynumber: 8.4 Consensus size: 44 67298 GAGCTCAGGT * * * * 67308 TGTCTATCAAATATACACCTGATGTCAATCAATTATACATCTCA 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCA * * 67352 TATCAATCAAATATACATCTCATGTCAATCAAATATTCATCTCA 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCA * 67396 TGTCAATCAAATATGCATCTCATGTCAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCA * 67440 TGTCAATCAAATATACATCTCATGTAAATCAAATATACATCTCA 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCA * * * 67484 TGTCAATCAAATATACATCACATGTCAATCAATTATACATCTAA 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCA 67528 TGTCAATCAAATATACATCTCATGTCAATC-AA-AT--A--T-A 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCA * * * 67565 ---CAATCAAATATACATTTGATTTCAATC--ATATACATCTCA 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCA * * * 67604 TGTCAATCAATTATACATCTCATGTCAATGAAAAATACATCTCA 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCA * * * 67648 TTTAAATCAATTATACAT 1 TGTCAATCAAATATACAT 67666 GTACATCTCA Statistics Matches: 275, Mismatches: 28, Indels: 22 0.85 0.09 0.07 Matches are distributed among these distances: 33 1 0.00 34 26 0.09 36 1 0.00 37 1 0.00 38 2 0.01 39 1 0.00 40 1 0.00 42 24 0.09 43 1 0.00 44 217 0.79 ACGTcount: A:0.41, C:0.21, G:0.05, T:0.34 Consensus pattern (44 bp): TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCA Found at i:67424 original size:66 final size:66 Alignment explanation

Indices: 67308--67665 Score: 452 Period size: 66 Copynumber: 5.6 Consensus size: 66 67298 GAGCTCAGGT * * * * * 67308 TGTCTATCAAATATACACCTGATGTCAATCAATTATACATCTCATATCAATCAAATATACATCTC 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTC 67373 A 66 A * * 67374 TGTCAATCAAATATTCATCTCATGTCAATCAAATATGCATCTCATGTCAATCAAATATACATCTC 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTC 67439 A 66 A * * 67440 TGTCAATCAAATATACATCTCATGTAAATCAAATATACATCTCATGTCAATCAAATATACATCAC 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTC 67505 A 66 A * * 67506 TGTCAATCAATTATACATCTAATGTCAATCAAATATACATCTCATGTCAATC-AA-AT--A--T- 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTC 67564 A 66 A * * * * 67565 ---CAATCAAATATACATTTGATTTCAATC--ATATACATCTCATGTCAATCAATTATACATCTC 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTC 67625 A 66 A * * * * * 67626 TGTCAATGAAAAATACATCTCATTTAAATCAATTATACAT 1 TGTCAATCAAATATACATCTCATGTCAATCAAATATACAT 67666 GTACATCTCA Statistics Matches: 254, Mismatches: 26, Indels: 24 0.84 0.09 0.08 Matches are distributed among these distances: 54 20 0.08 55 1 0.00 56 25 0.10 58 1 0.00 59 1 0.00 60 1 0.00 61 1 0.00 62 1 0.00 64 24 0.09 65 2 0.01 66 177 0.70 ACGTcount: A:0.41, C:0.21, G:0.05, T:0.34 Consensus pattern (66 bp): TGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTCATGTCAATCAAATATACATCTC A Found at i:67619 original size:76 final size:78 Alignment explanation

Indices: 67487--67642 Score: 226 Period size: 76 Copynumber: 2.0 Consensus size: 78 67477 CATCTCATGT 67487 CAATCAAATATACATCACATGTCAATCAATTATACATCTAATGTCAATCAAATATACATCTCATG 1 CAATCAAATATACATCACATGTCAATCAATTATACATCTAATGTCAATCAAATATACATCTCATG * 67552 TCAATCAAATATA 66 TCAATCAAAAATA *** * * * 67565 CAATCAAATATACATTTGATTTCAATC-A-TATACATCTCATGTCAATCAATTATACATCTCATG 1 CAATCAAATATACATCACATGTCAATCAATTATACATCTAATGTCAATCAAATATACATCTCATG * 67628 TCAATGAAAAATA 66 TCAATCAAAAATA 67641 CA 1 CA 67643 TCTCATTTAA Statistics Matches: 70, Mismatches: 8, Indels: 2 0.88 0.10 0.03 Matches are distributed among these distances: 76 46 0.66 77 1 0.01 78 23 0.33 ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32 Consensus pattern (78 bp): CAATCAAATATACATCACATGTCAATCAATTATACATCTAATGTCAATCAAATATACATCTCATG TCAATCAAAAATA Found at i:67621 original size:22 final size:22 Alignment explanation

Indices: 67565--67665 Score: 107 Period size: 22 Copynumber: 4.7 Consensus size: 22 67555 ATCAAATATA * * * 67565 CAATCAAATATACATTTGATTT 1 CAATCAAATATACATCTCATGT 67587 CAATC--ATATACATCTCATGT 1 CAATCAAATATACATCTCATGT * 67607 CAATCAATTATACATCTCATGT 1 CAATCAAATATACATCTCATGT * * * 67629 CAATGAAAAATACATCTCATTT 1 CAATCAAATATACATCTCATGT * * 67651 AAATCAATTATACAT 1 CAATCAAATATACAT 67666 GTACATCTCA Statistics Matches: 65, Mismatches: 12, Indels: 4 0.80 0.15 0.05 Matches are distributed among these distances: 20 17 0.26 22 48 0.74 ACGTcount: A:0.42, C:0.19, G:0.04, T:0.36 Consensus pattern (22 bp): CAATCAAATATACATCTCATGT Found at i:67642 original size:98 final size:99 Alignment explanation

Indices: 67466--67664 Score: 292 Period size: 98 Copynumber: 2.0 Consensus size: 99 67456 ATCTCATGTA 67466 AATCAAATATACATCTCATGTCAATCAAATATACATCACATGTCAATCAATTATACATCTAATGT 1 AATCAAATATACATCTCATGTCAATC-AATATACATCACATGTCAATCAATTATACATCTAATGT * * 67531 CAATCAAATATACATCTCATGTCAATCAAATATAC 65 CAATCAAAAATACATCTCATGTAAATCAAATATAC * * * * * 67566 AATCAAATATACATTTGATTTCAATC-ATATACATCTCATGTCAATCAATTATACATCTCATGTC 1 AATCAAATATACATCTCATGTCAATCAATATACATCACATGTCAATCAATTATACATCTAATGTC * * * 67630 AATGAAAAATACATCTCATTTAAATCAATTATAC 66 AATCAAAAATACATCTCATGTAAATCAAATATAC 67664 A 1 A 67665 TGTACATCTC Statistics Matches: 89, Mismatches: 10, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 98 66 0.74 100 23 0.26 ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33 Consensus pattern (99 bp): AATCAAATATACATCTCATGTCAATCAATATACATCACATGTCAATCAATTATACATCTAATGTC AATCAAAAATACATCTCATGTAAATCAAATATAC Found at i:68269 original size:35 final size:35 Alignment explanation

Indices: 68220--69308 Score: 806 Period size: 35 Copynumber: 30.3 Consensus size: 35 68210 CTAGATATAC * * 68220 ATCACTGAGATCAGGGTAAATACAGGGCACATTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * * 68255 ATCACTGGGCTCAGGGTAAATACAGGTCACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * 68290 ATCACTGGGATCAGGGTAAATACAGGTCACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * 68325 ATCACTGGGATCAGGGTAAATACAGGACACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * 68360 ATCACTGAGATCAGGGTAAATACAGGTCACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * 68395 ATCACTGGGATCAGGGTAAATACTGGACACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * 68430 ATCACTGAGATCAGAGTAAATACTGGACACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * 68465 ATCACTGAGATCAGGGTAAATATAGGACACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * ** * * * * 68500 ATCATTGACA-CACTGTATCACTGAGATCAGAGTAAATACTGG 1 ATCACTGAGATCAGGGTA--A---ATA-CAG-G-ACACACTGT * * * * 68542 ACACACTGTATCACAGGGCTCAGGGTAAATACTGGACACACTGT 1 A-TCACTG-A-GAT------CAGGGTAAATACAGGACACACTGT * * 68586 ATCACTGGGATCAGGGTAAATACAGGACACACGGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * * * 68621 ATCACAGGGCTCGGGGTAAATACAGGACACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * * * 68656 ATCACTGGGCTCAGGGTAAATATAGGTCACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * * 68691 ATCACAGGGCTCAGGGTAAATACAGGACACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT 68726 ATCACTGAGATCAGGGTAAATACAGGACACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT 68761 ATCACTGAGATCAGGGTAAATACAGGACACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * 68796 ATCACTGAGATCAGGGTAAATACAGGGCACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * ** * * * * * 68831 ATCACTGACA-CACTGTATCACTGAGATCAGGGTAAATACAGG 1 ATCACTGAGATCAGGGTA--A---ATA-CA-GG-ACACACTGT * * 68873 ACACACTGTATCACAGGGCTCAGGGTAAATACAGGACACACTGT 1 A-TCACTG-A-GA------TCAGGGTAAATACAGGACACACTGT * * * * 68917 ATCACAGGGCTCAGGGTAAATACAGGACTCACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * * * 68952 GTCTCT-AGGCTCAGGGTAAATGCAGGACACACTGT 1 ATCACTGA-GATCAGGGTAAATACAGGACACACTGT * * * * * 68987 ATCACTGGGCTCAGGGTAAATATAGGTCACACTGC 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * * * * 69022 ATCACTGGGCTCAGGGTAAATATAGGTCACACTGC 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * * * * * * 69057 ATCACTGGGCTAATGTTAAATATAGGGCACCACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACA-CACTGT * * * * * * * 69093 ATCTCTGGGCTAATGTTAAATATAGGACACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * * * * * 69128 ATCACTGGGCTTAAGGTAAATACAAGACACATTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * * * 69163 GTCACTGAGCTCAGGGTAAATATAGGTCACACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * ** * * ** 69198 ATCACTAAGCTTGGGGTAGATATAGGATTCACTGT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * * * * * * * 69233 ATAATTCAGCT-TGGGTAAATAAAGGATACACTTT 1 ATCACTGAGATCAGGGTAAATACAGGACACACTGT * * 69267 ATCACTGA-ACTCAGGGTAAATATAGGATACACT-T 1 ATCACTGAGA-TCAGGGTAAATACAGGACACACTGT 69301 -TCACTGAG 1 ATCACTGAG 69309 CTATATATTT Statistics Matches: 877, Mismatches: 135, Indels: 85 0.80 0.12 0.08 Matches are distributed among these distances: 33 7 0.01 34 35 0.04 35 717 0.82 36 34 0.04 39 4 0.00 40 4 0.00 41 4 0.00 42 12 0.01 43 18 0.02 44 15 0.02 45 7 0.01 46 4 0.00 47 4 0.00 50 2 0.00 52 10 0.01 ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23 Consensus pattern (35 bp): ATCACTGAGATCAGGGTAAATACAGGACACACTGT Found at i:68535 original size:51 final size:51 Alignment explanation

Indices: 68455--68554 Score: 175 Period size: 51 Copynumber: 2.0 Consensus size: 51 68445 GTAAATACTG * 68455 GACACACTGTATCACTGAGATCAGGGTAAATA-TAGGACACACTGTATCATT 1 GACACACTGTATCACTGAGATCAGAGTAAATACT-GGACACACTGTATCATT 68506 GACACACTGTATCACTGAGATCAGAGTAAATACTGGACACACTGTATCA 1 GACACACTGTATCACTGAGATCAGAGTAAATACTGGACACACTGTATCA 68555 CAGGGCTCAG Statistics Matches: 47, Mismatches: 1, Indels: 2 0.94 0.02 0.04 Matches are distributed among these distances: 51 46 0.98 52 1 0.02 ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24 Consensus pattern (51 bp): GACACACTGTATCACTGAGATCAGAGTAAATACTGGACACACTGTATCATT Found at i:68565 original size:86 final size:86 Alignment explanation

Indices: 68420--68589 Score: 297 Period size: 86 Copynumber: 2.0 Consensus size: 86 68410 GTAAATACTG * 68420 GACACACTGTATCACTGAGATCAGAGTAAATACTGGACACACTGTATCACTGAGATCAGGGTAAA 1 GACACACTGTATCACTGAGATCAGAGTAAATACTGGACACACTGTATCACAGAGATCAGGGTAAA 68485 TA-TAGGACACACTGTATCATT 66 TACT-GGACACACTGTATCATT * * 68506 GACACACTGTATCACTGAGATCAGAGTAAATACTGGACACACTGTATCACAGGGCTCAGGGTAAA 1 GACACACTGTATCACTGAGATCAGAGTAAATACTGGACACACTGTATCACAGAGATCAGGGTAAA 68571 TACTGGACACACTGTATCA 66 TACTGGACACACTGTATCA 68590 CTGGGATCAG Statistics Matches: 80, Mismatches: 3, Indels: 2 0.94 0.04 0.02 Matches are distributed among these distances: 86 79 0.99 87 1 0.01 ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23 Consensus pattern (86 bp): GACACACTGTATCACTGAGATCAGAGTAAATACTGGACACACTGTATCACAGAGATCAGGGTAAA TACTGGACACACTGTATCATT Found at i:68832 original size:331 final size:331 Alignment explanation

Indices: 68230--69170 Score: 1371 Period size: 331 Copynumber: 2.8 Consensus size: 331 68220 ATCACTGAGA * * * 68230 TCAGGGTAAATACAGGGCACATTGTATCACTGGGCTCAGGGTAAATACAGGTCACACTGTATCAC 1 TCAGGGTAAATACAGGACACACTGTATCACTGGGCTCAGGGTAAATACAGGACACACTGTATCAC * * * * * * 68295 TGGGATCAGGGTAAATACAGGTCACACTGTATCACTGGGATCAGGGTAAATACAGGACACACTGT 66 AGGGCTCAGGGTAAATACAGGACACACTGTATCACTGGGCTCAGGGTAAATATAGGTCACACTGT * * * 68360 ATCACTGAGATCAGGGTAAATACAGGTCACACTGTATCACTGGGATCAGGGTAAATACTGGACAC 131 ATCACTGGGCTCAGGGTAAATACAGGTCACACTGTATCACTGGGATCAGGGTAAATACAGGACAC * * * 68425 ACTGTATCACTGAGATCAGAGTAAATACTGGACACACTGTATCACTGAGATCAGGGTAAATATAG 196 ACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGTAAATACAG * * 68490 GACACACTGTATCATTGACACACTGTATCACTGAGATCAGAGTAAATACTGGACACACTGTATCA 261 GACACACTGTATCACTGACACACTGTATCACTGAGATCAGAGTAAATACAGGACACACTGTATCA 68555 CAGGGC 326 CAGGGC * * * 68561 TCAGGGTAAATACTGGACACACTGTATCACTGGGATCAGGGTAAATACAGGACACACGGTATCAC 1 TCAGGGTAAATACAGGACACACTGTATCACTGGGCTCAGGGTAAATACAGGACACACTGTATCAC * 68626 AGGGCTCGGGGTAAATACAGGACACACTGTATCACTGGGCTCAGGGTAAATATAGGTCACACTGT 66 AGGGCTCAGGGTAAATACAGGACACACTGTATCACTGGGCTCAGGGTAAATATAGGTCACACTGT * * * 68691 ATCACAGGGCTCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGTAAATACAGGACAC 131 ATCACTGGGCTCAGGGTAAATACAGGTCACACTGTATCACTGGGATCAGGGTAAATACAGGACAC 68756 ACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGTAAATACAG 196 ACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGTAAATACAG * * 68821 GGCACACTGTATCACTGACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCA 261 GACACACTGTATCACTGACACACTGTATCACTGAGATCAGAGTAAATACAGGACACACTGTATCA 68886 CAGGGC 326 CAGGGC * * * * 68892 TCAGGGTAAATACAGGACACACTGTATCACAGGGCTCAGGGTAAATACAGGACTCACTGTGTCTC 1 TCAGGGTAAATACAGGACACACTGTATCACTGGGCTCAGGGTAAATACAGGACACACTGTATCAC * 68957 TA-GGCTCAGGGTAAATGCAGGACACACTGTATCACTGGGCTCAGGGTAAATATAGGTCACACTG 66 -AGGGCTCAGGGTAAATACAGGACACACTGTATCACTGGGCTCAGGGTAAATATAGGTCACACTG * * * * * * * * * 69021 CATCACTGGGCTCAGGGTAAATATAGGTCACACTGCATCACTGGGCTAATGTTAAATATAGGGCA 130 TATCACTGGGCTCAGGGTAAATACAGGTCACACTGTATCACTGGGATCAGGGTAAATACAGGACA * * * * * * * * * * * 69086 CCACTGTATCTCTGGGCTAATGTTAAATATAGGACACACTGTATCACTGGGCTTAAGGTAAATAC 195 -CACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGTAAATAC * * * 69151 AAGACACATTGTGTCACTGA 259 AGGACACACTGTATCACTGA 69171 GCTCAGGGTA Statistics Matches: 546, Mismatches: 62, Indels: 3 0.89 0.10 0.00 Matches are distributed among these distances: 331 476 0.87 332 70 0.13 ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22 Consensus pattern (331 bp): TCAGGGTAAATACAGGACACACTGTATCACTGGGCTCAGGGTAAATACAGGACACACTGTATCAC AGGGCTCAGGGTAAATACAGGACACACTGTATCACTGGGCTCAGGGTAAATATAGGTCACACTGT ATCACTGGGCTCAGGGTAAATACAGGTCACACTGTATCACTGGGATCAGGGTAAATACAGGACAC ACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGTAAATACAG GACACACTGTATCACTGACACACTGTATCACTGAGATCAGAGTAAATACAGGACACACTGTATCA CAGGGC Found at i:68844 original size:16 final size:16 Alignment explanation

Indices: 68823--68854 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 68813 AAATACAGGG 68823 CACACTGTATCACTGA 1 CACACTGTATCACTGA 68839 CACACTGTATCACTGA 1 CACACTGTATCACTGA 68855 GATCAGGGTA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.31, C:0.31, G:0.12, T:0.25 Consensus pattern (16 bp): CACACTGTATCACTGA Found at i:68846 original size:51 final size:51 Alignment explanation

Indices: 68786--68886 Score: 193 Period size: 51 Copynumber: 2.0 Consensus size: 51 68776 GTAAATACAG * 68786 GACACACTGTATCACTGAGATCAGGGTAAATACAGGGCACACTGTATCACT 1 GACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACT 68837 GACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCAC 1 GACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCAC 68887 AGGGCTCAGG Statistics Matches: 49, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 51 49 1.00 ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21 Consensus pattern (51 bp): GACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACT Found at i:68896 original size:86 final size:86 Alignment explanation

Indices: 68751--68921 Score: 306 Period size: 86 Copynumber: 2.0 Consensus size: 86 68741 GTAAATACAG * 68751 GACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGTAAA 1 GACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACAGAGATCAGGGTAAA * 68816 TACAGGGCACACTGTATCACT 66 TACAGGACACACTGTATCACT * * 68837 GACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACAGGGCTCAGGGTAAA 1 GACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACAGAGATCAGGGTAAA 68902 TACAGGACACACTGTATCAC 66 TACAGGACACACTGTATCAC 68922 AGGGCTCAGG Statistics Matches: 81, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 86 81 1.00 ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20 Consensus pattern (86 bp): GACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACAGAGATCAGGGTAAA TACAGGACACACTGTATCACT Found at i:68947 original size:18 final size:18 Alignment explanation

Indices: 68857--68947 Score: 64 Period size: 18 Copynumber: 5.2 Consensus size: 18 68847 ATCACTGAGA 68857 TCAGGGTAAATACAGGAC 1 TCAGGGTAAATACAGGAC * ** * 68875 ACACTGT--ATCACAGGGC 1 TCAGGGTAAAT-ACAGGAC 68892 TCAGGGTAAATACAGGAC 1 TCAGGGTAAATACAGGAC * ** * 68910 ACACTGT--ATCACAGGGC 1 TCAGGGTAAAT-ACAGGAC 68927 TCAGGGTAAATACAGGAC 1 TCAGGGTAAATACAGGAC 68945 TCA 1 TCA 68948 CTGTGTCTCT Statistics Matches: 51, Mismatches: 16, Indels: 12 0.65 0.20 0.15 Matches are distributed among these distances: 16 4 0.08 17 20 0.39 18 23 0.45 19 4 0.08 ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18 Consensus pattern (18 bp): TCAGGGTAAATACAGGAC Found at i:68967 original size:156 final size:156 Alignment explanation

Indices: 68683--68993 Score: 471 Period size: 156 Copynumber: 2.0 Consensus size: 156 68673 AAATATAGGT * * * 68683 CACACTGTATCACAGGGCTCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGTAAATA 1 CACACTGTATCACAGAGATCAGGGTAAATACAGGACACACTGTATCACAGAGATCAGGGTAAATA * 68748 CAGGACACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGT 66 CAGGACACACTGTATCACAGAGATCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGT * 68813 AAATACAGGGCACACTGTATCACTGA 131 AAATACAGGACACACTGTATCACTGA * * * 68839 CACACTGTATCACTGAGATCAGGGTAAATACAGGACACACTGTATCACAGGGCTCAGGGTAAATA 1 CACACTGTATCACAGAGATCAGGGTAAATACAGGACACACTGTATCACAGAGATCAGGGTAAATA * * * * * * 68904 CAGGACACACTGTATCACAGGGCTCAGGGTAAATACAGGACTCACTGTGTCTCT-AGGCTCAGGG 66 CAGGACACACTGTATCACAGAGATCAGGGTAAATACAGGACACACTGTATCACTGA-GATCAGGG * 68968 TAAATGCAGGACACACTGTATCACTG 130 TAAATACAGGACACACTGTATCACTG 68994 GGCTCAGGGT Statistics Matches: 139, Mismatches: 15, Indels: 2 0.89 0.10 0.01 Matches are distributed among these distances: 155 1 0.01 156 138 0.99 ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20 Consensus pattern (156 bp): CACACTGTATCACAGAGATCAGGGTAAATACAGGACACACTGTATCACAGAGATCAGGGTAAATA CAGGACACACTGTATCACAGAGATCAGGGTAAATACAGGACACACTGTATCACTGAGATCAGGGT AAATACAGGACACACTGTATCACTGA Found at i:69459 original size:39 final size:39 Alignment explanation

Indices: 69416--69815 Score: 444 Period size: 39 Copynumber: 10.3 Consensus size: 39 69406 TTATCAGCCA * * 69416 TCTATGCTGTGGCAGTATGCTGTCTGACACTGTCAGTTT 1 TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTCT * * 69455 TCTATGGTGTGGCAGTATGCTGTCTGATACTGTCATTCT 1 TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTCT * ** * ** 69494 TCTATGCAGTGGCAGTATGCTGTCCAAAACTAACAGT-T 1 TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTCT * * * * * * 69532 GTCTTTGCTATGGCAGTAGGTTTTCTGATACTGTCAGTTT 1 -TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTCT * 69572 TCTATGCTGTGGCAGTATGCTCTCTGATACTGTCAGTCT 1 TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTCT * * * * * * * 69611 TCTATGCTGTGGCAGTGTGCTGCCTGACATTATCAGCCA 1 TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTCT * 69650 TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTGT 1 TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTCT * * 69689 TTTATGCTGCGGCAGTATGCTGTCTGATACTGTCAGTCT 1 TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTCT * * * * ** * * 69728 TCTATGCTGTGGCAGTGTGCTGCCTGACATTACCAGCCA 1 TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTCT * 69767 TCTATGCTGTGGCAGTATGCTGTCTGACA-TCGTCAGTCT 1 TCTATGCTGTGGCAGTATGCTGTCTGATACT-GTCAGTCT 69806 TCTATGCTGT 1 TCTATGCTGT 69816 AGTAGCAGAC Statistics Matches: 294, Mismatches: 64, Indels: 6 0.81 0.18 0.02 Matches are distributed among these distances: 38 2 0.01 39 291 0.99 40 1 0.00 ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37 Consensus pattern (39 bp): TCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTCT Found at i:69832 original size:117 final size:117 Alignment explanation

Indices: 69401--69815 Score: 584 Period size: 117 Copynumber: 3.5 Consensus size: 117 69391 GTCTGCTACA * 69401 TGACATTATCAGCCATCTATGCTGTGGCAGTATGCTGTCTGACACTGTCAGTTTTCTATGGTGTG 1 TGACATTATCAGCCATCTATGCTGTGGCAGTATGCTGTCTGACACTGTCAGTTTTCTATGCTGTG * * * 69466 GCAGTATGCTGTCTGATACTGTCATTCTTCTATGCAGTGGCAGTATGCTGTCC 66 GCAGTATGCTGTCTGATACTGTCAGTCTTCTATGCTGTGGCAGTGTGCTG-CC * * * * *** * * * * * * 69519 -AAAACTAACAGTTGTCTTTGCTATGGCAGTAGGTTTTCTGATACTGTCAGTTTTCTATGCTGTG 1 TGACATTATCAGCCATCTATGCTGTGGCAGTATGCTGTCTGACACTGTCAGTTTTCTATGCTGTG * 69583 GCAGTATGCTCTCTGATACTGTCAGTCTTCTATGCTGTGGCAGTGTGCTGCC 66 GCAGTATGCTGTCTGATACTGTCAGTCTTCTATGCTGTGGCAGTGTGCTGCC * * 69635 TGACATTATCAGCCATCTATGCTGTGGCAGTATGCTGTCTGATACTGTCAGTGTTT-TATGCTGC 1 TGACATTATCAGCCATCTATGCTGTGGCAGTATGCTGTCTGACACTGTCAGT-TTTCTATGCTGT 69699 GGCAGTATGCTGTCTGATACTGTCAGTCTTCTATGCTGTGGCAGTGTGCTGCC 65 GGCAGTATGCTGTCTGATACTGTCAGTCTTCTATGCTGTGGCAGTGTGCTGCC * * 69752 TGACATTACCAGCCATCTATGCTGTGGCAGTATGCTGTCTGACA-TCGTCAGTCTTCTATGCTGT 1 TGACATTATCAGCCATCTATGCTGTGGCAGTATGCTGTCTGACACT-GTCAGTTTTCTATGCTGT 69816 AGTAGCAGAC Statistics Matches: 257, Mismatches: 36, Indels: 9 0.85 0.12 0.03 Matches are distributed among these distances: 116 5 0.02 117 249 0.97 118 3 0.01 ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36 Consensus pattern (117 bp): TGACATTATCAGCCATCTATGCTGTGGCAGTATGCTGTCTGACACTGTCAGTTTTCTATGCTGTG GCAGTATGCTGTCTGATACTGTCAGTCTTCTATGCTGTGGCAGTGTGCTGCC Found at i:69833 original size:78 final size:78 Alignment explanation

Indices: 69691--69836 Score: 197 Period size: 78 Copynumber: 1.9 Consensus size: 78 69681 GTCAGTGTTT * * * * 69691 TATGCTGCGGCAGTATGCTGTCTGATACTGTCAGTCTTCTATGCTGTGGCAGTGTGCTGCCTGAC 1 TATGCTGCGGCAGTATGCTGTCTGACACTGTCAGTCTTCTATGCTGTAGCAGAGTACTGCCTGAC 69756 ATTACCAGCCATC 66 ATTACCAGCCATC * * * 69769 TATGCTGTGGCAGTATGCTGTCTGACA-TCGTCAGTCTTCTATGCTGTAGTAGCAG-ACTGTCTG 1 TATGCTGCGGCAGTATGCTGTCTGACACT-GTCAGTCTTCTATGCTGTAGCAG-AGTACTGCCTG 69832 ACATT 64 ACATT 69837 GTTTTAATGT Statistics Matches: 59, Mismatches: 7, Indels: 4 0.84 0.10 0.06 Matches are distributed among these distances: 77 1 0.02 78 57 0.97 79 1 0.02 ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34 Consensus pattern (78 bp): TATGCTGCGGCAGTATGCTGTCTGACACTGTCAGTCTTCTATGCTGTAGCAGAGTACTGCCTGAC ATTACCAGCCATC Found at i:72538 original size:54 final size:54 Alignment explanation

Indices: 72460--72820 Score: 521 Period size: 54 Copynumber: 6.7 Consensus size: 54 72450 AACGGGACCA * * * * ** 72460 ATCAGAAGCCACCGGTACCTCCAAAGTAGGTCACAACAAATATCTTCCAATAAA 1 ATCAGAAACCACCAGTACCCCCAAAGTAGGTCACAACAAATATCCTCCAATATC * 72514 ATCGGAAACCACCAGTACCCCCAAAGTAGGTCACAACAAATATCCTCCAATATC 1 ATCAGAAACCACCAGTACCCCCAAAGTAGGTCACAACAAATATCCTCCAATATC 72568 ATCAGAAACCACCAGTACCCCCAAAGTAGGTCACAACAAATATCCTCCAATATC 1 ATCAGAAACCACCAGTACCCCCAAAGTAGGTCACAACAAATATCCTCCAATATC * 72622 ATCAGAAACCACC-GTGACCCCCAAAGTAGGTCACAACAAATATCATCCAATATC 1 ATCAGAAACCACCAGT-ACCCCCAAAGTAGGTCACAACAAATATCCTCCAATATC * * * * 72676 ATCAGGAACCA-CTGTTACCTCCAAAGTTGGTCACAACAAATATCCTCCAATATC 1 ATCAGAAACCACCAG-TACCCCCAAAGTAGGTCACAACAAATATCCTCCAATATC * 72730 ATCAGAAACCACCAGTACCCCCAAAGTAGGTCACAACAAATATCCTCCAATATG 1 ATCAGAAACCACCAGTACCCCCAAAGTAGGTCACAACAAATATCCTCCAATATC * * * * 72784 ATTAGAAACCACCTA-TTCTCCCAAAGTTGGTCACAAC 1 ATCAGAAACCACC-AGTACCCCCAAAGTAGGTCACAAC 72821 TCAATGCAAC Statistics Matches: 280, Mismatches: 22, Indels: 10 0.90 0.07 0.03 Matches are distributed among these distances: 53 3 0.01 54 273 0.98 55 4 0.01 ACGTcount: A:0.39, C:0.31, G:0.11, T:0.19 Consensus pattern (54 bp): ATCAGAAACCACCAGTACCCCCAAAGTAGGTCACAACAAATATCCTCCAATATC Found at i:77070 original size:11 final size:11 Alignment explanation

Indices: 77054--77110 Score: 96 Period size: 11 Copynumber: 5.2 Consensus size: 11 77044 AATCCATGCC * 77054 CTGTGTATCGG 1 CTGTATATCGG * 77065 CTGTGTATCGG 1 CTGTATATCGG 77076 CTGTATATCGG 1 CTGTATATCGG 77087 CTGTATATCGG 1 CTGTATATCGG 77098 CTGTATATCGG 1 CTGTATATCGG 77109 CT 1 CT 77111 TGATTTCTTG Statistics Matches: 45, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 11 45 1.00 ACGTcount: A:0.14, C:0.19, G:0.30, T:0.37 Consensus pattern (11 bp): CTGTATATCGG Found at i:78942 original size:1 final size:1 Alignment explanation

Indices: 78936--78960 Score: 50 Period size: 1 Copynumber: 25.0 Consensus size: 1 78926 GGCAGGCAGG 78936 TTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTT 78961 AAGGCAAAAT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 24 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:80343 original size:42 final size:42 Alignment explanation

Indices: 80284--80485 Score: 306 Period size: 42 Copynumber: 4.8 Consensus size: 42 80274 TCATAGAAGA 80284 ACTCCTATACACAAGCCTATATACGAGACCAACTGTCTGGTT 1 ACTCCTATACACAAGCCTATATACGAGACCAACTGTCTGGTT 80326 ACTCCTATACACAAGCCTATATACGAGACCAACTGTCTGGTT 1 ACTCCTATACACAAGCCTATATACGAGACCAACTGTCTGGTT * * * 80368 ACTCCTATACACAAGCCTATATACGAGACCGA-TTTCATAGAAG-A 1 ACTCCTATACACAAGCCTATATACGAGACCAACTGTC-T-G--GTT 80412 ACTCCTATACACAAGCCTATATACGAGACCAACTGTCTGGTT 1 ACTCCTATACACAAGCCTATATACGAGACCAACTGTCTGGTT 80454 ACTCCTATACACAAGCC--TATACGAGA-CAACTG 1 ACTCCTATACACAAGCCTATATACGAGACCAACTG 80486 ACTGACTGGT Statistics Matches: 148, Mismatches: 6, Indels: 15 0.88 0.04 0.09 Matches are distributed among these distances: 39 6 0.04 40 9 0.06 41 4 0.03 42 91 0.61 43 2 0.01 44 32 0.22 45 4 0.03 ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24 Consensus pattern (42 bp): ACTCCTATACACAAGCCTATATACGAGACCAACTGTCTGGTT Found at i:80441 original size:86 final size:84 Alignment explanation

Indices: 80284--80485 Score: 306 Period size: 86 Copynumber: 2.4 Consensus size: 84 80274 TCATAGAAGA * 80284 ACTCCTATACACAAGCCTATATACGAGACCAACTGTCTGGTTACTCCTATACACAAGCCTATATA 1 ACTCCTATACACAAGCCTATATACGAGACCAACTGTCTGGTAACTCCTATACACAAGCCTATATA 80349 CGAGACCAACTGTCTGGTT 66 CGAGACCAACTGTCTGGTT * * 80368 ACTCCTATACACAAGCCTATATACGAGACCGA-TTTCATAGAAG-AACTCCTATACACAAGCCTA 1 ACTCCTATACACAAGCCTATATACGAGACCAACTGTC-T-G--GTAACTCCTATACACAAGCCTA 80431 TATACGAGACCAACTGTCTGGTT 62 TATACGAGACCAACTGTCTGGTT 80454 ACTCCTATACACAAGCC--TATACGAGA-CAACTG 1 ACTCCTATACACAAGCCTATATACGAGACCAACTG 80486 ACTGACTGGT Statistics Matches: 108, Mismatches: 5, Indels: 10 0.88 0.04 0.08 Matches are distributed among these distances: 83 5 0.05 84 42 0.39 85 1 0.01 86 59 0.55 87 1 0.01 ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24 Consensus pattern (84 bp): ACTCCTATACACAAGCCTATATACGAGACCAACTGTCTGGTAACTCCTATACACAAGCCTATATA CGAGACCAACTGTCTGGTT Found at i:80888 original size:25 final size:25 Alignment explanation

Indices: 80859--80934 Score: 125 Period size: 25 Copynumber: 3.0 Consensus size: 25 80849 TTCACACATG * * 80859 ATTTAAACTGTAGTCAAGTAGATTC 1 ATTTAAATTGTAGTCAGGTAGATTC 80884 ATTTAAATTGTAGTCAGGTAGATTC 1 ATTTAAATTGTAGTCAGGTAGATTC * 80909 ATTTAAATTGTAGTCGGGTAGATTC 1 ATTTAAATTGTAGTCAGGTAGATTC 80934 A 1 A 80935 CTAGTATTGT Statistics Matches: 48, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 25 48 1.00 ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38 Consensus pattern (25 bp): ATTTAAATTGTAGTCAGGTAGATTC Found at i:81852 original size:30 final size:30 Alignment explanation

Indices: 81818--81878 Score: 122 Period size: 30 Copynumber: 2.0 Consensus size: 30 81808 AGCGTCATTC 81818 TACAAGTAGTCAAATTTATCAACTCATAAT 1 TACAAGTAGTCAAATTTATCAACTCATAAT 81848 TACAAGTAGTCAAATTTATCAACTCATAAT 1 TACAAGTAGTCAAATTTATCAACTCATAAT 81878 T 1 T 81879 CAGAACAATC Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 30 31 1.00 ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34 Consensus pattern (30 bp): TACAAGTAGTCAAATTTATCAACTCATAAT Found at i:82124 original size:14 final size:14 Alignment explanation

Indices: 82105--82132 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 82095 TGCTATTTTT 82105 ATAAATTGATCTTC 1 ATAAATTGATCTTC 82119 ATAAATTGATCTTC 1 ATAAATTGATCTTC 82133 GTTTTAATAG Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43 Consensus pattern (14 bp): ATAAATTGATCTTC Found at i:83516 original size:36 final size:36 Alignment explanation

Indices: 83469--83576 Score: 153 Period size: 36 Copynumber: 3.0 Consensus size: 36 83459 CATGTCACCT * * 83469 ACGAGCCACCTACATGTGGCCGAGATATATTGCTAA 1 ACGAGCCACCTACACGTGGCCGAGATATATAGCTAA * * * 83505 ACGAGCCACCTACACGTGCCCGAGACATATAGCTGA 1 ACGAGCCACCTACACGTGGCCGAGATATATAGCTAA * * 83541 ACGAGCCACCTACACGTGGCTGAGATATATCGCTAA 1 ACGAGCCACCTACACGTGGCCGAGATATATAGCTAA 83577 CTAAAAATAA Statistics Matches: 62, Mismatches: 10, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 36 62 1.00 ACGTcount: A:0.31, C:0.29, G:0.22, T:0.19 Consensus pattern (36 bp): ACGAGCCACCTACACGTGGCCGAGATATATAGCTAA Found at i:85500 original size:51 final size:50 Alignment explanation

Indices: 85414--85709 Score: 304 Period size: 51 Copynumber: 5.9 Consensus size: 50 85404 AATAAAGGTC * 85414 AAACAGAGGCTGATATCA--GACGTCTTGTTAACATCAATAATTCACAGTG 1 AAACAGAGGCTGATATCACTGACGTCTTGTTAACATCAACAATTCA-AGTG * * * 85463 AAACAGAGGCTGATATCACTGACGTCTTGTTAACATCAACAATACAACTT 1 AAACAGAGGCTGATATCACTGACGTCTTGTTAACATCAACAATTCAAGTG * 85513 AAACAGAGGCTGATAT--CTGACGTCAATCTAAATGTTAACATCAATAATTCACAGTG 1 AAACAGAGGCTGATATCACTGACG----TCT---TGTTAACATCAACAATTCA-AGTG * * 85569 AAACAGAGGCTGATATCACTGACGACTTGTTAACATCAA-ATTTTCAAAGTG 1 AAACAGAGGCTGATATCACTGACGTCTTGTTAACATCAACA-ATTC-AAGTG * * * * * 85620 AAACAGAGGCTGATATCA--GATGTCATGTTAACATCAACAATACAACTA 1 AAACAGAGGCTGATATCACTGACGTCTTGTTAACATCAACAATTCAAGTG * * 85668 AAACAGAGGCTGATATCACCGACGTTTTGTT-A-ATCAACAATT 1 AAACAGAGGCTGATATCACTGACGTCTTGTTAACATCAACAATT 85710 ACCAATATTA Statistics Matches: 209, Mismatches: 21, Indels: 35 0.79 0.08 0.13 Matches are distributed among these distances: 48 36 0.17 49 37 0.18 50 28 0.13 51 61 0.29 52 4 0.02 54 2 0.01 55 17 0.08 56 18 0.09 58 6 0.03 ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26 Consensus pattern (50 bp): AAACAGAGGCTGATATCACTGACGTCTTGTTAACATCAACAATTCAAGTG Found at i:89025 original size:17 final size:18 Alignment explanation

Indices: 88987--89028 Score: 61 Period size: 18 Copynumber: 2.4 Consensus size: 18 88977 GTGAAGGAAC 88987 CAATCACTGATACGGTAT 1 CAATCACTGATACGGTAT 89005 CAATCACTGAT-CGAG-AT 1 CAATCACTGATACG-GTAT 89022 CAATCAC 1 CAATCAC 89029 CTACACAGAG Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 17 11 0.48 18 12 0.52 ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24 Consensus pattern (18 bp): CAATCACTGATACGGTAT Found at i:89129 original size:46 final size:47 Alignment explanation

Indices: 89062--89201 Score: 255 Period size: 47 Copynumber: 3.0 Consensus size: 47 89052 TTAGTGGACT 89062 CCTAGCTACTGGGTCATTACCTGCCATACTTGGTGT-CCCCACCAGA 1 CCTAGCTACTGGGTCATTACCTGCCATACTTGGTGTCCCCCACCAGA * 89108 CCTAGCTACTGGGTCATTACCTGCCATACTTGGTGTCCCCCACCAAA 1 CCTAGCTACTGGGTCATTACCTGCCATACTTGGTGTCCCCCACCAGA * 89155 CCTAGCTACTGGGTCATTACCTGCCATACTTAGTGTCCCCCACCAGA 1 CCTAGCTACTGGGTCATTACCTGCCATACTTGGTGTCCCCCACCAGA 89202 AGTTCTGGGG Statistics Matches: 90, Mismatches: 3, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 46 36 0.40 47 54 0.60 ACGTcount: A:0.21, C:0.36, G:0.18, T:0.26 Consensus pattern (47 bp): CCTAGCTACTGGGTCATTACCTGCCATACTTGGTGTCCCCCACCAGA Found at i:90331 original size:24 final size:24 Alignment explanation

Indices: 90311--90994 Score: 1019 Period size: 24 Copynumber: 28.5 Consensus size: 24 90301 GACGTACCGG 90311 AACTCAGAGATTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC * 90335 AACTCAGAGACTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC * 90359 AACTCAGAGACTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC * 90383 AACTCAGAGACTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC * 90407 AACTCAGAGATTGACTTCTACTAC 1 AACTCAGAGATTGACTTGTACTAC * * 90431 AACTCAGAGACTGACTTGTACTAA 1 AACTCAGAGATTGACTTGTACTAC * * 90455 AACTCAGAGACTGACTTGTACTAA 1 AACTCAGAGATTGACTTGTACTAC * 90479 AACTCAGAGATTGACTTGTACTAG 1 AACTCAGAGATTGACTTGTACTAC * 90503 AACTCAGAGATTGACTTATACTAC 1 AACTCAGAGATTGACTTGTACTAC * * 90527 AACTTAGAGATTGAGTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC 90551 AACTCAGAGATTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC * * 90575 AACTCTG-CATTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC * * 90598 AACTCAGAGACTGACTTGTACCAC 1 AACTCAGAGATTGACTTGTACTAC * ** 90622 AATTCAGAGGCTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC * 90646 AACTCAGAGATTGACTTGTACCAC 1 AACTCAGAGATTGACTTGTACTAC * * 90670 AATTCAGAGACTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC 90694 AACTCAGAGATTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC 90718 AACTCAGAGATTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC * * * 90742 AACTCAAAGACTGACTTGTACTAT 1 AACTCAGAGATTGACTTGTACTAC 90766 AACTCAGAGATTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC * 90790 AACTCAGAGATTGACTTCTACTAC 1 AACTCAGAGATTGACTTGTACTAC * * 90814 AACTCAGAGACTGACTTGTACTAA 1 AACTCAGAGATTGACTTGTACTAC * * 90838 AACTCAGAGATTGACTTGCACCAC 1 AACTCAGAGATTGACTTGTACTAC * * 90862 AACTCTGAGATTGACTTGTTCTAC 1 AACTCAGAGATTGACTTGTACTAC * 90886 AACTCAGAGATTGACTTATACTAC 1 AACTCAGAGATTGACTTGTACTAC * * 90910 AACTCAGAGATTGGCTTGTTCTAC 1 AACTCAGAGATTGACTTGTACTAC * * * 90934 AACTAAGAGATTGGCTTGTTCTAC 1 AACTCAGAGATTGACTTGTACTAC 90958 AACTCAGAGATTGACTTGTACTAC 1 AACTCAGAGATTGACTTGTACTAC 90982 AACTCAGAGATTG 1 AACTCAGAGATTG 90995 GTGTTTAAAT Statistics Matches: 598, Mismatches: 61, Indels: 2 0.90 0.09 0.00 Matches are distributed among these distances: 23 21 0.04 24 577 0.96 ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28 Consensus pattern (24 bp): AACTCAGAGATTGACTTGTACTAC Found at i:91290 original size:20 final size:20 Alignment explanation

Indices: 91265--91319 Score: 110 Period size: 20 Copynumber: 2.8 Consensus size: 20 91255 CTGCCAGGTG 91265 AGAGAACCAATCAGTGGGAC 1 AGAGAACCAATCAGTGGGAC 91285 AGAGAACCAATCAGTGGGAC 1 AGAGAACCAATCAGTGGGAC 91305 AGAGAACCAATCAGT 1 AGAGAACCAATCAGT 91320 CACAGCACAG Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 35 1.00 ACGTcount: A:0.42, C:0.20, G:0.27, T:0.11 Consensus pattern (20 bp): AGAGAACCAATCAGTGGGAC Found at i:91613 original size:18 final size:18 Alignment explanation

Indices: 91590--92053 Score: 490 Period size: 18 Copynumber: 25.8 Consensus size: 18 91580 CATTTTTGAG 91590 TAGGGTATACCTGTGGTA 1 TAGGGTATACCTGTGGTA ** 91608 TAGGGTATATATGTGGTA 1 TAGGGTATACCTGTGGTA * 91626 TAGGGCATACCTGTGGT- 1 TAGGGTATACCTGTGGTA * * 91643 TAAAGATATACCTGTGGTA 1 T-AGGGTATACCTGTGGTA 91662 TAGGGTATACCTGTGGT- 1 TAGGGTATACCTGTGGTA * 91679 TAAGGGTATACCAGTGGTA 1 T-AGGGTATACCTGTGGTA * * 91698 TAGGGTTTACCTTTGGGT- 1 TAGGGTATACCTGT-GGTA * 91716 TAGGGTATATCTGTGGTA 1 TAGGGTATACCTGTGGTA 91734 TAGGGTATACCTGTGGTA 1 TAGGGTATACCTGTGGTA * 91752 TAGGGTATACCAGTGGTA 1 TAGGGTATACCTGTGGTA * * 91770 TAGGGTTTACCTTTGGGT- 1 TAGGGTATACCTGT-GGTA * 91788 TAGGGTATATCTGTGGTA 1 TAGGGTATACCTGTGGTA * 91806 TAGGGTATACCTGTGGTT 1 TAGGGTATACCTGTGGTA * 91824 TAGGGTATACCTGTGGTT 1 TAGGGTATACCTGTGGTA 91842 TAGGGTATACCTGTGGTA 1 TAGGGTATACCTGTGGTA ** * 91860 TATAGTATACCTGTGGTT 1 TAGGGTATACCTGTGGTA 91878 TAGGGTATACCTGTGGTA 1 TAGGGTATACCTGTGGTA * ** 91896 TAGGGTTTATTTGTGG-A 1 TAGGGTATACCTGTGGTA 91913 TTAGGGTATACCTGTGGTA 1 -TAGGGTATACCTGTGGTA ** 91932 TATAGTATACCTGTGGTA 1 TAGGGTATACCTGTGGTA * 91950 TAGGGTATATCTGTGGTA 1 TAGGGTATACCTGTGGTA * ** 91968 TAGGGTTTATTTGTGG-A 1 TAGGGTATACCTGTGGTA * * * 91985 TTAGGGTATATCTGGGGTT 1 -TAGGGTATACCTGTGGTA * * * * 92004 TAGGGTTTATCTGTAGTT 1 TAGGGTATACCTGTGGTA * * 92022 TAGGGTACACCTGTGTTA 1 TAGGGTATACCTGTGGTA ** 92040 TAAAGTATACCTGT 1 TAGGGTATACCTGT 92054 AGTTTAGAAT Statistics Matches: 371, Mismatches: 63, Indels: 24 0.81 0.14 0.05 Matches are distributed among these distances: 17 10 0.03 18 352 0.95 19 9 0.02 ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38 Consensus pattern (18 bp): TAGGGTATACCTGTGGTA Found at i:92473 original size:18 final size:18 Alignment explanation

Indices: 92450--92704 Score: 251 Period size: 18 Copynumber: 14.2 Consensus size: 18 92440 NNNNNNNNNN 92450 TAGGGTATACCTGTGGTT 1 TAGGGTATACCTGTGGTT 92468 TAGGGTATACCTGTGGTT 1 TAGGGTATACCTGTGGTT * 92486 TAGGGTATACCTGTGGTA 1 TAGGGTATACCTGTGGTT ** 92504 TATAGTATACCTGTGGTT 1 TAGGGTATACCTGTGGTT * 92522 TAGGGTATACCTGTGGTA 1 TAGGGTATACCTGTGGTT * ** * 92540 TAGGGTTTATTTGTGGAT 1 TAGGGTATACCTGTGGTT * 92558 TAGGGTATACCTGTGGTA 1 TAGGGTATACCTGTGGTT ** * 92576 TATAGTATACCTGTGGTA 1 TAGGGTATACCTGTGGTT * * 92594 TAGGGTATATCTGTGGTA 1 TAGGGTATACCTGTGGTT * ** * 92612 TAGGGTTTATTTGTGGAT 1 TAGGGTATACCTGTGGTT * * 92630 TAGGGTATATCTGGGGTT 1 TAGGGTATACCTGTGGTT * * * 92648 TAGGGTTTATCTGTAGTT 1 TAGGGTATACCTGTGGTT * 92666 TAGGGTACACCTGT-GTT 1 TAGGGTATACCTGTGGTT ** * 92683 ATAAAGTATACCTGTAGTT 1 -TAGGGTATACCTGTGGTT 92702 TAG 1 TAG 92705 AATTACACAG Statistics Matches: 195, Mismatches: 40, Indels: 4 0.82 0.17 0.02 Matches are distributed among these distances: 17 3 0.02 18 189 0.97 19 3 0.02 ACGTcount: A:0.21, C:0.09, G:0.30, T:0.40 Consensus pattern (18 bp): TAGGGTATACCTGTGGTT Found at i:92567 original size:72 final size:72 Alignment explanation

Indices: 92450--92685 Score: 319 Period size: 72 Copynumber: 3.3 Consensus size: 72 92440 NNNNNNNNNN * * ** * 92450 TAGGGTATACCTGTGGTTTAGGGTATACCTGTGGTTTAGGGTATACCTGTGGTATATAGTATACC 1 TAGGGTATACCTGTGGTATAGGGTTTATTTGTGGATTAGGGTATACCTGTGGTATATAGTATACC 92515 TGTGGTT 66 TGTGGTT 92522 TAGGGTATACCTGTGGTATAGGGTTTATTTGTGGATTAGGGTATACCTGTGGTATATAGTATACC 1 TAGGGTATACCTGTGGTATAGGGTTTATTTGTGGATTAGGGTATACCTGTGGTATATAGTATACC * 92587 TGTGGTA 66 TGTGGTT * * * * ** * * 92594 TAGGGTATATCTGTGGTATAGGGTTTATTTGTGGATTAGGGTATATCTGGGGTTTAGGGTTTATC 1 TAGGGTATACCTGTGGTATAGGGTTTATTTGTGGATTAGGGTATACCTGTGGTATATAGTATACC * 92659 TGTAGTT 66 TGTGGTT * * 92666 TAGGGTACACCTGTGTTATA 1 TAGGGTATACCTGTGGTATA 92686 AAGTATACCT Statistics Matches: 145, Mismatches: 19, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 72 145 1.00 ACGTcount: A:0.20, C:0.08, G:0.31, T:0.40 Consensus pattern (72 bp): TAGGGTATACCTGTGGTATAGGGTTTATTTGTGGATTAGGGTATACCTGTGGTATATAGTATACC TGTGGTT Found at i:93291 original size:2 final size:2 Alignment explanation

Indices: 93284--93308 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 93274 ATGCATACCA 93284 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 93309 ATTAATTTTC Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:95976 original size:48 final size:48 Alignment explanation

Indices: 95905--96102 Score: 308 Period size: 48 Copynumber: 4.1 Consensus size: 48 95895 TAACTTACAG 95905 TGTAACCTGTTATTGTAGCATAGCTGTGATTCTGACTATAACATGGGA 1 TGTAACCTGTTATTGTAGCATAGCTGTGATTCTGACTATAACATGGGA * 95953 TGTAACCTGTTATTGTAGCATAGCTGTGATTCTGACTCTAACATAGGG- 1 TGTAACCTGTTATTGTAGCATAGCTGTGATTCTGACTATAACAT-GGGA ** * * * 96001 TGTCCCCTGTTATTGTAGCATAGCTGTGATTCTGACTGTAACGTGGGG 1 TGTAACCTGTTATTGTAGCATAGCTGTGATTCTGACTATAACATGGGA * * 96049 TGTAACCTATTATTGTAGCATAGCTGTGATTCTGACTATAACATGGAA 1 TGTAACCTGTTATTGTAGCATAGCTGTGATTCTGACTATAACATGGGA 96097 TGTAAC 1 TGTAAC 96103 AAGCTTACAA Statistics Matches: 136, Mismatches: 12, Indels: 4 0.89 0.08 0.03 Matches are distributed among these distances: 47 3 0.02 48 130 0.96 49 3 0.02 ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35 Consensus pattern (48 bp): TGTAACCTGTTATTGTAGCATAGCTGTGATTCTGACTATAACATGGGA Found at i:96213 original size:30 final size:30 Alignment explanation

Indices: 96176--96643 Score: 467 Period size: 30 Copynumber: 15.4 Consensus size: 30 96166 TAATAATATT * 96176 CTCTGTAATAGTAACCACAATTACAATGTG 1 CTCTGTAATAGTAACCACAATTACAATGTA * * * 96206 TTATGTAATAG-AACCCACAATTACAATGTG 1 CTCTGTAATAGTAA-CCACAATTACAATGTA * * * * * * * 96236 TTATGTTATAGTCATCACAATTACAAGGCA 1 CTCTGTAATAGTAACCACAATTACAATGTA * * * 96266 CTCTGTAATAGTCACCACAATTACAAGGCA 1 CTCTGTAATAGTAACCACAATTACAATGTA * * * 96296 CTCTGTAATAGTCACCACAATTACAAGGCA 1 CTCTGTAATAGTAACCACAATTACAATGTA * * * 96326 CTCTGTAATACAACAG-ACACCACAATTACTAGGCA 1 CTCTGTAAT-----AGTA-ACCACAATTACAATGTA * 96361 CTCTGTAATAGTCACCACAATTACAATGTA 1 CTCTGTAATAGTAACCACAATTACAATGTA * 96391 CTCTGTAATAG-ATACCACAATTACAATGTT 1 CTCTGTAATAGTA-ACCACAATTACAATGTA * * 96421 GTCTGTAATAGTCACCACAATTACAATGTA 1 CTCTGTAATAGTAACCACAATTACAATGTA * * * 96451 CTCTGTAATAGTTACCACAATTACAAGGCA 1 CTCTGTAATAGTAACCACAATTACAATGTA * * 96481 CTCTGTAATAGTCACCACAATTACAATTTA 1 CTCTGTAATAGTAACCACAATTACAATGTA * 96511 CTCTGTAATAATAACCACAATTACAATGTA 1 CTCTGTAATAGTAACCACAATTACAATGTA * * * * 96541 CTTTGTAATAGTAAGCATAATTGCAATGTA 1 CTCTGTAATAGTAACCACAATTACAATGTA * * * 96571 CTCTGTCATAGTAACCATAATTACAAGGTA 1 CTCTGTAATAGTAACCACAATTACAATGTA * * 96601 CTTTGTAATAGTAACCATAATTACAA-GATA 1 CTCTGTAATAGTAACCACAATTACAATG-TA * 96631 CTCTGTGATAGTA 1 CTCTGTAATAGTA 96644 TCTTTAATTA Statistics Matches: 378, Mismatches: 48, Indels: 24 0.84 0.11 0.05 Matches are distributed among these distances: 29 3 0.01 30 347 0.92 31 1 0.00 35 27 0.07 ACGTcount: A:0.38, C:0.21, G:0.12, T:0.30 Consensus pattern (30 bp): CTCTGTAATAGTAACCACAATTACAATGTA Found at i:105851 original size:24 final size:24 Alignment explanation

Indices: 105819--105870 Score: 86 Period size: 24 Copynumber: 2.2 Consensus size: 24 105809 ATTAGCCAAG * 105819 AGTTATTGCATCATTGAGTGAAAC 1 AGTTATTGCATCATTGAGTCAAAC * 105843 AGTTATTGCATCATTGAGTCAAAG 1 AGTTATTGCATCATTGAGTCAAAC 105867 AGTT 1 AGTT 105871 TTCATTCCAT Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 24 26 1.00 ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35 Consensus pattern (24 bp): AGTTATTGCATCATTGAGTCAAAC Found at i:109878 original size:15 final size:15 Alignment explanation

Indices: 109858--109892 Score: 61 Period size: 15 Copynumber: 2.3 Consensus size: 15 109848 ACAAAAAGCA * 109858 TTTCTGTTCATACTT 1 TTTCTGTTAATACTT 109873 TTTCTGTTAATACTT 1 TTTCTGTTAATACTT 109888 TTTCT 1 TTTCT 109893 TTCTCTGTGT 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:0.14, C:0.17, G:0.06, T:0.63 Consensus pattern (15 bp): TTTCTGTTAATACTT Found at i:110458 original size:50 final size:50 Alignment explanation

Indices: 110383--110651 Score: 511 Period size: 50 Copynumber: 5.4 Consensus size: 50 110373 TCTACGGACC * * 110383 CTGGACAAAGTAATAGCTCACCTGGACTTTCTCCTCTGTGACGTGGATTT 1 CTGGACAAAATAATAGCTCACCTGGACATTCTCCTCTGTGACGTGGATTT 110433 CTGGACAAAATAATAGCTCACCTGGACATTCTCCTCTGTGACGTGGATTT 1 CTGGACAAAATAATAGCTCACCTGGACATTCTCCTCTGTGACGTGGATTT * 110483 CTGGACAAAATAATAGCTCACCTGGACATTCCCCTCTGTGACGTGGATTT 1 CTGGACAAAATAATAGCTCACCTGGACATTCTCCTCTGTGACGTGGATTT 110533 CTGGACAAAATAATAGCTCACCTGGACATTCTCCTCTGTGACGTGGATTT 1 CTGGACAAAATAATAGCTCACCTGGACATTCTCCTCTGTGACGTGGATTT 110583 CTGGACAAAATAATAGCTCACCTGGACATTCTCCTCTGTGACGTGGATTT 1 CTGGACAAAATAATAGCTCACCTGGACATTCTCCTCTGTGACGTGGATTT 110633 CTGGACAAAATAATAGCTC 1 CTGGACAAAATAATAGCTC 110652 NNNNNNNNNN Statistics Matches: 215, Mismatches: 4, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 50 215 1.00 ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29 Consensus pattern (50 bp): CTGGACAAAATAATAGCTCACCTGGACATTCTCCTCTGTGACGTGGATTT Found at i:121061 original size:57 final size:57 Alignment explanation

Indices: 120982--121128 Score: 195 Period size: 57 Copynumber: 2.6 Consensus size: 57 120972 CACGGCCTGA * * * 120982 GGGTACTGTCGATGGAGGGAACCCTGACCTAGCAGACAAATTCTCTAACTTTTTATT 1 GGGTCCTGTGGATGGAGGGAACCCTGACCTAGCAGACAAATTCTATAACTTTTTATT * * * 121039 GGGTCCTGTGGATGGAGGGAACCCTGACCTAGCGGACCAATTCTATGACTTTTTATT 1 GGGTCCTGTGGATGGAGGGAACCCTGACCTAGCAGACAAATTCTATAACTTTTTATT * * ** * 121096 GGATCCTCTGGATAAAGGGAACCCTGACTTAGC 1 GGGTCCTGTGGATGGAGGGAACCCTGACCTAGC 121129 TGACTGATTG Statistics Matches: 79, Mismatches: 11, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 57 79 1.00 ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28 Consensus pattern (57 bp): GGGTCCTGTGGATGGAGGGAACCCTGACCTAGCAGACAAATTCTATAACTTTTTATT Found at i:125264 original size:28 final size:28 Alignment explanation

Indices: 125224--125282 Score: 118 Period size: 28 Copynumber: 2.1 Consensus size: 28 125214 TGATAGTTTG 125224 TCAGAATTAATGAAGTCTTAGCCTGGTC 1 TCAGAATTAATGAAGTCTTAGCCTGGTC 125252 TCAGAATTAATGAAGTCTTAGCCTGGTC 1 TCAGAATTAATGAAGTCTTAGCCTGGTC 125280 TCA 1 TCA 125283 ATTTTACCCC Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 31 1.00 ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32 Consensus pattern (28 bp): TCAGAATTAATGAAGTCTTAGCCTGGTC Found at i:125380 original size:28 final size:28 Alignment explanation

Indices: 125332--125838 Score: 539 Period size: 28 Copynumber: 17.6 Consensus size: 28 125322 CAGAGTTAGT * * 125332 AGTCTTGGCCTAGTCTCAGAGTTAATGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * * * 125360 AATTTTAGACTGGTCTCAGAGTTATGTAATGA 1 AGTCTTAGCCTGGTCTCAGAG---T-TAATGA 125392 AGTCTTAGCCTGGTCTCAGAGTTAATGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA 125420 AGTCTTAGCCTGGTCTCAGAGTTAATGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * 125448 AGTCTTAGCCTGGTGTCAGAGTTAATGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * * * 125476 AGTCTAAGCCTGGTCTCAGAGTGATTGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * * * 125504 AGTCTTAGCCTGGTGTCAGAGTGAGTGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * 125532 AGTCTTAGCCTGGTGTCAGAGTTAATGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * * 125560 AGTCTTAGCCTGGTGTCAGAGTGAATGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * * 125588 AGTTTTAGCCATTTCAGCCTCGTCTCAGAGTTAATAA 1 AG---T---C--TT-AGCCTGGTCTCAGAGTTAATGA * * * * 125625 AGTTTTATCCTGGTCCCAGGGTTAATGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * * 125653 AGTCTTAGCCTGGTCTCATAGTTAATAA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * * * * 125681 AGTTTTATCCTGGTCCCAGGGTTAATGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * * 125709 AGTCTCAGCCTGGTCTCAGAGTTAATAA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * * * * 125737 AGTTTTATCCTGGTCCCAGGGTTAATGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA * 125765 AGTCTTAGCCTGGTCTCAGAGTGT-GTGA 1 AGTCTTAGCCTGGTCTCAGAGT-TAATGA * * ** 125793 AGTCTTAGACTGGTCTCAGAGTGAGGGA 1 AGTCTTAGCCTGGTCTCAGAGTTAATGA 125821 AGTCTTAGCCTGGTCTCA 1 AGTCTTAGCCTGGTCTCA 125839 ATTTTACCCC Statistics Matches: 402, Mismatches: 62, Indels: 30 0.81 0.13 0.06 Matches are distributed among these distances: 28 348 0.87 29 4 0.01 31 2 0.00 32 24 0.06 34 2 0.00 36 2 0.00 37 20 0.05 ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32 Consensus pattern (28 bp): AGTCTTAGCCTGGTCTCAGAGTTAATGA Found at i:125728 original size:149 final size:149 Alignment explanation

Indices: 125463--125835 Score: 377 Period size: 149 Copynumber: 2.6 Consensus size: 149 125453 TAGCCTGGTG * * * * 125463 TCAGAGTTAATGAAGTCTAAGCCTGGTCTCAGAGTGATTGAAGTCTTAGCCTGGTGTCAGAGTGA 1 TCAGAGTTAATAAAGTCTAAGCCTGGTCCCAGAGTGAATGAAGTCTTAGCCTGGTCTCAGAGTGA * * ** * * * 125528 GTGAAGTCTTAGCCTGGTGTCAGAGTTAATGAAGTCTTAGCCTGGTGTCAGAGTGAATGAAGTTT 66 ATAAAGTCTTAGCCTGGTCCCAGAGTTAATGAAGTCTCAGCCTGGTCTCAGAGTGAATAAAGTTT 125593 TAGCCATTTCAGCCTCGTC 131 TAGCCATTTCAGCCTCGTC * * * * * * * 125612 TCAGAGTTAATAAAGTTTTATCCTGGTCCCAGGGTTAATGAAGTCTTAGCCTGGTCTCATAGTTA 1 TCAGAGTTAATAAAGTCTAAGCCTGGTCCCAGAGTGAATGAAGTCTTAGCCTGGTCTCAGAGTGA * * * * 125677 ATAAAGTTTTATCCTGGTCCCAGGGTTAATGAAGTCTCAGCCTGGTCTCAGAGTTAATAAAGTTT 66 ATAAAGTCTTAGCCTGGTCCCAGAGTTAATGAAGTCTCAGCCTGGTCTCAGAGTGAATAAAGTTT * 125742 T----A--T---CCTGGTC 131 TAGCCATTTCAGCCTCGTC * * * * * ** * 125752 CCAGGGTTAATGAAGTCTTAGCCTGGTCTCAGAGTGTGTGAAGTCTTAGACTGGTCTCAGAGTGA 1 TCAGAGTTAATAAAGTCTAAGCCTGGTCCCAGAGTGAATGAAGTCTTAGCCTGGTCTCAGAGTGA *** 125817 GGGAAGTCTTAGCCTGGTC 66 ATAAAGTCTTAGCCTGGTC 125836 TCAATTTTAC Statistics Matches: 183, Mismatches: 41, Indels: 9 0.79 0.18 0.04 Matches are distributed among these distances: 140 72 0.39 143 1 0.01 145 1 0.01 149 109 0.60 ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32 Consensus pattern (149 bp): TCAGAGTTAATAAAGTCTAAGCCTGGTCCCAGAGTGAATGAAGTCTTAGCCTGGTCTCAGAGTGA ATAAAGTCTTAGCCTGGTCCCAGAGTTAATGAAGTCTCAGCCTGGTCTCAGAGTGAATAAAGTTT TAGCCATTTCAGCCTCGTC Found at i:131671 original size:24 final size:24 Alignment explanation

Indices: 131644--131712 Score: 77 Period size: 24 Copynumber: 2.9 Consensus size: 24 131634 GGAACGATCG * 131644 CCAAGGTCGAGT-TTAGAACGGTCC 1 CCAAGGTCGAGTCTT-GAAAGGTCC 131668 CCAAGGTCGAGTCTTGAAAGGTCC 1 CCAAGGTCGAGTCTTGAAAGGTCC ** * * 131692 CCTCGATCTAGTCTTGAAAGG 1 CCAAGGTCGAGTCTTGAAAGG 131713 GGATCAGCTA Statistics Matches: 39, Mismatches: 5, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 24 37 0.95 25 2 0.05 ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23 Consensus pattern (24 bp): CCAAGGTCGAGTCTTGAAAGGTCC Found at i:132970 original size:29 final size:29 Alignment explanation

Indices: 132887--132974 Score: 131 Period size: 29 Copynumber: 3.0 Consensus size: 29 132877 ATTAACCAAT * * * 132887 AGTGTAGAATATTAATGTAATTATTCAAT 1 AGTGTAGAATATTAATGTAATAATTAAAC * 132916 AGTGTAGATTATTAATGTAATAATTAAAC 1 AGTGTAGAATATTAATGTAATAATTAAAC * 132945 AGTGTAGAATGTTAATGTAATAATTAAAC 1 AGTGTAGAATATTAATGTAATAATTAAAC 132974 A 1 A 132975 TTTCTTTTTT Statistics Matches: 53, Mismatches: 6, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 29 53 1.00 ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38 Consensus pattern (29 bp): AGTGTAGAATATTAATGTAATAATTAAAC Found at i:136757 original size:177 final size:176 Alignment explanation

Indices: 136461--136813 Score: 697 Period size: 177 Copynumber: 2.0 Consensus size: 176 136451 AATTCCGTTA 136461 AACATTTTCAGTTTCTTCTACCTTATGTTGCATGTAAATTTATTAATCTGTTGCATGATATTCTC 1 AACATTTTCAGTTTCTTCTACCTTATGTTGCATGTAAATTTATTAATCTGTTGCATGATATTCTC 136526 TGTAGTAACTCTCTGCATGAATGTATAAACATGAAAAAAGATTCTATATCGATGACAATGTTTCT 66 TGTAGTAACTCTCTGCATGAATGTATAAACATGAAAAAAGATTCTATATCGATGACAATGTTTCT 136591 TCTTTTTGAATAGGTCTCCAAGTTTCAAGCTGATATGTGCCGCAGC 131 TCTTTTTGAATAGGTCTCCAAGTTTCAAGCTGATATGTGCCGCAGC 136637 NAACATTTTCAGTTTCTTCTACCTTATGTTGCATGTAAATTTATTAATCTGTTGCATGATATTCT 1 -AACATTTTCAGTTTCTTCTACCTTATGTTGCATGTAAATTTATTAATCTGTTGCATGATATTCT 136702 CTGTAGTAACTCTCTGCATGAATGTATAAACATGAAAAAAGATTCTATATCGATGACAATGTTTC 65 CTGTAGTAACTCTCTGCATGAATGTATAAACATGAAAAAAGATTCTATATCGATGACAATGTTTC 136767 TTCTTTTTGAATAGGTCTCCAAGTTTCAAGCTGATATGTGCCGCAGC 130 TTCTTTTTGAATAGGTCTCCAAGTTTCAAGCTGATATGTGCCGCAGC 136814 TGCGAAAAAG Statistics Matches: 176, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 177 176 1.00 ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39 Consensus pattern (176 bp): AACATTTTCAGTTTCTTCTACCTTATGTTGCATGTAAATTTATTAATCTGTTGCATGATATTCTC TGTAGTAACTCTCTGCATGAATGTATAAACATGAAAAAAGATTCTATATCGATGACAATGTTTCT TCTTTTTGAATAGGTCTCCAAGTTTCAAGCTGATATGTGCCGCAGC Found at i:139742 original size:181 final size:178 Alignment explanation

Indices: 139433--139841 Score: 702 Period size: 181 Copynumber: 2.3 Consensus size: 178 139423 GCTGGCGAAG 139433 ATGACAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTC 1 ATGA-AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTC 139498 ATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTATTCTTTTGCAGATCAATTGTA 65 ATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTATTCTTTTGCAGATCAATTGTA * 139563 CATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTTCTGATAATTT 130 CATATATCAGAGGTGTGCATATTGCTAGGATTTTGA-TTTCCGATAATTT 139613 ATCGAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCT 1 AT-G-AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCT * * 139678 CGTTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGT 64 CATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTATTCTTTTGCAGATCAATTGT 139743 ACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTT 129 ACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTT * * 139793 ATGAAAAA-A--A--TTTTGAACTTCGTCATTTTTTGGCAAAATGTTGCATATA 1 ATGAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATA 139842 CATGTAGGGT Statistics Matches: 222, Mismatches: 5, Indels: 11 0.93 0.02 0.05 Matches are distributed among these distances: 173 37 0.17 175 1 0.00 177 1 0.00 178 5 0.02 179 1 0.00 180 16 0.07 181 160 0.72 182 1 0.00 ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37 Consensus pattern (178 bp): ATGAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCA TTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTATTCTTTTGCAGATCAATTGTAC ATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTT Found at i:147225 original size:13 final size:13 Alignment explanation

Indices: 147196--147228 Score: 52 Period size: 11 Copynumber: 2.7 Consensus size: 13 147186 ATAAATAAAA 147196 AAAATTCATATAT 1 AAAATTCATATAT 147209 --AATTCATATAT 1 AAAATTCATATAT 147220 AAAATTCAT 1 AAAATTCAT 147229 CAAATCTTCT Statistics Matches: 18, Mismatches: 0, Indels: 4 0.82 0.00 0.18 Matches are distributed among these distances: 11 11 0.61 13 7 0.39 ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39 Consensus pattern (13 bp): AAAATTCATATAT Found at i:149469 original size:16 final size:16 Alignment explanation

Indices: 149448--149478 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 149438 GAATTGTTCT * 149448 TTCTTTCTTTATTTAC 1 TTCTTTATTTATTTAC 149464 TTCTTTATTTATTTA 1 TTCTTTATTTATTTA 149479 ATATTTTCCC Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71 Consensus pattern (16 bp): TTCTTTATTTATTTAC Found at i:149545 original size:15 final size:15 Alignment explanation

Indices: 149525--149566 Score: 84 Period size: 15 Copynumber: 2.8 Consensus size: 15 149515 TACTTATTGA 149525 TAATTTTCCTACCTC 1 TAATTTTCCTACCTC 149540 TAATTTTCCTACCTC 1 TAATTTTCCTACCTC 149555 TAATTTTCCTAC 1 TAATTTTCCTAC 149567 TTTTACGGTT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 27 1.00 ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48 Consensus pattern (15 bp): TAATTTTCCTACCTC Found at i:149943 original size:20 final size:20 Alignment explanation

Indices: 149918--149959 Score: 75 Period size: 20 Copynumber: 2.1 Consensus size: 20 149908 ATATTGACTT 149918 TAATATATGTATGGGGATGA 1 TAATATATGTATGGGGATGA * 149938 TAATATATGTATGGGGGTGA 1 TAATATATGTATGGGGATGA 149958 TA 1 TA 149960 GGTTTTATGA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36 Consensus pattern (20 bp): TAATATATGTATGGGGATGA Found at i:150874 original size:16 final size:16 Alignment explanation

Indices: 150853--151082 Score: 201 Period size: 16 Copynumber: 15.4 Consensus size: 16 150843 TTTCTGGTAC * 150853 TTTACTGTTGGAATAG 1 TTTACTGTTAGAATAG * 150869 TTTACTGTTAAAATAG 1 TTTACTGTTAGAATAG 150885 TTTACTGTTAGAATAG 1 TTTACTGTTAGAATAG 150901 TTTACTGTTAG-A-A- 1 TTTACTGTTAGAATAG 150914 --TA--GTT-GAATAG 1 TTTACTGTTAGAATAG * 150925 TTTACTGTTTGAATAG 1 TTTACTGTTAGAATAG 150941 TTTACTGTTAG-A-A- 1 TTTACTGTTAGAATAG 150954 --TA--GTT-GAATAG 1 TTTACTGTTAGAATAG * 150965 TTTACTGTTTGAATAG 1 TTTACTGTTAGAATAG * 150981 TTTACTGTTTGAATAG 1 TTTACTGTTAGAATAG 150997 TTTACTGTTAGAATAG 1 TTTACTGTTAGAATAG 151013 TTTACTGTTAGAATAG 1 TTTACTGTTAGAATAG * * * * 151029 TTGAATAGTT-TACT-G 1 TTTACT-GTTAGAATAG * * 151044 TTAGAATAGTT-GAATAG 1 TT-TACT-GTTAGAATAG 151061 TTTACTGTTAGAATAG 1 TTTACTGTTAGAATAG 151077 TTTACT 1 TTTACT 151083 ACCATTAACA Statistics Matches: 181, Mismatches: 13, Indels: 40 0.77 0.06 0.17 Matches are distributed among these distances: 8 2 0.01 9 8 0.04 10 2 0.01 11 4 0.02 13 4 0.02 14 2 0.01 15 14 0.08 16 139 0.77 17 6 0.03 ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45 Consensus pattern (16 bp): TTTACTGTTAGAATAG Found at i:150927 original size:24 final size:24 Alignment explanation

Indices: 150895--151078 Score: 210 Period size: 24 Copynumber: 8.0 Consensus size: 24 150885 TTTACTGTTA 150895 GAATAGTTTACTGTTAGAATAGTT 1 GAATAGTTTACTGTTAGAATAGTT 150919 GAATAGTTTAC---T-G--T--TT 1 GAATAGTTTACTGTTAGAATAGTT 150935 GAATAGTTTACTGTTAGAATAGTT 1 GAATAGTTTACTGTTAGAATAGTT * 150959 GAATAGTTTACTGTTTGAATAGTT 1 GAATAGTTTACTGTTAGAATAGTT * * * * * 150983 TACT-GTTTGAATAGTT-TACT-GTT 1 GAATAGTTT-ACT-GTTAGAATAGTT 151006 AGAATAGTTTACTGTTAGAATAGTT 1 -GAATAGTTTACTGTTAGAATAGTT 151031 GAATAGTTTACTGTTAGAATAGTT 1 GAATAGTTTACTGTTAGAATAGTT 151055 GAATAGTTTACTGTTAGAATAGTT 1 GAATAGTTTACTGTTAGAATAGTT 151079 TACTACCATT Statistics Matches: 135, Mismatches: 11, Indels: 28 0.78 0.06 0.16 Matches are distributed among these distances: 16 13 0.10 18 1 0.01 19 1 0.01 20 2 0.01 21 1 0.01 22 1 0.01 23 10 0.07 24 96 0.71 25 10 0.07 ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44 Consensus pattern (24 bp): GAATAGTTTACTGTTAGAATAGTT Found at i:150939 original size:40 final size:40 Alignment explanation

Indices: 150880--151054 Score: 276 Period size: 40 Copynumber: 4.6 Consensus size: 40 150870 TTACTGTTAA 150880 AATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTG 1 AATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTG * 150920 AATAGTTTACTGTTTGAATAGTTTACTGTTAGAATAGTTG 1 AATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTG * 150960 AATAGTTTACTGTTTGAATAGTTTAC---T-G--T--TTG 1 AATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTG 150992 AATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTG 1 AATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTG 151032 AATAGTTTACTGTTAGAATAGTT 1 AATAGTTTACTGTTAGAATAGTT 151055 GAATAGTTTA Statistics Matches: 125, Mismatches: 2, Indels: 16 0.87 0.01 0.11 Matches are distributed among these distances: 32 28 0.22 34 1 0.01 35 1 0.01 36 2 0.02 37 1 0.01 38 1 0.01 40 91 0.73 ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45 Consensus pattern (40 bp): AATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTG Found at i:150949 original size:56 final size:56 Alignment explanation

Indices: 150863--151054 Score: 289 Period size: 56 Copynumber: 3.4 Consensus size: 56 150853 TTTACTGTTG * 150863 GAATAGTTTACTGTTAAAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTT 1 GAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTT * * * * * 150919 GAATAGTTTACTGTTTGAATAGTTTACTGTTAGAATAGTTGAATAGTT-TACT-GTTT 1 GAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTTACT-GTTAGAATAG-TT * 150975 GAATAGTTTACTGTTTGAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTT 1 GAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTT 151031 GAATAGTTTACTGTTAGAATAGTT 1 GAATAGTTTACTGTTAGAATAGTT 151055 GAATAGTTTA Statistics Matches: 121, Mismatches: 11, Indels: 8 0.86 0.08 0.06 Matches are distributed among these distances: 55 4 0.03 56 113 0.93 57 4 0.03 ACGTcount: A:0.31, C:0.05, G:0.19, T:0.44 Consensus pattern (56 bp): GAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTT Found at i:151033 original size:96 final size:96 Alignment explanation

Indices: 150863--151082 Score: 345 Period size: 96 Copynumber: 2.3 Consensus size: 96 150853 TTTACTGTTG * * 150863 GAATAGTTTACTGTTAAAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTGAATAGTTT 1 GAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTGAATAGTTG * 150928 ACTGTTTGAATAGTTTACTGTTAGAATAGTT 66 AATGTTTGAATAGTTTACTGTTAGAATAGTT * * * * 150959 GAATAGTTTACTGTTTGAATAGTTTACTGTTTGAATAGTTTACTGTTAGAATAGTTTACT-GTTA 1 GAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTGAATAGTT- 151023 GAATAG-TTGAATAGTTTACTGTTAGAATAGTT 65 GAAT-GTTTGAATAGTTTACTGTTAGAATAGTT 151055 GAATAGTTTACTGTTAGAATAGTTTACT 1 GAATAGTTTACTGTTAGAATAGTTTACT 151083 ACCATTAACA Statistics Matches: 114, Mismatches: 8, Indels: 4 0.90 0.06 0.03 Matches are distributed among these distances: 95 3 0.03 96 110 0.96 97 1 0.01 ACGTcount: A:0.31, C:0.05, G:0.19, T:0.44 Consensus pattern (96 bp): GAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTTACTGTTAGAATAGTTGAATAGTTG AATGTTTGAATAGTTTACTGTTAGAATAGTT Found at i:151075 original size:40 final size:40 Alignment explanation

Indices: 150890--151083 Score: 175 Period size: 40 Copynumber: 4.8 Consensus size: 40 150880 AATAGTTTAC * * * * * 150890 TGTTAGAATAGTTTACTGTTAGAATAGTTGAATAGTTTAC 1 TGTTTGAATAGTTTACTGTTAGAATAGTTTACTAGTTGAA * * * * 150930 TGTTTGAATAGTTTACTGTTAGAATAGTTGAATAGTTTAC 1 TGTTTGAATAGTTTACTGTTAGAATAGTTTACTAGTTGAA * 150970 TGTTTGAATAGTTTACTGTTTGAATAGTTTACT-GTTAGAA 1 TGTTTGAATAGTTTACTGTTAGAATAGTTTACTAGTT-GAA * * * 151010 TAGTTT-ACT-GTTAGAATAGTT-GAATAGTTTACT-GTTAGAA 1 T-GTTTGAATAGTT-TACT-GTTAGAATAGTTTACTAGTT-GAA 151050 TAG-TTGAATAGTTTACTGTTAGAATAGTTTACTA 1 T-GTTTGAATAGTTTACTGTTAGAATAGTTTACTA 151084 CCATTAACAT Statistics Matches: 134, Mismatches: 12, Indels: 15 0.83 0.07 0.09 Matches are distributed among these distances: 39 11 0.08 40 113 0.84 41 10 0.07 ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44 Consensus pattern (40 bp): TGTTTGAATAGTTTACTGTTAGAATAGTTTACTAGTTGAA Found at i:161368 original size:18 final size:18 Alignment explanation

Indices: 161348--161712 Score: 448 Period size: 18 Copynumber: 20.3 Consensus size: 18 161338 GGTGTTACCT * * 161348 GGACAACCAGGATTTAAT 1 GGACAACCTGGATTTAAC * 161366 GGACAACCTGG-TTTAAAT 1 GGACAACCTGGATTT-AAC * * * 161384 GGACAGCCAGGATTCAAC 1 GGACAACCTGGATTTAAC * * 161402 GGTCAACCCGGATTTAAC 1 GGACAACCTGGATTTAAC * 161420 GGACAACCCGGATTTAAC 1 GGACAACCTGGATTTAAC * * 161438 GGACAACCCGGATTTAAT 1 GGACAACCTGGATTTAAC * 161456 GGACAACCTGG-TTTAAAT 1 GGACAACCTGGATTT-AAC * * * 161474 GGACAGCCAGGATTTAAT 1 GGACAACCTGGATTTAAC * 161492 GGTCAACCTGGATTTAAC 1 GGACAACCTGGATTTAAC 161510 GGACAACCTGGATTTAAC 1 GGACAACCTGGATTTAAC * 161528 GGACAACCTGGATTTAAT 1 GGACAACCTGGATTTAAC * 161546 GGACAACCTGGTTTTAAC 1 GGACAACCTGGATTTAAC 161564 GGACAACCTGGATTTAAC 1 GGACAACCTGGATTTAAC 161582 GGACAACCTGGATTTAAC 1 GGACAACCTGGATTTAAC * * 161600 GGACAACCCGGATTTAAT 1 GGACAACCTGGATTTAAC * 161618 GGACAACCTGG-TTTAAAT 1 GGACAACCTGGATTT-AAC * * * 161636 GGACAGCCAGGATTTAAT 1 GGACAACCTGGATTTAAC * 161654 GGTCAACCTGGATTTAAC 1 GGACAACCTGGATTTAAC * 161672 GGACAACCCGGATTTAAC 1 GGACAACCTGGATTTAAC 161690 GGACAACCTGGATTTAAC 1 GGACAACCTGGATTTAAC 161708 GGACA 1 GGACA 161713 GCCAGGTTTT Statistics Matches: 306, Mismatches: 35, Indels: 12 0.87 0.10 0.03 Matches are distributed among these distances: 17 9 0.03 18 289 0.94 19 8 0.03 ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23 Consensus pattern (18 bp): GGACAACCTGGATTTAAC Found at i:161505 original size:90 final size:90 Alignment explanation

Indices: 161348--161712 Score: 518 Period size: 90 Copynumber: 4.1 Consensus size: 90 161338 GGTGTTACCT * * * * 161348 GGACAACCAGGATTTAATGGACAACCTGGTTTAAATGGACAGCCAGGATTCAACGGTCAACCCGG 1 GGACAACCTGGATTTAATGGACAACCTGGTTTAAATGGACAACCAGGATTTAACGGACAACCCGG 161413 ATTTAACGGACAACCCGGATTTAAC 66 ATTTAACGGACAACCCGGATTTAAC * * * * * 161438 GGACAACCCGGATTTAATGGACAACCTGGTTTAAATGGACAGCCAGGATTTAATGGTCAACCTGG 1 GGACAACCTGGATTTAATGGACAACCTGGTTTAAATGGACAACCAGGATTTAACGGACAACCCGG * 161503 ATTTAACGGACAACCTGGATTTAAC 66 ATTTAACGGACAACCCGGATTTAAC * * * * 161528 GGACAACCTGGATTTAATGGACAACCTGGTTTTAACGGACAACCTGGATTTAACGGACAACCTGG 1 GGACAACCTGGATTTAATGGACAACCTGGTTTAAATGGACAACCAGGATTTAACGGACAACCCGG * 161593 ATTTAACGGACAACCCGGATTTAAT 66 ATTTAACGGACAACCCGGATTTAAC * * * * 161618 GGACAACCTGG-TTTAAATGGACAGCCAGGATTT-AATGGTCAACCTGGATTTAACGGACAACCC 1 GGACAACCTGGATTT-AATGGACAACCTGG-TTTAAATGGACAACCAGGATTTAACGGACAACCC * 161681 GGATTTAACGGACAACCTGGATTTAAC 64 GGATTTAACGGACAACCCGGATTTAAC 161708 GGACA 1 GGACA 161713 GCCAGGTTTT Statistics Matches: 252, Mismatches: 21, Indels: 4 0.91 0.08 0.01 Matches are distributed among these distances: 89 3 0.01 90 246 0.98 91 3 0.01 ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23 Consensus pattern (90 bp): GGACAACCTGGATTTAATGGACAACCTGGTTTAAATGGACAACCAGGATTTAACGGACAACCCGG ATTTAACGGACAACCCGGATTTAAC Found at i:161849 original size:18 final size:18 Alignment explanation

Indices: 161825--161908 Score: 96 Period size: 18 Copynumber: 4.7 Consensus size: 18 161815 CGGATTTCCC * * 161825 GGACAACCAGGAATGCCC 1 GGACAACCAGGGATGCCA * 161843 GGTCAACCAGGGATGCCA 1 GGACAACCAGGGATGCCA 161861 GGACAACCAGGGATGCCA 1 GGACAACCAGGGATGCCA * * * * * 161879 GGTCAGCAAGGGTTACCA 1 GGACAACCAGGGATGCCA 161897 GGACAACCAGGG 1 GGACAACCAGGG 161909 GGTTTTCCCG Statistics Matches: 54, Mismatches: 12, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 18 54 1.00 ACGTcount: A:0.31, C:0.27, G:0.33, T:0.08 Consensus pattern (18 bp): GGACAACCAGGGATGCCA Found at i:161877 original size:36 final size:36 Alignment explanation

Indices: 161825--161908 Score: 114 Period size: 36 Copynumber: 2.3 Consensus size: 36 161815 CGGATTTCCC * * * * 161825 GGACAACCAGGAATGCCCGGTCAACCAGGGATGCCA 1 GGACAACCAGGGATGCCAGGTCAACAAGGGATACCA * * 161861 GGACAACCAGGGATGCCAGGTCAGCAAGGGTTACCA 1 GGACAACCAGGGATGCCAGGTCAACAAGGGATACCA 161897 GGACAACCAGGG 1 GGACAACCAGGG 161909 GGTTTTCCCG Statistics Matches: 42, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 36 42 1.00 ACGTcount: A:0.31, C:0.27, G:0.33, T:0.08 Consensus pattern (36 bp): GGACAACCAGGGATGCCAGGTCAACAAGGGATACCA Found at i:163511 original size:22 final size:22 Alignment explanation

Indices: 163483--163528 Score: 92 Period size: 22 Copynumber: 2.1 Consensus size: 22 163473 TTGATGTGTC 163483 ATTCCAAAAACTCAAGCAATAT 1 ATTCCAAAAACTCAAGCAATAT 163505 ATTCCAAAAACTCAAGCAATAT 1 ATTCCAAAAACTCAAGCAATAT 163527 AT 1 AT 163529 GCTATATCAG 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:0.50, C:0.22, G:0.04, T:0.24 Consensus pattern (22 bp): ATTCCAAAAACTCAAGCAATAT Found at i:166443 original size:2 final size:2 Alignment explanation

Indices: 166436--166512 Score: 145 Period size: 2 Copynumber: 38.5 Consensus size: 2 166426 TGTGCCAAGC 166436 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT * 166478 CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 166513 AGTTGTGTGA Statistics Matches: 73, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 2 73 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): CT Found at i:168978 original size:42 final size:42 Alignment explanation

Indices: 168960--169371 Score: 598 Period size: 42 Copynumber: 9.8 Consensus size: 42 168950 TCTAAATTTT * * * 168960 AGGACAGATCCATTGAATATAAGGAGAGACCCTTCAACTTTA 1 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTTTA 169002 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTTTA 1 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTTTA * 169044 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAAATTTA 1 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTTTA 169086 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTTTA 1 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTTTA * ** 169128 AGGACAGATCCTTTGGATATTAGGAGAGATCCTTTGGA-TATT- 1 AGGACAGATCCTTTGGATATTAGGAGAGA-CCCTTCAACT-TTA * * 169170 AGGACAGATCCTTGGGATATTAGGAGAGACCCTTCAACTGTA 1 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTTTA * ** 169212 AGGACAGATCCTTTGGATATTAGGAGAGATCCTTTGGA-TATT- 1 AGGACAGATCCTTTGGATATTAGGAGAGA-CCCTTCAACT-TTA * * 169254 AGGACAGATCCTTGGGATATTAGGAGAGACCCTTCAACTGTA 1 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTTTA * 169296 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTGTA 1 AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTTTA * * * 169338 AGGACAGATCCTTTGGATATCAGGACAGATCCTT 1 AGGACAGATCCTTTGGATATTAGGAGAGACCCTT 169372 GGGATATTAG Statistics Matches: 335, Mismatches: 27, Indels: 16 0.89 0.07 0.04 Matches are distributed among these distances: 41 12 0.04 42 310 0.93 43 13 0.04 ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28 Consensus pattern (42 bp): AGGACAGATCCTTTGGATATTAGGAGAGACCCTTCAACTTTA Found at i:169424 original size:42 final size:42 Alignment explanation

Indices: 169359--169459 Score: 105 Period size: 42 Copynumber: 2.4 Consensus size: 42 169349 TTTGGATATC * * * 169359 AGGACAGATCCTTGGGATATTAGGAGAGACCCT-TCAACTGTA 1 AGGACAGATCCTTTGAATATTAGGACAGACCCTCTCAAC-GTA * * * * 169401 AGGACAGATCCTTTGAATGTTAGGTCAGACCCTCTGAACGTT 1 AGGACAGATCCTTTGAATATTAGGACAGACCCTCTCAACGTA * * 169443 AGAACAGACCCTTTGAA 1 AGGACAGATCCTTTGAA 169460 CGACGCATTA Statistics Matches: 49, Mismatches: 9, Indels: 2 0.82 0.15 0.03 Matches are distributed among these distances: 42 45 0.92 43 4 0.08 ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25 Consensus pattern (42 bp): AGGACAGATCCTTTGAATATTAGGACAGACCCTCTCAACGTA Found at i:169452 original size:63 final size:63 Alignment explanation

Indices: 169070--169455 Score: 201 Period size: 63 Copynumber: 6.1 Consensus size: 63 169060 ATATTAGGAG * * * * * * * * 169070 AGACCCTTCAAATTTAAGGACAGATCCTTTGGATATTAGGAGAGACCCTT-CAACTTTAAGGAC 1 AGACCCTTCAACTGTAAGGACAGATCCTTTGAATATCAGGACAGACCCTTGGAACATT-AGAAC * ** * * * * * * * * * * 169133 AGATCCTTTGGA-TATTAGGAGAGATCCTTTGGATATTAGGACAGATCCTTGGGATATTAGGAG 1 AGA-CCCTTCAACTGTAAGGACAGATCCTTTGAATATCAGGACAGACCCTTGGAACATTAGAAC * * * * * * 169196 AGACCCTTCAACTGTAAGGACAGATCCTTTGGATATTAGGAGAGATCCTTTGG-ATATTAGGAC 1 AGACCCTTCAACTGTAAGGACAGATCCTTTGAATATCAGGACAGA-CCCTTGGAACATTAGAAC * ** * * * * * * * * * * 169259 AGATCCTTGGGA-TATTAGGAGAGA-CCCTTCAACTGTAAGGACAGATCCTTTGG-ATATTAGGA 1 AGACCCTT-CAACTGTAAGGACAGATCCTTTGAA-TATCAGGACAGA-CCCTTGGAACATTAGAA * 169321 G 63 C * * * * * * 169322 AGACCCTTCAACTGTAAGGACAGATCCTTTGGATATCAGGACAGATCCTTGGGATATTAGGAG 1 AGACCCTTCAACTGTAAGGACAGATCCTTTGAATATCAGGACAGACCCTTGGAACATTAGAAC * * * * 169385 AGACCCTTCAACTGTAAGGACAGATCCTTTGAATGTTAGGTCAGACCCTCT-GAACGTTAGAAC 1 AGACCCTTCAACTGTAAGGACAGATCCTTTGAATATCAGGACAGACCCT-TGGAACATTAGAAC 169448 AGACCCTT 1 AGACCCTT 169456 TGAACGACGC Statistics Matches: 254, Mismatches: 59, Indels: 20 0.76 0.18 0.06 Matches are distributed among these distances: 62 16 0.06 63 218 0.86 64 20 0.08 ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27 Consensus pattern (63 bp): AGACCCTTCAACTGTAAGGACAGATCCTTTGAATATCAGGACAGACCCTTGGAACATTAGAAC Found at i:172349 original size:2 final size:2 Alignment explanation

Indices: 172342--172397 Score: 112 Period size: 2 Copynumber: 28.0 Consensus size: 2 172332 NNNNNNNNNN 172342 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 172384 CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT 172398 GAGACTGATA Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 54 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:176366 original size:18 final size:18 Alignment explanation

Indices: 176295--176366 Score: 126 Period size: 18 Copynumber: 4.0 Consensus size: 18 176285 AAAGAAGCAA * 176295 CCTACTCCTCACAAACAA 1 CCTACTCCTCACAAACAG 176313 CCTACTCCTCACAAACAG 1 CCTACTCCTCACAAACAG * 176331 CCTACTCCTCAAAAACAG 1 CCTACTCCTCACAAACAG 176349 CCTACTCCTCACAAACAG 1 CCTACTCCTCACAAACAG 176367 TCCAATTCTC Statistics Matches: 51, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 51 1.00 ACGTcount: A:0.36, C:0.43, G:0.04, T:0.17 Consensus pattern (18 bp): CCTACTCCTCACAAACAG Found at i:177996 original size:19 final size:19 Alignment explanation

Indices: 177974--178013 Score: 62 Period size: 19 Copynumber: 2.1 Consensus size: 19 177964 TTTCGGATGC * * 177974 TGGAGGAGGTTAAGGTTTT 1 TGGAGCAGGTTAAAGTTTT 177993 TGGAGCAGGTTAAAGTTTT 1 TGGAGCAGGTTAAAGTTTT 178012 TG 1 TG 178014 TTGCGGGTGC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38 Consensus pattern (19 bp): TGGAGCAGGTTAAAGTTTT Found at i:178004 original size:177 final size:175 Alignment explanation

Indices: 177695--178656 Score: 1336 Period size: 177 Copynumber: 5.4 Consensus size: 175 177685 TCTAACCTAT * * * * * * 177695 TACTTGTCCTATCTTCACCAAACTTGCATGGATGGTGTGCCTTATGATACTGATGCACCAGACAG 1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA * * * * * * 177760 GCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTGTTGGACCAGG 66 GCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG * 177825 TTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAGTATCTTAGTTAC 131 TTAAAGTTTTTGTTGCAGGTGCCCTCTGAT-G-AGTATCTTAGTTAC * * * * * 177872 TGCTGGT-CTGTACTTCACCAAACTTGCATGGATGGTGTGCCTTATGATACTGATGCACCAGACA 1 TACTGGTCCT-AACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACA * * * * * 177936 GGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAG 65 AGCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTG * * * 178001 GTTAAAGTTTTTGTTGCGGGTGCCCAT-TGATAGCAATATCTAAGTTAC 130 GTTAAAGTTTTTGTTGCAGGTGCCC-TCTGAT-G-AGTATCTTAGTTAC * * * * * 178049 TACTGGTCCTAACTTCACCAAATTTGTATGGGTGATGCGTCATATGATACTGATGCACCTGACAA 1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA * 178114 GCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCTGG 66 GCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG * 178179 TTAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTAATCTTAGTTAC 131 TTAAAGTTTTTGTTGCAGGTGCCCTCTGATGAGT-ATCTTAGTTAC * 178225 TACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA 1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA * 178290 GCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCTGG 66 GCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG * 178355 TT-AAGTTTTTGTTGCAGGTGCCCTCTGATGATGATATCTTAGTTAT 131 TTAAAGTTTTTGTTGCAGGTGCCCTCTGATGA-G-TATCTTAGTTAC * 178401 TACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA 1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA * 178466 GCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGG 66 GCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG *** * 178531 TTAGATAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTAGTTAT 131 -T---TAAAGTTTTTGTTGCAGGTGCCCTCTGATGA-G-TATCTTAGTTAC * * * * * * 178582 TACTAGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCTGACAG 1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA 178647 GCTTGAATGC 66 GCTTGAATGC 178657 ATAGTCTGGT Statistics Matches: 727, Mismatches: 46, Indels: 20 0.92 0.06 0.03 Matches are distributed among these distances: 175 31 0.04 176 280 0.39 177 303 0.42 178 3 0.00 180 1 0.00 181 109 0.15 ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33 Consensus pattern (175 bp): TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA GCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG TTAAAGTTTTTGTTGCAGGTGCCCTCTGATGAGTATCTTAGTTAC Found at i:178496 original size:352 final size:352 Alignment explanation

Indices: 177692--178656 Score: 1391 Period size: 352 Copynumber: 2.7 Consensus size: 352 177682 GTATCTAACC * * * * * * 177692 TATTACTTGTCCTATCTTCACCAAACTTGCATGGATGGTGTGCCTTATGATACTGATGCACCAGA 1 TATTACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGA * * * * * * 177757 CAGGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTGTTGGACC 66 CAAGCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGC * * * * 177822 AGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAGT-ATCTTAGTTACTGCTGGT-CTGTAC 131 TGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGAT-G-ATTAATCTTAGTTACTACTGGTCCT-TAC * * * 177885 TTCACCAAACTTGCATGGATGGTGTGCCTTATGATACTGATGCACCAGACAGGCTTGAGTGCTGA 193 TTCACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGCACCTGACAGGCTTGAATGCTGA * * * 177950 ATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGT 258 ATCTGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCAGGTTAAAGTTTTTGT * 178015 TGCGGGTGCCCATTGATAGCAATATCTAAGT 323 TGCAGGTGCCCATTGATAG-AATATCTAAGT * * * * * 178046 TACTACTGGTCCTAACTTCACCAAATTTGTATGGGTGATGCGTCATATGATACTGATGCACCTGA 1 TATTACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGA * 178111 CAAGCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGC 66 CAAGCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGC * 178176 TGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTAATCTTAGTTACTACTGGTCCTAACTTC 131 TGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTAATCTTAGTTACTACTGGTCCTTACTTC * * * 178241 ACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAAGCTTGAATGCTGAATC 196 ACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAATC * 178306 TGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCTGGTT-AAGTTTTTGTTGC 261 TGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCAGGTTAAAGTTTTTGTTGC * 178370 AGGTGCCC-TCTGAT-GATGATATCTTAGT 326 AGGTGCCCAT-TGATAGA--ATATCTAAGT 178398 TATTACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGA 1 TATTACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGA * 178463 CAAGCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGC 66 CAAGCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGC *** * * * 178528 TGGTTAGATAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTAGTTATTACTAGTCCTT 131 TGG-T---TAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTA-ATCTTAGTTACTACTGGTCCTT * * 178593 ACTTCACCAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCTGACAGGCTTGAATGC 191 ACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGCACCTGACAGGCTTGAATGC 178657 ATAGTCTGGT Statistics Matches: 547, Mismatches: 54, Indels: 17 0.89 0.09 0.03 Matches are distributed among these distances: 350 1 0.00 351 2 0.00 352 161 0.29 353 130 0.24 354 145 0.27 356 30 0.05 357 78 0.14 ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33 Consensus pattern (352 bp): TATTACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGA CAAGCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGC TGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTAATCTTAGTTACTACTGGTCCTTACTTC ACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAATC TGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCAGGTTAAAGTTTTTGTTGC AGGTGCCCATTGATAGAATATCTAAGT Found at i:179345 original size:20 final size:20 Alignment explanation

Indices: 179322--179364 Score: 68 Period size: 20 Copynumber: 2.1 Consensus size: 20 179312 TATGATAAAG 179322 TATTGTATGATATGAAACAA 1 TATTGTATGATATGAAACAA * * 179342 TATTGTTTGATATGATACAA 1 TATTGTATGATATGAAACAA 179362 TAT 1 TAT 179365 GATATCATAT Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42 Consensus pattern (20 bp): TATTGTATGATATGAAACAA Found at i:179458 original size:18 final size:18 Alignment explanation

Indices: 179435--179469 Score: 54 Period size: 18 Copynumber: 1.9 Consensus size: 18 179425 TTGATATTTT 179435 ATGATA-TGATTATGTATC 1 ATGATATTG-TTATGTATC 179453 ATGATATTGTTATGTAT 1 ATGATATTGTTATGTAT 179470 AGTATTGTAT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 14 0.88 19 2 0.12 ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49 Consensus pattern (18 bp): ATGATATTGTTATGTATC Found at i:179642 original size:15 final size:15 Alignment explanation

Indices: 179585--179634 Score: 55 Period size: 15 Copynumber: 3.2 Consensus size: 15 179575 GTATCCTATG 179585 ATACAATATTGTATA 1 ATACAATATTGTATA * * * 179600 TTCTATAATATTGTATC 1 --ATACAATATTGTATA 179617 ATACAATATTGTATA 1 ATACAATATTGTATA 179632 ATA 1 ATA 179635 TGATATTGGT Statistics Matches: 27, Mismatches: 6, Indels: 2 0.77 0.17 0.06 Matches are distributed among these distances: 15 15 0.56 17 12 0.44 ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44 Consensus pattern (15 bp): ATACAATATTGTATA Found at i:179692 original size:15 final size:15 Alignment explanation

Indices: 179674--179798 Score: 101 Period size: 15 Copynumber: 7.8 Consensus size: 15 179664 ATCACATGGA 179674 ATTGTATTATATGAT 1 ATTGTATTATATGAT * 179689 ATTGTAATATTATATAAT 1 ATTG---TATTATATGAT * 179707 ATTGTATTATACGAT 1 ATTGTATTATATGAT * 179722 ATTGTATGATATGAT 1 ATTGTATTATATGAT 179737 ATTGGT-TTATATGAT 1 ATT-GTATTATATGAT * 179752 A-TGTTATCATATCACATGAA 1 ATTG-TAT--TAT---ATGAT 179772 ATTGTATTATATGAT 1 ATTGTATTATATGAT * 179787 ATTGTAATATAT 1 ATTGTATTATAT 179799 TTTATTGTGT Statistics Matches: 89, Mismatches: 9, Indels: 24 0.73 0.07 0.20 Matches are distributed among these distances: 13 1 0.01 14 2 0.02 15 54 0.61 16 2 0.02 17 3 0.03 18 17 0.19 20 8 0.09 21 2 0.02 ACGTcount: A:0.36, C:0.03, G:0.13, T:0.48 Consensus pattern (15 bp): ATTGTATTATATGAT Found at i:179701 original size:18 final size:18 Alignment explanation

Indices: 179678--179712 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 179668 CATGGAATTG * 179678 TATTATATGATATTGTAA 1 TATTATATAATATTGTAA 179696 TATTATATAATATTGTA 1 TATTATATAATATTGTA 179713 TTATACGATA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51 Consensus pattern (18 bp): TATTATATAATATTGTAA Found at i:179713 original size:98 final size:98 Alignment explanation

Indices: 179590--179796 Score: 294 Period size: 98 Copynumber: 2.1 Consensus size: 98 179580 CTATGATACA * 179590 ATATTGT-ATATTCTATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTCAGA-AA 1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTT-AGATAA * 179653 TATAG-AATAATATCACATGGAATTGTATTATATG 65 TAT-GTAATAATATCACATGAAATTGTATTATATG * * * * * 179687 ATATTGTAATATTATATAATATTGTATTATACGATATTGTATGATATGATATTGGTTTATATGAT 1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTAGATAAT * * 179752 ATGTTATCATATCACATGAAATTGTATTATATG 66 ATGTAATAATATCACATGAAATTGTATTATATG 179785 ATATTGTAATAT 1 ATATTGTAATAT 179797 ATTTTATTGT Statistics Matches: 98, Mismatches: 9, Indels: 5 0.88 0.08 0.04 Matches are distributed among these distances: 97 10 0.10 98 88 0.90 ACGTcount: A:0.38, C:0.05, G:0.13, T:0.45 Consensus pattern (98 bp): ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTAGATAAT ATGTAATAATATCACATGAAATTGTATTATATG Found at i:179806 original size:30 final size:30 Alignment explanation

Indices: 179674--179816 Score: 103 Period size: 30 Copynumber: 4.5 Consensus size: 30 179664 ATCACATGGA * 179674 ATTGTATTATATGATATTGTAATATTATATAAT 1 ATTGTATTATATGATATTGT-A-A-TATATGAT * 179707 ATTGTATTATACGATATTGT-ATGATATGAT 1 ATTGTATTATATGATATTGTAAT-ATATGAT * 179737 ATTGGT-TTATATGATA-TGTTATCATATCACATGAA 1 ATT-GTATTATATGATATTG-TA--ATAT---ATGAT ** 179772 ATTGTATTATATGATATTGTAATATATTTT 1 ATTGTATTATATGATATTGTAATATATGAT * * 179802 ATTGTGTCATATGAT 1 ATTGTATTATATGAT 179817 GCAATATGTA Statistics Matches: 90, Mismatches: 9, Indels: 25 0.73 0.07 0.20 Matches are distributed among these distances: 29 3 0.03 30 35 0.39 31 2 0.02 32 2 0.02 33 25 0.28 34 2 0.02 35 19 0.21 36 2 0.02 ACGTcount: A:0.34, C:0.03, G:0.13, T:0.49 Consensus pattern (30 bp): ATTGTATTATATGATATTGTAATATATGAT Found at i:180046 original size:13 final size:13 Alignment explanation

Indices: 180028--180052 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 180018 TGATGTATTA 180028 TGTAATATGATAT 1 TGTAATATGATAT 180041 TGTAATATGATA 1 TGTAATATGATA 180053 CTATATTGTA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44 Consensus pattern (13 bp): TGTAATATGATAT Found at i:181098 original size:20 final size:20 Alignment explanation

Indices: 181073--181125 Score: 70 Period size: 20 Copynumber: 2.6 Consensus size: 20 181063 ACATGATTCC * 181073 TATGATATAATATTGTATGA 1 TATGATATAATATTGTATAA * * 181093 TATGATATACTATTGTTTAA 1 TATGATATAATATTGTATAA * 181113 TATGATGTAATAT 1 TATGATATAATAT 181126 CATGTTATAT Statistics Matches: 28, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 28 1.00 ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47 Consensus pattern (20 bp): TATGATATAATATTGTATAA Found at i:181345 original size:16 final size:16 Alignment explanation

Indices: 181324--181361 Score: 58 Period size: 16 Copynumber: 2.4 Consensus size: 16 181314 TAGTAATCAC * 181324 TCTGTCCGTCCGTCCT 1 TCTGTCCGTCCGTCCG * 181340 TCTGTCGGTCCGTCCG 1 TCTGTCCGTCCGTCCG 181356 TCTGTC 1 TCTGTC 181362 ACTCTTCCGT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 16 20 1.00 ACGTcount: A:0.00, C:0.39, G:0.24, T:0.37 Consensus pattern (16 bp): TCTGTCCGTCCGTCCG Found at i:181581 original size:31 final size:31 Alignment explanation

Indices: 181541--181607 Score: 127 Period size: 31 Copynumber: 2.2 Consensus size: 31 181531 ACTATGCATA 181541 AGAA-GAATGGGCAAAGAGAGATAACTGCTG 1 AGAATGAATGGGCAAAGAGAGATAACTGCTG 181571 AGAATGAATGGGCAAAGAGAGATAACTGCTG 1 AGAATGAATGGGCAAAGAGAGATAACTGCTG 181602 AGAATG 1 AGAATG 181608 TTACCATTGT Statistics Matches: 36, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 30 4 0.11 31 32 0.89 ACGTcount: A:0.43, C:0.09, G:0.33, T:0.15 Consensus pattern (31 bp): AGAATGAATGGGCAAAGAGAGATAACTGCTG Found at i:182517 original size:50 final size:51 Alignment explanation

Indices: 182463--182581 Score: 145 Period size: 50 Copynumber: 2.4 Consensus size: 51 182453 ATGATACAAT * * * 182463 ATTGTAAAATATTATATTGGTTT-CTATAATA-TAGTATAATATCACATGAA 1 ATTGTATAATATAATATTGGTTTAATATAATATTAGT-TAATATCACATGAA * * * * 182513 ATTGTATAATATGATATT-GTTTAATATGATATTGGTTTATATCACATGAA 1 ATTGTATAATATAATATTGGTTTAATATAATATTAGTTAATATCACATGAA 182563 ATTGTATAATATAATATTG 1 ATTGTATAATATAATATTG 182582 AAATTTATAT Statistics Matches: 59, Mismatches: 7, Indels: 5 0.83 0.10 0.07 Matches are distributed among these distances: 49 4 0.07 50 52 0.88 51 3 0.05 ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45 Consensus pattern (51 bp): ATTGTATAATATAATATTGGTTTAATATAATATTAGTTAATATCACATGAA Found at i:182554 original size:15 final size:15 Alignment explanation

Indices: 182508--182551 Score: 61 Period size: 15 Copynumber: 2.9 Consensus size: 15 182498 ATAATATCAC * * 182508 ATGAAATTGTATAAT 1 ATGATATTGTTTAAT 182523 ATGATATTGTTTAAT 1 ATGATATTGTTTAAT 182538 ATGATATTGGTTTA 1 ATGATATT-GTTTA 182552 TATCACATGA Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 15 21 0.81 16 5 0.19 ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48 Consensus pattern (15 bp): ATGATATTGTTTAAT Found at i:182752 original size:15 final size:15 Alignment explanation

Indices: 182732--182763 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 182722 ATGCATCAAA 182732 ATACAATAAAGTATC 1 ATACAATAAAGTATC * 182747 ATACAATACAGTATC 1 ATACAATAAAGTATC 182762 AT 1 AT 182764 TCTATATTAT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28 Consensus pattern (15 bp): ATACAATAAAGTATC Found at i:182852 original size:20 final size:20 Alignment explanation

Indices: 182822--182877 Score: 69 Period size: 20 Copynumber: 2.8 Consensus size: 20 182812 ATGTACATTG * 182822 TAATATGATATTGCATCATA 1 TAATATGATATTGCATAATA * 182842 TAATACT-ATATTGTATAATA 1 TAATA-TGATATTGCATAATA * 182862 TATTATGATATTGCAT 1 TAATATGATATTGCAT 182878 GATGTGATCA Statistics Matches: 30, Mismatches: 4, Indels: 4 0.79 0.11 0.11 Matches are distributed among these distances: 19 1 0.03 20 28 0.93 21 1 0.03 ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45 Consensus pattern (20 bp): TAATATGATATTGCATAATA Found at i:193730 original size:36 final size:37 Alignment explanation

Indices: 193658--193731 Score: 123 Period size: 36 Copynumber: 2.0 Consensus size: 37 193648 ATAAGTCGGA * 193658 ATGTTAATCCCCCCGCTGCAGTGTGCAGTAATCTGTT 1 ATGTTAATCCCCCCGCTGCAGTGTGCAGTAAGCTGTT * 193695 ATGTTAAT-CCCCCGCTGCAGTGTGCAGTAGGCTGTT 1 ATGTTAATCCCCCCGCTGCAGTGTGCAGTAAGCTGTT 193731 A 1 A 193732 AGCAGTCTAG Statistics Matches: 35, Mismatches: 2, Indels: 1 0.92 0.05 0.03 Matches are distributed among these distances: 36 27 0.77 37 8 0.23 ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31 Consensus pattern (37 bp): ATGTTAATCCCCCCGCTGCAGTGTGCAGTAAGCTGTT Found at i:194695 original size:1 final size:1 Alignment explanation

Indices: 194689--194713 Score: 50 Period size: 1 Copynumber: 25.0 Consensus size: 1 194679 AACAGAGAAC 194689 GGGGGGGGGGGGGGGGGGGGGGGGG 1 GGGGGGGGGGGGGGGGGGGGGGGGG 194714 NAGTTTACCT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 24 1.00 ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00 Consensus pattern (1 bp): G Found at i:194893 original size:80 final size:80 Alignment explanation

Indices: 194804--195046 Score: 405 Period size: 80 Copynumber: 3.0 Consensus size: 80 194794 TTCATCACCT 194804 TTGTAAGGAGTTTATAAGTACAACTGTTACCAGAATGTATAGTTTATTTTTACCATACCTTAAAC 1 TTGTAAGGAGTTTATAAGTACAACTGTTACCAGAATGTATAGTTTATTTTTACCATACCTTAAAC 194869 TGTAAATTAGCATAA 66 TGTAAATTAGCATAA ** 194884 TTGTAAGGAGTTTATAAGTACAACTGTTACCAGAATGTATAGTTTATTTTTACCATACCCCAAAC 1 TTGTAAGGAGTTTATAAGTACAACTGTTACCAGAATGTATAGTTTATTTTTACCATACCTTAAAC 194949 TGTAAATTAGCATAA 66 TGTAAATTAGCATAA * * * * * 194964 TTGTAAGGAGTTTATAAATACAACTGTTATACCAGAATGTATAGTTTATTCTAATCATATCTTAA 1 TTGTAAGGAGTTTATAAGTACAACTG-T-TACCAGAATGTATAGTTTATTTTTACCATACCTTAA 195029 ACTGTAAATTAGCATAA 64 ACTGTAAATTAGCATAA 195046 T 1 T 195047 CTCTATAAAT Statistics Matches: 152, Mismatches: 9, Indels: 2 0.93 0.06 0.01 Matches are distributed among these distances: 80 103 0.68 81 1 0.01 82 48 0.32 ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37 Consensus pattern (80 bp): TTGTAAGGAGTTTATAAGTACAACTGTTACCAGAATGTATAGTTTATTTTTACCATACCTTAAAC TGTAAATTAGCATAA Found at i:199282 original size:16 final size:18 Alignment explanation

Indices: 199263--199295 Score: 52 Period size: 17 Copynumber: 1.9 Consensus size: 18 199253 AAAATTAATG 199263 TAAA-TTAATG-TATCAT 1 TAAATTTAATGTTATCAT 199279 TAAATTTAATGTTATCA 1 TAAATTTAATGTTATCA 199296 ACTACATCTT Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 4 0.27 17 6 0.40 18 5 0.33 ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45 Consensus pattern (18 bp): TAAATTTAATGTTATCAT Found at i:204188 original size:31 final size:31 Alignment explanation

Indices: 204153--204326 Score: 177 Period size: 31 Copynumber: 5.1 Consensus size: 31 204143 GTGTACACAG * 204153 GTACATAACAATAAGTCTTACCCCCAGGTGT 1 GTACATAACAGTAAGTCTTACCCCCAGGTGT 204184 GTACATAACAGTAAGTCTTACCCCCAGGTGT 1 GTACATAACAGTAAGTCTTACCCCCAGGTGT * 204215 GTAAACAGGTACATTACGGTAAGTCTTACCCCCAGGTGTGT 1 GT--ACA--T--A--ACAGTAAGTCTTACCCCCA-G-GTGT 204256 ACACAGGTACATAACAGTAAGTCTTACCCCCAGGTGT 1 ------GTACATAACAGTAAGTCTTACCCCCAGGTGT * 204293 GTATATAACAGTAAGTCTTACCCCCAGGTGT 1 GTACATAACAGTAAGTCTTACCCCCAGGTGT 204324 GTA 1 GTA 204327 AACAGGTACA Statistics Matches: 123, Mismatches: 4, Indels: 32 0.77 0.03 0.20 Matches are distributed among these distances: 31 65 0.53 33 3 0.02 35 1 0.01 37 5 0.04 38 1 0.01 39 36 0.29 40 1 0.01 41 5 0.04 43 1 0.01 45 3 0.02 47 2 0.02 ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26 Consensus pattern (31 bp): GTACATAACAGTAAGTCTTACCCCCAGGTGT Found at i:204188 original size:39 final size:39 Alignment explanation

Indices: 204142--204493 Score: 337 Period size: 39 Copynumber: 9.4 Consensus size: 39 204132 TTACCCCTGA * 204142 TGTGTACACAGGTACATAACAATAAGTCTTACCCCCA-G 1 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGG 204180 -GTGT------GTACATAACAGTAAGTCTTACCCCCAGG 1 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGG * * * 204212 TGTGTAAACAGGTACATTACGGTAAGTCTTACCCCCAGG 1 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGG 204251 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGG 1 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGG 204290 TGTGT----A--T--ATAACAGTAAGTCTTACCCCCAGG 1 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGG * * 204321 TGTGTAAACAGGTACATAACGGTAAGTCTTACCCCCAGG 1 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGG * * * * 204360 TGTGTAAACAGGTACAAAACAGTAAAAGACTTA-CCCCAGA 1 TGTGTACACAGGTACATAACAGT--AAGTCTTACCCCCAGG * * * * * * * * 204400 TATGTACATAGGAACAAAAAAGTAAAATTTTTA-CACCAGG 1 TGTGTACACAGGTACATAACAGT--AAGTCTTACCCCCAGG * * 204440 TGTGTGCACAGGTACATAACAGTAAGTCTTA-CCACAGG 1 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGG 204478 TGTGTCTACACAGGTA 1 TGTG--TACACAGGTA 204494 GATCATAGAA Statistics Matches: 262, Mismatches: 32, Indels: 38 0.79 0.10 0.11 Matches are distributed among these distances: 31 54 0.21 32 1 0.00 33 5 0.02 35 2 0.01 37 5 0.02 38 15 0.06 39 111 0.42 40 62 0.24 41 7 0.03 ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24 Consensus pattern (39 bp): TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGG Found at i:204243 original size:70 final size:73 Alignment explanation

Indices: 204142--204384 Score: 265 Period size: 70 Copynumber: 3.3 Consensus size: 73 204132 TTACCCCTGA * * 204142 TGTGTACACAGGTACATAACAATAAGTCTTACCCCCA-G-GTGT-GTACATAACAGTAAGTCTTA 1 TGTGTAAACAGGTACATAACAGTAAGTCTTACCCCCAGGTGTGTAGTACATAACAGTAAGTCTTA 204204 CCCCCAGG 66 CCCCCAGG * * 204212 TGTGTAAACAGGTACATTACGGTAAGTCTTACCCCCAGGTGTGTACACAGGTACATAACAGTAAG 1 TGTGTAAACAGGTACATAACAGTAAGTCTTACCCCCAGGTGTGT----A-GTACATAACAGTAAG 204277 TCTTACCCCCAGG 61 TCTTACCCCCAGG * 204290 TGTGT----A--T--ATAACAGTAAGTCTTACCCCCAGGTGTGTAAACAGGTACATAACGGTAAG 1 TGTGTAAACAGGTACATAACAGTAAGTCTTACCCCCAGGTGTGT----A-GTACATAACAGTAAG 204347 TCTTACCCCCAGG 61 TCTTACCCCCAGG * 204360 TGTGTAAACAGGTACAAAACAGTAA 1 TGTGTAAACAGGTACATAACAGTAA 204385 AAGACTTACC Statistics Matches: 148, Mismatches: 9, Indels: 24 0.82 0.05 0.13 Matches are distributed among these distances: 70 97 0.66 71 1 0.01 72 5 0.03 74 2 0.01 76 1 0.01 78 42 0.28 ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24 Consensus pattern (73 bp): TGTGTAAACAGGTACATAACAGTAAGTCTTACCCCCAGGTGTGTAGTACATAACAGTAAGTCTTA CCCCCAGG Found at i:204278 original size:109 final size:109 Alignment explanation

Indices: 204142--204384 Score: 441 Period size: 109 Copynumber: 2.2 Consensus size: 109 204132 TTACCCCTGA * 204142 TGTGTACACAGGTACATAACAATAAGTCTTACCCCCAGGTGTGTACATAACAGTAAGTCTTACCC 1 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGGTGTGTACATAACAGTAAGTCTTACCC * 204207 CCAGGTGTGTAAACAGGTACATTACGGTAAGTCTTACCCCCAGG 66 CCAGGTGTGTAAACAGGTACATAACGGTAAGTCTTACCCCCAGG * 204251 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGGTGTGTATATAACAGTAAGTCTTACCC 1 TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGGTGTGTACATAACAGTAAGTCTTACCC 204316 CCAGGTGTGTAAACAGGTACATAACGGTAAGTCTTACCCCCAGG 66 CCAGGTGTGTAAACAGGTACATAACGGTAAGTCTTACCCCCAGG * * 204360 TGTGTAAACAGGTACAAAACAGTAA 1 TGTGTACACAGGTACATAACAGTAA 204385 AAGACTTACC Statistics Matches: 129, Mismatches: 5, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 109 129 1.00 ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24 Consensus pattern (109 bp): TGTGTACACAGGTACATAACAGTAAGTCTTACCCCCAGGTGTGTACATAACAGTAAGTCTTACCC CCAGGTGTGTAAACAGGTACATAACGGTAAGTCTTACCCCCAGG Done.