Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr08 129432109 

Parameters: 2 7 7 80 10 50 1000

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

Length: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 350 characters in sequence are not A, C, G, or T


File 360 of 425

Found at i:111225370 original size:46 final size:46

Alignment explanation

Indices: 111225313--111225779 Score: 522 Period size: 46 Copynumber: 10.0 Consensus size: 46 111225303 AGTGTGCTCT * * 111225313 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * * * * 111225359 CTGATAAGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC 1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * * * 111225405 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC 1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * * 111225451 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * ** * * 111225497 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCACATGGC 1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCA-A---C * 111225547 AGCGTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC 1 --C-TGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * ** * 111225596 ATGACAAAAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGAC-ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC ** * * * * 111225643 AC-GACGGGAAATAAATAAGACCATGGTTGAAAGAGACCATGGCAGC 1 -CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * * 111225689 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * ** * * * 111225735 ATGACAAAAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA 1 CTGAC-ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCA 111225780 TCATGTCAAA Statistics Matches: 368, Mismatches: 42, Indels: 21 0.85 0.10 0.05 Matches are distributed among these distances: 46 251 0.68 47 74 0.20 49 1 0.00 50 1 0.00 52 1 0.00 53 40 0.11 ACGTcount: A:0.40, C:0.15, G:0.24, T:0.20 Consensus pattern (46 bp): CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC Found at i:111225618 original size:47 final size:47 Alignment explanation

Indices: 111225558--111225806 Score: 290 Period size: 47 Copynumber: 5.4 Consensus size: 47 111225548 GCGTGACATG 111225558 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAA 1 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAA ** * *** 111225605 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACACGAC-GGG 1 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAA * * * * ** 111225651 AAATAAATAAGACCATGGTTGAAAGAGACCATGGCAGCGTGAC-ATG 1 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAA 111225697 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAA 1 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAA * * * * * * 111225744 AAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATGTC--AA 1 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAA * * 111225789 AGATAAATAAGACCATGG 1 AAATGAATAAGACCATGG 111225807 ATGGGAGACG Statistics Matches: 170, Mismatches: 31, Indels: 4 0.83 0.15 0.02 Matches are distributed among these distances: 45 16 0.09 46 76 0.45 47 78 0.46 ACGTcount: A:0.44, C:0.15, G:0.22, T:0.18 Consensus pattern (47 bp): AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAA Found at i:111225735 original size:238 final size:239 Alignment explanation

Indices: 111225318--111225784 Score: 670 Period size: 238 Copynumber: 2.0 Consensus size: 239 111225308 GCTCTCTGAT ** * * * 111225318 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATAAGAAATGTGTAAGACCAT 1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAAAAAAAATGTGTAAGACCAT * * * *** * 111225383 GGTTGAAAGATACCATGGCAGCCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGC 66 GGTTGAAAGATACCATGGCAACCTGACAGGAAATAAATAAGACCATGGTTGAAAGAGACCATGGC * ** *** 111225448 AGCCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC-GGGAAATAAA 131 AGCCTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAAAAATAAA * * 111225512 TAAGACCATGGTTGAAAGATACCATGGCA-CATGGCAGCGTGAC 196 TAAGACCATAGTTGAAAGACACCATGGCATCATGGCAGCGTGAC 111225555 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAAAAATGTGTAAGACCA 1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGA-AAAAAAATGTGTAAGACCA * 111225620 TGGTTGAAAGATACCATGGCAACAC-GACGGGAAATAAATAAGACCATGGTTGAAAGAGACCATG 65 TGGTTGAAAGATACCATGGCAAC-CTGACAGGAAATAAATAAGACCATGGTTGAAAGAGACCATG * * 111225684 GCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAAAAATG 129 GCAGCCTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAAAAATA * * 111225749 AGTAAGACCATAGTTGAAAGACACTATGGCATCATG 194 AATAAGACCATAGTTGAAAGACACCATGGCATCATG 111225785 TCAAAGATAA Statistics Matches: 201, Mismatches: 25, Indels: 5 0.87 0.11 0.02 Matches are distributed among these distances: 237 42 0.21 238 123 0.61 239 32 0.16 240 4 0.02 ACGTcount: A:0.40, C:0.15, G:0.24, T:0.20 Consensus pattern (239 bp): ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAAAAAAAATGTGTAAGACCAT GGTTGAAAGATACCATGGCAACCTGACAGGAAATAAATAAGACCATGGTTGAAAGAGACCATGGC AGCCTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAAAAAAATAAA TAAGACCATAGTTGAAAGACACCATGGCATCATGGCAGCGTGAC Found at i:111237936 original size:25 final size:25 Alignment explanation

Indices: 111237902--111237952 Score: 102 Period size: 25 Copynumber: 2.0 Consensus size: 25 111237892 AAACAGAAAG 111237902 AAGAACAAATTAAGACATTCAATGC 1 AAGAACAAATTAAGACATTCAATGC 111237927 AAGAACAAATTAAGACATTCAATGC 1 AAGAACAAATTAAGACATTCAATGC 111237952 A 1 A 111237953 CTTGTTGATT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.53, C:0.16, G:0.12, T:0.20 Consensus pattern (25 bp): AAGAACAAATTAAGACATTCAATGC Found at i:111238923 original size:2 final size:2 Alignment explanation

Indices: 111238916--111238940 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 111238906 TCAAGTCTCC 111238916 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 111238941 CATAATTATC 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:111242601 original size:7 final size:7 Alignment explanation

Indices: 111242580--111242616 Score: 56 Period size: 7 Copynumber: 5.3 Consensus size: 7 111242570 TACTCTTATC * 111242580 TGATCAG 1 TGATAAG * 111242587 TGACAAG 1 TGATAAG 111242594 TGATAAG 1 TGATAAG 111242601 TGATAAG 1 TGATAAG 111242608 TGATAAG 1 TGATAAG 111242615 TG 1 TG 111242617 GTAGCTTTAG Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 7 27 1.00 ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27 Consensus pattern (7 bp): TGATAAG Found at i:111242651 original size:58 final size:57 Alignment explanation

Indices: 111242535--111242657 Score: 210 Period size: 58 Copynumber: 2.1 Consensus size: 57 111242525 ACTTCTGATC * 111242535 AGTGATAAGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA 1 AGTGATAAGTGACAAATGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA * * 111242592 AGTGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA 1 AGTGATAAGTGACAAATGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA 111242650 AGTGATAA 1 AGTGATAA 111242658 ATGTGATCAG Statistics Matches: 62, Mismatches: 3, Indels: 1 0.94 0.05 0.02 Matches are distributed among these distances: 57 28 0.45 58 34 0.55 ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30 Consensus pattern (57 bp): AGTGATAAGTGACAAATGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA Found at i:111255044 original size:40 final size:39 Alignment explanation

Indices: 111254879--111255062 Score: 138 Period size: 40 Copynumber: 4.6 Consensus size: 39 111254869 AAATTGAATG * * * 111254879 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T 1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT * * * * * * 111254919 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T * * * * * 111254959 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT * 111254999 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT * * * 111255038 GATATCCGGGTTAAGTCCCGTAGGC 1 -ATATCCGGGCTAAGACCCGAAGGC 111255063 CTTGGTGCGG Statistics Matches: 113, Mismatches: 26, Indels: 10 0.76 0.17 0.07 Matches are distributed among these distances: 37 4 0.04 38 2 0.02 39 3 0.03 40 104 0.92 ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT Found at i:111255045 original size:80 final size:80 Alignment explanation

Indices: 111254923--111255071 Score: 183 Period size: 80 Copynumber: 1.9 Consensus size: 80 111254913 GAAATTATAA * * * * 111254923 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCATTCG 1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCG 111254988 TGCGAGTCATTCTAT 66 TGCGAGTCATTCTAT * * * * * * * 111255003 CCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGCCTTG 1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGCATTC 111255067 GTGCG 65 GTGCG 111255072 GGTTACCATA Statistics Matches: 57, Mismatches: 11, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 79 1 0.02 80 56 0.98 ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23 Consensus pattern (80 bp): CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCG TGCGAGTCATTCTAT Found at i:111255087 original size:80 final size:81 Alignment explanation

Indices: 111254919--111255107 Score: 177 Period size: 80 Copynumber: 2.4 Consensus size: 81 111254909 GCTGGAAATT * * * * 111254919 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA * 111254984 TTCGTGCGAGTCATTC 66 TTCGTGCGAGTCATCC * * * * * * 111255000 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC * * * * 111255063 CTTGGTGCGGGTTA-CC 65 ATTCGTGCGAGTCATCC * * * * 111255079 ATAACCGGGGTATGTCCCGAAGGCGATTG 1 ATAACCGGGCTAAGACCCGAAGGCAATTG 111255108 ATCGAGTAGC Statistics Matches: 85, Mismatches: 21, Indels: 5 0.77 0.19 0.05 Matches are distributed among these distances: 79 2 0.02 80 83 0.98 ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23 Consensus pattern (81 bp): ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA TTCGTGCGAGTCATCC Found at i:111269032 original size:16 final size:17 Alignment explanation

Indices: 111269013--111269053 Score: 52 Period size: 15 Copynumber: 2.6 Consensus size: 17 111269003 TTTCAAAATT 111269013 TAAAAAATATAT-AAAC 1 TAAAAAATATATCAAAC * 111269029 T-AAAAATA-ATCAAAT 1 TAAAAAATATATCAAAC 111269044 TAAAAAATAT 1 TAAAAAATAT 111269054 GGACTAAATT Statistics Matches: 21, Mismatches: 1, Indels: 5 0.78 0.04 0.19 Matches are distributed among these distances: 14 2 0.10 15 11 0.52 16 8 0.38 ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27 Consensus pattern (17 bp): TAAAAAATATATCAAAC Found at i:111291250 original size:16 final size:15 Alignment explanation

Indices: 111291208--111291251 Score: 52 Period size: 16 Copynumber: 2.8 Consensus size: 15 111291198 TATGAACCGG * 111291208 CAAAAGCCGAAATGC 1 CAAAAGCCAAAATGC * 111291223 CAAAATGTCAAAATGC 1 CAAAA-GCCAAAATGC 111291239 CGAAAAGCCAAAA 1 C-AAAAGCCAAAA 111291252 GTTTGGCTAC Statistics Matches: 24, Mismatches: 3, Indels: 3 0.80 0.10 0.10 Matches are distributed among these distances: 15 5 0.21 16 15 0.62 17 4 0.17 ACGTcount: A:0.52, C:0.23, G:0.16, T:0.09 Consensus pattern (15 bp): CAAAAGCCAAAATGC Found at i:111291551 original size:29 final size:29 Alignment explanation

Indices: 111291475--111291585 Score: 91 Period size: 29 Copynumber: 3.9 Consensus size: 29 111291465 TGATTGTGAC * * * * 111291475 TGGGCCGAACGGGCCATATAGATGTGATT 1 TGGGCCTAATGGGCCATATACAGGTGATT ** 111291504 TGGGCCTAATGGGAAATATACAGGTGATT 1 TGGGCCTAATGGGCCATATACAGGTGATT * *** 111291533 TGGGCCTAGTGGGCCATATGA-ATACGA-T 1 TGGGCCTAATGGGCCATAT-ACAGGTGATT * * 111291561 TGGGCTTAATGGGCCAGATACAGGT 1 TGGGCCTAATGGGCCATATACAGGT 111291586 ATATGAATTT Statistics Matches: 62, Mismatches: 18, Indels: 5 0.73 0.21 0.06 Matches are distributed among these distances: 27 1 0.02 28 18 0.29 29 42 0.68 30 1 0.02 ACGTcount: A:0.26, C:0.15, G:0.33, T:0.25 Consensus pattern (29 bp): TGGGCCTAATGGGCCATATACAGGTGATT Found at i:111295054 original size:5 final size:6 Alignment explanation

Indices: 111295040--111295073 Score: 50 Period size: 6 Copynumber: 5.3 Consensus size: 6 111295030 TAATTTTCCC 111295040 TTTTCT TTTTCT TTTTCT TTTTCCT TCTTTCT TT 1 TTTTCT TTTTCT TTTTCT TTTT-CT T-TTTCT TT 111295074 CCCTGCTAAT Statistics Matches: 26, Mismatches: 0, Indels: 4 0.87 0.00 0.13 Matches are distributed among these distances: 6 17 0.65 7 6 0.23 8 3 0.12 ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79 Consensus pattern (6 bp): TTTTCT Found at i:111295055 original size:12 final size:13 Alignment explanation

Indices: 111295033--111295073 Score: 57 Period size: 12 Copynumber: 3.2 Consensus size: 13 111295023 AAAACCCTAA * 111295033 TTTTCCCTTTTCT 1 TTTTCCTTTTTCT 111295046 TTTT-CTTTTTCT 1 TTTTCCTTTTTCT 111295058 TTTTCCTTCTTTCT 1 TTTTCCTT-TTTCT 111295072 TT 1 TT 111295074 CCCTGCTAAT Statistics Matches: 25, Mismatches: 1, Indels: 3 0.86 0.03 0.10 Matches are distributed among these distances: 12 11 0.44 13 7 0.28 14 7 0.28 ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76 Consensus pattern (13 bp): TTTTCCTTTTTCT Found at i:111295148 original size:15 final size:15 Alignment explanation

Indices: 111295130--111295158 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 111295120 TTTATTCTTT 111295130 TATTATATTATTAAC 1 TATTATATTATTAAC 111295145 TATTATATTATTAA 1 TATTATATTATTAA 111295159 TTTCTTAAAT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55 Consensus pattern (15 bp): TATTATATTATTAAC Found at i:111295563 original size:42 final size:42 Alignment explanation

Indices: 111295516--111295599 Score: 168 Period size: 42 Copynumber: 2.0 Consensus size: 42 111295506 TATAATCCAT 111295516 TGGGATCCTGGATTTGTCACAACATCAAGCACTTGTTGAAGA 1 TGGGATCCTGGATTTGTCACAACATCAAGCACTTGTTGAAGA 111295558 TGGGATCCTGGATTTGTCACAACATCAAGCACTTGTTGAAGA 1 TGGGATCCTGGATTTGTCACAACATCAAGCACTTGTTGAAGA 111295600 AAATCCCAAT Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 42 42 1.00 ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29 Consensus pattern (42 bp): TGGGATCCTGGATTTGTCACAACATCAAGCACTTGTTGAAGA Found at i:111303344 original size:23 final size:23 Alignment explanation

Indices: 111303315--111303364 Score: 100 Period size: 23 Copynumber: 2.2 Consensus size: 23 111303305 TACGTTTGTT 111303315 TTTATCAAAATTGAAGTTGCAGG 1 TTTATCAAAATTGAAGTTGCAGG 111303338 TTTATCAAAATTGAAGTTGCAGG 1 TTTATCAAAATTGAAGTTGCAGG 111303361 TTTA 1 TTTA 111303365 CTTACCGAAA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 27 1.00 ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38 Consensus pattern (23 bp): TTTATCAAAATTGAAGTTGCAGG Found at i:111303851 original size:26 final size:26 Alignment explanation

Indices: 111303822--111303872 Score: 66 Period size: 26 Copynumber: 2.0 Consensus size: 26 111303812 ACCAGCACAC * * 111303822 CAATATCGCAGCAAAGCTGCCAGTAA 1 CAATAACGCAACAAAGCTGCCAGTAA ** 111303848 CAATAACGCAACGTAGCTGCCAGTA 1 CAATAACGCAACAAAGCTGCCAGTA 111303873 GCAGTAAGTG Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 26 21 1.00 ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16 Consensus pattern (26 bp): CAATAACGCAACAAAGCTGCCAGTAA Found at i:111309447 original size:18 final size:19 Alignment explanation

Indices: 111309424--111309462 Score: 62 Period size: 20 Copynumber: 2.1 Consensus size: 19 111309414 ATATATTCAC 111309424 ACATTTTCA-CAATTCAAT 1 ACATTTTCATCAATTCAAT 111309442 ACATTTTCATTCAATTCAAT 1 ACATTTTCA-TCAATTCAAT 111309462 A 1 A 111309463 TTAATACTCA Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 18 9 0.47 20 10 0.53 ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41 Consensus pattern (19 bp): ACATTTTCATCAATTCAAT Found at i:111310128 original size:25 final size:24 Alignment explanation

Indices: 111310102--111310181 Score: 81 Period size: 25 Copynumber: 3.2 Consensus size: 24 111310092 AATCCTAACT * 111310102 TTTTCTCCTTTCTTTCTCTTTTTC 1 TTTTCTCCTTTCCTTCTCTTTTTC * * 111310126 TTTTCTTTCTTTCCTTCTCTGTTTC 1 TTTTC-TCCTTTCCTTCTCTTTTTC * * 111310151 GTTTCTGCTTTCGCTT-TCTTTTTC 1 TTTTCTCCTTTC-CTTCTCTTTTTC 111310175 TATTTCT 1 T-TTTCT 111310182 ATTTATTTTT Statistics Matches: 46, Mismatches: 7, Indels: 5 0.79 0.12 0.09 Matches are distributed among these distances: 24 18 0.39 25 28 0.61 ACGTcount: A:0.01, C:0.26, G:0.05, T:0.68 Consensus pattern (24 bp): TTTTCTCCTTTCCTTCTCTTTTTC Found at i:111310132 original size:17 final size:18 Alignment explanation

Indices: 111310100--111310135 Score: 56 Period size: 17 Copynumber: 2.0 Consensus size: 18 111310090 AAAATCCTAA 111310100 CTTTTTCTCCTTTCTTTCT 1 CTTTTTCT-CTTTCTTTCT 111310119 CTTTTTCT-TTTCTTTCT 1 CTTTTTCTCTTTCTTTCT 111310136 TTCCTTCTCT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 17 9 0.53 19 8 0.47 ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72 Consensus pattern (18 bp): CTTTTTCTCTTTCTTTCT Found at i:111310155 original size:21 final size:21 Alignment explanation

Indices: 111310109--111310156 Score: 55 Period size: 21 Copynumber: 2.3 Consensus size: 21 111310099 ACTTTTTCTC * 111310109 CTTTCTTTCTCTTTTTCTTTT 1 CTTTCTTTCTCTTTCTCTTTT 111310130 CTTTCTTTC-C-TTCTCTGTTT 1 CTTTCTTTCTCTTTCTCT-TTT 111310150 CGTTTCT 1 C-TTTCT 111310157 GCTTTCGCTT Statistics Matches: 24, Mismatches: 1, Indels: 4 0.83 0.03 0.14 Matches are distributed among these distances: 19 5 0.21 20 5 0.21 21 14 0.58 ACGTcount: A:0.00, C:0.27, G:0.04, T:0.69 Consensus pattern (21 bp): CTTTCTTTCTCTTTCTCTTTT Found at i:111310221 original size:5 final size:5 Alignment explanation

Indices: 111310211--111310235 Score: 50 Period size: 5 Copynumber: 5.0 Consensus size: 5 111310201 GTTTTATTAG 111310211 ATATA ATATA ATATA ATATA ATATA 1 ATATA ATATA ATATA ATATA ATATA 111310236 TATTGATATT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 20 1.00 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (5 bp): ATATA Found at i:111313009 original size:2 final size:2 Alignment explanation

Indices: 111313002--111313040 Score: 69 Period size: 2 Copynumber: 19.5 Consensus size: 2 111312992 TGCTTCAACA * 111313002 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 111313041 GAACAATACC Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49 Consensus pattern (2 bp): AT Found at i:111316110 original size:21 final size:19 Alignment explanation

Indices: 111316077--111316115 Score: 60 Period size: 21 Copynumber: 1.9 Consensus size: 19 111316067 AAAATCCTAG 111316077 CTTTTTCTTCTTTCTTTCT 1 CTTTTTCTTCTTTCTTTCT 111316096 CTTTTTCTTTTCTTTCTTTC 1 CTTTTTC--TTCTTTCTTTC 111316116 CTTCTCTGTT Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 19 7 0.39 21 11 0.61 ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74 Consensus pattern (19 bp): CTTTTTCTTCTTTCTTTCT Found at i:111316112 original size:25 final size:25 Alignment explanation

Indices: 111316079--111316127 Score: 73 Period size: 25 Copynumber: 2.0 Consensus size: 25 111316069 AATCCTAGCT * 111316079 TTTTCTTCTTTCTTTCTCT-TTTTC 1 TTTTCTTCTTTCCTTCTCTGTTTTC 111316103 TTTTCTTTCTTTCCTTCTCTGTTTT 1 TTTTC-TTCTTTCCTTCTCTGTTTT 111316128 ATTTCTACTT Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 24 5 0.23 25 13 0.59 26 4 0.18 ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73 Consensus pattern (25 bp): TTTTCTTCTTTCCTTCTCTGTTTTC Found at i:111316127 original size:21 final size:21 Alignment explanation

Indices: 111316084--111316133 Score: 57 Period size: 21 Copynumber: 2.4 Consensus size: 21 111316074 TAGCTTTTTC * 111316084 TTCTTTCTTTCTCTTTTTCTT 1 TTCTTTCTTTCTCTTTCTCTT * 111316105 TTCTTTCTTTC-CTTCTCTGTT 1 TTCTTTCTTTCTCTT-TCTCTT * 111316126 TTATTTCT 1 TTCTTTCT 111316134 ACTTTGGTTT Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 20 3 0.12 21 22 0.88 ACGTcount: A:0.02, C:0.24, G:0.02, T:0.72 Consensus pattern (21 bp): TTCTTTCTTTCTCTTTCTCTT Found at i:111316132 original size:25 final size:25 Alignment explanation

Indices: 111316080--111316133 Score: 67 Period size: 25 Copynumber: 2.2 Consensus size: 25 111316070 ATCCTAGCTT * * 111316080 TTTC-TTCTTTCTTTCTCTTTTTCT 1 TTTCTTTCTTTCCTTCTCTTTTTCA 111316104 TTTCTTTCTTTCCTTCTCTGTTTT-A 1 TTTCTTTCTTTCCTTCTCT-TTTTCA 111316129 TTTCT 1 TTTCT 111316134 ACTTTGGTTT Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 24 4 0.15 25 18 0.69 26 4 0.15 ACGTcount: A:0.02, C:0.24, G:0.02, T:0.72 Consensus pattern (25 bp): TTTCTTTCTTTCCTTCTCTTTTTCA Found at i:111316168 original size:19 final size:19 Alignment explanation

Indices: 111316146--111316183 Score: 51 Period size: 19 Copynumber: 2.0 Consensus size: 19 111316136 TTTGGTTTTC 111316146 TTTT-TCTATTTTATTTATT 1 TTTTCTCTATTTT-TTTATT * 111316165 TTTTCTTTATTTTTTTATT 1 TTTTCTCTATTTTTTTATT 111316184 ATATATAATA Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 19 10 0.59 20 7 0.41 ACGTcount: A:0.13, C:0.05, G:0.00, T:0.82 Consensus pattern (19 bp): TTTTCTCTATTTTTTTATT Found at i:111316196 original size:5 final size:5 Alignment explanation

Indices: 111316186--111316238 Score: 106 Period size: 5 Copynumber: 10.6 Consensus size: 5 111316176 TTTTTATTAT 111316186 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA 1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA 111316236 ATA 1 ATA 111316239 CTTATATGTT Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 48 1.00 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (5 bp): ATATA Found at i:111325649 original size:14 final size:14 Alignment explanation

Indices: 111325649--111325718 Score: 50 Period size: 14 Copynumber: 4.4 Consensus size: 14 111325639 TCTTAGATAT * 111325649 GATATGGAATCTTA 1 GATATGCAATCTTA 111325663 GATATGATACAATCTTA 1 GATATG---CAATCTTA * 111325680 GATATGATATGCAATATTA 1 G--AT-AT--GCAATCTTA 111325699 GATATGCAATCTTA 1 GATATGCAATCTTA 111325713 GATATG 1 GATATG 111325719 ATATGCAATC Statistics Matches: 45, Mismatches: 3, Indels: 16 0.70 0.05 0.25 Matches are distributed among these distances: 14 20 0.44 16 2 0.04 17 10 0.22 19 10 0.22 20 2 0.04 22 1 0.02 ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36 Consensus pattern (14 bp): GATATGCAATCTTA Found at i:111325660 original size:36 final size:34 Alignment explanation

Indices: 111325620--111325739 Score: 145 Period size: 36 Copynumber: 3.4 Consensus size: 34 111325610 ATGGAAATAT * 111325620 AATCTTTAAGGATATGCAATCTTAGATATGATATGG 1 AATCTTT-A-GATATGCAATCTTAGATATGATATGC 111325656 AATC-TTAGATATGATACAATCTTAGATATGATATGC 1 AATCTTTAGATATG---CAATCTTAGATATGATATGC * 111325692 AAT-ATTAGATATGCAATCTTAGATATGATATGC 1 AATCTTTAGATATGCAATCTTAGATATGATATGC * 111325725 AATCTTGAAGATATG 1 AATCTT-TAGATATG 111325740 ATCTTGTAAT Statistics Matches: 75, Mismatches: 3, Indels: 13 0.82 0.03 0.14 Matches are distributed among these distances: 33 29 0.39 34 2 0.03 35 9 0.12 36 35 0.47 ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36 Consensus pattern (34 bp): AATCTTTAGATATGCAATCTTAGATATGATATGC Found at i:111325668 original size:33 final size:33 Alignment explanation

Indices: 111325630--111325739 Score: 157 Period size: 33 Copynumber: 3.2 Consensus size: 33 111325620 AATCTTTAAG * 111325630 GATATGCAATCTTAGATATGATATGGAATCTTA 1 GATATGCAATCTTAGATATGATATGCAATCTTA * 111325663 GATATGATACAATCTTAGATATGATATGCAATATTA 1 GATATG---CAATCTTAGATATGATATGCAATCTTA 111325699 GATATGCAATCTTAGATATGATATGCAATCTTGAA 1 GATATGCAATCTTAGATATGATATGCAATCTT--A 111325734 GATATG 1 GATATG 111325740 ATCTTGTAAT Statistics Matches: 69, Mismatches: 3, Indels: 8 0.86 0.04 0.10 Matches are distributed among these distances: 33 31 0.45 35 7 0.10 36 31 0.45 ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35 Consensus pattern (33 bp): GATATGCAATCTTAGATATGATATGCAATCTTA Found at i:111325736 original size:21 final size:19 Alignment explanation

Indices: 111325630--111325741 Score: 139 Period size: 19 Copynumber: 6.2 Consensus size: 19 111325620 AATCTTTAAG 111325630 GATATGCAATCTTAGATAT 1 GATATGCAATCTTAGATAT * 111325649 GATATGGAATCTTAGATAT 1 GATATGCAATCTTAGATAT 111325668 GATA--CAATCTTAGATAT 1 GATATGCAATCTTAGATAT * 111325685 GATATGCAA---TA-TTA- 1 GATATGCAATCTTAGATAT 111325699 GATATGCAATCTTAGATAT 1 GATATGCAATCTTAGATAT 111325718 GATATGCAATCTTGAAGATAT 1 GATATGCAATCTT--AGATAT 111325739 GAT 1 GAT 111325742 CTTGTAATCT Statistics Matches: 80, Mismatches: 4, Indels: 16 0.80 0.04 0.16 Matches are distributed among these distances: 14 9 0.11 15 2 0.03 16 2 0.03 17 18 0.22 18 2 0.03 19 38 0.47 21 9 0.11 ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36 Consensus pattern (19 bp): GATATGCAATCTTAGATAT Found at i:111325744 original size:33 final size:35 Alignment explanation

Indices: 111325620--111325744 Score: 127 Period size: 33 Copynumber: 3.6 Consensus size: 35 111325610 ATGGAAATAT * * 111325620 AATCTTTAAGGATATGCAATCTTAGATATGATATGG 1 AATCTTGAAGGATATG-AATCTTAGATATGATATGC * * 111325656 AATCTTAGATATGATA-CAATCTTAGATATGATATGC 1 AATCTT-GA-AGGATATGAATCTTAGATATGATATGC * 111325692 AATATT--A-GATATGCAATCTTAGATATGATATGC 1 AATCTTGAAGGATATG-AATCTTAGATATGATATGC 111325725 AATCTTGAA-GATATG-ATCTT 1 AATCTTGAAGGATATGAATCTT 111325745 GTAATCTTGG Statistics Matches: 76, Mismatches: 7, Indels: 15 0.78 0.07 0.15 Matches are distributed among these distances: 31 4 0.05 32 1 0.01 33 29 0.38 35 7 0.09 36 29 0.38 37 1 0.01 38 5 0.07 ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37 Consensus pattern (35 bp): AATCTTGAAGGATATGAATCTTAGATATGATATGC Found at i:111333983 original size:20 final size:19 Alignment explanation

Indices: 111333938--111333986 Score: 53 Period size: 20 Copynumber: 2.5 Consensus size: 19 111333928 AATTAATCTG * 111333938 TATTAACAGTTTTATGCAT 1 TATTAACAGTTTTATACAT ** 111333957 TAGTTAACAGTTTTGATATTT 1 TA-TTAACAGTTTT-ATACAT 111333978 TATTAACAG 1 TATTAACAG 111333987 ATATTTTATG Statistics Matches: 25, Mismatches: 3, Indels: 3 0.81 0.10 0.10 Matches are distributed among these distances: 19 2 0.08 20 18 0.72 21 5 0.20 ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47 Consensus pattern (19 bp): TATTAACAGTTTTATACAT Found at i:111335409 original size:17 final size:18 Alignment explanation

Indices: 111335377--111335411 Score: 54 Period size: 17 Copynumber: 2.0 Consensus size: 18 111335367 GTGTAGTTCA * 111335377 CCTGTGTGGACCCACACG 1 CCTGTATGGACCCACACG 111335395 CCTGTATGG-CCCACACG 1 CCTGTATGGACCCACACG 111335412 GCCCAATGGG Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 8 0.50 18 8 0.50 ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17 Consensus pattern (18 bp): CCTGTATGGACCCACACG Found at i:111348712 original size:44 final size:45 Alignment explanation

Indices: 111348659--111348761 Score: 127 Period size: 44 Copynumber: 2.3 Consensus size: 45 111348649 TGTCTTTGAC * * * 111348659 ATGGACTTACATGAATTATTCATGTCTCCAATGCCATA-TATAAT 1 ATGGACTTACATGAATCAATCATGTCTCCAAAGCCATATTATAAT ** * * 111348703 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT 1 ATGGACTTACATGAATCAATCATGTCTCCAAAGCCATA-TTATAAT 111348749 ATGGACTTACATG 1 ATGGACTTACATG 111348762 GCTCATTTCG Statistics Matches: 50, Mismatches: 7, Indels: 2 0.85 0.12 0.03 Matches are distributed among these distances: 44 32 0.64 46 18 0.36 ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34 Consensus pattern (45 bp): ATGGACTTACATGAATCAATCATGTCTCCAAAGCCATATTATAAT Found at i:111348760 original size:46 final size:44 Alignment explanation

Indices: 111348681--111348766 Score: 136 Period size: 46 Copynumber: 1.9 Consensus size: 44 111348671 GAATTATTCA * 111348681 TGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAATCC 1 TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCC * 111348725 TGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA 1 TGTCTCCAAAGCCATA--TATAATATGGACTTACATGGCTCA 111348767 TTTCGTTCTG Statistics Matches: 38, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 44 15 0.39 46 23 0.61 ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33 Consensus pattern (44 bp): TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCC Found at i:111352352 original size:8 final size:7 Alignment explanation

Indices: 111352331--111352520 Score: 67 Period size: 7 Copynumber: 26.1 Consensus size: 7 111352321 ACCCTATTTT 111352331 TATATT- 1 TATATTA 111352337 TATATTA 1 TATATTA 111352344 TATAGTTA 1 TATA-TTA * 111352352 TTCTATTA 1 -TATATTA * 111352360 TGTATTA 1 TATATTA 111352367 TTTATATTA 1 --TATATTA 111352376 TTATATTA 1 -TATATTA * 111352384 T-TATTT 1 TATATTA * 111352390 TACATTA 1 TATATTA 111352397 T-TATTTA 1 TATA-TTA 111352404 TATATTA 1 TATATTA * 111352411 T-TGTTA 1 TATATTA * 111352417 TATTTTTA 1 TA-TATTA * 111352425 CTTGTATTA 1 --TATATTA 111352434 TATATT- 1 TATATTA 111352440 TATTAATTA 1 TA-T-ATTA * 111352449 TTTA-TA 1 TATATTA * 111352455 TGTATTA 1 TATATTA 111352462 TATATTA 1 TATATTA * 111352469 TATTCACATA 1 TA-T-A-TTA 111352479 TATACTT- 1 TATA-TTA 111352486 TCATATTA 1 T-ATATTA 111352494 TATATTA 1 TATATTA 111352501 TA-ATTA 1 TATATTA 111352507 T-T-TTA 1 TATATTA 111352512 TATTATTA 1 TA-TATTA 111352520 T 1 T 111352521 GTCATTTTTT Statistics Matches: 142, Mismatches: 17, Indels: 48 0.69 0.08 0.23 Matches are distributed among these distances: 5 4 0.03 6 29 0.20 7 52 0.37 8 36 0.25 9 16 0.11 10 5 0.04 ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60 Consensus pattern (7 bp): TATATTA Found at i:111352360 original size:27 final size:26 Alignment explanation

Indices: 111352325--111352517 Score: 91 Period size: 24 Copynumber: 7.7 Consensus size: 26 111352315 TTTTTAACCC * 111352325 TATTTTTATATTTATATTATA-TAGTTA 1 TATTATTAT-TTTATATTATATTA-TTA 111352352 T-TCTATTATGTATTAT-TTATATTATTA 1 TAT-TATTAT-T-TTATATTATATTATTA * 111352379 TATTATTATTTTACA-T-TATTATT- 1 TATTATTATTTTATATTATATTATTA * 111352402 TATATATTATTGTTATATT-T-TTACTTG 1 TAT-TATTATT-TTATATTATATTA-TTA * 111352429 TATTA-TATATT-TATTA-ATTATT- 1 TATTATTATTTTATATTATATTATTA * * 111352451 TA-TATGTATTATATATTATATTCA-CA 1 TATTAT-TATTTTATATTATATT-ATTA * 111352477 TA-TA-TACTTTCATATTATA-TATTA 1 TATTATTA-TTTTATATTATATTATTA 111352501 TA--ATTATTTTATATTAT 1 TATTATTATTTTATATTAT 111352518 TATGTCATTT Statistics Matches: 133, Mismatches: 12, Indels: 46 0.70 0.06 0.24 Matches are distributed among these distances: 21 2 0.02 22 2 0.02 23 25 0.19 24 32 0.24 25 27 0.20 26 13 0.10 27 25 0.19 28 7 0.05 ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61 Consensus pattern (26 bp): TATTATTATTTTATATTATATTATTA Found at i:111352374 original size:16 final size:16 Alignment explanation

Indices: 111352333--111352471 Score: 82 Period size: 16 Copynumber: 8.9 Consensus size: 16 111352323 CCTATTTTTA 111352333 TATTTATATTATATAGT 1 TATTTATATTATATA-T * * 111352350 TA-TTCTATTATGTAT 1 TATTTATATTATATAT 111352365 TATTTATATTATTATAT 1 TATTTATATTA-TATAT * 111352382 TA-TTAT-TT-TACAT 1 TATTTATATTATATAT 111352395 TA-TTAT-TTATATAT 1 TATTTATATTATATAT * 111352409 TATTGT-TA-TAT-TTT 1 TATT-TATATTATATAT * * 111352423 TACTTGTATTATATATT 1 TATTTATATTATATA-T * 111352440 TATTAATTATT-TATAT 1 TATTTA-TATTATATAT 111352456 GTATTATATATTATAT 1 -TATT-TATATTATAT 111352472 TCACATATAT Statistics Matches: 95, Mismatches: 13, Indels: 27 0.70 0.10 0.20 Matches are distributed among these distances: 13 13 0.14 14 13 0.14 15 13 0.14 16 24 0.25 17 24 0.25 18 8 0.08 ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62 Consensus pattern (16 bp): TATTTATATTATATAT Found at i:111352519 original size:13 final size:13 Alignment explanation

Indices: 111352325--111352520 Score: 67 Period size: 13 Copynumber: 14.7 Consensus size: 13 111352315 TTTTTAACCC * 111352325 TATTTTTATATTTA 1 TATTATTAT-TTTA * 111352339 TATTA-TATAGTTA 1 TATTATTAT-TTTA 111352352 T-TCTATTATGTATTA 1 TAT-TATTAT-T-TTA 111352367 T-TTA-TATTATTA 1 TATTATTATT-TTA 111352379 TATTATTATTTTA 1 TATTATTATTTTA * 111352392 CATTATTA-TTTA 1 TATTATTATTTTA 111352404 TA-TATTATTGTTA 1 TATTATTATT-TTA * * * 111352417 TATTTTTA-CTTG 1 TATTATTATTTTA 111352429 TATTA-TATATTTA 1 TATTATTAT-TTTA * 111352442 T-TAATTA-TTTA 1 TATTATTATTTTA 111352453 TATGTATTATATATTA 1 TAT-TATTAT-T-TTA 111352469 TATTCACATATATACTTTCA 1 TATT---AT-TAT--TTT-A * 111352489 TATTA-TATATTA 1 TATTATTATTTTA 111352501 TA--ATTATTTTA 1 TATTATTATTTTA 111352512 TATTATTAT 1 TATTATTAT 111352521 GTCATTTTTT Statistics Matches: 140, Mismatches: 17, Indels: 51 0.67 0.08 0.25 Matches are distributed among these distances: 10 1 0.01 11 20 0.14 12 25 0.18 13 47 0.34 14 17 0.12 15 10 0.07 16 6 0.04 17 1 0.01 18 2 0.01 19 5 0.04 20 6 0.04 ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61 Consensus pattern (13 bp): TATTATTATTTTA Found at i:111352549 original size:21 final size:20 Alignment explanation

Indices: 111352491--111352570 Score: 67 Period size: 21 Copynumber: 3.9 Consensus size: 20 111352481 TACTTTCATA * 111352491 TTATATATTATA--ATTATT 1 TTATATATTATATCATTTTT * 111352509 TTATATTATTATGTCATTTTT 1 TTATA-TATTATATCATTTTT * 111352530 TTATACTATTATAT-TTTTTT 1 TTATA-TATTATATCATTTTT 111352550 ATCTATATATTATTATCATTT 1 -T-TATATATTA-TATCATTT 111352571 AAGTTTTAGC Statistics Matches: 49, Mismatches: 6, Indels: 9 0.77 0.09 0.14 Matches are distributed among these distances: 18 5 0.10 19 6 0.12 20 5 0.10 21 23 0.47 22 7 0.14 23 3 0.06 ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64 Consensus pattern (20 bp): TTATATATTATATCATTTTT Found at i:111352843 original size:17 final size:16 Alignment explanation

Indices: 111352820--111352878 Score: 59 Period size: 17 Copynumber: 3.6 Consensus size: 16 111352810 CCAATATATT 111352820 TTATATTTTTATATAA 1 TTATATTTTTATATAA * 111352836 TTATTATTCTTATA-AA 1 TTA-TATTTTTATATAA 111352852 -TATACTTTTTATTATATA 1 TTATA-TTTTTA-TATA-A 111352870 TTATATTTT 1 TTATATTTT 111352879 AAATCTATTA Statistics Matches: 35, Mismatches: 2, Indels: 10 0.74 0.04 0.21 Matches are distributed among these distances: 14 2 0.06 15 7 0.20 16 7 0.20 17 10 0.29 18 5 0.14 19 4 0.11 ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63 Consensus pattern (16 bp): TTATATTTTTATATAA Found at i:111354489 original size:2 final size:2 Alignment explanation

Indices: 111354482--111354515 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 111354472 ACATTTACTC 111354482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 111354516 TCATTTCAAT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:111355274 original size:9 final size:10 Alignment explanation

Indices: 111355262--111355328 Score: 59 Period size: 10 Copynumber: 6.8 Consensus size: 10 111355252 TCTTTCTCCC 111355262 TTTTCTTT-T 1 TTTTCTTTCT 111355271 TTTTCTTTCT 1 TTTTCTTTCT 111355281 TTTTCTTTCTAT 1 TTTTCTTTC--T 111355293 TTTTCTTTCT 1 TTTTCTTTCT * * 111355303 ATTTCATT-T 1 TTTTCTTTCT ** 111355312 TGGT-TTTCT 1 TTTTCTTTCT 111355321 TTTTCTTT 1 TTTTCTTT 111355329 TATTTATTTG Statistics Matches: 45, Mismatches: 8, Indels: 9 0.73 0.13 0.15 Matches are distributed among these distances: 8 2 0.04 9 13 0.29 10 20 0.44 12 10 0.22 ACGTcount: A:0.04, C:0.15, G:0.03, T:0.78 Consensus pattern (10 bp): TTTTCTTTCT Found at i:111355285 original size:6 final size:6 Alignment explanation

Indices: 111355262--111355329 Score: 50 Period size: 6 Copynumber: 11.5 Consensus size: 6 111355252 TCTTTCTCCC * * * * * 111355262 TTTTCT TTTTTT TCTTTCT TTTTCT TTCTAT TTTTC- -TTTCT ATTTCA 1 TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT ** 111355309 TTTTGG TTTTCT TTTTCT TTT 1 TTTTCT TTTTCT TTTTCT TTT 111355330 ATTTATTTGT Statistics Matches: 47, Mismatches: 12, Indels: 6 0.72 0.18 0.09 Matches are distributed among these distances: 4 4 0.09 6 38 0.81 7 5 0.11 ACGTcount: A:0.04, C:0.15, G:0.03, T:0.78 Consensus pattern (6 bp): TTTTCT Found at i:111355295 original size:12 final size:12 Alignment explanation

Indices: 111355270--111355306 Score: 60 Period size: 12 Copynumber: 3.2 Consensus size: 12 111355260 CCTTTTCTTT 111355270 TTTTTCTTTC-- 1 TTTTTCTTTCTA 111355280 TTTTTCTTTCTA 1 TTTTTCTTTCTA 111355292 TTTTTCTTTCTA 1 TTTTTCTTTCTA 111355304 TTT 1 TTT 111355307 CATTTTGGTT Statistics Matches: 25, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 10 10 0.40 12 15 0.60 ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78 Consensus pattern (12 bp): TTTTTCTTTCTA Found at i:111355318 original size:22 final size:22 Alignment explanation

Indices: 111355271--111355322 Score: 61 Period size: 22 Copynumber: 2.4 Consensus size: 22 111355261 CTTTTCTTTT * * 111355271 TTTTCTTTCTTTTTCTTTCTAT 1 TTTTCTTTCTATTTCTTTCTAG * 111355293 TTTTCTTTCTATTTCATTT-TGG 1 TTTTCTTTCTATTTC-TTTCTAG 111355315 TTTTCTTT 1 TTTTCTTT 111355323 TTCTTTTATT Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 22 23 0.88 23 3 0.12 ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75 Consensus pattern (22 bp): TTTTCTTTCTATTTCTTTCTAG Found at i:111356866 original size:23 final size:25 Alignment explanation

Indices: 111356842--111356920 Score: 88 Period size: 27 Copynumber: 3.0 Consensus size: 25 111356832 AGCAAATGAT * 111356842 TATAAAGTTAAAAT-AGATCTTATTA 1 TATAAA-TAAAAATAAGATCTTATTA 111356867 TATAAATAAAAATAAAAGATCTTATTA 1 TATAAATAAAAAT--AAGATCTTATTA * 111356894 TATAAACAAAAATAAAAGATCTTATTA 1 TATAAATAAAAAT--AAGATCTTATTA 111356921 AAAGGACATC Statistics Matches: 49, Mismatches: 2, Indels: 4 0.89 0.04 0.07 Matches are distributed among these distances: 24 6 0.12 25 6 0.12 27 37 0.76 ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34 Consensus pattern (25 bp): TATAAATAAAAATAAGATCTTATTA Found at i:111356892 original size:27 final size:27 Alignment explanation

Indices: 111356856--111356920 Score: 121 Period size: 27 Copynumber: 2.4 Consensus size: 27 111356846 AAGTTAAAAT * 111356856 AGATCTTATTATATAAATAAAAATAAA 1 AGATCTTATTATATAAACAAAAATAAA 111356883 AGATCTTATTATATAAACAAAAATAAA 1 AGATCTTATTATATAAACAAAAATAAA 111356910 AGATCTTATTA 1 AGATCTTATTA 111356921 AAAGGACATC Statistics Matches: 37, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 27 37 1.00 ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34 Consensus pattern (27 bp): AGATCTTATTATATAAACAAAAATAAA Found at i:111358506 original size:10 final size:10 Alignment explanation

Indices: 111358491--111358516 Score: 52 Period size: 10 Copynumber: 2.6 Consensus size: 10 111358481 AAACTCATCA 111358491 TTCATTTAAT 1 TTCATTTAAT 111358501 TTCATTTAAT 1 TTCATTTAAT 111358511 TTCATT 1 TTCATT 111358517 GCACAGAATG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 16 1.00 ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62 Consensus pattern (10 bp): TTCATTTAAT Found at i:111361754 original size:2 final size:2 Alignment explanation

Indices: 111361749--111361778 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 111361739 AAACACACAC 111361749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 111361779 GTAAATTTTA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:111363198 original size:21 final size:21 Alignment explanation

Indices: 111363157--111363198 Score: 50 Period size: 21 Copynumber: 2.0 Consensus size: 21 111363147 CGTGGTGCGT * * 111363157 GTACGGGGGCTGTGTGCTGGC 1 GTACGGAGGCTGGGTGCTGGC 111363178 GTACGGAGGCGTGGGTG-TGGC 1 GTACGGAGGC-TGGGTGCTGGC 111363199 TGTGGCACTA Statistics Matches: 18, Mismatches: 2, Indels: 2 0.82 0.09 0.09 Matches are distributed among these distances: 21 13 0.72 22 5 0.28 ACGTcount: A:0.07, C:0.17, G:0.55, T:0.21 Consensus pattern (21 bp): GTACGGAGGCTGGGTGCTGGC Found at i:111368072 original size:9 final size:9 Alignment explanation

Indices: 111368056--111368088 Score: 50 Period size: 9 Copynumber: 3.8 Consensus size: 9 111368046 TTTAATTAGA 111368056 AATTAATTT 1 AATTAATTT * 111368065 AGTTAATTT 1 AATTAATTT 111368074 AATTAA-TT 1 AATTAATTT 111368082 AATTAAT 1 AATTAAT 111368089 ATTTATTTTG Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 8 8 0.38 9 13 0.62 ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52 Consensus pattern (9 bp): AATTAATTT Found at i:111370941 original size:48 final size:44 Alignment explanation

Indices: 111370883--111371196 Score: 179 Period size: 47 Copynumber: 6.7 Consensus size: 44 111370873 GATTTGTGCA 111370883 CCAGTGTAAGACCATGTCTGGGACATGGCATCGACATCCAGATGAAAG 1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACAT--AGATGAAAG * * * * * 111370931 CTAGTGTAAGACATGTCTGGGGCATGCATCAGCCATATTATGAGAG 1 CCAGTGTAAGACATGTCTGGGACATGCATC-GACATA-GATGAAAG * 111370977 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGA-GATAAGTG 1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACATAGATGA-AA--G * * * * 111371025 CCA-TAGTAAGACATGTCTGGGACATGCATCGGCCTTGACAGAGATAG 1 CCAGT-GTAAGACATGTCTGGGACATGCATCGACATAGA-TGA-A-AG * * * ** * * 111371072 CCAATTTAAGACGTGTCTGGGACACCCATCGGCCA-AGAGTTG--TG 1 CCAGTGTAAGACATGTCTGGGACATGCATC-GACATAGA--TGAAAG * * * * * 111371116 CTAGTGTAAGACATGTTTAGGACATGCATCAGCACGCATATATGAGAG 1 CCAGTGTAAGACATGTCTGGGACATGCATC-G-A--CATAGATGAAAG 111371164 CCAGTGTAAGACCATGTCTGGGACATGGCATCG 1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCG 111371197 GCAATTTATA Statistics Matches: 206, Mismatches: 38, Indels: 43 0.72 0.13 0.15 Matches are distributed among these distances: 44 24 0.12 45 3 0.01 46 36 0.17 47 79 0.38 48 45 0.22 49 14 0.07 50 5 0.02 ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22 Consensus pattern (44 bp): CCAGTGTAAGACATGTCTGGGACATGCATCGACATAGATGAAAG Found at i:111371044 original size:94 final size:94 Alignment explanation

Indices: 111370883--111371199 Score: 330 Period size: 94 Copynumber: 3.4 Consensus size: 94 111370873 GATTTGTGCA * ** * 111370883 CCAGTGTAAGACCATGTCTGGGACATGGCATCGACATCCAGATGAA-AGCTAGTGTAAGACATGT 1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGAT-AAGTGCTAGTGTAAGACATGT * 111370947 CTGGGGCATGCATCAGCCATATTATGAGAG 65 CTGGGACATGCATCAGCCATATTATGAGAG * 111370977 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGATAAGTGCCA-TAGTAAGACATGT 1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGATAAGTGCTAGT-GTAAGACATGT * * * 111371041 CTGGGACATGCATCGGCC-T-TGACAGAGATAG 65 CTGGGACATGCATCAGCCATATTA-TGAG--AG * * * ** * 111371072 CCAATTTAAGA-CGTGTCTGGGACA-CCCATCGGCCA-AGAG-T-TGTGCTAGTGTAAGACATGT 1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATAGAGATAAGTGCTAGTGTAAGACATGT * * 111371132 TTAGGACATGCATCAGCACGCATA-TATGAGAG 65 CTGGGACATGCATCAG--C-CATATTATGAGAG 111371164 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA 1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA 111371200 ATTTATACCA Statistics Matches: 183, Mismatches: 26, Indels: 29 0.77 0.11 0.12 Matches are distributed among these distances: 91 29 0.16 92 15 0.08 93 32 0.17 94 94 0.51 95 13 0.07 ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22 Consensus pattern (94 bp): CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGATAAGTGCTAGTGTAAGACATGTC TGGGACATGCATCAGCCATATTATGAGAG Found at i:111379957 original size:47 final size:46 Alignment explanation

Indices: 111379851--111380163 Score: 203 Period size: 47 Copynumber: 6.7 Consensus size: 46 111379841 TGTGCACCAA * * * * * 111379851 TGTAAGACCATGTTTGGGACATGGCATCGGCATCCA-GACGAGGGCTAG 1 TGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACATGATGAGAGCCAG * * * 111379899 TGTAAGACATGTCTGGGACATGCATCAGCTATATTATGAGAGCCAG 1 TGTAAGACATGTCTGGGACATGCATCGGCTACATGATGAGAGCCAG * * 111379945 TGTAAGACCATGT-TGGGACATGGCATCGGC-ACAGAGATGAGTGCCAG 1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCTACA-TGATGAGAGCCAG * * * 111379992 AGTAAGACAAGTCTGGGACATGCATCGGCCTCGACA-GA-GATAGCCAG 1 TGTAAGACATGTCTGGGACATGCATCGG-CT--ACATGATGAGAGCCAG ** * * * * * 111380039 TGTAAGATGTATCTGGGACATGCATCGGC--CAAGA-GTTGTGCTAG 1 TGTAAGACATGTCTGGGACATGCATCGGCTACATGATG-AGAGCCAG * * * * 111380083 TGTAAGACATGTTTGGGACATGCATCAGC-ACGCATATATGAGAGCTAG 1 TGTAAGACATGTCTGGGACATGCATCGGCTA--CAT-GATGAGAGCCAG * 111380131 TGTAAAACCATGTCTGGGACATGGCATCGGCTA 1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCTA 111380164 TTTATCCCAT Statistics Matches: 208, Mismatches: 38, Indels: 35 0.74 0.14 0.12 Matches are distributed among these distances: 42 2 0.01 43 3 0.01 44 28 0.13 45 2 0.01 46 44 0.21 47 82 0.39 48 22 0.11 49 14 0.07 50 10 0.05 51 1 0.00 ACGTcount: A:0.28, C:0.19, G:0.30, T:0.22 Consensus pattern (46 bp): TGTAAGACATGTCTGGGACATGCATCGGCTACATGATGAGAGCCAG Found at i:111380011 original size:93 final size:91 Alignment explanation

Indices: 111379851--111380161 Score: 310 Period size: 93 Copynumber: 3.3 Consensus size: 91 111379841 TGTGCACCAA * * 111379851 TGTAAGACCATGTTTGGGACATGGCATCGGCATCCAGACGAGGGCTAGTGTAAGACATGTCTGGG 1 TGTAAGACCATG-TTGGGACATGGCATCGGCA-CAAGA-GAGTGCTAGTGTAAGACATGTCTGGG * 111379916 ACATGCATCAGCTATATTATGAGAGCCAG 63 ACATGCATCAGCTACATTATGAGAGCCAG * * * 111379945 TGTAAGACCATGTTGGGACATGGCATCGGCACAGAGATGAGTGCCAGAGTAAGACAAGTCTGGGA 1 TGTAAGACCATGTTGGGACATGGCATCGGCACA-AGA-GAGTGCTAGTGTAAGACATGTCTGGGA * * * 111380010 CATGCATCGGCCTCGACA-GA-GATAGCCAG 64 CATGCATCAG-CT--ACATTATGAGAGCCAG ** * * * 111380039 TGTAAGATGTAT-CTGGGACAT-GCATCGGC-CAAGAGTTGTGCTAGTGTAAGACATGTTTGGGA 1 TGTAAGA-CCATGTTGGGACATGGCATCGGCACAAGAG-AGTGCTAGTGTAAGACATGTCTGGGA * 111380101 CATGCATCAGC-ACGCATATATGAGAGCTAG 64 CATGCATCAGCTA--CAT-TATGAGAGCCAG * 111380131 TGTAAAACCATGTCTGGGACATGGCATCGGC 1 TGTAAGACCATGT-TGGGACATGGCATCGGC 111380162 TATTTATCCC Statistics Matches: 177, Mismatches: 26, Indels: 28 0.77 0.11 0.12 Matches are distributed among these distances: 87 1 0.01 89 2 0.01 90 2 0.01 91 36 0.20 92 16 0.09 93 70 0.40 94 45 0.25 95 3 0.02 96 2 0.01 ACGTcount: A:0.28, C:0.19, G:0.30, T:0.22 Consensus pattern (91 bp): TGTAAGACCATGTTGGGACATGGCATCGGCACAAGAGAGTGCTAGTGTAAGACATGTCTGGGACA TGCATCAGCTACATTATGAGAGCCAG Found at i:111381106 original size:19 final size:19 Alignment explanation

Indices: 111381082--111381122 Score: 73 Period size: 19 Copynumber: 2.2 Consensus size: 19 111381072 TGGGCCGTGT * 111381082 GGTTTTGATAGAATACCAA 1 GGTTTTGACAGAATACCAA 111381101 GGTTTTGACAGAATACCAA 1 GGTTTTGACAGAATACCAA 111381120 GGT 1 GGT 111381123 ATTCGAACAA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 21 1.00 ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29 Consensus pattern (19 bp): GGTTTTGACAGAATACCAA Found at i:111381351 original size:12 final size:13 Alignment explanation

Indices: 111381320--111381351 Score: 50 Period size: 12 Copynumber: 2.6 Consensus size: 13 111381310 GAAGAAAGGG 111381320 AGAAAAAAGAGAA 1 AGAAAAAAGAGAA 111381333 AG-AAAAAGA-AA 1 AGAAAAAAGAGAA 111381344 AGAAAAAA 1 AGAAAAAA 111381352 ATGGCAAAGA Statistics Matches: 18, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 11 4 0.22 12 12 0.67 13 2 0.11 ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00 Consensus pattern (13 bp): AGAAAAAAGAGAA Found at i:111382191 original size:15 final size:15 Alignment explanation

Indices: 111382171--111382201 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 111382161 TACCGAAAAC 111382171 TCAATATCCTTTCTT 1 TCAATATCCTTTCTT 111382186 TCAATATCCTTTCTT 1 TCAATATCCTTTCTT 111382201 T 1 T 111382202 TTAAGTCCGC Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55 Consensus pattern (15 bp): TCAATATCCTTTCTT Found at i:111386044 original size:39 final size:39 Alignment explanation

Indices: 111385986--111386145 Score: 275 Period size: 39 Copynumber: 4.1 Consensus size: 39 111385976 AATTATATTA * 111385986 CCAGCACAAAGCCTACGGGACTTTAGCCCGGATACATTT 1 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT * 111386025 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 1 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT * 111386064 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 1 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT * * 111386103 CTAGCACAAAGCCTGCAGGACTTTAGCCCGGATACATTT 1 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT 111386142 CCAG 1 CCAG 111386146 TGTCTTGCAT Statistics Matches: 115, Mismatches: 6, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 39 115 1.00 ACGTcount: A:0.26, C:0.31, G:0.23, T:0.21 Consensus pattern (39 bp): CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT Found at i:111390273 original size:26 final size:26 Alignment explanation

Indices: 111390235--111390344 Score: 184 Period size: 26 Copynumber: 4.2 Consensus size: 26 111390225 CATGAAATTC * 111390235 TTATCATGAAACATTTACCTAACCCA 1 TTATCATGGAACATTTACCTAACCCA 111390261 TTATCATGGAACATTTACCTAACCCA 1 TTATCATGGAACATTTACCTAACCCA * 111390287 TTATCATGGAACATTTACCTAACCTA 1 TTATCATGGAACATTTACCTAACCCA * * 111390313 TTATCATGGAATATTTACCTAACCTA 1 TTATCATGGAACATTTACCTAACCCA 111390339 TTATCA 1 TTATCA 111390345 ATTTGTATCA Statistics Matches: 81, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 81 1.00 ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35 Consensus pattern (26 bp): TTATCATGGAACATTTACCTAACCCA Found at i:111395196 original size:39 final size:39 Alignment explanation

Indices: 111395153--111395273 Score: 206 Period size: 39 Copynumber: 3.1 Consensus size: 39 111395143 AATTATATTA * * * 111395153 CCAGCACAAAACCTGCGAGACTTTAGCCCGGATACATTT 1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 111395192 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT * 111395231 CTAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 111395270 CCAG 1 CCAG 111395274 TGTCTTGCAT Statistics Matches: 77, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 39 77 1.00 ACGTcount: A:0.26, C:0.31, G:0.23, T:0.21 Consensus pattern (39 bp): CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT Found at i:111399864 original size:18 final size:18 Alignment explanation

Indices: 111399830--111399864 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 111399820 GCTCAATACG * 111399830 CTTCACTTCCTCTACTAT 1 CTTCACTTCCTCCACTAT * 111399848 CTTCACTTTCTCCACTA 1 CTTCACTTCCTCCACTA 111399865 AAATCGTGAA Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.17, C:0.40, G:0.00, T:0.43 Consensus pattern (18 bp): CTTCACTTCCTCCACTAT Found at i:111401979 original size:62 final size:62 Alignment explanation

Indices: 111401878--111402044 Score: 203 Period size: 62 Copynumber: 2.7 Consensus size: 62 111401868 CACATGCTCT * 111401878 TGTCCCTGGCCATGT-G-GTTTTATACAATGAACAATGAGTTACACAGCCTGGGAACACGCATG 1 TGTCCCTGGCC--GTAGCGTTTTATACAATGAACAATGAGTTACACAGCCAGGGAACACGCATG * * * * * * * 111401940 TGTTCCTGGCCGTATCGTTTTATACAATGAACAGTGAGTTACACGGCCAGGGTATACGCTTG 1 TGTCCCTGGCCGTAGCGTTTTATACAATGAACAATGAGTTACACAGCCAGGGAACACGCATG * * * 111402002 TGTCCCTGGCTGTAGGGTTTTATACAATGAACAATAAGTTACA 1 TGTCCCTGGCCGTAGCGTTTTATACAATGAACAATGAGTTACA 111402045 TAGTTGTTCA Statistics Matches: 89, Mismatches: 14, Indels: 4 0.83 0.13 0.04 Matches are distributed among these distances: 60 2 0.02 62 87 0.98 ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29 Consensus pattern (62 bp): TGTCCCTGGCCGTAGCGTTTTATACAATGAACAATGAGTTACACAGCCAGGGAACACGCATG Found at i:111402667 original size:15 final size:15 Alignment explanation

Indices: 111402649--111402692 Score: 54 Period size: 15 Copynumber: 2.9 Consensus size: 15 111402639 AGAAAGGGAG 111402649 AAAGAAAAAAAGAAA 1 AAAGAAAAAAAGAAA 111402664 AAAGAAAAGAAA-AAA 1 AAAGAAAA-AAAGAAA * * 111402679 ATAGAAAATAAGAA 1 AAAGAAAAAAAGAA 111402693 CTAACGTTAA Statistics Matches: 25, Mismatches: 2, Indels: 4 0.81 0.06 0.13 Matches are distributed among these distances: 14 2 0.08 15 20 0.80 16 3 0.12 ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05 Consensus pattern (15 bp): AAAGAAAAAAAGAAA Found at i:111402964 original size:20 final size:20 Alignment explanation

Indices: 111402924--111402960 Score: 58 Period size: 19 Copynumber: 1.9 Consensus size: 20 111402914 CCTGTAATTT 111402924 TCAACCAAGACCAATCCACA 1 TCAACCAAGACCAATCCACA * 111402944 TCAACCAA-TCCAATCCA 1 TCAACCAAGACCAATCCA 111402961 ACATATTTTC Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 19 8 0.50 20 8 0.50 ACGTcount: A:0.43, C:0.41, G:0.03, T:0.14 Consensus pattern (20 bp): TCAACCAAGACCAATCCACA Found at i:111407846 original size:13 final size:13 Alignment explanation

Indices: 111407825--111407876 Score: 95 Period size: 13 Copynumber: 4.0 Consensus size: 13 111407815 TAGTAATCAT * 111407825 ACACAGGCGTGTC 1 ACACGGGCGTGTC 111407838 ACACGGGCGTGTC 1 ACACGGGCGTGTC 111407851 ACACGGGCGTGTC 1 ACACGGGCGTGTC 111407864 ACACGGGCGTGTC 1 ACACGGGCGTGTC 111407877 CCTACCGAGC Statistics Matches: 38, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 13 38 1.00 ACGTcount: A:0.17, C:0.31, G:0.37, T:0.15 Consensus pattern (13 bp): ACACGGGCGTGTC Found at i:111411829 original size:54 final size:55 Alignment explanation

Indices: 111411751--111411868 Score: 139 Period size: 54 Copynumber: 2.2 Consensus size: 55 111411741 CTGCCAAAAC * ** 111411751 AACACGGGCGTGCGACACGCCCGTGCCTTGAAACCATGGCCAAACCTGTCAAATT 1 AACACGGGCATGCGACACGCCCGTGCCAAGAAACCATGGCCAAACCTGTCAAATT * * * * * * * 111411806 AACACGGG-ATGCGACACGTCCGTGCCAAGCAACCTTGGTCGAACCTGTTAGATT 1 AACACGGGCATGCGACACGCCCGTGCCAAGAAACCATGGCCAAACCTGTCAAATT 111411860 AACACGGGC 1 AACACGGGC 111411869 GTGGGAGAAG Statistics Matches: 52, Mismatches: 10, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 54 44 0.85 55 8 0.15 ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17 Consensus pattern (55 bp): AACACGGGCATGCGACACGCCCGTGCCAAGAAACCATGGCCAAACCTGTCAAATT Found at i:111412376 original size:23 final size:23 Alignment explanation

Indices: 111412350--111412395 Score: 56 Period size: 23 Copynumber: 2.0 Consensus size: 23 111412340 TATTCTATTT * 111412350 TCATACCCATGCCATTACTATGC 1 TCATACCCATGCCATTACCATGC * * * 111412373 TCATTCTCATGCTATTACCATGC 1 TCATACCCATGCCATTACCATGC 111412396 CAATGACACA Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 23 19 1.00 ACGTcount: A:0.24, C:0.33, G:0.09, T:0.35 Consensus pattern (23 bp): TCATACCCATGCCATTACCATGC Found at i:111413781 original size:19 final size:20 Alignment explanation

Indices: 111413749--111413786 Score: 51 Period size: 19 Copynumber: 1.9 Consensus size: 20 111413739 TGTTTAAAAA * * 111413749 TTTTTATTTATTATTTTATG 1 TTTTTACTTATTATCTTATG 111413769 TTTTTACTT-TTATCTTAT 1 TTTTTACTTATTATCTTAT 111413787 TTTAAGACTA Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 19 8 0.50 20 8 0.50 ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74 Consensus pattern (20 bp): TTTTTACTTATTATCTTATG Found at i:111418019 original size:30 final size:30 Alignment explanation

Indices: 111417983--111418049 Score: 134 Period size: 30 Copynumber: 2.2 Consensus size: 30 111417973 CTGTGTGCTA 111417983 GGCCGTGTGGCTACCACGGTCGCCTCGCAC 1 GGCCGTGTGGCTACCACGGTCGCCTCGCAC 111418013 GGCCGTGTGGCTACCACGGTCGCCTCGCAC 1 GGCCGTGTGGCTACCACGGTCGCCTCGCAC 111418043 GGCCGTG 1 GGCCGTG 111418050 GGGGCTTTTG Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 30 37 1.00 ACGTcount: A:0.09, C:0.39, G:0.36, T:0.16 Consensus pattern (30 bp): GGCCGTGTGGCTACCACGGTCGCCTCGCAC Found at i:111423639 original size:26 final size:26 Alignment explanation

Indices: 111423610--111423663 Score: 108 Period size: 26 Copynumber: 2.1 Consensus size: 26 111423600 ACCACAAAAG 111423610 TATGCCATTGAACTTATTGTTTTAGT 1 TATGCCATTGAACTTATTGTTTTAGT 111423636 TATGCCATTGAACTTATTGTTTTAGT 1 TATGCCATTGAACTTATTGTTTTAGT 111423662 TA 1 TA 111423664 AACTTAGTAG Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 28 1.00 ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50 Consensus pattern (26 bp): TATGCCATTGAACTTATTGTTTTAGT Found at i:111425587 original size:17 final size:17 Alignment explanation

Indices: 111425565--111425610 Score: 92 Period size: 17 Copynumber: 2.7 Consensus size: 17 111425555 TTTAGGATAA 111425565 ATTTTGATTGATTTATG 1 ATTTTGATTGATTTATG 111425582 ATTTTGATTGATTTATG 1 ATTTTGATTGATTTATG 111425599 ATTTTGATTGAT 1 ATTTTGATTGAT 111425611 ATATCTTGAA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 29 1.00 ACGTcount: A:0.24, C:0.00, G:0.17, T:0.59 Consensus pattern (17 bp): ATTTTGATTGATTTATG Found at i:111425600 original size:11 final size:10 Alignment explanation

Indices: 111425565--111425610 Score: 50 Period size: 8 Copynumber: 5.2 Consensus size: 10 111425555 TTTAGGATAA 111425565 ATTTTGATTG 1 ATTTTGATTG 111425575 A-TTT-A-TG 1 ATTTTGATTG 111425582 ATTTTGATTG 1 ATTTTGATTG 111425592 A-TTT-A-TG 1 ATTTTGATTG 111425599 ATTTTGATTG 1 ATTTTGATTG 111425609 AT 1 AT 111425611 ATATCTTGAA Statistics Matches: 30, Mismatches: 0, Indels: 12 0.71 0.00 0.29 Matches are distributed among these distances: 7 6 0.20 8 8 0.27 9 8 0.27 10 8 0.27 ACGTcount: A:0.24, C:0.00, G:0.17, T:0.59 Consensus pattern (10 bp): ATTTTGATTG Found at i:111428967 original size:47 final size:47 Alignment explanation

Indices: 111428897--111429026 Score: 233 Period size: 47 Copynumber: 2.7 Consensus size: 47 111428887 CATTCTCTAC 111428897 GCCAATGTCATGTCCCAGACATGGTCTTACACTGGCTATAATATTGTG 1 GCCAATG-CATGTCCCAGACATGGTCTTACACTGGCTATAATATTGTG * 111428945 GCCAATGCATGTCCCAGACATGGTCTTACACTGGCTATCATATTGTG 1 GCCAATGCATGTCCCAGACATGGTCTTACACTGGCTATAATATTGTG * 111428992 GCCGATGCATGTCCCAGACATGGTCTTACACTGGC 1 GCCAATGCATGTCCCAGACATGGTCTTACACTGGC 111429027 ACACAAGTAA Statistics Matches: 80, Mismatches: 2, Indels: 1 0.96 0.02 0.01 Matches are distributed among these distances: 47 73 0.91 48 7 0.09 ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28 Consensus pattern (47 bp): GCCAATGCATGTCCCAGACATGGTCTTACACTGGCTATAATATTGTG Found at i:111430582 original size:55 final size:55 Alignment explanation

Indices: 111430498--111430607 Score: 211 Period size: 55 Copynumber: 2.0 Consensus size: 55 111430488 GTGTGCTTGA 111430498 CCGTGTGTGCCAAGAATATCTGCAATTAGACTGTAAAACAAAAGAAAAACAAACT 1 CCGTGTGTGCCAAGAATATCTGCAATTAGACTGTAAAACAAAAGAAAAACAAACT * 111430553 CCGTGTGTGCCAAGAATATCTGCAATTAGACTGTAAAACAAAAGAAAAATAAACT 1 CCGTGTGTGCCAAGAATATCTGCAATTAGACTGTAAAACAAAAGAAAAACAAACT 111430608 AAGTTATTTA Statistics Matches: 54, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 55 54 1.00 ACGTcount: A:0.45, C:0.17, G:0.16, T:0.21 Consensus pattern (55 bp): CCGTGTGTGCCAAGAATATCTGCAATTAGACTGTAAAACAAAAGAAAAACAAACT Found at i:111432059 original size:40 final size:41 Alignment explanation

Indices: 111431988--111432100 Score: 131 Period size: 41 Copynumber: 2.8 Consensus size: 41 111431978 AAATAGGGCT * ** * 111431988 TTAGCGGCGTTTTTTGAAAAAACGCCG-TAAAAATTATA-CA 1 TTAGCGGCG-TTTTTGGAAAAACGCCGCTAAAAACCAGAGCA * * 111432028 TTAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAACCAGAGCA 1 TTAGCGGCGTTTTTGGAAAAACGCCGCTAAAAACCAGAGCA * * 111432069 ATAGCGGCGTTTTTGGTAAAACGCCGCTAAAA 1 TTAGCGGCGTTTTTGGAAAAACGCCGCTAAAA 111432101 GTCATATAAC Statistics Matches: 62, Mismatches: 9, Indels: 3 0.84 0.12 0.04 Matches are distributed among these distances: 39 14 0.23 40 17 0.27 41 31 0.50 ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25 Consensus pattern (41 bp): TTAGCGGCGTTTTTGGAAAAACGCCGCTAAAAACCAGAGCA Found at i:111432187 original size:15 final size:16 Alignment explanation

Indices: 111432158--111432192 Score: 63 Period size: 15 Copynumber: 2.2 Consensus size: 16 111432148 TAGTCTATAT 111432158 AACCCCTACAACCCTA 1 AACCCCTACAACCCTA 111432174 AACCCCTA-AACCCTA 1 AACCCCTACAACCCTA 111432189 AACC 1 AACC 111432193 TAATAAAACC Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 15 11 0.58 16 8 0.42 ACGTcount: A:0.40, C:0.49, G:0.00, T:0.11 Consensus pattern (16 bp): AACCCCTACAACCCTA Found at i:111432517 original size:19 final size:19 Alignment explanation

Indices: 111432486--111432532 Score: 78 Period size: 19 Copynumber: 2.5 Consensus size: 19 111432476 ATATTAGATT 111432486 TAAA-AAAAACATTGATAA 1 TAAATAAAAACATTGATAA * 111432504 TAAATAAAATCATTGATAA 1 TAAATAAAAACATTGATAA 111432523 TAAATAAAAA 1 TAAATAAAAA 111432533 TGAAATATAA Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 18 4 0.15 19 22 0.85 ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26 Consensus pattern (19 bp): TAAATAAAAACATTGATAA Found at i:111437092 original size:44 final size:44 Alignment explanation

Indices: 111437029--111437117 Score: 178 Period size: 44 Copynumber: 2.0 Consensus size: 44 111437019 ACTATCGCTT 111437029 TCATTTAGGTGTCAACTTTATTTTAACAGATGTTATGCCTTATA 1 TCATTTAGGTGTCAACTTTATTTTAACAGATGTTATGCCTTATA 111437073 TCATTTAGGTGTCAACTTTATTTTAACAGATGTTATGCCTTATA 1 TCATTTAGGTGTCAACTTTATTTTAACAGATGTTATGCCTTATA 111437117 T 1 T 111437118 GATGCTATAG Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 44 45 1.00 ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46 Consensus pattern (44 bp): TCATTTAGGTGTCAACTTTATTTTAACAGATGTTATGCCTTATA Found at i:111437869 original size:20 final size:20 Alignment explanation

Indices: 111437828--111437875 Score: 53 Period size: 20 Copynumber: 2.4 Consensus size: 20 111437818 TTATTATTTA 111437828 TTTTAGTTTTGATTCTAAAT 1 TTTTAGTTTTGATTCTAAAT * * 111437848 TTTTA-TTTTTATTTTAATAT 1 TTTTAGTTTTGATTCTAA-AT * 111437868 TTCTAGTT 1 TTTTAGTT 111437876 AAAATTTTAA Statistics Matches: 23, Mismatches: 3, Indels: 3 0.79 0.10 0.10 Matches are distributed among these distances: 19 10 0.43 20 11 0.48 21 2 0.09 ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67 Consensus pattern (20 bp): TTTTAGTTTTGATTCTAAAT Found at i:111437995 original size:18 final size:18 Alignment explanation

Indices: 111437969--111438021 Score: 52 Period size: 18 Copynumber: 2.9 Consensus size: 18 111437959 TATTTTGATA * 111437969 ATGAATTTTAAATTTTTT 1 ATGATTTTTAAATTTTTT * 111437987 ATGATTTTTATAATATTTT 1 ATGATTTTTA-AATTTTTT ** * 111438006 ATTTTTTTTTAATTTT 1 ATGATTTTTAAATTTT 111438022 ATTACTTTTA Statistics Matches: 28, Mismatches: 6, Indels: 2 0.78 0.17 0.06 Matches are distributed among these distances: 18 14 0.50 19 14 0.50 ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68 Consensus pattern (18 bp): ATGATTTTTAAATTTTTT Found at i:111450708 original size:22 final size:22 Alignment explanation

Indices: 111450681--111450722 Score: 84 Period size: 22 Copynumber: 1.9 Consensus size: 22 111450671 ACACTTAAAC 111450681 TTAAAATAATTATAAGTAATAT 1 TTAAAATAATTATAAGTAATAT 111450703 TTAAAATAATTATAAGTAAT 1 TTAAAATAATTATAAGTAAT 111450723 TTTTTATGTA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 20 1.00 ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40 Consensus pattern (22 bp): TTAAAATAATTATAAGTAATAT Found at i:111454011 original size:25 final size:24 Alignment explanation

Indices: 111453952--111454012 Score: 63 Period size: 25 Copynumber: 2.5 Consensus size: 24 111453942 ATAACTCGAA * 111453952 CGAGCATCCTGTTAACAGGCTTAT 1 CGAGCATCCTGTTAACAGGCTTAG 111453976 CGAGCATTCCTGTT-ACATGGTCCTT-G 1 CGAGCA-TCCTGTTAACA-GG--CTTAG 111454002 CGAGCATCCTG 1 CGAGCATCCTG 111454013 ATCGATAGTG Statistics Matches: 32, Mismatches: 1, Indels: 7 0.80 0.03 0.17 Matches are distributed among these distances: 24 9 0.28 25 14 0.44 26 6 0.19 27 3 0.09 ACGTcount: A:0.20, C:0.28, G:0.23, T:0.30 Consensus pattern (24 bp): CGAGCATCCTGTTAACAGGCTTAG Found at i:111454141 original size:18 final size:18 Alignment explanation

Indices: 111454118--111454153 Score: 72 Period size: 18 Copynumber: 2.0 Consensus size: 18 111454108 CGCCACCAAT 111454118 CTTTTTAGGTGTGATTGG 1 CTTTTTAGGTGTGATTGG 111454136 CTTTTTAGGTGTGATTGG 1 CTTTTTAGGTGTGATTGG 111454154 ATCACCTTTA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.11, C:0.06, G:0.33, T:0.50 Consensus pattern (18 bp): CTTTTTAGGTGTGATTGG Found at i:111455378 original size:17 final size:19 Alignment explanation

Indices: 111455334--111455397 Score: 60 Period size: 19 Copynumber: 3.4 Consensus size: 19 111455324 ATATATAACC * 111455334 TATAAAAAATAATAAATAA 1 TATAATAAATAATAAATAA 111455353 TATAGAATAAA-AATAAA-AA 1 TAT--AATAAATAATAAATAA ** 111455372 TATAATAAATGTTAAATAA 1 TATAATAAATAATAAATAA * 111455391 TAAAATA 1 TATAATA 111455398 TATTTAAATA Statistics Matches: 37, Mismatches: 4, Indels: 8 0.76 0.08 0.16 Matches are distributed among these distances: 17 6 0.16 18 4 0.11 19 16 0.43 20 6 0.16 21 5 0.14 ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28 Consensus pattern (19 bp): TATAATAAATAATAAATAA Found at i:111455392 original size:19 final size:18 Alignment explanation

Indices: 111455346--111455411 Score: 55 Period size: 19 Copynumber: 3.6 Consensus size: 18 111455336 TAAAAAATAA ** 111455346 TAAATAATATAGAATAAAAA 1 TAAATAATAT--AATAAATT 111455366 TAAA-AATATAATAAATGT 1 TAAATAATATAATAAAT-T * * 111455384 TAAATAATAAAATATATT 1 TAAATAATATAATAAATT 111455402 TAAAT-ATATA 1 TAAATAATATA 111455412 GGAAATAAGA Statistics Matches: 39, Mismatches: 5, Indels: 7 0.76 0.10 0.14 Matches are distributed among these distances: 17 10 0.26 18 10 0.26 19 15 0.38 20 4 0.10 ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33 Consensus pattern (18 bp): TAAATAATATAATAAATT Found at i:111455393 original size:31 final size:30 Alignment explanation

Indices: 111455335--111455395 Score: 77 Period size: 31 Copynumber: 2.0 Consensus size: 30 111455325 TATATAACCT * 111455335 ATAAAAAATAATAAATAATATAGAATAAAA 1 ATAAAAAATAATAAATAATAAAGAATAAAA ** * 111455365 ATAAAAATATAATAAATGTTAAATAATAAAA 1 ATAAAAA-ATAATAAATAATAAAGAATAAAA 111455396 TATATTTAAA Statistics Matches: 26, Mismatches: 4, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 30 7 0.27 31 19 0.73 ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26 Consensus pattern (30 bp): ATAAAAAATAATAAATAATAAAGAATAAAA Found at i:111455530 original size:3 final size:3 Alignment explanation

Indices: 111455522--111455703 Score: 53 Period size: 3 Copynumber: 60.3 Consensus size: 3 111455512 AAGTAAAAAT * * * * 111455522 ATA ATA ATA AT- ATA AAA ATG ATA AT- GTA A-A ATA ATA ATA ATA ATTT 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA * * * 111455568 GTGA AAA ATA A-A CATA ATAA ATA ATA AT- GTAA ATA ATA TATA ATA 1 AT-A ATA ATA ATA -ATA AT-A ATA ATA ATA AT-A ATA ATA -ATA ATA * * * * 111455613 A-A ATA AT- TTT ATA ATA TATA AT- ATA AAA ATA AGGT- ATA AAA ATA 1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA A--TA ATA ATA ATA * * * 111455657 A-A ACA ATTA ACA AT- ATA AAA ATA TATA TATA ATA ATA ATA ATA ATA 1 ATA ATA A-TA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA 111455703 A 1 A 111455704 ACATATAGGG Statistics Matches: 131, Mismatches: 26, Indels: 44 0.65 0.13 0.22 Matches are distributed among these distances: 2 17 0.13 3 91 0.69 4 22 0.17 5 1 0.01 ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32 Consensus pattern (3 bp): ATA Found at i:111455710 original size:37 final size:36 Alignment explanation

Indices: 111455632--111455710 Score: 88 Period size: 37 Copynumber: 2.2 Consensus size: 36 111455622 TATAATATAT * * 111455632 AATATAAAAATAAGGTATAAAAATAAAACAATTAAC 1 AATATAAAAATAAGATATAAAAATAAAACAATAAAC * * * 111455668 AATATAAAAATATATATATAATAATAATAATAATAAAC 1 AATATAAAAATA-AGATATAAAAATAA-AACAATAAAC 111455706 -ATATA 1 AATATA 111455711 GGGTTAAATT Statistics Matches: 36, Mismatches: 5, Indels: 3 0.82 0.11 0.07 Matches are distributed among these distances: 36 12 0.33 37 16 0.44 38 8 0.22 ACGTcount: A:0.66, C:0.04, G:0.03, T:0.28 Consensus pattern (36 bp): AATATAAAAATAAGATATAAAAATAAAACAATAAAC Found at i:111469778 original size:31 final size:31 Alignment explanation

Indices: 111469719--111469779 Score: 88 Period size: 31 Copynumber: 2.0 Consensus size: 31 111469709 CAATTCAGAA * 111469719 ACTTAAATAAAAAATTTTAAATAGTTTAATT 1 ACTTAAATAAAAAATTTTAAATAATTTAATT * 111469750 ACTTAAAT-AAAAATTTTCGAATAATTTAAT 1 ACTTAAATAAAAAATTTT-AAATAATTTAAT 111469780 GATCATTCTA Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 30 9 0.33 31 18 0.67 ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41 Consensus pattern (31 bp): ACTTAAATAAAAAATTTTAAATAATTTAATT Found at i:111472108 original size:107 final size:108 Alignment explanation

Indices: 111471908--111472123 Score: 398 Period size: 107 Copynumber: 2.0 Consensus size: 108 111471898 AAAAAACACG 111471908 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTATTAGAAATTTTATTATTT 1 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTATTAGAAATTTTATTATTT 111471973 AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA 66 AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA * * 111472016 TCAAAAATTTTAT-AGAGTAATTAACAAAAATTTTAATACAATTTTGTTTGAAATTTTATTATTT 1 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTATTAGAAATTTTATTATTT * 111472080 AAAACTTATTCTAACTTAACATATCATTGTTTTGTTAAACTAA 66 AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA 111472123 T 1 T 111472124 TTTTTGTTTA Statistics Matches: 105, Mismatches: 3, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 107 92 0.88 108 13 0.12 ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44 Consensus pattern (108 bp): TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTATTAGAAATTTTATTATTT AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA Found at i:111484340 original size:150 final size:150 Alignment explanation

Indices: 111484155--111484436 Score: 401 Period size: 150 Copynumber: 1.9 Consensus size: 150 111484145 CATAATTTTA * * * 111484155 TTAAAATATAATATATTTACAATATTATAATTTCTTGATTTTTTTTATTATAGATAATTA-TGTT 1 TTAAAATATAATATATTTACAATATTATAATTTCTTGA-TTTTCTTATTATAGAGAATCACT-TT * * 111484219 AATCTAATTTAAATAA-AAATTTAGTAAAAACAAAATTTATGTCTCTTT-GTAATTCATATACGT 64 AACCTAATTTAAATAATAAATTTAGTAAAAACAAAATTTATGTCTCTTTAGTAATTCATATACGC 111484282 AATTACGTGAATCGTGATTTGT 129 AATTACGTGAATCGTGATTTGT * * * 111484304 TTAATAATATAATATATTTATAATATT-TAAATTTCTTTATTTTCTTATTATAGAGAGTCACTTT 1 TTAA-AATATAATATATTTACAATATTAT-AATTTCTTGATTTTCTTATTATAGAGAATCACTTT * * * 111484368 AACCTAATTTAAATAATAATTTTAGTAAAAACAAAATTTATGTTTCTTTATTAATTCATATACGC 64 AACCTAATTTAAATAATAAATTTAGTAAAAACAAAATTTATGTCTCTTTAGTAATTCATATACGC 111484433 AATT 129 AATT 111484437 CATATTTTTA Statistics Matches: 117, Mismatches: 11, Indels: 8 0.86 0.08 0.06 Matches are distributed among these distances: 149 39 0.33 150 61 0.52 151 17 0.15 ACGTcount: A:0.39, C:0.07, G:0.06, T:0.47 Consensus pattern (150 bp): TTAAAATATAATATATTTACAATATTATAATTTCTTGATTTTCTTATTATAGAGAATCACTTTAA CCTAATTTAAATAATAAATTTAGTAAAAACAAAATTTATGTCTCTTTAGTAATTCATATACGCAA TTACGTGAATCGTGATTTGT Found at i:111487653 original size:46 final size:46 Alignment explanation

Indices: 111487601--111487913 Score: 439 Period size: 46 Copynumber: 6.8 Consensus size: 46 111487591 CTCTGACAGA 111487601 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG 1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG 111487647 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG 1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG * 111487693 AAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG 1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG * * 111487739 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG 1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG * * *** 111487785 AAATGTTTAAGACCATGGTTGAAAGATACCATGGCAACGTGACGGGG 1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-TATG ** * * * 111487832 AAATGAATAAGACCATGGTTGAATGATACCATGGCAACATGACA-G 1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG * * * * * 111487877 AAAATGAGTAAGGCCATAGTTGAAAGACACTATGGCA 1 -AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA 111487914 TCATGTCGAA Statistics Matches: 245, Mismatches: 20, Indels: 4 0.91 0.07 0.01 Matches are distributed among these distances: 45 1 0.00 46 205 0.84 47 39 0.16 ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22 Consensus pattern (46 bp): AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG Found at i:111496515 original size:49 final size:48 Alignment explanation

Indices: 111496456--111496676 Score: 195 Period size: 49 Copynumber: 4.6 Consensus size: 48 111496446 CACATCAAGT * 111496456 CGATGCCATGTCCTAGACAGGTCTTACACTGACTTTCATATAACGAGGC 1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTT-ATATAACGAGGC * * * * * * * 111496505 CGATGCCATGTCCCGGATAGGTCTTACCCTGGCTCTTATCTATCG-GTGT 1 CGATGCCATGTCCCAGACAGGTCTTACACTGACT-TTATATAACGAG-GC * * * 111496554 CGATGTCATGTCCCAGACAGGTCTTACACTGAC---ACATAAC-AAGC 1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTATATAACGAGGC * * ** 111496598 TGATGCCATGTCCCAGACAGGTTTTACACT-AGCTTGTATATCTCGAGGC 1 CGATGCCATGTCCCAGACAGGTCTTACACTGA-CTT-TATATAACGAGGC * * 111496647 CGATG-CATGTCCCAAACATGTCTTACACTG 1 CGATGCCATGTCCCAGACAGGTCTTACACTG 111496677 GCACACATAA Statistics Matches: 133, Mismatches: 29, Indels: 20 0.73 0.16 0.11 Matches are distributed among these distances: 43 1 0.01 44 29 0.22 45 4 0.03 48 26 0.20 49 71 0.53 50 2 0.02 ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28 Consensus pattern (48 bp): CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTATATAACGAGGC Found at i:111496709 original size:94 final size:93 Alignment explanation

Indices: 111496554--111496725 Score: 231 Period size: 94 Copynumber: 1.8 Consensus size: 93 111496544 CTATCGGTGT * * 111496554 CGATGTCATGTCCCAGACAGGTCTTACACTGACACATAACAAGCTGATGCCATGTCCCAGACAGG 1 CGATGTCATGTCCCAAACAGGTCTTACACTGACACATAACAAGCTGATGCCATGTCCCAGACAAG ** 111496619 TTTTACACTAGCTTGTATATCTCGAGGC 66 ACTTACACTAGCTTGTATATCTCGAGGC * *** 111496647 CGATG-CATGTCCCAAACATGTCTTACACTGGCACACATAATGTGGCTGATG-CATGTCCCAGAC 1 CGATGTCATGTCCCAAACAGGTCTTACACT-G-ACACATAA-CAAGCTGATGCCATGTCCCAGAC 111496710 AAGACTTACACTAGCT 63 AAGACTTACACTAGCT 111496726 CACATACCAC Statistics Matches: 68, Mismatches: 8, Indels: 5 0.84 0.10 0.06 Matches are distributed among these distances: 92 22 0.32 93 6 0.09 94 33 0.49 95 7 0.10 ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25 Consensus pattern (93 bp): CGATGTCATGTCCCAAACAGGTCTTACACTGACACATAACAAGCTGATGCCATGTCCCAGACAAG ACTTACACTAGCTTGTATATCTCGAGGC Found at i:111502030 original size:20 final size:20 Alignment explanation

Indices: 111502007--111502048 Score: 59 Period size: 20 Copynumber: 2.1 Consensus size: 20 111501997 TTTTAGAAAA 111502007 TTTTT-CAACTTTTTATATTT 1 TTTTTACAA-TTTTTATATTT * 111502027 TTTTTACGATTTTTATATTT 1 TTTTTACAATTTTTATATTT 111502047 TT 1 TT 111502049 CTAAGTTTTA Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 20 18 0.90 21 2 0.10 ACGTcount: A:0.19, C:0.07, G:0.02, T:0.71 Consensus pattern (20 bp): TTTTTACAATTTTTATATTT Found at i:111502057 original size:18 final size:18 Alignment explanation

Indices: 111502006--111502057 Score: 52 Period size: 18 Copynumber: 2.8 Consensus size: 18 111501996 TTTTTAGAAA * 111502006 ATTTTTC-AACTTTTTAT 1 ATTTTTCTAAGTTTTTAT * * 111502023 ATTTTTTTTACGATTTTTAT 1 A-TTTTTCTAAG-TTTTTAT 111502043 ATTTTTCTAAGTTTT 1 ATTTTTCTAAGTTTT 111502058 AATAAAATTT Statistics Matches: 27, Mismatches: 5, Indels: 5 0.73 0.14 0.14 Matches are distributed among these distances: 17 1 0.04 18 9 0.33 19 9 0.33 20 8 0.30 ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67 Consensus pattern (18 bp): ATTTTTCTAAGTTTTTAT Found at i:111502891 original size:15 final size:15 Alignment explanation

Indices: 111502871--111502902 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 111502861 GGGCTGCAGT * 111502871 TTTTTATGAAGATGA 1 TTTTTACGAAGATGA 111502886 TTTTTACGAAGATGA 1 TTTTTACGAAGATGA 111502901 TT 1 TT 111502903 GTTAACAGAC 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:0.31, C:0.03, G:0.19, T:0.47 Consensus pattern (15 bp): TTTTTACGAAGATGA Found at i:111508397 original size:11 final size:12 Alignment explanation

Indices: 111508367--111508399 Score: 50 Period size: 12 Copynumber: 2.8 Consensus size: 12 111508357 AATTTTATTT 111508367 AATTAATATTTAA 1 AATTAA-ATTTAA 111508380 AATTAAATTTAA 1 AATTAAATTTAA 111508392 AA-TAAATT 1 AATTAAATT 111508400 ATAGTTACTC Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 11 6 0.30 12 8 0.40 13 6 0.30 ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42 Consensus pattern (12 bp): AATTAAATTTAA Found at i:111510049 original size:19 final size:18 Alignment explanation

Indices: 111510015--111510072 Score: 89 Period size: 18 Copynumber: 3.2 Consensus size: 18 111510005 TACGACCATT * 111510015 TACGACACTATTTATGTA 1 TACGATACTATTTATGTA 111510033 TACGATACTATTTTATGTA 1 TACGATACTA-TTTATGTA * 111510052 TACGGTACTATTTATGTA 1 TACGATACTATTTATGTA 111510070 TAC 1 TAC 111510073 AGTACTGTTC Statistics Matches: 37, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 18 20 0.54 19 17 0.46 ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43 Consensus pattern (18 bp): TACGATACTATTTATGTA Found at i:111510077 original size:18 final size:18 Alignment explanation

Indices: 111510021--111510094 Score: 87 Period size: 18 Copynumber: 4.1 Consensus size: 18 111510011 CATTTACGAC 111510021 ACTATTTATGTATAC-GAT 1 ACTATTTATGTATACAG-T * 111510039 ACTATTTTATGTATACGGT 1 ACTA-TTTATGTATACAGT 111510058 ACTATTTATGTATACAGT 1 ACTATTTATGTATACAGT * * * 111510076 ACTGTTCACGTATACAGT 1 ACTATTTATGTATACAGT 111510094 A 1 A 111510095 GTTAGGATTG Statistics Matches: 50, Mismatches: 4, Indels: 4 0.86 0.07 0.07 Matches are distributed among these distances: 18 33 0.66 19 16 0.32 20 1 0.02 ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42 Consensus pattern (18 bp): ACTATTTATGTATACAGT Found at i:111514885 original size:2 final size:2 Alignment explanation

Indices: 111514880--111514918 Score: 69 Period size: 2 Copynumber: 19.5 Consensus size: 2 111514870 TCTCTCTCTC * 111514880 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 111514919 CTATTTTGGA Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51 Consensus pattern (2 bp): TA Found at i:111516955 original size:25 final size:25 Alignment explanation

Indices: 111516926--111516974 Score: 80 Period size: 25 Copynumber: 2.0 Consensus size: 25 111516916 CAAAGGAAAA ** 111516926 TCCTAATCTAATTCCTAATTTAAAG 1 TCCTAATAGAATTCCTAATTTAAAG 111516951 TCCTAATAGAATTCCTAATTTAAA 1 TCCTAATAGAATTCCTAATTTAAA 111516975 ATTTATAAGG Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 25 22 1.00 ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39 Consensus pattern (25 bp): TCCTAATAGAATTCCTAATTTAAAG Found at i:111521620 original size:25 final size:25 Alignment explanation

Indices: 111521591--111521641 Score: 75 Period size: 25 Copynumber: 2.0 Consensus size: 25 111521581 CAAAGAAAAA ** * 111521591 TCCTAATCTAATTTCTAATTTAAAG 1 TCCTAATAGAATTCCTAATTTAAAG 111521616 TCCTAATAGAATTCCTAATTTAAAG 1 TCCTAATAGAATTCCTAATTTAAAG 111521641 T 1 T 111521642 TTATAAGGAA Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 25 23 1.00 ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41 Consensus pattern (25 bp): TCCTAATAGAATTCCTAATTTAAAG Found at i:111524840 original size:21 final size:21 Alignment explanation

Indices: 111524814--111524854 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 111524804 ATCTGCTCAA * * 111524814 ACTCCACCTGTTTTGGAGTAC 1 ACTCCACCTGCTGTGGAGTAC 111524835 ACTCCACCTGCTGTGGAGTA 1 ACTCCACCTGCTGTGGAGTA 111524855 TCGCTCGTCT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29 Consensus pattern (21 bp): ACTCCACCTGCTGTGGAGTAC Found at i:111531792 original size:17 final size:18 Alignment explanation

Indices: 111531753--111531802 Score: 57 Period size: 17 Copynumber: 2.8 Consensus size: 18 111531743 TTTCTTTAAT 111531753 CTATTTTATATGTATTAC 1 CTATTTTATATGTATTAC * * * 111531771 TTATTTT-TATTTCTTAC 1 CTATTTTATATGTATTAC * 111531788 CTATTATATATGTAT 1 CTATTTTATATGTAT 111531803 ACATATAGTT Statistics Matches: 24, Mismatches: 7, Indels: 2 0.73 0.21 0.06 Matches are distributed among these distances: 17 13 0.54 18 11 0.46 ACGTcount: A:0.26, C:0.10, G:0.04, T:0.60 Consensus pattern (18 bp): CTATTTTATATGTATTAC Found at i:111532417 original size:26 final size:25 Alignment explanation

Indices: 111532381--111532475 Score: 91 Period size: 26 Copynumber: 3.6 Consensus size: 25 111532371 TTTACATAAC 111532381 ATTTATTTTAAACTTATTCATATATT 1 ATTTATTTTAAACTT-TTCATATATT * * * * * 111532407 ATTTATCTTAAATTTTTTTACATATC 1 ATTTATTTTAAA-CTTTTCATATATT * 111532433 ATTCATTTTAAACTTTTCCCATATATT 1 ATTTATTTTAAACTTTT--CATATATT * 111532460 ATTTATTTCAAACTTT 1 ATTTATTTTAAACTTT 111532476 CGCCTATACT Statistics Matches: 53, Mismatches: 13, Indels: 5 0.75 0.18 0.07 Matches are distributed among these distances: 25 4 0.08 26 28 0.53 27 21 0.40 ACGTcount: A:0.32, C:0.13, G:0.00, T:0.56 Consensus pattern (25 bp): ATTTATTTTAAACTTTTCATATATT Found at i:111532441 original size:52 final size:54 Alignment explanation

Indices: 111532347--111532465 Score: 163 Period size: 52 Copynumber: 2.2 Consensus size: 54 111532337 AGATGTCTTG * * * 111532347 TATATTATTTATTTTAAGTTTCTTTTTACATAACATTTATTTTAAACTTATT-CA 1 TATATTATTTATCTTAAGATTCTTTTTACATAACATTCATTTTAAACTT-TTCCA * 111532401 TATATTATTTATCTTAA-ATT-TTTTTACATATCATTCATTTTAAACTTTTCCCA 1 TATATTATTTATCTTAAGATTCTTTTTACATAACATTCATTTTAAACTTTT-CCA 111532454 TATATTATTTAT 1 TATATTATTTAT 111532466 TTCAAACTTT Statistics Matches: 59, Mismatches: 4, Indels: 5 0.87 0.06 0.07 Matches are distributed among these distances: 51 2 0.03 52 25 0.42 53 16 0.27 54 16 0.27 ACGTcount: A:0.31, C:0.11, G:0.01, T:0.57 Consensus pattern (54 bp): TATATTATTTATCTTAAGATTCTTTTTACATAACATTCATTTTAAACTTTTCCA Found at i:111533579 original size:25 final size:25 Alignment explanation

Indices: 111533545--111533595 Score: 102 Period size: 25 Copynumber: 2.0 Consensus size: 25 111533535 GCTTTCTTTG 111533545 AGAATGTTTCATCTGAGGTTCCCAT 1 AGAATGTTTCATCTGAGGTTCCCAT 111533570 AGAATGTTTCATCTGAGGTTCCCAT 1 AGAATGTTTCATCTGAGGTTCCCAT 111533595 A 1 A 111533596 TCTGATTCTG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35 Consensus pattern (25 bp): AGAATGTTTCATCTGAGGTTCCCAT Found at i:111540473 original size:72 final size:72 Alignment explanation

Indices: 111540373--111540523 Score: 266 Period size: 72 Copynumber: 2.1 Consensus size: 72 111540363 TTGGTTGTGA * * * 111540373 CTGCCATTGTTCTTGTCGGGATGGGTTTAGGAGTGTTTGATGCATGAGATAAGAAAGAGAGATAG 1 CTGCCATTGTTCTTGTCGAGATGAGTTTAGGAGTGTTTGATGCATGAGATAAGAAAAAGAGATAG 111540438 GTAGAAG 66 GTAGAAG * 111540445 CTGCCATTGTTCTTGTCGAGATGAGTTTAGGAGTGTTTGGTGCATGAGATAAGAAAAAGAGATAG 1 CTGCCATTGTTCTTGTCGAGATGAGTTTAGGAGTGTTTGATGCATGAGATAAGAAAAAGAGATAG 111540510 GTAGAAG 66 GTAGAAG 111540517 CTGCCAT 1 CTGCCAT 111540524 GGTTGATTTT Statistics Matches: 75, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 72 75 1.00 ACGTcount: A:0.28, C:0.10, G:0.32, T:0.29 Consensus pattern (72 bp): CTGCCATTGTTCTTGTCGAGATGAGTTTAGGAGTGTTTGATGCATGAGATAAGAAAAAGAGATAG GTAGAAG Found at i:111549020 original size:18 final size:18 Alignment explanation

Indices: 111548989--111549038 Score: 50 Period size: 18 Copynumber: 2.7 Consensus size: 18 111548979 ATAAATATAA 111548989 ATTTTGAAATTTTTATAAA-T 1 ATTTTG-AA-TTTTA-AAAGT 111549009 ATTTTGAATTTTAAAAGTT 1 ATTTTGAATTTTAAAAG-T 111549028 ATTTT-AATTTT 1 ATTTTGAATTTT 111549039 TTTTGTAATT Statistics Matches: 28, Mismatches: 0, Indels: 6 0.82 0.00 0.18 Matches are distributed among these distances: 17 3 0.11 18 11 0.39 19 8 0.29 20 6 0.21 ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58 Consensus pattern (18 bp): ATTTTGAATTTTAAAAGT Found at i:111549039 original size:19 final size:19 Alignment explanation

Indices: 111548960--111549020 Score: 58 Period size: 19 Copynumber: 3.4 Consensus size: 19 111548950 TATTATTCTA 111548960 GAATTTTTA-AAATATTTT 1 GAATTTTTATAAATATTTT *** 111548978 -AATAAATAT-AA-ATTTT 1 GAATTTTTATAAATATTTT 111548994 GAAATTTTTATAAATATTTT 1 G-AATTTTTATAAATATTTT 111549014 GAATTTT 1 GAATTTT 111549021 AAAAGTTATT Statistics Matches: 32, Mismatches: 6, Indels: 9 0.68 0.13 0.19 Matches are distributed among these distances: 16 5 0.16 17 7 0.22 18 6 0.19 19 8 0.25 20 6 0.19 ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52 Consensus pattern (19 bp): GAATTTTTATAAATATTTT Found at i:111549744 original size:30 final size:30 Alignment explanation

Indices: 111549705--111549767 Score: 83 Period size: 30 Copynumber: 2.1 Consensus size: 30 111549695 TCATTGGTTC * 111549705 AAATATCATTATGGAC-TTTATTTTTTAAAA 1 AAATATCATTATGGACAATT-TTTTTTAAAA * * 111549735 AAATCTCATTATGGACAATTTTTTTTATAA 1 AAATATCATTATGGACAATTTTTTTTAAAA 111549765 AAA 1 AAA 111549768 GTCAAAAATA Statistics Matches: 29, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 30 27 0.93 31 2 0.07 ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44 Consensus pattern (30 bp): AAATATCATTATGGACAATTTTTTTTAAAA Found at i:111551096 original size:8 final size:8 Alignment explanation

Indices: 111551085--111551112 Score: 56 Period size: 8 Copynumber: 3.5 Consensus size: 8 111551075 AACAATTAAA 111551085 TTAATATT 1 TTAATATT 111551093 TTAATATT 1 TTAATATT 111551101 TTAATATT 1 TTAATATT 111551109 TTAA 1 TTAA 111551113 GTGTGAAAAC Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 20 1.00 ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (8 bp): TTAATATT Done.