Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr04 ID=Chr04-JGI_221_v2.0

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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33

Warning! 912357 characters in sequence are not A, C, G, or T


File 139 of 198

Found at i:44273073 original size:21 final size:21

Alignment explanation

Indices: 44273044--44273136 Score: 98 Period size: 21 Copynumber: 4.4 Consensus size: 21 44273034 TTTGACGCTG 44273044 CTCTGCTTCCCTCGCTGTAGC 1 CTCTGCTTCCCTCGCTGTAGC * * * * 44273065 TTTTGCTTCCCTCGCTTTATC 1 CTCTGCTTCCCTCGCTGTAGC * 44273086 CTCTGCTTCCCTCGCTGCAGC 1 CTCTGCTTCCCTCGCTGTAGC * * * 44273107 CTGTACTTCTCTCGCTGCT-GC 1 CTCTGCTTCCCTCGCTG-TAGC 44273128 CTCTGCTTC 1 CTCTGCTTC 44273137 TCTTACTGCC Statistics Matches: 56, Mismatches: 15, Indels: 2 0.77 0.21 0.03 Matches are distributed among these distances: 21 56 1.00 ACGTcount: A:0.04, C:0.41, G:0.16, T:0.39 Consensus pattern (21 bp): CTCTGCTTCCCTCGCTGTAGC Found at i:44273131 original size:42 final size:42 Alignment explanation

Indices: 44273040--44273136 Score: 108 Period size: 42 Copynumber: 2.3 Consensus size: 42 44273030 AACTTTTGAC * * * * 44273040 GCTG-CTCTGCTTCCCTCGCTGTAGCTTTTGCTTCCCTCGCT 1 GCTGCCTCTGCTTCCCTCGCTGCAGCCTGTACTTCCCTCGCT * * * 44273081 -TTATCCTCTGCTTCCCTCGCTGCAGCCTGTACTTCTCTCGCT 1 GCT-GCCTCTGCTTCCCTCGCTGCAGCCTGTACTTCCCTCGCT 44273123 GCTGCCTCTGCTTC 1 GCTGCCTCTGCTTC 44273137 TCTTACTGCC Statistics Matches: 44, Mismatches: 9, Indels: 5 0.76 0.16 0.09 Matches are distributed among these distances: 40 1 0.02 42 42 0.95 43 1 0.02 ACGTcount: A:0.04, C:0.40, G:0.18, T:0.38 Consensus pattern (42 bp): GCTGCCTCTGCTTCCCTCGCTGCAGCCTGTACTTCCCTCGCT Found at i:44273292 original size:66 final size:66 Alignment explanation

Indices: 44273163--44273294 Score: 176 Period size: 66 Copynumber: 2.0 Consensus size: 66 44273153 GTTTTAAGCT * * ** * 44273163 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGT 1 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCTACATCCACTTTAAGTTGT 44273228 A 66 A * * * 44273229 GCTGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTACCTCCACTTTAAGTTG 1 GCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGATGCTACATCCACTTTAAGTTG 44273293 TA 65 TA 44273295 TAATTTGCTC Statistics Matches: 57, Mismatches: 8, Indels: 2 0.85 0.12 0.03 Matches are distributed among these distances: 66 53 0.93 67 4 0.07 ACGTcount: A:0.16, C:0.26, G:0.17, T:0.41 Consensus pattern (66 bp): GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCTACATCCACTTTAAGTTGT A Found at i:44278861 original size:9 final size:9 Alignment explanation

Indices: 44278847--44279095 Score: 116 Period size: 9 Copynumber: 28.8 Consensus size: 9 44278837 AAAATTATGC 44278847 TATGTAAGT 1 TATGTAAGT * 44278856 TTTGTAAGT 1 TATGTAAGT * * 44278865 CATATAAGT 1 TATGTAAGT 44278874 TATGTAAG- 1 TATGTAAGT 44278882 T-TGTAAGT 1 TATGTAAGT 44278890 TATGTAAGT 1 TATGTAAGT * 44278899 TAT-TTA-T 1 TATGTAAGT * * 44278906 TATGAAAAT 1 TATGTAAGT * 44278915 TAAGTAAGT 1 TATGTAAGT * 44278924 TATGTAATT 1 TATGTAAGT * 44278933 TACG-AA-T 1 TATGTAAGT * ** 44278940 AAT-TAAAAA 1 TATGT-AAGT * 44278949 AATGTAAGT 1 TATGTAAGT 44278958 TATGTAAG- 1 TATGTAAGT 44278966 T-TGTAAGT 1 TATGTAAGT 44278974 TATGTAAGT 1 TATGTAAGT * 44278983 TATGTATA-A 1 TATGTA-AGT 44278992 TAT-TAA-T 1 TATGTAAGT ** * 44278999 TAACTAACT 1 TATGTAAGT * 44279008 TATGTAATT 1 TATGTAAGT * * 44279017 TAAGTATAATAT 1 T-A-TGTAA-GT 44279029 TAATGTAAGT 1 T-ATGTAAGT 44279039 TATGTAAG- 1 TATGTAAGT 44279047 T-TGTAAGT 1 TATGTAAGT 44279055 TATGTAAGT 1 TATGTAAGT * 44279064 TAT-TTA-T 1 TATGTAAGT * * 44279071 TATGAAAAT 1 TATGTAAGT * 44279080 TAAGTAAGT 1 TATGTAAGT 44279089 TATGTAA 1 TATGTAA 44279096 TTTACGAATA Statistics Matches: 182, Mismatches: 38, Indels: 40 0.70 0.15 0.15 Matches are distributed among these distances: 7 31 0.17 8 21 0.12 9 113 0.62 10 5 0.03 11 8 0.04 12 4 0.02 ACGTcount: A:0.40, C:0.02, G:0.16, T:0.43 Consensus pattern (9 bp): TATGTAAGT Found at i:44278988 original size:34 final size:34 Alignment explanation

Indices: 44278847--44279144 Score: 94 Period size: 34 Copynumber: 8.9 Consensus size: 34 44278837 AAAATTATGC * * * 44278847 TATGTAAGTTTTGTAAGTCATATAAGTTATGT-AAG 1 TATGTAAGTTATGTAAGT--TGTAAGTTATGTAAAT * * * 44278882 T-TGTAAGTTATGTAAGTTATTTA-TTATGAAAAT 1 TATGTAAGTTATGTAAGTT-GTAAGTTATGTAAAT * * * * 44278915 TAAGTAAGTTATGTAA-TT-TACGAATAAT-TAAAAA 1 TATGTAAGTTATGTAAGTTGTA--AGTTATGT-AAAT * * 44278949 AATGTAAGTTATGTAAGTTGTAAGTTATGTAAGT 1 TATGTAAGTTATGTAAGTTGTAAGTTATGTAAAT * * * * 44278983 TATGTATA-ATAT-TAA-TTAACTAACTTATGTAATT 1 TATGTA-AGTTATGTAAGTT--GTAAGTTATGTAAAT * * * 44279017 TAAGTATA-ATAT-TAA--TGTAAGTTATGT-AAG 1 TATGTA-AGTTATGTAAGTTGTAAGTTATGTAAAT * * * 44279047 T-TGTAAGTTATGTAAGTTATTTA-TTATGAAAAT 1 TATGTAAGTTATGTAAGTT-GTAAGTTATGTAAAT * * * * 44279080 TAAGTAAGTTATGTAA-TT-TACGAATAAT-TAAAAA 1 TATGTAAGTTATGTAAGTTGTA--AGTTATGT-AAAT * 44279114 AATGTAAGTTATGTAAGTTGTAAGTTATGTA 1 TATGTAAGTTATGTAAGTTGTAAGTTATGTA 44279145 TAATATTAAT Statistics Matches: 195, Mismatches: 41, Indels: 55 0.67 0.14 0.19 Matches are distributed among these distances: 28 1 0.01 29 6 0.03 30 5 0.03 31 11 0.06 32 14 0.07 33 20 0.10 34 126 0.65 35 8 0.04 36 4 0.02 ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42 Consensus pattern (34 bp): TATGTAAGTTATGTAAGTTGTAAGTTATGTAAAT Found at i:44279170 original size:156 final size:162 Alignment explanation

Indices: 44278869--44279200 Score: 595 Period size: 165 Copynumber: 2.1 Consensus size: 162 44278859 GTAAGTCATA 44278869 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT 1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT 44278934 ACGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAAT 66 ACGAATAATTAAAAAAATGTAAG-T-TGTAAG-TGTAAGTTATGTAAGTTATGTATAATATTAAT 44278999 TAACTAACTTATGTAATTTAAGTATAATATTAATG 128 TAACTAACTTATGTAATTTAAGTATAATATTAATG 44279034 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT 1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT 44279099 ACGAATAATTAAAAAAATGTAAG-T-T-A-TGTAAG-T-TGTAAGTTATGTATAATATTAATTAA 66 ACGAATAATTAAAAAAATGTAAGTTGTAAGTGTAAGTTATGTAAGTTATGTATAATATTAATTAA 44279158 CTAACTTATGTAATTTAAGTATAATATTAATG 131 CTAACTTATGTAATTTAAGTATAATATTAATG 44279190 TAAGTTATGTA 1 TAAGTTATGTA 44279201 TAATATTAAT Statistics Matches: 167, Mismatches: 0, Indels: 9 0.95 0.00 0.05 Matches are distributed among these distances: 156 69 0.41 157 1 0.01 158 6 0.04 160 1 0.01 161 1 0.01 162 1 0.01 165 88 0.53 ACGTcount: A:0.41, C:0.02, G:0.14, T:0.42 Consensus pattern (162 bp): TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT ACGAATAATTAAAAAAATGTAAGTTGTAAGTGTAAGTTATGTAAGTTATGTATAATATTAATTAA CTAACTTATGTAATTTAAGTATAATATTAATG Found at i:44279190 original size:22 final size:22 Alignment explanation

Indices: 44279165--44279210 Score: 74 Period size: 22 Copynumber: 2.1 Consensus size: 22 44279155 TAACTAACTT * 44279165 ATGTAATTTAAGTATAATATTA 1 ATGTAAGTTAAGTATAATATTA * 44279187 ATGTAAGTTATGTATAATATTA 1 ATGTAAGTTAAGTATAATATTA 44279209 AT 1 AT 44279211 TAACAAAGTT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46 Consensus pattern (22 bp): ATGTAAGTTAAGTATAATATTA Found at i:44279194 original size:56 final size:56 Alignment explanation

Indices: 44279132--44279578 Score: 423 Period size: 65 Copynumber: 7.5 Consensus size: 56 44279122 TTATGTAAGT * * * 44279132 TGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAA 1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA ** 44279188 TGTAAGTTATGTATAATATTAATTAACAAAGTTATGTAATTTATGTATAATATTAA 1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA 44279244 TGTAATTAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA 1 TGT-A--AGTTATGT-A--TA---ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA ** * 44279309 TGTAAGTTATGTAATTTATGAATAATTATAAAAATGTAAGTTATGTAATTTATGTATAATACTAA 1 TGTAAGTTATG-----TAT-AAT-ATTA-ATTAAT-TAAGTTATGTAATTTATGTATAATATTAA 44279374 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA 1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA * * * * 44279430 TTAATTAAGTTATGTAATTTATGTATAATACTAATGTAAGTTATGT-ATAATAT-TAATTAATTA 1 -T--GTAAGTTATGT-A-TAATAT-TAAT--TAAT-TAAGTTATGTAAT-TTATGT-A-TAA-T- * * 44279493 AGTTA 52 ATTAA * 44279498 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA 1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA * * * 44279554 TGTAACTTATATATTA-ATTAATTAA 1 TGTAAGTTATGTATAATATTAATTAA 44279579 ATGATATGTA Statistics Matches: 330, Mismatches: 27, Indels: 69 0.77 0.06 0.16 Matches are distributed among these distances: 55 9 0.03 56 100 0.30 57 7 0.02 58 7 0.02 59 35 0.11 60 12 0.04 61 4 0.01 62 19 0.06 63 8 0.02 64 14 0.04 65 105 0.32 66 4 0.01 67 3 0.01 68 3 0.01 ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47 Consensus pattern (56 bp): TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA Found at i:44279232 original size:34 final size:34 Alignment explanation

Indices: 44279187--44279554 Score: 248 Period size: 34 Copynumber: 11.7 Consensus size: 34 44279177 TATAATATTA * ** 44279187 ATGTAAGTTATGTATAATATTAATTAACAAAGTT 1 ATGTAATTTATGTATAATATTAATTAATTAAGTT 44279221 ATGTAATTTATGTATAATATTAATGTAATT-AGTT 1 ATGTAATTTATGTATAATATTAAT-TAATTAAGTT 44279255 ATGTAATTTATG--T-ATATTAATTAATTAAGTT 1 ATGTAATTTATGTATAATATTAATTAATTAAGTT * 44279286 ATGTAATTTATGTATAATATTAA-T--GTAAGTT 1 ATGTAATTTATGTATAATATTAATTAATTAAGTT * * 44279317 ATGTAATTTATGAATAAT-TATAA-AAATGTAAGTT 1 ATGTAATTTATGTATAATAT-TAATTAAT-TAAGTT * * 44279351 ATGTAATTTATGTATAATACTAA-T--GTAAGTT 1 ATGTAATTTATGTATAATATTAATTAATTAAGTT * * * * 44279382 ATGT-A--TA-ATATTA-ATTAATTAAGTTATGTA 1 ATGTAATTTATGTATAATATTAATTAA-TTAAGTT * * 44279412 AT-TTATGTA--T--AATATTAATTAATTAAGTT 1 ATGTAATTTATGTATAATATTAATTAATTAAGTT * * 44279441 ATGTAATTTATGTATAATACTAA-T--GTAAGTT 1 ATGTAATTTATGTATAATATTAATTAATTAAGTT * * * * 44279472 ATGT-A--TA-ATATTA-ATTAATTAAGTTATGTA 1 ATGTAATTTATGTATAATATTAATTAA-TTAAGTT * * 44279502 AT-TTATGTA--T--AATATTAATTAATTAAGTT 1 ATGTAATTTATGTATAATATTAATTAATTAAGTT 44279531 ATGTAATTTATGTATAATATTAAT 1 ATGTAATTTATGTATAATATTAAT 44279555 GTAACTTATA Statistics Matches: 263, Mismatches: 35, Indels: 72 0.71 0.09 0.19 Matches are distributed among these distances: 26 8 0.03 27 10 0.04 28 4 0.02 29 18 0.07 30 50 0.19 31 72 0.27 32 7 0.03 33 3 0.01 34 88 0.33 35 3 0.01 ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47 Consensus pattern (34 bp): ATGTAATTTATGTATAATATTAATTAATTAAGTT Found at i:44279234 original size:90 final size:90 Alignment explanation

Indices: 44279132--44279578 Score: 625 Period size: 90 Copynumber: 4.9 Consensus size: 90 44279122 TTATGTAAGT * * * * 44279132 TGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAATGTAAGTTA 1 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA ** 44279197 TGTATAATATTAATTAACAAAGTTA 66 TGTATAATATTAATTAATTAAGTTA * 44279222 TGTAATTTATGTATAATATTAATGTAATT-AGTTATGTAATTTATGTATATTAATTAAT-TAAGT 1 TGTAATTTATGTATAATATTAAT-TAATTAAGTTATGTAATTTATGTATAAT-ATTAATGTAAGT * * 44279285 TATGTAATTTATGTATAATATTAATGTAAGTTA 64 TATGT-A--TA-ATATTA-ATTAAT-TAAGTTA * * * 44279318 TGTAATTTATGAATAAT-TATAA-AAATGTAAGTTATGTAATTTATGTATAATACTAATGTAAGT 1 TGTAATTTATGTATAATAT-TAATTAAT-TAAGTTATGTAATTTATGTATAATATTAATGTAAGT 44279381 TATGTATAATATTAATTAATTAAGTTA 64 TATGTATAATATTAATTAATTAAGTTA * 44279408 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATACTAATGTAAGTTA 1 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA 44279473 TGTATAATATTAATTAATTAAGTTA 66 TGTATAATATTAATTAATTAAGTTA * 44279498 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAACTTA 1 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA * * 44279563 TATATTA-ATTAATTAA 66 TGTATAATATTAATTAA 44279579 ATGATATGTA Statistics Matches: 322, Mismatches: 21, Indels: 29 0.87 0.06 0.08 Matches are distributed among these distances: 89 9 0.03 90 208 0.65 91 21 0.07 92 4 0.01 93 4 0.01 94 7 0.02 95 13 0.04 96 56 0.17 ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47 Consensus pattern (90 bp): TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA TGTATAATATTAATTAATTAAGTTA Found at i:44279473 original size:22 final size:22 Alignment explanation

Indices: 44279441--44279486 Score: 74 Period size: 22 Copynumber: 2.1 Consensus size: 22 44279431 TAATTAAGTT * 44279441 ATGTAATTTATGTATAATACTA 1 ATGTAAGTTATGTATAATACTA * 44279463 ATGTAAGTTATGTATAATATTA 1 ATGTAAGTTATGTATAATACTA 44279485 AT 1 AT 44279487 TAATTAAGTT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46 Consensus pattern (22 bp): ATGTAAGTTATGTATAATACTA Found at i:44280887 original size:108 final size:107 Alignment explanation

Indices: 44280699--44280903 Score: 268 Period size: 108 Copynumber: 1.9 Consensus size: 107 44280689 CGTAAAGGCA ** * * * 44280699 AAACGACACCGTTTTGTTTAAAAACCCCGAATCTTTGCGGCGTTTTCACCATAGCGCCACTAATG 1 AAACGACACCGTTTCATTAAAAAACCCCGAATATTTGCGGCGTTTTCACCATAACGCCACTAATG * * * * 44280764 TCGTTAATGTGCCAGGGAAAATGACACCGTTTGGTTTAATGT 66 CCGTTAATATGCCAGGCAAAACGACACCGTTTGGTTTAATGT ** * * 44280806 AAACGACACCGTTTCATTAAAAAAACCCCGACA-ATTTGCGGCGTTTTCGGCGTAATGCCACTAA 1 AAACGACACCGTTTCATT-AAAAAACCCCGA-ATATTTGCGGCGTTTTCACCATAACGCCACTAA 44280870 TGCCGTTAATATGCCAGGCAAAACGACACCGTTT 64 TGCCGTTAATATGCCAGGCAAAACGACACCGTTT 44280904 TATTTACAAA Statistics Matches: 83, Mismatches: 13, Indels: 3 0.84 0.13 0.03 Matches are distributed among these distances: 107 16 0.19 108 66 0.80 109 1 0.01 ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27 Consensus pattern (107 bp): AAACGACACCGTTTCATTAAAAAACCCCGAATATTTGCGGCGTTTTCACCATAACGCCACTAATG CCGTTAATATGCCAGGCAAAACGACACCGTTTGGTTTAATGT Found at i:44281279 original size:6 final size:6 Alignment explanation

Indices: 44281270--44281299 Score: 60 Period size: 6 Copynumber: 5.0 Consensus size: 6 44281260 GTATTTTGTT 44281270 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA 1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA 44281300 TTTCTTAAGT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 24 1.00 ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67 Consensus pattern (6 bp): ATTTTA Found at i:44281672 original size:15 final size:17 Alignment explanation

Indices: 44281633--44281665 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 44281623 CTAACCCGAC 44281633 CCTCTTAAAACCCTAAA 1 CCTCTTAAAACCCTAAA * 44281650 CCTCTTAAATCCCTAA 1 CCTCTTAAAACCCTAA 44281666 CTCTTAACCA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.36, C:0.36, G:0.00, T:0.27 Consensus pattern (17 bp): CCTCTTAAAACCCTAAA Found at i:44288927 original size:23 final size:23 Alignment explanation

Indices: 44288901--44288992 Score: 80 Period size: 23 Copynumber: 3.9 Consensus size: 23 44288891 GGACTCACCA 44288901 CAGCTTGTATGAGCTTACCGTTT 1 CAGCTTGTATGAGCTTACCGTTT * * 44288924 CAGC-TCTACGGAGCTTACCGTTT 1 CAGCTTGTA-TGAGCTTACCGTTT * 44288947 CAGCTCG-ATAGAGCTTACCGTTTAT 1 CAGCTTGTAT-GAGCTTACCG-TT-T * * 44288972 CAGCTCGGAATGAGCTTACCG 1 CAGCT-TGTATGAGCTTACCG 44288993 ATCATGGCTC Statistics Matches: 56, Mismatches: 6, Indels: 11 0.77 0.08 0.15 Matches are distributed among these distances: 22 3 0.05 23 32 0.57 24 2 0.04 25 6 0.11 26 11 0.20 27 2 0.04 ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30 Consensus pattern (23 bp): CAGCTTGTATGAGCTTACCGTTT Found at i:44292105 original size:62 final size:61 Alignment explanation

Indices: 44291987--44292167 Score: 186 Period size: 61 Copynumber: 2.9 Consensus size: 61 44291977 TTGGTCTTGT * * * * * 44291987 AACAAAATTAGCCCTCTAATGTTTACATATTCTATCAATTT-GATACTAAATATAAAATAATTC 1 AACAAATTTAGTCCTC-AATGTTTACAAATTCTATCAATTTAG-TACTAAATCTAAAA-AAATC * * * 44292050 AACAAATTTAGTCCTCAATGTTTACAAAATT-TATCATTTTAGTTCTAATTCTAAAAAAATC 1 AACAAATTTAGTCCTCAATGTTTAC-AAATTCTATCAATTTAGTACTAAATCTAAAAAAATC * * * * * * 44292111 AATAAATTTATTCCTCAATATTTACAAATTCTGTCAATTTAGTCCTAACTCTAAAAA 1 AACAAATTTAGTCCTCAATGTTTACAAATTCTATCAATTTAGTACTAAATCTAAAAA 44292168 TTTTAAAAAT Statistics Matches: 100, Mismatches: 15, Indels: 8 0.81 0.12 0.07 Matches are distributed among these distances: 60 5 0.05 61 48 0.48 62 28 0.28 63 19 0.19 ACGTcount: A:0.41, C:0.16, G:0.04, T:0.38 Consensus pattern (61 bp): AACAAATTTAGTCCTCAATGTTTACAAATTCTATCAATTTAGTACTAAATCTAAAAAAATC Found at i:44293361 original size:61 final size:61 Alignment explanation

Indices: 44293251--44293375 Score: 137 Period size: 61 Copynumber: 2.0 Consensus size: 61 44293241 TCAAAAATTG * * * * * * * 44293251 TTAGAGTTAGGACTAAATTGATAGATTTTGTAAATGTTGATGGCCAAATTTATT-AATTCTT 1 TTAGAATTAGAACTAAAATGACAAATTCTGTAAATGTTGAGGGCCAAATTTATTAAATT-TT * * 44293312 TTAGAATTAGAACTAAAATGACAAATTCTGTAAATAG-TGAGGGCTAAATTTGTTAAATTTT 1 TTAGAATTAGAACTAAAATGACAAATTCTGTAAAT-GTTGAGGGCCAAATTTATTAAATTTT 44293373 TTA 1 TTA 44293376 TATTTGGGAT Statistics Matches: 53, Mismatches: 9, Indels: 4 0.80 0.14 0.06 Matches are distributed among these distances: 61 48 0.91 62 5 0.09 ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40 Consensus pattern (61 bp): TTAGAATTAGAACTAAAATGACAAATTCTGTAAATGTTGAGGGCCAAATTTATTAAATTTT Found at i:44297667 original size:13 final size:13 Alignment explanation

Indices: 44297649--44297714 Score: 63 Period size: 13 Copynumber: 5.5 Consensus size: 13 44297639 AACTTTGAAT 44297649 TATTTAGTGATAA 1 TATTTAGTGATAA * 44297662 TATTTA--GA-AT 1 TATTTAGTGATAA 44297672 TATTTAGTGATAA 1 TATTTAGTGATAA 44297685 TATTTAG-GAT-- 1 TATTTAGTGATAA * * 44297695 GATTTAGTGACAA 1 TATTTAGTGATAA 44297708 TATTTAG 1 TATTTAG 44297715 GTAATGTCTA Statistics Matches: 42, Mismatches: 5, Indels: 12 0.71 0.08 0.20 Matches are distributed among these distances: 10 13 0.31 11 4 0.10 12 5 0.12 13 20 0.48 ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45 Consensus pattern (13 bp): TATTTAGTGATAA Found at i:44297671 original size:23 final size:23 Alignment explanation

Indices: 44297645--44297714 Score: 113 Period size: 23 Copynumber: 3.0 Consensus size: 23 44297635 TTTAAACTTT 44297645 GAATTATTTAGTGATAATATTTA 1 GAATTATTTAGTGATAATATTTA 44297668 GAATTATTTAGTGATAATATTTA 1 GAATTATTTAGTGATAATATTTA * * * 44297691 GGATGATTTAGTGACAATATTTA 1 GAATTATTTAGTGATAATATTTA 44297714 G 1 G 44297715 GTAATGTCTA Statistics Matches: 44, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 23 44 1.00 ACGTcount: A:0.37, C:0.01, G:0.17, T:0.44 Consensus pattern (23 bp): GAATTATTTAGTGATAATATTTA Found at i:44297800 original size:16 final size:16 Alignment explanation

Indices: 44297779--44297848 Score: 113 Period size: 16 Copynumber: 4.4 Consensus size: 16 44297769 TTTGGTTCGC * 44297779 TGTATTGGATTAGAGG 1 TGTAATGGATTAGAGG * 44297795 TGTATTGGATTAGAGG 1 TGTAATGGATTAGAGG 44297811 TGTAATGGATTAGAGG 1 TGTAATGGATTAGAGG * 44297827 TGTAATGGAATAGAGG 1 TGTAATGGATTAGAGG 44297843 TGTAAT 1 TGTAAT 44297849 AGCAAATCAA Statistics Matches: 52, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 16 52 1.00 ACGTcount: A:0.30, C:0.00, G:0.36, T:0.34 Consensus pattern (16 bp): TGTAATGGATTAGAGG Found at i:44298090 original size:25 final size:25 Alignment explanation

Indices: 44298058--44298112 Score: 69 Period size: 25 Copynumber: 2.2 Consensus size: 25 44298048 TAATTTAATC * 44298058 ATAT-TTAAACATAATTATTATT-AA 1 ATATATTAAACAT-ATTATAATTAAA * 44298082 ATATATTAAATATATTATAATTAAA 1 ATATATTAAACATATTATAATTAAA 44298107 ATATAT 1 ATATAT 44298113 AATTTAATAA Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 24 12 0.44 25 15 0.56 ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45 Consensus pattern (25 bp): ATATATTAAACATATTATAATTAAA Found at i:44301742 original size:28 final size:28 Alignment explanation

Indices: 44301711--44301765 Score: 92 Period size: 28 Copynumber: 2.0 Consensus size: 28 44301701 GCAAATCGGT * 44301711 AGAAAAGAAAAGAAAATAAACAGAGGGC 1 AGAAAAGAAAAGAAAAGAAACAGAGGGC * 44301739 AGAAAAGAAAAGAAAAGAAACGGAGGG 1 AGAAAAGAAAAGAAAAGAAACAGAGGG 44301766 AGCAAATCGG Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 28 25 1.00 ACGTcount: A:0.64, C:0.05, G:0.29, T:0.02 Consensus pattern (28 bp): AGAAAAGAAAAGAAAAGAAACAGAGGGC Found at i:44306653 original size:24 final size:25 Alignment explanation

Indices: 44306626--44306678 Score: 81 Period size: 25 Copynumber: 2.2 Consensus size: 25 44306616 CAGCTCGAAA * 44306626 GAGCATCTCGTTA-TTAGCTCTCAT 1 GAGCATCTCGATATTTAGCTCTCAT * 44306650 GAGCATCTCGATATTTGGCTCTCAT 1 GAGCATCTCGATATTTAGCTCTCAT 44306675 GAGC 1 GAGC 44306679 TTTCCGTTAT Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 24 12 0.46 25 14 0.54 ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34 Consensus pattern (25 bp): GAGCATCTCGATATTTAGCTCTCAT Found at i:44307404 original size:15 final size:16 Alignment explanation

Indices: 44307384--44307416 Score: 50 Period size: 15 Copynumber: 2.1 Consensus size: 16 44307374 GCTTACTCTA 44307384 TTTTATTTCCTCT-TT 1 TTTTATTTCCTCTGTT * 44307399 TTTTATTTTCTCTGTT 1 TTTTATTTCCTCTGTT 44307415 TT 1 TT 44307417 ATAGTATTTG Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 15 12 0.75 16 4 0.25 ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76 Consensus pattern (16 bp): TTTTATTTCCTCTGTT Found at i:44308184 original size:27 final size:26 Alignment explanation

Indices: 44308135--44308229 Score: 113 Period size: 25 Copynumber: 3.7 Consensus size: 26 44308125 CGTTTCGACC * * ** 44308135 CACAGCTTGTGTGAGTAAGCTAATTTT 1 CACAGCTCGTGTGAGCATTCTAA-TTT 44308162 CACAGCTCGTGTGAGCATTCTAA-TT 1 CACAGCTCGTGTGAGCATTCTAATTT * * 44308187 CACAGCTCGTATGAGCATTCTGATTT 1 CACAGCTCGTGTGAGCATTCTAATTT 44308213 -ACAGCTCGTGTGAGCAT 1 CACAGCTCGTGTGAGCAT 44308230 ACATGTACAT Statistics Matches: 60, Mismatches: 7, Indels: 4 0.85 0.10 0.06 Matches are distributed among these distances: 25 39 0.65 26 2 0.03 27 19 0.32 ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33 Consensus pattern (26 bp): CACAGCTCGTGTGAGCATTCTAATTT Found at i:44312197 original size:3 final size:3 Alignment explanation

Indices: 44312191--44312226 Score: 72 Period size: 3 Copynumber: 12.0 Consensus size: 3 44312181 CTACTACTAC 44312191 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 44312227 AATTGCTAAA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 33 1.00 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (3 bp): TAA Found at i:44313874 original size:132 final size:132 Alignment explanation

Indices: 44313634--44313919 Score: 518 Period size: 132 Copynumber: 2.2 Consensus size: 132 44313624 CGTTATTGTT * 44313634 GATCTGCTCCACTACTGCTTAGGGGGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA 1 GATCTGCTCCACTACTGCTTAGGGGGACAGAATCTGCAATATTCAACCTACTCCACTACTGCTTA * 44313699 AGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTTTATTGGGAAGATAAGATTCACCATCT 66 AGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTATATTGGGAAGATAAGATTCACCATCT 44313764 TC 131 TC * * 44313766 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATATTTAACCTACTCCACTACTGCTTA 1 GATCTGCTCCACTACTGCTTAGGGGGACAGAATCTGCAATATTCAACCTACTCCACTACTGCTTA * * 44313831 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATATTGGGAAGATAAGATTCACCATCT 66 AGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTATATTGGGAAGATAAGATTCACCATCT 44313896 TC 131 TC 44313898 GATCTGCTCCACTACTGCTTAG 1 GATCTGCTCCACTACTGCTTAG 44313920 NNNNNNNNNN Statistics Matches: 148, Mismatches: 6, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 132 148 1.00 ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31 Consensus pattern (132 bp): GATCTGCTCCACTACTGCTTAGGGGGACAGAATCTGCAATATTCAACCTACTCCACTACTGCTTA AGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTATATTGGGAAGATAAGATTCACCATCT TC Found at i:44324157 original size:132 final size:132 Alignment explanation

Indices: 44323920--44324800 Score: 1478 Period size: 132 Copynumber: 6.7 Consensus size: 132 44323910 NNNNNNNNNN * * * * 44323920 ACTGTATTGGGAAGATAAGATTCACCATATTAGATCTGCTCCACTACTGCTTAGGATGACAGAAT 1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT 44323985 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT 66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT 44324050 CC 131 CC * * 44324052 ACTGTATTGGGAAGATAAGATTCACCATTTTCGATCTGCTCCACTACTGATTAGGGTAACAGAAT 1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT 44324117 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT 66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT 44324182 CC 131 CC * * * * 44324184 ACTATATTGGGAAGATAAGAATCACCATCTTCGATCTGCTCCGCTACTGCTTAGGGTGACAGAAT 1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT * * 44324249 TTACAATCTTCAACCTACTCCACTACTGCTTAGGGT-AGTAGGACTAATGGCTTAAATCTGCTTC 66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGA-TAGGACTAATGGCTTAAATCTGCTTC 44324313 TCC 130 TCC * * * 44324316 ACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAAT 1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT * 44324381 CTGCAATCTTCAACCTACTCCACAACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT 66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT 44324446 CC 131 CC * * 44324448 ACTGTATTGGGAAGATAAGATTCACCATGTTCAATCTGCTCCACTACTGATTAGGGTGACAGAAT 1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT 44324513 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT 66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT * 44324578 AC 131 CC * * * * * 44324580 ACTGCATTGGGAAGATAAGATTCACCATCTTCGATATTCTCCACTACTGCTTAGGGTGGCAGAAT 1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT * 44324645 TTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT 66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT 44324710 CC 131 CC * 44324712 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTATTGCA-TAGGGTGACAGAA 1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG-ATTAGGGTGACAGAA * * 44324776 TCTGTAATCTTCAACCTATTCCACT 65 TCTGCAATCTTCAACCTACTCCACT 44324801 GCCAAATACA Statistics Matches: 698, Mismatches: 48, Indels: 6 0.93 0.06 0.01 Matches are distributed among these distances: 131 1 0.00 132 696 1.00 133 1 0.00 ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31 Consensus pattern (132 bp): ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT CC Found at i:44324390 original size:44 final size:44 Alignment explanation

Indices: 44324349--44324682 Score: 159 Period size: 44 Copynumber: 7.6 Consensus size: 44 44324339 ACCATCTTTG 44324349 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA 1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA * * * * * * * 44324393 ACCTACTCCACAACTGCTTAGGGTGATAGGA-CT--AATGGCTTAA 1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAAT--CTTCA * * * * * * * * * 44324436 ATCTGCTTCTCCACTGTATT-GGGAAGATAAGATTC-ACCATGTTCA 1 ATCTGCTCCACTACTG-ATTAGGG-TGA-CAGAATCTGCAATCTTCA 44324481 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA 1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA * * * * * * 44324525 ACCTACTCCACTACTGCTTAGGGTGATAGGA-CT--AATGGCTTAA 1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAAT--CTTCA * * * * * * * 44324568 ATCTGCTTCTAC-ACTGCATT-GGGAAGATAAGATTC-ACCATCTTCG 1 ATCTGC-TCCACTACTG-ATTAGGG-TGA-CAGAATCTGCAATCTTCA * * * * * 44324613 ATATTCTCCACTACTGCTTAGGGTGGCAGAATTTGCAATCTTCA 1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA * * * 44324657 ACCTACTCCACTACTGCTTAGGGTGA 1 ATCTGCTCCACTACTGATTAGGGTGA 44324683 TAGGACTAAT Statistics Matches: 206, Mismatches: 62, Indels: 44 0.66 0.20 0.14 Matches are distributed among these distances: 41 6 0.03 43 46 0.22 44 111 0.54 45 37 0.18 46 2 0.01 47 4 0.02 ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30 Consensus pattern (44 bp): ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA Found at i:44325949 original size:21 final size:20 Alignment explanation

Indices: 44325923--44325968 Score: 65 Period size: 21 Copynumber: 2.2 Consensus size: 20 44325913 GGTATAGCAG 44325923 GATCACCACATGCCCCAATCT 1 GATCACCACATGCCCC-ATCT ** 44325944 GATCACTTCATGCCCCATCT 1 GATCACCACATGCCCCATCT 44325964 GATCA 1 GATCA 44325969 ATATTTGAGC Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 20 9 0.39 21 14 0.61 ACGTcount: A:0.26, C:0.39, G:0.11, T:0.24 Consensus pattern (20 bp): GATCACCACATGCCCCATCT Found at i:44326954 original size:13 final size:12 Alignment explanation

Indices: 44326936--44327052 Score: 54 Period size: 13 Copynumber: 9.0 Consensus size: 12 44326926 TGACTTCTCC 44326936 TTTTTCTTTTTCT 1 TTTTTCTTTTT-T 44326949 TTTTTCTTCTCTTT 1 TTTTTCTT-T-TTT 44326963 TTTTTCCTTTTTT 1 TTTTT-CTTTTTT ** * 44326976 TTTGACTTCGATTT 1 TTTTTCTT--TTTT ** * 44326990 TTTTGATTTTTAA 1 TTTTTCTTTTT-T * 44327003 TTTTTGTTTTTT 1 TTTTTCTTTTTT * 44327015 GTTTTTGTTTTTT 1 -TTTTTCTTTTTT * * 44327028 TGTTTTGTTATTT 1 T-TTTTCTTTTTT * 44327041 TTTTTGTTTTTT 1 TTTTTCTTTTTT 44327053 CCTTTTTTTT Statistics Matches: 83, Mismatches: 13, Indels: 17 0.73 0.12 0.15 Matches are distributed among these distances: 12 16 0.19 13 46 0.55 14 16 0.19 15 5 0.06 ACGTcount: A:0.05, C:0.08, G:0.08, T:0.79 Consensus pattern (12 bp): TTTTTCTTTTTT Found at i:44326961 original size:12 final size:12 Alignment explanation

Indices: 44326929--44326975 Score: 53 Period size: 12 Copynumber: 4.0 Consensus size: 12 44326919 TTCGCCTTGA * 44326929 CTTCTCCTTTTT 1 CTTCTCTTTTTT * 44326941 CTTTTTCTTTTTT 1 C-TTCTCTTTTTT 44326954 CTTCTCTTTTTT 1 CTTCTCTTTTTT 44326966 -TTC-CTTTTTT 1 CTTCTCTTTTTT 44326976 TTTGACTTCG Statistics Matches: 31, Mismatches: 3, Indels: 4 0.82 0.08 0.11 Matches are distributed among these distances: 10 7 0.23 11 3 0.10 12 11 0.35 13 10 0.32 ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77 Consensus pattern (12 bp): CTTCTCTTTTTT Found at i:44326984 original size:27 final size:25 Alignment explanation

Indices: 44326925--44326993 Score: 61 Period size: 25 Copynumber: 2.7 Consensus size: 25 44326915 GGTTTTCGCC 44326925 TTGACTTCTCCTTTTTCTTTTTCTTTT 1 TTGACTTCT-CTTTTT-TTTTTCTTTT * 44326952 TT--CTTCTCTTTTTTTTCCTTTTTTT 1 TTGACTTCTCTTTTTTTT--TTCTTTT ** 44326977 TTGACTTCGATTTTTTT 1 TTGACTTCTCTTTTTTT 44326994 GATTTTTAAT Statistics Matches: 35, Mismatches: 3, Indels: 8 0.76 0.07 0.17 Matches are distributed among these distances: 23 3 0.09 24 6 0.17 25 13 0.37 27 13 0.37 ACGTcount: A:0.04, C:0.19, G:0.04, T:0.72 Consensus pattern (25 bp): TTGACTTCTCTTTTTTTTTTCTTTT Found at i:44327013 original size:7 final size:7 Alignment explanation

Indices: 44326988--44327052 Score: 57 Period size: 7 Copynumber: 9.9 Consensus size: 7 44326978 TGACTTCGAT 44326988 TTTTTTG 1 TTTTTTG * * 44326995 ATTTTTA 1 TTTTTTG * 44327002 ATTTTTG 1 TTTTTTG 44327009 TTTTTTG 1 TTTTTTG 44327016 -TTTTTG 1 TTTTTTG 44327022 TTTTTT- 1 TTTTTTG * 44327028 TGTTTTG 1 TTTTTTG * 44327035 -TTATT- 1 TTTTTTG 44327040 TTTTTTG 1 TTTTTTG 44327047 TTTTTT 1 TTTTTT 44327053 CCTTTTTTTT Statistics Matches: 46, Mismatches: 8, Indels: 8 0.74 0.13 0.13 Matches are distributed among these distances: 6 18 0.39 7 28 0.61 ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83 Consensus pattern (7 bp): TTTTTTG Found at i:44327014 original size:8 final size:8 Alignment explanation

Indices: 44327003--44327052 Score: 54 Period size: 8 Copynumber: 6.5 Consensus size: 8 44326993 TGATTTTTAA 44327003 TTTTTG-T 1 TTTTTGTT 44327010 TTTTTG-- 1 TTTTTGTT 44327016 TTTTTGTT 1 TTTTTGTT 44327024 TTTTTGTT 1 TTTTTGTT 44327032 TTGTTAT-TT 1 TT-TT-TGTT 44327041 TTTTTGTT 1 TTTTTGTT 44327049 TTTT 1 TTTT 44327053 CCTTTTTTTT Statistics Matches: 38, Mismatches: 0, Indels: 9 0.81 0.00 0.19 Matches are distributed among these distances: 6 6 0.16 7 7 0.18 8 18 0.47 9 6 0.16 10 1 0.03 ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86 Consensus pattern (8 bp): TTTTTGTT Found at i:44327059 original size:14 final size:12 Alignment explanation

Indices: 44326987--44327052 Score: 78 Period size: 13 Copynumber: 5.2 Consensus size: 12 44326977 TTGACTTCGA 44326987 TTTTTTTGATTTT 1 TTTTTTTG-TTTT * 44327000 TAATTTTTGTTTT 1 T-TTTTTTGTTTT 44327013 TTGTTTTTGTTTT 1 TT-TTTTTGTTTT * 44327026 TTTGTTTTGTTAT 1 TTT-TTTTGTTTT 44327039 TTTTTTTGTTTT 1 TTTTTTTGTTTT 44327051 TT 1 TT 44327053 CCTTTTTTTT Statistics Matches: 46, Mismatches: 4, Indels: 7 0.81 0.07 0.12 Matches are distributed among these distances: 12 11 0.24 13 29 0.63 14 6 0.13 ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83 Consensus pattern (12 bp): TTTTTTTGTTTT Found at i:44327062 original size:17 final size:17 Alignment explanation

Indices: 44326987--44327050 Score: 60 Period size: 17 Copynumber: 3.7 Consensus size: 17 44326977 TTGACTTCGA * 44326987 TTTTTTTGATTTT-TAAT 1 TTTTTTTG-TTTTGTTAT * * 44327004 TTTTGTT-TTTTGTTTTT 1 TTTTTTTGTTTTG-TTAT 44327021 GTTTTTTTGTTTTGTTAT 1 -TTTTTTTGTTTTGTTAT 44327039 TTTTTTTGTTTT 1 TTTTTTTGTTTT 44327051 TTCCTTTTTT Statistics Matches: 38, Mismatches: 5, Indels: 8 0.75 0.10 0.16 Matches are distributed among these distances: 15 4 0.11 17 20 0.53 18 9 0.24 19 5 0.13 ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83 Consensus pattern (17 bp): TTTTTTTGTTTTGTTAT Found at i:44331829 original size:11 final size:11 Alignment explanation

Indices: 44331813--44331837 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 44331803 ATTTTTTAAC 44331813 TTTAAAATACT 1 TTTAAAATACT 44331824 TTTAAAATACT 1 TTTAAAATACT 44331835 TTT 1 TTT 44331838 TTTAATTTTT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52 Consensus pattern (11 bp): TTTAAAATACT Found at i:44331857 original size:40 final size:40 Alignment explanation

Indices: 44331797--44331945 Score: 212 Period size: 40 Copynumber: 3.7 Consensus size: 40 44331787 TTTTATTTTA * * 44331797 TTTTTT-A-TTTTTTAACTTTAAAATACTTTTAAAATACT 1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT * * 44331835 TTTTTTAATTTTTTTAATTTTAAAATTTTTTTTAAATACT 1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT 44331875 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT 1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT 44331915 TTTTTTAATTTTTATTTTAATTTTTAAAATA 1 TTTTTTAA--TTT-TTTTAA-TTTTAAAATA 44331946 AATTTTTGGT Statistics Matches: 99, Mismatches: 6, Indels: 6 0.89 0.05 0.05 Matches are distributed among these distances: 38 6 0.06 39 1 0.01 40 73 0.74 42 3 0.03 43 6 0.06 44 10 0.10 ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64 Consensus pattern (40 bp): TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT Found at i:44331877 original size:29 final size:28 Alignment explanation

Indices: 44331823--44331878 Score: 69 Period size: 29 Copynumber: 1.9 Consensus size: 28 44331813 TTTAAAATAC * 44331823 TTTTAAAATACTTTTTTTAATTTTTTTAA 1 TTTTAAAATA-TTTTTTTAATCTTTTTAA 44331852 TTTTAAAAT-TTTTTTTAAATACTTTTT 1 TTTTAAAATATTTTTTT-AAT-CTTTTT 44331879 TTAATTTTTT Statistics Matches: 24, Mismatches: 1, Indels: 4 0.83 0.03 0.14 Matches are distributed among these distances: 27 7 0.29 28 3 0.12 29 14 0.58 ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66 Consensus pattern (28 bp): TTTTAAAATATTTTTTTAATCTTTTTAA Found at i:44331888 original size:8 final size:9 Alignment explanation

Indices: 44331834--44331895 Score: 54 Period size: 9 Copynumber: 6.4 Consensus size: 9 44331824 TTTAAAATAC 44331834 TTTTTTTAA 1 TTTTTTTAA 44331843 TTTTTTTAA 1 TTTTTTTAA ** 44331852 -TTTTAAAA 1 TTTTTTTAA 44331860 TTTTTTTTAAATA 1 -TTTTTTT--A-A 44331873 CTTTTTTTAA 1 -TTTTTTTAA 44331883 TTTTTTTAA 1 TTTTTTTAA 44331892 TTTT 1 TTTT 44331896 AAAATATTTT Statistics Matches: 43, Mismatches: 5, Indels: 10 0.74 0.09 0.17 Matches are distributed among these distances: 8 6 0.14 9 22 0.51 10 5 0.12 11 1 0.02 12 1 0.02 13 8 0.19 ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73 Consensus pattern (9 bp): TTTTTTTAA Found at i:44332329 original size:3 final size:3 Alignment explanation

Indices: 44332323--44332349 Score: 54 Period size: 3 Copynumber: 9.0 Consensus size: 3 44332313 AAACTACTAT 44332323 TAA TAA TAA TAA TAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA 44332350 AATTGCTAAA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 24 1.00 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (3 bp): TAA Found at i:44335363 original size:17 final size:17 Alignment explanation

Indices: 44335315--44335365 Score: 54 Period size: 17 Copynumber: 3.1 Consensus size: 17 44335305 TTGTTTATTT * 44335315 AATTTAATTA-ATTTT- 1 AATTAAATTATATTTTC * 44335330 ATTTAAATT-TATTTTTC 1 AATTAAATTATA-TTTTC 44335347 AATTAAATTATATTTTC 1 AATTAAATTATATTTTC 44335364 AA 1 AA 44335366 CCAACTTTTA Statistics Matches: 29, Mismatches: 3, Indels: 6 0.76 0.08 0.16 Matches are distributed among these distances: 15 8 0.28 16 4 0.14 17 15 0.52 18 2 0.07 ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57 Consensus pattern (17 bp): AATTAAATTATATTTTC Found at i:44336250 original size:29 final size:29 Alignment explanation

Indices: 44336208--44336267 Score: 120 Period size: 29 Copynumber: 2.1 Consensus size: 29 44336198 CATACAAGTC 44336208 ATACATAAATTTTCTATCATCCATTCTGG 1 ATACATAAATTTTCTATCATCCATTCTGG 44336237 ATACATAAATTTTCTATCATCCATTCTGG 1 ATACATAAATTTTCTATCATCCATTCTGG 44336266 AT 1 AT 44336268 TAAGATGTGC Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 29 31 1.00 ACGTcount: A:0.32, C:0.20, G:0.07, T:0.42 Consensus pattern (29 bp): ATACATAAATTTTCTATCATCCATTCTGG Found at i:44343227 original size:59 final size:60 Alignment explanation

Indices: 44343124--44343256 Score: 160 Period size: 59 Copynumber: 2.2 Consensus size: 60 44343114 TATATTAGTA * * * * ** * 44343124 GTCACCTAATTATTAGTAAATTTTTTTTTTGGCCATTCAACTATG-AAAGTTGCAAAATG 1 GTCACCCAACTATTAGTAAATTTCTTTTTTGACCACCCAACTATGAAAAGTTACAAAATG * * * * 44343183 GTCACCCCACTATTAGTAAATTTCTTTTTTGATCACCCAGCTATGAAAAGTTACAAAATT 1 GTCACCCAACTATTAGTAAATTTCTTTTTTGACCACCCAACTATGAAAAGTTACAAAATG 44343243 GTCACCCAACTATT 1 GTCACCCAACTATT 44343257 TAATTTTGTT Statistics Matches: 61, Mismatches: 12, Indels: 1 0.82 0.16 0.01 Matches are distributed among these distances: 59 36 0.59 60 25 0.41 ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37 Consensus pattern (60 bp): GTCACCCAACTATTAGTAAATTTCTTTTTTGACCACCCAACTATGAAAAGTTACAAAATG Found at i:44344164 original size:9 final size:9 Alignment explanation

Indices: 44344152--44344201 Score: 50 Period size: 8 Copynumber: 5.4 Consensus size: 9 44344142 TAATGTTTTT 44344152 AATTTTAAA 1 AATTTTAAA * 44344161 AATTTTGTTTAA 1 AA--TT-TTAAA 44344173 AATTTT-AA 1 AATTTTAAA 44344181 AATTTTAAA 1 AATTTTAAA 44344190 AA-TTTAAA 1 AATTTTAAA 44344198 AATT 1 AATT 44344202 AATTAAATAT Statistics Matches: 35, Mismatches: 1, Indels: 10 0.76 0.02 0.22 Matches are distributed among these distances: 8 16 0.46 9 9 0.26 10 2 0.06 11 2 0.06 12 6 0.17 ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48 Consensus pattern (9 bp): AATTTTAAA Found at i:44344181 original size:8 final size:8 Alignment explanation

Indices: 44344168--44344198 Score: 53 Period size: 8 Copynumber: 3.9 Consensus size: 8 44344158 AAAAATTTTG 44344168 TTTAAAAT 1 TTTAAAAT 44344176 TTTAAAAT 1 TTTAAAAT * 44344184 TTTAAAAA 1 TTTAAAAT 44344192 TTTAAAA 1 TTTAAAA 44344199 ATTAATTAAA Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 8 22 1.00 ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45 Consensus pattern (8 bp): TTTAAAAT Found at i:44362095 original size:2 final size:2 Alignment explanation

Indices: 44362088--44362112 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 44362078 AGTCATTTGA 44362088 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 44362113 AACAAAAATC 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:44367058 original size:22 final size:22 Alignment explanation

Indices: 44366976--44367055 Score: 112 Period size: 22 Copynumber: 3.7 Consensus size: 22 44366966 AATCTTCAAG 44366976 GATATGCAATCTT---AGATAT 1 GATATGCAATCTTAGAAGATAT 44366995 GATATGCAATCTTAGAAGATAT 1 GATATGCAATCTTAGAAGATAT 44367017 GATATGCAATCTTAGAAGATAT 1 GATATGCAATCTTAGAAGATAT * * 44367039 GATTTTGTAATCTTAGA 1 GA-TATGCAATCTTAGA 44367056 GATTTAATTT Statistics Matches: 55, Mismatches: 2, Indels: 4 0.90 0.03 0.07 Matches are distributed among these distances: 19 13 0.24 22 30 0.55 23 12 0.22 ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36 Consensus pattern (22 bp): GATATGCAATCTTAGAAGATAT Found at i:44367302 original size:23 final size:23 Alignment explanation

Indices: 44367258--44367302 Score: 54 Period size: 23 Copynumber: 2.0 Consensus size: 23 44367248 TCTTATTTTG * * 44367258 TTGATTTGTGTATAATTTATTTA 1 TTGATTTGTATATAATTGATTTA ** 44367281 TTGATTTGTATATTGTTGATTT 1 TTGATTTGTATATAATTGATTT 44367303 CAAATCTCTT Statistics Matches: 18, Mismatches: 4, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 23 18 1.00 ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62 Consensus pattern (23 bp): TTGATTTGTATATAATTGATTTA Found at i:44367732 original size:15 final size:16 Alignment explanation

Indices: 44367707--44367741 Score: 63 Period size: 15 Copynumber: 2.2 Consensus size: 16 44367697 TTAAAATATG 44367707 TATATTTTTATTTTTT 1 TATATTTTTATTTTTT 44367723 TATA-TTTTATTTTTT 1 TATATTTTTATTTTTT 44367738 TATA 1 TATA 44367742 ATTCACACAC Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 15 15 0.79 16 4 0.21 ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77 Consensus pattern (16 bp): TATATTTTTATTTTTT Found at i:44367777 original size:23 final size:22 Alignment explanation

Indices: 44367750--44367792 Score: 68 Period size: 23 Copynumber: 1.9 Consensus size: 22 44367740 TAATTCACAC * 44367750 ACATATATATTTTTCTTATATGT 1 ACATATATATATTT-TTATATGT 44367773 ACATATATATATTTTTATAT 1 ACATATATATATTTTTATAT 44367793 TTTATAATTT Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 22 6 0.32 23 13 0.68 ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56 Consensus pattern (22 bp): ACATATATATATTTTTATATGT Found at i:44367882 original size:3 final size:3 Alignment explanation

Indices: 44367874--44367938 Score: 130 Period size: 3 Copynumber: 21.7 Consensus size: 3 44367864 TCACATGACC 44367874 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 44367922 ATT ATT ATT ATT ATT AT 1 ATT ATT ATT ATT ATT AT 44367939 ATTCTTTAAA Statistics Matches: 62, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 62 1.00 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (3 bp): ATT Found at i:44371278 original size:2 final size:2 Alignment explanation

Indices: 44371271--44371296 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 44371261 TATCAACATC 44371271 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 44371297 TCACTTTTAA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:44371861 original size:40 final size:40 Alignment explanation

Indices: 44371817--44371955 Score: 133 Period size: 37 Copynumber: 3.5 Consensus size: 40 44371807 ACATATCAGT * 44371817 TTGACACCCAGTGCCTCATCGGATAATTTGAAGTAGTAAA 1 TTGACACCCAGTGCCTCATCGGATAATCTGAAGTAGTAAA * * * * 44371857 TTGACACCCAGCGTCTCATC-GATTAAACTG-A--AGTAAG 1 TTGACACCCAGTGCCTCATCGGA-TAATCTGAAGTAGTAAA * * * 44371894 TTGGCACCCAGTGCCTCATCGAATAAATCTGAAGTAATAAA 1 TTGACACCCAGTGCCTCATCGGAT-AATCTGAAGTAGTAAA * * * 44371935 TTGAAACCCGGTGTCTCATCG 1 TTGACACCCAGTGCCTCATCG 44371956 ACTCGAAGTC Statistics Matches: 77, Mismatches: 16, Indels: 11 0.74 0.15 0.11 Matches are distributed among these distances: 37 23 0.30 38 6 0.08 39 4 0.05 40 23 0.30 41 21 0.27 ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26 Consensus pattern (40 bp): TTGACACCCAGTGCCTCATCGGATAATCTGAAGTAGTAAA Found at i:44381274 original size:17 final size:18 Alignment explanation

Indices: 44381248--44381287 Score: 64 Period size: 17 Copynumber: 2.3 Consensus size: 18 44381238 TTCTTCTCTC * 44381248 AATTTTTTTTATTTT-AT 1 AATTTATTTTATTTTCAT 44381265 AATTTATTTTATTTTCAT 1 AATTTATTTTATTTTCAT 44381283 AATTT 1 AATTT 44381288 TAAAAATGTC Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 17 14 0.67 18 7 0.33 ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70 Consensus pattern (18 bp): AATTTATTTTATTTTCAT Found at i:44385250 original size:30 final size:30 Alignment explanation

Indices: 44385216--44385292 Score: 84 Period size: 30 Copynumber: 2.6 Consensus size: 30 44385206 ACAGTAGAAC * * 44385216 AAGATGAAGATTAAGAT-AATGTTAGAGATG 1 AAGATGAAGATCAAGATCAA-GGTAGAGATG * * 44385246 AAGATCAAGATCAAGATCAAGGTAGAGCTG 1 AAGATGAAGATCAAGATCAAGGTAGAGATG * * 44385276 GAGATGAAGATGAAGAT 1 AAGATGAAGATCAAGAT 44385293 GAAGATGATG Statistics Matches: 39, Mismatches: 7, Indels: 2 0.81 0.15 0.04 Matches are distributed among these distances: 30 37 0.95 31 2 0.05 ACGTcount: A:0.45, C:0.05, G:0.29, T:0.21 Consensus pattern (30 bp): AAGATGAAGATCAAGATCAAGGTAGAGATG Found at i:44385262 original size:36 final size:36 Alignment explanation

Indices: 44385215--44385298 Score: 98 Period size: 36 Copynumber: 2.3 Consensus size: 36 44385205 CACAGTAGAA * * 44385215 CAAGATGAAGATTAAGATA-ATGTTAGAGATGAAGAT 1 CAAGATGAAGATCAAGATAGA-GCTAGAGATGAAGAT * * * 44385251 CAAGATCAAGATCAAGGTAGAGCTGGAGATGAAGAT 1 CAAGATGAAGATCAAGATAGAGCTAGAGATGAAGAT * 44385287 GAAGATGAAGAT 1 CAAGATGAAGAT 44385299 GATGAGCCTG Statistics Matches: 40, Mismatches: 7, Indels: 2 0.82 0.14 0.04 Matches are distributed among these distances: 36 39 0.98 37 1 0.03 ACGTcount: A:0.45, C:0.06, G:0.29, T:0.20 Consensus pattern (36 bp): CAAGATGAAGATCAAGATAGAGCTAGAGATGAAGAT Found at i:44385299 original size:12 final size:12 Alignment explanation

Indices: 44385241--44385300 Score: 50 Period size: 12 Copynumber: 5.0 Consensus size: 12 44385231 ATAATGTTAG * 44385241 AGATGAAGATCA 1 AGATGAAGATGA * * 44385253 AGATCAAGATCA 1 AGATGAAGATGA * * * 44385265 AGGT-AGAGCTGG 1 AGATGA-AGATGA 44385277 AGATGAAGATGA 1 AGATGAAGATGA 44385289 AGATGAAGATGA 1 AGATGAAGATGA 44385301 TGAGCCTGAA Statistics Matches: 38, Mismatches: 8, Indels: 4 0.76 0.16 0.08 Matches are distributed among these distances: 11 1 0.03 12 36 0.95 13 1 0.03 ACGTcount: A:0.45, C:0.07, G:0.32, T:0.17 Consensus pattern (12 bp): AGATGAAGATGA Found at i:44385632 original size:70 final size:70 Alignment explanation

Indices: 44385544--44385677 Score: 241 Period size: 70 Copynumber: 1.9 Consensus size: 70 44385534 ATTAAAAATA 44385544 ATTGTATTATATTTTTACATCAATAATATATTTATTTACAATTTACCAAAAAAATGAATAAATTA 1 ATTGTATTATATTTTTACATCAATAATATATTTATTTACAATTTACCAAAAAAATGAATAAATTA 44385609 TTTGT 66 TTTGT * * * 44385614 ATTGTATTGTATTTTTACATCAATAATATATTTATTTACAATTTTCCCAAAAAATGAATAAATT 1 ATTGTATTATATTTTTACATCAATAATATATTTATTTACAATTTACCAAAAAAATGAATAAATT 44385678 GTTTTTTTAT Statistics Matches: 61, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 70 61 1.00 ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46 Consensus pattern (70 bp): ATTGTATTATATTTTTACATCAATAATATATTTATTTACAATTTACCAAAAAAATGAATAAATTA TTTGT Found at i:44386656 original size:20 final size:19 Alignment explanation

Indices: 44386615--44386674 Score: 65 Period size: 20 Copynumber: 3.2 Consensus size: 19 44386605 TTTAAATATA 44386615 TATAAATATATTATTTTAT 1 TATAAATATATTATTTTAT 44386634 TATAAAGTATATTATTATT-T 1 TATAAA-TATATTATT-TTAT 44386654 TAT---TATATTAATTTTAT 1 TATAAATATATT-ATTTTAT 44386671 TATA 1 TATA 44386675 TTTTTATATT Statistics Matches: 36, Mismatches: 0, Indels: 11 0.77 0.00 0.23 Matches are distributed among these distances: 16 8 0.22 17 7 0.19 19 6 0.17 20 13 0.36 21 2 0.06 ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58 Consensus pattern (19 bp): TATAAATATATTATTTTAT Found at i:44386681 original size:11 final size:13 Alignment explanation

Indices: 44386621--44386676 Score: 55 Period size: 14 Copynumber: 4.5 Consensus size: 13 44386611 TATATATAAA 44386621 TATATTATTTTAT 1 TATATTATTTTAT * * * 44386634 TATA-AAGTATA- 1 TATATTATTTTAT 44386645 T-TATTATTTTAT 1 TATATTATTTTAT 44386657 TATATTAATTTTAT 1 TATATT-ATTTTAT 44386671 TATATT 1 TATATT 44386677 TTTATATTTT Statistics Matches: 33, Mismatches: 6, Indels: 7 0.72 0.13 0.15 Matches are distributed among these distances: 10 2 0.06 11 5 0.15 12 5 0.15 13 8 0.24 14 13 0.39 ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62 Consensus pattern (13 bp): TATATTATTTTAT Found at i:44395464 original size:24 final size:25 Alignment explanation

Indices: 44395405--44395466 Score: 81 Period size: 28 Copynumber: 2.4 Consensus size: 25 44395395 TATTGTAAAA * 44395405 ATTTGCACTTTGGTGCTTATCGATATT 1 ATTTGCACTTCGGTGCTTATC-A-ATT 44395432 ATTTTGCACTTCGGTGCTTATC-ATT 1 A-TTTGCACTTCGGTGCTTATCAATT 44395457 ATTTGCACTT 1 ATTTGCACTT 44395467 TGTACTTAGT Statistics Matches: 33, Mismatches: 1, Indels: 5 0.85 0.03 0.13 Matches are distributed among these distances: 24 9 0.27 25 4 0.12 27 1 0.03 28 19 0.58 ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48 Consensus pattern (25 bp): ATTTGCACTTCGGTGCTTATCAATT Found at i:44396396 original size:15 final size:15 Alignment explanation

Indices: 44396376--44396406 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 44396366 TCATATTTAA 44396376 ATCATTTCTAAACAT 1 ATCATTTCTAAACAT 44396391 ATCATTTCTAAACAT 1 ATCATTTCTAAACAT 44396406 A 1 A 44396407 CTCGGTTAAC 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:0.42, C:0.19, G:0.00, T:0.39 Consensus pattern (15 bp): ATCATTTCTAAACAT Found at i:44397020 original size:8 final size:8 Alignment explanation

Indices: 44397007--44397295 Score: 416 Period size: 8 Copynumber: 36.1 Consensus size: 8 44396997 ATCCATTTGG * 44397007 ATGTATGC 1 ATGTATGT 44397015 ATGTATGT 1 ATGTATGT 44397023 ATGTATGT 1 ATGTATGT 44397031 ATGTATGT 1 ATGTATGT * 44397039 ATGTGTGT 1 ATGTATGT * 44397047 ATGTGTGT 1 ATGTATGT * 44397055 ATGTGTGT 1 ATGTATGT * 44397063 ATGTGTGT 1 ATGTATGT * 44397071 ATGTGTGT 1 ATGTATGT * 44397079 ATGTGTGT 1 ATGTATGT * 44397087 ATGTGTGT 1 ATGTATGT * 44397095 ATGTGTGT 1 ATGTATGT * 44397103 ATGTGTGT 1 ATGTATGT * 44397111 ATGTGTGT 1 ATGTATGT * 44397119 ATGTGTGT 1 ATGTATGT * 44397127 GTGTATGT 1 ATGTATGT * 44397135 GTGTATGT 1 ATGTATGT * 44397143 GTGTATGT 1 ATGTATGT * * 44397151 GTGTGTGT 1 ATGTATGT 44397159 ATGTATGT 1 ATGTATGT 44397167 ATGTATGT 1 ATGTATGT 44397175 ATGTATGT 1 ATGTATGT 44397183 ATGTATGT 1 ATGTATGT 44397191 ATGTATGT 1 ATGTATGT 44397199 ATGTATGT 1 ATGTATGT 44397207 ATGTATGT 1 ATGTATGT 44397215 ATGTATGT 1 ATGTATGT * 44397223 GTGTATGT 1 ATGTATGT 44397231 ATGTATGT 1 ATGTATGT 44397239 ATGTATGT 1 ATGTATGT 44397247 ATGTATGT 1 ATGTATGT 44397255 ATGTATGT 1 ATGTATGT 44397263 ATGTATGT 1 ATGTATGT 44397271 ATGTATGT 1 ATGTATGT 44397279 ATGTATGT 1 ATGTATGT 44397287 ATGTATGT 1 ATGTATGT 44397295 A 1 A 44397296 ACATTCCCCA Statistics Matches: 272, Mismatches: 9, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 8 272 1.00 ACGTcount: A:0.19, C:0.00, G:0.31, T:0.49 Consensus pattern (8 bp): ATGTATGT Found at i:44397410 original size:10 final size:10 Alignment explanation

Indices: 44397394--44397428 Score: 54 Period size: 10 Copynumber: 3.5 Consensus size: 10 44397384 CTTCTACTTG 44397394 ATTTTATAAGT 1 ATTTTATAA-T 44397405 -TTTTATAAT 1 ATTTTATAAT 44397414 ATTTTATAAT 1 ATTTTATAAT 44397424 ATTTT 1 ATTTT 44397429 TTATTTTTAC Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 9 1 0.04 10 22 0.96 ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63 Consensus pattern (10 bp): ATTTTATAAT Found at i:44397987 original size:6 final size:7 Alignment explanation

Indices: 44397970--44397995 Score: 52 Period size: 7 Copynumber: 3.7 Consensus size: 7 44397960 TTTAAATTCG 44397970 AAAAAGT 1 AAAAAGT 44397977 AAAAAGT 1 AAAAAGT 44397984 AAAAAGT 1 AAAAAGT 44397991 AAAAA 1 AAAAA 44397996 AATACAAAAG Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 19 1.00 ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12 Consensus pattern (7 bp): AAAAAGT Found at i:44398312 original size:43 final size:43 Alignment explanation

Indices: 44398264--44398351 Score: 113 Period size: 43 Copynumber: 2.0 Consensus size: 43 44398254 TATCAGCACG * *** * 44398264 ATCTTGCTTAAAGTGATAGGTCCTTTTATCAACGATTAAATTT 1 ATCTTGCTCAAAGTGATAAAACCTTTTATCAACGATCAAATTT * * 44398307 ATCTTGCTCAAAGTGATAAAACCTTTTATCGATGATCAAATTT 1 ATCTTGCTCAAAGTGATAAAACCTTTTATCAACGATCAAATTT 44398350 AT 1 AT 44398352 TCTCCATGAT Statistics Matches: 38, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 43 38 1.00 ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40 Consensus pattern (43 bp): ATCTTGCTCAAAGTGATAAAACCTTTTATCAACGATCAAATTT Found at i:44400399 original size:14 final size:14 Alignment explanation

Indices: 44400380--44400406 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 44400370 ACAAAACAAT 44400380 ATGACTAACTAAAC 1 ATGACTAACTAAAC 44400394 ATGACTAACTAAA 1 ATGACTAACTAAA 44400407 ATACGACTAA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22 Consensus pattern (14 bp): ATGACTAACTAAAC Found at i:44402632 original size:2 final size:2 Alignment explanation

Indices: 44402627--44402651 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 44402617 CTATATATAT 44402627 AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG A 44402652 AAGTATTTTA 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:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:44411081 original size:50 final size:51 Alignment explanation

Indices: 44410959--44411085 Score: 184 Period size: 51 Copynumber: 2.5 Consensus size: 51 44410949 AAAGGTCGCA * * * 44410959 TGTGTAGTACCATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACG 1 TGTGTAGTACTATGTGCAGGCTACTATGCGAACCGGAAAGCTTCGATCACG * ** 44411010 TGTGTAGTACTATGTGCAGGCTACTATGTGAACCGGAAAG-TTTTATCACG 1 TGTGTAGTACTATGTGCAGGCTACTATGCGAACCGGAAAGCTTCGATCACG * 44411060 TGTGTAGTACTATGTGAAGGCTACTA 1 TGTGTAGTACTATGTGCAGGCTACTA 44411086 CATGTATCGA Statistics Matches: 69, Mismatches: 7, Indels: 1 0.90 0.09 0.01 Matches are distributed among these distances: 50 33 0.48 51 36 0.52 ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31 Consensus pattern (51 bp): TGTGTAGTACTATGTGCAGGCTACTATGCGAACCGGAAAGCTTCGATCACG Found at i:44413315 original size:15 final size:14 Alignment explanation

Indices: 44413294--44413329 Score: 54 Period size: 15 Copynumber: 2.5 Consensus size: 14 44413284 ATAATCCTTA * 44413294 ATAATTATCTTAAT 1 ATAATTATCCTAAT 44413308 ATTAATTATCCTAAT 1 A-TAATTATCCTAAT 44413323 ATAATTA 1 ATAATTA 44413330 AAATAGAGTC Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 14 7 0.35 15 13 0.65 ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47 Consensus pattern (14 bp): ATAATTATCCTAAT Found at i:44417105 original size:84 final size:84 Alignment explanation

Indices: 44416964--44417119 Score: 212 Period size: 84 Copynumber: 1.9 Consensus size: 84 44416954 GGCTCGTACA * * 44416964 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCAATGCCACTGTCCCAGACAGGGT 1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCAATGCCACTGTCCCAGACAGGGT 44417029 CGTACACAAATCAACTACG 66 CGTACACAAATCAACTACG 44417048 ATGCC-ACTGTCCCAGACATGGTCTTACACGT-ATACACA-AGTCAATGCCAAC-GTCCCAGACA 1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAT-CACATA-TCAATGCC-ACTGTCCCAGACA * * 44417109 TGGTCTTACAC 62 GGGTCGTACAC 44417120 GAAAATACAT Statistics Matches: 64, Mismatches: 4, Indels: 8 0.84 0.05 0.11 Matches are distributed among these distances: 83 5 0.08 84 57 0.89 85 2 0.03 ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22 Consensus pattern (84 bp): ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCAATGCCACTGTCCCAGACAGGGT CGTACACAAATCAACTACG Found at i:44417119 original size:43 final size:41 Alignment explanation

Indices: 44416962--44417120 Score: 157 Period size: 43 Copynumber: 3.8 Consensus size: 41 44416952 AAGGCTCGTA * * 44416962 CAATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCACATAT 1 CAATGCC-ACTGTCCCAGACATGGTCTTACACGTAA-CACA-AT * * 44417005 CAATGCCACTGTCCCAGACAGGGTCGTACAC--AA-ATCAACT 1 CAATGCCACTGTCCCAGACATGGTCTTACACGTAACA-CAA-T * 44417045 ACGATGCCACTGTCCCAGACATGGTCTTACACGTATACACAAGT 1 -CAATGCCACTGTCCCAGACATGGTCTTACACGTA-ACACAA-T 44417089 CAATGCCAAC-GTCCCAGACATGGTCTTACACG 1 CAATGCC-ACTGTCCCAGACATGGTCTTACACG 44417121 AAAATACATA Statistics Matches: 98, Mismatches: 9, Indels: 18 0.78 0.07 0.14 Matches are distributed among these distances: 39 2 0.02 40 3 0.03 41 30 0.31 42 2 0.02 43 53 0.54 44 7 0.07 45 1 0.01 ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21 Consensus pattern (41 bp): CAATGCCACTGTCCCAGACATGGTCTTACACGTAACACAAT Found at i:44419881 original size:34 final size:34 Alignment explanation

Indices: 44419838--44419905 Score: 127 Period size: 34 Copynumber: 2.0 Consensus size: 34 44419828 TCTATACTTG 44419838 GGTATCACGATACCCATTTCATGATGGGACAAAA 1 GGTATCACGATACCCATTTCATGATGGGACAAAA * 44419872 GGTATCACGATACCCATTTCGTGATGGGACAAAA 1 GGTATCACGATACCCATTTCATGATGGGACAAAA 44419906 ATGGCACAAA Statistics Matches: 33, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 34 33 1.00 ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24 Consensus pattern (34 bp): GGTATCACGATACCCATTTCATGATGGGACAAAA Found at i:44421913 original size:15 final size:15 Alignment explanation

Indices: 44421893--44421924 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 44421883 CATTTCACTA * 44421893 TTATGTCTTTTGTAT 1 TTATGTCTTTTATAT 44421908 TTATGTCTTTTATAT 1 TTATGTCTTTTATAT 44421923 TT 1 TT 44421925 TGCATGCATA 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:0.16, C:0.06, G:0.09, T:0.69 Consensus pattern (15 bp): TTATGTCTTTTATAT Found at i:44423583 original size:37 final size:35 Alignment explanation

Indices: 44423520--44423589 Score: 88 Period size: 37 Copynumber: 1.9 Consensus size: 35 44423510 ATTTCCAAAA * 44423520 TAATATCATTTTAATAGTTTAATATTAAATTTAATT 1 TAATATCATCTTAATAGTTTAATATT-AATTTAATT * 44423556 TAATACTCATCTTAATAGTATT-TTATTAATTTAA 1 TAATA-TCATCTTAATAGT-TTAATATTAATTTAA 44423590 GATTAATGTG Statistics Matches: 30, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 36 12 0.40 37 16 0.53 38 2 0.07 ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51 Consensus pattern (35 bp): TAATATCATCTTAATAGTTTAATATTAATTTAATT Found at i:44425502 original size:3 final size:3 Alignment explanation

Indices: 44425494--44425556 Score: 85 Period size: 3 Copynumber: 21.7 Consensus size: 3 44425484 AAAACCCTAT * * 44425494 AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG 1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG * 44425542 AA- AA- AAA AAG AAG AA 1 AAG AAG AAG AAG AAG AA 44425557 AATCTAAGAG Statistics Matches: 54, Mismatches: 5, Indels: 2 0.89 0.08 0.03 Matches are distributed among these distances: 2 4 0.07 3 50 0.93 ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00 Consensus pattern (3 bp): AAG Found at i:44425518 original size:21 final size:21 Alignment explanation

Indices: 44425494--44425556 Score: 112 Period size: 21 Copynumber: 3.1 Consensus size: 21 44425484 AAAACCCTAT 44425494 AAGAAGAAGAAAAAGAAGAAG 1 AAGAAGAAGAAAAAGAAGAAG 44425515 AAGAAGAAGAAAAAGAAGAAG 1 AAGAAGAAGAAAAAGAAGAAG 44425536 AAGAAGAA-AAAAA-AAGAAG 1 AAGAAGAAGAAAAAGAAGAAG 44425555 AA 1 AA 44425557 AATCTAAGAG Statistics Matches: 42, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 19 8 0.19 20 5 0.12 21 29 0.69 ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00 Consensus pattern (21 bp): AAGAAGAAGAAAAAGAAGAAG Found at i:44429835 original size:20 final size:20 Alignment explanation

Indices: 44429793--44429842 Score: 57 Period size: 20 Copynumber: 2.5 Consensus size: 20 44429783 AACCGATAAA * 44429793 ATCGATACCAAGAGAAAATT 1 ATCGATACCAAGAGAAAAGT * 44429813 ATCGATACCAA-ATAAAAGGT 1 ATCGATACCAAGAGAAAA-GT * 44429833 ATCAATACCA 1 ATCGATACCA 44429843 TTTCATTTAA Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 19 5 0.19 20 21 0.81 ACGTcount: A:0.50, C:0.18, G:0.12, T:0.20 Consensus pattern (20 bp): ATCGATACCAAGAGAAAAGT Found at i:44429944 original size:136 final size:136 Alignment explanation

Indices: 44429700--44429977 Score: 556 Period size: 136 Copynumber: 2.0 Consensus size: 136 44429690 TTGAGATGAA 44429700 AATACCATTTCATTTAATTCACCTGCAACAAAAGTTATCGATACTTAATTTTAACATTTAATGCC 1 AATACCATTTCATTTAATTCACCTGCAACAAAAGTTATCGATACTTAATTTTAACATTTAATGCC 44429765 TTGATTCAGTGACCATTAAACCGATAAAATCGATACCAAGAGAAAATTATCGATACCAAATAAAA 66 TTGATTCAGTGACCATTAAACCGATAAAATCGATACCAAGAGAAAATTATCGATACCAAATAAAA 44429830 GGTATC 131 GGTATC 44429836 AATACCATTTCATTTAATTCACCTGCAACAAAAGTTATCGATACTTAATTTTAACATTTAATGCC 1 AATACCATTTCATTTAATTCACCTGCAACAAAAGTTATCGATACTTAATTTTAACATTTAATGCC 44429901 TTGATTCAGTGACCATTAAACCGATAAAATCGATACCAAGAGAAAATTATCGATACCAAATAAAA 66 TTGATTCAGTGACCATTAAACCGATAAAATCGATACCAAGAGAAAATTATCGATACCAAATAAAA 44429966 GGTATC 131 GGTATC 44429972 AATACC 1 AATACC 44429978 GGTGATAGTA Statistics Matches: 142, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 136 142 1.00 ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30 Consensus pattern (136 bp): AATACCATTTCATTTAATTCACCTGCAACAAAAGTTATCGATACTTAATTTTAACATTTAATGCC TTGATTCAGTGACCATTAAACCGATAAAATCGATACCAAGAGAAAATTATCGATACCAAATAAAA GGTATC Found at i:44429971 original size:20 final size:20 Alignment explanation

Indices: 44429929--44429977 Score: 55 Period size: 20 Copynumber: 2.5 Consensus size: 20 44429919 AACCGATAAA * 44429929 ATCGATACCAAGAGAAAATT 1 ATCGATACCAAGAGAAAAGT * 44429949 ATCGATACCAA-ATAAAAGGT 1 ATCGATACCAAGAGAAAA-GT * 44429969 ATCAATACC 1 ATCGATACC 44429978 GGTGATAGTA Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 19 5 0.20 20 20 0.80 ACGTcount: A:0.49, C:0.18, G:0.12, T:0.20 Consensus pattern (20 bp): ATCGATACCAAGAGAAAAGT Found at i:44431252 original size:17 final size:16 Alignment explanation

Indices: 44431230--44431263 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 44431220 GGGGATAGCG 44431230 TTTGTTTGATGTTTATT 1 TTTGTTTG-TGTTTATT * 44431247 TTTGTTTGTTTTTATT 1 TTTGTTTGTGTTTATT 44431263 T 1 T 44431264 CATAATATTT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 16 8 0.50 17 8 0.50 ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76 Consensus pattern (16 bp): TTTGTTTGTGTTTATT Found at i:44444427 original size:16 final size:16 Alignment explanation

Indices: 44444406--44444437 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 44444396 GTGGAGTGGA 44444406 ACTCCACAGTTTTGGC 1 ACTCCACAGTTTTGGC 44444422 ACTCCACAGTTTTGGC 1 ACTCCACAGTTTTGGC 44444438 GAAGTTCTAC 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:0.19, C:0.31, G:0.19, T:0.31 Consensus pattern (16 bp): ACTCCACAGTTTTGGC Found at i:44455775 original size:10 final size:10 Alignment explanation

Indices: 44455762--44455801 Score: 57 Period size: 9 Copynumber: 4.2 Consensus size: 10 44455752 CTTTACAATA 44455762 TTTTATATTT 1 TTTTATATTT 44455772 TTTTATA-TT 1 TTTTATATTT 44455781 TTTTA-ATTT 1 TTTTATATTT * 44455790 TTTTCTATTT 1 TTTTATATTT 44455800 TT 1 TT 44455802 AATAAATTTT Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 8 1 0.04 9 13 0.48 10 13 0.48 ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80 Consensus pattern (10 bp): TTTTATATTT Found at i:44455781 original size:17 final size:18 Alignment explanation

Indices: 44455759--44455804 Score: 60 Period size: 18 Copynumber: 2.7 Consensus size: 18 44455749 ATTCTTTACA 44455759 ATATTTTAT-ATTTTTTT 1 ATATTTTATAATTTTTTT * 44455776 ATATTTTTTAATTTTTTT 1 ATATTTTATAATTTTTTT * 44455794 CTATTTT-TAAT 1 ATATTTTATAAT 44455805 AAATTTTGAA Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 17 12 0.46 18 14 0.54 ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74 Consensus pattern (18 bp): ATATTTTATAATTTTTTT Found at i:44455789 original size:18 final size:19 Alignment explanation

Indices: 44455762--44455801 Score: 64 Period size: 18 Copynumber: 2.2 Consensus size: 19 44455752 CTTTACAATA 44455762 TTTTATATTTTTTTATATT 1 TTTTATATTTTTTTATATT * 44455781 TTTTA-ATTTTTTTCTATT 1 TTTTATATTTTTTTATATT 44455799 TTT 1 TTT 44455802 AATAAATTTT Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 18 15 0.75 19 5 0.25 ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80 Consensus pattern (19 bp): TTTTATATTTTTTTATATT Found at i:44457130 original size:14 final size:13 Alignment explanation

Indices: 44457103--44457128 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 44457093 AAGATATAAC 44457103 CAGATTTTTTTTT 1 CAGATTTTTTTTT 44457116 CAGATTTTTTTTT 1 CAGATTTTTTTTT 44457129 TCTTTCTTTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69 Consensus pattern (13 bp): CAGATTTTTTTTT Found at i:44459733 original size:25 final size:25 Alignment explanation

Indices: 44459704--44459762 Score: 118 Period size: 25 Copynumber: 2.4 Consensus size: 25 44459694 ATTATATCTA 44459704 ATGTTTTATGAGATACTGACTTTTT 1 ATGTTTTATGAGATACTGACTTTTT 44459729 ATGTTTTATGAGATACTGACTTTTT 1 ATGTTTTATGAGATACTGACTTTTT 44459754 ATGTTTTAT 1 ATGTTTTAT 44459763 CTTGATTGCA Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 34 1.00 ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54 Consensus pattern (25 bp): ATGTTTTATGAGATACTGACTTTTT Found at i:44462198 original size:41 final size:41 Alignment explanation

Indices: 44462137--44462323 Score: 313 Period size: 41 Copynumber: 4.6 Consensus size: 41 44462127 TTTAAACAGA * 44462137 TTCACTGGCACTTCA-CCTGCTAGGCTTATAGCCTGATTCAG 1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTGATTCAG * * 44462178 TTCACCGACACTTAGTCTGCTAGGCTTATAGCCTGATTCAG 1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG * 44462219 TTCACCGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAG 1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG * 44462260 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAA 1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG 44462301 TTCACCGGCACTTAGCCTGCTAG 1 TTCACCGGCACTTAGCCTGCTAG 44462324 ACGTAAAGTC Statistics Matches: 137, Mismatches: 8, Indels: 2 0.93 0.05 0.01 Matches are distributed among these distances: 40 1 0.01 41 136 0.99 ACGTcount: A:0.20, C:0.29, G:0.20, T:0.30 Consensus pattern (41 bp): TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG Found at i:44462346 original size:82 final size:82 Alignment explanation

Indices: 44462136--44462351 Score: 256 Period size: 82 Copynumber: 2.6 Consensus size: 82 44462126 ATTTAAACAG * * * * ** * * 44462136 ATTCACTGGCACTTCA-CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAGTCTGCTA 1 ATTCACCGGCACTT-AGCCTGCTAGACGTAAAGCCTGAAACAGTTCACCGGCACTTAGCCTGCTA 44462200 GGCTTATAGCCTGATTCA 65 GGCTTATAGCCTGATTCA * *** * ** 44462218 GTTCACCGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAG 1 ATTCACCGGCACTTAGCCTGCTAGACGTAAAGCCTGAAACAGTTCACCGGCACTTAGCCTGCTAG 44462283 GCTTATAGCCTGATTCA 66 GCTTATAGCCTGATTCA * 44462300 ATTCACCGGCACTTAGCCTGCTAGACGTAAAGTCC-GAAACATTTCACCGGCA 1 ATTCACCGGCACTTAGCCTGCTAGACGTAAAG-CCTGAAACAGTTCACCGGCA 44462352 ATTAATCTGA Statistics Matches: 119, Mismatches: 13, Indels: 4 0.88 0.10 0.03 Matches are distributed among these distances: 81 1 0.01 82 116 0.97 83 2 0.02 ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29 Consensus pattern (82 bp): ATTCACCGGCACTTAGCCTGCTAGACGTAAAGCCTGAAACAGTTCACCGGCACTTAGCCTGCTAG GCTTATAGCCTGATTCA Found at i:44464074 original size:34 final size:31 Alignment explanation

Indices: 44464015--44464076 Score: 79 Period size: 31 Copynumber: 1.9 Consensus size: 31 44464005 TGTTTTGTTT 44464015 TTATTATAATAACATTATAATATATAAATTA 1 TTATTATAATAACATTATAATATATAAATTA * * 44464046 TTATTATTATAACCTTTATAAATAATATAAA 1 TTATTATAATAA-CATTAT-AAT-ATATAAA 44464077 ATCTATATAT Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 31 11 0.42 32 5 0.19 33 3 0.12 34 7 0.27 ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45 Consensus pattern (31 bp): TTATTATAATAACATTATAATATATAAATTA Found at i:44474327 original size:46 final size:43 Alignment explanation

Indices: 44474001--44474781 Score: 232 Period size: 44 Copynumber: 18.0 Consensus size: 43 44473991 CAGATCGAGC * ** * ** * * 44474001 CTTATCTCCCTGAAGTTACAGTAGAGTAGACTAATTAACCAAGT 1 CTTATCT-CCTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT * * * 44474045 CTTATCCTCCTGAAGTTGCAAC-GAGGCAGACTAAAGATGGTAAAT 1 CTTAT-CTCCTGAAGTTGCAGCGGA-GCAGACTAAAGA-AGCAAAT * * * ** 44474090 CTTATCTCCTTGAAGTTTCAGTGGAGCAGATTAAAGCCG-ACAAT 1 CTTATCTCC-TGAAGTTGCAGCGGAGCAGACTAAAGAAGCA-AAT * * * * * * 44474134 CCTATCTCGCTGAAGTTGCAGTGG-GCGGA-TTAA-AACCTTAGAT 1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGC--AAAT * * * * * * * * 44474177 ATTATCTCTCTGAAGTTGTAG-AGAGCAGA-T--CGCATCTAGT 1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT * ** * 44474217 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGT 1 CTTATCT-CCTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT * * 44474261 CTTATCTTCCTAAAGTTGCAGC-GAGGCAGACTGAAAGATGGCAAAT 1 CTTATC-TCCTGAAGTTGCAGCGGA-GCAGACT-AAAGA-AGCAAAT * * * 44474307 CTTATCTCCTTGAAGTTGCAGAGGAGCAGA-TTAA-AACCGACAAT 1 CTTATCTCC-TGAAGTTGCAGCGGAGCAGACTAAAGAAGC-A-AAT * * ** * * * 44474351 CATATCTCCCTGAAGTTGCAGTGGAGC-GGGTTAA-AACCTTAGAT 1 CTTATCT-CCTGAAGTTGCAGCGGAGCAGACTAAAGAAGC--AAAT * * * * * * * 44474395 CTTATCTCTCTGAAGTTGCAG-AGAGTAGA-T--CGCATCTAGT 1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT * * * ** * 44474435 CTTATCTCCCTGACGTTGTAGTGGAGCAGACTAATTAAGCAAGT 1 CTTATCT-CCTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT * * * 44474479 CTTATCCTCCTGAAGTTACAGC-GAGGCAGACTGAAGATGGCAAAT 1 CTTAT-CTCCTGAAGTTGCAGCGGA-GCAGACTAAAGA-AGCAAAT * * * ** 44474524 CTTATCTCCTTGAAGTTGCGGTGGAGCAGATTAAAGCCG-ACAAT 1 CTTATCTCC-TGAAGTTGCAGCGGAGCAGACTAAAGAAGCA-AAT * * * * * 44474568 CCTATCTCGCTGAAGTTGCAGCGGA-CGGA-TTAA-AACCTTAGAT 1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGC--AAAT * * * * * * * 44474611 CTTATCTCTCTAAAGTTGCAG-AGAGCAGA-T--CGCATCTACT 1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT * * * 44474651 CTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAGT 1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT * * * 44474695 CTTATCCTCTTGAAGTTGCAGC-GAGGCAGACTGAAGATGGCAAAT 1 CTTAT-CTCCTGAAGTTGCAGCGGA-GCAGACTAAAGA-AGCAAAT * * * * 44474740 CTTATCTCCTTGAAATTGCAGTGGAGCAAACTAAATAAGCAA 1 CTTATCTCC-TGAAGTTGCAGCGGAGCAGACTAAAGAAGCAA 44474782 CACCTGATAA Statistics Matches: 544, Mismatches: 136, Indels: 114 0.69 0.17 0.14 Matches are distributed among these distances: 40 57 0.10 41 22 0.04 42 19 0.03 43 73 0.13 44 235 0.43 45 104 0.19 46 32 0.06 47 2 0.00 ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27 Consensus pattern (43 bp): CTTATCTCCTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT Found at i:44474676 original size:216 final size:216 Alignment explanation

Indices: 44474001--44474767 Score: 1246 Period size: 216 Copynumber: 3.5 Consensus size: 216 44473991 CAGATCGAGC * * * * * 44474001 CTTATCTCCCTGAAGTTACAGTAGAGTAGACTAATTAACCAAGTCTTATCCTCCTGAAGTTGCAA 1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTGCAG * * * 44474066 CGAGGCAGACTAAAGATGGTAAATCTTATCTCCTTGAAGTTTCAGTGGAGCAGATTAAAGCCGAC 66 CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGAC * * * 44474131 AATCCTATCTCGCTGAAGTTGCAGTGGGCGGATTAAAACCTTAGATATTATCTCTCTGAAGTTGT 131 AATCCTATCTCGCTGAAGTTGCAGTGGACGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC 44474196 AGAGAGCAGATCGCATCTAGT 196 AGAGAGCAGATCGCATCTAGT * * 44474217 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCTTCCTAAAGTTGCAG 1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTGCAG * * 44474282 CGAGGCAGACTGAAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGAGGAGCAGATTAAAACCGA 66 CGAGGCAGACTG-AAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGA * * * 44474347 CAATCATATCTCCCTGAAGTTGCAGTGGAGCGGGTTAAAACCTTAGATCTTATCTCTCTGAAGTT 130 CAATCCTATCTCGCTGAAGTTGCAGTGGA-CGGATTAAAACCTTAGATCTTATCTCTCTGAAGTT * 44474412 GCAGAGAGTAGATCGCATCTAGT 194 GCAGAGAGCAGATCGCATCTAGT * * * 44474435 CTTATCTCCCTGACGTTGTAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTACAG 1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTGCAG * 44474500 CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCGGTGGAGCAGATTAAAGCCGAC 66 CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGAC * * 44474565 AATCCTATCTCGCTGAAGTTGCAGCGGACGGATTAAAACCTTAGATCTTATCTCTCTAAAGTTGC 131 AATCCTATCTCGCTGAAGTTGCAGTGGACGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC * 44474630 AGAGAGCAGATCGCATCTACT 196 AGAGAGCAGATCGCATCTAGT * * * 44474651 CTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAGTCTTATCCTCTTGAAGTTGCAG 1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTGCAG * 44474716 CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAATTGCAGTGGAGCA 66 CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCA 44474768 AACTAAATAA Statistics Matches: 507, Mismatches: 42, Indels: 4 0.92 0.08 0.01 Matches are distributed among these distances: 216 232 0.46 217 149 0.29 218 126 0.25 ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28 Consensus pattern (216 bp): CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTGCAG CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGAC AATCCTATCTCGCTGAAGTTGCAGTGGACGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC AGAGAGCAGATCGCATCTAGT Found at i:44477915 original size:44 final size:43 Alignment explanation

Indices: 44477833--44477915 Score: 105 Period size: 44 Copynumber: 1.9 Consensus size: 43 44477823 GCCTTGTGAG * 44477833 TATTCGAAATAAGGACACACGGCCGTGTCCTAGCCTGTGTATA 1 TATTCGAAATAAGGACACACGGCCGTGTCCAAGCCTGTGTATA * * * 44477876 TATTCGAAAATAGGGTCACACGGTCGTGTCGCAAG-CTGTG 1 TATTCG-AAATAAGGACACACGGCCGTGTC-CAAGCCTGTG 44477916 CTCGAAACTA Statistics Matches: 34, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 43 6 0.18 44 25 0.74 45 3 0.09 ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25 Consensus pattern (43 bp): TATTCGAAATAAGGACACACGGCCGTGTCCAAGCCTGTGTATA Found at i:44488791 original size:14 final size:14 Alignment explanation

Indices: 44488772--44488805 Score: 59 Period size: 14 Copynumber: 2.4 Consensus size: 14 44488762 TAAGTTTAGT 44488772 TTTATTGTTTAAAG 1 TTTATTGTTTAAAG * 44488786 TTTATTGTTTAAAT 1 TTTATTGTTTAAAG 44488800 TTTATT 1 TTTATT 44488806 TATTCCTTAA Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 14 19 1.00 ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65 Consensus pattern (14 bp): TTTATTGTTTAAAG Found at i:44501684 original size:7 final size:7 Alignment explanation

Indices: 44501672--44501700 Score: 51 Period size: 7 Copynumber: 4.3 Consensus size: 7 44501662 ATACAATAGA 44501672 TATTTAT 1 TATTTAT 44501679 TATTTAT 1 TATTTAT 44501686 TATTTAT 1 TATTTAT 44501693 TA-TTAT 1 TATTTAT 44501699 TA 1 TA 44501701 AATGAAAGAT Statistics Matches: 22, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 6 6 0.27 7 16 0.73 ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69 Consensus pattern (7 bp): TATTTAT Found at i:44501959 original size:15 final size:16 Alignment explanation

Indices: 44501939--44501974 Score: 56 Period size: 15 Copynumber: 2.3 Consensus size: 16 44501929 AAATAAAGTA * 44501939 AAAGAATAAAA-AAAC 1 AAAGAAGAAAAGAAAC 44501954 AAAGAAGAAAAGAAAC 1 AAAGAAGAAAAGAAAC 44501970 AAAGA 1 AAAGA 44501975 CCATTCGAAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 10 0.53 16 9 0.47 ACGTcount: A:0.78, C:0.06, G:0.14, T:0.03 Consensus pattern (16 bp): AAAGAAGAAAAGAAAC Found at i:44502392 original size:17 final size:18 Alignment explanation

Indices: 44502370--44502403 Score: 52 Period size: 17 Copynumber: 1.9 Consensus size: 18 44502360 TAAATGAGTT 44502370 AATTAGGAT-TAAATTGG 1 AATTAGGATATAAATTGG * 44502387 AATTAGGGTATAAATTG 1 AATTAGGATATAAATTG 44502404 AAAAGAAAAT Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 8 0.53 18 7 0.47 ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35 Consensus pattern (18 bp): AATTAGGATATAAATTGG Found at i:44511259 original size:43 final size:43 Alignment explanation

Indices: 44511195--44511401 Score: 256 Period size: 43 Copynumber: 4.9 Consensus size: 43 44511185 TACCGTAACA * * * * 44511195 ATGCC-ATATCCCAGATATGGTCTTACATGTAATCTCGTATCG 1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG ** * * * 44511237 ATGCCAATAAGCCAGCCATGGTCTTACACGAAATCACATATCA 1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG * * * 44511280 ATGGCAATATCCCAGACACGGTCTTACACGAAATCACATATCG 1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG * * 44511323 ATGCCAATGTCCCAGACATGGTCTTACACGAAGTCTCATATCG 1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG * * 44511366 ATGCCAA-ATCCCAGATATGGTCTTACACGTAATCTC 1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTC 44511402 GGTAACCCTA Statistics Matches: 140, Mismatches: 24, Indels: 2 0.84 0.14 0.01 Matches are distributed among these distances: 42 30 0.21 43 110 0.79 ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26 Consensus pattern (43 bp): ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG Found at i:44513685 original size:29 final size:29 Alignment explanation

Indices: 44513643--44513700 Score: 107 Period size: 29 Copynumber: 2.0 Consensus size: 29 44513633 ACCACTGCAA * 44513643 ACGGCGGTGCCGTCACTGGAGATCGGTGG 1 ACGGCGGTGCCGTCACCGGAGATCGGTGG 44513672 ACGGCGGTGCCGTCACCGGAGATCGGTGG 1 ACGGCGGTGCCGTCACCGGAGATCGGTGG 44513701 CCGGTGCAGT Statistics Matches: 28, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 29 28 1.00 ACGTcount: A:0.14, C:0.26, G:0.45, T:0.16 Consensus pattern (29 bp): ACGGCGGTGCCGTCACCGGAGATCGGTGG Found at i:44514556 original size:11 final size:11 Alignment explanation

Indices: 44514532--44514569 Score: 51 Period size: 11 Copynumber: 3.5 Consensus size: 11 44514522 TCTTATATTC 44514532 TTTATATTTTT 1 TTTATATTTTT 44514543 TTTAT-TTTTAT 1 TTTATATTTT-T * 44514554 TTTATAATTTT 1 TTTATATTTTT 44514565 TTTAT 1 TTTAT 44514570 TTCCTTCACT Statistics Matches: 24, Mismatches: 1, Indels: 4 0.83 0.03 0.14 Matches are distributed among these distances: 10 4 0.17 11 17 0.71 12 3 0.12 ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79 Consensus pattern (11 bp): TTTATATTTTT Found at i:44518955 original size:5 final size:5 Alignment explanation

Indices: 44518935--44518982 Score: 69 Period size: 5 Copynumber: 9.2 Consensus size: 5 44518925 TTTTTATGTT * 44518935 TTATA TATATTA TTATA TTATA TTATA TTATA TTGTA TTATA TTATA T 1 TTATA T-TA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA T 44518983 AAGTAAAAAT Statistics Matches: 39, Mismatches: 2, Indels: 4 0.87 0.04 0.09 Matches are distributed among these distances: 5 32 0.82 6 4 0.10 7 3 0.08 ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60 Consensus pattern (5 bp): TTATA Found at i:44519701 original size:3 final size:3 Alignment explanation

Indices: 44519693--44519757 Score: 58 Period size: 3 Copynumber: 21.7 Consensus size: 3 44519683 AATAAGAATT * * * * * * 44519693 TTA TTA TTA TTA TTA TTG TTA ATA TAA TAA TAA TTA TTA TTA TTG TTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA * * 44519741 ATA TAA TTA TTA TTA TT 1 TTA TTA TTA TTA TTA TT 44519758 TTTAATGATT Statistics Matches: 50, Mismatches: 12, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 3 50 1.00 ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58 Consensus pattern (3 bp): TTA Found at i:44519728 original size:27 final size:27 Alignment explanation

Indices: 44519698--44519757 Score: 102 Period size: 27 Copynumber: 2.2 Consensus size: 27 44519688 GAATTTTATT 44519698 ATTATTATTATTGTTAATATAATAATA 1 ATTATTATTATTGTTAATATAATAATA * * 44519725 ATTATTATTATTGTTAATATAATTATT 1 ATTATTATTATTGTTAATATAATAATA 44519752 ATTATT 1 ATTATT 44519758 TTTAATGATT Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 27 31 1.00 ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57 Consensus pattern (27 bp): ATTATTATTATTGTTAATATAATAATA Found at i:44519746 original size:21 final size:22 Alignment explanation

Indices: 44519717--44519763 Score: 78 Period size: 21 Copynumber: 2.2 Consensus size: 22 44519707 ATTGTTAATA 44519717 TAATAATAATTATTATTATTGT 1 TAATAATAATTATTATTATTGT * 44519739 TAAT-ATAATTATTATTATTTT 1 TAATAATAATTATTATTATTGT 44519760 TAAT 1 TAAT 44519764 GATTGTAATT Statistics Matches: 24, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 21 20 0.83 22 4 0.17 ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57 Consensus pattern (22 bp): TAATAATAATTATTATTATTGT Found at i:44528730 original size:17 final size:18 Alignment explanation

Indices: 44528708--44528741 Score: 52 Period size: 17 Copynumber: 1.9 Consensus size: 18 44528698 CAAATGAGTT 44528708 AATTAGGAT-TAAATTGG 1 AATTAGGATATAAATTGG * 44528725 AATTAGGGTATAAATTG 1 AATTAGGATATAAATTG 44528742 AAAAGAAAAT Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 8 0.53 18 7 0.47 ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35 Consensus pattern (18 bp): AATTAGGATATAAATTGG Found at i:44529094 original size:37 final size:36 Alignment explanation

Indices: 44529043--44529115 Score: 92 Period size: 37 Copynumber: 2.0 Consensus size: 36 44529033 GAATATTAAC * * * * 44529043 TTGAAAATGGAAAAGTTAATTTTGAATTGAATTGTGA 1 TTGAAAATGAAAAAGTGAA-ATTGAATTGAAATGTGA * 44529080 TTGAAAGTGAAAAAGTGAAATTGAATTGAAATGTGA 1 TTGAAAATGAAAAAGTGAAATTGAATTGAAATGTGA 44529116 ATATGGAGAC Statistics Matches: 31, Mismatches: 5, Indels: 1 0.84 0.14 0.03 Matches are distributed among these distances: 36 15 0.48 37 16 0.52 ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33 Consensus pattern (36 bp): TTGAAAATGAAAAAGTGAAATTGAATTGAAATGTGA Found at i:44531111 original size:42 final size:42 Alignment explanation

Indices: 44531061--44531160 Score: 173 Period size: 42 Copynumber: 2.4 Consensus size: 42 44531051 CTATACGAAT ** * 44531061 GGCACTAAGTGTGCGAAATTAAAATGACGATGTTGAATAACG 1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG 44531103 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG 1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG 44531145 GGCACTAAGTGTGCGA 1 GGCACTAAGTGTGCGA 44531161 TACCAAGATC Statistics Matches: 55, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 42 55 1.00 ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20 Consensus pattern (42 bp): GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG Found at i:44539485 original size:29 final size:30 Alignment explanation

Indices: 44539450--44539506 Score: 98 Period size: 29 Copynumber: 1.9 Consensus size: 30 44539440 CAATTCGATT 44539450 AAAAAATCATTAAAAATTTAA-AAAAATAA 1 AAAAAATCATTAAAAATTTAAGAAAAATAA * 44539479 AAAAAATTATTAAAAATTTAAGAAAAAT 1 AAAAAATCATTAAAAATTTAAGAAAAAT 44539507 TTGGTTCAAT Statistics Matches: 26, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 29 20 0.77 30 6 0.23 ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26 Consensus pattern (30 bp): AAAAAATCATTAAAAATTTAAGAAAAATAA Found at i:44554525 original size:27 final size:26 Alignment explanation

Indices: 44554495--44554570 Score: 73 Period size: 26 Copynumber: 2.8 Consensus size: 26 44554485 AGAGATGGAA 44554495 GCCTTTATGGCAAATCTTGTAAAGAA-G 1 GCCTTTATGGCAAA-CTT-TAAAGAATG * ** 44554522 GCCTTTGTGGCGCACTTTAAAGAATG 1 GCCTTTATGGCAAACTTTAAAGAATG * * 44554548 ACCTTTATGGCAACCTTCTAAAG 1 GCCTTTATGGCAAACTT-TAAAG 44554571 GAAACGCCTC Statistics Matches: 39, Mismatches: 8, Indels: 4 0.76 0.16 0.08 Matches are distributed among these distances: 25 7 0.18 26 16 0.41 27 16 0.41 ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30 Consensus pattern (26 bp): GCCTTTATGGCAAACTTTAAAGAATG Found at i:44557957 original size:18 final size:19 Alignment explanation

Indices: 44557914--44557958 Score: 60 Period size: 18 Copynumber: 2.5 Consensus size: 19 44557904 AAATCAAAAT 44557914 ATTGTGAG-AGTTAAAAGC 1 ATTGTGAGTAGTTAAAAGC 44557932 A-TGATGAGTA-TTAAAAGC 1 ATTG-TGAGTAGTTAAAAGC 44557950 ATTGTGAGT 1 ATTGTGAGT 44557959 GAAAGAATGA Statistics Matches: 24, Mismatches: 0, Indels: 6 0.80 0.00 0.20 Matches are distributed among these distances: 17 2 0.08 18 19 0.79 19 3 0.12 ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31 Consensus pattern (19 bp): ATTGTGAGTAGTTAAAAGC Found at i:44565166 original size:31 final size:30 Alignment explanation

Indices: 44565095--44565184 Score: 78 Period size: 31 Copynumber: 3.0 Consensus size: 30 44565085 GTGACCAATT 44565095 AAAAAAA--ATAGTTAAGTGACCAAAAAAG 1 AAAAAAATCATAGTTAAGTGACCAAAAAAG * * 44565123 AAACAAATTCATAGTTAAGTGGCCAAATTAAA- 1 AAA-AAAATCATAGTTAAGTGACCAAA--AAAG * * * 44565155 AAAAAAATCATAATTGAGAGACCAGAAAAA 1 AAAAAAATCATAGTTAAGTGACCA-AAAAA 44565185 AATTTAACCC Statistics Matches: 49, Mismatches: 7, Indels: 10 0.74 0.11 0.15 Matches are distributed among these distances: 28 3 0.06 29 3 0.06 30 3 0.06 31 32 0.65 32 5 0.10 33 3 0.06 ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18 Consensus pattern (30 bp): AAAAAAATCATAGTTAAGTGACCAAAAAAG Found at i:44566537 original size:27 final size:27 Alignment explanation

Indices: 44566499--44566560 Score: 79 Period size: 27 Copynumber: 2.3 Consensus size: 27 44566489 GGTGCAGAAT ** 44566499 CATCATCATCATTTTCAACAACAGCAA 1 CATCATCATCATCATCAACAACAGCAA ** 44566526 CATCATCATCATCATCTGCAACAGCAA 1 CATCATCATCATCATCAACAACAGCAA * 44566553 CAACATCA 1 CATCATCA 44566561 ACAGCAGTGG Statistics Matches: 30, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 27 30 1.00 ACGTcount: A:0.40, C:0.32, G:0.05, T:0.23 Consensus pattern (27 bp): CATCATCATCATCATCAACAACAGCAA Found at i:44571275 original size:20 final size:20 Alignment explanation

Indices: 44571250--44571300 Score: 68 Period size: 20 Copynumber: 2.5 Consensus size: 20 44571240 AAATTATAAA * 44571250 AATAAAAATTATTAAACTTT 1 AATAAAAATTATTAAAATTT 44571270 AATAAAAAGTT-TTAAAATTT 1 AATAAAAA-TTATTAAAATTT * 44571290 ACTAAAAATTA 1 AATAAAAATTA 44571301 GAAAAAATAT Statistics Matches: 27, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 19 2 0.07 20 23 0.85 21 2 0.07 ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37 Consensus pattern (20 bp): AATAAAAATTATTAAAATTT Found at i:44571323 original size:18 final size:18 Alignment explanation

Indices: 44571302--44571345 Score: 70 Period size: 18 Copynumber: 2.4 Consensus size: 18 44571292 TAAAAATTAG 44571302 AAAAAATATAAAATTGTA 1 AAAAAATATAAAATTGTA * 44571320 AAAAAATATAAAATTTTA 1 AAAAAATATAAAATTGTA * 44571338 TAAAAATA 1 AAAAAATA 44571346 ATTAAAAAGA Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 18 24 1.00 ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30 Consensus pattern (18 bp): AAAAAATATAAAATTGTA Found at i:44579206 original size:195 final size:195 Alignment explanation

Indices: 44578874--44579267 Score: 754 Period size: 195 Copynumber: 2.0 Consensus size: 195 44578864 AACCACATAC 44578874 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCTGCACCGCTCACATCGAAAACACTACT 1 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCTGCACCGCTCACATCGAAAACACTACT * 44578939 TATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCGGAATAACCAC 66 TATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCAC * 44579004 AAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCATAACCATATTATAA 131 AAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATAA 44579069 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAG-TCGCACCGCTCACATCGAAAACACTAC 1 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCT-GCACCGCTCACATCGAAAACACTAC 44579133 TTATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCA 65 TTATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCA 44579198 CAAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATA 130 CAAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATA 44579263 A 195 A 44579264 TCAA 1 TCAA 44579268 GCAAAATAAC Statistics Matches: 196, Mismatches: 2, Indels: 2 0.98 0.01 0.01 Matches are distributed among these distances: 194 1 0.01 195 195 0.99 ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26 Consensus pattern (195 bp): TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCTGCACCGCTCACATCGAAAACACTACT TATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCAC AAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATAA Found at i:44580028 original size:31 final size:31 Alignment explanation

Indices: 44579992--44580055 Score: 119 Period size: 31 Copynumber: 2.1 Consensus size: 31 44579982 TTCACTTACT * 44579992 TTACTTGTCACATCAATATCACATTCCACAA 1 TTACTTGTCACATCAACATCACATTCCACAA 44580023 TTACTTGTCACATCAACATCACATTCCACAA 1 TTACTTGTCACATCAACATCACATTCCACAA 44580054 TT 1 TT 44580056 CGACAAACAT Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 32 1.00 ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33 Consensus pattern (31 bp): TTACTTGTCACATCAACATCACATTCCACAA Found at i:44585251 original size:28 final size:28 Alignment explanation

Indices: 44585199--44585256 Score: 75 Period size: 28 Copynumber: 2.1 Consensus size: 28 44585189 GTTCTCTCAA * 44585199 AAATTAAAATTAAATTATATATTTTTAT 1 AAATTAAAATTAAATTATATATTTTAAT 44585227 AAATTAAAATATAAATTGAT-T-TTTTAAT 1 AAATTAAAAT-TAAATT-ATATATTTTAAT 44585255 AA 1 AA 44585257 CTTATATCTT Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 28 18 0.67 29 7 0.26 30 2 0.07 ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47 Consensus pattern (28 bp): AAATTAAAATTAAATTATATATTTTAAT Found at i:44589264 original size:30 final size:29 Alignment explanation

Indices: 44589210--44589277 Score: 82 Period size: 30 Copynumber: 2.3 Consensus size: 29 44589200 AGATTAGGAT * 44589210 TAATTTAATTTTTCTTAAAATAAATAAAG 1 TAATTTAATTTTTATTAAAATAAATAAAG * * * 44589239 TAATTTAGTTTTTATATAGAATAAATGAAG 1 TAATTTAATTTTTAT-TAAAATAAATAAAG * 44589269 TAATATAAT 1 TAATTTAAT 44589278 ATTAAGATGC Statistics Matches: 32, Mismatches: 6, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 29 13 0.41 30 19 0.59 ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44 Consensus pattern (29 bp): TAATTTAATTTTTATTAAAATAAATAAAG Done.