Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr14

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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31

Warning! 4503000 characters in sequence are not A, C, G, or T


File 58 of 770

Found at i:16875498 original size:29 final size:29

Alignment explanation

Indices: 16875456--16875714 Score: 419 Period size: 29 Copynumber: 8.7 Consensus size: 29 16875446 GCGAATGATT 16875456 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16875485 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16875514 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16875543 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16875572 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16875601 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC * 16875630 GAGGCACTATGTGTGTGAGATCAGTAATCGAGTAATC 1 GAGGCACTA--TGTGTGCG---AG--ATC-AGTAATC * 16875667 GAGGCACTATGTGTGCGAGATCAGTAATT 1 GAGGCACTATGTGTGCGAGATCAGTAATC * 16875696 GAGGCACTGTGTGTGCGAG 1 GAGGCACTATGTGTGCGAG 16875715 TTTTTCAACA Statistics Matches: 218, Mismatches: 4, Indels: 16 0.92 0.02 0.07 Matches are distributed among these distances: 29 178 0.82 30 3 0.01 31 7 0.03 32 2 0.01 34 2 0.01 35 7 0.03 36 3 0.01 37 16 0.07 ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25 Consensus pattern (29 bp): GAGGCACTATGTGTGCGAGATCAGTAATC Found at i:16875673 original size:37 final size:37 Alignment explanation

Indices: 16875623--16875694 Score: 135 Period size: 37 Copynumber: 1.9 Consensus size: 37 16875613 GTGCGAGATC * 16875623 AGTAATCGAGGCACTATGTGTGTGAGATCAGTAATCG 1 AGTAATCGAGGCACTATGTGTGCGAGATCAGTAATCG 16875660 AGTAATCGAGGCACTATGTGTGCGAGATCAGTAAT 1 AGTAATCGAGGCACTATGTGTGCGAGATCAGTAAT 16875695 TGAGGCACTG Statistics Matches: 34, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 37 34 1.00 ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26 Consensus pattern (37 bp): AGTAATCGAGGCACTATGTGTGCGAGATCAGTAATCG Found at i:16879074 original size:49 final size:49 Alignment explanation

Indices: 16879014--16879276 Score: 447 Period size: 49 Copynumber: 5.4 Consensus size: 49 16879004 TACATATATG * * * * * * 16879014 TGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAAAGTGGATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA * 16879063 TGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 16879112 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 16879161 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 16879210 TGTGAT-AGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA * 16879258 TGTGATAAGGCCTAATGGC 1 TGTGATGAGGCCTAATGGC 16879277 TAATGTAAAA Statistics Matches: 207, Mismatches: 6, Indels: 2 0.96 0.03 0.01 Matches are distributed among these distances: 48 48 0.23 49 159 0.77 ACGTcount: A:0.28, C:0.09, G:0.33, T:0.29 Consensus pattern (49 bp): TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA Found at i:16879427 original size:37 final size:37 Alignment explanation

Indices: 16879377--16879498 Score: 226 Period size: 37 Copynumber: 3.3 Consensus size: 37 16879367 GGAATATGTT * 16879377 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 16879414 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA * 16879451 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 16879488 CCGGGTAAGAC 1 CCGGGTAAGAC 16879499 TTCTTTTATA Statistics Matches: 83, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 37 83 1.00 ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21 Consensus pattern (37 bp): CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA Found at i:16881386 original size:39 final size:40 Alignment explanation

Indices: 16881305--16881388 Score: 98 Period size: 39 Copynumber: 2.1 Consensus size: 40 16881295 GAGAATTGAG ** * * * 16881305 AGTGATGTATCCGGACTAAGTTCCAAAGAGCATTCGTGCT 1 AGTGATGTATCCGGACTAAGGCCCAAAGAGCAATCATACT * * 16881345 AGTGATGTATCCGGGCT-AGGCCCGAAGAGCAATCATACT 1 AGTGATGTATCCGGACTAAGGCCCAAAGAGCAATCATACT 16881384 AGTGA 1 AGTGA 16881389 CGTGTATTCG Statistics Matches: 37, Mismatches: 7, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 39 21 0.57 40 16 0.43 ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24 Consensus pattern (40 bp): AGTGATGTATCCGGACTAAGGCCCAAAGAGCAATCATACT Found at i:16881628 original size:29 final size:29 Alignment explanation

Indices: 16881586--16881863 Score: 533 Period size: 29 Copynumber: 9.7 Consensus size: 29 16881576 GCGAATGATT 16881586 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16881615 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16881644 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16881673 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16881702 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16881731 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16881760 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16881789 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC * 16881818 GAGGCACTATGTGTGCGAGATCAGTAATT 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16881847 GAGGCAC--TGTGTGCGAG 1 GAGGCACTATGTGTGCGAG 16881864 TTTTTCAACA Statistics Matches: 248, Mismatches: 1, Indels: 2 0.99 0.00 0.01 Matches are distributed among these distances: 27 10 0.04 29 238 0.96 ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24 Consensus pattern (29 bp): GAGGCACTATGTGTGCGAGATCAGTAATC Found at i:16885275 original size:49 final size:49 Alignment explanation

Indices: 16885162--16885473 Score: 536 Period size: 49 Copynumber: 6.4 Consensus size: 49 16885152 TACATATATG * * * * * 16885162 TGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAAAGTG-ATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA * * 16885210 TGTGATGAGGCCTAATGGCCGATGCGATGAATGTGAAAGTGTATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 16885259 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 16885308 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 16885357 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA * 16885406 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA 1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA * 16885455 TGTGATAAGGCCTAATGGC 1 TGTGATGAGGCCTAATGGC 16885474 TAATGTAAAA Statistics Matches: 257, Mismatches: 6, Indels: 1 0.97 0.02 0.00 Matches are distributed among these distances: 48 38 0.15 49 219 0.85 ACGTcount: A:0.28, C:0.09, G:0.33, T:0.29 Consensus pattern (49 bp): TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA Found at i:16885624 original size:37 final size:37 Alignment explanation

Indices: 16885574--16885695 Score: 226 Period size: 37 Copynumber: 3.3 Consensus size: 37 16885564 GGAATATGTT * 16885574 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 16885611 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA * 16885648 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 16885685 CCGGGTAAGAC 1 CCGGGTAAGAC 16885696 TTCTTTTATA Statistics Matches: 83, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 37 83 1.00 ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21 Consensus pattern (37 bp): CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA Found at i:16887586 original size:39 final size:40 Alignment explanation

Indices: 16887505--16887588 Score: 98 Period size: 39 Copynumber: 2.1 Consensus size: 40 16887495 GAGAATTGAG ** * * * 16887505 AGTGATGTATCCGGACTAAGTTCCAAAGAGCATTCGTGCT 1 AGTGATGTATCCGGACTAAGGCCCAAAGAGCAATCATACT * * 16887545 AGTGATGTATCCGGGCT-AGGCCCGAAGAGCAATCATACT 1 AGTGATGTATCCGGACTAAGGCCCAAAGAGCAATCATACT 16887584 AGTGA 1 AGTGA 16887589 CGTGTATTCG Statistics Matches: 37, Mismatches: 7, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 39 21 0.57 40 16 0.43 ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24 Consensus pattern (40 bp): AGTGATGTATCCGGACTAAGGCCCAAAGAGCAATCATACT Found at i:16887827 original size:29 final size:29 Alignment explanation

Indices: 16887785--16888119 Score: 640 Period size: 29 Copynumber: 11.7 Consensus size: 29 16887775 GCGAATGATT 16887785 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16887814 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16887843 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16887872 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16887901 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16887930 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16887959 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16887988 GAGGCAC-ATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16888016 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16888045 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC * 16888074 GAGGCACTATGTGTGCGAGATCAGTAATT 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16888103 GAGGCAC--TGTGTGCGAG 1 GAGGCACTATGTGTGCGAG 16888120 TTTTTCAACA Statistics Matches: 304, Mismatches: 1, Indels: 4 0.98 0.00 0.01 Matches are distributed among these distances: 27 10 0.03 28 28 0.09 29 266 0.88 ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24 Consensus pattern (29 bp): GAGGCACTATGTGTGCGAGATCAGTAATC Found at i:16891010 original size:37 final size:37 Alignment explanation

Indices: 16890960--16891044 Score: 152 Period size: 37 Copynumber: 2.3 Consensus size: 37 16890950 GGAATATGTT * 16890960 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA * 16890997 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 16891034 CCGGGTAAGAC 1 CCGGGTAAGAC 16891045 TTCTTTTATA Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 37 46 1.00 ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21 Consensus pattern (37 bp): CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA Found at i:16892937 original size:39 final size:40 Alignment explanation

Indices: 16892856--16892939 Score: 98 Period size: 39 Copynumber: 2.1 Consensus size: 40 16892846 GAGAATTGAG ** * * * 16892856 AGTGATGTATCCGGACTAAGTTCCAAAGAGCATTCGTGCT 1 AGTGATGTATCCGGACTAAGGCCCAAAGAGCAATCATACT * * 16892896 AGTGATGTATCCGGGCT-AGGCCCGAAGAGCAATCATACT 1 AGTGATGTATCCGGACTAAGGCCCAAAGAGCAATCATACT 16892935 AGTGA 1 AGTGA 16892940 CGTGTATTCG Statistics Matches: 37, Mismatches: 7, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 39 21 0.57 40 16 0.43 ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24 Consensus pattern (40 bp): AGTGATGTATCCGGACTAAGGCCCAAAGAGCAATCATACT Found at i:16893178 original size:29 final size:29 Alignment explanation

Indices: 16893136--16893471 Score: 640 Period size: 29 Copynumber: 11.7 Consensus size: 29 16893126 GCGAATGATT 16893136 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16893165 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16893194 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16893223 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16893252 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16893281 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16893310 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16893339 GAGGCAC-ATGTGTGCGAGATCAGT-ATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16893366 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC 16893395 GAGGCACTATGTGTGCGAGATCAGTAATC 1 GAGGCACTATGTGTGCGAGATCAGTAATC * 16893424 GAGGCACTATGTGTGCGAGATCAGTAATT 1 GAGGCACTATGTGTGCGAGATCAGTAATC * 16893453 GAGGCACTGTGTGTGCGAG 1 GAGGCACTATGTGTGCGAG 16893472 TTTTTCAACA Statistics Matches: 303, Mismatches: 2, Indels: 4 0.98 0.01 0.01 Matches are distributed among these distances: 27 10 0.03 28 34 0.11 29 259 0.85 ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24 Consensus pattern (29 bp): GAGGCACTATGTGTGCGAGATCAGTAATC Found at i:16896360 original size:37 final size:37 Alignment explanation

Indices: 16896310--16896431 Score: 226 Period size: 37 Copynumber: 3.3 Consensus size: 37 16896300 GGAATATGTT * 16896310 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 16896347 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA * 16896384 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT 1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA 16896421 CCGGGTAAGAC 1 CCGGGTAAGAC 16896432 TTCTTTTATA Statistics Matches: 83, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 37 83 1.00 ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21 Consensus pattern (37 bp): CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA Found at i:16898888 original size:30 final size:30 Alignment explanation

Indices: 16898847--16898912 Score: 123 Period size: 30 Copynumber: 2.2 Consensus size: 30 16898837 AGATGGATCA 16898847 ATAAGAATGTGTATTGACTATCAACAGCTCG 1 ATAA-AATGTGTATTGACTATCAACAGCTCG 16898878 ATAAAATGTGTATTGACTATCAACAGCTCG 1 ATAAAATGTGTATTGACTATCAACAGCTCG 16898908 ATAAA 1 ATAAA 16898913 GTTACGATAA Statistics Matches: 35, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 30 31 0.89 31 4 0.11 ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29 Consensus pattern (30 bp): ATAAAATGTGTATTGACTATCAACAGCTCG Found at i:16908146 original size:15 final size:15 Alignment explanation

Indices: 16908126--16908163 Score: 51 Period size: 15 Copynumber: 2.5 Consensus size: 15 16908116 AATTTCCATG 16908126 TTCATATATC-ATAAT 1 TTCATATATCTAT-AT * 16908141 TTCATATTTCTATAT 1 TTCATATATCTATAT 16908156 TTCATATA 1 TTCATATA 16908164 ACATCATTTT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 15 18 0.90 16 2 0.10 ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53 Consensus pattern (15 bp): TTCATATATCTATAT Found at i:16913550 original size:20 final size:20 Alignment explanation

Indices: 16913492--16913572 Score: 76 Period size: 20 Copynumber: 4.0 Consensus size: 20 16913482 TCATATAATT * * 16913492 AGTAGTTCATCCATAT-AACC 1 AGTAATTCATCCATTTCAA-C * * 16913512 AGTAATTTAT-CAGTATCAAC 1 AGTAATTCATCCA-TTTCAAC * * 16913532 AGTAATTCATTCATTTCAAT 1 AGTAATTCATCCATTTCAAC 16913552 AGTAATTCATCCATTTCAAC 1 AGTAATTCATCCATTTCAAC 16913572 A 1 A 16913573 TAGCTTATTC Statistics Matches: 51, Mismatches: 7, Indels: 6 0.80 0.11 0.09 Matches are distributed among these distances: 19 2 0.04 20 45 0.88 21 4 0.08 ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36 Consensus pattern (20 bp): AGTAATTCATCCATTTCAAC Found at i:16913804 original size:22 final size:22 Alignment explanation

Indices: 16913779--16913827 Score: 80 Period size: 22 Copynumber: 2.2 Consensus size: 22 16913769 ACGCTCTTTT * 16913779 GAGCTGAATAGTCAGCTCATAC 1 GAGCTGAACAGTCAGCTCATAC * 16913801 GAGCTGAACAGTCAGCTCATAT 1 GAGCTGAACAGTCAGCTCATAC 16913823 GAGCT 1 GAGCT 16913828 TAAATGGTAA Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 22 25 1.00 ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22 Consensus pattern (22 bp): GAGCTGAACAGTCAGCTCATAC Found at i:16913872 original size:23 final size:23 Alignment explanation

Indices: 16913730--16913874 Score: 100 Period size: 23 Copynumber: 6.3 Consensus size: 23 16913720 AAGCTCCTCC * 16913730 TGAGCTGATAAACAATAAGCTC-TA 1 TGAGCTG--AAACAGTAAGCTCATA * * * * 16913754 TTGAGCTGAAACAATACGCTCTTT 1 -TGAGCTGAAACAGTAAGCTCATA * * 16913778 TGAGCTG-AATAGTCAGCTCATA 1 TGAGCTGAAACAGTAAGCTCATA * * 16913800 CGAGCTG-AACAGTCAGCTCATA 1 TGAGCTGAAACAGTAAGCTCATA * ** 16913822 TGAGCTTAAATGGTAAGCTCCA-A 1 TGAGCTGAAACAGTAAGCT-CATA * 16913845 TGAGCTGAAACAGTAAGCTCTTA 1 TGAGCTGAAACAGTAAGCTCATA * 16913868 CGAGCTG 1 TGAGCTG 16913875 TGGTGAGTCC Statistics Matches: 96, Mismatches: 20, Indels: 10 0.76 0.16 0.08 Matches are distributed among these distances: 22 35 0.36 23 51 0.53 24 3 0.03 25 7 0.07 ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26 Consensus pattern (23 bp): TGAGCTGAAACAGTAAGCTCATA Found at i:16919569 original size:20 final size:21 Alignment explanation

Indices: 16919527--16919568 Score: 84 Period size: 21 Copynumber: 2.0 Consensus size: 21 16919517 ATGAATACAT 16919527 ATAAATTAGCTCTATCAAAAA 1 ATAAATTAGCTCTATCAAAAA 16919548 ATAAATTAGCTCTATCAAAAA 1 ATAAATTAGCTCTATCAAAAA 16919569 TTAACACGTA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 21 1.00 ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29 Consensus pattern (21 bp): ATAAATTAGCTCTATCAAAAA Found at i:16921341 original size:50 final size:52 Alignment explanation

Indices: 16921266--16921522 Score: 259 Period size: 53 Copynumber: 4.8 Consensus size: 52 16921256 ACGCGGGTAC * * * * 16921266 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCCTT-TTTA-AAA 1 CTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTCCTTATAAA * * 16921316 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA 1 CTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT-CCTTATAAA * * * * 16921369 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA 1 CTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCC-TT-CCTTATA--AA * * * * * * 16921424 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAA 1 CTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT-CCTTATAAA * 16921477 CCTTACCAATTGTCCATGCCTTGGCATGGTCTTACATGGTATCCTT 1 -CTTACC-ATTG-CCATGCCTTGACATGGTCTTACATGGTATCCTT 16921523 AAACCCTAAT Statistics Matches: 172, Mismatches: 25, Indels: 14 0.82 0.12 0.07 Matches are distributed among these distances: 50 40 0.23 52 5 0.03 53 46 0.27 54 5 0.03 55 45 0.26 56 31 0.18 ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37 Consensus pattern (52 bp): CTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTCCTTATAAA Found at i:16921458 original size:108 final size:111 Alignment explanation

Indices: 16921314--16921515 Score: 322 Period size: 108 Copynumber: 1.8 Consensus size: 111 16921304 TCCTTTTTAA * * 16921314 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA 1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA 16921377 -TG-CCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT 65 TTGTCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT * * * 16921422 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT 1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT 16921487 TGTCCATGCCTTGGCATGGTCTTACATGG 66 TGTCCATGCCTTGGCATGGTCTTACATGG 16921516 TATCCTTAAA Statistics Matches: 85, Mismatches: 5, Indels: 5 0.89 0.05 0.05 Matches are distributed among these distances: 107 1 0.01 108 49 0.58 109 7 0.08 110 2 0.02 111 26 0.31 ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35 Consensus pattern (111 bp): AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT TGTCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT Found at i:16928949 original size:55 final size:53 Alignment explanation

Indices: 16928759--16929013 Score: 236 Period size: 55 Copynumber: 4.8 Consensus size: 53 16928749 ACGCGGGTAC * * * * * 16928759 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA 1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA * * 16928808 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA 1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA * * * 16928861 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA 1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AA * *** 16928916 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA 1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA * * * * 16928969 CCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT 1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGGATCCTT 16929014 AAACCCTAAT Statistics Matches: 173, Mismatches: 22, Indels: 16 0.82 0.10 0.08 Matches are distributed among these distances: 49 38 0.22 50 1 0.01 52 2 0.01 53 49 0.28 54 10 0.06 55 71 0.41 56 2 0.01 ACGTcount: A:0.21, C:0.25, G:0.17, T:0.36 Consensus pattern (53 bp): CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA Found at i:16928950 original size:108 final size:110 Alignment explanation

Indices: 16928806--16929006 Score: 318 Period size: 108 Copynumber: 1.8 Consensus size: 110 16928796 ATCCTTTTGA * * 16928806 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA 1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA 16928869 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT 65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT * * * 16928914 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT 1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT * 16928979 TTCCATGCCTTGGCATGGTCTTACATGG 66 TGCCATGCCTTGGCATGGTCTTACATGG 16929007 TATCCTTAAA Statistics Matches: 84, Mismatches: 6, Indels: 4 0.89 0.06 0.04 Matches are distributed among these distances: 107 1 0.01 108 49 0.58 109 7 0.08 110 27 0.32 ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35 Consensus pattern (110 bp): AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT Found at i:16930387 original size:20 final size:20 Alignment explanation

Indices: 16930342--16930407 Score: 60 Period size: 20 Copynumber: 3.3 Consensus size: 20 16930332 CATTTTTATT * * * 16930342 CGTATAAACTGTAATTCATT 1 CGTATAACCAGTAATTCATC * ** * 16930362 CATATAATTAGTAGTTCATC 1 CGTATAACCAGTAATTCATC 16930382 CGTATAACCAGTAATTCATC 1 CGTATAACCAGTAATTCATC * 16930402 GGTATA 1 CGTATA 16930408 TCAATAATTT Statistics Matches: 35, Mismatches: 11, Indels: 0 0.76 0.24 0.00 Matches are distributed among these distances: 20 35 1.00 ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36 Consensus pattern (20 bp): CGTATAACCAGTAATTCATC Found at i:16930684 original size:23 final size:23 Alignment explanation

Indices: 16930637--16930750 Score: 90 Period size: 23 Copynumber: 5.0 Consensus size: 23 16930627 TTGAGATGAT * * 16930637 AAACAATAAGCTCTGTT-GAGTTG 1 AAACAGTAAGCTCT-TTCGAGCTG * 16930660 AAACAATAAGCTCTTTCGAGCTG 1 AAACAGTAAGCTCTTTCGAGCTG ** * 16930683 -AACAGTAAGCTAATACGAGCTG 1 AAACAGTAAGCTCTTTCGAGCTG * ** 16930705 AAACGGTAAGCTCCAAT-GAGCTG 1 AAACAGTAAGCT-CTTTCGAGCTG * * 16930728 AAATAGTAAGCTCTTACGAGCTG 1 AAACAGTAAGCTCTTTCGAGCTG 16930751 TGGTGAGTCT Statistics Matches: 73, Mismatches: 14, Indels: 8 0.77 0.15 0.08 Matches are distributed among these distances: 22 21 0.29 23 51 0.70 24 1 0.01 ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24 Consensus pattern (23 bp): AAACAGTAAGCTCTTTCGAGCTG Found at i:16932702 original size:27 final size:28 Alignment explanation

Indices: 16932645--16932714 Score: 115 Period size: 27 Copynumber: 2.5 Consensus size: 28 16932635 AAACTTGTAC * 16932645 AGCACTAAGTGTGCGAGTTTGATCATGT 1 AGCACTAAGTGTGCGAGTTTGATCATAT * 16932673 AGCACTAAGTGTGCGAG-TTGATTATAT 1 AGCACTAAGTGTGCGAGTTTGATCATAT 16932700 AGCACTAAGTGTGCG 1 AGCACTAAGTGTGCG 16932715 GACACACTAT Statistics Matches: 40, Mismatches: 2, Indels: 1 0.93 0.05 0.02 Matches are distributed among these distances: 27 23 0.57 28 17 0.43 ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30 Consensus pattern (28 bp): AGCACTAAGTGTGCGAGTTTGATCATAT Found at i:16936062 original size:48 final size:46 Alignment explanation

Indices: 16935908--16936143 Score: 141 Period size: 48 Copynumber: 4.9 Consensus size: 46 16935898 ACGTTAAGTT * * * * * * * 16935908 GCCGATGCCATGTCCCAGACATGGTCTTACACTATCTCTCAAAACAAT 1 GCCGATGCCATGTCCCAGACTTGGTC-TACACTAGCACAC-ATATAAC * * ** *** 16935956 GCCGATGCTATGTCCCAGACATGGTCTTACACTAGCATTCATATTGTG 1 GCCGATGCCATGTCCCAGACTTGGTC-TACACTAGCACACATA-TAAC ** * * * 16936004 GCTAACGCCATATCCTAGACTTGGTCTAACACTAGCACACATATCAAC 1 GCCGATGCCATGTCCCAGACTTGGTCT-ACACTAGCACACATAT-AAC * * *** 16936052 GCCGATGCCATGTCCCAGA-TATGGTCGTACACTAGCTCTCATGATGTT 1 GCCGATGCCATGTCCCAGACT-TGGTC-TACACTAGCACACAT-ATAAC * * 16936100 TCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATAT 1 GCCGATGCCATGTCCCAGACTTGGTC-TACACTAGCACACATAT 16936144 TAACCAAATG Statistics Matches: 145, Mismatches: 36, Indels: 15 0.74 0.18 0.08 Matches are distributed among these distances: 47 7 0.05 48 135 0.93 49 3 0.02 ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27 Consensus pattern (46 bp): GCCGATGCCATGTCCCAGACTTGGTCTACACTAGCACACATATAAC Found at i:16936110 original size:96 final size:96 Alignment explanation

Indices: 16935908--16936143 Score: 278 Period size: 96 Copynumber: 2.5 Consensus size: 96 16935898 ACGTTAAGTT * * * * * * * 16935908 GCCGATGCCATGTCCCAGACATGGTCTTACACTATCTCTCAAAACAATGCCGATGCTATGTCCCA 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCA * 16935973 GACATGGTCTTACACTAGCATTCATATTGTG 66 GACATGGTCGTACACTAGCATTCATATTGTG ** * * * * * 16936004 GCTAACGCCATATCCTAGACTTGGTCTAACACTAGCACACATATCAACGCCGATGCCATGTCCCA 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCA * * 16936069 GATATGGTCGTACACTAGC-TCTCATGA-TGTT 66 GACATGGTCGTACACTAGCAT-TCAT-ATTGTG * 16936100 TCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATAT 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATAT 16936144 TAACCAAATG Statistics Matches: 113, Mismatches: 25, Indels: 4 0.80 0.18 0.03 Matches are distributed among these distances: 95 1 0.01 96 111 0.98 97 1 0.01 ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27 Consensus pattern (96 bp): GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCA GACATGGTCGTACACTAGCATTCATATTGTG Found at i:16949962 original size:40 final size:40 Alignment explanation

Indices: 16949898--16950082 Score: 205 Period size: 40 Copynumber: 4.7 Consensus size: 40 16949888 GCTACTCGTT * * * 16949898 CAAATGCCTTCTGGACATAGCCCGG-TTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAATAACTCGCA * * * 16949938 CAAATGCCTTTGGGACTTAACCCGGATTTAATAACTCACA 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCGCA * 16949978 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCGCA * * * * * * 16950018 CCAATGCCTTCGGG-CTTAGCTCGGATATAGTCACTAAGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACT-CGCA * 16950058 CAAA-GCCTTCAGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 16950083 CATCATTTGA Statistics Matches: 124, Mismatches: 18, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 39 24 0.19 40 98 0.79 41 2 0.02 ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCGCA Found at i:16958111 original size:39 final size:39 Alignment explanation

Indices: 16957902--16958113 Score: 225 Period size: 40 Copynumber: 5.4 Consensus size: 39 16957892 GAATCACGTA * * * ** 16957902 CCTTCGGAATTTAACCGGATATAGCT-ACTCGTTCAAATG 1 CCTTCGGGACTTAGCCGGATATAG-TAACTCGCACAAATG * * 16957941 CCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG * * 16957981 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATG 1 CCTTCGGGACTT-AGCCGGATATAGTAACTCGCACAAATG * * 16958021 CCTTCGGGACTTAACCGGATTTAGTAACTCGCAC-AATG 1 CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG * * * 16958059 CCTTC-GGATCTTAGTCGGATATAGTCACTTAGCACAAA-G 1 CCTTCGGGA-CTTAGCCGGATATAGTAAC-TCGCACAAATG 16958098 CCTTCGGGACTTAGCC 1 CCTTCGGGACTTAGCC 16958114 CGGACATCAT Statistics Matches: 148, Mismatches: 18, Indels: 14 0.82 0.10 0.08 Matches are distributed among these distances: 37 3 0.02 38 24 0.16 39 49 0.33 40 71 0.48 41 1 0.01 ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26 Consensus pattern (39 bp): CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG Found at i:16960663 original size:13 final size:13 Alignment explanation

Indices: 16960645--16960669 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 16960635 GCTTTATTTA 16960645 TTAAACTAATTAT 1 TTAAACTAATTAT 16960658 TTAAACTAATTA 1 TTAAACTAATTA 16960670 ACTGATTTAA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44 Consensus pattern (13 bp): TTAAACTAATTAT Found at i:16964730 original size:79 final size:82 Alignment explanation

Indices: 16964590--16964774 Score: 229 Period size: 79 Copynumber: 2.3 Consensus size: 82 16964580 TCGAATGATG * * * 16964590 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT * 16964654 CGTGCGAGTTAATA-AA 66 CGTGCGAGTCAATATAA * ** 16964670 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT * 16964732 TCGTGCGAGTCACTATAA 65 TCGTGCGAGTCAATATAA ** 16964750 -CCGGGCTTCGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 16964775 AGCGAGTCGT Statistics Matches: 91, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 1 0.01 79 56 0.62 80 34 0.37 ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24 Consensus pattern (82 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT CGTGCGAGTCAATATAA Found at i:16964782 original size:40 final size:40 Alignment explanation

Indices: 16964591--16964782 Score: 151 Period size: 40 Copynumber: 4.8 Consensus size: 40 16964581 CGAATGATGT * * * * * 16964591 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT 1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAAC ** * * * * * 16964631 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT 1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTCACTAAAC * * * 16964671 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAAC 1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC * 16964710 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA- 1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AAC * * 16964750 CCGGGCTT-CGTCCCGAAGGCATTTGAGCGAGTC 1 CCGGG-TTAAGTCCCGAAGGCATTTGTGCGAGTC 16964783 GTTATATCCG Statistics Matches: 126, Mismatches: 20, Indels: 12 0.80 0.13 0.08 Matches are distributed among these distances: 39 33 0.26 40 82 0.65 41 11 0.09 ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23 Consensus pattern (40 bp): CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC Found at i:16964805 original size:79 final size:79 Alignment explanation

Indices: 16964590--16964807 Score: 183 Period size: 79 Copynumber: 2.7 Consensus size: 79 16964580 TCGAATGATG * * * * ** * 16964590 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGA-TCCGAAGGCAT 1 TCCGGGCTAAG-CCCGAAGGCATTTGAGC-AAGTCACTAAACCCGGGTTA-AATTCCGAAGGCAT * 16964653 TCGTGCGAGTTAATAAA 63 TCGTGCGAGTCAATAAA * * * * 16964670 TCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTACTAAACCCGGGTTAAGTCCCGAAGGCATTCG 1 TCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGGCATTCG * 16964735 TGCGAGTCACTATAA 66 TGCGAGTCAATA-AA ** * ** * * 16964750 -CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCGTTATATCC-GGTTAAATTCCGAAGG 1 TCCGGGCTAAG-CCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGG 16964808 TACGTGATTT Statistics Matches: 113, Mismatches: 21, Indels: 9 0.79 0.15 0.06 Matches are distributed among these distances: 79 69 0.61 80 44 0.39 ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24 Consensus pattern (79 bp): TCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGGCATTCG TGCGAGTCAATAAA Found at i:16975205 original size:31 final size:31 Alignment explanation

Indices: 16975161--16975262 Score: 123 Period size: 31 Copynumber: 3.1 Consensus size: 31 16975151 CCTTTTCATA * 16975161 TTTCATATCTCATAATACTGGGCCGAAGCCTTTTCAT 1 TTTCATATTTCATAATACTGGGCCGAAG-C----C-T 16975198 GTTTCATATTTCATAATACTGGGCCGAAGCCT 1 -TTTCATATTTCATAATACTGGGCCGAAGCCT * 16975230 TTTCATATTTCATATTACTGGGCCGAAGCCT 1 TTTCATATTTCATAATACTGGGCCGAAGCCT 16975261 TT 1 TT 16975263 ACTGTAAACG Statistics Matches: 62, Mismatches: 2, Indels: 7 0.87 0.03 0.10 Matches are distributed among these distances: 31 32 0.52 32 1 0.02 33 1 0.02 37 1 0.02 38 27 0.44 ACGTcount: A:0.24, C:0.23, G:0.16, T:0.38 Consensus pattern (31 bp): TTTCATATTTCATAATACTGGGCCGAAGCCT Found at i:16975245 original size:38 final size:38 Alignment explanation

Indices: 16975138--16975245 Score: 180 Period size: 38 Copynumber: 2.8 Consensus size: 38 16975128 TCAATCATGC * * 16975138 ACTGGGCCGTAGCCCTTTTCATATTTCATATCTCATAAT 1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTTCATAAT * 16975177 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT 1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT 16975215 ACTGGGCCGAAGCCTTTTCATATTTCATATT 1 ACTGGGCCGAAGCCTTTTCATATTTCATATT 16975246 ACTGGGCCGA Statistics Matches: 65, Mismatches: 4, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 38 54 0.83 39 11 0.17 ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39 Consensus pattern (38 bp): ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT Found at i:16975500 original size:24 final size:24 Alignment explanation

Indices: 16975454--16975572 Score: 154 Period size: 24 Copynumber: 5.0 Consensus size: 24 16975444 GCTTTATCAT * 16975454 ATAACTGGAGGCCT-AGCCTCTTTTA 1 ATAACTGG-GGCATAAGCC-CTTTTA * 16975479 ATAACTGGGGCCA-AAGCCCTTTCA 1 ATAACTGGGG-CATAAGCCCTTTTA 16975503 ATAACTGGGGCATAAGCCCTTTT- 1 ATAACTGGGGCATAAGCCCTTTTA ** 16975526 ATAACTGGGGCATAAGCCCTTTCG 1 ATAACTGGGGCATAAGCCCTTTTA 16975550 ATAACTGGGGCATAAGCCCTTTT 1 ATAACTGGGGCATAAGCCCTTTT 16975573 TCACTTCCTC Statistics Matches: 85, Mismatches: 5, Indels: 9 0.86 0.05 0.09 Matches are distributed among these distances: 23 24 0.28 24 48 0.56 25 13 0.15 ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28 Consensus pattern (24 bp): ATAACTGGGGCATAAGCCCTTTTA Found at i:16975533 original size:47 final size:48 Alignment explanation

Indices: 16975454--16975572 Score: 172 Period size: 47 Copynumber: 2.5 Consensus size: 48 16975444 GCTTTATCAT * 16975454 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCCA-AAGCCCTTTCA 1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGG-CATAAGCCCTTTCA * 16975503 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTCG 1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA 16975550 ATAACTGGGGCATAAGCCCTTTT 1 ATAACTGGGGCATAAGCCCTTTT 16975573 TCACTTCCTC Statistics Matches: 66, Mismatches: 2, Indels: 6 0.89 0.03 0.08 Matches are distributed among these distances: 46 2 0.03 47 43 0.65 48 9 0.14 49 12 0.18 ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28 Consensus pattern (48 bp): ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA Found at i:16975648 original size:20 final size:20 Alignment explanation

Indices: 16975623--16975682 Score: 102 Period size: 20 Copynumber: 3.0 Consensus size: 20 16975613 TATGATTACC 16975623 TCATGTGCATATCATACATA 1 TCATGTGCATATCATACATA * * 16975643 TCATGTGCGTATCATACATT 1 TCATGTGCATATCATACATA 16975663 TCATGTGCATATCATACATA 1 TCATGTGCATATCATACATA 16975683 CCATATTTAT Statistics Matches: 36, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 36 1.00 ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37 Consensus pattern (20 bp): TCATGTGCATATCATACATA Found at i:16975757 original size:25 final size:25 Alignment explanation

Indices: 16975725--16975772 Score: 69 Period size: 25 Copynumber: 1.9 Consensus size: 25 16975715 ATACATAAAC * * * 16975725 CCTAGGGGTATAATGGTCATTTTTA 1 CCTAGGGGCAAAACGGTCATTTTTA 16975750 CCTAGGGGCAAAACGGTCATTTT 1 CCTAGGGGCAAAACGGTCATTTT 16975773 CATATTATAA Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 25 20 1.00 ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33 Consensus pattern (25 bp): CCTAGGGGCAAAACGGTCATTTTTA Found at i:16978471 original size:49 final size:50 Alignment explanation

Indices: 16978259--16978483 Score: 229 Period size: 49 Copynumber: 4.5 Consensus size: 50 16978249 CTGGTACGCA * * * 16978259 TAGTAGCCTGCAATTAGTACTACACATGCGAT-CAATTATCCGGTATACG 1 TAGTAGCCTGCACTTAGTACTACACATGCGATCCAATCATCCGGTACACG * * * * * * * * 16978308 TAGTTGCCTACACTTAGTACTACATATGTGATCTAACCATCTGATACACG 1 TAGTAGCCTGCACTTAGTACTACACATGCGATCCAATCATCCGGTACACG * * * ** * ** * * 16978358 TAGTAGCTTGCACTTAGTACTACACACGTGATTGAAGTTATTGGGTACGCA 1 TAGTAGCCTGCACTTAGTACTACACATGCGATCCAA-TCATCCGGTACACG 16978409 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAATCATCCGGTACACG 1 TAGTAGCCTGCACTTAGTACTACACATGCGATCCAATCATCCGGTACACG * 16978458 TAGTAGCATGCACTTAGTACTACACA 1 TAGTAGCCTGCACTTAGTACTACACA 16978484 CATGACCTCA Statistics Matches: 138, Mismatches: 36, Indels: 4 0.78 0.20 0.02 Matches are distributed among these distances: 49 61 0.44 50 42 0.30 51 35 0.25 ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28 Consensus pattern (50 bp): TAGTAGCCTGCACTTAGTACTACACATGCGATCCAATCATCCGGTACACG Found at i:16984255 original size:49 final size:48 Alignment explanation

Indices: 16984200--16984375 Score: 228 Period size: 49 Copynumber: 3.6 Consensus size: 48 16984190 TCTGGTACGC * 16984200 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGCACA 1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACA * * * * 16984248 AGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAATTATCGGGTATGC- 1 A-TAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAATTATCCGGTA--CA * * 16984300 ATACTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGTACA 1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACA 16984348 CATAGTAGCCTGCACTTAGTACTACACA 1 -ATAGTAGCCTGCACTTAGTACTACACA 16984376 CATGACCTAC Statistics Matches: 108, Mismatches: 13, Indels: 13 0.81 0.10 0.10 Matches are distributed among these distances: 47 1 0.01 48 1 0.01 49 65 0.60 50 2 0.02 51 37 0.34 52 1 0.01 53 1 0.01 ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25 Consensus pattern (48 bp): ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACA Found at i:16984332 original size:100 final size:100 Alignment explanation

Indices: 16984188--16984376 Score: 317 Period size: 100 Copynumber: 1.9 Consensus size: 100 16984178 TAGACAAGGC * * * 16984188 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGCACA-AGTA 1 TATCGGGTACGCATACTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGCACACA-TA 16984252 GTAGCCTGCACTTAGTACTACACACGTGATCGAAAT 65 GTAGCCTGCACTTAGTACTACACACGTGATCGAAAT * * 16984288 TATCGGGTATGCATACTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGTACACATAG 1 TATCGGGTACGCATACTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGCACACATAG 16984353 TAGCCTGCACTTAGTACTACACAC 66 TAGCCTGCACTTAGTACTACACAC 16984377 ATGACCTACA Statistics Matches: 83, Mismatches: 5, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 100 82 0.99 101 1 0.01 ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25 Consensus pattern (100 bp): TATCGGGTACGCATACTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGCACACATAG TAGCCTGCACTTAGTACTACACACGTGATCGAAAT Found at i:16984658 original size:27 final size:27 Alignment explanation

Indices: 16984628--16984681 Score: 72 Period size: 27 Copynumber: 2.0 Consensus size: 27 16984618 TCATACAACC * * 16984628 CATGTAATAGTAATTTAACATTCAATT 1 CATGTAACAATAATTTAACATTCAATT ** 16984655 CATGTAACAATAATTTGCCATTCAATT 1 CATGTAACAATAATTTAACATTCAATT 16984682 TCACATGACA Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 27 23 1.00 ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39 Consensus pattern (27 bp): CATGTAACAATAATTTAACATTCAATT Found at i:16986848 original size:19 final size:19 Alignment explanation

Indices: 16986813--16986850 Score: 51 Period size: 19 Copynumber: 2.0 Consensus size: 19 16986803 TTGCAATTTA * 16986813 AATTTTTATTTTCTTTTCT 1 AATTTTTATTTTATTTTCT 16986832 AATTTTTCA-TTTATTTTCT 1 AATTTTT-ATTTTATTTTCT 16986851 TCTGACAGGT Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 19 16 0.94 20 1 0.06 ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71 Consensus pattern (19 bp): AATTTTTATTTTATTTTCT Found at i:16992729 original size:87 final size:87 Alignment explanation

Indices: 16992582--16992741 Score: 250 Period size: 87 Copynumber: 1.8 Consensus size: 87 16992572 GTGACGAGAT * * 16992582 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAATATATGGCAAT 1 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTCGAAAGATATGGCAAT 16992647 AAGTGTGCATGCTGGAAATATA 66 AAGTGTGCATGCTGGAAATATA * * * 16992669 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAAGGGTATGGCAC 1 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTCGAAAGATATGGCAA * 16992733 TATGTGTGC 65 TAAGTGTGC 16992742 GGGCTTAAAT Statistics Matches: 66, Mismatches: 6, Indels: 2 0.89 0.08 0.03 Matches are distributed among these distances: 87 65 0.98 88 1 0.02 ACGTcount: A:0.29, C:0.14, G:0.30, T:0.27 Consensus pattern (87 bp): TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTCGAAAGATATGGCAAT AAGTGTGCATGCTGGAAATATA Found at i:16992734 original size:29 final size:29 Alignment explanation

Indices: 16992582--16992712 Score: 253 Period size: 29 Copynumber: 4.5 Consensus size: 29 16992572 GTGACGAGAT 16992582 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA 16992611 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA * 16992640 TGGCAATAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA 16992669 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA 16992698 TGGCACTAAGTGTGC 1 TGGCACTAAGTGTGC 16992713 GAGCTCGAAG Statistics Matches: 100, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 29 100 1.00 ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27 Consensus pattern (29 bp): TGGCACTAAGTGTGCATGCTGGAAATATA Found at i:16992759 original size:87 final size:87 Alignment explanation

Indices: 16992582--16992770 Score: 247 Period size: 87 Copynumber: 2.2 Consensus size: 87 16992572 GTGACGAGAT * * 16992582 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAATATATGGCAAT 1 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTCGAAAGATATGGCAAT * * 16992647 AAGTGTGCATGCTGGAAATATA 66 AAGTGTGCAGGCTGGAAATACA * * * 16992669 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAAGGGTATGGCAC 1 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTCGAAAGATATGGCAA * * * * 16992733 TATGTGTGCGGGCT-TAAATCGCA 65 TAAGTGTGCAGGCTGGAAAT-ACA 16992756 TGGCACTAAGTGTGC 1 TGGCACTAAGTGTGC 16992771 GAAATCGAGT Statistics Matches: 89, Mismatches: 11, Indels: 4 0.86 0.11 0.04 Matches are distributed among these distances: 86 4 0.04 87 84 0.94 88 1 0.01 ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26 Consensus pattern (87 bp): TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTCGAAAGATATGGCAAT AAGTGTGCAGGCTGGAAATACA Found at i:17000766 original size:6 final size:6 Alignment explanation

Indices: 17000755--17000796 Score: 50 Period size: 6 Copynumber: 7.0 Consensus size: 6 17000745 TTAAAACTAC * * 17000755 TTTTTA TTTTTA TTTTTA -TTATA TTTTATA ATTTTA TTTTTA 1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA TTTTTA TTTTTA 17000797 ATTATTAATT Statistics Matches: 30, Mismatches: 4, Indels: 4 0.79 0.11 0.11 Matches are distributed among these distances: 5 4 0.13 6 21 0.70 7 5 0.17 ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76 Consensus pattern (6 bp): TTTTTA Found at i:17000816 original size:28 final size:24 Alignment explanation

Indices: 17000713--17000801 Score: 74 Period size: 24 Copynumber: 3.6 Consensus size: 24 17000703 TTTAAAAACA * 17000713 TTTATTTATTATTTTATGTTTATAAT 1 TTTATTT-TTATTATAT-TTTATAAT * ** * 17000739 TTT-TTATTAAAACTACTTTT-TATT 1 TTTATTTTTATTA-TA-TTTTATAAT 17000763 TTTATTTTTATTATATTTTATAAT 1 TTTATTTTTATTATATTTTATAAT 17000787 TTTATTTTTAATTAT 1 TTTATTTTT-ATTAT 17000802 TAATTTTGGT Statistics Matches: 49, Mismatches: 9, Indels: 11 0.71 0.13 0.16 Matches are distributed among these distances: 23 4 0.08 24 23 0.47 25 18 0.37 26 4 0.08 ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69 Consensus pattern (24 bp): TTTATTTTTATTATATTTTATAAT Found at i:17002336 original size:46 final size:44 Alignment explanation

Indices: 17002232--17002339 Score: 144 Period size: 44 Copynumber: 2.4 Consensus size: 44 17002222 TGTCTTTGAC ** * * * 17002232 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT 1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT * 17002276 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT 1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT 17002322 ATGGACTTACATGGCTCA 1 ATGGACTTACATGGCTCA 17002340 TTTCGTTCTG Statistics Matches: 56, Mismatches: 6, Indels: 2 0.88 0.09 0.03 Matches are distributed among these distances: 44 33 0.59 46 23 0.41 ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33 Consensus pattern (44 bp): ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT Found at i:17008034 original size:55 final size:54 Alignment explanation

Indices: 17007964--17008071 Score: 128 Period size: 55 Copynumber: 2.0 Consensus size: 54 17007954 ATAGGTTCGA * * * * 17007964 CCACAGTTGTTCCACATGG-GTGTGTTGCACGCCCGTGTTGTTTTGGCAGGCTCAC 1 CCACAGTTCTTCCACACGGAGTGTCTT--ACGCCCATGTTGTTTTGGCAGGCTCAC * * 17008019 CCACGGTTCTTCCACACGGACGTGTCTTATGCCCATGTTGTTTTGGCAGGCTC 1 CCACAGTTCTTCCACACGGA-GTGTCTTACGCCCATGTTGTTTTGGCAGGCTC 17008072 GACCACGACC Statistics Matches: 45, Mismatches: 6, Indels: 4 0.82 0.11 0.07 Matches are distributed among these distances: 55 39 0.87 57 6 0.13 ACGTcount: A:0.13, C:0.29, G:0.27, T:0.31 Consensus pattern (54 bp): CCACAGTTCTTCCACACGGAGTGTCTTACGCCCATGTTGTTTTGGCAGGCTCAC Found at i:17009612 original size:22 final size:22 Alignment explanation

Indices: 17009577--17009619 Score: 59 Period size: 22 Copynumber: 2.0 Consensus size: 22 17009567 TGAGCTGTTA ** 17009577 CCTTGGGTTGGGTTCAGTATTC 1 CCTTGGGTAAGGTTCAGTATTC * 17009599 CCTTGGGTAAGGTTCGGTATT 1 CCTTGGGTAAGGTTCAGTATT 17009620 ACTTCGCAAA Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.12, C:0.16, G:0.33, T:0.40 Consensus pattern (22 bp): CCTTGGGTAAGGTTCAGTATTC Found at i:17021449 original size:48 final size:49 Alignment explanation

Indices: 17021374--17021597 Score: 230 Period size: 48 Copynumber: 4.7 Consensus size: 49 17021364 TAAGTTGCCA * * 17021374 ATGCCATGTCCTAGACATGGTCTTACACT-GGATCATATGTCAAAGCCG 1 ATGCCATGTCCCAGACATGGTCTTACACTAGCATCATATGTCAAAGCCG * ** * 17021422 ATGCCATGTCCCAGACATGGTCGTACACTAGC-TC-TCATAACAATGCCG 1 ATGCCATGTCCCAGACATGGTCTTACACTAGCATCAT-ATGTCAAAGCCG * * * 17021470 ATGCCATGTCCCAGACTTGGTCTTACACTAGCACGCATATTGT---GGCCG 1 ATGCCATGTCCCAGACATGGTCTTACACTAGCA-TCATA-TGTCAAAGCCG * *** 17021518 ATGCCATGTCCCAGACATGGTCTTACACTAGCATACATA--TCAACGTTA 1 ATGCCATGTCCCAGACATGGTCTTACACTAGCAT-CATATGTCAAAGCCG * 17021566 ATGCCATGTCCCAAACATGGTCTTACACTAGC 1 ATGCCATGTCCCAGACATGGTCTTACACTAGC 17021598 TCTCATGATG Statistics Matches: 147, Mismatches: 19, Indels: 20 0.79 0.10 0.11 Matches are distributed among these distances: 45 1 0.01 47 1 0.01 48 140 0.95 49 1 0.01 50 2 0.01 51 2 0.01 ACGTcount: A:0.27, C:0.29, G:0.19, T:0.26 Consensus pattern (49 bp): ATGCCATGTCCCAGACATGGTCTTACACTAGCATCATATGTCAAAGCCG Found at i:17021538 original size:96 final size:96 Alignment explanation

Indices: 17021370--17021597 Score: 266 Period size: 96 Copynumber: 2.4 Consensus size: 96 17021360 AGGTTAAGTT * * * * * 17021370 GCCAATGCCATGTCCTAGACATGGTCTTACACT-GGA-TCATA-TGTCAAAGCCGATGCCATGTC 1 GCCAATGCCATGTCCCAAACATGGTCTTACACTAGCACGCATATTGT---GGCCGATGCCATGTC * * 17021432 CCAGACATGGTCGTACACTAGC-TCTCATAACAAT 63 CCAGACATGGTCGTACACTAGCAT-ACATAACAAC * * * 17021466 GCCGATGCCATGTCCCAGACTTGGTCTTACACTAGCACGCATATTGTGGCCGATGCCATGTCCCA 1 GCCAATGCCATGTCCCAAACATGGTCTTACACTAGCACGCATATTGTGGCCGATGCCATGTCCCA * * 17021531 GACATGGTCTTACACTAGCATACATATCAAC 66 GACATGGTCGTACACTAGCATACATAACAAC ** 17021562 GTTAATGCCATGTCCCAAACATGGTCTTACACTAGC 1 GCCAATGCCATGTCCCAAACATGGTCTTACACTAGC 17021598 TCTCATGATG Statistics Matches: 113, Mismatches: 15, Indels: 8 0.83 0.11 0.06 Matches are distributed among these distances: 96 103 0.91 97 3 0.03 98 4 0.04 99 3 0.03 ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25 Consensus pattern (96 bp): GCCAATGCCATGTCCCAAACATGGTCTTACACTAGCACGCATATTGTGGCCGATGCCATGTCCCA GACATGGTCGTACACTAGCATACATAACAAC Found at i:17031714 original size:38 final size:39 Alignment explanation

Indices: 17031662--17031804 Score: 234 Period size: 39 Copynumber: 3.7 Consensus size: 39 17031652 GAATGTTCGA 17031662 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT 1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT * * 17031701 GTGATA-CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT 1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT * 17031739 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT 1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT * 17031778 GTGATATCCGGGTTAAGTCCCGAAGGC 1 GTGATATCCGGGCTAAG-CCCGAAGGC 17031805 CTTTGTGCGG Statistics Matches: 95, Mismatches: 7, Indels: 3 0.90 0.07 0.03 Matches are distributed among these distances: 38 35 0.37 39 51 0.54 40 9 0.09 ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22 Consensus pattern (39 bp): GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT Found at i:17031750 original size:77 final size:79 Alignment explanation

Indices: 17031663--17031844 Score: 269 Period size: 77 Copynumber: 2.3 Consensus size: 79 17031653 AATGTTCGAG 17031663 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATA-CCGGGCTAAG-CCCGAAGGC 1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC 17031726 AATTGTGCGAGTTA 66 AATTGTGCGAGTTA * 17031740 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC 1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC ** * 17031805 CTTTGTGCGGGTTA 66 AATTGTGCGAGTTA ** * * 17031819 CCATAACCGGGCTATGTCCCGAAGGC 1 TGATATCCGGGCTAAG-CCCGAAGGC 17031845 GTTTGAACGA Statistics Matches: 94, Mismatches: 8, Indels: 3 0.90 0.08 0.03 Matches are distributed among these distances: 77 44 0.47 78 9 0.10 79 32 0.34 80 9 0.10 ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23 Consensus pattern (79 bp): TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC AATTGTGCGAGTTA Found at i:17039540 original size:39 final size:39 Alignment explanation

Indices: 17039486--17039629 Score: 225 Period size: 39 Copynumber: 3.7 Consensus size: 39 17039476 GAATGTTCGA * 17039486 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGTAAATT 1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT * * * 17039525 GTGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT 1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT * 17039564 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT 1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT * 17039603 GTGATATCCGGGTTAAGTCCCGAAGGC 1 GTGATATCCGGGCTAAG-CCCGAAGGC 17039630 CTTTGTGCGG Statistics Matches: 94, Mismatches: 10, Indels: 1 0.90 0.10 0.01 Matches are distributed among these distances: 39 85 0.90 40 9 0.10 ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23 Consensus pattern (39 bp): GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT Found at i:17039576 original size:78 final size:79 Alignment explanation

Indices: 17039487--17039669 Score: 260 Period size: 78 Copynumber: 2.3 Consensus size: 79 17039477 AATGTTCGAG * 17039487 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGTAAATTGTGATACCCGGGCTAAG-CCCGAAGGC 1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATACCCGGGCTAAGTCCCGAAGGC 17039551 AATTGTGCGAGTTA 66 AATTGTGCGAGTTA * * 17039565 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC 1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATACCCGGGCTAAGTCCCGAAGGC ** * 17039630 CTTTGTGCGGGTTA 66 AATTGTGCGAGTTA ** * * 17039644 CCATAACCGGGCTATGTCCCGAAGGC 1 TGATATCCGGGCTAAG-CCCGAAGGC 17039670 GTTTGAACGA Statistics Matches: 93, Mismatches: 10, Indels: 2 0.89 0.10 0.02 Matches are distributed among these distances: 78 52 0.56 79 32 0.34 80 9 0.10 ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23 Consensus pattern (79 bp): TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATACCCGGGCTAAGTCCCGAAGGC AATTGTGCGAGTTA Found at i:17041376 original size:49 final size:49 Alignment explanation

Indices: 17041318--17041506 Score: 236 Period size: 50 Copynumber: 3.8 Consensus size: 49 17041308 GTAGCCAAAC * * 17041318 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT 1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT * * * 17041367 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC 1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-AAT * * * 17041417 TATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT 1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-T * * * 17041468 TAT-TGGGCACGCATAGTAGTCTGCACTTAGTACTACACA 1 TATCT-GGTACACATAGTAGCCTGCACTTAGTACTACACA 17041507 TGCGACCTAG Statistics Matches: 122, Mismatches: 14, Indels: 6 0.86 0.10 0.04 Matches are distributed among these distances: 49 42 0.34 50 47 0.39 51 33 0.27 ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27 Consensus pattern (49 bp): TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT Found at i:17041449 original size:50 final size:49 Alignment explanation

Indices: 17041315--17041506 Score: 235 Period size: 49 Copynumber: 3.9 Consensus size: 49 17041305 TATGTAGCCA * * * 17041315 AACTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACC 1 AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC * * 17041364 AATTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC 1 AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC * * 17041413 TAACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCG 1 -AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CC * * * 17041464 AAGTTAT-TGG-GCACGCATAGTAGTCTGCACTTAGTACTACACA 1 AA-CTATCTGGTACACG--TAGTAGCCTGCACTTAGTACTACACA 17041507 TGCGACCTAG Statistics Matches: 125, Mismatches: 13, Indels: 8 0.86 0.09 0.05 Matches are distributed among these distances: 49 48 0.38 50 48 0.38 51 29 0.23 ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27 Consensus pattern (49 bp): AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC Found at i:17041533 original size:101 final size:99 Alignment explanation

Indices: 17041315--17041515 Score: 267 Period size: 99 Copynumber: 2.0 Consensus size: 99 17041305 TATGTAGCCA * * * * * * 17041315 AACTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG 1 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGCACACA * 17041380 TAGTAGCCTGCACTTAGTACTACACACGTGACCT 66 TAGTAGCCTGCACTTAGTACTACACACGCGACCT * ** * 17041414 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATTGGGCACG 1 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGCACA * * 17041479 CATAGTAGTCTGCACTTAGTACTACACATGCGACCT 64 CATAGTAGCCTGCACTTAGTACTACACACGCGACCT 17041515 A 1 A 17041516 GCTACATATA Statistics Matches: 87, Mismatches: 13, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 99 43 0.49 100 3 0.03 101 41 0.47 ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26 Consensus pattern (99 bp): AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGCACACA TAGTAGCCTGCACTTAGTACTACACACGCGACCT Found at i:17042848 original size:30 final size:30 Alignment explanation

Indices: 17042812--17042871 Score: 111 Period size: 30 Copynumber: 2.0 Consensus size: 30 17042802 AAGATGAGTT 17042812 AATTTTGCCTTTATTTTCCCTTTTTATTTC 1 AATTTTGCCTTTATTTTCCCTTTTTATTTC * 17042842 AATTTTGGCTTTATTTTCCCTTTTTATTTC 1 AATTTTGCCTTTATTTTCCCTTTTTATTTC 17042872 TTTTAATTAC Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 30 29 1.00 ACGTcount: A:0.13, C:0.18, G:0.05, T:0.63 Consensus pattern (30 bp): AATTTTGCCTTTATTTTCCCTTTTTATTTC Found at i:17045721 original size:45 final size:45 Alignment explanation

Indices: 17045653--17045783 Score: 199 Period size: 45 Copynumber: 2.9 Consensus size: 45 17045643 TATCGTACGG * * 17045653 TACTATTCTGGCCTTTGAACCTAGCAGGCTATGATGCCGGTGAGA 1 TACTATTCAGGCCTTTGAACCTAGCAGGCTATAATGCCGGTGAGA * 17045698 TACTATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA 1 TACTATTCAGGCCTTTGAACCTAGCAGGCTATAATGCCGGTGAGA * * ** 17045743 TAGTATTCGGGCCTTCAAACCTAGCAGGCTATAATGCCGGT 1 TACTATTCAGGCCTTTGAACCTAGCAGGCTATAATGCCGGT 17045784 AAAATTATAT Statistics Matches: 78, Mismatches: 8, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 45 78 1.00 ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27 Consensus pattern (45 bp): TACTATTCAGGCCTTTGAACCTAGCAGGCTATAATGCCGGTGAGA Found at i:17072915 original size:7 final size:7 Alignment explanation

Indices: 17072903--17072939 Score: 65 Period size: 7 Copynumber: 5.3 Consensus size: 7 17072893 AGTATACTAA 17072903 TTTAGGG 1 TTTAGGG 17072910 TTTAGGG 1 TTTAGGG 17072917 TTTAGGG 1 TTTAGGG 17072924 TTTAGGG 1 TTTAGGG * 17072931 TTTAAGG 1 TTTAGGG 17072938 TT 1 TT 17072940 AACAAATATA Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 7 29 1.00 ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46 Consensus pattern (7 bp): TTTAGGG Found at i:17089742 original size:29 final size:29 Alignment explanation

Indices: 17089700--17089761 Score: 79 Period size: 29 Copynumber: 2.1 Consensus size: 29 17089690 ATATAATGAG ** * 17089700 ATTGGACCTAATGGGCCATTTGAATGTGA 1 ATTGGACCTAATGGGCCAAATGAACGTGA * * 17089729 ATTGGGCCTGATGGGCCAAATGAACGTGA 1 ATTGGACCTAATGGGCCAAATGAACGTGA 17089758 ATTG 1 ATTG 17089762 AATGGTTGGA Statistics Matches: 28, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 29 28 1.00 ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27 Consensus pattern (29 bp): ATTGGACCTAATGGGCCAAATGAACGTGA Found at i:17097444 original size:29 final size:27 Alignment explanation

Indices: 17097402--17097519 Score: 107 Period size: 29 Copynumber: 4.2 Consensus size: 27 17097392 GTGAGCATGA 17097402 ATATAA-TGAGATTGGGCCTAATGGGCC 1 ATATAAGTGA-ATTGGGCCTAATGGGCC * 17097429 ATATGAATGTGAATTGGGCCTGATGGGCC 1 ATAT-AA-GTGAATTGGGCCTAATGGGCC 17097458 ATATAAACGTGAATTGGGCTGCT--TGGGCC 1 ATAT-AA-GTGAATTGGGC--CTAATGGGCC * * * 17097487 ATATAAATGATATTGGGCCTAGTGGGTC 1 ATATAAGTGA-ATTGGGCCTAATGGGCC 17097515 ATATA 1 ATATA 17097520 CATGTTTGTA Statistics Matches: 78, Mismatches: 5, Indels: 15 0.80 0.05 0.15 Matches are distributed among these distances: 26 2 0.03 27 7 0.09 28 21 0.27 29 43 0.55 30 3 0.04 31 2 0.03 ACGTcount: A:0.28, C:0.14, G:0.30, T:0.29 Consensus pattern (27 bp): ATATAAGTGAATTGGGCCTAATGGGCC Found at i:17103186 original size:19 final size:19 Alignment explanation

Indices: 17103162--17103204 Score: 86 Period size: 19 Copynumber: 2.3 Consensus size: 19 17103152 CATGGGCTTT 17103162 GCCAGTTTGGGCCATGTGG 1 GCCAGTTTGGGCCATGTGG 17103181 GCCAGTTTGGGCCATGTGG 1 GCCAGTTTGGGCCATGTGG 17103200 GCCAG 1 GCCAG 17103205 AAATGGGCCG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 24 1.00 ACGTcount: A:0.12, C:0.23, G:0.42, T:0.23 Consensus pattern (19 bp): GCCAGTTTGGGCCATGTGG Found at i:17103191 original size:10 final size:10 Alignment explanation

Indices: 17103162--17103222 Score: 56 Period size: 9 Copynumber: 6.3 Consensus size: 10 17103152 CATGGGCTTT * 17103162 GCCAGTTTGG 1 GCCAGTGTGG 17103172 GCCA-TGTGG 1 GCCAGTGTGG * 17103181 GCCAGTTTGG 1 GCCAGTGTGG 17103191 GCCA-TGTGG 1 GCCAGTGTGG ** 17103200 GCCAGAAATGG 1 GCCAG-TGTGG 17103211 GCC-GTGTGG 1 GCCAGTGTGG 17103220 GCC 1 GCC 17103223 CCACGGGCTC Statistics Matches: 41, Mismatches: 7, Indels: 7 0.75 0.13 0.13 Matches are distributed among these distances: 9 22 0.54 10 13 0.32 11 6 0.15 ACGTcount: A:0.13, C:0.23, G:0.43, T:0.21 Consensus pattern (10 bp): GCCAGTGTGG Found at i:17103213 original size:20 final size:19 Alignment explanation

Indices: 17103169--17103222 Score: 72 Period size: 19 Copynumber: 2.8 Consensus size: 19 17103159 TTTGCCAGTT ** 17103169 TGGGCCATGTGGGCCAGTT 1 TGGGCCATGTGGGCCAGAA 17103188 TGGGCCATGTGGGCCAGAAA 1 TGGGCCATGTGGGCCAG-AA * 17103208 TGGGCCGTGTGGGCC 1 TGGGCCATGTGGGCC 17103223 CCACGGGCTC Statistics Matches: 31, Mismatches: 3, Indels: 1 0.89 0.09 0.03 Matches are distributed among these distances: 19 17 0.55 20 14 0.45 ACGTcount: A:0.13, C:0.22, G:0.44, T:0.20 Consensus pattern (19 bp): TGGGCCATGTGGGCCAGAA Found at i:17103798 original size:34 final size:34 Alignment explanation

Indices: 17103749--17103825 Score: 127 Period size: 34 Copynumber: 2.3 Consensus size: 34 17103739 TCATTGCATT * 17103749 ACTGATACTGTTACTGTAATGGGCTAAGGCCCAC 1 ACTGATACTGCTACTGTAATGGGCTAAGGCCCAC * * 17103783 ATTGATACTGCTACTGTTATGGGCTAAGGCCCAC 1 ACTGATACTGCTACTGTAATGGGCTAAGGCCCAC 17103817 ACTGATACT 1 ACTGATACT 17103826 TGATTGTTAC Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 34 39 1.00 ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29 Consensus pattern (34 bp): ACTGATACTGCTACTGTAATGGGCTAAGGCCCAC Found at i:17107412 original size:46 final size:46 Alignment explanation

Indices: 17107359--17107534 Score: 203 Period size: 46 Copynumber: 3.8 Consensus size: 46 17107349 TGGTTGAGCA * * 17107359 TCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATACGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG * * * * * * 17107405 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTA-ACTAGGCA 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATACGA-ACG * * 17107452 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG * * 17107498 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 17107535 GCGGGTTACA Statistics Matches: 106, Mismatches: 19, Indels: 10 0.79 0.14 0.07 Matches are distributed among these distances: 45 1 0.01 46 70 0.66 47 34 0.32 48 1 0.01 ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29 Consensus pattern (46 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG Found at i:17107515 original size:93 final size:93 Alignment explanation

Indices: 17107356--17107526 Score: 288 Period size: 93 Copynumber: 1.8 Consensus size: 93 17107346 GGATGGTTGA * * 17107356 GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATACGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATACGAACGCCCGAACTCGTTGAGT 17107421 TGAGTCCGAGTTCGTGAAATGTAACTAG 66 TGAGTCCGAGTTCGTGAAATGTAACTAG * * * * 17107449 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATACGAACGCCCGAACTCGTTGAGT 17107514 TGAGTCCGAGTTC 66 TGAGTCCGAGTTC 17107527 ACTTATGGGC Statistics Matches: 72, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 93 72 1.00 ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATACGAACGCCCGAACTCGTTGAGT TGAGTCCGAGTTCGTGAAATGTAACTAG Found at i:17114233 original size:22 final size:23 Alignment explanation

Indices: 17114208--17114250 Score: 70 Period size: 22 Copynumber: 1.9 Consensus size: 23 17114198 TATCCCCACA * 17114208 TGGAGTGTAG-GGCTGGACGGAG 1 TGGAGTGTAGAGGATGGACGGAG 17114230 TGGAGTGTAGAGGATGGACGG 1 TGGAGTGTAGAGGATGGACGG 17114251 GTAGGACTTC Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 22 10 0.53 23 9 0.47 ACGTcount: A:0.21, C:0.07, G:0.53, T:0.19 Consensus pattern (23 bp): TGGAGTGTAGAGGATGGACGGAG Found at i:17115453 original size:26 final size:25 Alignment explanation

Indices: 17115423--17115479 Score: 69 Period size: 26 Copynumber: 2.2 Consensus size: 25 17115413 ATACCTTTAG 17115423 CTATTAGAACTTAATTAATTAATTAA 1 CTATTAGAACTT-ATTAATTAATTAA ** * 17115449 CTATTTAGTCCTTTTTAATTAATTAA 1 CTA-TTAGAACTTATTAATTAATTAA 17115475 CTATT 1 CTATT 17115480 GAAAGAATAA Statistics Matches: 27, Mismatches: 3, Indels: 3 0.82 0.09 0.09 Matches are distributed among these distances: 25 2 0.07 26 18 0.67 27 7 0.26 ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49 Consensus pattern (25 bp): CTATTAGAACTTATTAATTAATTAA Found at i:17116492 original size:27 final size:27 Alignment explanation

Indices: 17116452--17116505 Score: 72 Period size: 27 Copynumber: 2.0 Consensus size: 27 17116442 AGGTACAACC * * 17116452 CATGTAATAGTAATTTAACATTCAATT 1 CATGTAACAATAATTTAACATTCAATT ** 17116479 CATGTAACAATAATTTGCCATTCAATT 1 CATGTAACAATAATTTAACATTCAATT 17116506 TCACATGACA Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 27 23 1.00 ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39 Consensus pattern (27 bp): CATGTAACAATAATTTAACATTCAATT Found at i:17126954 original size:25 final size:25 Alignment explanation

Indices: 17126926--17126975 Score: 91 Period size: 25 Copynumber: 2.0 Consensus size: 25 17126916 GGACGAAGAG 17126926 TAGGAAGCAAGGAATTACTCAAGGA 1 TAGGAAGCAAGGAATTACTCAAGGA * 17126951 TAGGAAGCAATGAATTACTCAAGGA 1 TAGGAAGCAAGGAATTACTCAAGGA 17126976 AAGCCGATTG Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 25 24 1.00 ACGTcount: A:0.44, C:0.12, G:0.26, T:0.18 Consensus pattern (25 bp): TAGGAAGCAAGGAATTACTCAAGGA Found at i:17131667 original size:123 final size:123 Alignment explanation

Indices: 17131448--17131786 Score: 597 Period size: 123 Copynumber: 2.8 Consensus size: 123 17131438 GAATTATGTG * 17131448 AAATGAAATATGGATGTGTAATGATTATTGACATATGTGTGTATGAGTATTTGAATGGTACCCGG 1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG * 17131513 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGA 66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA 17131571 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG 1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG 17131636 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA 66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA * * * * * 17131694 AAATGAAATATGGATGTGTAATGATTATTGATTTATGTGTGCATGAGCAATTGAATGATACCCGG 1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG * * 17131759 GCTAAGTCCCGAAGACATTTATGCTAGT 66 GCTAAGTCCCGAAGGCAATTATGCTAGT 17131787 AATTATATCC Statistics Matches: 207, Mismatches: 9, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 123 207 1.00 ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34 Consensus pattern (123 bp): AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA Found at i:17131810 original size:40 final size:40 Alignment explanation

Indices: 17131755--17131997 Score: 292 Period size: 40 Copynumber: 6.1 Consensus size: 40 17131745 TGAATGATAC * * * * ** 17131755 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT * * * * 17131795 CCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGACTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-TTATAT * 17131835 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT * 17131875 CCGGGCTAATACCC-AAGGCATTTGTGCAAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT * * 17131914 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT * * ** * 17131954 CCGGGCTAAGACCCGAGGGCATTCGTGCGTGTGGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT 17131994 CCGG 1 CCGG 17131998 TTGTATTCCG Statistics Matches: 180, Mismatches: 20, Indels: 6 0.87 0.10 0.03 Matches are distributed among these distances: 39 39 0.22 40 139 0.77 41 2 0.01 ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT Found at i:17131923 original size:79 final size:80 Alignment explanation

Indices: 17131755--17131997 Score: 303 Period size: 79 Copynumber: 3.0 Consensus size: 80 17131745 TGAATGATAC * * * * * * 17131755 CCGGGCTAAGT-CCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAATT 1 CCGGGCTAA-TACCCGAAGGCATTTGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATTT * * 17131819 GTGCTAG-TGACTATAT 65 GTGCAAGTTG-TTATAT * * 17131835 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATATCCGGGCTAATACCC-AAGGCATTTG 1 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATTTG 17131899 TGCAAGTTGTTATAT 66 TGCAAGTTGTTATAT * * * 17131914 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATATCCGGGCTAAGACCCGAGGGCATTCG 1 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATTTG ** * 17131979 TGCGTGTGGTTATAT 66 TGCAAGTTGTTATAT 17131994 CCGG 1 CCGG 17131998 TTGTATTCCG Statistics Matches: 143, Mismatches: 17, Indels: 6 0.86 0.10 0.04 Matches are distributed among these distances: 79 72 0.50 80 71 0.50 ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28 Consensus pattern (80 bp): CCGGGCTAATACCCGAAGGCATTTGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATTTG TGCAAGTTGTTATAT Found at i:17138961 original size:40 final size:40 Alignment explanation

Indices: 17138906--17139149 Score: 301 Period size: 40 Copynumber: 6.1 Consensus size: 40 17138896 TGAATGATAC * * * * ** 17138906 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT * * * * 17138946 CCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGACTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-TTATAT * 17138986 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT * 17139026 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT * * 17139066 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT * * ** * 17139106 CCGGGCTAAGACCCGAGGGCATTCGTGCGTGTGGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT 17139146 CCGG 1 CCGG 17139150 TTGTATTCCG Statistics Matches: 182, Mismatches: 20, Indels: 4 0.88 0.10 0.02 Matches are distributed among these distances: 40 180 0.99 41 2 0.01 ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT Found at i:17143571 original size:47 final size:47 Alignment explanation

Indices: 17143517--17143976 Score: 749 Period size: 47 Copynumber: 9.7 Consensus size: 47 17143507 GATTTTATGC * * * 17143517 GATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCGATGT 1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT 17143564 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT 1 GATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGT 17143613 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT 1 GATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGT 17143662 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT 1 GATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGT * * 17143711 GATGAATGTGAAAGTGTATATACGTGATAAGGCCGAATGGCCGATGT 1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT * * 17143758 GATGAATGTGAAATTGTATATATGTGATAAGTCCTAATGGCCGATGT 1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT 17143805 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT 1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT 17143852 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT 1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT * * * * 17143899 TATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAACGT 1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT * * 17143946 GATGGATGTGAAAGTGTATAAATGTGATAAG 1 GATGAATGTGAAAGTGTATATATGTGATAAG 17143977 TCCCGAAGGG Statistics Matches: 393, Mismatches: 18, Indels: 4 0.95 0.04 0.01 Matches are distributed among these distances: 47 250 0.64 49 143 0.36 ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30 Consensus pattern (47 bp): GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT Found at i:17151502 original size:24 final size:24 Alignment explanation

Indices: 17151403--17151495 Score: 159 Period size: 24 Copynumber: 3.9 Consensus size: 24 17151393 AAGGCTGTCA 17151403 GGAGAAGATTTAGGAGCTGATAAG 1 GGAGAAGATTTAGGAGCTGATAAG * 17151427 GGAGATGATTTAGGAGCTGATAAG 1 GGAGAAGATTTAGGAGCTGATAAG * * 17151451 GGAGAGGATTTAGGAGCTGATAAA 1 GGAGAAGATTTAGGAGCTGATAAG 17151475 GGAGAAGATTTAGGAGCTGAT 1 GGAGAAGATTTAGGAGCTGAT 17151496 CACGGAGCAG Statistics Matches: 65, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 24 65 1.00 ACGTcount: A:0.35, C:0.04, G:0.38, T:0.23 Consensus pattern (24 bp): GGAGAAGATTTAGGAGCTGATAAG Found at i:17156002 original size:89 final size:90 Alignment explanation

Indices: 17155807--17156002 Score: 322 Period size: 89 Copynumber: 2.2 Consensus size: 90 17155797 GAAAATCTTA * * 17155807 GTAAGGTAATTTGTTTAATGAATTTGAAAGATTTTTTATTTGTTGAATATTGATCTGAACATAAA 1 GTAAGGTAATTTGTTTAATGAATTTGAAAGATTTGTTATTTATTGAATATTGATCTGAACATAAA * 17155872 TGAATTCATCTGACTGTAAATCTCG 66 TGAATTCATCTGACTGTAAATCCCG * 17155897 GTAAGGTAATTTGTTTAATGAATTTGAAAGATTTGTTATTTATTGAATA-TGATCTGAACATAGA 1 GTAAGGTAATTTGTTTAATGAATTTGAAAGATTTGTTATTTATTGAATATTGATCTGAACATAAA * * 17155961 TGAATTCATCTGACTGTAAGTCCCT 66 TGAATTCATCTGACTGTAAATCCCG * 17155986 GTAAGGTAATTGGTTTA 1 GTAAGGTAATTTGTTTA 17156003 TGTTGATGGA Statistics Matches: 99, Mismatches: 7, Indels: 1 0.93 0.07 0.01 Matches are distributed among these distances: 89 52 0.53 90 47 0.47 ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41 Consensus pattern (90 bp): GTAAGGTAATTTGTTTAATGAATTTGAAAGATTTGTTATTTATTGAATATTGATCTGAACATAAA TGAATTCATCTGACTGTAAATCCCG Found at i:17158569 original size:46 final size:46 Alignment explanation

Indices: 17158251--17158569 Score: 417 Period size: 46 Copynumber: 7.0 Consensus size: 46 17158241 TTTGACATGA * * * * * 17158251 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT * * * * 17158297 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCATGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT * * * * 17158343 TGCCAT-GTATCTTTCAAACATGGTCTTATTCATTTCATATCACGC 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT * * * 17158388 TGCCACGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT * * 17158434 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT * * * 17158480 TGCCATAGAATCTTTCAACCATGGTCTTACACATTTCATATCAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT * 17158526 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAG 17158570 AGAGCACACT Statistics Matches: 248, Mismatches: 23, Indels: 4 0.90 0.08 0.01 Matches are distributed among these distances: 45 43 0.17 46 205 0.83 ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39 Consensus pattern (46 bp): TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT Found at i:17160656 original size:11 final size:11 Alignment explanation

Indices: 17160640--17160691 Score: 50 Period size: 11 Copynumber: 4.5 Consensus size: 11 17160630 CTTTCTTTAT 17160640 ATAATAATAAA 1 ATAATAATAAA * 17160651 ATAATAACAAA 1 ATAATAATAAA * * 17160662 ATGTATTATTAAA 1 A--TAATAATAAA * 17160675 ATATTAATAAA 1 ATAATAATAAA 17160686 ATAATA 1 ATAATA 17160692 TTTATCTAAT Statistics Matches: 33, Mismatches: 6, Indels: 4 0.77 0.14 0.09 Matches are distributed among these distances: 11 25 0.76 13 8 0.24 ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33 Consensus pattern (11 bp): ATAATAATAAA Found at i:17162436 original size:22 final size:22 Alignment explanation

Indices: 17162406--17162463 Score: 107 Period size: 22 Copynumber: 2.6 Consensus size: 22 17162396 TCAGTGCTAG 17162406 TAATCACTTTTACACCTTTCGCA 1 TAAT-ACTTTTACACCTTTCGCA 17162429 TAATACTTTTACACCTTTCGCA 1 TAATACTTTTACACCTTTCGCA 17162451 TAATACTTTTACA 1 TAATACTTTTACA 17162464 TGCTTTACAA Statistics Matches: 35, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 22 31 0.89 23 4 0.11 ACGTcount: A:0.29, C:0.26, G:0.03, T:0.41 Consensus pattern (22 bp): TAATACTTTTACACCTTTCGCA Found at i:17166253 original size:39 final size:40 Alignment explanation

Indices: 17166153--17166343 Score: 176 Period size: 39 Copynumber: 4.8 Consensus size: 40 17166143 TCGAATGATG * * * * 17166153 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTAATAAA * * * 17166193 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTAATAAA * * 17166233 TCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAATAAA * * * * 17166272 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TCATATAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAATA-AA ** * 17166312 -CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT 17166344 CGTTATATCC Statistics Matches: 122, Mismatches: 23, Indels: 12 0.78 0.15 0.08 Matches are distributed among these distances: 39 62 0.51 40 53 0.43 41 7 0.06 ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAATAAA Found at i:17166293 original size:79 final size:81 Alignment explanation

Indices: 17166153--17166336 Score: 227 Period size: 79 Copynumber: 2.3 Consensus size: 81 17166143 TCGAATGATG * * * 17166153 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT 17166217 CGTGCGAGTTAATA-AA 66 CGTGCGAG-TAATATAA * ** 17166233 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT * 17166295 TCGTGCGAGTCATATAA 65 TCGTGCGAGTAATATAA ** 17166312 -CCGGGCTTCGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 17166337 AGCGAGTCGT Statistics Matches: 91, Mismatches: 9, Indels: 9 0.83 0.08 0.08 Matches are distributed among these distances: 78 13 0.14 79 60 0.66 80 18 0.20 ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24 Consensus pattern (81 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT CGTGCGAGTAATATAA Found at i:17171316 original size:71 final size:71 Alignment explanation

Indices: 17171232--17171395 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 17171222 CGATTTGTCT 17171232 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 17171297 CTTTCA 66 CTTTCA 17171303 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 17171368 CTTTCA 66 CTTTCA 17171374 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 17171396 GATACATCTC Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:17171433 original size:71 final size:70 Alignment explanation

Indices: 17171232--17171429 Score: 258 Period size: 71 Copynumber: 2.8 Consensus size: 70 17171222 CGATTTGTCT * * * * 17171232 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 17171297 CTTTCA 65 CTTTCA * * * * 17171303 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 17171368 CTTTCA 65 CTTTCA * * 17171374 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC 17171430 TACAGGGTGT Statistics Matches: 120, Mismatches: 6, Indels: 5 0.92 0.05 0.04 Matches are distributed among these distances: 68 22 0.18 69 1 0.01 70 1 0.01 71 96 0.80 ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34 Consensus pattern (70 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC TTTCA Found at i:17178391 original size:71 final size:71 Alignment explanation

Indices: 17178305--17178468 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 17178295 CGATTTGTCT 17178305 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 17178370 CTTTCA 66 CTTTCA 17178376 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 17178441 CTTTCA 66 CTTTCA 17178447 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 17178469 GATACATCTC Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:17178506 original size:71 final size:70 Alignment explanation

Indices: 17178305--17178502 Score: 258 Period size: 71 Copynumber: 2.8 Consensus size: 70 17178295 CGATTTGTCT * * * * 17178305 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 17178370 CTTTCA 65 CTTTCA * * * * 17178376 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 17178441 CTTTCA 65 CTTTCA * * 17178447 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC 17178503 TACAGGGTGT Statistics Matches: 120, Mismatches: 6, Indels: 5 0.92 0.05 0.04 Matches are distributed among these distances: 68 22 0.18 69 1 0.01 70 1 0.01 71 96 0.80 ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34 Consensus pattern (70 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC TTTCA Found at i:17183637 original size:79 final size:82 Alignment explanation

Indices: 17183497--17183681 Score: 229 Period size: 79 Copynumber: 2.3 Consensus size: 82 17183487 TCGAATGATG * * * 17183497 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT * 17183561 CGTGCGAGTTAATA-AA 66 CGTGCGAGTCAATATAA * ** 17183577 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT * 17183639 TCGTGCGAGTCACTATAA 65 TCGTGCGAGTCAATATAA ** 17183657 -CCGGGCTTCGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 17183682 AGCGAGTCGT Statistics Matches: 91, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 1 0.01 79 56 0.62 80 34 0.37 ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24 Consensus pattern (82 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT CGTGCGAGTCAATATAA Found at i:17183689 original size:40 final size:40 Alignment explanation

Indices: 17183498--17183689 Score: 151 Period size: 40 Copynumber: 4.8 Consensus size: 40 17183488 CGAATGATGT * * * * * 17183498 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT 1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAAC ** * * * * * 17183538 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT 1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTCACTAAAC * * * 17183578 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAAC 1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC * 17183617 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA- 1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AAC * * 17183657 CCGGGCTT-CGTCCCGAAGGCATTTGAGCGAGTC 1 CCGGG-TTAAGTCCCGAAGGCATTTGTGCGAGTC 17183690 GTTATATCCG Statistics Matches: 126, Mismatches: 20, Indels: 12 0.80 0.13 0.08 Matches are distributed among these distances: 39 33 0.26 40 82 0.65 41 11 0.09 ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23 Consensus pattern (40 bp): CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC Found at i:17183712 original size:79 final size:79 Alignment explanation

Indices: 17183497--17183714 Score: 183 Period size: 79 Copynumber: 2.7 Consensus size: 79 17183487 TCGAATGATG * * * * ** * 17183497 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGA-TCCGAAGGCAT 1 TCCGGGCTAAG-CCCGAAGGCATTTGAGC-AAGTCACTAAACCCGGGTTA-AATTCCGAAGGCAT * 17183560 TCGTGCGAGTTAATAAA 63 TCGTGCGAGTCAATAAA * * * * 17183577 TCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTACTAAACCCGGGTTAAGTCCCGAAGGCATTCG 1 TCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGGCATTCG * 17183642 TGCGAGTCACTATAA 66 TGCGAGTCAATA-AA ** * ** * * 17183657 -CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCGTTATATCC-GGTTAAATTCCGAAGG 1 TCCGGGCTAAG-CCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGG 17183715 TACGTGATTC Statistics Matches: 113, Mismatches: 21, Indels: 9 0.79 0.15 0.06 Matches are distributed among these distances: 79 69 0.61 80 44 0.39 ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24 Consensus pattern (79 bp): TCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGGCATTCG TGCGAGTCAATAAA Found at i:17191676 original size:40 final size:40 Alignment explanation

Indices: 17191510--17191677 Score: 160 Period size: 40 Copynumber: 4.2 Consensus size: 40 17191500 CATTTGAATG * * * 17191510 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT * * 17191550 ATGTCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT * * * * ** 17191590 ATATCCAGGCTAAGACCCGAAGGCAATGGTGCAAGTTACC 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT * * * * 17191630 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT * 17191670 GTATCCGG 1 ATATCCGG 17191678 TTAAATCCCG Statistics Matches: 100, Mismatches: 24, Indels: 8 0.76 0.18 0.06 Matches are distributed among these distances: 39 3 0.03 40 93 0.93 41 4 0.04 ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT Found at i:17193685 original size:46 final size:46 Alignment explanation

Indices: 17193412--17193685 Score: 372 Period size: 46 Copynumber: 6.0 Consensus size: 46 17193402 TTTGACATGA * * * * 17193412 TGCCATAGTATCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT * * * * 17193458 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT * * 17193504 TGCCAAT-GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT 1 TGCC-ATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT ** * * 17193550 TGCCATGGTATCTTTCAACCATTATGTTATTCATTTCATATCAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT * 17193596 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT * 17193642 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG 1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAG 17193686 AGAGCACACT Statistics Matches: 209, Mismatches: 16, Indels: 6 0.90 0.07 0.03 Matches are distributed among these distances: 45 6 0.03 46 201 0.96 47 2 0.01 ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41 Consensus pattern (46 bp): TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT Found at i:17195827 original size:11 final size:11 Alignment explanation

Indices: 17195811--17195862 Score: 59 Period size: 11 Copynumber: 4.5 Consensus size: 11 17195801 CTTTCTTTAT 17195811 ATAATAATAAA 1 ATAATAATAAA 17195822 ATAATAATAAA 1 ATAATAATAAA * * 17195833 ATGTATTATTAAA 1 A--TAATAATAAA * 17195846 ATATTAATAAA 1 ATAATAATAAA 17195857 ATAATA 1 ATAATA 17195863 TTTATCTAAT Statistics Matches: 35, Mismatches: 4, Indels: 4 0.81 0.09 0.09 Matches are distributed among these distances: 11 26 0.74 13 9 0.26 ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35 Consensus pattern (11 bp): ATAATAATAAA Found at i:17196057 original size:24 final size:24 Alignment explanation

Indices: 17196030--17196084 Score: 101 Period size: 24 Copynumber: 2.3 Consensus size: 24 17196020 CTTCATAGTT 17196030 ATTCATCTATTTAATTTGGTCCTA 1 ATTCATCTATTTAATTTGGTCCTA * 17196054 ATTCATTTATTTAATTTGGTCCTA 1 ATTCATCTATTTAATTTGGTCCTA 17196078 ATTCATC 1 ATTCATC 17196085 CTTAAAATAT Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 24 29 1.00 ACGTcount: A:0.25, C:0.16, G:0.07, T:0.51 Consensus pattern (24 bp): ATTCATCTATTTAATTTGGTCCTA Found at i:17203828 original size:26 final size:26 Alignment explanation

Indices: 17203776--17203830 Score: 67 Period size: 26 Copynumber: 2.1 Consensus size: 26 17203766 AACACACCAA * * * 17203776 TATCGCAGCAAGGTTGCCGGTAACAG 1 TATCGCAGCAAAGCTGCCAGTAACAG 17203802 TATCGCAGCAAAGCTGCCAG-AATCAG 1 TATCGCAGCAAAGCTGCCAGTAA-CAG 17203828 TAT 1 TAT 17203831 ATGTAGCAAA Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 25 2 0.08 26 23 0.92 ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20 Consensus pattern (26 bp): TATCGCAGCAAAGCTGCCAGTAACAG Found at i:17203855 original size:27 final size:27 Alignment explanation

Indices: 17203825--17203877 Score: 88 Period size: 27 Copynumber: 2.0 Consensus size: 27 17203815 CTGCCAGAAT * 17203825 CAGTATATGTAGCAAAGCCACTAGTAG 1 CAGTATATGTAGCAAAGCCACCAGTAG * 17203852 CAGTATATGTGGCAAAGCCACCAGTA 1 CAGTATATGTAGCAAAGCCACCAGTA 17203878 TAATACACTT Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 27 24 1.00 ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21 Consensus pattern (27 bp): CAGTATATGTAGCAAAGCCACCAGTAG Found at i:17204027 original size:27 final size:27 Alignment explanation

Indices: 17203983--17204052 Score: 70 Period size: 27 Copynumber: 2.6 Consensus size: 27 17203973 ATTATAACAC * 17203983 AAATCAGTCA-TTTGCCCTCGAGGGGTA 1 AAAT-AGTCATTTTACCCTCGAGGGGTA ** 17204010 AAATAGTCATTTTACCCTTTAGGGGTA 1 AAATAGTCATTTTACCCTCGAGGGGTA *** 17204037 TTTTAGTCATTTTACC 1 AAATAGTCATTTTACC 17204053 AGTCTTGGGG Statistics Matches: 36, Mismatches: 6, Indels: 2 0.82 0.14 0.05 Matches are distributed among these distances: 26 5 0.14 27 31 0.86 ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37 Consensus pattern (27 bp): AAATAGTCATTTTACCCTCGAGGGGTA Found at i:17207483 original size:27 final size:27 Alignment explanation

Indices: 17207453--17207650 Score: 114 Period size: 27 Copynumber: 7.4 Consensus size: 27 17207443 AAAGAAAGAC * * 17207453 TTGTGGCAATCTC-TGTAATGGGAGCCT 1 TTGTGGCAATC-CATGTAAAGGAAGCCT * 17207480 TTGTGGCTATCCATGTAAAGGAAGCCT 1 TTGTGGCAATCCATGTAAAGGAAGCCT * * * * * 17207507 TTTTGGCTA-CCCTATAAAAGAAGCCT 1 TTGTGGCAATCCATGTAAAGGAAGCCT * * * * * 17207533 GTATTGCTATTCATGTAAAGGAAGCCT 1 TTGTGGCAATCCATGTAAAGGAAGCCT * * * * * * 17207560 TTCTCGCTACCCATGTAAAAGAAGCTT 1 TTGTGGCAATCCATGTAAAGGAAGCCT * * * * 17207587 TTGTGCCTATCAATGTAAAGGAAGCCA 1 TTGTGGCAATCCATGTAAAGGAAGCCT ** * * 17207614 AAGTGCCTAA-CCATGTAAAGGAAGCCC 1 TTGTGGC-AATCCATGTAAAGGAAGCCT 17207641 TTGTGGCAAT 1 TTGTGGCAAT 17207651 TCGAATAAAG Statistics Matches: 130, Mismatches: 37, Indels: 8 0.74 0.21 0.05 Matches are distributed among these distances: 26 23 0.18 27 106 0.82 28 1 0.01 ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29 Consensus pattern (27 bp): TTGTGGCAATCCATGTAAAGGAAGCCT Found at i:17207532 original size:53 final size:54 Alignment explanation

Indices: 17207475--17207612 Score: 179 Period size: 53 Copynumber: 2.6 Consensus size: 54 17207465 CTGTAATGGG * * 17207475 AGCCTTTGTGGCTATCCATGTAAAGGAAGCCTTTTTGGCTACCC-TATAAAAGA 1 AGCCTTTGTGGCTATCCATGTAAAGGAAGCCTTTCTCGCTACCCATATAAAAGA * * * * * 17207528 AGCCTGTATTGCTATTCATGTAAAGGAAGCCTTTCTCGCTACCCATGTAAAAGA 1 AGCCTTTGTGGCTATCCATGTAAAGGAAGCCTTTCTCGCTACCCATATAAAAGA * * * 17207582 AGCTTTTGTGCCTATCAATGTAAAGGAAGCC 1 AGCCTTTGTGGCTATCCATGTAAAGGAAGCC 17207613 AAAGTGCCTA Statistics Matches: 70, Mismatches: 14, Indels: 1 0.82 0.16 0.01 Matches are distributed among these distances: 53 38 0.54 54 32 0.46 ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30 Consensus pattern (54 bp): AGCCTTTGTGGCTATCCATGTAAAGGAAGCCTTTCTCGCTACCCATATAAAAGA Found at i:17220368 original size:17 final size:18 Alignment explanation

Indices: 17220348--17220383 Score: 56 Period size: 19 Copynumber: 2.0 Consensus size: 18 17220338 GGAAAATAAA 17220348 GAAATGA-AAAAAAAAAG 1 GAAATGAGAAAAAAAAAG 17220365 GAAATGATGAAAAAAAAAG 1 GAAATGA-GAAAAAAAAAG 17220384 AGTGTGGATG Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 17 7 0.41 19 10 0.59 ACGTcount: A:0.72, C:0.00, G:0.19, T:0.08 Consensus pattern (18 bp): GAAATGAGAAAAAAAAAG Found at i:17222176 original size:41 final size:43 Alignment explanation

Indices: 17222127--17222240 Score: 144 Period size: 41 Copynumber: 2.7 Consensus size: 43 17222117 ATATGTGTTC * * 17222127 GTGTAAGACTATAGCTGGGCTATGGCATCGA-TATATG-ATAT 1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT * * 17222168 GTGTAAGACCATAGCTGGGCTATGGCAT-TATTATGTGAAGAT 1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT * ** 17222210 GTGTAAGACCATAGTTGAACTATGGCATCGA 1 GTGTAAGACCATAGCTGGGCTATGGCATCGA 17222241 GAAACGAAGT Statistics Matches: 62, Mismatches: 8, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 40 1 0.02 41 32 0.52 42 28 0.45 43 1 0.02 ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30 Consensus pattern (43 bp): GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT Found at i:17224290 original size:15 final size:14 Alignment explanation

Indices: 17224272--17224304 Score: 57 Period size: 14 Copynumber: 2.4 Consensus size: 14 17224262 AACCTAACCC * 17224272 AAAAAAAAACAAAG 1 AAAAAAAAAAAAAG 17224286 AAAAAAAAAAAAAG 1 AAAAAAAAAAAAAG 17224300 AAAAA 1 AAAAA 17224305 CTTACCCAAA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 14 18 1.00 ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00 Consensus pattern (14 bp): AAAAAAAAAAAAAG Found at i:17224945 original size:15 final size:16 Alignment explanation

Indices: 17224928--17224961 Score: 59 Period size: 17 Copynumber: 2.1 Consensus size: 16 17224918 TAAATACTAT 17224928 TATATACATATATATTA 1 TATATACATATATA-TA 17224945 TATATACATATATATA 1 TATATACATATATATA 17224961 T 1 T 17224962 TTTAAATACC Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 3 0.18 17 14 0.82 ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47 Consensus pattern (16 bp): TATATACATATATATA Found at i:17225067 original size:2 final size:2 Alignment explanation

Indices: 17225056--17225087 Score: 50 Period size: 2 Copynumber: 17.0 Consensus size: 2 17225046 TTTTATGTAC 17225056 AT AT -T AT AT AT AT AT AT AT AT AT AT AT A- AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 17225088 TTGTACATAT Statistics Matches: 28, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 1 2 0.07 2 26 0.93 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:17232365 original size:68 final size:69 Alignment explanation

Indices: 17232111--17232373 Score: 330 Period size: 70 Copynumber: 3.7 Consensus size: 69 17232101 GAGTTAAGCC * * * 17232111 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT 1 TTTTAATTTTTG-TTTT--AAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT 17232176 GAGGTAT 63 GAGGTAT * * * * * * 17232183 TTTCAATTTTTGTGTTTTAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGA 1 TTTTAATTTTTGT-TTTAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGA 17232248 GGTAT 65 GGTAT * * 17232253 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCTG 1 TTTTAATTTTTGTTTT--AAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTG 17232317 AGGTAT 64 AGGTAT * * * * 17232323 TTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT 1 TTTTAATTTTTGTTTTAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCT 17232374 TTTAATTTTT Statistics Matches: 165, Mismatches: 23, Indels: 10 0.83 0.12 0.05 Matches are distributed among these distances: 68 31 0.19 69 3 0.02 70 84 0.51 71 33 0.20 72 14 0.08 ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38 Consensus pattern (69 bp): TTTTAATTTTTGTTTTAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAG GTAT Found at i:17232418 original size:121 final size:123 Alignment explanation

Indices: 17232253--17232498 Score: 381 Period size: 121 Copynumber: 2.0 Consensus size: 123 17232243 GTTGAGGTAT 17232253 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCTG 1 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG * * * 17232317 AGGTATTTTTAGTTTAT-GTTTTAAATT-GACTCATATTGCGAGAGGTGAGTTAAGCC 66 AGGTATTTTCAATTTATAGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC * * 17232373 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT 1 TTTTAATTTTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT * * * 17232438 GAGGTATTTTCAATTTTTGAGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCC 65 GAGGTATTTTCAATTTAT-AGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC 17232498 T 1 T 17232499 CAGGTCACGC Statistics Matches: 113, Mismatches: 8, Indels: 5 0.90 0.06 0.04 Matches are distributed among these distances: 120 12 0.11 121 40 0.35 122 24 0.21 124 9 0.08 125 28 0.25 ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39 Consensus pattern (123 bp): TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG AGGTATTTTCAATTTATAGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC Found at i:17232437 original size:262 final size:259 Alignment explanation

Indices: 17231946--17232535 Score: 1033 Period size: 262 Copynumber: 2.3 Consensus size: 259 17231936 TCAAGGAAAA * 17231946 TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTGTTGTTT 1 TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTTT 17232011 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGTTT 66 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGTTT 17232076 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCA 131 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCA * 17232141 TATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTAA-T 196 TATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGAGTTTTAATT 17232204 T-AACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTTT 1 TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTTT 17232268 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGG-CACGCTGAGGTATTTTTAGTTT 66 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTA---TT--TTT 17232332 ATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATC 126 A-GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATC 17232397 AACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGAGTTT 190 AACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGAGTTT 17232462 TAATT 255 TAATT * * * * * * 17232467 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTT 1 TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTTT 17232532 TCAA 66 TCAA 17232536 TTTACGTTGT Statistics Matches: 316, Mismatches: 8, Indels: 10 0.95 0.02 0.03 Matches are distributed among these distances: 256 12 0.04 257 104 0.33 258 1 0.00 259 2 0.01 261 4 0.01 262 130 0.41 263 2 0.01 264 61 0.19 ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37 Consensus pattern (259 bp): TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTTT TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGTTT TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCA TATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGAGTTTTAATT Found at i:17232494 original size:72 final size:71 Alignment explanation

Indices: 17232395--17232813 Score: 311 Period size: 72 Copynumber: 5.8 Consensus size: 71 17232385 TTTTTCAAAA * * 17232395 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGAGT 1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCT-AGT 17232460 TTTAATT 65 TTTAATT * * 17232467 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCT-GTT 1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTAGTT 17232531 TTCAATT 66 TT-AATT * * * * ** * *** * * * *** 17232538 T--ACGT--TGTT-CAAGA-ATCAACTCATATTGCGAGAGGTAGGTTGA-ACCTTTT-AATTTCT 1 TCAAC-TCATATTGCGAGAGGTGAGTTGAGCCT-CG-G-GGCACGCTGAGGTATTTTCAATTTCT * ** 17232595 ACTTTTTCAAAA 62 A-GTTTT-AATT * * * 17232607 TCAACTCA-ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT-GTT 1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTAGTT * ** 17232670 GTCAAAAAAA 66 -T---TAATT * * 17232680 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTATGT 1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTA-GT 17232745 TTTAATT 65 TTTAATT * * ** 17232752 TCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATTTC 1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GGCACGCTGAGGTATTTTCAATTTC 17232814 CGTTTTTCAA Statistics Matches: 263, Mismatches: 60, Indels: 46 0.71 0.16 0.12 Matches are distributed among these distances: 66 5 0.02 67 12 0.05 68 8 0.03 69 16 0.06 70 15 0.06 71 14 0.05 72 101 0.38 73 19 0.07 74 69 0.26 75 1 0.00 76 3 0.01 ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35 Consensus pattern (71 bp): TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTAGTT TTAATT Found at i:17232723 original size:74 final size:73 Alignment explanation

Indices: 17232603--17232813 Score: 257 Period size: 74 Copynumber: 2.9 Consensus size: 73 17232593 CTACTTTTTC * * 17232603 AAAATCAACTCA-ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCT 17232667 GT-TGTCAAA 66 -TATGT-AAA * * 17232676 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTT-T 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCT *** 17232740 TATGTTTT 66 TATGTAAA ** * * * 17232748 AATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATTT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GACACGCTGAGGTATTTTCAATTT 17232813 C 64 C 17232814 CGTTTTTCAA Statistics Matches: 119, Mismatches: 14, Indels: 8 0.84 0.10 0.06 Matches are distributed among these distances: 72 33 0.28 73 18 0.15 74 68 0.57 ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31 Consensus pattern (73 bp): AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCT TATGTAAA Found at i:17232822 original size:14 final size:14 Alignment explanation

Indices: 17232803--17232837 Score: 52 Period size: 14 Copynumber: 2.5 Consensus size: 14 17232793 CGCTGAGGTA 17232803 TTTTCAATTTCCGT 1 TTTTCAATTTCCGT * 17232817 TTTTCAATTTCTGT 1 TTTTCAATTTCCGT * 17232831 CTTTCAA 1 TTTTCAA 17232838 AAAAAATCAA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 14 19 1.00 ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57 Consensus pattern (14 bp): TTTTCAATTTCCGT Found at i:17232851 original size:164 final size:164 Alignment explanation

Indices: 17232656--17233316 Score: 863 Period size: 164 Copynumber: 4.0 Consensus size: 164 17232646 GCTGAGGTAA * * * 17232656 TTTCAATTTCTG--TTGTCAAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCA 1 TTTCAATTTCTGCCTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA * *** * 17232719 CGCTGAGGTATTTTCAATTTT-TATGT-TTTAATTTCAACTCGTATTGCGAGAGGCGAGTTGAGC 65 CGCTGAGGTAATTTCAATTTTGT-TGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGC 17232782 CTCAGGTCACACGCTGAGGTATTTTCAATTTCCGTT 129 CTCAGGTCACACGCTGAGGTATTTTCAATTTCCGTT * * 17232818 TTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACA 1 TTTCAATTTCTGCCTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA * * 17232883 CGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGC 65 CGCTGAGGTAATTTCAATTT-TGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGC * * * 17232948 CTCAGGTCATACGCCGAGGTATTTTCAATTTTCGTT 129 CTCAGGTCACACGCTGAGGTATTTTCAATTTCCGTT * 17232984 TTTCAATTTTTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC 1 TTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC * * * 17233049 GCTGAGGTAATTTCAATTTTGTTGTCAAAAAAGTCAACTCGTATTACGAGAGGTGAGTTGAGCCT 66 GCTGAGGTAATTTCAATTTTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCCT * * 17233114 CAGATCACACG-TCGAGGTATTTTCAATTTCCATT 131 CAGGTCACACGCT-GAGGTATTTTCAATTTCCGTT * * 17233148 TTTCAATTTCTGCCTTTCAAAAAAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCG 1 TTTCAATTTCTGCCTTTC------AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA * * * *** 17233213 GGACACGCTGAGGTAATTTCAATTTCTATTTTC--AAAATTCAACTCATATTGCGAGAAATGAGT 60 GGACACGCTGAGGTAATTTCAATTT-TGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGT * * * 17233276 TGAGCCTCAAG--ACACGTTGAGGTATTTTCAATTTCTGTT 124 TGAGCCTCAGGTCACACGCTGAGGTATTTTCAATTTCCGTT 17233315 TT 1 TT 17233317 CAAAAAATCA Statistics Matches: 444, Mismatches: 40, Indels: 25 0.87 0.08 0.05 Matches are distributed among these distances: 162 12 0.03 163 2 0.00 164 150 0.34 165 69 0.16 166 81 0.18 167 26 0.06 168 1 0.00 169 34 0.08 170 64 0.14 171 5 0.01 ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34 Consensus pattern (164 bp): TTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC GCTGAGGTAATTTCAATTTTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCCT CAGGTCACACGCTGAGGTATTTTCAATTTCCGTT Found at i:17232943 original size:74 final size:77 Alignment explanation

Indices: 17232818--17232978 Score: 220 Period size: 74 Copynumber: 2.1 Consensus size: 77 17232808 AATTTCCGTT * * * 17232818 TTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGG-AC 1 TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCAC * 17232882 ACGCTGAGGTAA 66 ACGCCGAGGTAA * * 17232894 TTTCAATTTCTGT-TGTC-AAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCA 1 TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-CA * * 17232957 TACGCCGAGGTAT 65 CACGCCGAGGTAA 17232970 TTTCAATTT 1 TTTCAATTT 17232979 TCGTTTTTCA Statistics Matches: 75, Mismatches: 8, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 74 39 0.52 75 3 0.04 76 33 0.44 ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32 Consensus pattern (77 bp): TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCAC ACGCCGAGGTAA Found at i:17233105 original size:73 final size:75 Alignment explanation

Indices: 17233000--17233142 Score: 211 Period size: 73 Copynumber: 1.9 Consensus size: 75 17232990 TTTTTGCCTT * * 17233000 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACG-CTGAGGTAATTT 1 TCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGTC-GAGGTAATTT 17233062 CAATTTTGTTG 65 CAATTTTGTTG * * * 17233073 TCAAAAAAGTCAACTCGTATTACGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTATTTTC 1 TCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC 17233138 AATTT 66 AATTT 17233143 CCATTTTTCA Statistics Matches: 62, Mismatches: 5, Indels: 4 0.87 0.07 0.06 Matches are distributed among these distances: 73 41 0.66 75 20 0.32 76 1 0.02 ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29 Consensus pattern (75 bp): TCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC AATTTTGTTG Done.