Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold1532

Parameters: 2 7 7 80 10 50 500

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

Length: 1715538
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29

Warning! 192937 characters in sequence are not A, C, G, or T


File 3 of 5

Found at i:533327 original size:2 final size:2

Alignment explanation

Indices: 533320--533389 Score: 113 Period size: 2 Copynumber: 35.0 Consensus size: 2 533310 TAAATTATAT * * * 533320 TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TG TC TG TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 533362 TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC 533390 AAGGTAAAGT Statistics Matches: 62, Mismatches: 6, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 2 62 1.00 ACGTcount: A:0.00, C:0.46, G:0.04, T:0.50 Consensus pattern (2 bp): TC Found at i:538380 original size:17 final size:17 Alignment explanation

Indices: 538358--538393 Score: 72 Period size: 17 Copynumber: 2.1 Consensus size: 17 538348 CTGTCCTTCT 538358 TACCTTTTAAGGAGAAC 1 TACCTTTTAAGGAGAAC 538375 TACCTTTTAAGGAGAAC 1 TACCTTTTAAGGAGAAC 538392 TA 1 TA 538394 TCCCATAATC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 19 1.00 ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31 Consensus pattern (17 bp): TACCTTTTAAGGAGAAC Found at i:538551 original size:2 final size:2 Alignment explanation

Indices: 538544--538625 Score: 155 Period size: 2 Copynumber: 41.0 Consensus size: 2 538534 TGCACATGCA * 538544 TC TC TC TC TC TC TC TC GC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 538586 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 538626 ACACACACAC Statistics Matches: 78, Mismatches: 2, Indels: 0 0.98 0.03 0.00 Matches are distributed among these distances: 2 78 1.00 ACGTcount: A:0.00, C:0.50, G:0.01, T:0.49 Consensus pattern (2 bp): TC Found at i:538630 original size:2 final size:2 Alignment explanation

Indices: 538625--538664 Score: 53 Period size: 2 Copynumber: 20.0 Consensus size: 2 538615 CTCTCTCTCT ** * 538625 CA CA CA CA CA CA CA CA CA CA CA TG CA CG CA CA CA CA CA CA 1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA 538665 AACCAGGTTA Statistics Matches: 32, Mismatches: 6, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.45, C:0.47, G:0.05, T:0.03 Consensus pattern (2 bp): CA Found at i:540483 original size:2 final size:2 Alignment explanation

Indices: 540476--540514 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 540466 TGGGATCCTT 540476 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 540515 GATAAATATC Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:551884 original size:1 final size:1 Alignment explanation

Indices: 551878--551906 Score: 58 Period size: 1 Copynumber: 29.0 Consensus size: 1 551868 TAGGCTTTGA 551878 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 551907 TGCGCACTTT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 28 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:553304 original size:21 final size:21 Alignment explanation

Indices: 553280--553345 Score: 57 Period size: 21 Copynumber: 3.2 Consensus size: 21 553270 GTTTTGGCAG 553280 AAGTATTAAGTTTCCGCTAAA 1 AAGTATTAAGTTTCCGCTAAA * * ** * 553301 AAGTA-CACACTTTTGGC--AG 1 AAGTATTA-AGTTTCCGCTAAA 553320 AAGTATTAAGTTTCCGCTAAA 1 AAGTATTAAGTTTCCGCTAAA 553341 AAGTA 1 AAGTA 553346 CACACTAGCC Statistics Matches: 31, Mismatches: 10, Indels: 8 0.63 0.20 0.16 Matches are distributed among these distances: 19 12 0.39 20 2 0.06 21 17 0.55 ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30 Consensus pattern (21 bp): AAGTATTAAGTTTCCGCTAAA Found at i:553315 original size:40 final size:40 Alignment explanation

Indices: 553271--553351 Score: 162 Period size: 40 Copynumber: 2.0 Consensus size: 40 553261 CATTTCTACG 553271 TTTTGGCAGAAGTATTAAGTTTCCGCTAAAAAGTACACAC 1 TTTTGGCAGAAGTATTAAGTTTCCGCTAAAAAGTACACAC 553311 TTTTGGCAGAAGTATTAAGTTTCCGCTAAAAAGTACACAC 1 TTTTGGCAGAAGTATTAAGTTTCCGCTAAAAAGTACACAC 553351 T 1 T 553352 AGCCATTATT Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 40 41 1.00 ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31 Consensus pattern (40 bp): TTTTGGCAGAAGTATTAAGTTTCCGCTAAAAAGTACACAC Found at i:558778 original size:60 final size:60 Alignment explanation

Indices: 558710--558893 Score: 332 Period size: 60 Copynumber: 3.1 Consensus size: 60 558700 CATATAAATC * * 558710 AGCATCAGGACGATTAACACAGTTCTGGAAAAATCTCCTCCACGACCCTCGTTATAATGT 1 AGCATCAGGACGATTAACACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT 558770 AGCATCAGGACGATTAACACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT 1 AGCATCAGGACGATTAACACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT ** 558830 AGCATCAGGACGATTATTACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT 1 AGCATCAGGACGATTAACACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT 558890 AGCA 1 AGCA 558894 ATGTCCTTTT Statistics Matches: 120, Mismatches: 4, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 60 120 1.00 ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24 Consensus pattern (60 bp): AGCATCAGGACGATTAACACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT Found at i:571657 original size:18 final size:18 Alignment explanation

Indices: 571636--571677 Score: 66 Period size: 18 Copynumber: 2.3 Consensus size: 18 571626 CTCTTGATTT 571636 AGCTATATAGCTTGAAAA 1 AGCTATATAGCTTGAAAA * * 571654 AGCTATATAGCTTTATAA 1 AGCTATATAGCTTGAAAA 571672 AGCTAT 1 AGCTAT 571678 TCAAACTAGC Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 18 22 1.00 ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33 Consensus pattern (18 bp): AGCTATATAGCTTGAAAA Found at i:575806 original size:19 final size:19 Alignment explanation

Indices: 575782--575818 Score: 65 Period size: 19 Copynumber: 1.9 Consensus size: 19 575772 CTCATGAAAT 575782 TTTTTTTTCAAAGTGCGTA 1 TTTTTTTTCAAAGTGCGTA * 575801 TTTTTTTTCAAGGTGCGT 1 TTTTTTTTCAAAGTGCGT 575819 TAGCACACAT Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 19 17 1.00 ACGTcount: A:0.16, C:0.11, G:0.19, T:0.54 Consensus pattern (19 bp): TTTTTTTTCAAAGTGCGTA Found at i:576115 original size:2 final size:2 Alignment explanation

Indices: 576071--576095 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 576061 CATCACTTCA 576071 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 576096 NNNNNNNNNN Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:578213 original size:20 final size:20 Alignment explanation

Indices: 578188--578228 Score: 73 Period size: 20 Copynumber: 2.0 Consensus size: 20 578178 GTTGTGTTTT * 578188 TAAAATACGTGTGAAGATTG 1 TAAAATACGTGTGAAAATTG 578208 TAAAATACGTGTGAAAATTG 1 TAAAATACGTGTGAAAATTG 578228 T 1 T 578229 CTCTTCCTTT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32 Consensus pattern (20 bp): TAAAATACGTGTGAAAATTG Found at i:581915 original size:229 final size:228 Alignment explanation

Indices: 581513--581944 Score: 855 Period size: 229 Copynumber: 1.9 Consensus size: 228 581503 TGTAAATTTC 581513 ATGCAGACGACGCAATGGATGACACGAACTCTATTTATTTTGGTAAATGTTTTCATACAGTTTGA 1 ATGCAGACGACGCAATGGATGACACGAACTCTATTTATTTTGGTAAATGTTTTCATACAGTTTGA 581578 ATTGAAAAAAATTACATGGGTATCAATTCTAAATGGCTTGTATTATAAACCAGATATTCTTTTTC 66 ATTGAAAAAAATTACATGGGTATCAATTCTAAATGGCTTGTATTATAAACCAGATATTCTTTTTC 581643 CAACAGAAATTATATCTAAGTAAGAATTTTTTCCAACTTCTTTTCTTATTTGTTATCTCGTGTTG 131 CAACAGAAATTATATCTAAGTAAGAATTTTTTCCAACTTCTTTTCTTATTTGTTATCTCGTGTTG 581708 TTTTGTTATAAAAAAAATGTTGTTGTTTATACT 196 TTTTGTTATAAAAAAAATGTTGTTGTTTATACT 581741 ANTGCAGACGACGCAATGGATGACACGAACTCTATTTATTTTGGTAAATGTTTTCATACAGTTTG 1 A-TGCAGACGACGCAATGGATGACACGAACTCTATTTATTTTGGTAAATGTTTTCATACAGTTTG 581806 AATTGAAAAAAATTACATGGGTATCAATTCTAAATGGCTTGTATTATAAACCAGATATTCTTTTT 65 AATTGAAAAAAATTACATGGGTATCAATTCTAAATGGCTTGTATTATAAACCAGATATTCTTTTT 581871 CCAACAGAAATTATATCTAAGTAAGAATTTTTTCCAACTTCTTTTCTTATTTGTTATCTCGTGTT 130 CCAACAGAAATTATATCTAAGTAAGAATTTTTTCCAACTTCTTTTCTTATTTGTTATCTCGTGTT 581936 GTTTTGTTA 195 GTTTTGTTA 581945 ATGTTGTTGT Statistics Matches: 203, Mismatches: 0, Indels: 1 1.00 0.00 0.00 Matches are distributed among these distances: 228 1 0.00 229 202 1.00 ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41 Consensus pattern (228 bp): ATGCAGACGACGCAATGGATGACACGAACTCTATTTATTTTGGTAAATGTTTTCATACAGTTTGA ATTGAAAAAAATTACATGGGTATCAATTCTAAATGGCTTGTATTATAAACCAGATATTCTTTTTC CAACAGAAATTATATCTAAGTAAGAATTTTTTCCAACTTCTTTTCTTATTTGTTATCTCGTGTTG TTTTGTTATAAAAAAAATGTTGTTGTTTATACT Found at i:582045 original size:2 final size:2 Alignment explanation

Indices: 582038--582110 Score: 146 Period size: 2 Copynumber: 36.5 Consensus size: 2 582028 TGATGAATAA 582038 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 582080 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 582111 GTGACATATG Statistics Matches: 71, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 71 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:583169 original size:21 final size:23 Alignment explanation

Indices: 583109--583167 Score: 118 Period size: 23 Copynumber: 2.6 Consensus size: 23 583099 AAACGAGACA 583109 TCGCGCTAACACACAACACGCCG 1 TCGCGCTAACACACAACACGCCG 583132 TCGCGCTAACACACAACACGCCG 1 TCGCGCTAACACACAACACGCCG 583155 TCGCGCTAACACA 1 TCGCGCTAACACA 583168 ACTTTGCACA Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 36 1.00 ACGTcount: A:0.31, C:0.42, G:0.17, T:0.10 Consensus pattern (23 bp): TCGCGCTAACACACAACACGCCG Found at i:583178 original size:31 final size:31 Alignment explanation

Indices: 583143--583206 Score: 119 Period size: 31 Copynumber: 2.1 Consensus size: 31 583133 CGCGCTAACA 583143 CACAACACGCCGTCGCGCTAACACAACTTTG 1 CACAACACGCCGTCGCGCTAACACAACTTTG * 583174 CACAACACGCCGTCGCGCTAACGCAACTTTG 1 CACAACACGCCGTCGCGCTAACACAACTTTG 583205 CA 1 CA 583207 AGTTTCACAG Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 32 1.00 ACGTcount: A:0.28, C:0.39, G:0.17, T:0.16 Consensus pattern (31 bp): CACAACACGCCGTCGCGCTAACACAACTTTG Found at i:584371 original size:31 final size:31 Alignment explanation

Indices: 584333--584620 Score: 354 Period size: 31 Copynumber: 10.1 Consensus size: 31 584323 CTGTGAAACT * 584333 TGCAAAGTTGCGTTAGCGCGACGGCGTGTTG 1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 584364 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 584395 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG * 584426 TGCAAAGTTGTGTTAGCGCAACGGCGTG-T- 1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG * * 584455 T------TTATGTTAGTGCGACGGCGTG-T- 1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG * * 584478 TGC------GTGTTAGCGCGATGGCATGTTG 1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 584503 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 584534 TGCAAAGTTGTGTTAGCGCGACGGCGTG-T- 1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 584563 T-----G-TGTGTTAGCGCGACGGCGTGTTG 1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 584588 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 584619 TG 1 TG 584621 TGTTAGCGCG Statistics Matches: 228, Mismatches: 11, Indels: 36 0.83 0.04 0.13 Matches are distributed among these distances: 23 55 0.24 24 3 0.01 25 4 0.02 29 2 0.01 30 3 0.01 31 161 0.71 ACGTcount: A:0.15, C:0.16, G:0.39, T:0.30 Consensus pattern (31 bp): TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG Found at i:584470 original size:54 final size:54 Alignment explanation

Indices: 584403--584631 Score: 276 Period size: 54 Copynumber: 4.2 Consensus size: 54 584393 TGTGCAAAGT * * 584403 TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCAACGGCGTGTTT 1 TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG * * * * 584457 TATGTTAGTGCGACGGCGTG-T-TGC------GTGTTAGCGCGATGGCATGTTGTGCAAAG 1 TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGC--G-TGT----TG 584510 TTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 1 -TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 584565 TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 1 TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG 584619 TGTGTTAGCGCGA 1 TGTGTTAGCGCGA 584632 TGTCTCGTTT Statistics Matches: 149, Mismatches: 10, Indels: 32 0.78 0.05 0.17 Matches are distributed among these distances: 46 14 0.09 48 1 0.01 49 3 0.02 52 3 0.02 53 1 0.01 54 103 0.69 55 2 0.01 56 3 0.02 59 3 0.02 60 1 0.01 62 15 0.10 ACGTcount: A:0.14, C:0.16, G:0.39, T:0.31 Consensus pattern (54 bp): TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG Found at i:584485 original size:23 final size:23 Alignment explanation

Indices: 584435--584502 Score: 73 Period size: 23 Copynumber: 3.0 Consensus size: 23 584425 GTGCAAAGTT * ** 584435 GTGTTAGCGCAACGGCGTGTTTT 1 GTGTTAGCGCGACGGCGTGTTGC * * 584458 ATGTTAGTGCGACGGCGTGTTGC 1 GTGTTAGCGCGACGGCGTGTTGC * * 584481 GTGTTAGCGCGATGGCATGTTG 1 GTGTTAGCGCGACGGCGTGTTG 584503 TGCAAAGTTG Statistics Matches: 36, Mismatches: 9, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 23 36 1.00 ACGTcount: A:0.13, C:0.16, G:0.38, T:0.32 Consensus pattern (23 bp): GTGTTAGCGCGACGGCGTGTTGC Found at i:584548 original size:85 final size:85 Alignment explanation

Indices: 584459--584620 Score: 288 Period size: 85 Copynumber: 1.9 Consensus size: 85 584449 GCGTGTTTTA * * 584459 TGTTAGTGCGACGGCGTGTTGCGTGTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGA 1 TGTTAGCGCGACGGCGTGTTGCGTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGA 584524 CGGCGTGTTGTGCAAAGTTG 66 CGGCGTGTTGTGCAAAGTTG * * 584544 TGTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGA 1 TGTTAGCGCGACGGCGTGTTGCGTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGA 584609 CGGCGTGTTGTG 66 CGGCGTGTTGTG 584621 TGTTAGCGCG Statistics Matches: 73, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 85 73 1.00 ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30 Consensus pattern (85 bp): TGTTAGCGCGACGGCGTGTTGCGTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGA CGGCGTGTTGTGCAAAGTTG Found at i:584562 original size:108 final size:108 Alignment explanation

Indices: 584373--584587 Score: 376 Period size: 108 Copynumber: 2.0 Consensus size: 108 584363 GTGCAAAGTT * 584373 GTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTG 1 GTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTG * * 584438 TTAGCGCAACGGCGTGTTTTATGTTAGTGCGACGGCGTGTTGC 66 TTAGCGCAACGGCGTGTTGTATGTTAGCGCGACGGCGTGTTGC * 584481 GTGTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTG 1 GTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTG * * 584546 TTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTG 66 TTAGCGCAACGGCGTGTTGTATGTTAGCGCGACGGCGTGTTG 584588 TGCAAAGTTG Statistics Matches: 101, Mismatches: 6, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 108 101 1.00 ACGTcount: A:0.14, C:0.16, G:0.39, T:0.30 Consensus pattern (108 bp): GTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTG TTAGCGCAACGGCGTGTTGTATGTTAGCGCGACGGCGTGTTGC Found at i:584571 original size:23 final size:23 Alignment explanation

Indices: 584542--584589 Score: 96 Period size: 23 Copynumber: 2.1 Consensus size: 23 584532 TGTGCAAAGT 584542 TGTGTTAGCGCGACGGCGTGTTG 1 TGTGTTAGCGCGACGGCGTGTTG 584565 TGTGTTAGCGCGACGGCGTGTTG 1 TGTGTTAGCGCGACGGCGTGTTG 584588 TG 1 TG 584590 CAAAGTTGTG Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 25 1.00 ACGTcount: A:0.08, C:0.17, G:0.44, T:0.31 Consensus pattern (23 bp): TGTGTTAGCGCGACGGCGTGTTG Found at i:584602 original size:139 final size:135 Alignment explanation

Indices: 584344--584633 Score: 390 Period size: 139 Copynumber: 2.1 Consensus size: 135 584334 GCAAAGTTGC * * 584344 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTT 1 GTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTT * 584409 AGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCAACGGCGTGTTTTATGTTAGTGCGACGGC 66 AGCGCGACGGCGTGTTGT----AGTTGTGTTAGCGCAACGGCGTGTTTTATGTTAGCGCGACGGC 584474 GTGTTGCGT 127 GTGTTGCGT 584483 GTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTT 1 GTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTT * * 584548 AGCGCGACGGCGTG-T-T-G-TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGA 66 AGCGCGACGGCGTGTTGTAGTTGTGTTAGCGCAACGGCGTG-T-T------TTATGTTAGCGCGA * 584609 CGGCGTGTTGTGT 123 CGGCGTGTTGCGT 584622 GTTAGCGCGATG 1 GTTAGCGCGATG 584634 TCTCGTTTAT Statistics Matches: 137, Mismatches: 6, Indels: 16 0.86 0.04 0.10 Matches are distributed among these distances: 131 19 0.14 132 2 0.01 133 1 0.01 137 1 0.01 138 1 0.01 139 113 0.82 ACGTcount: A:0.15, C:0.16, G:0.39, T:0.30 Consensus pattern (135 bp): GTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTT AGCGCGACGGCGTGTTGTAGTTGTGTTAGCGCAACGGCGTGTTTTATGTTAGCGCGACGGCGTGT TGCGT Found at i:586765 original size:21 final size:22 Alignment explanation

Indices: 586726--586775 Score: 75 Period size: 21 Copynumber: 2.3 Consensus size: 22 586716 AAAAGAAGTC 586726 ATTTTCACACATTGATGCATGA 1 ATTTTCACACATTGATGCATGA * * 586748 ATTTTC-CATATTGGTGCATGA 1 ATTTTCACACATTGATGCATGA 586769 ATTTTCA 1 ATTTTCA 586776 AGAACAACTT Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 21 19 0.76 22 6 0.24 ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42 Consensus pattern (22 bp): ATTTTCACACATTGATGCATGA Found at i:589576 original size:16 final size:16 Alignment explanation

Indices: 589555--589586 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 589545 TTCTACAACA * 589555 ACATAGCTTTGCACAT 1 ACATAGCTTTACACAT 589571 ACATAGCTTTACACAT 1 ACATAGCTTTACACAT 589587 TGTCTTTACC Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.34, C:0.25, G:0.09, T:0.31 Consensus pattern (16 bp): ACATAGCTTTACACAT Found at i:591893 original size:12 final size:12 Alignment explanation

Indices: 591876--591903 Score: 56 Period size: 12 Copynumber: 2.3 Consensus size: 12 591866 CATTAAGACA 591876 ACAACTACACTG 1 ACAACTACACTG 591888 ACAACTACACTG 1 ACAACTACACTG 591900 ACAA 1 ACAA 591904 GGAATATCCA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 16 1.00 ACGTcount: A:0.46, C:0.32, G:0.07, T:0.14 Consensus pattern (12 bp): ACAACTACACTG Found at i:595077 original size:1 final size:1 Alignment explanation

Indices: 595073--595119 Score: 67 Period size: 1 Copynumber: 47.0 Consensus size: 1 595063 TTTTTGTGGG ** * 595073 TTTTTTTTGGTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 595120 GGGGGGGGGG Statistics Matches: 42, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 1 42 1.00 ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94 Consensus pattern (1 bp): T Found at i:595088 original size:10 final size:10 Alignment explanation

Indices: 595059--595121 Score: 65 Period size: 10 Copynumber: 6.3 Consensus size: 10 595049 TTTGTTGTGG 595059 TGGTTTTTTGT 1 TGGTTTTTT-T * 595070 GGGTTTTTTT 1 TGGTTTTTTT 595080 TGGTTTTTTT 1 TGGTTTTTTT * 595090 TTGTTTTTTT 1 TGGTTTTTTT * 595100 T-TTTTTTTT 1 TGGTTTTTTT ** 595109 TTTTTTTTTT 1 TGGTTTTTTT 595119 TGG 1 TGG 595122 GGGGGGGGGT Statistics Matches: 45, Mismatches: 6, Indels: 3 0.83 0.11 0.06 Matches are distributed among these distances: 9 8 0.18 10 29 0.64 11 8 0.18 ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83 Consensus pattern (10 bp): TGGTTTTTTT Found at i:596854 original size:18 final size:17 Alignment explanation

Indices: 596831--596866 Score: 54 Period size: 18 Copynumber: 2.1 Consensus size: 17 596821 TAATATTTAT 596831 ATCTATTAAATCTTATTA 1 ATCTATTAAATC-TATTA * 596849 ATCTATTATATCTATTA 1 ATCTATTAAATCTATTA 596866 A 1 A 596867 ACCTTACAAT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 17 6 0.35 18 11 0.65 ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50 Consensus pattern (17 bp): ATCTATTAAATCTATTA Found at i:598276 original size:21 final size:21 Alignment explanation

Indices: 598250--598346 Score: 126 Period size: 21 Copynumber: 4.7 Consensus size: 21 598240 TACACCATAG 598250 CATAGCATAGCATTGAAATCT 1 CATAGCATAGCATTGAAATCT * 598271 CATAGCATAGCATTGGAATCT 1 CATAGCATAGCATTGAAATCT * * 598292 CATAGCATAACATTGGAATCT 1 CATAGCATAGCATTGAAATCT 598313 CATAGCATAGCA-T-ACAATCT 1 CATAGCATAGCATTGA-AATCT * * 598333 CATAGAATCGCATT 1 CATAGCATAGCATT 598347 CGTCATATCA Statistics Matches: 68, Mismatches: 6, Indels: 4 0.87 0.08 0.05 Matches are distributed among these distances: 20 16 0.24 21 52 0.76 ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28 Consensus pattern (21 bp): CATAGCATAGCATTGAAATCT Found at i:598534 original size:5 final size:5 Alignment explanation

Indices: 598521--598554 Score: 50 Period size: 5 Copynumber: 6.8 Consensus size: 5 598511 GTTCAAATCT * * 598521 CATAG CATAC CATAG CATAG CATAG CATAC CATA 1 CATAG CATAG CATAG CATAG CATAG CATAG CATA 598555 TCATTAAGCC Statistics Matches: 26, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 5 26 1.00 ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21 Consensus pattern (5 bp): CATAG Found at i:598536 original size:10 final size:10 Alignment explanation

Indices: 598521--598554 Score: 59 Period size: 10 Copynumber: 3.4 Consensus size: 10 598511 GTTCAAATCT 598521 CATAGCATAC 1 CATAGCATAC * 598531 CATAGCATAG 1 CATAGCATAC 598541 CATAGCATAC 1 CATAGCATAC 598551 CATA 1 CATA 598555 TCATTAAGCC Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 10 22 1.00 ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21 Consensus pattern (10 bp): CATAGCATAC Found at i:598604 original size:21 final size:21 Alignment explanation

Indices: 598578--598631 Score: 90 Period size: 21 Copynumber: 2.6 Consensus size: 21 598568 CATTTCAATT * 598578 TCTCATAGCATAGCATACAAA 1 TCTCATAGCATACCATACAAA 598599 TCTCATAGCATACCATACAAA 1 TCTCATAGCATACCATACAAA * 598620 TCTCATACCATA 1 TCTCATAGCATA 598632 TCATTAAAAT Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 21 31 1.00 ACGTcount: A:0.41, C:0.28, G:0.06, T:0.26 Consensus pattern (21 bp): TCTCATAGCATACCATACAAA Found at i:627568 original size:445 final size:441 Alignment explanation

Indices: 626428--627764 Score: 2162 Period size: 441 Copynumber: 3.0 Consensus size: 441 626418 CCTAGACCCA 626428 GACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAA 1 GACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAA * * * * 626493 ATCAATAGTACAACTAAGTGTATAATTATTGTTCTTTGTTTAAAGTTTTAAGTCCTTCTGTCTAA 66 ATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGTCAAA * * 626558 GTATATTCAAGAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAATTTTTTAGGTCT 131 GTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAATTTTTTAGGTCA * 626623 AGGTCACAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATG-TCACAAGTTAAAA 196 AGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATGAT-ACAAGTTAAAA * * * 626687 GTCTGTATATTAAAGGAGTCTTGTGTTATGGCCCAGACAATATTTTTTATGAAAAGCTTGACCTT 260 GTCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGGACAATATTTTTTATGAAAAGCTTGACCTT * * 626752 GAAGAACAAAATAAGTCAAGGTCAAAACTTTTGGTGGCCTGCACTCCTTCTCAATACCATGTACC 325 GAAGAACAAAATAGGTCAAGGTCAAAACTTTTGGTGGCCTGCACTCCTTCTCAATACCATCTACC * * * 626817 TATGTTCCAAGTTTTAAGTCTTAATGTCAAAGGGTATTAAAGTTAC-GACTCA 390 TATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTACGGCCT-G 626869 GACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAA 1 GACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAA * 626934 ATCAATAGTACACCTGAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGTCAAA 66 ATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGTCAAA * * * * 626999 GTAAATTCAGGACTTGAACAATGAAGTTTTTTCAAATTTGACCTTGAAATAAAATTTTTAGGTCA 131 GTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAATTTTTTAGGTCA * 627064 AGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATGACACAAGTTAAAAG 196 AGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAAGTTAAAAG * 627129 TCTGTATGTTAAAAGAGTCTTGTGTTATGGTCCGGACAATATTTTTTTATG-AAAGCTTGA-CTT 261 TCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGGACAATA-TTTTTTATGAAAAGCTTGACCTT * * 627192 CGAAGAACAAAATAGGTCAAGGTCAAAACTTTTGGTGGCGC-GCACTCTTTCTAAATACCATCTA 325 -GAAGAACAAAATAGGTCAAGGTCAAAACTTTTGGTGGC-CTGCACTCCTTCTCAATACCATCTA * 627256 CCTATGTTCCAAATTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTACGGCCTG 388 CCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTACGGCCTG * * 627310 GACAAAATTTTATTATTTTTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATAAT 1 GACAAAATTTTATTA-TCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTC--AT-AT * * * * 627375 ATTATTCAATAGTACACCTAAGTGTATTATTATTGTCCTTTGTTTAAGGTTTGAAGTCCTTCTGT 62 ATAAATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGT * * *** 627440 CAAAGTATATTCAGGAGTTGAACAATGAAGTTTTTCCTAATATGACCTTGAAATTTTTTTTTTAG 127 CAAAGTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAATTTTTTAG * 627505 GTCAAGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAAGTTA 192 GTCAAGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAAGTTA * * * 627570 AAAGTCTGTAAGTTAAAGGAGTCTTGTGTTATGGTCCGGATAATATTTTTTATGAAAAGCCTGAC 257 AAAGTCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGGACAATATTTTTTATGAAAAGCTTGAC * * 627635 CTTGAAAAACAAAATAGGTCAAGGTCAAAACTGTTGGTGGCCTGCACTCCTTCTCAATACCATCT 322 CTTGAAGAACAAAATAGGTCAAGGTCAAAACTTTTGGTGGCCTGCACTCCTTCTCAATACCATCT * * 627700 ACCTATCTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTTAAGTTACGGCCTG 387 ACCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTACGGCCTG 627755 GACAAAATTT 1 GACAAAATTT 627765 GGATGAAGAA Statistics Matches: 830, Mismatches: 54, Indels: 20 0.92 0.06 0.02 Matches are distributed among these distances: 440 3 0.00 441 410 0.49 442 53 0.06 444 12 0.01 445 349 0.42 446 3 0.00 ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36 Consensus pattern (441 bp): GACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAA ATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGTCAAA GTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAATTTTTTAGGTCA AGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAAGTTAAAAG TCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGGACAATATTTTTTATGAAAAGCTTGACCTTG AAGAACAAAATAGGTCAAGGTCAAAACTTTTGGTGGCCTGCACTCCTTCTCAATACCATCTACCT ATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTACGGCCTG Found at i:628530 original size:17 final size:17 Alignment explanation

Indices: 628505--628537 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 628495 CTGGTACTGT * 628505 ACCAGTTATCGGCTAAG 1 ACCAATTATCGGCTAAG 628522 ACCAATTATCGGCTAA 1 ACCAATTATCGGCTAA 628538 ACTGAGAGTT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24 Consensus pattern (17 bp): ACCAATTATCGGCTAAG Found at i:633116 original size:165 final size:167 Alignment explanation

Indices: 632595--633308 Score: 881 Period size: 165 Copynumber: 4.2 Consensus size: 167 632585 AAAGAATCAT * * * 632595 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGCTTTACTCTGA-ATATTCCTTTGTTTAAC 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCT-ATATATTCCTATGTTAAAC * * * * * * 632659 TTTGACCCCCCCCCCATTTTGGCCCCACCCTACCCCTGGGGATCATGATTTTCACAACTATGAAT 65 TTCGA---CCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAA * ** 632724 CTACACTACCTGAGGATGCTTCCACACAAGAATCAGCTTTC 127 ATACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * ** 632765 CTGACTGATTAGTTTCT--GAA-AAGATTTTTAAAGATTTACTCTATATATTCAAATGTTAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT * * * ** 632827 TC-AACCCCCTATTGTGGCCCAACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTAC 66 TCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAAATAC * * * * 632891 ACTATCTAAGGTTGCTTCCACACAAGTGTCAGCTTTC 131 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * * * * 632928 CTGGCTGATTAGTTTCCGAGAAGAAGATTTTTAAAGATTTACTCTATACATACCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT * * 632993 TCGA-CCCCCCATTGTGGCCCCATCCTACCCCCGGGGGT-ATGATTTTCACAACATTGAAAATAC 66 TCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAAATAC * * 633056 ACTACCTGAGGATGCTTCCACACTAGTTTCAGCTTTG 131 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC 633093 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT * * 633158 TCGACCCCCCCCCCGTTGTGGCCCCACCCTTCCCCCGGGGGTCATGATTTTCACAACTTTGAATC 66 TCGA---CCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA-- * 633223 TACACTACATGTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC 126 -A-A-TACA-CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * * 633269 CTGG-T-CTTATGGTTCATGAGAAGAAGATTTTTGAAA-ATTT 1 CTGGCTGATTA-GTTTC-TGAGAAGAAGATTTTT-AAAGATTT 633309 CTCGAAAATT Statistics Matches: 474, Mismatches: 51, Indels: 32 0.85 0.09 0.06 Matches are distributed among these distances: 163 101 0.21 165 121 0.26 166 72 0.15 167 37 0.08 168 3 0.01 169 31 0.07 170 35 0.07 173 1 0.00 174 4 0.01 175 9 0.02 176 57 0.12 177 3 0.01 ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33 Consensus pattern (167 bp): CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT TCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAAATAC ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC Found at i:635433 original size:21 final size:21 Alignment explanation

Indices: 635407--635503 Score: 135 Period size: 21 Copynumber: 4.7 Consensus size: 21 635397 TACACCATAG 635407 CATAGCATAGCATTGAAATCT 1 CATAGCATAGCATTGAAATCT 635428 CATAGCATAGCATTGAAATCT 1 CATAGCATAGCATTGAAATCT * 635449 CATAGCATAGCATTGGAATCT 1 CATAGCATAGCATTGAAATCT * 635470 CATACCATAGCA-T-ACAATCT 1 CATAGCATAGCATTGA-AATCT * * 635490 CATAGAATCGCATT 1 CATAGCATAGCATT 635504 CGTCATATCA Statistics Matches: 68, Mismatches: 6, Indels: 4 0.87 0.08 0.05 Matches are distributed among these distances: 20 15 0.22 21 53 0.78 ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28 Consensus pattern (21 bp): CATAGCATAGCATTGAAATCT Found at i:635469 original size:42 final size:41 Alignment explanation

Indices: 635407--635525 Score: 141 Period size: 42 Copynumber: 2.9 Consensus size: 41 635397 TACACCATAG * 635407 CATAGCATAGCATTGAAATCTCATAGCATAGCATTGA-AATCT 1 CATAGCATAGCATTGAAATCTCATACCATAGCA-T-ACAATCT * 635449 CATAGCATAGCATTGGAATCTCATACCATAGCATACAATCT 1 CATAGCATAGCATTGAAATCTCATACCATAGCATACAATCT * * ** * 635490 CATAGAATCGCATTCGTCATATCATACCATAGCATA 1 CATAGCATAGCATT-GAAATCTCATACCATAGCATA 635526 GCATACAACA Statistics Matches: 68, Mismatches: 7, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 40 1 0.01 41 18 0.26 42 49 0.72 ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28 Consensus pattern (41 bp): CATAGCATAGCATTGAAATCTCATACCATAGCATACAATCT Found at i:635698 original size:15 final size:15 Alignment explanation

Indices: 635678--635706 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 635668 GTTCAAATCT 635678 CATAGCATACCATAG 1 CATAGCATACCATAG 635693 CATAGCATACCATA 1 CATAGCATACCATA 635707 TCATTAAGCC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21 Consensus pattern (15 bp): CATAGCATACCATAG Found at i:635756 original size:21 final size:21 Alignment explanation

Indices: 635730--635809 Score: 108 Period size: 21 Copynumber: 3.8 Consensus size: 21 635720 CATTTCAATT 635730 TCTCATAGCATAGCATACAAA 1 TCTCATAGCATAGCATACAAA 635751 TCTCATAGCATAGCATACAAA 1 TCTCATAGCATAGCATACAAA * * 635772 TCTCATAGCATATCATTA-ACA 1 TCTCATAGCATAGCA-TACAAA * * 635793 TCGCATACCATAGCATA 1 TCTCATAGCATAGCATA 635810 GCATAAATTT Statistics Matches: 53, Mismatches: 5, Indels: 3 0.87 0.08 0.05 Matches are distributed among these distances: 20 2 0.04 21 49 0.92 22 2 0.04 ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26 Consensus pattern (21 bp): TCTCATAGCATAGCATACAAA Found at i:636580 original size:163 final size:168 Alignment explanation

Indices: 636303--636724 Score: 656 Period size: 163 Copynumber: 2.5 Consensus size: 168 636293 TCACACTTTT ** * 636303 TTGTAAGCGCTCTCATGCCTACAAATTTTGACATATTTTCATTAAATGTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCC-AC--A-TTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA * * * 636368 CTACTATTACCTTGATCAAGTTCGAAAATCAGAATTGGTCGATAC-TTTT-TTGGAGTTATGGGA 62 CCACTATTACCTTGGTCAAGTTCGAAAATCAGAATTGGTCAATACTTTTTGTTGGAGTTATGGGA 636431 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC 127 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC 636473 TTGTAAGCGCTCTCATG-C-C-TTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC 1 TTGTAAGCGCTCTCATGCCACATTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC * 636535 TATTACCTTGGTCAAGTTCGAAAATCAGCATTGGTCAATACTTTTTGTTGGAGTTATGGGACTTT 66 TATTACCTTGGTCAAGTTCGAAAATCAGAATTGGTCAATACTTTTTGTTGGAGTTATGGGACTTT * 636600 GACCACAATAATGACTTCGTTTTATCCAAAAATTGACC 131 GACCACAATAATGACTCCGTTTTATCCAAAAATTGACC 636638 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCC-AC--A-TTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA * 636703 CCACTATAACCTTGGTCAAGTT 62 CCACTATTACCTTGGTCAAGTT 636725 TCTAAATTAG Statistics Matches: 234, Mismatches: 9, Indels: 16 0.90 0.03 0.06 Matches are distributed among these distances: 163 77 0.33 164 4 0.02 165 72 0.31 166 1 0.00 167 1 0.00 168 1 0.00 169 1 0.00 170 17 0.07 172 60 0.26 ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37 Consensus pattern (168 bp): TTGTAAGCGCTCTCATGCCACATTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC TATTACCTTGGTCAAGTTCGAAAATCAGAATTGGTCAATACTTTTTGTTGGAGTTATGGGACTTT GACCACAATAATGACTCCGTTTTATCCAAAAATTGACC Found at i:637999 original size:4 final size:4 Alignment explanation

Indices: 637992--638044 Score: 54 Period size: 4 Copynumber: 13.0 Consensus size: 4 637982 TGATGATTGG * * * 637992 ATGA ATGA ATGGA ATGA ATGA ATGA ATG- ATAGA TTGA TTGA ATGA ATAA 1 ATGA ATGA AT-GA ATGA ATGA ATGA ATGA AT-GA ATGA ATGA ATGA ATGA 638041 ATGA 1 ATGA 638045 TTGTTTTAAT Statistics Matches: 42, Mismatches: 4, Indels: 6 0.81 0.08 0.12 Matches are distributed among these distances: 3 2 0.05 4 35 0.83 5 5 0.12 ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28 Consensus pattern (4 bp): ATGA Found at i:640555 original size:26 final size:26 Alignment explanation

Indices: 640526--640585 Score: 111 Period size: 26 Copynumber: 2.3 Consensus size: 26 640516 CAAGGGAGAT * 640526 TGGCATTCTTTGTATGGCCACCAAAA 1 TGGCATTCTTTGAATGGCCACCAAAA 640552 TGGCATTCTTTGAATGGCCACCAAAA 1 TGGCATTCTTTGAATGGCCACCAAAA 640578 TGGCATTC 1 TGGCATTC 640586 ACCTGACATA Statistics Matches: 33, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 26 33 1.00 ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30 Consensus pattern (26 bp): TGGCATTCTTTGAATGGCCACCAAAA Found at i:648789 original size:21 final size:21 Alignment explanation

Indices: 648763--648804 Score: 66 Period size: 21 Copynumber: 2.0 Consensus size: 21 648753 GGAGCTGCCA * 648763 TCAAAGAAGAAGGTTCCAACG 1 TCAAAGAAGAAGGGTCCAACG * 648784 TCAAAGAAGACGGGTCCAACG 1 TCAAAGAAGAAGGGTCCAACG 648805 ATGAAGAAGA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.40, C:0.21, G:0.26, T:0.12 Consensus pattern (21 bp): TCAAAGAAGAAGGGTCCAACG Found at i:648811 original size:21 final size:21 Alignment explanation

Indices: 648787--648845 Score: 82 Period size: 21 Copynumber: 2.8 Consensus size: 21 648777 TCCAACGTCA * 648787 AAGAAGACGGGTCCAACGATG 1 AAGAAGACGGGTCCAACGAGG * * 648808 AAGAAGACTGTTCCAACGAGG 1 AAGAAGACGGGTCCAACGAGG * 648829 AAAAAGACGGGTCCAAC 1 AAGAAGACGGGTCCAAC 648846 TCGGGAGAGT Statistics Matches: 32, Mismatches: 6, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 21 32 1.00 ACGTcount: A:0.41, C:0.20, G:0.29, T:0.10 Consensus pattern (21 bp): AAGAAGACGGGTCCAACGAGG Found at i:648812 original size:42 final size:42 Alignment explanation

Indices: 648766--648845 Score: 108 Period size: 42 Copynumber: 1.9 Consensus size: 42 648756 GCTGCCATCA * 648766 AAGAAGAAGGTTCCAACG-TCAAAGAAGACGGGTCCAACGATG 1 AAGAAGAAGGTTCCAACGAGCAAA-AAGACGGGTCCAACGATG ** * 648808 AAGAAGACTGTTCCAACGAGGAAAAAGACGGGTCCAAC 1 AAGAAGAAGGTTCCAACGAGCAAAAAGACGGGTCCAAC 648846 TCGGGAGAGT Statistics Matches: 33, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 42 30 0.91 43 3 0.09 ACGTcount: A:0.41, C:0.20, G:0.28, T:0.11 Consensus pattern (42 bp): AAGAAGAAGGTTCCAACGAGCAAAAAGACGGGTCCAACGATG Found at i:649754 original size:166 final size:166 Alignment explanation

Indices: 649479--650937 Score: 2061 Period size: 166 Copynumber: 8.8 Consensus size: 166 649469 GTGAATATGC * 649479 AAAATAAACAAAGTAC-TCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCAC 1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC * * 649543 AATATGGCATGCCAAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTAAG 65 AATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG ** 649608 AAATT-TTTGACGGAAATTTGTTTGAAAATTTTGGCTA 130 -AATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA * * 649645 AAAATAAACAAAGTAC-TCA-TTACACAGGAAGTTGACGTCCAATTGGTACAAAAATACATCCCA 1 AAAATAAACAAAGT-CGTCATTTA-ACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCA * ** ** * * * * 649708 CGATAAAGCATGCTTATACAAATACTGTGTAAAAATTTCGAGCATCTGCGATGAACAGTTGCTGA 64 CAATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGA 649773 GAATTCTTTGACAAAAATTTGTTTGAAAATGTTT-GCTA 129 GAATTCTTTGACAAAAATTTGTTTGAAAAT-TTTGGCTA * * * * 649811 AAAATAAATAAAGTCGTCATTTAACAGGAAGTTGACATCTGATTGGTACAAAAACATATCCCACA 1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA * * * * * * * 649876 ATTTGGCATACCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGTGATTAATAGCTGCTGAGA 66 ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA * ** 649941 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA 131 ATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA * * * * 649977 AAAATAAATAAAGTCGTCATTTAACAGGAAGTTGACGTCCAATTGGTACAAAAATACATCTCA-A 1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA * 650041 GATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG 66 -ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG 650106 AATTCTTTGACAAAAATTTGTTTGAAAATGTTT-GCTA 130 AATTCTTTGACAAAAATTTGTTTGAAAAT-TTTGGCTA ** * 650143 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGATATCTGATTGGTACAAAAATATATCCCACA 1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA * * * * 650208 ATATGGCATGCCATAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGA 66 ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA * 650273 ATTCTTTGACAAAAATTTGTTTGAAAATTTTTGCTA 131 ATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA * * 650309 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCTGATTGGTACAAAAATATATCCCACA 1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA * * * 650374 ATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA 66 ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA * ** 650439 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA 131 ATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA * * * 650475 AAAATAAACAAAGTAC-TCATATAACAGGAAGTTGACGTCCAATTGGTACAAAAATACATCCCAC 1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC * * ** * * * 650539 GATATAGCATGCTTATACAAATACTGTGTAAAAATTTCAAGCATCTGCTATAAACAGTTGCTGAG 65 AATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG * 650604 AATTCTTTGACAAAAATTTGTTTGAAAATTTTTGCTA 130 AATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA * 650641 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACA 1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA * * * * * * 650706 ATATGGCATGCCTATACAAATATTGTGTAAAATTTTTAAGCATCTGCGATAGATAGTTGCTGAGA 66 ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA * * * 650771 ATTCTTTGACGAAAATTTGTTTGAAAATTTTAGTTAA 131 ATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCT-A * * * * 650808 AAAATAAGCAAAGTCATCATTTAAGAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG 1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA ** * * 650873 ATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA 66 ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 650938 TAAATGCGAC Statistics Matches: 1157, Mismatches: 123, Indels: 25 0.89 0.09 0.02 Matches are distributed among these distances: 165 16 0.01 166 1012 0.87 167 129 0.11 ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30 Consensus pattern (166 bp): AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA ATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA Found at i:650973 original size:4 final size:4 Alignment explanation

Indices: 650964--651007 Score: 70 Period size: 4 Copynumber: 11.0 Consensus size: 4 650954 TTTTGTTACG * * 650964 GACA GACA GACA GACA GACA GACT GACG GACA GACA GACA GACA 1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA 651008 CACAAGGGTA Statistics Matches: 37, Mismatches: 3, Indels: 0 0.93 0.08 0.00 Matches are distributed among these distances: 4 37 1.00 ACGTcount: A:0.45, C:0.25, G:0.27, T:0.02 Consensus pattern (4 bp): GACA Found at i:652969 original size:21 final size:21 Alignment explanation

Indices: 652945--653227 Score: 326 Period size: 21 Copynumber: 13.6 Consensus size: 21 652935 TTTTTATAAA 652945 TTCCAACTTTAAAGTTGGAAT 1 TTCCAACTTTAAAGTTGGAAT ** 652966 TTCCAACTTTAATCTTGGAAT 1 TTCCAACTTTAAAGTTGGAAT * * 652987 TTCCAACTTTAATGTTAGAAT 1 TTCCAACTTTAAAGTTGGAAT * 653008 TTCCAACTTTAAAGGTGGAAT 1 TTCCAACTTTAAAGTTGGAAT * 653029 TTCCAACTTTAAAGTT-GATTT 1 TTCCAACTTTAAAGTTGGA-AT ** 653050 TTCCAA-TTTAAAAGTTAAAAT 1 TTCCAACTTT-AAAGTTGGAAT * * 653071 TACAAAC-TTAACAGTTGGAAT 1 TTCCAACTTTAA-AGTTGGAAT ** 653092 TTCCAACTTTAATCTTGGAAT 1 TTCCAACTTTAAAGTTGGAAT * 653113 TTCCAACTTTCAAGTT-G-AT 1 TTCCAACTTTAAAGTTGGAAT * * 653132 TTCCAACTTTCAAGTT-GATTT 1 TTCCAACTTTAAAGTTGGA-AT 653153 TTCCAACTTTAAAGTTGGAAT 1 TTCCAACTTTAAAGTTGGAAT ** 653174 TTCCAACTTTAATCTTGGAAT 1 TTCCAACTTTAAAGTTGGAAT * 653195 TTCCAACTTTCAAGTTGGAAT 1 TTCCAACTTTAAAGTTGGAAT 653216 TTCCAACTTTAA 1 TTCCAACTTTAA 653228 TATTGGGATT Statistics Matches: 222, Mismatches: 31, Indels: 18 0.82 0.11 0.07 Matches are distributed among these distances: 19 19 0.09 20 8 0.04 21 188 0.85 22 7 0.03 ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40 Consensus pattern (21 bp): TTCCAACTTTAAAGTTGGAAT Found at i:656057 original size:22 final size:23 Alignment explanation

Indices: 656014--656070 Score: 107 Period size: 22 Copynumber: 2.5 Consensus size: 23 656004 CCACCTAAGA 656014 TTAAGGCGGATTCCTTTTTTGTT 1 TTAAGGCGGATTCCTTTTTTGTT 656037 TTAAGGCGGATTCC-TTTTTGTT 1 TTAAGGCGGATTCCTTTTTTGTT 656059 TTAAGGCGGATT 1 TTAAGGCGGATT 656071 TTTATTACCC Statistics Matches: 34, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 22 20 0.59 23 14 0.41 ACGTcount: A:0.16, C:0.12, G:0.25, T:0.47 Consensus pattern (23 bp): TTAAGGCGGATTCCTTTTTTGTT Found at i:661443 original size:74 final size:74 Alignment explanation

Indices: 661322--661468 Score: 294 Period size: 74 Copynumber: 2.0 Consensus size: 74 661312 TACAGGATCA 661322 AGAAGACACAAAGAATTGGGCTTAACATTTCTACCTCCTCCTTTGTCAATGTTTTTGAGGTGTCT 1 AGAAGACACAAAGAATTGGGCTTAACATTTCTACCTCCTCCTTTGTCAATGTTTTTGAGGTGTCT 661387 AGCTCGCTT 66 AGCTCGCTT 661396 AGAAGACACAAAGAATTGGGCTTAACATTTCTACCTCCTCCTTTGTCAATGTTTTTGAGGTGTCT 1 AGAAGACACAAAGAATTGGGCTTAACATTTCTACCTCCTCCTTTGTCAATGTTTTTGAGGTGTCT 661461 AGCTCGCT 66 AGCTCGCT 661469 GATATCTAGT Statistics Matches: 73, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 74 73 1.00 ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35 Consensus pattern (74 bp): AGAAGACACAAAGAATTGGGCTTAACATTTCTACCTCCTCCTTTGTCAATGTTTTTGAGGTGTCT AGCTCGCTT Found at i:663005 original size:172 final size:172 Alignment explanation

Indices: 662719--663345 Score: 961 Period size: 172 Copynumber: 3.6 Consensus size: 172 662709 TCACACTTTT * * 662719 TTGTAAGCGCTCTCATGCCTACAAATTTTTACGGATTTTCATTAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATGAAATTTATACCAAATGTTTATA * * 662784 CCACTATTACCTTGGTCAAGTTCGAAAATCAACATTGGTCGATACTTTTTGTTGGAGTTATGGGA 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA ** 662849 CTTTGACCACAATAATGACTTTGTTTTATCCAAAAATTGACC 131 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC * * * 662891 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTTATGAAATCTATACCAAATGTGTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATGAAATTTATACCAAATGTTTATA * * 662956 CCACTAATA-CTTCGGTCAAGTTCGAAAATCAGCTTTGGTCAATACTTTTTGTTGGAGTTATGGG 66 CCACTAATACCTT-GGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG * 663020 ACTTTGACCACAATAATGACTCCGTTTTATCCTAAAATTGACC 130 ACTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC * * * * 663063 TTGTAAGCGCTCTAATGCCTACAAATTTTGACGGATTTTCAAT-TAATTTATAACAAATGTTTGT 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTC-ATGAAATTTATACCAAATGTTTAT * * * 663127 ACCACTAATACTTTGGTCAAGTTCGTAAATCAGCATTGGTCGATGCTTTTTGTTGGAGTTATGGG 65 ACCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG * * 663192 ACTTTGACCACAATAATGACTCCGTTTTATCCCATAATTGACC 130 ACTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC * * * 663235 TTGTAAGTGCTCTCATGCCTACAAATTTTGTCGGATTTACATGAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATGAAATTTATACCAAATGTTTATA * * ** * 663300 TCACTAATACCGTGGTCAAGTTCCTAAATCAGCCTTGGTCGATACT 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACT 663346 AGTATACTGC Statistics Matches: 412, Mismatches: 39, Indels: 8 0.90 0.08 0.02 Matches are distributed among these distances: 171 5 0.01 172 403 0.98 173 4 0.01 ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37 Consensus pattern (172 bp): TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATGAAATTTATACCAAATGTTTATA CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC Found at i:668305 original size:11 final size:11 Alignment explanation

Indices: 668289--668313 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 668279 AGTTTTCGTT 668289 GTTTTGGGTCA 1 GTTTTGGGTCA 668300 GTTTTGGGTCA 1 GTTTTGGGTCA 668311 GTT 1 GTT 668314 AGCCCAATAC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.08, C:0.08, G:0.36, T:0.48 Consensus pattern (11 bp): GTTTTGGGTCA Found at i:696504 original size:2 final size:2 Alignment explanation

Indices: 696497--696555 Score: 118 Period size: 2 Copynumber: 29.5 Consensus size: 2 696487 NNNNNNNNNN 696497 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 696539 CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT C 696556 CTTTTTCCTT Statistics Matches: 57, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 57 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:697334 original size:17 final size:17 Alignment explanation

Indices: 697312--697379 Score: 65 Period size: 17 Copynumber: 4.3 Consensus size: 17 697302 CCCATTGGCC * 697312 TGGCCTGGCCTCAAAGT 1 TGGCCTGGCCTCAAAAT * 697329 TGGCCTGGCCTC--ACT 1 TGGCCTGGCCTCAAAAT * 697344 T---TTGGCCTCAAAAT 1 TGGCCTGGCCTCAAAAT * 697358 TGGCCTGGCCTCAAATT 1 TGGCCTGGCCTCAAAAT 697375 TGGCC 1 TGGCC 697380 ACTACAACAA Statistics Matches: 41, Mismatches: 5, Indels: 10 0.73 0.09 0.18 Matches are distributed among these distances: 12 7 0.17 14 3 0.07 15 3 0.07 17 28 0.68 ACGTcount: A:0.16, C:0.31, G:0.25, T:0.28 Consensus pattern (17 bp): TGGCCTGGCCTCAAAAT Found at i:697349 original size:29 final size:29 Alignment explanation

Indices: 697317--697379 Score: 99 Period size: 29 Copynumber: 2.2 Consensus size: 29 697307 TGGCCTGGCC * ** 697317 TGGCCTCAAAGTTGGCCTGGCCTCACTTT 1 TGGCCTCAAAATTGGCCTGGCCTCAAATT 697346 TGGCCTCAAAATTGGCCTGGCCTCAAATT 1 TGGCCTCAAAATTGGCCTGGCCTCAAATT 697375 TGGCC 1 TGGCC 697380 ACTACAACAA Statistics Matches: 31, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 29 31 1.00 ACGTcount: A:0.17, C:0.30, G:0.24, T:0.29 Consensus pattern (29 bp): TGGCCTCAAAATTGGCCTGGCCTCAAATT Found at i:697452 original size:11 final size:11 Alignment explanation

Indices: 697430--697459 Score: 51 Period size: 11 Copynumber: 2.6 Consensus size: 11 697420 CTTTACATAT 697430 TTGATGTTTTTA 1 TTGAT-TTTTTA 697442 TTGATTTTTTA 1 TTGATTTTTTA 697453 TTGATTT 1 TTGATTT 697460 ATTTTCAATG Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 11 13 0.72 12 5 0.28 ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70 Consensus pattern (11 bp): TTGATTTTTTA Found at i:700812 original size:3 final size:3 Alignment explanation

Indices: 700804--700855 Score: 86 Period size: 3 Copynumber: 17.3 Consensus size: 3 700794 TGGCACGATT * * 700804 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATT ATC ATC ATC ATC ATT ATC 1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC 700852 ATC A 1 ATC A 700856 ATCTAATGAA Statistics Matches: 45, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 3 45 1.00 ACGTcount: A:0.35, C:0.29, G:0.00, T:0.37 Consensus pattern (3 bp): ATC Found at i:702802 original size:2 final size:2 Alignment explanation

Indices: 702795--702848 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 702785 CTGAAACAAA 702795 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 702837 TC TC TC TC TC TC 1 TC TC TC TC TC TC 702849 ATGTATTTTT Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:703958 original size:15 final size:15 Alignment explanation

Indices: 703938--703972 Score: 70 Period size: 15 Copynumber: 2.3 Consensus size: 15 703928 ATTTTTTCTG 703938 CAATGATCAATGAAC 1 CAATGATCAATGAAC 703953 CAATGATCAATGAAC 1 CAATGATCAATGAAC 703968 CAATG 1 CAATG 703973 GCACAGTTGA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 20 1.00 ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20 Consensus pattern (15 bp): CAATGATCAATGAAC Found at i:704542 original size:18 final size:18 Alignment explanation

Indices: 704519--704556 Score: 67 Period size: 18 Copynumber: 2.1 Consensus size: 18 704509 TGGTCCCAAA 704519 TCAAATTTTGGCCTGGCC 1 TCAAATTTTGGCCTGGCC * 704537 TCAAATTTTGGCCTTGCC 1 TCAAATTTTGGCCTGGCC 704555 TC 1 TC 704557 TACTTTGGCC Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37 Consensus pattern (18 bp): TCAAATTTTGGCCTGGCC Found at i:705657 original size:18 final size:18 Alignment explanation

Indices: 705626--705697 Score: 94 Period size: 18 Copynumber: 4.1 Consensus size: 18 705616 ATGTTTATAG 705626 AGGCCAAA-TTTGAGGCC 1 AGGCCAAATTTTGAGGCC 705643 AGGCCAAATTTTGAGGCC 1 AGGCCAAATTTTGAGGCC * * 705661 AGGACAAAATTTG-GAGCC 1 AGGCCAAATTTTGAG-GCC * 705679 AGGCCTAATTTTGAGGCC 1 AGGCCAAATTTTGAGGCC 705697 A 1 A 705698 AACGTGAGGC Statistics Matches: 47, Mismatches: 5, Indels: 5 0.82 0.09 0.09 Matches are distributed among these distances: 17 9 0.19 18 37 0.79 19 1 0.02 ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21 Consensus pattern (18 bp): AGGCCAAATTTTGAGGCC Found at i:705802 original size:65 final size:65 Alignment explanation

Indices: 705707--705836 Score: 244 Period size: 65 Copynumber: 2.0 Consensus size: 65 705697 AAACGTGAGG 705707 CAAGACCAACTTTGAGGACAGACCAGGCCAATGCGGCCAGGCCAGGTTTTAGAGTATGCCAAAAA 1 CAAGACCAACTTTGAGGACAGACCAGGCCAATGCGGCCAGGCCAGGTTTTAGAGTATGCCAAAAA 705772 NCAAGACCAAC-TTGAGGACAGACCAGGCCAATGCGGCCAGGCCAGGTTTTAGAGTATGCCAAAA 1 -CAAGACCAACTTTGAGGACAGACCAGGCCAATGCGGCCAGGCCAGGTTTTAGAGTATGCCAAAA 705836 A 65 A 705837 GAATGCACAC Statistics Matches: 64, Mismatches: 0, Indels: 1 0.98 0.00 0.02 Matches are distributed among these distances: 65 54 0.84 66 10 0.16 ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15 Consensus pattern (65 bp): CAAGACCAACTTTGAGGACAGACCAGGCCAATGCGGCCAGGCCAGGTTTTAGAGTATGCCAAAAA Found at i:706455 original size:2 final size:2 Alignment explanation

Indices: 706448--706472 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 706438 TATGGTCGGC 706448 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 706473 NNNNNNNNNN Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:708401 original size:2 final size:2 Alignment explanation

Indices: 708394--708452 Score: 118 Period size: 2 Copynumber: 29.5 Consensus size: 2 708384 TAAGTTTATC 708394 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 708436 AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG A 708453 TCAATGTTCG Statistics Matches: 57, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 57 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:715384 original size:3 final size:3 Alignment explanation

Indices: 715376--715442 Score: 55 Period size: 3 Copynumber: 21.3 Consensus size: 3 715366 TGTGAAATTA * * * 715376 ATC ATC ATC ATC ATC ACC ACC ATC ATC GATAC ATGT ATC ATC ATC A-C 1 ATC ATC ATC ATC ATC ATC ATC ATC ATC -AT-C AT-C ATC ATC ATC ATC * 715423 AATC ATC TTC ATC ATC ATC A 1 -ATC ATC ATC ATC ATC ATC A 715443 CTGTCAAATG Statistics Matches: 53, Mismatches: 7, Indels: 8 0.78 0.10 0.12 Matches are distributed among these distances: 2 1 0.02 3 44 0.83 4 7 0.13 5 1 0.02 ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30 Consensus pattern (3 bp): ATC Found at i:721221 original size:41 final size:41 Alignment explanation

Indices: 721176--721320 Score: 272 Period size: 41 Copynumber: 3.5 Consensus size: 41 721166 ATACTGATAT 721176 ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG 1 ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG * 721217 ACGTATACGTCTCTGGTACTGTTTGGTTGGTACTGTCAGGG 1 ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG 721258 ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG 1 ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG * 721299 ACGTATATGTCCCTGGTACTGT 1 ACGTATACGTCCCTGGTACTGT 721321 ATACATGTAC Statistics Matches: 101, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 41 101 1.00 ACGTcount: A:0.15, C:0.19, G:0.30, T:0.35 Consensus pattern (41 bp): ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG Found at i:728309 original size:22 final size:22 Alignment explanation

Indices: 728283--728882 Score: 1092 Period size: 22 Copynumber: 27.3 Consensus size: 22 728273 CTGTTTTTCG 728283 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728305 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728327 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT * * 728349 TCGATTTTTACCTGGTTTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728371 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728393 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728415 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728437 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728459 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728481 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728503 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728525 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728547 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728569 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728591 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728613 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728635 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728657 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728679 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728701 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728723 TAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT * 728745 TAGATTTTTACCTTGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT * 728767 TAGATTTTTACCTGGTTTTTGT 1 TAGATTTTTACCTGGTCTTTGT * 728789 AAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT * 728811 CAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT * * * * * 728833 TAAATCTTAACCTTGTTTTTGT 1 TAGATTTTTACCTGGTCTTTGT * 728855 AAGATTTTTACCTGGTCTTTGT 1 TAGATTTTTACCTGGTCTTTGT 728877 TAGATT 1 TAGATT 728883 CGTTATCCTC Statistics Matches: 555, Mismatches: 23, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 22 555 1.00 ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55 Consensus pattern (22 bp): TAGATTTTTACCTGGTCTTTGT Found at i:729801 original size:45 final size:46 Alignment explanation

Indices: 729737--729847 Score: 181 Period size: 45 Copynumber: 2.5 Consensus size: 46 729727 GCATCTCATT * 729737 GTGTGTTTAAGCATGCATGTACCTTTTTTGTGGTGAAGTGTTGA-A 1 GTGTGTTTAAGCATGCATGTACCTTTTTTGGGGTGAAGTGTTGACA * * 729782 GTGTGTTTAGGCATGCATGTACCTTTTTTGGGGTGAAGTGTTTACA 1 GTGTGTTTAAGCATGCATGTACCTTTTTTGGGGTGAAGTGTTGACA 729828 -TGTGTTTAAGCATGCATGTA 1 GTGTGTTTAAGCATGCATGTA 729848 GTACTACCTT Statistics Matches: 61, Mismatches: 4, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 45 60 0.98 46 1 0.02 ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41 Consensus pattern (46 bp): GTGTGTTTAAGCATGCATGTACCTTTTTTGGGGTGAAGTGTTGACA Found at i:729926 original size:55 final size:55 Alignment explanation

Indices: 729858--730004 Score: 258 Period size: 55 Copynumber: 2.7 Consensus size: 55 729848 GTACTACCTT * * * 729858 TTTTTAGTGGTGAAGTGTTTAAGCGTACCTTATTGGTAAAGTGTTTGAGCCTACC 1 TTTTTGGTGGTGAAGTGTTTAAGCCTACCTTTTTGGTAAAGTGTTTGAGCCTACC * 729913 TTTTTGGTGGTGAAGTGTTTGAGCCTACCTTTTTGGTAAAGTGTTTGAGCCTACC 1 TTTTTGGTGGTGAAGTGTTTAAGCCTACCTTTTTGGTAAAGTGTTTGAGCCTACC 729968 TTTTTGGTGGTGAAGTGTTTAAGCCTACCTTTTTGGT 1 TTTTTGGTGGTGAAGTGTTTAAGCCTACCTTTTTGGT 730005 GGTGAAGTGT Statistics Matches: 87, Mismatches: 5, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 55 87 1.00 ACGTcount: A:0.18, C:0.13, G:0.27, T:0.43 Consensus pattern (55 bp): TTTTTGGTGGTGAAGTGTTTAAGCCTACCTTTTTGGTAAAGTGTTTGAGCCTACC Found at i:729931 original size:29 final size:29 Alignment explanation

Indices: 729858--730020 Score: 221 Period size: 29 Copynumber: 5.8 Consensus size: 29 729848 GTACTACCTT * * * 729858 TTTTTAGTGGTGAAGTGTTTAAGCGTACC 1 TTTTTGGTGGTGAAGTGTTTGAGCCTACC * * 729887 -TTAT--TGGTAAAGTGTTTGAGCCTACC 1 TTTTTGGTGGTGAAGTGTTTGAGCCTACC 729913 TTTTTGGTGGTGAAGTGTTTGAGCCTACC 1 TTTTTGGTGGTGAAGTGTTTGAGCCTACC * 729942 -TTTT--TGGTAAAGTGTTTGAGCCTACC 1 TTTTTGGTGGTGAAGTGTTTGAGCCTACC * 729968 TTTTTGGTGGTGAAGTGTTTAAGCCTACC 1 TTTTTGGTGGTGAAGTGTTTGAGCCTACC 729997 TTTTTGGTGGTGAAGTGTTTGAGC 1 TTTTTGGTGGTGAAGTGTTTGAGC 730021 ATGTCCTGGG Statistics Matches: 118, Mismatches: 10, Indels: 12 0.84 0.07 0.09 Matches are distributed among these distances: 26 40 0.34 27 7 0.06 28 7 0.06 29 64 0.54 ACGTcount: A:0.18, C:0.12, G:0.28, T:0.42 Consensus pattern (29 bp): TTTTTGGTGGTGAAGTGTTTGAGCCTACC Found at i:733582 original size:3 final size:3 Alignment explanation

Indices: 733574--733607 Score: 68 Period size: 3 Copynumber: 11.3 Consensus size: 3 733564 AGTTGGATGA 733574 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A 1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A 733608 ATAACAAGAC Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 31 1.00 ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32 Consensus pattern (3 bp): ATC Found at i:734258 original size:93 final size:93 Alignment explanation

Indices: 734099--734321 Score: 383 Period size: 93 Copynumber: 2.4 Consensus size: 93 734089 TAATGGAGCG * 734099 GTACCACCAAACACCCTGGATATGAAGTAAAACAACAGAGGTTATTATATCAGTGATTTATCCTT 1 GTACCACCAAACACCCTGGATATGAAGTAAAACAACACAGGTTATTATATCAGTGATTTATCCTT 734164 GTCACATGTATAGAAAACTGATGAAGCA 66 GTCACATGTATAGAAAACTGATGAAGCA * 734192 GTACCACCAAACACCCCGGATATGAAGTAAAACAACACAGGTTATTATATCAGTGATTTATCCTT 1 GTACCACCAAACACCCTGGATATGAAGTAAAACAACACAGGTTATTATATCAGTGATTTATCCTT 734257 GTCACATGTATAGAAAACTGATGAAGCA 66 GTCACATGTATAGAAAACTGATGAAGCA * * * * * 734285 GTTCCATCAGACACCCTGGATGTGAAGTTAAACAACA 1 GTACCACCAAACACCCTGGATATGAAGTAAAACAACA 734322 GACACTATTT Statistics Matches: 122, Mismatches: 8, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 93 122 1.00 ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25 Consensus pattern (93 bp): GTACCACCAAACACCCTGGATATGAAGTAAAACAACACAGGTTATTATATCAGTGATTTATCCTT GTCACATGTATAGAAAACTGATGAAGCA Found at i:739032 original size:11 final size:11 Alignment explanation

Indices: 739016--739040 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 739006 TTGAGAACGT 739016 TGTCAAAAAAG 1 TGTCAAAAAAG 739027 TGTCAAAAAAG 1 TGTCAAAAAAG 739038 TGT 1 TGT 739041 ACTAATTTGA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24 Consensus pattern (11 bp): TGTCAAAAAAG Found at i:739151 original size:1 final size:1 Alignment explanation

Indices: 739145--739172 Score: 56 Period size: 1 Copynumber: 28.0 Consensus size: 1 739135 AGCACCACTA 739145 CCCCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC 739173 GACCTTGCAA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 27 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:747332 original size:11 final size:12 Alignment explanation

Indices: 747314--747341 Score: 56 Period size: 12 Copynumber: 2.3 Consensus size: 12 747304 AATTGAATGC 747314 ATTTTTTTTTTT 1 ATTTTTTTTTTT 747326 ATTTTTTTTTTT 1 ATTTTTTTTTTT 747338 ATTT 1 ATTT 747342 AAATACAACT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 16 1.00 ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89 Consensus pattern (12 bp): ATTTTTTTTTTT Found at i:749639 original size:2 final size:2 Alignment explanation

Indices: 749632--749697 Score: 78 Period size: 2 Copynumber: 33.0 Consensus size: 2 749622 AGGGTTAACG * ** ** * 749632 AT AT AT AT AT AT AT AT AT AT AT AN NN NN NT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 749674 AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT 749698 CCCTTCTAGT Statistics Matches: 60, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 60 1.00 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.45 Consensus pattern (2 bp): AT Found at i:750619 original size:2 final size:2 Alignment explanation

Indices: 750612--750710 Score: 130 Period size: 2 Copynumber: 50.5 Consensus size: 2 750602 TGATGTTTGA 750612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG -G 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG * * * * * 750652 AG GG GG AG GG AG GG GG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG * 750694 AG AG AG AG AA AG AG AG A 1 AG AG AG AG AG AG AG AG A 750711 AACCAGCTTG Statistics Matches: 87, Mismatches: 8, Indels: 4 0.88 0.08 0.04 Matches are distributed among these distances: 1 2 0.02 2 85 0.98 ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00 Consensus pattern (2 bp): AG Found at i:754651 original size:3 final size:3 Alignment explanation

Indices: 754643--754670 Score: 56 Period size: 3 Copynumber: 9.3 Consensus size: 3 754633 AAACGTACAA 754643 CCT CCT CCT CCT CCT CCT CCT CCT CCT C 1 CCT CCT CCT CCT CCT CCT CCT CCT CCT C 754671 TTCTTCTTCT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 25 1.00 ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32 Consensus pattern (3 bp): CCT Found at i:754675 original size:3 final size:3 Alignment explanation

Indices: 754669--754730 Score: 124 Period size: 3 Copynumber: 20.7 Consensus size: 3 754659 CTCCTCCTCC 754669 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT 1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT 754717 TCT TCT TCT TCT TC 1 TCT TCT TCT TCT TC 754731 CTGCTCCTCA Statistics Matches: 59, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 59 1.00 ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66 Consensus pattern (3 bp): TCT Found at i:754771 original size:12 final size:15 Alignment explanation

Indices: 754741--754779 Score: 60 Period size: 15 Copynumber: 2.6 Consensus size: 15 754731 CTGCTCCTCA 754741 TCGTCCTCAATCTCG 1 TCGTCCTCAATCTCG * 754756 TCGTCCTCATTCTCG 1 TCGTCCTCAATCTCG * 754771 TCATCCTCA 1 TCGTCCTCA 754780 TCCCAATTCT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 15 22 1.00 ACGTcount: A:0.13, C:0.41, G:0.10, T:0.36 Consensus pattern (15 bp): TCGTCCTCAATCTCG Found at i:764973 original size:2 final size:2 Alignment explanation

Indices: 764966--765027 Score: 88 Period size: 2 Copynumber: 31.0 Consensus size: 2 764956 GTAGACGTGT ** ** 764966 TA TA TA TA TA TA TA TA TA NN NN TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 765008 TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA 765028 ATTTTAAGCT Statistics Matches: 56, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 56 1.00 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.47 Consensus pattern (2 bp): TA Found at i:769194 original size:14 final size:14 Alignment explanation

Indices: 769175--769209 Score: 52 Period size: 14 Copynumber: 2.5 Consensus size: 14 769165 ATTCAAGATT * 769175 CGAGATTGGAAATA 1 CGAGATTCGAAATA * 769189 CGAGATTCGAAGTA 1 CGAGATTCGAAATA 769203 CGAGATT 1 CGAGATT 769210 TGAGATTCAA 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:0.37, C:0.11, G:0.29, T:0.23 Consensus pattern (14 bp): CGAGATTCGAAATA Found at i:770005 original size:2 final size:2 Alignment explanation

Indices: 770000--770046 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 769990 TTTTTTTTAT 770000 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 770042 TC TC T 1 TC TC T 770047 GAGATGTCAA Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:772011 original size:2 final size:2 Alignment explanation

Indices: 772004--772103 Score: 155 Period size: 2 Copynumber: 50.0 Consensus size: 2 771994 CAGTACCAGT 772004 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * * * * * 772046 TC TC TC TC TC TC TG TT TC TC TC GC TC TC TG TC TC TC TG TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 772088 TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC 772104 AACTGTTGGG Statistics Matches: 89, Mismatches: 9, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 2 89 1.00 ACGTcount: A:0.00, C:0.46, G:0.04, T:0.50 Consensus pattern (2 bp): TC Found at i:774247 original size:305 final size:304 Alignment explanation

Indices: 773692--774304 Score: 1003 Period size: 305 Copynumber: 2.0 Consensus size: 304 773682 CGTGCAGGTG * 773692 AATAATATATAAATAATGCCTGTTTGGGAGGGTAACAGTTGAATTTGCACCCCGAGAAAACCATT 1 AATAATATATAAATAATGCCTGTTTGGGAGGGTAACAGTTGAAATTGCACCCCGAGAAAACCATT * * 773757 GTCAACCGACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGCCAATTTCAACTGTTATCCT 66 GTCAACCGACCCAAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGCCAATTTCAACTGTTATCCT * ** * 773822 CCCAAACAGATACCATTTATTTTGCTATACTGAATGTCTTAATTTTAAAGAAAATTTTACTGCTT 131 CCCAAACAGACACCATTTATTTTGCTATACTGAATGTCTTAATTTTAAAGAAAACATCACTGCTT * * * * 773887 TTATATAGGAATAACTTTAATTCTACAGCGAACCGTACGCGCATAATTTTCGCGCATGTAACAAT 196 TTAGATAGGAATAACGTGAATTCTAAAGCGAACCGTACGCGCATAATTTTCGCGCATGTAACAAT * 773952 TTGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGT 261 TCGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGT * * * 773996 AATATTATATAAATAGTGCCTGTTTGGGAGGGTAACAGTTGAAATTGACATCCCGAGAAAACCAT 1 AATAATATATAAATAATGCCTGTTTGGGAGGGTAACAGTTGAAATTG-CACCCCGAGAAAACCAT * * * 774061 TGTCAACCGACCCAAAGCGGAGGTTGACAATGTTTTTCGAGGGGTGTCAATTTTAACTGTTATCC 65 TGTCAACCGACCCAAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGCCAATTTCAACTGTTATCC * * * 774126 TCCCAAACAGGCACTATTTATTTTGTTATACTGAATGTCTTAATTTTAAAGAAAACATCACTGCT 130 TCCCAAACAGACACCATTTATTTTGCTATACTGAATGTCTTAATTTTAAAGAAAACATCACTGCT * 774191 TTTAGATAGGAATAACGTGAATTC-AAAGGCGAACCGTACGCGCATGATTTTCGCGCATGTAACA 195 TTTAGATAGGAATAACGTGAATTCTAAA-GCGAACCGTACGCGCATAATTTTCGCGCATGTAACA 774255 ATTCGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGT 259 ATTCGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGT 774301 AATA 1 AATA 774305 GGACAGATTA Statistics Matches: 285, Mismatches: 22, Indels: 3 0.92 0.07 0.01 Matches are distributed among these distances: 304 46 0.16 305 239 0.84 ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31 Consensus pattern (304 bp): AATAATATATAAATAATGCCTGTTTGGGAGGGTAACAGTTGAAATTGCACCCCGAGAAAACCATT GTCAACCGACCCAAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGCCAATTTCAACTGTTATCCT CCCAAACAGACACCATTTATTTTGCTATACTGAATGTCTTAATTTTAAAGAAAACATCACTGCTT TTAGATAGGAATAACGTGAATTCTAAAGCGAACCGTACGCGCATAATTTTCGCGCATGTAACAAT TCGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGT Found at i:774388 original size:62 final size:62 Alignment explanation

Indices: 774310--774433 Score: 203 Period size: 62 Copynumber: 2.0 Consensus size: 62 774300 TAATAGGACA * * 774310 GATTATGAACTGCGTCTAAACCAATCATATTTAAGTATTTAACATGAAAGTATAACAAAACG 1 GATTATGAACTACGTCTAAACCAATCAGATTTAAGTATTTAACATGAAAGTATAACAAAACG * * * 774372 GATTATGAACTACGTCTTAACCATTCAGATTTCAGTATTTAACATGAAAGTATAACAAAACG 1 GATTATGAACTACGTCTAAACCAATCAGATTTAAGTATTTAACATGAAAGTATAACAAAACG 774434 TTTTTTCTAG Statistics Matches: 57, Mismatches: 5, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 62 57 1.00 ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30 Consensus pattern (62 bp): GATTATGAACTACGTCTAAACCAATCAGATTTAAGTATTTAACATGAAAGTATAACAAAACG Found at i:776749 original size:17 final size:19 Alignment explanation

Indices: 776712--776749 Score: 53 Period size: 17 Copynumber: 2.1 Consensus size: 19 776702 GGACATGGAG * 776712 CTAAAATATTAACATGGAT 1 CTAAAATATTAACATGCAT 776731 CTAAAATA-T-ACATGCAT 1 CTAAAATATTAACATGCAT 776748 CT 1 CT 776750 TAGTTTTTAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 17 9 0.50 18 1 0.06 19 8 0.44 ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32 Consensus pattern (19 bp): CTAAAATATTAACATGCAT Found at i:780266 original size:14 final size:14 Alignment explanation

Indices: 780247--780276 Score: 51 Period size: 14 Copynumber: 2.1 Consensus size: 14 780237 ATCCCCAAAA * 780247 CTCTCTTCCTCTCT 1 CTCTCTCCCTCTCT 780261 CTCTCTCCCTCTCT 1 CTCTCTCCCTCTCT 780275 CT 1 CT 780277 GGATTTTCTA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47 Consensus pattern (14 bp): CTCTCTCCCTCTCT Found at i:783909 original size:3 final size:3 Alignment explanation

Indices: 783901--783927 Score: 54 Period size: 3 Copynumber: 9.0 Consensus size: 3 783891 ACCATCAGTT 783901 TCA TCA TCA TCA TCA TCA TCA TCA TCA 1 TCA TCA TCA TCA TCA TCA TCA TCA TCA 783928 GTTTTCGCTG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 24 1.00 ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33 Consensus pattern (3 bp): TCA Found at i:784588 original size:2 final size:2 Alignment explanation

Indices: 784581--784637 Score: 114 Period size: 2 Copynumber: 28.5 Consensus size: 2 784571 TTTATATTCG 784581 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 784623 GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA G 784638 NNNNNNNNNN Statistics Matches: 55, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 55 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:790568 original size:2 final size:2 Alignment explanation

Indices: 790561--790627 Score: 134 Period size: 2 Copynumber: 33.5 Consensus size: 2 790551 ATATTCTTCG 790561 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 790603 GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA G 790628 TATAAACTCA Statistics Matches: 65, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 65 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:794497 original size:59 final size:60 Alignment explanation

Indices: 794422--794581 Score: 207 Period size: 59 Copynumber: 2.6 Consensus size: 60 794412 GCAGGGAGGA 794422 ACAACTCACTAAAGGATTGCTGTAAACAAAAC-ACCAGCTGTAAATGGGCTGTTATACAT 1 ACAACTCACTAAAGGATTGCTGTAAACAAAACAACCAGCTGTAAATGGGCTGTTATACAT * * 794481 ACAACTCATTAAAGGATTGCTGTAAACAAAACAACCAGCTGTAAATGTGCTGTTAATA-AT 1 ACAACTCACTAAAGGATTGCTGTAAACAAAACAACCAGCTGTAAATGGGCTGTT-ATACAT * * * * * * 794541 ATAATTCACGACAATGATTGCTGTAAAAAAAAACAAACAGC 1 ACAACTCACTA-AAGGATTGCTGT-AAACAAAACAACCAGC 794582 AAGATGTGAA Statistics Matches: 88, Mismatches: 9, Indels: 5 0.86 0.09 0.05 Matches are distributed among these distances: 59 31 0.35 60 29 0.33 61 14 0.16 62 14 0.16 ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24 Consensus pattern (60 bp): ACAACTCACTAAAGGATTGCTGTAAACAAAACAACCAGCTGTAAATGGGCTGTTATACAT Found at i:794515 original size:30 final size:30 Alignment explanation

Indices: 794421--794515 Score: 76 Period size: 30 Copynumber: 3.2 Consensus size: 30 794411 GGCAGGGAGG * 794421 AACAACTCACTAAAGGATTGCTGTAAACAA 1 AACAACTCATTAAAGGATTGCTGTAAACAA * 794451 AAC-AC-CAGCTGTAAATGG---GCTGTTATAC-A 1 AACAACTCA--T-TAAA-GGATTGCTG-TAAACAA * 794480 TACAACTCATTAAAGGATTGCTGTAAACAA 1 AACAACTCATTAAAGGATTGCTGTAAACAA 794510 AACAAC 1 AACAAC 794516 CAGCTGTAAA Statistics Matches: 49, Mismatches: 5, Indels: 22 0.64 0.07 0.29 Matches are distributed among these distances: 27 2 0.04 28 6 0.12 29 14 0.29 30 19 0.39 31 6 0.12 32 2 0.04 ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22 Consensus pattern (30 bp): AACAACTCATTAAAGGATTGCTGTAAACAA Found at i:794532 original size:30 final size:30 Alignment explanation

Indices: 794439--794533 Score: 83 Period size: 30 Copynumber: 3.2 Consensus size: 30 794429 ACTAAAGGAT 794439 TGCTGTAAACAAAAC-ACCAGCTGTAAATG 1 TGCTGTAAACAAAACAACCAGCTGTAAATG * * * * 794468 GGCTGTTATAC-ATACAACTCA--T-TAAAGG 1 TGCTG-TAAACAAAACAAC-CAGCTGTAAATG 794496 ATTGCTGTAAACAAAACAACCAGCTGTAAATG 1 --TGCTGTAAACAAAACAACCAGCTGTAAATG 794528 TGCTGT 1 TGCTGT 794534 TAATAATATA Statistics Matches: 49, Mismatches: 8, Indels: 17 0.66 0.11 0.23 Matches are distributed among these distances: 28 5 0.10 29 14 0.29 30 22 0.45 31 3 0.06 32 5 0.10 ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25 Consensus pattern (30 bp): TGCTGTAAACAAAACAACCAGCTGTAAATG Found at i:796216 original size:2 final size:2 Alignment explanation

Indices: 796209--796249 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 796199 TCTATTTGTC 796209 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 796250 TTTTCATGCA Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:798771 original size:2 final size:2 Alignment explanation

Indices: 798764--798814 Score: 88 Period size: 2 Copynumber: 26.5 Consensus size: 2 798754 GATTAGTTGA 798764 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 798805 -G AG AG AG AG A 1 AG AG AG AG AG A 798815 AGGGGGGTAA Statistics Matches: 47, Mismatches: 0, Indels: 4 0.92 0.00 0.08 Matches are distributed among these distances: 1 2 0.04 2 45 0.96 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:799712 original size:3 final size:3 Alignment explanation

Indices: 799691--799787 Score: 88 Period size: 3 Copynumber: 32.3 Consensus size: 3 799681 GACGATGAAT * * 799691 ATG ATG TTG ATG ATA ATG ATG ATG ACT- ATG ATG ATG ATG ATG ATG 1 ATG ATG ATG ATG ATG ATG ATG ATG A-TG ATG ATG ATG ATG ATG ATG * * * ** * * * 799736 ACG ACG AAG AAA ATA ATA ATG ATG ATG ATG ATG ATG ATT ATG ATG ATG 1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG 799784 ATG A 1 ATG A 799788 AACTAAATAA Statistics Matches: 81, Mismatches: 11, Indels: 4 0.84 0.11 0.04 Matches are distributed among these distances: 2 1 0.01 3 79 0.98 4 1 0.01 ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31 Consensus pattern (3 bp): ATG Found at i:801169 original size:20 final size:21 Alignment explanation

Indices: 801139--801177 Score: 71 Period size: 20 Copynumber: 1.9 Consensus size: 21 801129 TAAAAACTTT 801139 TTTTGAAAGATTTACCTGTAA 1 TTTTGAAAGATTTACCTGTAA 801160 TTTT-AAAGATTTACCTGT 1 TTTTGAAAGATTTACCTGT 801178 CGATAATGTT Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 20 14 0.78 21 4 0.22 ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46 Consensus pattern (21 bp): TTTTGAAAGATTTACCTGTAA Found at i:815133 original size:2 final size:2 Alignment explanation

Indices: 815120--815153 Score: 50 Period size: 2 Copynumber: 17.0 Consensus size: 2 815110 ACTTTATTCT * * 815120 AG AG AG AA AG AG AG AG AG AA AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 815154 TGTGTTTGTT Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00 Consensus pattern (2 bp): AG Found at i:815137 original size:12 final size:12 Alignment explanation

Indices: 815120--815150 Score: 62 Period size: 12 Copynumber: 2.6 Consensus size: 12 815110 ACTTTATTCT 815120 AGAGAGAAAGAG 1 AGAGAGAAAGAG 815132 AGAGAGAAAGAG 1 AGAGAGAAAGAG 815144 AGAGAGA 1 AGAGAGA 815151 GAGTGTGTTT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 19 1.00 ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00 Consensus pattern (12 bp): AGAGAGAAAGAG Found at i:815158 original size:2 final size:2 Alignment explanation

Indices: 815153--815196 Score: 70 Period size: 2 Copynumber: 22.0 Consensus size: 2 815143 GAGAGAGAGA * * 815153 GT GT GT TT GT TT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT 1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT 815195 GT 1 GT 815197 ACTTCTAAAA Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55 Consensus pattern (2 bp): GT Found at i:816983 original size:11 final size:11 Alignment explanation

Indices: 816945--816988 Score: 52 Period size: 11 Copynumber: 4.0 Consensus size: 11 816935 GGTCCACTCG * 816945 GGGTTCACTTT 1 GGGTTTACTTT * 816956 GGGTTTACTGT 1 GGGTTTACTTT 816967 GGGTTTACTTT 1 GGGTTTACTTT * * 816978 GAGTTTCCTTT 1 GGGTTTACTTT 816989 TGAGAATTGC Statistics Matches: 28, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 11 28 1.00 ACGTcount: A:0.09, C:0.14, G:0.27, T:0.50 Consensus pattern (11 bp): GGGTTTACTTT Found at i:821249 original size:66 final size:66 Alignment explanation

Indices: 821143--821275 Score: 248 Period size: 66 Copynumber: 2.0 Consensus size: 66 821133 ATATATTTGC 821143 TACACTAAAAATAATTTAAATGAACATTTAAGCTAGAACATAATAGTTGATTAACAGATCAGAAA 1 TACACTAAAAATAATTTAAATGAACATTTAAGCTAGAACATAATAGTTGATTAACAGATCAGAAA 821208 A 66 A * * 821209 TACACTAAAAATAATTTTAATGAACATTTAAGTTAGAACATAATAGTTGATTAACAGATCAGAAA 1 TACACTAAAAATAATTTAAATGAACATTTAAGCTAGAACATAATAGTTGATTAACAGATCAGAAA 821274 A 66 A 821275 T 1 T 821276 TGATTGAAAA Statistics Matches: 65, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 66 65 1.00 ACGTcount: A:0.50, C:0.10, G:0.11, T:0.29 Consensus pattern (66 bp): TACACTAAAAATAATTTAAATGAACATTTAAGCTAGAACATAATAGTTGATTAACAGATCAGAAA A Found at i:830189 original size:8 final size:8 Alignment explanation

Indices: 830176--830267 Score: 94 Period size: 8 Copynumber: 11.5 Consensus size: 8 830166 TTTCCTGTGC * 830176 GTCCGTCA 1 GTCCGTCT 830184 GTCCGTCT 1 GTCCGTCT * 830192 GTCTGTCT 1 GTCCGTCT * 830200 GTCCGCCT 1 GTCCGTCT 830208 GTCCGTCT 1 GTCCGTCT * 830216 GTCCGTCC 1 GTCCGTCT 830224 GTCCGTCT 1 GTCCGTCT * 830232 GTCTGTCT 1 GTCCGTCT * * 830240 GGCTGTCT 1 GTCCGTCT * * 830248 GTCTGTCC 1 GTCCGTCT * 830256 GTCTGTCT 1 GTCCGTCT 830264 GTCC 1 GTCC 830268 CACTTCAGTT Statistics Matches: 71, Mismatches: 13, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 8 71 1.00 ACGTcount: A:0.01, C:0.36, G:0.26, T:0.37 Consensus pattern (8 bp): GTCCGTCT Found at i:830195 original size:4 final size:4 Alignment explanation

Indices: 830188--830266 Score: 86 Period size: 4 Copynumber: 19.8 Consensus size: 4 830178 CCGTCAGTCC * * * * * * 830188 GTCT GTCT GTCT GTCC GCCT GTCC GTCT GTCC GTCC GTCC GTCT GTCT 1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT * * 830236 GTCT GGCT GTCT GTCT GTCC GTCT GTCT GTC 1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTC 830267 CCACTTCAGT Statistics Matches: 63, Mismatches: 12, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 4 63 1.00 ACGTcount: A:0.00, C:0.34, G:0.27, T:0.39 Consensus pattern (4 bp): GTCT Found at i:831779 original size:21 final size:21 Alignment explanation

Indices: 831753--831796 Score: 70 Period size: 21 Copynumber: 2.1 Consensus size: 21 831743 TTTTAGATTC 831753 GCACGAGCTCTCGCATACGTT 1 GCACGAGCTCTCGCATACGTT * * 831774 GCACGAGCTCTCGGATTCGTT 1 GCACGAGCTCTCGCATACGTT 831795 GC 1 GC 831797 GTTTTAGTGC Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 21 21 1.00 ACGTcount: A:0.16, C:0.32, G:0.27, T:0.25 Consensus pattern (21 bp): GCACGAGCTCTCGCATACGTT Found at i:834574 original size:2 final size:2 Alignment explanation

Indices: 834567--834591 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 834557 TTCTACAAAT 834567 GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA G 834592 TTTTTTTTAG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:841362 original size:2 final size:2 Alignment explanation

Indices: 841355--841397 Score: 77 Period size: 2 Copynumber: 21.5 Consensus size: 2 841345 NNNNNNNNNN * 841355 GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 841397 G 1 G 841398 GGGGGGGGAA Statistics Matches: 39, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): GA Found at i:846577 original size:135 final size:134 Alignment explanation

Indices: 846299--846583 Score: 321 Period size: 134 Copynumber: 2.1 Consensus size: 134 846289 TGACCCCTAA * * * * * * 846299 ACCATATATATTCATGTTTCTGATATCAAGGGGCATCAAATGTTTTGTAGGTCATGAGCCCTGTG 1 ACCATATATATTCTTGTTCCTGATATCAAGGGGCATCAAACGGTATGTAGGTCATGAGCCCCGTG * * * * * 846364 GGTGGTCCTGATCCCCTCAAACAGCAAGTCCCTTAATATCTTAAAATCAGTTGAGATCCCCACCC 66 GGTGGTCATGACCCCCTCAAACAGCAAGTCACTGAATATCTGAAAATCAGTTGAGATCCCCACCC 846429 TTAC 131 TTAC * 846433 ACCATATATATTCTTGTTCCTTG-TGTCAAGGGGCATCAAACGGTATGTAGGTCATG-GACCCCG 1 ACCATATATATTCTTGTTCC-TGATATCAAGGGGCATCAAACGGTATGTAGGTCATGAG-CCCCG * * * * 846496 -GGGATGGTCATGACCCCCCTCGAACAGGAAGTGCAC-GAATATCTCGAAAA-CGGTTGAGATTC 64 TGGG-TGGTCATGA-CCCCCTCAAACAGCAAGT-CACTGAATATCT-GAAAATCAGTTGAGATCC 846558 CCACCCCTT-C 125 CCA-CCCTTAC 846568 ACCATATATATTCTTG 1 ACCATATATATTCTTG 846584 ATCCAAAGGT Statistics Matches: 128, Mismatches: 16, Indels: 13 0.82 0.10 0.08 Matches are distributed among these distances: 133 4 0.03 134 59 0.46 135 54 0.42 136 11 0.09 ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28 Consensus pattern (134 bp): ACCATATATATTCTTGTTCCTGATATCAAGGGGCATCAAACGGTATGTAGGTCATGAGCCCCGTG GGTGGTCATGACCCCCTCAAACAGCAAGTCACTGAATATCTGAAAATCAGTTGAGATCCCCACCC TTAC Found at i:852265 original size:19 final size:19 Alignment explanation

Indices: 852241--852293 Score: 70 Period size: 19 Copynumber: 2.8 Consensus size: 19 852231 GGTGTGGCAG * * 852241 ATCACGTAAATCACGCGAA 1 ATCACGTTAATCACGCCAA ** 852260 ATCACGTTAATCATACCAA 1 ATCACGTTAATCACGCCAA 852279 ATCACGTTAATCACG 1 ATCACGTTAATCACG 852294 GTATTGCTTC Statistics Matches: 28, Mismatches: 6, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 19 28 1.00 ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23 Consensus pattern (19 bp): ATCACGTTAATCACGCCAA Found at i:855003 original size:22 final size:22 Alignment explanation

Indices: 854979--855097 Score: 150 Period size: 22 Copynumber: 5.4 Consensus size: 22 854969 TACTTAACGA * * * 854979 TTACTTAAAGGTGACGGAAATA 1 TTACTTAAATGTGACTGAAATG * 855001 TTACTGAAATGTGACTGAAATG 1 TTACTTAAATGTGACTGAAATG * * 855023 TTACTGAAATGTGACTGAAAGG 1 TTACTTAAATGTGACTGAAATG * 855045 TTACTTAAATGTGACTGAAAGG 1 TTACTTAAATGTGACTGAAATG * 855067 TTACTTAAATGTGACT-TAATGG 1 TTACTTAAATGTGACTGAAAT-G 855089 TTACTTAAA 1 TTACTTAAA 855098 GGTAACGGAA Statistics Matches: 88, Mismatches: 8, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 21 2 0.02 22 86 0.98 ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33 Consensus pattern (22 bp): TTACTTAAATGTGACTGAAATG Found at i:855085 original size:11 final size:11 Alignment explanation

Indices: 854989--855082 Score: 98 Period size: 11 Copynumber: 8.5 Consensus size: 11 854979 TTACTTAAAG * 854989 GTGACGGAAAT 1 GTGACTGAAAT * * 855000 ATTACTGAAAT 1 GTGACTGAAAT 855011 GTGACTGAAAT 1 GTGACTGAAAT * 855022 GTTACTGAAAT 1 GTGACTGAAAT * 855033 GTGACTGAAAG 1 GTGACTGAAAT * * 855044 GTTACTTAAAT 1 GTGACTGAAAT * 855055 GTGACTGAAAG 1 GTGACTGAAAT * * 855066 GTTACTTAAAT 1 GTGACTGAAAT 855077 GTGACT 1 GTGACT 855083 TAATGGTTAC Statistics Matches: 65, Mismatches: 18, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 11 65 1.00 ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31 Consensus pattern (11 bp): GTGACTGAAAT Found at i:866349 original size:2 final size:2 Alignment explanation

Indices: 866342--866425 Score: 159 Period size: 2 Copynumber: 42.0 Consensus size: 2 866332 TATGTTGACA * 866342 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 866384 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 866426 ATTGTTTACT Statistics Matches: 80, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 2 80 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:867984 original size:4 final size:4 Alignment explanation

Indices: 867977--868071 Score: 79 Period size: 4 Copynumber: 24.2 Consensus size: 4 867967 ACTCTCTCTT * * * * * * * * 867977 TCTG TCTG TCTG TCCG TCCG TCCG TCCG TCCG TCCG TCTG TCCG TCCG 1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG * 868025 T-TCG TCCG TCTG TCTG TCTG TCTG TCTG --TG TCTG TCTG TCTG TCTG 1 TCT-G TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG 868071 T 1 T 868072 GTGTGTGTGT Statistics Matches: 81, Mismatches: 6, Indels: 8 0.85 0.06 0.08 Matches are distributed among these distances: 2 2 0.02 4 79 0.98 ACGTcount: A:0.00, C:0.34, G:0.25, T:0.41 Consensus pattern (4 bp): TCTG Found at i:868047 original size:12 final size:12 Alignment explanation

Indices: 867977--868071 Score: 88 Period size: 12 Copynumber: 8.1 Consensus size: 12 867967 ACTCTCTCTT * 867977 TCTGTCTGTCTG 1 TCTGTCCGTCTG * * 867989 TCCGTCCGTCCG 1 TCTGTCCGTCTG * * 868001 TCCGTCCGTCCG 1 TCTGTCCGTCTG * 868013 TCTGTCCGTCCG 1 TCTGTCCGTCTG 868025 T-TCGTCCGTCTG 1 TCT-GTCCGTCTG * 868037 TCTGTCTGTCTG 1 TCTGTCCGTCTG 868049 TCTGT--GTCTG 1 TCTGTCCGTCTG * 868059 TCTGTCTGTCTG 1 TCTGTCCGTCTG 868071 T 1 T 868072 GTGTGTGTGT Statistics Matches: 73, Mismatches: 6, Indels: 8 0.84 0.07 0.09 Matches are distributed among these distances: 10 10 0.14 11 1 0.01 12 61 0.84 13 1 0.01 ACGTcount: A:0.00, C:0.34, G:0.25, T:0.41 Consensus pattern (12 bp): TCTGTCCGTCTG Found at i:868058 original size:14 final size:14 Alignment explanation

Indices: 868039--868067 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 868029 TCCGTCTGTC 868039 TGTCTGTCTGTCTG 1 TGTCTGTCTGTCTG 868053 TGTCTGTCTGTCTG 1 TGTCTGTCTGTCTG 868067 T 1 T 868068 CTGTGTGTGT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.00, C:0.21, G:0.28, T:0.52 Consensus pattern (14 bp): TGTCTGTCTGTCTG Found at i:868058 original size:18 final size:18 Alignment explanation

Indices: 868035--868083 Score: 80 Period size: 18 Copynumber: 2.7 Consensus size: 18 868025 TTCGTCCGTC 868035 TGTCTGTCTGTCTGTCTG 1 TGTCTGTCTGTCTGTCTG 868053 TGTCTGTCTGTCTGTCTG 1 TGTCTGTCTGTCTGTCTG * * 868071 TGTGTGTGTGTCT 1 TGTCTGTCTGTCT 868084 CTCTCTCTCT Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 29 1.00 ACGTcount: A:0.00, C:0.18, G:0.31, T:0.51 Consensus pattern (18 bp): TGTCTGTCTGTCTGTCTG Found at i:868086 original size:2 final size:2 Alignment explanation

Indices: 868081--868112 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 868071 TGTGTGTGTG 868081 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 868113 ACTCAGAAAA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Done.