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 5 of 5

Found at i:1331581 original size:58 final size:58

Alignment explanation

Indices: 1331508--1331644 Score: 256 Period size: 58 Copynumber: 2.4 Consensus size: 58 1331498 CTTGGTGAGA 1331508 ACAGTTTCTCTATAGCTTGGTAAGACCACCTAAAATTTATCTATAGCTTGGAGAAAAC 1 ACAGTTTCTCTATAGCTTGGTAAGACCACCTAAAATTTATCTATAGCTTGGAGAAAAC * 1331566 ACAGTTTCTCTATAGCTTGGTAAGACCACCTAAAATTTCTCTATAGCTTGGAGAAAAC 1 ACAGTTTCTCTATAGCTTGGTAAGACCACCTAAAATTTATCTATAGCTTGGAGAAAAC * 1331624 ACAGTTTCTCTATAGTTTGGT 1 ACAGTTTCTCTATAGCTTGGT 1331645 GATAAAACAG Statistics Matches: 77, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 58 77 1.00 ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34 Consensus pattern (58 bp): ACAGTTTCTCTATAGCTTGGTAAGACCACCTAAAATTTATCTATAGCTTGGAGAAAAC Found at i:1331654 original size:27 final size:27 Alignment explanation

Indices: 1331547--1331643 Score: 113 Period size: 27 Copynumber: 3.4 Consensus size: 27 1331537 CTAAAATTTA 1331547 TCTATAGCTTGGAGAAAACACAGTTTC 1 TCTATAGCTTGGAGAAAACACAGTTTC * * * * 1331574 TCTATAGCTTGGTAAGACCACCTAAAATTTC 1 TCTATAGCTTGG--AGA-AAAC-ACAGTTTC 1331605 TCTATAGCTTGGAGAAAACACAGTTTC 1 TCTATAGCTTGGAGAAAACACAGTTTC * 1331632 TCTATAGTTTGG 1 TCTATAGCTTGG 1331644 TGATAAAACA Statistics Matches: 57, Mismatches: 9, Indels: 8 0.77 0.12 0.11 Matches are distributed among these distances: 27 29 0.51 28 2 0.04 29 6 0.11 30 2 0.04 31 18 0.32 ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33 Consensus pattern (27 bp): TCTATAGCTTGGAGAAAACACAGTTTC Found at i:1332482 original size:2 final size:2 Alignment explanation

Indices: 1332475--1332529 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 1332465 AATGAAAGAA 1332475 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 1332517 CT CT CT CT CT CT C 1 CT CT CT CT CT CT C 1332530 ACATGACAAT Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:1335860 original size:2 final size:2 Alignment explanation

Indices: 1335853--1335890 Score: 76 Period size: 2 Copynumber: 19.0 Consensus size: 2 1335843 GCACCTACAG 1335853 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 1335891 CAAGAAGAAA Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1337078 original size:16 final size:16 Alignment explanation

Indices: 1337057--1337091 Score: 61 Period size: 16 Copynumber: 2.2 Consensus size: 16 1337047 TTTATTCATT 1337057 TTTTTTGGTATATATA 1 TTTTTTGGTATATATA * 1337073 TTTTTTTGTATATATA 1 TTTTTTGGTATATATA 1337089 TTT 1 TTT 1337092 ATAGGCACTT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69 Consensus pattern (16 bp): TTTTTTGGTATATATA Found at i:1340767 original size:28 final size:28 Alignment explanation

Indices: 1340732--1340788 Score: 114 Period size: 28 Copynumber: 2.0 Consensus size: 28 1340722 AGAAATACGG 1340732 CTAGGCATGTACTGTGTTTGACCATGCA 1 CTAGGCATGTACTGTGTTTGACCATGCA 1340760 CTAGGCATGTACTGTGTTTGACCATGCA 1 CTAGGCATGTACTGTGTTTGACCATGCA 1340788 C 1 C 1340789 CTACAAATGT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 29 1.00 ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32 Consensus pattern (28 bp): CTAGGCATGTACTGTGTTTGACCATGCA Found at i:1346644 original size:23 final size:24 Alignment explanation

Indices: 1346596--1346645 Score: 59 Period size: 24 Copynumber: 2.1 Consensus size: 24 1346586 TTTAATAACC * 1346596 AAAAAACACCAAAAATCTAATTTA 1 AAAAAACACCAAAAATCTAATATA * 1346620 AAAAAAC-CCAAACAATTTAA-ATA 1 AAAAAACACCAAA-AATCTAATATA 1346643 AAA 1 AAA 1346646 TTTTCATAGT Statistics Matches: 23, Mismatches: 2, Indels: 3 0.82 0.07 0.11 Matches are distributed among these distances: 23 10 0.43 24 13 0.57 ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18 Consensus pattern (24 bp): AAAAAACACCAAAAATCTAATATA Found at i:1350535 original size:24 final size:24 Alignment explanation

Indices: 1350501--1350550 Score: 91 Period size: 24 Copynumber: 2.1 Consensus size: 24 1350491 TTATTAAAGG * 1350501 GATTCCTTATGGAGTGAGCAGTTT 1 GATTCCCTATGGAGTGAGCAGTTT 1350525 GATTCCCTATGGAGTGAGCAGTTT 1 GATTCCCTATGGAGTGAGCAGTTT 1350549 GA 1 GA 1350551 GGGGAATAAA Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34 Consensus pattern (24 bp): GATTCCCTATGGAGTGAGCAGTTT Found at i:1352709 original size:32 final size:32 Alignment explanation

Indices: 1352668--1352761 Score: 152 Period size: 32 Copynumber: 2.9 Consensus size: 32 1352658 TTCAGGCAAA 1352668 GGGGTCATTTTTCTACGTAGAATAATGACCGG 1 GGGGTCATTTTTCTACGTAGAATAATGACCGG ** 1352700 GGGGTCATTTTTCGGCGTAGAATAATGACCGG 1 GGGGTCATTTTTCTACGTAGAATAATGACCGG * * 1352732 GGGGTCATTATTCTACGTAGAAAAATGACC 1 GGGGTCATTTTTCTACGTAGAATAATGACC 1352762 CCCGGTCATT Statistics Matches: 56, Mismatches: 6, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 32 56 1.00 ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29 Consensus pattern (32 bp): GGGGTCATTTTTCTACGTAGAATAATGACCGG Found at i:1352772 original size:31 final size:32 Alignment explanation

Indices: 1352668--1352779 Score: 145 Period size: 32 Copynumber: 3.5 Consensus size: 32 1352658 TTCAGGCAAA * 1352668 GGGGTCATTTTTCTACGTAGAATAATGACCGG 1 GGGGTCATTATTCTACGTAGAATAATGACCGG * ** 1352700 GGGGTCATTTTTCGGCGTAGAATAATGACCGG 1 GGGGTCATTATTCTACGTAGAATAATGACCGG * * 1352732 GGGGTCATTATTCTACGTAGAAAAATGACC-C 1 GGGGTCATTATTCTACGTAGAATAATGACCGG ** 1352763 CCGGTCATTATTCTACG 1 GGGGTCATTATTCTACG 1352780 GGGGTCATTA Statistics Matches: 71, Mismatches: 9, Indels: 1 0.88 0.11 0.01 Matches are distributed among these distances: 31 15 0.21 32 56 0.79 ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29 Consensus pattern (32 bp): GGGGTCATTATTCTACGTAGAATAATGACCGG Found at i:1354520 original size:12 final size:12 Alignment explanation

Indices: 1354503--1354528 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 1354493 ATTTCAGCAG 1354503 CATTATCATCAT 1 CATTATCATCAT 1354515 CATTATCATCAT 1 CATTATCATCAT 1354527 CA 1 CA 1354529 AAGACAATAT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38 Consensus pattern (12 bp): CATTATCATCAT Found at i:1373311 original size:13 final size:13 Alignment explanation

Indices: 1373293--1373318 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 1373283 ATGGGGTTCA 1373293 TATAATTAATAAT 1 TATAATTAATAAT 1373306 TATAATTAATAAT 1 TATAATTAATAAT 1373319 AATCCTATAA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46 Consensus pattern (13 bp): TATAATTAATAAT Found at i:1380130 original size:15 final size:15 Alignment explanation

Indices: 1380092--1380270 Score: 126 Period size: 15 Copynumber: 11.3 Consensus size: 15 1380082 TCATTTCACT ** 1380092 CTACACTACACTACA 1 CTACACTATGCTACA * * * 1380107 CTTCGCTATGCAACA 1 CTACACTATGCTACA 1380122 CTACACTATGCTACA 1 CTACACTATGCTACA * * 1380137 CTGA-ACTACGCTTCA 1 CT-ACACTATGCTACA 1380152 CTACACTATGCTACGCAACA 1 CTACACTATGCT-----ACA 1380172 CTACACTATGCTACGTTA 1 CTACACTATGCTAC---A * * 1380190 CCATACACTTTGCTACG 1 -C-TACACTATGCTACA 1380207 CTACACTATGCTACA 1 CTACACTATGCTACA 1380222 CTACACTATGCTACA 1 CTACACTATGCTACA * * 1380237 CTACGCTACGCTACA 1 CTACACTATGCTACA * ** 1380252 CTACATTACACTACA 1 CTACACTATGCTACA 1380267 CTAC 1 CTAC 1380271 CCTAAATCAC Statistics Matches: 131, Mismatches: 21, Indels: 24 0.74 0.12 0.14 Matches are distributed among these distances: 14 1 0.01 15 100 0.76 16 2 0.02 18 1 0.01 19 1 0.01 20 26 0.20 ACGTcount: A:0.31, C:0.35, G:0.08, T:0.26 Consensus pattern (15 bp): CTACACTATGCTACA Found at i:1380165 original size:20 final size:20 Alignment explanation

Indices: 1380142--1380256 Score: 106 Period size: 20 Copynumber: 5.8 Consensus size: 20 1380132 CTACACTGAA * 1380142 CTACGCTTCACTACACTATG 1 CTACGCTACACTACACTATG * 1380162 CTACGCAACACTACACTATG 1 CTACGCTACACTACACTATG * * 1380182 CTACGTTAC-CATACACTTTG 1 CTACGCTACAC-TACACTATG ** ** 1380202 CTACGCTACACTATGCTACA 1 CTACGCTACACTACACTATG * ** * 1380222 CTACACTATGCTACACTACG 1 CTACGCTACACTACACTATG 1380242 CTACGCTACACTACA 1 CTACGCTACACTACA 1380257 TTACACTACA Statistics Matches: 73, Mismatches: 20, Indels: 4 0.75 0.21 0.04 Matches are distributed among these distances: 19 1 0.01 20 71 0.97 21 1 0.01 ACGTcount: A:0.30, C:0.35, G:0.10, T:0.26 Consensus pattern (20 bp): CTACGCTACACTACACTATG Found at i:1380345 original size:20 final size:20 Alignment explanation

Indices: 1380320--1380368 Score: 62 Period size: 20 Copynumber: 2.5 Consensus size: 20 1380310 TCATTTCACT ** 1380320 CTACACTTCACTATGCTACG 1 CTACACTTCACTAAACTACG * 1380340 CTACACTACACTAAACTACG 1 CTACACTTCACTAAACTACG * 1380360 CTACGCTTC 1 CTACACTTC 1380369 GCTACAATAC Statistics Matches: 24, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 20 24 1.00 ACGTcount: A:0.29, C:0.37, G:0.08, T:0.27 Consensus pattern (20 bp): CTACACTTCACTAAACTACG Found at i:1380373 original size:25 final size:25 Alignment explanation

Indices: 1380329--1380383 Score: 65 Period size: 25 Copynumber: 2.2 Consensus size: 25 1380319 TCTACACTTC * * 1380329 ACTATGCTACGCTACACTACACTAA 1 ACTACGCTACGCTACACTACAATAA * * * 1380354 ACTACGCTACGCTTCGCTACAATAC 1 ACTACGCTACGCTACACTACAATAA 1380379 ACTAC 1 ACTAC 1380384 CCTAAATCAC Statistics Matches: 25, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 25 25 1.00 ACGTcount: A:0.33, C:0.35, G:0.09, T:0.24 Consensus pattern (25 bp): ACTACGCTACGCTACACTACAATAA Found at i:1380405 original size:113 final size:116 Alignment explanation

Indices: 1380202--1380486 Score: 432 Period size: 113 Copynumber: 2.5 Consensus size: 116 1380192 ATACACTTTG * ** 1380202 CTACGCTACACTATGCTACACTACACTATGCTACACTACGCTACGCTACACTACATTACACTACA 1 CTACACTACACTATGCTACACTACACTACACTACACTACGCTACGCTACACTAC--TACACTACA 1380267 CTACCCTAAATCACAATACACAATGTCCTTGAAATACTCTACTTCATTTCACT 64 CTACCCTAAATCACAATACACAATGTCCTTGAAATACTCTACTTCATTTCACT * * * * * 1380320 CTACACTTCACTATGCTACGCTACACTACACTAAACTACGCTACGCTTCGCTAC-A-A-TACACT 1 CTACACTACACTATGCTACACTACACTACACTACACTACGCTACGCTACACTACTACACTACACT 1380382 ACCCTAAATCACAATACACAATGTCCTTGAAATACTCTACTTCATTTCACT 66 ACCCTAAATCACAATACACAATGTCCTTGAAATACTCTACTTCATTTCACT ** * 1380433 CTACACTACACTACACTACACTACACTACACTACACTACACTACGCTACACTAC 1 CTACACTACACTATGCTACACTACACTACACTACACTACGCTACGCTACACTAC 1380487 ACTACATTGC Statistics Matches: 151, Mismatches: 16, Indels: 5 0.88 0.09 0.03 Matches are distributed among these distances: 113 103 0.68 114 1 0.01 115 1 0.01 118 46 0.30 ACGTcount: A:0.34, C:0.34, G:0.05, T:0.27 Consensus pattern (116 bp): CTACACTACACTATGCTACACTACACTACACTACACTACGCTACGCTACACTACTACACTACACT ACCCTAAATCACAATACACAATGTCCTTGAAATACTCTACTTCATTTCACT Found at i:1380441 original size:5 final size:5 Alignment explanation

Indices: 1380433--1380622 Score: 326 Period size: 5 Copynumber: 38.0 Consensus size: 5 1380423 TCATTTCACT * 1380433 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACG CTACA 1 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA * * * * 1380483 CTACA CTACA TTGCA CTACA CTATA CTACA CTACA CTACA CTACA TTACA 1 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA * 1380533 TTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA 1 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA 1380583 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA 1 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA 1380623 AGTCACAATT Statistics Matches: 175, Mismatches: 10, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 5 175 1.00 ACGTcount: A:0.39, C:0.38, G:0.01, T:0.22 Consensus pattern (5 bp): CTACA Found at i:1381773 original size:18 final size:18 Alignment explanation

Indices: 1381746--1381800 Score: 71 Period size: 18 Copynumber: 3.2 Consensus size: 18 1381736 TCTTTCTTTC 1381746 TTTC-TTTTTTTTTGTCT 1 TTTCTTTTTTTTTTGTCT 1381763 TTTCTTTTTTTTTTGGTC- 1 TTTCTTTTTTTTTT-GTCT * 1381781 TTTCTATTTTTTTT-TCT 1 TTTCTTTTTTTTTTGTCT 1381798 TTT 1 TTT 1381801 TCAGTCAAAA Statistics Matches: 34, Mismatches: 1, Indels: 6 0.83 0.02 0.15 Matches are distributed among these distances: 16 2 0.06 17 7 0.21 18 22 0.65 19 3 0.09 ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82 Consensus pattern (18 bp): TTTCTTTTTTTTTTGTCT Found at i:1381774 original size:19 final size:19 Alignment explanation

Indices: 1381740--1381795 Score: 69 Period size: 19 Copynumber: 2.9 Consensus size: 19 1381730 ATCTCTTCTT * * 1381740 TCTTTCTTTCTTTTTTTTTG 1 TCTTTCTAT-TTTTTTTTGG 1381760 TCTTTTCT-TTTTTTTTTGG 1 TC-TTTCTATTTTTTTTTGG 1381779 TCTTTCTATTTTTTTTT 1 TCTTTCTATTTTTTTTT 1381796 CTTTTTCAGT Statistics Matches: 33, Mismatches: 1, Indels: 5 0.85 0.03 0.13 Matches are distributed among these distances: 18 5 0.15 19 20 0.61 20 3 0.09 21 5 0.15 ACGTcount: A:0.02, C:0.12, G:0.05, T:0.80 Consensus pattern (19 bp): TCTTTCTATTTTTTTTTGG Found at i:1381802 original size:18 final size:17 Alignment explanation

Indices: 1381746--1381802 Score: 62 Period size: 17 Copynumber: 3.2 Consensus size: 17 1381736 TCTTTCTTTC 1381746 TTTCTTTTTTTTTGTC-T 1 TTTCTTTTTTTTT-TCTT * * 1381763 TTTCTTTTTTTTTTGGTC 1 TTTCTTTTTTTTTT-CTT 1381781 TTTCTATTTTTTTTTCTT 1 TTTCT-TTTTTTTTTCTT 1381799 TTTC 1 TTTC 1381803 AGTCAAAAGC Statistics Matches: 33, Mismatches: 4, Indels: 5 0.79 0.10 0.12 Matches are distributed among these distances: 16 1 0.03 17 13 0.39 18 10 0.30 19 9 0.27 ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81 Consensus pattern (17 bp): TTTCTTTTTTTTTTCTT Found at i:1382462 original size:126 final size:126 Alignment explanation

Indices: 1382237--1382485 Score: 392 Period size: 126 Copynumber: 2.0 Consensus size: 126 1382227 GATAAACGAG * * * 1382237 TAACTATTAAATATCCGTTGTATTATATTCTAAAACTAAGGTATTTCTTAAAGGAAATTCCAGGT 1 TAACTATCAAATATCCGTTGTAATATATTCTAAAACTAAGGTATTTCTTAAAGGAAATGCCAGGT * * * * 1382302 ATTGTACATGTAATGTATTTGGTTGGTACTAGAAGTCGCCACACGTCATCCATATACTGAA 66 ATTGTACATGTAACGTATTTGATTGGTACTAGAAGTCGCCACAAGTCATCCAAATACTGAA * * 1382363 TAACTATCAAATATCCGTTGTAATATATTTTAGAA-TGAAGGTATTTCTTAAAGGAAATGCCAGG 1 TAACTATCAAATATCCGTTGTAATATATTCTAAAACT-AAGGTATTTCTTAAAGGAAATGCCAGG * 1382427 TATTGTACATGTAACGTATTTGATTGGTATTAGAAGTCGCCACAAGTCATCCAAATACT 65 TATTGTACATGTAACGTATTTGATTGGTACTAGAAGTCGCCACAAGTCATCCAAATACT 1382486 TTTGTAAATA Statistics Matches: 112, Mismatches: 10, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 125 1 0.01 126 111 0.99 ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35 Consensus pattern (126 bp): TAACTATCAAATATCCGTTGTAATATATTCTAAAACTAAGGTATTTCTTAAAGGAAATGCCAGGT ATTGTACATGTAACGTATTTGATTGGTACTAGAAGTCGCCACAAGTCATCCAAATACTGAA Found at i:1382522 original size:37 final size:37 Alignment explanation

Indices: 1382472--1382545 Score: 121 Period size: 37 Copynumber: 2.0 Consensus size: 37 1382462 GTCGCCACAA * * 1382472 GTCATCCAAATACTTTTGTAAATATGATACTGTTTAC 1 GTCATCCAAATACTTTTGTAAATATCAGACTGTTTAC * 1382509 GTCATCCATATACTTTTGTAAATATCAGACTGTTTAC 1 GTCATCCAAATACTTTTGTAAATATCAGACTGTTTAC 1382546 TTTAATTTTT Statistics Matches: 34, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 37 34 1.00 ACGTcount: A:0.31, C:0.18, G:0.11, T:0.41 Consensus pattern (37 bp): GTCATCCAAATACTTTTGTAAATATCAGACTGTTTAC Found at i:1383249 original size:19 final size:19 Alignment explanation

Indices: 1383225--1383263 Score: 69 Period size: 19 Copynumber: 2.1 Consensus size: 19 1383215 CAGAAGAACA 1383225 AATGTAGCTTATTGTGTCC 1 AATGTAGCTTATTGTGTCC * 1383244 AATGTAGCTTGTTGTGTCC 1 AATGTAGCTTATTGTGTCC 1383263 A 1 A 1383264 TCCTATCAAT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41 Consensus pattern (19 bp): AATGTAGCTTATTGTGTCC Found at i:1385639 original size:16 final size:16 Alignment explanation

Indices: 1385620--1385651 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 1385610 TGTATGGATG * 1385620 AATGAATGAGTAAATA 1 AATGAATGACTAAATA 1385636 AATGAATGACTAAATA 1 AATGAATGACTAAATA 1385652 CTGAATTATA 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:0.56, C:0.03, G:0.16, T:0.25 Consensus pattern (16 bp): AATGAATGACTAAATA Found at i:1387534 original size:52 final size:50 Alignment explanation

Indices: 1387443--1387542 Score: 150 Period size: 52 Copynumber: 2.0 Consensus size: 50 1387433 CTATTAATAT * 1387443 CCACGTAGACTAAAAATTTCCACGACCATCAAGCACCCCCACCCCCCCCCC 1 CCACGTAGACTAAAAATTTCCACGACCATCAACCACCCCC-CCCCCCCCCC * 1387494 NCCACGTAGACTAAAAATTTCCACGACCATC-ACC-CCCCCCCCCTCCCCC 1 -CCACGTAGACTAAAAATTTCCACGACCATCAACCACCCCCCCCCCCCCCC 1387543 AATAATCGAC Statistics Matches: 46, Mismatches: 2, Indels: 3 0.90 0.04 0.06 Matches are distributed among these distances: 49 9 0.20 50 5 0.11 51 2 0.04 52 30 0.65 ACGTcount: A:0.27, C:0.52, G:0.07, T:0.13 Consensus pattern (50 bp): CCACGTAGACTAAAAATTTCCACGACCATCAACCACCCCCCCCCCCCCCC Found at i:1390970 original size:15 final size:15 Alignment explanation

Indices: 1390950--1390981 Score: 64 Period size: 15 Copynumber: 2.1 Consensus size: 15 1390940 TTTCCTTTTG 1390950 TGCTTCATGCGGTTA 1 TGCTTCATGCGGTTA 1390965 TGCTTCATGCGGTTA 1 TGCTTCATGCGGTTA 1390980 TG 1 TG 1390982 AAGGTTAGAA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 17 1.00 ACGTcount: A:0.12, C:0.19, G:0.28, T:0.41 Consensus pattern (15 bp): TGCTTCATGCGGTTA Found at i:1396721 original size:2 final size:2 Alignment explanation

Indices: 1396714--1396740 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 1396704 CCGAGCCGCA 1396714 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 T 1396741 NNNNNNNNNN Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:1398800 original size:2 final size:2 Alignment explanation

Indices: 1398795--1398842 Score: 96 Period size: 2 Copynumber: 24.0 Consensus size: 2 1398785 AGAAGTATAT 1398795 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 1398837 AG AG AG 1 AG AG AG 1398843 CACACAACAG Statistics Matches: 46, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:1402075 original size:32 final size:32 Alignment explanation

Indices: 1402038--1402099 Score: 115 Period size: 32 Copynumber: 1.9 Consensus size: 32 1402028 AATGCTATTC * 1402038 ATTCTTTAGAATATTCCAAGATGATAAGATCA 1 ATTCTTTAGAATATTCCAAGATGACAAGATCA 1402070 ATTCTTTAGAATATTCCAAGATGACAAGAT 1 ATTCTTTAGAATATTCCAAGATGACAAGAT 1402100 AGATTTTAGA Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 29 1.00 ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34 Consensus pattern (32 bp): ATTCTTTAGAATATTCCAAGATGACAAGATCA Found at i:1407138 original size:4 final size:4 Alignment explanation

Indices: 1407092--1407130 Score: 53 Period size: 4 Copynumber: 10.0 Consensus size: 4 1407082 AAGAGTTGGG * * 1407092 GTTT -TTT GTTT GTTT GTTT GTTT GTTT TTTT TTTT GTTT 1 GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT 1407131 TTTTTTTTAC Statistics Matches: 32, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 3 3 0.09 4 29 0.91 ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82 Consensus pattern (4 bp): GTTT Found at i:1407138 original size:12 final size:12 Alignment explanation

Indices: 1407093--1407134 Score: 66 Period size: 12 Copynumber: 3.5 Consensus size: 12 1407083 AGAGTTGGGG 1407093 TTTTTTGTTTGT 1 TTTTTTGTTTGT * 1407105 TTGTTTGTTTGT 1 TTTTTTGTTTGT * 1407117 TTTTTTTTTTGT 1 TTTTTTGTTTGT 1407129 TTTTTT 1 TTTTTT 1407135 TTTTACAAAA Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 12 27 1.00 ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86 Consensus pattern (12 bp): TTTTTTGTTTGT Found at i:1407162 original size:19 final size:19 Alignment explanation

Indices: 1407138--1407180 Score: 77 Period size: 19 Copynumber: 2.3 Consensus size: 19 1407128 TTTTTTTTTT * 1407138 TACAAAAATTGAACACTTG 1 TACAAAAACTGAACACTTG 1407157 TACAAAAACTGAACACTTG 1 TACAAAAACTGAACACTTG 1407176 TACAA 1 TACAA 1407181 TTTTACAACC Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 19 23 1.00 ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23 Consensus pattern (19 bp): TACAAAAACTGAACACTTG Found at i:1409440 original size:2 final size:2 Alignment explanation

Indices: 1409433--1409471 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 1409423 GACTGGCTCT 1409433 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 1409472 TTATTCAATA 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:1413524 original size:2 final size:2 Alignment explanation

Indices: 1413517--1413572 Score: 103 Period size: 2 Copynumber: 27.5 Consensus size: 2 1413507 GTCAGTTTAT 1413517 GA GA GA GA GA GA GA GA GA GA GA GA GNA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA GA GA GA GA GA 1413560 GA GA GA GA GA GA G 1 GA GA GA GA GA GA G 1413573 TTGTACATGT Statistics Matches: 53, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 2 51 0.96 3 2 0.04 ACGTcount: A:0.48, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1420271 original size:2 final size:2 Alignment explanation

Indices: 1420264--1420300 Score: 67 Period size: 2 Copynumber: 19.0 Consensus size: 2 1420254 AGATAAATAT 1420264 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1420301 TGACCACATG Statistics Matches: 34, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 1 1 0.03 2 33 0.97 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:1424293 original size:2 final size:2 Alignment explanation

Indices: 1424286--1424370 Score: 163 Period size: 2 Copynumber: 43.0 Consensus size: 2 1424276 TAGAATAATA 1424286 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 1424328 CT C- 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 1424369 CT 1 CT 1424371 ACGTGTATGA Statistics Matches: 82, Mismatches: 0, Indels: 2 0.98 0.00 0.02 Matches are distributed among these distances: 1 1 0.01 2 81 0.99 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:1426455 original size:2 final size:2 Alignment explanation

Indices: 1426448--1426479 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 1426438 GGCGTAATAT 1426448 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 1426480 NCTACGACGA 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:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1428783 original size:2 final size:2 Alignment explanation

Indices: 1428776--1428827 Score: 104 Period size: 2 Copynumber: 26.0 Consensus size: 2 1428766 TTGGTGTAAT 1428776 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 1428818 GA GA GA GA GA 1 GA GA GA GA GA 1428828 ATTGTTTTAA Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1431154 original size:21 final size:21 Alignment explanation

Indices: 1431128--1431176 Score: 98 Period size: 21 Copynumber: 2.3 Consensus size: 21 1431118 GCATCGTCCA 1431128 CAAACAATTGTCGTAAAATTG 1 CAAACAATTGTCGTAAAATTG 1431149 CAAACAATTGTCGTAAAATTG 1 CAAACAATTGTCGTAAAATTG 1431170 CAAACAA 1 CAAACAA 1431177 AGGTCGTATT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 28 1.00 ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24 Consensus pattern (21 bp): CAAACAATTGTCGTAAAATTG Found at i:1431182 original size:21 final size:21 Alignment explanation

Indices: 1431137--1431184 Score: 78 Period size: 21 Copynumber: 2.3 Consensus size: 21 1431127 ACAAACAATT ** 1431137 GTCGTAAAATTGCAAACAATT 1 GTCGTAAAATTGCAAACAAAG 1431158 GTCGTAAAATTGCAAACAAAG 1 GTCGTAAAATTGCAAACAAAG 1431179 GTCGTA 1 GTCGTA 1431185 TTTCCGAAGT Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 21 25 1.00 ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25 Consensus pattern (21 bp): GTCGTAAAATTGCAAACAAAG Found at i:1450270 original size:58 final size:58 Alignment explanation

Indices: 1450189--1450304 Score: 160 Period size: 58 Copynumber: 2.0 Consensus size: 58 1450179 AAAATTCTAA * * ** 1450189 TTAGTTTTCTGCACCATTTATTGCAGAGGGTGAAAAATTCTGACCTCACAAATTTTGT 1 TTAGTTTTCCGCACCATTTATTGCAAAAAGTGAAAAATTCTGACCTCACAAATTTTGT * * * * 1450247 TTAGTTTTCCGCACTATTTATTGCAAAAAGTGAGAAATTCTGTCCTCGCAAATTTTGT 1 TTAGTTTTCCGCACCATTTATTGCAAAAAGTGAAAAATTCTGACCTCACAAATTTTGT 1450305 AGCAAACCAA Statistics Matches: 50, Mismatches: 8, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 58 50 1.00 ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39 Consensus pattern (58 bp): TTAGTTTTCCGCACCATTTATTGCAAAAAGTGAAAAATTCTGACCTCACAAATTTTGT Found at i:1459671 original size:191 final size:190 Alignment explanation

Indices: 1459347--1459727 Score: 744 Period size: 191 Copynumber: 2.0 Consensus size: 190 1459337 TTAAGTACCC 1459347 TTTATGTTACGAGCCCCTGATAAGGAAGAAACTTTAATGTATGATTTGATTAATTGTGTACCTTT 1 TTTATGTTACGAGCCCCTGATAAGGAAGAAACTTTAATGTATGATTTGATTAATTGTGTACCTTT 1459412 GTTACGCCGATTGCGCCAATGTTTCCTCCATACGTTGTCGTTGCATGTCCACATCCGACGAAACC 66 GTTACGCCGATTGCGCCAATGTTTCCTCCATACGTTGTCGTTGCATGTCCACATCCGACGAAACC * 1459477 CGCTATCAGACTACAGAACCCCTCAATGGCTATTCCTCGATTAACACTTTGTGCTGGTGG 131 CGCTATCAGACTACAGAACCCCTCAATGGCTATTCCTCGATTAACACTATGTGCTGGTGG 1459537 NTTTATGTTACGAGCCCCTGATAAGGAAGAAACTTTAATGTATGATTTGATTAATTGTGTACCTT 1 -TTTATGTTACGAGCCCCTGATAAGGAAGAAACTTTAATGTATGATTTGATTAATTGTGTACCTT 1459602 TGTTACGCCGATTGCGCCAATGTTTCCTCCATACGTTGTCGTTGCATGTCCACATCCGACGAAAC 65 TGTTACGCCGATTGCGCCAATGTTTCCTCCATACGTTGTCGTTGCATGTCCACATCCGACGAAAC 1459667 CCGCTATCAGACTACAGAACCCCTCAATGGCTATTCCTCGATTAACACTATGTGCTGGTGG 130 CCGCTATCAGACTACAGAACCCCTCAATGGCTATTCCTCGATTAACACTATGTGCTGGTGG 1459728 GGGAGGAAGA Statistics Matches: 189, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 191 189 1.00 ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32 Consensus pattern (190 bp): TTTATGTTACGAGCCCCTGATAAGGAAGAAACTTTAATGTATGATTTGATTAATTGTGTACCTTT GTTACGCCGATTGCGCCAATGTTTCCTCCATACGTTGTCGTTGCATGTCCACATCCGACGAAACC CGCTATCAGACTACAGAACCCCTCAATGGCTATTCCTCGATTAACACTATGTGCTGGTGG Found at i:1461508 original size:2 final size:2 Alignment explanation

Indices: 1461501--1461549 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 1461491 TGTTGTTAAA 1461501 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 1461543 AG AG AG A 1 AG AG AG A 1461550 TTTATTTTTA Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1463966 original size:2 final size:2 Alignment explanation

Indices: 1463959--1464024 Score: 132 Period size: 2 Copynumber: 33.0 Consensus size: 2 1463949 AAGCATGAAT 1463959 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 1464001 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 1464025 TTTTCAGTCT Statistics Matches: 64, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 64 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1472942 original size:250 final size:244 Alignment explanation

Indices: 1472501--1473049 Score: 752 Period size: 250 Copynumber: 2.2 Consensus size: 244 1472491 ATCAACACCA * * 1472501 GCATAGAGAGAACCAGACAAACCAGATACTGTAATGTAAC-A-AAAACATTATTACAAATGGCAT 1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATGGCAT * ** * * 1472564 AAAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAG 66 AAAGAGAACCAGACAAACAAGGTAGTCTAACATAACAACAAAACATTATTACAAATGACAAAGAG * * * * 1472629 AGAATCAGACAAACACGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGAA 131 AGAACCAGACAAACACGGTACTGTAATGTAACAACAAAACATTATAACAAATGGCAAAGAGAGAA 1472694 CCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATGGTA-A-ATG 196 CCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTAT--TACATATG * 1472743 GCATAGAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCAT 1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATGGCAT * * * 1472808 AGAGAGTACCAGACAAACAAGGTACCAGTACTATTACATAACAACGAAACATTATTACAAATGAC 66 AAAGAGAACCAGACAAACAAGGT---AGT-CTA--ACATAACAACAAAACATTATTACAAATGAC 1472873 AAAGAGAGAACCAGACAAAC-CAGGTACTGTAATGTAACAACAAAACATTATAACAAA-GGACAA 125 AAAGAGAGAACCAGACAAACAC-GGTACTGTAATGTAACAACAAAACATTATAACAAATGG-CAA * * * * 1472936 AGAGAGAACCAGACAACCAATGTATTGTAATGTAACAACCAAACATTATTACATATG 188 AGAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACATATG * * * 1472993 ACATAGAGAGAACCAGACAAACAAGG-ATCTGTAATATAACAACCAAACATTATTACA 1 GCATAGAGAGAACCAGACAAACAAGGTA-CTGTAATGTAACAACAAAACATTATTACA 1473050 TTGTACAACC Statistics Matches: 271, Mismatches: 23, Indels: 18 0.87 0.07 0.06 Matches are distributed among these distances: 242 37 0.14 243 1 0.00 244 43 0.16 247 3 0.01 248 4 0.01 249 5 0.02 250 178 0.66 ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18 Consensus pattern (244 bp): GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATGGCAT AAAGAGAACCAGACAAACAAGGTAGTCTAACATAACAACAAAACATTATTACAAATGACAAAGAG AGAACCAGACAAACACGGTACTGTAATGTAACAACAAAACATTATAACAAATGGCAAAGAGAGAA CCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACATATG Found at i:1472944 original size:189 final size:183 Alignment explanation

Indices: 1472505--1473049 Score: 733 Period size: 189 Copynumber: 3.0 Consensus size: 183 1472495 ACACCAGCAT * * 1472505 AGAGAGAACCAGACAAACCAGATACTGTAATGTAAC-A-AAAACATTATTACAAATGGCATAA-A 1 AGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAATGGCA-AAGA 1472567 GAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGA 65 GAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGA * * * ** * * 1472632 ATCAGACAAACACGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCAT 130 ACCAGACAAACAAGGTAGTCTAACATAACAACAAAACATTATTACAAATGACAA * * *** * 1472686 AGAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATGGTAAATGGCATAGAG 1 AGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAATGGCAAAGAG * 1472751 AGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGTA 66 AGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGAA * 1472816 CCAGACAAACAAGGTACCAGTACTATTACATAACAACGAAACATTATTACAAATGACAA 131 CCAGACAAACAAGGT---AGT-CTA--ACATAACAACAAAACATTATTACAAATGACAA 1472875 AGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAA-GGACAAAGA 1 AGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAATGG-CAAAGA * * * * * * 1472939 GAGAACCAGACAACCAATGTATTGTAATGTAACAACCAAACATTATTACATATGACATAGAGAGA 65 GAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGA * * 1473004 ACCAGACAAACAAGG-A-TCTGTAATATAACAACCAAACATTATTACA 130 ACCAGACAAACAAGGTAGTC--TAACATAACAACAAAACATTATTACA 1473050 TTGTACAACC Statistics Matches: 321, Mismatches: 31, Indels: 22 0.86 0.08 0.06 Matches are distributed among these distances: 181 33 0.10 182 2 0.01 183 120 0.37 184 1 0.00 185 3 0.01 186 3 0.01 187 2 0.01 188 2 0.01 189 155 0.48 ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18 Consensus pattern (183 bp): AGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAATGGCAAAGAG AGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGAA CCAGACAAACAAGGTAGTCTAACATAACAACAAAACATTATTACAAATGACAA Found at i:1473050 original size:61 final size:61 Alignment explanation

Indices: 1472501--1473049 Score: 737 Period size: 61 Copynumber: 8.9 Consensus size: 61 1472491 ATCAACACCA * * 1472501 GCATAGAGAGAACCAGACAAACCAGATACTGTAATGTAAC-A-AAAACATTATTACAAATG 1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG * * 1472560 GCATAAAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATG 1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG * * * 1472621 GCATAGAGAGAATCAGACAAACACGGTAGTGTAATGTAACAACAAAACATTATTACAAATG 1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG * *** 1472682 GCATAGAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATGGTAAATG 1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG * 1472743 GCATAGAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATG 1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG * * * * 1472804 GCATAGAGAGTACCAGACAAACAAGGTACCAGTACTATTACATAACAACGAAACATTATTACAAA 1 GCATAGAGAGAACCAGACAAACAAGGTA-CTGTA--A-T--GTAACAACAAAACATTATTACAAA 1472869 TG 60 TG * * * * 1472871 ACAAAGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAA-G 1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG * * * * * * 1472931 GACAAAGAGAGAACCAGACAACCAATGTATTGTAATGTAACAACCAAACATTATTACATATG 1 G-CATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG * * * 1472993 ACATAGAGAGAACCAGACAAACAAGG-ATCTGTAATATAACAACCAAACATTATTACA 1 GCATAGAGAGAACCAGACAAACAAGGTA-CTGTAATGTAACAACAAAACATTATTACA 1473050 TTGTACAACC Statistics Matches: 437, Mismatches: 42, Indels: 20 0.88 0.08 0.04 Matches are distributed among these distances: 59 36 0.08 60 3 0.01 61 338 0.77 62 4 0.01 63 1 0.00 64 2 0.00 65 1 0.00 66 4 0.01 67 48 0.11 ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18 Consensus pattern (61 bp): GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG Found at i:1477935 original size:10 final size:9 Alignment explanation

Indices: 1477915--1477939 Score: 50 Period size: 9 Copynumber: 2.8 Consensus size: 9 1477905 ACTTCCATAC 1477915 AAAAAACAA 1 AAAAAACAA 1477924 AAAAAACAA 1 AAAAAACAA 1477933 AAAAAAC 1 AAAAAAC 1477940 TAACGCCACC Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 16 1.00 ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00 Consensus pattern (9 bp): AAAAAACAA Found at i:1487662 original size:20 final size:21 Alignment explanation

Indices: 1487637--1487680 Score: 63 Period size: 20 Copynumber: 2.1 Consensus size: 21 1487627 TCTGATATTA 1487637 AATAAAATTTGC-TTCCCAAC 1 AATAAAATTTGCATTCCCAAC * * 1487657 AATAAAATTTTCATTGCCAAC 1 AATAAAATTTGCATTCCCAAC 1487678 AAT 1 AAT 1487681 GCAGCTAGTT Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 20 11 0.52 21 10 0.48 ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32 Consensus pattern (21 bp): AATAAAATTTGCATTCCCAAC Found at i:1494192 original size:48 final size:48 Alignment explanation

Indices: 1494129--1494230 Score: 161 Period size: 48 Copynumber: 2.1 Consensus size: 48 1494119 ATTTTTACAG 1494129 CTTTGAAATTTTTATGAAGTGTTAAGCT-AAAACAAAAAGACATTTGCT 1 CTTTGAAATTTTTATGAAGTGTTAAGCTAAAAACAAAAA-ACATTTGCT 1494177 CTTTGAAATTTTTATGAAGTGTTAAGCTAAAAAAAACAAAAAACATTTGCT 1 CTTTGAAATTTTTATGAAGTGTTAAGCT---AAAAACAAAAAACATTTGCT 1494228 CTT 1 CTT 1494231 ATAAACAAGA Statistics Matches: 50, Mismatches: 0, Indels: 5 0.91 0.00 0.09 Matches are distributed among these distances: 48 28 0.56 51 12 0.24 52 10 0.20 ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35 Consensus pattern (48 bp): CTTTGAAATTTTTATGAAGTGTTAAGCTAAAAACAAAAAACATTTGCT Found at i:1500063 original size:24 final size:23 Alignment explanation

Indices: 1500031--1500079 Score: 64 Period size: 23 Copynumber: 2.1 Consensus size: 23 1500021 AGAAAAGAGA 1500031 AATTGACAAAAATTATTAAAA-TTT 1 AATTGAC-AAAATT-TTAAAAGTTT * 1500055 AATTTACAAAATTTTAAAAGTTT 1 AATTGACAAAATTTTAAAAGTTT 1500078 AA 1 AA 1500080 CAAATTTACA Statistics Matches: 23, Mismatches: 1, Indels: 3 0.85 0.04 0.11 Matches are distributed among these distances: 22 6 0.26 23 11 0.48 24 6 0.26 ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39 Consensus pattern (23 bp): AATTGACAAAATTTTAAAAGTTT Found at i:1504908 original size:42 final size:43 Alignment explanation

Indices: 1504849--1504930 Score: 121 Period size: 42 Copynumber: 1.9 Consensus size: 43 1504839 ACTATAATAA * 1504849 TTGTAGTTCCATCAATAATTGA-GATGCGTAAGAGAATATCTT 1 TTGTAGTTCCATCAATAATTGATGATACGTAAGAGAATATCTT * * * 1504891 TTGTAGTTCCGTCAATAATTGATGATATGTAGGAGAATAT 1 TTGTAGTTCCATCAATAATTGATGATACGTAAGAGAATAT 1504931 TTATAATAGT Statistics Matches: 35, Mismatches: 4, Indels: 1 0.88 0.10 0.03 Matches are distributed among these distances: 42 21 0.60 43 14 0.40 ACGTcount: A:0.33, C:0.10, G:0.21, T:0.37 Consensus pattern (43 bp): TTGTAGTTCCATCAATAATTGATGATACGTAAGAGAATATCTT Found at i:1504981 original size:45 final size:45 Alignment explanation

Indices: 1504845--1505080 Score: 212 Period size: 46 Copynumber: 5.3 Consensus size: 45 1504835 AATAACTATA * * ** * 1504845 ATAATTGTAGTTCCATCAATAATTGAGATGCGTAAGAGAATATCT 1 ATAATTGTAGTTCCATCAATAATCGGGATATGTAGGAGAATATCT * * * * 1504890 -T--TTGTAGTTCCGTCAATAATTGATGATATGTAGGAGAATATTT 1 ATAATTGTAGTTCCATCAATAATCG-GGATATGTAGGAGAATATCT * * * 1504933 ATAATAGTAGTTCCTTCAGTAATCAGGGATAT-TAGGAGAATATCT 1 ATAATTGTAGTTCCATCAATAATC-GGGATATGTAGGAGAATATCT * * * * * 1504978 ATAATTGTATTTCCGTCAATGATCGGGAATGTGTTGGAGAATATCT 1 ATAATTGTAGTTCCATCAATAATCGGG-ATATGTAGGAGAATATCT * * * 1505024 ATAATTGTAGTTCCATCAATAATCGTGGATATGTGGGAAAATATAT 1 ATAATTGTAGTTCCATCAATAATCG-GGATATGTAGGAGAATATCT * 1505070 AT-TTTGTAGTT 1 ATAATTGTAGTT 1505081 TCATTGACAT Statistics Matches: 156, Mismatches: 27, Indels: 16 0.78 0.14 0.08 Matches are distributed among these distances: 42 20 0.13 43 15 0.10 44 5 0.03 45 42 0.27 46 71 0.46 47 3 0.02 ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37 Consensus pattern (45 bp): ATAATTGTAGTTCCATCAATAATCGGGATATGTAGGAGAATATCT Found at i:1504986 original size:91 final size:88 Alignment explanation

Indices: 1504827--1505055 Score: 214 Period size: 91 Copynumber: 2.5 Consensus size: 88 1504817 CTAACGGGTT * ** * 1504827 TGTAGGAGAATAACTATAATAATTGTAGTTCCATCAATAAT--TGAGATGCGTAAGAGAATATCT 1 TGTAGGAGAATATCTATAAT-A--GTAGTTCCATCAATAATCGTG-GAT-ATTAGGAGAATATCT * * 1504890 TTTGTAGTTCCGTCAATAATTGATG-ATA 61 TTTGTAGTTCCGTCAATAATCG-GGAATA * * * 1504918 TGTAGGAGAATATTTATAATAGTAGTTCCTTCAGTAATCAG-GGATATTAGGAGAATATCTATAA 1 TGTAGGAGAATATCTATAATAGTAGTTCCATCAATAATC-GTGGATATTAGGAGAATATCT-T-- * * * 1504982 TTGTATTTCCGTCAATGATCGGGAATG 62 TTGTAGTTCCGTCAATAATCGGGAATA * * 1505009 TGTTGGAGAATATCTATAATTGTAGTTCCATCAATAATCGTGGATAT 1 TGTAGGAGAATATCTATAATAGTAGTTCCATCAATAATCGTGGATAT 1505056 GTGGGAAAAT Statistics Matches: 113, Mismatches: 17, Indels: 16 0.77 0.12 0.11 Matches are distributed among these distances: 88 27 0.24 89 4 0.04 90 4 0.04 91 78 0.69 ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36 Consensus pattern (88 bp): TGTAGGAGAATATCTATAATAGTAGTTCCATCAATAATCGTGGATATTAGGAGAATATCTTTTGT AGTTCCGTCAATAATCGGGAATA Found at i:1506799 original size:62 final size:62 Alignment explanation

Indices: 1506702--1506823 Score: 244 Period size: 62 Copynumber: 2.0 Consensus size: 62 1506692 AAATCAGGAA 1506702 AACAGCTTGAATTGAATCAGGTGAGGCAGAATTTATATCTATCAATTACAGAAAGATTATAT 1 AACAGCTTGAATTGAATCAGGTGAGGCAGAATTTATATCTATCAATTACAGAAAGATTATAT 1506764 AACAGCTTGAATTGAATCAGGTGAGGCAGAATTTATATCTATCAATTACAGAAAGATTAT 1 AACAGCTTGAATTGAATCAGGTGAGGCAGAATTTATATCTATCAATTACAGAAAGATTAT 1506824 TTATAAAAGT Statistics Matches: 60, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 62 60 1.00 ACGTcount: A:0.40, C:0.11, G:0.18, T:0.30 Consensus pattern (62 bp): AACAGCTTGAATTGAATCAGGTGAGGCAGAATTTATATCTATCAATTACAGAAAGATTATAT Found at i:1515361 original size:172 final size:166 Alignment explanation

Indices: 1515135--1515738 Score: 784 Period size: 167 Copynumber: 3.6 Consensus size: 166 1515125 TCCAAGAGGG * * * * * * 1515135 TCATGATTTTCACAAATTTGAATCTACATTACCCGAGGAAGCTTCCAAACAAGTTTCAGCTTTTC 1 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC * * * * * 1515200 TGGCTGAATAATTTTTTAGAAGAAGATTTTTAAAGATTTACTCAATATATTCCCATGTTAAACTT 66 TGGCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAAC-T * ** 1515265 TGACCCCCCCCCCCCAGTAAGGCCCCACCCTACCCCTGGGGA 130 TGA----CCCCCCCCATTGTGGCCCCACCCTACCCC-GGGGA * * * * * * 1515307 TCTTGTTTTTCACTACTTTGAATCTACACTACCTAAGGATGCTTCCCCACAAGTTTCATCTTTCC 1 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC * 1515372 TGGCTGACTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAACTT 66 TGGCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAACTT * * ** * * 1515437 CAACCCCTTCATTGTGGCCCCACCTTACCCCCGGGGG 131 GACCCCCCCCATTGTGGCCCCACCCTA-CCCCGGGGA * 1515474 TCATGATTTTCACAACTTTGAATCTACACTACCTGATGATGCTTCCACACAAGTTTCAGCTTTCC 1 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC * * 1515539 TGGCTGATTAGTTTTTGAGAGGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAACTT 66 TGGCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAACTT * * 1515604 GA---CCCCCATTGTGGCCCCACCCTATCCCC-AGAA 131 GACCCCCCCCATTGTGGCCCCACCCTA-CCCCGGGGA 1515637 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC 1 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC * * * * 1515702 TGGCTTAATGGTTCTTGAGAAGAAGATTTTTGAAGAT 66 TGGCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGAT 1515739 GACTCTCAAA Statistics Matches: 380, Mismatches: 51, Indels: 11 0.86 0.12 0.02 Matches are distributed among these distances: 163 96 0.25 164 23 0.06 167 144 0.38 168 4 0.01 171 3 0.01 172 110 0.29 ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34 Consensus pattern (166 bp): TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC TGGCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAACTT GACCCCCCCCATTGTGGCCCCACCCTACCCCGGGGA Found at i:1533820 original size:26 final size:25 Alignment explanation

Indices: 1533770--1533848 Score: 98 Period size: 22 Copynumber: 3.4 Consensus size: 25 1533760 GTGCCACATG * 1533770 ATATATATAAAGAAAA-C-TACA-T 1 ATATATATAAAGAAAATCGTATATT 1533792 ATATATATAAAGAAAATCGTATATTT 1 ATATATATAAAGAAAATCGTATA-TT 1533818 ATATATATAAAGAAAAT-G-ATA-T 1 ATATATATAAAGAAAATCGTATATT 1533840 ATATATATA 1 ATATATATA 1533849 NNNNNNNNNN Statistics Matches: 52, Mismatches: 1, Indels: 8 0.85 0.02 0.13 Matches are distributed among these distances: 22 26 0.50 23 1 0.02 24 6 0.12 25 1 0.02 26 18 0.35 ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34 Consensus pattern (25 bp): ATATATATAAAGAAAATCGTATATT Found at i:1535260 original size:20 final size:20 Alignment explanation

Indices: 1535237--1535326 Score: 85 Period size: 20 Copynumber: 4.4 Consensus size: 20 1535227 TGGTTATATA 1535237 TATATATACA-CGATTTTCTT 1 TATATATACATCG-TTTTCTT * 1535257 TATATATA-TTCAGTTTTCTT 1 TATATATACATC-GTTTTCTT * * 1535277 TATATATATATCGTATTCATT 1 TATATATACATCGTTTTC-TT * * 1535298 ATATATATATATCATTTTCTT 1 -TATATATACATCGTTTTCTT 1535319 TATATATA 1 TATATATA 1535327 TAAATATACG Statistics Matches: 60, Mismatches: 5, Indels: 10 0.80 0.07 0.13 Matches are distributed among these distances: 20 37 0.62 21 7 0.12 22 16 0.27 ACGTcount: A:0.32, C:0.10, G:0.03, T:0.54 Consensus pattern (20 bp): TATATATACATCGTTTTCTT Found at i:1535327 original size:20 final size:20 Alignment explanation

Indices: 1535205--1535375 Score: 137 Period size: 22 Copynumber: 7.8 Consensus size: 20 1535195 ATATATCGCG 1535205 ATTTTCTTTATATATATATC 1 ATTTTCTTTATATATATATC * * * * 1535225 AGTGGTTATATATATATATACAC 1 A-T-TTTCTTTATATATATA-TC 1535248 GATTTTCTTTATATATAT-TC 1 -ATTTTCTTTATATATATATC 1535268 AGTTTTCTTTATATATATATC 1 A-TTTTCTTTATATATATATC * * 1535289 GTATTCATTATATATATATATC 1 ATTTTC-TT-TATATATATATC 1535311 ATTTTCTTTATATATATAAATATAC 1 ATTTTC-TT-TATATAT--ATAT-C * 1535336 GATTTTCTTTATATATATATGT 1 -ATTTTCTTTATATATATAT-C 1535358 AGTTTTCTTTATATATAT 1 A-TTTTCTTTATATATAT 1535376 CATGTGGCAC Statistics Matches: 123, Mismatches: 15, Indels: 24 0.76 0.09 0.15 Matches are distributed among these distances: 19 1 0.01 20 22 0.18 21 6 0.05 22 71 0.58 23 2 0.02 24 12 0.10 25 3 0.02 26 6 0.05 ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54 Consensus pattern (20 bp): ATTTTCTTTATATATATATC Found at i:1542511 original size:85 final size:86 Alignment explanation

Indices: 1542352--1542523 Score: 265 Period size: 85 Copynumber: 2.0 Consensus size: 86 1542342 ACAATATCAA * * * 1542352 AACCAATAAAAATGTAGTAACAAACCAGCTTCCTTTTCCATATTTGATCGGAGGTTGACGTTCGA 1 AACCAATAAAAATATAGTAACAAACCAGCTTCCTTTTACATATTTGATCGGAGCTTGACGTTCGA 1542417 AGTTATGCTATTTATACTTTT 66 AGTTATGCTATTTATACTTTT * ** * 1542438 AACCAATAAAAATATAGTAACAAATCATTTTCCTTTTACAT-TTTGATCGGAGCTTGACGTTGGA 1 AACCAATAAAAATATAGTAACAAACCAGCTTCCTTTTACATATTTGATCGGAGCTTGACGTTCGA * 1542502 AGTTATGCTATTTCTACTTTT 66 AGTTATGCTATTTATACTTTT 1542523 A 1 A 1542524 TCAATAGTTC Statistics Matches: 78, Mismatches: 8, Indels: 1 0.90 0.09 0.01 Matches are distributed among these distances: 85 42 0.54 86 36 0.46 ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38 Consensus pattern (86 bp): AACCAATAAAAATATAGTAACAAACCAGCTTCCTTTTACATATTTGATCGGAGCTTGACGTTCGA AGTTATGCTATTTATACTTTT Found at i:1547017 original size:8 final size:8 Alignment explanation

Indices: 1547004--1547048 Score: 63 Period size: 8 Copynumber: 5.6 Consensus size: 8 1546994 TGCGTCTACA 1547004 GACAGACG 1 GACAGACG 1547012 GACAGACG 1 GACAGACG * * 1547020 GACGGACA 1 GACAGACG 1547028 GACAGACG 1 GACAGACG * 1547036 GACGGACG 1 GACAGACG 1547044 GACAG 1 GACAG 1547049 GGTGAAACCA Statistics Matches: 31, Mismatches: 6, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 8 31 1.00 ACGTcount: A:0.36, C:0.24, G:0.40, T:0.00 Consensus pattern (8 bp): GACAGACG Found at i:1547018 original size:12 final size:12 Alignment explanation

Indices: 1547001--1547038 Score: 67 Period size: 12 Copynumber: 3.2 Consensus size: 12 1546991 AGTTGCGTCT 1547001 ACAGACAGACGG 1 ACAGACAGACGG * 1547013 ACAGACGGACGG 1 ACAGACAGACGG 1547025 ACAGACAGACGG 1 ACAGACAGACGG 1547037 AC 1 AC 1547039 GGACGGACAG Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 12 24 1.00 ACGTcount: A:0.39, C:0.26, G:0.34, T:0.00 Consensus pattern (12 bp): ACAGACAGACGG Found at i:1549811 original size:1 final size:1 Alignment explanation

Indices: 1549807--1549850 Score: 88 Period size: 1 Copynumber: 44.0 Consensus size: 1 1549797 CCCCCCCCCC 1549807 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1549851 TATNNNNNNN Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 43 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:1549905 original size:12 final size:12 Alignment explanation

Indices: 1549891--1549930 Score: 53 Period size: 12 Copynumber: 3.2 Consensus size: 12 1549881 CCCCCCCCAA * 1549891 AAAAAAAAACAAA 1 AAAAAAAAA-AAC 1549904 AAAAAAAAAAAC 1 AAAAAAAAAAAC * 1549916 AAAACAAAAAAC 1 AAAAAAAAAAAC 1549928 AAA 1 AAA 1549931 GTTATTATCA Statistics Matches: 25, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 12 16 0.64 13 9 0.36 ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00 Consensus pattern (12 bp): AAAAAAAAAAAC Found at i:1549909 original size:15 final size:15 Alignment explanation

Indices: 1549889--1549926 Score: 67 Period size: 15 Copynumber: 2.5 Consensus size: 15 1549879 CCCCCCCCCC 1549889 AAAAAAAAAAACAAA 1 AAAAAAAAAAACAAA 1549904 AAAAAAAAAAACAAA 1 AAAAAAAAAAACAAA 1549919 ACAAAAAA 1 A-AAAAAA 1549927 CAAAGTTATT Statistics Matches: 22, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 15 16 0.73 16 6 0.27 ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00 Consensus pattern (15 bp): AAAAAAAAAAACAAA Found at i:1549914 original size:20 final size:20 Alignment explanation

Indices: 1549889--1549926 Score: 67 Period size: 20 Copynumber: 1.9 Consensus size: 20 1549879 CCCCCCCCCC 1549889 AAAAAAAAAAACAAAAAAAA 1 AAAAAAAAAAACAAAAAAAA * 1549909 AAAAAACAAAACAAAAAA 1 AAAAAAAAAAACAAAAAA 1549927 CAAAGTTATT Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 17 1.00 ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00 Consensus pattern (20 bp): AAAAAAAAAAACAAAAAAAA Found at i:1569840 original size:2 final size:2 Alignment explanation

Indices: 1569835--1569868 Score: 59 Period size: 2 Copynumber: 17.0 Consensus size: 2 1569825 CGCGCGCGCG * 1569835 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CC CA CA 1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA 1569869 TACGTGTAAG Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00 Consensus pattern (2 bp): CA Found at i:1570109 original size:27 final size:27 Alignment explanation

Indices: 1570079--1570131 Score: 70 Period size: 27 Copynumber: 2.0 Consensus size: 27 1570069 CACATCCAAT * 1570079 TGAACACCTCTTAAACACACGTTCAAG 1 TGAACACCTCATAAACACACGTTCAAG * * * 1570106 TGAACATCTCATATACACACTTTCAA 1 TGAACACCTCATAAACACACGTTCAA 1570132 TACAACTCCA Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 27 22 1.00 ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26 Consensus pattern (27 bp): TGAACACCTCATAAACACACGTTCAAG Found at i:1573506 original size:22 final size:22 Alignment explanation

Indices: 1573453--1573514 Score: 72 Period size: 21 Copynumber: 2.9 Consensus size: 22 1573443 GGCGAAGGAG * * * 1573453 CGAAAGTGCGAGGATGTGACGG 1 CGAAAGTGCGAAGATGCGACGA * 1573475 C-AAAGCGCGAAGATGCGACGA 1 CGAAAGTGCGAAGATGCGACGA * 1573496 CGAAAGTGCGAAGTTGCGA 1 CGAAAGTGCGAAGATGCGA 1573515 AGGCAAAGAA Statistics Matches: 33, Mismatches: 6, Indels: 2 0.80 0.15 0.05 Matches are distributed among these distances: 21 17 0.52 22 16 0.48 ACGTcount: A:0.32, C:0.18, G:0.39, T:0.11 Consensus pattern (22 bp): CGAAAGTGCGAAGATGCGACGA Found at i:1578633 original size:2 final size:2 Alignment explanation

Indices: 1578628--1578671 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 1578618 CAGTCTGTGT 1578628 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 1578670 GA 1 GA 1578672 TATCCTTTAC Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1579220 original size:19 final size:19 Alignment explanation

Indices: 1579196--1579236 Score: 82 Period size: 19 Copynumber: 2.2 Consensus size: 19 1579186 TAAATCTTTT 1579196 TATCAATTTCATAGATATA 1 TATCAATTTCATAGATATA 1579215 TATCAATTTCATAGATATA 1 TATCAATTTCATAGATATA 1579234 TAT 1 TAT 1579237 ATAGATATAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 22 1.00 ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44 Consensus pattern (19 bp): TATCAATTTCATAGATATA Found at i:1579234 original size:2 final size:2 Alignment explanation

Indices: 1579229--1579296 Score: 100 Period size: 2 Copynumber: 34.0 Consensus size: 2 1579219 AATTTCATAG * * * 1579229 AT AT AT AT AT AG AT AT AT AT AT AG AT AT AT AT AT AG 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 * 1579271 AT AG AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT 1579297 TTATCAAGAA Statistics Matches: 58, Mismatches: 8, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 2 58 1.00 ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44 Consensus pattern (2 bp): AT Found at i:1579242 original size:12 final size:12 Alignment explanation

Indices: 1579225--1579296 Score: 121 Period size: 12 Copynumber: 6.2 Consensus size: 12 1579215 TATCAATTTC 1579225 ATAGATATATAT 1 ATAGATATATAT 1579237 ATAGATATATAT 1 ATAGATATATAT 1579249 ATAGATATATAT 1 ATAGATATATAT 1579261 ATAG--ATATAT 1 ATAGATATATAT 1579271 ATAGATATATAT 1 ATAGATATATAT * 1579283 ATATATATATAT 1 ATAGATATATAT 1579295 AT 1 AT 1579297 TTATCAAGAA Statistics Matches: 57, Mismatches: 1, Indels: 4 0.92 0.02 0.06 Matches are distributed among these distances: 10 10 0.18 12 47 0.82 ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43 Consensus pattern (12 bp): ATAGATATATAT Found at i:1580775 original size:3 final size:3 Alignment explanation

Indices: 1580767--1580804 Score: 76 Period size: 3 Copynumber: 12.7 Consensus size: 3 1580757 TCCATTTCAA 1580767 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA 1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA 1580805 GACTTGTACT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32 Consensus pattern (3 bp): CAT Found at i:1585842 original size:20 final size:20 Alignment explanation

Indices: 1585819--1585864 Score: 74 Period size: 20 Copynumber: 2.3 Consensus size: 20 1585809 ACAATACTGA 1585819 ATCATAGGATACAATACAAT 1 ATCATAGGATACAATACAAT ** 1585839 ATCATATTATACAATACAAT 1 ATCATAGGATACAATACAAT 1585859 ATCATA 1 ATCATA 1585865 CTTTACAAAA Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 24 1.00 ACGTcount: A:0.50, C:0.15, G:0.04, T:0.30 Consensus pattern (20 bp): ATCATAGGATACAATACAAT Found at i:1585871 original size:20 final size:20 Alignment explanation

Indices: 1585827--1585877 Score: 77 Period size: 20 Copynumber: 2.5 Consensus size: 20 1585817 GAATCATAGG 1585827 ATACAATACAATATCATATT 1 ATACAATACAATATCATATT 1585847 ATACAATACAATATCATACTT 1 ATACAATACAATATCATA-TT * 1585868 -TACAAAACAA 1 ATACAATACAA 1585878 ATAAGTTCTT Statistics Matches: 29, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 20 27 0.93 21 2 0.07 ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29 Consensus pattern (20 bp): ATACAATACAATATCATATT Found at i:1593857 original size:176 final size:176 Alignment explanation

Indices: 1591819--1594503 Score: 3530 Period size: 176 Copynumber: 15.1 Consensus size: 176 1591809 TCCCATCCCA ** * 1591819 ATGTATCACAAGAGTTTTATAAATAAACTGATATTGTACATACCAGCAACTTGTCCACAGGAAGC 1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC * * * * 1591884 GCTATTGAGGAATGGTGGGTCAATGCAAGAGGTGTCTTCCACCTGAATATCCTCTTTACCTTTAT 66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT * * 1591949 TGAAAAGAAAAAAGGACAAAATGTCTTATATGGTTAACCGAAGTAC 131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC * * * 1591995 ATGCATCACAAGAGTTTTATTTATAAATCAATATATTGTACATACCAGCAACTTGTCCACAGGAA 1 ATGTATCACAAGAGTTTTATTGATAAA-CTA-ATATTGTACATACCAGCAACTTGTCCACAGGAA * * * * * * 1592060 GCGCTATTGAGGAACGGTGGGTCGATTCGAGAAGTGTCTTCCACCTGAGTATCATCTTCAGCTTT 64 GCGCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTT * 1592125 ATTGAAGAGAAAAAAGGAC--AATGTCTCATATGGTTAACAGATTGAAGTAC 129 ATTGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAAC--A--GAAGTAC * * * * 1592175 ATGTATCACAAGAGCTTT-TTAAGTAAACTGATATTGTACATACCAGCAACTTGTCCACCGGAAG 1 ATGTATCACAAGAGTTTTATTGA-TAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAG * * * 1592239 CGCTATTGAGGAATGGTGGGTCAATGCAAGAAGTGTCTTCCACCTGAGTATCATCTTCATCTTTA 65 CGCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTA * * * 1592304 TTGAGGAGAAAAAAAGGACAAAATGTCTAATATGGTTTACAGAAGTAC 130 TTGAAGAG-AAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC * * 1592352 ATGTATCACAAGAGTTTTATTGATGAACTAGTATTGTACATACCAGCAACTTGTCCACAGGAAGC 1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC * * 1592417 GCTATTGAGGAATGGTGGGTCAATGCAAGAAGTGTCTTCCACCTGAGTATCCTCTTCATCTTTAT 66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT * * * * * * 1592482 TGAAGAGAAATAAGAACAAAATGTCTTAAAT-ATTAAACGGATGTAC 131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTT-AACAGAAGTAC * * * * * 1592528 ATGAATCATAAGAGTTTTATTAATAAACTAATATATTGTACATACCAGCAAGTTTTCCACAGGAA 1 ATGTATCACAAGAGTTTTATTGATAAACT-A-ATATTGTACATACCAGCAACTTGTCCACAGGAA * * * * * 1592593 GCGCTATTGAGGAATGGTGGGTCATTGCAAGAGGTGTCTTCCACCTGAATATCCTCTTTACCTTT 64 GCGCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTT * * 1592658 ATTGAAAAGAAAAAAGGACAAATTTAATGACTTATATGGTTAACAGAAGTAC 129 ATTGAAGAGAAAAAAGGAC-AA---AATGTCTTATATGGTTAACAGAAGTAC * * * * 1592710 ATGTATCACAAGAGTTTTATTGATTAACTGATATTGTACATACCAGCAACTTGTCCACCGGAAGA 1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC * * * 1592775 GCTATTGAGGAACGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAGTATCCTCTCCATCTTTAT 66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT * * * * * 1592840 TGACGAGAAAAAAAGGACAAAATGTGTAATATGGTTTACAGAAGAAC 131 TGAAGAG-AAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC * * 1592887 ATGTAGCACAAGAGTTTTATTGATAAACTAGTATTGTACATACCAGCAACTTGTCCACAGGAAGC 1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC * * 1592952 GCTATTGAGGAATGGTGGGTCAATGCAAGAAGTGTCTTCCACCTGAGTATCCTCTTCATCTTTAT 66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT * * * * * * 1593017 TGAAGAGAAATAAGAACAAAATGTCTTAAAT-ATTAAACGGATGTAC 131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTT-AACAGAAGTAC * * * * * * 1593063 ATGAATCATAAGAGTTTTATTAATAAACTAATATATTGTACATACGAGCAAGTTTTCCACAGGAA 1 ATGTATCACAAGAGTTTTATTGATAAACT-A-ATATTGTACATACCAGCAACTTGTCCACAGGAA * * * * * 1593128 GCGCTATTGAGGAATGGTGGGTCATTGCAAGAAGTGTCCTCCACCTGAATATCCTCTTTACCTTT 64 GCGCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTT * * 1593193 ATTGAAAAGAAAAAAGGACAAATTTAATGACTTATATGGTTAACAGAAGTAC 129 ATTGAAGAGAAAAAAGGAC-AA---AATGTCTTATATGGTTAACAGAAGTAC * * 1593245 ATGTATCACAAGAGTTTCATTGATAAACTGATATTGTACATACCAGCAACTTGTCCACAGGAAGC 1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC * * * * * * 1593310 GCTATTGAGGAATGGTGGGTCAATTCGAGAGGTGTCTTCCATCTGAATATCATCATCAGCTTTAT 66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT * * * * 1593375 TGAAGAGAAAATAGGACAAAGTGTCTTATATGGTTTACAGATTGAAATAC 131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGG-TTA-ACA--GAAGTAC * * * * * 1593425 ATGTAGCACAAGAGTTTTATTGATTAACTGATATTGTACATACCAGCAACTTGTCCACCGGAAGA 1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC * * * 1593490 GCTATTGAGGAACGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAGTATCCTCTCCATCTTTAT 66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT * * * * * 1593555 TGACGAGAAAAAAAGGACAAAATGTGTAATATGGTTTACAGAAGAAC 131 TGAAGAG-AAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC * * 1593602 ATGTAGCACAAGAGTTTTATTGATAAACTGATATTGTACATACCAGCAACTTGTCCACAGGAAGC 1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC * * * * * * 1593667 GCTATTGAGGAATGGAT-GGTCGATTCGAGAAGTGTCTTCCATCTCAATATCTTCTTCAGCTTTA 66 GCTATTGAGGAATGG-TGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTA * * 1593731 TTGAAGAGAAAAAAGGACAAAGTGTCTTATATGGTTAACAGAAGTGC 130 TTGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC ** * 1593778 ATGTATCACAAGAGTTTTATAAATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGA 1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC * * * 1593843 GCTATTGAGGAATGGTGGGTCAATGCGAGAGGTGTCTTCCACCTGAATATCCTCTTTACCTTTAT 66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT * * 1593908 TGAAAAGAAAAAAGGACAAAGTGTCTTATATGGTTAACAGAAGTAC 131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC * * 1593954 ATGTATCACAAGAGTTTTATCGATAAACTGATATTGTACATACCAGCAACTTGTCCACAGGAAGC 1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC * * ** * * 1594019 GCTATTGAGGAATGGTGGGTCAATTCGAGAAGTGTCTTCCATCACAATATCATCTTCAGCTTTAT 66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT * * * 1594084 TGAAGGGAAAAAAGGACAAAATGTCTAATATGGTTTACAGAAGTAC 131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC * * * 1594130 ATGTATCACAAGAGTTTTATTGATAAACTAGTATTGTACATACCAGCAACTTGTCCACGGGAAGA 1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC * ** ** * 1594195 GCTATTGAGGAATGGTGGGTCAATGCAAGAAGTCCCTTCCACCTGCGTATCATCTTCATCTTTAT 66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT *** 1594260 TGAAGAGAAAAAAACCCAAAATGTCTTATATGGTTAACAGAAGTAC 131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC * * 1594306 ATGTATCACAAGAGTTTTATTAATAAATTAATATATTGTACATACCAGCAACTTGTCCACAGGAA 1 ATGTATCACAAGAGTTTTATTGATAAACT-A-ATATTGTACATACCAGCAACTTGTCCACAGGAA * * ** * * * * 1594371 GCGCTTTTGAGGAATGGTGGGTCGATTTGAGAAGTGTCTTCCATCAGAATATCATCTTCAGCTTT 64 GCGCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTT * * * * 1594436 ATTGAAGAGAAAAAAAGACATAATGACTTATTTGGTTAACAGATA-TAC 129 ATTGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGA-AGTAC * 1594484 ATGCATCACAAGAGTTTTAT 1 ATGTATCACAAGAGTTTTAT 1594504 AAATAAGGCC Statistics Matches: 2197, Mismatches: 274, Indels: 74 0.86 0.11 0.03 Matches are distributed among these distances: 175 5 0.00 176 691 0.31 177 415 0.19 178 567 0.26 179 24 0.01 180 354 0.16 181 49 0.02 182 88 0.04 183 4 0.00 ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29 Consensus pattern (176 bp): ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC Found at i:1599741 original size:24 final size:24 Alignment explanation

Indices: 1599714--1599761 Score: 87 Period size: 24 Copynumber: 2.0 Consensus size: 24 1599704 CAACGAAATC 1599714 ACTGCCACTTTTAACACCTTGTTT 1 ACTGCCACTTTTAACACCTTGTTT * 1599738 ACTGCCACTTTTAACATCTTGTTT 1 ACTGCCACTTTTAACACCTTGTTT 1599762 GAAAATTCGC Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 23 1.00 ACGTcount: A:0.21, C:0.27, G:0.08, T:0.44 Consensus pattern (24 bp): ACTGCCACTTTTAACACCTTGTTT Found at i:1600450 original size:16 final size:16 Alignment explanation

Indices: 1600429--1600468 Score: 53 Period size: 16 Copynumber: 2.5 Consensus size: 16 1600419 ATTACAGTCA * 1600429 ACTCGTAACCAAACTG 1 ACTCGTAACCAAACAG * 1600445 ACTCGTACCCAAACAG 1 ACTCGTAACCAAACAG * 1600461 ACTTGTAA 1 ACTCGTAA 1600469 TCAGATTGTT Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 16 20 1.00 ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20 Consensus pattern (16 bp): ACTCGTAACCAAACAG Found at i:1604942 original size:2 final size:2 Alignment explanation

Indices: 1604899--1604931 Score: 66 Period size: 2 Copynumber: 16.5 Consensus size: 2 1604889 GGGCTTACAA 1604899 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 1604932 GGATGCACAC Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:1608251 original size:12 final size:12 Alignment explanation

Indices: 1608234--1608260 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 1608224 ATACACACAC 1608234 GTACATAAACTA 1 GTACATAAACTA 1608246 GTACATAAACTA 1 GTACATAAACTA 1608258 GTA 1 GTA 1608261 ATTACATTGA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26 Consensus pattern (12 bp): GTACATAAACTA Found at i:1608750 original size:2 final size:2 Alignment explanation

Indices: 1608743--1608783 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 1608733 TACAAACTAA 1608743 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1608784 ATTCAGAAAT 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:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:1615768 original size:2 final size:2 Alignment explanation

Indices: 1615761--1615822 Score: 124 Period size: 2 Copynumber: 31.0 Consensus size: 2 1615751 NNNNNNNNNN 1615761 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 1615803 TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC 1615823 AATATGTGTT Statistics Matches: 60, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 60 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1616055 original size:21 final size:20 Alignment explanation

Indices: 1616018--1616059 Score: 50 Period size: 21 Copynumber: 2.0 Consensus size: 20 1616008 CCCATGAGTC * 1616018 TTTGTTTAGTTTTTAAACATG 1 TTTGTTTAGTTTATAAA-ATG 1616039 TTTGTTTA-TCTTATAAAATG 1 TTTGTTTAGT-TTATAAAATG 1616059 T 1 T 1616060 ATGCATAATA Statistics Matches: 19, Mismatches: 1, Indels: 3 0.83 0.04 0.13 Matches are distributed among these distances: 20 5 0.26 21 14 0.74 ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57 Consensus pattern (20 bp): TTTGTTTAGTTTATAAAATG Found at i:1618847 original size:4 final size:4 Alignment explanation

Indices: 1618838--1618873 Score: 54 Period size: 4 Copynumber: 9.0 Consensus size: 4 1618828 TACCCTTGTG * * 1618838 TGTC TGTC TGTC CGTC CGTC TGTC TGTC TGTC TGTC 1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC 1618874 CGTCCGTAAC Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 4 30 1.00 ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44 Consensus pattern (4 bp): TGTC Found at i:1618860 original size:12 final size:12 Alignment explanation

Indices: 1618843--1618880 Score: 58 Period size: 12 Copynumber: 3.2 Consensus size: 12 1618833 TTGTGTGTCT 1618843 GTCTGTCCGTCC 1 GTCTGTCCGTCC * * 1618855 GTCTGTCTGTCT 1 GTCTGTCCGTCC 1618867 GTCTGTCCGTCC 1 GTCTGTCCGTCC 1618879 GT 1 GT 1618881 AACAAAAATT Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 12 22 1.00 ACGTcount: A:0.00, C:0.34, G:0.26, T:0.39 Consensus pattern (12 bp): GTCTGTCCGTCC Found at i:1618863 original size:20 final size:20 Alignment explanation

Indices: 1618838--1618877 Score: 71 Period size: 20 Copynumber: 2.0 Consensus size: 20 1618828 TACCCTTGTG 1618838 TGTCTGTCTGTCCGTCCGTC 1 TGTCTGTCTGTCCGTCCGTC * 1618858 TGTCTGTCTGTCTGTCCGTC 1 TGTCTGTCTGTCCGTCCGTC 1618878 CGTAACAAAA Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.00, C:0.33, G:0.25, T:0.42 Consensus pattern (20 bp): TGTCTGTCTGTCCGTCCGTC Found at i:1619306 original size:166 final size:167 Alignment explanation

Indices: 1618904--1619444 Score: 890 Period size: 166 Copynumber: 3.3 Consensus size: 167 1618894 GTTGCATTTA * * 1618904 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT 1618969 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 1619034 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT 131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * * 1619071 TCTCAGCAA-TGGTATATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATA 1 TCTCAGCAACT-ATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATA * * 1619135 TCGTGGGATCTATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTT 65 TCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT * * * 1619200 TTT-GCCAAAATTTTCAAACAAATTTCCGTCAAAGAAT 130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * 1619237 TCTCAGCAACTATTTATCGGAGATGCTTGAAATTTTAACACACTATTTGTTTAGTCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT * * 1619302 CGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTT-AATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 1619366 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT 131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 1619403 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACA 1619445 NNNNNNNNNN Statistics Matches: 343, Mismatches: 28, Indels: 7 0.91 0.07 0.02 Matches are distributed among these distances: 165 22 0.06 166 198 0.58 167 123 0.36 ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38 Consensus pattern (167 bp): TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT Found at i:1621298 original size:34 final size:34 Alignment explanation

Indices: 1621253--1621320 Score: 109 Period size: 34 Copynumber: 2.0 Consensus size: 34 1621243 TAGGCATTTG * * 1621253 AAATGCTTTATGCTCCACAGATGTTTCAGTATTC 1 AAATGCATTATGCTCCACAGATATTTCAGTATTC * 1621287 AAATGCATTATGCTCTACAGATATTTCAGTATTC 1 AAATGCATTATGCTCCACAGATATTTCAGTATTC 1621321 CTTTCAATTG Statistics Matches: 31, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 34 31 1.00 ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38 Consensus pattern (34 bp): AAATGCATTATGCTCCACAGATATTTCAGTATTC Found at i:1624368 original size:39 final size:39 Alignment explanation

Indices: 1624310--1625049 Score: 1063 Period size: 39 Copynumber: 19.0 Consensus size: 39 1624300 TCCTGCCAGA * 1624310 CTGTGTGGAGTTATTAACAGGTAGGATGACTGTATCAGT 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * 1624349 CAGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT ** * 1624388 CAATGTGGAGTTATAAACAGGTAGGATGACTGTATCTGT 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT ** * * * 1624427 CAATGTGGAGTTATAAACAGGTAGGGTGACTGTAACAGA 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * * 1624466 CTGTGTGGAGTTATAAACATGTAGGGTGACTGTATCAGA 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * 1624505 CTCTGTGGAGTTATAAACAGGTAGGATGACTGTATC-CT 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * * 1624543 ACTGTGTGGAGTTATTAACAGGAAGGATGACTGTATC-CT 1 -CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * 1624582 ACTGTGTGGAGTTATAAACAGGTAGGATGACTGTATC-CT 1 -CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * 1624621 ACTGTGTGGAGTTATAAACAGGTAGGGTGACTGTATCAGA 1 -CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * 1624661 CTGTGTGGAGTTGTTAACAGGTAGGATGACTGTATCAGT 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * 1624700 CTGTGGGGAGTTATAAAGAGGTAGGATGACTGTATCAGT 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * * 1624739 CTGTGGGGAGTTATAGACAGGTAGGGTGACTGTATCAGT 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * * 1624778 CAGTGGGGAGTTATAAACAGGTAGGGTGACTGTATCAGT 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * * 1624817 CTGTGTGGAGTTGTTAACAGGTAGGATGACTGTATCAGA 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT 1624856 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * * 1624895 CTGTGGGGAGTTATAAACAGGTAGGGTGACTGTATCAGA 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * 1624934 CTGTGTGGAGTTATTAACAGGTAGGATGACTGTATCAGA 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT 1624973 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT * * 1625012 CTGTGGGGAGTTATAAACAGGTAGGGTGACTGTATCAG 1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAG 1625050 NNNNNNNNNN Statistics Matches: 642, Mismatches: 57, Indels: 4 0.91 0.08 0.01 Matches are distributed among these distances: 39 642 1.00 ACGTcount: A:0.28, C:0.11, G:0.32, T:0.29 Consensus pattern (39 bp): CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT Found at i:1625424 original size:39 final size:39 Alignment explanation

Indices: 1625366--1626580 Score: 1878 Period size: 39 Copynumber: 31.2 Consensus size: 39 1625356 NNNNNNNNNN * 1625366 TCAGTCTGTG-GGAGTTATAAACAGGTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * * 1625404 TCAGTCTGTGTGGAGTTATAAAGAGGAAGGAGGGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGG-GTGACTGTA * 1625444 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * 1625483 TCAGTCTGTGGGGAGTTATAAACAGGCAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * * 1625522 TCAGTCTGTGGGGAGTTATAAAGAGGTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1625561 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1625600 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * * 1625639 TCAGTCTGTGGGGAGTTATAAAGAGGTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1625678 TCAGTCTGTGTGGAGTTATAGACAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * 1625717 TCAGTCTGTGGGGAGTTATAAACAGGCAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * ** 1625756 TCAGTCAGTGTGGAGTTATAAAGGGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * 1625795 TCAGTCTGTGGGGAGTTATAAACAGGTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1625834 TCAGACTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * 1625873 TCAGTCAGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1625912 TCAGTCAGTGTGGAGTTATAAACAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA ** 1625951 TCAGTCAATGTGGAGTTATAAACAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA ** * 1625990 TCAGTCAATGTGGAGTTATAAACAGGTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1626029 TCAGTCTGTGGGGAGTTATAAACAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * 1626068 TCAGTCTGTGGGGAGTTATAAACAGGTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * 1626107 TC-CTACTGTGTGGAGTTATAAACAGGTAGGATGACTGTA 1 TCAGT-CTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * * 1626146 TCAGTCTGTGGGGAGTTATAAACAGTTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1626185 TCAGTCTGTGTGGAGTTATAAACAGGTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * 1626224 TC-CTACTGTGTGGAGTTATAAACAGGTAGGATGACTGTA 1 TCAGT-CTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1626263 TCAGTCTGTGGGGAGTTATAAACAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * * 1626302 TCAGTCTGTGGGGAGTTATAGACAGGTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA 1626341 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * * * 1626380 TCAGTCTATGGGGAGTTATTAACAGGTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1626419 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1626458 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * 1626497 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA * * 1626536 TCAGTCTGTGGGGAGTTATAAACAGGTAGGATGACTGTA 1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA 1626575 TCAGTC 1 TCAGTC 1626581 AGTGGAGATA Statistics Matches: 1096, Mismatches: 75, Indels: 11 0.93 0.06 0.01 Matches are distributed among these distances: 38 12 0.01 39 1046 0.95 40 38 0.03 ACGTcount: A:0.27, C:0.10, G:0.34, T:0.29 Consensus pattern (39 bp): TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA Found at i:1631135 original size:24 final size:24 Alignment explanation

Indices: 1631107--1631156 Score: 100 Period size: 24 Copynumber: 2.1 Consensus size: 24 1631097 TTCTATCAGT 1631107 TTAAGGAAATAAATAATATCATTA 1 TTAAGGAAATAAATAATATCATTA 1631131 TTAAGGAAATAAATAATATCATTA 1 TTAAGGAAATAAATAATATCATTA 1631155 TT 1 TT 1631157 GATAAAGAAG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 26 1.00 ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36 Consensus pattern (24 bp): TTAAGGAAATAAATAATATCATTA Found at i:1632293 original size:22 final size:22 Alignment explanation

Indices: 1632268--1632321 Score: 81 Period size: 22 Copynumber: 2.5 Consensus size: 22 1632258 AATCGCACCT * 1632268 TCGCCATCGCAACTTCGCACTC 1 TCGCCTTCGCAACTTCGCACTC * * 1632290 TCGCCTTCGCATCTTCGCACTT 1 TCGCCTTCGCAACTTCGCACTC 1632312 TCGCCTTCGC 1 TCGCCTTCGC 1632322 CTTTTTATAA Statistics Matches: 29, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 22 29 1.00 ACGTcount: A:0.11, C:0.44, G:0.15, T:0.30 Consensus pattern (22 bp): TCGCCTTCGCAACTTCGCACTC Found at i:1645153 original size:32 final size:33 Alignment explanation

Indices: 1645087--1645163 Score: 138 Period size: 33 Copynumber: 2.4 Consensus size: 33 1645077 GATTTTGGTC 1645087 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG 1 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG * 1645120 TCAATATTCAACGTTGAAAAATGA-CCCCCGGG 1 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG 1645152 TCAATTTTCAAC 1 TCAATTTTCAAC 1645164 CCGGGTCAAT Statistics Matches: 42, Mismatches: 2, Indels: 1 0.93 0.04 0.02 Matches are distributed among these distances: 32 19 0.45 33 23 0.55 ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26 Consensus pattern (33 bp): TCAATTTTCAACGTTGAAAAATGACCCCCCGGG Found at i:1645775 original size:21 final size:20 Alignment explanation

Indices: 1645751--1645815 Score: 60 Period size: 21 Copynumber: 3.1 Consensus size: 20 1645741 TGAATGGGTG 1645751 ATATCACCTATTCGAATTTGA 1 ATATCACCTATTC-AATTTGA * * 1645772 ATATCACCT-TTACAAATTGGGG 1 ATATCACCTATT-C-AATT-TGA * 1645794 ATATCACTTATTCAATTTGA 1 ATATCACCTATTCAATTTGA 1645814 AT 1 AT 1645816 GAGTGTTATC Statistics Matches: 35, Mismatches: 6, Indels: 7 0.73 0.12 0.15 Matches are distributed among these distances: 20 5 0.14 21 18 0.51 22 10 0.29 23 2 0.06 ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38 Consensus pattern (20 bp): ATATCACCTATTCAATTTGA Found at i:1646250 original size:10 final size:10 Alignment explanation

Indices: 1646222--1646252 Score: 55 Period size: 10 Copynumber: 3.2 Consensus size: 10 1646212 AAATAGATAA 1646222 ATTTTCTTAT 1 ATTTTCTTAT 1646232 ATTTT-TTAT 1 ATTTTCTTAT 1646241 ATTTTCTTAT 1 ATTTTCTTAT 1646251 AT 1 AT 1646253 ATATAAATAA Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 9 9 0.45 10 11 0.55 ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71 Consensus pattern (10 bp): ATTTTCTTAT Found at i:1646352 original size:2 final size:2 Alignment explanation

Indices: 1646345--1646419 Score: 105 Period size: 2 Copynumber: 37.5 Consensus size: 2 1646335 CACTTTGATA ** ** * 1646345 CT CT CT CT CT CT CT CT CT CT CT CT NN NN NT 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 1646387 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1646420 ATATTTAACA Statistics Matches: 69, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 69 1.00 ACGTcount: A:0.00, C:0.47, G:0.00, T:0.47 Consensus pattern (2 bp): CT Found at i:1648034 original size:13 final size:14 Alignment explanation

Indices: 1648005--1648038 Score: 52 Period size: 13 Copynumber: 2.5 Consensus size: 14 1647995 GGGTCTATAC * 1648005 TCAATATTAATAAA 1 TCAATAATAATAAA 1648019 TCAATAATAA-AAA 1 TCAATAATAATAAA 1648032 TCAATAA 1 TCAATAA 1648039 AAACTTATTC Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 13 10 0.53 14 9 0.47 ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29 Consensus pattern (14 bp): TCAATAATAATAAA Found at i:1648295 original size:12 final size:13 Alignment explanation

Indices: 1648268--1648299 Score: 57 Period size: 12 Copynumber: 2.5 Consensus size: 13 1648258 TCTTCTTTTA 1648268 TTAAATTTTAAAC 1 TTAAATTTTAAAC 1648281 TTAAATTTT-AAC 1 TTAAATTTTAAAC 1648293 TTAAATT 1 TTAAATT 1648300 GTTTCGTCTT Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 12 10 0.53 13 9 0.47 ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50 Consensus pattern (13 bp): TTAAATTTTAAAC Found at i:1650856 original size:15 final size:15 Alignment explanation

Indices: 1650836--1650866 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 1650826 TGCTTCATAT 1650836 ATTGAGTAAAGGAAA 1 ATTGAGTAAAGGAAA 1650851 ATTGAGTAAAGGAAA 1 ATTGAGTAAAGGAAA 1650866 A 1 A 1650867 GCTAGCTTAC Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19 Consensus pattern (15 bp): ATTGAGTAAAGGAAA Found at i:1654641 original size:10 final size:10 Alignment explanation

Indices: 1654626--1654656 Score: 53 Period size: 10 Copynumber: 3.1 Consensus size: 10 1654616 TGTGGCTCTG 1654626 AAACATACAC 1 AAACATACAC * 1654636 AAACATACAT 1 AAACATACAC 1654646 AAACATACAC 1 AAACATACAC 1654656 A 1 A 1654657 TTACAAGACA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 10 19 1.00 ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13 Consensus pattern (10 bp): AAACATACAC Found at i:1658553 original size:2 final size:2 Alignment explanation

Indices: 1658546--1658603 Score: 116 Period size: 2 Copynumber: 29.0 Consensus size: 2 1658536 TACAAATAAA 1658546 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 1658588 CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT 1658604 GTAGCAACTC Statistics Matches: 56, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 56 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1662624 original size:134 final size:134 Alignment explanation

Indices: 1662402--1662732 Score: 374 Period size: 134 Copynumber: 2.5 Consensus size: 134 1662392 TATAATCATG * * * * * * * 1662402 ACCCCTCAACCATATATATTCATGTTTCTGATGTCAAGGGGCATCAAATGTTATGTAGGTTATGG 1 ACCCCTTAACCATATATATTCTTGTTCCTTATGTCAAGGGGCATCAAAAGGTATGTAGGTAATGG * * * 1662467 GCCCTGTGGGTGGTCCTGACCCCCTCAAACACCAAGTCCCTTAATATCTTC-AAAACTGTTGAGA 66 GCCCTGTGGGTGGTCCTGACCCCCTCAAACACCAAGTCCATGAATATC-TCGAAAACGGTTGAGA 1662531 TCCCC 130 TCCCC * * * 1662536 A-CCCTTAAACCATATATATTCTTGTTCCTTATGTCAAGGGGCATCAAACGGTATGTACGTCATG 1 ACCCCTT-AACCATATATATTCTTGTTCCTTATGTCAAGGGGCATCAAAAGGTATGTAGGTAATG * * ** * 1662600 GGCCC-G-GGGATGGTCGTGACCCCCCTCGAACAGGAAGTGCATGAATATCTCGAAAACGGTTGA 65 GGCCCTGTGGG-TGGTCCTGA-CCCCCTCAAACACCAAGTCCATGAATATCTCGAAAACGGTTGA 1662663 GATCCCC 128 GATCCCC * * * 1662670 ACCCCTTAACCGTATGTATTCTTGATCCTTA----AA-GGGCATCAAAAGGTATGTAGGTAATGG 1 ACCCCTTAACCATATATATTCTTGTTCCTTATGTCAAGGGGCATCAAAAGGTATGTAGGTAATGG 1662730 GCC 66 GCC 1662733 TCAGGGTTAA Statistics Matches: 170, Mismatches: 22, Indels: 15 0.82 0.11 0.07 Matches are distributed among these distances: 129 27 0.16 130 2 0.01 132 3 0.02 133 15 0.09 134 118 0.69 135 5 0.03 ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27 Consensus pattern (134 bp): ACCCCTTAACCATATATATTCTTGTTCCTTATGTCAAGGGGCATCAAAAGGTATGTAGGTAATGG GCCCTGTGGGTGGTCCTGACCCCCTCAAACACCAAGTCCATGAATATCTCGAAAACGGTTGAGAT CCCC Found at i:1663879 original size:2 final size:2 Alignment explanation

Indices: 1663872--1663935 Score: 128 Period size: 2 Copynumber: 32.0 Consensus size: 2 1663862 TGTATGCATA 1663872 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 1663914 CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT 1663936 ATTAAAGTGG Statistics Matches: 62, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 62 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1668072 original size:30 final size:29 Alignment explanation

Indices: 1668030--1668116 Score: 97 Period size: 30 Copynumber: 2.9 Consensus size: 29 1668020 CCATTGCATC * 1668030 TTCGCTCTTCGCCGTCGCA-TCTTCGCACT 1 TTCGCTCTTCGCCGTCGCACTC-TCGCACA * 1668059 TTCGCTCCTTCGCCGTTGCACTCTCGCACA 1 TTCGCT-CTTCGCCGTCGCACTCTCGCACA * 1668089 TTCGCT-TTCGCAACTTCGCACTCTCGCA 1 TTCGCTCTTCGC--CGTCGCACTCTCGCA 1668117 TCTCCGACTT Statistics Matches: 50, Mismatches: 4, Indels: 7 0.82 0.07 0.11 Matches are distributed among these distances: 28 5 0.10 29 6 0.12 30 37 0.74 31 2 0.04 ACGTcount: A:0.10, C:0.41, G:0.16, T:0.32 Consensus pattern (29 bp): TTCGCTCTTCGCCGTCGCACTCTCGCACA Found at i:1673282 original size:166 final size:165 Alignment explanation

Indices: 1672853--1674358 Score: 1897 Period size: 166 Copynumber: 9.2 Consensus size: 165 1672843 CTTCTACTCA * * 1672853 AATAG-TTTTGAGAAGAAGATTTTTAAAAAATTTT-TCTATATA----TA---AAAA-TTTAT-C 1 AATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC * * * * * 1672907 CCCCATTGTGGCCCCGCCCTACCCCCAGGGACCATGATTTGAACAAACTTAAAACTACATTATCT 65 CCCCATTGTGGCCCCACCCTA-CCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCT * *** * * 1672972 GAGGATGCTTACACGCCAATTTGAGCTTTCTTGGCCA 129 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT * * * * * 1673009 AAAAGTTTTT-A-AA-AAGATTTTTAAAGATTTTGTCTATATATTCCTGTATAATAA-TTTATCC 1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAA-AACTTGATCC * * * 1673070 CCCAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGAATCTACATTACCT 65 CCCCATTGTGGCCCCACCCTACCCC-AGGGACCATGATTTGAACAAACTTGAATCTACACTACCT * 1673135 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCA 129 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT * 1673172 AATAGATTTTGAGAAGAAGATTTTTAAAGATTTTCT-TAATATATTCCTATGTAAAACTTGATCC 1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCT-ATATATTCCTATGTAAAACTTGATCC * * * * * 1673236 CCCTATTGTTGCCCCACCCTACCTCCTGGGACTATGATTTGAACAAACTTGAATCTACACTACCA 65 CCCCATTGTGGCCCCACCCTACC-CCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCT 1673301 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT 129 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT * 1673338 TATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCT-TAATATATTCCTATGTAAAACTTGATCC 1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCT-ATATATTCCTATGTAAAACTTGATCC * * * 1673402 CCCCATTGTGGCCCCACCCTACCCCCTGGGACCATGATTTGAACATACTTGAATCTACACTACTT 65 CCCCATTGTGGCCCCACCCTA-CCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCT * * * 1673467 GAGGATGCTTCCACTCAAATTTAAGCTTTCCTGGTCT 129 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT * * * * ** * 1673504 AACAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCCATTTATTCCTATGTAAAAATCCATTCC 1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCC * * * * * * 1673569 CCCATTGTAGCCCCACCATACCACAAGGGACTATGATTTCAACAAACTGGAATCTACACTACCTG 66 CCCATTGTGGCCCCACCCTACC-CCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTG * * * * 1673634 AGGATGCTTCCATTTTAATTTGAGCTTTTCTAGCCT 130 AGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT * 1673670 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATATAAAACTTGATCCC 1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCC * * * 1673735 CCCATTGTTGCCCCACCCTACTCACAGGCACCATGATTTGAACAAACTTGAATCTACACTACCTG 66 CCCATTGTGGCCCCACCCTAC-CCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTG * * * * 1673800 AGGATGCTTTCATTTTAATTTGAGCTTTCCTGACCT 130 AGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT 1673836 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCC 1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCC * * * * 1673901 CCCATTGTTGCCCCACCCTATCCCCAGGGACTATGATTTGAACAAACTTGAATCTACACTATCTA 66 CCCATTGTGGCCCCACCCTA-CCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTG * * * 1673966 AGGATGCTTCCATTTTAATTTGAGCTTTTCTGGCCT 130 AGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT * * 1674002 GATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATATAAAACTTGATCCC 1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGAT-CC * * 1674067 CCCCATTGTTGCCCCACCCTACCCACAGGGACCATGATTTGAACAAACTTGAATCTACACTATCT 65 CCCCATTGTGGCCCCACCCTACCC-CAGGGACCATGATTTGAACAAACTTGAATCTACACTACCT * * * 1674132 AAGGATGCTTCCATTTTAATTTGAGC-TTCTCTGGCCT 129 GAGGATGCTTCCACTTAAATTTGAGCTTTC-CTGGCCT * * * 1674169 GATACTTTTTGAGAAGAAGATTTATT-AAGATTTTCTCTAAATATTCCTATGTAAAACTTGATCC 1 AATAGTTTTTGAGAAGAAGATTT-TTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC * 1674233 CCCTC-TTGTGGCCCTCA--CTACCCCCGGGGACCATGATTTGAACAAACCTT-AATCTACACTA 65 CCC-CATTGTGGCCC-CACCCTA-CCCCAGGGACCATGATTTGAACAAA-CTTGAATCTACACTA * * ** * * * * * 1674294 CCTGAGGATGCCTCAACACAAGTTTAAGCTTTTCAGGCCG 126 CCTGAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT 1674334 AATAGTTTTTGAGAAGAAGATTTTT 1 AATAGTTTTTGAGAAGAAGATTTTT 1674359 GAAAAATACC Statistics Matches: 1203, Mismatches: 115, Indels: 56 0.88 0.08 0.04 Matches are distributed among these distances: 153 8 0.01 154 17 0.01 155 2 0.00 156 5 0.00 157 4 0.00 158 1 0.00 161 2 0.00 162 11 0.01 163 95 0.08 164 3 0.00 165 87 0.07 166 806 0.67 167 160 0.13 168 2 0.00 ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34 Consensus pattern (165 bp): AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCC CCCATTGTGGCCCCACCCTACCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGA GGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT Found at i:1676215 original size:2 final size:2 Alignment explanation

Indices: 1676208--1676256 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 1676198 GGTATGCATA 1676208 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 1676250 CT CT CT C 1 CT CT CT C 1676257 AAAATAACGT Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:1677590 original size:11 final size:11 Alignment explanation

Indices: 1677560--1677591 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 1677550 TAAAGACGAT * 1677560 CTTTAAGCCAC 1 CTTTAAGCTAC 1677571 CTTTAAGCTAC 1 CTTTAAGCTAC 1677582 CTTTAAGCTA 1 CTTTAAGCTA 1677592 TAAGTATTGC Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34 Consensus pattern (11 bp): CTTTAAGCTAC Found at i:1677650 original size:22 final size:22 Alignment explanation

Indices: 1677600--1677652 Score: 70 Period size: 22 Copynumber: 2.4 Consensus size: 22 1677590 TATAAGTATT * 1677600 GCTTAAAGGTGGCTTAAAGAAA 1 GCTTAAAGATGGCTTAAAGAAA * ** 1677622 GCGTAAAGATGGCTTAAAGGCA 1 GCTTAAAGATGGCTTAAAGAAA 1677644 GCTTAAAGA 1 GCTTAAAGA 1677653 CTATCTTTAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 26 1.00 ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21 Consensus pattern (22 bp): GCTTAAAGATGGCTTAAAGAAA Found at i:1677673 original size:11 final size:11 Alignment explanation

Indices: 1677657--1677685 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 1677647 TAAAGACTAT 1677657 CTTTAAGCCAC 1 CTTTAAGCCAC 1677668 CTTTAAGCCAC 1 CTTTAAGCCAC 1677679 CTTTAAG 1 CTTTAAG 1677686 GACAACTTAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:1677733 original size:11 final size:11 Alignment explanation

Indices: 1677717--1677745 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 1677707 GTCCAAACTT 1677717 CTTTAAGCCAC 1 CTTTAAGCCAC 1677728 CTTTAAGCCAC 1 CTTTAAGCCAC 1677739 CTTTAAG 1 CTTTAAG 1677746 GACAACTTAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:1677749 original size:60 final size:60 Alignment explanation

Indices: 1677656--1677805 Score: 300 Period size: 60 Copynumber: 2.5 Consensus size: 60 1677646 TTAAAGACTA 1677656 TCTTTAAGCCACCTTTAAGCCACCTTTAAGGACAACTTATAGGTCCTTAATGTCCAAACT 1 TCTTTAAGCCACCTTTAAGCCACCTTTAAGGACAACTTATAGGTCCTTAATGTCCAAACT 1677716 TCTTTAAGCCACCTTTAAGCCACCTTTAAGGACAACTTATAGGTCCTTAATGTCCAAACT 1 TCTTTAAGCCACCTTTAAGCCACCTTTAAGGACAACTTATAGGTCCTTAATGTCCAAACT 1677776 TCTTTAAGCCACCTTTAAGCCACCTTTAAG 1 TCTTTAAGCCACCTTTAAGCCACCTTTAAG 1677806 CCACCTTTAA Statistics Matches: 90, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 60 90 1.00 ACGTcount: A:0.29, C:0.27, G:0.11, T:0.32 Consensus pattern (60 bp): TCTTTAAGCCACCTTTAAGCCACCTTTAAGGACAACTTATAGGTCCTTAATGTCCAAACT Found at i:1677793 original size:11 final size:11 Alignment explanation

Indices: 1677777--1677841 Score: 121 Period size: 11 Copynumber: 5.9 Consensus size: 11 1677767 GTCCAAACTT 1677777 CTTTAAGCCAC 1 CTTTAAGCCAC 1677788 CTTTAAGCCAC 1 CTTTAAGCCAC 1677799 CTTTAAGCCAC 1 CTTTAAGCCAC * 1677810 CTTTAAGCTAC 1 CTTTAAGCCAC 1677821 CTTTAAGCCAC 1 CTTTAAGCCAC 1677832 CTTTAAGCCA 1 CTTTAAGCCA 1677842 TTAAAAAAAA Statistics Matches: 52, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 11 52 1.00 ACGTcount: A:0.28, C:0.34, G:0.09, T:0.29 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:1679056 original size:112 final size:112 Alignment explanation

Indices: 1678859--1679081 Score: 401 Period size: 112 Copynumber: 2.0 Consensus size: 112 1678849 AACCCTGACG ** * * 1678859 TGCACCTGGGCACACGACACACCTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT 1 TGCACCTGGGCACACGACACAAATGCTGTGTATAACTTGTATATTCTGTGTTAGTTCCAGGGGTT * 1678924 TTCTTAAGTTGGACAAACAATAGACTTTAATTAGATATACACAAACA 66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA 1678971 TGCACCTGGGCACACGACACAAATGCTGTGTATAACTTGTATATTCTGTGTTAGTTCCAGGGGTT 1 TGCACCTGGGCACACGACACAAATGCTGTGTATAACTTGTATATTCTGTGTTAGTTCCAGGGGTT 1679036 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAAC 66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAAC 1679082 GAACAAAACT Statistics Matches: 106, Mismatches: 5, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 112 106 1.00 ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32 Consensus pattern (112 bp): TGCACCTGGGCACACGACACAAATGCTGTGTATAACTTGTATATTCTGTGTTAGTTCCAGGGGTT TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA Found at i:1679302 original size:2 final size:2 Alignment explanation

Indices: 1679295--1679344 Score: 91 Period size: 2 Copynumber: 25.0 Consensus size: 2 1679285 CGGATGAACT * 1679295 GA GA GA GA GA GA AA 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 1679337 GA GA GA GA 1 GA GA GA GA 1679345 TTTTTTTCAC Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): GA Found at i:1679701 original size:22 final size:22 Alignment explanation

Indices: 1679673--1679733 Score: 70 Period size: 22 Copynumber: 2.8 Consensus size: 22 1679663 AATATTGACT * 1679673 TAAAGGCCACTTAAAGACAGTG 1 TAAAGGCCACTTAAAGACAGCG * * 1679695 TAAAGG-CAGTGTAAAGAGAGCG 1 TAAAGGCCACT-TAAAGACAGCG * 1679717 TAAATGCCACTTAAAGA 1 TAAAGGCCACTTAAAGA 1679734 TGCTTAAAGG Statistics Matches: 32, Mismatches: 5, Indels: 4 0.78 0.12 0.10 Matches are distributed among these distances: 21 3 0.09 22 26 0.81 23 3 0.09 ACGTcount: A:0.43, C:0.15, G:0.25, T:0.18 Consensus pattern (22 bp): TAAAGGCCACTTAAAGACAGCG Found at i:1679749 original size:11 final size:11 Alignment explanation

Indices: 1679726--1679775 Score: 75 Period size: 11 Copynumber: 4.6 Consensus size: 11 1679716 GTAAATGCCA * 1679726 CTTAAAGAT-G 1 CTTAAAGGTGG 1679736 CTTAAAGGTGG 1 CTTAAAGGTGG 1679747 CTTAAAGGTGG 1 CTTAAAGGTGG * 1679758 CTTAAAGGTAG 1 CTTAAAGGTGG 1679769 CTTAAAG 1 CTTAAAG 1679776 AAGTTTGGAC Statistics Matches: 37, Mismatches: 2, Indels: 1 0.93 0.05 0.03 Matches are distributed among these distances: 10 8 0.22 11 29 0.78 ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28 Consensus pattern (11 bp): CTTAAAGGTGG Found at i:1679872 original size:11 final size:11 Alignment explanation

Indices: 1679856--1679885 Score: 51 Period size: 11 Copynumber: 2.7 Consensus size: 11 1679846 CCTTTTAGCT * 1679856 CCTTTAAGTCA 1 CCTTTAAGCCA 1679867 CCTTTAAGCCA 1 CCTTTAAGCCA 1679878 CCTTTAAG 1 CCTTTAAG 1679886 GACTTGCTTA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33 Consensus pattern (11 bp): CCTTTAAGCCA Found at i:1681071 original size:4 final size:4 Alignment explanation

Indices: 1681062--1681097 Score: 54 Period size: 4 Copynumber: 9.0 Consensus size: 4 1681052 TCTAGCCTTG * * 1681062 TGTC TGTC TGTC CGTC CGTC TGTC TGTC TGTC TGTC 1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC 1681098 CGTCCGTAAC Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 4 30 1.00 ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44 Consensus pattern (4 bp): TGTC Done.