Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2673

Parameters: 2 7 7 80 10 50 1000

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

Length: 42711
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:1634 original size:20 final size:20

Alignment explanation

Indices: 1609--1683 Score: 71 Period size: 20 Copynumber: 3.6 Consensus size: 20 1599 CCGTGGACTC * 1609 AATGTATCGATACTATTCAT 1 AATGTATCAATACTATTCAT * 1629 AATGTATCAATAC-ATGAACAGT 1 AATGTATCAATACTAT--TCA-T * * 1651 GATGTATCAATACTATTCAC 1 AATGTATCAATACTATTCAT * 1671 AATGTATCGATAC 1 AATGTATCAATAC 1684 ATGAACAATG Statistics Matches: 44, Mismatches: 7, Indels: 8 0.75 0.12 0.14 Matches are distributed among these distances: 19 2 0.05 20 23 0.52 21 4 0.09 22 13 0.30 23 2 0.05 ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33 Consensus pattern (20 bp): AATGTATCAATACTATTCAT Found at i:1656 original size:22 final size:21 Alignment explanation

Indices: 1630--1696 Score: 66 Period size: 22 Copynumber: 3.1 Consensus size: 21 1620 ACTATTCATA 1630 ATGTATCAATACATGAACAGTG 1 ATGTATCAATACATGAACA-TG ** 1652 ATGTATCAATACTATTCACA-- 1 ATGTATCAATAC-ATGAACATG * 1672 ATGTATCGATACATGAACAATG 1 ATGTATCAATACATGAAC-ATG 1694 ATG 1 ATG 1697 AATAGTGATG Statistics Matches: 36, Mismatches: 5, Indels: 8 0.73 0.10 0.16 Matches are distributed among these distances: 19 4 0.11 20 12 0.33 22 15 0.42 23 5 0.14 ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30 Consensus pattern (21 bp): ATGTATCAATACATGAACATG Found at i:1669 original size:42 final size:42 Alignment explanation

Indices: 1610--1696 Score: 138 Period size: 42 Copynumber: 2.1 Consensus size: 42 1600 CGTGGACTCA * * * 1610 ATGTATCGATACTATTCATAATGTATCAATACATGAACAGTG 1 ATGTATCAATACTATTCACAATGTATCAATACATGAACAATG * 1652 ATGTATCAATACTATTCACAATGTATCGATACATGAACAATG 1 ATGTATCAATACTATTCACAATGTATCAATACATGAACAATG 1694 ATG 1 ATG 1697 AATAGTGATG Statistics Matches: 41, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 42 41 1.00 ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32 Consensus pattern (42 bp): ATGTATCAATACTATTCACAATGTATCAATACATGAACAATG Found at i:2855 original size:34 final size:35 Alignment explanation

Indices: 2817--2883 Score: 102 Period size: 36 Copynumber: 1.9 Consensus size: 35 2807 CCTTACAACA 2817 CTATC-TTTCAA-GGCTAAGATAGAAACCTCTCTCT 1 CTATCTTTTCAAGGGCTAAGATAG-AACCTCTCTCT 2851 CTATCTTTTTCAAGGGCTAAGATAGAACCTCTC 1 CTATC-TTTTCAAGGGCTAAGATAGAACCTCTC 2884 AATCACTTAG Statistics Matches: 30, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 34 5 0.17 36 14 0.47 37 11 0.37 ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33 Consensus pattern (35 bp): CTATCTTTTCAAGGGCTAAGATAGAACCTCTCTCT Found at i:3356 original size:13 final size:13 Alignment explanation

Indices: 3338--3363 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 3328 CAATTTTTTG 3338 TGTATCGATACAT 1 TGTATCGATACAT 3351 TGTATCGATACAT 1 TGTATCGATACAT 3364 ACTTGGTGTA 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:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:3378 original size:32 final size:33 Alignment explanation

Indices: 3318--3381 Score: 94 Period size: 32 Copynumber: 2.0 Consensus size: 33 3308 TACAAGCCAA ** * 3318 TGTATCGATACAATTTTTTGTGTATCGATACAT 1 TGTATCGATACAATACTTGGTGTATCGATACAT 3351 TGTATCGATAC-ATACTTGGTGTATCGATACA 1 TGTATCGATACAATACTTGGTGTATCGATACA 3382 AGTTTGGCTA Statistics Matches: 28, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 32 17 0.61 33 11 0.39 ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41 Consensus pattern (33 bp): TGTATCGATACAATACTTGGTGTATCGATACAT Found at i:5521 original size:23 final size:24 Alignment explanation

Indices: 5476--5522 Score: 62 Period size: 23 Copynumber: 2.0 Consensus size: 24 5466 CAAAGAATTG * 5476 AACACAAATTCAATTAAGCACAAA 1 AACACAAATTCAATTAAGAACAAA 5500 AACACAAA-TCAATTGAA-AACAAA 1 AACACAAATTCAATT-AAGAACAAA 5523 TTTTCAACAA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 23 11 0.52 24 10 0.48 ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15 Consensus pattern (24 bp): AACACAAATTCAATTAAGAACAAA Found at i:6568 original size:84 final size:84 Alignment explanation

Indices: 6413--6577 Score: 201 Period size: 84 Copynumber: 2.0 Consensus size: 84 6403 CATTTTCCAC * * * * 6413 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC 1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC 6478 TCATTGATTTACTTTCATT 66 TCATTGATTTACTTTCATT * * 6497 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA 1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA * * * 6559 CACTTATTGATTTATTTTC 63 AACTCATTGATTTACTTTC 6578 TTCTTTGAGT Statistics Matches: 69, Mismatches: 9, Indels: 6 0.82 0.11 0.07 Matches are distributed among these distances: 82 6 0.09 83 9 0.13 84 54 0.78 ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52 Consensus pattern (84 bp): TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC TCATTGATTTACTTTCATT Found at i:8140 original size:34 final size:35 Alignment explanation

Indices: 8102--8168 Score: 102 Period size: 36 Copynumber: 1.9 Consensus size: 35 8092 CCTTACAACA 8102 CTATC-TTTCAA-GGCTAAGATAGAAACCTCTCTCT 1 CTATCTTTTCAAGGGCTAAGATAG-AACCTCTCTCT 8136 CTATCTTTTTCAAGGGCTAAGATAGAACCTCTC 1 CTATC-TTTTCAAGGGCTAAGATAGAACCTCTC 8169 AATCACTTAG Statistics Matches: 30, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 34 5 0.17 36 14 0.47 37 11 0.37 ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33 Consensus pattern (35 bp): CTATCTTTTCAAGGGCTAAGATAGAACCTCTCTCT Found at i:8645 original size:13 final size:13 Alignment explanation

Indices: 8627--8652 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 8617 CAATTTTTTG 8627 TGTATCGATACAT 1 TGTATCGATACAT 8640 TGTATCGATACAT 1 TGTATCGATACAT 8653 ACTTGGTGTA 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:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:8667 original size:32 final size:33 Alignment explanation

Indices: 8607--8670 Score: 94 Period size: 32 Copynumber: 2.0 Consensus size: 33 8597 TACAAGCCAA ** * 8607 TGTATCGATACAATTTTTTGTGTATCGATACAT 1 TGTATCGATACAATACTTGGTGTATCGATACAT 8640 TGTATCGATAC-ATACTTGGTGTATCGATACA 1 TGTATCGATACAATACTTGGTGTATCGATACA 8671 AGTTTGGCTA Statistics Matches: 28, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 32 17 0.61 33 11 0.39 ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41 Consensus pattern (33 bp): TGTATCGATACAATACTTGGTGTATCGATACAT Found at i:12234 original size:338 final size:338 Alignment explanation

Indices: 11603--12281 Score: 1135 Period size: 338 Copynumber: 2.0 Consensus size: 338 11593 TTTCTATGGC * 11603 ATGGTAAGAGATATGTGTTGAAAAAGAGAAGATTGATAGATGAATAGCCCATCTAACTGATCCTC 1 ATGGTAAGAGATATGTGCTGAAAAAGAGAAGATTGATAGATGAATAGCCCATCTAACTGATCCTC * * * * * 11668 GACGGTCATTACGAAATAACCAAAATTTTAGAGTTGCCAATGATCATTTCGGGTTAGGCATGATT 66 GACGGTCATCACGAAATAACCAAAATGTTAGAGTTGCCAATGATCATTTCGGGCTAGGCACGATC * * 11733 GGATGCCTATTGAAACTTATGTATTGAGTTACGAAACTCAAGACATCGATCTCATGGTCTACGTA 131 GGATGCCTATTGAAACCTATGTATTGAGTTACGAAACTCAAGACATCGATCTCATGATCTACGTA 11798 CTTCAAAGATTCGTCGATTGGTTCAAGAGTTGGTTACGCACAAAAAGGTAAGAACCTCCTCGTGA 196 CTTCAAAGATTCGTCGATTGGTTCAAGAGTTGGTTACGCACAAAAAGGTAAGAACCTCCTCGTGA * * * 11863 CGTAAAAAATCGGTACCTTACTAGCTTCACTTTGACTTGGCATTGGTTTCATTGGTTTCGACTCG 261 CGTAAAAAATCAGTACCTTACTAGCTACACTTTGACTTGACATTGGTTTCATTGGTTTCGACTCG 11928 ATATTATTTCAAT 326 ATATTATTTCAAT * * 11941 ATGGTAAGAGATATGTGCTGAAAAAGAGATGATTGATAGATGAATAGCTCATCTAACTGATCCTC 1 ATGGTAAGAGATATGTGCTGAAAAAGAGAAGATTGATAGATGAATAGCCCATCTAACTGATCCTC * * * 12006 GACGGTCATCATGAAATGACCAAAATGTTAGAGTTGCCATTGATCATTTCGGGCTAGGCACGATC 66 GACGGTCATCACGAAATAACCAAAATGTTAGAGTTGCCAATGATCATTTCGGGCTAGGCACGATC * 12071 GGATGCCTATTGAAACCTATGTATTGAGTTACGAAACAT-GAGACATCGATCTCATGATCTACGT 131 GGATGCCTATTGAAACCTATGTATTGAGTTACGAAAC-TCAAGACATCGATCTCATGATCTACGT * * * 12135 ACTTCAAATATTCGTCGATTGGTTCAAGAGTTGGTTACGCACAAAGAGGTACGAACCTCCTCGTG 195 ACTTCAAAGATTCGTCGATTGGTTCAAGAGTTGGTTACGCACAAAAAGGTAAGAACCTCCTCGTG * * * 12200 ACGTAAAAAATCAGTACTTTATTAGCTACACTTTGACTTGACATTGGTTTCATTGGTTTTGACTC 260 ACGTAAAAAATCAGTACCTTACTAGCTACACTTTGACTTGACATTGGTTTCATTGGTTTCGACTC 12265 GATATTATTTCAAT 325 GATATTATTTCAAT 12279 ATG 1 ATG 12282 ATCCCCTTGA Statistics Matches: 317, Mismatches: 23, Indels: 2 0.93 0.07 0.01 Matches are distributed among these distances: 338 316 1.00 339 1 0.00 ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31 Consensus pattern (338 bp): ATGGTAAGAGATATGTGCTGAAAAAGAGAAGATTGATAGATGAATAGCCCATCTAACTGATCCTC GACGGTCATCACGAAATAACCAAAATGTTAGAGTTGCCAATGATCATTTCGGGCTAGGCACGATC GGATGCCTATTGAAACCTATGTATTGAGTTACGAAACTCAAGACATCGATCTCATGATCTACGTA CTTCAAAGATTCGTCGATTGGTTCAAGAGTTGGTTACGCACAAAAAGGTAAGAACCTCCTCGTGA CGTAAAAAATCAGTACCTTACTAGCTACACTTTGACTTGACATTGGTTTCATTGGTTTCGACTCG ATATTATTTCAAT Found at i:14540 original size:13 final size:13 Alignment explanation

Indices: 14522--14547 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 14512 ACACCAAAGT 14522 ATGTATCGATACA 1 ATGTATCGATACA 14535 ATGTATCGATACA 1 ATGTATCGATACA 14548 CAAAAAATTG 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:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:14545 original size:33 final size:33 Alignment explanation

Indices: 14503--14567 Score: 96 Period size: 33 Copynumber: 2.0 Consensus size: 33 14493 TAGCCAAACT * * 14503 TGTATCGATACAC-CAAAGTATGTATCGATACAA 1 TGTATCGATACACAAAAAAT-TGTATCGATACAA 14536 TGTATCGATACACAAAAAATTGTATCGATACA 1 TGTATCGATACACAAAAAATTGTATCGATACA 14568 TTGGCTTGTA Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 33 25 0.86 34 4 0.14 ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28 Consensus pattern (33 bp): TGTATCGATACACAAAAAATTGTATCGATACAA Found at i:16295 original size:20 final size:20 Alignment explanation

Indices: 16270--16396 Score: 94 Period size: 20 Copynumber: 5.8 Consensus size: 20 16260 GTAAAAAGAC 16270 AGAATGTATCGATACATTGA 1 AGAATGTATCGATACATTGA * 16290 AGAATGTATCGATACATTCA 1 AGAATGTATCGATACATTGA * 16310 TA-CATGTATCGATACATTGA 1 -AGAATGTATCGATACATTGA * * * 16330 AAAATGTTTTGATACATCTGGGTAAA 1 AGAATGTATCGATACAT-T--G---A 16356 AGACAAAGTGTATCGATACATTGA 1 AG---AA-TGTATCGATACATTGA * 16380 AAAATGTATCGATACAT 1 AGAATGTATCGATACAT 16397 CTGGGTAAAA Statistics Matches: 85, Mismatches: 10, Indels: 24 0.71 0.08 0.20 Matches are distributed among these distances: 19 1 0.01 20 60 0.71 21 4 0.05 23 1 0.01 24 2 0.02 26 2 0.02 27 1 0.01 29 3 0.04 30 11 0.13 ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31 Consensus pattern (20 bp): AGAATGTATCGATACATTGA Found at i:16392 original size:90 final size:91 Alignment explanation

Indices: 16222--16396 Score: 282 Period size: 90 Copynumber: 1.9 Consensus size: 91 16212 TTTTAACTAG * 16222 ATGTATCGATACACTGAAAAATGTATTGATATATCTAGGTAAAAAGACAGAATGTATCGATACAT 1 ATGTATCGATACACTGAAAAATGTATTGATACATCTAGGTAAAAAGACAGAATGTATCGATACAT * 16287 TGAAGAATGTATCGATACATTCATAC 66 TGAAAAATGTATCGATACATTCATAC * * * 16313 ATGTATCGATACATTGAAAAATGTTTTGATACATCTGGGT-AAAAGACA-AAGTGTATCGATACA 1 ATGTATCGATACACTGAAAAATGTATTGATACATCTAGGTAAAAAGACAGAA-TGTATCGATACA 16376 TTGAAAAATGTATCGATACAT 65 TTGAAAAATGTATCGATACAT 16397 CTGGGTAAAA Statistics Matches: 78, Mismatches: 5, Indels: 3 0.91 0.06 0.03 Matches are distributed among these distances: 89 2 0.03 90 40 0.51 91 36 0.46 ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30 Consensus pattern (91 bp): ATGTATCGATACACTGAAAAATGTATTGATACATCTAGGTAAAAAGACAGAATGTATCGATACAT TGAAAAATGTATCGATACATTCATAC Found at i:21353 original size:59 final size:59 Alignment explanation

Indices: 21187--22184 Score: 615 Period size: 59 Copynumber: 17.0 Consensus size: 59 21177 TAAAATCTAT * * * 21187 AACTCCATGGCACCC-TTTTCAAAGTCCACAA-TATCGTGACACCCTTTTTAAAG-CTCAC 1 AACTTCATGGCACCCTTTTTCAAAGTCCACAACT-TCGTGGCACCCTTTTCAAAGTC-CAC * * * * * 21245 AAC-TCTTTGGCACCC-TTTTAAAAGCCCACAACTTTGTGGCATCCTTTTTCAAAGTCCAC 1 AACTTC-ATGGCACCCTTTTTCAAAGTCCACAACTTCGTGGCA-CCCTTTTCAAAGTCCAC * * * * * ** * * 21304 AACTTTAAGGAACCCTTTTTCAAAGTCCGCAACTTTGTGGCACCCTTTTCATTGTTCAT 1 AACTTCATGGCACCCTTTTTCAAAGTCCACAACTTCGTGGCACCCTTTTCAAAGTCCAC * * * * * * * 21363 AACTCCATGGCA-CCTTTTTCTAAAGTACAGAACTCCACTCTATGCCACCCTCTTCAAAGTCCAT 1 AACTTCATGGCACCCTTTTTC-AAAGTCCACAACT----TC-GTGGCACCCTTTTCAAAGTCCAC ** * 21427 AAC-TCAATGGTGCCCTTTCTT-AAAGTCCACAACTTTGTGGCACCCTTTTTCAAAGTCCAC 1 AACTTC-ATGGCACCCTTT-TTCAAAGTCCACAACTTCGTGGCACCC-TTTTCAAAGTCCAC * * * * * * 21487 AAC-TC-TGTAGC-CCCCTTTTCAAAGTCCACAACTCCATGGCAACCCTTTCCAAACTCCAT 1 AACTTCATG--GCACCCTTTTTCAAAGTCCACAACTTCGTGGC-ACCCTTTTCAAAGTCCAC * ** * * * * * 21546 AACTCCGCGACACCC-TTTT-AAAGTCTACAATTTTGTGGCACCCTTTT-AGAGTCCAC 1 AACTTCATGGCACCCTTTTTCAAAGTCCACAACTTCGTGGCACCCTTTTCAAAGTCCAC * * * 21602 AACTCCGTGGCA-CCTTTTT-AAAGTCCACAACTTCGTGGCACCCTTTTGAAAGTCCAC 1 AACTTCATGGCACCCTTTTTCAAAGTCCACAACTTCGTGGCACCCTTTTCAAAGTCCAC * * * * 21659 AAC-TCAATGGCACCCCTTTCCAAAGTCCACAACTCCGTGGCACCCTTTT-AAAGTCTAC 1 AACTTC-ATGGCACCCTTTTTCAAAGTCCACAACTTCGTGGCACCCTTTTCAAAGTCCAC * * 21717 AAC-TCAATGGCACCCTTTTCCAAAGTCCACAAC-TCGGTGGCACCCTTTTTCAAAGCCCAC 1 AACTTC-ATGGCACCCTTTTTCAAAGTCCACAACTTC-GTGGCACCC-TTTTCAAAGTCCAC * * * * * * *** * * 21777 AACTCCGTGGCA-CTTTTTTCTAAGTCCACAATTTTAG-GGCATAATTTTTTAAAGTCAAC 1 AACTTCATGGCACCCTTTTTCAAAGTCCACAA-CTTCGTGGCA-CCCTTTTCAAAGTCCAC * * * * 21836 AACTCCATGACA-CATTTTTCAAAGTCCATAACTTCGTGGCACCCTTTTCAAAGTCCAC 1 AACTTCATGGCACCCTTTTTCAAAGTCCACAACTTCGTGGCACCCTTTTCAAAGTCCAC * * * * * * * 21894 AACTCCGTGGCACCCTTTTTCAAAGTCTACAACTTCATGGCACCCTTCTCAAAGTCAAT 1 AACTTCATGGCACCCTTTTTCAAAGTCCACAACTTCGTGGCACCCTTTTCAAAGTCCAC * * * * * 21953 AAC-TCTGTGGCACCCCTTTTCAAAGTCCAC-AC-TCTATGGCACCCTTCTT-AAAGTCTAT 1 AACTTC-ATGGCACCCTTTTTCAAAGTCCACAACTTC-GTGGCACCCTT-TTCAAAGTCCAC * ** * * * * 22011 AACTTCGTGGTGCCCCTTTTCAAAGTCCATAACTTCGTGGCACCCCTTCTCATAGTCCAC 1 AACTTCATGGCACCCTTTTTCAAAGTCCACAACTTCGTGGCA-CCCTTTTCAAAGTCCAC * * * * * *** * * 22071 AACTTCGTGACA-CCTCTTTT-AAAGTCAATAATTTCGTGGCATTATTTT-AAAGTTCAT 1 AACTTCATGGCACCCT-TTTTCAAAGTCCACAACTTCGTGGCACCCTTTTCAAAGTCCAC * * * * * 22128 AAC-TCTGTGGCA-CCTTTTT-AAAGTTCGCAACTTCGTCGCACCCTTTT-AAAGCCCAC 1 AACTTC-ATGGCACCCTTTTTCAAAGTCCACAACTTCGTGGCACCCTTTTCAAAGTCCAC 22184 A 1 A 22185 CAAGTTAGTG Statistics Matches: 740, Mismatches: 153, Indels: 96 0.75 0.15 0.10 Matches are distributed among these distances: 55 2 0.00 56 78 0.11 57 44 0.06 58 186 0.25 59 289 0.39 60 94 0.13 61 3 0.00 63 2 0.00 64 35 0.05 65 5 0.01 66 2 0.00 ACGTcount: A:0.26, C:0.31, G:0.12, T:0.30 Consensus pattern (59 bp): AACTTCATGGCACCCTTTTTCAAAGTCCACAACTTCGTGGCACCCTTTTCAAAGTCCAC Found at i:21598 original size:28 final size:28 Alignment explanation

Indices: 21194--22184 Score: 525 Period size: 30 Copynumber: 33.8 Consensus size: 28 21184 TATAACTCCA 21194 TGGCACCCTTTTCAAAGTCCACAA-TATCG 1 TGGCACCCTTTT-AAAGTCCACAACT-TCG * * 21223 TGACACCCTTTTTAAAG-CTCACAAC-TCTT 1 TGGCACCC-TTTTAAAGTC-CACAACTTC-G * * 21252 TGGCACCCTTTTAAAAGCCCACAACTTTG 1 TGGCACCCTTTT-AAAGTCCACAACTTCG * ** 21281 TGGCATCCTTTTTCAAAGTCCACAACTTTA 1 TGGCA-CCCTTTT-AAAGTCCACAACTTCG * * * * 21311 AGGAACCCTTTTTCAAAGTCCGCAACTTTG 1 TGGCACCC-TTTT-AAAGTCCACAACTTCG ** * * * * 21341 TGGCACCCTTTTCATTGTTCATAACTCCA 1 TGGCACCCTTTT-AAAGTCCACAACTTCG * * * * 21370 TGGCACCTTTTTCTAAAGTACAGAACTCCACTCTA 1 TGGCACC-CTTT-TAAAGTCCACAACT----TC-G * * * * 21405 TGCCACCCTCTTCAAAGTCCATAAC-TCAA 1 TGGCACCCT-TTTAAAGTCCACAACTTC-G ** * 21434 TGGTGCCCTTTCTTAAAGTCCACAACTTTG 1 TGGCACCC-TT-TTAAAGTCCACAACTTCG 21464 TGGCACCCTTTTTCAAAGTCCACAAC-TCTG 1 TGGCACCC-TTTT-AAAGTCCACAACTTC-G * * * * 21494 TAGCCCCCTTTTCAAAGTCCACAACTCCA 1 TGGCACCCTTTT-AAAGTCCACAACTTCG * * * * 21523 TGGCAACCCTTTCCAAACTCCATAACTCCG 1 TGGC-ACCCTTT-TAAAGTCCACAACTTCG * * * * * 21553 CGACACCCTTTTAAAGTCTACAATTTTG 1 TGGCACCCTTTTAAAGTCCACAACTTCG * * 21581 TGGCACCCTTTTAGAGTCCACAACTCCG 1 TGGCACCCTTTTAAAGTCCACAACTTCG * 21609 TGGCACCTTTTTAAAGTCCACAACTTCG 1 TGGCACCCTTTTAAAGTCCACAACTTCG * 21637 TGGCACCCTTTTGAAAGTCCACAAC-TCAA 1 TGGCACCCTTTT-AAAGTCCACAACTTC-G * * 21666 TGGCACCCCTTTCCAAAGTCCACAACTCCG 1 TGGCA-CCCTTT-TAAAGTCCACAACTTCG * * 21696 TGGCACCCTTTTAAAGTCTACAAC-TCAA 1 TGGCACCCTTTTAAAGTCCACAACTTC-G 21724 TGGCACCCTTTTCCAAAGTCCACAAC-TCGG 1 TGGCACCCTTTT--AAAGTCCACAACTTC-G * * 21754 TGGCACCCTTTTTCAAAGCCCACAACTCCG 1 TGGCACCC-TTTT-AAAGTCCACAACTTCG ** * * * 21784 TGGCACTTTTTTCTAAGTCCACAATTTTAG 1 TGGCACCCTTTT-AAAGTCCACAA-CTTCG *** * * * 21814 -GGCATAATTTTTTAAAGTCAACAACTCCA 1 TGGC--ACCCTTTTAAAGTCCACAACTTCG * ** * 21843 TGACACATTTTTCAAAGTCCATAACTTCG 1 TGGCACCCTTTT-AAAGTCCACAACTTCG * 21872 TGGCACCCTTTTCAAAGTCCACAACTCCG 1 TGGCACCCTTTT-AAAGTCCACAACTTCG * * 21901 TGGCACCCTTTTTCAAAGTCTACAACTTCA 1 TGGCACCC-TTTT-AAAGTCCACAACTTCG * * * 21931 TGGCACCCTTCTCAAAGTCAATAAC-TCTG 1 TGGCACCCTT-TTAAAGTCCACAACTTC-G * 21960 TGGCACCCCTTTTCAAAGTCCAC-AC-TCTA 1 TGGCA-CCCTTTT-AAAGTCCACAACTTC-G * * 21989 TGGCACCCTTCTTAAAGTCTATAACTTCG 1 TGGCACCCTT-TTAAAGTCCACAACTTCG * 22018 TGGTGC-CCCTTTTCAAAGTCCATAACTTCG 1 T-G-GCACCCTTTT-AAAGTCCACAACTTCG * * 22048 TGGCACCCCTTCTCATAGTCCACAACTTCG 1 TGGCA-CCCTT-TTAAAGTCCACAACTTCG * * * * 22078 TGACACCTCTTTTAAAGTCAATAATTTCG 1 TGGCACC-CTTTTAAAGTCCACAACTTCG *** * * 22107 TGGCATTATTTTAAAGTTCATAAC-TCTG 1 TGGCACCCTTTTAAAGTCCACAACTTC-G * * * 22135 TGGCACCTTTTTAAAGTTCGCAACTTCG 1 TGGCACCCTTTTAAAGTCCACAACTTCG * * 22163 TCGCACCCTTTTAAAGCCCACA 1 TGGCACCCTTTTAAAGTCCACA 22185 CAAGTTAGTG Statistics Matches: 749, Mismatches: 156, Indels: 115 0.73 0.15 0.11 Matches are distributed among these distances: 27 3 0.00 28 172 0.23 29 241 0.32 30 294 0.39 31 18 0.02 34 12 0.02 35 9 0.01 ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30 Consensus pattern (28 bp): TGGCACCCTTTTAAAGTCCACAACTTCG Found at i:21949 original size:147 final size:146 Alignment explanation

Indices: 21194--22096 Score: 682 Period size: 147 Copynumber: 6.1 Consensus size: 146 21184 TATAACTCCA * * * * ** 21194 TGGCACCCTTTTCAAAGTCCACAA-TATCGTG-ACACCCTTTTTAAAG-CTCACAACTCTTTGGC 1 TGGCACCCTTTTCAAAGTCCACAACTCTAGGGCAC-CCCTTTTCAAAGTC-CACAACTCCATGGC * * * * * * **** * 21256 ACCCTTTTAAAAGCCCACAACTTTGTGGCATCCTTTTTCAAAGTCCACAACTTTAAGGAACCCTT 64 A-CCTTTTTAAAGTCTATAACTTCGTGGCA-CCCTTTTCAAAGTCCACAACTCCGTGGCACCCTT * * 21321 TTTCAAAGTCCGCAACTTTG 127 TTTCAAAGTCCACAACTTCG ** * * * * * * * 21341 TGGCACCCTTTTCATTGTTCATAACTCCATGGCA-CCTTTTTCTAAAGTACAGAACTCCACTCTA 1 TGGCACCCTTTTCAAAGTCCACAACTCTAGGGCACCCCTTTTC-AAAGTCCACAACT---C-C-A * * * * * ** * ** 21405 TGCCACCCTCTTCAAAGTCCATAAC-TCAATGGTGCCCTTTCTTAAAGTCCACAACTTTGTGGCA 60 TGGCA-CCTTTTTAAAGTCTATAACTTC-GTGGCACCCTTT-TCAAAGTCCACAACTCCGTGGCA 21469 CCCTTTTTCAAAGTCCACAAC-TCTG 122 CCCTTTTTCAAAGTCCACAACTTC-G * * * * * * * * ** * 21494 TAGCCCCCTTTTCAAAGTCCACAACTCCATGGCAACCCTTTCCAAACTCCATAACTCCGCGACAC 1 TGGCACCCTTTTCAAAGTCCACAACTCTAGGGCACCCCTTTTCAAAGTCCACAACTCCATGGCAC * * * * * 21559 CCTTTTAAAGTCTACAATTTTGTGGCACCCTTTT-AGAGTCCACAACTCCGTGGCA-CCTTTTT- 66 CTTTTTAAAGTCTATAACTTCGTGGCACCCTTTTCAAAGTCCACAACTCCGTGGCACCCTTTTTC 21621 AAAGTCCACAACTTCG 131 AAAGTCCACAACTTCG * * * * * 21637 TGGCACCCTTTTGAAAGTCCACAACTCAATGGCACCCCTTTCCAAAGTCCACAACTCCGTGGCAC 1 TGGCACCCTTTTCAAAGTCCACAACTCTAGGGCACCCCTTTTCAAAGTCCACAACTCCATGGCAC * * * * 21702 CCTTTTAAAGTCTACAAC-TCAATGGCACCCTTTTCCAAAGTCCACAACTCGGTGGCACCCTTTT 66 CTTTTTAAAGTCTATAACTTC-GTGGCACCCTTTT-CAAAGTCCACAACTCCGTGGCACCCTTTT * * 21766 TCAAAGCCCACAACTCCG 129 TCAAAGTCCACAACTTCG ** * * * **** * * * 21784 TGGCACTTTTTTCTAAGTCCACAATTTTAGGGCATAATTTTTTAAAGTCAACAACTCCATGACAC 1 TGGCACCCTTTTCAAAGTCCACAACTCTAGGGCACCCCTTTTCAAAGTCCACAACTCCATGGCAC * * 21849 ATTTTTCAAAGTCCATAACTTCGTGGCACCCTTTTCAAAGTCCACAACTCCGTGGCACCCTTTTT 66 CTTTTT-AAAGTCTATAACTTCGTGGCACCCTTTTCAAAGTCCACAACTCCGTGGCACCCTTTTT * * 21914 CAAAGTCTACAACTTCA 130 CAAAGTCCACAACTTCG * * * * 21931 TGGCACCCTTCTCAAAGTCAATAACTCT-GTGGCACCCCTTTTCAAAGTCCAC-ACTCTATGGCA 1 TGGCACCCTTTTCAAAGTCCACAACTCTAG-GGCACCCCTTTTCAAAGTCCACAACTCCATGGCA * * * * 21994 CCCTTCTTAAAGTCTATAACTTCGTGGTGC-CCCTTTTCAAAGTCCATAACTTCGTGGCACCCCT 65 -CCTTTTTAAAGTCTATAACTTCGT-G-GCACCCTTTTCAAAGTCCACAACTCCGTGGCACCCTT * * 22058 TCTCATAGTCCACAACTTCG 127 TTTCAAAGTCCACAACTTCG * 22078 TGACACCTCTTTT-AAAGTC 1 TGGCACC-CTTTTCAAAGTC 22097 AATAATTTCG Statistics Matches: 600, Mismatches: 129, Indels: 54 0.77 0.16 0.07 Matches are distributed among these distances: 142 1 0.00 143 98 0.16 144 9 0.01 145 37 0.06 146 34 0.06 147 257 0.43 148 44 0.07 149 4 0.01 150 1 0.00 151 1 0.00 152 7 0.01 153 101 0.17 154 6 0.01 ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30 Consensus pattern (146 bp): TGGCACCCTTTTCAAAGTCCACAACTCTAGGGCACCCCTTTTCAAAGTCCACAACTCCATGGCAC CTTTTTAAAGTCTATAACTTCGTGGCACCCTTTTCAAAGTCCACAACTCCGTGGCACCCTTTTTC AAAGTCCACAACTTCG Found at i:22056 original size:88 final size:88 Alignment explanation

Indices: 21188--22071 Score: 438 Period size: 88 Copynumber: 10.0 Consensus size: 88 21178 AAAATCTATA * * * * * 21188 ACTCCATGGCACCCTT-TTCAAAGTCCACAA-TATCGTGACACCCTTTTTAAAG-CTCACAAC-T 1 ACTCCATGGCACCCTTCTTCAAAGTCTACAACT-TCATGGCACCCTTTTCAAAGTC-CATAACTT * * * 21249 CTTTGGCA-CCCTTTTAAAAGCCCAC 64 C-GTGGCACCCCTTTTCAAAGTCCAC *** * * * * * * ** 21274 AACTTTGTGGCATCCTTTTTCAAAGTCCACAACTTTAAGGAACCCTTTTTCAAAGTCCGCAACTT 1 -ACTCCATGGCACCCTTCTTCAAAGTCTACAACTTCATGGCACCC-TTTTCAAAGTCCATAACTT * ** * * 21339 TGTGGCA-CCCTTTTCATTGTTCATA 64 CGTGGCACCCCTTTTCAAAGTCCA-C * * * * 21364 ACTCCATGGCA-CCTTTTTCTAAAGTAC-AGAACTCCACTCTATGCCACCCTCTTCAAAGTCCAT 1 ACTCCATGGCACCCTTCTTC-AAAGT-CTACAACT----TC-ATGGCACCCTTTTCAAAGTCCAT * ** * 21427 AAC-TCAATGG-TGCCCTTTCTTAAAGTCCAC 59 AACTTC-GTGGCACCCCTTT-TCAAAGTCCAC *** * * * * 21457 AACTTTGTGGCACCCTTTTTCAAAGTCCACAAC-TC-TGTAGCCCCCTTTTCAAAGTCCACAACT 1 -ACTCCATGGCACCCTTCTTCAAAGTCTACAACTTCATG--GCACCCTTTTCAAAGTCCATAACT * * * * * * 21520 CCATGGCAACCCTTTCCAAACTCCATA 63 TCGTGGCACCCCTTTTCAAAGTCCA-C ** * * ** * * * 21547 ACTCCGCGACACCCTT-TT-AAAGTCTACAATTTTGTGGCACCCTTTT-AGAGTCCACAACTCCG 1 ACTCCATGGCACCCTTCTTCAAAGTCTACAACTTCATGGCACCCTTTTCAAAGTCCATAACTTCG * 21609 TGGCA--CCTTTTTAAAGTCCAC 66 TGGCACCCCTTTTCAAAGTCCAC * * * * * * 21630 AACTTCGTGGCACCCTT-TTGAAAGTCCACAAC-TCAATGGCACCCCTTTCCAAAGTCCACAACT 1 -ACTCCATGGCACCCTTCTTCAAAGTCTACAACTTC-ATGGCA-CCCTTTTCAAAGTCCATAACT * * 21693 CCGTGGCA-CCCTTTT-AAAGTCTAC 63 TCGTGGCACCCCTTTTCAAAGTCCAC * * * * * 21717 AACTCAATGGCACCCTT-TTCCAAAGTCCACAAC-TCGGTGGCACCCTTTTTCAAAGCCCACAAC 1 -ACTCCATGGCACCCTTCTT-CAAAGTCTACAACTTC-ATGGCACCC-TTTTCAAAGTCCATAAC * ** * 21780 TCCGTGGCA-CTTTTTTCTAAGTCCAC 62 TTCGTGGCACCCCTTTTCAAAGTCCAC * ** * *** * * * * * ** 21806 AATTTTAGGGCATAATTTTTTAAAGTCAACAACTCCATGACACATTTTTCAAAGTCCATAACTTC 1 -ACTCCATGGCACCCTTCTTCAAAGTCTACAACTTCATGGCACCCTTTTCAAAGTCCATAACTTC 21871 GTGGCA-CCCTTTTCAAAGTCCAC 65 GTGGCACCCCTTTTCAAAGTCCAC * * * * 21894 AACTCCGTGGCACCCTTTTTCAAAGTCTACAACTTCATGGCACCCTTCTCAAAGTCAATAAC-TC 1 -ACTCCATGGCACCCTTCTTCAAAGTCTACAACTTCATGGCACCCTTTTCAAAGTCCATAACTTC 21958 TGTGGCACCCCTTTTCAAAGTCCAC 65 -GTGGCACCCCTTTTCAAAGTCCAC * * * 21983 ACTCTATGGCACCCTTCTT-AAAGTCTATAACTTCGTGGTGC-CCCTTTTCAAAGTCCATAACTT 1 ACTCCATGGCACCCTTCTTCAAAGTCTACAACTTCAT-G-GCACCCTTTTCAAAGTCCATAACTT * * 22046 CGTGGCACCCCTTCTCATAGTCCAC 64 CGTGGCACCCCTTTTCAAAGTCCAC 22071 A 1 A 22072 ACTTCGTGAC Statistics Matches: 621, Mismatches: 134, Indels: 83 0.74 0.16 0.10 Matches are distributed among these distances: 84 28 0.05 85 15 0.02 86 25 0.04 87 97 0.16 88 232 0.37 89 148 0.24 90 13 0.02 92 1 0.00 93 25 0.04 94 29 0.05 95 8 0.01 ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30 Consensus pattern (88 bp): ACTCCATGGCACCCTTCTTCAAAGTCTACAACTTCATGGCACCCTTTTCAAAGTCCATAACTTCG TGGCACCCCTTTTCAAAGTCCAC Found at i:22259 original size:31 final size:31 Alignment explanation

Indices: 22175--22274 Score: 128 Period size: 31 Copynumber: 3.2 Consensus size: 31 22165 GCACCCTTTT * 22175 AAAGCCCACACAAGTTAGTGGTAACCCTTTTCC 1 AAAGCCCACACAAGTTGGTGGTAA-CC-TTTCC * * 22208 AAAGCCCACACAAGTTGGTGGTATCCTTTCA 1 AAAGCCCACACAAGTTGGTGGTAACCTTTCC * * * 22239 AAAGCCCACAAAAGTCGGTGGCAACCTTTCC 1 AAAGCCCACACAAGTTGGTGGTAACCTTTCC 22270 AAAGC 1 AAAGC 22275 ATAGCATCTT Statistics Matches: 59, Mismatches: 8, Indels: 2 0.86 0.12 0.03 Matches are distributed among these distances: 31 35 0.59 32 2 0.03 33 22 0.37 ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21 Consensus pattern (31 bp): AAAGCCCACACAAGTTGGTGGTAACCTTTCC Found at i:22322 original size:33 final size:33 Alignment explanation

Indices: 22282--22619 Score: 266 Period size: 31 Copynumber: 10.5 Consensus size: 33 22272 AGCATAGCAT * * 22282 CTTTTCAAAAGCCCACATAAGTCGGTGGCAACT 1 CTTTTCAAAAGCCCACACAAGTCGGTGGCAACC * ** * * 22315 TTTTTCAAAAGCATACACAAGTTGGTGGC-ATC 1 CTTTTCAAAAGCCCACACAAGTCGGTGGCAACC ** 22347 C-TTTCAAAAGCCCACACAAGTTAGTGGCAACC 1 CTTTTCAAAAGCCCACACAAGTCGGTGGCAACC * * * * 22379 CTTTT-TAAAGCCCACATAAATCGATGGCAACC 1 CTTTTCAAAAGCCCACACAAGTCGGTGGCAACC * * * 22411 C-TTTC-AAAGCTCACACTAGTCGATGGCAACC 1 CTTTTCAAAAGCCCACACAAGTCGGTGGCAACC * * * 22442 CTTTTTAAAAGCCTACACAAGTCGGTGGTAA-C 1 CTTTTCAAAAGCCCACACAAGTCGGTGGCAACC * * * * * 22474 C-TTTCTAAAGCTCACACAAGTTGGTGG-TA-T 1 CTTTTCAAAAGCCCACACAAGTCGGTGGCAACC * * * 22504 CTTTTCAAAAGCCCATAGAAGTCAGTGGCAACC 1 CTTTTCAAAAGCCCACACAAGTCGGTGGCAACC * * ** * 22537 CTTTTC-AAAGCCCACAGAAAATCAATGGCAACA 1 CTTTTCAAAAGCCCACA-CAAGTCGGTGGCAACC * * * 22570 CTTTTTAAAAGGCCACACAAGTTGGTGGCAA-C 1 CTTTTCAAAAGCCCACACAAGTCGGTGGCAACC * 22602 CTTTCCAAAAGCCCACAC 1 CTTTTCAAAAGCCCACAC 22620 GAGTTGGCAG Statistics Matches: 236, Mismatches: 59, Indels: 21 0.75 0.19 0.07 Matches are distributed among these distances: 30 2 0.01 31 91 0.39 32 56 0.24 33 78 0.33 34 9 0.04 ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24 Consensus pattern (33 bp): CTTTTCAAAAGCCCACACAAGTCGGTGGCAACC Found at i:23095 original size:51 final size:51 Alignment explanation

Indices: 23001--23165 Score: 186 Period size: 51 Copynumber: 3.2 Consensus size: 51 22991 CTTGTTATTT * * * * 23001 TTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTAGAACCCTCATCACCA 1 TTAAGCCCAA-GTCGCTAGCCTTGAATCAGCACATTAGCACCCTCATCACCA * * * * 23053 TTGAGCCCAAGTCGCTAGCCTTGAATCAGCACATTGGCACCCTTATCACCT 1 TTAAGCCCAAGTCGCTAGCCTTGAATCAGCACATTAGCACCCTCATCACCA * * * * * * 23104 TTAAGCCTAAGTCGTTGGCCTTGAATCAGCACATTAGCACCTTTTATCACCT 1 TTAAGCCCAAGTCGCTAGCCTTGAATCAGCACATTAGCACC-CTCATCACCA 23156 TTAAGCCCAA 1 TTAAGCCCAA 23166 CATCATTGGC Statistics Matches: 97, Mismatches: 15, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 51 71 0.73 52 26 0.27 ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28 Consensus pattern (51 bp): TTAAGCCCAAGTCGCTAGCCTTGAATCAGCACATTAGCACCCTCATCACCA Found at i:23202 original size:53 final size:52 Alignment explanation

Indices: 23016--23188 Score: 170 Period size: 51 Copynumber: 3.3 Consensus size: 52 23006 TCCAATGTCG * * * * * * * * 23016 TTGGCCTTGAATCAGCACATTAGAACC-CTCATCACCATTGAGCCCAAGTCG 1 TTGGCCTTGAATCAACACATTAGCACCTTTTATCACCTTTAAGCCCAAATCA * * * * * * * * 23067 CTAGCCTTGAATCAGCACATTGGCACC-CTTATCACCTTTAAGCCTAAGTCG 1 TTGGCCTTGAATCAACACATTAGCACCTTTTATCACCTTTAAGCCCAAATCA * 23118 TTGGCCTTGAATCAGCACATTAGCACCTTTTATCACCTTTAAGCCCAACATCA 1 TTGGCCTTGAATCAACACATTAGCACCTTTTATCACCTTTAAGCCCAA-ATCA 23171 TTGGCCTTGAATCAACAC 1 TTGGCCTTGAATCAACAC 23189 GTTGTCACTT Statistics Matches: 104, Mismatches: 16, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 51 67 0.64 52 18 0.17 53 19 0.18 ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27 Consensus pattern (52 bp): TTGGCCTTGAATCAACACATTAGCACCTTTTATCACCTTTAAGCCCAAATCA Found at i:23209 original size:53 final size:52 Alignment explanation

Indices: 23070--23209 Score: 131 Period size: 53 Copynumber: 2.7 Consensus size: 52 23060 CAAGTCGCTA * * * ** * * * 23070 GCCTTGAATCAGCACATTGGCACC-CTTATCACCTTTAAGCCTAAGTCGTTG 1 GCCTTGAATCAACACATTAGCACCTTTTAAAACCTTTAAGCCCAAATCATTG * ** 23121 GCCTTGAATCAGCACATTAGCACCTTTTATCACCTTTAAGCCCAACATCATTG 1 GCCTTGAATCAACACATTAGCACCTTTTAAAACCTTTAAGCCCAA-ATCATTG * * 23174 GCCTTGAATCAACACGTT-GTCACTTTTTAAAACCTT 1 GCCTTGAATCAACACATTAG-CACCTTTTAAAACCTT 23210 CTGTCCAAAG Statistics Matches: 76, Mismatches: 10, Indels: 4 0.84 0.11 0.04 Matches are distributed among these distances: 51 23 0.30 52 19 0.25 53 34 0.45 ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31 Consensus pattern (52 bp): GCCTTGAATCAACACATTAGCACCTTTTAAAACCTTTAAGCCCAAATCATTG Found at i:23318 original size:52 final size:52 Alignment explanation

Indices: 23230--23346 Score: 171 Period size: 52 Copynumber: 2.2 Consensus size: 52 23220 CCTAATGCCG * * 23230 CTAGCCTTGAATCAGCACATTGGCACGCTTACCATCTTTAAATCCAATGTCA 1 CTAGCCTTGAATCAGCACAATAGCACGCTTACCATCTTTAAATCCAATGTCA * * * * 23282 TTAGCCTTGAATCAGCACAATAGCACTCTTATCATCTTTAAGTCCAATGTCA 1 CTAGCCTTGAATCAGCACAATAGCACGCTTACCATCTTTAAATCCAATGTCA * 23334 CAAGCCTTGAATC 1 CTAGCCTTGAATC 23347 TGCATATTGG Statistics Matches: 57, Mismatches: 8, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 52 57 1.00 ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30 Consensus pattern (52 bp): CTAGCCTTGAATCAGCACAATAGCACGCTTACCATCTTTAAATCCAATGTCA Found at i:24194 original size:25 final size:21 Alignment explanation

Indices: 24126--24204 Score: 115 Period size: 21 Copynumber: 3.8 Consensus size: 21 24116 AACATAAGTA 24126 AATGTTATCGATACATGCTTGT 1 AATG-TATCGATACATGCTTGT 24148 AATGTATCGATACATGCTTGT 1 AATGTATCGATACATGCTTGT * * 24169 AATGTATCGATACATTCTT-C 1 AATGTATCGATACATGCTTGT * 24189 AATGTATTGATACATG 1 AATGTATCGATACATG 24205 TAGGCAAATT Statistics Matches: 53, Mismatches: 4, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 20 14 0.26 21 35 0.66 22 4 0.08 ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39 Consensus pattern (21 bp): AATGTATCGATACATGCTTGT Found at i:29127 original size:16 final size:16 Alignment explanation

Indices: 29106--29139 Score: 59 Period size: 16 Copynumber: 2.1 Consensus size: 16 29096 GTTCAAGACT 29106 TAGTTACAATCACAAA 1 TAGTTACAATCACAAA * 29122 TAGTTACAATCACGAA 1 TAGTTACAATCACAAA 29138 TA 1 TA 29140 AGGATTGATC Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.47, C:0.18, G:0.09, T:0.26 Consensus pattern (16 bp): TAGTTACAATCACAAA Found at i:33631 original size:13 final size:13 Alignment explanation

Indices: 33613--33638 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 33603 GGCAGTAGTT 33613 TTGTATCGATACA 1 TTGTATCGATACA 33626 TTGTATCGATACA 1 TTGTATCGATACA 33639 ACACTTATGT 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:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TTGTATCGATACA Found at i:34571 original size:49 final size:49 Alignment explanation

Indices: 34412--34828 Score: 410 Period size: 49 Copynumber: 8.6 Consensus size: 49 34402 CAAAGAATGA * * * * * 34412 CAATGTGCTGATTCATGGCCAGTGACATTAGACTTAAAGAAGAA--TGC 1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC ** * * * * * 34459 CAATGTGCCTGAGACAAGGCCAACGACATTGGGCTTAGGAATGTTAAAGATGC 1 CAATGTG-CTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GATGAAGGTGC ** * * 34512 CAATGTGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGC 1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC 34561 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGGTTAAGGTGC 1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT-G--AAGGTGC * * * 34613 CAATGTGCTAATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGTGC 1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC * * 34662 CAATGTGCTTATTCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGC 1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC * * * * 34711 CAATATGCTGATTTAAGGCCAGCGATATTGGGC-T-----T----GTGC 1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC * * 34750 CAATGTGCTGATTCAAGGCCAGCGACATTGG-CTTTAAGATGGAGGTGC 1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC * * * 34798 CAATATGTTGATTCAAGGCCAGCGATATTGG 1 CAATGTGCTGATTCAAGGCCAGCGACATTGG 34829 GCTTGTGCCA Statistics Matches: 312, Mismatches: 39, Indels: 37 0.80 0.10 0.10 Matches are distributed among these distances: 38 1 0.00 39 33 0.11 43 1 0.00 44 1 0.00 47 7 0.02 48 55 0.18 49 126 0.40 50 5 0.02 51 4 0.01 52 69 0.22 53 10 0.03 ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26 Consensus pattern (49 bp): CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC Found at i:34627 original size:101 final size:97 Alignment explanation

Indices: 34412--34828 Score: 424 Period size: 101 Copynumber: 4.3 Consensus size: 97 34402 CAAAGAATGA * * * * * ** 34412 CAATGTGCTGATTCATGGCCAGTGACATTAGACTTAAAGAAGAA-TGCCAATGTGCCTGAGACAA 1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTGCCAATGTG-CTGATTCAA * * * * 34476 GGCCAACGACATTGGGCTTAGGAATGTTAAAGATGC 65 GGCCAACGACATTGGTCTTA--AA-GATGAAGGTGC ** 34512 CAATGTGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA 1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAA-GTGCCAATGTGCTGATTCAA * 34577 GGCCAGCGACATTGGTCTTAAAGATGGTTAAGGTGC 65 GGCCAACGACATTGGTCTTAAAGAT-G--AAGGTGC * * * * * * 34613 CAATGTGCTAATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGTGCCAATGTGCTTATTCAA 1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAA-GTGCCAATGTGCTGATTCAA 34678 GGCCAACGACATTGGTCTTAAAGATGAAGGTGC 65 GGCCAACGACATTGGTCTTAAAGATGAAGGTGC * * * 34711 CAATATGCTGATTTAAGGCCAGCGATATTGGGC-T-----T---GTGCCAATGTGCTGATTCAAG 1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTGCCAATGTGCTGATTCAAG * * * 34767 GCCAGCGACATTGG-CTTTAAGATGGAGGTGC 66 GCCAACGACATTGGTCTTAAAGATGAAGGTGC * * 34798 CAATATGTTGATTCAAGGCCAGCGATATTGG 1 CAATGTGCTGATTCAAGGCCAGCGATATTGG 34829 GCTTGTGCCA Statistics Matches: 280, Mismatches: 32, Indels: 23 0.84 0.10 0.07 Matches are distributed among these distances: 87 44 0.16 88 33 0.12 92 1 0.00 97 1 0.00 98 35 0.12 99 2 0.01 100 40 0.14 101 114 0.41 102 10 0.04 ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26 Consensus pattern (97 bp): CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTGCCAATGTGCTGATTCAAG GCCAACGACATTGGTCTTAAAGATGAAGGTGC Found at i:34699 original size:150 final size:148 Alignment explanation

Indices: 34412--34741 Score: 405 Period size: 150 Copynumber: 2.2 Consensus size: 148 34402 CAAAGAATGA * * * * 34412 CAATGTGCTGATTCATGGCCAGTGACATTAGACTTAAAGAAGAATGCCAATGTGCCTGAGACAAG 1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGAATGCCAATGTGCCTAAGACAAG * * * * 34477 GCCAACGACATTGGGCTTAGGAATGTTAAAGATGCCAATGTGCTGATTCAAGGCCAATGATATTG 66 GCCAACGACATCGGGCTTA-GAATGATAAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTG 34542 GACTTAAAGATGAAGGTGC 130 GACTTAAAGATGAAGGTGC * * * 34561 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGGTTAAGGTGCCAATGTG-CTAAT 1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-AG--AA--TGCCAATGTGCCTAAG * * * * * 34625 TCAAGGCCAACGACATCGGTCTTA-AA-GATGAAGGTGCCAATGTGCTTATTCAAGGCCAACGAC 61 ACAAGGCCAACGACATCGGGCTTAGAATGATAAAGATGCCAATGTGCTGATTCAAGGCCAACGAC * 34688 ATTGGTCTTAAAGATGAAGGTGC 126 ATTGGACTTAAAGATGAAGGTGC * * * 34711 CAATATGCTGATTTAAGGCCAGCGATATTGG 1 CAATGTGCTGATTCAAGGCCAGCGACATTGG 34742 GCTTGTGCCA Statistics Matches: 156, Mismatches: 20, Indels: 9 0.84 0.11 0.05 Matches are distributed among these distances: 149 36 0.23 150 82 0.53 151 2 0.01 152 2 0.01 153 24 0.15 154 10 0.06 ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25 Consensus pattern (148 bp): CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGAATGCCAATGTGCCTAAGACAAG GCCAACGACATCGGGCTTAGAATGATAAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGG ACTTAAAGATGAAGGTGC Found at i:34761 original size:39 final size:39 Alignment explanation

Indices: 34707--34867 Score: 171 Period size: 39 Copynumber: 3.9 Consensus size: 39 34697 AAAGATGAAG * 34707 GTGCCAATATGCTGATTTAAGGCCAGCGATATTGGGCTT 1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT * * 34746 GTGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGCTTTAAGAT 1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC--T----T * 34790 GGAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGGCTT 1 ----GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT * * 34833 GTGCCAATGTGCTGATTCAAGGCTAGCGATATTGG 1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGG 34868 ACTTTGAAGA Statistics Matches: 102, Mismatches: 9, Indels: 22 0.77 0.07 0.17 Matches are distributed among these distances: 38 3 0.03 39 62 0.61 40 1 0.01 43 1 0.01 44 1 0.01 47 1 0.01 48 30 0.29 49 3 0.03 ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29 Consensus pattern (39 bp): GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT Found at i:34820 original size:87 final size:88 Alignment explanation

Indices: 34658--34877 Score: 343 Period size: 87 Copynumber: 2.5 Consensus size: 88 34648 AAAGATGAAG * * * * 34658 GTGCCAATGTGCTTATTCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGAT 1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTTAAGATGAAGGTGCCAATATGCTGAT * 34723 TTAAGGCCAGCGATATTGGGCTT 66 TCAAGGCCAGCGATATTGGGCTT * * 34746 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGG-CTTTAAGATGGAGGTGCCAATATGTTGAT 1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTTAAGATGAAGGTGCCAATATGCTGAT 34810 TCAAGGCCAGCGATATTGGGCTT 66 TCAAGGCCAGCGATATTGGGCTT * * 34833 GTGCCAATGTGCTGATTCAAGGCTAGCGATATTGGACTTTGAAGA 1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTT-AAGA 34878 AGACGCCACC Statistics Matches: 122, Mismatches: 8, Indels: 3 0.92 0.06 0.02 Matches are distributed among these distances: 87 81 0.66 88 37 0.30 89 4 0.03 ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28 Consensus pattern (88 bp): GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTTAAGATGAAGGTGCCAATATGCTGAT TCAAGGCCAGCGATATTGGGCTT Found at i:34933 original size:29 final size:30 Alignment explanation

Indices: 34894--35018 Score: 161 Period size: 29 Copynumber: 4.3 Consensus size: 30 34884 CACCAACTTG 34894 TGTGGGCTTTTGAAAGGGTTG-CACTAACT 1 TGTGGGCTTTTGAAAGGGTTGCCACTAACT * 34923 TGTGTGCTTTTG-AA-GGTTGCCACTAACT 1 TGTGGGCTTTTGAAAGGGTTGCCACTAACT * * * 34951 TGTAGGC-TTTGAAAGGGGTGCCACTGACT 1 TGTGGGCTTTTGAAAGGGTTGCCACTAACT * 34980 TGTGGGCTTTTGAAAAGGG-TGCCACTGACT 1 TGTGGGCTTTTG-AAAGGGTTGCCACTAACT 35010 TGTGGGCTT 1 TGTGGGCTT 35019 AAAAAGAGAA Statistics Matches: 85, Mismatches: 6, Indels: 9 0.85 0.06 0.09 Matches are distributed among these distances: 27 9 0.11 28 17 0.20 29 29 0.34 30 24 0.28 31 6 0.07 ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34 Consensus pattern (30 bp): TGTGGGCTTTTGAAAGGGTTGCCACTAACT Found at i:34951 original size:59 final size:60 Alignment explanation

Indices: 34882--35013 Score: 155 Period size: 57 Copynumber: 2.2 Consensus size: 60 34872 TGAAGAAGAC * * * * * 34882 GCCACCAACTTGTGTGGGCTTTTGAAAGGGTTG-CACTAACTTGTGTGCTTTTG-AAGGTT 1 GCCACTAACTTGTGTAGGC-TTTGAAAGGGGTGCCACTAACTTGTGGGCTTTTGAAAGGGT * 34941 GCCACTAAC-T-TGTAGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTTGAAAAGGGT 1 GCCACTAACTTGTGTAGGCTTTGAAAGGGGTGCCACTAACTTGTGGGCTTTTG-AAAGGGT * 35000 GCCACTGACTTGTG 1 GCCACTAACTTGTG 35014 GGCTTAAAAA Statistics Matches: 61, Mismatches: 7, Indels: 8 0.80 0.09 0.11 Matches are distributed among these distances: 56 12 0.20 57 24 0.39 58 1 0.02 59 21 0.34 60 1 0.02 61 2 0.03 ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32 Consensus pattern (60 bp): GCCACTAACTTGTGTAGGCTTTGAAAGGGGTGCCACTAACTTGTGGGCTTTTGAAAGGGT Found at i:34994 original size:30 final size:30 Alignment explanation

Indices: 34894--35018 Score: 159 Period size: 30 Copynumber: 4.3 Consensus size: 30 34884 CACCAACTTG * 34894 TGTGGGCTTTTGAAAGGGTTG-CACTAACT 1 TGTGGGCTTTTGAAAGGGGTGCCACTAACT * * 34923 TGTGTGCTTTTG-AA-GGTTGCCACTAACT 1 TGTGGGCTTTTGAAAGGGGTGCCACTAACT * * 34951 TGTAGGC-TTTGAAAGGGGTGCCACTGACT 1 TGTGGGCTTTTGAAAGGGGTGCCACTAACT * * 34980 TGTGGGCTTTTGAAAAGGGTGCCACTGACT 1 TGTGGGCTTTTGAAAGGGGTGCCACTAACT 35010 TGTGGGCTT 1 TGTGGGCTT 35019 AAAAAGAGAA Statistics Matches: 85, Mismatches: 7, Indels: 7 0.86 0.07 0.07 Matches are distributed among these distances: 27 9 0.11 28 17 0.20 29 29 0.34 30 30 0.35 ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34 Consensus pattern (30 bp): TGTGGGCTTTTGAAAGGGGTGCCACTAACT Found at i:35046 original size:33 final size:33 Alignment explanation

Indices: 34999--35978 Score: 617 Period size: 33 Copynumber: 30.6 Consensus size: 33 34989 TTGAAAAGGG * * * 34999 TGCCACTGACTTGTGGGCTTAAAAAGAGAAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA 35032 TGCCACGGAGTTGTGGACTT-AAAAG-G---G- 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * 35059 TACCATGGAGTTGTGGACTT-AAAAG-G---G- 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * 35086 TGCCACGGAGTTGTGGACTTAAAAGGAGCAAGG 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA ** * * * 35119 TGCCTTGGAGTTCTGGACTTAAAAGGAAAAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * 35152 TGCCATGGAGTTGTGGATTTAAAAGGA-ACAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGA-AAGA * 35185 TGCCATGGAGTTGTGGACTT-AAAAG-G---G- 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * 35212 TACCACAGAGTTGTGGACTTAAAAAGAAAAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * * 35245 GTGCCACAGAGTTGTGGGCTT-AAAAGGGAAAAGGG 1 -TGCCACGGAGTTGTGGACTTAAAAAGAG-AAA-GA * 35280 TGCCACGGAGTCGTGGACTT-AAAAG-G---G- 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * 35307 TGCCCCGGAGTTGTGGACAT-AAAAGGGAAAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAG-AAAGA ** * 35340 GTGCCACGGAGTCATGGACTTAAAAGGA-ACAAGA 1 -TGCCACGGAGTTGTGGACTTAAAAAGAGA-AAGA * 35374 TGCCACGGAGTTGTGGACTT-AAAAGGGAAATGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAA-GA * * * * 35407 TGCCATGGAGTTGTGGATTTAACAGGA-ATAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGA-AAGA * 35440 TGCCACGAAGTTGTGGACTT-AAAAGAGAAAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAG-AAAGA * * 35473 TGCCACGAAGTTGTGGACTTAAAAGGA-ACAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGA-AAGA * * * * 35506 TGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * 35539 GTACCACGGAGTTGTGGGCTT-AAAAG-G---G- 1 -TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * 35567 TGCCACGGAGTTATGGACTTAAAAGGAAAAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * * 35600 GTGCCACAGAGTTGTGGACTTAAAAGGAAAAATA 1 -TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * 35634 TGCCACGGAGTTGTGGACTTAAAAGGA-ACAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGA-AAGA * 35667 TGCCACGGAGATGTGGACTT-AAAAG-G---G- 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * 35694 TGCCACGGAGTTCTGGACTTTAAAAGGAAAAAGAA 1 TGCCACGGAGTTGTGGAC-TTAAAAAGAGAAAG-A * * * * 35729 TGCCATGGAGTTGTGGGCTTAAAAGGAAAAAGAA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAG-A * * * * 35763 TGCCACGAAGTTGTGGGCTTAAAAGGAAAAAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAG-AGAAAGA * * 35797 GTGCCACAGAGTTGTGGGCTT-AAAAG-G---G- 1 -TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * 35825 TGCCACAGAGTTATGGACTTAAAAGGA-ACAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGA-AAGA * * * * * 35858 TGCCACAGAGTTGTGGGCTTAGAATGAAAAAGA 1 TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * * * 35891 GTGCCACAGAGTTCTGGGCTTAAAAAGAAAAATA 1 -TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA * * * 35925 GTGCCACAGAGTTTTGGACTT-AAAAGGGAAAAGA 1 -TGCCACGGAGTTGTGGACTTAAAAAGAG-AAAGA * * 35959 TACCACGAAGTTGTGGACTT 1 TGCCACGGAGTTGTGGACTT 35979 TGACAAAAGA Statistics Matches: 775, Mismatches: 107, Indels: 130 0.77 0.11 0.13 Matches are distributed among these distances: 27 133 0.17 28 24 0.03 29 7 0.01 31 1 0.00 32 31 0.04 33 313 0.40 34 222 0.29 35 44 0.06 ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20 Consensus pattern (33 bp): TGCCACGGAGTTGTGGACTTAAAAAGAGAAAGA Found at i:35252 original size:34 final size:34 Alignment explanation

Indices: 35205--35978 Score: 724 Period size: 33 Copynumber: 23.8 Consensus size: 34 35195 TTGTGGACTT * * * * 35205 AAAAGGGTACCACAGAGTTGTGGACTTAAAAAGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * * 35239 AAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGG 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * 35273 AAAAGGGTGCCACGGAGTCGTGGACTTAAAA-G- 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * * 35305 ----G-GTGCCCCGGAGTTGTGGACATAAAAGGG 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA ** 35334 AAAAGAGTGCCACGGAGTCATGGACTTAAAAGGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * 35368 ACAAGA-TGCCACGGAGTTGTGGACTTAAAAGGG 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * * * 35401 AAATGA-TGCCATGGAGTTGTGGATTTAACAGGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * 35434 ATAAGA-TGCCACGAAGTTGTGGACTTAAAA-GA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * 35466 GAAAAGA-TGCCACGAAGTTGTGGACTTAAAAGGA 1 -AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * * 35500 ACAAGA-TGCCACGGAGTTGTGGGCTTAGAAGGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * 35533 AAAAGAGTACCACGGAGTTGTGGGCTTAAAA-G- 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * 35565 ----G-GTGCCACGGAGTTATGGACTTAAAAGGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * 35594 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * 35628 AAAATA-TGCCACGGAGTTGTGGACTTAAAAGGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * 35661 ACAAGA-TGCCACGGAGATGTGGACTTAAAA-G- 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * 35692 ----G-GTGCCACGGAGTTCTGGACTTTAAAAGGA 1 AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGA * * * 35722 AAAAGAATGCCATGGAGTTGTGGGCTTAAAAGGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * * 35756 AAAAGAATGCCACGAAGTTGTGGGCTTAAAAGGAA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGG-A * * 35791 AAAAGAGTGCCACAGAGTTGTGGGCTTAAAA-G- 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * 35823 ----G-GTGCCACAGAGTTATGGACTTAAAAGGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * * * * 35852 ACAAGA-TGCCACAGAGTTGTGGGCTTAGAATGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * * * 35885 AAAAGAGTGCCACAGAGTTCTGGGCTTAAAAAGA 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * * * 35919 AAAATAGTGCCACAGAGTTTTGGACTTAAAAGGG 1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA * * 35953 AAAAGA-TACCACGAAGTTGTGGACTT 1 AAAAGAGTGCCACGGAGTTGTGGACTT 35979 TGACAAAAGA Statistics Matches: 623, Mismatches: 82, Indels: 71 0.80 0.11 0.09 Matches are distributed among these distances: 27 84 0.13 28 12 0.02 29 1 0.00 32 3 0.00 33 240 0.39 34 239 0.38 35 44 0.07 ACGTcount: A:0.37, C:0.13, G:0.31, T:0.19 Consensus pattern (34 bp): AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA Found at i:35267 original size:61 final size:60 Alignment explanation

Indices: 35159--35272 Score: 165 Period size: 61 Copynumber: 1.9 Consensus size: 60 35149 AGATGCCATG * * * ** 35159 GAGTTGTGGATTTAAAAGGAACAAGATGCCATGGAGTTGTGGACTTAAAAGGGTACCACA 1 GAGTTGTGGACTTAAAAAGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGGTACCACA * 35219 GAGTTGTGGACTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGG 1 GAGTTGTGGACTTAAAAAGAAAAAGA-TGCCACAGAGTTGTGGACTTAAAAGGG 35273 AAAAGGGTGC Statistics Matches: 47, Mismatches: 6, Indels: 1 0.87 0.11 0.02 Matches are distributed among these distances: 60 23 0.49 61 24 0.51 ACGTcount: A:0.36, C:0.11, G:0.32, T:0.22 Consensus pattern (60 bp): GAGTTGTGGACTTAAAAAGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGGTACCACA Found at i:35315 original size:27 final size:27 Alignment explanation

Indices: 35273--35333 Score: 95 Period size: 27 Copynumber: 2.3 Consensus size: 27 35263 CTTAAAAGGG * 35273 AAAAGGGTGCCACGGAGTCGTGGACTT 1 AAAAGGGTGCCACGGAGTCGTGGACAT * * 35300 AAAAGGGTGCCCCGGAGTTGTGGACAT 1 AAAAGGGTGCCACGGAGTCGTGGACAT 35327 AAAAGGG 1 AAAAGGG 35334 AAAAGAGTGC Statistics Matches: 31, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 27 31 1.00 ACGTcount: A:0.30, C:0.16, G:0.38, T:0.16 Consensus pattern (27 bp): AAAAGGGTGCCACGGAGTCGTGGACAT Found at i:35592 original size:27 final size:28 Alignment explanation

Indices: 35532--35851 Score: 151 Period size: 27 Copynumber: 10.2 Consensus size: 28 35522 GCTTAGAAGG * * * 35532 AAAAAGAGTACCACGGAGTTGTGGGCTT 1 AAAAGGAGTGCCACGGAGTTGTGGACTT * 35560 AAAAGG-GTGCCACGGAGTTATGGACTT 1 AAAAGGAGTGCCACGGAGTTGTGGACTT * 35587 AAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTT 1 AAAA-G-----GAGTGCCACGGAGTTGTGGACTT * 35621 AAAAGGAAAAATATGCCACGGAGTTGTGGACTT 1 AAAAGG----A-GTGCCACGGAGTTGTGGACTT * 35654 AAAAGGAACAAGATGCCACGGAGATGTGGACTT 1 AAAAGG----AG-TGCCACGGAGTTGTGGACTT * 35687 AAAAGG-GTGCCACGGAGTTCTGGACTTT 1 AAAAGGAGTGCCACGGAGTTGTGGAC-TT * * 35715 AAAAGGAAAAAGAATGCCATGGAGTTGTGGGCTT 1 AAAAGG----AG--TGCCACGGAGTTGTGGACTT * * 35749 AAAAGGAAAAAGAATGCCACGAAGTTGTGGGCTT 1 AAAAGG----AG--TGCCACGGAGTTGTGGACTT * * 35783 AAAAGGAAAAAAGAGTGCCACAGAGTTGTGGGCTT 1 AAAA-G------GAGTGCCACGGAGTTGTGGACTT * * 35818 AAAAGG-GTGCCACAGAGTTATGGACTT 1 AAAAGGAGTGCCACGGAGTTGTGGACTT 35845 AAAAGGA 1 AAAAGGA 35852 ACAAGATGCC Statistics Matches: 241, Mismatches: 22, Indels: 58 0.75 0.07 0.18 Matches are distributed among these distances: 27 63 0.26 28 17 0.07 32 1 0.00 33 57 0.24 34 62 0.26 35 38 0.16 37 2 0.01 41 1 0.00 ACGTcount: A:0.37, C:0.13, G:0.31, T:0.19 Consensus pattern (28 bp): AAAAGGAGTGCCACGGAGTTGTGGACTT Found at i:35733 original size:35 final size:34 Alignment explanation

Indices: 35694--35974 Score: 269 Period size: 34 Copynumber: 8.5 Consensus size: 34 35684 CTTAAAAGGG * * * 35694 TGCCACGGAGTTCTGGACTTTAAAAGGAAAAAGAA 1 TGCCACAGAGTTGTGGGC-TTAAAAGGAAAAAGAA ** 35729 TGCCATGGAGTTGTGGGCTTAAAAGGAAAAAGAA 1 TGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGAA * 35763 TGCCAC-GAAGTTGTGGGCTTAAAAGGAAAAAAGAG 1 TGCCACAG-AGTTGTGGGCTTAAAAGG-AAAAAGAA 35798 TGCCACAGAGTTGTGGGCTTAAAAGG-----G-- 1 TGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGAA * * * 35825 TGCCACAGAGTTATGGACTTAAAAGGAACAAG-A 1 TGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGAA * * * 35858 TGCCACAGAGTTGTGGGCTTAGAATGAAAAAGAG 1 TGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGAA * * * * 35892 TGCCACAGAGTTCTGGGCTTAAAAAGAAAAATAG 1 TGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGAA * * * 35926 TGCCACAGAGTTTTGGACTTAAAAGGGAAAAG-A 1 TGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGAA * 35959 TACCAC-GAAGTTGTGG 1 TGCCACAG-AGTTGTGG 35975 ACTTTGACAA Statistics Matches: 210, Mismatches: 25, Indels: 24 0.81 0.10 0.09 Matches are distributed among these distances: 27 24 0.11 29 1 0.00 32 2 0.01 33 40 0.19 34 96 0.46 35 46 0.22 36 1 0.00 ACGTcount: A:0.37, C:0.13, G:0.29, T:0.20 Consensus pattern (34 bp): TGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGAA Found at i:35897 original size:67 final size:68 Alignment explanation

Indices: 35818--35946 Score: 179 Period size: 67 Copynumber: 1.9 Consensus size: 68 35808 TTGTGGGCTT * * * * 35818 AAAAGGGTGCCACAGAGTTATGGACTTAAAAGGAACAAGA-TGCCACAGAGTTGTGGGCTTAGAA 1 AAAAGAGTGCCACAGAGTTATGGACTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGACTTAGAA 35882 TGA 66 TGA * * * * 35885 AAAAGAGTGCCACAGAGTTCTGGGCTTAAAAAGAAAAATAGTGCCACAGAGTTTTGGACTTA 1 AAAAGAGTGCCACAGAGTTATGGACTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGACTTA 35947 AAAGGGAAAA Statistics Matches: 53, Mismatches: 8, Indels: 1 0.85 0.13 0.02 Matches are distributed among these distances: 67 34 0.64 68 19 0.36 ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21 Consensus pattern (68 bp): AAAAGAGTGCCACAGAGTTATGGACTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGACTTAGAA TGA Found at i:39030 original size:32 final size:33 Alignment explanation

Indices: 38967--39034 Score: 95 Period size: 33 Copynumber: 2.1 Consensus size: 33 38957 CGTTACAAGC * * 38967 CAATGTATCGATACATTTGGTCATGTATCGATA 1 CAATGTATCGATAAACTTGGTCATGTATCGATA 39000 CAATGTATCGATAGAACTT-GT-ATGTATCGATA 1 CAATGTATCGATA-AACTTGGTCATGTATCGATA 39032 CAA 1 CAA 39035 ATAGTTAAGG Statistics Matches: 32, Mismatches: 2, Indels: 3 0.86 0.05 0.08 Matches are distributed among these distances: 32 14 0.44 33 15 0.47 34 3 0.09 ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34 Consensus pattern (33 bp): CAATGTATCGATAAACTTGGTCATGTATCGATA Found at i:39121 original size:13 final size:13 Alignment explanation

Indices: 39103--39127 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 39093 TACAGTGGTC 39103 ATGTATCGATACA 1 ATGTATCGATACA 39116 ATGTATCGATAC 1 ATGTATCGATAC 39128 TGTGCATTAT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): ATGTATCGATACA Done.