Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2942

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: 45771
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:2394 original size:7 final size:7

Alignment explanation

Indices: 2382--2411 Score: 60 Period size: 7 Copynumber: 4.3 Consensus size: 7 2372 TTTTCTAAGA 2382 AAAATTC 1 AAAATTC 2389 AAAATTC 1 AAAATTC 2396 AAAATTC 1 AAAATTC 2403 AAAATTC 1 AAAATTC 2410 AA 1 AA 2412 GCCGATAAAT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 23 1.00 ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27 Consensus pattern (7 bp): AAAATTC Found at i:2910 original size:25 final size:24 Alignment explanation

Indices: 2854--2904 Score: 70 Period size: 25 Copynumber: 2.1 Consensus size: 24 2844 ATTAATAACT 2854 AGTTAAGTT-AATTAAATTATGATTA 1 AGTTAA-TTAAATTAAATTA-GATTA 2879 AGTTAATTAAATTAAATTA-ATTA 1 AGTTAATTAAATTAAATTAGATTA 2902 AGT 1 AGT 2905 CTTAATCAAA Statistics Matches: 25, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 23 7 0.28 24 2 0.08 25 16 0.64 ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43 Consensus pattern (24 bp): AGTTAATTAAATTAAATTAGATTA Found at i:7273 original size:43 final size:43 Alignment explanation

Indices: 7199--7566 Score: 459 Period size: 43 Copynumber: 8.6 Consensus size: 43 7189 AATATTTTGC * * * * * 7199 ACGCCGCTATAGAACATGACCTTTAGTGGCACTTTTACAACAA 1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA * * * * * 7242 ACGCTGCTAAAGAACATGGCATTTAGCGGCACTTTTTCCACAA 1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA * * * * * 7285 ACGCCGTTAAAGAAAATAACCTTTAGTGGCGCTTTTCCCAAAA 1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA * 7328 ACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA 1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA * * * 7371 ATGCCACTAAAGAACATGACCTTTAGCGGCGTTTTTCCCACAA 1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA * * 7414 ACGCCGCTATAGAACATGACCTTTAGCGGCGTTTTTCCCACAA 1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA * * 7457 ACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACGA 1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA * * * * 7500 ACACCGCTATAGAACA-GACCTTTACCGACGCTTTTCCCACAA 1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA * * * 7542 ACGCCGATAAAGAATATGACTTTTA 1 ACGCCGCTAAAGAACATGACCTTTA 7567 AAAAATATTT Statistics Matches: 283, Mismatches: 41, Indels: 2 0.87 0.13 0.01 Matches are distributed among these distances: 42 35 0.12 43 248 0.88 ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24 Consensus pattern (43 bp): ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA Found at i:7875 original size:17 final size:18 Alignment explanation

Indices: 7839--7876 Score: 51 Period size: 18 Copynumber: 2.2 Consensus size: 18 7829 ATTTAGAATC 7839 AAAACTAAAATAAATAAT 1 AAAACTAAAATAAATAAT * * 7857 AAAATTAAATTAAAT-AT 1 AAAACTAAAATAAATAAT 7874 AAA 1 AAA 7877 GATATCAATA Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 17 5 0.28 18 13 0.72 ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26 Consensus pattern (18 bp): AAAACTAAAATAAATAAT Found at i:9432 original size:48 final size:47 Alignment explanation

Indices: 9331--9742 Score: 218 Period size: 48 Copynumber: 8.7 Consensus size: 47 9321 TCATTTGTGC * 9331 GCTAGTATAAGA-CATGTCTGGGACAT-GCATCAGCCACATT---ATGAGA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-G---CATTGAGATGAGA * * 9377 GCCAGTGTAAGACCATGTTTGGGACATGGCATCTGCATTGAGATGAGA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGAGATGAGA * * * 9425 GCTAGTGTAAGA-CGTGTCTGGGACAT-GCATCGGCCTCGAGATGTA-A 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGAGATG-AGA * * * * * 9471 GCCAGTGTAAGA-CATGTATGGGATAT-GCATCG-AGT-ACGAT-ATGT 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCATTGA-GATGA-GA * * * 9515 G-TCAGTGAAAGACCATGTCTGGGACATGGCAACAGCACGTAT-AGA-G-GT 1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATC-GCA--T-TGAGATGAGA * * * * 9563 GTTAGTGTAAGACCATGTCTAGGACATGGCATCAGCATGGATATGTGAGA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGAGA--TGAGA * * * * ** * 9613 GCTAATGTAAGACCATGTCTGGGACATGGCATTGGCCTCGATTTCGATA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCA-TCGCATTGAGAT-GAGA * * 9662 G-TCAGTGTACGACCATGTATGGGACATGGCATCG-ACTT--GATGGATGA 1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGCA-TTGAGAT-GA-GA * 9709 GCCAGTGTAAGACCATGTCTGGGACATGGCATCG 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCG 9743 GTATTACACC Statistics Matches: 285, Mismatches: 51, Indels: 59 0.72 0.13 0.15 Matches are distributed among these distances: 42 1 0.00 43 1 0.00 44 12 0.04 45 17 0.06 46 62 0.22 47 58 0.20 48 63 0.22 49 31 0.11 50 37 0.13 51 3 0.01 ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25 Consensus pattern (47 bp): GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCATTGAGATGAGA Found at i:13572 original size:46 final size:46 Alignment explanation

Indices: 13522--13694 Score: 185 Period size: 46 Copynumber: 3.7 Consensus size: 46 13512 TTGAGCATCT 13522 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC 1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC * * * 13568 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC 1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCC * * 13615 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGACG-CC 1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC * * * 13660 CAAGCTGGTTGAGTTGAGTCCGAGTTCGCTTATGG 1 GAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG 13695 GCGGGTTACA Statistics Matches: 106, Mismatches: 11, Indels: 20 0.77 0.08 0.15 Matches are distributed among these distances: 42 2 0.02 43 5 0.05 45 7 0.07 46 55 0.52 47 29 0.27 48 3 0.03 50 4 0.04 51 1 0.01 ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29 Consensus pattern (46 bp): GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC Found at i:13675 original size:93 final size:93 Alignment explanation

Indices: 13516--13687 Score: 283 Period size: 93 Copynumber: 1.8 Consensus size: 93 13506 GGATGGTTGA * * * 13516 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT 13581 TGAGTCCGAGTTCGTGAGATGTAACTAG 66 TGAGTCCGAGTTCGTGAGATGTAACTAG * * 13609 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGACG-CCCAAGCTGGTTGAG 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGAG 13673 TTGAGTCCGAGTTCG 65 TTGAGTCCGAGTTCG 13688 CTTATGGGCG Statistics Matches: 73, Mismatches: 5, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 92 4 0.05 93 69 0.95 ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT TGAGTCCGAGTTCGTGAGATGTAACTAG Found at i:21233 original size:114 final size:108 Alignment explanation

Indices: 21033--21328 Score: 281 Period size: 114 Copynumber: 2.7 Consensus size: 108 21023 AGATAAAATG * * * * * * * * * 21033 TTTTTTGTGGCGTTTTTGATAAAGTGCCACTAA-AGCTCGATCTATAGCTGCGTTTTTCAAAAAG 1 TTTTTTGCGGAGTTTTTCAAAAAGCGCCGCTAATA-CTCGATCTATAGCGGCATTTTTAAAAAAG * * * * 21097 CGCCGCTAGTGACACTAAAGCTCAACATAAAACGATGTGGTTTTG-TTTAA 65 CGCCGCTAATGACACTAAAGCT---CA-AAAACG--G-CGTTGTGCTTAAA * * 21147 TTTTTTGCGGTGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGCGGCATTTTTTAAAAAGC 1 TTTTTTGCGGAGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGCGGCATTTTTAAAAAAGC * * * 21212 GCTGCTAATGCCACTAAAGCTCAAACACGGCGTTGTGCTTAAA 66 GCCGCTAATGACACTAAAGCTCAAAAACGGCGTTGTGCTTAAA ** ** * * * 21255 TTTTTTGCGGAGTTTTTTGAAAAGCGCCGCTAATGGTCGACCTATAGTGGCACTTTTAAAAAAGC 1 TTTTTTGCGGAGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGCGGCATTTTTAAAAAAGC 21320 GCCGCTAAT 66 GCCGCTAAT 21329 ACTAGATCTA Statistics Matches: 154, Mismatches: 26, Indels: 10 0.81 0.14 0.05 Matches are distributed among these distances: 107 5 0.03 108 69 0.45 110 5 0.03 111 2 0.01 114 72 0.47 115 1 0.01 ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33 Consensus pattern (108 bp): TTTTTTGCGGAGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGCGGCATTTTTAAAAAAGC GCCGCTAATGACACTAAAGCTCAAAAACGGCGTTGTGCTTAAA Found at i:21340 original size:40 final size:40 Alignment explanation

Indices: 21274--21351 Score: 111 Period size: 40 Copynumber: 1.9 Consensus size: 40 21264 GAGTTTTTTG ** * 21274 AAAAGCGCCGCTAATGGTCGACCTATAGTGGCACTTTTAA 1 AAAAGCGCCGCTAATACTAGACCTATAGTGGCACTTTTAA * * 21314 AAAAGCGCCGCTAATACTAGATCTATAGTGGCATTTTT 1 AAAAGCGCCGCTAATACTAGACCTATAGTGGCACTTTT 21352 TATAGCGACG Statistics Matches: 33, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 40 33 1.00 ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28 Consensus pattern (40 bp): AAAAGCGCCGCTAATACTAGACCTATAGTGGCACTTTTAA Found at i:31719 original size:22 final size:21 Alignment explanation

Indices: 31689--31754 Score: 64 Period size: 19 Copynumber: 3.2 Consensus size: 21 31679 TACAAATTAA 31689 ATCTCCAAGATTACAAGATCAT 1 ATCTCCAAGATTAC-AGATCAT * * * 31711 ATCTTCAAGATTGCATATCAT 1 ATCTCCAAGATTACAGATCAT * * 31732 ATCT--AAGATTGCATATCAT 1 ATCTCCAAGATTACAGATCAT 31751 ATCT 1 ATCT 31755 AAGATTGTAT Statistics Matches: 41, Mismatches: 3, Indels: 3 0.87 0.06 0.06 Matches are distributed among these distances: 19 19 0.46 21 10 0.24 22 12 0.29 ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35 Consensus pattern (21 bp): ATCTCCAAGATTACAGATCAT Found at i:31741 original size:19 final size:19 Alignment explanation

Indices: 31706--31803 Score: 164 Period size: 19 Copynumber: 5.2 Consensus size: 19 31696 AGATTACAAG 31706 ATCATATCTTCAAGATTGCAT 1 ATCATATC-T-AAGATTGCAT 31727 ATCATATCTAAGATTGCAT 1 ATCATATCTAAGATTGCAT 31746 ATCATATCTAAGATTG--T 1 ATCATATCTAAGATTGCAT 31763 ATCATATCTAAGATTGCAT 1 ATCATATCTAAGATTGCAT 31782 ATCATATCTAAGATTGCAT 1 ATCATATCTAAGATTGCAT 31801 ATC 1 ATC 31804 CTTAAAGATT Statistics Matches: 75, Mismatches: 0, Indels: 6 0.93 0.00 0.07 Matches are distributed among these distances: 17 17 0.23 19 49 0.65 20 1 0.01 21 8 0.11 ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38 Consensus pattern (19 bp): ATCATATCTAAGATTGCAT Found at i:31770 original size:36 final size:37 Alignment explanation

Indices: 31706--31803 Score: 153 Period size: 36 Copynumber: 2.6 Consensus size: 37 31696 AGATTACAAG 31706 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT 1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATTGCAT 31746 ATCATATCTAAGATTG-TATCATATCTAAGATTGCAT 1 ATCATATCTAAGATTGATATCATATCTAAGATTGCAT 31782 ATCATATCTAAGATTGCATATC 1 ATCATATCTAAGATTG-ATATC 31804 CTTAAAGATT Statistics Matches: 56, Mismatches: 0, Indels: 6 0.90 0.00 0.10 Matches are distributed among these distances: 36 36 0.64 38 11 0.20 39 1 0.02 40 8 0.14 ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38 Consensus pattern (37 bp): ATCATATCTAAGATTGATATCATATCTAAGATTGCAT Found at i:33246 original size:26 final size:26 Alignment explanation

Indices: 33210--33264 Score: 110 Period size: 26 Copynumber: 2.1 Consensus size: 26 33200 TTATACATGA 33210 CATATCATCATATATGACCAAGTATC 1 CATATCATCATATATGACCAAGTATC 33236 CATATCATCATATATGACCAAGTATC 1 CATATCATCATATATGACCAAGTATC 33262 CAT 1 CAT 33265 GCTTAACAAA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 29 1.00 ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31 Consensus pattern (26 bp): CATATCATCATATATGACCAAGTATC Found at i:34015 original size:17 final size:19 Alignment explanation

Indices: 33993--34031 Score: 55 Period size: 19 Copynumber: 2.2 Consensus size: 19 33983 TGTACAAAAC * 33993 TATAAT-TC-GTCAATTTA 1 TATAATATCTGTCAATTCA 34010 TATAATATCTGTCAATTCA 1 TATAATATCTGTCAATTCA 34029 TAT 1 TAT 34032 TCCAGAATGC Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 17 6 0.32 18 2 0.11 19 11 0.58 ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46 Consensus pattern (19 bp): TATAATATCTGTCAATTCA Found at i:34149 original size:24 final size:24 Alignment explanation

Indices: 34074--34150 Score: 68 Period size: 24 Copynumber: 3.2 Consensus size: 24 34064 AGCACTTTCA * * 34074 AGCCATAAT-AGGAAGCTTATGTG 1 AGCCATAATCGGGAAGCTCATGTG * *** 34097 AGTCATGTAA-CGGGAAGCTCATAAA 1 AGCCA--TAATCGGGAAGCTCATGTG 34122 AGCCATAATCGGGAAGCTCATGTG 1 AGCCATAATCGGGAAGCTCATGTG 34146 AGCCA 1 AGCCA 34151 ATATCGTGTA Statistics Matches: 40, Mismatches: 10, Indels: 7 0.70 0.18 0.12 Matches are distributed among these distances: 23 7 0.17 24 17 0.43 25 16 0.40 ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21 Consensus pattern (24 bp): AGCCATAATCGGGAAGCTCATGTG Found at i:34323 original size:25 final size:26 Alignment explanation

Indices: 34210--34349 Score: 64 Period size: 25 Copynumber: 5.6 Consensus size: 26 34200 CTTTTATCGT * * 34210 GAAGCTCTTGAGAGC-C-AATTATCAG 1 GAAGCTCATGAGAGCTCAAATAAT-AG * * 34235 GAAGCTCAT-ACGAGCT-ATA-AATCAA 1 GAAGCTCATGA-GAGCTCAAATAAT-AG * * 34260 GAAGCTCAAGAGAG-TCATATAATAG 1 GAAGCTCATGAGAGCTCAAATAATAG * * * * 34285 GATGCTTATAAGAGCT-AAATAATGG 1 GAAGCTCATGAGAGCTCAAATAATAG * 34310 GAAGCTCATGAGAGC-CAAGT-ATCAG 1 GAAGCTCATGAGAGCTCAAATAAT-AG * * 34335 GACGCTCATAAGAGC 1 GAAGCTCATGAGAGC 34350 AGTGGTGTGT Statistics Matches: 87, Mismatches: 19, Indels: 18 0.70 0.15 0.15 Matches are distributed among these distances: 24 4 0.05 25 77 0.89 26 6 0.07 ACGTcount: A:0.39, C:0.17, G:0.24, T:0.21 Consensus pattern (26 bp): GAAGCTCATGAGAGCTCAAATAATAG Found at i:34346 original size:50 final size:49 Alignment explanation

Indices: 34210--34349 Score: 131 Period size: 50 Copynumber: 2.8 Consensus size: 49 34200 CTTTTATCGT * * * 34210 GAAGCTCTTGAGAGCCAATTATCAGGAAGCTCATACGAGCTATAAATCAA 1 GAAGCTCATGAGAGCCAA-TATCAGGAAGCTCATAAGAGCTAAAAATCAA * * * * ** 34260 GAAGCTCAAGAGAGTCATATAAT-AGGATGCTTATAAGAGCTAAATAAT-GG 1 GAAGCTCATGAGAGCCA-AT-ATCAGGAAGCTCATAAGAGCTAAA-AATCAA * 34310 GAAGCTCATGAGAGCCAAGTATCAGGACGCTCATAAGAGC 1 GAAGCTCATGAGAGCCAA-TATCAGGAAGCTCATAAGAGC 34350 AGTGGTGTGT Statistics Matches: 72, Mismatches: 13, Indels: 10 0.76 0.14 0.11 Matches are distributed among these distances: 49 3 0.04 50 63 0.88 51 6 0.08 ACGTcount: A:0.39, C:0.17, G:0.24, T:0.21 Consensus pattern (49 bp): GAAGCTCATGAGAGCCAATATCAGGAAGCTCATAAGAGCTAAAAATCAA Found at i:35411 original size:15 final size:15 Alignment explanation

Indices: 35391--35420 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 35381 CATTTTATTT * 35391 ATATTAGGATAATTA 1 ATATTAAGATAATTA 35406 ATATTAAGATAATTA 1 ATATTAAGATAATTA 35421 TTAGGATTAT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40 Consensus pattern (15 bp): ATATTAAGATAATTA Found at i:35448 original size:27 final size:26 Alignment explanation

Indices: 35387--35449 Score: 63 Period size: 27 Copynumber: 2.3 Consensus size: 26 35377 ACTCCATTTT 35387 ATTTATATTAGGATAATTAATATTAAG 1 ATTT-TATTAGGATAATTAATATTAAG * * * * 35414 ATAATTATTAGGATTATTTAATTTTAGG 1 AT-TTTATTAGGA-TAATTAATATTAAG 35442 ATTTTATT 1 ATTTTATT 35450 TTAATTATCT Statistics Matches: 29, Mismatches: 5, Indels: 4 0.76 0.13 0.11 Matches are distributed among these distances: 27 15 0.52 28 14 0.48 ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51 Consensus pattern (26 bp): ATTTTATTAGGATAATTAATATTAAG Found at i:35464 original size:10 final size:10 Alignment explanation

Indices: 35445--35476 Score: 57 Period size: 10 Copynumber: 3.3 Consensus size: 10 35435 TTTTAGGATT 35445 TTAT-TTTAA 1 TTATCTTTAA 35454 TTATCTTTAA 1 TTATCTTTAA 35464 TTATCTTTAA 1 TTATCTTTAA 35474 TTA 1 TTA 35477 AATGTGTAAC Statistics Matches: 22, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 9 4 0.18 10 18 0.82 ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62 Consensus pattern (10 bp): TTATCTTTAA Found at i:36844 original size:46 final size:44 Alignment explanation

Indices: 36737--36844 Score: 135 Period size: 44 Copynumber: 2.4 Consensus size: 44 36727 TGTCTTTGAC ** * * * 36737 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT 1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT * * 36781 ATGGACTTACATTGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT 1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT 36827 ATGGACTTACATGGCTCA 1 ATGGACTTACATGGCTCA 36845 TTTCTGTTCT Statistics Matches: 54, Mismatches: 8, Indels: 2 0.84 0.12 0.03 Matches are distributed among these distances: 44 32 0.59 46 22 0.41 ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34 Consensus pattern (44 bp): ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT Found at i:42056 original size:25 final size:26 Alignment explanation

Indices: 41999--42104 Score: 153 Period size: 26 Copynumber: 4.2 Consensus size: 26 41989 TGAAATGCCC * 41999 ATCATGGAACATTTAGCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT 42025 ATCATGGAACATTTACCT-ACCCATT 1 ATCATGGAACATTTACCTAACCCATT * * * 42050 ATTATGGAATATTTACCTAATCCATT 1 ATCATGGAACATTTACCTAACCCATT * 42076 ATCATGGAACATTTTCCTAACCC-TT 1 ATCATGGAACATTTACCTAACCCATT 42101 ATCA 1 ATCA 42105 ATTTGTACCA Statistics Matches: 71, Mismatches: 8, Indels: 3 0.87 0.10 0.04 Matches are distributed among these distances: 25 29 0.41 26 42 0.59 ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35 Consensus pattern (26 bp): ATCATGGAACATTTACCTAACCCATT Found at i:42064 original size:51 final size:51 Alignment explanation

Indices: 42002--42102 Score: 150 Period size: 51 Copynumber: 2.0 Consensus size: 51 41992 AATGCCCATC * 42002 ATGGAACATTTAGCTAACCCATTATCATGGAACATTTACCT-ACCCATTATT 1 ATGGAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCC-TTATT * * * 42053 ATGGAATATTTACCTAATCCATTATCATGGAACATTTTCCTAACCCTTAT 1 ATGGAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCCTTAT 42103 CAATTTGTAC Statistics Matches: 45, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 51 41 0.91 52 4 0.09 ACGTcount: A:0.33, C:0.23, G:0.09, T:0.36 Consensus pattern (51 bp): ATGGAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCCTTATT Done.