Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold948

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: 39749
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:577 original size:27 final size:27

Alignment explanation

Indices: 540--612 Score: 94 Period size: 27 Copynumber: 2.7 Consensus size: 27 530 AAAAGCCACC * * * 540 CTTTGTGTTTGTCAACAATGGTGGTTA 1 CTTTGTATTTGTCAAAAATGATGGTTA * 567 CTTTGTATTTGTCAAAAATGATGGTTC 1 CTTTGTATTTGTCAAAAATGATGGTTA 594 CTTT-TAGTTTGTCAAAAAT 1 CTTTGTA-TTTGTCAAAAAT 613 TATAGCTTAT Statistics Matches: 41, Mismatches: 4, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 26 2 0.05 27 39 0.95 ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45 Consensus pattern (27 bp): CTTTGTATTTGTCAAAAATGATGGTTA Found at i:740 original size:13 final size:13 Alignment explanation

Indices: 721--754 Score: 59 Period size: 13 Copynumber: 2.6 Consensus size: 13 711 TCTCTCAAGC 721 ATCCCTCTCTTGT 1 ATCCCTCTCTTGT * 734 ATTCCTCTCTTGT 1 ATCCCTCTCTTGT 747 ATCCCTCT 1 ATCCCTCT 755 TCAATTTTTT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 13 19 1.00 ACGTcount: A:0.09, C:0.38, G:0.06, T:0.47 Consensus pattern (13 bp): ATCCCTCTCTTGT Found at i:4372 original size:16 final size:16 Alignment explanation

Indices: 4345--4384 Score: 64 Period size: 16 Copynumber: 2.6 Consensus size: 16 4335 CGCGCTGTTT 4345 GTTTCA-CCTTATAAA 1 GTTTCAGCCTTATAAA 4360 GTTTCAGCCTTATAAA 1 GTTTCAGCCTTATAAA * 4376 GTTGCAGCC 1 GTTTCAGCC 4385 AAACTTGACT Statistics Matches: 23, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 15 6 0.26 16 17 0.74 ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35 Consensus pattern (16 bp): GTTTCAGCCTTATAAA Found at i:4617 original size:32 final size:33 Alignment explanation

Indices: 4580--4675 Score: 92 Period size: 32 Copynumber: 2.9 Consensus size: 33 4570 TGAAATAGTT 4580 ATTTAAATTA-TTATTTTTATTAAATAATTA-A 1 ATTTAAATTACTTATTTTTATTAAATAATTATA * * * 4611 TCTTTAACATATACTTATTTATT-TAAAAAAATTATA 1 -ATTTAA-AT-TACTTATTT-TTATTAAATAATTATA * 4647 ATTTAAA-TACTTATTTATATTAAATAATT 1 ATTTAAATTACTTATTTTTATTAAATAATT 4676 TTTAAAATAT Statistics Matches: 51, Mismatches: 7, Indels: 12 0.73 0.10 0.17 Matches are distributed among these distances: 31 1 0.02 32 22 0.43 33 2 0.04 34 3 0.06 35 20 0.39 36 3 0.06 ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51 Consensus pattern (33 bp): ATTTAAATTACTTATTTTTATTAAATAATTATA Found at i:4824 original size:14 final size:14 Alignment explanation

Indices: 4805--4907 Score: 69 Period size: 14 Copynumber: 7.7 Consensus size: 14 4795 TAGACATTAA 4805 ATATTAATATATTT 1 ATATTAATATATTT 4819 ATATTAATAT-TTAT 1 ATATTAATATATT-T * * 4833 ATGTTATTA-ATTT 1 ATATTAATATATTT * 4846 ATATT-ATATA--A 1 ATATTAATATATTT * 4857 ATTTTAATATATTT 1 ATATTAATATATTT 4871 AT-TTAATTATATTAT 1 ATATTAA-TATATT-T * 4886 ATTTTAAT-TATTT 1 ATATTAATATATTT * 4899 -TATTTATAT 1 ATATTAATAT 4908 TATATTTATG Statistics Matches: 70, Mismatches: 9, Indels: 21 0.70 0.09 0.21 Matches are distributed among these distances: 11 4 0.06 12 12 0.17 13 14 0.20 14 32 0.46 15 4 0.06 16 4 0.06 ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60 Consensus pattern (14 bp): ATATTAATATATTT Found at i:4829 original size:20 final size:18 Alignment explanation

Indices: 4812--4916 Score: 68 Period size: 15 Copynumber: 6.2 Consensus size: 18 4802 TAAATATTAA 4812 TATATTTATATTAATATT 1 TATATTTATATTAATATT * 4830 TATATGT-TATT-A-ATT 1 TATATTTATATTAATATT * * 4845 TATA-TTATATAAATTTT 1 TATATTTATATTAATATT 4862 AATATATTTAT-TTAATTATAT 1 --TATATTTATATTAA-TAT-T * 4883 TATATTT-TA--ATTATT 1 TATATTTATATTAATATT 4898 T-TATTTATATT-ATATT 1 TATATTTATATTAATATT 4914 TAT 1 TAT 4917 GTATATTATA Statistics Matches: 66, Mismatches: 8, Indels: 27 0.65 0.08 0.27 Matches are distributed among these distances: 14 6 0.09 15 14 0.21 16 10 0.15 17 8 0.12 18 7 0.11 19 14 0.21 20 6 0.09 21 1 0.02 ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62 Consensus pattern (18 bp): TATATTTATATTAATATT Found at i:4873 original size:33 final size:32 Alignment explanation

Indices: 4806--4887 Score: 89 Period size: 33 Copynumber: 2.6 Consensus size: 32 4796 AGACATTAAA * * 4806 TATTAATATAT-TTATATTAATATTTATATGT 1 TATTAATTTATATTATATAAATATTTATATGT * 4837 TATTAATTTATATTATATAAAT-TTTAATATATT 1 TATTAATTTATATTATATAAATATTT-ATAT-GT 4870 TATTTAA-TTATATTATAT 1 TA-TTAATTTATATTATAT 4888 TTTAATTATT Statistics Matches: 44, Mismatches: 3, Indels: 6 0.83 0.06 0.11 Matches are distributed among these distances: 31 13 0.30 32 13 0.30 33 14 0.32 34 4 0.09 ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59 Consensus pattern (32 bp): TATTAATTTATATTATATAAATATTTATATGT Found at i:4925 original size:20 final size:18 Alignment explanation

Indices: 4812--4926 Score: 69 Period size: 20 Copynumber: 6.2 Consensus size: 18 4802 TAAATATTAA * 4812 TATATTTATATTAATAT-T 1 TATATTTAT-TTATTATAT * 4830 TATATGTTATTAATTTATAT 1 TATAT-TTATTTA-TTATAT * * 4850 TATA-TAAATT-TTA-A- 1 TATATTTATTTATTATAT 4864 TATATTTATTTAATTATAT 1 TATATTTATTT-ATTATAT * * 4883 TATATTTTAATTATTTTATT 1 TATA-TTTATTTATTATA-T 4903 TATATTATATTTATGTATAT 1 TATATT-TATTTAT-TATAT 4923 TATA 1 TATA 4927 AAATTATATA Statistics Matches: 74, Mismatches: 11, Indels: 22 0.69 0.10 0.21 Matches are distributed among these distances: 14 4 0.05 15 5 0.07 16 3 0.04 17 3 0.04 18 11 0.15 19 18 0.24 20 27 0.36 21 3 0.04 ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61 Consensus pattern (18 bp): TATATTTATTTATTATAT Found at i:5591 original size:27 final size:27 Alignment explanation

Indices: 5559--5629 Score: 90 Period size: 27 Copynumber: 2.6 Consensus size: 27 5549 AATCACTCAT * 5559 TATTTGTCAAAAATTGT-GATTACTTTG 1 TATTTGTCAAAAATGGTAG-TTACTTTG * * * 5586 TGTTTGTCAAAAATGGTAGTTTCTTTT 1 TATTTGTCAAAAATGGTAGTTACTTTG 5613 TATTTGTCAAAAATGGT 1 TATTTGTCAAAAATGGT 5630 GGCATGTTGT Statistics Matches: 38, Mismatches: 5, Indels: 2 0.84 0.11 0.04 Matches are distributed among these distances: 27 37 0.97 28 1 0.03 ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48 Consensus pattern (27 bp): TATTTGTCAAAAATGGTAGTTACTTTG Found at i:5753 original size:13 final size:13 Alignment explanation

Indices: 5737--5762 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 5727 TCTTAAGCAT 5737 CTCTCTTGTATCC 1 CTCTCTTGTATCC 5750 CTCTCTTGTATCC 1 CTCTCTTGTATCC 5763 ATCTTCAATT 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:0.08, C:0.38, G:0.08, T:0.46 Consensus pattern (13 bp): CTCTCTTGTATCC Found at i:9806 original size:27 final size:26 Alignment explanation

Indices: 9775--9865 Score: 105 Period size: 27 Copynumber: 3.5 Consensus size: 26 9765 AAACCACTCA * 9775 TTGTTTGTCAAAAATTGTGGTTACTT 1 TTGTTTGTCAAAAATGGTGGTTACTT * 9801 TGTGTTTGTCAAAAATGGTGGTTTCTTT 1 T-TGTTTGTCAAAAATGGTGGTTAC-TT * * * 9829 TTATTTGTCAAAAATGGTGG-CA-TG 1 TTGTTTGTCAAAAATGGTGGTTACTT 9853 TTGTTTGTCAAAA 1 TTGTTTGTCAAAA 9866 TTTGTGGCTA Statistics Matches: 56, Mismatches: 7, Indels: 6 0.81 0.10 0.09 Matches are distributed among these distances: 24 13 0.23 26 1 0.02 27 39 0.70 28 3 0.05 ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46 Consensus pattern (26 bp): TTGTTTGTCAAAAATGGTGGTTACTT Found at i:10374 original size:23 final size:23 Alignment explanation

Indices: 10348--10412 Score: 70 Period size: 23 Copynumber: 3.1 Consensus size: 23 10338 TTGATGATTG 10348 ATTGAGTTTATAGATTTTATTTT 1 ATTGAGTTTATAGATTTTATTTT * * 10371 ATTGAG-TT-T-GA--TGA-TTG 1 ATTGAGTTTATAGATTTTATTTT 10388 ATTGAGTTTATAGATTTTATTTT 1 ATTGAGTTTATAGATTTTATTTT 10411 AT 1 AT 10413 GTTAAAAGGT Statistics Matches: 32, Mismatches: 4, Indels: 12 0.67 0.08 0.25 Matches are distributed among these distances: 17 8 0.25 18 4 0.12 19 1 0.03 20 4 0.12 21 1 0.03 22 4 0.12 23 10 0.31 ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57 Consensus pattern (23 bp): ATTGAGTTTATAGATTTTATTTT Found at i:10381 original size:40 final size:40 Alignment explanation

Indices: 10321--10412 Score: 166 Period size: 40 Copynumber: 2.3 Consensus size: 40 10311 AATCTTTGAT * * 10321 ATTTCATTTTAGTGAGTTTGATGATTGATTGAGTTTATAG 1 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG 10361 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG 1 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG 10401 ATTTTATTTTAT 1 ATTTTATTTTAT 10413 GTTAAAAGGT Statistics Matches: 50, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 40 50 1.00 ACGTcount: A:0.25, C:0.01, G:0.18, T:0.55 Consensus pattern (40 bp): ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG Found at i:10403 original size:17 final size:17 Alignment explanation

Indices: 10333--10396 Score: 56 Period size: 17 Copynumber: 3.4 Consensus size: 17 10323 TTCATTTTAG 10333 TGAGTTTGATGATTGAT 1 TGAGTTTGATGATTGAT * * 10350 TGAGTTTATAGATTTTATTTTAT 1 TGAG-TT-T-GA--TGA-TTGAT 10373 TGAGTTTGATGATTGAT 1 TGAGTTTGATGATTGAT 10390 TGAGTTT 1 TGAGTTT 10397 ATAGATTTTA Statistics Matches: 37, Mismatches: 4, Indels: 12 0.70 0.08 0.23 Matches are distributed among these distances: 17 15 0.41 18 4 0.11 19 1 0.03 20 4 0.11 21 1 0.03 22 4 0.11 23 8 0.22 ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53 Consensus pattern (17 bp): TGAGTTTGATGATTGAT Found at i:10503 original size:21 final size:20 Alignment explanation

Indices: 10463--10503 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 20 10453 GATTTTAATG ** 10463 ATTTATTTAATTTTTGTTAT 1 ATTTATTTAATTTTCATTAT 10483 ATTTATGTTAATTTTCATTAT 1 ATTTAT-TTAATTTTCATTAT 10504 GATGATTTGT Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 20 6 0.33 21 12 0.67 ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66 Consensus pattern (20 bp): ATTTATTTAATTTTCATTAT Found at i:12055 original size:155 final size:155 Alignment explanation

Indices: 11886--12386 Score: 425 Period size: 154 Copynumber: 3.2 Consensus size: 155 11876 TGGCCATCGA * * 11886 ATCGCTTCTATGCCAAAGGTATAGT-TTTAGGGTAGGTTTACCTTTTTCTTATTATTTTTACG-C 1 ATCGCTTCTATGCCAAAGGTATA-TATTTAGGATAGGTTTATCTTTTTCTTATTATTTTTACGTC * * 11949 TCTTTAGGGTTACCAAGATACTTTCACATCG-AAG-ATATACCTTAA-AGGCATTTTCGTAACTT 65 T-TTTAAGATTACCAAGATACTTTCACATCGAAAGTAT-TACC-TAAGA-GCATTTTCGTAACTT * * * * 12011 TTCTAAAATCGAGTGCTAGATAGTTACCAG 126 TTCTAAAACCAAGTCCTAGATAGTCACCAG * * * * * * * * 12041 GTCGTTTCTATGCCAATGGTGTATATTTATGATAGGTTTGTCTTTTTCTTATCA-TTTTGCGTCT 1 ATCGCTTCTATGCCAAAGGTATATATTTAGGATAGGTTTATCTTTTTCTTATTATTTTTACGTCT * ** * * * 12105 TTTAAGATTATCGGGATACTTTCACGTCGAAAGTATTACCTAAGAGCATTTTCTTAATTTTTCTA 66 TTTAAGATTACCAAGATACTTTCACATCGAAAGTATTACCTAAGAGCATTTTCGTAACTTTTCTA * 12170 AAACCAAGTCCTAGATAGTCACTAG 131 AAACCAAGTCCTAGATAGTCACCAG * * * * * 12195 ATCGCTTCTGTGCCAAAAGTATATATTTAGAATATGTTTATCTTTTTATTTATTATTTTATA--T 1 ATCGCTTCTATGCCAAAGGTATATATTTAGGATAGGTTTATCTTTTT-CTTATTATTTT-TACGT * * * * * * * 12258 CTTTTAAGATTATCGAGATACTTTTACGTCGAAGGTA-TACCCCAAG-GCATTTT-GTTAA-TTC 64 CTTTTAAGATTACCAAGATACTTTCACATCGAAAGTATTA-CCTAAGAGCATTTTCG-TAACTTT * * * * * 12319 ACTAGAACCAAATCCTAAATAGTCAGCA- 127 TCTAAAACCAAGTCCTAGATAGTCACCAG * * * 12347 AGTCACTTTTATGCCAAAGGTATGTATTTAGGAATAGGTT 1 A-TCGCTTCTATGCCAAAGGTATATATTTAGG-ATAGGTT 12387 CGTCATTTTA Statistics Matches: 279, Mismatches: 55, Indels: 25 0.78 0.15 0.07 Matches are distributed among these distances: 152 1 0.00 153 48 0.17 154 126 0.45 155 98 0.35 156 5 0.02 157 1 0.00 ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40 Consensus pattern (155 bp): ATCGCTTCTATGCCAAAGGTATATATTTAGGATAGGTTTATCTTTTTCTTATTATTTTTACGTCT TTTAAGATTACCAAGATACTTTCACATCGAAAGTATTACCTAAGAGCATTTTCGTAACTTTTCTA AAACCAAGTCCTAGATAGTCACCAG Found at i:14483 original size:16 final size:16 Alignment explanation

Indices: 14459--14493 Score: 61 Period size: 16 Copynumber: 2.2 Consensus size: 16 14449 TCGGTAGATG * 14459 AATCGCCCATCTAATT 1 AATCACCCATCTAATT 14475 AATCACCCATCTAATT 1 AATCACCCATCTAATT 14491 AAT 1 AAT 14494 TTTCGATGGT 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:0.37, C:0.29, G:0.03, T:0.31 Consensus pattern (16 bp): AATCACCCATCTAATT Found at i:14897 original size:13 final size:13 Alignment explanation

Indices: 14879--14904 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 14869 CATTATTCCA 14879 TGTATCGATACAT 1 TGTATCGATACAT 14892 TGTATCGATACAT 1 TGTATCGATACAT 14905 GGATCTTTGT 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:16190 original size:52 final size:51 Alignment explanation

Indices: 16078--16193 Score: 128 Period size: 51 Copynumber: 2.3 Consensus size: 51 16068 CAATTCTCTG ** * * * 16078 CAATCGGGGATATTCCATCTCTGATTTTATTTTCAAAACACTAATTTCCTA 1 CAATCGGGGATACCCCAACTCTGATTTTATTTCCAAAACACCAATTTCCTA * * 16129 TAATCGGGGATACCCCAACT-TCGATTTTATTTCCAAAAACACCAATTT-TTCA 1 CAATCGGGGATACCCCAACTCT-GATTTTATTTCC-AAAACACCAATTTCCT-A 16181 CAATCGGGGATAC 1 CAATCGGGGATAC 16194 TACAACCCCG Statistics Matches: 54, Mismatches: 8, Indels: 5 0.81 0.12 0.07 Matches are distributed among these distances: 50 1 0.02 51 28 0.52 52 25 0.46 ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34 Consensus pattern (51 bp): CAATCGGGGATACCCCAACTCTGATTTTATTTCCAAAACACCAATTTCCTA Found at i:16252 original size:28 final size:27 Alignment explanation

Indices: 16183--16258 Score: 100 Period size: 27 Copynumber: 2.8 Consensus size: 27 16173 ATTTTTCACA * 16183 ATCGGGGATACTACAACCCCGTTAATC 1 ATCGGGGATACTCCAACCCCGTTAATC * 16210 ATCGGGGATACTCCAACCCCGTT-ATT 1 ATCGGGGATACTCCAACCCCGTTAATC * 16236 TTCGAAGGGATACTCCAACCCCG 1 ATCG--GGGATACTCCAACCCCG 16259 GCTTCATTTC Statistics Matches: 44, Mismatches: 3, Indels: 3 0.88 0.06 0.06 Matches are distributed among these distances: 26 5 0.11 27 22 0.50 28 17 0.39 ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22 Consensus pattern (27 bp): ATCGGGGATACTCCAACCCCGTTAATC Found at i:16401 original size:52 final size:51 Alignment explanation

Indices: 16242--16621 Score: 185 Period size: 52 Copynumber: 7.3 Consensus size: 51 16232 TATTTTCGAA ** * * * *** * 16242 GGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCG 1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCAAAATCG * * * ** * 16293 GTGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCA 1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTC-AAAATCG * * * 16345 GGGATACTCCAGCTCCGATTTTATTTTCAAAAACACCAATTTTTCACAATCG 1 GGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTTCAAAATCG * * ** * * ** 16397 GGGATACTCTAACCCC-A-TTAATCATCGAGGATACTCCAACCTCGTTATTTCCGAA--- 1 GGGATACTCCAACCCCGATTTTATTTTC-A--AAACACCAA-----TT-TTTCAAAATCG ** * * * *** * 16452 GGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCG 1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCAAAATCG * * * ** * 16503 GGGATACTCTAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCA 1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTC-AAAATCG * * * * 16555 GGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCACAATCG 1 GGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAA-TTTTTCAAAATCG * 16608 AGGATACTCCAACC 1 GGGATACTCCAACC 16622 TCGTTATTTC Statistics Matches: 239, Mismatches: 72, Indels: 34 0.69 0.21 0.10 Matches are distributed among these distances: 48 5 0.02 49 2 0.01 50 7 0.03 51 69 0.29 52 79 0.33 53 40 0.17 54 8 0.03 55 15 0.06 56 1 0.00 57 7 0.03 58 6 0.03 ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31 Consensus pattern (51 bp): GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCAAAATCG Found at i:16497 original size:210 final size:209 Alignment explanation

Indices: 16102--16731 Score: 976 Period size: 210 Copynumber: 3.0 Consensus size: 209 16092 CCATCTCTGA * * * * * * 16102 TTTTATTTTCAAAACACTAA-TTTCCTATAATCGGGGATACCCCAACTTCGATTTTATTTCCAAA 1 TTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAA 16166 AACACCAATTTTTCACAATCGGGGATACTACAACCCCGTTAATCATCGGGGATACTCCAACCCCG 66 AACACCAATTTTTCACAATCGGGGATACT-CAACCCCGTTAATCATCGGGGATACTCCAACCCCG * * 16231 TTATTTTCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCGGTG 130 TTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCGGAG 16296 ATACTCCAACCCCGG 195 ATACTCCAACCCCGG * 16311 TTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTTCAAA 1 TTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAA * * * 16376 AACACCAATTTTTCACAATCGGGGATACTCTAACCCCATTAATCATCGAGGATACTCCAACCTCG 66 AACACCAATTTTTCACAATCGGGGATACTC-AACCCCGTTAATCATCGGGGATACTCCAACCCCG * 16441 TTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCGGGG 130 TTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCGGAG * 16506 ATACTCTAACCCCGG 195 ATACTCCAACCCCGG 16521 TTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAA 1 TTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAA * * * * 16586 AACACCAATTTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCCACCC 66 AACACCAA-TTTTTCACAATCGGGGATACT-CAACCCCGTTA-ATCATCGGGGATACTCCAACCC ** * * * * 16651 CGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTA-TTCTCAAAATATTGATTTCTCATAATTG 128 CGTTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTC-CAAAATATTGATTTCTCAAAATCG 16715 GAGATACTCCAACCCCG 192 GAGATACTCCAACCCCG 16732 TTATTTCCGA Statistics Matches: 386, Mismatches: 29, Indels: 9 0.91 0.07 0.02 Matches are distributed among these distances: 209 20 0.05 210 247 0.64 211 31 0.08 212 88 0.23 ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31 Consensus pattern (209 bp): TTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAA AACACCAATTTTTCACAATCGGGGATACTCAACCCCGTTAATCATCGGGGATACTCCAACCCCGT TATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCGGAGA TACTCCAACCCCGG Found at i:16799 original size:78 final size:79 Alignment explanation

Indices: 16635--16803 Score: 193 Period size: 78 Copynumber: 2.2 Consensus size: 79 16625 TTATTTCATC * * 16635 GGGGATACTCCCACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCTCAAAATATT 1 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCTCAAAATATC * * 16700 GATTTCTCATAATT 66 GATTTCTCACAACT * ** * * * 16714 GGAGATACTCCAACCCCGTTATTTCCGA-GGGATACTCCAATCCCGATG-TTT-TTTTC-TAATC 1 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCG--GCTTTATTCTCAAAAT- 16775 ATCGATTTCTCACAACT 63 ATCGATTTCTCACAACT 16792 GGGGATACTCCA 1 GGGGATACTCCA 16804 GCCTCGTCAT Statistics Matches: 76, Mismatches: 11, Indels: 7 0.81 0.12 0.07 Matches are distributed among these distances: 77 3 0.04 78 45 0.59 79 27 0.36 80 1 0.01 ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30 Consensus pattern (79 bp): GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCTCAAAATATC GATTTCTCACAACT Found at i:21909 original size:13 final size:13 Alignment explanation

Indices: 21891--21951 Score: 71 Period size: 13 Copynumber: 5.2 Consensus size: 13 21881 ATACAAAGAT 21891 CAATGTATCGATA 1 CAATGTATCGATA 21904 CAATGTATCGATA 1 CAATGTATCGATA 21917 C-A--T-T-GA-A 1 CAATGTATCGATA * 21924 TAATGTATCGATA 1 CAATGTATCGATA 21937 CAATGTATCGATA 1 CAATGTATCGATA 21950 CA 1 CA 21952 TTGAATAATG Statistics Matches: 40, Mismatches: 2, Indels: 12 0.74 0.04 0.22 Matches are distributed among these distances: 7 1 0.03 8 3 0.08 9 1 0.03 10 2 0.05 11 1 0.03 12 3 0.08 13 29 0.73 ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): CAATGTATCGATA Found at i:21915 original size:33 final size:33 Alignment explanation

Indices: 21873--21971 Score: 164 Period size: 33 Copynumber: 3.0 Consensus size: 33 21863 AAATTCCCAG ** 21873 ATGTATCGATACAAAG-ATCAATGTATCGATACA 1 ATGTATCGATACATTGAAT-AATGTATCGATACA 21906 ATGTATCGATACATTGAATAATGTATCGATACA 1 ATGTATCGATACATTGAATAATGTATCGATACA 21939 ATGTATCGATACATTGAATAATGTATCGATACA 1 ATGTATCGATACATTGAATAATGTATCGATACA 21972 TTTCCTTGGC Statistics Matches: 63, Mismatches: 2, Indels: 2 0.94 0.03 0.03 Matches are distributed among these distances: 33 61 0.97 34 2 0.03 ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31 Consensus pattern (33 bp): ATGTATCGATACATTGAATAATGTATCGATACA Found at i:21930 original size:20 final size:20 Alignment explanation

Indices: 21905--21973 Score: 89 Period size: 20 Copynumber: 3.8 Consensus size: 20 21895 GTATCGATAC 21905 AATGTATCGATACATTGAAT 1 AATGTATCGATACATTGAAT 21925 AATGTATCGATAC------- 1 AATGTATCGATACATTGAAT 21938 AATGTATCGATACATTGAAT 1 AATGTATCGATACATTGAAT 21958 AATGTATCGATACATT 1 AATGTATCGATACATT 21974 TCCTTGGCAG Statistics Matches: 42, Mismatches: 0, Indels: 14 0.75 0.00 0.25 Matches are distributed among these distances: 13 13 0.31 20 29 0.69 ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35 Consensus pattern (20 bp): AATGTATCGATACATTGAAT Found at i:22118 original size:21 final size:20 Alignment explanation

Indices: 22092--22130 Score: 69 Period size: 21 Copynumber: 1.9 Consensus size: 20 22082 GTTGGGACCT 22092 TGTATCGATACATTCTAGAAA 1 TGTATCGATACATT-TAGAAA 22113 TGTATCGATACATTTAGA 1 TGTATCGATACATTTAGA 22131 CAAAAATGTG Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 20 4 0.22 21 14 0.78 ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36 Consensus pattern (20 bp): TGTATCGATACATTTAGAAA Found at i:24457 original size:20 final size:20 Alignment explanation

Indices: 24432--24506 Score: 69 Period size: 20 Copynumber: 3.6 Consensus size: 20 24422 ACCCAGAATA * 24432 TATCGATACAATGAGAAATG 1 TATCGATACATTGAGAAATG * * 24452 TATCGATTCATTTGAAAAACATG 1 TATCGATACA-TTG-AGAA-ATG * * * 24475 TATCGATATATTTAGTAATG 1 TATCGATACATTGAGAAATG 24495 TATCGATACATT 1 TATCGATACATT 24507 TCCTTAGCAG Statistics Matches: 43, Mismatches: 9, Indels: 6 0.74 0.16 0.10 Matches are distributed among these distances: 20 23 0.53 21 4 0.09 22 5 0.12 23 11 0.26 ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36 Consensus pattern (20 bp): TATCGATACATTGAGAAATG Done.