Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold939

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: 12254
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:1662 original size:23 final size:23

Alignment explanation

Indices: 1619--1676 Score: 61 Period size: 20 Copynumber: 2.7 Consensus size: 23 1609 AAAAAATGAA * * 1619 ATAAATAAAATTATATTTATATT 1 ATAAATAAAATTAAATATATATT * 1642 ATAAATAAAA-TAAAT-GATA-T 1 ATAAATAAAATTAAATATATATT 1662 ATAAAT-AAATTAAAT 1 ATAAATAAAATTAAAT 1677 TAGTTAAATT Statistics Matches: 32, Mismatches: 2, Indels: 5 0.82 0.05 0.13 Matches are distributed among these distances: 19 3 0.09 20 12 0.38 21 3 0.09 22 4 0.12 23 10 0.31 ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38 Consensus pattern (23 bp): ATAAATAAAATTAAATATATATT Found at i:1727 original size:9 final size:9 Alignment explanation

Indices: 1713--1771 Score: 56 Period size: 9 Copynumber: 7.0 Consensus size: 9 1703 AATATATATA 1713 TAATAGAAT 1 TAATAGAAT 1722 TAATAGAAT 1 TAATAGAAT * * 1731 AGAATA-TAT 1 -TAATAGAAT 1740 TAAT---A- 1 TAATAGAAT 1745 TAATAGAAT 1 TAATAGAAT 1754 TAATAGAAT 1 TAATAGAAT 1763 TAATAGAAT 1 TAATAGAAT 1772 AGAATATATT Statistics Matches: 42, Mismatches: 3, Indels: 10 0.76 0.05 0.18 Matches are distributed among these distances: 5 4 0.10 6 1 0.02 8 4 0.10 9 29 0.69 10 4 0.10 ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34 Consensus pattern (9 bp): TAATAGAAT Found at i:1750 original size:23 final size:23 Alignment explanation

Indices: 1722--1795 Score: 95 Period size: 23 Copynumber: 3.4 Consensus size: 23 1712 ATAATAGAAT 1722 TAATAGAATAGAATATATTAATA 1 TAATAGAATAGAATATATTAATA * * 1745 TAATAGAAT--TA-ATA-GAAT- 1 TAATAGAATAGAATATATTAATA 1763 TAATAGAATAGAATATATTAATA 1 TAATAGAATAGAATATATTAATA 1786 TAATAGAATA 1 TAATAGAATA 1796 TAGAATAGAA Statistics Matches: 42, Mismatches: 4, Indels: 10 0.75 0.07 0.18 Matches are distributed among these distances: 18 9 0.21 19 3 0.07 20 4 0.10 21 4 0.10 22 3 0.07 23 19 0.45 ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34 Consensus pattern (23 bp): TAATAGAATAGAATATATTAATA Found at i:1751 original size:32 final size:30 Alignment explanation

Indices: 1703--1797 Score: 106 Period size: 32 Copynumber: 3.2 Consensus size: 30 1693 TATATATATT 1703 AATATATATATAATAGAATTAATAGAATAG 1 AATATATATATAATAGAATTAATAGAATAG * 1733 AATATATTAATATAATAGAATTAATAGAAT-T 1 AATATA-T-ATATAATAGAATTAATAGAATAG * * * * 1764 AATAGA-ATAGAATA-TATTAATATAATAG 1 AATATATATATAATAGAATTAATAGAATAG 1792 AATATA 1 AATATA 1798 GAATAGAATA Statistics Matches: 55, Mismatches: 7, Indels: 8 0.79 0.10 0.11 Matches are distributed among these distances: 27 10 0.18 28 12 0.22 30 6 0.11 31 6 0.11 32 21 0.38 ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35 Consensus pattern (30 bp): AATATATATATAATAGAATTAATAGAATAG Found at i:1766 original size:41 final size:41 Alignment explanation

Indices: 1686--1815 Score: 178 Period size: 41 Copynumber: 3.2 Consensus size: 41 1676 TTAGTTAAAT * * 1686 TAGAATATATATATATTAATAT-ATA-TA-TAATAGAATTAA 1 TAGAATAGA-ATATATTAATATAATAGAATTAATAGAATTAA 1725 TAGAATAGAATATATTAATATAATAGAATTAATAGAATTAA 1 TAGAATAGAATATATTAATATAATAGAATTAATAGAATTAA 1766 TAGAATAGAATATATTAATATAATAGAATATAGAATAGAA-TAA 1 TAGAATAGAATATATTAATATAATAGAAT-T--AATAGAATTAA 1809 TAGAATA 1 TAGAATA 1816 TATAATAGAA Statistics Matches: 83, Mismatches: 2, Indels: 8 0.89 0.02 0.09 Matches are distributed among these distances: 38 12 0.14 39 11 0.13 40 1 0.01 41 41 0.49 42 1 0.01 43 10 0.12 44 7 0.08 ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35 Consensus pattern (41 bp): TAGAATAGAATATATTAATATAATAGAATTAATAGAATTAA Found at i:1804 original size:12 final size:13 Alignment explanation

Indices: 1728--1831 Score: 81 Period size: 13 Copynumber: 8.1 Consensus size: 13 1718 GAATTAATAG * * 1728 AATAGAATATATT 1 AATAGAATAGAAT * 1741 AATATAATAGAATT 1 AATAGAATAGAA-T * 1755 AATAGAATTA-ATAG 1 AATAGAA-TAGA-AT * * 1769 AATAGAATATATT 1 AATAGAATAGAAT * 1782 AATATAATAGAAT 1 AATAGAATAGAAT 1795 -ATAGAATAGAAT 1 AATAGAATAGAAT * 1807 AATAGAATA-TAT 1 AATAGAATAGAAT 1819 AATAGAAT-GAAT 1 AATAGAATAGAAT 1831 A 1 A 1832 TTCTAATATA Statistics Matches: 72, Mismatches: 13, Indels: 13 0.73 0.13 0.13 Matches are distributed among these distances: 12 24 0.33 13 29 0.40 14 16 0.22 15 3 0.04 ACGTcount: A:0.58, C:0.00, G:0.11, T:0.32 Consensus pattern (13 bp): AATAGAATAGAAT Found at i:1839 original size:24 final size:22 Alignment explanation

Indices: 1812--1861 Score: 68 Period size: 20 Copynumber: 2.3 Consensus size: 22 1802 AGAATAATAG 1812 AATATATAATAGAATGAATATTCT 1 AATATATAA-A-AATGAATATTCT 1836 -A-ATATAAAAATGAATATTCT 1 AATATATAAAAATGAATATTCT 1856 AATATA 1 AATATA 1862 AATTAGATAA Statistics Matches: 24, Mismatches: 0, Indels: 6 0.80 0.00 0.20 Matches are distributed among these distances: 20 12 0.50 21 2 0.08 22 9 0.38 23 1 0.04 ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36 Consensus pattern (22 bp): AATATATAAAAATGAATATTCT Found at i:1849 original size:20 final size:20 Alignment explanation

Indices: 1824--1863 Score: 80 Period size: 20 Copynumber: 2.0 Consensus size: 20 1814 TATATAATAG 1824 AATGAATATTCTAATATAAA 1 AATGAATATTCTAATATAAA 1844 AATGAATATTCTAATATAAA 1 AATGAATATTCTAATATAAA 1864 TTAGATAATA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35 Consensus pattern (20 bp): AATGAATATTCTAATATAAA Found at i:1874 original size:14 final size:14 Alignment explanation

Indices: 1855--1887 Score: 57 Period size: 14 Copynumber: 2.4 Consensus size: 14 1845 ATGAATATTC * 1855 TAATATAAATTAGA 1 TAATATAAATTAAA 1869 TAATATAAATTAAA 1 TAATATAAATTAAA 1883 TAATA 1 TAATA 1888 AGATAATAAG Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 14 18 1.00 ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36 Consensus pattern (14 bp): TAATATAAATTAAA Found at i:5493 original size:10 final size:10 Alignment explanation

Indices: 5478--5504 Score: 54 Period size: 10 Copynumber: 2.7 Consensus size: 10 5468 TATAGCCCTA 5478 TATTTTCTAT 1 TATTTTCTAT 5488 TATTTTCTAT 1 TATTTTCTAT 5498 TATTTTC 1 TATTTTC 5505 ATTTTTATTA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 17 1.00 ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70 Consensus pattern (10 bp): TATTTTCTAT Found at i:6154 original size:9 final size:11 Alignment explanation

Indices: 6135--6166 Score: 64 Period size: 11 Copynumber: 2.9 Consensus size: 11 6125 CAGAATCTCA 6135 TAAATATATAT 1 TAAATATATAT 6146 TAAATATATAT 1 TAAATATATAT 6157 TAAATATATA 1 TAAATATATA 6167 GAAATAATAT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 21 1.00 ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44 Consensus pattern (11 bp): TAAATATATAT Found at i:6175 original size:13 final size:13 Alignment explanation

Indices: 6159--6227 Score: 68 Period size: 13 Copynumber: 5.2 Consensus size: 13 6149 ATATATATTA 6159 AATATATAGAAAT 1 AATATATAGAAAT * 6172 AATATAGAGTCTAAAT 1 AATATATAG---AAAT 6188 AATATATAGAAAT 1 AATATATAGAAAT * 6201 -ATATATAGATAT 1 AATATATAGAAAT * * 6213 AAAATATAGATAT 1 AATATATAGAAAT 6226 AA 1 AA 6228 AATAAAAATT Statistics Matches: 48, Mismatches: 4, Indels: 8 0.80 0.07 0.13 Matches are distributed among these distances: 12 11 0.23 13 25 0.52 16 12 0.25 ACGTcount: A:0.58, C:0.01, G:0.09, T:0.32 Consensus pattern (13 bp): AATATATAGAAAT Found at i:6176 original size:22 final size:22 Alignment explanation

Indices: 6135--6206 Score: 65 Period size: 22 Copynumber: 3.0 Consensus size: 22 6125 CAGAATCTCA * 6135 TAAATATATATTAAATATATAT 1 TAAATATATATGAAATATATAT 6157 TAAATATATA-GAAATAATATAGAGT 1 TAAATATATATGAAAT-ATAT--A-T 6182 CTAAATAATATATAGAAATATATAT 1 -TAAAT-ATATAT-GAAATATATAT 6207 AGATATAAAA Statistics Matches: 41, Mismatches: 1, Indels: 13 0.75 0.02 0.24 Matches are distributed among these distances: 21 4 0.10 22 14 0.34 24 1 0.02 25 2 0.05 26 6 0.15 27 5 0.12 28 4 0.10 29 5 0.12 ACGTcount: A:0.56, C:0.01, G:0.06, T:0.38 Consensus pattern (22 bp): TAAATATATATGAAATATATAT Found at i:6228 original size:13 final size:13 Alignment explanation

Indices: 6203--6231 Score: 58 Period size: 13 Copynumber: 2.2 Consensus size: 13 6193 ATAGAAATAT 6203 ATATAGATATAAA 1 ATATAGATATAAA 6216 ATATAGATATAAA 1 ATATAGATATAAA 6229 ATA 1 ATA 6232 AAAATTTGAT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31 Consensus pattern (13 bp): ATATAGATATAAA Found at i:6274 original size:13 final size:14 Alignment explanation

Indices: 6251--6280 Score: 53 Period size: 13 Copynumber: 2.2 Consensus size: 14 6241 TTCTATAGAT 6251 AATAGAATAAATAG 1 AATAGAATAAATAG 6265 AATA-AATAAATAG 1 AATAGAATAAATAG 6278 AAT 1 AAT 6281 TTCGAATTTG Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 13 12 0.75 14 4 0.25 ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23 Consensus pattern (14 bp): AATAGAATAAATAG Found at i:10305 original size:18 final size:18 Alignment explanation

Indices: 10282--10317 Score: 54 Period size: 18 Copynumber: 2.0 Consensus size: 18 10272 ATTAGGATGC 10282 CCTTCCTTCCCCCGTTCT 1 CCTTCCTTCCCCCGTTCT * * 10300 CCTTCCTTTCCCCTTTCT 1 CCTTCCTTCCCCCGTTCT 10318 TTCATTTATT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.00, C:0.53, G:0.03, T:0.44 Consensus pattern (18 bp): CCTTCCTTCCCCCGTTCT Found at i:10334 original size:18 final size:18 Alignment explanation

Indices: 10313--10356 Score: 88 Period size: 18 Copynumber: 2.4 Consensus size: 18 10303 TCCTTTCCCC 10313 TTTCTTTCATTTATTTAT 1 TTTCTTTCATTTATTTAT 10331 TTTCTTTCATTTATTTAT 1 TTTCTTTCATTTATTTAT 10349 TTTCTTTC 1 TTTCTTTC 10357 TTTTTATGCG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 26 1.00 ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73 Consensus pattern (18 bp): TTTCTTTCATTTATTTAT Found at i:10346 original size:22 final size:22 Alignment explanation

Indices: 10312--10359 Score: 64 Period size: 22 Copynumber: 2.2 Consensus size: 22 10302 TTCCTTTCCC 10312 CTTTCTTTCATTTATTTAT-TTT 1 CTTTCTTTCATTTATTT-TCTTT 10334 CTTTCATTT-ATTTATTTTCTTT 1 CTTTC-TTTCATTTATTTTCTTT 10356 CTTT 1 CTTT 10360 TTATGCGAAA Statistics Matches: 24, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 21 1 0.04 22 20 0.83 23 3 0.12 ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73 Consensus pattern (22 bp): CTTTCTTTCATTTATTTTCTTT Found at i:10833 original size:9 final size:9 Alignment explanation

Indices: 10819--10856 Score: 51 Period size: 9 Copynumber: 4.2 Consensus size: 9 10809 TCAAATAGAA 10819 TTAAATAAT 1 TTAAATAAT 10828 TTAAATAAT 1 TTAAATAAT * 10837 TAAAATAA- 1 TTAAATAAT 10845 TTAAACTAAT 1 TTAAA-TAAT 10855 TT 1 TT 10857 TTAAAATTTT Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 8 4 0.16 9 19 0.76 10 2 0.08 ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42 Consensus pattern (9 bp): TTAAATAAT Found at i:10833 original size:19 final size:18 Alignment explanation

Indices: 10806--10855 Score: 50 Period size: 18 Copynumber: 2.7 Consensus size: 18 10796 AAAAAATGAA 10806 AATTCAAATAGAATT-AAAT 1 AATTCAAAT--AATTAAAAT * 10825 AATTTAAATAATTAAAAT 1 AATTCAAATAATTAAAAT 10843 AATT-AAACTAATT 1 AATTCAAA-TAATT 10856 TTTAAAATTT Statistics Matches: 28, Mismatches: 1, Indels: 5 0.82 0.03 0.15 Matches are distributed among these distances: 17 7 0.25 18 13 0.46 19 8 0.29 ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36 Consensus pattern (18 bp): AATTCAAATAATTAAAAT Found at i:10889 original size:21 final size:23 Alignment explanation

Indices: 10870--10922 Score: 70 Period size: 24 Copynumber: 2.2 Consensus size: 23 10860 AAATTTTAAA 10870 TAGAATTATTATATTCTTAATTAT 1 TAGAATTATTATATTCTTAA-TAT * 10894 TATAATTATTATATTCTATCAATAT 1 TAGAATTATTATATTCT-T-AATAT 10919 TAGA 1 TAGA 10923 TTGAATATTA Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 24 16 0.64 25 7 0.28 26 2 0.08 ACGTcount: A:0.40, C:0.06, G:0.04, T:0.51 Consensus pattern (23 bp): TAGAATTATTATATTCTTAATAT Found at i:10931 original size:12 final size:12 Alignment explanation

Indices: 10914--10940 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 10904 ATATTCTATC 10914 AATATTAGATTG 1 AATATTAGATTG 10926 AATATTAGATTG 1 AATATTAGATTG 10938 AAT 1 AAT 10941 CTACCATTAT 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:0.44, C:0.00, G:0.15, T:0.41 Consensus pattern (12 bp): AATATTAGATTG Found at i:10969 original size:14 final size:14 Alignment explanation

Indices: 10950--11005 Score: 78 Period size: 14 Copynumber: 4.0 Consensus size: 14 10940 TCTACCATTA 10950 TTATATTAAATATG 1 TTATATTAAATATG * 10964 TTATATTAAGAT-TA 1 TTATATTAA-ATATG 10978 TTATATTAAATATG 1 TTATATTAAATATG * 10992 TTATATTAAGTATG 1 TTATATTAAATATG 11006 GCATTCAAAA Statistics Matches: 37, Mismatches: 3, Indels: 4 0.84 0.07 0.09 Matches are distributed among these distances: 13 2 0.05 14 33 0.89 15 2 0.05 ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50 Consensus pattern (14 bp): TTATATTAAATATG Found at i:10986 original size:28 final size:28 Alignment explanation

Indices: 10946--11001 Score: 112 Period size: 28 Copynumber: 2.0 Consensus size: 28 10936 TGAATCTACC 10946 ATTATTATATTAAATATGTTATATTAAG 1 ATTATTATATTAAATATGTTATATTAAG 10974 ATTATTATATTAAATATGTTATATTAAG 1 ATTATTATATTAAATATGTTATATTAAG 11002 TATGGCATTC Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50 Consensus pattern (28 bp): ATTATTATATTAAATATGTTATATTAAG Found at i:11482 original size:24 final size:24 Alignment explanation

Indices: 11455--11517 Score: 108 Period size: 24 Copynumber: 2.6 Consensus size: 24 11445 TTTATTTATA * 11455 TATTTTATATTAAATTCGAAATTC 1 TATTTAATATTAAATTCGAAATTC * 11479 TATTAAATATTAAATTCGAAATTC 1 TATTTAATATTAAATTCGAAATTC 11503 TATTTAATATTAAAT 1 TATTTAATATTAAAT 11518 ATATTCAATT Statistics Matches: 36, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 24 36 1.00 ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48 Consensus pattern (24 bp): TATTTAATATTAAATTCGAAATTC Found at i:11531 original size:25 final size:26 Alignment explanation

Indices: 11498--11599 Score: 102 Period size: 25 Copynumber: 4.0 Consensus size: 26 11488 TTAAATTCGA 11498 AATTCTATTTA-ATATTAAATATATTC 1 AATT-TATTTATATATTAAATATATTC * * 11524 AATTTATTTATATATT-ATTTTATTC 1 AATTTATTTATATATTAAATATATTC * * 11549 AATTTATTTATATATTCAATTTATT- 1 AATTTATTTATATATTAAATATATTC * * * 11574 TATATATTATATATATTATATATATT 1 AATTTATT-TATATATTAAATATATT 11600 TTCTTTTAAT Statistics Matches: 65, Mismatches: 8, Indels: 6 0.82 0.10 0.08 Matches are distributed among these distances: 25 35 0.54 26 30 0.46 ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58 Consensus pattern (26 bp): AATTTATTTATATATTAAATATATTC Found at i:11536 original size:17 final size:17 Alignment explanation

Indices: 11516--11599 Score: 71 Period size: 17 Copynumber: 5.4 Consensus size: 17 11506 TTAATATTAA 11516 ATATATTCAATTTA-TT 1 ATATATTCAATTTATTT 11532 -TATA-T--A-TTATTT 1 ATATATTCAATTTATTT 11544 -TAT-T-CAATTTATTT 1 ATATATTCAATTTATTT 11558 ATATATTCAATTTATTT 1 ATATATTCAATTTATTT * 11575 ATATATT-ATATATATTAT 1 ATATATTCA-ATTTATT-T 11593 ATATATT 1 ATATATT 11600 TTCTTTTAAT Statistics Matches: 57, Mismatches: 1, Indels: 18 0.75 0.01 0.24 Matches are distributed among these distances: 11 3 0.05 12 6 0.11 13 1 0.02 14 7 0.12 15 7 0.12 16 2 0.04 17 23 0.40 18 8 0.14 ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60 Consensus pattern (17 bp): ATATATTCAATTTATTT Found at i:11586 original size:9 final size:9 Alignment explanation

Indices: 11509--11599 Score: 61 Period size: 9 Copynumber: 10.6 Consensus size: 9 11499 ATTCTATTTA * 11509 ATATTAAAT 1 ATATTATAT 11518 ATATTCA-AT 1 ATATT-ATAT * 11527 TTATT-TAT 1 ATATTATAT 11535 ATATTAT-T 1 ATATTATAT * 11543 TTATTCA-AT 1 ATATT-ATAT * 11552 TTATT-TAT 1 ATATTATAT 11560 ATATTCA-AT 1 ATATT-ATAT * 11569 TTATT-TAT 1 ATATTATAT 11577 ATATTATAT 1 ATATTATAT 11586 ATATTATAT 1 ATATTATAT 11595 ATATT 1 ATATT 11600 TTCTTTTAAT Statistics Matches: 66, Mismatches: 6, Indels: 20 0.72 0.07 0.22 Matches are distributed among these distances: 8 23 0.35 9 42 0.64 10 1 0.02 ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58 Consensus pattern (9 bp): ATATTATAT Done.