Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00170.F1

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, 917

Length: 1529
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28


Found at i:311 original size:33 final size:33

Alignment explanation

Indices: 262--342 Score: 99 Period size: 33 Copynumber: 2.5 Consensus size: 33 252 GGAAATCCCG * * * 262 AAACCTGAAATACCTAAAATGCCTGAGTTGCCA 1 AAACCTGAATTGCCTAAAATGCCGGAGTTGCCA * * 295 AAACCTGAATTGCCTAAAGTTCCGGAGTTGCCA 1 AAACCTGAATTGCCTAAAATGCCGGAGTTGCCA * * 328 AAGCCCGAATTGCCT 1 AAACCTGAATTGCCT 343 GAGGTTCCCA Statistics Matches: 41, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 33 41 1.00 ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22 Consensus pattern (33 bp): AAACCTGAATTGCCTAAAATGCCGGAGTTGCCA Found at i:377 original size:51 final size:51 Alignment explanation

Indices: 310--458 Score: 190 Period size: 51 Copynumber: 2.9 Consensus size: 51 300 TGAATTGCCT * * * * * 310 AAAGTTCCGGAGTTGCCAAAGCCCGAATTGCCTGAGGTTCCCAAGTTTCCG 1 AAAGTTCCAGAGTTGCCAAAGCCAGAATTACCTAAGGTTCCCGAGTTTCCG * * * * 361 AAAGTTCCAGAATTGCCAAAACCAGAATTACCCAAGGTTCCTGAGTTTCCG 1 AAAGTTCCAGAGTTGCCAAAGCCAGAATTACCTAAGGTTCCCGAGTTTCCG * * * 412 AAAGTTCCAGAGTTGCCAAAGCCTGAATTTCCTAAGATTCCCGAGTT 1 AAAGTTCCAGAGTTGCCAAAGCCAGAATTACCTAAGGTTCCCGAGTT 459 GAAAAAACCT Statistics Matches: 82, Mismatches: 16, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 51 82 1.00 ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25 Consensus pattern (51 bp): AAAGTTCCAGAGTTGCCAAAGCCAGAATTACCTAAGGTTCCCGAGTTTCCG Found at i:424 original size:18 final size:18 Alignment explanation

Indices: 353--425 Score: 53 Period size: 18 Copynumber: 4.2 Consensus size: 18 343 GAGGTTCCCA 353 AGTTTCCGAAAGTTCCAG 1 AGTTTCCGAAAGTTCCAG * * * 371 AATTGCC-AAA--ACCAG 1 AGTTTCCGAAAGTTCCAG * * * * * 386 AATTACCCAAGGTTCCTG 1 AGTTTCCGAAAGTTCCAG 404 AGTTTCCGAAAGTTCCAG 1 AGTTTCCGAAAGTTCCAG 422 AGTT 1 AGTT 426 GCCAAAGCCT Statistics Matches: 40, Mismatches: 12, Indels: 6 0.69 0.21 0.10 Matches are distributed among these distances: 15 10 0.25 16 2 0.05 17 3 0.08 18 25 0.62 ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26 Consensus pattern (18 bp): AGTTTCCGAAAGTTCCAG Found at i:584 original size:33 final size:33 Alignment explanation

Indices: 544--878 Score: 273 Period size: 33 Copynumber: 10.2 Consensus size: 33 534 TCCGGAGTTA * * 544 CCAAAGCCAGAATTTCCTAAAGTTCCTGAAGTG 1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG * * * * 577 CCCAAGCCTGAATTACCCAAAGCTCCTG-AGTTG 1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAG-TG * * * * * 610 CCAAAACCTGAATTACCAAAAGTTCCTG-AGTTA 1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAG-TG * * 643 CCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTG 1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG * * * * 676 CCTAAGCCAGAATTGCCTAAAGTTCCTGAGGTA 1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG * * * * 709 CCTAAGTCGGAATTGCCCAAAGCTCCTGAAGTG 1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG * * * * * 742 CCCAAGCCTGAATTACCCAAAGCTCCCG-AGTTG 1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAG-TG * ** ** * * 775 CCAAAACTTGAATCACCAAAAGTTCCTG-AGTTA 1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAG-TG * 808 CCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTG 1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG * * * 841 CCTAAGCCAGAATTGCCCAAAGCTCCTGAATTG 1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG 874 CCAAA 1 CCAAA 879 AATTCCTGAG Statistics Matches: 249, Mismatches: 49, Indels: 8 0.81 0.16 0.03 Matches are distributed among these distances: 32 4 0.02 33 242 0.97 34 3 0.01 ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22 Consensus pattern (33 bp): CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG Found at i:608 original size:66 final size:66 Alignment explanation

Indices: 529--878 Score: 319 Period size: 66 Copynumber: 5.3 Consensus size: 66 519 TGAAGCACCA * * * * * * * 529 AAAGTTCCGGAGTTACCAAAGCCAGAATTTCCTAAAGTTCCTGAAGTGCCCAAGCCTGAATTACC 1 AAAGCTCCTGAGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCC 594 C 66 C * * * * 595 AAAGCTCCTGAGTTGCCAAAACCTGAATTACCAAAAGTTCCTG-AGTTACCAAAGCCAGAATTGC 1 AAAGCTCCTGAGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAG-TGCCAAAGCCAGAATTGC * 659 CT 65 CC * * * * * * * * * 661 AAAGTTCCTGAGGTGCCTAAGCCAGAATTGCCTAAAGTTCCTGAGGTACCTAAGTCGGAATTGCC 1 AAAGCTCCTGAGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCC 726 C 66 C * * * * * * ** ** 727 AAAGCTCCTGAAG-TGCCCAAGCCTGAATTACCCAAAGCTCCCG-AGTTGCCAAAACTTGAATCA 1 AAAGCTCCTG-AGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAG-TGCCAAAGCCAGAATTG * 790 CCA 64 CCC * * * * 793 AAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTGCCTAAGCCAGAATTGCC 1 AAAGCTCCTGAGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCC 858 C 66 C * 859 AAAGCTCCTGAATTGCCAAA 1 AAAGCTCCTGAGTTGCCAAA 879 AATTCCTGAG Statistics Matches: 219, Mismatches: 59, Indels: 12 0.76 0.20 0.04 Matches are distributed among these distances: 65 5 0.02 66 209 0.95 67 5 0.02 ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22 Consensus pattern (66 bp): AAAGCTCCTGAGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCC C Found at i:621 original size:99 final size:99 Alignment explanation

Indices: 493--705 Score: 291 Period size: 99 Copynumber: 2.2 Consensus size: 99 483 TCCAGAGATG * * * * * 493 CCCAATGCTCCTAAATTGTCAAAATCTGAAGCACCAAAAGTTCCGGAGTTACCAAAGCCAGAATT 1 CCCAAAGCTCCTGAGTTGCCAAAACCTGAAGCACCAAAAGTTCCGGAGTTACCAAAGCCAGAATT * * 558 TCCTAAAGTTCCTGAAGTGCCCAAGCCTGAATTA 66 GCCTAAAGTTCCTGAAGTGCCCAAGCCAGAATTA ** * 592 CCCAAAGCTCCTGAGTTGCCAAAACCTGAATTACCAAAAGTTCCTGAGTTACCAAAGCCAGAATT 1 CCCAAAGCTCCTGAGTTGCCAAAACCTGAAGCACCAAAAGTTCCGGAGTTACCAAAGCCAGAATT * * * 657 GCCTAAAGTTCCTGAGGTGCCTAAGCCAGAATTG 66 GCCTAAAGTTCCTGAAGTGCCCAAGCCAGAATTA * * 691 CCTAAAGTTCCTGAG 1 CCCAAAGCTCCTGAG 706 GTACCTAAGT Statistics Matches: 99, Mismatches: 15, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 99 99 1.00 ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23 Consensus pattern (99 bp): CCCAAAGCTCCTGAGTTGCCAAAACCTGAAGCACCAAAAGTTCCGGAGTTACCAAAGCCAGAATT GCCTAAAGTTCCTGAAGTGCCCAAGCCAGAATTA Found at i:643 original size:18 final size:17 Alignment explanation

Indices: 583--647 Score: 62 Period size: 18 Copynumber: 3.8 Consensus size: 17 573 AGTGCCCAAG * 583 CCTGAATTACCCAAAGCT 1 CCTGAATTACCAAAAG-T * * 601 CCTGAGTTGCCAAAA-- 1 CCTGAATTACCAAAAGT 616 CCTGAATTACCAAAAGTT 1 CCTGAATTACCAAAAG-T * 634 CCTGAGTTACCAAA 1 CCTGAATTACCAAA 648 GCCAGAATTG Statistics Matches: 38, Mismatches: 6, Indels: 6 0.76 0.12 0.12 Matches are distributed among these distances: 15 13 0.34 18 25 0.66 ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23 Consensus pattern (17 bp): CCTGAATTACCAAAAGT Found at i:679 original size:18 final size:18 Alignment explanation

Indices: 656--713 Score: 59 Period size: 18 Copynumber: 3.4 Consensus size: 18 646 AAGCCAGAAT 656 TGCCTAAAGTTCCTGAGG 1 TGCCTAAAGTTCCTGAGG * ** 674 TGCCT-AAG--CCAGAAT 1 TGCCTAAAGTTCCTGAGG 689 TGCCTAAAGTTCCTGAGG 1 TGCCTAAAGTTCCTGAGG * 707 TACCTAA 1 TGCCTAA 714 GTCGGAATTG Statistics Matches: 30, Mismatches: 7, Indels: 6 0.70 0.16 0.14 Matches are distributed among these distances: 15 9 0.30 16 3 0.10 17 3 0.10 18 15 0.50 ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26 Consensus pattern (18 bp): TGCCTAAAGTTCCTGAGG Found at i:745 original size:18 final size:18 Alignment explanation

Indices: 722--767 Score: 53 Period size: 15 Copynumber: 2.7 Consensus size: 18 712 AAGTCGGAAT 722 TGCCCAAAGCTCCTGAAG 1 TGCCCAAAGCTCCTGAAG * 740 TGCCC-AAG--CCTGAAT 1 TGCCCAAAGCTCCTGAAG * 755 TACCCAAAGCTCC 1 TGCCCAAAGCTCC 768 CGAGTTGCCA Statistics Matches: 23, Mismatches: 2, Indels: 6 0.74 0.06 0.19 Matches are distributed among these distances: 15 10 0.43 16 3 0.13 17 3 0.13 18 7 0.30 ACGTcount: A:0.28, C:0.37, G:0.17, T:0.17 Consensus pattern (18 bp): TGCCCAAAGCTCCTGAAG Found at i:879 original size:99 final size:99 Alignment explanation

Indices: 526--879 Score: 327 Period size: 99 Copynumber: 3.6 Consensus size: 99 516 ATCTGAAGCA * * * * * * * 526 CCAAAAGTTCC-GGAGTTACCAAAGCCAGAATTTCCTAAAGTTCCTGAAGTGCCCAAGCCTGAAT 1 CCAAAAGTTCCTGAAG-TGCCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCAAAACCTGAAT * * * * * * 590 TACCCAAAGCTCCTGAGTTGCCAAAACCTGAATTA 65 TACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTG * * * * * * * 625 CCAAAAGTTCCTG-AGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAGCCAGAAT 1 CCAAAAGTTCCTGAAG-TGCCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCAAAACCTGAAT * * * * * * 689 TGCCTAAAGTTCCTGAGGTACCTAAGTCGGAATTG 65 TACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTG * * * * * * * 724 CCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCG-AGTTGCCAAAACTTGAAT 1 CCAAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCCCAAAGCTCCTGAAG-TGCCAAAACCTGAAT * 788 CACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTG 65 TACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTG * * * 823 CCTAAAGTTCCTGAAGTGCCTAAGCCAGAATTGCCCAAAGCTCCTGAATTGCCAAAA 1 CCAAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCAAAA 880 ATTCCTGAGT Statistics Matches: 209, Mismatches: 42, Indels: 8 0.81 0.16 0.03 Matches are distributed among these distances: 98 1 0.00 99 204 0.98 100 4 0.02 ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22 Consensus pattern (99 bp): CCAAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCAAAACCTGAATT ACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTG Found at i:885 original size:18 final size:18 Alignment explanation

Indices: 850--920 Score: 51 Period size: 18 Copynumber: 4.1 Consensus size: 18 840 GCCTAAGCCA * ** 850 GAATTGCCCAAAGCTCCT 1 GAATTGCCAAAAATTCCT 868 GAATTGCCAAAAATTCCT 1 GAATTGCCAAAAATTCCT * * 886 GAGTT--CACAAAA--CCA 1 GAATTGCCA-AAAATTCCT * 901 GAATTGCCTAAAATTCCT 1 GAATTGCCAAAAATTCCT 919 GA 1 GA 921 GGTACCAAAA Statistics Matches: 40, Mismatches: 8, Indels: 10 0.69 0.14 0.17 Matches are distributed among these distances: 15 6 0.15 16 6 0.15 17 5 0.12 18 23 0.57 ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24 Consensus pattern (18 bp): GAATTGCCAAAAATTCCT Found at i:885 original size:51 final size:51 Alignment explanation

Indices: 830--1029 Score: 146 Period size: 51 Copynumber: 4.0 Consensus size: 51 820 TTGCCTAAAG * * 830 TTCCTGAAGTGCCTAAGCCAGAATTGCCCAAAGCTCCTGAATTGCCAAAAA 1 TTCCTGAAGTGCCTAAGCCAGAATTGCCCAAAACTCCTGAATTACCAAAAA * * * * * ** 881 TTCCTG-AGTTCACAAAACCAGAATTGCCTAAAATTCCTGAGGTACC-AAAA 1 TTCCTGAAGTGC-CTAAGCCAGAATTGCCCAAAACTCCTGAATTACCAAAAA * * * * * * 931 --CCAGAATTGCCTAAAGTGACTGAGTTG-CCAAAACT--TGAATTACCAAAAG 1 TTCCTGAAGTGCCT-AA--GCCAGAATTGCCCAAAACTCCTGAATTACCAAAAA * * 980 TTTCTGAGGTGCCTAAGCCAGAATTG-CCAAAAGCTCCTGAATTACCAAAA 1 TTCCTGAAGTGCCTAAGCCAGAATTGCCCAAAA-CTCCTGAATTACCAAAA 1030 CCTCAATTAC Statistics Matches: 109, Mismatches: 29, Indels: 22 0.68 0.18 0.14 Matches are distributed among these distances: 48 24 0.22 49 10 0.09 50 16 0.15 51 59 0.54 ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23 Consensus pattern (51 bp): TTCCTGAAGTGCCTAAGCCAGAATTGCCCAAAACTCCTGAATTACCAAAAA Found at i:886 original size:150 final size:150 Alignment explanation

Indices: 718--1029 Score: 329 Period size: 150 Copynumber: 2.1 Consensus size: 150 708 ACCTAAGTCG * * * * * * * * 718 GAATTGCCCAAAGCTCCTGAAGTGC-CCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAAAC 1 GAATTGCCAAAAACTCCTG-AGTGCACAAAACCAGAATTACCCAAAACTCCCGAGGTACCAAAAC ** ** * * * 782 TTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTGCCTAAG 65 CAGAATCACCAAAAGTGACTGAGTTACCAAAACCAGAATTACCAAAAGTTCCTGAAGTGCCTAAG * 847 CCAGAATTGCCCAAAGCTCCT 130 CCAGAATTGCCAAAAGCTCCT * * * * * * 868 GAATTGCCAAAAATTCCTGAGTTCACAAAACCAGAATTGCCTAAAATTCCTGAGGTACCAAAACC 1 GAATTGCCAAAAACTCCTGAGTGCACAAAACCAGAATTACCCAAAACTCCCGAGGTACCAAAACC ** * * ** * * 933 AGAATTGCCTAAAGTGACTGAGTTGCCAAAACTTGAATTACCAAAAGTTTCTGAGGTGCCTAAGC 66 AGAATCACCAAAAGTGACTGAGTTACCAAAACCAGAATTACCAAAAGTTCCTGAAGTGCCTAAGC 998 CAGAATTGCCAAAAGCTCCT 131 CAGAATTGCCAAAAGCTCCT * 1018 GAATTACCAAAA 1 GAATTGCCAAAA 1030 CCTCAATTAC Statistics Matches: 130, Mismatches: 31, Indels: 2 0.80 0.19 0.01 Matches are distributed among these distances: 149 4 0.03 150 126 0.97 ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22 Consensus pattern (150 bp): GAATTGCCAAAAACTCCTGAGTGCACAAAACCAGAATTACCCAAAACTCCCGAGGTACCAAAACC AGAATCACCAAAAGTGACTGAGTTACCAAAACCAGAATTACCAAAAGTTCCTGAAGTGCCTAAGC CAGAATTGCCAAAAGCTCCT Found at i:1043 original size:99 final size:98 Alignment explanation

Indices: 895--1145 Score: 268 Period size: 99 Copynumber: 2.5 Consensus size: 98 885 TGAGTTCACA * * * * * ** 895 AAACCAGAATTGCCTAAAATTCCTGAGGTACCAAAACCAGAATTGCCTAAAGTGACTGAGTTGCC 1 AAACCAGAATTGCC-AAAACTCCTGAGTTACCAAAACCTGAATTACCTAAAGTGACCGAGTTAAC ** * * * * 960 AAAACTTGAATTACCAAAAGTTTCTGAGGTGCCT 65 AAAACCAGAATTACCAAAAGTTCCAGAGGTACCG * * * * ** * 994 AAGCCAGAATTGCCAAAAGCTCCTGAATTACCAAAACCTCAATTACCTAAAATTCCCGGGTTAAC 1 AAACCAGAATTGCCAAAA-CTCCTGAGTTACCAAAACCTGAATTACCTAAAGTGACCGAGTTAAC * * 1059 AAAACCAGAATTGCCTAAAGTTCCAGAGGTACCG 65 AAAACCAGAATTACCAAAAGTTCCAGAGGTACCG * 1093 AAACCAGAATTGCCCAAAACTCCTGAGTTGCCAAAACCTGAATTACCTAAAGT 1 AAACCAGAATTG-CCAAAACTCCTGAGTTACCAAAACCTGAATTACCTAAAGT 1146 TCCTGAATTG Statistics Matches: 123, Mismatches: 27, Indels: 4 0.80 0.18 0.03 Matches are distributed among these distances: 98 4 0.03 99 113 0.92 100 6 0.05 ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22 Consensus pattern (98 bp): AAACCAGAATTGCCAAAACTCCTGAGTTACCAAAACCTGAATTACCTAAAGTGACCGAGTTAACA AAACCAGAATTACCAAAAGTTCCAGAGGTACCG Found at i:1157 original size:33 final size:33 Alignment explanation

Indices: 868--1151 Score: 237 Period size: 33 Copynumber: 8.6 Consensus size: 33 858 CAAAGCTCCT * * 868 GAATTGCCAAAAATTCCTGAGTT-CACAAAACCA 1 GAATTGCCTAAAGTTCCTGAGTTAC-CAAAACCA * * 901 GAATTGCCTAAAATTCCTGAGGTACCAAAACCA 1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA ** * ** 934 GAATTGCCTAAAGTGACTGAGTTGCCAAAACTT 1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA * * * * * * * 967 GAATTACCAAAAGTTTCTGAGGTGCCTAAGCCA 1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA * * * * 1000 GAATTGCCAAAAGCTCCTGAATTACCAAAACCT 1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA * * * * * * 1033 CAATTACCTAAAATTCCCGGGTTAACAAAACCA 1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA * * * 1066 GAATTGCCTAAAGTTCCAGAGGTACCGAAACCA 1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA * ** * * 1099 GAATTGCCCAAAACTCCTGAGTTGCCAAAACCT 1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA * 1132 GAATTACCTAAAGTTCCTGA 1 GAATTGCCTAAAGTTCCTGA 1152 ATTGCCTAGC Statistics Matches: 193, Mismatches: 57, Indels: 2 0.77 0.23 0.01 Matches are distributed among these distances: 33 192 0.99 34 1 0.01 ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23 Consensus pattern (33 bp): GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA Done.