Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00548.P3

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: 7518
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31


Found at i:2010 original size:18 final size:18

Alignment explanation


    Indices: 1987--2075  Score: 106
    Period size: 18  Copynumber: 4.9  Consensus size: 18

       1977 CGTTTACGGT

                              
       1987 ACTATTCACGTATACAGC
          1 ACTATTCACGTATACAGC

                             *
       2005 ACTATTCACGTATACAGT
          1 ACTATTCACGTATACAGC

                    *      *  
       2023 ACTATTCAAGTATACGGC
          1 ACTATTCACGTATACAGC

                  *   *    * *
       2041 ACTATTTACGAATACGGT
          1 ACTATTCACGTATACAGC

               *             
       2059 ACTGTTCACGTATACAG
          1 ACTATTCACGTATACAG

       2076 TAGTTGGGAT


Statistics
Matches: 59,  Mismatches: 12, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  18   59  1.00

ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30


Consensus pattern (18 bp):   
ACTATTCACGTATACAGC

Found at i:2036 original size:36 final size:36

Alignment explanation


    Indices: 1985--2075  Score: 128
    Period size: 36  Copynumber: 2.5  Consensus size: 36

       1975 ACCGTTTACG

                                          *     
       1985 GTACTATTCACGTATACAGCACTATTCACGTATACA
          1 GTACTATTCACGTATACAGCACTATTCACGAATACA

                      *      *        *        *
       2021 GTACTATTCAAGTATACGGCACTATTTACGAATACG
          1 GTACTATTCACGTATACAGCACTATTCACGAATACA

                 *             
       2057 GTACTGTTCACGTATACAG
          1 GTACTATTCACGTATACAG

       2076 TAGTTGGGAT


Statistics
Matches: 47,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  36   47  1.00

ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31


Consensus pattern (36 bp):   
GTACTATTCACGTATACAGCACTATTCACGAATACA

Found at i:7159 original size:72 final size:72

Alignment explanation


    Indices: 7066--7377  Score: 269
    Period size: 72  Copynumber: 4.3  Consensus size: 72

       7056 TCCCATCAAC

                            **         *  *       ***       *    *           
       7066 TATTGGAAA-CTTGACCACTCTCGAAGTTCTTCATCTTTCCAATAACAGCTTATCAGGTGAAATT
          1 TATTGGAAACCTT-ACTTCTCTCGAAGCTCATCATCTTAATAATAACAACTTAACAGGTGAAATT

               *     
       7130 CC-GCTGGT
         65 CCTCCT-GT

                                    *  *          *                          
       7138 TATTGGAAACCTTACTTCTCTCG-TGCGCATCAGTCTTGATAATAACAACTTAACAGGTGAAATT
          1 TATTGGAAACCTTACTTCTCTCGAAGCTCATCA-TCTTAATAATAACAACTTAACAGGTGAAATT

                    
       7202 CCTCCTGT
         65 CCTCCTGT

                     *     *             * * **               *  *           
       7210 TATT-GAAAACTTGAGTTCTCTCGGAA-CACTTTTTCTTAATAATAACAAATTGACAGGTGAAAT
          1 TATTGGAAACCTT-ACTTCTCTC-GAAGCTCATCATCTTAATAATAACAACTTAACAGGTGAAAT

                   *  
       7273 TCCAT-CGGT
         64 TCC-TCCTGT

                       *            * *            *                         
       7282 TATTGGAAACCGTACTTCTCTC-ATGTTCATCAATCTTAGTAATAACAACTTAACAGGTGAAATT
          1 TATTGGAAACCTTACTTCTCTCGAAGCTCATC-ATCTTAATAATAACAACTTAACAGGTGAAATT

                    
       7346 CCTCCTGT
         65 CCTCCTGT

                             *      
       7354 TATTGGAAACCTTACTTTTCTCGA
          1 TATTGGAAACCTTACTTCTCTCGA

       7378 GGCCTTTGAT


Statistics
Matches: 190,  Mismatches: 38, Indels: 23
        0.76            0.15        0.09

Matches are distributed among these distances:
  70    1  0.01
  71   15  0.08
  72  157  0.83
  73   17  0.09

ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35


Consensus pattern (72 bp):   
TATTGGAAACCTTACTTCTCTCGAAGCTCATCATCTTAATAATAACAACTTAACAGGTGAAATTC
CTCCTGT

Done.