Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold759

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: 7171
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31


Found at i:1598 original size:100 final size:100

Alignment explanation


    Indices: 1484--2420  Score: 1441
    Period size: 100  Copynumber: 9.4  Consensus size: 100

       1474 TGCAATGTCG

                                                                             
       1484 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCAG
          1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCAG

                                               
       1549 CCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA
         66 CCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA

                                            *                                
       1584 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCCGTTCCACCGCACCGTCAGGGAAGTAAGATCAG
          1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCAG

                                               
       1649 CCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA
         66 CCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA

               *          *                 *                                
       1684 GGGGAACCAGATCCCCCGTCGTAGCTTCAATCCGTTCCACCGCACCGTCAGGGAAGTAAGATCAG
          1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCAG

                                               
       1749 CCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA
         66 CCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA

               *          *                 *                                
       1784 GGGGAACCAGATCCCCCGTCGTAGCTTCAATCCGTTCCACCGCACCGTCAGGGAAGTAAGATCAG
          1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCAG

                                               
       1849 CCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA
         66 CCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA

               *          *                 *                                
       1884 GGGGAACCAGATCCCCCGTCGTAGCTTCAATCCGTTCCACCGCACCGTCAGGGAAGTAAGATCAG
          1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCAG

                                       *       
       1949 CCGCTGTGGCTTCAATCTTTTTAATTGCAATATCA
         66 CCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA

                                          *         *    *     * *          *
       1984 GGGAAACCAGATCCGCCGTCGTAGCTTCAACCTGTTCCACTGCACTG-CTAAGAAAGTAAGATCC
          1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTC-AGGGAAGTAAGATCA

               *              *         *       
       2048 GCCACTGTGGCTTCAATCGTTTTAATTGCAATATCA
         65 GCCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA

                                                    *    *     *            *
       2084 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCC
          1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTC-AGGGAAGTAAGATCA

                *        *              *       
       2148 GCCGTTGTGGCTTTAATCTTTTTAATTGCAATATCA
         65 GCCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA

                                                    *    *     *            *
       2184 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCC
          1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTC-AGGGAAGTAAGATCA

                             *                * 
       2248 GCCGCTGTGGCTTCAATGTTTTTAATTGTAATATTA
         65 GCCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA

            *                                       *    *     *            *
       2284 AGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCC
          1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTC-AGGGAAGTAAGATCA

                *                       *       
       2348 GCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
         65 GCCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA

                 *                               
       2384 GGGAATCCAGATCCGCCGTCGTAGCTTCAATCTGTTC
          1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTC

       2421 ACTGCACTGC


Statistics
Matches: 803,  Mismatches: 33, Indels: 2
        0.96            0.04        0.00

Matches are distributed among these distances:
  99    1  0.00
 100  802  1.00

ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27


Consensus pattern (100 bp):   
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCAG
CCGCTGTGGCTTCAATCTTTTTAATTGTAATATCA

Found at i:2744 original size:132 final size:132

Alignment explanation


    Indices: 2440--2721  Score: 537
    Period size: 132  Copynumber: 2.1  Consensus size: 132

       2430 CTAAGGAGGT

                                                                             
       2440 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTA
          1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTA

                                                                             
       2505 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCATCGATCTGCTCCACTACTGCTTAGGGAG
         66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCATCGATCTGCTCCACTACTGCTTAGGGAG

              
       2570 AC
        131 AC

                                                         *    *              
       2572 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTATAATTTCTGGCTTCAATGTA
          1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTA

                          *                                                  
       2637 CTCCACTGTAACCATAGGGAGGTAAAATCTGCCATCATCGATCTGCTCCACTACTGCTTAGGGAG
         66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCATCGATCTGCTCCACTACTGCTTAGGGAG

              
       2702 AC
        131 AC

                              
       2704 AAGATCTGAAATCTTCAA
          1 AAGATCTGAAATCTTCAA

       2722 CCTGCTCCAC


Statistics
Matches: 147,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 132  147  1.00

ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27


Consensus pattern (132 bp):   
AAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTA
CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCATCGATCTGCTCCACTACTGCTTAGGGAG
AC

Found at i:4046 original size:22 final size:22

Alignment explanation


    Indices: 4021--4066  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       4011 TTAGCCTCTC

                  *                
       4021 CATTTTTA-CTTTTTCATTTTTT
          1 CATTTTCATCTTTTT-ATTTTTT

                                  
       4043 CATTTTCATCTTTTTATTTTTT
          1 CATTTTCATCTTTTTATTTTTT

              
       4065 CA
          1 CA

       4067 CATCACTTCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22   16  0.73
  23    6  0.27

ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70


Consensus pattern (22 bp):   
CATTTTCATCTTTTTATTTTTT

Found at i:6294 original size:20 final size:20

Alignment explanation


    Indices: 6265--6304  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       6255 TAAAGGTCTT

                                
       6265 TAATGCATATGATGCGATGC
          1 TAATGCATATGATGCGATGC

                 *              
       6285 TAATGTATATGATGCGATGC
          1 TAATGCATATGATGCGATGC

       6305 ATGAGGTGAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33


Consensus pattern (20 bp):   
TAATGCATATGATGCGATGC
Done.