Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: MAG.C2.12_contig_108

Parameters: 2 5 7 80 10 50 2000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 2000

Length: 7842
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25


Found at i:1577 original size:18 final size:18

Alignment explanation


    Indices: 1551--1589  Score: 50
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       1541 AAATTCCCTG

                      * **    
       1551 GTTTCTTTGGCTGTTTTA
          1 GTTTCTTTGGATCGTTTA

                *             
       1569 GTTTGTTTGGATCGTTTA
          1 GTTTCTTTGGATCGTTTA

               
       1587 GTT
          1 GTT

       1590 ACCTTGCAAA


Statistics
Matches: 17,  Mismatches: 4, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.08, C:0.08, G:0.26, T:0.59


Consensus pattern (18 bp):   
GTTTCTTTGGATCGTTTA

Found at i:1634 original size:27 final size:27

Alignment explanation


    Indices: 1590--1646  Score: 86
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       1580 TCGTTTAGTT

                       *         *     
       1590 ACCTTGCAAACTAAATAAACCGCATAA
          1 ACCTTGCAAACCAAATAAACCACATAA

                         *        *    
       1617 ACCTTGCAAACCAGATAAACCATATAA
          1 ACCTTGCAAACCAAATAAACCACATAA

               
       1644 ACC
          1 ACC

       1647 AGACAAAGAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.47, C:0.28, G:0.07, T:0.18


Consensus pattern (27 bp):   
ACCTTGCAAACCAAATAAACCACATAA

Found at i:1645 original size:18 final size:18

Alignment explanation


    Indices: 1604--1653  Score: 58
    Period size: 18  Copynumber: 2.8  Consensus size: 18

       1594 TGCAAACTAA

                   **       * 
       1604 ATAAACCGCATAAACCTT
          1 ATAAACCAGATAAACCAT

            **                
       1622 GCAAACCAGATAAACCAT
          1 ATAAACCAGATAAACCAT

                      *   
       1640 ATAAACCAGACAAA
          1 ATAAACCAGATAAA

       1654 GAAATAAGCC


Statistics
Matches: 24,  Mismatches: 8, Indels: 0
        0.75            0.25        0.00

Matches are distributed among these distances:
  18   24  1.00

ACGTcount: A:0.52, C:0.26, G:0.08, T:0.14


Consensus pattern (18 bp):   
ATAAACCAGATAAACCAT

Found at i:1653 original size:27 final size:27

Alignment explanation


    Indices: 1596--1660  Score: 67
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       1586 AGTTACCTTG

                 *         *        ***
       1596 CAAACTAAATAAACCGCATAAACCTTG
          1 CAAACCAAATAAACCACATAAACCAGA

                   *        *          
       1623 CAAACCAGATAAACCATATAAACCAGA
          1 CAAACCAAATAAACCACATAAACCAGA

                 *      
       1650 CAAA-GAAATAA
          1 CAAACCAAATAA

       1661 GCCGAATGGC


Statistics
Matches: 29,  Mismatches: 9, Indels: 1
        0.74            0.23        0.03

Matches are distributed among these distances:
  26    5  0.17
  27   24  0.83

ACGTcount: A:0.55, C:0.23, G:0.08, T:0.14


Consensus pattern (27 bp):   
CAAACCAAATAAACCACATAAACCAGA
Done.