Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1078

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: 29049
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:20984 original size:42 final size:42

Alignment explanation


    Indices: 20876--21083  Score: 197
    Period size: 42  Copynumber: 4.9  Consensus size: 42

      20866 TGAGATGCCA

                       *               * **   *         
      20876 ATGCCATATCCTAGACATGGTCTTACATGGGATCACAAATATCG
          1 ATGCCATATCCCAGACATGGTCTTACACGAAATCTC--ATATCG

                     *                      **    *     
      20920 ATGCCGATAGCCCAG-CTATGGTCTTACACGATGTCTCGTATCG
          1 ATGCC-ATATCCCAGAC-ATGGTCTTACACGAAATCTCATATCG

                   *                         *   *    
      20963 ATGCCATGTCCCAGACATGGTCTTACACGAAATTTCAAATCG
          1 ATGCCATATCCCAGACATGGTCTTACACGAAATCTCATATCG

                           *         *                 
      21005 ATGCCATATCCCAGATATGGTCTTATACGAAATC-CATAAT-G
          1 ATGCCATATCCCAGACATGGTCTTACACGAAATCTCAT-ATCG

                           *         *   *        
      21046 ATGCCATATCCCAGATATGGTCTTATACGTAATCTCAT
          1 ATGCCATATCCCAGACATGGTCTTACACGAAATCTCAT

      21084 TAACCCTAAT


Statistics
Matches: 138,  Mismatches: 21, Indels: 12
        0.81            0.12        0.07

Matches are distributed among these distances:
  41   36  0.26
  42   63  0.46
  43   11  0.08
  44    6  0.04
  45   22  0.16

ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29


Consensus pattern (42 bp):   
ATGCCATATCCCAGACATGGTCTTACACGAAATCTCATATCG

Found at i:21066 original size:83 final size:85

Alignment explanation


    Indices: 20876--21070  Score: 216
    Period size: 87  Copynumber: 2.3  Consensus size: 85

      20866 TGAGATGCCA

                       *               * **  **                        *     
      20876 ATGCCATATCCTAGACATGGTCTTACATGGGATCACAAATATCGATGCCGATAGCCCAGCTATGG
          1 ATGCCATATCCCAGACATGGTCTTACACGAAATTTC-AA-ATCGATGCCGATAGCCCAGATATGG

                      **    *     
      20941 TCTTACACGATGTCTCGTATCG
         64 TCTTACACGAAATCTCATATCG

                   *                                           *             
      20963 ATGCCATGTCCCAGACATGGTCTTACACGAAATTTCAAATCGATGCC-ATATCCCAGATATGGTC
          1 ATGCCATATCCCAGACATGGTCTTACACGAAATTTCAAATCGATGCCGATAGCCCAGATATGGTC

               *                 
      21027 TTATACGAAATC-CATAAT-G
         66 TTACACGAAATCTCAT-ATCG

                           *         
      21046 ATGCCATATCCCAGATATGGTCTTA
          1 ATGCCATATCCCAGACATGGTCTTA

      21071 TACGTAATCT


Statistics
Matches: 92,  Mismatches: 15, Indels: 6
        0.81            0.13        0.05

Matches are distributed among these distances:
  83   26  0.28
  84   26  0.28
  85    9  0.10
  86    2  0.02
  87   29  0.32

ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28


Consensus pattern (85 bp):   
ATGCCATATCCCAGACATGGTCTTACACGAAATTTCAAATCGATGCCGATAGCCCAGATATGGTC
TTACACGAAATCTCATATCG

Found at i:21096 original size:41 final size:40

Alignment explanation


    Indices: 20966--21079  Score: 111
    Period size: 41  Copynumber: 2.8  Consensus size: 40

      20956 CGTATCGATG

                *       *         *        *  *     **
      20966 CCATGTCCCAGACATGGTCTTACACGAAATTTCAAATCGATG
          1 CCATATCCCAGATATGGTCTTATACGAAA-TCCATAT-GAAC

                                                   **
      21008 CCATATCCCAGATATGGTCTTATACGAAATCCATAATGATG
          1 CCATATCCCAGATATGGTCTTATACGAAATCCAT-ATGAAC

                                      *    
      21049 CCATATCCCAGATATGGTCTTATACGTAATC
          1 CCATATCCCAGATATGGTCTTATACGAAATC

      21080 TCATTAACCC


Statistics
Matches: 65,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  41   37  0.57
  42   28  0.43

ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29


Consensus pattern (40 bp):   
CCATATCCCAGATATGGTCTTATACGAAATCCATATGAAC

Found at i:22809 original size:25 final size:25

Alignment explanation


    Indices: 22776--22833  Score: 80
    Period size: 25  Copynumber: 2.3  Consensus size: 25

      22766 ATGAGCTGTA

                              *      
      22776 AACAATAAGCTCCTCCGAGCTAAAT
          1 AACAATAAGCTCCTCCGAACTAAAT

                        *  *     *   
      22801 AACAATAAGCTCTTCTGAACTGAAT
          1 AACAATAAGCTCCTCCGAACTAAAT

                    
      22826 AACAATAA
          1 AACAATAA

      22834 ACTCATATGA


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  25   29  1.00

ACGTcount: A:0.45, C:0.22, G:0.10, T:0.22


Consensus pattern (25 bp):   
AACAATAAGCTCCTCCGAACTAAAT

Found at i:24768 original size:74 final size:75

Alignment explanation


    Indices: 24684--24826  Score: 252
    Period size: 75  Copynumber: 1.9  Consensus size: 75

      24674 TCCTATATCC

                                                                             
      24684 CTAAACCGTGTAACTCTCT-TTTTGCAATGCATAAACAAATTGATGTCACACGACCAAGTCACAC
          1 CTAAACCGTGTAACTCTCTGTTTTGCAATGCATAAACAAATTGATGTCACACGACCAAGTCACAC

                      
      24748 GCCCATGTCG
         66 GCCCATGTCG

                *                            *                   *           
      24758 CTAACCCGTGTAACTCTCTGTTTTGCAATGCATGAACAAATTGATGTCACACGGCCAAGTCACAC
          1 CTAAACCGTGTAACTCTCTGTTTTGCAATGCATAAACAAATTGATGTCACACGACCAAGTCACAC

                
      24823 GCCC
         66 GCCC

      24827 GTGTGCCAGG


Statistics
Matches: 65,  Mismatches: 3, Indels: 1
        0.94            0.04        0.01

Matches are distributed among these distances:
  74   18  0.28
  75   47  0.72

ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25


Consensus pattern (75 bp):   
CTAAACCGTGTAACTCTCTGTTTTGCAATGCATAAACAAATTGATGTCACACGACCAAGTCACAC
GCCCATGTCG

Done.