Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3269

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: 45882
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:6860 original size:27 final size:27

Alignment explanation


    Indices: 6830--7007  Score: 205
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       6820 ATATTGAGTC

                    *       *   *    * 
       6830 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                             *  *      
       6857 CGCACACTTAGTGCTACGTAATCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                        
       6884 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAGTCAAA-T

                          **   *     * 
       6912 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                 *   ** 
       6939 CGCACACTTAGTGC-ATCATATTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAAAT

                          *            
       6966 CGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                           
       6993 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       7008 GTACAATTTA


Statistics
Matches: 130,  Mismatches: 18, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
  27  106  0.82
  28   24  0.18

ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAAAT

Found at i:6969 original size:82 final size:81

Alignment explanation


    Indices: 6851--7006  Score: 233
    Period size: 82  Copynumber: 1.9  Consensus size: 81

       6841 TGCTATATAA

                                   *                       *                 
       6851 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
          1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA

                             
       6916 CACTTAGTGCCGCATGG
         65 CACTTAGTGCCGCATGG

                *                      *   **                                
       6933 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
          1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA

                      
       6997 CACTTAGTGC
         65 CACTTAGTGC

       7007 TGTACAATTT


Statistics
Matches: 67,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  81   16  0.24
  82   51  0.76

ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27


Consensus pattern (81 bp):   
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG

Found at i:15864 original size:39 final size:39

Alignment explanation


    Indices: 15821--16025  Score: 288
    Period size: 39  Copynumber: 5.3  Consensus size: 39

      15811 TGCCTCTGGA

                             *       *             
      15821 ACTTAGCCCGGATATAACATCAGCAAGAATGCCTTCGGG
          1 ACTTAGCCCGGATATAATATCAGCACGAATGCCTTCGGG

                     *                             
      15860 ACTTAGCCCAGATATAATATCAGCACGAATGCCTTCGGG
          1 ACTTAGCCCGGATATAATATCAGCACGAATGCCTTCGGG

                               *                   
      15899 ACTTAGCCCGGATATAATACCAGCACGAATGCCTTCGGG
          1 ACTTAGCCCGGATATAATATCAGCACGAATGCCTTCGGG

                 ** *                              
      15938 ACTTAATCAGGATATAATATCAGCACGAATGCCTTCGGG
          1 ACTTAGCCCGGATATAATATCAGCACGAATGCCTTCGGG

                               *          *    *    
      15977 ACTTAGCCCGGATATAAATCTCA-CAC-AAGGCCTGCGGG
          1 ACTTAGCCCGGATAT-AATATCAGCACGAATGCCTTCGGG

            *          
      16015 TCTTAGCCCGG
          1 ACTTAGCCCGG

      16026 TTAAAATCCT


Statistics
Matches: 149,  Mismatches: 16, Indels: 3
        0.89            0.10        0.02

Matches are distributed among these distances:
  38   20  0.13
  39  123  0.83
  40    6  0.04

ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22


Consensus pattern (39 bp):   
ACTTAGCCCGGATATAATATCAGCACGAATGCCTTCGGG

Found at i:23962 original size:39 final size:39

Alignment explanation


    Indices: 23919--24026  Score: 180
    Period size: 39  Copynumber: 2.8  Consensus size: 39

      23909 ACATCAATAT

                      *                            
      23919 GAATGCCTTCAGGACTTAGCCCGAATATAATACCAGCAC
          1 GAATGCCTTCGGGACTTAGCCCGAATATAATACCAGCAC

                              *             *      
      23958 GAATGCCTTCGGGACTTAACCCGAATATAATATCAGCAC
          1 GAATGCCTTCGGGACTTAGCCCGAATATAATACCAGCAC

                                   *      
      23997 GAATGCCTTCGGGACTTAGCCCGGATATAA
          1 GAATGCCTTCGGGACTTAGCCCGAATATAA

      24027 ATCTCACACA


Statistics
Matches: 64,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  39   64  1.00

ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22


Consensus pattern (39 bp):   
GAATGCCTTCGGGACTTAGCCCGAATATAATACCAGCAC

Found at i:29930 original size:50 final size:46

Alignment explanation


    Indices: 29826--29930  Score: 122
    Period size: 50  Copynumber: 2.2  Consensus size: 46

      29816 GACAGGACAG

                 *               *                  *     
      29826 GACAGAAATGAGCCATGTAAGTCCATATCAGTTATATGGCTTTGGA
          1 GACAGGAATGAGCCATGTAAGCCCATATCAGTTATATGGCATTGGA

              *                                                
      29872 GATAGGAATGAGCCATGTAAGCCCATATAATACA-TATATATGGCATTGGA
          1 GACAGGAATGAGCCATGTAAGCCC--AT-AT-CAGT-TATATGGCATTGGA

                     
      29922 GACAGGAAT
          1 GACAGGAAT

      29931 AATTCATGTA


Statistics
Matches: 49,  Mismatches: 5, Indels: 6
        0.82            0.08        0.10

Matches are distributed among these distances:
  46   21  0.43
  48    2  0.04
  49    3  0.06
  50   23  0.47

ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26


Consensus pattern (46 bp):   
GACAGGAATGAGCCATGTAAGCCCATATCAGTTATATGGCATTGGA
Done.