Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold610

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: 17415
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:13874 original size:40 final size:38

Alignment explanation


    Indices: 13818--13920  Score: 109
    Period size: 40  Copynumber: 2.6  Consensus size: 38

      13808 TCGAATGATG

                                   *              * 
      13818 TCCGGCTAAGTCCCGAAGGC-TTTGTGCTGAGTGACCATA
          1 TCCGGCTAAGT-CCGAAGGCATTGGTGC-GAGTGACCAAA

                                             *  *   
      13857 TCCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACTAAA
          1 TCCGG-CTAAG-TCCGAAGGCATTGGTGCGAGTGACCAAA

                                    
      13897 TCCGGGCTAAGTCCGAAGAGCATT
          1 TCC-GGCTAAGTCCGAAG-GCATT

      13921 CATGCTAGCG


Statistics
Matches: 55,  Mismatches: 4, Indels: 9
        0.81            0.06        0.13

Matches are distributed among these distances:
  39   12  0.22
  40   34  0.62
  41    9  0.16

ACGTcount: A:0.25, C:0.23, G:0.28, T:0.23


Consensus pattern (38 bp):   
TCCGGCTAAGTCCGAAGGCATTGGTGCGAGTGACCAAA

Found at i:13938 original size:79 final size:80

Alignment explanation


    Indices: 13854--14051  Score: 224
    Period size: 80  Copynumber: 2.5  Consensus size: 80

      13844 CTGAGTGACC

                                         **       *                          
      13854 ATATCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAATCCGGGCTAAG-TCCGAAGA
          1 ATATCCGGACTAAG-TCCCGAAGAGCATTCATGCGAGTGA-TAAATCCGGGCTAAGTTCCGAAGA

                             
      13916 GCATTCATGCTAGCGAT
         64 GCATTCATGCTAGCGAT

            *       *                        *      **                       
      13933 GTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGC
          1 ATATCCGGACTAAGTCCCGAAGAGCATTCATGCGAGTGATAAATCCGGGCTAAGTTCCGAAGAGC

                *      *   
      13998 ATTCGTGCTAGTGAT
         66 ATTCATGCTAGCGAT

                          *            *      *     
      14013 ATATCCGTG-CTAAATCCCGAAGAGCAATCATGCTAGTGA
          1 ATATCCG-GACTAAGTCCCGAAGAGCATTCATGCGAGTGA

      14052 CGTGTATTCG


Statistics
Matches: 102,  Mismatches: 13, Indels: 7
        0.84            0.11        0.06

Matches are distributed among these distances:
  78    1  0.01
  79   31  0.30
  80   69  0.68
  81    1  0.01

ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24


Consensus pattern (80 bp):   
ATATCCGGACTAAGTCCCGAAGAGCATTCATGCGAGTGATAAATCCGGGCTAAGTTCCGAAGAGC
ATTCATGCTAGCGAT

Found at i:13953 original size:40 final size:40

Alignment explanation


    Indices: 13896--14051  Score: 242
    Period size: 40  Copynumber: 3.9  Consensus size: 40

      13886 GAGTTACTAA

                                              *     
      13896 ATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGCGATGT
          1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT

                                                    
      13935 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
          1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT

                         *             *          * 
      13975 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
          1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT

                 *     *            *            
      14015 ATCCGTGCTAAATCCCGAAGAGCAATCATGCTAGTGA
          1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA

      14052 CGTGTATTCG


Statistics
Matches: 107,  Mismatches: 9, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  39   13  0.12
  40   94  0.88

ACGTcount: A:0.27, C:0.22, G:0.26, T:0.24


Consensus pattern (40 bp):   
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT

Done.