Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1870

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: 4198
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.20


Found at i:199 original size:64 final size:64

Alignment explanation


    Indices: 120--241  Score: 199
    Period size: 64  Copynumber: 1.9  Consensus size: 64

        110 CGTTTGGTTG

                                                *                           
        120 GGGGGGAGGGACGGATGCTGGGGAGGGACTCGTTGCGCACGCTTGGCCCTCCGCATGTTAGAGA
          1 GGGGGGAGGGACGGATGCTGGGGAGGGACTCGTTGCCCACGCTTGGCCCTCCGCATGTTAGAGA

                      *      * *                          *           
        184 GGGGGGAGGGCCGGATGGTTGGGAGGGACTCGTTGCCCACGCTTGGGCCTCCGCATGT
          1 GGGGGGAGGGACGGATGCTGGGGAGGGACTCGTTGCCCACGCTTGGCCCTCCGCATGT

        242 GCTATCGGTG


Statistics
Matches: 53,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  64   53  1.00

ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18


Consensus pattern (64 bp):   
GGGGGGAGGGACGGATGCTGGGGAGGGACTCGTTGCCCACGCTTGGCCCTCCGCATGTTAGAGA

Found at i:755 original size:102 final size:102

Alignment explanation


    Indices: 579--765  Score: 315
    Period size: 102  Copynumber: 1.8  Consensus size: 102

        569 GGCCAGGTGC

                                       *          *                          
        579 ACGGTGCGCGCCCTGCCCGCCCCCTGGTGTGGGGGCGGTCGGGGCGCACACCATGCGGAGCACCG
          1 ACGGTGCGCGCCCTGCCCGCCCCCTGGGGTGGGGGCGGGCGGGGCGCACACCATGCGGAGCACCG

                                                 
        644 GTGCGCGCCTCGCCCACCCTCGGCTGCGGGCGGGAGA
         66 GTGCGCGCCTCGCCCACCCTCGGCTGCGGGCGGGAGA

                                                               *             
        681 ACGGTGCGCGCCCAT-CCCGCCCCCTGGGGTCGGGGGCGGGCGGGGCGCACGCCATGCGGAGCA-
          1 ACGGTGCGCGCCC-TGCCCGCCCCCTGGGGT-GGGGGCGGGCGGGGCGCACACCATGCGGAGCAC

                                  
        744 CGGTGCGCGCCTCGCCCACCCT
         64 CGGTGCGCGCCTCGCCCACCCT

        766 GGGGGGTGCG


Statistics
Matches: 80,  Mismatches: 3, Indels: 4
        0.92            0.03        0.05

Matches are distributed among these distances:
 102   49  0.61
 103   31  0.39

ACGTcount: A:0.09, C:0.41, G:0.41, T:0.10


Consensus pattern (102 bp):   
ACGGTGCGCGCCCTGCCCGCCCCCTGGGGTGGGGGCGGGCGGGGCGCACACCATGCGGAGCACCG
GTGCGCGCCTCGCCCACCCTCGGCTGCGGGCGGGAGA

Found at i:836 original size:64 final size:62

Alignment explanation


    Indices: 676--851  Score: 168
    Period size: 64  Copynumber: 2.8  Consensus size: 62

        666 GCTGCGGGCG

                *                                             **         *  
        676 GGAGAACGGTGCGCGCCCATCCCGCCCCCTGGGGT-CGGGGGCGG-GCGGGGCGCACGCCATGC
          1 GGAGCACGGTGCGCGCCC-TCCCGCCCCCTGGGGTGC-GGGGCGGCGCGGCACGCACGCCAGGC

                                     *                                       
        738 GGAGCACGGTGCGCG-CCTCGCC-CACCCTGGGGGGTGCGGGGCGGCCGCGGCACGCAC-CC-GG
          1 GGAGCACGGTGCGCGCCCTC-CCGCCCCCT--GGGGTGCGGGGCGG-CGCGGCACGCACGCCAGG

              
        799 CC
         62 -C

                                                                
        801 AGGAGCACGGTGCGCGCCCTTCCCGCCCCCTGGGGTG-GGGGCGGTCGCGGC
          1 -GGAGCACGGTGCGCGCCC-TCCCGCCCCCTGGGGTGCGGGGCGG-CGCGGC

        852 GCACACCGTG


Statistics
Matches: 96,  Mismatches: 7, Indels: 21
        0.77            0.06        0.17

Matches are distributed among these distances:
  60    7  0.07
  61    4  0.04
  62   27  0.28
  63   17  0.18
  64   30  0.31
  65    4  0.04
  66    7  0.07

ACGTcount: A:0.08, C:0.39, G:0.45, T:0.09


Consensus pattern (62 bp):   
GGAGCACGGTGCGCGCCCTCCCGCCCCCTGGGGTGCGGGGCGGCGCGGCACGCACGCCAGGC
Done.