Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2597

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: 3035
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30


Found at i:1989 original size:13 final size:13

Alignment explanation


    Indices: 1971--2027  Score: 51
    Period size: 13  Copynumber: 3.9  Consensus size: 13

       1961 ACAACACTTA

                         
       1971 TGTATCGATACAT
          1 TGTATCGATACAT

                              
       1984 TGTATCGATACAACACTT
          1 TGTATCGAT---ACA--T

                        * 
       2002 ATGTATCGATACCT
          1 -TGTATCGATACAT

                        
       2016 TGTATCGATACA
          1 TGTATCGATACA

       2028 AACTTTATGT


Statistics
Matches: 36,  Mismatches: 2, Indels: 12
        0.72            0.04        0.24

Matches are distributed among these distances:
  13   20  0.56
  14    1  0.03
  16    5  0.14
  18    1  0.03
  19    9  0.25

ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:2002 original size:32 final size:32

Alignment explanation


    Indices: 1921--2046  Score: 181
    Period size: 32  Copynumber: 4.0  Consensus size: 32

       1911 CGTAGCTTAT

                            *                
       1921 ATTGTATCGATACAAAAACTTATG--TC-ATAC
          1 ATTGTATCGATAC-AACACTTATGTATCGATAC

                                            
       1951 ATTGTATCGA-ACAACACTTATGTATCGATAC
          1 ATTGTATCGATACAACACTTATGTATCGATAC

                                            
       1982 ATTGTATCGATACAACACTTATGTATCGATAC
          1 ATTGTATCGATACAACACTTATGTATCGATAC

            *                                
       2014 CTTGTATCGATACAA-ACTTTATGTATCGATAC
          1 ATTGTATCGATACAACAC-TTATGTATCGATAC

             
       2046 A
          1 A

       2047 AATCGTTGAA


Statistics
Matches: 88,  Mismatches: 3, Indels: 8
        0.89            0.03        0.08

Matches are distributed among these distances:
  28    9  0.10
  29    2  0.02
  30   12  0.14
  31   16  0.18
  32   49  0.56

ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34


Consensus pattern (32 bp):   
ATTGTATCGATACAACACTTATGTATCGATAC

Found at i:2048 original size:19 final size:18

Alignment explanation


    Indices: 1953--2048  Score: 88
    Period size: 19  Copynumber: 5.8  Consensus size: 18

       1943 TGTCATACAT

                               
       1953 TGTATCGA-ACAACACTTA
          1 TGTATCGATACAA-ACTTA

                              
       1971 TGTATCGATAC--A--T-
          1 TGTATCGATACAAACTTA

                               
       1984 TGTATCGATACAACACTTA
          1 TGTATCGATACAA-ACTTA

                              
       2003 TGTATCGATAC---C-T-
          1 TGTATCGATACAAACTTA

                               
       2016 TGTATCGATACAAACTTTA
          1 TGTATCGATACAAAC-TTA

                          
       2035 TGTATCGATACAAA
          1 TGTATCGATACAAA

       2049 TCGTTGAAAT


Statistics
Matches: 65,  Mismatches: 0, Indels: 25
        0.72            0.00        0.28

Matches are distributed among these distances:
  13   22  0.34
  14    2  0.03
  15    1  0.02
  16    3  0.05
  18   10  0.15
  19   27  0.42

ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33


Consensus pattern (18 bp):   
TGTATCGATACAAACTTA
Done.