Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1192

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: 5071
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30


Found at i:3184 original size:13 final size:13

Alignment explanation


    Indices: 3166--3190  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3156 ATAATGCACA

                         
       3166 GTATCGATACATT
          1 GTATCGATACATT

                        
       3179 GTATCGATACAT
          1 GTATCGATACAT

       3191 GACCACTGTA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (13 bp):   
GTATCGATACATT

Found at i:3187 original size:33 final size:32

Alignment explanation


    Indices: 3145--3207  Score: 90
    Period size: 33  Copynumber: 1.9  Consensus size: 32

       3135 CACCTTCAGA

                            *                
       3145 TGTATCGATACATAATGCACAGTATCGATACAT
          1 TGTATCGATACATAA-CCACAGTATCGATACAT

                         *     *          
       3178 TGTATCGATACATGACCACTGTATCGATAC
          1 TGTATCGATACATAACCACAGTATCGATAC

       3208 TTGCAAAGAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  32   13  0.48
  33   14  0.52

ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30


Consensus pattern (32 bp):   
TGTATCGATACATAACCACAGTATCGATACAT

Found at i:3295 original size:19 final size:20

Alignment explanation


    Indices: 3271--3322  Score: 81
    Period size: 20  Copynumber: 2.6  Consensus size: 20

       3261 CTTAACTGTT

                                 
       3271 TGTATCGATACAT-A-CAAGA
          1 TGTATCGATACATGACCAA-A

                                
       3290 TGTATCGATACATGACCAAA
          1 TGTATCGATACATGACCAAA

                         
       3310 TGTATCGATACAT
          1 TGTATCGATACAT

       3323 TGGTTTTGTA


Statistics
Matches: 31,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
  19   13  0.42
  20   15  0.48
  21    3  0.10

ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29


Consensus pattern (20 bp):   
TGTATCGATACATGACCAAA

Done.