Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1047

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: 197917
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32


File 2 of 2

Found at i:189968 original size:32 final size:32

Alignment explanation


    Indices: 189927--189989  Score: 117
    Period size: 32  Copynumber: 2.0  Consensus size: 32

     189917 ACAAAACTTA

                                            
     189927 TGTATCGATACAACACTTATGTATCGATACAT
          1 TGTATCGATACAACACTTATGTATCGATACAT

                                    *      
     189959 TGTATCGATACAACACTTATGTATTGATACA
          1 TGTATCGATACAACACTTATGTATCGATACA

     189990 AATCATGGAA


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   30  1.00

ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35


Consensus pattern (32 bp):   
TGTATCGATACAACACTTATGTATCGATACAT

Found at i:191202 original size:13 final size:13

Alignment explanation


    Indices: 191184--191209  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

     191174 TACAGCAAGT

                         
     191184 ATGTATCGATACA
          1 ATGTATCGATACA

                         
     191197 ATGTATCGATACA
          1 ATGTATCGATACA

     191210 CAAAAAATTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31


Consensus pattern (13 bp):   
ATGTATCGATACA

Found at i:197374 original size:20 final size:20

Alignment explanation


    Indices: 197346--197386  Score: 73
    Period size: 20  Copynumber: 2.0  Consensus size: 20

     197336 ATCCTGGAAA

                                
     197346 TTCTATGTATCGATACATTT
          1 TTCTATGTATCGATACATTT

                *               
     197366 TTCTTTGTATCGATACATTT
          1 TTCTATGTATCGATACATTT

             
     197386 T
          1 T

     197387 GTATCGATAC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.22, C:0.15, G:0.10, T:0.54


Consensus pattern (20 bp):   
TTCTATGTATCGATACATTT

Found at i:197403 original size:13 final size:13

Alignment explanation


    Indices: 197370--197423  Score: 81
    Period size: 13  Copynumber: 4.0  Consensus size: 13

     197360 ACATTTTTCT

                         
     197370 TTGTATCGATACA
          1 TTGTATCGATACA

                           
     197383 TTTTGTATCGATACA
          1 --TTGTATCGATACA

                         
     197398 TTGTATCGATACA
          1 TTGTATCGATACA

            *            
     197411 CTGTATCGATACA
          1 TTGTATCGATACA

     197424 GGGTGATTAT


Statistics
Matches: 38,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  13   25  0.66
  15   13  0.34

ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39


Consensus pattern (13 bp):   
TTGTATCGATACA

Found at i:197410 original size:28 final size:26

Alignment explanation


    Indices: 197370--197423  Score: 81
    Period size: 28  Copynumber: 2.0  Consensus size: 26

     197360 ACATTTTTCT

                           *            
     197370 TTGTATCGATACATTTTGTATCGATACA
          1 TTGTATCGATACA--CTGTATCGATACA

                                      
     197398 TTGTATCGATACACTGTATCGATACA
          1 TTGTATCGATACACTGTATCGATACA

     197424 GGGTGATTAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  26   12  0.48
  28   13  0.52

ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39


Consensus pattern (26 bp):   
TTGTATCGATACACTGTATCGATACA

Done.