Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_6185

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: 8086
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31


Found at i:1259 original size:16 final size:17

Alignment explanation


    Indices: 1232--1265  Score: 61
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       1222 AAATGGATTT

                             
       1232 AATAGAAATTAAATAGA
          1 AATAGAAATTAAATAGA

                             
       1249 AATAG-AATTAAATAGA
          1 AATAGAAATTAAATAGA

             
       1265 A
          1 A

       1266 TTCTCTAATT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   12  0.71
  17    5  0.29

ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24


Consensus pattern (17 bp):   
AATAGAAATTAAATAGA

Found at i:2203 original size:16 final size:16

Alignment explanation


    Indices: 2172--2215  Score: 72
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       2162 TAGTATTTTA

                      *     
       2172 TACTAGCGT-GTTATT
          1 TACTAGCGTATTTATT

                            
       2187 TACTAGCGTATTTATT
          1 TACTAGCGTATTTATT

                         
       2203 TACTAGCGTATTT
          1 TACTAGCGTATTT

       2216 GCTCTTTCTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  15    9  0.33
  16   18  0.67

ACGTcount: A:0.23, C:0.14, G:0.16, T:0.48


Consensus pattern (16 bp):   
TACTAGCGTATTTATT

Found at i:5305 original size:16 final size:17

Alignment explanation


    Indices: 5284--5316  Score: 59
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       5274 GAATCGAAAT

                             
       5284 AAAAAAAAAATA-TCAG
          1 AAAAAAAAAATAGTCAG

                             
       5300 AAAAAAAAAATAGTCAG
          1 AAAAAAAAAATAGTCAG

       5317 CAATACAAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   12  0.75
  17    4  0.25

ACGTcount: A:0.73, C:0.06, G:0.09, T:0.12


Consensus pattern (17 bp):   
AAAAAAAAAATAGTCAG

Done.