Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1524

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: 6069
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30


Found at i:49 original size:13 final size:13

Alignment explanation


    Indices: 31--55  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

         21 CAAAGATCAG

                         
         31 TGTATCGATACAA
          1 TGTATCGATACAA

                        
         44 TGTATCGATACA
          1 TGTATCGATACA

         56 TTTGAGTAAG


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


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:132 original size:33 final size:33

Alignment explanation


    Indices: 95--161  Score: 98
    Period size: 33  Copynumber: 2.0  Consensus size: 33

         85 AGTAGCTTAA

                                             
         95 ATTGTATCGATACAAAAAAATATGTATCGATAC
          1 ATTGTATCGATACAAAAAAATATGTATCGATAC

                           * ***             
        128 ATTGTATCGATACAACATTTTATGTATCGATAC
          1 ATTGTATCGATACAAAAAAATATGTATCGATAC

             
        161 A
          1 A

        162 AATCGTTGAA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   30  1.00

ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34


Consensus pattern (33 bp):   
ATTGTATCGATACAAAAAAATATGTATCGATAC

Found at i:135 original size:13 final size:13

Alignment explanation


    Indices: 117--141  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        107 CAAAAAAATA

                         
        117 TGTATCGATACAT
          1 TGTATCGATACAT

                        
        130 TGTATCGATACA
          1 TGTATCGATACA

        142 ACATTTTATG


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):   
TGTATCGATACAT

Found at i:724 original size:32 final size:33

Alignment explanation


    Indices: 688--753  Score: 98
    Period size: 33  Copynumber: 2.0  Consensus size: 33

        678 TTCAACGATC

                                             
        688 TGTATCGATACATA-AATGTTGTATCGATACAA
          1 TGTATCGATACATATAATGTTGTATCGATACAA

                           ** *              
        720 TGTATCGATACATATTTTTTTGTATCGATACAA
          1 TGTATCGATACATATAATGTTGTATCGATACAA

             
        753 T
          1 T

        754 TTAAGCTACT


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  32   14  0.47
  33   16  0.53

ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41


Consensus pattern (33 bp):   
TGTATCGATACATATAATGTTGTATCGATACAA

Found at i:725 original size:13 final size:13

Alignment explanation


    Indices: 707--731  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        697 ACATAAATGT

                         
        707 TGTATCGATACAA
          1 TGTATCGATACAA

                        
        720 TGTATCGATACA
          1 TGTATCGATACA

        732 TATTTTTTTG


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


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:959 original size:50 final size:52

Alignment explanation


    Indices: 833--948  Score: 202
    Period size: 52  Copynumber: 2.3  Consensus size: 52

        823 CACTAATCTT

                                                                
        833 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
          1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA

                                                                 
        885 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATAACA-T-T-AAA
          1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGAT-ACATTATAAAA

                          
        935 TGTATCGATACATG
          1 TGTATCGATACATG

        949 TAGATAAATT


Statistics
Matches: 63,  Mismatches: 0, Indels: 4
        0.94            0.00        0.06

Matches are distributed among these distances:
  50   17  0.27
  51    1  0.02
  52   42  0.67
  53    3  0.05

ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29


Consensus pattern (52 bp):   
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA

Found at i:4180 original size:22 final size:22

Alignment explanation


    Indices: 4155--4198  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4145 GCAGTCAGGA

                                  
       4155 GCATCTCGTCATGCAATGAATG
          1 GCATCTCGTCATGCAATGAATG

                                  
       4177 GCATCTCGTCATGCAATGAATG
          1 GCATCTCGTCATGCAATGAATG

       4199 TCATTTGATC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27


Consensus pattern (22 bp):   
GCATCTCGTCATGCAATGAATG
Done.