Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2656

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: 10389
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34


Found at i:164 original size:22 final size:23

Alignment explanation


    Indices: 139--184  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        129 CAACCAAACC

                                    
        139 AATTCA-ACATATTT-TCAAGATA
          1 AATTCATACATATTTAT-AAGATA

                   *               
        161 AATTCATGCATATTTATAAGATA
          1 AATTCATACATATTTATAAGATA

             
        184 A
          1 A

        185 CGTCATCACA


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  22    6  0.29
  23   14  0.67
  24    1  0.05

ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37


Consensus pattern (23 bp):   
AATTCATACATATTTATAAGATA

Found at i:190 original size:23 final size:23

Alignment explanation


    Indices: 146--190  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        136 ACCAATTCAA

                             *     
        146 CATATTTTCAAGATAAATTCATG
          1 CATATTTTCAAGATAAAGTCATG

                             *     
        169 CATATTTAT-AAGATAACGTCAT
          1 CATATTT-TCAAGATAAAGTCAT

        191 CACATACCCA


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  23   18  0.95
  24    1  0.05

ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38


Consensus pattern (23 bp):   
CATATTTTCAAGATAAAGTCATG

Found at i:7792 original size:22 final size:23

Alignment explanation


    Indices: 7767--7812  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       7757 CAACCAAACC

                                    
       7767 AATTCA-ACATATTT-TCAAGATA
          1 AATTCATACATATTTAT-AAGATA

                   *               
       7789 AATTCATGCATATTTATAAGATA
          1 AATTCATACATATTTATAAGATA

             
       7812 A
          1 A

       7813 CGTCATCACA


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  22    6  0.29
  23   14  0.67
  24    1  0.05

ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37


Consensus pattern (23 bp):   
AATTCATACATATTTATAAGATA

Found at i:7818 original size:23 final size:23

Alignment explanation


    Indices: 7774--7818  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       7764 ACCAATTCAA

                             *     
       7774 CATATTTTCAAGATAAATTCATG
          1 CATATTTTCAAGATAAAGTCATG

                             *     
       7797 CATATTTAT-AAGATAACGTCAT
          1 CATATTT-TCAAGATAAAGTCAT

       7819 CACATACCCA


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  23   18  0.95
  24    1  0.05

ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38


Consensus pattern (23 bp):   
CATATTTTCAAGATAAAGTCATG

Found at i:10379 original size:13 final size:13

Alignment explanation


    Indices: 10361--10389  Score: 58
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      10351 ATTTTACCAA

                         
      10361 TTTCTTCAATAAT
          1 TTTCTTCAATAAT

                         
      10374 TTTCTTCAATAAT
          1 TTTCTTCAATAAT

               
      10387 TTT
          1 TTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59


Consensus pattern (13 bp):   
TTTCTTCAATAAT
Done.