Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1646

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, 868

Length: 1448
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31


Found at i:888 original size:9 final size:10

Alignment explanation


    Indices: 839--896  Score: 53
    Period size: 10  Copynumber: 5.3  Consensus size: 10

        829 TTTATTCTCT

                       
        839 AAAAAAATAGA
          1 AAAAAAATA-A

                        
        850 TAAAAGAAATAA
          1 -AAAA-AAATAA

             *    *   
        862 ATAAAACTAA
          1 AAAAAAATAA

                        
        872 GTAAAAAAATAA
          1 --AAAAAAATAA

                      
        884 AAAAAAATAA
          1 AAAAAAATAA

               
        894 AAA
          1 AAA

        897 GACCACCTTT


Statistics
Matches: 39,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
  10   18  0.46
  11    3  0.08
  12   13  0.33
  13    5  0.13

ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14


Consensus pattern (10 bp):   
AAAAAAATAA

Found at i:1129 original size:16 final size:15

Alignment explanation


    Indices: 1098--1138  Score: 55
    Period size: 16  Copynumber: 2.6  Consensus size: 15

       1088 GGTACTAGGC

                  *         
       1098 GCGTGGAGGATGGCGT
          1 GCGTGGTGG-TGGCGT

                            
       1114 GCGGTGGTGGTGGCGT
          1 GC-GTGGTGGTGGCGT

                     
       1130 GCGTGGTGG
          1 GCGTGGTGG

       1139 CAGCTAGGAG


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  15    7  0.30
  16   10  0.43
  17    6  0.26

ACGTcount: A:0.05, C:0.12, G:0.61, T:0.22


Consensus pattern (15 bp):   
GCGTGGTGGTGGCGT
Done.