Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold935

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: 4079
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32


Found at i:1385 original size:16 final size:16

Alignment explanation


    Indices: 1346--1388  Score: 59
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       1336 CAAAAGCCAA

                             
       1346 TTTCAAAGTAATGTAAG
          1 TTTC-AAGTAATGTAAG

             **             
       1363 TAACAAGTAATGTAAG
          1 TTTCAAGTAATGTAAG

                      
       1379 TTTCAAGTAA
          1 TTTCAAGTAA

       1389 ACATGACGCG


Statistics
Matches: 22,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  16   20  0.91
  17    2  0.09

ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33


Consensus pattern (16 bp):   
TTTCAAGTAATGTAAG

Found at i:2933 original size:10 final size:9

Alignment explanation


    Indices: 2918--2952  Score: 54
    Period size: 9  Copynumber: 4.0  Consensus size: 9

       2908 TTTATTTCAT

                     
       2918 AAAAAAAAC
          1 AAAAAAAAC

                     
       2927 AAAAAAAAC
          1 AAAAAAAAC

                     
       2936 AAAAAAAA-
          1 AAAAAAAAC

                *    
       2944 AAAACAAAC
          1 AAAAAAAAC

       2953 GAACACTGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
   8    7  0.29
   9   17  0.71

ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00


Consensus pattern (9 bp):   
AAAAAAAAC

Found at i:2943 original size:13 final size:13

Alignment explanation


    Indices: 2918--2951  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       2908 TTTATTTCAT

                     *   
       2918 AAAAA-AAACAAA
          1 AAAAACAAAAAAA

                         
       2930 AAAAACAAAAAAA
          1 AAAAACAAAAAAA

                     
       2943 AAAAACAAA
          1 AAAAACAAA

       2952 CGAACACTGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12    5  0.25
  13   15  0.75

ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00


Consensus pattern (13 bp):   
AAAAACAAAAAAA
Done.