Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1986

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: 7302
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37


Found at i:939 original size:30 final size:29

Alignment explanation


    Indices: 905--961  Score: 69
    Period size: 29  Copynumber: 1.9  Consensus size: 29

        895 AAATATTTTT

                             *            
        905 ATATTAATATTTATAATTAAATTTTAAAAA
          1 ATATTAATATTTA-AATGAAATTTTAAAAA

                 **           *        
        935 ATATTTTTATTTAAATGATATTTTAAA
          1 ATATTAATATTTAAATGAAATTTTAAA

        962 TTAATTTAAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  29   12  0.52
  30   11  0.48

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51


Consensus pattern (29 bp):   
ATATTAATATTTAAATGAAATTTTAAAAA

Found at i:1177 original size:19 final size:20

Alignment explanation


    Indices: 1137--1175  Score: 60
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       1127 AAAAATATTA

                      *          
       1137 ATTTTAATATTTTTAAAAAAT
          1 ATTTTAATATATTT-AAAAAT

                              
       1158 ATTTTAATATATTTAAAA
          1 ATTTTAATATATTTAAAA

       1176 TAATTTAAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    4  0.24
  21   13  0.76

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (20 bp):   
ATTTTAATATATTTAAAAAT

Found at i:1182 original size:19 final size:20

Alignment explanation


    Indices: 1139--1183  Score: 56
    Period size: 19  Copynumber: 2.2  Consensus size: 20

       1129 AAATATTAAT

                    *           *
       1139 TTTAATATTTTTAAAAAATAT
          1 TTTAATATATTT-AAAAATAA

                                
       1160 TTTAATATATTT-AAAATAA
          1 TTTAATATATTTAAAAATAA

                 
       1179 TTTAA
          1 TTTAA

       1184 ATTCAATCAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  19   11  0.50
  21   11  0.50

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (20 bp):   
TTTAATATATTTAAAAATAA

Found at i:3027 original size:38 final size:38

Alignment explanation


    Indices: 2984--3070  Score: 147
    Period size: 38  Copynumber: 2.3  Consensus size: 38

       2974 AAAATAATTG

                                           *      
       2984 AAATATAAATATGATATAATATAAGAAATGTTTTTAAA
          1 AAATATAAATATGATATAATATAAGAAATGTATTTAAA

                                                  
       3022 AAATATAAATATGATATAATATAAGAAATGTATTTAAA
          1 AAATATAAATATGATATAATATAAGAAATGTATTTAAA

              * *      
       3060 AAGTTTAAATA
          1 AAATATAAATA

       3071 AATATATAAT


Statistics
Matches: 46,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  38   46  1.00

ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36


Consensus pattern (38 bp):   
AAATATAAATATGATATAATATAAGAAATGTATTTAAA

Found at i:4460 original size:159 final size:158

Alignment explanation


    Indices: 4172--4488  Score: 607
    Period size: 159  Copynumber: 2.0  Consensus size: 158

       4162 AAAGTGAGAA

                                       *                                     
       4172 AAACGAAATTGGTTAATGCAAAAAAAATTGAAAGGGATCTTAACAACACCCATTTGCTAAGGGGA
          1 AAACGAAATTGGTTAATGCAAAAAAAAATGAAAGGGATCTTAACAACACCCATTTGCTAAGGGGA

                                                                             
       4237 ATCAGAAAATGAAGTTCTTTCTTAAGCTAAAACATGGCAAAATGCTTTCCCAGTGGGGACCAAAA
         66 ATCAGAAAATGAAGTTCTTTCTTAAGCTAAAACATGGCAAAATGCTTTCCCAGTGGGGACCAAAA

                                        
       4302 TCTTTTTTGTCATTTTCTGAAGTCAAAT
        131 TCTTTTTTGTCATTTTCTGAAGTCAAAT

                                                                           * 
       4330 AAACGAAATTGGTTAATGCAAAAAAAAAATGAAAGGGATCTTAACAACACCCATTTGCTAAGGTG
          1 AAACGAAATTGGTTAATGC-AAAAAAAAATGAAAGGGATCTTAACAACACCCATTTGCTAAGGGG

                                                                             
       4395 AATCAGAAAATGAAGTTCTTTCTTAAGCTAAAACATGGCAAAATGCTTTCCCAGTGGGGACCAAA
         65 AATCAGAAAATGAAGTTCTTTCTTAAGCTAAAACATGGCAAAATGCTTTCCCAGTGGGGACCAAA

                                         
       4460 ATCTTTTTTGTCATTTTCTGAAGTCAAAT
        130 ATCTTTTTTGTCATTTTCTGAAGTCAAAT

       4489 TAATGTGAAT


Statistics
Matches: 156,  Mismatches: 2, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
 158   19  0.12
 159  137  0.88

ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28


Consensus pattern (158 bp):   
AAACGAAATTGGTTAATGCAAAAAAAAATGAAAGGGATCTTAACAACACCCATTTGCTAAGGGGA
ATCAGAAAATGAAGTTCTTTCTTAAGCTAAAACATGGCAAAATGCTTTCCCAGTGGGGACCAAAA
TCTTTTTTGTCATTTTCTGAAGTCAAAT
Done.