Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold591

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: 5475
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36


Found at i:2807 original size:28 final size:30

Alignment explanation


    Indices: 2750--2809  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2740 CATATCTGTC

                           *              
       2750 TGAATATATAAAATATATATATAAATAAAA
          1 TGAATATATAAAATAGATATATAAATAAAA

                                 *    *    
       2780 TGAATAT-TAAATATAGATATTTAAAAAAAA
          1 TGAATATATAAA-ATAGATATATAAATAAAA

       2810 ATTGAAGTAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    4  0.15
  30   22  0.85

ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33


Consensus pattern (30 bp):   
TGAATATATAAAATAGATATATAAATAAAA

Found at i:3016 original size:22 final size:22

Alignment explanation


    Indices: 2985--3036  Score: 61
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       2975 AGTAGATTTA

                                    
       2985 TTTTACTATTTAAAAATTAT-TAT
          1 TTTTA-TA-TTAAAAATTATATAT

                       * *        
       3008 TTTTATATTAATATTTATATAT
          1 TTTTATATTAAAAATTATATAT

                   
       3030 TTTTATA
          1 TTTTATA

       3037 ATCAAATTTA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  21    9  0.35
  22   12  0.46
  23    5  0.19

ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62


Consensus pattern (22 bp):   
TTTTATATTAAAAATTATATAT

Found at i:3045 original size:22 final size:21

Alignment explanation


    Indices: 3001--3046  Score: 58
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       2991 TATTTAAAAA

                           *     
       3001 TTATTATTTTTATATTAATAT
          1 TTATTATTTTTATATCAATAT

                                   
       3022 TTATATATTTTTATAATCAA-AT
          1 TTAT-TATTTTTAT-ATCAATAT

               
       3044 TTA
          1 TTA

       3047 AATAAAAATA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  21    4  0.18
  22   14  0.64
  23    4  0.18

ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61


Consensus pattern (21 bp):   
TTATTATTTTTATATCAATAT

Found at i:3533 original size:34 final size:34

Alignment explanation


    Indices: 3490--3559  Score: 140
    Period size: 34  Copynumber: 2.1  Consensus size: 34

       3480 AATATATTCG

                                              
       3490 TATAAGTTTATAAGATAATAGCTTACCAAGTTTA
          1 TATAAGTTTATAAGATAATAGCTTACCAAGTTTA

                                              
       3524 TATAAGTTTATAAGATAATAGCTTACCAAGTTTA
          1 TATAAGTTTATAAGATAATAGCTTACCAAGTTTA

              
       3558 TA
          1 TA

       3560 ATAACGCTTT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   36  1.00

ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39


Consensus pattern (34 bp):   
TATAAGTTTATAAGATAATAGCTTACCAAGTTTA

Found at i:4719 original size:23 final size:24

Alignment explanation


    Indices: 4667--4725  Score: 66
    Period size: 23  Copynumber: 2.5  Consensus size: 24

       4657 TAATAAATTT

                *                  *
       4667 AAAATTTAAAATTTTATTTTATGT
          1 AAAAATTAAAATTTTATTTTATGA

            **                      
       4691 TTAAATTAAAATTTTA-TTTATGA
          1 AAAAATTAAAATTTTATTTTATGA

                  *     
       4714 AAAAATAAAAAT
          1 AAAAATTAAAAT

       4726 AATTTTTTAT


Statistics
Matches: 28,  Mismatches: 7, Indels: 1
        0.78            0.19        0.03

Matches are distributed among these distances:
  23   15  0.54
  24   13  0.46

ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46


Consensus pattern (24 bp):   
AAAAATTAAAATTTTATTTTATGA
Done.