Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold666

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: 11992
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.28

Warning! 1729 characters in sequence are not A, C, G, or T


Found at i:938 original size:12 final size:11

Alignment explanation


    Indices: 918--961  Score: 61
    Period size: 11  Copynumber: 3.7  Consensus size: 11

        908 AACTAGCTCT

                       
        918 TTTTTTTTCAA
          1 TTTTTTTTCAA

                         
        929 TTTATTTTTCAAA
          1 TTT-TTTTTC-AA

                        
        942 TTTTTTTTTCAA
          1 -TTTTTTTTCAA

                    
        954 TTTTTTTT
          1 TTTTTTTT

        962 TTCACAACTT


Statistics
Matches: 30,  Mismatches: 0, Indels: 6
        0.83            0.00        0.17

Matches are distributed among these distances:
  11   11  0.37
  12    8  0.27
  13    8  0.27
  14    3  0.10

ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75


Consensus pattern (11 bp):   
TTTTTTTTCAA

Found at i:943 original size:13 final size:13

Alignment explanation


    Indices: 917--965  Score: 73
    Period size: 13  Copynumber: 3.8  Consensus size: 13

        907 GAACTAGCTC

                         
        917 TTTTTTTTTC-AA
          1 TTTTTTTTTCAAA

               *         
        929 TTTATTTTTCAAA
          1 TTTTTTTTTCAAA

                        *
        942 TTTTTTTTTCAAT
          1 TTTTTTTTTCAAA

                       
        955 TTTTTTTTTCA
          1 TTTTTTTTTCA

        966 CAACTTGATA


Statistics
Matches: 33,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  12    9  0.27
  13   24  0.73

ACGTcount: A:0.18, C:0.08, G:0.00, T:0.73


Consensus pattern (13 bp):   
TTTTTTTTTCAAA

Found at i:962 original size:12 final size:12

Alignment explanation


    Indices: 917--962  Score: 74
    Period size: 12  Copynumber: 3.8  Consensus size: 12

        907 GAACTAGCTC

                        
        917 TTTTTTTTTCAA
          1 TTTTTTTTTCAA

               *         
        929 TTTATTTTTCAAA
          1 TTTTTTTTTC-AA

                        
        942 TTTTTTTTTCAA
          1 TTTTTTTTTCAA

                     
        954 TTTTTTTTT
          1 TTTTTTTTT

        963 TCACAACTTG


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  12   20  0.65
  13   11  0.35

ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76


Consensus pattern (12 bp):   
TTTTTTTTTCAA

Found at i:1024 original size:12 final size:12

Alignment explanation


    Indices: 1007--1060  Score: 83
    Period size: 12  Copynumber: 4.6  Consensus size: 12

        997 GGAAACTAGT

                        
       1007 TTTTTTTTCGAA
          1 TTTTTTTTCGAA

                        
       1019 TTTTTTTTCGAA
          1 TTTTTTTTCGAA

                        
       1031 TTTTTTTT-GAA
          1 TTTTTTTTCGAA

                     * *
       1042 TTTTTTTTCTAG
          1 TTTTTTTTCGAA

                   
       1054 TTTTTTT
          1 TTTTTTT

       1061 CGAGAAACTA


Statistics
Matches: 39,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  11   11  0.28
  12   28  0.72

ACGTcount: A:0.13, C:0.06, G:0.07, T:0.74


Consensus pattern (12 bp):   
TTTTTTTTCGAA

Found at i:1034 original size:23 final size:23

Alignment explanation


    Indices: 1008--1063  Score: 85
    Period size: 23  Copynumber: 2.4  Consensus size: 23

        998 GAAACTAGTT

                                   
       1008 TTTTTTTCGAATTTTTTTTCGAA
          1 TTTTTTTCGAATTTTTTTTCGAA

                   *            * *
       1031 TTTTTTTTGAATTTTTTTTCTAG
          1 TTTTTTTCGAATTTTTTTTCGAA

                      
       1054 TTTTTTTCGA
          1 TTTTTTTCGA

       1064 GAAACTACTA


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  23   29  1.00

ACGTcount: A:0.14, C:0.07, G:0.09, T:0.70


Consensus pattern (23 bp):   
TTTTTTTCGAATTTTTTTTCGAA

Found at i:4272 original size:20 final size:20

Alignment explanation


    Indices: 4249--4295  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       4239 TAGCTCCAAC

                     *          
       4249 CAGCTTATTTGAGCTCAATT
          1 CAGCTTATTCGAGCTCAATT

                 *              
       4269 CAGCTCATTCGAGCTCAATT
          1 CAGCTTATTCGAGCTCAATT

            *      
       4289 TAGCTTA
          1 CAGCTTA

       4296 CTTTCAGCTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36


Consensus pattern (20 bp):   
CAGCTTATTCGAGCTCAATT

Found at i:10135 original size:20 final size:20

Alignment explanation


    Indices: 10107--10171  Score: 78
    Period size: 20  Copynumber: 3.2  Consensus size: 20

      10097 TCTTAGTGCA

                *    *           
      10107 AGCTGATTTTAGCTCCAA-TC
          1 AGCTCATTTGAGCT-CAATTC

                                
      10127 AGCTCATTTGAGCTCAATTC
          1 AGCTCATTTGAGCTCAATTC

                    *          *
      10147 AGCTCATTCGAGCTCAATTT
          1 AGCTCATTTGAGCTCAATTC

                 
      10167 AGCTC
          1 AGCTC

      10172 GTTAATTTTA


Statistics
Matches: 40,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  19    3  0.08
  20   37  0.93

ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34


Consensus pattern (20 bp):   
AGCTCATTTGAGCTCAATTC
Done.