Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3374

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: 28448
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:236 original size:29 final size:29

Alignment explanation


    Indices: 202--275  Score: 105
    Period size: 29  Copynumber: 2.6  Consensus size: 29

        192 ATAATCAACA

                              *          *
        202 CGCACACTTAGTGCCATGTACTTT-AAACT
          1 CGCACACTTAGTGCCATGCA-TTTCAAACC

                                      *  
        231 CGCACACTTAGTGCCATGCATTTCAAGCC
          1 CGCACACTTAGTGCCATGCATTTCAAACC

                            
        260 CGCACACTTAGTGCCA
          1 CGCACACTTAGTGCCA

        276 ATCTCACAAC


Statistics
Matches: 41,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  28    3  0.07
  29   38  0.93

ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26


Consensus pattern (29 bp):   
CGCACACTTAGTGCCATGCATTTCAAACC

Found at i:15165 original size:14 final size:14

Alignment explanation


    Indices: 15146--15194  Score: 71
    Period size: 14  Copynumber: 3.4  Consensus size: 14

      15136 CAATCCATTG

                          
      15146 AAAGAGAAAAAGAA
          1 AAAGAGAAAAAGAA

                       *  
      15160 AAAGAGAAAAATAA
          1 AAAGAGAAAAAGAA

                   *       
      15174 AAAGAGTGAAAAGAA
          1 AAAGAG-AAAAAGAA

                  
      15189 AAAGAG
          1 AAAGAG

      15195 TGGAAAAAGT


Statistics
Matches: 31,  Mismatches: 3, Indels: 1
        0.89            0.09        0.03

Matches are distributed among these distances:
  14   19  0.61
  15   12  0.39

ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04


Consensus pattern (14 bp):   
AAAGAGAAAAAGAA

Found at i:15185 original size:15 final size:15

Alignment explanation


    Indices: 15153--15201  Score: 64
    Period size: 15  Copynumber: 3.3  Consensus size: 15

      15143 TTGAAAGAGA

                          *
      15153 AAAAGAAAAAGAG-A
          1 AAAAGAAAAAGAGTG

                *          
      15167 AAAATAAAAAGAGTG
          1 AAAAGAAAAAGAGTG

                            
      15182 AAAAGAAAAAGAGTGG
          1 AAAAGAAAAAGAGT-G

                
      15198 AAAA
          1 AAAA

      15202 AGTGATAAAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  14   12  0.40
  15   13  0.43
  16    5  0.17

ACGTcount: A:0.71, C:0.00, G:0.22, T:0.06


Consensus pattern (15 bp):   
AAAAGAAAAAGAGTG

Found at i:24114 original size:27 final size:26

Alignment explanation


    Indices: 24097--24166  Score: 95
    Period size: 27  Copynumber: 2.6  Consensus size: 26

      24087 ATATTAAGTC

                                       
      24097 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTCAGTGCTATAT-ATCAACT

                    *                   
      24124 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTCAGTGCTATAT-ATC-AACT

                    *      
      24152 CGCACACTTAGTGCT
          1 CGCACACTCAGTGCT

      24167 GTACAATTTA


Statistics
Matches: 41,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  27   22  0.54
  28   19  0.46

ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27


Consensus pattern (26 bp):   
CGCACACTCAGTGCTATATATCAACT

Found at i:24160 original size:28 final size:28

Alignment explanation


    Indices: 24097--24194  Score: 135
    Period size: 28  Copynumber: 3.5  Consensus size: 28

      24087 ATATTAAGTC

                    *                   
      24097 CGCACACTCAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
      24124 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                           *  *    *    *
      24152 CGCACACTTAGTGCTGTACAATTTAAACC
          1 CGCACACTTAGTGCTATATAA-TCAAACT

                          
      24181 CGCACACTTAGTGC
          1 CGCACACTTAGTGC

      24195 CAATCTCATG


Statistics
Matches: 64,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  27   22  0.34
  28   23  0.36
  29   19  0.30

ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27


Consensus pattern (28 bp):   
CGCACACTTAGTGCTATATAATCAAACT

Done.