Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1487

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: 18912
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32


Found at i:5927 original size:27 final size:27

Alignment explanation


    Indices: 5897--6074  Score: 205
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       5887 ATATTGAGTC

                    *       *   *    * 
       5897 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                             *  *      
       5924 CGCACACTTAGTGCTACGTAATCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                        
       5951 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAGTCAAA-T

                          **   *     * 
       5979 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                 *   ** 
       6006 CGCACACTTAGTGC-ATCATATTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAAAT

                          *            
       6033 CGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                           
       6060 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       6075 GTACAATTTA


Statistics
Matches: 130,  Mismatches: 18, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
  27  106  0.82
  28   24  0.18

ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAAAT

Found at i:6036 original size:82 final size:81

Alignment explanation


    Indices: 5918--6073  Score: 233
    Period size: 82  Copynumber: 1.9  Consensus size: 81

       5908 TGCTATATAA

                                   *                       *                 
       5918 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
          1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA

                             
       5983 CACTTAGTGCCGCATGG
         65 CACTTAGTGCCGCATGG

                *                      *   **                                
       6000 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
          1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA

                      
       6064 CACTTAGTGC
         65 CACTTAGTGC

       6074 TGTACAATTT


Statistics
Matches: 67,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  81   16  0.24
  82   51  0.76

ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27


Consensus pattern (81 bp):   
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG

Found at i:10852 original size:22 final size:21

Alignment explanation


    Indices: 10827--10868  Score: 66
    Period size: 22  Copynumber: 2.0  Consensus size: 21

      10817 TTTGAACCAT

                                  
      10827 TACCAATTCGTACCAAATTCCA
          1 TACCAATTCGTACC-AATTCCA

                 *              
      10849 TACCATTTCGTACCAATTCC
          1 TACCAATTCGTACCAATTCC

      10869 CAAATACCAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    6  0.32
  22   13  0.68

ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31


Consensus pattern (21 bp):   
TACCAATTCGTACCAATTCCA

Found at i:16459 original size:19 final size:19

Alignment explanation


    Indices: 16437--16503  Score: 55
    Period size: 19  Copynumber: 3.4  Consensus size: 19

      16427 ACAAGTGAGG

                               
      16437 AAAAAGAAAAAGAGAATGA
          1 AAAAAGAAAAAGAGAATGA

                             *   
      16456 AAAAGAGCAAAAAGAGATTGA
          1 AAAA-AG-AAAAAGAGAATGA

            *  **               
      16477 GAAGTGAAAAAGA-AATTGA
          1 AAAAAGAAAAAGAGAA-TGA

             *      
      16496 AGAAAGAA
          1 AAAAAGAA

      16504 GAGAAATGAA


Statistics
Matches: 36,  Mismatches: 9, Indels: 6
        0.71            0.18        0.12

Matches are distributed among these distances:
  18    1  0.03
  19   18  0.50
  20    3  0.08
  21   14  0.39

ACGTcount: A:0.66, C:0.01, G:0.24, T:0.09


Consensus pattern (19 bp):   
AAAAAGAAAAAGAGAATGA
Done.